Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_011190252.1 DP_RS15240 3-phosphoshikimate 1-carboxyvinyltransferase
Query= BRENDA::Q3MAV9 (426 letters) >NCBI__GCF_000025945.1:WP_011190252.1 Length = 451 Score = 332 bits (851), Expect = 1e-95 Identities = 183/412 (44%), Positives = 262/412 (63%), Gaps = 8/412 (1%) Query: 13 VDATVEIPGSKSITNRALLVAALAQGDSTLENALFSEDSEYFAKCVEQLGIPITLNPHLA 72 VD +V +PGSKS+T RAL+ AALA+G+STL L SED+EY + + Q+G+ I H Sbjct: 40 VDVSVAVPGSKSLTQRALIAAALAEGESTLHGPLVSEDTEYSSAALRQVGVTID---HEE 96 Query: 73 QIQVSGKGGDIPAKQADLFVGLAGTAARFITALVALGNGEYRLDGVPRMRERPMGDLVTV 132 +V G G I +F+G GTA RF+T++++LGN + LDG RM ERP+ L+T Sbjct: 97 SWRVQGNAGRIAPCAEPIFLGNNGTATRFLTSVLSLGNSRFVLDGDKRMAERPIEPLMTA 156 Query: 133 LQNSGIKINFEGNSGFMPYTIYGQQFAGGHFRLKANQTSQQLSALLMIAPYAQQDTTIEV 192 LQ G+ ++ ++G P I AGG L ++SQ LS+LL++APYA++ + V Sbjct: 157 LQGWGVDVSSMHDTGCPPLVINSTGLAGGMTVLPEGKSSQYLSSLLLVAPYAREVAELRV 216 Query: 193 EGTLVSQSYVKMTCRLMADFGVDVTQTDDNQFHIKAGQRYQARHYTIEPDASNASYFFAA 252 EG + S+ Y+ MT +M+ FG+ V + D ++ Y+ + Y++E DAS+ASYF+AA Sbjct: 217 EGEVFSKPYITMTLDVMSRFGIHVEYSSDYKYFKIPRGIYRGQDYSVEGDASSASYFWAA 276 Query: 253 AAVTGGRVRVNHLTKQSCQGDILWLNVLEQMGCQV-LEGEDYTEVIGPEQLQGIDVDMND 311 AAVTGGRVRV +++ S QGD+ + +L +MGC + +EG T + L+GI VDM D Sbjct: 277 AAVTGGRVRVENVSVSSLQGDVKLVPLLGRMGCGLSIEGGGIT-LASTGMLEGISVDMAD 335 Query: 312 MSDLVQTLGAIAPYANSPVIIRNVEHIRYKETERIRAVVTELRRLGVKVEEFADGMKIE- 370 M D+V TL +A +A I+N+ H+R KE +R+ AVVTEL R+G +VEE +D M I Sbjct: 336 MPDVVPTLAVVAAFAEGKTHIQNIGHLRIKECDRLHAVVTELTRMGAEVEEHSDSMVIHG 395 Query: 371 --PTPINPAAIETYHDHRMAMAFAVTGLKTPGIVIQDPGCTAKTFPDYFTRF 420 ++ A IETY DHRMAM+ AV GLK PG+ I GC AK+FPD++ RF Sbjct: 396 KGGRDLHGATIETYDDHRMAMSMAVAGLKVPGVEISGEGCVAKSFPDFWQRF 447 Lambda K H 0.320 0.136 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: 480 Number of extensions: 24 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: 426 Length of database: 451 Length adjustment: 32 Effective length of query: 394 Effective length of database: 419 Effective search space: 165086 Effective search space used: 165086 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 (21.8 bits) S2: 51 (24.3 bits)
Align candidate WP_011190252.1 DP_RS15240 (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.9134.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-140 453.7 0.0 3.3e-140 453.5 0.0 1.0 1 lcl|NCBI__GCF_000025945.1:WP_011190252.1 DP_RS15240 3-phosphoshikimate 1- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025945.1:WP_011190252.1 DP_RS15240 3-phosphoshikimate 1-carboxyvinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 453.5 0.0 3.3e-140 3.3e-140 2 410 .. 43 448 .. 42 451 .] 0.96 Alignments for each domain: == domain 1 score: 453.5 bits; conditional E-value: 3.3e-140 TIGR01356 2 eikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg.lkep 69 ++++pgsKS+++Ral++aaLaege++++++L seDt+++ alr+ G+++ ++e++ ++g++g ++ lcl|NCBI__GCF_000025945.1:WP_011190252.1 43 SVAVPGSKSLTQRALIAAALAEGESTLHGPLVSEDTEYSSAALRQVGVTID-HEESWRVQGNAGrIAPC 110 689************************************************.689*******9966666 PP TIGR01356 70 eaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisg 138 + + lgn Gt++R+lt+vl+l ++ +vl+gd+++ +RPie+l++aL+ g++++s +++g++Pl+i++ lcl|NCBI__GCF_000025945.1:WP_011190252.1 111 AEPIFLGNNGTATRFLTSVLSLGNSRFVLDGDKRMAERPIEPLMTALQGWGVDVSSMHDTGCPPLVINS 179 6******************************************************************** PP TIGR01356 139 p.lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede.r 205 + l gg++ l SsQy+s+lll ap+a + +l+++g ++ s+pyi +tL+++++fg++ve + + + lcl|NCBI__GCF_000025945.1:WP_011190252.1 180 TgLAGGMTVLPEGKSSQYLSSLLLVAPYAREVAELRVEG-EVFSKPYITMTLDVMSRFGIHVEYSSDyK 247 98888999999999**************99888888888.*************************9988 PP TIGR01356 206 kivvkggqkykqkevevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadvevee 274 +++++g y+ ++++vegDaSsA++f aaaa+tg++v+ven+ +s+qgd++++ +L +mG+ +++e lcl|NCBI__GCF_000025945.1:WP_011190252.1 248 YFKIPRGI-YRGQDYSVEGDASSASYFWAAAAVTGGRVRVENVSVSSLQGDVKLVPLLGRMGCGLSIEG 315 88999875.99999******************************************************* PP TIGR01356 275 qrdvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklG 343 +++ ++ l+g+ +d+++++D +ptlav+aafAeg+t+i+ni +lR+kE+dR++a+++eL+++G lcl|NCBI__GCF_000025945.1:WP_011190252.1 316 G-GITLASTGMLEGIS--VDMADMPDVVPTLAVVAAFAEGKTHIQNIGHLRIKECDRLHAVVTELTRMG 381 *.7****999******..*************************************************** PP TIGR01356 344 veveeledgllieGkk.kelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevle 410 +evee +d+++i+Gk + l+ga+++tydDHR+am++av+gl++ +vei +++cvaksfP+F++ + lcl|NCBI__GCF_000025945.1:WP_011190252.1 382 AEVEEHSDSMVIHGKGgRDLHGATIETYDDHRMAMSMAVAGLKVP-GVEISGEGCVAKSFPDFWQRFA 448 ****************9***************************9.******************9765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (415 nodes) Target sequences: 1 (451 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: 11.47 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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