Align Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized)
to candidate WP_015931476.1 MNOD_RS23565 amino acid permease
Query= TCDB::P15993 (457 letters) >NCBI__GCF_000022085.1:WP_015931476.1 Length = 475 Score = 428 bits (1100), Expect = e-124 Identities = 204/456 (44%), Positives = 306/456 (67%), Gaps = 8/456 (1%) Query: 3 EGQQH-GEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFL 61 E Q H + L RGLK+RHIQLIA+GGAIG GLFLG+ I AGPG++L YA+ G + F Sbjct: 12 EEQAHEAKDLVRGLKDRHIQLIAIGGAIGVGLFLGAGRAISQAGPGLVLSYALGGLVTFF 71 Query: 62 IMRQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFW 121 IMR LGE+++ PVAGSF+ FA +Y +AGFA+GW+YW ++V+ MAE+TAVG Y+ +W Sbjct: 72 IMRALGELLMHRPVAGSFATFAEEYVSPWAGFATGWSYWFMWVVSGMAEITAVGVYVHYW 131 Query: 122 YPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNG- 180 +P++P W+ A + V+ +NL V +FGE+EFWFA++KV+A+VA+++ G ++ G G Sbjct: 132 FPDVPQWIPALITLCVLYGLNLIAVGLFGELEFWFALVKVVAIVALLLIGPAVIIFGLGE 191 Query: 181 -GPQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATN 239 G A+ +NLW GGF P G G+V+ + I+MF++ G+EL+G+TA EA NPE+++P+ATN Sbjct: 192 LGTTASFTNLWSHGGFFPTGVLGVVLTLQIVMFAYQGVELLGVTAGEAQNPERTLPRATN 251 Query: 240 QVIYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSV 299 V+YRIL+FYIG+L +++SL+PW +++ + SPF+L+F ++G A +N VV+TAA S Sbjct: 252 SVVYRILVFYIGALLIIMSLVPWNQLSPNESPFILVFDKIGIPGAAGIINFVVITAAASS 311 Query: 300 YNSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAF 359 NS ++ RML+ LAQ G AP+A +V+ R VP I SA V L V++NY PE F Sbjct: 312 CNSGIFSTGRMLYTLAQFGQAPRAFGTVNARHVPAAGITASAAVMLLGVVLNYFVPEQVF 371 Query: 360 GLLMALVVSALVINWAMISLAHMKFRR---AKQEQGVVTRFPALLYPLGNWICLLFMAAV 416 + ++ + + WA+I +AH+ +R+ A + V R P P NW + F+A V Sbjct: 372 VYVTSVALVGALWTWALIVIAHLGYRKAVAAGEAAPVSYRMPG--SPYTNWFVVAFLALV 429 Query: 417 LVIMLMTPGMAISVYLIPVWLIVLGIGYLFKEKTAK 452 V + + G +++Y+ PVW +LG+GY + K Sbjct: 430 SVFLGLDEGTRVALYVAPVWFALLGVGYQLTKMLTK 465 Lambda K H 0.328 0.141 0.434 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: 646 Number of extensions: 32 Number of successful extensions: 3 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: 457 Length of database: 475 Length adjustment: 33 Effective length of query: 424 Effective length of database: 442 Effective search space: 187408 Effective search space used: 187408 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 24 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