Alignments for a candidate for aroC in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Methylobacterium nodulans ORS 2060

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_015928554.1 MNOD_RS09040 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_000022085.1:WP_015928554.1
          Length = 371

 Score =  436 bits (1122), Expect = e-127
 Identities = 225/364 (61%), Positives = 266/364 (73%), Gaps = 17/364 (4%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+ N+ G LFRVTTFGESHG ALGC+VDG PP IPL  A++Q +LDRRRPG SR+TTQRR
Sbjct: 1   MSHNSFGHLFRVTTFGESHGPALGCVVDGCPPLIPLEAAEIQAELDRRRPGQSRFTTQRR 60

Query: 61  EPDQVKILSGVFEG-------VTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQ 113
           EPD V+ILSGVF         +TTGT I L+IEN DQRS+DYS I+D +RPGHADYTYE 
Sbjct: 61  EPDTVRILSGVFADDRTGGRQLTTGTPIALMIENVDQRSKDYSEIRDTYRPGHADYTYEA 120

Query: 114 KYGLRDYRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIK--DWS 171
           KYG+RDYRGGGRSSARETA RVAAGAIA+K L    G+ IRG L Q+G   +D    DW+
Sbjct: 121 KYGIRDYRGGGRSSARETAARVAAGAIARKVLP---GVTIRGALVQLGPHAIDRARFDWN 177

Query: 172 QVEQNPFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIA 231
           +V  NPFFCPD        E++  ++K+G SIGA + VVA GVP GLG PV+ +LDAD+A
Sbjct: 178 EVGNNPFFCPDAVAAVQWAEILDEIRKDGSSIGAVIEVVAEGVPPGLGAPVYGKLDADLA 237

Query: 232 HALMSINAVKGVEIGDGFDVVALRGSQNRDEIT-----KDGFQSNHAGGILGGISSGQQI 286
            A+MSINAVKGVEIGDGF    LRG +N DE+         F +NHAGGILGGISSGQ I
Sbjct: 238 AAMMSINAVKGVEIGDGFAAATLRGEENADEMRPGNGGAPAFLANHAGGILGGISSGQPI 297

Query: 287 IAHMALKPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLR 346
           +   A+KPTSSI  P  ++ R     E++TKGRHDPCVGIRAVP+ EAM+A VL DH LR
Sbjct: 298 VCRFAVKPTSSILTPRASVTRDNRPAEVVTKGRHDPCVGIRAVPVGEAMMACVLADHYLR 357

Query: 347 QRAQ 350
            R Q
Sbjct: 358 HRGQ 361


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: 479
Number of extensions: 13
Number of successful extensions: 6
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: 371
Length adjustment: 30
Effective length of query: 331
Effective length of database: 341
Effective search space:   112871
Effective search space used:   112871
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_015928554.1 MNOD_RS09040 (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.7078.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-132  428.1   0.0   1.3e-132  427.9   0.0    1.0  1  lcl|NCBI__GCF_000022085.1:WP_015928554.1  MNOD_RS09040 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000022085.1:WP_015928554.1  MNOD_RS09040 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.9   0.0  1.3e-132  1.3e-132       1     349 [.      10     360 ..      10     362 .. 0.96

  Alignments for each domain:
  == domain 1  score: 427.9 bits;  conditional E-value: 1.3e-132
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfe....G 65 
                                               +r+ttfGeSHg+alg+++dG+P+ ++l++++iq el+rRrpgqsr+t++r+E D+v+ilsGvf     G
  lcl|NCBI__GCF_000022085.1:WP_015928554.1  10 FRVTTFGESHGPALGCVVDGCPPLIPLEAAEIQAELDRRRPGQSRFTTQRREPDTVRILSGVFAddrtG 78 
                                               89************************************************************9533332 PP

                                 TIGR00033  66 ...kTtGaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGav 131
                                                   TtG+Pial+i+N d+rskdy++i++++RPgHadyty+ KYgi+d++gggrsSaReTaarvaaGa+
  lcl|NCBI__GCF_000022085.1:WP_015928554.1  79 grqLTTGTPIALMIENVDQRSKDYSEIRDTYRPGHADYTYEAKYGIRDYRGGGRSSARETAARVAAGAI 147
                                               3446***************************************************************** PP

                                 TIGR00033 132 akklLketagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvG 200
                                               a+k L     + i + +v+lg  ++++  ++    +++ ++p++cpda a+ +  e++d+++kdg s+G
  lcl|NCBI__GCF_000022085.1:WP_015928554.1 148 ARKVLPG---VTIRGALVQLGPHAIDRARFDW---NEVGNNPFFCPDAVAAVQWAEILDEIRKDGSSIG 210
                                               *****87...89**************988884...78999***************************** PP

                                 TIGR00033 201 gvvevvvsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirr 268
                                               +v+evv+++vp glG p++ klda la+a++sinAvKgveiGdGF+aa+ rG e  De+     +   +
  lcl|NCBI__GCF_000022085.1:WP_015928554.1 211 AVIEVVAEGVPPGLGAPVYGKLDADLAAAMMSINAVKGVEIGDGFAAATLRGEENADEMRPGnGGAPAF 279
                                               ***********************************************************988577789* PP

                                 TIGR00033 269 ktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamva 337
                                                +n+ GGi+GGi+ G++i+ r avKp+++i +p+++v+ +++++  +tkgRhDpcv +ravpv Eam+a
  lcl|NCBI__GCF_000022085.1:WP_015928554.1 280 LANHAGGILGGISSGQPIVCRFAVKPTSSILTPRASVTRDNRPAEVVTKGRHDPCVGIRAVPVGEAMMA 348
                                               ********************************************************************* PP

                                 TIGR00033 338 lvladallekra 349
                                                vlad++l++r+
  lcl|NCBI__GCF_000022085.1:WP_015928554.1 349 CVLADHYLRHRG 360
                                               *********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (371 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: 9.96
//
[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