Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate HSERO_RS20525 HSERO_RS20525 alpha-glucosidase
Query= BRENDA::F9VPH0 (641 letters) >FitnessBrowser__HerbieS:HSERO_RS20525 Length = 803 Score = 219 bits (557), Expect = 5e-61 Identities = 161/562 (28%), Positives = 258/562 (45%), Gaps = 48/562 (8%) Query: 56 EEHIVGLGEKATELDRKRFRYVMYNVDAGAYK-RFQDPLYANIPFFISIYK--GKATGYF 112 EE GLGE+A +++R Y M N+DA Y R DPLY +IPF+I+ G G F Sbjct: 149 EEMYFGLGERAGDMNRAGQSYEMRNIDAMGYSARNTDPLYKHIPFYITWLPKTGAGFGLF 208 Query: 113 VNSASKVIIDVG------FTHYSKVIITIPHKDVEIYVFEGP-TPEKVIEKYTDVTGKPY 165 ++ S D+G HY T PH D++ Y P TP ++T +TG+P Sbjct: 209 YDTLSDCRFDMGRELDNYHGHYR--YFTAPHGDLDYYFIASPGTPLAATRRFTWLTGRPA 266 Query: 166 LPPKWAFGYLISRFSYFPQ-DEIVKLLDLMKEFKVTGIFLDIDYMDS--------YKLFT 216 PKW GY S SY D V++ + + + I D ++ S +F Sbjct: 267 WMPKWGLGYSGSTMSYTDAPDAQVQMGQFIAKCREHDILCDSFHLSSGYTSIGPKRYVFH 326 Query: 217 WDKEKFPDVKKFIEEVHGRGVKIITIVDHSIKADQNYDVFLSGLGKYCETDKGELFVGKL 276 W+ EKFPD F+ + + + + D G +GE + Sbjct: 327 WNTEKFPDPHGFVRSYLDASIHLCANIKPCLLRDHPQFEQARQAGLLICDSQGEPAWVQF 386 Query: 277 WPGNSVYPDFFREETRKWWSELISK-WLSQGIDGIWLDMNEPTDFSQYKEGGDRLLLAFP 335 W Y DF T WW + + L G+ W D NE ++ GD F Sbjct: 387 WDEVGAYLDFTNPATLDWWRANVKQALLDYGVSATWNDNNEFEVWT-----GDAYAHGFG 441 Query: 336 KNVIHYHKGKKVYHELVRNAYPYYEAMATYEGFKNKEEVFILTRGGYAGIQKFAGIWTGD 395 + + K + L+ A + A + F+++R G AG+Q++ W+GD Sbjct: 442 QQY-PVRQAKVLQTMLMMQASRQAQLEAAPQ-----RRPFLVSRSGGAGMQRYVQTWSGD 495 Query: 396 NTPSWDDLKLQLQLILGLSISGIAYIGIDIGGFQGRGFEKIDNSLELLVKYFEIAMFFPM 455 N SW+ L+ L++ LGL++SG++ IG DIGGF G + ELLV++ +F P Sbjct: 496 NYTSWETLRYNLKMGLGLALSGVSNIGHDIGGFSGPA-----PAPELLVRWVAFGVFMPR 550 Query: 456 FRTHKGKDGIDTEPTFLPDYYKERVKRVIETRYNFLSYIYSLAIEAHETGHPIIRPLFYE 515 F H D ++ ++ +I+ RY F+ Y+Y L ++ + P++RP F E Sbjct: 551 FSIHSWNDDKTVNEPWMYPEVTAQIAALIKLRYRFIPYLYELLWQSTQDYQPVLRPTFAE 610 Query: 516 FPDDENTYRIDDEYLVGKHVLYAPIIEKSD-KRIVYLPRKSKWMEFWNQEISEGWVNSKS 574 FP D D+ ++G +L AP++E+ +R VYLP ++W+ +W+ E EG + Sbjct: 611 FPHDRRCLDECDDMMLGSAMLVAPVVEQGQTERRVYLPSGARWVSYWSGERYEG--GQEI 668 Query: 575 NLP-------IYIREGSLIQLD 589 +LP + +REG++I ++ Sbjct: 669 SLPAPWDQPVMLLREGAVIPMN 690 Lambda K H 0.321 0.142 0.432 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: 1314 Number of extensions: 77 Number of successful extensions: 8 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: 641 Length of database: 803 Length adjustment: 40 Effective length of query: 601 Effective length of database: 763 Effective search space: 458563 Effective search space used: 458563 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