Align trehalose-6-phosphate hydrolase (TreA;BSU07810) (EC 3.2.1.93) (characterized)
to candidate 201365 SO2213 oligo-1,6-glucosidase (NCBI ptt file)
Query= CAZy::CAB12610.1 (561 letters) >FitnessBrowser__MR1:201365 Length = 540 Score = 316 bits (809), Expect = 2e-90 Identities = 182/531 (34%), Positives = 280/531 (52%), Gaps = 53/531 (9%) Query: 8 WWKKAVVYQIYPKSFNDTTGNGVGDLNGIIEKLDYLKTLQVDVLWLTPIYDSPQHDNGYD 67 WW+ AV+YQIYP+S DT G+GVGDL GII KLDY+ +L VD +W++P + SP D GYD Sbjct: 6 WWRGAVIYQIYPRSLLDTNGDGVGDLRGIITKLDYIASLNVDAIWISPFFKSPMADFGYD 65 Query: 68 IRDYYSIYPEYGTMEDFERLVSEAHKRDLKVVMDLVVNHTSTEHKWFREAISSIDSPYRD 127 I DY I P +G+M+DF+ L+ +AH+R +KV++D V++HTS +H WF E+ S +P D Sbjct: 66 ISDYREIDPLFGSMQDFDELIEKAHQRGIKVIIDQVLSHTSDQHAWFIESRESRTNPKAD 125 Query: 128 FYIWKKPQENGSVPTNWESKFGGSAWELDEASGQYYLHLFDVTQADLNWENEEVRKHVYD 187 +Y+W P+E+G+ P NW + FGG AWE + QYYLH F +Q D+N+ N +VR+ V D Sbjct: 126 WYVWADPREDGTPPNNWLAIFGGCAWEWEPRRQQYYLHNFLRSQPDINFHNPDVRQAVLD 185 Query: 188 MMHFWFEKGIDGFRLDVINL-----ISKDQRFPNAEEGDGRSFYTDGPRVH--------- 233 + FW +KG+DGFRLD I + +D E+ GR F D P + Sbjct: 186 NVEFWLKKGVDGFRLDAITFCFHDELLRDNPAKPKEKRQGRGFSEDNPYAYQYHYYNNDR 245 Query: 234 ----EFLHEMNEKVFSHYDSMTVGEMSS-TTVDHCIRYTNPDNKELDMTFSFHHLKVDYP 288 +F+ + + + + ++T+GE+S+ ++ YT D++ L M +SF L DY Sbjct: 246 PQTIQFIEALRQLINRYPGTVTLGEVSAEDSLAVMAAYTKGDDR-LHMAYSFELLTDDY- 303 Query: 289 NGEKWALAPFDFLKLKEILSDWQTGMHAGGGWNALFWCNHDQPRVVSRYGDDGAYRVKSA 348 +++ + + + G GW NHD RV SR+G G A Sbjct: 304 ----------SAAYIRQTVEALENSI--GDGWPCWAIGNHDVQRVASRWG-RGKQTSDMA 350 Query: 349 KMLATAIHMMQGTPYIYQGEELGMTNPKFTDISSYRDVESLNMYHAFKEKGMADQDITAI 408 KML + ++G+ YQGEELG+T + +D + F Sbjct: 351 KMLNAMLCSLRGSVCSYQGEELGLTEVPI-EFHELQDPFGKTFWPMF------------- 396 Query: 409 LQAKSRDNSRTPVQWDA-TENGGFTTGTPWIPVAGNYREINAEAALRDQNSVFYHYQKLI 467 K RD RTP+ W+ + GF+ +PW+P+A +R + + D +SV + Y++ + Sbjct: 397 ---KGRDGCRTPMPWEQYADFSGFSQVSPWLPIAAAHRALAVDLQEADCHSVLHGYRQFL 453 Query: 468 QIRKMYDIVTEGTYEIIAKDDPNIFAYLRHGSNEKLLVINNFYGTEAAFTL 518 RK Y + E + +P + ++R +KLLV N E +L Sbjct: 454 AWRKCYPALITSEIEFLDAPEP-LLVFVRKLGEQKLLVCFNLLDAETQLSL 503 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: 911 Number of extensions: 47 Number of successful extensions: 7 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: 540 Length adjustment: 36 Effective length of query: 525 Effective length of database: 504 Effective search space: 264600 Effective search space used: 264600 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 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