Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate AZOBR_RS27990 AZOBR_RS27990 ABC transporter permease
Query= TCDB::O30832 (290 letters) >FitnessBrowser__azobra:AZOBR_RS27990 Length = 310 Score = 99.4 bits (246), Expect = 9e-26 Identities = 81/277 (29%), Positives = 132/277 (47%), Gaps = 8/277 (2%) Query: 16 PAVILLFLWMIVPLSMTLYFSFLRYNLLMPG--MESFTGWDNYYYFLTDPAFSAALTNTI 73 PA+++L ++P L S +L+ PG + NY L D F ++ + Sbjct: 32 PALVVLGGITLLPGLFLLGVSLTPLSLVNPGTVFDFSDPLGNYRELLRDARFHNSVLLQL 91 Query: 74 LLVVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSALVWKNMFMNPVNG 133 L + + + G+ +ALLL+ +R + P + P V AL+WK ++ V+ Sbjct: 92 HLSATSVGLQLAAGLGVALLLNVRARFFEAIRAAFLIPMVLPPIVVALIWKILYTPDVSP 151 Query: 134 MFAHIARGLGLPPFDFLSQAPLA--SIIGIVAWQWLPFATLILLTALQSLDREQMEAAEM 191 + + GLP ++ LA +I WQW PF L++L LQ + E +EAA + Sbjct: 152 LH-RLLEEAGLPVDSLITDPTLAIWAIAVAETWQWFPFTMLMVLATLQLIPDEPLEAARI 210 Query: 192 DGASALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNGGPGTASTNITYLVYA 251 DGA+ F HI + +L A+ V L + I L F I V TNGGPGTA+ Y + Sbjct: 211 DGANRRQVFRHIILAYLRPALVVCGLFRLIDSLKAFPLIYVLTNGGPGTATEVTNYYGFI 270 Query: 252 QSLLNYDVGGGSAGGIVAVVLANIVAI-FLMRMIGKN 287 ++ N+ G A I ++L + A+ +L+ +G N Sbjct: 271 EA-FNFSY-WGYASAIAVLMLGGVFAVSWLVGRLGWN 305 Lambda K H 0.329 0.142 0.429 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: 226 Number of extensions: 13 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: 290 Length of database: 310 Length adjustment: 27 Effective length of query: 263 Effective length of database: 283 Effective search space: 74429 Effective search space used: 74429 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 (21.8 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