Align glycerol kinase; EC 2.7.1.30 (characterized)
to candidate H281DRAFT_04229 H281DRAFT_04229 glycerol kinase
Query= CharProtDB::CH_121461 (502 letters) >FitnessBrowser__Burk376:H281DRAFT_04229 Length = 499 Score = 636 bits (1641), Expect = 0.0 Identities = 300/497 (60%), Positives = 389/497 (78%), Gaps = 1/497 (0%) Query: 3 EKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLV 62 + +YI+ALDQGTTSSRA++ D N++S +Q+EFEQIYP+PGWVEH+P EIW+TQ+ Sbjct: 2 QDQYILALDQGTTSSRAMLFDRLGNVVSTAQKEFEQIYPRPGWVEHNPQEIWSTQAGVAA 61 Query: 63 EVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLE 122 E + +A ++ IAAIGITNQRETTIVW++ETG PIYNAIVWQ RRTA+ C+ LK GLE Sbjct: 62 EAVTRAGMNGTSIAAIGITNQRETTIVWDRETGHPIYNAIVWQDRRTADFCDQLKEQGLE 121 Query: 123 DYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVT 182 +R+ TGL ID YFS TK++WILD+VEG+RE+A++G L FGTVD+WL+W T+G +HVT Sbjct: 122 AKVRAKTGLPIDSYFSATKIRWILDNVEGAREKAKQGRLAFGTVDSWLVWNFTKGGLHVT 181 Query: 183 DYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPISG 242 D TNASRTMLFNIHTL WDD++L+ LDIPR MLPEVR SSEVYG T ++IP++G Sbjct: 182 DVTNASRTMLFNIHTLKWDDELLDALDIPRSMLPEVRPSSEVYGPTKT-TVFASKIPLAG 240 Query: 243 IAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYA 302 IAGDQ AALFGQ+C + GM KNTYGTGCF++MNTG+K ++S+N L+TTIA ++NYA Sbjct: 241 IAGDQHAALFGQMCTESGMVKNTYGTGCFLVMNTGDKPIESKNNLVTTIAWQIGDQINYA 300 Query: 303 LEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYAR 362 LEG++F+ GA +QWLRD + +I +A + E A V + +GVY+VPAF GLGAP+W+ AR Sbjct: 301 LEGSIFIGGAVVQWLRDGLGIIKNAAEIETLARGVPHCDGVYLVPAFAGLGAPHWNARAR 360 Query: 363 GAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQF 422 G +FG+TRG + HI RA L+SIAYQ+ DVL+AM+ADSGIR+ LRVDGGA ANN LMQF Sbjct: 361 GTLFGVTRGTTSAHIARAALDSIAYQSLDVLKAMEADSGIRIGELRVDGGACANNLLMQF 420 Query: 423 QSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNY 482 Q+DILG RP+V E TALGAAYLAGLAVG+W++++ELQ + ++R F P +E + Sbjct: 421 QADILGVDAVRPKVSETTALGAAYLAGLAVGYWKDVNELQSQWKLDRRFTPALEQADVEE 480 Query: 483 RYAGWKKAVKRAMAWEE 499 GWK+A++ A AW + Sbjct: 481 CLDGWKRAIRAAKAWAD 497 Lambda K H 0.318 0.134 0.404 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: 774 Number of extensions: 20 Number of successful extensions: 2 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: 502 Length of database: 499 Length adjustment: 34 Effective length of query: 468 Effective length of database: 465 Effective search space: 217620 Effective search space used: 217620 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: 52 (24.6 bits)
Align candidate H281DRAFT_04229 H281DRAFT_04229 (glycerol kinase)
to HMM TIGR01311 (glpK: glycerol kinase (EC 2.7.1.30))
# 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.carbon/TIGR01311.hmm # target sequence database: /tmp/gapView.15263.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01311 [M=496] Accession: TIGR01311 Description: glycerol_kin: glycerol kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-229 748.3 1.2 1.7e-229 748.1 1.2 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_04229 H281DRAFT_04229 glycerol kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_04229 H281DRAFT_04229 glycerol kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 748.1 1.2 1.7e-229 1.7e-229 1 496 [] 4 495 .. 