Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 3606951 Dshi_0379 inner-membrane translocator (RefSeq)
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__Dino:3606951 Length = 358 Score = 126 bits (316), Expect = 1e-33 Identities = 92/302 (30%), Positives = 152/302 (50%), Gaps = 21/302 (6%) Query: 140 IQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYS-YALLSSYFGLSFWVLLPLSGIF 198 + LI+ + A GLNI+ G G + LG F AVGAY+ Y L++++ L+ + + L G+ Sbjct: 54 VPFLIWAIAAIGLNILTGYCGQVSLGTGGFMAVGAYACYKLMTAFPDLNIAICVLLGGVI 113 Query: 199 AALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTD--VTKGTFGISSIPKATLFG 256 A GV+ G P LR++G YLA+ TLA + + L N G + P+ T+FG Sbjct: 114 TAAVGVLFGLPSLRIKGFYLAVATLA-AQFFLVWLFNKVPWFYNYSASGQINAPERTMFG 172 Query: 257 IPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALRED 316 P + A K + LA + A++ L R IGR+W A+R+ Sbjct: 173 YAITG-----------PNADAAPK---YLFCLAFLFVLAWLARNLTRGTIGRSWMAIRDM 218 Query: 317 EIACRSLGINTVTTKLTAFATGAMFAGFAGS-FFAARQGFVS-PESFVFLESAVILAIVV 374 +IA +G+N + KLTAFA + F G AG+ FF+ G V E+F +S ++L +++ Sbjct: 219 DIAAEIIGVNPLKAKLTAFAVSSFFVGVAGALFFSVYLGAVEVGEAFGINQSFLVLFMII 278 Query: 375 LGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKP 434 +GG+GS+ G A +V LL+ + L + + ++ G ++ ++ +P Sbjct: 279 IGGLGSIFGSLAGAAFIVLLPVLLKNVMVGSLGWDTAIAAH-FEFVVLGGLIIFFLIVEP 337 Query: 435 RG 436 G Sbjct: 338 HG 339 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: 501 Number of extensions: 30 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: 358 Length adjustment: 31 Effective length of query: 432 Effective length of database: 327 Effective search space: 141264 Effective search space used: 141264 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