GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloB in Caulobacter crescentus NA1000

Align Hydroxyacylglutathione hydrolase; EC 3.1.2.6; Glyoxalase II; Glx II (uncharacterized)
to candidate CCNA_02959 CCNA_02959 Zn-dependent hydrolase, glyoxalase II family

Query= curated2:Q4FP49
         (239 letters)



>FitnessBrowser__Caulo:CCNA_02959
          Length = 286

 Score = 83.2 bits (204), Expect = 5e-21
 Identities = 58/190 (30%), Positives = 86/190 (45%), Gaps = 34/190 (17%)

Query: 14  SYLIVDKAKNIACVIDP-------------SEAKPVIKYLEDKNIHLKYILNTHHHYDHV 60
           SYL+VD A   A +IDP             + A  ++  + D+ +HL Y+L TH H DH+
Sbjct: 17  SYLVVDPATKTAAIIDPVLDFEPKAGKLSTTSADALLAAVRDQGLHLAYVLETHAHADHL 76

Query: 61  GGNKELKEKYGAS-VIGYK-----------GDKDRIPE---IDILVGDQDIWHEENFQAK 105
                ++ K GA  VIG K            + D  P+    D+L+ + D          
Sbjct: 77  SAADLIRRKTGAKIVIGAKITEVQKTFIPVFESDARPDGAVFDVLMEEGDALPLGELSIA 136

Query: 106 IFHIPGHTLGHICFYFYNEESVFTGDTLFSLGCGKIFE----GTYSQMYNSLMKIKALPE 161
             H PGHT    C  +   ++ F GDTLF    G        G    +Y S+ K+ ALP+
Sbjct: 137 ALHTPGHT--PACMTYRIGDAAFVGDTLFMPDYGTARADFPGGDARTLYRSIQKVLALPD 194

Query: 162 KTKIYCGHEY 171
           +T+I+ GH+Y
Sbjct: 195 ETRIFVGHDY 204


Lambda     K      H
   0.319    0.139    0.419 

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: 150
Number of extensions: 6
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: 239
Length of database: 286
Length adjustment: 25
Effective length of query: 214
Effective length of database: 261
Effective search space:    55854
Effective search space used:    55854
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 (21.7 bits)
S2: 47 (22.7 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