Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012173009.1 AZC_RS23020 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_000010525.1:WP_012173009.1 Length = 420 Score = 391 bits (1004), Expect = e-113 Identities = 222/421 (52%), Positives = 286/421 (67%), Gaps = 18/421 (4%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MA +V KFGGTSV +ERI VA VK+ +AG +V VVVSAMSG+TN L+ + Sbjct: 1 MARLVMKFGGTSVANIERIRNVARHVKREVDAGYEVAVVVSAMSGKTNELVAWCKESSAL 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 PRE D +V++GEQVT LL++ L G+ A S+ G Q+ I TD AH ARI ID T Sbjct: 61 YDPREYDAVVASGEQVTSGLLAITLQSMGLKARSWQGWQIPISTDEAHGSARIQEIDGTA 120 Query: 121 IRADLKAGRVVVVAGFQGVD-GNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY 179 + AG V V+AGFQG+ G ITTLGRGGSDT+ VA+AAA+ A+ C IYTDVDGVY Sbjct: 121 LNTGFAAGEVAVIAGFQGMHLPTGRITTLGRGGSDTSAVAVAAAIGAERCDIYTDVDGVY 180 Query: 180 TTDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQ------ 233 TTDPRVVP+A+RLD+I FEEMLEMASLG+KVLQ+R+VE A + V V SF+ Sbjct: 181 TTDPRVVPKAKRLDRIAFEEMLEMASLGAKVLQVRSVELAMVHQVRTFVRSSFEDPDAPH 240 Query: 234 ----EGPGTLITIDDEEE----SMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPI 285 E GTLI DEEE ME +++GIAF++DEA+++IR V D PGVA + P+ Sbjct: 241 MGTVESAGTLIC--DEEEIVANQMEARVVTGIAFSKDEAQVSIRRVEDKPGVAAAVFVPL 298 Query: 286 SAANVEVDMIVQNVAHD-NTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKV 344 + A++ VDMIVQNV+ D TTD TFTV DY A ++L + I G T++ KV Sbjct: 299 ADAHINVDMIVQNVSADGRTTDITFTVPTADYERAKDVLNKARDTITFETIEGATDVTKV 358 Query: 345 SIVGVGMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFEL 404 S++G+GMRSHAGVA+ F+ALA + INI+ I+TSEIK+S++I+ Y ELAVR LH+ + L Sbjct: 359 SVIGIGMRSHAGVAADAFKALAAKGINIRAITTSEIKISILIDAAYTELAVRTLHSLYGL 418 Query: 405 D 405 D Sbjct: 419 D 419 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: 439 Number of extensions: 17 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: 412 Length of database: 420 Length adjustment: 31 Effective length of query: 381 Effective length of database: 389 Effective search space: 148209 Effective search space used: 148209 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_012173009.1 AZC_RS23020 (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.7843.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-126 406.0 11.5 1.1e-125 405.8 11.5 1.0 1 lcl|NCBI__GCF_000010525.1:WP_012173009.1 AZC_RS23020 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010525.1:WP_012173009.1 AZC_RS23020 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.8 11.5 1.1e-125 1.1e-125 4 404 .. 4 416 .. 1 419 [. 0.95 Alignments for each domain: == domain 1 score: 405.8 bits; conditional E-value: 1.1e-125 TIGR00656 4 iVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprer 72 V+KFGGtsv+++eri+++a++v++e+ g++v VVvSAms++t+elv+ + s pre lcl|NCBI__GCF_000010525.1:WP_012173009.1 4 LVMKFGGTSVANIERIRNVARHVKREVDAGYEVAVVVSAMSGKTNELVAWC------KESSALYDPREY 66 69*************************************************......8999999***** PP TIGR00656 73 delvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvva 141 d +v+ GE+++s ll+ l+ g ka++ +g++ +i Td+ +g+A+i+e++ L + g + v+a lcl|NCBI__GCF_000010525.1:WP_012173009.1 67 DAVVASGEQVTSGLLAITLQSMGLKARSWQGWQIPISTDEAHGSARIQEIDG-TALNTGFAAGEVAVIA 134 ***************************************************9.9*************** PP TIGR00656 142 GFiGat.eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEale 209 GF+G+ G+iTtLGRGGSD++A+++aaa+ A+r++iyTDV+GvyttDPrvv++ak++d+i++eE+le lcl|NCBI__GCF_000010525.1:WP_012173009.1 135 GFQGMHlPTGRITTLGRGGSDTSAVAVAAAIGAERCDIYTDVDGVYTTDPRVVPKAKRLDRIAFEEMLE 203 ****98579************************************************************ PP TIGR00656 210 lAtlGakvlhpralelaveakvpilvrsskek.........e.egTlitn.......kkensslvkaia 261 +A+lGakvl+ r++ela+ +v +vrss+e e +gTli++ ++e ++v++ia lcl|NCBI__GCF_000010525.1:WP_012173009.1 204 MASLGAKVLQVRSVELAMVHQVRTFVRSSFEDpdaphmgtvEsAGTLICDeeeivanQMEA-RVVTGIA 271 *****************************9843333334333489***9988888644554.5****** PP TIGR00656 262 leknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLk 326 ++k+ a+++++ + +k+g++a +f La+++invd+i+q s t+i+++v + d ++ak++L+ lcl|NCBI__GCF_000010525.1:WP_012173009.1 272 FSKDEAQVSIR--RVEDKPGVAAAVFVPLADAHINVDMIVQNVSAdgrtTDITFTVPTADYERAKDVLN 338 ***********..****************************99877889******************** PP TIGR00656 327 eesgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaek 395 + + + +e +e d+++vs++g g++++ Gva+ +fkal+ k+ini i++se+kis+l+d +++e lcl|NCBI__GCF_000010525.1:WP_012173009.1 339 KARDTITFETIEGATDVTKVSVIGIGMRSHAGVAADAFKALAAKGINIRAITTSEIKISILIDAAYTEL 407 ********************************************************************* PP TIGR00656 396 avrklhekl 404 avr+lh+ + lcl|NCBI__GCF_000010525.1:WP_012173009.1 408 AVRTLHSLY 416 ******976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (420 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 7.65 // [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