Alignments for a candidate for aroC in Brevundimonas sp. GW460-12-10-14-LB2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Brevundimonas sp. GW460-12-10-14-LB2

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_066552034.1 A4249_RS08790 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_001636925.1:WP_066552034.1
          Length = 361

 Score =  379 bits (973), Expect = e-110
 Identities = 202/361 (55%), Positives = 251/361 (69%), Gaps = 13/361 (3%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+ NT G LFRVTT+GESHG A+GC+VDG PP IPLTEADLQ  LD+R+PG SR+ TQR+
Sbjct: 1   MSHNTFGHLFRVTTWGESHGPAIGCVVDGCPPMIPLTEADLQPWLDQRKPGGSRFVTQRK 60

Query: 61  EPDQVKILSGVFEG----VTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYG 116
           E D  +ILSGVF+     VTTGT I +LIEN DQRS+DY  I   +RPGHADY Y+ KYG
Sbjct: 61  ESDTARILSGVFDDGDGPVTTGTPISILIENEDQRSKDYGEIARAYRPGHADYAYQAKYG 120

Query: 117 LRDYRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGD--IPLDIKDWSQVE 174
           +RD+RGGGRSSARETA RVAAGA+A+K L +  G++IR  + Q+G   I  D  D+  V 
Sbjct: 121 VRDHRGGGRSSARETASRVAAGAVARKVLGD--GVKIRAGVVQIGPHRIAPDQIDFDAVH 178

Query: 175 QNPFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHAL 234
            N  F    + +   +  +  ++K G S+GA V +  +GVPAG G P++ +LD ++A AL
Sbjct: 179 TNQLFAASAEVVGDWEAYLDGIRKAGSSVGAVVALEVTGVPAGWGAPLYGKLDGELAAAL 238

Query: 235 MSINAVKGVEIGDGFDVVALRGSQNRDEITKD-----GFQSNHAGGILGGISSGQQIIAH 289
           MSINA KGVEIG GF+   L G QN DE+  D      F SN AGG+LGGIS+GQ + A 
Sbjct: 239 MSINAAKGVEIGAGFEAAELTGEQNADEMRLDLNKQPVFLSNKAGGVLGGISTGQPVTAR 298

Query: 290 MALKPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRA 349
           +A KPTSSI    +TI R GEE ++ TKGRHDPCV +RAVP+ EAM A VL D  LR RA
Sbjct: 299 VAFKPTSSILTLRQTITRDGEETDLRTKGRHDPCVALRAVPVVEAMAACVLADAHLRHRA 358

Query: 350 Q 350
           Q
Sbjct: 359 Q 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: 425
Number of extensions: 19
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: 361
Length adjustment: 29
Effective length of query: 332
Effective length of database: 332
Effective search space:   110224
Effective search space used:   110224
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_066552034.1 A4249_RS08790 (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.2090266.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-129  417.0   0.0   3.3e-129  416.8   0.0    1.0  1  NCBI__GCF_001636925.1:WP_066552034.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001636925.1:WP_066552034.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.8   0.0  3.3e-129  3.3e-129       1     350 [.      10     359 ..      10     360 .. 0.97

  Alignments for each domain:
  == domain 1  score: 416.8 bits;  conditional E-value: 3.3e-129
                             TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfe.G...kTtG 69 
                                           +r+tt+GeSHg+a+g+++dG+P+ ++lte+d+q+ l++R+pg sr+ ++rkE+D+ +ilsGvf  G    TtG
  NCBI__GCF_001636925.1:WP_066552034.1  10 FRVTTWGESHGPAIGCVVDGCPPMIPLTEADLQPWLDQRKPGGSRFVTQRKESDTARILSGVFDdGdgpVTTG 82 
                                           89************************************************************96433356*** PP

                             TIGR00033  70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagi 142
                                           +Pi++li+N+d+rskdy +i++ +RPgHady+y+ KYg++d++gggrsSaReTa rvaaGava+k L +  g+
  NCBI__GCF_001636925.1:WP_066552034.1  83 TPISILIENEDQRSKDYGEIARAYRPGHADYAYQAKYGVRDHRGGGRSSARETASRVAAGAVARKVLGD--GV 153
                                           *******************************************************************99..9* PP

                             TIGR00033 143 eivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglG 215
                                           +i a vv++g  ++  ++++    ++++++++++++ae     e+++d ++k+g svG+vv + v++vp+g+G
  NCBI__GCF_001636925.1:WP_066552034.1 154 KIRAGVVQIGPHRIAPDQID---FDAVHTNQLFAASAEVVGDWEAYLDGIRKAGSSVGAVVALEVTGVPAGWG 223
                                           ***********888876666...48999********************************************* PP

                             TIGR00033 216 eplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGGieGGitnGedir 287
                                            pl+ kld+ela+al+sinA+KgveiG+GFeaa+ +G +  De+ l+ +++  + +n+ GG++GGi++G++++
  NCBI__GCF_001636925.1:WP_066552034.1 224 APLYGKLDGELAAALMSINAAKGVEIGAGFEAAELTGEQNADEMRLDlNKQPVFLSNKAGGVLGGISTGQPVT 296
                                           ***********************************************888999******************** PP

                             TIGR00033 288 vriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekras 350
                                            r+a+Kp+++i + ++t++ +++e+  +tkgRhDpcv++ravpvvEam a vlada l++ra+
  NCBI__GCF_001636925.1:WP_066552034.1 297 ARVAFKPTSSILTLRQTITRDGEETDLRTKGRHDPCVALRAVPVVEAMAACVLADAHLRHRAQ 359
                                           ***********************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (361 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: 00:00:00.00
# Mc/sec: 16.79
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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