Alignments for a candidate for gatB in Azohydromonas australica DSM 1124

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Azohydromonas australica DSM 1124

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_028996924.1 H537_RS0104395 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000430725.1:WP_028996924.1
          Length = 483

 Score =  412 bits (1058), Expect = e-119
 Identities = 213/473 (45%), Positives = 308/473 (65%), Gaps = 4/473 (0%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E VIGLE H +L T SK+FS +   FGA PN+  + +DLA PG LPV N+ AV+ A+R 
Sbjct: 10  YEVVIGLETHAQLSTASKIFSGASTAFGAAPNTQASAVDLALPGTLPVPNRGAVERAIRF 69

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITRLH 122
            +A+  ++A +S F RKNYFYPD PK YQISQ++ P+ + G I+  V  + KR+ +TR H
Sbjct: 70  GLAVGAKVARQSIFARKNYFYPDLPKGYQISQYEIPVVQGGVIEFLVGEQKKRVNLTRAH 129

Query: 123 MEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGVS 180
           +EEDAGKS H+  + L  +DLNR GTPL+EIVSEP++RS  EA  Y   L +++ + G+ 
Sbjct: 130 LEEDAGKSLHEDYHGLTGIDLNRAGTPLLEIVSEPEMRSSLEAVGYARSLHALVVWLGIC 189

Query: 181 DVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGGE 240
           D  M+EGS RCDAN+S+R  G E FGT+ E+KNLNSF ++++ ++YE + Q +++  G  
Sbjct: 190 DGNMQEGSFRCDANVSVRKPG-EPFGTRREIKNLNSFRFLQQAIDYEVQWQIDQIEDGLS 248

Query: 241 IGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDERK 300
           I Q T  FD  +G+T  MR KE + DYRYFP+PD+ PL I+ AW ERV+  +PELP    
Sbjct: 249 IEQATVLFDPDSGETRAMRSKEDAHDYRYFPDPDLPPLVIEPAWVERVKAGMPELPQAMA 308

Query: 301 AKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVELL 360
            ++  + GLPAYDA ++T +   + ++E+  +     KL +NWLMG   + LN     + 
Sbjct: 309 DRFQQQDGLPAYDAGMVTQSLAFARYYEAARDACKQPKLVANWLMGEYAKRLNAEGRGIE 368

Query: 361 DTKLTPENLAGMIKLIEDGTMSSKIAKKVFPEL-AAKGGNAKQIMEDNGLVQISDEATLL 419
           +  + P  L  +I  I DGT+S+   ++VF  L + +G +   ++E  GL Q+SD   L 
Sbjct: 369 EAPVAPATLGALIARIADGTISNNGGRQVFDALWSGEGSDVDALIEAKGLKQMSDTGALE 428

Query: 420 KFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
             V + L  NE+SV +++ GK KA   LVGQ+MKASKG+ANP L  +LLK++L
Sbjct: 429 AIVEQVLAANEKSVAEFRAGKDKAFNALVGQVMKASKGKANPALAGELLKKKL 481


Lambda     K      H
   0.313    0.133    0.373 

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: 573
Number of extensions: 24
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: 475
Length of database: 483
Length adjustment: 34
Effective length of query: 441
Effective length of database: 449
Effective search space:   198009
Effective search space used:   198009
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate WP_028996924.1 H537_RS0104395 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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/TIGR00133.hmm
# target sequence database:        /tmp/gapView.2537487.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-160  520.1   0.0   2.8e-160  519.9   0.0    1.0  1  NCBI__GCF_000430725.1:WP_028996924.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000430725.1:WP_028996924.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  519.9   0.0  2.8e-160  2.8e-160       4     480 ..      10     481 ..       7     482 .. 0.98

  Alignments for each domain:
  == domain 1  score: 519.9 bits;  conditional E-value: 2.8e-160
                             TIGR00133   4 yelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsev 76 
                                           ye+viGlE+H ql t+sK+F+ +s+ +    pNt+ ++v+l+lPG+lPv+N+ av+ A+  +la+++k+    
  NCBI__GCF_000430725.1:WP_028996924.1  10 YEVVIGLETHAQLSTASKIFSGASTAFGA-APNTQASAVDLALPGTLPVPNRGAVERAIRFGLAVGAKVA-RQ 80 
                                           99*************************99.9*************************************65.69 PP

                             TIGR00133  77 svFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkdkqslvDfN 149
                                           s+F+RK+YfYpDlPkgyqi+q+++P++++G++e  + e++k+++++r hlEeD+gks ++    +  + +D+N
  NCBI__GCF_000430725.1:WP_028996924.1  81 SIFARKNYFYPDLPKGYQISQYEIPVVQGGVIEFLVGEQKKRVNLTRAHLEEDAGKSLHEDY--HGLTGIDLN 151
                                           ***********************************************************944..58999**** PP

                             TIGR00133 150 RsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKNln 222
                                           R+g+PLlEiV++P+++s+ ea+ + ++l++++ +l+i dg+++eGs+R+D+Nvs+r k  e +gtr EiKNln
  NCBI__GCF_000430725.1:WP_028996924.1 152 RAGTPLLEIVSEPEMRSSLEAVGYARSLHALVVWLGICDGNMQEGSFRCDANVSVR-KPGEPFGTRREIKNLN 223
                                           ********************************************************.667889********** PP

                             TIGR00133 223 slksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkek 295
                                           s++ +++ai+yE++ q++ +++g +++q+t  fd  +  t ++R+Ke+++DYRYfp+Pdlpp++i++ +v++ 
  NCBI__GCF_000430725.1:WP_028996924.1 224 SFRFLQQAIDYEVQWQIDQIEDGLSIEQATVLFDPDSGETRAMRSKEDAHDYRYFPDPDLPPLVIEPAWVER- 295
                                           ***********************************************************************9. PP

                             TIGR00133 296 veeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkisla 368
                                           v++ +pelP+a+  r++++ gl ++da ++++ l +++++e +  + k+pkl++nW++ e +++Ln++   ++
  NCBI__GCF_000430725.1:WP_028996924.1 296 VKAGMPELPQAMADRFQQQDGLPAYDAGMVTQSLAFARYYEAARDACKQPKLVANWLMGEYAKRLNAEGRGIE 368
                                           ************************************************************************* PP

                             TIGR00133 369 eallkpeelaeliklikegkisqksakelleellen.kkdpkklieklgliqisdekelvkiveevikenpke 440
                                           ea ++p +l +li+ i +g+is+  ++++++ l +  ++d+++lie++gl q+sd+ +l +ive+v++ n+k+
  NCBI__GCF_000430725.1:WP_028996924.1 369 EAPVAPATLGALIARIADGTISNNGGRQVFDALWSGeGSDVDALIEAKGLKQMSDTGALEAIVEQVLAANEKS 441
                                           *******************************99875499********************************** PP

                             TIGR00133 441 vekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           v ++++gk+ka++ lvGqvmk +kg+a+p+ + +llk++l
  NCBI__GCF_000430725.1:WP_028996924.1 442 VAEFRAGKDKAFNALVGQVMKASKGKANPALAGELLKKKL 481
                                           **************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (483 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: 31.77
//
[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 2024 update 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 original 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