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_RS14635 RR42_RS14635 proline-specific permease
Query= TCDB::P15993 (457 letters) >FitnessBrowser__Cup4G11:RR42_RS14635 Length = 466 Score = 373 bits (957), Expect = e-108 Identities = 190/445 (42%), Positives = 278/445 (62%), Gaps = 5/445 (1%) Query: 5 QQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMR 64 Q+ + L+RGL RHI+ +ALG AIGTGLF GSAS IQ+AGP ++L Y I G +++MR Sbjct: 2 QEQSQGLQRGLSARHIRFMALGSAIGTGLFYGSASAIQTAGPAVLLAYVIGGAAVYMVMR 61 Query: 65 QLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPE 124 LGEM V PVAGSF +A G AGF GW Y ++V +A++TA G Y+ FW+P+ Sbjct: 62 ALGEMAVRNPVAGSFGQYASTGLGPLAGFLLGWTYAFEMIVVCLADVTAFGIYMGFWFPD 121 Query: 125 IPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSG----NG 180 +P W+ +I +NL +VKVFGE+EFW +++KV A+VAMI G ++ G +G Sbjct: 122 VPRWIWVLGIVFLIGGLNLLSVKVFGELEFWLSLLKVGAIVAMIGGGVAIMLFGFGMADG 181 Query: 181 GPQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQ 240 G + NLW GGF+P+G G++ A++MF+FGG+E++GITA EA +P++ IP+A N Sbjct: 182 GVATGIHNLWTHGGFMPNGIAGVIASFAVVMFAFGGIEIIGITAGEARDPQRVIPRAINA 241 Query: 241 VIYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVY 300 V RIL+FY+ +LAVL+SL PW R+ ++ SPFV IF LG A LNIVV++AA+S Sbjct: 242 VPLRILLFYVLTLAVLMSLYPWHRIGSEGSPFVQIFSRLGIGSAAAVLNIVVISAAVSAI 301 Query: 301 NSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFG 360 NS ++ RML+G+A Q AP+ ASV ++GVP T++V A V++NY+ PE F Sbjct: 302 NSDIFGAGRMLYGMAVQRQAPRIFASVSRKGVPWMTVVVMAFALLAGVVLNYVMPEDVFT 361 Query: 361 LLMALVVSALVINWAMISLAHMKFRRAKQEQGVVT-RFPALLYPLGNWICLLFMAAVLVI 419 L+ ++ A V W MI L+ + RR V +FP +P+ FM + + Sbjct: 362 LIASIATFATVWVWLMILLSQVALRRRMSRAEVAALKFPVPFWPVAPLAATAFMLFIFGV 421 Query: 420 MLMTPGMAISVYLIPVWLIVLGIGY 444 + P ++ + VWL++L + + Sbjct: 422 LGWFPQTRAALLVGAVWLLLLVVAW 446 Score = 25.8 bits (55), Expect = 0.003 Identities = 23/102 (22%), Positives = 44/102 (43%), Gaps = 9/102 (8%) Query: 361 LLMALVVSALVINWAMISLAHMKFRRAKQEQGVVTRFPAL-LYPLGNWICLLFMAAVLVI 419 +L+A V+ + M +L M R G ++ + L PL ++ A +++ Sbjct: 45 VLLAYVIGGAAVYMVMRALGEMAVRNPVA--GSFGQYASTGLGPLAGFLLGWTYAFEMIV 102 Query: 420 MLMTPGMAISVYL------IPVWLIVLGIGYLFKEKTAKAVK 455 + + A +Y+ +P W+ VLGI +L +VK Sbjct: 103 VCLADVTAFGIYMGFWFPDVPRWIWVLGIVFLIGGLNLLSVK 144 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: 653 Number of extensions: 44 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 457 Length of database: 466 Length adjustment: 33 Effective length of query: 424 Effective length of database: 433 Effective search space: 183592 Effective search space used: 183592 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