Align Glycerol uptake facilitator protein 3 (characterized)
to candidate 208652 DVU3133 glycerol uptake facilitator protein
Query= SwissProt::F9UTW9 (240 letters) >MicrobesOnline__882:208652 Length = 251 Score = 186 bits (473), Expect = 3e-52 Identities = 105/242 (43%), Positives = 139/242 (57%), Gaps = 7/242 (2%) Query: 1 MMKDPLALQLLGEFLGTFILILLGDGVVAGVTLNKSKAQNAGWVAITLGWGFAVTMGVYA 60 M + L ++L EF+GT +LI+ G G VA +T+ K N W IT GWG AV +G+ A Sbjct: 1 MKEISLGKEMLSEFMGTMVLIIFGAGNVA-MTVLFGKTLNITWDNITFGWGLAVLLGIMA 59 Query: 61 SSFMSPAHLNPAVSLGMAVAGKFPWAYVIPYSAAQIAGGVIGGLVVWLHYYPHWQATK-D 119 S AH+NPAVSL +A G+FPW V+PYS AQ+AGG G +V+L + W Sbjct: 60 G-LPSGAHINPAVSLALAATGRFPWRKVLPYSVAQVAGGFAGAAIVFLDFKAKWLGVDPQ 118 Query: 120 AGAILGIFATGPGIRR-YFWNFISEVIGTFVLVFGLLA---FTKGQFTAGLNPIVVGILI 175 + GIF T P I Y FI ++IGT VL+FG+LA F + P++V LI Sbjct: 119 LASTAGIFCTFPAITTSYLPGFIDQIIGTAVLMFGILAIGDFAGKNNVGWMGPVLVAALI 178 Query: 176 IAIGLSLGGTTGYAINPARDLGPRIAHAVLPIANKGTSDWAYSWVPIAGPLVGGALGALL 235 +AIG+SLG GYAINPARD GPR V + VPI GP++GG LGA + Sbjct: 179 VAIGMSLGAMHGYAINPARDFGPRFFALVAGFTQPNLMEPGIVLVPIVGPIIGGPLGAFI 238 Query: 236 FN 237 ++ Sbjct: 239 YD 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: 251 Number of extensions: 19 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: 251 Length adjustment: 24 Effective length of query: 216 Effective length of database: 227 Effective search space: 49032 Effective search space used: 49032 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