Alignments for a candidate for gatA in Azoarcus sp. BH72

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Azoarcus sp. BH72

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_011763908.1 AZO_RS00865 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000061505.1:WP_011763908.1
          Length = 487

 Score =  461 bits (1185), Expect = e-134
 Identities = 241/488 (49%), Positives = 330/488 (67%), Gaps = 7/488 (1%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           + +  ++EL++ +  +++   +L      RI   +  + AF+ +D E A A A+  D  +
Sbjct: 1   MINASVSELRRALDTRQVSSVELATLFLDRIAERNPALNAFITIDREGALAAARAADARI 60

Query: 63  DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122
              +  G L G+P+  KD   T+G+ TTC SK+L +F   YDA VV RL+DA AV++GK 
Sbjct: 61  AAGTA-GPLTGIPLAHKDLFCTEGVLTTCGSKMLADFVSPYDAHVVSRLKDAGAVSLGKT 119

Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182
           NMDEFAMGSS E+S Y   +NPW+   +PGGSSGGSAAAVAA  VP + GSDTGGS+RQP
Sbjct: 120 NMDEFAMGSSNESSHYGAVRNPWDTTRIPGGSSGGSAAAVAARLVPLATGSDTGGSVRQP 179

Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242
           AS  GV G+KPTYG VSRYG++A+ASSLDQ G    + ED A LL A++G D  DST  +
Sbjct: 180 ASHTGVTGIKPTYGVVSRYGMIAYASSLDQGGAFGASAEDCALLLTAMAGFDPRDSTCLD 239

Query: 243 VDVPDFLSSLTGD-----IKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEV 297
               D+ ++L        + GL+I +P+E+  EG+  + R +V AAL     LGA   EV
Sbjct: 240 RPAEDYAAALAPTAGGKPLAGLRIGLPREFFAEGMADDVRAAVDAALDQYRALGAVTVEV 299

Query: 298 SLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKR 357
           SLP++K A+  YY+++ +EAS+NL+RFDG+RYG+R     +L D+Y ++RAEGFG EVKR
Sbjct: 300 SLPNAKLAVPAYYVIAPAEASSNLSRFDGVRYGHRAAEYGDLNDMYCKSRAEGFGAEVKR 359

Query: 358 RIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKD 417
           RI++GT+ LS GYYDAYY +AQK+R LI +DF+  F + DVI GPT+PT A+ IGE   D
Sbjct: 360 RILVGTYVLSHGYYDAYYLQAQKLRRLIAQDFQAAFAQCDVIAGPTSPTTAWAIGEKADD 419

Query: 418 PLTMYANDILTIPVNLAGVPGISVPCGLADG-LPLGLQIIGKHFDESTVYRVAHAFEQAT 476
           P+ MY +DI TI VNLAG+PG+S PCG   G LP+GLQ+IG +F ES +   AH ++QA+
Sbjct: 420 PVQMYLSDIYTIAVNLAGLPGLSHPCGFGAGRLPVGLQLIGNYFGESRLLATAHQYQQAS 479

Query: 477 DHHKAKPE 484
           D H  +PE
Sbjct: 480 DWHLQRPE 487


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: 572
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: 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_011763908.1 AZO_RS00865 (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.6663.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.7e-181  587.5   0.0   1.1e-180  587.3   0.0    1.0  1  lcl|NCBI__GCF_000061505.1:WP_011763908.1  AZO_RS00865 Asp-tRNA(Asn)/Glu-tR


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000061505.1:WP_011763908.1  AZO_RS00865 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 !  587.3   0.0  1.1e-180  1.1e-180       2     465 ..      10     480 ..       9     481 .. 0.98

  Alignments for each domain:
  == domain 1  score: 587.3 bits;  conditional E-value: 1.1e-180
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdn 68 
                                               +++l++++vs++e+++ +l+ri + +  +naf+++++e al++a++ d+++a  +  +l+gip+a Kd 
  lcl|NCBI__GCF_000061505.1:WP_011763908.1  10 RRALDTRQVSSVELATLFLDRIAERNPALNAFITIDREGALAAARAADARIAaGTaGPLTGIPLAHKDL 78 
                                               678899*********************************************975536************ PP

                                 TIGR00132  69 iavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneerv 137
                                               ++++++ ttc+Sk+L ++vspyda+Vv rlk+aga+ +GktN+DEFamGss e+S +g+++nP++++r+
  lcl|NCBI__GCF_000061505.1:WP_011763908.1  79 FCTEGVLTTCGSKMLADFVSPYDAHVVSRLKDAGAVSLGKTNMDEFAMGSSNESSHYGAVRNPWDTTRI 147
                                               ********************************************************************* PP

                                 TIGR00132 138 pGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakk 206
                                               pGGSsgGsaaavaa lvpla gsDTGgS+RqPAs++gv G+KPtYG+vSRyG++ayasSldq G + ++
  lcl|NCBI__GCF_000061505.1:WP_011763908.1 148 PGGSSGGSAAAVAARLVPLATGSDTGGSVRQPASHTGVTGIKPTYGVVSRYGMIAYASSLDQGGAFGAS 216
                                               ********************************************************************* PP

                                 TIGR00132 207 vedialvldvisgkDkkDstslevkveelleelkk.....dlkglkvgvvkelseesldkevkekfekl 270
                                                ed al+l +++g D +Dst l+ + e++  +l+       l gl++g+ +e++ e++ ++v+++++++
  lcl|NCBI__GCF_000061505.1:WP_011763908.1 217 AEDCALLLTAMAGFDPRDSTCLDRPAEDYAAALAPtaggkPLAGLRIGLPREFFAEGMADDVRAAVDAA 285
                                               *****************************999887555556889************************* PP

                                 TIGR00132 271 lekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfg 339
                                               l++ ++lga  vevslp+ kla+++Yy+i+p+Eassnl+r+dg+ryG+r+ e+ +l+++y k+R+egfg
  lcl|NCBI__GCF_000061505.1:WP_011763908.1 286 LDQYRALGAVTVEVSLPNAKLAVPAYYVIAPAEASSNLSRFDGVRYGHRAAEYGDLNDMYCKSRAEGFG 354
                                               ********************************************************************* PP

                                 TIGR00132 340 eevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplem 408
                                               +evkrRi++G+y+ls++yyd+yy++Aqk+r+li+++f+ +f ++Dvi++pt+pt+a  +geka+dp++m
  lcl|NCBI__GCF_000061505.1:WP_011763908.1 355 AEVKRRILVGTYVLSHGYYDAYYLQAQKLRRLIAQDFQAAFAQCDVIAGPTSPTTAWAIGEKADDPVQM 423
                                               ********************************************************************* PP

                                 TIGR00132 409 ylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                               ylsD++t+ +nlaGlp++s P+g     lp+Glq+ig++f +++ll  a++++qa d
  lcl|NCBI__GCF_000061505.1:WP_011763908.1 424 YLSDIYTIAVNLAGLPGLSHPCGFGAGRLPVGLQLIGNYFGESRLLATAHQYQQASD 480
                                               ****************************************************99865 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.06
//
[ok]

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