Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_041466196.1 CPAR_RS10150 lysine-sensitive aspartokinase 3
Query= BRENDA::Q57991 (473 letters) >NCBI__GCF_000020505.1:WP_041466196.1 Length = 470 Score = 308 bits (788), Expect = 3e-88 Identities = 191/474 (40%), Positives = 281/474 (59%), Gaps = 32/474 (6%) Query: 4 VMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVRDIA 63 VMKFGGTSVG+ +R V + ++KK +VV+ SA S +TN L++I+ +A R + Sbjct: 3 VMKFGGTSVGTAAAMRQVIANIAEKKKTSAPLVVL-SACSGITNKLIQIADEAGSGR-LK 60 Query: 64 KVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPKSRD 123 + + +R+ H I E I +EE++ V + I + LE++ G+ +GELT +SRD Sbjct: 61 EALKLVGEVRQFHLDLIGELIGNEELRAAVIEKIGVYLTRLERLTEGIEIVGELTERSRD 120 Query: 124 YILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSAR----VKRLEVKERLL 179 SFGE LS+ + + A+ + G L+ +ITD+ +G AR R E + Sbjct: 121 RFCSFGELLSTSVFAAALNEAGVPCEWLDVRTV-MITDDRYGFARPLAETCRKNTTEIIK 179 Query: 180 PLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTTD 239 PLL G + V G+IG+TE G TTLGRGGSD SAAL G L ++ IEIWTDV GV TTD Sbjct: 180 PLLDAGTVVVTQGYIGSTESGRTTTLGRGGSDLSAALFGAWLHSESIEIWTDVDGVMTTD 239 Query: 240 PRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLIT 299 PR+VP AR I +++ EA ELAY GAKVLHP TI PA+EK IP+ V NT+ P+S+GTLIT Sbjct: 240 PRMVPEARSIRVMTFSEAAELAYLGAKVLHPDTIAPAVEKNIPVFVLNTWHPDSKGTLIT 299 Query: 300 NDMEM-----SDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQ 354 ND E+ +VK+I+ K A++NI M G G + +F ++V +IS Sbjct: 300 NDPELLAGKSHGGLVKSIAVKKGQAILNIRSNRMFGRHGFMSELFDVFERFAISVEMIS- 358 Query: 355 GSSETNISLVVSEEDVDKA-LKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAG 413 +SE ++SL V + V + +KAL + + +V ++ V +SVVG Sbjct: 359 -TSEVSVSLTVDDGSVGETFIKAL---------------SSLGEVEIEHKVATVSVVGDN 402 Query: 414 MRGAKGIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKF 467 +R ++G+AG+IF ++ N++MI+QG+SE+N+ V+DE D+ V LH +F Sbjct: 403 LRMSRGVAGRIFNSL--RNVNLRMISQGASEINVGVVVDESDVAPAVAALHCEF 454 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: 523 Number of extensions: 23 Number of successful extensions: 8 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: 470 Length adjustment: 33 Effective length of query: 440 Effective length of database: 437 Effective search space: 192280 Effective search space used: 192280 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_041466196.1 CPAR_RS10150 (lysine-sensitive aspartokinase 3)
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.6914.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-122 394.7 1.4 3.6e-122 394.5 1.4 1.0 1 lcl|NCBI__GCF_000020505.1:WP_041466196.1 CPAR_RS10150 lysine-sensitive as Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020505.1:WP_041466196.1 CPAR_RS10150 lysine-sensitive aspartokinase 3 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 394.5 1.4 3.6e-122 3.6e-122 4 441 .. 2 455 .. 1 456 [. 0.95 Alignments for each domain: == domain 1 score: 394.5 bits; conditional E-value: 3.6e-122 TIGR00657 4 iVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee...kelieki 69 +V+KFGGtSvg++ +++v + ++k k ++VV+SA +g+T++L+++a+++ s++ +l+ ++ lcl|NCBI__GCF_000020505.1:WP_041466196.1 2 VVMKFGGTSVGTAAAMRQVIANIAEKK-KTSAPLVVLSACSGITNKLIQIADEAGSGRLkeaLKLVGEV 69 9******************99998888.5559*************************996666677899 PP TIGR00657 70 rekhlealeela.sqalkeklkallekeleevkk............ereldlilsvGEklSaallaaal 125 r+ hl+ + el+ +++l++ + + + l+ +++ er++d+ s+GE lS++++aaal lcl|NCBI__GCF_000020505.1:WP_041466196.1 70 RQFHLDLIGELIgNEELRAAVIEKIGVYLTRLERltegieivgeltERSRDRFCSFGELLSTSVFAAAL 138 **************999999999998888888888999******************************* PP TIGR00657 126 eelgvkavsllgaeagiltdsefgrAk....vleeikterleklleegiivvvaGFiGatekgeittLG 190 +e g ++l+ + +++td+++g A+ + ++ +te +++ll++g++vv++G+iG+te+g++ttLG lcl|NCBI__GCF_000020505.1:WP_041466196.1 139 NEAG-VPCEWLDVRTVMITDDRYGFARplaeTCRKNTTEIIKPLLDAGTVVVTQGYIGSTESGRTTTLG 206 ****.99********************99988899999******************************* PP TIGR00657 191 RGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlep 259 RGGSDl+Aal +a l+ + +ei+tDVdG++t+DPr+vpeAr + +++ Ea+ELa+lGakvLhp+t+ p lcl|NCBI__GCF_000020505.1:WP_041466196.1 207 RGGSDLSAALFGAWLHSESIEIWTDVDGVMTTDPRMVPEARSIRVMTFSEAAELAYLGAKVLHPDTIAP 275 ********************************************************************* PP TIGR00657 260 amrakipivvkstfnpeaeGTlivaksk....seeepavkalsldknqalvsvsgttmk..pgilaevf 322 a++++ip++v +t+ p+++GTli+++ + +++ vk+++++k qa+++++++ m g+++e+f lcl|NCBI__GCF_000020505.1:WP_041466196.1 276 AVEKNIPVFVLNTWHPDSKGTLITNDPEllagKSHGGLVKSIAVKKGQAILNIRSNRMFgrHGFMSELF 344 ********************************9999**********************999******** PP TIGR00657 323 galaeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmks 391 ++ ++v++i+ +se s+s++vd+ ++ ++ +k+++ l+eve+e+k+a+vs+vG++++ lcl|NCBI__GCF_000020505.1:WP_041466196.1 345 DVFERFAISVEMIS--TSEVSVSLTVDDGSVGETF------IKALSSLGEVEIEHKVATVSVVGDNLRM 405 **************..88889*****988765443......457899********************** PP TIGR00657 392 apgvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441 gva++if+ L++ +n +mis +sei++ vvvde+d+ av alh +++ lcl|NCBI__GCF_000020505.1:WP_041466196.1 406 SRGVAGRIFNSLRN--VNLRMISqgASEINVGVVVDESDVAPAVAALHCEFF 455 ************98..9******99***********************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (470 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: 8.89 // [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