Alignments for a candidate for gatB in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Methanosarcina acetivorans C2A

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_011024400.1 MA_RS23595 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000007345.1:WP_011024400.1
          Length = 495

 Score =  342 bits (878), Expect = 1e-98
 Identities = 198/496 (39%), Positives = 302/496 (60%), Gaps = 40/496 (8%)

Query: 7   IGLEVHVEL-KTKSKIFSSSPTPF-GAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKAAM 64
           IGLE+HV+L K K+K+F    T +  A  NT T  I LG PG LPVLNK+ VE A+K  +
Sbjct: 11  IGLEIHVQLNKLKTKMFCGCSTDYHNAAPNTHTCPICLGLPGTLPVLNKKVVEAAIKVGL 70

Query: 65  ALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRLHLE 124
           AL  EIA +T+F RKNYFYPD PK +Q++Q+D PI   G + IE       +GITR H+E
Sbjct: 71  ALEGEIAEETQFHRKNYFYPDLPKGFQVTQYDYPIVSKGKVVIEGEDGEHVVGITRAHME 130

Query: 125 EDAGKLTHTGD-GYS---LVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGV 180
           ED GKL H G  G S   L+D+NR G PL+E V+EPD+R+P+EA  +L+K ++I++Y  V
Sbjct: 131 EDPGKLVHIGSIGKSKGVLIDYNRSGMPLIETVTEPDMRSPKEARRFLDKFRNILEYLDV 190

Query: 181 SDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGF 240
            D  + EG++R DAN+S+       +GT+ E+KN++S   V++ L +E  RQ+ V+  G 
Sbjct: 191 FDGNL-EGAMRVDANVSV------HWGTRVEVKNISSHKGVERALLYEIMRQKNVIRRGG 243

Query: 241 FIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDER 300
            I QETR +DE    T+ MR KE ++DYRYF EPDL+ + I D W   +K ++PELPD +
Sbjct: 244 TIVQETRHFDEGRGVTLSMRTKEEAEDYRYFREPDLMPMRITD-WIPAIKETLPELPDAK 302

Query: 301 RKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNW----LMGEVS------ 350
           R R+IE+ G     A  LT    +ADF+E    KG + K A+ W     +GE++      
Sbjct: 303 RTRFIEQYGITDMHARALTSKIMLADFYEGVCAKGVDPKIAATWTADVFLGELNYRDLAI 362

Query: 351 --------AYLNAEQKELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAE 402
                    +++A+  E+ + +     +  ++ L  +G IS + A +V + +++  G  E
Sbjct: 363 SSYGGKTIGFIHAKDPEVEN-SFKGSDMVELVTLFAEGKISDRAAVEVIRTILD--GTEE 419

Query: 403 K----IVKEKGLVQISDEGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKG 458
           K    I++EKGL +  D+ ++ K V E +  N  +++D+  G ++++ FLVGQ+MK +KG
Sbjct: 420 KTPSQIIEEKGLFKAEDD-LVTKAVAETIAENAAAVQDYLGGTEKSLNFLVGQVMKKTKG 478

Query: 459 QANPPMVNKILLEEIK 474
            A+     +++L+E+K
Sbjct: 479 TADAKTARELILKELK 494


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: 635
Number of extensions: 30
Number of successful extensions: 6
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: 495
Length adjustment: 34
Effective length of query: 442
Effective length of database: 461
Effective search space:   203762
Effective search space used:   203762
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: 52 (24.6 bits)

Align candidate WP_011024400.1 MA_RS23595 (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.3435553.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-172  560.3   0.0   4.8e-172  558.7   0.0    1.6  1  NCBI__GCF_000007345.1:WP_011024400.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000007345.1:WP_011024400.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  558.7   0.0  4.8e-172  4.8e-172       6     480 ..       9     493 ..       5     494 .. 0.95

  Alignments for each domain:
  == domain 1  score: 558.7 bits;  conditional E-value: 4.8e-172
                             TIGR00133   6 lviGlEvHvqln.tksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsevs 77 
                                           + iGlE+Hvqln +k+K+Fc cs+++++a pNt++cp+clglPG+lPvlNk++v++A+k++lal+ + ++e +
  NCBI__GCF_000007345.1:WP_011024400.1   9 IRIGLEIHVQLNkLKTKMFCGCSTDYHNAAPNTHTCPICLGLPGTLPVLNKKVVEAAIKVGLALEGE-IAEET 80 
                                           679*********99*****************************************************.5679* PP

                             TIGR00133  78 vFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk.dkqslvDfN 149
                                           +F+RK+YfYpDlPkg+q+tq+d+Pi+++Gk+ ie e++e+ +gi+r h+EeD+gk+++ +s   +k  l+D+N
  NCBI__GCF_000007345.1:WP_011024400.1  81 QFHRKNYFYPDLPKGFQVTQYDYPIVSKGKVVIEGEDGEHVVGITRAHMEEDPGKLVHIGSIGkSKGVLIDYN 153
                                           ***********************************************************997548899***** PP

                             TIGR00133 150 RsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKNln 222
                                           Rsg+PL+E Vt+Pd++s+kear fl k+r+il+yl+++dg+l eG+mRvD+Nvs++       gtrvE+KN++
  NCBI__GCF_000007345.1:WP_011024400.1 154 RSGMPLIETVTEPDMRSPKEARRFLDKFRNILEYLDVFDGNL-EGAMRVDANVSVH------WGTRVEVKNIS 219
                                           ******************************************.9************......99********* PP

                             TIGR00133 223 slksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkek 295
                                           s k++e+a+ yEi+Rqk+++++g +++qetr+fde + +t+s+R Kee+eDYRYf+ePdl+p+ i++ +    
  NCBI__GCF_000007345.1:WP_011024400.1 220 SHKGVERALLYEIMRQKNVIRRGGTIVQETRHFDEGRGVTLSMRTKEEAEDYRYFREPDLMPMRITDWI-PA- 290
                                           ******************************************************************975.55. PP

                             TIGR00133 296 veeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkisla 368
                                           ++e+lpelP+akr+r+ ++yg+ +  a+ l+s   l+d +e v     +pk a++W  + +lgeLn++++ ++
  NCBI__GCF_000007345.1:WP_011024400.1 291 IKETLPELPDAKRTRFIEQYGITDMHARALTSKIMLADFYEGVCAKGVDPKIAATWTADVFLGELNYRDLAIS 363
                                           9*******************************************************************99998 PP

                             TIGR00133 369 ea.................llkpeelaeliklikegkisqksakelleellen..kkdpkklieklgliqisd 422
                                                               +k ++++el+ l+ egkis+++a e+++++l+   +k p+++ie++gl++ +d
  NCBI__GCF_000007345.1:WP_011024400.1 364 SYggktigfihakdpevenSFKGSDMVELVTLFAEGKISDRAAVEVIRTILDGteEKTPSQIIEEKGLFKAED 436
                                           6555556655555665555788899**************************8766999************999 PP

                             TIGR00133 423 ekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           +  ++k+v e i+en+ +v++y+ g ek+l+flvGqvmkktkg ad+k++ +l+ + l
  NCBI__GCF_000007345.1:WP_011024400.1 437 D-LVTKAVAETIAENAAAVQDYLGGTEKSLNFLVGQVMKKTKGTADAKTARELILKEL 493
                                           8.99************************************************998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (495 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: 8.37
//
[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 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