Alignments for a candidate for gatD in Archaeoglobus veneficus SNP6

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatD in Archaeoglobus veneficus SNP6

Align glutamyl-tRNA(Gln) amidotransferase subunit D (EC 6.3.5.7) (characterized)
to candidate WP_013682980.1 ARCVE_RS01330 Glu-tRNA(Gln) amidotransferase subunit GatD

Query= metacyc::MONOMER-14998
         (435 letters)



>NCBI__GCF_000194625.1:WP_013682980.1
          Length = 416

 Score =  389 bits (999), Expect = e-113
 Identities = 210/412 (50%), Positives = 282/412 (68%), Gaps = 13/412 (3%)

Query: 19  GDMVLVEKPDVTYEGMVLDRADDADDRHIVLKLENGYNIGVEISDARIELLEKGSEPRIE 78
           G  V ++     +EG+ +  +  +     VLKL+NGYN+G    +  IE++E+G  P+ E
Sbjct: 7   GKRVRIKAKGRIFEGIAMPSSTGS----FVLKLDNGYNLGFSEYEL-IEVIEEG-RPKEE 60

Query: 79  LPPVEAAEDPELPDVSIISTGGTVASIIDYRTGAVHPAFTADDLLRANPELLDIANIRGR 138
           +   E A+  ELP+V IISTGGT+AS +DYRTGAV   F+A++++   PE+ +I N+   
Sbjct: 61  I--AELAKKEELPNVKIISTGGTIASKVDYRTGAVTSQFSAEEIVSDVPEIAEICNVDAM 118

Query: 139 AVFNILSENMKPEYWVETARAVYGEIKDGADGVVVAHGTDTMHYTSAALSFMLRTPVPVV 198
            ++NILSENMK ++W+E AR VY  IKDG +GV++ HGTDTM YT++AL+FML TP PVV
Sbjct: 119 LLYNILSENMKAKHWIELAREVYKAIKDGYEGVIITHGTDTMAYTASALAFMLSTPSPVV 178

Query: 199 FTGAQRSSDRPSSDASLNIQCSVRAATSEIAEVTVCMHATMDDLSCHLHRGVKVRKMHTS 258
           F GAQRSSDRPSSDA++N+ C+ + A S++ EV V MHA+  D  CH+HRGVKVRK HTS
Sbjct: 179 FVGAQRSSDRPSSDAAMNLVCAAKTAISDLGEVVVVMHASTSDDFCHIHRGVKVRKCHTS 238

Query: 259 RRDTFRSMNALPLAEVT-PDG-IKILEENYRKRGSDELELSDRVEERVAFIKSYPGISPD 316
           RRD FRS+N  PL  V+ P G I+ L    R RG  EL L DR+EE+V  +K +PG+ PD
Sbjct: 239 RRDAFRSINNPPLGVVSYPSGDIRWLSSRIR-RGERELRLKDRLEEKVVLVKFFPGLKPD 297

Query: 317 IIKWHLDEGYRGIVIEGTGLGHCPDTLIPVIGEAHDMGVPVAMTSQCLNGRVNMNVYSTG 376
           ++ ++ D+GYRG V+EGTGLGH     +  I    +  V V MTSQCL GRV   VY TG
Sbjct: 298 VLDYYYDKGYRGFVLEGTGLGHVSTDWVDTISRIAEDSV-VVMTSQCLWGRVCDRVYDTG 356

Query: 377 RRLLQAGVIPCDDMLPEVAYVKMCWVLGQTDDPEMAREMMRENIAGEINERT 428
           R LLQAGVI  +DMLPEVA +K+ W+LG   D E A+ +++ N+ GEIN  T
Sbjct: 357 RYLLQAGVIEGEDMLPEVALIKLMWLLGNY-DVEEAKRLVKVNLVGEINPTT 407


