Alignments for a candidate for gatA in Bacillus alkalinitrilicus DSM 22532

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Bacillus alkalinitrilicus DSM 22532

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_078429292.1 BK574_RS15995 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_002019605.1:WP_078429292.1
          Length = 486

 Score =  769 bits (1986), Expect = 0.0
 Identities = 374/486 (76%), Positives = 435/486 (89%), Gaps = 1/486 (0%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           MS+    I++L   +H KE+ +S+LV+ SY+RI AVD+KV+AF+ LDEERAR YAK+LDE
Sbjct: 1   MSVLGGSISDLHNRLHNKEVSVSELVNASYERINAVDEKVKAFVTLDEERARGYAKKLDE 60

Query: 61  AVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIG 120
           A++  +E GLLFG+P G+KDNIVT+GL TTCSSK+L NF+P+++ATV++ LQ A++VTIG
Sbjct: 61  ALNSNAERGLLFGIPAGIKDNIVTRGLTTTCSSKLLANFEPMHNATVIENLQGAQSVTIG 120

Query: 121 KLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIR 180
           KLNMDEFAMGSSTENS +  T+NPWN D VPGGSSGGSAA+VAAGEV FSLGSDTGGSIR
Sbjct: 121 KLNMDEFAMGSSTENSGFFNTRNPWNTDYVPGGSSGGSAASVAAGEVVFSLGSDTGGSIR 180

Query: 181 QPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTS 240
           QPAS+CGVVGLKPTYGRVSR+GLVAFASSLDQIGPITRTVEDNA +LQ ++G DKMDSTS
Sbjct: 181 QPASYCGVVGLKPTYGRVSRFGLVAFASSLDQIGPITRTVEDNALVLQVLAGYDKMDSTS 240

Query: 241 ANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLP 300
           AN+D  D+LS+LT D+KGLKIAVPKEYL EGV ++ +  +L +LKVLEGLGATWEEVSLP
Sbjct: 241 ANIDTSDYLSALTEDVKGLKIAVPKEYLAEGVHEDVKNRILESLKVLEGLGATWEEVSLP 300

Query: 301 HSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIM 360
           HSKYA+ATYYLL+SSEASANLARFDG+RYG R+DNA NLI++YK+TR+ GFG+EVKRRIM
Sbjct: 301 HSKYAVATYYLLASSEASANLARFDGVRYGVRSDNAANLIEMYKETRSNGFGDEVKRRIM 360

Query: 361 LGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLT 420
           LGT+ALSSGYYDAYYKKAQKVRTLIKKDFEDVFE YDVI+GPT PT AFKIGE   DPLT
Sbjct: 361 LGTYALSSGYYDAYYKKAQKVRTLIKKDFEDVFENYDVIIGPTAPTTAFKIGEKVNDPLT 420

Query: 421 MYANDILTIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHAFEQATDHH 479
           MYANDILTIPVNLAGVP IS+PCGL + GLP+GLQ+IGKHFDE+TVYRVAHAFEQATDHH
Sbjct: 421 MYANDILTIPVNLAGVPAISIPCGLGENGLPIGLQVIGKHFDENTVYRVAHAFEQATDHH 480

Query: 480 KAKPEL 485
           KAKPEL
Sbjct: 481 KAKPEL 486


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: 774
Number of extensions: 28
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: 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_078429292.1 BK574_RS15995 (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.781.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.9e-209  679.9   0.2     1e-208  679.7   0.2    1.0  1  lcl|NCBI__GCF_002019605.1:WP_078429292.1  BK574_RS15995 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002019605.1:WP_078429292.1  BK574_RS15995 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 !  679.7   0.2    1e-208    1e-208       2     465 ..      12     478 ..      11     479 .. 0.99

  Alignments for each domain:
  == domain 1  score: 679.7 bits;  conditional E-value: 1e-208
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKd 67 
                                               ++ l++kevs++e++++++eri+av++k++af+++++e+a   akkld++++   e  +l+gip+++Kd
  lcl|NCBI__GCF_002019605.1:WP_078429292.1  12 HNRLHNKEVSVSELVNASYERINAVDEKVKAFVTLDEERARGYAKKLDEALNsnAErGLLFGIPAGIKD 80 
                                               67899********************************************999754435*********** PP

                                 TIGR00132  68 niavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneer 136
                                               ni++++++ttc+Sk+L n+ + ++atV+e+l+ a+ ++iGk N+DEFamGsste+S f  t+nP+n+++
  lcl|NCBI__GCF_002019605.1:WP_078429292.1  81 NIVTRGLTTTCSSKLLANFEPMHNATVIENLQGAQSVTIGKLNMDEFAMGSSTENSGFFNTRNPWNTDY 149
                                               ********************************************************************* PP

                                 TIGR00132 137 vpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilak 205
                                               vpGGSsgGsaa+vaa++v+++lgsDTGgSiRqPAs+cgvvGlKPtYG+vSR+Glva+asSldqiG++++
  lcl|NCBI__GCF_002019605.1:WP_078429292.1 150 VPGGSSGGSAASVAAGEVVFSLGSDTGGSIRQPASYCGVVGLKPTYGRVSRFGLVAFASSLDQIGPITR 218
                                               ********************************************************************* PP

                                 TIGR00132 206 kvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekl 274
                                               +ved alvl+v++g+Dk+Dsts++++++++l++l++d+kglk++v ke+  e+++++vk+++ + l++l
  lcl|NCBI__GCF_002019605.1:WP_078429292.1 219 TVEDNALVLQVLAGYDKMDSTSANIDTSDYLSALTEDVKGLKIAVPKEYLAEGVHEDVKNRILESLKVL 287
                                               ********************************************************************* PP

                                 TIGR00132 275 eelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevk 343
                                               e lga+++evslp++k+a+a+Yy++++sEas+nlar+dg+ryG r +++ +l e+y++tRs+gfg+evk
  lcl|NCBI__GCF_002019605.1:WP_078429292.1 288 EGLGATWEEVSLPHSKYAVATYYLLASSEASANLARFDGVRYGVRSDNAANLIEMYKETRSNGFGDEVK 356
                                               ********************************************************************* PP

                                 TIGR00132 344 rRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsD 412
                                               rRimlG+yals++yyd+yykkAqkvrtli+++fe++fe++Dvi++ptapt+afk+gek +dpl+my++D
  lcl|NCBI__GCF_002019605.1:WP_078429292.1 357 RRIMLGTYALSSGYYDAYYKKAQKVRTLIKKDFEDVFENYDVIIGPTAPTTAFKIGEKVNDPLTMYAND 425
                                               ********************************************************************* PP

                                 TIGR00132 413 vltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                               +lt+p+nlaG+pais+P+g  e+glpiGlq+igk+fd++++++va+a+eqa+d
  lcl|NCBI__GCF_002019605.1:WP_078429292.1 426 ILTIPVNLAGVPAISIPCGLGENGLPIGLQVIGKHFDENTVYRVAHAFEQATD 478
                                               **************************************************987 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.50
//
[ok]

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

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Protein sequences (fasta format)
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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