GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Sinorhizobium fredii NGR234

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_164924158.1 NGR_RS12135 aspartate aminotransferase family protein

Query= BRENDA::P42588
         (459 letters)



>NCBI__GCF_000018545.1:WP_164924158.1
          Length = 399

 Score =  219 bits (559), Expect = 1e-61
 Identities = 133/384 (34%), Positives = 212/384 (55%), Gaps = 20/384 (5%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD-PLRAMLAKTLA 134
           L+   G  ++D   G  + ++GH +P +V A++ Q A++  H   L D P +  LA+ L 
Sbjct: 26  LIAEDGTRYLDFAAGVAVNSLGHAHPHLVEALKAQ-AEKLWHVSNLYDVPGQESLARRLT 84

Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSAT 191
           A+T       FF NSG E++E A+K A+ Y   +G   +F  I   GAFHG+++  ++A 
Sbjct: 85  AVTFADRV--FFTNSGAEALECAIKTARRYHFAKGHPERFHVITFEGAFHGRTIATIAAG 142

Query: 192 AKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPP 251
            +  + + F P  PGF  VPFG+I A++ A+N      D+ AA+++EPIQGEGG+ L   
Sbjct: 143 GQQKYIEGFGPKAPGFYQVPFGDIAAVKNAIN------DETAAILIEPIQGEGGIRLASK 196

Query: 252 GYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGA 311
            ++  +R LCDE+G L+ILDEVQ G+GRTGK+FA E   + PDI+ +AK +GGG  P+GA
Sbjct: 197 EFMQELRALCDEYGLLLILDEVQCGVGRTGKLFAHEWSGITPDIMAVAKGIGGG-FPLGA 255

Query: 312 TIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371
            +ATE   + +      H +T+GGNPLA A   A ++V+L +           +   G  
Sbjct: 256 CLATEAAAAGMVAG--THGSTYGGNPLAMAVGNAVLDVVLAEGFLENVRDVALVFRQGLA 313

Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPL 431
            L   +PD+++E RG G+++ I+    ++      +  R   L+A        +R+ PPL
Sbjct: 314 SLKDRFPDVIEEIRGDGLMLGIK---AKVPCADVLKAIRAEKLLAVPAGE-NVLRLLPPL 369

Query: 432 TLTIEQCELVIKAARKALAAMRVS 455
             T  +    +    +A  A+R +
Sbjct: 370 ITTAAEAREGLARLERAAEAVRAA 393


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: 400
Number of extensions: 20
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: 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 Apr 09 2024. 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