Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_010528243.1 GQW_RS0112430 bifunctional aspartate kinase/homoserine dehydrogenase I
Query= reanno::Btheta:351931 (811 letters) >NCBI__GCF_000220155.1:WP_010528243.1 Length = 811 Score = 825 bits (2132), Expect = 0.0 Identities = 438/813 (53%), Positives = 572/813 (70%), Gaps = 4/813 (0%) Query: 1 MKVMKFGGTSVGSVNSILSVKRIVESAGEPVIVVVSALGGITDKLINTSKMAAAGDSAYE 60 MKV+KFGGTSVG+ +I VK IVE ++VVVSA GGITD+LI + AA G+ Y Sbjct: 1 MKVLKFGGTSVGTAENIKKVKEIVEGQKGQIVVVVSAFGGITDRLIRAAHKAAEGNPVYA 60 Query: 61 GEFREIVYRHVEMIKEVIPAGAGQVALQRQIGELLNELKDIFQGIYLIRDLSPKTSDTIV 120 + I+ H+++I + P A A++ + + +ELK I +G++LIR+LS K+ +I Sbjct: 61 TDIDNIIDDHLQIIDTLFPDIAANTAIRNGVEPIFDELKSINKGVFLIRELSEKSLASIS 120 Query: 121 SYGERLSSIIVAELIDEAKWFDSRTFIKTEKKHNKHTIDADLTNQLVKEAFHSIPKVSLV 180 GERLSS I+A + A+WFDSR +IKT ++ + D T + ++E + +SL Sbjct: 121 GIGERLSSKIIAAYLG-ARWFDSRLYIKTFVEYGRVHADLVYTYKHLREIQPQLADLSLF 179 Query: 181 PGFISSDKVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTDVDGFMTADPRVISTAYTI 240 PGFISS+ G+ T LGRGGSDYTA+I+A+A DA LEIWTDVDGFMTADP+VIS AY I Sbjct: 180 PGFISSN-ARGENTTLGRGGSDYTASILASAFDAEMLEIWTDVDGFMTADPKVISRAYCI 238 Query: 241 SELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQETSNPQSKA 300 LSY EA EL +FGAKV+YPPTI PV KNIPI IKNTFNP GT+I + Sbjct: 239 EHLSYAEAMELSHFGAKVIYPPTILPVYQKNIPITIKNTFNPSAPGTLINGRQETAGQRQ 298 Query: 301 IKGISSINDTSLITVQGLGMVGVIGVNYRIFKALAKNGISVFLVSQASSENSTSIGVRNA 360 IKGISSI SL+T+QG+GMVGV G++ R+F +LA I+V L+SQASSENS SI + ++ Sbjct: 299 IKGISSIKSVSLLTIQGIGMVGVSGISMRLFASLAAKNINVILISQASSENSISIVIDSS 358 Query: 361 DADLACEVLNEEFAKEIEMGEISPILAERNLATVAIVGENMKHTPGIAGKLFGTLGRNGI 420 +LA + +EF +E+ IS I+ + +A VAIVGENMKHT GIAG LF ++G+NG+ Sbjct: 359 QTELAKMAIEQEFKRELSERHISNIIIDNEMAVVAIVGENMKHTTGIAGLLFNSVGKNGV 418 Query: 421 NVIACAQGASETNISFVVDSKSLRKSLNVIHDSFFLSEYQVLNLFICGIGTVGGSLVEQI 480 NV A AQGASE NISFV+ K ++K+LNVIH++FFLS+Y LNLF+ G GTVG L+ +I Sbjct: 419 NVYAIAQGASELNISFVIKEKDIKKALNVIHEAFFLSDYSRLNLFLVGKGTVGSRLIHKI 478 Query: 481 RCQQQKLMMENGLKLHVVGIIDAAKAMFSREGFDLANFREELQKKGKDSNLQTIRDEIVG 540 Q+ KL+ N LK+ +VG+ +F +EG D E+L+K+G ++ RD+I+ Sbjct: 479 ATQRDKLIKNNSLKIRLVGLAGRNSMIFDKEGLDPNTAIEKLEKEGTPGDVSQFRDKIIE 538 Query: 541 MNIFNSVFVDCTASPDIASLYKDLLQHNVSVVAANKIAASSAYENYRELKTIARQRGVKY 600 MN+ NSVFVDC+AS ++ASLY LL+ NVSVV ANKIA+SS+YE YR+LK AR++GVK+ Sbjct: 539 MNMANSVFVDCSASDEVASLYLSLLEANVSVVTANKIASSSSYETYRKLKETARKKGVKF 598 Query: 601 LFETNVGAGLPIINTINDLIHSGDKILKIEAVLSGTLNYIFNKISADIPFSRTIKMAQEE 660 +ETNVGAGLPII INDL+ SG+KILK+EAVLSGTLNYI N +S P S+ I A+E+ Sbjct: 599 FYETNVGAGLPIIAPINDLVRSGEKILKMEAVLSGTLNYIVNSVSEKKPLSQVIIEAKEK 658 Query: 661 RYSEPDPRIDLSGKDVIRKLVILAREAGYHIEQEDVEKNLFVPNDFFE-GSLDDFWKRVP 719 YSEPDPRIDLSG DV+RK +ILAREAGY +E VE FVP + + SLD F +++ Sbjct: 659 GYSEPDPRIDLSGTDVVRKALILAREAGYPLESSGVEVEPFVPQQYLDLPSLDLFLEKIA 718 Query: 720 SLDADFEARRQVLEKEHKHWRFVAKL-EDGKASVGLQEVGANHPFYGLEGSNNIILLTTE 778 LD FE RRQ E+K R+ A + +GKA VGL EV HPF+ LEGSNNI+L+ +E Sbjct: 719 ELDITFEKRRQKALAENKKLRYAAHMTANGKAKVGLIEVDHKHPFFDLEGSNNIVLIWSE 778 Query: 779 RYKEYPMMIQGYGAGAGVTAAGVFADIMSIANV 811 Y E+PM I+GYGAGA VTAAGV ADI+ +ANV Sbjct: 779 HYFEHPMQIKGYGAGADVTAAGVLADIIKVANV 811 Lambda K H 0.317 0.135 0.377 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: 1454 Number of extensions: 59 Number of successful extensions: 7 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: 811 Length of database: 811 Length adjustment: 41 Effective length of query: 770 Effective length of database: 770 Effective search space: 592900 Effective search space used: 592900 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_010528243.1 GQW_RS0112430 (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.1532308.