Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate AZOBR_RS25735 AZOBR_RS25735 alpha-amylase
Query= CAZy::AAS80455.1 (528 letters) >FitnessBrowser__azobra:AZOBR_RS25735 Length = 537 Score = 588 bits (1515), Expect = e-172 Identities = 299/539 (55%), Positives = 365/539 (67%), Gaps = 27/539 (5%) Query: 2 WWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGYD 61 WW+ VIYQVYPRSFQD+NGDGVGDL G+ RL +L++LGVDALW+SP Y SPM DFGYD Sbjct: 7 WWQSGVIYQVYPRSFQDSNGDGVGDLPGILARLDHLQTLGVDALWVSPIYPSPMADFGYD 66 Query: 62 VADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASRNSPKRD 121 V+DY V P+FGT++DF+RLL E H G+K+++D VPNH+S HPWF SR+SR+ PKRD Sbjct: 67 VSDYTGVHPLFGTMEDFERLLAELHRRGMKLILDFVPNHSSDRHPWFQASRSSRDDPKRD 126 Query: 122 WYIWKDPAPDGGPPNNWQSFFGGPAWTLDEATGQYYLHQFLPEQPDLNWRNPEVREAIYE 181 WYIW+D APDGGPPNNW S FGG AW D ATGQYY H +L EQPDLNWRNP +REA+ + Sbjct: 127 WYIWRDAAPDGGPPNNWLSEFGGGAWEWDAATGQYYYHAYLKEQPDLNWRNPALREAMLD 186 Query: 182 VMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPETYAY 241 +R WL RGVDGFRVD + L +D FRD P NP WR GM R + + T DQPE + Sbjct: 187 ALRVWLDRGVDGFRVDAIHHLIKDAQFRDNPPNPGWREGMSPVRRLIRLHTVDQPEVHDA 246 Query: 242 VREMRQVLDEFSEPGRERVMVGEIYLPYPQLVRYYQA---GCHLPFNFHLIFRGLPDWRP 298 + MR+V D + G +R+++GE YLP QL+ YY A G LPFNFHL+ W Sbjct: 247 IAAMRRVADGY---GPDRLLIGEAYLPIDQLMAYYGADLTGFQLPFNFHLL---STPWEA 300 Query: 299 ENLARIVEEYESLLTRWDWPNWVLGNHDQPRLASRLGEAQARVAAMLLFTLRGTPTWYYG 358 + LA ++ YE+ L WPNWVLGNHD+ R+ASRLG QARVAAMLL TLRGTPT Y G Sbjct: 301 KALAALIRTYEAALPPGGWPNWVLGNHDRSRVASRLGRGQARVAAMLLLTLRGTPTLYQG 360 Query: 359 DEIGMKNGEIPPEKVQDPAALRQKDRLGEHNLPP---GRDPERTPMQWDDTPFAGFSTVE 415 DEIGM + IPP++VQDP E N+P GRDP RTP+ WD P GF+T E Sbjct: 361 DEIGMTDVAIPPDRVQDP---------WEKNIPGLGLGRDPVRTPIPWDGGPRGGFTTGE 411 Query: 416 PWLPVNPDYKTRNVAAQEQDPRSMLHLVRRLIALRK-DPDLLYGAYRTYRAREGVYAYLR 474 PWLP+ PD++ NVAAQ DP SML L R L++LR+ +P L G Y A V Y R Sbjct: 412 PWLPLGPDHERVNVAAQAADPSSMLALHRALLSLRRAEPALSVGRYEPVSAENDVLVYER 471 Query: 475 GEG---WLVALNLTEKEKALE-LPRGGRVVLSTHLDR-EERVGERLFLRPDEGVAVRLD 528 G + V LNL+ E+ ++ +P + LSTHLDR E V L LRPDEGV + D Sbjct: 472 RHGRDRFRVLLNLSAAERTVDAVPDAAHIRLSTHLDRGGEPVSGALRLRPDEGVVIGFD 530 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: 1232 Number of extensions: 75 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: 528 Length of database: 537 Length adjustment: 35 Effective length of query: 493 Effective length of database: 502 Effective search space: 247486 Effective search space used: 247486 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 Apr 09 2024. 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