Align trehalase (TreF;b3519) (EC 3.2.1.28) (characterized)
to candidate BWI76_RS26700 BWI76_RS26700 alpha,alpha-trehalase
Query= CAZy::AAC76544.1 (549 letters) >FitnessBrowser__Koxy:BWI76_RS26700 Length = 550 Score = 993 bits (2568), Expect = 0.0 Identities = 469/549 (85%), Positives = 504/549 (91%) Query: 1 MLNQKIQNPNPDELMIEVDLCYELDPYELKLDEMIEAEPEPEMIEGLPASDALTPADRYL 60 M +QK++N + DEL IE D CYE DPYELKLDEM +AEPEPE+IEGLPASDALTPADRYL Sbjct: 1 MFSQKLRNVDDDELRIENDPCYEADPYELKLDEMFDAEPEPEIIEGLPASDALTPADRYL 60 Query: 61 ELFEHVQSAKIFPDSKTFPDCAPKMDPLDILIRYRKVRRHRDFDLRKFVENHFWLPEVYS 120 ELF HVQ ++IF DSKTFPDCAPK DPLDILI YR+VRR FDLR+FVE+HFWLP+ + Sbjct: 61 ELFAHVQKSRIFADSKTFPDCAPKQDPLDILIHYRRVRRTPGFDLRQFVEDHFWLPDSRA 120 Query: 121 SEYVSDPQNSLKEHIDQLWPVLTREPQDHIPWSSLLALPQSYIVPGGRFSETYYWDSYFT 180 +YVSDP SLKEHID LWPVLTREPQDHIPWSSLLALPQSYIVPGGRFSETYYWDSYFT Sbjct: 121 EDYVSDPNRSLKEHIDNLWPVLTREPQDHIPWSSLLALPQSYIVPGGRFSETYYWDSYFT 180 Query: 181 MLGLAESGREDLLKCMADNFAWMIENYGHIPNGNRTYYLSRSQPPVFALMVELFEEDGVR 240 MLGLAESGREDLLKCMADNFAWMIE YGHIPNGNRTYYLSRSQPPVFALMVELFEEDGVR Sbjct: 181 MLGLAESGREDLLKCMADNFAWMIEIYGHIPNGNRTYYLSRSQPPVFALMVELFEEDGVR 240 Query: 241 GARRYLDHLKMEYAFWMDGAESLIPNQAYRHVVRMPDGSLLNRYWDDRDTPRDESWLEDV 300 GA+RYLDHL+MEY+FWMDGAESLIPNQAYRHVVRMPDGSLLNRYWDDRDTPRDESW EDV Sbjct: 241 GAKRYLDHLQMEYSFWMDGAESLIPNQAYRHVVRMPDGSLLNRYWDDRDTPRDESWREDV 300 Query: 301 ETAKHSGRPPNEVYRDLRAGAASGWDYSSRWLRDTGRLASIRTTQFIPIDLNAFLFKLES 360 ETAKHSGRPPNEVYRDLRAGA SGWDYSSRWLRD RLASIRTTQFIPIDLNAFLFKLE+ Sbjct: 301 ETAKHSGRPPNEVYRDLRAGAESGWDYSSRWLRDITRLASIRTTQFIPIDLNAFLFKLEN 360 Query: 361 AIANISALKGEKETEALFRQKASARRDAVNRYLWDDENGIYRDYDWRREQLALFSAAAIV 420 IAN+S LKG++ETEA FRQKAS RR AV RYLWDDE+G +RDYDWRREQLALFSAA+IV Sbjct: 361 TIANLSGLKGDRETEAAFRQKASDRRAAVTRYLWDDESGCFRDYDWRREQLALFSAASIV 420 Query: 421 PLYVGMANHEQADRLANAVRSRLLTPGGILASEYETGEQWDKPNGWAPLQWMAIQGFKMY 480 LYVGMA HEQADRLA+AVR+RLLTPGGI+A+EYE+GEQWDKPNGWAPLQWMA+QGFKMY Sbjct: 421 ALYVGMATHEQADRLADAVRARLLTPGGIMATEYESGEQWDKPNGWAPLQWMAVQGFKMY 480 Query: 481 GDDLLGDEIARSWLKTVNQFYLEQHKLIEKYHIADGVPREGGGGEYPLQDGFGWTNGVVR 540 G D LGDEIA+SWL+TVN +Y + +KLIEKYHIA P EGGGGEYPLQDGFGWTNGVVR Sbjct: 481 GQDPLGDEIAQSWLQTVNHYYKQHYKLIEKYHIASATPHEGGGGEYPLQDGFGWTNGVVR 540 Query: 541 RLIGLYGEP 549 RLIGLYGEP Sbjct: 541 RLIGLYGEP 549 Lambda K H 0.319 0.138 0.434 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: 1350 Number of extensions: 72 Number of successful extensions: 1 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: 549 Length of database: 550 Length adjustment: 36 Effective length of query: 513 Effective length of database: 514 Effective search space: 263682 Effective search space used: 263682 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 (21.7 bits) S2: 53 (25.0 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