Alignments for a candidate for gatB in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Halomonas desiderata SP1

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_086509866.1 BZY95_RS10435 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_002151265.1:WP_086509866.1
          Length = 489

 Score =  448 bits (1152), Expect = e-130
 Identities = 233/486 (47%), Positives = 328/486 (67%), Gaps = 13/486 (2%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M +ETVIGLEVHV+L T SK+FS +   FGAEPN+    +DL  PGVLPV+N+ AV  A+
Sbjct: 1   MQWETVIGLEVHVQLATRSKIFSGASTAFGAEPNTQACAVDLGLPGVLPVLNEAAVAMAV 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119
           +  +A++ EI   S FDRKNYFYPD PK YQ SQ  QPI   G ++I + DG TK I + 
Sbjct: 61  KFGLAIHAEIPEVSVFDRKNYFYPDLPKGYQTSQMYQPIVGAGVVEITLEDGTTKPIRVH 120

Query: 120 RLHMEEDAGKSTH------KGE-YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRS 172
             H+EEDAGKS H      KG   + +DLNR GTPL+EIVSEPD+RS KEA AYL+ + S
Sbjct: 121 HAHLEEDAGKSLHELFSSGKGHGMTGIDLNRAGTPLLEIVSEPDMRSAKEAAAYLKAIHS 180

Query: 173 IIQYTGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQE 232
           I+ Y G+SD  M EGS+RCD N+S+RP GQE FGT+AE+KN+NSF +V + + +E +RQ 
Sbjct: 181 IVTYLGISDGNMAEGSMRCDVNVSVRPKGQEAFGTRAEIKNVNSFRFVERAIAFEVERQI 240

Query: 233 EELLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTI 292
           E L  GG++ QETR FD    +T  MR KE ++DYRYFP PD++P+ +D A+ + +R  +
Sbjct: 241 ELLEDGGKVVQETRLFDPERDETRSMRTKEEANDYRYFPCPDLLPVVLDKAYIDHLRDNL 300

Query: 293 PELPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYL 352
           PELP E++A++ NELGL AYDA VL+ T+EM+D+F+   E   D K  +NW+ G +   L
Sbjct: 301 PELPAEKRARFENELGLSAYDASVLSATREMADYFDEVREVCGDAKQAANWVQGELAGAL 360

Query: 353 NKNQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPEL-AAKGGNAKQIMEDNGLVQ 411
           N+  + + D+ ++   L  ++  + D T++ K AK+VF  L   +G +A  I+E  GL Q
Sbjct: 361 NRENLAIKDSPVSARQLGELVARVLDDTINGKAAKQVFQALWNGQGTSADDIIEAQGLKQ 420

Query: 412 ISDEATLLKFVNEALDNNEQSVEDYKNG----KGKAMGFLVGQIMKASKGQANPQLVNQL 467
           ++D   +   +++ + ++   V  Y++     +GK +G+ VGQ+MKAS+G ANPQ VN+L
Sbjct: 421 VTDTGAIEAMIDQVIADSPAQVAQYRDAEPDKRGKMIGYFVGQVMKASRGTANPQQVNEL 480

Query: 468 LKQELD 473
           LKQ+LD
Sbjct: 481 LKQKLD 486


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: 623
Number of extensions: 30
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: 489
Length adjustment: 34
Effective length of query: 441
Effective length of database: 455
Effective search space:   200655
Effective search space used:   200655
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: 52 (24.6 bits)

Align candidate WP_086509866.1 BZY95_RS10435 (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.32236.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-175  570.1   0.0   1.8e-175  570.0   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086509866.1  BZY95_RS10435 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509866.1  BZY95_RS10435 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 !  570.0   0.0  1.8e-175  1.8e-175       3     480 ..       2     485 ..       1     486 [. 0.97

  Alignments for each domain:
  == domain 1  score: 570.0 bits;  conditional E-value: 1.8e-175
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               ++e viGlEvHvql t+sK+F+ +s+ +   +pNt+ c+v+lglPG+lPvlN+ av++A+k +la++++
  lcl|NCBI__GCF_002151265.1:WP_086509866.1   2 QWETVIGLEVHVQLATRSKIFSGASTAFGA-EPNTQACAVDLGLPGVLPVLNEAAVAMAVKFGLAIHAE 69 
                                               7899************************99.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesd 139
                                                + evsvFdRK+YfYpDlPkgyq +q ++Pi+  G++ei le++  k i++++ hlEeD+gks ++  +
  lcl|NCBI__GCF_002151265.1:WP_086509866.1  70 -IPEVSVFDRKNYFYPDLPKGYQTSQMYQPIVGAGVVEITLEDGTtKPIRVHHAHLEEDAGKSLHELFS 137
                                               .778************************************998766*******************9765 PP

                                 TIGR00133 140 k...dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsir 205
                                                   + ++ +D+NR+g+PLlEiV++Pd++sakea+a+lk +++i+ yl+isdg++ eGsmR+DvNvs+r
  lcl|NCBI__GCF_002151265.1:WP_086509866.1 138 SgkgHGMTGIDLNRAGTPLLEIVSEPDMRSAKEAAAYLKAIHSIVTYLGISDGNMAEGSMRCDVNVSVR 206
                                               544677899************************************************************ PP

                                 TIGR00133 206 lkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDY 274
                                               +kGqe++gtr+EiKN+ns++ +e+ai +E+eRq++ll++g +v+qetr fd ++  t s+R Kee++DY
  lcl|NCBI__GCF_002151265.1:WP_086509866.1 207 PKGQEAFGTRAEIKNVNSFRFVERAIAFEVERQIELLEDGGKVVQETRLFDPERDETRSMRTKEEANDY 275
                                               ********************************************************************* PP

                                 TIGR00133 275 RYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklik 343
                                               RYfp Pdl p+++d+ ++++ ++ +lpelP +kr+r+++e+gls++da vl + +e++d+f+ev ++ +
  lcl|NCBI__GCF_002151265.1:WP_086509866.1 276 RYFPCPDLLPVVLDKAYIDH-LRDNLPELPAEKRARFENELGLSAYDASVLSATREMADYFDEVREVCG 343
                                               *******************9.************************************************ PP

                                 TIGR00133 344 epklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellen.kkdpkkl 411
                                               ++k+a+nW+  el+g Ln++++ ++++ +++ +l el++ + +++i++k+ak++++ l +  +++++ +
  lcl|NCBI__GCF_002151265.1:WP_086509866.1 344 DAKQAANWVQGELAGALNRENLAIKDSPVSARQLGELVARVLDDTINGKAAKQVFQALWNGqGTSADDI 412
                                               ********************************************************999865899**** PP

                                 TIGR00133 412 ieklgliqisdekelvkiveevikenpkevekyk....sgkekalkflvGqvmkktkgradpkevekll 476
                                               ie++gl q++d+ ++ +++++vi++ p +v +y+    +++ k+++++vGqvmk ++g a+p++v++ll
  lcl|NCBI__GCF_002151265.1:WP_086509866.1 413 IEAQGLKQVTDTGAIEAMIDQVIADSPAQVAQYRdaepDKRGKMIGYFVGQVMKASRGTANPQQVNELL 481
                                               *********************************98888899**************************** PP

                                 TIGR00133 477 kell 480
                                               k++l
  lcl|NCBI__GCF_002151265.1:WP_086509866.1 482 KQKL 485
                                               *998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (489 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: 11.75
//
[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