Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate Ga0059261_2310 Ga0059261_2310 Beta-glucosidase-related glycosidases
Query= SwissProt::E7CY69 (757 letters) >FitnessBrowser__Korea:Ga0059261_2310 Length = 762 Score = 236 bits (602), Expect = 3e-66 Identities = 188/596 (31%), Positives = 273/596 (45%), Gaps = 50/596 (8%) Query: 69 TCFPPAAGLSSSWNPELIHKVGEAMAEECIQEKVAVILGPGVNIKRNPLGGRCFEYWSED 128 T FP G ++S++P L + A + E + P V++ R+ GR E ED Sbjct: 134 TIFPVPVGEAASFDPALAERTAAAASYEAAAAGIDWTFAPMVDVARDQRWGRTMEGAGED 193 Query: 129 PYLAGHEAIGIVEGVQS---KGVGTSL---KHFAANNQETDRLRVDA-RISPRALREIYF 181 +L A V+G Q K + T + KHFAA L + +S R LRE+YF Sbjct: 194 VHLGNLFAAARVKGFQGASLKAIDTMMACAKHFAAYGAAEAGLDYNTVDVSERTLREVYF 253 Query: 182 PAFEHIVKKAQPWTIMCSYNRINGVHSAQNHWLLTDVLRDEWGFDGIVMSDWGADH---D 238 P F+ A + M S+N I+G+ S N WL+ VLRDEW + G V+SD+ D D Sbjct: 254 PPFQAAFG-AGALSAMSSFNEISGIPSNGNEWLMRTVLRDEWKYQGFVVSDYTGDMEMID 312 Query: 239 RGASLNA----------GLNLEMPPSYTDDQIVYAVRDGLITPAQLDRMAQGMIDLVNKT 288 G + +A G+++ M + D + V G + A++D + ++ + K Sbjct: 313 HGFAADAREATKIAFMAGVDMSMTSGFYRDHLPDLVEKGEVPMARVDESVRKVLAI--KA 370 Query: 289 RAAMSIDNYRFDVDAHDEVAH-----------QAAIESIVMLKNDDAILPLNAGPVANPS 337 + + D +R +D E A + A +SIV+LKN+ +LPL G Sbjct: 371 KLGLFEDPFR-RIDEKREAARSRTKATLALSREMAKKSIVLLKNEGDVLPLRKGG----- 424 Query: 338 ATPQKIAVIGEFARTPRYQGGGSSHITPTKMTSFLDTLAER--GIKADFAPGFTLDLEPA 395 QKIA+IG FA G K+ L+T G A +E Sbjct: 425 ---QKIAIIGPFAAGQHDLNGPWCVYGDNKLAIDLETGVRNALGKNAQITVVEGSQVEAP 481 Query: 396 DPALESEAVETAKNADVVLMFLGLPEAVESEGFDRDTLDMPAKQIALLEQVAAANQNVVV 455 P AV A+NADVVL+ +G E + E R ++ +PA Q AL E VAA + V+V Sbjct: 482 LPGGIEAAVAAARNADVVLLAIGESERMSGEAQSRTSITVPAPQQALAEAVAATGKPVIV 541 Query: 456 VLSNGSVITVAPWAKNAKGILESWLLGQSGGPALADVIFGQVSPSGKLAQSIPLDINDDP 515 VL NG + + KNA IL +W LG G A+ADV+FG SPSG+L S P + P Sbjct: 542 VLKNGRALALEGAVKNAPAILVTWFLGSESGNAIADVLFGDYSPSGRLPMSFPREPGQQP 601 Query: 516 SMLNWPGEEGHVDYGEGVFAGYR-YYDTYGKAVDYPFGYGLSYATFEITGVAVAK---TG 571 + G + + Y+ +Y + + YPFG+GL+Y + + K Sbjct: 602 FYYSHK-PTGRPNPSDDKLEEYKTHYRSIPNSALYPFGHGLTYGKIDYANLTPDKGTLAW 660 Query: 572 ANTATVTATVTNTSDVDAAETVQVYVVPGKADVARPKHELKGFTKAFLKAGESKTV 627 TAT+TN A E VQ+Y+ A + RP ELK F K L G S+TV Sbjct: 661 DGEIAFTATITNRGTRAAEEVVQLYIRDRAASITRPVRELKAFRKIALAPGASETV 716 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: 1250 Number of extensions: 63 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: 757 Length of database: 762 Length adjustment: 40 Effective length of query: 717 Effective length of database: 722 Effective search space: 517674 Effective search space used: 517674 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