a2m2html output for tmp.a2m

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:

- T0383 Hypothetical Protein SP_1558, Streptococcus pneumoniae TIGR4, 127 res
- gi|62528163|ref|ZP_00389421.1|_1:124 COG4835: Uncharacterized protein conserved in bacteria [Streptococcus thermophilus LMD-9]
- gi|55738381|gb|AAV62022.1|_1:124 conserved hypothetical protein [Streptococcus thermophilus CNRZ1066]
- gi|55822396|ref|YP_140837.1| hypothetical protein str0421 [Streptococcus thermophilus CNRZ1066]
- gi|55820508|ref|YP_138950.1| conserved hypothetical protein, [Streptococcus thermophilus LMG 18311]
- gi|55736493|gb|AAV60135.1| conserved hypothetical protein, [Streptococcus thermophilus LMG 18311]
- gi|14973049|gb|AAK75645.1|_2:128 hypothetical protein SP_1558 [Streptococcus pneumoniae TIGR4]
- gi|15901401|ref|NP_346005.1| hypothetical protein SP1558 [Streptococcus pneumoniae TIGR4]
- gi|66879340|ref|ZP_00404363.1| COG4835: Uncharacterized protein conserved in bacteria [Streptococcus pneumoniae TIGR4]
- gi|15459070|gb|AAL00220.1|_2:128 Hypothetical protein [Streptococcus pneumoniae R6]
- gi|15903459|ref|NP_359009.1| hypothetical protein spr1416 [Streptococcus pneumoniae R6]
- gi|71853266|gb|AAZ51289.1|_1:124 transposase [Streptococcus pyogenes MGAS5005]
- gi|50903109|gb|AAT86824.1| Transposase [Streptococcus pyogenes MGAS10394]
- gi|13622031|gb|AAK33787.1| hypothetical protein SPy0864 [Streptococcus pyogenes M1 GAS]
- gi|94994158|ref|YP_602256.1| hypothetical cytosolic protein [Streptococcus pyogenes MGAS10750]
- gi|94992239|ref|YP_600338.1| hypothetical cytosolic protein [Streptococcus pyogenes MGAS2096]
- gi|94990238|ref|YP_598338.1| hypothetical cytosolic protein [Streptococcus pyogenes MGAS10270]
- gi|94988357|ref|YP_596458.1| hypothetical cytosolic protein [Streptococcus pyogenes MGAS9429]
- gi|94547666|gb|ABF37712.1| hypothetical cytosolic protein [Streptococcus pyogenes MGAS10750]
- gi|94545747|gb|ABF35794.1| hypothetical cytosolic protein [Streptococcus pyogenes MGAS2096]
- gi|94543746|gb|ABF33794.1| hypothetical cytosolic protein [Streptococcus pyogenes MGAS10270]
- gi|94541865|gb|ABF31914.1| hypothetical cytosolic protein [Streptococcus pyogenes MGAS9429]
- gi|71802411|gb|AAX71764.1| transposase [Streptococcus pyogenes MGAS6180]
- gi|50914035|ref|YP_060007.1| Transposase [Streptococcus pyogenes MGAS10394]
- gi|19748091|gb|AAL97569.1| hypothetical protein [Streptococcus pyogenes MGAS8232]
- gi|28811431|dbj|BAC64363.1| hypothetical protein [Streptococcus pyogenes SSI-1]
- gi|21904313|gb|AAM79192.1| conserved hypothetical protein [Streptococcus pyogenes MGAS315]
