Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate 8499281 DvMF_0059 phosphoglucosamine mutase (RefSeq)
Query= SwissProt::Q68BJ6 (456 letters) >FitnessBrowser__Miya:8499281 Length = 450 Score = 219 bits (558), Expect = 1e-61 Identities = 163/467 (34%), Positives = 237/467 (50%), Gaps = 29/467 (6%) Query: 1 MGK-LFGTFGVRGIAN-EEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLK 58 MGK LFGT G+RG N +T + AL++G+A GT R G R VV+G+DTR+SG + + Sbjct: 1 MGKRLFGTDGLRGQVNIYPMTADVALRLGLAAGTHF-RNGNRRHRVVIGKDTRLSGYVFE 59 Query: 59 DALISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGM 118 AL +GL + G DV VG PTPAI + T + AD G VI+ASHNP NGIK + +G Sbjct: 60 SALTAGLCAAGMDVYLVGPLPTPAIAFLTRNMRADLGVVISASHNPFMDNGIKFFDKDGF 119 Query: 119 GLKKEREAIVEELFFSEDFHRAKWN-----EIGELRK-EDIIKPYIEAIKNRVDVEAIKK 172 L E E + ++ D+ +W+ +G K ED YI +KN + Sbjct: 120 KLPDEMENKITDMVLDPDW---QWDYPAPERVGRAAKIEDSPGRYIVYLKNSFPAH-LTL 175 Query: 173 RRPFVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVK 232 VV+D +NGA P L ELG +V+ + P+G N +L + K Sbjct: 176 DGMRVVLDCANGANYKVAPLALEELGAEVIKIGTEPNG----LNINHQCGSLYPGVAAGK 231 Query: 233 AL--GADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENG--GGLLVTTIATS 288 L AD G+A DGDADR + +DE G + GD+ AL AD +LR LV T+ ++ Sbjct: 232 VLETRADVGLALDGDADRLIVVDEKGTVLDGDQIMALCADDMLRRGALRNNTLVATVMSN 291 Query: 289 NLLDDIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAK 348 L+ K G K++RT VGD V A+ +GGE++G +IF D DG M + Sbjct: 292 MALEVYMKERGCKLLRTPVGDRYVVEAMRREGANLGGEQSGHLIFMDHGTTGDGLMAALQ 351 Query: 349 IVEIFAKSGKKFSELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTK 408 I+ I + + SEL +L + Q HVE RK + + + K++ G Sbjct: 352 ILRIMRERDRPLSELAGQLQLFPQELINVHVE--RKIPFEQCQPVLDGVA-KVEAELG-- 406 Query: 409 IIFDDGWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEALK 455 D G VL+R SGTE + R+ E + E+ + L + +++ L+ Sbjct: 407 ---DRGRVLLRYSGTEAVCRVMVEGEDPEQVKRLASLLAETVQKHLR 450 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: 27 Number of successful extensions: 5 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: 450 Length adjustment: 33 Effective length of query: 423 Effective length of database: 417 Effective search space: 176391 Effective search space used: 176391 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