(c) 1992-2000 Regents of the University of California, Santa Cruz
Sequence Alignment and Modeling Software System
http://www.cse.ucsc.edu/research/compbio/sam.html
Citations (SAM, SAM-T99, HMMs)
- R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
- K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting remote protein homologies, Bioinformatics 14(10):846-856, 1998.
- A. Krogh et al., Hidden Markov models in computational biology: Applications to protein modeling, JMB 235:1501-1531, Feb 1994.
Sequence numbers correspond to the following labels:
-
- T0498 L1c, E coli, 56 residues
-
- gi|99032573|pdb|2GI9|A_1:56 Chain A, Backbone Conformational Constraints In A Microcrystalline U- 15n-Labeled Protein By 3d Dipolar-Shift Solid-State Nmr Spectroscopy [Taxonomy]
- gi|161760905|pdb|2JU6|X Chain X, Solid-State Protein Structure Determination With Proton- Detected Triple Resonance 3d Magic-Angle Spinning Nmr Spectroscopy [Taxonomy]
- gi|163931020|pdb|2QMT|A Chain A, Crystal Polymorphism Of Protein Gb1 Examined By Solid-State Nmr And X-Ray Diffraction [Taxonomy]
- gi|183448054|pdb|2JSV|X Chain X, Dipole Tensor-Based Refinement For Atomic-Resolution Structure Determination Of A Nanocrystalline Protein By Solid-State Nmr Spectroscopy [Taxonomy]
-
-
- gi|34810871|pdb|1P7E|A_1:56 Chain A, Gb3 Solution Structure Obtained By Refinement Of X-Ray Structure With Dipolar Couplings [Taxonomy]
- gi|34810872|pdb|1P7F|A Chain A, Gb3 Solution Structure Obtained By Refinement Of X-Ray Structure With Dipolar Couplings [Taxonomy]
- gi|126031555|pdb|2OED|A Chain A, Gb3 Solution Structure Obtained By Refinement Of X-Ray Structure With Dipolar Couplings [Taxonomy]
-
- gi|1065200|pdb|1FCC|C_1:56 Chain C, Crystal Structure Of The C2 Fragment Of Streptococcal Protein G In Complex With The Fc Domain Of Human Igg [Taxonomy]
- gi|157875391|pdb|1FCC|D Chain D, Crystal Structure Of The C2 Fragment Of Streptococcal Protein G In Complex With The Fc Domain Of Human Igg [Taxonomy]
-
- gi|5542539|pdb|3GB1|A_1:56 Chain A, Structures Of B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|157831155|pdb|1GB1|A Chain A, A Novel, Highly Stable Fold Of The Immunoglobulin Binding Domain Of Streptococcal Protein G [Taxonomy]
- gi|157833473|pdb|1PGA|A Chain A, Two Crystal Structures Of The B1 Immunoglobulin-Binding Domain Of Streptococcal Protein G And Comparison With Nmr [Taxonomy]
- gi|157833474|pdb|1PGB|A Chain A, Two Crystal Structures Of The B1 Immunoglobulin-Binding Domain Of Streptoccocal Protein G And Comparison With Nmr [Taxonomy]
- gi|157835028|pdb|2GB1|A Chain A, A Novel, Highly Stable Fold Of The Immunoglobulin Binding Domain Of Streptococcal Protein G [Taxonomy]
-
- gi|14278227|pdb|1IBX|B_1:56 Chain B, Nmr Structure Of Dff40 And Dff45 N-Terminal Domain Complex
-
- gi|119390478|pdb|2NMQ|A_1:55 Chain A, Simultaneous Determination Of Protein Structure And Dynamics Using Rdcs [Taxonomy]
-
- gi|157883859|pdb|2I2Y|A_1:56 Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc [Taxonomy]
-
-
- gi|158428903|pdb|2J52|A_1:56 Chain A, Solution Structure Of Gb1 Domain Protein G And Low And High Pressure. [Taxonomy]
- gi|158428904|pdb|2J53|A Chain A, Solution Structure Of Gb1 Domain Protein G And Low And High Pressure [Taxonomy]
-
-
- gi|15988267|pdb|1FD6|A_2:57 Chain A, Delta0: A Computationally Designed Core Variant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
-
-
-
- gi|157835190|pdb|2IGH|A_6:61 Chain A, Determination Of The Solution Structures Of Domains Ii And Iii Of Protein G From Streptococcus By 1h Nmr [Taxonomy]
-
