Alignments for a candidate for aroC in Geobacter uraniireducens Rf4

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Geobacter uraniireducens Rf4

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_011938713.1 GURA_RS09220 chorismate synthase

Query= SwissProt::O66493
         (398 letters)



>NCBI__GCF_000016745.1:WP_011938713.1
          Length = 393

 Score =  430 bits (1106), Expect = e-125
 Identities = 226/399 (56%), Positives = 287/399 (71%), Gaps = 15/399 (3%)

Query: 7   RFLTAGESHGKGLTAILEGIPANLPLSEEEINHELRRRQRGYGRGGRMKIEKDTAEILSG 66
           R+LTAGESHG  LTAI+EGIPA L LSEE+IN +L RRQ GYGRGGRM IEKD  EILSG
Sbjct: 3   RYLTAGESHGPQLTAIIEGIPAGLSLSEEQINIDLARRQCGYGRGGRMLIEKDQVEILSG 62

Query: 67  VRFGKTLGSPIALFIRNRDWENWKEKMAIEGEPSPSVVPFTRPRPGHADLSGGIKYNQRD 126
           VR+GKT+GSPI L +RNRDWENW EKM+         +  TR RPGHADL G +KYN  D
Sbjct: 63  VRWGKTIGSPITLCVRNRDWENWHEKMSPHERFHDDKIRVTRSRPGHADLPGAMKYNHHD 122

Query: 127 LRNILERASARETAARVAVGAVCKKFLSEFGIKIGSFVVSIGQKEVEELKDKSYFANPEK 186
           +RNILER+SARETA RVAVGAV K  LS+F I++  FV  +G   ++ ++          
Sbjct: 123 VRNILERSSARETAVRVAVGAVAKALLSQFEIEVCGFVAELG--GIKAIRPSL------P 174

Query: 187 LLSYHEKAEDSELRIPFPEKDEEFKTYIDEVKEKGESLGGVFEVFALNVPPGLGSHIQWD 246
           L +  + A  SEL       +EE K  ID V+++G+++GGV EV A+ VPPGLGSH+QWD
Sbjct: 175 LAALKDMAAKSELFTYDKSVEEEMKRLIDTVRDEGDTVGGVIEVNAVGVPPGLGSHVQWD 234

Query: 247 RRIDGRIAQAMMSIQAIKGVEIGLGFEAARRFGSQVHDEIGW-------SEGKGYFRHSN 299
           R++D R+A A++SIQA KGVEIG+GF+AA   GS+VHDEI +        E  G++R SN
Sbjct: 235 RKLDARLAMAVLSIQAFKGVEIGIGFQAAASTGSKVHDEIFYDSARIAHGEQSGFYRKSN 294

Query: 300 NLGGTEGGITNGMPIVVRVAMKPIPTLKNPLRSVDIETKEEMKAGKERTDIVAVPAASVV 359
           N GG EGGI+NG  IVVR AMKPIPTL  PLRSVDI +KE  +A  ER+D+ AVPAASVV
Sbjct: 295 NAGGIEGGISNGEEIVVRAAMKPIPTLYKPLRSVDIVSKEPYEATVERSDVCAVPAASVV 354

Query: 360 GEAMLAIVLADALLEKLGGDFMEEVKKRFEDYVNHVKSF 398
            EA++AI LADA + K GGD + E+K+ ++ Y++++++F
Sbjct: 355 AEAVVAIELADAFMVKFGGDSITEIKRNYQSYLDYLRAF 393


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: 482
Number of extensions: 17
Number of successful extensions: 3
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: 393
Length adjustment: 31
Effective length of query: 367
Effective length of database: 362
Effective search space:   132854
Effective search space used:   132854
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_011938713.1 GURA_RS09220 (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.2914.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-129  417.2   0.1   2.8e-129  417.0   0.1    1.0  1  lcl|NCBI__GCF_000016745.1:WP_011938713.1  GURA_RS09220 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016745.1:WP_011938713.1  GURA_RS09220 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.0   0.1  2.8e-129  2.8e-129       1     349 [.       2     372 ..       2     374 .. 0.92

  Alignments for each domain:
  == domain 1  score: 417.0 bits;  conditional E-value: 2.8e-129
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               +r++t+GeSHg++l+aii+G+Pagl+l+ee+i+ +l+rR+ g++r+ rm  E+D+veilsGv+ GkT G
  lcl|NCBI__GCF_000016745.1:WP_011938713.1   2 FRYLTAGESHGPQLTAIIEGIPAGLSLSEEQINIDLARRQCGYGRGGRMLIEKDQVEILSGVRWGKTIG 70 
                                               89******************************************************************* PP

                                 TIGR00033  70 aPiallikNkd.......vrskdyed......ikelpRPgHadytylkKYgikd.regggrsSaReTaa 124
                                               +Pi+l ++N+d       +++++           ++ RPgHad+ +  KY+ +d r++++rsSaReTa+
  lcl|NCBI__GCF_000016745.1:WP_011938713.1  71 SPITLCVRNRDwenwhekMSPHE--RfhddkiRVTRSRPGHADLPGAMKYNHHDvRNILERSSARETAV 137
                                               ***********988887744433..133455567899******************************** PP

                                 TIGR00033 125 rvaaGavakklLketagieivayvvklgevelee.esakeiskerldkspvrcpdaeaekemeeeidka 192
                                               rva+Gavak+lL++  +ie+ ++v +lg +++ + +      k+ ++ks+++ +d++ e+em+ +id++
  lcl|NCBI__GCF_000016745.1:WP_011938713.1 138 RVAVGAVAKALLSQ-FEIEVCGFVAELGGIKAIRpSLPLAALKDMAAKSELFTYDKSVEEEMKRLIDTV 205
                                               **************.55************7665505555889999999********************* PP

                                 TIGR00033 193 kkdgdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDel 259
                                               +++gd+vGgv+ev + +vp glG  +++++klda+la a+lsi+A+KgveiG GF+aa  +Gs+++De+
  lcl|NCBI__GCF_000016745.1:WP_011938713.1 206 RDEGDTVGGVIEVNAVGVPPGLGshVQWDRKLDARLAMAVLSIQAFKGVEIGIGFQAAASTGSKVHDEI 274
                                               ***********************9999*****************************************9 PP

                                 TIGR00033 260 vle........ddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRh 320
                                                ++        + ++ rk+nn GGieGGi+nGe+i+vr+a+Kpipt++kpl++vd+  ke+++at++R+
  lcl|NCBI__GCF_000016745.1:WP_011938713.1 275 FYDsariahgeQSGFYRKSNNAGGIEGGISNGEEIVVRAAMKPIPTLYKPLRSVDIVSKEPYEATVERS 343
                                               87621111112445679**************************************************** PP

                                 TIGR00033 321 DpcvvpravpvvEamvalvladallekra 349
                                               D+c+vp+a++v+Ea+va+ lada++ k++
  lcl|NCBI__GCF_000016745.1:WP_011938713.1 344 DVCAVPAASVVAEAVVAIELADAFMVKFG 372
                                               ***********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (393 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.26
//
[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