Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_020177124.1 A3OQ_RS0119490 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_000385335.1:WP_020177124.1 Length = 412 Score = 398 bits (1023), Expect = e-115 Identities = 225/412 (54%), Positives = 289/412 (70%), Gaps = 10/412 (2%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 MA +V KFGGTSV V+RI VA V++ + G DI VVVSAMSG+TN L+D + S Sbjct: 1 MARLVMKFGGTSVADVDRIRNVARHVQREVEAGYDIAVVVSAMSGKTNELVDWCRVASRF 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120 PRE D +V+ GEQVT LLA+ L G+PA S+ G QV ILT AH ARI ID Sbjct: 61 YDPREYDAVVAAGEQVTAGLLAIVLQDMGIPARSWQGWQVPILTSDAHGSARIADIDGSA 120 Query: 121 IQRDIKAGR-VVVVAGFQGV-DEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 178 I + + + V V+AGFQG+ E G I+TLGRGGSDT+ VA+AAA+KA+ C IYTDVDGV Sbjct: 121 IFKAFEERKEVAVIAGFQGLHQETGRISTLGRGGSDTSAVAIAAAIKAERCDIYTDVDGV 180 Query: 179 YTTDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQE---- 234 YTTDPR+VAKA+RLD++ FEEMLEMASLG+KVLQ+R+VE A Y V V SF + Sbjct: 181 YTTDPRIVAKARRLDRVAFEEMLEMASLGAKVLQVRSVELAMVYKVKTFVRSSFDDPLDP 240 Query: 235 GPGTLITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMI 294 PGTLI DEE+ +EQ +++GIAF+R+EA++T+R V D PGVA I P++ AN+ VDMI Sbjct: 241 KPGTLI-CDEEDILEQQVVTGIAFSREEAQITLRRVADNPGVAAAIFMPLAEANINVDMI 299 Query: 295 VQNVAHDNT--TDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRS 352 +Q V DNT TD TFTV D+ A +L+ ++G G +++ K+S +GVGMRS Sbjct: 300 IQ-VVSDNTVATDITFTVPVVDFERARAILEKAQPQIGYGTLQGASDVVKISAIGVGMRS 358 Query: 353 HAGVASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404 H GVA+R F+ALA++ INI+ I+TSEIK SV+IE Y ELAVR LH+ + LD Sbjct: 359 HPGVAARAFKALAEKGINIRAITTSEIKFSVLIEAAYTELAVRTLHSLYGLD 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: 421 Number of extensions: 16 Number of successful extensions: 6 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: 412 Length adjustment: 31 Effective length of query: 381 Effective length of database: 381 Effective search space: 145161 Effective search space used: 145161 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_020177124.1 A3OQ_RS0119490 (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.1072.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-125 405.7 5.1 1.3e-125 405.5 5.1 1.0 1 lcl|NCBI__GCF_000385335.1:WP_020177124.1 A3OQ_RS0119490 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000385335.1:WP_020177124.1 A3OQ_RS0119490 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.5 5.1 1.3e-125 1.3e-125 4 404 .. 4 407 .. 1 410 [. 0.95 Alignments for each domain: == domain 1 score: 405.5 bits; conditional E-value: 1.3e-125 TIGR00656 4 iVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprer 72 V+KFGGtsv++++ri+++a++v +e++ g++ VVvSAms++t+elv+ ++ s pre lcl|NCBI__GCF_000385335.1:WP_020177124.1 4 LVMKFGGTSVADVDRIRNVARHVQREVEAGYDIAVVVSAMSGKTNELVDWC------RVASRFYDPREY 66 69*************************************************......7999999***** PP TIGR00656 73 delvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLee.giivvv 140 d +v+ GE++++ ll+ +l++ g a++ +g++ +ilT+d +g+A+i +++ + +++ ee + + v+ lcl|NCBI__GCF_000385335.1:WP_020177124.1 67 DAVVAAGEQVTAGLLAIVLQDMGIPARSWQGWQVPILTSDAHGSARIADIDG-SAIFKAFEErKEVAVI 134 ****************************************************.99999988725699** PP TIGR00656 141 aGFiGa.teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 aGF+G +e G+i tLGRGGSD++A+++aaa+kA+r++iyTDV+GvyttDPr+v +a+++d++++eE+l lcl|NCBI__GCF_000385335.1:WP_020177124.1 135 AGFQGLhQETGRISTLGRGGSDTSAVAIAAAIKAERCDIYTDVDGVYTTDPRIVAKARRLDRVAFEEML 203 *****72567*********************************************************** PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsske....keegTlitn..kkensslvkaialeknvarltv 271 e+A+lGakvl+ r++ela+ +kv+ +vrss++ ++ gTli++ + ++++v++ia++++ a++t+ lcl|NCBI__GCF_000385335.1:WP_020177124.1 204 EMASLGAKVLQVRSVELAMVYKVKTFVRSSFDdpldPKPGTLICDeeDILEQQVVTGIAFSREEAQITL 272 ******************************963332579*****955344457**************** PP TIGR00656 272 egegmlgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaeles 336 + +++++g++a if Lae++invd+i+q s+ t+i+++v d ++a ++L++ + ++++ lcl|NCBI__GCF_000385335.1:WP_020177124.1 273 R--RVADNPGVAAAIFMPLAEANINVDMIIQVVSDntvaTDITFTVPVVDFERARAILEKAQPQIGYGT 339 *..****************************999889999***************************** PP TIGR00656 337 leveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekl 404 l+ +d+ ++s++g+g++++pGva+++fkal+ek+ini i++se+k svl++ +++e avr+lh+ + lcl|NCBI__GCF_000385335.1:WP_020177124.1 340 LQGASDVVKISAIGVGMRSHPGVAARAFKALAEKGINIRAITTSEIKFSVLIEAAYTELAVRTLHSLY 407 *****************************************************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (412 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.94 // [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