Alignments for a candidate for aroC in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Shewanella loihica PV-4

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate 5209968 Shew_2416 chorismate synthase (RefSeq)

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__PV4:5209968
          Length = 364

 Score =  552 bits (1422), Expect = e-162
 Identities = 275/359 (76%), Positives = 311/359 (86%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+GN+IGQ F VTTFGESHG ALGCI+DG PPG+ + EAD+QHDLDRRRPGTSRYTT RR
Sbjct: 1   MSGNSIGQNFVVTTFGESHGKALGCIIDGCPPGLAIDEADMQHDLDRRRPGTSRYTTARR 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           EPDQVKILSGVFEG TTGTSIGL+IENTDQRSQDYS IKD FRPGHADYTY+QKYGLRDY
Sbjct: 61  EPDQVKILSGVFEGQTTGTSIGLVIENTDQRSQDYSNIKDQFRPGHADYTYQQKYGLRDY 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSARETAMRVAAGA+AKKYL +  GIEI+G L+Q+G I  +I D+ QVE N FF 
Sbjct: 121 RGGGRSSARETAMRVAAGAVAKKYLKQVHGIEIKGYLSQLGPICAEILDFDQVEHNAFFF 180

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           PD  K++ LDE MR LKK GDSIGAKV+VVA+ VP GLGEPVFDRLDADIAHALM INAV
Sbjct: 181 PDAAKLEQLDEYMRELKKSGDSIGAKVSVVATNVPVGLGEPVFDRLDADIAHALMGINAV 240

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIGDGF VV  +GS++RD ++ +GF SNHAGGILGGISSGQ I+AH+A+KPTSSI+V
Sbjct: 241 KGVEIGDGFAVVNQKGSEHRDLMSPEGFASNHAGGILGGISSGQPIVAHIAMKPTSSISV 300

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359
           PG ++   GE  E++TKGRHDPCVGIRAVPIAEAMLAIVLMDHLLR RAQN +V++  P
Sbjct: 301 PGESMTVQGERAEVVTKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRHRAQNMNVESITP 359


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: 468
Number of extensions: 8
Number of successful extensions: 1
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 5209968 Shew_2416 (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.27334.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.8e-145  469.6   0.5   3.2e-145  469.5   0.5    1.0  1  lcl|FitnessBrowser__PV4:5209968  Shew_2416 chorismate synthase (R


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209968  Shew_2416 chorismate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.5   0.5  3.2e-145  3.2e-145       1     350 [.      10     350 ..      10     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: 469.5 bits;  conditional E-value: 3.2e-145
                        TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPiallikN 78 
                                      + +ttfGeSHgkalg+iidG+P+gl ++e+d+q++l+rRrpg+sr+t+ r+E D+v+ilsGvfeG+TtG+ i l+i+N
  lcl|FitnessBrowser__PV4:5209968  10 FVVTTFGESHGKALGCIIDGCPPGLAIDEADMQHDLDRRRPGTSRYTTARREPDQVKILSGVFEGQTTGTSIGLVIEN 87 
                                      569*************************************************************************** PP

                        TIGR00033  79 kdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagieivayvvklgevel 156
                                      +d+rs+dy++ik+++RPgHadyty++KYg++d++gggrsSaReTa+rvaaGavakk+Lk+ +giei++y+++lg +++
  lcl|FitnessBrowser__PV4:5209968  88 TDQRSQDYSNIKDQFRPGHADYTYQQKYGLRDYRGGGRSSARETAMRVAAGAVAKKYLKQVHGIEIKGYLSQLGPICA 165
                                      *****************************************************************************9 PP

                        TIGR00033 157 eeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplfdkldaelasallsin 234
                                      e   ++     +++++ +++pda + +++ e++ ++kk+gds+G++v+vv++nvpvglGep+fd+lda +a+al++in
  lcl|FitnessBrowser__PV4:5209968 166 EILDFD-----QVEHNAFFFPDAAKLEQLDEYMRELKKSGDSIGAKVSVVATNVPVGLGEPVFDRLDADIAHALMGIN 238
                                      965544.....69999************************************************************** PP

                        TIGR00033 235 AvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkek 312
                                      AvKgveiGdGF+ ++++Gse+ D +    +   + +n+ GGi+GGi+ G++i+ +ia+Kp+++i+ p ++++++++ +
  lcl|FitnessBrowser__PV4:5209968 239 AVKGVEIGDGFAVVNQKGSEHRDLMS--PE--GFASNHAGGILGGISSGQPIVAHIAMKPTSSISVPGESMTVQGERA 312
                                      ***********************554..33..589**************************************99999 PP

                        TIGR00033 313 akatkgRhDpcvvpravpvvEamvalvladallekras 350
                                        +tkgRhDpcv +ravp++Eam+a+vl+d+ll++ra+
  lcl|FitnessBrowser__PV4:5209968 313 EVVTKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRHRAQ 350
                                      9999*******************************987 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.97
//
[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