Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_019868370.1 METMI_RS0121545 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_000384075.1:WP_019868370.1 Length = 408 Score = 582 bits (1499), Expect = e-171 Identities = 305/405 (75%), Positives = 342/405 (84%), Gaps = 2/405 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MAL V KFGGTSVGTVERI+ VAEKVKK + GD +VVVVSAMSGETNRLIG+A ++ Q Sbjct: 1 MALYVYKFGGTSVGTVERIKAVAEKVKKAHDLGDQIVVVVSAMSGETNRLIGMAKEMQVQ 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P RE+DV++STGEQVT+ALLSMAL + G A SYTG QV+ILTDS+HTKARI IDD+ Sbjct: 61 PTEREMDVLISTGEQVTVALLSMALHEIGCDACSYTGGQVKILTDSSHTKARIRKIDDSR 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 I A LK G+VVVVAGFQGVD + NITTLGRGGSDTT VALAAALKADEC I+TDVDGVYT Sbjct: 121 IHAHLKQGKVVVVAGFQGVDEHDNITTLGRGGSDTTAVALAAALKADECLIFTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDPRV P+ARRLD+ITFEEMLEMASLGSKVLQIR+VEFAGKYNV LRVL SF EG GTLI Sbjct: 181 TDPRVEPKARRLDRITFEEMLEMASLGSKVLQIRSVEFAGKYNVALRVLSSFTEGNGTLI 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300 T EE ME +ISGIAFNRDEAKLTI GVPD PGVA ILGPI+ AN+EVDMI+QN+A Sbjct: 241 TY--EESPMESALISGIAFNRDEAKLTITGVPDRPGVASTILGPIADANIEVDMIIQNIA 298 Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360 D TTDFTFT+HRNDY A IL+QT A++GAR GD I KVSIVGVGMRSHAG+AS Sbjct: 299 DDATTDFTFTIHRNDYQRAKTILEQTCADLGARAVTGDDTIVKVSIVGVGMRSHAGIAST 358 Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 405 MF+ LA E INI+MISTSEIK+SVV++EKY+ELAVRALH AF+LD Sbjct: 359 MFKTLASEGINIRMISTSEIKISVVVDEKYMELAVRALHAAFKLD 403 Lambda K H 0.317 0.133 0.362 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: 547 Number of extensions: 17 Number of successful extensions: 3 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: 408 Length adjustment: 31 Effective length of query: 381 Effective length of database: 377 Effective search space: 143637 Effective search space used: 143637 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_019868370.1 METMI_RS0121545 (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.2415.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.1e-136 439.0 13.7 1e-135 438.8 13.7 1.0 1 lcl|NCBI__GCF_000384075.1:WP_019868370.1 METMI_RS0121545 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384075.1:WP_019868370.1 METMI_RS0121545 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 438.8 13.7 1e-135 1e-135 2 406 .. 2 402 .. 1 403 [. 0.98 Alignments for each domain: == domain 1 score: 438.8 bits; conditional E-value: 1e-135 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 l V KFGGtsvg +erik++a++v+k+ g++ vVVvSAms++t++l+ +a + ++ ++++r lcl|NCBI__GCF_000384075.1:WP_019868370.1 2 ALYVYKFGGTSVGTVERIKAVAEKVKKAHDLGDQIVVVVSAMSGETNRLIGMA------KEMQVQPTER 64 688*************************************************9......9********* PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 e+d l+s+GE++++alls+al+e g +a +++g++ ilTd+++++A+i++++ +r+ L++g++vv lcl|NCBI__GCF_000384075.1:WP_019868370.1 65 EMDVLISTGEQVTVALLSMALHEIGCDACSYTGGQVKILTDSSHTKARIRKIDD-SRIHAHLKQGKVVV 132 *****************************************************9.************** PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 vaGF+G +e+ +iTtLGRGGSD+tA++laaalkAd++ i+TDV+GvyttDPrv ++a+++d+i++eE+l lcl|NCBI__GCF_000384075.1:WP_019868370.1 133 VAGFQGVDEHDNITTLGRGGSDTTAVALAAALKADECLIFTDVDGVYTTDPRVEPKARRLDRITFEEML 201 ********************************************************************* PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltvege 274 e+A+lG kvl+ r++e+a +++v ++v ss+ + +gTlit +e l+++ia++++ a+lt++ lcl|NCBI__GCF_000384075.1:WP_019868370.1 202 EMASLGSKVLQIRSVEFAGKYNVALRVLSSFTEGNGTLITYeesPMESA-LISGIAFNRDEAKLTIT-- 267 ***************************************9866455555.*****************.. PP TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleve 340 g+ +++g++++i + +a+++i vd+i+q ++ t+ +++++++d ++ak +L+++ +++ + + + lcl|NCBI__GCF_000384075.1:WP_019868370.1 268 GVPDRPGVASTILGPIADANIEVDMIIQNIADdatTDFTFTIHRNDYQRAKTILEQTCADLGARAVTGD 336 9****************************998888********************************** PP TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 + +vsivg+g++++ G+as +fk l+ ++ini mis+se+kisv+vdek++e avr+lh+++++ lcl|NCBI__GCF_000384075.1:WP_019868370.1 337 DTIVKVSIVGVGMRSHAGIASTMFKTLASEGINIRMISTSEIKISVVVDEKYMELAVRALHAAFKL 402 **************************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (408 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: 12.10 // [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