Align trehalose-6-phosphate hydrolase (TreA;BSU07810) (EC 3.2.1.93) (characterized)
to candidate 5209418 Shew_1889 alpha amylase, catalytic region (RefSeq)
Query= CAZy::CAB12610.1 (561 letters) >FitnessBrowser__PV4:5209418 Length = 541 Score = 322 bits (825), Expect = 2e-92 Identities = 187/534 (35%), Positives = 278/534 (52%), Gaps = 53/534 (9%) Query: 5 QTPWWKKAVVYQIYPKSFNDTTGNGVGDLNGIIEKLDYLKTLQVDVLWLTPIYDSPQHDN 64 Q WW+ AV+YQIYP+S D+ G+GVGDL GII KLDY+ +L VD +W++P + SP D Sbjct: 3 QLSWWRGAVIYQIYPRSLMDSNGDGVGDLQGIISKLDYIASLNVDAIWISPFFKSPMKDF 62 Query: 65 GYDIRDYYSIYPEYGTMEDFERLVSEAHKRDLKVVMDLVVNHTSTEHKWFREAISSIDSP 124 GYDI DY +I P +GTM DF+ L+ +AH +KV++D V++HTS +H WF E+ S D+ Sbjct: 63 GYDISDYRAIDPLFGTMADFDELIDKAHGLGIKVIIDQVLSHTSDQHAWFSESRQSRDNA 122 Query: 125 YRDFYIWKKPQENGSVPTNWESKFGGSAWELDEASGQYYLHLFDVTQADLNWENEEVRKH 184 +D+Y+W P +G+ P NW + FGG AWE + QYYLH F +Q DLN+ N +VR+ Sbjct: 123 KQDWYVWADPNPDGTAPNNWLAIFGGCAWEWEPRRQQYYLHNFLTSQPDLNFHNPDVRQA 182 Query: 185 VYDMMHFWFEKGIDGFRLDVINLISKDQRF----PNAEE-GDGRSFYTDGPRVHE----- 234 V D + FW +KG+DGFRLD I D++ P E+ GR F D P ++ Sbjct: 183 VLDNVKFWLDKGVDGFRLDAITFCYHDEQLRDNPPKPEDKRQGRGFSEDNPYAYQYHYYN 242 Query: 235 --------FLHEMNEKVFSHYDSMTVGEMSS-TTVDHCIRYTNPDNKELDMTFSFHHLKV 285 F+ E+ + + +T+GE+SS ++ YT D++ L M +SF L Sbjct: 243 NTRPQTVGFIEELRALINQYPGVVTLGEVSSEDSLATMAEYTQGDDR-LHMAYSFELLTD 301 Query: 286 DYPNGEKWALAPFDFLKLKEILSDWQTGMHAGGGWNALFWCNHDQPRVVSRYGDDGAYRV 345 D+ +P E L G GW NHD RV +R+G D A+ Sbjct: 302 DF--------SPAYIRHTVEALE-----QSIGDGWPCWAIGNHDVQRVATRWGRD-AFNS 347 Query: 346 KSAKMLATAIHMMQGTPYIYQGEELGMTNPKFTDISSYRDVESLNMYHAFKEKGMADQDI 405 AKML + ++G+ YQGEELG+ + +D + + F Sbjct: 348 DMAKMLNAMLCSLRGSVCSYQGEELGLGEVEIA-YEQLQDPFGITFWPMF---------- 396 Query: 406 TAILQAKSRDNSRTPVQWDATEN-GGFTTGTPWIPVAGNYREINAEAALRDQNSVFYHYQ 464 K RD RTP+ W N GF+ TPW+PV +++ + + + S+ HY+ Sbjct: 397 ------KGRDGCRTPMPWRHDANHAGFSDNTPWLPVPADHKAVAVDVQEANPESILNHYR 450 Query: 465 KLIQIRKMYDIVTEGTYEIIAKDDPNIFAYLRHGSNEKLLVINNFYGTEAAFTL 518 ++ RK++ I+ G + I D + + R + LLV N G +F+L Sbjct: 451 HMLAWRKLHPILVTGDIKFIESTDA-LLVFERRLGEQTLLVAFNLSGQPQSFSL 503 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: 941 Number of extensions: 50 Number of successful extensions: 5 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