GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Sinorhizobium meliloti 1021

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate SMc00778 SMc00778 oxidoreductase

Query= uniprot:B2T9V3
         (247 letters)



>FitnessBrowser__Smeli:SMc00778
          Length = 255

 Score =  154 bits (389), Expect = 2e-42
 Identities = 99/253 (39%), Positives = 143/253 (56%), Gaps = 20/253 (7%)

Query: 1   MTQRLAGKTALITAAGQGIGLATAELFAREGARV------------IATDIRIDGLAGKP 48
           M  RL GK ALI+    G GLA +ELFAREGA V            +A  +R +G     
Sbjct: 1   MAGRLHGKIALISGGAGGCGLAASELFAREGAAVGIVDLPQSQGEAVAARLRSEGFRAAF 60

Query: 49  VEARKLDVRD-DAAIKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMY 107
             A   D R    A++ ++ E+G + VLFN AG +     LE + E+WD    +NV++M+
Sbjct: 61  ASADASDERQVTQAVERVSGELGPITVLFNHAGTIVIRPFLETTAEEWDRLMAVNVRSMF 120

Query: 108 RMIRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGV 167
            M RA LP M+D GGGSI+  +S+ S+V   P    Y+ +K A     +SVA +F  R +
Sbjct: 121 LMTRAVLPQMIDAGGGSIV-CTSSISAVAATPMEVLYNTTKGACHMFARSVAVEFRDRNI 179

Query: 168 RCNAICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLG 227
           RCNA+CPG + + +  QR V +    G  +D   AA  A+Q  GR+ +P+E+A  ALYL 
Sbjct: 180 RCNAVCPGFIQT-AHGQREVEELTRYG--VDVSDAAIAAQQ--GRMCRPDEVAKAALYLA 234

Query: 228 SDESSFTTGHAHV 240
           S+++SF +G AH+
Sbjct: 235 SEDASFVSG-AHL 246


Lambda     K      H
   0.320    0.133    0.381 

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: 147
Number of extensions: 8
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 247
Length of database: 255
Length adjustment: 24
Effective length of query: 223
Effective length of database: 231
Effective search space:    51513
Effective search space used:    51513
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