GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Desulfovibrio vulgaris Hildenborough

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 207835 DVU2347 acetylornithine aminotransferase

Query= BRENDA::P42588
         (459 letters)



>MicrobesOnline__882:207835
          Length = 399

 Score =  198 bits (504), Expect = 2e-55
 Identities = 126/366 (34%), Positives = 197/366 (53%), Gaps = 32/366 (8%)

Query: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAK-----QPLHSQELLDPLRAMLAKT 132
           D +G+E+ID L G  + ++GH +P +   +  Q  K        + +E LD    +  K 
Sbjct: 37  DHEGREYIDLLSGIAVTSLGHCHPELAEVMARQARKLVHVSNLFYQEEQLD----LAEKL 92

Query: 133 LAALTPGKLKYSFFCNSGTESVEAALKLAKAY-QSPRG--KFTFIATSGAFHGKSLGALS 189
           L+ L   K   +FFCNSG E+ EAA+KLA+ Y Q  RG      +  +GAFHG++L  ++
Sbjct: 93  LSTLHCTK---AFFCNSGAEANEAAIKLARRYMQRVRGVDAHEVVTLTGAFHGRTLATVA 149

Query: 190 ATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILP 249
           AT +  F+  F P+  GFR   +G+I+A+R A+          A V++E +QGEGGV   
Sbjct: 150 ATGQERFQDGFAPMPAGFRQAEWGDIDALRAAITPA------TAGVLVEMVQGEGGVRPM 203

Query: 250 PPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPI 309
              Y  AV  LC E G L+++DE+QTG+ RTG+ +A +H  V+PDI+  AKAL  G +P+
Sbjct: 204 TQDYARAVADLCREKGVLLMVDEIQTGLCRTGRFWAHQHYGVEPDIVTSAKALANG-LPM 262

Query: 310 GATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDG 369
           GA + T+EV          H TTFG   L  + A AT++++    L  +A   G   ++ 
Sbjct: 263 GAMMTTDEVAQGFVAGS--HATTFGAGALVSSVAAATLDIMKRDRLDERATAVGGRAMER 320

Query: 370 FRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNA--KTIRI 427
           FR +  + P  ++E RG G+++ I    +        E++++ V      NN   K +R+
Sbjct: 321 FRAIGAKLPGTIEEVRGYGLMIGIVLTFS------GKEVWKELVARGFVCNNTQEKVLRL 374

Query: 428 EPPLTL 433
            P LT+
Sbjct: 375 VPALTI 380


Lambda     K      H
   0.320    0.135    0.393 

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: 382
Number of extensions: 20
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: 459
Length of database: 399
Length adjustment: 32
Effective length of query: 427
Effective length of database: 367
Effective search space:   156709
Effective search space used:   156709
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