Alignments for a candidate for gatB in Methanobacterium lacus AL-21

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Methanobacterium lacus AL-21

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (uncharacterized)
to candidate WP_013643917.1 METBO_RS01615 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B

Query= curated2:O27341
         (449 letters)



>NCBI__GCF_000191585.1:WP_013643917.1
          Length = 452

 Score =  679 bits (1752), Expect = 0.0
 Identities = 326/446 (73%), Positives = 385/446 (86%)

Query: 1   MKCGLEIHVQLDTRSKLFCRCPTDYQEAPPNTNICPVCLNQPGAKPYPPNRSALEGALKI 60
           MKCGLEIHVQL T SKLFC C T+Y++A  NTNICPVCLNQPGAKPYPPN++AL+ A+KI
Sbjct: 1   MKCGLEIHVQLKTDSKLFCSCHTNYKDAKANTNICPVCLNQPGAKPYPPNKAALDAAIKI 60

Query: 61  ALMLDCRINPEITYFMRKHYNYPDLPSGYQRTSIPVGLEGELNGVRIREVHIEEDPGQYK 120
           ALML C I+PE+TYF RKHY+YPDL SGYQRTSIP+G  GELNGVRI +VHIEEDPGQYK
Sbjct: 61  ALMLGCDISPEVTYFQRKHYDYPDLSSGYQRTSIPIGSGGELNGVRIYDVHIEEDPGQYK 120

Query: 121 PDQGTVDFNRSGIPLIEIVTEPDMTSPEEARNFLRELIRVLEYSGCARGEGTMRADVNIS 180
           PD GTVDFNRSGIPLIEIVT PDM SPEEAR FLRELIRVL+YSG ARGEG+MRADVNIS
Sbjct: 121 PDMGTVDFNRSGIPLIEIVTHPDMKSPEEARKFLRELIRVLDYSGSARGEGSMRADVNIS 180

Query: 181 LEGGKRVEIKNINSIKGAYKALKFEMIRQKNLLKRGVEVKQETRAFLESQMITVSMRLKE 240
           +EGGKR EIKNINSIKGAYKAL+FEM+RQKNLLKRG+E+KQETRAFLESQMITV MRLKE
Sbjct: 181 IEGGKRAEIKNINSIKGAYKALQFEMVRQKNLLKRGIEIKQETRAFLESQMITVPMRLKE 240

Query: 241 EAEDYRYIPDPDLPPMKFTDEVVEGLRERIPEAPHLKVKRFMEEYGLREEDARVLTSELE 300
           EAEDYRYIPDPDLPPM+  ++ VE +RE +PE  H+K +RF+ EYG+  + A+V+TSELE
Sbjct: 241 EAEDYRYIPDPDLPPMQAEEDAVEIIREAMPEPAHIKTERFVNEYGISRDHAKVITSELE 300

Query: 301 LADAFEEVAGSIDPEFAALWMRDELKRVLYYNKISFAESMITPGDIIELLAMIRKKEITS 360
           LADAFEEVA S+DPEFAALWMRDELKRV+YYNK+SF ES IT   I++LL M++ K+IT+
Sbjct: 301 LADAFEEVANSVDPEFAALWMRDELKRVIYYNKMSFKESEITASQIVDLLKMLQNKKITA 360

Query: 361 KAAKKIIEEMPLNKKGPREIATEMGLIGIIDESEVIRAVEQAIRENPGAVEDYHAGKEAA 420
           KA K+I+E++P N + P  IA EMGL G++ E +V+ A++Q ++ENP AV DY  GK+ A
Sbjct: 361 KAGKRIMEKLPRNSQMPSTIAEEMGLTGVVTEDQVVDAIKQVVKENPDAVSDYFEGKKNA 420

Query: 421 INFLVGQVMRMTRGKAEPERTVELIK 446
           INFLVGQVMR+TRGKA+P  T +L++
Sbjct: 421 INFLVGQVMRLTRGKADPTETNKLLE 446


Lambda     K      H
   0.317    0.137    0.391 

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: 746
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: 449
Length of database: 452
Length adjustment: 33
Effective length of query: 416
Effective length of database: 419
Effective search space:   174304
Effective search space used:   174304
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: 51 (24.3 bits)

