Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_011911705.1 PST_RS02425 phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >NCBI__GCF_000013785.1:WP_011911705.1 Length = 856 Score = 819 bits (2116), Expect = 0.0 Identities = 399/463 (86%), Positives = 433/463 (93%) Query: 1 MSTAKAPTLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLS 60 MS+AKAP LPASIFRAYDIRGVVGD+LT ETAYW+GRAIGSESLA+GEP V+VGRDGRLS Sbjct: 394 MSSAKAPNLPASIFRAYDIRGVVGDSLTTETAYWVGRAIGSESLAKGEPNVSVGRDGRLS 453 Query: 61 GPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIV 120 GPELV+ LIQGL+D GC VSD+GMVPTPVLYYAAN+L GKSGVMLTGSHNPPDYNGFKIV Sbjct: 454 GPELVQHLIQGLLDSGCDVSDIGMVPTPVLYYAANILAGKSGVMLTGSHNPPDYNGFKIV 513 Query: 121 VAGETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCG 180 +AG+TLANEQIQ LR+RIE NDL+SGVG VEQVD+L RYF+QIR DIAMAKPMKVVVDCG Sbjct: 514 IAGDTLANEQIQVLRKRIETNDLSSGVGKVEQVDVLERYFEQIRSDIAMAKPMKVVVDCG 573 Query: 181 NGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLA 240 NGVAGVIAP+LIEALGC+VIPLYCEVDGNFPNHHPDPGKPENL DLIAKVK+E ADLGLA Sbjct: 574 NGVAGVIAPKLIEALGCTVIPLYCEVDGNFPNHHPDPGKPENLVDLIAKVKSEKADLGLA 633 Query: 241 FDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGR 300 FDGDGDRVGVVTN GT+IYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRL LISGYGGR Sbjct: 634 FDGDGDRVGVVTNAGTMIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLTPLISGYGGR 693 Query: 301 PVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDS 360 PVMWKTGHSLIKKKMKE+GALLAGEMSGH+FFKERWFGFDDGIYSAARLLEILSQD+RD+ Sbjct: 694 PVMWKTGHSLIKKKMKESGALLAGEMSGHIFFKERWFGFDDGIYSAARLLEILSQDKRDA 753 Query: 361 EHVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLV 420 E VF+AFP DISTPEINITVTE+SKF I++ALQRDA+WGE N+ TLDGVRVDYPKGWGL+ Sbjct: 754 EQVFAAFPCDISTPEINITVTEESKFTIMDALQRDAKWGEANLITLDGVRVDYPKGWGLI 813 Query: 421 RASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 RASNTTPVLVLRFEAD+EEEL RI+ VFR QL +V L +PF Sbjct: 814 RASNTTPVLVLRFEADSEEELSRIQDVFRGQLLSVAPDLKLPF 856 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: 1192 Number of extensions: 38 Number of successful extensions: 1 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: 856 Length adjustment: 38 Effective length of query: 425 Effective length of database: 818 Effective search space: 347650 Effective search space used: 347650 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: 54 (25.4 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