Alignments for a candidate for aroC in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Pyrolobus fumarii 1A

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_014026153.1 PYRFU_RS02980 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_000223395.1:WP_014026153.1
          Length = 393

 Score =  291 bits (744), Expect = 3e-83
 Identities = 172/359 (47%), Positives = 223/359 (62%), Gaps = 16/359 (4%)

Query: 2   AGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRRE 61
           AG++ G LFRVTTFGESHG ALG +VDGVP G+PL+E D+  +L  RRPG  R+ T RRE
Sbjct: 3   AGSSFGLLFRVTTFGESHGSALGVVVDGVPAGMPLSERDVYKELLLRRPG-HRWATARRE 61

Query: 62  PDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLR--D 119
           PD+ +ILSGVFEG TTG  I +++ N D  S+ Y  ++   RPGHAD  Y  KYG    D
Sbjct: 62  PDKPEILSGVFEGRTTGHPIAIVVWNRDVDSRPYEEVRCKPRPGHADLAYVLKYGWENWD 121

Query: 120 YRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPL-------DIKDWSQ 172
           YRGGGR+S RET  RVAAGA+AKK L    G+ + G L ++G + L        ++++  
Sbjct: 122 YRGGGRASGRETVGRVAAGAVAKKLLLAA-GLTVYGRLAEIGGLELVDPRAEPSVEEFLA 180

Query: 173 VEQNPFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAH 232
              +P    D      +  ++   + EGDS+G  V VVA GVP GLG+PVFD+L AD+A 
Sbjct: 181 ARHSPVRVHDRRLEQEVMRVIEEARAEGDSLGGVVEVVAFGVPPGLGDPVFDKLKADLAK 240

Query: 233 ALMSINAVKGVEIGDGFDVVALRGSQNRDEITKDGFQSNHA----GGILGGISSGQQIIA 288
           ALMSI    G E+G GF +  ++GS+ RD I     Q        GG+LGG+S G  I  
Sbjct: 241 ALMSIPGAVGFEVGLGFRLARMKGSEARDPIRLVNGQPRPVGPAHGGMLGGLSVGTPIRL 300

Query: 289 HMALKPTSSITVPGRTINRFGEEVEMIT-KGRHDPCVGIRAVPIAEAMLAIVLMDHLLR 346
            +A KPTSSI  P  T N      + I+ KGRHDP + +RAV +AEAM+AI L DH+LR
Sbjct: 301 RIAFKPTSSIPRPIETWNLCENRPDTISVKGRHDPALVVRAVAVAEAMVAITLADHMLR 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: 417
Number of extensions: 24
Number of successful extensions: 8
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: 393
Length adjustment: 30
Effective length of query: 331
Effective length of database: 363
Effective search space:   120153
Effective search space used:   120153
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: 50 (23.9 bits)

Align candidate WP_014026153.1 PYRFU_RS02980 (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.5692.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-122  393.4   0.0   5.1e-122  393.1   0.0    1.0  1  lcl|NCBI__GCF_000223395.1:WP_014026153.1  PYRFU_RS02980 chorismate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000223395.1:WP_014026153.1  PYRFU_RS02980 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.1   0.0  5.1e-122  5.1e-122       1     347 [.      11     360 ..      11     363 .. 0.96

  Alignments for each domain:
  == domain 1  score: 393.1 bits;  conditional E-value: 5.1e-122
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               +r+ttfGeSHg alg+++dG+Pag++l+e d+ kel  Rrpg+ r ++ r+E D+ eilsGvfeG+TtG
  lcl|NCBI__GCF_000223395.1:WP_014026153.1  11 FRVTTFGESHGSALGVVVDGVPAGMPLSERDVYKELLLRRPGH-RWATARREPDKPEILSGVFEGRTTG 78 
                                               89****************************************9.************************* PP

                                 TIGR00033  70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikd..regggrsSaReTaarvaaGavakklL 136
                                                Pia+++ N+dv+s++ye+++ +pRPgHad++y+ KYg ++  ++gggr+S+ReT++rvaaGavakklL
  lcl|NCBI__GCF_000223395.1:WP_014026153.1  79 HPIAIVVWNRDVDSRPYEEVRCKPRPGHADLAYVLKYGWENwdYRGGGRASGRETVGRVAAGAVAKKLL 147
                                               **************************************98777************************** PP

                                 TIGR00033 137 ketagieivayvvklgeveleeesakeiskerldk..spvrcpdaeaekemeeeidkakkdgdsvGgvv 203
                                                  ag+ + + + ++g +el +  a+   +e l++  spvr+ d++ e+e+  +i++a+ +gds+Ggvv
  lcl|NCBI__GCF_000223395.1:WP_014026153.1 148 LA-AGLTVYGRLAEIGGLELVDPRAEPSVEEFLAArhSPVRVHDRRLEQEVMRVIEEARAEGDSLGGVV 215
                                               99.89************999988888444554444459******************************* PP

                                 TIGR00033 204 evvvsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnn 272
                                               evv+ +vp glG+p+fdkl+a la+al+si+ + g+e+G GF++a+++Gsea D++ l +++ r +   
  lcl|NCBI__GCF_000223395.1:WP_014026153.1 216 EVVAFGVPPGLGDPVFDKLKADLAKALMSIPGAVGFEVGLGFRLARMKGSEARDPIRLVNGQPRPVGPA 284
                                               ********************************************************************* PP

                                 TIGR00033 273 sGGieGGitnGedirvriavKpiptikkplktvdletkekakat.kgRhDpcvvpravpvvEamvalvl 340
                                                GG++GG++ G++ir+ria+Kp+++i +p +t +l ++ + +++ kgRhDp+ v+rav v+Eamva++l
  lcl|NCBI__GCF_000223395.1:WP_014026153.1 285 HGGMLGGLSVGTPIRLRIAFKPTSSIPRPIETWNLCENRPDTISvKGRHDPALVVRAVAVAEAMVAITL 353
                                               ***********************************9999999999************************ PP

                                 TIGR00033 341 adallek 347
                                               ad++l++
  lcl|NCBI__GCF_000223395.1:WP_014026153.1 354 ADHMLRN 360
                                               ****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (393 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.25
//
[ok]

This GapMind analysis is from Apr 10 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