Align invertase (CscA) (EC 3.2.1.26) (characterized)
to candidate BWI76_RS23410 BWI76_RS23410 glycosyl hydrolase family 32
Query= CAZy::CAA57219.1 (477 letters) >FitnessBrowser__Koxy:BWI76_RS23410 Length = 477 Score = 562 bits (1448), Expect = e-164 Identities = 267/478 (55%), Positives = 337/478 (70%), Gaps = 4/478 (0%) Query: 1 MTQSRLHAAQNALAKLHERRGNTFYPHFHLAPPAGWMNDPNGLIWFNDRYHAFYQHHPMS 60 MT S A Q AK HE +YP +HLA AGW+NDPNGL+WF+ YHAFYQHHP S Sbjct: 1 MTYSIPRAEQELQAK-HEELNLRWYPRYHLAARAGWINDPNGLVWFDGWYHAFYQHHPYS 59 Query: 61 EHWGPMHWGHATSDDMIHWQHEPIALAPGDENDKDGCFSGSAVDDNGVLSLIYTGHVWLD 120 WGPMHWGHA S D++HW+H P+ALAP DKDGCFSGSAV D L+LIYTGH + Sbjct: 60 TQWGPMHWGHARSKDLVHWEHLPVALAPEGPEDKDGCFSGSAVVDGDTLALIYTGHKFHG 119 Query: 121 GAGNDDAIREVQCLATSRDGIHFEKQGVILTPPEGIMHFRDPKVWREADTWWMVVGAKDP 180 ++ + +VQCLATSRDGIHFE+QG+++ P G+ HFRDPKVWRE D+W+M+VGA+D Sbjct: 120 DPSDEANLYQVQCLATSRDGIHFERQGIVVDTPPGMHHFRDPKVWREGDSWYMIVGARD- 178 Query: 181 GNTGQILLYRGSSLREWTFDRVLAHADAGESYMWECPDFFSLGDQHYLMFSPQGMNAEGY 240 G+TGQ+ LYR + LR+W VL A+ YMWECPDFF+L +H LMFSPQG+ A+GY Sbjct: 179 GDTGQVRLYRSADLRQWQDAGVLDEAEKEMGYMWECPDFFALNGKHILMFSPQGLAAKGY 238 Query: 241 SYRNRFQSGVIPGMWSPGRLFAQSGHFTELDNGHDFYAPQSFVAKDGRRIVIGWMDMWES 300 RN FQSG + G W PG+ F + G F E+D+GHDFYAPQSF+ DGRRIVIGW+DMWES Sbjct: 239 RNRNLFQSGYLLGEWQPGQAFVREGEFVEMDHGHDFYAPQSFLTPDGRRIVIGWLDMWES 298 Query: 301 PMPSKREGWAGCMTLARELS-ESNGKLLQRPVHEAESLRQQHQSISPRTISNKYVLQ-EN 358 P+P +++GWAG ++L RELS ++ +L RP E ES+R T+ N+ EN Sbjct: 299 PLPEQQDGWAGMLSLPRELSLSADNRLQMRPAKEVESMRGASFPWPVTTLKNQQTTTVEN 358 Query: 359 AQAVEIQLQWALKNSDAEHYGLQLGAGMRLYIDNQSERLVLWRYYPHENLDGYRSIPLPQ 418 +A+E+ L W +S AE YGL LG G+R+Y+D Q +RLVL R+YP L G RS+PL + Sbjct: 359 CEAMEVILHWDCASSSAEQYGLSLGDGLRVYVDAQMQRLVLERHYPQYGLCGTRSVPLTE 418 Query: 419 GDMLALRIFIDTSSVEVFINDGEAVMSSRIYPQPEERELSLYASHGVAVLQHGALWQL 476 G L LRIF D+SSVEVF+NDGEA +SSRIYP REL+L++ G A L+ WQL Sbjct: 419 GADLKLRIFFDSSSVEVFVNDGEACLSSRIYPDAARRELALFSWSGSAYLKEAGAWQL 476 Lambda K H 0.320 0.136 0.446 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: 999 Number of extensions: 64 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: 477 Length of database: 477 Length adjustment: 33 Effective length of query: 444 Effective length of database: 444 Effective search space: 197136 Effective search space used: 197136 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 (21.8 bits) S2: 51 (24.3 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