Alignments for a candidate for gatA in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Malonomonas rubra DSM 5091

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_072908350.1 BUB13_RS09635 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_900142125.1:WP_072908350.1
          Length = 485

 Score =  539 bits (1389), Expect = e-158
 Identities = 275/478 (57%), Positives = 354/478 (74%), Gaps = 2/478 (0%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           M L D  I++L++ +   E    +L      RI A +DKV +F+ + E  A A A E D+
Sbjct: 1   MQLNDLTISQLREKLASGETTSVELTKAFLARIAATNDKVNSFITVCEAEALAAAAEADQ 60

Query: 61  AVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIG 120
            +        + G+P+ VKD   T  +RTTC SKIL+N+   YDAT + +L++  AV IG
Sbjct: 61  RI-AAGNAAPMTGIPLAVKDIFNTLDVRTTCGSKILDNYVSPYDATAIAKLREQGAVIIG 119

Query: 121 KLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIR 180
           KLNMDEFAMGSS ENSA    KNPW+L+ VPGGSSGGSAAA+AAG+   +LG+DTGGSIR
Sbjct: 120 KLNMDEFAMGSSNENSAAGPVKNPWDLERVPGGSSGGSAAAIAAGQALATLGTDTGGSIR 179

Query: 181 QPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTS 240
           QPAS CGVVGLKPTYGRVSRYG++A+ASSLDQ+GP+ R VED A LL A++G D MDSTS
Sbjct: 180 QPASHCGVVGLKPTYGRVSRYGVIAYASSLDQVGPLARNVEDCATLLGAVAGYDPMDSTS 239

Query: 241 ANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLP 300
            +  VPD+L++L   +KG KI +PKEY  +G+  + +++V AA+   +GLGA   EVSLP
Sbjct: 240 VDTPVPDYLATLKDGVKGKKIGLPKEYFIDGLDADVKKAVDAAIATYKGLGAEIVEVSLP 299

Query: 301 HSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIM 360
           H+ YA+A YYL++++EAS+NLAR+DG+RYG R D  + LI +Y QTRA GFG+EVKRRIM
Sbjct: 300 HTDYAVACYYLIATAEASSNLARYDGVRYGVRKDEGEGLIGMYSQTRAAGFGDEVKRRIM 359

Query: 361 LGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLT 420
           LGT+ALSSGYYDAYY KAQKVRTLI++DF D FEK D+++ P  PTPAFKIGE T DPL 
Sbjct: 360 LGTYALSSGYYDAYYLKAQKVRTLIRQDFLDAFEKVDLLLTPVAPTPAFKIGEKTDDPLQ 419

Query: 421 MYANDILTIPVNLAGVPGISVPCG-LADGLPLGLQIIGKHFDESTVYRVAHAFEQATD 477
           MY +DI TIP+NLAG+ GIS+PCG  ++GLP+GLQ++GK F E+ + + A AFE  TD
Sbjct: 420 MYLSDIFTIPLNLAGLCGISLPCGNSSEGLPIGLQLLGKPFAEAEILQAAWAFENTTD 477


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: 631
Number of extensions: 18
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: 485
Length adjustment: 34
Effective length of query: 451
Effective length of database: 451
Effective search space:   203401
Effective search space used:   203401
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_072908350.1 BUB13_RS09635 (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.28460.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-198  646.2   0.0   1.7e-198  646.0   0.0    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072908350.1  BUB13_RS09635 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072908350.1  BUB13_RS09635 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 !  646.0   0.0  1.7e-198  1.7e-198       2     465 ..      12     477 ..      11     478 .. 0.99

  Alignments for each domain:
  == domain 1  score: 646.0 bits;  conditional E-value: 1.7e-198
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdn 68 
                                               +e+l + e++++e+++++l+ri a++dk+n+f++v++ +al++a++ d+++a  +  +++gip+avKd 
  lcl|NCBI__GCF_900142125.1:WP_072908350.1  12 REKLASGETTSVELTKAFLARIAATNDKVNSFITVCEAEALAAAAEADQRIAaGNaAPMTGIPLAVKDI 80 
                                               678889999******************************************975546************ PP

                                 TIGR00132  69 iavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneerv 137
                                               +++ d++ttc+SkiL+nyvspydat + +l+e+ga+iiGk N+DEFamGss e+Sa g++knP++ erv
  lcl|NCBI__GCF_900142125.1:WP_072908350.1  81 FNTLDVRTTCGSKILDNYVSPYDATAIAKLREQGAVIIGKLNMDEFAMGSSNENSAAGPVKNPWDLERV 149
                                               ********************************************************************* PP

                                 TIGR00132 138 pGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakk 206
                                               pGGSsgGsaaa+aa+++  +lg+DTGgSiRqPAs+cgvvGlKPtYG+vSRyG++ayasSldq+G+la++
  lcl|NCBI__GCF_900142125.1:WP_072908350.1 150 PGGSSGGSAAAIAAGQALATLGTDTGGSIRQPASHCGVVGLKPTYGRVSRYGVIAYASSLDQVGPLARN 218
                                               ********************************************************************* PP

                                 TIGR00132 207 vedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekle 275
                                               ved a +l +++g+D +Dsts++++v+++l +lk+ +kg k+g+ ke++ ++ld +vk+++++++ + +
  lcl|NCBI__GCF_900142125.1:WP_072908350.1 219 VEDCATLLGAVAGYDPMDSTSVDTPVPDYLATLKDGVKGKKIGLPKEYFIDGLDADVKKAVDAAIATYK 287
                                               ********************************************************************* PP

                                 TIGR00132 276 elgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkr 344
                                                lgaeivevslp+ ++a+a Yy+i+++Eassnlarydg+ryG r +e + l  +y++tR++gfg+evkr
  lcl|NCBI__GCF_900142125.1:WP_072908350.1 288 GLGAEIVEVSLPHTDYAVACYYLIATAEASSNLARYDGVRYGVRKDEGEGLIGMYSQTRAAGFGDEVKR 356
                                               ********************************************************************* PP

                                 TIGR00132 345 RimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDv 413
                                               RimlG+yals++yyd+yy+kAqkvrtli+++f ++fe+vD++++p+apt afk+gek++dpl+mylsD+
  lcl|NCBI__GCF_900142125.1:WP_072908350.1 357 RIMLGTYALSSGYYDAYYLKAQKVRTLIRQDFLDAFEKVDLLLTPVAPTPAFKIGEKTDDPLQMYLSDI 425
                                               ********************************************************************* PP

                                 TIGR00132 414 ltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                               +t+p+nlaGl++is+P+g++++glpiGlq+ gk f++ ++l++a a+e+++d
  lcl|NCBI__GCF_900142125.1:WP_072908350.1 426 FTIPLNLAGLCGISLPCGNSSEGLPIGLQLLGKPFAEAEILQAAWAFENTTD 477
                                               **********************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (485 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: 9.73
//
[ok]

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