Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_013402170.1 CALHY_RS01030 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000166355.1:WP_013402170.1 Length = 449 Score = 267 bits (683), Expect = 5e-76 Identities = 169/461 (36%), Positives = 253/461 (54%), Gaps = 18/461 (3%) Query: 1 MGKLFGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEA 60 MGKLFGT GVRG+AN+++T E A +G A G + E ++KP +++G+DTR+S +ML+ A Sbjct: 1 MGKLFGTDGVRGVANKELTCELAFDLGRA-GAYVLTETKQKPKILIGKDTRISCDMLEAA 59 Query: 61 LISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGL 120 L +GL SVG DV G+ TPA+ K D G +I+ASHNP E+NGIK G L Sbjct: 60 LCAGLTSVGADVYLAGVITTPAIAHLVKSHGFDAGIMISASHNPYEFNGIKFFNSQGFKL 119 Query: 121 KKEREAIVEELFFKEDFD---RAKWYEIGEVRREDIIKPYIEAIKSKVDVEAIKKRKPFV 177 + E +E++ ++ A++ IG V R D+ K Y E +KS ++ + K K + Sbjct: 120 SDQIEEKIEDIILNRKWNEVPHAQFDAIGRVNRVDLKKNYQEYLKSTLNGASFKGLK--I 177 Query: 178 VVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGAD 237 V+D +NGA P + ELG +V+ +N QPDG N E +LK + V AD Sbjct: 178 VIDCANGAAYKIAPEVFEELGAEVVVINNQPDG--TNINKECGSTHLKMLQQEVVKNKAD 235 Query: 238 FGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKG---GGLLVTTVATSNLLDDI 294 FG+A DGDADR +F+DE G + GDK L+A LK++G LV TV ++ L Sbjct: 236 FGIAYDGDADRTLFVDEEGSIVDGDKIMLLLAQN-LKQQGKLQRNTLVVTVMSNMGLFVA 294 Query: 295 AKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFA 354 AK+ G + TKVGD V + E +IGGE++G +I + DG +T ++ ++ Sbjct: 295 AKELGINLEVTKVGDRYVLEKMLEGGYSIGGEQSGHIILLDFATTGDGILTSLQLTKLIK 354 Query: 355 KSGKKFSELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDG 414 +SGKK S+L + Y Q+ VE + + +K + + +G G Sbjct: 355 ESGKKLSDLAKIMKVYPQVLVNAKVENGKKDLYSKDPVILEAIKKVEEKLNG------KG 408 Query: 415 WVLVRASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEKALS 455 VL+R SGTEP+IR+ E + E+ ++ + L+E LS Sbjct: 409 RVLIRPSGTEPLIRVMIEGEDYEEIKKDAHELASLIESRLS 449 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: 544 Number of extensions: 25 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: 449 Length adjustment: 33 Effective length of query: 422 Effective length of database: 416 Effective search space: 175552 Effective search space used: 175552 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