Alignments for a candidate for gatA in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Polaromonas naphthalenivorans CJ2

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_086000551.1 PNAP_RS00835 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000015505.1:WP_086000551.1
          Length = 507

 Score =  435 bits (1119), Expect = e-126
 Identities = 232/457 (50%), Positives = 308/457 (67%), Gaps = 16/457 (3%)

Query: 42  AFLALDEERARAYAKELDEAVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDP 101
           AFLALD + + A A+  D  +    E   L G+P+  KD  VT+   TT  SK+L N+  
Sbjct: 48  AFLALDADVSLAQARAADARL-AAGERTPLLGVPLAHKDVFVTRDFPTTAGSKMLANYRS 106

Query: 102 IYDATVVQRLQ----DAEAVTIGKLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGG 157
            +DATVV RL      A  VT+GKLN DEFAMGS  ENSAY+  +NPW+   VPGGSSGG
Sbjct: 107 PFDATVVSRLGVGPGGAGMVTLGKLNCDEFAMGSGNENSAYQKVQNPWDTSRVPGGSSGG 166

Query: 158 SAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPIT 217
           SAAAVAA  VP + G+DTGGSIRQPAS  G+ G+KPTYGR SRYG+VAFASSLDQ GP+ 
Sbjct: 167 SAAAVAARLVPAATGTDTGGSIRQPASLTGITGIKPTYGRCSRYGMVAFASSLDQAGPMA 226

Query: 218 RTVEDNAFLLQAISGVDK-MDSTSANVDVPDFLSSLTG---------DIKGLKIAVPKEY 267
           R+  D A LL A++G D   DSTS ++   D+ + L            +KGL+I +P ++
Sbjct: 227 RSALDCALLLSAMAGPDPDRDSTSLDMPAVDYATDLIAARTDGTSAKPLKGLRIGLPTQF 286

Query: 268 LGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSSSEASANLARFDGI 327
            G G   +   +V  AL   E LGAT  +VSLP ++ ++  YY+++ +EAS+NL+RFDG+
Sbjct: 287 FGAGCAPDVLAAVRGALSEFEKLGATLVDVSLPLTELSIPVYYVIAPAEASSNLSRFDGV 346

Query: 328 RYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAYYKKAQKVRTLIKK 387
           RYG+R  +  +L D+YK++R+EGFG+E  RRIM+GT+ LS GYYDAYY KAQK+R LI +
Sbjct: 347 RYGHRAAHYTDLTDMYKKSRSEGFGDEATRRIMIGTYVLSHGYYDAYYLKAQKIRRLIAQ 406

Query: 388 DFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIPVNLAGVPGISVPCGL-A 446
           DF+  F + DVI GP +PT A+KIGE + DP+  Y  DI T+  +LAG+PG+SVP G  A
Sbjct: 407 DFQTAFAQCDVIAGPVSPTVAWKIGEKSDDPVASYLADIYTLSSSLAGLPGMSVPAGFGA 466

Query: 447 DGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483
            G+P+GLQ+IG +F E+ +   AH F+ ATD H+  P
Sbjct: 467 GGMPVGLQLIGNYFKEAQLLGAAHQFQLATDWHQKAP 503


Lambda     K      H
   0.315    0.134    0.381 

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: 614
Number of extensions: 29
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: 485
Length of database: 507
Length adjustment: 34
Effective length of query: 451
Effective length of database: 473
Effective search space:   213323
Effective search space used:   213323
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate WP_086000551.1 PNAP_RS00835 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A 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/TIGR00132.hmm
# target sequence database:        /tmp/gapView.9753.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00132  [M=466]
Accession:   TIGR00132
Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     4e-166  539.3   0.0   4.7e-166  539.1   0.0    1.0  1  lcl|NCBI__GCF_000015505.1:WP_086000551.1  PNAP_RS00835 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_086000551.1  PNAP_RS00835 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  539.1   0.0  4.7e-166  4.7e-166       3     464 ..      20     496 ..      18     498 .. 0.95

  Alignments for each domain:
  == domain 1  score: 539.1 bits;  conditional E-value: 4.7e-166
                                 TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdni 69 
                                               ++l + ++s++ev++++l+ri ++   + afl+++++ +l++a++ d+++a  e ++l g+p+a Kd++
  lcl|NCBI__GCF_000015505.1:WP_086000551.1  20 AKLAAGDISSVEVTQHFLNRIGQHAG-LGAFLALDADVSLAQARAADARLAaGErTPLLGVPLAHKDVF 87 
                                               567788999***************99.**********************9985547************* PP

                                 TIGR00132  70 avkdiettcaSkiLenyvspydatVverlk....eagaliiGktNlDEFamGsstetSafgvtknPene 134
                                               +++d++tt++Sk+L ny+sp+datVv rl      ag++++Gk N DEFamGs+ e+Sa++ ++nP+++
  lcl|NCBI__GCF_000015505.1:WP_086000551.1  88 VTRDFPTTAGSKMLANYRSPFDATVVSRLGvgpgGAGMVTLGKLNCDEFAMGSGNENSAYQKVQNPWDT 156
                                               *****************************7333369********************************* PP

                                 TIGR00132 135 ervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGil 203
                                               +rvpGGSsgGsaaavaa lvp a g+DTGgSiRqPAs++g+ G+KPtYG+ SRyG+va+asSldq G++
  lcl|NCBI__GCF_000015505.1:WP_086000551.1 157 SRVPGGSSGGSAAAVAARLVPAATGTDTGGSIRQPASLTGITGIKPTYGRCSRYGMVAFASSLDQAGPM 225
                                               ********************************************************************* PP

                                 TIGR00132 204 akkvedialvldvisgkD.kkDstslevkveelleelkk.........dlkglkvgvvkelseesldke 262
                                               a++  d al+l++++g D  +Dstsl+++  ++ ++l +          lkgl++g+  ++++ ++  +
  lcl|NCBI__GCF_000015505.1:WP_086000551.1 226 ARSALDCALLLSAMAGPDpDRDSTSLDMPAVDYATDLIAartdgtsakPLKGLRIGLPTQFFGAGCAPD 294
                                               ******************559*******98877654432223355444699****************** PP

                                 TIGR00132 263 vkekfekllekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelya 331
                                               v ++++ +l ++e+lga++v+vslp  +l++++Yy+i+p+Eassnl+r+dg+ryG+r+ ++++l+++y+
  lcl|NCBI__GCF_000015505.1:WP_086000551.1 295 VLAAVRGALSEFEKLGATLVDVSLPLTELSIPVYYVIAPAEASSNLSRFDGVRYGHRAAHYTDLTDMYK 363
                                               ********************************************************************* PP

                                 TIGR00132 332 ktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklge 400
                                               k+Rsegfg+e  rRim+G+y+ls++yyd+yy+kAqk+r+li+++f+ +f ++Dvi++p++pt+a k+ge
  lcl|NCBI__GCF_000015505.1:WP_086000551.1 364 KSRSEGFGDEATRRIMIGTYVLSHGYYDAYYLKAQKIRRLIAQDFQTAFAQCDVIAGPVSPTVAWKIGE 432
                                               ********************************************************************* PP

                                 TIGR00132 401 kaedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqal 464
                                               k +dp+++yl+D++t+  +laGlp++svP+g    g+p+Glq+ig++f++ +ll +a++++ a+
  lcl|NCBI__GCF_000015505.1:WP_086000551.1 433 KSDDPVASYLADIYTLSSSLAGLPGMSVPAGFGAGGMPVGLQLIGNYFKEAQLLGAAHQFQLAT 496
                                               ********************************************************99998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (507 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: 11.28
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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