Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 3610346 Dshi_3727 ABC transporter related (RefSeq)
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__Dino:3610346 Length = 246 Score = 166 bits (419), Expect = 6e-46 Identities = 101/258 (39%), Positives = 150/258 (58%), Gaps = 17/258 (6%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 +L+ + L + FGGL A++ SF+A IT +IGPNGAGKTT+FN I+G KP G + Sbjct: 4 ILQTDRLGISFGGLRAVDAISFDALPNQITTVIGPNGAGKTTLFNLISGALKPGSGSVNL 63 Query: 74 NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133 + + + L + A +AR+FQ LF +TV ENL +A ++++ + + + Sbjct: 64 DGRDVTRAGPAEL------QRAGLARSFQITNLFFDMTVRENLRLA--TQVLEPASHLMR 115 Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193 L G + E I ARF +L D+ + G L +G QRRLEIA + P++L Sbjct: 116 PLRRTGRAANKVDELI--ARF-----ELHDKVHEQVGYLSHGEQRRLEIAMCLACEPKVL 168 Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253 LDEP G++ ++ AL++ + SILLIEHD+ +VM +SDHV+V+ GQKI+D Sbjct: 169 MLDEPTQGMSHADTEETEALIRGLTDHV--SILLIEHDIGIVMAVSDHVIVMHQGQKIAD 226 Query: 254 GTPDHVKNDPRVIAAYLG 271 GTP V+ +P V AAY G Sbjct: 227 GTPTEVRANPAVQAAYFG 244 Lambda K H 0.318 0.136 0.386 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: 191 Number of extensions: 13 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: 292 Length of database: 246 Length adjustment: 25 Effective length of query: 267 Effective length of database: 221 Effective search space: 59007 Effective search space used: 59007 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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