- gi|21910121|ref|NP_664389.1| hypothetical protein SpyM3_0585 [Streptococcus pyogenes MGAS315]
- gi|28896180|ref|NP_802530.1| hypothetical protein SPs1268 [Streptococcus pyogenes SSI-1]
- gi|19745934|ref|NP_607070.1| hypothetical protein spyM18_0925 [Streptococcus pyogenes MGAS8232]
- gi|15674892|ref|NP_269066.1| hypothetical protein SPy0864 [Streptococcus pyogenes M1 GAS]
- gi|71903316|ref|YP_280119.1| transposase [Streptococcus pyogenes MGAS6180]
- gi|71910484|ref|YP_282034.1| transposase [Streptococcus pyogenes MGAS5005]
- gi|76563355|gb|ABA45939.1|_1:124 conserved hypothetical protein [Streptococcus agalactiae A909]
- gi|22534369|gb|AAN00214.1| protein of unknown function [Streptococcus agalactiae 2603V/R]
- gi|22537490|ref|NP_688341.1| hypothetical protein SAG1343 [Streptococcus agalactiae 2603V/R]
- gi|24412993|emb|CAD47072.1| unknown [Streptococcus agalactiae NEM316]
- gi|76788298|ref|YP_329984.1| hypothetical protein SAK_1374 [Streptococcus agalactiae A909]
- gi|25011455|ref|NP_735850.1| hypothetical protein gbs1413 [Streptococcus agalactiae NEM316]
- gi|77414519|ref|ZP_00790666.1| protein of unknown function [Streptococcus agalactiae 515]
- gi|77411141|ref|ZP_00787493.1| protein of unknown function [Streptococcus agalactiae CJB111]
- gi|77162759|gb|EAO73718.1| protein of unknown function [Streptococcus agalactiae CJB111]
- gi|77159442|gb|EAO70606.1| protein of unknown function [Streptococcus agalactiae 515]
- gi|76798772|ref|ZP_00780988.1| Protein of unknown function (DUF1149) superfamily [Streptococcus agalactiae 18RS21]
- gi|76585879|gb|EAO62421.1| Protein of unknown function (DUF1149) superfamily [Streptococcus agalactiae 18RS21]
- gi|77409291|ref|ZP_00785996.1|_1:124 protein of unknown function [Streptococcus agalactiae COH1]
- gi|77172088|gb|EAO75252.1| protein of unknown function [Streptococcus agalactiae COH1]
- gi|24379350|ref|NP_721305.1|_1:124 hypothetical protein SMU.898 [Streptococcus mutans UA159]
- gi|24377276|gb|AAN58611.1| conserved hypothetical protein [Streptococcus mutans UA159]
- gi|81096796|ref|ZP_00875126.1|_1:124 conserved hypothetical protein [Streptococcus suis 89/1591]
- gi|80977148|gb|EAP40701.1| conserved hypothetical protein [Streptococcus suis 89/1591]
- gi|62464138|ref|ZP_00383437.1|_1:130 COG4835: Uncharacterized protein conserved in bacteria [Lactococcus lactis subsp. cremoris SK11]
- gi|12724566|gb|AAK05661.1|_1:130 UNKNOWN PROTEIN [Lactococcus lactis subsp. lactis Il1403]
- gi|15673545|ref|NP_267719.1| hypothetical protein L5610 [Lactococcus lactis subsp. lactis Il1403]
