Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_012674034.1 SULAZ_RS07315 aspartate kinase
Query= SwissProt::C3JXY0 (413 letters) >NCBI__GCF_000021545.1:WP_012674034.1 Length = 411 Score = 454 bits (1167), Expect = e-132 Identities = 237/403 (58%), Positives = 307/403 (76%), Gaps = 3/403 (0%) Query: 1 MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60 M LIVQK+GGTSVG++ERI+ VA K+KK D G+ +VVV SAM+GET+RLI L + +S Sbjct: 1 MPLIVQKYGGTSVGNIERIKNVARKIKKAVDEGNQVVVVSSAMTGETDRLIGLTRELSN- 59 Query: 61 QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120 +P PRE D++V+TGEQV I L+A+AL + GVPA+S TG QV I+TD+ HTKARI +ID Sbjct: 60 -RPNPREQDMVVATGEQVAIGLVAIALQELGVPAISLTGWQVPIITDNVHTKARIKKIDT 118 Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180 +IR L G+VV+VAGFQGV E G+ITTLGRGGSDT+ VALAAALKAD C+IYTDV GV Sbjct: 119 HRIRKHLDEGKVVIVAGFQGVSEDGDITTLGRGGSDTSAVALAAALKADVCEIYTDVPGV 178 Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240 +T DPR+V A+++ I++EEM+EMASLGSKV+QIR+VEF KY V + V SF + GT Sbjct: 179 FTADPRIVENARKIPVISYEEMMEMASLGSKVMQIRSVEFGAKYGVKIHVRSSFNDEEGT 238 Query: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV 300 I ++E E ME+ ++ GI+ E+++T+ VPD PGVA K+ + NI VDMIVQNV Sbjct: 239 WI-MEENEEMEKVVVRGISHELKESRITVVRVPDKPGVAAKLFKALGDKNIVVDMIVQNV 297 Query: 301 SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360 SH TD +FTV++ + D AE I + AKE+GA +V + KIAK+S+VG+GM++H+GVA Sbjct: 298 SHKGFTDISFTVNKTDADYAEEIAREVAKEVGAEDVERNDKIAKISVVGLGMKTHSGVAG 357 Query: 361 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAF 403 +MFE L KE INI ISTSEIK+S +I+EKY ELAVRALH AF Sbjct: 358 KMFEVLYKEGINIYAISTSEIKISCLIDEKYAELAVRALHEAF 400 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: 478 Number of extensions: 14 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: 411 Length adjustment: 31 Effective length of query: 382 Effective length of database: 380 Effective search space: 145160 Effective search space used: 145160 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_012674034.1 SULAZ_RS07315 (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.21480.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-152 492.7 13.5 5.9e-149 482.8 13.5 2.0 1 lcl|NCBI__GCF_000021545.1:WP_012674034.1 SULAZ_RS07315 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021545.1:WP_012674034.1 SULAZ_RS07315 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 482.8 13.5 5.9e-149 5.9e-149 1 441 [. 1 401 [. 1 402 [. 0.99 Alignments for each domain: == domain 1 score: 482.8 bits; conditional E-value: 5.9e-149 TIGR00657 1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekelieki 69 m liVqK+GGtSvgn+erik+va+ +kk+ +gnqvvVV SAm g Td+L+ l +++s+++ lcl|NCBI__GCF_000021545.1:WP_012674034.1 1 MPLIVQKYGGTSVGNIERIKNVARKIKKAVDEGNQVVVVSSAMTGETDRLIGLTRELSNRP-------- 61 569**********************************************************........ PP TIGR00657 70 rekhlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllga 138 + +re+d+++++GE++++ l+a al+elgv a+sl+g+ lcl|NCBI__GCF_000021545.1:WP_012674034.1 62 ------------N--------------------PREQDMVVATGEQVAIGLVAIALQELGVPAISLTGW 98 ............5....................8*********************************** PP TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207 + +i+td+ +++A+ +++i+t+r+ k+l+eg++v+vaGF+G++e+g+ittLGRGGSD++A++lAaalkA lcl|NCBI__GCF_000021545.1:WP_012674034.1 99 QVPIITDNVHTKAR-IKKIDTHRIRKHLDEGKVVIVAGFQGVSEDGDITTLGRGGSDTSAVALAAALKA 166 **************.****************************************************** PP TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpe 276 d++eiytDV+G++taDPriv++Ar+++ isyeE++E+aslG+kv++ r++e+ ++++++i+v+s+fn+e lcl|NCBI__GCF_000021545.1:WP_012674034.1 167 DVCEIYTDVPGVFTADPRIVENARKIPVISYEEMMEMASLGSKVMQIRSVEFGAKYGVKIHVRSSFNDE 235 ********************************************************************* PP TIGR00657 277 aeGTlivakskseeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqsssets.. 343 eGT+i+++++++e++ v+++s++ ++++++v ++++kpg++a++f+al ++++ vd+i+q++s+++ lcl|NCBI__GCF_000021545.1:WP_012674034.1 236 -EGTWIMEENEEMEKVVVRGISHELKESRITVVRVPDKPGVAAKLFKALGDKNIVVDMIVQNVSHKGft 303 .***************************************************************98899 PP TIGR00657 344 .isfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeninie 411 isf+v+k+dad a+e+ ++v +e e+ve ++k+a++s+vG gmk++ gva+k+fe+L +e+ini lcl|NCBI__GCF_000021545.1:WP_012674034.1 304 dISFTVNKTDADYAEEIA-REVAKEVGAEDVERNDKIAKISVVGLGMKTHSGVAGKMFEVLYKEGINIY 371 9****************6.6899********************************************** PP TIGR00657 412 missseikisvvvdekdaekavealheklv 441 +is+seikis+++dek+ae av+alhe+++ lcl|NCBI__GCF_000021545.1:WP_012674034.1 372 AISTSEIKISCLIDEKYAELAVRALHEAFI 401 ****************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (411 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06 # Mc/sec: 2.60 // [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