Align trehalose-6-phosphate hydrolase (TreA;BSU07810) (EC 3.2.1.93) (characterized)
to candidate 6937506 Sama_1662 alpha amylase, catalytic region (RefSeq)
Query= CAZy::CAB12610.1 (561 letters) >FitnessBrowser__SB2B:6937506 Length = 544 Score = 325 bits (833), Expect = 3e-93 Identities = 189/546 (34%), Positives = 289/546 (52%), Gaps = 60/546 (10%) Query: 7 PWWKKAVVYQIYPKSFNDTTGNGVGDLNGIIEKLDYLKTLQVDVLWLTPIYDSPQHDNGY 66 PWW+ A +YQIYP+S D+ G+G+GDL GIIE+LDY+ +L VD +W++P + SP D GY Sbjct: 5 PWWRGAAIYQIYPRSLKDSNGDGIGDLQGIIERLDYIASLNVDAIWISPFFRSPMKDFGY 64 Query: 67 DIRDYYSIYPEYGTMEDFERLVSEAHKRDLKVVMDLVVNHTSTEHKWFREAISSIDSPYR 126 DI DY + P +GTM+DF+ L+++AH LKVV+D V++HTS EH WF E+ S D+P Sbjct: 65 DISDYLDVDPMFGTMDDFDELIAKAHSLGLKVVIDQVLSHTSDEHAWFAESRQSRDNPKA 124 Query: 127 DFYIWKKPQENGSVPTNWESKFGGSAWELDEASGQYYLHLFDVTQADLNWENEEVRKHVY 186 D+Y+W P+E+G+ P NW + FGG AWE + QYYLH F +Q DLN+ E VR+ V Sbjct: 125 DWYVWADPREDGTPPNNWLAIFGGCAWEWEPRRQQYYLHNFLKSQPDLNFHCEAVRQAVL 184 Query: 187 DMMHFWFEKGIDGFRLDVINLISKDQRFPN-----AEEGDGRSFYTDGPRVHE------- 234 + + FW +KG+DGFRLD I D+ + A++ GR F D P ++ Sbjct: 185 NNVEFWLKKGVDGFRLDAITFCFHDKALRDNPAKPADKRQGRGFSEDNPYAYQYHWYNNE 244 Query: 235 ------FLHEMNEKVFSHYDSMTVGEMSS-TTVDHCIRYTNPDNKELDMTFSFHHLKVDY 287 F+ ++ + + ++T+GE+SS ++ YT DN+ L M +SF L DY Sbjct: 245 RPETLGFIEDLRALIDRYPGAVTLGEVSSEDSLATMAEYTRGDNR-LHMAYSFELLTKDY 303 Query: 288 PNGEKWALAPFDFLKLKEILSDWQTGMHAGGGWNALFWCNHDQPRVVSRYGDDGAYRVKS 347 G ++ + + + G GW NHD RV+SR+G G + Sbjct: 304 SAG-----------YIRSTVEALEGAI--GDGWPCWAIGNHDVERVISRWG-QGKGTPQM 349 Query: 348 AKMLATAIHMMQGTPYIYQGEELGMTNPKFTDISSYRDVESLNMYHAFKEKGMADQDITA 407 AKML+ + ++G+ +YQGEELG+T + +D + + F Sbjct: 350 AKMLSAMLGCLRGSLCVYQGEELGLTEADI-PFDALQDPFGIAFWPNF------------ 396 Query: 408 ILQAKSRDNSRTPVQWDAT-ENGGF----TTGTPWIPVAGNYREINAEAALRDQNSVFYH 462 K RD RTP+ W A E GF + PW+P+ +R +N A + +SV Sbjct: 397 ----KGRDGCRTPMPWQAEGEYMGFGATASGAMPWLPLPEEHRALNVAAQSANPDSVLNQ 452 Query: 463 YQKLIQIRKMYDIVTEGTYEIIAKDDPNIFAYLRHGSNEKLLVINNFYGTEAAFTLPDSL 522 + + + R+ + G + I +P + A+ R S++K+L + N T+P S Sbjct: 453 FSRFMAWRRTQPALVTGEIKFIDSKEP-VLAFERVSSDKKVLCVFNLSDKPQTMTVPGS- 510 Query: 523 APDEWK 528 + WK Sbjct: 511 --EPWK 514 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: 923 Number of extensions: 51 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: 544 Length adjustment: 36 Effective length of query: 525 Effective length of database: 508 Effective search space: 266700 Effective search space used: 266700 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