Query 025301
Match_columns 255
No_of_seqs 68 out of 70
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 04:27:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025301.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025301hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10250 O-FucT: GDP-fucose pr 99.1 7E-11 1.5E-15 106.6 3.4 123 94-226 174-330 (351)
2 PF01531 Glyco_transf_11: Glyc 94.1 0.067 1.5E-06 49.1 4.4 84 111-222 163-254 (298)
3 PF05830 NodZ: Nodulation prot 71.9 5.6 0.00012 38.5 4.4 132 75-225 134-285 (321)
4 KOG3705 Glycoprotein 6-alpha-L 68.1 4.4 9.5E-05 41.0 2.8 106 112-226 363-475 (580)
5 TIGR02898 spore_YhcN_YlaJ spor 56.1 21 0.00045 31.1 4.5 89 98-197 51-155 (158)
6 KOG3849 GDP-fucose protein O-f 43.0 30 0.00065 33.7 3.8 77 94-171 211-310 (386)
7 PF03620 IBV_3C: IBV 3C protei 36.0 17 0.00038 29.4 0.9 45 22-71 47-91 (93)
8 TIGR01668 YqeG_hyp_ppase HAD s 29.7 39 0.00084 28.3 2.1 84 90-188 3-86 (170)
9 PF01320 Colicin_Pyocin: Colic 26.8 23 0.00049 28.2 0.2 31 116-158 45-75 (85)
10 PF10245 MRP-S22: Mitochondria 26.1 13 0.00028 34.8 -1.6 41 60-107 196-236 (243)
11 PF02390 Methyltransf_4: Putat 25.7 59 0.0013 28.3 2.6 76 95-172 50-137 (195)
12 PF14399 Transpep_BrtH: NlpC/p 25.6 61 0.0013 29.1 2.7 41 146-186 73-114 (317)
13 PF11305 DUF3107: Protein of u 23.6 44 0.00095 26.0 1.2 47 130-178 4-53 (74)
14 PRK06319 DNA topoisomerase I/S 20.7 1.5E+02 0.0033 32.0 4.8 68 102-174 13-87 (860)
No 1
>PF10250 O-FucT: GDP-fucose protein O-fucosyltransferase; InterPro: IPR019378 This is a family of conserved proteins representing the enzyme responsible for adding O-fucose to EGF (epidermal growth factor-like) repeats. Six highly conserved cysteines are present as well as a DXD-like motif (ERD), conserved in mammals, Drosophila, and Caenorhabditis elegans. Both features are characteristic of several glycosyltransferase families. The enzyme is a membrane-bound protein released by proteolysis and, as for most glycosyltransferases, is strongly activated by manganese []. ; PDB: 3ZY6_A 3ZY3_A 3ZY5_A 3ZY2_A 3ZY4_A.
Probab=99.07 E-value=7e-11 Score=106.61 Aligned_cols=123 Identities=22% Similarity=0.268 Sum_probs=64.3
Q ss_pred ccchhHHHHHHHHHHHh----CCccEEEEeeC-ccccccccccc----------------------cccccCCCCCCCCC
Q 025301 94 MAAEKLRDAADKIKALL----VDYDSIHVRRG-DRLKTRKDRYG----------------------VDRSLFPHLDRDTR 146 (255)
Q Consensus 94 ~~a~~L~~~v~~I~~~l----gdfDavHVRRG-D~~~~~k~r~~----------------------v~r~l~P~ld~dts 146 (255)
-.++.++++|++++.++ |.|-|+|+|+| |+. +. -.++ -.....|.
