Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_090444689.1 BLS63_RS12570 phosphomannomutase CpsG
Query= BRENDA::Q8PGN7 (450 letters) >NCBI__GCF_900100495.1:WP_090444689.1 Length = 454 Score = 541 bits (1393), Expect = e-158 Identities = 269/449 (59%), Positives = 331/449 (73%), Gaps = 5/449 (1%) Query: 5 LPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAGLR 64 L FKAYDIRG++ ELNED+A RIG A A LD VV+G D+RL+S L++AL+ GL Sbjct: 4 LTCFKAYDIRGQLGAELNEDIAYRIGRAYAQFLDAKKVVIGGDMRLSSEPLKQALANGLM 63 Query: 65 ASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTGL 124 +G DVID+G+ GTEEVYF +L GGV VTASHNP+D+NGMKLVR A+PIS DTGL Sbjct: 64 DAGCDVIDLGMTGTEEVYFAAFHLDVDGGVEVTASHNPIDFNGMKLVRRGAQPISGDTGL 123 Query: 125 FAIRDTVAADTAAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAGLI 184 I+ + +T AY++HLL Y+ LKPLKLVVNAGNG AG + Sbjct: 124 KDIQGLAQTNDFPAVAQRGQLTRQTCLDAYIDHLLGYLKSDQLKPLKLVVNAGNGAAGHV 183 Query: 185 VDLL-----APHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWD 239 +D L A EF++V H+PDG+FPNGIPNPLLPENR ATA AVK + AD GIAWD Sbjct: 184 IDALEQRFQAMGAKVEFIKVHHQPDGSFPNGIPNPLLPENRAATADAVKAHNADMGIAWD 243 Query: 240 GDFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPV 299 GDFDRCF FD GRFIEGYY+VGLLA+A L K PG K++HDPRLTWNT++ VE AGG + Sbjct: 244 GDFDRCFLFDENGRFIEGYYIVGLLAEAFLNKAPGAKIIHDPRLTWNTIDIVERAGGQAI 303 Query: 300 LCKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADL 359 K+GHAFIKE+MR ENA+YGGEMSAHHYFR+FAY DSGMIPWLL+AEL+S G+SLA L Sbjct: 304 QSKTGHAFIKERMRKENAIYGGEMSAHHYFRDFAYCDSGMIPWLLVAELISTRGQSLAQL 363 Query: 360 VEARMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLRSSN 419 ++ RM +PCSGEIN++V DAKA + V++HYA P+ D TDGIS +F +WR +LRSSN Sbjct: 364 LDERMAAYPCSGEINYRVNDAKAVIQAVLDHYAEQEPKRDTTDGISLEFAEWRMSLRSSN 423 Query: 420 TEPLLRLNVETRGDAALLETRTQEISNLL 448 TEPLLRLN+E+R + AL++ + I L+ Sbjct: 424 TEPLLRLNIESRANPALVQQQRAVIEGLI 452 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: 640 Number of extensions: 20 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: 454 Length adjustment: 33 Effective length of query: 417 Effective length of database: 421 Effective search space: 175557 Effective search space used: 175557 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