Align Aspartokinase 3; Aspartate kinase 3; Aspartokinase III; EC 2.7.2.4 (characterized)
to candidate WP_010530910.1 ON01_RS10040 aspartate kinase
Query= SwissProt::P94417 (454 letters) >NCBI__GCF_000224785.1:WP_010530910.1 Length = 448 Score = 500 bits (1287), Expect = e-146 Identities = 247/449 (55%), Positives = 344/449 (76%), Gaps = 3/449 (0%) Query: 1 MKVVKFGGSSLASGAQLDKVFHIVTSDPARKAVVVSAPGKHYAEDTKVTDLLIACAEQYL 60 MKVVKFGGSS+A+ AQ+ K I+ D RK VVVSAPGK + +D K+TDLLI +E L Sbjct: 1 MKVVKFGGSSVANDAQIRKAGSIIADDSERKFVVVSAPGKRFKDDVKITDLLIELSELVL 60 Query: 61 ATGSAPELAEAVVERYALIANELQLGQSIIEKIRDDLFTLLEGDKSNPEQY-LDAVKASG 119 S + ++ R++ I N+L+L QSI+ I + L + ++P+Q D +K+ G Sbjct: 61 NNKSHEKKFAEIMARFSEIVNDLELPQSILADIEQSIQNTL--NTNSPDQIKADGLKSIG 118 Query: 120 EDNNAKLIAAYFRYKGVKAEYVNPKDAGLFVTNEPGNAQVLPESYQNLYRLRERDGLIIF 179 ED++AK+++ + + KG+ A YVNPKDAG+ V+NEPGNAQVLPES+ +Y +R RDG+++ Sbjct: 119 EDSSAKIVSEHLKTKGLNAHYVNPKDAGIIVSNEPGNAQVLPESFTKIYEMRARDGILVI 178 Query: 180 PGFFGFSKDGDVITFSRSGSDITGSILANGLQADLYENFTDVDAVYSVNPSFVENPKEIS 239 PGFFGF+K+G ++TFSR GSDITGSI+A G+QADLYENFTDVD+VY+VNP+ V NP++I+ Sbjct: 179 PGFFGFTKNGGLMTFSRGGSDITGSIVAAGVQADLYENFTDVDSVYAVNPAIVSNPEKIT 238 Query: 240 ELTYREMRELSYAGFSVFHDEALIPAFRAGIPVQIKNTNNPSAEGTRVVSKRDNTNGPVV 299 LTY+EMRELSY+GF VFHDEAL+PAF+A IPV IKNTNNP++ GT +VS ++ VV Sbjct: 239 TLTYKEMRELSYSGFGVFHDEALMPAFQAEIPVCIKNTNNPASPGTMIVSDKNPHTRCVV 298 Query: 300 GIASDTGFCSIYISKYLMNREIGFGRRALQILEEHGLTYEHVPSGIDDMTIILRQGQMDA 359 GIASDTGF ++Y+SKYLMNRE+GFGR+ LQILE+ G+++EH PSGID+M++I+R Q+ A Sbjct: 299 GIASDTGFSNLYVSKYLMNRELGFGRKLLQILEDEGISFEHAPSGIDNMSVIIRDSQLTA 358 Query: 360 ATERSVIKRIEEDLHADEVIVEHHLALIMVVGEAMRHNVGTTARAAKALSEAQVNIEMIN 419 E +VI RI+ +L+ + + +++ A+IMVVGE M VG ++A A +EA ++IEMIN Sbjct: 359 EKEINVINRIKSELNPETISIDYGFAMIMVVGEGMMSAVGIAEKSAAAFAEANISIEMIN 418 Query: 420 QGSSEVSMMFGVKEAEERKAVQALYQEFF 448 QGSSEVS+MFG+++ + AV++LYQ+FF Sbjct: 419 QGSSEVSVMFGIRKDKLDLAVKSLYQKFF 447 Lambda K H 0.316 0.134 0.370 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: 619 Number of extensions: 19 Number of successful extensions: 2 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: 454 Length of database: 448 Length adjustment: 33 Effective length of query: 421 Effective length of database: 415 Effective search space: 174715 Effective search space used: 174715 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_010530910.1 ON01_RS10040 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))
