Alignments for a candidate for mmsA in Desulfacinum hydrothermale DSM 13146

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Desulfacinum hydrothermale DSM 13146

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 WP_084058850.1 B9A12_RS14640 L-glutamate gamma-semialdehyde dehydrogenase

Query= curated2:Q5L025
         (488 letters)



>NCBI__GCF_900176285.1:WP_084058850.1
          Length = 994

 Score =  245 bits (626), Expect = 5e-69
 Identities = 160/450 (35%), Positives = 242/450 (53%), Gaps = 18/450 (4%)

Query: 26  ETLEVPNP-ATGEVLARVPISTKEDVDQAVQAAKKAFATWKDVPVPKRARIMFSFHHLLN 84
           ET    NP  T +V+  V  + ++   +AV AAK+AFA W+D P  +RA  +F       
Sbjct: 519 ETFSSTNPNRTDQVVGVVASAGEKKAREAVAAAKEAFAAWRDTPPRERAEYLFRAAQAAR 578

Query: 85  QHHEELAELVVQENGKAYKEAYGEIQRGIECVEFAAGAPTLLMG--ESLSNIAEEIDSEM 142
               ELA L V E GK++KEA G++   I+ +E+  G   + +G    + N+  E+ S +
Sbjct: 579 SRRYELAALQVYEVGKSWKEADGDVCEAIDFLEYY-GREMIRLGAPRRMGNVPGEV-SHL 636

Query: 143 FRYPLGVVAGITPFNFPMMVPLWMFPLAIVCGNTFVLKPSERTPILANKLAELFTEAGAP 202
           F  P GV A + P+NFP  + + M   A+V GNT V KP+ ++P++   L  +F EA  P
Sbjct: 637 FYEPRGVAAVVAPWNFPFAISVGMTSAALVTGNTVVYKPASQSPVIGYWLYRIFQEAKLP 696

Query: 203 PGVLNVVHG-AHEVVNALIDHEDIRAISFVGSQPVAKYVYERTAAQG------KRVQALS 255
            GVLN + G   ++ + L+ H D+  I+F GS+ V   + ER A         K V A  
Sbjct: 697 KGVLNFLPGPGAKIGDFLVTHPDVAMIAFTGSKEVGLRIIERAAKTPPDAHFVKNVVAEM 756

Query: 256 GAKNHHIVMPDADVETAVQHVISSAFGSAGQRCMACSAVVIVGEN-ETFVRRLKQKADEL 314
           G KN  I+  DAD++ AV HV+ SAFG  GQ+C ACS ++++ EN    + RL+  A+ L
Sbjct: 757 GGKNAIIIDADADLDEAVVHVLHSAFGYQGQKCSACSRLIVLEENYHKLLERLRAAAESL 816

Query: 315 IIGNGMDPEVLLTPVIRQSHREKVLGYIQKGIEEGAVLLRDGRKEMDDRPEGNFLGPTIF 374
            +G   D + ++  VI    REK+L YI+ G  EG VL+    +   +   G F+  TIF
Sbjct: 817 ELGPVEDAKNVMGAVIDAKAREKILEYIEIGKREGKVLV----ERPVEGSNGYFVPLTIF 872

Query: 375 DYVTPDMTIAKEEIFAPVLSLLRANDLDEALSYIRKSRYGNGATIYTKDAKAVRKFREEA 434
             + P+  +A+EEIF PVLS+++  D DEAL     ++Y     ++++  + + K R   
Sbjct: 873 TDIRPEHRLAQEEIFGPVLSVMKVRDFDEALEVANSTQYALTGAVFSRSPENIEKARRRF 932

Query: 435 DAGMLGINVG-VPATMAFFPFSGWKDSFYG 463
             G L IN G   A +   PF G+K S  G
Sbjct: 933 RVGNLYINRGSTGAIVERHPFGGFKMSGVG 962


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: 1038
Number of extensions: 49
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: 994
Length adjustment: 39
Effective length of query: 449
Effective length of database: 955
Effective search space:   428795
Effective search space used:   428795
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 Apr 09 2024. 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 2024 update 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