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Sequence Alignment and Modeling Software System
http://www.soe.ucsc.edu/research/compbio/sam.html

Citations (SAM, SAM-T99, HMMs)

Sequence numbers correspond to the following labels:

    • T0308 ARL6, Homo sapiens, 165 res
    • gi|68371244|ref|XP_709240.1|_15:175 PREDICTED: similar to RAB1A, member RAS oncogene family isoform 2 [Danio rerio]
    • gi|88193099|pdb|2FOL|A_26:186 Chain A, Crystal Structure Of Human Rab1a In Complex With Gdp [Taxonomy]
    • gi|88192430|pdb|2BCG|Y_9:169 Chain Y, Structure Of Doubly Prenylated Ypt1:gdi Complex [Taxonomy]
    • gi|68357838|ref|XP_684705.1|_10:169 PREDICTED: similar to RAB35, member RAS oncogene family (predicted) [Danio rerio]
    • gi|12084568|pdb|1G17|B_4:163 Chain B, Crystal Structure Of Sec4-Guanosine-5'-(Beta,Gamma)- Imidotriphosphate [Taxonomy]
    • gi|12084567|pdb|1G17|A Chain A, Crystal Structure Of Sec4-Guanosine-5'-(Beta,Gamma)- Imidotriphosphate [Taxonomy]
    • gi|6435686|pdb|1CXZ|A_6:179 Chain A, Crystal Structure Of Human Rhoa Complexed With The Effector Domain Of The Protein Kinase PknPRK1 [Taxonomy]
    • gi|3318980|pdb|1A2B| Human Rhoa Complexed With Gtp Analogue [Taxonomy]
    • gi|13096780|pdb|1HE1|D_3:176 Chain D, Crystal Structure Of The Complex Between The Gap Domain Of The Pseudomonas Aeruginosa Exos Toxin And Human Rac [Taxonomy]
    • gi|13096779|pdb|1HE1|C Chain C, Crystal Structure Of The Complex Between The Gap Domain Of The Pseudomonas Aeruginosa Exos Toxin And Human Rac [Taxonomy]
    • gi|76621149|ref|XP_587868.2|_9:169 PREDICTED: similar to cell line NK14 derived transforming oncogene [Bos taurus]
    • gi|55670772|pdb|1X86|H_8:181 Chain H, Crystal Structure Of The DhPH DOMAINS OF LEUKEMIA- Assiociated Rhogef In Complex With Rhoa [Taxonomy]
    • gi|55670770|pdb|1X86|F Chain F, Crystal Structure Of The DhPH DOMAINS OF LEUKEMIA- Assiociated Rhogef In Complex With Rhoa [Taxonomy]
    • gi|55670768|pdb|1X86|D Chain D, Crystal Structure Of The DhPH DOMAINS OF LEUKEMIA- Assiociated Rhogef In Complex With Rhoa [Taxonomy]
    • gi|55670766|pdb|1X86|B Chain B, Crystal Structure Of The DhPH DOMAINS OF LEUKEMIA- Assiociated Rhogef In Complex With Rhoa [Taxonomy]
    • gi|46015652|pdb|1S1C|B_7:180 Chain B, Crystal Structure Of The Complex Between The Human Rhoa And Rho-Binding Domain Of Human Rocki [Taxonomy]
    • gi|46015651|pdb|1S1C|A Chain A, Crystal Structure Of The Complex Between The Human Rhoa And Rho-Binding Domain Of Human Rocki [Taxonomy]
    • gi|21466031|pdb|1LB1|H_7:180 Chain H, Crystal Structure Of The Dbl And Pleckstrin Homology Domains Of Dbs In Complex With Rhoa [Taxonomy]
    • gi|21466029|pdb|1LB1|F Chain F, Crystal Structure Of The Dbl And Pleckstrin Homology Domains Of Dbs In Complex With Rhoa [Taxonomy]
    • gi|21466027|pdb|1LB1|D Chain D, Crystal Structure Of The Dbl And Pleckstrin Homology Domains Of Dbs In Complex With Rhoa [Taxonomy]
    • gi|21466025|pdb|1LB1|B Chain B, Crystal Structure Of The Dbl And Pleckstrin Homology Domains Of Dbs In Complex With Rhoa [Taxonomy]
