Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Phaeo:GFF2274 Length = 503 Score = 331 bits (849), Expect = 3e-95 Identities = 188/490 (38%), Positives = 285/490 (58%), Gaps = 1/490 (0%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 +L+ E + K + GV AL L++ G VHAL G NGAGKST + +L GI Q D G I++ Sbjct: 7 VLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIV 66 Query: 66 NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125 PV + P +A A GI I QEL ++VAENI+LG PR+ +VD L +T Sbjct: 67 AEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELEAKTN 126 Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185 +L+ L+ +A + + LS+A Q+VEIA+A + D + +I DEPT+++ + E LF+ Sbjct: 127 AILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLFEV 186 Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELT 245 I L QG GI Y+SHR+ E+ +I D S+ RDG + + A+ + +++ + ++G++L Sbjct: 187 ISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRKLD 246 Query: 246 RIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGL 305 ++ E L+V LS F D++ ++R+GE++G YGL+G+GR+E ++GL Sbjct: 247 LSRNEAHHELG-EVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGL 305 Query: 306 TVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSS 365 SGS+ L G + I P I G+SLV EDRK GLVL + N+ L L + Sbjct: 306 RNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQVDDLKA 365 Query: 366 WSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEP 425 + E + + +L I+T + V ++SGGNQQK+V+ K LS P L+ DEP Sbjct: 366 GPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEP 425 Query: 426 TRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTAL 485 TRGID G+K EI++LL G A IV+SSE PE+LH++DRI GR++ T + Sbjct: 426 TRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEV 485 Query: 486 SQEALLRLAS 495 ++E L+ S Sbjct: 486 TEENLIAAIS 495 Score = 73.2 bits (178), Expect = 2e-17 Identities = 56/229 (24%), Positives = 101/229 (44%), Gaps = 5/229 (2%) Query: 24 DGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAAGI 83 D +R G V G GAG++ L G+ +GSI L+GA V P +A+ GI Sbjct: 274 DVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGI 333 Query: 84 AMITQELEP---IPYMTVAENIWLGR-EPRRAGCIVDNKALNRRTRELLDSLEFDVDATS 139 +++ ++ + + M +N+ L + + +AG V + A + D L+ Sbjct: 334 SLVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWK 393 Query: 140 PM-HRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAGIVY 198 + LS Q + I K S V+I+DEPT I + +R L AQG ++ Sbjct: 394 QLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIV 453 Query: 199 VSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELTRI 247 +S + E+ +AD G + + ++ ++L+ I G + ++ Sbjct: 454 ISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISGLDTEKV 502 Lambda K H 0.319 0.135 0.381 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: 26 Number of successful extensions: 6 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: 495 Length of database: 503 Length adjustment: 34 Effective length of query: 461 Effective length of database: 469 Effective search space: 216209 Effective search space used: 216209 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