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:

- T0349 PaT90, Pseudomonas Aeruginosa, 75 res
- gi|78694054|ref|ZP_00858568.1|_1:75 conserved hypothetical protein [Bradyrhizobium sp. BTAi1]
- gi|78519609|gb|EAP32906.1| conserved hypothetical protein [Bradyrhizobium sp. BTAi1]
- gi|27377643|ref|NP_769172.1|_1:75 hypothetical protein bsr2532 [Bradyrhizobium japonicum USDA 110]
- gi|27350788|dbj|BAC47797.1| bsr2531 [Bradyrhizobium japonicum USDA 110]
- gi|39934116|ref|NP_946392.1|_1:75 hypothetical protein RPA1041 [Rhodopseudomonas palustris CGA009]
- gi|39647964|emb|CAE26484.1| conserved hypothetical protein [Rhodopseudomonas palustris CGA009]
- gi|85714243|ref|ZP_01045231.1|_1:75 hypothetical protein NB311A_14867 [Nitrobacter sp. Nb-311A]
- gi|85698690|gb|EAQ36559.1| hypothetical protein NB311A_14867 [Nitrobacter sp. Nb-311A]
- gi|83854855|ref|ZP_00948385.1|_1:70 hypothetical protein NAS141_09006 [Sulfitobacter sp. NAS-14.1]
- gi|83842698|gb|EAP81865.1| hypothetical protein NAS141_09006 [Sulfitobacter sp. NAS-14.1]
- gi|83941378|ref|ZP_00953840.1|_1:70 hypothetical protein EE36_04078 [Sulfitobacter sp. EE-36]
- gi|83847198|gb|EAP85073.1| hypothetical protein EE36_04078 [Sulfitobacter sp. EE-36]
- gi|91975695|ref|YP_568354.1|_1:74 hypothetical protein RPD_1215 [Rhodopseudomonas palustris BisB5]
- gi|91682151|gb|ABE38453.1| hypothetical protein RPD_1215 [Rhodopseudomonas palustris BisB5]
- gi|77741293|ref|ZP_00809777.1|_1:73 conserved hypothetical protein [Rhodopseudomonas palustris BisA53]
- gi|77698939|gb|EAO90087.1| conserved hypothetical protein [Rhodopseudomonas palustris BisA53]
- gi|77655221|gb|EAO86896.1|_49:122 hypothetical protein RPDDRAFT_3396 [Rhodopseudomonas palustris BisB5]
- gi|23347192|gb|AAN29346.1|_1:74 conserved hypothetical protein [Brucella suis 1330]
- gi|62195519|gb|AAX73819.1| conserved hypothetical protein [Brucella abortus biovar 1 str. 9-941]
- gi|82699314|ref|YP_413888.1| hypothetical protein BAB1_0428 [Brucella melitensis biovar Abortus 2308]
- gi|62289387|ref|YP_221180.1| hypothetical protein BruAb1_0423 [Brucella abortus biovar 1 str. 9-941]
- gi|82615415|emb|CAJ10384.1| conserved hypothetical protein [Brucella melitensis biovar Abortus]
- gi|23501304|ref|NP_697431.1| hypothetical protein BR0400 [Brucella suis 1330]
- gi|17983543|gb|AAL52714.1|_5:78 Hypothetical Protein [Brucella melitensis 16M]
- gi|17987816|ref|NP_540450.1| hypothetical protein BMEI1533 [Brucella melitensis 16M]
- gi|15073778|emb|CAC45419.1|_1:70 HYPOTHETICAL/UNKNOWN PROTEIN [Sinorhizobium meliloti]
- gi|15964600|ref|NP_384953.1| HYPOTHETICAL/UNKNOWN PROTEIN [Sinorhizobium meliloti 1021]
