Alignments for a candidate for gabD in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabD in Dechlorosoma suillum PS

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate Dsui_0437 Dsui_0437 succinate-semialdehyde dehydrogenase

Query= BRENDA::P25526
         (482 letters)



>FitnessBrowser__PS:Dsui_0437
          Length = 483

 Score =  688 bits (1775), Expect = 0.0
 Identities = 340/485 (70%), Positives = 397/485 (81%), Gaps = 5/485 (1%)

Query: 1   MKLNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRA 60
           MKL DSNL RQQ  +NG+W+   +     V NPA+G +L  VP+ GA ETRAAI AA+ A
Sbjct: 1   MKLEDSNLLRQQCYLNGQWVGGESD--FPVHNPASGAELARVPRFGAAETRAAIAAADAA 58

Query: 61  LPAWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFA 120
            PAWR+ TAKER  +LR WF LM +H DDLA LMT EQGKPLAEA+GE++YAASF+EWFA
Sbjct: 59  WPAWRSRTAKERTGVLRRWFELMNQHADDLALLMTSEQGKPLAEARGEVAYAASFVEWFA 118

Query: 121 EEGKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180
           EE KR YG+TIP   ADKR++VIKQPIGV AAITPWNFPAAMITRK  PALAAGCT+V+K
Sbjct: 119 EEAKRAYGETIPAVAADKRMLVIKQPIGVCAAITPWNFPAAMITRKVAPALAAGCTVVVK 178

Query: 181 PASQTPFSALALAELAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQ 240
           PA QTP +ALALAELA RAG PAGVFNV+TG   A+G ELTSNP VRKLSFTGSTE+GR 
Sbjct: 179 PAEQTPLTALALAELAHRAGFPAGVFNVITGDPVAIGGELTSNPTVRKLSFTGSTEVGRL 238

Query: 241 LMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDG 300
           LM QCA  IKK+SLELGGNAPFIVFDDADLD AVEGA+ SK+RN GQTCVCANRL VQDG
Sbjct: 239 LMGQCAPSIKKLSLELGGNAPFIVFDDADLDAAVEGAMISKYRNTGQTCVCANRLLVQDG 298

Query: 301 VYDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKA 360
           +Y+ FA +L   V+ L +G+G + GVT GPLID  A+AKVE HIADA+  GARV+ GG+ 
Sbjct: 299 IYEAFAARLAAKVATLKVGEGTEAGVTQGPLIDADALAKVEAHIADAVAHGARVLAGGRR 358

Query: 361 HER---GGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAY 417
           HER   GG FFQPT+L DV    +V++EETFGP+APLFRF+ E + IA AN TEFGLA+Y
Sbjct: 359 HERYREGGAFFQPTVLADVTPQMRVAREETFGPVAPLFRFQTEEEAIALANATEFGLASY 418

Query: 418 FYARDLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKY 477
           FY+RD+ R+FRVGEALEYG+VG+NTG+ISNEVAPFGGIK SGLGREGSKYG+E+YLE+KY
Sbjct: 419 FYSRDIGRIFRVGEALEYGMVGVNTGLISNEVAPFGGIKQSGLGREGSKYGLEEYLEVKY 478

Query: 478 MCIGL 482
           +C+GL
Sbjct: 479 LCLGL 483


Lambda     K      H
   0.318    0.135    0.395 

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: 745
Number of extensions: 18
Number of successful extensions: 3
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: 482
Length of database: 483
Length adjustment: 34
Effective length of query: 448
Effective length of database: 449
Effective search space:   201152
Effective search space used:   201152
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 (21.7 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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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