Align Tonoplast intrinsic protein-a (transports water, urea, glycerol and gases (CO2 and NH3) (characterized)
to candidate Ac3H11_4644 Aquaporin Z
Query= TCDB::Q9XG70 (247 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4644 Length = 248 Score = 91.3 bits (225), Expect = 2e-23 Identities = 71/235 (30%), Positives = 104/235 (44%), Gaps = 24/235 (10%) Query: 15 PDCIQALIVEFICTFLFVFAGVGSAMAANKLNGDPLVSLFF--VAMAHALVVAVTISAGF 72 P +Q EF+ TF F G GSA+ A P + + F V++A L V A Sbjct: 19 PTSLQKWSAEFLGTFWLTFGGCGSAVLAAAF---PQLGIGFLGVSLAFGLTVLTGAYALG 75 Query: 73 RISGGHLNPAVTLGLCMGGHITVFRSILYWIDQLLASVAACALLNYLTAGLETPVHTLAN 132 ISGGH NPAV++GL +GG V Y + Q+L ++ A +L + G P + Sbjct: 76 PISGGHFNPAVSVGLALGGRFKVSELPGYVVAQVLGAIVAAGVLYLIATG--KPGADIGG 133 Query: 133 GVSYGQG------------IIMEVILTFSLLFTVYTTIVDPKKGILEGMGPLLTGLVVGA 180 + G G ++ EV+LT L + + EG+G + GL + Sbjct: 134 FATNGYGEHSPGGYGLLAAVVAEVVLTAVFLIVILGV---TSRRAAEGVGGMAIGLCLTL 190 Query: 181 NIMAGGPFSGASMNPARSFGPAFV--SGIWTDHWVYWVGPLIGGGLAGFICENFF 233 + P + S+NPARS GPA S ++ WV+W P+ G L I F Sbjct: 191 IHLISIPVTNTSVNPARSTGPALFGPSYALSELWVFWAAPIAGALLGAAIYRGLF 245 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: 224 Number of extensions: 16 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: 247 Length of database: 248 Length adjustment: 24 Effective length of query: 223 Effective length of database: 224 Effective search space: 49952 Effective search space used: 49952 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