Alignments for a candidate for gatA in Methanothermobacter thermautotrophicus Delta H

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Methanothermobacter thermautotrophicus Delta H

Align Glutamyl-tRNA(Gln) amidotransferase subunit A, chloroplastic/mitochondrial; Glu-AdT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_048061065.1 MTH_RS07145 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= SwissProt::Q9LI77
         (537 letters)



>NCBI__GCF_000008645.1:WP_048061065.1
          Length = 451

 Score =  318 bits (814), Expect = 4e-91
 Identities = 191/445 (42%), Positives = 252/445 (56%), Gaps = 30/445 (6%)

Query: 59  TAVEIAKSYLSRIRLTEPQLKCFLHV-SENVLKDAQEIDQRIAKGEELGPLAGVLIGVKD 117
           TA E  + +L RI      +  FL V  E  +K A+EID RIA G+E G LAG++IGVK 
Sbjct: 16  TASENLEKFLKRIEAKNDDINAFLEVRGEEAIKRAEEIDARIASGKETGKLAGLVIGVKS 75

Query: 118 NICTQGMPSTAASRILEHYRPPFDATAVKKIKELGGIVVGKTNMDEFGMGSTTEASAFQV 177
           NI  +    +AAS+ LE+Y   +DAT +++IKE  GI++G TNMDEF  GS+TE S F  
Sbjct: 76  NINVEDFNVSAASKTLENYTGSYDATVIRRIKEEDGIIIGMTNMDEFAAGSSTETSFFGP 135

Query: 178 TANPWDLSRVPGGSSGGSAAAVAARQCMVSLGSDTGGSVRQPASFCGVVGLKPTYGRVSR 237
           T NP    R+PGGSSGGSAAAVAA  C ++LGSDTGGS+R PAS CGV+G KPTYG VSR
Sbjct: 136 TDNPAAPGRIPGGSSGGSAAAVAAGMCDLALGSDTGGSIRNPASHCGVMGFKPTYGAVSR 195

Query: 238 FGLMAYASSLDVIGCFGSTVADAGMLLHAISGYDRFDSTSSKQDVPEFQSQFLSVDHFES 297
            GL+  A S D IG   + V+   + L  ISGYD  D T+             S D    
Sbjct: 196 QGLLDLAMSFDQIGPLAADVSGISLALDVISGYDPADPTTLDS----------SPDLEVE 245

Query: 298 KPLNGVKVGIIRETLEDGVDSGVRSATQEAASHLEALGCILTEVSLPSFSLGLPAYYVIA 357
           + L G++VG++RE LE   D  +    Q     +E  G  + E+      L LP YY+I 
Sbjct: 246 RELKGLRVGVVREFLE-VTDEAIDEVIQGKLGAMEDEGAEIVELDFGYIDLCLPTYYLIN 304

Query: 358 SSESSSNLSRYDGVRYGNQVMAEELNKLYECSRGEGFGGEVKMRILMGTYALSAGYYDAY 417
             E  S   +YDG +YG+++              +  G EV  RI MG+Y         Y
Sbjct: 305 YVEFFSATRKYDGRKYGHRI-------------EDVCGSEVLRRIHMGSYISQKELSGKY 351

Query: 418 YKRAQQVRTLIRKDFKAALEQNDILISPAAPSAAYKIGEKKDDPLAMYAGDIMTVNVNLA 477
           YKRA Q R+LIR++    L   DI+  P  P   + +GE+  +P+ MYA D++TV  NLA
Sbjct: 352 YKRALQARSLIRREITGLLSHVDIIAGPTVPKLPHTLGEEL-EPMEMYAYDVLTVIANLA 410

