Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_012473759.1 CPHAMN1_RS01510 bifunctional aspartate kinase/homoserine dehydrogenase I
Query= reanno::Cola:Echvi_2000 (815 letters) >NCBI__GCF_000020545.1:WP_012473759.1 Length = 819 Score = 675 bits (1742), Expect = 0.0 Identities = 354/819 (43%), Positives = 515/819 (62%), Gaps = 8/819 (0%) Query: 1 MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60 MK++KFGG+SI N E I+ V II + +V SA VT+ LL+ A A + Sbjct: 1 MKVLKFGGTSIENSERIRNVLGIIRGAIKDSPVIIVVSAIRKVTDLLLEAAVAAGSGDAG 60 Query: 61 YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120 Y L +E H ++V+ L+ + +++ + ELGD+ +G+ L+++ S+R+ + Sbjct: 61 YREKLVTIENIHGDLVRDLIDLSRRNEVQEVLTDELQELGDILYGVSLLRDLSDRSKALI 120 Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSHD 180 LSFGER S I++ +G+ SY DAR L+ TD A+V+ +++LI FK Sbjct: 121 LSFGERFSARIISTFFCQEGLDASYTDARKLIVTDTNHCDARVDMSASSELISAWFKEER 180 Query: 181 DIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVYT 240 + V+TG+IG+ G TT+GR GSDYTA+I + GA++++IWTDV G +ADP+ V Sbjct: 181 GVPVVTGYIGAAPDGTATTLGRGGSDYTATILGSVAGADEIQIWTDVDGFFSADPKRVKD 240 Query: 241 AFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRIS----KD 296 A+ +P +SY EAMELSH GAKV+ P ++ PAMK+ IPI I+N++ PD GTRIS D Sbjct: 241 AYVLPFISYGEAMELSHSGAKVLHPYSVHPAMKKGIPITIRNSYNPDVEGTRISAPEGND 300 Query: 297 SGEGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSIC 356 +G GK + G+SS++++ +LN G G+V V G++ R F LA + INII ISQASSE SI Sbjct: 301 TGSGKPVTGLSSINDVVLLNFSGSGMVGVPGIASRLFSCLARHKINIIFISQASSEQSIS 360 Query: 357 VAIASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQA 416 +AI A +A+ ++E+EF E+ +++ + +A+IAVVG+ M +PG S +F+ Sbjct: 361 LAINLVQAEKARLLLEQEFAAELAVRQIESLTFRKHIAIIAVVGKQMPGHPGVSAHLFET 420 Query: 417 LGRNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGK 476 LG+N +NV A+AQG++E+NIS VI D KAL+ +HE+F LS KV H+F+ G G I K Sbjct: 421 LGKNGINVIAVAQGANEMNISFVIDSHDEDKALHCVHESFLLSRRKV-HVFIAGTGTIAK 479 Query: 477 ALTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLAT--VGPPDENDEPMDMDK 534 +L I L++E LD+ + GMAN+R + G DL+ G D D Sbjct: 480 SLIGQIRDHSLTLRKEKELDVVVSGMANTRMHVSDDAGIDLSRWESGLKPRTDGKTVSD- 538 Query: 535 FIGTMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLA 594 ++ + N N++FVDCTAS +VA Y +L S + +VT NK +G E Y+ + + Sbjct: 539 YVDYIKSRNLHNTIFVDCTASAEVAACYPDLLASNISVVTANKLGTAGSWELYETISEAL 598 Query: 595 GQRGVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSEV 654 RF YETNV AGLP+INTL DL SGD + RIE VLSG+++YIF+EL KG FSE+ Sbjct: 599 HASNARFLYETNVGAGLPIINTLNDLRNSGDRIVRIEGVLSGTLSYIFNELRKGRKFSEI 658 Query: 655 VAQAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVP 714 V A++ GYTEPDPR+DLSG D ARK LILGRE G L +ED+E +S+VPE SV Sbjct: 659 VRSARDAGYTEPDPREDLSGADFARKFLILGRELGYRLDYEDIECESLVPESLRGEMSVE 718 Query: 715 EFFKKLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDNM 774 EF ++L D +Q + EA G + + + GKA++G+ +L +P L G++N+ Sbjct: 719 EFMERLGGIDAAYQTRISEAAETGMTIAYAGEISEGKARIGVKTLPVSNPVAGLNGTENL 778 Query: 775 ILFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRLGNY 813 ++FTT+RY D P++V+GPGAG +VTA GVFADI+R+ +Y Sbjct: 779 VVFTTDRYLDTPLVVKGPGAGGEVTAGGVFADILRIASY 817 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: 1412 Number of extensions: 53 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: 819 Length adjustment: 41 Effective length of query: 774 Effective length of database: 778 Effective search space: 602172 Effective search space used: 602172 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_012473759.1 CPHAMN1_RS01510 (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.10303.