Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_013010708.1 DACET_RS07120 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_000025725.1:WP_013010708.1 Length = 404 Score = 432 bits (1111), Expect = e-126 Identities = 222/402 (55%), Positives = 298/402 (74%), Gaps = 2/402 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 M ++V KFGGTSVG++ERI VA + K +D G D+VV VSAM+GET+RLI+L K+I E Sbjct: 1 MGIVVMKFGGTSVGSLERIRNVANIIAKKKDEGHDVVVTVSAMAGETDRLINLLKEIDED 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120 PRE D +V TGE + L+A LI G PAVS TG Q ++TD +++K+RIL I A R Sbjct: 61 FSPREYDQLVHTGETASSPLVAQTLISMGYPAVSLTGYQFGMITDGSYSKSRILDIKADR 120 Query: 121 IQRDIKAGRVVVVAGFQGVDEK-GNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY 179 I ++++ G++ + AGFQGVD K +I TLGRGGSDTT VA+AAALKA C+IYTDVDG+Y Sbjct: 121 IFKELEKGKICICAGFQGVDPKTDDINTLGRGGSDTTAVAIAAALKATVCEIYTDVDGIY 180 Query: 180 TTDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTL 239 T DPR+V A++LDKI++ EMLE+ASLG+KVLQ R VE + V + VL S +E PGTL Sbjct: 181 TADPRIVKNAKKLDKISYNEMLELASLGAKVLQSRCVELGMNHDVDILVLSSLEEKPGTL 240 Query: 240 ITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 299 +T ++EE MEQ +++G+ ++++AK+T+ VPD+PG+A I I+A N+ VD+IVQNV+ Sbjct: 241 VTKEDEE-MEQVVVTGVVSDKNQAKITLTEVPDSPGIASTIFNKIAAENINVDVIVQNVS 299 Query: 300 HDNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASR 359 + TD +FTV + D A V +A E+GA+E + D +IAKVSIVGVGMRSH+GVA++ Sbjct: 300 KEGNTDLSFTVQKTDLIRAKDVCSQVAKEIGAKEVLADGDIAKVSIVGVGMRSHSGVAAK 359 Query: 360 MFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAF 401 MF LA+ +N+ MI+TSEIKVS V+EEKY ELAVR LH AF Sbjct: 360 MFTLLAEMGVNLMMITTSEIKVSCVVEEKYSELAVRTLHEAF 401 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: 470 Number of extensions: 22 Number of successful extensions: 4 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: 404 Length adjustment: 31 Effective length of query: 381 Effective length of database: 373 Effective search space: 142113 Effective search space used: 142113 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_013010708.1 DACET_RS07120 (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.1172738.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.5e-133 429.0 15.1 1.1e-132 428.9 15.1 1.0 1 NCBI__GCF_000025725.1:WP_013010708.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000025725.1:WP_013010708.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 428.9 15.1 1.1e-132 1.1e-132 1 406 [. 1 403 [. 1 404 [] 0.97 Alignments for each domain: == domain 1 score: 428.9 bits; conditional E-value: 1.1e-132 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 + ++V+KFGGtsvgs eri+++a+i+ k++ eg++vvV vSAm+++td+l++l + i ++ spre d NCBI__GCF_000025725.1:WP_013010708.1 1 MGIVVMKFGGTSVGSLERIRNVANIIAKKKDEGHDVVVTVSAMAGETDRLINLL------KEIDEDFSPREYD 67 579************************************************999......89*********** PP TIGR00656 74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146 +lv +GE+ ss+l+++ l g+ a++l+g + g++Td+++ + +i +++ r+++ Le+g+i + aGF+G NCBI__GCF_000025725.1:WP_013010708.1 68 QLVHTGETASSPLVAQTLISMGYPAVSLTGYQFGMITDGSYSKSRILDIKA-DRIFKELEKGKICICAGFQGV 139 ***************************************************.********************* PP TIGR00656 147 teeG.eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvl 218 + + +i tLGRGGSD+tA+++aaalkA +eiyTDV+G+yt+DPr+v++akk+dkisy+E+lelA+lGakvl NCBI__GCF_000025725.1:WP_013010708.1 140 DPKTdDINTLGRGGSDTTAVAIAAALKATVCEIYTDVDGIYTADPRIVKNAKKLDKISYNEMLELASLGAKVL 212 *99846******************************************************************* PP TIGR00656 219 hpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltvegegmlgkrgilaeifk 288 + r +el ++ +v ilv ss e++ gTl+t+ ++e+ +v+++ +kn+a++t++ ++ +++gi+++if+ NCBI__GCF_000025725.1:WP_013010708.1 213 QSRCVELGMNHDVDILVLSSLEEKPGTLVTKedeEMEQ-VVVTGVVSDKNQAKITLT--EVPDSPGIASTIFN 282 ******************************96433444.599***************..************** PP TIGR00656 289 aLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapG 358 +a e+invd+i+q s+ t++s++v+++d+ +ak++ ++ ++++ +++ + d+a+vsivg+g+++++G NCBI__GCF_000025725.1:WP_013010708.1 283 KIAAENINVDVIVQNVSKegnTDLSFTVQKTDLIRAKDVCSQVAKEIGAKEVLADGDIAKVSIVGVGMRSHSG 355 **************9988888**************************************************** PP TIGR00656 359 vaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 va+++f+ l+e ++n++mi++se+k+s +v+ek++e avr+lhe+++e NCBI__GCF_000025725.1:WP_013010708.1 356 VAAKMFTLLAEMGVNLMMITTSEIKVSCVVEEKYSELAVRTLHEAFVE 403 **********************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (404 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: 00:00:00.01 # Mc/sec: 15.06 // [ok]
This GapMind analysis is from Jul 25 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