Align 6-P-β-galactosidase (Gan1D) (EC 3.2.1.86) (characterized)
to candidate 16800 b2716 cryptic 6-phospho-beta-glucosidase (NCBI)
Query= CAZy::AHL67640.1 (478 letters) >FitnessBrowser__Keio:16800 Length = 474 Score = 334 bits (856), Expect = 4e-96 Identities = 188/488 (38%), Positives = 273/488 (55%), Gaps = 36/488 (7%) Query: 9 FPPEFLWGAASAAYQVEGAWNEDGKGLSVWDVFAKQPGRT---------FKGTNGDV--- 56 FP FLWG A AA Q EGA+ E KGL+ D+ R F+ + + Sbjct: 4 FPESFLWGGALAANQSEGAFREGDKGLTTVDMIPHGEHRMAVKLGLEKRFQLRDDEFYPS 63 Query: 57 --AVDHYHRYQEDVALMAEMGLKAYRFSVSWSRVFPDGNGAV-NEKGLDFYDRLIEELRN 113 A D YHRY+ED+ALMAEMG K +R S++WSR+FP G+ N++G+ FY + EE + Sbjct: 64 HEATDFYHRYKEDIALMAEMGFKVFRTSIAWSRLFPQGDEITPNQQGIAFYRSVFEECKK 123 Query: 114 HGIEPIVTLYHWDVPQALMDAYGAWESRRIIDDFDRYAVTLFQRFGDRVKYWVTLNEQNI 173 +GIEP+VTL H+DVP L+ YG+W +R++++ F RYA T F+ F VKYW+T NE NI Sbjct: 124 YGIEPLVTLCHFDVPMHLVTEYGSWRNRKLVEFFSRYARTCFEAFDGLVKYWLTFNEINI 183 Query: 174 FISFGYR-LGL-HPPGVKDMKRMYEANHIANLANAKVIQSFRHYVPDGKIGPSFAYSPMY 231 + + GL G + Y+A H +A+A + P ++G A Y Sbjct: 184 MLHSPFSGAGLVFEEGENQDQVKYQAAHHQLVASALATKIAHEVNPQNQVGCMLAGGNFY 243 Query: 232 PYDSRPENVLAFENAEEFQNHWWMDVYAWGMYPQAAWNYLESQGLEPTVAPGDWELLQAA 291 PY +PE+V A + +N +++DV A G YP + +G+ APGD E+L+ Sbjct: 244 PYSCKPEDVWAALEKDR-ENLFFIDVQARGTYPAYSARVFREKGVTINKAPGDDEILKNT 302 Query: 292 KPDFMGVNYYQTTTVEHNPPDGVGEGVMNTTGKKGTSTSSGIPGLFKTVRNPHVDTTNWD 351 DF+ +YY + MN + +S + K++RNP++ ++W Sbjct: 303 V-DFVSFSYYASRCASAE---------MN-------ANNSSAANVVKSLRNPYLQVSDWG 345 Query: 352 WAIDPVGLRIGLRRIANRYQLPILITENGLGEFDTLEPGDIVNDDYRIDYLRRHVQEIQR 411 W IDP+GLRI + + +RYQ P+ + ENGLG D +NDDYRI YLR H++ + Sbjct: 346 WGIDPLGLRITMNMMYDRYQKPLFLVENGLGAKDEFAANGEINDDYRISYLREHIRAMGE 405 Query: 412 AITDGVDVLGYCAWSFTDLLSWLNG-YQKRYGFVYVNRDDESEKDLRRIKKKSFYWYQRV 470 AI DG+ ++GY W DL+S G KRYGFV+V+RDD L R +KKSF+WY++V Sbjct: 406 AIADGIPLMGYTTWGCIDLVSASTGEMSKRYGFVFVDRDDAGNGTLTRTRKKSFWWYKKV 465 Query: 471 IETNGAEL 478 I +NG +L Sbjct: 466 IASNGEDL 473 Lambda K H 0.320 0.139 0.448 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: 729 Number of extensions: 53 Number of successful extensions: 7 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: 478 Length of database: 474 Length adjustment: 33 Effective length of query: 445 Effective length of database: 441 Effective search space: 196245 Effective search space used: 196245 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