GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Dechlorosoma suillum PS

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 Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase

Query= curated2:Q5L025
         (488 letters)



>FitnessBrowser__PS:Dsui_0105
          Length = 476

 Score =  236 bits (601), Expect = 2e-66
 Identities = 162/471 (34%), Positives = 231/471 (49%), Gaps = 10/471 (2%)

Query: 14  YIGGQWVASSGTETLEVPNPATGEVLARVPISTKEDVDQAVQAAKKAFATWKDVPVPKRA 73
           YIGGQWVA  G   ++V NPAT  V+ARVP  T  D D+A +AA  AF  W  +   +R 
Sbjct: 8   YIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPAWAALSGAERG 67

Query: 74  RIMFSFHHLLNQHHEELAELVVQENGKAYKEAYGEIQRGIECVEFAAGAPTLLMGESLSN 133
             +      L    +EL  L+  E G   K A   +Q G     FAA A     G +   
Sbjct: 68  AFLQKIADGLKARQDELGRLIASEVGMPVKLAT-RVQAGNPIFTFAACARIAAEGFAEER 126

Query: 134 IAEEIDSEMFRYPLGVVAGITPFNFPMMVPLWMFPLAIVCGNTFVLKPSERTPILANKLA 193
           I + +   + + P G VA ITP+NFP+         A+  G T VLKPSE  P+ A  LA
Sbjct: 127 IGQSL---VLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLNAFLLA 183

Query: 194 ELFTEAGAPPGVLNVVHGAHEVVN-ALIDHEDIRAISFVGSQPVAKYVYERTAAQGKRVQ 252
           E+   AG P GV N+V G   VV  AL  H  + A+SF GS    K V    AA  KRV 
Sbjct: 184 EVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATVKRVS 243

Query: 253 ALSGAKNHHIVMPDADVETAVQHVISSAFGSAGQRCMACSAVVIVGENETFVRRLK-QKA 311
              G K+  +V+PDAD+  AV+  ++  F ++GQ C A + +++  E       L  Q A
Sbjct: 244 LELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALAVQAA 303

Query: 312 DELIIGNGMDPEVLLTPVIRQSHREKVLGYIQKGIEEGAVLLRDGRKEMDDRPEGNFLGP 371
               +G+ +     L P++    R++V   I++ + +GA LL  G    +  P G ++ P
Sbjct: 304 AAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAPEGLPTGYYVRP 363

Query: 372 TIFDYVTPDMTIAKEEIFAPVLSLLRANDLDEALSYIRKSRYGNGATIYTKDAKAVRKFR 431
           T+F  V PD  +A+EE+F PVL++L   D  EA +    + YG  A +++ +      F 
Sbjct: 364 TVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEEARALAFA 423

Query: 432 EEADAGMLGINVGVPATMAFFPFSGWKDSFYGDLHVNGKDGVNFYTRKKMI 482
               AG + IN      +A  PF G+K S YG     G+ GV  +   + I
Sbjct: 424 RRLRAGQVDINGAFFNLLA--PFGGFKQSGYG--RELGRHGVEDFLETQSI 470


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: 520
Number of extensions: 30
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: 488
Length of database: 476
Length adjustment: 34
Effective length of query: 454
Effective length of database: 442
Effective search space:   200668
Effective search space used:   200668
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: 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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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