Query 036083
Match_columns 404
No_of_seqs 159 out of 284
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 09:16:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036083.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036083hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00466 SRA SET and RING fi 100.0 2.2E-62 4.8E-67 439.8 17.3 153 202-363 2-155 (155)
2 PF02182 SAD_SRA: SAD/SRA doma 100.0 2.8E-60 6.1E-65 424.6 14.0 153 202-363 1-155 (155)
3 COG3440 Predicted restriction 96.0 3.5E-05 7.7E-10 76.7 -11.6 139 210-361 10-150 (301)
4 PF12218 End_N_terminal: N ter 47.9 5.2 0.00011 32.6 -0.4 49 301-365 11-59 (67)
5 COG0097 RplF Ribosomal protein 40.5 21 0.00046 33.9 2.4 25 316-340 148-172 (178)
6 COG2897 SseA Rhodanese-related 31.2 46 0.001 33.6 3.2 12 271-282 235-246 (285)
7 PF13356 DUF4102: Domain of un 24.2 1.3E+02 0.0028 24.4 4.1 46 329-387 16-65 (89)
8 PF07543 PGA2: Protein traffic 18.4 5.9E+02 0.013 23.3 7.5 26 116-148 98-123 (140)
9 PRK03999 translation initiatio 17.2 3.5E+02 0.0076 24.2 5.6 36 328-363 15-52 (129)
10 PF08207 EFP_N: Elongation fac 16.7 2.7E+02 0.0058 21.4 4.2 34 328-361 9-43 (58)
No 1
>smart00466 SRA SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. Domain in SET domain containing proteins and in Deinococcus radiodurans DRA1533.
Probab=100.00 E-value=2.2e-62 Score=439.77 Aligned_cols=153 Identities=48% Similarity=0.805 Sum_probs=144.6
Q ss_pred CCcccCCCCccccceeccHHHHHHhccCCCcCCCcccccCCCCCCCCCCCCCceEEEEecCCCCCCCCCCCeEEEEccCC
Q 036083 202 AKRIGDIPGVHVGHQFYSRAEMVAVGFHSHWLNGIDYMGMSYKGDYKNYIFPLAVAIVLSGMYEDDLDNAEDVVYTGQGG 281 (404)
Q Consensus 202 ~k~iG~VPGV~VGD~F~~R~El~~vGLH~~~qaGIdy~g~~~~g~~~~~~~~gA~SIVlSGgYeDD~D~GD~LiYTGqGG 281 (404)
.++||+||||+|||||+||+|||++|||+++|+||||++.+. +.++|+|||+||+|+||+|+||+|+|||+||
T Consensus 2 ~~~~G~vpGv~vGd~f~~R~el~~~GlH~~~~~GI~~~~~~~-------~~~~A~SIV~SggYedd~D~gd~liYtG~gg 74 (155)
T smart00466 2 KHIFGPVPGVEVGDIFFFRVELCLVGLHRPTQAGIDGLTADE-------GEPGATSVVSSGGYEDDTDDGDVLIYTGQGG 74 (155)
T ss_pred CceEeCCCCccCCCEEcchhHhhhhcccCcccCCcccccccC-------CCccEEEEEECCCccCcccCCCEEEEEccCC
Confidence 579999999999999999999999999999999999987542 3689999999999999999999999999999
Q ss_pred CCCCCCccccccccccchhHHHHHhhhCCCCEEEEeccCCCCCCCC-ceeEecceEEEEEEEEeecCcceEEEEEEEEEe
Q 036083 282 HNLTGDKRQIRDQKLERGNLALKNCVDQDLPVRVIRGHDCSSSYTG-KVYTYDGLYKVVKYWAEKGLSGFTVFKYRLRRL 360 (404)
Q Consensus 282 ~d~~g~krQ~~DQkLerGNlAL~nS~~~g~PVRVIRG~k~~s~~ap-kgYRYDGLYkVv~yW~EkGk~G~~V~KFkL~Rl 360 (404)
++. +++|+.||+|++||+||++||++++|||||||+++.+.++| ++|||||||+|++||.++|++||.||||+|+|+
T Consensus 75 ~~~--~~~~~~dQkl~~gNlAL~~S~~~~~PVRViRg~~~~~~~~p~~gyrYDGLY~V~~~w~e~g~~G~~v~kfkL~R~ 152 (155)
T smart00466 75 RDM--THGQPEDQKLERGNLALEASCRKGIPVRVVRGMKGYSKYAPGKGYIYDGLYRIVDYWREVGKSGFLVFKFKLVRI 152 (155)
T ss_pred ccC--CCCCccccEecchhHHHHHHHhcCCceEEEccccccCCCCCCCeEEECcEEEEEEEEEecCCCCcEEEEEEEEeC