- gi|1064973|pdb|1IGC|A_6:61 Chain A, Igg1 Fab Fragment (Mopc21) Complex With Domain Iii Of Protein G From Streptococcus [Taxonomy]
- gi|157831452|pdb|1IGD|A Chain A, The Third Igg-Binding Domain From Streptococcal Protein G: An Analysis By X-Ray Crystallography Of The Structure Alone And In A Complex With Fab [Taxonomy]
- gi|157835188|pdb|2IGD|A Chain A, Anisotropic Structure Of Protein G Igg-Binding Domain Iii At 1.1 Angstrom Resolution [Taxonomy]
-
- gi|149243209|pdb|2PLP|A_1:54 Chain A, Ultra High Resolution Backbone Conformation Of Protein Gb1 From Residual Dipolar Couplings Alone [Taxonomy]
-
- gi|38492880|pdb|1Q10|A_1:56 Chain A, Ensemble Of 40 Structures Of The Dimeric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|38492881|pdb|1Q10|B Chain B, Ensemble Of 40 Structures Of The Dimeric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
-
-
-
-
-
- gi|15988266|pdb|1FCL|A_1:56 Chain A, Delta1.5: A Computationally Designed Core Variant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
-
- gi|21465426|pdb|1EM7|A_1:56 Chain A, Helix Variant Of The B1 Domain From Streptococcal Protein G [Taxonomy]
-
- gi|7245924|pdb|1QKZ|A_6:61 Chain A, Fab Fragment (Mn14c11.6) In Complex With A Peptide Antigen Derived From Neisseria Meningitidis P1.7 Serosubtype Antigen And Domain Ii From Streptococcal Protein G [Taxonomy]
-
- gi|71041692|pdb|1UWX|A_5:60 Chain A, P1.2 Serosubtype Antigen Derived From N. Meningitidis Pora In Complex With Fab Fragment [Taxonomy]
- gi|71041693|pdb|1UWX|B Chain B, P1.2 Serosubtype Antigen Derived From N. Meningitidis Pora In Complex With Fab Fragment [Taxonomy]
-
-
-
- gi|157835189|pdb|2IGG|A_6:61 Chain A, Determination Of The Solution Structures Of Domains Ii And Iii Of Protein G From Streptococcus By 1h Nmr [Taxonomy]
-
-
-
-
- gi|109157407|pdb|2CWB|A_7:62 Chain A, Solution Structure Of The Ubiquitin-Associated Domain Of Human Bmsc-Ubp And Its Complex With Ubiquitin
- gi|110591203|pdb|2DEN|A Chain A, Solution Structure Of The Ubiquitin-Associated Domain Of Human Bmsc-Ubp And Its Complex With Ubiquitin
-
-
-
- gi|161761023|pdb|2ON8|A_1:56 Chain A, Gbeta1 Stabilization By In Vitro Evolution And Computational Design [Taxonomy]
-
- gi|164519462|pdb|2ONQ|A_1:56 Chain A, Gbeta1 Stabilization By In Vitro Evolution And Computational Design [Taxonomy]
-
- gi|24987790|pdb|1MPE|A_1:56 Chain A, Ensemble Of 20 Structures Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987791|pdb|1MPE|B Chain B, Ensemble Of 20 Structures Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987792|pdb|1MPE|C Chain C, Ensemble Of 20 Structures Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987793|pdb|1MPE|D Chain D, Ensemble Of 20 Structures Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987819|pdb|1MVK|A Chain A, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987820|pdb|1MVK|B Chain B, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987821|pdb|1MVK|C Chain C, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987822|pdb|1MVK|D Chain D, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987823|pdb|1MVK|E Chain E, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987824|pdb|1MVK|F Chain F, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987825|pdb|1MVK|G Chain G, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987826|pdb|1MVK|H Chain H, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987827|pdb|1MVK|I Chain I, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987828|pdb|1MVK|J Chain J, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987829|pdb|1MVK|K Chain K, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987830|pdb|1MVK|L Chain L, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