T Consensus 174 ~~~~~i~~~a~~~i~~~~~~~~~yiavHlR~~~D~~-~~-C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~------ 245 (351)
T PF10250_consen 174 RFSPEIRELADKFIKRLLAGGGPYIAVHLRRGKDWF-SA-CEFKGERHLLASPRCWGKKSINPEKKRRNGCCPS------ 245 (351)
T ss_dssp -B-HHHHHHHHHHHHHH----SSEEEEEE--SHHHH-HH-HCT-T----TTTHHHH-GGGTT-----HHHHS--------
T ss_pred ecCHHHHHHHHHHHHHhhcccCceEEEeecccCchH-hh-cccCCchHHHHHhHhhccccccchhhhhcCCCCC------
Confidence 46788999999999887 39999999999 980 00 0000 00011221
Q ss_pred hHHHHHhhhccc--CCCcEEEEecCCC--CCCCCchhhhhcceeeccch---HHhhcccCcchhhHHHHHHHHHhCCcee
Q 025301 147 PEAILCRIKNWV--PPGRTLFIASNER--TPGFFSPLAVRYNLAYSSNF---SDILDLVVENNYQLFMVERLILMGARTF 219 (255)
Q Consensus 147 pe~i~~~~~~~v--~~gr~LYIATdE~--~~~fF~pL~~~y~v~~LdDF---~~l~~~~~~N~Y~l~mVD~lV~srgktf 219 (255)
.+.+...++..+ ...++||||||+. ....+++|++.|...+..+. .++++++.. .++.|||++|+++|..|
T Consensus 246 ~~~~~~~i~~~~~~~~~~~vYiAtd~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~--~~~a~vD~~i~~~s~~F 323 (351)
T PF10250_consen 246 TPQEAKQILRALGKNNTTVVYIATDEIYGGERRLDPLKNMFPNVVTKDDLLSHEELEPLND--DQLAMVDQEICSRSDVF 323 (351)
T ss_dssp HHHHHHHHHHHHHHHT-SEEEEEESS-----------HHHHHHHHGGGT--EE--S-------S--HHHHHHHHHHSSEE
T ss_pred hHHHHHHHHHHhccCCCCEEEEecCcccccchhHHHHHHHhhhhEeccccCCHHHhhhccc--cchhHHHHHHHhcCCEE
Confidence 233444444333 3469999999994 34577888888875441111 122333333 66779999999999999
Q ss_pred Eeecccc
Q 025301 220 IKTYKED 226 (255)
Q Consensus 220 vgTf~~~ 226 (255)
|||..|.
T Consensus 324 igt~~St 330 (351)
T PF10250_consen 324 IGTCGST 330 (351)
T ss_dssp EE-TT-H
T ss_pred EecCcch
Confidence 9999873
No 2
>PF01531 Glyco_transf_11: Glycosyl transferase family 11; InterPro: IPR002516 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 11 GT11 from CAZY comprises enzymes with only one known activity; galactoside 2-L-fucosyltransferase (2.4.1.69 from EC). Some of the proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Galactoside 2-L-fucosyltransferase 1 (2.4.1.69 from EC) and Galactoside 2-L-fucosyltransferase 2 (2.4.1.69 from EC) belong to the Hh blood group system and are associated with H/h and Se/se antigens.; GO: 0008107 galactoside 2-alpha-L-fucosyltransferase activity, 0005975 carbohydrate metabolic process, 0016020 membrane
Probab=94.11 E-value=0.067 Score=49.05 Aligned_cols=84 Identities=15% Similarity=0.176 Sum_probs=46.2
Q ss_pred CCccEEEEeeCccccccccccccccccCCCCCCCCChHHHHHh---hhcccCCCcEEEEecCCCCCCCCchhhhhcc---
Q 025301 111 VDYDSIHVRRGDRLKTRKDRYGVDRSLFPHLDRDTRPEAILCR---IKNWVPPGRTLFIASNERTPGFFSPLAVRYN--- 184 (255)
Q Consensus 111 gdfDavHVRRGD~~~~~k~r~~v~r~l~P~ld~dtspe~i~~~---~~~~v~~gr~LYIATdE~~~~fF~pL~~~y~--- 184 (255)
...-+|||||||.......+ ..++. .+++-..+. +++. .++-++||.||+.+- .++.+.
T Consensus 163 ~~~V~VHIRRGDy~~~~~~~-----~~~~~----~~~~Yy~~Ai~~i~~~-~~~~~f~ifSDD~~w-----~k~~l~~~~ 227 (298)
T PF01531_consen 163 SNSVCVHIRRGDYVSNGNHN-----WKHGI----CDKDYYKKAIEYIREK-VKNPKFFIFSDDIEW-----CKENLKFSN 227 (298)
T ss_pred CCeEEEEEEchhcccccccc-----ccCCC----CCHHHHHHHHHHHHHh-CCCCEEEEEcCCHHH-----HHHHHhhcC
Confidence 38899999999997654210 11111 224444333 3332 246689999997542 222221
Q ss_pred --eeeccchHHhhcccCcchhhHHHHHHHHHhCCceeEee
Q 025301 185 --LAYSSNFSDILDLVVENNYQLFMVERLILMGARTFIKT 222 (255)
Q Consensus 185 --v~~LdDF~~l~~~~~~N~Y~l~mVD~lV~srgktfvgT 222 (255)
+.+..+ .-+..|=..++.++.+|.+
T Consensus 228 ~~~~~~~~-------------~~~~~Dl~lms~C~~~Iis 254 (298)
T PF01531_consen 228 GDVYFSGN-------------NSPYEDLYLMSQCKHFIIS 254 (298)
T ss_pred CcEEEECC-------------CCHHHHHHHHHhCCcEEEC
Confidence 111111 1224566667889999988
No 3
>PF05830 NodZ: Nodulation protein Z (NodZ); InterPro: IPR008716 The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3SIX_A 2HLH_A 2HHC_A 3SIW_A 2OCX_A.
