Query psy9523
Match_columns 107
No_of_seqs 114 out of 200
Neff 4.6
Searched_HMMs 46136
Date Fri Aug 16 21:48:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9523.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9523hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3887|consensus 100.0 5.1E-41 1.1E-45 269.9 5.7 101 7-107 166-266 (347)
2 PF04670 Gtr1_RagA: Gtr1/RagA 100.0 7.7E-38 1.7E-42 243.1 1.4 78 18-95 151-232 (232)
3 KOG3886|consensus 99.9 1.7E-24 3.6E-29 172.9 2.8 84 16-99 151-236 (295)
4 PF08066 PMC2NT: PMC2NT (NUC01 44.3 63 0.0014 21.5 4.5 67 27-102 14-81 (91)
5 COG2966 Uncharacterized conser 39.4 1.3E+02 0.0028 23.9 6.4 57 46-102 33-100 (250)
6 PF08655 DASH_Ask1: DASH compl 39.1 42 0.00091 22.0 3.0 35 28-62 16-50 (66)
7 cd01833 XynB_like SGNH_hydrola 33.9 1E+02 0.0022 20.9 4.4 50 46-95 99-153 (157)
8 cd01832 SGNH_hydrolase_like_1 29.1 1.4E+02 0.003 20.7 4.5 51 45-95 129-182 (185)
9 COG1126 GlnQ ABC-type polar am 26.1 1.6E+02 0.0035 23.9 4.8 28 64-102 156-183 (240)
10 PF13492 GAF_3: GAF domain; PD 25.9 1.2E+02 0.0025 19.1 3.4 21 48-68 5-25 (129)
11 PF14234 DUF4336: Domain of un 24.8 46 0.001 27.3 1.6 19 62-80 140-158 (285)
12 cd05397 NT_Pol-beta-like Nucle 24.2 1.3E+02 0.0028 17.6 3.2 27 47-73 2-28 (49)
13 PF01042 Ribonuc_L-PSP: Endori 24.1 1.5E+02 0.0032 20.1 3.8 27 17-46 67-93 (121)
14 PF01096 TFIIS_C: Transcriptio 22.1 51 0.0011 18.9 1.0 17 57-73 3-19 (39)
No 1
>KOG3887|consensus
Probab=100.00 E-value=5.1e-41 Score=269.88 Aligned_cols=101 Identities=76% Similarity=1.168 Sum_probs=98.7
Q ss_pred hhhccCCCCceeeEEeecccchhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhcCcceEeeeeccceEEEecCCCCCCch
Q psy9523 7 YSWDSGGYDQITLSFHLTSIYDHSIFEAFSKVIQKLIPQLPTLENLLNILINNSGIEKAFLFDVVSKIYIATDSSPVDMQ 86 (107)
Q Consensus 7 ~~l~~~~~~~~~i~~~~TSI~D~SLy~AwS~IVq~LiP~~~~le~~L~~~~~~~~aeev~LFe~~T~L~IAtds~~~D~~ 86 (107)
=+|.|+|.++++++||+|||||||+|+|||||||+|||++|+||++||.|+++++.+|+||||+.||+||||||+|+|++
T Consensus 166 d~l~d~gle~v~vsf~LTSIyDHSIfEAFSkvVQkLipqLptLEnlLnif~s~S~ieKafLFDv~SKIYiaTDS~PVdmq 245 (347)
T KOG3887|consen 166 DELADAGLEKVQVSFYLTSIYDHSIFEAFSKVVQKLIPQLPTLENLLNIFISNSKIEKAFLFDVLSKIYIATDSSPVDMQ 245 (347)
T ss_pred HHHHhhhhccceEEEEEeeecchHHHHHHHHHHHHHhhhchhHHHHHHHHhhccchhhhhhhhhhheeEEecCCCcchhH
Confidence 36889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHhhhcccCC
Q psy9523 87 SYELCCDMVDLVIDVSGIYGK 107 (107)
Q Consensus 87 ~fE~~sd~I~v~~d~~~iY~~ 107 (107)
.||+|||||||.+|+++|||.
