Align 6-P-β-glucosidase (PbgA) (EC 3.2.1.86) (characterized)
to candidate AZOBR_RS16895 AZOBR_RS16895 beta-glucosidase
Query= CAZy::AAB49339.1 (466 letters) >FitnessBrowser__azobra:AZOBR_RS16895 Length = 482 Score = 327 bits (837), Expect = 7e-94 Identities = 181/473 (38%), Positives = 257/473 (54%), Gaps = 44/473 (9%) Query: 1 SFPKNFLWGSATAAYQVEGAWNQDGKGPSIWDLYSKLPGTTFEGTNGDIAADHYNRYKED 60 +FP F+WG++T++YQ+EGA G+GPS+WD +S G G GD+A DHYNRY ED Sbjct: 39 AFPDKFVWGASTSSYQIEGAVTAGGRGPSVWDTFSHSFGKVANGDTGDVACDHYNRYAED 98 Query: 61 VKTMAEMGLKTYRFSIAWTRIFPEGSGKINEKGIEFYSNLIDELLKYNIEPMITLYHWDL 120 V MA+ G+ YRFS+AW R+ P G+G N +G++FY L D LL I P LYHWDL Sbjct: 99 VDLMAKAGMNAYRFSVAWPRVQPTGTGPANAEGLDFYDRLTDALLAKGIAPWPCLYHWDL 158 Query: 121 PQALQDKYAGWESREIIDDFVEYARVCFKNFGDRVKYWIVMNEPNVFIGLGYGIALHPPG 180 PQALQD+ GW +R+I F +YA++ GDR K+W ++NEP+V G+G+ H PG Sbjct: 159 PQALQDR-GGWTNRDIAGWFTDYAQLVAARIGDRAKHWTMLNEPSVHAIFGHGLGGHAPG 217 Query: 181 GKDRKKELNAGHITALANAKAIKLFREI--VPNGMIGSSIAYGPAYAASESEEDKLALEK 238 + A H LA A+K R +G+ ++ P + L+ Sbjct: 218 MTGKGNYFKAIHHQNLAQGMALKALRAAGGAKGWQLGTVLSLQPVWPVG-------GLDA 270 Query: 239 YYNYNVWW---W----FDPYFKGEYPADMLKYNQEKYGAPEILDGDMELLKSAKSDFIGI 291 Y ++ W W DP +GEYP ++L+ AP + GD+E ++ DF+GI Sbjct: 271 NYAASLMWDAVWNRACLDPLLRGEYP-ELLRDG----FAPLVKAGDLEAIRQ-PIDFLGI 324 Query: 292 NYYCTQMIADNKEGVGYNGMNTTGEKNSQKENGVPGLFKNVRNTNLEYTDWDWAIDPDGL 351 NYY + G+ G + E G P T W ++PDG+ Sbjct: 325 NYYSRMHQQPDPAGLFGTGYGSPPE-------GTP------------TTGMGWPVEPDGI 365 Query: 352 RYGMVQLKERY-NLPIIISENGLGAVDPIDEEGNIQDIPRIDYLREHIIACEKAIEEGVD 410 +++LK+ Y N P+ + ENG + +G +QD RI YLR HI+A +A+EEGVD Sbjct: 366 AEILIELKQEYGNPPVYVMENGAAYPEQTGPKGFVQDNDRISYLRRHILAGHQALEEGVD 425 Query: 411 LLGYCTWSYIDLLSWLNGYKKQYGFIYVDRKNNLERKKKASYFWYKDVIASNG 463 L G+ WS +D W GY++++G I VDR+ LER+ KASY WY DVI G Sbjct: 426 LRGWFVWSLLDNFEWAEGYQRRFGLIEVDRQ-TLERRPKASYHWYADVIRKKG 477 Lambda K H 0.317 0.138 0.435 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: 783 Number of extensions: 48 Number of successful extensions: 6 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: 466 Length of database: 482 Length adjustment: 33 Effective length of query: 433 Effective length of database: 449 Effective search space: 194417 Effective search space used: 194417 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: 41 (21.6 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