Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate GFF3089 HP15_3032 amino acid ABC transporter, inner membrane subunit
Query= uniprot:B2TBJ8 (250 letters) >FitnessBrowser__Marino:GFF3089 Length = 247 Score = 95.1 bits (235), Expect = 1e-24 Identities = 61/202 (30%), Positives = 97/202 (48%), Gaps = 9/202 (4%) Query: 15 LLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPLLIQMFLV 74 L+ T+ L F SL L L L+ + ++S + A Y + RG P L+ M L Sbjct: 24 LMDGAIVTIELAFLSLALSVALGLIGASAKLSQSRVAKGIATTYTTLIRGVPDLVMMLLF 83 Query: 75 YYGMGQFGV-IRESFLWPVLR-------EPYMCAVLSLALCTAGYTAEIIRGGLMAVPVG 126 YYG GQ V + ++W +P++ V+++ L Y E RG +AV G Sbjct: 84 YYG-GQVAVNMLSDYIWEAYEIDFFFQFDPFISGVVTIGLIFGAYMTETFRGAFLAVETG 142 Query: 127 QIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGVAQQ 186 QIEA + G + F RR++ P +R LP +L+K+TAL S++ + ++ VA++ Sbjct: 143 QIEAARAYGFTRFHTFRRIMLPQMMRHALPGLGNNWQVLLKTTALVSIIGLTDMVRVAEE 202 Query: 187 IIQQTYRTTEVFICAALIYLFL 208 + FI A +YL L Sbjct: 203 AAKAERMPFHFFIPVAFVYLAL 224 Lambda K H 0.331 0.143 0.431 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: 157 Number of extensions: 8 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: 250 Length of database: 247 Length adjustment: 24 Effective length of query: 226 Effective length of database: 223 Effective search space: 50398 Effective search space used: 50398 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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