Align trehalose-6-phosphate hydrolase (TreA;BSU07810) (EC 3.2.1.93) (characterized)
to candidate GFF2114 Psest_2157 trehalose synthase
Query= CAZy::CAB12610.1 (561 letters) >FitnessBrowser__psRCH2:GFF2114 Length = 1108 Score = 243 bits (620), Expect = 3e-68 Identities = 175/546 (32%), Positives = 251/546 (45%), Gaps = 96/546 (17%) Query: 8 WWKKAVVYQIYPKSFNDTTGNGVGDLNGIIEKLDYLKTLQVDVLWLTPIYDSPQHDNGYD 67 W+K AVVYQ++ KSF D+ +GVGD G+I+KLDY+ L V+ +WL P Y SP+ D+GYD Sbjct: 16 WYKDAVVYQVHLKSFYDSNNDGVGDFAGLIDKLDYIADLGVNTIWLLPFYPSPRRDDGYD 75 Query: 68 IRDYYSIYPEYGTMEDFERLVSEAHKRDLKVVMDLVVNHTSTEHKWFREAISS-IDSPYR 126 I DY ++PEYGTM D R ++EAHKR L+V+ +LV+NHTS +H WF+ A + S R Sbjct: 76 IADYRGVHPEYGTMADARRFIAEAHKRGLRVITELVINHTSDQHPWFQRARKARKGSAAR 135 Query: 127 DFYIWKKPQENGSVPTNWESKFGGSAWELDEASGQYYLHLFDVTQADLNWENEEVRKHVY 186 +FY+W E S W D + QY+ H F Q DLN++N +V K V Sbjct: 136 NFYVWSDTDEKYDGTRIIFLDTEKSNWTWDPVAKQYFWHRFYSHQPDLNFDNPQVMKAVL 195 Query: 187 DMMHFWFEKGIDGFRLDVINLISKDQRFPNAEEGDGRSFYTDGPRVHEFLHEMNEKVFSH 246 +M +W + GIDG RLD I P E DG + + P H L + ++ ++ Sbjct: 196 AVMRYWLDMGIDGLRLDAI---------PYLVERDGTN-NENLPETHAVLKAIRAEIDAN 245 Query: 247 Y-DSMTVGEMSSTTVDHCIRYTNPD---NKELDMTFSFHHLKVDYPNGEKWALAPFDFLK 302 Y D M + E + D + + D E M F F + Y A+A D Sbjct: 246 YPDRMLLAEANQWPEDTQLYFGGEDGGPGDECHMAFHFPLMPRMY-----MAIAQEDRFP 300 Query: 303 LKEILSDWQTGMHAGGGWNALFWCNHDQ---PRVVSR--------YGDDGAYRV------ 345 + +IL QT A+F NHD+ V R Y D R+ Sbjct: 301 ITDILR--QTPDIPENCQWAIFLRNHDELTLEMVTDRERDYLWNYYASDKRARINLGIRR 358 Query: 346 ----------KSAKMLATAIHMMQGTPYIYQGEELGMTNPKFTDISSYRDVESLNMYHAF 395 + ++L + + M GTP IY G+E+GM + F Sbjct: 359 RLAPLLERDRRRIELLNSLLLSMPGTPVIYYGDEIGMGDNIFLG---------------- 402 Query: 396 KEKGMADQDITAILQAKSRDNSRTPVQWDATENGGFTTGTP--------WIPVAGNYREI 447 RD RTP+QW NGGF+ P P+ G Y I Sbjct: 403 -----------------DRDGVRTPMQWSVDRNGGFSRADPPNLVLPPVMDPLYG-YYTI 444 Query: 448 NAEAALRDQNSVFYHYQKLIQIRKMYDIVTEGTYEIIAKDDPNIFAYLR-----HGSNEK 502 N EA RD +S+ ++++ IRK + GT +++A + I AYLR +G E Sbjct: 445 NVEAQQRDPHSLLNWTRRMLTIRKQFKAFGRGTLKMLAPSNRRILAYLREFTGANGDTEI 504 Query: 503 LLVINN 508 + + N Sbjct: 505 IFCVAN 510 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: 1488 Number of extensions: 67 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: 561 Length of database: 1108 Length adjustment: 41 Effective length of query: 520 Effective length of database: 1067 Effective search space: 554840 Effective search space used: 554840 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: 55 (25.8 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