Align trehalose-6-phosphate hydrolase (TreC;KP1_0530) (EC 3.2.1.93) (characterized)
to candidate AZOBR_RS04510 AZOBR_RS04510 trehalose synthase
Query= CAZy::BAG86620.1 (551 letters) >FitnessBrowser__azobra:AZOBR_RS04510 Length = 562 Score = 230 bits (587), Expect = 1e-64 Identities = 180/592 (30%), Positives = 262/592 (44%), Gaps = 101/592 (17%) Query: 7 WWQNGVIYQIYPKSFQDTTGSGTGDLRGVTARLDYLQKLGVDAIWLTPFYVSPQVDNGYD 66 W++N VIY + +F D G G GD +G+ RLDYLQ LGV +WL PF SP D+GYD Sbjct: 6 WYKNAVIYNLSVGTFMDANGDGIGDFQGLQRRLDYLQGLGVTCLWLGPFQPSPMRDHGYD 65 Query: 67 VANYTAIDPSYGTMADFDALVAEAKARGIRIVLDMVLNHTSTEHEWFRQS-LNKESPYRQ 125 VA+Y +DP YGT+ DF K RGIR+++D+V+NHTS +H WF+ + + +SPYR Sbjct: 66 VADYYNVDPRYGTLGDFVEFSHACKQRGIRVIIDLVVNHTSDQHPWFQAARKDPDSPYRD 125 Query: 126 FYIWRDGEPDALPNNWRSKFGG---NAWQWHADSGQYYLHLFAIEQADLNWENPAVRAEL 182 +Y+W D +PD F G W W ++ YY H F Q DLN NP V+AEL Sbjct: 126 WYVWSDKKPDDADQG--VVFPGVQKTTWSWDKEARAYYFHRFYEFQPDLNTANPEVQAEL 183 Query: 183 KKVCEFWADRGVDGLRLDVVNLISKDQTFPCDLDGDGRRFYTDGPRV-HEFLQEMSRD-- 239 KV FW + GV G R+D V + T D+ ++F D R EF+Q D Sbjct: 184 LKVMGFWIELGVSGFRMDAVPFVI--ATKGPDVKKPKQQF--DMLRTFREFVQWRCGDAV 239 Query: 240 VFTPRNLMTVGEMSSTSLEHCQQYAALDGRELSMTFNFHHLKVDYPGGEKWTLARPDYVA 299 + N++ + Q+Y DG + M FNF + + + LA D Sbjct: 240 LLAEANVLPTVD---------QEYFGDDGDRMQMVFNFQVNQNLF-----YALATADTRP 285 Query: 300 L-KALFRHWQQGMHNRAWNALFWCNHDQ-----------PRIVSRFGDEGE---YRVTAA 344 L KAL W LF NHD+ R+ FG + + Y Sbjct: 286 LAKALDVTRVPRPSTNQW-GLFLRNHDELDLGRLTEAQRKRVFDAFGPDKDMQLYDRGIR 344 Query: 345 KMLAMVLHG--------------MQGTPYIYQGEEIGMTNPHFSSISDYRDVESHNMFIE 390 + LA +L G + GTP + G+EIGM + Sbjct: 345 RRLAPMLRGDRRWLELAYSLLFTLPGTPVLRYGDEIGMGDD------------------- 385 Query: 391 RAAQGQSPDELLAILASKSRDNSRTPMPWHAGENGGFSDGEPWI-----GLGDNYQEINV 445 L+ R+ +RTPM W GGF+ + + G Y+ IN Sbjct: 386 --------------LSLPERECARTPMQWSDEPQGGFTKADDPVHPVISGGAYGYERINA 431 Query: 446 EAALADPDSVFYTYQQLITLRKTLPLLTWGDYEDLLPEHPSLWCYRRQWQGQTLVVAANL 505 DP ++ +++I +RK P + WGD++ L ++ R W+ +++V NL Sbjct: 432 AHQRRDPSALLNWTERIIRMRKECPEIGWGDFQVLPTGSNAVLAIRYDWRNNSVLVVHNL 491 Query: 506 -SRELQAWQPAEAPGEWKMIISNYAE--TTPRPTG---LTLRPFEAIWWLQG 551 R + + GE +++ AE P G L L P+ W+ G Sbjct: 492 DDRPHEIALAVDGTGESPRLVNLLAEDHNDPEEDGRHRLVLEPYGYRWYRLG 543 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: 1021 Number of extensions: 71 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 551 Length of database: 562 Length adjustment: 36 Effective length of query: 515 Effective length of database: 526 Effective search space: 270890 Effective search space used: 270890 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: 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