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 GFF4342 PS417_22235 aromatic amino acid transporter
Query= TCDB::P15993 (457 letters) >FitnessBrowser__WCS417:GFF4342 Length = 473 Score = 621 bits (1601), Expect = 0.0 Identities = 306/449 (68%), Positives = 356/449 (79%), Gaps = 9/449 (2%) Query: 10 QLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLGEM 69 +LKRGLKNRHIQLIALGGAIGTGLFLGSA V++SAGP +ILGYAI GFIAF+IMRQLGEM Sbjct: 10 ELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEM 69 Query: 70 VVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPTWV 129 +VEEPVAGSFSHFA+KYWG FAGF SGWN W+LY+LV M+ELTAVGKY+ +W+PEIPTWV Sbjct: 70 IVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYVHYWWPEIPTWV 129 Query: 130 SAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNGGPQATVSNL 189 SAA FFV+IN INL NVKVFGE EFWFAIIKV+A+V MI G +LL SG GGPQA+V+NL Sbjct: 130 SAAAFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGTGGPQASVTNL 189 Query: 190 WDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRILIFY 249 W+ GGF PHG GLVM MAIIMFSFGGLE++G TAAEAD P IPKA NQVIYRILIFY Sbjct: 190 WEHGGFFPHGVGGLVMAMAIIMFSFGGLEMLGFTAAEADKPRTVIPKAINQVIYRILIFY 249 Query: 250 IGSLAVLLSLMPWTRVTA---------DTSPFVLIFHELGDTFVANALNIVVLTAALSVY 300 IG+L VLLSL PW + A SPFV +F LG A+ LN VVLTAALSVY Sbjct: 250 IGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSDTAAHILNFVVLTAALSVY 309 Query: 301 NSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFG 360 NS YCNSRML G+A+QG+APKALA +DKRGVPV +IL SA +T + VL+NYL P+ A Sbjct: 310 NSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAITLVAVLMNYLIPQHALE 369 Query: 361 LLMALVVSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIM 420 LLM+LVV+ LVINWAMIS +H KFR+ G V F AL YP GN++CL F+ +LVIM Sbjct: 370 LLMSLVVATLVINWAMISFSHFKFRQHMNRTGQVPLFKALWYPYGNYVCLAFVVFILVIM 429 Query: 421 LMTPGMAISVYLIPVWLIVLGIGYLFKEK 449 LM PG+ +SV+ IPVW++ + + Y K K Sbjct: 430 LMIPGIQVSVFAIPVWVMFMAVCYGIKNK 458 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: 712 Number of extensions: 29 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: 473 Length adjustment: 33 Effective length of query: 424 Effective length of database: 440 Effective search space: 186560 Effective search space used: 186560 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