Align PTS lactose transporter subunit IIC, component of PTS-type lactose transporter, IIC-IIB-IIA (characterized)
to candidate 7026215 Shewana3_3357 diguanylate phosphodiesterase (RefSeq)
Query= TCDB::U5MFA1 (445 letters) >FitnessBrowser__ANA3:7026215 Length = 610 Score = 124 bits (312), Expect = 6e-33 Identities = 72/198 (36%), Positives = 111/198 (56%), Gaps = 14/198 (7%) Query: 228 LERVVQSLPGILLLM--FVAQLFWVIGIHGNQMIKPIREPLLLGAITVNMSAFEQGKEVP 285 +E + Q+ G+ L M + + W G+HG+ LL+G M VP Sbjct: 132 IEGLQQASLGVQLFMRILLTHVLWCFGVHGDNAYL-----LLIGVDNGLMQL------VP 180 Query: 286 NIITMPFWDVYMSIGGSGLTIGLLIAVMIATRRKEMKEIAKLSIGPGLFNINEPVIFGMP 345 ++ F D+++ GGSG T+ L+IA+ I + + IAK++ +FNINE +I+G+P Sbjct: 181 HLTASQFMDLFILYGGSGATLSLIIAIFIGAKDSATRHIAKIATPFAIFNINEILIYGLP 240 Query: 346 IMLNPILAIPFIITPLVTGSIGYFATLTGFAGKAVVMVPWTTPPLINAWLSTAGSMGAVV 405 I+ NP L +PFI++PLV + Y A G PW TPPL+NA+++ +G M AV Sbjct: 241 IIFNPRLLVPFILSPLVNFILAYSAIHVGLLSFEGHSFPWITPPLLNAYIA-SGHMSAVF 299 Query: 406 TQLICIVVAVLIYLPFVK 423 Q++ I + VLIYLPFV+ Sbjct: 300 FQVLLIGLGVLIYLPFVR 317 Lambda K H 0.328 0.142 0.419 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: 552 Number of extensions: 36 Number of successful extensions: 2 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: 445 Length of database: 610 Length adjustment: 35 Effective length of query: 410 Effective length of database: 575 Effective search space: 235750 Effective search space used: 235750 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: 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