Align glycerol facilitator-aquaporin (characterized)
to candidate Echvi_1769 Echvi_1769 Glycerol uptake facilitator and related permeases (Major Intrinsic Protein Family)
Query= CharProtDB::CH_012828 (289 letters) >FitnessBrowser__Cola:Echvi_1769 Length = 244 Score = 160 bits (404), Expect = 3e-44 Identities = 100/280 (35%), Positives = 150/280 (53%), Gaps = 42/280 (15%) Query: 9 YITEFVGTALLIIMGNGAVANVELKGTKAHAQSWMIIGWGYGLGVMLPAVAFGNIT-SQI 67 YI EF+GT LL++MG G VANV LK TK + W++I + LGV + V G + + + Sbjct: 4 YIAEFIGTGLLLLMGAGVVANVVLKQTKGNNSGWIVITTAWALGVFIGVVVAGPYSGAHL 63 Query: 68 NPAFTLGLAASGLFPWAHVAQYIIAQVLGAMFGQLLIVMVYRPYYLKTQNPNAILGTFST 127 NPA ++GLA +GLF W+ V Y++AQ+LGA G L ++Y+ ++ T +PN F+T Sbjct: 64 NPAVSVGLAVAGLFEWSLVPGYVLAQILGAGAGSSLAWLIYKDHFDLTDDPNLKFAPFAT 123 Query: 128 IDNVDDNSEKTRLGATINGFLNEFLGSFVLFFGAVAATNIFFGSQSITWMTNYLKGQGAD 187 + + S + FL+E +G+FVL + +T GA+ Sbjct: 124 APAIRNLS---------SNFLSEVVGTFVLILVILYST-------------------GAN 155 Query: 188 VSSSDVMNQIWVQASGASASKMIAHLFLGFLVMGLVVALGGPTGPGLNPARDFGPRLVHS 247 + + I + A GA L + LV + +ALGG TG +NPARD GPRL H Sbjct: 156 LEDPN-NTPIGLGALGA--------LPVALLVWVIGLALGGTTGYAINPARDLGPRLAHQ 206 Query: 248 LLPKSVLGEAKGSSKWWYAWVPVLAPILASLAAVALFKMI 287 LP + KGSS W Y+WVP++ P++ + A A F ++ Sbjct: 207 FLPI----KGKGSSDWAYSWVPIVGPLMGASLAAATFLIL 242 Lambda K H 0.323 0.138 0.426 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: 317 Number of extensions: 28 Number of successful extensions: 4 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: 289 Length of database: 244 Length adjustment: 25 Effective length of query: 264 Effective length of database: 219 Effective search space: 57816 Effective search space used: 57816 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 47 (22.7 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