Align Glucose kinase (characterized, see rationale)
to candidate WP_017222136.1 A923_RS0113155 glucokinase
Query= uniprot:Q8P6M4 (344 letters) >NCBI__GCF_000276805.1:WP_017222136.1 Length = 319 Score = 182 bits (461), Expect = 1e-50 Identities = 103/322 (31%), Positives = 163/322 (50%), Gaps = 6/322 (1%) Query: 23 LAADVGGTHVRVGRVSHGADAPIELSQYRTYRCADHASLDAILADFLRDSRAVDAVVIAS 82 + ADVGGT++R+ A LS+ + + CA+ +L+A LA + + Sbjct: 4 VVADVGGTNIRLAVCDLETGA---LSELKEFACAEFVTLEAALAQYFAALSGEITHLCVG 60 Query: 83 AGVALDDGRFISNNLPWTIAPRQLRDTLGVRAVHLVNDFEAVAYAAPQMEQRAVVQLSGP 142 +++ + NL W + + L+D L + ++H++ND+ A++ A P + +Q+ Sbjct: 61 IACPVENDHVVMTNLNWEFSKQALQDKLKLASLHIINDYTAISLAVPFLSAEEKIQIGAG 120 Query: 143 TPRHAQPGGPILVVGPGTGLGAAVWINGPRQPTVLATEAGQVALASNDPDTAQVLRILAR 202 Q G V GPGTGLG + + + L E G V+ N P+ A +L +L Sbjct: 121 ---ECQTDGVTAVFGPGTGLGVSHIVKAAGKWISLDGEGGHVSFTPNTPEQADILCLLQT 177 Query: 203 DASYLPIEHVLSGPGLRNLYLALCELHAATPIHPLPADITHAALHSDDALARRCLQLFCA 262 ++ E +LSG GL NLY LC L P D+T AAL +AR+ L +FC Sbjct: 178 QFGHVSAERILSGQGLVNLYKCLCTLSEQEAKFDQPKDVTKAALDGSCDIARKSLAVFCQ 237 Query: 263 LLGSAVGDMALAYGASGGVYLAGGILPSIGQFLAASDFRERFLAKGRMRPVLERIPVKLV 322 ++G G++AL +GG+Y+AGGI+P F AS+FR F KGR + L IP L+ Sbjct: 238 VMGGFAGNLALNLACTGGIYIAGGIVPRFVDFFQASEFRRCFEEKGRFKDYLTAIPTFLI 297 Query: 323 EHGQLGVLGAASWYLQHHTEVS 344 H G+LGA+ + Q T ++ Sbjct: 298 THDNPGLLGASVYLRQELTSIN 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: 299 Number of extensions: 12 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: 344 Length of database: 319 Length adjustment: 28 Effective length of query: 316 Effective length of database: 291 Effective search space: 91956 Effective search space used: 91956 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