Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_009140673.1 HMPREF9452_RS03215 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000225705.1:WP_009140673.1 Length = 447 Score = 177 bits (450), Expect = 5e-49 Identities = 138/458 (30%), Positives = 213/458 (46%), Gaps = 25/458 (5%) Query: 3 KLFGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALI 62 K FGT G RG ANE + + A KIG G KK V++G+DTR+S M + AL+ Sbjct: 2 KYFGTDGFRGRANEGLNVDHAFKIGRFVGWYYGARRGKKARVIIGKDTRLSSYMFESALV 61 Query: 63 SGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKK 122 SGL++ G D + + PTP V + D G +ITASHNP NGIKL+ G + + Sbjct: 62 SGLVASGADAYMLHVIPTPGVSYEVVDGGFDCGVMITASHNPYTDNGIKLVNHEGYKMDE 121 Query: 123 EREAIVEE-LFFKEDFDRAKWYEIGEVRREDIIKPYIEAIKSKVDVEAIKKRKPFVVVDT 181 + ++E+ + K + A IG D ++ I S + + + +D Sbjct: 122 DVLELIEDYIDGKSEVPLATGENIG--CTVDYMQGRNRYIASLISSCGFSLQGMKIGLDC 179 Query: 182 SNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGVA 241 +NG+ S + LG + +N P+GY N +++ V G D G A Sbjct: 180 ANGSASSVARPVFDALGAETHVINNAPNGY--NINVACGSTHIEGLQRFVVENGLDIGFA 237 Query: 242 QDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNL----LDDIAKK 297 DGDADR + +DE G + GD L K G L +TV + + + Sbjct: 238 YDGDADRCLAVDERGHLVDGD--LILYVCGTYLNKYGRLAKSTVVPTVMGNFGFFRALEA 295 Query: 298 HGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSG 357 G +T VGD V + EN +GGE++G +IF + DG +T +++E+ Sbjct: 296 AGLNYEKTDVGDKYVYACMRENGYNLGGEQSGHIIFGDLAKTGDGILTSLRIMEVLRAER 355 Query: 358 KKFSELIDELPKYYQIKTKRHVEGDRHAIVNK---VAEMARERGYTVDTTDGAKIIFEDG 414 +K SEL + Y Q V D+ A++N A +A+ Y + +G Sbjct: 356 EKLSELTRPVKLYPQQLVNVRV-SDKDAVMNGEDIKAAIAQAEEY----------LEGNG 404 Query: 415 WVLVRASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEK 452 V VRASGTEP++R+ +EA ++ + + + LEK Sbjct: 405 RVFVRASGTEPLVRVLTEAPDEKLCTKAGAIVLTALEK 442 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: 512 Number of extensions: 26 Number of successful extensions: 5 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: 447 Length adjustment: 33 Effective length of query: 422 Effective length of database: 414 Effective search space: 174708 Effective search space used: 174708 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