Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 5210370 Shew_2813 phosphopentomutase (RefSeq)
Query= reanno::MR1:200397 (404 letters) >FitnessBrowser__PV4:5210370 Length = 405 Score = 714 bits (1844), Expect = 0.0 Identities = 348/404 (86%), Positives = 373/404 (92%) Query: 1 MKRTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEGKADTGRKGPLALPNLARLG 60 MKRTVIMMLDSFGVGAA DA FGD GS+TFGHIAKACAEGKA+ GR+GPL LPNLA+LG Sbjct: 1 MKRTVIMMLDSFGVGAAKDAEAFGDTGSNTFGHIAKACAEGKANDGREGPLKLPNLAKLG 60 Query: 61 LAHAAMESTGAFAPGFADNVDLIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH 120 LA AA ESTG+FA GF D+V++IGAYGHA ELSSGKDTPSGHWEMAGVPVL+EWGYFS+ Sbjct: 61 LALAAKESTGSFAEGFGDDVEVIGAYGHADELSSGKDTPSGHWEMAGVPVLYEWGYFSDL 120 Query: 121 QNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQIAC 180 ++SFPKELTDKIL RAGL GFLGNCHASGT ILEELGEEHM SG PIFYTSADSVFQIAC Sbjct: 121 KDSFPKELTDKILERAGLSGFLGNCHASGTAILEELGEEHMTSGLPIFYTSADSVFQIAC 180 Query: 181 HEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAKTV 240 HE TFGLENLY LC+IAREELEPYNIGRVIARPF GTGPSDFARTGNRKDY++EPP+KTV Sbjct: 181 HEETFGLENLYTLCQIAREELEPYNIGRVIARPFVGTGPSDFARTGNRKDYAVEPPSKTV 240 Query: 241 LDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTNFV 300 LDKLK AGGEVVSVGKIADIYA+CGITKKVKA GLEALFDATL +VK AG+ TIVFTNFV Sbjct: 241 LDKLKEAGGEVVSVGKIADIYAHCGITKKVKATGLEALFDATLEQVKQAGDRTIVFTNFV 300 Query: 301 DFDSHYGHRRDVAGYAKGLEYFDARLPEMLALLDEDDLLILTADHGCDPTWQGTDHTREY 360 DFDSHYGHRRD+AGYA+ LEYFD+RLPEMLALL E+DLL+LTADHGCDPTWQGTDHTRE Sbjct: 301 DFDSHYGHRRDIAGYARALEYFDSRLPEMLALLGEEDLLLLTADHGCDPTWQGTDHTRER 360 Query: 361 VPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI 404 VPVLAYGAGL GSLGRRNSFADIGQSIASYF LEPMEYGESF+ Sbjct: 361 VPVLAYGAGLAPGSLGRRNSFADIGQSIASYFGLEPMEYGESFV 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: 734 Number of extensions: 15 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: 405 Length adjustment: 31 Effective length of query: 373 Effective length of database: 374 Effective search space: 139502 Effective search space used: 139502 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 5210370 Shew_2813 (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.28493.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-169 550.1 0.0 1.3e-169 550.0 0.0 1.0 1 lcl|FitnessBrowser__PV4:5210370 Shew_2813 phosphopentomutase (Re Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5210370 Shew_2813 phosphopentomutase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 550.0 0.0 1.3e-169 1.3e-169 1 381 [] 3 402 .. 3 402 .. 0.98 Alignments for each domain: == domain 1 score: 550.0 bits; conditional E-value: 1.3e-169 TIGR01696 1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk..........lnlpnleklGlgkiee......lagvdave 62 r+ +++lds+G+G+a+da+ f+d G++t+ghia+a+++ l+lpnl+klGl+ + + +g + lcl|FitnessBrowser__PV4:5210370 3 RTVIMMLDSFGVGAAKDAEAFGDTGSNTFGHIAKACAEgkandgregpLKLPNLAKLGLALAAKestgsfAEGFGDDV 80 6789*********************************99*********************9998899998899999** PP TIGR01696 63 evlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkpasGtvildelGe 136 ev+++y++++e+ssGkdt++Ghwe+aG+++l e+++fs ++fp+el dk+ erag+ +lgn++asGt+il+elGe lcl|FitnessBrowser__PV4:5210370 81 EVIGAYGHADELSSGKDTPSGHWEMAGVPVLYEWGYFSdlkDSFPKELTDKILERAGLSgFLGNCHASGTAILEELGE 158 **************************************9999****************99****************** PP TIGR01696 137 ehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfkrtsnrhdyalk 213 ehm +G +i+ytsadsv+qia+hee+++le+ly lc++are+l y+iGr+iarpfvG + +f rt+nr+dya++ lcl|FitnessBrowser__PV4:5210370 159 EHMTSGLPIFYTSADSVFQIACHEETFGLENLYTLCQIAREELE--PYNIGRVIARPFVGTgPSDFARTGNRKDYAVE 234 ******************************************96..5*************99**************** PP TIGR01696 214 pfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftg.isfanlvdfdalyGhrrdk 290 p++ktvldklk+++ +v+s+Gkiadiy+ +Gitkkv+++++++++d++++++k++++ i+f+n+vdfd+ yGhrrd lcl|FitnessBrowser__PV4:5210370 235 PPSKTVLDKLKEAGGEVVSVGKIADIYAHCGITKKVKATGLEALFDATLEQVKQAGDRtIVFTNFVDFDSHYGHRRDI 312 *********************************************************99******************* PP TIGR01696 291 eGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkvkkgqalesaetfadiGatla 368 +Gya+ale fd+rlpe+l++l e+dll+ltadhG+dpt++Gtdhtre +pvl+y+ +g +l+++++fadiG+++a lcl|FitnessBrowser__PV4:5210370 313 AGYARALEYFDSRLPEMLALLGEEDLLLLTADHGCDPTWQGTDHTRERVPVLAYGAGLAPG-SLGRRNSFADIGQSIA 389 *************************************************************.**************** PP TIGR01696 369 dnfntskpeyGks 381 +f+ + +eyG s lcl|FitnessBrowser__PV4:5210370 390 SYFGLEPMEYGES 402 ***********86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (381 nodes) Target sequences: 1 (405 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.31 // [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