Align Beta-galactosidase BgaT; Beta-gal; EC 3.2.1.23 (characterized)
to candidate HSERO_RS01350 HSERO_RS01350 beta-galactosidase
Query= SwissProt::Q9X6C6 (645 letters) >FitnessBrowser__HerbieS:HSERO_RS01350 Length = 658 Score = 712 bits (1838), Expect = 0.0 Identities = 350/654 (53%), Positives = 441/654 (67%), Gaps = 13/654 (1%) Query: 2 LGVCYYPEHWPRERWSEDARRMRELGLAYVRVGEFAWALLEPEPGRLDWAWLDEAVAVLA 61 LGVCYYPEHWP W DA+RM+ LG+ VR+GEFAW+ +EP PG L W WLD A+ VLA Sbjct: 5 LGVCYYPEHWPEAMWDSDAQRMKALGIKQVRIGEFAWSRIEPSPGELRWDWLDRAIEVLA 64 Query: 62 QAGLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYHEETRRIVT 121 + GL+VV+ TPTATPPKWL+DR+ ++L VD GR+R FG RRHY FSS Y EE++RIV Sbjct: 65 RHGLEVVMCTPTATPPKWLIDRHDDVLAVDANGRQRAFGSRRHYDFSSDSYFEESQRIVR 124 Query: 122 LLGERYGKHPAVAGFQTDNEYGCHGTVRCYCERCQDAFRKWLEERYGSIDVLNEAWGTVF 181 LLGERYG+HPAV +QTDNEYGCH TV Y Q FR+WL +RYGSID LN AWGTVF Sbjct: 125 LLGERYGQHPAVTAWQTDNEYGCHQTVVSYSASAQRRFRQWLRQRYGSIDALNTAWGTVF 184 Query: 182 WSQRYRTFQEVELPNLTVAEANPSHLLDYYRFASEQVRRYNRLQVEILRAHAPGKFVTHN 241 WS YR+F E++ P TV EA+PSH LDY RFAS++V RYNR+QVEILRA +PG+ + HN Sbjct: 185 WSMEYRSFDEIDAPIGTVTEAHPSHRLDYRRFASDEVARYNRMQVEILRALSPGRLMVHN 244 Query: 242 FMGFFTDLNPFPLGEDLDFASWDSYPLGFTDLMPLPEEEKLRYARTGHPDVAAFHHDLYR 301 FM F + + +P+ DLD A+WDSYPLG ++M + K R+ RTGHPD A+F+HDLYR Sbjct: 245 FMQMFLEFDHYPVAADLDVATWDSYPLGALEVMWFDDATKARWLRTGHPDFASFNHDLYR 304 Query: 302 AVGRGRFWVMEQQPGPVNWAPHNPNPAPGMVRLWTWEALANGAEVVSYFRWRQVPFAQEQ 361 + FWVMEQQPGPVNWA NP+P PGMVRLW+WEA A+GA VSYFRWRQ PFAQEQ Sbjct: 305 GMSAQPFWVMEQQPGPVNWAHWNPHPLPGMVRLWSWEAFAHGAGCVSYFRWRQCPFAQEQ 364 Query: 362 MHAGLHRPDYAPDAAFFEVQRVVEEL-------GALSLPPPGQAPVALVYDPEAPWVYEV 414 +HAGL+RPD D E ++V E+ GAL+ P + VAL++D +A W++++ Sbjct: 365 LHAGLNRPDNRLDVGGSEAEQVAREIITVEQAQGALAQP---RGKVALLFDYDAKWLFDI 421 Query: 415 QPHGAEWNYLALVFLFYSVARRLGLDVDIVPPGAALQGYRLVLVPSLPIVREKALNAFRE 474 G ++ Y F +Y+ R LGLDVDI+P A L GY +++VP LPIV + E Sbjct: 422 HFQGIDFEYQRFAFQYYATLRALGLDVDILPLHAKLDGYAMIVVPPLPIVPDDLPGRIAE 481 Query: 475 ADGIVLFGPRSGSKNENFHIPQGLPPGPLQALLPLKVVRVESLPPGLREEVEGPWGRFSS 534 + + +FGPRSGSK + IP LPPGPLQ LLP++V RVESL P + E V+ Sbjct: 482 SGALSVFGPRSGSKTRSLQIPATLPPGPLQQLLPMRVWRVESLRPNVTEPVQFGAHSGQG 541 Query: 535 GLWREWVETD---LSPLLRFADGLGALFRAGRYLYLAAWPSPELLGALLVGLAQEGGLSP 591 WR+ +E D L L +F DG A+ R R YLA L A LA++ GL+P Sbjct: 542 AHWRDLIEADGEGLQTLAQFGDGHPAIVRKERAHYLAGIFDDALTSACFEQLARDAGLAP 601 Query: 592 KPLPSGLRLRWRGHLVFAFNYGPEEVVLPVPSGVRFRLGGPRLSPYEVAVWEEG 645 + LP GLRL+ RG L FAFNY + LP G +F +G +L P VAV+ G Sbjct: 602 QRLPEGLRLQERGGLCFAFNYSDAAITLPQAQGAQFLVGQAQLEPQGVAVYRTG 655 Lambda K H 0.322 0.142 0.469 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: 1542 Number of extensions: 80 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: 645 Length of database: 658 Length adjustment: 38 Effective length of query: 607 Effective length of database: 620 Effective search space: 376340 Effective search space used: 376340 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 (21.9 bits) S2: 54 (25.4 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