Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate Dsui_0636 Dsui_0636 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= uniprot:Q31RN9 (396 letters) >FitnessBrowser__PS:Dsui_0636 Length = 245 Score = 103 bits (258), Expect = 4e-27 Identities = 73/232 (31%), Positives = 127/232 (54%), Gaps = 25/232 (10%) Query: 180 LRPVSSND-------WSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLS---VT 229 L PV S + ++GL T+A +L + V +L +G ++ + R ++P RWLS Sbjct: 11 LTPVPSGETTYLGWLFTGLQWTVALSLSAWVIALVVGSIVGVLR--TVPN-RWLSGFAAV 67 Query: 230 YIELFRGLPLVTILFFGQVMVPLML---------DSEWRIDRILRAIVGLTIFLSAYLAE 280 Y+E FR +PL+ LF ++P +L S+ + + L A++ L +F +A +AE Sbjct: 68 YVECFRNVPLLVQLFSWYFVLPELLPPALGNAYKQSDPLLQQFLAAMLCLGLFTAARVAE 127 Query: 281 TVRGGLQAIPQGQFEAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSI 340 VR G++++P+GQ A A+G L Q YR ++LP A RI +P + FLN+ +++ + + Sbjct: 128 QVRAGIESLPRGQRNAGLAMGFTLAQVYRHVLLPMAFRIIVPPLTSEFLNIFKNSAVATT 187 Query: 341 VGLLELLGISRSILANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRL 392 +GL+EL SR Y + E ++ + +LY + L RRLE+++ Sbjct: 188 IGLIEL---SRQAQQLVDYTAQPYEAFIAVTLLYVCINVTVMFLMRRLEEKV 236 Lambda K H 0.329 0.142 0.471 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: 264 Number of extensions: 11 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: 396 Length of database: 245 Length adjustment: 27 Effective length of query: 369 Effective length of database: 218 Effective search space: 80442 Effective search space used: 80442 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: 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