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_011951530.1 SWIT_RS03485 amino acid permease
Query= TCDB::P15993 (457 letters) >NCBI__GCF_000016765.1:WP_011951530.1 Length = 455 Score = 296 bits (758), Expect = 9e-85 Identities = 166/449 (36%), Positives = 256/449 (57%), Gaps = 10/449 (2%) Query: 5 QQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMR 64 +Q L+RGL R + +I +GGAIGTGLF+GS I AGPG++L Y +A I+ +M Sbjct: 10 RQREAGLERGLTRRQLTMIGIGGAIGTGLFMGSGLAIGYAGPGVLLSYLLAAVISLAVMF 69 Query: 65 QLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPE 124 L EM V P AGSF A Y AG+ + W YW V++ +E AVG Y+ FW P Sbjct: 70 SLAEMAVLNPTAGSFGTHAELYISPLAGWIARWTYWAEMVILIGSEAVAVGHYLSFWLPG 129 Query: 125 IPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFG-GWLLFSGNGGPQ 183 +P W+S + I +N+ V FG +E+W + IKV A++A I+ G G +L G G P Sbjct: 130 LPVWLSILLSGGGILFVNMRAVGSFGTVEYWLSAIKVAAILAFILLGLGMVL--GVGTPA 187 Query: 184 ATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIY 243 +SN GG LP G G+ M I +FSF G+E++ + A EAD+P +++P A ++ Sbjct: 188 IGLSNYMVDGGPLPFGMKGVWMGAMIAIFSFFGIEMIAVAAGEADDPGKAVPHAMRTLLV 247 Query: 244 RILIFYIGSLAVLLSLMPWT---RVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVY 300 R+ +FY+ S+A++L+++PW+ D SPFV +F G A+ +N VVL AALS Sbjct: 248 RLCLFYLLSIAIILAIVPWSSSGAAVVDQSPFVKVFAGFGIVGAASVMNFVVLCAALSAM 307 Query: 301 NSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFG 360 NS +Y SRMLF LA+ G+AP + ++ VP LVS L + + L+P AF Sbjct: 308 NSSLYMASRMLFSLARAGDAPASFGVLNGAAVPARAALVSGLGILIAAAVALLSPR-AFE 366 Query: 361 LLMALVVSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIM 420 ++ + + + W +I + H +FRR +G+ R P +P+ I L + A++ M Sbjct: 367 YMLGIALFGGLFTWMLILVTHFRFRRRVGTEGLAYRAP--FFPVPQCIGLAGLLAIVAAM 424 Query: 421 LMTPGM-AISVYLIPVWLIVLGIGYLFKE 448 L++ G+ ISV + WL+++ + +L ++ Sbjct: 425 LVSGGIWRISVAIGVPWLLLVALLFLLRK 453 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: 587 Number of extensions: 41 Number of successful extensions: 6 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: 455 Length adjustment: 33 Effective length of query: 424 Effective length of database: 422 Effective search space: 178928 Effective search space used: 178928 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