Alignments for a candidate for gatD in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatD in Methanosarcina acetivorans C2A

Align glutamyl-tRNA(Gln) amidotransferase subunit D (EC 6.3.5.7) (characterized)
to candidate WP_011021336.1 MA_RS06825 Glu-tRNA(Gln) amidotransferase subunit GatD

Query= metacyc::MONOMER-14998
         (435 letters)



>NCBI__GCF_000007345.1:WP_011021336.1
          Length = 424

 Score =  389 bits (999), Expect = e-113
 Identities = 206/425 (48%), Positives = 277/425 (65%), Gaps = 23/425 (5%)

Query: 19  GDMVLVEKPDVTYEGMVLDRADDADDRHIVLKLENGYNIGVEISDARIELLEKGSEP--- 75
           GD V +E+    YEG V+   +     +I +K+++GYN G  I   RI LLE   E    
Sbjct: 6   GDWVRIERNGTVYEGKVMPSMEG----YITIKMKSGYNAGFSIDKVRITLLENNGETANG 61

Query: 76  -----------RIELPPVEAAEDPELPDVSIISTGGTVASIIDYRTGAVHPAFTADDLLR 124
                        ELP        +LP ++I+STGGT+AS IDYRTGAV   FTADD+L 
Sbjct: 62  SRNGGKGCKTNEEELPE----PGKKLPKIAILSTGGTIASKIDYRTGAVTSQFTADDILA 117

Query: 125 ANPELLDIANIRGRAVFNILSENMKPEYWVETARAVYGEIKDGADGVVVAHGTDTMHYTS 184
           A PEL +IA+ +GR + +ILSENM  + W   ++AV  EI+ GADGV+V HGTDTM Y++
Sbjct: 118 AIPELKEIADFKGRVISSILSENMDSDSWQNLSKAVVEEIEAGADGVIVTHGTDTMMYSA 177

Query: 185 AALSFMLRTPVPVVFTGAQRSSDRPSSDASLNIQCSVRAATSEIAEVTVCMHATMDDLSC 244
           AALSFM++TPVP+VF G+QRS+DRPSSD ++N  C+ R A S+IAEV V MH T  D  C
Sbjct: 178 AALSFMIKTPVPIVFVGSQRSADRPSSDNAMNAICAARVAISDIAEVVVVMHGTTSDDFC 237

Query: 245 HLHRGVKVRKMHTSRRDTFRSMNALPLAEVTPDGIKILE-ENYRKRGSDELELSDRVEER 303
            +HRG KVRK+HTSRRD F+S+N+LP+  V     +I    +Y +RG   L+    +E +
Sbjct: 238 EIHRGTKVRKLHTSRRDAFKSVNSLPVGTVDYGTGEIKTFIDYTRRGEKALKFKPGMEPK 297

Query: 304 VAFIKSYPGISPDIIKWHLDEGYRGIVIEGTGLGHCPDTLIPVIGEAHDMGVPVAMTSQC 363
            A +K  PG  P ++ +++  GY+G+V+EGTGLGH     IP++ +A D  +PV +TSQC
Sbjct: 298 CALVKFTPGADPTVLDYYISNGYKGLVVEGTGLGHISTKWIPLLRKATDAKMPVIVTSQC 357

Query: 364 LNGRVNMNVYSTGRRLLQAGVIPCDDMLPEVAYVKMCWVLGQTDDPEMAREMMRENIAGE 423
           LNGR+   VY TGR +L+AG I  +D LPE A VK+ WVLGQTDD E A  M+RE+++GE
Sbjct: 358 LNGRICDRVYDTGRDMLKAGAIEGEDTLPETALVKLMWVLGQTDDFEKAAGMLREDLSGE 417

