Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_066327343.1 BLR17_RS04505 aspartate kinase
Query= BRENDA::P08660 (449 letters) >NCBI__GCF_900100165.1:WP_066327343.1 Length = 418 Score = 167 bits (422), Expect = 8e-46 Identities = 119/365 (32%), Positives = 183/365 (50%), Gaps = 29/365 (7%) Query: 6 VSKFGGTSVADFDAMNRSADIVLSDANVR--LVVLSASAGITNLLVALAEGLEPGERFEK 63 V KFGG SV D + D VL A + L+V+SA TN L + + Sbjct: 3 VFKFGGASVKDAAGIRNVYD-VLQKAGYQDVLLVVSAMGKTTNALEVVIKNY-------- 53 Query: 64 LDAIRNIQFAILERLRYPNVIREEI---------ERLLENITVLAEAAALATSPALT--- 111 D + ++ E +Y N I ++ + E+ + L A SP Sbjct: 54 FDKSPELNASVQEIKKYHNQILLDLFEDENHAVFAAVNEHFSDLEYFLAHNKSPNYNFVY 113 Query: 112 DELVSHGELMSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLL 171 D++VS GE++ST + + ++ QW DVR ++TN+ + AE D EL + Sbjct: 114 DQIVSMGEIISTTVLSYYMNFMGIETQWIDVRNYIKTNNNYRDAEVDW----ELTQSNIS 169 Query: 172 PRLN-EGLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTD 230 + + L ITQGF+GS+ TTTLGR GSDYTAA+ A L+A V IW DVPG+ D Sbjct: 170 KNIKTKSLNITQGFLGSDENNFTTTLGREGSDYTAAIFAYCLNAESVTIWKDVPGVMNAD 229 Query: 231 PRVVSAAKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVC 290 PR A +++I++ EA E+A +GA V+HP TL P + +IP+ V S +P GT+V Sbjct: 230 PRYFENASLLNQISYREAIELAFYGATVIHPKTLQPLQKKEIPLHVKSFINPLLKGTVVS 289 Query: 291 NKTENPPLFRALALRRNQTLLTLHSLNM-LHSRGFLAEVFGILARHNISVDLITTSEVSV 349 P ++R Q L++L S++ ++E+FG+ I V+LI S +S Sbjct: 290 KGATLEPFMPCFIVKREQLLISLSSIDFSFIMEENISEIFGLFHEFKIKVNLIQNSAISF 349 Query: 350 ALTLD 354 ++ ++ Sbjct: 350 SVCVE 354 Lambda K H 0.320 0.135 0.376 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: 304 Number of extensions: 8 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: 449 Length of database: 418 Length adjustment: 32 Effective length of query: 417 Effective length of database: 386 Effective search space: 160962 Effective search space used: 160962 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_066327343.1 BLR17_RS04505 (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.2692795.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-81 260.4 0.0 2.1e-81 260.2 0.0 1.1 1 NCBI__GCF_900100165.1:WP_066327343.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066327343.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.2 0.0 2.1e-81 2.1e-81 5 351 .. 3 354 .. 1 385 [. 0.88 Alignments for each domain: == domain 1 score: 260.2 bits; conditional E-value: 2.1e-81 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhle 75 V KFGG Sv+++ i++v + ++k+ + +v+ VvSAm+++T+aL ++++ ++ ++ +++i++ h + NCBI__GCF_900100165.1:WP_066327343.1 3 VFKFGGASVKDAAGIRNVYDVLQKAGYQ--DVLLVVSAMGKTTNALEVVIKNYFDKSPelNASVQEIKKYHNQ 73 89*******************9999955..5***************999999877665587888999999988 PP TIGR00657 76 aleelasqalkeklkallekeleevkk..........ereldlilsvGEklSaallaaaleelgvkavsllga 138 +l l +++ ++ + a++++++ ++ + +d i+s+GE +S+++l+ +++ g + ++++ NCBI__GCF_900100165.1:WP_066327343.1 74 ILLDLFEDENHA-VFAAVNEHFSDLEYflahnkspnyNFVYDQIVSMGEIISTTVLSYYMNFMG-IETQWIDV 144 887766543333.33444444444444567778999999*************************.78899*** PP TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeve 211 ++ i t++++++A+v e +++++ k ++ + + +++GF+G++e++ +ttLGR GSD+tAa+ A +l+A+ v NCBI__GCF_900100165.1:WP_066327343.1 145 RNYIKTNNNYRDAEVDWELTQSNISKNIKTKSLNITQGFLGSDENNFTTTLGREGSDYTAAIFAYCLNAESVT 217 ************************************************************************* PP TIGR00657 212 iytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTliva 284 i++DV+G++ aDPr+ ++A +l++isy+Ea ELa +Ga v+hp+tl+p+ +++ip++vks np +GT++ + NCBI__GCF_900100165.1:WP_066327343.1 218 IWKDVPGVMNADPRYFENASLLNQISYREAIELAFYGATVIHPKTLQPLQKKEIPLHVKSFINPLLKGTVVSK 290 ***********************************************************************99 PP TIGR00657 285 kskseeepavkalsldknqalvsvsgttmk...pgilaevfgalaeakvnvdlilqsssetsisfvvdke 351 + ep + ++++q l+s+s+ + ++e+fg +e k++v+li +s isf v e NCBI__GCF_900100165.1:WP_066327343.1 291 GAT--LEPFMPCFIVKREQLLISLSSIDFSfimEENISEIFGLFHEFKIKVNLIQ--NS--AISFSVCVE 354 966..55899999999*******9999999888888999***************8..33..244444333 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (418 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: 18.24 // [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