Align trehalose-6-phosphate hydrolase (TreC;KP1_0530) (EC 3.2.1.93) (characterized)
to candidate CCNA_02368 CCNA_02368 alpha-glucosidase
Query= CAZy::BAG86620.1 (551 letters) >FitnessBrowser__Caulo:CCNA_02368 Length = 547 Score = 320 bits (821), Expect = 7e-92 Identities = 190/533 (35%), Positives = 271/533 (50%), Gaps = 48/533 (9%) Query: 7 WWQNGVIYQIYPKSFQDTTGSGTGDLRGVTARLDYLQKLGVDAIWLTPFYVSPQVDNGYD 66 WW+ VIYQ+YP+SF D+ G G GDL G+TA LD++ LGV+ +WL+PF+ SP D GYD Sbjct: 26 WWRGAVIYQVYPRSFADSNGDGVGDLPGITAHLDHIASLGVEGVWLSPFFTSPMKDFGYD 85 Query: 67 VANYTAIDPSYGTMADFDALVAEAKARGIRIVLDMVLNHTSTEHEWFRQSLNKESPYR-Q 125 V+NY +DP +GT+ADFDAL+A A A G++I++D+V +HTS EH WF +S S + Sbjct: 86 VSNYCDVDPIFGTLADFDALIARAHALGLKIIIDLVFSHTSDEHPWFVESRQDRSNAKAD 145 Query: 126 FYIWRDGEPD-ALPNNWRSKFGGNAWQWHADSGQYYLHLFAIEQADLNWENPAVRAELKK 184 +++W D +PD + P+NW+S FGG AW W A GQYY+H F Q LN NPAV+ L Sbjct: 146 WFVWADAKPDGSPPSNWQSVFGGPAWTWDARRGQYYMHNFLSSQPQLNLHNPAVQEALLA 205 Query: 185 VCEFWADRGVDGLRLDVVNLISKDQTF----PCDLDGDGRRFYTDGPRVH--------EF 232 V +FW D+GVDG R D +N D P G R + ++H +F Sbjct: 206 VTQFWIDKGVDGFRFDAINFSMHDPALTDNPPLPPGGKRTRPFDFQDKIHNQSHADIPKF 265 Query: 233 LQEMSRDVFTPRNLMTVGEMSSTSLEHCQQYAALDGRELSMTFNFHHLKVDYPGGEKWTL 292 L + +V E+ E + L+ + F +L D GE Sbjct: 266 LSRLRALTDAAGGRFSVAEVGGDHAEREMKLFTAGEDRLNSAYGFLYLYADKLIGE---- 321 Query: 293 ARPDYVALKALFRHWQQGMHNRAWNALFWCNHDQPRIVSRFGDEGEYRVTAAKMLAMVLH 352 P A+ W G W + + NHD PR VSR+ EG R A++ ++L Sbjct: 322 MIPQGAAM------W-PGEAGEGWPSWTFSNHDAPRAVSRWA-EGRDRKAFAELCLLLLM 373 Query: 353 GMQGTPYIYQGEEIGMTNPHFSSISDYRDVESHNMFIERAAQGQSPDELLAILASKSRDN 412 G++G ++YQGEE+G+ H ER Q P+ + + RD Sbjct: 374 GLRGNVFVYQGEELGLPQAHVP--------------FERL---QDPEAIANWPQTLGRDG 416 Query: 413 SRTPMPWHAGE-NGGFSDGEPWIGLGDNYQEINVEAALADPDSVFYTYQQLITLRKTLPL 471 +RTPMPW +G N GFS EPW+ + + + V+A ADP S ++LI LR+ P Sbjct: 417 ARTPMPWVSGALNAGFSGVEPWLPVDPEHLPLAVDAQEADPASTLNVARRLIGLRRAYPA 476 Query: 472 LTWGDYEDLLPEHPSLWCYRRQWQGQTLVVAANLSRELQAWQPAEAPGEWKMI 524 L G + P L ++R +++A NL E W P W +I Sbjct: 477 LRTGAITFIDTNSP-LLIFQRGEGADAVLLAFNLGFETVTW---SLPDGWTLI 525 Lambda K H 0.320 0.136 0.446 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: 954 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: 551 Length of database: 547 Length adjustment: 36 Effective length of query: 515 Effective length of database: 511 Effective search space: 263165 Effective search space used: 263165 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: 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