Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate AZOBR_RS27990 AZOBR_RS27990 ABC transporter permease
Query= uniprot:D8IPH8 (292 letters) >FitnessBrowser__azobra:AZOBR_RS27990 Length = 310 Score = 151 bits (382), Expect = 2e-41 Identities = 90/272 (33%), Positives = 153/272 (56%), Gaps = 9/272 (3%) Query: 16 PSLLVMLVLGLVPTVAAINLALKNRVLRYPDSDYVW---LRNLERLMSDRRFLNAIEVSA 72 P+L+V+ + L+P + + ++L L P + + + L N L+ D RF N++ + Sbjct: 32 PALVVLGGITLLPGLFLLGVSLTPLSLVNPGTVFDFSDPLGNYRELLRDARFHNSVLLQL 91 Query: 73 VWEVVTVLGAVIVGIAIAVYLFENVHGKWRQAMCVLLITPVLLPRVSAAFIWKFMYSPLT 132 +V + G+ +A+ L NV ++ +A+ + P++LP + A IWK +Y+P Sbjct: 92 HLSATSVGLQLAAGLGVALLL--NVRARFFEAIRAAFLIPMVLPPIVVALIWKILYTPDV 149 Query: 133 GILGWLLGLVGIHDTAFLSDPALALYAVALVDIWQWGLFFAVIVLKLLETLPPEPLEAAR 192 L LL G+ + ++DP LA++A+A+ + WQW F ++VL L+ +P EPLEAAR Sbjct: 150 SPLHRLLEEAGLPVDSLITDPTLAIWAIAVAETWQWFPFTMLMVLATLQLIPDEPLEAAR 209 Query: 193 LDYARTWQVYAYIALPMLKGPLISLVFIKMVESLRSFDLIYVMTKGGPGVATETLDMYAY 252 +D A QV+ +I L L+ L+ ++++SL++F LIYV+T GGPG ATE + Y + Sbjct: 210 IDGANRRQVFRHIILAYLRPALVVCGLFRLIDSLKAFPLIYVLTNGGPGTATEVTNYYGF 269 Query: 253 AQGIGLSGKVSYASTMAVLMMIATTLIFTLIW 284 + S YAS +AVLM+ +F + W Sbjct: 270 IEAFNFS-YWGYASAIAVLMLGG---VFAVSW 297 Lambda K H 0.328 0.141 0.439 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: 234 Number of extensions: 10 Number of successful extensions: 1 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: 292 Length of database: 310 Length adjustment: 27 Effective length of query: 265 Effective length of database: 283 Effective search space: 74995 Effective search space used: 74995 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 (21.7 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