    • gi|93279886|pdb|2G6B|A_10:172 Chain A, Crystal Structure Of Human Rab26 In Complex With A Gtp Analogue [Taxonomy]
    • gi|76624275|ref|XP_588442.2|_36:197 PREDICTED: similar to Ras-related protein Rab-18 isoform 4 [Bos taurus]
    • gi|42543203|pdb|1OIV|B_30:190 Chain B, X-Ray Structure Of The Small G Protein Rab11a In Complex With Gdp [Taxonomy]
    • gi|42543202|pdb|1OIV|A Chain A, X-Ray Structure Of The Small G Protein Rab11a In Complex With Gdp [Taxonomy]
    • gi|49903967|gb|AAH76433.1|_3:176 Ras-related C3 botulinum toxin substrate 3 (rho family, small GTP binding protein Rac3) [Danio rerio]
    • gi|57526488|ref|NP_001002754.1| ras-related C3 botulinum toxin substrate 3 (rho family, small GTP binding protein Rac3) [Danio rerio]
    • gi|83753568|pdb|1X3S|A_15:176 Chain A, Crystal Structure Of Human Rab18 In Complex With Gppnhp [Taxonomy]
    • gi|3402099|pdb|1AM4|F_3:177 Chain F, Complex Between Cdc42hs.Gmppnp And P50 Rhogap (H. Sapiens) [Taxonomy]
    • gi|3402097|pdb|1AM4|E Chain E, Complex Between Cdc42hs.Gmppnp And P50 Rhogap (H. Sapiens) [Taxonomy]
    • gi|3402095|pdb|1AM4|D Chain D, Complex Between Cdc42hs.Gmppnp And P50 Rhogap (H. Sapiens) [Taxonomy]
    • gi|76638452|ref|XP_598212.2|_34:199 PREDICTED: similar to RAB33B, member RAS oncogene family [Bos taurus]
    • gi|76639295|ref|XP_871153.1|_62:222 PREDICTED: similar to RAB35, member RAS oncogene family (predicted) [Bos taurus]
    • gi|9257040|pdb|1DPF|A_5:178 Chain A, Crystal Structure Of A Mg-Free Form Of Rhoa Complexed With Gdp [Taxonomy]
    • gi|83754993|pdb|2EW1|A_27:187 Chain A, Crystal Structure Of Rab30 In Complex With A Gtp Analogue [Taxonomy]
    • gi|76661316|ref|XP_873392.1|_8:169 PREDICTED: similar to RAB18, member RAS oncogene family (predicted) [Bos taurus]
    • gi|13096554|pdb|1FOE|H_3:176 Chain H, Crystal Structure Of Rac1 In Complex With The Guanine Nucleotide Exchange Region Of Tiam1 [Taxonomy]
    • gi|13096552|pdb|1FOE|F Chain F, Crystal Structure Of Rac1 In Complex With The Guanine Nucleotide Exchange Region Of Tiam1 [Taxonomy]
    • gi|13096550|pdb|1FOE|D Chain D, Crystal Structure Of Rac1 In Complex With The Guanine Nucleotide Exchange Region Of Tiam1 [Taxonomy]
    • gi|13096548|pdb|1FOE|B Chain B, Crystal Structure Of Rac1 In Complex With The Guanine Nucleotide Exchange Region Of Tiam1 [Taxonomy]
    • gi|58177306|pdb|1XCG|F_3:176 Chain F, Crystal Structure Of Human Rhoa In Complex With DhPH Fragment Of Pdzrhogef [Taxonomy]
    • gi|58177304|pdb|1XCG|B Chain B, Crystal Structure Of Human Rhoa In Complex With DhPH Fragment Of Pdzrhogef [Taxonomy]
    • gi|85082713|ref|XP_956972.1|_9:170 hypothetical protein ( (NM_017382) RAB11a, member RAS oncogene family [Mus musculus] sp|Q9JLX1|R11A_MOUSE RAS-RELATED PROTEIN RAB-11A gb|AAF36458.1|AF127669_1 (AF127669) small GTPase [Mus musculus] ) [Neurospora crassa OR74A]
