Align Rhamnulokinase (EC 2.7.1.5) (characterized)
to candidate YP_002823364.1 NGR_b11580 carbohydrate kinase
Query= reanno::HerbieS:HSERO_RS22200 (459 letters) >NCBI__GCF_000018545.1:YP_002823364.1 Length = 481 Score = 276 bits (707), Expect = 8e-79 Identities = 177/467 (37%), Positives = 241/467 (51%), Gaps = 26/467 (5%) Query: 1 IAVFDIGKTNIKLTLVDEHGQELAVRRRPNQPRQDGPYPHHDVAAIEAWLLENLAALARQ 60 +AV D+GKTN+KL+ G + N R P+ HHD+ A+ W+ E LA L+R+ Sbjct: 2 VAVLDVGKTNVKLSAAAADGTIVETLSVANPVRPGPPWRHHDLRALSEWVFETLATLSRR 61 Query: 61 WRIRAIVPVTHGATAALVDEA-----GLVLPVADYEHDFALPPAH--RPYESLRPPFAQS 113 A V HG+ L G LP+ DYE PA Y L F Sbjct: 62 HAFGAFVTAGHGSGGVLTGADPDAGDGAALPMIDYEQSL---PADIGETYAPLAGSFLDR 118 Query: 114 ASPLLGMGLNLGRQLYWQSQRYPDAFARARYLLMYPQYWSWRLSGVAAGELSSLGCHTDL 173 S + + RQLYW Q P AFA+AR+ L PQYW+WRL+GVAA E S LG + L Sbjct: 119 GSATMHCATHQARQLYWMEQHEPQAFAKARWYLGVPQYWAWRLTGVAASETSFLGAQSHL 178 Query: 174 WQPGQQCYSSLLAQCNWTPLMPPLRAAWERLGPLRPELAQRTGLPADCAVLCGVHDSNAS 233 W ++ ++ +++ W LMPP AW+ L P+RPEL +R LP VL G HDS+ + Sbjct: 179 WNVAERRWAPIVSARGWERLMPPFARAWQALAPVRPELVRRFDLPNGLPVLTGGHDSSLN 238 Query: 234 LLRYLRGTGGGPRIVLSSGTWLIAAALDGCVSGLREEADMLANVNVLGAPVACMRFMGGR 293 RY G V+S+GTW++ + + L E M N +V G P+ + MGGR Sbjct: 239 HYRY-HAAGLRDFTVISTGTWIVGFSGSTPLERLDEHRGMTLNSDVFGDPLGGILTMGGR 297 Query: 294 EFAQIAGDDLPCS---AEQLQALIDAQVFALPCFSECGGPFAGR--RGSIVGQAPQQPGS 348 EF++IAG + P E L L++ + FA+P F + G F G RG I+G + P Sbjct: 298 EFSRIAGRNPPAEDVPLEILARLLEERTFAIPSFGDNDGLFPGSAGRGRIIGPSADTPME 357 Query: 349 RYALATLYCALMTAYCLDALDAPGEIVVEGSFTANPHFAALLAALV-SRTVYRSSDASGT 407 R ALA LYCAL+T CL+AL + +V++GSF +P +A L+AAL+ R V+ + DA G Sbjct: 358 RKALALLYCALLTVECLEALGSDRFVVLDGSFLRDPLYAQLVAALLPDRQVHFNLDAYGV 417 Query: 408 TLGGWLL----DRWERAPETATLPA-LLPAEPLALRGLAAYREDWLR 449 G LL R AP +P L EP LA Y DW R Sbjct: 418 AAGAALLAGQGTRRNPAPLILGVPTHLEEIEP----ELARYAADWRR 460 Lambda K H 0.322 0.137 0.437 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: 648 Number of extensions: 41 Number of successful extensions: 5 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: 459 Length of database: 481 Length adjustment: 33 Effective length of query: 426 Effective length of database: 448 Effective search space: 190848 Effective search space used: 190848 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: 51 (24.3 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