Align Amino-acid permease RocE (characterized)
to candidate 1937132 b3795 predicted transporter (NCBI)
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__Keio:1937132 Length = 461 Score = 300 bits (767), Expect = 9e-86 Identities = 164/466 (35%), Positives = 260/466 (55%), Gaps = 13/466 (2%) Query: 6 DNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTML 65 DN +LQR +++RH+ +I+LGG IG G F+G T+ AGP +L+Y++ G +F M Sbjct: 3 DNKPELQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGP-SVLLAYIIAGLFVFFIMR 61 Query: 66 CLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPH 125 +GE+ PV+GSF YA +++SP FG+ W YW W E + G +Q WFP Sbjct: 62 SMGEMLFLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPE 121 Query: 126 IDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILG-GAAMFGLIDLKG 184 + WI L+ AL+ + N + + E EFWF+ IK+ I++ I++G G FG + G Sbjct: 122 MAQWIPALIAVALVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVIGLGVIFFGFGN--G 179 Query: 185 GEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQ 244 G+ F G F G K L + V ++QG ELIG+ AGE+++P+ T+ ++ + Sbjct: 180 GQSIGFSNLTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSAVGK 239 Query: 245 TVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVA 304 +WR L+F+V +I VI + PW + G SPFV F +IGI AA I+NFV+L A LS Sbjct: 240 VLWRILIFYVGAIFVIVTIFPWNEIGSNGSPFVLTFAKIGITAAAGIINFVVLTAALSGC 299 Query: 305 NSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAV----ACLSLLTKFAQAE 360 NSG+Y+ R+LYA+A Q A+ K ++ GVP+ + V++A+ +CL+ + + Sbjct: 300 NSGMYSCGRMLYALAKNRQLPAAMAKVSRHGVPVAGVAVSIAILLIGSCLNYI--IPNPQ 357 Query: 361 TVYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLN 420 V++ + S + + V W I +SQ+ FRR + I F++ L+P + + Sbjct: 358 RVFVYVYSASVLPGMVPWFVILISQLRFRRAH---KAAIASHPFRSILFPWANYVTMAFL 414 Query: 421 TVVLISLAFDPEQRIALYCGVPFMIICYIIYHVVIKKRQQANRQLE 466 VLI + F+ + R++L+ G+ FM+ IY V R +LE Sbjct: 415 ICVLIGMYFNEDTRMSLFVGIIFMLAVTAIYKVFGLNRHGKAHKLE 460 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: 578 Number of extensions: 26 Number of successful extensions: 7 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: 461 Length adjustment: 33 Effective length of query: 434 Effective length of database: 428 Effective search space: 185752 Effective search space used: 185752 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