Alignments for a candidate for DAPtransferase in Desulfovibrio oxyclinae DSM 11498

GapMind for Amino acid biosynthesis

Alignments for a candidate for DAPtransferase in Desulfovibrio oxyclinae DSM 11498

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_018125202.1 B149_RS0110945 LL-diaminopimelate aminotransferase

Query= BRENDA::O66630
         (387 letters)



>NCBI__GCF_000375485.1:WP_018125202.1
          Length = 388

 Score =  468 bits (1204), Expect = e-136
 Identities = 228/385 (59%), Positives = 290/385 (75%), Gaps = 1/385 (0%)

Query: 2   FEFSDRLKVLPPYLFAELDRKKQEKIEQGVDVIDLGVGDPDMPTPKPIVEAAKKALENPE 61
           F+ +DRL  LPPYLFA +D+ K E   QG+D+I LG+GDPD+PTP+ I++A  +  + P 
Sbjct: 4   FKLADRLATLPPYLFAAIDKAKAEVAAQGIDIISLGIGDPDLPTPEFIIDALHEGAKKPV 63

Query: 62  NHKYPSYVGKYEFRKAVADWYKRRFDVDLDPNTEVITLIGSKEGIAHFPLAFVNPGDIVL 121
           NH+YPSYVG  E+R AVADWY++RF+V+LDP +EV++LIGSKEGIAHFPLA+VNPGD+VL
Sbjct: 64  NHQYPSYVGMLEYRTAVADWYRQRFNVELDPESEVVSLIGSKEGIAHFPLAYVNPGDLVL 123

Query: 122 CPDPAYPVYRIGAIFAGGTPYTVPLKEENNFLPDLDSIPEDVAKKAKIIWINYPNNPTSA 181
              P YPVY     FAGG    +PL EEN+FL DLD++ +D   +AK+I++ YPNNPT+A
Sbjct: 124 VATPNYPVYPAATGFAGGEVQFLPLLEENDFLVDLDAVDDDTWARAKMIFVCYPNNPTAA 183

Query: 182 PPTLEFYKKLVDWAKEYNVIIASDNAYSEI-YTGQEKPPSILQVPGAKDVAIEFHSLSKT 240
             T EFY++LV  AKE+NVI+ SD AYSEI Y    KP SIL+V G KDVAIEFHSLSKT
Sbjct: 184 TATKEFYERLVQKAKEFNVIVVSDLAYSEIYYDPSNKPLSILEVEGGKDVAIEFHSLSKT 243

Query: 241 YNMTGWRIGMAVGNKELVAGLGKVKTNVDSGQFGAVQDAGIVALNLPEEEVEKIRDVYRE 300
           YNMTGWR+ MAVGN++L+AGLGK+K NVDSG F AVQ+AGI AL   E   EK R +Y+E
Sbjct: 244 YNMTGWRVAMAVGNEQLIAGLGKIKENVDSGIFQAVQEAGIAALRHGEPHAEKFRAIYKE 303

Query: 301 RKKIMTEALEKIGLEIYRSDYTFYLWIKVPEGYTSAEFVGRLIDEAGIVCTPGNGFGEYG 360
           R+ ++ +AL  IG++    + +FY+W KVPEG TSA+FV  ++ + G+V TPGNGFG  G
Sbjct: 304 RRDVVCKALSDIGIQHRVPEASFYVWAKVPEGNTSADFVTNVLKQTGVVLTPGNGFGTPG 363

Query: 361 EGYFRISLTVPTERLLEAAERIKNL 385
           EGYFRISLTV  + L EA  RI  L
Sbjct: 364 EGYFRISLTVNNDLLKEAVSRISKL 388


Lambda     K      H
   0.317    0.139    0.413 

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: 525
Number of extensions: 21
Number of successful extensions: 2
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: 387
Length of database: 388
Length adjustment: 30
Effective length of query: 357
Effective length of database: 358
Effective search space:   127806
Effective search space used:   127806
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: 50 (23.9 bits)

