GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Pseudomonas simiae WCS417

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF3484 PS417_17840 betaine-aldehyde dehydrogenase

Query= BRENDA::Q8VWZ1
         (503 letters)



>FitnessBrowser__WCS417:GFF3484
          Length = 486

 Score =  352 bits (902), Expect = e-101
 Identities = 187/466 (40%), Positives = 279/466 (59%), Gaps = 19/466 (4%)

Query: 27  NINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSAASGSLRARYLRAIAAKIK 86
           N NP+T   IG++ +   E+V LAV AAK A  +     W+      RAR +R +   I+
Sbjct: 19  NYNPATGEAIGEVASGGAEEVALAVAAAKEAFPK-----WANTPAKERARLMRKLGELIE 73

Query: 87  EKKDELGKLESIDCGKPLEEALADLDDVVAC-FEYYAGLAEELDSKQKAPISLPMDT-FK 144
           +    L +LE++D G P+ +    L    +  F+++A +   +D       S P+D    
Sbjct: 74  QNVPHLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDGH-----SYPVDDQML 128

Query: 145 SYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSELASVTCLELGEICKEV 204
           +Y L +P+GV  L++PWN PF+ ATWK AP LA G  A+LK SEL+ +T  ELG +  E 
Sbjct: 129 NYTLYQPVGVCGLVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTANELGRLAVEA 188

Query: 205 GLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTTAAQLVKPVSLELGGK 264
           G+P GVLN++ G G  AG +L  HPDV  ISFTG +ATG KIM TA   +K  S+ELGGK
Sbjct: 189 GIPNGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAG--LKKYSMELGGK 246

Query: 265 SPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIAVEFVDKLVKWAENIKIS 324
           SP+++FED DL++  +  +F  F  NG+ C+A SR+ + ES+  +FV +    A+ + + 
Sbjct: 247 SPVLIFEDADLERALDSALFTIFSLNGERCTAGSRIFIQESVYPQFVAEFAARAKRLIVG 306

Query: 325 DPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGG-----RRPEHLKKGYFVEPTI 379
           DP +   ++G ++++A Y KV   I     EGAT+L GG       P HL KG F++PT+
Sbjct: 307 DPQDPKTQVGSMITQAHYDKVTGYIKIGIEEGATLLAGGLDRPANLPAHLSKGQFIQPTV 366

Query: 380 ITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAVMSNDLERCERLSKA 439
             DV   M+I +EE+FGPV+ +  F  E EA+ LANDT YGL S + + D+ +  RL++ 
Sbjct: 367 FADVNNKMRIAQEEIFGPVVCLIPFKDEAEALQLANDTEYGLASYIWTQDIGKAHRLARG 426

Query: 440 LQAGIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENYLSVKQV 485
           ++AG+V+IN      ++ P+GG+K SG GRE G++  E +  +K V
Sbjct: 427 IEAGMVFINSQNVRDLRQPFGGVKGSGTGREGGQYSFEVFAEIKNV 472


Lambda     K      H
   0.317    0.134    0.402 

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: 587
Number of extensions: 19
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: 503
Length of database: 486
Length adjustment: 34
Effective length of query: 469
Effective length of database: 452
Effective search space:   211988
Effective search space used:   211988
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 (21.6 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