Align ABC transporter permease (characterized, see rationale)
to candidate AZOBR_RS31200 AZOBR_RS31200 sugar ABC transporter permease
Query= uniprot:A0A166R405 (325 letters) >FitnessBrowser__azobra:AZOBR_RS31200 Length = 325 Score = 132 bits (331), Expect = 2e-35 Identities = 97/303 (32%), Positives = 156/303 (51%), Gaps = 9/303 (2%) Query: 20 YLGLAGALLAMVALFSVLSSHFLSYDTFSTLANQIPD---LMVLAVGMTFVLIIGGIDLS 76 +L L +V F + ++ F ++ + + N + D L + AVGMTFV++ GGIDLS Sbjct: 5 FLPLLVTSAVLVVGFLLCAAQFPNFASLRVVGNLLTDNAFLGITAVGMTFVILSGGIDLS 64 Query: 77 VGSVLALAASAVSVAILGWGWSVLPAALLGMAVAALAGTITGSITVAWRIPSFIVSLGVL 136 VG+V+ ++V I GW + A + +AVA G G++ +++P FIV+L + Sbjct: 65 VGAVIGFTTVLLAVLIEQGGWHPVSAFAVALAVAGGFGAAMGAVIHVFQMPPFIVTLAGM 124 Query: 137 EMARGLAYQMTGSRTAYIGDAFAWLSN-PIAF-GISPSFIIALLIIFIAQAVLT---RTV 191 +ARGL + ++ +A L + + F G + ALL++ + A + T Sbjct: 125 FVARGLGFVLSTDSIPINHPLYAELGDLALRFDGGGKLTLPALLMLGVVAAAVVCAHWTR 184 Query: 192 FGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADPNAGSGLE 251 FG L +G N ++ L G+ + V++L GLLAG+A + A A +G+E Sbjct: 185 FGANLYALGGNRQSAELMGVPVGRTTVAVYALSGLLAGLAGIVFSLYTGAGYSLAATGVE 244 Query: 252 LQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEP-TKRIITGAVIVVA 310 L I AVVIGGT L GG G VI TF GVLI ++ + G+ +I G ++ V Sbjct: 245 LDTITAVVIGGTQLTGGYGYVIGTFIGVLIQGLIQTYITFDGSLSSWWTKIAIGVLLFVF 304 Query: 311 VVL 313 ++L Sbjct: 305 ILL 307 Lambda K H 0.325 0.139 0.393 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: 268 Number of extensions: 9 Number of successful extensions: 3 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: 325 Length of database: 325 Length adjustment: 28 Effective length of query: 297 Effective length of database: 297 Effective search space: 88209 Effective search space used: 88209 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 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