Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate Echvi_1827 Echvi_1827 aspartate kinase
Query= BRENDA::P08660 (449 letters) >FitnessBrowser__Cola:Echvi_1827 Length = 423 Score = 172 bits (435), Expect = 2e-47 Identities = 123/404 (30%), Positives = 201/404 (49%), Gaps = 20/404 (4%) Query: 1 MSEIVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGER 60 M++ +V KFGG SV D A+ ++I+ + +V++ ++ G T AL E L + Sbjct: 1 MTKAIVYKFGGASVKDAAAIKNLSNILFNRLRSPMVIVVSAIGKTTN--ALEEILRL--K 56 Query: 61 FEKLDAIRNIQFAILERLRYPNVIREE---IERLLENITV-LAEAAALATSPALTDE--- 113 ++ +D NI L + EE + ++ENI + LA + + DE Sbjct: 57 YDGVDFYSNITILRKNHLAICQELFEEGDLVFGMVENIFLQLARVLEVPLTKENYDEYYD 116 Query: 114 -LVSHGELMSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLP 172 +V GEL+ST + L R W D R + T+D F A+ D A +L+P Sbjct: 117 RVVGFGELLSTKIIHAYLCHRQQYCIWQDARDFILTDDNFRFAKVDWEQTARQCQQKLVP 176 Query: 173 RLNEGLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPR 232 L + V+TQGF+GS G+ TTLGR GSD++AA+ A++L A V IW DVPG+ DP+ Sbjct: 177 VLKQLPVVTQGFVGSTKDGQPTTLGREGSDFSAAIFAKSLGAESVTIWKDVPGVLNADPK 236 Query: 233 VVSAAKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNK 292 + D + + EAAEM +GA V+HP T+ P + IP+FV S P GT++ + Sbjct: 237 RFEETVKFDRLDYKEAAEMTFYGASVIHPRTIKPLANAKIPLFVRSFLQPEEQGTVIGDF 296 Query: 293 TENPPLFRALALRRNQTLLTLHSLNMLH-SRGFLAEVFGILARHNISVDLITTSEVSVAL 351 E + ++ Q L+T + + + +V+ L R + +LI +S +++++ Sbjct: 297 GEGSINVPTIVVKDRQVLVTFEVTDFTFINESHMHQVYAELDRLKLRANLIQSSAITISI 356 Query: 352 TLDTTGSTSTGDTLLTQSLLMELSALCRVEVEEGLALVALIGND 395 D + + LL E+ + +V+ EGL LV + D Sbjct: 357 CTDR-------ELFKLEQLLEEMKGIFKVKYNEGLQLVTVKNYD 393 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: 322 Number of extensions: 10 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: 423 Length adjustment: 32 Effective length of query: 417 Effective length of database: 391 Effective search space: 163047 Effective search space used: 163047 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 Echvi_1827 Echvi_1827 (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.27178.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-77 246.5 0.0 3.5e-77 246.3 0.0 1.0 1 lcl|FitnessBrowser__Cola:Echvi_1827 Echvi_1827 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_1827 Echvi_1827 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 246.3 0.0 3.5e-77 3.5e-77 2 385 .. 3 390 .. 2 419 .. 0.86 Alignments for each domain: == domain 1 score: 246.3 bits; conditional E-value: 3.5e-77 TIGR00657 2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekirekhl 74 + iV+KFGG Sv+++ ik++ +i+ ++ + ++v+VvSA++++T+aL e+ + ++ + + i+ +r++hl lcl|FitnessBrowser__Cola:Echvi_1827 3 KAIVYKFGGASVKDAAAIKNLSNILFNRL--RSPMVIVVSAIGKTTNALEEILRLKYDGVDfYSNITILRKNHL 74 579***********************999..668********************999999978899999***** PP TIGR00657 75 ealeela.sqalkeklkallekeleevkk...........ereldlilsvGEklSaallaaaleelgvkavsll 136 ++ +el + + ++e+ + ++ + ++ +d+++ +GE lS++++ a+l++++ ++ + lcl|FitnessBrowser__Cola:Echvi_1827 75 AICQELFeEG---DLVFGMVENIFLQLARvlevpltkenyDEYYDRVVGFGELLSTKIIHAYLCHRQ-QYCIWQ 144 **99998553...444455555555555556689999999***************************.9***** PP TIGR00657 137 gaeagiltdsefgrAk....vleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalk 206 +a+ iltd++f+ Ak +++ +++l ++l++ vv++GF+G+t++g+ ttLGR GSD++Aa+ A+ l+ lcl|FitnessBrowser__Cola:Echvi_1827 145 DARDFILTDDNFRFAKvdweQTARQCQQKLVPVLKQL-PVVTQGFVGSTKDGQPTTLGREGSDFSAAIFAKSLG 217 ****************544333333344444444443.56779******************************* PP TIGR00657 207 AdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGT 280 A+ v i++DV+G++ aDP+ +e+ + d ++y+Ea+E++ +Ga v+hprt++p+++akip++v+s +pe++GT lcl|FitnessBrowser__Cola:Echvi_1827 218 AESVTIWKDVPGVLNADPKRFEETVKFDRLDYKEAAEMTFYGASVIHPRTIKPLANAKIPLFVRSFLQPEEQGT 291 ************************************************************************** PP TIGR00657 281 livakskseeepavkalsldknqalvsvsgttmk...pgilaevfgalaeakvnvdlilqsssetsisfvvdke 351 +i+ + + +v ++ +++ q+lv+ + t + +v l + k +li ss +is++ d+e lcl|FitnessBrowser__Cola:Echvi_1827 292 VIGDFGE--GSINVPTIVVKDRQVLVTFEVTDFTfinESHMHQVYAELDRLKLRANLIQ--SSAITISICTDRE 361 ***9966..5578999999999999999988888778999999**************98..5556899999887 PP TIGR00657 352 dadkakellkkkvkeekaleevevekklalvslv 385 k ++ll +e k + +v+++++l lv++ lcl|FitnessBrowser__Cola:Echvi_1827 362 LF-KLEQLL----EEMKGIFKVKYNEGLQLVTVK 390 64.455553....466677779999999988875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (423 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: 00:00:00.02 # Mc/sec: 7.59 // [ok]
This GapMind analysis is from Apr 09 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