GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Phyllobacterium brassicacearum STM 196

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate WP_106711603.1 CU102_RS13315 succinyl-diaminopimelate desuccinylase

Query= BRENDA::Q9KQ52
         (377 letters)



>NCBI__GCF_003010955.1:WP_106711603.1
          Length = 398

 Score =  283 bits (723), Expect = 8e-81
 Identities = 161/393 (40%), Positives = 224/393 (56%), Gaps = 22/393 (5%)

Query: 1   MTDS--PVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFE-----DTTNFW 53
           MT S  PV  LA +LI+  S+TPA+ G    +   L  LGF +E  VF      D  N +
Sbjct: 1   MTSSIDPVQNLA-QLIACPSITPAEGGALSALQAMLAPLGFSVERPVFSEAGTPDVENLY 59

Query: 54  ARRGTQSPLFVFAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAV 113
           ARR    P  +FAGHTDVVP G    W  PPF   + +G ++GRGA DMKG +AC + AV
Sbjct: 60  ARRSGNGPHLMFAGHTDVVPVGDEGAWTVPPFSAEIRNGEMYGRGAVDMKGGIACFVAAV 119

Query: 114 ERFIAEHPDHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGD 173
            R + ++   +GS+ F+IT DEEGP INGT +++E   AR E  D  IVGEP++   +GD
Sbjct: 120 ARHLEKNGALKGSVSFVITGDEEGPSINGTGKLLEWAKARGEKWDAAIVGEPTNPDKLGD 179

Query: 174 VVKNGRRGSITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSF 233
           ++K GRRGS++G + V G QGH AYPHLA+NPV   +  +  L    +DEG   F PT+ 
Sbjct: 180 MIKIGRRGSLSGTVVVHGVQGHAAYPHLADNPVRGLVTLVDSLLYPVFDEGTKDFQPTNL 239

Query: 234 QIPNLQAGTGASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLD------------AHG 281
           ++  +  G  A NVIP      FN RF+   T E +   +H+ LD            +  
Sbjct: 240 EVTTIDVGNPAVNVIPATATATFNVRFNDTWTGETLMAEIHNRLDQASRRHKLRPGKSEP 299

Query: 282 LDYDVKW-TLSGQPFLTDTGELLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVV 340
           ++YD+ W       FLT   +L+  + +++E+V    P L T+GGTSD RFI      VV
Sbjct: 300 VNYDLNWRNRVSHVFLTHEEKLIGTLSSSIEKVTGNRPQLSTSGGTSDARFIKDY-CPVV 358

Query: 341 ELGPVNATIHKVNECVRIADLEKLTDMYQKTLN 373
           E G V  T+H V+E V +ADLE LT +Y++ ++
Sbjct: 359 EFGLVGKTMHMVDERVALADLETLTQVYERFIS 391


Lambda     K      H
   0.318    0.135    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: 468
Number of extensions: 31
Number of successful extensions: 4
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: 377
Length of database: 398
Length adjustment: 30
Effective length of query: 347
Effective length of database: 368
Effective search space:   127696
Effective search space used:   127696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_106711603.1 CU102_RS13315 (succinyl-diaminopimelate 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.2898748.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-128  414.7   0.0     2e-128  414.4   0.0    1.0  1  NCBI__GCF_003010955.1:WP_106711603.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106711603.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.4   0.0    2e-128    2e-128       5     369 ..      11     392 ..       8     393 .. 0.97

  Alignments for each domain:
  == domain 1  score: 414.4 bits;  conditional E-value: 2e-128
                             TIGR01246   5 akeLisrksvtPndagaqeliaerLkklgfeieilefe.....dtknlwatrgteepvlvfaGhtDvvPaGel 72 
                                           + +Li  +s+tP++ ga++ +++ L  lgf++e+  f      d++nl+a+r  + p+l+faGhtDvvP+G++
  NCBI__GCF_003010955.1:WP_106711603.1  11 LAQLIACPSITPAEGGALSALQAMLAPLGFSVERPVFSeagtpDVENLYARRSGNGPHLMFAGHTDVVPVGDE 83 
                                           578*****************************99877533344899*************************** PP

                             TIGR01246  73 ekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetl 145
                                            +W+ +pf++e+r+G +ygrGa+Dmkg++a+fv+a+ r+++kn   kGs+s++it Deeg +i+Gt k++e+ 
  NCBI__GCF_003010955.1:WP_106711603.1  84 GAWTVPPFSAEIRNGEMYGRGAVDMKGGIACFVAAVARHLEKNGALKGSVSFVITGDEEGPSINGTGKLLEWA 156
                                           ************************************************************************* PP

                             TIGR01246 146 kerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDe 218
                                           k+r e+ d a+vgeP+  +klGD+ikiGrrGs++g++ ++G+qGh aYPh+a+nPv  +v ++  l+   +De
  NCBI__GCF_003010955.1:WP_106711603.1 157 KARGEKWDAAIVGEPTNPDKLGDMIKIGRRGSLSGTVVVHGVQGHAAYPHLADNPVRGLVTLVDSLLYPVFDE 229
                                           ************************************************************************* PP

                             TIGR01246 219 GneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkh............kldY 279
                                           G++ f+p++l+++ i++g+ a nviP+ ++++fn+rf+  ++ e+l  ++++ ld+              ++Y
  NCBI__GCF_003010955.1:WP_106711603.1 230 GTKDFQPTNLEVTTIDVGNPAVNVIPATATATFNVRFNDTWTGETLMAEIHNRLDQAsrrhklrpgksePVNY 302
                                           *******************************************************988999999999988*** PP

                             TIGR01246 280 elewk.lsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneav 351
                                           +l+w+ + ++ flt+e+kli ++ ++ie+v++++p+lstsGGtsDarfi+++ + vve+Glv +t+h v+e+v
  NCBI__GCF_003010955.1:WP_106711603.1 303 DLNWRnRVSHVFLTHEEKLIGTLSSSIEKVTGNRPQLSTSGGTSDARFIKDY-CPVVEFGLVGKTMHMVDERV 374
                                           ****7257999*****************************************.******************** PP

                             TIGR01246 352 kiedleklsevyekllee 369
                                            ++dle l++vye+++++
  NCBI__GCF_003010955.1:WP_106711603.1 375 ALADLETLTQVYERFISD 392
                                           **************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (398 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.74
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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