Align aspartate kinase 1; EC 2.7.2.4 (characterized)
to candidate WP_005808827.1 DHAF_RS18265 aspartate kinase
Query= CharProtDB::CH_090816 (404 letters) >NCBI__GCF_000021925.1:WP_005808827.1 Length = 409 Score = 419 bits (1078), Expect = e-122 Identities = 223/406 (54%), Positives = 286/406 (70%), Gaps = 4/406 (0%) Query: 1 MKIIVQKFGGTSVKDDKGRKLALGHIKEAISEGYKVVVVVSAMGRKGDPYATDSLLGLLY 60 M+++VQKFGGTSV + R + EA+ EGY VVVVSA+GR GDPYATD+ + L+ Sbjct: 1 MRVLVQKFGGTSVSSAERRAQVAAKVSEAVREGYSPVVVVSAIGRSGDPYATDTFINLVN 60 Query: 61 GDQSAISPREQDLLLSCGETISSVVFTSMLLDNGVKAAALTGAQAGFLTNDQHTNAKIIE 120 G RE DLL+SCGE IS VV TS L G++A LTG QAG +TND + +A+II Sbjct: 61 GITLESPKREMDLLMSCGEIISGVVLTSTLKSMGLEAILLTGGQAGIITNDCYGDARIIR 120 Query: 121 MKPERLFSVLANHDAVVVAGFQGATEKGDTTTIGRGGSDTSAAALGAAVDAEYIDIFTDV 180 ++P+ + L+ VVV GFQG TE G TT+GRGGSDT+A+ALG A++AE IDI+TDV Sbjct: 121 VEPKGILDHLSEGRVVVVTGFQGVTEDGQVTTLGRGGSDTTASALGVALNAEAIDIYTDV 180 Query: 181 EGVMTADPRVVENAKPLPVVTYTEICNLAYQGAKVISPRAVEIAMQAKVPIRVRSTYSND 240 EG+MTADPR+VE+A+ L VVTY EIC+LA+QGAKVI PRAVEIAMQ +PI ++ T+S+ Sbjct: 181 EGIMTADPRIVEDARILDVVTYNEICHLAHQGAKVIHPRAVEIAMQRNIPIWIKCTFSDA 240 Query: 241 KGTLVTS-HHSSKVGSDVF-ERLITGIAHVKDVTQFKVPAK--IGQYNVQTEVFKAMANA 296 +GTLVTS G+D+ +R ITGIAH +VTQ +VP V ++FK MA A Sbjct: 241 RGTLVTSIQPDMGAGTDITGDRTITGIAHTPNVTQIQVPTHDVADVLQVDKQIFKGMALA 300 Query: 297 GISVDFFNITPSEIVYTVAGNKTETAQRILMDMGYDPMVTRNCAKVSAVGAGIMGVPGVT 356 ISVDF ++ P ++YTV E A +IL ++G+ P CAKVS VGAGI GVPGV Sbjct: 301 DISVDFISVQPESVLYTVPDEIAEKAMKILDNLGFKPTAVPGCAKVSIVGAGIAGVPGVM 360 Query: 357 SKIVSALSEKEIPILQSADSHTTIWVLVHEADMVPAVNALHEEFEL 402 + +V ALS+ + ILQSADSHTTIWVLV++ DMVPAV ALH++F L Sbjct: 361 ANMVEALSDAGVRILQSADSHTTIWVLVNKEDMVPAVQALHKKFLL 406 Lambda K H 0.316 0.131 0.364 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: 490 Number of extensions: 21 Number of successful extensions: 3 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: 404 Length of database: 409 Length adjustment: 31 Effective length of query: 373 Effective length of database: 378 Effective search space: 140994 Effective search space used: 140994 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_005808827.1 DHAF_RS18265 (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.2183.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-132 426.8 7.9 5e-132 426.7 7.9 1.0 1 lcl|NCBI__GCF_000021925.1:WP_005808827.1 DHAF_RS18265 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_005808827.1 DHAF_RS18265 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 426.7 7.9 5e-132 5e-132 2 405 .. 2 405 .. 1 407 [. 0.98 Alignments for each domain: == domain 1 score: 426.7 bits; conditional E-value: 5e-132 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 + VqKFGGtsv s er+ ++a +v ++++eg+++vVVvSA+++++d +++ + +++l++ i e+ +r lcl|NCBI__GCF_000021925.1:WP_005808827.1 2 RVLVQKFGGTSVSSAERRAQVAAKVSEAVREGYSPVVVVSAIGRSGDPYATDT-FINLVNGITLESPKR 69 689**************************************************.*************** PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 e+d+l+s+GE +s ++l+s l+ g +a+ l+g++agi+T+d +g+A+i ++++ + +l+ L eg +vv lcl|NCBI__GCF_000021925.1:WP_005808827.1 70 EMDLLMSCGEIISGVVLTSTLKSMGLEAILLTGGQAGIITNDCYGDARIIRVEP-KGILDHLSEGRVVV 137 ******************************************************.9************* PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 v+GF+G te+G++TtLGRGGSD+tA +l+ al+A+ ++iyTDVeG++t+DPr+ve+a+ +d ++y+E++ lcl|NCBI__GCF_000021925.1:WP_005808827.1 138 VTGFQGVTEDGQVTTLGRGGSDTTASALGVALNAEAIDIYTDVEGIMTADPRIVEDARILDVVTYNEIC 206 ********************************************************************* PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn.........kkensslvkaialeknvar 268 lA++Gakv+hpra+e+a++ ++pi ++ +++ +gTl+t+ + +++ +++ia+++nv++ lcl|NCBI__GCF_000021925.1:WP_005808827.1 207 HLAHQGAKVIHPRAVEIAMQRNIPIWIKCTFSDARGTLVTSiqpdmgagtDITGDRTITGIAHTPNVTQ 275 *****************************************999887766666669************* PP TIGR00656 269 ltvegegmlgkrgilaeifkaLaeeeinvdlisqtesetsislvvdeedvdeakkaLkeesgaaelesl 337 ++v ++++++ + +ifk +a ++i+vd+is + s+ ++v +e +++a k+L + +++ lcl|NCBI__GCF_000021925.1:WP_005808827.1 276 IQVPTHDVADVLQVDKQIFKGMALADISVDFISVQP--ESVLYTVPDEIAEKAMKILDNL----GFKPT 338 **********************************99..9******************998....58899 PP TIGR00656 338 eveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 v ++a+vsivgag+ ++pGv++++++al++ +++il++++s+t+i+vlv+++d++ av++lh+k+ lcl|NCBI__GCF_000021925.1:WP_005808827.1 339 AVP-GCAKVSIVGAGIAGVPGVMANMVEALSDAGVRILQSADSHTTIWVLVNKEDMVPAVQALHKKFL 405 998.*************************************************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (409 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: 00:00:00.02 # Mc/sec: 7.49 // [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