Align Phosphoglucomutase; PGM; EC 5.4.2.2; Glucose phosphomutase (uncharacterized)
to candidate WP_011989366.1 CKL_RS03915 phosphoglucomutase
Query= curated2:P40390 (460 letters) >NCBI__GCF_000016505.1:WP_011989366.1 Length = 506 Score = 162 bits (411), Expect = 2e-44 Identities = 146/484 (30%), Positives = 225/484 (46%), Gaps = 50/484 (10%) Query: 13 DIRGIVGKT------LTDDAAYFIGRAIAA-----KAAEKGIARIALGRDGRLSGPELME 61 DIRGI K LT + I R K E +IA+G D RLSG E Sbjct: 13 DIRGIATKNPEKEVNLTVERVKLITRGFIKWIKNKKNLENNKIKIAIGIDSRLSGLEFKR 72 Query: 62 HIQRGLTDSGISVLNVGMVTTPMLYFAAVN---ECGGSGVMITGSHNPPDYNGFKMMLGG 118 I L + G V + G+ TTP ++ V C G+ +MITGSH P YNG K Sbjct: 73 CICEELLNLGCYVYDCGLCTTPAMFMTTVTGSYRCHGA-IMITGSHLPYYYNGLKFFTES 131 Query: 119 DTLAGEAIQELL--AIVEKDGFVAADKQGSVTEKDISGAYHDHIV--------GHVKLKR 168 E I+ +L A+ + D V + +G++ + D Y +V V R Sbjct: 132 GGCEKEDIKYILNRALNKYDNSVHS--RGNIFKIDFIDEYSGILVKKIREGINSKVNYNR 189 Query: 169 PIN---IAIDAGNGVGGAFAGKLYKGLGNEVT-ELFCEVDGNFPNHHPDPSKPENLQDLI 224 P++ I +DAGNG GG FA K+ + LG ++ F DG FPNH P+P E + + Sbjct: 190 PLSELKIIVDAGNGAGGFFANKVLEPLGAKIEGSQFIIPDGKFPNHLPNPEDKEAMHSIK 249 Query: 225 AALKNGDAEIGLAFDGDADRLGVVTKDGNIIYPDRQLMLFAQDVLNRNPGAKVIFDVKST 284 A+ A++G+ FD D DR +V G I + + L + VL PG ++ D ++ Sbjct: 250 EAVIKNKADLGIIFDADVDRAAIVDCSGREINRNALIALISTIVLEEYPGTTIVTDSVTS 309 Query: 285 RLLAPWIKEHGGEAIMEKTGH-----SFIKSAMKKTGALVAGEMSGHVFFKERWFGFDDG 339 L+ +I+E GG+ K G+ I+ + G +A E SGH FKE +F DDG Sbjct: 310 DGLSEFIQELGGKHHRFKRGYRNVINEGIRLNNQNEGCYLAIETSGHAAFKENYF-LDDG 368 Query: 340 LYAGARLLEILSASDNPSEVLDNLPQSISTPELNIS-----LPEG--SNGHQVIEELAAK 392 Y A++L ++ + + +++L Q++ P ++ L E G +++EEL Sbjct: 369 AYLIAKVLIKMARLKSEGKSIEDLIQNMKMPVESLEFRFDILDENFKEYGDKILEELKLY 428 Query: 393 AE-FEGATEII-TIDGLRVEF----PDGFGLMRASNTTPILVLRFEADTQAAIERIQNRF 446 E EG +E+ +G+R+ G+ L+R S P+L L E D I ++ Sbjct: 429 IEKVEGWSEVSPNYEGIRINCCSFKGSGWLLLRLSLHEPVLCLNIECDLSGYSNIIIDKL 488 Query: 447 KAVI 450 K+ + Sbjct: 489 KSFL 492 Lambda K H 0.318 0.138 0.402 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: 556 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: 460 Length of database: 506 Length adjustment: 34 Effective length of query: 426 Effective length of database: 472 Effective search space: 201072 Effective search space used: 201072 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 (21.7 bits) S2: 52 (24.6 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