Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_038018174.1 HA49_RS13070 phosphomannomutase/phosphoglucomutase
Query= BRENDA::Q8PGN7 (450 letters) >NCBI__GCF_000757425.2:WP_038018174.1 Length = 459 Score = 476 bits (1225), Expect = e-139 Identities = 237/458 (51%), Positives = 322/458 (70%), Gaps = 10/458 (2%) Query: 1 MPMTLPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALS 60 M L FKAYDIRG++ EL+ D+A RIG A L+ VV+G DVRL S L+ +L+ Sbjct: 1 MSTKLSCFKAYDIRGKLDVELDCDVAYRIGRAYGQFLNPKKVVIGGDVRLTSENLKLSLA 60 Query: 61 AGLRASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISS 120 GL+ SG DVID+G GTEEVYF T +L A GG+ VTASHNP+DYNGMKLV+E ++PIS Sbjct: 61 RGLQDSGVDVIDLGTTGTEEVYFATSHLNADGGIEVTASHNPLDYNGMKLVKEFSKPISG 120 Query: 121 DTGLFAIRDTVAADTAAPGEPTASEQSRTDKTA---YLEHLLSYVDRSTL-KPLKLVVNA 176 DTGL I+ +A + + P + + + Y+ +L+++D + +P+KLVVN+ Sbjct: 121 DTGLRDIQ-RLAEENSFPDVVNSQRGTYNQLSTLVQYVSMILNFIDLKNISRPIKLVVNS 179 Query: 177 GNGGAGLIVD-----LLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNG 231 GNG AG ++D + +P F+++ H PDGNFPNGIPNPLLP+ R T AV + Sbjct: 180 GNGAAGHVIDEIEKIFIEKKVPISFIKIHHNPDGNFPNGIPNPLLPDCRQDTTDAVIAHN 239 Query: 232 ADFGIAWDGDFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQV 291 AD GIA+DGDFDRCF FD G FIEGYY+VGLLA++ L K K++HDPRL+WNT++ V Sbjct: 240 ADMGIAFDGDFDRCFLFDECGCFIEGYYIVGLLAESFLEKNVNEKIIHDPRLSWNTIDIV 299 Query: 292 EEAGGIPVLCKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQ 351 GGIPV K+GHAFIKEKMRSE+AVYGGEMSAHHYFR+F Y DSGMIPWLL+ EL+ Sbjct: 300 TTCGGIPVESKTGHAFIKEKMRSEDAVYGGEMSAHHYFRDFFYCDSGMIPWLLVVELLCV 359 Query: 352 SGRSLADLVEARMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQW 411 +L+ LV R+ K+P SGEIN + + ++ + +Y ++ +D+ DG+S +F W Sbjct: 360 KNTTLSSLVNKRIDKYPASGEININLKNPSVAIDYIHSYYKGIAVNIDFLDGLSIEFENW 419 Query: 412 RFNLRSSNTEPLLRLNVETRGDAALLETRTQEISNLLR 449 RFNLRSSNTEP++RLNVE++G+ +L++ +TQE+ ++L+ Sbjct: 420 RFNLRSSNTEPVVRLNVESKGNKSLMQLKTQELLDILK 457 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: 575 Number of extensions: 22 Number of successful extensions: 3 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: 459 Length adjustment: 33 Effective length of query: 417 Effective length of database: 426 Effective search space: 177642 Effective search space used: 177642 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