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_013842849.1 DESRU_RS14595 amino acid permease
Query= TCDB::P15993 (457 letters) >NCBI__GCF_000215085.1:WP_013842849.1 Length = 462 Score = 389 bits (1000), Expect = e-113 Identities = 191/440 (43%), Positives = 285/440 (64%), Gaps = 4/440 (0%) Query: 9 EQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLGE 68 E L RGLK RHIQLIA+GGAIG GLFLGS++ I++AGP ++L Y IAG F+++R LGE Sbjct: 7 EGLHRGLKERHIQLIAIGGAIGVGLFLGSSTAIKTAGPSLMLSYLIAGLAIFIVLRALGE 66 Query: 69 MVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPTW 128 M V P++GSF +A + G G+ + W YW ++V+ MAE+TA G Y+ FW+P+ P W Sbjct: 67 MAVTYPLSGSFGAYANMFIGPVYGYLTSWTYWFMWVVTCMAEITAAGIYMTFWFPDTPQW 126 Query: 129 VSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLF--SGNGGPQATV 186 A V++ +NL +VK +GE EFWFA+IKV+ ++AMI+ GG ++F GN G + Sbjct: 127 AWALAALVIMTVVNLISVKHYGEFEFWFALIKVVTIIAMILIGGAMIFFGIGNNGVPIGI 186 Query: 187 SNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRIL 246 SNL GGF GFTG + + ++ F++ G+EL+G+TA EA+NP++++P A N+V++RIL Sbjct: 187 SNLTAHGGFFAKGFTGPALALVMVAFAYLGMELIGVTAGEAENPQKTLPSAINKVLWRIL 246 Query: 247 IFYIGSLAVLLSLMPWTRV-TADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVY 305 IFY+G+L ++L L PW + + SPFVL F ++G A +N VVLTAALS NS ++ Sbjct: 247 IFYVGALFIILCLFPWNEIDPSKGSPFVLTFSKVGIPAAAGIINFVVLTAALSSCNSGIF 306 Query: 306 CNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMAL 365 RML+ LA Q AP + GVPVN I +SA + V++NYL P F + ++ Sbjct: 307 STGRMLYTLALQKKAPAFFGKLSGSGVPVNGIFISAAFLCIGVVLNYLVPAKVFEYVTSV 366 Query: 366 VVSALVINWAMISLAHMKFRRA-KQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMTP 424 V W +I +A + +R++ EQ +FP L+PL +++ L F+A V+++M + Sbjct: 367 TTIGAVWVWGIILVAQINYRKSLSPEQVSQLKFPTPLWPLTSYLTLAFLALVVIMMAFSE 426 Query: 425 GMAISVYLIPVWLIVLGIGY 444 G I++Y+ PVW +L + Y Sbjct: 427 GTRIALYVGPVWFGLLLLSY 446 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: 611 Number of extensions: 34 Number of successful extensions: 4 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: 462 Length adjustment: 33 Effective length of query: 424 Effective length of database: 429 Effective search space: 181896 Effective search space used: 181896 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