Alignments for a candidate for aroA in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Denitrovibrio acetiphilus DSM 12809

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_013012189.1 DACET_RS14910 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::K9RIB8
         (448 letters)



>NCBI__GCF_000025725.1:WP_013012189.1
          Length = 426

 Score =  323 bits (827), Expect = 9e-93
 Identities = 178/421 (42%), Positives = 256/421 (60%), Gaps = 6/421 (1%)

Query: 28  SLSGSIRVPGDKSISHRALMLGALAEGETRIEGLLLGEDPRSTAKCFQAMGALVSDLNTE 87
           S+ G++RVP DKSISHR+ ML ++A+G  R+   LL  D ++T    +A+G    +    
Sbjct: 9   SIKGTVRVPSDKSISHRSFMLLSMAKGRGRVIDPLLSADTKATMAAMRAVGVQFEETVNG 68

Query: 88  LVRVKGIGLGNLLEPVDVLDAGNSGTTLRLMLGILASHAGRFFSITGDSSLRSRPMSRVV 147
            V +   G  N  EP DV+D  NSGT+ RL+ G+ A    +++ +TGD+S+R RPM RV+
Sbjct: 69  FV-ITSDGYQNFKEPSDVIDCMNSGTSARLLTGVFAP-TNKYYVLTGDNSMRKRPMDRVI 126

Query: 148 KPLEQMGAQIWGRDNNSKAPLAVRGENLKPIHYHSPIASAQVKSCVLLAGLSVEGKTTVT 207
            PL +MGA+   RDN SK PL +      P+   +   SAQVKS +LLAG+  EG TT T
Sbjct: 127 LPLTEMGAKFAARDNGSKLPLTILPSVTNPVELTASTKSAQVKSAILLAGVQTEGVTTYT 186

Query: 208 EPALSRDHSERMLQAFGAKLDIDTQTNSVSVNGPVKLYGQSVVVPGDISSAAFWLVAGAI 267
           E A++R+H+E ML A GA L +D     +SV G   L    VVVPGD SSAAF+L    +
Sbjct: 187 EKAVTRNHTEIMLSALGANLTVDGL--KISVEGAADLRSIDVVVPGDFSSAAFFLGGTLM 244

Query: 268 VSDSELLIENVGVNPTRTGVLEALEMMGAEIARENEREVAGEPVADLRVRSSKLKGCTIE 327
             +SEL++ENVG+NPTR+G+L  L  MG +   ++ER  A E + D+ ++S   +GCTI+
Sbjct: 245 FDNSELILENVGLNPTRSGMLNVLTQMGVKYEIDSERGGA-EKLGDICIKSQSFEGCTID 303

Query: 328 GDIIPRLIDEIPILAVAAVFAEGTTVIKDAAELRVKESDRITVMANQLNSMGARITELDD 387
           GDI+  +IDE+P++A   +FA     I++A ELRVKESDRI      L  +GA + E +D
Sbjct: 304 GDIVANMIDELPMVATLGLFANSPVTIRNAKELRVKESDRIEATLYNLRQLGAEVEEYED 363

Query: 388 GMEITGGTPLTG-AELDSFTDHRIAMSLAIAALNASGTTTINRAEAASVSYPDFFETIKR 446
           GM++     +   AEL +F DHR+AM   + A    G  T++  +   VS+P F ET + 
Sbjct: 364 GMKVYPIKSVNDKAELKAFDDHRMAMIAIMLAKRFGGNITVDDMQCVDVSFPTFIETFES 423

Query: 447 I 447
           +
Sbjct: 424 L 424


Lambda     K      H
   0.316    0.132    0.363 

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: 453
Number of extensions: 18
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: 448
Length of database: 426
Length adjustment: 32
Effective length of query: 416
Effective length of database: 394
Effective search space:   163904
Effective search space used:   163904
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_013012189.1 DACET_RS14910 (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.27709.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-117  378.0   0.3   3.1e-117  377.8   0.3    1.0  1  lcl|NCBI__GCF_000025725.1:WP_013012189.1  DACET_RS14910 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025725.1:WP_013012189.1  DACET_RS14910 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.8   0.3  3.1e-117  3.1e-117       1     412 [.      12     424 ..      12     426 .] 0.95

  Alignments for each domain:
  == domain 1  score: 377.8 bits;  conditional E-value: 3.1e-117
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg..lk 67 
                                               g +++p++KSishR+++l ++a+g+ +v ++L s+Dt+at+ a+r+ G+++ee+ + +vi+  g+  +k
  lcl|NCBI__GCF_000025725.1:WP_013012189.1  12 GTVRVPSDKSISHRSFMLLSMAKGRGRVIDPLLSADTKATMAAMRAVGVQFEETVNGFVITSDGYqnFK 80 
                                               789*************************************************9988888876655559* PP

                                 TIGR01356  68 epeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlai 136
                                               ep++++d+ nsGt+aRlltgv a +++ +vltgd+s++kRP++r++ +L e+ga++ ++++ ++lPl+i
  lcl|NCBI__GCF_000025725.1:WP_013012189.1  81 EPSDVIDCMNSGTSARLLTGVFAPTNKYYVLTGDNSMRKRPMDRVILPLTEMGAKFAARDNGSKLPLTI 149
                                               ********************************************************************* PP

                                 TIGR01356 137 sgplkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeeder 205
                                                  ++ ++   + + S+Q+ksa+lla+    q++++++++ek ++r+++ei+L  l++    ++++   
  lcl|NCBI__GCF_000025725.1:WP_013012189.1 150 LPSVTNPVELTASTKSAQVKSAILLAG---VQTEGVTTYTEKAVTRNHTEIMLSALGAN---LTVDGL- 211
                                               *97776666667788************...6889**********************988...999876. PP

                                 TIGR01356 206 kivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveve 273
                                               ki+v+g +  ++ +v v+gD+SsAaffl   ++  + e+ +en+g n+t+ +  +++vL +mG + e++
  lcl|NCBI__GCF_000025725.1:WP_013012189.1 212 KISVEGAADLRSIDVVVPGDFSSAAFFLGGTLMFDNsELILENVGLNPTRSG--MLNVLTQMGVKYEID 278
                                               *******9999999*******************9999***************..999************ PP

                                 TIGR01356 274 eqr.......dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaa 334
                                               ++r       d+ ++ +++++g ++    v+++iDelp++a+l++fA+ + +i+n++elRvkEsdRi+a
  lcl|NCBI__GCF_000025725.1:WP_013012189.1 279 SERggaeklgDICIK-SQSFEGCTIdGDIVANMIDELPMVATLGLFANSPVTIRNAKELRVKESDRIEA 346
                                               ***************.678******66889*************************************** PP

                                 TIGR01356 335 iaeeLeklGveveeledgllieGkkkelkg.avvdtydDHRiamalavlglaaegeveiedaecvaksf 402
                                               +  +L++lG+evee edg+++++ k ++++ a+++ +dDHR+am   +l+ +  g+++++d +cv++sf
  lcl|NCBI__GCF_000025725.1:WP_013012189.1 347 TLYNLRQLGAEVEEYEDGMKVYPIK-SVNDkAELKAFDDHRMAMIAIMLAKRFGGNITVDDMQCVDVSF 414
                                               ************************6.66555************************************** PP

                                 TIGR01356 403 PeFfevleql 412
                                               P F+e  e+l
  lcl|NCBI__GCF_000025725.1:WP_013012189.1 415 PTFIETFESL 424
                                               *****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (426 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: 10.03
//
[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