Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate HSERO_RS23930 HSERO_RS23930 beta-D-glucoside glucohydrolase
Query= SwissProt::E7CY69 (757 letters) >FitnessBrowser__HerbieS:HSERO_RS23930 Length = 784 Score = 252 bits (643), Expect = 6e-71 Identities = 198/659 (30%), Positives = 308/659 (46%), Gaps = 78/659 (11%) Query: 69 TCFPPAAGLSSSWNPELIHKVGEAMAEECIQEKVAVILGPGVNIKRNPLGGRCFEYWSED 128 T FP GL+SSW+ +++ + AEE + + + P V+I R+P GR E + ED Sbjct: 133 TTFPIGLGLASSWDMDVVARAMRVSAEEAAADSIDMTFAPMVDISRDPRWGRTSEGFGED 192 Query: 129 PYLAGHEAIGIVEGVQ-------SKGVGTSLKHFAANNQ-ETDRLRVDARISPRALREIY 180 PYL A V +Q + V S+KHFA E R + P+ + Y Sbjct: 193 PYLVSRIAEVSVRALQGDTKPIAANRVMASVKHFALYGAVEGGRDYNVVNMDPQRMYNDY 252 Query: 181 FPAFEHIVKKAQPWTIMCSYNRINGVHSAQNHWLLTDVLRDEWGFDGIVMSDWGA----- 235 P + + A +M + N ING + N WLL D+LR +WGF G+ +SD GA Sbjct: 253 LPPYRAAID-AGAGAVMVALNSINGAPATSNTWLLQDLLRRDWGFKGLTVSDHGAITELV 311 Query: 236 -----DHDRGA---SLNAGLNLEMPPSYTDDQIVYAVRDGLITPAQLDRMAQGMI----D 283 +D A S+ AG ++ M Q+ VR G ++ +LD + ++ D Sbjct: 312 NHGVAQNDSEAARLSMKAGTDMSMADQVYIKQLPELVRSGKVSQQELDNAVRDILGAKYD 371 Query: 284 L-------VNKTRAAMSIDNYRFDVDAHDEVAHQAAIESIVMLKNDDAILPLNAGPVANP 336 L V RAA + D H A + A +S+V+L+N +A LPL Sbjct: 372 LGLFKDPYVRIGRAADDPPDVYADSRLHRRDAREVAQQSMVLLENRNAALPLKKNA---- 427 Query: 337 SATPQKIAVIGEFARTP-----RYQGGGSSHITPTKMTSFLDTLAERGIKADFAPGFTLD 391 +IA++G A + + G T T L +G K +A G + Sbjct: 428 -----RIALVGPLADSHIDMLGSWSAAGKDKQTITLRQGLQAALGGQG-KLVYARGANIT 481 Query: 392 -----------LEPADP----------ALESEAVETAKNADVVLMFLGLPEAVESEGFDR 430 L DP A+ EAV+ A++ADV++ +G + E R Sbjct: 482 EDKHIVDYLNFLNWDDPEVVQDKRSPKAMIDEAVKAARHADVIVAAVGESRGMSHESSSR 541 Query: 431 DTLDMPAKQIALLEQVAAANQNVVVVLSNGSVITVAPWAKNAKGILESWLLGQSGGPALA 490 +L +P Q+ LL+ + A + +V+VL NG + + +NA ILE+W G GG A+A Sbjct: 542 TSLSLPQSQLDLLKALKATGKPLVLVLMNGRPLDLNWARENASAILETWYTGTEGGNAIA 601 Query: 491 DVIFGQVSPSGKLAQSIPLDINDDPSMLNWPGEEGHVDYGEGVFAGY--RYYDTYGKAVD 548 D++FG V+PSGKL + P + PS N P G Y EG Y +Y+D + Sbjct: 602 DILFGDVNPSGKLPITFPRSVGQIPSYYNHP-RVGR-PYTEGKPGNYTSQYFDEPNGPL- 658 Query: 549 YPFGYGLSYATFEITGVAVAKTGANT---ATVTATVTNTSDVDAAETVQVYVVPGKADVA 605 YPFGYGLSY F+++ V++++ + + TV N A VQ+Y+ A V Sbjct: 659 YPFGYGLSYTEFKLSEVSLSQPSMSADGKVEASVTVKNVGRRAGATVVQLYLRDVAASVV 718 Query: 606 RPKHELKGFTKAFLKAGESKTVAIDLDERAFAYWSEKYNDWHVEAGEYAIEVGVSSRDI 664 RP ELK F K L+ GE K V +D +A ++++ K ++ E GE+ +++G+ S+++ Sbjct: 719 RPVKELKDFRKVMLQPGEEKQVQFSIDRKALSFYNAKL-EYVAEPGEFQVQIGLDSKEV 776 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: 1312 Number of extensions: 59 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 757 Length of database: 784 Length adjustment: 41 Effective length of query: 716 Effective length of database: 743 Effective search space: 531988 Effective search space used: 531988 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