Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate Synpcc7942_1001 Synpcc7942_1001 aspartate kinase
Query= BRENDA::P74569 (600 letters) >FitnessBrowser__SynE:Synpcc7942_1001 Length = 616 Score = 703 bits (1814), Expect = 0.0 Identities = 392/606 (64%), Positives = 459/606 (75%), Gaps = 15/606 (2%) Query: 1 MALIVQKFGGTSVGTVERIQAVAQRIKRTVQGGNSLVVVVSAMGKSTDVLVDLAQQISPN 60 MALIVQK+GGTSVG+VERI AVAQRI +TV GN +VVVVSAMG STD L+ LA IS N Sbjct: 20 MALIVQKYGGTSVGSVERITAVAQRIAQTVAAGNQVVVVVSAMGHSTDELLKLANAISAN 79 Query: 61 PCRREMDMLLSTGEQVSIALLSLALQEIDQPAISLTGAQVGIVTEAEHSRARILEIRPDR 120 P RRE+DMLL+TGEQVSIALLS+AL E AIS+TGAQVGI+TEA HSRARILEI P R Sbjct: 80 PSRRELDMLLATGEQVSIALLSMALHEQGCDAISMTGAQVGIITEAHHSRARILEIDPQR 139 Query: 121 LEHHLREGKVVVVAGFQGISSVEH---LEITTLGRGGSDTSAVALAAALKADFCEIYTDV 177 L+ L G+VVVVAGFQGI+S + EITTLGRGGSDTSAVALAAAL AD CEIYTDV Sbjct: 140 LQSQLDAGRVVVVAGFQGIASSDRTALTEITTLGRGGSDTSAVALAAALNADRCEIYTDV 199 Query: 178 PGILTTDPRLVPEAQLMAEITCDEMLELASLGAKVLHPRAVEIARNYGIPLVVRSSWSDE 237 PGILTTDPRLVPEA L+ EITCDEMLELASLGA VLHPRAVEIARNYG+ LVVRSSW+ E Sbjct: 200 PGILTTDPRLVPEAHLLEEITCDEMLELASLGASVLHPRAVEIARNYGVRLVVRSSWTQE 259 Query: 238 PGTKVVAPPVQ-NRSLVGLEIAKAVDGVEYDADQAKVALLRVPDRPGVASKLFRDIAQQQ 296 PGT VVAPP + +RSL GLEI + VDG+ D DQAKVALL VPDRPG+A+ LF ++AQ+ Sbjct: 260 PGTGVVAPPRRSDRSLQGLEIGRPVDGLALDTDQAKVALLHVPDRPGIAASLFGEMAQRG 319 Query: 297 VDIDLIIQSIHDGNSNDIAFTVVKDLLNTAEAVTSAIAPALRSYPEADQEAEIIVEKGIA 356 V++DLIIQSIH+GNSNDI+FTV + L AEA T+ + AD E E +A Sbjct: 320 VNVDLIIQSIHEGNSNDISFTVSQADLEKAEAGTTQLL--------ADLGGEQQSEAAVA 371 Query: 357 KIAIAGAGMIGRPGIAAKMFKTLADVGVNIEMISTSEVKVSCVIDQRDADRAIAALSNAF 416 K++I+G G++GRPGIAA+MF LA G+NI+MISTSEVKVSCVI D RAIAAL +F Sbjct: 372 KVSISGVGIVGRPGIAAQMFSALAQGGINIQMISTSEVKVSCVIAAADQQRAIAALQESF 431 Query: 417 GVTLSPPKNQTD--TSHLPAVRGVALDQDQAQIAIRHVPDRPGMAAQLFTALAEANISVD 474 + + TD T+ LPAVRGVALD+DQA++AI +VPD PGMAA +F LA+ ISVD Sbjct: 432 ELEEAIAATATDACTTDLPAVRGVALDRDQARLAILNVPDLPGMAATIFQILADRQISVD 491 Query: 475 MIIQSQRCRINQGTPCRDIAFMVAEGDSSQAEAILQPLIKDWLDAAIVVNKAIAKVSIVG 534 MIIQSQR RI+ G PCRDIA + D+ A A LQ D ++ + IAKVSIVG Sbjct: 492 MIIQSQRGRIHNGQPCRDIACTLPPADAELAAAALQ-AFADQHGCSLEIQTEIAKVSIVG 550 Query: 535 SGMIGHPGVAAHFFAALAQENINIEMIATSEIKISCVVPQDRGVDALKAAHSAFNLAGTK 594 SGM+ PGVAA FAALA INI MIATSEIK+SC+V + V+AL+ H+AF LA + Sbjct: 551 SGMVQQPGVAAQMFAALANHGINIHMIATSEIKVSCIVDASQAVEALQTVHAAFGLASDR 610 Query: 595 TVTVPA 600 + VPA Sbjct: 611 RIEVPA 616 Lambda K H 0.318 0.132 0.366 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: 965 Number of extensions: 35 Number of successful extensions: 17 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: 600 Length of database: 616 Length adjustment: 37 Effective length of query: 563 Effective length of database: 579 Effective search space: 325977 Effective search space used: 325977 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: 53 (25.0 bits)
Align candidate Synpcc7942_1001 Synpcc7942_1001 (aspartate kinase)
to HMM TIGR00656 (aspartate kinase, monofunctional class (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/TIGR00656.hmm # target sequence database: /tmp/gapView.29330.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00656 [M=407] Accession: TIGR00656 Description: asp_kin_monofn: aspartate kinase, monofunctional class 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-165 535.5 14.0 1.4e-131 425.2 8.5 2.0 2 lcl|FitnessBrowser__SynE:Synpcc7942_1001 Synpcc7942_1001 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1001 Synpcc7942_1001 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 425.2 8.5 1.4e-131 1.4e-131 1 406 [. 