Align Glycerol kinase; EC 2.7.1.30; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK (uncharacterized)
to candidate 3607827 Dshi_1235 xylulokinase (RefSeq)
Query= curated2:C6E1L8 (495 letters) >FitnessBrowser__Dino:3607827 Length = 480 Score = 162 bits (411), Expect = 2e-44 Identities = 148/475 (31%), Positives = 213/475 (44%), Gaps = 33/475 (6%) Query: 5 LSIDQGTTSSRATLYAASGETLATVSRPLVQHYPNPGWVEHAAQEIWEGQLACIAEAIAK 64 L +D GT++ + ++ + L S PL P PG E + W G LA AE A+ Sbjct: 3 LGLDIGTSAVKGLVWDGA-RVLGAASAPLKVQVPVPGASEQDPEAWWRGILAVCAELSAQ 61 Query: 65 AGIAPAKVAGIGITNQRETTVVWERETGEPLHRAIVWQDRRTA-ELTESLKEQGLEAMVR 123 G A +V+ IG++ Q V + G L AI+W D R E E GL A Sbjct: 62 PGWA--EVSAIGLSGQMHGAVCLGPD-GAVLRPAILWNDNRAVREAAEMAALPGLAA--- 115 Query: 124 ERTGLLLDPYFSASKLSWLLDRVDGLRRRAERGEVCFGTIDSWLMFKLSGGKSHLTDISN 183 R G+ P F A KL+WL L W+ +L G +T+ S Sbjct: 116 -RVGVPPMPGFPAPKLAWLARTEPELHAAT----TMVMQAKDWVGMRLHGRA--VTEYSE 168 Query: 184 ASRTMLFNINTLEWDEELLRLFRIPRGMLPEVRGSAAGFGHTSAQVAGA-----EIPIAG 238 A+ T+ + +WD E L + R +P + G SA A A +P+ Sbjct: 169 AAGTLWLDQAARDWDREALAFSGLERAQMPALGAGTDLAGPLSAAAAAALGLKPGVPVIR 228 Query: 239 VAGDQQAALFGQGCFAPGMAKATFGTGAFVVMNSGARLGVGDGVLSTIAWQLPGEAVQYA 298 GD G G APG A + GT ++ S A G++ + A +PG +Q A Sbjct: 229 GGGDAMVGAAGIGVVAPGQAMISLGTSGQYLVASEAHRPNPAGLVHSFAHCVPGAYIQMA 288 Query: 299 LEGSIFIAGAAVQWLQEGLGLIASAREVEAL--AASVSDSAGV-YFVPALSGLGTPYWDP 355 ++ A + WL LG R V L AA +D A V F+P L+G TP+ DP Sbjct: 289 ---AMLNGAAPMAWLAGVLG-----RSVPDLLAAAETADPAHVPLFLPYLTGERTPHGDP 340 Query: 356 YARGVIAGLTRGSTKAHLARAALEAIAFQTLDAIRAMEKASGIALKELRVDGGAAADNLL 415 AR GL+ GS + RA ++AIA+ DA + +A A L + GGA +D L+ Sbjct: 341 EARAGFEGLSHGSGPGEMMRAVVDAIAYSFADAQAVLGEAGVRAASPLAIGGGARSD-LV 399 Query: 416 LQIQADLLGVPVLRPRCTE-STSLGAAFLAGIGAGVLDTSAIAAQWALDRRFEPQ 469 LQ AD+L VPV RP + +LGAA LA +G+G + + +A + F P+ Sbjct: 400 LQTLADVLEVPVQRPASADLGPALGAAKLAAVGSGAMPAARLADPPEIGAVFHPR 454 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: 601 Number of extensions: 35 Number of successful extensions: 6 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: 480 Length adjustment: 34 Effective length of query: 461 Effective length of database: 446 Effective search space: 205606 Effective search space used: 205606 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 Apr 09 2024. 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