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 BWI76_RS00660 BWI76_RS00660 ABC transporter
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Koxy:BWI76_RS00660 Length = 503 Score = 530 bits (1365), Expect = e-155 Identities = 275/492 (55%), Positives = 360/492 (73%), Gaps = 2/492 (0%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 +L ++GI+++FPGV+AL+NV + L PG VTALIGENGAGKSTLVK++TGIY+P EGEIL Sbjct: 7 LLSLKGITKVFPGVRALENVQLDLWPGKVTALIGENGAGKSTLVKVMTGIYQPEEGEILY 66 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRF-RTIDWQTMNSRS 138 P + ++A G+TAIHQETVLFDEL+V ENIF+G T + +DW M+ ++ Sbjct: 67 KAIPIQLPNPESAHKVGITAIHQETVLFDELSVTENIFVGQYLHTGLLKKLDWPAMHRKA 126 Query: 139 KALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFR 198 +LT LE IDP LK LSIAQRH+VAIARALS EA++VI+DEPTAALS+ EI + ++ Sbjct: 127 SEILTRLEVQIDPRATLKTLSIAQRHMVAIARALSFEAQVVILDEPTAALSQHEILEFYQ 186 Query: 199 IVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRD 258 IV LK+ GKAILFISHKFDE++E+AD + + R G ++ +V MMVGR Sbjct: 187 IVERLKQDGKAILFISHKFDEIFELADYYTIL-RDGVYVSSGAINDITEERMVAMMVGRA 245 Query: 259 VENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFG 318 + +PK+D G VLE+++ H TEF ISF+LRKGEILG YGL+GAGR+EL Q+L G Sbjct: 246 ITQTYPKVDCIPGETVLEVKDLCHPTEFAHISFSLRKGEILGFYGLVGAGRTELMQALSG 305 Query: 319 ITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTS 378 ++ P SG +VL+G+ + P DAI AGIV VPEER + G + +PI QN++LP L++ + Sbjct: 306 VSHPSSGDIVLKGKPMRFRQPADAISAGIVCVPEERQKQGAIIALPIAQNISLPQLSKLN 365 Query: 379 RRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDE 438 G L A E+ LA +YA RL ++A + V TLSGGNQQKVVIGKWLAT P+VIILDE Sbjct: 366 PGGVLNDAREWRLADEYASRLQVKAFSWRQAVETLSGGNQQKVVIGKWLATHPEVIILDE 425 Query: 439 PTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAE 498 PTKGIDIGSKAAVH F+SEL ++GL++IMVSSELPE++GM+DR++VM EGL + E Sbjct: 426 PTKGIDIGSKAAVHQFMSELVSQGLAVIMVSSELPEVMGMADRIIVMHEGLMVAEYRAGE 485 Query: 499 LSPEALVRAATG 510 + E +V AA+G Sbjct: 486 ATAETIVSAASG 497 Score = 69.7 bits (169), Expect = 2e-16 Identities = 53/227 (23%), Positives = 107/227 (47%), Gaps = 8/227 (3%) Query: 288 DISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGI 347 ++ L G++ + G GAG+S L + + GI +P G+++ + I + +P+ A + GI Sbjct: 25 NVQLDLWPGKVTALIGENGAGKSTLVKVMTGIYQPEEGEILYKAIPIQLPNPESAHKVGI 84 Query: 348 VYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALS 407 + +E L + + +N+ + T G L+ + A+ RK +E L + Sbjct: 85 TAIHQETV---LFDELSVTENIFVGQYLHT---GLLKKLDWPAMHRKASEILTRLEVQID 138 Query: 408 --VPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSI 465 + TLS + V I + L+ +V+ILDEPT + + + L +G +I Sbjct: 139 PRATLKTLSIAQRHMVAIARALSFEAQVVILDEPTAALSQHEILEFYQIVERLKQDGKAI 198 Query: 466 IMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATGNA 512 + +S + EI ++D ++++G+ +++ E +V G A Sbjct: 199 LFISHKFDEIFELADYYTILRDGVYVSSGAINDITEERMVAMMVGRA 245 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: 681 Number of extensions: 31 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 512 Length of database: 503 Length adjustment: 34 Effective length of query: 478 Effective length of database: 469 Effective search space: 224182 Effective search space used: 224182 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