Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_050462753.1 AKL27_RS10445 aspartate kinase
Query= SwissProt::C3JXY0 (413 letters) >NCBI__GCF_001189915.1:WP_050462753.1 Length = 417 Score = 517 bits (1331), Expect = e-151 Identities = 276/417 (66%), Positives = 329/417 (78%), Gaps = 12/417 (2%) Query: 1 MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60 MAL V K+GGTS+GS ERI+ VA +V K+ DAG +VVV SAMSGETNRL+ LAK I Sbjct: 1 MALYVHKYGGTSMGSTERIKNVAKRVAKWHDAGHQVVVVPSAMSGETNRLLGLAKDIMA- 59 Query: 61 QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120 QP RELD++ STGEQV++ALLAMAL G AVSY G QV I TDSA TKARI IDD Sbjct: 60 -QPDQRELDMLASTGEQVSVALLAMALQAIGKEAVSYAGWQVPIKTDSAFTKARIRSIDD 118 Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180 KIR DL AG++V+V GFQGVD GNITTLGRGGSDT+ VA+AAA+KA EC IYTDVDGV Sbjct: 119 AKIRKDLNAGKIVIVTGFQGVDANGNITTLGRGGSDTSAVAVAAAIKAAECLIYTDVDGV 178 Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKE---- 236 YTTDPRVVS A+RL +TFEEMLEMASLGSKVLQIR+VEFAG Y +P RVL S + Sbjct: 179 YTTDPRVVSEARRLKTVTFEEMLEMASLGSKVLQIRSVEFAGNYKMPTRVLSSLTDPLMP 238 Query: 237 -----GPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANI 291 GTLI+ +E+ +MEQ I+GIAF+RDEAK+T+ GVPD PG+A++ILGPI+ ANI Sbjct: 239 LEEETTSGTLISFEEDTNMEQATITGIAFSRDEAKITVLGVPDRPGIAYQILGPIADANI 298 Query: 292 EVDMIVQNVSHDNTTDFTFTVHRNEYDAAERILQNTAK-EIGAREVVGDTKIAKVSIVGV 350 EVDMI+QN S + TDFTFTV R EY A +L N+ K IGA +VGDTK++KVS+VGV Sbjct: 299 EVDMIIQNQSVEGKTDFTFTVPRAEYAKAIEVLNNSVKSHIGAASIVGDTKVSKVSVVGV 358 Query: 351 GMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDA 407 GMRSH G+AS+MF L++E +NIQMISTSEIK+SV+I+EKY+ELAVRALH AF+LD+ Sbjct: 359 GMRSHVGIASQMFRTLSEEGVNIQMISTSEIKISVLIDEKYMELAVRALHKAFDLDS 415 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: 505 Number of extensions: 12 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: 417 Length adjustment: 31 Effective length of query: 382 Effective length of database: 386 Effective search space: 147452 Effective search space used: 147452 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_050462753.1 AKL27_RS10445 (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.16642.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-133 431.4 10.7 4.1e-130 420.7 10.7 2.0 1 lcl|NCBI__GCF_001189915.1:WP_050462753.1 AKL27_RS10445 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001189915.1:WP_050462753.1 AKL27_RS10445 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 420.7 10.7 4.1e-130 4.1e-130 1 440 [. 1 411 [. 1 413 [. 0.96 Alignments for each domain: == domain 1 score: 420.7 bits; conditional E-value: 4.1e-130 TIGR00657 1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekelieki 69 mal V K+GGtS+g+ erik+vak+v k + g+qvvVV SAm+g T++L+ la+ ++ ++ lcl|NCBI__GCF_001189915.1:WP_050462753.1 1 MALYVHKYGGTSMGSTERIKNVAKRVAKWHDAGHQVVVVPSAMSGETNRLLGLAKDIMAQP-------- 61 6788*********************************************************........ PP TIGR00657 70 rekhlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllga 138 +reld++ s+GE++S+alla+al++ g +avs+ g+ lcl|NCBI__GCF_001189915.1:WP_050462753.1 62 ------------D--------------------QRELDMLASTGEQVSVALLAMALQAIGKEAVSYAGW 98 ............3....................79********************************** PP TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207 + +i tds+f++A+ +++i+ +++ k l++g+iv+v+GF+G++ +g+ittLGRGGSD++A+++Aaa+kA lcl|NCBI__GCF_001189915.1:WP_050462753.1 99 QVPIKTDSAFTKAR-IRSIDDAKIRKDLNAGKIVIVTGFQGVDANGNITTLGRGGSDTSAVAVAAAIKA 166 **************.****************************************************** PP TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkst.... 272 e+ iytDVdG+yt+DPr+v+eArrl+++++eE+lE+aslG+kvL+ r++e+a ++k p +v s+ lcl|NCBI__GCF_001189915.1:WP_050462753.1 167 AECLIYTDVDGVYTTDPRVVSEARRLKTVTFEEMLEMASLGSKVLQIRSVEFAGNYKMPTRVLSSltdp 235 **************************************************************9973333 PP TIGR00657 273 ....fnpeaeGTlivaksk.seeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlil 336 ++++ GTli +++ ++e+ ++++++++++a+++v g++++pgi+ +++g +a+a+++vd+i+ lcl|NCBI__GCF_001189915.1:WP_050462753.1 236 lmplEEETTSGTLISFEEDtNMEQATITGIAFSRDEAKITVLGVPDRPGIAYQILGPIADANIEVDMII 304 3332466789****9887779999********************************************* PP TIGR00657 337 qsss...etsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifea 402 q++s +t +f+v++ ++ ka e+l+++vk++ ++ ++k+++vs+vG gm+s+ g+a+++f + lcl|NCBI__GCF_001189915.1:WP_050462753.1 305 QNQSvegKTDFTFTVPRAEYAKAIEVLNNSVKSHIGAASIVGDTKVSKVSVVGVGMRSHVGIASQMFRT 373 9999655555*********************************************************** PP TIGR00657 403 Laeeniniemissseikisvvvdekdaekavealhekl 440 L+ee++ni+mis+seikisv++dek++e av+alh+++ lcl|NCBI__GCF_001189915.1:WP_050462753.1 374 LSEEGVNIQMISTSEIKISVLIDEKYMELAVRALHKAF 411 ************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (417 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: 00:00:00.07 # Mc/sec: 2.52 // [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