Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate Ga0059261_1954 Ga0059261_1954 phosphoglucosamine mutase (EC 5.4.2.10)
Query= SwissProt::Q68BJ6 (456 letters) >FitnessBrowser__Korea:Ga0059261_1954 Length = 461 Score = 224 bits (572), Expect = 3e-63 Identities = 159/443 (35%), Positives = 231/443 (52%), Gaps = 32/443 (7%) Query: 3 KLFGTFGVRGIAN-EEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61 K FGT G+RG N +T A+++GMA G +R G + VV+G+DTR+SG M+++AL Sbjct: 19 KYFGTDGIRGKTNVTPMTAAMAMQVGMAAGAHFRR-GDHKHRVVIGKDTRLSGYMIENAL 77 Query: 62 ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 ++G S G DV+ VG PTPA+ T+ AD G +I+ASHNP NGIKL P+G L Sbjct: 78 VAGFTSVGMDVVLVGPMPTPAVAMLTHSMRADMGVMISASHNPYADNGIKLFGPDGYKLS 137 Query: 122 KEREAIVEELFFSEDFHRAKWNEIGELRK-EDIIKPYIEAIKNRVDVEAIKKRRPFVVVD 180 E +E L E A +IG ++ ED YI K+ E ++ VVVD Sbjct: 138 DADELAIEALIDGE-IPLAPAADIGRAKRIEDAKGRYIHFAKSTFP-EDLRLDGLKVVVD 195 Query: 181 TSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADFGV 240 +NGA P L ELG +VV++ PDG N + E V A GA G+ Sbjct: 196 CANGAAYQVAPSALWELGAEVVAIGVTPDG--KNINDQVGSTAPLTLCETVVASGAHIGI 253 Query: 241 AQDGDADRAVFIDENGRFIQGDKTFALVADAVLRE---NGGGLLVTTIATSNLLDDIAKR 297 A DGDADR + +DE G + GD+ A +A R+ +GGGL+ T ++ L +A + Sbjct: 254 ALDGDADRLIVVDEQGEVVDGDQLMATIASGWARQGRLSGGGLVATVMSNLGLERHLAAQ 313 Query: 298 NGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAKSG 357 G ++RTKVGD V + + +GGE++G +I D+ DG + +++ ++G Sbjct: 314 -GLGLVRTKVGDRYVLEKMRASGYNVGGEQSGHIILSDYATTGDGLVAALQVLAELVRAG 372 Query: 358 KKFSELI---DELP---KYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIF 411 SE++ D LP K +F + +E + V AE DGT Sbjct: 373 APASEVLHRFDPLPQLLKNVRFSGGKPLENETVKSVIAAAE---------TELDGT---- 419 Query: 412 DDGWVLVRASGTEPIIRIFSEAK 434 G VL+RASGTEP+IR+ +E + Sbjct: 420 --GRVLIRASGTEPVIRVMAEGE 440 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: 548 Number of extensions: 35 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: 461 Length adjustment: 33 Effective length of query: 423 Effective length of database: 428 Effective search space: 181044 Effective search space used: 181044 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