Confidence 986 45789999999999999999999999999999998777888 699999999999999999999999999999999
Q ss_pred CCC
Q 036083 361 EGQ 363 (404)
Q Consensus 361 pGQ 363 (404)
|||
T Consensus 153 ~gQ 155 (155)
T smart00466 153 PGQ 155 (155)
T ss_pred CCC
Confidence 998
No 2
>PF02182 SAD_SRA: SAD/SRA domain; InterPro: IPR003105 This domain has been termed SRA-YDG, for SET and Ring finger Associated, and because of the conserved YDG motif within the domain. Further characteristics of the domain are the conservation of up to 13 evenly spaced glycine residues and a VRV(I/V)RG motif. The domain is mainly found in plants and animals and in bacteria. In animals, this domain is associated with the Np95-like ring finger protein and the related gene product Np97, which contains PHD and RING FINGER domains and which is an important determinant in cell cycle progression. Np95 is a chromatin-associated ubiquitin ligase, binding to histones is direct and shows a remarkable preference for histone H3 and its N-terminal tail. The SRA-YDG domain contained in Np95 is indispensable both for the interaction with histones and for chromatin binding in vivo [, ]. In plants the SRA-YDG domain is associated with the SET domain, found in a family of histone methyl transferases, and in bacteria it is found in association with HNH, a non-specific nuclease motif [, ].; GO: 0042393 histone binding; PDB: 2ZO1_B 2ZKD_A 2ZO0_B 2ZKF_A 2ZKG_B 3FDE_A 3F8I_A 2ZO2_B 3F8J_B 2ZKE_A ....
Probab=100.00 E-value=2.8e-60 Score=424.62 Aligned_cols=153 Identities=59% Similarity=0.912 Sum_probs=125.5
Q ss_pred CCcccCCCCccccceeccHHHHHHhccCCCcCCCcccccCCCCCCCCCCCCCceEEEEecCCCCCCCCCCCeEEEEccCC
Q 036083 202 AKRIGDIPGVHVGHQFYSRAEMVAVGFHSHWLNGIDYMGMSYKGDYKNYIFPLAVAIVLSGMYEDDLDNAEDVVYTGQGG 281 (404)
Q Consensus 202 ~k~iG~VPGV~VGD~F~~R~El~~vGLH~~~qaGIdy~g~~~~g~~~~~~~~gA~SIVlSGgYeDD~D~GD~LiYTGqGG 281 (404)
+|+|||||||+|||||++|+||+++|+|+++|+|||+++..+ .++|+|||+||+|+||+|+||+|||||+||
T Consensus 1 ~k~~G~ipGv~vG~~f~~r~~~~~~G~H~~~~~GI~g~~~~g--------~~~A~SIV~Sg~y~dd~D~gd~l~YtG~gg 72 (155)
T PF02182_consen 1 EKRFGHIPGVEVGDWFPYRMELSIVGLHGPTQAGIDGMKKEG--------GPVAYSIVLSGGYEDDEDNGDVLIYTGQGG 72 (155)
T ss_dssp -TSSS--TT--TT-EESSHHHHHHTTSS--SS-SEEEETTTE--------SEEEEEEEESSSSTTCEECSSEEEEE-SSS
T ss_pred CCcEeCCCCccCccEEhHHHHHhHhccCCCccCCeecccCCC--------ceeeEEEEECCCcccccCCCCEEEEEcCCC
Confidence 478999999999999999999999999999999999987653 278999999999999999999999999999
Q ss_pred CCCCCCccccccccccchhHHHHHhhhCCCCEEEEeccCCCCCCCCc-e-eEecceEEEEEEEEeecCcceEEEEEEEEE
Q 036083 282 HNLTGDKRQIRDQKLERGNLALKNCVDQDLPVRVIRGHDCSSSYTGK-V-YTYDGLYKVVKYWAEKGLSGFTVFKYRLRR 359 (404)
Q Consensus 282 ~d~~g~krQ~~DQkLerGNlAL~nS~~~g~PVRVIRG~k~~s~~apk-g-YRYDGLYkVv~yW~EkGk~G~~V~KFkL~R 359 (404)
++..+++ |..||+|++||+||.+|+++++|||||||+++.+.|+|+ + |||||||+|++||.++|++|+.||||+|+|
T Consensus 73 ~~~~~~~-~~~dQ~l~~gN~AL~~S~~~~~PVRViR~~~~~~~~ap~~g~yrYDGLY~V~~~w~~~g~~G~~v~kF~L~R 151 (155)
