GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Pontibacter ramchanderi LP43

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_101446556.1 BD749_RS17050 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_002846395.1:WP_101446556.1
          Length = 478

 Score =  412 bits (1059), Expect = e-119
 Identities = 223/459 (48%), Positives = 307/459 (66%), Gaps = 5/459 (1%)

Query: 6   HKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGR 65
           H + +++  I   ++    LV+     I+    ++ AFL + EE A A A  +D+ +   
Sbjct: 5   HSLRDIRSDIANGQVSCRQLVEHYLHNIKQ-QPELNAFLEIFEEEAYAQADAVDKKL-AS 62

Query: 66  SEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMD 125
              G L GM IG+KD +  +G     SS+IL  F  +Y AT VQRL   +A+ IG+ N D
Sbjct: 63  GHAGKLAGMVIGLKDVLAYEGHSLQASSQILNGFKSLYTATAVQRLLAEDAIIIGRQNCD 122

Query: 126 EFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASF 185
           EFAMG+S ENS++    N  +   VPGGSSGGSA AV A     S+GSDTGGS+RQPASF
Sbjct: 123 EFAMGASNENSSFGPVLNADDKTRVPGGSSGGSAVAVQADLCLASIGSDTGGSVRQPASF 182

Query: 186 CGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDV 245
           CGVVGLKPTY R+SRYGL+A+ASS DQIG I+++VED A LL+ ++G D+ DST ++  V
Sbjct: 183 CGVVGLKPTYSRISRYGLIAYASSFDQIGVISKSVEDAALLLEVMAGSDEYDSTVSHRPV 242

Query: 246 PDFLSSLTGDIKGLKIAVPKE-YLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKY 304
           P +   L  D K  KI   ++ +  EG+  E +ES+L    +L+  G   E V  P+  Y
Sbjct: 243 PAYSQMLQTD-KKYKIGYIRDCFESEGLDAEVKESILGVKDMLQEAGHEVEAVEFPYLDY 301

Query: 305 ALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTF 364
            + TYY+L+++EAS+NL RFDG++YGYR++NA +L  LYK+TRAEGFG EV+RRIMLGTF
Sbjct: 302 MVPTYYILTTAEASSNLGRFDGVKYGYRSENATDLTSLYKKTRAEGFGPEVQRRIMLGTF 361

Query: 365 ALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYAN 424
            LS+ YYDAYY KAQ+VR LIK+  +++ + YD ++ PT PT AF++ ENT +PL MY  
Sbjct: 362 VLSADYYDAYYTKAQRVRRLIKEKTDELLQNYDFLILPTAPTTAFRLEENTANPLAMYLA 421

Query: 425 DILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDE 462
           DI T+  +LAGVP IS+P G  A+GL +GLQ++ + F+E
Sbjct: 422 DIFTVQASLAGVPAISIPVGRDANGLSIGLQLMTRSFEE 460


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: 598
Number of extensions: 35
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: 478
Length adjustment: 34
Effective length of query: 451
Effective length of database: 444
Effective search space:   200244
Effective search space used:   200244
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_101446556.1 BD749_RS17050 (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.1754402.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-175  570.4   0.2   1.7e-175  570.2   0.2    1.0  1  NCBI__GCF_002846395.1:WP_101446556.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101446556.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  570.2   0.2  1.7e-175  1.7e-175       3     463 ..      12     473 ..      10     476 .. 0.97

  Alignments for each domain:
  == domain 1  score: 570.2 bits;  conditional E-value: 1.7e-175
                             TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkd 73 
                                           + + + +vs ++++e++l++i+++ + +nafle+ +e+a+++a+++dkk+a  +  klag++i++Kd++a ++
  NCBI__GCF_002846395.1:WP_101446556.1  12 SDIANGQVSCRQLVEHYLHNIKQQPE-LNAFLEIFEEEAYAQADAVDKKLAsGHaGKLAGMVIGLKDVLAYEG 83 
                                           56788999**************9998.***********************974536***************** PP

                             TIGR00132  74 iettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsa 146
                                            ++ ++S+iL++++s y at v+rl +++a+iiG+ N DEFamG+s e+S fg++ n  +++rvpGGSsgGsa
  NCBI__GCF_002846395.1:WP_101446556.1  84 HSLQASSQILNGFKSLYTATAVQRLLAEDAIIIGRQNCDEFAMGASNENSSFGPVLNADDKTRVPGGSSGGSA 156
                                           ************************************************************************* PP

                             TIGR00132 147 aavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisg 219
                                            av adl+  ++gsDTGgS+RqPAsfcgvvGlKPtY ++SRyGl+ayasS+dqiG+++k+ved+al+l+v++g
  NCBI__GCF_002846395.1:WP_101446556.1 157 VAVQADLCLASIGSDTGGSVRQPASFCGVVGLKPTYSRISRYGLIAYASSFDQIGVISKSVEDAALLLEVMAG 229
                                           ************************************************************************* PP

                             TIGR00132 220 kDkkDstslevkveelleelkkdlkglkvgvvkelse.esldkevkekfekllekleelgaeivevslpsvkl 291
                                           +D+ Dst  + +v+ + + l++  k+ k+g++++++e e+ld evke++  +++ l+e g+e++ v++p++++
  NCBI__GCF_002846395.1:WP_101446556.1 230 SDEYDSTVSHRPVPAYSQMLQT-DKKYKIGYIRDCFEsEGLDAEVKESILGVKDMLQEAGHEVEAVEFPYLDY 301
                                           ******************9999.9**********765278********************************* PP

                             TIGR00132 292 alaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykk 364
                                           ++++Yyi++++Eassnl r+dg++yG+r e++++l+ ly+ktR+egfg ev+rRimlG+++ls++yyd+yy+k
  NCBI__GCF_002846395.1:WP_101446556.1 302 MVPTYYILTTAEASSNLGRFDGVKYGYRSENATDLTSLYKKTRAEGFGPEVQRRIMLGTFVLSADYYDAYYTK 374
                                           ************************************************************************* PP

                             TIGR00132 365 AqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekgl 437
                                           Aq+vr+li+++ ++l++++D+++ ptapt+af+l+e++++pl+myl+D++tv a+laG+pais+P+g + +gl
  NCBI__GCF_002846395.1:WP_101446556.1 375 AQRVRRLIKEKTDELLQNYDFLILPTAPTTAFRLEENTANPLAMYLADIFTVQASLAGVPAISIPVGRDANGL 447
                                           ************************************************************************* PP

                             TIGR00132 438 piGlqiigkafddkkllsvakaleqa 463
                                           +iGlq+++++f++ +ll +++ + ++
  NCBI__GCF_002846395.1:WP_101446556.1 448 SIGLQLMTRSFEEPQLLAFSNYILDK 473
                                           *******************9887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (478 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 25.51
//
[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