Alignments for a candidate for gatB in Pseudarthrobacter sulfonivorans Ar51

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Pseudarthrobacter sulfonivorans Ar51

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_058929563.1 AU252_RS03710 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_001484605.1:WP_058929563.1
          Length = 502

 Score =  389 bits (999), Expect = e-112
 Identities = 207/484 (42%), Positives = 304/484 (62%), Gaps = 14/484 (2%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           ++ V+G EVHVEL TKSK+FSS+P  FG E NT  + +DLG PGVLPV+N+ A+E ++K 
Sbjct: 16  YDPVLGFEVHVELNTKSKMFSSAPNVFGDEPNTNVNEVDLGMPGVLPVVNRVAIESSIKI 75

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVG-GKTKRIGITRL 121
            +ALNC+IA    F RK YFYPD PK +Q SQ++ PI  +G+++IE+  G   R+ I R 
Sbjct: 76  GLALNCKIAESCTFARKQYFYPDTPKNFQTSQYEDPIAYDGYLDIELSDGTIFRVEIERA 135

Query: 122 HLEEDAGKLTHTGDG--------YSLVDFNRQGTPLVEIVSEP----DIRTPEEAYAYLE 169
           H+EEDAGKLTH G          +SLVD+NR G PLVEIV++P      R PE A AY+ 
Sbjct: 136 HMEEDAGKLTHMGGAAGRIQGADFSLVDYNRSGVPLVEIVTKPIEGAGSRAPELAKAYVA 195

Query: 170 KLKSIIQYTGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEE 229
            ++ I++  GVSD KME G++RCDAN+SLRP G+E FG ++E KN+NS   V+  + +E 
Sbjct: 196 AVREIVKNLGVSDAKMERGNVRCDANVSLRPHGRERFGIRSETKNVNSLRAVEHAVRYEI 255

Query: 230 KRQEQVLLSGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERV 289
           +R   VL +G  I QETR + E T+ T   R K  +DDYRYFPEPDLV +    EW E +
Sbjct: 256 QRHAAVLDAGNPIIQETRHWHEDTRTTTSGRPKSDADDYRYFPEPDLVPIVASREWVEEL 315

Query: 290 KASIPELPDERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEV 349
           +A++PE P  RRKR   + G++  +   + +   + D  EET+  GA A  A  W MGE+
Sbjct: 316 RATLPEPPAARRKRLQSDWGYSDLEFRDV-VNAGVMDEIEETIAAGASASVARKWWMGEI 374

Query: 350 SAYLNAEQKELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKG 409
                    +   + + P  +  + +++E G I++K+A +V   ++   G   +IV+++G
Sbjct: 375 VGRAKNADVDPGQLGVQPATIVELNRMVEDGKINNKMATEVLDGVLAGEGTPAEIVEKRG 434

Query: 410 LVQISDEGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKIL 469
           L  +SD+G LL+ +  AL   P   +  + GK +AIG +VG +MKA++GQA+   V +++
Sbjct: 435 LAVVSDDGPLLEAIDAALAAQPDVADKIRAGKLQAIGAIVGGVMKATRGQADAGRVKELI 494

Query: 470 LEEI 473
           L ++
Sbjct: 495 LAKL 498


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: 623
Number of extensions: 33
Number of successful extensions: 5
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: 502
Length adjustment: 34
Effective length of query: 442
Effective length of database: 468
Effective search space:   206856
Effective search space used:   206856
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_058929563.1 AU252_RS03710 (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.15888.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-140  455.0   0.0   1.6e-140  454.8   0.0    1.0  1  lcl|NCBI__GCF_001484605.1:WP_058929563.1  AU252_RS03710 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_058929563.1  AU252_RS03710 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.8   0.0  1.6e-140  1.6e-140       1     480 [.      13     498 ..      13     499 .. 0.96

  Alignments for each domain:
  == domain 1  score: 454.8 bits;  conditional E-value: 1.6e-140
                                 TIGR00133   1 kieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalaln 69 
                                               +++y+ v+G+EvHv lntksK+F++++n + + +pNtnv+ v+lg+PG+lPv+N+ a+++ +k++laln
  lcl|NCBI__GCF_001484605.1:WP_058929563.1  13 MEKYDPVLGFEVHVELNTKSKMFSSAPNVFGD-EPNTNVNEVDLGMPGVLPVVNRVAIESSIKIGLALN 80 
                                               578999**************************.************************************ PP

                                 TIGR00133  70 skivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqyke 137
                                               +k ++e  +F+RK+YfYpD Pk++q +q++ Pia dG+l+iel+++   +++ier h+EeD+gk+++ +
  lcl|NCBI__GCF_001484605.1:WP_058929563.1  81 CK-IAESCTFARKQYFYPDTPKNFQTSQYEDPIAYDGYLDIELSDGTiFRVEIERAHMEEDAGKLTHMG 148
                                               **.5689************************************9988789*****************98 PP

                                 TIGR00133 138 sdk.....dkqslvDfNRsgvPLlEiVtkPd....lksakearaflkklrqilryleisdgdleeGsmR 197
                                                       +++slvD+NRsgvPL+EiVtkP      + ++ a+a++  +r+i++ l++sd+++e G++R
  lcl|NCBI__GCF_001484605.1:WP_058929563.1 149 GAAgriqgADFSLVDYNRSGVPLVEIVTKPIegagSRAPELAKAYVAAVREIVKNLGVSDAKMERGNVR 217
                                               7655577899********************733335778999*************************** PP

                                 TIGR00133 198 vDvNvsirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslR 266
                                               +D+Nvs+r++G+e++g r E KN+nsl+++e+a+ yEi+R  ++l  g+ + qetr+++e + +t s R
  lcl|NCBI__GCF_001484605.1:WP_058929563.1 218 CDANVSLRPHGRERFGIRSETKNVNSLRAVEHAVRYEIQRHAAVLDAGNPIIQETRHWHEDTRTTTSGR 286
                                               ********************************************************************* PP

                                 TIGR00133 267 kKeeseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldaf 335
                                                K ++ DYRYfpePdl+pi+ + e+v+e ++++lpe P a+r+rl+++ g s+ + + +v ++ ++d  
  lcl|NCBI__GCF_001484605.1:WP_058929563.1 287 PKSDADDYRYFPEPDLVPIVASREWVEE-LRATLPEPPAARRKRLQSDWGYSDLEFRDVV-NAGVMDEI 353
                                               ****************************.***********************99999877.57788999 PP

                                 TIGR00133 336 eevvklikepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellen 404
                                               ee   + +++  a +W + e++g+ ++ +++  +  ++p +++el +++++gki++k+a e+l+ +l  
  lcl|NCBI__GCF_001484605.1:WP_058929563.1 354 EETIAAGASASVARKWWMGEIVGRAKNADVDPGQLGVQPATIVELNRMVEDGKINNKMATEVLDGVLAG 422
                                               9999999999*********************************************************** PP

                                 TIGR00133 405 kkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkeve 473
                                               ++ p +++ek+gl  +sd+  l ++++++++ +p+   k ++gk +a++ +vG vmk t+g+ad+ +v+
  lcl|NCBI__GCF_001484605.1:WP_058929563.1 423 EGTPAEIVEKRGLAVVSDDGPLLEAIDAALAAQPDVADKIRAGKLQAIGAIVGGVMKATRGQADAGRVK 491
                                               ********************************************************************* PP

                                 TIGR00133 474 kllkell 480
                                               +l+  +l
  lcl|NCBI__GCF_001484605.1:WP_058929563.1 492 ELILAKL 498
                                               *998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (502 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.19
//
[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