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 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 300 bits (767), Expect = 1e-85 Identities = 171/485 (35%), Positives = 271/485 (55%), Gaps = 2/485 (0%) Query: 12 VAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQ 71 + K YAGV AL +++ G L G NG+GKST + I+ G+ AG++ + G Sbjct: 15 ITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAGQEHV 74 Query: 72 FNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTRELLDSL 131 P + AAG+ +I Q+ P ++VAENI + + +A+ R LD + Sbjct: 75 TLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARAALDRI 134 Query: 132 EFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTA 191 +D + + L VAQ QLV I +A + Q++IMDEPT+A+ E E + L IR L Sbjct: 135 GVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGIIRMLKE 194 Query: 192 QGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELTRIDHKV 251 +G +++VSH+L+E+ ++++ + R+G V G ++ D L + G+++ + Sbjct: 195 EGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDVPEVPPS- 253 Query: 252 GRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSG 311 A T +QV L +AG F DIS LR GE+LGI GL+G GR+ ++GL D+G Sbjct: 254 DVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALFGLVTPDAG 313 Query: 312 SVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSSWSLINA 371 S+ + G P+P+G P+A A + V EDR GL L+ SIL N+A+ +S ++ Sbjct: 314 SILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDAHTSGGFLDM 373 Query: 372 RKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDE 431 + A D ++RL++K +E PV S+SGGNQQ+V LA+ LS P L+ + P+ G+D Sbjct: 374 TGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLILNGPSVGVDV 433 Query: 432 GAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTALSQEALL 491 G+K +I+ ++ + R G IV+S + PELL R+ V + GR++ TAL+++ L Sbjct: 434 GSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDALEGTALTEDDLA 493 Query: 492 -RLAS 495 RLAS Sbjct: 494 HRLAS 498 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: 545 Number of extensions: 24 Number of successful extensions: 6 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: 498 Length adjustment: 34 Effective length of query: 461 Effective length of database: 464 Effective search space: 213904 Effective search space used: 213904 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