Align candidate WP_018125202.1 B149_RS0110945 (LL-diaminopimelate aminotransferase)
to HMM TIGR03540 (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/TIGR03540.hmm
# target sequence database:        /tmp/gapView.16829.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03540  [M=383]
Accession:   TIGR03540
Description: DapC_direct: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-185  603.1   0.0   1.1e-185  602.9   0.0    1.0  1  lcl|NCBI__GCF_000375485.1:WP_018125202.1  B149_RS0110945 LL-diaminopimelat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000375485.1:WP_018125202.1  B149_RS0110945 LL-diaminopimelate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  602.9   0.0  1.1e-185  1.1e-185       1     382 [.       5     387 ..       5     388 .] 0.99

  Alignments for each domain:
  == domain 1  score: 602.9 bits;  conditional E-value: 1.1e-185
                                 TIGR03540   1 klaerleklPPylfaeidklkaekkakGvdvidlgiGdPdlptpkeivealkkaaekpenhryPsyeGl 69 
                                               kla+rl++lPPylfa+idk+kae++a+G+d+i+lgiGdPdlptp+ i++al + a+kp nh+yPsy+G+
  lcl|NCBI__GCF_000375485.1:WP_018125202.1   5 KLADRLATLPPYLFAAIDKAKAEVAAQGIDIISLGIGDPDLPTPEFIIDALHEGAKKPVNHQYPSYVGM 73 
                                               589****************************************************************** PP

                                 TIGR03540  70 layrkavadwykkrfgveldpetevlsliGskeGiahlplafvnpGdivlvpdPgyPvykistllagge 138
                                               l+yr avadwy++rf+veldpe+ev+sliGskeGiah+pla+vnpGd+vlv+ P yPvy  +t +agge
  lcl|NCBI__GCF_000375485.1:WP_018125202.1  74 LEYRTAVADWYRQRFNVELDPESEVVSLIGSKEGIAHFPLAYVNPGDLVLVATPNYPVYPAATGFAGGE 142
                                               ********************************************************************* PP

                                 TIGR03540 139 pyelPlkeendflPdldaipedvlkkakilflnyPnnPtsavadkeffkevvefakeyniivvhdaays 207
                                               ++ lPl+eendfl dlda+++d++ +ak++f+ yPnnPt+a+a+kef++++v+ ake n+ivv+d ays
  lcl|NCBI__GCF_000375485.1:WP_018125202.1 143 VQFLPLLEENDFLVDLDAVDDDTWARAKMIFVCYPNNPTAATATKEFYERLVQKAKEFNVIVVSDLAYS 211
                                               ********************************************************************* PP

                                 TIGR03540 208 eivfd.eykalsflevdgakdvaielhslsktynmtGWrigfavGnkeliaalgkvksnvdsGvfqaiq 275
                                               ei++d  +k+ls+lev+g kdvaie+hslsktynmtGWr+++avGn++lia+lgk+k+nvdsG+fqa+q
  lcl|NCBI__GCF_000375485.1:WP_018125202.1 212 EIYYDpSNKPLSILEVEGGKDVAIEFHSLSKTYNMTGWRVAMAVGNEQLIAGLGKIKENVDSGIFQAVQ 280
                                               ****9457899********************************************************** PP

                                 TIGR03540 276 eaaiaaleeeeevvkelrkvykkrrdllvealkkiGldvkkpkatfylWvkvPeGytsaefakklleea 344
                                               ea+iaal++ e   ++ r++yk+rrd++++al +iG++ + p+a+fy+W+kvPeG tsa+f++++l+++
  lcl|NCBI__GCF_000375485.1:WP_018125202.1 281 EAGIAALRHGEPHAEKFRAIYKERRDVVCKALSDIGIQHRVPEASFYVWAKVPEGNTSADFVTNVLKQT 349
                                               ********************************************************************* PP

                                 TIGR03540 345 gvvvtpGvgfGesGeGyirisltvseerlkeaverlkk 382
                                               gvv+tpG+gfG+ GeGy+risltv+++ lkeav+r++k
  lcl|NCBI__GCF_000375485.1:WP_018125202.1 350 GVVLTPGNGFGTPGEGYFRISLTVNNDLLKEAVSRISK 387
                                               ************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (383 nodes)
Target sequences:                          1  (388 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: 6.76
//
[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