Alignments for a candidate for mmsA in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Desulfovibrio vulgaris Hildenborough

Align Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase

Query= curated2:Q5L025
         (488 letters)



>MicrobesOnline__882:208845
          Length = 1006

 Score =  232 bits (591), Expect = 5e-65
 Identities = 160/460 (34%), Positives = 237/460 (51%), Gaps = 16/460 (3%)

Query: 14  YIGGQWVASSGTETLEVPNPAT-GEVLARVPISTKEDVDQAVQAAKKAFATWKDVPVPKR 72
           YIGG+ V ++  + +   NPA   EV+A +  + + ++D A+ AAKKA  TW+D     R
Sbjct: 515 YIGGRDVTTA--DLIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKAALTWRDTSPADR 572

Query: 73  ARIMFSFHHLLNQHHEELAELVVQENGKAYKEAYGEIQRGIECVEFAAGAPTLLMGESLS 132
           A  +     +  +   EL+   V E GK + +AY ++  GI+ +E+ A     L      
Sbjct: 573 AAYLRRAADICRKRIWELSAWQVVEVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPRRM 632

Query: 133 NIAEEIDSEMFRYPLGVVAGITPFNFPMMVPLWMFPLAIVCGNTFVLKPSERTPILANKL 192
             A    + +F  P G+ A I P+NFP  + + M   AIV GN  + KPS  +  +   L
Sbjct: 633 GRAPGEHNHLFYQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGYNL 692

Query: 193 AELFTEAGAPPGVLNVVHGAHEVV-NALIDHEDIRAISFVGSQPVAKYVYERTA------ 245
           AE+F EAG P GV N   G   ++ + L++H DI  I F GS  V   + E+ A      
Sbjct: 693 AEVFREAGLPEGVFNYCPGRSSIMGDYLVEHPDISLICFTGSMEVGLRIQEKAAKVQPGQ 752

Query: 246 AQGKRVQALSGAKNHHIVMPDADVETAVQHVISSAFGSAGQRCMACSAVVIVGE-NETFV 304
            Q KRV A  G KN  I+  DAD++ AV  V+ SAFG  GQ+C ACS V+++    + F+
Sbjct: 753 RQCKRVIAEMGGKNATIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDAIYDRFI 812

Query: 305 RRLKQKADELIIGNGMDPEVLLTPVIRQSHREKVLGYIQKGIEEGAVLLRDGRKEMDDRP 364
            RL + A  + IG   DP   + PV   + ++ V  YI+   EEG VLL    K  D   
Sbjct: 813 ERLVKAASSIHIGPSEDPSNYMGPVADATLQKNVSDYIRIAEEEGRVLL----KRTDLPA 868

Query: 365 EGNFLGPTIFDYVTPDMTIAKEEIFAPVLSLLRANDLDEALSYIRKSRYGNGATIYTKDA 424
           EG ++  TI   + P+  IA+EEIF PVL+++RA   DEALS    +R+     ++++  
Sbjct: 869 EGCYVPLTIVGDIRPEHRIAQEEIFGPVLAVMRAATFDEALSIANGTRFALTGAVFSRSP 928

Query: 425 KAVRKFREEADAGMLGINVG-VPATMAFFPFSGWKDSFYG 463
           + + K R E   G L +N G   A +   PF G+  S  G
Sbjct: 929 EHLDKARREFRVGNLYLNKGSTGALVERQPFGGFAMSGVG 968


Lambda     K      H
   0.319    0.136    0.396 

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: 1009
Number of extensions: 37
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: 488
Length of database: 1006
Length adjustment: 39
Effective length of query: 449
Effective length of database: 967
Effective search space:   434183
Effective search space used:   434183
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 (21.8 bits)
S2: 54 (25.4 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