Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_068010615.1 PsAD2_RS21780 ROK family protein
Query= reanno::SB2B:6937235 (310 letters) >NCBI__GCF_001623255.1:WP_068010615.1 Length = 311 Score = 168 bits (426), Expect = 1e-46 Identities = 112/295 (37%), Positives = 149/295 (50%), Gaps = 9/295 (3%) Query: 5 GIDLGGTKIELVTLNEKGEEVFRKRVPTPKD-YRATLEAVAGLVHDSEKETGQVS-SVGI 62 GIDLGGTKIE +E V KR+ TPK+ Y ++A+ ++H E+ +G +G+ Sbjct: 6 GIDLGGTKIEATAFDEAWAVVESKRIATPKETYEGLVDALCEMIHWLEEVSGNKDLPIGV 65 Query: 63 GIPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGAGK 122 GIPG S TG+ +N +G+ + D+ + LGR V ND NCFA+SE+V G G Sbjct: 66 GIPGFYSKRTGKFLTANLP-ASGRTLHDDIISKLGRAVTFENDCNCFALSEAVLGAGRSY 124 Query: 123 TLVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLPW--MTADEFNSTRCFCGNADC 180 VFG ILGTG G G N G NG GE+GH +P+ MT +C CG C Sbjct: 125 DTVFGLILGTGVGGGCCSNGHTVSGLNGAAGEYGHLGIPYAAMTKLGLEPLKCGCGRTGC 184 Query: 181 IETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGE-PLAEAAFGRFIDRLARALAHVINL 239 ET+++G G R G+A I G+ P+ E R +LA L + Sbjct: 185 FETYLAGPGISRLANHVTGKAVDAQTITKAAAAGDVPMQEVM--RLWSQLAAELVAALQC 242 Query: 240 -LDPDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAA 293 LDPD IVLGGG+S I I + LP +L + G SSG RGAA Sbjct: 243 SLDPDCIVLGGGLSKIPNIERTIAQALPGKLLNHTEPPMICVAQFGDSSGTRGAA 297 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: 325 Number of extensions: 18 Number of successful extensions: 3 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: 311 Length adjustment: 27 Effective length of query: 283 Effective length of database: 284 Effective search space: 80372 Effective search space used: 80372 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 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