Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_051060823.1 CDO52_RS21155 phospho-sugar mutase
Query= BRENDA::C6L2F4 (596 letters) >NCBI__GCF_002263495.1:WP_051060823.1 Length = 559 Score = 284 bits (726), Expect = 8e-81 Identities = 213/563 (37%), Positives = 273/563 (48%), Gaps = 63/563 (11%) Query: 12 ALEAAVNFWRSVDRREETQKETLELLKNLTEDELAKLFLARLEFGTAGLRGRMGAGFSRM 71 +L W D T+ E +L + LA+ F ARLEFGTAGLRG +GAG +RM Sbjct: 12 SLRGQAEAWLEQDPDPRTRDELKAILDAGDDAALAERFGARLEFGTAGLRGALGAGPNRM 71 Query: 72 NDVTIQQTTQGYCAFLVDVFGEDGKDRGVVIGFDARHNSRRFAQLTAAVFLSKGFRVQLF 131 N VT+ + G +L G R VVIG+DARH S FA+ TAAV G L Sbjct: 72 NRVTVMRAAAGVARWL-------GSGRCVVIGYDARHRSADFAEDTAAVLTGAGCTALLL 124 Query: 132 SDIVHTPMVPYTVVAANCIAGIMITASHNPKADNGYKVYAAN-----GAQIIPPMDSEIS 186 + TP++ Y V A AGIM+TASHNP DNGYKVY G+QI+ P+D+EIS Sbjct: 125 PRPLPTPVLAYAVRALGADAGIMVTASHNPPQDNGYKVYMGGEGPGAGSQIVAPVDAEIS 184 Query: 187 AFINSNLDFWSDVDEYFDSKTGMLTEKAANSSLLEDPLNTYVDAYIKDIAADLCVAEQQG 246 A I++ G ++E S T VD I + A G Sbjct: 185 AAIDA---------------VGPVSELKVGSGW------TVVDEEIVERYLGAITAVPLG 223 Query: 247 SD--LKFMYTAMHGVGTPMVKKMLAAFGFNDNLLTVDAQCTPDPEFPTVAFPNPEEKGAL 304 SD + YT +HGVG ++ GF L V Q PDP+FPTVAFPNPEE GA+ Sbjct: 224 SDRAVSVTYTPLHGVGASTLRAAFERVGFPAPRL-VPEQAEPDPDFPTVAFPNPEEPGAM 282 Query: 305 DLAFQEADSHGLTLVIANDPDADRFAAAEKCDGRWYQFTGDELGAILGAYAIKLREGQGI 364 DLA ++G LV+ANDPDADR A A G TGDE+G +L Y ++ G Sbjct: 283 DLALAVGRANGSDLVVANDPDADRVAVAVPGHG---LLTGDEIGGLLAEYILRHTAG--- 336 Query: 365 SKSKMALICSAVSSRMLQKIAKENGCTFAETMTGFKWMENKAIEMEAEGLIPVFVYEEAL 424 + + VS+ +L KIA + G ET+TGFKW+ G VF YEEAL Sbjct: 337 --GDRVVATTIVSAGLLPKIAADYGVRCVETLTGFKWLARAG----GPGERNVFSYEEAL 390 Query: 425 GYAL----SQRVRDKDGVSAAAVWMQMAIDL-YSRGQTVMDFLMSLRKRYGYFVTRNSYF 479 GY L S+ V DKDG+SAA MA + G+T++D L +RYG T Sbjct: 391 GYCLGGDTSRPVADKDGISAALAVAAMAAEAKRDGGRTLLDLLDDQARRYGLHRTAQVAV 450 Query: 480 ICPDPRLIQGLFKDFANGGNYPKQLGPFTIRRIRDVGRGYDSEEQCSFPSNCEMLTVYLD 539 D L+ + P+ G + I D G + P+ + L L Sbjct: 451 RVSDLALLADTMRRLR--AEPPRAFGSLEVEAIEDFAEG-----RGDLPAT-DALRYRLG 502 Query: 540 N--GAVVTLRGSGTEPKLKYYAE 560 A +TLR SGTEPKLK Y E Sbjct: 503 GPARARITLRPSGTEPKLKAYLE 525 Lambda K H 0.320 0.135 0.398 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: 833 Number of extensions: 45 Number of successful extensions: 10 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: 596 Length of database: 559 Length adjustment: 36 Effective length of query: 560 Effective length of database: 523 Effective search space: 292880 Effective search space used: 292880 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 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