Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_012675675.1 PERMA_RS08105 aspartate kinase
Query= SwissProt::C3JXY0 (413 letters) >NCBI__GCF_000021565.1:WP_012675675.1 Length = 410 Score = 446 bits (1146), Expect = e-130 Identities = 233/403 (57%), Positives = 308/403 (76%), Gaps = 3/403 (0%) Query: 1 MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60 M LIVQKFGGTSVGS+ERI+ VA+K+K+ + G+ +VVV SAM+GET+RL+ L + +S Sbjct: 1 MPLIVQKFGGTSVGSIERIKNVANKIKRAVEEGNKVVVVSSAMAGETDRLLTLTRELSS- 59 Query: 61 QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120 +P PRE D++VSTGEQV I L+++AL + G+ AVS TG QV I TD AHTKARI +ID Sbjct: 60 -KPDPREQDMVVSTGEQVAIGLISIALKEMGIDAVSLTGWQVPIYTDDAHTKARIKKIDT 118 Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180 +I ++L GRVV+VAGFQG+ + G+ITTLGRGGSDTT VALAAAL AD C+IYTDV GV Sbjct: 119 GRILSELDKGRVVIVAGFQGISDYGDITTLGRGGSDTTAVALAAALNADVCEIYTDVTGV 178 Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240 +T DPR+V A+++ I++EEM+EMASLGSKV+QIR+VEFA KY V + V SF E GT Sbjct: 179 FTADPRIVENAKKIPVISYEEMMEMASLGSKVMQIRSVEFAAKYGVKIHVKSSFIEEDGT 238 Query: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV 300 I ++E E ME+ ++ GI+ + E+++T+ VPD PG+A K+ + NI VDMIVQNV Sbjct: 239 WI-VEENEEMEKVVVRGISHDLKESRITVVQVPDKPGIAAKLFKALGDRNIVVDMIVQNV 297 Query: 301 SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360 SH+ TD +FTV++ + + AE I + AKEIGA+ V + +IAK+S+VG+GM++HAG A Sbjct: 298 SHEGYTDISFTVNKIDAEYAEEIAKEVAKEIGAKGVERNDRIAKISVVGLGMKTHAGTAG 357 Query: 361 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAF 403 +MFE L +E INI ISTSEIK+S +I+EKY ELAVRALH AF Sbjct: 358 KMFEVLYREGINIYAISTSEIKISCLIDEKYAELAVRALHEAF 400 Lambda K H 0.316 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: 469 Number of extensions: 14 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: 413 Length of database: 410 Length adjustment: 31 Effective length of query: 382 Effective length of database: 379 Effective search space: 144778 Effective search space used: 144778 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_012675675.1 PERMA_RS08105 (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.8806.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-138 448.7 15.1 1.1e-138 448.5 15.1 1.0 1 lcl|NCBI__GCF_000021565.1:WP_012675675.1 PERMA_RS08105 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021565.1:WP_012675675.1 PERMA_RS08105 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 448.5 15.1 1.1e-138 1.1e-138 2 406 .. 2 402 .. 1 403 [. 0.98 Alignments for each domain: == domain 1 score: 448.5 bits; conditional E-value: 1.1e-138 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 liVqKFGGtsvgs+erik++a++++++++eg+kvvVV SAm+++td+l++l+ + s+++ pr lcl|NCBI__GCF_000021565.1:WP_012675675.1 2 PLIVQKFGGTSVGSIERIKNVANKIKRAVEEGNKVVVVSSAMAGETDRLLTLT------RELSSKPDPR 64 59***************************************************......899******* PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 e+d++vs+GE++++ l+s al+e g +a++l+g++ +i Tdd +++A+ik+++t r+l+ L++g +v+ lcl|NCBI__GCF_000021565.1:WP_012675675.1 65 EQDMVVSTGEQVAIGLISIALKEMGIDAVSLTGWQVPIYTDDAHTKARIKKIDT-GRILSELDKGRVVI 132 ******************************************************.************** PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 vaGF+G G+iTtLGRGGSD+tA++laaal+Ad +eiyTDV Gv+t+DPr+ve+akki+ isyeE++ lcl|NCBI__GCF_000021565.1:WP_012675675.1 133 VAGFQGISDYGDITTLGRGGSDTTAVALAAALNADVCEIYTDVTGVFTADPRIVENAKKIPVISYEEMM 201 ********************************************************************* PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitnkkens..slvkaialeknvarltvegeg 275 e+A+lG kv++ r++e+a +++v+i v+ss+ +e+gT i++++e+ +v++i+++ + +r+tv+ + lcl|NCBI__GCF_000021565.1:WP_012675675.1 202 EMASLGSKVMQIRSVEFAAKYGVKIHVKSSFIEEDGTWIVEENEEMekVVVRGISHDLKESRITVV--Q 268 ****************************************9444333469****************..* PP TIGR00656 276 mlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslevee 341 + +k+gi+a++fkaL++++i vd+i+q s+ t+is++v++ d++ a+++ ke+ ++++ + +e + lcl|NCBI__GCF_000021565.1:WP_012675675.1 269 VPDKPGIAAKLFKALGDRNIVVDMIVQNVSHegyTDISFTVNKIDAEYAEEIAKEVAKEIGAKGVERND 337 ***************************9998899*********************************** PP TIGR00656 342 dlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 +a++s+vg g++ + G a+++f++l ++ini is+se+kis l+dek+ae avr+lhe+++e lcl|NCBI__GCF_000021565.1:WP_012675675.1 338 RIAKISVVGLGMKTHAGTAGKMFEVLYREGINIYAISTSEIKISCLIDEKYAELAVRALHEAFIE 402 ***************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (410 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: 7.82 // [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