Lambda     K      H
   0.318    0.135    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: 539
Number of extensions: 22
Number of successful extensions: 4
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: 435
Length of database: 416
Length adjustment: 32
Effective length of query: 403
Effective length of database: 384
Effective search space:   154752
Effective search space used:   154752
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_013682980.1 ARCVE_RS01330 (Glu-tRNA(Gln) amidotransferase subunit GatD)
to HMM TIGR02153 (gatD: glutamyl-tRNA(Gln) amidotransferase, subunit D (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/TIGR02153.hmm
# target sequence database:        /tmp/gapView.3699937.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02153  [M=405]
Accession:   TIGR02153
Description: gatD_arch: glutamyl-tRNA(Gln) amidotransferase, subunit D
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-182  592.5   0.0   2.1e-182  592.3   0.0    1.0  1  NCBI__GCF_000194625.1:WP_013682980.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000194625.1:WP_013682980.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  592.3   0.0  2.1e-182  2.1e-182       1     404 [.      18     408 ..      18     409 .. 0.97

  Alignments for each domain:
  == domain 1  score: 592.3 bits;  conditional E-value: 2.1e-182
                             TIGR02153   1 vfeGvvlpstelseediivlklknGYnvgvkkeeveeievleeekeeklekleeeiekkeelekvsilstGGt 73 
                                           +feG+ +ps    +++ +vlkl+nGYn+g+++ e+  iev+ee +++   +  +e +kkeel++v+i+stGGt
  NCBI__GCF_000194625.1:WP_013682980.1  18 IFEGIAMPS----STGSFVLKLDNGYNLGFSEYEL--IEVIEEGRPK---EEIAELAKKEELPNVKIISTGGT 81 
                                           69*******....6799*************99998..9999999996...589999***************** PP

                             TIGR02153  74 iaskvdYetGavkpaltaeelleavpelkeianikaravlnilsenmkPesWikiaeevakaleegadgvvva 146
                                           iaskvdY+tGav+++++aee+++ vpe+ ei+n++a  ++nilsenmk ++Wi++a+ev+ka+++g++gv+++
  NCBI__GCF_000194625.1:WP_013682980.1  82 IASKVDYRTGAVTSQFSAEEIVSDVPEIAEICNVDAMLLYNILSENMKAKHWIELAREVYKAIKDGYEGVIIT 154
                                           ************************************************************************* PP

                             TIGR02153 147 hGtDtmaytaaaLsFmlkklpvPvvlvGaqRssDRPssDaalnliaavkvakediaevvvvmhgetsDtyvlv 219
                                           hGtDtmayta+aL+Fml++ p+Pvv+vGaqRssDRPssDaa+nl++a+k a +d++evvvvmh++tsD+++++
  NCBI__GCF_000194625.1:WP_013682980.1 155 HGTDTMAYTASALAFMLST-PSPVVFVGAQRSSDRPSSDAAMNLVCAAKTAISDLGEVVVVMHASTSDDFCHI 226
                                           *******************.***************************************************** PP

                             TIGR02153 220 hrgvkvrkmhtsRRDaFksinslPlakvdpkekeiellredyrkrgekelelkdkleekvalvkfyPGlspei 292
                                           hrgvkvrk+htsRRDaF+sin+ Pl+ v + ++ i+   +++ +rge+el lkd+leekv+lvkf+PGl+p++
  NCBI__GCF_000194625.1:WP_013682980.1 227 HRGVKVRKCHTSRRDAFRSINNPPLGVVSYPSGDIRW-LSSRIRRGERELRLKDRLEEKVVLVKFFPGLKPDV 298
                                           ******************************9877765.5667889999************************* PP

                             TIGR02153 293 lealvdkgykgivieGtGlGhvsedlievikkavddgvvvvmtsqclyGrvnlnvYstGRellkaGvieaedm 365
                                           l+++ dkgy+g+v+eGtGlGhvs+d++++i ++ +d  vvvmtsqcl+Grv+++vY+tGR ll+aGvie+edm
  NCBI__GCF_000194625.1:WP_013682980.1 299 LDYYYDKGYRGFVLEGTGLGHVSTDWVDTISRIAED-SVVVMTSQCLWGRVCDRVYDTGRYLLQAGVIEGEDM 370
                                           ********************************9999.7899******************************** PP

                             TIGR02153 366 lpevayvklmwvLgqteeleevrkllkknlageieertl 404
                                           lpeva++klmw+Lg+++  ee+++l+k nl+gei+++t+
  NCBI__GCF_000194625.1:WP_013682980.1 371 LPEVALIKLMWLLGNYDV-EEAKRLVKVNLVGEINPTTR 408
                                           ****************98.77778***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (416 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 16.85
//
[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