Align trehalose-6-phosphate hydrolase (TreA;BSU07810) (EC 3.2.1.93) (characterized)
to candidate N515DRAFT_3393 N515DRAFT_3393 alpha-glucosidase
Query= CAZy::CAB12610.1 (561 letters) >FitnessBrowser__Dyella79:N515DRAFT_3393 Length = 541 Score = 316 bits (809), Expect = 2e-90 Identities = 186/539 (34%), Positives = 282/539 (52%), Gaps = 58/539 (10%) Query: 5 QTPWWKKAVVYQIYPKSFNDTTGNGVGDLNGIIEKLDYLKTLQVDVLWLTPIYDSPQHDN 64 +TPWW+ AV+YQIYP+SF DT G+GVGDL GI+E+LDY+ L VD +W+ P + SP D Sbjct: 3 ETPWWRGAVIYQIYPRSFLDTDGDGVGDLPGIVERLDYIAGLGVDAIWIAPFFRSPMADF 62 Query: 65 GYDIRDYYSIYPEYGTMEDFERLVSEAHKRDLKVVMDLVVNHTSTEHKWFREAISSIDSP 124 GYDI DY ++ P +GT++DF+RL+++AH LKV++D V++HTS +H+WF+E+ +S D+P Sbjct: 63 GYDIADYRAVDPLFGTIDDFDRLLAKAHALGLKVMIDQVLSHTSDQHEWFKESRASRDNP 122 Query: 125 YRDFYIWKKPQENGSVPTNWESKFGGSAWELDEASGQYYLHLFDVTQADLNWENEEVRKH 184 D+Y+W +++G+ P NW S FGG AW+ + GQYYLH F +Q DLN+ + +V++ Sbjct: 123 KADWYVWADARDDGTPPNNWMSLFGGVAWQWEPRRGQYYLHNFLTSQPDLNFHHPDVQRA 182 Query: 185 VYDMMHFWFEKGIDGFRLDVINLISKDQRF------PNAEEGDGRSFYTDGPRVHE---- 234 V D + FW +KG+DG RLD IN D++ P A GR F D P + Sbjct: 183 VLDNVQFWLDKGVDGLRLDAINFCFHDRQLRDNPPKPQAMR-VGRGFSPDNPYAFQYHYY 241 Query: 235 ---------FLHEMNEKVFSHYDSMTVGEMSS-TTVDHCIRYTNPDNKELDMTFSFHHLK 284 FL E+ + + + +GE+SS ++ YT L M +SF L Sbjct: 242 NNTQPENLAFLEELRGLLDRYPGAAALGEISSEDSLATMAEYTT--GHRLHMGYSFELLT 299 Query: 285 VDYPNGEKWALAPFDFLKLKEILSDWQTGMHAGGGWNALFWCNHDQPRVVSRYG----DD 340 D F ++ + + M GW NHD RV+SR+G + Sbjct: 300 AD-----------FSAAYIRGTVERLEAQMTE--GWPCWAISNHDVERVLSRWGREARGN 346 Query: 341 GAYRVKSAKMLATAIHMMQGTPYIYQGEELGMTNPKFTDISSYRDVESLNMYHAFKEKGM 400 G V+ A +L + ++G+ +YQGEEL +T E+ Y A ++ Sbjct: 347 GDASVRLANLLTAMVCSLRGSVCVYQGEELALT-------------EAEVPYEALQD--- 390 Query: 401 ADQDITAILQAKSRDNSRTPVQWDATENGGFTTGTPWIPVAGNYREINAEAALRDQNSVF 460 IT K RD RTP+ WD + N GF++G PW+PV +R + D S Sbjct: 391 -PYGITFWPNFKGRDGCRTPMPWDESANAGFSSGAPWLPVPAGHRALAVSRQELDPASAL 449 Query: 461 YHYQKLIQIRKMYDIVTEGTYEIIAKDDPNIFAYLRHGSNEKLLVINNFYGTEAAFTLP 519 + ++ +Q R+ + G + +P + A+ R + E +L N A LP Sbjct: 450 HGFRGFMQWRQAQPELRWGAIGFLDTPEP-VLAFTRTHAGETVLAAFNLGSAPVAVALP 507 Lambda K H 0.318 0.135 0.423 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: 897 Number of extensions: 50 Number of successful extensions: 4 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: 561 Length of database: 541 Length adjustment: 36 Effective length of query: 525 Effective length of database: 505 Effective search space: 265125 Effective search space used: 265125 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: 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