GapMind for catabolism of small carbon sources

 

Alignments for a candidate for QDPR in Echinicola vietnamensis KMM 6221, DSM 17526

Align oxygen-insensitive NAD(P)H nitroreductase; EC 1.-.-.-; EC 1.5.1.34 (characterized)
to candidate Echvi_0893 Echvi_0893 Nitroreductase

Query= CharProtDB::CH_002389
         (217 letters)



>FitnessBrowser__Cola:Echvi_0893
          Length = 215

 Score = 79.0 bits (193), Expect = 6e-20
 Identities = 61/202 (30%), Positives = 101/202 (50%), Gaps = 10/202 (4%)

Query: 10  RHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYV 69
           R++TK  +  K +  E+ + I    + SPSS+  QP+  IV +  E K ++   A     
Sbjct: 10  RYATKKMNG-KAVPQEKVDYILEAARLSPSSSGLQPYRVIVVTDPEIKEKMKPIA----- 63

Query: 70  FNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHR 129
           +++ ++ DASH++VF A     +  +K V  +          +  A  ++    ++ +  
Sbjct: 64  WDQSQITDASHILVFAAWENYTEEKIKAVFKETLTARGLPLDKMDAYRERLWGMYSQLP- 122

Query: 130 KDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVV 189
           ++ H  A   AKQ Y+  G  +   A   +DA P+EGFD   LDA  GLKE G  S VV+
Sbjct: 123 EEWH--AHHAAKQAYIAFGTAIAAAAEQKVDATPMEGFDPEGLDALLGLKELGLKSAVVL 180

Query: 190 PVGHHSVE-DFNATLPKSRLPQ 210
           P+G+   E D+ A + K R P+
Sbjct: 181 PLGYRDEENDWLAGMKKFRTPK 202


Lambda     K      H
   0.317    0.131    0.379 

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: 132
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: 217
Length of database: 215
Length adjustment: 22
Effective length of query: 195
Effective length of database: 193
Effective search space:    37635
Effective search space used:    37635
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: 45 (21.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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