Alignments for a candidate for aroA in Rhizobium leguminosarum WSM1325

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Rhizobium leguminosarum WSM1325

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_012759631.1 RLEG_RS21630 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::C3MC80
         (448 letters)



>NCBI__GCF_000023185.1:WP_012759631.1
          Length = 452

 Score =  775 bits (2000), Expect = 0.0
 Identities = 391/447 (87%), Positives = 419/447 (93%)

Query: 1   MSHGLSPRPATAKKSADLKGTVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTG 60
           M +G +P+PATA+KSA L G+VRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTG
Sbjct: 1   MLNGSAPKPATARKSAGLTGSVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTG 60

Query: 61  KAMQAMGAKIRKEGDTWIINGVGNGALLAPEAPLDFGNAGTGCRLTMGLVGVYDFDSTFI 120
           +AMQAMGA+IRKEG+ W+I+G GNGALLAP+APLDFGNAGTG RLTMGLVG YDF STF 
Sbjct: 61  RAMQAMGARIRKEGEQWVIDGTGNGALLAPDAPLDFGNAGTGVRLTMGLVGTYDFRSTFT 120

Query: 121 GDASLTKRPMGRVLDPLREMGVQVKSAEGDRLPVTLRGPKTPNPITYRVPMASAQVKSAV 180
           GDASL+KRPMGRVL+PLREMGVQV ++EGDRLPVTLRGP TP+PI YRVPMASAQVKSAV
Sbjct: 121 GDASLSKRPMGRVLNPLREMGVQVSASEGDRLPVTLRGPGTPSPIRYRVPMASAQVKSAV 180

Query: 181 LLAGLNTPGITTVIEPVMTRDHTEKMLQGFGANLSVETDTAGVRTIRLEGRGKLTGQVID 240
           LLAGLNTPGITTVIEPVMTRDHTEKMLQGFGA LSVETD+ GVRTIRLEGRGKL GQVID
Sbjct: 181 LLAGLNTPGITTVIEPVMTRDHTEKMLQGFGAALSVETDSEGVRTIRLEGRGKLAGQVID 240

Query: 241 VPGDPSSTAFPLVAALLVPGSDVTILNVLMNPTRTGLILTLQEMGANIEVMNPRLAGGED 300
           VPGDPSSTAFPLVAALLVPGSD+TI+NVLMNPTRTGLILTLQEMGA+IEV N RLAGGED
Sbjct: 241 VPGDPSSTAFPLVAALLVPGSDITIVNVLMNPTRTGLILTLQEMGADIEVANARLAGGED 300

Query: 301 VADLRVRYSELKGVTVPEERAPSMIDEYPVLAVAAAFAEGATVMNGLDELRVKESDRLSA 360
           VADLRVR+SELKGVTVPEERAPSMIDEYP+LAVAA FAEGAT+M GL+ELRVKESDRLSA
Sbjct: 301 VADLRVRHSELKGVTVPEERAPSMIDEYPILAVAACFAEGATIMKGLEELRVKESDRLSA 360

Query: 361 VADGLKLNGVDCDEGEASLVVRGRPGGKGLGNAAGGQVKTHLDHRIAMSFLVLGLASEHP 420
           VADGLKLNGVDCDEGE  L+VRGRP GKGLGNAA G+V THLDHRIAMSFLV+GLASEHP
Sbjct: 361 VADGLKLNGVDCDEGEDFLIVRGRPDGKGLGNAADGRVSTHLDHRIAMSFLVMGLASEHP 420

Query: 421 VTVDDATMIATSFPEFMDLMTGLGATI 447
           VT+DDA MIATSFPEFM LMTGLGA I
Sbjct: 421 VTIDDAAMIATSFPEFMQLMTGLGAKI 447


