Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_018123593.1 B149_RS0102550 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_000375485.1:WP_018123593.1 Length = 414 Score = 391 bits (1004), Expect = e-113 Identities = 212/412 (51%), Positives = 287/412 (69%), Gaps = 2/412 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 M ++VQKFGGTSV ++ +V +KV + G+ VVVV+SAM+GETNRL+ LAN+ + Sbjct: 1 MNIVVQKFGGTSVASLSTQLEVMKKVMRPYREGNKVVVVLSAMAGETNRLLALANEWVTT 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P E+D +VSTGEQV+ AL SM L +G+ A S G Q I TD + KARI+ ID T Sbjct: 61 PDAAEMDSLVSTGEQVSCALFSMLLKNQGIRARSVLGFQAPIRTDCSFGKARIVDIDTTA 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 + L+ V+VVAGFQG + ITTLGRGGSDT+ VA+AAAL A+ C+IYTDV GV+T Sbjct: 121 LFEMLEDHDVLVVAGFQGCEDGKRITTLGRGGSDTSAVAMAAALNAEVCEIYTDVPGVFT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDP + A ++D+I ++EMLEMAS+G+KVLQIR+VEFA KYNV + V +F + GTL+ Sbjct: 181 TDPNICSDATKIDRIAYDEMLEMASMGAKVLQIRSVEFAKKYNVTVHVRSTFSDEQGTLV 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300 E++ ME ++SGIA+++D+A++T+ V D PGV+ I P++ + VDMIVQN + Sbjct: 241 C--QEDDDMEAVLVSGIAYDKDQARITLVHVEDRPGVSAAIFSPLAERKILVDMIVQNPS 298 Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360 + TD TFTV + D L++L+ IG + + ++++KVSI+GVGMR+H+GVASR Sbjct: 299 KGSKTDMTFTVPKADIKQTLKVLEDLRYEIGYEDLLSSSDVSKVSIIGVGMRNHSGVASR 358 Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE 412 F ALA E+INI MISTSEIKVS +I+EKY ELAVR LH F L Q E Sbjct: 359 AFRALADENINILMISTSEIKVSFLIDEKYTELAVRTLHKEFALHEGGIQQE 410 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: 417 Number of extensions: 12 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: 414 Length adjustment: 31 Effective length of query: 381 Effective length of database: 383 Effective search space: 145923 Effective search space used: 145923 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_018123593.1 B149_RS0102550 (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.22015.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-139 450.2 6.8 4.1e-139 450.0 6.8 1.0 1 lcl|NCBI__GCF_000375485.1:WP_018123593.1 B149_RS0102550 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000375485.1:WP_018123593.1 B149_RS0102550 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 450.0 6.8 4.1e-139 4.1e-139 1 406 [. 1 402 [. 1 403 [. 0.98 Alignments for each domain: == domain 1 score: 450.0 bits; conditional E-value: 4.1e-139 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 ++++VqKFGGtsv+s + ++ k+v++ ++eg+kvvVV+SAm+++t++l++la + + lcl|NCBI__GCF_000375485.1:WP_018123593.1 1 MNIVVQKFGGTSVASLSTQLEVMKKVMRPYREGNKVVVVLSAMAGETNRLLALA------NEWVTTPDA 63 689***************************************************......78889999* PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 +e+d lvs+GE++s al+s++l+++g +a+++ g +a+i+Td +fg+A+i +++t L+e+Le++++ lcl|NCBI__GCF_000375485.1:WP_018123593.1 64 AEMDSLVSTGEQVSCALFSMLLKNQGIRARSVLGFQAPIRTDCSFGKARIVDIDT-TALFEMLEDHDVL 131 *******************************************************.************* PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G + +iTtLGRGGSD++A+++aaal+A+ +eiyTDV+Gv+ttDP++ ++a kid+i+y+E+ lcl|NCBI__GCF_000375485.1:WP_018123593.1 132 VVAGFQGCEDGKRITTLGRGGSDTSAVAMAAALNAEVCEIYTDVPGVFTTDPNICSDATKIDRIAYDEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltveg 273 le+A++Gakvl+ r++e+a++++v + vrs+++ e+gTl+++ ++e lv++ia++k++ar+t++ lcl|NCBI__GCF_000375485.1:WP_018123593.1 201 LEMASMGAKVLQIRSVEFAKKYNVTVHVRSTFSDEQGTLVCQeddDMEAV-LVSGIAYDKDQARITLV- 267 *****************************************976555555.*****************. PP TIGR00656 274 egmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslev 339 ++ +++g+ a if+ Lae++i vd+i+q +s+ t+++++v + d++++ k+L++ ++++e+l lcl|NCBI__GCF_000375485.1:WP_018123593.1 268 -HVEDRPGVSAAIFSPLAERKILVDMIVQNPSKgskTDMTFTVPKADIKQTLKVLEDLRYEIGYEDLLS 335 .******************************98889********************************* PP TIGR00656 340 eedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 +d+ +vsi+g+g+++++Gvas++f al+++ninilmis+se+k+s+l+dek++e avr+lh+++ + lcl|NCBI__GCF_000375485.1:WP_018123593.1 336 SSDVSKVSIIGVGMRNHSGVASRAFRALADENINILMISTSEIKVSFLIDEKYTELAVRTLHKEFAL 402 ****************************************************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (414 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: 10.46 // [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