Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_010936305.1 DET_RS02825 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_000011905.1:WP_010936305.1 Length = 430 Score = 253 bits (645), Expect = 1e-71 Identities = 162/452 (35%), Positives = 240/452 (53%), Gaps = 29/452 (6%) Query: 4 LFGTFGVRGIANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDALIS 63 LFGT G+R + +E + E ALK+G + G +R VV+ D+R S +K L Sbjct: 3 LFGTSGIRRLVDERLM-EIALKVGFSVGKRYRR-------VVLAGDSRTSTPAIKRILSG 54 Query: 64 GLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKE 123 L+S G DV+D+G+ PTP + + F D G ++TASHN EYNGIK L P+G Sbjct: 55 ALVSAGADVVDIGLVPTPTLAFMVRDF--DAGLMVTASHNTAEYNGIKFLNPDGSAFSYL 112 Query: 124 REAIVEELFFSEDFHRAKWNEIGELRK-EDIIKPYIEAIKNRVDVEAIKKRRPFVVVDTS 182 ++ + + S H KW+ G++ ++ ++E I + K R VVVD Sbjct: 113 QQQEITKDVESSRAHPMKWDSFGQINAFPSTVEKHMEHILGYLP----DKCRLKVVVDCG 168 Query: 183 NGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADFGVAQ 242 GA S+ P+LL+ +G +V+S+N G FP PEP ENL G ++ VK AD G+A Sbjct: 169 GGAASVITPWLLQRMGSRVISLNDTTHGFFP-HPPEPLAENLSGLIQTVKESDADLGIAH 227 Query: 243 DGDADRAVFIDENGRFIQGDKTFALVADAVLRENGGGLLVTTIATSNLLDDIAKRNGAKV 302 DGDADR V +D++G FI GDK L A A + +VTT+ S +D++ G KV Sbjct: 228 DGDADRMVAVDKHGNFISGDKMLVLFARAARADK----VVTTLDASMAVDEM----GFKV 279 Query: 303 MRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAKSGKKFSE 362 +RT VGD V+ L+ G GGE G +FP+ L DG A+++ + S + SE Sbjct: 280 IRTAVGDNYVSEE-LKRQGNFGGEPCGAWVFPESSLCPDGIYAAARLLNLV--SHQPLSE 336 Query: 363 LIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFDDGWVLVRASG 422 LI ++P+Y + G A+V + + + DG K+ DGW+L+R SG Sbjct: 337 LISDIPEYSMKRGSVEGSGLNLALVEESLQCLNPLSSSL--LDGIKLNLKDGWLLIRPSG 394 Query: 423 TEPIIRIFSEAKSEEKAREYLELGIKLLEEAL 454 TEP IR+ +EA++ E + G+K L+ L Sbjct: 395 TEPKIRLTAEARTPEYCETIYQTGLKCLKSCL 426 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: 490 Number of extensions: 34 Number of successful extensions: 8 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: 430 Length adjustment: 32 Effective length of query: 424 Effective length of database: 398 Effective search space: 168752 Effective search space used: 168752 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