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 H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family
Query= TCDB::P15993 (457 letters) >FitnessBrowser__Burk376:H281DRAFT_04042 Length = 506 Score = 651 bits (1680), Expect = 0.0 Identities = 318/449 (70%), Positives = 368/449 (81%), Gaps = 2/449 (0%) Query: 5 QQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMR 64 QQ G LKRGLKNRHIQLIALGGAIGTGLFLGSASV+Q+AGP +ILGYAI G IAF+IMR Sbjct: 51 QQDG--LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMR 108 Query: 65 QLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPE 124 QLGEMV +EPVAGSFSHFAYKYWG F GF SGWNYWVLYVLV+MAELTAVG Y+ +W+P Sbjct: 109 QLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPG 168 Query: 125 IPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNGGPQA 184 +PTWVSA V F INAINL NVK +GE EFWFAIIKV+AV+ MI+FGG+LL SG+GGPQA Sbjct: 169 VPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQA 228 Query: 185 TVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYR 244 ++SNLW GGF PHGF GL M+A+IMFSFGGLEL+GITAAEAD P++SIPKA NQVIYR Sbjct: 229 SISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYR 288 Query: 245 ILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCV 304 ILIFYI SLAVLLSL PW V A SPFV+IF ++G T AN LN+VVLTAALSVYNS V Sbjct: 289 ILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGV 348 Query: 305 YCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMA 364 Y NSRML+GLA+QGNAP+AL VD+RGVP I +SAL T CV++NYL P A GLLMA Sbjct: 349 YANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMA 408 Query: 365 LVVSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMTP 424 LVV+ALV+NWA+ISL H+K RRA G F + +P+ NWICL FMA +LVI+ MTP Sbjct: 409 LVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILAMTP 468 Query: 425 GMAISVYLIPVWLIVLGIGYLFKEKTAKA 453 G+++SV L+PVWL+V+ GY FK + A A Sbjct: 469 GLSVSVLLVPVWLVVMWAGYAFKRRRAAA 497 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: 775 Number of extensions: 41 Number of successful extensions: 1 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: 506 Length adjustment: 34 Effective length of query: 423 Effective length of database: 472 Effective search space: 199656 Effective search space used: 199656 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