Alignments for a candidate for gatB in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Polaromonas naphthalenivorans CJ2

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_011799605.1 PNAP_RS00830 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000015505.1:WP_011799605.1
          Length = 485

 Score =  412 bits (1060), Expect = e-119
 Identities = 216/473 (45%), Positives = 304/473 (64%), Gaps = 4/473 (0%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E VIG E H +L T SK+FS +P  FGAEPN+  + +D A PG LPV+NK AV  A+  
Sbjct: 13  YEVVIGFETHTQLTTQSKLFSRAPIAFGAEPNTQASAVDFALPGALPVMNKGAVQRAIEF 72

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITRLH 122
            +A+N  IA +S F RKNYFYPD PK YQISQF+ P+ + G ++  +DGE K + + R H
Sbjct: 73  GLAVNAHIAEKSIFARKNYFYPDLPKGYQISQFEIPVVQGGVVEFFLDGEKKSVRLVRAH 132

Query: 123 MEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGVS 180
           +EEDAGKS H+    +  +DLNR GTPL+EIV+EPD+RS  EA AY ++L  I+ + G+ 
Sbjct: 133 LEEDAGKSLHEDFIGMSGIDLNRAGTPLLEIVTEPDMRSTAEAVAYAKELHKIVTWIGIC 192

Query: 181 DVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGGE 240
           D  M+EGS RCDAN+S+R  G E  GT+ E+KNLNSF ++++ ++YE + Q E++  G E
Sbjct: 193 DGNMQEGSFRCDANVSVRKPG-EPLGTRREIKNLNSFKFMQQAMDYEVRWQIEQIEDGHE 251

Query: 241 IGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDERK 300
           I Q T  FD  TG+T  MR KE + DYRYFP+PD+ PL I   W E+ R  + ELP    
Sbjct: 252 IQQATVLFDPDTGETRSMRSKEDAADYRYFPDPDLPPLVIGRDWVEKTRSEMSELPRVMA 311

Query: 301 AKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVELL 360
           A++V + GLP YDA  LT +K  + +FE+        KL SNW+MG ++  LN  +  + 
Sbjct: 312 ARFVADYGLPEYDAGQLTQSKATAAYFEAVATASKSPKLASNWVMGELSRRLNAEEKSIE 371

Query: 361 DTKLTPENLAGMIKLIEDGTMSSKIAKKVFPEL-AAKGGNAKQIMEDNGLVQISDEATLL 419
            + ++   LA +I  I DGT+++  A++VF  L   +G +   ++E  GL  +SD   L 
Sbjct: 372 ASAVSALQLAALIGRIADGTIANNAARQVFDALWTGEGLDVDALIEAKGLKSMSDTGELE 431

Query: 420 KFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
             ++  L  N ++VE+ K G  KA   LVGQ MKA+KG+ANP  VN+LLK++L
Sbjct: 432 TIIDGVLAANAKNVEEVKAGNAKAFNALVGQAMKATKGKANPAQVNELLKKKL 484


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: 561
Number of extensions: 25
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: 485
Length adjustment: 34
Effective length of query: 441
Effective length of database: 451
Effective search space:   198891
Effective search space used:   198891
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_011799605.1 PNAP_RS00830 (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.19298.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-163  530.1   0.0   2.6e-163  529.9   0.0    1.0  1  lcl|NCBI__GCF_000015505.1:WP_011799605.1  PNAP_RS00830 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011799605.1  PNAP_RS00830 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 !  529.9   0.0  2.6e-163  2.6e-163       4     480 ..      13     484 ..      10     485 .] 0.98

  Alignments for each domain:
  == domain 1  score: 529.9 bits;  conditional E-value: 2.6e-163
                                 TIGR00133   4 yelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnski 72 
                                               ye+viG+E+H+ql t+sKlF++++  +   +pNt+ ++v+++lPGalPv+Nk av+ A+  +la+n++ 
  lcl|NCBI__GCF_000015505.1:WP_011799605.1  13 YEVVIGFETHTQLTTQSKLFSRAPIAFGA-EPNTQASAVDFALPGALPVMNKGAVQRAIEFGLAVNAH- 79 
                                               99*************************99.**************************************. PP

                                 TIGR00133  73 vsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkd 141
                                               ++e+s+F+RK+YfYpDlPkgyqi+q+++P++++G++e  l++++k++++ r hlEeD+gks ++     
  lcl|NCBI__GCF_000015505.1:WP_011799605.1  80 IAEKSIFARKNYFYPDLPKGYQISQFEIPVVQGGVVEFFLDGEKKSVRLVRAHLEEDAGKSLHEDFI-- 146
                                               668************************************************************9665.. PP

                                 TIGR00133 142 kqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqe 210
                                                +s +D+NR+g+PLlEiVt+Pd++s+ ea+a+ k+l++i+ +++i dg+++eGs+R+D+Nvs+r k  e
  lcl|NCBI__GCF_000015505.1:WP_011799605.1 147 GMSGIDLNRAGTPLLEIVTEPDMRSTAEAVAYAKELHKIVTWIGICDGNMQEGSFRCDANVSVR-KPGE 214
                                               79**************************************************************.6678 PP

                                 TIGR00133 211 kegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpe 279
                                                 gtr EiKNlns+k +++a++yE+  q++ +++g+e++q+t  fd  +  t s+R+Ke+++DYRYfp+
  lcl|NCBI__GCF_000015505.1:WP_011799605.1 215 PLGTRREIKNLNSFKFMQQAMDYEVRWQIEQIEDGHEIQQATVLFDPDTGETRSMRSKEDAADYRYFPD 283
                                               899****************************************************************** PP

                                 TIGR00133 280 PdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepkla 348
                                               Pdlpp++i  ++v++ ++ ++ elP+ + +r++ +ygl e+da  l++ +  + +fe v++++k+pkla
  lcl|NCBI__GCF_000015505.1:WP_011799605.1 284 PDLPPLVIGRDWVEK-TRSEMSELPRVMAARFVADYGLPEYDAGQLTQSKATAAYFEAVATASKSPKLA 351
                                               **************9.9**************************************************** PP

                                 TIGR00133 349 vnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellen.kkdpkklieklg 416
                                                nW++ el ++Ln+++ s++++++++ +la+li  i +g+i++ +a+++++ l +  + d+++lie++g
  lcl|NCBI__GCF_000015505.1:WP_011799605.1 352 SNWVMGELSRRLNAEEKSIEASAVSALQLAALIGRIADGTIANNAARQVFDALWTGeGLDVDALIEAKG 420
                                               ***************************************************99875499********** PP

                                 TIGR00133 417 liqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               l ++sd+ el  i++ v++ n+k+ve+ k+g  ka++ lvGq+mk tkg+a+p++v++llk++l
  lcl|NCBI__GCF_000015505.1:WP_011799605.1 421 LKSMSDTGELETIIDGVLAANAKNVEEVKAGNAKAFNALVGQAMKATKGKANPAQVNELLKKKL 484
                                               *************************************************************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.23
//
[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