Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_013518959.1 ALIDE2_RS11525 aspartate kinase
Query= SwissProt::C3JXY0 (413 letters) >NCBI__GCF_000204645.1:WP_013518959.1 Length = 423 Score = 513 bits (1322), Expect = e-150 Identities = 268/421 (63%), Positives = 332/421 (78%), Gaps = 12/421 (2%) Query: 1 MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60 MAL V K+GGTS+GS ERI VA +V K+ AG +VVV SAMSGETNRL+ LAK ++ Sbjct: 1 MALFVHKYGGTSMGSTERIRNVAKRVAKWARAGHQVVVVPSAMSGETNRLLALAKDLAPA 60 Query: 61 QQPLP--RELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQI 118 + RE D++ +TGEQ + ALLA+AL G+ AVSY G QV I TDS++TKARI I Sbjct: 61 RASAAFHREQDMLAATGEQASSALLAIALQAEGMEAVSYAGWQVPIRTDSSYTKARIESI 120 Query: 119 DDQKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVD 178 DD+++R DL AGRVV++ GFQG+D++GNITTLGRGGSDT+ VA+AAA+KADEC IYTDVD Sbjct: 121 DDKRVRADLDAGRVVIITGFQGIDDEGNITTLGRGGSDTSAVAVAAAMKADECLIYTDVD 180 Query: 179 GVYTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSF---- 234 GVYTTDPRVVS A+RL ++FEEMLEMASLGSKVLQIR+VEFAGKY VP+RVL SF Sbjct: 181 GVYTTDPRVVSQARRLKSVSFEEMLEMASLGSKVLQIRSVEFAGKYKVPMRVLSSFTPWD 240 Query: 235 -----KEGPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGA 289 + GTLIT +E+E MEQ ++SGIAFNRDE K+++ GVPD PG+A++ILGP++ A Sbjct: 241 IDINEEAKSGTLITFEEDEQMEQAVVSGIAFNRDETKISVLGVPDKPGIAYQILGPVADA 300 Query: 290 NIEVDMIVQNVSHDNTTDFTFTVHRNEY-DAAERILQNTAKEIGAREVVGDTKIAKVSIV 348 NIEVD+I+QN+S D TDF+FTV+ N++ E + + +GA+EVVGDT I KVSIV Sbjct: 301 NIEVDVIIQNISKDGRTDFSFTVNHNDHARTLELLREKVVPALGAQEVVGDTAICKVSIV 360 Query: 349 GVGMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAP 408 G+GMRSH GVA++MF L++E INIQMISTSEIK SVVIE+KYLELAVRALH AF+LD P Sbjct: 361 GIGMRSHVGVAAKMFRVLSEEGINIQMISTSEIKTSVVIEDKYLELAVRALHKAFDLDQP 420 Query: 409 A 409 A Sbjct: 421 A 421 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: 528 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: 423 Length adjustment: 32 Effective length of query: 381 Effective length of database: 391 Effective search space: 148971 Effective search space used: 148971 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_013518959.1 ALIDE2_RS11525 (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.23257.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-128 414.2 7.8 3.4e-128 414.0 7.8 1.0 1 lcl|NCBI__GCF_000204645.1:WP_013518959.1 ALIDE2_RS11525 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204645.1:WP_013518959.1 ALIDE2_RS11525 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 414.0 7.8 3.4e-128 3.4e-128 2 406 .. 2 417 .. 1 418 [. 0.95 Alignments for each domain: == domain 1 score: 414.0 bits; conditional E-value: 3.4e-128 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 l V K+GGts+gs+eri+++ak+v k + g++vvVV SAms++t++l++la +l+ a ++ +r lcl|NCBI__GCF_000204645.1:WP_013518959.1 2 ALFVHKYGGTSMGSTERIRNVAKRVAKWARAGHQVVVVPSAMSGETNRLLALA--KDLAPARASAAFHR 68 689**************************************************..69************ PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 e+d+l ++GE+ ssall+ al+++g++a+++ g++ +i+Td+++++A+i++++ +r+ L+ g +v+ lcl|NCBI__GCF_000204645.1:WP_013518959.1 69 EQDMLAATGEQASSALLAIALQAEGMEAVSYAGWQVPIRTDSSYTKARIESIDD-KRVRADLDAGRVVI 136 *****************************************************9.************** PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 ++GF+G + eG+iTtLGRGGSD++A+++aaa+kAd++ iyTDV+GvyttDPrvv++a++++++s+eE+l lcl|NCBI__GCF_000204645.1:WP_013518959.1 137 ITGFQGIDDEGNITTLGRGGSDTSAVAVAAAMKADECLIYTDVDGVYTTDPRVVSQARRLKSVSFEEML 205 ********************************************************************* PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrssk.........ekeegTlitn....kkensslvkaialek 264 e+A+lG kvl+ r++e+a ++kvp++v ss+ e ++gTlit ++e+ +v++ia+++ lcl|NCBI__GCF_000204645.1:WP_013518959.1 206 EMASLGSKVLQIRSVEFAGKYKVPMRVLSSFtpwdidineEAKSGTLITFeedeQMEQA-VVSGIAFNR 273 *****************************973333333213349****98666555555.********* PP TIGR00656 265 nvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesg 330 + ++++v g+ +k+gi+ +i + +a+++i vd+i+q s+ t+ s++v+++d ++ ++L+e++ lcl|NCBI__GCF_000204645.1:WP_013518959.1 274 DETKISVL--GVPDKPGIAYQILGPVADANIEVDVIIQNISKdgrTDFSFTVNHNDHARTLELLREKVV 340 ********..9****************************998888*******************98765 PP TIGR00656 331 .aaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavr 398 a++ +++ + +++vsivg g++++ Gva+++f +l+e++ini mis+se+k sv+++ k++e avr lcl|NCBI__GCF_000204645.1:WP_013518959.1 341 pALGAQEVVGDTAICKVSIVGIGMRSHVGVAAKMFRVLSEEGINIQMISTSEIKTSVVIEDKYLELAVR 409 2778***************************************************************** PP TIGR00656 399 klheklee 406 +lh+++ + lcl|NCBI__GCF_000204645.1:WP_013518959.1 410 ALHKAFDL 417 ****9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (423 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: 10.72 // [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