Align beta-galactosidase (EC 3.2.1.23) (characterized)
to candidate Ga0059261_2642 Ga0059261_2642 Beta-galactosidase
Query= BRENDA::B9LW38 (700 letters) >FitnessBrowser__Korea:Ga0059261_2642 Length = 685 Score = 367 bits (941), Expect = e-105 Identities = 219/640 (34%), Positives = 322/640 (50%), Gaps = 51/640 (7%) Query: 3 LGVCYFPEHWPSEEWERDVAAMADAGLEYVRMAEFSWGVLEPERGTFDFEWLDEAIELIG 62 LG ++PE WP E W D+ M G VR+ E++W +EPE G +D +WL A+ L Sbjct: 36 LGSAWYPEQWPEERWAEDLRLMKAHGANVVRIGEYAWSRMEPEEGKYDMDWLVRAVRLAA 95 Query: 63 DHGMQAVLCTPTATPPKWLVDERPSIRQEDPDGTVREHGSRRHYCFNSDAYREETARIVE 122 + ++ V+ TP+ TPP W+ + P + Q +G HG RR + +S YR+ +IVE Sbjct: 96 KYDIKVVIGTPSDTPPAWMTQKYPDVSQIQSNGQKVGHGGRRQFSISSKRYRDFCRQIVE 155 Query: 123 RVTERYADSPHVAGWQTDNEFGCHETVRCYCDDCADAFRTWLADRYGDIDRLNEAWGNAF 182 R+ + P+V GWQ NE T Y + A+ WL RYG +DRLN AW + Sbjct: 156 RMAQALGKEPNVMGWQIGNE----PTDESYDAEARAAWVAWLQQRYGTLDRLNAAWTTQY 211 Query: 183 WSQQYGSFDEIDPPGPTPAEHHPSRLLAYARFSSDSVVEYNRLHADLIR-EADPDWFVTH 241 WSQ+Y +D++ + +P +L RF + V+++R D IR ADP F+T Sbjct: 212 WSQRYTRWDQVPFSND---KANPGWMLEVKRFITAQWVDFHRNQRDAIRAHADPAQFITV 268 Query: 242 NF--MGRFPTLNAYDVSEDLDRVAWDSY-PTGFVQDRYDGEASPDQLRAGDPDQVGMDHD 298 NF +G + Y + DLD +WD+Y +G ++ P + G HD Sbjct: 269 NFGGLGWANRFDRYAANRDLDFTSWDNYVGSGHLK----------------PYRNGATHD 312 Query: 299 IYRSALDRPFWVMEQQPGDVNWPPHCPQPGEGAMRLWAHHAAAHGADAVLYFRWRRCLEG 358 + R R FWVME QPG VNW G R A A HG+D +LY++WR L G Sbjct: 313 LVRGWKRRNFWVMEIQPGFVNWAGVSNMLYPGETRRMAWQAIGHGSDGILYWQWRNALNG 372 Query: 359 QEQYHAGLRKADGSPDRGYADAAHTSEEFA---TLDGASHVDAPVAVVFDYDSLWALNAQ 415 QE H + DG P YA+ E A L +H + VA++ DY S WA++ Q Sbjct: 373 QETMHGSIIGPDGKPLPVYAEVQQIGREMAKATPLIAGTHPVSDVAILQDYASRWAIDFQ 432 Query: 416 PHAPDFDYWALQEAFYGAVRGRGVQVDVV-PPSADLSGYAAVVAPALHLVTEDLADRLTD 474 H D+D + +Y ++ VD+V +A LSGY VVAP+L++++E A RLTD Sbjct: 433 LHHRDYDQIEVLLDYYQPLKDARGAVDIVEAEAAPLSGYKLVVAPSLNVISETTAKRLTD 492 Query: 475 YIAGGGEVLFGPRTGVKDAENKLRPMSQPGPLTDLVGATVDQHESLPRRLETTVRRVGDP 534 Y+ GGG ++ GPR+G+KD+ N L P QPGPL +L+G V+Q +L Sbjct: 493 YVRGGGHLILGPRSGMKDSYNALEPQRQPGPLAELLGGRVEQFYAL-------------- 538 Query: 535 TDDSEEIAAPPVSFRTWAEWLDPDAAEPQYAY---DVDGPADGRPAVVTNTVGDGQVTYC 591 D++ ++ + WAE L A + Q +G DG+PAV++ VG G++TY Sbjct: 539 -DEAVDVGGGKATI--WAEQLSTSAPDTQVLLRYGKANGWLDGKPAVISRAVGKGRITYV 595 Query: 592 GVWPESDLADALASDLLDRAGVRYAERLPDGVRIGYRGGR 631 G + + L L A V +P V + R G+ Sbjct: 596 GALVDDAVMKTLIDGALRDAKVARDFPVPAEVELMTREGQ 635 Lambda K H 0.318 0.137 0.444 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: 1570 Number of extensions: 108 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: 700 Length of database: 685 Length adjustment: 39 Effective length of query: 661 Effective length of database: 646 Effective search space: 427006 Effective search space used: 427006 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: 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