Alignments for a candidate for gatA in Caulobacter crescentus NA1000

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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original publication.

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

GapMind for Amino acid biosynthesis