Alignments for a candidate for aroC in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Kyrpidia tusciae DSM 2912

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_041305460.1 BTUS_RS08555 chorismate synthase

Query= SwissProt::O66493
         (398 letters)



>NCBI__GCF_000092905.1:WP_041305460.1
          Length = 386

 Score =  443 bits (1140), Expect = e-129
 Identities = 228/390 (58%), Positives = 284/390 (72%), Gaps = 8/390 (2%)

Query: 6   LRFLTAGESHGKGLTAILEGIPANLPLSEEEINHELRRRQRGYGRGGRMKIEKDTAEILS 65
           LRFLTAGESHG  LTAI+EG+P+ LP+    I+ +LRRRQ+G+GRGGRM+IE D  EI S
Sbjct: 2   LRFLTAGESHGPELTAIVEGLPSRLPIRSALIDEQLRRRQQGHGRGGRMRIESDRVEITS 61

Query: 66  GVRFGKTLGSPIALFIRNRDWENWKEKMAIEGEPSPSVVPFTRPRPGHADLSGGIKYNQR 125
           G+RFG TLG+P+ + IRNRDWENWK KMA+EG+P P   P T+PRPGHADL+G +KYN  
Sbjct: 62  GLRFGLTLGTPLTMRIRNRDWENWKTKMAVEGDPPPEAKPVTKPRPGHADLAGVLKYNHD 121

Query: 126 DLRNILERASARETAARVAVGAVCKKFLSEFGIKIGSFVVSIGQKEVEELKDKSYFANPE 185
           D+RN+LER+SAR TA  VAVG+V ++ L+ FGI+I S VV IG  E ++         P+
Sbjct: 122 DVRNVLERSSARNTATLVAVGSVARQLLAPFGIRIFSHVVEIGGVEAKKF--------PK 173

Query: 186 KLLSYHEKAEDSELRIPFPEKDEEFKTYIDEVKEKGESLGGVFEVFALNVPPGLGSHIQW 245
            L    + AE S +R   PE  E+    ID+ + +G +LGGVFEV AL VPPGLGS+   
Sbjct: 174 TLEQIADAAELSTVRCADPEAAEKMVEAIDQARREGNTLGGVFEVVALGVPPGLGSYAHP 233

Query: 246 DRRIDGRIAQAMMSIQAIKGVEIGLGFEAARRFGSQVHDEIGWSEGKGYFRHSNNLGGTE 305
           DRR+DGR+A A+MSIQAIKGVE+GLGF AAR  GS+VHDEIG+   KGY R +N+ GG E
Sbjct: 234 DRRLDGRLAGALMSIQAIKGVEVGLGFTAARLPGSEVHDEIGYDPEKGYTRDTNHAGGIE 293

Query: 306 GGITNGMPIVVRVAMKPIPTLKNPLRSVDIETKEEMKAGKERTDIVAVPAASVVGEAMLA 365
           GG++NG P+VVR AMKPIPTL  PLRSVDI +KE  +A  ER+D  AVPAA+VVGEAM A
Sbjct: 294 GGVSNGQPVVVRAAMKPIPTLYKPLRSVDIHSKESFQASVERSDTCAVPAAAVVGEAMTA 353

Query: 366 IVLADALLEKLGGDFMEEVKKRFEDYVNHV 395
            VLA    EK  GD +EEVK ++  Y+  V
Sbjct: 354 WVLALCFREKFSGDSLEEVKAQYRAYMEMV 383


Lambda     K      H
   0.317    0.137    0.394 

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: 475
Number of extensions: 17
Number of successful extensions: 2
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: 398
Length of database: 386
Length adjustment: 31
Effective length of query: 367
Effective length of database: 355
Effective search space:   130285
Effective search space used:   130285
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_041305460.1 BTUS_RS08555 (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.2893.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-127  411.9   0.0   1.2e-127  411.7   0.0    1.0  1  lcl|NCBI__GCF_000092905.1:WP_041305460.1  BTUS_RS08555 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_041305460.1  BTUS_RS08555 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.7   0.0  1.2e-127  1.2e-127       1     347 [.       2     363 ..       2     367 .. 0.94

  Alignments for each domain:
  == domain 1  score: 411.7 bits;  conditional E-value: 1.2e-127
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               lr++t+GeSHg++l+ai++GlP+ l++  + i ++l+rR++g++r+ rmr E+D+vei+sG++ G T G
  lcl|NCBI__GCF_000092905.1:WP_041305460.1   2 LRFLTAGESHGPELTAIVEGLPSRLPIRSALIDEQLRRRQQGHGRGGRMRIESDRVEITSGLRFGLTLG 70 
                                               699****************************************************************** PP

                                 TIGR00033  70 aPiallikNkd...........vrskdyedikelpRPgHadytylkKYgikd.regggrsSaReTaarv 126
                                               +P+++ i+N+d            ++ +  +  ++pRPgHad++++ KY+ +d r+ ++rsSaR Ta++v
  lcl|NCBI__GCF_000092905.1:WP_041305460.1  71 TPLTMRIRNRDwenwktkmaveGDPPPEAKPVTKPRPGHADLAGVLKYNHDDvRNVLERSSARNTATLV 139
                                               ***********8887776663333334444899************************************ PP

                                 TIGR00033 127 aaGavakklLketagieivayvvklgeveleeesak.eiskerldkspvrcpdaeaekemeeeidkakk 194
                                               a+G+va++lL+   gi+i ++vv++g ve+++   + e + ++++ s+vrc+d+ea+++m+e id+a++
  lcl|NCBI__GCF_000092905.1:WP_041305460.1 140 AVGSVARQLLAP-FGIRIFSHVVEIGGVEAKKFPKTlEQIADAAELSTVRCADPEAAEKMVEAIDQARR 207
                                               ************.88***************9877667778888888*********************** PP

                                 TIGR00033 195 dgdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvl 261
                                               +g+++Ggv evv+ +vp glG   + +++ld++la al+si+A+Kgve+G GF+aa+ +Gse++De+ +
  lcl|NCBI__GCF_000092905.1:WP_041305460.1 208 EGNTLGGVFEVVALGVPPGLGsyAHPDRRLDGRLAGALMSIQAIKGVEVGLGFTAARLPGSEVHDEIGY 276
                                               *********************98899******************************************* PP

                                 TIGR00033 262 e.ddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvprav 329
                                               + +++++r tn+ GGieGG++nG++++vr+a+Kpipt++kpl++vd++ ke+ +a+++R+D c+vp+a+
  lcl|NCBI__GCF_000092905.1:WP_041305460.1 277 DpEKGYTRDTNHAGGIEGGVSNGQPVVVRAAMKPIPTLYKPLRSVDIHSKESFQASVERSDTCAVPAAA 345
                                               *999***************************************************************** PP

                                 TIGR00033 330 pvvEamvalvladallek 347
                                               +v Eam+a vla  + ek
  lcl|NCBI__GCF_000092905.1:WP_041305460.1 346 VVGEAMTAWVLALCFREK 363
                                               ***********9666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (386 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: 10.38
//
[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