GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Caulobacter crescentus NA1000

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate CCNA_02385 CCNA_02385 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::A0A0D5ZBC4
         (539 letters)



>FitnessBrowser__Caulo:CCNA_02385
          Length = 459

 Score =  561 bits (1445), Expect = e-164
 Identities = 267/453 (58%), Positives = 347/453 (76%), Gaps = 2/453 (0%)

Query: 82  KWTVDSWKSKKALQLP-EYPDQAELESVLKTLDAFPPIVFAGEARSLEEKLGEAAMGNAF 140
           +WT  +W++K A  LP +YPD   +E V +TL   PP+VFAGEAR L+ +LGE A G AF
Sbjct: 4   RWTPAAWRAKPAKHLPTDYPDMGAVERVEQTLRQMPPLVFAGEARRLKSQLGEVAEGRAF 63

Query: 141 LLQGGDCAESFKEFNANNIRDTFRILLQMGAVLMFGGQMPVIKVGRMAGQFAKPRSDPFE 200
           LLQGGDCAESFKEF+A+NIRDTFR++LQM  VL F G  PV+KVGR+AGQFAKPRS+P E
Sbjct: 64  LLQGGDCAESFKEFHADNIRDTFRLILQMAVVLTFAGGKPVVKVGRIAGQFAKPRSEPIE 123

Query: 201 EKNGVKLPSYRGDNVNGDSFDEKSRIPDPQRMIRAYCQSAATLNLLRAFATGGYAAMQRV 260
            +  V LPSYRGD +NG  F+E  R+PDP R+++AY QSAATLNLLRAFA+GGYA +  +
Sbjct: 124 VQGDVTLPSYRGDIINGMDFNEAERVPDPDRLLKAYGQSAATLNLLRAFASGGYADLYNI 183

Query: 261 TQWNLDFTEHSEQGDRYRELASRVDEALGFMAAAGLTVD-HPIMTTTEFWTSHECLLLPY 319
            +W L F   S QG RYREL+ ++ EAL FM+A G+T D  P +   EF+TSHE LLL +
Sbjct: 184 HRWTLGFVGDSPQGARYRELSEKISEALTFMSAVGVTPDTQPDLRRVEFFTSHEALLLGF 243

Query: 320 EQSLTRLDSTSGRYYDCSAHFLWAGERTRQLDGAHVEFLRGVANPLGIKVSDKMDPNELV 379
           E+++TR+DSTSG +YD SAH LW GERTRQLDGAHVEF+RGV NP+G+K    M+ ++L+
Sbjct: 244 EEAMTRVDSTSGDWYDTSAHLLWIGERTRQLDGAHVEFMRGVKNPIGLKCGPTMEGDDLL 303

Query: 380 KLIEILNPQNKAGRITVITRMGAENMRVKLPHLIRAVRRAGQIVTWVSDPMHGNTIKAPC 439
           +LI++LNP N+ GR+T+  R G++ +  +LP L++A + AG+ V W +DPMHGNT+KA  
Sbjct: 304 RLIDVLNPHNEPGRLTLYGRFGSDKIADRLPRLMKATKSAGRSVVWATDPMHGNTLKAST 363

Query: 440 GLKTRPFDSIRAEVRAFFDVHEQEGSHPGGVHLEMTGQNVTECIGGSRTVTFDDLGSRYH 499
           G KTRPFD I +EV++F ++ + EG HPGGVHLEMTGQNVTEC+GG+R V+  DL  RYH
Sbjct: 364 GYKTRPFDRILSEVKSFVEIAQAEGVHPGGVHLEMTGQNVTECLGGARAVSETDLADRYH 423

Query: 500 THCDPRLNASQSLELAFIIAERLRKRRINSPQL 532
           THCDPRLN  Q+LELAF++AE+L+  R +  +L
Sbjct: 424 THCDPRLNGEQALELAFLVAEKLKAARDDQRRL 456


