Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate N515DRAFT_3389 N515DRAFT_3389 alpha-glucosidase
Query= BRENDA::P21517 (604 letters) >FitnessBrowser__Dyella79:N515DRAFT_3389 Length = 673 Score = 305 bits (781), Expect = 4e-87 Identities = 201/566 (35%), Positives = 279/566 (49%), Gaps = 34/566 (6%) Query: 48 VPMHKQRSQPQPGVTAWRAAIDLSSGQPRRRYSFKLLWHDRQRWFTPQGFSRMPPARLEQ 107 V MH + P W+ + SS + + Y F+L W+ G S P+ + Sbjct: 97 VAMHWASNDPTGTFDYWQGTVPASSSE--KYYRFQLNDGSASAWYNAAGTSSSEPSSGDF 154 Query: 108 FAVDVPDIG-PQWAADQIFYQIFPDRFARSLPREAEQDHVYYHHAAGQEIILRDWDEPVT 166 + + P P W + + YQIFPDRF Q Y + GQ W V Sbjct: 155 YLI--PGFKTPDWMKNGVIYQIFPDRFYNGDTSNDVQTGQYSY--GGQSTQKVAWGGSVF 210 Query: 167 AQAGGST---FYGGDLDGISEKLPYLKK-LGVTALYLNPVFKAPSVHKYDTEDYRHVDPQ 222 A GS F+GGDL G+ +KL Y+K+ LG +YLNPVF +P+ HKYDTEDY HVDP Sbjct: 211 ATGSGSNNLVFFGGDLAGVDQKLGYIKQTLGANIVYLNPVFTSPTNHKYDTEDYYHVDPA 270 Query: 223 FGGDGALLRL----RHNTQQLGMRLVLDGVFNHSGDSHAWFDRHNR-GTGGACHNPESPW 277 FG + L L +T ++LDGVFNH+GD+ WFDR+N T GA + S W Sbjct: 271 FGSNTTLQTLIADVHASTNGPKGYVMLDGVFNHTGDTSQWFDRYNWWSTQGAYESTSSTW 330 Query: 278 RDWYSFSD-DGTALDWLGYASLPKLDY--QSESLVNEIYRGEDSIVRHWLKAPWNMDGWR 334 +Y+F GT + GY+++PKLDY ++ N+IY S+V+ WL +P+ +DGWR Sbjct: 331 YGYYTFQQWPGTYSSFYGYSTMPKLDYGASGSAVRNQIYGSTSSVVKTWLSSPYGIDGWR 390 Query: 335 LDVVHML---GEAGGARNNMQHVAGITEAAKETQPEAYIVGEHFGDARQWLQADVE-DAA 390 LD + G G N Q +A + A K A I+GE +G+A W E D+A Sbjct: 391 LDAPQYIDAGGNNGSDAINHQIMAELRTAVKAVNANAEILGEFWGNANPWTGNGKEWDSA 450 Query: 391 MNYRGFTFPLWGFLANTDISYDPQQIDAQTCMAWMDNYRAGLSHQQQLRMFNQLDSHDTA 450 +NY GFT P+ ++ D S + I A +W+ RA Q M N L SHD Sbjct: 451 LNYDGFTQPVSEWITGYDYSGNAASIPASQFDSWLHGTRANYPGNVQQTMANFLSSHDIQ 510 Query: 451 RFKTLLGRDIARLPLAVVWLFTWPGVPCIYYGDEVGLDGKNDPFCRKPFPWQVEKQDTAL 510 RF G DI + LA+++ T+ G P IYYGDE G+ G NDP R+ F W A Sbjct: 511 RFAQRAGGDIWKTYLALIFQMTYVGTPTIYYGDEYGMQGGNDPDNRRTFDWTQGSTTNAA 570 Query: 511 FALYQRMIALRKKSQALRHGGCQVLYAEDN--VVVFVRVLNQQRVLVAINR-GEACEVVL 567 AL Q++IA+R + ALR G L +D+ + + R RV VA+N A V + Sbjct: 571 VALTQKLIAIRNQYAALRTGSFMSLLTDDSNKLYAYGRFDASHRVAVALNNDSTAHSVTV 630 Query: 568 PASPFLNAVQWQCKEGHGQLTDGILA 593 P WQ +G +L+ Sbjct: 631 PV--------WQLSMANGSAVTDLLS 648 Lambda K H 0.322 0.138 0.451 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: 1226 Number of extensions: 74 Number of successful extensions: 9 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: 673 Length adjustment: 38 Effective length of query: 566 Effective length of database: 635 Effective search space: 359410 Effective search space used: 359410 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: 54 (25.4 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