Alignments for a candidate for gatB in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Methanococcus maripaludis C5

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (uncharacterized)
to candidate WP_011868517.1 MMARC5_RS03800 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= curated2:Q57624
         (472 letters)



>NCBI__GCF_000016125.1:WP_011868517.1
          Length = 469

 Score =  700 bits (1807), Expect = 0.0
 Identities = 326/466 (69%), Positives = 407/466 (87%)

Query: 6   EDVKMKCGLEIHVQIDTKSKLFCNCSTNYLDAEPNTNVCPVCLGLPGAKPLPPNKKAVEV 65
           ED+ MKCGLEIHVQ+DT SKLFC C TNY D EPNTN+CPVC+G PGAKP+PPNKKA+++
Sbjct: 3   EDLSMKCGLEIHVQVDTNSKLFCQCPTNYKDVEPNTNICPVCIGHPGAKPMPPNKKAIDM 62

Query: 66  AIMVAKMLGCKIVVDEDIYFQRKHYDYPDLPSGYQRTSTPIGVDGEFMGIGIHEVHLEED 125
           AIMVAKMLGC++V+D+DIYFQRKHY+YPDLPSGYQ+TS PIG  G+F+G+GI EVHLEED
Sbjct: 63  AIMVAKMLGCEMVIDKDIYFQRKHYNYPDLPSGYQKTSVPIGEHGKFLGVGITEVHLEED 122

Query: 126 PGQYNPSFGIVDYNRSGTPLIEIVTKPDIKSPEEAREFLKQLMTLFRYLGCLRGEGTMRA 185
           PGQY P  G VDYNRSGTPLIEIVT PD+KSPEEAREFL+QL+ LFRY+G LRGEGTMRA
Sbjct: 123 PGQYKPDLGTVDYNRSGTPLIEIVTDPDMKSPEEAREFLRQLLRLFRYIGNLRGEGTMRA 182

Query: 186 DVNISIEYMGVQGNRVEVKNVNSIKGVYKVLKYELIRQKNIIKRGGEVKRETRAFLESQM 245
           D NISI+Y G+QGNRVEVKNVNSI+GVYKVLKYELIRQKN+++RGGE+K ETRAF+ESQM
Sbjct: 183 DTNISIKYNGIQGNRVEVKNVNSIRGVYKVLKYELIRQKNVLRRGGEIKLETRAFMESQM 242

Query: 246 ITKAMRSKETAEDYRYIPDPDIQPIVISEKWVKEIEEKMPETPLAKKKRFVEEYGIDEED 305
           ITK MRSKETA+DYRYIPDPD+QPIV++ +WV+++E +MPETP+ K+KRFVE+YGI E+D
Sbjct: 243 ITKGMRSKETADDYRYIPDPDLQPIVLNNEWVEKVEAQMPETPMNKEKRFVEQYGIKEDD 302

Query: 306 AKVLVSDLDMAEMFEEVVKSLGVNKENVDLAVTWIRNELRRSLQYHKVDLYESGVKAEHI 365
           AKVLVSDL++A++FE+VV  LG +K+ + LAVTWIRNEL+R L Y+K++ +E+ ++ EH+
Sbjct: 303 AKVLVSDLELADVFEKVVAELGNDKDGISLAVTWIRNELKRVLVYNKLEFFETNLRPEHM 362

Query: 366 VELIKLIKEGVISQKIAKEIVDLLVINRGKKMPKELVEELGLTVIRDEDALVKAVEEAIK 425
           VELI  IK+  ISQKI K I++ +V ++G+K PKEL+ E+GLTVI D   L KA EEAIK
Sbjct: 363 VELINSIKDKTISQKIGKTIIEQMVEHKGEKTPKELINEMGLTVIEDTSELEKACEEAIK 422

Query: 426 NNPKAVEDYLNGKKEALNFLMGQVMRLTRGRADPKRVIELLKERLD 471
           N+ KA+EDY +G + ALN ++GQVM+LTRGRA+P  V+E+LK+++D
Sbjct: 423 NSEKAIEDYKSGNQRALNSVVGQVMKLTRGRAEPATVVEILKKKID 468


