Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate RR42_RS03385 RR42_RS03385 sugar kinase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1965 (306 letters) >FitnessBrowser__Cup4G11:RR42_RS03385 Length = 309 Score = 293 bits (749), Expect = 5e-84 Identities = 156/296 (52%), Positives = 197/296 (66%), Gaps = 3/296 (1%) Query: 6 PSVVVFGEALTDVVQHSPGRWQGYPGGAPWNVARAMSRLGVPTAFAGSISTDSLGDELAQ 65 P+ VVFGEALTD+V W G PGG+ WNVAR +RLGVPTAFAG+IS D+LGD+LA+ Sbjct: 7 PAYVVFGEALTDMVHQGGQDWLGLPGGSCWNVARVGARLGVPTAFAGAISADTLGDQLAE 66 Query: 66 QSKAAGLDMRFLQRVDADPLVAIVPSSHPPRYFFAGE--ADLLFDVDQLPAGWLDAARLC 123 S AGLD+RFLQRV+ PL+A V + HPP+YFF G+ ADL FD ++LP GW AAR Sbjct: 67 ASAEAGLDLRFLQRVERSPLLAFVGAQHPPQYFFVGDDSADLYFDPERLPPGWRQAARTV 126 Query: 124 HFSCISLARQPLGDRLVEVARRVKEEDKLISYDPNWRNLMDTRYRELTFPAMVELADIIK 183 HF +SLARQPL RL A + + K I++DPN+R M + F M LAD IK Sbjct: 127 HFGSLSLARQPLAARLCTEATQARAAGKRIAFDPNFRTPMRAPEYQAVFAHMAGLADYIK 186 Query: 184 LSDEDLRQIYPGLNEEQALHTLRTMNASAQILFTRGAKGMALYAADVKFEQPAIAVEVAD 243 +SDEDLR +YP L+E AL LR + A++L TRGA GM L D EQP AV+V D Sbjct: 187 VSDEDLRGLYPALDEHAALAALRALAPQARVLLTRGADGMTLLHGDGACEQPVFAVDVVD 246 Query: 244 TVGAGDSSMAGWLASTLLGIQEPHAR-LEFSAACASVSCSHAGAYAPSREEVEDLL 298 TVG GD++M GW+A LL + AR ++AA A+V+ + AGAY+P+ EV LL Sbjct: 247 TVGCGDAAMGGWMAGLLLDPEATLARQARWAAATAAVAATRAGAYSPTVAEVSVLL 302 Lambda K H 0.320 0.133 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: 288 Number of extensions: 7 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: 306 Length of database: 309 Length adjustment: 27 Effective length of query: 279 Effective length of database: 282 Effective search space: 78678 Effective search space used: 78678 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 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