Alignments for a candidate for aroA in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Pseudomonas stutzeri RCH2

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate GFF1943 Psest_1986 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>FitnessBrowser__psRCH2:GFF1943
          Length = 747

 Score =  474 bits (1220), Expect = e-138
 Identities = 247/424 (58%), Positives = 308/424 (72%), Gaps = 2/424 (0%)

Query: 7   PSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGASIQVI 66
           P   L+G + VPGDKSISHR+++L ++AEG T+V+GFL G D LA + A + MG  I+  
Sbjct: 319 PGGSLTGHLRVPGDKSISHRSIMLGSLAEGTTEVEGFLEGEDALATIQAFRDMGVVIEGP 378

Query: 67  EDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQRRPMK 126
               +  V GVG+ GL+APP  +  GNSGT++RLLSGLLA QPF+T LTGD+SL +RPM 
Sbjct: 379 HQGRV-TVHGVGLHGLKAPPGPIYLGNSGTSMRLLSGLLAAQPFDTTLTGDASLSKRPMN 437

Query: 127 RIIDPLTLMGAKIDSTGNV-PPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGLYARGKT 185
           R+  PL  MGA I++  +  PPL I G  RL+G+HY++PMASAQVKSCLLLAGLYA G+T
Sbjct: 438 RVAKPLREMGAVIETAPDGRPPLTIRGGQRLSGMHYEMPMASAQVKSCLLLAGLYAAGQT 497

Query: 186 CITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAFFIVAAT 245
            +TEPAP+RDHTER+L+ F Y +     +  V  G KL+A  I +P DISSAAFF+VAA+
Sbjct: 498 SVTEPAPTRDHTERMLRGFGYPVTVKGSTALVEPGHKLQATHIEVPADISSAAFFMVAAS 557

Query: 246 ITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHARLKGIDI 305
           I  GS I L  VGVNPTR GVI++LK+MG DI + +  E   EP ADI VR A+LKGIDI
Sbjct: 558 IAQGSEIVLEHVGVNPTRTGVIDILKLMGGDISLENPREVGGEPVADIRVRGAQLKGIDI 617

Query: 306 PPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGIAAESLP 365
           P D VPL IDEFPVL +AAA A+G+T LR A ELRVKE+DRI  M DGLQ LG+ AE  P
Sbjct: 618 PEDLVPLAIDEFPVLFVAAACAEGRTTLRGAEELRVKESDRIQVMADGLQTLGVKAEPTP 677

Query: 366 DGVIIQGGTLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFVELANEV 425
           DG++I+GG +  GEV ++ DHRIAM+F+VA   A GPVRI +C NV TSFPNF+ LA   
Sbjct: 678 DGIVIEGGAIGSGEVWAHGDHRIAMSFSVAALRASGPVRIHDCANVATSFPNFLALAQRA 737

Query: 426 GMNV 429
           GM V
Sbjct: 738 GMQV 741


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: 925
Number of extensions: 45
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: 747
Length adjustment: 36
Effective length of query: 402
Effective length of database: 711
Effective search space:   285822
Effective search space used:   285822
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 GFF1943 Psest_1986 (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.11043.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.3e-131  424.3   0.0   3.3e-131  423.8   0.0    1.2  1  lcl|FitnessBrowser__psRCH2:GFF1943  Psest_1986 3-phosphoshikimate 1-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1943  Psest_1986 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.8   0.0  3.3e-131  3.3e-131       1     413 [.     325     738 ..     325     740 .. 0.96

  Alignments for each domain:
  == domain 1  score: 423.8 bits;  conditional E-value: 3.3e-131
                           TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..lkepeae 72 
                                         g++++pg+KSishR+++l++Laeg+t+v+++L++eD lat++a+r++G+ +e  ++++++++gvg   lk p   
  lcl|FitnessBrowser__psRCH2:GFF1943 325 GHLRVPGDKSISHRSIMLGSLAEGTTEVEGFLEGEDALATIQAFRDMGVVIEgPHQGRVTVHGVGLhgLKAPPGP 399
                                         689*************************************************666*********988899999** PP

                           TIGR01356  73 ldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplkg.give 146
                                         ++lgnsGt++Rll+g+la+++++++ltgd sl+kRP++r+ ++Lre+ga ie +  +g++Pl+i+g++++ g+++
  lcl|FitnessBrowser__psRCH2:GFF1943 400 IYLGNSGTSMRLLSGLLAAQPFDTTLTGDASLSKRPMNRVAKPLREMGAVIETAP-DGRPPLTIRGGQRLsGMHY 473
                                         ****************************************************887.69*********8888**** PP

                           TIGR01356 147 lsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykqkeve 221
                                           ++aS+Q+ks+llla+   l a + + v+e+  +r+++e++L  ++     v+++ + +  v++g+k + +++e
  lcl|FitnessBrowser__psRCH2:GFF1943 474 EMPMASAQVKSCLLLAG---LYAAGQTSVTEPAPTRDHTERMLRGFGYP---VTVKGS-TALVEPGHKLQATHIE 541
                                         *****************...66778888999***********9998876...777766.889****9999999** PP

                           TIGR01356 222 vegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dvevegasklk 287
                                         v++D+SsAaff++aa i+++ e+++e++g n+t+++  +i++L+ mG+d+++e+ r        d++v+ga +lk
  lcl|FitnessBrowser__psRCH2:GFF1943 542 VPADISSAAFFMVAASIAQGsEIVLEHVGVNPTRTG--VIDILKLMGGDISLENPRevggepvaDIRVRGA-QLK 613
                                         *******************99***************..788****************************75.7** PP

                           TIGR01356 288 gvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkkke 361
                                         g+++ +  v+ +iDe+p+l v+aa+Aeg t+++++eelRvkEsdRi+++a+ L++lGv++e+++dg++ieG+   
  lcl|FitnessBrowser__psRCH2:GFF1943 614 GIDIpEDLVPLAIDEFPVLFVAAACAEGRTTLRGAEELRVKESDRIQVMADGLQTLGVKAEPTPDGIVIEGG--A 686
                                         ****88999***************************************************************..6 PP

                           TIGR01356 362 lkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlg 413
                                         + +++v  ++DHRiam+++v++l+a+g+v+i+d + va+sfP+F+ ++++ g
  lcl|FitnessBrowser__psRCH2:GFF1943 687 IGSGEVWAHGDHRIAMSFSVAALRASGPVRIHDCANVATSFPNFLALAQRAG 738
                                         *********************************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (747 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: 18.72
//
[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