Alignments for a candidate for aroA in Chlorobaculum parvum NCIB 8327

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Chlorobaculum parvum NCIB 8327

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_012501549.1 CPAR_RS01510 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::B8CWX4
         (430 letters)



>NCBI__GCF_000020505.1:WP_012501549.1
          Length = 434

 Score =  280 bits (716), Expect = 6e-80
 Identities = 175/433 (40%), Positives = 255/433 (58%), Gaps = 17/433 (3%)

Query: 12  KGEIN-IPGDKSISHRSVIFTSLAEGRSLIRGFLESEDCLNTLRAFQMMGVNI--EKIKP 68
           +GE++ +P DKSISHR+ I  SLAEG + I  F    D  +TL   + +G+++  +++  
Sbjct: 5   QGEVSSLPPDKSISHRAAIIGSLAEGTTEITNFSGGFDNQSTLSVLRDLGISVRQDEVPA 64

Query: 69  GE------YIVNGVGLYGLKEPGDVIDCGNSGTGMRLLCGLLAPQPFYSVLTGDNSLRNR 122
           G+       ++   GL+  +EP + + C NSG+ MR++ G+LA QPF S L GD SL  R
Sbjct: 65  GDGRIVRHVVIESNGLWSFREPSEPLMCNNSGSTMRMMAGILAAQPFRSELVGDASLMKR 124

Query: 123 PMGRVVNPLRQMGASIWCRDGGYAPLSIKGEK-LEGISYTLPVASAQVKSSLLLAGLYSQ 181
           PM RV +PLR MGA I   D G AP+ I G K L+ I Y LPV SAQVKS + LA L++ 
Sbjct: 125 PMKRVADPLRMMGADISLSDAGTAPVVINGTKDLKTIEYLLPVPSAQVKSLVALAALHAD 184

Query: 182 GDVFLTEPGPSRDHTERMLKGFGVKVYKKGNSIKLPHSEDTK-LTPQEVLIPGDISSAAF 240
           G   + EP  SRDHTE ML   G++   + + ++    +  K +  +   +P D S+A F
Sbjct: 185 GQSKIIEPIRSRDHTELML---GLETIDRPDGVREIIIDGRKPIAAKPFKVPADPSAACF 241

Query: 241 FIVASLITPGSEILLKNVGLNPTRCGIIDVVRQMGGNLELLNVREVNGEKSADILVK-YS 299
            I   L+   SEI+L++V LNPTR   IDV+++ G  L + NVR   GE   DI+V+  S
Sbjct: 242 MIALGLLGERSEIVLRDVCLNPTRVAYIDVLQEAGAGLGIENVRSEGGEPVGDIVVRSCS 301

Query: 300 ELEGVHI-DGDIIPRLIDEIPVIAVLASQARGETVIRDAAELKVKETDRIKATVTELGKS 358
            L  + I D  ++  +IDE+P++AVL++ A GE  + +A EL+ KE+DRI+A V+ L + 
Sbjct: 302 SLAPLRISDHAVVAGVIDELPMLAVLSAFATGEFELHNATELRTKESDRIEAVVSNLERL 361

Query: 359 GVDIEELPDGMVIKG-PCSIIGGVKLESYKDHRIAMSLAVAGLLAEEQITIKNSECINTS 417
           G   E+ PDG V+KG P        +E + DHRIAMS A+A   A   + + + E    S
Sbjct: 362 GFACEQYPDGFVVKGRPTVNREEAVIECFDDHRIAMSFAIAAEAAGASLRLSDREVAGVS 421

Query: 418 FPQFNKLLQKLIQ 430
           FP F  L++ L Q
Sbjct: 422 FPNFFALIESLKQ 434


Lambda     K      H
   0.317    0.138    0.392 

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: 448
Number of extensions: 31
Number of successful extensions: 6
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: 430
Length of database: 434
Length adjustment: 32
Effective length of query: 398
Effective length of database: 402
Effective search space:   159996
Effective search space used:   159996
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: 51 (24.3 bits)

Align candidate WP_012501549.1 CPAR_RS01510 (3-phosphoshikimate 1-carboxyvinyltransferase)
to HMM TIGR01356 (aroA: 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))

