Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate 3609008 Dshi_2397 phosphoglucosamine mutase (RefSeq)
Query= SwissProt::Q68BJ6 (456 letters) >FitnessBrowser__Dino:3609008 Length = 447 Score = 214 bits (544), Expect = 6e-60 Identities = 156/454 (34%), Positives = 227/454 (50%), Gaps = 48/454 (10%) Query: 3 KLFGTFGVRGIANEE-ITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61 KLFGT GVRG AN +T E AL++G A G +R+ VV+G+DTR+SG M + AL Sbjct: 4 KLFGTDGVRGTANTAPMTAEMALRLGAAAGRYFRRDQSAAHRVVIGKDTRLSGYMFETAL 63 Query: 62 ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +G STG +V+ +G PTPA+ T AD G +I+ASHNP + NGIK P+G L Sbjct: 64 TAGFTSTGMNVLLLGPIPTPAVALLTQSMRADVGVMISASHNPADDNGIKFFGPDGYKLS 123 Query: 122 KEREAIVEELFFSEDFHRAKWNEIGELRK-EDIIKPYIEAIKN----RVDVEAIKKRRPF 176 E +EE+ + D A+ IG ++ +D + YIE K + ++ +K Sbjct: 124 DAAEEEIEEI-LAGDIRPAQAPNIGRAKRIDDGLGRYIERAKRTFPAHLRLDGLK----- 177 Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGA 236 VVVD +NGA P +L ELG V+ V P+G N + + E V + GA Sbjct: 178 VVVDCANGAAYKVAPAVLWELGADVIPVGVSPNGR--NINRDCGSTAPQTAAEAVVSHGA 235 Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFAL-----VADAVLRENGGGLLVTTIATSNLL 291 D G+ DGDADR + +DENG GD+ AL A +LR+N LV T+ ++ L Sbjct: 236 DVGICLDGDADRVMILDENGELADGDQLMALFATRWAAQGLLRDN---TLVATVMSNLGL 292 Query: 292 DDIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVE 351 + G K++RT VGD V A+ + +GGE++G ++ D DG M + + Sbjct: 293 EYYLNDLGLKLVRTAVGDRYVVEAMRKGGWNLGGEQSGHIVMLDHGTTGDGLMAGLQFLA 352 Query: 352 IFAKSGKKFSELIDELPKYYQ-FKTKRHVEGD--------RKAIVAKVAELAEKKGYKID 402 + G+ SEL Q + R G + AI A A+L+ K Sbjct: 353 EMVQQGRSASELKHSFTTVPQRLENVRFGAGQDPLAAASVKSAIAAAEAQLSGK------ 406 Query: 403 TTDGTKIIFDDGWVLVRASGTEPIIRIFSEAKSE 436 G +L+R SGTEP++R+ +E + E Sbjct: 407 -----------GRLLIRKSGTEPLVRVMAECEDE 429 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: 527 Number of extensions: 29 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: 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 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