GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Erythrobacter gangjinensis K7-2

Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate WP_047007388.1 AAW01_RS11455 SDR family oxidoreductase

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



>NCBI__GCF_001010925.1:WP_047007388.1
          Length = 266

 Score =  107 bits (268), Expect = 2e-28
 Identities = 88/274 (32%), Positives = 132/274 (48%), Gaps = 35/274 (12%)

Query: 9   GKTVIVTGASS------GIGKAIVDELLSLKVKVANFDLTDNGEKHE------NLLFQKV 56
           GKT++VTG+        GI +A  DE  +  V     D   +G   E       +   + 
Sbjct: 6   GKTIVVTGSGKEKGLGQGILQAFADEGANCVVSDVRLDDEVDGVADELRQRGAKVATVQC 65

Query: 57  DVTSREQVEASVAAVVEHFGTVDAVVNNAGINI---PRLLVDPKDPHGQYELDDATFEKI 113
           DV+     +A VA  ++HFG+VD  VNNAGI     P L VD  D           ++++
Sbjct: 66  DVSDAASCQALVAQALDHFGSVDVFVNNAGIGFKMKPLLDVDTADE----------WDQV 115

Query: 114 TMINQKGLYLVSQAVGRLLV-AKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSW 172
             +N  G +  +QA  R +V A K G IIN+AS+A   G     AY  +K  +   TR+ 
Sbjct: 116 LAVNLSGAFYCTQAAARAMVDAGKGGRIINIASQAAKTGFPHLPAYVSSKHGMVGLTRAS 175

Query: 173 AKELGKYGVRVVGIAPGIMEATGL---RTLAYEEALGYTRGKTVEEIRAGYASTTTTPLG 229
           A ELG +G+ V  I P  +  TGL   +   + + LG+ +   VE+  A  A+    P+G
Sbjct: 176 AVELGAHGITVNAICPNHV-TTGLGAQQNEYFSKLLGFAK---VEDYLANMAA--KNPMG 229

Query: 230 RSGKLSEVADLVAYYISDRSSYITGITTNVAGGK 263
           R G  S+ A    +  SD + Y+TG   N++GG+
Sbjct: 230 RPGLPSDTAAACLWLASDEAVYVTGEALNISGGE 263


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: 192
Number of extensions: 15
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: 266
Length adjustment: 25
Effective length of query: 241
Effective length of database: 241
Effective search space:    58081
Effective search space used:    58081
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