Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate WP_043744689.1 AMB_RS14985 transcriptional regulator
Query= SwissProt::P23917 (302 letters) >NCBI__GCF_000009985.1:WP_043744689.1 Length = 297 Score = 324 bits (830), Expect = 2e-93 Identities = 168/300 (56%), Positives = 203/300 (67%), Gaps = 10/300 (3%) Query: 1 MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTV 60 +RIGIDLGGTKTE IAL +G +L R R+ T R Y TI TI LV+ E G +V Sbjct: 3 LRIGIDLGGTKTEAIALDLSGRELARQRVATARGSYDGTIATIKGLVEGLESRLGAAASV 62 Query: 61 GMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAA 120 G+GIPG+ISP TG++KNANSTWL G+P D+DL L R VRLANDA+C A+SEA DGA A Sbjct: 63 GIGIPGTISPRTGLIKNANSTWLIGKPLDRDLETALGRPVRLANDADCFALSEATDGAGA 122 Query: 121 GAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCGK 180 G TVF VI+GTG G G+ +GR G N AGEWGHNPLPW ++ E R CYCG+ Sbjct: 123 GFDTVFGVILGTGVGGGIVAHGRLLSGPNAIAGEWGHNPLPWPEDAE---RPGPACYCGR 179 Query: 181 QGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHVV 240 GCIETF+SG G A D+ G L + L D A AL RYE RLA++LA V+ Sbjct: 180 SGCIETFLSGPGLARDH----GGGLSAEQ---LATSDDAAAGAALARYERRLARALAAVI 232 Query: 241 NILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAWLWP 300 N++DP VIVLGGG+S +DRLY+ V L + FVF +T +R +HGDSSGVRGAAWLWP Sbjct: 233 NVIDPHVIVLGGGLSKLDRLYRNVPALWEGFVFSDHVDTLLRPPRHGDSSGVRGAAWLWP 292 Lambda K H 0.318 0.137 0.418 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: 342 Number of extensions: 17 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: 302 Length of database: 297 Length adjustment: 27 Effective length of query: 275 Effective length of database: 270 Effective search space: 74250 Effective search space used: 74250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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