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 RR42_RS28305 RR42_RS28305 proline-specific permease
Query= TCDB::P15993 (457 letters) >FitnessBrowser__Cup4G11:RR42_RS28305 Length = 472 Score = 424 bits (1090), Expect = e-123 Identities = 205/455 (45%), Positives = 303/455 (66%), Gaps = 8/455 (1%) Query: 3 EGQQHGEQ-LKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFL 61 E + H E+ L RGLK+RHIQ+IA+GGAIG GLFLG+ I AGPG++L YAI G F Sbjct: 10 EERVHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFF 69 Query: 62 IMRQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFW 121 IMR LGE+++ PV+GSF+ +A ++ G FAGFA+GW+YW ++V+ MAE+TAV Y+ +W Sbjct: 70 IMRALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYW 129 Query: 122 YPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNG- 180 +P++P W+ A V+ +N V VFGE+EFWFA+IKV+ +VAMI+ G ++F G Sbjct: 130 FPDVPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTP 189 Query: 181 -GPQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATN 239 GP A+ SNLW GGF+P G G+V+ + I+MF++ G+EL+G+TA EA NPE+ +P ATN Sbjct: 190 LGPTASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATN 249 Query: 240 QVIYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSV 299 V++RILIFY+G+L ++++L+PW + SPFV +F +G A +N+VV+TAA S Sbjct: 250 GVVWRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASS 309 Query: 300 YNSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAF 359 NS ++ RML+ LAQ G AP+A V + VP I SA + + VL+NY+ PE F Sbjct: 310 CNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVF 369 Query: 360 GLLMALVVSALVINWAMISLAHMKFRR---AKQEQGVVTRFPALLYPLGNWICLLFMAAV 416 + ++ + + W++I +AH+ +R+ A + + V R P P NW+ + FM AV Sbjct: 370 VWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGA--PYANWLVVAFMIAV 427 Query: 417 LVIMLMTPGMAISVYLIPVWLIVLGIGYLFKEKTA 451 V++ + PG +++Y+ PVW +LGIGY F + A Sbjct: 428 AVLLSLDPGTRVALYVAPVWFALLGIGYRFTKSRA 462 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: 649 Number of extensions: 29 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: 472 Length adjustment: 33 Effective length of query: 424 Effective length of database: 439 Effective search space: 186136 Effective search space used: 186136 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