GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Lentibacillus jeotgali Grbi

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_010529623.1 ON01_RS03495 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000224785.1:WP_010529623.1
          Length = 489

 Score =  727 bits (1876), Expect = 0.0
 Identities = 358/487 (73%), Positives = 419/487 (86%), Gaps = 5/487 (1%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           MSLFDH I +L+ ++HKKEI   DLVD SY RI  VDD+V+AFL LDEE+AR+ AK+LD 
Sbjct: 1   MSLFDHSIKQLEGMLHKKEISAEDLVDASYNRIHEVDDQVKAFLTLDEEQARSQAKQLDA 60

Query: 61  AVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFD-PIYDATVVQRLQDAEAVTI 119
           A D   E+  LF +P G+KDNIVTKGLRTTC S+ L+NFD P+Y+ATVV++L   + VT+
Sbjct: 61  APD---ENAQLFAIPAGIKDNIVTKGLRTTCGSQFLKNFDDPLYNATVVEKLNTEKTVTV 117

Query: 120 GKLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSI 179
           GKLNMDEFAMGSSTEN++Y  T+NPWN D VPGGSSGGSAA+VAAGEV FSLGSDTGGSI
Sbjct: 118 GKLNMDEFAMGSSTENTSYTPTRNPWNTDYVPGGSSGGSAASVAAGEVLFSLGSDTGGSI 177

Query: 180 RQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDST 239
           RQPASFCGVVG+KPTYGRVSR+GLVAFASSLDQIGPITR+VEDNA +L+ ISG DKMDST
Sbjct: 178 RQPASFCGVVGMKPTYGRVSRFGLVAFASSLDQIGPITRSVEDNARILEIISGHDKMDST 237

Query: 240 SANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSL 299
           SA+VDVP +   LTGD+KG+KIAVPKEYL EGV  E +E+V++ALKV E LGA WEEVSL
Sbjct: 238 SADVDVPSYTDKLTGDVKGMKIAVPKEYLAEGVAPEVKEAVMSALKVYESLGAEWEEVSL 297

Query: 300 PHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRI 359
           PHSKYA+A YYLL+SSEASANLARFDG+RYG R+D ADN++D++  +R+EGFG+EVKRRI
Sbjct: 298 PHSKYAVAAYYLLASSEASANLARFDGVRYGVRSDKADNMMDMFTYSRSEGFGDEVKRRI 357

Query: 360 MLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPL 419
           MLGTFALSSGYYDAYYKKAQKVRTLIK DF+++ + YDV++GPT PTPAFK+GE   DPL
Sbjct: 358 MLGTFALSSGYYDAYYKKAQKVRTLIKNDFDNILKDYDVVIGPTAPTPAFKVGEKIDDPL 417

Query: 420 TMYANDILTIPVNLAGVPGISVPCGLA-DGLPLGLQIIGKHFDESTVYRVAHAFEQATDH 478
           TMYANDILTIPVNLAGVPGISVPCG + +GLP+GLQIIG  F E TVYR AHA+EQATDH
Sbjct: 418 TMYANDILTIPVNLAGVPGISVPCGFSEEGLPIGLQIIGNAFAEGTVYRAAHAYEQATDH 477

Query: 479 HKAKPEL 485
           H  +P+L
Sbjct: 478 HTKRPQL 484


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: 747
Number of extensions: 26
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: 489
Length adjustment: 34
Effective length of query: 451
Effective length of database: 455
Effective search space:   205205
Effective search space used:   205205
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_010529623.1 ON01_RS03495 (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.3032861.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-204  665.7   0.2   2.1e-204  665.5   0.2    1.0  1  NCBI__GCF_000224785.1:WP_010529623.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010529623.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  665.5   0.2  2.1e-204  2.1e-204       3     465 ..      13     476 ..      11     477 .. 0.99

  Alignments for each domain:
  == domain 1  score: 665.5 bits;  conditional E-value: 2.1e-204
                             TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkvakekklagipiavKdniavkdie 75 
                                            +l+kke+s++++++++++ri++v+d+++afl++++e+a ++ak+ld++ +++ +l+ ip+++Kdni++k+++
  NCBI__GCF_000224785.1:WP_010529623.1  13 GMLHKKEISAEDLVDASYNRIHEVDDQVKAFLTLDEEQARSQAKQLDAAPDENAQLFAIPAGIKDNIVTKGLR 85 
                                           5899********************************************997778******************* PP

                             TIGR00132  76 ttcaSkiLenyv.spydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaa 147
                                           ttc+S++L+n+  + y+atVve+l+++ ++++Gk N+DEFamGsste+  + +t+nP+n+++vpGGSsgGsaa
  NCBI__GCF_000224785.1:WP_010529623.1  86 TTCGSQFLKNFDdPLYNATVVEKLNTEKTVTVGKLNMDEFAMGSSTENTSYTPTRNPWNTDYVPGGSSGGSAA 158
                                           ***********7356********************************************************** PP

                             TIGR00132 148 avaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgk 220
                                           +vaa++v ++lgsDTGgSiRqPAsfcgvvG+KPtYG+vSR+Glva+asSldqiG+++++ved a +l++isg+
  NCBI__GCF_000224785.1:WP_010529623.1 159 SVAAGEVLFSLGSDTGGSIRQPASFCGVVGMKPTYGRVSRFGLVAFASSLDQIGPITRSVEDNARILEIISGH 231
                                           ************************************************************************* PP

                             TIGR00132 221 DkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklal 293
                                           Dk+Dsts++v+v++++ +l+ d+kg+k++v ke+  e++  evke++ ++l++ e+lgae++evslp++k+a+
  NCBI__GCF_000224785.1:WP_010529623.1 232 DKMDSTSADVDVPSYTDKLTGDVKGMKIAVPKEYLAEGVAPEVKEAVMSALKVYESLGAEWEEVSLPHSKYAV 304
                                           ************************************************************************* PP

                             TIGR00132 294 aiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAq 366
                                           a+Yy++++sEas+nlar+dg+ryG r +++++++++++ +Rsegfg+evkrRimlG++als++yyd+yykkAq
  NCBI__GCF_000224785.1:WP_010529623.1 305 AAYYLLASSEASANLARFDGVRYGVRSDKADNMMDMFTYSRSEGFGDEVKRRIMLGTFALSSGYYDAYYKKAQ 377
                                           ************************************************************************* PP

                             TIGR00132 367 kvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpi 439
                                           kvrtli+++f+++++++Dv+++ptapt afk+gek +dpl+my++D+lt+p+nlaG+p+isvP+g +e+glpi
  NCBI__GCF_000224785.1:WP_010529623.1 378 KVRTLIKNDFDNILKDYDVVIGPTAPTPAFKVGEKIDDPLTMYANDILTIPVNLAGVPGISVPCGFSEEGLPI 450
                                           ************************************************************************* PP

                             TIGR00132 440 Glqiigkafddkkllsvakaleqald 465
                                           Glqiig+af++ +++++a+a+eqa+d
  NCBI__GCF_000224785.1:WP_010529623.1 451 GLQIIGNAFAEGTVYRAAHAYEQATD 476
                                           ***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (489 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 32.09
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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