GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Flavobacterium glycines Gm-149

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_066324795.1 BLR17_RS07430 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= curated2:B0KBN4
         (488 letters)



>NCBI__GCF_900100165.1:WP_066324795.1
          Length = 465

 Score =  328 bits (840), Expect = 3e-94
 Identities = 185/446 (41%), Positives = 264/446 (59%), Gaps = 9/446 (2%)

Query: 8   IHELRELLKKREVSALEVTKSYLERIKEVEPKIDALITITEDFALQRAKEADEKIKNGED 67
           I ++ + L  +++S   + +  L+ +K+     +++ ++ +  AL+ A + D KI NGE 
Sbjct: 5   IKKIHQQLVSKQISCTALVQEKLDLLKQ--NTYNSVNSVLDTLALELAAKVDAKIANGET 62

Query: 68  TALT-GIPVIIKDNISTEGIKTTCSSKMLENYIPPYNATVVEKLLEEGVIILGKSNLDEF 126
             L  GIP  IKD    +G  TT SS++L NY  PY AT ++KLL+ G I L K N D F
Sbjct: 63  IGLLEGIPFGIKDVYMVQGTYTTASSELLRNYKSPYTATAIQKLLDAGAIPLAKENCDSF 122

Query: 127 AMGSSTENSAFKTTKNPWDLSRVPGGSSGGSAAAIAADEAAFALGSDTGGSIRQPASLCG 186
             GSS+EN+ F   KN  +   V GGSSGGSA  +A +   F++G DTGGSIRQPA    
Sbjct: 123 GHGSSSENTIFGAVKNAINPELVGGGSSGGSAVNVAKEYTVFSIGGDTGGSIRQPAGYNH 182

Query: 187 VVGMKPTYGLVSRYGLVAFASSLDQIGPFTKDVTDCAIVLNTIIGHDPKDSTSLKIDKPD 246
           + G+KPTYG +SRYGL+A+ASS D +GP  K + D  IVLN + G DPKD TS+   +  
Sbjct: 183 IYGLKPTYGRISRYGLMAYASSTDCVGPLAKSIEDIRIVLNVMSGKDPKDQTSIASTEIS 242

Query: 247 YTSYLKEDIKGLRIGVAKEFF-GEGIEEGVKETVQESIKVLQDLGAEIIDISIPYVEYAL 305
             +    ++K   IG  K F   E I+  +K     S++ ++  G E+ ++     +  +
Sbjct: 243 EDAIATSEVK--TIGYFKNFIESEAIDAQIKADFLASVEKIKAKGIEVKELDFFKSDILV 300

Query: 306 PAYYIIASAEASSNLARYDGIRYGH-IAGKYEDLIDMYMVTRSEGFGKEVKRRIMLGTYA 364
             YY +A AE +SNL+R DG  YG+ I G  E+LID Y VTRSE F +E KRRI+ G   
Sbjct: 301 STYYTLAMAETASNLSRLDGTNYGNRIEG--ENLIDTYAVTRSENFSEETKRRIVGGNQV 358

Query: 365 LSSGYYDAYYKKALKVRTLIKNDFEKAFEKCDVIIGPTSPTVAFKIGERANDPLAMYLAD 424
           LS G+ D  Y K L +R  I  +F K F++ DVI+ P +P+   KIG+   DPLAMYL+D
Sbjct: 359 LSQGFSDEIYLKGLALRDQISENFSKDFQEVDVILSPVTPSTPPKIGDSLKDPLAMYLSD 418

Query: 425 IYTVSVNIAGLPGISIPCGLSDGLPV 450
            YTV  ++  LP I++P G + GL +
Sbjct: 419 AYTVGFSLGQLPTITVPQGTTTGLQI 444


Lambda     K      H
   0.316    0.136    0.380 

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: 544
Number of extensions: 27
Number of successful extensions: 3
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: 465
Length adjustment: 33
Effective length of query: 455
Effective length of database: 432
Effective search space:   196560
Effective search space used:   196560
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.

Links

Downloads

Related tools

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