Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate RR42_RS30175 RR42_RS30175 beta-glucosidase
Query= SwissProt::E7CY69 (757 letters) >FitnessBrowser__Cup4G11:RR42_RS30175 Length = 708 Score = 322 bits (824), Expect = 6e-92 Identities = 229/677 (33%), Positives = 337/677 (49%), Gaps = 61/677 (9%) Query: 26 AWHLQGVESKGIPSYMITDGPHGLRKSLASSAGETDLDDSVPATCFPPAAGLSSSWNPEL 85 A +++GV GIP + D GLR TD D AT P + +++NP L Sbjct: 58 AGYVKGVPRLGIPPLKLADASLGLR--------HTDGPDDC-ATALPAGLAIGATFNPSL 108 Query: 86 IHKVGEAMAEECIQEKVAVILGPGVNIKRNPLGGRCFEYWSEDPYLAGHEAIGIVEGVQS 145 +G + +E V LG G+N+ R+ GR FEY SEDP L+G IV G Q Sbjct: 109 ARTIGNLIGKEARARDFNVALGGGINLVRDVRNGRNFEYISEDPLLSGLIGAEIVSGTQE 168 Query: 146 KGVGTSLKHFAANNQETDRLRVDARISPRALREIYFPAFEHIVKKAQPWTIMCSYNRING 205 +GV LKH + N ET++ +DA I P A RE AF+ ++K+QP +M +YN +NG Sbjct: 169 EGVIAVLKHVSLNASETNKFFLDAIIDPAAHRESDLLAFQIAIEKSQPGALMGAYNLVNG 228 Query: 206 VHSAQNHWLLTDVLRDEWGFDGIVMSDWGADHD-----RGASLNAGLNLEMPPSYTDDQI 260 ++ N +L + ++D GF G VMSDW A + G +AG L+ + + + Sbjct: 229 AYACGNRAILQETIKDAMGFKGWVMSDWLAVYGWEFALSGLDQHAGAQLDKQ-EWFNGPL 287 Query: 261 VYAVRDGLITPAQLDRMAQGMIDLVNKTRAAMSIDNYR----FDVDAHDEVAHQAAIESI 316 A G + ++ M + M+ ++ A+ ID R D AH+ VA QAA E I Sbjct: 288 RQAYEQGKVPKERISDMVRRML----RSYYAIGIDQQRAAAPVDFAAHNAVALQAAREGI 343 Query: 317 VMLKNDDAILPLNAGPVANPSATPQKIAVIGEFARTPRYQGGGSSHITPT---------K 367 V+LKN+ LPL AG Q+IA+IG +A+T G GSS + PT + Sbjct: 344 VLLKNEGQALPLAAGR--------QRIAIIGGYAQTGVLSGDGSSQVMPTSGYAAQVPLR 395 Query: 368 MTSFLDTLAERGIKADFAPGFTLDLEPADPALE-----SEAVETAKNADVVLMFLGLPEA 422 L T R + L A + ++AV AK AD+V+MF EA Sbjct: 396 SHPLLGTTVMRLFGSSPLAALRKQLPEAIIEFDCGAHIADAVAMAKRADIVVMFAYRHEA 455 Query: 423 VESEGFDRDTLDMPAKQIALLEQVAAANQNVVVVLSNGSVITVAPWAKNAKGILESWLLG 482 E FD + +P Q AL+E VA N+N++VVL G+ + + PW A+ I+++W G Sbjct: 456 ---ERFDSPDMTLPFGQDALIEAVANENRNLIVVLQTGNPVAM-PWRDKARAIVQAWFPG 511 Query: 483 QSGGPALADVIFGQVSPSGKLAQSIPLDINDDPSMLNWPGEEGH------VDYGEGVFAG 536 Q G A+A+V+ G+++PSG+L S P D+ P PG + V Y EG G Sbjct: 512 QLGAQAIAEVLTGKINPSGRLPISFPFDVGQTPHP-TLPGSDVELGTPIKVHYHEGAEVG 570 Query: 537 YRYYDTYGKAVDYPFGYGLSYATFEITGVAVAKTGANTATVTATVTNTSDVDAAETVQVY 596 YR++ G+ + FG+GLSYATF + V A + TV TVTNT + QVY Sbjct: 571 YRWFAKTGRQPLFGFGHGLSYATFAYRDLEV--VDAESLTVAFTVTNTGARQGDDVPQVY 628 Query: 597 VVPGKADVARPKHELKGFTKAFLKAGESKTVAIDLDERAFAYWSEKYNDWHVEAGEYAIE 656 + D + L GF + L+ GES V I D R A + + W +EAG+Y I Sbjct: 629 LTDAAGDW---RMRLLGFERVSLRPGESARVRITADPRLLACFQSELGCWRMEAGQYRIA 685 Query: 657 VGVSSRDIADTVAVALD 673 +G S++D+ ++ + L+ Sbjct: 686 LGRSAQDLELSIELCLE 702 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: 1172 Number of extensions: 54 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 757 Length of database: 708 Length adjustment: 40 Effective length of query: 717 Effective length of database: 668 Effective search space: 478956 Effective search space used: 478956 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