GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Pseudomonas fluorescens GW456-L13

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate PfGW456L13_3622 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)

Query= curated2:Q72L58
         (471 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3622
          Length = 474

 Score =  191 bits (486), Expect = 3e-53
 Identities = 147/466 (31%), Positives = 233/466 (50%), Gaps = 35/466 (7%)

Query: 9   RVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLNERLLEEAEAVDPGL-PLAGLVVAVKD 67
           R+  GEV+PLE+     + ++  DP LGA ++++    + A A+DP   PLAG+ + +KD
Sbjct: 17  RLKSGEVTPLELVNLAAREIEIQDPALGAVVAIDIEGAQRA-ALDPKAGPLAGVPILIKD 75

Query: 68  -NIATRGLRTTAGSRLLENFVPPY-EATAVARLKALGALVLGKTNLDEFGMGSSTEHSAF 125
            NI  +G  T  GSRL E+ VP   ++  V+RL+  GA++LGKT   EF     TE    
Sbjct: 76  TNIDVKGFATRHGSRLYEDAVPAQVDSEFVSRLRNAGAIILGKTKTPEFAGDFVTEPEWQ 135

Query: 126 FPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAFCGVYGLKPTYGRV 185
            P +NP +P    GGSSGGSA A+ A + P+A G+D GGS+R PA+ CGV GLKP+ GR 
Sbjct: 136 GPCRNPRNPQYASGGSSGGSACAVGAGMVPVAHGTDCGGSIRVPASVCGVVGLKPSRGRT 195

Query: 186 SRFGLIA-YASSLDQIGPMARSVRDLALLMDAVAGPDP-LDATSLDLPPRFQEALEGPLP 243
                +  +   LD    + R+VRD ALL+D ++G +P     +   PP + E L+   P
Sbjct: 196 PVGPHVGEFVGGLDSEHVLTRTVRDSALLLDVLSGYEPGAPYAAPPAPPSWLECLKTRSP 255

Query: 244 PLRLGVVREALAGNS--PGVERALEEALKVFRELGLSVREVSWPSLPQALAAYYILAPAE 301
            L++        G+S    + +A+  A+    + G  +R  +WP + +A AA  +    E
Sbjct: 256 RLKIAFACARPDGSSIDETIHKAILNAVDFLSKDGHELRPFNWPDMTKAGAAAALFWQME 315

Query: 302 ASSNLARYDGTLYGRRAEGEEVEGMMEATRALFGLEVKRRVLVGTFVLSSGYYEAYYGRA 361
             + L  +     G     ++VE +   T   +    +R  L           + ++ RA
Sbjct: 316 IEA-LMEHKAQTRGYPISVQDVEWI---TYEFYKCSTQRTAL-----------DVHHARA 360

Query: 362 QAFRRRLKAEAQALFREVDLLLLPTTPHP-----AFPFGARRDPLAMYRE----DLYTVG 412
              + ++  +    F ++D+L+ PT          F     R     Y+       +T  
Sbjct: 361 T--QNKVSHDMADSFTDIDVLITPTVALAPPLIGGFVATGERHLDEWYKNAYAFSPFTEV 418

Query: 413 ANLTGLPALSFPAG-FEGHLPVGLQLLAPWGEDERLLRAALAFEEA 457
            NLTG PA+S P G  E  LP+G+Q++  +G++E +LR A   E +
Sbjct: 419 FNLTGQPAISIPVGIMENGLPIGMQIVGKFGDEETILRLASEVERS 464


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: 476
Number of extensions: 22
Number of successful extensions: 5
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: 474
Length adjustment: 33
Effective length of query: 438
Effective length of database: 441
Effective search space:   193158
Effective search space used:   193158
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