Align aspartate kinase 1; EC 2.7.2.4 (characterized)
to candidate WP_013075566.1 BTUS_RS07805 aspartate kinase
Query= CharProtDB::CH_090816 (404 letters) >NCBI__GCF_000092905.1:WP_013075566.1 Length = 407 Score = 428 bits (1101), Expect = e-124 Identities = 225/404 (55%), Positives = 293/404 (72%), Gaps = 4/404 (0%) Query: 1 MKIIVQKFGGTSVKDDKGRKLALGHIKEAISEGYKVVVVVSAMGRKGDPYATDSLLGLLY 60 M+I+VQKFGGTS+ D+ R+ A+ H+++A+++ ++VVVVVSAMGR+G PYATD+LLGL+ Sbjct: 1 MRILVQKFGGTSLAGDEPRQWAVHHVEKALAQEFRVVVVVSAMGRQGAPYATDTLLGLI- 59 Query: 61 GDQSAISPREQDLLLSCGETISSVVFTSMLLDNGVKAAALTGAQAGFLTNDQHTNAKIIE 120 A +PRE DLLLSCGE IS+V F ++L + ++A ALTG QAG +T + A I+E Sbjct: 60 -PPGASTPRETDLLLSCGEIISAVSFAALLRTHKIRATALTGGQAGIVTESEFGAAPILE 118 Query: 121 MKPERLFSVLANHDAVVVAGFQGATEKGDTTTIGRGGSDTSAAALGAAVDAEYIDIFTDV 180 +KP R+ L VVVAGFQG T G+ TT+GRGGSDT+AAALG A+DAE +DIFTDV Sbjct: 119 VKPGRIIRELEQGHVVVVAGFQGRTADGEITTLGRGGSDTTAAALGVALDAERVDIFTDV 178 Query: 181 EGVMTADPRVVENAKPLPVVTYTEICNLAYQGAKVISPRAVEIAMQAKVPIRVRSTYSND 240 EG+MTADPR+V +A+ LP TYTEICNLAYQGAKVI PRAVEIAM+ +P+RVR+T S+D Sbjct: 179 EGIMTADPRIVRDARRLPQATYTEICNLAYQGAKVIHPRAVEIAMRKNIPVRVRATMSDD 238 Query: 241 KGTLVTS--HHSSKVGSDVFERLITGIAHVKDVTQFKVPAKIGQYNVQTEVFKAMANAGI 298 +GTLVT+ G D +RL+TGI + Q K+ G V VF+AMA+AGI Sbjct: 239 EGTLVTNVEDDGRLEGRDPGDRLVTGITQTSRIVQIKIAQPSGAPPVHRAVFQAMADAGI 298 Query: 299 SVDFFNITPSEIVYTVAGNKTETAQRILMDMGYDPMVTRNCAKVSAVGAGIMGVPGVTSK 358 SVDF N+ P + +TV+ + A++IL ++G + + +CAKVS VGAGI GVPGV ++ Sbjct: 299 SVDFINVGPGGVAFTVSEAEAGRAEKILRNLGVEVEIVPDCAKVSVVGAGIAGVPGVMAR 358 Query: 359 IVSALSEKEIPILQSADSHTTIWVLVHEADMVPAVNALHEEFEL 402 IV AL+E+ + ILQSADSHTTIW LV E DM AV ALH F L Sbjct: 359 IVGALAEEGVEILQSADSHTTIWCLVREGDMNRAVCALHRRFGL 402 Lambda K H 0.316 0.131 0.364 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: 493 Number of extensions: 18 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: 404 Length of database: 407 Length adjustment: 31 Effective length of query: 373 Effective length of database: 376 Effective search space: 140248 Effective search space used: 140248 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_013075566.1 BTUS_RS07805 (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.23508.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-129 416.6 0.9 6.4e-129 416.4 0.9 1.0 1 lcl|NCBI__GCF_000092905.1:WP_013075566.1 BTUS_RS07805 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092905.1:WP_013075566.1 BTUS_RS07805 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 416.4 0.9 6.4e-129 6.4e-129 1 405 [. 1 401 [. 1 403 [. 0.96 Alignments for each domain: == domain 1 score: 416.4 bits; conditional E-value: 6.4e-129 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + + VqKFGGts++++e ++ a ++v k+l ++ +vvVVvSAm++++ +++ + ll+l+ +++p lcl|NCBI__GCF_000092905.1:WP_013075566.1 1 MRILVQKFGGTSLAGDEPRQWAVHHVEKALAQEFRVVVVVSAMGRQGAPYATDT-LLGLI--PPGASTP 66 5799**************************************************.78776..56789** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re+d+l+s+GE +s++ ++ +lr + +a+al+g++agi+T++efg A i e+++ r++ Le+g +v lcl|NCBI__GCF_000092905.1:WP_013075566.1 67 RETDLLLSCGEIISAVSFAALLRTHKIRATALTGGQAGIVTESEFGAAPILEVKP-GRIIRELEQGHVV 134 *******************************************************.************* PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G+t +GeiTtLGRGGSD+tAa+l+ al+A+rv+i+TDVeG++t+DPr+v++a+++++ +y+E+ lcl|NCBI__GCF_000092905.1:WP_013075566.1 135 VVAGFQGRTADGEITTLGRGGSDTTAAALGVALDAERVDIFTDVEGIMTADPRIVRDARRLPQATYTEI 203 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn.........kkens..slvkaialekn 265 ++lA++Gakv+hpra+e+a+++++p++vr + + +egTl+tn + + +lv++i+ + lcl|NCBI__GCF_000092905.1:WP_013075566.1 204 CNLAYQGAKVIHPRAVEIAMRKNIPVRVRATMSDDEGTLVTNveddgrlegRD--PgdRLVTGITQTSR 270 ******************************************99998665433..2559********** PP TIGR00656 266 varltvegegmlgkrgilaeifkaLaeeeinvdlisqtesetsislvvdeedvdeakkaLkeesgaael 334 + ++++ + g + + +f+a+a+++i+vd+i+ ++ ++++v+e ++ +a+k+L++ lcl|NCBI__GCF_000092905.1:WP_013075566.1 271 IVQIKIA--QPSGAPPVHRAVFQAMADAGISVDFINVGP--GGVAFTVSEAEAGRAEKILRNLG----- 330 *******..999***************************..9*******************996..... PP TIGR00656 335 esleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhek 403 ++e+ d+a+vs+vgag+ ++pGv+++i+ al+e++++il++++s+t+i+ lv+e d+++av +lh++ lcl|NCBI__GCF_000092905.1:WP_013075566.1 331 VEVEIVPDCAKVSVVGAGIAGVPGVMARIVGALAEEGVEILQSADSHTTIWCLVREGDMNRAVCALHRR 399 66888999************************************************************9 PP TIGR00656 404 le 405 + lcl|NCBI__GCF_000092905.1:WP_013075566.1 400 FG 401 96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (407 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.25 // [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