GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Dechlorosoma suillum PS

Align succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase

Query= BRENDA::Q0K2K1
         (483 letters)



>FitnessBrowser__PS:Dsui_0105
          Length = 476

 Score =  322 bits (826), Expect = 1e-92
 Identities = 198/469 (42%), Positives = 255/469 (54%), Gaps = 8/469 (1%)

Query: 11  SHCLIDGEWTGAQSGAELAVCNPATGERIGSVPLAGAAEAEQAVRAAERALPAWRAQTGK 70
           S   I G+W      A + V NPAT   I  VP   A +A++A RAA  A PAW A +G 
Sbjct: 5   SRFYIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPAWAALSGA 64

Query: 71  ARAAVLRRWADLMLAHQEDLARLMTAEQGKPLPEARGEVAYAASFLEWFGEEAKRVDGEV 130
            R A L++ AD + A Q++L RL+ +E G P+  A    A    F         R+  E 
Sbjct: 65  ERGAFLQKIADGLKARQDELGRLIASEVGMPVKLATRVQAGNPIFTF---AACARIAAEG 121

Query: 131 LASPRSSQKMLVLREPVGVCAAITPWNFPAAMITRKVGPALAAGCTIIVKPAEQTPLTAL 190
            A  R  Q  LVL+ P G  A ITPWNFP   I  KVG ALAAGCT+++KP+E  PL A 
Sbjct: 122 FAEERIGQS-LVLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLNAF 180

Query: 191 ALAVLGEQAGVPRGVLQVVTGDAVQIGGVLCASPVVRKLSFTGSTAIGKLLMAQCAGTVK 250
            LA + E AG+P GV  +VTG    +G  L A P +  +SFTGSTA GK + A  A TVK
Sbjct: 181 LLAEVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATVK 240

Query: 251 KLSLELGGNAPLIIFDDADLDRAVEGILASKFRNSGQTCVCANRIYVHDRVYDEVARRLV 310
           ++SLELGG +  ++  DADL  AV+G +A  F NSGQ C    R+ V    Y E A   V
Sbjct: 241 RVSLELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALAV 300

Query: 311 SAVEQLRPGHGVDSGVTQGPLIDADAVAKVEAHIADALAQGATVLTGGQRHALG---GTF 367
            A      G  +  G   GPL+      +V A I  A+A GA +L GG     G   G +
Sbjct: 301 QAAAAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAPEGLPTGYY 360

Query: 368 FAPTVLANATASMRVAREETFGPLAPLFRFTSEAEVVAMANDTESGLAAYFFSRDMAKIW 427
             PTV         +AREE FGP+  +  +  EAE  A+AN T+ GLAA  +S + A+  
Sbjct: 361 VRPTVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEEARAL 420

Query: 428 RVAQGLEYGMVGINTGLISNEVAPFGGVKQSGLGREGSRHGIDEYLETK 476
             A+ L  G V IN G   N +APFGG KQSG GRE  RHG++++LET+
Sbjct: 421 AFARRLRAGQVDIN-GAFFNLLAPFGGFKQSGYGRELGRHGVEDFLETQ 468


Lambda     K      H
   0.319    0.133    0.390 

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: 600
Number of extensions: 25
Number of successful extensions: 4
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: 483
Length of database: 476
Length adjustment: 34
Effective length of query: 449
Effective length of database: 442
Effective search space:   198458
Effective search space used:   198458
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: 51 (24.3 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