GapMind for catabolism of small carbon sources

 

Aligments for a candidate for arcB in Desulfovibrio vulgaris Miyazaki F

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate 8500677 DvMF_1425 aspartate carbamoyltransferase catalytic subunit (RefSeq)

Query= curated2:Q8DJW4
         (310 letters)



>lcl|FitnessBrowser__Miya:8500677 DvMF_1425 aspartate
           carbamoyltransferase catalytic subunit (RefSeq)
          Length = 325

 Score = 95.5 bits (236), Expect = 1e-24
 Identities = 89/305 (29%), Positives = 134/305 (43%), Gaps = 22/305 (7%)

Query: 13  RDLLSIADLSRAEAEYLLDLAAQMK------IGKVAPQCPKVLGLLFQKASTRTRVSFTV 66
           +DLL +  L+RAE  +LLD AAQ        + KV     K + L F + STRT+ SF V
Sbjct: 12  KDLLDVTQLTRAELFHLLDTAAQFHDINRRPVKKVPTLKGKSVVLFFAEPSTRTKTSFDV 71

Query: 67  AMYQLGGQVIDLNPQSTQVGRGEPLTDTARVLDRYL-DAVAIRTYGQAELQLFADYARIP 125
           A  +L      L    + + +GE L DTA  L     D + IR       Q  A+     
Sbjct: 72  AGKRLSADTFSLAKSGSSLSKGESLKDTALTLQAMTPDIIVIRHSSSGAAQFLAERLDCS 131

Query: 126 VINALTD-REHPCQILADLLTLRESFG-TLAGLTLCYIGD--GNNVAHSLLLGCALLGVN 181
           V+NA      HP Q L D  +LR+ +G T  G TL  +GD   + VA S +   + LGV 
Sbjct: 132 VVNAGDGWHAHPTQALLDCYSLRQVWGDTFEGRTLLILGDIAHSRVARSNVHLLSSLGVK 191

Query: 182 IRVASPPQFAPLADIVAQAKALSGGKSEVAVLTDPQAAAKGAHALYT-DVWASMGQEAEA 240
           +R+ +P    P                 V +      A +G  A+    +     Q    
Sbjct: 192 VRLCAPRTLLPAGV----------HNWPVTIFNRLDDAVQGVDAVMCLRLQLERQQAGLL 241

Query: 241 GDRQPIFQPYQINDHLLALADPRAIVLHCLPAHRDEEITASVLEGPQSRVWEQAENRLHV 300
            D +   Q + ++   L +A P A VLH  P +R  EI++ + + P+S + +Q    +  
Sbjct: 242 PDLREYAQRFCLSPRHLTMAAPSARVLHPGPMNRGLEISSVLADAPESLILDQVAAGVAT 301

Query: 301 QKALL 305
           + A+L
Sbjct: 302 RMAIL 306


Lambda     K      H
   0.321    0.135    0.392 

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: 200
Number of extensions: 8
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 310
Length of database: 325
Length adjustment: 27
Effective length of query: 283
Effective length of database: 298
Effective search space:    84334
Effective search space used:    84334
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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