-
-
-
-
-
-
-
-
- gi|157833481|pdb|1PGX|A_14:69 Chain A, The 1.66 Angstroms X-Ray Structure Of The B2 Immunoglobulin- Binding Domain Of Streptococcal Protein G And Comparison To The Nmr Structure Of The B1 Domain [Taxonomy]
-
- gi|157831156|pdb|1GB4|A_2:57 Chain A, Hyperthermophilic Variant Of The B1 Domain From Streptococcal Protein G, Nmr, 47 Structures [Taxonomy]
-
-
-
-
-
-
-
- gi|24159073|pdb|1MI0|A_10:65 Chain A, Crystal Structure Of The Redesigned Protein G Variant Nug2 [Taxonomy]
- gi|24159074|pdb|1MI0|B Chain B, Crystal Structure Of The Redesigned Protein G Variant Nug2 [Taxonomy]
-
-
-
-
-
- gi|24159072|pdb|1MHX|A_10:65 Chain A, Crystal Structures Of The Redesigned Protein G Variant Nug1 [Taxonomy]
-
-
-
-
-
-
- T0498 L1c, E coli, 56 residues
10 20 30 40 50
| | | | |
1 ...T.TYKL.IL..N.LKQAKEEAIKELVDAGTAEKYIKLIANAKTVEGVWTLKDEIKTFTVTE.
2 ...M.QYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE.
3 ...M.QYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYFNDNGVDGEWTYDDATKTFTVTE.
4 ...M.QYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE.
5 ...T.TYKL.VI..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE.
6 ...M.TYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE.
7 ...M.QYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEs
8 ...-.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE.
9 ...M.QYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEg
10 ...M.QYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEg
11 ...M.TYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDAATKTFTVTE.
12 ...M.QYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEg
13 m..T.TFKL.II..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGIDGEWTYDDATKTFTVTE.
14 pavT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE.
15 pavT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE.
16 pavT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE.
17 pavT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE.
18 ...-.TYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVT-.
19 ...M.QYKV.IL..N.GKTLKGETTTEAVDAATAEKVVKQFFNDNGVDGEWTYDDATKTFTVTE.
20 pktD.TYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEk
21 pktD.TYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEk
22 pktD.TYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEk
23 m..T.TYKL.VI..N.GKTLKGETTTKTVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEm
24 ...T.TFKL.II..N.GKTLKGETTTEAVDAATAEKVLKQYINDNGIDGEWTYDDATKTWTVTE.
25 ...T.TYKL.IL..N.GKTLKGETTTEAVDAETAERVFKEYAKKNGVDGEWTYDDATKTFTVTE.
26 pavT.TYKL.VI..N.GKTLKGETTTKAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEk
27 pavT.TYKL.VI..N.GKTLKGETTTKAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEk
28 pavT.TYKL.VI..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEk
29 pavT.TYKL.VI..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEk
30 pavT.TYKL.VI..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEk
31 pavT.TYKL.VI..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEk
32 gshM.QYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTYTVTEg
33 ep.MdTYKL.IL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEk
34 hhhH.QYKL.AL..N.GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEg
35 pavT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEi
36 pavT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEm
37 ...M.QFKL.II..N.GKTLKGEITLEAVDAAEAEKKFKQYANDNGIDGEWTYDDATKTFTVTE.
38 ...M.QFKL.II..N.GKTLKGEITIEAVDAAEAEKFFKQYANDNGIDGEWTYDDATKTFTVTE.
39 ...M.QYKV.IL..N.GKTLKGETTTEAVDAATFEKVVKQFFNDNGVDGEWTYDDATKTFTVTE.
