Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_037574568.1 BS73_RS20470 aspartate kinase
Query= BRENDA::P9WPX3 (421 letters) >NCBI__GCF_000744815.1:WP_037574568.1 Length = 425 Score = 550 bits (1418), Expect = e-161 Identities = 282/425 (66%), Positives = 349/425 (82%), Gaps = 4/425 (0%) Query: 1 MALVVQKYGGSSVADAERIRRVAERIVATKKQGNDVVVVVSAMGDTTDDLLDLAQQVCPA 60 M LVVQKYGGSSVADAE I+RVA RIV TKK G++VVVVVSAMGDTTD+L+DLA++V P Sbjct: 1 MGLVVQKYGGSSVADAEGIKRVARRIVDTKKAGHEVVVVVSAMGDTTDELIDLAEEVSPI 60 Query: 61 PPPRELDMLLTAGERISNALVAMAIESLGAHARSFTGSQAGVITTGTHGNAKIIDVTPGR 120 P RELDMLLTAGERIS AL+AMAI+SLG A+SFTGSQAGVIT H A+IIDVTPGR Sbjct: 61 PGGRELDMLLTAGERISMALLAMAIKSLGHEAQSFTGSQAGVITDSVHNKARIIDVTPGR 120 Query: 121 LQTALEEGRVVLVAGFQGVSQDTKDVTTLGRGGSDTTAVAMAAALGADVCEIYTDVDGIF 180 ++T+L+EG + +VAGFQGVSQD+K++TTLGRGGSDTTAVA+AAAL A+VCEIYTDVDG+F Sbjct: 121 IRTSLDEGNIAIVAGFQGVSQDSKNITTLGRGGSDTTAVALAAALDAEVCEIYTDVDGVF 180 Query: 181 SADPRIVRNARKLDTVTFEEMLEMAACGAKVLMLRCVEYARRHNIPVHVRSSYSDRPGTV 240 +ADPR+V+ ARK+D + FE+MLE+A+ G+KVL+ RCVEYARR+NIP+HVRSS+S GT Sbjct: 181 TADPRVVKKARKIDEIAFEDMLELASSGSKVLLHRCVEYARRYNIPIHVRSSFSGLQGTW 240 Query: 241 VVGSIKD---VPMEDPILTGVAHDRSEAKVTIVGLPDIPGYAAKVFRAVADADVNIDMVL 297 V + ME I++GVAHD SEAK+T+VG+PD PG AA++FRA+ADA++NIDMV+ Sbjct: 241 VRNKEESEGAAEMEQAIISGVAHDTSEAKITVVGVPDKPGEAARIFRAIADAEINIDMVV 300 Query: 298 QNVSKVEDGKTDITFTCSRDVGPAAVEKLDSLRNEIGFSQLLYDDHIGKVSLIGAGMRSH 357 QNVS+ TDI+FT + G A+E L+ ++ IG+ L YDD IGK+SL+GAGMRS+ Sbjct: 301 QNVSQATTSLTDISFTLPKTEGRKAIEALEKVQAGIGYDSLRYDDQIGKISLVGAGMRSN 360 Query: 358 PGVTATFCEALAAVGVNIELISTSEIRISVLCRDTELDKAVVALHEAFGLGGD-EEATVY 416 PGVTATF EAL+ GVNIELISTSEIRISV+ R ++++AV A+H AFGL D +EA VY Sbjct: 361 PGVTATFFEALSNAGVNIELISTSEIRISVVTRADDVNQAVQAVHSAFGLDSDSDEAVVY 420 Query: 417 AGTGR 421 GTGR Sbjct: 421 GGTGR 425 Lambda K H 0.318 0.134 0.376 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: 506 Number of extensions: 15 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: 421 Length of database: 425 Length adjustment: 32 Effective length of query: 389 Effective length of database: 393 Effective search space: 152877 Effective search space used: 152877 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_037574568.1 BS73_RS20470 (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.815660.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-129 417.9 12.9 2.5e-129 417.7 12.9 1.0 1 NCBI__GCF_000744815.1:WP_037574568.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037574568.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.7 12.9 2.5e-129 2.5e-129 1 405 [. 1 409 [. 1 411 [. 0.97 Alignments for each domain: == domain 1 score: 417.7 bits; conditional E-value: 2.5e-129 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 + l+VqK+GG+sv++ e+ik++a+++++++k g++vvVVvSAm+ +tdel++la e +s + re d NCBI__GCF_000744815.1:WP_037574568.1 1 MGLVVQKYGGSSVADAEGIKRVARRIVDTKKAGHEVVVVVSAMGDTTDELIDLA------EEVSPIPGGRELD 67 579***************************************************......799********** PP TIGR00656 74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146 +l+ GE++s+all++a++ lg++a++++g +ag++Td+ +++A+i ++ + r+ L+eg i +vaGF+G NCBI__GCF_000744815.1:WP_037574568.1 68 MLLTAGERISMALLAMAIKSLGHEAQSFTGSQAGVITDSVHNKARIIDVTP-GRIRTSLDEGNIAIVAGFQGV 139 ***************************************************.********************9 PP TIGR00656 147 teeG.eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvl 218 ++ +iTtLGRGGSD+tA++laaal+A+ +eiyTDV+Gv+t+DPrvv++a+kid+i++e++lelA+ G kvl NCBI__GCF_000744815.1:WP_037574568.1 140 SQDSkNITTLGRGGSDTTAVALAAALDAEVCEIYTDVDGVFTADPRVVKKARKIDEIAFEDMLELASSGSKVL 212 888736******************************************************************* PP TIGR00656 219 hpralelaveakvpilvrsskekeegTlitn........kkensslvkaialeknvarltvegegmlgkrgil 283 r +e+a ++++pi vrss++ +gT + n ++e+ +++++a++ a++tv+ g+ +k+g + NCBI__GCF_000744815.1:WP_037574568.1 213 LHRCVEYARRYNIPIHVRSSFSGLQGTWVRNkeesegaaEMEQA-IISGVAHDTSEAKITVV--GVPDKPGEA 282 *******************************7777776555555.*****************..9******** PP TIGR00656 284 aeifkaLaeeeinvdlisqtese.....tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivga 351 a+if a+a++ein+d+++q s+ t+is+++ +++ +a +aL++++ ++++sl ++ ++ ++s+vga NCBI__GCF_000744815.1:WP_037574568.1 283 ARIFRAIADAEINIDMVVQNVSQattslTDISFTLPKTEGRKAIEALEKVQAGIGYDSLRYDDQIGKISLVGA 355 ******************9988888889********************************************* PP TIGR00656 352 glveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 g++++pGv++ f+al++ ++ni is+se++isv+ + d+++av+++h+++ NCBI__GCF_000744815.1:WP_037574568.1 356 GMRSNPGVTATFFEALSNAGVNIELISTSEIRISVVTRADDVNQAVQAVHSAFG 409 ***************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (425 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: 00:00:00.00 # Mc/sec: 21.01 // [ok]
This GapMind analysis is from Jul 26 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