Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_009545860.1 CCE_RS09765 mannose-1-phosphate guanylyltransferase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000017845.1:WP_009545860.1 Length = 841 Score = 197 bits (502), Expect = 8e-55 Identities = 133/442 (30%), Positives = 223/442 (50%), Gaps = 19/442 (4%) Query: 4 LFGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALIS 63 LFG GV G+AN ITPEFA+K+G A+G+ LK + VVV RD R M+ +LIS Sbjct: 384 LFGQRGVTGLANIDITPEFAVKLGAAYGSTLKAGSQ----VVVSRDQRGFSRMISRSLIS 439 Query: 64 GLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKE 123 GL+SVG ++ ++ P + T GG + A + ++ I+ + G+ + K Sbjct: 440 GLMSVGINIQNLEATAIPISRTMTPKLGVSGGVHLRAHPDRTDHILIEFFDDQGINIPKS 499 Query: 124 REAIVEELFFKEDFDRAKWYEIGEVR-REDIIKPYIEAIKSKVDVEAIKKRKPFVVVDTS 182 +E +E +FKED R +IG + +I Y E ++++D+E+I P +V+D Sbjct: 500 QEKKIEGAYFKEDLRRVGIPDIGNMSYPAQVIDTYRETFETQLDIESISNSDPKIVIDYV 559 Query: 183 NGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGVAQ 242 G LP LL + GC I +NA + E E L + ++V+A+ A+ G Sbjct: 560 YGVSGAILPQLLTKFGCDAIVLNASLRQ--TTVSTEERESLLHQLGQVVEAVKANLGAQV 617 Query: 243 DGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNLLDDIAKKHGAKV 302 + ++ + +DE+G I+G+ AL+ + + +V V S+ ++ IA++H KV Sbjct: 618 SANGEQFILVDESGLSIRGEWLTALMVNTIFTAYPRSTVVVPVEASSAVEQIARRHDGKV 677 Query: 303 MRTKVGDLIVARALYEN-NGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKKFS 361 +RTK + A N N ++GG + G IFP+ G D ++AK++E+ A + Sbjct: 678 IRTKSNPTALMEAAQMNPNVSLGGSGDTGFIFPQLHPGFDAMFSLAKLLEMLATQERSLV 737 Query: 362 ELIDELP----KYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKII--FEDGW 415 ++ ELP K Y ++ V+G A++ + E+ ++ DG KII D W Sbjct: 738 QIQAELPRICHKSYILRCPWKVKG---ALMRYLVEIHNPE--QLELIDGVKIINPQNDNW 792 Query: 416 VLVRASGTEPIIRIFSEAKSKE 437 VL+ EP + I + + +E Sbjct: 793 VLILPDAGEPFVHIVANSDDRE 814 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: 822 Number of extensions: 38 Number of successful extensions: 7 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: 841 Length adjustment: 37 Effective length of query: 418 Effective length of database: 804 Effective search space: 336072 Effective search space used: 336072 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: 53 (25.0 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