Probab=71.85 E-value=5.6 Score=38.45 Aligned_cols=132 Identities=15% Similarity=0.260 Sum_probs=61.0
Q ss_pred eecccccccccccCCCcccccchhHHHHHHHHHHHh-CCc--cEEEEeeCccccccccccccccccCCCCCCCCChHHHH
Q 025301 75 CKDRKNHSALMLPHSFLPSMAAEKLRDAADKIKALL-VDY--DSIHVRRGDRLKTRKDRYGVDRSLFPHLDRDTRPEAIL 151 (255)
Q Consensus 75 Ce~e~~~~~v~rp~~~l~~~~a~~L~~~v~~I~~~l-gdf--DavHVRRGD~~~~~k~r~~v~r~l~P~ld~dtspe~i~ 151 (255)
|+-+++++ | +.+| -..+....-+++|..+. .++ -+||||+|...- .+-|=..-+.++.-+
T Consensus 134 c~~~aeR~-i---f~sl--kpR~eIqarID~iy~ehf~g~~~IGVHVRhGngeD-----------~~~h~~~~~D~e~~L 196 (321)
T PF05830_consen 134 CDEEAERE-I---FSSL--KPRPEIQARIDAIYREHFAGYSVIGVHVRHGNGED-----------IMDHAPYWADEERAL 196 (321)
T ss_dssp S-HHHHHH-H---HHHS---B-HHHHHHHHHHHHHHTTTSEEEEEEE--------------------------HHHHHHH
T ss_pred chhHHHHH-H---HHhC--CCCHHHHHHHHHHHHHHcCCCceEEEEEeccCCcc-----------hhccCccccCchHHH
Confidence 66666443 2 3344 34566777778876665 466 789999996631 111100111233222
Q ss_pred ----Hhhh--cccCC--CcEEEEecCCCCCCCCchhhhhcc-e-eeccchHHh-hcccCc-----chhhHHHHHHHHHhC
Q 025301 152 ----CRIK--NWVPP--GRTLFIASNERTPGFFSPLAVRYN-L-AYSSNFSDI-LDLVVE-----NNYQLFMVERLILMG 215 (255)
Q Consensus 152 ----~~~~--~~v~~--gr~LYIATdE~~~~fF~pL~~~y~-v-~~LdDF~~l-~~~~~~-----N~Y~l~mVD~lV~sr 215 (255)
..+. ....+ .-.||+|||+.. .-+.|+++|- + ..-++|..- -+++.. ++-.-++||-..+++
T Consensus 197 ~~V~~ai~~ak~~~~~k~~~IFLATDSae--Vid~fr~~FPdiiti~k~F~~~~~g~Lhs~~~g~~gg~~ALIDM~LLSr 274 (321)
T PF05830_consen 197 RQVCTAIDKAKALAPPKPVRIFLATDSAE--VIDQFRKKFPDIITIPKQFPASQAGPLHSAAVGIEGGESALIDMYLLSR 274 (321)
T ss_dssp HHHHHHHHHHHTS--SS-EEEEEEES-HH--HHHHHHHHSTTEE----------------HHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHhccCCCCeeEEEecCcHH--HHHHHHHHCCCeEEcccccCCCCCCcCcccccccchHHHHHHHHHHHHh
Confidence 2221 11233 466999999875 4677777774 2 333445321 112222 445568999999999
Q ss_pred CceeE-eeccc
Q 025301 216 ARTFI-KTYKE 225 (255)
Q Consensus 216 gktfv-gTf~~ 225 (255)
..+-| =|..|
T Consensus 275 CD~LIr~~ptS 285 (321)
T PF05830_consen 275 CDYLIRFPPTS 285 (321)
T ss_dssp SSEEEEESTT-
T ss_pred CCeEEEcCCCc
Confidence 99999 47777
No 4
>KOG3705 consensus Glycoprotein 6-alpha-L-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=68.12 E-value=4.4 Score=41.00 Aligned_cols=106 Identities=16% Similarity=0.194 Sum_probs=66.0
Q ss_pred CccEEEEeeCccccccccccccccccCCCCCCCCChHHHHHhhhcccCC-CcEEEEecCCCCCCCCchhhhhcc-eeecc
