Align trehalose-6-phosphate hydrolase (TreA;BSU07810) (EC 3.2.1.93) (characterized)
to candidate PP_4059 PP_4059 fused trehalose synthase B/maltokinase
Query= CAZy::CAB12610.1 (561 letters) >FitnessBrowser__Putida:PP_4059 Length = 1106 Score = 240 bits (612), Expect = 2e-67 Identities = 173/567 (30%), Positives = 260/567 (45%), Gaps = 93/567 (16%) Query: 8 WWKKAVVYQIYPKSFNDTTGNGVGDLNGIIEKLDYLKTLQVDVLWLTPIYDSPQHDNGYD 67 W+K AV+YQ++ KSF D+ +G+GD G+I KLDY+ L V+ LWL P Y SP+ D+GYD Sbjct: 16 WYKDAVIYQLHIKSFFDSNNDGIGDFAGLISKLDYIAELGVNTLWLLPFYPSPRRDDGYD 75 Query: 68 IRDYYSIYPEYGTMEDFERLVSEAHKRDLKVVMDLVVNHTSTEHKWFREA-ISSIDSPYR 126 I +Y +++P+YG+M D R ++EAHKR L+V+ +LV+NHTS +H WF+ A + S R Sbjct: 76 IAEYKAVHPDYGSMADARRFIAEAHKRGLRVITELVINHTSDQHPWFQRARHAKRGSKAR 135 Query: 127 DFYIWKKPQENGSVPTNWESKFGGSAWELDEASGQYYLHLFDVTQADLNWENEEVRKHVY 186 +FY+W + S W D +GQY+ H F Q DLN++N +V K V Sbjct: 136 EFYVWSDDDQKYDGTRIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDNPQVLKAVI 195 Query: 187 DMMHFWFEKGIDGFRLDVINLISKDQRFPNAEEGDGRSFYTDGPRVHEFLHEMNEKVFSH 246 +M FW + G+DG RLD I P E DG + + H+ L + ++ ++ Sbjct: 196 GVMRFWLDLGVDGLRLDAI---------PYLIERDGTN-NENLAETHDVLKAIRAEIDAN 245 Query: 247 Y-DSMTVGEMSSTTVDHCIRYTNPDNKELDMTFSFHHLKVDYPNGEKWALAPFDFLKLKE 305 Y D M + E + D + D E M F F + Y ALA D + + Sbjct: 246 YPDRMLLAEANQWPEDTRPYFGEGDGDECHMAFHFPLMPRMY-----MALAMEDRFPITD 300 Query: 306 ILSDWQTGMHAGGGWNALFWCNHDQ---PRVVSR--------YGDDGAYRV--------- 345 IL + A W A+F NHD+ V R Y +D R+ Sbjct: 301 ILRQ-TPEIPANCQW-AIFLRNHDELTLEMVTDRERDYLWNYYAEDRRARINLGIRRRLA 358 Query: 346 -------KSAKMLATAIHMMQGTPYIYQGEELGMTNPKFTDISSYRDVESLNMYHAFKEK 398 + ++L + + M GTP +Y G+ELGM + N+Y Sbjct: 359 PLLQRDRRRIELLTSLLLSMPGTPTLYYGDELGMGD---------------NIY------ 397 Query: 399 GMADQDITAILQAKSRDNSRTPVQWDATENGGFTTGTP--------WIPVAGNYREINAE 450 RD RTP+QW NGGF+ P P+ G Y+ +N E Sbjct: 398 ------------LGDRDGVRTPMQWSPDRNGGFSRADPQRLVLPPIMDPLYG-YQTVNVE 444 Query: 451 AALRDQNSVFYHYQKLIQIRKMYDIVTEGTYEIIAKDDPNIFAYLRH-----GSNEKLLV 505 A D +S+ ++++ +RK G+ + + I AY+R G+ E +L Sbjct: 445 AQSHDPHSLLNWTRRMLAVRKQQKAFGRGSLRTLTPSNRRILAYIREYTDADGNTEVILC 504 Query: 506 INNFYGTEAAFTLPDSLAPDEWKAEVL 532 + N A L S D+ E+L Sbjct: 505 VANVSRAAQAAELELSQYADKVPVEML 531 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: 1482 Number of extensions: 74 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: 1106 Length adjustment: 41 Effective length of query: 520 Effective length of database: 1065 Effective search space: 553800 Effective search space used: 553800 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