Align β-galactosidase (GKGal1A;GK2337) (Gal1A) (EC 3.2.1.23) (characterized)
to candidate BWI76_RS19550 BWI76_RS19550 phospho-cellobiase
Query= CAZy::BAD76622.1 (455 letters) >FitnessBrowser__Koxy:BWI76_RS19550 Length = 464 Score = 417 bits (1073), Expect = e-121 Identities = 215/462 (46%), Positives = 293/462 (63%), Gaps = 20/462 (4%) Query: 10 PDDFLWGGAVTSFQTEGAWNEGGKGLSIVDARP----------IPKGHSDWKVAVDFYHR 59 P FLWGGA + Q EGA+ E GKGL+ D +P +P +A+DFYHR Sbjct: 5 PQAFLWGGATAANQVEGAYLEDGKGLTTSDVQPRGVFGDVVERVPGDSGIKDIAIDFYHR 64 Query: 60 YKEDIALFKELGFTAYRTSIAWTRIFPDG-EGEPNEAGLAFYDAVFDELRANGIEPVITL 118 Y EDI+LF E+GF R SIAW RIFP G E +PNEAGLAFYD +FDE+ + I P++TL Sbjct: 65 YPEDISLFAEMGFNCLRVSIAWARIFPHGDEAQPNEAGLAFYDKLFDEMAKHNITPLVTL 124 Query: 119 YHFDLPLALAKKYNGFASRKVVDLFERYARTVFERYRGKVNYWLTFNEQNLVLEQPHLWG 178 H+++P AL K Y G+ +RKV+ FERYARTVFERY+ KV WLTFNE N+ L P + G Sbjct: 125 SHYEMPWALVKNYGGWGNRKVIGFFERYARTVFERYQAKVKLWLTFNEINMSLHAP-MTG 183 Query: 179 AICPEDEDPEAFAYRVCHNVFIAHAKAVKALREIAPEAKIGGMVTYLTTYPATCRPEDAL 238 P D +A Y+ H+ +A A A KA +I PE KIG M+ YP +C+P+D Sbjct: 184 VGLPADSS-KAEVYQAIHHQLVASALAAKACHDIVPEGKIGNMLLGGLMYPLSCKPDDIF 242 Query: 239 ANVQAKELFIDFFFDVFARGAYPRYVTNQLEKKGICLPLEAGDEELLRSQTVDFLSFSYY 298 +Q + FF DV RGAYP Y+ GI L + D L+ +TVDF+SFSYY Sbjct: 243 ETLQQNRSW-QFFGDVQCRGAYPGYMLRYFRDNGINLDITDADRAALK-ETVDFISFSYY 300 Query: 299 QSQIVRHQEQDERIIKG----LEPNPYLPKTKWGWAIDPIGLRIALKDVYARYEMPIFIT 354 + V E+ + +G + PNP+L ++WGW IDP+GLR L ++ RY+ P+FI Sbjct: 301 MTGCVTADEELNKKARGNILSMVPNPHLASSEWGWQIDPLGLRTLLNVLWDRYQKPLFIV 360 Query: 355 ENGIGLEEELNENGTVDDDERIDYLRRHIEQMKMAMEEGVEVIGYLMWGATDLLS-SQGE 413 ENG+G ++++ +G+++DD RI YL H+ Q++ A+E+GVE++GY WG DL+S S+ E Sbjct: 361 ENGLGAKDKVEADGSINDDYRISYLNDHLVQVREAIEDGVELMGYTSWGPIDLVSASKAE 420 Query: 414 MRKRYGVIFVNRDDENLRDLKRYKKKSFYWFQRVIRTNGEEL 455 M KRYG I+V+RDD+ L R +KKSF+W++ VI TNG L Sbjct: 421 MSKRYGFIYVDRDDDGNGTLARSRKKSFWWYKEVIATNGGSL 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: 653 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: 464 Length adjustment: 33 Effective length of query: 422 Effective length of database: 431 Effective search space: 181882 Effective search space used: 181882 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