Align β-galactosidase (GKGal1A;GK2337) (Gal1A) (EC 3.2.1.23) (characterized)
to candidate BWI76_RS22295 BWI76_RS22295 6-phospho-beta-glucosidase
Query= CAZy::BAD76622.1 (455 letters) >FitnessBrowser__Koxy:BWI76_RS22295 Length = 474 Score = 419 bits (1076), Expect = e-121 Identities = 217/474 (45%), Positives = 302/474 (63%), Gaps = 33/474 (6%) Query: 10 PDDFLWGGAVTSFQTEGAWNEGGKGLSIVDARPIPKGHSDWKV----------------- 52 P FLWGGA+ + Q+EGAW EGGKG + VD IP G V Sbjct: 5 PQGFLWGGALAANQSEGAWLEGGKGPTTVDM--IPHGAHRLAVKLGQEKRFAPRDDEFYP 62 Query: 53 ---AVDFYHRYKEDIALFKELGFTAYRTSIAWTRIFPDG-EGEPNEAGLAFYDAVFDELR 108 A+DFYHRYKEDIAL E+GF+ +RTSIAW+R+FP G E EPN G+AFY ++F+E + Sbjct: 63 SHEAIDFYHRYKEDIALMAEMGFSVFRTSIAWSRLFPKGDEQEPNPEGIAFYRSLFEECK 122 Query: 109 ANGIEPVITLYHFDLPLALAKKYNGFASRKVVDLFERYARTVFERYRGKVNYWLTFNEQN 168 + IEP++TL HFD+P+ L +Y + +RK+V+ F RYART FE + G V YWLTFNE N Sbjct: 123 KHNIEPLVTLCHFDVPMHLVTEYGSWRNRKMVEFFTRYARTCFEAFDGLVKYWLTFNEIN 182 Query: 169 LVLEQPHLW-GAICPEDEDPEAFAYRVCHNVFIAHAKAVKALREIAPEAKIGGMVTYLTT 227 ++L P G + E E+ E Y+ H+ +A A A K E+ P+ ++G M+ Sbjct: 183 IMLHSPFSGAGLVFEEGENQEQVKYQAAHHELVASALATKIAHEVNPQNQVGCMLAGGNF 242 Query: 228 YPATCRPEDALANVQAKELFIDFFFDVFARGAYPRYVTNQLEKKGICLPLEAGDEELLRS 287 YP +C+PED ++ K+ FF DV ARGAYP + +KG+ + EAGD+E+LR Sbjct: 243 YPYSCKPEDVWMALE-KDRENLFFIDVQARGAYPVWAARVFREKGVTIAKEAGDDEILR- 300 Query: 288 QTVDFLSFSYYQSQIVRHQ-----EQDERIIKGLEPNPYLPKTKWGWAIDPIGLRIALKD 342 TVDF+SFSYY S+ + I+K L+ NPY+ ++WGW IDP+GLRI + Sbjct: 301 HTVDFVSFSYYASRCASAEMNAGNTSAANIVKSLK-NPYIKASEWGWGIDPLGLRITMNM 359 Query: 343 VYARYEMPIFITENGIGLEEELNENGTVDDDERIDYLRRHIEQMKMAMEEGVEVIGYLMW 402 +Y RY+ P+F+ ENG+G +E++ NG ++DD RI YLR HI+ M A+E+G+ V+GY W Sbjct: 360 MYDRYQKPLFLVENGLGARDEIDANGEINDDYRISYLREHIQAMGDAIEDGIPVMGYTSW 419 Query: 403 GATDLLS-SQGEMRKRYGVIFVNRDDENLRDLKRYKKKSFYWFQRVIRTNGEEL 455 G DL+S S GEM KRYG ++V+RDD L R +KKSF+W+++VI +NGE+L Sbjct: 420 GCIDLVSASTGEMSKRYGFVYVDRDDAGHGTLARRRKKSFWWYKKVIASNGEDL 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: 699 Number of extensions: 46 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