Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate GFF2212 HP15_2166 glycerol kinase
Query= reanno::Smeli:SM_b21009 (497 letters) >FitnessBrowser__Marino:GFF2212 Length = 490 Score = 572 bits (1473), Expect = e-167 Identities = 283/492 (57%), Positives = 356/492 (72%), Gaps = 3/492 (0%) Query: 1 MGGYILAIDQGTTSTRAIVFDGNQKIAGVGQKEFKQHFPKSGWVEHDPEEIWQTVVSTVK 60 M YIL+IDQGTTS+RAI+FD I Q+EF QHFP SGWVEH+PE++W +V T Sbjct: 1 MSQYILSIDQGTTSSRAILFDLQGNIHATRQQEFPQHFPASGWVEHNPEDLWSSVKQTCD 60 Query: 61 EAIEKSGITANDIAAIGITNQRETVVVWDRETGKPIHNAIVWQDRRTAAFCDKLKKKGLE 120 + + +++ A+GITNQRET VVWDR+TG+P++NAIVWQDRRTA++C+ LK +GLE Sbjct: 61 AVMAEECGDRDEVIAVGITNQRETTVVWDRQTGEPVYNAIVWQDRRTASYCESLKSEGLE 120 Query: 121 KTFVKKTGLLLDPYFSGTKLNWLLSNVKGAQVRAAKGELCFGTIDTFLIWRLTGGECFCT 180 KTGLL+DPYFS TKL W+L NV G + RA +GEL FGT+D+FL+WRLTGG T Sbjct: 121 PWVSSKTGLLVDPYFSATKLRWILENVAGVRERAERGELAFGTVDSFLLWRLTGGREHRT 180 Query: 181 DATNASRTLLYNIAENAWDDELTEVLRVPKEMLPEVKDCAADFGVTDPSLFGAAIPILGV 240 DATNASRTLL+NI WD EL ++ +P+ +LPEV D A FG + +LGV Sbjct: 181 DATNASRTLLFNIHNQKWDPELLQLFDIPESLLPEVMDSADQFGRITEGGALSGTSVLGV 240 Query: 241 AGDQQAATIGQACFKPGMLKSTYGTGCFALLNTGKDMVRSKNRLLTTIAYRLDGETTYAL 300 AGDQQAA GQ CF GM KSTYGTGCF +LNTG ++SK+RLLTT+AYR++G+ TYAL Sbjct: 241 AGDQQAALFGQTCFGIGMAKSTYGTGCFLMLNTGDKALQSKHRLLTTVAYRVNGKPTYAL 300 Query: 301 EGSIFVAGAAVQWLRDGLKVIKAAPDTGSLAESADPSQEVYLVPAFTGLGAPHWDPDARG 360 EGSIF+AGA +QWLRDGL++I+ A +T LAE VYLVPAFTGLGAP+WDP+ARG Sbjct: 301 EGSIFIAGATIQWLRDGLRLIRDACETEPLAEGTPVDHGVYLVPAFTGLGAPYWDPNARG 360 Query: 361 AIFGMTRNTGPAEFARAALEAVCYQTRDLLEAMHKDWRRNGNDTVLRVDGGMVASDWTMQ 420 AIFG+TR+TG E A L++VCYQT+DL +AM KD R N LRVDGGMVA++W +Q Sbjct: 361 AIFGLTRDTGIKEIVTAGLQSVCYQTKDLQKAMEKDGIRPVN---LRVDGGMVANNWVLQ 417 Query: 421 RLSDLLDAPVDRPVILETTALGVAWLAGSRAGVWPNQEAFAKSWARDRRFEPHMDEATRK 480 L+D+L A VDRP ++ETTALG A+LAG AGV+ + E + W DR FEP M + R Sbjct: 418 FLADILGARVDRPSLVETTALGAAYLAGLEAGVYGSLEELSDLWRCDRNFEPVMTKEHRD 477 Query: 481 VKLKGWRSAVKR 492 GW AV++ Sbjct: 478 KLYDGWSQAVQK 489 Lambda K H 0.319 0.134 0.415 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: 830 Number of extensions: 33 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: 497 Length of database: 490 Length adjustment: 34 Effective length of query: 463 Effective length of database: 456 Effective search space: 211128 Effective search space used: 211128 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
