Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_028990562.1 G579_RS0113315 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_000423825.1:WP_028990562.1 Length = 406 Score = 547 bits (1409), Expect = e-160 Identities = 285/407 (70%), Positives = 333/407 (81%), Gaps = 1/407 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 MALIVQKFGGTSVG+ ERI VA KV G+ +VVVVSAMSGET+RLI LA+++ + Sbjct: 1 MALIVQKFGGTSVGSPERIRNVANKVLAEMAKGNQVVVVVSAMSGETDRLIKLAREMHAR 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120 P RELD+++STGEQVTIALLAM L G PA SYTG QV I TDS HTKARI+ ID R Sbjct: 61 PPERELDMLISTGEQVTIALLAMGLESLGQPARSYTGGQVAIQTDSVHTKARIVSIDEHR 120 Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 I+ D+ AGRVVVVAGFQGVD GNITTLGRGGSDTT VA+AAALKADEC IYTDVDGVYT Sbjct: 121 IREDLAAGRVVVVAGFQGVDAAGNITTLGRGGSDTTAVAIAAALKADECHIYTDVDGVYT 180 Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLI 240 TDPR+ +A+RLD+ITFEEMLEMASLG+KVLQ R+VEFAGKY+VP+RVL SF EGPGTL+ Sbjct: 181 TDPRIEPRARRLDRITFEEMLEMASLGAKVLQTRSVEFAGKYNVPVRVLSSFAEGPGTLV 240 Query: 241 TLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAH 300 T EE +ME+ +SGIAFNR+EAK+TI GVPD PG+A ILG +SAA++ VDMI+QNV+ Sbjct: 241 TC-EEAAMEEAKVSGIAFNRNEAKITIVGVPDRPGIAHSILGAVSAASINVDMIIQNVSE 299 Query: 301 DNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASRM 360 TDFTFTV RND++ AL+++Q I E+ A GD I K+SIVGVGMRSHAG+A+ M Sbjct: 300 HGKTDFTFTVERNDFDKALEIVQKIGRELDAEAVQGDNRIVKISIVGVGMRSHAGIAATM 359 Query: 361 FEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPA 407 FE LA+ENINIQMISTSEIK+SVV++EKYLELAVRALH AF LD A Sbjct: 360 FETLARENINIQMISTSEIKISVVVDEKYLELAVRALHEAFGLDKAA 406 Lambda K H 0.317 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: 547 Number of extensions: 15 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: 406 Length adjustment: 31 Effective length of query: 381 Effective length of database: 375 Effective search space: 142875 Effective search space used: 142875 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_028990562.1 G579_RS0113315 (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.9199.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-145 470.6 12.9 4e-142 460.3 12.9 2.0 1 lcl|NCBI__GCF_000423825.1:WP_028990562.1 G579_RS0113315 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000423825.1:WP_028990562.1 G579_RS0113315 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 460.3 12.9 4e-142 4e-142 1 441 [. 1 401 [. 1 402 [. 0.98 Alignments for each domain: == domain 1 score: 460.3 bits; conditional E-value: 4e-142 TIGR00657 1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekelieki 69 maliVqKFGGtSvg+ eri++va+ v++e +kgnqvvVVvSAm+g Td+L++la++++ ++ lcl|NCBI__GCF_000423825.1:WP_028990562.1 1 MALIVQKFGGTSVGSPERIRNVANKVLAEMAKGNQVVVVVSAMSGETDRLIKLAREMHARP-------- 61 89***********************************************************........ PP TIGR00657 70 rekhlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllga 138 + ereld+++s+GE++++alla+ le+lg+ a+s++g+ lcl|NCBI__GCF_000423825.1:WP_028990562.1 62 ------------P--------------------ERELDMLISTGEQVTIALLAMGLESLGQPARSYTGG 98 ............7....................8*********************************** PP TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207 + i tds +++A+ +++i+++r+ + l +g +vvvaGF+G++ g+ittLGRGGSD+tA+++AaalkA lcl|NCBI__GCF_000423825.1:WP_028990562.1 99 QVAIQTDSVHTKAR-IVSIDEHRIREDLAAGRVVVVAGFQGVDAAGNITTLGRGGSDTTAVAIAAALKA 166 **************.****************************************************** PP TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpe 276 de++iytDVdG+yt+DPri p Arrld i++eE+lE+aslGakvL+ r++e+a ++++p++v s+f + lcl|NCBI__GCF_000423825.1:WP_028990562.1 167 DECHIYTDVDGVYTTDPRIEPRARRLDRITFEEMLEMASLGAKVLQTRSVEFAGKYNVPVRVLSSFAEG 235 ******************************************************************998 PP TIGR00657 277 aeGTlivakskseeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqsssets.. 343 +GTl++ ++ +ee +v+++++++n+a++++ g++++pgi+ ++ga++ a++nvd+i+q++se++ lcl|NCBI__GCF_000423825.1:WP_028990562.1 236 -PGTLVTCEEAAMEEAKVSGIAFNRNEAKITIVGVPDRPGIAHSILGAVSAASINVDMIIQNVSEHGkt 303 .**********9****************************************************77777 PP TIGR00657 344 .isfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeninie 411 +f+v+++d dka e+ +k+ e + e v+ ++++ ++s+vG gm+s+ g+aa++fe+La+enini+ lcl|NCBI__GCF_000423825.1:WP_028990562.1 304 dFTFTVERNDFDKALEIV-QKIGRELDAEAVQGDNRIVKISIVGVGMRSHAGIAATMFETLARENINIQ 371 7****************8.57999999999*************************************** PP TIGR00657 412 missseikisvvvdekdaekavealheklv 441 mis+seikisvvvdek+ e av+alhe++ lcl|NCBI__GCF_000423825.1:WP_028990562.1 372 MISTSEIKISVVVDEKYLELAVRALHEAFG 401 ***************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (406 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 3.87 // [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