Alignments for a candidate for DAPtransferase in Methanothermobacter thermautotrophicus str. Delta H

GapMind for Amino acid biosynthesis

Alignments for a candidate for DAPtransferase in Methanothermobacter thermautotrophicus str. Delta H

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_202943321.1 MTH_RS00260 LL-diaminopimelate aminotransferase

Query= BRENDA::O26158
         (410 letters)



>NCBI__GCF_000008645.1:WP_202943321.1
          Length = 411

 Score =  832 bits (2148), Expect = 0.0
 Identities = 410/410 (100%), Positives = 410/410 (100%)

Query: 1   MVTVNENYLLLKSSYIFSEINRRVEEFQRKNPDADIIRMGIGDVTRPLPEAVVEAFHRAV 60
           MVTVNENYLLLKSSYIFSEINRRVEEFQRKNPDADIIRMGIGDVTRPLPEAVVEAFHRAV
Sbjct: 2   MVTVNENYLLLKSSYIFSEINRRVEEFQRKNPDADIIRMGIGDVTRPLPEAVVEAFHRAV 61

Query: 61  DEMAEEETFRGYGPEQGYPFLREAIAENDYASRGVDITADEIFISDGAKCDTGNIQEIFG 120
           DEMAEEETFRGYGPEQGYPFLREAIAENDYASRGVDITADEIFISDGAKCDTGNIQEIFG
Sbjct: 62  DEMAEEETFRGYGPEQGYPFLREAIAENDYASRGVDITADEIFISDGAKCDTGNIQEIFG 121

Query: 121 LDNVVAVTDPVYPVYVESNVMAGRAGPADDDGRYSGLVYLPCTEENSFIPSLPEERVDLI 180
           LDNVVAVTDPVYPVYVESNVMAGRAGPADDDGRYSGLVYLPCTEENSFIPSLPEERVDLI
Sbjct: 122 LDNVVAVTDPVYPVYVESNVMAGRAGPADDDGRYSGLVYLPCTEENSFIPSLPEERVDLI 181

Query: 181 YLCYPNNPTGTTLTEKQLAEWVDYARDSGSLILFDAAYEAYIQEDGIPHSIYEVEGAREV 240
           YLCYPNNPTGTTLTEKQLAEWVDYARDSGSLILFDAAYEAYIQEDGIPHSIYEVEGAREV
Sbjct: 182 YLCYPNNPTGTTLTEKQLAEWVDYARDSGSLILFDAAYEAYIQEDGIPHSIYEVEGAREV 241

Query: 241 AIEFRSFSKNAGFTGTRCAFTVVPEELEVPDSSGRMHSVRELWNRRQTTKFNGVSYPVQR 300
           AIEFRSFSKNAGFTGTRCAFTVVPEELEVPDSSGRMHSVRELWNRRQTTKFNGVSYPVQR
Sbjct: 242 AIEFRSFSKNAGFTGTRCAFTVVPEELEVPDSSGRMHSVRELWNRRQTTKFNGVSYPVQR 301

Query: 301 AAEAVYTPEGQREIRESIDYYMENARIIRESLERAGLRYYGGVNAPYIWIRTPEGMDSWQ 360
           AAEAVYTPEGQREIRESIDYYMENARIIRESLERAGLRYYGGVNAPYIWIRTPEGMDSWQ
Sbjct: 302 AAEAVYTPEGQREIRESIDYYMENARIIRESLERAGLRYYGGVNAPYIWIRTPEGMDSWQ 361

Query: 361 FFDTLLNDAEVVGTPGSGFGPSGEGYFRLTAFNSFRNTVKAMERISELSF 410
           FFDTLLNDAEVVGTPGSGFGPSGEGYFRLTAFNSFRNTVKAMERISELSF
Sbjct: 362 FFDTLLNDAEVVGTPGSGFGPSGEGYFRLTAFNSFRNTVKAMERISELSF 411


Lambda     K      H
   0.317    0.136    0.403 

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: 800
Number of extensions: 19
Number of successful extensions: 1
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: 410
Length of database: 411
Length adjustment: 31
Effective length of query: 379
Effective length of database: 380
Effective search space:   144020
Effective search space used:   144020
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: 50 (23.9 bits)

