Query 013030
Match_columns 451
No_of_seqs 60 out of 62
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 08:49:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013030.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013030hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12483 GIDE: E3 Ubiquitin li 97.8 0.00015 3.1E-09 64.6 9.6 101 310-417 18-121 (160)
2 cd06094 RP_Saci_like RP_Saci_l 80.8 1.4 3.1E-05 38.0 2.7 24 323-346 1-24 (89)
3 PTZ00234 variable surface prot 65.1 34 0.00074 36.7 8.9 13 223-235 371-383 (433)
4 COG5015 Uncharacterized conser 62.0 8 0.00017 35.7 3.1 34 237-270 46-80 (132)
5 COG1200 RecG RecG-like helicas 45.1 60 0.0013 37.0 7.0 46 387-432 106-152 (677)
6 KOG0887 60S ribosomal protein 36.2 27 0.00058 31.6 2.2 46 257-314 30-75 (111)
7 KOG1016 Predicted DNA helicase 35.2 19 0.00041 42.2 1.4 16 7-22 1199-1214(1387)
8 PF10281 Ish1: Putative stress 29.1 48 0.001 23.8 2.1 17 364-380 6-22 (38)
9 PF05834 Lycopene_cycl: Lycope 28.2 2.1E+02 0.0046 28.9 7.2 44 348-392 198-243 (374)
10 PF13869 NUDIX_2: Nucleotide h 28.2 8.5 0.00018 37.2 -2.4 35 373-407 21-55 (188)
11 KOG0558 Dihydrolipoamide trans 27.9 19 0.00042 38.5 -0.1 31 381-411 77-110 (474)
12 PF11432 DUF3197: Protein of u 27.7 72 0.0016 29.1 3.4 59 323-395 19-86 (113)
13 COG4303 EutB Ethanolamine ammo 26.5 53 0.0012 35.1 2.8 27 361-388 421-447 (453)
14 cd04488 RecG_wedge_OBF RecG_we 26.1 1E+02 0.0022 22.6 3.6 27 389-415 45-71 (75)
15 cd00780 NTF2 Nuclear transport 25.3 59 0.0013 27.4 2.4 39 233-271 41-89 (119)
16 PF02037 SAP: SAP domain; Int 23.7 70 0.0015 22.7 2.2 17 365-381 7-23 (35)
17 cd04486 YhcR_OBF_like YhcR_OBF 23.3 1.1E+02 0.0023 25.2 3.5 28 388-415 43-70 (78)
18 PTZ00382 Variant-specific surf 22.4 41 0.00088 29.0 0.9 19 220-238 77-95 (96)
19 KOG2362 Uncharacterized Fe-S p 22.0 58 0.0013 34.2 2.0 17 385-401 316-332 (336)
20 cd00165 S4 S4/Hsp/ tRNA synthe 21.8 1.1E+02 0.0024 21.7 2.9 37 364-400 16-52 (70)
21 KOG2057 Predicted equilibrativ 21.5 2.9E+02 0.0063 29.9 6.9 16 43-58 324-339 (499)
22 PF03144 GTP_EFTU_D2: Elongati 20.7 83 0.0018 24.1 2.2 19 382-400 5-23 (74)
23 PRK06437 hypothetical protein; 20.5 1.1E+02 0.0024 24.4 2.9 37 365-402 21-64 (67)
No 1
>PF12483 GIDE: E3 Ubiquitin ligase; InterPro: IPR022170 This domain family is found in bacteria, archaea and eukaryotes, and is typically between 150 and 163 amino acids in length. There is a single completely conserved residue E that may be functionally important. GIDE is an E3 ubiquitin ligase which is involved in inducing apoptosis. ; GO: 0016881 acid-amino acid ligase activity
