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 17628 b3567 fused D-xylose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Keio:17628 Length = 513 Score = 342 bits (876), Expect = 2e-98 Identities = 196/502 (39%), Positives = 305/502 (60%), Gaps = 13/502 (2%) Query: 18 PAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPN--EG 75 P +LEM+ I++ F VKA+DNV + L+ G + +L GENG+GKSTL+K+L GIY EG Sbjct: 2 PYLLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEG 61 Query: 76 EILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMN 135 EI+ G + + G+ IHQE L ELTV ENIFLG+ T +D+ M Sbjct: 62 EIIFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEI-THNGIMDYDLMT 120 Query: 136 SRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDD 195 R + LL + +I P R+ DL + Q+ LV IA+AL+ + R++I+DEPTA+L+ +E Sbjct: 121 LRCQKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSI 180 Query: 196 LFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMV 255 L I+R L++ G A ++ISHK +E+ I+D V R + + +D+I+ MMV Sbjct: 181 LLDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMS-EDDIITMMV 239 Query: 256 GRDVENVFPKIDVAIGGPVLEIRNYS-------HRTEFRDISFTLRKGEILGVYGLIGAG 308 GR++ ++P G +L I + + H D+SF+L++GEILG+ GL+GAG Sbjct: 240 GRELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAG 299 Query: 309 RSELSQSLFGITK-PLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQ 367 R+E Q LFG+ GK+ ++G+++ I + Q AI GI VPE+R R G+ M + + Sbjct: 300 RTETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGK 359 Query: 368 NMTLPSLAR-TSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKW 426 N+TL +L + T L A E + ++L ++ ++ + +G LSGGNQQK ++ + Sbjct: 360 NITLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARC 419 Query: 427 LATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMK 486 L P+++ILDEPT+GIDIG+K ++ I++L +G+++I++SSELPE++G+SDRVLVM Sbjct: 420 LLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMH 479 Query: 487 EGLSAGIFERAELSPEALVRAA 508 EG L+ E ++ AA Sbjct: 480 EGKLKANLINHNLTQEQVMEAA 501 Score = 74.7 bits (182), Expect = 7e-18 Identities = 62/229 (27%), Positives = 111/229 (48%), Gaps = 16/229 (6%) Query: 288 DISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLS--GKMVLEGQEITIHSPQDAIRA 345 ++ L GEI+ + G G+G+S L + L GI S G+++ G+EI +D R Sbjct: 22 NVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEIIFAGEEIQASHIRDTERK 81 Query: 346 GIVYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAA 405 GI + +E L + + +N+ L + + G + ++ L ++L L + Sbjct: 82 GIAIIHQELA---LVKELTVLENIFLGN--EITHNGIM----DYDLMTLRCQKL-LAQVS 131 Query: 406 LSVP----VGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAE 461 LS+ VG L G QQ V I K L +++ILDEPT + + + I +L Sbjct: 132 LSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLDIIRDLQQH 191 Query: 462 GLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510 G++ I +S +L E+ +SD + V+++G G + A +S + ++ G Sbjct: 192 GIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVG 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: 580 Number of extensions: 34 Number of successful extensions: 12 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: 513 Length adjustment: 35 Effective length of query: 477 Effective length of database: 478 Effective search space: 228006 Effective search space used: 228006 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