Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate GFF3451 PS417_17665 ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >FitnessBrowser__WCS417:GFF3451 Length = 286 Score = 161 bits (408), Expect = 1e-44 Identities = 91/288 (31%), Positives = 169/288 (58%), Gaps = 6/288 (2%) Query: 1 MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMN 60 +NL L Q++NGL LG +Y L+++G T+++G++ +NFAHG +++GA+I Y + S N Sbjct: 2 LNLYLFQILNGLGLGMIYFLISVGLTIIFGLLNFVNFAHGAFFLLGAYICYTAV-SLTGN 60 Query: 61 FFVALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVG--ANT 118 F++AL++A L A L VIE + + + H + ++ +G++ +++ V + G + Sbjct: 61 FWLALLIAPLVVAALAWVIERVLIQRIYHLPHMFQILVTLGIALIIQEASVMIWGPVGKS 120 Query: 119 RAFPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAA 178 A P+ ++ V +G +L ++ S ++ + L +++++T+ G +RA S ++ Sbjct: 121 VAVPELLRGVLV-VGDFVYPYYRLFLIVFSGLVGLGLWLLLERTRFGALVRAGSESTETV 179 Query: 179 QLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGII 238 L+G N+ R S TFALG ALAG AGVL A +P +G +FV V+GG+G Sbjct: 180 SLLGTNIFRLFSMTFALGVALAGVAGVLFA-PLRGAQPFVGPEILGVAFVVVVIGGMGSF 238 Query: 239 PGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGK 286 GA +GG ++G++++ T ++YG + ++++VRP G+ G+ Sbjct: 239 SGALVGGLLVGVVQSLMTTL-WPQGASLMIYGAMAVVILVRPYGLFGR 285 Lambda K H 0.330 0.146 0.407 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: 244 Number of extensions: 10 Number of successful extensions: 5 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: 286 Length adjustment: 26 Effective length of query: 266 Effective length of database: 260 Effective search space: 69160 Effective search space used: 69160 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