Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate SMc02438 SMc02438 aspartate kinase
Query= SwissProt::C3JXY0 (413 letters) >FitnessBrowser__Smeli:SMc02438 Length = 424 Score = 389 bits (999), Expect = e-113 Identities = 216/423 (51%), Positives = 291/423 (68%), Gaps = 18/423 (4%) Query: 1 MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAK---AI 57 MA IV KFGGTSV + RI VA VK+ DAG ++ VV+SAMSG+TN L+ + + Sbjct: 1 MARIVMKFGGTSVADLNRIHNVARHVKREVDAGHEVAVVVSAMSGKTNELVGWVENMPKV 60 Query: 58 SGDQQPL--PRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARI 115 +G P RE D +V++GEQVT LLA+AL G+ A S+ G Q+ I TD+AH ARI Sbjct: 61 AGSNAPFYDAREYDAVVASGEQVTSGLLAIALQSMGINARSWQGWQLPIKTDNAHGAARI 120 Query: 116 LQIDDQKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYT 175 L+ID + + G+V VVAGFQG+ + TLGRGGSDT+ VA+AAA+KAD C IYT Sbjct: 121 LEIDGADVIRRMGEGQVAVVAGFQGLGPDNRLATLGRGGSDTSAVAIAAAVKADRCDIYT 180 Query: 176 DVDGVYTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFK 235 DVDGVYTTDPR+ A+RL KI FEEMLEMASLG+KVLQ+R+VE A + V V SF+ Sbjct: 181 DVDGVYTTDPRIEPKARRLKKIAFEEMLEMASLGAKVLQVRSVELAMVHKVRTFVRSSFE 240 Query: 236 E-----------GPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILG 284 + PGTLI DE+E +EQ +++GIA+ +DEA++++R + D PGV+ I G Sbjct: 241 DPDAPGMGDLMNPPGTLI-CDEDEIVEQEVVTGIAYAKDEAQISLRRLADRPGVSAAIFG 299 Query: 285 PISGANIEVDMIVQNVSHDNT-TDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIA 343 P++ A+I VDMIVQN+S D + TD TFTV + D A R+L + ++IG + ++ + Sbjct: 300 PLAEAHINVDMIVQNISEDGSKTDMTFTVPSGDVDKALRVLGDNKEKIGYDVIQSESGLV 359 Query: 344 KVSIVGVGMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAF 403 KVS++G+GMRSHAGVA+ F ALA + INI+ I+TSEIK+S++I+ Y ELAVR LH+ + Sbjct: 360 KVSVIGIGMRSHAGVAASAFRALADKGINIKAITTSEIKISILIDGPYAELAVRTLHSVY 419 Query: 404 ELD 406 LD Sbjct: 420 GLD 422 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: 462 Number of extensions: 20 Number of successful extensions: 5 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: 424 Length adjustment: 32 Effective length of query: 381 Effective length of database: 392 Effective search space: 149352 Effective search space used: 149352 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 SMc02438 SMc02438 (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.4625.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-128 414.6 3.8 2.8e-128 414.3 3.8 1.1 1 lcl|FitnessBrowser__Smeli:SMc02438 SMc02438 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc02438 SMc02438 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 414.3 3.8 2.8e-128 2.8e-128 3 405 .. 3 420 .. 1 422 [. 0.93 Alignments for each domain: == domain 1 score: 414.3 bits; conditional E-value: 2.8e-128 TIGR00656 3 liVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdei...sprerde 74 iV+KFGGtsv++ +ri+++a++v++e+ g++v VVvSAms++t+elv +e ++ ++ ++ re d lcl|FitnessBrowser__Smeli:SMc02438 3 RIVMKFGGTSVADLNRIHNVARHVKREVDAGHEVAVVVSAMSGKTNELVGWVE--NMPKVAGSNApfyDAREYDA 75 59**************************************************8..55444444434559****** PP TIGR00656 75 lvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGatee 149 +v+ GE+++s ll+ al+ g +a++ +g++ +i Td+ +g A+i e++ ++ ++ eg++ vvaGF+G + lcl|FitnessBrowser__Smeli:SMc02438 76 VVASGEQVTSGLLAIALQSMGINARSWQGWQLPIKTDNAHGAARILEIDG-ADVIRRMGEGQVAVVAGFQGLGPD 149 **************************************************.8999999***************** PP TIGR00656 150 GeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhprale 224 + tLGRGGSD++A+++aaa+kAdr++iyTDV+GvyttDPr+ ++a++++ki++eE+le+A+lGakvl+ r++e lcl|FitnessBrowser__Smeli:SMc02438 150 NRLATLGRGGSDTSAVAIAAAVKADRCDIYTDVDGVYTTDPRIEPKARRLKKIAFEEMLEMASLGAKVLQVRSVE 224 *************************************************************************** PP TIGR00656 225 laveakvpilvrsske..........ke.egTlitn..kkensslvkaialeknvarltvegegmlgkrgilaei 286 la+ kv +vrss+e + gTli++ + ++++v++ia+ k+ a+++++ +++++g+ a i lcl|FitnessBrowser__Smeli:SMc02438 225 LAMVHKVRTFVRSSFEdpdapgmgdlMNpPGTLICDedEIVEQEVVTGIAYAKDEAQISLR--RLADRPGVSAAI 297 **************973333333332244799**9955444558*****************..************ PP TIGR00656 287 fkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveap 357 f+ Lae++invd+i+q se t+++++v dvd+a ++L + +++++++ ++ e++l +vs++g g++++ lcl|FitnessBrowser__Smeli:SMc02438 298 FGPLAEAHINVDMIVQNISEdgskTDMTFTVPSGDVDKALRVLGDNKEKIGYDVIQSESGLVKVSVIGIGMRSHA 372 ******************999999*************************************************** PP TIGR00656 358 Gvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 Gva+ +f al++k+ini+ i++se+kis+l+d+ +ae avr+lh+++ lcl|FitnessBrowser__Smeli:SMc02438 373 GVAASAFRALADKGINIKAITTSEIKISILIDGPYAELAVRTLHSVYG 420 ********************************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (424 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.74 // [ok]
This GapMind analysis is from Apr 09 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