Probab=97.80 E-value=0.00015 Score=64.63 Aligned_cols=101 Identities=21% Similarity=0.288 Sum_probs=67.0
Q ss_pred cccceeeeeeeeceEEeecCCceeEEE-EeCCCCeeeEeeecceeEecCCCCCCCCHHHHHHHHhcC-CCCCCceeEEee
Q 013030 310 TWGLRSLERRAVDFYISDFQSGLRALV-KTGYGARVTPYVDDSLAIDVNPGKEELSPEFIRWLAERN-LSSDDRIMRLKE 387 (451)
Q Consensus 310 ~Wglr~~Er~~~DFYISDfqSGlRALV-KaG~GakVtp~V~es~vvd~g~~~kdlS~~f~~WL~erN-LSsd~r~mRlkE 387 (451)
.|.+.+..+..+.||+.| ..-|.+| ....++.+.--.+-+..... .......+..|+...- +. .+=.||+|
T Consensus 18 ~~~~v~~~~~~vPF~L~D--~tg~v~V~~~p~~a~l~l~~v~~~f~p~---~~~~~~~~~~~~~~~~~~~--~~G~r~~E 90 (160)
T PF12483_consen 18 SWRTVSSGTSEVPFYLED--GTGRVRVVDDPEGAELDLETVYDRFEPS---PSSPPDGLFGFFSGERELE--PKGYRYTE 90 (160)
T ss_pred cEEEEEcceeEcCEEEEC--CceEEEEecCcccCccceeeEEEEeEEC---CCCccceeeeeeccceecc--ccccEEEE
Confidence 499999999999999999 4455555 56666655322222221111 1133333444333222 11 33479999
Q ss_pred eeeeeCCeEEEEEEEE-ecCceeEEeCCCCc
Q 013030 388 GYIKEGSTVSVMGVVQ-RNDNVLMIVPPPEP 417 (451)
Q Consensus 388 GyIkEGstVSVmGvvq-r~~~~lmIvpP~e~ 417 (451)
-.|.+|++|.|+|.+. ..|..++|-+|.+.
T Consensus 91 ~~L~~G~~ltvvGe~~~~~~g~~~i~~p~~g 121 (160)
T PF12483_consen 91 EILPVGTPLTVVGELVRDGDGNLVIQPPKDG 121 (160)
T ss_pred EEcCCCCEEEEEEEEEEcCCCcEEEeCCCCC
Confidence 9999999999999995 55568999999986
No 2
>cd06094 RP_Saci_like RP_Saci_like, retropepsin family. Retropepsin on retrotransposons with long terminal repeats (LTR) including Saci-1, -2 and -3 of Schistosoma mansoni. Retropepsins are related to fungal and mammalian pepsins. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified
Probab=80.75 E-value=1.4 Score=37.98 Aligned_cols=24 Identities=46% Similarity=0.616 Sum_probs=20.7
Q ss_pred eEEeecCCceeEEEEeCCCCeeeE
Q 013030 323 FYISDFQSGLRALVKTGYGARVTP 346 (451)
Q Consensus 323 FYISDfqSGlRALVKaG~GakVtp 346 (451)
|||.|++||+|+||-||..-.|-|
T Consensus 1 l~v~D~~s~~~fLVDTGA~vSviP 24 (89)
T cd06094 1 LHVRDRTSGLRFLVDTGAAVSVLP 24 (89)
T ss_pred CeeEECCCCcEEEEeCCCceEeec
Confidence 799999999999999998755554
No 3
>PTZ00234 variable surface protein Vir12; Provisional
Probab=65.15 E-value=34 Score=36.68 Aligned_cols=13 Identities=8% Similarity=0.332 Sum_probs=8.5
Q ss_pred HHHHHHHhhhhhc
Q 013030 223 CCVAALFGWNTFW 235 (451)
Q Consensus 223 ~~v~al~iWN~~~ 235 (451)
|+|+++|+|-+|+
T Consensus 371 ~ailGtifFlfyy 383 (433)
T PTZ00234 371 ASIIGVLVFLFFF 383 (433)
T ss_pred HHHHHHHHHhhhh
Confidence 6777777775543
No 4
>COG5015 Uncharacterized conserved protein [Function unknown]
Probab=62.00 E-value=8 Score=35.71 Aligned_cols=34 Identities=24% Similarity=0.397 Sum_probs=30.7
