Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate H281DRAFT_04410 H281DRAFT_04410 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >FitnessBrowser__Burk376:H281DRAFT_04410 Length = 452 Score = 194 bits (492), Expect = 6e-54 Identities = 147/452 (32%), Positives = 220/452 (48%), Gaps = 24/452 (5%) Query: 3 KLFGTFGVRGIANE-EITPEFALKIGMAFGTLLKREGR-----ERPLVVVGRDTRVSGEM 56 + FGT G+RG E ITPEF L++G A G +L R RP V++G+DTRVSG M Sbjct: 4 RYFGTDGIRGKVGEGPITPEFVLRLGYAAGKVLVGADRWARTGTRPTVLIGKDTRVSGYM 63 Query: 57 LKDALISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPN 116 L+ AL +G + G DV+ G PTP I + T G VI+ASHNP NGIK + Sbjct: 64 LEAALEAGFSAAGVDVMLAGPMPTPGIAYLTRALRLAAGVVISASHNPYYDNGIKFFSAD 123 Query: 117 GMGLKKEREAIVEELFFSEDFHRAKWNEIGELRK-EDIIKPYIEAIKNRVDVEAIKKRRP 175 G L E E+ +EE A ++G+ R+ +D YIE K+ A R Sbjct: 124 GNKLPDEVESQIEE-HLELPLACASSEQLGKARRLDDAAGRYIEFCKSTFPA-AFDLRGL 181 Query: 176 FVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALG 235 +VVD ++GA P++ ELG +++ + P+G N + V+A Sbjct: 182 KLVVDCAHGAAYDVAPHVFHELGAEIIPIGVAPNGF--NINDGVGATAPDALVRAVRANH 239 Query: 236 ADFGVAQDGDADRAVFIDENGRFIQGDK-TFALVADAVLRENGGGLLVTTIATSNLLDDI 294 AD G+A DGDADR +D GR GD+ + LV D + + V T+ T+ ++ Sbjct: 240 ADLGIALDGDADRLQVVDAAGRLYNGDELLYVLVKDRIATDGKVEGAVGTLMTNMAVEVA 299 Query: 295 AKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFA 354 + G K +R VGD V L E+ +G E +G ++ D DG ++ ++ Sbjct: 300 LQAAGVKFVRAAVGDRYVLEQLREHGWQLGAEGSGHILSLDRHSTGDGIVSALLVLAAMK 359 Query: 355 KSGKKFSELIDELPKYYQ--FKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFD 412 +S K +EL+D + + Q + + D K A +A + D +G Sbjct: 360 RSDKTLAELLDGVTLFPQKLINVRMKPDADWKGSDAIRRAIASAE----DALNGR----- 410 Query: 413 DGWVLVRASGTEPIIRIFSEAKSEEKAREYLE 444 G VL+RASGTEP++R+ EA+ + A + E Sbjct: 411 -GRVLIRASGTEPVLRVMVEAEHADDALRHAE 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: 545 Number of extensions: 31 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: 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