Alignments for a candidate for mmsA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Acidovorax sp. GW101-3H11

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= reanno::pseudo1_N1B4:Pf1N1B4_1229
         (505 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1496
          Length = 500

 Score =  243 bits (621), Expect = 9e-69
 Identities = 154/444 (34%), Positives = 239/444 (53%), Gaps = 13/444 (2%)

Query: 10  QKVKLLIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQT--WKL 67
           ++V  +I G    + +  W  + +PAT+ V+A+ P + AA++  A+++A RAF +  W+ 
Sbjct: 20  RRVGNVIGGVSGPALSGRWLPVTDPATEMVVAEAPDSDAADIARAVASAQRAFDSHVWRG 79

Query: 68  TPIGARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEG-DIFRGLEVVEHACSIGSL 126
                R +++ +L  LI  H+  ++ + + + GK    A   D+  G E V +     + 
Sbjct: 80  LRPADREKLLFRLSELIERHADELSALETLQSGKLQGIARAIDVQAGAEFVRYMAGWATK 139

Query: 127 QMGEFAEN---VAGGV-DTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKP 182
             G+  +N   + G    TYT R+P+GV   I P+NFP  I LW    A+A G T VLKP
Sbjct: 140 LEGQTLDNSIPIPGPQWVTYTRREPVGVVGAIVPWNFPLAIALWKIAPALAAGCTVVLKP 199

Query: 183 SEQDPMSTMLLVELAIEAGIPPGVLNVVHG-GKDVVDALCTHKDIKAVSFVGSTAVGTHV 241
           SE  P++ + L  LA+EAGIP GVLNVV G G     AL  H  ++ +SF GSTAVG  V
Sbjct: 200 SEDTPLTALRLAHLALEAGIPEGVLNVVCGRGATAGAALIAHPGVRKLSFTGSTAVGKVV 259

Query: 242 YDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATS-VVVLVGA 300
              A ++  R    +G K+ AVV+ DA+  Q    +    F   GQ C A+S ++V    
Sbjct: 260 GHAAVENMARFTLELGGKSPAVVMEDADPSQVAQGIATGIFFHQGQVCTASSRLLVHRSL 319

Query: 301 AKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDI 360
            ++ L +L  +AQ +++ +G +  T  GP+ SK   AR++D I S   EGA L   G  +
Sbjct: 320 YRRVLDELAGIAQGMRIGSGFDAATQFGPLTSKAHFARVMDFIASAKAEGATLVAGGERV 379

Query: 361 SVPGYEKGNFVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTG 420
               ++ G FV PT+F+  T +M++  +E+FGPVL V   D ++ AIA  N  P+G    
Sbjct: 380 ----HDAGCFVQPTIFADTTAQMRVVREEVFGPVLAVAPFDDVEDAIAAANDTPYGLAAS 435

Query: 421 LFTQSGAAARKFQTEIDVGQVGIN 444
           L+TQS + A +    +  G V +N
Sbjct: 436 LWTQSLSHAHRIVPRLQAGVVWVN 459


Lambda     K      H
   0.319    0.135    0.397 

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: 573
Number of extensions: 30
Number of successful extensions: 6
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: 505
Length of database: 500
Length adjustment: 34
Effective length of query: 471
Effective length of database: 466
Effective search space:   219486
Effective search space used:   219486
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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Protein sequences (fasta format)
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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