Alignments for a candidate for mmsA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Cupriavidus basilensis 4G11

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 RR42_RS34225 RR42_RS34225 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__Cup4G11:RR42_RS34225
          Length = 506

 Score =  588 bits (1517), Expect = e-172
 Identities = 288/492 (58%), Positives = 360/492 (73%), Gaps = 3/492 (0%)

Query: 6   HLIGGELIAD-TGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKR 64
           H I G  +A  +GR  DVFNP+TG A R V L   +    A+ AA AAF AW +TPP +R
Sbjct: 15  HYINGSRVASASGRAQDVFNPATGAAARSVALGSADEAGTAVAAAAAAFAAWADTPPIRR 74

Query: 65  AQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSR 124
           A+V+ RF QL+  + + +  +I+ EHGK   DA GE+ RGI+ +E+A   P++LKG+Y+ 
Sbjct: 75  ARVMQRFLQLMNQHRDTLAAMITAEHGKVFSDAQGEVSRGIDIIEFACGIPQLLKGDYTD 134

Query: 125 NVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLI 184
            V   +D W+  QP+GVV GITPFNFP MVP WM+P+A+A GNTF+LKPSERDPS++L +
Sbjct: 135 QVSTGMDNWTLRQPLGVVVGITPFNFPCMVPCWMFPIALAAGNTFVLKPSERDPSASLFM 194

Query: 185 AELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRVQ 244
           A+L  EAGLP GV NVV GDK  VDALI  PEVKA+SFVGSTPIA+YI       GKRVQ
Sbjct: 195 ADLLTEAGLPAGVFNVVQGDKVVVDALIAHPEVKAVSFVGSTPIAQYISERSAHFGKRVQ 254

Query: 245 ALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVPQ 304
           ALGGAKNH V+MPDAD++ AV AL+GA YGS GERCMAIS+AV VGD +AD ++  L  +
Sbjct: 255 ALGGAKNHLVVMPDADIEQAVDALIGAGYGSAGERCMAISIAVLVGD-VADKILPLLAER 313

Query: 305 IKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFFL 364
           +K L IG G +   +MGP+VT  A +++ GY+  GVA+GA LVVDGR  +V GHE GFF 
Sbjct: 314 VKALVIGNGMNAEAEMGPIVTRQALERIEGYVGLGVAEGATLVVDGRDCRVPGHEAGFFT 373

Query: 365 GGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARL 424
           GGTLFD VTP M IYKEEIFGPVL  VRV    +A+QL+NDHE+GNG   +T DG  AR 
Sbjct: 374 GGTLFDNVTPAMRIYKEEIFGPVLGCVRVKDFAQAVQLVNDHEFGNGVACYTSDGGVARE 433

Query: 425 FCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRWPQR 484
           F   I+VGMVG+NVP+PVP+A+H FGGWKRSLFGD HAYG +GVRFYTK+K++ QRWP  
Sbjct: 434 FARRIQVGMVGINVPIPVPMAWHGFGGWKRSLFGDTHAYGEEGVRFYTKQKSVMQRWPD- 492

Query: 485 KSHEAAQFAFPS 496
              + A+FA P+
Sbjct: 493 SIGKGAEFAMPT 504


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: 768
Number of extensions: 27
Number of successful extensions: 2
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: 506
Length adjustment: 34
Effective length of query: 464
Effective length of database: 472
Effective search space:   219008
Effective search space used:   219008
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 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources