GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Pseudovibrio axinellae Ad2

Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_068003992.1 PsAD2_RS06355 SDR family oxidoreductase

Query= reanno::Koxy:BWI76_RS01745
         (267 letters)



>NCBI__GCF_001623255.1:WP_068003992.1
          Length = 263

 Score =  128 bits (322), Expect = 1e-34
 Identities = 91/271 (33%), Positives = 135/271 (49%), Gaps = 32/271 (11%)

Query: 5   LNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDI--HGGDKHQSS----GNYNFWPT 58
           + L  K+  VTGGA GIG AI    L  GA V + D     G+  Q +    G+  F   
Sbjct: 1   MKLDRKVAIVTGGAQGIGYAIAQRFLEDGAKVMISDADERAGEAAQEALSEFGHVAFCHC 60

Query: 59  DISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNI 118
           D+    +V   V + +  FG ID LVNNAGV          A      L+E  F++++ +
Sbjct: 61  DVGVRLDVRNMVANTLDEFGDIDVLVNNAGVT---------AAGDFLTLSEDDFDRVLQV 111

Query: 119 NQKGVFLMSQAVARQMVKQ-----RSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRS 173
           N KG FL SQAVAR MV++      +G+I+N+SS + +     Q  Y  +K  LN  T  
Sbjct: 112 NLKGAFLCSQAVARHMVEKIEEGGSAGIIINISSVNSVLAIPEQVPYTVSKGGLNQLTNV 171

Query: 174 WSKELGKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSG 233
            +  L K+GIRV G+ PG +E   L+    +E+          ++ +  S+   PLGR G
Sbjct: 172 SAVALAKYGIRVNGIGPGSIETDMLKAVVQDES----------KMNKVLSRT--PLGRLG 219

Query: 234 RLTEVADFVCYLLSERASYMTGVTTNIAGGK 264
           + +E+A    +L S+ ASY++G T    G +
Sbjct: 220 QPSEIAGVASFLASDDASYVSGQTIFADGAR 250


Lambda     K      H
   0.315    0.132    0.378 

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: 173
Number of extensions: 10
Number of successful extensions: 5
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: 267
Length of database: 263
Length adjustment: 25
Effective length of query: 242
Effective length of database: 238
Effective search space:    57596
Effective search space used:    57596
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: 42 (22.0 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