Align Glycerol kinase; EC 2.7.1.30; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK (uncharacterized)
to candidate Ga0059261_2623 Ga0059261_2623 Glycerol kinase
Query= curated2:C6E1L8 (495 letters) >FitnessBrowser__Korea:Ga0059261_2623 Length = 496 Score = 411 bits (1057), Expect = e-119 Identities = 220/485 (45%), Positives = 304/485 (62%), Gaps = 9/485 (1%) Query: 4 LLSIDQGTTSSRATLYAASGETLATVSRPLVQHYPNPGWVEHAAQEIWEGQLACIAEAIA 63 +L+IDQGTT+++A L AA G + + SR + YP PGW E +A +IWE A IAE +A Sbjct: 6 ILAIDQGTTNTKALLVAADGSVVISRSRSMQVTYPQPGWAEQSASDIWEAVAALIAELVA 65 Query: 64 KAGIAPAKVAGIGITNQRETTVVWERETGEPLHRAIVWQDRRTAELTESLKEQGLEAMVR 123 A A++A + I+NQRET V+WE +TG P+ A++WQ R+AE L+ GLE + Sbjct: 66 AA--PDAQIAALAISNQRETVVLWEADTGRPVAPAVIWQCARSAERCADLRAAGLEDAIV 123 Query: 124 ERTGLLLDPYFSASKLSWLLDRVDGLRRRAERGEVCFGTIDSWLMFKLSGGKSHLTDISN 183 R+GL +DP F A+K+ WLLD + G R RA GE+ GTIDSWL++ L+GGK H TD SN Sbjct: 124 ARSGLGIDPLFPAAKIGWLLDTIPGARDRANAGEIKCGTIDSWLLWNLTGGKVHATDHSN 183 Query: 184 ASRTMLFNINTLEWDEELLRLFRIPRGMLPEVRGSAAGFGHTSAQVAG--AEIPIAGVAG 241 ASRT LFN++TL+WD EL R+F +P +LP + S GFG + + A P+ + G Sbjct: 184 ASRTQLFNLDTLDWDAELARIFDVPLAILPRIAPSDGGFGTVAPGLTALPAGTPVQVLLG 243 Query: 242 DQQAALFGQGCFAPGMAKATFGTGAFVVMNSGARLGVGDGVLSTIAWQLPGEAVQYALEG 301 D AALF G APG KAT GTG+ ++ + R+ G+ STIAW G Q+A+EG Sbjct: 244 DSHAALFAHGILAPGRVKATIGTGSSLMAATAGRVRSSHGLSSTIAWSRTGTGAQHAIEG 303 Query: 302 SIFIAGAAVQWLQEGLGLIASAREVEALAASVSDSAGVYFVPALSGLGTPYWDPYARGVI 361 +I ++G A + LGL A + + LAASV S GV FVPAL+GLG P+W ARG I Sbjct: 304 NISVSGHAAAFATALLGL-ADEQALTDLAASVESSEGVVFVPALAGLGAPHWQTGARGTI 362 Query: 362 AGLTRGSTKAHLARAALEAIAFQTLDAIRAMEKASGIALKELRVDGGAAADNLLLQIQAD 421 +G+T + AH+ARA LEAIA Q D + A+ GI L EL +DGGAA + LL Q+ AD Sbjct: 363 SGMTLATRPAHVARATLEAIALQIGDVLDAIAADLGIDLPELSIDGGAARNALLAQLLAD 422 Query: 422 LLGVPVLRPRCTESTSLGAAFLAGIGAGVLDTSAIAAQWALDRRFEPQMERNLREELHRG 481 L G ++RP E+++LG A +A G+ D+ A+AA RFEP++ + RE + Sbjct: 423 LTGRTIVRPEIAEASALGVARMAADALGLADSGAMAAA----DRFEPKLAEDAREAIRGN 478 Query: 482 WQKCV 486 W++ + Sbjct: 479 WRESI 483 Lambda K H 0.319 0.134 0.399 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: 652 Number of extensions: 27 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: 495 Length of database: 496 Length adjustment: 34 Effective length of query: 461 Effective length of database: 462 Effective search space: 212982 Effective search space used: 212982 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 (21.8 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