Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate BWI76_RS04140 BWI76_RS04140 phosphopentomutase
Query= BRENDA::P0A6K6 (407 letters) >FitnessBrowser__Koxy:BWI76_RS04140 Length = 407 Score = 790 bits (2041), Expect = 0.0 Identities = 379/406 (93%), Positives = 394/406 (97%) Query: 1 MKRAFIMVLDSFGIGATEDAERFGDVGADTLGHIAEACAKGEADNGRKGPLNLPNLTRLG 60 MKRAFIMVLDSFGIGATEDA+RFGDVG+DT+GHIAEACAKGEADNGRKGPLNLPNLTRLG Sbjct: 1 MKRAFIMVLDSFGIGATEDADRFGDVGSDTMGHIAEACAKGEADNGRKGPLNLPNLTRLG 60 Query: 61 LAKAHEGSTGFIPAGMDGNAEVIGAYAWAHEMSSGKDTPSGHWEIAGVPVLFEWGYFSDH 120 L KAHEGSTG + AGMDG+AEVIGAYAWAHE+SSGKDTPSGHWEIAGVPVLF+WGYF +H Sbjct: 61 LVKAHEGSTGKVAAGMDGSAEVIGAYAWAHELSSGKDTPSGHWEIAGVPVLFDWGYFPEH 120 Query: 121 ENSFPQELLDKLVERANLPGYLGNCHSSGTVILDQLGEEHMKTGKPIFYTSADSVFQIAC 180 ENSFPQELLDKLV+RANLPGYLGNCHSSGTVILDQLGEEHMKTGKPIFYTSADSVFQIAC Sbjct: 121 ENSFPQELLDKLVKRANLPGYLGNCHSSGTVILDQLGEEHMKTGKPIFYTSADSVFQIAC 180 Query: 181 HEETFGLDKLYELCEIAREELTNGGYNIGRVIARPFIGDKAGNFQRTGNRHDLAVEPPAP 240 HEET+GLDKLYELCEIAREELT GGYNIGRVIARPFIGDKAGNFQRTGNRHDLAVEPPAP Sbjct: 181 HEETYGLDKLYELCEIAREELTEGGYNIGRVIARPFIGDKAGNFQRTGNRHDLAVEPPAP 240 Query: 241 TVLQKLVDEKHGQVVSVGKIADIYANCGITKKVKATGLDALFDATIKEMKEAGDNTIVFT 300 TVLQKLVDEK GQVVSVGKIADIYANCGITKKVKATGLDALFDAT+KEMKEAGD TIVFT Sbjct: 241 TVLQKLVDEKKGQVVSVGKIADIYANCGITKKVKATGLDALFDATVKEMKEAGDETIVFT 300 Query: 301 NFVDFDSSWGHRRDVAGYAAGLELFDRRLPELMSLLRDDDILILTADHGCDPTWTGTDHT 360 NFVDFDSSWGHRRDVAGYAAGLELFDRRLPELM L+ +DDILILTADHGCDPTWTGTDHT Sbjct: 301 NFVDFDSSWGHRRDVAGYAAGLELFDRRLPELMELVGEDDILILTADHGCDPTWTGTDHT 360 Query: 361 REHIPVLVYGPKVKPGSLGHRETFADIGQTLAKYFGTSDMEYGKAM 406 REHIPVL+YGPKVKPGSLGHRETFADIGQTLA YFGTS M+YGK M Sbjct: 361 REHIPVLIYGPKVKPGSLGHRETFADIGQTLATYFGTSAMDYGKNM 406 Lambda K H 0.318 0.138 0.422 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: 820 Number of extensions: 28 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: 407 Length of database: 407 Length adjustment: 31 Effective length of query: 376 Effective length of database: 376 Effective search space: 141376 Effective search space used: 141376 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate BWI76_RS04140 BWI76_RS04140 (phosphopentomutase)
to HMM TIGR01696 (deoB: phosphopentomutase (EC 5.4.2.7))
# 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/TIGR01696.hmm # target sequence database: /tmp/gapView.18252.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01696 [M=381] Accession: TIGR01696 Description: deoB: phosphopentomutase 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-205 668.5 0.0 1.5e-205 668.3 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS04140 BWI76_RS04140 phosphopentomutase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS04140 BWI76_RS04140 phosphopentomutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 668.3 0.0 1.5e-205 1.5e-205 1 380 [. 3 404 .. 3 405 .. 0.99 Alignments for each domain: == domain 1 score: 668.3 bits; conditional E-value: 1.5e-205 TIGR01696 1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk..........lnlpnleklGlgkiee......l 55 r+f++vlds+GiG++eda++f+d+G+dt+ghiaea++k lnlpnl++lGl k++e lcl|FitnessBrowser__Koxy:BWI76_RS04140 3 RAFIMVLDSFGIGATEDADRFGDVGSDTMGHIAEACAKgeadngrkgpLNLPNLTRLGLVKAHEgstgkvA 73 89******************************************************************999 PP TIGR01696 56 agvdaveevlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgn 122 ag+d+++ev+++ya+++e+ssGkdt++GhweiaG+++l+++++f+ n+fp+elldkl++ra+++ +lgn lcl|FitnessBrowser__Koxy:BWI76_RS04140 74 AGMDGSAEVIGAYAWAHELSSGKDTPSGHWEIAGVPVLFDWGYFPeheNSFPQELLDKLVKRANLPgYLGN 144 9********************************************9999********************** PP TIGR01696 123 kpasGtvildelGeehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarp 193 +++sGtvild+lGeehmktGk+i+ytsadsv+qia+hee+ +l++lyelce+are+l++++y+iGr+iarp lcl|FitnessBrowser__Koxy:BWI76_RS04140 145 CHSSGTVILDQLGEEHMKTGKPIFYTSADSVFQIACHEETYGLDKLYELCEIAREELTEGGYNIGRVIARP 215 *********************************************************************** PP TIGR01696 194 fvGe.aGnfkrtsnrhdyalkpfaktvldklkdeky.dvisiGkiadiydgeGitkkvrtksnmdgldkvi 262 f+G+ aGnf+rt+nrhd+a++p+a+tvl+kl+dek +v+s+Gkiadiy+++Gitkkv+++++++++d+++ lcl|FitnessBrowser__Koxy:BWI76_RS04140 216 FIGDkAGNFQRTGNRHDLAVEPPAPTVLQKLVDEKKgQVVSVGKIADIYANCGITKKVKATGLDALFDATV 286 ***********************************99********************************** PP TIGR01696 263 kelkedftg.isfanlvdfdalyGhrrdkeGyaaaleefdarlpellsklreddlliltadhGndptatGt 332 ke+ke++++ i+f+n+vdfd+++Ghrrd++Gyaa+le fd+rlpel+ ++ edd+liltadhG+dpt+tGt lcl|FitnessBrowser__Koxy:BWI76_RS04140 287 KEMKEAGDEtIVFTNFVDFDSSWGHRRDVAGYAAGLELFDRRLPELMELVGEDDILILTADHGCDPTWTGT 357 ********99************************************************************* PP TIGR01696 333 dhtreyipvlvyspkvkkgqalesaetfadiGatladnfntskpeyGk 380 dhtre+ipvl+y+pkvk+g +l+++etfadiG+tla +f+ts ++yGk lcl|FitnessBrowser__Koxy:BWI76_RS04140 358 DHTREHIPVLIYGPKVKPG-SLGHRETFADIGQTLATYFGTSAMDYGK 404 *******************.***************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (381 nodes) Target sequences: 1 (407 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: 00:00:00.01 # Mc/sec: 8.99 // [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