Align candidate WP_013643917.1 METBO_RS01615 (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.16738.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-172  560.2   0.5   1.9e-172  560.0   0.5    1.0  1  lcl|NCBI__GCF_000191585.1:WP_013643917.1  METBO_RS01615 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000191585.1:WP_013643917.1  METBO_RS01615 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 !  560.0   0.5  1.9e-172  1.9e-172       6     480 ..       1     449 [.       1     450 [. 0.98

  Alignments for each domain:
  == domain 1  score: 560.0 bits;  conditional E-value: 1.9e-172
                                 TIGR00133   6 lviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPv.lNkeavkkAlklalalnskiv 73 
                                               +++GlE+Hvql t sKlFc+c +++++ak Ntn+cpvcl++PGa+P+ +Nk a+ +A+k+al+l++ i 
  lcl|NCBI__GCF_000191585.1:WP_013643917.1   1 MKCGLEIHVQLKTDSKLFCSCHTNYKDAKANTNICPVCLNQPGAKPYpPNKAALDAAIKIALMLGCDIS 69 
                                               79*********************************************99******************** PP

                                 TIGR00133  74 sevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkdk 142
                                                ev++F+RKhY+YpDl +gyq+t+  +Pi+++G    el++    ++i  +h+EeD+g  qyk    ++
  lcl|NCBI__GCF_000191585.1:WP_013643917.1  70 PEVTYFQRKHYDYPDLSSGYQRTS--IPIGSGG----ELNG----VRIYDVHIEEDPG--QYK----PD 122
                                               ************************..*******....7888....*************..799....66 PP

                                 TIGR00133 143 qslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqek 211
                                               +++vDfNRsg+PL+EiVt+Pd+ks++ear+fl++l ++l y++ ++g   eGsmR+DvN+si+      
  lcl|NCBI__GCF_000191585.1:WP_013643917.1 123 MGTVDFNRSGIPLIEIVTHPDMKSPEEARKFLRELIRVLDYSGSARG---EGSMRADVNISIE------ 182
                                               9**********************************************...*************...... PP

                                 TIGR00133 212 egtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpeP 280
                                                g+r+EiKN+ns+k+ +ka+++E+ Rqk+llk+g e+kqetraf e+++itv +R Kee+eDYRY+p+P
  lcl|NCBI__GCF_000191585.1:WP_013643917.1 183 GGKRAEIKNINSIKGAYKALQFEMVRQKNLLKRGIEIKQETRAFLESQMITVPMRLKEEAEDYRYIPDP 251
                                               9******************************************************************** PP

                                 TIGR00133 281 dlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklav 349
                                               dlpp++ +e+ v+  ++e +pe  ++k +r+++eyg+s + akv++s+lel+dafeev++++++ + a+
  lcl|NCBI__GCF_000191585.1:WP_013643917.1 252 DLPPMQAEEDAVEI-IREAMPEPAHIKTERFVNEYGISRDHAKVITSELELADAFEEVANSVDP-EFAA 318
                                               **********9988.********9************************************9988.**** PP

                                 TIGR00133 350 nWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgli 418
                                                W+++el+++++++k+s++e+ +++++++ l+k+++++ki++k++k+++e+l  n ++p++++e++gl+
  lcl|NCBI__GCF_000191585.1:WP_013643917.1 319 LWMRDELKRVIYYNKMSFKESEITASQIVDLLKMLQNKKITAKAGKRIMEKLPRNSQMPSTIAEEMGLT 387
                                               ********************************************************************* PP

                                 TIGR00133 419 qisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                                ++ e+++v+++++v+kenp++v +y +gk++a++flvGqvm+ t+g+adp+e++kll+  l
  lcl|NCBI__GCF_000191585.1:WP_013643917.1 388 GVVTEDQVVDAIKQVVKENPDAVSDYFEGKKNAINFLVGQVMRLTRGKADPTETNKLLEVEL 449
                                               *********************************************************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (452 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: 10.83
//
[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