GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Sphingomonas indica Dd16

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_085219215.1 B9N75_RS13220 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_900177405.1:WP_085219215.1
          Length = 497

 Score =  437 bits (1123), Expect = e-127
 Identities = 235/471 (49%), Positives = 312/471 (66%), Gaps = 14/471 (2%)

Query: 26  VDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMPIGVKDNIVTK 85
           V E+Y    A    + AF+    + A A A + D    G +   L  G+PIG+KD   TK
Sbjct: 26  VAEAYNAAVAGAKALNAFVIETPDHALAAADQADRDRAGGTLKPLS-GVPIGMKDLFATK 84

Query: 86  GLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTENSAYKLTKNPW 145
           G++TT  S +LE F P+Y++TV QRL DA A  +GKLNMD+FAMGSS E S +    +PW
Sbjct: 85  GVQTTAGSHMLEGFTPVYESTVSQRLWDAGAGMLGKLNMDQFAMGSSNETSYFGNVISPW 144

Query: 146 ------NLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTYGRVS 199
                 N    PGGSSGGS+AAVAA   P + G+DTGGSIRQPA+F G+ G+KPTYGR S
Sbjct: 145 RRGDGGNAPLAPGGSSGGSSAAVAARLCPGATGTDTGGSIRQPAAFTGISGIKPTYGRCS 204

Query: 200 RYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLTGDIKGL 259
           R+G+VAF+SSLDQ GP+ R V D A LL+A+SG D  DSTS  +DVP + ++L+ D++G 
Sbjct: 205 RWGIVAFSSSLDQAGPMARDVRDCAILLEAMSGFDPKDSTSLQMDVPAWDANLSADLRGK 264

Query: 260 KIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSSSEASA 319
           K+ +PKEY  +G+  E   +    +   +  GA   E+SLPH+KYAL TYY+++ +EAS+
Sbjct: 265 KVGIPKEYRIDGIPAEIDRAWEQGIAWAKDAGAEIVEISLPHTKYALPTYYIIAPAEASS 324

Query: 320 NLARFDGIRYGYR-----TDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAY 374
           NLAR+DG+RYG R     +     L ++YK TRA GFG EVKRRIM+GT+ LS+G+YDAY
Sbjct: 325 NLARYDGVRYGQRVAGEGSGTGAGLAEMYKATRAAGFGAEVKRRIMIGTYVLSAGFYDAY 384

Query: 375 YKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIPVNLA 434
           + +AQKVR LI +DF+  FE  DVI+ PT P+ +F +GE + DP+ MY ND+  +P +LA
Sbjct: 385 FNQAQKVRALIARDFQKAFETVDVILTPTAPSASFALGEKSADPIAMYLNDVFAVPASLA 444

Query: 435 GVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPE 484
           G+P +SVP  L D GLPLGLQIIG+ FDE  V     A E       A+PE
Sbjct: 445 GLPAMSVPAALDDQGLPLGLQIIGRAFDEQGVLNAGLAIEHRAG-FTARPE 494


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: 621
Number of extensions: 30
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: 485
Length of database: 497
Length adjustment: 34
Effective length of query: 451
Effective length of database: 463
Effective search space:   208813
Effective search space used:   208813
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_085219215.1 B9N75_RS13220 (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.1117858.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-169  550.2   0.0   2.2e-169  550.0   0.0    1.0  1  NCBI__GCF_900177405.1:WP_085219215.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085219215.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  550.0   0.0  2.2e-169  2.2e-169       5     463 ..      16     486 ..      12     489 .. 0.96

  Alignments for each domain:
  == domain 1  score: 550.0 bits;  conditional E-value: 2.2e-169
                             TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdie 75 
                                           +k+  +s++ev+e++++++   k  +naf+  t+++al++a++ d++ a  + k+l g+pi++Kd +a+k+++
  NCBI__GCF_900177405.1:WP_085219215.1  16 VKDGAFSAREVAEAYNAAVAGAKA-LNAFVIETPDHALAAADQADRDRAgGTlKPLSGVPIGMKDLFATKGVQ 87 
                                           667778889999999999988888.*********************99975558******************* PP

                             TIGR00132  76 ttcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPe......neervpGGSs 142
                                           tt++S++Le+++++y++tV +rl +aga ++Gk N+D FamGss etS+fg +  P+      n    pGGSs
  NCBI__GCF_900177405.1:WP_085219215.1  88 TTAGSHMLEGFTPVYESTVSQRLWDAGAGMLGKLNMDQFAMGSSNETSYFGNVISPWrrgdggNAPLAPGGSS 160
                                           ********************************************************633333366789***** PP

                             TIGR00132 143 gGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvld 215
                                           gGs+aavaa l+p a g+DTGgSiRqPA+f+g+ G+KPtYG+ SR+G+va++sSldq G++a++v d a++l+
  NCBI__GCF_900177405.1:WP_085219215.1 161 GGSSAAVAARLCPGATGTDTGGSIRQPAAFTGISGIKPTYGRCSRWGIVAFSSSLDQAGPMARDVRDCAILLE 233
                                           ************************************************************************* PP

                             TIGR00132 216 visgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslps 288
                                           ++sg D kDstsl+++v+ +  +l +dl+g kvg+ ke++ ++++ e+++++e+ +   ++ gaeive+slp+
  NCBI__GCF_900177405.1:WP_085219215.1 234 AMSGFDPKDSTSLQMDVPAWDANLSADLRGKKVGIPKEYRIDGIPAEIDRAWEQGIAWAKDAGAEIVEISLPH 306
                                           ************************************************************************* PP

                             TIGR00132 289 vklalaiYyiispsEassnlarydgiryGkrveelks.....lkelyaktRsegfgeevkrRimlGayalske 356
                                            k+al++Yyii+p+Eassnlarydg+ryG+rv    s     l e+y++tR++gfg+evkrRim+G+y+ls++
  NCBI__GCF_900177405.1:WP_085219215.1 307 TKYALPTYYIIAPAEASSNLARYDGVRYGQRVAGEGSgtgagLAEMYKATRAAGFGAEVKRRIMIGTYVLSAG 379
                                           ********************************9998889999******************************* PP

                             TIGR00132 357 yydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvP 429
                                            yd+y+++Aqkvr li+++f+k+fe vDvi++ptap  +f lgek +dp++myl+Dv+ vpa+laGlpa+svP
  NCBI__GCF_900177405.1:WP_085219215.1 380 FYDAYFNQAQKVRALIARDFQKAFETVDVILTPTAPSASFALGEKSADPIAMYLNDVFAVPASLAGLPAMSVP 452
                                           ************************************************************************* PP

                             TIGR00132 430 lgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                           ++ +++glp+Glqiig+afd++ +l+++ a+e++
  NCBI__GCF_900177405.1:WP_085219215.1 453 AALDDQGLPLGLQIIGRAFDEQGVLNAGLAIEHR 486
                                           ***************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (497 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: 17.99
//
[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