Alignments for a candidate for dapE in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Paraburkholderia bryophila 376MFSha3.1

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate H281DRAFT_00597 H281DRAFT_00597 succinyldiaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>FitnessBrowser__Burk376:H281DRAFT_00597
          Length = 379

 Score =  474 bits (1221), Expect = e-138
 Identities = 232/376 (61%), Positives = 282/376 (75%), Gaps = 4/376 (1%)

Query: 6   SLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRR----GTKAP 61
           +L L ++LI+R SVTPDD+ CQ+LL ERL  +GF  E +      N+W  +    G    
Sbjct: 4   TLALTEQLIARASVTPDDQHCQRLLIERLSALGFEHETIESNGVTNLWAVKRGVDGRAGK 63

Query: 62  VVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHP 121
           ++ FAGHTDVVPTGP+E+W S PFEP  RDG+LYGRGAADMKTSIA FV A E FVA HP
Sbjct: 64  LLAFAGHTDVVPTGPLEQWQSAPFEPTHRDGKLYGRGAADMKTSIAGFVVASEEFVAAHP 123

Query: 122 NHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRG 181
            H+GSIA LITSDEEG A DGT KVV+ L+AR E +DYCIVGEPT+  + GD +KNGRRG
Sbjct: 124 RHRGSIAFLITSDEEGPATDGTVKVVEALQARGERMDYCIVGEPTSSTQFGDTVKNGRRG 183

Query: 182 SLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGG 241
           S+SG L VKG QGHIAYPHLA NPVH  APAL EL  E WD+GNEYFPPT++Q+SNI+ G
Sbjct: 184 SMSGKLVVKGVQGHIAYPHLARNPVHLLAPALAELVAERWDDGNEYFPPTTWQVSNIHSG 243

Query: 242 TGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGK 301
           TGATNVIPG  +V FNFRFST ST  GL+QRVHAILD+HG++YDLQW+ SG PFLT  G 
Sbjct: 244 TGATNVIPGHADVMFNFRFSTASTVEGLQQRVHAILDRHGLEYDLQWTVSGLPFLTPHGD 303

Query: 302 LTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDI 361
           L++    AI +  G+  ELSTTGGTSDGRFI  I Q+++E GP NA+IH+I+E++ +  I
Sbjct: 304 LSNALAKAIKDETGVSTELSTTGGTSDGRFIARICQQVVEFGPLNASIHKIDEHIDVAHI 363

Query: 362 PKLSAVYEGILARLLA 377
             L  VY  +L +L+A
Sbjct: 364 EPLKNVYRRVLEQLIA 379


Lambda     K      H
   0.317    0.135    0.400 

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: 506
Number of extensions: 18
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: 381
Length of database: 379
Length adjustment: 30
Effective length of query: 351
Effective length of database: 349
Effective search space:   122499
Effective search space used:   122499
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 H281DRAFT_00597 H281DRAFT_00597 (succinyldiaminopimelate desuccinylase)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

# 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/TIGR01246.hmm
# target sequence database:        /tmp/gapView.26989.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01246  [M=370]
Accession:   TIGR01246
Description: dapE_proteo: succinyl-diaminopimelate desuccinylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.7e-165  535.0   0.0   5.4e-165  534.8   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00597  H281DRAFT_00597 succinyldiaminop


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00597  H281DRAFT_00597 succinyldiaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.8   0.0  5.4e-165  5.4e-165       3     370 .]       6     377 ..       4     377 .. 0.98

  Alignments for each domain:
  == domain 1  score: 534.8 bits;  conditional E-value: 5.4e-165
                                    TIGR01246   3 elakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgt....eepvlvfaGht 64 
                                                  +l+++Li r svtP+d+ +q l++erL++lgfe e++e ++++nlwa ++       + l+faGht
  lcl|FitnessBrowser__Burk376:H281DRAFT_00597   6 ALTEQLIARASVTPDDQHCQRLLIERLSALGFEHETIESNGVTNLWAVKRGvdgrAGKLLAFAGHT 71 
                                                  6899******************************************9775557767889******* PP

                                    TIGR01246  65 DvvPaGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDe 130
                                                  DvvP+G+le+W+s pfep++rdGklygrGaaDmk+s+a fvva+e+fv++++ h+Gs+++litsDe
  lcl|FitnessBrowser__Burk376:H281DRAFT_00597  72 DVVPTGPLEQWQSAPFEPTHRDGKLYGRGAADMKTSIAGFVVASEEFVAAHPRHRGSIAFLITSDE 137
                                                  ****************************************************************** PP

                                    TIGR01246 131 egeaidGtkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhk 196
                                                  eg a dGt+kvve l++r e +dy++vgeP+s+ + GD++k+GrrGs++gkl +kG+qGh+aYPh+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00597 138 EGPATDGTVKVVEALQARGERMDYCIVGEPTSSTQFGDTVKNGRRGSMSGKLVVKGVQGHIAYPHL 203
                                                  ****************************************************************** PP

                                    TIGR01246 197 aenPvhkavpvlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevsee 262
                                                  a+nPvh ++p+l+el+a+++D+Gne+fpp+  q++ni++gtga+nviPg+++v+fn+rfs+ +++e
  lcl|FitnessBrowser__Burk376:H281DRAFT_00597 204 ARNPVHLLAPALAELVAERWDDGNEYFPPTTWQVSNIHSGTGATNVIPGHADVMFNFRFSTASTVE 269
                                                  ****************************************************************** PP

                                    TIGR01246 263 elkskvekildkhkldYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfia 328
                                                   l+++v++ild+h+l+Y+l+w++sg pflt +g+l +++a+ai+  ++ ++elst+GGtsD+rfia
  lcl|FitnessBrowser__Burk376:H281DRAFT_00597 270 GLQQRVHAILDRHGLEYDLQWTVSGLPFLTPHGDLSNALAKAIKDETGVSTELSTTGGTSDGRFIA 335
                                                  ****************************************************************** PP

                                    TIGR01246 329 klgaevvelGlvndtihkvneavkiedleklsevyeklleel 370
                                                  ++ ++vve+G++n++ihk++e++ ++ +e l++vy+++le+l
  lcl|FitnessBrowser__Burk376:H281DRAFT_00597 336 RICQQVVEFGPLNASIHKIDEHIDVAHIEPLKNVYRRVLEQL 377
                                                  ***************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (379 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: 00:00:00.01
# Mc/sec: 8.09
//
[ok]

This GapMind analysis is from Apr 09 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