Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AZOBR_RS32410 AZOBR_RS32410 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__azobra:AZOBR_RS32410 Length = 355 Score = 205 bits (521), Expect = 2e-57 Identities = 122/344 (35%), Positives = 178/344 (51%), Gaps = 33/344 (9%) Query: 105 RHFLKIALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDL 164 R F L+ + + V AI G S Y+ I +I+V+L+ LN V G AGLL + Sbjct: 26 RRFAWTLLLLAVAFGAVPAAIVGTGSS--YLAQIAITTMIFVILSASLNHVTGTAGLLSI 83 Query: 165 GYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLA 224 G+ AFY +GAY+ ALLS+ GL F V LP +G+ AAL+G ++ P +RL Y A+ TL Sbjct: 84 GHAAFYGIGAYAAALLSTKLGLPFIVTLPAAGLIAALFGFLVALPTMRLVSIYFAVATLG 143 Query: 225 FGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLF 284 GE+I +VL+NW DVT+G GI IP LFG D + + Sbjct: 144 IGEMIYVVLLNWVDVTRGPMGIRGIPPIELFGWQADTL------------------LTRY 185 Query: 285 YLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGF 344 + + + +V RL G A ALRED+ S+GIN K+ +F FAG Sbjct: 186 LAVAVIAVACVWVLHRLTHSYYGNALRALREDDQCADSMGINVERLKIESFVVATFFAGI 245 Query: 345 AGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFL 404 AG+ A +++P++F F+ES +ILA+VV+GG+GSL G + A+ M+ E LR++ Sbjct: 246 AGALLAHTSAYIAPDNFRFMESILILAMVVVGGLGSLPGAVVGALFMIVLPEALRDIGD- 304 Query: 405 KLIFGPDFTPELYRMLIFGLAMVVVMLFKPRGFVGSREPTAFLR 448 YRM+ G M + +L P+G + F+R Sbjct: 305 ------------YRMIAVGATMFLSILLLPKGMLAEGTALGFVR 336 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: 478 Number of extensions: 27 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: 463 Length of database: 355 Length adjustment: 31 Effective length of query: 432 Effective length of database: 324 Effective search space: 139968 Effective search space used: 139968 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 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