Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_110805493.1 C8J30_RS08890 carbohydrate kinase
Query= reanno::Dino:3609413 (308 letters) >NCBI__GCF_003217355.1:WP_110805493.1 Length = 307 Score = 360 bits (923), Expect = e-104 Identities = 185/306 (60%), Positives = 220/306 (71%) Query: 1 MILCAGEALIDMLPRALPDGTAGFAPVAGGAVFNTAVALGRLGADVGLVTGLSRDLFGEV 60 MIL GEALIDMLPR G A FAP AGG+VFNTA+ALGRLGA+ G ++G+S DLFGEV Sbjct: 1 MILSCGEALIDMLPRQSTAGEAAFAPYAGGSVFNTAIALGRLGAEAGFLSGISTDLFGEV 60 Query: 61 LMTALAAADVDSDMAVLSDRPTTLAFVTLTDGHAQYAFYDENTAGRMLAPADMPDPGPEV 120 L+ LAA+ VD+ +++ SDRPTTLAFV L DGHA YAFYDENTAGRM+ PA++P V Sbjct: 61 LIETLAASKVDAGLSIRSDRPTTLAFVKLVDGHASYAFYDENTAGRMITPAELPAIPAAV 120 Query: 121 GTLFFGGISLAVEPCAAAYEALCLKAAAGRVVMLDPNIRPGFIKDETTFRARIDRMLAVT 180 +FFGGISL V+PC YEAL + AA RV MLDPNIRPGFI+DE +RAR++RM+A+ Sbjct: 121 KAMFFGGISLPVDPCGGTYEALMAREAASRVTMLDPNIRPGFIRDEAAYRARLNRMIALA 180 Query: 181 DIVKVSDEDLAWLMGPGDLAESAAALRARGPAVVCVTRGGAGVEAHTATGITHVAAEAVE 240 DIVKVSDEDL WL GPG++ A L ARG +V VT G G A + + V Sbjct: 181 DIVKVSDEDLRWLEGPGEIEALARGLLARGTKLVFVTEGSTGAHAFSVELSLFEPSHKVT 240 Query: 241 VVDTVGAGDTFNAGFLAGLAEAGALDKDRLRALDAPVLTSALRLGAQAAAITVSRAGANP 300 VVDTVGAGDTFNAG LA L A L K + DA ++++ L LG AAAITVSRAGANP Sbjct: 241 VVDTVGAGDTFNAGVLAALDRADKLTKAEVATADAALISACLTLGNAAAAITVSRAGANP 300 Query: 301 PWRDEL 306 PW +EL Sbjct: 301 PWAEEL 306 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: 260 Number of extensions: 7 Number of successful extensions: 1 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: 307 Length adjustment: 27 Effective length of query: 281 Effective length of database: 280 Effective search space: 78680 Effective search space used: 78680 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