Alignments for a candidate for aroA in Rhizobium johnstonii 3841

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Rhizobium johnstonii 3841

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_011649931.1 RL_RS00575 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q9R4E4
         (455 letters)



>NCBI__GCF_000009265.1:WP_011649931.1
          Length = 452

 Score =  770 bits (1989), Expect = 0.0
 Identities = 388/449 (86%), Positives = 417/449 (92%)

Query: 1   MSHGASSRPATARKSSGLSGTVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTG 60
           M +G++S+PATARKS+GL+G+VRIPGDKSISHRSFM GGLASGETRITGLLEGEDVINTG
Sbjct: 1   MLNGSASKPATARKSAGLTGSVRIPGDKSISHRSFMIGGLASGETRITGLLEGEDVINTG 60

Query: 61  KAMQAMGARIRKEGDTWIIDGVGNGGLLAPEAPLDFGNAATGCRLTMGLVGVYDFDSTFI 120
           +AMQAMGARIRKEG  W+I+G GNG LLAP+APLDFGNA TG RLTMGLVG YDF STFI
Sbjct: 61  RAMQAMGARIRKEGAQWVIEGTGNGALLAPDAPLDFGNAGTGVRLTMGLVGTYDFHSTFI 120

Query: 121 GDASLTKRPMGRVLNPLREMGVQVKSEDGDRLPVTLRGPKTPTPITYRVPMASAQVKSAV 180
           GDASL+KRPMGRVLNPLREMGVQV + +GDRLPVTLRGP TP+PI YRVPMASAQVKSAV
Sbjct: 121 GDASLSKRPMGRVLNPLREMGVQVSASEGDRLPVTLRGPGTPSPIRYRVPMASAQVKSAV 180

Query: 181 LLAGLNTPGITTVIEPIMTRDHTEKMLQGFGANLTVETDADGVRTIRLEGRGKLTGQVID 240
           LLAGLNTPG+TTVIEP+MTRDHTEKMLQGFGA L+VETD DGVRTIRLEGRGKL GQVID
Sbjct: 181 LLAGLNTPGVTTVIEPVMTRDHTEKMLQGFGAALSVETDGDGVRTIRLEGRGKLAGQVID 240

Query: 241 VPGDPSSTAFPLVAALLVPGSDVTILNVLMNPTRTGLILTLQEMGADIEVINPRLAGGED 300
           VPGDPSSTAFPLVAAL+VPGSD+TI+NVLMNPTRTGLILTLQEMGADIEV+N RLAGGED
Sbjct: 241 VPGDPSSTAFPLVAALIVPGSDITIVNVLMNPTRTGLILTLQEMGADIEVVNARLAGGED 300

Query: 301 VADLRVRSSTLKGVTVPEDRAPSMIDEYPILAVAAAFAEGATVMNGLEELRVKESDRLSA 360
           VADLRVR S LKGVTVPEDRAPSMIDEYPILAVAA FAEGATVM GLEELRVKESDRLSA
Sbjct: 301 VADLRVRHSELKGVTVPEDRAPSMIDEYPILAVAACFAEGATVMKGLEELRVKESDRLSA 360

Query: 361 VANGLKLNGVDCDEGETSLVVRGRPDGKGLGNASGAAVATHLDHRIAMSFLVMGLVSENP 420
           VA+GLKLNGVDCDEGE  L+VRGRPDGKGLGNA+   V+THLDHRIAMSFLV+GL SE+ 
Sbjct: 361 VADGLKLNGVDCDEGEDFLIVRGRPDGKGLGNAADGRVSTHLDHRIAMSFLVLGLASEHA 420

Query: 421 VTVDDATMIATSFPEFMDLMAGLGAKIEL 449
           VT+DDA MIATSFPEFM LM GLGAKIEL
Sbjct: 421 VTIDDAAMIATSFPEFMQLMTGLGAKIEL 449


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: 891
Number of extensions: 23
Number of successful extensions: 1
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: 452
Length adjustment: 33
Effective length of query: 422
Effective length of database: 419
Effective search space:   176818
Effective search space used:   176818
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_011649931.1 RL_RS00575 (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.3685140.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-137  445.3   0.0   1.1e-137  445.1   0.0    1.0  1  NCBI__GCF_000009265.1:WP_011649931.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000009265.1:WP_011649931.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.1   0.0  1.1e-137  1.1e-137       1     414 [.      20     445 ..      20     446 .. 0.96

  Alignments for each domain:
  == domain 1  score: 445.1 bits;  conditional E-value: 1.1e-137
                             TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg..lkepea 71 
                                           g+++ipg+KSishR++++++La+get++t+lL++eD+++t +a++++Ga++++e+ ++vieg g+  l  p+a
  NCBI__GCF_000009265.1:WP_011649931.1  20 GSVRIPGDKSISHRSFMIGGLASGETRITGLLEGEDVINTGRAMQAMGARIRKEGAQWVIEGTGNgaLLAPDA 92 
                                           789***********************************************************998999***** PP

                             TIGR01356  72 eldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkgg 143
                                            ld+gn+Gt +Rl++g++ ++++++++ gd sl+kRP++r++++Lre+g++++++e  ++lP++++gp  +++
  NCBI__GCF_000009265.1:WP_011649931.1  93 PLDFGNAGTGVRLTMGLVGTYDFHSTFIGDASLSKRPMGRVLNPLREMGVQVSASE-GDRLPVTLRGPgTPSP 164
                                           *****************************************************988.58*********8888* PP

                             TIGR01356 144 ivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede..rkivvkggqk 214
                                           i +  ++aS+Q+ksa+lla+   l++ ++++v+e++++r+++e++L+ ++++  +ve + +  r+i+++g +k
  NCBI__GCF_000009265.1:WP_011649931.1 165 IRYRVPMASAQVKSAVLLAG---LNTPGVTTVIEPVMTRDHTEKMLQGFGAA-LSVETDGDgvRTIRLEGRGK 233
                                           ********************...8999***********************98.9999998899********** PP

                             TIGR01356 215 ykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dv 278
                                            + + ++v+gD+Ss+af+l+aa+i ++ ++t+ n+++n+t+++  +i +L+emGad+ev + r        d+
  NCBI__GCF_000009265.1:WP_011649931.1 234 LAGQVIDVPGDPSSTAFPLVAALIVPGsDITIVNVLMNPTRTG--LILTLQEMGADIEVVNARlaggedvaDL 304
                                           66666**********************9***************..777************************* PP

                             TIGR01356 279 evegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveele 350
                                           +v+ +s+lkgv+v + +++s+iDe+p+lav+a+fAeg t++k++eelRvkEsdR++a+a+ L+  Gv+++e+e
  NCBI__GCF_000009265.1:WP_011649931.1 305 RVR-HSELKGVTVpEDRAPSMIDEYPILAVAACFAEGATVMKGLEELRVKESDRLSAVADGLKLNGVDCDEGE 376
                                           ***.689******9999******************************************************** PP

                             TIGR01356 351 dgllieGkk.....kelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlga 414
                                           d+l+++G+       +  +++v+t+ DHRiam++ vlgla e+ v+i+da+++a+sfPeF++++  lga
  NCBI__GCF_000009265.1:WP_011649931.1 377 DFLIVRGRPdgkglGNAADGRVSTHLDHRIAMSFLVLGLASEHAVTIDDAAMIATSFPEFMQLMTGLGA 445
                                           ********999666666779*********************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (452 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 20.11
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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