Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 6936793 Sama_0975 phosphopentomutase (RefSeq)
Query= reanno::MR1:200397 (404 letters) >FitnessBrowser__SB2B:6936793 Length = 407 Score = 729 bits (1882), Expect = 0.0 Identities = 349/404 (86%), Positives = 380/404 (94%) Query: 1 MKRTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEGKADTGRKGPLALPNLARLG 60 MKRT+I+MLDSFG+GAA DA KFGDVGSDTFGHIA+ CAEGKA+ GR+G L LPNL+RLG Sbjct: 1 MKRTIILMLDSFGIGAADDADKFGDVGSDTFGHIAQMCAEGKANNGREGELKLPNLSRLG 60 Query: 61 LAHAAMESTGAFAPGFADNVDLIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH 120 LAHAA E+TGAFAPGF DNVD+IGAYGH QELSSGKDTPSGHWEMAGVPVLFEWGYFSEH Sbjct: 61 LAHAAKEATGAFAPGFGDNVDIIGAYGHCQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH 120 Query: 121 QNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQIAC 180 QNSFPKELTDKIL RAGL FLGNCHASGTTILEELGEEHM++GKPIFYTSADSVFQIAC Sbjct: 121 QNSFPKELTDKILERAGLTEFLGNCHASGTTILEELGEEHMKTGKPIFYTSADSVFQIAC 180 Query: 181 HEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAKTV 240 HE +FGLENLYRLCEIAREELEPYNIGRVIARPF GTGPSDFARTGNR+DY++EPP+KTV Sbjct: 181 HEESFGLENLYRLCEIAREELEPYNIGRVIARPFVGTGPSDFARTGNRRDYAVEPPSKTV 240 Query: 241 LDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTNFV 300 LDKLK AGGEVVSVGKI+DIYA+CGITKKVKA+GLE LFDATL ++K AG+NTIVFTNFV Sbjct: 241 LDKLKQAGGEVVSVGKISDIYAHCGITKKVKASGLEDLFDATLEQIKQAGDNTIVFTNFV 300 Query: 301 DFDSHYGHRRDVAGYAKGLEYFDARLPEMLALLDEDDLLILTADHGCDPTWQGTDHTREY 360 DFDSHYGHRRDV+GYAK LEYFDARLPE++ALL+E DLL+LTADHGCDPTWQGTDHTRE+ Sbjct: 301 DFDSHYGHRRDVSGYAKALEYFDARLPELMALLEEGDLLLLTADHGCDPTWQGTDHTREF 360 Query: 361 VPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI 404 VPVLAYGAGL+AGSLG+R SFADIGQSIASYF L MEYGESF+ Sbjct: 361 VPVLAYGAGLEAGSLGKRGSFADIGQSIASYFGLAAMEYGESFM 404 Lambda K H 0.318 0.137 0.412 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: 735 Number of extensions: 18 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: 404 Length of database: 407 Length adjustment: 31 Effective length of query: 373 Effective length of database: 376 Effective search space: 140248 Effective search space used: 140248 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 6936793 Sama_0975 (phosphopentomutase (RefSeq))
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.29530.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-175 567.1 0.0 8.9e-175 567.0 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6936793 Sama_0975 phosphopentomutase (Re Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6936793 Sama_0975 phosphopentomutase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 567.0 0.0 8.9e-175 8.9e-175 1 381 [] 3 402 .. 3 402 .. 0.98 Alignments for each domain: == domain 1 score: 567.0 bits; conditional E-value: 8.9e-175 TIGR01696 1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk..........lnlpnleklGlgkiee......lagvdav 61 r+ +++lds+GiG+a+da++f+d+G+dt+ghia+ +++ l+lpnl++lGl+++ + +g ++ lcl|FitnessBrowser__SB2B:6936793 3 RTIILMLDSFGIGAADDADKFGDVGSDTFGHIAQMCAEgkanngregeLKLPNLSRLGLAHAAKeatgafAPGFGDN 79 678999******************************9999*********************99989999999***** PP TIGR01696 62 eevlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkpasGtvildel 134 +++++y++ +e+ssGkdt++Ghwe+aG+++l+e+++fs n+fp+el dk+ erag+ +lgn++asGt+il+el lcl|FitnessBrowser__SB2B:6936793 80 VDIIGAYGHCQELSSGKDTPSGHWEMAGVPVLFEWGYFSehqNSFPKELTDKILERAGLTeFLGNCHASGTTILEEL 156 ***************************************9999***************998**************** PP TIGR01696 135 GeehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfkrtsnrhdy 210 GeehmktGk+i+ytsadsv+qia+hee ++le+ly+lce+are+l y+iGr+iarpfvG + +f rt+nr dy lcl|FitnessBrowser__SB2B:6936793 157 GEEHMKTGKPIFYTSADSVFQIACHEESFGLENLYRLCEIAREELE--PYNIGRVIARPFVGTgPSDFARTGNRRDY 231 ********************************************96..5*************99************* PP TIGR01696 211 alkpfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftg.isfanlvdfdalyGh 286 a++p++ktvldklk+++ +v+s+Gki+diy+ +Gitkkv++ +++d++d++++++k+++++ i+f+n+vdfd+ yGh lcl|FitnessBrowser__SB2B:6936793 232 AVEPPSKTVLDKLKQAGGEVVSVGKISDIYAHCGITKKVKASGLEDLFDATLEQIKQAGDNtIVFTNFVDFDSHYGH 308 ***************************************************************************** PP TIGR01696 287 rrdkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkvkkgqalesaetfadi 363 rrd++Gya+ale fdarlpel+++l e dll+ltadhG+dpt++Gtdhtre++pvl+y+ g +l+++ +fadi lcl|FitnessBrowser__SB2B:6936793 309 RRDVSGYAKALEYFDARLPELMALLEEGDLLLLTADHGCDPTWQGTDHTREFVPVLAYGAGLEAG-SLGKRGSFADI 384 ***************************************************************99.*********** PP TIGR01696 364 GatladnfntskpeyGks 381 G+++a +f+ + +eyG s lcl|FitnessBrowser__SB2B:6936793 385 GQSIASYFGLAAMEYGES 402 ****************86 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: 10.68 // [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