    • gi|32414965|ref|XP_327962.1| hypothetical protein ( (NM_017382) RAB11a, member RAS oncogene family [Mus musculus] sp|Q9JLX1|R11A_MOUSE RAS-RELATED PROTEIN RAB-11A gb|AAF36458.1|AF127669_1 (AF127669) small GTPase [Mus musculus] ) [Neurospora crassa OR74A]
    • gi|28918054|gb|EAA27736.1| hypothetical protein ( (NM_017382) RAB11a, member RAS oncogene family [Mus musculus] sp|Q9JLX1|R11A_MOUSE RAS-RELATED PROTEIN RAB-11A gb|AAF36458.1|AF127669_1 (AF127669) small GTPase [Mus musculus] ) [Neurospora crassa]
    • gi|6980759|pdb|1CC0|C_5:178 Chain C, Crystal Structure Of The Rhoa.Gdp-Rhogdi Complex [Taxonomy]
    • gi|6980757|pdb|1CC0|A Chain A, Crystal Structure Of The Rhoa.Gdp-Rhogdi Complex [Taxonomy]
    • gi|30750043|pdb|1OW3|B_5:178 Chain B, Crystal Structure Of Rhoa.Gdp.Mgf3-In Complex With Rhogap [Taxonomy]
    • gi|2981782|pdb|1FTN| Crystal Structure Of The Human RhoaGDP COMPLEX [Taxonomy]
    • gi|15826631|pdb|1HH4|B_3:176 Chain B, Rac1-Rhogdi Complex Involved In Nadph Oxidase Activation [Taxonomy]
    • gi|15826630|pdb|1HH4|A Chain A, Rac1-Rhogdi Complex Involved In Nadph Oxidase Activation [Taxonomy]
    • gi|76645968|ref|XP_879487.1|_23:184 PREDICTED: similar to RAB37, member RAS oncogene family isoform 3 [Bos taurus]
    • gi|76668547|ref|XP_585448.2|_223:383 PREDICTED: similar to RAB14, member RAS oncogene family [Bos taurus]
    • gi|85544637|pdb|2F7S|B_26:197 Chain B, The Crystal Structure Of Human Rab27b Bound To Gdp [Taxonomy]
    • gi|85544636|pdb|2F7S|A Chain A, The Crystal Structure Of Human Rab27b Bound To Gdp [Taxonomy]
    • gi|82408217|pdb|2C2H|B_3:176 Chain B, Crystal Structure Of The Human Rac3 In Complex With Gdp [Taxonomy]
    • gi|82408216|pdb|2C2H|A Chain A, Crystal Structure Of The Human Rac3 In Complex With Gdp [Taxonomy]
    • gi|30749373|pdb|1KMQ|A_8:181 Chain A, Crystal Structure Of A Constitutively Activated Rhoa Mutant (Q63l) [Taxonomy]
    • gi|55667303|ref|XP_528758.1|_75:235 PREDICTED: similar to c-K-ras2 protein isoform b; Kirsten rat sarcoma-2 viral (v-Ki-ras2) oncogene homolog; transforming protein p21; c-Kirsten-ras protein; K-ras p21 protein; oncogene KRAS2; c-K-ras protein; PR310 c-K-ras oncogene; cellular c-Ki-ras2 proto-o... [Pan troglodytes]
    • gi|76658667|ref|XP_870111.1|_37:202 PREDICTED: similar to Ras-related protein Rab-33A (Small GTP-binding protein S10) isoform 2 [Bos taurus]
    • gi|60593433|pdb|1OIX|A_30:190 Chain A, X-Ray Structure Of The Small G Protein Rab11a In Complex With Gdp And Pi [Taxonomy]
    • gi|42543204|pdb|1OIW|A Chain A, X-Ray Structure Of The Small G Protein Rab11a In Complex With Gtpgammas [Taxonomy]
    • gi|76645964|ref|XP_869879.1|_29:191 PREDICTED: similar to Ras-related protein Rab-37 isoform 1 [Bos taurus]
    • gi|13096181|pdb|1HUQ|A_3:164 Chain A, 1.8a Crystal Structure Of The Monomeric Gtpase Rab5c (Mouse) [Taxonomy]
    • gi|50344776|ref|NP_001002061.1|_3:176 ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) [Danio rerio]
    • gi|47940026|gb|AAH71369.1| Ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) [Danio rerio]
