Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_004511964.1 GMET_RS09500 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_000012925.1:WP_004511964.1 Length = 405 Score = 485 bits (1248), Expect = e-141 Identities = 251/404 (62%), Positives = 319/404 (78%), Gaps = 2/404 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MAL+VQK+GGTS+G++ERI VA++V K +AG+D+VVVVSAMSGETN+L+ LAN++ E Sbjct: 1 MALVVQKYGGTSMGSIERIRNVAKRVAKTYDAGNDMVVVVSAMSGETNKLVALANEVCEF 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P RE DV+V++GEQV+IALL+M L G A SY G QV I+TDS +KARI I D Sbjct: 61 PDNREYDVLVASGEQVSIALLAMCLKSMGYKAKSYHGWQVPIITDSVFSKARIEEIPDAK 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 +RADLK G +VVVAGFQG+D +GN+TTLGRGGSDT+ VA+AAA+KAD C+IYTDVDGVYT Sbjct: 121 VRADLKDGTIVVVAGFQGIDKDGNVTTLGRGGSDTSAVAMAAAMKADVCEIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDP + AR++DKI+++EMLE+ASLG+KVLQIR+VEFA KYNV + V SF + GT++ Sbjct: 181 TDPNICEDARKIDKISYDEMLELASLGAKVLQIRSVEFAKKYNVDIHVRSSFNDNQGTMV 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300 T +D++ ME ++SGIA++++EAK+ + GVPD PG+A KIL +S AN+ VDMIVQNV+ Sbjct: 241 TKEDKD--MEAVLVSGIAYDKNEAKIAVLGVPDKPGIAAKILSSLSDANISVDMIVQNVS 298 Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360 + TDFTFTV + D+ AL I K+ A I A D +I+KVSIVGVGMRSHAGVA++ Sbjct: 299 GGDLTDFTFTVTKADFKKALAITKEIATEIKATGVSADESISKVSIVGVGMRSHAGVATK 358 Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFEL 404 MF+ LA E INIQMISTSEIKVSVVI+ KY ELAVR LH AF L Sbjct: 359 MFQTLANEGINIQMISTSEIKVSVVIDAKYTELAVRVLHEAFGL 402 Lambda K H 0.317 0.133 0.362 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: 451 Number of extensions: 13 Number of successful extensions: 2 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: 412 Length of database: 405 Length adjustment: 31 Effective length of query: 381 Effective length of database: 374 Effective search space: 142494 Effective search space used: 142494 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: 50 (23.9 bits)
Align candidate WP_004511964.1 GMET_RS09500 (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.22924.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-136 442.0 17.4 1.2e-136 441.9 17.4 1.0 1 lcl|NCBI__GCF_000012925.1:WP_004511964.1 GMET_RS09500 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012925.1:WP_004511964.1 GMET_RS09500 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 441.9 17.4 1.2e-136 1.2e-136 1 406 [. 1 402 [. 1 403 [. 0.97 Alignments for each domain: == domain 1 score: 441.9 bits; conditional E-value: 1.2e-136 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + l+VqK+GGts+gs+eri+++ak+v k++ g+++vVVvSAms++t++lv+la + + + + + lcl|NCBI__GCF_000012925.1:WP_004511964.1 1 MALVVQKYGGTSMGSIERIRNVAKRVAKTYDAGNDMVVVVSAMSGETNKLVALA------NEVCEFPDN 63 579***************************************************......8999***** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re d lv+ GE++s+all++ l+ g+ka++++g++ +i+Td+ f +A+i+e+ ++ L++g+iv lcl|NCBI__GCF_000012925.1:WP_004511964.1 64 REYDVLVASGEQVSIALLAMCLKSMGYKAKSYHGWQVPIITDSVFSKARIEEIPD-AKVRADLKDGTIV 131 *****************************************************98.99*********** PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G +++G++TtLGRGGSD++A+++aaa+kAd +eiyTDV+GvyttDP++ e+a+kidkisy+E+ lcl|NCBI__GCF_000012925.1:WP_004511964.1 132 VVAGFQGIDKDGNVTTLGRGGSDTSAVAMAAAMKADVCEIYTDVDGVYTTDPNICEDARKIDKISYDEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltveg 273 lelA+lGakvl+ r++e+a++++v i vrss++ ++gT +t+ ++e lv++ia++kn a+++v lcl|NCBI__GCF_000012925.1:WP_004511964.1 201 LELASLGAKVLQIRSVEFAKKYNVDIHVRSSFNDNQGTMVTKedkDMEA-VLVSGIAYDKNEAKIAVL- 267 *****************************************97433444.6*****************. PP TIGR00656 274 egmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslev 339 g+ +k+gi+a+i + L++++i+vd+i+q s t+ +++v + d ++a ++ ke ++++ + ++ lcl|NCBI__GCF_000012925.1:WP_004511964.1 268 -GVPDKPGIAAKILSSLSDANISVDMIVQNVSGgdlTDFTFTVTKADFKKALAITKEIATEIKATGVSA 335 .9***************************9988889**********************99999****** PP TIGR00656 340 eedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 +e + +vsivg+g++++ Gva+++f+ l++++ini mis+se+k+sv++d k++e avr lhe++ + lcl|NCBI__GCF_000012925.1:WP_004511964.1 336 DESISKVSIVGVGMRSHAGVATKMFQTLANEGINIQMISTSEIKVSVVIDAKYTELAVRVLHEAFGL 402 ***************************************************************9965 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (405 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: 00:00:00.01 # Mc/sec: 11.46 // [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