Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate Pf6N2E2_5676 Aspartokinase (EC 2.7.2.4)
Query= SwissProt::C3JXY0 (413 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 Length = 413 Score = 745 bits (1923), Expect = 0.0 Identities = 392/413 (94%), Positives = 401/413 (97%) Query: 1 MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60 MALIVQKFGGTSVG+VERIEQVADKVKKFR+AGDDLVVVLSAMSGETNRLIDLAK ISGD Sbjct: 1 MALIVQKFGGTSVGTVERIEQVADKVKKFREAGDDLVVVLSAMSGETNRLIDLAKQISGD 60 Query: 61 QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120 QQP+PRELDVIVSTGEQVTIALLAMAL KRGVPAVSYTG+QVRILTDSAH KARILQIDD Sbjct: 61 QQPVPRELDVIVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHNKARILQIDD 120 Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180 QKIR DLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV Sbjct: 121 QKIRGDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180 Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240 YTTDPRVV VAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT Sbjct: 181 YTTDPRVVPVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240 Query: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV 300 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPIS ANIEVDMIVQNV Sbjct: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANIEVDMIVQNV 300 Query: 301 SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360 SHDNTTDFTFTVHRN+Y +AE IL+ TA EIGAREVVGDTKIAKVSIVGVGMRSHAGVAS Sbjct: 301 SHDNTTDFTFTVHRNDYQSAEAILKKTAGEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360 Query: 361 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE 413 RMFE+LAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDA A+ GE Sbjct: 361 RMFESLAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAAAQPGE 413 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: 700 Number of extensions: 22 Number of successful extensions: 1 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: 413 Length adjustment: 31 Effective length of query: 382 Effective length of database: 382 Effective search space: 145924 Effective search space used: 145924 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 Pf6N2E2_5676 (Aspartokinase (EC 2.7.2.4))
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.14779.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-135 436.9 12.8 4.3e-135 436.8 12.8 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 Aspartokinase (EC 2.7.2.4) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 Aspartokinase (EC 2.7.2.4) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 436.8 12.8 4.3e-135 4.3e-135 1 406 [. 1 405 [. 1 406 [. 0.97 Alignments for each domain: == domain 1 score: 436.8 bits; conditional E-value: 4.3e-135 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleais 64 + liVqKFGGtsvg +eri+++a++v+k + g++ vVV+SAms++t++l++la+ + + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 1 MALIVQKFGGTSVGTVERIEQVADKVKKFREAGDDLVVVLSAMSGETNRLIDLAK----QISGD 60 579***************************************************5....44556 PP TIGR00656 65 deisprerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerL 128 +++ pre d +vs+GE++++all++al ++gv a++++g++ ilTd+ +++A+i +++ +++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 61 QQPVPRELDVIVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHNKARILQIDD-QKI 123 7889*******************************************************9.*** PP TIGR00656 129 lelLeegiivvvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrv 192 L+ g +vvvaGF+G +e+G+iTtLGRGGSD+t ++laaalkAd+++iyTDV+GvyttDPrv lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 124 RGDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTDPRV 187 **************************************************************** PP TIGR00656 193 veeakkidkisyeEalelAtlGakvlhpralelaveakvpilvrsskekeegTlitn....kke 252 v+ a+++dki++eE+le+A+lG kvl+ ra+e+a +++vp++v +s+++ gTlit ++e lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 188 VPVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGTLITIdeeeSME 251 *******************************************************985555666 PP TIGR00656 253 nsslvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvv 313 ++ ++++ia++++ a+lt++ g+ + +g++ +i + ++ ++i vd+i+q s+ t+ +++v lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 252 QP-IISGIAFNRDEAKLTIR--GVPDTPGVAFKILGPISAANIEVDMIVQNVSHdntTDFTFTV 312 66.*****************..9****************************9988999****** PP TIGR00656 314 deedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmi 377 +++d ++a+++Lk++ g+++ +++ + ++a+vsivg+g++++ Gvas++f+ l+++ ini mi lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 313 HRNDYQSAEAILKKTAGEIGAREVVGDTKIAKVSIVGVGMRSHAGVASRMFESLAKESINIQMI 376 **************************************************************** PP TIGR00656 378 sssetkisvlvdekdaekavrklheklee 406 s+se+k+sv+++ek++e avr+lh ++e+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 377 STSEIKVSVVIEEKYLELAVRALHTAFEL 405 **************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (413 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.23 // [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