Align Rhamnulokinase; RhaB; EC 2.7.1.5; ATP:L-rhamnulose phosphotransferase; L-rhamnulose 1-kinase; Rhamnulose kinase (uncharacterized)
to candidate 350803 BT1275 L-fuculose kinase (NCBI ptt file)
Query= curated2:Q8A1A3 (485 letters) >FitnessBrowser__Btheta:350803 Length = 476 Score = 444 bits (1142), Expect = e-129 Identities = 223/471 (47%), Positives = 303/471 (64%), Gaps = 5/471 (1%) Query: 2 KQNFFAVDLGATSGRTILGSFIEGGLNLEEINRFPNHLIEVGGHFYWDIYALYRHIIDGL 61 + + AVD G SGR I GS ++G L LEEI+RF N +++G H YWD AL+ + GL Sbjct: 6 RNTYLAVDFGGGSGRVIAGSLLQGKLELEEIHRFTNRQVKLGNHVYWDFPALFEDMKTGL 65 Query: 62 KLVAHRGESIASIGIDTWGVDFVLLGKDGNLLRQPYAYRDPHTVGAPEAFFSRISRSEVY 121 KL A +G + IGIDTWGVDF L+ K GNLL P YRD T G P+ F + + Y Sbjct: 66 KLAAQKGYHVKGIGIDTWGVDFGLIDKKGNLLGNPVCYRDARTDGMPDKVFQILDAQKHY 125 Query: 122 GKTGIQVMNFNSLFQLDTLRRNHDSALEAADKVLFMPDALSYMLTGKMVTEYTIASTAQL 181 TGIQVM N+LFQL ++++N D LE A ++LFMPD SY LTG EY IAST++L Sbjct: 126 ACTGIQVMPINTLFQLYSMQQNQDVLLEVAQRLLFMPDLFSYYLTGVANNEYCIASTSEL 185 Query: 182 VNAHTQRLEPELLKAVGLQEENFGRFVFPGEKIGTLTEEVQKITGLGAIPVIAVAGHDTG 241 ++A + + ++A+GL E FG + PG GTL EE+ + TGLG + +IAV HDT Sbjct: 186 LDARQRNWSMDTIRALGLPEHLFGEIILPGTVRGTLKEEIGRETGLGPVDIIAVGSHDTA 245 Query: 242 SAVAAVPALDRNFAYLSSGTWSLMGVETDAPVITAETEALNFTNEGGVEGTIRLLKNICG 301 SAVAAVPA + A+LSSGTWSL+GVE D P++T E FTNEGGV G IR L+NI G Sbjct: 246 SAVAAVPATEGQVAFLSSGTWSLLGVEVDEPILTEEARLAQFTNEGGVGGHIRFLQNITG 305 Query: 302 MWLLERCRLNW----GDTSYPELITEADSCEPFRSLINPDDDCFANPADMEQAIREYCRT 357 +W+L+R W + SY ++ +A E ++I DD F NP +ME A+ YCR Sbjct: 306 LWILQRLMSEWKLRGEEQSYDTILPQAADAE-IDTIIPVDDAEFMNPENMETALLNYCRN 364 Query: 358 TGQPVPEQRGQIVRCIFESLALRYRQVLENLRALSPRPIETLHVIGGGSRNDLLNQFTAN 417 VP + ++V+C+ +SLA +YR+ + L P PI L++IGGGS+N LLNQ TAN Sbjct: 365 HSLKVPGNKAEMVKCVLQSLAFKYREAVAQLNRCLPSPIHRLNIIGGGSQNKLLNQLTAN 424 Query: 418 AIGIPVVAGPSEATAIGNVMIQAMTVGEATDVAGMRQLISRSIPLKTYHPQ 468 A+GIPV AGP EATA+GN++ QAM GE + + +R+++S S+ + Y+P+ Sbjct: 425 ALGIPVYAGPVEATAMGNILTQAMAKGEISSLREIREVVSHSVTPQVYYPE 475 Lambda K H 0.321 0.137 0.411 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: 582 Number of extensions: 25 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: 485 Length of database: 476 Length adjustment: 34 Effective length of query: 451 Effective length of database: 442 Effective search space: 199342 Effective search space used: 199342 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: 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