T Consensus 246 ~YElC~d~IDV~iDl~~iYg~ 266 (347)
T KOG3887|consen 246 SYELCCDMIDVTIDLSSIYGL 266 (347)
T ss_pred HHHHHHhhhheeeehHHhhCC
Confidence 999999999999999999993
No 2
>PF04670 Gtr1_RagA: Gtr1/RagA G protein conserved region; InterPro: IPR006762 GTR1 was first identified in Saccharomyces cerevisiae (Baker's yeast) as a suppressor of a mutation in RCC1. RCC1 catalyzes guanine nucleotide exchange on Ran, a well characterised nuclear Ras-like small G protein that plays an essential role in the import and export of proteins and RNAs across the nuclear membrane through the nuclear pore complex. RCC1 is located inside the nucleus, bound to chromatin. The concentration of GTP within the cell is ~30 times higher than the concentration of GDP, thus resulting in the preferential production of the GTP form of Ran by RCC1 within the nucleus. Gtr1p is located within both the cytoplasm and the nucleus and has been reported to play a role in cell growth. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1 and Rag A and Gtr1p belong to the sixth subfamily of the Ras-like small GTPase superfamily []. ; GO: 0005525 GTP binding, 0005634 nucleus, 0005737 cytoplasm; PDB: 3R7W_B 2Q3F_B 3LLU_A.
Probab=100.00 E-value=7.7e-38 Score=243.12 Aligned_cols=78 Identities=55% Similarity=0.930 Sum_probs=69.8
Q ss_pred eeEEeecccchhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhcCcceEeeeeccceEEEecCC-CCCC---chhHHHHHH
Q psy9523 18 TLSFHLTSIYDHSIFEAFSKVIQKLIPQLPTLENLLNILINNSGIEKAFLFDVVSKIYIATDS-SPVD---MQSYELCCD 93 (107)
Q Consensus 18 ~i~~~~TSI~D~SLy~AwS~IVq~LiP~~~~le~~L~~~~~~~~aeev~LFe~~T~L~IAtds-~~~D---~~~fE~~sd 93 (107)
+++||+|||||||||+|||+|||+||||++.||++|+.||.+|+|+||||||++||||||||+ +|+| ++|||+|||
T Consensus 151 ~~~~~~TSI~D~Sly~A~S~Ivq~LiP~~~~le~~L~~~~~~c~a~ev~LFd~~T~L~Ia~ds~~~~~~~~~~~fE~~S~ 230 (232)
T PF04670_consen 151 DITFFLTSIWDESLYEAWSKIVQKLIPNLSTLENLLNNFCSSCNADEVFLFDRSTFLYIATDSRSPVDERDMQRFEKCSD 230 (232)
T ss_dssp SEEEEEE-TTSTHHHHHHHHHHHTTSTTHCCCCCCCCHHHCCCTEEEEEEEETTT--ECEE-S-S------HHHHHHHHH
T ss_pred ceEEEeccCcCcHHHHHHHHHHHHHcccHHHHHHHHHHHHHhcCCcEEEEEeeeeEEEEEeccCCCccccccccHHHHhh
Confidence 699999999999999999999999999999999999999999999999999999999999999 8887 999999999
Q ss_pred HH
Q psy9523 94 MV 95 (107)
Q Consensus 94 ~I 95 (107)
||
T Consensus 231 ii 232 (232)
T PF04670_consen 231 II 232 (232)
T ss_dssp HH
T ss_pred cC
Confidence 97
No 3
>KOG3886|consensus
Probab=99.89 E-value=1.7e-24 Score=172.86 Aligned_cols=84 Identities=20% Similarity=0.332 Sum_probs=78.4
Q ss_pred ceeeEEeecccchhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhcCcceEeeeeccceEEEecCC--CCCCchhHHHHHH
Q psy9523 16 QITLSFHLTSIYDHSIFEAFSKVIQKLIPQLPTLENLLNILINNSGIEKAFLFDVVSKIYIATDS--SPVDMQSYELCCD 93 (107)
Q Consensus 16 ~~~i~~~~TSI~D~SLy~AwS~IVq~LiP~~~~le~~L~~~~~~~~aeev~LFe~~T~L~IAtds--~~~D~~~fE~~sd 93 (107)
+..+.||+|||||||||||||.||+.++||.+.+|+.|..|.+..+|+|++||||+|||+||+-+ +..|.||||++||
T Consensus 151 ~~~~~~f~TsiwDetl~KAWS~iv~~lipn~~~~e~~Lr~fg~~~ea~eviLfEr~tflvI~~~q~~~~~~~hrfekisn 230 (295)
T KOG3886|consen 151 PLECKCFPTSIWDETLYKAWSSIVYNLIPNVSALESKLRNFGEILEALEVILFERATFLVISHYQIKEMRDAHRFEKISN 230 (295)
T ss_pred cccccccccchhhHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHhHHHHHHHHhhhheeeehhhhhccccccccccHHH
Confidence 56789999999999999999999999999999999999999999999999999999999999655 5677799999999
Q ss_pred HHHHHH
Q psy9523 94 MVDLVI 99 (107)
Q Consensus 94 ~I~v~~ 99 (107)
|+|-+.
