Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate 5210165 Shew_2609 inner-membrane translocator (RefSeq)
Query= uniprot:D8IUY4 (309 letters) >FitnessBrowser__PV4:5210165 Length = 297 Score = 161 bits (408), Expect = 2e-44 Identities = 97/307 (31%), Positives = 168/307 (54%), Gaps = 14/307 (4%) Query: 2 DIFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVA 61 ++ IQ IINGL++G +Y ++ + + +VY ++NFA G+ L+VGA V + L Q Sbjct: 4 ELLIQLIINGLIVGLLYGVVGMCFVLVYKSTQIVNFAQGEFLLVGAWVCWAFLTYFQ--- 60 Query: 62 PGLPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAMM 121 LP V + + V +L++ I RP+ P ++ ++ IG+SI Q+L Sbjct: 61 --LPFFVGFLFTLC----FMAVFGVLLQMIVLRPMIGEPIISVIMVTIGLSIFFQSLTKW 114 Query: 122 IWGRSPLPFPQVMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMRATA 181 I+G SP +PQV + + I G I +M +A+L M L + +K G AMRATA Sbjct: 115 IFGVSPQSYPQVFDTQSIAIFGLNIELAYLMSTVIAILIMAAFFLFFKYSKHGLAMRATA 174 Query: 182 ENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAVL 241 + ++A +G+ +V +++ I A ++A AGV+ + G+K F A +L Sbjct: 175 FDQQVAQSLGISVKQVFAMSWGIAATVSATAGVVIGMVNGVSDSLSTI--GIKVFPAVIL 232 Query: 242 GGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGIM 301 GG+ +I GA++GG+++G++E++ + D +G+ Y DI F VL+++L +P G+ Sbjct: 233 GGLDSIVGAIVGGVVIGVLENIAEFF--DSQWLHIGNMY-DIAPFYVLLVILWFKPYGLF 289 Query: 302 GERVADR 308 G R +R Sbjct: 290 GTRDIER 296 Lambda K H 0.328 0.144 0.416 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: 238 Number of extensions: 16 Number of successful extensions: 3 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: 309 Length of database: 297 Length adjustment: 27 Effective length of query: 282 Effective length of database: 270 Effective search space: 76140 Effective search space used: 76140 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: 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