GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligB in Magnetospirillum magneticum AMB-1

Align protocatechuate 4,5-dioxygenase (subunit 1/2) (EC 1.13.11.8) (characterized)
to candidate WP_011382705.1 AMB_RS01310 protocatechuate 3,4-dioxygenase subunit beta

Query= BRENDA::G2IQQ3
         (302 letters)



>NCBI__GCF_000009985.1:WP_011382705.1
          Length = 278

 Score =  253 bits (646), Expect = 4e-72
 Identities = 126/284 (44%), Positives = 177/284 (62%), Gaps = 13/284 (4%)

Query: 1   MARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYND 60
           MA++  GI  +H+P +G AI      + YW P F G+ P+  W+ +    PDV ++VYND
Sbjct: 1   MAKIVGGINVTHVPYIGRAIAGNLQQDAYWKPFFDGFPPVHAWLDKV--KPDVAVVVYND 58

Query: 61  HASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIM 120
           H   F ++ +PTF+IG A  +  ADEGWG   V   KG  DL+WH+  SLI  EFD+T  
Sbjct: 59  HGLNFFLDKMPTFSIGAAAEYSNADEGWGIPTVAPFKGDQDLSWHLIDSLIEAEFDLTTC 118

Query: 121 NQMDVDHGCTVPLSMIFGEPEEWPCK-----VIPFPVNVVTYPPPSGKRCFALGDSIRAA 175
            +M VDH  T+PL ++      WP +      +P   N V +P PS KRC A G +I  A
Sbjct: 119 QEMLVDHAFTLPLELL------WPTRNAALRTVPICQNTVQFPLPSAKRCLAFGRAINKA 172

Query: 176 VESFPEDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRE 235
           +ES+  D  V V GTGG+SHQL+G RAG INK+FDL F+DKL+SDP+ +++  +   +  
Sbjct: 173 IESWDSDARVVVLGTGGLSHQLEGTRAGFINKKFDLEFMDKLVSDPDWVTQYSNEDLVEL 232

Query: 236 SGSEGIELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQ 279
           +G++GIEL+ WL  RGAL  KV+ ++T YHIP SNTA G + ++
Sbjct: 233 TGTQGIELLNWLTCRGALGGKVKAVHTNYHIPISNTAAGLLAME 276


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: 278
Number of extensions: 13
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: 278
Length adjustment: 26
Effective length of query: 276
Effective length of database: 252
Effective search space:    69552
Effective search space used:    69552
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 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