Lambda     K      H
   0.316    0.135    0.385 

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: 869
Number of extensions: 27
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: 448
Length of database: 452
Length adjustment: 33
Effective length of query: 415
Effective length of database: 419
Effective search space:   173885
Effective search space used:   173885
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_012759631.1 RLEG_RS21630 (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.22396.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-139  450.4   0.0   3.3e-139  450.2   0.0    1.0  1  lcl|NCBI__GCF_000023185.1:WP_012759631.1  RLEG_RS21630 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023185.1:WP_012759631.1  RLEG_RS21630 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.2   0.0  3.3e-139  3.3e-139       1     414 [.      20     445 ..      20     446 .. 0.96

  Alignments for each domain:
  == domain 1  score: 450.2 bits;  conditional E-value: 3.3e-139
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg..lk 67 
                                               g+++ipg+KSishR++++++La+get++t+lL++eD+++t +a++++Ga++++e+e++vi+g g+  l 
  lcl|NCBI__GCF_000023185.1:WP_012759631.1  20 GSVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGRAMQAMGARIRKEGEQWVIDGTGNgaLL 88 
                                               789***********************************************************998899* PP

                                 TIGR01356  68 epeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlai 136
                                                p+a ld+gn+Gt +Rl++g++ ++++ +++tgd sl+kRP++r++++Lre+g++++++e  ++lP+++
  lcl|NCBI__GCF_000023185.1:WP_012759631.1  89 APDAPLDFGNAGTGVRLTMGLVGTYDFRSTFTGDASLSKRPMGRVLNPLREMGVQVSASE-GDRLPVTL 156
                                               *********************************************************988.58****** PP

                                 TIGR01356 137 sgp.lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede 204
                                               +gp  +++i +  ++aS+Q+ksa+lla+   l++ ++++v+e++++r+++e++L+ ++++  +ve + e
  lcl|NCBI__GCF_000023185.1:WP_012759631.1 157 RGPgTPSPIRYRVPMASAQVKSAVLLAG---LNTPGITTVIEPVMTRDHTEKMLQGFGAA-LSVETDSE 221
                                               ***8888*********************...8999***********************88.88888777 PP

                                 TIGR01356 205 ..rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270
                                                 r+i+++g +k + + ++v+gD+Ss+af+l+aa++ ++ ++t+ n+++n+t+++  +i +L+emGad+
  lcl|NCBI__GCF_000023185.1:WP_012759631.1 222 gvRTIRLEGRGKLAGQVIDVPGDPSSTAFPLVAALLVPGsDITIVNVLMNPTRTG--LILTLQEMGADI 288
                                               78**********66666*********************99***************..777********* PP

                                 TIGR01356 271 eveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsd 330
                                               ev++ r        d++v+ +s+lkgv+v +++++s+iDe+p+lav+a+fAeg t +k++eelRvkEsd
  lcl|NCBI__GCF_000023185.1:WP_012759631.1 289 EVANARlaggedvaDLRVR-HSELKGVTVpEERAPSMIDEYPILAVAACFAEGATIMKGLEELRVKESD 356
                                               *******************.689******99************************************** PP

                                 TIGR01356 331 RiaaiaeeLeklGveveeledgllieGkk.....kelkgavvdtydDHRiamalavlglaaegeveied 394
                                               R++a+a+ L+  Gv+++e+ed+l+++G+       +  +++v+t+ DHRiam++ v+gla e++v+i+d
  lcl|NCBI__GCF_000023185.1:WP_012759631.1 357 RLSAVADGLKLNGVDCDEGEDFLIVRGRPdgkglGNAADGRVSTHLDHRIAMSFLVMGLASEHPVTIDD 425
                                               ****************************999666666779***************************** PP

                                 TIGR01356 395 aecvaksfPeFfevleqlga 414
                                               a+++a+sfPeF++++  lga
  lcl|NCBI__GCF_000023185.1:WP_012759631.1 426 AAMIATSFPEFMQLMTGLGA 445
                                               ****************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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.87
//
[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