Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_089302368.1 CHB84_RS15705 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_900188115.1:WP_089302368.1 Length = 444 Score = 229 bits (585), Expect = 1e-64 Identities = 157/446 (35%), Positives = 232/446 (52%), Gaps = 22/446 (4%) Query: 1 MGKLFGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRK-KPLVVVGRDTRVSGEMLKE 59 M +LFGT GVRG+AN ++TPE AM + + +L R +P+ VVGRD R SGEML Sbjct: 1 MARLFGTDGVRGLANGELTPELAMAVAASAARVLAAHDRSHRPVAVVGRDPRASGEMLDA 60 Query: 60 ALISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMG 119 A+++GL S G DV VG+ PTPAV AD G +I+ASHNP NGIKL G Sbjct: 61 AVVAGLTSAGADVRRVGVLPTPAVAHLVADIGADLGVMISASHNPMPDNGIKLFADGGHK 120 Query: 120 LKKEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIE--AIKSKVDVEAIKKRKPF 176 L E +EE + R E+G V +D + Y++ + + ++ ++ Sbjct: 121 LPDGIEDEIEE-GLHANGTRPTGAEVGRVAELDDALDRYVDHLLVAAPQRLDGLR----- 174 Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGA 236 VVVD +NGA + P R G V+ +NA+PDG N +L V GA Sbjct: 175 VVVDCANGAATFAAPEAYRRAGADVVAINAEPDGV--NINDACGSTHLDSLQAAVVEHGA 232 Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLK--EKGGGLLVTTVATSNLLDDI 294 D GVA DGDADR + ++ G + GD+ A++A A+ K E +V TV ++ L Sbjct: 233 DLGVAHDGDADRCLAVNSAGEVVDGDEILAVLALAMAKSGELVDQTVVATVMSNLGLHLA 292 Query: 295 AKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFA 354 ++HG ++ T VGD V L ++GGE++G ++ P H DG +T +++ Sbjct: 293 MREHGLQLRTTAVGDRYVLDELRAGGYSLGGEQSGHLVLPAHATTGDGLLTALRLMGAVT 352 Query: 355 KSGKKFSELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDG 414 SGK +EL + + Q+ V D+ A+V + + R VD +G + E G Sbjct: 353 ASGKPLAELAGVMRRLPQVLVNVRV-ADKDAVVE--SRLVRS---AVDDVEGE--LGEQG 404 Query: 415 WVLVRASGTEPIIRIFSEAKSKEKAQ 440 VL+R SGTE ++R+ EA ++ AQ Sbjct: 405 RVLLRPSGTEQLVRVMVEAPDQDTAQ 430 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: 526 Number of extensions: 28 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: 444 Length adjustment: 33 Effective length of query: 422 Effective length of database: 411 Effective search space: 173442 Effective search space used: 173442 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