GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Caulobacter crescentus NA1000

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate CCNA_01906 CCNA_01906 allophanate hydrolase

Query= curated2:Q67KJ2
         (488 letters)



>FitnessBrowser__Caulo:CCNA_01906
          Length = 594

 Score =  191 bits (485), Expect = 6e-53
 Identities = 172/481 (35%), Positives = 235/481 (48%), Gaps = 60/481 (12%)

Query: 17  SAVEIAESALSRIAQ---VEPAVGAFITVAADHVIERAKKLDARRKAGDTELGPLAGVPI 73
           SA  +A SAL+ I     ++P V   + +    V+ +A+ +DAR  AG+T   PLAGVP 
Sbjct: 20  SAESVARSALAAIEAYDAIQPQVWT-LRLPEAAVLAQARAVDARIAAGETL--PLAGVPF 76

Query: 74  AVKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKANMDEFAMGSSGESS 133
           AVKDNI  + + TT A      Y +   ATVVE+L AAGA+++GK N+D+FA G  G  S
Sbjct: 77  AVKDNIDVADLATTAACPGF-AYTAGRSATVVEQLLAAGAVLVGKTNLDQFATGLVGTRS 135

Query: 134 AFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAAFTGIVGLKPTYG 193
            +G  R  ++   V GGSSSGSA AVAAG    ALGTDT GS R PAAF  +VGLKP+ G
Sbjct: 136 PYGAPRCVFNQAFVSGGSSSGSAVAVAAGLVAFALGTDTAGSGRVPAAFNHLVGLKPSKG 195

Query: 194 YVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRD--ATNAGRTPPALKFGGEP 251
             S  G+V    SLD +     D++   R+  V+A  D  D  +  A +  PAL      
Sbjct: 196 RWSTRGLVPACRSLDCISVFAADLDGAGRVDAVLAAFDPEDPYSRPAPQPEPAL------ 249

Query: 252 SLSGVRLGVPKE----LLGPGIDPGVKARVEEAIAQLEELGATVEECSL-PSTEYALSAY 306
           +L+G+R+ +P+       G G    + A    A+A+L+  GA   E  + P  + A   Y
Sbjct: 250 TLAGLRVAIPRPEQRIFFGDGESEALYA---SAVARLQAAGAVAVEVDMAPLLDAAKLLY 306

Query: 307 YVIAVAEASSNL-----ARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIMLGTY 361
               VAE ++ +     A    +    RA   GGL            G E  R    G Y
Sbjct: 307 SGPWVAERTAAVEPLLRAAPSAIEPTVRAIVQGGLAVT---------GVETFR----GLY 353

Query: 362 VLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIGEKVDDPVSMYLG 421
            L A      YRRA           E  +   DAL  PTTP T + +     +P+++   
Sbjct: 354 ALEA------YRRAA----------EAVWAAADALFLPTTP-TIYTVKALKAEPLALNAN 396

Query: 422 -DICTIPVNLAGLPAVSVPCGF-VDGLPVGMQLIGKPFADTQILQIAWAYQKVTKHHEAR 479
             + T  VNL  L A++VP GF  DG   G+  IG  FAD  +L +A  Y +     E  
Sbjct: 397 LGLYTNFVNLLDLSALAVPAGFRADGTGFGVTFIGPAFADRALLDLAAVYLETFPMAETP 456

Query: 480 P 480
           P
Sbjct: 457 P 457


Lambda     K      H
   0.318    0.135    0.391 

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: 703
Number of extensions: 37
Number of successful extensions: 4
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: 488
Length of database: 594
Length adjustment: 35
Effective length of query: 453
Effective length of database: 559
Effective search space:   253227
Effective search space used:   253227
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 Aug 03 2021. The underlying query database was built on Aug 03 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