Align Glycerol uptake facilitator protein 3 (characterized)
to candidate RR42_RS29350 RR42_RS29350 glycerol uptake facilitator or water-selective channels
Query= SwissProt::F9UTW9 (240 letters) >FitnessBrowser__Cup4G11:RR42_RS29350 Length = 241 Score = 58.9 bits (141), Expect = 9e-14 Identities = 70/238 (29%), Positives = 107/238 (44%), Gaps = 33/238 (13%) Query: 6 LALQLLGEFLGTFIL--ILLGDGVVAGVTL--NKSKAQNAGWVAITLGWGFAVTMGVYAS 61 L Q+ GE +GT +L +++G G++A N + A A +A T+G G V + V+ Sbjct: 4 LPRQIAGEVIGTALLLAVVIGSGIMAERLAGGNVAVALLANTLA-TVG-GLYVLIEVFGP 61 Query: 62 SFMSPAHLNPAVSLGMAVAGKFPWAYVIPYSAAQIAGGVIGGLVVWLHYYPHWQATKDAG 121 +S AH NPAVS+ MAV G+ P + PY AQ+AG V+G WL H Sbjct: 62 --ISGAHFNPAVSMVMAVKGELPRYALAPYIVAQLAGAVLG---AWL---AHAMFDVSIL 113 Query: 122 AILGIFATGPGIRRYFWNFISEVIGTFVLVFGLLAFTKGQFTAGLNPIVVGILIIAIGLS 181 + +GPG +I+E + T L+ +L G+ P +V I A Sbjct: 114 QLSAKMRSGPG------QWIAEAVATAGLILVILRAPDGR-----APAMVASYIGA-AYW 161 Query: 182 LGGTTGYAINPARDLGPRIAHAVLPIANKGTSDWAYSWVPIAGPLVGGALGALLFNVL 239 +T +A NPA G +++ IA + + L+G +G LL L Sbjct: 162 FTASTSFA-NPAAAFGRMFSNSFAGIAPASVPGF------VLAELLGACIGLLLHTAL 212 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: 173 Number of extensions: 12 Number of successful extensions: 1 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: 241 Length adjustment: 23 Effective length of query: 217 Effective length of database: 218 Effective search space: 47306 Effective search space used: 47306 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