Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate WP_057507033.1 ABB28_RS02115 diaminopimelate decarboxylase
Query= reanno::Dyella79:N515DRAFT_4002 (853 letters) >NCBI__GCF_001431535.1:WP_057507033.1 Length = 864 Score = 863 bits (2229), Expect = 0.0 Identities = 474/860 (55%), Positives = 589/860 (68%), Gaps = 15/860 (1%) Query: 1 MKFGGTSVATLPRWQNIRELVASRRAE-GARVLVVVSALTGITDALKQMC-AQEDKGKRV 58 +KFGGTSV+ RW I +L R E G+RVLVVVSAL+G+T+ L + D RV Sbjct: 13 LKFGGTSVSRRHRWDTIGKLAKKRAEETGSRVLVVVSALSGVTNELTAIADGAADSRARV 72 Query: 59 EAARAIAQRHYDLLDHMQLAVPATLAERLSELAMLAEDGPGAMGELAWAALVQAHGELMS 118 A + +RH LD ++L A L ERL+ L L +D A L W A V GEL+S Sbjct: 73 AA---LVERHQAFLDELELP-RAVLGERLAALQALLDDARAAARTLDWQAEVLGQGELLS 128 Query: 119 SALGAAFLSHAGLPTEWLDARDCLAAVA-LPNQNERTKLLSAMVEARPDPALNARL-AEL 176 S++GAA+L GL W+DAR L A+ LPNQ+ ++ LS + + D A R A+ Sbjct: 129 SSIGAAYLHQNGLDMGWMDARQWLDALPPLPNQSPWSQRLSVNCQWKSDEAWAQRFRAQP 188 Query: 177 GEVFITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVP 236 + ITQGFIAR A G T +LGRGGSDTSA+YFGALL A RVEIWTDV GMF+ANP+ VP Sbjct: 189 TRLLITQGFIARHADGGTAILGRGGSDTSAAYFGALLGASRVEIWTDVPGMFSANPKDVP 248 Query: 237 GARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGPEVRE 296 ARLL RLDY EAQEIA+TGAKVLHPR + P R+ VPM I DT RPEL GT I Sbjct: 249 DARLLTRLDYYEAQEIATTGAKVLHPRSIKPCRDAGVPMAILDTERPELPGTSIDGSAAP 308 Query: 297 HAPSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVTVSLD 356 P VKAIS R GI LVSME +GMWQQVGFLADVF FK+HGLSVDLIGSAETNVTVSLD Sbjct: 309 -VPGVKAISRRNGIVLVSMEGIGMWQQVGFLADVFGLFKKHGLSVDLIGSAETNVTVSLD 367 Query: 357 PTENLLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEFGQIRVH 416 P+ENL+++D +AAL++DL+++C+VK+I PCAAITLVGRGMRS+LH LS V A FG+ RVH Sbjct: 368 PSENLVNTDVLAALSADLSQICKVKIIVPCAAITLVGRGMRSLLHKLSDVWATFGRERVH 427 Query: 417 LISQSSNNLNLTFVVDENVVDDLLPHLHELLIAAGALRTDDSALFGPSWQALYGSGEVAA 476 +ISQSSN+LNLTFV+DE D LLP LH LI +GA+ +++A+FGP W+ + +G V Sbjct: 428 MISQSSNDLNLTFVIDETDADGLLPILHAELIDSGAMPVEETAVFGPRWREI--AGTVRP 485 Query: 477 PAASWWRTAERERLLRLGAERTPRYVYHLPTVRQQARELKSLGAVDRLHYAVKANTHPAI 536 WWR +R LL+L TPRYVYHLPTVR +AR L ++ +D+ +YA+KAN+HPAI Sbjct: 486 RGTPWWR-GQRAHLLQLAEAGTPRYVYHLPTVRARARALAAITPIDQRYYAIKANSHPAI 544 Query: 537 LKALAEEGFGFECVSPGELKAVLAAVPESAP--LLFTPNFAPRADYEWALTTRATISLDA 594 L+ L EGFG ECVS GELK V +P +P +LFTP+F PR ++E A T+++D Sbjct: 545 LETLEAEGFGLECVSHGELKHVFNVLPGLSPRRVLFTPSFCPREEFEAAFALGVTVTVDN 604 Query: 595 LYQLENWGELFRGREIVLRVDLGRGLGHHEKVRTGGSGSKFGLPVELVDSFLRLADAHGV 654 + L+ W +LFR RE+ LRVDLGRG GHH KVRTGG SKFGLP+ VD F+R A G Sbjct: 605 VEALQRWPDLFRNRELWLRVDLGRGEGHHAKVRTGGKESKFGLPMARVDEFVRAATELGT 664 Query: 655 IVRGLHAHLGSGILDEGHWGEVYGQLASLAERIGSVAFLDIGGGLGVPSHPGEARLDIAA 714 + GLHAHLGSG+ HW + +LA A RIG+V +DIGGG+ +P + D+ A Sbjct: 665 TIVGLHAHLGSGVETAQHWRLMCDELAGFARRIGTVQTIDIGGGMPIPYSEEDEPFDLEA 724 Query: 715 LDRVLRSVKAAYPHYQLWMEPGRYLVADAGVLLARVTQQKGKGSWRYLGVDTGMNSLIRP 774 L VKA +P ++L +EPGRYLVA++GVLL R TQ K R +G+D GMN+LIRP Sbjct: 725 WAEGLAEVKAVHPAFRLAIEPGRYLVAESGVLLTRCTQVVEKEGVRRVGLDAGMNTLIRP 784 Query: 775 ALYEAWHEIVNLTRLDEPATGLFQVVGPICESGDVLGTDRRLP-EAQEGDVVLVAQAGAY 833 ALY+AWH+I NL+R A F VVGPICES DV G R+LP DV++VA AGAY Sbjct: 785 ALYDAWHDIENLSRQGGYAEAAFDVVGPICESSDVFGKRRKLPASTAPDDVMVVADAGAY 844 Query: 834 GKVMSSPYNMRDEAEEVILD 853 G VM+S YN R E IL+ Sbjct: 845 GYVMASTYNQRAMPREDILE 864 Lambda K H 0.319 0.135 0.398 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: 1866 Number of extensions: 87 Number of successful extensions: 9 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: 853 Length of database: 864 Length adjustment: 42 Effective length of query: 811 Effective length of database: 822 Effective search space: 666642 Effective search space used: 666642 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 WP_057507033.1 ABB28_RS02115 (diaminopimelate decarboxylase)
