Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate GFF641 PGA1_c06550 phosphoglucosamine mutase GlmM
Query= SwissProt::Q68BJ6 (456 letters) >FitnessBrowser__Phaeo:GFF641 Length = 448 Score = 209 bits (533), Expect = 1e-58 Identities = 153/474 (32%), Positives = 237/474 (50%), Gaps = 48/474 (10%) Query: 1 MGKLFGTFGVRGIAN-EEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKD 59 M K FGT GVRG AN +T + AL+IG A G +R+ VV+G+DTR+SG M + Sbjct: 1 MRKFFGTDGVRGTANIHPMTADMALRIGAAVGRYFRRDASGVHRVVIGKDTRLSGYMFES 60 Query: 60 ALISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMG 119 AL +GL STG +V+ +G PTPA+ T AD G +I+ASHNP NGIK P+G Sbjct: 61 ALTAGLTSTGMNVLLLGPVPTPAVGLMTRSMRADLGVMISASHNPAADNGIKFFGPDGFK 120 Query: 120 L----KKEREAIVE---ELFFSEDFHRAKWNEIGELRKEDIIKPYIEAIKNRVDVEAIKK 172 L + E EA++E E +++ RAK + R + +K ++ + ++ +K Sbjct: 121 LSDTVEMELEALIEAGVEPAQAQNIGRAKRIDDARFRYGERVK---SSLPRDIRLDGLK- 176 Query: 173 RRPFVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVK 232 VV+D +NGA P +L ELG +V+ V PDG N + + E V Sbjct: 177 ----VVIDCANGAAHRAAPEILWELGAEVIPVGVSPDG--TNINRDCGSTHPGTAAETVV 230 Query: 233 ALGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVA-----DAVLRENGGGLLVTTIAT 287 A GA G+ DGDADR + ID+ G+ GD+ AL+A D VL G LV+T+ + Sbjct: 231 AHGAHVGICLDGDADRVIIIDDTGKVADGDQLMALLATRWAEDGVL---AGNALVSTVMS 287 Query: 288 SNLLDDIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTA 347 + L+ G + RT VGD V + E +GGE++G ++ D+ DG M Sbjct: 288 NLGLERHLAARGIALERTAVGDRYVVERMREGGFNLGGEQSGHIVMTDYATTGDGLMAGL 347 Query: 348 KIVEIFAKSGKKFSEL------IDELPKYYQFKT-KRHVEGDRKAIVAKVAELAEKKGYK 400 + ++ K S+L + +L K +F + +E D+ +VAE Sbjct: 348 HFLAEMVRADKPASQLAQQFAPVPQLLKNVRFAAGQTPLESDQVQTAIRVAE-------- 399 Query: 401 IDTTDGTKIIFDDGWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEAL 454 + + G +L+R SGTEP++R+ +E + + ++ + +E A+ Sbjct: 400 -------ETLAGQGRLLIRKSGTEPLVRVMAECEDAKVLTAAVDSVVAAVEAAV 446 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: 481 Number of extensions: 29 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: 448 Length adjustment: 33 Effective length of query: 423 Effective length of database: 415 Effective search space: 175545 Effective search space used: 175545 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 17 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