GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Shewanella oneidensis MR-1

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate 200848 SO1683 3-oxoacyl-(acyl-carrier-protein) reductase, putative (NCBI ptt file)

Query= BRENDA::Q99714
         (261 letters)



>FitnessBrowser__MR1:200848
          Length = 252

 Score =  143 bits (360), Expect = 4e-39
 Identities = 96/257 (37%), Positives = 134/257 (52%), Gaps = 12/257 (4%)

Query: 8   VKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFA--PADV 65
           +K  V VITGGA GLGLA A      GA   L+D+     E     LG++        D+
Sbjct: 3   LKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYALDI 62

Query: 66  TSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTH---TLEDFQRVLDVNL 122
           T E+DV    A     FG+++V VN AGI         K G+     + + FQ V++VNL
Sbjct: 63  TDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNL 122

Query: 123 MGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPI 182
            GTF   R  A  M ++     GQ GVI+N +S+A   G VGQ+ Y+ASK G+  M++  
Sbjct: 123 TGTFLCGREAAAAMIES-----GQAGVIVNISSLAK-AGNVGQSNYAASKAGVAAMSVGW 176

Query: 183 ARDLAPIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIE 242
           A++LA   IR   +APG+  T +  ++  +    L   VP   RLG   E A  V+ IIE
Sbjct: 177 AKELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPV-GRLGHAEEIASTVRFIIE 235

Query: 243 NPFLNGEVIRLDGAIRM 259
           N ++NG V  +DG IR+
Sbjct: 236 NDYVNGRVFEVDGGIRL 252


Lambda     K      H
   0.318    0.135    0.385 

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: 153
Number of extensions: 13
Number of successful extensions: 6
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: 261
Length of database: 252
Length adjustment: 24
Effective length of query: 237
Effective length of database: 228
Effective search space:    54036
Effective search space used:    54036
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: 47 (22.7 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