Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate BWI76_RS04245 BWI76_RS04245 bifunctional aspartate kinase/homoserine dehydrogenase I
Query= BRENDA::P00561 (820 letters) >FitnessBrowser__Koxy:BWI76_RS04245 Length = 820 Score = 1495 bits (3871), Expect = 0.0 Identities = 756/820 (92%), Positives = 794/820 (96%) Query: 1 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTI GQDA Sbjct: 1 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTIGGQDA 60 Query: 61 LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120 L NI+DAERIFAELL GLA AQPGFPLAQLK FV+QEFAQIKHVLHGISLLGQCPDS+NA Sbjct: 61 LTNIADAERIFAELLQGLADAQPGFPLAQLKAFVEQEFAQIKHVLHGISLLGQCPDSVNA 120 Query: 121 ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP 180 +LICRGEK+SIAIMAG+LEARGHNVTVI+PVEKLLAVGHYLESTVDIAESTRRIAAS+IP Sbjct: 121 SLICRGEKLSIAIMAGLLEARGHNVTVINPVEKLLAVGHYLESTVDIAESTRRIAASQIP 180 Query: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV Sbjct: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240 Query: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300 PDARLLKSMSYQEAMELSYFGAKVLHPRTI PIAQFQIPCLIKNTGNPQAPGTLIGASRD Sbjct: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTIAPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300 Query: 301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360 ED+LPVKGISNLNNMAMF+VSGPGMKGMVGMAARVFA MSRA ISVVLITQSSSEYSISF Sbjct: 301 EDDLPVKGISNLNNMAMFNVSGPGMKGMVGMAARVFATMSRAGISVVLITQSSSEYSISF 360 Query: 361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420 CVPQSDC RA+R M++EFYLELKEGLLEPL++ ERLAIISVVGDGMRTLRGISAKFFAAL Sbjct: 361 CVPQSDCARAKRVMEDEFYLELKEGLLEPLSIMERLAIISVVGDGMRTLRGISAKFFAAL 420 Query: 421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL 480 ARANINIVAIAQGSSERSISVVV+NDDATTGVRVTHQMLFNTDQVIEVFVIG+GGVGGAL Sbjct: 421 ARANINIVAIAQGSSERSISVVVSNDDATTGVRVTHQMLFNTDQVIEVFVIGIGGVGGAL 480 Query: 481 LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL 540 +EQ+KRQQSWLK+KHIDLRVCGVANS+ALLTNVHGLNLE+W++ELA+AKE FNLGRLIRL Sbjct: 481 IEQIKRQQSWLKSKHIDLRVCGVANSRALLTNVHGLNLEHWRDELAEAKEAFNLGRLIRL 540 Query: 541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR 600 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSS+DYYHQLR+AA SR Sbjct: 541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSLDYYHQLRHAASSSR 600 Query: 601 RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA 660 RKFLYDTNVGAGLPVIENLQNLLNAGDEL++FSGILSGSLS+IFGKLDEG+SFSEAT LA Sbjct: 601 RKFLYDTNVGAGLPVIENLQNLLNAGDELLRFSGILSGSLSFIFGKLDEGVSFSEATRLA 660 Query: 661 REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 720 REMGYTEPDPRDDLSG+DVARKLLILARETGRELEL+DI +EP LPA F+A GDV +FMA Sbjct: 661 REMGYTEPDPRDDLSGVDVARKLLILARETGRELELSDIIVEPALPAGFDASGDVDSFMA 720 Query: 721 NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF 780 L LDD FA+RVAKARDEGKVLRYVGNI+EDG CRVKIA VDGNDPLFKVKNGENALAF Sbjct: 721 RLPSLDDEFASRVAKARDEGKVLRYVGNIEEDGTCRVKIAAVDGNDPLFKVKNGENALAF 780 Query: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV Sbjct: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820 Lambda K H 0.319 0.135 0.384 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: 1881 Number of extensions: 50 Number of successful extensions: 4 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: 820 Length of database: 820 Length adjustment: 42 Effective length of query: 778 Effective length of database: 778 Effective search space: 605284 Effective search space used: 605284 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: 56 (26.2 bits)
