Align Tonoplast intrinsic protein-a (transports water, urea, glycerol and gases (CO2 and NH3) (characterized)
to candidate AZOBR_RS03835 AZOBR_RS03835 aquaporin Z
Query= TCDB::Q9XG70 (247 letters) >FitnessBrowser__azobra:AZOBR_RS03835 Length = 246 Score = 99.4 bits (246), Expect = 6e-26 Identities = 74/218 (33%), Positives = 107/218 (49%), Gaps = 20/218 (9%) Query: 24 EFICTFLFVFAGVGSAMAANKLNGDPLVSLFFVAMAHALVVAVTISAGFRISGGHLNPAV 83 EF+ TF VF G GSA+ + + + L V++A L V + ISG HLNPAV Sbjct: 10 EFLGTFWLVFGGCGSAVLSAAFP-EVGIGLTGVSLAFGLTVLTMAYSVGHISGCHLNPAV 68 Query: 84 TLGLCMGGHITVFRSILYWIDQLLASVAACALLNYLTAGLETPVHTLANGVS---YGQ-- 138 T+GL GG + Y I Q++ + A A++ Y+ A + A G++ YG+ Sbjct: 69 TVGLWAGGRFPAKDILPYVIAQVVGAFLA-AMVLYVIATGKADWSLAAKGLAANGYGEHS 127 Query: 139 --------GIIMEVILTFSLLFTVYTTIVDPKKGILEGMGPLLTGLVVGANIMAGGPFSG 190 G+++EV+LTF L + + + G PL GL + + P + Sbjct: 128 PGAYNLTSGLLIEVVLTFMFLIVI---LGSTDRRAPAGFAPLAIGLALTLIHLISIPVTN 184 Query: 191 ASMNPARSFGPAFVSGIWT--DHWVYWVGPLIGGGLAG 226 S+NPARS GPA V G W W +WV PL+GG L G Sbjct: 185 TSVNPARSTGPALVVGGWALQQLWAFWVAPLVGGLLGG 222 Score = 25.8 bits (55), Expect = 9e-04 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 10/73 (13%) Query: 21 LIVEFICTFLFVFAGVGSAMAANKLNGDPLVSLFFVAMAHALVVAVTISAGFRISGGHLN 80 L++E + TF+F+ +GS PL + + H + + VT ++ +N Sbjct: 137 LLIEVVLTFMFLIVILGSTDRRAPAGFAPLAIGLALTLIHLISIPVTNTS--------VN 188 Query: 81 PAVTLG--LCMGG 91 PA + G L +GG Sbjct: 189 PARSTGPALVVGG 201 Lambda K H 0.327 0.142 0.443 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: 215 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 247 Length of database: 246 Length adjustment: 24 Effective length of query: 223 Effective length of database: 222 Effective search space: 49506 Effective search space used: 49506 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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