GapMind for catabolism of small carbon sources

 

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

Align Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized)
to candidate 200453 SO1275 succinate-semialdehyde dehydrogenase (NCBI ptt file)

Query= SwissProt::Q02253
         (535 letters)



>FitnessBrowser__MR1:200453
          Length = 482

 Score =  226 bits (577), Expect = 1e-63
 Identities = 143/472 (30%), Positives = 241/472 (51%), Gaps = 9/472 (1%)

Query: 43  FIDGKFVESKSDKWIDIHNPATNEVVGRVPQSTKAEMEAAVAACKRAFPAWADTSILSRQ 102
           +I+G++ ++ S + + I NPAT  V+  VP   +AE +AA+AA + A PAW   +   R 
Sbjct: 14  YINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALPAWRALTAKERG 73

Query: 103 QVLLRYQQLIKENLKEIARLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMLGETMPS 162
             L R+ +L+ EN  ++A L+T EQGK L +A+G+V      +E        + G+T+P 
Sbjct: 74  AKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAEEAKRIYGDTIPG 133

Query: 163 ITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGATMLLA 222
              D  +   + P+GV A I P+NFPA +       A+  G T ++KP+ + P   + LA
Sbjct: 134 HQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPFTALALA 193

Query: 223 KLLQDSGAPDGTLNIIHGQHEAV-NFICDHPDIKAISFVGSNQAGEYIFERGSRNGKRVQ 281
            L + +G P G  ++I G   A+ N +C +P ++ +SF GS   G  +  + +   K++ 
Sbjct: 194 VLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGSTNVGIKLMAQCAPTLKKLS 253

Query: 282 ANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTA-VLVGEAKKWLPELVERA 340
             +G     +V  DAN +  +   + A +  AGQ C+  +   V  G   ++  +L    
Sbjct: 254 LELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFAEKLSMAV 313

Query: 341 KNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGAKEGASILLDGRKIKVKGYENGNFVG 400
             L+V  G   G   GPLI   A E+V + ++   K+GA++L  G+  ++     GNF  
Sbjct: 314 AKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKVHEL----GGNFFE 369

Query: 401 PTIISNVKPSMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGNGTAIFTTNGAIARKY 460
           PT+++N   SM   +EE FGP+  + +   +D+ IK  ND  +G     +  + ++  K 
Sbjct: 370 PTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRDISLVWKV 429

Query: 461 AHMVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTI 512
           A  ++ G VGVN  + +   +  F G +SS  G      K GI+ Y ++K I
Sbjct: 430 AESLEYGMVGVNTGL-ISTEVAPFGGMKSSGLGREG--SKYGIEEYLEIKYI 478


Lambda     K      H
   0.318    0.133    0.389 

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: 530
Number of extensions: 35
Number of successful extensions: 4
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: 535
Length of database: 482
Length adjustment: 34
Effective length of query: 501
Effective length of database: 448
Effective search space:   224448
Effective search space used:   224448
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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