T PF02182_consen 73 NDLSGNK-QPKDQKLERGNLALANSMKTGNPVRVIRGYKLKSSYAPKGGIYRYDGLYKVVKYWREKGKSGFKVFKFKLVR 151 (155)
T ss_dssp B--TTT--B-S---SSHHHHHHHHHSGGS-EEEEEEEGGGGGTTS-SSS-EEEEEEEEEEEEEEEE-TTSSEEEEEEEEE
T ss_pred ccccccc-ccccccccchhHHHHHHHhcCCCeEEEeecCCCCccCCcCCCEEeCcEEEEEEEEEEeCCCCcEEEEEEEEE
Confidence 9987655 999999999999999999999999999999999999994 6 999999999999999999999999999999
Q ss_pred eCCC
Q 036083 360 LEGQ 363 (404)
Q Consensus 360 lpGQ 363 (404)
+|||
T Consensus 152 ~~gQ 155 (155)
T PF02182_consen 152 LPGQ 155 (155)
T ss_dssp -TSS
T ss_pred CCCC
Confidence 9998
No 3
>COG3440 Predicted restriction endonuclease [Defense mechanisms]
Probab=96.04 E-value=3.5e-05 Score=76.69 Aligned_cols=139 Identities=12% Similarity=-0.054 Sum_probs=113.4
Q ss_pred Cccccceecc-HHHHHHhccCCCcCCCcccccCCCCCCCCCCCCCceEEEEecCCCCCCCCCCCeEEEEccCCCCCCCCc
Q 036083 210 GVHVGHQFYS-RAEMVAVGFHSHWLNGIDYMGMSYKGDYKNYIFPLAVAIVLSGMYEDDLDNAEDVVYTGQGGHNLTGDK 288 (404)
Q Consensus 210 GV~VGD~F~~-R~El~~vGLH~~~qaGIdy~g~~~~g~~~~~~~~gA~SIVlSGgYeDD~D~GD~LiYTGqGG~d~~g~k 288 (404)
++.++..+-. +.+..-.+.|-|++.++.+.+.+ .+.+++.+|+|+++.+.+++..||+-|+.... .
T Consensus 10 sf~~~~a~~~i~~~~~~~a~~kp~l~l~v~~~~~-----------~~~~~~n~~~~~~e~~~~f~~l~~~~g~~~~~--~ 76 (301)
T COG3440 10 SFSQRNASLKIFGGNREAAPHKPILLLDVGRKIS-----------TFFITENQGIYETELIEPFIQLWSFFGPKLQK--Y 76 (301)
T ss_pred chhhhhhhhhhcccccccCCcCceeehhhHhhhh-----------cccccccccccchhccchHHHHHhhcCccccc--C
Confidence 5555666655 66777889999999999865432 46799999999999999999999999986322 2
Q ss_pred cccccccccchhHHHHHhhhCCCCEEEEeccCCCCCCCC-ceeEecceEEEEEEEEeecCcceEEEEEEEEEeC
Q 036083 289 RQIRDQKLERGNLALKNCVDQDLPVRVIRGHDCSSSYTG-KVYTYDGLYKVVKYWAEKGLSGFTVFKYRLRRLE 361 (404)
Q Consensus 289 rQ~~DQkLerGNlAL~nS~~~g~PVRVIRG~k~~s~~ap-kgYRYDGLYkVv~yW~EkGk~G~~V~KFkL~Rlp 361 (404)
.+..-+.+..|+.+++.+++.+-|-++||++.....+.| ..|-|-|+|.+-..|.++.-.+++++.|...+++
T Consensus 77 ~~~~p~~~l~~d~~~h~~~k~~~~~l~~~~~~~~~e~v~~~~~d~el~~~~~~~~~~~~l~~~L~~~~~~~~~~ 150 (301)
T COG3440 77 GVDAPFELLQGDGKWHLDIKEGFDGLSIRTLPTEKEFVEYHYIDDELEQSLQYHQGEKRLIDDLISIWRKEVLQ 150 (301)
T ss_pred CCCCchHHhhccchhhhcccccCCccccCCCccHhhhhhhhhccHHHHHHHHhhcccchhHHHHHHHHHHHHHH
Confidence 244556667899999999999999999999887665666 5788999999999999999999999999998873
No 4
>PF12218 End_N_terminal: N terminal extension of bacteriophage endosialidase; InterPro: IPR024429 This entry represents the N-terminal extension domain of endosialidases which is approximately 70 amino acids in length. The two N-terminal domains (this domain and the beta propeller) assemble in the compact 'cap' whereas the C-terminal domain forms an extended tail-like structure. The very N-terminal part of the 'cap' region (residues 246 to 312) holds the only alpha-helix of the protein and is presumably the residual part of the deleted N-terminal head-binding domain [].; PDB: 3JU4_A 3GVL_A 3GVK_B 3GVJ_A 1V0E_B 1V0F_E.