Q 025301 112 DYDSIHVRRGDRLKTRKDRYGVDRSLFPHLDRDTRPEAILCRIKNWVPP-GRTLFIASNERTPGFFSPLAVRYN-LAYSS 189 (255)
Q Consensus 112 dfDavHVRRGD~~~~~k~r~~v~r~l~P~ld~dtspe~i~~~~~~~v~~-gr~LYIATdE~~~~fF~pL~~~y~-v~~Ld 189 (255)
---++||||-|+.... ...||-.+--+--|.++.-++..-++ .|.+|+|||.+. ..+--+.+|- --+.+
T Consensus 363 PivGvhvRRTDKVGTE-------AAfH~~eEYM~~vE~~f~~le~rg~~~~rRiflAsDDp~--vv~EAk~kYPnYe~ig 433 (580)
T KOG3705|consen 363 PIVGVHVRRTDKVGTE-------AAFHALEEYMEWVEIWFKVLEKRGKPLERRIFLASDDPT--VVPEAKNKYPNYEVIG 433 (580)
T ss_pred ceeeEEEEecccccch-------hhhhhHHHHHHHHHHHHHHHHHhCCchhheEEEecCCch--hchHhhccCCCcEEec
Confidence 5679999999997443 34555433333456666665554333 789999999654 4555666663 34444
Q ss_pred chHHhhc-ccCc----chhhHHHHHHHHHhCCceeEeecccc
Q 025301 190 NFSDILD-LVVE----NNYQLFMVERLILMGARTFIKTYKED 226 (255)
Q Consensus 190 DF~~l~~-~~~~----N~Y~l~mVD~lV~srgktfvgTf~~~ 226 (255)
|=+--|- .++. +..|-.++|--+.|...-.|-||.|-
T Consensus 434 d~eia~~A~l~nRYTd~sL~GvIlDIh~LS~~d~LVCTFSSQ 475 (580)
T KOG3705|consen 434 DTEIAKTAQLNNRYTDASLMGVILDIHILSKVDYLVCTFSSQ 475 (580)
T ss_pred cHHHHHHhhccccchhhhhhheeeeeeeecccceEEEechHH
Confidence 4333332 2222 45566677777888888888888775
No 5
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic 40-residue C-terminal domain that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=56.08 E-value=21 Score=31.08 Aligned_cols=89 Identities=18% Similarity=0.255 Sum_probs=51.1
Q ss_pred hHHHHHHHHHHHh---CC-ccEEEEeeCccccccccccccccccCCCCCCCCChHHHHHhh----hcccCCCcEEEEecC
Q 025301 98 KLRDAADKIKALL---VD-YDSIHVRRGDRLKTRKDRYGVDRSLFPHLDRDTRPEAILCRI----KNWVPPGRTLFIASN 169 (255)
Q Consensus 98 ~L~~~v~~I~~~l---gd-fDavHVRRGD~~~~~k~r~~v~r~l~P~ld~dtspe~i~~~~----~~~v~~gr~LYIATd 169 (255)
.+.++|++|+++. .+ =||-=|.-|+-+.. ||+ +=.+. .+...++|...+ +...|.++.+||++|
T Consensus 51 ~~~~~A~~Ia~~v~~v~~V~dA~vvVtg~~A~V-----gv~--~~~~~-~~~~~~~iK~~Va~~Vk~~dp~~~~VyVsaD 122 (158)
T TIGR02898 51 DLYDVADEIASEAAKVKGVKDATVVITGNYAYV-----GVD--LTNGL-EGSVTDELKEKVAETVKSTDNRIANVYVSAD 122 (158)
T ss_pred hHHHHHHHHHHHHhcCCCCceEEEEEECCEEEE-----EEE--cCCCc-chhhHHHHHHHHHHHHHhhCCCcceEEEEcC
Confidence 4567777776655 34 45555666887653 221 11111 122345555444 466778999999997
Q ss_pred CCCCCCCchhhhhcc-e-------eeccchHHhhcc
Q 025301 170 ERTPGFFSPLAVRYN-L-------AYSSNFSDILDL 197 (255)
Q Consensus 170 E~~~~fF~pL~~~y~-v-------~~LdDF~~l~~~ 197 (255)
+.||+-++.--+ + -|+++|.++...
