Alignments for a candidate for dapE in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Phaeobacter inhibens BS107

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate GFF3587 PGA1_c36420 succinyl-diaminopimelate desuccinylase DapE

Query= SwissProt::Q9JYL2
         (381 letters)



>FitnessBrowser__Phaeo:GFF3587
          Length = 385

 Score =  259 bits (662), Expect = 9e-74
 Identities = 152/371 (40%), Positives = 205/371 (55%), Gaps = 8/371 (2%)

Query: 8   ELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRRGTKAP--VVCF 65
           +L  +LI   SVTP++     LL + L   GF    +  G+  N+  R G K     + F
Sbjct: 10  QLTADLIRCASVTPEEGGALVLLDKVLSAAGFTCTRVDRGEVSNLIARWGDKGHPRTMGF 69

Query: 66  AGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHPNHQG 125
            GHTDVVP G    W   PF   E+DG LYGRGA DMK+ +A FV A    V   P   G
Sbjct: 70  NGHTDVVPVGDTNAWTVDPFGAEEKDGFLYGRGATDMKSGVAAFVAAAIDLVQTTPP-DG 128

Query: 126 SIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRGSLSG 185
           +I L IT DEEGDA+DGTT ++D +    E +  C+VGEPT  DK+G+MIK GRRGSLS 
Sbjct: 129 AILLTITGDEEGDAIDGTTALLDHMDREGEQMAVCLVGEPTCPDKMGEMIKIGRRGSLSA 188

Query: 186 NLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTGAT 245
             TV G QGH AYPH A NP++     +  L     D+G E+F  ++  +  I+ G  AT
Sbjct: 189 WFTVTGVQGHSAYPHRAKNPLNAMVRLMDRLASHELDQGTEHFDASTLAVVTIDTGNPAT 248

Query: 246 NVIPGELNVKFNFRFSTESTEAGLKQRVHA----ILDKHGVQYDLQWSCSGQPFLTQAGK 301
           NVIP +     N RF+   T A L   + A         GV   ++   SG+ F+T  G 
Sbjct: 249 NVIPAQTRSTVNIRFNDAHTGAELSDWLRAEAARAAKDFGVDIAVEIKVSGESFITPPGP 308

Query: 302 LTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDI 361
           L+D+  AA+    G + +LSTTGGTSD RF+K     ++E+G    T+HQ++E V +  I
Sbjct: 309 LSDLVSAAVETETGRKPQLSTTGGTSDARFVKNHC-PVVEVGLVGKTMHQVDERVEIAQI 367

Query: 362 PKLSAVYEGIL 372
            +L ++Y  IL
Sbjct: 368 HQLKSIYGRIL 378


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: 424
Number of extensions: 22
Number of successful extensions: 5
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: 385
Length adjustment: 30
Effective length of query: 351
Effective length of database: 355
Effective search space:   124605
Effective search space used:   124605
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 GFF3587 PGA1_c36420 (succinyl-diaminopimelate desuccinylase DapE)
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.4644.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.2e-118  382.3   0.0   1.4e-118  382.1   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3587  PGA1_c36420 succinyl-diaminopime


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3587  PGA1_c36420 succinyl-diaminopimelate desuccinylase DapE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.1   0.0  1.4e-118  1.4e-118       3     368 ..      10     379 ..       8     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 382.1 bits;  conditional E-value: 1.4e-118
                          TIGR01246   3 elakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgt..eepvlvfaGhtDvvPaGelekWs 76 
                                        +l+ +Li+  svtP++ ga+ l+++ L++ gf++ ++  +++ nl a+ g   +  ++ f GhtDvvP+G++++W+
  lcl|FitnessBrowser__Phaeo:GFF3587  10 QLTADLIRCASVTPEEGGALVLLDKVLSAAGFTCTRVDRGEVSNLIARWGDkgHPRTMGFNGHTDVVPVGDTNAWT 85 
                                        6899*******************************************998854456899***************** PP

                          TIGR01246  77 sdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetlkerdeli 152
                                         dpf +ee+dG+lygrGa+Dmk+++aafv+aa + v+  +   G + l it Deeg+aidGt+++++ +    e++
  lcl|FitnessBrowser__Phaeo:GFF3587  86 VDPFGAEEKDGFLYGRGATDMKSGVAAFVAAAIDLVQTTP-PDGAILLTITGDEEGDAIDGTTALLDHMDREGEQM 160
                                        *********************************9998776.58********************************* PP

                          TIGR01246 153 dyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffppssl 228
                                          ++vgeP++ +k+G++ikiGrrGs+++ ++++G+qGh aYPh+a+nP++ +v+++ +l++ +lD+G+e+f +s l
  lcl|FitnessBrowser__Phaeo:GFF3587 161 AVCLVGEPTCPDKMGEMIKIGRRGSLSAWFTVTGVQGHSAYPHRAKNPLNAMVRLMDRLASHELDQGTEHFDASTL 236
                                        **************************************************************************** PP

                          TIGR01246 229 qianieagtgasnviPgelkvkfnlrfssevseeel....kskvekildkhkldYelewklsgepfltkegklikk 300
                                         +  i++g+ a+nviP++ + + n+rf+  ++ +el    + + ++  +++++d  +e k+sge+f+t  g l + 
  lcl|FitnessBrowser__Phaeo:GFF3587 237 AVVTIDTGNPATNVIPAQTRSTVNIRFNDAHTGAELsdwlRAEAARAAKDFGVDIAVEIKVSGESFITPPGPLSDL 312
                                        *****************************9998776111166777788899************************* PP

                          TIGR01246 301 vaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklle 368
                                        v +a+e  +++kp+lst+GGtsDarf+++  + vve+Glv +t+h+v+e+v+i+++++l+++y ++l+
  lcl|FitnessBrowser__Phaeo:GFF3587 313 VSAAVETETGRKPQLSTTGGTSDARFVKNH-CPVVEVGLVGKTMHQVDERVEIAQIHQLKSIYGRILR 379
                                        *****************************9.********************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (385 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.91
//
[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