Probab=47.90 E-value=5.2 Score=32.59 Aligned_cols=49 Identities=27% Similarity=0.417 Sum_probs=23.7
Q ss_pred HHHHHhhhCCCCEEEEeccCCCCCCCCceeEecceEEEEEEEEeecCcceEEEEEEEEEeCCCCC
Q 036083 301 LALKNCVDQDLPVRVIRGHDCSSSYTGKVYTYDGLYKVVKYWAEKGLSGFTVFKYRLRRLEGQPI 365 (404)
Q Consensus 301 lAL~nS~~~g~PVRVIRG~k~~s~~apkgYRYDGLYkVv~yW~EkGk~G~~V~KFkL~RlpGQP~ 365 (404)
.||-.++...++=++|-|.-. .|+|.. -+..+-|.=-+|-.+|+||||-
T Consensus 11 ~A~~a~l~a~~~g~~IDg~Gl-------------TykVs~---lPd~srf~N~rF~~eri~gqpl 59 (67)
T PF12218_consen 11 AAITAALEASPVGRKIDGAGL-------------TYKVSS---LPDISRFKNARFVYERIPGQPL 59 (67)
T ss_dssp HHHHHHHHHS-TTS-EE-TT--------------EEEESS------GGGEES-EEEE-SSTT--E
T ss_pred HHHHHHHhccCCCeEEecCCc-------------eEEEee---CccHHhhccceEEEeecCCCce
Confidence 566666665554444444211 144432 4456677777899999999994
No 5
>COG0097 RplF Ribosomal protein L6P/L9E [Translation, ribosomal structure and biogenesis]
Probab=40.55 E-value=21 Score=33.94 Aligned_cols=25 Identities=40% Similarity=0.547 Sum_probs=20.0
Q ss_pred EeccCCCCCCCCceeEecceEEEEE
Q 036083 316 IRGHDCSSSYTGKVYTYDGLYKVVK 340 (404)
Q Consensus 316 IRG~k~~s~~apkgYRYDGLYkVv~ 340 (404)
||.+..+.+|.++|.+|||.|.+.+
T Consensus 148 Ir~~r~pepykgKgi~ydge~I~~K 172 (178)
T COG0097 148 IRAARKPEPYKGKGIRYDGEYIRRK 172 (178)
T ss_pred HHhccCCCCCCCcceEEcCEEEEEe
Confidence 4555556789999999999998875
No 6
>COG2897 SseA Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=31.17 E-value=46 Score=33.59 Aligned_cols=12 Identities=42% Similarity=0.689 Sum_probs=9.4
Q ss_pred CCeEEEEccCCC
Q 036083 271 AEDVVYTGQGGH 282 (404)
Q Consensus 271 GD~LiYTGqGG~ 282 (404)
.++|+|||+|-.
T Consensus 235 ~~vI~yCgsG~~ 246 (285)
T COG2897 235 KEVIVYCGSGVR 246 (285)
T ss_pred CCEEEEcCCchH
Confidence 368999999854
No 7
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=24.19 E-value=1.3e+02 Score=24.38 Aligned_cols=46 Identities=41% Similarity=0.630 Sum_probs=25.6
Q ss_pred eeEec---ceEEEEEEEEeecCcceEEEEEEEEEeCCCCCCCccccccccCCCCC-Cchhhhh
Q 036083 329 VYTYD---GLYKVVKYWAEKGLSGFTVFKYRLRRLEGQPILTTNQVRFINGRVPQ-SLSEIRG 387 (404)
Q Consensus 329 gYRYD---GLYkVv~yW~EkGk~G~~V~KFkL~RlpGQP~L~~~~v~f~~g~iP~-s~sei~~ 387 (404)
...|| |||..+. ++|...|.|+. |..|. ...+.-|..|. |+++-|.