- gi|23003673|ref|ZP_00047327.1|_1:126 hypothetical protein Lgas_03001712 [Lactobacillus gasseri ATCC 33323]
- gi|58254298|gb|AAV42535.1|_1:125 hypothetical protein LBA0658 [Lactobacillus acidophilus NCFM]
- gi|58336981|ref|YP_193566.1| hypothetical protein LBA0658 [Lactobacillus acidophilus NCFM]
- gi|42518757|ref|NP_964687.1|_1:126 hypothetical protein LJ0832 [Lactobacillus johnsonii NCC 533]
- gi|41583043|gb|AAS08653.1| hypothetical protein LJ_0832 [Lactobacillus johnsonii NCC 533]
- gi|29342796|gb|AAO80560.1|_1:122 conserved hypothetical protein [Enterococcus faecalis V583]
- gi|29375336|ref|NP_814490.1| hypothetical protein EF0742 [Enterococcus faecalis V583]
- gi|81428094|ref|YP_395093.1|_1:126 hypothetical protein LSA0480 [Lactobacillus sakei subsp. sakei 23K]
- gi|78609735|emb|CAI54781.1| Hypothetical protein [Lactobacillus sakei subsp. sakei 23K]
- gi|104773702|ref|YP_618682.1|_1:127 hypothetical protein Ldb0592 [Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842]
- gi|103422783|emb|CAI97422.1| Conserved hypothetical protein [Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842]
- gi|62515590|ref|ZP_00386991.1| COG4835: Uncharacterized protein conserved in bacteria [Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365]
- gi|62514719|ref|ZP_00386216.1|_1:125 COG4835: Uncharacterized protein conserved in bacteria [Lactobacillus casei ATCC 334]
- gi|16412859|emb|CAC95663.1|_1:124 lin0430 [Listeria innocua]
- gi|16799507|ref|NP_469775.1| hypothetical protein lin0430 [Listeria innocua Clip11262]
- gi|47096598|ref|ZP_00234187.1|_1:124 conserved hypothetical protein [Listeria monocytogenes str. 1/2a F6854]
- gi|47015058|gb|EAL06002.1| conserved hypothetical protein [Listeria monocytogenes str. 1/2a F6854]
- gi|16409785|emb|CAC98486.1| lmo0407 [Listeria monocytogenes]
- gi|16802452|ref|NP_463937.1| hypothetical protein lmo0407 [Listeria monocytogenes EGD-e]
- gi|46906645|ref|YP_013034.1|_1:124 hypothetical protein LMOf2365_0427 [Listeria monocytogenes str. 4b F2365]
- gi|47091553|ref|ZP_00229350.1| conserved hypothetical protein [Listeria monocytogenes str. 4b H7858]
- gi|47020230|gb|EAL10966.1| conserved hypothetical protein [Listeria monocytogenes str. 4b H7858]
- gi|46879910|gb|AAT03211.1| conserved hypothetical protein [Listeria monocytogenes str. 4b F2365]
- gi|77409470|ref|ZP_00786162.1|_1:88 protein of unknown function [Streptococcus agalactiae COH1]
- gi|77171913|gb|EAO75090.1| protein of unknown function [Streptococcus agalactiae COH1]
