GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacIIC in Shewanella sp. ANA-3

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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