Alignments for a candidate for gatA in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Steroidobacter denitrificans DSM 18526

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_066922914.1 ACG33_RS06390 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_001579945.1:WP_066922914.1
          Length = 484

 Score =  488 bits (1256), Expect = e-142
 Identities = 249/477 (52%), Positives = 328/477 (68%), Gaps = 1/477 (0%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           + EL + +  +     +L      RI+ ++  + AF+ +  E A A A++ D  +    E
Sbjct: 6   LAELGEGLRARRFSSIELARHFLDRIERLNPTLNAFITVTAETALAAAEQADRRL-AAGE 64

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            G L G+P+  KD   T G+ TTC+S++L NF   YDATVV RL  A AV +GK NMDEF
Sbjct: 65  EGALIGVPLAHKDIFCTDGILTTCASRMLSNFVAPYDATVVARLSRAGAVMLGKANMDEF 124

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSS E S Y   +NPW+LD VPGGSSGGSAAAVAA  VP S G+DTGGSIRQPA+   
Sbjct: 125 AMGSSNETSWYGPVRNPWDLDKVPGGSSGGSAAAVAARLVPASTGTDTGGSIRQPAALTS 184

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           + GLKP+YGRVSRYG++AFASSLDQ G +TR+  D A LL  ++G D +DSTS +  VPD
Sbjct: 185 LTGLKPSYGRVSRYGMIAFASSLDQAGTLTRSAHDAALLLAQMAGFDPLDSTSVDTPVPD 244

Query: 248 FLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALA 307
           ++  L   + GLKI V KE+   G+ +E    V  AL+V   LGA   EVSLP+   ++ 
Sbjct: 245 YVGLLAQPLTGLKIGVLKEFFERGLDEEIERRVREALEVYRRLGAQLVEVSLPNLPLSVP 304

Query: 308 TYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALS 367
            YY+++ +E S+NL+RFDG+R+G+R D+  +L+DLYK++RAEGFG EVKRRIM GT+ LS
Sbjct: 305 AYYVVAPAECSSNLSRFDGVRFGHRCDSPVDLLDLYKRSRAEGFGEEVKRRIMTGTYVLS 364

Query: 368 SGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDIL 427
           +GYYDAYY +AQKVR LI  DF   F + DV++GPTTP+PAF IG  + DP+TMY NDI 
Sbjct: 365 AGYYDAYYLRAQKVRRLIADDFARAFSQVDVLMGPTTPSPAFAIGTKSDDPVTMYLNDIY 424

Query: 428 TIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPE 484
           T  VNLAG+P +SVPCG  DGLP+GLQI+G HF E+ +  VAH +++ T  H+  P+
Sbjct: 425 TSGVNLAGLPAMSVPCGFQDGLPVGLQIVGPHFAEARLLNVAHVYQRETQWHERIPK 481


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: 627
Number of extensions: 27
Number of successful extensions: 2
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: 484
Length adjustment: 34
Effective length of query: 451
Effective length of database: 450
Effective search space:   202950
Effective search space used:   202950
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_066922914.1 ACG33_RS06390 (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.22174.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.1e-185  601.1   0.0     8e-185  600.9   0.0    1.0  1  lcl|NCBI__GCF_001579945.1:WP_066922914.1  ACG33_RS06390 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001579945.1:WP_066922914.1  ACG33_RS06390 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.9   0.0    8e-185    8e-185       6     465 ..      14     474 ..       9     475 .. 0.98

  Alignments for each domain:
  == domain 1  score: 600.9 bits;  conditional E-value: 8e-185
                                 TIGR00132   6 kkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..kekklagipiavKdniavk 72 
                                                ++++s+ e+++++l+rie+ + ++naf++vt+e+al++a++ d+++a  +e  l+g+p+a Kd +++ 
  lcl|NCBI__GCF_001579945.1:WP_066922914.1  14 RARRFSSIELARHFLDRIERLNPTLNAFITVTAETALAAAEQADRRLAagEEGALIGVPLAHKDIFCTD 82 
                                               56778889999***********************************9984447**************** PP

                                 TIGR00132  73 diettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGS 141
                                               +i ttcaS++L+n+v+pydatVv rl +aga+++Gk+N+DEFamGss etS +g+++nP++ ++vpGGS
  lcl|NCBI__GCF_001579945.1:WP_066922914.1  83 GILTTCASRMLSNFVAPYDATVVARLSRAGAVMLGKANMDEFAMGSSNETSWYGPVRNPWDLDKVPGGS 151
                                               ********************************************************************* PP

                                 TIGR00132 142 sgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedi 210
                                               sgGsaaavaa lvp + g+DTGgSiRqPA++++  GlKP+YG+vSRyG++a+asSldq G l+++ +d+
  lcl|NCBI__GCF_001579945.1:WP_066922914.1 152 SGGSAAAVAARLVPASTGTDTGGSIRQPAALTSLTGLKPSYGRVSRYGMIAFASSLDQAGTLTRSAHDA 220
                                               ********************************************************************* PP

                                 TIGR00132 211 alvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelga 279
                                               al+l++++g D  Dsts++++v++++  l++ l glk+gv+ke++e +ld+e++++++++le+ ++lga
  lcl|NCBI__GCF_001579945.1:WP_066922914.1 221 ALLLAQMAGFDPLDSTSVDTPVPDYVGLLAQPLTGLKIGVLKEFFERGLDEEIERRVREALEVYRRLGA 289
                                               ********************************************************************* PP

                                 TIGR00132 280 eivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRiml 348
                                               ++vevslp++ l++++Yy+++p+E ssnl+r+dg+r+G+r + + +l +ly+++R+egfgeevkrRim 
  lcl|NCBI__GCF_001579945.1:WP_066922914.1 290 QLVEVSLPNLPLSVPAYYVVAPAECSSNLSRFDGVRFGHRCDSPVDLLDLYKRSRAEGFGEEVKRRIMT 358
                                               ********************************************************************* PP

                                 TIGR00132 349 GayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvp 417
                                               G+y+ls++yyd+yy++Aqkvr+li+d+f  +f++vDv+++pt+p  af +g k +dp++myl+D++t  
  lcl|NCBI__GCF_001579945.1:WP_066922914.1 359 GTYVLSAGYYDAYYLRAQKVRRLIADDFARAFSQVDVLMGPTTPSPAFAIGTKSDDPVTMYLNDIYTSG 427
                                               ********************************************************************* PP

                                 TIGR00132 418 anlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                               +nlaGlpa+svP+g + +glp+Glqi+g +f++ +ll+va+ ++++++
  lcl|NCBI__GCF_001579945.1:WP_066922914.1 428 VNLAGLPAMSVPCGFQ-DGLPVGLQIVGPHFAEARLLNVAHVYQRETQ 474
                                               ****************.8*************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (484 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.73
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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