GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligB in Pandoraea thiooxydans ATSB16

Align protocatechuate 4,5-dioxygenase (subunit 1/2) (EC 1.13.11.8) (characterized)
to candidate WP_047212489.1 PATSB16_RS02570 protocatechuate 3,4-dioxygenase

Query= BRENDA::G2IQQ3
         (302 letters)



>NCBI__GCF_001931675.1:WP_047212489.1
          Length = 280

 Score =  336 bits (862), Expect = 3e-97
 Identities = 152/280 (54%), Positives = 212/280 (75%), Gaps = 3/280 (1%)

Query: 1   MARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYND 60
           MAR+  GI +SH+PA+GAAI  G + + YW P+F+G  P R+W+      PD+ I++YND
Sbjct: 1   MARIVAGIGTSHVPAIGAAIDHGKTADPYWRPLFEGVAPAREWLAAIA--PDIAIVIYND 58

Query: 61  HASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLIL-DEFDMTI 119
           HAS F +++ PTFA+G AETF P DEG+GPR VP  +G+P+ AWH+A+SLIL D FD+ +
Sbjct: 59  HASRFALDVTPTFALGMAETFAPHDEGYGPRAVPVCEGNPEFAWHLAESLILKDGFDLAM 118

Query: 120 MNQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESF 179
           +++M VDHG TVPLS++FG+P  WPC+VIP  VNV+ YP P+ +RC  LG ++R A++S+
Sbjct: 119 VSEMTVDHGLTVPLSLLFGQPTRWPCQVIPLCVNVIQYPQPTAQRCHQLGQALRRAIDSY 178

Query: 180 PEDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSE 239
             D  V V+GTGGMSHQLQG RAGLIN ++D  ++D++ +DP  L+ + H + LRE+GSE
Sbjct: 179 APDAKVAVFGTGGMSHQLQGERAGLINPDYDRMWLDRMETDPGSLAVIGHAELLREAGSE 238

Query: 240 GIELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQ 279
           G+E++MWLIMRGAL E VR ++ FYH+PASNTA G + L+
Sbjct: 239 GLEIIMWLIMRGALDEAVRRVHRFYHVPASNTAYGLLALE 278


Lambda     K      H
   0.319    0.138    0.439 

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: 296
Number of extensions: 10
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: 280
Length adjustment: 26
Effective length of query: 276
Effective length of database: 254
Effective search space:    70104
Effective search space used:    70104
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