Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate GFF3737 Psest_3806 Phosphomannomutase
Query= BRENDA::P26276 (463 letters) >FitnessBrowser__psRCH2:GFF3737 Length = 857 Score = 814 bits (2103), Expect = 0.0 Identities = 397/463 (85%), Positives = 431/463 (93%) Query: 1 MSTAKAPTLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLS 60 MS+AKAP LPASIFRAYDIRGVVGD+LT ETAYW+GRAIGSESLA+GEP V+VGRDGRLS Sbjct: 395 MSSAKAPNLPASIFRAYDIRGVVGDSLTTETAYWVGRAIGSESLAKGEPNVSVGRDGRLS 454 Query: 61 GPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIV 120 GPELV+ LIQGL+D GC VSD+GMVPTPVLYYAAN+L GKSGVMLTGSHNPPDYNGFKIV Sbjct: 455 GPELVQHLIQGLLDSGCDVSDIGMVPTPVLYYAANILAGKSGVMLTGSHNPPDYNGFKIV 514 Query: 121 VAGETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCG 180 +AG+TLANEQIQ LR+RIE NDL+SGVG VEQVD+L RYF+QIR DIAMAKPMKVVVDCG Sbjct: 515 IAGDTLANEQIQTLRKRIENNDLSSGVGKVEQVDVLERYFQQIRSDIAMAKPMKVVVDCG 574 Query: 181 NGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLA 240 NGVAGVIAP++IEALGC+VIPLYC+VDGNFPNHHPDPGKPENL DLIAKVK+E ADLGLA Sbjct: 575 NGVAGVIAPRMIEALGCTVIPLYCDVDGNFPNHHPDPGKPENLVDLIAKVKSEKADLGLA 634 Query: 241 FDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGR 300 FDGDGDRVGVVTN GT+IY DRLLMLFAKDVVSRNPGADIIFDVKCTRRL LISGYGGR Sbjct: 635 FDGDGDRVGVVTNAGTMIYADRLLMLFAKDVVSRNPGADIIFDVKCTRRLTPLISGYGGR 694 Query: 301 PVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDS 360 PVMWKTGHSLIKKKMKE+GALLAGEMSGH+FFKERWFGFDDGIYSAARLLEILSQD+RD+ Sbjct: 695 PVMWKTGHSLIKKKMKESGALLAGEMSGHIFFKERWFGFDDGIYSAARLLEILSQDKRDA 754 Query: 361 EHVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLV 420 E VF+AFP DISTPEINITVTE+SKF I++ALQRDAQWGE N+ TLDGVRVDYPKGWGL+ Sbjct: 755 EQVFAAFPCDISTPEINITVTEESKFTIMDALQRDAQWGEANLITLDGVRVDYPKGWGLI 814 Query: 421 RASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 RASNTTPVLVLRFEAD+EEEL RI+ VFR QL V L +PF Sbjct: 815 RASNTTPVLVLRFEADSEEELSRIQDVFRAQLLNVAPDLKLPF 857 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: 1147 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: 857 Length adjustment: 38 Effective length of query: 425 Effective length of database: 819 Effective search space: 348075 Effective search space used: 348075 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 17 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