GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Caulobacter crescentus NA1000

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate CCNA_02479 CCNA_02479 aryl-alcohol dehydrogenase

Query= BRENDA::P22144
         (363 letters)



>FitnessBrowser__Caulo:CCNA_02479
          Length = 366

 Score = 85.5 bits (210), Expect = 2e-21
 Identities = 80/266 (30%), Positives = 114/266 (42%), Gaps = 22/266 (8%)

Query: 21  DAPEISEPT--DVLVQVKKTGICGSDIHFYAHGRIGNFVLTKPMVLGHESAGTVVQVGKG 78
           +A +I  P   ++LV+V  TG+C +D+      R  +    +P+VLGHE AG V QVG G
Sbjct: 18  EALDIEPPRAGEILVRVVATGVCHTDMVM----RDQHLPTPQPVVLGHEGAGVVEQVGPG 73

Query: 79  VTSLKVGDNVAIEPGIPSRF---SDEYKSGHYNLCPHMAFAATPNSKEGEPNPP------ 129
           V  + VGD+V +      R    SD   +  +   P     A  +   G           
Sbjct: 74  VAKVAVGDHVVMTFNSCGRCPSCSDHAPTYCHEFFPRNFMGAREDGSSGLSKGSEVIHAN 133

Query: 130 ----GTLCKYFKSPEDFLVKLPDHVSLE-LGALVEPLSVGVHASKLG-SVAFGDYVAVFG 183
                +   Y    E   VK+     LE LG L   +  G  A      V  G  + VFG
Sbjct: 134 IFGQSSFATYALCHERNAVKVDKTAPLERLGPLGCGVMTGAGAVMNALKVPAGRSLVVFG 193

Query: 184 AGPVGLLAAAVAKTFGAKGVIVVDIFDNKLKMAKDIGAATHTFNSKTGGSEELIKAFGGN 243
           AG VGL A   AK  GA  +I +DI   +L +A ++G A H  N   GG  E I+A  G 
Sbjct: 194 AGAVGLSAVLAAKAIGAGPIIAIDINPERLALALELG-ADHALNGAEGGVVEKIQAITGT 252

Query: 244 VPNVVLECTGAEPCIKLGVDAIAPGG 269
             +  ++ T     ++  VD +   G
Sbjct: 253 GAHFSIDTTANLKVMRQAVDCLGARG 278


Lambda     K      H
   0.318    0.138    0.411 

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: 348
Number of extensions: 22
Number of successful extensions: 4
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: 363
Length of database: 366
Length adjustment: 29
Effective length of query: 334
Effective length of database: 337
Effective search space:   112558
Effective search space used:   112558
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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