GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Dyadobacter tibetensis Y620-1

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_025763648.1 X939_RS0112665 aspartate carbamoyltransferase catalytic subunit

Query= BRENDA::Q51742
         (315 letters)



>NCBI__GCF_000566685.1:WP_025763648.1
          Length = 307

 Score =  119 bits (297), Expect = 1e-31
 Identities = 97/316 (30%), Positives = 157/316 (49%), Gaps = 21/316 (6%)

Query: 2   VVSLAGRDLLCLQDYTAEEIWTILETAKMFKIWQKIGKPHRL---LEGKTLAMIFQKPST 58
           +  L+ R LL +++    +I TILETA  FK  + I +P +    L   T+A +F + ST
Sbjct: 1   MTKLSVRHLLGIKNLNESDIHTILETATQFK--EVINRPIKKVPSLRDITIANVFFENST 58

Query: 59  RTRVSFEVAMAHLGGHALYLNAQDLQLRRGETIADTAR-VLSRYVDAIMARVYDHKDVED 117
           RTR+SFE+A   L    +  ++    +++GET+ DT   +L+  VD I+ R         
Sbjct: 59  RTRLSFELAEKRLSADVVNFSSSGSSVKKGETLLDTVNNILAMKVDMIVMRHSSPGAPHY 118

Query: 118 LAKYATVPVIN-GLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGD--GNNVAHSLMIA 174
           LA + +  V+N G     HP QAL D  ++ EK G + G K+  +GD   + VA S +  
Sbjct: 119 LANHISANVVNAGDGTHEHPTQALLDAFSMQEKLGDLAGKKIAIIGDITHSRVALSNIFC 178

Query: 175 GTKLGADVVVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYT-DVWA 233
             KLGA+V+V  P    P         ++  E G   ++ HD   A++  DV     +  
Sbjct: 179 LQKLGAEVMVCGPSTLIP---------KHLGELG--VKISHDVRAALQWCDVANVLRIQL 227

Query: 234 SMGQEAEAEERRKIFRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWD 293
              Q       R+  + + +NK ++     D + MH  P +RG E++ D  DS +S++ +
Sbjct: 228 ERQQIKYFPSLREYAQFYGINKQMLDEVDKDIVLMHPGPINRGVELSSDAADSHHSIILN 287

Query: 294 QAENRLHAQKAVLALV 309
           Q EN +  + AVL L+
Sbjct: 288 QVENGVAIRMAVLYLL 303


Lambda     K      H
   0.319    0.134    0.400 

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: 183
Number of extensions: 8
Number of successful extensions: 4
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: 315
Length of database: 307
Length adjustment: 27
Effective length of query: 288
Effective length of database: 280
Effective search space:    80640
Effective search space used:    80640
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 (21.8 bits)
S2: 48 (23.1 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