Align glycerol facilitator-aquaporin (characterized)
to candidate CA265_RS07865 CA265_RS07865 aquaporin
Query= CharProtDB::CH_012828 (289 letters) >FitnessBrowser__Pedo557:CA265_RS07865 Length = 246 Score = 162 bits (409), Expect = 9e-45 Identities = 98/280 (35%), Positives = 143/280 (51%), Gaps = 40/280 (14%) Query: 9 YITEFVGTALLIIMGNGAVANVELKGTKAHAQSWMIIGWGYGLGVMLPAVAFGNIT-SQI 67 Y+ EF+GTAL+I++GNG VANV LKGTK + W++I + L V + V G + + + Sbjct: 4 YLAEFIGTALMILLGNGVVANVVLKGTKGNNSGWIVITTAWALAVFVGVVVAGPYSGAHL 63 Query: 68 NPAFTLGLAASGLFPWAHVAQYIIAQVLGAMFGQLLIVMVYRPYYLKTQNPNAILGTFST 127 NP TLGLA F WA YIIAQ+ GAM G L+ ++Y+ ++ T + F+T Sbjct: 64 NPIVTLGLAIGKGFSWALAPFYIIAQLAGAMTGSFLVWLIYKDHFDATDDQGLKAAPFAT 123 Query: 128 IDNVDDNSEKTRLGATINGFLNEFLGSFVLFFGAVAATNIFFGSQSITWMTNYLKGQGAD 187 + + S + L+E +G+FVL F T+ G++ L GA Sbjct: 124 APAIRNIS---------SNLLSEIIGTFVLIFVIFYFTDASMGTKETVTTPIGLGSMGA- 173 Query: 188 VSSSDVMNQIWVQASGASASKMIAHLFLGFLVMGLVVALGGPTGPGLNPARDFGPRLVHS 247 + + FLV + +ALGG TG +NPARD GPR++H Sbjct: 174 -------------------------IPVAFLVWVIGLALGGTTGYAINPARDLGPRIIHF 208 Query: 248 LLPKSVLGEAKGSSKWWYAWVPVLAPILASLAAVALFKMI 287 L+P + KG S W YAWVP++ PI+ S+ A F +I Sbjct: 209 LIPM----KGKGGSDWSYAWVPIVGPIIGSVLAAVAFLLI 244 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: 298 Number of extensions: 15 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: 1 Length of query: 289 Length of database: 246 Length adjustment: 25 Effective length of query: 264 Effective length of database: 221 Effective search space: 58344 Effective search space used: 58344 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