Align trehalose-6-phosphate hydrolase (TreC;KP1_0530) (EC 3.2.1.93) (characterized)
to candidate 3610517 Dshi_3898 alpha amylase catalytic region (RefSeq)
Query= CAZy::BAG86620.1 (551 letters) >FitnessBrowser__Dino:3610517 Length = 526 Score = 272 bits (696), Expect = 2e-77 Identities = 198/570 (34%), Positives = 270/570 (47%), Gaps = 81/570 (14%) Query: 7 WWQNGVIYQIYPKSFQDTTGSGTGDLRGVTARLDYLQKLGVDAIWLTPFYVSPQVDNGYD 66 W +N VIYQ+YP+SF DTTG+G GDL GVT +LDY+ LGVD IWL+PFY SP D GYD Sbjct: 7 WPENPVIYQVYPRSFLDTTGTGEGDLPGVTRQLDYIAGLGVDGIWLSPFYPSPFCDGGYD 66 Query: 67 VANYTAIDPSYGTMADFDALVAEAKARGIRIVLDMVLNHTSTEHEWFRQSLNKESPYRQF 126 +A++ A+D +GT+ DFDALVA A +R+++D+VLNHTS H+WF +SL +E + Sbjct: 67 IADHCAVDRRFGTLDDFDALVARAHDLDLRVMIDLVLNHTSDTHDWFAKSLAREEGFEDV 126 Query: 127 YIW----RDGEPDALPNNWRSKFGGNAWQWHADSGQYYLHLFAIEQADLNWENPAVRAEL 182 YIW +DG P P+NW S FG AW+WH QY LH F Q LN N V L Sbjct: 127 YIWADPCKDGSP---PSNWLSFFGEAAWRWHPQRAQYCLHKFLPCQPCLNHYNDRVHERL 183 Query: 183 KKVCEFWADRGVDGLRLDVVNLISKDQTFPCD----------LDGDGRRFYTDGPRVHEF 232 ++ FW DRGVDG R D V D F + + G YT +H+ Sbjct: 184 NRITRFWRDRGVDGFRYDAVTSFFYDPGFRDNPPAAEAEAALIPGPSNNPYTFQEHIHDV 243 Query: 233 L-------QEMSRDVFTPRNLMTVGEMSS--TSLEHCQQYAALDGRELSMTFNFHHLKVD 283 L E R++ P + +GE+++ S+E ++ D + +D Sbjct: 244 LPNECAAFAETLREMAGP-DAYLLGEINNGPRSVEVTCKFTGPDRLDAGYA-------ID 295 Query: 284 YPGGEKWTLARPDYVALKALFRHWQQGMHNRAWNALFWCN-HDQPRIVSRFGDEGEYRVT 342 P P L+ L + W +W N HDQ R VS FGD G Sbjct: 296 LPE------RGPSTEVLRDLLTRLEDA---EGWT--WWLNSHDQKRAVSSFGDGG---AA 341 Query: 343 AAKMLAMVLHGMQGTPYIYQGEEIGMTNPHFSSISDYRDVESHNMFIERAAQGQSPDELL 402 AKMLA L + G ++QGEE+G + + P +L+ Sbjct: 342 DAKMLAAFLCALPGPLLLFQGEELGQPQAELEKV-----------------ELTDPYDLM 384 Query: 403 AILASKSRDNSRTPMPWHAGENG-GFSDGEPWIGLGDNYQEINVEAALADPDSVFYTYQQ 461 S R+ +R PM W + GFS PW+ + ++ V ADP SV Y+ Sbjct: 385 YWPDSVGRNGARAPMAWDDTQPACGFSKAVPWLPMA-RAEQGGVAQQEADPASVLAFYRD 443 Query: 462 LITLRKTLPLLTWGDYEDLLPEHPSLWCYRRQWQGQTLV--VAANLSRELQAWQPAEAPG 519 + R+ L L + L + P C R + + TLV VAAN+S Q P + Sbjct: 444 ALARRRDLGL---AEATMELEDAPDA-CIRFRLRVGTLVVQVAANMSGAPQDLAPRQGA- 498 Query: 520 EWKMIISNYAETTPRPTGLTLRPFEAIWWL 549 K I+ +T P G L P A WWL Sbjct: 499 --KRIL----QTKPPAPGSNLPPRSAAWWL 522 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: 932 Number of extensions: 43 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 551 Length of database: 526 Length adjustment: 35 Effective length of query: 516 Effective length of database: 491 Effective search space: 253356 Effective search space used: 253356 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: 52 (24.6 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