Alignments for a candidate for gatB in Desulfurobacterium atlanticum DSM 15668

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Desulfurobacterium atlanticum DSM 15668

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_089322288.1 CHB58_RS01305 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_900188395.1:WP_089322288.1
          Length = 485

 Score =  479 bits (1233), Expect = e-140
 Identities = 244/486 (50%), Positives = 342/486 (70%), Gaps = 11/486 (2%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           M FE VIGLEVH +L T +KIF S    FG   NT    + LG PG LPVLNK+AVE+A+
Sbjct: 1   MEFEAVIGLEVHAQLLTDTKIFCSCRNRFGDPPNTNVCPVCLGMPGSLPVLNKKAVEYAV 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEV-GGKTKRIGIT 119
           KAA+ALNC+I T + F RK+YFYPD PKAYQI+Q++ P  E+GWIEIE   G  K+I I 
Sbjct: 61  KAALALNCKINTYSIFARKHYFYPDLPKAYQITQYELPFAEHGWIEIEKPDGTKKKIRIR 120

Query: 120 RLHLEEDAGKLTHTGDGY---SLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQ 176
           R+H+EEDAGK  H G+GY   S VD NR GTPL+EIVSEPDI +PEEA  Y++KL+ I+ 
Sbjct: 121 RIHMEEDAGKTLH-GEGYDQNSYVDLNRAGTPLIEIVSEPDISSPEEARLYMQKLRDILV 179

Query: 177 YTGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVL 236
           + GV+D  +EEGSLRCDAN+S+RP G ++ GT+TE+KN+NSF F+QK LE+E +RQ +V+
Sbjct: 180 WIGVNDGNLEEGSLRCDANVSIRPKGSDKLGTRTEIKNVNSFRFIQKALEYEIERQIKVV 239

Query: 237 LSGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPEL 296
             G  + QETR YD     T  MR KE ++DYRYFPEPDL  L ID EW + +KAS+PEL
Sbjct: 240 KGGGEVVQETRLYDSQKNITKTMRTKEEAEDYRYFPEPDLPPLIIDSEWLDSIKASLPEL 299

Query: 297 PDERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQK-GAEAKQASNWLMGEVSAYLNA 355
           PD  ++R++++     YDA +L   + +A FFE  V     E K+ +N+++ +    LN 
Sbjct: 300 PDSVKERFVKDYSLTPYDASILVKERALAHFFESAVSSYSGEPKKVANFIISDFLGILNE 359

Query: 356 EQKELADVALTPEGLAGMIKLIEKGTISSKIAKK-VFKELIEKGGDAEKIVKEKGLVQIS 414
           E+  ++DV + PE +A ++ L++KGTIS ++AK+ V  E+++ G   EKIVKEKGLVQIS
Sbjct: 360 EKIGISDVKVKPEYIAELLTLVDKGTISLRVAKEDVLPEMVKTGKSPEKIVKEKGLVQIS 419

Query: 415 DEGVLLKLVTEALDNNPQSIEDFKNGKD----RAIGFLVGQIMKASKGQANPPMVNKILL 470
           DE  L++++   L+ N +++  +K G D    +A+ FL+GQ+MK +KG+ANP ++N+++ 
Sbjct: 420 DESALVEIIEAVLNKNEKAVNQYKTGDDKKKTKAVKFLIGQVMKETKGKANPKVLNELIP 479

Query: 471 EEIKKR 476
           + + K+
Sbjct: 480 KILDKK 485


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: 687
Number of extensions: 36
Number of successful extensions: 6
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: 485
Length adjustment: 34
Effective length of query: 442
Effective length of database: 451
Effective search space:   199342
Effective search space used:   199342
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_089322288.1 CHB58_RS01305 (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.26156.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-193  630.0   0.5   1.3e-193  629.9   0.5    1.0  1  lcl|NCBI__GCF_900188395.1:WP_089322288.1  CHB58_RS01305 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900188395.1:WP_089322288.1  CHB58_RS01305 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 !  629.9   0.5  1.3e-193  1.3e-193       2     480 ..       1     482 [.       1     483 [. 0.97

