Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_089300214.1 CHB84_RS04545 phospho-sugar mutase
Query= BRENDA::C6L2F4 (596 letters) >NCBI__GCF_900188115.1:WP_089300214.1 Length = 560 Score = 244 bits (624), Expect = 5e-69 Identities = 194/577 (33%), Positives = 268/577 (46%), Gaps = 63/577 (10%) Query: 11 GALEAAVNFWRSVDRREETQKETLELLKNLTED------ELAKLFLARLEFGTAGLRGRM 64 G LEAA W + D E + E +L EL L FGTAGLRG + Sbjct: 6 GVLEAARR-WAAGDVDERCRAELHDLADRAASGDTEAAAELDDRMSGPLTFGTAGLRGPL 64 Query: 65 GAGFSRMNDVTIQQTTQGYCAFLVDVFGEDGKDRGVVIGFDARHNSRRFAQLTAAVFLSK 124 AG + +N + +TT G +L + G G V++G DARH S A A V Sbjct: 65 RAGPNGINRAVVARTTAGVARWLEE-HGHTGAR--VLVGRDARHGSAELATEAAGVLCGA 121 Query: 125 GFRVQLFSDIVHTPMVPYTVVAANCIAGIMITASHNPKADNGYKVYAANGAQIIPPMDSE 184 G V +F + V TP++ + V AGI ITASHNP +DNGYK+Y A+GAQI+PP D+E Sbjct: 122 GLTVSVFDEPVPTPVLAFAVRDLGAAAGIQITASHNPASDNGYKLYDASGAQIVPPADAE 181 Query: 185 ISAFINSNLDFWSDVDEYFDSKTGMLTEKAANSSLLEDPLNTYVDAYIKDIAADLCVAEQ 244 ISA I + + S + P VD Y+ A + Sbjct: 182 ISASIEAAPE----------------VRSLTRSRAWDRPDPAVVDRYVSRAAT---MPRG 222 Query: 245 QGSDLKFMYTAMHGVGTPMVKKMLAAFGFNDNLLTVDAQCTPDPEFPTVAFPNPEEKGAL 304 ++ T +HGVG L GF D+++ V Q PDP+FPTV +PNPEE GA Sbjct: 223 TARGIRVALTPLHGVGADTAVAALHHAGF-DDVVVVAEQAEPDPDFPTVPYPNPEEAGAC 281 Query: 305 DLAFQEADSHGLTLVIANDPDADRFAA-------AEKCDGRWYQFTGDELGAILGAYAIK 357 D + A S L +A DPDADR A + G + TGDE G +LG + + Sbjct: 282 DRLLELAASCRADLAVALDPDADRCALGIPTRHDSHDVSGGFRMLTGDETGTLLGEHVLA 341 Query: 358 LREGQGISKSKMALICSAVSSRMLQKIAKENGCTFAETMTGFKWMENKAIEMEAEGLIPV 417 + +A + VSS L +A+ + ++AET+TGFKW+ A G V Sbjct: 342 SLDRARHPDPVVA--TTIVSSSALAALARAHRASYAETLTGFKWLVR-----AAGGDRLV 394 Query: 418 FVYEEALGY-ALSQRVRDKDGVSAAAVWMQMAIDLYSRGQTVMDFLMSLRKRYGYFVTRN 476 + YEEALG A VRDKDG++AA + +A + G ++ L L +G ++T Sbjct: 395 YAYEEALGVCADPAAVRDKDGITAAVLAADLAASRKAAGSSIGQMLDELATEHGVYLTAP 454 Query: 477 SYFICPDPRLIQGLFKDFANGGNYPKQLGPFTIRRIRDVGRGYDSEEQCSFPSNCEMLTV 536 R + G+ + + + P+QL T+ I D+ G D T+ Sbjct: 455 VTVRVRSSRELPGIMRQLRS--DPPRQLAGRTV-TIDDLLPGSD--------------TL 497 Query: 537 YLDNGAV-VTLRGSGTEPKLKYYAETSSTDPEQGLAE 572 L V V +R SGTEPK+K Y E PEQG E Sbjct: 498 RLTGAGVRVVVRPSGTEPKIKAYLEVVEPPPEQGSPE 534 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: 780 Number of extensions: 41 Number of successful extensions: 8 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: 560 Length adjustment: 36 Effective length of query: 560 Effective length of database: 524 Effective search space: 293440 Effective search space used: 293440 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