Align Rhamnulokinase; RhaB; EC 2.7.1.5; ATP:L-rhamnulose phosphotransferase; L-rhamnulose 1-kinase; Rhamnulose kinase (uncharacterized)
to candidate 16887 b2803 L-fuculokinase (NCBI)
Query= curated2:Q8A1A3 (485 letters) >FitnessBrowser__Keio:16887 Length = 482 Score = 147 bits (372), Expect = 6e-40 Identities = 122/383 (31%), Positives = 181/383 (47%), Gaps = 22/383 (5%) Query: 71 IASIGIDTWGVDFVLLGKDGNLLRQPYAYRDPHTVGAPEAFFSRISRSEVYGKTGIQVMN 130 I I + T+GVD L+ K GNLL +++ P T + IS + +G+ + Sbjct: 84 IRGIAVTTFGVDGALVDKQGNLLYPIISWKCPRTAAVMDNIERLISAQRLQAISGVGAFS 143 Query: 131 FNSLFQLDTLRRNHDSALEAADKVLFMPDALSYMLTGKMVTEYTIASTAQLVNAHTQRLE 190 FN+L++L L+ NH LE A LF+ +++ LTG+ T+ T+A T+Q+++ + Sbjct: 144 FNTLYKLVWLKENHPQLLERAHAWLFISSLINHRLTGEFTTDITMAGTSQMLDIQQRDFS 203 Query: 191 PELLKAVGLQEENFGRFVFPGEKIGTLTEEVQKITGLG-AIPVIAVAGHDTGSAVAAVPA 249 P++L+A G+ F R V GE+IGTL + GL IPVI+ AGHDT A+ A Sbjct: 204 PQILQATGIPRRLFPRLVEAGEQIGTLQNSAAAMLGLPVGIPVIS-AGHDTQFALFGAGA 262 Query: 250 LDRNFAYLSSGTWSLMGVETDAPVITAETEALNFTNEGGVEGTIRLLKNICGMWL----L 305 ++N LSSGTW ++ V + + ++ T E + L N WL L Sbjct: 263 -EQNEPVLSSGTWEILMVRSAQVDTSLLSQYAGSTCELDSQAG---LYNPGMQWLASGVL 318 Query: 306 ERCR-LNW-GDTSYPELITEADSCEPFRSLINPDDDCFANPADMEQAIREYCRTTGQPVP 363 E R L W +T + LI EA LI P D D+ + G + Sbjct: 319 EWVRKLFWTAETPWQMLIEEA-------RLIAPGADGVKMQCDLLSC--QNAGWQGVTLN 369 Query: 364 EQRGQIVRCIFESLALRYRQVLENLRALSPRPIETLHVIGGGSRNDLLNQFTANAIGIPV 423 RG R E L + ++ L+ L + L ++GGGSRN L NQ AN + IPV Sbjct: 370 TTRGHFYRAALEGLTAQLQRNLQMLEKIGHFKASELLLVGGGSRNTLWNQIKANMLDIPV 429 Query: 424 -VAGPSEATAIGNVMIQAMTVGE 445 V +E T G + VGE Sbjct: 430 KVLDDAETTVAGAALFGWYGVGE 452 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: 512 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 485 Length of database: 482 Length adjustment: 34 Effective length of query: 451 Effective length of database: 448 Effective search space: 202048 Effective search space used: 202048 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: 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