Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_103231575.1 C1634_RS03120 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_002899945.2:WP_103231575.1 Length = 460 Score = 294 bits (753), Expect = 4e-84 Identities = 178/456 (39%), Positives = 260/456 (57%), Gaps = 15/456 (3%) Query: 6 GTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPL-VVVGRDTRVSGEMLKEALISG 64 GT G G N+ +TP +K AFGT L+ KK L +++GRD R+SG+M+ + + Sbjct: 12 GTIG--GKVNDNLTPLDVVKFASAFGTWLQNNKNKKDLTLIIGRDARISGQMVSSLVTAT 69 Query: 65 LLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKER 124 L +G +V+D+G++ TP V+ NADGG ++TASHNP ++N +KLL G + E Sbjct: 70 LQGLGINVVDLGLSTTPTVEIMVPELNADGGIILTASHNPKQWNALKLLNEKGEFITGEN 129 Query: 125 EAIVEELFFKEDFDRAKWYEIGEVR-REDIIKPYIEAIKS--KVDVEAIKKRKPFVVVDT 181 A V L EDF+ A+ ++G+ RED +I+ I VD EAIK + VV+D Sbjct: 130 GAEVLALAESEDFNYAEVDDLGQYETREDAFDIHIKQILDLPMVDAEAIKAKNFKVVLDA 189 Query: 182 SNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGVA 241 N G + +P LL LGC+ + + +P G+FP NPEP +E+L + E+VK AD G+ Sbjct: 190 VNSTGGIAIPMLLDTLGCETVKLYCEPTGHFP-HNPEPLKEHLGDICELVKKENADLGIV 248 Query: 242 QDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNLLDDIAKKHGAK 301 D D DR IDE G + T VAD +LK K G+ V+ +++S L D+A H ++ Sbjct: 249 VDPDVDRLALIDEKGEMFGEEYTLVAVADYLLKHK-NGVAVSNLSSSRALRDVAHTHNSE 307 Query: 302 VMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKKFS 361 + VG++ V + E N IGGE NGG+I+P+ GRD + VA + AK K S Sbjct: 308 YFASAVGEVNVVTLMKEKNAVIGGEGNGGIIYPDLHYGRDSLVGVALFLTHLAKENKTVS 367 Query: 362 ELIDELPKYYQIKTKRHV--EGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDGWVLVR 419 EL P Y+ K K + E D AI++K+ + + V DG KI FE+ WV +R Sbjct: 368 ELRAGYPSYFMGKKKIELTPEIDVDAILSKMEQ--EYKNEEVSVVDGVKIDFENNWVHLR 425 Query: 420 ASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEKALS 455 S TEPIIRI++EAKS+E+A + LG +++ K S Sbjct: 426 KSNTEPIIRIYTEAKSQEEADK---LGDDIIAKIKS 458 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: 545 Number of extensions: 35 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: 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