Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate GFF2319 PGA1_c23510 aspartokinase LysC
Query= SwissProt::A4VJB4 (412 letters) >FitnessBrowser__Phaeo:GFF2319 Length = 412 Score = 399 bits (1026), Expect = e-116 Identities = 217/413 (52%), Positives = 292/413 (70%), Gaps = 7/413 (1%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 M ++V KFGGTSV ++RI + A++V G +++V+VSAMSG+TN L+ + S Sbjct: 1 MPVLVMKFGGTSVANLDRIRRAAKRVGVEVAKGYNVIVIVSAMSGKTNELVGWVNETSPL 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120 RE D +VS+GE VT L+A+ L + +PA S+ G QV + T SAH++ARI +I + Sbjct: 61 FDAREYDAVVSSGENVTAGLMALTLQEMDIPARSWQGWQVPLKTTSAHSQARIEEIPPEN 120 Query: 121 IQRDIKAG-RVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY 179 I G RV VVAGFQG+ +G ITTLGRGGSDTT VA AAA +A+ C IYTDVDGVY Sbjct: 121 INAKFGEGMRVAVVAGFQGISPEGRITTLGRGGSDTTAVAFAAAFEAERCDIYTDVDGVY 180 Query: 180 TTDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQE---GP 236 TTDPR+ KA++LDKI FEEMLE+ASLG+KVLQ R+VE A +Y V LRVL SF+E Sbjct: 181 TTDPRICDKARKLDKIAFEEMLELASLGAKVLQTRSVELAMRYKVKLRVLSSFEEQSDEA 240 Query: 237 GTLITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQ 296 GTL+ DEEE ME +++G+A++RDEAKLT++ V D PG+A I +S A V VDMIVQ Sbjct: 241 GTLV-CDEEEIMESNVVAGVAYSRDEAKLTVQSVADRPGIAAHIFTALSEAGVNVDMIVQ 299 Query: 297 NVAHDNTTDFTFTVHRNDYNNALQVLQGI--AAEMGAREAIGDTNIAKVSIVGVGMRSHA 354 +++ + TD TF+ + A Q LQ + E+ E + D ++AKVS+VG+GMRS + Sbjct: 300 DISDEGRTDMTFSCPTDQVVRAEQALQAVKEKGELNYAELLADRDVAKVSVVGIGMRSQS 359 Query: 355 GVASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPA 407 GVA++MF+ L+ E INI++I+TSEIK+SV+I+ KY+ELAV+ALH AFELD A Sbjct: 360 GVAAKMFKVLSDEGINIKVITTSEIKISVLIDRKYMELAVQALHDAFELDKAA 412 Lambda K H 0.317 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: 417 Number of extensions: 10 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: 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate GFF2319 PGA1_c23510 (aspartokinase LysC)
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.20717.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-129 418.5 7.5 1.7e-129 418.3 7.5 1.0 1 lcl|FitnessBrowser__Phaeo:GFF2319 PGA1_c23510 aspartokinase LysC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF2319 PGA1_c23510 aspartokinase LysC # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 418.3 7.5 1.7e-129 1.7e-129 3 406 .. 3 408 .. 1 409 [. 0.95 Alignments for each domain: == domain 1 score: 418.3 bits; conditional E-value: 1.7e-129 TIGR00656 3 liVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdelvsv 78 + V+KFGGtsv++ +ri++aak+v e+ +g++v+V+vSAms++t+elv + + +s re d +vs lcl|FitnessBrowser__Phaeo:GFF2319 3 VLVMKFGGTSVANLDRIRRAAKRVGVEVAKGYNVIVIVSAMSGKTNELVGWV------NETSPLFDAREYDAVVSS 72 78**************************************************......8999999*********** PP TIGR00656 79 GEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegi.ivvvaGFiGateeGeiT 153 GE +++ l++ l+e + a++ +g++ ++ T + + +A+i+e+ + e++ eg+ + vvaGF+G eG+iT lcl|FitnessBrowser__Phaeo:GFF2319 73 GENVTAGLMALTLQEMDIPARSWQGWQVPLKTTSAHSQARIEEIPP-ENINAKFGEGMrVAVVAGFQGISPEGRIT 147 **********************************************.88888888875489*************** PP TIGR00656 154 tLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralelavea 229 tLGRGGSD+tA++ aaa +A+r++iyTDV+GvyttDPr+ ++a+k+dki++eE+lelA+lGakvl+ r++ela+++ lcl|FitnessBrowser__Phaeo:GFF2319 148 TLGRGGSDTTAVAFAAAFEAERCDIYTDVDGVYTTDPRICDKARKLDKIAFEEMLELASLGAKVLQTRSVELAMRY 223 **************************************************************************** PP TIGR00656 230 kvpilvrsskeke...egTlitnkkens..slvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdli 300 kv+++v ss+e++ +gTl+++++e ++v ++a++++ a+ltv+ ++++++gi+a+if+aL+e+++nvd+i lcl|FitnessBrowser__Phaeo:GFF2319 224 KVKLRVLSSFEEQsdeAGTLVCDEEEIMesNVVAGVAYSRDEAKLTVQ--SVADRPGIAAHIFTALSEAGVNVDMI 297 ********998654468*****954433236*****************..************************** PP TIGR00656 301 sqtese...tsislvvdeedvdeakkaLkeesgaae..lesleveedlavvsivgaglveapGvaseifkaleekn 371 +q s+ t+++++ + +v +a++aL++++++ e + +l ++d+a+vs+vg g+++++Gva+++fk+l++++ lcl|FitnessBrowser__Phaeo:GFF2319 298 VQDISDegrTDMTFSCPTDQVVRAEQALQAVKEKGElnYAELLADRDVAKVSVVGIGMRSQSGVAAKMFKVLSDEG 373 **9987788********************99877666699999********************************* PP TIGR00656 372 inilmisssetkisvlvdekdaekavrklheklee 406 ini+ i++se+kisvl+d k++e av++lh+++e+ lcl|FitnessBrowser__Phaeo:GFF2319 374 INIKVITTSEIKISVLIDRKYMELAVQALHDAFEL 408 *********************************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 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.59 // [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