Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate Synpcc7942_0150 Synpcc7942_0150 Dolichyl-phosphate beta-D-mannosyltransferase
Query= BRENDA::Q2PCE3 (246 letters) >FitnessBrowser__SynE:Synpcc7942_0150 Length = 388 Score = 97.1 bits (240), Expect = 5e-25 Identities = 66/215 (30%), Positives = 114/215 (53%), Gaps = 4/215 (1%) Query: 8 LTIVLATLNEIDNLPRLCSDIDSILKNTKI-KYQLLFVDDNSSDGTREFIIEYCNKNKLS 66 L++V+ T NE +N+ L ++ +L +Y+L+ VDD+S D T + K + Sbjct: 26 LSLVIPTFNEAENIQPLLLQLNELLDRALADRYELIVVDDDSPDRTWALAEQLQPKLPML 85 Query: 67 KYIFNEYKKSTLIARYQGINNADGKYIILMDSDLQHPPKYLLNIYNSLLKHNDIVIASRY 126 + + + A G A G+ + ++D DLQHPP+ LL + ++ D+ +ASR Sbjct: 86 TVLRRQGDRGLATAVVYGWQRAQGEILGVIDGDLQHPPETLLALIQTMQAGADLAVASRN 145 Query: 127 VKGGSTGNRKPIRGIISRGASLMAQLLL-KSSRQIKDPISCYIGFRKGLKLDIDE-GWRG 184 V GG + R + SRGA L+ L+L + ++ DP+S Y R+ +LD+ RG Sbjct: 146 VSGGGVSDWSVWRRLGSRGAQLLGLLILPEVLGRVSDPMSGYFMVRRS-RLDLPSLQPRG 204 Query: 185 YEIGIFLRASNNNVKVKEIPYRFAERENGKSKVTS 219 Y+I + + A +++E+ + F ER G+SKVT+ Sbjct: 205 YKILLEVIAKGQIRQIREVGFIFRERSQGESKVTA 239 Lambda K H 0.320 0.140 0.396 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: 198 Number of extensions: 8 Number of successful extensions: 3 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: 246 Length of database: 388 Length adjustment: 27 Effective length of query: 219 Effective length of database: 361 Effective search space: 79059 Effective search space used: 79059 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: 48 (23.1 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