Alignments for a candidate for aroA in Novosphingobium aromaticivorans DSM 12444

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Novosphingobium aromaticivorans DSM 12444

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_011444984.1 SARO_RS06630 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q9R4E4
         (455 letters)



>NCBI__GCF_000013325.1:WP_011444984.1
          Length = 441

 Score =  473 bits (1217), Expect = e-138
 Identities = 252/434 (58%), Positives = 302/434 (69%), Gaps = 1/434 (0%)

Query: 8   RPATARKSSGLSGTVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGKAMQAMG 67
           RP     +  L G + +PGDKSISHRS M G LA GETR+TGLLEGEDV++T  AM+AMG
Sbjct: 2   RPRRFTANGPLKGRIGVPGDKSISHRSIMLGALAVGETRVTGLLEGEDVLSTAAAMRAMG 61

Query: 68  ARIRKEGD-TWIIDGVGNGGLLAPEAPLDFGNAATGCRLTMGLVGVYDFDSTFIGDASLT 126
           A I ++ D  W + GVG GGLL P+  LD GN+ T  RL MGLV  +   +TF+GDASL+
Sbjct: 62  ATIERDADGMWHVHGVGVGGLLQPQQALDMGNSGTSTRLLMGLVATHPITATFVGDASLS 121

Query: 127 KRPMGRVLNPLREMGVQVKSEDGDRLPVTLRGPKTPTPITYRVPMASAQVKSAVLLAGLN 186
           KRPMGRV++PL  MG +  +  G RLP+TLRG     PI YR+P+ASAQVKSAVLLAGLN
Sbjct: 122 KRPMGRVIDPLSTMGAEFTASPGGRLPLTLRGISPAVPIEYRLPVASAQVKSAVLLAGLN 181

Query: 187 TPGITTVIEPIMTRDHTEKMLQGFGANLTVETDADGVRTIRLEGRGKLTGQVIDVPGDPS 246
           TPG+TTVIEPI TRDH+E+ML+GFGA LTV+  ADG R IR+ G  +L  Q I VPGDPS
Sbjct: 182 TPGVTTVIEPIPTRDHSERMLRGFGAELTVDVAADGARVIRVRGEAELKPQDIAVPGDPS 241

Query: 247 STAFPLVAALLVPGSDVTILNVLMNPTRTGLILTLQEMGADIEVINPRLAGGEDVADLRV 306
           S AF +VAALLV GSD+ + NV +NPTR  L   L+ MG  IE +N R  GGE VADLRV
Sbjct: 242 SAAFFVVAALLVEGSDLVVENVGLNPTRAALFDVLRLMGGSIEELNRREVGGEPVADLRV 301

Query: 307 RSSTLKGVTVPEDRAPSMIDEYPILAVAAAFAEGATVMNGLEELRVKESDRLSAVANGLK 366
           R S L G+ V     PSM+DE+P+L VAAA A+G TV  GLEELRVKESDR+SA+   L+
Sbjct: 302 RHSLLTGIDVDPAVVPSMVDEFPVLFVAAALAKGRTVTTGLEELRVKESDRISAMRAALE 361

Query: 367 LNGVDCDEGETSLVVRGRPDGKGLGNASGAAVATHLDHRIAMSFLVMGLVSENPVTVDDA 426
           L G    E E  L++ G       G A GA+V THLDHRIAMS  + G+ S N V VDD 
Sbjct: 362 LAGATVTETEDGLIIDGTGGDPLPGTAEGASVVTHLDHRIAMSMAIAGIASRNGVEVDDT 421

Query: 427 TMIATSFPEFMDLM 440
             IATSFP F  L+
Sbjct: 422 RPIATSFPVFESLL 435


Lambda     K      H
   0.316    0.135    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: 715
Number of extensions: 32
Number of successful extensions: 4
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: 455
Length of database: 441
Length adjustment: 33
Effective length of query: 422
Effective length of database: 408
Effective search space:   172176
Effective search space used:   172176
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_011444984.1 SARO_RS06630 (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.21377.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.6e-127  409.9   0.2   6.6e-127  409.7   0.2    1.0  1  lcl|NCBI__GCF_000013325.1:WP_011444984.1  SARO_RS06630 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013325.1:WP_011444984.1  SARO_RS06630 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.7   0.2  6.6e-127  6.6e-127       1     411 [.      14     437 ..      14     440 .. 0.96

  Alignments for each domain:
  == domain 1  score: 409.7 bits;  conditional E-value: 6.6e-127
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               g+i +pg+KSishR+++l+aLa get+vt+lL++eD+l+t  a+r++Ga++e++ ++ ++++gvg   l
  lcl|NCBI__GCF_000013325.1:WP_011444984.1  14 GRIGVPGDKSISHRSIMLGALAVGETRVTGLLEGEDVLSTAAAMRAMGATIERDaDGMWHVHGVGVggL 82 
                                               7899************************************************666********99888* PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                                +p+++ld+gnsGt++Rll+g++a+++ + ++ gd sl+kRP++r++++L+ +gae+ ++   g+lPl+
  lcl|NCBI__GCF_000013325.1:WP_011444984.1  83 LQPQQALDMGNSGTSTRLLMGLVATHPITATFVGDASLSKRPMGRVIDPLSTMGAEFTASP-GGRLPLT 150
                                               **********************************************************987.69***** PP

                                 TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksf.gveveee 202
                                               ++g +++ +i +  + aS+Q+ksa+lla+   l++ ++++v+e++ +r++ e++L  ++++  v+v  +
  lcl|NCBI__GCF_000013325.1:WP_011444984.1 151 LRGISPAvPIEYRLPVASAQVKSAVLLAG---LNTPGVTTVIEPIPTRDHSERMLRGFGAElTVDVAAD 216
                                               ***97777*********************...8999**********************97636777777 PP

                                 TIGR01356 203 derkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270
                                                 r i+v+g+++ k+++++v+gD+SsAaff++aa++ ++ +++ven+g n+t++   +++vL+ mG+++
  lcl|NCBI__GCF_000013325.1:WP_011444984.1 217 GARVIRVRGEAELKPQDIAVPGDPSSAAFFVVAALLVEGsDLVVENVGLNPTRAA--LFDVLRLMGGSI 283
                                               77********999999********************9999*************99..888********* PP

                                 TIGR01356 271 eveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsd 330
                                               e  + r        d++v+ +s l g++v ++ v+s+ De+p+l v+aa+A+g t+ +++eelRvkEsd
  lcl|NCBI__GCF_000013325.1:WP_011444984.1 284 EELNRRevggepvaDLRVR-HSLLTGIDVdPAVVPSMVDEFPVLFVAAALAKGRTVTTGLEELRVKESD 351
                                               *999999************.688******89************************************** PP

                                 TIGR01356 331 RiaaiaeeLeklGveveeledgllieGkk.....kelkgavvdtydDHRiamalavlglaaegeveied 394
                                               Ri+a++++Le  G++v+e+edgl+i G+       + +ga+v t+ DHRiam++a++g+a +++ve++d
  lcl|NCBI__GCF_000013325.1:WP_011444984.1 352 RISAMRAALELAGATVTETEDGLIIDGTGgdplpGTAEGASVVTHLDHRIAMSMAIAGIASRNGVEVDD 420
                                               ***************************999899999999****************************** PP

                                 TIGR01356 395 aecvaksfPeFfevleq 411
                                               +  +a+sfP F  +le+
  lcl|NCBI__GCF_000013325.1:WP_011444984.1 421 TRPIATSFPVFESLLES 437
                                               ************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (441 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: 00:00:00.02
# Mc/sec: 8.44
//
[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