Alignments for a candidate for gatB in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Kyrpidia tusciae DSM 2912

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_013076725.1 BTUS_RS14015 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000092905.1:WP_013076725.1
          Length = 475

 Score =  603 bits (1555), Expect = e-177
 Identities = 296/474 (62%), Positives = 369/474 (77%), Gaps = 1/474 (0%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           M FETVIGLEVHVEL TK+KIF    T FGA  NT    + LG+PGVLPVLN+ A+E AM
Sbjct: 1   MEFETVIGLEVHVELATKTKIFCGCSTEFGAPPNTHVCPVCLGHPGVLPVLNRRALELAM 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITR 120
           KAA+ALNCEIA ++KFDRKNYFYPD PKAYQISQ+DKPIGE+GW+EIE     KRIGI R
Sbjct: 61  KAALALNCEIARESKFDRKNYFYPDLPKAYQISQYDKPIGEHGWVEIETADGPKRIGIIR 120

Query: 121 LHLEEDAGKLTHTGDG-YSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTG 179
           +HLEEDAGKL H  DG +SLVDFNR G PL+EIVSEPD+R+PEEA AYLEKLK+I+QY  
Sbjct: 121 VHLEEDAGKLMHGADGLHSLVDFNRVGVPLIEIVSEPDMRSPEEARAYLEKLKAIMQYCE 180

Query: 180 VSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSG 239
           +SD +MEEGSLRCDANISLRP G  EFGTKTE+KN+NSF  VQ+GLEHE++RQ ++L SG
Sbjct: 181 ISDVRMEEGSLRCDANISLRPAGTSEFGTKTEIKNMNSFRNVQRGLEHEQERQREILASG 240

Query: 240 FFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDE 299
             + QETRR+DEA  +T+ MR KE + DYRYFPEPDLV L ID+EW  RV+ SIPELPD 
Sbjct: 241 GQVVQETRRWDEAAGRTLPMRSKEEAHDYRYFPEPDLVTLSIDEEWVRRVRESIPELPDA 300

Query: 300 RRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKE 359
           RR+R++E+ G  AYDA VLT ++ +ADFFEE  +   +AK  SNW+MGE+  ++N    E
Sbjct: 301 RRRRFVEQYGLPAYDAGVLTASRGVADFFEEAARHAGDAKAVSNWMMGELLGHMNQSGLE 360

Query: 360 LADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVL 419
           + DV +TP GLA +I+LI  GTIS+KI K VF E+   G + + +++E+GLVQISDEG L
Sbjct: 361 IRDVKVTPRGLARLIELIADGTISTKIGKTVFAEMFATGKEPDVVIEEQGLVQISDEGAL 420

Query: 420 LKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEI 473
             LV   ++ NP+S+ D++ GK +A+G LVGQ+MK +KG+ANP +VNK+L E +
Sbjct: 421 AALVDRVIEANPKSVADYRGGKGKALGALVGQVMKETKGKANPQVVNKLLRERL 474


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: 711
Number of extensions: 25
Number of successful extensions: 2
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: 475
Length adjustment: 33
Effective length of query: 443
Effective length of database: 442
Effective search space:   195806
Effective search space used:   195806
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_013076725.1 BTUS_RS14015 (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.27718.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-190  619.8   0.0   1.6e-190  619.6   0.0    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013076725.1  BTUS_RS14015 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013076725.1  BTUS_RS14015 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 !  619.6   0.0  1.6e-190  1.6e-190       2     480 ..       1     474 [.       1     475 [] 0.99

  Alignments for each domain:
  == domain 1  score: 619.6 bits;  conditional E-value: 1.6e-190
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               +e+e viGlEvHv l tk+K+Fc cs+e+   +pNt+vcpvclg PG+lPvlN++a++ A+k alaln+
  lcl|NCBI__GCF_000092905.1:WP_013076725.1   1 MEFETVIGLEVHVELATKTKIFCGCSTEFGA-PPNTHVCPVCLGHPGVLPVLNRRALELAMKAALALNC 68 
                                               689**************************99.************************************* PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesd 139
                                               +i    s+FdRK+YfYpDlPk+yqi+q+d+Pi+e+G +eie+ ++ k+igi r+hlEeD+gk+++  + 
  lcl|NCBI__GCF_000092905.1:WP_013076725.1  69 EIA-RESKFDRKNYFYPDLPKAYQISQYDKPIGEHGWVEIETADGPKRIGIIRVHLEEDAGKLMHGADG 136
                                               *66.69***********************************************************9886 PP

                                 TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208
                                                  +slvDfNR gvPL+EiV++Pd++s++eara+l+kl++i++y eisd  +eeGs+R+D+N+s+r+ G
  lcl|NCBI__GCF_000092905.1:WP_013076725.1 137 --LHSLVDFNRVGVPLIEIVSEPDMRSPEEARAYLEKLKAIMQYCEISDVRMEEGSLRCDANISLRPAG 203
                                               ..7****************************************************************** PP

                                 TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277
                                               ++++gt+ EiKN+ns++++++ +e+E eRq ++l++g +v+qetr +de+  +t+ +R+Kee++DYRYf
  lcl|NCBI__GCF_000092905.1:WP_013076725.1 204 TSEFGTKTEIKNMNSFRNVQRGLEHEQERQREILASGGQVVQETRRWDEAAGRTLPMRSKEEAHDYRYF 272
                                               ********************************************************************* PP

                                 TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346
                                               pePdl+++ idee+v++ v+e +pelP+a+r r++++ygl ++da vl++ + ++d fee+++ ++++k
  lcl|NCBI__GCF_000092905.1:WP_013076725.1 273 PEPDLVTLSIDEEWVRR-VRESIPELPDARRRRFVEQYGLPAYDAGVLTASRGVADFFEEAARHAGDAK 340
                                               ****************9.*************************************************** PP

                                 TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415
                                               ++ nW++ ellg++n++ +++ ++ ++p  la+li+li +g+is k++k+++ e++ ++k+p+ +ie++
  lcl|NCBI__GCF_000092905.1:WP_013076725.1 341 AVSNWMMGELLGHMNQSGLEIRDVKVTPRGLARLIELIADGTISTKIGKTVFAEMFATGKEPDVVIEEQ 409
                                               ********************************************************************* PP

                                 TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               gl+qisde +l ++v+ vi+ npk+v +y+ gk kal+ lvGqvmk+tkg+a+p+ v+kll+e+l
  lcl|NCBI__GCF_000092905.1:WP_013076725.1 410 GLVQISDEGALAALVDRVIEANPKSVADYRGGKGKALGALVGQVMKETKGKANPQVVNKLLRERL 474
                                               ***************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (475 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: 00:00:00.02
# Mc/sec: 10.77
//
[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