Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_028310659.1 H566_RS0105535 phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >NCBI__GCF_000482785.1:WP_028310659.1 Length = 464 Score = 496 bits (1276), Expect = e-145 Identities = 247/460 (53%), Positives = 328/460 (71%), Gaps = 4/460 (0%) Query: 7 PTLPAS-IFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELV 65 P +PA+ +F+AYDIRGVV LT + IG++I + + RG+ +GRDGR SGP L Sbjct: 6 PNVPAAGLFKAYDIRGVVTTALTPDAVRQIGQSIATLARERGQTAAVIGRDGRESGPALA 65 Query: 66 KQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGET 125 K L GL G V D+G+V TP+LY+A L +GVM+TGSHNPP+YNG K+VVAGE Sbjct: 66 KALSDGLRAGGLDVVDIGLVATPMLYFATYELGIPTGVMVTGSHNPPEYNGLKMVVAGEA 125 Query: 126 LANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAG 185 + + I LR RI + LA+G G DI RY ++I D+ +++P+K+V+D GNGV G Sbjct: 126 IYGDTITGLRTRIAEGKLATGEGGYRTDDIAERYLQRIVGDVKLSRPIKIVIDAGNGVPG 185 Query: 186 VIAPQLIEALGCSVIP-LYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGD 244 AP+L + LG +V+ L+CEVDG FPNHHPDP P NL+D++A ++ +A++GLAFDGD Sbjct: 186 AYAPELFKRLGATVVKELFCEVDGTFPNHHPDPADPHNLEDVMAALRETDAEIGLAFDGD 245 Query: 245 GDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMW 304 GDR+GVVT TG II+PDR LMLFA+DV+SRNPG +IFDVKC+R + ++ GG P++W Sbjct: 246 GDRLGVVTKTGNIIWPDRQLMLFARDVLSRNPGQQVIFDVKCSRHVGNVVREAGGVPLLW 305 Query: 305 KTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVF 364 +TGHSL+K K+KETGA LAGEMSGHVFFKERW+GFDDG+Y+ ARLLEILS+ + D V Sbjct: 306 RTGHSLVKAKLKETGAPLAGEMSGHVFFKERWYGFDDGLYTGARLLEILSKVE-DPSAVL 364 Query: 365 SAFPSDISTPEINITVTEDSKFAIIEALQRDAQW-GEGNITTLDGVRVDYPKGWGLVRAS 423 A P+ STPE+ + E F ++E LQ+ A++ G I T+DGVR ++P G+GL R S Sbjct: 365 EALPNASSTPELKLETAEGENFTLVEKLQQTAKFEGTTEIITIDGVRAEFPDGFGLARPS 424 Query: 424 NTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 NTTPV+VLRFEAD E LERI+ FR + AV + +PF Sbjct: 425 NTTPVVVLRFEADNPEALERIQAQFRKAILAVAPEVKLPF 464 Lambda K H 0.319 0.138 0.410 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: 643 Number of extensions: 26 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: 463 Length of database: 464 Length adjustment: 33 Effective length of query: 430 Effective length of database: 431 Effective search space: 185330 Effective search space used: 185330 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 (21.7 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