T Consensus 123 ---pd~~~Ri~~~~~~i~~G~pv~~~~~e~~~iv~R 155 (158)
T TIGR02898 123 ---PDTVERIRRYGKGIKEGRPVEGFLDELAEIVRR 155 (158)
T ss_pred ---HHHHHHHHHHHHHhHcCCChHHHHHHHHHHHHh
Confidence 568888776543 2 455555555443
No 6
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=42.96 E-value=30 Score=33.72 Aligned_cols=77 Identities=26% Similarity=0.421 Sum_probs=45.1
Q ss_pred ccchhHHHHHHH-HHHHhC-CccEEEEeeCccc-------cc--ccccc------ccccc---cCCCCCCCCChHHHHHh
Q 025301 94 MAAEKLRDAADK-IKALLV-DYDSIHVRRGDRL-------KT--RKDRY------GVDRS---LFPHLDRDTRPEAILCR 153 (255)
Q Consensus 94 ~~a~~L~~~v~~-I~~~lg-dfDavHVRRGD~~-------~~--~k~r~------~v~r~---l~P~ld~dtspe~i~~~ 153 (255)
.+|.+.++.+.+ |.+.|- -|-+||.|-|--- +. .+.=| |-.++ |.|.+- --|-++|++.
T Consensus 211 ~WS~r~~e~~k~fI~a~L~rpfvgiHLRng~DWvraCehikd~~~~hlfASpQClGy~~~~gaLt~e~C-~Psk~~I~rq 289 (386)
T KOG3849|consen 211 RWSSRITEQAKKFISANLARPFVGIHLRNGADWVRACEHIKDTTNRHLFASPQCLGYGHHLGALTKEIC-SPSKQQILRQ 289 (386)
T ss_pred HHHHHHHHHHHHHHHHhcCcceeEEEeecCchHHHHHHHhcccCCCccccChhhccccccccccchhhh-CccHHHHHHH
Confidence 467777787766 556665 9999999987421 11 00000 00011 111100 1136789999
Q ss_pred hhcccCC---CcEEEEecCCC
Q 025301 154 IKNWVPP---GRTLFIASNER 171 (255)
Q Consensus 154 ~~~~v~~---gr~LYIATdE~ 171 (255)
++.+|.. -.-||+|||..
T Consensus 290 ik~~v~si~dakSVfVAsDs~ 310 (386)
T KOG3849|consen 290 IKEKVGSIGDAKSVFVASDSD 310 (386)
T ss_pred HHHHHhhhcccceEEEeccch
Confidence 9988876 45899999953
No 7
>PF03620 IBV_3C: IBV 3C protein; InterPro: IPR005296 These proteins are the product of ORF 3C from Infectious bronchitis virus. Currently, the function of this protein remains unknown.
Probab=36.03 E-value=17 Score=29.36 Aligned_cols=45 Identities=22% Similarity=0.324 Sum_probs=33.8
Q ss_pred hhHHHHHHhhhccccceeEEeeeccccccccccccccceeeeecCCCcee
Q 025301 22 KIWYHVLMTSMKLGARGVAHVEGVSRVNLNDNRRYSNLLLINRTASPLSW 71 (255)
Q Consensus 22 ~~W~~~~~~~~k~g~~~~~~~~~vs~~~l~~~~~~~~~~lI~R~f~~~~W 71 (255)
.+||-|.. -+|++|++++.+.++-+-..+++. ..+|.-.|-.|+|
T Consensus 47 Lfwytw~v---~pgak~~afvY~~tygkkln~pel--E~VivneFPkNg~ 91 (93)
T PF03620_consen 47 LFWYTWVV---VPGAKGTAFVYNHTYGKKLNNPEL--EAVIVNEFPKNGW 91 (93)
T ss_pred HHhhheee---ccCCceeEEeeccccccccCchhh--hhhhhhhcccCCC
Confidence 58999986 689999999999999885455442 2455556766777
No 8
>TIGR01668 YqeG_hyp_ppase HAD superfamily (subfamily IIIA) phosphatase, TIGR01668. This family consists of sequences from fungi, plants, cyanobacteria, gram-positive bacteria and Deinococcus. There is presently no characterization of any sequence in this family.
