Align Probable inositol transporter 2 (characterized)
to candidate Echvi_2810 Echvi_2810 MFS transporter, sugar porter (SP) family
Query= SwissProt::Q9C757 (580 letters) >FitnessBrowser__Cola:Echvi_2810 Length = 450 Score = 176 bits (445), Expect = 2e-48 Identities = 114/348 (32%), Positives = 192/348 (55%), Gaps = 20/348 (5%) Query: 32 AFSAGIGGLLFGYDTGVISGALLYIRDDFKSVDRNTWLQEM-IVSMAVAGAIVGAAIGGW 90 AF + G LFG+DT VISGA L ++ +++ D W I+S+A+ G ++GA +GG Sbjct: 9 AFIVSLTGFLFGFDTAVISGANLPLKALWQTSD---WFHGFFIMSVALWGTVIGALLGGI 65 Query: 91 ANDKLGRRSAILMADFLFLLGAIIMAAAPNPSLLVVGRVFVGLGVGMASMTAPLYISEAS 150 LGR++ + +FL+ A+ A A +P + R G+ +G +S+ AP Y+SE S Sbjct: 66 PCHHLGRKNTLFWIGVMFLVSALGTALATDPFVFSFYRFVGGVAIGASSIAAPTYVSEIS 125 Query: 151 PAKIRGALVSTNGFLITGGQFLSYLINLAFTDV--TGTWRWMLGIAGIPALLQFVLMFTL 208 A RG V I G ++Y+ N V WRWML IPA++ + + Sbjct: 126 QAYQRGRRVGLYQINIVSGILVAYVSNYLLQGVGDHNDWRWMLAAEIIPAIIYLAFILDI 185 Query: 209 PESPRWLYRKGREEE-AKAILRRIYSAEDVEQEIRALKDSVETEILEEGSSEKINMIKLC 267 PESPRWL K ++E A+ +L++I + + ++Q + ++K S + +KL Sbjct: 186 PESPRWLILKQKDESAAQKVLKKITTGK-IDQLLLSIKH----------DSLRSKKMKLF 234 Query: 268 KAKTVRRGLIAGVGLQVFQQFVGINTVMYYSPTIVQLAGFASNRTALLLSLVTAGLNAFG 327 AK +AG+ + +F Q GIN ++YY+P I++ AGF + T+LL ++ N Sbjct: 235 SAKNRLPLFLAGI-IAIFNQLSGINFILYYAPEIMEKAGFVTT-TSLLGAVCIGFTNLIF 292 Query: 328 SIISIYFIDRIGRKKLLIISLFGVIISLGILTGVFYEAATHAPAISSL 375 ++I + ID+ GRK+L++I G IISLG+++ FY++++ ++S+ Sbjct: 293 TLIGMSLIDKTGRKQLMLIGSMGYIISLGLVSYGFYDSSSPLFILTSI 340 Score = 51.6 bits (122), Expect = 7e-11 Identities = 27/108 (25%), Positives = 51/108 (47%) Query: 455 FALLGLGLYIIFFSPGMGTVPWIVNSEIYPLRFRGICGGIAATANWISNLIVAQSFLSLT 514 F L + ++I G G V W+ SEI+P + R + A +W ++ L Sbjct: 335 FILTSILIFIAAHGIGQGAVIWVFISEIFPNKVRAMGQSFGAGVHWGGAAMITLFGAVLI 394 Query: 515 EAIGTSWTFLIFGVISVIALLFVMVCVPETKGMPMEEIEKMLERRSME 562 + + F++F + ++ +FV +PETKG+ +E + L ++ E Sbjct: 395 DTLMPFQIFMVFMALMILQFVFVWRYMPETKGLELENLHSKLAQKLYE 442 Lambda K H 0.324 0.139 0.425 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: 620 Number of extensions: 37 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 580 Length of database: 450 Length adjustment: 35 Effective length of query: 545 Effective length of database: 415 Effective search space: 226175 Effective search space used: 226175 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 52 (24.6 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