40 pavT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEv
41 pavT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEv
42 palT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANENGVDGVWTYDDATKTFTVTEm
43 palT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANENGVDGVWTYDDATKTFTVTEm
44 pavT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEm
45 pavT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEm
46 pavT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEm
47 pavT.TYKL.VI..N.GKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEm
48 m..T.TFKL.II..N.GKTLKGEITIEAVDAAEAEKIFKQYANDNGIDGEWTYDDATKTFTVTE.
49 palT.TYKL.VI..N.GKTLKGETTTKAVDVETAEKAFKQYANENGVDGVWTYDDATKTFTVTEm
50 palT.TYKL.IV..K.GNTFSGETTTKAVDAETAEKAFKQYANENGVYGEWSYDDATKTFTVTEk
51 palT.TYKL.IV..K.GNTFSGETTTKAIDAATAEKEFKQYATANGVDGEWSYDDATKTFTVTEk
52 palT.TYKL.IV..K.GNTFSGETTTKAVDAETAEKAFKQYATANNVDGEWSYDDATKTFTVTEk
53 palT.TYKL.IV..K.GNTFSGETTTKAVDAETAEKAFKQYATANNVDGEWSYDDATKTFTVTEk
54 palT.TYKL.IV..K.GNTFSGETTTKAIDAATAEKEFKQYATANNVDGEWSYDDATKTFTVTEk
55 ha.MdTYKL.VIvlN.GTTFTY--TTEAVDAATAEKVFKQYANDNGVDGEWTYADATKTFTVTE.
56 palT.TYKL.VV..K.GNTFSGETTTKAIDTATAEKEFKQYATANNVDGEWSYDDATKTFTVTEk
57 palT.TYKL.VV..K.GNTFSGETTTKAIDTATAEKEFKQYATANNVDGEWSYDDATKTFTVTEk
58 palT.TYKL.IV..K.GNTFSGETTTKAIDAATAEKEFKQYATANNVDGEWSYDYATKTFTVTEk
59 palT.TYRL.VI..K.GVTFSGETATKAVDAATAEQAFRQYANDNGVTGEWAYDAATKTFTVTEa
60 ha.MdTYKLfIV..I.GDRVV-VVTTEAVDAATAEKVFKQYANDNGVDGEWTYDDAAKTFTVTE.
61 palT.TYRL.VI..K.GVTFSGETATKAVDAATAEQTFRQYANDNGITGEWAYDTATKTFTVTEa
62 palT.SYKL.VI..K.GATFSGETATKAVDAAVAEQTFRDYANKNGVDGVWAYDAATKTFTVTEq
63 palT.SYKL.VI..K.GATFSGETATKAVDAAVAEQTFRDYANKNGVDGVWAYDAATKTFTVTEq
64 ...-.----.--..-.---MKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEk
65 ...-.MYYL.VV..NkGQNAFYETLTKAVDAETARNAFIQSLKDDGVQGVWTYDDATKTFTVQA.
66 ...T.TYKL.IL..N.LKQAKEEAIKELVDAGTAEKYIKLIANAKTVEGVWTLKDEIKTFTVTE.
1 ..
2 ..
3 ..
4 ..
5 ..
6 ..
7 ge
8 ..
9 sh
10 sh
11 ..
12 sm
13 ..
14 ..
15 ..
16 ..
17 ..
18 ..
19 ..
20 pe
21 pe
22 pe
23 dp
24 ..
25 ..
26 pe
27 pe
28 pe
29 pe
30 pe
31 pe
32 sc
33 pe
34 sq
35 de
36 ..
37 ..
38 ..
39 ..
40 nt
41 nt
42 vt
43 vt
44 vt
45 vt
46 vt
47 vt
48 ..
49 vt
50 pa
51 pa
52 pa
53 pa
54 pa
55 ..
56 pa
57 pa
58 pa
59 le
60 ..
61 le
62 pv
63 pv
64 pe
65 ..
66 ..