Align Rhamnulokinase (EC 2.7.1.5) (characterized)
to candidate WP_062735671.1 AYX06_RS10180 rhamnulokinase
Query= reanno::Koxy:BWI76_RS00680 (488 letters) >NCBI__GCF_001580365.1:WP_062735671.1 Length = 487 Score = 319 bits (818), Expect = 1e-91 Identities = 196/491 (39%), Positives = 266/491 (54%), Gaps = 27/491 (5%) Query: 4 RHCVAVDLGASSGRVMLASYQPGQQTLALREIHRFTNSLQKVD-----GFDCWDLDSLEG 58 R AVDLGA+SGRV+L + G+ L LR + RF N ++ G W++ L Sbjct: 3 RTVAAVDLGATSGRVILGGIEDGR--LRLRHLARFPNQPVRLHEGGRTGLH-WNITELHR 59 Query: 59 EIRRGLEKVCEQGILIDSIGIDTWGVDYVLLDKRGQRVGLPVSYRDSRTQGLMRHAEAQL 118 + GL + QG L+ SIGID+W VDY LL + G+ +G P SYRD RT + ++ Sbjct: 60 SLTAGLAQALRQGELVVSIGIDSWAVDYALL-RDGRMLGAPYSYRDERTAVGVEAVHGRV 118 Query: 119 GRAEIYRRSGIQFLPFNTLYQLRALVEQQPELVSQAAHALLIPDYFSFRLTGNMNWEYTN 178 E++ R+G+Q LPFNT+YQL V++ + A LL+PD + LTG E TN Sbjct: 119 SPEELHARTGLQHLPFNTVYQLA--VDRVRGDLDLADRMLLVPDLIGYWLTGRQVAEATN 176 Query: 179 ATTTQLVNINSDSWDEDLLNWSGAPREWFGTPTHPGNVIGHWICPQGNHI------PVVA 232 A+TT L++ + WD L++ G PRE F PG IG + + V A Sbjct: 177 ASTTGLLDARTRQWDTGLMDRLGYPRELFAPVVTPGTRIGELLPDVAAELGAAPGLAVTA 236 Query: 233 VASHDTASAVIASPLASKNAAYLSSGTWSLMGFESKIPCTSDAALRANITNEGGAEGRYR 292 V SHDTASAV+A P AA++SSGTWSL+G E P + + AN TNEGG +GR R Sbjct: 237 VGSHDTASAVVAVPTTDDAAAFISSGTWSLVGIELDAPVLTPESRAANFTNEGGLDGRVR 296 Query: 293 VLKNIMGLWLLQRVLRE---------QNVSDLPALIARTAALPACRFVIDCNDDRFINPD 343 LKN+ GLWLL +R Q SDL AL+A AA+ V+D D+RF P Sbjct: 297 FLKNVSGLWLLSESIRTWDGPGASDAQRSSDLAALLAEAAAVTRPVSVVDATDERFTAPG 356 Query: 344 DMSAEIQAACRESGQPVPDTDAELARCIFDSLALLYTRVLNELAALRGQPFSQLHIVGGG 403 DM A + A C E G P T AE+ RCI +SLA Y + + L G+ +H+VGGG Sbjct: 357 DMPARVVAWCEERGLEPPRTRAEVVRCILESLAAAYATTIEQAEHLSGKRIRTIHVVGGG 416 Query: 404 CQNELLNQLCADACGITVVAGPVEASTLGNIGIQLMTLDEL-NNVDEFRQVVRQNYALTT 462 QN LL QL AD G TV AGPVEA+ +GN+ +Q + +++ R +V + Sbjct: 417 SQNALLCQLTADRTGRTVAAGPVEATAVGNVLVQARAAGLVTGDLEALRGIVATTFEPVR 476 Query: 463 FTPNPENEIAR 473 + P + AR Sbjct: 477 YQPRTVTDTAR 487 Lambda K H 0.320 0.135 0.413 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: 615 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: 488 Length of database: 487 Length adjustment: 34 Effective length of query: 454 Effective length of database: 453 Effective search space: 205662 Effective search space used: 205662 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 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