Align Aquaporin-3, Aqp-3 of 271 aas (characterized)
to candidate H281DRAFT_05734 H281DRAFT_05734 aquaporin Z
Query= TCDB::729057658 (271 letters) >FitnessBrowser__Burk376:H281DRAFT_05734 Length = 246 Score = 84.7 bits (208), Expect = 2e-21 Identities = 64/197 (32%), Positives = 97/197 (49%), Gaps = 19/197 (9%) Query: 46 GPVPAAFVVGLTLAWIAWVFGPVSGAHVNPVVSLMMLLVRKVWFLDALIYIVAQLLGSMA 105 G V + GLT+ +A+ G +SG H+NP VS+ + + + D + YIVAQ++G++ Sbjct: 41 GFVGVSLAFGLTVLTMAYAIGHISGCHLNPAVSVGLTVAGRFPARDLVPYIVAQVVGAVP 100 Query: 106 GSWI---------GTLAVPAVDAGNTLGMTTISANITVGQAIGLEIVATALLLLVILSAV 156 G+ + G V + A N G + + ++ A E V T L VIL A Sbjct: 101 GAAVLALIASGKPGFELVASGFASNGYGERS-PGHYSLAAAFVCEAVMTGFFLFVILGAT 159 Query: 157 DELRPKPWNVGNVTIFPFIFGATLALLASLLGDLTGASMNPARSFGPAV-VNNNFTD-LW 214 D+ P P G L L+ + +T S+NPARS GPA+ V D LW Sbjct: 160 DKRAP-------AGFAPIAIGLCLTLIHLVSIPVTNTSVNPARSTGPALFVGGAAVDQLW 212 Query: 215 VYIVGPFIGALLATVLY 231 ++ + P IGA++A VLY Sbjct: 213 LFWIAPIIGAVIAGVLY 229 Lambda K H 0.326 0.140 0.433 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: 192 Number of extensions: 15 Number of successful extensions: 5 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: 271 Length of database: 246 Length adjustment: 24 Effective length of query: 247 Effective length of database: 222 Effective search space: 54834 Effective search space used: 54834 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: 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