Align Alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate N515DRAFT_3393 N515DRAFT_3393 alpha-glucosidase
Query= reanno::ANA3:7025148 (540 letters) >FitnessBrowser__Dyella79:N515DRAFT_3393 Length = 541 Score = 744 bits (1922), Expect = 0.0 Identities = 350/522 (67%), Positives = 407/522 (77%), Gaps = 9/522 (1%) Query: 1 MSELTWWRGAVIYQIYPRSLLDTNGDGVGDLRGIITKLDYIASLNVDAIWISPFFKSPMA 60 MSE WWRGAVIYQIYPRS LDT+GDGVGDL GI+ +LDYIA L VDAIWI+PFF+SPMA Sbjct: 1 MSETPWWRGAVIYQIYPRSFLDTDGDGVGDLPGIVERLDYIAGLGVDAIWIAPFFRSPMA 60 Query: 61 DFGYDISDYREVDPLFGTMQDFDELIEKAHQRGIKVIIDQVLSHTSDQHAWFCESRESRT 120 DFGYDI+DYR VDPLFGT+ DFD L+ KAH G+KV+IDQVLSHTSDQH WF ESR SR Sbjct: 61 DFGYDIADYRAVDPLFGTIDDFDRLLAKAHALGLKVMIDQVLSHTSDQHEWFKESRASRD 120 Query: 121 NPKADWYVWAEPKEDGTAPNNWLAIFGGCAWEWEPRRQQYYLHNFLRSQPDINFHNPDVR 180 NPKADWYVWA+ ++DGT PNNW+++FGG AW+WEPRR QYYLHNFL SQPD+NFH+PDV+ Sbjct: 121 NPKADWYVWADARDDGTPPNNWMSLFGGVAWQWEPRRGQYYLHNFLTSQPDLNFHHPDVQ 180 Query: 181 QAVLDNVEFWLKKGVDGFRLDAITFCYHDEQLRDNPPKPKDKRQGRGFSEDNPYAYQYHY 240 +AVLDNV+FWL KGVDG RLDAI FC+HD QLRDNPPKP+ R GRGFS DNPYA+QYHY Sbjct: 181 RAVLDNVQFWLDKGVDGLRLDAINFCFHDRQLRDNPPKPQAMRVGRGFSPDNPYAFQYHY 240 Query: 241 YNNDRPQTILFIEELRQLINRYPGAVTLGEVSAEDSLAVMAAYTKGEDRLHMAYSFELLT 300 YNN +P+ + F+EELR L++RYPGA LGE+S+EDSLA MA YT G RLHM YSFELLT Sbjct: 241 YNNTQPENLAFLEELRGLLDRYPGAAALGEISSEDSLATMAEYTTGH-RLHMGYSFELLT 299 Query: 301 DDYSAAYIRQTVEALEASIGDGWPCWAIGNHDAQRVASRWGR-----GKQTSDMVKMLNA 355 D+SAAYIR TVE LEA + +GWPCWAI NHD +RV SRWGR G + + +L A Sbjct: 300 ADFSAAYIRGTVERLEAQMTEGWPCWAISNHDVERVLSRWGREARGNGDASVRLANLLTA 359 Query: 356 MVNSLRGSVCSYQGEELGLTEAPIEYHELQDPFGKTFWPMFKGRDGCRTPMPWEQNADFS 415 MV SLRGSVC YQGEEL LTEA + Y LQDP+G TFWP FKGRDGCRTPMPW+++A+ + Sbjct: 360 MVCSLRGSVCVYQGEELALTEAEVPYEALQDPYGITFWPNFKGRDGCRTPMPWDESAN-A 418 Query: 416 GFSQVTPWLPIAQAHRALAVDVQEADSQSMLHGYRQFLAWRKGYPALVEGEIEFLDAPEP 475 GFS PWLP+ HRALAV QE D S LHG+R F+ WR+ P L G I FLD PEP Sbjct: 419 GFSSGAPWLPVPAGHRALAVSRQELDPASALHGFRGFMQWRQAQPELRWGAIGFLDTPEP 478 Query: 476 LLVFVRTSGEQKLLVCFNLQDTEQALSLDALSIQQEITGHGL 517 +L F RT + +L FNL A++L + I GHGL Sbjct: 479 VLAFTRTHAGETVLAAFNLGSAPVAVALPLAG--ERIGGHGL 518 Lambda K H 0.320 0.137 0.436 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: 1027 Number of extensions: 33 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: 540 Length of database: 541 Length adjustment: 35 Effective length of query: 505 Effective length of database: 506 Effective search space: 255530 Effective search space used: 255530 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: 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