Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate BWI76_RS07360 BWI76_RS07360 phenylalanine transporter
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Koxy:BWI76_RS07360 Length = 458 Score = 576 bits (1485), Expect = e-169 Identities = 277/441 (62%), Positives = 344/441 (78%) Query: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 69 L RGL+NRHIQLIALGGAIGTGLFLG +Q AGP+++LGYA+ G++AF+IMRQLGEMV Sbjct: 18 LHRGLQNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYAVAGIVAFLIMRQLGEMV 77 Query: 70 AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 129 +EPV+GSF+HFAYKYWG F GFLSGWNYWV++VLV MAELTA G Y+ YW P VPTW+ Sbjct: 78 VEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWLPDVPTWIW 137 Query: 130 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQASISNLW 189 A F INA+NL NV+ YGE EFWFA+IKV+A+IGMI FG ++L GHGG +A I NLW Sbjct: 138 AAAFFLIINAVNLVNVRLYGEAEFWFALIKVLAIIGMIGFGLWMLFGGHGGSKAGIDNLW 197 Query: 190 SHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIFYI 249 HGGFF G+HGL LAVIMFSFGGLELIGITAAEA P+KSIPKAVNQV+YRIL+FYI Sbjct: 198 KHGGFFATGWHGLIMSLAVIMFSFGGLELIGITAAEAQNPEKSIPKAVNQVVYRILLFYI 257 Query: 250 CSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYANSRM 309 SL VLL+LYPW E+ + SPFVMIF + S + A+ LN V+L A+LSVYNSGVY+NSRM Sbjct: 258 GSLVVLLALYPWVEIQSDSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGVYSNSRM 317 Query: 310 LYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMALVVAAL 369 L+GL+ QGNAP+ L +V +RGVP ++ LS + T V++NYL+P +ALGLLMALVVA L Sbjct: 318 LFGLSVQGNAPKFLARVSKRGVPVNSLLLSGIITSLVVVLNYLLPQKALGLLMALVVATL 377 Query: 370 VLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILAMTPGLSVSV 429 +LNW +I L HLK R A G FK+ P SN+IC+AF+ALILV++ G+ +S Sbjct: 378 LLNWIMICLAHLKFRAAQRRKGREPKFKALLSPASNYICIAFLALILVLMCTIDGMRLSA 437 Query: 430 LLVPLWLVVMWAGYAFKRRRA 450 +L+P+W++ ++A + RR A Sbjct: 438 ILLPVWILFLFAAFKTLRRTA 458 Lambda K H 0.327 0.140 0.440 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: 605 Number of extensions: 19 Number of successful extensions: 1 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: 461 Length of database: 458 Length adjustment: 33 Effective length of query: 428 Effective length of database: 425 Effective search space: 181900 Effective search space used: 181900 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 (21.7 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