GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Epibacterium ulvae U95

Align Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplastic; 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 2; DAHP synthase 2; PhDAHP2; Phospho-2-keto-3-deoxyheptonate aldolase 2; EC 2.5.1.54 (characterized)
to candidate WP_090217168.1 CV091_RS03245 3-deoxy-7-phosphoheptulonate synthase class II

Query= SwissProt::A0A067XGX8
         (512 letters)



>NCBI__GCF_002796795.1:WP_090217168.1
          Length = 456

 Score =  527 bits (1357), Expect = e-154
 Identities = 260/448 (58%), Positives = 333/448 (74%), Gaps = 4/448 (0%)

Query: 60  TKWNLESWKTKPAFQLPDYPDKVELESVLKTLSTYPPIVFAGEARNLEEKLGEAALGNAF 119
           T W   +W+ KP  Q+PDY D   L +V   LS YPP+VFAGEAR L+++LG A  G AF
Sbjct: 2   TTWQKTNWRNKPRIQMPDYTDADALNAVEAQLSKYPPLVFAGEARRLKQQLGAAGRGEAF 61

Query: 120 LLQGGDCAESFKEFSANNIRDTFRVMLQMGVVLMFGGQMPVIKVGRMAGQFAKPRSDPFE 179
           LLQGGDCAESF +FSA+ IRDTF+VMLQM +VL +G ++PV+KVGRMAGQFAKPRS P E
Sbjct: 62  LLQGGDCAESFDQFSADAIRDTFKVMLQMAMVLTYGAKVPVVKVGRMAGQFAKPRSAPTE 121

Query: 180 EKDGVKLPSYRGDNVNGDAFDEKSRIPDPHRMVRAYTQSVATLNLLRAFASGGYAAMQRV 239
             DG++LPSYRGD +N  AF  ++RIP+P +M++AYTQ+ ATLNLLRAF++GGYA + +V
Sbjct: 122 TIDGLELPSYRGDIINDLAFTPEARIPNPQKMLQAYTQAAATLNLLRAFSTGGYADINQV 181

Query: 240 NQWNLDFTDQSEQGDRYRELAHRVDEAMGFMTAAGLTVD--HTIMTTTDFWTSHECLLLP 297
           + W L FT+ SE+ D YR++A+R+ + + FM AAG+  D  HT+ +  DF+TSHE LLL 
Sbjct: 182 HAWTLGFTE-SEKVDAYRDMANRITDTLDFMNAAGVNKDTAHTLHSV-DFYTSHEGLLLE 239

Query: 298 YEQALTREDSTSGLYYDCSAHMIWVGERTRQLDGAHVEFLRGIANPLGIKVSHKMDPDEL 357
           YE+ALTREDSTSG +   S HMIW+G+RTRQ DGAHVEF  G+ NP+G+K       ++L
Sbjct: 240 YEEALTREDSTSGDWLAGSGHMIWIGDRTRQPDGAHVEFCSGVLNPIGLKCGPTTTAEDL 299

Query: 358 VKLIDILNPQNKPGRITVITRMGADNMRVKLPHLIRAVRGAGQIVTWVSDPMHGNTTKAP 417
             L+  LNP+N+ GR+T+I R GA      LP L++AV+  G  VTWV DPMHGNT K+ 
Sbjct: 300 KVLMKKLNPENEEGRLTLIARFGAGKAAEHLPRLVQAVKEEGATVTWVCDPMHGNTIKSS 359

Query: 418 CGLKTRSFDSIRAELRAFFDVHEQEGSYPGGVHLEMTGQNVTECVGGSRTITYNDLSSRY 477
            G KTR F+++  E+R FF+VH  EG+ PGGVH EMTGQ+VTEC GG R +T  DLS+RY
Sbjct: 360 TGYKTRPFENVLREVRDFFEVHNAEGTVPGGVHFEMTGQDVTECTGGIRAVTDEDLSARY 419

Query: 478 HTHCDPRLNASQALELAFAIAERLRRRR 505
           HT CDPRLNASQ+LELAF +AE L  +R
Sbjct: 420 HTACDPRLNASQSLELAFLVAEELSNQR 447


