Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_085772645.1 B1812_RS16990 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_002117405.1:WP_085772645.1 Length = 411 Score = 402 bits (1034), Expect = e-117 Identities = 220/409 (53%), Positives = 289/409 (70%), Gaps = 6/409 (1%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 M +V KFGGTSV TVERI VA VK+ G D+ VVVSAMSG+TN L+ K+ + Sbjct: 1 MPRLVMKFGGTSVATVERIHNVARHVKREIAAGYDVAVVVSAMSGKTNELVAWCKEAARL 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120 RE D +V++GEQVT LLA+AL +GV A S+ G Q +LTD++H ARI+ I+ + Sbjct: 61 HDMREYDAVVASGEQVTSGLLAIALQAQGVAARSWQGWQTPVLTDASHGAARIMSIEPEG 120 Query: 121 IQRDIKAGRVVVVAGFQGVDE-KGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY 179 I VVAGFQG+ + G ITTLGRGGSDT+ VALAAA+ A+ C IYTDVDGVY Sbjct: 121 IIEGFGRKETAVVAGFQGIHKPSGRITTLGRGGSDTSAVALAAAIGAERCDIYTDVDGVY 180 Query: 180 TTDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEG---- 235 TTDPRVV+KA+R+D+I FEEMLEMASLG+KV+Q+R+VE A K+ +P V SF + Sbjct: 181 TTDPRVVSKARRMDRIAFEEMLEMASLGAKVMQVRSVELALKHDMPTYVRSSFDDPDDPR 240 Query: 236 PGTLITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIV 295 PGTLI EE+ ME +++G+AF+RDEA++T+R V D PGVA + P++ A + VDMIV Sbjct: 241 PGTLICR-EEDIMESQVVTGVAFSRDEAQITLRRVIDKPGVAASVFMPLAEAGINVDMIV 299 Query: 296 QNVAHDNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAG 355 Q ++ D+ TD TFTV +D++ A +L+ E+G G ++AKVS+VGVGMRSHAG Sbjct: 300 QTISDDSMTDMTFTVAASDFDRARALLEKAKGEIGFAALAGAKDVAKVSVVGVGMRSHAG 359 Query: 356 VASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404 VA++ F ALA++ +NI+ ISTSEIK SV+I+ Y ELAVR LHT + LD Sbjct: 360 VAAKGFRALAEKGVNIRAISTSEIKFSVLIDAAYTELAVRTLHTLYGLD 408 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: 423 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: 412 Length of database: 411 Length adjustment: 31 Effective length of query: 381 Effective length of database: 380 Effective search space: 144780 Effective search space used: 144780 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_085772645.1 B1812_RS16990 (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.9047.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-128 413.1 6.8 7.1e-128 413.0 6.8 1.0 1 lcl|NCBI__GCF_002117405.1:WP_085772645.1 B1812_RS16990 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002117405.1:WP_085772645.1 B1812_RS16990 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 413.0 6.8 7.1e-128 7.1e-128 4 404 .. 4 405 .. 1 408 [. 0.95 Alignments for each domain: == domain 1 score: 413.0 bits; conditional E-value: 7.1e-128 TIGR00656 4 iVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprer 72 V+KFGGtsv+ +eri+++a++v++e+ g++v VVvSAms++t+elv+ + re lcl|NCBI__GCF_002117405.1:WP_085772645.1 4 LVMKFGGTSVATVERIHNVARHVKREIAAGYDVAVVVSAMSGKTNELVAWC------KEAARLHDMREY 66 69*************************************************......666777789*** PP TIGR00656 73 delvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvva 141 d +v+ GE+++s ll+ al+++gv a++ +g++ ++lTd+++g A+i ++++ e ++e ++ vva lcl|NCBI__GCF_002117405.1:WP_085772645.1 67 DAVVASGEQVTSGLLAIALQAQGVAARSWQGWQTPVLTDASHGAARIMSIEP-EGIIEGFGRKETAVVA 134 ****************************************************.99999999999***** PP TIGR00656 142 GFiGat.eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEale 209 GF+G G+iTtLGRGGSD++A++laaa+ A+r++iyTDV+GvyttDPrvv++a+++d+i++eE+le lcl|NCBI__GCF_002117405.1:WP_085772645.1 135 GFQGIHkPSGRITTLGRGGSDTSAVALAAAIGAERCDIYTDVDGVYTTDPRVVSKARRMDRIAFEEMLE 203 ****75269************************************************************ PP TIGR00656 210 lAtlGakvlhpralelaveakvpilvrsske....keegTlitn..kkensslvkaialeknvarltve 272 +A+lGakv++ r++ela + ++p vrss++ ++ gTli+ + +s++v+++a++++ a++t++ lcl|NCBI__GCF_002117405.1:WP_085772645.1 204 MASLGAKVMQVRSVELALKHDMPTYVRSSFDdpddPRPGTLICReeDIMESQVVTGVAFSRDEAQITLR 272 *****************************853222569*****966444457***************** PP TIGR00656 273 gegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesle 338 +++k+g++a +f Lae++invd+i+qt s+ t+++++v+ d d+a ++L++ +g++++ l lcl|NCBI__GCF_002117405.1:WP_085772645.1 273 --RVIDKPGVAASVFMPLAEAGINVDMIVQTISDdsmTDMTFTVAASDFDRARALLEKAKGEIGFAALA 339 ..******************************99999******************************** PP TIGR00656 339 veedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekl 404 +d+a+vs+vg+g++++ Gva++ f al+ek++ni is+se+k svl+d +++e avr+lh + lcl|NCBI__GCF_002117405.1:WP_085772645.1 340 GAKDVAKVSVVGVGMRSHAGVAAKGFRALAEKGVNIRAISTSEIKFSVLIDAAYTELAVRTLHTLY 405 ***************************************************************866 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: 00:00:00.01 # Mc/sec: 9.90 // [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