Align 6-phospho-β-glycosidase (GK1856) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate BWI76_RS22380 BWI76_RS22380 6-phospho-beta-glucosidase
Query= CAZy::BAD76141.1 (470 letters) >FitnessBrowser__Koxy:BWI76_RS22380 Length = 466 Score = 477 bits (1227), Expect = e-139 Identities = 240/464 (51%), Positives = 316/464 (68%), Gaps = 9/464 (1%) Query: 11 YRFPAGFWWGSATSATQIEGAANEGGKGKNIWDHWYEQEPHRFFQGVGPEVASDFYHRYK 70 Y+FP GF+WG+A S Q EG +N+ ++IWD W+ ++P RF+Q +GP+ D YH+Y Sbjct: 4 YQFPEGFFWGAAASGPQTEGISNK--PHRSIWDSWFAEQPERFYQQIGPQTVCDTYHQYP 61 Query: 71 EDIALMKEIGHNSFRFSISWSRLIPD-GVGEVNPEAVRFYNAVIDELLANGIEPFVNLYH 129 +D+ALMK G NSFR SI WSRLI D G NP+AVRFY+A +DE++ NGIEP +NLYH Sbjct: 62 QDVALMKRTGFNSFRTSIQWSRLIDDFETGAPNPDAVRFYHAYLDEMIENGIEPMINLYH 121 Query: 130 FDMPLAMQT-IGGWENREVVDAYARYASLCFQLFGDRVKTWFTHNEPIVPVEGGYLYDFH 188 FDMP A+Q GG+E+ V D +AR+A F+LFG +VK W T NEPIVPVEGGYLYDFH Sbjct: 122 FDMPEALQKQYGGFESAHVTDLFARFARTAFELFGHKVKYWITFNEPIVPVEGGYLYDFH 181 Query: 189 YPNVVDFRRAVQVAYHTMIAHAKAVAAFRRAAIPDGKIGIILNLTPSYPRSQHPADVKAA 248 YP D R A QVA++ M+AHAKAV FR A+ + +IG++LNLTPSY R+ D KAA Sbjct: 182 YPCKKDGRLAAQVAFNIMLAHAKAVREFRTLAL-ESEIGVVLNLTPSYTRNDSAEDKKAA 240 Query: 249 HIADLLFNRSFLDPAVKGEYPQDLIELLDEYGFLPVTKANDRELIKENTIDLLGINYYQP 308 ADL FNRSFLDP VK ++P++L E+L + LP D ELI + +D LG+NYY P Sbjct: 241 WYADLFFNRSFLDPLVKHQFPKELCEILAAHDCLPEVTKADVELISGSRVDFLGVNYYVP 300 Query: 309 RRVKAKENMPNPDAPFLPERFFDYYAMPGRKMNPYR-GWEIYEKGIYDILINIKENYGNI 367 RRVKA+E+ D F PE +F+ Y P + NPYR EI + IYDI NI++NYGN Sbjct: 301 RRVKARESDYTLDY-FTPEFYFENYVNPEGRFNPYRDNNEILPQAIYDIAANIRDNYGNK 359 Query: 368 ECFISENGMGVE-GEERFRDESGMIHDDYRIEFIREHLKWVHRAIEEGVNVKGYHLWTFM 426 + F++E G+ ++ E E G+I D +RI + EHL +HRAI +G N G H WTF+ Sbjct: 360 KWFLAEIGIAMDIDSEGEPGEDGVIDDSFRIGLMEEHLVQLHRAIADGANCFGVHQWTFI 419 Query: 427 DNWSWTNAYKNRYGLVAVDLENGLKRTIKKSGYWFKSLAENNGF 470 DNWSW N++K RYG ++L+ G +R IK++ WF LA +NGF Sbjct: 420 DNWSWINSFKRRYGFWRLNLQTG-ERQIKRNALWFAELATSNGF 462 Lambda K H 0.321 0.140 0.446 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: 823 Number of extensions: 45 Number of successful extensions: 9 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: 470 Length of database: 466 Length adjustment: 33 Effective length of query: 437 Effective length of database: 433 Effective search space: 189221 Effective search space used: 189221 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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