GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Shewanella halifaxensis HAW-EB4

Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_012277980.1 SHAL_RS15025 gamma-carboxygeranoyl-CoA hydratase

Query= reanno::pseudo5_N2C3_1:AO356_01590
         (273 letters)



>NCBI__GCF_000019185.1:WP_012277980.1
          Length = 293

 Score =  245 bits (625), Expect = 9e-70
 Identities = 133/254 (52%), Positives = 172/254 (67%), Gaps = 2/254 (0%)

Query: 15  GVATLWLSRESKNNAFNAEMIRELILALDHVSSDPNLRFLLIRGRGKHFSAGADLAWMQQ 74
           GVA + L R  K+NAF+  MI E+I  L+H S++   + L+I+  GK+FSAGADL WM++
Sbjct: 26  GVAQMVLDRADKHNAFDEVMISEMIKVLEHFSANVQCQVLVIKANGKNFSAGADLNWMRK 85

Query: 75  SAELDYHTNLDDARELAELMYNLAKLKIPTLAVVQGAAFGGALGLISACDMAIGADEAQF 134
            A++D+  NL DA ELA+LM  L K   PT+A+VQGAAFGGALGLI   D+AI    A F
Sbjct: 86  QAKMDFGQNLSDANELAKLMSLLDKFPKPTIALVQGAAFGGALGLICCSDIAIANQRASF 145

Query: 135 CLSEVRIGLAPAVISPFVVQAIGERAARRYALTAERFDGQRAKEIGLLSESYPVETLDQQ 194
           CLSEV++GL PAVISP+V +A+G+RAARRY LTAERFD Q+A E+ ++ E    + LD  
Sbjct: 146 CLSEVKLGLIPAVISPYVTRAMGQRAARRYMLTAERFDVQKALELQVIHEVN--DDLDAA 203

Query: 195 VEQWIDNLLLNSPAAMRASKELLREVGNGALTPALRRYTENAIARIRVSPEGQEGLRAFL 254
            +  ID LL NSP  M   K LL  + +G +      YT   IARIRVS EGQEGL AF 
Sbjct: 204 AQPMIDALLCNSPLGMTWVKTLLLSLEDGVIDQNTLDYTSERIARIRVSEEGQEGLNAFF 263

Query: 255 QKRAPNWQAESNNN 268
           +KR+P W A ++ N
Sbjct: 264 EKRSPQWPATTDFN 277


Lambda     K      H
   0.318    0.133    0.382 

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: 232
Number of extensions: 5
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: 273
Length of database: 293
Length adjustment: 26
Effective length of query: 247
Effective length of database: 267
Effective search space:    65949
Effective search space used:    65949
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 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