Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_011373653.1 SUDEN_RS10580 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000012965.1:WP_011373653.1 Length = 446 Score = 233 bits (593), Expect = 1e-65 Identities = 157/466 (33%), Positives = 247/466 (53%), Gaps = 35/466 (7%) Query: 3 KLFGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALI 62 KLFGT GVRG A +T E AM++ MA G K ++VG+DTR SG M++ A++ Sbjct: 2 KLFGTDGVRGEAGTFLTAELAMRVAMAAGIYFKAHSITNK-ILVGKDTRRSGYMIENAIV 60 Query: 63 SGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKK 122 SGL ++G DVI +G PTPA+ + T++ D G +I+ASHN E NGIK + G L Sbjct: 61 SGLTAIGYDVIQIGPMPTPAIAFITENMRCDAGIMISASHNSFEDNGIKFFDGRGDKLPH 120 Query: 123 EREAIVEELFFKEDF---DRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPFVV 178 E +E++FF +D + + IG+ +R +D+I YI +K+ + + + +V Sbjct: 121 SVEEEIEKIFFDKDTILEAQTQGKYIGKAKRIDDVIGRYIVQLKNSFPRD-LSLKDMRIV 179 Query: 179 VDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADF 238 +D +NGAG + P +L ELG +VI ++ +PDG+ N + K+ E V AD Sbjct: 180 LDAANGAGYMVGPTVLEELGAEVIVLHNKPDGF--NINDSCGALHTKDVCESVVKYRADL 237 Query: 239 GVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKG---GGLLVTTVATSNLLDDIA 295 G+A DGDADR V +DENG + GD+ + A + ++G GG +V+TV ++ LDD Sbjct: 238 GIALDGDADRVVIVDENGVVVDGDQLLGALG-AFMSDRGTLKGGGIVSTVMSNRGLDDFM 296 Query: 296 KKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAK 355 G K+ R+ VGD V + + GGE++G VI + DG ++ +V+ + K Sbjct: 297 SDKGLKLFRSDVGDKNVLEVMKKEGINFGGEQSGHVIISDFAKTGDGLVSALQVLALLLK 356 Query: 356 SGKKFSELIDELPKYYQ------IKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKI 409 + +K S+ + Y Q +KTK+ V + + K+ E+ + Sbjct: 357 TSQKASKALRPFALYPQKLVNIKVKTKK-VLSEIDGLDEKLKELDENGVHH--------- 406 Query: 410 IFEDGWVLVRASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEKALS 455 LVR SGTE +R+ E K +K Y++ +E +KAL+ Sbjct: 407 -------LVRYSGTENKLRVLLECKDAKKMNLYMDEMVEFFQKALN 445 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: 502 Number of extensions: 27 Number of successful extensions: 7 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: 446 Length adjustment: 33 Effective length of query: 422 Effective length of database: 413 Effective search space: 174286 Effective search space used: 174286 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