Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_010961099.1 MCA_RS09075 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_000008325.1:WP_010961099.1 Length = 447 Score = 203 bits (517), Expect = 8e-57 Identities = 148/441 (33%), Positives = 226/441 (51%), Gaps = 18/441 (4%) Query: 5 FGTFGVRG-IANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDALIS 63 FGT G+RG + + ITP+F LK+G A G + RE R V++G+DTR+SG M + AL + Sbjct: 6 FGTDGIRGRVGDYPITPDFMLKLGWAAGCVFAREMPGRR-VLIGKDTRISGYMFESALEA 64 Query: 64 GLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKE 123 G + G D +G PTPA+ + T A G VI+ASHNP NGIK P+GM L E Sbjct: 65 GFSAAGVDTQLLGPMPTPAVAYLTRTLRAQAGVVISASHNPYYDNGIKFFGPDGMKLPDE 124 Query: 124 REAIVEELFFSEDFHRAKWNEIGE-LRKEDIIKPYIEAIKNRVDVEAIKKRRPFVVVDTS 182 E ++E+ + + + IG+ R D YIE K+ + + + +VVD + Sbjct: 125 LELLIED-YLGRPMTTVECSHIGKATRIVDAAGRYIEFCKSTIPL-GMHFSGMKIVVDCA 182 Query: 183 NGAGSLTLPYLLRELGCKVVSVNAHPDG-HFPARNPEPNEENLKGFMEIVKALGADFGVA 241 +G+ P + EL V ++ PDG + R + ENL+ + V AD G+A Sbjct: 183 HGSTYHVAPDVFSELRATVSTLGVAPDGLNINDRVGATDPENLR---QTVLEENADLGIA 239 Query: 242 QDGDADRAVFIDENGRFIQGDKTFALVADAVLRENG-GGLLVTTIATSNLLDDIAKRNGA 300 DGD DR + +D G + GD+ ++A+A E G +V T+ ++ L+ +R G Sbjct: 240 LDGDGDRLIMVDHRGEVVDGDELLFVIANARHAEGELKGSVVGTLMSNLGLEQAIRRLGL 299 Query: 301 KVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAKSGKKF 360 + R VGD V +LE+ +GGE +G +I D DG ++ +++ +SGK Sbjct: 300 EFRRAAVGDRYVMEMMLEHGSMLGGEGSGHIICRDRTTTGDGIVSALQVLAEIVRSGKTL 359 Query: 361 SELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFDDGWVLVRA 420 EL + KY Q +V + +A V L +K +++ G D G VL+R Sbjct: 360 HELKQGMRKYPQRLV--NVRLAERVSLASV-PLVQKVKAEVEAELG-----DSGRVLLRP 411 Query: 421 SGTEPIIRIFSEAKSEEKARE 441 SGTEP+IR+ E E + RE Sbjct: 412 SGTEPLIRVMVEGADEGQVRE 432 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: 517 Number of extensions: 32 Number of successful extensions: 6 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: 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