Alignments for a candidate for DAPtransferase in Desulfobacter vibrioformis DSM 8776

GapMind for Amino acid biosynthesis

Alignments for a candidate for DAPtransferase in Desulfobacter vibrioformis DSM 8776

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_035237791.1 Q366_RS07615 LL-diaminopimelate aminotransferase

Query= BRENDA::O26158
         (410 letters)



>NCBI__GCF_000745975.1:WP_035237791.1
          Length = 408

 Score =  520 bits (1338), Expect = e-152
 Identities = 246/408 (60%), Positives = 314/408 (76%), Gaps = 2/408 (0%)

Query: 1   MVTVNENYLLLKSSYIFSEINRRVEEFQRKNPDADIIRMGIGDVTRPLPEAVVEAFHRAV 60
           M+T NENY  L +SY+F++I +RV+ +Q  NPD ++IR+GIGDVT PLP AVV+ F + V
Sbjct: 1   MITANENYNKLNASYLFADIAKRVQLYQDSNPDKEVIRLGIGDVTLPLPPAVVQGFQKGV 60

Query: 61  DEMAEEETFRGYGPEQGYPFLREAIAENDYASRGVDITADEIFISDGAKCDTGNIQEIFG 120
           DEM+ + TFRGYGPEQGY FLR+AIA  D+ SRG DI ADEIF+SDGAKCDTGN QE+F 
Sbjct: 61  DEMSADATFRGYGPEQGYLFLRQAIAAGDFQSRGADIEADEIFVSDGAKCDTGNFQELFS 120

Query: 121 LDNVVAVTDPVYPVYVESNVMAGRAGPADDDGRYSGLVYLPCTEENSFIPSLPEERVDLI 180
            +  +A+ DPVYPVY+++NVMAGR G   D GRY G+VY+ C +EN F+P LP+  VDLI
Sbjct: 121 NNITIAIPDPVYPVYLDTNVMAGRTGEFKD-GRYQGIVYMDCLKENGFMPDLPDAPVDLI 179

Query: 181 YLCYPNNPTGTTLTEKQLAEWVDYARDSGSLILFDAAYEAYIQEDGIPHSIYEVEGAREV 240
           YLC+PNNPTG+T T  QLA WV+YARD+ +LILFDAAYEA+I++  +P SIYE+ GA+EV
Sbjct: 180 YLCFPNNPTGSTATRDQLAAWVNYARDNKALILFDAAYEAFIRDTDLPRSIYEIPGAKEV 239

Query: 241 AIEFRSFSKNAGFTGTRCAFTVVPEELEVPDSSGRMHSVRELWNRRQTTKFNGVSYPVQR 300
           A+EFRSFSK AGFTGTRC FTVVP+   +  +SG   S+  +WNRRQ+TKFNGVSYPVQ+
Sbjct: 240 AVEFRSFSKTAGFTGTRCGFTVVPKSCMIYTASGSKVSLHNMWNRRQSTKFNGVSYPVQK 299

Query: 301 AAEAVYTPEGQREIRESIDYYMENARIIRESLERAGLRYYGGVNAPYIWIRTPEGMDSWQ 360
           AAEAVY+P GQ +I+ +IDYY+ NA+++ +++   G  + GG NAPYIWI    G DSW+
Sbjct: 300 AAEAVYSPGGQAQIKANIDYYLANAQVVCQTMTDLGFDHVGGKNAPYIWI-DGNGRDSWE 358

Query: 361 FFDTLLNDAEVVGTPGSGFGPSGEGYFRLTAFNSFRNTVKAMERISEL 408
           FFD LL+ A VV TPG GFG  G  Y R++AFNS  N  KAM R+ ++
Sbjct: 359 FFDLLLDKAGVVCTPGQGFGRCGAQYIRISAFNSPENVAKAMARVKDV 406


