Align Permease IIC component (characterized, see rationale)
to candidate 7026215 Shewana3_3357 diguanylate phosphodiesterase (RefSeq)
Query= uniprot:A0A0H2UNC6 (448 letters) >FitnessBrowser__ANA3:7026215 Length = 610 Score = 118 bits (295), Expect = 6e-31 Identities = 79/249 (31%), Positives = 125/249 (50%), Gaps = 25/249 (10%) Query: 209 FTALVPGFVVAFVVIFINGLLVAMGTDIFKVIAIPFGFVSNLTNSWIGLMIIY--LLTQL 266 F +V GF+ F V VA + + + PF + L + +G+ + LLT + Sbjct: 103 FFPIVIGFIGLFAV-------VAEASIFLEWLFAPF--IEGLQQASLGVQLFMRILLTHV 153 Query: 267 LWIVGIHGANIVFAFVSPIALANMAENAAGGHFAVAGEFSNMFVIAGGSGATLGLCLYIA 326 LW G+HG N A++ I + N A +F ++F++ GGSGATL L + I Sbjct: 154 LWCFGVHGDN---AYLLLIGVDNGLMQLVP--HLTASQFMDLFILYGGSGATLSLIIAIF 208 Query: 327 FASKSEQLKAIGRASVVPALFNINEPLIFGLPIIYNPALAIPFILAPMVTATIYYVANSL 386 +K + I + + A+FNINE LI+GLPII+NP L +PFIL+P+V + Y A + Sbjct: 209 IGAKDSATRHIAKIATPFAIFNINEILIYGLPIIFNPRLLVPFILSPLVNFILAYSAIHV 268 Query: 387 NFIKPIIAQVPWPTPVGIGAFLGTADLRAVLVALVCAFAAFLVYLPFIR---------VY 437 + PW TP + A++ + + AV ++ L+YLPF+R + Sbjct: 269 GLLSFEGHSFPWITPPLLNAYIASGHMSAVFFQVLLIGLGVLIYLPFVRRFSLMSEHYEF 328 Query: 438 DQKLVKEEQ 446 D +L+K Q Sbjct: 329 DSELIKRVQ 337 Lambda K H 0.329 0.142 0.426 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: 622 Number of extensions: 35 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: 448 Length of database: 610 Length adjustment: 35 Effective length of query: 413 Effective length of database: 575 Effective search space: 237475 Effective search space used: 237475 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 (21.8 bits) S2: 52 (24.6 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