Align Glycerol kinase; EC 2.7.1.30; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK (uncharacterized)
to candidate RR42_RS16765 RR42_RS16765 glycerol kinase
Query= curated2:Q47ER3 (502 letters) >FitnessBrowser__Cup4G11:RR42_RS16765 Length = 507 Score = 256 bits (653), Expect = 2e-72 Identities = 174/502 (34%), Positives = 251/502 (50%), Gaps = 15/502 (2%) Query: 9 VLALDQGTTSTRAILFGRKGDIHGVAQQEITQHYPQPGWVEHDAEEIWQAQLAVARAALR 68 +LA+D+GT+ TRA + G + + + + P+PG VE DA + + +AV RA + Sbjct: 8 ILAIDEGTSGTRAAVVAADGHVSCLEYTTLQVNTPRPGVVEQDANAVLEKTIAVCRATIA 67 Query: 69 DNGILAKQIVAVGMTNQRETTVLWDRSSGEPLHRAIVWQDRRTAGLCDELTTAGHAGLFR 128 +IVA+G+ QR T VLWD SG + A+VWQD R AG L A L Sbjct: 68 RARQAQLRIVALGIATQRATAVLWDTRSGRAIVPAMVWQDTRYAGELGALAPAWDKTLLE 127 Query: 129 E--RTGLVLDAYFSGTKLKWLLDHI---PGARSRAERGELAFGTIDSWLTWKLSGGRAHV 183 + R V Y W H+ P G LAFGTID+WL W LS RA V Sbjct: 128 QVGRPVGVRSPYL------WAARHLRDTPEVAEALRAGSLAFGTIDTWLLWHLSTERACV 181 Query: 184 TDPSNASRTLLFDIHRCCWDEELLALLDIPMALLPRIVDSSGEIATIAAEWLGAEIPLSG 243 T P+NA+ + + + L L P ALLP + + + A LG ++P+ Sbjct: 182 TTPTNATSASAYVLAGHRYHLGWLDALGFPHALLPALRQDADDFGRTRAALLGIDVPILA 241 Query: 244 IAGDQQAATFGQVCLQHGMAKNTYGTGCFLLMNTGQAPMASC--HRLLTTIGWQRQGKTT 301 AGDQ A G CL+ G + +GTG F+ + G P A + T+ +RQ + Sbjct: 242 CAGDQLAGAAGLGCLERGQSMCVHGTGSFVDLVIGPQPPAKAGLYDGTLTMTARRQHDVS 301 Query: 302 YL-LEGSVFMGGATVQWLRDGLGLISSADQIESLAASVADNGGVYLVPAHTGLGAPYWDP 360 +L +E V G+ + W+ + L SA QI +LAA+V GV +PA TGL P P Sbjct: 302 HLSVETFVATTGSALNWVCEKLRWFESAKQISALAATVDAARGVTFLPALTGLRVPQMQP 361 Query: 361 FARGALFGMTRGTTRAHIARAALEAIAFQSADVLQAMEKDAGQSLSELRVDGGAARNDLL 420 AR +L G++ +T+A +A A LE IA + ++A E+ AG ++EL V GG + +D L Sbjct: 362 EARASLTGISIASTQAEVAYAILEGIAHAVSSCMEANEEVAGVPVAELIVGGGLSGSDAL 421 Query: 421 MQFQADLLGVPVVRPQVTETTAL-GAAYLAGLAVGFWQDEAELTALWRADRRFEPSMAED 479 +Q QADL G+P+ R + T+ +L G A+ AG + W + A D FEP + D Sbjct: 422 LQIQADLTGMPIRRMRETDRASLRGIAFFAGSSGLLWDSLQDARATNETDAVFEPRLGAD 481 Query: 480 RRSALFADWHRAVERSLHWANA 501 +R A WH V L A + Sbjct: 482 QRGERRALWHARVASELRHAQS 503 Lambda K H 0.321 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: 604 Number of extensions: 30 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: 502 Length of database: 507 Length adjustment: 34 Effective length of query: 468 Effective length of database: 473 Effective search space: 221364 Effective search space used: 221364 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 (21.9 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