GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Methylocystis bryophila S285

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_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein

Query= curated2:Q81QR5
         (486 letters)



>NCBI__GCF_002117405.1:WP_085772038.1
          Length = 506

 Score =  201 bits (510), Expect = 6e-56
 Identities = 141/466 (30%), Positives = 221/466 (47%), Gaps = 15/466 (3%)

Query: 7   KRVKNHINGEWVESTGTEVEAVPNPATGKIIAYVPLSPKEDVEKAVEAAKAAYETWSKVP 66
           KR  N I G+WV   G E     +P TG  I  V      DVE A++AA  A + W K P
Sbjct: 17  KRYDNFIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHKAKDAWGKTP 76

Query: 67  VPNRSRQLYKYLQLLQENKEELAKIITLENGKTLTDAT-GEVQRGIEAVELATSAPNLMM 125
              R+  L K  Q L +N   LA + T++NGK + + T  ++   I+             
Sbjct: 77  AAERANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQE 136

Query: 126 GQALPNIASGIDGSIWRYPIGVVAGITPFNFPMMIPLWMFPLAIACGNTFVLKTSERTPL 185
           G +L  I        +  P+GVV  I P+NFP+++  W    A+A GN  VLK +E+TP+
Sbjct: 137 G-SLSEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQTPM 195

Query: 186 LAERLVELFYEAGFPKGVLNLVQG-GKDVVNSILENKDIQAVSFVGSEPVARYVYETGTK 244
               + EL  +   P GVLN+V G G +    +  NK I  ++F G     R + +   +
Sbjct: 196 SILAVAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYAAE 254

Query: 245 HGKRVQALAGAKNHAIVM------PDCNLEKTVQGVIGSAFASSGERCMACSVVAVVDEI 298
           +   V    G K+  I         D  L+K ++G    A  + GE C   S   V   I
Sbjct: 255 NLIPVTLELGGKSPNIFFADVMAEDDAFLDKALEGFASFAL-NQGEVCTCPSRALVQRSI 313

Query: 299 ADEFIDVLVAETKKLKVGDGFHEDNYVGPLIRESHKERVLGYINSGVADGATLLVDGRK- 357
            D+F++  +A   K++ G        +G        E++L Y++ G  +GA +L+ G + 
Sbjct: 314 YDKFMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLIGGERS 373

Query: 358 -IKEEVGEGYFVGATIFDGVNQEMKIWQDEIFAPVLSIVRVKDLEEGIKLTNQSKFANGA 416
            ++ E+ EGY++  T  +G N+ M+++Q+EIF PV+S+   +  EE +++ N + +  GA
Sbjct: 374 VLEGELKEGYYMQPTALEGHNR-MRVFQEEIFGPVVSVTTFETEEEALQIANDTLYGLGA 432

Query: 417 VIYTSNGKHAQTFRDNIDAGMIGVNVNVPAPMAFFAFAGNKASFFG 462
            ++T +G  A      I AG +  N     P A  AF G K S  G
Sbjct: 433 GLWTRDGSRAYRCGRAIRAGRVWTNCYHAYP-AHAAFGGYKQSGIG 477


Lambda     K      H
   0.317    0.135    0.392 

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: 538
Number of extensions: 23
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: 486
Length of database: 506
Length adjustment: 34
Effective length of query: 452
Effective length of database: 472
Effective search space:   213344
Effective search space used:   213344
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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