Align glycerol kinase; EC 2.7.1.30 (characterized)
to candidate BWI76_RS27515 BWI76_RS27515 glycerol kinase
Query= CharProtDB::CH_121461 (502 letters) >FitnessBrowser__Koxy:BWI76_RS27515 Length = 503 Score = 967 bits (2500), Expect = 0.0 Identities = 470/502 (93%), Positives = 492/502 (98%) Query: 1 MTEKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSST 60 MT+KKYIVALDQGTTSSRAVVMDHDANI+SVSQREFEQIYP+PGWVEHDPMEIWA+QSST Sbjct: 1 MTDKKYIVALDQGTTSSRAVVMDHDANIVSVSQREFEQIYPRPGWVEHDPMEIWASQSST 60 Query: 61 LVEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDG 120 LVEVLAKADISSD+IAAIGITNQRET IVWE+ETGKPIYNAIVWQCRRTAEICE LKRDG Sbjct: 61 LVEVLAKADISSDEIAAIGITNQRETAIVWERETGKPIYNAIVWQCRRTAEICEQLKRDG 120 Query: 121 LEDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVH 180 +E+YIR TGLV+DPYFSGTKVKWILDHVEG+RERA+RGELLFGTVDTWLIWKMTQGRVH Sbjct: 121 MEEYIRKATGLVVDPYFSGTKVKWILDHVEGARERAKRGELLFGTVDTWLIWKMTQGRVH 180 Query: 181 VTDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPI 240 VTDYTNASRTMLFNIH LDWDDKML+ LDIPR MLPEVR+SSEVYGQTNIGGKGGTRIPI Sbjct: 181 VTDYTNASRTMLFNIHELDWDDKMLDALDIPRAMLPEVRKSSEVYGQTNIGGKGGTRIPI 240 Query: 241 SGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVN 300 +GIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAV S +GLLTTIACGP GEVN Sbjct: 241 AGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVTSTHGLLTTIACGPRGEVN 300 Query: 301 YALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPY 360 YALEGAVFMAGASIQWLRDEMKLI+DA+DSEYFATKV++TNGVYVVPAFTGLGAPYWDPY Sbjct: 301 YALEGAVFMAGASIQWLRDEMKLISDAFDSEYFATKVKDTNGVYVVPAFTGLGAPYWDPY 360 Query: 361 ARGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLM 420 ARGAIFGLTRGVN+NHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLM Sbjct: 361 ARGAIFGLTRGVNSNHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLM 420 Query: 421 QFQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTER 480 QFQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTER Sbjct: 421 QFQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTER 480 Query: 481 NYRYAGWKKAVKRAMAWEEHDE 502 NYRY+GWKKAVKRA+AWEEHDE Sbjct: 481 NYRYSGWKKAVKRALAWEEHDE 502 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: 970 Number of extensions: 20 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: 502 Length of database: 503 Length adjustment: 34 Effective length of query: 468 Effective length of database: 469 Effective search space: 219492 Effective search space used: 219492 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 BWI76_RS27515 BWI76_RS27515 (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.29849.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-234 765.3 0.9 1.2e-234 765.1 0.9 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS27515 BWI76_RS27515 glycerol kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS27515 BWI76_RS27515 glycerol kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 765.1 0.9 1.2e-234 1.2e-234 1 496 [] 5 497 .. 5 497 .. 0.99 Alignments for each domain: == domain 1 score: 765.1 bits; conditional E-value: 1.2e-234 TIGR01311 1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeei 71 k+i+a+DqGttssra+v+d+++++v+ +q+e++qi+p++gwvEhdp+ei++s+ ++l e+l+k++i+++ei lcl|FitnessBrowser__Koxy:BWI76_RS27515 5 KYIVALDQGTTSSRAVVMDHDANIVSVSQREFEQIYPRPGWVEHDPMEIWASQSSTLVEVLAKADISSDEI 75 69********************************************************************* PP TIGR01311 72 aaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWll 142 aaiGitnqREt++vW++etgkp++naivWq++rta+i+e+lk+++ ee++r+ tGL++++Yfs+tK++W+l lcl|FitnessBrowser__Koxy:BWI76_RS27515 76 AAIGITNQRETAIVWERETGKPIYNAIVWQCRRTAEICEQLKRDGMEEYIRKATGLVVDPYFSGTKVKWIL 146 *********************************************************************** PP TIGR01311 143 dnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPe 213 d+ve++r++a++gellfGtvdtwli+k+t+g+vhvtd+tNASRt+l+n+++l+wd+++l++++ip+++lPe lcl|FitnessBrowser__Koxy:BWI76_RS27515 147 DHVEGARERAKRGELLFGTVDTWLIWKMTQGRVHVTDYTNASRTMLFNIHELDWDDKMLDALDIPRAMLPE 217 *********************************************************************** PP TIGR01311 214 irsssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglL 284 +r+ssevyg+++ ++++pi+g++Gdqqaal+gqlc+k+g+aKntYgtGcF+l+ntGek+v+s+hglL lcl|FitnessBrowser__Koxy:BWI76_RS27515 218 VRKSSEVYGQTNIGGKGGTRIPIAGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVTSTHGLL 288 **************9******************************************************** PP TIGR01311 285 ttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyW 355 tt+a+ g+ +yalEG+v++aGa +qwlrd++kli++a ++e +a++v+d++gvy+VPaf+GL+aPyW lcl|FitnessBrowser__Koxy:BWI76_RS27515 289 TTIACGPRGEV--NYALEGAVFMAGASIQWLRDEMKLISDAFDSEYFATKVKDTNGVYVVPAFTGLGAPYW 357 *****999877..6********************************************************* PP TIGR01311 356 dsdArgtivGltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilg 426 d+ Arg+i+Gltr+++++hi+ra+le++a+q+rd+leam++d+g+++++L+vDGg+++nn+lmq+q+dilg lcl|FitnessBrowser__Koxy:BWI76_RS27515 358 DPYARGAIFGLTRGVNSNHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDILG 428 *********************************************************************** PP TIGR01311 427 vkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496 ++verp+v e+talGaA++aglavg+w++++el+++a e ++f+p ++++er+ +y+ wk+av+r+l w lcl|FitnessBrowser__Koxy:BWI76_RS27515 429 TRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIE-REFRPGIETTERNYRYSGWKKAVKRALAW 497 ************************************9997.**************************988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (496 nodes) Target sequences: 1 (503 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8.54 // [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