Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate 17247 b3176 phosphoglucosamine mutase (NCBI)
Query= SwissProt::Q68BJ6 (456 letters) >FitnessBrowser__Keio:17247 Length = 445 Score = 203 bits (517), Expect = 8e-57 Identities = 145/448 (32%), Positives = 220/448 (49%), Gaps = 26/448 (5%) Query: 3 KLFGTFGVRG-IANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61 K FGT G+RG + + ITP+F LK+G A G +L R G + +++G+DTR+SG ML+ AL Sbjct: 5 KYFGTDGIRGRVGDAPITPDFVLKLGWAAGKVLARHGSRK--IIIGKDTRISGYMLESAL 62 Query: 62 ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +GL + G + G PTPA+ + T F A+ G VI+ASHNP NGIK +G L Sbjct: 63 EAGLAAAGLSALFTGPMPTPAVAYLTRTFRAEAGIVISASHNPFYDNGIKFFSIDGTKLP 122 Query: 122 KEREAIVEELFFSEDFHRAKWNEIGEL-RKEDIIKPYIEAIK----NRVDVEAIKKRRPF 176 E + E ++ E+G+ R D YIE K N + + +K Sbjct: 123 DAVEEAI-EAEMEKEISCVDSAELGKASRIVDAAGRYIEFCKATFPNELSLSELK----- 176 Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGA 236 +VVD +NGA P +LRELG V+++ P+G N E +++ V A A Sbjct: 177 IVVDCANGATYHIAPNVLRELGANVIAIGCEPNG--VNINAEVGATDVRALQARVLAEKA 234 Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENG-GGLLVTTIATSNLLDDIA 295 D G+A DGD DR + +D G + GD+ ++A LR+ G V T+ ++ L+ Sbjct: 235 DLGIAFDGDGDRVIMVDHEGNKVDGDQIMYIIAREGLRQGQLRGGAVGTLMSNMGLELAL 294 Query: 296 KRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAK 355 K+ G R KVGD V + E IG E +G VI D DG + +++ A+ Sbjct: 295 KQLGIPFARAKVGDRYVLEKMQEKGWRIGAENSGHVILLDKTTTGDGIVAGLQVLAAMAR 354 Query: 356 SGKKFSELIDELPKYYQFKTK-RHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFDDG 414 + +L + + Q R+ G + E + K T + + + G Sbjct: 355 NHMSLHDLCSGMKMFPQILVNVRYTAGS--------GDPLEHESVKAVTAEVEAALGNRG 406 Query: 415 WVLVRASGTEPIIRIFSEAKSEEKAREY 442 VL+R SGTEP+IR+ E + E + E+ Sbjct: 407 RVLLRKSGTEPLIRVMVEGEDEAQVTEF 434 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: 526 Number of extensions: 39 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: 445 Length adjustment: 33 Effective length of query: 423 Effective length of database: 412 Effective search space: 174276 Effective search space used: 174276 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