# 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/TIGR00657.hmm # target sequence database: /tmp/gapView.4048514.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00657 [M=442] Accession: TIGR00657 Description: asp_kinases: aspartate kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-85 273.6 0.8 2e-85 273.4 0.8 1.0 1 NCBI__GCF_000224785.1:WP_010530910.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010530910.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 273.4 0.8 2e-85 2e-85 5 441 .. 3 447 .. 1 448 [] 0.92 Alignments for each domain: == domain 1 score: 273.4 bits; conditional E-value: 2e-85 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAma.......gvTdaLvelaekvsseee.kelieki 69 V+KFGG+Sv+n +i+k+ i+ ++e + +VVvSA++ ++Td L+el+e v ++++ +++ ++i NCBI__GCF_000224785.1:WP_010530910.1 3 VVKFGGSSVANDAQIRKAGSIIADDSERK---FVVVSAPGkrfkddvKITDLLIELSELVLNNKShEKKFAEI 72 89**********************99555...******98333344459************9999888999** PP TIGR00657 70 rekhlealeela.sqalkeklkallekeleevkk.ereldlilsvGEklSaallaaaleelgvkavsllgaea 140 +++ e+++ l+ +q++ + +++ +++ l+ + + d + s+GE+ Sa+++++ l+++g +a + ++a NCBI__GCF_000224785.1:WP_010530910.1 73 MARFSEIVNDLElPQSILADIEQSIQNTLNTNSPdQIKADGLKSIGEDSSAKIVSEHLKTKGLNAHYVNPKDA 145 ***********************99999988766577899**********************99999999*** PP TIGR00657 141 giltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiy 213 gi+ ++e g+A+ + ++ ++ ++ + i v+ GF+G t++g + t RGGSD+t +++Aa ++Ad e + NCBI__GCF_000224785.1:WP_010530910.1 146 GIIVSNEPGNAQ-VLPESFTKIYEMRARDGILVIPGFFGFTKNGGLMTFSRGGSDITGSIVAAGVQADLYENF 217 ************.66666667777777777******************************************* PP TIGR00657 214 tDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivaks 286 tDVd +y P iv+++ ++ +++y+E+ EL+++G v+h ++l pa +a+ip+ +k+t np ++GT+iv+++ NCBI__GCF_000224785.1:WP_010530910.1 218 TDVDSVYAVNPAIVSNPEKITTLTYKEMRELSYSGFGVFHDEALMPAFQAEIPVCIKNTNNPASPGTMIVSDK 290 ************************************************************************8 PP TIGR00657 287 kseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkak 357 + ++ v ++++d+ + + vs+ m+ g+ +++++l++++++ + ++ ++s ++ ++++ ++k NCBI__GCF_000224785.1:WP_010530910.1 291 N-PHTRCVVGIASDTGFSNLYVSKYLMNreLGFGRKLLQILEDEGISFEHAPSGID--NMSVIIRDSQLTAEK 360 8.6679*********************9999******************9985555..677888888765555 PP TIGR00657 358 ellk.kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdek 427 e+ + +k+e + e+++++ ++a++ +vG+gm sa g+a k ++a ae+ni+iemi sse+++ + ++++ NCBI__GCF_000224785.1:WP_010530910.1 361 EINViNRIKSELNPETISIDYGFAMIMVVGEGMMSAVGIAEKSAAAFAEANISIEMINqgSSEVSVMFGIRKD 433 553357899*************************************************99************* PP TIGR00657 428 daekavealheklv 441 + + av+ l++k++ NCBI__GCF_000224785.1:WP_010530910.1 434 KLDLAVKSLYQKFF 447 ************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (448 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 28.31 // [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