GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaG in Caulobacter crescentus NA1000

Align protocatechuate 3,4-dioxygenase (subunit 2/2) (EC 1.13.11.3) (characterized)
to candidate CCNA_02491 CCNA_02491 protocatechuate 3,4-dioxygenase beta chain

Query= BRENDA::Q0SH27
         (237 letters)



>FitnessBrowser__Caulo:CCNA_02491
          Length = 235

 Score =  268 bits (685), Expect = 7e-77
 Identities = 127/228 (55%), Positives = 156/228 (68%), Gaps = 1/228 (0%)

Query: 7   HFEAGHEANAPLLFPEYKTTRLRSPKNDLILIPQRLGEITGPVFGDADVAKGEN-DMTHA 65
           +F+       P L   Y +T  RSP+  L+ IP  L E TGP      +  G   D+T  
Sbjct: 4   NFKREDAGQPPSLHAPYASTVPRSPRQPLVRIPHTLTETTGPSNAWPRLMGGAMADLTTQ 63

Query: 66  NGGEAQGQRIIVHGRVLDSAGKPIPDTLIEVWQANAGGRYRHKMDSWPAPLDPHFNGVAR 125
           +    QGQRIIV GRVLD  G+P+P+T++E+WQANA GRY HK D W APLDP+F G  R
Sbjct: 64  HKAMPQGQRIIVSGRVLDEDGRPVPNTVMEIWQANAAGRYIHKKDQWDAPLDPNFTGAGR 123

Query: 126 CLTDKQGHYEFTTIKPGAYPWGNHHNAWRPAHIHFSLFGQAFTQRLVTQMYFPDDPFFFQ 185
            +TD +G Y+F +I+PGAYPWGNHHNAWRPAHIH SL G AF  RLVTQMYFPDDP    
Sbjct: 124 VITDDEGRYQFVSIRPGAYPWGNHHNAWRPAHIHLSLLGPAFATRLVTQMYFPDDPLIEI 183

Query: 186 DPIYNSVPEAARERMISTFDYDHTRDNWAVGFKFDIVLRGRDATPFED 233
           DPI N+VP   R+R++S FD + T+ NWA+G+ FD+VLRGRD TPFED
Sbjct: 184 DPIANAVPLPYRQRLVSRFDIEATKPNWALGYLFDVVLRGRDQTPFED 231


Lambda     K      H
   0.322    0.140    0.458 

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: 237
Number of extensions: 8
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: 237
Length of database: 235
Length adjustment: 23
Effective length of query: 214
Effective length of database: 212
Effective search space:    45368
Effective search space used:    45368
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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