Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_018945701.1 B1A74_RS00670 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_001995255.1:WP_018945701.1 Length = 417 Score = 572 bits (1473), Expect = e-168 Identities = 295/410 (71%), Positives = 352/410 (85%), Gaps = 2/410 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 MAL+V KFGGTSVGT ERI VAE+ R+ G +V+VVSAMSGET+RL+ LA +++ + Sbjct: 1 MALLVLKFGGTSVGTTERIRAVAERALHLREEGHQLVIVVSAMSGETDRLLGLANELNPR 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120 RELDV++STGEQVTIALLAMAL +G PA SYTG QV I TDSA+ KARI ID R Sbjct: 61 VDGRELDVLLSTGEQVTIALLAMALEAKGCPARSYTGAQVTIRTDSAYNKARIRSIDDAR 120 Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 ++ D++AGR+VVVAGFQGVDE G ITTLGRGGSDTT VALAAALKADEC+IYTDVDGVYT Sbjct: 121 VRDDLEAGRIVVVAGFQGVDEDGAITTLGRGGSDTTAVALAAALKADECRIYTDVDGVYT 180 Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLI 240 TDPR+V +A+RL+++TFEEMLEMASLGSKVLQIRAVEFAGKY+VPLRVL SF EGPGTLI Sbjct: 181 TDPRLVPQARRLERVTFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLSSFGEGPGTLI 240 Query: 241 TLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAH 300 T +E+ ++EQ +++GIAFN++EA+LT+ GVPD PGVA +ILGP++ AN+EVDMIVQNV Sbjct: 241 TTEEDAAVEQALVAGIAFNQNEAQLTVGGVPDQPGVAHRILGPVADANIEVDMIVQNVGE 300 Query: 301 D-NTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASR 359 D TTDFTFTVHRNDY AL++LQG A E+GARE GD +I K+S+VGVGMRSHAG+ASR Sbjct: 301 DGRTTDFTFTVHRNDYEKALELLQGAADELGAREVSGDVHIVKISVVGVGMRSHAGIASR 360 Query: 360 MFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFEL-DAPAG 408 MFEAL++ENINI+MISTSEIK+SVV++EKYLELAVRALH AFEL + PAG Sbjct: 361 MFEALSRENINIRMISTSEIKISVVVDEKYLELAVRALHDAFELEEEPAG 410 Lambda K H 0.317 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: 542 Number of extensions: 14 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: 417 Length adjustment: 31 Effective length of query: 381 Effective length of database: 386 Effective search space: 147066 Effective search space used: 147066 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_018945701.1 B1A74_RS00670 (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.2716.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-135 438.7 6.8 1.3e-135 438.5 6.8 1.0 1 lcl|NCBI__GCF_001995255.1:WP_018945701.1 B1A74_RS00670 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001995255.1:WP_018945701.1 B1A74_RS00670 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 438.5 6.8 1.3e-135 1.3e-135 2 406 .. 2 404 .. 1 405 [. 0.98 Alignments for each domain: == domain 1 score: 438.5 bits; conditional E-value: 1.3e-135 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 l V KFGGtsvg +eri+++a+++l+ +eg++ v+VvSAms++td+l+ la + + + r lcl|NCBI__GCF_001995255.1:WP_018945701.1 2 ALLVLKFGGTSVGTTERIRAVAERALHLREEGHQLVIVVSAMSGETDRLLGLA------NELNPRVDGR 64 689**************************************************......89999***** PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 e d l+s+GE++++all++al+++g a++++g++ i+Td+ +++A+i++++ r+ + Le g ivv lcl|NCBI__GCF_001995255.1:WP_018945701.1 65 ELDVLLSTGEQVTIALLAMALEAKGCPARSYTGAQVTIRTDSAYNKARIRSIDD-ARVRDDLEAGRIVV 132 *****************************************************9.9************* PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 vaGF+G +e+G iTtLGRGGSD+tA++laaalkAd++ iyTDV+GvyttDPr+v++a++++++++eE+l lcl|NCBI__GCF_001995255.1:WP_018945701.1 133 VAGFQGVDEDGAITTLGRGGSDTTAVALAAALKADECRIYTDVDGVYTTDPRLVPQARRLERVTFEEML 201 ********************************************************************* PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltvege 274 e+A+lG kvl+ ra+e+a +++vp++v ss+ + gTlit ++ lv +ia+++n a+ltv lcl|NCBI__GCF_001995255.1:WP_018945701.1 202 EMASLGSKVLQIRAVEFAGKYNVPLRVLSSFGEGPGTLITTeedAAVEQALVAGIAFNQNEAQLTVG-- 268 ****************************************9555333347*****************.. PP TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaeleslev 339 g+ +++g++ +i + +a+++i vd+i+q +e t+ +++v+++d ++a ++L+ ++++ ++++ lcl|NCBI__GCF_001995255.1:WP_018945701.1 269 GVPDQPGVAHRILGPVADANIEVDMIVQNVGEdgrtTDFTFTVHRNDYEKALELLQGAADELGAREVSG 337 9*****************************999999********************************* PP TIGR00656 340 eedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 + + ++s+vg+g++++ G+as++f+al+ +nini mis+se+kisv+vdek++e avr+lh+++e+ lcl|NCBI__GCF_001995255.1:WP_018945701.1 338 DVHIVKISVVGVGMRSHAGIASRMFEALSRENINIRMISTSEIKISVVVDEKYLELAVRALHDAFEL 404 ****************************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (417 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: 10.31 // [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