Alignments for a candidate for gatA in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Methanosarcina acetivorans C2A

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_048066007.1 MA_RS23590 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000007345.1:WP_048066007.1
          Length = 475

 Score =  507 bits (1306), Expect = e-148
 Identities = 253/468 (54%), Positives = 338/468 (72%), Gaps = 8/468 (1%)

Query: 17  KKEIKISDLVDESYKRIQAVD-DKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMP 75
           K +IK S   + +   ++ ++  K+  ++ + ++     A E  + +D     G L G+P
Sbjct: 11  KDKIKESSAEEVTAGYLEVIEKSKINGYITVSDK-----ALEQAKKIDVEGHEGPLAGVP 65

Query: 76  IGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTEN 135
           I +KDNI   GL  +C SKILE + P ++A V+++L DA AV +GK N+DEFAMGSSTE 
Sbjct: 66  IAIKDNISVVGLPNSCGSKILEGYVPPFNAHVIEKLLDAGAVILGKTNLDEFAMGSSTET 125

Query: 136 SAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTY 195
           S Y  T NPW+L+ VPGGSSGGSAA VAAGE PF+LGSDTGGS+R PA+FCGVVGLKPTY
Sbjct: 126 SYYGPTANPWDLERVPGGSSGGSAAVVAAGEAPFALGSDTGGSVRCPAAFCGVVGLKPTY 185

Query: 196 GRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLTGD 255
           G VSRYG+VA+A+SL+Q+GP+   VED A L+  I+G D+ DSTS +    ++  +L  D
Sbjct: 186 GAVSRYGVVAYANSLEQVGPLANNVEDIAILMDVIAGYDRRDSTSID-SKTEYQKALVDD 244

Query: 256 IKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSSS 315
           +KGLKI VPKE+ GEG+     ++V  A+   E LGAT +EVS+P+  YALA+YY+++ S
Sbjct: 245 VKGLKIGVPKEFFGEGIHPGVEKAVWNAIHKFESLGATRQEVSMPNINYALASYYIIAMS 304

Query: 316 EASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAYY 375
           EAS+NLARFDG RYG+R  N +N   +  +TRAEGFG EVKRRI+LGT+ALS+GY+D YY
Sbjct: 305 EASSNLARFDGTRYGFRA-NGENWHAMVSKTRAEGFGTEVKRRILLGTYALSAGYHDKYY 363

Query: 376 KKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIPVNLAG 435
            KA KVRTL+K+DF+      D+++ PT P PAF+IGE  +DPLT+Y +D+ T P+NLAG
Sbjct: 364 LKALKVRTLVKQDFDKALSTVDLLMAPTMPNPAFRIGEKIEDPLTLYLSDVNTCPINLAG 423

Query: 436 VPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483
           VP +SVPCG  DGLP+GLQI+GK FDE TV R A+ FE+ TD+H  +P
Sbjct: 424 VPSVSVPCGFTDGLPVGLQIMGKPFDEPTVLRAAYTFEKNTDYHTKRP 471


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: 636
Number of extensions: 29
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: 475
Length adjustment: 34
Effective length of query: 451
Effective length of database: 441
Effective search space:   198891
Effective search space used:   198891
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: 51 (24.3 bits)

Align candidate WP_048066007.1 MA_RS23590 (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.16745.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.8e-194  631.1   0.0   6.9e-194  630.8   0.0    1.0  1  NCBI__GCF_000007345.1:WP_048066007.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000007345.1:WP_048066007.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  630.8   0.0  6.9e-194  6.9e-194       8     465 ..      15     465 ..       7     466 .. 0.96

  Alignments for each domain:
  == domain 1  score: 630.8 bits;  conditional E-value: 6.9e-194
                             TIGR00132   8 kevsikevleeilerieavkdkinaflevtkekalkkakkldkkvakekklagipiavKdniavkdiettcaS 80 
                                           ke s++ev+  +le ie+  +kin +++v+++ al++akk+d +  +e +lag+pia+Kdni+v +++ +c+S
  NCBI__GCF_000007345.1:WP_048066007.1  15 KESSAEEVTAGYLEVIEK--SKINGYITVSDK-ALEQAKKIDVEG-HEGPLAGVPIAIKDNISVVGLPNSCGS 83 
                                           566667777777777765..578*****9876.*********977.668************************ PP

                             TIGR00132  81 kiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaavaadl 153
                                           kiLe+yv+p++a+V+e+l +aga+i+GktNlDEFamGsstetS++g+t+nP++ ervpGGSsgGsaa+vaa++
  NCBI__GCF_000007345.1:WP_048066007.1  84 KILEGYVPPFNAHVIEKLLDAGAVILGKTNLDEFAMGSSTETSYYGPTANPWDLERVPGGSSGGSAAVVAAGE 156
                                           ************************************************************************* PP

                             TIGR00132 154 vplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkkDst 226
                                           +p+algsDTGgS+R+PA+fcgvvGlKPtYG+vSRyG+vaya+Sl+q+G+la++vedia+++dvi+g+D +Dst
  NCBI__GCF_000007345.1:WP_048066007.1 157 APFALGSDTGGSVRCPAAFCGVVGLKPTYGAVSRYGVVAYANSLEQVGPLANNVEDIAILMDVIAGYDRRDST 229
                                           ************************************************************************* PP

                             TIGR00132 227 slevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyii 299
                                           s+++k+ e+ ++l +d+kglk+gv ke+++e+++ +v++++ ++++k+e+lga+ +evs+p++++ala Yyii
  NCBI__GCF_000007345.1:WP_048066007.1 230 SIDSKT-EYQKALVDDVKGLKIGVPKEFFGEGIHPGVEKAVWNAIHKFESLGATRQEVSMPNINYALASYYII 301
                                           ****77.7999**9*********************************************************** PP

                             TIGR00132 300 spsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtli 372
                                           ++sEassnlar+dg ryG r++  + ++ +++ktR+egfg+evkrRi+lG+yals++y dkyy+kA kvrtl+
  NCBI__GCF_000007345.1:WP_048066007.1 302 AMSEASSNLARFDGTRYGFRANGEN-WHAMVSKTRAEGFGTEVKRRILLGTYALSAGYHDKYYLKALKVRTLV 373
                                           *********************9999.*********************************************** PP

                             TIGR00132 373 idefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiig 445
                                           +++f+k+++ vD++++pt+p  af++gek edpl+ ylsDv t p+nlaG+p++svP+g + +glp+Glqi+g
  NCBI__GCF_000007345.1:WP_048066007.1 374 KQDFDKALSTVDLLMAPTMPNPAFRIGEKIEDPLTLYLSDVNTCPINLAGVPSVSVPCGFT-DGLPVGLQIMG 445
                                           *************************************************************.8********** PP

                             TIGR00132 446 kafddkkllsvakaleqald 465
                                           k fd+ ++l++a+++e+++d
  NCBI__GCF_000007345.1:WP_048066007.1 446 KPFDEPTVLRAAYTFEKNTD 465
                                           ****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (475 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 15.28
//
[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