GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Crocosphaera subtropica ATCC 51142

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 WP_009544566.1 CCE_RS13000 SDR family NAD(P)-dependent oxidoreductase

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_000017845.1:WP_009544566.1
          Length = 271

 Score =  101 bits (251), Expect = 2e-26
 Identities = 71/208 (34%), Positives = 104/208 (50%), Gaps = 18/208 (8%)

Query: 8   VKGLVAVITGGASGLGLATAERLVGQGASAVLL------DLPNSGGEAQAKKLGNNCVFA 61
           V G  A++TG + G+G A A  L  QG   +LL      +L     E QA +     +  
Sbjct: 3   VLGKTALVTGASRGIGRAIALELAQQGIKRLLLVARNRVNLTAVAEEIQATEAKIEVIIL 62

Query: 62  PADVTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVN 121
           P D+ +   V TA+A A   +G +D+ VNCAG+A  S     K  Q   +ED    L VN
Sbjct: 63  PLDIRNSVSVTTAIAQAWRDYGPIDILVNCAGVAHQSSFLYSKLSQ---VED---ELSVN 116

Query: 122 LMGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLP 181
           LMGT+++ R+VA  M   +      +G IIN +S+         A YSA+K  ++G T  
Sbjct: 117 LMGTYHITRVVARRMAAQK------QGTIINVSSLMGKIAAPTMATYSATKFALLGFTQA 170

Query: 182 IARDLAPIGIRVMTIAPGLFGTPLLTSL 209
           +  +LAP  IRV+ + P L  T ++  L
Sbjct: 171 LRSELAPYNIRVIALLPSLTDTDMVQGL 198


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: 125
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: 261
Length of database: 271
Length adjustment: 25
Effective length of query: 236
Effective length of database: 246
Effective search space:    58056
Effective search space used:    58056
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 Apr 09 2024. 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