Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_036259295.1 DL86_RS05875 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000746085.1:WP_036259295.1 Length = 449 Score = 214 bits (545), Expect = 5e-60 Identities = 149/454 (32%), Positives = 233/454 (51%), Gaps = 33/454 (7%) Query: 3 KLFGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALI 62 K FGT G+RG AN ITPE AMK+ A G + +R G + V+G+DTR+S M++ A++ Sbjct: 4 KHFGTDGIRGRANVAITPELAMKVAQATGVVFQR-GDHRHRAVIGKDTRLSSYMIEYAMV 62 Query: 63 SGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKK 122 +G SVG D + +G PTPAV T AD G +I+ASHNP E NGIKL P+G L Sbjct: 63 AGFASVGMDSLLLGPMPTPAVAMLTHSMRADIGVMISASHNPFEDNGIKLFGPDGYKLSD 122 Query: 123 EREAIVEELFFKE-DFDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPFVVVD 180 E EA +E + K+ +K ++G R E YIE K + + + +VVD Sbjct: 123 EVEAKIEAMLAKDFALKLSKPADLGRAMRVEGDRARYIEFAKRTL-LRTLSLDGLRIVVD 181 Query: 181 TSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGV 240 +NGA P L ELG +V ++ +PDG+ R + ++ V+ + AD GV Sbjct: 182 CANGAAYKVAPEALWELGAEVFSIGVEPDGFNINRGVGSTAP--QALVKKVREMRADIGV 239 Query: 241 AQDGDADRAVFIDENGRFIQGDKTFALVADAVLKE----KGGGLLVTTVATSNLLDDIAK 296 A DGDADR + +DE G+ + GD+ A +A + E K G +V TV ++ L+ + Sbjct: 240 ALDGDADRVIIVDEMGKIVDGDQLMAAIAQSWKDEGRLTKPG--IVATVMSNLGLERYLE 297 Query: 297 KHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKS 356 G + RT VGD V + +N +GGE++G +I ++ DG + +++ I + Sbjct: 298 DVGLSLARTPVGDRYVLEHMRQNGYNLGGEQSGHIILSDYCTTGDGLVAALQLMAIVKRE 357 Query: 357 GKKFSEL------IDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKII 410 K S++ + ++ K K R +E D ++ + RE G Sbjct: 358 SKPVSQVCRRFEPLPQVLKNVTFKAGRPLEDD--GVIRAIEAGRRELG------------ 403 Query: 411 FEDGWVLVRASGTEPIIRIFSEAKSKEKAQEYLN 444 G +++R SGTEP+IR+ E + + + ++ Sbjct: 404 -NAGRLVIRPSGTEPVIRVMGEGDNLDVVERIVD 436 Lambda K H 0.317 0.138 0.391 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: 531 Number of extensions: 23 Number of successful extensions: 6 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: 455 Length of database: 449 Length adjustment: 33 Effective length of query: 422 Effective length of database: 416 Effective search space: 175552 Effective search space used: 175552 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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