Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_028950461.1 Q385_RS0104175 aspartate kinase
Query= SwissProt::C3JXY0 (413 letters) >NCBI__GCF_000619805.1:WP_028950461.1 Length = 411 Score = 454 bits (1167), Expect = e-132 Identities = 237/403 (58%), Positives = 307/403 (76%), Gaps = 3/403 (0%) Query: 1 MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60 M LIVQK+GGTSVG++ERI+ VA K+KK D G+ +VVV SAM+GET+RLI L + +S Sbjct: 1 MPLIVQKYGGTSVGNIERIKNVAKKIKKAVDEGNQVVVVSSAMTGETDRLIGLTRELSS- 59 Query: 61 QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120 +P PRE D++V+TGEQV I L+A+AL + GVPA+S TG QV I+TD+ HTKARI +ID Sbjct: 60 -RPNPREQDMVVATGEQVAIGLVAIALQELGVPAISLTGWQVPIITDNVHTKARIKKIDT 118 Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180 +IR L G+VV+VAGFQGV E G+ITTLGRGGSDT+ VALAAALKAD C+IYTDV GV Sbjct: 119 HRIRKHLDEGKVVIVAGFQGVSEDGDITTLGRGGSDTSAVALAAALKADVCEIYTDVTGV 178 Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240 +T DPR+V A+++ I++EEM+EMASLGSKV+QIR+VEF KY V + V SF + GT Sbjct: 179 FTADPRIVENARKIPVISYEEMMEMASLGSKVMQIRSVEFGAKYGVKIHVRSSFNDEEGT 238 Query: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV 300 I ++E E ME+ ++ GI+ E+++T+ VPD PGVA K+ + NI VDMIVQNV Sbjct: 239 WI-MEENEEMEKVVVRGISHELKESRITVVRVPDKPGVAAKLFKALGEKNIVVDMIVQNV 297 Query: 301 SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360 SH TD +FTV++ + D AE I + AKE+GA +V + KIAK+S+VG+GM++H+GVA Sbjct: 298 SHKGFTDISFTVNKTDADYAEEIAREVAKEVGAEDVERNDKIAKISVVGLGMKTHSGVAG 357 Query: 361 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAF 403 +MFE L KE INI ISTSEIK+S +I+EKY ELAVRALH AF Sbjct: 358 KMFEVLYKEGINIYAISTSEIKISCLIDEKYAELAVRALHEAF 400 Lambda K H 0.316 0.133 0.357 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: 468 Number of extensions: 13 Number of successful extensions: 4 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: 413 Length of database: 411 Length adjustment: 31 Effective length of query: 382 Effective length of database: 380 Effective search space: 145160 Effective search space used: 145160 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_028950461.1 Q385_RS0104175 (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.1283.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-143 462.2 15.5 9e-143 462.0 15.5 1.0 1 lcl|NCBI__GCF_000619805.1:WP_028950461.1 Q385_RS0104175 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000619805.1:WP_028950461.1 Q385_RS0104175 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 462.0 15.5 9e-143 9e-143 2 406 .. 2 402 .. 1 403 [. 0.98 Alignments for each domain: == domain 1 score: 462.0 bits; conditional E-value: 9e-143 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 liVqK+GGtsvg++erik++ak+++k++ eg++vvVV SAm ++td+l+ l+ + s+ ++pr lcl|NCBI__GCF_000619805.1:WP_028950461.1 2 PLIVQKYGGTSVGNIERIKNVAKKIKKAVDEGNQVVVVSSAMTGETDRLIGLT------RELSSRPNPR 64 59*************************************************99......899******* PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 e+d++v++GE++++ l++ al+elgv a++l+g++ +i+Td+ +++A+ik+++t +r+ + L+eg++v+ lcl|NCBI__GCF_000619805.1:WP_028950461.1 65 EQDMVVATGEQVAIGLVAIALQELGVPAISLTGWQVPIITDNVHTKARIKKIDT-HRIRKHLDEGKVVI 132 ******************************************************.************** PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 vaGF+G e+G+iTtLGRGGSD++A++laaalkAd +eiyTDV Gv+t+DPr+ve+a+ki+ isyeE++ lcl|NCBI__GCF_000619805.1:WP_028950461.1 133 VAGFQGVSEDGDITTLGRGGSDTSAVALAAALKADVCEIYTDVTGVFTADPRIVENARKIPVISYEEMM 201 ********************************************************************* PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitnkkens..slvkaialeknvarltvegeg 275 e+A+lG kv++ r++e+ +++v+i vrss++ eegT i++++e+ +v++i++e + +r+tv+ lcl|NCBI__GCF_000619805.1:WP_028950461.1 202 EMASLGSKVMQIRSVEFGAKYGVKIHVRSSFNDEEGTWIMEENEEMekVVVRGISHELKESRITVV--R 268 ****************************************9444333469****************..* PP TIGR00656 276 mlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslevee 341 + +k+g++a++fkaL+e++i vd+i+q s+ t+is++v+++d+d a+++ +e+ ++++ e++e + lcl|NCBI__GCF_000619805.1:WP_028950461.1 269 VPDKPGVAAKLFKALGEKNIVVDMIVQNVSHkgfTDISFTVNKTDADYAEEIAREVAKEVGAEDVERND 337 ****************************999999*********************************** PP TIGR00656 342 dlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 ++a++s+vg g++ ++Gva+++f++l +++ini is+se+kis l+dek+ae avr+lhe+++e lcl|NCBI__GCF_000619805.1:WP_028950461.1 338 KIAKISVVGLGMKTHSGVAGKMFEVLYKEGINIYAISTSEIKISCLIDEKYAELAVRALHEAFIE 402 ***************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (411 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: 00:00:00.02 # Mc/sec: 6.65 // [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