GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Caulobacter crescentus NA1000

Align Maleylacetoacetate isomerase; MAAI; GSTZ1-1; Glutathione S-transferase zeta 1; EC 5.2.1.2; EC 2.5.1.18 (characterized)
to candidate CCNA_02569 CCNA_02569 glutathione S-transferase

Query= SwissProt::P57113
         (216 letters)



>FitnessBrowser__Caulo:CCNA_02569
          Length = 209

 Score = 59.3 bits (142), Expect = 5e-14
 Identities = 47/170 (27%), Positives = 76/170 (44%), Gaps = 4/170 (2%)

Query: 17  SWRVRIALALKGIDYEIVPINLIKDGGQQFSEEFQTLNPMKQVPALKIDGITIGQSLAIL 76
           SW +R  LALK    +   + +    G+   +E   ++P +  PAL+   + I  SLAI 
Sbjct: 12  SWSLRPWLALKRAGVDFTELEVALRRGEATGDEIGCISPSRLAPALRDGDLVIWDSLAIC 71

Query: 77  EYLEETRPIPRLLPQDPQKRAIVRMISDLIASGIQPLQN---LSVLKQVGQENQMPWAQK 133
           EYL E  P  +L P DP  RA+ R     + SG Q L+    +++ +   + +     QK
Sbjct: 72  EYLAERYPDAKLWPDDPVLRALGRSACAEMHSGFQALRGECPMALDEPPRKLDLSEATQK 131

Query: 134 AITSGFNALEKILQSTAGKYCVGDEVSMADVCLAPQVANAERFKVDLSPY 183
            +         +L  + G + +GD  S+AD    P       + V L+ Y
Sbjct: 132 NVRRIVALWTGLLARSHGPFLLGD-WSIADAFYTPVATRFRTYDVRLADY 180


Lambda     K      H
   0.319    0.135    0.392 

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: 120
Number of extensions: 4
Number of successful extensions: 1
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: 216
Length of database: 209
Length adjustment: 21
Effective length of query: 195
Effective length of database: 188
Effective search space:    36660
Effective search space used:    36660
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 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