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 PP_1059 PP_1059 Uncharacterized amino acid permease YtnA
Query= TCDB::P15993 (457 letters) >FitnessBrowser__Putida:PP_1059 Length = 472 Score = 393 bits (1010), Expect = e-114 Identities = 194/440 (44%), Positives = 278/440 (63%), Gaps = 3/440 (0%) Query: 8 GEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLG 67 G LKR L RHI+L+ALG IG GLFLGSA I+ AGP I+L Y I G +IMR LG Sbjct: 15 GGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALG 74 Query: 68 EMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPT 127 EM V PVAGSFS +A Y G AGF +GWNYW L+++ +AE+TAV Y+ W+P++P Sbjct: 75 EMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAIYMGIWFPDVPR 134 Query: 128 WVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFG-GWLLFS-GNGGPQAT 185 W+ A + A+NL VK FGE EFWFA+IK++ ++AM++ G G + F GN G Sbjct: 135 WIWALAALGSMGAVNLVAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFGNDGVAVG 194 Query: 186 VSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRI 245 +SNLW GGF+P+G TG++M + ++MF++ G+E++G+TA EA NP+++IP+A V +RI Sbjct: 195 ISNLWSNGGFMPNGVTGVLMSLQMVMFAYLGVEMIGLTAGEARNPQKTIPQAIGSVFWRI 254 Query: 246 LIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVY 305 L+FY+G+L V+LS+ PW + + SPFV+ F LG A +N VV+TAALS N ++ Sbjct: 255 LLFYVGALFVILSIYPWNEIGSQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIF 314 Query: 306 CNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMAL 365 RML+ LAQ G AP A A K GVP N +L+S L VL NYL PE F + ++ Sbjct: 315 STGRMLYSLAQNGQAPAAFARTSKNGVPRNALLLSIGALLLGVLANYLVPEKVFVWVTSI 374 Query: 366 VVSALVINWAMISLAHMKFRRA-KQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMTP 424 + W MI LA +KFR + ++ L+PL +++ L F+ V+ +M Sbjct: 375 ATFGAIWTWVMILLAQLKFRAGLTTAERKALKYRMWLWPLSSYLALAFLVLVVGLMAYFE 434 Query: 425 GMAISVYLIPVWLIVLGIGY 444 +++Y+ P +L++L + Y Sbjct: 435 DTRVALYIGPAFLVLLTVLY 454 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: 671 Number of extensions: 26 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: 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