Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011020190.1 MA_RS00690 aspartate kinase, monofunctional class
Query= BRENDA::Q57991 (473 letters) >NCBI__GCF_000007345.1:WP_011020190.1 Length = 472 Score = 464 bits (1194), Expect = e-135 Identities = 243/469 (51%), Positives = 333/469 (71%), Gaps = 11/469 (2%) Query: 1 MTTVMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVR 60 M VMKFGGTSVG G++IRHVA+++ + +E + +VVV SA+ VT+ L+E ++ A Sbjct: 1 MKIVMKFGGTSVGDGKKIRHVAQLLKRYHEEGNQIVVVTSALGGVTDRLLENARLASTKG 60 Query: 61 DIAKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPK 120 ++ V +F + KH++A+++AI+ + +EV +++D RIEELEK LIG+ YLGELT + Sbjct: 61 KVSLVKEFKTELTNKHHEAVKDAIEDPRVAKEVLQVLDLRIEELEKALIGICYLGELTSR 120 Query: 121 SRDYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSARV--KRLEVKERL 178 S DYI S+GERL++PI+SGA+R LG SI GGEAGI+T +++G+AR K E+ + Sbjct: 121 SIDYISSYGERLAAPIVSGAVRSLGAASIEYTGGEAGIVTTSDYGNARPLEKTYELVLKR 180 Query: 179 LPLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTT 238 L E I VVTGFIG E+G ITTLGR GSD+SA+++G L AD I +W +V+G+ TT Sbjct: 181 LGCRLESHILVVTGFIGENEDGIITTLGRSGSDFSASILGAALKADEIWLWKEVNGIMTT 240 Query: 239 DPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLI 298 DPR+VP A+ IP++SY EAMEL+YFGA VLHPRTIEPAM + IP+ VKNTF PE GTL+ Sbjct: 241 DPRIVPEAKTIPQISYAEAMELSYFGANVLHPRTIEPAMREHIPVRVKNTFNPEFPGTLV 300 Query: 299 TNDMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQGSSE 358 + +VKA+S IKNVALINI GA M G GT AR+F AL VN+++ISQGSSE Sbjct: 301 VAEKFQCRHVVKAVSLIKNVALINISGAEMPGTVGTVARLFTALARAGVNIVMISQGSSE 360 Query: 359 TNISLVVSEEDVDKALKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAGMRGAK 418 +N+S VVSE V+ ALKAL EF N ++++++ D++VCV++VVGAGM G Sbjct: 361 SNLSFVVSESHVESALKALHAEF---------NREIVKEITSDRNVCVVAVVGAGMAGTP 411 Query: 419 GIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKF 467 G+A ++F A+ S NI MI+QGSS+ NISFV+ E D V+ LH++F Sbjct: 412 GVAKRVFGALGNSMINIIMISQGSSQYNISFVVREGDAFAAVKTLHDEF 460 Lambda K H 0.316 0.135 0.364 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: 585 Number of extensions: 22 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: 473 Length of database: 472 Length adjustment: 33 Effective length of query: 440 Effective length of database: 439 Effective search space: 193160 Effective search space used: 193160 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_011020190.1 MA_RS00690 (aspartate kinase, monofunctional class)
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.27270.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-144 467.7 2.7 2.6e-144 467.5 2.7 1.0 1 lcl|NCBI__GCF_000007345.1:WP_011020190.1 MA_RS00690 aspartate kinase, mon Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007345.1:WP_011020190.1 MA_RS00690 aspartate kinase, monofunctional class # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 467.5 2.7 2.6e-144 2.6e-144 2 441 .. 1 461 [. 1 462 [. 0.96 Alignments for each domain: == domain 1 score: 467.5 bits; conditional E-value: 2.6e-144 TIGR00657 2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee....keli 66 ++iV+KFGGtSvg++++i++va+++k+ +e+gnq vVV SA +gvTd+L+e a+ +s + + ke+ lcl|NCBI__GCF_000007345.1:WP_011020190.1 1 MKIVMKFGGTSVGDGKKIRHVAQLLKRYHEEGNQIVVVTSALGGVTDRLLENARLASTKGKvslvKEFK 69 679*****************************************************9999989999999 PP TIGR00657 67 ekirekhlealeela.sqalkeklkallekeleevkk............ereldlilsvGEklSaalla 122 +++ +kh ea++ ++ + +++++ ++l+ ++ee++k +r+ d+i s+GE+l+a++++ lcl|NCBI__GCF_000007345.1:WP_011020190.1 70 TELTNKHHEAVKDAIeDPRVAKEVLQVLDLRIEELEKaligicylgeltSRSIDYISSYGERLAAPIVS 138 99************999999***************99******************************** PP TIGR00657 123 aaleelgvkavsllgaeagiltdsefgrAk...vleeikterleklleegiivvvaGFiGatekgeitt 188 +a+++lg+ +++++g+eagi+t+s +g+A+ +++e +rl le +i vv+GFiG +e+g itt lcl|NCBI__GCF_000007345.1:WP_011020190.1 139 GAVRSLGAASIEYTGGEAGIVTTSDYGNARpleKTYELVLKRLGCRLES-HILVVTGFIGENEDGIITT 206 ******************************7666666666666666665.599**************** PP TIGR00657 189 LGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtl 257 LGR GSD++A++l+aalkAde++++++V+Gi+t+DPrivpeA+ +++isy+Ea+EL+++Ga vLhprt+ lcl|NCBI__GCF_000007345.1:WP_011020190.1 207 LGRSGSDFSASILGAALKADEIWLWKEVNGIMTTDPRIVPEAKTIPQISYAEAMELSYFGANVLHPRTI 275 ********************************************************************* PP TIGR00657 258 epamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfga 324 epamr ip++vk+tfnpe +GTl+va++ + + vka+sl kn al+++sg++m +g++a++f+a lcl|NCBI__GCF_000007345.1:WP_011020190.1 276 EPAMREHIPVRVKNTFNPEFPGTLVVAEKF-QCRHVVKAVSLIKNVALINISGAEMPgtVGTVARLFTA 343 ****************************66.6669*********************999********** PP TIGR00657 325 laeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksap 393 la+a+vn+++i+q sse+++sfvv+++++++a ++l+ ++ + + ++e++ ++++++v++vGagm+++p lcl|NCBI__GCF_000007345.1:WP_011020190.1 344 LARAGVNIVMISQGSSESNLSFVVSESHVESALKALH-AEFNREIVKEITSDRNVCVVAVVGAGMAGTP 411 ***********************************96.68899999*********************** PP TIGR00657 394 gvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441 gva+++f aL ++ ini mis ss+++is+vv+e da +av++lh++++ lcl|NCBI__GCF_000007345.1:WP_011020190.1 412 GVAKRVFGALGNSMINIIMISqgSSQYNISFVVREGDAFAAVKTLHDEFE 461 ***********************************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (472 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.01 // [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