Lambda     K      H
   0.318    0.133    0.393 

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: 688
Number of extensions: 23
Number of successful extensions: 3
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: 539
Length of database: 459
Length adjustment: 34
Effective length of query: 505
Effective length of database: 425
Effective search space:   214625
Effective search space used:   214625
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate CCNA_02385 CCNA_02385 (3-deoxy-7-phosphoheptulonate synthase)
to HMM TIGR01358 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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/TIGR01358.hmm
# target sequence database:        /tmp/gapView.12452.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01358  [M=443]
Accession:   TIGR01358
Description: DAHP_synth_II: 3-deoxy-7-phosphoheptulonate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.7e-242  788.8   0.0   6.6e-242  788.6   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02385  CCNA_02385 3-deoxy-7-phosphohept


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02385  CCNA_02385 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  788.6   0.0  6.6e-242  6.6e-242       1     442 [.       5     449 ..       5     450 .. 0.99

  Alignments for each domain:
  == domain 1  score: 788.6 bits;  conditional E-value: 6.6e-242
                             TIGR01358   1 wsleswrskpaaqlP.eyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkev 72 
                                           w++++wr+kpa++lP +yPd++a+e+v++tl+++PPlv+age+++lk++l+eva+G+afllqgGdcaesfke+
  lcl|FitnessBrowser__Caulo:CCNA_02385   5 WTPAAWRAKPAKHLPtDYPDMGAVERVEQTLRQMPPLVFAGEARRLKSQLGEVAEGRAFLLQGGDCAESFKEF 77 
                                           89*************99******************************************************** PP

                             TIGR01358  73 eadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarvp 145
                                           +adnird++r++lqmavvlt+++++PvvkvgriaGq+akPrsepie++++vtlpsyrGd+ing++f+ea+rvp
  lcl|FitnessBrowser__Caulo:CCNA_02385  78 HADNIRDTFRLILQMAVVLTFAGGKPVVKVGRIAGQFAKPRSEPIEVQGDVTLPSYRGDIINGMDFNEAERVP 150
                                           ************************************************************************* PP

                             TIGR01358 146 dperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvaeae 218
                                           dp+rl++ay +saatlnllra++sgGyadl+++h+W+l fv++sp+gary++l+e+i+eal+fmsavgv++++
  lcl|FitnessBrowser__Caulo:CCNA_02385 151 DPDRLLKAYGQSAATLNLLRAFASGGYADLYNIHRWTLGFVGDSPQGARYRELSEKISEALTFMSAVGVTPDT 223
                                           **********************************************************************998 PP

                             TIGR01358 219 ..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikvgps 289
                                             +l+rve++tshealll +eea+trvds++g+++d+sahllWiGertrqldgahvef+rgvknPig+k+gp+
  lcl|FitnessBrowser__Caulo:CCNA_02385 224 qpDLRRVEFFTSHEALLLGFEEAMTRVDSTSGDWYDTSAHLLWIGERTRQLDGAHVEFMRGVKNPIGLKCGPT 296
                                           899********************************************************************** PP

                             TIGR01358 290 meadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGyktrr 362
                                           me+d+ll+li+vl+P+nePGrltl+ r+G++kia++lP+l++a+k+aGr+vvW+tdpmhGntl+a++Gyktr 
  lcl|FitnessBrowser__Caulo:CCNA_02385 297 MEGDDLLRLIDVLNPHNEPGRLTLYGRFGSDKIADRLPRLMKATKSAGRSVVWATDPMHGNTLKASTGYKTRP 369
                                           ************************************************************************* PP

                             TIGR01358 363 fddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqslelaflv 435
                                           fd+ilsevk+f+e+++aeG+hpGGvhle+tG++vteclGGar+++etdla+ry+t+cdPrln eq+lelaflv
  lcl|FitnessBrowser__Caulo:CCNA_02385 370 FDRILSEVKSFVEIAQAEGVHPGGVHLEMTGQNVTECLGGARAVSETDLADRYHTHCDPRLNGEQALELAFLV 442
                                           ************************************************************************* PP

                             TIGR01358 436 aeklrea 442
                                           aekl++a
  lcl|FitnessBrowser__Caulo:CCNA_02385 443 AEKLKAA 449
                                           ****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (459 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: 00:00:00.02
# Mc/sec: 9.74
//
[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:

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