T Consensus 231 I~kqfk 236 (295)
T KOG3886|consen 231 IIKQFK 236 (295)
T ss_pred HHHHhh
Confidence 999763
No 4
>PF08066 PMC2NT: PMC2NT (NUC016) domain; InterPro: IPR012588 Exosomes are nano-compartments that function in the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA) [, ]. Exosomes occur in both archaea and eukaryotes, and have a similar overall structure to each other and to bacterial/organelle PNPases (polynucleotide phosphorylases; 2.7.7.8 from EC) [], consisting of a barrel structure composed of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. There are two types of exosomes in eukaryotes, cytoplasmic exosomes that are responsible for 3'-5' exoribonuclease degradation of mRNAs, and nuclear exosomes that degrade pre-mRNAs (such as nonsense transcripts) and degrade rRNAs, snRNAs and snoRNAs. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. There are several accessory proteins that help degrade, unwind or polyadenylate RNA substrate before they enter the exosome. This entry represents the N-terminal domain of Rrp6 (exosome component 10 in humans), a nuclear exosome accessory factor that interacts with the bottom of the hexameric PH-ring opposite the cap. Rrp6 functions as a hydrolytic exonuclease, and is homologous to RNase-D in Escherichia coli. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0006396 RNA processing, 0000176 nuclear exosome (RNase complex)
Probab=44.27 E-value=63 Score=21.49 Aligned_cols=67 Identities=21% Similarity=0.342 Sum_probs=45.0
Q ss_pred chhHHHHHH-HHHHHHHcCChHHHHHHHHHHHHhcCcceEeeeeccceEEEecCCCCCCchhHHHHHHHHHHHHhhh
Q psy9523 27 YDHSIFEAF-SKVIQKLIPQLPTLENLLNILINNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMVDLVIDVS 102 (107)
Q Consensus 27 ~D~SLy~Aw-S~IVq~LiP~~~~le~~L~~~~~~~~aeev~LFe~~T~L~IAtds~~~D~~~fE~~sd~I~v~~d~~ 102 (107)
=|...|+.+ ..+-+.+--+.+.|-++++.+....+...-...-. |..-+| .+|+.++|.+|-+++=.
T Consensus 14 ~D~~Fy~s~dp~f~~~ld~~s~rll~l~n~ll~~~~~~~~~~~~~--------~~~d~d-~~~~~vvd~~D~LlEk~ 81 (91)
T PF08066_consen 14 QDYDFYRSFDPEFAESLDEQSQRLLSLINSLLKSAGSKSNISSPD--------DVDDVD-ERWDSVVDVNDSLLEKA 81 (91)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhccccccccCCC--------ccccHH-HHHHHHHHHHHHHHHHH
Confidence 467788888 66666666667778888888887776654332222 332233 48999999999887643
No 5
>COG2966 Uncharacterized conserved protein [Function unknown]
Probab=39.43 E-value=1.3e+02 Score=23.94 Aligned_cols=57 Identities=18% Similarity=0.199 Sum_probs=44.8
Q ss_pred hHHHHHHHHHHHHhcCcceEeeeeccceEEEecCCC-----------CCCchhHHHHHHHHHHHHhhh
Q psy9523 46 LPTLENLLNILINNSGIEKAFLFDVVSKIYIATDSS-----------PVDMQSYELCCDMVDLVIDVS 102 (107)
Q Consensus 46 ~~~le~~L~~~~~~~~aeev~LFe~~T~L~IAtds~-----------~~D~~~fE~~sd~I~v~~d~~ 102 (107)
....|+.+++.++.-|.+++.+|.-+|-+++.++.. +.....++++++.=++..++.
T Consensus 33 s~rve~~~~ria~a~g~~~~~~~vt~t~Ii~s~~~~~~~~i~~~r~~~~~~~nl~kvs~v~~i~~~v~ 100 (250)
T COG2966 33 SYRVEETMNRIARALGLESVESFVTPTAIILSTEDDDTSCVTLVRVIPDRGINLEKVSEVNRISRAVE 100 (250)
T ss_pred HhHHHHHHHHHHHHcCCCcceeeccCceEEEEeccCCCCcceEEEecCCCCccHHHHHHHHHHHHHHH
Confidence 356899999999999999999999999999997651 224456778777766665553
No 6
>PF08655 DASH_Ask1: DASH complex subunit Ask1; InterPro: IPR013964 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules [].