Q ss_pred hhhHHhhhhhCCcccccc-cCCCcEEEEEEEEEec
Q 013030 237 RKAIISYIARYPDAELRN-AKNGQFVKISGVVTCG 270 (451)
Q Consensus 237 ~~~i~rfl~k~Pdt~Lr~-akdGQ~VKItG~VtCG 270 (451)
.+...+.++++|+.++.+ .+||++|.|+|.++.-
T Consensus 46 tK~~yKqik~np~vefcg~~kdg~~vrlrg~a~f~ 80 (132)
T COG5015 46 TKPYYKQIKKNPEVEFCGMDKDGVMVRLRGRAEFV 80 (132)
T ss_pred ChHHHHHHhhCCCeEEEEecCCceEEEEeeeEEec
Confidence 678999999999999976 7999999999998864
No 5
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=45.06 E-value=60 Score=36.95 Aligned_cols=46 Identities=24% Similarity=0.284 Sum_probs=31.9
Q ss_pred eeeeeeCCeEEEEEEEEecCceeEEeCCCCcccccce-eeeeccccc
Q 013030 387 EGYIKEGSTVSVMGVVQRNDNVLMIVPPPEPITTGCQ-WAKCIVPAS 432 (451)
Q Consensus 387 EGyIkEGstVSVmGvvqr~~~~lmIvpP~e~vsTGcq-w~kcllP~~ 432 (451)
+..+++|++|.|.|-++|.+..+=|+-|.=-+-..+. ..+.+.|+|
T Consensus 106 ~~~~~~G~~v~v~Gk~~~~~~~~~~~hpe~~~~~~~~~~~~~i~PvY 152 (677)
T COG1200 106 KKKLKVGERVIVYGKVKRFKGGLQITHPEYIVNDDGSELEERLTPVY 152 (677)
T ss_pred HhhCCCCCEEEEEEEEeeccCceEEEcceEEecCCCcccccceeeee
Confidence 3457799999999999998776666655544433333 566677765
No 6
>KOG0887 consensus 60S ribosomal protein L35A/L37 [Translation, ribosomal structure and biogenesis]
Probab=36.16 E-value=27 Score=31.60 Aligned_cols=46 Identities=37% Similarity=0.597 Sum_probs=34.5
Q ss_pred CCcEEEEEEEEEecccccccCcCCCCceeEEeeeEEEecCCCCCCCCCCCccccccce
Q 013030 257 NGQFVKISGVVTCGNVPLESSFQKVPRCIYTSTSLYEYRGWGSKAANPTHRRFTWGLR 314 (451)
Q Consensus 257 dGQ~VKItG~VtCG~vPLeSsfqKv~RCVYtSt~LyEyrgw~sk~an~kh~~f~Wglr 314 (451)
+--+|||.|+ ...=|++|-.-.||+|.+-.=.+-|+ ++.+..|+..
T Consensus 30 ~t~llkIEGv----~skeEa~fYlGkR~~yvYKa~~~~~~--------~k~RvIWGkV 75 (111)
T KOG0887|consen 30 NTSLLKIEGV----YSKEEASFYLGKRCVYVYKAKPEVRG--------SKTRVIWGKV 75 (111)
T ss_pred CcEEEEEecc----cchhhhheeecCcEEEEEecCCCCCC--------ceEEEEEEEE
Confidence 3348999997 45678899889999998765544444 7888889864
No 7
>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]
Probab=35.21 E-value=19 Score=42.15 Aligned_cols=16 Identities=56% Similarity=0.889 Sum_probs=14.7
Q ss_pred ccccCCceeeeCCCCC
Q 013030 7 SHQLSNGLYVSGRPEQ 22 (451)
Q Consensus 7 sHqLsnGLyVSGrpeq 22 (451)
-|||.+||||+|+|-|
T Consensus 1199 qH~Lps~l~v~~qp~q 1214 (1387)
T KOG1016|consen 1199 QHQLPSGLYVKLQPGQ 1214 (1387)
T ss_pred ccccCccceEecCCcc
Confidence 5999999999999984
No 8
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=29.09 E-value=48 Score=23.75 Aligned_cols=17 Identities=12% Similarity=0.477 Sum_probs=14.7
Q ss_pred CHHHHHHHHhcCCCCCC
Q 013030 364 SPEFIRWLAERNLSSDD 380 (451)
Q Consensus 364 S~~f~~WL~erNLSsd~ 380 (451)
..+|+.||.++|+....
