GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Burkholderia phytofirmans PsJN

Align Maleylacetoacetate isomerase; MAAI; GSTZ1-1; Glutathione S-transferase zeta 1; EC 5.2.1.2; EC 2.5.1.18 (characterized)
to candidate BPHYT_RS17615 BPHYT_RS17615 Glutathione S-transferase domain

Query= SwissProt::P57113
         (216 letters)



>FitnessBrowser__BFirm:BPHYT_RS17615
          Length = 203

 Score = 70.9 bits (172), Expect = 2e-17
 Identities = 55/176 (31%), Positives = 83/176 (47%), Gaps = 8/176 (4%)

Query: 7   VLYSYFRSSCSWRVRIALALKGIDYEIVPINLIKDGGQQFSEEFQTLNPMKQVPALKIDG 66
           VLYS      S R R+ L  KG+D+EI  ++L         E+   +NP  QVP L    
Sbjct: 3   VLYSGTTCPFSQRCRLVLFEKGMDFEIRDVDLFNK-----PEDIAVMNPYGQVPILVERD 57

Query: 67  ITIGQSLAILEYLEETRPIPRLLPQDPQKRAIVRM-ISDLIASGIQPLQNLSVLKQVGQE 125
           + + +S  I EY++E  P P+L+P DP +RA  R+ + +        +  L   K    E
Sbjct: 58  LILYESNIINEYIDERFPHPQLMPADPVQRARARLFLLNFEKELFVHVGTLENEKGKAAE 117

Query: 126 NQMPWAQKAITSGFNALEKILQSTAGKYCVGDEVSMADVCLAPQVANAERFKVDLS 181
                A+ AI      L  I      KY +G+E SM DV +AP +   + + ++LS
Sbjct: 118 KNHEKARLAIRDRLTQLAPIF--LKNKYMLGEEFSMLDVAIAPLLWRLDHYGIELS 171


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: 96
Number of extensions: 5
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: 216
Length of database: 203
Length adjustment: 21
Effective length of query: 195
Effective length of database: 182
Effective search space:    35490
Effective search space used:    35490
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