Align Amino-acid permease RocE (characterized)
to candidate GFF1065 PS417_05405 D-alanine/D-serine/glycine permease
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__WCS417:GFF1065 Length = 472 Score = 320 bits (821), Expect = 5e-92 Identities = 168/446 (37%), Positives = 256/446 (57%), Gaps = 4/446 (0%) Query: 8 GNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCL 67 G L+R + RH+ +++LG IG G FLG+ I AGP +LSY++GG + + M L Sbjct: 15 GGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGP-AIMLSYIIGGLAILVIMRAL 73 Query: 68 GELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHID 127 GE+AV PV+GSF YA ++ P GF GW YW W VTC E + M WFP Sbjct: 74 GEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTP 133 Query: 128 VWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQ 187 WIW L M +N I KAF E EFWF+ IKI+ I+ +I GG + G Sbjct: 134 RWIWALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVI-GGVGIIAFGFGNDGVA 192 Query: 188 APFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVW 247 + G PNG++ +L+++ V FA+ G E+IG+ AGE+++P+KTIP +I W Sbjct: 193 LGISNLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFW 252 Query: 248 RTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSG 307 R L+F+V ++ VI + PW + G SPFV FE++GI AA I+NFV++ A LS N G Sbjct: 253 RILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGG 312 Query: 308 LYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLL 367 ++++ R+LY++A GQA KT+ GVP +L++++ L +L + E V++ + Sbjct: 313 IFSTGRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKVFVWVT 372 Query: 368 SLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISL 427 S+A A W+ I L+Q+ FR+ + LK++ LYPV + L +V+ + Sbjct: 373 SIATFGAIWTWLMILLAQLKFRKSL--SPAEQAGLKYRMWLYPVSSYLALAFLLLVVGLM 430 Query: 428 AFDPEQRIALYCGVPFMIICYIIYHV 453 A+ P+ RIALY G F+++ ++++V Sbjct: 431 AYFPDTRIALYVGPVFLVLLTVLFYV 456 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: 592 Number of extensions: 32 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: 472 Length adjustment: 33 Effective length of query: 434 Effective length of database: 439 Effective search space: 190526 Effective search space used: 190526 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 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