Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate Pf1N1B4_835 Trehalose-6-phosphate hydrolase (EC 3.2.1.93)
Query= CAZy::AAS80455.1 (528 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 Length = 549 Score = 328 bits (840), Expect = 4e-94 Identities = 213/567 (37%), Positives = 306/567 (53%), Gaps = 66/567 (11%) Query: 3 WKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGYDV 62 W+ +VIYQ+YP+SF G+ GDL GV +L YL LGVD LW++PF +SP +D GYD+ Sbjct: 4 WQRSVIYQIYPKSFHSHAGNPTGDLLGVVAKLDYLHWLGVDCLWITPFLRSPQRDNGYDI 63 Query: 63 ADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASRNSPKRDW 122 +DY +DP +GT+ D + L+ EA G+K+++D+V NHTS EH WF ++R+S ++P RD+ Sbjct: 64 SDYYAIDPSYGTMADCELLIAEAGKRGIKLMLDIVVNHTSIEHTWFQQARSSLDNPYRDF 123 Query: 123 YIWKDPAPDGGPPNNWQSFFGGPAWTLDEATGQYYLHQFLPEQPDLNWRNPEVREAIYEV 182 YIW+D PNNW+S FGG AW + TGQYYLH F Q DLNW NP+VR ++++ Sbjct: 124 YIWRD------QPNNWESKFGGSAWEYEAQTGQYYLHLFDHTQADLNWDNPQVRAEVFKM 177 Query: 183 MRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPETYAYV 242 MRFW +GV GFR+DV+ L+++ F ++ N D R F D P + Y+ Sbjct: 178 MRFWRDKGVGGFRLDVINLISKPADFPED--NSDGRR-----------FYTDGPNVHEYL 224 Query: 243 REMRQVLDEFSEPGRERVMVGEI-YLPYPQLVRYYQ---AGCHLPFNFHLI---FRGLPD 295 ++M + + E G + + VGE+ +RY + + FNFH + + L Sbjct: 225 QQMHREVFE----GHDLINVGEMSSTSLEHCIRYSRPESKELSMTFNFHHLKVDYPNLQK 280 Query: 296 WRPEN-----LARIVEEYES-LLTRWDWPNWVLGNHDQPRLASRLGE------AQARVAA 343 W + L RI+ ++++ + W NHDQPR+ SR G A++ Sbjct: 281 WVRADFDFLALKRILSDWQTGMQAGGGWNALFWCNHDQPRVVSRFGHDGEHRVVSAKMLG 340 Query: 344 MLLFTLRGTPTWYYGDEIGMKN-GEIPPEKVQDPAAL---RQKDRLGEHN-------LPP 392 L L+GTP Y G+E+GM N G ++ +D L R K G + + Sbjct: 341 TALHFLQGTPFVYQGEELGMTNPGFDHIDQYRDVETLNIFRLKREAGSSDVDNMAAIMQK 400 Query: 393 GRDPERTPMQWDDTPFAGFSTVEPWLPVNPDYKTRNVAAQEQDPRSMLHLVRRLIALRKD 452 RD RTPM W+ P AGFS VEPW+ V + NVA Q DP S+LH R+LIALR+ Sbjct: 401 SRDNGRTPMHWNTEPNAGFSAVEPWIGVPANAAQINVAHQLDDPDSVLHHYRQLIALRRS 460 Query: 453 PDLLY-GAYRTYRARE-GVYAYLR---GEGWLVALNLTEKEKALELP-------RGGRVV 500 L+ G YR ++AY+R GE LV N +ELP +V Sbjct: 461 ETLMSDGVYRQLLPEHTQIWAYVREGQGERLLVLNNFYGTPCEVELPPEVINESMVQSLV 520 Query: 501 LSTHLDREERVGERLFLRPDEGVAVRL 527 +S + D R ++FLRP E +RL Sbjct: 521 ISNYPDCPPR-NRQVFLRPYESFVLRL 546 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: 1044 Number of extensions: 56 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: 549 Length adjustment: 35 Effective length of query: 493 Effective length of database: 514 Effective search space: 253402 Effective search space used: 253402 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