- gi|74421645|gb|ABA05844.1|_4:77 conserved hypothetical protein [Nitrobacter winogradskyi Nb-255]
- gi|75676775|ref|YP_319196.1| hypothetical protein Nwi_2591 [Nitrobacter winogradskyi Nb-255]
- gi|90425825|ref|YP_534195.1|_1:72 hypothetical protein RPC_4353 [Rhodopseudomonas palustris BisB18]
- gi|90107839|gb|ABD89876.1| conserved hypothetical protein [Rhodopseudomonas palustris BisB18]
- gi|78495617|ref|ZP_00847837.1| conserved hypothetical protein [Rhodopseudomonas palustris BisB18]
- gi|56676972|gb|AAV93638.1|_1:68 conserved hypothetical protein [Silicibacter pomeroyi DSS-3]
- gi|56695235|ref|YP_165583.1| hypothetical protein SPO0320 [Silicibacter pomeroyi DSS-3]
- gi|86139018|ref|ZP_01057589.1|_1:69 hypothetical protein MED193_10703 [Roseobacter sp. MED193]
- gi|85824249|gb|EAQ44453.1| hypothetical protein MED193_10703 [Roseobacter sp. MED193]
- gi|17738992|gb|AAL41651.1|_23:96 hypothetical protein [Agrobacterium tumefaciens str. C58]
- gi|17934545|ref|NP_531335.1| hypothetical protein Atu0635 [Agrobacterium tumefaciens str. C58]
- gi|15155582|gb|AAK86442.1| AGR_C_1126p [Agrobacterium tumefaciens str. C58]
- gi|15887976|ref|NP_353657.1| hypothetical protein AGR_C_1126 [Agrobacterium tumefaciens str. C58]
- gi|89070186|ref|ZP_01157514.1|_1:68 hypothetical protein OG2516_16591 [Oceanicola granulosus HTCC2516]
- gi|89044202|gb|EAR50353.1| hypothetical protein OG2516_16591 [Oceanicola granulosus HTCC2516]
- gi|86356522|ref|YP_468414.1|_1:73 hypothetical protein RHE_CH00876 [Rhizobium etli CFN 42]
- gi|86280624|gb|ABC89687.1| hypothetical conserved protein [Rhizobium etli CFN 42]
- gi|77388741|gb|ABA79926.1|_1:68 conserved hypothetical protein [Rhodobacter sphaeroides 2.4.1]
- gi|77464323|ref|YP_353827.1| hypothetical protein RSP_0749 [Rhodobacter sphaeroides 2.4.1]
- gi|84683978|ref|ZP_01011880.1|_1:68 hypothetical protein RB2654_16056 [Rhodobacterales bacterium HTCC2654]
- gi|84667731|gb|EAQ14199.1| hypothetical protein RB2654_16056 [Rhodobacterales bacterium HTCC2654]
- gi|85705713|ref|ZP_01036810.1|_1:68 hypothetical protein ROS217_10447 [Roseovarius sp. 217]
- gi|85669703|gb|EAQ24567.1| hypothetical protein ROS217_10447 [Roseovarius sp. 217]
- gi|84515723|ref|ZP_01003084.1|_1:68 hypothetical protein SKA53_13776 [Loktanella vestfoldensis SKA53]
- gi|84510165|gb|EAQ06621.1| hypothetical protein SKA53_13776 [Loktanella vestfoldensis SKA53]
- gi|84500216|ref|ZP_00998482.1|_1:68 hypothetical protein OB2597_09749 [Oceanicola batsensis HTCC2597]
- gi|84392150|gb|EAQ04418.1| hypothetical protein OB2597_09749 [Oceanicola batsensis HTCC2597]
- gi|83952380|ref|ZP_00961111.1|_1:67 hypothetical protein ISM_09521 [Roseovarius nubinhibens ISM]
