GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Caulobacter crescentus NA1000

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate CCNA_02525 CCNA_02525 aspartate carbamoyltransferase

Query= curated2:Q8DJW4
         (310 letters)



>FitnessBrowser__Caulo:CCNA_02525
          Length = 332

 Score =  109 bits (273), Expect = 8e-29
 Identities = 104/327 (31%), Positives = 159/327 (48%), Gaps = 35/327 (10%)

Query: 4   RFVMETLRGR-------DLLSIADLSRAEAEYLLDLA-AQMKIGKVAPQCPKVLGLL--- 52
           R  +ET+R R         LS  DL+  +A  LLDLA A + + +   Q  K L +L   
Sbjct: 10  REAIETIRARVFAFPKRHFLSAGDLNAPQAADLLDLADAFVALNR---QTSKTLDILKGR 66

Query: 53  -----FQKASTRTRVSFTVAMYQLGGQVIDLNPQSTQVGRGEPLTDTARVLDRYL-DAVA 106
                F + STRT+ SF +A  +LG  V+++NP+++ V +GE L DTA  L+    D + 
Sbjct: 67  TLMNLFFENSTRTQSSFELAGKRLGADVVNMNPKTSSVAKGETLIDTAVTLNAMRPDLLV 126

Query: 107 IRTYGQAELQLFADYARIPVINALT-DREHPCQILADLLTLRESFGTLAGLTLCYIGD-- 163
           +R        L +      V+NA     EHP Q L D L++R +FG ++GLT+   GD  
Sbjct: 127 VRHASSGAASLLSQKVSGHVVNAGDGQHEHPTQALLDALSIRRAFGRVSGLTVAICGDVL 186

Query: 164 GNNVAHSLLLGCALLGVNIRVASPPQFAPLADIVAQAKALSGGKSEVAVLTDPQAAAKGA 223
            + VA S +     LG ++R+  PP   P     AQA+     +  VAV  D ++   GA
Sbjct: 187 HSRVARSNVALLHTLGASVRLVGPPTLMP-----AQAE-----RWGVAVHHDMKSGLAGA 236

Query: 224 H-ALYTDVWASMGQEAEAGDRQPIFQPYQINDHLLALADPRAIVLHCLPAHRDEEITASV 282
              +   +     Q A     +  F+ Y ++   L+ A P A V+H  P +R  EI + V
Sbjct: 237 DVVMMLRLQLERMQGAFVPSTREYFRFYGLDREKLSRAAPGAKVMHPGPMNRGVEIDSDV 296

Query: 283 LEGPQ-SRVWEQAENRLHVQKALLASL 308
            + P  S + +Q E  +  + A+LASL
Sbjct: 297 ADDPAVSLIQDQVEMGVAARMAVLASL 323


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: 231
Number of extensions: 15
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: 310
Length of database: 332
Length adjustment: 28
Effective length of query: 282
Effective length of database: 304
Effective search space:    85728
Effective search space used:    85728
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 (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