Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF1060 Psest_1093 ABC-type branched-chain amino acid transport system, permease component
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__psRCH2:GFF1060 Length = 335 Score = 106 bits (264), Expect = 1e-27 Identities = 82/275 (29%), Positives = 125/275 (45%), Gaps = 31/275 (11%) Query: 37 LLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHT 96 L + L A N+++GYAGLL G+ AF+A G Y+ M S + +GL T Sbjct: 56 LCFALFACAFNLLLGYAGLLSFGHAAFFATGGYITGYMLSSY-------------SGLST 102 Query: 97 SLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGP 156 L I+ L + G + G ++ +G Y A++TL +++ F + P T G Sbjct: 103 ELGIL--AGTLASTVLGGLFGMLAIRRQGIYFAMITLALAQLV--FFVFVQAP--FTGGE 156 Query: 157 KGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAW 216 GL + +FGL D+ + YY L + V+ I R S G+ Sbjct: 157 NGLQGVPRGHLFGL----------VDMKNNMAMYYFVLAVFVLGFAIIQRTIHSPYGQVL 206 Query: 217 MAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIV 276 AIRE+E A ++G N KLLAF + A+ G++GA S S ++ Sbjct: 207 KAIRENEPRAVSLGYNVDRHKLLAFVISAALAGLAGATKTVVFQLASLTDAHWHMSGEVI 266 Query: 277 AMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPL 311 M +LGG+G I G ++GA ++ L L GPL Sbjct: 267 LMTLLGGVGTILGPLVGATVVVTLQSSLS--NGPL 299 Lambda K H 0.328 0.144 0.430 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: 292 Number of extensions: 20 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: 358 Length of database: 335 Length adjustment: 29 Effective length of query: 329 Effective length of database: 306 Effective search space: 100674 Effective search space used: 100674 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 (21.7 bits) S2: 49 (23.5 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