Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_083924279.1 D471_RS0121390 aspartate kinase
Query= BRENDA::P26512 (421 letters) >NCBI__GCF_000341125.1:WP_083924279.1 Length = 435 Score = 280 bits (716), Expect = 6e-80 Identities = 178/416 (42%), Positives = 238/416 (57%), Gaps = 25/416 (6%) Query: 5 VQKYGGSSLESAERIRNVAERIVATKKAGNDVVVVCSAMGDTTDELLELAAAVNPVPPAR 64 V K+GGSSL + ER+R A R A ++G + VV SA GDTTD LL AA V R Sbjct: 29 VWKFGGSSLATTERVRAAARRAGAAYRSGGPLAVVVSAQGDTTDALLSRAADVGSTAAGR 88 Query: 65 EMDMLLTAGERISNALVAMAIESLGAEAQSFTGSQAGVLTTERHGNARIVDVTPGRVREA 124 E+D LL GE S AL+A+A++ LG A + TGSQ+G+L T RHG +V V P R+ Sbjct: 89 ELDQLLATGENASAALMAIALQGLGVPAVAVTGSQSGILATGRHGTGVVVAVDPERILRV 148 Query: 125 LDEGKICIVAGFQGVNKETRDVTTLGRGGSDTTAVALAAALNADVCEIYSDVDGVYTADP 184 LD GK+ +VAGFQG N+E DV TLGRGGSD++A ALAA L A C+I +DV GVYTADP Sbjct: 149 LDGGKVAVVAGFQGTNEE-GDVITLGRGGSDSSAAALAAGLGAHDCDILTDVAGVYTADP 207 Query: 185 RIVPNAQKLEKLSFEEMLELAAVGSKILVLRSVEYARAFNVPLRVRSSYSNDPGTLI--- 241 RI P+AQ + + + M E+A G++++ R+VE A +V LRVRSS+ PGT I Sbjct: 208 RICPSAQLMPVVPNDVMAEMAFAGARVMHTRAVEIAALHDVELRVRSSFEQTPGTRIPLR 267 Query: 242 --AGSMEDIPVEEAVLTGVATDKSEAKVTVLGISDKPGEAAKVFRALADAEINIDMVLQN 299 G +E +P AV+ D A+V + A ++R LA I +DM Sbjct: 268 GDGGMVETVPAAWAVV----HDLDVARVELSAGGAGGATVADLYRRLARRGITVDM---- 319 Query: 300 VSSVEDGTTDIT--FTCPRSD---GRRAMEILKKLQVQG-NWTNVLYDDQVGKVSLVGAG 353 V S DG +T T RSD RRA+E +V G + V+ D++V +VS+VG G Sbjct: 320 VGSARDGRGGLTSGMTVRRSDVPEVRRALE-----RVAGPSRGRVVVDEEVARVSVVGTG 374 Query: 354 MKSHPGVTAEFMEALRDVNVNIELISTSEIRISVLIREDDLDAAARALHEQFQLGG 409 + S P TA + LR + +STS+ RI V + A R LH++F L G Sbjct: 375 LLSRPEYTARMLSCLRTAGIEASALSTSQARICVTVPSASATLAVRRLHQEFGLDG 430 Lambda K H 0.314 0.131 0.355 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: 403 Number of extensions: 16 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: 421 Length of database: 435 Length adjustment: 32 Effective length of query: 389 Effective length of database: 403 Effective search space: 156767 Effective search space used: 156767 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: 42 (22.0 bits) S2: 51 (24.3 bits)
Align candidate WP_083924279.1 D471_RS0121390 (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.1176.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-96 310.4 0.2 4.8e-84 268.9 0.1 2.0 2 lcl|NCBI__GCF_000341125.1:WP_083924279.1 D471_RS0121390 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000341125.1:WP_083924279.1 D471_RS0121390 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 40.2 0.0 1.2e-14 1.2e-14 5 57 .. 29 81 .. 26 86 .. 0.93 2 ! 268.9 0.1 4.8e-84 4.8e-84 103 441 .. 87 427 .. 78 428 .. 0.95 Alignments for each domain: == domain 1 score: 40.2 bits; conditional E-value: 1.2e-14 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekv 57 V KFGG+S+++ er++++a++ +++++g + +VVvSA +++TdaL++ a v lcl|NCBI__GCF_000341125.1:WP_083924279.1 29 VWKFGGSSLATTERVRAAARRAGAAYRSGGPLAVVVSAQGDTTDALLSRAADV 81 89********************************************9987665 PP == domain 2 score: 268.9 bits; conditional E-value: 4.8e-84 TIGR00657 103 ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegii 171 reld +l++GE+ Saal+a al+ lgv av+++g+++gil+++++g + ++ ++ er++ +l+ g++ lcl|NCBI__GCF_000341125.1:WP_083924279.1 87 GRELDQLLATGENASAALMAIALQGLGVPAVAVTGSQSGILATGRHGTGV-VVAVDPERILRVLDGGKV 154 689***********************************************.****************** PP TIGR00657 172 vvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeE 240 vvaGF+G++e+g++ tLGRGGSD +Aa+lAa l+A+ ++i tDV G+ytaDPri p+A++++ + + lcl|NCBI__GCF_000341125.1:WP_083924279.1 155 AVVAGFQGTNEEGDVITLGRGGSDSSAAALAAGLGAHDCDILTDVAGVYTADPRICPSAQLMPVVPNDV 223 ********************************************************************* PP TIGR00657 241 alELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivaksk...seeepavkalsldknqalv 306 ++E+a Ga+v+h r++e+a+ ++++++v+s+f+++ +GT i + +e pa a+ +d + a+v lcl|NCBI__GCF_000341125.1:WP_083924279.1 224 MAEMAFAGARVMHTRAVEIAALHDVELRVRSSFEQT-PGTRIPLRGDggmVETVPAAWAVVHDLDVARV 291 ***********************************9.*****999889988888999************ PP TIGR00657 307 svsgttmkpgilaevfgalaeakvnvdlilqsss.ets...isfvvdkedadkakellkkkvkeekale 371 ++s + ++a++ ++la++++ vd++ + + + ++v ++d+++ ++l++ + + lcl|NCBI__GCF_000341125.1:WP_083924279.1 292 ELSAGGAGGATVADLYRRLARRGITVDMVGSARDgR-GgltSGMTVRRSDVPEVRRALER--VAGPSRG 357 *****************************9665542.244458**************964..5566667 PP TIGR00657 372 evevekklalvslvGagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealhekl 440 +v v++++a vs+vG g+ s+p +a++++ L+ ++i ++s+s+ +i+v v++ a+ av+ lh+++ lcl|NCBI__GCF_000341125.1:WP_083924279.1 358 RVVVDEEVARVSVVGTGLLSRPEYTARMLSCLRTAGIEASALSTSQARICVTVPSASATLAVRRLHQEF 426 8******************************************************************99 PP TIGR00657 441 v 441 lcl|NCBI__GCF_000341125.1:WP_083924279.1 427 G 427 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (435 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: 2.76 // [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