Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate AZOBR_RS27990 AZOBR_RS27990 ABC transporter permease
Query= uniprot:D4GP36 (317 letters) >FitnessBrowser__azobra:AZOBR_RS27990 Length = 310 Score = 109 bits (273), Expect = 7e-29 Identities = 66/190 (34%), Positives = 108/190 (56%), Gaps = 3/190 (1%) Query: 109 LVLGLFLAILLDHGIRFSEKFQTVYLLPMSLSFVVTAQLWLWMFNVESGILNLVVTTLGF 168 L GL +A+LL+ RF E + +L+PM L +V A +W ++ + L+ ++ G Sbjct: 102 LAAGLGVALLLNVRARFFEAIRAAFLIPMVLPPIVVALIWKILYTPDVSPLHRLLEEAGL 161 Query: 169 NPVDWL-GNPSIALGAVILALIWQFSGYTMVVYLAGLQSIPDDQFEAARVDGASITRTYL 227 PVD L +P++A+ A+ +A WQ+ +TM++ LA LQ IPD+ EAAR+DGA+ + + Sbjct: 162 -PVDSLITDPTLAIWAIAVAETWQWFPFTMLMVLATLQLIPDEPLEAARIDGANRRQVFR 220 Query: 228 RIIVPQLKEASVSAAVVLMVFALKAFTFLYALVGRYRPPNGTDILATLMVRRAFKFGEWA 287 II+ L+ A V + ++ +LKAF +Y L P T++ AF F W Sbjct: 221 HIILAYLRPALVVCGLFRLIDSLKAFPLIYVLTNG-GPGTATEVTNYYGFIEAFNFSYWG 279 Query: 288 YSAAIATMLL 297 Y++AIA ++L Sbjct: 280 YASAIAVLML 289 Lambda K H 0.326 0.140 0.424 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: 261 Number of extensions: 8 Number of successful extensions: 2 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: 317 Length of database: 310 Length adjustment: 27 Effective length of query: 290 Effective length of database: 283 Effective search space: 82070 Effective search space used: 82070 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 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