Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate AZOBR_RS25905 AZOBR_RS25905 glycerol kinase
Query= reanno::Smeli:SM_b21009 (497 letters) >FitnessBrowser__azobra:AZOBR_RS25905 Length = 501 Score = 625 bits (1613), Expect = 0.0 Identities = 301/492 (61%), Positives = 371/492 (75%), Gaps = 2/492 (0%) Query: 3 GYILAIDQGTTSTRAIVFDGNQKIAGVGQKEFKQHFPKSGWVEHDPEEIWQTVVSTVKEA 62 G++LAIDQGTTSTRAIVFD AGV ++EF QH+P GWVEHDPE+IW+ V+ ++ A Sbjct: 5 GHVLAIDQGTTSTRAIVFDRRGVPAGVARREFAQHYPADGWVEHDPEDIWRDTVAVMRGA 64 Query: 63 IEKSGITANDIAAIGITNQRETVVVWDRETGKPIHNAIVWQDRRTAAFCDKLKKKGLEKT 122 ++++G++A DIAAIGITNQRET VVWDR TG+P+H AIVWQDRRT+ C KL ++G Sbjct: 65 VDEAGLSAADIAAIGITNQRETTVVWDRRTGEPVHRAIVWQDRRTSDLCRKLVEEGCGPL 124 Query: 123 FVKKTGLLLDPYFSGTKLNWLLSNVKGAQVRAAKGELCFGTIDTFLIWRLTGGECFCTDA 182 +KTGLL+D YFS TK+ W+L +V GA+ RA +GELCFGTID+FL+ RLTGG TDA Sbjct: 125 VRRKTGLLIDSYFSATKIAWILDHVPGARERAERGELCFGTIDSFLLHRLTGGRVHATDA 184 Query: 183 TNASRTLLYNIAENAWDDELTEVLRVPKEMLPEVKDCAADFGVTDPSLFGAAIPILGVAG 242 TNASR+++++I WDDEL + R+P+ M+PEV D +A+FG T+P L G AIPI G+AG Sbjct: 185 TNASRSMVFDIHRQDWDDELLALFRIPRAMMPEVLDSSAEFGATEPDLLGRAIPITGIAG 244 Query: 243 DQQAATIGQACFKPGMLKSTYGTGCFALLNTGKDMVRSKNRLLTTIAYRLDGETTYALEG 302 DQQAAT GQACF+PGM+KSTYGTGCFALLNTG + V S++ +LTT+AYRLDG TTYALEG Sbjct: 245 DQQAATFGQACFQPGMVKSTYGTGCFALLNTGDEPVESRSNMLTTVAYRLDGRTTYALEG 304 Query: 303 SIFVAGAAVQWLRDGLKVIKAAPDTGSLAESADPSQEVYLVPAFTGLGAPHWDPDARGAI 362 SIF+AGAA++WLRDGL +I A T +A S VYLVPAF GLGAPHWDP AR AI Sbjct: 305 SIFIAGAAIKWLRDGLGIITHASQTDDMATRVPDSHGVYLVPAFVGLGAPHWDPQARAAI 364 Query: 363 FGMTRNTGPAEFARAALEAVCYQTRDLLEAMHKDW--RRNGNDTVLRVDGGMVASDWTMQ 420 FG+T + GPA ARAALEAV +QTRDL +AM DW LRVDGGM A+DW Q Sbjct: 365 FGLTLDAGPAHIARAALEAVAFQTRDLRDAMVSDWSAAHTATSDALRVDGGMAANDWLCQ 424 Query: 421 RLSDLLDAPVDRPVILETTALGVAWLAGSRAGVWPNQEAFAKSWARDRRFEPHMDEATRK 480 L+D+LD PV+RP ++ETTALG A LAG + GV+ +Q A A +W DRRFEP MD A R Sbjct: 425 FLADVLDLPVERPAVIETTALGAAGLAGLKVGVYRDQAALAGAWRCDRRFEPRMDAAKRV 484 Query: 481 VKLKGWRSAVKR 492 GW AV+R Sbjct: 485 RLYDGWLDAVRR 496 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: 838 Number of extensions: 26 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: 497 Length of database: 501 Length adjustment: 34 Effective length of query: 463 Effective length of database: 467 Effective search space: 216221 Effective search space used: 216221 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 AZOBR_RS25905 AZOBR_RS25905 (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.27537.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-213 695.1 0.0 2.3e-213 694.9 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS25905 AZOBR_RS25905 glycerol kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS25905 AZOBR_RS25905 glycerol kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 694.9 0.0 2.3e-213 2.3e-213 2 493 .. 