GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroA in Marinobacter adhaerens HP15

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate GFF1397 HP15_1364 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>FitnessBrowser__Marino:GFF1397
          Length = 742

 Score =  483 bits (1243), Expect = e-141
 Identities = 251/425 (59%), Positives = 312/425 (73%), Gaps = 3/425 (0%)

Query: 7   PSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGASIQVI 66
           P   ++G+I VPGDKS+SHR+++L A+A+G T+V GFL G D+LA + A + MG +I+  
Sbjct: 313 PGGAITGDIRVPGDKSMSHRSIMLGALADGVTEVKGFLEGEDSLATLQAFRDMGVTIEG- 371

Query: 67  EDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQRRPMK 126
            D+  + + GVGM GLQAP   L  GNSGTA+RL +GLLA QPF++ LTGD+SL  RPM 
Sbjct: 372 PDDGFVRIHGVGMHGLQAPRGPLYLGNSGTAMRLFAGLLAAQPFDSELTGDASLSGRPMG 431

Query: 127 RIIDPLTLMGAKIDST-GNVPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGLYARGKT 185
           R+ DPL  MGA ID+  G  PPLKI G  +L+GIHY++P+ASAQVKSCLLLAGLYA G T
Sbjct: 432 RVADPLRAMGAVIDTAEGGRPPLKIRGGQKLSGIHYEMPVASAQVKSCLLLAGLYAEGST 491

Query: 186 CITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAFFIVAAT 245
            +TEPAP+RDHTER+L  F Y + +D  +  VSGGGKL A +I +P DISS+AFF+VAA+
Sbjct: 492 SVTEPAPTRDHTERMLAGFGYHVHRDGATASVSGGGKLTATNIDVPADISSSAFFLVAAS 551

Query: 246 ITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHARLKGIDI 305
           I PGS + L  VG+NPTR+GVIN+L  MGA+IE+    E   EP AD+ VR A L+GIDI
Sbjct: 552 IAPGSNLILRHVGMNPTRVGVINILNQMGANIEILDEREIGGEPVADLRVRSAELQGIDI 611

Query: 306 PPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGIAAESLP 365
           P DQVPL IDEFPVL IAAA A G+TVLR A ELRVKE+DRI  M DGL  LG+     P
Sbjct: 612 PEDQVPLAIDEFPVLFIAAACANGRTVLRGAEELRVKESDRIQVMADGLAALGVETTVTP 671

Query: 366 DGVIIQGG-TLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFVELANE 424
           DG+II GG T+ GG VNS+ DHRIAM+FAVA   A G + + +C NV TSFP FVELA  
Sbjct: 672 DGIIIDGGQTIGGGTVNSHGDHRIAMSFAVASLRAAGDITVNDCANVATSFPGFVELAQG 731

Query: 425 VGMNV 429
            G+N+
Sbjct: 732 TGINI 736


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: 968
Number of extensions: 42
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: 742
Length adjustment: 36
Effective length of query: 402
Effective length of database: 706
Effective search space:   283812
Effective search space used:   283812
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 GFF1397 HP15_1364 (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.5006.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.9e-130  419.7   0.0   8.6e-130  419.2   0.0    1.2  1  lcl|FitnessBrowser__Marino:GFF1397  HP15_1364 3-phosphoshikimate 1-c


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1397  HP15_1364 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.2   0.0  8.6e-130  8.6e-130       1     413 [.     319     733 ..     319     735 .. 0.96

  Alignments for each domain:
  == domain 1  score: 419.2 bits;  conditional E-value: 8.6e-130
                           TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..lkepeae 72 
                                         g+i++pg+KS+shR+++l+aLa+g t+v+++L++eD latl+a+r++G+++e  +++ + i+gvg+  l+ p   
  lcl|FitnessBrowser__Marino:GFF1397 319 GDIRVPGDKSMSHRSIMLGALADGVTEVKGFLEGEDSLATLQAFRDMGVTIEgPDDGFVRIHGVGMhgLQAPRGP 393
                                         79**************************************************6669999*****9999******* PP

                           TIGR01356  73 ldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplkg.give 146
                                         l+lgnsGt++Rl  g+la+++++++ltgd sl+ RP++r+ ++Lr++ga i+ +e  g++Pl+i+g++k+ gi++
  lcl|FitnessBrowser__Marino:GFF1397 394 LYLGNSGTAMRLFAGLLAAQPFDSELTGDASLSGRPMGRVADPLRAMGAVIDTAE-GGRPPLKIRGGQKLsGIHY 467
                                         ****************************************************988.69*********7777**** PP

                           TIGR01356 147 lsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykqkeve 221
                                           + aS+Q+ks+llla+   l a++ + v+e+  +r+++e++L+ ++ +   v+++   + +v gg+k + ++++
  lcl|FitnessBrowser__Marino:GFF1397 468 EMPVASAQVKSCLLLAG---LYAEGSTSVTEPAPTRDHTERMLAGFGYH---VHRDGA-TASVSGGGKLTATNID 535
                                         *****************...67789999999***********9998877...999887.*********88888** PP

                           TIGR01356 222 vegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dvevegasklk 287
                                         v++D+Ss affl+aa i+++ ++ ++++g+n+t+ +  +i++L++mGa++e+ ++r        d++v+ + +l+
  lcl|FitnessBrowser__Marino:GFF1397 536 VPADISSSAFFLVAASIAPGsNLILRHVGMNPTRVG--VINILNQMGANIEILDEReiggepvaDLRVR-SAELQ 607
                                         ********************9***************..888**************99************.578** PP

                           TIGR01356 288 gvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkkke 361
                                         g+++ + +v+ +iDe+p+l ++aa+A+g t+++++eelRvkEsdRi+++a+ L++lGve+++++dg++i G+ ++
  lcl|FitnessBrowser__Marino:GFF1397 608 GIDIpEDQVPLAIDEFPVLFIAAACANGRTVLRGAEELRVKESDRIQVMADGLAALGVETTVTPDGIIIDGG-QT 681
                                         ****99******************************************************************.6* PP

                           TIGR01356 362 lkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlg 413
                                         + g++v++++DHRiam++av++l+a+g ++++d + va+sfP F+e+++  g
  lcl|FitnessBrowser__Marino:GFF1397 682 IGGGTVNSHGDHRIAMSFAVASLRAAGDITVNDCANVATSFPGFVELAQGTG 733
                                         **********************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (742 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: 16.04
//
[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