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-124 401.5 0.0 3.6e-124 401.1 0.0 1.2 1 lcl|NCBI__GCF_000020545.1:WP_012473759.1 CPHAMN1_RS01510 bifunctional asp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020545.1:WP_012473759.1 CPHAMN1_RS01510 bifunctional aspartate kinase/homoserine dehydrogenase I # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 401.1 0.0 3.6e-124 3.6e-124 5 441 .. 3 461 .. 1 462 [. 0.96 Alignments for each domain: == domain 1 score: 401.1 bits; conditional E-value: 3.6e-124 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekire 71 V+KFGGtS+ n eri++v i+ + k+ +v++VvSA+ +vTd L+e a + s++ e++ +i++ lcl|NCBI__GCF_000020545.1:WP_012473759.1 3 VLKFGGTSIENSERIRNVLGIIRGAI-KDSPVIIVVSAIRKVTDLLLEAAVAAGSGDAgyREKLVTIEN 70 89************************.777***********************999999999999**** PP TIGR00657 72 khlealeelasqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleel 128 h + + l+ + +++++++l el+e+ +r+++lils+GE+ Sa++++ ++++ lcl|NCBI__GCF_000020545.1:WP_012473759.1 71 IHGDLVRDLIDLSRRNEVQEVLTDELQELGDilygvsllrdlsDRSKALILSFGERFSARIISTFFCQE 139 **********88999999999999999998899************************************ PP TIGR00657 129 gvkavsllgaeagiltdsefgrAkvleeikterleklleeg.iivvvaGFiGatekgeittLGRGGSDl 196 g ++s+++a++ i+td ++ +A+v ++++e + + +e+ ++vv+G+iGa ++g ttLGRGGSD+ lcl|NCBI__GCF_000020545.1:WP_012473759.1 140 G-LDASYTDARKLIVTDTNHCDARVDMSASSELISAWFKEErGVPVVTGYIGAAPDGTATTLGRGGSDY 207 *.999*******************9999999999999999989************************** PP TIGR00657 197 tAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamraki 265 tA++l++ +Ade++i+tDVdG ++aDP+ v++A l+ isy Ea+EL+++GakvLhp +++pam+++i lcl|NCBI__GCF_000020545.1:WP_012473759.1 208 TATILGSVAGADEIQIWTDVDGFFSADPKRVKDAYVLPFISYGEAMELSHSGAKVLHPYSVHPAMKKGI 276 ********************************************************************* PP TIGR00657 266 pivvkstfnpeaeGTlivaksk..seeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakv 330 pi +++++np+ eGT i a++ + ++v++ls+ ++ +l++ sg++m pgi++++f++la++k+ lcl|NCBI__GCF_000020545.1:WP_012473759.1 277 PITIRNSYNPDVEGTRISAPEGndTGSGKPVTGLSSINDVVLLNFSGSGMVgvPGIASRLFSCLARHKI 345 ******************99777777889**************************************** PP TIGR00657 331 nvdlilqsssetsisfvvdkedadkakellk...kkvkeekaleevevekklalvslvGagmksapgva 396 n++ i+q sse+sis++++ +a+ka ll+ ++++ +++e++++ k++a++++vG++m ++pgv lcl|NCBI__GCF_000020545.1:WP_012473759.1 346 NIIFISQASSEQSISLAINLVQAEKARLLLEqefAAELAVRQIESLTFRKHIAIIAVVGKQMPGHPGVS 414 ****************************99966656677799999************************ PP TIGR00657 397 akifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441 a++fe+L +++in+ +++ ++e++is+v+d++d +ka++++he + lcl|NCBI__GCF_000020545.1:WP_012473759.1 415 AHLFETLGKNGINVIAVAqgANEMNISFVIDSHDEDKALHCVHESFL 461 ******************99************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (819 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: 00:00:00.02 # Mc/sec: 17.28 // [ok]
This GapMind analysis is from Apr 10 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