6 497 .. 5 500 .. 0.98 Alignments for each domain: == domain 1 score: 694.9 bits; conditional E-value: 2.3e-213 TIGR01311 2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaee 70 ++aiDqGtts+raivfd++g + a++e+ q++p +gwvEhdp++i++++v+v++ a+++++ +a++ lcl|FitnessBrowser__azobra:AZOBR_RS25905 6 HVLAIDQGTTSTRAIVFDRRGVPAGVARREFAQHYPADGWVEHDPEDIWRDTVAVMRGAVDEAGLSAAD 74 589****************************************************************** PP TIGR01311 71 iaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlr 139 iaaiGitnqREttvvWd++tg+p++ aivWqd+rt++++++l ee+ +r+ktGL++++YfsatK++ lcl|FitnessBrowser__azobra:AZOBR_RS25905 75 IAAIGITNQRETTVVWDRRTGEPVHRAIVWQDRRTSDLCRKLVEEGCGPLVRRKTGLLIDSYFSATKIA 143 ********************************************************************* PP TIGR01311 140 WlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipk 208 W+ld+v+++r++ae+gel+fGt+d++l+++Ltgg+vh+td+tNASR +++++++++wd+ell+lf+ip+ lcl|FitnessBrowser__azobra:AZOBR_RS25905 144 WILDHVPGARERAERGELCFGTIDSFLLHRLTGGRVHATDATNASRSMVFDIHRQDWDDELLALFRIPR 212 ********************************************************************* PP TIGR01311 209 ellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkv 277 +++Pe+ +ss+ +g +e++ ll++++pitg++Gdqqaa +gq+c+++g++K+tYgtGcF llntG+++v lcl|FitnessBrowser__azobra:AZOBR_RS25905 213 AMMPEVLDSSAEFGATEPD-LLGRAIPITGIAGDQQAATFGQACFQPGMVKSTYGTGCFALLNTGDEPV 280 ******************9.************************************************* PP TIGR01311 278 iskhglLttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPa 346 s++++Lttvay+l+g+++ yalEGs+++aGaa++wlrd l++i++a++++++a++v+ds+gvy+VPa lcl|FitnessBrowser__azobra:AZOBR_RS25905 281 ESRSNMLTTVAYRLDGRTT--YALEGSIFIAGAAIKWLRDGLGIITHASQTDDMATRVPDSHGVYLVPA 347 ****************986..************************************************ PP TIGR01311 347 fsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileamekdagvevk....vLkvDGgl 411 f GL+aP+Wd++Ar++i+Glt ++ +hiaraaleavafq+rd+ +am +d + + +L+vDGg+ lcl|FitnessBrowser__azobra:AZOBR_RS25905 348 FVGLGAPHWDPQARAAIFGLTLDAGPAHIARAALEAVAFQTRDLRDAMVSDWSAAHTatsdALRVDGGM 416 ***************************************************99544444559******* PP TIGR01311 412 sknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepemdeeere 480 ++n++l+q+ ad+l+++verp v ettalGaA +agl+vgv++++ l+ ++ + ++fep+md+++r lcl|FitnessBrowser__azobra:AZOBR_RS25905 417 AANDWLCQFLADVLDLPVERPAVIETTALGAAGLAGLKVGVYRDQAALAGAWRCD-RRFEPRMDAAKRV 484 ******************************************************8.************* PP TIGR01311 481 kkykkwkeavers 493 + y w +av+r lcl|FitnessBrowser__azobra:AZOBR_RS25905 485 RLYDGWLDAVRRV 497 **********997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (496 nodes) Target sequences: 1 (501 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: 10.84 // [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