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_02696 CCNA_02696 AtzE family amidohydrolase

Query= curated2:Q72L58
         (471 letters)



>FitnessBrowser__Caulo:CCNA_02696
          Length = 464

 Score =  253 bits (645), Expect = 1e-71
 Identities = 186/475 (39%), Positives = 248/475 (52%), Gaps = 52/475 (10%)

Query: 5   EIRARVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLN-ERLLEEAEAVDPGL------- 56
           EI   V  G V+   V +A L R+Q LD G+ AF ++  ER L  AEAVD  L       
Sbjct: 8   EIAGEVRAGRVTARAVTEATLSRIQRLDGGINAFTAVTAERALAAAEAVDADLAAGRPVG 67

Query: 57  PLAGLVVAVKDNIATRGLRTTAGSRLLENFVPP-YEATAVARLKALGALVLGKTNLDEFG 115
           PLAG+  AVK+     GL T AGS++     PP ++AT V RL A GA+++G  N+DEF 
Sbjct: 68  PLAGVPFAVKNLFDLEGLPTLAGSKIRRAAAPPAHDATLVQRLTAAGAVLVGALNMDEFA 127

Query: 116 MGSSTEHSAFFPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAFCGV 175
            G  TE++   P +NP DP R+ GGSSGGSAAA+AA L PL LGSDT GS+R PA  CGV
Sbjct: 128 YGFVTENAHDGPVRNPHDPTRIAGGSSGGSAAAVAAGLVPLTLGSDTNGSIRIPAGLCGV 187

Query: 176 YGLKPTYGRVSRFGLIAYASSLDQIGPMARSVRDLALLMDAVAGPDPLDATSLDLPPRFQ 235
           +GLKPTYGR+SR G+  +  SLD +GP ARSV DLAL  D + GPDP   +   +  R  
Sbjct: 188 FGLKPTYGRLSRQGVFPFVESLDHVGPFARSVEDLALAYDVLQGPDP---SGDPICIRDA 244

Query: 236 EALEGPL-----PPLRLGVVREAL-AGNSPGVERALEEALKVFRELGLSVREVSWPSLPQ 289
           E L G L      PLR+GV+      G  P V  AL            +  EV+  +   
Sbjct: 245 EPLAGRLDALAEQPLRVGVLGGWFQQGAFPEVLAALGRVADALE----ARDEVTLQNAQA 300

Query: 290 ALAAYYILAPAEASSNLARYDGTLYGRRAEGEEVEGMMEATRAL-FGLEVKRRVLVGTFV 348
           A AA + L                     EG E+     A RA+ +   V+ R+L G  +
Sbjct: 301 ARAAAFCLT------------------AFEGGELHHEDLARRAMDYDPAVRDRLLAGA-L 341

Query: 349 LSSGYYEAYYGRAQAFRRRLKAEAQALFREVDLLLLPTTPHPAFPFGARRDPL----AMY 404
           L +G  EA    AQ FR   + E + +F+  D+LL P +  PA P G     +       
Sbjct: 342 LPAGVAEA----AQRFRTIFRDEVREVFQRYDILLAPASVCPAPPIGQATMEMDGVPVSV 397

Query: 405 REDL--YTVGANLTGLPALSFPAGFEGHLPVGLQLLAPWGEDERLLRAALAFEEA 457
           R++L  +T   +  GLP L+ P    G LP+G+Q++AP   ++    AAL  + A
Sbjct: 398 RKNLGAFTQPISYVGLPVLAAPVNRPGQLPIGVQIIAPPWREDLAFAAALRLQRA 452


Lambda     K      H
   0.319    0.137    0.395 

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: 581
Number of extensions: 29
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: 471
Length of database: 464
Length adjustment: 33
Effective length of query: 438
Effective length of database: 431
Effective search space:   188778
Effective search space used:   188778
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: 51 (24.3 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