Align Tonoplast intrinsic protein-a (transports water, urea, glycerol and gases (CO2 and NH3) (characterized)
to candidate GFF4011 PS417_20545 porin
Query= TCDB::Q9XG70 (247 letters) >FitnessBrowser__WCS417:GFF4011 Length = 233 Score = 92.0 bits (227), Expect = 9e-24 Identities = 68/220 (30%), Positives = 106/220 (48%), Gaps = 21/220 (9%) Query: 22 IVEFICTFLFVFAGVGSAMAANKLNGDPLVSLFFVAMAHALVVAVTISAGFRISGGHLNP 81 I E + TF V G GSA+ A + L V++A L V A ISG HLNP Sbjct: 8 ITEGLGTFWLVLGGCGSAVLAAAFPAVG-IGLLGVSLAFGLTVLTMAFAIGHISGCHLNP 66 Query: 82 AVTLGLCMGGHITVFRSILYWIDQLLASVAACALLNYLTAGLETPVHTLANGVS---YGQ 138 AV++GL +GG Y + Q++ A ALL ++ +G P LA+G++ YG+ Sbjct: 67 AVSVGLVVGGRFPARELPAYIVAQVVGGTIAAALLYFIASG--KPGFELASGLASNGYGE 124 Query: 139 ----------GIIMEVILTFSLLFTVYTTIVDPKKGILEGMGPLLTGLVVGANIMAGGPF 188 G + E+++T +F V ++ G+ P+ GL + + P Sbjct: 125 HSPGGYSMVAGFVCELVMT--AMFVVIILGATDRRA-PPGLAPVAIGLALTLIHLISIPV 181 Query: 189 SGASMNPARSFGPAFVSGIWT--DHWVYWVGPLIGGGLAG 226 + S+NPARS GPA + G W W++W+ P++G + G Sbjct: 182 TNTSVNPARSTGPALIVGGWAIQQLWMFWLAPILGAVIGG 221 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: 212 Number of extensions: 18 Number of successful extensions: 3 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: 233 Length adjustment: 23 Effective length of query: 224 Effective length of database: 210 Effective search space: 47040 Effective search space used: 47040 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