Alignments for a candidate for aroC in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Desulfovibrio vulgaris Miyazaki F

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate 8500660 DvMF_1408 chorismate synthase (RefSeq)

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__Miya:8500660
          Length = 353

 Score =  366 bits (939), Expect = e-106
 Identities = 187/351 (53%), Positives = 241/351 (68%), Gaps = 4/351 (1%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYT---T 57
           M+GNT G++FR+TT+GESHG  LG +VDG P G+PL E+ +Q +LD RRPG++      T
Sbjct: 1   MSGNTFGRIFRLTTYGESHGPGLGGVVDGCPAGVPLDESVIQRELDLRRPGSASAGLAGT 60

Query: 58  QRREPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGL 117
            R+EPD V++LSGVFEGVTTGT IG  I N DQRS+DY  +  ++RPGHAD TY+ KYGL
Sbjct: 61  ARKEPDTVRLLSGVFEGVTTGTPIGFHIANEDQRSRDYGDLAKLYRPGHADITYDAKYGL 120

Query: 118 RDYRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNP 177
           RD+RGGGR+S RET  RVA GA+A   LA    IE+R    ++G +P D+ D +  +   
Sbjct: 121 RDFRGGGRASGRETVSRVAGGAVALALLA-MHDIEVRAYTVEIGGVPADVVDPAGAQGRL 179

Query: 178 FFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSI 237
           FF PDPD + A + L+  ++ EGD++G  V V A+GVPAGLGEPVFD+LDA +AHA+MS+
Sbjct: 180 FFSPDPDVVPAWESLVHDVRAEGDTLGGIVQVEATGVPAGLGEPVFDKLDALLAHAMMSV 239

Query: 238 NAVKGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSS 297
            AVK VE+G G +   LRGS+N D I   GF +NHAGGILGGIS+GQ I+    +KP  S
Sbjct: 240 GAVKAVEVGAGLEAARLRGSENNDPIIPGGFHTNHAGGILGGISNGQPIVVRATVKPIPS 299

Query: 298 ITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQR 348
           I     TI+  G    +   GRHD C   R VP+ +AM A+VL D LL QR
Sbjct: 300 IAQEQITIDTNGRPAPLRVGGRHDICAIPRVVPVLKAMAALVLADSLLLQR 350


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: 435
Number of extensions: 17
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: 361
Length of database: 353
Length adjustment: 29
Effective length of query: 332
Effective length of database: 324
Effective search space:   107568
Effective search space used:   107568
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 8500660 DvMF_1408 (chorismate synthase (RefSeq))
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.13313.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.5e-121  391.6   0.0   1.7e-121  391.4   0.0    1.0  1  lcl|FitnessBrowser__Miya:8500660  DvMF_1408 chorismate synthase (R


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8500660  DvMF_1408 chorismate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  391.4   0.0  1.7e-121  1.7e-121       1     348 [.      10     350 ..      10     353 .] 0.95

  Alignments for each domain:
  == domain 1  score: 391.4 bits;  conditional E-value: 1.7e-121
                         TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsr...ltrmrkEeDeveilsGvfeGkTtGaPial 74 
                                       +rltt+GeSHg+ lg ++dG+Pag++l+e+ iq+el+ Rrpg++      + rkE D+v++lsGvfeG TtG+Pi +
  lcl|FitnessBrowser__Miya:8500660  10 FRLTTYGESHGPGLGGVVDGCPAGVPLDESVIQRELDLRRPGSASaglAGTARKEPDTVRLLSGVFEGVTTGTPIGF 86 
                                       89****************************************865222579************************** PP

                         TIGR00033  75 likNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagieivayvvkl 151
                                        i N+d+rs+dy d+++l+RPgHad ty  KYg++d +gggr+S+ReT+ rva Gava +lL+  ++ie+ ay+v++
  lcl|FitnessBrowser__Miya:8500660  87 HIANEDQRSRDYGDLAKLYRPGHADITYDAKYGLRDFRGGGRASGRETVSRVAGGAVALALLAM-HDIEVRAYTVEI 162
                                       ***************************************************************9.66********** PP

                         TIGR00033 152 geveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplfdkldaelas 228
                                       g v ++        +  ++ + ++ pd++   + e +++ ++ +gd++Gg+v+v +++vp+glGep+fdklda la+
  lcl|FitnessBrowser__Miya:8500660 163 GGVPADVVD-----PAGAQGRLFFSPDPDVVPAWESLVHDVRAEGDTLGGIVQVEATGVPAGLGEPVFDKLDALLAH 234
                                       **9998533.....44566688999**************************************************** PP

                         TIGR00033 229 allsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGedirvriavKpiptikkplktv 305
                                       a++s+ AvK+ve+G+G eaa+ rGse nD++        ++tn+ GGi+GGi+nG++i+vr++vKpip+i++++ t+
  lcl|FitnessBrowser__Miya:8500660 235 AMMSVGAVKAVEVGAGLEAARLRGSENNDPIIP----GGFHTNHAGGILGGISNGQPIVVRATVKPIPSIAQEQITI 307
                                       *****************************9985....4699************************************ PP

                         TIGR00033 306 dletkekakatkgRhDpcvvpravpvvEamvalvladallekr 348
                                       d++++++  +  gRhD c++pr+vpv  am alvlad ll +r
  lcl|FitnessBrowser__Miya:8500660 308 DTNGRPAPLRVGGRHDICAIPRVVPVLKAMAALVLADSLLLQR 350
                                       **************************************99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (353 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: 00:00:00.01
# Mc/sec: 7.89
//
[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