Align β-galactosidase (GalD) (EC 3.2.1.23) (characterized)
to candidate N515DRAFT_3226 N515DRAFT_3226 Beta-galactosidase GanA
Query= CAZy::ABA39423.1 (579 letters) >FitnessBrowser__Dyella79:N515DRAFT_3226 Length = 532 Score = 636 bits (1641), Expect = 0.0 Identities = 310/518 (59%), Positives = 385/518 (74%), Gaps = 5/518 (0%) Query: 63 AAPATQTPMPQFVSKDGKHALMVDGAPFLILGAQVNNSSNYPGVMDKVWPAMQVLGPNTV 122 A+PA MP+ V++ G+HAL+VDG PFLILGAQVNNSSN+P ++D+VWPA+ L NTV Sbjct: 18 ASPALAEDMPRLVAEHGRHALLVDGKPFLILGAQVNNSSNWPAMLDEVWPAIGQLHANTV 77 Query: 123 QVPIAWEQVEPEEGKFDFSFVDTLLAQAREHKVRLVLLWFATWKNNGPAYAPHWVKTDNQ 182 QVPIAWEQ+EP+EG+FDFSF+DTL+ QAREH+VRLVLLWFATWKNNGP+YAP WVK D++ Sbjct: 78 QVPIAWEQIEPKEGQFDFSFLDTLVEQAREHRVRLVLLWFATWKNNGPSYAPSWVKLDDR 137 Query: 183 RFPRVVTREGKAIGSLSPHAQATLDADRKAFVAFMQHLKQVDPQ-HTVIMIQPENEPGTY 241 RFPR++ REG+ + SLSP A ATL+ADRKAFV M HL+++D + HTVIM+Q ENE GTY Sbjct: 138 RFPRLMNREGRRLNSLSPLASATLEADRKAFVQLMTHLRKIDGERHTVIMVQVENESGTY 197 Query: 242 GSVRDFSPMAQKLFDGPVPDELLKRLNKQPGSWAQVFGADADEIFHAWSIGRYIDQVAEA 301 G+ RD SPMA K+F G VP+ LL+ K G+W+QVFG DA E FHAW + +I+QV A Sbjct: 198 GTDRDHSPMADKVFAGSVPEALLRATGKPAGNWSQVFGNDAAEFFHAWHVAHFIEQVTAA 257 Query: 302 GKQAYPLPMYVNAALRGPFNPGQPGQYASGGPTDNVLDVWKAAGPHIDLLAPDIYMPEYR 361 GK YPLPMY NAALR PFNPG PG Y SGGPTDNVL VWKAA P +D+LAPDIY P+Y+ Sbjct: 258 GKAVYPLPMYANAALRDPFNPGPPGAYESGGPTDNVLHVWKAAAPSLDVLAPDIYKPDYK 317 Query: 362 MYTTVLERYARPDNALFVAETGNRPEYARYLFPTLGHDGVGWSAFGMDYTRYSNYPLGAK 421 Y+T LERYAR DN LFVAETGN YARY++ +G +GWS FGMD+T YSNYPLGA+ Sbjct: 318 HYSTYLERYARKDNPLFVAETGNDKVYARYVYAAVGAGAIGWSPFGMDFTGYSNYPLGAR 377 Query: 422 HVNEETLAPFALGFKLVSLGMRPFAKAASEGKLHGTAEEPGQAVQELKLNDRWSATITYG 481 V+++TLA FA +++++ A AA GKL G AE L L + W A + +G Sbjct: 378 KVDDDTLAMFAANYRVLAPMAGELAAAAYAGKLWGAAEPDDTHEATLDLGE-WQAHLGFG 436 Query: 482 VPQFWFKGEPP-GNPEPIGAALIAELGPDEFLVTGYHVRVTLHPASEATANMLYDRVEEG 540 Q F EPP GNP+ G ALIA+L P+E+LV VRV+ PA + L DRVEEG Sbjct: 437 --QLQFGTEPPKGNPDHAGGALIAQLAPNEYLVVARDVRVSFSPAHGRKPDFLLDRVEEG 494 Query: 541 QYDGDTWQFQRNWNGDQTDYGVNFSSAPQLLKIKLATY 578 YD W F+R WNGDQTD+G+NF P++L+++LATY Sbjct: 495 HYDHGRWVFRRLWNGDQTDWGLNFIGEPRVLRVRLATY 532 Lambda K H 0.317 0.134 0.419 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: 1126 Number of extensions: 52 Number of successful extensions: 3 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: 579 Length of database: 532 Length adjustment: 36 Effective length of query: 543 Effective length of database: 496 Effective search space: 269328 Effective search space used: 269328 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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