Alignments for a candidate for gatB in Methanosarcina mazei Go1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Methanosarcina mazei Go1

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (uncharacterized)
to candidate WP_011033177.1 MM_RS06355 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B

Query= curated2:Q8THJ0
         (495 letters)



>NCBI__GCF_000007065.1:WP_011033177.1
          Length = 495

 Score =  954 bits (2466), Expect = 0.0
 Identities = 473/495 (95%), Positives = 483/495 (97%)

Query: 1   MVYENPDGIRIGLEIHVQLNKLKTKMFCGCSTDYHNAAPNTHTCPICLGLPGTLPVLNKK 60
           MVYENPDGIRIGLEIHVQLNKLKTKMFCGCSTDYHNAAPNTHTCP+CLGLPG LPVLNKK
Sbjct: 1   MVYENPDGIRIGLEIHVQLNKLKTKMFCGCSTDYHNAAPNTHTCPVCLGLPGALPVLNKK 60

Query: 61  VVEAAIKVGLALEGEIAEETQFHRKNYFYPDLPKGFQVTQYDYPIVSKGKVVIEGEDGEH 120
            VEAAIKVGLALEGEIAEETQFHRKNYFYPDLPKGFQVTQYDYPIVSKGKVVIEGEDGEH
Sbjct: 61  AVEAAIKVGLALEGEIAEETQFHRKNYFYPDLPKGFQVTQYDYPIVSKGKVVIEGEDGEH 120

Query: 121 VVGITRAHMEEDPGKLVHIGSIGKSKGVLIDYNRSGMPLIETVTEPDMRSPKEARRFLDK 180
           VVGITRAHMEEDPGKLVHIGSI KSKGVLIDYNRSGMPLIETVTEPDMRSPKEARRFLDK
Sbjct: 121 VVGITRAHMEEDPGKLVHIGSIEKSKGVLIDYNRSGMPLIETVTEPDMRSPKEARRFLDK 180

Query: 181 FRNILEYLDVFDGNLEGAMRVDANVSVHWGTRVEVKNISSHKGVERALLYEIMRQKNVIR 240
           FRNILEYLDVFDGNLEGAMRVDANVSVHWGTRVEVKNISSHKGVERALLYEIMRQKNVIR
Sbjct: 181 FRNILEYLDVFDGNLEGAMRVDANVSVHWGTRVEVKNISSHKGVERALLYEIMRQKNVIR 240

Query: 241 RGGTIVQETRHFDEGRGVTLSMRTKEEAEDYRYFREPDLMPMRITDWIPAIKETLPELPD 300
           RGG I QETRHFDEGRGVT+SMRTKEEAEDYRYFREPDLMPMR+T WIPAIKETLPELPD
Sbjct: 241 RGGKITQETRHFDEGRGVTISMRTKEEAEDYRYFREPDLMPMRVTGWIPAIKETLPELPD 300

Query: 301 AKRTRFIEQYGITDMHARALTSKIMLADFYEGVCAKGVDPKIAATWTADVFLGELNYRDL 360
           AKR RF+EQYGITDMHARALTSKIMLADFYEGVCAKGVDPK+AATWTADV LGELNYRDL
Sbjct: 301 AKRARFMEQYGITDMHARALTSKIMLADFYEGVCAKGVDPKVAATWTADVLLGELNYRDL 360

Query: 361 AISSYGGKTIGFIHAKDPEVENSFKGSDMVELVTLFAEGKISDRAAVEVIRTILDGTEEK 420
           AISSY G+TIGFIHAKDPEVENSFK SDMVELVTLFAEGK+SDRAAVEVIRTILDG EEK
Sbjct: 361 AISSYDGRTIGFIHAKDPEVENSFKVSDMVELVTLFAEGKVSDRAAVEVIRTILDGNEEK 420

Query: 421 TPSQIIEEKGLFKAEDDLVTKAVAETIAENAAAVQDYLGGTEKSLNFLVGQVMKKTKGTA 480
           +PSQIIEEKGLFKAEDDLVT+AVAETIAEN AAVQDYLGGTEKSLNFLVGQVMKKTKGTA
Sbjct: 421 SPSQIIEEKGLFKAEDDLVTRAVAETIAENEAAVQDYLGGTEKSLNFLVGQVMKKTKGTA 480

