Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_041661596.1 AFER_RS00570 aspartate kinase
Query= BRENDA::P26512 (421 letters) >NCBI__GCF_000023265.1:WP_041661596.1 Length = 409 Score = 439 bits (1129), Expect = e-128 Identities = 233/411 (56%), Positives = 307/411 (74%), Gaps = 6/411 (1%) Query: 1 MALVVQKYGGSSLESAERIRNVAERIVATKKAGNDVVVVCSAMGDTTDELLELAAAVNPV 60 MAL+VQK+GG+S+ +RIR VA+ + T GN VVVV SAMG TTD+L+ LA Sbjct: 1 MALLVQKFGGTSVGDVDRIRGVADHVARTVHRGNKVVVVVSAMGKTTDDLIRLAHEATDG 60 Query: 61 P-PAREMDMLLTAGERISNALVAMAIESLGAEAQSFTGSQAGVLTTERHGNARIVDVTPG 119 P PAREMDMLLTAGERIS ALVAMA+ LG EA+SFTGSQAG++T H A+I+++ P Sbjct: 61 PAPAREMDMLLTAGERISAALVAMALSDLGVEAESFTGSQAGIITDTDHTRAKILEIRPH 120 Query: 120 RVREALDEGKICIVAGFQGVNKETRDVTTLGRGGSDTTAVALAAALNADVCEIYSDVDGV 179 R+ EA++ + +VAGFQGV+ E RDVTTLGRGGSDTTAVALAA L+ADVCEIY+DV GV Sbjct: 121 RLLEAIESHIVPVVAGFQGVSTE-RDVTTLGRGGSDTTAVALAARLDADVCEIYTDVSGV 179 Query: 180 YTADPRIVPNAQKLEKLSFEEMLELAAVGSKILVLRSVEYARAFNVPLRVRSSYSNDPGT 239 +TADPR+VP A+K+ ++SFEEMLELAA G ++L LRSVE AR F VPL VRSS++ +PGT Sbjct: 180 FTADPRVVPRARKIPRISFEEMLELAASGGRVLALRSVEAARNFRVPLHVRSSFTWEPGT 239 Query: 240 LIAGSMEDIPVEEAVLTGVATDKSEAKVTVLGISDKPGEAAKVFRALADAEINIDMVLQN 299 + E+ +E+AV++ +A D SE KVTV+G+ D PG AA++FR +A+ +N+DM++QN Sbjct: 240 WVV--EEEPSMEQAVVSAIAHDASEVKVTVVGVPDHPGVAARLFRHVAEQGVNVDMIVQN 297 Query: 300 VSSVEDGTTDITFTCPRSDGRRAMEILKKLQVQGNWTNVLYDDQVGKVSLVGAGMKSHPG 359 VS G TDI+FT P++D RA+E + + +V+ D+ +G+VSLVGAGMK+HPG Sbjct: 298 VSL--QGHTDISFTAPKADRARALEATRAAAAEVGAVDVILDEGIGRVSLVGAGMKTHPG 355 Query: 360 VTAEFMEALRDVNVNIELISTSEIRISVLIREDDLDAAARALHEQFQLGGE 410 VTA E L + +NIE+ISTS IRIS ++R + L+ A +ALHE F+L E Sbjct: 356 VTARMFETLAEKGINIEMISTSAIRISCVVRAEVLEDAVQALHEAFELDRE 406 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: 453 Number of extensions: 22 Number of successful extensions: 7 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: 409 Length adjustment: 31 Effective length of query: 390 Effective length of database: 378 Effective search space: 147420 Effective search space used: 147420 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: 50 (23.9 bits)
Align candidate WP_041661596.1 AFER_RS00570 (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.18313.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-131 424.1 9.3 3.4e-131 423.9 9.3 1.0 1 lcl|NCBI__GCF_000023265.1:WP_041661596.1 AFER_RS00570 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023265.1:WP_041661596.1 AFER_RS00570 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 423.9 9.3 3.4e-131 3.4e-131 1 406 [. 1 403 [. 1 404 [. 0.97 Alignments for each domain: == domain 1 score: 423.9 bits; conditional E-value: 3.4e-131 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + l VqKFGGtsvg+++ri+ +a++v +++++g+kvvVVvSAm+k+td l+ la+ ea+ lcl|NCBI__GCF_000023265.1:WP_041661596.1 1 MALLVQKFGGTSVGDVDRIRGVADHVARTVHRGNKVVVVVSAMGKTTDDLIRLAH-----EATDGPAPA 64 5799**************************************************4.....777777778 PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re+d+l+ GE++s+al+++al +lgv+ae+++g +agi+Td +++Aki e+ + +rLle +e +i++ lcl|NCBI__GCF_000023265.1:WP_041661596.1 65 REMDMLLTAGERISAALVAMALSDLGVEAESFTGSQAGIITDTDHTRAKILEIRP-HRLLEAIESHIVP 132 9******************************************************.************* PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G +e ++TtLGRGGSD+tA++laa l+Ad +eiyTDV+Gv+t+DPrvv++a+ki++is+eE+ lcl|NCBI__GCF_000023265.1:WP_041661596.1 133 VVAGFQGVSTERDVTTLGRGGSDTTAVALAARLDADVCEIYTDVSGVFTADPRVVPRARKIPRISFEEM 201 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltveg 273 lelA G +vl r++e a + vp+ vrss+ e gT +++ ++e+ +v+aia++ ++tv+ lcl|NCBI__GCF_000023265.1:WP_041661596.1 202 LELAASGGRVLALRSVEAARNFRVPLHVRSSFTWEPGTWVVEeepSMEQA-VVSAIAHDASEVKVTVV- 268 *****************************************988778887.*******9999999999. PP TIGR00656 274 egmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslev 339 g+ +++g++a++f +ae+++nvd+i+q s t+is++ + d +a +a ++ +++ ++ + lcl|NCBI__GCF_000023265.1:WP_041661596.1 269 -GVPDHPGVAARLFRHVAEQGVNVDMIVQNVSLqghTDISFTAPKADRARALEATRAAAAEVGAVDVIL 336 .9***************************9765566*******************99999999****** PP TIGR00656 340 eedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 +e++ vs+vgag++ +pGv++++f+ l+ek+ini mis+s ++is +v+ + +e+av++lhe++e+ lcl|NCBI__GCF_000023265.1:WP_041661596.1 337 DEGIGRVSLVGAGMKTHPGVTARMFETLAEKGINIEMISTSAIRISCVVRAEVLEDAVQALHEAFEL 403 *****************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (409 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 9.19 // [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