Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate 6938122 Sama_2243 phosphoglucosamine mutase (RefSeq)
Query= SwissProt::Q68BJ6 (456 letters) >FitnessBrowser__SB2B:6938122 Length = 452 Score = 218 bits (555), Expect = 3e-61 Identities = 160/456 (35%), Positives = 233/456 (51%), Gaps = 31/456 (6%) Query: 3 KLFGTFGVRGIANE-EITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61 K FGT GVRG E ITP+FA+K+G A GT++ G + V++G+DTR+SG ML+ A+ Sbjct: 4 KYFGTDGVRGKVGEFPITPDFAMKLGWAAGTVMAASGTKE--VIIGKDTRLSGYMLESAM 61 Query: 62 ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +G + G +V G PTPAI + T+ F AD G VI+ASHNP NGIK G L Sbjct: 62 EAGFCAAGVNVALTGPLPTPAIAYLTSTFRADAGVVISASHNPYYDNGIKFFSNTGTKLT 121 Query: 122 KEREAIVEELFFSEDFHRAKW----NEIGELRK-EDIIKPYIEAIK----NRVDVEAIKK 172 E+E +E L S A +++G++R+ D YIE K N + + +K Sbjct: 122 DEQELEIERLLVSAIEGGAMTCVASDKLGKVRRINDAAGRYIEFCKGTFPNSLSLTGLK- 180 Query: 173 RRPFVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVK 232 +VVD+++GA + RELG +V+S+N PDG N ++ V Sbjct: 181 ----IVVDSAHGAAYHIAKNVYRELGAEVISINDKPDG--ININEHCGATHMDSLQTAVM 234 Query: 233 ALGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLR--ENGGGLLVTTIATSNL 290 AD G+A DGDADR + +D G+ I GD L+A + + E G++ T + SNL Sbjct: 235 IHEADLGIALDGDADRLMMVDSKGQVIDGDALLYLLAKSAQQRGEQVSGVIGTLM--SNL 292 Query: 291 LDDIAKRN-GAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKI 349 + A N G R KVGD V L E +GGE +G ++ DF D + + ++ Sbjct: 293 GFEQALANLGIPFKRAKVGDRYVVELLKETGWRLGGENSGHLLMLDFTTTGDAIVASLQV 352 Query: 350 VEIFAKSGKKFSELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKI 409 + +SG ++ I EL + Q + G+ A V + T + Sbjct: 353 LRALLESGAGLADAITELNMFPQVLINVRLNGN-----AAVGLSHPSVSDAVATAESA-- 405 Query: 410 IFDDGWVLVRASGTEPIIRIFSEAKSEEKAREYLEL 445 + +DG VL+R SGTEP+IR+ EAK KA +Y EL Sbjct: 406 LGNDGRVLLRKSGTEPLIRVMVEAKDAVKANQYAEL 441 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: 494 Number of extensions: 30 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: 452 Length adjustment: 33 Effective length of query: 423 Effective length of database: 419 Effective search space: 177237 Effective search space used: 177237 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