GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroC in Phyllobacterium endophyticum PEPV15

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_106715655.1 CU100_RS06510 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_003010935.1:WP_106715655.1
          Length = 364

 Score =  426 bits (1094), Expect = e-124
 Identities = 223/367 (60%), Positives = 266/367 (72%), Gaps = 16/367 (4%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+ NT G LFRVTT+GESHGLALGC+VDG PPGI  +EA++Q  LD+R+PG SRYTTQRR
Sbjct: 1   MSHNTFGHLFRVTTWGESHGLALGCVVDGCPPGISFSEAEIQSYLDKRKPGQSRYTTQRR 60

Query: 61  EPDQVKILSGVF---EGVT---TGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQK 114
           EPDQVK+LSG     +G+T   TGT I ++IENTDQRS+DY  I   +RPGHADYTY+ K
Sbjct: 61  EPDQVKVLSGFMLQDDGMTMISTGTPISMMIENTDQRSKDYGDIARQYRPGHADYTYDVK 120

Query: 115 YGLRDYRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIK--DWSQ 172
           YG+RDYRGGGRSSARETA RVAAGAIA+K +    G+ +RG L  MG   +D    DW +
Sbjct: 121 YGIRDYRGGGRSSARETAARVAAGAIARKVVP---GLLVRGALVGMGIHSIDRSRWDWDE 177

Query: 173 VEQNPFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAH 232
           V  NPFF PD   +D     +  ++K G SIGA V VVA  VPAGLG PV+ +LD DIA 
Sbjct: 178 VGNNPFFTPDLQSVDVFASYLDGIRKAGSSIGAVVEVVAENVPAGLGAPVYGKLDQDIAS 237

Query: 233 ALMSINAVKGVEIGDGFDVVALRGSQNRDEIT--KDG---FQSNHAGGILGGISSGQQII 287
            LMSINAVKGVEIGDGFD   L G +N DE+    DG   F SNHAGGILGGISSG  ++
Sbjct: 238 NLMSINAVKGVEIGDGFDTARLTGEENADEMRMGNDGKPIFLSNHAGGILGGISSGAPVV 297

Query: 288 AHMALKPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQ 347
           A  A+KPTSSI  P R+I+  G +VE++T+GRHDPCVGIRAVPI EAM+A  + DH LR 
Sbjct: 298 ARFAVKPTSSILTPRRSIDADGNQVEVMTRGRHDPCVGIRAVPIGEAMVACAIADHYLRH 357

Query: 348 RAQNADV 354
           R Q   +
Sbjct: 358 RGQTGRI 364


Lambda     K      H
   0.319    0.138    0.404 

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: 478
Number of extensions: 14
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: 361
Length of database: 364
Length adjustment: 29
Effective length of query: 332
Effective length of database: 335
Effective search space:   111220
Effective search space used:   111220
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: 49 (23.5 bits)

Align candidate WP_106715655.1 CU100_RS06510 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))

# 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/TIGR00033.hmm
# target sequence database:        /tmp/gapView.2182697.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00033  [M=351]
Accession:   TIGR00033
Description: aroC: chorismate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-124  400.1   0.1   4.5e-124  399.9   0.1    1.0  1  NCBI__GCF_003010935.1:WP_106715655.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106715655.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.9   0.1  4.5e-124  4.5e-124       1     350 [.      10     360 ..      10     361 .. 0.96

  Alignments for each domain:
  == domain 1  score: 399.9 bits;  conditional E-value: 4.5e-124
                             TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvf...eGkT... 67 
                                           +r+tt+GeSHg alg+++dG+P+g++ +e++iq++l++R+pgqsr+t++r+E D+v++lsG +    G T   
  NCBI__GCF_003010935.1:WP_106715655.1  10 FRVTTWGESHGLALGCVVDGCPPGISFSEAEIQSYLDKRKPGQSRYTTQRREPDQVKVLSGFMlqdDGMTmis 82 
                                           89***********************************************************864447988555 PP

                             TIGR00033  68 tGaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketa 140
                                           tG+Pi+++i+N+d+rskdy di++++RPgHadyty +KYgi+d++gggrsSaReTaarvaaGa+a+k +    
  NCBI__GCF_003010935.1:WP_106715655.1  83 TGTPISMMIENTDQRSKDYGDIARQYRPGHADYTYDVKYGIRDYRGGGRSSARETAARVAAGAIARKVVPG-- 153
                                           7******************************************************************9987.. PP

                             TIGR00033 141 gieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvg 213
                                            + + + +v +g  +++++  +    +++ ++p++ pd +  +    ++d ++k+g s+G+vvevv++nvp+g
  NCBI__GCF_003010935.1:WP_106715655.1 154 -LLVRGALVGMGIHSIDRSRWD---WDEVGNNPFFTPDLQSVDVFASYLDGIRKAGSSIGAVVEVVAENVPAG 222
                                           .569999999999999987777...478999****************************************** PP

                             TIGR00033 214 lGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGGieGGitnGed 285
                                           lG p++ kld  +as l+sinAvKgveiGdGF++a+ +G e  De+ +  d+k  + +n+ GGi+GGi+ G +
  NCBI__GCF_003010935.1:WP_106715655.1 223 LGAPVYGKLDQDIASNLMSINAVKGVEIGDGFDTARLTGEENADEMRMGnDGKPIFLSNHAGGILGGISSGAP 295
                                           ***********************************************9989999******************* PP

                             TIGR00033 286 irvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekras 350
                                           ++ r avKp+++i +p++++d ++++   +t+gRhDpcv +ravp+ Eamva  +ad++l++r++
  NCBI__GCF_003010935.1:WP_106715655.1 296 VVARFAVKPTSSILTPRRSIDADGNQVEVMTRGRHDPCVGIRAVPIGEAMVACAIADHYLRHRGQ 360
                                           *************************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (364 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.68
//
[ok]

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

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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