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: 576
Number of extensions: 21
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: 410
Length of database: 408
Length adjustment: 31
Effective length of query: 379
Effective length of database: 377
Effective search space:   142883
Effective search space used:   142883
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_035237791.1 Q366_RS07615 (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.12614.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-176  572.4   0.0   2.8e-176  572.2   0.0    1.0  1  lcl|NCBI__GCF_000745975.1:WP_035237791.1  Q366_RS07615 LL-diaminopimelate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745975.1:WP_035237791.1  Q366_RS07615 LL-diaminopimelate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.2   0.0  2.8e-176  2.8e-176       2     400 ..       3     405 ..       2     407 .. 0.98

  Alignments for each domain:
  == domain 1  score: 572.2 bits;  conditional E-value: 2.8e-176
                                 TIGR03542   2 kvnehflklkssylfseiakkvkefrkknpeadiirlgiGdvtqPlakaviealkeaveelaseetfrG 70 
                                               + ne+++kl++sylf++iak+v+ ++ +np++++irlgiGdvt Pl++av++ +++ v+e++ + tfrG
  lcl|NCBI__GCF_000745975.1:WP_035237791.1   3 TANENYNKLNASYLFADIAKRVQLYQDSNPDKEVIRLGIGDVTLPLPPAVVQGFQKGVDEMSADATFRG 71 
                                               57******************************************************************* PP

                                 TIGR03542  71 yGpeqGldllreaiaeeeykgr...idpeeifisdGakcdvarllelfgsdktvavqdPvyPvyvdsav 136
                                               yGpeqG+ +lr+aia  ++++r   i+++eif+sdGakcd+++++elf+++ t+a+ dPvyPvy+d++v
  lcl|NCBI__GCF_000745975.1:WP_035237791.1  72 YGPEQGYLFLRQAIAAGDFQSRgadIEADEIFVSDGAKCDTGNFQELFSNNITIAIPDPVYPVYLDTNV 140
                                               *********************999********************************************* PP

                                 TIGR03542 137 laGragvldddgkykkivylpctkenefiPelpeekkvdiiylCsPnnPtGtvltkeqlkelvdyaken 205
                                               +aGr+g+++ dg+y+ ivy+ c+ken+f+P+lp+ + vd+iylC+PnnPtG+++t++ql ++v+ya++n
  lcl|NCBI__GCF_000745975.1:WP_035237791.1 141 MAGRTGEFK-DGRYQGIVYMDCLKENGFMPDLPDAP-VDLIYLCFPNNPTGSTATRDQLAAWVNYARDN 207
                                               *****9997.69************************.******************************** PP

                                 TIGR03542 206 dslilfdaayeafisdpslPksiyeiegakecaieirsfsktlGftGvrlgytvvPkelkvedg....e 270
                                               ++lilfdaayeafi+d +lP+siyei+gake+a+e+rsfskt+GftG+r+g+tvvPk  ++ ++     
  lcl|NCBI__GCF_000745975.1:WP_035237791.1 208 KALILFDAAYEAFIRDTDLPRSIYEIPGAKEVAVEFRSFSKTAGFTGTRCGFTVVPKSCMIYTAsgskV 276
                                               **********************************************************98877667778 PP

                                 TIGR03542 271 slkklWerllctkfnGaslivqraaeavlakeglqqikeaisyymenarilrkaleaaglkvyGGenaP 339
                                               sl+++W+r+++tkfnG+s++vq+aaeav+++ g+ qik  i+yy+ na+++ +++++ g+   GG+naP
  lcl|NCBI__GCF_000745975.1:WP_035237791.1 277 SLHNMWNRRQSTKFNGVSYPVQKAAEAVYSPGGQAQIKANIDYYLANAQVVCQTMTDLGFDHVGGKNAP 345
                                               9******************************************************************** PP

                                 TIGR03542 340 ylWvklpegissedffdkllkeaevvgtPGsGfGssGeGfvrlsalgkredivealerike 400
                                               y+W+  + g +s++ffd ll +a vv tPG+GfG++G  ++r+sa+++ e++++a+ r+k+
  lcl|NCBI__GCF_000745975.1:WP_035237791.1 346 YIWIDGN-GRDSWEFFDLLLDKAGVVCTPGQGFGRCGAQYIRISAFNSPENVAKAMARVKD 405
                                               ****965.69************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (408 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.18
//
[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