    • gi|4557959|pdb|1ZBD|A_8:169 Chain A, Structural Basis Of Rab Effector Specificity: Crystal Structure Of The Small G Protein Rab3a Complexed With The Effector Domain Of Rabphilin-3a [Taxonomy]
    • gi|13096378|pdb|1G4U|R_3:176 Chain R, Crystal Structure Of The Salmonella Tyrosine Phosphatase And Gtpase Activating Protein Sptp Bound To Rac1 [Taxonomy]
    • gi|68443483|ref|XP_701100.1|_10:171 PREDICTED: similar to RAP2A, member of RAS oncogene family [Danio rerio]
    • gi|50741401|ref|XP_419573.1|_14:174 PREDICTED: similar to RAB4A, member RAS oncogene family; Oncogene RAB4; RAB4, member RAS oncogene family [Gallus gallus]
    • gi|66361571|pdb|2BME|D_11:171 Chain D, High Resolution Structure Of Gppnhp-Bound Human Rab4a [Taxonomy]
    • gi|66361570|pdb|2BME|C Chain C, High Resolution Structure Of Gppnhp-Bound Human Rab4a [Taxonomy]
    • gi|66361569|pdb|2BME|B Chain B, High Resolution Structure Of Gppnhp-Bound Human Rab4a [Taxonomy]
    • gi|66361568|pdb|2BME|A Chain A, High Resolution Structure Of Gppnhp-Bound Human Rab4a [Taxonomy]
    • gi|66361567|pdb|2BMD|A Chain A, High Resolution Structure Of Gdp-Bound Human Rab4a [Taxonomy]
    • gi|6730595|pdb|3RAP|S_3:164 Chain S, The Small G Protein Rap2 In A Non Catalytic Complex With Gtp [Taxonomy]
    • gi|6730594|pdb|3RAP|R Chain R, The Small G Protein Rap2 In A Non Catalytic Complex With Gtp [Taxonomy]
    • gi|3318816|pdb|2RAP| The Small G Protein Rap2a In Complex With Gtp [Taxonomy]
    • gi|2780995|pdb|1KAO| Crystal Structure Of The Small G Protein Rap2a With Gdp [Taxonomy]
    • gi|83754940|pdb|2ERY|B_5:166 Chain B, The Crystal Structure Of The Ras Related Protein Rras2 (Rras2) In The Gdp Bound State [Taxonomy]
    • gi|83754939|pdb|2ERY|A Chain A, The Crystal Structure Of The Ras Related Protein Rras2 (Rras2) In The Gdp Bound State [Taxonomy]
    • gi|68405670|ref|XP_693356.1|_234:394 PREDICTED: similar to Transforming protein p21/H-Ras-1 (c-H-ras) [Danio rerio]
    • gi|51247937|pdb|1VG9|H_9:173 Chain H, The Crystal Structures Of The Rep-1 Protein In Complex With C-Terminally Truncated Rab7 Protein [Taxonomy]
    • gi|51247935|pdb|1VG9|F Chain F, The Crystal Structures Of The Rep-1 Protein In Complex With C-Terminally Truncated Rab7 Protein [Taxonomy]
    • gi|51247933|pdb|1VG9|D Chain D, The Crystal Structures Of The Rep-1 Protein In Complex With C-Terminally Truncated Rab7 Protein [Taxonomy]
    • gi|51247931|pdb|1VG9|B Chain B, The Crystal Structures Of The Rep-1 Protein In Complex With C-Terminally Truncated Rab7 Protein [Taxonomy]
    • gi|51247925|pdb|1VG1|A Chain A, Gdp-Bound Rab7 [Taxonomy]
    • gi|642532|gb|AAB08927.1|_21:182 ras-related small GTP binding protein Rab5 [Taxonomy]
    • gi|508285|gb|AAA74081.1| Rab5c-like protein, similar to Canis familiaris Rab5c protein, PIR Accession Number S38625 [Taxonomy]
    • gi|50760525|ref|XP_425821.1|_31:194 PREDICTED: similar to solute carrier family 26, member 9 isoform a; anion transporter/exchanger-9 [Gallus gallus]
