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 YP_008920792.1 CA_C3453 gamma-aminobutyrate permease
Query= TCDB::P15993 (457 letters) >NCBI__GCF_000008765.1:YP_008920792.1 Length = 477 Score = 309 bits (792), Expect = 1e-88 Identities = 171/460 (37%), Positives = 265/460 (57%), Gaps = 16/460 (3%) Query: 5 QQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPG-IILGYAIAGFIAFLIM 63 + + ++KR LK RH+ +IA+GGAIGTG+F+ I AGPG ++ YA G + + +M Sbjct: 6 ETNSNEVKRSLKARHLNMIAMGGAIGTGIFIALGDTIHQAGPGGALVAYACIGVMVYFLM 65 Query: 64 RQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYP 123 LGEM PV+GSF +A K+ GFA GWNYW + + AE+ A G ++FW+ Sbjct: 66 TGLGEMATFMPVSGSFETYASKFVDESVGFALGWNYWYNWAITVAAEMVAGGMAMKFWFK 125 Query: 124 EIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNGGPQ 183 +P + + +F V+I A+NL +VK +GE E+WFA IKVI V+ +I G + GG + Sbjct: 126 GVPAVIWSILFLVLIVALNLLSVKAYGESEYWFAGIKVITVIVFLIVGTATILGIIGGHK 185 Query: 184 ATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIY 243 + N + G + M+ I FSF G ELVGI A E++NP++SIPKA N + + Sbjct: 186 IGLRNFTIKDAPFVGGVKSIFMVFLIAGFSFQGTELVGIAAGESENPKKSIPKAINTIFW 245 Query: 244 RILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSC 303 RILIFY+G++ V+ +++P+T+ SPF ++F G A +N V+LT+ LS NS Sbjct: 246 RILIFYLGTIFVVSAIIPYTQAGVKISPFTMVFERAGIPIAAAIMNAVILTSVLSCGNSG 305 Query: 304 VYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLM 363 +Y +SRML+ +A++G APK L ++ RGVPV + ++ +V + C L A + + L+ Sbjct: 306 MYASSRMLYAMAKEGKAPKILGKLNSRGVPVYALALTTIVASACFLTGLYAESTVYVWLV 365 Query: 364 ALVVSALVINWAMISLAHMKFRRA----KQEQGVVTRFPALLYPLGNWICLLFMAAVLVI 419 A A + WA I++ H +FR+A K++ + + A L+P+G I L V++ Sbjct: 366 AASGLAGFLAWAGIAVCHYRFRKAYVAQKRDLNKLI-YRAKLFPIGPVIALALCVVVILG 424 Query: 420 MLMT---------PGMAISVYLIPVWLIVLGIGYLFKEKT 450 +T G+ S +P++ I L IGY K KT Sbjct: 425 QGITYFQADKIDWTGVITSYIGLPIF-IALWIGYKIKHKT 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: 568 Number of extensions: 30 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: 477 Length adjustment: 33 Effective length of query: 424 Effective length of database: 444 Effective search space: 188256 Effective search space used: 188256 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 24 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