Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate CCNA_00886 CCNA_00886 aspartokinase
Query= SwissProt::A4VJB4 (412 letters) >FitnessBrowser__Caulo:CCNA_00886 Length = 415 Score = 392 bits (1008), Expect = e-114 Identities = 221/415 (53%), Positives = 287/415 (69%), Gaps = 13/415 (3%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 M+ +V KFGGTSV +ERI +VA V G + VVVSAMSG+TN L+ Sbjct: 1 MSRLVMKFGGTSVADLERIRRVARLVAAEVATGKQVAVVVSAMSGKTNELVAWTDGAGRA 60 Query: 61 PV-----PRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQ 115 E D +V++GEQVT LLAM L G A S+ G QV ILTD AH +ARI + Sbjct: 61 AAGLPESDDEYDAVVASGEQVTAGLLAMTLRNMGHKARSFLGWQVPILTDEAHGRARIEE 120 Query: 116 IDAQRIQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDV 175 I + ++ G + V+AGFQGV ITTLGRGGSDT+ VA+AAA+K D C IYTDV Sbjct: 121 IPPENLEECFANGEIAVIAGFQGVTPNRRITTLGRGGSDTSAVAIAAAVKGD-CDIYTDV 179 Query: 176 DGVYTTDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQE- 234 DGVYTTDPR+ +KA+RL KI++EEMLEMASLG+KVLQ R+VE A + VP+RVL SF E Sbjct: 180 DGVYTTDPRIESKARRLAKISYEEMLEMASLGAKVLQTRSVEMAMAHRVPVRVLSSFVEP 239 Query: 235 ----GPGTLITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVE 290 G GT++ DEEE ME+ I+SG+A++RDEAK+T+ G+PD PGV+ +I G ++ ANV Sbjct: 240 GEAPGQGTIVC-DEEEIMEKRIVSGVAYSRDEAKITLLGLPDHPGVSSQIFGRLAEANVN 298 Query: 291 VDMIVQNVAHD-NTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVG 349 VDMIVQ+ A +T + FTV + D A++++Q E+G + ++AKVS++GVG Sbjct: 299 VDMIVQSRARSADTANMEFTVGKRDATRAVEIVQAAQKEIGFEAVAVNEDVAKVSVIGVG 358 Query: 350 MRSHAGVASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404 MRSHAGVA MF+ALA++NINIQ+ISTSEIK+SV+I+ Y ELAVRALH + LD Sbjct: 359 MRSHAGVAQSMFQALAEKNINIQVISTSEIKISVLIDAAYTELAVRALHAVYGLD 413 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: 445 Number of extensions: 22 Number of successful extensions: 6 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: 415 Length adjustment: 31 Effective length of query: 381 Effective length of database: 384 Effective search space: 146304 Effective search space used: 146304 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 CCNA_00886 CCNA_00886 (aspartokinase)
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.32055.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-132 426.5 10.4 6.3e-132 426.3 10.4 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_00886 CCNA_00886 aspartokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_00886 CCNA_00886 aspartokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 426.3 10.4 6.3e-132 6.3e-132 4 405 .. 4 411 .. 1 413 [. 0.94 Alignments for each domain: == domain 1 score: 426.3 bits; conditional E-value: 6.3e-132 TIGR00656 4 iVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdei....sprer 72 V+KFGGtsv++ eri+++a++v +e+ gk+v VVvSAms++t+elv+ ++ a + + s+ e lcl|FitnessBrowser__Caulo:CCNA_00886 4 LVMKFGGTSVADLERIRRVARLVAAEVATGKQVAVVVSAMSGKTNELVAWTDG-----AGRAAAglpeSDDEY 71 69*************************************************82.....2222223334899** PP TIGR00656 73 delvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiG 145 d +v+ GE++++ ll++ lr+ g+ka+++ g++ +ilTd+ +g+A+i+e+ + e+L+e ++g i v+aGF+G lcl|FitnessBrowser__Caulo:CCNA_00886 72 DAVVASGEQVTAGLLAMTLRNMGHKARSFLGWQVPILTDEAHGRARIEEIPP-ENLEECFANGEIAVIAGFQG 143 ****************************************************.******************** PP TIGR00656 146 ateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvl 218 t + +iTtLGRGGSD++A+++aaa+k d ++iyTDV+GvyttDPr+ ++a++++kisyeE+le+A+lGakvl lcl|FitnessBrowser__Caulo:CCNA_00886 144 VTPNRRITTLGRGGSDTSAVAIAAAVKGD-CDIYTDVDGVYTTDPRIESKARRLAKISYEEMLEMASLGAKVL 215 ***************************76.9****************************************** PP TIGR00656 219 hpralelaveakvpilvrssk.....ekeegTlitnkkens..slvkaialeknvarltvegegmlgkrgila 284 + r++e+a++ vp++v ss+ + +gT +++++e ++v+++a++++ a++t+ g+ +++g+ + lcl|FitnessBrowser__Caulo:CCNA_00886 216 QTRSVEMAMAHRVPVRVLSSFvepgeAPGQGTIVCDEEEIMekRIVSGVAYSRDEAKITLL--GLPDHPGVSS 286 *****************9997433323459*****955533348*****************..99******** PP TIGR00656 285 eifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgagl 353 +if++Lae+++nvd+i+q++++ +++++v ++d+++a+++ ++ ++++++e + v+ed+a+vs++g+g+ lcl|FitnessBrowser__Caulo:CCNA_00886 287 QIFGRLAEANVNVDMIVQSRARsadtANMEFTVGKRDATRAVEIVQAAQKEIGFEAVAVNEDVAKVSVIGVGM 359 ********************99989889********************************************* PP TIGR00656 354 veapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 +++ Gva+ +f+al+eknini is+se+kisvl+d +++e avr+lh+++ lcl|FitnessBrowser__Caulo:CCNA_00886 360 RSHAGVAQSMFQALAEKNINIQVISTSEIKISVLIDAAYTELAVRALHAVYG 411 ************************************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (415 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: 11.68 // [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