Aligments for a candidate for dapE in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Aligments for a candidate for dapE in Sphingomonas koreensis DSMZ 15582

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate Ga0059261_0797 Ga0059261_0797 succinyldiaminopimelate desuccinylase (EC 3.5.1.18)

Query= SwissProt::Q9JYL2
         (381 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_0797 Ga0059261_0797
           succinyldiaminopimelate desuccinylase (EC 3.5.1.18)
          Length = 373

 Score =  262 bits (669), Expect = 1e-74
 Identities = 152/377 (40%), Positives = 214/377 (56%), Gaps = 14/377 (3%)

Query: 7   LELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKN------IWLRRGTKA 60
           +EL K LI+ PS+TP       +L   L  +GF  +    G+  +      + +R     
Sbjct: 5   VELTKALIAAPSITPAHGSVFDVLEAALRPLGFTVDRFVAGEAPDGPVENLLAVRNAGPG 64

Query: 61  PVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKH 120
           P   FAGH DVVP G  E W S  FEP  R   LYGRGA DMK SIA F  A     A  
Sbjct: 65  PHFAFAGHLDVVPPG--EGWTSGAFEPEVRGDLLYGRGAVDMKGSIAAFAAAVAALPAS- 121

Query: 121 PNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRR 180
               G+++L+IT DEEG A  GT  ++D + A     D C+VGEPT+  +LGD IK GRR
Sbjct: 122 ----GTLSLIITGDEEGPATYGTLALMDRMAAAGLTPDMCLVGEPTSAHRLGDTIKIGRR 177

Query: 181 GSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNING 240
           GS   ++ V G+QGH+AYPHLA NP+     AL E+     DEG ++F P++ +  ++  
Sbjct: 178 GSTVIDIEVPGRQGHVAYPHLADNPIPRLVRALAEIDAIELDEGTDWFQPSNIETIDLTV 237

Query: 241 GTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAG 300
           G  ATNVIPG+ + + + RF+ +     L +R+  I+  H     ++    G+ FLT+ G
Sbjct: 238 GNPATNVIPGKASARLSIRFNDQHRGQDLIERIERIVHAHAPAGIVRGRVYGEAFLTEPG 297

Query: 301 KLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLND 360
            L+ +   AI    GI  ELST+GGTSD RF+  I   ++E G  NAT+H+++E V L+D
Sbjct: 298 TLSTLISDAIEVETGIRPELSTSGGTSDARFLSRIC-PVVEFGLLNATMHKLDEAVALDD 356

Query: 361 IPKLSAVYEGILARLLA 377
           + KL+A+YE +L R+ A
Sbjct: 357 LHKLTAIYETLLRRVYA 373


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: 392
Number of extensions: 27
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: 373
Length adjustment: 30
Effective length of query: 351
Effective length of database: 343
Effective search space:   120393
Effective search space used:   120393
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 Ga0059261_0797 Ga0059261_0797 (succinyldiaminopimelate desuccinylase (EC 3.5.1.18))
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.11281.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-113  365.4   0.0   1.8e-113  365.2   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0797  Ga0059261_0797 succinyldiaminopi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0797  Ga0059261_0797 succinyldiaminopimelate desuccinylase (EC 3.5.1.18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  365.2   0.0  1.8e-113  1.8e-113       1     369 [.       4     370 ..       4     371 .. 0.96

  Alignments for each domain:
  == domain 1  score: 365.2 bits;  conditional E-value: 1.8e-113
                                 TIGR01246   1 vlelakeLisrksvtPndagaqeliaerLkklgfeieilefed.....tknlwatrgt.eepvlvfaGh 63 
                                               v+el+k Li  +s+tP+   + +++++ L+ lgf++++   ++     ++nl+a r+    p+++faGh
  lcl|FitnessBrowser__Korea:Ga0059261_0797   4 VVELTKALIAAPSITPAHGSVFDVLEAALRPLGFTVDRFVAGEapdgpVENLLAVRNAgPGPHFAFAGH 72 
                                               5799********************************9988876233336888887777679******** PP

                                 TIGR01246  64 tDvvPaGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeeg 132
                                                DvvP G  e W+s +fepe+r   lygrGa+Dmkgs+aaf +a+           G+lsl+it Deeg
  lcl|FitnessBrowser__Korea:Ga0059261_0797  73 LDVVPPG--EGWTSGAFEPEVRGDLLYGRGAVDMKGSIAAFAAAVA-----ALPASGTLSLIITGDEEG 134
                                               *******..9*******************************99987.....44568************* PP

                                 TIGR01246 133 eaidGtkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPv 201
                                                a +Gt ++++ + +   ++d+++vgeP+s+++lGD+ikiGrrGs   ++++ G qGhvaYPh+a+nP+
  lcl|FitnessBrowser__Korea:Ga0059261_0797 135 PATYGTLALMDRMAAAGLTPDMCLVGEPTSAHRLGDTIKIGRRGSTVIDIEVPGRQGHVAYPHLADNPI 203
                                               ********************************************************************* PP

                                 TIGR01246 202 hkavpvlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvek 270
                                               +++v++l+e+ ai+lDeG++ f+ps+++  ++++g+ a+nviPg+++++  +rf+ ++  ++l +++e+
  lcl|FitnessBrowser__Korea:Ga0059261_0797 204 PRLVRALAEIDAIELDEGTDWFQPSNIETIDLTVGNPATNVIPGKASARLSIRFNDQHRGQDLIERIER 272
                                               ********************************************************************* PP

                                 TIGR01246 271 ildkhkldYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGl 339
                                               i+++h     ++ ++ ge+flt+ g l + + +aie  ++++pelstsGGtsDarf+ ++ + vve+Gl
  lcl|FitnessBrowser__Korea:Ga0059261_0797 273 IVHAHAPAGIVRGRVYGEAFLTEPGTLSTLISDAIEVETGIRPELSTSGGTSDARFLSRI-CPVVEFGL 340
                                               ************************************************************.******** PP

                                 TIGR01246 340 vndtihkvneavkiedleklsevyekllee 369
                                               +n+t+hk++eav ++dl+kl+++ye+ll++
  lcl|FitnessBrowser__Korea:Ga0059261_0797 341 LNATMHKLDEAVALDDLHKLTAIYETLLRR 370
                                               ***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (373 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: 7.82
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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