Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_055437364.1 ASC41_RS14495 bifunctional aspartate kinase/homoserine dehydrogenase I
Query= reanno::Cola:Echvi_2000 (815 letters) >NCBI__GCF_001418085.1:WP_055437364.1 Length = 814 Score = 722 bits (1863), Expect = 0.0 Identities = 370/814 (45%), Positives = 560/814 (68%), Gaps = 3/814 (0%) Query: 1 MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60 M+++KFGG+S+ + +NI KV +I+E S+K+ V SA GG+T++LL+ N+A+ + ++ Sbjct: 1 MQVLKFGGTSVGSSKNINKVITILEDYSKKDKVICVVSAVGGITDKLLKAGNLAKDNNKN 60 Query: 61 YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120 Y T + ++ +H++++++L+P Q + + + + +L +L GI+LI E S +T D + Sbjct: 61 YKTEYKSIKAKHIKVLEELIP-QNNAAIIKELDGKLKKLKNLLDGIFLINELSPQTSDRL 119 Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHF-KSH 179 +SFGE LS+FI+A L+++G+ + + L+ T+ + A+V F+TTN IQ++F ++ Sbjct: 120 VSFGELLSSFIIAETLKSRGVNAVRKNTQQLIVTNSNYTKAEVIFETTNNNIQEYFNEAT 179 Query: 180 DDIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVY 239 DI ++ GFI + G+TTT+GR GSDYTA+I AAAL E++EIWTDVSG+ T +P+LV Sbjct: 180 QDITLLPGFISKSYLGKTTTLGRGGSDYTAAIVAAALKTERLEIWTDVSGMYTTNPKLVK 239 Query: 240 TAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSG- 298 A+ I ++SY+EAMELSHFGAKV++P T+QP + +IPI+IKNT KP+E GT IS + Sbjct: 240 QAYPIERISYHEAMELSHFGAKVLYPPTVQPVLSLNIPIHIKNTLKPNEFGTIISNEGNT 299 Query: 299 EGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICVA 358 + GI+++++I++L +QG G+V + G S+R F TL+ INIILI+QASSEHSIC Sbjct: 300 KSSTATGITNINDIALLTLQGNGMVGIPGFSKRLFETLSQEKINIILITQASSEHSICFG 359 Query: 359 IASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALG 418 I+ DA +A++ I F +EI +D I + ++++IA+VG+NM+ + G SG+MF ALG Sbjct: 360 ISKDDAIQAETAINLAFEHEISKHRIDPITVEQNLSIIALVGDNMKSHQGISGKMFSALG 419 Query: 419 RNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGKAL 478 +NN+N+ AIAQG+SE NISAVI + D++KALN +HE FF ++ K L++F+ G+G +G+ L Sbjct: 420 KNNINIRAIAQGASERNISAVIAEKDVEKALNTIHERFFGNNIKQLNVFITGIGNVGEKL 479 Query: 479 TKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDKFIGT 538 IHQQ L++ LD++I GMANS+ M F+ +G DL + + +D F+ Sbjct: 480 IDQIHQQSNYLKKNLKLDVRIVGMANSKKMIFNAEGIDLNDWASKFHHADKSTLDGFLEK 539 Query: 539 MTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAGQRG 598 +N NS+FVD TA+ V+ +YE L S + +V NK A S YK L+ LA + Sbjct: 540 AKALNLRNSIFVDITANDAVSKMYEHYLRSSIAVVACNKIACSSTYSNYKLLQDLALKYN 599 Query: 599 VRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSEVVAQA 658 FFYETNV AGLP+INTL +L+ SGD V I+AVLSGS+N++F+ F + V +A Sbjct: 600 TPFFYETNVGAGLPIINTLNNLVSSGDKVTSIQAVLSGSLNFVFNNFSDKTNFHDTVKRA 659 Query: 659 KEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPEFFK 718 + +GYTEPDPR DLSG+DVARKILIL RE G + E +E S + + ++ +V +F+K Sbjct: 660 QFEGYTEPDPRIDLSGIDVARKILILARENGGAMEIESIENDSFLTKANLESDTVDDFYK 719 Query: 719 KLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDNMILFT 778 L+ + HFQ+L A AK +L+++A +NGKAKVGL + HPF+ L+G DN+++F Sbjct: 720 TLKTEEAHFQKLYASAKAKNCQLKYVAEFKNGKAKVGLKEIPEGHPFYNLEGKDNIVMFY 779 Query: 779 TERYNDFPMIVRGPGAGADVTAAGVFADIIRLGN 812 TERY + P+IV+G GAGADVTA+G+FADII+ G+ Sbjct: 780 TERYPEQPLIVKGAGAGADVTASGLFADIIKAGS 813 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: 1557 Number of extensions: 76 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: 815 Length of database: 814 Length adjustment: 41 Effective length of query: 774 Effective length of database: 773 Effective search space: 598302 Effective search space used: 598302 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_055437364.1 ASC41_RS14495 (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.1078584.