Alignments for a candidate for aroC in Acidimicrobium ferrooxidans DSM 10331

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Acidimicrobium ferrooxidans DSM 10331

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_015799113.1 AFER_RS08890 chorismate synthase

Query= SwissProt::P9WPY1
         (401 letters)



>NCBI__GCF_000023265.1:WP_015799113.1
          Length = 392

 Score =  392 bits (1007), Expect = e-114
 Identities = 213/387 (55%), Positives = 265/387 (68%), Gaps = 13/387 (3%)

Query: 1   MLRWITAGESHGRALVAVVEGMVAGVHVTSADIADQLARRRLGYGRGARMTFERDAVTVL 60
           MLRW+T GESHGRAL  ++EG+ AG+ +    I+ +LARRRLGYGRG RM FE+DA+T++
Sbjct: 1   MLRWLTGGESHGRALAVIIEGVPAGLELVGDAISAELARRRLGYGRGPRMRFEQDALTII 60

Query: 61  SGIRHGSTLGGPIAIEIGNTEWP-KWETVMAADPVDPAELADVARNAPLTRPRPGHADYA 119
            G+RHG TLG PI +EI N+EW  KW   M+ DP   A          LT PRPGHAD A
Sbjct: 61  GGVRHGRTLGSPIVLEIANSEWERKWTEEMSPDPGQTAR--------KLTAPRPGHADLA 112

Query: 120 GMLKYGFDDARPVLERASARETAARVAAGTVARAFLRQALGVEVLSHVISIGASAPYEGP 179
           G+ KYGFDDAR VLERASARETAARVAAG VA+A L   LGV ++SHV+ +GA+      
Sbjct: 113 GLQKYGFDDARNVLERASARETAARVAAGAVAKALL-GVLGVGIVSHVVQLGAARVSVET 171

Query: 180 PPRAEDLPAIDASPVRAYDKAAEADMIAQIEAAKKDGDTLGGVVEAVALGLPVGLGSFTS 239
            P   D   IDAS VR  D A EA MIA++ AA K GD+LGG  + VA G+PVGLGS+  
Sbjct: 172 VPTLGDRERIDASEVRCLDPAVEAAMIAEVRAAAKVGDSLGGAAQVVAHGVPVGLGSYVH 231

Query: 240 GDHRLDSQLAAAVMGIQAIKGVEIGDGFQTARRRGSRAHDEMYPGPDGVVRSTNRAGGLE 299
            D RLD  L  A++ I A+K V IG G + A  RGS AHD +      + R T+RAGG+E
Sbjct: 232 WDRRLDGLLGQALLSIPAVKAVSIGAGLEVAGVRGSLAHDAIVGSQ--LERPTDRAGGIE 289

Query: 300 GGMTNGQPLRVRAAMKPISTVPR-ALATVDLATGDEAVAIHQRSDVCAVPAAGVVVETMV 358
           GG++NG P+   A MKP++T+ R  + TVDLATG+ ++A  +R+DV AVPA GVV E MV
Sbjct: 290 GGVSNGSPIVATAWMKPLATLNRPVIETVDLATGERSIAFRERTDVTAVPAMGVVAEAMV 349

Query: 359 ALVLARAALEKFGGDSLAETQRNIAAY 385
           ALVLA  AL KFGGDS+AE +RN  +Y
Sbjct: 350 ALVLADEALRKFGGDSIAEFRRNAESY 376


Lambda     K      H
   0.317    0.133    0.380 

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: 533
Number of extensions: 27
Number of successful extensions: 5
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: 401
Length of database: 392
Length adjustment: 31
Effective length of query: 370
Effective length of database: 361
Effective search space:   133570
Effective search space used:   133570
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 WP_015799113.1 AFER_RS08890 (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.2581.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-116  375.1   0.3   1.8e-116  374.9   0.3    1.0  1  lcl|NCBI__GCF_000023265.1:WP_015799113.1  AFER_RS08890 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023265.1:WP_015799113.1  AFER_RS08890 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  374.9   0.3  1.8e-116  1.8e-116       1     350 [.       2     363 ..       2     364 .. 0.94

  Alignments for each domain:
  == domain 1  score: 374.9 bits;  conditional E-value: 1.8e-116
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               lr++t GeSHg+al++ii+G+Paglel  + i+ el+rRr g++r+ rmr E+D+++i++Gv++G+T G
  lcl|NCBI__GCF_000023265.1:WP_015799113.1   2 LRWLTGGESHGRALAVIIEGVPAGLELVGDAISAELARRRLGYGRGPRMRFEQDALTIIGGVRHGRTLG 70 
                                               699****************************************************************** PP

                                 TIGR00033  70 aPiallikNkd........vrskdyed..ikelpRPgHadytylkKYgikd.regggrsSaReTaarva 127
                                               +Pi l i N +        +++++ +   + + pRPgHad+++l+KYg++d r+ ++r+SaReTaarva
  lcl|NCBI__GCF_000023265.1:WP_015799113.1  71 SPIVLEIANSEwerkwteeMSPDPGQTarKLTAPRPGHADLAGLQKYGFDDaRNVLERASARETAARVA 139
                                               ***********6666666554444443668899******************9***************** PP

                                 TIGR00033 128 aGavakklLketagieivayvvklgeveleeesak.eiskerldkspvrcpdaeaekemeeeidkakkd 195
                                               aGavak+lL    g+ iv++vv+lg  +++ e++     +er+d+s+vrc+d+  e++m +e+  a k 
  lcl|NCBI__GCF_000023265.1:WP_015799113.1 140 AGAVAKALLGV-LGVGIVSHVVQLGAARVSVETVPtLGDRERIDASEVRCLDPAVEAAMIAEVRAAAKV 207
                                               *********99.89************777766555334699**************************** PP

                                 TIGR00033 196 gdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle 262
                                               gds+Gg  +vv+++vpvglG  ++++++ld+ l++allsi+AvK+v iG+G e a vrGs a+D +v  
  lcl|NCBI__GCF_000023265.1:WP_015799113.1 208 GDSLGGAAQVVAHGVPVGLGsyVHWDRRLDGLLGQALLSIPAVKAVSIGAGLEVAGVRGSLAHDAIVG- 275
                                               ********************999*****************************************8886. PP

                                 TIGR00033 263 ddkirrktnnsGGieGGitnGedirvriavKpiptikkpl.ktvdletkekakatkgRhDpcvvpravp 330
                                                 +++r t++ GGieGG++nG++i+  + +Kp +t+++p  +tvdl+t e   a ++R D+++vp+ ++
  lcl|NCBI__GCF_000023265.1:WP_015799113.1 276 -SQLERPTDRAGGIEGGVSNGSPIVATAWMKPLATLNRPViETVDLATGERSIAFRERTDVTAVPAMGV 343
                                               .5799*********************************9648*************************** PP

                                 TIGR00033 331 vvEamvalvladallekras 350
                                               v+Eamvalvlad++l+k++ 
  lcl|NCBI__GCF_000023265.1:WP_015799113.1 344 VAEAMVALVLADEALRKFGG 363
                                               ***************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (392 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.05
//
[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