Align Aspartokinase 3; Aspartate kinase 3; Aspartokinase III; EC 2.7.2.4 (characterized)
to candidate WP_022948116.1 H035_RS0106110 aspartate kinase
Query= SwissProt::P94417 (454 letters) >NCBI__GCF_000421465.1:WP_022948116.1 Length = 455 Score = 285 bits (729), Expect = 2e-81 Identities = 169/456 (37%), Positives = 263/456 (57%), Gaps = 16/456 (3%) Query: 3 VVKFGGSSLASGAQLDKVFHIVTSDPARKAVVVSAPGKHYAEDTKVTDLLIACA------ 56 V KFGGSS+AS Q++KV IV +D R+ VVVSAPG+ +++ KVTD LI A Sbjct: 6 VCKFGGSSVASAGQIEKVKQIVQADKRRRYVVVSAPGRSRSDEQKVTDHLINIATSGAHF 65 Query: 57 -EQYLATGSAPELAEAVVERYALIANELQLGQS-IIEKIRDDLFTLLEGDKSNPEQYLDA 114 +Q L+ + E +AV+E++ IA+EL + I+ ++ DL T LEGD+ + Sbjct: 66 RDQRLSI-TPNESKKAVLEKFTRIASELGVDAGDILASLKKDLATSLEGDRR-----IAF 119 Query: 115 VKASGEDNNAKLIAAYFRYKGVKAEYVNPKDAGLFVTNEPGNAQVLPESYQNLYRLRERD 174 + + GE NA+++A YF+ G+ A P+D GL V+++ A+VL E+Y N+ L D Sbjct: 120 LASRGEHYNARIVAEYFQNSGMTARARLPEDFGLLVSDDYLGAKVLSEAYANIAELTSED 179 Query: 175 GLIIFPGFFGFSKDGDVITFSRSGSDITGSILANGLQADLYENFTDVDAVYSVNPSFVEN 234 G+ + PGF+G ++ G+V FSR GSD+TG +A + AD YEN+TDV V+ V+PS + Sbjct: 180 GIAVIPGFYGVTQAGEVAVFSRGGSDLTGGEVAYAIDADTYENWTDVSGVFEVDPSLIPE 239 Query: 235 PKEISELTYREMRELSYAGFSVFHDEALIPAFRAGIPVQIKNTNNPSAEGTRVVSKRDNT 294 + I LT++E+R LS GF+VFH +A++ IP+ I+NTN P GT ++++R Sbjct: 240 ARAIPRLTFKEIRLLSSKGFNVFHLDAMLSCKERKIPIHIRNTNRPQEPGTIILNERVPE 299 Query: 295 NGPVVGIASDTGFCSIYISKYLMNREIGFGRRALQILEEHGLTYEHVPSGIDDMTIILRQ 354 G +VGIA IY+ K ++ E+GF LQI +E + H P+ DD+ +++ Q Sbjct: 300 EG-IVGIARLENMAYIYLEKDMLGEEVGFTASLLQIFQEFNINTYHYPTDKDDIAVLVNQ 358 Query: 355 GQMDAATERSVIKRIEEDLHADEVIVEHHLALIMVVGEAMRHNVGTTARAAKALSEAQVN 414 + + + IE+ L D + V ++LA+I VG ++ N A ALS + Sbjct: 359 DDL-TGNINDLRRHIEKKLKPDYMDVVYNLAIITPVGLGLKGNSYPIVDALLALSRNHIP 417 Query: 415 IEMINQGSSEVSMMFGVKEAEERKAVQALYQEFFAG 450 IEMI+Q S++ GV +A A++ LY + G Sbjct: 418 IEMIDQAPSQICFHIGVSQAVADDALKILYDQLIKG 453 Lambda K H 0.316 0.134 0.370 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: 480 Number of extensions: 20 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: 454 Length of database: 455 Length adjustment: 33 Effective length of query: 421 Effective length of database: 422 Effective search space: 177662 Effective search space used: 177662 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: 51 (24.3 bits)
Align candidate WP_022948116.1 H035_RS0106110 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (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/TIGR00657.hmm # target sequence database: /tmp/gapView.7955.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00657 [M=442] Accession: TIGR00657 Description: asp_kinases: aspartate kinase 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-72 231.4 0.0 1.3e-72 231.2 0.0 1.0 1 lcl|NCBI__GCF_000421465.1:WP_022948116.1 H035_RS0106110 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000421465.1:WP_022948116.1 H035_RS0106110 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 231.2 0.0 1.3e-72 1.3e-72 4 441 .. 