Query psy11123
Match_columns 285
No_of_seqs 153 out of 395
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 18:36:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11123.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11123hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03366 YEATS: YEATS family; 100.0 6.4E-33 1.4E-37 217.8 9.1 81 150-233 1-81 (84)
2 KOG3149|consensus 100.0 2.1E-28 4.6E-33 225.2 12.4 135 127-264 13-156 (249)
3 COG5033 TFG3 Transcription ini 99.9 9E-27 1.9E-31 209.6 8.4 97 130-232 14-112 (225)
4 PF09154 DUF1939: Domain of un 48.8 10 0.00022 28.1 1.3 14 195-208 36-49 (57)
5 PLN00172 ubiquitin conjugating 39.5 92 0.002 26.6 6.0 47 148-196 28-75 (147)
6 PHA01750 hypothetical protein 38.4 69 0.0015 25.1 4.5 28 31-58 40-74 (75)
7 PF09278 MerR-DNA-bind: MerR, 36.8 1.3E+02 0.0028 21.4 5.6 43 19-61 16-64 (65)
8 PF06600 DUF1140: Protein of u 33.3 72 0.0016 26.7 4.1 64 3-67 32-96 (107)
9 PF04000 Sas10_Utp3: Sas10/Utp 31.5 1.4E+02 0.0031 22.1 5.3 58 29-86 3-78 (85)
10 PF15361 RIC3: Resistance to i 30.7 50 0.0011 28.8 3.0 23 37-59 128-150 (152)
11 COG4898 Uncharacterized protei 28.4 41 0.00088 28.2 1.9 21 41-61 81-101 (115)
12 smart00212 UBCc Ubiquitin-conj 27.1 2.5E+02 0.0054 23.3 6.5 47 149-197 27-74 (145)
13 PF11559 ADIP: Afadin- and alp 26.3 92 0.002 26.3 3.8 31 21-51 121-151 (151)
14 PF07544 Med9: RNA polymerase 23.1 1.3E+02 0.0028 23.4 3.8 44 19-62 36-81 (83)
15 PF10224 DUF2205: Predicted co 22.2 3.4E+02 0.0073 21.5 6.0 45 17-61 7-51 (80)
16 PF05308 Mito_fiss_reg: Mitoch 21.8 1.1E+02 0.0024 29.0 3.7 37 5-46 106-142 (253)
17 cd00089 HR1 Protein kinase C-r 21.3 3.5E+02 0.0076 20.1 6.4 45 19-63 6-65 (72)
18 PF04508 Pox_A_type_inc: Viral 20.6 89 0.0019 19.5 1.9 22 33-54 1-22 (23)
19 PRK09737 EcoKI restriction-mod 20.6 2E+02 0.0044 27.6 5.4 44 28-71 375-418 (461)
20 PF10186 Atg14: UV radiation r 20.5 2.2E+02 0.0049 25.7 5.4 47 17-63 37-93 (302)
No 1
>PF03366 YEATS: YEATS family; InterPro: IPR005033 Named the YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF small subunit', this family also contains the GAS41 protein. All these proteins are thought to have a transcription stimulatory activity.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3QRL_A 2L7E_A 3FK3_C 3RLS_A.
