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.5826.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 18.34
//
[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