  Alignments for each domain:
  == domain 1  score: 629.9 bits;  conditional E-value: 1.3e-193
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               +e+e+viGlEvH ql t +K+Fc+c n++ + +pNtnvcpvclg+PG+lPvlNk+av+ A+k alaln+
  lcl|NCBI__GCF_900188395.1:WP_089322288.1   1 MEFEAVIGLEVHAQLLTDTKIFCSCRNRFGD-PPNTNVCPVCLGMPGSLPVLNKKAVEYAVKAALALNC 68 
                                               689****************************.************************************* PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykes 138
                                               ki+  +s+F+RKhYfYpDlPk+yqitq++lP+ae+G +eie+ ++  k+i+i+r+h+EeD+gk+ + e 
  lcl|NCBI__GCF_900188395.1:WP_089322288.1  69 KIN-TYSIFARKHYFYPDLPKAYQITQYELPFAEHGWIEIEKPDGTkKKIRIRRIHMEEDAGKTLHGEG 136
                                               *77.5************************************98765499**************999865 PP

                                 TIGR00133 139 dkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlk 207
                                                 d+ s+vD+NR+g+PL+EiV++Pd++s++ear +++klr il ++++ dg+leeGs+R+D+Nvsir+k
  lcl|NCBI__GCF_900188395.1:WP_089322288.1 137 -YDQNSYVDLNRAGTPLIEIVSEPDISSPEEARLYMQKLRDILVWIGVNDGNLEEGSLRCDANVSIRPK 204
                                               .589***************************************************************** PP

                                 TIGR00133 208 GqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRY 276
                                               G++k gtr EiKN+ns++ i+ka+eyEieRq+k++k g ev+qetr +d +k+it ++R Kee+eDYRY
  lcl|NCBI__GCF_900188395.1:WP_089322288.1 205 GSDKLGTRTEIKNVNSFRFIQKALEYEIERQIKVVKGGGEVVQETRLYDSQKNITKTMRTKEEAEDYRY 273
                                               ********************************************************************* PP

                                 TIGR00133 277 fpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvkl.ike 344
                                               fpePdlpp+ id e++++ +++ lpelP+  ++r++k+y l  +da +lv+++ l++ fe++v++ ++e
  lcl|NCBI__GCF_900188395.1:WP_089322288.1 274 FPEPDLPPLIIDSEWLDS-IKASLPELPDSVKERFVKDYSLTPYDASILVKERALAHFFESAVSSySGE 341
                                               ***************999.9****************************************987661678 PP

                                 TIGR00133 345 pklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksake.lleellenkkdpkkli 412
                                               pk+++n+i++++lg Ln++ki ++++ +kpe++ael+ l+++g+is + ake +l e+++++k+p+k++
  lcl|NCBI__GCF_900188395.1:WP_089322288.1 342 PKKVANFIISDFLGILNEEKIGISDVKVKPEYIAELLTLVDKGTISLRVAKEdVLPEMVKTGKSPEKIV 410
                                               8*************************************************955**************** PP

                                 TIGR00133 413 eklgliqisdekelvkiveevikenpkevekyk....sgkekalkflvGqvmkktkgradpkevekllk 477
                                               +++gl+qisde++lv+i+e+v+++n+k+v +yk    ++k ka+kfl+Gqvmk+tkg+a+pk  ++l+ 
  lcl|NCBI__GCF_900188395.1:WP_089322288.1 411 KEKGLVQISDESALVEIIEAVLNKNEKAVNQYKtgddKKKTKAVKFLIGQVMKETKGKANPKVLNELIP 479
                                               *********************************998888999**************************9 PP

                                 TIGR00133 478 ell 480
                                               ++l
  lcl|NCBI__GCF_900188395.1:WP_089322288.1 480 KIL 482
                                               998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (485 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: 9.83
//
[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