- gi|83836053|gb|EAP75351.1| hypothetical protein ISM_09521 [Roseovarius nubinhibens ISM]
- gi|89358591|ref|ZP_01196413.1|_1:73 conserved hypothetical protein [Xanthobacter autotrophicus Py2]
- gi|89352768|gb|EAS18047.1| conserved hypothetical protein [Xanthobacter autotrophicus Py2]
- gi|68191197|gb|EAN05854.1|_1:67 hypothetical protein MesoDRAFT_1972 [Mesorhizobium sp. BNC1]
- gi|69278224|ref|ZP_00613435.1| hypothetical protein MesoDRAFT_1972 [Mesorhizobium sp. BNC1]
- gi|99078712|ref|YP_611970.1|_3:71 hypothetical protein TM1040_3741 [Silicibacter sp. TM1040]
- gi|99035850|gb|ABF62708.1| conserved hypothetical protein [Silicibacter sp. TM1040]
- gi|69300052|ref|ZP_00621928.1| hypothetical protein RoseDRAFT_2261 [Silicibacter sp. TM1040]
- gi|69937107|ref|ZP_00631828.1|_1:68 conserved hypothetical/unknown protein [Paracoccus denitrificans PD1222]
- gi|69151716|gb|EAN64905.1| conserved hypothetical/unknown protein [Paracoccus denitrificans PD1222]
- gi|89052979|ref|YP_508430.1|_1:68 hypothetical protein Jann_0488 [Jannaschia sp. CCS1]
- gi|88862528|gb|ABD53405.1| hypothetical protein Jann_0488 [Jannaschia sp. CCS1]
- gi|71368069|ref|ZP_00658579.1|_1:70 conserved hypothetical protein [Nocardioides sp. JS614]
- gi|71156222|gb|EAO06639.1| conserved hypothetical protein [Nocardioides sp. JS614]
- gi|83945355|ref|ZP_00957703.1|_1:65 hypothetical protein OA2633_14251 [Oceanicaulis alexandrii HTCC2633]
- gi|83851189|gb|EAP89046.1| hypothetical protein OA2633_14251 [Oceanicaulis alexandrii HTCC2633]
- gi|83594283|ref|YP_428035.1|_1:65 hypothetical protein Rru_A2951 [Rhodospirillum rubrum ATCC 11170]
- gi|83577197|gb|ABC23748.1| conserved hypothetical protein [Rhodospirillum rubrum ATCC 11170]
- gi|103487805|ref|YP_617366.1|_5:65 hypothetical protein Sala_2324 [Sphingopyxis alaskensis RB2256]
- gi|98977882|gb|ABF54033.1| hypothetical protein Sala_2324 [Sphingopyxis alaskensis RB2256]

              10        20        30          40        50        60   
              |         |         |           |         |         |   
   1 MRELLRTNDAVLLSAVGALLDGADIGHLVLD.QNMS.ILEGSLGVIPRRVLVHEDDLAGARRLLT
   2 MRELVRTNDVVLISAVGALLDGAEIHYLVMD.QNMS.ILEGSVGVIPRRVLVHPDDLRSARQVLT
   3 MKELVRTNDIVLVSAVGALLDGADIHHLVLD.QNMS.IIEGSLGILPRRILVHEDDNLQARRLLT
   4 MRELVRTNDMVLVSAIGALLDGANIHHLVLD.QNMS.IIEGSLGILPRRILVHEDDAQEARQLLT
   5 MRELLRTNDAVLLSAVGALLDGADIGHLVLD.QNMS.ILEGSLGVIPRRVLVHEDDLAGARRLLT
   6 MRELVRTNDLVLVSAIGALLDGAGIFYLVLD.QNMS.VIEGSLGVLPRRILVNDDDNRAARQLLI
   7 MKELLRTTDPTIIAFASALLQGEDIDCFPLD.VNMS.VLEGGIGIFPRRLMVHDDDHSAATRVLR
   8 MKELLRTTDPTIIAFASALLQGEDIDCFPLD.VNMS.VLEGGIGIFPRRLMVHDDDHTAATRVLL
