GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Caulobacter crescentus NA1000

Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate CCNA_01747 CCNA_01747 3-oxoacyl-(acyl-carrier protein) reductase

Query= CharProtDB::CH_091826
         (259 letters)



>FitnessBrowser__Caulo:CCNA_01747
          Length = 246

 Score =  104 bits (260), Expect = 2e-27
 Identities = 78/257 (30%), Positives = 128/257 (49%), Gaps = 19/257 (7%)

Query: 3   QVAVVIGGGQTLGAFLCEGLAQAGYHVAVADLNESNANRLADTINSRYGAGRAYGFKVDA 62
           + A+V G    +G  +   L   G HV ++   ES    L   +  R     A     + 
Sbjct: 7   KTALVTGATGGIGGAIARALHAQGAHVVLSGTRESALAELKAELGER-----ASTVVANL 61

Query: 63  TDEASVEALARAVDETFGRA-DLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSR 121
           +D   V+ L    +E  G   D+++ +AGV +   I + +  D+D  ++VNL GYF  SR
Sbjct: 62  SDAEQVDGLVAKAEEAAGAPLDIVIANAGVTRDGLIVRMKDEDWDTVIKVNLEGYFRLSR 121

Query: 122 EFSKLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHS 181
             +K M++    GRII I S  G  G+   + Y+A+K G +G +++LA +LA  G+TV+ 
Sbjct: 122 AAAKGMMKRRA-GRIIGITSIVGVTGNPGQTNYAASKAGMIGFSKALAQELASRGVTVNC 180

Query: 182 LMLGNLLKSPMFQSLLPQYAEKLGITPEEVEPYYVDKVPLKRGCDYQDVLNVLLFYASDK 241
           +  G  + SPM  +L  Q  +K GI         +  +P  +  +  D+    ++ ASD+
Sbjct: 181 VAPG-FIASPMTDALNEQ--QKAGI---------LSTIPAGKLGEGADIAAACVYLASDQ 228

Query: 242 AAYCTGQSINVTGGQVM 258
           A Y TGQ+++V GG  M
Sbjct: 229 AGYVTGQTLHVNGGMAM 245


Lambda     K      H
   0.319    0.136    0.387 

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: 178
Number of extensions: 8
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: 259
Length of database: 246
Length adjustment: 24
Effective length of query: 235
Effective length of database: 222
Effective search space:    52170
Effective search space used:    52170
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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.

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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