Align β-galactosidase (GKGal1A;GK2337) (Gal1A) (EC 3.2.1.23) (characterized)
to candidate 16800 b2716 cryptic 6-phospho-beta-glucosidase (NCBI)
Query= CAZy::BAD76622.1 (455 letters) >FitnessBrowser__Keio:16800 Length = 474 Score = 411 bits (1057), Expect = e-119 Identities = 213/479 (44%), Positives = 299/479 (62%), Gaps = 37/479 (7%) Query: 7 SIIPDDFLWGGAVTSFQTEGAWNEGGKGLSIVDARPIPKGHSDWKVAV------------ 54 S+ P+ FLWGGA+ + Q+EGA+ EG KGL+ VD P H + ++AV Sbjct: 2 SVFPESFLWGGALAANQSEGAFREGDKGLTTVDMIP----HGEHRMAVKLGLEKRFQLRD 57 Query: 55 ----------DFYHRYKEDIALFKELGFTAYRTSIAWTRIFPDG-EGEPNEAGLAFYDAV 103 DFYHRYKEDIAL E+GF +RTSIAW+R+FP G E PN+ G+AFY +V Sbjct: 58 DEFYPSHEATDFYHRYKEDIALMAEMGFKVFRTSIAWSRLFPQGDEITPNQQGIAFYRSV 117 Query: 104 FDELRANGIEPVITLYHFDLPLALAKKYNGFASRKVVDLFERYARTVFERYRGKVNYWLT 163 F+E + GIEP++TL HFD+P+ L +Y + +RK+V+ F RYART FE + G V YWLT Sbjct: 118 FEECKKYGIEPLVTLCHFDVPMHLVTEYGSWRNRKLVEFFSRYARTCFEAFDGLVKYWLT 177 Query: 164 FNEQNLVLEQPHLW-GAICPEDEDPEAFAYRVCHNVFIAHAKAVKALREIAPEAKIGGMV 222 FNE N++L P G + E E+ + Y+ H+ +A A A K E+ P+ ++G M+ Sbjct: 178 FNEINIMLHSPFSGAGLVFEEGENQDQVKYQAAHHQLVASALATKIAHEVNPQNQVGCML 237 Query: 223 TYLTTYPATCRPEDALANVQAKELFIDFFFDVFARGAYPRYVTNQLEKKGICLPLEAGDE 282 YP +C+PED A ++ K+ FF DV ARG YP Y +KG+ + GD+ Sbjct: 238 AGGNFYPYSCKPEDVWAALE-KDRENLFFIDVQARGTYPAYSARVFREKGVTINKAPGDD 296 Query: 283 ELLRSQTVDFLSFSYYQSQIVR-----HQEQDERIIKGLEPNPYLPKTKWGWAIDPIGLR 337 E+L++ TVDF+SFSYY S+ + ++K L NPYL + WGW IDP+GLR Sbjct: 297 EILKN-TVDFVSFSYYASRCASAEMNANNSSAANVVKSLR-NPYLQVSDWGWGIDPLGLR 354 Query: 338 IALKDVYARYEMPIFITENGIGLEEELNENGTVDDDERIDYLRRHIEQMKMAMEEGVEVI 397 I + +Y RY+ P+F+ ENG+G ++E NG ++DD RI YLR HI M A+ +G+ ++ Sbjct: 355 ITMNMMYDRYQKPLFLVENGLGAKDEFAANGEINDDYRISYLREHIRAMGEAIADGIPLM 414 Query: 398 GYLMWGATDLLS-SQGEMRKRYGVIFVNRDDENLRDLKRYKKKSFYWFQRVIRTNGEEL 455 GY WG DL+S S GEM KRYG +FV+RDD L R +KKSF+W+++VI +NGE+L Sbjct: 415 GYTTWGCIDLVSASTGEMSKRYGFVFVDRDDAGNGTLTRTRKKSFWWYKKVIASNGEDL 473 Lambda K H 0.321 0.140 0.430 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: 683 Number of extensions: 44 Number of successful extensions: 8 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: 455 Length of database: 474 Length adjustment: 33 Effective length of query: 422 Effective length of database: 441 Effective search space: 186102 Effective search space used: 186102 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