Align trehalose-6-phosphate hydrolase (TreA;BSU07810) (EC 3.2.1.93) (characterized)
to candidate WP_086510098.1 BZY95_RS11685 DUF3459 domain-containing protein
Query= CAZy::CAB12610.1 (561 letters) >NCBI__GCF_002151265.1:WP_086510098.1 Length = 550 Score = 297 bits (761), Expect = 6e-85 Identities = 183/554 (33%), Positives = 272/554 (49%), Gaps = 64/554 (11%) Query: 8 WWKKAVVYQIYPKSFNDTTGNGVGDLNGIIEKLDYLKTLQVDVLWLTPIYDSPQHDNGYD 67 WW+ AV+YQIYP+SF D+ G G+GDL G+I++LDY+ +L VD +WL P + SP D GYD Sbjct: 12 WWRGAVIYQIYPRSFQDSRGAGIGDLQGVIDRLDYIASLNVDAIWLAPFFTSPMKDFGYD 71 Query: 68 IRDYYSIYPEYGTMEDFERLVSEAHKRDLKVVMDLVVNHTSTEHKWFREAISSIDSPYRD 127 + DY + P +GT++DF+RLV AH R L+V +D V++H+S +H WF E+ SS D+P D Sbjct: 72 VSDYRGVDPTFGTLDDFDRLVEAAHARGLRVTIDQVLSHSSDQHPWFAESRSSRDNPKAD 131 Query: 128 FYIWKKPQENGSVPTNWESKFGGSAWELDEASGQYYLHLFDVTQADLNWENEEVRKHVYD 187 +Y+W + +GS PTNW++ FGGSAW+ D QYYLH F V Q DLN+ N EV + + + Sbjct: 132 WYVWADARSDGSPPTNWQAIFGGSAWQWDTRRCQYYLHNFLVEQPDLNFHNPEVVEAILE 191 Query: 188 MMHFWFEKGIDGFRLDVINLIS----KDQ-------------RFPNAEEGDGRSFYTDGP 230 + FW E+G+DGFRLD +N + KD R N + P Sbjct: 192 EVRFWLERGVDGFRLDAVNFCTHGPLKDNPPREKIVEGFIGVRPDNPYAFQRHLYDKTQP 251 Query: 231 RVHEFLHEMNEKVFSHYDSMTVGEMSSTTVDHCIRYTNPDNKELDMTFSFHHLKVDYPNG 290 FL + + + + T+GE+ + K L M +SF+ L Sbjct: 252 ENLAFLERLRALLDEYPSTTTIGEVGDDDSLGVMSEYTQGGKRLHMCYSFNLLTDKATPA 311 Query: 291 EKWALAPFDFLKLKEILSDWQTGMHAGGGWNALFWCNHDQPRVVSRYGDDGAYRVKSAKM 350 + LAP ++ + G GW NHD RV +R+ + A + ++ Sbjct: 312 D--LLAPLTEMEAR-----------IGDGWPCWAVGNHDITRVATRW--NVASDMAKLRL 356 Query: 351 LATAIHMMQGTPYIYQGEELGMTNPKFTDISSYRDVESLNMYHAFKEKGMADQDITAILQ 410 + +G+ +YQGEELG+T + T E+ + IT Sbjct: 357 YLAFLLTQRGSICLYQGEELGLTEAELT-----------------FEQLVDPAGITFWPS 399 Query: 411 AKSRDNSRTPVQWDATE-NGGFTTGTPWIPVAGNYREINAEAALRDQNSVFYHYQKLIQI 469 K RD RTP+ W A +GGFTT TPW+PV + + + RD S+ Y+ + Sbjct: 400 YKGRDGCRTPMPWVADALHGGFTTATPWLPVPEAHLALAVDRQERDPGSLLNAYRDFLLF 459 Query: 470 RKMYDIVTEGT--YEIIAKDDPNIFAYLRHGSNEKLLVINNFYGTEAAFTLP-------- 519 R+ + +G Y + D + + R +++LLV NF + P Sbjct: 460 RRNQPALVKGDIHYHPLQGD---VICFERLHGDDRLLVALNFANDPCTLSAPLDARPLAG 516 Query: 520 -DSLAPDEWKAEVL 532 SL W AE L Sbjct: 517 APSLVNGRWTAERL 530 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: 908 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: 550 Length adjustment: 36 Effective length of query: 525 Effective length of database: 514 Effective search space: 269850 Effective search space used: 269850 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 24 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