Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate AZOBR_RS07040 AZOBR_RS07040 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >FitnessBrowser__azobra:AZOBR_RS07040 Length = 455 Score = 222 bits (565), Expect = 2e-62 Identities = 154/447 (34%), Positives = 229/447 (51%), Gaps = 34/447 (7%) Query: 4 LFGTFGVRGIAN-EEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDALI 62 LFGT G+RG AN + +T E AL++ MA L R G R VV+G+DTR+SG +L+ AL Sbjct: 5 LFGTDGIRGTANIDPMTAETALRVAMA-SALQFRRGDHRHRVVIGKDTRLSGYLLEPALT 63 Query: 63 SGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKK 122 +G +S G DV+ +G PTPA+ T AD G +I+ASHNP + NGIKL P+G L Sbjct: 64 AGFISMGMDVVLLGPLPTPAVAMLTRSLRADLGVMISASHNPYQDNGIKLFGPDGYKLSD 123 Query: 123 EREAIVE---------ELFFSEDFHRAKWNEIGELRKEDIIKPYIEAIKNRVDVEAIKKR 173 E +E +L S D RA R ED YIE +KN ++ Sbjct: 124 AVELAIETRMGQPFAPDLAGSADLGRAS-------RLEDSTGRYIEYVKNTFP-RGLRLD 175 Query: 174 RPFVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKA 233 +VVD +NGA P +L ELG V+ V +PDG N + + E V A Sbjct: 176 GLRIVVDCANGAAYRVAPKVLYELGADVIPVGVNPDG--LNINKDCGATATRTLQEQVVA 233 Query: 234 LGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVAD--AVLRENGGGLLVTTIATSNLL 291 GA G+A DGDADR + +DE GR + GD+ AL+A A + GG +V T+ ++ + Sbjct: 234 HGAHLGIALDGDADRLIMVDEAGRVVDGDQVMALIASSWAQAQTLKGGGVVATVMSNLGM 293 Query: 292 DDIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVE 351 + + G ++RT VGD V + E+ +GGE++G V+ D+ DG + +++ Sbjct: 294 ERHLQGLGIALVRTPVGDRYVVEHMREHGYNVGGEQSGHVVLSDYSTTGDGLIAALQVLA 353 Query: 352 IFAKSGKKFSELIDEL--PKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKI 409 + +SG + + + ++ P + R G + +A V + DG Sbjct: 354 VLIQSGGRAASEVCQVFAPVPQKLTNVRFAAGSKPLEIASV---------QAAIRDGEAR 404 Query: 410 IFDDGWVLVRASGTEPIIRIFSEAKSE 436 + G +L+R SGTEP+IR+ +E E Sbjct: 405 LNGSGRILIRKSGTEPVIRVMAEGDDE 431 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: 507 Number of extensions: 28 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: 455 Length adjustment: 33 Effective length of query: 423 Effective length of database: 422 Effective search space: 178506 Effective search space used: 178506 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