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.10841.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-89 284.9 0.0 7.9e-89 284.6 0.0 1.1 1 lcl|NCBI__GCF_001431535.1:WP_057507033.1 ABB28_RS02115 diaminopimelate de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057507033.1 ABB28_RS02115 diaminopimelate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 284.6 0.0 7.9e-89 7.9e-89 3 441 .. 10 459 .. 8 460 .. 0.89 Alignments for each domain: == domain 1 score: 284.6 bits; conditional E-value: 7.9e-89 TIGR00657 3 liVqKFGGtSvgnverikkvakivkkeke.kgnqvvVVvSAmagvTdaLvelaekvsseeekeliekir 70 +iV+KFGGtSv r + + k+ kk++e g v+VVvSA +gvT++L ++a+ + + + + ++++ lcl|NCBI__GCF_001431535.1:WP_057507033.1 10 WIVLKFGGTSVSRRHRWDTIGKLAKKRAEeTGSRVLVVVSALSGVTNELTAIADGAADSR--ARVAALV 76 8***********************9987516899*************************9..7899999 PP TIGR00657 71 ekhlealeela.sqalkeklkallekeleevkk....ereldlilsvGEklSaallaaaleelgv.... 130 e+h + l+el+ + a+ + a+l++ l+ +++ ++++l GE lS+++ aa+l++ g lcl|NCBI__GCF_001431535.1:WP_057507033.1 77 ERHQAFLDELElPRAVLGERLAALQALLDDARAaartLDWQAEVLGQGELLSSSIGAAYLHQNGLdmgw 145 ***********99888777666666666666666544667899********************987787 PP TIGR00657 131 .kavsllgaeagiltdsefgrAk...vleeikterleklleeg..iivvvaGFiGatekgeittLGRGG 193 +a+++l+a ++ +s +++ + ++++ + + +++ + +++GFi+ + +g + LGRGG lcl|NCBI__GCF_001431535.1:WP_057507033.1 146 mDARQWLDALPPLPNQSPWSQRLsvnCQWKSDEAWAQRF-RAQptRLLITQGFIARHADGGTAILGRGG 213 889999999999999999998777432333333333444.444479*********************** PP TIGR00657 194 SDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamr 262 SD++Aa +a+l+A++vei+tDV+G ++a P+ vp+Ar+l ++y Ea+E+a+ GakvLhpr+++p++ lcl|NCBI__GCF_001431535.1:WP_057507033.1 214 SDTSAAYFGALLGASRVEIWTDVPGMFSANPKDVPDARLLTRLDYYEAQEIATTGAKVLHPRSIKPCRD 282 ********************************************************************* PP TIGR00657 263 akipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeak 329 a++p+ + +t pe +GT i ++ p vka+s ++ +lvs++g +m +g+la+vfg ++++ lcl|NCBI__GCF_001431535.1:WP_057507033.1 283 AGVPMAILDTERPELPGTSIDGSAA--PVPGVKAISRRNGIVLVSMEGIGMWqqVGFLADVFGLFKKHG 349 ***********************66..5589*******************9888*************** PP TIGR00657 330 vnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaak 398 +vdli s et+++ +d ++ + +l +++++++v++ a ++lvG gm+s ++ lcl|NCBI__GCF_001431535.1:WP_057507033.1 350 LSVDLIG--SAETNVTVSLDPSENLVNTDVLAALSADLSQICKVKIIVPCAAITLVGRGMRSLLHKLSD 416 ******9..667888888887775555566667889********************************* PP TIGR00657 399 ifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441 + ++ +e ++mis s++ ++++v+de+da+ ++ lh++l+ lcl|NCBI__GCF_001431535.1:WP_057507033.1 417 VWATFGRER--VHMISqsSNDLNLTFVIDETDADGLLPILHAELI 459 *******65..6666655899********************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (864 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: 12.15 // [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