Align Glycerol kinase; EC 2.7.1.30; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK (uncharacterized)
to candidate BWI76_RS07670 BWI76_RS07670 carbohydrate kinase
Query= curated2:Q0BC36 (500 letters) >FitnessBrowser__Koxy:BWI76_RS07670 Length = 506 Score = 377 bits (967), Expect = e-109 Identities = 204/497 (41%), Positives = 297/497 (59%), Gaps = 19/497 (3%) Query: 4 QYILALDQGTTSSRAMLFDRQGNIVSIAQKEFEQIYPQPGWVEHDPQEIWSTQAGVAAEA 63 ++I+ALD+GTT+++A++ D +G +V + P+ GWVE + + V A+A Sbjct: 7 EFIIALDEGTTNAKAVVLDSRGQVVVKFSQPLAIQTPREGWVEQSGEVLVDASLEVIAKA 66 Query: 64 VTRTGLNGTSIAAIGITNQRETTIVWDRETGQPVYNAIVWQDRRTADFCDSLKKQGLEAK 123 V G ++AA+ I+NQRET I W R++G+P+ AI WQ R+A FCD L+ E + Sbjct: 67 VAHVGAE--NVAALAISNQRETAIGWYRQSGKPINAAITWQCSRSAAFCDELRHSDKEQQ 124 Query: 124 VRAKTGLPIDSYFSATKIRWILDNVPGARDKARQGKLAFGTVDSWLVWNFTKHELHVTDV 183 ++A TGLPI FSA+K+RW+L+++P R A +G++ GT+DSWL+WN T+ + D Sbjct: 125 IKAVTGLPIAPLFSASKMRWLLESLPEGRALAERGEICLGTIDSWLLWNLTQGDAFSCDY 184 Query: 184 TNASRTMLFNIHTREWDSELLELLDIPRSMLPDVKASSEIYGHTK-TTVFASKIPLAGIA 242 +NA+RT L N+ T +WD ++L L IPR+ LP++K SS ++G+T+ IP+ + Sbjct: 185 SNAARTQLLNLQTGQWDDDMLALFQIPRAALPEIKPSSGLFGYTRGLNAIPDGIPVMAMV 244 Query: 243 GDQHAALFGQMCTTSGMVKNTYGTGCFLMMNTGDKPIESK----NNLVTTIAWQIGDDVQ 298 GD HAALFG G VK TYGTG +M P++S + L TTIAW GD + Sbjct: 245 GDSHAALFGHALGELGCVKATYGTGSSVM-----APVKSAQCDIDALATTIAWHDGDSIT 299 Query: 299 YALEGSIFIAGAVVQWLRDGVGI-----IKTAAEIEALAASVPHTDGVYLVPAFAGLGAP 353 Y LEG+I G V W+ D G+ + A E+ L ASV T GVY VPA GLGAP Sbjct: 300 YGLEGNIPHTGDAVAWMADSTGLSELSDAELAHELNTLPASVDSTLGVYFVPALTGLGAP 359 Query: 354 HWNARARGSVFGVTRGTTSAHLARAALDAIAYQSLDVLAAMEADSGISIGELRVDGGASA 413 W+ ARG + G++RG AHL RAAL++I YQ DV+ AM + L VDGG + Sbjct: 360 WWDDSARGVICGLSRGVKRAHLIRAALESITYQIADVVVAMRQQDDFHLTALMVDGGPTK 419 Query: 414 NDLLMQFQADLLGVDAVRPQITETTALGAAYLAGLAIGYWKNLDEVRSQWQLDRRFAPSM 473 ND LMQ+QADLLG +R + E +A+GAA LA A+ ++ ++++ F P M Sbjct: 420 NDWLMQYQADLLGCPVMRSDVAELSAIGAALLARKALNP-GSVTDLKAFLTEHSEFIPDM 478 Query: 474 PKEQ-VEQRMAGWQRAV 489 + Q +++R W+ AV Sbjct: 479 ARHQRLQKRWQEWRHAV 495 Lambda K H 0.318 0.132 0.398 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: 665 Number of extensions: 23 Number of successful extensions: 5 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: 500 Length of database: 506 Length adjustment: 34 Effective length of query: 466 Effective length of database: 472 Effective search space: 219952 Effective search space used: 219952 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)
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