Align Glycerol uptake facilitator protein 3 (characterized)
to candidate Echvi_1769 Echvi_1769 Glycerol uptake facilitator and related permeases (Major Intrinsic Protein Family)
Query= SwissProt::F9UTW9 (240 letters) >FitnessBrowser__Cola:Echvi_1769 Length = 244 Score = 231 bits (590), Expect = 8e-66 Identities = 119/238 (50%), Positives = 148/238 (62%), Gaps = 9/238 (3%) Query: 11 LGEFLGTFILILLGDGVVAGVTLNKSKAQNAGWVAITLGWGFAVTMGVYASSFMSPAHLN 70 + EF+GT +L+L+G GVVA V L ++K N+GW+ IT W V +GV + S AHLN Sbjct: 5 IAEFIGTGLLLLMGAGVVANVVLKQTKGNNSGWIVITTAWALGVFIGVVVAGPYSGAHLN 64 Query: 71 PAVSLGMAVAGKFPWAYVIPYSAAQIAGGVIGGLVVWLHYYPHWQATKDAGAILGIFATG 130 PAVS+G+AVAG F W+ V Y AQI G G + WL Y H+ T D FAT Sbjct: 65 PAVSVGLAVAGLFEWSLVPGYVLAQILGAGAGSSLAWLIYKDHFDLTDDPNLKFAPFATA 124 Query: 131 PGIRRYFWNFISEVIGTFVLVFGLLAFTKGQF---------TAGLNPIVVGILIIAIGLS 181 P IR NF+SEV+GTFVL+ +L T L + V +L+ IGL+ Sbjct: 125 PAIRNLSSNFLSEVVGTFVLILVILYSTGANLEDPNNTPIGLGALGALPVALLVWVIGLA 184 Query: 182 LGGTTGYAINPARDLGPRIAHAVLPIANKGTSDWAYSWVPIAGPLVGGALGALLFNVL 239 LGGTTGYAINPARDLGPR+AH LPI KG+SDWAYSWVPI GPL+G +L A F +L Sbjct: 185 LGGTTGYAINPARDLGPRLAHQFLPIKGKGSSDWAYSWVPIVGPLMGASLAAATFLIL 242 Score = 22.7 bits (47), Expect = 0.007 Identities = 28/109 (25%), Positives = 43/109 (39%), Gaps = 19/109 (17%) Query: 6 LALQLLGEFLGTFILILLGDGVVAGVTLNKSKAQNAGWVAITLG--------WGFAVTMG 57 L+ L E +GTF+LIL+ ++ N N LG W + +G Sbjct: 130 LSSNFLSEVVGTFVLILV---ILYSTGANLEDPNNTPIGLGALGALPVALLVWVIGLALG 186 Query: 58 VYASSFMSPAH-LNPAVS---LGMAVAGKFPWAYVIPYSAAQIAGGVIG 102 ++PA L P ++ L + G WA YS I G ++G Sbjct: 187 GTTGYAINPARDLGPRLAHQFLPIKGKGSSDWA----YSWVPIVGPLMG 231 Lambda K H 0.325 0.143 0.459 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: 285 Number of extensions: 16 Number of successful extensions: 3 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: 240 Length of database: 244 Length adjustment: 23 Effective length of query: 217 Effective length of database: 221 Effective search space: 47957 Effective search space used: 47957 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 (21.6 bits) S2: 46 (22.3 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