Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate H281DRAFT_05513 H281DRAFT_05513 branched-chain amino acid transport system permease protein
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__Burk376:H281DRAFT_05513 Length = 597 Score = 130 bits (326), Expect = 2e-34 Identities = 95/306 (31%), Positives = 148/306 (48%), Gaps = 36/306 (11%) Query: 138 FGIQI---LIYVMLAW-GLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLP 193 FGI I Y +A G+N++VGL+G + LG AFYA+GAY+ L S G + Sbjct: 36 FGIHIAQSFCYTAIAVIGVNLLVGLSGQMSLGQAAFYAIGAYASVLTSLKLGWPIAASVL 95 Query: 194 LSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKAT 253 AA G ++G LR RG YLA+ TLA G ++ ++ W +T GT G+S +P+ Sbjct: 96 FGVAVAAAVGTVVGVFALRTRGLYLAMTTLAVGFVVSILAQRWVGLTGGTMGLSGVPQ-- 153 Query: 254 LFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEAL 313 + F T G +I+ Y++ ++ + + IGR A Sbjct: 154 ---VDFGDTIHG--------------EIWYLYVVGGTLLVVQILNDYVFDSRIGRCLLAT 196 Query: 314 REDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIV 373 R+ E S+GI + FA A AG +G FA + GFV ++F S +L Sbjct: 197 RDSEAFAASVGIKVPIVRSAIFAVSAALAGLSGGLFAHQSGFVGSDAFSVTLSLSLLIAA 256 Query: 374 VLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFK 433 V+GG+G A I + GT +L M+ ++L+ G D Y ++++G M++V+L Sbjct: 257 VIGGLG-------ARIGPLAGTAIL--MTIVELVAGLD----RYGLMVYGGIMLLVLLVF 303 Query: 434 PRGFVG 439 P+G G Sbjct: 304 PQGAAG 309 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: 673 Number of extensions: 40 Number of successful extensions: 5 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: 597 Length adjustment: 35 Effective length of query: 428 Effective length of database: 562 Effective search space: 240536 Effective search space used: 240536 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: 52 (24.6 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