Align trehalose-6-phosphate hydrolase (TreC;KP1_0530) (EC 3.2.1.93) (characterized)
to candidate BWI76_RS02960 BWI76_RS02960 glucohydrolase
Query= CAZy::BAG86620.1 (551 letters) >FitnessBrowser__Koxy:BWI76_RS02960 Length = 551 Score = 1038 bits (2683), Expect = 0.0 Identities = 482/550 (87%), Positives = 507/550 (92%) Query: 1 MNHLPHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVTARLDYLQKLGVDAIWLTPFYVSPQ 60 MN LP WWQNGVIYQIYPKSFQDTTG+GTGDLRGVT+RLDYLQKLGVDAIWLTPFYVSPQ Sbjct: 1 MNTLPLWWQNGVIYQIYPKSFQDTTGTGTGDLRGVTSRLDYLQKLGVDAIWLTPFYVSPQ 60 Query: 61 VDNGYDVANYTAIDPSYGTMADFDALVAEAKARGIRIVLDMVLNHTSTEHEWFRQSLNKE 120 VDNGYDVANYTAIDP+YGT+ DFD LVA+A ARGIRIVLDMVLNHTSTEH WFR++LNKE Sbjct: 61 VDNGYDVANYTAIDPTYGTLDDFDELVAQAHARGIRIVLDMVLNHTSTEHAWFREALNKE 120 Query: 121 SPYRQFYIWRDGEPDALPNNWRSKFGGNAWQWHADSGQYYLHLFAIEQADLNWENPAVRA 180 SPYRQFYIWRDGEP PNNWRSKFGGNAWQWHA+S QYYLHLFA+EQADLNWENPAVRA Sbjct: 121 SPYRQFYIWRDGEPTTPPNNWRSKFGGNAWQWHAESEQYYLHLFAVEQADLNWENPAVRA 180 Query: 181 ELKKVCEFWADRGVDGLRLDVVNLISKDQTFPCDLDGDGRRFYTDGPRVHEFLQEMSRDV 240 ELKKVCEFWADRGVDGLRLDVVNLISKDQTFP D DGDGRRFYTDGPR HEFLQEMSRDV Sbjct: 181 ELKKVCEFWADRGVDGLRLDVVNLISKDQTFPSDTDGDGRRFYTDGPRAHEFLQEMSRDV 240 Query: 241 FTPRNLMTVGEMSSTSLEHCQQYAALDGRELSMTFNFHHLKVDYPGGEKWTLARPDYVAL 300 FTPR LMTVGEMSST+L HCQQYAALDG ELSMTFNFHHLKVDYPGGEKWTLARPD+VAL Sbjct: 241 FTPRGLMTVGEMSSTTLAHCQQYAALDGGELSMTFNFHHLKVDYPGGEKWTLARPDFVAL 300 Query: 301 KALFRHWQQGMHNRAWNALFWCNHDQPRIVSRFGDEGEYRVTAAKMLAMVLHGMQGTPYI 360 K+LFRHWQQGMHNRAWNALFWCNHDQPRIVSRFGDEGEYRV AAKMLAMVLHGMQGTPYI Sbjct: 301 KSLFRHWQQGMHNRAWNALFWCNHDQPRIVSRFGDEGEYRVPAAKMLAMVLHGMQGTPYI 360 Query: 361 YQGEEIGMTNPHFSSISDYRDVESHNMFIERAAQGQSPDELLAILASKSRDNSRTPMPWH 420 YQGEEIGMTNPHF I+DYRDVESHNMFIERAAQGQ PDELLAILASKSRDNSRTPM W+ Sbjct: 361 YQGEEIGMTNPHFMRITDYRDVESHNMFIERAAQGQDPDELLAILASKSRDNSRTPMQWN 420 Query: 421 AGENGGFSDGEPWIGLGDNYQEINVEAALADPDSVFYTYQQLITLRKTLPLLTWGDYEDL 480 ++GGFS GEPWI L DNY+EIN EAA ADP+SVFYTYQQLI LRK+ P+LTWGDY+DL Sbjct: 421 NADHGGFSAGEPWIALCDNYREINAEAAQADPESVFYTYQQLIALRKSAPVLTWGDYQDL 480 Query: 481 LPEHPSLWCYRRQWQGQTLVVAANLSRELQAWQPAEAPGEWKMIISNYAETTPRPTGLTL 540 LPEHPSLWCYRRQWQGQTLVV ANLSRE Q WQP GEW M++SNYAE RP +TL Sbjct: 481 LPEHPSLWCYRRQWQGQTLVVVANLSREFQRWQPEAMSGEWGMLMSNYAEAANRPAAMTL 540 Query: 541 RPFEAIWWLQ 550 RPFEA+WWLQ Sbjct: 541 RPFEAVWWLQ 550 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: 1392 Number of extensions: 55 Number of successful extensions: 1 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: 551 Length adjustment: 36 Effective length of query: 515 Effective length of database: 515 Effective search space: 265225 Effective search space used: 265225 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)
Align candidate BWI76_RS02960 BWI76_RS02960 (glucohydrolase)
