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.8891.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: 00:00:00.02
# Mc/sec: 11.93
//
[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:

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:

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:

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:

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