GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroC in Caulobacter crescentus NA1000

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate CCNA_03256 CCNA_03256 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__Caulo:CCNA_03256
          Length = 372

 Score =  415 bits (1067), Expect = e-121
 Identities = 218/363 (60%), Positives = 259/363 (71%), Gaps = 16/363 (4%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+ NT G LFRVTT+GESHG ALGC+VDG PPGI LT   +Q  LD+RRPG  ++ TQR+
Sbjct: 1   MSHNTFGHLFRVTTWGESHGPALGCVVDGCPPGIALTAEMIQVFLDKRRPGNGKFVTQRQ 60

Query: 61  EPDQVKILSGVFEGV------TTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQK 114
           EPD V+ILSGVFE        TTGT I L+IENTDQRS+DYS I   FRPGHADY Y  K
Sbjct: 61  EPDAVRILSGVFEDARSNGQRTTGTPISLMIENTDQRSKDYSEIAQAFRPGHADYAYFAK 120

Query: 115 YGLRDYRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIK--DWSQ 172
           YG+RDYRGGGRSSARETA RVAAGA+A+  +    G+ +R  L Q+G   +D    DW+Q
Sbjct: 121 YGVRDYRGGGRSSARETAARVAAGAVARLIIP---GVTVRAALVQIGPHKIDRSNWDWAQ 177

Query: 173 VEQNPFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAH 232
            EQNP++ PD   +   +E +  ++K G S GA V V A+GVPAG G P++ +LDA++A 
Sbjct: 178 TEQNPYWSPDAAIVPVWEEHLEKIRKAGSSTGAVVEVEATGVPAGWGAPLYAKLDAELAA 237

Query: 233 ALMSINAVKGVEIGDGFDVVALRGSQNRDEITK--DG---FQSNHAGGILGGISSGQQII 287
           ALMSINA KGVEIGDGFD  AL G  N D +    DG   FQSNHAGGILGGISSGQ I+
Sbjct: 238 ALMSINAAKGVEIGDGFDSAALTGEDNADTMRMGDDGQPVFQSNHAGGILGGISSGQPIV 297

Query: 288 AHMALKPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQ 347
           A +A KPTSSI +P  T+N  GEE+E+ TKGRHDPCVGIR VP+ EAM A VL D  LR 
Sbjct: 298 ARVAFKPTSSILIPRETVNEAGEEIELRTKGRHDPCVGIRGVPVVEAMTACVLADAFLRH 357

Query: 348 RAQ 350
           R Q
Sbjct: 358 RGQ 360


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: 415
Number of extensions: 13
Number of successful extensions: 5
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: 372
Length adjustment: 30
Effective length of query: 331
Effective length of database: 342
Effective search space:   113202
Effective search space used:   113202
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 CCNA_03256 CCNA_03256 (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.10985.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-130  421.5   0.0   1.3e-130  421.3   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03256  CCNA_03256 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03256  CCNA_03256 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.3   0.0  1.3e-130  1.3e-130       1     350 [.      10     360 ..      10     361 .. 0.96

  Alignments for each domain:
  == domain 1  score: 421.3 bits;  conditional E-value: 1.3e-130
                             TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfe.....G.kT 67 
                                           +r+tt+GeSHg+alg+++dG+P+g+ lt+e+iq  l++Rrpg++++ ++r+E D+v+ilsGvfe     G +T
  lcl|FitnessBrowser__Caulo:CCNA_03256  10 FRVTTWGESHGPALGCVVDGCPPGIALTAEMIQVFLDKRRPGNGKFVTQRQEPDAVRILSGVFEdarsnGqRT 82 
                                           89************************************************************9744444446* PP

                             TIGR00033  68 tGaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketa 140
                                           tG+Pi+l+i+N+d+rskdy++i++ +RPgHady+y+ KYg++d++gggrsSaReTaarvaaGava+  +    
  lcl|FitnessBrowser__Caulo:CCNA_03256  83 TGTPISLMIENTDQRSKDYSEIAQAFRPGHADYAYFAKYGVRDYRGGGRSSARETAARVAAGAVARLIIPG-- 153
                                           *****************************************************************977655.. PP

                             TIGR00033 141 gieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvg 213
                                            + + a +v++g  ++++++ +     +++++p   pda      ee ++k++k+g s G+vvev +++vp+g
  lcl|FitnessBrowser__Caulo:CCNA_03256 154 -VTVRAALVQIGPHKIDRSNWDW---AQTEQNPYWSPDAAIVPVWEEHLEKIRKAGSSTGAVVEVEATGVPAG 222
                                           .99**************998884...68899****************************************** PP

                             TIGR00033 214 lGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGGieGGitnGed 285
                                           +G pl+ kldaela+al+sinA+KgveiGdGF++a  +G +  D + +  d++  +++n+ GGi+GGi+ G++
  lcl|FitnessBrowser__Caulo:CCNA_03256 223 WGAPLYAKLDAELAAALMSINAAKGVEIGDGFDSAALTGEDNADTMRMGdDGQPVFQSNHAGGILGGISSGQP 295
                                           ***********************************************99677889****************** PP

                             TIGR00033 286 irvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekras 350
                                           i+ r+a+Kp+++i  p++tv+ +++e   +tkgRhDpcv +r vpvvEam+a vlada+l++r++
  lcl|FitnessBrowser__Caulo:CCNA_03256 296 IVARVAFKPTSSILIPRETVNEAGEEIELRTKGRHDPCVGIRGVPVVEAMTACVLADAFLRHRGQ 360
                                           *************************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (372 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: 00:00:00.01
# Mc/sec: 7.66
//
[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