Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_086509008.1 BZY95_RS05705 phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >NCBI__GCF_002151265.1:WP_086509008.1 Length = 469 Score = 581 bits (1497), Expect = e-170 Identities = 288/468 (61%), Positives = 353/468 (75%), Gaps = 6/468 (1%) Query: 1 MSTAKAPTLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLS 60 MS A ++PASIFRAYDIRG+V DTLT T IGRAIGSE+ AR E V V RDGRLS Sbjct: 1 MSQATNSSVPASIFRAYDIRGIVDDTLTETTVEQIGRAIGSEAAARNESTVVVARDGRLS 60 Query: 61 GPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGK-SGVMLTGSHNPPDYNGFKI 119 GP L + L++GL G V D+GMVPTPVLY+A ++LEG SGVM+TGSHNPPDYNGFKI Sbjct: 61 GPRLSEALMRGLTAAGRDVIDIGMVPTPVLYFATHILEGTASGVMVTGSHNPPDYNGFKI 120 Query: 120 VVAGETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDC 179 V+ GETL+ E I AL RIE +LA G GSV D+ Y ++I DI + +P+K VVDC Sbjct: 121 VLGGETLSGEAITALYRRIESGNLAEGQGSVRHADVRDAYLERIVGDIKLERPLKAVVDC 180 Query: 180 GNGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGL 239 GNGVAG + P+LIE LG IPL+ E+DG FPNHHPDPGK ENL+D++ VK AD+GL Sbjct: 181 GNGVAGELGPKLIEMLGAETIPLFAEIDGTFPNHHPDPGKVENLQDVMRTVKETGADIGL 240 Query: 240 AFDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGG 299 AFDGDGDR+GVVT +G +IYPD L+M FA+D++SRNPGA +IFDVKCT L ++ GG Sbjct: 241 AFDGDGDRLGVVTPSGKLIYPDHLMMAFAEDMLSRNPGARVIFDVKCTGNLAGVVERAGG 300 Query: 300 RPVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEI----LSQ 355 P MW+TGHSLIK +MKETGA LAGEMSGH+FF+ERW+GFDDGIY AARLLEI LS Sbjct: 301 TPEMWRTGHSLIKARMKETGAQLAGEMSGHIFFQERWYGFDDGIYGAARLLEILAKHLST 360 Query: 356 DQRDSEHVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEGNI-TTLDGVRVDYP 414 D++ F+ +P DISTPEIN+ VT+++KF ++E L R+ +G+ + TTLDG+RVDYP Sbjct: 361 QGMDADAFFARYPQDISTPEINVHVTDENKFELVEKLAREGDFGDDGVKTTLDGIRVDYP 420 Query: 415 KGWGLVRASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVP 462 GWGL RASNTTPVLVLRFE ++ LERI+ F + LK VD +L +P Sbjct: 421 DGWGLCRASNTTPVLVLRFEGKSDAALERIRNRFADALKQVDPALTLP 468 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: 671 Number of extensions: 27 Number of successful extensions: 4 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: 463 Length of database: 469 Length adjustment: 33 Effective length of query: 430 Effective length of database: 436 Effective search space: 187480 Effective search space used: 187480 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