Aligments for a candidate for gatB in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Aligments for a candidate for gatB in Acidovorax sp. GW101-3H11

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate Ac3H11_3339 Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit B (EC 6.3.5.7)

Query= metacyc::MONOMER-13956
         (476 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3339
          Length = 482

 Score =  422 bits (1085), Expect = e-122
 Identities = 220/469 (46%), Positives = 303/469 (64%), Gaps = 3/469 (0%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           +E VIG E H +L T+SKIFS +PT FGAE NTQ   +DL  PG LPV+N+EAV  A+K 
Sbjct: 9   YEVVIGFETHTQLATQSKIFSRAPTAFGAEPNTQACAVDLALPGTLPVMNREAVACAIKL 68

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRLH 122
            +AL   IA  + F RKNYFYPD PK YQISQF+ P+ + G +   +G + K + + R H
Sbjct: 69  GLALGSHIAEKSIFARKNYFYPDLPKGYQISQFEIPVVQGGEVSFFLGDEKKTVRLVRAH 128

Query: 123 LEEDAGKLTHTGD-GYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGVS 181
           LEEDAGK  H    G S +D NR GTPL+EIV+EPD+ + +EA AY ++L  I+ + G+ 
Sbjct: 129 LEEDAGKSLHEDFIGQSGIDLNRAGTPLLEIVTEPDMSSSDEAVAYAKELHKIVTWIGIC 188

Query: 182 DCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGFF 241
           D  M+EGS RCDAN+S+R  GQ   GT+ E+KNLNSF F+Q+ +++E + Q + +  G  
Sbjct: 189 DGNMQEGSFRCDANVSVRKPGQP-LGTRREIKNLNSFKFMQQAIDYEIRWQIEQIEDGHA 247

Query: 242 IQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDERR 301
           IQQ T  +D  T +T  MR KE + DYRYFP+PDL  L+I ++W E  +A + ELP    
Sbjct: 248 IQQATVLFDPDTGETRAMRTKEDAADYRYFPDPDLPPLHISEQWIEEQRAQMAELPRTMA 307

Query: 302 KRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKELA 361
            R++ + G   YDA  LT +K MA +FE   +   +AK ASNW+MGEVS  LN  +  + 
Sbjct: 308 TRFVADYGLPEYDATTLTQSKAMAAYFEAVAKACGQAKLASNWIMGEVSRRLNMAEIGIE 367

Query: 362 DVALTPEGLAGMIKLIEKGTISSKIAKKVFKEL-IEKGGDAEKIVKEKGLVQISDEGVLL 420
              ++   LA +I  I  GTIS+  AK+VF  L   +G D + +++ KGL Q++D G L 
Sbjct: 368 QAPVSSAQLAALIARIADGTISNNAAKQVFDALWTSEGQDVDAVIEAKGLKQMNDSGALE 427

Query: 421 KLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKIL 469
           K++ E +  N  ++  F+ GKD+A   LVGQIMKASKG+ANP  VN++L
Sbjct: 428 KIIDEVIAANADNVAQFRAGKDKAFNALVGQIMKASKGKANPTQVNELL 476


Lambda     K      H
   0.314    0.134    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: 569
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: 476
Length of database: 482
Length adjustment: 34
Effective length of query: 442
Effective length of database: 448
Effective search space:   198016
Effective search space used:   198016
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 Ac3H11_3339 (Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit B (EC 6.3.5.7))
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.23058.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   8.2e-173  561.2   0.0   9.3e-173  561.0   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339  Aspartyl-tRNA(Asn) amidotransfer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339  Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamy
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  561.0   0.0  9.3e-173  9.3e-173       4     480 ..       9     480 ..       6     481 .. 0.98

  Alignments for each domain:
  == domain 1  score: 561.0 bits;  conditional E-value: 9.3e-173
                                        TIGR00133   4 yelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlkla 65 
                                                      ye+viG+E+H+ql t+sK+F+++++ +   +pNt+ c+v+l+lPG+lPv+N+eav+ A+kl+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339   9 YEVVIGFETHTQLATQSKIFSRAPTAFGA-EPNTQACAVDLALPGTLPVMNREAVACAIKLG 69 
                                                      99*************************99.******************************** PP

                                        TIGR00133  66 lalnskivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlE 127
                                                      lal+s+ ++e+s+F+RK+YfYpDlPkgyqi+q+++P++++G+++  l +++k++++ r hlE
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339  70 LALGSH-IAEKSIFARKNYFYPDLPKGYQISQFEIPVVQGGEVSFFLGDEKKTVRLVRAHLE 130
                                                      ******.668**************************************************** PP

                                        TIGR00133 128 eDtgksqykesdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdg 189
                                                      eD+gks ++      qs +D+NR+g+PLlEiVt+Pd++s++ea+a+ k+l++i+ +++i dg
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 131 EDAGKSLHEDFI--GQSGIDLNRAGTPLLEIVTEPDMSSSDEAVAYAKELHKIVTWIGICDG 190
                                                      ********9665..7*********************************************** PP

                                        TIGR00133 190 dleeGsmRvDvNvsirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqe 251
                                                      +++eGs+R+D+Nvs+r  G +  gtr EiKNlns+k +++ai+yEi  q++ +++g+ ++q+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 191 NMQEGSFRCDANVSVRKPG-QPLGTRREIKNLNSFKFMQQAIDYEIRWQIEQIEDGHAIQQA 251
                                                      ****************555.5689999*********************************** PP

                                        TIGR00133 252 trafdekksitvslRkKeeseDYRYfpePdlppieideevvkekveeklpelPeakrirlkk 313
                                                      t  fd  +  t ++R Ke+++DYRYfp+Pdlpp++i+e++++e  ++++ elP+++ +r++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 252 TVLFDPDTGETRAMRTKEDAADYRYFPDPDLPPLHISEQWIEE-QRAQMAELPRTMATRFVA 312
                                                      *******************************************.9***************** PP

                                        TIGR00133 314 eyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkislaeallkpe 375
                                                      +ygl e+da +l++ + ++ +fe v+k+ +++kla nWi+ e+ ++Ln  +i +++a +++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 313 DYGLPEYDATTLTQSKAMAAYFEAVAKACGQAKLASNWIMGEVSRRLNMAEIGIEQAPVSSA 374
                                                      ************************************************************** PP

                                        TIGR00133 376 elaeliklikegkisqksakelleellen.kkdpkklieklgliqisdekelvkiveevike 436
                                                      +la+li+ i +g+is+ +ak++++ l +  ++d++++ie++gl q++d  +l ki++evi+ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 375 QLAALIARIADGTISNNAAKQVFDALWTSeGQDVDAVIEAKGLKQMNDSGALEKIIDEVIAA 436
                                                      ************************9987659******************************* PP

                                        TIGR00133 437 npkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                                      n+++v ++++gk+ka++ lvGq+mk +kg+a+p++v++ll+ +l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 437 NADNVAQFRAGKDKAFNALVGQIMKASKGKANPTQVNELLRAKL 480
                                                      ***************************************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (482 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: 7.84
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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