Align candidate GFF2212 HP15_2166 (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.24347.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-216 703.0 0.0 9.2e-216 702.8 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF2212 HP15_2166 glycerol kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF2212 HP15_2166 glycerol kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 702.8 0.0 9.2e-216 9.2e-216 1 492 [. 3 489 .. 3 490 .] 0.99 Alignments for each domain: == domain 1 score: 702.8 bits; conditional E-value: 9.2e-216 TIGR01311 1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiG 75 ++i++iDqGttssrai+fd +g++ a+ q+e+ q+fp +gwvEh+p+++++sv++++ ++++ + +e++a+G lcl|FitnessBrowser__Marino:GFF2212 3 QYILSIDQGTTSSRAILFDLQGNIHATRQQEFPQHFPASGWVEHNPEDLWSSVKQTCDAVMAEECGDRDEVIAVG 77 69************************************************************************* PP TIGR01311 76 itnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveevrk 150 itnqREttvvWd++tg+p++naivWqd+rta+++e+lk+e+ e +++ktGL++++YfsatKlrW+l+nv +vr+ lcl|FitnessBrowser__Marino:GFF2212 78 ITNQRETTVVWDRQTGEPVYNAIVWQDRRTASYCESLKSEGLEPWVSSKTGLLVDPYFSATKLRWILENVAGVRE 152 *************************************************************************** PP TIGR01311 151 aaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevygeie 225 +ae+gel fGtvd++l+++Ltgg++h td+tNASRtll+n++++kwd ell+lf+ip++llPe+++s++++g i+ lcl|FitnessBrowser__Marino:GFF2212 153 RAERGELAFGTVDSFLLWRLTGGREHRTDATNASRTLLFNIHNQKWDPELLQLFDIPESLLPEVMDSADQFGRIT 227 *************************************************************************** PP TIGR01311 226 ekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkptkya 300 e + +++ + gv+Gdqqaal+gq+c+ g+aK+tYgtGcFl+lntG+k++ skh+lLttvay+++gk + ya lcl|FitnessBrowser__Marino:GFF2212 228 EG-GALSGTSVLGVAGDQQAALFGQTCFGIGMAKSTYGTGCFLMLNTGDKALQSKHRLLTTVAYRVNGKPT--YA 299 *9.89999***********************************************************9875..** PP TIGR01311 301 lEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehi 375 lEGs+++aGa++qwlrd l+li++a e+e+la+ + ++gvy+VPaf+GL+aPyWd++Arg+i+Gltr+t ++i lcl|FitnessBrowser__Marino:GFF2212 300 LEGSIFIAGATIQWLRDGLRLIRDACETEPLAEGTPVDHGVYLVPAFTGLGAPYWDPNARGAIFGLTRDTGIKEI 374 *************************************************************************** PP TIGR01311 376 araaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalGaAlaaglav 450 ++a l++v++q++d+ +amekd + +L+vDGg+++nn+++q+ adilg +v rp+ +ettalGaA++agl++ lcl|FitnessBrowser__Marino:GFF2212 375 VTAGLQSVCYQTKDLQKAMEKDGI-RPVNLRVDGGMVANNWVLQFLADILGARVDRPSLVETTALGAAYLAGLEA 448 *********************985.5557********************************************** PP TIGR01311 451 gvwkseeeleksaeaeektfepemdeeerekkykkwkeaver 492 gv+ s+eel++ ++ + ++fep m++e+r+k y w++av++ lcl|FitnessBrowser__Marino:GFF2212 449 GVYGSLEELSDLWRCD-RNFEPVMTKEHRDKLYDGWSQAVQK 489 ***************8.***********************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (496 nodes) Target sequences: 1 (490 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10.80 // [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