Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_041097278.1 SUTH_RS04025 phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >NCBI__GCF_000828635.1:WP_041097278.1 Length = 473 Score = 500 bits (1287), Expect = e-146 Identities = 257/464 (55%), Positives = 322/464 (69%), Gaps = 17/464 (3%) Query: 8 TLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQ 67 TL IF+AYDIRG+V TLTA+T IG+A+GSE++AR + +GRDGRLSGP L Sbjct: 3 TLAPEIFKAYDIRGIVRTTLTADTVRRIGQALGSEAVARDIKAIVIGRDGRLSGPALASA 62 Query: 68 LIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLA 127 L G+ G V D+G VPTP+ Y+AA+ L +S V +TGSHNPP+YNG K+V+ G+TL Sbjct: 63 LADGITRTGVDVIDIGCVPTPMTYFAAHELGTESCVSVTGSHNPPEYNGLKMVLGGQTLY 122 Query: 128 NEQIQALRERIEKN--------DLAS-----GVGSVEQVDILPRYFKQIRDDIAMAKPMK 174 E IQ LR RIEKN D AS G G V + Y +I D+ +++PMK Sbjct: 123 GEMIQDLRRRIEKNAASAVPPGDTASHNFCQGRGVVRHASVHQAYLDRIVGDVKLSRPMK 182 Query: 175 VVVDCGNGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAEN 234 +V+DCGNGVAG +AP+L +GC V L+CEVDGNFPNHHPDP KPENL DL ++ Sbjct: 183 IVIDCGNGVAGGVAPELFRRMGCEVTELFCEVDGNFPNHHPDPSKPENLVDLQRALRETG 242 Query: 235 ADLGLAFDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALI 294 A+LGLAFDGDGDR+GVVT G II+PDR LMLFA DV+ RNPGA II+DVKC+R L I Sbjct: 243 AELGLAFDGDGDRLGVVTRDGEIIFPDRQLMLFAADVLVRNPGAQIIYDVKCSRWLAESI 302 Query: 295 SGYGGRPVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILS 354 GGRP+MW TGH+LIK K+KETGA LAGEMSGH+FFKERWFGFDD +Y+ ARLLEI+S Sbjct: 303 RHQGGRPLMWNTGHALIKTKLKETGAPLAGEMSGHMFFKERWFGFDDALYTGARLLEIVS 362 Query: 355 QDQRDSEHVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQW---GEGNITTLDGVRV 411 + DS P+ ISTPE+NI + E A++ L+ + G + T+DGVR Sbjct: 363 R-WEDSNWPLKNLPNAISTPELNIKMNEGEPHALVAKLRAGGKKLLPGARELITIDGVRA 421 Query: 412 DYPKGWGLVRASNTTPVLVLRFEADTEEELERIKTVFRNQLKAV 455 +Y G+GL RASNTTPV+VLRFEADT+ L RI+ FR+ L+ + Sbjct: 422 EYADGFGLARASNTTPVVVLRFEADTQAALTRIQAEFRSALETL 465 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: 658 Number of extensions: 25 Number of successful extensions: 4 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: 473 Length adjustment: 33 Effective length of query: 430 Effective length of database: 440 Effective search space: 189200 Effective search space used: 189200 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 Apr 09 2024. 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