Align Tonoplast intrinsic protein-a (transports water, urea, glycerol and gases (CO2 and NH3) (characterized)
to candidate 354244 BT4718 putative aquaporin (NCBI ptt file)
Query= TCDB::Q9XG70 (247 letters) >FitnessBrowser__Btheta:354244 Length = 222 Score = 92.8 bits (229), Expect = 5e-24 Identities = 71/220 (32%), Positives = 106/220 (48%), Gaps = 19/220 (8%) Query: 26 ICTFLFVFAGVGSAMAANKLNGD--PLVSLFFVAMAHALVVAVTISAGFRISGGHLNPAV 83 I T + V G GSA+ A + G V VA+A L V A ISG H+NPA+ Sbjct: 2 IGTMVLVLMGCGSAVFAGSMAGTVGAGVGTVGVALAFGLSVVAMAYAIGGISGCHINPAI 61 Query: 84 TLGLCMGGHITVFRSILYWIDQLLASVAACALLNYL--TAGLETPVHTLANGVSYG---Q 138 TLG+ + G + + +Y + Q++ ++ A+L L T G + P T +NG G Q Sbjct: 62 TLGVFLSGRMNGKDAGMYMLFQVIGAIIGSAILYALVTTGGHDGPTATGSNGFGDGEMLQ 121 Query: 139 GIIMEVILTFSLLFTVYTTIVDPKKGILEGMGPLLTGLVVGANIMAGG----PFSGASMN 194 I EV+ TF + V + DPKKG GL +G +++ P +G S+N Sbjct: 122 AFIAEVVFTFIFVLVVLGS-TDPKKG-----AGAFAGLAIGLSLVLVHIVCIPITGTSVN 175 Query: 195 PARSFGPAFVSG--IWTDHWVYWVGPLIGGGLAGFICENF 232 PARS GPA G + W++ V P +G ++ + F Sbjct: 176 PARSIGPALFQGGEALSQLWLFIVAPFVGAAVSALVWNYF 215 Score = 29.3 bits (64), Expect = 7e-05 Identities = 27/106 (25%), Positives = 47/106 (44%), Gaps = 12/106 (11%) Query: 16 DCIQALIVEFICTFLFVFAGVGSAMAANKLNGDPLVSL-FFVAMAHALVVAVTISAGFRI 74 + +QA I E + TF+FV +GS DP F +A L + + I Sbjct: 118 EMLQAFIAEVVFTFIFVLVVLGST--------DPKKGAGAFAGLAIGLSLVLVHIVCIPI 169 Query: 75 SGGHLNPAVTLG--LCMGGHITVFRSILYWIDQLLASVAACALLNY 118 +G +NPA ++G L GG + + L+ + + + + + NY Sbjct: 170 TGTSVNPARSIGPALFQGGE-ALSQLWLFIVAPFVGAAVSALVWNY 214 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: 232 Number of extensions: 22 Number of successful extensions: 3 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: 222 Length adjustment: 23 Effective length of query: 224 Effective length of database: 199 Effective search space: 44576 Effective search space used: 44576 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