Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate SMc00637 SMc00637 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >FitnessBrowser__Smeli:SMc00637 Length = 450 Score = 219 bits (557), Expect = 2e-61 Identities = 147/453 (32%), Positives = 237/453 (52%), Gaps = 30/453 (6%) Query: 3 KLFGTFGVRGIANE-KITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEAL 61 + FGT G+RG +N +TP+ AM++G+A GT+ R G + VV+G+DTR+SG ML+ A+ Sbjct: 4 RYFGTDGIRGQSNIFPMTPDLAMRVGIAVGTIF-RNGAHRHRVVIGKDTRLSGYMLENAM 62 Query: 62 ISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 ++G + G DV +G PTP V T+ AD G +I+ASHN NGIKL P+G L Sbjct: 63 VAGFTAAGLDVFLLGPIPTPGVAMLTRSLRADIGVMISASHNAFRDNGIKLFGPDGYKLS 122 Query: 122 KEREAIVEELFFKE-DFDRAKWYEIGEVRRED-IIKPYIEAIKSKVDVEAIKKRKPFVVV 179 + E +E+L ++ AK +IG +R D I YIE K + + K + + Sbjct: 123 DDIEQKIEDLLEQDMSGQLAKPEDIGRAKRVDGDIYRYIEQAKRTLPRDVTLKGLR-IAI 181 Query: 180 DTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFG 239 D +NGA P L ELG +V+T+ +P+G N E + + V + AD G Sbjct: 182 DCANGAAYKVAPSALWELGAEVVTIGTEPNGV--NINLECGSTHPAALQKKVHEVRADIG 239 Query: 240 VAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKE---KGGGLLVTTVATSNL-LDDIA 295 +A DGDADR + +DE G I GD+ A++AD+ + KGGG+ T + SNL L+ Sbjct: 240 IALDGDADRVLIVDEEGAVIDGDQLMAVIADSWAADGMLKGGGIAATVM--SNLGLERYL 297 Query: 296 KKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAK 355 + K+ RTKVGD V + ++ +GGE++G ++ + DG + +++ + + Sbjct: 298 QARRLKLHRTKVGDRYVVEQMRQDGLNVGGEQSGHIVLSDFGTTGDGLVAALQILAVVKR 357 Query: 356 SGKKFSELIDELPKYYQIKTKRHVEGDR----HAIVNKVAEMARERGYTVDTTDGAKIIF 411 GK SE+ Q+ V + A+ +AE + + Sbjct: 358 QGKTVSEICRRFEPVPQVLKNVRVSAGKPLEDAAVQQAIAEAEAQ-------------LA 404 Query: 412 EDGWVLVRASGTEPIIRIFSEAKSKEKAQEYLN 444 ++G +L+R SGTEP+IR+ +E + + + ++ Sbjct: 405 KNGRLLIRPSGTEPLIRVMAEGDDRGQVERIVD 437 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: 546 Number of extensions: 27 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: 450 Length adjustment: 33 Effective length of query: 422 Effective length of database: 417 Effective search space: 175974 Effective search space used: 175974 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 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