Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_010438017.1 G7G_RS0102615 3-phosphoshikimate 1-carboxyvinyltransferase
Query= BRENDA::C3MC80 (448 letters) >NCBI__GCF_000192475.1:WP_010438017.1 Length = 452 Score = 450 bits (1158), Expect = e-131 Identities = 248/448 (55%), Positives = 305/448 (68%), Gaps = 9/448 (2%) Query: 3 HGLSPRPATAKKSADLKGTVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGKA 62 HG +P P T+ L GT +PGDKSISHRS + G +A GETRI+GLLEGEDV++T KA Sbjct: 4 HG-TPIPMTSHPCGPLTGTAEVPGDKSISHRSLILGAMAVGETRISGLLEGEDVLDTAKA 62 Query: 63 MQAMGAKIRKEGD-TWIINGVGNGALLAPEAPLDFGNAGTGCRLTMGLVGVYDFDSTFIG 121 M+A GA++ G W ++GVG G P+ +D GN+GTG RL MG + +TF G Sbjct: 63 MRAFGAEVTDHGGGEWSVHGVGVGGFAEPDQVIDCGNSGTGVRLIMGAMATSPITATFTG 122 Query: 122 DASLTKRPMGRVLDPLREMGVQVKSAEGDRLPVTLRGPKTPNPITYRVPMASAQVKSAVL 181 DASL KRPM RV DPL G Q G RLP+T+ G P P+ Y VP+ SAQVKSAVL Sbjct: 123 DASLNKRPMARVTDPLALFGTQSVGRNGGRLPMTIVGAADPIPVRYEVPVPSAQVKSAVL 182 Query: 182 LAGLNTPGITTVIEPVMTRDHTEKMLQGFGANLSVETDTAGVRTIRLEGRGKLTGQVIDV 241 LAGLN PG T VIE TRDH+E+ML GFGA ++VE DT R I L GR +L QVI V Sbjct: 183 LAGLNAPGKTVVIEKEATRDHSERMLAGFGAEITVE-DTDEGRVITLTGRPELKPQVIAV 241 Query: 242 PGDPSSTAFPLVAALLVPGSDVTILNVLMNPTRTGLILTLQEMGANIEVMNPRLAGGEDV 301 P DPSS AFP+ AAL+ PGSDV + + +NPTR GL TL+EMGA++ N R GGE V Sbjct: 242 PRDPSSAAFPVCAALITPGSDVLVPGIGLNPTRAGLFTTLREMGADLTYENEREEGGEPV 301 Query: 302 ADLRVRYS-ELKGVTVPEERAPSMIDEYPVLAVAAAFAEGATVMNGLDELRVKESDRLSA 360 ADLR +YS +KG++VP ERA SMIDEYPVL+V AA A G +M G+ ELRVKESDR+ A Sbjct: 302 ADLRAKYSPNMKGISVPPERAASMIDEYPVLSVVAANATGTMMMGGVKELRVKESDRIDA 361 Query: 361 VADGLKLNGVDCDEGEASLVVRGRPGGKGLGNAAGGQV-KTHLDHRIAMSFLVLGLASEH 419 +A GL+ NGV DEG+ V G G+G GG + ++ LDHRIAMSF+V+G+ ++ Sbjct: 362 MARGLRANGVTVDEGDDWWSVE----GLGIGGVPGGGICESFLDHRIAMSFMVMGMGAKK 417 Query: 420 PVTVDDATMIATSFPEFMDLMTGLGATI 447 V+VDD IATSFP F LMTGLGA + Sbjct: 418 AVSVDDGGPIATSFPIFEPLMTGLGAKL 445 Lambda K H 0.316 0.135 0.385 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: 728 Number of extensions: 53 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 448 Length of database: 452 Length adjustment: 33 Effective length of query: 415 Effective length of database: 419 Effective search space: 173885 Effective search space used: 173885 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
Align candidate WP_010438017.1 G7G_RS0102615 (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.1873256.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-118 382.7 0.0 1.1e-118 382.6 0.0 1.0 1 NCBI__GCF_000192475.1:WP_010438017.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000192475.1:WP_010438017.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 382.6 0.0 1.1e-118 1.1e-118 2 414 .. 21 443 .. 20 444 .. 0.96 Alignments for each domain: == domain 1 score: 382.6 bits; conditional E-value: 1.1e-118 TIGR01356 2 eikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..lkepea 71 ++pg+KSishR+l+l+a+a get++ +lL++eD+l t +a+r++Ga+v+++ ++e+ ++gvg ++ep++ NCBI__GCF_000192475.1:WP_010438017.1 21 TAEVPGDKSISHRSLILGAMAVGETRISGLLEGEDVLDTAKAMRAFGAEVTDHgGGEWSVHGVGVggFAEPDQ 93 6789***********************************************666********99888****** PP TIGR01356 72 eldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkgg 143 ++d+gnsGt +Rl++g++a+++ + ++tgd sl+kRP+ r++++L +g + ++ g+lP++i g + + NCBI__GCF_000192475.1:WP_010438017.1 94 VIDCGNSGTGVRLIMGAMATSPITATFTGDASLNKRPMARVTDPLALFGTQSVGRN-GGRLPMTIVGAaDPIP 165 ***************************************************99988.69********96666* PP TIGR01356 144 ivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede.rkivvkggqky 215 + + + S+Q+ksa+lla+ l+a + ++v+ek+ +r++ e++L+ ++++ ++ve +de r i+++g + NCBI__GCF_000192475.1:WP_010438017.1 166 VRYEVPVPSAQVKSAVLLAG---LNAPGKTVVIEKEATRDHSERMLAGFGAE-ITVEDTDEgRVITLTGRPEL 234 ********************...8999***********************99.****9999888999999889 PP TIGR01356 216 kqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dve 279 k++ ++v+ D+SsAaf++ aa+it++ +v v ++g n+t+++ ++++L+emGad+++e++r d++ NCBI__GCF_000192475.1:WP_010438017.1 235 KPQVIAVPRDPSSAAFPVCAALITPGsDVLVPGIGLNPTRAG--LFTTLREMGADLTYENEReeggepvaDLR 305 9999**************************************..888************************** PP TIGR01356 280 vegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeled 351 + + ++kg+ v +++++s+iDe+p+l+v+aa A g+ ++ +++elRvkEsdRi a+a+ L++ Gv+v+e+ d NCBI__GCF_000192475.1:WP_010438017.1 306 AKYSPNMKGISVpPERAASMIDEYPVLSVVAANATGTMMMGGVKELRVKESDRIDAMARGLRANGVTVDEGDD 378 ************99*********************************************************** PP TIGR01356 352 gllieGkk..kelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlga 414 + ++eG g+ +++ DHRiam++ v+g+ a++ v ++d + +a+sfP F ++ lga NCBI__GCF_000192475.1:WP_010438017.1 379 WWSVEGLGigGVPGGGICESFLDHRIAMSFMVMGMGAKKAVSVDDGGPIATSFPIFEPLMTGLGA 443 *******99455555899***************************************99999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (415 nodes) Target sequences: 1 (452 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: 00:00:00.00 # Mc/sec: 25.67 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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:
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