Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012970316.1 ALVIN_RS05455 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_000025485.1:WP_012970316.1 Length = 409 Score = 587 bits (1513), Expect = e-172 Identities = 305/409 (74%), Positives = 354/409 (86%), Gaps = 3/409 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MALIVQK+GGTSVG++ERI+ VAE+VK++R+ GD VVVVVSAMSGET+RLI LA Q+ E+ Sbjct: 1 MALIVQKYGGTSVGSIERIQAVAERVKRWRDQGDQVVVVVSAMSGETDRLIKLAKQLQER 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P PRELDV++STGEQVTIALLSMAL +G PA SYTG QV ILTDSAH KARI ID Sbjct: 61 PEPRELDVLLSTGEQVTIALLSMALTAQGCPARSYTGAQVHILTDSAHNKARIRDIDAAR 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 +RADL+AGRVVVVAGFQG+D G+ITTLGRGGSDT+ VA+AAALKADECQIYTDVDGVYT Sbjct: 121 VRADLEAGRVVVVAGFQGIDEQGDITTLGRGGSDTSAVAIAAALKADECQIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDPRV P+AR+LD+ITFEEMLEMASLGSKVLQIR+VEFAGKY VPLRVL SF+EG GTLI Sbjct: 181 TDPRVEPKARKLDRITFEEMLEMASLGSKVLQIRSVEFAGKYRVPLRVLSSFEEGEGTLI 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNV- 299 + +D + +E ISGIAF+RDEAKLT+ GVPD PGVA +ILGPI+ AN+EVDMIVQNV Sbjct: 241 SFEDND--VEDAKISGIAFSRDEAKLTVLGVPDQPGVAHRILGPIAEANIEVDMIVQNVG 298 Query: 300 AHDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVAS 359 A ++TTDFTFTVHRNDY ALEIL++TA +GAR+ GD +I K+S+VGVGMRSHAG+AS Sbjct: 299 ADESTTDFTFTVHRNDYAPALEILQRTANELGARQVTGDASIVKISLVGVGMRSHAGIAS 358 Query: 360 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPA 408 RMF +LAKE INI+MISTSEIK+SVV++EKYLEL VR LH AF L PA Sbjct: 359 RMFASLAKEGINIRMISTSEIKISVVVDEKYLELGVRTLHDAFGLGQPA 407 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: 550 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: 409 Length adjustment: 31 Effective length of query: 381 Effective length of database: 378 Effective search space: 144018 Effective search space used: 144018 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_012970316.1 ALVIN_RS05455 (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.16245.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-137 443.5 6.9 4.3e-137 443.3 6.9 1.0 1 lcl|NCBI__GCF_000025485.1:WP_012970316.1 ALVIN_RS05455 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025485.1:WP_012970316.1 ALVIN_RS05455 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 443.3 6.9 4.3e-137 4.3e-137 1 404 [. 1 401 [. 1 404 [. 0.97 Alignments for each domain: == domain 1 score: 443.3 bits; conditional E-value: 4.3e-137 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + liVqK+GGtsvgs+eri+++a++v++ +g++vvVVvSAms++td+l++la ++ ++ + p lcl|NCBI__GCF_000025485.1:WP_012970316.1 1 MALIVQKYGGTSVGSIERIQAVAERVKRWRDQGDQVVVVVSAMSGETDRLIKLA------KQLQERPEP 63 579***************************************************......9******** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re d l+s+GE++++alls+al ++g a++++g++ ilTd+ +++A+i++++ r+ Le g +v lcl|NCBI__GCF_000025485.1:WP_012970316.1 64 RELDVLLSTGEQVTIALLSMALTAQGCPARSYTGAQVHILTDSAHNKARIRDIDA-ARVRADLEAGRVV 131 *******************************************************.9************ PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G +e+G+iTtLGRGGSD++A+++aaalkAd+++iyTDV+GvyttDPrv ++a+k+d+i++eE+ lcl|NCBI__GCF_000025485.1:WP_012970316.1 132 VVAGFQGIDEQGDITTLGRGGSDTSAVAIAAALKADECQIYTDVDGVYTTDPRVEPKARKLDRITFEEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn..kkensslvkaialeknvarltvege 274 le+A+lG kvl+ r++e+a ++ vp++v ss+e+ egTli + ++ +++ia++++ a+ltv lcl|NCBI__GCF_000025485.1:WP_012970316.1 201 LEMASLGSKVLQIRSVEFAGKYRVPLRVLSSFEEGEGTLISFedNDVEDAKISGIAFSRDEAKLTVL-- 267 ****************************************87543334469****************.. PP TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaeleslev 339 g+ +++g++ +i + +ae++i vd+i+q + t+ +++v+++d a ++L+++ ++++ +++ lcl|NCBI__GCF_000025485.1:WP_012970316.1 268 GVPDQPGVAHRILGPIAEANIEVDMIVQNVGAdestTDFTFTVHRNDYAPALEILQRTANELGARQVTG 336 9**************************986555566********************************* PP TIGR00656 340 eedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekl 404 + + ++s+vg+g++++ G+as++f+ l++++ini mis+se+kisv+vdek++e vr+lh+++ lcl|NCBI__GCF_000025485.1:WP_012970316.1 337 DASIVKISLVGVGMRSHAGIASRMFASLAKEGINIRMISTSEIKISVVVDEKYLELGVRTLHDAF 401 **************************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (409 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: 10.52 // [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