Align β-galactosidase (A4-β-Gal) (EC 3.2.1.23) (characterized)
to candidate BPHYT_RS22765 BPHYT_RS22765 beta-galactosidase
Query= CAZy::BAA28362.1 (645 letters) >FitnessBrowser__BFirm:BPHYT_RS22765 Length = 660 Score = 694 bits (1791), Expect = 0.0 Identities = 350/656 (53%), Positives = 442/656 (67%), Gaps = 15/656 (2%) Query: 2 LGVCYYPEHWPKERWKEDARRMREAGLSHVRIGEFAWALLEPEPGRLEWGWLDEAIATLA 61 LGVCYYPEHWP+ W++DARRM+ G+ VRI EFAW+ +EP PG +WGWLD +I L Sbjct: 3 LGVCYYPEHWPESMWQDDARRMKALGIEQVRIAEFAWSRIEPTPGEYDWGWLDRSIDVLG 62 Query: 62 AEGLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVT 121 A GL+VV+ TPTATPPKWL+DR+P+ILPV +GR R FG RRHY FSSP Y +++I T Sbjct: 63 AAGLQVVMCTPTATPPKWLIDRHPDILPVGADGRPRAFGSRRHYDFSSPSYFAASQKICT 122 Query: 122 LLAERYGGLEAVAGFQTDNEYGCHDTVRCYCPRCQEAFRGWLEARYGTIEALNEAWGTAF 181 +AERYG AVA +QTDNE+GCH TV Y P FR WL+ARY TI+ALN AWGT F Sbjct: 123 AVAERYGKHPAVAYWQTDNEFGCHHTVVSYSPAAVGRFREWLKARYQTIDALNRAWGTVF 182 Query: 182 WSQRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQVRAFNRLQVEILRAHAPGKFVTHN 241 WS YRSF E++ P TV E +PSH LDY RFASD+V +NR+QVEI+RAH+PG+ V HN Sbjct: 183 WSMEYRSFDEIDAPVATVTEAHPSHRLDYRRFASDEVARYNRMQVEIIRAHSPGRPVAHN 242 Query: 242 FMGFFTDLDAFALAQDLDFASWDSYPLGFTDLMPLPPEEKLRYARTGHPDVAAFHHDLYR 301 FM FT+ D + +A DLD A+WDSYPLG + PE K R+ R+GHPD A+F+HD+YR Sbjct: 243 FMQLFTEFDHYKVAADLDVATWDSYPLGALEEQWFAPEVKARWLRSGHPDFASFNHDVYR 302 Query: 302 GVGRGRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVSYFRWRQAPFAQEQ 361 G+ + FWVMEQQPGPVNWA NP+P PGMVRLW+WEA AHGA VSYFRWRQAPFAQEQ Sbjct: 303 GMSKLPFWVMEQQPGPVNWALWNPAPLPGMVRLWSWEAFAHGAGCVSYFRWRQAPFAQEQ 362 Query: 362 MHAGLHRPDSAPDQGFFEAKRVAEE----LAALALPPVA-QAPVALVFDYEAAWIYEVQP 416 MHAGL+ PD+ D G EA +VA E LAA A A ++ VALV+DYEA W++E+ P Sbjct: 363 MHAGLNTPDNRLDVGGNEASQVAGEIRTVLAANADADAAVRSKVALVYDYEAKWLFEIHP 422 Query: 417 QGAEWSYLGLVYLFYSALRRLGLDVDVVPPGASLRGYAFAVVPSLPIVREEALEAFREAE 476 QGA++ Y + +YSALR LGLDVDVVP A L GY+ VVP LP+V E + + Sbjct: 423 QGADFHYPRFAFEYYSALRALGLDVDVVPVDAPLDGYSLIVVPPLPVVPEAFAQRLASSG 482 Query: 477 GPVLFGPRSGSKTETFQIPKELPPGPLQALLPLKVVRVESLPPGLLE---VAEGALGRFP 533 V+ GPR+GSKT+ QIP LPPG L ++LPL+V RVES+ P + E +A+G Sbjct: 483 AQVVLGPRTGSKTKDLQIPANLPPGALTSVLPLRVWRVESMRPNVTEAVRLADGESAGEA 542 Query: 534 LGL---WREWVEAPLKPLL----TFQDGKGALYREGRYLYLAAWPSPELAGRLLSALAAE 586 G WR++++ L F DG A + G + YLA+ L RL + +A E Sbjct: 543 DGFARHWRDFIDTDAAQSLDVRARFADGHPAYVQGGAFHYLASLFDDALTVRLFARIAQE 602 Query: 587 AGLKVLSLPEGLRLRRRGTWVFAFNYGPEAVEAPASEGARFLLGSRRVGPYDLAVW 642 AGL+ + L + +R+ RRG + FNYG E + GSR + P +AV+ Sbjct: 603 AGLETMPLGDSVRVSRRGALTYVFNYGDETHTLSGVADDALVFGSRAIEPQGVAVY 658 Lambda K H 0.322 0.139 0.454 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: 1445 Number of extensions: 87 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: 660 Length adjustment: 38 Effective length of query: 607 Effective length of database: 622 Effective search space: 377554 Effective search space used: 377554 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