Align β-galactosidase (GKGal1A;GK2337) (Gal1A) (EC 3.2.1.23) (characterized)
to candidate 17781 b3721 cryptic phospho-beta-glucosidase B (NCBI)
Query= CAZy::BAD76622.1 (455 letters) >FitnessBrowser__Keio:17781 Length = 470 Score = 416 bits (1068), Expect = e-120 Identities = 218/462 (47%), Positives = 293/462 (63%), Gaps = 20/462 (4%) Query: 10 PDDFLWGGAVTSFQTEGAWNEGGKGLSIVDARPI-------PK--GHSDWK-VAVDFYHR 59 P+ FLWGGA + Q EGAW E GKG+S D +P P+ G + K VA+DFYHR Sbjct: 5 PETFLWGGATAANQVEGAWQEDGKGISTSDLQPHGVMGKMEPRILGKENIKDVAIDFYHR 64 Query: 60 YKEDIALFKELGFTAYRTSIAWTRIFPDG-EGEPNEAGLAFYDAVFDELRANGIEPVITL 118 Y EDIALF E+GFT R SIAW RIFP G E EPNEAGLAFYD +FDE+ GI+P++TL Sbjct: 65 YPEDIALFAEMGFTCLRISIAWARIFPQGDEVEPNEAGLAFYDRLFDEMAQAGIKPLVTL 124 Query: 119 YHFDLPLALAKKYNGFASRKVVDLFERYARTVFERYRGKVNYWLTFNEQNLVLEQPHLWG 178 H+++P L K Y G+A+R V+D FE YARTVF RY+ KV WLTFNE N+ L P + Sbjct: 125 SHYEMPYGLVKNYGGWANRAVIDHFEHYARTVFTRYQHKVALWLTFNEINMSLHAP--FT 182 Query: 179 AICPEDEDPEAFAYRVCHNVFIAHAKAVKALREIAPEAKIGGMVTYLTTYPATCRPEDAL 238 + +E EA Y+ H+ +A A+AVKA + PEAKIG M+ YP TC+P+D L Sbjct: 183 GVGLAEESGEAEVYQAIHHQLVASARAVKACHSLLPEAKIGNMLLGGLVYPLTCQPQDML 242 Query: 239 ANVQAKELFIDFFFDVFARGAYPRYVTNQLEKKGICLPLEAGDEELLRSQTVDFLSFSYY 298 ++ ++ FF DV ARG YP Y+ I + + D E L+ TVDF+SFSYY Sbjct: 243 QAMEENRRWM-FFGDVQARGQYPGYMQRFFRDHNITIEMTESDAEDLK-HTVDFISFSYY 300 Query: 299 QSQIVRHQEQDERIIKG----LEPNPYLPKTKWGWAIDPIGLRIALKDVYARYEMPIFIT 354 + V H E + +G + PNP+L ++WGW IDP+GLR+ L ++ RY+ P+FI Sbjct: 301 MTGCVSHDESINKNAQGNILNMIPNPHLKSSEWGWQIDPVGLRVLLNTLWDRYQKPLFIV 360 Query: 355 ENGIGLEEELNENGTVDDDERIDYLRRHIEQMKMAMEEGVEVIGYLMWGATDLLS-SQGE 413 ENG+G ++ + +G++ DD RI YL H+ Q+ A+ +GV+++GY WG DL+S S + Sbjct: 361 ENGLGAKDSVEADGSIQDDYRIAYLNDHLVQVNEAIADGVDIMGYTSWGPIDLVSASHSQ 420 Query: 414 MRKRYGVIFVNRDDENLRDLKRYKKKSFYWFQRVIRTNGEEL 455 M KRYG I+V+RDD L R +KKSF W+ VI+T G L Sbjct: 421 MSKRYGFIYVDRDDNGEGSLTRTRKKSFGWYAEVIKTRGLSL 462 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: 644 Number of extensions: 34 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: 470 Length adjustment: 33 Effective length of query: 422 Effective length of database: 437 Effective search space: 184414 Effective search space used: 184414 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