Probab=99.98 E-value=6.4e-33 Score=217.82 Aligned_cols=81 Identities=43% Similarity=0.814 Sum_probs=68.0
Q ss_pred ceeEEEEEEcCCCCCccccceeeeEEEEeCCCCCCCceeEeecCCeEEEeeeeeeEEEEEEEEEecCCCCcceEEEEEEe
Q psy11123 150 THKWTVYVRNCESNPESIVRHIAHVKFMLHESYAPNNVVIVRKAPFKITREGWGEFPMKITIGFVDRENNRNVELVHPVN 229 (285)
Q Consensus 150 THkWtVYVR~~~~e~edls~~IkKVtF~LHpSF~pnp~rvV~~PPFeVtE~GWGEF~I~I~I~Fk~~~~~k~v~i~H~L~ 229 (285)
||+|+||||+++++ +++.+|+||+|+||||| +||+|+|++|||+|+|+|||||+|.|+|+|++.++.++++|.|+|+
T Consensus 1 th~W~v~Vr~~~~~--d~~~~i~kV~f~LHpsF-~~p~r~v~~pPFevte~GWGeF~i~I~i~f~~~~~~~~~~~~h~L~ 77 (84)
T PF03366_consen 1 THKWTVYVRGLDNE--DLSYFIKKVTFKLHPSF-PNPVRVVTKPPFEVTETGWGEFEIPIKIHFKDPSNEKPVTIQHDLK 77 (84)
T ss_dssp -EEEEEEEEECCCT----TTTEEEEEEES-TTS-SS-EEECSSTTEEEEEEESS--EEEEEEECCCGGCTCEEEEEEE--
T ss_pred CcEEEEEEEeCCCC--CccceEEEEEEECCCCC-CCCceEecCCCCEEEEeEeccEEEEEEEEEeCCCCCCcEEEEEEEE
Confidence 79999999999987 79999999999999999 5899999999999999999999999999999976667799999999
Q ss_pred eCCC
Q psy11123 230 FLHV 233 (285)
Q Consensus 230 L~~~ 233 (285)
|+++
T Consensus 78 l~~~ 81 (84)
T PF03366_consen 78 LHQD 81 (84)
T ss_dssp SSSC
T ss_pred cCCC
Confidence 9865
No 2
>KOG3149|consensus
Probab=99.95 E-value=2.1e-28 Score=225.20 Aligned_cols=135 Identities=31% Similarity=0.455 Sum_probs=112.9
Q ss_pred ceeeeEEECccccccCCCCCCCCceeEEEEEEcCCCCCccccceeeeEEEEeCCCCCCCceeEeecCCeEEEeeeeeeEE
Q psy11123 127 QRNFRFYVGTMCKALGSPACGQSTHKWTVYVRNCESNPESIVRHIAHVKFMLHESYAPNNVVIVRKAPFKITREGWGEFP 206 (285)
Q Consensus 127 ~r~~~IViGn~a~~l~~~~~~~~THkWtVYVR~~~~e~edls~~IkKVtF~LHpSF~pnp~rvV~~PPFeVtE~GWGEF~ 206 (285)
+...+|++||.|+.++++.++.+||.|+||||+...+ +++.||+||+|+||+|| +||+|+|++|||+|+|+|||+|+
T Consensus 13 ~~~~~iv~G~~a~~~~~~~~~~~th~w~v~v~~~~~e--d~~~~V~KV~f~LH~sf-~~P~Rvv~~pPf~i~EtGwgeF~ 89 (249)
T KOG3149|consen 13 TISVPIVPGNRAAILGKRLPDGFTHIWEVYVRGPGKE--DISAFVDKVVFKLHESF-PNPRRVVESPPFEITETGWGEFE 89 (249)
T ss_pred eEEeeeecCccccccCCCCCcccceeeEEEecCcCcc--ccceeeeeeeeeccccc-ccccccccCCCceEEeeccccce
Confidence 4556999999999999988889999999999999877 79999999999999999 79999999999999999999999
Q ss_pred EEEEEEEecCCCCcceEEEEEEeeCCCCCCC-cc-------cccccceEEEeeccccce-eeeecCc
Q psy11123 207 MKITIGFVDRENNRNVELVHPVNFLHVKSII-PI-------ISLETPIDVVLSLSETVL-EYLMDAD 264 (285)
