GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__MR1:200453 SO1275 succinate-semialdehyde
           dehydrogenase (NCBI ptt file)
          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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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