Probab=29.67 E-value=39 Score=28.32 Aligned_cols=84 Identities=15% Similarity=0.215 Sum_probs=45.8
Q ss_pred CcccccchhHHHHHHHHHHHhCCccEEEEeeCccccccccccccccccCCCCCCCCChHHHHHhhhcccCCCcEEEEecC
Q 025301 90 FLPSMAAEKLRDAADKIKALLVDYDSIHVRRGDRLKTRKDRYGVDRSLFPHLDRDTRPEAILCRIKNWVPPGRTLFIASN 169 (255)
Q Consensus 90 ~l~~~~a~~L~~~v~~I~~~lgdfDavHVRRGD~~~~~k~r~~v~r~l~P~ld~dtspe~i~~~~~~~v~~gr~LYIATd 169 (255)
++|.|-.+++++|.-.+..+.| +.++=+....-.-..+ ...++|. ..++++.+++ .|-.|+|+||
T Consensus 3 ~~~~~~~~~~~~i~~~~~~~~~-v~~vv~D~Dgtl~~~~-----~~~~~pg------v~e~L~~Lk~---~g~~l~I~Sn 67 (170)
T TIGR01668 3 CLPHAIVKTLNDLTIDLLKKVG-IKGVVLDKDNTLVYPD-----HNEAYPA------LRDWIEELKA---AGRKLLIVSN 67 (170)
T ss_pred cCcccccCchhhCCHHHHHHCC-CCEEEEecCCccccCC-----CCCcChh------HHHHHHHHHH---cCCEEEEEeC
Confidence 4566667788888888776653 4444333311111000 0012221 2345555554 6889999999
Q ss_pred CCCCCCCchhhhhcceeec
Q 025301 170 ERTPGFFSPLAVRYNLAYS 188 (255)
Q Consensus 170 E~~~~fF~pL~~~y~v~~L 188 (255)
......-..+.+++.+.++
T Consensus 68 ~~~~~~~~~~~~~~gl~~~ 86 (170)
T TIGR01668 68 NAGEQRAKAVEKALGIPVL 86 (170)
T ss_pred CchHHHHHHHHHHcCCEEE
Confidence 8644455556566666543
No 9
>PF01320 Colicin_Pyocin: Colicin immunity protein / pyocin immunity protein; InterPro: IPR023802 Bacterial colicin and pyocin immunity proteins [, ] can bind specifically to the DNase-type colicins and pyocins and inhibit their bactericidal activity. The 1.8-angstrom crystal structure of the ImmE7 protein consists of four antiparallel alpha-helices []. Sequence similarities between colicins E2, A and E1 [] are less striking. The colicin E2 (pyocin) immunity protein does not share similarity with either the colicin E3 or cloacin DF13 [] immunity proteins. Pyocin protects a cell that harbours the plasmid ColE2 encoding colicin E2 against colicin E2; it is thus essential both for autonomous replication and colicin E2 immunity []. This entry represents the structural domain of colicin and pyocin immunity proteins.; GO: 0015643 toxin binding, 0030153 bacteriocin immunity; PDB: 1GXH_A 1GXG_A 1MZ8_C 2ERH_A 1ZNV_C 1AYI_A 1UNK_A 2JBG_A 7CEI_A 1CEI_A ....
Probab=26.78 E-value=23 Score=28.19 Aligned_cols=31 Identities=29% Similarity=0.633 Sum_probs=24.3
Q ss_pred EEEeeCccccccccccccccccCCCCCCCCChHHHHHhhhccc
Q 025301 116 IHVRRGDRLKTRKDRYGVDRSLFPHLDRDTRPEAILCRIKNWV 158 (255)
Q Consensus 116 vHVRRGD~~~~~k~r~~v~r~l~P~ld~dtspe~i~~~~~~~v 158 (255)
-|-..+|++ .||.-+++-|||.|++.+++|=
T Consensus 45 eHP~gSDLI------------fYP~~~~edsPegIv~~vKeWR 75 (85)
T PF01320_consen 45 EHPDGSDLI------------FYPEDGREDSPEGIVKEVKEWR 75 (85)
T ss_dssp --TTTTHHH------------HS-STTSTSSHHHHHHHHHHHH
T ss_pred CCCCCCcee------------eeCCCCCCCCHHHHHHHHHHHH
Confidence 478888887 4788889999999999999874
No 10
>PF10245 MRP-S22: Mitochondrial 28S ribosomal protein S22; InterPro: IPR019374 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is the conserved N terminus and central portion of the mitochondrial small subunit 28S ribosomal protein S22. Mammalian mitochondria carry out the synthesis of 13 polypeptides that are essential for oxidative phosphorylation and, hence, for the synthesis of the majority of the ATP used by eukaryotic organisms. The number of proteins produced by prokaryotes is smaller, reflected in the lower number of ribosomal proteins present in them [].
