Alignments for a candidate for gatA in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_012408045.1 NPUN_RS06670 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000020025.1:WP_012408045.1
          Length = 486

 Score =  558 bits (1439), Expect = e-163
 Identities = 281/482 (58%), Positives = 358/482 (74%), Gaps = 4/482 (0%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I EL Q + KKE    ++  E+ +RI+A++ K+ +FL +  ERA   A  +D  +    E
Sbjct: 4   IRELHQQLVKKERSAVEITQEALERIEALEPKLHSFLCVTAERALEQAGAVDAKIAAGEE 63

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            GLL G+P+G+KDN+ TKG+ TTC+S+ILENF P Y++T  Q+L DA AV +GK N+DEF
Sbjct: 64  IGLLAGIPVGIKDNLCTKGIPTTCASRILENFVPPYESTATQKLADAGAVMVGKTNLDEF 123

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSSTENSAY++T NPWNL  VPGGSSGGSAAAV++ E   +LGSDTGGSIRQPASFCG
Sbjct: 124 AMGSSTENSAYQVTANPWNLSRVPGGSSGGSAAAVSSQECVVALGSDTGGSIRQPASFCG 183

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           VVG+KPTYG VSRYGLVA+ASSLDQIGP   TVED A LL AI+G D  DSTS  V +P+
Sbjct: 184 VVGMKPTYGLVSRYGLVAYASSLDQIGPFANTVEDAAILLNAIAGHDPKDSTSLKVAIPN 243

Query: 248 FLSSLTGDIK---GLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKY 304
           + +S   D K    L+I + KE  GEG+     ++V  A+ VL+ LGA    +S P  +Y
Sbjct: 244 YAASFKPDFKPRGQLRIGIVKETFGEGLDSVVEQAVTKAVDVLQSLGAEIHIISCPRFRY 303

Query: 305 ALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTF 364
            L TYY+++ SEASANLAR+DG++YGYR  +ADNL+ +Y +TRA GFG EVKRRIM+GT+
Sbjct: 304 GLPTYYIIAPSEASANLARYDGVKYGYRAPDADNLLSMYTRTRATGFGTEVKRRIMIGTY 363

Query: 365 ALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYAN 424
           ALS+GYYDAYY KAQKVRTLIK+DFE  F   DV+V PT+PT AFK GE T DPL+MY  
Sbjct: 364 ALSAGYYDAYYLKAQKVRTLIKEDFEKAFRVVDVLVCPTSPTTAFKAGEKTTDPLSMYLT 423

Query: 425 DILTIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483
           D++TIPVNLAG+P +S+PCG  D GLP+GLQ+IG    E  +++VA+A+EQAT  H  KP
Sbjct: 424 DLMTIPVNLAGLPSLSLPCGFDDQGLPIGLQLIGNVLREDQLFQVAYAYEQATTWHLRKP 483

Query: 484 EL 485
           ++
Sbjct: 484 QI 485


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: 611
Number of extensions: 25
Number of successful extensions: 3
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: 486
Length adjustment: 34
Effective length of query: 451
Effective length of database: 452
Effective search space:   203852
Effective search space used:   203852
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_012408045.1 NPUN_RS06670 (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.3695329.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.8e-206  671.2   0.0   4.4e-206  671.0   0.0    1.0  1  NCBI__GCF_000020025.1:WP_012408045.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020025.1:WP_012408045.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  671.0   0.0  4.4e-206  4.4e-206       2     465 ..       8     477 ..       7     478 .. 0.98

  Alignments for each domain:
  == domain 1  score: 671.0 bits;  conditional E-value: 4.4e-206
                             TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKdniav 71 
                                           +++l+kke s++e+++e leriea + k+++fl vt+e+al++a ++d+k+a  +e  +lagip+++Kdn+++
  NCBI__GCF_000020025.1:WP_012408045.1   8 HQQLVKKERSAVEITQEALERIEALEPKLHSFLCVTAERALEQAGAVDAKIAagEEiGLLAGIPVGIKDNLCT 80 
                                           78999**********************************************9976656*************** PP

                             TIGR00132  72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgG 144
                                           k+i+ttcaS+iLen+v+py++t +++l +aga+++GktNlDEFamGsste+Sa++vt+nP+n +rvpGGSsgG
  NCBI__GCF_000020025.1:WP_012408045.1  81 KGIPTTCASRILENFVPPYESTATQKLADAGAVMVGKTNLDEFAMGSSTENSAYQVTANPWNLSRVPGGSSGG 153
                                           ************************************************************************* PP

                             TIGR00132 145 saaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvi 217
                                           saaav+ +++++algsDTGgSiRqPAsfcgvvG+KPtYGlvSRyGlvayasSldqiG++a++ved+a++l++i
  NCBI__GCF_000020025.1:WP_012408045.1 154 SAAAVSSQECVVALGSDTGGSIRQPASFCGVVGMKPTYGLVSRYGLVAYASSLDQIGPFANTVEDAAILLNAI 226
                                           ************************************************************************* PP

                             TIGR00132 218 sgkDkkDstslevkveelleelkkdlk...glkvgvvkelseesldkevkekfekllekleelgaeivevslp 287
                                           +g+D kDstsl+v+++++  + k d k   +l++g+vke ++e+ld+ v++++ k++++l++lgaei  +s+p
  NCBI__GCF_000020025.1:WP_012408045.1 227 AGHDPKDSTSLKVAIPNYAASFKPDFKprgQLRIGIVKETFGEGLDSVVEQAVTKAVDVLQSLGAEIHIISCP 299
                                           ********************99995543338****************************************** PP

                             TIGR00132 288 svklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydk 360
                                           ++++ l++Yyii+psEas+nlarydg++yG+r+ ++++l  +y++tR+ gfg+evkrRim+G+yals++yyd+
  NCBI__GCF_000020025.1:WP_012408045.1 300 RFRYGLPTYYIIAPSEASANLARYDGVKYGYRAPDADNLLSMYTRTRATGFGTEVKRRIMIGTYALSAGYYDA 372
                                           ************************************************************************* PP

                             TIGR00132 361 yykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkk 433
                                           yy+kAqkvrtli+++fek+f+ vDv+v+pt+pt+afk gek++dpl+myl+D++t+p+nlaGlp++s+P+g +
  NCBI__GCF_000020025.1:WP_012408045.1 373 YYLKAQKVRTLIKEDFEKAFRVVDVLVCPTSPTTAFKAGEKTTDPLSMYLTDLMTIPVNLAGLPSLSLPCGFD 445
                                           ************************************************************************* PP

                             TIGR00132 434 ekglpiGlqiigkafddkkllsvakaleqald 465
                                           ++glpiGlq+ig+++ +++l++va+a+eqa++
  NCBI__GCF_000020025.1:WP_012408045.1 446 DQGLPIGLQLIGNVLREDQLFQVAYAYEQATT 477
                                           ****************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (486 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 0.02s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.31
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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