Align glycerol facilitator-aquaporin (characterized)
to candidate 8500047 DvMF_0810 major intrinsic protein (RefSeq)
Query= CharProtDB::CH_012828 (289 letters) >FitnessBrowser__Miya:8500047 Length = 252 Score = 90.5 bits (223), Expect = 3e-23 Identities = 70/235 (29%), Positives = 105/235 (44%), Gaps = 44/235 (18%) Query: 10 ITEFVGTALLIIMGNGAVANVELKGTKAHAQSWMIIGWGYGLGVMLPAVAFGNITSQINP 69 ++EF+GT +LII G G VA L G K +W I +G+GL V+L +A + INP Sbjct: 11 VSEFMGTMVLIIFGAGNVAMTVLFG-KGLNITWDNITFGWGLAVLLGIMAGLPSGAHINP 69 Query: 70 AFTLGLAASGLFPWAHVAQYIIAQVLGAMFGQLLIVMVYRPYYLKTQNPNA-ILGTFSTI 128 A T+ LAA+G FPW V Y AQV G G ++ + + ++ A G F T Sbjct: 70 AVTVALAATGRFPWKKVLPYSAAQVAGGFAGAAIVFIDFHAKWVGVDPQLASTAGIFCTF 129 Query: 129 DNVDDNSEKTRLGATINGFLNEFLGSFVLFFGAVAATNIFFGSQSITWMTNYLKGQGADV 188 + + + GF+++ +G+ L FG + A F +I W Sbjct: 130 PAITT--------SYLPGFIDQIIGTAALMFG-ILAIGDFASKNNIGW------------ 168 Query: 189 SSSDVMNQIWVQASGASASKMIAHLFLGFLVMGLVVALGGPTGPGLNPARDFGPR 243 I + + LV+ + ++LG G +NPARDFGPR Sbjct: 169 ---------------------IGGILVALLVVAIGMSLGAMHGYAINPARDFGPR 202 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: 251 Number of extensions: 19 Number of successful extensions: 4 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: 289 Length of database: 252 Length adjustment: 25 Effective length of query: 264 Effective length of database: 227 Effective search space: 59928 Effective search space used: 59928 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