GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dpkA in Desulfoscipio geothermicus DSM 3669

Align Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase; Pyr2C/Pip2C reductase; N-methyl-L-amino acid dehydrogenase; NMAADH; EC 1.5.1.21; EC 1.4.1.17 (characterized)
to candidate WP_092484923.1 BM299_RS12810 Ldh family oxidoreductase

Query= SwissProt::Q5FB93
         (341 letters)



>NCBI__GCF_900115975.1:WP_092484923.1
          Length = 343

 Score =  132 bits (333), Expect = 1e-35
 Identities = 83/247 (33%), Positives = 123/247 (49%), Gaps = 5/247 (2%)

Query: 13  PFTELQSLLQAIFQRHGCSEAVARVLAHNCASAQRDGAHSHGVFRMPGYVSTLASGWVDG 72
           P  +L+ +   + + +G  E  A + A    SA   G  SHG+  +P YV  +  G VD 
Sbjct: 5   PAADLKKICVDVLKGYGVPEENADITASVMISASLRGIDSHGIAYLPVYVERIKRGVVDP 64

Query: 73  QATPQVSDVAAGYVRVDAAGGFAQPALAAARELLVAKARSAGIAVLAIHNSHHFAALWPD 132
           +A P++    A    VD   G  Q     A  L V KA ++    + + NS HF  +   
Sbjct: 65  KAQPEIVTETANTAVVDCKNGLGQVGGVFAMNLAVKKALASNTGFVGLRNSGHFGMVSYY 124

Query: 133 VEPFAEEGLVALSVVNSMTCVVPHGARKPLFGTNPIAFAAPCAEHDPIVFDMATSAMAHG 192
               A+   + L++ N+ + V P G  +PLFGTNPI+FA P  +   IV D ATSA+A  
Sbjct: 125 TMQAAKNNCIGLAMTNAPSSVAPFGGMEPLFGTNPISFAFPVKDRPDIVIDFATSAIART 184

Query: 193 DVQIAARAGQQLPEGMGVDADGQPTTDPKAILEG--GALLPFGGHKGSALSMMVELLAAA 250
            ++  A   Q++PEG  +  +G      K   EG  G LLP  G KG  L+++ E+L+A 
Sbjct: 185 KLRNMAAEKQEIPEGWALSKEGYMA---KTADEGYEGVLLPAAGVKGYGLAIIAEVLSAV 241

Query: 251 LTGGHFS 257
           LTG  F+
Sbjct: 242 LTGAAFT 248


Lambda     K      H
   0.318    0.132    0.398 

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: 213
Number of extensions: 10
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: 341
Length of database: 343
Length adjustment: 29
Effective length of query: 312
Effective length of database: 314
Effective search space:    97968
Effective search space used:    97968
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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