Align 5'-fluoro-5'-deoxy-adenosine phosphorylase (EC 2.4.2.1) (characterized)
to candidate WP_011840388.1 RSPH17029_RS02465 S-methyl-5'-thioadenosine phosphorylase
Query= metacyc::MONOMER-15923 (299 letters) >NCBI__GCF_000015985.1:WP_011840388.1 Length = 290 Score = 265 bits (678), Expect = 7e-76 Identities = 142/266 (53%), Positives = 171/266 (64%), Gaps = 5/266 (1%) Query: 15 LGIIGGSGLYEFPGLTDPEEFPVETPYGPPSAPPVVGTVGGRWVAFLARHGTGHRIPPSR 74 +G+IGGSG+YE GL D VETP+G PS + G + G +AFL RHG GH P+ Sbjct: 5 IGVIGGSGVYEIDGLEDAVWTKVETPWGDPSDEILTGRLDGVPMAFLPRHGRGHVHSPTT 64 Query: 75 IPVRANLYALKALGVTEVVSVSAVGSLREEYAPGHLVVPDQIIDRTRGGRPATFFSSGVV 134 +P RAN+ ALK LGVT++VSVSA GS R E APG V+ DQ IDR+ R +FF SG V Sbjct: 65 VPYRANIDALKRLGVTDLVSVSACGSFRGEMAPGDFVIVDQFIDRSFA-RAKSFFGSGCV 123 Query: 135 VHVSLADPYCPRLRAALTDAARAAHPTVHPAGTYLCMEGPQFSTRAESQLYRAWGMDVIG 194 HVSLA P C RL A +AAR TVH GTYLCMEGPQFST AES LY++WG VIG Sbjct: 124 AHVSLAHPTCGRLSALCAEAARGTGVTVHEGGTYLCMEGPQFSTLAESLLYKSWGCHVIG 183 Query: 195 MTAQPEAKLAREAELCYAGLSLVTDYDCWHTGHDSVDARTVAEVMAANVIAARAVLSGLA 254 MT PEAKLAREAE+CYA +++VTDYD WH H VD + + AN AR +++GL Sbjct: 184 MTNMPEAKLAREAEICYASVAMVTDYDSWHPHHGEVDITAIIATLGANADHARGLVAGLP 243 Query: 255 HATAPADCACHH----ALDGAVLTDP 276 C H ALD A++T P Sbjct: 244 ARLGTERDLCPHGCDRALDHALMTAP 269 Lambda K H 0.319 0.135 0.415 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: 280 Number of extensions: 9 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: 299 Length of database: 290 Length adjustment: 26 Effective length of query: 273 Effective length of database: 264 Effective search space: 72072 Effective search space used: 72072 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: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. 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