Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 288 bits (738), Expect = 2e-82 Identities = 166/486 (34%), Positives = 275/486 (56%), Gaps = 15/486 (3%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 ++EM+ I + FPG+ A DNV++ + G + AL+GENGAGKSTL+ +L G+Y+P +GEILV Sbjct: 4 VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139 G+P A G+ +HQ +L ++ TV ENI LG P + + +K Sbjct: 64 KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKI----NIKKAAK 119 Query: 140 ALLTALES---NIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDL 196 A+ T + +DP +++D+S+ + V I + L A I+I DEPTAAL+ +EI +L Sbjct: 120 AVETISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITEL 179 Query: 197 FRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVG 256 +I++ L +GK+I+ I+HK E+ E+ D V R +S TP D + MMVG Sbjct: 180 IQIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTP-DSLAAMMVG 238 Query: 257 RDVENVFPKIDVAIGGPVLEIRNYSHR-----TEFRDISFTLRKGEILGVYGLIGAGRSE 311 R+V K VL+I++ + T D+ + GEILGV G+ G G++E Sbjct: 239 REVNFSVEKDPAQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTE 298 Query: 312 LSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTL 371 L +++ G+ KP G + L GQ+IT +P+ AG+ ++P++R +HGL L + +N+ L Sbjct: 299 LIEAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVL 358 Query: 372 PSLART--SRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLAT 429 + + S G L + A + E D+R + LSGGNQQK +I + + Sbjct: 359 QTYYQKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDR 418 Query: 430 APKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGL 489 +P ++I +PT+G+D+G+ ++H + + +G +++++S EL E++ +SDR+ V+ EG Sbjct: 419 SPDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGK 478 Query: 490 SAGIFE 495 I + Sbjct: 479 IVAIVD 484 Score = 84.0 bits (206), Expect = 1e-20 Identities = 60/225 (26%), Positives = 113/225 (50%), Gaps = 10/225 (4%) Query: 288 DISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGI 347 +++ +++GEI + G GAG+S L LFG+ +P G+++++G+ + I P A R GI Sbjct: 22 NVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILVKGKPVKITDPNVANRLGI 81 Query: 348 VYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFA--LARKYAERLDLRAAA 405 V + L + +N+ L + ++ A + ++++Y +D A Sbjct: 82 GMVHQH---FMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVETISKQYGLAVDPYAKI 138 Query: 406 LSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSI 465 + VG QQ+V I K L +++I DEPT + + + +L +EG SI Sbjct: 139 QDISVGM-----QQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQIMKKLVSEGKSI 193 Query: 466 IMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510 I+++ +L EI+ + DR V++ G G + +E +P++L G Sbjct: 194 ILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVG 238 Lambda K H 0.320 0.137 0.382 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 609 Number of extensions: 31 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 512 Length of database: 509 Length adjustment: 35 Effective length of query: 477 Effective length of database: 474 Effective search space: 226098 Effective search space used: 226098 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory