Align Amino-acid permease RocE (characterized)
to candidate WP_053544618.1 CDES_RS05420 amino acid permease
Query= SwissProt::P39137 (467 letters) >NCBI__GCF_001277995.1:WP_053544618.1 Length = 468 Score = 266 bits (679), Expect = 1e-75 Identities = 144/438 (32%), Positives = 234/438 (53%), Gaps = 4/438 (0%) Query: 15 MKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGELAVAF 74 +++RH+ I+LG IGTG F G+ I AGP +L YL+GG +++ + LGE++V Sbjct: 14 LRARHIHFIALGSAIGTGLFYGSAGAIQAAGP-SVLLVYLLGGAVVYFMLRALGEMSVHH 72 Query: 75 PVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVWIWCLV 134 PV GSF Y + G+ GW++ + C + + G M WFP W+W Sbjct: 73 PVRGSFAVYTRAHLGGWAGYITGWMFAFEMLIVCLADLTAIGIYMNFWFPDTPQWVWVAA 132 Query: 135 FAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAPFLTHF 194 ++ N + + F E E F+ +K+ ++ I+ GGAA+ E A + Sbjct: 133 TLLIVGGANLASVRWFGELEVVFTIVKVTAVIAMIV-GGAAILAFGLGSNAEVAGISNLW 191 Query: 195 YEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRTLVFFV 254 G FPNGI+ M+ I V FAF GTE+IGVA E+E+PEK+IP+++ R L+F+V Sbjct: 192 EHGGFFPNGIEGMIAAFILVLFAFGGTEIIGVAGSEAEEPEKSIPKAVNTVPVRILLFYV 251 Query: 255 LSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSGLYASTRI 314 +I+VI + PW ESPFV +F+ +G+ +AA ++N V++ A LS N+ L+ + R+ Sbjct: 252 GAILVILALNPWPSITGEESPFVQIFDTLGVNWAAGLLNLVVITAALSAINADLFGAGRV 311 Query: 315 LYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLLSLAGMSA 374 L +A E A KA+GK + GVP+ + I+ + V + ++ E V+ ++ SLA + Sbjct: 312 LTGLAKENLAPKAMGKIAKNGVPIMTTIIMIIVLIVGVILNAVLPERVFEIVASLATFAT 371 Query: 375 QVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISLAFDPEQR 434 W+ I L+Q+ RR+ E ++E LKF P YP + + + Sbjct: 372 VYVWLMILLAQVGSRRRMSAE--EVETLKFPVPFYPFGQYFAILFIAFTFGIMVWYENYH 429 Query: 435 IALYCGVPFMIICYIIYH 452 + L GV F+++ I+Y+ Sbjct: 430 LPLAVGVGFLVLMTILYY 447 Lambda K H 0.329 0.142 0.438 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: 539 Number of extensions: 34 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: 467 Length of database: 468 Length adjustment: 33 Effective length of query: 434 Effective length of database: 435 Effective search space: 188790 Effective search space used: 188790 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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