Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate 14712 b0576 phenylalanine transporter (NCBI)
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Keio:14712 Length = 458 Score = 571 bits (1471), Expect = e-167 Identities = 274/444 (61%), Positives = 345/444 (77%) Query: 6 QQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQL 65 Q+ L RGL NRHIQLIALGGAIGTGLFLG +Q AGP+++LGY + G+IAF+IMRQL Sbjct: 15 QEPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQL 74 Query: 66 GEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVP 125 GEMV +EPV+GSF+HFAYKYWG F GFLSGWNYWV++VLV MAELTA G Y+ YW+P VP Sbjct: 75 GEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVP 134 Query: 126 TWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQASI 185 TW+ A F INA+NL NV+ YGETEFWFA+IKV+A+IGMI FG +LL SGHGG +ASI Sbjct: 135 TWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLLFSGHGGEKASI 194 Query: 186 SNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRIL 245 NLW +GGFF G++GL LAVIMFSFGGLELIGITAAEA +P+KSIPKAVNQV+YRIL Sbjct: 195 DNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVVYRIL 254 Query: 246 IFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYA 305 +FYI SL VLL+LYPW EV + SPFVMIF + S + A+ LN V+L A+LSVYNSGVY+ Sbjct: 255 LFYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGVYS 314 Query: 306 NSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMALV 365 NSRML+GL+ QGNAP+ L +V RRGVP ++ LS T V++NYL+P +A GLLMALV Sbjct: 315 NSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLLMALV 374 Query: 366 VAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILAMTPGL 425 VA L+LNW +I L HL+ R AM G FK+ +P N++C+AF+ +IL+++ + Sbjct: 375 VATLLLNWIMICLAHLRFRAAMRRQGRETQFKALLYPFGNYLCIAFLGMILLLMCTMDDM 434 Query: 426 SVSVLLVPLWLVVMWAGYAFKRRR 449 +S +L+P+W+V ++ + RR+ Sbjct: 435 RLSAILLPVWIVFLFMAFKTLRRK 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: 614 Number of extensions: 20 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