Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate H281DRAFT_02777 H281DRAFT_02777 alpha-glucosidase
Query= CAZy::AAS80455.1 (528 letters) >FitnessBrowser__Burk376:H281DRAFT_02777 Length = 524 Score = 615 bits (1585), Expect = e-180 Identities = 305/515 (59%), Positives = 365/515 (70%), Gaps = 25/515 (4%) Query: 2 WWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGYD 61 WW+ VIYQVYPRSFQD+NGDG+GDL G+ RLPYL LG+DA+WLSP Y SPM DFGYD Sbjct: 6 WWQRGVIYQVYPRSFQDSNGDGIGDLAGITSRLPYLAGLGIDAVWLSPIYPSPMADFGYD 65 Query: 62 VADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASRNSPKRD 121 VADYCD+DP+FGTL DF + + AH LGLKVL+D VPNH+S HPWF ESR+SR +PKRD Sbjct: 66 VADYCDIDPMFGTLGDFKQFADRAHELGLKVLLDFVPNHSSDRHPWFEESRSSRENPKRD 125 Query: 122 WYIWKDPAPDGGPPNNWQSFFGGPAWTLDEATGQYYLHQFLPEQPDLNWRNPEVREAIYE 181 WY+W+DPAPDGGPPNNW S GG AW DE TGQYY H FL EQPDLNWRNP+VR A+ + Sbjct: 126 WYLWRDPAPDGGPPNNWLSRMGGSAWEWDERTGQYYYHAFLREQPDLNWRNPQVRRAMDD 185 Query: 182 VMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPETYAY 241 V+RFWL RGVDGFRVDVLWLL +D FRD P NP + PG + R L +TEDQPE + Sbjct: 186 VLRFWLDRGVDGFRVDVLWLLIKDSQFRDNPPNPAYEPGQPEHHRQLQTYTEDQPEVHEI 245 Query: 242 VREMRQVLDEFSEPGRERVMVGEIYLPYPQLVRYYQA---GCHLPFNFHLIFRGLPDWRP 298 VR MR LDE+ ERV++GEIYLP PQLVRYY A G +PFNF L+ W Sbjct: 246 VRSMRATLDEYG----ERVLIGEIYLPVPQLVRYYGANGDGADMPFNFQLLNAA---WNA 298 Query: 299 ENLARIVEEYESLLTRWDWPNWVLGNHDQPRLASRLGEAQARVAAMLLFTLRGTPTWYYG 358 +AR++ +Y+S L WPNWVLGNHD PR+ASR+G AQARVAA+LL TLRGTPT YYG Sbjct: 299 GEIARMIRDYDSALPVHAWPNWVLGNHDNPRVASRVGAAQARVAAVLLLTLRGTPTLYYG 358 Query: 359 DEIGMKNGEIPPEKVQDPAALRQKDRLGEHNLPPGRDPERTPMQWDDT-PFAGFSTVEPW 417 DEIGM +GEI P++VQDPA +RQ D + GRDPERTPMQWD P AGF+ W Sbjct: 359 DEIGMTDGEISPDRVQDPAEIRQPD------IGQGRDPERTPMQWDAALPGAGFTNGRSW 412 Query: 418 LPVNPDYKTRNVAAQEQDPRSMLHLVRRLIALRK-DPDLLYGAYRTYRAREGVYAY---L 473 LP++ D +V AQ+ DP SML L RRL+ LR+ + L+ GA A V + Sbjct: 413 LPISTD---TSVRAQDGDPSSMLSLYRRLLELRRSNAALVQGAIENVAASGDVLTFERHY 469 Query: 474 RGEGWLVALNLTEKEKALELPRGGRVVLSTHLDRE 508 RG+ +ALN+ + ++ PR G V+LST RE Sbjct: 470 RGQRLFIALNMGAADAVMQ-PRSGVVLLSTLAGRE 503 Lambda K H 0.321 0.141 0.466 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: 1155 Number of extensions: 70 Number of successful extensions: 6 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: 528 Length of database: 524 Length adjustment: 35 Effective length of query: 493 Effective length of database: 489 Effective search space: 241077 Effective search space used: 241077 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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