Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_084055894.1 B9A12_RS02180 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_900176285.1:WP_084055894.1 Length = 464 Score = 236 bits (601), Expect = 2e-66 Identities = 159/448 (35%), Positives = 247/448 (55%), Gaps = 29/448 (6%) Query: 1 MGKLFGTFGVRGIANE-EITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKD 59 MG LFGT G+RGIANE +T + ALK+GM L R +RP +V+G+DTR+SG M++ Sbjct: 1 MGDLFGTDGIRGIANEYPMTTDIALKVGMGAAHLF-RNRHQRPKIVIGKDTRLSGYMIET 59 Query: 60 ALISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMG 119 A+ +G+ + G DV+ VG PTP I + T AD G VI+ASHNP EYNGIK+ G Sbjct: 60 AITAGICALGVDVLLVGPLPTPGIAFITTSMRADAGIVISASHNPYEYNGIKIFAGTGFK 119 Query: 120 LKKEREAIVEELFFSEDFHRAKWNEIGEL----RKEDIIKPYIEAIKN----RVDVEAIK 171 L E E +E L + + R E+ E+ R +D YI +KN + +E ++ Sbjct: 120 LPDEVEGEIERLILTGEIDRIPRPEVSEIGRAKRIDDAYGRYIVYLKNTFPRNLTLEGLR 179 Query: 172 KRRPFVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIV 231 +V+D ++GA P + ELG KV+ V P+G N E + + +V Sbjct: 180 -----IVLDCAHGAAYKVAPAVFEELGAKVIVVGDRPNG--KNINWECGSLHPESMARLV 232 Query: 232 KALGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENGGGLLVTTIAT--SN 289 + A G+A DGDADR + DE G + GD+ A+ A L+E G T +AT SN Sbjct: 233 REHQAHVGLAFDGDADRVILADEKGDILDGDQLMAICAKH-LQELGRLKRNTVVATVMSN 291 Query: 290 LLDDIAKRN-GAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAK 348 + ++A R+ G +++RT VGD V +++++ +GGE++G +IF D DG ++ + Sbjct: 292 MGLEVALRSMGIRLVRTAVGDRYVVEKMIQDDYCLGGEQSGHIIFLDHSTTGDGILSALQ 351 Query: 349 IVEIFAKSGKKFSELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTK 408 ++ + ++ + SEL + ++ Q T ++V K + +V E+ KI+ T G+ Sbjct: 352 VLAVMLEAQRPLSELKTVMERFPQ--TLKNVSVAEKGKIEEVPEIMACAS-KIEETLGS- 407 Query: 409 IIFDDGWVLVRASGTEPIIRIFSEAKSE 436 DG +L+R SGTEP+IR+ E + E Sbjct: 408 ----DGRLLIRPSGTEPVIRVMIEGRDE 431 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: 557 Number of extensions: 27 Number of successful extensions: 7 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: 464 Length adjustment: 33 Effective length of query: 423 Effective length of database: 431 Effective search space: 182313 Effective search space used: 182313 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