Probab=39.13 E-value=42 Score=21.98 Aligned_cols=35 Identities=9% Similarity=0.217 Sum_probs=28.6
Q ss_pred hhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhcCc
Q psy9523 28 DHSIFEAFSKVIQKLIPQLPTLENLLNILINNSGI 62 (107)
Q Consensus 28 D~SLy~AwS~IVq~LiP~~~~le~~L~~~~~~~~a 62 (107)
|+.+=.|++.|-++++|.+...-...+...++++.
T Consensus 16 D~N~s~~~~iit~~IlP~v~rY~~~s~~i~~~~~f 50 (66)
T PF08655_consen 16 DSNFSRCHRIITDKILPAVERYGESSEKIWDSAKF 50 (66)
T ss_pred HHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHhH
Confidence 77888999999999999998877777776666654
No 7
>cd01833 XynB_like SGNH_hydrolase subfamily, similar to Ruminococcus flavefaciens XynB. Most likely a secreted hydrolase with xylanase activity. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=33.89 E-value=1e+02 Score=20.93 Aligned_cols=50 Identities=12% Similarity=0.085 Sum_probs=36.4
Q ss_pred hHHHHHHHHHHHHhcCc--ceEeeeeccceE---EEecCCCCCCchhHHHHHHHH
Q psy9523 46 LPTLENLLNILINNSGI--EKAFLFDVVSKI---YIATDSSPVDMQSYELCCDMV 95 (107)
Q Consensus 46 ~~~le~~L~~~~~~~~a--eev~LFe~~T~L---~IAtds~~~D~~~fE~~sd~I 95 (107)
...+.+.+..+|..-+. ..+.++|..+.. ..+.|.-|....-|+++.+.+
T Consensus 99 ~~~~n~~l~~~~~~~~~~~~~v~~vd~~~~~~~~~~~~Dg~Hpn~~Gy~~~a~~~ 153 (157)
T cd01833 99 IAEYNAAIPGVVADLRTAGSPVVLVDMSTGYTTADDLYDGLHPNDQGYKKMADAW 153 (157)
T ss_pred HHHHHHHHHHHHHHHhcCCCCEEEEecCCCCCCcccccCCCCCchHHHHHHHHHH
Confidence 44555566666665443 568999988875 467899999999999987754
No 8
>cd01832 SGNH_hydrolase_like_1 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid. Myxobacterial members of this subfamily have been reported to be involved in adventurous gliding motility.
Probab=29.11 E-value=1.4e+02 Score=20.72 Aligned_cols=51 Identities=12% Similarity=0.109 Sum_probs=33.3
Q ss_pred ChHHHHHHHHHHHHhcCcceEeeeecc---ceEEEecCCCCCCchhHHHHHHHH
Q psy9523 45 QLPTLENLLNILINNSGIEKAFLFDVV---SKIYIATDSSPVDMQSYELCCDMV 95 (107)
Q Consensus 45 ~~~~le~~L~~~~~~~~aeev~LFe~~---T~L~IAtds~~~D~~~fE~~sd~I 95 (107)
.+..+.+.|..+|...++.-+=+++.. ..-..+.|.-|....-|+++.+.|
T Consensus 129 ~~~~~n~~l~~~a~~~~v~~vd~~~~~~~~~~~~~~~DgiHpn~~G~~~~A~~i 182 (185)
T cd01832 129 RLAAYNAVIRAVAARYGAVHVDLWEHPEFADPRLWASDRLHPSAAGHARLAALV 182 (185)
T ss_pred HHHHHHHHHHHHHHHcCCEEEecccCcccCCccccccCCCCCChhHHHHHHHHH
Confidence 355677778888777654444333321 111356788889999999998876
No 9
>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]
Probab=26.13 E-value=1.6e+02 Score=23.88 Aligned_cols=28 Identities=36% Similarity=0.599 Sum_probs=21.5
Q ss_pred eEeeeeccceEEEecCCCCCCchhHHHHHHHHHHHHhhh
Q psy9523 64 KAFLFDVVSKIYIATDSSPVDMQSYELCCDMVDLVIDVS 102 (107)
Q Consensus 64 ev~LFe~~T~L~IAtds~~~D~~~fE~~sd~I~v~~d~~ 102 (107)
++.|||=+| |..|| |++.+.++|+.++.
