Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011736129.1 PPRO_RS11225 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_000015045.1:WP_011736129.1 Length = 404 Score = 469 bits (1206), Expect = e-137 Identities = 241/404 (59%), Positives = 309/404 (76%), Gaps = 2/404 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MAL+VQK+GGTSVG +RI VA++V + +AG++++VV+SAMSGETNRL+ LAN++ E Sbjct: 1 MALVVQKYGGTSVGNPDRIRNVAKRVARTCDAGNELIVVLSAMSGETNRLVSLANEMCEL 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P RE D +VSTGEQVTIALL+M L G A SY G QV I+TD TKARI I+D Sbjct: 61 PHGREYDTLVSTGEQVTIALLAMHLKSMGYKAKSYLGWQVPIITDDTATKARIERIEDAR 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 IRADL G +V+VAGFQG+D NGNITTLGRGGSDT+ VALAAALKAD C+IYTDVDGVYT Sbjct: 121 IRADLNEGTIVIVAGFQGIDANGNITTLGRGGSDTSAVALAAALKADVCEIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDP + +AR+++ I+++EMLE+ASLG+KVLQIR+VEFA KYNV + V S + GT++ Sbjct: 181 TDPNICKEARKMESISYDEMLELASLGAKVLQIRSVEFAKKYNVNVHVRSSLNDNTGTMV 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300 T E + ME ++SG+A++++EAK+ + GV D PG A +IL +S A++ VDMIVQNV+ Sbjct: 241 T--RENKDMEGILVSGVAYDKNEAKIVVMGVADKPGTAARILSALSDASIPVDMIVQNVS 298 Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360 DFTFTV++ D A++I Q A + ARE I D I+K+SIVG+GMRSHAGVA+ Sbjct: 299 QAGLADFTFTVNKTDLKQAMQITNQVAGELQAREVISDEKISKISIVGLGMRSHAGVATT 358 Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFEL 404 MF ALA +INIQ ISTSEIK+SV+I++KY ELAVR LH AF L Sbjct: 359 MFSALAAANINIQTISTSEIKISVIIDDKYTELAVRVLHEAFNL 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: 19 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: 404 Length adjustment: 31 Effective length of query: 381 Effective length of database: 373 Effective search space: 142113 Effective search space used: 142113 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_011736129.1 PPRO_RS11225 (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.19617.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-135 437.1 15.3 3.7e-135 437.0 15.3 1.0 1 lcl|NCBI__GCF_000015045.1:WP_011736129.1 PPRO_RS11225 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011736129.1 PPRO_RS11225 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 437.0 15.3 3.7e-135 3.7e-135 1 406 [. 1 402 [. 1 403 [. 0.98 Alignments for each domain: == domain 1 score: 437.0 bits; conditional E-value: 3.7e-135 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + l+VqK+GGtsvg+ +ri+++ak+v ++ g++ +VV+SAms++t++lv+la + + + + lcl|NCBI__GCF_000015045.1:WP_011736129.1 1 MALVVQKYGGTSVGNPDRIRNVAKRVARTCDAGNELIVVLSAMSGETNRLVSLA------NEMCELPHG 63 579***************************************************......899****** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re d+lvs+GE++++all++ l+ g+ka+++ g++ +i+Tdd+ ++A+i++++ r+ L+eg+iv lcl|NCBI__GCF_000015045.1:WP_011736129.1 64 REYDTLVSTGEQVTIALLAMHLKSMGYKAKSYLGWQVPIITDDTATKARIERIED-ARIRADLNEGTIV 131 ******************************************************9.9************ PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 +vaGF+G + +G+iTtLGRGGSD++A++laaalkAd +eiyTDV+GvyttDP++ +ea+k+++isy+E+ lcl|NCBI__GCF_000015045.1:WP_011736129.1 132 IVAGFQGIDANGNITTLGRGGSDTSAVALAAALKADVCEIYTDVDGVYTTDPNICKEARKMESISYDEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltveg 273 lelA+lGakvl+ r++e+a++++v++ vrss + + gT +t ++e+ lv+++a++kn a+++v+ lcl|NCBI__GCF_000015045.1:WP_011736129.1 201 LELASLGAKVLQIRSVEFAKKYNVNVHVRSSLNDNTGTMVTRenkDMEG-ILVSGVAYDKNEAKIVVM- 267 *****************************************96444444.5*****************. PP TIGR00656 274 egmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslev 339 g+++k+g++a+i +aL++++i vd+i+q s+ + +++v+++d+++a ++ +++ g+++ +++ lcl|NCBI__GCF_000015045.1:WP_011736129.1 268 -GVADKPGTAARILSALSDASIPVDMIVQNVSQaglADFTFTVNKTDLKQAMQITNQVAGELQAREVIS 335 .9****************************999888999****************************** PP TIGR00656 340 eedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 +e++ ++sivg g++++ Gva+ +f+al+ nini +is+se+kisv++d k++e avr lhe++ + lcl|NCBI__GCF_000015045.1:WP_011736129.1 336 DEKISKISIVGLGMRSHAGVATTMFSALAAANINIQTISTSEIKISVIIDDKYTELAVRVLHEAFNL 402 ***************************************************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (404 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: 10.29 // [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