Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_011373268.1 SUDEN_RS08595 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_000012965.1:WP_011373268.1 Length = 403 Score = 429 bits (1102), Expect = e-124 Identities = 222/402 (55%), Positives = 299/402 (74%), Gaps = 1/402 (0%) Query: 3 LIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQPV 62 LIVQKFGGTSVG +ERI+ VA +V + + G+D+VVVVSAMSGETN+L+ A+ S+ P Sbjct: 2 LIVQKFGGTSVGDLERIQNVASRVCETKKAGNDVVVVVSAMSGETNKLLAYAEHFSKNPQ 61 Query: 63 PRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQRIQ 122 E+D+++S+GE+VT +LLA+AL + G AVS TG + I+TD+ HTKARI +ID + Sbjct: 62 RAEVDMLLSSGERVTASLLAIALSEMGCEAVSMTGRKAGIVTDNIHTKARIEEIDPTAMN 121 Query: 123 RDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182 + IK G++VVVAGFQG+ + GN+TTLGRGGSD + VA+A A+KAD C+IYTDV G++TTD Sbjct: 122 KAIKDGKIVVVAGFQGISQDGNVTTLGRGGSDLSAVAIAGAIKADLCEIYTDVSGIFTTD 181 Query: 183 PRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLITL 242 PR+ +A++LDKI+++EMLE+ASLG+KVLQ R+VE A K +V L SF GTLIT Sbjct: 182 PRIEPRAKKLDKISYDEMLELASLGAKVLQNRSVELAKKLNVNLVTRTSFSNEEGTLIT- 240 Query: 243 DEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAHDN 302 EE ME+P++SGIA ++++A++++ GV D PG+A I +S +V +DMI+QNV HD Sbjct: 241 KEENIMEKPLVSGIALDKNQARVSLVGVKDRPGIASDIFTKLSNNSVNIDMIIQNVGHDG 300 Query: 303 TTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASRMFE 362 + FTV ND +A +V+ E E D NI KVSIVGVGM+SH GVA++ F Sbjct: 301 KANIDFTVPVNDLADAKKVMDSFVKESEVDEVSYDENICKVSIVGVGMKSHTGVAAKAFS 360 Query: 363 ALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404 +A ENINI MISTSEIK+S++I EKY ELAVRALH+A+ELD Sbjct: 361 VMAAENININMISTSEIKISMIIAEKYAELAVRALHSAYELD 402 Lambda K H 0.317 0.133 0.357 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: 459 Number of extensions: 15 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: 412 Length of database: 403 Length adjustment: 31 Effective length of query: 381 Effective length of database: 372 Effective search space: 141732 Effective search space used: 141732 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_011373268.1 SUDEN_RS08595 (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.9621.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-144 468.2 16.7 1.4e-144 468.0 16.7 1.0 1 lcl|NCBI__GCF_000012965.1:WP_011373268.1 SUDEN_RS08595 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012965.1:WP_011373268.1 SUDEN_RS08595 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 468.0 16.7 1.4e-144 1.4e-144 2 406 .. 1 401 [. 1 402 [. 0.98 Alignments for each domain: == domain 1 score: 468.0 bits; conditional E-value: 1.4e-144 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 +liVqKFGGtsvg+ eri+++a++v +++k g++vvVVvSAms++t++l++ a e +s+++ ++ lcl|NCBI__GCF_000012965.1:WP_011373268.1 1 MLIVQKFGGTSVGDLERIQNVASRVCETKKAGNDVVVVVSAMSGETNKLLAYA------EHFSKNPQRA 63 79***************************************************......7********* PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 e d+l+s GE+++++ll+ al e g +a++++g +agi+Td+ +++A+i+e+++ + + +++g+ivv lcl|NCBI__GCF_000012965.1:WP_011373268.1 64 EVDMLLSSGERVTASLLAIALSEMGCEAVSMTGRKAGIVTDNIHTKARIEEIDP-TAMNKAIKDGKIVV 131 ******************************************************.9************* PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 vaGF+G ++G++TtLGRGGSDl+A+++a a+kAd +eiyTDV+G++ttDPr+ ++akk+dkisy+E+l lcl|NCBI__GCF_000012965.1:WP_011373268.1 132 VAGFQGISQDGNVTTLGRGGSDLSAVAIAGAIKADLCEIYTDVSGIFTTDPRIEPRAKKLDKISYDEML 200 ********************************************************************* PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltvege 274 elA+lGakvl++r++ela++ +v++++r s+++eegTlit+ +e++ lv++ial+kn+ar++++ lcl|NCBI__GCF_000012965.1:WP_011373268.1 201 ELASLGAKVLQNRSVELAKKLNVNLVTRTSFSNEEGTLITKeenIMEKP-LVSGIALDKNQARVSLV-- 266 ****************************************966455666.*****************.. PP TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleve 340 g+ +++gi++ if+ L+++++n+d+i+q ++ +i+++v +d+ +akk++ +++++ e+++++++ lcl|NCBI__GCF_000012965.1:WP_011373268.1 267 GVKDRPGIASDIFTKLSNNSVNIDMIIQNVGHdgkANIDFTVPVNDLADAKKVMDSFVKESEVDEVSYD 335 99**************************9877777********************************** PP TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 e++++vsivg+g+++++Gva+++f++++ +nini mis+se+kis+++ ek+ae avr+lh+++e+ lcl|NCBI__GCF_000012965.1:WP_011373268.1 336 ENICKVSIVGVGMKSHTGVAAKAFSVMAAENININMISTSEIKISMIIAEKYAELAVRALHSAYEL 401 ***************************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (403 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.73 // [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