Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate 208653 DVU3134 glycerol kinase
Query= SwissProt::O66131 (496 letters) >MicrobesOnline__882:208653 Length = 497 Score = 638 bits (1645), Expect = 0.0 Identities = 313/495 (63%), Positives = 373/495 (75%), Gaps = 1/495 (0%) Query: 1 MNQYMLAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIA 60 M+ Y+LA+DQGTTSSRAILF ++G+I ++QKEFTQ +PQPGWVEHNANEI+ + V+ Sbjct: 1 MSNYVLALDQGTTSSRAILFTREGDIKQISQKEFTQIYPQPGWVEHNANEIFDTQSWVMR 60 Query: 61 SVLSEAQVKPEQVAGIGITNQRETTVVWEKDTGNPIYNAIVWQSRQTAGICDELKAKGYD 120 L EA + V GITNQRETTVVW+K TG P+YNAIVWQ R+TAG CDELKA+G Sbjct: 61 ECLQEAGIGAADVVAAGITNQRETTVVWDKATGAPVYNAIVWQDRRTAGFCDELKARGLA 120 Query: 121 PLFRKKTGLLIDAYFSGTKVKWILDHVDGARERAERGELLFGTIDTWLIWKLSGGRVHVT 180 +FRKKTGL++DAYFSGTKV+WILD+V GAR +AE+GELLFGTIDTWLIW L+ G+ HVT Sbjct: 121 DVFRKKTGLVLDAYFSGTKVRWILDNVPGARAKAEKGELLFGTIDTWLIWNLTKGKAHVT 180 Query: 181 DYSNASRTLMFNIHTLEWDDELLDILGVPKAMLPEVRPSSEVYAKTAPYHFFGVEVPIAG 240 D SNASRTLMFNI+T WDDELL IL VP++MLP V SSEV P F G +PIAG Sbjct: 181 DSSNASRTLMFNINTGAWDDELLGILDVPRSMLPRVTGSSEVVGDIHP-EFLGKAIPIAG 239 Query: 241 AAGDQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVASKHGLLTTIAWGIDGKVEYA 300 AGDQQAA +G AC GMAKNTYGTGCFMLMNTG + +S++ LL+T+AW YA Sbjct: 240 NAGDQQAATYGNACLKPGMAKNTYGTGCFMLMNTGTEVRSSQNNLLSTVAWTTPSGRFYA 299 Query: 301 LEGSIFVAGSAIQWLRDGLRMIKTAADSETYAEKVESTDGVYVVPAFIGLGTPYWDSEVR 360 LEGS+F+AG+ +QWLRDGL +IK A + E A V GVY+VPAF GLG P+WD R Sbjct: 300 LEGSVFIAGAVVQWLRDGLGIIKAAPEVEQLALSVPDNGGVYLVPAFAGLGAPHWDQYAR 359 Query: 361 GAVFGLTRGTTKEHFIRATLESLAYQTKDVLAVMEADSGISLTTLRVDGGAVKNNFLMQF 420 G + G+TRG TK H RA LES+A QT D++ M+ DSGI L LR DGGA +NN LMQF Sbjct: 360 GTMVGITRGATKAHIARAALESIALQTLDIMDCMQKDSGIKLAALRADGGATRNNLLMQF 419 Query: 421 QSDLLAVPVERPVVNETTALGAAYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDDKRTM 480 Q+D+L VPVERP V ETTALGAAYLAGLA G+W S D+IA WQL+RRFEP M DDKR Sbjct: 420 QADVLGVPVERPKVTETTALGAAYLAGLATGFWKSEDEIATMWQLDRRFEPNMSDDKRQH 479 Query: 481 LYDGWKKAVRAAMAF 495 L W++AV A A+ Sbjct: 480 LVYEWQRAVERAKAW 494 Lambda K H 0.319 0.134 0.406 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: 783 Number of extensions: 30 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: 496 Length of database: 497 Length adjustment: 34 Effective length of query: 462 Effective length of database: 463 Effective search space: 213906 Effective search space used: 213906 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 (21.7 bits) S2: 52 (24.6 bits)
