Align fused aspartate kinase/homoserine dehydrogenase 2 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 203139 SO4055 aspartokinase II/homoserine dehydrogenase, methionine-sensitive (NCBI ptt file)
Query= ecocyc::ASPKINIIHOMOSERDEHYDROGII-MONOMER (810 letters) >FitnessBrowser__MR1:203139 Length = 797 Score = 571 bits (1472), Expect = e-167 Identities = 342/802 (42%), Positives = 480/802 (59%), Gaps = 22/802 (2%) Query: 14 LHKFGGSSLADVKCYLRVAGIMAEYSQPDDMMVVSAAGSTTNQLINWLKLSQTDRLSAHQ 73 LHKFGGSSLAD CY RVA I+ + DD++VVSAAG TTN L L L +++L + Sbjct: 6 LHKFGGSSLADADCYRRVAHILLTHGHSDDLVVVSAAGKTTNFLYKLLSLRDSNQLWQEE 65 Query: 74 VQQTLRRYQCDLISGLLPAEEADSLISAFVSDLERLAALLDSGI-NDAVYAEVVGHGEVW 132 +Q L YQ LI LL E+A L +D +L +LL + ND + VV GE W Sbjct: 66 LQ-VLISYQQGLIEQLLSNEQARDLRERLTTDKAQLISLLSLDVRNDYQISHVVSFGERW 124 Query: 133 SARLMSAVLNQQGLPAAWLDAREFLRAERAAQPQVDEGLSYPLLQQLLVQHPGKRLVVTG 192 SARLM+A+L + G+ A+ +DA L A+ AA PQ+ S +Q LL HP +RLV+TG Sbjct: 125 SARLMAALLRESGVAASHVDACSILVADEAAVPQIRVQESRAKVQALLAAHPNERLVITG 184 Query: 193 FISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADPRKVKDACLLPLL 252 FI N G+T+LLGRNGSD+SA+ I +LA + RVTIW+DV GV++ADP K+ DA LL + Sbjct: 185 FICANERGDTLLLGRNGSDFSASLIASLADIERVTIWTDVEGVFNADPNKINDAKLLKSM 244 Query: 253 RLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIERVLASGTGARIVT 312 L EA LARL +PVLH+RTLQP+ +E+ L +R SY T I +S A +VT Sbjct: 245 SLAEADRLARLGSPVLHSRTLQPLFNTEVSLAVRSSYASHTDFTLIAPH-SSSASAPVVT 303 Query: 313 SHDDVCLIEFQVPASQDFKLAHKEIDQILKRAQVRPLAVGVHNDRQLLQFCYTSEVADSA 372 + + V L F++ +DQ+++ A + PLA V + Q L+ YT+E Sbjct: 304 NLNAVVLFGFKIAGD-----VASLLDQLVE-AGLTPLAHWV-SAHQRLELAYTAENQKQV 356 Query: 373 LKILD---EAGLPGELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQPVEFTWQSDDG 429 K+LD EA +L++ L LVA+V A H R + +L + + + D Sbjct: 357 QKLLDAQAEALGIRDLQINTELGLVALVSADAE----HYRRSFARLLSRDAKPLFSGD-- 410 Query: 430 ISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFGKGNIGSRWLELFAREQSTLSARTG 489 +SLV ++ L Q +H+ KRIG++L G GNIG W++LF +L+ Sbjct: 411 LSLVTLVPQSQVNLLTQKVHRRCAGPRKRIGVLLLGVGNIGEAWVKLFKSVSPSLNQELE 470 Query: 490 FEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPYDDLVVLDVT 549 + L G+V S ++L+ G+D F++EA E LF + D+L+ LD++ Sbjct: 471 AQVELVGLVTSSKALIKSKGVDLQSWQQEFDNEATPWQYEHLFEQLEQLNCDELIALDIS 530 Query: 550 ASQQLADQYLDFASHGFHVISANKLAGASDSNKYRQIHDAFEKTGRHWLYNATVGAGLPI 609 AS L QY +F G H++SANKLAG+ YR++ + W YNA+ GAGLPI Sbjct: 531 ASASLTLQYPEFFERGIHMVSANKLAGSGPLPFYRELKEQLGYRRLFWRYNASCGAGLPI 590 Query: 610 NHTVRDLIDSGDTILSISGIFSGTLSWLFLQFDGSVPFTELVDQAWQQGLTEPDPRDDLS 669 H + DL +SGD++ ++ GIFSGTL WLF ++D S PF+ELV +A G+TEPDPRDDLS Sbjct: 591 QHALNDLRNSGDSVEAVGGIFSGTLCWLFEKYDTSKPFSELVIEARGLGITEPDPRDDLS 650 Query: 670 GKDVMRKLVILAREAGYNIEPDQVRVESLVPAHCEGGSIDHFFENGDELNEQMVQRLEAA 729 G+D+ RKL+ILARE G IE + + + SLVPAH ++ F EL+++++Q+ AA Sbjct: 651 GRDMQRKLLILAREIGLEIELEDIELRSLVPAHLADIPLEQFLARIGELDDELLQQYGAA 710 Query: 730 REMGLVLRYVARFDANG---KARVGVEAVREDHPLASLLPCDNVFAIESRWYRDNPLVIR 786 E VLRYVA D +G KA VG++ + HP A+L P DNVF I S +Y+ NPL+IR Sbjct: 711 AEQNKVLRYVASLDNSGAVLKAEVGLQWIDASHPYANLTPGDNVFVIRSAFYQGNPLIIR 770 Query: 787 GPGAGRDVTAGAIQSDINRLAQ 808 GPGAGR+VTA A+QSD+ ++ + Sbjct: 771 GPGAGREVTAAAVQSDLTQICR 792 Lambda K H 0.320 0.135 0.397 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: 1491 Number of extensions: 60 Number of successful extensions: 6 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: 810 Length of database: 797 Length adjustment: 41 Effective length of query: 769 Effective length of database: 756 Effective search space: 581364 Effective search space used: 581364 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: 55 (25.8 bits)
