Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_092056201.1 BQ4888_RS08050 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_900111775.1:WP_092056201.1 Length = 410 Score = 498 bits (1281), Expect = e-145 Identities = 248/404 (61%), Positives = 324/404 (80%), Gaps = 2/404 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MAL+VQK+GGTSVGT++RI VA +V K + G+DVVV+VSAMSGETN+L+ LAN++ E Sbjct: 1 MALVVQKYGGTSVGTIDRIRNVARRVAKTYDEGNDVVVIVSAMSGETNKLVALANEMCEF 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P RE DV+V+TGEQV+++LLSM L G A SY G Q+ I+TDS +KARI IDD Sbjct: 61 PSEREYDVLVATGEQVSMSLLSMCLQSMGYKAKSYCGFQIPIVTDSVFSKARIEKIDDKK 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 IR DLK+G +++VAGFQG+D +GNITTLGRGGSDT+ VA+AAA+KAD C+I+TDVDG+YT Sbjct: 121 IREDLKSGTIIIVAGFQGIDKDGNITTLGRGGSDTSAVAVAAAIKADVCEIFTDVDGIYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDPR+VP+A +++K++++EMLEMASLGSKVLQIR+VEFA KY V + V SF + PGTL+ Sbjct: 181 TDPRIVPEASKMEKVSYDEMLEMASLGSKVLQIRSVEFAKKYGVVVHVRSSFNDNPGTLV 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300 T +D + ME ++SGI +N+DEAK+++ VPD PG+A KI P+S AN+ VDMI+QNV+ Sbjct: 241 TKEDAD--MEAVLVSGITYNKDEAKISVLRVPDKPGIAAKIFSPLSHANITVDMIIQNVS 298 Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360 H+ TD TFTV ++D+ AL+I+++TA GA D +IAKVSIVGVGMRSH+GVAS+ Sbjct: 299 HEGFTDLTFTVPKSDFKKALKIVEETAKETGAASVTSDESIAKVSIVGVGMRSHSGVASK 358 Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFEL 404 MF+ L++E +NIQMISTSEIKVS VI+ KY ELAVR LH AF+L Sbjct: 359 MFQTLSQEGVNIQMISTSEIKVSCVIDSKYTELAVRVLHEAFDL 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: 461 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: 410 Length adjustment: 31 Effective length of query: 381 Effective length of database: 379 Effective search space: 144399 Effective search space used: 144399 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_092056201.1 BQ4888_RS08050 (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.7521.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-137 444.9 14.5 1.6e-137 444.7 14.5 1.0 1 lcl|NCBI__GCF_900111775.1:WP_092056201.1 BQ4888_RS08050 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900111775.1:WP_092056201.1 BQ4888_RS08050 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 444.7 14.5 1.6e-137 1.6e-137 1 405 [. 1 401 [. 1 403 [. 0.98 Alignments for each domain: == domain 1 score: 444.7 bits; conditional E-value: 1.6e-137 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + l+VqK+GGtsvg ++ri+++a++v k++ eg++vvV+vSAms++t++lv+la + + + +s+ lcl|NCBI__GCF_900111775.1:WP_092056201.1 1 MALVVQKYGGTSVGTIDRIRNVARRVAKTYDEGNDVVVIVSAMSGETNKLVALA------NEMCEFPSE 63 579***************************************************......89******* PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re d lv++GE++s++lls+ l+ g+ka+++ g + +i+Td+ f +A+i++++ +++ e L+ g+i+ lcl|NCBI__GCF_900111775.1:WP_092056201.1 64 REYDVLVATGEQVSMSLLSMCLQSMGYKAKSYCGFQIPIVTDSVFSKARIEKIDD-KKIREDLKSGTII 131 ******************************************************9.************* PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 +vaGF+G +++G+iTtLGRGGSD++A+++aaa+kAd +ei+TDV+G+yttDPr+v+ea k++k+sy+E+ lcl|NCBI__GCF_900111775.1:WP_092056201.1 132 IVAGFQGIDKDGNITTLGRGGSDTSAVAVAAAIKADVCEIFTDVDGIYTTDPRIVPEASKMEKVSYDEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltveg 273 le+A+lG kvl+ r++e+a++++v + vrss++ + gTl+t+ ++e lv++i+++k+ a+++v lcl|NCBI__GCF_900111775.1:WP_092056201.1 201 LEMASLGSKVLQIRSVEFAKKYGVVVHVRSSFNDNPGTLVTKedaDMEAV-LVSGITYNKDEAKISVL- 267 *****************************************976555555.*****************. PP TIGR00656 274 egmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslev 339 + +k+gi+a+if+ L++++i vd+i+q s+ t+++++v + d ++a k+ +e+ ++++ s+ lcl|NCBI__GCF_900111775.1:WP_092056201.1 268 -RVPDKPGIAAKIFSPLSHANITVDMIIQNVSHegfTDLTFTVPKSDFKKALKIVEETAKETGAASVTS 335 .****************************9998899********************************* PP TIGR00656 340 eedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 +e +a+vsivg+g+++++Gvas++f+ l+++++ni mis+se+k+s ++d k++e avr lhe++ lcl|NCBI__GCF_900111775.1:WP_092056201.1 336 DESIAKVSIVGVGMRSHSGVASKMFQTLSQEGVNIQMISTSEIKVSCVIDSKYTELAVRVLHEAFD 401 ***************************************************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (410 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: 11.70 // [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