Lambda     K      H
   0.319    0.134    0.401 

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: 658
Number of extensions: 20
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: 512
Length of database: 456
Length adjustment: 34
Effective length of query: 478
Effective length of database: 422
Effective search space:   201716
Effective search space used:   201716
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate WP_090217168.1 CV091_RS03245 (3-deoxy-7-phosphoheptulonate synthase class II)
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.2359771.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-212  691.4   0.0   2.5e-212  691.1   0.0    1.0  1  NCBI__GCF_002796795.1:WP_090217168.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002796795.1:WP_090217168.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  691.1   0.0  2.5e-212  2.5e-212       1     442 [.       4     446 ..       4     447 .. 0.99

  Alignments for each domain:
  == domain 1  score: 691.1 bits;  conditional E-value: 2.5e-212
                             TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkeve 73 
                                           w++  wr+kp  q+P+y da+al+av+++l+++PPlv+age+++lk++l+++ +GeafllqgGdcaesf++++
  NCBI__GCF_002796795.1:WP_090217168.1   4 WQKTNWRNKPRIQMPDYTDADALNAVEAQLSKYPPLVFAGEARRLKQQLGAAGRGEAFLLQGGDCAESFDQFS 76 
                                           77899******************************************************************** PP

                             TIGR01358  74 adnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarvpd 146
                                           ad ird+++v+lqma+vltyga++Pvvkvgr+aGq+akPrs+p+e+ dg++lpsyrGd+in  af+ +ar+p+
  NCBI__GCF_002796795.1:WP_090217168.1  77 ADAIRDTFKVMLQMAMVLTYGAKVPVVKVGRMAGQFAKPRSAPTETIDGLELPSYRGDIINDLAFTPEARIPN 149
                                           ************************************************************************* PP

                             TIGR01358 147 perlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvaeae. 218
                                           p+++++ay+++aatlnllra+ +gGyad+++vh+W+l f+ +s++ + y+++a++i+++l fm+a+gv++++ 
  NCBI__GCF_002796795.1:WP_090217168.1 150 PQKMLQAYTQAAATLNLLRAFSTGGYADINQVHAWTLGFT-ESEKVDAYRDMANRITDTLDFMNAAGVNKDTa 221
                                           ***************************************8.58999*********************988776 PP

                             TIGR01358 219 .alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikvgpsm 290
                                            +l+ v++ytshe lll+yeealtr+ds++g++   s+h++WiG+rtrq dgahvef +gv nPig+k+gp++
  NCBI__GCF_002796795.1:WP_090217168.1 222 hTLHSVDFYTSHEGLLLEYEEALTREDSTSGDWLAGSGHMIWIGDRTRQPDGAHVEFCSGVLNPIGLKCGPTT 294
                                           69*********************************************************************** PP

                             TIGR01358 291 eadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGyktrrf 363
                                           +a++l  l+++l+Pene Grltli+r+Ga k ae+lP+l++avk++G++v+Wv+dpmhGnt+++++Gyktr f
  NCBI__GCF_002796795.1:WP_090217168.1 295 TAEDLKVLMKKLNPENEEGRLTLIARFGAGKAAEHLPRLVQAVKEEGATVTWVCDPMHGNTIKSSTGYKTRPF 367
                                           ************************************************************************* PP

                             TIGR01358 364 ddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqslelaflva 436
                                           +++l ev+ ffevh+aeGt pGGvh e+tG+dvtec+GG r++t++dl+ ry+tacdPrlna+qslelaflva
  NCBI__GCF_002796795.1:WP_090217168.1 368 ENVLREVRDFFEVHNAEGTVPGGVHFEMTGQDVTECTGGIRAVTDEDLSARYHTACDPRLNASQSLELAFLVA 440
                                           ************************************************************************* PP

                             TIGR01358 437 eklrea 442
                                           e l ++
  NCBI__GCF_002796795.1:WP_090217168.1 441 EELSNQ 446
                                           *99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (456 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 20.47
//
[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