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-126 409.1 6.3 1.7e-126 408.8 6.3 1.1 1 NCBI__GCF_001418085.1:WP_055437364.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001418085.1:WP_055437364.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 408.8 6.3 1.7e-126 1.7e-126 5 441 .. 3 458 .. 1 459 [. 0.95 Alignments for each domain: == domain 1 score: 408.8 bits; conditional E-value: 1.7e-126 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhle 75 V+KFGGtSvg+ ++i+kv i++ ++k+ +v+ VvSA++g+Td+L++ + ++++++ k++ + i++kh++ NCBI__GCF_001418085.1:WP_055437364.1 3 VLKFGGTSVGSSKNINKVITILEDYSKKD-KVICVVSAVGGITDKLLKAGNLAKDNNKnyKTEYKSIKAKHIK 74 99*****************9998888666.***************************9999999********* PP TIGR00657 76 aleelasqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgvkavsll 136 leel++q+ ++ + + l+ +l+++k+ +++ d+++s+GE lS+ ++a++l+++gv+av NCBI__GCF_001418085.1:WP_055437364.1 75 VLEELIPQNNAA-IIKELDGKLKKLKNlldgiflinelsPQTSDRLVSFGELLSSFIIAETLKSRGVNAVR-K 145 ******865555.555556666666667999***********************************76665.6 PP TIGR00657 137 gaeagiltdsefgrAkvleeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207 + ++ i+t+s++++A+v+ e+++++++++ +e i ++ GFi + g++ttLGRGGSD+tAa++Aaalk NCBI__GCF_001418085.1:WP_055437364.1 146 NTQQLIVTNSNYTKAEVIFETTNNNIQEYFNEAtqDITLLPGFISKSYLGKTTTLGRGGSDYTAAIVAAALKT 218 88999************************9999889************************************* PP TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGT 280 +++ei+tDV+G yt+ P++v++A ++ isy+Ea+EL+++GakvL+p t++p+ ++ipi++k+t p++ GT NCBI__GCF_001418085.1:WP_055437364.1 219 ERLEIWTDVSGMYTTNPKLVKQAYPIERISYHEAMELSHFGAKVLYPPTVQPVLSLNIPIHIKNTLKPNEFGT 291 ************************************************************************* PP TIGR00657 281 livakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdke 351 +i ++ + ++++ +++++ ++ al++++g++m pg+ +++f++l+++k+n++li+q sse+si f ++k+ NCBI__GCF_001418085.1:WP_055437364.1 292 IISNEGN-TKSSTATGITNINDIALLTLQGNGMVgiPGFSKRLFETLSQEKINIILITQASSEHSICFGISKD 363 *****98.5559************************************************************* PP TIGR00657 352 dadkakellk...kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseik 419 da +a+++ + +++ +++ + +++ve++l++++lvG++mks+ g+ +k+f+aL ++nini++i+ +se++ NCBI__GCF_001418085.1:WP_055437364.1 364 DAIQAETAINlafEHEISKHRIDPITVEQNLSIIALVGDNMKSHQGISGKMFSALGKNNINIRAIAqgASERN 436 *999999988888889999***********************************************9****** PP TIGR00657 420 isvvvdekdaekavealheklv 441 is v+ ekd+eka++++he+++ NCBI__GCF_001418085.1:WP_055437364.1 437 ISAVIAEKDVEKALNTIHERFF 458 *******************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (814 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 48.42 // [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