Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate H281DRAFT_00016 H281DRAFT_00016 beta-glucosidase
Query= SwissProt::E7CY69 (757 letters) >FitnessBrowser__Burk376:H281DRAFT_00016 Length = 763 Score = 302 bits (774), Expect = 4e-86 Identities = 225/702 (32%), Positives = 331/702 (47%), Gaps = 62/702 (8%) Query: 23 GGDAWHLQGVESKGIPSYMITDGPHGLRKSLASSAGETDLDDSVPATCFPPAAGLSSSWN 82 G H+ G+ + IP++ IT+GP G+ G D AT P + L++S++ Sbjct: 88 GNSIRHIPGIPALSIPTFRITNGPVGI--------GAGDCVPQDRATALPMSMALAASFD 139 Query: 83 PELIHKVGEAMAEECIQEKVAVILGPGVNIKRNPLGGRCFEYWSEDPYLAGHEAIGIVEG 142 P L G+ + E + V+ PG+N R GGR FEY SEDP LAG A + G Sbjct: 140 PTLARAYGDVLGREARMLGLHVVEAPGMNAVRVGQGGRNFEYLSEDPVLAGVIAENEIRG 199 Query: 143 VQSKGVGTSLKHFAANNQETDRLRVDARISPRALREIYFPAFEHIVKKAQPWTIMCSYNR 202 Q+ GV KHF N QE +R V + R L EIY F V++ ++MCSYNR Sbjct: 200 AQATGVIAMAKHFILNEQEANRNTVSVVVDDRTLHEIYLLPFGVSVRRGNVASVMCSYNR 259 Query: 203 INGVHSAQNHWLLTDVLRDEWGFDGIVMSDWGADHDRGASLNAGLNLEMPPS--YTDDQI 260 I ++ + L +LR E GF G V SD+GA H +LNAGL+LEM +T + Sbjct: 260 IGSTYACETPRALNAILRGELGFMGYVQSDFGATHSTAPALNAGLDLEMQSGIWFTPPNL 319 Query: 261 VYAVRDGLITPAQLDR------MAQGMIDLVNKTRAAMSIDNYRFDVDAHDEVAHQAAIE 314 A+ G +T A +++ + ++ A +D+ D + A + Sbjct: 320 NAALATGQLTMATVNQALTRRYTQMFKAGIFDRPVARTPLDSTTIQNDGTE--ARVIGEQ 377 Query: 315 SIVMLKNDDAILPLNAGPVANPSATPQKIAVIGE--FARTPRYQGGGSSHITPT----KM 368 S V+LKN +LPL S + I ++G + G GSS + PT Sbjct: 378 SAVLLKNSGNLLPL--------SGAVKSITIVGHNTYVDDAIAGGSGSSRVVPTYTVGPQ 429 Query: 369 TSFLDTLAERGIKADFAPGFTLDLEPADPALESEAVETAKNADVVLMFLGLPEAVESEGF 428 + L + G A TL P D ++++ A ADV ++ G+ V EG Sbjct: 430 QGITNVLRQLGSSATVK---TL-AAPNDGSMDAAVAAAAATADVAIVMAGV---VTGEGS 482 Query: 429 DRDTLDMPAKQIALLEQVAAANQNVVVVLSNGSVITVAPWAKNAKGILESWLLGQSGGPA 488 DR L +P Q L+ VA N+ +VVL +G + + PW ILE+W GQ G Sbjct: 483 DRPDLSLPKGQDKLIAAVANRNERTIVVLKDGDPV-LMPWVDQVPAILETWYSGQEDGNV 541 Query: 489 LADVIFGQVSPSGKLAQSIPLDINDDPSML--NWPGEEGH---VDYGEGVFAGYRYYDTY 543 +A ++FG +PSGKL + P D P+ + +PG G V Y EG+ GYR+YDT Sbjct: 542 VARLLFGLANPSGKLPVTYPRLATDTPTSMPDRYPGTSGSDPVVQYSEGLLVGYRWYDTR 601 Query: 544 GKAVDYPFGYGLSYATFEITGVAVAK---TGANTATVTATVTNTSDVDAAETVQVYV-VP 599 + FG+GLSY +F+I+ V V+ TG V TV NT + AE QVY+ +P Sbjct: 602 QVKPLFAFGHGLSYTSFKISDVQVSPRGYTGNGPILVALTVENTGLREGAEVAQVYLGLP 661 Query: 600 GKADVARPKHELKGFTKAFLKAGESKTVAIDL----DERAFAYWSEKYNDWHVEAGEYAI 655 ++ P L F K LK GE + +++ + A +YW W + AG Y + Sbjct: 662 --PNLGEPTKRLIAFQKVLLKPGEKRALSMYIYPINGFHALSYWDNAAQSWKIAAGTYTV 719 Query: 656 EVGVSSRDIAD----TVAVAL--DGDGKTQPLTEWSTYG-EW 690 VG +S +I TV VA+ GDG + + +G +W Sbjct: 720 YVGNASDNIVAQSTFTVNVAMRDTGDGDDNVSRDPAPFGWDW 761 Lambda K H 0.315 0.132 0.393 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: 1271 Number of extensions: 59 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: 757 Length of database: 763 Length adjustment: 40 Effective length of query: 717 Effective length of database: 723 Effective search space: 518391 Effective search space used: 518391 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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