Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_012473902.1 CPHAMN1_RS02285 phosphomannomutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000020545.1:WP_012473902.1 Length = 460 Score = 184 bits (467), Expect = 5e-51 Identities = 139/459 (30%), Positives = 214/459 (46%), Gaps = 18/459 (3%) Query: 5 FGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALISG 64 FGT G R I ++ T + +A V VG DTR Sbjct: 5 FGTDGWRAIIADEYTFDNLKLASLATADYFLDLPEALNGVCVGYDTRFMSPEFARYTAEV 64 Query: 65 LLSVGCDV-IDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKE 123 L S G V + APTPAV ++ GG VITASHNPP YNG K+ G E Sbjct: 65 LSSRGLRVFLSDSFAPTPAVSLFSRDKQLAGGIVITASHNPPHYNGFKIKASYGGSALPE 124 Query: 124 REAIVEELFFKEDFDRAKWYEIGEVRREDIIKPYIEAIKSKVDVEAIKKRKPFVVVDTSN 183 +++E+ + D + + DI Y++ + S +D++ I+K + + Sbjct: 125 SISVIEKNLNETDPGTTIEPDESLIETADIKGYYLQYLLSHIDLDTIRKSHLHIAHNAMF 184 Query: 184 GAGSLTLPYLL--RELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGVA 241 G+G + +L ++ C +N DG NPEP ++ FM K G+ Sbjct: 185 GSGQHIMDSILGTTQVDCYHCRLNPGFDGI----NPEPIPRYIRNFMTFCKKTKPAAGII 240 Query: 242 QDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGG-GLLVTTVATSNLLDDIAKKHGA 300 DGDADR +DEN +I K FA+V ++++K G + T A ++++D I +KH Sbjct: 241 NDGDADRICMLDENADYIDSHKIFAIVLKYLVEDKRKTGEVAKTFALTDVIDKICRKHNL 300 Query: 301 KVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKKF 360 + VG V++ + + IGGEE+GG+ ++ RDG ++EI AK K Sbjct: 301 TLHLLPVGFKHVSKLMTTRDILIGGEESGGIGITSYLPERDGIYIGLLILEIMAKKKKTL 360 Query: 361 S----ELIDELPKYYQIKTKRHVEGDR-HAIVNKVAEMARERGYTVDTT-----DGAKII 410 S EL DE +Y + ++ ++ +++ K + ER T T DG K Sbjct: 361 SGLVQELFDEYGSFYYNRIDLPIDEEKKQSLIAKASRGDLERIATYRVTGFNALDGFKYH 420 Query: 411 FEDGWVLVRASGTEPIIRIFSEAKSKEKAQEYLNLGIEL 449 FE GW+L+R SGTEP++R++ EA S EK E L+ + L Sbjct: 421 FEGGWLLIRLSGTEPVLRLYCEADSPEKVDEALDYAMAL 459 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: 506 Number of extensions: 25 Number of successful extensions: 4 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: 460 Length adjustment: 33 Effective length of query: 422 Effective length of database: 427 Effective search space: 180194 Effective search space used: 180194 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