Align Glycerol uptake facilitator protein 3 (characterized)
to candidate 8500047 DvMF_0810 major intrinsic protein (RefSeq)
Query= SwissProt::F9UTW9 (240 letters) >FitnessBrowser__Miya:8500047 Length = 252 Score = 182 bits (462), Expect = 5e-51 Identities = 100/237 (42%), Positives = 138/237 (58%), Gaps = 7/237 (2%) Query: 6 LALQLLGEFLGTFILILLGDGVVAGVTLNKSKAQNAGWVAITLGWGFAVTMGVYASSFMS 65 L +++ EF+GT +LI+ G G VA +T+ K N W IT GWG AV +G+ A S Sbjct: 6 LGREMVSEFMGTMVLIIFGAGNVA-MTVLFGKGLNITWDNITFGWGLAVLLGIMAG-LPS 63 Query: 66 PAHLNPAVSLGMAVAGKFPWAYVIPYSAAQIAGGVIGGLVVWLHYYPHWQATK-DAGAIL 124 AH+NPAV++ +A G+FPW V+PYSAAQ+AGG G +V++ ++ W + Sbjct: 64 GAHINPAVTVALAATGRFPWKKVLPYSAAQVAGGFAGAAIVFIDFHAKWVGVDPQLASTA 123 Query: 125 GIFATGPGIRR-YFWNFISEVIGTFVLVFGLLA---FTKGQFTAGLNPIVVGILIIAIGL 180 GIF T P I Y FI ++IGT L+FG+LA F + I+V +L++AIG+ Sbjct: 124 GIFCTFPAITTSYLPGFIDQIIGTAALMFGILAIGDFASKNNIGWIGGILVALLVVAIGM 183 Query: 181 SLGGTTGYAINPARDLGPRIAHAVLPIANKGTSDWAYSWVPIAGPLVGGALGALLFN 237 SLG GYAINPARD GPR V + VPI GPL+GG LGA +++ Sbjct: 184 SLGAMHGYAINPARDFGPRFFALVAGFTQPNLMEPGIVLVPIVGPLIGGPLGAFIYD 240 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: 247 Number of extensions: 15 Number of successful extensions: 5 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: 240 Length of database: 252 Length adjustment: 24 Effective length of query: 216 Effective length of database: 228 Effective search space: 49248 Effective search space used: 49248 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