Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate GFF3717 Psest_3786 Glycosidases
Query= CAZy::AAS80455.1 (528 letters) >FitnessBrowser__psRCH2:GFF3717 Length = 539 Score = 237 bits (604), Expect = 9e-67 Identities = 179/547 (32%), Positives = 246/547 (44%), Gaps = 110/547 (20%) Query: 1 MWWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGY 60 +W++ A IYQ+ P F+D+NGDG GDL G+ RL Y++ LG A+WL PFY+SP +D GY Sbjct: 4 LWYRNAAIYQIDPTLFRDSNGDGCGDLRGITERLDYIRGLGCTAVWLMPFYQSPFEDAGY 63 Query: 61 DVADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASRNSPKR 120 D++D+ VD FG L D LLE+A LGL V+++LV HTS +H WF E+R RNSP R Sbjct: 64 DISDHLQVDERFGDLADIVALLEKAEELGLHVIIELVVQHTSIQHKWFQEARRDRNSPYR 123 Query: 121 DWYIWKDPAPDGGPPNNWQSFFGGPAWTLDEATGQYYLHQFLPEQPDLNWRNPEVREAIY 180 D+YIW D D P WT DE GQYY H F +PDL+ NP V I Sbjct: 124 DYYIWADEPDDFMEP--IFPTVEDSIWTWDEEAGQYYRHLFYKHEPDLDLTNPRVIHEIE 181 Query: 181 EVMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPETYA 240 +M FWLR GV GFR+D + + G + G W T +PET Sbjct: 182 RIMSFWLRLGVSGFRIDAAVHMVR------QAGGGELEKGYWLLEHMRDFVTMRRPET-- 233 Query: 241 YVREMRQVLDEFSEPGRERVMVGEIYLPYPQLVRYY-----QAGCHLPF--NFHLIFRGL 293 V++GEI + V Y+ + L F N HL F L Sbjct: 234 -------------------VLLGEIDTDPDKYVEYFGDEADRVTLLLDFWTNNHL-FLSL 273 Query: 294 PDWRPENLARIVEEYESLLTRWDWPNWVLGNHDQ-------------------------- 327 + E L R + + + W+ NHD+ Sbjct: 274 ARQQAEPLVRALNSQPLPPSHSQYALWI-RNHDELSLDRLEEDERNEVMDTFAPDENMRA 332 Query: 328 ------PRLASRLGEAQARVAA--MLLFTLRGTPTWYYGDEIGMKNGEIPPEKVQDPAAL 379 RLA L + R+AA LLF+L GTP YG+EIGM + PE++ Sbjct: 333 YNRGIRRRLAPMLDGDERRIAATHALLFSLPGTPIIRYGEEIGMGDDLDRPERL------ 386 Query: 380 RQKDRLGEHNLPPGRDPERTPMQWDDTPFAGFSTVE-----PWLPVNP-DYKTRNVAAQE 433 RTPMQW + P AGFS + P + P Y+ NV AQ Sbjct: 387 ----------------AVRTPMQWSNEPNAGFSCTKGELAAPVIDEGPFTYEKINVFAQT 430 Query: 434 QDPRSML----HLVRRLIALRKDPDLLYGAYRTYRAREGVYAYLR---GEGWLVALNLTE 486 S++ +++R I LR ++ G T + +R G L+ +NL + Sbjct: 431 LRSDSLMARTGNMIRTRIGLR---EIGIGKRTTVEVNDPAVFAIRHDNGSTVLMLVNLAD 487 Query: 487 KEKALEL 493 +E +E+ Sbjct: 488 QETTVEI 494 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: 1009 Number of extensions: 48 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 528 Length of database: 539 Length adjustment: 35 Effective length of query: 493 Effective length of database: 504 Effective search space: 248472 Effective search space used: 248472 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