GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Enterococcus termitis LMG 8895

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_069663619.1 BCR25_RS10830 amidase

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_001730305.1:WP_069663619.1
          Length = 486

 Score =  154 bits (389), Expect = 7e-42
 Identities = 137/489 (28%), Positives = 229/489 (46%), Gaps = 61/489 (12%)

Query: 18  KEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMPIG 77
           K++ +++ +D+  +++   + ++ AF+  D E A+   K  D      +++G  FG+PI 
Sbjct: 14  KKLSVTEWIDDREQQLNKRNPELNAFVDWDAEAAKKQYKAND------TQNGPFFGLPIP 67

Query: 78  VKD-NIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTENS 136
           +K      KG++ +  S++ +          VQ L+    + +GK N  EF   + ++  
Sbjct: 68  LKMLGQDKKGMKASSGSRLFKEQRATSTDHFVQGLERLGFIPLGKTNAPEFGFKNISDPL 127

Query: 137 AYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTYG 196
            Y   KNPWNLD  PGGSSGG+AAAVA+G  P +  SD GGSIR PASF G++GLKPT G
Sbjct: 128 IYGPAKNPWNLDYSPGGSSGGAAAAVASGLFPIAGASDGGGSIRIPASFSGLIGLKPTRG 187

Query: 197 R--VSRYGLVAF-ASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLT 253
              V   G   +  +S+D    +T ++ D   L   + G +K  +    V   ++     
Sbjct: 188 SMPVGPNGWRGWQGASID--FALTVSMRDTETLFYHLRGTEK--AAPYQVPKAEWSHQAA 243

Query: 254 GDIKGLKIA-VPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLP-HSKYALATYYL 311
            + K LKIA + +  +G  V  EA ++V  A+  LE  G    EVS P + +  + +YYL
Sbjct: 244 TEKKSLKIAFLTESPVGTPVSSEAVKAVHNAVDFLEKQGHQVTEVSYPVNGRQLIDSYYL 303

Query: 312 LSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYY 371
           ++ +E +   A F+GI+   +   +   ++L                +  G +       
Sbjct: 304 MNGAETA---AMFEGIQESLQRPLSKADMEL----------------MTWGIYQYGIQLS 344

Query: 372 DAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKI-----GENTKDPLT------ 420
            + Y ++ ++        E +FE+YD+ + PT    A KI      E  +  L       
Sbjct: 345 ASQYTRSLQLWDQAAYKMEQLFEEYDLFLTPTAADTAPKIDAELQSEQIRKELAQAETLS 404

Query: 421 ----------MYANDILTIP----VNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTV 465
                     M+   +   P     NL G P IS+P  +A+ GLPLG+Q +     E  +
Sbjct: 405 QKQLQELIYDMFEKSLTITPFTQLANLTGQPAISLPTHVAESGLPLGVQFMASKGREDLL 464

Query: 466 YRVAHAFEQ 474
           ++V   FE+
Sbjct: 465 FQVGELFEK 473


Lambda     K      H
   0.315    0.134    0.381 

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: 470
Number of extensions: 16
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 485
Length of database: 486
Length adjustment: 34
Effective length of query: 451
Effective length of database: 452
Effective search space:   203852
Effective search space used:   203852
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: 52 (24.6 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