Query: 481 DAKTARELILKELKG 495
           DAKTARELI+KELKG
Sbjct: 481 DAKTARELIVKELKG 495


Lambda     K      H
   0.317    0.136    0.393 

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: 1002
Number of extensions: 26
Number of successful extensions: 1
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: 495
Length of database: 495
Length adjustment: 34
Effective length of query: 461
Effective length of database: 461
Effective search space:   212521
Effective search space used:   212521
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_011033177.1 MM_RS06355 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B)
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.11047.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-172  560.9   0.0   2.8e-172  559.4   0.0    1.5  1  lcl|NCBI__GCF_000007065.1:WP_011033177.1  MM_RS06355 Asp-tRNA(Asn)/Glu-tRN


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000007065.1:WP_011033177.1  MM_RS06355 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  559.4   0.0  2.8e-172  2.8e-172       6     480 ..       9     493 ..       5     494 .. 0.95

  Alignments for each domain:
  == domain 1  score: 559.4 bits;  conditional E-value: 2.8e-172
                                 TIGR00133   6 lviGlEvHvqln.tksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskiv 73 
                                               + iGlE+Hvqln +k+K+Fc cs+++++a pNt++cpvclglPGalPvlNk+av++A+k++lal+ + +
  lcl|NCBI__GCF_000007065.1:WP_011033177.1   9 IRIGLEIHVQLNkLKTKMFCGCSTDYHNAAPNTHTCPVCLGLPGALPVLNKKAVEAAIKVGLALEGE-I 76 
                                               679*********99*****************************************************.5 PP

                                 TIGR00133  74 sevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk.d 141
                                               +e ++F+RK+YfYpDlPkg+q+tq+d+Pi+++Gk+ ie e++e+ +gi+r h+EeD+gk+++ +s + +
  lcl|NCBI__GCF_000007065.1:WP_011033177.1  77 AEETQFHRKNYFYPDLPKGFQVTQYDYPIVSKGKVVIEGEDGEHVVGITRAHMEEDPGKLVHIGSIEkS 145
                                               679*************************************************************98757 PP

                                 TIGR00133 142 kqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqe 210
                                               k  l+D+NRsg+PL+E Vt+Pd++s+kear fl k+r+il+yl+++dg+l eG+mRvD+Nvs++     
  lcl|NCBI__GCF_000007065.1:WP_011033177.1 146 KGVLIDYNRSGMPLIETVTEPDMRSPKEARRFLDKFRNILEYLDVFDGNL-EGAMRVDANVSVH----- 208
                                               8899**********************************************.9************..... PP

                                 TIGR00133 211 kegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpe 279
                                                 gtrvE+KN++s k++e+a+ yEi+Rqk+++++g +++qetr+fde + +t+s+R Kee+eDYRYf+e
  lcl|NCBI__GCF_000007065.1:WP_011033177.1 209 -WGTRVEVKNISSHKGVERALLYEIMRQKNVIRRGGKITQETRHFDEGRGVTISMRTKEEAEDYRYFRE 276
                                               .99****************************************************************** PP

                                 TIGR00133 280 PdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepkla 348
                                               Pdl+p+ ++   +   ++e+lpelP+akr+r++++yg+ +  a+ l+s   l+d +e v     +pk a
  lcl|NCBI__GCF_000007065.1:WP_011033177.1 277 PDLMPMRVTGW-IPA-IKETLPELPDAKRARFMEQYGITDMHARALTSKIMLADFYEGVCAKGVDPKVA 343
                                               ********986.566.9**************************************************** PP

                                 TIGR00133 349 vnWileellgeLnkkkislaea.................llkpeelaeliklikegkisqksakellee 400
                                               ++W  + llgeLn++++ ++                    +k ++++el+ l+ egk+s+++a e++++
  lcl|NCBI__GCF_000007065.1:WP_011033177.1 344 ATWTADVLLGELNYRDLAISSYdgrtigfihakdpevenSFKVSDMVELVTLFAEGKVSDRAAVEVIRT 412
                                               ***************999876555656655555665565788899************************ PP

                                 TIGR00133 401 llen..kkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgra 467
                                               +l+   +k+p+++ie++gl++ +d+  ++++v e i+en+ +v++y+ g ek+l+flvGqvmkktkg a
  lcl|NCBI__GCF_000007065.1:WP_011033177.1 413 ILDGneEKSPSQIIEEKGLFKAEDD-LVTRAVAETIAENEAAVQDYLGGTEKSLNFLVGQVMKKTKGTA 480
                                               **8656999************9998.99***************************************** PP

                                 TIGR00133 468 dpkevekllkell 480
                                               d+k++ +l+ + l
  lcl|NCBI__GCF_000007065.1:WP_011033177.1 481 DAKTARELIVKEL 493
                                               *******998876 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: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 2.75
//
[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