Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_057687434.1 ABB28_RS16370 phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >NCBI__GCF_001431535.1:WP_057687434.1 Length = 779 Score = 536 bits (1382), Expect = e-157 Identities = 269/455 (59%), Positives = 338/455 (74%), Gaps = 7/455 (1%) Query: 6 APTLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELV 65 A +L A IFRAYDIRGVVG+ LT + A IG+AIGSE LA+G V +GRDGRLSGPEL Sbjct: 315 AASLAAGIFRAYDIRGVVGEELTPKVAALIGQAIGSEVLAQGLREVVIGRDGRLSGPELA 374 Query: 66 KQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGET 125 L +GL GC V D+G+ PTPV+Y+A++ L S V +TGSHNPP+YNGFKIV+AG+T Sbjct: 375 AGLAEGLRRAGCDVIDIGLAPTPVVYFASHHLRTGSCVAVTGSHNPPEYNGFKIVIAGQT 434 Query: 126 LANEQIQALRERIEKNDLA--SGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGV 183 L+ + + AL +RI + LA S G+ +Q ++ Y ++I DD+ + +P+KVV D GNGV Sbjct: 435 LSGDAVTALYQRIVEGRLAQASSPGNYQQREVNDDYVRRIADDVQLERPLKVVADAGNGV 494 Query: 184 AGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDG 243 AG + L+EA+G VIPLYC+VDGNFPNHHPDP +P NL+DL+ VK +ADLG+AFDG Sbjct: 495 AGALVQPLLEAIGADVIPLYCDVDGNFPNHHPDPSEPANLQDLVQTVKRFDADLGIAFDG 554 Query: 244 DGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVM 303 DGDR+GVVT GTII+ DRLLMLFA DV+ RNPGA +I+DVKCT +L + +GG P+M Sbjct: 555 DGDRLGVVTPDGTIIFADRLLMLFAADVLLRNPGAMVIYDVKCTGKLADFVLRHGGSPMM 614 Query: 304 WKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHV 363 WKTGHSLIK +M ET A LAGEMSGH FF+ERWFGFDDG+Y+AARLLEIL+ + + V Sbjct: 615 WKTGHSLIKARMAETDAELAGEMSGHFFFRERWFGFDDGLYAAARLLEILALREETPQEV 674 Query: 364 FSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGE-----GNITTLDGVRVDYPKGWG 418 P ISTPEI + V + + A++ + AQ G+ G I+T+DG+RVD+ GWG Sbjct: 675 LEELPQSISTPEIKVPVADGTPHALVSLVVSAAQSGDNPFVGGRISTIDGLRVDFADGWG 734 Query: 419 LVRASNTTPVLVLRFEADTEEELERIKTVFRNQLK 453 LVRASNTTPVLVLRFEADTEE LERIK FR QL+ Sbjct: 735 LVRASNTTPVLVLRFEADTEEALERIKAQFRTQLQ 769 Lambda K H 0.319 0.138 0.410 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: 919 Number of extensions: 43 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: 463 Length of database: 779 Length adjustment: 37 Effective length of query: 426 Effective length of database: 742 Effective search space: 316092 Effective search space used: 316092 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: 53 (25.0 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