Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_059152208.1 V474_RS14540 aspartate kinase
Query= SwissProt::Q88EI9 (411 letters) >NCBI__GCF_001046635.1:WP_059152208.1 Length = 419 Score = 407 bits (1047), Expect = e-118 Identities = 227/419 (54%), Positives = 290/419 (69%), Gaps = 12/419 (2%) Query: 1 MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60 MA IV KFGGTS+ ERI +VA VK+ +EAG ++ VV+SAMSGET+RL++ ++ Sbjct: 1 MARIVMKFGGTSMAGSERIRRVAGIVKRQQEAGHEVAVVVSAMSGETDRLVNFCREANAL 60 Query: 61 PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120 P E DV+V++GEQVT LL + L G A S+ G QV I TD +H KARI +ID Sbjct: 61 YDPAEYDVVVASGEQVTSGLLALTLQAIGCKARSWQGWQVPIKTDDAHAKARIEEIDADA 120 Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 + A + G + V+ GFQGV G +TTLGRGGSDT+ VA+AAA+KAD C IYTDVDGVYT Sbjct: 121 LIASMAAGEIAVIPGFQGVSPEGRVTTLGRGGSDTSAVAVAAAVKADRCDIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEG----- 235 TDPR+V +AR+L +T+EEMLE+AS+GSKVLQ RSV A K V ++VL SF + Sbjct: 181 TDPRIVAKARKLPLVTYEEMLELASVGSKVLQTRSVSLAMKEKVRVQVLSSFIDETAPAA 240 Query: 236 ---PGTLITIDEE---ESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNI 289 PGTLI DEE ME+ +I+GIA +++EAK+T+ VPD PG I P++ SNI Sbjct: 241 DTIPGTLIVSDEELEGSDMERQLITGIAADKNEAKVTLTRVPDRPGAVASIFAPLAESNI 300 Query: 290 EVDMIVQNVAHD-NTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGV 348 VDMI+QNVA D TD TFTV +++ +AQ++LE IG +I D +AK+S+VGV Sbjct: 301 NVDMIIQNVAKDKGETDVTFTVPQSDLARAQAMLEERKDSIGYYRLIADGNVAKISVVGV 360 Query: 349 GMRSHAGVASCMFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLDAPA 407 GMRSHAGVAS MF+ LA INI ISTSEIKVSV+++ ELAVR LHTA+ LDA A Sbjct: 361 GMRSHAGVASTMFKTLADRGINIIAISTSEIKVSVLIDTDETELAVRVLHTAYGLDAAA 419 Lambda K H 0.316 0.133 0.358 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: 406 Number of extensions: 16 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: 411 Length of database: 419 Length adjustment: 31 Effective length of query: 380 Effective length of database: 388 Effective search space: 147440 Effective search space used: 147440 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_059152208.1 V474_RS14540 (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.1807183.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-126 408.3 11.8 2.2e-126 408.1 11.8 1.0 1 NCBI__GCF_001046635.1:WP_059152208.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001046635.1:WP_059152208.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 408.1 11.8 2.2e-126 2.2e-126 3 405 .. 3 414 .. 1 416 [. 0.95 Alignments for each domain: == domain 1 score: 408.1 bits; conditional E-value: 2.2e-126 TIGR00656 3 liVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdel 75 iV+KFGGts+++seri+++a iv+++ + g++v VVvSAms++td+lv++ + + p+e d + NCBI__GCF_001046635.1:WP_059152208.1 3 RIVMKFGGTSMAGSERIRRVAGIVKRQQEAGHEVAVVVSAMSGETDRLVNFC------REANALYDPAEYDVV 69 59*************************************************9......67888889******* PP TIGR00656 76 vsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGate 148 v+ GE+++s ll+ l++ g ka++ +g++ +i Tdd + +A+i+e++ L+ ++ g i v+ GF+G NCBI__GCF_001046635.1:WP_059152208.1 70 VASGEQVTSGLLALTLQAIGCKARSWQGWQVPIKTDDAHAKARIEEIDA-DALIASMAAGEIAVIPGFQGVSP 141 *************************************************.999******************** PP TIGR00656 149 eGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpr 221 eG++TtLGRGGSD++A+++aaa+kAdr++iyTDV+GvyttDPr+v +a+k++ ++yeE+lelA++G kvl+ r NCBI__GCF_001046635.1:WP_059152208.1 142 EGRVTTLGRGGSDTSAVAVAAAVKADRCDIYTDVDGVYTTDPRIVAKARKLPLVTYEEMLELASVGSKVLQTR 214 ************************************************************************* PP TIGR00656 222 alelaveakvpilvrssk........ekeegTlitn.......kkensslvkaialeknvarltvegegmlgk 279 ++ la++ kv + v ss+ ++ gTli++ ++e + l+++ia +kn a++t++ + ++ NCBI__GCF_001046635.1:WP_059152208.1 215 SVSLAMKEKVRVQVLSSFidetapaaDTIPGTLIVSdeelegsDMERQ-LITGIAADKNEAKVTLT--RVPDR 284 **************99973333332133379****9887776555555.*****************..***** PP TIGR00656 280 rgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsi 348 +g a if Lae++invd+i+q ++ t+++++v + d+ +a+++L+e+++ +++ +l + ++a++s+ NCBI__GCF_001046635.1:WP_059152208.1 285 PGAVASIFAPLAESNINVDMIIQNVAKdkgeTDVTFTVPQSDLARAQAMLEERKDSIGYYRLIADGNVAKISV 357 **********************997766677****************************************** PP TIGR00656 349 vgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 vg+g++++ Gvas +fk l++++ini+ is+se+k+svl+d+ ++e avr lh ++ NCBI__GCF_001046635.1:WP_059152208.1 358 VGVGMRSHAGVASTMFKTLADRGINIIAISTSEIKVSVLIDTDETELAVRVLHTAYG 414 *****************************************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (419 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 16.36 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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