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 GFF4632 PS417_23700 aromatic amino acid transporter
Query= TCDB::P15993 (457 letters) >FitnessBrowser__WCS417:GFF4632 Length = 467 Score = 617 bits (1592), Expect = 0.0 Identities = 301/453 (66%), Positives = 363/453 (80%), Gaps = 9/453 (1%) Query: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLGEMV 70 LKRGLKNRHIQLIALGGAIGTGLFLGSA V++SAGP +ILGYAIAGFIAFLIMRQLGEM+ Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMI 70 Query: 71 VEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPTWVS 130 VEEPVAGSFSHFA+KYWG +AGF +GWNYWVLYVLV MAELTAVGKYIQFW+P+IPTWVS Sbjct: 71 VEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIPTWVS 130 Query: 131 AAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNGGPQATVSNLW 190 A VFFV +N IN NVK FGE EFWFAIIKV+A+V MI+ G +LLFSG GGPQA+VSNLW Sbjct: 131 ALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTGGPQASVSNLW 190 Query: 191 DQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRILIFYI 250 GGF P+G GL+M MA IMFSFGGLELVGITAAEA P + IPKA NQV+YRILIFY+ Sbjct: 191 SHGGFFPNGGMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRILIFYV 250 Query: 251 GSLAVLLSLMPWTRV---------TADTSPFVLIFHELGDTFVANALNIVVLTAALSVYN 301 G+L VLLSL PW ++ SPFV IF +G+ A+ LN VVLTAALSVYN Sbjct: 251 GALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVLTAALSVYN 310 Query: 302 SCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGL 361 S VYCNSRMLFGLA+QG+APK+L ++K+GVP+ + +SALVT LCV++NY+AP+SA L Sbjct: 311 SGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYVAPQSALEL 370 Query: 362 LMALVVSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIML 421 L ALVV++L+INWA+IS+ H+KFR+A EQGV F +P N++CL FM ++ +ML Sbjct: 371 LFALVVASLMINWALISITHIKFRKAMGEQGVTPSFKTFWFPFSNYLCLAFMVMIISVML 430 Query: 422 MTPGMAISVYLIPVWLIVLGIGYLFKEKTAKAV 454 PG++ SVY +PVW+ ++ + Y + + + AV Sbjct: 431 AIPGISESVYAMPVWVGIIYVAYRLRVRRSHAV 463 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: 741 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: 467 Length adjustment: 33 Effective length of query: 424 Effective length of database: 434 Effective search space: 184016 Effective search space used: 184016 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