- gi|56808916|ref|ZP_00366625.1|_1:93 COG4835: Uncharacterized protein conserved in bacteria [Streptococcus pyogenes M49 591]
- gi|77406292|ref|ZP_00783358.1|_1:71 protein of unknown function [Streptococcus agalactiae H36B]
- gi|77175104|gb|EAO77907.1| protein of unknown function [Streptococcus agalactiae H36B]

                 10           20                  30             40    
                 |            |                   |              |    
   1 .SNAMNLKR.E.QEFVSQYHFD...A..R..NFE.W..E.N..ENG..APETK.V..DVNFQ..L
   2 .---MDLIH.E.KVFVNRYHYD...V..R..NHE.W..E.K..ENG..VPKTN.V..EVTFQ..L
   3 .---MDLIH.E.KVFVNRYHYD...V..R..NHE.W..E.K..ENG..VPKTN.V..EVTFQ..L
   4 mEKDMNLKR.E.QEFVSQYHFD...A..R..NFE.W..E.N..ENG..APETK.V..DVNFQ..L
   5 mEKDMNLKR.E.QEFVSQYHFD...A..R..NFE.W..E.N..ENG..APETK.V..DVNFQ..L
   6 .---MQLVR.E.KEFVNQYHYD...A..R..NLE.W..E.K..ENG..TPETN.F..EVTFQ..L
   7 .---MEVIR.E.QEFVNQYHYD...A..R..NLE.W..E.E..ENG..TPKTN.F..EVTFQ..L
   8 .---MEVIR.E.QEFVNQYHYD...A..R..NLE.W..E.E..ENG..TPKTN.F..EVTFQ..L
   9 .---MEIVR.Q.KEFVNQYHYD...A..R..NLE.W..E.K..ENG..TPETD.V..EVTFQ..L
  10 .---MEIIR.D.KEFVNQYHFD...A..R..NHA.W..E.K..ENG..IPETK.L..KVDFQ..L
  11 .-MTLTIER.E.QEFVNQFHYD...A..R..NYE.W..E.K..ENG..TPETN.L..NVQFQ..L
  12 .-MALTIER.E.QEFVNQFHYD...A..R..NYE.W..E.K..ENG..TPETN.L..NVQFQ..L
  13 .---MDFKNmT.PIIVRSFHYD...L..N..DEQkV..K.N..EVN..VSLRQ.VyqDLDDG..S
  14 .---MDFEK.QtPVTVQSFHYD...L..V..DEG.VaaK.S..EVN..PGIRK.L..DVSGD..D
  15 .---MDFKNmT.PIVVRSFHYD...L..N..DEQkV..K.N..EVN..VSLRQ.VyqDLEDG..S
  16 .---MEIKR.Q.QEIVEAYHYD...M..RvpDSE.V..E.T..DLR..VSFSP.I..EVEEE..N
  17 .---MQTKK.D.PISVDAFHFD...R..V..SPD.A..E.P..QQNiqVSLVK.I..DADDE..Y
  18 .---MEFNK.QtPIIVRAFHYD...L..L..DEP.E..EkN..EVN..VAIRQ.V..VATGEdgV
  19 .---METKR.Y.PIAVESFHYD...LvkQ..GTP.V..K.N..DLQ..VAMRQ.I..EWS-D..P
  20 .---MDIVT.N.KIVVEKYNFEttmE..E..NQP.F..E.NkiELE..VHEVEpV..DGNVE..L
  21 .---MDIVT.N.KIVVEKYNFEtivE..E..NEQ.F..E.NkiELE..VHEVEpV..NGNVE..L
  22 .---MDIVT.N.KIVVEKYNFEtimE..E..NEQ.F..E.NkiELE..VHEVEpV..NGNVE..L
  23 .--------.-.----------...-..-..---.-..-.-..---..-----.-..---FQ..L
  24 .---MQLVR.E.KEFVNQYHYD...A..R..NLE.W..E.K..ENG..TPETN.F..EVTFQ..L
  25 .--------.-.----------...-..-..---.-..-.-..---..-----.-..-----..-


              50            60          70        80        90       10
              |             |           |         |         |         
   1 LQH.D.QENQV....TSLIVILSFMIVFDK..FVISGTISQVNHIDGRIVNEPSELNQEEVETLA
   2 HHK.D.KEANN....TSVVAVLQFMIVRDE..FVISGIISQMNHIQNRIVNNPKDFSQEEAEYLA
   3 HHK.D.KEANN....TSVVAVLQFMIVRDE..FVISGIVSQMNHIQNRIVNNPKDFSQEEAEYLA
