Alignments for a candidate for aroC in Sphingomonas wittichii RW1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Sphingomonas wittichii RW1

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_012050943.1 SWIT_RS24090 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_000016765.1:WP_012050943.1
          Length = 356

 Score =  390 bits (1002), Expect = e-113
 Identities = 200/357 (56%), Positives = 257/357 (71%), Gaps = 10/357 (2%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+ N+ G++FR +T+GESHG A+G +VDG PPG+ L+EAD+Q  LD+RRPGTSR+TTQR+
Sbjct: 1   MSFNSFGRVFRFSTWGESHGPAIGAVVDGCPPGLELSEADIQPWLDKRRPGTSRFTTQRQ 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           EPDQV+ILSGVFEG TTGT I L+I+N DQRS+DYS +   +RPGHADY Y+ KYG RD+
Sbjct: 61  EPDQVRILSGVFEGRTTGTPISLMIDNVDQRSKDYSEVALAYRPGHADYAYDAKYGFRDH 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLD--IKDWSQVEQNPF 178
           RGGGRSSARETA RVAAGA+A+  + E   + IR  L ++G   +D    D + +++NPF
Sbjct: 121 RGGGRSSARETASRVAAGAVARLVIPE---VRIRAYLIELGGDRIDPAAFDDAAIDENPF 177

Query: 179 FCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSIN 238
           FCPD       + ++   +K G S+GA V  VA GVPAG G P++ +LD+++A A MSIN
Sbjct: 178 FCPDRAAAARWEAIVDDARKAGSSVGAVVECVAEGVPAGWGAPLYAKLDSELAAACMSIN 237

Query: 239 AVKGVEIGDGFDVVALRGSQNRDEIT-----KDGFQSNHAGGILGGISSGQQIIAHMALK 293
           AVKGVEIGDGF    L G  N D +      K  F +NHAGGI GGI++GQ ++  +ALK
Sbjct: 238 AVKGVEIGDGFAAARLTGETNADPMRPGNDGKPVFLANHAGGIAGGIATGQPVVVRIALK 297

Query: 294 PTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQ 350
           PTSSI  P  TI R G+  ++ TKGRHDPCVGIRA P+ EAM+A+VL D  L  RAQ
Sbjct: 298 PTSSILTPVETIGRDGKAADIRTKGRHDPCVGIRAAPVLEAMVALVLADQKLLHRAQ 354


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: 399
Number of extensions: 13
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: 356
Length adjustment: 29
Effective length of query: 332
Effective length of database: 327
Effective search space:   108564
Effective search space used:   108564
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_012050943.1 SWIT_RS24090 (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.14173.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-135  437.0   0.0   2.7e-135  436.8   0.0    1.0  1  lcl|NCBI__GCF_000016765.1:WP_012050943.1  SWIT_RS24090 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016765.1:WP_012050943.1  SWIT_RS24090 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.8   0.0  2.7e-135  2.7e-135       1     349 [.      10     353 ..      10     355 .. 0.98

  Alignments for each domain:
  == domain 1  score: 436.8 bits;  conditional E-value: 2.7e-135
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               +r+ t+GeSHg+a+ga++dG+P+glel+e+diq+ l++Rrpg+sr+t++r+E D+v+ilsGvfeG+TtG
  lcl|NCBI__GCF_000016765.1:WP_012050943.1  10 FRFSTWGESHGPAIGAVVDGCPPGLELSEADIQPWLDKRRPGTSRFTTQRQEPDQVRILSGVFEGRTTG 78 
                                               799****************************************************************** PP

                                 TIGR00033  70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138
                                               +Pi+l+i+N d+rskdy++++  +RPgHady+y  KYg++d++gggrsSaReTa rvaaGava+  + e
  lcl|NCBI__GCF_000016765.1:WP_012050943.1  79 TPISLMIDNVDQRSKDYSEVALAYRPGHADYAYDAKYGFRDHRGGGRSSARETASRVAAGAVARLVIPE 147
                                               ****************************************************************99999 PP

                                 TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207
                                                  ++i ay+++lg  +++   +++    ++d++p++cpd+ a+++ e+++d a+k+g svG+vve+v+
  lcl|NCBI__GCF_000016765.1:WP_012050943.1 148 ---VRIRAYLIELGGDRIDPAAFDD---AAIDENPFFCPDRAAAARWEAIVDDARKAGSSVGAVVECVA 210
                                               ...89**********9999877775...89*************************************** PP

                                 TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGG 275
                                               ++vp+g+G pl+ kld+ela+a +sinAvKgveiGdGF+aa+ +G    D++    d+k  + +n+ GG
  lcl|NCBI__GCF_000016765.1:WP_012050943.1 211 EGVPAGWGAPLYAKLDSELAAACMSINAVKGVEIGDGFAAARLTGETNADPMRPGnDGKPVFLANHAGG 279
                                               ****************************************************9877999********** PP

                                 TIGR00033 276 ieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladal 344
                                               i GGi++G++++vria+Kp+++i +p +t+  ++k +  +tkgRhDpcv +ra+pv Eamvalvlad+ 
  lcl|NCBI__GCF_000016765.1:WP_012050943.1 280 IAGGIATGQPVVVRIALKPTSSILTPVETIGRDGKAADIRTKGRHDPCVGIRAAPVLEAMVALVLADQK 348
                                               ************************************9999***************************99 PP

                                 TIGR00033 345 lekra 349
                                               l +ra
  lcl|NCBI__GCF_000016765.1:WP_012050943.1 349 LLHRA 353
                                               98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (356 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: 10.68
//
[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