Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 7023823 Shewana3_1043 phosphopentomutase (RefSeq)
Query= reanno::MR1:200397 (404 letters) >FitnessBrowser__ANA3:7023823 Length = 404 Score = 812 bits (2097), Expect = 0.0 Identities = 397/404 (98%), Positives = 402/404 (99%) Query: 1 MKRTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEGKADTGRKGPLALPNLARLG 60 MKRTVIMMLDSFGVGAAGDAAKFGD+GSDTFGHIAKACAEG+AD GR+GPL LPNLARLG Sbjct: 1 MKRTVIMMLDSFGVGAAGDAAKFGDLGSDTFGHIAKACAEGEADIGREGPLTLPNLARLG 60 Query: 61 LAHAAMESTGAFAPGFADNVDLIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH 120 LAHAAMESTGAFAPGFADNV+LIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH Sbjct: 61 LAHAAMESTGAFAPGFADNVELIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH 120 Query: 121 QNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQIAC 180 QNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQIAC Sbjct: 121 QNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQIAC 180 Query: 181 HEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAKTV 240 HEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAKTV Sbjct: 181 HEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAKTV 240 Query: 241 LDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTNFV 300 LDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTNFV Sbjct: 241 LDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTNFV 300 Query: 301 DFDSHYGHRRDVAGYAKGLEYFDARLPEMLALLDEDDLLILTADHGCDPTWQGTDHTREY 360 DFDSHYGHRRDVAGYAKGLEYFD+RLPEMLALLDEDDLLILTADHGCDPTWQGTDHTREY Sbjct: 301 DFDSHYGHRRDVAGYAKGLEYFDSRLPEMLALLDEDDLLILTADHGCDPTWQGTDHTREY 360 Query: 361 VPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI 404 VPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI Sbjct: 361 VPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI 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: 810 Number of extensions: 22 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: 404 Length adjustment: 31 Effective length of query: 373 Effective length of database: 373 Effective search space: 139129 Effective search space used: 139129 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 7023823 Shewana3_1043 (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.23415.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-171 556.3 0.0 1.7e-171 556.2 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7023823 Shewana3_1043 phosphopentomutase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7023823 Shewana3_1043 phosphopentomutase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 556.2 0.0 1.7e-171 1.7e-171 1 381 [] 3 402 .. 3 402 .. 0.98 Alignments for each domain: == domain 1 score: 556.2 bits; conditional E-value: 1.7e-171 TIGR01696 1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk..........lnlpnleklGlgkiee......lagvdav 61 r+ +++lds+G+G+a daa+f+d G+dt+ghia+a+++ l+lpnl++lGl+++ +g ++ lcl|FitnessBrowser__ANA3:7023823 3 RTVIMMLDSFGVGAAGDAAKFGDLGSDTFGHIAKACAEgeadigregpLTLPNLARLGLAHAAMestgafAPGFADN 79 6789*********************************99*********************9877789999999**** PP TIGR01696 62 eevlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkpasGtvildel 134 e +++y++++e+ssGkdt++Ghwe+aG+++l+e+++fs n+fp+el dk+ rag+ +lgn++asGt+il+el lcl|FitnessBrowser__ANA3:7023823 80 VELIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSehqNSFPKELTDKILARAGLDgFLGNCHASGTTILEEL 156 ***************************************9999*****************9**************** PP TIGR01696 135 GeehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfkrtsnrhdy 210 Geehm++Gk+i+ytsadsv+qia+he +++le+ly+lce+are+l y+iGr+iarpf G + +f rt+nr+dy lcl|FitnessBrowser__ANA3:7023823 157 GEEHMRSGKPIFYTSADSVFQIACHEGTFGLENLYRLCEIAREELE--PYNIGRVIARPFDGTgPSDFARTGNRKDY 231 ********************************************96..5*************99************* PP TIGR01696 211 alkpfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftg.isfanlvdfdalyGh 286 +l+p+aktvldklk ++ +v+s+Gkiadiy+ +Gitkkv+++++++++d+++ e+k ++++ i+f+n+vdfd+ yGh lcl|FitnessBrowser__ANA3:7023823 232 SLEPPAKTVLDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENtIVFTNFVDFDSHYGH 308 ************************************************************99*************** PP TIGR01696 287 rrdkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkvkkgqalesaetfadi 363 rrd++Gya++le fd+rlpe+l++l eddlliltadhG+dpt++Gtdhtrey+pvl+y+ k g +l+++++fadi lcl|FitnessBrowser__ANA3:7023823 309 RRDVAGYAKGLEYFDSRLPEMLALLDEDDLLILTADHGCDPTWQGTDHTREYVPVLAYGAGLKAG-SLGRRNSFADI 384 *****************************************************************.*********** PP TIGR01696 364 GatladnfntskpeyGks 381 G+++a +f+ + +eyG s lcl|FitnessBrowser__ANA3:7023823 385 GQSIASYFKLEPMEYGES 402 ****************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (381 nodes) Target sequences: 1 (404 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: 6.98 // [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