Align Alpha,alpha-phosphotrehalase (EC 3.2.1.93) (characterized)
to candidate Pf1N1B4_835 Trehalose-6-phosphate hydrolase (EC 3.2.1.93)
Query= reanno::pseudo3_N2E3:AO353_15985 (549 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 Length = 549 Score = 1050 bits (2714), Expect = 0.0 Identities = 491/549 (89%), Positives = 517/549 (94%) Query: 1 MQDWQRSVIYQIYPKSFHSHAGNPTGDLLGVVAKLDYLQWLGVDCLWITPFLRSPQRDNG 60 MQDWQRSVIYQIYPKSFHSHAGNPTGDLLGVVAKLDYL WLGVDCLWITPFLRSPQRDNG Sbjct: 1 MQDWQRSVIYQIYPKSFHSHAGNPTGDLLGVVAKLDYLHWLGVDCLWITPFLRSPQRDNG 60 Query: 61 YDISDYYAIDPSYGTMADCELLIAEAGKRGIKLMLDIVVNHTSIEHSWFQQARSSLDNPY 120 YDISDYYAIDPSYGTMADCELLIAEAGKRGIKLMLDIVVNHTSIEH+WFQQARSSLDNPY Sbjct: 61 YDISDYYAIDPSYGTMADCELLIAEAGKRGIKLMLDIVVNHTSIEHTWFQQARSSLDNPY 120 Query: 121 RDFYIWRDQPNNWESKFGGSAWEYEAQTGQYFLHLFDHTQADLNWDNPQVRAEVFKLMRF 180 RDFYIWRDQPNNWESKFGGSAWEYEAQTGQY+LHLFDHTQADLNWDNPQVRAEVFK+MRF Sbjct: 121 RDFYIWRDQPNNWESKFGGSAWEYEAQTGQYYLHLFDHTQADLNWDNPQVRAEVFKMMRF 180 Query: 181 WRDKGVGGFRLDVINLISKPADFPEDHTDGRRFYTDGPNVHEYLQEMHREVFEGHDLINV 240 WRDKGVGGFRLDVINLISKPADFPED++DGRRFYTDGPNVHEYLQ+MHREVFEGHDLINV Sbjct: 181 WRDKGVGGFRLDVINLISKPADFPEDNSDGRRFYTDGPNVHEYLQQMHREVFEGHDLINV 240 Query: 241 GEMSSTSLEHCIRYSRPDSKELSMTFNFHHLKVDYPNMQKWVRADFDFLELKRILSDWQT 300 GEMSSTSLEHCIRYSRP+SKELSMTFNFHHLKVDYPN+QKWVRADFDFL LKRILSDWQT Sbjct: 241 GEMSSTSLEHCIRYSRPESKELSMTFNFHHLKVDYPNLQKWVRADFDFLALKRILSDWQT 300 Query: 301 GMQAGGGWNALFWCNHDQPRVVSRFGDDGEHRVVSAKMLGTALHFLQGTPFIYQGEELGM 360 GMQAGGGWNALFWCNHDQPRVVSRFG DGEHRVVSAKMLGTALHFLQGTPF+YQGEELGM Sbjct: 301 GMQAGGGWNALFWCNHDQPRVVSRFGHDGEHRVVSAKMLGTALHFLQGTPFVYQGEELGM 360 Query: 361 TNPGFERIEQYRDVETLNIYRLKREAGESEASSMAAIMQKSRDNSRTPMQWSALPNAGFS 420 TNPGF+ I+QYRDVETLNI+RLKREAG S+ +MAAIMQKSRDN RTPM W+ PNAGFS Sbjct: 361 TNPGFDHIDQYRDVETLNIFRLKREAGSSDVDNMAAIMQKSRDNGRTPMHWNTEPNAGFS 420 Query: 421 SSEPWIGVPANAMQINVENQLDDTTSVLHHYRQLIALRRSEPLIQDGVYRQLLPTHKQVW 480 + EPWIGVPANA QINV +QLDD SVLHHYRQLIALRRSE L+ DGVYRQLLP H Q+W Sbjct: 421 AVEPWIGVPANAAQINVAHQLDDPDSVLHHYRQLIALRRSETLMSDGVYRQLLPEHTQIW 480 Query: 481 VYLREGEGERLLVVNNFYGTACEVELPERVITDCMLQRLVISNYPDSEVRKQQLFLRPYE 540 Y+REG+GERLLV+NNFYGT CEVELP VI + M+Q LVISNYPD R +Q+FLRPYE Sbjct: 481 AYVREGQGERLLVLNNFYGTPCEVELPPEVINESMVQSLVISNYPDCPPRNRQVFLRPYE 540 Query: 541 SFVLHLTDH 549 SFVL LTDH Sbjct: 541 SFVLRLTDH 549 Lambda K H 0.321 0.137 0.436 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: 1402 Number of extensions: 54 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: 549 Length of database: 549 Length adjustment: 36 Effective length of query: 513 Effective length of database: 513 Effective search space: 263169 Effective search space used: 263169 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 (21.9 bits) S2: 53 (25.0 bits)
Align candidate Pf1N1B4_835 (Trehalose-6-phosphate hydrolase (EC 3.2.1.93))
