Align α-glucosidase (CmmB) (EC 3.2.1.20) (characterized)
to candidate HSERO_RS11645 HSERO_RS11645 alpha-amylase
Query= CAZy::BAI67603.1 (567 letters) >FitnessBrowser__HerbieS:HSERO_RS11645 Length = 1121 Score = 208 bits (530), Expect = 8e-58 Identities = 171/554 (30%), Positives = 255/554 (46%), Gaps = 82/554 (14%) Query: 20 WRDAVVYQVYLRSFRDANGDGIGDLGGLSQGLDAIAALGCDAIWLNPCYASPQRDHGYDI 79 ++DAV+YQ++++S+ DAN DGIGD GL Q LD I LG + IWL P Y SP+RD GYDI Sbjct: 10 YKDAVIYQIHVKSYFDANDDGIGDFAGLIQKLDYITGLGVNTIWLLPFYPSPRRDDGYDI 69 Query: 80 ADYLTIDPAYGTLEEFDEVVRRAHELGLRVLMDMVANHCSSDHAWFQAALAAEPGSDERA 139 ++Y + P YG + + + AHE GLRV+ ++V NH S H WFQ A A PGS R Sbjct: 70 SEYKNVHPDYGNMSDVRRFIAAAHEHGLRVITELVINHTSDQHPWFQRARRARPGSVARN 129 Query: 140 RFIFRDGLGPDGELPPNNWDSVFGGLAWTRVTERDGRPGQWYLHSFDTSQPDFDWRHPAV 199 +++ D + D+ W V + ++ H F + QPD ++ +P V Sbjct: 130 FYVWSDDDKSYADTRIIFVDTEKSNWTWDPVAK------AYFWHRFYSHQPDLNFDNPHV 183 Query: 200 AEHFENVLRFWFERGVDGFRIDVAHGHFKDAALPDHPGGRGPDAGHNHGMWDQPEVHDLY 259 + NV+ FW + G+DG R+D L + G + PE H + Sbjct: 184 LKAVLNVMSFWLDLGIDGLRLDAV------PYLIEREGTSNENL---------PETHAIL 228 Query: 260 RSWRALGDAYEPEKYFVGE--IWVPSPDRLADYL-RPDELHNAFSFDLLVQPWNA----D 312 + RA D+ P++ + E +W P+ + Y DE H AF F L+ + + A D Sbjct: 229 KRIRAEMDSKYPDRMLLAEANMW---PEDVQQYFGDSDECHMAFHFPLMPRMYMALASQD 285 Query: 313 RFRKAIETGLAVGRGWPA---WT--LANHD--VHRAVTRYGQEQPLDEALP---TDMIAA 362 RF I L PA W L NHD VT ++ + P + Sbjct: 286 RF--PITDILRQTPDIPADCQWAIFLRNHDELTLEMVTDAERDYLWNHYAPDRRARINLG 343 Query: 363 ARRRGPADLDRGLRRARAAAALALALPGSMYLYQGEELGLPEVLDLPDAARQDPIWTRSN 422 RRR ++R RR + + L++PG+ +Y G+E+G+ + + L D Sbjct: 344 IRRRLAPLVERDWRRIQLLNSFLLSMPGTPVIYYGDEIGMGDNIHLGD------------ 391 Query: 423 GTELGRDGCRIPLPWTREGRTFGFSDAAAATTWLP---QPAW-FGAFARATQAADPDSML 478 RDG R P+ WT + R GFS A LP P + + Q+AD SML Sbjct: 392 -----RDGVRTPMQWTPD-RNGGFSRVDPARLVLPLLMDPQYGYQTINVEAQSADRHSML 445 Query: 479 SLHRDLLATRRTHL---RGTEPIVWLSPAGAEVLAFRRGDVVVVTNFGSAPFTPPSAWGA 535 + R LL R+ H RG+ +V+ P+ ++ A+ R FT P GA Sbjct: 446 NWMRRLLNVRKQHQAFGRGSLALVY--PSNRKIFAYLR------------EFTDPRPGGA 491 Query: 536 LSPLLASQPLTGSA 549 +L ++ SA Sbjct: 492 TETILCVANVSQSA 505 Lambda K H 0.321 0.138 0.454 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: 1858 Number of extensions: 115 Number of successful extensions: 5 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: 567 Length of database: 1121 Length adjustment: 41 Effective length of query: 526 Effective length of database: 1080 Effective search space: 568080 Effective search space used: 568080 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: 55 (25.8 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