Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_106718999.1 CU100_RS23075 aspartate kinase
Query= SwissProt::Q88EI9 (411 letters) >NCBI__GCF_003010935.1:WP_106718999.1 Length = 417 Score = 404 bits (1039), Expect = e-117 Identities = 220/416 (52%), Positives = 291/416 (69%), Gaps = 13/416 (3%) Query: 1 MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60 MA IV KFGGTSV I+RI VA VK+ +AG ++ VV+SAM+G+TN L+ +Q + Sbjct: 1 MARIVMKFGGTSVADIDRIRNVARHVKREVDAGHEVAVVVSAMAGKTNELVAWTRQTSPM 60 Query: 61 PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120 RE D IV++GEQVT LL +AL GV A S+ G Q+ I TD++H ARIL ID Sbjct: 61 HDAREYDAIVASGEQVTAGLLAIALQAMGVHARSWQGWQIPIKTDNAHGAARILDIDGSF 120 Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 + EG+V V++GFQG+ I+TLGRGGSDT+ VA+AA++KAD C IYTDVDGVYT Sbjct: 121 LIERFAEGQVAVISGFQGIGPDNRISTLGRGGSDTSAVAIAASVKADRCDIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKE------ 234 TDPRV P+ARRL +I+FEEMLEMASLG+KVLQ+RSVE A + V V SF++ Sbjct: 181 TDPRVEPKARRLSRISFEEMLEMASLGAKVLQVRSVELAMVHKVRTFVRSSFEDPDAPGM 240 Query: 235 -----GPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNI 289 PGTLI DEEE +EQ +++GIA+ +DEA++++R V D PG++ I GP++ S+I Sbjct: 241 GDLINPPGTLI-CDEEEIVEQQVVTGIAYAKDEAQISLRRVADRPGISAAIFGPLAESHI 299 Query: 290 EVDMIVQNVAHDNT-TDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGV 348 VDMIVQNV+ D T TD TFTV + +KA VLEN EIG + + + KVS++G+ Sbjct: 300 NVDMIVQNVSEDGTKTDMTFTVPSGDLDKALVVLENVKAEIGCDIIQSEAGMVKVSVIGI 359 Query: 349 GMRSHAGVASCMFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404 GMRSHAGVA+ F ALA + INI+ I+TSEIK+S++++ Y ELAVR LH+ + LD Sbjct: 360 GMRSHAGVAATAFRALADKGINIRAITTSEIKISILIDGPYAELAVRTLHSVYGLD 415 Lambda K H 0.316 0.133 0.358 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: 425 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: 411 Length of database: 417 Length adjustment: 31 Effective length of query: 380 Effective length of database: 386 Effective search space: 146680 Effective search space used: 146680 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_106718999.1 CU100_RS23075 (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.525945.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-126 406.9 6.4 6e-126 406.6 6.4 1.1 1 NCBI__GCF_003010935.1:WP_106718999.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106718999.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 406.6 6.4 6e-126 6e-126 3 405 .. 3 413 .. 1 415 [. 0.95 Alignments for each domain: == domain 1 score: 406.6 bits; conditional E-value: 6e-126 TIGR00656 3 liVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdel 75 iV+KFGGtsv++++ri+++a++v++e+ g++v VVvSAm+++t+elv+ + +++s re d + NCBI__GCF_003010935.1:WP_106718999.1 3 RIVMKFGGTSVADIDRIRNVARHVKREVDAGHEVAVVVSAMAGKTNELVAWT------RQTSPMHDAREYDAI 69 59**************************************************......788999999****** PP TIGR00656 76 vsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGate 148 v+ GE++++ ll+ al++ gv+a++ +g++ +i Td+ +g A+i +++ + L+e+ +eg++ v+ GF+G NCBI__GCF_003010935.1:WP_106718999.1 70 VASGEQVTAGLLAIALQAMGVHARSWQGWQIPIKTDNAHGAARILDIDG-SFLIERFAEGQVAVISGFQGIGP 141 *************************************************.*********************** PP TIGR00656 149 eGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpr 221 + +i tLGRGGSD++A+++aa++kAdr++iyTDV+GvyttDPrv ++a+++ +is+eE+le+A+lGakvl+ r NCBI__GCF_003010935.1:WP_106718999.1 142 DNRISTLGRGGSDTSAVAIAASVKADRCDIYTDVDGVYTTDPRVEPKARRLSRISFEEMLEMASLGAKVLQVR 214 ************************************************************************* PP TIGR00656 222 alelaveakvpilvrsskek..........e.egTlitn..kkensslvkaialeknvarltvegegmlgkrg 281 ++ela+ kv +vrss+e + gTli++ + ++++v++ia+ k+ a+++++ +++++g NCBI__GCF_003010935.1:WP_106718999.1 215 SVELAMVHKVRTFVRSSFEDpdapgmgdliNpPGTLICDeeEIVEQQVVTGIAYAKDEAQISLR--RVADRPG 285 *****************985333333322233688998844334458*****************..******* PP TIGR00656 282 ilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivg 350 i a if+ Lae++invd+i+q se t+++++v d+d+a +L++++ +++ + ++ e ++ +vs++g NCBI__GCF_003010935.1:WP_106718999.1 286 ISAAIFGPLAESHINVDMIVQNVSEdgtkTDMTFTVPSGDLDKALVVLENVKAEIGCDIIQSEAGMVKVSVIG 358 ************************99999******************************************** PP TIGR00656 351 aglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 g++++ Gva+ +f al++k+ini i++se+kis+l+d+ +ae avr+lh+++ NCBI__GCF_003010935.1:WP_106718999.1 359 IGMRSHAGVAATAFRALADKGINIRAITTSEIKISILIDGPYAELAVRTLHSVYG 413 ***************************************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 30.65 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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