Probab=26.08 E-value=13 Score=34.78 Aligned_cols=41 Identities=20% Similarity=0.428 Sum_probs=29.6
Q ss_pred eeeeecCCCceeeeeeecccccccccccCCCcccccchhHHHHHHHHH
Q 025301 60 LLINRTASPLSWFMECKDRKNHSALMLPHSFLPSMAAEKLRDAADKIK 107 (255)
Q Consensus 60 ~lI~R~f~~~~WyrvCe~e~~~~~v~rp~~~l~~~~a~~L~~~v~~I~ 107 (255)
+---||||++.||-+..+.. .. +-..|| ++.+|.+||+-|.
T Consensus 196 LrSTRHfG~m~fyL~~~~~i-d~---LL~dmi---~~~~l~dA~~Li~ 236 (243)
T PF10245_consen 196 LRSTRHFGPMAFYLVWNKKI-DG---LLYDMI---QRDRLDDAVNLIR 236 (243)
T ss_pred HhccCccchhHHHHHHccCc-HH---HHHHHH---HhhHHHHHHHHHH
Confidence 33448999999999987776 22 224555 7778999998664
No 11
>PF02390 Methyltransf_4: Putative methyltransferase ; InterPro: IPR003358 This entry represents tRNA (guanine-N-7) methyltransferase (2.1.1.33 from EC), which catalyses the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. Capping of the pre-mRNA 5' end by addition a monomethylated guanosine cap (m(7)G) is an essential and the earliest modification in the biogenesis of mRNA []. The reaction is catalysed by three enzymes: triphosphatase, guanylyltransferase, and tRNA (guanine-N-7) methyltransferase [, ].; GO: 0008176 tRNA (guanine-N7-)-methyltransferase activity, 0006400 tRNA modification; PDB: 3DXZ_A 3DXY_A 3DXX_A 3CKK_A 3P2I_B 3P2K_D 3P2E_A 3MTE_B 3PB3_B 1YZH_B ....
Probab=25.70 E-value=59 Score=28.32 Aligned_cols=76 Identities=20% Similarity=0.335 Sum_probs=37.9
Q ss_pred cchhHHHHHHHHHHHhCCccEEEEeeCcccccccccc---cccc------ccCCC---CCCCCChHHHHHhhhcccCCCc
Q 025301 95 AAEKLRDAADKIKALLVDYDSIHVRRGDRLKTRKDRY---GVDR------SLFPH---LDRDTRPEAILCRIKNWVPPGR 162 (255)
Q Consensus 95 ~a~~L~~~v~~I~~~lgdfDavHVRRGD~~~~~k~r~---~v~r------~l~P~---ld~dtspe~i~~~~~~~v~~gr 162 (255)
..+++..++.++... +..-+++-+||....-..-+ .|++ ..||. --+..--++.++.+...+.+|.
