GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Amantichitinum ursilacus IGB-41

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_053938969.1 WG78_RS16670 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>NCBI__GCF_001294205.1:WP_053938969.1
          Length = 466

 Score =  234 bits (598), Expect = 4e-66
 Identities = 144/453 (31%), Positives = 236/453 (52%), Gaps = 11/453 (2%)

Query: 9   GGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRAQVL 68
           G  + AD   T  V NP+TGE +  +P   +   ++AI+AA+AA+PAWR+    +R+Q+L
Sbjct: 17  GAWIDADNQETVPVNNPATGEIIAHIPKLGKAETRRAIEAAQAAWPAWRSKTAKERSQIL 76

Query: 69  FRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSRNVGP 128
            ++  L+ AN + +  +++ E GK + +A GE+      +E+       ++G+       
Sbjct: 77  RKWNDLMLANVDDLALILTSEQGKPLAEARGEITYAASYIEWFAEEARRIEGDIIAPPSN 136

Query: 129 NIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLIAELF 188
           +       QPIGV A ITP+NFPA +       A+A G   +LKP+ + P S L +A L 
Sbjct: 137 DRRILVLKQPIGVTAAITPWNFPAAMITRKVGPALAAGCPMVLKPATQTPLSALALAVLA 196

Query: 189 HEAGLPKGVLNVVHGDKGAVDA-LIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRVQALG 247
             AG+P G+ NV+ G    +   L  +P V+ ++F GST +   +  +     K++    
Sbjct: 197 ERAGVPAGIFNVLTGSSTEIGGELTASPIVRKITFTGSTEVGAKLIEQSAPTIKKMSMEL 256

Query: 248 GAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVPQIKG 307
           G     ++  DADLD AV   +G+ Y + G+ C+  +  + V   + DA  QKL   +  
Sbjct: 257 GGNAPFIVFDDADLDAAVQGAIGSKYRNSGQTCVCAN-RLLVQAGVYDAFAQKLADAVNA 315

Query: 308 LKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFFLGGT 367
           LK+G G   G+  GPL+   A  K+  +I     +GA+++  G+ + +     G F   T
Sbjct: 316 LKVGNGVDDGVTQGPLIDDKAIAKIEEHIADATGKGAQVLTGGKRHAL----GGTFFEPT 371

Query: 368 LFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARLF-- 425
           +   VTP M + +EE FGP+  + +  + EEA+ + ND E+G  +  +TRD   AR+F  
Sbjct: 372 ILTGVTPAMKVAREETFGPLAPLFKFETEEEAIAMANDTEFGLASYFYTRD--LARIFRV 429

Query: 426 CDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFG 458
            + +E GMVG+N  L +      FGG K+S  G
Sbjct: 430 AEGLEYGMVGINAGL-ISSEVAPFGGVKQSGLG 461


Lambda     K      H
   0.319    0.137    0.411 

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: 581
Number of extensions: 33
Number of successful extensions: 5
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: 498
Length of database: 466
Length adjustment: 34
Effective length of query: 464
Effective length of database: 432
Effective search space:   200448
Effective search space used:   200448
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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