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 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