Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate Ga0059261_0833 Ga0059261_0833 Glycerol kinase
Query= reanno::Smeli:SM_b21009 (497 letters) >FitnessBrowser__Korea:Ga0059261_0833 Length = 491 Score = 451 bits (1160), Expect = e-131 Identities = 240/495 (48%), Positives = 318/495 (64%), Gaps = 12/495 (2%) Query: 1 MGGYILAIDQGTTSTRAIVFDGNQKIAGVGQKEFKQHFPKSGWVEHDPEEIWQTVVSTVK 60 MG +L ID+GTTSTRA++F + + E QH+P G VEHD EIW+ + Sbjct: 1 MGEKLLVIDEGTTSTRAMLFAPDGTLLASRSAELAQHYPAPGLVEHDAAEIWEKTLGCAV 60 Query: 61 EAIEKSGITANDIAAIGITNQRETVVVWDRETGKPIHNAIVWQDRRTAAFCDKLKKKGLE 120 +E +G A+ IAAIGITNQRET+V WD+ TG+P+ AIVWQDRR+AA C +LK+ G E Sbjct: 61 AMVEAAG-GADRIAAIGITNQRETIVFWDKATGEPLAPAIVWQDRRSAAICRELKEAGEE 119 Query: 121 KTFVKKTGLLLDPYFSGTKLNWLLSNVKGAQVRAAKGELCFGTIDTFLIWRLTGGE---- 176 +TGLLLDPYFSGTK+ W ++N Q+R A L GT++++L+W+LT E Sbjct: 120 PGVQARTGLLLDPYFSGTKIAWAMAN--WPQLREAGDRLAIGTVESWLVWKLTANEKRGG 177 Query: 177 CFCTDATNASRTLLYNIAENAWDDELTEVLRVPKEMLPEVKDCAADFGVTDPSLFGAAIP 236 TDATNASRTLL + W D L ++ P+ L E+ DCA FG T +LFG IP Sbjct: 178 LHITDATNASRTLLMGLGSGGWSDGLIDLFGAPRAALAEIVDCAGRFGET--TLFGGPIP 235 Query: 237 ILGVAGDQQAATIGQACFKPGMLKSTYGTGCFALLNTGKDMVRSKNRLLTTIAYRLDGET 296 I G+AGDQQAATIGQAC PG K+T+GTG F L N G+ SK+RLL+T+ ++L G Sbjct: 236 ICGMAGDQQAATIGQACLSPGDTKATFGTGAFVLTNAGERQPASKHRLLSTVLWQLGGRR 295 Query: 297 TYALEGSIFVAGAAVQWLRDGLKVIKAAPDTGSLAESADPSQEVYLVPAFTGLGAPHWDP 356 TYA+EGS+FVAG+ V+WLRD L +I++A +T LA S + VY VPA TGLGAP W+P Sbjct: 296 TYAIEGSVFVAGSVVKWLRDSLGLIESAGETEVLARSVPDNGGVYFVPALTGLGAPWWEP 355 Query: 357 DARGAIFGMTRNTGPAEFARAALEAVCYQTRDLLEAMHKDWRRNGNDTVLRVDGGMVASD 416 +ARGAI G++ + A RAALEA+ +Q+ DL A D + + LR+DGGM+ +D Sbjct: 356 EARGAISGLSLASTRAHVVRAALEAMAHQSHDLKAAFAAD---GADWSSLRIDGGMITND 412 Query: 417 WTMQRLSDLLDAPVDRPVILETTALGVAWLAGSRAGVWPNQEAFAKSWARDRRFEPHMDE 476 W Q L+D+LD V+RP ETTALG A LAG G++ + A + RF P M Sbjct: 413 WIAQDLADVLDLTVERPDFTETTALGAAMLAGVGYGLFAGLDEAAAMRGKVERFAPGMKV 472 Query: 477 ATRKVKLKGWRSAVK 491 R +L GW++AV+ Sbjct: 473 EARDARLAGWKAAVE 487 Lambda K H 0.319 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: 772 Number of extensions: 30 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: 497 Length of database: 491 Length adjustment: 34 Effective length of query: 463 Effective length of database: 457 Effective search space: 211591 Effective search space used: 211591 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