Alignments for a candidate for gatA in Desulfurobacterium atlanticum DSM 15668

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Desulfurobacterium atlanticum DSM 15668

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_089322320.1 CHB58_RS01475 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_900188395.1:WP_089322320.1
          Length = 487

 Score =  563 bits (1450), Expect = e-165
 Identities = 278/477 (58%), Positives = 364/477 (76%), Gaps = 3/477 (0%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           M L +  + EL  LI KKEIK S++ +E + RI+  + K+ A++ +++E++   AK  D 
Sbjct: 1   MELINKSLKELSSLIAKKEIKPSEITEELFSRIEETESKLNAYITVEKEKSIEAAKLKDR 60

Query: 61  AVDGRSEHGL--LFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVT 118
            ++  SE  +  LFG+P+ +KDNI+ +G + TC+SK+L++F   YDATV+++L++  A+ 
Sbjct: 61  ELEKLSETEIPDLFGIPLSIKDNILVEGQKMTCASKMLKDFIAPYDATVIKKLREKGAIF 120

Query: 119 IGKLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGS 178
           IGK N+DEFAMGSSTE S + +T+NPW+L+ VPGGSSGGSAAAVAA     SLGSDTGGS
Sbjct: 121 IGKNNLDEFAMGSSTETSFFGVTRNPWDLERVPGGSSGGSAAAVAARSALASLGSDTGGS 180

Query: 179 IRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDS 238
           IRQP S CGVVG+KPTYGRVSRYGL AFASSLDQIGPIT+ +EDNAFLL  ISG+D  D+
Sbjct: 181 IRQPCSLCGVVGMKPTYGRVSRYGLTAFASSLDQIGPITKNIEDNAFLLNIISGLDSKDA 240

Query: 239 TSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVS 298
           TSA + VP++L +L  +IKGLK  +PKEY  EG+  E +E V+ A K LE LG   EE+S
Sbjct: 241 TSAKLPVPNYLEALDNEIKGLKAGLPKEYFIEGIDPEVKEKVMEAAKTLEKLGVEVEEIS 300

Query: 299 LPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRR 358
           LPH+ YA+ TYY+++ +EAS+NL RFDG+RY YR     +LID+Y +TRAEGFGNEVKRR
Sbjct: 301 LPHTSYAVETYYIIAPAEASSNLGRFDGVRYTYRAKEYTDLIDMYCKTRAEGFGNEVKRR 360

Query: 359 IMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDP 418
           IM+GT+ LS+GYYDAYY KAQKVRTLI +DF++ FEK D IV P +PT AFKIGE T DP
Sbjct: 361 IMIGTYTLSAGYYDAYYLKAQKVRTLIYQDFQNAFEKVDFIVTPVSPTTAFKIGEKTDDP 420

Query: 419 LTMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQ 474
           + MY +DI TI VNLAG+PG+S+PCG  + GLP+G+Q+IGK FDE T+Y V +  E+
Sbjct: 421 IKMYLSDIFTIAVNLAGLPGLSMPCGFDSKGLPVGVQLIGKAFDEETLYSVGYKLEK 477


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: 642
Number of extensions: 28
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: 487
Length adjustment: 34
Effective length of query: 451
Effective length of database: 453
Effective search space:   204303
Effective search space used:   204303
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_089322320.1 CHB58_RS01475 (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.1017908.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.6e-205  666.8   0.2   9.9e-205  666.6   0.2    1.0  1  NCBI__GCF_900188395.1:WP_089322320.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900188395.1:WP_089322320.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  666.6   0.2  9.9e-205  9.9e-205       3     465 ..      13     480 ..      11     481 .. 0.98

  Alignments for each domain:
  == domain 1  score: 666.6 bits;  conditional E-value: 9.9e-205
                             TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva....ke.kklagipiavKdnia 70 
                                           +l+ kke++ +e++ee+  rie++++k+na+++v+kek++++ak  d++++    +e   l+gip+++Kdni 
  NCBI__GCF_900188395.1:WP_089322320.1  13 SLIAKKEIKPSEITEELFSRIEETESKLNAYITVEKEKSIEAAKLKDRELEklseTEiPDLFGIPLSIKDNIL 85 
                                           6799****************************************9999988775333349************* PP

                             TIGR00132  71 vkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsg 143
                                           v++ ++tcaSk+L+++++pydatV+++l+e+ga+ iGk NlDEFamGsstetS+fgvt+nP++ ervpGGSsg
  NCBI__GCF_900188395.1:WP_089322320.1  86 VEGQKMTCASKMLKDFIAPYDATVIKKLREKGAIFIGKNNLDEFAMGSSTETSFFGVTRNPWDLERVPGGSSG 158
                                           ************************************************************************* PP

                             TIGR00132 144 GsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldv 216
                                           Gsaaavaa ++  +lgsDTGgSiRqP s+cgvvG+KPtYG+vSRyGl+a+asSldqiG+++k++ed a++l++
  NCBI__GCF_900188395.1:WP_089322320.1 159 GSAAAVAARSALASLGSDTGGSIRQPCSLCGVVGMKPTYGRVSRYGLTAFASSLDQIGPITKNIEDNAFLLNI 231
                                           ************************************************************************* PP

                             TIGR00132 217 isgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsv 289
                                           isg D+kD ts++ +v+++le+l +++kglk g+ ke++ e++d evkek+ ++ ++le+lg+e++e+slp+ 
  NCBI__GCF_900188395.1:WP_089322320.1 232 ISGLDSKDATSAKLPVPNYLEALDNEIKGLKAGLPKEYFIEGIDPEVKEKVMEAAKTLEKLGVEVEEISLPHT 304
                                           ************************************************************************* PP

                             TIGR00132 290 klalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyy 362
                                           ++a+ +Yyii+p+Eassnl r+dg+ry +r++e+++l ++y ktR+egfg+evkrRim+G+y+ls++yyd+yy
  NCBI__GCF_900188395.1:WP_089322320.1 305 SYAVETYYIIAPAEASSNLGRFDGVRYTYRAKEYTDLIDMYCKTRAEGFGNEVKRRIMIGTYTLSAGYYDAYY 377
                                           ************************************************************************* PP

                             TIGR00132 363 kkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkek 435
                                           +kAqkvrtli ++f+++fe+vD+iv+p++pt+afk+gek++dp++mylsD++t+ +nlaGlp++s+P+g ++k
  NCBI__GCF_900188395.1:WP_089322320.1 378 LKAQKVRTLIYQDFQNAFEKVDFIVTPVSPTTAFKIGEKTDDPIKMYLSDIFTIAVNLAGLPGLSMPCGFDSK 450
                                           ************************************************************************* PP

                             TIGR00132 436 glpiGlqiigkafddkkllsvakaleqald 465
                                           glp+G+q+igkafd+++l+sv+++le++l+
  NCBI__GCF_900188395.1:WP_089322320.1 451 GLPVGVQLIGKAFDEETLYSVGYKLEKELK 480
                                           **************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (487 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: 16.90
//
[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