Align Phosphomannomutase/phosphoglucomutase; PMM / PGM; EC 5.4.2.2; EC 5.4.2.8 (uncharacterized)
to candidate WP_009545950.1 CCE_RS03375 phosphoglucosamine mutase
Query= curated2:Q88C93 (463 letters) >NCBI__GCF_000017845.1:WP_009545950.1 Length = 485 Score = 145 bits (366), Expect = 3e-39 Identities = 134/453 (29%), Positives = 210/453 (46%), Gaps = 45/453 (9%) Query: 9 LPDS-IFRAYDIRGVVGKTLHAETA----YWIGRAIGAQSLAQGEPQVSVGRDGRLSGPM 63 LP+S +F IRG G+ L A A +W G+ + +++ G V +G+D R S M Sbjct: 31 LPNSPLFGTDGIRGKAGELLTAPFALQLGFWAGQVLKSKTTTPGP--VMIGQDSRNSSDM 88 Query: 64 LVEQLIKGLVDAGCNVSDVGLVPTPALYYAANVLAGKSGVMLTGSHNPSDYNGFKIV-IA 122 L + GL AG V +GL PTP + Y +G+M++ SHNP + NG K Sbjct: 89 LAMAMAAGLTSAGLEVWQLGLCPTPCVAYLTRHSEAIAGIMISASHNPPEDNGIKFFNTD 148 Query: 123 GDTLANEQIQALLTRLKTN-----DLTLAQGRVEKVEILDRYFKQIVGD----VKLAKKL 173 G L++ Q + L+ N D A G++ L + Q + D + + Sbjct: 149 GTKLSSSLGQEIEDGLRGNLLLSVDEIAAWGKILYEPTLVNTYCQFLQDSLPPSLSCQGM 208 Query: 174 KVVVDCGNGAAGVVAPQLIEALGCEVIPLFCEVDGNFPNHHPDPGKPENLEDLIAKVKET 233 K+V+D GA+ VAP + +ALG EVI L +G+ N + +L L A ++E Sbjct: 209 KIVLDLAWGASVNVAPAMFKALGAEVICLHETANGDRINVNCG---STHLHVLQAAIQEH 265 Query: 234 GADIGLAFDGDGDRVGVVTNTGSIVYPDRLLMLFAQDVLSRN--PGAEIIFDVKCTRRLT 291 AD+G AFDGD DRV V +TG +V D +L L+ + +L R P +I V Sbjct: 266 QADMGFAFDGDADRVMAVDSTGKVVDGDYILYLWGKSLLERGNLPNNLLIGTVMANLGFE 325 Query: 292 PLIEQHGGRALMWKTGHSLIKKKMKQTGSLLAGEMSGHIFIKERWYGFD-DGIYSAARLL 350 + GG+ + G ++ +M +TG++L GE SGHI YG DG+ +A L Sbjct: 326 RAWQGLGGQLVRTSVGDRYVQSQMWETGAMLGGEQSGHIICHH--YGVSGDGVQTALHLA 383 Query: 351 EILSKTEQS----AENLFAAFPNDISTPEINIDVTDEGK---FSIIDALQRDADWGEANL 403 ++ ++ S +N F +P + N+ + D K + LQ+ E + Sbjct: 384 ALVHESGVSLAELVKNSFDTYPQILR----NVRLEDREKLRYWQECQPLQQAIAQAEVGM 439 Query: 404 TTIDGVRVDYANGWGLVRASNTTPVLVLRFEAD 436 G LVRAS T P++ + E++ Sbjct: 440 G---------ETGRVLVRASGTEPLIRVMVESE 463 Lambda K H 0.319 0.138 0.406 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: 539 Number of extensions: 28 Number of successful extensions: 4 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: 463 Length of database: 485 Length adjustment: 33 Effective length of query: 430 Effective length of database: 452 Effective search space: 194360 Effective search space used: 194360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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