Align Amino-acid permease RocE (characterized)
to candidate AO356_15120 AO356_15120 amino acid transporter
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_15120 Length = 476 Score = 478 bits (1231), Expect = e-139 Identities = 221/458 (48%), Positives = 329/458 (71%), Gaps = 3/458 (0%) Query: 3 TNQDNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFL 62 TN G ++ M++RH+ M++LGGVIGTG FL +G+T+NQAGP+GAV++Y++G ++++ Sbjct: 8 TNTRTG--FKQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALMVYM 65 Query: 63 TMLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRW 122 M+CLGELAV P +GSF TYAT+F+ P G+ WLYWL W V EF +AG LM RW Sbjct: 66 VMMCLGELAVQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILMSRW 125 Query: 123 FPHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDL 182 FP VWIW +FA ++F+ N ++ + FAE+EFW S IK+L +++F+++GG A+ GL+++ Sbjct: 126 FPDTPVWIWSALFAGVVFLTNVVSVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGLLNI 185 Query: 183 KGGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSI 242 L++F +GLFP G + +T++ V+FAF GTELIG+AAGE++DP++ +PR+I Sbjct: 186 DQAHSIG-LSNFTREGLFPTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVPRAI 244 Query: 243 KQTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLS 302 + TV R VFFV +I V+A ++P +QAG+VESPFV VF IGIPY+ADIMNFVI+ ALLS Sbjct: 245 RTTVLRLAVFFVGTIFVLATLLPREQAGLVESPFVTVFTYIGIPYSADIMNFVIISALLS 304 Query: 303 VANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETV 362 ANSGLYA++R+L+ ++++G K + G P+ ++IV+MA SLL+ A+T+ Sbjct: 305 AANSGLYAASRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAASLLSSVFAADTI 364 Query: 363 YMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTV 422 Y+ L+S++G++ V W++I+ SQI FRR Y+ GG I DLKF+ YP +PL L ++ Sbjct: 365 YLALVSISGLAVVVVWMSIAASQIAFRRHYVANGGDIRDLKFRVRGYPWVPLGALVCCSL 424 Query: 423 VLISLAFDPEQRIALYCGVPFMIICYIIYHVVIKKRQQ 460 + +AFDPEQR+ALY G+PF+ CY +Y++ K R++ Sbjct: 425 ACVGIAFDPEQRVALYFGLPFIAWCYFVYYITRKSRER 462 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: 581 Number of extensions: 19 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: 467 Length of database: 476 Length adjustment: 33 Effective length of query: 434 Effective length of database: 443 Effective search space: 192262 Effective search space used: 192262 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