T Consensus 6 ~~~L~~wL~~~gi~~~~ 22 (38)
T PF10281_consen 6 DSDLKSWLKSHGIPVPK 22 (38)
T ss_pred HHHHHHHHHHcCCCCCC
Confidence 46899999999998774
No 9
>PF05834 Lycopene_cycl: Lycopene cyclase protein; InterPro: IPR008671 This family consists of lycopene beta and epsilon cyclase proteins. Carotenoids with cyclic end groups are essential components of the photosynthetic membranes in all plants, algae, and cyanobacteria. These lipid-soluble compounds protect against photo-oxidation, harvest light for photosynthesis, and dissipate excess light energy absorbed by the antenna pigments. The cyclisation of lycopene (psi, psi-carotene) is a key branch point in the pathway of carotenoid biosynthesis. Two types of cyclic end groups are found in higher plant carotenoids: the beta and epsilon rings. Carotenoids with two beta rings are ubiquitous, and those with one beta and one epsilon ring are common; however, carotenoids with two epsilon rings are rare [].; GO: 0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 0016117 carotenoid biosynthetic process
Probab=28.20 E-value=2.1e+02 Score=28.87 Aligned_cols=44 Identities=20% Similarity=0.368 Sum_probs=32.3
Q ss_pred eecceeEecCC--CCCCCCHHHHHHHHhcCCCCCCceeEEeeeeeee
Q 013030 348 VDDSLAIDVNP--GKEELSPEFIRWLAERNLSSDDRIMRLKEGYIKE 392 (451)
Q Consensus 348 V~es~vvd~g~--~~kdlS~~f~~WL~erNLSsd~r~mRlkEGyIkE 392 (451)
++|.+.++... +..++...+.+||+++|+.... ++|-|.|+|--
T Consensus 198 lvE~T~fs~~~~~~~~~~~~~l~~~l~~~g~~~~~-i~~~E~G~IPm 243 (374)
T PF05834_consen 198 LVEETSFSPRPALPEEELKARLRRYLERLGIDDYE-ILEEERGVIPM 243 (374)
T ss_pred EEEEEEEcCCCCCCHHHHHHHHHHHHHHcCCCcee-EEEeecceeec
Confidence 55666655544 3346778899999998888654 88999998865
No 10
>PF13869 NUDIX_2: Nucleotide hydrolase; PDB: 3MDG_B 2J8Q_B 3Q2S_A 3P5T_D 3BAP_A 2CL3_A 3P6Y_A 3Q2T_B 3BHO_A 3N9U_A ....
Probab=28.16 E-value=8.5 Score=37.23 Aligned_cols=35 Identities=43% Similarity=0.582 Sum_probs=28.2
Q ss_pred hcCCCCCCceeEEeeeeeeeCCeEEEEEEEEecCc
Q 013030 373 ERNLSSDDRIMRLKEGYIKEGSTVSVMGVVQRNDN 407 (451)
Q Consensus 373 erNLSsd~r~mRlkEGyIkEGstVSVmGvvqr~~~ 407 (451)
|+..+..+|.+|++|-|-++|++-||-||+==|..
T Consensus 21 ekd~s~~~rl~rl~~~y~~~GmRrsVe~Vllvh~h 55 (188)
T PF13869_consen 21 EKDPSVAARLQRLKENYEKEGMRRSVEGVLLVHEH 55 (188)
T ss_dssp -SSSSHHHHHHHHHHHHHHHSSEEEEEEEEEEEET
T ss_pred ccccCHHHHHHHHHHHHHHhCCceEEEEEEEEecC
Confidence 34566678999999999999999999998754443
No 11
>KOG0558 consensus Dihydrolipoamide transacylase (alpha-keto acid dehydrogenase E2 subunit) [Energy production and conversion]
Probab=27.91 E-value=19 Score=38.47 Aligned_cols=31 Identities=32% Similarity=0.440 Sum_probs=21.7
Q ss_pred ceeEEeeeeeeeCCeEEE---EEEEEecCceeEE
Q 013030 381 RIMRLKEGYIKEGSTVSV---MGVVQRNDNVLMI 411 (451)
Q Consensus 381 r~mRlkEGyIkEGstVSV---mGvvqr~~~~lmI 411 (451)
|-..+||.|+||||||+= +.-||-+.+-.-|
T Consensus 77 ~Ev~vkeWfVKEGDtVeqFd~lCEVQSDKAsvtI 110 (474)
T KOG0558|consen 77 AEVTVKEWFVKEGDTVEQFDPLCEVQSDKASVTI 110 (474)
T ss_pred eeeeeeeehhhcCCcHHHhcchhhcccccceEEE
Confidence 567899999999999874 3445555544433
No 12
>PF11432 DUF3197: Protein of unknown function (DUF3197); InterPro: IPR024443 This domain, whose function is unknown, is found in bacterial proteins.; PDB: 1WN9_A 1WNA_A.
