Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_013429174.1 CALKRO_RS00500 phosphoglucomutase/phosphomannomutase family protein
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000166775.1:WP_013429174.1 Length = 471 Score = 234 bits (597), Expect = 5e-66 Identities = 159/467 (34%), Positives = 228/467 (48%), Gaps = 23/467 (4%) Query: 5 FGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALISG 64 FGT G R I + T E K+ A +K +G +V+G D R + Sbjct: 4 FGTGGWRAIIGDDFTKENIQKVAQAVSIYMKEKGIDSDGIVLGYDRRFLSDKAARWFSEV 63 Query: 65 LLSVGCDVIDVG-IAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKE 123 L + G V + +APTP V + K N GA +TASHNP +YNGIKL G E Sbjct: 64 LSANGIKVFFINKVAPTPLVMFTVKKLNTKFGATVTASHNPADYNGIKLFIEEGRDAPFE 123 Query: 124 REAIVEEL---FFKEDFDRAKWYEIGEVRREDIIKP---YIEAIKSKVDVEAIKKRKPFV 177 + +E + + R K+ + E +II P YI+AI S +D+EAIKKRK + Sbjct: 124 VTSEIETIANSLLSDSIKRLKFEKAIENGWIEIIDPFDDYIDAILSMIDIEAIKKRKLRI 183 Query: 178 VVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGAD 237 ++D G +L +L C V T++ + D F R P P L +V G D Sbjct: 184 LLDPMYGVSRTSLQTILITARCDVDTIHERHDTLFGGRLPSPTTSTLYRLKHLVVEKGYD 243 Query: 238 FGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKG-GGLLVTTVATSNLLDDIAK 296 G+ DGDADR IDE G FI + L+ LK KG G +V +AT++LLD IA Sbjct: 244 LGIGTDGDADRVGIIDEIGNFIHPNDILVLLYYYFLKYKGWKGPVVRNLATTHLLDRIAS 303 Query: 297 KHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKS 356 G K VG ++ + E IGGE +GG+ H+ G+DG +VE+ K+ Sbjct: 304 SFGEKCYEVPVGFKYISAKMEETGAIIGGESSGGLTIKGHIKGKDGIFAATLLVELICKT 363 Query: 357 GKKFSELIDELPKYYQIKTKRHVEGD---RHAIVNKVAEMARERGY---------TVDTT 404 G+K SE+++E+ + Y I VE D K+ E+ ++ + V Sbjct: 364 GRKLSEILEEIHRIYGILYM--VENDFSFEPEEKEKIWEILFDKKHLPDFPFEISNVSYI 421 Query: 405 DGAKIIFED-GWVLVRASGTEPIIRIFSEAKSKEKAQEYLNLGIELL 450 DG K+ F++ GWVL R SGTEP++RI+SE + K A+E + E L Sbjct: 422 DGVKVYFKNGGWVLARFSGTEPLLRIYSEMEEKVHAEEVCKIFAEFL 468 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: 585 Number of extensions: 34 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: 471 Length adjustment: 33 Effective length of query: 422 Effective length of database: 438 Effective search space: 184836 Effective search space used: 184836 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