# 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/TIGR01356.hmm
# target sequence database:        /tmp/gapView.24714.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01356  [M=415]
Accession:   TIGR01356
Description: aroA: 3-phosphoshikimate 1-carboxyvinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.8e-109  351.2   0.0   4.3e-109  351.0   0.0    1.0  1  lcl|NCBI__GCF_000020505.1:WP_012501549.1  CPAR_RS01510 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020505.1:WP_012501549.1  CPAR_RS01510 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.0   0.0  4.3e-109  4.3e-109       4     413 ..      10     433 ..       6     434 .] 0.92

  Alignments for each domain:
  == domain 1  score: 351.0 bits;  conditional E-value: 4.3e-109
                                 TIGR01356   4 kipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee...ke.....elviegv 63 
                                               ++p++KSishRa ++++Laeg+t++tn+  + D ++tl++lr+lG++v+ +e   ++     ++vie +
  lcl|NCBI__GCF_000020505.1:WP_012501549.1  10 SLPPDKSISHRAAIIGSLAEGTTEITNFSGGFDNQSTLSVLRDLGISVRqDEvpaGDgrivrHVVIESN 78 
                                               58**********************************************943333222222225677777 PP

                                 TIGR01356  64 gg..lkepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeeg 130
                                               g   ++ep++ l ++nsG t+R++ g+la++++ ++l gd sl kRP++r+ ++Lr++ga+i+ ++ +g
  lcl|NCBI__GCF_000020505.1:WP_012501549.1  79 GLwsFREPSEPLMCNNSGSTMRMMAGILAAQPFRSELVGDASLMKRPMKRVADPLRMMGADISLSD-AG 146
                                               768899999******************************************************877.79 PP

                                 TIGR01356 131 slPlaisgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgve 198
                                               ++P++i+g++ +  i +l +  S+Q+ks + laa   l+a++ + ++e++ sr+++e++L l       
  lcl|NCBI__GCF_000020505.1:WP_012501549.1 147 TAPVVINGTKDLkTIEYLLPVPSAQVKSLVALAA---LHADGQSKIIEPIRSRDHTELMLGLET----- 207
                                               *********9998999******************...88899999999***********97644..... PP

                                 TIGR01356 199 veeede.rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLee 265
                                               +++ d+ r+i++ g + ++ k ++v++D+S+A+f++a++++ ++ e++++++  n+t+     i+vL+e
  lcl|NCBI__GCF_000020505.1:WP_012501549.1 208 IDRPDGvREIIIDGRKPIAAKPFKVPADPSAACFMIALGLLGERsEIVLRDVCLNPTRVA--YIDVLQE 274
                                               67777779******99988888**********************9*************99..888**** PP

                                 TIGR01356 266 mGadveveeqr........dvevegasklkgvkv.d.idvdsliDelptlavlaafAegetriknieel 324
                                                Ga + +e+ r        d++v++ s+l ++++ d + v+ +iDelp+lavl+afA ge +++n+ el
  lcl|NCBI__GCF_000020505.1:WP_012501549.1 275 AGAGLGIENVRseggepvgDIVVRSCSSLAPLRIsDhAVVAGVIDELPMLAVLSAFATGEFELHNATEL 343
                                               *******999999*********************9757899**************************** PP

                                 TIGR01356 325 RvkEsdRiaaiaeeLeklGveveeledgllieGkk.kelkgavvdtydDHRiamalavlglaaegevei 392
                                               R kEsdRi+a++++Le+lG  +e+ +dg++++G+   + ++av++++dDHRiam++a+++ aa + +++
  lcl|NCBI__GCF_000020505.1:WP_012501549.1 344 RTKESDRIEAVVSNLERLGFACEQYPDGFVVKGRPtVNREEAVIECFDDHRIAMSFAIAAEAAGASLRL 412
                                               **********************************8555566**************************** PP

                                 TIGR01356 393 edaecvaksfPeFfevleqlg 413
                                                d e++ +sfP+Ff ++e+l+
  lcl|NCBI__GCF_000020505.1:WP_012501549.1 413 SDREVAGVSFPNFFALIESLK 433
                                               *****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (434 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: 00:00:00.02
# Mc/sec: 8.17
//
[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