    • gi|67464498|pdb|1Z2C|C_5:178 Chain C, Crystal Structure Of Mdia1 Gbd-Fh3 In Complex With Rhoc- Gmppnp [Taxonomy]
    • gi|67464496|pdb|1Z2C|A Chain A, Crystal Structure Of Mdia1 Gbd-Fh3 In Complex With Rhoc- Gmppnp [Taxonomy]
    • gi|2392389|pdb|1JAH|_3:163 H-Ras P21 Protein Mutant G12p, Complexed With Guanosine-5'-[beta,Gamma-Methylene] Triphosphate And Magnesium [Taxonomy]
    • gi|576243|pdb|1PLK| C-H-Ras P21 Protein Mutant With Gly 12 Replaced By Pro (G12p) Complexed With Guanosine-Triphosphate [Taxonomy]
    • gi|14277769|pdb|1I4T|D_3:176 Chain D, Crystal Structure Analysis Of Rac1-Gmppnp In Complex With Arfaptin [Taxonomy]
    • gi|68372738|ref|XP_685892.1|_39:204 PREDICTED: similar to Ras-related protein Rab-33A (Small GTP-binding protein S10) [Danio rerio]
    • gi|58332274|ref|NP_001011285.1|_3:176 Novel protein similar to ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) [Xenopus tropicalis]
    • gi|56789686|gb|AAH87999.1| Novel protein similar to ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) [Xenopus tropicalis]
    • gi|89272958|emb|CAJ82940.1| Novel protein similar to ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) [Xenopus tropicalis]
    • gi|5107569|pdb|1CLU|A_3:163 Chain A, H-Ras Complexed With Diaminobenzophenone-Beta,Gamma-Imido- Gtp [Taxonomy]
    • gi|2392390|pdb|1JAI| H-Ras P21 Protein Mutant G12p, Complexed With Guanosine-5'-[beta,Gamma-Methylene] Triphosphate And Manganese [Taxonomy]
    • gi|494936|pdb|821P| C-H-Ras P21 Protein (Residues 1 - 166) Mutant With Gly 12 Replaced By Pro (G12p) Complex With Guanosine-5'-[b,G-Imido] Triphosphate [Taxonomy]
    • gi|576244|pdb|1PLL| C-H-Ras P21 Protein Mutant With Gly 12 Replaced By Pro (G12p) Complexed With Guanosine-Diphosphate [Taxonomy]
    • gi|576242|pdb|1PLJ| C-H-Ras P21 Protein Mutant With Gly 12 Replaced By Pro (G12p) Complexed With P3-1-(2-Nitrophenyl)ethyl- Guanosine-5'-(B,G-Imido)-Triphosphate [Taxonomy]
    • gi|76658483|ref|XP_589241.2|_20:181 PREDICTED: similar to Ras-related protein Rab-5A isoform 1 [Bos taurus]
    • gi|76658481|ref|XP_869695.1| PREDICTED: similar to Ras-related protein Rab-5A isoform 2 [Bos taurus]
    • gi|40889551|pdb|1R2Q|A_6:167 Chain A, Crystal Structure Of Human Rab5a Gtpase Domain At 1.05 A Resolution [Taxonomy]
    • gi|27066008|pdb|1N6H|A Chain A, Crystal Structure Of Human Rab5a [Taxonomy]
    • gi|55670035|pdb|1TU3|E_7:168 Chain E, Crystal Structure Of Rab5 Complex With Rabaptin5 C-Terminal Domain [Taxonomy]
    • gi|55670034|pdb|1TU3|D Chain D, Crystal Structure Of Rab5 Complex With Rabaptin5 C-Terminal Domain [Taxonomy]
    • gi|55670033|pdb|1TU3|C Chain C, Crystal Structure Of Rab5 Complex With Rabaptin5 C-Terminal Domain [Taxonomy]
    • gi|55670032|pdb|1TU3|B Chain B, Crystal Structure Of Rab5 Complex With Rabaptin5 C-Terminal Domain [Taxonomy]
    • gi|55670031|pdb|1TU3|A Chain A, Crystal Structure Of Rab5 Complex With Rabaptin5 C-Terminal Domain [Taxonomy]
    • gi|55664283|ref|XP_529151.1|_37:202 PREDICTED: similar to Ras-related protein Rab-33A (Small GTP-binding protein S10) [Pan troglodytes]
