Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_020563310.1 A3OW_RS0110035 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_000372865.1:WP_020563310.1 Length = 406 Score = 583 bits (1503), Expect = e-171 Identities = 306/408 (75%), Positives = 347/408 (85%), Gaps = 2/408 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MAL V KFGGTSVG+VERI+ VAEKVK+ + GD +VVVVSAMSGETNRLI LA I +Q Sbjct: 1 MALYVYKFGGTSVGSVERIKAVAEKVKQAHDLGDRIVVVVSAMSGETNRLIALAKDIQKQ 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P RELDV+VSTGEQVT+ALL+MAL + G PA S+TG QV+ILTDS+HTKARI IDD+ Sbjct: 61 PNARELDVLVSTGEQVTVALLAMALEEIGCPAYSFTGGQVKILTDSSHTKARIRDIDDSR 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 +RA L G VVVVAGFQGVD +GNITTLGRGGSDTT VALAAALKADEC I+TDVDGVYT Sbjct: 121 MRARLDQGNVVVVAGFQGVDEHGNITTLGRGGSDTTAVALAAALKADECLIFTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDPR+ P+ARRLDKITFEEMLEMASLGSKVLQIR+VEFAGKYNV LRVL SF EG GTLI Sbjct: 181 TDPRIEPKARRLDKITFEEMLEMASLGSKVLQIRSVEFAGKYNVALRVLSSFTEGKGTLI 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300 T +D + ME +ISGIAFNRDEAKLTI GVPD PGVA +ILGPI+ AN+EVDMIVQN+A Sbjct: 241 TYEDSQ--MESALISGIAFNRDEAKLTITGVPDKPGVASRILGPIAEANIEVDMIVQNIA 298 Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360 D+TTDFTFTVHRNDYL A E L+ T A +GA++ GD I K+SIVGVGMRSHAG+AS Sbjct: 299 EDDTTDFTFTVHRNDYLRAKESLELTRAELGAKKVTGDDAIVKISIVGVGMRSHAGIAST 358 Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPA 408 MF+ALA E INI+MISTSEIK+SVV++EKYLELAVR LH+AF+LD A Sbjct: 359 MFQALASEGINIKMISTSEIKISVVVDEKYLELAVRTLHSAFKLDQAA 406 Lambda K H 0.317 0.133 0.362 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: 551 Number of extensions: 14 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_020563310.1 A3OW_RS0110035 (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.24535.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-138 446.6 12.1 4.9e-138 446.4 12.1 1.0 1 lcl|NCBI__GCF_000372865.1:WP_020563310.1 A3OW_RS0110035 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000372865.1:WP_020563310.1 A3OW_RS0110035 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 446.4 12.1 4.9e-138 4.9e-138 2 406 .. 2 402 .. 1 403 [. 0.98 Alignments for each domain: == domain 1 score: 446.4 bits; conditional E-value: 4.9e-138 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 l V KFGGtsvgs+erik++a++v+++ g++ vVVvSAms++t++l++la + i+++++ r lcl|NCBI__GCF_000372865.1:WP_020563310.1 2 ALYVYKFGGTSVGSVERIKAVAEKVKQAHDLGDRIVVVVSAMSGETNRLIALA------KDIQKQPNAR 64 688**************************************************......9********* PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 e d lvs+GE++++all++al+e g a +++g++ ilTd+++++A+i++++ +r+ +L++g +vv lcl|NCBI__GCF_000372865.1:WP_020563310.1 65 ELDVLVSTGEQVTVALLAMALEEIGCPAYSFTGGQVKILTDSSHTKARIRDIDD-SRMRARLDQGNVVV 132 *****************************************************9.************** PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 vaGF+G +e+G+iTtLGRGGSD+tA++laaalkAd++ i+TDV+GvyttDPr+ ++a+++dki++eE+l lcl|NCBI__GCF_000372865.1:WP_020563310.1 133 VAGFQGVDEHGNITTLGRGGSDTTAVALAAALKADECLIFTDVDGVYTTDPRIEPKARRLDKITFEEML 201 ********************************************************************* PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltvege 274 e+A+lG kvl+ r++e+a +++v ++v ss+ + +gTlit ++e l+++ia++++ a+lt++ lcl|NCBI__GCF_000372865.1:WP_020563310.1 202 EMASLGSKVLQIRSVEFAGKYNVALRVLSSFTEGKGTLITYedsQMES-ALISGIAFNRDEAKLTIT-- 267 ****************************************87534444.6*****************.. PP TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleve 340 g+ +k+g++++i + +ae++i vd+i+q +e t+ +++v+++d +ak+ L+ + +++ +++ + lcl|NCBI__GCF_000372865.1:WP_020563310.1 268 GVPDKPGVASRILGPIAEANIEVDMIVQNIAEddtTDFTFTVHRNDYLRAKESLELTRAELGAKKVTGD 336 9******************************99999**********************9********** PP TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 + ++sivg+g++++ G+as +f+al+ ++ini+mis+se+kisv+vdek++e avr+lh+++++ lcl|NCBI__GCF_000372865.1:WP_020563310.1 337 DAIVKISIVGVGMRSHAGIASTMFQALASEGINIKMISTSEIKISVVVDEKYLELAVRTLHSAFKL 402 ***************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.62 // [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