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); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized)
to candidate AZOBR_RS31000 AZOBR_RS31000 aldehyde dehydrogenase

Query= BRENDA::Q9STS1
         (503 letters)



>FitnessBrowser__azobra:AZOBR_RS31000
          Length = 479

 Score =  312 bits (799), Expect = 2e-89
 Identities = 186/480 (38%), Positives = 262/480 (54%), Gaps = 14/480 (2%)

Query: 8   RQLFIGGQWTEPVLRKT-LPVVNPATEDIIGYIPAATSEDVELAVEAARKAFTRNNGKDW 66
           +  +IGG WTEP    T + V+NPATE + G +     ED + AV AA  AF       +
Sbjct: 5   QSFYIGGAWTEPAAGATVMEVLNPATEQVSGTVALGGPEDAQRAVAAAHAAFD-----GF 59

Query: 67  ARATGAVRAKYLRAIAAKVIERKSELANLEAIDCGKPLDEAAWDMDDVAGCFEYYADLAE 126
           +R     R + L A+ A   +R  E+A+    + G PL      +   A  F   A    
Sbjct: 60  SRTPLNERLELLAAVCALFEKRMDEVADAITEEMGAPLAA----LSKPAQAFMGLAHFKT 115

Query: 127 GLDAKQKTPLSLPMDTFKGYILKEPIGVVGMITPWNYPLLMAVWKVAPSLAAGCTAILKP 186
            L+A ++ P      T +  IL+EP+GV  MITPWN+P+     KVAP+LA GCT +LKP
Sbjct: 116 ALEAAREYPFERTRGTTR--ILREPVGVCAMITPWNWPINQIACKVAPALATGCTMVLKP 173

Query: 187 SELASLTCLELADICREVGLPPGVLNILTGLGTEAGAPLASHPHVDKIVFTGSTTTGSSI 246
           SE A  +    A+I  E G+P GV N+  G G   G  LASHP VD +  TGST  G+S+
Sbjct: 174 SEFAPYSAWIFAEILHEAGVPAGVFNMFYGDGAVVGPVLASHPLVDMVSLTGSTRAGASV 233

Query: 247 MTSAAKLVKPVSLELGGKSPIIVFDDVDIDKAVEWTMFGCFWTNGQICSATSRLLVHERI 306
             +AA  +K VSLELGGKS  I+ +  D+ KAV   +       GQ C+A SR+ V    
Sbjct: 234 SHNAADSIKRVSLELGGKSANIICESADLTKAVTHGVRSMMSNTGQSCNAPSRMYVPASR 293

Query: 307 ADEFLDKLVKWTKNIKISDPFEEGCRLGPVVSKGQYERVLKFVSNARNEGATVLCGGV-R 365
            DE      +    + + DP  +   +GP+ ++ QYERV + +     EGAT+LCGG  R
Sbjct: 294 LDEAETIAAQVCARLVVGDPRGDRTGVGPIANQRQYERVQRLIQAGIEEGATLLCGGPGR 353

Query: 366 PEHLKKGYFVEPAIVSNVTTSMEIWREEVFGPALCVKTFSTEDEAIQLANDSQYGLAGAV 425
           P+ L++G++ +P + S  T  M I REE+FGP L ++ +   +EAI+ ANDS YGL+G V
Sbjct: 354 PDGLERGFYAKPTVFSRATDGMTIMREEIFGPVLTIRPYEDIEEAIRSANDSLYGLSGYV 413

Query: 426 LSNDLERCDRVSKAFQAGIVWVNCSQPCFCQAPWGGTKRSGFGRELGEWGLENYLSVKQV 485
            +  ++    V+K  + G+V +N        AP+GG K+SG GRE GE G E +L  K V
Sbjct: 414 YAGTVDEARAVAKRLRTGMVHLN-GASIDLAAPFGGYKQSGIGREWGEVGFEEFLETKSV 472


Lambda     K      H
   0.318    0.135    0.421 

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: 637
Number of extensions: 27
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: 479
Length adjustment: 34
Effective length of query: 469
Effective length of database: 445
Effective search space:   208705
Effective search space used:   208705
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 (21.7 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