Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate RR42_RS06370 RR42_RS06370 aspartate kinase
Query= SwissProt::C3JXY0 (413 letters) >FitnessBrowser__Cup4G11:RR42_RS06370 Length = 416 Score = 519 bits (1336), Expect = e-152 Identities = 276/416 (66%), Positives = 328/416 (78%), Gaps = 12/416 (2%) Query: 1 MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60 MALIV K+GGTS+GS ERI+ VA +V K+ AG +VVV SAMSGETNRL+ LAK IS Sbjct: 1 MALIVHKYGGTSMGSPERIKNVAKRVAKWHRAGHRVVVVPSAMSGETNRLLGLAKEISA- 59 Query: 61 QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120 QP PRELD++ +TGEQ + ALLA+AL GV A+SYTG QV + TDS+HTKARI IDD Sbjct: 60 -QPSPRELDMLAATGEQASSALLAIALQSEGVDAISYTGWQVPVKTDSSHTKARIESIDD 118 Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180 ++I DL AGRVVVV GFQG+D+ GNITTLGRGGSDT+ VA+AAA++A+EC IYTDVDGV Sbjct: 119 ERILADLDAGRVVVVTGFQGIDDNGNITTLGRGGSDTSAVAIAAAIEAEECLIYTDVDGV 178 Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKE---- 236 YTTDPRVV A+RLD+ITFEEMLEMASLGSKVLQIR+VEFAGKY V RVL S + Sbjct: 179 YTTDPRVVEDARRLDQITFEEMLEMASLGSKVLQIRSVEFAGKYRVKTRVLSSLTDPLMP 238 Query: 237 -----GPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANI 291 GTLIT +E ME +ISGIAF RDEAK+T+ GVPD PG+A++ILGP++ ANI Sbjct: 239 LEQEMHSGTLITFEENSEMEAAVISGIAFARDEAKITVLGVPDKPGIAYQILGPVADANI 298 Query: 292 EVDMIVQNVSHDNTTDFTFTVHRNEYDAAERILQNTAK-EIGAREVVGDTKIAKVSIVGV 350 +VDMI+QN S D TDFTFTV R EY A IL ++ K IGA V GD K++KVS+VGV Sbjct: 299 DVDMIIQNQSVDGKTDFTFTVPRGEYQRALAILNDSVKAHIGAASVSGDPKVSKVSVVGV 358 Query: 351 GMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 406 GMRSH G+AS+MF L++E INIQMISTSEIK+SV+I+EKY+ELAVRALH FELD Sbjct: 359 GMRSHVGIASKMFRTLSEEGINIQMISTSEIKISVLIDEKYMELAVRALHKVFELD 414 Lambda K H 0.316 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: 517 Number of extensions: 19 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: 413 Length of database: 416 Length adjustment: 31 Effective length of query: 382 Effective length of database: 385 Effective search space: 147070 Effective search space used: 147070 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 RR42_RS06370 RR42_RS06370 (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.9078.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-130 421.1 7.5 2.8e-130 420.9 7.5 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS06370 RR42_RS06370 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS06370 RR42_RS06370 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 420.9 7.5 2.8e-130 2.8e-130 1 406 [. 1 413 [. 1 414 [. 0.95 Alignments for each domain: == domain 1 score: 420.9 bits; conditional E-value: 2.8e-130 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + liV K+GGts+gs erik++ak+v k + g++vvVV SAms++t++l+ la + is ++sp lcl|FitnessBrowser__Cup4G11:RR42_RS06370 1 MALIVHKYGGTSMGSPERIKNVAKRVAKWHRAGHRVVVVPSAMSGETNRLLGLA------KEISAQPSP 63 579***************************************************......9******** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re d+l ++GE+ ssall+ al+ +gv+a++++g++ ++ Td+++++A+i++++ er+l L+ g +v lcl|FitnessBrowser__Cup4G11:RR42_RS06370 64 RELDMLAATGEQASSALLAIALQSEGVDAISYTGWQVPVKTDSSHTKARIESIDD-ERILADLDAGRVV 131 ******************************************************9.************* PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vv+GF+G + +G+iTtLGRGGSD++A+++aaa++A+++ iyTDV+GvyttDPrvve+a+++d+i++eE+ lcl|FitnessBrowser__Cup4G11:RR42_RS06370 132 VVTGFQGIDDNGNITTLGRGGSDTSAVAIAAAIEAEECLIYTDVDGVYTTDPRVVEDARRLDQITFEEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrss.........kekeegTlitn..kkens.slvkaialek 264 le+A+lG kvl+ r++e+a ++ v+ +v ss +e ++gTlit ++e++ ++++ia+ + lcl|FitnessBrowser__Cup4G11:RR42_RS06370 201 LEMASLGSKVLQIRSVEFAGKYRVKTRVLSSltdplmpleQEMHSGTLITFeeNSEMEaAVISGIAFAR 269 ****************************99844444433234459****97563344356********* PP TIGR00656 265 nvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesg 330 + a++tv g+ +k+gi+ +i + +a+++i+vd+i+q +s t+ +++v + + ++a ++L++ ++ lcl|FitnessBrowser__Cup4G11:RR42_RS06370 270 DEAKITVL--GVPDKPGIAYQILGPVADANIDVDMIIQNQSVdgkTDFTFTVPRGEYQRALAILNDSVK 336 ********..9****************************987777********************9986 PP TIGR00656 331 a.aelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavr 398 a ++ s++ + ++ +vs+vg+g++++ G+as++f l+e++ini mis+se+kisvl+dek++e avr lcl|FitnessBrowser__Cup4G11:RR42_RS06370 337 AhIGAASVSGDPKVSKVSVVGVGMRSHVGIASKMFRTLSEEGINIQMISTSEIKISVLIDEKYMELAVR 405 61469**************************************************************** PP TIGR00656 399 klheklee 406 +lh+++e+ lcl|FitnessBrowser__Cup4G11:RR42_RS06370 406 ALHKVFEL 413 ******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (416 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.10 // [ok]
This GapMind analysis is from Apr 09 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