GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Caldicellulosiruptor kronotskyensis 2002

Align glutamate-tRNAGln ligase (EC 6.1.1.24) (characterized)
to candidate WP_013430673.1 CALKRO_RS08745 glutamate--tRNA ligase

Query= BRENDA::Q9X2I8
         (487 letters)



>NCBI__GCF_000166775.1:WP_013430673.1
          Length = 480

 Score =  433 bits (1114), Expect = e-126
 Identities = 219/478 (45%), Positives = 311/478 (65%), Gaps = 20/478 (4%)

Query: 24  LVRVRFAPSPTGHLHVGGARTALFNWMFARKEGGKFILRIEDTDTERSSREYEQQILESL 83
           +VRVRFAPSPTG LH+GGARTALFN++FA+K  GKFILRIEDTD ERS  E+ + I+ SL
Sbjct: 1   MVRVRFAPSPTGQLHIGGARTALFNYLFAKKHNGKFILRIEDTDLERSREEWAKGIMRSL 60

Query: 84  RWCGLDWDEGPDIGGDFGPYRQSERLEIYREYAEKLVEDKRAYYVVYDKE--DPSKELFT 141
           RW G++WDEGPD+GGDFGPY QS+R EIY EY +KL+E+ +AYY    +E  +  +E+  
Sbjct: 61  RWLGIEWDEGPDVGGDFGPYFQSQRKEIYLEYIKKLLEEGKAYYCFCTQEEIEREREIAR 120

Query: 142 TYEYPHEYKEK---------------GHPVTIKFKV-LPGKTSFEDLLKGYMEFDNSTLE 185
             + P++Y +K               G    ++ K  + G T   D+++G +EF N  L+
Sbjct: 121 QQKIPYKYSKKCRNISLEEAKKRIKNGEKAVVRIKAPVEGTTVVHDIIRGDVEFSNDQLD 180

Query: 186 DFIIMKSNGFPTYNFAVVVDDHLMRISHVFRGEDHLSNTPKQLMIYEAFGWEAPVFMHIP 245
           DFII+KS+G PTYNF  V+DD+LM+ISHV R E+HLSNTPKQL+IYEA   + P F H+P
Sbjct: 181 DFIILKSDGNPTYNFVCVIDDYLMKISHVIRAEEHLSNTPKQLIIYEALNIQPPQFAHVP 240

Query: 246 LILGSDRTPLSKRHGATSVEHFRREGILSRALMNYLALLGWRVEGDE-IFTIEEKLQSFD 304
           +IL  DR+ LSKRHGATSVE F   G L  A++NYL LLGW    D  I +++E +Q F+
Sbjct: 241 MILAPDRSKLSKRHGATSVEEFFENGYLKEAIVNYLLLLGWSPGEDRTIISLDEAIQKFE 300

Query: 305 PKDISNKGVIFDYQKLEWVNGKHMRRIDLEDLKREFIEWAKYAGKEIPSVDERYFSETLR 364
            +++S    I+D  KL W+NG +++ ID++DL      +    G +I S D+ Y    L+
Sbjct: 301 LENVSKNAAIYDINKLTWINGYYLKEIDIDDLYERMKYFYSKNGIDISSFDKEYVKSVLK 360

Query: 365 ICREKVNTLSQLYDIMYPFMNDDYEYEKDYVEKFLKREEAERVLEEAKKAFKDLNSWNME 424
           + REKV TL+++      F + +YEYE+  VEK+   +   + L+      K++  ++ E
Sbjct: 361 LVREKVKTLAEVVSASSYFFDSNYEYEQKGVEKYFTADNL-KYLQLLLNDLKNVQPFSAE 419

Query: 425 EIEKTLRDLSEKGLASKKVVFQLIRGAVTGKLVTPGLFETIEVLGKERTLKRLERTLQ 482
           EIEK +R  +E+       +   IR  ++G+ VTPGLFE +EVLGK+  + R+E+TL+
Sbjct: 420 EIEKLVRSKAEEFNTKAANLIHTIRMCISGRTVTPGLFEMMEVLGKDEVINRIEKTLK 477


Lambda     K      H
   0.320    0.139    0.416 

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: 708
Number of extensions: 36
Number of successful extensions: 6
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: 487
Length of database: 480
Length adjustment: 34
Effective length of query: 453
Effective length of database: 446
Effective search space:   202038
Effective search space used:   202038
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 (21.8 bits)
S2: 52 (24.6 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