Align Sucrose alpha-glucosidase (EC 3.2.1.48) (characterized)
to candidate AO353_25135 AO353_25135 glycosyl hydrolase family 32
Query= reanno::pseudo1_N1B4:Pf1N1B4_5116 (489 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25135 Length = 489 Score = 961 bits (2485), Expect = 0.0 Identities = 444/489 (90%), Positives = 468/489 (95%) Query: 1 MSAALEIAQHALSDGLSRVTDDYRPGYHLAPPAGWMNDPNGVVYFRGEYHVFYQHHPFDA 60 MS++L++AQ ALSDGLSRV DYRPGYH+APPAGWMNDPNGVVYFRGEYHVFYQH+PF+A Sbjct: 1 MSSSLDLAQRALSDGLSRVIHDYRPGYHIAPPAGWMNDPNGVVYFRGEYHVFYQHYPFEA 60 Query: 61 KWGPMYWGHAKSADLVHWQHLPIALAPGDDFDRDGCFSGSAVVCGDTLALIYTGHTWLGE 120 KWGPMYWGHAKSADLVHWQHLPIALAPGDDFDRDGCFSGSAVVCGDTLALIYTGHTWLGE Sbjct: 61 KWGPMYWGHAKSADLVHWQHLPIALAPGDDFDRDGCFSGSAVVCGDTLALIYTGHTWLGE 120 Query: 121 VGDERYIRQVQCLATSTDGIQFVKHGAVIDTAPQDTIMHFRDPKVWQEDDGWYLIAGARL 180 GDER IRQVQCLATS DGI+FVKHGAVI+T PQDTIMHFRDPKVW+EDD WYLIAGARL Sbjct: 121 AGDERSIRQVQCLATSIDGIRFVKHGAVIETPPQDTIMHFRDPKVWKEDDCWYLIAGARL 180 Query: 181 GDVPLLPLYRSTDLHSWEFLDYVSSGSEGDGYMWECPDLFRLNGRDVLLYSPQGMQPEGY 240 GD+PLLPLYRSTDLH+WEFL YVS GSEGDGYMWECPDLFRLNGRDVLLYSPQGMQP+GY Sbjct: 181 GDIPLLPLYRSTDLHAWEFLGYVSGGSEGDGYMWECPDLFRLNGRDVLLYSPQGMQPQGY 240 Query: 241 ERLNKYQTGYRVGRLDSQWHFTGGPFIELDNGHDFYAAQTLLAADGRRLVWAWLDMWESP 300 ERLNKYQTGYRVGRLDS+WHFTGGPFIELDNGHDFYAAQTLLAADGRRL+WAWLDMWESP Sbjct: 241 ERLNKYQTGYRVGRLDSEWHFTGGPFIELDNGHDFYAAQTLLAADGRRLLWAWLDMWESP 300 Query: 301 MPSQAHHWCGMLGVPRELELHADRLCVYPARELTALRMAPLPGVSWWEGSGSRWVPEVNG 360 MPS+AHHWCGMLG+PRELEL ADRLCVYPARELTALR APLPG WW+ SG+RWVPEV G Sbjct: 301 MPSKAHHWCGMLGLPRELELRADRLCVYPARELTALRKAPLPGTPWWDESGTRWVPEVKG 360 Query: 361 DMLEIHVHLDLRGCTSGHLGIALRCSDDGHEETLLYYDASLQRLVLDRSRAGAQVTGQRS 420 DMLEIHVHLDL GCT GHLGIALRCSDDG+EETLLYYDASLQRLVLDRSR+GAQ TGQRS Sbjct: 361 DMLEIHVHLDLLGCTDGHLGIALRCSDDGYEETLLYYDASLQRLVLDRSRSGAQATGQRS 420 Query: 421 VSIDPTQERLELRVFLDRSSIEVFDENGRFSLSSRLYPRPDSLGVKLFANGSGGRVSIPK 480 VSIDPTQERLELRVFLDRSSIEVFDENGRFSLSSRLYP+P SLGVKL A+GSGGRVSIP+ Sbjct: 421 VSIDPTQERLELRVFLDRSSIEVFDENGRFSLSSRLYPQPGSLGVKLLASGSGGRVSIPR 480 Query: 481 AWPLASGWL 489 AWPLASGWL Sbjct: 481 AWPLASGWL 489 Lambda K H 0.321 0.140 0.465 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: 1228 Number of extensions: 55 Number of successful extensions: 1 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: 489 Length of database: 489 Length adjustment: 34 Effective length of query: 455 Effective length of database: 455 Effective search space: 207025 Effective search space used: 207025 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 (21.9 bits) S2: 52 (24.6 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