Align Amino-acid permease RocE (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 311 bits (798), Expect = 2e-89 Identities = 167/456 (36%), Positives = 263/456 (57%), Gaps = 14/456 (3%) Query: 1 MNTNQDNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIM 60 M TN + LQR ++ RH+ +++LG IG G FLG+ I AGP +LSYL+GG + Sbjct: 1 MQTN----DSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGP-AILLSYLLGGVAI 55 Query: 61 FLTMLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQ 120 F+ M LGE+AV PV+GSF YA ++ P G+ GW YW W +TC E + G M Sbjct: 56 FIIMRALGEMAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMG 115 Query: 121 RWFPHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAM-FGL 179 WFP + WIW L M +N KA+ E EFWF+ IK++ I+L I+ GGA + FGL Sbjct: 116 VWFPDVPQWIWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGL 175 Query: 180 IDLKGGEQAPF-LTHFYEDGLF-PNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKT 237 G + P +++ + G F PNG K ML+ + V FA+ G E+IG+ AGE+++P+K+ Sbjct: 176 ----GNQGVPTGISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKS 231 Query: 238 IPRSIKQTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVIL 297 IP +I WR L+F+V ++ VI + PW + G SPFV FE++GI AA I+NFV+L Sbjct: 232 IPDAINSVFWRILIFYVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVL 291 Query: 298 IALLSVANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFA 357 A LS N G+Y++ R+L+ +A +GQA + T+ G+P +++V++ +L + Sbjct: 292 TAALSSCNGGIYSTGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYL 351 Query: 358 QAETVYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGL 417 V++ + S A A W + ++Q+ +RR + L F+ P +P + L Sbjct: 352 VPAKVFVWVTSAATFGAIWTWGIVLITQMKYRRGL--SEAQRSQLVFRMPFFPYASYLAL 409 Query: 418 TLNTVVLISLAFDPEQRIALYCGVPFMIICYIIYHV 453 +V+ + + P+ R+AL G ++++ ++Y+V Sbjct: 410 AFLVLVVGLMGYFPDTRVALIVGPLWLVLLTVLYYV 445 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: 569 Number of extensions: 24 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: 454 Length adjustment: 33 Effective length of query: 434 Effective length of database: 421 Effective search space: 182714 Effective search space used: 182714 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