Align Glycerol kinase; EC 2.7.1.30; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK (uncharacterized)
to candidate WP_084076315.1 BUB04_RS08485 hypothetical protein
Query= curated2:Q9X6C9 (495 letters) >NCBI__GCF_900129305.1:WP_084076315.1 Length = 516 Score = 127 bits (318), Expect = 1e-33 Identities = 135/453 (29%), Positives = 197/453 (43%), Gaps = 35/453 (7%) Query: 3 YLLALDQGTTSSWAILFTLEGEVVAVAQRAFAQHYPEPGLVEHDPWEIWESQLWAAKEAL 62 Y +D GT+S+ A++F V +A G E DP ++ ++ A + Sbjct: 13 YTCGIDIGTSSTKAVVFDPSLRKVFSVSVPYAFTDTREGAAELDPDQVADA---AIRCLS 69 Query: 63 RRAGVGPEAVLALGIANQRET--TLVWERDTGRPLHPAIVWQDRRTASLCEALRERGLEG 120 R A G +A L A+ TL+ +G PL + W D R +R G Sbjct: 70 RCAAHGAQAGTPLAFASFSSALHTLMAVDRSGNPLGGCLTWADVRPMEAIGTVRSFGN-- 127 Query: 121 LFRARTGLLLDPYFSATKLLWLLERVPGLRERAERGEVCFGTVDTWLLWNLTGGRVHATD 180 RTG ++ K+LWL R P +A R F T+ ++L LTG V D Sbjct: 128 -IYERTGCPPHAIYTPAKILWLRRRRPEAYRKAAR----FVTLKEYILHRLTGRWV--AD 180 Query: 181 PTNASRTLLFHLETLTWDEELLRVLGIPKALLPEVRPSDG----DFGETLPGLLGAPIPI 236 AS L +L WD ELLR L + + L + +DG +GA P+ Sbjct: 181 FGVASGGGLLNLHEKGWDRELLRALELQEDSLSPL--ADGTTVLSMKREWEERIGARFPL 238 Query: 237 RGVLGDQQAALLGQAALGAGEGKCTYGTGAFLLLNTGERPVWAEGGLLTTLAWHLEGKAA 296 GD Q A LG + T GT + + + E + + G T + L+ + Sbjct: 239 VLGSGDGQLANLGAGTYASRRFVATVGTSGAVRVFSPEARLDSRG---RTWCYMLD-RDT 294 Query: 297 YALEGSVFVAGAAVGWLR-----EVGLLGESHEV-ESLARQVED----AGGVYFVPAFTG 346 Y G++ G +GWLR E G G + V E L+R E+ AGG+ F+P TG Sbjct: 295 YVTGGAINNGGIVLGWLRSRLAYEYGEDGVAVPVYEDLSRMAEEVPPGAGGLLFLPFLTG 354 Query: 347 LGAPHWDPYARGAILGLTRGTTRAHLARAALEGVAFSVGEVAWAMAGAAGLGLKALKADG 406 P W+ ARG +LGL HL RAA+EGVAF + + AG + G Sbjct: 355 ERTPDWNAAARGVVLGLGMEHGFRHLVRAAMEGVAFRLNANFLVLQELAGEARDVI-ISG 413 Query: 407 GMAQNDLFLEIQADLLGVPVLRPRVTETTALGA 439 G+ + ++L+I AD+LG P+L E + LGA Sbjct: 414 GVTHSRVWLQILADVLGRPLLLYPGAENSTLGA 446 Lambda K H 0.320 0.138 0.434 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: 697 Number of extensions: 27 Number of successful extensions: 4 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: 516 Length adjustment: 34 Effective length of query: 461 Effective length of database: 482 Effective search space: 222202 Effective search space used: 222202 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 24 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