Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate Pf6N2E2_2809 Periplasmic beta-glucosidase (EC 3.2.1.21)
Query= SwissProt::E7CY69 (757 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2809 Length = 763 Score = 244 bits (623), Expect = 1e-68 Identities = 198/666 (29%), Positives = 305/666 (45%), Gaps = 93/666 (13%) Query: 69 TCFPPAAGLSSSWNPELIHKVGEAMAEECIQEKVAVILGPGVNIKRNPLGGRCFEYWSED 128 T FP L+SSW+ + I++ G A+E + + + P V+I R+P GR E + ED Sbjct: 113 TIFPIPLALASSWDMDAIYRSGRVAAQEAAADSLDITFAPMVDISRDPRWGRTSEGFGED 172 Query: 129 PYLAGHEAIGIVEGVQSKG------VGTSLKHFAANNQ-ETDRLRVDARISPRALREIYF 181 YL A +V+ Q G + S+KHFA E R +SP + + Y Sbjct: 173 TYLVSRIAGVMVKAFQGNGANAADSIMASVKHFALYGAVEGGRDYNTVDMSPLKMYQDYL 232 Query: 182 PAFEHIVKKAQPWTIMCSYNRINGVHSAQNHWLLTDVLRDEWGFDGIVMSDWGA------ 235 P + + A +M + N INGV + N WL+ D+LR EWGF G+ +SD GA Sbjct: 233 PPYRAAI-DAGAGGVMVALNSINGVPATANTWLMNDLLRKEWGFKGLAVSDHGAIFELIK 291 Query: 236 -----DHDRGASL--NAGLNLEMPPSYTDDQIVYAVRDGLITPAQLDRMAQGMIDLVNKT 288 D A L AG+++ M S ++ ++ G I + +D + + L K Sbjct: 292 HGVAKDGREAAKLAIKAGIDMSMNDSLYGKELPGLLKAGEIEQSDIDNAVREV--LAAKY 349 Query: 289 RAAMSIDNYRFDVDAHDEVA--------HQA-----AIESIVMLKNDDAILPLNAGPVAN 335 + D Y A D+ A H+A A S+V+L+N + LPL Sbjct: 350 DMGLFKDPYLRIGKAEDDPADTYAESRMHRADARDVARRSLVLLENRNQTLPLK------ 403 Query: 336 PSATPQKIAVIGEFARTP-RYQGGGSSHITPTKMTSFLDTLAERGIKADF---------- 384 KIA++G A+ P G ++ P + + D + R + AD Sbjct: 404 ---KTAKIALVGPLAKAPIDMMGSWAAAGRPAQSVTLFDGMT-RALGADSKLIYARGANI 459 Query: 385 ----------------APGFTLDLEPADPALESEAVETAKNADVVLMFLGLPEAVESEGF 428 AP D PA L EAV+ AK+ADVV+ +G + E Sbjct: 460 TGDKKVLDYLNFLNFDAPEVVDDPRPAQ-VLIDEAVKAAKDADVVVAAVGESRGMSHESS 518 Query: 429 DRDTLDMPAKQIALLEQVAAANQNVVVVLSNGSVITVAPWAKNAKGILESWLLGQSGGPA 488 R L++PA Q L++ + A + +V+VL NG +++ + A ILE+W G GG A Sbjct: 519 SRTELNIPASQRELIKALKATGKPLVLVLMNGRPLSLLEEKQQADAILETWFSGTEGGNA 578 Query: 489 LADVIFGQVSPSGKLAQSIPLDINDDPSMLNWPGEEGHVDYGE-------GVFAGYRYYD 541 +ADV+FG +PSGKL + P + P+ N H+ G G + + D Sbjct: 579 IADVLFGDYNPSGKLPITFPRSVGQIPTYYN------HLSIGRPFTPGKPGNYTSQYFDD 632 Query: 542 TYGKAVDYPFGYGLSYATFEITGVAVAKTGAN-TATVTATVT--NTSDVDAAETVQVYVV 598 T G YPFGYGLSY F ++ +A++ T N T + A+VT NT D VQ+Y+ Sbjct: 633 TTGPL--YPFGYGLSYTEFSLSDMALSSTTLNKTGKLDASVTLENTGKRDGETVVQLYIQ 690 Query: 599 PGKADVARPKHELKGFTKAFLKAGESKTVAIDLDERAFAYWSEKYNDWHVEAGEYAIEVG 658 + RP ELK F K LKAGE K + + E +++ + + E G++ +++G Sbjct: 691 DVTGSIIRPVKELKNFRKVMLKAGEKKVIHFTITEDDLKFFNAQLK-YAAEPGKFNVQIG 749 Query: 659 VSSRDI 664 + S+D+ Sbjct: 750 LDSQDV 755 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: 1270 Number of extensions: 63 Number of successful extensions: 6 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: 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