Align candidate 208653 DVU3134 (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.28293.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-226 736.2 1.3 7.7e-226 736.0 1.3 1.0 1 lcl|MicrobesOnline__882:208653 DVU3134 glycerol kinase Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:208653 DVU3134 glycerol kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 736.0 1.3 7.7e-226 7.7e-226 1 496 [] 3 494 .. 3 494 .. 0.99 Alignments for each domain: == domain 1 score: 736.0 bits; conditional E-value: 7.7e-226 TIGR01311 1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiGitnq 79 ++++a+DqGttssrai+f++eg++ ++qke++qi+p++gwvEh+++ei++++ v++e l++++i a++++a Gitnq lcl|MicrobesOnline__882:208653 3 NYVLALDQGTTSSRAILFTREGDIKQISQKEFTQIYPQPGWVEHNANEIFDTQSWVMRECLQEAGIGAADVVAAGITNQ 81 59***************************************************************************** PP TIGR01311 80 REttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveevrkaaeegell 158 REttvvWdk+tg p++naivWqd+rta +++elk+++ + +r+ktGL+l++Yfs+tK+rW+ldnv+++r++ae+gell lcl|MicrobesOnline__882:208653 82 RETTVVWDKATGAPVYNAIVWQDRRTAGFCDELKARGLADVFRKKTGLVLDAYFSGTKVRWILDNVPGARAKAEKGELL 160 ******************************************************************************* PP TIGR01311 159 fGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevygeieekellkeevpit 237 fGt+dtwli++Lt+gk+hvtd +NASRtl++n++t +wd+ell ++++p+++lP+++ ssev+g+i+++ +l++++pi+ lcl|MicrobesOnline__882:208653 161 FGTIDTWLIWNLTKGKAHVTDSSNASRTLMFNINTGAWDDELLGILDVPRSMLPRVTGSSEVVGDIHPE-FLGKAIPIA 238 *********************************************************************.********* PP TIGR01311 238 gvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkptkyalEGsvavaGaavqwlr 316 g +Gdqqaa +g++clk+g+aKntYgtGcF+l+ntG+++ s+++lL+tva+++ + + yalEGsv++aGa+vqwlr lcl|MicrobesOnline__882:208653 239 GNAGDQQAATYGNACLKPGMAKNTYGTGCFMLMNTGTEVRSSQNNLLSTVAWTTPSGR--FYALEGSVFIAGAVVQWLR 315 *****************************************************98766..6****************** PP TIGR01311 317 dnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileame 395 d l++ik a eve+la sv+d++gvy+VPaf+GL+aP+Wd+ Argt+vG+tr++tk+hiaraale++a+q+ di+++m+ lcl|MicrobesOnline__882:208653 316 DGLGIIKAAPEVEQLALSVPDNGGVYLVPAFAGLGAPHWDQYARGTMVGITRGATKAHIARAALESIALQTLDIMDCMQ 394 ******************************************************************************* PP TIGR01311 396 kdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepem 474 kd+g+++++L++DGg+++nnllmq+qad+lgv+verpkv+ettalGaA++agla+g+wkse+e+++ ++ + ++fep+m lcl|MicrobesOnline__882:208653 395 KDSGIKLAALRADGGATRNNLLMQFQADVLGVPVERPKVTETTALGAAYLAGLATGFWKSEDEIATMWQLD-RRFEPNM 472 **********************************************************************8.******* PP TIGR01311 475 deeerekkykkwkeaverslkw 496 ++++r++ + +w++aver++ w lcl|MicrobesOnline__882:208653 473 SDDKRQHLVYEWQRAVERAKAW 494 *******************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (496 nodes) Target sequences: 1 (497 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10.50 // [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