Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_051378059.1 H566_RS0104985 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000482785.1:WP_051378059.1 Length = 392 Score = 160 bits (405), Expect = 7e-44 Identities = 115/333 (34%), Positives = 182/333 (54%), Gaps = 37/333 (11%) Query: 110 IALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAF 169 +AL LL + + A++ L + +L+Y + GLNI +G AG+++ +AF Sbjct: 78 LALAGLLAFGALATALREDPFPLLIL----CTLLLYATVCLGLNIQIGYAGVVNFSAMAF 133 Query: 170 YAVGAYSYALLSSYFG-LSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEI 228 + VG+Y+ A L++ L +L L+G AAL G +L FPVLR RG Y ++VT+AF + Sbjct: 134 FGVGSYAAAWLTTNAPTLPHLAVLALAGGAAALVGAMLLFPVLRTRGHYASLVTVAFAVL 193 Query: 229 IRLVLINWTDVTKGTFGISS---IPKATLFGIPF--DATAGGFAKLFHLPISSAYYKIFL 283 R ++ +V + TFG + +P ++FG F D G F+ ++ + I L Sbjct: 194 FR----SFMEVNE-TFGGAQGMKLPGLSMFGHDFNDDIELFGLTFTFYAGYAAVAFAIAL 248 Query: 284 FYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAG 343 L L T R+ R IG ++A+R DEIA GIN K+TAF G FAG Sbjct: 249 SALAL---------TWRIERSWIGVNFDAVRSDEIAAACFGINIARWKITAFLIGNAFAG 299 Query: 344 FAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSF 403 AG+ FA GFV+P +F F +S V+L+I+VLGG+G+L GI AA++++ E L+ + Sbjct: 300 VAGALFALMTGFVAPNNFNFGDSLVMLSILVLGGLGNLWGILPAALIVIILPEKLQAI-- 357 Query: 404 LKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRG 436 + YR L++ A++ ++LF+P+G Sbjct: 358 -----------QEYRFLLYAAAVIAILLFRPQG 379 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: 565 Number of extensions: 41 Number of successful extensions: 4 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: 463 Length of database: 392 Length adjustment: 32 Effective length of query: 431 Effective length of database: 360 Effective search space: 155160 Effective search space used: 155160 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: 51 (24.3 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