Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate CA265_RS09655 CA265_RS09655 aspartate kinase
Query= BRENDA::Q9S702 (559 letters) >FitnessBrowser__Pedo557:CA265_RS09655 Length = 437 Score = 233 bits (593), Expect = 1e-65 Identities = 170/470 (36%), Positives = 257/470 (54%), Gaps = 50/470 (10%) Query: 86 VMKFGGSSVASAERMIQVAKLILSFPDEKPVVVLSAMAKTTNKLL------MAGEK---A 136 ++KFGG+SV S ERM ++ +I P+E+ +VVLSA++ TTN L+ +AG+K + Sbjct: 3 ILKFGGTSVGSPERMTKLLDIIN--PNEEQIVVLSAVSGTTNSLVEIANYFLAGDKKKGS 60 Query: 137 VCCGVTNVDTIEELSYIKELHIRTAHELGVETAVIAEHLEGLEQLLKGVAMMKELTLRSR 196 C V N+ + ++ L E G E VI H L L + T Sbjct: 61 EC--VENLYQKYKTFVVELLPAAEFQEQGNE--VIDYHFGFLAGLANDI-----FTSIEE 111 Query: 197 DYLVSFGECMSTRLFAAYLNKIGHKARQYDAFEIGIITTDDFTNADILEATYPAVSKKL- 255 +++ GE +ST L+ YL IG + A + + TD+ DI P +K L Sbjct: 112 KVVLAQGELLSTTLYHIYLKSIGVPSVLLPALDF--MKTDEDNEPDI-----PFTTKHLT 164 Query: 256 -LGDWSKENALPVVTGFLGKGWRSCAVTTLGRGGSDLTATTIGKALGLREIQVWKDVDGV 314 L + K+N L + G++ + V L RGGSD TA+ +G A+ E+Q+W D+DG+ Sbjct: 165 PLLEQHKDNKLFITQGYICRNSFG-EVDNLRRGGSDYTASLLGAAILAEEVQIWTDIDGM 223 Query: 315 LTCDPNIYCGAQPVPHLTFDEAAELAYFGAQVLHPLSMRPAREGNIPVRVKNSYNPTAPG 374 DP I G +P+ L+FDEAAELAYFGA++LHP S+ PA++ IPVR+ N+ P+A G Sbjct: 224 HNNDPRIVKGTKPIAQLSFDEAAELAYFGAKILHPQSVFPAQKYKIPVRLLNTMEPSAAG 283 Query: 375 TVITRSRDMSKAVLTSIVLKRNVTMLDITSTRMLGQYGFLAKVFSTFEKLGISVDVVATS 434 T+IT D + + SI K +T + I S+RML YGFL +VF FE+ +D++ TS Sbjct: 284 TLIT--HDSERGKIKSIAAKDGITAIRIQSSRMLLAYGFLRRVFEVFERYKTPIDMITTS 341 Query: 435 EVSISLTLDPSKFCSRELIQHELDQVVEELEKIAVVNLLRHRSIISLIGNVQRSSFILEK 494 EV++SLT+D + L Q++EELE V + + SI+ ++G+ F EK Sbjct: 342 EVAVSLTIDETA---------HLPQIIEELESFGTVEVDTNHSIVCVVGD-----FGSEK 387 Query: 495 -GF--RVLR-TNGINVQMISQGASKVNISLIVNDDEAEHCVKALHSAFFE 540 GF RVL I ++MIS G S N+SL++ + +++LH+ FE Sbjct: 388 HGFASRVLEGLKHIPIRMISYGGSNYNVSLLILSEYKTEALRSLHNRLFE 437 Lambda K H 0.319 0.133 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: 475 Number of extensions: 21 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: 559 Length of database: 437 Length adjustment: 34 Effective length of query: 525 Effective length of database: 403 Effective search space: 211575 Effective search space used: 211575 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: 52 (24.6 bits)
Align candidate CA265_RS09655 CA265_RS09655 (aspartate kinase)
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.3381.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-90 288.1 0.0 7.9e-90 287.9 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS09655 CA265_RS09655 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS09655 CA265_RS09655 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 287.9 0.0 7.9e-90 7.9e-90 5 442 .] 3 437 .] 1 437 [] 0.87 Alignments for each domain: == domain 1 score: 287.9 bits; conditional E-value: 7.9e-90 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee...kelieki 69 ++KFGGtSvg+ er+ k+ +i+ ++ + +VV+SA++g+T++Lve+a+ + +++ e +e++ lcl|FitnessBrowser__Pedo557:CA265_RS09655 3 ILKFGGTSVGSPERMTKLLDIINPNE----EQIVVLSAVSGTTNSLVEIANYFLAGDKkkgSECVENL 66 79********************9887....779********************999965555555555 PP TIGR00657 70 rekhlealeela.sqalkeklkallekeleevkk.......ereldlilsvGEklSaallaaaleelg 129 +k + + el + +e+ ++++++++ + + e+ ++l+ GE lS++l +l++ g lcl|FitnessBrowser__Pedo557:CA265_RS09655 67 YQKYKTFVVELLpAAEFQEQGNEVIDYHFGFLAGlandiftSIEEKVVLAQGELLSTTLYHIYLKSIG 134 55555555555545555666666666665555549999*99999************************ PP TIGR00657 130 vkavsllgaeagiltdsefgrAkvleeikterleklleeg...iivvvaGFiGatekgeittLGRGGS 194 v +v l a + td+ + +t+ l++lle+ ++ +++G+i ++ ge+ L RGGS lcl|FitnessBrowser__Pedo557:CA265_RS09655 135 VPSVLL-PALDFMKTDEDNEPDI---PFTTKHLTPLLEQHkdnKLFITQGYICRNSFGEVDNLRRGGS 198 777755.5555666776554444...455555555555433448************************ PP TIGR00657 195 DltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamr 262 D+tA+ll+aa+ A+ev+i+tD+dG + DPriv+ ++ ++++s++Ea+ELa++Gak+Lhp+++ pa + lcl|FitnessBrowser__Pedo557:CA265_RS09655 199 DYTASLLGAAILAEEVQIWTDIDGMHNNDPRIVKGTKPIAQLSFDEAAELAYFGAKILHPQSVFPAQK 266 ******************************************************************** PP TIGR00657 263 akipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaea 328 +kip++ +t++p+a GTli+ +s+ + ++k+++ ++ + + ++++ m +g+l +vf+ ++ lcl|FitnessBrowser__Pedo557:CA265_RS09655 267 YKIPVRLLNTMEPSAAGTLITHDSE---RGKIKSIAAKDGITAIRIQSSRMLlaYGFLRRVFEVFERY 331 ***********************55...568********************999************** PP TIGR00657 329 kvnvdlilqsssetsisfvvdked.adkakellkkkvkeekaleevevekklalvslvGagmksapgv 395 k +d+i+ +se +s+++d++ ++++ e+ ++ +++vev+++ ++v +vG+ +++ g lcl|FitnessBrowser__Pedo557:CA265_RS09655 332 KTPIDMIT--TSEVAVSLTIDETAhLPQIIEE-------LESFGTVEVDTNHSIVCVVGDFGSEKHGF 390 ********..8888899999987656666665.......578************************** PP TIGR00657 396 aakifeaLaeeniniemis..sseikisvvvdekdaekavealheklve 442 a++++e L++ i+i+mis s++++s+++ +++ ++a++ lh++l+e lcl|FitnessBrowser__Pedo557:CA265_RS09655 391 ASRVLEGLKH--IPIRMISygGSNYNVSLLILSEYKTEALRSLHNRLFE 437 *********9..********99************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (437 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: 11.69 // [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