Alignments for a candidate for gatA in Rhodomicrobium vannielii ATCC 17100

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Rhodomicrobium vannielii ATCC 17100

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_049779603.1 RVAN_RS07965 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000166055.1:WP_049779603.1
          Length = 523

 Score =  492 bits (1267), Expect = e-143
 Identities = 257/483 (53%), Positives = 341/483 (70%), Gaps = 9/483 (1%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           MSL +  +++ +  +  KEI  ++L +     I+A +D ++A+L +  ++A   AK+ DE
Sbjct: 1   MSLNELTLSDARDKLRAKEITATELTEACLSAIEAGNDALKAYLVVTADKALEQAKKSDE 60

Query: 61  AVDGRSEHG-LLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTI 119
            +   ++    L G+P+G+KD   T G+RTT  S IL NF+P Y++TV Q L DA AV +
Sbjct: 61  RLAANAKDARALEGIPLGIKDLFCTDGVRTTAGSHILGNFEPPYESTVTQNLWDAGAVML 120

Query: 120 GKLNMDEFAMGSSTENSAYKLTKNPWNL-----DTVPGGSSGGSAAAVAAGEVPFSLGSD 174
           GKLNMDEFAMGSSTE S Y  T NPW       + VPGGSSGGS++AVAAG    +  SD
Sbjct: 121 GKLNMDEFAMGSSTETSYYGQTVNPWRAKDSDENLVPGGSSGGSSSAVAAGLCLGATASD 180

Query: 175 TGGSIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVD 234
           TGGSIRQPA+F G VG+KPTYGR SRYG+VAFASSLDQ GPITR+++D A +LQA++  D
Sbjct: 181 TGGSIRQPAAFTGTVGIKPTYGRCSRYGMVAFASSLDQAGPITRSIKDAALMLQAMASYD 240

Query: 235 KMDSTSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATW 294
             DSTS +  +PD   +LT   KGLKI VPKEY  +G+ KE        + +    GA  
Sbjct: 241 LKDSTSVDRPLPDLEKALTQKFKGLKIGVPKEYRVDGMSKEIEALWEKGIDIYRQAGAEI 300

Query: 295 EEVSLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNE 354
            ++SLPH+K AL  YY+++ +EAS+NLAR+DG+RYG R D  D ++D+Y++TR+ GFG E
Sbjct: 301 VDISLPHTKAALPAYYIVAPAEASSNLARYDGVRYGLRADGRD-IVDMYEETRSHGFGAE 359

Query: 355 VKRRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIG-E 413
           VKRRI++GT+ LS+GYYDAYY KAQKVR+LIK+DF+D FE  DV++ PTTPTPAF +G +
Sbjct: 360 VKRRILIGTYVLSAGYYDAYYLKAQKVRSLIKRDFDDAFETVDVVLTPTTPTPAFGLGSK 419

Query: 414 NTKDPLTMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAF 472
              DP+ MY NDI T+ VN+AG+PG+SVP GL A+GLPLGLQ+IGK FDE+TV R     
Sbjct: 420 KDADPVEMYLNDIFTVTVNMAGLPGLSVPGGLSAEGLPLGLQLIGKPFDEATVLRAGQVI 479

Query: 473 EQA 475
           E A
Sbjct: 480 EDA 482


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: 704
Number of extensions: 36
Number of successful extensions: 6
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: 523
Length adjustment: 34
Effective length of query: 451
Effective length of database: 489
Effective search space:   220539
Effective search space used:   220539
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_049779603.1 RVAN_RS07965 (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.3825615.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.5e-181  587.5   0.0   1.1e-180  587.3   0.0    1.0  1  NCBI__GCF_000166055.1:WP_049779603.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166055.1:WP_049779603.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  587.3   0.0  1.1e-180  1.1e-180       3     464 ..      13     483 ..      11     485 .. 0.97

  Alignments for each domain:
  == domain 1  score: 587.3 bits;  conditional E-value: 1.1e-180
                             TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva...ke.kklagipiavKdniav 71 
                                           ++l +ke++++e++e++l +iea +d ++a+l vt++kal++akk+d+++a   k+ + l gip+++Kd +++
  NCBI__GCF_000166055.1:WP_049779603.1  13 DKLRAKEITATELTEACLSAIEAGNDALKAYLVVTADKALEQAKKSDERLAanaKDaRALEGIPLGIKDLFCT 85 
                                           67899*******************************************99987545359************** PP

                             TIGR00132  72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....eneervpG 139
                                            +++tt++S+iL n+ +py++tV+++l +aga+++Gk N+DEFamGsstetS++g t nP      +e+ vpG
  NCBI__GCF_000166055.1:WP_049779603.1  86 DGVRTTAGSHILGNFEPPYESTVTQNLWDAGAVMLGKLNMDEFAMGSSTETSYYGQTVNPwrakdSDENLVPG 158
                                           ************************************************************6655558899*** PP

                             TIGR00132 140 GSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedial 212
                                           GSsgGs+ avaa+l+  a +sDTGgSiRqPA+f+g+vG+KPtYG+ SRyG+va+asSldq G+++++++d+al
  NCBI__GCF_000166055.1:WP_049779603.1 159 GSSGGSSSAVAAGLCLGATASDTGGSIRQPAAFTGTVGIKPTYGRCSRYGMVAFASSLDQAGPITRSIKDAAL 231
                                           ************************************************************************* PP

                             TIGR00132 213 vldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevs 285
                                           +l++++ +D kDsts++ + ++l ++l+++ kglk+gv ke++ ++++ke+++ +ek ++  ++ gaeiv++s
  NCBI__GCF_000166055.1:WP_049779603.1 232 MLQAMASYDLKDSTSVDRPLPDLEKALTQKFKGLKIGVPKEYRVDGMSKEIEALWEKGIDIYRQAGAEIVDIS 304
                                           ************************************************************************* PP

                             TIGR00132 286 lpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyy 358
                                           lp+ k al++Yyi++p+Eassnlarydg+ryG r++  + + ++y +tRs+gfg+evkrRi++G+y+ls++yy
  NCBI__GCF_000166055.1:WP_049779603.1 305 LPHTKAALPAYYIVAPAEASSNLARYDGVRYGLRADGRD-IVDMYEETRSHGFGAEVKRRILIGTYVLSAGYY 376
                                           ***********************************9988.********************************* PP

                             TIGR00132 359 dkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaed.plemylsDvltvpanlaGlpaisvPl 430
                                           d+yy+kAqkvr+li+++f+++fe vDv+++pt+pt af lg+k++  p+emyl+D++tv++n+aGlp++svP 
  NCBI__GCF_000166055.1:WP_049779603.1 377 DAYYLKAQKVRSLIKRDFDDAFETVDVVLTPTTPTPAFGLGSKKDAdPVEMYLNDIFTVTVNMAGLPGLSVPG 449
                                           *****************************************998756************************** PP

                             TIGR00132 431 gkkekglpiGlqiigkafddkkllsvakaleqal 464
                                           g + +glp+Glq+igk fd+ ++l++++ +e+a+
  NCBI__GCF_000166055.1:WP_049779603.1 450 GLSAEGLPLGLQLIGKPFDEATVLRAGQVIEDAV 483
                                           ****************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (523 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: 00:00:00.01
# Mc/sec: 18.58
//
[ok]

This GapMind analysis is from Jul 25 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:

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