Align Amino-acid permease RocE (characterized)
to candidate BWI76_RS06245 BWI76_RS06245 proline-specific permease ProY
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__Koxy:BWI76_RS06245 Length = 456 Score = 302 bits (774), Expect = 1e-86 Identities = 162/445 (36%), Positives = 252/445 (56%), Gaps = 6/445 (1%) Query: 6 DNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTML 65 ++ N+L+R + +RH+ ++LG IGTG F G+ I AGP +L+Y++GG ++ M Sbjct: 2 ESSNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGP-SVLLAYIIGGVAAYIIMR 60 Query: 66 CLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPH 125 LGE++V P + SF YA ++ P G+ GW Y + + + G M WFP Sbjct: 61 ALGEMSVHNPAASSFSRYAQDYLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPA 120 Query: 126 IDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILG-GAAMFGLIDLKG 184 + W+W L ++ +N ++ K F E EFWFS K+ I++ I+ G G ++G+ + G Sbjct: 121 VPHWVWVLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMILAGFGIIIWGIGN--G 178 Query: 185 GEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQ 244 G+ + G F NG M++++ V FA+ G E+IG+ AGE++DPEK+IPR+I Sbjct: 179 GQPTGIHNLWSNGGFFSNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINS 238 Query: 245 TVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVA 304 R LVF+V ++ VI + PW Q G SPFV F+ +GI +AA I+NFV+L A LS Sbjct: 239 VPMRILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHLGITFAASILNFVVLTASLSAI 298 Query: 305 NSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYM 364 NS ++ R+L+ MA +G A K KT++RGVP +++V ++ + E V++ Sbjct: 299 NSDVFGVGRMLHGMAEQGSAPKMFAKTSRRGVPWVTVMVMTIALLFAVYLNYIMPENVFL 358 Query: 365 VLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVL 424 V+ SLA + WI I LSQI FRR+ E K LKFK P +IGL ++ Sbjct: 359 VIASLATFATVWVWIMILLSQIAFRRRLPPEEAKA--LKFKVPGGVTTTVIGLLFLVFII 416 Query: 425 ISLAFDPEQRIALYCGVPFMIICYI 449 + + P+ RI+LY G ++I+ I Sbjct: 417 GLIGYHPDTRISLYVGFAWIILLLI 441 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: 583 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: 456 Length adjustment: 33 Effective length of query: 434 Effective length of database: 423 Effective search space: 183582 Effective search space used: 183582 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