Align Amino-acid permease RocE (characterized)
to candidate RR42_RS28305 RR42_RS28305 proline-specific permease
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__Cup4G11:RR42_RS28305 Length = 472 Score = 308 bits (788), Expect = 3e-88 Identities = 161/429 (37%), Positives = 252/429 (58%), Gaps = 6/429 (1%) Query: 11 LQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGEL 70 L R +K RH+ MI++GG IG G FLG G I AGP G +LSY +GG +F M LGEL Sbjct: 19 LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGP-GLMLSYAIGGVAIFFIMRALGEL 77 Query: 71 AVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVWI 130 + PVSGSF TYA +F+ P GFA GW YW W VT E + + WFP + WI Sbjct: 78 LLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWI 137 Query: 131 WCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMF-GLIDLKGGEQAP 189 L A+++++N + F E EFWF+ IK++ I+ I++G A +F G+ L G A Sbjct: 138 PALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPL--GPTAS 195 Query: 190 FLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRT 249 F + G P G +++T+ V FA+QG ELIGV AGE+++PEK +P + VWR Sbjct: 196 FSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRI 255 Query: 250 LVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSGLY 309 L+F+V ++I++ ++PW + SPFV VFE+IG+P AA I+N V++ A S NSG++ Sbjct: 256 LIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIF 315 Query: 310 ASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLLSL 369 ++ R+LY +A GQA +A G+ + + VP ++ + A+ + +L + E V++ + S+ Sbjct: 316 STGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTSI 375 Query: 370 AGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISLAF 429 + + + W I ++ + +R+ G+++ + F+ P P + + V + L+ Sbjct: 376 SLVGSLWTWSIIMIAHLGYRKAI--AAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSL 433 Query: 430 DPEQRIALY 438 DP R+ALY Sbjct: 434 DPGTRVALY 442 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: 548 Number of extensions: 23 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