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.13366.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-261 854.9 0.0 1.5e-261 854.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 Trehalose-6-phosphate hydrolase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 Trehalose-6-phosphate hydrolase (EC 3.2.1.93) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 854.7 0.0 1.5e-261 1.5e-261 2 543 .. 4 545 .. 3 546 .. 0.99 Alignments for each domain: == domain 1 score: 854.7 bits; conditional E-value: 1.5e-261 TIGR02403 2 lkkkviyqiyPksfkdskgkgvGdlkGiiekldylkkLgvdviWltPiyksPqkDnGyDvsdyla 66 ++++viyqiyPksf+++ g+ +Gdl G++ kldyl++Lgvd++W+tP+++sPq+DnGyD+sdy+a lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 4 WQRSVIYQIYPKSFHSHAGNPTGDLLGVVAKLDYLHWLGVDCLWITPFLRSPQRDNGYDISDYYA 68 99*************************************************************** PP TIGR02403 67 idpefGtledfeeLvkeakkrnikimlDlvlnhtsteheWfkkalag.dekyrdfyilrdekgkl 130 idp++Gt++d+e L++ea kr+ik+mlD+v+nhts+eh Wf++a+++ d++yrdfyi+rd + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 69 IDPSYGTMADCELLIAEAGKRGIKLMLDIVVNHTSIEHTWFQQARSSlDNPYRDFYIWRD----Q 129 ***********************************************************5....6 PP TIGR02403 131 PtnWeskfGGsaWeleeetekyyLhLfdktqaDLnWeneevreevadvvkfwldkGvkGfrlDvi 195 P+nWeskfGGsaWe+e++t++yyLhLfd+tqaDLnW+n++vr+ev+++++fw+dkGv GfrlDvi lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 130 PNNWESKFGGSAWEYEAQTGQYYLHLFDHTQADLNWDNPQVRAEVFKMMRFWRDKGVGGFRLDVI 194 9**************************************************************** PP TIGR02403 196 nliskdelfeddeegdgrkfytDgpkvheylkelneevfekdkdlltvGelssttiekcikyskl 260 nlisk+++f++d+ +dgr+fytDgp+vheyl+++++evfe +dl++vGe+sst++e+ci+ys++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 195 NLISKPADFPEDN-SDGRRFYTDGPNVHEYLQQMHREVFE-GHDLINVGEMSSTSLEHCIRYSRP 257 ***********96.89***********************8.************************ PP TIGR02403 261 eekeLsmvftfhhLkvDyengekwtkakfdfaklkeilkewqeelqkengwnalflnnhDqPrav 325 e+keLsm+f+fhhLkvDy+n +kw++a+fdf +lk+il++wq+++q+++gwnalf++nhDqPr+v lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 258 ESKELSMTFNFHHLKVDYPNLQKWVRADFDFLALKRILSDWQTGMQAGGGWNALFWCNHDQPRVV 322 ***************************************************************** PP TIGR02403 326 srfgddeeyreesakmlaaaihllrGtpyiyqGeeiGmtnpkfekiedykDveslnaykalkkkg 390 srfg+d+e+r+ sakml++a+h+l+Gtp++yqGee+Gmtnp f++i++y+Dve+ln+++ ++++g lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 323 SRFGHDGEHRVVSAKMLGTALHFLQGTPFVYQGEELGMTNPGFDHIDQYRDVETLNIFRLKREAG 387 ***************************************************************** PP TIGR02403 391 kseeevlailkaksrDnsrtpmqWdeeknaGfstekpwlkvaknykeinvekeledeesvfkfyk 455 s+ + +a +++ksrDn+rtpm+W+ e naGfs+ +pw+ v +n+++inv ++l+d +sv+++y+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 388 SSDVDNMAAIMQKSRDNGRTPMHWNTEPNAGFSAVEPWIGVPANAAQINVAHQLDDPDSVLHHYR 452 ***************************************************************** PP TIGR02403 456 kliklrkeeeviaeGeyealekddpkvlaylrelkkekllvlanfsgeekkvklpeelks....a 516 +li+lr++e+++++G y++l+ ++ +++ay+re + e+llvl+nf+g+ ++v+lp e+ + + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 453 QLIALRRSETLMSDGVYRQLLPEHTQIWAYVREGQGERLLVLNNFYGTPCEVELPPEVINesmvQ 517 *******************************************************9998878888 PP TIGR02403 517 kvllsnyeeaekk.aklelkPyeaivle 543 ++++sny + + +++ l+Pye++vl+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 518 SLVISNYPDCPPRnRQVFLRPYESFVLR 545 999******9988799********9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (544 nodes) Target sequences: 1 (549 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.03 # Mc/sec: 9.88 // [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