Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate Ac3H11_1109 ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1109 Length = 513 Score = 261 bits (667), Expect = 4e-74 Identities = 162/500 (32%), Positives = 268/500 (53%), Gaps = 21/500 (4%) Query: 19 GIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERV 78 GI KR+P VVA V V EI +++GENGAGKSTL+KI+ G +KPD G + NG+ V Sbjct: 2 GITKRYPAVVANSGVSLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGSVFFNGQAV 61 Query: 79 EFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSK 138 + +P +A GI+++ Q +L D +TVAEN++L G ++L+ + ++ Sbjct: 62 QVRNPQEARALGIAMVFQHFSLFDTLTVAENVWL------GLDKSLTLAEVTQRISAKAA 115 Query: 139 ELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEI 198 E G P V L+ + Q VEI +AL+ P+++ +DEPTS LT + E+LF + Sbjct: 116 E----YGLDIDPLRPVHTLSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKLFVV 171 Query: 199 IEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGREVE 258 + L S G S++++SH+L E+ + V+R GK G E ++ ++M+G E Sbjct: 172 LRKLASEGCSILYISHKLHEIRALCTACTVLRGGKVTGVCNPSEETNASLSRLMIGAEPP 231 Query: 259 FFPHGIETRPGEIALEVRNL------KWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETML 312 H + G L V+ L ++ + ++ FEV+ GEV+G AG+ G G+ E + Sbjct: 232 ALEHR-AVQTGATVLRVKGLSLPRADQFGVDLIDLQFEVKAGEVVGIAGVSGNGQKELLY 290 Query: 313 LVFGVNQK-ESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPS 371 + G +Q+ E I V G+ P +G+ +PE+R +G V M + N++L Sbjct: 291 ALSGEDQRAEPASIQVTGQNAGRMGPGQRRALGLHFVPEERLGRGAVPTMGLAHNLLLTR 350 Query: 372 LKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNAD 431 + G + ++ +ED ++R ++K + ++LSGGN QK ++ + + N Sbjct: 351 KNAVGGSGWIKVGALQKH-AEDIIQRFNVKAGGPHSAAKSLSGGNLQKFIVGREIDANPK 409 Query: 432 ILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITA 491 +LI +PT G+DVGA A+I I L G AV+++S EL E+ + DR+ V+ +G ++ Sbjct: 410 LLIVSQPTWGVDVGAAAQIRGSILALRDAGCAVLVVSEELDELFEICDRLHVVAKGRLSP 469 Query: 492 VLDNREKRVTQEEIMYYASG 511 + E T E I + SG Sbjct: 470 SVQRAE--ATVERIGEWMSG 487 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: 596 Number of extensions: 38 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: 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