20 433 .. 20 434 .. 0.95 2 ! 113.7 0.2 5.2e-37 5.2e-37 255 404 .. 450 604 .. 436 607 .. 0.94 Alignments for each domain: == domain 1 score: 425.2 bits; conditional E-value: 1.4e-131 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + liVqK+GGtsvgs+eri ++a+++ +++ g++vvVVvSAm+++tdel++la +ais ++s+ lcl|FitnessBrowser__SynE:Synpcc7942_1001 20 MALIVQKYGGTSVGSVERITAVAQRIAQTVAAGNQVVVVVSAMGHSTDELLKLA------NAISANPSR 82 579***************************************************......8******** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re d+l+++GE++s+alls+al+e+g +a++++g++ gi+T++++ +A+i e+++ +rL ++L+ g +v lcl|FitnessBrowser__SynE:Synpcc7942_1001 83 RELDMLLATGEQVSIALLSMALHEQGCDAISMTGAQVGIITEAHHSRARILEIDP-QRLQSQLDAGRVV 150 *******************************************************.************* PP TIGR00656 139 vvaGFiG.....ateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidki 202 vvaGF+G +t eiTtLGRGGSD++A++laaal+Adr+eiyTDV+G++ttDPr+v+ea+ +++i lcl|FitnessBrowser__SynE:Synpcc7942_1001 151 VVAGFQGiassdRTALTEITTLGRGGSDTSAVALAAALNADRCEIYTDVPGILTTDPRLVPEAHLLEEI 219 *******54433355689*************************************************** PP TIGR00656 203 syeEalelAtlGakvlhpralelaveakvpilvrsskekeegTlitn......kkens.......slvk 258 + +E+lelA+lGa vlhpra+e+a +++v ++vrss +e gT +++ + s ++v lcl|FitnessBrowser__SynE:Synpcc7942_1001 220 TCDEMLELASLGASVLHPRAVEIARNYGVRLVVRSSWTQEPGTGVVApprrsdR---SlqgleigRPVD 285 **********************************************98876651...2445566699** PP TIGR00656 259 aialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakka 324 ++al+ ++a++++ ++ +++gi+a +f+ +a++++nvdli+q+ e ++is++v++ d+++a++ lcl|FitnessBrowser__SynE:Synpcc7942_1001 286 GLALDTDQAKVALL--HVPDRPGIAASLFGEMAQRGVNVDLIIQSIHEgnsNDISFTVSQADLEKAEAG 352 *************9..9****************************9999999**************998 PP TIGR00656 325 LkeesgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekda 393 ++ +++ + + e +a+vsi+g+g+v+ pG+a+++f+al++ +ini mis+se+k+s ++ +d lcl|FitnessBrowser__SynE:Synpcc7942_1001 353 TTQLLADLG-GEQQSEAAVAKVSISGVGIVGRPGIAAQMFSALAQGGINIQMISTSEVKVSCVIAAADQ 420 888877777.66778899*************************************************** PP TIGR00656 394 ekavrklheklee 406 ++a+ +l+e++e+ lcl|FitnessBrowser__SynE:Synpcc7942_1001 421 QRAIAALQESFEL 433 **********987 PP == domain 2 score: 113.7 bits; conditional E-value: 5.2e-37 TIGR00656 255 slvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese........tsislvvde 315 + v+++al++++arl++ ++ + +g++a+if++La+++i+vd+i+q++ +i+ ++ lcl|FitnessBrowser__SynE:Synpcc7942_1001 450 PAVRGVALDRDQARLAIL--NVPDLPGMAATIFQILADRQISVDMIIQSQRGrihngqpcRDIACTLPP 516 489***************..****************************9944788899999******** PP TIGR00656 316 edvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetki 384 d++ a +aL+++ ++ + +sle++ ++a+vsivg+g+v++pGva+++f+al++++ini mi++se+k+ lcl|FitnessBrowser__SynE:Synpcc7942_1001 517 ADAELAAAALQAFADQHG-CSLEIQTEIAKVSIVGSGMVQQPGVAAQMFAALANHGINIHMIATSEIKV 584 *************98888.************************************************** PP TIGR00656 385 svlvdekdaekavrklhekl 404 s +vd +a++a +++h+++ lcl|FitnessBrowser__SynE:Synpcc7942_1001 585 SCIVDASQAVEALQTVHAAF 604 *****************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (616 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 15.27 // [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