Alignments for a candidate for aroA in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Pseudomonas putida KT2440

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate PP_1770 PP_1770 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>FitnessBrowser__Putida:PP_1770
          Length = 746

 Score =  466 bits (1198), Expect = e-135
 Identities = 245/430 (56%), Positives = 306/430 (71%), Gaps = 6/430 (1%)

Query: 3   YQTIPSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGAS 62
           +Q  P   L+G I VPGDKSISHR+++L ++AEG T+V+GFL G D LA + A + MG  
Sbjct: 314 FQAQPGGRLNGRIRVPGDKSISHRSIMLGSLAEGTTEVEGFLEGEDALATLQAFRDMGV- 372

Query: 63  IQVIEDENI--LVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSL 120
             VIE  N   + + GVG+ GL+ PP  L  GNSGT++RLLSGLLAGQPF+  +TGD+SL
Sbjct: 373 --VIEGPNHGRVTIHGVGLHGLKPPPGPLYVGNSGTSMRLLSGLLAGQPFDVTMTGDASL 430

Query: 121 QRRPMKRIIDPLTLMGAKIDS-TGNVPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGL 179
            +RPM R+ +PL  MGA +++     PPL I G  +L G+ Y LPMASAQVKSCLLLAGL
Sbjct: 431 SKRPMNRVANPLREMGAVVETGPDGRPPLTIRGGHKLKGLTYTLPMASAQVKSCLLLAGL 490

Query: 180 YARGKTCITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAF 239
           YA GKT +TEPAP+RDHTER+L+ F Y++        +  GGKL A  I +P DISSAAF
Sbjct: 491 YAEGKTTVTEPAPTRDHTERMLRGFGYSVDSHGPVASLQSGGKLTATRIEVPADISSAAF 550

Query: 240 FIVAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHAR 299
           F+VAA+I  GS + L  VG+NPTR GVI++L++MG DI + +  E   EP AD+ VR A+
Sbjct: 551 FLVAASIAEGSELVLEHVGINPTRTGVIDILRLMGGDITLENQREVGGEPVADLRVRGAK 610

Query: 300 LKGIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGI 359
           LKGIDIP   VPL IDEFPVL +AAA A+G+TVLR A ELRVKE+DRI  M DGL  LGI
Sbjct: 611 LKGIDIPEALVPLAIDEFPVLFVAAACAEGRTVLRGAEELRVKESDRIQVMADGLTTLGI 670

Query: 360 AAESLPDGVIIQGGTLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFV 419
             E  PDG+II GG + GGEV+ + DHRIAMAF+VA   A  P+RI +C NV TSFPNF+
Sbjct: 671 KCEPTPDGIIIDGGQMGGGEVHGHGDHRIAMAFSVASLRASAPIRIHDCANVATSFPNFL 730

Query: 420 ELANEVGMNV 429
            L  EVG+ V
Sbjct: 731 ALCAEVGIRV 740


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: 935
Number of extensions: 40
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: 746
Length adjustment: 36
Effective length of query: 402
Effective length of database: 710
Effective search space:   285420
Effective search space used:   285420
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 PP_1770 PP_1770 (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.28146.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.7e-130  419.8   0.0   6.9e-130  419.5   0.0    1.1  1  lcl|FitnessBrowser__Putida:PP_1770  PP_1770 3-phosphoshikimate 1-car


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1770  PP_1770 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.5   0.0  6.9e-130  6.9e-130       1     413 [.     324     737 ..     324     739 .. 0.95

  Alignments for each domain:
  == domain 1  score: 419.5 bits;  conditional E-value: 6.9e-130
                           TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..lkepeae 72 
                                         g+i++pg+KSishR+++l++Laeg+t+v+++L++eD latl+a+r++G+ +e  ++++++i+gvg   lk p   
  lcl|FitnessBrowser__Putida:PP_1770 324 GRIRVPGDKSISHRSIMLGSLAEGTTEVEGFLEGEDALATLQAFRDMGVVIEgPNHGRVTIHGVGLhgLKPPPGP 398
                                         79**************************************************66699*******988899999** PP

                           TIGR01356  73 ldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplkg.give 146
                                         l++gnsGt++Rll+g+la ++++v++tgd sl+kRP++r+ ++Lre+ga +e    +g++Pl+i+g+ k+ g ++
  lcl|FitnessBrowser__Putida:PP_1770 399 LYVGNSGTSMRLLSGLLAGQPFDVTMTGDASLSKRPMNRVANPLREMGAVVETGP-DGRPPLTIRGGHKLkGLTY 472
                                         ***************************************************9866.79*********8888**** PP

                           TIGR01356 147 lsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykqkeve 221
                                           ++aS+Q+ks+llla+   l a++ ++v+e+  +r+++e++L  ++     v+ +     +++ g+k + +++e
  lcl|FitnessBrowser__Putida:PP_1770 473 TLPMASAQVKSCLLLAG---LYAEGKTTVTEPAPTRDHTERMLRGFGYS---VDSHGP-VASLQSGGKLTATRIE 540
                                         *****************...67789999999***********9887755...888876.77888888877778** PP

                           TIGR01356 222 vegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dvevegasklk 287
                                         v++D+SsAaffl+aa i+++ e+++e++g+n+t+++  +i++L+ mG+d+++e+qr        d++v+ga klk
  lcl|FitnessBrowser__Putida:PP_1770 541 VPADISSAAFFLVAASIAEGsELVLEHVGINPTRTG--VIDILRLMGGDITLENQRevggepvaDLRVRGA-KLK 612
                                         *******************99***************..788****************************75.7** PP

                           TIGR01356 288 gvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkkke 361
                                         g+++ ++ v+ +iDe+p+l v+aa+Aeg t+++++eelRvkEsdRi+++a+ L++lG+++e+++dg++i G+  +
  lcl|FitnessBrowser__Putida:PP_1770 613 GIDIpEALVPLAIDEFPVLFVAAACAEGRTVLRGAEELRVKESDRIQVMADGLTTLGIKCEPTPDGIIIDGG--Q 685
                                         ****99******************************************************************..6 PP

                           TIGR01356 362 lkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlg 413
                                         + g++v++++DHRiama++v++l+a+++++i+d + va+sfP+F+ + +++g
  lcl|FitnessBrowser__Putida:PP_1770 686 MGGGEVHGHGDHRIAMAFSVASLRASAPIRIHDCANVATSFPNFLALCAEVG 737
                                         *********************************************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (746 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 16.63
//
[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