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_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= TCDB::P15993 (457 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 403 bits (1036), Expect = e-117 Identities = 195/444 (43%), Positives = 283/444 (63%), Gaps = 7/444 (1%) Query: 6 QHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQ 65 Q + L+RGL+ RHI+L+ALG AIG GLFLGSA+ I+ AGP I+L Y + G F+IMR Sbjct: 2 QTNDSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMRA 61 Query: 66 LGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEI 125 LGEM V+ PVAGSFS +A Y G G+ +GWNYW ++++ +AE+TAVG Y+ W+P++ Sbjct: 62 LGEMAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDV 121 Query: 126 PTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLF--SGNGGPQ 183 P W+ A V + A+NL VK +GE EFWFA+IKV+ +V MI+ GG ++ GN G Sbjct: 122 PQWIWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGVP 181 Query: 184 ATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIY 243 +SNLW GGF+P+G G++M + ++MF++ G+E++G+TA EADNP++SIP A N V + Sbjct: 182 TGISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVFW 241 Query: 244 RILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSC 303 RILIFY+G+L V++S+ PW + SPFV+ F LG A +N VVLTAALS N Sbjct: 242 RILIFYVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLTAALSSCNGG 301 Query: 304 VYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLM 363 +Y RMLF LAQQG AP+ A G+P +LVS + VL+NYL P F + Sbjct: 302 IYSTGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPAKVFVWVT 361 Query: 364 ALVVSALVINWAMISLAHMKFRRA---KQEQGVVTRFPALLYPLGNWICLLFMAAVLVIM 420 + + W ++ + MK+RR Q +V R P +P +++ L F+ V+ +M Sbjct: 362 SAATFGAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMP--FFPYASYLALAFLVLVVGLM 419 Query: 421 LMTPGMAISVYLIPVWLIVLGIGY 444 P +++ + P+WL++L + Y Sbjct: 420 GYFPDTRVALIVGPLWLVLLTVLY 443 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: 678 Number of extensions: 38 Number of successful extensions: 2 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: 454 Length adjustment: 33 Effective length of query: 424 Effective length of database: 421 Effective search space: 178504 Effective search space used: 178504 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