Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate N515DRAFT_3019 N515DRAFT_3019 beta-glucosidase
Query= SwissProt::E7CY69 (757 letters) >FitnessBrowser__Dyella79:N515DRAFT_3019 Length = 737 Score = 311 bits (796), Expect = 1e-88 Identities = 226/682 (33%), Positives = 326/682 (47%), Gaps = 65/682 (9%) Query: 24 GDAWHLQGVESKGIPSYMITDGPHGLRKSLASSAGETDLDDSVPATCFPPAAGLSSSWNP 83 G A ++ +E GIP+ +D G+ S G+ AT P +++W+P Sbjct: 82 GSAGYIPALERVGIPAIQESDAGLGVASSERMRPGDY-------ATPLPAGPVTAATWDP 134 Query: 84 ELIHKVGEAMAEECIQEKVAVILGPGVNIKRNPLGGRCFEYWSEDPYLAGHEAIGIVEGV 143 ++ + G + E + V+L G N+ R P GR FEY EDP LAG + G+ Sbjct: 135 KVAFRGGAMIGGEAHAKGFNVLLAGGTNLMREPRNGRNFEYAGEDPLLAGTMVGEAIRGI 194 Query: 144 QSKGVGTSLKHFAANNQETDRLRVDARISPRALREIYFPAFEHIVKKAQPWTIMCSYNRI 203 +S+ V +++KHFA N+QET R VD RI +A+RE AFE +++ +P ++MCSYN++ Sbjct: 195 ESQHVVSTIKHFALNDQETARTTVDVRIGEQAMRESDLLAFELAIERGKPGSVMCSYNKL 254 Query: 204 NGVHSAQNHWLLTDVLRDEWGFDGIVMSDWGADHDRGASLNAGLNLEMPPSYTDDQIVY- 262 NG + +N +LL VL+ +W + G VMSDWG H ++NAGL+ E D I + Sbjct: 255 NGDWACENDYLLNQVLKRDWKYPGFVMSDWGGVHSAAKAVNAGLDQESAAEIFDKDIYFD 314 Query: 263 -AVRDGLITPAQLDRMAQGMIDLVNKTRAAMSIDNY-----RFDVDAHDEVAHQAAIESI 316 +RD L M+ + ++ A + + D A+ VA + Sbjct: 315 KPLRDALAKGEVKQARIDDMVRRILRSFFAAGVFEHPAKKAPIDEKANLAVARETLEAGA 374 Query: 317 VMLKNDDAILPLNAGPVANPSATPQKIAVIGEFARTPRYQGGGSSHITPTKMTSFLDTLA 376 V+L+ND+ +LPL+ A + IAVIG A GGGSS +T A Sbjct: 375 VLLRNDNQLLPLDV-------ARLESIAVIGAHADKGVLAGGGSSLVTAKGGN------A 421 Query: 377 ERGIKADFAPGFTLDLEPADP--ALES----------------EAVETAKNADVVLMFLG 418 G+K PG + P P AL+S A A + V ++F+ Sbjct: 422 VPGLKPSDWPGPVM-YHPYSPLKALQSMAPKAKVQFTGGDDVAAAAALAAKSQVAVVFV- 479 Query: 419 LPEAVESEGFDRDTLDMPAKQIALLEQVAAANQNVVVVLSNGSVITVAPWAKNAKGILES 478 + E FD L +P Q AL+ VA AN +VVL NGS + + PW + +LE Sbjct: 480 --QKWAGEDFDARDLSLPDGQDALVTAVAKANPRTIVVLENGSPVAM-PWLEQVGAVLEV 536 Query: 479 WLLGQSGGPALADVIFGQVSPSGKLAQSIPLDINDDPSMLNWPGEEG------HVDYG-E 531 W G G +A+++ G+V+PSG+L S P D+ P PG G VDY E Sbjct: 537 WYPGGDAGNGIANLLSGKVNPSGRLPLSWPRDVLQLPRP-ELPGAGGSGALPQSVDYAIE 595 Query: 532 GVFAGYRYYDTYGKAVDYPFGYGLSYATFEITGVAVAKTGANTATVTATVTNTSDVDAAE 591 G GYR+Y + +PFGYGLSY +FE G T T T TV NT A+ Sbjct: 596 GANVGYRWYQSKDLQPLFPFGYGLSYTSFE-HGALKVDTKDGKVTATVTVRNTGKRAGAD 654 Query: 592 TVQVYV-VPGKADVARPKHELKGFTKAFLKAGESKTVAIDLDERAFAYWSEKYNDWHVEA 650 QVYV VPG L GF+K FLK GE + ++I L+ + A + + W V Sbjct: 655 VAQVYVQVPG-----AKARRLAGFSKVFLKPGEQRELSIPLERKLLADFDTARHGWVVRG 709 Query: 651 GEYAIEVGVSSRDIADTVAVAL 672 GEY + G SS D+ AV L Sbjct: 710 GEYVVSEGRSSADLGRPAAVQL 731 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: 1423 Number of extensions: 66 Number of successful extensions: 7 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: 737 Length adjustment: 40 Effective length of query: 717 Effective length of database: 697 Effective search space: 499749 Effective search space used: 499749 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