Alignments for a candidate for gatB in Thermocrinis albus DSM 14484

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Thermocrinis albus DSM 14484

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_012991604.1 THAL_RS02810 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000025605.1:WP_012991604.1
          Length = 470

 Score =  473 bits (1217), Expect = e-138
 Identities = 237/472 (50%), Positives = 330/472 (69%), Gaps = 6/472 (1%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           M  E VIGLE+HV+L+T+SK+F S P  FGAE NT    + LG PG LPVLNK AVE A+
Sbjct: 1   MELEPVIGLEIHVQLETRSKLFCSCPVEFGAEPNTNVCPVCLGLPGTLPVLNKRAVELAL 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITR 120
           +AA+ALNCEI   + F RKNYFYPD PK YQISQ++ P+  NG++E++     KR+ I R
Sbjct: 61  RAAIALNCEINLVSVFARKNYFYPDLPKGYQISQYEHPLAVNGFVEVQ----GKRVRIRR 116

Query: 121 LHLEEDAGKLTHTGDGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGV 180
           LHLEEDAGK  H G G + +DFNR GTPL+EIV+EPDI +P+ A  +LE L++I++Y GV
Sbjct: 117 LHLEEDAGKNIHEG-GKTYLDFNRAGTPLIEIVTEPDIDSPQMAREFLETLRNIMRYAGV 175

Query: 181 SDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGF 240
           S   ME+G LRCD N+SLRP G  E GTK E+KN+NSF FVQK +E E +RQ++++ +G 
Sbjct: 176 SRADMEKGQLRCDINVSLRPKGSRELGTKVEIKNVNSFRFVQKAIESEIERQKRIITTGG 235

Query: 241 FIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDER 300
            + QETR +D +T  T  MR KE + DYRYFP+PDL+ L + +++ + +++S+PELP ER
Sbjct: 236 SVIQETRTFDPSTGLTYPMRTKEEAHDYRYFPDPDLLPLVLTEDFVQEIRSSMPELPHER 295

Query: 301 RKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAE-AKQASNWLMGEVSAYLNAEQKE 359
           + R +E      Y+A +LT  KE+ DFFEE  +  +E  K   NWL+ ++   L   Q  
Sbjct: 296 KMRLMEVYALGEYEAKILTDLKEVGDFFEEAARHFSEDPKLLCNWLLNDLLGNLRERQMS 355

Query: 360 LADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVL 419
           + D  +TP  LA +++LI KGT+SS++AK V KE++E G D ++IV+EKGL QISDE  +
Sbjct: 356 IEDSPVTPLHLARLVELIHKGTLSSRLAKDVLKEMVETGKDPQEIVREKGLTQISDEQAI 415

Query: 420 LKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLE 471
            ++V + L + P   +  + G+++ + F VGQ+MKA+KG+ANP +V KIL E
Sbjct: 416 REIVLQVLASFPSEADRLRKGEEKLLSFFVGQVMKATKGKANPQVVQKILRE 467


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: 613
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: 470
Length adjustment: 33
Effective length of query: 443
Effective length of database: 437
Effective search space:   193591
Effective search space used:   193591
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: 51 (24.3 bits)

Align candidate WP_012991604.1 THAL_RS02810 (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.11634.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.6e-185  600.7   0.0   9.6e-185  600.6   0.0    1.0  1  lcl|NCBI__GCF_000025605.1:WP_012991604.1  THAL_RS02810 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025605.1:WP_012991604.1  THAL_RS02810 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 !  600.6   0.0  9.6e-185  9.6e-185       3     479 ..       2     468 ..       1     470 [] 0.97

  Alignments for each domain:
  == domain 1  score: 600.6 bits;  conditional E-value: 9.6e-185
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               e e viGlE+Hvql+t+sKlFc+c+ e+   +pNtnvcpvclglPG+lPvlNk+av+ Al  a aln++
  lcl|NCBI__GCF_000025605.1:WP_012991604.1   2 ELEPVIGLEIHVQLETRSKLFCSCPVEFGA-EPNTNVCPVCLGLPGTLPVLNKRAVELALRAAIALNCE 69 
                                               67889***********************99.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140
                                               i+  vsvF+RK+YfYpDlPkgyqi+q++ P+a +G +e++     k+++i+rlhlEeD+gk+ +++   
  lcl|NCBI__GCF_000025605.1:WP_012991604.1  70 IN-LVSVFARKNYFYPDLPKGYQISQYEHPLAVNGFVEVQG----KRVRIRRLHLEEDAGKNIHEGG-- 131
                                               76.5*******************************776644....77******************76.. PP

                                 TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209
                                                  +++DfNR+g+PL+EiVt+Pd+ s++ ar+fl+ lr+i+ry ++s++d+e+G +R+D+Nvs+r+kG+
  lcl|NCBI__GCF_000025605.1:WP_012991604.1 132 --KTYLDFNRAGTPLIEIVTEPDIDSPQMAREFLETLRNIMRYAGVSRADMEKGQLRCDINVSLRPKGS 198
                                               ..58***************************************************************** PP

                                 TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfp 278
                                               ++ gt+vEiKN+ns++ ++kaie EieRqk+++++g +v qetr+fd ++  t  +R Kee++DYRYfp
  lcl|NCBI__GCF_000025605.1:WP_012991604.1 199 RELGTKVEIKNVNSFRFVQKAIESEIERQKRIITTGGSVIQETRTFDPSTGLTYPMRTKEEAHDYRYFP 267
                                               ********************************************************************* PP

                                 TIGR00133 279 ePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvkli.kepk 346
                                               +Pdl p++++e++v+e ++  +pelP+++++rl++ y l e++ak+l++ +e+ d fee+++   ++pk
  lcl|NCBI__GCF_000025605.1:WP_012991604.1 268 DPDLLPLVLTEDFVQE-IRSSMPELPHERKMRLMEVYALGEYEAKILTDLKEVGDFFEEAARHFsEDPK 335
                                               ***************9.******************************************987651567* PP

                                 TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415
                                               l  nW+l++llg+L+++++s++++ ++p +la+l++li++g++s++ ak++l+e++e++kdp+++++++
  lcl|NCBI__GCF_000025605.1:WP_012991604.1 336 LLCNWLLNDLLGNLRERQMSIEDSPVTPLHLARLVELIHKGTLSSRLAKDVLKEMVETGKDPQEIVREK 404
                                               ********************************************************************* PP

                                 TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkel 479
                                               gl+qisde+++ +iv +v++  p e  + ++g ek+l f+vGqvmk tkg+a+p+ v+k+l+e+
  lcl|NCBI__GCF_000025605.1:WP_012991604.1 405 GLTQISDEQAIREIVLQVLASFPSEADRLRKGEEKLLSFFVGQVMKATKGKANPQVVQKILREV 468
                                               *************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (470 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: 10.11
//
[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