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|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|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|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|15459070|gb|AAL00220.1|_3:128 Hypothetical protein [Streptococcus pneumoniae R6]
- gi|15903459|ref|NP_359009.1| hypothetical protein spr1416 [Streptococcus pneumoniae R6]
- gi|14973049|gb|AAK75645.1|_3:128 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|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|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|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|12724566|gb|AAK05661.1|_3:130 UNKNOWN PROTEIN [Lactococcus lactis subsp. lactis Il1403]
- gi|15673545|ref|NP_267719.1| hypothetical protein L5610 [Lactococcus lactis subsp. lactis Il1403]
- gi|16412859|emb|CAC95663.1|_1:124 lin0430 [Listeria innocua]
- gi|16799507|ref|NP_469775.1| hypothetical protein lin0430 [Listeria innocua Clip11262]
- gi|62464138|ref|ZP_00383437.1|_4:130 COG4835: Uncharacterized protein conserved in bacteria [Lactococcus lactis subsp. cremoris SK11]
- 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|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|62514719|ref|ZP_00386216.1|_1:125 COG4835: Uncharacterized protein conserved in bacteria [Lactobacillus casei ATCC 334]
- 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|58254298|gb|AAV42535.1|_8:125 hypothetical protein LBA0658 [Lactobacillus acidophilus NCFM]
- gi|58336981|ref|YP_193566.1| hypothetical protein LBA0658 [Lactobacillus acidophilus NCFM]
- gi|42518757|ref|NP_964687.1|_8:126 hypothetical protein LJ0832 [Lactobacillus johnsonii NCC 533]
- gi|41583043|gb|AAS08653.1| hypothetical protein LJ_0832 [Lactobacillus johnsonii NCC 533]
- gi|23003673|ref|ZP_00047327.1|_8:126 hypothetical protein Lgas_03001712 [Lactobacillus gasseri ATCC 33323]
- gi|77409470|ref|ZP_00786162.1|_3:88 protein of unknown function [Streptococcus agalactiae COH1]
- gi|77171913|gb|EAO75090.1| protein of unknown function [Streptococcus agalactiae COH1]
- gi|104773702|ref|YP_618682.1|_7:127 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|77406292|ref|ZP_00783358.1|_2:71 protein of unknown function [Streptococcus agalactiae H36B]
- gi|77175104|gb|EAO77907.1| protein of unknown function [Streptococcus agalactiae H36B]
- gi|56808916|ref|ZP_00366625.1|_1:89 COG4835: Uncharacterized protein conserved in bacteria [Streptococcus pyogenes M49 591]

              10        20                 30        40               5
              |         |                  |         |                
   1 SNAMNLKREQEFVSQYHFDA...R...NFEW..E.NENGAPETKVDVNFQL...LQHDQ....EN
   2 ---MEVIREQEFVNQYHYDA...R...NLEW..E.EENGTPKTNFEVTFQL...ANRDE....AA
   3 ---MEVIREQEFVNQYHYDA...R...NLEW..E.EENGTPKTNFEVTFQL...ANRDE....AA
   4 ---MQLVREKEFVNQYHYDA...R...NLEW..E.KENGTPETNFEVTFQL...IDKDE....QQ
   5 -KDMNLKREQEFVSQYHFDA...R...NFEW..E.NENGAPETKVDVNFQL...LQHDQ....EN
   6 -KDMNLKREQEFVSQYHFDA...R...NFEW..E.NENGAPETKVDVNFQL...LQHDQ....EN
   7 ---MEIVRQKEFVNQYHYDA...R...NLEW..E.KENGTPETDVEVTFQL...VEKNE....EL
   8 ---MEIIRDKEFVNQYHFDA...R...NHAW..E.KENGIPETKLKVDFQL...IEQNR....AE
   9 ---MDLIHEKVFVNRYHYDV...R...NHEW..E.KENGVPKTNVEVTFQL...HHKDK....EA
  10 ---MDLIHEKVFVNRYHYDV...R...NHEW..E.KENGVPKTNVEVTFQL...HHKDK....EA
  11 ---MDIVTNKIVVEKYNFET...I...VEEN..EqFENKIELEVHEVEPVN...GNVEL....MS
  12 ---LTIEREQEFVNQFHYDA...R...NYEW..E.KENGTPETNLNVQFQL...VPKEQ....LE
  13 ---MDIVTNKIVVEKYNFET...T...MEENq.P.FENKIELEVHEVEPVD...GNVEL....MA
  14 ----TIEREQEFVNQFHYDA...R...NYEW..E.KENGTPETNLNVQFQL...VPKEQ....LE
  15 ---MDIVTNKIVVEKYNFET...I...MEEN..EqFENKIELEVHEVEPVN...GNVEL....MS
  16 ---MEIKRQQEIVEAYHYDM...R...VPDS..E.VETDLRVSFSPIEVEE...ENYPE....--
  17 ---METKRYPIAVESFHYDL...V...KQGT..P.VKNDLQVAMRQIEWSDpakQDELK....KG
  18 ---MQTKKDPISVDAFHFDR...V...SPDA..E.PQQNIQVSLVKIDADD...EYLQEadlkAG
  19 ---------PVTVQSFHYDL...V...DEGVaaK.SEVNPGIRKLDVSGDD...EHSEE....EG
  20 ---------PIVVRSFHYDLndeQ...KVKN..E.VNVSLRQVYQDLEDGS...QDEGK....NG
  21 ---------PIIVRSFHYDLndeQ...KVKN..E.VNVSLRQVYQDLDDGS...QDEGK....TG
  22 --------------------...-...----..-.---------------L...ANRDE....AA
  23 --------TPIIVRAFHYDL...LdepEEKN..E.VNVAIRQVVATGEDGV...EDAGE....AG
  24 --------------------...-...----..-.----------------...-----....--
  25 ---MQLVREKEFVNQYHYDA...R...NLEW..E.KENGTPETNFEVTFQL...IDKDE....QQ