5 451 .. 2 452 .. 0.88 Alignments for each domain: == domain 1 score: 231.2 bits; conditional E-value: 1.3e-72 TIGR00657 4 iVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAm.......agvTdaLvelaekvsseee... 62 V+KFGG+Sv+++ +i+kv +iv+++k+ + VVvSA+ ++vTd+L+++a + + ++ lcl|NCBI__GCF_000421465.1:WP_022948116.1 5 FVCKFGGSSVASAGQIEKVKQIVQADKRRR---YVVVSAPgrsrsdeQKVTDHLINIATSGAHFRDqrl 70 69*************************666...9999997444444469*********99888887566 PP TIGR00657 63 ....keliekirekhlealeela..sqalkeklkallekeleevkkereldlilsvGEklSaallaaal 125 +e +++ ek ++++el + + lk++l++ le +r + + s+GE+ a+++a+++ lcl|NCBI__GCF_000421465.1:WP_022948116.1 71 sitpNESKKAVLEKFTRIASELGvdAGDILASLKKDLATSLEG---DRRIAFLASRGEHYNARIVAEYF 136 6666555566666666666666542333444444444444444...*********************** PP TIGR00657 126 eelgvkavsllgaeagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGS 194 ++ g+ a++ l + g+l ++ ++ Ak + +++ +++++l +e+ i v+ GF G+t+ ge+ + RGGS lcl|NCBI__GCF_000421465.1:WP_022948116.1 137 QNSGMTARARLPEDFGLLVSDDYLGAK-VLSEAYANIAELTSEDGIAVIPGFYGVTQAGEVAVFSRGGS 204 ***************************.99999999********************************* PP TIGR00657 195 DltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamra 263 Dlt +A a++Ad e +tDV+G++ DP ++peAr ++ ++++E L+s G v+h +++ +++ lcl|NCBI__GCF_000421465.1:WP_022948116.1 205 DLTGGEVAYAIDADTYENWTDVSGVFEVDPSLIPEARAIPRLTFKEIRLLSSKGFNVFHLDAMLSCKER 273 ********************************************************************* PP TIGR00657 264 kipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakv 330 kipi++++t p+++GT+i +++++ee + +++ +n+a + +++ +g+ a ++++ +e ++ lcl|NCBI__GCF_000421465.1:WP_022948116.1 274 KIPIHIRNTNRPQEPGTIILNERVPEE--GIVGIARLENMAYIYLEKDMLGeeVGFTASLLQIFQEFNI 340 **********************99655..899***********9999888788************9999 PP TIGR00657 331 nvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaaki 399 n ++++ i+ v+++d+ + l+++++++ + ++v +la+++ vG g+k++ + + lcl|NCBI__GCF_000421465.1:WP_022948116.1 341 NTYHYP--TDKDDIAVLVNQDDLTGNINDLRRHIEKKLKPDYMDVVYNLAIITPVGLGLKGNSYPIVDA 407 887765..88889*********99999999999************************************ PP TIGR00657 400 feaLaeeniniemissseikisvv..vdekdaekavealheklv 441 + aL+++ i+iemi + +i++ v++ a+ a++ l+++l+ lcl|NCBI__GCF_000421465.1:WP_022948116.1 408 LLALSRNHIPIEMIDQAPSQICFHigVSQAVADDALKILYDQLI 451 ***************77777776611567778889999998886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (455 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: 9.54 // [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