Query: 478 GLPAMVLPCGLVEGGPSGLPVGLQM 502
           G+PA  +P G V     G+PVGLQ+
Sbjct: 411 GIPAASIPAGDV----GGVPVGLQL 431


Lambda     K      H
   0.316    0.133    0.375 

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: 576
Number of extensions: 25
Number of successful extensions: 5
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: 537
Length of database: 451
Length adjustment: 34
Effective length of query: 503
Effective length of database: 417
Effective search space:   209751
Effective search space used:   209751
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_048061065.1 MTH_RS07145 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A)
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.6957.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.9e-181  588.8   0.0   4.5e-181  588.6   0.0    1.0  1  lcl|NCBI__GCF_000008645.1:WP_048061065.1  MTH_RS07145 Asp-tRNA(Asn)/Glu-tR


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008645.1:WP_048061065.1  MTH_RS07145 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  588.6   0.0  4.5e-181  4.5e-181       3     461 ..       8     449 ..       6     451 .] 0.98

  Alignments for each domain:
  == domain 1  score: 588.6 bits;  conditional E-value: 4.5e-181
                                 TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..kek.klagipiavKdn 68 
                                               +++k++ ++++e+le++l+riea++d+inaflev+ e+a+k+a+++d+++a  ke+ klag++i+vK+n
  lcl|NCBI__GCF_000008645.1:WP_048061065.1   8 DMIKNHGLTASENLEKFLKRIEAKNDDINAFLEVRGEEAIKRAEEIDARIAsgKETgKLAGLVIGVKSN 76 
                                               68999*********************************************9976645************ PP

                                 TIGR00132  69 iavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneerv 137
                                               i+v+d+++++aSk+Leny+++ydatV++r+ke++ +iiG+tN+DEFa+GsstetS+fg+t+nP++  r+
  lcl|NCBI__GCF_000008645.1:WP_048061065.1  77 INVEDFNVSAASKTLENYTGSYDATVIRRIKEEDGIIIGMTNMDEFAAGSSTETSFFGPTDNPAAPGRI 145
                                               ********************************************************************* PP

                                 TIGR00132 138 pGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakk 206
                                               pGGSsgGsaaavaa++++lalgsDTGgSiR+PAs+cgv+G+KPtYG+vSR+Gl+++a+S+dqiG+la++
  lcl|NCBI__GCF_000008645.1:WP_048061065.1 146 PGGSSGGSAAAVAAGMCDLALGSDTGGSIRNPASHCGVMGFKPTYGAVSRQGLLDLAMSFDQIGPLAAD 214
                                               ********************************************************************* PP

                                 TIGR00132 207 vedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekle 275
                                               v+ i+l ldvisg+D +D+t+l+++++    e++++lkgl+vgvv+e+ e+ +d++++e ++ +l ++e
  lcl|NCBI__GCF_000008645.1:WP_048061065.1 215 VSGISLALDVISGYDPADPTTLDSSPD---LEVERELKGLRVGVVREFLEV-TDEAIDEVIQGKLGAME 279
                                               ************************998...4445559**************.***************** PP

                                 TIGR00132 276 elgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkr 344
                                               ++gaeive+++ +++l+l++Yy+i+++E++s++++ydg++yG+r+e+++              g+ev r
  lcl|NCBI__GCF_000008645.1:WP_048061065.1 280 DEGAEIVELDFGYIDLCLPTYYLINYVEFFSATRKYDGRKYGHRIEDVC--------------GSEVLR 334
                                               *************************************************..............****** PP

                                 TIGR00132 345 RimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDv 413
                                               Ri++G+y+++ke ++kyyk+A ++r+li++e+++l+++vD+i++pt+p+l+++lge+ e p+emy++Dv
  lcl|NCBI__GCF_000008645.1:WP_048061065.1 335 RIHMGSYISQKELSGKYYKRALQARSLIRREITGLLSHVDIIAGPTVPKLPHTLGEELE-PMEMYAYDV 402
                                               ***********************************************************.********* PP

                                 TIGR00132 414 ltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakale 461
                                               ltv+anlaG+pa+s+P+g+   g+p+Glq+++k  dd +++s++++++
  lcl|NCBI__GCF_000008645.1:WP_048061065.1 403 LTVIANLAGIPAASIPAGDV-GGVPVGLQLQAKPGDDGMIVSAMREIA 449
                                               ********************.6*********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (451 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.58
//
[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