Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_011602471.1 FRAAL_RS05560 phosphomannomutase/phosphoglucomutase
Query= BRENDA::Q8PGN7 (450 letters) >NCBI__GCF_000058485.1:WP_011602471.1 Length = 452 Score = 313 bits (802), Expect = 7e-90 Identities = 184/445 (41%), Positives = 251/445 (56%), Gaps = 5/445 (1%) Query: 8 FKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAGLRASG 67 FKAYD+RG VP E + ++AR G A LD +V HD+R +S L A + G + G Sbjct: 8 FKAYDVRGVVPAEFDAEIARLTGAAFVRLLDAERIVTAHDMRESSIPLAAAFAEGAASQG 67 Query: 68 RDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTGLFAI 127 DV+ GL T+ +YF L G M TASHNP YNG+KL R A PI +TGL I Sbjct: 68 ADVVLAGLGSTDLLYFAAGSLDIPGA-MFTASHNPAKYNGIKLCRAGAAPIGQETGLAEI 126 Query: 128 RDTVAADTAAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAGLIVDL 187 R V A + S Y+ HL + VD S ++PL + V+AGNG GL V Sbjct: 127 RAMVEQGVPAGPGRVGTVTSSDLLADYVRHLHTLVDLSGIRPLTVAVDAGNGMGGLTVPA 186 Query: 188 LAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWDGDFDRCFF 247 LP V ++ E DG+FPN NP+ P N AV+ GAD G+A+DGD DRCF Sbjct: 187 TLAGLPLTVVPLYFELDGSFPNHEANPIEPANLRDLQAAVRAAGADIGLAFDGDADRCFV 246 Query: 248 FDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPVLCKSGHAF 307 D G + + L+A LA++PGG ++H+ ++ E V E GGIPV + GH+F Sbjct: 247 VDERGEIVSPSVITALVADRELAREPGGTIIHNVIVSKGVPELVTERGGIPVRTRVGHSF 306 Query: 308 IKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADLVEARMQKF 367 IK +M A++GGE S H YFR+F ADSGM+ L + + R L+DL+ A ++ Sbjct: 307 IKAEMARTGAIFGGEHSGHFYFRDFWRADSGMLAALHVLAALGGQPRPLSDLL-AGYGRY 365 Query: 368 PCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADF--GQWRFNLRSSNTEPLLR 425 SGEIN +VAD A++ V + YA + ++D+ DG++ F G W FNLR SNTEPLLR Sbjct: 366 SASGEINSEVADVVAAMQAVEKAYAPHAADVDHLDGLTISFADGSW-FNLRPSNTEPLLR 424 Query: 426 LNVETRGDAALLETRTQEISNLLRG 450 LNVE +AA+ R + ++ + G Sbjct: 425 LNVEGPDEAAMRRLRDEVLARVRGG 449 Lambda K H 0.319 0.136 0.404 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: 534 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: 450 Length of database: 452 Length adjustment: 33 Effective length of query: 417 Effective length of database: 419 Effective search space: 174723 Effective search space used: 174723 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