Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate Synpcc7942_2132 Synpcc7942_2132 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >FitnessBrowser__SynE:Synpcc7942_2132 Length = 472 Score = 211 bits (536), Expect = 5e-59 Identities = 146/461 (31%), Positives = 233/461 (50%), Gaps = 25/461 (5%) Query: 4 LFGTFGVRGIANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDALIS 63 LFGT G+RG E +T A ++G G +L++ G +R VVVG+D+R S ML AL S Sbjct: 26 LFGTDGIRGRVGEHLTAPLAQQVGFWTGQVLRQAGGDRGPVVVGQDSRNSSNMLAMALSS 85 Query: 64 GLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKE 123 GL + G +V+ +G+ PTP + + T+H A GG +I+ASHNPP NGIK+ +G L ++ Sbjct: 86 GLAAAGVEVLHLGLCPTPGVAYLTHHSEAIGGVMISASHNPPGDNGIKVFGADGSKLDRQ 145 Query: 124 REAIVEELFFSE--DFHRAKWNEIGELRKEDIIKPYIEAIK----NRVDVEAIKKRRPFV 177 +A +E + W + + + Y AI R +++ +K + Sbjct: 146 LQAAIEAGLRGQQTSLPATTWGQ--HYYQPQLADHYQAAIAQSLGQRANLQGLK-----I 198 Query: 178 VVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGAD 237 V+D + GA +L P L RELG +V++++ PDG+ N +L V GAD Sbjct: 199 VLDLAWGAAALLAPRLFRELGAEVIALHDLPDGN--QINVNCGSTHLARLQAAVLEQGAD 256 Query: 238 FGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLREN--GGGLLVTTIATSNLLDDIA 295 G A DGDADR + +D GR + GD L + ++ G +VTT+ + + Sbjct: 257 MGFAFDGDADRVLAVDGRGRSVDGDHILFLWGRELEQQQQLPGQAIVTTVMANLGFERAW 316 Query: 296 KRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAK 355 + G + +RT VGD V + +GGE++G ++ + L DG +T A + + Sbjct: 317 QAVGGEFVRTAVGDQYVQAEMQARGAMLGGEQSGHILCRHYALTGDGTLTAAHVAALVQA 376 Query: 356 SGKKFSELIDELPKYYQ--FKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFDD 413 SG ++L+D+ + Y + R + DR+ A L + TD + D Sbjct: 377 SGVSLADLVDQSFRPYPQLLRNVRVEDRDRRCNWQNCAALTQ--AIAAAETD----MGDR 430 Query: 414 GWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEAL 454 G VLVRASGTEP++RI EA+ ++ + +++ E L Sbjct: 431 GRVLVRASGTEPLLRIMVEAEEAQQVEHWTTHLVQVAESHL 471 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: 466 Number of extensions: 24 Number of successful extensions: 5 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: 472 Length adjustment: 33 Effective length of query: 423 Effective length of database: 439 Effective search space: 185697 Effective search space used: 185697 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