Alignments for a candidate for gatA in Frankia alni ACN14a

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Frankia alni ACN14a

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_011606923.1 FRAAL_RS25510 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000058485.1:WP_011606923.1
          Length = 519

 Score =  481 bits (1239), Expect = e-140
 Identities = 252/462 (54%), Positives = 321/462 (69%), Gaps = 3/462 (0%)

Query: 19  EIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMPIGV 78
           E+   +    +  RI  VDD + AFL +D E A A A+ +DE        G L G+P+ +
Sbjct: 44  ELSAVEATQAALDRIAKVDDTIHAFLHVDTEGALAAARSVDERRAAGERLGPLAGVPLAL 103

Query: 79  KDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTENSAY 138
           KD +  +G+ TTC S+ILE +   YDATVV RL+ A+ V +GK+NMDEFAMGSSTENSAY
Sbjct: 104 KDVLTARGMPTTCGSRILEGWHAPYDATVVGRLRAADVVLLGKVNMDEFAMGSSTENSAY 163

Query: 139 KLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTYGRV 198
             T+NPW+   +PGGSSGGSAAAVAA E P ++G+DTGGSIRQPA+ CG+VG+KPTYG V
Sbjct: 164 GPTRNPWDTTRIPGGSSGGSAAAVAAFEAPLAIGTDTGGSIRQPAAVCGLVGVKPTYGGV 223

Query: 199 SRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSL-TGDIK 257
           SRYGLVAF+SSLDQ GP+ RTV D A L  AI+G D +DSTS +V VP  + +    DI+
Sbjct: 224 SRYGLVAFSSSLDQAGPLARTVTDAALLHAAIAGHDPLDSTSVDVPVPAVVEAAGRRDIR 283

Query: 258 GLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSSSEA 317
           GL+I V +E  GEG     + +  AA++ L  LGA   EVS PH  YALA YYL++ SE 
Sbjct: 284 GLRIGVVRELAGEGYDPGVQAAFAAAVETLTELGAEVVEVSCPHFTYALAAYYLIAPSEC 343

Query: 318 SANLARFDGIRYGYRT--DNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAYY 375
           S+NLARFD +R+G R   D      ++  +TR  GFG EVKRRI+LGT+ALSSGYYDAYY
Sbjct: 344 SSNLARFDAMRFGLRVGDDGQAGAEEVMSRTREAGFGPEVKRRIILGTYALSSGYYDAYY 403

Query: 376 KKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIPVNLAG 435
            +AQKVRTLI +DF   +E+ DV+V PTTPTPAF +G    DP+ MY +D+ TIP NLAG
Sbjct: 404 GQAQKVRTLISRDFAAAYERVDVLVSPTTPTPAFPLGSKVDDPVAMYLSDLCTIPSNLAG 463

Query: 436 VPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATD 477
            P +S+P GLADGLP+G+QI+   F +  +Y V  A E+A D
Sbjct: 464 GPAMSLPAGLADGLPVGIQIMAPPFADDRLYLVGGALEEALD 505


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: 662
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: 485
Length of database: 519
Length adjustment: 34
Effective length of query: 451
Effective length of database: 485
Effective search space:   218735
Effective search space used:   218735
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)

Align candidate WP_011606923.1 FRAAL_RS25510 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (EC 6.3.5.-))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00132.hmm
# target sequence database:        /tmp/gapView.1018107.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00132  [M=466]
Accession:   TIGR00132
Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-192  626.3   0.0   1.9e-192  626.1   0.0    1.0  1  NCBI__GCF_000058485.1:WP_011606923.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000058485.1:WP_011606923.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  626.1   0.0  1.9e-192  1.9e-192       4     465 ..      39     505 ..      36     506 .. 0.98

  Alignments for each domain:
  == domain 1  score: 626.1 bits;  conditional E-value: 1.9e-192
                             TIGR00132   4 llkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKdniavkd 73 
                                           ++ + e+s++e++++ l+ri +v+d+i+afl+v++e al++a+++d++ a  ++  +lag+p+a+Kd+++ ++
  NCBI__GCF_000058485.1:WP_011606923.1  39 AIAAGELSAVEATQAALDRIAKVDDTIHAFLHVDTEGALAAARSVDERRAagERlGPLAGVPLALKDVLTARG 111
                                           6778899****************************************998864456***************** PP

                             TIGR00132  74 iettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsa 146
                                           ++ttc+S+iLe++++pydatVv rl++a+++++Gk N+DEFamGsste+Sa+g+t+nP++++r+pGGSsgGsa
  NCBI__GCF_000058485.1:WP_011606923.1 112 MPTTCGSRILEGWHAPYDATVVGRLRAADVVLLGKVNMDEFAMGSSTENSAYGPTRNPWDTTRIPGGSSGGSA 184
                                           ************************************************************************* PP

                             TIGR00132 147 aavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisg 219
                                           aavaa+++pla+g+DTGgSiRqPA++cg vG+KPtYG vSRyGlva++sSldq G+la++v+d+al++++i+g
  NCBI__GCF_000058485.1:WP_011606923.1 185 AAVAAFEAPLAIGTDTGGSIRQPAAVCGLVGVKPTYGGVSRYGLVAFSSSLDQAGPLARTVTDAALLHAAIAG 257
                                           ************************************************************************* PP

                             TIGR00132 220 kDkkDstslevkveelleelkk.dlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvkl 291
                                           +D  Dsts++v+v+ ++e++ + d++gl++gvv+el +e++d +v+++f++++e+l+elgae+vevs+p++ +
  NCBI__GCF_000058485.1:WP_011606923.1 258 HDPLDSTSVDVPVPAVVEAAGRrDIRGLRIGVVRELAGEGYDPGVQAAFAAAVETLTELGAEVVEVSCPHFTY 330
                                           **************9999887669************************************************* PP

                             TIGR00132 292 alaiYyiispsEassnlarydgiryGkrveelks..lkelyaktRsegfgeevkrRimlGayalskeyydkyy 362
                                           ala+Yy+i+psE ssnlar+d++r+G rv ++ +  ++e++++tR++gfg evkrRi+lG+yals++yyd+yy
  NCBI__GCF_000058485.1:WP_011606923.1 331 ALAAYYLIAPSECSSNLARFDAMRFGLRVGDDGQagAEEVMSRTREAGFGPEVKRRIILGTYALSSGYYDAYY 403
                                           *******************************99988999********************************** PP

                             TIGR00132 363 kkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkek 435
                                            +Aqkvrtli ++f  ++e vDv+vspt+pt af lg+k +dp++mylsD++t+p nlaG pa+s+P+g + +
  NCBI__GCF_000058485.1:WP_011606923.1 404 GQAQKVRTLISRDFAAAYERVDVLVSPTTPTPAFPLGSKVDDPVAMYLSDLCTIPSNLAGGPAMSLPAGLA-D 475
                                           ***********************************************************************.8 PP

                             TIGR00132 436 glpiGlqiigkafddkkllsvakaleqald 465
                                           glp+G+qi++  f+d++l+ v+ ale+ald
  NCBI__GCF_000058485.1:WP_011606923.1 476 GLPVGIQIMAPPFADDRLYLVGGALEEALD 505
                                           *************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (519 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 17.77
//
[ok]

This GapMind analysis is from Jul 25 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:

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
the source code
instructions for running GapMind on your computer
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