Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_084932971.1 HA51_RS05635 xylose ABC transporter ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >NCBI__GCF_002095475.1:WP_084932971.1 Length = 506 Score = 427 bits (1098), Expect = e-124 Identities = 233/500 (46%), Positives = 326/500 (65%), Gaps = 12/500 (2%) Query: 4 LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDA--GTL 61 LL++ I K F VKAL +L + G VM+L GENG+GKST+MK+L G+Y G + Sbjct: 2 LLEMNHITKRFGAVKALDDISLRLDAGEVMSLCGENGSGKSTLMKILCGLYPHGDFDGEI 61 Query: 62 LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAE 121 + G + ++ GI IIHQEL L+ QLT+ ENIFLG E + RFG +D +TM Sbjct: 62 QFAGDRIQAQTIRDTERKGIVIIHQELALVRQLTVMENIFLGAE-LGRFGLVDDETMTLR 120 Query: 122 ADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181 +LLA++ L D VG+L +G QQ+VEIA+ L+ + +++I+DEPT +LT+ ETE L Sbjct: 121 CQQLLARVKLDVAPDTKVGELGLGQQQLVEIARALNKQVRLLILDEPTSSLTEQETEVLL 180 Query: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK 241 +I L+ G +YISH++ E+ I D + V RDGQ IA R A L+ED +I MMVGR+ Sbjct: 181 SIINNLREHGIACIYISHKLNEVKAISDTICVIRDGQHIATRPAAGLSEDDIITMMVGRE 240 Query: 242 LEDQYPHLDKAPGDIRLKVDNLCG--------PGVNDVSFTLRKGEILGVSGLMGAGRTE 293 L YPH G+ L+V NL VN+VSF+L++GEILG++GL+GAGRTE Sbjct: 241 LTALYPHQPHEIGETILEVKNLTAWHPVNRHVRRVNNVSFSLKRGEILGIAGLVGAGRTE 300 Query: 294 LMKVLYGALP-RTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMS 352 ++ L+G P R G + ++G V ++ +A+GI + EDRK+DG+V M V +N++ Sbjct: 301 TVQCLFGVWPGRWQGDIAINGKLVKIHDCREAIAHGIAMVPEDRKKDGIVPLMGVGKNIT 360 Query: 353 LTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMT 412 L AL FS ++ A EQQA++D IR VKT S E AIG LSGGNQQK +A+ L+ Sbjct: 361 LAALDQFSHRLSTVDEAAEQQAINDAIRRLRVKTSSPELAIGRLSGGNQQKAILAKCLLL 420 Query: 413 RPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGH 472 PK+LILDEPTRG+DVGA++EIY LIN G+++I++SSE+PEVLG+SDR++VMHEG Sbjct: 421 NPKILILDEPTRGIDVGARQEIYLLINALVQQGIAVIVISSELPEVLGLSDRVLVMHEGQ 480 Query: 473 LSGEFTREQATQEVLMAAAV 492 + + TQE +M AA+ Sbjct: 481 IKADLINNNLTQEQVMEAAL 500 Lambda K H 0.318 0.137 0.380 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: 650 Number of extensions: 33 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: 501 Length of database: 506 Length adjustment: 34 Effective length of query: 467 Effective length of database: 472 Effective search space: 220424 Effective search space used: 220424 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 24 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