Alignments for a candidate for gatB in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Thermomonospora curvata DSM 43183

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_012853877.1 TCUR_RS17535 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000024385.1:WP_012853877.1
          Length = 500

 Score =  397 bits (1021), Expect = e-115
 Identities = 212/483 (43%), Positives = 304/483 (62%), Gaps = 13/483 (2%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           +E V+G+E H+EL T +K+F   PT FGA  NTQ   + LG PG LPV NK A+E  +K 
Sbjct: 16  YEPVLGVETHIELGTATKMFCGCPTTFGAPPNTQVCPVCLGLPGSLPVTNKAAIEGIIKI 75

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRLH 122
            +ALNC IA   +F RKNYFYPD PK YQISQ+D+P+  +G++++EV G+T RIGI R+H
Sbjct: 76  GLALNCTIAEWCRFARKNYFYPDMPKNYQISQYDEPLCVDGYLDVEVDGETFRIGIERVH 135

Query: 123 LEEDAGKLTHTGDG--------YSLVDFNRQGTPLVEIVSEPDIRT----PEEAYAYLEK 170
           +EED GK  H G          YSLVD+NR G PLVEIV++P   T    P  A AY  +
Sbjct: 136 MEEDTGKSLHVGGATGRIHGADYSLVDYNRAGIPLVEIVTKPITGTGDKAPLVARAYATE 195

Query: 171 LKSIIQYTGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEK 230
           L+ +++  GVSD +MEEGS+RCD N+SL P G  E+GT+TE KN+NS   V++ + HE +
Sbjct: 196 LRELVRALGVSDVRMEEGSMRCDINVSLAPRGATEWGTRTETKNVNSLRSVERAVRHEIE 255

Query: 231 RQEQVLLSGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVK 290
           RQ  VL SG  + QETR + E T  T   R KE + DYRYFPEPDLV L    EW E+++
Sbjct: 256 RQAAVLESGGKVVQETRHFHEDTGTTTPGRSKEEAQDYRYFPEPDLVPLAPSREWVEQLR 315

Query: 291 ASIPELPDERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVS 350
           AS+PELP  RR+R   E G    +   + +     D  E+TV+ G     A  W M E+S
Sbjct: 316 ASLPELPAARRRRVQAEWGLTDLELRDV-VNAGALDLIEQTVKAGCAPGPARKWWMNELS 374

Query: 351 AYLNAEQKELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGL 410
                +  EL ++ +TP  +A +  LI++G+++ K+A++VF+ ++   GD +++V  +GL
Sbjct: 375 RRATEQGVELDELPITPAQVARVQALIDEGSLNDKLARQVFEGVLAGEGDPDEVVAARGL 434

Query: 411 VQISDEGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILL 470
             +SDEG L  +V + +  N  + +  + GK  A G LVG +MKA++GQA+     +++L
Sbjct: 435 KVVSDEGELAAIVDQVIAENADAADKVRAGKVAAAGALVGAVMKATRGQADAARARELIL 494

Query: 471 EEI 473
           +++
Sbjct: 495 QKL 497


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: 567
Number of extensions: 18
Number of successful extensions: 4
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: 500
Length adjustment: 34
Effective length of query: 442
Effective length of database: 466
Effective search space:   205972
Effective search space used:   205972
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_012853877.1 TCUR_RS17535 (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.1004717.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.5e-151  488.6   0.0   9.7e-151  488.4   0.0    1.0  1  NCBI__GCF_000024385.1:WP_012853877.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000024385.1:WP_012853877.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.4   0.0  9.7e-151  9.7e-151       3     480 ..      15     497 ..      13     498 .. 0.97

  Alignments for each domain:
  == domain 1  score: 488.4 bits;  conditional E-value: 9.7e-151
                             TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivse 75 
                                           +ye v+G+E+H+ l+t++K+Fc c++ +   +pNt+vcpvclglPG+lPv Nk a++  +k++laln+  ++e
  NCBI__GCF_000024385.1:WP_012853877.1  15 KYEPVLGVETHIELGTATKMFCGCPTTFGA-PPNTQVCPVCLGLPGSLPVTNKAAIEGIIKIGLALNCT-IAE 85 
                                           7999************************99.**************************************.668 PP

                             TIGR00133  76 vsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk.....dkq 143
                                              F+RK+YfYpD+Pk+yqi+q+d P++ dG+l++e++++  +igier+h+EeDtgks + +  +     +++
  NCBI__GCF_000024385.1:WP_012853877.1  86 WCRFARKNYFYPDMPKNYQISQYDEPLCVDGYLDVEVDGETFRIGIERVHMEEDTGKSLHVGGATgrihgADY 158
                                           ************************************************************987766687899* PP

                             TIGR00133 144 slvDfNRsgvPLlEiVtkPdlksake....araflkklrqilryleisdgdleeGsmRvDvNvsirlkGqeke 212
                                           slvD+NR+g+PL+EiVtkP   ++++    ara+  +lr+++r l++sd  +eeGsmR+D+Nvs+ ++G ++ 
  NCBI__GCF_000024385.1:WP_012853877.1 159 SLVDYNRAGIPLVEIVTKPITGTGDKaplvARAYATELRELVRALGVSDVRMEEGSMRCDINVSLAPRGATEW 231
                                           *********************99987344469***************************************** PP

                             TIGR00133 213 gtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppi 285
                                           gtr E KN+nsl+s+e+a+ +EieRq ++l++g +v+qetr+f+e + +t   R+Kee++DYRYfpePdl+p+
  NCBI__GCF_000024385.1:WP_012853877.1 232 GTRTETKNVNSLRSVERAVRHEIERQAAVLESGGKVVQETRHFHEDTGTTTPGRSKEEAQDYRYFPEPDLVPL 304
                                           ************************************************************************* PP

                             TIGR00133 286 eideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellg 358
                                             + e+v++ +++ lpelP a+r r++ e gl + + + +v ++  ld  e+ vk+   p  a +W ++el +
  NCBI__GCF_000024385.1:WP_012853877.1 305 APSREWVEQ-LRASLPELPAARRRRVQAEWGLTDLELRDVV-NAGALDLIEQTVKAGCAPGPARKWWMNELSR 375
                                           ********9.***********************99999877.567889************************* PP

                             TIGR00133 359 eLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkive 431
                                           +  ++ ++l e  ++p ++a++ +li+eg +++k a++++e +l  ++dp++++ ++gl  +sde el +iv+
  NCBI__GCF_000024385.1:WP_012853877.1 376 RATEQGVELDELPITPAQVARVQALIDEGSLNDKLARQVFEGVLAGEGDPDEVVAARGLKVVSDEGELAAIVD 448
                                           ************************************************************************* PP

                             TIGR00133 432 evikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           +vi+en+++  k ++gk +a + lvG vmk t+g+ad++++ +l+ ++l
  NCBI__GCF_000024385.1:WP_012853877.1 449 QVIAENADAADKVRAGKVAAAGALVGAVMKATRGQADAARARELILQKL 497
                                           *******************************************998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (500 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 18.59
//
[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