Alignments for a candidate for gatB in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Steroidobacter denitrificans DSM 18526

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_066919679.1 ACG33_RS06395 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_001579945.1:WP_066919679.1
          Length = 483

 Score =  482 bits (1240), Expect = e-140
 Identities = 236/481 (49%), Positives = 344/481 (71%), Gaps = 9/481 (1%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M++ETVIGLE+H +L T SK+FS +P  +GA PN+  N++DL YPGVLPV+N+ AV  A+
Sbjct: 1   MNWETVIGLEIHAQLATRSKIFSSAPTAYGAAPNTQANLVDLGYPGVLPVLNRSAVQMAV 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119
           +  +A+  +IA  S F RKNYFYPD PK YQISQ+++PI E G + I + DGE K IGIT
Sbjct: 61  KFGLAVGADIAARSVFARKNYFYPDLPKGYQISQYEKPIVERGSLQIVLEDGERKTIGIT 120

Query: 120 RLHMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYT 177
           R H+EEDAGKS H+  + L  +DLNR GTPL+EIVSEPD+RS +EA AY++K+ ++++Y 
Sbjct: 121 RAHLEEDAGKSLHEDFHGLTGIDLNRAGTPLLEIVSEPDMRSAREAVAYMKKIHTLVRYL 180

Query: 178 GVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLS 237
            + D  M+EGS RCDAN+S+RP GQ KFGT+ E+KNLNSF Y+ K + +E  RQ E +  
Sbjct: 181 EICDGNMQEGSFRCDANVSVRPLGQSKFGTRCEIKNLNSFRYIEKAINHEVARQIEIIEG 240

Query: 238 GGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPD 297
           GG I QETR +D    +T  +R KE ++DYRYFP+PD++P+ +D ++ E+VR ++PELPD
Sbjct: 241 GGTIRQETRLYDPDKDETRALRSKEEANDYRYFPDPDLLPVVLDPSFIEQVRISLPELPD 300

Query: 298 ERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTI-----EH-GADVKLTSNWLMGGVNEY 351
           ++ A+Y+ + GL AYDA +LT ++EM D++E+ +     EH G   KL +NW+MG ++  
Sbjct: 301 QKAARYLEQFGLSAYDAGILTASREMGDYYEAVLAALGAEHGGGHEKLAANWIMGELSAA 360

Query: 352 LNKNQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQ 411
           LNK+ +E+  +++    LAG+++ I DGT+S KIAK+VF  + A G +A  ++E  GL Q
Sbjct: 361 LNKDGLEIARSRVDARRLAGLLERIVDGTISGKIAKEVFEAMWADGLDADAVIEAKGLRQ 420

Query: 412 ISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQE 471
           I+D A +   +   +  N + + +Y++GK K  GF VGQ+MKA+ G+ANP  +N+LLK++
Sbjct: 421 ITDTAAIETVIESVMAANPKQLAEYRSGKDKLFGFFVGQVMKATGGKANPAQLNELLKKK 480

Query: 472 L 472
           L
Sbjct: 481 L 481


Lambda     K      H
   0.313    0.133    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: 622
Number of extensions: 19
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: 475
Length of database: 483
Length adjustment: 34
Effective length of query: 441
Effective length of database: 449
Effective search space:   198009
Effective search space used:   198009
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_066919679.1 ACG33_RS06395 (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.2579580.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.9e-177  574.9   0.0   6.6e-177  574.7   0.0    1.0  1  NCBI__GCF_001579945.1:WP_066919679.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001579945.1:WP_066919679.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  574.7   0.0  6.6e-177  6.6e-177       2     480 ..       1     481 [.       1     482 [. 0.98

  Alignments for each domain:
  == domain 1  score: 574.7 bits;  conditional E-value: 6.6e-177
                             TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivs 74 
                                           +++e viGlE+H ql t+sK+F+++++ +    pNt+ + v+lg+PG+lPvlN++av++A+k +la+++ i  
  NCBI__GCF_001579945.1:WP_066919679.1   1 MNWETVIGLEIHAQLATRSKIFSSAPTAYGA-APNTQANLVDLGYPGVLPVLNRSAVQMAVKFGLAVGADIA- 71 
                                           57899************************99.9*************************************65. PP

                             TIGR00133  75 evsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslv 146
                                             svF+RK+YfYpDlPkgyqi+q+++Pi+e G+l+i le++e k+igi+r hlEeD+gks ++    +  + +
  NCBI__GCF_001579945.1:WP_066919679.1  72 ARSVFARKNYFYPDLPKGYQISQYEKPIVERGSLQIVLEDGErKTIGITRAHLEEDAGKSLHEDF--HGLTGI 142
                                           69***********************************99887799*****************944..58999* PP

                             TIGR00133 147 DfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiK 219
                                           D+NR+g+PLlEiV++Pd++sa ea+a++kk+++++rylei dg+++eGs+R+D+Nvs+r+ Gq+k+gtr EiK
  NCBI__GCF_001579945.1:WP_066919679.1 143 DLNRAGTPLLEIVSEPDMRSAREAVAYMKKIHTLVRYLEICDGNMQEGSFRCDANVSVRPLGQSKFGTRCEIK 215
                                           ************************************************************************* PP

                             TIGR00133 220 NlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevv 292
                                           Nlns++ iekai++E++Rq+++++ g ++ qetr +d  k  t +lR+Kee++DYRYfp+Pdl p+++d++++
  NCBI__GCF_001579945.1:WP_066919679.1 216 NLNSFRYIEKAINHEVARQIEIIEGGGTIRQETRLYDPDKDETRALRSKEEANDYRYFPDPDLLPVVLDPSFI 288
                                           ************************************************************************* PP

                             TIGR00133 293 kekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep......klavnWileellge 359
                                           ++ v+  lpelP++k +r+ +++gls++da +l++ +e+ d++e v  +++ +      kla+nWi+ el + 
  NCBI__GCF_001579945.1:WP_066919679.1 289 EQ-VRISLPELPDQKAARYLEQFGLSAYDAGILTASREMGDYYEAVLAALGAEhgggheKLAANWIMGELSAA 360
                                           *9.*******************************************9988877788998************** PP

                             TIGR00133 360 Lnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkivee 432
                                           Lnk  +++a + +++  la l++ i +g+is+k+ake++e +  ++ d++++ie++gl qi+d+ ++  ++e 
  NCBI__GCF_001579945.1:WP_066919679.1 361 LNKDGLEIARSRVDARRLAGLLERIVDGTISGKIAKEVFEAMWADGLDADAVIEAKGLRQITDTAAIETVIES 433
                                           ************************************************************************* PP

                             TIGR00133 433 vikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           v++ npk++ +y+sgk+k+++f+vGqvmk t g+a+p++ ++llk++l
  NCBI__GCF_001579945.1:WP_066919679.1 434 VMAANPKQLAEYRSGKDKLFGFFVGQVMKATGGKANPAQLNELLKKKL 481
                                           **********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (483 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 26.44
//
[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