Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate 3607127 Dshi_0549 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= uniprot:A8LLL4 (385 letters) >FitnessBrowser__Dino:3607127 Length = 272 Score = 110 bits (274), Expect = 6e-29 Identities = 75/244 (30%), Positives = 125/244 (51%), Gaps = 15/244 (6%) Query: 148 VTATTPP----EFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYAL 203 V PP E T +NY L + +G+ R N+L + I T + +++ AA+AL Sbjct: 38 VALEAPPVWIFEPTLSNYREALFE----DGVLRTLINSLIIAISTTFLALVLGVPAAFAL 93 Query: 204 AWMEFPGRA-LLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAI 262 A EF G+ L I ++ P+ LAL P + +G+ ++ L + F +P+ I Sbjct: 94 ARFEFRGKKDLWFWFITNRMISPIVLAL-PFFLIARNLGLLDKHITLILIYLTFNLPIVI 152 Query: 263 YLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAK 322 +++ + G+P D+ E A+++GA+ F I KI LPL+ P +A AIF F+++WN+L+ Sbjct: 153 WIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMPGVAVSAIFSFIFSWNELMFGL 212 Query: 323 VFLIDATGQTTVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVF-FSMQRFLVRGLLA 381 + M +E G +I+AT+ I +P+L+F + LVRGL Sbjct: 213 ILTRSEAKTAPAMAVSFMEGYNLPYG--KIMATSTL--IVIPVLIFALIASKQLVRGLTM 268 Query: 382 GSVK 385 G+VK Sbjct: 269 GAVK 272 Lambda K H 0.323 0.138 0.419 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: 214 Number of extensions: 9 Number of successful extensions: 2 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: 385 Length of database: 272 Length adjustment: 28 Effective length of query: 357 Effective length of database: 244 Effective search space: 87108 Effective search space used: 87108 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 48 (23.1 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