Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate N515DRAFT_2990 N515DRAFT_2990 phosphomannomutase / phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >FitnessBrowser__Dyella79:N515DRAFT_2990 Length = 779 Score = 553 bits (1424), Expect = e-161 Identities = 270/459 (58%), Positives = 337/459 (73%), Gaps = 3/459 (0%) Query: 8 TLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQ 67 T+ +IFRAYD+RG+VG +L + A +G++IG+ +G + VGRDGRLSGPEL Sbjct: 321 TVDPTIFRAYDVRGIVGKSLNTDVARLLGQSIGTVMREKGLREIVVGRDGRLSGPELTAA 380 Query: 68 LIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLA 127 L GL + G V D+G VPTPV+YYAA SGV +TGSHNPPDYNGFKIVV GETL+ Sbjct: 381 LSDGLREAGIDVIDIGAVPTPVVYYAAYRFNTGSGVAVTGSHNPPDYNGFKIVVGGETLS 440 Query: 128 NEQIQALRERIEKNDLA-SGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGV 186 IQ L RI N+L G GS+ Q+D++P Y ++I D+ + MKVVVDCGNG+ G Sbjct: 441 EGSIQDLYRRIAANELERGGKGSLRQIDVVPDYVERITSDVQAGRRMKVVVDCGNGIPGS 500 Query: 187 IAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGD 246 +APQ++E +GC VI LYC+VDG FPNHHPDP P NL+DLI VK+ ADLG+AFDGDGD Sbjct: 501 VAPQVLEGIGCEVIQLYCDVDGTFPNHHPDPSDPHNLEDLILAVKSTGADLGVAFDGDGD 560 Query: 247 RVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKT 306 R+GVVT TG II+PDR LMLFA+DV+SR PGA II+DVKCT L I GG P+MW+T Sbjct: 561 RLGVVTKTGEIIFPDRTLMLFARDVLSRQPGATIIYDVKCTGHLKGQILDAGGSPLMWRT 620 Query: 307 GHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILS--QDQRDSEHVF 364 GHSLIK KM+ETGA LAGEMSGH FFKERW+GFDDGIY+ ARLLEIL+ D+R E +F Sbjct: 621 GHSLIKSKMRETGAELAGEMSGHFFFKERWYGFDDGIYAGARLLEILAGDLDERTPEQIF 680 Query: 365 SAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASN 424 + P +STPE+ I + E + IE ++ A +G+ +TT+DGVR D+P GWGLVR SN Sbjct: 681 ATCPKGVSTPELKIEMKEGEHYKFIEKFRQSASFGDAALTTIDGVRADWPDGWGLVRPSN 740 Query: 425 TTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 TTP+LVLRF+AD + L+RI+ VFR QL AVD +L +PF Sbjct: 741 TTPILVLRFDADNDAALKRIQNVFREQLHAVDPALKLPF 779 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: 945 Number of extensions: 33 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 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