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_025763134.1 X939_RS0110055 N-acetylornithine carbamoyltransferase

Query= reanno::HerbieS:HSERO_RS07185
         (304 letters)



>NCBI__GCF_000566685.1:WP_025763134.1
          Length = 316

 Score =  123 bits (309), Expect = 5e-33
 Identities = 104/328 (31%), Positives = 156/328 (47%), Gaps = 46/328 (14%)

Query: 3   IKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFEA 62
           +KH+L F D T  +   +I    V KR    +       ++T+ ++F  +S RTR+S + 
Sbjct: 1   MKHFLSFEDVT--DLSQLITSGIVAKRN--PFGDQELGKNKTIGLLFFNSSLRTRISTQK 56

Query: 63  GMHQMGGAAIYLNTRDSQLG------------RGEPVEDAAQVMSRMCDVIMIRTYG--- 107
               +G   I +N      G            + E V++AA V+   CD+I IR++    
Sbjct: 57  AAQNLGLNVITMNVGQDGWGLEMEEGVVMNGDKAEHVKEAAAVIGSYCDIIGIRSFASLT 116

Query: 108 ------QEII-ERFAKHSRVPVINGLTNEQHPCQVLADVFTYIEHHGSIQGKIV-AWVGD 159
                 QEI+ ++F K++ VP++N  +  +HP Q LAD  T  E     + K+V  W+  
Sbjct: 117 DREKDYQEIVFQQFKKYAGVPIVNLESATRHPLQSLADCITIEEFKLKERPKVVLTWLPH 176

Query: 160 AN-------NMLYSWLQAAEVFGFHVNVSTPKGYDIDPAQVSPGNKNYTFFADPADACQD 212
                    N    W+  A+V    + V+ PKGYD+ P  V  G   Y    D   A + 
Sbjct: 177 FKPLPQAVANSFCEWMNHADV---ELVVTHPKGYDLSPEFVGKGQVIY----DQNKALEG 229

Query: 213 ADLVTTDVWTSMGFEAENNARLKAFDGWIVDQAKMARAKKDALFMHCLPAHRGEEVAAEV 272
           AD V    W+S  FE      L +   W++ +AKMA    +  FMHCLP  R  +VA EV
Sbjct: 230 ADFVYGKNWSS--FEPYGQV-LNSDPSWMITEAKMALTD-NGKFMHCLPLRRNMKVADEV 285

Query: 273 IDGPQSVVWEEAENR-LHVQKALLEYLV 299
           +DGP+S+V E+A NR    Q AL E L+
Sbjct: 286 LDGPRSLVIEQAANREWSAQAALREILI 313


Lambda     K      H
   0.321    0.135    0.409 

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: 214
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: 304
Length of database: 316
Length adjustment: 27
Effective length of query: 277
Effective length of database: 289
Effective search space:    80053
Effective search space used:    80053
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 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