      0            60         70        80        90       100       11
     |             |          |         |         |         |         
   1 QV....TSLIVILSFMIVFDKF.VISGTISQVNHIDGRIVNEPSELNQEEVETLARPCLNMLNRL
   2 KV....TSIVAVLQFVIVRDEF.VISGVISQIAHIQGRLINEPSEFSQDEVENLAAPLLEIVKRL
   3 KV....TSIVAVLQFVIVRDEF.VISGVISQMAHIQGRLINEPSEFSQDEVENLAAPLLEIVKRL
   4 KE....TVIVSVLQFVIVKEEF.VISGVISQMVRILDRLVDKPSEFTQEEVESLAAPLLDMVKRL
   5 QV....TSLIVILSFMIVFDKF.VISGTISQVNHIDGRIVNEPNELNQEEVETLARPCLNMLNRL
   6 QV....TSLIVILSFMIVFDKF.VISGTISQVNHIDGRIVNEPSELNQEEVETLARPCLNMLNRL
   7 NE....TTVVAVLQFMIVRDEF.VLSGVLSQMVKIKDRLVNQPSEFSQEEVATLAAPLLDILKRM
   8 NR....TSMITILRFMIVLDHF.VISGAMSQAVHLPNRLVEEPTEFTDEEKRVLVEPLLDILKRM
   9 NN....TSVVAVLQFMIVRDEF.VISGIISQMNHIQNRIVNNPKDFSQEEAEYLAAPLLDTLQRL
  10 NN....TSVVAVLQFMIVRDEF.VISGIVSQMNHIQNRIVNNPKDFSQEEAEYLAAPLLDTLQRL
  11 KG....KIFKITIPFLLVLENF.RIDGRISRIIQLKD-FFGDFSDLEAVDVEGLSNPLIDYIKRL
  12 KLgegdTGIHAVLTYLIVLDNI.VLSGFVSQLNYVRGQIIKEQEELEQEELAQLAAPLFELLKRL
  13 KG....KIFKITIPFLLVLENF.RIDGRISRIIQLKD-FFGQFSDLEAKDVEGLSNPLIDYIKRL
  14 KLgdrdTGIHAVLTYLIVLDNI.VLSGFVSQLNYVRGKIIKEQEELEQEELAQLAAPLFDLLQRL
  15 KG....KIFKITIPFLLVLENF.RIDGRISRIIQLKD-FFGDFSDLEAVDVEGLSNPLIDYIKRL
  16 NS....SALVARLEFRIVFDEF.VLSGAISQINHIIDRKIEKQEDISQEEVDELVRPLFSIVERL
  17 NL....FQMMIPFDVVPDDAGF.EISGKITQIVQVLD-YFGEANELPQAELGKLSRPLVETIETL
  18 NI....YQIVTPFQVMPQGSGF.AVSGQISRVVQLLD-FFGTPDEIEQKEMMKLSRPLIEYIETL
  19 SY....YDVAVFFDVIPAPAEF.EVSGAIHQIVQIKN-YHGDGTDISNADWQLLSRPLVEYIETL
  20 KY....FEIAVPFEVSPAPGDF.TVSGVITRVVQFVD-YFGDGSDLEPSEYQLLSRPLVEEIETL
  21 KY....FEIAVPFEVSPAPGDF.TVSGVITRVVQFVD-YFGDGTDLEPSDYQLLSRPLVEQIETL
  22 KV....TSIVAVLQFVIVRDEX.VISGVISQIAHIQGRLINEPSEFSQDEVENLAAPLLEIVKRL
  23 GY....YEVAVVYDVTPDEDNIiEISGVNTQVVQLLG-YHGDGQDLDQETYRLLSRPLVEYIETL
  24 --....------LQFVIVRDEF.VISGVISQMAHIQGRLINEPSEFSQDEVENLAAPLLEIVKRL
  25 KE....TVIVSVLQFVIVKEEF.VISGVISQMVRILDRLVDKPSELRK-----------------


      0       120       
     |         |       
   1 TYEVTEIALDLPGINLEF
   2 TYEVTEIALDRPGVTLEF
   3 TYEVTEIALDRPGVTLEF
   4 TYEVTEIALDRPGIHLEF
   5 TYEVTEIALDLPGINLEF
   6 TYEVTEIALDLPGINLEF
   7 TYEVTEIALDKEGVSLEF
   8 TYEVTEIAFDAPGVNLEF
   9 TYEVTEIALDRPGINLEF
  10 TYEVTEIALDRPGINLEF
  11 TYDVTEIAFDEPGVSLDF
  12 VYETTEVALDQPGINLGF
  13 TYDVTEIAFDEPGVSLDF
  14 VYETTEVALDHPGINLEF
  15 TYDVTEIAFDEPGVSLDF
  16 SYEVTEIALDRPGVQLNF
  17 TYQVTAVALDQG-VNLQF
  18 TYQVTAVALNEG-IQLQF
  19 TYEVTQVTFDKP-VNLNF
  20 TYEITQLTLDHP-VNLSF
  21 TYEITQLTLDHP-VNLSF
  22 TYEVTEIALDRPGVTLEF
  23 TYEVSQVALDEP-INLDF
  24 TYEVTEIALDRPGVTLEF
  25 ------------------