Align Glycerol kinase; EC 2.7.1.30; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK (uncharacterized)
to candidate H281DRAFT_04146 H281DRAFT_04146 xylulokinase
Query= curated2:Q12GA2 (497 letters) >FitnessBrowser__Burk376:H281DRAFT_04146 Length = 514 Score = 154 bits (389), Expect = 7e-42 Identities = 143/489 (29%), Positives = 224/489 (45%), Gaps = 40/489 (8%) Query: 1 MTYLLALDQGTSSSRSIVFDELGHIVAQAQQELPQIYPKPGWVEHDPMEIWRTQ---LAT 57 M Y++ +D GT S+++++ D+ G IVA P+P W E P ++ +A Sbjct: 1 MDYVIGVDIGTQSTKALLVDQHGAIVAHHASSYQPDTPRPLWAEQWPAVWFKAVTECIAA 60 Query: 58 AREALGKAGLKASDIRALGITNQRETTVVWHRATGQPIHNAIVWQDRRAEATCAQLREQG 117 +AG+ A+ I+A+ +++ + + + +P++ ++W DRRA +R Sbjct: 61 CVRKAKEAGVAANSIKAVCVSSLYGGSGIPVDSDMRPLYPCLIWMDRRATDQVEWVRNNV 120 Query: 118 KEALIQSKTGLLIDAYFSGTKLKWLLDNVPGVRAQAERGELAFGTIDSWLMWQLTGGALH 177 + + TG +D+Y+ TK+ WL D+ P V AQ F ++++++ LTG Sbjct: 121 DLDRLYTITGNGVDSYYGYTKMLWLRDHEPDVWAQTR----YFLPPNAYVIYMLTGEI-- 174 Query: 178 ATDVSNASRT-MLFNVRTNQWDAELLDLLGIPASLMPQVLPSS--------AHYGETRPE 228 A D S+A ++++ W E LD+LGIPA++MP+ L S + + E Sbjct: 175 AVDHSSAGNIGGIYDIAKRDWSDEALDMLGIPATMMPERLVESSEVVGSLLSQWTEELGL 234 Query: 229 LLGHAIAIGGVAGDQQSALFGQACFKAGMAKNTYGTGCFMLMHTGTQFQTSHNGLLTTSA 288 G AI GGV D A F +AG GT M Q + +GL++ Sbjct: 235 AAGTAIVAGGV--DAAVATFAAGVSRAGQHVAMIGTS--MCWGYINQTVDARHGLISMPH 290 Query: 289 AQTTAHPEFAMEGSVFVGGAVVQWLRDGL-HA-IQGS-----GEVQAL----AQSVP-DS 336 + G++ GA V W RD HA I+ + G+ L A VP S Sbjct: 291 VFNGQRDIYVFGGAI-TAGASVTWYRDQFCHAEIEAARATPHGDPHRLLEDNAAKVPAGS 349 Query: 337 GGVMMVPAFTGLGAPYWKPDARGTITGLTRGTTVAHIARAALESIAYQSAALLQAMSRDA 396 GVM +P G +P W A G GL+ T AH+ RA LE +++ ++A + A Sbjct: 350 DGVMFLPYLMGERSPVWDAKASGAFVGLSLFHTRAHLYRAVLEGVSFALKHNIEAGRKGA 409 Query: 397 VSSGAAPLAELRVDGGACANDLLMQFQADLLGIPVLRPAVIETTALGAAYLAGLSSGVYR 456 S +L V GGA +DL MQ AD+ G PV A+GAA LA L G+ Sbjct: 410 QSLE----DKLVVVGGAAHSDLWMQIIADITGYPVYTIEQEVEAAMGAALLAALGVGLV- 464 Query: 457 STDELSGMW 465 S + G W Sbjct: 465 SQEAAQGGW 473 Lambda K H 0.318 0.131 0.395 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: 610 Number of extensions: 28 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: 497 Length of database: 514 Length adjustment: 34 Effective length of query: 463 Effective length of database: 480 Effective search space: 222240 Effective search space used: 222240 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 (21.8 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