Alignments for a candidate for gatA in Heliomicrobium modesticaldum Ice1 Ice1; ATCC 51547

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Heliomicrobium modesticaldum Ice1 Ice1; ATCC 51547

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_012284007.1 HM1_RS13775 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000019165.1:WP_012284007.1
          Length = 487

 Score =  579 bits (1492), Expect = e-170
 Identities = 285/485 (58%), Positives = 371/485 (76%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           M L+     EL  L+ +KE+  +++V     R+QA++ K++AF+ L  ++A   A  +D 
Sbjct: 1   MKLYTKTAHELHDLLVRKEVSATEIVKTQADRMQALEPKIRAFVTLTVDKALEQAARVDA 60

Query: 61  AVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIG 120
            +      G L G+P+ +KDN+ T G+RTTCSSKIL NF P YDATVV +L++A AV +G
Sbjct: 61  KIAAGEAIGPLEGIPMAIKDNMCTDGVRTTCSSKILNNFVPPYDATVVTKLKEAGAVMMG 120

Query: 121 KLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIR 180
           K N+DEFAMGSSTENS +  T NPW+++ VPGGSSGGSAA+VAAG+  FSLGSDTGGSIR
Sbjct: 121 KTNLDEFAMGSSTENSGFFATCNPWDIERVPGGSSGGSAASVAAGQAVFSLGSDTGGSIR 180

Query: 181 QPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTS 240
           QPA+FCGVVGLKPTYG VSR+GL+AFASSLDQIGP TR V D A ++ AI+G D  DSTS
Sbjct: 181 QPAAFCGVVGLKPTYGAVSRFGLIAFASSLDQIGPFTRDVRDCAHVMNAIAGHDAKDSTS 240

Query: 241 ANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLP 300
           A VD PD+ S L   IKG ++ +PKEY G+G+  E +E +  A+K +E LGA   E SLP
Sbjct: 241 APVDYPDYTSLLGKPIKGWRVGLPKEYFGDGMDPEVKEVIEKAVKTIEDLGAEVAECSLP 300

Query: 301 HSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIM 360
           H++YAL  YYL++ +EAS+NLAR+DG+RYGYR+++AD+LI ++K+TRAEGFG+EVKRRIM
Sbjct: 301 HTEYALPVYYLIAPAEASSNLARYDGVRYGYRSESADDLITMFKKTRAEGFGDEVKRRIM 360

Query: 361 LGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLT 420
           LGT+ALSSGYYDAYY KA KVRTLIK DF+  FEK+DVI+ PTTPT AFK G+ T +PL 
Sbjct: 361 LGTYALSSGYYDAYYLKALKVRTLIKNDFDQAFEKFDVILSPTTPTVAFKFGDRTDNPLQ 420

Query: 421 MYANDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHK 480
           MY +DI T+ VNLAG+PG+S+  G A G+P+GLQIIGK FDE+ + ++A+A+E+AT  H 
Sbjct: 421 MYLSDIYTLSVNLAGIPGLSINAGFAKGMPVGLQIIGKPFDEARLLQIAYAYEEATGCHS 480

Query: 481 AKPEL 485
             P+L
Sbjct: 481 KMPDL 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: 642
Number of extensions: 26
Number of successful extensions: 2
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: 487
Length adjustment: 34
Effective length of query: 451
Effective length of database: 453
Effective search space:   204303
Effective search space used:   204303
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_012284007.1 HM1_RS13775 (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.3476828.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.7e-204  664.3   0.0   5.4e-204  664.1   0.0    1.0  1  NCBI__GCF_000019165.1:WP_012284007.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019165.1:WP_012284007.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  664.1   0.0  5.4e-204  5.4e-204       2     464 ..      12     476 ..      11     478 .. 0.99

  Alignments for each domain:
  == domain 1  score: 664.1 bits;  conditional E-value: 5.4e-204
                             TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKdniav 71 
                                           ++ll++kevs++e++++  +r++a + ki+af+++t +kal++a+++d+k+a  +   +l gip+a+Kdn+++
  NCBI__GCF_000019165.1:WP_012284007.1  12 HDLLVRKEVSATEIVKTQADRMQALEPKIRAFVTLTVDKALEQAARVDAKIAagEAiGPLEGIPMAIKDNMCT 84 
                                           67899**********************************************9954456*************** PP

                             TIGR00132  72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgG 144
                                            +++ttc+SkiL+n+v+pydatVv++lkeaga+++GktNlDEFamGsste+S f +t nP++ ervpGGSsgG
  NCBI__GCF_000019165.1:WP_012284007.1  85 DGVRTTCSSKILNNFVPPYDATVVTKLKEAGAVMMGKTNLDEFAMGSSTENSGFFATCNPWDIERVPGGSSGG 157
                                           ************************************************************************* PP

                             TIGR00132 145 saaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvi 217
                                           saa+vaa++++++lgsDTGgSiRqPA+fcgvvGlKPtYG+vSR+Gl+a+asSldqiG+++++v d a v+++i
  NCBI__GCF_000019165.1:WP_012284007.1 158 SAASVAAGQAVFSLGSDTGGSIRQPAAFCGVVGLKPTYGAVSRFGLIAFASSLDQIGPFTRDVRDCAHVMNAI 230
                                           ************************************************************************* PP

                             TIGR00132 218 sgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvk 290
                                           +g+D+kDsts+ v+ +++++ l k +kg +vg+ ke++++++d evke +ek+++++e+lgae+ e slp+ +
  NCBI__GCF_000019165.1:WP_012284007.1 231 AGHDAKDSTSAPVDYPDYTSLLGKPIKGWRVGLPKEYFGDGMDPEVKEVIEKAVKTIEDLGAEVAECSLPHTE 303
                                           ************************************************************************* PP

                             TIGR00132 291 lalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyyk 363
                                           +al++Yy+i+p+Eassnlarydg+ryG+r e +++l  +++ktR+egfg+evkrRimlG+yals++yyd+yy+
  NCBI__GCF_000019165.1:WP_012284007.1 304 YALPVYYLIAPAEASSNLARYDGVRYGYRSESADDLITMFKKTRAEGFGDEVKRRIMLGTYALSSGYYDAYYL 376
                                           ************************************************************************* PP

                             TIGR00132 364 kAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekg 436
                                           kA kvrtli+++f+++fe+ Dvi+spt+pt+afk+g+++++pl+mylsD++t+ +nlaG+p++s+ +g + kg
  NCBI__GCF_000019165.1:WP_012284007.1 377 KALKVRTLIKNDFDQAFEKFDVILSPTTPTVAFKFGDRTDNPLQMYLSDIYTLSVNLAGIPGLSINAGFA-KG 448
                                           **********************************************************************.8* PP

                             TIGR00132 437 lpiGlqiigkafddkkllsvakaleqal 464
                                           +p+Glqiigk fd+ +ll++a+a+e+a+
  NCBI__GCF_000019165.1:WP_012284007.1 449 MPVGLQIIGKPFDEARLLQIAYAYEEAT 476
                                           *************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (487 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 30.51
//
[ok]

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

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