Query: 424 INERT 428
           I E T
Sbjct: 418 ITECT 422


Lambda     K      H
   0.318    0.135    0.395 

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: 538
Number of extensions: 25
Number of successful extensions: 4
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: 435
Length of database: 424
Length adjustment: 32
Effective length of query: 403
Effective length of database: 392
Effective search space:   157976
Effective search space used:   157976
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_011021336.1 MA_RS06825 (Glu-tRNA(Gln) amidotransferase subunit GatD)
to HMM TIGR02153 (gatD: glutamyl-tRNA(Gln) amidotransferase, subunit D (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/TIGR02153.hmm
# target sequence database:        /tmp/gapView.3711095.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02153  [M=405]
Accession:   TIGR02153
Description: gatD_arch: glutamyl-tRNA(Gln) amidotransferase, subunit D
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-183  596.4   0.1   1.3e-183  596.2   0.1    1.0  1  NCBI__GCF_000007345.1:WP_011021336.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000007345.1:WP_011021336.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  596.2   0.1  1.3e-183  1.3e-183       1     404 [.      17     423 ..      17     424 .] 0.97

  Alignments for each domain:
  == domain 1  score: 596.2 bits;  conditional E-value: 1.3e-183
                             TIGR02153   1 vfeGvvlpstelseediivlklknGYnvgvkkeeveeievleeekeek..........lekleeeiekkeele 63 
                                           v+eG v+ps    +e++i++k+k+GYn g+++++v+ i++le++ e++           ++ ee +e+ ++l+
  NCBI__GCF_000007345.1:WP_011021336.1  17 VYEGKVMPS----MEGYITIKMKSGYNAGFSIDKVR-ITLLENNGETAngsrnggkgcKTNEEELPEPGKKLP 84 
                                           79*******....78********************7.999999988878999**9996666667788999*** PP

                             TIGR02153  64 kvsilstGGtiaskvdYetGavkpaltaeelleavpelkeianikaravlnilsenmkPesWikiaeevakal 136
                                           k+ ilstGGtiask+dY+tGav++++ta+++l+a+pelkeia++k+r +++ilsenm+ +sW++++++v++++
  NCBI__GCF_000007345.1:WP_011021336.1  85 KIAILSTGGTIASKIDYRTGAVTSQFTADDILAAIPELKEIADFKGRVISSILSENMDSDSWQNLSKAVVEEI 157
                                           ************************************************************************* PP

                             TIGR02153 137 eegadgvvvahGtDtmaytaaaLsFmlkklpvPvvlvGaqRssDRPssDaalnliaavkvakediaevvvvmh 209
                                           e+gadgv+v+hGtDtm+y+aaaLsFm+k+ pvP+v+vG+qRs+DRPssD+a+n i+a++va +diaevvvvmh
  NCBI__GCF_000007345.1:WP_011021336.1 158 EAGADGVIVTHGTDTMMYSAAALSFMIKT-PVPIVFVGSQRSADRPSSDNAMNAICAARVAISDIAEVVVVMH 229
                                           *****************************.******************************************* PP

                             TIGR02153 210 getsDtyvlvhrgvkvrkmhtsRRDaFksinslPlakvdpkekeiellredyrkrgekelelkdkleekvalv 282
                                           g+tsD+++++hrg+kvrk htsRRDaFks+nslP+++vd+ ++ei ++  dy++rgek l++k+++e k+alv
  NCBI__GCF_000007345.1:WP_011021336.1 230 GTTSDDFCEIHRGTKVRKLHTSRRDAFKSVNSLPVGTVDYGTGEI-KTFIDYTRRGEKALKFKPGMEPKCALV 301
                                           ****************************************87665.56789********************** PP

                             TIGR02153 283 kfyPGlspeilealvdkgykgivieGtGlGhvsedlievikkavddgvvvvmtsqclyGrvnlnvYstGRell 355
                                           kf+PG +p +l++++++gykg+v+eGtGlGh+s+++i+ ++ka+d++++v++tsqcl+Gr++++vY+tGR++l
  NCBI__GCF_000007345.1:WP_011021336.1 302 KFTPGADPTVLDYYISNGYKGLVVEGTGLGHISTKWIPLLRKATDAKMPVIVTSQCLNGRICDRVYDTGRDML 374
                                           ************************************************************************* PP

                             TIGR02153 356 kaGvieaedmlpevayvklmwvLgqteeleevrkllkknlageieertl 404
                                           kaG+ie+ed+lpe+a+vklmwvLgqt+++e++  +l+++l+gei+e+t+
  NCBI__GCF_000007345.1:WP_011021336.1 375 KAGAIEGEDTLPETALVKLMWVLGQTDDFEKAAGMLREDLSGEITECTQ 423
                                           *********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (424 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: 26.94
//
[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