Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_011654706.1 RL_RS25550 carbohydrate kinase
Query= reanno::Dino:3609413 (308 letters) >NCBI__GCF_000009265.1:WP_011654706.1 Length = 318 Score = 219 bits (558), Expect = 7e-62 Identities = 127/310 (40%), Positives = 172/310 (55%), Gaps = 7/310 (2%) Query: 1 MILCAGEALIDMLPRALPDGTAGFAPVAGGAVFNTAVALGRLGADVGLVTGLSRDLFGEV 60 MI+ G+ALID LP ALP+G +G+ PV GG+ N A A+GRLG VG + GLS D FG + Sbjct: 1 MIVVCGDALIDFLPVALPEGGSGYIPVCGGSCCNIATAIGRLGGKVGFMGGLSEDFFGAM 60 Query: 61 LMTALAAADVDSDMAVLSDRPTTLAFVTLTDGHAQYAFYDENTAGRMLAPADMPDPGPEV 120 L+ A +D A TTLAFV L D +YAFYD +A R P G EV Sbjct: 61 LVQQFNEAGIDLRYATRLPFDTTLAFVRLGDDEPEYAFYDSGSAARHWTLKGAPSLGTEV 120 Query: 121 GTLFFGGISLAVEPCAAAYEALCLKAAAGRVVMLDPNIRPGFIKDETTFRARIDRMLAVT 180 L G ++L P ++A E+L RV+ +DPN RPG +D +R R++R+ + Sbjct: 121 DVLHIGSVTLIHPPVSSACESLFENEQGKRVLSIDPNCRPGLAQDPEAYRQRLNRLCGMA 180 Query: 181 DIVKVSDEDLAWL---MGPGDLAESAAALRARGPAVVCVTRGGAGVEAHTATG-ITHVAA 236 DIVK+S DL ++ +GP AES + RA+ +V V+RG G + A G + V A Sbjct: 181 DIVKLSVTDLGFMQPGVGPHSAAESWLSNRAK---IVLVSRGAGGATVYLAGGRVVEVPA 237 Query: 237 EAVEVVDTVGAGDTFNAGFLAGLAEAGALDKDRLRALDAPVLTSALRLGAQAAAITVSRA 296 VVDTVGAGD AGFL L ++G L +D + AL AL A A++ Sbjct: 238 RPARVVDTVGAGDALIAGFLTHLQQSGDLHRDSIGALTGDRARKALEFAAHVASLACEHR 297 Query: 297 GANPPWRDEL 306 G++PPWR E+ Sbjct: 298 GSDPPWRREI 307 Lambda K H 0.320 0.136 0.398 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: 216 Number of extensions: 10 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: 308 Length of database: 318 Length adjustment: 27 Effective length of query: 281 Effective length of database: 291 Effective search space: 81771 Effective search space used: 81771 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 (21.8 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