GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligJ in Sinorhizobium meliloti 1021

Align 4-oxalmesaconate hydratase; OMA hydratase; Gallate degradation protein B; EC 4.2.1.83 (characterized)
to candidate SMc00503 SMc00503 hypothetical protein

Query= SwissProt::Q88JX8
         (258 letters)



>FitnessBrowser__Smeli:SMc00503
          Length = 244

 Score =  319 bits (817), Expect = 4e-92
 Identities = 154/240 (64%), Positives = 182/240 (75%), Gaps = 5/240 (2%)

Query: 19  QKSALVVSAHSADFVWRAGGAIALHAEQGYAMHVVCLSFGERGESAKLWRKGEMTEAKVK 78
           QK+ LVVSAHSADFVWRAGGAIA HA QGYA+ VVCLSFGERGESAKLW+K  MT   VK
Sbjct: 3   QKTGLVVSAHSADFVWRAGGAIAAHARQGYAVTVVCLSFGERGESAKLWKKSGMTLETVK 62

Query: 79  DARREEAMAAAEILGA-SVEFFDIGDYPMRADKDTLFRLADVYRRVQPEFVLSHSLKDPY 137
             RR EA  AA+ LG   + F+D+GDYP++   +   RL D+YR ++PEF+L+HS +DPY
Sbjct: 63  ADRRREAENAAKALGVHDILFYDLGDYPIQVTPEAFDRLVDLYREIRPEFMLTHSRQDPY 122

Query: 138 NYDHPLAMHLAQEARIIAQAEGYKPGEKIVGAPPVYAFEPHQPEQCEWRPDTFLDITSVW 197
           N+DHP+A   AQ AR+IAQA G+KP   ++GAPPVY FEPHQPEQC W+P+  LDIT VW
Sbjct: 123 NFDHPMATEFAQHARVIAQAHGHKPSTPVLGAPPVYLFEPHQPEQCNWKPNFLLDITDVW 182

Query: 198 DKKYAAIQCMAGQEHLWEYYTRVALQRGVQAKRNVGITSARNIVYAEGLQSVFPRVTENL 257
           +KK AAI+CM GQEHLWEYYTRVALQRGVQA RN    S   I Y E  ++VFP VT  L
Sbjct: 183 EKKLAAIKCMEGQEHLWEYYTRVALQRGVQASRN----SDYKITYGEAYEAVFPHVTGTL 238


Lambda     K      H
   0.320    0.132    0.408 

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: 273
Number of extensions: 10
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: 258
Length of database: 244
Length adjustment: 24
Effective length of query: 234
Effective length of database: 220
Effective search space:    51480
Effective search space used:    51480
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: 46 (22.3 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