GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Shewanella oneidensis MR-1

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate 199807 SO0619 succinylglutamic semialdehyde dehydrogenase (NCBI ptt file)

Query= reanno::Caulo:CCNA_01360
         (500 letters)



>FitnessBrowser__MR1:199807
          Length = 487

 Score =  171 bits (433), Expect = 5e-47
 Identities = 142/457 (31%), Positives = 215/457 (47%), Gaps = 15/457 (3%)

Query: 7   HFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQRR 66
           HFI GQ   G  G      +P  G++  R   A+A ++N A+  A+ AQ  W       R
Sbjct: 3   HFIKGQWHTG-KGHDVASSNPANGEIIWRGQTATAEQVNAAVDAAREAQFDWFILGFDAR 61

Query: 67  ARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLKGEYTQ 126
            +++  ++  LE +  ELA  ++ E GK   ++  ++   +  I  +    +   G  T 
Sbjct: 62  LKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYNKRTGTETN 121

Query: 127 GAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPVRL 186
               G  V    +P GVVA   P+NFP  +P     PA+  GN+ + KPSE  P V   +
Sbjct: 122 DTPAGRAVLR-HKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVFKPSELTPKVAELM 180

Query: 187 AELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQR-AGAAGKRV 245
             L  ++GLP GVLN+V G+ D  +A+  HP +  + F GSS     + Q+ AG  GK +
Sbjct: 181 VTLWEKSGLPAGVLNLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240

Query: 246 QAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERC-MALPVVVPVGEKTATALREKLV 304
               G  N  ++   AD+  AV DI+ +AY S+G+RC  A  + V  GE+   AL  KLV
Sbjct: 241 ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQ-GDALVAKLV 299

Query: 305 AAIGGLRVGV-STDPDAHYGPVVS-AAHKARIESYIQMGVDEGAELVVDGRGFSLQGHEE 362
            A+  ++VG  +  P    G ++S AA K  + +   +    G  LV       L   + 
Sbjct: 300 EAVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLLSLGGVPLV------ELMHLQA 353

Query: 363 GF-FVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNG 421
           G   V P L D V   S    +E FGP+LQ+VR    ++ I LA++ +YG    I   + 
Sbjct: 354 GTGLVSPGLID-VTAVSELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSR 412

Query: 422 DAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSG 458
           +    F  ++  G+V  N  I        FGG   SG
Sbjct: 413 EDYEYFLARIRAGIVNWNKQITGASGAAPFGGVGASG 449


Lambda     K      H
   0.320    0.137    0.409 

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: 606
Number of extensions: 29
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: 500
Length of database: 487
Length adjustment: 34
Effective length of query: 466
Effective length of database: 453
Effective search space:   211098
Effective search space used:   211098
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: 52 (24.6 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