Align Glucose kinase (characterized, see rationale)
to candidate WP_047007751.1 AAW01_RS12295 glucokinase
Query= uniprot:Q8P6M4 (344 letters) >NCBI__GCF_001010925.1:WP_047007751.1 Length = 324 Score = 168 bits (425), Expect = 2e-46 Identities = 112/320 (35%), Positives = 164/320 (51%), Gaps = 8/320 (2%) Query: 23 LAADVGGTHVRVGRVSHGADAPIELSQYRTYRCADHASLDAILADFLRDSRAVDA---VV 79 + D+GGTH R +H D I + + T DHAS D+ R + D V Sbjct: 4 VTVDIGGTHARFAIATHADDGSITMDEPVTLHTDDHASFQTAWEDY-RAQKGGDIPSRVA 62 Query: 80 IASAGVALDDGRFISNNLPWTIAPRQLRDTLGVRAVHLVNDFEAVAYAAPQMEQRAVVQL 139 +A AG + +NN PW I P +++ LGV + +VNDFEAVA+A + + + L Sbjct: 63 MAIAGPVGGEVIRFTNN-PWIIRPALVKEKLGVDSFKIVNDFEAVAHAVARAGEDEYLHL 121 Query: 140 SGPTPRHAQPGGPILVVGPGTGLGAA-VWINGPRQPTVLATEAGQVALASNDPDTAQVLR 198 +GP P G + V+GPGTGLG A ++ V ATE G + A D +L Sbjct: 122 TGPEGP-LPPTGRLTVMGPGTGLGVAHLYREADGTYRVSATEGGHIDFAPLDSIEDAILA 180 Query: 199 ILARDASYLPIEHVLSGPGLRNLYLALCELHAATPIHPLPADITHAALHSDDALARRCLQ 258 L + + + +E V++GP + ++Y L L + +I ++ +D+LA + Sbjct: 181 RLRKRHTRVSVERVVAGPAISDIYHTLASLERKSVPELDDVEIWTRGMNGEDSLAAAAVD 240 Query: 259 LFCALLGSAVGDMALAYGASGGVYLAGGILPSIGQFLAASDFRERFLAKGRMRPVLERIP 318 FC LGS GDMALA+GA V +AGG+ + L S F ERF AKGR ++ +P Sbjct: 241 RFCLSLGSVAGDMALAHGAK-AVVIAGGLGYRLRDHLPKSGFAERFRAKGRFAGLMAGLP 299 Query: 319 VKLVEHGQLGVLGAASWYLQ 338 VKL+ H Q G+ GAA+ Y Q Sbjct: 300 VKLITHPQPGLFGAAAAYCQ 319 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: 405 Number of extensions: 24 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: 324 Length adjustment: 28 Effective length of query: 316 Effective length of database: 296 Effective search space: 93536 Effective search space used: 93536 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