Lambda     K      H
   0.317    0.137    0.388 

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: 778
Number of extensions: 27
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: 472
Length of database: 469
Length adjustment: 33
Effective length of query: 439
Effective length of database: 436
Effective search space:   191404
Effective search space used:   191404
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_011868517.1 MMARC5_RS03800 (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.3674168.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-176  574.0   4.6   1.2e-176  573.8   4.6    1.0  1  NCBI__GCF_000016125.1:WP_011868517.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016125.1:WP_011868517.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  573.8   4.6  1.2e-176  1.2e-176       3     480 ..       4     467 ..       2     468 .. 0.97

  Alignments for each domain:
  == domain 1  score: 573.8 bits;  conditional E-value: 1.2e-176
                             TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPv.lNkeavkkAlklalalnskivs 74 
                                           +  +++GlE+Hvq++t+sKlFc+c++++++ +pNtn+cpvc+g PGa+P+ +Nk+a+ +A+++a++l++++v 
  NCBI__GCF_000016125.1:WP_011868517.1   4 DLSMKCGLEIHVQVDTNSKLFCQCPTNYKDVEPNTNICPVCIGHPGAKPMpPNKKAIDMAIMVAKMLGCEMVI 76 
                                           5789**********************************************99*****************9765 PP

                             TIGR00133  75 .evsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkdkqslv 146
                                            + ++F+RKhY+YpDlP+gyq t+  +Pi+e+G    ++ +    +gi+++hlEeD+g  qyk    ++ ++v
  NCBI__GCF_000016125.1:WP_011868517.1  77 dKDIYFQRKHYNYPDLPSGYQKTS--VPIGEHG----KFLG----VGITEVHLEEDPG--QYK----PDLGTV 133
                                           489*********************..*******....5556....*************..799....669*** PP

                             TIGR00133 147 DfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiK 219
                                           D+NRsg+PL+EiVt Pd+ks++ear+fl++l +++ry++  +g   eG+mR+D N+si++ G   +g+rvE+K
  NCBI__GCF_000016125.1:WP_011868517.1 134 DYNRSGTPLIEIVTDPDMKSPEEAREFLRQLLRLFRYIGNLRG---EGTMRADTNISIKYNG--IQGNRVEVK 201
                                           *******************************************...*************886..689****** PP

                             TIGR00133 220 NlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevv 292
                                           N+ns+++++k+++yE++Rqk++l++g e+k etraf e+++it  +R+Ke++ DYRY+p+Pdl+pi++++e+v
  NCBI__GCF_000016125.1:WP_011868517.1 202 NVNSIRGVYKVLKYELIRQKNVLRRGGEIKLETRAFMESQMITKGMRSKETADDYRYIPDPDLQPIVLNNEWV 274
                                           ************************************************************************* PP

                             TIGR00133 293 kekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep....klavnWileellgeLn 361
                                           ++ ve+++pe+P +k +r++++yg++e+dakvlvsdlel+d+fe+vv  +++      lav+Wi++el+++L 
  NCBI__GCF_000016125.1:WP_011868517.1 275 EK-VEAQMPETPMNKEKRFVEQYGIKEDDAKVLVSDLELADVFEKVVAELGNDkdgiSLAVTWIRNELKRVLV 346
                                           *9.******************************************998887775777899************* PP

                             TIGR00133 362 kkkislaeallkpeelaeliklikegkisqksakelleellen..kkdpkklieklgliqisdekelvkivee 432
                                           ++k+++ e++l+pe+++eli+ ik+++isqk++k+++e+++e+  +k pk+li+++gl+ i+d++el k++ee
  NCBI__GCF_000016125.1:WP_011868517.1 347 YNKLEFFETNLRPEHMVELINSIKDKTISQKIGKTIIEQMVEHkgEKTPKELINEMGLTVIEDTSELEKACEE 419
                                           ******************************************9767889************************ PP

                             TIGR00133 433 vikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           +ik+ +k++e+yksg ++al+ +vGqvmk t+gra+p++v+++lk+++
  NCBI__GCF_000016125.1:WP_011868517.1 420 AIKNSEKAIEDYKSGNQRALNSVVGQVMKLTRGRAEPATVVEILKKKI 467
                                           *********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (469 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 22.27
//
[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