T Consensus 16 ~~~~D~~~GL~l~v~------~~G~kt~~~r~-~~~gk------~~~~~lG~~p~~sl~~AR~ 65 (89)
T PF13356_consen 16 YEVSDGVPGLYLRVT------PSGSKTFYFRY-RINGK------RRRITLGRYPELSLAEARE 65 (89)
T ss_dssp EEEEEESTTEEEEE-------TTS-EEEEEEE-EETTE------EEEEEEEECTTS-HHHHHH
T ss_pred EEEEeCCCCcEEEEE------eCCCeEEEEEE-Eecce------EEEeccCCCccCCHHHHHH
Confidence 35566 8887765 67777777777 65555 23344556654 4444433
No 8
>PF07543 PGA2: Protein trafficking PGA2; InterPro: IPR011431 A Saccharomyces cerevisiae (Baker's yeast) member of this family (PGA2, P53903 from SWISSPROT) is a single pass membrane protein which has been implicated in protein trafficking [, ].
Probab=18.44 E-value=5.9e+02 Score=23.29 Aligned_cols=26 Identities=23% Similarity=0.037 Sum_probs=17.8
Q ss_pred CCCCcchHHHHHHHHHHHHHHHHhhHHHHHHhh
Q 036083 116 NFAEKSDHAKVKETLRLFNKYYLQGVQEEEQRC 148 (404)
Q Consensus 116 ~~~~~s~r~kV~~~lr~F~~~y~~l~qeee~r~ 148 (404)
+-=++++|.++++.++. |.++++++.
T Consensus 98 ~~WGkkaRrRqkk~~k~-------l~~~~e~~~ 123 (140)
T PF07543_consen 98 FGWGKKARRRQKKQQKK-------LEEAEEQRR 123 (140)
T ss_pred ccccHHHHHHHHHHHHH-------HHHHHHHHH
Confidence 44578899999998773 445555553
No 9
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=17.22 E-value=3.5e+02 Score=24.17 Aligned_cols=36 Identities=17% Similarity=0.103 Sum_probs=29.1
Q ss_pred ceeEecc-eEEEEEEEE-eecCcceEEEEEEEEEeCCC
Q 036083 328 KVYTYDG-LYKVVKYWA-EKGLSGFTVFKYRLRRLEGQ 363 (404)
Q Consensus 328 kgYRYDG-LYkVv~yW~-EkGk~G~~V~KFkL~RlpGQ 363 (404)
..+.||| +|.|+++-. -+|+.|...++.+|+-+..-
T Consensus 15 ~~i~~~g~p~~V~~~~~~kpGkhg~a~vr~k~knL~tG 52 (129)
T PRK03999 15 SYVVIDGEPCKIVEISKSKPGKHGSAKARIVAIGIFDG 52 (129)
T ss_pred CEEEECCEEEEEEEEEeecCCCCCcEEEEEEEEECCCC
Confidence 4689999 999999854 56776888999999987644
No 10
>PF08207 EFP_N: Elongation factor P (EF-P) KOW-like domain; InterPro: IPR013185 This entry represents the N-terminal domain of homologues of elongation factor P, which probably are translation initiation factors. ; PDB: 3TRE_A 1YBY_A 1IZ6_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H 3OYY_B.
Probab=16.65 E-value=2.7e+02 Score=21.39 Aligned_cols=34 Identities=26% Similarity=0.356 Sum_probs=27.0
Q ss_pred ceeEecc-eEEEEEEEEeecCcceEEEEEEEEEeC
Q 036083 328 KVYTYDG-LYKVVKYWAEKGLSGFTVFKYRLRRLE 361 (404)
Q Consensus 328 kgYRYDG-LYkVv~yW~EkGk~G~~V~KFkL~Rlp 361 (404)
..+.||| ||.|.++-.-+...|...++.+|+-+.
T Consensus 9 ~~i~~~g~~~~V~~~~~~k~gkg~a~v~~klknl~ 43 (58)
T PF08207_consen 9 MVIEIDGEPYVVLDFQHVKPGKGGAFVRVKLKNLR 43 (58)
T ss_dssp SEEEETTEEEEEEEEEEECCTTSSSEEEEEEEETT
T ss_pred CEEEECCEEEEEEEEEEECCCCCCeEEEEEEEECC
Confidence 4577776 899999977776668889999998764
Done!