T Consensus 50 ~~~~v~~a~~~~~~~--~l~Nv~~~~~da~~~l~~~~~~~~v~~i~i~FPDPWpK~rH~krRl~~~~fl~~~~~~L~~gG 127 (195)
T PF02390_consen 50 RKKRVAKALRKAEKR--GLKNVRFLRGDARELLRRLFPPGSVDRIYINFPDPWPKKRHHKRRLVNPEFLELLARVLKPGG 127 (195)
T ss_dssp -HHHHHHHHHHHHHH--TTSSEEEEES-CTTHHHHHSTTTSEEEEEEES-----SGGGGGGSTTSHHHHHHHHHHEEEEE
T ss_pred chHHHHHHHHHHHhh--cccceEEEEccHHHHHhhcccCCchheEEEeCCCCCcccchhhhhcCCchHHHHHHHHcCCCC
Confidence 444566666666555 67888888888653111000 1110 01221 1111223455556666677888
Q ss_pred EEEEecCCCC
Q 025301 163 TLFIASNERT 172 (255)
Q Consensus 163 ~LYIATdE~~ 172 (255)
.|+++||-.+
T Consensus 128 ~l~~~TD~~~ 137 (195)
T PF02390_consen 128 ELYFATDVEE 137 (195)
T ss_dssp EEEEEES-HH
T ss_pred EEEEEeCCHH
Confidence 8888888544
No 12
>PF14399 Transpep_BrtH: NlpC/p60-like transpeptidase
Probab=25.56 E-value=61 Score=29.09 Aligned_cols=41 Identities=10% Similarity=0.072 Sum_probs=34.7
Q ss_pred ChHHHHHhhhcccCCCcEEEEecCCCCCCCCchh-hhhccee
Q 025301 146 RPEAILCRIKNWVPPGRTLFIASNERTPGFFSPL-AVRYNLA 186 (255)
Q Consensus 146 spe~i~~~~~~~v~~gr~LYIATdE~~~~fF~pL-~~~y~v~ 186 (255)
+++++++.+++.+..|+.|.|.+|.-.-+|+... +.+|--|
T Consensus 73 ~~~~~~~~l~~~l~~g~pv~~~~D~~~lpy~~~~~~~~~~~H 114 (317)
T PF14399_consen 73 SPDEAWEELKEALDAGRPVIVWVDMYYLPYRPNYYKKHHADH 114 (317)
T ss_pred CHHHHHHHHHHHHhCCCceEEEeccccCCCCccccccccCCc
Confidence 5889999999999999999999999999998885 4554333
No 13
>PF11305 DUF3107: Protein of unknown function (DUF3107); InterPro: IPR021456 Some members in this family of proteins are annotated as ATP-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=23.55 E-value=44 Score=26.01 Aligned_cols=47 Identities=15% Similarity=0.409 Sum_probs=37.8
Q ss_pred cccc---ccccCCCCCCCCChHHHHHhhhcccCCCcEEEEecCCCCCCCCch
Q 025301 130 RYGV---DRSLFPHLDRDTRPEAILCRIKNWVPPGRTLFIASNERTPGFFSP 178 (255)
Q Consensus 130 r~~v---~r~l~P~ld~dtspe~i~~~~~~~v~~gr~LYIATdE~~~~fF~p 178 (255)
++|| .|++ .++.+.++|++.+.+.+-+..+..+.--||++...++=|
T Consensus 4 kIGi~~~~REl--~ies~~s~dev~~~v~~Al~~~~~~l~LtD~kGr~~lVp 53 (74)
T PF11305_consen 4 KIGIQNVAREL--VIESDQSADEVEAAVTDALADGSGVLTLTDEKGRRVLVP 53 (74)
T ss_pred EEeeecCCceE--EEecCCCHHHHHHHHHHHHhCCCceEEEEeCCCCEEEEE
Confidence 4555 3555 478889999999999999999978888899998876654
No 14
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=20.75 E-value=1.5e+02 Score=31.95 Aligned_cols=68 Identities=13% Similarity=0.270 Sum_probs=43.0
Q ss_pred HHHHHHHHhC-CccEE----EEeeCccccccccccccc--cccCCCCCCCCChHHHHHhhhcccCCCcEEEEecCCCCCC
Q 025301 102 AADKIKALLV-DYDSI----HVRRGDRLKTRKDRYGVD--RSLFPHLDRDTRPEAILCRIKNWVPPGRTLFIASNERTPG 174 (255)
Q Consensus 102 ~v~~I~~~lg-dfDav----HVRRGD~~~~~k~r~~v~--r~l~P~ld~dtspe~i~~~~~~~v~~gr~LYIATdE~~~~ 174 (255)
-|.+|..-|| +|--. |||-=-. ..+||+ -...|.+...-..+.+++.|++.+..-..||||||.---|
T Consensus 13 kak~I~~~Lg~~~~V~as~GHl~dLp~-----~~~~~~~~~~f~p~y~~~~~k~~~~~~ik~~~k~ad~iilAtDpDREG 87 (860)
T PRK06319 13 KIKTLQKLLGEGFIFASSLGHIVDLPA-----KEFGIDIENDFEPDYQILPDKEEVINKICKLAKKCDVVYLSPDPDREG 87 (860)
T ss_pred HHHHHHHHhCCCCEEEecccCcccCCc-----ccCCcCCCCCCCcceEECccHHHHHHHHHHHHHhCCEEEECCCCCcch
Confidence 4677888888 66432 5554211 113442 2233544433456789999999998889999999965544
Done!