GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Amantichitinum ursilacus IGB-41

Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate WP_053937509.1 WG78_RS09155 3-oxoacyl-ACP reductase FabG

Query= metacyc::MONOMER-13092
         (266 letters)



>NCBI__GCF_001294205.1:WP_053937509.1
          Length = 247

 Score =  129 bits (324), Expect = 6e-35
 Identities = 90/267 (33%), Positives = 135/267 (50%), Gaps = 33/267 (12%)

Query: 5   LNIAGKTVIVTGASSGIGKAIVDELLSLKVKVANFDLTDNGEKHENLLFQ---------K 55
           +++ GK  +VTGAS GIG+AI  EL  L   V     +  G        Q         +
Sbjct: 1   MSLEGKVALVTGASRGIGQAIALELGRLGATVVGTATSQEGADAITAYLQAAGLKGHGLR 60

Query: 56  VDVTSREQVEASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKITM 115
           + VT     EA V+ + +  G +  +VNNAGI    LL+  KD           ++ I  
Sbjct: 61  LQVTEDGACEALVSQIEKDSGAIAVLVNNAGITRDNLLMRMKDDE---------WDAIMA 111

Query: 116 INQKGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKE 175
            N K +Y +S+AV R ++  + G I+N+AS  G  G+ GQ+ Y+  KAA++ +T+S A+E
Sbjct: 112 TNLKPVYQLSKAVIRGMMKARWGRIVNIASVVGATGNPGQTNYSAAKAALFGFTKSLARE 171

Query: 176 LGKYGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLS 235
           +G  G+ V  +APG ++    R L  E+     + K VE I           LGR G   
Sbjct: 172 IGSRGITVNAVAPGFIDTDMTRGLPDEQ-----KAKLVESI----------ALGRLGAAQ 216

Query: 236 EVADLVAYYISDRSSYITGITTNVAGG 262
           ++AD VA+  SD++ YITG T +V GG
Sbjct: 217 DIADAVAFLSSDKAGYITGNTLHVNGG 243


Lambda     K      H
   0.313    0.131    0.361 

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: 155
Number of extensions: 10
Number of successful extensions: 4
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: 266
Length of database: 247
Length adjustment: 24
Effective length of query: 242
Effective length of database: 223
Effective search space:    53966
Effective search space used:    53966
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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