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 7024900 Shewana3_2074 ABC transporter related (RefSeq)
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__ANA3:7024900 Length = 499 Score = 335 bits (860), Expect = 2e-96 Identities = 185/494 (37%), Positives = 307/494 (62%), Gaps = 8/494 (1%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 ILE++ IS+ +PGVKAL++VS+ L G V AL+GENGAGKSTLVK++TG + G+IL Sbjct: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139 G P F + A AG++ ++QE L LTVA+N+FLG+ PR R I ++ M + ++ Sbjct: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPR-RLGLIHFKKMYADAR 122 Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199 A+LT + +ID + L D SIA + L+AIAR +++ A+++++DEPTA+L KE+ LF I Sbjct: 123 AVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182 Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDV 259 + LK +G AI+FI+H D++Y+I+D V R + ++ + PQ +++ M+GR + Sbjct: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVL-RNGQFIGEYLTAELPQPKLIEAMLGRSL 241 Query: 260 ENVF------PKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELS 313 + + +L + + S + + ++ T+ KG+ +G+ GL+G+GRSE+ Sbjct: 242 QEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVC 301 Query: 314 QSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPS 373 ++FG+ SG + L GQ++ + P DAI AGI PE+R G+ P+ I +N+ L Sbjct: 302 NAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILAL 361 Query: 374 LARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKV 433 AR +L + +A+ + ++L + P+ LSGGNQQKV++ +WLA P + Sbjct: 362 QARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPIL 421 Query: 434 IILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGI 493 ++LDEPT+GIDIG+ A + I L EG+S+++ SSEL E++ S++V+V+++ + Sbjct: 422 LVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRE 481 Query: 494 FERAELSPEALVRA 507 AEL+ + +++A Sbjct: 482 LSGAELTSQHVMQA 495 Score = 94.4 bits (233), Expect = 9e-24 Identities = 67/235 (28%), Positives = 116/235 (49%), Gaps = 6/235 (2%) Query: 278 RNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIH 337 ++Y D+S L GE+ + G GAG+S L + + G G ++ G+ + Sbjct: 12 KHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFN 71 Query: 338 SPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAE 397 +P DA +AGI V +E L + + QN+ L R R G + +A AR Sbjct: 72 TPMDAQKAGISTVYQEVN---LVPNLTVAQNLFLGYEPR--RLGLIHFKKMYADARAVLT 126 Query: 398 RLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISE 457 + L +S P+ S QQ + I + +A + KV++LDEPT +D + G +++ Sbjct: 127 QFKLDID-VSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQ 185 Query: 458 LAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATGNA 512 L A+G++I+ ++ L ++ +SDR+ V++ G G + AEL L+ A G + Sbjct: 186 LKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRS 240 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: 538 Number of extensions: 30 Number of successful extensions: 7 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: 499 Length adjustment: 34 Effective length of query: 478 Effective length of database: 465 Effective search space: 222270 Effective search space used: 222270 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 Sep 17 2021. 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