GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Phaeobacter inhibens BS107

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate GFF294 PGA1_c03060 aspartate carbamoyltransferase PyrB

Query= curated2:Q8TKT5
         (302 letters)



>FitnessBrowser__Phaeo:GFF294
          Length = 331

 Score = 86.3 bits (212), Expect = 9e-22
 Identities = 90/310 (29%), Positives = 136/310 (43%), Gaps = 18/310 (5%)

Query: 2   KRDVLSITDLSKEEIYELLESAADL-KAKRKAGESTEYLKNKSLGMIFEKSSTRTRVSFE 60
           +R +L I  L   EI  +L+ A    +  R+  +    L   +   +F ++STRT+ SFE
Sbjct: 15  QRHLLGIEPLKPHEITAILDLADSYAELNRRPDKHANALSGLTQVNMFFENSTRTQASFE 74

Query: 61  VAMTDFGGHALYLNSRDIQVGRGETIEDTARTLSGYLHGLMARVMSHD-TVEKLAKYSTM 119
           +A    G   + +  +   + +GET+ DTA TL+     L+     H   V+ LA+    
Sbjct: 75  IAGKRLGADVMNMAMQASSIKKGETLIDTAMTLNAMHPDLLVVRHPHSGAVDLLAQKVNC 134

Query: 120 PVINALSDR-EHPCQILGDFMTIMEFKKKFEGLKFAWVGD--GNNVCNSALLGSAIMGME 176
            V+NA   R EHP Q L D +TI   K +   L  A  GD   + V  S L+    M   
Sbjct: 135 AVLNAGDGRHEHPTQALLDALTIRRAKGRLHRLNIAICGDVAHSRVARSNLILLGKMENR 194

Query: 177 FAVACPKGYEPK--AEFLEQAKALGGKFTITDDPKVAAKDADIIYT-DVWVSMGDEAEQE 233
             +  P    P   A+F  +         I DD +   KD D++    +     D     
Sbjct: 195 IRLIGPPTLVPGHFADFGAE---------IYDDMREGLKDVDVVMMLRLQKERMDGGFIP 245

Query: 234 KRLREFASFQVNTELLGVAKPDVIVMHCLPARRGLEITDEVMDGPN-SVIFEEAENRLHA 292
                +  + ++ E L +AKPD IVMH  P  RG+EI   + D  N SVI E+ E  +  
Sbjct: 246 SEREYYHRYGLDAEKLALAKPDAIVMHPGPMNRGVEIDGTLADDINRSVIQEQVEMGVAV 305

Query: 293 QKALILKLMR 302
           + A +  L R
Sbjct: 306 RMAAMDLLAR 315


Lambda     K      H
   0.318    0.134    0.378 

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: 203
Number of extensions: 9
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: 302
Length of database: 331
Length adjustment: 27
Effective length of query: 275
Effective length of database: 304
Effective search space:    83600
Effective search space used:    83600
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: 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