Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate Echvi_1218 Echvi_1218 aspartate kinase
Query= BRENDA::P08660 (449 letters) >FitnessBrowser__Cola:Echvi_1218 Length = 439 Score = 249 bits (637), Expect = 1e-70 Identities = 148/448 (33%), Positives = 255/448 (56%), Gaps = 16/448 (3%) Query: 6 VSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGERF---E 62 + KFGGTSV + M++ D++ D +++VLSA +G TN LV + E L G++ E Sbjct: 3 IMKFGGTSVGKPERMHQVKDLITRDNERKIIVLSALSGTTNALVGIGEALAEGKKDLAKE 62 Query: 63 KLDAIRNIQFAILERLRYPNVIREEIERLL-ENITVLAEAAALATSPALTDELVSHGELM 121 ++D + + L R++ E+++ E+ L ++ + A+ ++++ GEL+ Sbjct: 63 RIDTLHAHYQEFYKALLESEAGRKKAEKIIKEHFEFLNIILKISFNEAINRDILAQGELL 122 Query: 122 STLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVIT 181 ST LF +L+E+D+ A + + M ++ +EP++A +++ L + L IT Sbjct: 123 STKLFYTLLQEKDIPAIFLPALEYMSIDEN---SEPEVAKISDRLKAILKNYDKDALFIT 179 Query: 182 QGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRID 241 QG+I ++ L RGGSDYTA+L+ A+ AS V+IWTD+ G++ DPRVV + I Sbjct: 180 QGYICKNHRNEVDNLKRGGSDYTASLIGAAIKASVVEIWTDIDGMHNNDPRVVDKTRPIA 239 Query: 242 EIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFRA 301 +++F EAAE+A FGAK+LHPA++ PA +IPV + ++ P A GT + E +A Sbjct: 240 QLSFDEAAELAYFGAKILHPASIWPAQTYNIPVKLLNTMQPEAPGTTI-TAEETGKGVKA 298 Query: 302 LALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGSTST 361 +A + + + S ML + GFL +VF I ++ +D+ITTSEV+V++T+D Sbjct: 299 IAAKDGIIAVKIKSSRMLLAYGFLRKVFEIFEKYKTPIDMITTSEVAVSVTID------- 351 Query: 362 GDTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICYG 421 D + ++MEL E++ +V + GN +++ G+ KEV L+ F +RM+ YG Sbjct: 352 -DDTHLKEIIMELEKFGNTEIDYKQTIVCVAGNMIAENTGMIKEVVVALQDFPVRMVSYG 410 Query: 422 ASSHNLCFLVPGEDAEQVVQKLHSNLFE 449 S +N+ LV + + +Q+L+ LF+ Sbjct: 411 GSRNNVSILVDTKYKNEALQRLNDELFQ 438 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: 378 Number of extensions: 14 Number of successful extensions: 5 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: 439 Length adjustment: 32 Effective length of query: 417 Effective length of database: 407 Effective search space: 169719 Effective search space used: 169719 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_1218 Echvi_1218 (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.24351.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-89 285.4 1.0 5.2e-89 285.2 1.0 1.0 1 lcl|FitnessBrowser__Cola:Echvi_1218 Echvi_1218 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_1218 Echvi_1218 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 285.2 1.0 5.2e-89 5.2e-89 5 441 .. 3 437 .. 1 438 [. 0.90 Alignments for each domain: == domain 1 score: 285.2 bits; conditional E-value: 5.2e-89 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee...keliekirekhle 75 ++KFGGtSvg+ er+++v +++++++e + ++V+SA +g+T+aLv + e + ++++ ke i+++ ++ e lcl|FitnessBrowser__Cola:Echvi_1218 3 IMKFGGTSVGKPERMHQVKDLITRDNERK---IIVLSALSGTTNALVGIGEALAEGKKdlaKERIDTLHAHYQE 73 79**********************99555...***********************9987776666666666666 PP TIGR00657 76 aleela.sqalkeklkallekeleevkk.......ereldlilsvGEklSaallaaaleelgvkavsllgaeag 141 ++l s+a ++k ++++++++e ++ e+ + il+ GE lS++l+ +l+e+++ a+ l + e lcl|FitnessBrowser__Cola:Echvi_1218 74 FYKALLeSEAGRKKAEKIIKEHFEFLNIilkisfnEAINRDILAQGELLSTKLFYTLLQEKDIPAIFLPALEYM 147 66666667777777777777777666558899999999999**********************99999888877 PP TIGR00657 142 iltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytD 215 + +++ + +++ + + ++k +++ + +++G+i ++ +e+ L RGGSD+tA+l++aa+kA++vei+tD lcl|FitnessBrowser__Cola:Echvi_1218 148 SIDENSEPEVA-KISDRLKAILKNYDKDALFITQGYICKNHRNEVDNLKRGGSDYTASLIGAAIKASVVEIWTD 220 66655544444.5788888888999999********************************************** PP TIGR00657 216 VdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskse 289 +dG + DPr+v ++r ++++s++Ea+ELa++Gak+Lhp+++ pa ++ip+ +t++pea+GT i+a+++ lcl|FitnessBrowser__Cola:Echvi_1218 221 IDGMHNNDPRVVDKTRPIAQLSFDEAAELAYFGAKILHPASIWPAQTYNIPVKLLNTMQPEAPGTTITAEET-- 292 **********************************************************************55.. PP TIGR00657 290 eepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellk 361 + vka++ ++ + v+++++ m +g+l +vf++ ++ k +d+i+ +se +s ++d++ + ke+ lcl|FitnessBrowser__Cola:Echvi_1218 293 -GKGVKAIAAKDGIIAVKIKSSRMLlaYGFLRKVFEIFEKYKTPIDMIT--TSEVAVSVTIDDD--THLKEI-- 359 .688********************999**********************..7765666666654..444444.. PP TIGR00657 362 kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekdaekav 433 ++e+++++++e++ k +v + G+ ++++ g++++++ aL++ ++++m+s s ++s++vd k+ ++a+ lcl|FitnessBrowser__Cola:Echvi_1218 360 --IMELEKFGNTEIDYKQTIVCVAGNMIAENTGMIKEVVVALQD--FPVRMVSygGSRNNVSILVDTKYKNEAL 429 ..688999**********************************99..9******999****************** PP TIGR00657 434 ealheklv 441 + l ++l+ lcl|FitnessBrowser__Cola:Echvi_1218 430 QRLNDELF 437 ****9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (439 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: 11.40 // [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