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 N515DRAFT_3653 N515DRAFT_3653 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= TCDB::P15993 (457 letters) >FitnessBrowser__Dyella79:N515DRAFT_3653 Length = 453 Score = 408 bits (1049), Expect = e-118 Identities = 197/438 (44%), Positives = 288/438 (65%), Gaps = 6/438 (1%) Query: 9 EQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLGE 68 + L+R L RHI +ALG AIG GLFLGSA+ I AGP ++ Y G + F+IMR LGE Sbjct: 3 QHLQRRLTPRHITFMALGMAIGAGLFLGSANAINLAGPSVLFAYLFGGAMIFIIMRALGE 62 Query: 69 MVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPTW 128 M V +PVAGSFS +A++Y G FAG+ +GWNYW+L V V MAE TAVG Y++ W+PE+P W Sbjct: 63 MAVHDPVAGSFSTYAHRYLGPFAGYLTGWNYWILMVGVGMAESTAVGIYMRQWFPELPQW 122 Query: 129 VSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSG--NGGPQATV 186 + +I +NL VKV+GEMEFWF +IKV+ VV MI+ G +++ G NGG + Sbjct: 123 IWVFGSVAMIGGLNLMAVKVYGEMEFWFTLIKVVTVVLMILGGAGMIWLGWGNGGQPVGL 182 Query: 187 SNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRIL 246 +NLW GG+ PHGFTG+V+ + +++F+FGG+E +G+ A EA PE++IP+A N V++RIL Sbjct: 183 ANLWSHGGWFPHGFTGMVLALPVVVFAFGGIETIGMAAGEAAQPERTIPRAVNSVLWRIL 242 Query: 247 IFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVYC 306 IFY+G+L V++++ PW ++ SPFV F +LG A +N VV+TAALS +NS + Sbjct: 243 IFYVGALFVIMAIYPWDQLGTQGSPFVTTFGKLGIPQAAGLINFVVITAALSGFNSTTFS 302 Query: 307 NSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMALV 366 SRML+ L+ + AP L V + GVPV +LV+ V++NYL PE F ++M+++ Sbjct: 303 GSRMLYSLSTKAQAPAFLGQVSEHGVPVRAVLVTLACLVFGVVLNYLLPERIFAMMMSIL 362 Query: 367 VSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMTPGM 426 V W M+ +AH FRR + T FP +PL + +CLLF+A VL ++ + Sbjct: 363 AFNTVWTWMMVLIAHYSFRR----RHGATAFPLRAWPLTSVVCLLFLAFVLFMLGYSADT 418 Query: 427 AISVYLIPVWLIVLGIGY 444 +++Y+ W+++L + Y Sbjct: 419 RVALYVGAGWVVLLSLAY 436 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: 709 Number of extensions: 46 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: 453 Length adjustment: 33 Effective length of query: 424 Effective length of database: 420 Effective search space: 178080 Effective search space used: 178080 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 17 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