Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_083780243.1 BTUS_RS15280 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000092905.1:WP_083780243.1 Length = 383 Score = 206 bits (523), Expect = 1e-57 Identities = 125/347 (36%), Positives = 195/347 (56%), Gaps = 38/347 (10%) Query: 91 EGELDISTEKSFFHRHFLK-IALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLA 149 E + ++ E+ +R+ LK ++L ALLL AI ++ N I +L+Y++L Sbjct: 36 ERKTNVWIEQQQRNRNLLKWVSLAALLL----AAAIWPWWVDDRFLLNVMINVLLYMVLG 91 Query: 150 WGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFP 209 G++++ G AGL LGY FY +GAY+ ALL + G+SFW LP S L ++ G P Sbjct: 92 MGMHLIFGTAGLPFLGYAGFYGIGAYTAALLMTR-GVSFWAALPASVAAVCLVALLFGAP 150 Query: 210 VLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKL 269 +LRLRG+Y + +LA GEII L IN D+T G GI IPK FG A Sbjct: 151 ILRLRGEYFMLGSLALGEIIHLT-INNLDITGGPNGIVGIPKPRWFGGTLSQPAD----- 204 Query: 270 FHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVT 329 +YL+L + +++ + L++ +GR+W ALREDE+A ++G+ T Sbjct: 205 -------------FYYLLLVVVLVSIALLTYLQKSTVGRSWLALREDELAAEAVGVPTYR 251 Query: 330 TKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAI 389 KL F G+ +AG AG+F AAR G V+P SF + S ++ I+++GGMGSL G+ + + Sbjct: 252 RKLQLFVLGSAWAGVAGAFLAARMGIVTPGSFTLMNSVQMIGIIIVGGMGSLPGVVLGTV 311 Query: 390 VMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRG 436 +M+G E +R ++ +R++IFG+A++ V+ F+PRG Sbjct: 312 LMIGLPEFVRALAD-------------WRLVIFGVAIMAVLRFRPRG 345 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: 506 Number of extensions: 35 Number of successful extensions: 5 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: 383 Length adjustment: 32 Effective length of query: 431 Effective length of database: 351 Effective search space: 151281 Effective search space used: 151281 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