Alignments for a candidate for gatA in Novosphingobium aromaticivorans DSM 12444

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Novosphingobium aromaticivorans DSM 12444

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_011446472.1 SARO_RS14365 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000013325.1:WP_011446472.1
          Length = 494

 Score =  440 bits (1131), Expect = e-128
 Identities = 231/480 (48%), Positives = 321/480 (66%), Gaps = 7/480 (1%)

Query: 2   SLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEA 61
           +L D  I  ++  + + +   +++       ++A    + AF+    E A   A ++D  
Sbjct: 3   NLTDLGIAAIRDGVARGDFTATEVATAFNAAVEAAQPALNAFIVTTPEEALEAAGKVDAD 62

Query: 62  VDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGK 121
                  G + G+PIG+KD   T+G +TT +SKILE F P Y++TV Q+L DA A  +GK
Sbjct: 63  RTAGRPLGKMAGVPIGMKDLFATRGTQTTAASKILEGFMPEYESTVSQKLWDAGAGMLGK 122

Query: 122 LNMDEFAMGSSTENSAYKLTKNPWNL--DTVP---GGSSGGSAAAVAAGEVPFSLGSDTG 176
           LN+D+FAMGSS E SA+    +PW    DT P   GGSSGGS++AVAA   P + G+DTG
Sbjct: 123 LNLDQFAMGSSNETSAFGNVISPWRRPGDTAPLAPGGSSGGSSSAVAARIAPAATGTDTG 182

Query: 177 GSIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKM 236
           GSIRQPA+F G+ G+KPTYGR SR+G+VAFASSLDQ GP+ R V D A +L+A++G D  
Sbjct: 183 GSIRQPAAFTGISGIKPTYGRCSRWGIVAFASSLDQAGPMARDVADCAIMLEAMAGFDPK 242

Query: 237 DSTSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEE 296
           DSTS ++ VP++ ++L  D++G K+ +P+EY  +G+  +   S    +  L+  GA   E
Sbjct: 243 DSTSLDMPVPEWTANLDPDMRGKKVGIPREYRLDGMDPDVARSWEDGIAWLKDAGAEIVE 302

Query: 297 VSLPHSKYALATYYLLSSSEASANLARFDGIRYGYR-TDNADNLIDLYKQTRAEGFGNEV 355
           +SLPH+KYAL TYY+++ +EAS+NLAR+DG+RYG R       L D+Y  TRA GFG EV
Sbjct: 303 ISLPHTKYALPTYYIIAPAEASSNLARYDGVRYGLRDLPEGAGLQDMYAATRAAGFGPEV 362

Query: 356 KRRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENT 415
           KRRI++GT+ LS+G+YDAYY +AQKVRTLI  DF + F + DVI+ PT P+ AF +GE +
Sbjct: 363 KRRILIGTYVLSAGFYDAYYTQAQKVRTLISHDFTNAFREVDVILAPTAPSSAFALGEKS 422

Query: 416 KDPLTMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQ 474
            DPL MY ND+ ++P +LAG+P +SVP GL  +GLPLGLQ+IG+ FDE  V     A EQ
Sbjct: 423 ADPLEMYLNDVFSVPASLAGLPAMSVPAGLDRNGLPLGLQVIGRAFDEQGVLNAGLALEQ 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: 613
Number of extensions: 34
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: 494
Length adjustment: 34
Effective length of query: 451
Effective length of database: 460
Effective search space:   207460
Effective search space used:   207460
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_011446472.1 SARO_RS14365 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A)
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.23552.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-172  560.6   0.0   1.5e-172  560.4   0.0    1.0  1  lcl|NCBI__GCF_000013325.1:WP_011446472.1  SARO_RS14365 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013325.1:WP_011446472.1  SARO_RS14365 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  560.4   0.0  1.5e-172  1.5e-172       5     463 ..      16     483 ..      12     486 .. 0.96

  Alignments for each domain:
  == domain 1  score: 560.4 bits;  conditional E-value: 1.5e-172
                                 TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKdnia 70 
                                               + + +++++ev++++++++ea +  +naf+ +t+e+al++a k+d++ +  +   k+ag+pi++Kd +a
  lcl|NCBI__GCF_000013325.1:WP_011446472.1  16 VARGDFTATEVATAFNAAVEAAQPALNAFIVTTPEEALEAAGKVDADRTagRPlGKMAGVPIGMKDLFA 84 
                                               5667788999***********************************98776555569************* PP

                                 TIGR00132  71 vkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPene..... 134
                                               +++++tt+aSkiLe++++ y++tV ++l +aga ++Gk NlD FamGss etSafg +  P+ +     
  lcl|NCBI__GCF_000013325.1:WP_011446472.1  85 TRGTQTTAASKILEGFMPEYESTVSQKLWDAGAGMLGKLNLDQFAMGSSNETSAFGNVISPWRRpgdta 153
                                               *************************************************************75422211 PP

                                 TIGR00132 135 ervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGil 203
                                                  pGGSsgGs+ avaa ++p a g+DTGgSiRqPA+f+g+ G+KPtYG+ SR+G+va+asSldq G++
  lcl|NCBI__GCF_000013325.1:WP_011446472.1 154 PLAPGGSSGGSSSAVAARIAPAATGTDTGGSIRQPAAFTGISGIKPTYGRCSRWGIVAFASSLDQAGPM 222
                                               5789***************************************************************** PP

                                 TIGR00132 204 akkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfeklle 272
                                               a++v d a++l++++g D kDstsl+++v+e++ +l  d++g kvg+ +e++ +++d +v++++e+ + 
  lcl|NCBI__GCF_000013325.1:WP_011446472.1 223 ARDVADCAIMLEAMAGFDPKDSTSLDMPVPEWTANLDPDMRGKKVGIPREYRLDGMDPDVARSWEDGIA 291
                                               ********************************************************************* PP

                                 TIGR00132 273 kleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrve.elkslkelyaktRsegfge 340
                                                l++ gaeive+slp+ k+al++Yyii+p+Eassnlarydg+ryG r   e   l+++ya+tR++gfg 
  lcl|NCBI__GCF_000013325.1:WP_011446472.1 292 WLKDAGAEIVEISLPHTKYALPTYYIIAPAEASSNLARYDGVRYGLRDLpEGAGLQDMYAATRAAGFGP 360
                                               ***********************************************7615555*************** PP

                                 TIGR00132 341 evkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemy 409
                                               evkrRi++G+y+ls++ yd+yy++Aqkvrtli ++f+++f+evDvi++ptap +af lgek +dplemy
  lcl|NCBI__GCF_000013325.1:WP_011446472.1 361 EVKRRILIGTYVLSAGFYDAYYTQAQKVRTLISHDFTNAFREVDVILAPTAPSSAFALGEKSADPLEMY 429
                                               ********************************************************************* PP

                                 TIGR00132 410 lsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               l+Dv+ vpa+laGlpa+svP+g +++glp+Glq+ig+afd++ +l+++ aleq+
  lcl|NCBI__GCF_000013325.1:WP_011446472.1 430 LNDVFSVPASLAGLPAMSVPAGLDRNGLPLGLQVIGRAFDEQGVLNAGLALEQR 483
                                               ************************************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (494 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: 00:00:00.03
# Mc/sec: 7.30
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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