Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_093427781.1 BM272_RS05535 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_900112605.1:WP_093427781.1 Length = 413 Score = 587 bits (1512), Expect = e-172 Identities = 308/409 (75%), Positives = 347/409 (84%), Gaps = 1/409 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MALIVQK+GGTSVGT ERIE VA++V R AGDDVVVVVSAMSGETNRL+ LA ++ + Sbjct: 1 MALIVQKYGGTSVGTPERIEAVADQVCARRRAGDDVVVVVSAMSGETNRLVELAGRVDPE 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 RELDV+++TGEQVTIALL+MAL +R A SYTG+QVRILTDSA+ KARIL ID H Sbjct: 61 ANGRELDVLLATGEQVTIALLAMALERRECEARSYTGSQVRILTDSAYNKARILDIDGEH 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 +R+DL GRVVVVAGFQG+D G+ITTLGRGGSDTT VALAAALKADECQI+TDVDGVYT Sbjct: 121 VRSDLGHGRVVVVAGFQGIDEAGSITTLGRGGSDTTAVALAAALKADECQIFTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDPRVVP ARRL++ITFEEMLEMASLGSKVLQIRAVEFAGKY+VPLRVL SFQEGPGTLI Sbjct: 181 TDPRVVPGARRLERITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLSSFQEGPGTLI 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300 T+D+ + MEQP+ISGIAFNRDEAK+TIRGVPDTPG+A +ILGPI AN+EVDMI+QNV Sbjct: 241 TVDEGDNDMEQPVISGIAFNRDEAKVTIRGVPDTPGIASRILGPIGDANIEVDMIIQNVG 300 Query: 301 HD-NTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVAS 359 D TTDFTFTVHRNDY +EIL+ A GARE GD I KVS+VGVGMRSHAG+A Sbjct: 301 ADGGTTDFTFTVHRNDYQRVVEILQALAEEFGAREVAGDDRIVKVSLVGVGMRSHAGIAG 360 Query: 360 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPA 408 MF ALA E INIQMI+TSEIK+SVVI+EKYLEL VRALH AF L+ A Sbjct: 361 TMFRALADEGINIQMIATSEIKISVVIDEKYLELGVRALHQAFNLEEAA 409 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: 588 Number of extensions: 18 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: 413 Length adjustment: 31 Effective length of query: 381 Effective length of database: 382 Effective search space: 145542 Effective search space used: 145542 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_093427781.1 BM272_RS05535 (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.1895032.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-133 430.9 6.8 2.9e-133 430.7 6.8 1.0 1 NCBI__GCF_900112605.1:WP_093427781.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900112605.1:WP_093427781.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 430.7 6.8 2.9e-133 2.9e-133 1 406 [. 1 405 [. 1 406 [. 0.98 Alignments for each domain: == domain 1 score: 430.7 bits; conditional E-value: 2.9e-133 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 + liVqK+GGtsvg eri+++a++v ++ + g++vvVVvSAms++t++lvela + e + re d NCBI__GCF_900112605.1:WP_093427781.1 1 MALIVQKYGGTSVGTPERIEAVADQVCARRRAGDDVVVVVSAMSGETNRLVELA------GRVDPEANGRELD 67 579***************************************************......799999******* PP TIGR00656 74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146 l+++GE++++all++al++++ +a++++g + ilTd+ +++A+i +++ e++ + L +g +vvvaGF+G NCBI__GCF_900112605.1:WP_093427781.1 68 VLLATGEQVTIALLAMALERRECEARSYTGSQVRILTDSAYNKARILDIDG-EHVRSDLGHGRVVVVAGFQGI 139 ***************************************************.9******************** PP TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219 +e G iTtLGRGGSD+tA++laaalkAd+++i+TDV+GvyttDPrvv+ a+++++i++eE+le+A+lG kvl+ NCBI__GCF_900112605.1:WP_093427781.1 140 DEAGSITTLGRGGSDTTAVALAAALKADECQIFTDVDGVYTTDPRVVPGARRLERITFEEMLEMASLGSKVLQ 212 ************************************************************************* PP TIGR00656 220 pralelaveakvpilvrsskekeegTlitn.....kkensslvkaialeknvarltvegegmlgkrgilaeif 287 ra+e+a +++vp++v ss+++ gTlit ++e++ ++++ia++++ a++t++ g+ + +gi+++i NCBI__GCF_900112605.1:WP_093427781.1 213 IRAVEFAGKYSVPLRVLSSFQEGPGTLITVdegdnDMEQP-VISGIAFNRDEAKVTIR--GVPDTPGIASRIL 282 *****************************87888788888.*****************..9************ PP TIGR00656 288 kaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglvea 356 + +++++i vd+i+q + t+ +++v+++d ++ +++L++ ++++ +++ + + +vs+vg+g++++ NCBI__GCF_900112605.1:WP_093427781.1 283 GPIGDANIEVDMIIQNVGAdggtTDFTFTVHRNDYQRVVEILQALAEEFGAREVAGDDRIVKVSLVGVGMRSH 355 ***************99877888************************************************** PP TIGR00656 357 pGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 G+a+ +f al++++ini mi++se+kisv++dek++e vr+lh+++ + NCBI__GCF_900112605.1:WP_093427781.1 356 AGIAGTMFRALADEGINIQMIATSEIKISVVIDEKYLELGVRALHQAFNL 405 **********************************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (413 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: 00:00:00.00 # Mc/sec: 25.53 // [ok]
This GapMind analysis is from Jul 25 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