Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_019614405.1 G327_RS0108835 phosphoglucomutase/phosphomannomutase family protein
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000381745.1:WP_019614405.1 Length = 470 Score = 197 bits (500), Expect = 8e-55 Identities = 143/463 (30%), Positives = 221/463 (47%), Gaps = 27/463 (5%) Query: 5 FGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALISG 64 FGT G R I ++ T + + ++ E V+G D R + + Sbjct: 4 FGTGGWRSIIGDEFTKANVCLVAQSLANIMMIEDVVNKGFVIGYDRRFLSDKASKWFAEV 63 Query: 65 LLSVGCDVIDVG-IAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMG---- 119 L G V + PTP V K A ITASHNP +YNGIK+ G Sbjct: 64 LAGNGIKVSFIDKFVPTPIVMHKAKAMGTIYSACITASHNPSDYNGIKVFIEGGRDADEI 123 Query: 120 ----LKKEREAIVEELFFKEDFDRAKWYEIGEVRREDIIKPYIEAIKSKVDVEAIKKRKP 175 ++ + EAI DF++A E G++ + + +++++ +DVEAIK+ Sbjct: 124 ITEKIETQIEAINSADIQALDFEKA--VEDGQIVVINPMNEFVDSVLDLLDVEAIKQANL 181 Query: 176 FVVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALG 235 V++D G L +L C V +N + F P P+ L + +V A G Sbjct: 182 RVLIDPMFGVAKNALQTVLITGRCDVDVINDGENPAFGGLMPSPSAATLYQLKHLVVAKG 241 Query: 236 ADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLK-EKGGGLLVTTVATSNLLDDI 294 D GV DGDADR IDE G F+ ++ L+ ++K +K G +V +AT+++LD I Sbjct: 242 YDIGVGTDGDADRIGIIDEKGNFVHPNEVLILLYYYLIKYKKQSGSVVRNIATTHILDKI 301 Query: 295 AKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFA 354 A HG K VG ++ + ++ IGGE +GG+ H+ G+D + +VE+ A Sbjct: 302 AADHGQKSFEVPVGFKHISSQMEADDSLIGGESSGGLTIRGHIKGKDSVFAASLLVEMIA 361 Query: 355 KSGKKFSELIDELPKYYQIKTKRHVEGD-------RHAIVNK--VAEMARERGYTVDT-- 403 +GKK SEL++E+ Y EGD + I NK V + E Y ++ Sbjct: 362 VTGKKISELLEEIYDIYGYSYT--AEGDCTFKAEQKEVIYNKVYVEKQLPEFQYDIERVS 419 Query: 404 -TDGAKIIFED-GWVLVRASGTEPIIRIFSEAKSKEKAQEYLN 444 DG K+ F++ GWV+ R SGTEP++RIFSE +S+ A+ +N Sbjct: 420 YADGLKVYFKNGGWVIARFSGTEPLLRIFSEMESQTIAEGIVN 462 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: 529 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: 455 Length of database: 470 Length adjustment: 33 Effective length of query: 422 Effective length of database: 437 Effective search space: 184414 Effective search space used: 184414 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