Align glucokinase (EC 2.7.1.2) (characterized)
to candidate AZOBR_RS11685 AZOBR_RS11685 hypothetical protein
Query= reanno::SB2B:6937235 (310 letters) >FitnessBrowser__azobra:AZOBR_RS11685 Length = 299 Score = 266 bits (679), Expect = 6e-76 Identities = 138/295 (46%), Positives = 177/295 (60%), Gaps = 1/295 (0%) Query: 3 RSGIDLGGTKIELVTLNEKGEEVFRKRVPTPKDYRATLEAVAGLVHDSEKETGQV-SSVG 61 R G+DLGGTKI L G E R R TP+ Y TL+A+AG V E+ G+ ++VG Sbjct: 2 RIGVDLGGTKIAATLLAPDGTERARHRADTPRGYAETLQALAGAVAALEERAGRRDATVG 61 Query: 62 IGIPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGAG 121 + +PG+V A G V+ N WL+G+P DL L R VRIANDAN F +SE++DG AG Sbjct: 62 LCLPGIVDAAAGTVRAVNLPWLDGRPFAADLARALDRPVRIANDANAFVLSEAMDGAAAG 121 Query: 122 KTLVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLPWMTADEFNSTRCFCGNADCI 181 LVFG ILGTG G GI + ++ G N + GEWGHNPLPW ++ C CG CI Sbjct: 122 APLVFGIILGTGVGGGIVADRRILPGANALAGEWGHNPLPWRVTEDGPPVPCGCGREGCI 181 Query: 182 ETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVINLLD 241 ET + G G R GE + EI A G+ A A R D LARALA V+NLLD Sbjct: 182 ETLLCGAGLARLHLWRTGETLTPPEIAARAQSGDAPARATLDRHADALARALAAVVNLLD 241 Query: 242 PDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWLW 296 PDV+V+GGG+S + +YE +PA ++ L T+ ++ HGA SG+RGAAWLW Sbjct: 242 PDVVVVGGGLSELPGLYEAVPARWGRWALSPAPRTRFLRARHGAESGMRGAAWLW 296 Lambda K H 0.318 0.138 0.424 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: 281 Number of extensions: 12 Number of successful extensions: 2 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: 310 Length of database: 299 Length adjustment: 27 Effective length of query: 283 Effective length of database: 272 Effective search space: 76976 Effective search space used: 76976 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 (21.6 bits) S2: 48 (23.1 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