Align β-galactosidase (A4-β-Gal) (EC 3.2.1.23) (characterized)
to candidate H281DRAFT_03229 H281DRAFT_03229 beta-galactosidase
Query= CAZy::BAA28362.1 (645 letters) >FitnessBrowser__Burk376:H281DRAFT_03229 Length = 661 Score = 692 bits (1786), Expect = 0.0 Identities = 347/660 (52%), Positives = 438/660 (66%), Gaps = 23/660 (3%) Query: 2 LGVCYYPEHWPKERWKEDARRMREAGLSHVRIGEFAWALLEPEPGRLEWGWLDEAIATLA 61 LGVCYYPEHWP+ W++DARRM+ G+ VRI EFAW+ +EP PG +W WLD AI L Sbjct: 3 LGVCYYPEHWPESMWEDDARRMKALGIEQVRIAEFAWSRIEPTPGEYDWAWLDRAIEVLG 62 Query: 62 AEGLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVT 121 A GL+VV+ TPTATPPKWL+DR+P+ILP+ +GR R FG RRHY FSSP Y +++I T Sbjct: 63 AAGLQVVMCTPTATPPKWLIDRHPDILPIGADGRPRAFGSRRHYDFSSPSYFSASQKICT 122 Query: 122 LLAERYGGLEAVAGFQTDNEYGCHDTVRCYCPRCQEAFRGWLEARYGTIEALNEAWGTAF 181 +AERYG AVA +QTDNE+GCH TV Y P FR WL+ARY TI+ LN AWGT F Sbjct: 123 AIAERYGKHPAVAYWQTDNEFGCHHTVVSYSPAAVARFREWLKARYTTIDELNRAWGTVF 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 + P+ K R+ R+GHPD A+F+HD+YR Sbjct: 243 FMQLFTEFDHYKVAADLDVAAWDSYPLGALEEQWFAPDVKARWLRSGHPDFASFNHDVYR 302 Query: 302 GVGRGRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVSYFRWRQAPFAQEQ 361 G+ + FWVMEQQPGPVNWA NP+P PGMVRLW+WEA AHGA VSYFRWRQAPFAQEQ Sbjct: 303 GMSKLPFWVMEQQPGPVNWAQWNPAPLPGMVRLWSWEAFAHGAGCVSYFRWRQAPFAQEQ 362 Query: 362 MHAGLHRPDSAPDQGFFEAKRVAEE----LAALALPPVA-QAPVALVFDYEAAWIYEVQP 416 MHAGL+ PD+ D G EA +VA E LAA A A ++ VALV+DYEA W++E+ P Sbjct: 363 MHAGLNTPDNRLDVGGSEAAQVASEIRTVLAANAHADAAVRSKVALVYDYEAKWLFEIHP 422 Query: 417 QGAEWSYLGLVYLFYSALRRLGLDVDVVPPGASLRGYAFAVVPSLPIVREEALEAFREAE 476 QGA++ Y + +YSALR LGLDVDVVP ASL GY+ VVP LP+V + + Sbjct: 423 QGADFHYPRFAFEYYSALRALGLDVDVVPVDASLDGYSLIVVPPLPVVPADLAARLASSG 482 Query: 477 GPVLFGPRSGSKTETFQIPKELPPGPLQALLPLKVVRVESLPPGLLEV----------AE 526 V+ GPR+GSKT+ QIP LPPG L +LPL+V RVES+ P + E E Sbjct: 483 AQVVLGPRTGSKTQDLQIPANLPPGALADVLPLRVWRVESMRPNVTEAVRLAGTQDASVE 542 Query: 527 GALGRFPLGLWREWVEA----PLKPLLTFQDGKGALYREGRYLYLAAWPSPELAGRLLSA 582 + R WR+++E+ L F DG+ A R G + YLA+ L RL Sbjct: 543 DGVARH----WRDFIESKDTNSFDVLARFADGQPAYVRSGAFHYLASLFDDALTTRLFEQ 598 Query: 583 LAAEAGLKVLSLPEGLRLRRRGTWVFAFNYGPEAVEAPASEGARFLLGSRRVGPYDLAVW 642 +A AG++ + L E +R+ R G + FNYG A + F++GS V P +AV+ Sbjct: 599 IAQRAGVETVRLGESVRISRCGALTYVFNYGDNAHTITGAADNAFVIGSSTVEPQGVAVY 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: 1440 Number of extensions: 81 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: 661 Length adjustment: 38 Effective length of query: 607 Effective length of database: 623 Effective search space: 378161 Effective search space used: 378161 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