Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_066329102.1 BLR17_RS14640 bifunctional aspartate kinase/homoserine dehydrogenase I
Query= reanno::Cola:Echvi_2000 (815 letters) >NCBI__GCF_900100165.1:WP_066329102.1 Length = 815 Score = 768 bits (1982), Expect = 0.0 Identities = 389/814 (47%), Positives = 570/814 (70%), Gaps = 2/814 (0%) Query: 1 MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60 M+++KFGG+S+AN +NI+ V I+ K++K+ +V SA VT+ L A+ A ++ES Sbjct: 1 MRVLKFGGTSVANAKNIKLVLDIVLNKAKKDKLIVVVSALSKVTDLLQLAASKAAANDES 60 Query: 61 YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120 Y I+ E+EK+HL+ +K+L+PV +QS+ L+ +K N L + G +L+ E S RT D + Sbjct: 61 YKEIVAEIEKKHLDALKELIPVSEQSSLLSHIKRIINHLETILDGCFLLGELSARTSDTI 120 Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSHD 180 LSFGE LS++I+A L+ +SY D+R+L+KT++ +G A VNF+ TN L F ++D Sbjct: 121 LSFGELLSSYIIAEALKQNLKNSSYKDSRELIKTNNNYGKAAVNFEVTNSLTTAFFANND 180 Query: 181 -DIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVY 239 + V+ GFI S+ TT+GR GSDYTA+I A AL A+++EIWTDV+G+ TA+P++V Sbjct: 181 AQVVVMPGFIASSLDEINTTLGRGGSDYTAAILAGALNADELEIWTDVNGMFTANPKIVK 240 Query: 240 TAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDS-G 298 A I +SY EAMELSHFGAKV++P T+QP ++++IPI+IKNTF+P+ GT IS S Sbjct: 241 QAQPIATISYQEAMELSHFGAKVLYPPTIQPVLRKNIPIHIKNTFEPEAEGTYISNVSVS 300 Query: 299 EGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICVA 358 G ++GIS +DNI+++ ++GPG++ V G S+R F L+N GIN+I I+QASSEHSIC+ Sbjct: 301 NGIPVRGISHIDNITLITLEGPGMIGVSGSSKRLFEVLSNEGINVIFITQASSEHSICIG 360 Query: 359 IASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALG 418 I + DA A++ I + F EI ++D + ++ +IA+VGENM+++ G SGRMF LG Sbjct: 361 ILNSDAEVAENAINKAFEIEIAQNKIDPCIVEQNLCIIALVGENMKNHQGLSGRMFSTLG 420 Query: 419 RNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGKAL 478 +NNVN+ AIAQG+SE NISAVI + D++KALN LHE FF + K L+LF++GVG +G+ Sbjct: 421 KNNVNIRAIAQGASERNISAVINERDVKKALNTLHENFFEENTKQLNLFVMGVGNVGEKF 480 Query: 479 TKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDKFIGT 538 + IHQQ K L+E +++++ ++NSR M F ED DL + EN E + + FI Sbjct: 481 IEQIHQQKKFLKENLKINVRVIALSNSRKMLFDEDAIDLNSWQAALENGETANKELFIEK 540 Query: 539 MTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAGQRG 598 + +N NS+FVD TA+ DVA IYE+ L VG+VT NK A + + YK LKKL+ Q Sbjct: 541 VAALNLRNSIFVDITANADVAAIYERFLKQSVGVVTCNKIACASAYDNYKNLKKLSRQYN 600 Query: 599 VRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSEVVAQA 658 F +ETNV AGLP+I+T+++L+ SGD VH+I+AVLSGS+N+IF+ ++ F +VV +A Sbjct: 601 APFLFETNVGAGLPIIDTVKNLIASGDKVHKIQAVLSGSLNFIFNNFDENNSFHDVVKEA 660 Query: 659 KEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPEFFK 718 +G+TEPDP+ DLSG+DVARKILIL RE+G + E++E S +P C + +FFK Sbjct: 661 GVQGFTEPDPKIDLSGIDVARKILILIRESGYKMEIENIENNSFLPAACMATTNNEDFFK 720 Query: 719 KLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDNMILFT 778 L +++ HF+ +L EA AK +L+F+A NGKA VGL + +HPF+ L+G DN++LF Sbjct: 721 SLIEYNSHFEGILAEAKAKDSRLKFVAEFINGKANVGLQFIPKDHPFYNLEGKDNIVLFY 780 Query: 779 TERYNDFPMIVRGPGAGADVTAAGVFADIIRLGN 812 T+RY D P++++G GAGA VTA+G+FAD+IR+GN Sbjct: 781 TDRYVDQPLLIKGAGAGAAVTASGIFADVIRIGN 814 Lambda K H 0.317 0.134 0.375 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: 1443 Number of extensions: 67 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: 815 Length of database: 815 Length adjustment: 41 Effective length of query: 774 Effective length of database: 774 Effective search space: 599076 Effective search space used: 599076 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 (21.7 bits) S2: 56 (26.2 bits)
