Align Maltose or maltodextrin glucosidase (EC 3.2.1.20) (characterized)
to candidate CCNA_02369 CCNA_02369 alpha-amylase
Query= reanno::Korea:Ga0059261_1581 (604 letters) >FitnessBrowser__Caulo:CCNA_02369 Length = 604 Score = 686 bits (1771), Expect = 0.0 Identities = 347/602 (57%), Positives = 417/602 (69%), Gaps = 18/602 (2%) Query: 9 TLLAGTVASA---------QTAAPAELRARAAETEVLYFLLPDRFENGDPSNDRGGLRGD 59 TLLA T SA AAP R + EV+YF+LPDRFENGD +ND GG Sbjct: 10 TLLAMTAVSALGMDAMTTAAAAAPDPYLQRKPQDEVIYFVLPDRFENGDATNDHGGPALG 69 Query: 60 RLTTGFDPAHKGFFHGGDLKGLIRRLDYIQSLGASAIWLGPIYKNKPVQGGPGQETAGYH 119 L GFDPA GF+HGGDLKG+ RRLDYIQ LGA+A+WL PI+ N+ VQG PGQE+A +H Sbjct: 70 ALADGFDPARAGFYHGGDLKGVTRRLDYIQGLGATAVWLAPIFVNRAVQGPPGQESAAHH 129 Query: 120 GYWITDFTRVDPHFGTNDEMKAFVDAAHARGIKVYLDIITNHTADVIQYRECPKSACDYR 179 GYWITDFT VDPH GT + KA VDAAHARG+KVY+DI+ NHTADVIQY+ECP + C YR Sbjct: 130 GYWITDFTDVDPHLGTKADFKALVDAAHARGMKVYMDIVLNHTADVIQYKECPDNRCAYR 189 Query: 180 SRADYPYQRKGGVKGAAINPGFAGDGVQTPENFAKLSDPNYAYTTVVPEAERTVKVPAWL 239 +DYPY R+GGV GA IN GF G ++F+KL P++AYT VP + K PAWL Sbjct: 190 GVSDYPYVRRGGVDGAPINDGFDG------KDFSKLKRPDWAYTPYVPPGQERAKTPAWL 243 Query: 240 NDPIHYHNRGNTTFRNESSTMGDFVGLDDLMTESPRVLQGFIDIYGAWIDQFGIDGFRID 299 NDPI+YHNRG++TF ESS +GDF LD + TE PRV++GFI++YG WID FGIDG+RID Sbjct: 244 NDPIYYHNRGDSTFAGESSLLGDFATLDGVFTEHPRVVEGFIEVYGRWIDDFGIDGYRID 303 Query: 300 TARHVNPEFWQGFSKAMIERAKARGIPNFHIFGEVANEGDVGDLALHTRVHQLPSVLDFG 359 TARHVNPEFWQ F AM+ RAKA+GI NFHIFGEV + DV LA H +V +LP+VLDF Sbjct: 304 TARHVNPEFWQAFVPAMLARAKAKGIENFHIFGEVF-DADVATLARHVKVDKLPTVLDFA 362 Query: 360 FRAAVQHTVAGEKGPDMLAAMFDRDALYEGGAEAALRLPTFISNHDHGRFSTDVRKAFPK 419 F+AAV G GPD LA++F D +YEGG A +LPTF+ NHD GR V KA PK Sbjct: 363 FQAAVTDVALGRAGPDRLASVFAGDVVYEGGEATARQLPTFLGNHDMGRIGHFVLKAHPK 422 Query: 420 ASDDEVLARVKLAHAMLLLLRGVPTIYSGDEQGFVSDGNDQDAREDMFPSKVAIYNDNRL 479 DD +LAR+ LA+A++L RGVPTIY GDEQGF DG+ D+REDMFPS+VA YNDNRL Sbjct: 423 IGDDALLARITLANAIMLTARGVPTIYYGDEQGFTGDGDYADSREDMFPSQVASYNDNRL 482 Query: 480 LGTDKTTADSNFDTGHPLYMEISKLSAIRKATPALSRGRQVTRAYDEKPGLFAVSRFDPA 539 +G+ + F T LY I+ L+ +R TPAL GRQVTR + KPGL A SR Sbjct: 483 VGSSAKGPRTAFQTDSVLYRRIAALAKLRGMTPALREGRQVTRIAEGKPGLLAFSRL--M 540 Query: 540 SGAEVLVAFNTSAAPITRQVEVGVSSTAFAPLVGQCAASASAPGSVTVTLPAFGYVACVA 599 +G EVL FNTS PI +V V + S A+ L G C +SA APGS V L F Y+ CV+ Sbjct: 541 AGTEVLAVFNTSDKPIKARVPVEMGSAAWKSLHGACISSAVAPGSYAVELAPFDYMICVS 600 Query: 600 AG 601 G Sbjct: 601 EG 602 Lambda K H 0.319 0.136 0.411 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: 1211 Number of extensions: 58 Number of successful extensions: 4 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: 604 Length of database: 604 Length adjustment: 37 Effective length of query: 567 Effective length of database: 567 Effective search space: 321489 Effective search space used: 321489 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 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