Align candidate 203139 SO4055 (aspartokinase II/homoserine dehydrogenase, methionine-sensitive (NCBI ptt file))
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.2539515.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-67 213.9 0.0 3.7e-67 213.2 0.0 1.2 1 FitnessBrowser__MR1:203139 Domain annotation for each sequence (and alignments): >> FitnessBrowser__MR1:203139 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 213.2 0.0 3.7e-67 3.7e-67 6 438 .. 7 431 .. 4 434 .. 0.83 Alignments for each domain: == domain 1 score: 213.2 bits; conditional E-value: 3.7e-67 TIGR00657 6 qKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekirekhlealeela.sqalk 86 KFGG+S+++++ ++va+i++ + ++ + +VVvSA +++T+ L +l + +s++ +e+++++ + + +e+l +++ + FitnessBrowser__MR1:203139 7 HKFGGSSLADADCYRRVAHILLTHGHS--DDLVVVSAAGKTTNFLYKLLSLRDSNQLwQEELQVLISYQQGLIEQLLsNEQAR 87 6*******************9999855..589************************997777777777766777766444444 PP TIGR00657 87 eklkallekeleevkk.......ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterl 162 ++l+ + +++ + + ++s+GE+ Sa+l+aa+l+e g a+s ++a + +++d++ ++++++++ FitnessBrowser__MR1:203139 88 DLRERLTTDKAQLISLlsldvrnDYQISHVVSFGERWSARLMAALLRESG-VAASHVDACSILVADEAAVPQI-RVQESRAKV 168 4444444444444433777887799999**********************.7788888888888877655544.788888888 PP TIGR00657 163 eklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalE 243 ++ll + v++GFi a+e g++ +LGR+GSD++A+l+A++ + ++v i+tDV+G++ aDP+++++A++l+++s +Ea FitnessBrowser__MR1:203139 169 QALLAAHpnERLVITGFICANERGDTLLLGRNGSDFSASLIASLADIERVTIWTDVEGVFNADPNKINDAKLLKSMSLAEADR 251 888888776899*********************************************************************** PP TIGR00657 244 LaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmkpgilaevfgala 326 La+lG+ vLh rtl+p+ + ++ + v+s++ +++ Tli ++s+s ++p v+ + + +l+ +++ g +a ++ +l FitnessBrowser__MR1:203139 252 LARLGSPVLHSRTLQPLFNTEVSLAVRSSYASHTDFTLIAPHSSSASAPVVT---NLNAVVLFGFKIA----GDVASLLDQLV 327 ******************************************8866655554...4444455544444....55688888888 PP TIGR00657 327 eakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeenin 409 ea+ + s+ ++ ++++ e+ ++ ++ll ++ e+ +++++++++l lv+lv+a+ +++ a++++ a+ FitnessBrowser__MR1:203139 328 EAGLTPLAHWVSA-HQRLELAYTAENQKQVQKLL-DAQAEALGIRDLQINTELGLVALVSADAEHYRRSFARLLSRDAK---- 404 9998887777444.4679**************98.5678888999*******************988877777766555.... PP TIGR00657 410 iemissseikisvvvdekdaekavealhe 438 + s + +++++v++++++ +++++h+ FitnessBrowser__MR1:203139 405 --PLFSGDLSLVTLVPQSQVNLLTQKVHR 431 ..344577888888888888888888886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (797 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: 24.00 // [ok]
This GapMind analysis is from Jul 25 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