Alignments for a candidate for aroA in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Pseudomonas fluorescens FW300-N2E2

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate Pf6N2E2_2518 Cyclohexadienyl dehydrogenase (EC 1.3.1.12)(EC 1.3.1.43) / 5-Enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19)

Query= BRENDA::Q83E11
         (438 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2518
          Length = 735

 Score =  452 bits (1163), Expect = e-131
 Identities = 235/424 (55%), Positives = 302/424 (71%), Gaps = 2/424 (0%)

Query: 7   PSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGASIQVI 66
           P   LSG I VPGDKSISHR+++L ++AEG T+V+GFL G D LA + A + MG  I+  
Sbjct: 307 PGGSLSGRIRVPGDKSISHRSIMLGSLAEGVTEVEGFLEGEDALATLQAFRDMGVVIEGP 366

Query: 67  EDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQRRPMK 126
               +  + GVG+ GL+  P  +  GNSGT++RLLSGLLA Q F++ LTGD+SL +RPM 
Sbjct: 367 HHGRV-TIHGVGLHGLKPAPGPIYLGNSGTSMRLLSGLLAAQDFDSTLTGDASLSKRPMN 425

Query: 127 RIIDPLTLMGAKIDSTGNV-PPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGLYARGKT 185
           R+ +PL  MGA I++  +  PP+ I G  +L G+ Y +PMASAQVKSCLLLAGLYA GKT
Sbjct: 426 RVANPLREMGAVIETAADGRPPMIIRGGNKLKGLTYTMPMASAQVKSCLLLAGLYAEGKT 485

Query: 186 CITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAFFIVAAT 245
            +TEPAP+RDHTER+L+ F Y +  D  +  V  G KL A  I +PGDISS+AFF+VAA+
Sbjct: 486 TVTEPAPTRDHTERMLRGFGYPVTVDGATASVESGNKLTATHIEVPGDISSSAFFLVAAS 545

Query: 246 ITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHARLKGIDI 305
           I  GS + L  VG+NPTR GVI++L++MGADI + +  E   EP AD+ VR A+LKGI+I
Sbjct: 546 IAEGSDLVLEHVGINPTRTGVIDILRLMGADITLENQREVGGEPVADLRVRAAKLKGIEI 605

Query: 306 PPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGIAAESLP 365
           P   VPL IDEFPVL +AAA A+G+TVL  A ELRVKE+DRI  M DGL  LG+  +  P
Sbjct: 606 PEALVPLAIDEFPVLFVAAACAEGRTVLTGAEELRVKESDRIQVMADGLLALGVKCQPTP 665

Query: 366 DGVIIQGGTLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFVELANEV 425
           DG+II GG + GGEV+ + DHRIAMAF+VA   A  P+RI +C NV TSFPNF+ L  +V
Sbjct: 666 DGIIIDGGQIGGGEVHGHGDHRIAMAFSVASLRASAPIRIHDCANVATSFPNFLALCAQV 725

Query: 426 GMNV 429
           G+ V
Sbjct: 726 GIRV 729


Lambda     K      H
   0.318    0.137    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: 900
Number of extensions: 46
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: 438
Length of database: 735
Length adjustment: 36
Effective length of query: 402
Effective length of database: 699
Effective search space:   280998
Effective search space used:   280998
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate Pf6N2E2_2518 (Cyclohexadienyl dehydrogenase (EC 1.3.1.12)(EC 1.3.1.43) / 5-Enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19))
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.12432.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   4.7e-131  423.3   0.0   6.2e-131  422.9   0.0    1.1  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2518  Cyclohexadienyl dehydrogenase (E


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2518  Cyclohexadienyl dehydrogenase (EC 1.3.1.12)(EC 1.3.1.43) / 5-Enolpyruv
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.9   0.0  6.2e-131  6.2e-131       1     413 [.     313     726 ..     313     728 .. 0.96

  Alignments for each domain:
  == domain 1  score: 422.9 bits;  conditional E-value: 6.2e-131
                                      TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegv 63 
                                                    g+i++pg+KSishR+++l++Laeg t+v+++L++eD latl+a+r++G+ +e  ++++++i+gv
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2518 313 GRIRVPGDKSISHRSIMLGSLAEGVTEVEGFLEGEDALATLQAFRDMGVVIEgPHHGRVTIHGV 376
                                                    79**************************************************666********* PP

                                      TIGR01356  64 gg..lkepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeies 125
                                                    g   lk +   ++lgnsGt++Rll+g+la+++++++ltgd sl+kRP++r+ ++Lre+ga ie 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2518 377 GLhgLKPAPGPIYLGNSGTSMRLLSGLLAAQDFDSTLTGDASLSKRPMNRVANPLREMGAVIET 440
                                                    9876666669*****************************************************8 PP

                                      TIGR01356 126 keeegslPlaisgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieit 188
                                                    +  +g++P+ i+g++k+ g ++  ++aS+Q+ks+llla+   l a++ ++v+e+  +r+++e++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2518 441 AA-DGRPPMIIRGGNKLkGLTYTMPMASAQVKSCLLLAG---LYAEGKTTVTEPAPTRDHTERM 500
                                                    87.69*********8888*********************...67789999999*********** PP

                                      TIGR01356 189 LkllksfgveveeederkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgen 251
                                                    L  ++     v+++   + +v+ g+k + +++ev+gD+Ss affl+aa i+++ ++++e++g+n
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2518 501 LRGFGYP---VTVDGA-TASVESGNKLTATHIEVPGDISSSAFFLVAASIAEGsDLVLEHVGIN 560
                                                    9988866...888776.99*******88889*********************99********** PP

                                      TIGR01356 252 stqgdkaiiivLeemGadveveeqr........dvevegasklkgvkv.didvdsliDelptla 306
                                                    +t+++  +i++L+ mGad+++e+qr        d++v+ a klkg+++ ++ v+ +iDe+p+l 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2518 561 PTRTG--VIDILRLMGADITLENQRevggepvaDLRVR-AAKLKGIEIpEALVPLAIDEFPVLF 621
                                                    *****..788****************************.789******99************** PP

                                      TIGR01356 307 vlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkkkelkgavvdty 370
                                                    v+aa+Aeg t+++++eelRvkEsdRi+++a+ L +lGv++++++dg++i G+  ++ g++v+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2518 622 VAAACAEGRTVLTGAEELRVKESDRIQVMADGLLALGVKCQPTPDGIIIDGG--QIGGGEVHGH 683
                                                    ****************************************************..7********* PP

                                      TIGR01356 371 dDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlg 413
                                                    +DHRiama++v++l+a+++++i+d + va+sfP+F+ + +q+g
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2518 684 GDHRIAMAFSVASLRASAPIRIHDCANVATSFPNFLALCAQVG 726
                                                    **************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (735 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: 00:00:00.01
# Mc/sec: 18.05
//
[ok]

This GapMind analysis is from Apr 09 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