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-116 375.0 3.2 3e-116 375.0 3.2 1.6 2 NCBI__GCF_000220155.1:WP_010528243.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000220155.1:WP_010528243.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 375.0 3.2 3e-116 3e-116 5 441 .. 3 453 .. 1 454 [. 0.94 2 ? -1.8 0.0 0.064 0.064 33 148 .. 542 575 .. 524 607 .. 0.55 Alignments for each domain: == domain 1 score: 375.0 bits; conditional E-value: 3e-116 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhle 75 V+KFGGtSvg++e+ikkv +iv+ +k g q vVVvSA +g+Td+L+ a+k+ +++ ++ i++i ++hl+ NCBI__GCF_000220155.1:WP_010528243.1 3 VLKFGGTSVGTAENIKKVKEIVEGQK--G-QIVVVVSAFGGITDRLIRAAHKAAEGNPvyATDIDNIIDDHLQ 72 89*********************999..5.99*********************999988999*********** PP TIGR00657 76 aleela.sqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgvkavsl 135 ++++l a ++ +++ +e ++e+k+ e++l+ i +GE+lS++++aa+l ++ NCBI__GCF_000220155.1:WP_010528243.1 73 IIDTLFpDIAANTAIRNGVEPIFDELKSinkgvflirelsEKSLASISGIGERLSSKIIAAYLGARW------ 139 *****96667777888899999999999999*******************************97765...... PP TIGR00657 136 lgaeagiltdsefgrAkvleeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalk 206 ++++ i t e+gr + + t +++ ++ + + ++ GFi ++ ge ttLGRGGSD+tA++lA+a + NCBI__GCF_000220155.1:WP_010528243.1 140 FDSRLYIKTFVEYGRVH-ADLVYTYKHLREIQPQlaDLSLFPGFISSNARGENTTLGRGGSDYTASILASAFD 211 9**************99.55555555544444444589*********************************** PP TIGR00657 207 AdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeG 279 A+ +ei+tDVdG +taDP++++ A ++++sy+Ea+EL+++Gakv++p t+ p+ +++ipi +k+tfnp+a+G NCBI__GCF_000220155.1:WP_010528243.1 212 AEMLEIWTDVDGFMTADPKVISRAYCIEHLSYAEAMELSHFGAKVIYPPTILPVYQKNIPITIKNTFNPSAPG 284 ************************************************************************* PP TIGR00657 280 Tlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdk 350 Tli + ++ + ++k++s+ k+ +l++++g +m +gi ++f la +++nv+li+q sse+sis+v+d NCBI__GCF_000220155.1:WP_010528243.1 285 TLINGRQETAGQRQIKGISSIKSVSLLTIQGIGMVgvSGISMRLFASLAAKNINVILISQASSENSISIVIDS 357 ********9999************************************************************* PP TIGR00657 351 edadkakellk...kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..ssei 418 ++++ ak + + k +++e+ ++++ +++++a+v++vG++mk++ g+a+ +f+ + ++++n+ +i+ +se NCBI__GCF_000220155.1:WP_010528243.1 358 SQTELAKMAIEqefKRELSERHISNIIIDNEMAVVAIVGENMKHTTGIAGLLFNSVGKNGVNVYAIAqgASEL 430 **999999988777788999***********************************************9***** PP TIGR00657 419 kisvvvdekdaekavealheklv 441 +is+v++ekd +ka++++he+++ NCBI__GCF_000220155.1:WP_010528243.1 431 NISFVIKEKDIKKALNVIHEAFF 453 *********************98 PP == domain 2 score: -1.8 bits; conditional E-value: 0.064 TIGR00657 33 gnqvvVVvSAmagvTdaLvelaekvsseeekeliekirekhlealeelasqalkeklkallekeleevkkere 105 n+v+V +SA +v ++l e s + NCBI__GCF_000220155.1:WP_010528243.1 542 ANSVFVDCSASDEVASLYLSLLEANVSVVT------------------------------------------- 571 347777777777777777766666555553........................................... PP TIGR00657 106 ldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsef 148 +++ NCBI__GCF_000220155.1:WP_010528243.1 572 ---------------------------------------ANKI 575 .......................................2222 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (811 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: 22.54 // [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