GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pantoea rwandensis LMG 26275

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_084935308.1 HA51_RS14510 3-oxoacyl-ACP reductase FabG

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_002095475.1:WP_084935308.1
          Length = 244

 Score =  126 bits (316), Expect = 5e-34
 Identities = 85/255 (33%), Positives = 132/255 (51%), Gaps = 15/255 (5%)

Query: 7   SVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVT 66
           S +G VA++TG + G+G A AE LV +GA  V      SG EA +  LG+N      +VT
Sbjct: 2   SFEGKVALVTGASRGIGRAIAETLVARGAKVVGTATSESGAEAISAYLGDNGKGLLLNVT 61

Query: 67  SEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTF 126
               +++ L   + +FG VD+ VN AGI   +    +K       +++  +LD NL   F
Sbjct: 62  DAASIESVLEKVRAEFGEVDILVNNAGITRDNLLMRMKD------DEWADILDTNLTSVF 115

Query: 127 NVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDL 186
            + + V   M +       + G II   SV    G  GQA Y+A+K G++G +  +AR++
Sbjct: 116 RLSKAVLRAMMKK------RVGRIITIGSVVGTMGNAGQANYAAAKAGLIGFSKSLAREI 169

Query: 187 APIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQ--AIIENP 244
           A  GI V  +APG   T +  +L E   + + ++VP   RLGDP E A+ V   A  E  
Sbjct: 170 ASRGITVNVVAPGFIETDMTRALNEDQRSGILAEVP-AGRLGDPQEIANAVAFLASDEAS 228

Query: 245 FLNGEVIRLDGAIRM 259
           ++ GE + ++G + M
Sbjct: 229 YITGETLHVNGGMYM 243


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: 8
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: 261
Length of database: 244
Length adjustment: 24
Effective length of query: 237
Effective length of database: 220
Effective search space:    52140
Effective search space used:    52140
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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