Align ribulokinase (EC 2.7.1.16) (characterized)
to candidate 3607115 Dshi_0537 carbohydrate kinase FGGY (RefSeq)
Query= BRENDA::Q9KBQ3 (563 letters) >FitnessBrowser__Dino:3607115 Length = 497 Score = 200 bits (509), Expect = 1e-55 Identities = 160/534 (29%), Positives = 241/534 (45%), Gaps = 52/534 (9%) Query: 5 YTIGVDYGTESGRAVLIDLSNGQELADHVTPYRHGVIDQYLPNTNIKLGHEWALQHPLDY 64 Y + D GTES R + D+ NG +A H PY T G A Q+P D+ Sbjct: 3 YFLAADGGTESLRVRIYDI-NGVCVASHAEPYE----------TTFSPGAR-AEQNPEDW 50 Query: 65 VEVLTTSVPAVMKESGVDADDVIGIGVDFTACTMLPVDEEGQPLCLLAQYKDNPHSWVKL 124 L + A + E+G+ + + + T+CT++ +D+ G+PL P L Sbjct: 51 WICLCKASRASLAEAGLAGEQIDAMAYATTSCTVVALDKAGKPL--------RP---ALL 99 Query: 125 WKHHAAQDKANAINEMAEKRGEAFLPRYGGKISSEWMIAKVWQILDEAEDVYNRTDQFLE 184 W A +A A+ + R G +S+EWMI K I DVY+ E Sbjct: 100 WMDVRADQEAEAVLATGDARLRLNSDG-AGPVSAEWMIPKALWIKRNEPDVYDAAATICE 158 Query: 185 ATDWIVSQMTGKIVKNSCTAGYKAIWHKREGYPSNEFFKALD-PRLEHLTTTKLRGDIVP 243 D++ ++TG+ + G + + R+G + AL P L K + Sbjct: 159 YQDYLTLRLTGERCASLNNVGLRWHYANRDGGWAESLVTALGMPDL----VEKWPARVAA 214 Query: 244 LGERAGGLLPEMAEKMGLNPGIAVAVGNVDAHAAVPAVGVTTPGKLVMAMGTSICHMLLG 303 GE G L P+ AE +GL P + G DA + +GV+ PG+L + G+S + Sbjct: 215 PGEVVGSLTPDAAEALGLTPKTKLVQGGADALIGMIGLGVSQPGQLCLITGSSHLQFGVT 274 Query: 304 EKEQEVEGMCGVVEDGIIPGYLGYEAGQSAVGDIFAWFVKHGVSAATFDEAQEKGVNVHA 363 EK GM G D + PG E GQ++ G I W + DE Sbjct: 275 EKPFHAPGMWGAYADIVYPGRHIVEGGQTSTGSIINWLRRFVGGEFDIDE---------- 324 Query: 364 LLEEKASQLRPGESGLLALDWWNGNRSILVDTELSGMLLGYTLQTKPEEIYRALLEATAF 423 + KA+ L PG GL+ D + GNR+ D G + G TL +P ++RA++E + Sbjct: 325 -MNRKAAALPPGSEGLVVQDHFQGNRTPYTDARSRGAITGLTLAHEPHHVFRAIMEGISM 383 Query: 424 GTRAIVDAFHGRGVEVHELYACGGLPQKNHLLMQIFADVTNREIKVAASKQTPALGAAMF 483 GTRAI+D+F G E E+ A GG + L MQI AD +++ AS P LG+A+ Sbjct: 384 GTRAILDSFAKGGYEGSEMVAGGGATNSD-LFMQIHADTAGIPVRIPASTDGPTLGSAIL 442 Query: 484 ASVAAGSEVGGYDSIEE---AAKKMGRVKDETFKPIPEHVAIYEKLYQEYVTLH 534 A+ AG + +I+E A K GRV +P P+ V YE++Y Y+ L+ Sbjct: 443 AAHGAGY----FATIDEGIAAMVKPGRV----IEPNPKAVQAYEEIYARYLALY 488 Lambda K H 0.317 0.134 0.402 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: 659 Number of extensions: 33 Number of successful extensions: 6 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: 563 Length of database: 497 Length adjustment: 35 Effective length of query: 528 Effective length of database: 462 Effective search space: 243936 Effective search space used: 243936 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 (21.6 bits) S2: 52 (24.6 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