Q Consensus 207 I~I~I~Fk~~~~~k~v~i~H~L~L~~~~tg~-~t-------~g~et~v~v~l~~~e~~~-e~~~~~~ 264 (285)
|.|+|||.+..+++++.+.|+|+++..+.+. +. ...++..-=+-..+..++ +++|.++
T Consensus 90 i~i~i~f~d~~~~~~v~~~~~l~l~~~~~p~~~~~~~~~~~~~~~~~~~r~~v~~~~~~~e~~f~~~ 156 (249)
T KOG3149|consen 90 IQIEIFFTDDANEKKVTLYHDLKLHSYGAPPVPHEESTKKTFVNPTISLRIPVVREGVDVEIVFPDP 156 (249)
T ss_pred EEEEEEeccCCCCceeeeeeeEEeeccCCCCccchhhhcccccccchhcccccccccccceeecCCC
Confidence 9999999998888889999999998775431 11 111111111223467788 9999987
No 3
>COG5033 TFG3 Transcription initiation factor IIF, auxiliary subunit [Transcription]
Probab=99.93 E-value=9e-27 Score=209.59 Aligned_cols=97 Identities=29% Similarity=0.536 Sum_probs=85.6
Q ss_pred eeEEECccccccCCC--CCCCCceeEEEEEEcCCCCCccccceeeeEEEEeCCCCCCCceeEeecCCeEEEeeeeeeEEE
Q psy11123 130 FRFYVGTMCKALGSP--ACGQSTHKWTVYVRNCESNPESIVRHIAHVKFMLHESYAPNNVVIVRKAPFKITREGWGEFPM 207 (285)
Q Consensus 130 ~~IViGn~a~~l~~~--~~~~~THkWtVYVR~~~~e~edls~~IkKVtF~LHpSF~pnp~rvV~~PPFeVtE~GWGEF~I 207 (285)
.+|+.| .|+.++.. .+-.+||-|.||||+..++ +++.||+||+|+||||| +||.|++.+|||+|.|+|||||+|
T Consensus 14 r~Iipg-ea~~~~~e~~~P~r~th~w~v~v~~~g~E--~~~~iv~KVifkLH~Tf-~NP~Rti~~pPFeI~EtGWGEF~i 89 (225)
T COG5033 14 RVIIPG-EAKPLGNEERFPVRHTHIWLVFVRAPGKE--DIATIVKKVIFKLHPTF-SNPTRTIESPPFEIKETGWGEFDI 89 (225)
T ss_pred ceeccC-ccccCCccccCCchhhEEEEEEEeCCCCc--chhhhhheeeEEecccc-CCCcccccCCCcEEEecccccceE
Confidence 355555 99999885 4567899999999999887 89999999999999999 699999999999999999999999
Q ss_pred EEEEEEecCCCCcceEEEEEEeeCC
Q psy11123 208 KITIGFVDRENNRNVELVHPVNFLH 232 (285)
Q Consensus 208 ~I~I~Fk~~~~~k~v~i~H~L~L~~ 232 (285)
.|+|||.+..+++ +|.|+|.|..
T Consensus 90 ~I~iff~~~age~--~~~fyl~f~~ 112 (225)
T COG5033 90 QIKIFFAEKAGEK--TIHFYLHFGD 112 (225)
T ss_pred EEEEEEecCCCce--Eeehhhhccc
Confidence 9999999999977 6667666643
No 4
>PF09154 DUF1939: Domain of unknown function (DUF1939); InterPro: IPR015237 This entry represents a C-terminal domain associated with prokaryotic alpha-amylases. It adopts a secondary structure consisting of an eight-stranded antiparallel beta-sheet containing a Greek key motif. Its exact function has not, as yet, been determined []. ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds; PDB: 1MXD_A 1MWO_A 1MXG_A 1W9X_A 2DIE_A 1VJS_A 1BPL_B 1BLI_A 1OB0_A 1E3Z_A ....