   4 LQH.D.QENQV....TSLIVILSFMIVFDK..FVISGTISQVNHIDGRIVNEPSELNQEEVETLA
   5 LQH.D.QENQV....TSLIVILSFMIVFDK..FVISGTISQVNHIDGRIVNEPNELNQEEVETLA
   6 IDK.D.EQQKE....TVIVSVLQFVIVKEE..FVISGVISQMVRILDRLVDKPSEFTQEEVESLA
   7 ANR.D.EAAKV....TSIVAVLQFVIVRDE..FVISGVISQMAHIQGRLINEPSEFSQDEVENLA
   8 ANR.D.EAAKV....TSIVAVLQFVIVRDE..FVISGVISQIAHIQGRLINEPSEFSQDEVENLA
   9 VEK.N.EELNE....TTVVAVLQFMIVRDE..FVLSGVLSQMVKIKDRLVNQPSEFSQEEVATLA
  10 IEQ.N.RAENR....TSMITILRFMIVLDH..FVISGAMSQAVHLPNRLVEEPTEFTDEEKRVLV
  11 VPK.E.QLEKLgdrdTGIHAVLTYLIVLDN..IVLSGFVSQLNYVRGKIIKEQEELEQEELAQLA
  12 VPK.E.QLEKLgegdTGIHAVLTYLIVLDN..IVLSGFVSQLNYVRGQIIKEQEELEQEELAQLA
  13 QDE.G.KTGKY....FEIAVPFEVSPAPGD..FTVSGVITRVVQFVD-YFGDGTDLEPSDYQLLS
  14 EHS.E.EEGSY....YDVAVFFDVIPAPAE..FEVSGAIHQIVQIKN-YHGDGTDISNADWQLLS
  15 QDE.G.KNGKY....FEIAVPFEVSPAPGD..FTVSGVITRVVQFVD-YFGDGSDLEPSEYQLLS
  16 YPE.-.---NS....SALVARLEFRIVFDE..FVLSGAISQINHIIDRKIEKQEDISQEEVDELV
  17 LQEaDlKAGNI....YQIVTPFQVMPQGSG..FAVSGQISRVVQLLD-FFGTPDEIEQKEMMKLS
  18 EDA.G.EAGGY....YEVAVVYDVTPDEDNi.IEISGVNTQVVQLLG-YHGDGQDLDQETYRLLS
  19 AKQ.D.ELKKG....NLFQMMIPFDVVPDDagFEISGKITQIVQVLD-YFGEANELPQAELGKLS
  20 MAK.G.KIFKI....T-----IPFLLVLEN..FRIDGRISRIIQLKD-FFGQFSDLEAKDVEGLS
  21 MSK.G.KIFKI....T-----IPFLLVLEN..FRIDGRISRIIQLKD-FFGDFSDLEAVDVEGLS
  22 MSK.G.KIFKI....T-----IPFLLVLEN..FRIDGRISRIIQLKD-FFGDFSDLEAVDVEGLS
  23 ANR.D.EAAKV....TSIVAVLQFVIVRDE..XVISGVISQIAHIQGRLINEPSEFSQDEVENLA
  24 IDK.D.EQQKE....TVIVSVLQFVIVKEE..FVISGVISQMVRILDRLVDKPSELRKRKLNP--
  25 ---.-.-----....-----MLQFVIVRDE..FVISGVISQMAHIQGRLINEPSEFSQDEVENLA


      0       110       120          
     |         |         |          
   1 RPCLNMLNRLTYEVTEIALDLPGINLEF...
   2 APLLDTLQRLTYEVTEIALDRPGINLEF...
   3 APLLDTLQRLTYEVTEIALDRPGINLEF...
   4 RPCLNMLNRLTYEVTEIALDLPGINLEF...
   5 RPCLNMLNRLTYEVTEIALDLPGINLEF...
   6 APLLDMVKRLTYEVTEIALDRPGIHLEFkn.
   7 APLLEIVKRLTYEVTEIALDRPGVTLEFns.
   8 APLLEIVKRLTYEVTEIALDRPGVTLEFns.
   9 APLLDILKRMTYEVTEIALDKEGVSLEF...
  10 EPLLDILKRMTYEVTEIAFDAPGVNLEF...
  11 APLFDLLQRLVYETTEVALDHPGINLEF...
  12 APLFELLKRLVYETTEVALDQPGINLGF...
  13 RPLVEQIETLTYEITQLTLDHP-VNLSFksn
  14 RPLVEYIETLTYEVTQVTFDKP-VNLNFkae
  15 RPLVEEIETLTYEITQLTLDHP-VNLSFksn
  16 RPLFSIVERLSYEVTEIALDRPGVQLNFqqs
  17 RPLIEYIETLTYQVTAVALNE-GIQLQFtah
  18 RPLVEYIETLTYEVSQVALDEP-INLDFepn
  19 RPLVETIETLTYQVTAVALDQ-GVNLQFgas
  20 NPLIDYIKRLTYDVTEIAFDEPGVSLDFnan
  21 NPLIDYIKRLTYDVTEIAFDEPGVSLDFnan
  22 NPLIDYIKRLTYDVTEIAFDEPGVSLDFnan
  23 APLLEIVKRLTYEVTEIALDRPGVTLEFns.
  24 ----------------------------...
  25 APLLEIVKRLTYEVTEIALDRPGVTLEFns.