4 495 .. 0.99 Alignments for each domain: == domain 1 score: 748.1 bits; conditional E-value: 1.7e-229 TIGR01311 1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealeklei 66 ++i+a+DqGttssra++fd+ g++v++aqke++qi+p++gwvEh+p+ei++++ v+aea++++++ lcl|FitnessBrowser__Burk376:H281DRAFT_04229 4 QYILALDQGTTSSRAMLFDRLGNVVSTAQKEFEQIYPRPGWVEHNPQEIWSTQAGVAAEAVTRAGM 69 69**************************************************************** PP TIGR01311 67 kaeeiaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstY 132 + + iaaiGitnqREtt+vWd+etg+p++naivWqd+rta+++++lke++ e ++r+ktGLp+++Y lcl|FitnessBrowser__Burk376:H281DRAFT_04229 70 NGTSIAAIGITNQRETTIVWDRETGHPIYNAIVWQDRRTADFCDQLKEQGLEAKVRAKTGLPIDSY 135 ****************************************************************** PP TIGR01311 133 fsatKlrWlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwde 198 fsatK+rW+ldnve++r++a++g+l fGtvd+wl++++t+g+ hvtdvtNASRt+l+n++tlkwd+ lcl|FitnessBrowser__Burk376:H281DRAFT_04229 136 FSATKIRWILDNVEGAREKAKQGRLAFGTVDSWLVWNFTKGGLHVTDVTNASRTMLFNIHTLKWDD 201 ****************************************************************** PP TIGR01311 199 ellelfkipkellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgt 264 ell++++ip+++lPe+r+ssevyg ++++ ++ +++p++g++Gdq+aal+gq+c+++g++KntYgt lcl|FitnessBrowser__Burk376:H281DRAFT_04229 202 ELLDALDIPRSMLPEVRPSSEVYGPTKTT-VFASKIPLAGIAGDQHAALFGQMCTESGMVKNTYGT 266 ***************************99.9*********************************** PP TIGR01311 265 GcFlllntGekkviskhglLttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeevek 330 GcFl++ntG+k++ sk++l+tt+a+++g++ +yalEGs++++Ga+vqwlrd l++ik+a+e+e+ lcl|FitnessBrowser__Burk376:H281DRAFT_04229 267 GCFLVMNTGDKPIESKNNLVTTIAWQIGDQI--NYALEGSIFIGGAVVQWLRDGLGIIKNAAEIET 330 ****************************987..5******************************** PP TIGR01311 331 laksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileamek 396 la+ v++ +gvy+VPaf+GL+aP+W+++Argt++G+tr+tt++hiaraal+++a+q+ d+l+ame+ lcl|FitnessBrowser__Burk376:H281DRAFT_04229 331 LARGVPHCDGVYLVPAFAGLGAPHWNARARGTLFGVTRGTTSAHIARAALDSIAYQSLDVLKAMEA 396 ****************************************************************** PP TIGR01311 397 dagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleks 462 d+g+++ +L+vDGg+++nnllmq+qadilgv+ +rpkv ettalGaA++aglavg+wk+ +el+++ lcl|FitnessBrowser__Burk376:H281DRAFT_04229 397 DSGIRIGELRVDGGACANNLLMQFQADILGVDAVRPKVSETTALGAAYLAGLAVGYWKDVNELQSQ 462 ****************************************************************** PP TIGR01311 463 aeaeektfepemdeeerekkykkwkeaverslkw 496 ++ + ++f+p+ +++ e+ + wk+a++ ++ w lcl|FitnessBrowser__Burk376:H281DRAFT_04229 463 WKLD-RRFTPALEQADVEECLDGWKRAIRAAKAW 495 ***8.************************99988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (496 nodes) Target sequences: 1 (499 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: 00:00:00.03 # Mc/sec: 7.20 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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