GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Enterococcus termitis LMG 8895

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_069663669.1 BCR25_RS11100 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_001730305.1:WP_069663669.1
          Length = 489

 Score =  631 bits (1628), Expect = 0.0
 Identities = 310/481 (64%), Positives = 386/481 (80%), Gaps = 2/481 (0%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           L+D  +TEL  L+  KEI  +DL + +  RI+  +  V +F+ + EE+A   AK +D  +
Sbjct: 4   LYDKSLTELHDLLVSKEITATDLTNATLDRIKETEKDVDSFITISEEKALELAKAID--L 61

Query: 63  DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122
            G +E   L G+PIG+KDNIVTK + TT +SK+L NF+PIYDATV+ +L  ++ + +GKL
Sbjct: 62  KGITESNPLAGIPIGIKDNIVTKDILTTAASKMLHNFNPIYDATVMDKLYQSDMIPVGKL 121

Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182
           NMDEFAMG+STE S +K TKN W+   VPGGSSGGSAAAVAAG+VP SLGSDTGGSIRQP
Sbjct: 122 NMDEFAMGASTETSYFKKTKNAWDHTKVPGGSSGGSAAAVAAGQVPVSLGSDTGGSIRQP 181

Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242
           ASF G+VG+KPTYGRVSR+GL+AF+SSLDQIGP+TR V+DNA  L AISG D+ D TSA 
Sbjct: 182 ASFNGIVGMKPTYGRVSRFGLIAFSSSLDQIGPMTRNVQDNALALNAISGFDEKDGTSAG 241

Query: 243 VDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHS 302
           V VPDF + LTGDIKG+K+A+PKEYLGEGV    RE+VL A +  + LGAT EEVSLPHS
Sbjct: 242 VSVPDFTAGLTGDIKGMKVALPKEYLGEGVDAGVREAVLKAAETFKALGATVEEVSLPHS 301

Query: 303 KYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLG 362
           KY +A YY+++SSEAS+NL RFDGIRYGYR++N  NL D+Y  +R+EGFG EVKRRIMLG
Sbjct: 302 KYGVAVYYIIASSEASSNLQRFDGIRYGYRSENVKNLEDVYVNSRSEGFGLEVKRRIMLG 361

Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMY 422
           TF+LS+GYYDAY+KKA +VRTLIK+DF+ VFE YD+I+GP +PT AF +GEN  DP+TMY
Sbjct: 362 TFSLSAGYYDAYFKKAGQVRTLIKQDFDKVFETYDIIIGPASPTVAFGLGENINDPITMY 421

Query: 423 ANDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAK 482
            ND+LTIPVNLAG+PG+SVP G ++GLP+GLQIIGK FDEST+Y+ A+AFEQATD H  K
Sbjct: 422 MNDLLTIPVNLAGLPGMSVPAGFSEGLPVGLQIIGKAFDESTMYKAAYAFEQATDFHTKK 481

Query: 483 P 483
           P
Sbjct: 482 P 482


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: 725
Number of extensions: 24
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: 489
Length adjustment: 34
Effective length of query: 451
Effective length of database: 455
Effective search space:   205205
Effective search space used:   205205
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_069663669.1 BCR25_RS11100 (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.242610.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.5e-198  644.1   0.9   7.4e-198  643.9   0.9    1.0  1  NCBI__GCF_001730305.1:WP_069663669.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069663669.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  643.9   0.9  7.4e-198  7.4e-198       2     465 ..      13     476 ..      12     477 .. 0.99

  Alignments for each domain:
  == domain 1  score: 643.9 bits;  conditional E-value: 7.4e-198
                             TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkvake.kklagipiavKdniavkd 73 
                                           ++ll++ke++++++++++l+ri+++++++++f+++++ekal+ ak++d k  +e ++lagipi++Kdni++kd
  NCBI__GCF_001730305.1:WP_069663669.1  13 HDLLVSKEITATDLTNATLDRIKETEKDVDSFITISEEKALELAKAIDLKGITEsNPLAGIPIGIKDNIVTKD 85 
                                           678999******************************************88765647***************** PP

                             TIGR00132  74 iettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsa 146
                                           i tt+aSk+L+n++++ydatV+ +l +++++ +Gk N+DEFamG+stetS+f+ tkn +++++vpGGSsgGsa
  NCBI__GCF_001730305.1:WP_069663669.1  86 ILTTAASKMLHNFNPIYDATVMDKLYQSDMIPVGKLNMDEFAMGASTETSYFKKTKNAWDHTKVPGGSSGGSA 158
                                           ************************************************************************* PP

                             TIGR00132 147 aavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisg 219
                                           aavaa++vp++lgsDTGgSiRqPAsf g+vG+KPtYG+vSR+Gl+a++sSldqiG+++++v+d al l++isg
  NCBI__GCF_001730305.1:WP_069663669.1 159 AAVAAGQVPVSLGSDTGGSIRQPASFNGIVGMKPTYGRVSRFGLIAFSSSLDQIGPMTRNVQDNALALNAISG 231
                                           ************************************************************************* PP

                             TIGR00132 220 kDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvkla 292
                                            D+kD ts+ v+v++++  l+ d+kg+kv++ ke+ +e++d +v+e++ k+ e++++lga+++evslp++k+ 
  NCBI__GCF_001730305.1:WP_069663669.1 232 FDEKDGTSAGVSVPDFTAGLTGDIKGMKVALPKEYLGEGVDAGVREAVLKAAETFKALGATVEEVSLPHSKYG 304
                                           ************************************************************************* PP

                             TIGR00132 293 laiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkA 365
                                           +a+Yyii++sEassnl+r+dgiryG+r e++k+l+++y+++Rsegfg evkrRimlG++ ls++yyd+y+kkA
  NCBI__GCF_001730305.1:WP_069663669.1 305 VAVYYIIASSEASSNLQRFDGIRYGYRSENVKNLEDVYVNSRSEGFGLEVKRRIMLGTFSLSAGYYDAYFKKA 377
                                           ************************************************************************* PP

                             TIGR00132 366 qkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglp 438
                                            +vrtli+++f+k+fe +D+i++p++pt+af lge+ +dp++my++D+lt+p+nlaGlp++svP+g + +glp
  NCBI__GCF_001730305.1:WP_069663669.1 378 GQVRTLIKQDFDKVFETYDIIIGPASPTVAFGLGENINDPITMYMNDLLTIPVNLAGLPGMSVPAGFS-EGLP 449
                                           ********************************************************************.7*** PP

                             TIGR00132 439 iGlqiigkafddkkllsvakaleqald 465
                                           +Glqiigkafd+++++++a+a+eqa+d
  NCBI__GCF_001730305.1:WP_069663669.1 450 VGLQIIGKAFDESTMYKAAYAFEQATD 476
                                           ************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (489 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 33.59
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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