Alignments for a candidate for aroG in Caulobacter crescentus NA1000

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.20178.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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.14
//
[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