Alignments for a candidate for aroA in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Pseudomonas simiae WCS417

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate GFF1599 PS417_08135 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>FitnessBrowser__WCS417:GFF1599
          Length = 736

 Score =  446 bits (1148), Expect = e-130
 Identities = 237/424 (55%), Positives = 299/424 (70%), Gaps = 2/424 (0%)

Query: 7   PSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGASIQVI 66
           P   LSG I VPGDKSISHR+++L ++AEG T+V+GFL G D LA + A + MG  I+  
Sbjct: 308 PGGRLSGRIRVPGDKSISHRSIMLGSLAEGVTEVEGFLEGEDALATLQAFRDMGVVIEGP 367

Query: 67  EDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQRRPMK 126
               +  + GVG+ GL+  P  +  GNSGT++RLLSGLLA Q F++VLTGD+SL +RPM 
Sbjct: 368 HHGRV-TIHGVGLHGLKPAPGPIYLGNSGTSMRLLSGLLAAQSFDSVLTGDASLSKRPMS 426

Query: 127 RIIDPLTLMGAKIDS-TGNVPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGLYARGKT 185
           R+  PL  MGA I++     PPL I G   L G+ Y +PMASAQVKSCLLLAGLYA GKT
Sbjct: 427 RVAKPLREMGAVIETGPEGRPPLTIRGGQSLKGLAYAMPMASAQVKSCLLLAGLYAEGKT 486

Query: 186 CITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAFFIVAAT 245
            + EPAP+RDHTER+L+ F Y +  +  +  V  G  L A  I +PGDISS+AFF+VAA+
Sbjct: 487 VVAEPAPTRDHTERMLRGFGYPVAVEGATASVESGHALAATHIEVPGDISSSAFFLVAAS 546

Query: 246 ITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHARLKGIDI 305
           I  GS + L  VGVNPTR GVI++L++MGADI + +  E   EP AD+ VR A LKGI+I
Sbjct: 547 IAEGSELLLEHVGVNPTRTGVIDILRLMGADITLENQREVGGEPVADLRVRAAALKGIEI 606

Query: 306 PPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGIAAESLP 365
           P   VPL IDEFPVL +AAA A+G+TVLR A ELRVKE+DRI  M DGL  LG+  E   
Sbjct: 607 PEALVPLAIDEFPVLFVAAACAEGRTVLRGAQELRVKESDRIQVMADGLLALGVKCEPTA 666

Query: 366 DGVIIQGGTLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFVELANEV 425
           DG+II GG + GGEV+++ DHRIAMAF+VA   A  P+RIR+C NV TSFPNF+ L  +V
Sbjct: 667 DGIIIDGGLIGGGEVHAHGDHRIAMAFSVASLRAATPIRIRDCANVATSFPNFLTLCAQV 726

Query: 426 GMNV 429
           G+ V
Sbjct: 727 GIRV 730


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: 903
Number of extensions: 43
Number of successful extensions: 6
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: 736
Length adjustment: 36
Effective length of query: 402
Effective length of database: 700
Effective search space:   281400
Effective search space used:   281400
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 GFF1599 PS417_08135 (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.2911.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     2e-128  414.7   0.0   2.7e-128  414.2   0.0    1.2  1  lcl|FitnessBrowser__WCS417:GFF1599  PS417_08135 3-phosphoshikimate 1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1599  PS417_08135 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.2   0.0  2.7e-128  2.7e-128       1     413 [.     314     727 ..     314     729 .. 0.96

  Alignments for each domain:
  == domain 1  score: 414.2 bits;  conditional E-value: 2.7e-128
                           TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..lkepeae 72 
                                         g+i++pg+KSishR+++l++Laeg t+v+++L++eD latl+a+r++G+ +e  ++++++i+gvg   lk +   
  lcl|FitnessBrowser__WCS417:GFF1599 314 GRIRVPGDKSISHRSIMLGSLAEGVTEVEGFLEGEDALATLQAFRDMGVVIEgPHHGRVTIHGVGLhgLKPAPGP 388
                                         79**************************************************666*********9876666669* PP

                           TIGR01356  73 ldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplkg.give 146
                                         ++lgnsGt++Rll+g+la++s+++vltgd sl+kRP+ r+ ++Lre+ga ie    eg++Pl+i+g++++ g  +
  lcl|FitnessBrowser__WCS417:GFF1599 389 IYLGNSGTSMRLLSGLLAAQSFDSVLTGDASLSKRPMSRVAKPLREMGAVIETGP-EGRPPLTIRGGQSLkGLAY 462
                                         ****************************************************876.69*********8888**** PP

                           TIGR01356 147 lsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykqkeve 221
                                           ++aS+Q+ks+llla+   l a++ ++v e+  +r+++e++L  ++     v +e   + +v+ g++ + +++e
  lcl|FitnessBrowser__WCS417:GFF1599 463 AMPMASAQVKSCLLLAG---LYAEGKTVVAEPAPTRDHTERMLRGFGYP---VAVEGA-TASVESGHALAATHIE 530
                                         *****************...778899****************9998876...777665.889**999999999** PP

                           TIGR01356 222 vegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dvevegasklk 287
                                         v+gD+Ss affl+aa i+++ e+ +e++g n+t+++  +i++L+ mGad+++e+qr        d++v+ a  lk
  lcl|FitnessBrowser__WCS417:GFF1599 531 VPGDISSSAFFLVAASIAEGsELLLEHVGVNPTRTG--VIDILRLMGADITLENQRevggepvaDLRVR-AAALK 602
                                         *******************99***************..788****************************.789** PP

                           TIGR01356 288 gvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkkke 361
                                         g+++ ++ v+ +iDe+p+l v+aa+Aeg t++++++elRvkEsdRi+++a+ L +lGv++e+++dg++i G+   
  lcl|FitnessBrowser__WCS417:GFF1599 603 GIEIpEALVPLAIDEFPVLFVAAACAEGRTVLRGAQELRVKESDRIQVMADGLLALGVKCEPTADGIIIDGG--L 675
                                         ****99******************************************************************..6 PP

                           TIGR01356 362 lkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlg 413
                                         + g++v+ ++DHRiama++v++l+a+ +++i d + va+sfP+F+ + +q+g
  lcl|FitnessBrowser__WCS417:GFF1599 676 IGGGEVHAHGDHRIAMAFSVASLRAATPIRIRDCANVATSFPNFLTLCAQVG 727
                                         99********************************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (736 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.64
//
[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