to HMM TIGR02403 (treC: alpha,alpha-phosphotrehalase (EC 3.2.1.93))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR02403.hmm # target sequence database: /tmp/gapView.11828.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02403 [M=544] Accession: TIGR02403 Description: trehalose_treC: alpha,alpha-phosphotrehalase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-262 856.0 0.0 7.2e-262 855.8 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS02960 BWI76_RS02960 glucohydrolase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS02960 BWI76_RS02960 glucohydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 855.8 0.0 7.2e-262 7.2e-262 1 542 [. 7 548 .. 7 550 .. 0.99 Alignments for each domain: == domain 1 score: 855.8 bits; conditional E-value: 7.2e-262 TIGR02403 1 klkkkviyqiyPksfkdskgkgvGdlkGiiekldylkkLgvdviWltPiyksPqkDnGyDvsdylaidpef 71 ++++ viyqiyPksf+d++g+g+Gdl+G++++ldyl+kLgvd+iWltP+y+sPq DnGyDv++y+aidp++ lcl|FitnessBrowser__Koxy:BWI76_RS02960 7 WWQNGVIYQIYPKSFQDTTGTGTGDLRGVTSRLDYLQKLGVDAIWLTPFYVSPQVDNGYDVANYTAIDPTY 77 79********************************************************************* PP TIGR02403 72 GtledfeeLvkeakkrnikimlDlvlnhtsteheWfkkalagdekyrdfyilrdek.gklPtnWeskfGGs 141 Gtl+df+eLv++a++r+i+i+lD+vlnhtsteh+Wf++al+++++yr+fyi+rd + +++P+nW+skfGG+ lcl|FitnessBrowser__Koxy:BWI76_RS02960 78 GTLDDFDELVAQAHARGIRIVLDMVLNHTSTEHAWFREALNKESPYRQFYIWRDGEpTTPPNNWRSKFGGN 148 *******************************************************999************* PP TIGR02403 142 aWeleeetekyyLhLfdktqaDLnWeneevreevadvvkfwldkGvkGfrlDvinliskdelfeddeegdg 212 aW++++e+e+yyLhLf+++qaDLnWen++vr+e+++v++fw+d+Gv+G+rlDv+nliskd++f+ d++gdg lcl|FitnessBrowser__Koxy:BWI76_RS02960 149 AWQWHAESEQYYLHLFAVEQADLNWENPAVRAELKKVCEFWADRGVDGLRLDVVNLISKDQTFPSDTDGDG 219 *********************************************************************** PP TIGR02403 213 rkfytDgpkvheylkelneevfekdkdlltvGelssttiekcikyskleekeLsmvftfhhLkvDyengek 283 r+fytDgp+ he+l+e++++vf+ + l+tvGe+sstt+ +c++y++l+ eLsm+f+fhhLkvDy+ gek lcl|FitnessBrowser__Koxy:BWI76_RS02960 220 RRFYTDGPRAHEFLQEMSRDVFT-PRGLMTVGEMSSTTLAHCQQYAALDGGELSMTFNFHHLKVDYPGGEK 289 **********************8.*********************************************** PP TIGR02403 284 wtkakfdfaklkeilkewqeelqkengwnalflnnhDqPravsrfgddeeyreesakmlaaaihllrGtpy 354 wt+a++df++lk+++++wq++++ + +wnalf++nhDqPr+vsrfgd++eyr+ +akmla+++h ++Gtpy lcl|FitnessBrowser__Koxy:BWI76_RS02960 290 WTLARPDFVALKSLFRHWQQGMH-NRAWNALFWCNHDQPRIVSRFGDEGEYRVPAAKMLAMVLHGMQGTPY 359 **********************9.89********************************************* PP TIGR02403 355 iyqGeeiGmtnpkfekiedykDveslnaykalkkkgkseeevlailkaksrDnsrtpmqWdeeknaGfste 425 iyqGeeiGmtnp+f +i+dy+Dves n++ + ++g++ +e+lail++ksrDnsrtpmqW++ +++Gfs++ lcl|FitnessBrowser__Koxy:BWI76_RS02960 360 IYQGEEIGMTNPHFMRITDYRDVESHNMFIERAAQGQDPDELLAILASKSRDNSRTPMQWNNADHGGFSAG 430 *********************************************************************** PP TIGR02403 426 kpwlkvaknykeinvekeledeesvfkfykkliklrkeeeviaeGeyealekddpkvlaylrelkkekllv 496 +pw+++ +ny+ein+e++++d esvf++y++li+lrk+ +v+++G+y++l+ ++p++++y+r+++ ++l+v lcl|FitnessBrowser__Koxy:BWI76_RS02960 431 EPWIALCDNYREINAEAAQADPESVFYTYQQLIALRKSAPVLTWGDYQDLLPEHPSLWCYRRQWQGQTLVV 501 *********************************************************************** PP TIGR02403 497 lanfsgeekkvklpeelksakvllsnyeeaekk.aklelkPyeaivl 542 +an+s e ++ + ++ + ++ +l+sny ea+++ a+++l+P+ea+++ lcl|FitnessBrowser__Koxy:BWI76_RS02960 502 VANLSREFQRWQPEAMSGEWGMLMSNYAEAANRpAAMTLRPFEAVWW 548 *****88777777777778***********9999**********987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (544 nodes) Target sequences: 1 (551 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.55 // [ok]
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