Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_043743902.1 AMB_RS08455 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_000009985.1:WP_043743902.1 Length = 291 Score = 166 bits (419), Expect = 8e-46 Identities = 95/298 (31%), Positives = 156/298 (52%), Gaps = 12/298 (4%) Query: 4 FVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAG 63 F+Q L +GLT G+IY L +G+ ++Y +INFA G+ M+GG A + I+ Sbjct: 5 FLQYLFSGLTSGAIYALAGLGFAIIYNASHVINFAQGEFIMIGGMATATMVAAGVPIYLA 64 Query: 64 LPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQ 123 +P+A+ +++ VAM E+ A P R + + +I IG SI + Q+ Sbjct: 65 IPLAMAASMLVGVAM----------EKFAIEPARNADVVTIIIITIGASIFMRGAAQLIW 114 Query: 124 GPRNKPIPPMVSSV-YQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQD 182 +P ++ + + + I+AV + + WY NRT G+A T + Sbjct: 115 DKEFHSLPAFSGETPIAVMGATLMPQSLWVFGISAVAIALLWYFFNRTMFGKAMLGTSHN 174 Query: 183 RKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVLGG 242 R A L+GV V + + +F + A L AV G + + ++ G G+K F+AAVLGG Sbjct: 175 RLAAQLVGVAVKRVLLASFALSALLGAVGGIV-VTPITFTNYEAGIMLGLKGFSAAVLGG 233 Query: 243 IGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVEKV 300 +G+ GA+ GGL++G+ E++ S Y + AYKD F I+ FVL F P+G+ G+ ++V Sbjct: 234 LGNGTGAIIGGLIVGIAEAMASGYLSSAYKDAIAFIIILFVLFFMPSGLFGKRGTDRV 291 Lambda K H 0.329 0.143 0.421 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: 267 Number of extensions: 15 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: 300 Length of database: 291 Length adjustment: 26 Effective length of query: 274 Effective length of database: 265 Effective search space: 72610 Effective search space used: 72610 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