Probab=27.70 E-value=72 Score=29.06 Aligned_cols=59 Identities=27% Similarity=0.524 Sum_probs=34.0
Q ss_pred eEEeecCC-----ceeEEEEeCCCCeeeEeeecceeEecCCCC----CCCCHHHHHHHHhcCCCCCCceeEEeeeeeeeC
Q 013030 323 FYISDFQS-----GLRALVKTGYGARVTPYVDDSLAIDVNPGK----EELSPEFIRWLAERNLSSDDRIMRLKEGYIKEG 393 (451)
Q Consensus 323 FYISDfqS-----GlRALVKaG~GakVtp~V~es~vvd~g~~~----kdlS~~f~~WL~erNLSsd~r~mRlkEGyIkEG 393 (451)
.||+|.|. +..++|..|. ++.+.++. .|+-. ..+=.||.+||.+++. +++|-.+-.|
T Consensus 19 ~liTDwQd~R~~ARYa~ll~~gk----~~llt~dA---FGPafG~~G~~ALaELv~wl~~~G~-------~f~EaVl~p~ 84 (113)
T PF11432_consen 19 YLITDWQDQRPQARYALLLRGGK----EPLLTPDA---FGPAFGPEGERALAELVRWLQERGA-------RFYEAVLSPS 84 (113)
T ss_dssp EEEEE--SSCCC--EEEEEE-SS-----EEEEEEE---ESTTS-TTHHHHHHHHHHHHHHTT--------EEEEEEE-GG
T ss_pred EEEeccccchhhhhhhhheecCC----cccccccc---cCcccCccHHHHHHHHHHHHHHcCC-------chhheecCHH
Confidence 68999886 3456666555 45555554 23322 2345689999999984 6778776665
Q ss_pred Ce
Q 013030 394 ST 395 (451)
Q Consensus 394 st 395 (451)
+-
T Consensus 85 e~ 86 (113)
T PF11432_consen 85 EF 86 (113)
T ss_dssp GH
T ss_pred HH
Confidence 53
No 13
>COG4303 EutB Ethanolamine ammonia-lyase, large subunit [Amino acid transport and metabolism]
Probab=26.53 E-value=53 Score=35.09 Aligned_cols=27 Identities=30% Similarity=0.622 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHHhcCCCCCCceeEEeee
Q 013030 361 EELSPEFIRWLAERNLSSDDRIMRLKEG 388 (451)
Q Consensus 361 kdlS~~f~~WL~erNLSsd~r~mRlkEG 388 (451)
.-..+||++||.+.++..++|+ +...|
T Consensus 421 lrP~~EFe~wl~~mGi~~~Grl-t~~ag 447 (453)
T COG4303 421 LRPIPEFERWLERMGIMANGRL-TKRAG 447 (453)
T ss_pred CCCchHHHHHHHHhCcccCCce-eccCC
Confidence 5678999999999999999974 54443
No 14
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=26.07 E-value=1e+02 Score=22.60 Aligned_cols=27 Identities=37% Similarity=0.466 Sum_probs=22.4
Q ss_pred eeeeCCeEEEEEEEEecCceeEEeCCC
Q 013030 389 YIKEGSTVSVMGVVQRNDNVLMIVPPP 415 (451)
Q Consensus 389 yIkEGstVSVmGvvqr~~~~lmIvpP~ 415 (451)
.+++|+++.|.|.+++..+.+-|..|.
T Consensus 45 ~~~~G~~~~v~Gkv~~~~~~~qi~~P~ 71 (75)
T cd04488 45 QLPPGTRVRVSGKVKRFRGGLQIVHPE 71 (75)
T ss_pred cCCCCCEEEEEEEEeecCCeeEEeCCc
Confidence 378899999999999988877776664
No 15
>cd00780 NTF2 Nuclear transport factor 2 (NTF2) domain plays an important role in the trafficking of macromolecules, ions and small molecules between the cytoplasm and nucleus. This bi-directional transport of macromolecules across the nuclear envelope requires many soluble factors that includes GDP-binding protein Ran (RanGDP). RanGDP is required for both import and export of proteins and poly(A) RNA. RanGDP also has been implicated in cell cycle control, specifically in mitotic spindle assembly. In interphase cells, RanGDP is predominately nuclear and thought to be GTP bound, but it is also present in the cytoplasm, probably in the GDP-bound state. NTF2 mediates the nuclear import of RanGDP. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins.
