Aligments for a candidate for gatA in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Aligments for a candidate for gatA in Sphingomonas koreensis DSMZ 15582

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate Ga0059261_0838 Ga0059261_0838 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases

Query= curated2:Q9RTA9
         (482 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_0838 Ga0059261_0838
           Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and
           related amidases
          Length = 453

 Score =  160 bits (406), Expect = 6e-44
 Identities = 148/484 (30%), Positives = 213/484 (44%), Gaps = 71/484 (14%)

Query: 7   AAQLARAVQSGETTPQQLLHGALARAEAVR-GLNALVSLN-SHAEEQAAAVQGRMQAGET 64
           A  +A A+ +GET+ +     A+AR EA    +NA+V  + + A E A      +  GE 
Sbjct: 21  ALGIAAAIAAGETSARAQCELAIARIEADDDAINAVVVRDFARALEAADRADAAVARGER 80

Query: 65  LPLAGVPIVVKDNINVTGTRTTCGSRMLANYVSPYTATAAQKLQGAGAVIVGKANMDEFA 124
            P  GVP+ VK+  +V G  T+ G     + ++   A   Q+++ AGAVI+GK N+    
Sbjct: 81  RPFLGVPMTVKEAFDVEGLPTSWGFAHARDTIATSDAVVVQRMKAAGAVILGKTNVAPGL 140

Query: 125 MGSSTESSASGPTLNPWDHERVPGGSSGGSAVAVAAGISPVSLGSDTGGSVRQPAALCGV 184
               +++   G T NP D  R  GGSSGGSA A+AAG     +GSD GGS+R PAA CGV
Sbjct: 141 ADWQSDNVVYGRTANPRDLSRTAGGSSGGSAAALAAGFVTAEIGSDIGGSIRVPAAFCGV 200

Query: 185 YGFKPTYGRVSRYGLVAYASS-----LDQIGPFARSAEDLALLMNVIAGHDPRDATSLDA 239
           +G KP+Y  +  YG     S      L  +GP AR A DLA +++++A       T L  
Sbjct: 201 WGHKPSYELIDPYGHRFPGSDGASPPLGVVGPMARDAADLAAMLDILAD------TPLPR 254

Query: 240 PARFAVGGADSLRGLRVGVIRESLGGNTPGVEAALGATLDALRGAGAVVGEVS--IPELE 297
             RF   G   +  L             P +  AL     A   AG  +   S  +P+L 
Sbjct: 255 AGRFLGPGGKQILLLD----SHPAAPTDPAIRGALDRLDAAANQAGIHIARSSDLLPDLA 310

Query: 298 YAIAAYYLIAMPEASSNLARYDGMVYGERVPGGDVTRSMTLTREQGFGQEVQRRILLGTY 357
               AY             +   + +    PG +                       G  
Sbjct: 311 AQHRAY------------CKMLAITFARGAPGPN-----------------------GQA 335

Query: 358 ALSSGYYDAYYAKAMKVRRLIADEFTTAFGQYDVLVTPTSPFPAFRRGEKASDPLAMYAA 417
           A  S ++D   A+A + RR+    ++  F ++D +VTP +   AF   +   +   M   
Sbjct: 336 ASLSDWFDQLDAQA-RNRRI----WSRLFDEFDAVVTPANVVTAFPHRDDPYNERRMTVD 390

Query: 418 DVDT------VAVNLA---GLPALSVPAGFEEVDGKRLPVGVQFIAPALQDERLLALAGA 468
             DT      V   +A   GLPA + PAG    DG  LPVG+Q IA    D R +A+A  
Sbjct: 391 GQDTSYDAQLVWAGIATYPGLPATAFPAG-TTADG--LPVGLQVIADYRDDHRAIAIADL 447

Query: 469 LEAV 472
           L  V
Sbjct: 448 LHGV 451


Lambda     K      H
   0.316    0.132    0.372 

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: 539
Number of extensions: 34
Number of successful extensions: 4
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: 482
Length of database: 453
Length adjustment: 33
Effective length of query: 449
Effective length of database: 420
Effective search space:   188580
Effective search space used:   188580
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 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis