GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Azospirillum brasilense Sp245

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate AZOBR_RS26825 AZOBR_RS26825 aldehyde dehydrogenase

Query= BRENDA::Q93YB2
         (503 letters)



>FitnessBrowser__azobra:AZOBR_RS26825
          Length = 494

 Score =  299 bits (765), Expect = 2e-85
 Identities = 183/482 (37%), Positives = 268/482 (55%), Gaps = 16/482 (3%)

Query: 10  LFINGDWKAPVLNKRIPVINPATQNIIGDIPAATKEDVDVAVAAAKTALTRNKGADWATA 69
           L I G+ +     K   V+NPAT ++I       + DVD AV AA  A    +GA WA  
Sbjct: 18  LLIGGELRPAATGKTFDVVNPATGDVIATAADGGERDVDAAVRAAVAA----QGA-WARL 72

Query: 70  SGAVRARYLRAIAAKVTEKKPELAKLESIDCGKPL-DEAAWDIDDVAGCFEYYADLAEKL 128
           S   R R L     ++     E+ +L +++ GK +  E+  +   VA    +Y  LA +L
Sbjct: 73  SARERGRLLVECGRRLVGHAEEIGRLLALETGKAIRTESRVEASLVADTLTFYGGLASEL 132

Query: 129 DARQKAPVSLPMDTFKSHVLREPIGVVGLITPWNYPMLMATWKVAPALAAGCAAILKPSE 188
              +  P    M TF     REPIGVVG I PWN P+ +   K+APAL AG A I+K +E
Sbjct: 133 KG-ETVPFHPKMLTFTQ---REPIGVVGAIIPWNVPLYLMALKIAPALVAGNAVIVKSAE 188

Query: 189 LASLTCLELGEICKEVGLPPGVLNILTGLGPEAGAPLATHPDVDKVAFTGSSATGSKIMT 248
            A L  L + ++  ++ LPPGVLNIL+G GP  GAPL THP V KV FTGS  TG  I  
Sbjct: 189 EAPLAALRVIQVMNQL-LPPGVLNILSGDGPGCGAPLVTHPGVGKVTFTGSVETGKIISH 247

Query: 249 AAAQLVKPVSLELGGKSPLVVFEDVDLDKAAEWAIFGC-FWTNGQICSATSRLILHESIA 307
            AA  + PV+LELGGKSP++V  D DLDKA + A+ G  F   GQ C+A+SR+ +HES+ 
Sbjct: 248 LAADKLIPVTLELGGKSPMIVMGDADLDKAIDGAVAGMRFTRQGQSCTASSRIFVHESLH 307

Query: 308 TEFLNRIVKWIKNIKISDPLEEGCRLGPVVSEGQYEKILKFVSNAKSEGATILTGGS--- 364
             F++++   +  + + DPL+E   +G ++S  Q+E++  +++  ++    I    S   
Sbjct: 308 DAFIDKLKAKVDAMTMGDPLDEATDIGTIISPQQFERVQSYIALGETTAGAIAHRCSALP 367

Query: 365 RPEHLKKGFFIEPTIITDVTTNMQIWREEVFGPVLCVKTFSTEEEAIDLANDTVYGLGAA 424
             E L +G F++P + T +  + ++ REE+FGPV CV  F   E+A+ +AND+ +GL A 
Sbjct: 368 TDERLARGLFVQPVLFTGLANDHRLAREEIFGPVTCVIAFRDYEDALAMANDSDFGLAAT 427

Query: 425 VISNDLERCERVTKAFKAGIVWVNCSQPCFTQAPWGGVKRSGFGRELG-EWGLDNYLSVK 483
           + + DL      T+  +AG V VN +        +GG K+SG G+E   E  LD++   K
Sbjct: 428 IWTRDLRTALDATRRLQAGFVQVNQNLVVQPGLSYGGFKQSGLGKEASLEAMLDHFTHKK 487

Query: 484 QV 485
            V
Sbjct: 488 TV 489


Lambda     K      H
   0.318    0.135    0.416 

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: 534
Number of extensions: 27
Number of successful extensions: 6
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: 494
Length adjustment: 34
Effective length of query: 469
Effective length of database: 460
Effective search space:   215740
Effective search space used:   215740
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