Probab=25.29 E-value=59 Score=27.40 Aligned_cols=39 Identities=21% Similarity=0.426 Sum_probs=28.6
Q ss_pred hhcchhhHHhhhhhCC--cc-------cccccC-CCcEEEEEEEEEecc
Q 013030 233 TFWGRKAIISYIARYP--DA-------ELRNAK-NGQFVKISGVVTCGN 271 (451)
Q Consensus 233 ~~~~~~~i~rfl~k~P--dt-------~Lr~ak-dGQ~VKItG~VtCG~ 271 (451)
.+.++.+|..+|..+| .+ +..... .+=+|.|+|.|+.++
T Consensus 41 ~~~g~~~I~~~l~~lp~~~~~~~i~~~d~q~~~~~~ili~V~G~~~~~~ 89 (119)
T cd00780 41 QVTGRDAIVEKLSSLPFQKTKHKITTVDSQPTPSGGVIVMVTGSLKLDE 89 (119)
T ss_pred EecCHHHHHHHHHhCCCcceEEEEEEEeeeEcCCCCEEEEEEEEEEECC
Confidence 3567899999999999 33 222233 666799999999886
No 16
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=23.72 E-value=70 Score=22.67 Aligned_cols=17 Identities=35% Similarity=0.456 Sum_probs=14.4
Q ss_pred HHHHHHHHhcCCCCCCc
Q 013030 365 PEFIRWLAERNLSSDDR 381 (451)
Q Consensus 365 ~~f~~WL~erNLSsd~r 381 (451)
.+|+.+|+++||+..|.
T Consensus 7 ~eLk~~l~~~gL~~~G~ 23 (35)
T PF02037_consen 7 AELKEELKERGLSTSGK 23 (35)
T ss_dssp HHHHHHHHHTTS-STSS
T ss_pred HHHHHHHHHCCCCCCCC
Confidence 68999999999999983
No 17
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=23.26 E-value=1.1e+02 Score=25.17 Aligned_cols=28 Identities=18% Similarity=0.217 Sum_probs=23.8
Q ss_pred eeeeeCCeEEEEEEEEecCceeEEeCCC
Q 013030 388 GYIKEGSTVSVMGVVQRNDNVLMIVPPP 415 (451)
Q Consensus 388 GyIkEGstVSVmGvvqr~~~~lmIvpP~ 415 (451)
.-+++|++|.|-|.++...+..=|.++.
T Consensus 43 ~~~~~Gd~V~vtG~v~ey~g~tql~~~~ 70 (78)
T cd04486 43 ADVAVGDLVRVTGTVTEYYGLTQLTAVS 70 (78)
T ss_pred CCCCCCCEEEEEEEEEeeCCeEEEccCC
Confidence 3568899999999999999877777765
No 18
>PTZ00382 Variant-specific surface protein (VSP); Provisional
Probab=22.44 E-value=41 Score=28.97 Aligned_cols=19 Identities=11% Similarity=0.223 Sum_probs=13.4
Q ss_pred hhHHHHHHHHhhhhhcchh
Q 013030 220 PIFCCVAALFGWNTFWGRK 238 (451)
Q Consensus 220 ~i~~~v~al~iWN~~~~~~ 238 (451)
.+++++++++.|-++|+||
T Consensus 77 ~~v~~lv~~l~w~f~~r~k 95 (96)
T PTZ00382 77 AVVGGLVGFLCWWFVCRGK 95 (96)
T ss_pred hHHHHHHHHHhheeEEeec
Confidence 4556777788887777654
No 19
>KOG2362 consensus Uncharacterized Fe-S protein [General function prediction only]
Probab=22.02 E-value=58 Score=34.24 Aligned_cols=17 Identities=47% Similarity=0.546 Sum_probs=14.9
Q ss_pred EeeeeeeeCCeEEEEEE
Q 013030 385 LKEGYIKEGSTVSVMGV 401 (451)
Q Consensus 385 lkEGyIkEGstVSVmGv 401 (451)
++||||+.|++|.|+.-
T Consensus 316 ~~~g~I~vGd~Vyv~~k 332 (336)
T KOG2362|consen 316 VNEGTIKVGDTVYVLYK 332 (336)
T ss_pred cccceEEeCCEEEEEec
Confidence 56899999999999864