    • gi|76618740|ref|XP_883986.1|_20:181 PREDICTED: similar to RAB5B, member RAS oncogene family isoform 6 [Bos taurus]
    • gi|76618732|ref|XP_871705.1| PREDICTED: similar to RAB5B, member RAS oncogene family isoform 3 [Bos taurus]
    • gi|90109691|pdb|2FV8|A_25:198 Chain A, The Crystal Structure Of Rhob In The Gdp-Bound State [Taxonomy]
    • gi|27066016|pdb|1N6N|A_6:167 Chain A, Crystal Structure Of Human Rab5a A30r Mutant Complex With Gppnhp [Taxonomy]
    • gi|27066012|pdb|1N6L|A_6:167 Chain A, Crystal Structure Of Human Rab5a A30p Mutant Complex With Gtp [Taxonomy]
    • gi|27066010|pdb|1N6K|A Chain A, Crystal Structure Of Human Rab5a A30p Mutant Complex With Gdp And Aluminum Fluoride [Taxonomy]
    • gi|27066009|pdb|1N6I|A Chain A, Crystal Structure Of Human Rab5a A30p Mutant Complex With Gdp [Taxonomy]
    • gi|24158631|pdb|1GZS|C_5:179 Chain C, Crystal Structure Of The Complex Between The Gef Domain Of The Salmonella Typhimurium Sope Toxin And Human Cdc42 [Taxonomy]
    • gi|24158629|pdb|1GZS|A Chain A, Crystal Structure Of The Complex Between The Gef Domain Of The Salmonella Typhimurium Sope Toxin And Human Cdc42 [Taxonomy]
    • gi|29726779|pdb|1NVX|R_3:163 Chain R, Structural Evidence For Feedback Activation By Rasgtp Of The Ras-Specific Nucleotide Exchange Factor Sos [Taxonomy]
    • gi|29726778|pdb|1NVX|Q Chain Q, Structural Evidence For Feedback Activation By Rasgtp Of The Ras-Specific Nucleotide Exchange Factor Sos [Taxonomy]
    • gi|29726770|pdb|1NVU|R Chain R, Structural Evidence For Feedback Activation By Rasgtp Of The Ras-Specific Nucleotide Exchange Factor Sos [Taxonomy]
    • gi|29726769|pdb|1NVU|Q Chain Q, Structural Evidence For Feedback Activation By Rasgtp Of The Ras-Specific Nucleotide Exchange Factor Sos [Taxonomy]
    • gi|24987571|pdb|1LF5|A Chain A, Crystal Structure Of Rasa59g In The Gdp-Bound Form [Taxonomy]
    • gi|24987567|pdb|1LF0|A Chain A, Crystal Structure Of Rasa59g In The Gtp-Bound Form [Taxonomy]
    • gi|9719734|gb|AAF97836.1|_14:174 Contains similarity to ras-related GTP binding protein from Oryza sativa gb|D13758 and is a member of the Ras PF|00071 family. [Arabidopsis thaliana]
    • gi|68365242|ref|XP_706751.1|_5:182 PREDICTED: similar to aplysia ras-related homolog A2 isoform 2 [Danio rerio]
    • gi|27066018|pdb|1N6O|A_6:167 Chain A, Crystal Structure Of Human Rab5a A30k Mutant Complex With Gppnhp [Taxonomy]
    • gi|7546358|pdb|1EES|A_3:177 Chain A, Solution Structure Of Cdc42hs Complexed With A Peptide Derived From P-21 Activated Kinase, Nmr, 20 Structures [Taxonomy]
    • gi|27066019|pdb|1N6P|A_6:167 Chain A, Crystal Structure Of Human Rab5a A30e Mutant Complex With Gppnhp [Taxonomy]
    • gi|55630750|ref|XP_519779.1|_7:192 PREDICTED: similar to RAB2, member RAS oncogene family; small GTP binding protein RAB2A [Pan troglodytes]
    • gi|55663888|ref|XP_529084.1|_91:255 PREDICTED: similar to Ras-related protein Rab-9B (Rab-9L) (RAB9-like protein) [Pan troglodytes]