   9 MRELVRTNDVVLISAIGALMDGAQIHYLVMD.QNMS.ILEGSVGVIPRRVLVHPDDLSSARQVLT
  10 MRELVRTNDIVLLSAIGALLDGGRIHYLVLD.QNMS.VIEGSVGVLPRRLLVHDDDITTARQILT
  11 LRELVRTNDVVLISAIGALMDGAQIHYLVMD.QNMS.ILEGSVGVIPRRVLVHPDDLSSARQVLT
  12 MIELIRTNDSVLLSFAEALMKEAGIAYFIAD.TNMS.IIEGSLGVLPRRLMVDEDQMEEARQILI
  13 MIELIRTNDSVLLSFAEALMKEAGIAYFIAD.TNMS.IIEGSLGVLPRRLMVDEDQMEEARQILI
  14 MKELIRTNDAVLLSFAESLMKDAGIGCFIAD.QDMS.ILEGSLGLLPRRFLVAEDDADRARRILI
  15 -QELVRTNDMVLVSAVGALLDGAGIFHLVLD.QNMS.VLEGSLGVLPRRVLVNDGDNRAARRLLA
  16 MRELVRTNDVVLVSAIGALLDAARIHHLVLD.QNMS.VIEGSVGVIPRRILVHDDDNQEARQLLT
  17 MKELLRSTDPTVMAFASALLEGEDIDCFQMD.VNMS.ILEGGIGIFPRRMMVRDEDYDRALRVVT
  18 MKELLRSTDPTVLAFASALLEGEDIDCFQMD.VNMS.ILEGGIGIFPRRLMVRDEDYSQAKRAMV
  19 MRELIRTNDAVLLSFAESLMKDAGIHCLIAD.QAMS.ILEGSLGLLPRRFLVEEDRAGEARRILV
  20 MKELLRSTDPTVIAFAKALLGGEGIDCFEMD.VNMS.ILEGSIGILPRRLMVRTDDHTAALRVCR
  21 MHELIRANDPVLLSYAESLMKDAGIHCFIAD.QGMS.VLEGSLGMLPRRLLVDEEMADQARRILI
  22 MKELLRTTDPTIIAFATALLQGEDIDAFPVD.VHMS.VLEGSIGILPRRLFVPEEDWDRACRVMS
  23 MKELLRTTDPTIIAFASALLSGEGIPAFPMD.VHMS.TLEGSIGILPRRLMVRADDYVRARRVLT
  24 MKQLLRTNDIASIAFAQALLQGEGIDCFEMD.VNMS.ILEGSIGIFPRRLMVATADYEEARTTLI
  25 MKELLRTNDVTVIAFATALLDAEGIDWFTFD.DNMS.IMEGSIGIMPRRLMVHDRDLFMAEAVMR
  26 MKQLMRTNNPADMAFAQALLQGEGIDWFEMD.VNMS.VLEGSIGILPRRLMVKSEDHDRAATVMK
  27 MKLLLRSTDPATIAFAQALLQGEGIDCFEMD.VNMS.VLEGGIGIFPRRLMVRERDHARAERALQ
  28 MHELVRTNDLVLIGAIEALFQSAQIGHMVAD.QYMS.VMEGTIGILPRRLLVVDEDVDRARRLLK
  29 MIELIRTNDAVALSFIESLLRDAGINYLIAD.QNMS.IMEGSLGVLPRRVLVAEDQADEARQILG
  30 MKELLRSTDPTVLAFATALLNGEGIDCFEMD.VNMS.VLEGGIGIFPRRLLVHADDLEDARVVMR
  31 MKELLRTTDPLLITRAADLLAAEGIQSFPLD.QHMS.VLEGSLGILPRRLMVADRDLFMARAILR
  32 MLEILRSNDPTIIAFATALLRGEDIEVFEMD.VHMS.GLEGSIGILPRRLLVRRAEAAAAEVVLR
  33 MAELVRTNDPVAISVVEGLLTSAEIPYEVAD.RNMS.VLDGLIEVIKVRILVPDERAADARELMA
  34 MIEVLATNDPVKLSFAQAVLKEAGIEAVTLDeQTAS.TFGGALPWIKRRILVREQDRDRAKALLA
  35 MVELVSTDDPVLLSWLMAQLADAEIGAVVFD.SHTTaLLPGTLGLIQSRVMVGDDDLDAARRILA
  36 --ELVRLPNGAEAELLRGRLESAGVHAVCFD.AGMN.IAESVGLMIPVRIMVLDEDLGEARALMA


           70     
           |     
   1 DAGLAHELRSDD
   2 DAGLAHELRGDD
   3 DAGLGHELRPDE
   4 EAGLSHELRGDD
   5 DAGLAHELRSDD
   6 EAGLAHELRPDD
   7 DNDIPTG-----
   8 DNDIPTG-----
   9 DAGLAHELRTD-
  10 DAGLGHELRS--
  11 DAGLAHELRTD-
  12 DAKIEHELRDN-
  13 DAKIEHELRDN-
  14 DAGLELE-----
  15 EAGLAHELRPDD
  16 EAGLAHELR---
  17 DNDIP-------
  18 DNEIPL------
  19 DAGLGDELRNE-
  20 DNDID-------
  21 DAGLGGELRD--
  22 DNGIP-------
  23 ENGIE-------
  24 DNGFS-------
  25 DGEID-------
  26 DNGFD-------
  27 DNGI--------
  28 EAGFGAALRD--
  29 DAGL--------
  30 DNDLPV------
  31 DNRIH-------
  32 DNELP-------
  33 EAELGDW-----
  34 E-----------
  35 Q-----------
  36 ------------