Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_013537643.1 THEAM_RS04490 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000185805.1:WP_013537643.1 Length = 449 Score = 228 bits (582), Expect = 2e-64 Identities = 165/460 (35%), Positives = 242/460 (52%), Gaps = 32/460 (6%) Query: 3 KLFGTFGVRGIANE-KITPEFAMKIGMAFGTLLKRE-GRKKPLVVVGRDTRVSGEMLKEA 60 +LFGT G+RGIAN +TPE KIG+A+G L + +K VVVG+DTR+S +M+K A Sbjct: 6 RLFGTDGIRGIANRYPLTPEMVQKIGLAYGVYLNAKFPDRKHTVVVGQDTRLSSDMIKAA 65 Query: 61 LISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGL 120 LISGL S G DV+D G+ PTPAV + K + GG +++ASHNP EYNG+K G Sbjct: 66 LISGLNSAGVDVLDAGVVPTPAVSFLIKEGDFSGGVMVSASHNPYEYNGLKFFNHLGKKF 125 Query: 121 KKEREAIVEELFF-KEDFDRAKWYEIGEV-RREDIIKPYIEAIKSKVDVEAIKKRKPFVV 178 + E +E + F K + RA + +G V +++++ Y + ++S A K + Sbjct: 126 SEAEEGGLELVVFNKYELPRANYDNLGRVFNGKNLVESYKKHLESAGRYLAGLK----IG 181 Query: 179 VDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADF 238 +D +NGA P + LG KV T NA+PDG N + ++ + V LG Sbjct: 182 LDCANGATYQIAPEVFSALGAKVFTFNAEPDG--KNINDGCGALHPEKLAKKVVELGLHL 239 Query: 239 GVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNLLDDIAKKH 298 G A DGD DR + ++E G I GD+ AL+A V TV ++ L+ ++ Sbjct: 240 GFAYDGDGDRCIAVNERGEVIDGDQLIALLALHFADRSKEA--VATVMSNLGLELFLREK 297 Query: 299 GAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMT---VAKVVEIFAK 355 G ++ RT VGD VA + E +GGE++G +I E DG +T VA +V+ K Sbjct: 298 GFRLHRTPVGDRFVAEKMDEVGAAVGGEQSGHIIVKEFAETGDGILTSVLVASIVKSLRK 357 Query: 356 SGKKFSELIDELP-KYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDG 414 + L +P K +K K +R + KV RE G K++ G Sbjct: 358 PASEVLSLFKPVPQKLKNVKVKEKPPLER---LEKVQRAIRE---------GEKLLEGRG 405 Query: 415 WVLVRASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEKAL 454 VLVR SGTEP++RI EA+S E + IE++E+A+ Sbjct: 406 RVLVRYSGTEPLLRIMVEAESPELIERV----IEMVEEAV 441 Lambda K H 0.317 0.138 0.391 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: 581 Number of extensions: 26 Number of successful extensions: 7 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: 455 Length of database: 449 Length adjustment: 33 Effective length of query: 422 Effective length of database: 416 Effective search space: 175552 Effective search space used: 175552 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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