No 20
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=21.77 E-value=1.1e+02 Score=21.69 Aligned_cols=37 Identities=14% Similarity=0.233 Sum_probs=24.9
Q ss_pred CHHHHHHHHhcCCCCCCceeEEeeeeeeeCCeEEEEE
Q 013030 364 SPEFIRWLAERNLSSDDRIMRLKEGYIKEGSTVSVMG 400 (451)
Q Consensus 364 S~~f~~WL~erNLSsd~r~mRlkEGyIkEGstVSVmG 400 (451)
..+.++|+++..+.-+++...-..-.|+.|++|.+-+
T Consensus 16 r~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~~ 52 (70)
T cd00165 16 RSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDG 52 (70)
T ss_pred HHHHHHHHHcCCEEECCEEccCCccCcCCCCEEEEcC
Confidence 4566777777777777766544555677777776653
No 21
>KOG2057 consensus Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=21.51 E-value=2.9e+02 Score=29.86 Aligned_cols=16 Identities=38% Similarity=0.617 Sum_probs=11.5
Q ss_pred cccccCCceeecccCC
Q 013030 43 KKSGELGKMFDIPVDG 58 (451)
Q Consensus 43 kksgeLGkmfdi~v~~ 58 (451)
|-||+|--.||-....
T Consensus 324 kssgdl~dLFDgsa~s 339 (499)
T KOG2057|consen 324 KSSGDLDDLFDGSAPS 339 (499)
T ss_pred cccccHHHHhcCcCCC
Confidence 5678888888875443
No 22
>PF03144 GTP_EFTU_D2: Elongation factor Tu domain 2; InterPro: IPR004161 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA []. This domain is structurally related to the C-terminal domain of EF2 (IPR004160 from INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3MCA_A 3AGJ_E 1SKQ_B 1JNY_A 1S0U_A 1ZUN_B 3SFS_W 3UOQ_W 2H5E_B 2XEX_A ....
Probab=20.70 E-value=83 Score=24.06 Aligned_cols=19 Identities=32% Similarity=0.482 Sum_probs=17.3
Q ss_pred eeEEeeeeeeeCCeEEEEE
Q 013030 382 IMRLKEGYIKEGSTVSVMG 400 (451)
Q Consensus 382 ~mRlkEGyIkEGstVSVmG 400 (451)
..|+..|-|+.||+|.+++
T Consensus 5 ~grV~sG~l~~gd~v~~~~ 23 (74)
T PF03144_consen 5 TGRVYSGTLKKGDKVRVLP 23 (74)
T ss_dssp EEEEEESEEETTEEEEEES
T ss_pred EEEEEEeEEcCCCEEEECc
Confidence 3689999999999999988
No 23
>PRK06437 hypothetical protein; Provisional
Probab=20.48 E-value=1.1e+02 Score=24.35 Aligned_cols=37 Identities=11% Similarity=0.191 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCCCCC-------ceeEEeeeeeeeCCeEEEEEEE
Q 013030 365 PEFIRWLAERNLSSDD-------RIMRLKEGYIKEGSTVSVMGVV 402 (451)
Q Consensus 365 ~~f~~WL~erNLSsd~-------r~mRlkEGyIkEGstVSVmGvv 402 (451)
..+..+|++.|+..+. +++. .|=.|++||+|.++=.+
T Consensus 21 ~tv~dLL~~Lgi~~~~vaV~vNg~iv~-~~~~L~dgD~Veiv~~V 64 (67)
T PRK06437 21 LTVNDIIKDLGLDEEEYVVIVNGSPVL-EDHNVKKEDDVLILEVF 64 (67)
T ss_pred CcHHHHHHHcCCCCccEEEEECCEECC-CceEcCCCCEEEEEecc
Confidence 3588899999998654 5444 67789999999887544
Done!