Align candidate WP_066329102.1 BLR17_RS14640 (bifunctional aspartate kinase/homoserine dehydrogenase I)
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.2442477.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-128 413.9 7.1 4.7e-128 413.9 7.1 1.7 2 NCBI__GCF_900100165.1:WP_066329102.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066329102.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 413.9 7.1 4.7e-128 4.7e-128 5 442 .] 3 460 .. 1 460 [. 0.94 2 ? -1.6 0.2 0.056 0.056 314 361 .. 476 527 .. 462 563 .. 0.59 Alignments for each domain: == domain 1 score: 413.9 bits; conditional E-value: 4.7e-128 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhle 75 V+KFGGtSv+n+++ik v +iv+++++k+ + +VVvSA ++vTd L a+k+ ++e ke++++i++khl+ NCBI__GCF_900100165.1:WP_066329102.1 3 VLKFGGTSVANAKNIKLVLDIVLNKAKKD-KLIVVVSALSKVTDLLQLAASKAAANDEsyKEIVAEIEKKHLD 74 99************************777.****************999999999888899************ PP TIGR00657 76 aleelasqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgvkavsll 136 al+el++ + + l + +++ ++++++ r+ d+ils+GE lS+ ++a+al++ k+ s+ NCBI__GCF_900100165.1:WP_066329102.1 75 ALKELIPVSEQSSLLSHIKRIINHLETildgcfllgelsARTSDTILSFGELLSSYIIAEALKQNL-KNSSYK 146 ******989999999999999999888999********************************9998.****** PP TIGR00657 137 gaeagiltdsefgrAkvleeikterlek.lleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalk 206 ++++ i t++++g+A ++ + t+ l++ + ++ ++vv+ GFi+++ + ttLGRGGSD+tAa+lA al+ NCBI__GCF_900100165.1:WP_066329102.1 147 DSRELIKTNNNYGKAA-VNFEVTNSLTTaFFANNdaQVVVMPGFIASSLDEINTTLGRGGSDYTAAILAGALN 218 ****************.55555555555144444689************************************ PP TIGR00657 207 AdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeG 279 Ade+ei+tDV+G +ta P+iv++A+ +++isy+Ea+EL+++GakvL+p t++p+ r++ipi++k+tf+peaeG NCBI__GCF_900100165.1:WP_066329102.1 219 ADELEIWTDVNGMFTANPKIVKQAQPIATISYQEAMELSHFGAKVLYPPTIQPVLRKNIPIHIKNTFEPEAEG 291 ************************************************************************* PP TIGR00657 280 Tlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdk 350 T i + s+ ++ +v+++s+ +n +l++++g++m +g +++f+ l+++++nv+ i+q sse+si + + + NCBI__GCF_900100165.1:WP_066329102.1 292 TYISNVSV-SNGIPVRGISHIDNITLITLEGPGMIgvSGSSKRLFEVLSNEGINVIFITQASSEHSICIGILN 363 ******88.555***********************99*****************************9999999 PP TIGR00657 351 edadkakellk...kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..ssei 418 +da+ a+++ + + + +++++ + ve++l++++lvG++mk++ g+ +++f++L ++n+ni++i+ +se+ NCBI__GCF_900100165.1:WP_066329102.1 364 SDAEVAENAINkafEIEIAQNKIDPCIVEQNLCIIALVGENMKNHQGLSGRMFSTLGKNNVNIRAIAqgASER 436 999999999986666677889999999****************************************9***** PP TIGR00657 419 kisvvvdekdaekavealheklve 442 +is v++e+d++ka+++lhe+++e NCBI__GCF_900100165.1:WP_066329102.1 437 NISAVINERDVKKALNTLHENFFE 460 **********************85 PP == domain 2 score: -1.6 bits; conditional E-value: 0.056 TIGR00657 314 k.pgilaevfgalaeak....vnvdlilqsssetsisfvvdkedadkakellk 361 +++++++++ + k +nv +i++s+s+ + f d d+++ +++l+ NCBI__GCF_900100165.1:WP_066329102.1 476 VgEKFIEQIHQQKKFLKenlkINVRVIALSNSR-KMLFDEDAIDLNSWQAALE 527 336677777766554444455999999988874.3334334444555555544 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (815 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: 34.70 // [ok]
This GapMind analysis is from Jul 26 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