Align Amino-acid permease RocE (characterized)
to candidate BPHYT_RS21680 BPHYT_RS21680 amino acid permease-associated protein
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__BFirm:BPHYT_RS21680 Length = 476 Score = 292 bits (748), Expect = 1e-83 Identities = 153/454 (33%), Positives = 256/454 (56%), Gaps = 10/454 (2%) Query: 10 QLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGE 69 +L+ +K RH+ MI+LGGVIG G F+G+G + QAGP AVLS+L+ G ++ L M LGE Sbjct: 9 ELKAGLKQRHMTMIALGGVIGAGLFVGSGVVVQQAGP-AAVLSFLITGALVVLVMRMLGE 67 Query: 70 LAVAFPVSGSFQTYAT------KFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWF 123 +A A P GSF YA + GF GW+YW W + A+E ++ +L+Q W Sbjct: 68 MACAMPAVGSFYEYARLAFGGKRASGNLAGFLTGWMYWYFWVIVVAVEAVAGAKLVQFWL 127 Query: 124 PHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLK 183 P + W LV + N ++ ++ E EFWF+ IK+ I++F+ LGG + GL Sbjct: 128 PDVPAWAISLVLLVTLTATNLVSVGSYGEFEFWFASIKVAAIMVFLFLGGMYVLGLWPAA 187 Query: 184 GGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIK 243 A T GL P GI +L + + G E++ +AA E+++P K + ++ Sbjct: 188 KHVTAVLPTLLSHGGLMPKGIGPVLSGAVAATGFYFGAEIVTIAAAEAQEPAKAVAKATN 247 Query: 244 QTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSV 303 + R LVF+V SI+++ ++PW + +P+V+ + +GIP AA +MN ++L A+LS Sbjct: 248 SVITRVLVFYVGSILLVVALVPWNSPKMA-TPYVSALDAMGIPAAASVMNAIVLTAVLSA 306 Query: 304 ANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVY 363 NSGLYA++R+++A+ G A AL K N+RGVP+ ++++ S++ + +TV+ Sbjct: 307 LNSGLYAASRMIFALTRHGDAPAALAKVNRRGVPVRAILIGTVFGYASVVMSYVSPDTVF 366 Query: 364 MVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVV 423 L++ G A ++ I++SQ+ R + R+ E L+ + YP L + + + Sbjct: 367 AFLVNSYGTVAIFVYVLIAISQLKLRARIERDAP--EKLRVRMWCYPYLTWVAIIGMVGI 424 Query: 424 LISLAFDPEQRIALYCGVPFMIICYIIYHVVIKK 457 L+++AF PEQR L+ GV + + + Y + ++K Sbjct: 425 LVAMAFIPEQRQPLWFGVASLGVLLLAYLLRVRK 458 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: 515 Number of extensions: 28 Number of successful extensions: 6 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