GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatB in Lentibacillus jeotgali Grbi

Align glutamyl-tRNAGln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_010529624.1 ON01_RS03500 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000224785.1:WP_010529624.1
          Length = 476

 Score =  765 bits (1976), Expect = 0.0
 Identities = 380/476 (79%), Positives = 421/476 (88%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           MNFET+IGLEVHVELKT+SKIFS SP  FG E N+  + IDLGYPGVLPVLN+EAV +AM
Sbjct: 1   MNFETIIGLEVHVELKTESKIFSPSPNAFGDEPNSNINPIDLGYPGVLPVLNEEAVNYAM 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITR 120
           KAA+ALNC+IAT+TKFDRKNYFYPDNPKAYQISQFD+PIGENGWIEIEV G+ KRIGITR
Sbjct: 61  KAALALNCDIATNTKFDRKNYFYPDNPKAYQISQFDQPIGENGWIEIEVNGEKKRIGITR 120

Query: 121 LHLEEDAGKLTHTGDGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGV 180
           LH+EEDAGKLTH  DG+SLVDFNRQGTPL+EIVSEPDIRTPEEAYAYLEKLK+IIQYTGV
Sbjct: 121 LHMEEDAGKLTHQDDGHSLVDFNRQGTPLIEIVSEPDIRTPEEAYAYLEKLKNIIQYTGV 180

Query: 181 SDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGF 240
           SDCKMEEGSLRCDAN+S+RPIGQEEFG KTELKNLNSF+FVQKGLE EEKRQE+ LLSG 
Sbjct: 181 SDCKMEEGSLRCDANLSIRPIGQEEFGVKTELKNLNSFSFVQKGLEFEEKRQEKELLSGG 240

Query: 241 FIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDER 300
            I QETRRYDE TK+TILMRVKEGSDDYRYFPEPDLV LYID+EWKER++A IPELPD R
Sbjct: 241 EILQETRRYDEKTKETILMRVKEGSDDYRYFPEPDLVPLYIDEEWKERIRAEIPELPDTR 300

Query: 301 RKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKEL 360
           ++RYI EL    YDA VLT +KEMADFFEE V  GA+ KQASNWLMG+V AY+N   KEL
Sbjct: 301 KQRYINELELPEYDAAVLTSSKEMADFFEEAVNHGADIKQASNWLMGDVLAYMNKHYKEL 360

Query: 361 ADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVLL 420
            ++ALTPE LA MIKLIE GTISSKIAKKVF EL+E GGD EKIVKEKGLVQISDEG L 
Sbjct: 361 NELALTPEALATMIKLIEDGTISSKIAKKVFAELVENGGDPEKIVKEKGLVQISDEGQLT 420

Query: 421 KLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIKKR 476
           +++T+ LD N QSI D+KNGKDRAI +LVGQ+MK +KGQANPPMVNKIL +EI KR
Sbjct: 421 EIITKVLDENEQSIIDYKNGKDRAIKYLVGQVMKVTKGQANPPMVNKILQQEIDKR 476


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: 863
Number of extensions: 32
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: 476
Length of database: 476
Length adjustment: 33
Effective length of query: 443
Effective length of database: 443
Effective search space:   196249
Effective search space used:   196249
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_010529624.1 ON01_RS03500 (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.947750.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-191  621.2   3.0     6e-191  621.0   3.0    1.0  1  NCBI__GCF_000224785.1:WP_010529624.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010529624.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  621.0   3.0    6e-191    6e-191       2     480 ..       1     473 [.       1     474 [. 0.98

  Alignments for each domain:
  == domain 1  score: 621.0 bits;  conditional E-value: 6e-191
                             TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivs 74 
                                           +++e +iGlEvHv l t+sK+F+ ++n + + +pN+n++p++lg+PG+lPvlN+eav+ A+k alaln+ i  
  NCBI__GCF_000224785.1:WP_010529624.1   1 MNFETIIGLEVHVELKTESKIFSPSPNAFGD-EPNSNINPIDLGYPGVLPVLNEEAVNYAMKAALALNCDIA- 71 
                                           689****************************.**************************************66. PP

                             TIGR00133  75 evsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkdkqslvD 147
                                             ++FdRK+YfYpD Pk+yqi+q+d+Pi+e+G +eie+++++k+igi+rlh+EeD+gk++++ +    +slvD
  NCBI__GCF_000224785.1:WP_010529624.1  72 TNTKFDRKNYFYPDNPKAYQISQFDQPIGENGWIEIEVNGEKKRIGITRLHMEEDAGKLTHQDD---GHSLVD 141
                                           599**********************************************************955...59**** PP

                             TIGR00133 148 fNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKN 220
                                           fNR g+PL+EiV++Pd+++++ea a+l+kl++i++y+++sd+++eeGs+R+D+N+sir+ Gqe++g + E+KN
  NCBI__GCF_000224785.1:WP_010529624.1 142 FNRQGTPLIEIVSEPDIRTPEEAYAYLEKLKNIIQYTGVSDCKMEEGSLRCDANLSIRPIGQEEFGVKTELKN 214
                                           ************************************************************************* PP

                             TIGR00133 221 lnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvk 293
                                           lns++ ++k +e+E +Rq+k+l +g e+ qetr +dek++ t+ +R Ke s DYRYfpePdl+p+ idee+ +
  NCBI__GCF_000224785.1:WP_010529624.1 215 LNSFSFVQKGLEFEEKRQEKELLSGGEILQETRRYDEKTKETILMRVKEGSDDYRYFPEPDLVPLYIDEEWKE 287
                                           **********************************************************************955 PP

                             TIGR00133 294 ekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkis 366
                                            ++++++pelP+++++r+ +e++l e+da vl+s +e++d fee+v+  ++ k+a nW++ ++l+++nk+  +
  NCBI__GCF_000224785.1:WP_010529624.1 288 -RIRAEIPELPDTRKQRYINELELPEYDAAVLTSSKEMADFFEEAVNHGADIKQASNWLMGDVLAYMNKHYKE 359
                                           .5*********************************************************************** PP

                             TIGR00133 367 laeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenpk 439
                                           l+e +l+pe+la++ikli++g+is+k+ak+++ el+en++dp+k+++++gl+qisde +l++i+ +v++en++
  NCBI__GCF_000224785.1:WP_010529624.1 360 LNELALTPEALATMIKLIEDGTISSKIAKKVFAELVENGGDPEKIVKEKGLVQISDEGQLTEIITKVLDENEQ 432
                                           ************************************************************************* PP

                             TIGR00133 440 evekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           ++ +yk+gk++a+k+lvGqvmk tkg+a+p  v+k+l++ +
  NCBI__GCF_000224785.1:WP_010529624.1 433 SIIDYKNGKDRAIKYLVGQVMKVTKGQANPPMVNKILQQEI 473
                                           *************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (476 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: 00:00:00.00
# Mc/sec: 26.64
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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