Align candidate WP_202943321.1 MTH_RS00260 (LL-diaminopimelate aminotransferase)
to HMM TIGR03542 (LL-diaminopimelate aminotransferase (EC 2.6.1.83))

# 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/TIGR03542.hmm
# target sequence database:        /tmp/gapView.2900412.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03542  [M=402]
Accession:   TIGR03542
Description: DAPAT_plant: LL-diaminopimelate aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.7e-210  683.2   0.0   6.5e-210  683.0   0.0    1.0  1  NCBI__GCF_000008645.1:WP_202943321.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000008645.1:WP_202943321.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  683.0   0.0  6.5e-210  6.5e-210       2     400 ..       4     408 ..       3     410 .. 0.99

  Alignments for each domain:
  == domain 1  score: 683.0 bits;  conditional E-value: 6.5e-210
                             TIGR03542   2 kvnehflklkssylfseiakkvkefrkknpeadiirlgiGdvtqPlakaviealkeaveelaseetfrGyGpe 74 
                                           +vne++l+lkssy+fsei+++v+ef++knp+adiir+giGdvt+Pl++av+ea+++av+e+a+eetfrGyGpe
  NCBI__GCF_000008645.1:WP_202943321.1   4 TVNENYLLLKSSYIFSEINRRVEEFQRKNPDADIIRMGIGDVTRPLPEAVVEAFHRAVDEMAEEETFRGYGPE 76 
                                           79*********************************************************************** PP

                             TIGR03542  75 qGldllreaiaeeeykgr...idpeeifisdGakcdvarllelfgsdktvavqdPvyPvyvdsavlaGragvl 144
                                           qG+++lreaiae++y++r   i+++eifisdGakcd+++++e+fg d++vav+dPvyPvyv+s+v+aGrag +
  NCBI__GCF_000008645.1:WP_202943321.1  77 QGYPFLREAIAENDYASRgvdITADEIFISDGAKCDTGNIQEIFGLDNVVAVTDPVYPVYVESNVMAGRAGPA 149
                                           *******************99**************************************************** PP

                             TIGR03542 145 dddgkykkivylpctkenefiPelpeekkvdiiylCsPnnPtGtvltkeqlkelvdyakendslilfdaayea 217
                                           dddg+y+ +vylpct+en+fiP+lpee+ vd+iylC+PnnPtGt+lt++ql e+vdya++++slilfdaayea
  NCBI__GCF_000008645.1:WP_202943321.1 150 DDDGRYSGLVYLPCTEENSFIPSLPEER-VDLIYLCYPNNPTGTTLTEKQLAEWVDYARDSGSLILFDAAYEA 221
                                           ****************************.******************************************** PP

                             TIGR03542 218 fisdpslPksiyeiegakecaieirsfsktlGftGvrlgytvvPkelkvedg....eslkklWerllctkfnG 286
                                           +i+++ +P+siye+ega+e+aie+rsfsk++GftG+r+++tvvP+el+v d+    +s+++lW+r+++tkfnG
  NCBI__GCF_000008645.1:WP_202943321.1 222 YIQEDGIPHSIYEVEGAREVAIEFRSFSKNAGFTGTRCAFTVVPEELEVPDSsgrmHSVRELWNRRQTTKFNG 294
                                           ***************************************************99999***************** PP

                             TIGR03542 287 aslivqraaeavlakeglqqikeaisyymenarilrkaleaaglkvyGGenaPylWvklpegissedffdkll 359
                                           +s++vqraaeav+++eg+++i+e+i+yymenari+r++le+agl++yGG+naPy+W+++peg++s++ffd+ll
  NCBI__GCF_000008645.1:WP_202943321.1 295 VSYPVQRAAEAVYTPEGQREIRESIDYYMENARIIRESLERAGLRYYGGVNAPYIWIRTPEGMDSWQFFDTLL 367
                                           ************************************************************************* PP

                             TIGR03542 360 keaevvgtPGsGfGssGeGfvrlsalgkredivealerike 400
                                           ++aevvgtPGsGfG+sGeG++rl+a+++ +++v+a+eri+e
  NCBI__GCF_000008645.1:WP_202943321.1 368 NDAEVVGTPGSGFGPSGEGYFRLTAFNSFRNTVKAMERISE 408
                                           ***************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (411 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: 25.65
//
[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