Align Tonoplast intrinsic protein-a (transports water, urea, glycerol and gases (CO2 and NH3) (characterized)
to candidate SMc01870 SMc01870 aquaporin Z
Query= TCDB::Q9XG70 (247 letters) >FitnessBrowser__Smeli:SMc01870 Length = 228 Score = 93.2 bits (230), Expect = 4e-24 Identities = 71/221 (32%), Positives = 107/221 (48%), Gaps = 18/221 (8%) Query: 21 LIVEFICTFLFVFAGVGSAMAANKLNGDPLVSLFFVAMAHALVVAVTISAGFRISGGHLN 80 L VEF+ TF V G GSA+ A + + L V+ A L V A ISGGH N Sbjct: 5 LSVEFLGTFWLVLGGCGSAVLAAAFP-EVGIGLLGVSFAFGLTVLTMAYAVGGISGGHFN 63 Query: 81 PAVTLGLCMGGHITVFRSILYWIDQLLASVAACALLNYLTAG-LETPVHTLA-------- 131 PAV++GL + G + + Y + Q+ ++AA A+L + +G + + A Sbjct: 64 PAVSVGLAVAGRMPPASLVGYILAQVTGAIAAAAVLYVIASGKADFQLGGFAANGYGEHS 123 Query: 132 -NGVSYGQGIIMEVILT-FSLLFTVYTTIVDPKKGILEGMGPLLTGLVVGANIMAGGPFS 189 G S ++ EV++T F LL + +T + G P+ GL + + P + Sbjct: 124 PGGYSLTAALVTEVVMTAFFLLIILGST----HSRVPVGFAPIAIGLGLTLIHLVSIPVT 179 Query: 190 GASMNPARSFGPAFVSGIW--TDHWVYWVGPLIGGGLAGFI 228 S+NPARS G A G W + W++WV PLIG +AG + Sbjct: 180 NTSVNPARSTGQALFVGDWAISQLWLFWVAPLIGAVIAGIV 220 Score = 27.3 bits (59), Expect = 3e-04 Identities = 21/94 (22%), Positives = 43/94 (45%), Gaps = 9/94 (9%) Query: 20 ALIVEFICTFLFVFAGVGSAMAANKLNGDPLVSLFFVAMAHALVVAVTISAGFRISGGHL 79 AL+ E + T F+ +GS + + P+ + + H + + VT ++ + Sbjct: 132 ALVTEVVMTAFFLLIILGSTHSRVPVGFAPIAIGLGLTLIHLVSIPVTNTS--------V 183 Query: 80 NPAVTLGLCM-GGHITVFRSILYWIDQLLASVAA 112 NPA + G + G + + L+W+ L+ +V A Sbjct: 184 NPARSTGQALFVGDWAISQLWLFWVAPLIGAVIA 217 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: 202 Number of extensions: 13 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: 2 Length of query: 247 Length of database: 228 Length adjustment: 23 Effective length of query: 224 Effective length of database: 205 Effective search space: 45920 Effective search space used: 45920 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