Align Rhamnulokinase (EC 2.7.1.5) (characterized)
to candidate SM_b20489 SM_b20489 carbohydrate kinase
Query= reanno::HerbieS:HSERO_RS22200 (459 letters) >FitnessBrowser__Smeli:SM_b20489 Length = 490 Score = 279 bits (713), Expect = 2e-79 Identities = 177/461 (38%), Positives = 244/461 (52%), Gaps = 18/461 (3%) Query: 1 IAVFDIGKTNIKLTLVDEHGQELAVRRRPNQPRQDGPYPHHDVAAIEAWLLENLAALARQ 60 +AV D+GKTN+KL+ V G + PN+ P+ HHD+ + W+ E LA L+R+ Sbjct: 11 VAVLDVGKTNVKLSAVAADGTLVETISVPNRVLPGPPWRHHDLTRLGGWVFETLAVLSRR 70 Query: 61 WRIRAIVPVTHGATAALVDEA-----GLVLPVADYEHDFALPPAHRP-YESLRPPFAQSA 114 + A+V HG+ L G LP+ DYE LPP R Y L F Sbjct: 71 HGLAAVVAAGHGSGGVLTGADPDVGDGAALPMIDYEQP--LPPDIRDGYSPLAGTFLDRG 128 Query: 115 SPLLGMGLNLGRQLYWQSQRYPDAFARARYLLMYPQYWSWRLSGVAAGELSSLGCHTDLW 174 S + + RQLYW +R PDAF +AR+ L PQYW+WRLSGVAA E S LG + LW Sbjct: 129 SATMHGATHQARQLYWMEEREPDAFGKARWYLGLPQYWAWRLSGVAASEASFLGAQSHLW 188 Query: 175 QPGQQCYSSLLAQCNWTPLMPPLRAAWERLGPLRPELAQRTGLPADCAVLCGVHDSNASL 234 ++ +S +++ W LMPP AW+ LG +RPEL +R GLPA+ VL G HDS+ + Sbjct: 189 NVAERRFSPIVSARGWERLMPPFSKAWQTLGWIRPELVRRFGLPAEMRVLTGGHDSSLNH 248 Query: 235 LRYLRGTGGGPRIVLSSGTWLIAAALDGCVSGLREEADMLANVNVLGAPVACMRFMGGRE 294 RY G V+S+GTW++ + + L E M N +V G + + MGGRE Sbjct: 249 YRY-HAAGLRDFTVISTGTWIVGFSRSTPIERLDEHRGMTLNSDVFGNRLGGILTMGGRE 307 Query: 295 FAQIAGDDLP---CSAEQLQALIDAQVFALPCFSECGGPFAGR--RGSIVGQAPQQPGSR 349 F+ IAG + P E L L+ + A P F + G F G RG I+G A + R Sbjct: 308 FSHIAGSNPPTDDAPIEVLGRLVAQRTIAAPSFGDDDGLFPGSAGRGRILGPAAETAMER 367 Query: 350 YALATLYCALMTAYCLDALDAPGEIVVEGSFTANPHFAALLAALV-SRTVYRSSDASGTT 408 ALA LYCAL+T C++AL A +V++GSF +P +A ++AAL+ R V + DA G Sbjct: 368 KALALLYCALLTVECIEALSADRLVVLDGSFLRDPLYAGVVAALLPERQVRFNLDAYGVA 427 Query: 409 LGGWLLDRWERAPETATLPALLPAEPLALRG--LAAYREDW 447 G LL E + A L AL + LA L+ Y +W Sbjct: 428 AGAALLAGHETREKPAPL-ALSESIDLARLNPDLSRYAANW 467 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: 612 Number of extensions: 34 Number of successful extensions: 4 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: 490 Length adjustment: 33 Effective length of query: 426 Effective length of database: 457 Effective search space: 194682 Effective search space used: 194682 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 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