Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_012965550.1 FERP_RS05220 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000025505.1:WP_012965550.1 Length = 324 Score = 98.6 bits (244), Expect = 3e-25 Identities = 95/341 (27%), Positives = 150/341 (43%), Gaps = 53/341 (15%) Query: 110 IALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVM-LAWGLNIVVGLAGLLDLGYVA 168 I LI L P P+G Y+ FG+ L ++ L+W +I+VG G ++LG+ Sbjct: 12 IGLIVALTLPFYT-----PEG---YLFLFGMLFLFLILVLSW--DIIVGYTGQVNLGHTV 61 Query: 169 FYAVGAYSYALLS-----SYFGLSFWVLLP--------LSGIFAALWGVILGFPVLRLRG 215 F +GAY+ ALL F + + P + GI AAL+G +GF LRL+G Sbjct: 62 FVGLGAYTAALLQVPSRFESFSSALASMPPQNQFLSILIGGIVAALFGAAIGFVTLRLKG 121 Query: 216 DYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPIS 275 Y A+VT + + ++DV G G S + L P Sbjct: 122 YYFALVTAILPLVFIQTVYVFSDVFGGEEGFSIGLERALSQSPV---------------- 165 Query: 276 SAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAF 335 YY F +L+ L M Y+ + +G + A+R+DE +LGI+ V K+ AF Sbjct: 166 VRYYVAFAVFLLCFLAM--RYIV----KSDLGYRFMAVRDDEELAEALGIDVVKYKVLAF 219 Query: 336 ATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGT 395 + FAG AG+ + V P+ + +I+ VLGG+G+L G I I++ Sbjct: 220 TISSFFAGVAGATIVLYRITVGPDLYDIPLMLMIILSAVLGGLGTLYGPLIGGIIVY--- 276 Query: 396 ELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRG 436 LL+ + +I F + ++ ++ V L P G Sbjct: 277 -LLKNLFLKTMIPQGAFVND---EIVLYAILIAVALLSPEG 313 Lambda K H 0.330 0.145 0.432 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: 441 Number of extensions: 32 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 463 Length of database: 324 Length adjustment: 30 Effective length of query: 433 Effective length of database: 294 Effective search space: 127302 Effective search space used: 127302 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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