GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloB in Methanospirillum lacunae Ki8-1

Align Hydroxyacylglutathione hydrolase GloC; Accessory type II glyoxalase; Glyoxalase II 2; GlxII-2; EC 3.1.2.6 (characterized)
to candidate WP_109969325.1 DK846_RS12745 MBL fold metallo-hydrolase

Query= SwissProt::P75849
         (215 letters)



>NCBI__GCF_003173355.1:WP_109969325.1
          Length = 223

 Score = 66.2 bits (160), Expect = 4e-16
 Identities = 61/201 (30%), Positives = 97/201 (48%), Gaps = 21/201 (10%)

Query: 8   VTAFSQNCSLIWCEQTRLAALVDPGGDAE---KIKQEVDDSGLTLMQILLTHGHLDHVGA 64
           V   + NC +I  ++  L     P   A+    I+  ++     L  I+LTH H+DHVG 
Sbjct: 10  VDGVNGNCFIIVRDELTLIDTGMPKNSAKIVTYIQDTLNRKPSDLKTIILTHFHIDHVGD 69

Query: 65  AAELAQHYGVPVFGPEKEDEFW----LQGLP--AQSRMFGLE-----ECQPLTPDRWLNE 113
           A ++ +  G  V   E + ++     +Q +P      +F L        +P+ P+  L +
Sbjct: 70  ADDIKKLSGAKVAIHEADADYVAGRKIQPVPKGVMGWIFKLLIPLFFGSRPVEPEIKLKD 129

Query: 114 GDTISIGNVTLQVLHCPGHTPGHVVFFDDRAKLLISGDVI-FKGGVGRSDFPRGDHNQLI 172
           GDTI+     L  +H PGHTPG +  FD  +K+L +GDV+ F G   R      D N++ 
Sbjct: 130 GDTIA----GLISIHTPGHTPGSICLFDPASKILFAGDVLRFNGNKIRIGPSSLDLNEIK 185

Query: 173 SSIKDKLLPLGDDVIFIPGHG 193
            SI +K+  +  D I + GHG
Sbjct: 186 QSI-NKIAAIDFD-IMLSGHG 204


Lambda     K      H
   0.321    0.142    0.453 

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: 175
Number of extensions: 13
Number of successful extensions: 2
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: 215
Length of database: 223
Length adjustment: 22
Effective length of query: 193
Effective length of database: 201
Effective search space:    38793
Effective search space used:    38793
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: 45 (21.9 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