GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Dyella japonica UNC79MFTsu3.2

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate N515DRAFT_3479 N515DRAFT_3479 glutathione S-transferase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5292
         (211 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3479
          Length = 210

 Score = 66.2 bits (160), Expect = 4e-16
 Identities = 64/208 (30%), Positives = 89/208 (42%), Gaps = 22/208 (10%)

Query: 1   MELYTYYRSTSSYRVRIALALKGLDYQALPVNLIAAPGGEHRQPAYLAINPQGRVPALRT 60
           + LY Y  S + ++VR  L    L Y+ +PV++     GE RQP YL INP G VPA+  
Sbjct: 2   LTLYDYLPSQNGWKVRQLLRHLDLPYRTVPVSIFE---GEGRQPGYLRINPTGTVPAIAL 58

Query: 61  DEGALLVQSPAIIEYLEERYPQVPLLSADLTVRAHERGVAALIGCDIHPLHNVSVLNKLR 120
           ++G  L +S AI+ YL E  P +P    D   RA       L   +       SV+  LR
Sbjct: 59  EDGRTLAESNAILAYLAEGTPYLP---GDAYGRA-----KVLQWLNFEQERVESVIGSLR 110

Query: 121 QW---GHDETQVTEWIGHWISQGLAAVEQL---MGDDGYCFGAAPGLADVYLIPQLYAAE 174
            W   G    +    +      GL A+  L   +G   +    + G+AD+ L      A+
Sbjct: 111 YWTLTGQLAKRGPALVELKREAGLRALSMLDAELGTRPFVASESYGIADIALFAYASRAD 170

Query: 175 RFNVSLQAYPR----IRRVAALAAGHPA 198
                L  Y      I RV A   GH A
Sbjct: 171 EAGFDLAPYSHFQAWIERVRA-QPGHLA 197


Lambda     K      H
   0.320    0.137    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: 114
Number of extensions: 2
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: 211
Length of database: 210
Length adjustment: 21
Effective length of query: 190
Effective length of database: 189
Effective search space:    35910
Effective search space used:    35910
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