Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_085636384.1 MGEO_RS08970 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_002115805.1:WP_085636384.1 Length = 447 Score = 212 bits (539), Expect = 2e-59 Identities = 154/447 (34%), Positives = 224/447 (50%), Gaps = 34/447 (7%) Query: 3 KLFGTFGVRGIANE-EITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61 KLFGT GVRG AN +T + AL+IG A G +++ + VV+G+DTR SG M ++AL Sbjct: 4 KLFGTDGVRGTANAYPMTADMALRIGAAVGRHFRQDSKGVHRVVIGKDTRQSGYMFENAL 63 Query: 62 ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +GL STG +V+ +G PTPA+ T AD G +I+ASHNP NGIK P+G L Sbjct: 64 TAGLTSTGMNVLLLGPVPTPAVGLLTPSMRADLGIMISASHNPARDNGIKFFGPDGFKLS 123 Query: 122 KEREAIVEELF-------FSEDFHRAKWNEIGELRKEDIIKPYIEAIKNRVDVEAIKKRR 174 EA +E L +E+ RAK + G R ++ +K A + ++ +K Sbjct: 124 DADEAEIEALIETGVEPAQAENIGRAKRIDDGRFRYQERVKSTFPA---DLRLDGLK--- 177 Query: 175 PFVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKAL 234 VV+D +NGA P +L ELG V+ + P+G L V A Sbjct: 178 --VVIDCANGAAYKAAPEVLWELGADVIPLGVTPNGSNINEGCGSTHPQLAA--AAVVAH 233 Query: 235 GADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLREN--GGGLLVTTIATSNLLD 292 GAD G+ DGDADR + IDE G+ GD+ AL+A E G+LV T+ ++ L+ Sbjct: 234 GADIGICLDGDADRVILIDETGQVADGDQIMALMAARWAEEQRLRDGVLVATVMSNLGLE 293 Query: 293 DIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEI 352 G ++ RT VGD V A+ +GGE++G ++ D+ DG M + + Sbjct: 294 RFLDGRGLRLERTGVGDRYVVEAMRRGGWNLGGEQSGHIVMTDYATTGDGLMAGLQFLGE 353 Query: 353 FAKSGKKFSEL---IDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKI 409 ++GK S L D +P+ ++V D VA L E K D Sbjct: 354 MCRTGKPASALARSFDPVPQLL-----KNVRYD-----PSVAPL-ETASVKAAIADAEAR 402 Query: 410 IFDDGWVLVRASGTEPIIRIFSEAKSE 436 + G +L+R SGTEP+IR+ +E + E Sbjct: 403 LNGSGRLLIRKSGTEPLIRVMAECEDE 429 Lambda K H 0.317 0.139 0.396 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: 534 Number of extensions: 29 Number of successful extensions: 7 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: 456 Length of database: 447 Length adjustment: 33 Effective length of query: 423 Effective length of database: 414 Effective search space: 175122 Effective search space used: 175122 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