GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Lentibacillus jeotgali Grbi

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_010530226.1 ON01_RS06595 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= curated2:B8HY89
         (482 letters)



>NCBI__GCF_000224785.1:WP_010530226.1
          Length = 462

 Score =  325 bits (832), Expect = 3e-93
 Identities = 196/472 (41%), Positives = 268/472 (56%), Gaps = 27/472 (5%)

Query: 6   ELHQQLVSKERSAKEITQDALEKIQQLEPKVHAFLTLTAEQALAQAERVDQQIATGTEIG 65
           EL   + SK+ S  E+T   L +I  ++P +H+++T   E AL QA   +Q I  G   G
Sbjct: 11  ELAPLIESKQLSPVELTNHLLTRIDTIDPTIHSYITPLPELALKQAREAEQNIMHGRYKG 70

Query: 66  LLAGIPIAIKDNLCTKGIPTTCGSKILQGFIPPYESTVTSRLAAAGAVMVGKTNLDEFAM 125
            L GIP+ IKDN  TKGI TT GSK+   FIP   +    +L AAG +M+GK N+ E A+
Sbjct: 71  PLHGIPVGIKDNYYTKGIRTTAGSKLFVDFIPNKTAPAAEKLLAAGGIMLGKLNMHELAL 130

Query: 126 GSSTENSAYQLTANPWDLQRVPGGSSGGSAAAVAAGETLIALGSDTGGSIRQPASFCGVV 185
           GS+  N  +  T NPW++  +PGGSSGGS+AA+AAG T +A G+DT GSIR PA+ CGV 
Sbjct: 131 GSTGTNLTFGTTRNPWNIHHMPGGSSGGSSAALAAGLTTLATGTDTFGSIRLPAAMCGVY 190

Query: 186 GLKPTYGLVSRYGLVAYASSLDQIGPFATNVEDAALLLGAIAGHDPQDSTSLNVPIPDYT 245
           GLKPTYGLVS   +   A SLD  GP A +V D AL+L  +AG D  D  SL V  PDY 
Sbjct: 191 GLKPTYGLVSTSNMFPSAWSLDTAGPMARSVSDLALMLNDMAGFDANDPASLRVSTPDYA 250

Query: 246 QFLIPDLKGKKIGIIQETYGEGLDPQVEQVTHKAIQQLEELGAEVREISCPRFRYGLPTY 305
           + L   ++G +IG I   Y EGLD +VE++   AI+ L+ LGAE+REI  P       + 
Sbjct: 251 EDLNKGIRGIRIG-IPTYYLEGLDTEVERLFKNAIETLQNLGAEIREIVIPELSMSTFSG 309

Query: 306 YIIAPSEASANLARYDGVKYGFRSPDPENLLSMYTRTRAEGFGPEVKRRIMIGTYALSAG 365
           Y I   EASA    Y+                 + +T +E +G + +  ++ GT   +  
Sbjct: 310 YSIVAGEASA--FHYE-----------------WLQTHSEDYGADNRIFLLSGTLTNT-- 348

Query: 366 YYDAYYLKAQKVRTLIKQDFEAAFEQVDVLVCPTAP--TTAFAAGAKTADPLSMYLSDLM 423
               + +KAQ+ R  + + F  A E VD+++ PT P  T AFA      +   +      
Sbjct: 349 ---PHCVKAQQARRKMIEAFHNALESVDIMLGPTIPITTPAFAQNWVEQNLEVIRRCLPF 405

Query: 424 TIPVNLAGLPGLSLPCGFDQQGLPIGLQLIGNVLREDLVFQVAYAYEQATPW 475
           T PVNL G P LS+P G D +GLP G+Q IGN L E  + QVA+A+E+  P+
Sbjct: 406 TSPVNLLGTPSLSMPMGLDLRGLPAGMQFIGNHLSEKQLLQVAHAWERINPF 457


Lambda     K      H
   0.317    0.134    0.388 

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: 518
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: 482
Length of database: 462
Length adjustment: 33
Effective length of query: 449
Effective length of database: 429
Effective search space:   192621
Effective search space used:   192621
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Jul 26 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:

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