Alignments for a candidate for aroC in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Bacteroides thetaiotaomicron VPI-5482

Align chorismate synthase (EC 4.2.3.5) (characterized)
to candidate 351612 BT2084 chorismate synthase (NCBI ptt file)

Query= BRENDA::B5AAU3
         (442 letters)



>FitnessBrowser__Btheta:351612
          Length = 358

 Score =  365 bits (936), Expect = e-105
 Identities = 188/351 (53%), Positives = 240/351 (68%), Gaps = 5/351 (1%)

Query: 56  NIFGDYFQVATYGESHGGGVGCVISGCPPRIPLTEEDMQGDLDRRRPGQSRITTPRKETD 115
           N FG+ F++ ++GESHG GVG VI G P  I + EE +Q +L+RRRPGQS +TTPRKE D
Sbjct: 3   NSFGNIFRLTSFGESHGKGVGGVIDGFPSGITIDEEFVQQELNRRRPGQSILTTPRKEAD 62

Query: 116 TCKILSGTYEGMTTGTPIHVFVPNTDQRGGDYTEMAKAYRPSHADLTYDLKYGVRSVQGG 175
             + LSG +EG +TG PI   V N +Q   DY  + + YRPSHAD TY +KYG+R  +GG
Sbjct: 63  KVEFLSGIFEGKSTGCPIGFIVWNENQHSNDYNNLKEVYRPSHADYTYKVKYGIRDHRGG 122

Query: 176 GRSSARETIGRVAAGAVAKKILKLKCGVEILAFVSKVHQVVLPEDAVDYETLTLDQIESN 235
           GRSSARETI RV AGA+AK  L+ + G+ I A+ S+V  + L     DY+   LD IE+N
Sbjct: 123 GRSSARETISRVVAGALAKLALR-QLGISITAYTSQVGAIKLEGTYSDYD---LDLIETN 178

Query: 236 ICRCPDPEYAQKMIDAIDKVRINGNSIGGVVTCIARNVPRGLGSPVFDKLEALLAKAMLS 295
             RCPDPE A++M D I KV+  G++IGG +TC+ +  P GLG PVF KL A L  AMLS
Sbjct: 179 DVRCPDPEKAKEMADLIYKVKGEGDTIGGTLTCVIKGCPIGLGQPVFGKLHAALGNAMLS 238

Query: 296 LPASKGFEIGSGFAGTDLTGSEHNDEFYMDEGGNVRTRTNRSGGVQGGISNGETIYFKVA 355
           + A+K FE G GF G  + GSE ND F+ +  G + T TN SGG+QGGISNG+ IYF+V 
Sbjct: 239 INAAKAFEYGEGFKGLKMKGSEQNDVFF-NNNGRIETHTNHSGGIQGGISNGQDIYFRVV 297

Query: 356 FKPTATIGKKQNTVTRDHEDIELLTRGRHDPCVVPRAVPMVETMAALVLMD 406
           FKP AT+  +Q TV  D  D  L  RGRHD CV+PRAVP+VE MAA+ ++D
Sbjct: 298 FKPIATLLMEQETVNIDGVDTTLKARGRHDACVLPRAVPIVEAMAAMTILD 348


Lambda     K      H
   0.317    0.135    0.396 

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: 460
Number of extensions: 26
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: 442
Length of database: 358
Length adjustment: 31
Effective length of query: 411
Effective length of database: 327
Effective search space:   134397
Effective search space used:   134397
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 351612 BT2084 (chorismate synthase (NCBI ptt file))
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.18369.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.7e-140  453.2   0.1   3.1e-140  453.0   0.1    1.0  1  lcl|FitnessBrowser__Btheta:351612  BT2084 chorismate synthase (NCBI


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:351612  BT2084 chorismate synthase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.0   0.1  3.1e-140  3.1e-140       1     348 [.       9     354 ..       9     357 .. 0.98

  Alignments for each domain:
  == domain 1  score: 453.0 bits;  conditional E-value: 3.1e-140
                          TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPialli 76 
                                        +rlt fGeSHgk +g +idG+P+g++++ee +q+el+rRrpgqs+lt++rkE+D+ve+lsG+feGk tG Pi +++
  lcl|FitnessBrowser__Btheta:351612   9 FRLTSFGESHGKGVGGVIDGFPSGITIDEEFVQQELNRRRPGQSILTTPRKEADKVEFLSGIFEGKSTGCPIGFIV 84 
                                        89************************************************************************** PP

                          TIGR00033  77 kNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagieivayvvklg 152
                                         N++++s+dy+++ke++RP+Hadyty +KYgi+d++gggrsSaReT+ rv+aGa+ak  L++  gi i+ay++++g
  lcl|FitnessBrowser__Btheta:351612  85 WNENQHSNDYNNLKEVYRPSHADYTYKVKYGIRDHRGGGRSSARETISRVVAGALAKLALRQ-LGISITAYTSQVG 159
                                        **************************************************************.88*********** PP

                          TIGR00033 153 eveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplfdkldaelas 228
                                         ++le ++ + +  + ++++ vrcpd+e++kem ++i k+k +gd++Gg +++v+++ p glG+p+f kl+a+l++
  lcl|FitnessBrowser__Btheta:351612 160 AIKLEGTYSD-YDLDLIETNDVRCPDPEKAKEMADLIYKVKGEGDTIGGTLTCVIKGCPIGLGQPVFGKLHAALGN 234
                                        *****97776.68999************************************************************ PP

                          TIGR00033 229 allsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGedirvriavKpiptikkplkt 304
                                        a+lsinA+K++e G+GF+  +++Gse nD +  ++++i+++tn+sGGi+GGi+nG+di++r+++Kpi+t+  +++t
  lcl|FitnessBrowser__Btheta:351612 235 AMLSINAAKAFEYGEGFKGLKMKGSEQNDVFFNNNGRIETHTNHSGGIQGGISNGQDIYFRVVFKPIATLLMEQET 310
                                        **************************************************************************** PP

                          TIGR00033 305 vdletkekakatkgRhDpcvvpravpvvEamvalvladallekr 348
                                        v++++ +++  ++gRhD cv+pravp+vEam a++++d +l ++
  lcl|FitnessBrowser__Btheta:351612 311 VNIDGVDTTLKARGRHDACVLPRAVPIVEAMAAMTILDYYLLDK 354
                                        **************************************988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (358 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: 12.19
//
[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