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 PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 327 bits (838), Expect = 6e-94 Identities = 202/498 (40%), Positives = 282/498 (56%), Gaps = 8/498 (1%) Query: 1 MARPLLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDA 60 +A ++L A + K YA P L + LSLRAG V AL G NGAGKST ++ G+ Sbjct: 11 LANEVVLAASGLGKTYAQ-PVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTT 69 Query: 61 GSILLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKAL 120 G + G EA G+ M+ QEL +P +TVAEN++L P R G I +K L Sbjct: 70 GHMTYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWI-SHKRL 128 Query: 121 NRRTRELLDSLEFD-VDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEA 179 + + + D +D +P+ L + Q+VEIA+ DC V+I+DEPT+ + E Sbjct: 129 RQLATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREV 188 Query: 180 QTLFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGI 239 LF I RL A+G IVY+SHRL EL ++A + RDG V + LV + Sbjct: 189 ALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLM 248 Query: 240 VGQEL-TRIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEF 298 VG+EL ID +GR L+VD L R + ++S ++R GEI GI GL+G+GR+E Sbjct: 249 VGRELGEHID--LGRRQLGAPLLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGRTEL 306 Query: 299 LNCIYGLTVADSGSVTLQGKPMPIGL--PKATINAGMSLVTEDRKDSGLVLTGSILSNIA 356 L IYG ADSG + L P + + PKA + AG++L+TEDRK GL+LT SI +NIA Sbjct: 307 LRLIYGADRADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIA 366 Query: 357 LSAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTE 416 L +S ++++ E LAE ++ ++I++ + V +SGGNQQKVV+ + L + Sbjct: 367 LGNLGAVSRAGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERD 426 Query: 417 PVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRL 476 LL DEPTRGID GAK +IY LL + R G A +VVSS+ EL+ + DRIAV GRL Sbjct: 427 CQVLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRL 486 Query: 477 VTISTDTALSQEALLRLA 494 + SQ+ LL A Sbjct: 487 IDTFARDHWSQDQLLAAA 504 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: 589 Number of extensions: 28 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: 495 Length of database: 524 Length adjustment: 34 Effective length of query: 461 Effective length of database: 490 Effective search space: 225890 Effective search space used: 225890 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