Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate Echvi_1279 Echvi_1279 Glycerol kinase
Query= SwissProt::O66131 (496 letters) >FitnessBrowser__Cola:Echvi_1279 Length = 500 Score = 417 bits (1071), Expect = e-121 Identities = 209/493 (42%), Positives = 315/493 (63%), Gaps = 9/493 (1%) Query: 3 QYMLAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIASV 62 Q++L+IDQGT+ ++A++F+ +G+ V A ++ G VE + +I+ +VL + Sbjct: 6 QFILSIDQGTSGTKALVFDAQGKQVAKATVPLKTHYLDGGLVEQDPEDIYQNVLKAVGIC 65 Query: 63 LSEAQVKP---EQVAGIGITNQRETTVVWEKDTGNPIYNAIVWQSRQTAGICDELKAKGY 119 L++ Q + + + GI+NQRET ++W+K+ G P+Y A+VWQ +++ G+CD LKA G Sbjct: 66 LADFQFQGHPLDAITSCGISNQRETFLLWDKN-GAPLYQAVVWQCKRSIGVCDRLKAAGL 124 Query: 120 DPLFRKKTGLLIDAYFSGTKVKWILDHVDGARERAERGELLFGTIDTWLIWKLSGGRVHV 179 +PL + KTGL+ID YFSGTK+ W+ ++ + GE FGT+DTWL+++L+ G ++ Sbjct: 125 EPLIKDKTGLIIDPYFSGTKLIWLYENDPAIATAIDAGEAYFGTVDTWLLYRLTEGNHYL 184 Query: 180 TDYSNASRTLMFNIHTLEWDDELLDILGVPKAMLPEVRPSSEVYAKTAPYHFFGVEVPIA 239 TD++NASRTL FN+ TL+WD ELLD +G+ LP VRPSS + T +PI Sbjct: 185 TDFTNASRTLFFNLDTLDWDRELLDNMGLSGLQLPAVRPSSAEFGVTDFEGLLDAPLPIF 244 Query: 240 GAAGDQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVASKHGLLTTIAWGIDGKVEY 299 GD AA FG+ACF G AK T GTGC +LMN G++ +S HG+++TI W + +V Y Sbjct: 245 AMIGDSHAAAFGEACFEPGTAKATMGTGCSVLMNVGDERKSSGHGMVSTICWSTEAQVSY 304 Query: 300 ALEGSIFVAGSAIQWLRDGLRMIKTAADSETYAEKVESTDGVYVVPAFIGLGTPYWDSEV 359 ALEG I G+ I+WL++ L +I+ + ++E A+ V S GVY+VPAF GLG P+WD + Sbjct: 305 ALEGVIVTCGATIEWLKNELGLIQDSRETEAMAKAVTSNQGVYLVPAFSGLGAPHWDMKR 364 Query: 360 RGAVFGLTRGTTKEHFIRATLESLAYQTKDVLAVMEADSGISLTTLRVDGGAVKNNFLMQ 419 + ++ G+T + K H +RA LES+ YQ KDV++ ME D+ + L L VDGG N F++ Sbjct: 365 KASLVGMTFDSGKNHIVRAALESIPYQIKDVISAMEEDAQLDLEALNVDGGITANGFVID 424 Query: 420 FQSDLLAVPVERPVVNETTALGAAYLAGLAVGYWNSRDDIAAQWQLERRFE--PKMDDDK 477 F +DLL PV R + + +ALGAAYLAGL G + D+A QL+++ + P D Sbjct: 425 FLADLLEKPVARVGIADVSALGAAYLAGLKAGVFK---DLAHLQQLQQKQQTVPNGPADS 481 Query: 478 RTMLYDGWKKAVR 490 Y GW++AV+ Sbjct: 482 IKAAYAGWQRAVK 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: 637 Number of extensions: 29 Number of successful extensions: 4 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: 500 Length adjustment: 34 Effective length of query: 462 Effective length of database: 466 Effective search space: 215292 Effective search space used: 215292 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)
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