Alignments for a candidate for gatB in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Dechlorosoma suillum PS

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate Dsui_0884 Dsui_0884 glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, B subunit

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



>FitnessBrowser__PS:Dsui_0884
          Length = 485

 Score =  445 bits (1144), Expect = e-129
 Identities = 234/476 (49%), Positives = 325/476 (68%), Gaps = 9/476 (1%)

Query: 2   NFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMK 61
           N+E VIG+E H +L T+SKIFS S T FGA+ N Q S +DL  PGVLPVLN+ AVE A+K
Sbjct: 5   NWEVVIGIETHAQLSTQSKIFSGSSTAFGAQPNVQASAVDLALPGVLPVLNRGAVECAIK 64

Query: 62  AAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKR----IG 117
             +++  E+A  + F RKNYFYPD PK YQISQF+ P+   G + I+VG   K     + 
Sbjct: 65  FGLSIGAEVAAKSVFARKNYFYPDLPKGYQISQFELPVVVGGGVRIQVGQGDKAYEKVVR 124

Query: 118 ITRLHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQ 176
           +TR HLEEDAGK  H    G S +D NR GTPL+EIV+EPD+ +  EA AY + L ++++
Sbjct: 125 LTRAHLEEDAGKSLHEDFHGKSGIDLNRAGTPLLEIVTEPDMCSSAEAVAYAKALHALVR 184

Query: 177 YTGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVL 236
           + G+ D  M+EGS RCDAN+S+R  G E  GT+ E+KNLNSF F+Q+ +++E + Q   L
Sbjct: 185 WIGICDGNMQEGSFRCDANVSVRRPG-EPLGTRREIKNLNSFRFLQQAIDYEIQWQIDTL 243

Query: 237 LSGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPEL 296
             G  IQQ T  +D  + +T +MR KE + DYRYFP+PDL+ L I  EW ER KA++PEL
Sbjct: 244 EDGGKIQQATVLFDPDSGETRVMRTKEDAHDYRYFPDPDLLPLVISREWVERTKATLPEL 303

Query: 297 PDERRKRYIEELGFAAYDAMVLTLTKEMADFFEE--TVQKGAEAKQASNWLMGEVSAYLN 354
           P+ +R+R++E+LG +AYDA  LT + E+AD+F+   T    A AK A+NW+MGE+SA LN
Sbjct: 304 PEAKRQRFMEQLGLSAYDATALTASLEVADYFDAVVTAAGAANAKSAANWVMGELSARLN 363

Query: 355 AEQKELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIE-KGGDAEKIVKEKGLVQI 413
            E K++A   ++   LAG+I  I   TIS+ IAKKVF+ L    G  A+++++++GL QI
Sbjct: 364 KEDKDIAASPVSAAQLAGLIARIADNTISNNIAKKVFEALWNGDGASADEVIEKQGLKQI 423

Query: 414 SDEGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKIL 469
           +D G + KLV E L  N  ++ ++K GK++A   LVGQ+MKA+KG+ANP  VN +L
Sbjct: 424 TDTGAIEKLVDEVLAANAANVAEYKAGKEKAFNALVGQVMKAAKGKANPQQVNDLL 479


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: 560
Number of extensions: 23
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 Dsui_0884 Dsui_0884 (glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, B subunit)
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.24806.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   7.5e-165  535.0   0.0   8.5e-165  534.8   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_0884  Dsui_0884 glutamyl-tRNA(Gln) and


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0884  Dsui_0884 glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, B subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.8   0.0  8.5e-165  8.5e-165       3     480 ..       5     483 ..       3     484 .. 0.97

  Alignments for each domain:
  == domain 1  score: 534.8 bits;  conditional E-value: 8.5e-165
                         TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsevsvF 79 
                                       ++e+viG+E+H ql t+sK+F+ +s+ +   +pN + ++v+l+lPG+lPvlN+ av+ A+k +l +++++   +svF
  lcl|FitnessBrowser__PS:Dsui_0884   5 NWEVVIGIETHAQLSTQSKIFSGSSTAFGA-QPNVQASAVDLALPGVLPVLNRGAVECAIKFGLSIGAEVA-AKSVF 79 
                                       789*************************99.9*************************************55.6**** PP

                         TIGR00133  80 dRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke....keigierlhlEeDtgksqykesdkdkqslvDfNRsg 152
                                       +RK+YfYpDlPkgyqi+q++lP++ +G ++i++ +++    k ++++r hlEeD+gks ++    +  s +D+NR+g
  lcl|FitnessBrowser__PS:Dsui_0884  80 ARKNYFYPDLPKGYQISQFELPVVVGGGVRIQVGQGDkayeKVVRLTRAHLEEDAGKSLHEDF--HGKSGIDLNRAG 154
                                       ********************************99888788899*****************954..5799******** PP

                         TIGR00133 153 vPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKNlnslksiek 229
                                       +PLlEiVt+Pd+ s+ ea+a+ k l++++r+++i dg+++eGs+R+D+Nvs+r    e  gtr EiKNlns++ +++
  lcl|FitnessBrowser__PS:Dsui_0884 155 TPLLEIVTEPDMCSSAEAVAYAKALHALVRWIGICDGNMQEGSFRCDANVSVRRP-GEPLGTRREIKNLNSFRFLQQ 230
                                       *****************************************************55.577999*************** PP

                         TIGR00133 230 aieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkekveeklpelPea 306
                                       ai+yEi+ q++ l++g +++q+t  fd  +  t  +R Ke+++DYRYfp+Pdl p++i+ e+v++ ++++lpelPea
  lcl|FitnessBrowser__PS:Dsui_0884 231 AIDYEIQWQIDTLEDGGKIQQATVLFDPDSGETRVMRTKEDAHDYRYFPDPDLLPLVISREWVER-TKATLPELPEA 306
                                       ****************************************************************9.99********* PP

                         TIGR00133 307 krirlkkeyglseedakvlvsdlelldafeevvklikep..klavnWileellgeLnkkkislaeallkpeelaeli 381
                                       kr+r+++++gls++da  l++ le++d+f+ vv++++ +  k a+nW++ el ++Lnk++ ++a++ +++ +la li
  lcl|FitnessBrowser__PS:Dsui_0884 307 KRQRFMEQLGLSAYDATALTASLEVADYFDAVVTAAGAAnaKSAANWVMGELSARLNKEDKDIAASPVSAAQLAGLI 383
                                       *********************************998766669*********************************** PP

                         TIGR00133 382 klikegkisqksakelleellen.kkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvG 457
                                       + i +++is+ +ak+++e l +  + +++++iek+gl qi+d+ ++ k+v+ev++ n+ +v +yk+gkeka++ lvG
  lcl|FitnessBrowser__PS:Dsui_0884 384 ARIADNTISNNIAKKVFEALWNGdGASADEVIEKQGLKQITDTGAIEKLVDEVLAANAANVAEYKAGKEKAFNALVG 460
                                       ******************999866999************************************************** PP

                         TIGR00133 458 qvmkktkgradpkevekllkell 480
                                       qvmk +kg+a+p++v+ llk +l
  lcl|FitnessBrowser__PS:Dsui_0884 461 QVMKAAKGKANPQQVNDLLKAKL 483
                                       *******************9887 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.66
//
[ok]

This GapMind analysis is from Apr 09 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