Align 6-P-β-galactosidase (Gan1D) (EC 3.2.1.86) (characterized)
to candidate 17781 b3721 cryptic phospho-beta-glucosidase B (NCBI)
Query= CAZy::AHL67640.1 (478 letters) >FitnessBrowser__Keio:17781 Length = 470 Score = 343 bits (879), Expect = 9e-99 Identities = 191/484 (39%), Positives = 270/484 (55%), Gaps = 33/484 (6%) Query: 6 LKPFPPEFLWGAASAAYQVEGAWNEDGKGLSVWD-----VFAKQPGRTFKGTN-GDVAVD 59 +K FP FLWG A+AA QVEGAW EDGKG+S D V K R N DVA+D Sbjct: 1 MKAFPETFLWGGATAANQVEGAWQEDGKGISTSDLQPHGVMGKMEPRILGKENIKDVAID 60 Query: 60 HYHRYQEDVALMAEMGLKAYRFSVSWSRVFPDGNGAV-NEKGLDFYDRLIEELRNHGIEP 118 YHRY ED+AL AEMG R S++W+R+FP G+ NE GL FYDRL +E+ GI+P Sbjct: 61 FYHRYPEDIALFAEMGFTCLRISIAWARIFPQGDEVEPNEAGLAFYDRLFDEMAQAGIKP 120 Query: 119 IVTLYHWDVPQALMDAYGAWESRRIIDDFDRYAVTLFQRFGDRVKYWVTLNEQNIFISFG 178 +VTL H+++P L+ YG W +R +ID F+ YA T+F R+ +V W+T NE N+ + Sbjct: 121 LVTLSHYEMPYGLVKNYGGWANRAVIDHFEHYARTVFTRYQHKVALWLTFNEINMSLHAP 180 Query: 179 YRLGLHPPGVKDMKRMYEANHIANLANAKVIQSFRHYVPDGKIGPSFAYSPMYPYDSRPE 238 + G+ +Y+A H +A+A+ +++ +P+ KIG +YP +P+ Sbjct: 181 FT-GVGLAEESGEAEVYQAIHHQLVASARAVKACHSLLPEAKIGNMLLGGLVYPLTCQPQ 239 Query: 239 NVLAFENAEEFQNHWWM---DVYAWGMYPQAAWNYLESQGLEPTVAPGDWELLQAAKPDF 295 ++L A E +N WM DV A G YP + + + D E L+ DF Sbjct: 240 DML---QAME-ENRRWMFFGDVQARGQYPGYMQRFFRDHNITIEMTESDAEDLKHTV-DF 294 Query: 296 MGVNYYQTTTVEHNPPDGVGEGVMNTTGKKGTSTSSGIPGLFKTVRNPHVDTTNWDWAID 355 + +YY T V H+ + + + + + NPH+ ++ W W ID Sbjct: 295 ISFSYYMTGCVSHD--ESINKNAQGN--------------ILNMIPNPHLKSSEWGWQID 338 Query: 356 PVGLRIGLRRIANRYQLPILITENGLGEFDTLEPGDIVNDDYRIDYLRRHVQEIQRAITD 415 PVGLR+ L + +RYQ P+ I ENGLG D++E + DDYRI YL H+ ++ AI D Sbjct: 339 PVGLRVLLNTLWDRYQKPLFIVENGLGAKDSVEADGSIQDDYRIAYLNDHLVQVNEAIAD 398 Query: 416 GVDVLGYCAWSFTDLLSWLNG-YQKRYGFVYVNRDDESEKDLRRIKKKSFYWYQRVIETN 474 GVD++GY +W DL+S + KRYGF+YV+RDD E L R +KKSF WY VI+T Sbjct: 399 GVDIMGYTSWGPIDLVSASHSQMSKRYGFIYVDRDDNGEGSLTRTRKKSFGWYAEVIKTR 458 Query: 475 GAEL 478 G L Sbjct: 459 GLSL 462 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: 747 Number of extensions: 43 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: 470 Length adjustment: 33 Effective length of query: 445 Effective length of database: 437 Effective search space: 194465 Effective search space used: 194465 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