Align Rhamnulokinase RhaK in alpha-proteobacteria (EC 2.7.1.5) (characterized)
to candidate YP_002824801.1 NGR_c02500 carbohydrate kinase contains FGGY family domain
Query= reanno::Smeli:SMc03003 (462 letters) >NCBI__GCF_000018545.1:YP_002824801.1 Length = 456 Score = 735 bits (1897), Expect = 0.0 Identities = 363/456 (79%), Positives = 398/456 (87%) Query: 3 MKTVAVIDIGKTNAKVALVDLERFEEIAVRKSGNGVSDDGPYPHFDTERLWRFVLDSLAA 62 MKTVAVIDIGKTNAK+ALVDLE+FEEIAVRK+ N V DG YPHFD E LWRF+LDSLAA Sbjct: 1 MKTVAVIDIGKTNAKIALVDLEQFEEIAVRKTPNVVVKDGLYPHFDVEYLWRFILDSLAA 60 Query: 63 LHREHPVDAISVTTHGATAVLLDEAGELALPVLDYEFTGPDALAEEYEKARPPFTETGSA 122 LHRE PVDAISVTTHGATAVLL++AGELA+PVLDYE+ GPDAL+EEY +ARPPF+ETGSA Sbjct: 61 LHRERPVDAISVTTHGATAVLLNDAGELAMPVLDYEYAGPDALSEEYGQARPPFSETGSA 120 Query: 123 RLPMGLNVGAQLFWQQRMFPEHFARVATILTYAQYWSYRLTGVRTNELTSLGCHTDLWNP 182 RLPMGLNVGAQLFWQQRMFP FA VATILTYAQYWSYRLTGV TNELTSLGCHTDLWNP Sbjct: 121 RLPMGLNVGAQLFWQQRMFPRDFAEVATILTYAQYWSYRLTGVATNELTSLGCHTDLWNP 180 Query: 183 KAATFSSMVDEQGWRHLFAPVRRAGDVLGPLLRQVADETGLPPETPVHCGIHDSNASLLP 242 K ATFS+MV+ +GW LFAPVR+A +V+G LL +A+ TGLP PV+CGIHDSNASLLP Sbjct: 181 KTATFSTMVEARGWTPLFAPVRKADEVIGGLLPALAEATGLPDRLPVYCGIHDSNASLLP 240 Query: 243 HLITRQAPFSVASTGTWVVMLAVGAEPVKLDERRDTLINVNALGDPVPSARFMGGRAYSL 302 HL+TR APFSV STGTWVVM++VG E V+LDERRDTLINVNALGDPVPSARFMGGRA+SL Sbjct: 241 HLLTRSAPFSVVSTGTWVVMMSVGGEQVELDERRDTLINVNALGDPVPSARFMGGRAFSL 300 Query: 303 LIGDDPPTASPEAEASVLEQGHMLLPSLPGGSGPFPAARPHWTADEDKLAPAERLAVVSF 362 LIGDDPP S EAE VL +G MLLPS+PGGSGPFP+A P WT +ED L PAERLA VSF Sbjct: 301 LIGDDPPPPSAEAERRVLAEGRMLLPSVPGGSGPFPSAEPRWTVNEDNLTPAERLAAVSF 360 Query: 363 HLALMTATCLDLIGARGEILVEGPFALNDAYLRMLAAATGRPVLANRLNSTGTSLGAACL 422 HL+LMTATCLDLIGARGEI+VEGPFA N AYLRMLAAATGR VLANRL+STGTSLGAACL Sbjct: 361 HLSLMTATCLDLIGARGEIVVEGPFAANSAYLRMLAAATGRLVLANRLSSTGTSLGAACL 420 Query: 423 VAGARVRTGAEAIPAAKPDAYAAYAEAWRRRTAAHV 458 VAGA +RTGAEA A P +Y YA W+R TA HV Sbjct: 421 VAGATIRTGAEAFSEAVPRSYVDYAHKWQRLTAEHV 456 Lambda K H 0.319 0.134 0.409 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: 703 Number of extensions: 35 Number of successful extensions: 1 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: 462 Length of database: 456 Length adjustment: 33 Effective length of query: 429 Effective length of database: 423 Effective search space: 181467 Effective search space used: 181467 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 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