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_013842624.1 DESRU_RS13380 amino acid permease
Query= TCDB::P15993 (457 letters) >NCBI__GCF_000215085.1:WP_013842624.1 Length = 486 Score = 259 bits (663), Expect = 1e-73 Identities = 152/442 (34%), Positives = 242/442 (54%), Gaps = 7/442 (1%) Query: 9 EQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLGE 68 ++ RGLK+RH+QLIALGG IG+G FLG+ VI SAGP L Y + G I F +M +GE Sbjct: 17 QKFNRGLKSRHLQLIALGGIIGSGYFLGTGYVIDSAGPAACLAYLLGGLIVFCVMLCMGE 76 Query: 69 MVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPTW 128 + V P++ SF +A + GW+YW+ +V AE+ A G + ++P + T Sbjct: 77 LAVAIPISSSFVTYANDFISPAWACGMGWSYWLTWVFYVPAEMIAAGIIMNHFFPAVGTI 136 Query: 129 VSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNGGPQATV-- 186 A F ++I INL+ V FGE+EFW AIIK+ A++ +I L+FSG G + + Sbjct: 137 WWAIGFGLIITIINLSYVGTFGELEFWLAIIKIFAIIMFVIL-AILVFSGLLGKEGFMGT 195 Query: 187 SNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRIL 246 S L +GGF P G +++ M II+ +F G E++G+ A E+ PE++IP A V +RI+ Sbjct: 196 SILLGEGGFTPKGSWAVLLTMVIILVNFQGSEIIGLAAGESKEPEKTIPAAVKNVTWRII 255 Query: 247 IFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVYC 306 Y+ + +L+++ PW + + S F + G + + VVLTAA+S NS +Y Sbjct: 256 ALYVIPVFLLVTIFPWGKAGLEESVFAAALNLYGFKWAGGLFSFVVLTAAISCSNSGLYG 315 Query: 307 NSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYL-APESAFGLLMAL 365 +R ++ LA++G AP L +++ GVP N +S +CV+ L + ++ F +L+AL Sbjct: 316 CTRAVYALAREGMAPGWLGKLNRNGVPQNATFLSIAGCWICVMAYTLDSSQTIFTILLAL 375 Query: 366 VVSALVINWAMISLAHMKFRRAKQEQGV---VTRFPALLYPLGNWICLLFMAAVLVIMLM 422 + I W I + + FRR + +G +F L+P + A L ++ Sbjct: 376 SGFSGAIAWISICWSQLNFRRKLRREGFDAGQLKFRTPLFPYLTHFAIWIQVACLGVIAF 435 Query: 423 TPGMAISVYLIPVWLIVLGIGY 444 + IS+Y+ LI+ I Y Sbjct: 436 NEDLRISLYIGLPLLILPMIWY 457 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: 681 Number of extensions: 43 Number of successful extensions: 5 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: 486 Length adjustment: 33 Effective length of query: 424 Effective length of database: 453 Effective search space: 192072 Effective search space used: 192072 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