Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate 3607123 Dshi_0545 HAD-superfamily hydrolase, subfamily IA, variant 3 (RefSeq)
Query= SwissProt::O06995 (226 letters) >FitnessBrowser__Dino:3607123 Length = 246 Score = 73.2 bits (178), Expect = 4e-18 Identities = 72/237 (30%), Positives = 110/237 (46%), Gaps = 36/237 (15%) Query: 4 VIFDLDGVITDTAEYHFLAWKHIAEQIDIPFDRDMN-ERLKGISREESLESILIF----- 57 VIFD DGVI D+ E LA + + F D+ E ++ +SL++I + Sbjct: 23 VIFDFDGVIADS-EVISLATLQASLKA---FGMDLTIEEIRQKFLGKSLKTISTYVDQHS 78 Query: 58 -GGAETKYTNAEKQELMHRKNRDYQMLISKLTPEDLLPGIGRLLCQLKNENIKIGLASSS 116 A + NA + EL Y ++L P LP + +LL +L + +ASS Sbjct: 79 SSQAAADFGNAWQAEL-------YSRFRAELKP---LPHLEKLLFELAETATRFCIASSG 128 Query: 117 --RNAPKILRRLAIIDDFHAIVDPTTLAKGKPDPDIFLTAAAMLDVSPADCAAIEDAEAG 174 L +++ D F + +++GKP PD+FL AA LDVSP+ C IED+ G Sbjct: 129 TFERINVALSAMSMSDCFDHVFSSEQVSRGKPAPDLFLMAAEALDVSPSRCLVIEDSLYG 188 Query: 175 ISAIKSAGMFAVGV-----------GQGQPML--GADLVVRQTSDLTLELLHEEWEQ 218 I A K+AGM VG G+ +L GAD+++ D+ L + +Q Sbjct: 189 IRAAKAAGMRGVGFLGGAHLQGIVEQHGKTLLENGADMILASHQDIAARLAPKRTQQ 245 Lambda K H 0.319 0.136 0.390 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: 113 Number of extensions: 4 Number of successful extensions: 2 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: 226 Length of database: 246 Length adjustment: 23 Effective length of query: 203 Effective length of database: 223 Effective search space: 45269 Effective search space used: 45269 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 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 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