GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Dechlorosoma suillum PS

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate Dsui_0437 Dsui_0437 succinate-semialdehyde dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_515
         (500 letters)



>FitnessBrowser__PS:Dsui_0437
          Length = 483

 Score =  245 bits (625), Expect = 3e-69
 Identities = 157/462 (33%), Positives = 240/462 (51%), Gaps = 6/462 (1%)

Query: 10  YLNGHVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPAWSEQSSLRRS 69
           YLNG     +S     V NPA+GA  ARV         AA+A+A AA+PAW  +++  R+
Sbjct: 14  YLNGQWVGGESD--FPVHNPASGAELARVPRFGAAETRAAIAAADAAWPAWRSRTAKERT 71

Query: 70  RVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSDN 129
            V+ ++ EL+++H D+LA +++ E GK L++A GEV      VE+          +    
Sbjct: 72  GVLRRWFELMNQHADDLALLMTSEQGKPLAEARGEVAYAASFVEWFAEEAKRAYGETIPA 131

Query: 130 IGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLMA 189
           +        ++QP+GVCA +TP+NFP  +    +  AL AG   ++KP+E+ P  +L +A
Sbjct: 132 VAADKRMLVIKQPIGVCAAITPWNFPAAMITRKVAPALAAGCTVVVKPAEQTPLTALALA 191

Query: 190 RLLTEAGLPDGVFNVVQGDKVAVDA-LLQHPDIEAISFVGSTPIAEYIHQQGTAHGKRVQ 248
            L   AG P GVFNV+ GD VA+   L  +P +  +SF GST +   +  Q     K++ 
Sbjct: 192 ELAHRAGFPAGVFNVITGDPVAIGGELTSNPTVRKLSFTGSTEVGRLLMGQCAPSIKKLS 251

Query: 249 ALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPRI 308
              G     IV  DADLD A +  + + Y + G+ C+  +  +    + +   A+L  ++
Sbjct: 252 LELGGNAPFIVFDDADLDAAVEGAMISKYRNTGQTCVCANRLLVQDGIYEAFAARLAAKV 311

Query: 309 DQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGAEQGFFVG 368
             LK+G G + G   GPL+ A+  AKVE  I   VA GAR++  GR  +    E G F  
Sbjct: 312 ATLKVGEGTEAGVTQGPLIDADALAKVEAHIADAVAHGARVLAGGRRHE-RYREGGAFFQ 370

Query: 369 ATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARAF 428
            T+   VT +M + ++E FGPV  + R      A+AL NA EFG     ++RD G     
Sbjct: 371 PTVLADVTPQMRVAREETFGPVAPLFRFQTEEEAIALANATEFGLASYFYSRDIGRIFRV 430

Query: 429 ARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFG-DHHAYGEE 469
             +++ GMVG+N  + +      FGG K+S  G +   YG E
Sbjct: 431 GEALEYGMVGVNTGL-ISNEVAPFGGIKQSGLGREGSKYGLE 471


Lambda     K      H
   0.321    0.137    0.415 

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: 547
Number of extensions: 21
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: 500
Length of database: 483
Length adjustment: 34
Effective length of query: 466
Effective length of database: 449
Effective search space:   209234
Effective search space used:   209234
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