Align candidate BWI76_RS04245 BWI76_RS04245 (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.22504.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-155 502.1 0.1 9.8e-155 501.8 0.1 1.1 1 lcl|FitnessBrowser__Koxy:BWI76_RS04245 BWI76_RS04245 bifunctional aspar Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS04245 BWI76_RS04245 bifunctional aspartate kinase/homoserine dehydrogenase I # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 501.8 0.1 9.8e-155 9.8e-155 5 441 .. 3 460 .. 1 461 [. 0.97 Alignments for each domain: == domain 1 score: 501.8 bits; conditional E-value: 9.8e-155 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee....keliekire 71 V+KFGGtSv+n+er+ +va+i+++++++g qv++V+SA+a++T++Lv+++ek+ +++ + +e+i++ lcl|FitnessBrowser__Koxy:BWI76_RS04245 3 VLKFGGTSVANAERFLRVADILESNARQG-QVATVLSAPAKITNHLVAMIEKTIGGQDaltnIADAERIFA 72 99************************999.***************************999988899***** PP TIGR00657 72 khlealeelasqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgv 130 + l++l+ +++ + ++lka++e+e++++k+ ++ ++ ++++GEklS+a++a++le++g lcl|FitnessBrowser__Koxy:BWI76_RS04245 73 ELLQGLADAQPGFPLAQLKAFVEQEFAQIKHvlhgisllgqcpDSVNASLICRGEKLSIAIMAGLLEARG- 142 **********************************************************************. PP TIGR00657 131 kavsllgaeagiltdsefgrAkvleeikterleklleeg.iivvvaGFiGatekgeittLGRGGSDltAal 200 ++v+++++++++l+ +++++++v + ++t+r+++ ++v++aGF++ +ekge+++LGR+GSD++Aa+ lcl|FitnessBrowser__Koxy:BWI76_RS04245 143 HNVTVINPVEKLLAVGHYLESTVDIAESTRRIAASQIPAdHMVLMAGFTAGNEKGELVVLGRNGSDYSAAV 213 **********************888888888877666555******************************* PP TIGR00657 201 lAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvks 271 lAa+l+Ad++ei+tDVdG+yt+DPr+vp+Ar+l+++sy+Ea+EL+++GakvLhprt+ p+++++ip+++k+ lcl|FitnessBrowser__Koxy:BWI76_RS04245 214 LAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTIAPIAQFQIPCLIKN 284 *********************************************************************** PP TIGR00657 272 tfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsss 340 t+np+a+GTli+a+++ e++ +vk++s+ +n+a+++vsg++mk +g++a+vf ++++a+++v+li+qsss lcl|FitnessBrowser__Koxy:BWI76_RS04245 285 TGNPQAPGTLIGASRD-EDDLPVKGISNLNNMAMFNVSGPGMKgmVGMAARVFATMSRAGISVVLITQSSS 354 **************99.666*************************************************** PP TIGR00657 341 etsisfvvdkedadkakellk...kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeni 408 e+sisf+v+++d+ +ak++++ +++e le++++ ++la++s+vG+gm++ g+ ak+f+aLa++ni lcl|FitnessBrowser__Koxy:BWI76_RS04245 355 EYSISFCVPQSDCARAKRVMEdefYLELKEGLLEPLSIMERLAIISVVGDGMRTLRGISAKFFAALARANI 425 ********************9877668999***************************************** PP TIGR00657 409 niemis..sseikisvvvdekdaekavealheklv 441 ni++i+ sse++isvvv+++da++ v+++h++l+ lcl|FitnessBrowser__Koxy:BWI76_RS04245 426 NIVAIAqgSSERSISVVVSNDDATTGVRVTHQMLF 460 ********************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (820 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: 00:00:00.03 # Mc/sec: 11.79 // [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