Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate GFF1350 HP15_1320 aspartate kinase: aspartate kinase, monofunctional class
Query= BRENDA::O69077 (412 letters) >FitnessBrowser__Marino:GFF1350 Length = 412 Score = 623 bits (1606), Expect = 0.0 Identities = 324/408 (79%), Positives = 360/408 (88%), Gaps = 1/408 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MAL+VQKFGGTSVGT ERIE VAEKV +FR+ G DVVVVVSAMSGETNRLI LAN IME+ Sbjct: 1 MALLVQKFGGTSVGTTERIEAVAEKVSRFRKEGHDVVVVVSAMSGETNRLIALANNIMEE 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P PRE+DV+VSTGEQVTIALLSMAL K G A SYTG+QVRILTDS+HTKARI ID+ Sbjct: 61 PTPREMDVLVSTGEQVTIALLSMALQKLGCEARSYTGSQVRILTDSSHTKARIKQIDEQR 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 +R DL AGRVVVVAGFQG+D +GNITTLGRGGSDTT VALAAAL+ADECQIYTDVDGVYT Sbjct: 121 MREDLDAGRVVVVAGFQGIDESGNITTLGRGGSDTTAVALAAALRADECQIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDPRVV ARRL++ITFEEMLEMASLGSKVLQIR+VEFAGKYNVPLRVL SFQEG GTLI Sbjct: 181 TDPRVVDTARRLERITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLSSFQEGEGTLI 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300 T++D E +MEQP++SGIAFNRDEAKLTI GVPDTPG A +IL P+S AN+EVDMIVQNV Sbjct: 241 TLED-ENAMEQPVVSGIAFNRDEAKLTIAGVPDTPGSALRILKPVSDANIEVDMIVQNVG 299 Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360 DN T FTFTVHRND+ A E+L++ A +GARE GD+ IAKVSIVGVGMRSHAGVA++ Sbjct: 300 EDNRTAFTFTVHRNDFKRAKEVLQRVADELGAREVAGDSKIAKVSIVGVGMRSHAGVATQ 359 Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPA 408 MFEAL+ E INIQMISTSEIK+SVVI+EKYLELAVRALH+AFELD PA Sbjct: 360 MFEALSNEGINIQMISTSEIKISVVIDEKYLELAVRALHSAFELDKPA 407 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: 573 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: 412 Length adjustment: 31 Effective length of query: 381 Effective length of database: 381 Effective search space: 145161 Effective search space used: 145161 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 GFF1350 HP15_1320 (aspartate kinase: aspartate kinase, monofunctional class)
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.22378.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-142 460.7 12.7 2.6e-142 460.5 12.7 1.0 1 lcl|FitnessBrowser__Marino:GFF1350 HP15_1320 aspartate kinase: aspa Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1350 HP15_1320 aspartate kinase: aspartate kinase, monofunctional class # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 460.5 12.7 2.6e-142 2.6e-142 1 406 [. 1 403 [. 1 404 [. 0.98 Alignments for each domain: == domain 1 score: 460.5 bits; conditional E-value: 2.6e-142 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdel 75 + l VqKFGGtsvg +eri+++a++v + keg++vvVVvSAms++t++l++la ++i +e++pre+d l lcl|FitnessBrowser__Marino:GFF1350 1 MALLVQKFGGTSVGTTERIEAVAEKVSRFRKEGHDVVVVVSAMSGETNRLIALA------NNIMEEPTPREMDVL 69 5799**************************************************......8999*********** PP TIGR00656 76 vsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGateeG 150 vs+GE++++alls+al++lg +a++++g + ilTd+++++A+ik+++ +r+ e L+ g +vvvaGF+G +e G lcl|FitnessBrowser__Marino:GFF1350 70 VSTGEQVTIALLSMALQKLGCEARSYTGSQVRILTDSSHTKARIKQIDE-QRMREDLDAGRVVVVAGFQGIDESG 143 ************************************************9.************************* PP TIGR00656 151 eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralel 225 +iTtLGRGGSD+tA++laaal Ad+++iyTDV+GvyttDPrvv++a+++++i++eE+le+A+lG kvl+ r++e+ lcl|FitnessBrowser__Marino:GFF1350 144 NITTLGRGGSDTTAVALAAALRADECQIYTDVDGVYTTDPRVVDTARRLERITFEEMLEMASLGSKVLQIRSVEF 218 *************************************************************************** PP TIGR00656 226 aveakvpilvrsskekeegTlitn....kkensslvkaialeknvarltvegegmlgkrgilaeifkaLaeeein 296 a +++vp++v ss+++ egTlit +e++ +v++ia++++ a+lt+ g+ + +g + +i k +++++i lcl|FitnessBrowser__Marino:GFF1350 219 AGKYNVPLRVLSSFQEGEGTLITLedenAMEQP-VVSGIAFNRDEAKLTIA--GVPDTPGSALRILKPVSDANIE 290 **********************98555466666.*****************..9********************* PP TIGR00656 297 vdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkale 368 vd+i+q +e t+ +++v+++d ++ak++L+++ ++++ +++ ++++a+vsivg+g++++ Gva+++f+al+ lcl|FitnessBrowser__Marino:GFF1350 291 VDMIVQNVGEdnrTAFTFTVHRNDFKRAKEVLQRVADELGAREVAGDSKIAKVSIVGVGMRSHAGVATQMFEALS 365 *******999889************************************************************** PP TIGR00656 369 ekninilmisssetkisvlvdekdaekavrklheklee 406 +++ini mis+se+kisv++dek++e avr+lh+++e+ lcl|FitnessBrowser__Marino:GFF1350 366 NEGINIQMISTSEIKISVVIDEKYLELAVRALHSAFEL 403 ************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (412 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: 00:00:00.01 # Mc/sec: 11.78 // [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