T Consensus 156 ~vmLFDEPT--------SALDP---Elv~EVL~vm~~LA 183 (240)
T COG1126 156 KVMLFDEPT--------SALDP---ELVGEVLDVMKDLA 183 (240)
T ss_pred CEEeecCCc--------ccCCH---HHHHHHHHHHHHHH
Confidence 788888776 45676 78888888887764
No 10
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=25.91 E-value=1.2e+02 Score=19.10 Aligned_cols=21 Identities=38% Similarity=0.585 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHhcCcceEeee
Q psy9523 48 TLENLLNILINNSGIEKAFLF 68 (107)
Q Consensus 48 ~le~~L~~~~~~~~aeev~LF 68 (107)
.++..++.+++..+++.++||
T Consensus 5 l~~~i~~~l~~~~~~~~~~l~ 25 (129)
T PF13492_consen 5 LLERILELLRELLGADRAALF 25 (129)
T ss_dssp HHHHHHHHHHHHST-SEEEEE
T ss_pred HHHHHHHHHHHHhCCCEEEEE
Confidence 578889999999999998877
No 11
>PF14234 DUF4336: Domain of unknown function (DUF4336)
Probab=24.85 E-value=46 Score=27.28 Aligned_cols=19 Identities=32% Similarity=0.422 Sum_probs=18.0
Q ss_pred cceEeeeeccceEEEecCC
Q psy9523 62 IEKAFLFDVVSKIYIATDS 80 (107)
Q Consensus 62 aeev~LFe~~T~L~IAtds 80 (107)
..|+++|+|.|+-.|.||.
T Consensus 140 ~~EvvFfHk~SkTLIvTDl 158 (285)
T PF14234_consen 140 FQEVVFFHKPSKTLIVTDL 158 (285)
T ss_pred eeEEEEEECCCCeEEhhhc
Confidence 7899999999999999986
No 12
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are
Probab=24.23 E-value=1.3e+02 Score=17.63 Aligned_cols=27 Identities=7% Similarity=0.017 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHhcCcceEeeeeccce
Q psy9523 47 PTLENLLNILINNSGIEKAFLFDVVSK 73 (107)
Q Consensus 47 ~~le~~L~~~~~~~~aeev~LFe~~T~ 73 (107)
+.+++.-+.+...++..+++||=...+
T Consensus 2 ~~l~~i~~~l~~~~~~~~v~lfGS~ar 28 (49)
T cd05397 2 ELLDIIKERLKKLVPGYEIVVYGSLVR 28 (49)
T ss_pred HHHHHHHHHHHhhcCCcEEEEECCcCC
Confidence 456667777777888999999976543
No 13
>PF01042 Ribonuc_L-PSP: Endoribonuclease L-PSP; InterPro: IPR006175 This domain is found in endoribonuclease, that is active on single-stranded mRNA and inhibits protein synthesis by cleavage of mRNA []. Previously it was thought to inhibit protein synthesis initiation []. This endoribonuclease may also be involved in the regulation of purine biosynthesis []. ; PDB: 3GTZ_B 3V4D_E 1J7H_A 3R0P_D 2IG8_A 1QD9_B 3L7Q_E 3VCZ_A 3QUW_A 2EWC_K ....
Probab=24.13 E-value=1.5e+02 Score=20.07 Aligned_cols=27 Identities=26% Similarity=0.515 Sum_probs=23.7
Q ss_pred eeeEEeecccchhHHHHHHHHHHHHHcCCh
Q psy9523 17 ITLSFHLTSIYDHSIFEAFSKVIQKLIPQL 46 (107)
Q Consensus 17 ~~i~~~~TSI~D~SLy~AwS~IVq~LiP~~ 46 (107)
+++++|.|++.| |.++.++-...+|..
T Consensus 67 v~~~~yl~d~~~---~~~~~~v~~~~f~~~ 93 (121)
T PF01042_consen 67 VKVTVYLTDMSD---FPAVNEVWKEFFPDH 93 (121)
T ss_dssp EEEEEEESSGGG---HHHHHHHHHHHSTSS
T ss_pred eeeeehhhhhhh---hHHHHHHHHHHhccc
Confidence 689999999988 888899988888776
No 14
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=22.08 E-value=51 Score=18.89 Aligned_cols=17 Identities=18% Similarity=0.464 Sum_probs=12.5
Q ss_pred HHhcCcceEeeeeccce
Q psy9523 57 INNSGIEKAFLFDVVSK 73 (107)
Q Consensus 57 ~~~~~aeev~LFe~~T~ 73 (107)
|..||.++++.|+..|+
T Consensus 3 Cp~Cg~~~a~~~~~Q~r 19 (39)
T PF01096_consen 3 CPKCGHNEAVFFQIQTR 19 (39)
T ss_dssp -SSS-SSEEEEEEESSS
T ss_pred CcCCCCCeEEEEEeecc
Confidence 55799999999988764
Done!