Probab=48.83 E-value=10 Score=28.09 Aligned_cols=14 Identities=50% Similarity=1.282 Sum_probs=10.4
Q ss_pred eEEEeeeeeeEEEE
Q psy11123 195 FKITREGWGEFPMK 208 (285)
Q Consensus 195 FeVtE~GWGEF~I~ 208 (285)
-.+.+.|||+|+++
T Consensus 36 vtid~dG~~~f~v~ 49 (57)
T PF09154_consen 36 VTIDEDGWGEFPVP 49 (57)
T ss_dssp EEE-TTSEEEEEE-
T ss_pred EEECCCeEEEEEEC
Confidence 45789999999986
No 5
>PLN00172 ubiquitin conjugating enzyme; Provisional
Probab=39.47 E-value=92 Score=26.61 Aligned_cols=47 Identities=11% Similarity=0.275 Sum_probs=29.6
Q ss_pred CCceeEEEEEEcCCCCCccccceeeeEEEEeCCCCC-CCceeEeecCCeE
Q psy11123 148 QSTHKWTVYVRNCESNPESIVRHIAHVKFMLHESYA-PNNVVIVRKAPFK 196 (285)
Q Consensus 148 ~~THkWtVYVR~~~~e~edls~~IkKVtF~LHpSF~-pnp~rvV~~PPFe 196 (285)
++.++|.+.+.|+.+.+ -..-+=++.+.+.+.|- ..|.+.+..+.|+
T Consensus 28 ~nl~~w~~~i~GP~~tp--yegg~f~~~i~fp~~YP~~pP~v~f~t~i~H 75 (147)
T PLN00172 28 ENLFRWTASIIGPSDSP--YAGGVFFLSILFPPDYPFKPPKVQFTTKIYH 75 (147)
T ss_pred CChheEEEEEECCCCCC--CCCCEEEEEEECCcccCCCCCEEEEecCccc
Confidence 46999999999988765 22223367788888883 1233334444443
No 6
>PHA01750 hypothetical protein
Probab=38.40 E-value=69 Score=25.05 Aligned_cols=28 Identities=21% Similarity=0.306 Sum_probs=14.1
Q ss_pred HHHHHHhhhhhHHH-------HHHHHHHHHHHHHH
Q psy11123 31 ISTETAFLESQAVR-------LSDELNETLRLFRA 58 (285)
Q Consensus 31 f~~E~~~ke~e~~~-------Id~rl~~~~~~l~~ 58 (285)
.+.|+.+...||.. |++.+.+-.+-+||
T Consensus 40 V~~ELdNL~~ei~~~kikqDnl~~qv~eik~k~dk 74 (75)
T PHA01750 40 VNSELDNLKTEIEELKIKQDELSRQVEEIKRKLDK 74 (75)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhcc
Confidence 34455555555554 44445544444444
No 7
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=36.80 E-value=1.3e+02 Score=21.39 Aligned_cols=43 Identities=19% Similarity=0.275 Sum_probs=27.0
Q ss_pred hHHHHHHHH------HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHhhh
Q psy11123 19 DESKVRDYL------LREISTETAFLESQAVRLSDELNETLRLFRALKR 61 (285)
Q Consensus 19 ~~~ki~~ii------~~ef~~E~~~ke~e~~~Id~rl~~~~~~l~~Lr~ 61 (285)
++..|+.++ ...-..-....+..+++|++++....++.+.|..
T Consensus 16 sL~eI~~~l~l~~~~~~~~~~~~~~l~~~~~~i~~~i~~L~~~~~~L~~ 64 (65)
T PF09278_consen 16 SLEEIRELLELYDQGDPPCADRRALLEEKLEEIEEQIAELQALRAQLEH 64 (65)
T ss_dssp -HHHHHHHHHHCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 355666666 2233344456677888888888877777666653
No 8
>PF06600 DUF1140: Protein of unknown function (DUF1140); InterPro: IPR009520 This entry is represented by Bacteriophage bIL286, Orf36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several short, hypothetical phage and bacterial proteins. The function of this family is unknown.
