Align Glycerol kinase; EC 2.7.1.30; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK (uncharacterized)
to candidate WP_089137208.1 CES79_RS10945 gluconokinase
Query= curated2:Q7NC65 (508 letters) >NCBI__GCF_002217945.1:WP_089137208.1 Length = 520 Score = 172 bits (435), Expect = 3e-47 Identities = 141/484 (29%), Positives = 225/484 (46%), Gaps = 25/484 (5%) Query: 6 YIITLDEGTTSCRSIVFDKQAKIVSVAQNEFTQYFPQSGWVEHDPLEIWNTQLSTMQSVK 65 Y+I +D GTTS ++++FD K+ + N + Y E DP EI++ + + +V Sbjct: 3 YMIGVDIGTTSVKTVLFDNVGKVQGYSNNLYPLYQDVPDMAEEDPDEIFSAIVDGLTTVL 62 Query: 66 NKAQIKSVNVEAVGITNQRETVVLWNKETGLPVYNAIVWQDRRTSEYCETLTKHV--DKV 123 KA + ++ V + +++L + E P+ AI W D R +Y + L ++ ++ Sbjct: 63 RKANLSKGELKGVSFSAAMHSLILLD-ENHKPMTRAITWADNRAVKYADQLRENGVGKQI 121 Query: 124 REKTGLIINPYFSGTKIRWILKNVPLAQKTLKAGKLLAGTIDSWLIWKLTGGKVHATDVS 183 EKTG I+P TK+ W+ + + G I ++I+KL G V D S Sbjct: 122 YEKTGTPIHPMTPFTKLIWLRNE---HKDLFDKARWFVG-IKEYVIYKLFG--VLKEDYS 175 Query: 184 NASRTLLFNIHTMDWDQELLDLFEIPRSILPE-VKSSSEVYGYVEPSLWSQRATAKVPIT 242 A+ T +FNI MDWD + L+L + R LPE V ++ V G E P Sbjct: 176 IANATGMFNIFKMDWDDQALELAGVTRDKLPELVDTTDTVSGMNEDYARVIGIDPDTPFV 235 Query: 243 GVAGDQQSALFGQLCLKPGMVKNTYGTGCFTLMNIGEKPIMSKNKLLTTVAWKLGKKKPV 302 A D A G + PG+V T GT + + I K ++ + L K Sbjct: 236 MGASDGPLANLGVNAIDPGVVAVTIGTSGAVRVVTDKPKIDPKGRVF---CYYLAPGK-- 290 Query: 303 YALEGSVFIAGAAVQWIRDGL----RLIYDAAESDFY---ANLASKQDTHQVYLV--PSF 353 + + G V G +W+RD L ++ + + D Y +ASK L+ P Sbjct: 291 WVVGGPVNNGGIVFRWVRDQLFAPEKITAEQMKIDSYDLLTEIASKIPAGSDGLIFHPFL 350 Query: 354 TGLGAPYWDSYSRGAIFGLERGTKKEHIIKATLESIVFQTNDLIKAMSSDVGKKIEVVKV 413 G AP WD+ +RG+ FGL R + H+++A LE IV+ ++ A+ VGK + ++ Sbjct: 351 GGERAPIWDANARGSFFGLTRKHTRAHMVRAALEGIVYNLYTVLIALEEVVGKPVS-IQA 409 Query: 414 DGGATRSEYIMQFQSSISGVNVIRPKNIESTALGATFLAGLAVGYWKDLKELEKLVKVDK 473 GG RS Q + I +V P+++E TALGA L ++G DL E++K V V Sbjct: 410 TGGFARSALWRQMLADIFEQDVTIPESVEGTALGAAVLGMYSLGLIDDLSEVKKFVGVTN 469 Query: 474 EFKP 477 P Sbjct: 470 VHHP 473 Lambda K H 0.317 0.133 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: 571 Number of extensions: 34 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: 508 Length of database: 520 Length adjustment: 35 Effective length of query: 473 Effective length of database: 485 Effective search space: 229405 Effective search space used: 229405 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 (21.7 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