Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate 17628 b3567 fused D-xylose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Keio:17628 Length = 513 Score = 385 bits (990), Expect = e-111 Identities = 227/503 (45%), Positives = 317/503 (63%), Gaps = 18/503 (3%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDA--GEI 71 +L+ K I K F V A+DNV + EIVSL GENG+GKSTL+K+L G+ + GEI Sbjct: 4 LLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63 Query: 72 LVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDEN 131 + GE ++ D +KGI++IHQEL L +TV ENIFL G + T + +D + Sbjct: 64 IFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFL------GNEITHNGIMDYD 117 Query: 132 YMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEE 191 M R ++LL + SPD V +L Q+Q+VEI KAL K+ R++ +DEPT+SLT +E Sbjct: 118 LMTLRCQKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQE 177 Query: 192 TERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKM 251 T L +II L+ GI+ +++SH+L+EV ISD I V+RDG+ IG D II M Sbjct: 178 TSILLDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITM 237 Query: 252 MVGREVE-FFPHGIETRPGEIALEVRNLKWKD------KVKNVSFEVRKGEVLGFAGLVG 304 MVGRE+ +P+ T EI W +V +VSF +++GE+LG AGLVG Sbjct: 238 MVGRELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVG 297 Query: 305 AGRTETMLLVFGVNQKE-SGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTV 363 AGRTET+ +FGV + G IY++G++V+I+N + AI GI ++PEDRK G+V M V Sbjct: 298 AGRTETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAV 357 Query: 364 KDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLA 423 NI L +L K + LD+ E++ + +++L +KT S LSGGNQQK +LA Sbjct: 358 GKNITLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILA 417 Query: 424 KWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVV 483 + L N ILI DEPTRGID+GAK EI+++I +L QG AVI+ISSELPE+L LSDR++V Sbjct: 418 RCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLV 477 Query: 484 MWEGEITAVLDNREKRVTQEEIM 506 M EG++ A L N +TQE++M Sbjct: 478 MHEGKLKANLINH--NLTQEQVM 498 Lambda K H 0.319 0.138 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: 662 Number of extensions: 31 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 520 Length of database: 513 Length adjustment: 35 Effective length of query: 485 Effective length of database: 478 Effective search space: 231830 Effective search space used: 231830 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 (21.7 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