Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_012047340.1 BBTA_RS35575 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_000015165.1:WP_012047340.1 Length = 418 Score = 396 bits (1018), Expect = e-115 Identities = 219/417 (52%), Positives = 289/417 (69%), Gaps = 14/417 (3%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 M +V KFGGTSV ++RI VA VK+ D G ++ VVVSAMSG+TN L+ + S Sbjct: 1 MGRLVLKFGGTSVANIDRIRNVARHVKREVDAGHEVAVVVSAMSGKTNELVAWCTEASPM 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQID-AQ 119 RE D +V++GEQVT LLA+ L G+ A S+ G Q+ I T AH ARI+ ID ++ Sbjct: 61 HDAREYDAVVASGEQVTSGLLAIVLQSMGIQARSWQGWQIPIKTSDAHASARIVDIDGSE 120 Query: 120 RIQRDIKAGRVVVVAGFQGVDEKGN-ITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 178 IQR + V V+AGFQG++ N ITTLGRGGSDT+ VA+AAA+KAD C IYTDVDGV Sbjct: 121 LIQRFQERKEVAVIAGFQGINPATNRITTLGRGGSDTSAVAIAAAIKADRCDIYTDVDGV 180 Query: 179 YTTDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSF------ 232 YTTDPRVV KA+RLDKI FE+MLE+AS G+KVLQ+R+VE +++P+ V SF Sbjct: 181 YTTDPRVVPKAKRLDKIAFEDMLELASQGAKVLQVRSVELGMVHNMPIFVRSSFDKPEDI 240 Query: 233 ----QEGPGTLITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAAN 288 ++ PGTLI EE+ ME +++GIAF++DEA++++R + D PG+A I GP++ AN Sbjct: 241 DPHAKQPPGTLI-CSEEQIMENHVVTGIAFSKDEAQISVRQIEDKPGIAASIFGPLADAN 299 Query: 289 VEVDMIVQNVAHD-NTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVG 347 + VDMIVQNV+ D TTD TFTV DYN A + + ++G + T++AKVS++G Sbjct: 300 INVDMIVQNVSEDGKTTDLTFTVPATDYNRARETIAAAKDKIGYQRLDTATDVAKVSVIG 359 Query: 348 VGMRSHAGVASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404 GMRSHAGVA++ F ALA NINI+ I+TSEIK SV+I+ Y ELAVR LHT + LD Sbjct: 360 SGMRSHAGVAAKGFAALAARNINIRAITTSEIKFSVLIDAVYTELAVRTLHTLYGLD 416 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: 414 Number of extensions: 14 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: 418 Length adjustment: 31 Effective length of query: 381 Effective length of database: 387 Effective search space: 147447 Effective search space used: 147447 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_012047340.1 BBTA_RS35575 (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.8319.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-125 404.4 6.7 3.3e-125 404.2 6.7 1.0 1 lcl|NCBI__GCF_000015165.1:WP_012047340.1 BBTA_RS35575 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015165.1:WP_012047340.1 BBTA_RS35575 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 404.2 6.7 3.3e-125 3.3e-125 4 404 .. 4 413 .. 1 416 [. 0.94 Alignments for each domain: == domain 1 score: 404.2 bits; conditional E-value: 3.3e-125 TIGR00656 4 iVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprer 72 V KFGGtsv++++ri+++a++v++e+ g++v VVvSAms++t+elv+ s re lcl|NCBI__GCF_000015165.1:WP_012047340.1 4 LVLKFGGTSVANIDRIRNVARHVKREVDAGHEVAVVVSAMSGKTNELVAWC------TEASPMHDAREY 66 699***********************************************9......678888899*** PP TIGR00656 73 delvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvva 141 d +v+ GE+++s ll+ +l+ g +a++ +g++ +i T+d + +A+i +++ e + e++ + v+a lcl|NCBI__GCF_000015165.1:WP_012047340.1 67 DAVVASGEQVTSGLLAIVLQSMGIQARSWQGWQIPIKTSDAHASARIVDIDGSELIQRFQERKEVAVIA 135 ****************************************************5555555566789**** PP TIGR00656 142 GFiGateeG.eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEale 209 GF+G + +iTtLGRGGSD++A+++aaa+kAdr++iyTDV+GvyttDPrvv++ak++dki++e++le lcl|NCBI__GCF_000015165.1:WP_012047340.1 136 GFQGINPATnRITTLGRGGSDTSAVAIAAAIKADRCDIYTDVDGVYTTDPRVVPKAKRLDKIAFEDMLE 204 ****9976528********************************************************** PP TIGR00656 210 lAtlGakvlhpralelaveakvpilvrsskek.........e.egTlitn...kkensslvkaialekn 265 lA++Gakvl+ r++el + ++pi+vrss++k + gTli++ +en ++v++ia++k+ lcl|NCBI__GCF_000015165.1:WP_012047340.1 205 LASQGAKVLQVRSVELGMVHNMPIFVRSSFDKpedidphakQpPGTLICSeeqIMEN-HVVTGIAFSKD 272 *****************************975333333332457*****96644555.5********** PP TIGR00656 266 varltvegegmlgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesg 330 a+++v+ ++ +k+gi+a if+ La+++invd+i+q se t+++++v +d ++a +++ + ++ lcl|NCBI__GCF_000015165.1:WP_012047340.1 273 EAQISVR--QIEDKPGIAASIFGPLADANINVDMIVQNVSEdgktTDLTFTVPATDYNRARETIAAAKD 339 *******..*******************************99999************************ PP TIGR00656 331 aaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrk 399 ++++++l++ d+a+vs++g+g++++ Gva++ f+al+ +nini i++se+k svl+d ++e avr+ lcl|NCBI__GCF_000015165.1:WP_012047340.1 340 KIGYQRLDTATDVAKVSVIGSGMRSHAGVAAKGFAALAARNINIRAITTSEIKFSVLIDAVYTELAVRT 408 ********************************************************************* PP TIGR00656 400 lhekl 404 lh + lcl|NCBI__GCF_000015165.1:WP_012047340.1 409 LHTLY 413 **866 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (418 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: 8.47 // [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