Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate WP_066328323.1 BLR17_RS01490 glycosyl hydrolase
Query= SwissProt::E7CY69 (757 letters) >NCBI__GCF_900100165.1:WP_066328323.1 Length = 744 Score = 389 bits (999), Expect = e-112 Identities = 231/699 (33%), Positives = 370/699 (52%), Gaps = 43/699 (6%) Query: 9 VKDLTLEEKASLTSGGDAWHLQGVESKGIPSYMITDGPHGLRKSLASSAGETDLDDSVPA 68 + +TLEEK + G + GV GIP + DGP G+R+ ++ + + D+ A Sbjct: 53 ISKMTLEEKIGMLHGNSMFANGGVPRLGIPELKMADGPLGVREEISRDSWKPAGLDNDFA 112 Query: 69 TCFPPAAGLSSSWNPELIHKVGEAMAEECIQEKVAVILGPGVNIKRNPLGGRCFEYWSED 128 T +P + L+++WN + G ++ +E ++L P +NI R PLGGR +EY +ED Sbjct: 113 TYYPASGALAATWNTRMASLFGNSVGQELRARDKDMLLSPAINIVRTPLGGRTYEYMTED 172 Query: 129 PYLAGHEAIGIVEGVQSKGVGTSLKHFAANNQETDRLRVDARISPRALREIYFPAFEHIV 188 P+L A+ +V +Q V +KHFAANNQET+R VD +I R LREIY P FE + Sbjct: 173 PFLNKKMAVPLVVSLQDNDVMACVKHFAANNQETNRDFVDVQIDERTLREIYLPTFEATI 232 Query: 189 KKAQPWTIMCSYNRINGVHSAQNHWLLTDVLRDEWGFDGIVMSDWGADHDRGASLNAGLN 248 K+ +++M +YN+ G + +N ++L +LRDEWGF G+V+SDW A H SL GL+ Sbjct: 233 KEGNVYSVMGAYNKFRGEYLCENDYMLNTILRDEWGFKGVVVSDWAAVHSTVKSLQNGLD 292 Query: 249 LEMPPS------YTDDQIVYAVRDGLITPAQLDRMAQGMIDLVNKTRAAMSIDNYR--FD 300 +EM + D+++ AV+ G ++ ++D+ + ++ ++ + +A D + Sbjct: 293 IEMGSKKPFNEYFLADKLIAAVKAGEVSEKEIDKHVKRILHVLFQVKAMDGKDRVKGSLA 352 Query: 301 VDAHDEVAHQAAIESIVMLKNDDAILPLNAGPVANPSATPQKIAVIGEFARTPRYQGGGS 360 ++H + A++ A E++V+LKN++ LPL + + IAVIG A GG Sbjct: 353 TESHYQDAYEIASEAVVLLKNNNNALPLKLDGI-------KSIAVIGNNATKKNALGGFG 405 Query: 361 SHITPTKMTSFLDTLAER---GIKADFAPGF-------------------TLDLEPADPA 398 + + + + L+ L R IK ++A G+ + ++ D A Sbjct: 406 AGVKTKREITPLEGLKNRLPASIKINYAEGYLERYEKKNKGNLGNITSKGPVTIDQLDDA 465 Query: 399 LESEAVETAKNADVVLMFLGLPEAVESEGFDRDTLDMPAKQIALLEQVAAANQNVVVVLS 458 EA+E KN+ ++F G E+E DR L +P Q L+++V A N +VV+ Sbjct: 466 KLQEALEAVKNSGAAIIFAGSNRDYETEASDRKDLKLPFGQEELIKKVLAINPKTIVVMI 525 Query: 459 NGSVITVAPWAKNAKGILESWLLGQSGGPALADVIFGQVSPSGKLAQSIPLDINDDPSML 518 G+ + +K ++ SW G GG ALADV+ G+V+PSGKL ++P + D P+ Sbjct: 526 AGAPFEMEEISKKTNALVWSWFNGSEGGNALADVLLGKVNPSGKLPWTMPKKLMDSPAHA 585 Query: 519 --NWPGEEGHVDYGEGVFAGYRYYDTYGKAVDYPFGYGLSYATFEITGVAVAKTGAN--- 573 ++PG++ V+Y EG+ GYR++DT + YPFGYGLSY F K N Sbjct: 586 TNSFPGDK-TVNYAEGILVGYRWFDTKKISPMYPFGYGLSYTNFTFGKAFSDKEIYNNDE 644 Query: 574 TATVTATVTNTSDVDAAETVQVYVVPGKADVARPKHELKGFTKAFLKAGESKTVAIDLDE 633 T+ + NT VD E VQ+Y + + R ELKGFTK +KAG ++ V I + Sbjct: 645 VITIAVDLKNTGKVDGKEVVQLYSSKTDSKIDRAAQELKGFTKILVKAGATQKVIIKVPV 704 Query: 634 RAFAYWSEKYNDWHVEAGEYAIEVGVSSRDIADTVAVAL 672 + AY+ W VE G+Y +++G SSRDI + V + Sbjct: 705 KELAYYDVANKKWTVEPGKYKLKLGNSSRDIKKEIDVII 743 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: 1279 Number of extensions: 56 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: 744 Length adjustment: 40 Effective length of query: 717 Effective length of database: 704 Effective search space: 504768 Effective search space used: 504768 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 24 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