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_005812351.1 DHAF_RS06640 amino acid permease
Query= TCDB::P15993 (457 letters) >NCBI__GCF_000021925.1:WP_005812351.1 Length = 452 Score = 516 bits (1329), Expect = e-151 Identities = 246/449 (54%), Positives = 327/449 (72%), Gaps = 4/449 (0%) Query: 2 MEGQQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFL 61 M Q++G + RGLKNRHIQ+IALGGAIGTGLF GSA+ I+ AGP I Y I G + F Sbjct: 1 MSNQENG--MHRGLKNRHIQMIALGGAIGTGLFYGSAATIELAGPAITFSYLIGGLVIFF 58 Query: 62 IMRQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFW 121 IMR LGEM V+EPV+GSFSHFAYKYWG F GF SGWNYW Y++V+MAELTAVG YI FW Sbjct: 59 IMRMLGEMAVDEPVSGSFSHFAYKYWGEFPGFLSGWNYWFNYIVVSMAELTAVGIYINFW 118 Query: 122 YPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNGG 181 +P+IP W++A V V++ +NL +V FGE EFWFAI+KV+A++ MI+FG +L+FSG G Sbjct: 119 FPDIPHWLTALVCLVLVTLLNLISVGTFGEFEFWFAIVKVVAIIGMIVFGLFLIFSGING 178 Query: 182 PQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQV 241 NLW GGF+P+G G++ + +MFSFGG+EL+GITA EADNP++SIPKA NQV Sbjct: 179 EATGFDNLWIHGGFIPNGMIGILFSLVPVMFSFGGIELIGITAGEADNPQKSIPKAINQV 238 Query: 242 IYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYN 301 ++RILIFY+G+L+VL+ L PW +V AD SPFV+IF ++G A LNIVVLTAALSVYN Sbjct: 239 MWRILIFYVGALSVLMVLYPWNQVGADGSPFVMIFSKIGIPAAATLLNIVVLTAALSVYN 298 Query: 302 SCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGL 361 S VY N RML+ LA QGNAPK A ++KRG+PV +LVS+ +T + V++N+L P F Sbjct: 299 SGVYSNGRMLYSLAMQGNAPKLFAKLNKRGIPVAGVLVSSGITLVGVILNFLLPGKIFTY 358 Query: 362 LMALVVSALVINWAMISLAHMKFRRAK--QEQGVVTRFPALLYPLGNWICLLFMAAVLVI 419 LMA+ + A VI W I + ++KFR+AK Q +G F L+P N+ C F+ ++++ Sbjct: 359 LMAVAIIAAVITWTTIIIVNLKFRKAKIAQGEGDALHFKTPLHPYTNYFCAAFLVMIVIL 418 Query: 420 MLMTPGMAISVYLIPVWLIVLGIGYLFKE 448 M T M ++V ++P+WL++L I + K+ Sbjct: 419 MAFTESMKMAVLVLPIWLLILWISFKIKK 447 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: 680 Number of extensions: 33 Number of successful extensions: 2 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: 452 Length adjustment: 33 Effective length of query: 424 Effective length of database: 419 Effective search space: 177656 Effective search space used: 177656 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