GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Dietzia timorensis ID05-A0528

Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate WP_067472746.1 BJL86_RS11635 mycofactocin-coupled SDR family oxidoreductase

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



>NCBI__GCF_001659785.1:WP_067472746.1
          Length = 271

 Score = 67.8 bits (164), Expect = 2e-16
 Identities = 76/283 (26%), Positives = 120/283 (42%), Gaps = 44/283 (15%)

Query: 9   GKTVIVTGASSGIGKAIVDELLSLKVKVANFDLTDNGE--------------KHENL--- 51
           GK V +TG + G G+       +   K+   D+ D                 + E L   
Sbjct: 6   GKVVYITGIARGQGRKYATRFAAEGAKIIGCDIADKASAWTRYPASTPEDMAETEKLVAE 65

Query: 52  ----LFQKV-DVTSREQVEASVAAVVEHFG-TVDAVVNNAGI-NIPRLLVDPKDPHGQYE 104
               LF +V DV      +  VA  V HFG  +D VV NAGI N  +L          +E
Sbjct: 66  AGGELFARVGDVRDLAFQQQLVADGVAHFGGRLDIVVANAGICNWGKL----------WE 115

Query: 105 LDDATFEKITMINQKGLYLVSQA-VGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKA 163
           +D+  +     IN  G +   +A +  +L A   G I  ++S AGL+    Q+AY+ +K 
Sbjct: 116 MDEEQWNDTIDINLTGYWKTLKASIPHMLEAGNGGAITLLSSVAGLKSMPMQAAYSASKH 175

Query: 164 AVYSYTRSWAKELGKYGVRVVGIAP-GIMEATGLRTLAYEEALGYTRGKTVEEIRAGYAS 222
            V    ++ AKELG++G+RV  + P G++   G +     E         + E    +  
Sbjct: 176 GVVGLAQTAAKELGRHGIRVNTVHPYGVLTPMGGKDEGAHEVF-----NDMPEFLPHFEP 230

Query: 223 TTTTPLGRSGKLSEVADLVAYYISDRSSYITGITTNVAGGKTR 265
                +    K  ++AD V +  S+++  ITG T  V  G T+
Sbjct: 231 ILGMGM---AKTDDIADSVLFLSSEQARTITGTTFTVDMGATK 270


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: 188
Number of extensions: 7
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: 266
Length of database: 271
Length adjustment: 25
Effective length of query: 241
Effective length of database: 246
Effective search space:    59286
Effective search space used:    59286
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