Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_084935209.1 HA51_RS14055 sugar ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >NCBI__GCF_002095475.1:WP_084935209.1 Length = 494 Score = 417 bits (1073), Expect = e-121 Identities = 230/498 (46%), Positives = 327/498 (65%), Gaps = 12/498 (2%) Query: 15 LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74 L+A+GI K FPGV A+DNV + + +L+GENGAGKSTL+K L G+ +PD G I + Sbjct: 6 LEAEGISKFFPGVKALDNVSLRIKPGSVHALMGENGAGKSTLMKCLIGMYRPDKGTIRIK 65 Query: 75 GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMY 134 GE V+F +DA + GIS+IHQELNL MTVAENI+L E ++ VD + Sbjct: 66 GEPVQFQDTMDALRSGISMIHQELNLVPYMTVAENIWLGREPMK------YGFVDHGKLN 119 Query: 135 TRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETER 194 +++ELL+ + + D +V L+ A +QMVEI KA+ I+ MDEPTS+LT E Sbjct: 120 KQTQELLNRLNIRLKADRMVGELSIAAQQMVEIAKAVSWNSDIVIMDEPTSALTETEVAH 179 Query: 195 LFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVG 254 LF II L+ +G +++++SH++DE+ I+D I + RDG +G EF ++I MVG Sbjct: 180 LFTIIRDLREQGKAIIYISHKMDEIFTITDEISIFRDGTWVGSNNTSEFTRQSLITQMVG 239 Query: 255 REV-EFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETMLL 313 RE+ + FP G L VRNL KD+ +++F VRKGE+LG AGLVGAGR+E M Sbjct: 240 RELTQLFPK-FNGEIGADVLTVRNLTCKDRFTDINFTVRKGEILGVAGLVGAGRSEVMES 298 Query: 314 VFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLK 373 +FG+ +SG++ ++G V+I +P AI+ G+ + EDRK GL L ++V +N+ + ++ Sbjct: 299 LFGMESFDSGEVLIDGVPVKIDSPSTAIEKGMAFLTEDRKKSGLFLVLSVMENMSIVNMP 358 Query: 374 K-ISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADI 432 +S+ G V + ++ E +++L+IKTP++ QI NLSGGNQQKV++A+WL I Sbjct: 359 DYVSKAGFVSHMKMAQDCMEQ-IRKLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKI 417 Query: 433 LIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAV 492 LI DEPTRGIDVGAKAEI+R+I ELA +G A+IM+SSELPEIL +SDR++VM G IT + Sbjct: 418 LILDEPTRGIDVGAKAEIYRLISELANRGVAIIMVSSELPEILGMSDRVMVMHGGRITGI 477 Query: 493 LDNREKRVTQEEIMYYAS 510 LD E QE I+ AS Sbjct: 478 LDKEE--ANQETILSLAS 493 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: 699 Number of extensions: 39 Number of successful extensions: 8 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: 494 Length adjustment: 34 Effective length of query: 486 Effective length of database: 460 Effective search space: 223560 Effective search space used: 223560 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 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