Align Glucose kinase (characterized, see rationale)
to candidate WP_057508150.1 ABB28_RS08110 glucokinase
Query= uniprot:Q8P6M4 (344 letters) >NCBI__GCF_001431535.1:WP_057508150.1 Length = 335 Score = 174 bits (441), Expect = 3e-48 Identities = 109/317 (34%), Positives = 162/317 (51%), Gaps = 7/317 (2%) Query: 23 LAADVGGTHVRVGRVSHGADAPIELSQYRTYRCADHASLDAILADFLR--DSRAVDAVVI 80 L AD+GGT+ R +P+ R + D SL +L+ D+ A V Sbjct: 9 LVADIGGTNARFALADTADSSPLLEDSIREFPVVDFPSLGDAARHYLQEVDAEASRGVFA 68 Query: 81 ASAGVALDDGRFISNNLPWTIAPRQLRDTLGVRAVHLVNDFEAVAYAAPQMEQRAVVQLS 140 + V D+ R N PW I+ + LG +HL+NDF A A A ++ + VVQ+ Sbjct: 69 VAGRVDGDEARI--TNHPWVISRSRTAAMLGFSELHLINDFAAQAMAISLLQPKDVVQIG 126 Query: 141 GPTPRHAQPGGPIL--VVGPGTGLGAAVWINGPRQPTVLATEAGQVALASNDPDTAQVLR 198 G + + G P V+GPGTGLG + + L TE G V+ P+ ++L Sbjct: 127 GASWSPRRSGAPANYGVIGPGTGLGVGGLVIRHDRCFPLETEGGHVSFPPGTPEEIRILE 186 Query: 199 ILARDASYLPIEHVLSGPGLRNLYLALCELHAATPIHPLPADITHAALHSDDALARRCLQ 258 IL+ + E ++ GPGL N++ A+CE+ P H PAD+T A + D A R + Sbjct: 187 ILSETFGRVSNERLICGPGLVNIHRAVCEMAGFDPGHLKPADVT-ARAGAGDPQAMRAVD 245 Query: 259 LFCALLGSAVGDMALAYGASGGVYLAGGILPSIGQFLAASDFRERFLAKGRMRPVLERIP 318 LFCA+ G+ GD+ L GA GV+L GG++P + + L S FR+RF KGR ++ R+P Sbjct: 246 LFCAIFGAIAGDLVLIQGAWDGVFLTGGLVPRMLESLQHSGFRQRFEHKGRFSSIMGRVP 305 Query: 319 VKLVEHGQLGVLGAASW 335 V H G+LGAA++ Sbjct: 306 SLAVIHPNPGLLGAAAY 322 Lambda K H 0.321 0.136 0.410 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: 364 Number of extensions: 17 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: 344 Length of database: 335 Length adjustment: 28 Effective length of query: 316 Effective length of database: 307 Effective search space: 97012 Effective search space used: 97012 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 (21.9 bits) S2: 49 (23.5 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