Probab=33.29 E-value=72 Score=26.71 Aligned_cols=64 Identities=13% Similarity=0.007 Sum_probs=47.4
Q ss_pred ccccccccccCCCCchhHHHHHHHHHHHH-HHHHHhhhhhHHHHHHHHHHHHHHHHHhhhhhhhhh
Q psy11123 3 EDGERNDVTTHPSPTLDESKVRDYLLREI-STETAFLESQAVRLSDELNETLRLFRALKRSVVTQY 67 (285)
Q Consensus 3 ~~~~~~~~~~~~a~~~~~~ki~~ii~~ef-~~E~~~ke~e~~~Id~rl~~~~~~l~~Lr~~iv~~y 67 (285)
++.-++|+.+.++..-+-+--++.=..|| .+|+..+=+++.+||. +..=-.-||.=|+..|+.|
T Consensus 32 a~~~~~K~ae~g~~vrTs~yWKs~~n~efyi~E~~~~l~~l~e~Dr-~~~Ws~kLHQdr~kFV~kY 96 (107)
T PF06600_consen 32 ADINAHKLAENGNCVRTSAYWKSVGNAEFYIKEIYQKLSQLAEIDR-LFHWSSKLHQDRYKFVSKY 96 (107)
T ss_pred HHHHHHHHHhcccccchhHHHHHhhcHHHHHHHHHHHHHHHHHHHH-HhhHHHHHHHHHHHHHHHH
Confidence 34446778888887777776677666665 5899999999999984 4555556777788888887
No 9
>PF04000 Sas10_Utp3: Sas10/Utp3/C1D family; InterPro: IPR007146 This family contains Utp3 and LCP5 which are components of the U3 ribonucleoprotein complex []. It also includes the Homo sapiens (Human) C1D protein and Saccharomyces cerevisiae (Baker's yeast) YHR081W (rrp47), an exosome-associated protein required for the 3' processing of stable RNAs [] and Sas10 which has been identified as a regulator of chromatin silencing []. This entry also includes the human protein Neuroguidin, an initiation factor 4E (eIF4E)-binding protein [].
Probab=31.47 E-value=1.4e+02 Score=22.11 Aligned_cols=58 Identities=17% Similarity=0.234 Sum_probs=34.3
Q ss_pred HHHHHHHHhhhhhHHHHHHHHHH----HHHH-----HHHhh------hhhhhhhhcccC---CCCCcchhHHHhhh
Q psy11123 29 REISTETAFLESQAVRLSDELNE----TLRL-----FRALK------RSVVTQYYATNR---SNRRVHPTIVKAEE 86 (285)
Q Consensus 29 ~ef~~E~~~ke~e~~~Id~rl~~----~~~~-----l~~Lr------~~iv~~yy~~~~---~~~~~hpaikk~l~ 86 (285)
++|+..+...+..+..+.+.... ...- |..++ |++..-||--.+ .++..||.++++..
T Consensus 3 ~~l~~~l~~~~~~l~~l~~~~~~~~~~~l~~~~g~sl~~~K~~~llaY~~~~~~~~~lk~~g~~~~~hpv~~~L~r 78 (85)
T PF04000_consen 3 KELSESLDEVEESLQPLLEKVKEEKEEELSPSDGISLLQAKNQLLLAYIINLLFYMYLKLSGVDPKDHPVMKELVR 78 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHhccCCCcccccHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCChHHHHHHH
Confidence 46666777777777666655521 1111 44444 555555554433 45588999998875
No 10
>PF15361 RIC3: Resistance to inhibitors of cholinesterase homologue 3
Probab=30.71 E-value=50 Score=28.84 Aligned_cols=23 Identities=17% Similarity=0.333 Sum_probs=20.5
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHh
Q psy11123 37 FLESQAVRLSDELNETLRLFRAL 59 (285)
Q Consensus 37 ~ke~e~~~Id~rl~~~~~~l~~L 59 (285)
.-+.||+++++||.|+-++|.+|
T Consensus 128 ~~~~eL~qLq~rL~qTE~~m~ki 150 (152)
T PF15361_consen 128 ITDYELAQLQERLAQTERAMEKI 150 (152)
T ss_pred chHHHHHHHHHHHHHHHHHHHHH
Confidence 44679999999999999999986
No 11
>COG4898 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.40 E-value=41 Score=28.17 Aligned_cols=21 Identities=19% Similarity=0.347 Sum_probs=18.4
Q ss_pred hHHHHHHHHHHHHHHHHHhhh
Q psy11123 41 QAVRLSDELNETLRLFRALKR 61 (285)
Q Consensus 41 e~~~Id~rl~~~~~~l~~Lr~ 61 (285)
.+++||+.|++-.|.||||=-
T Consensus 81 RvEEI~D~lMqeIRyLDKLvD 101 (115)
T COG4898 81 RVEEIDDPLMQEIRYLDKLVD 101 (115)
T ss_pred ehhhhccHHHHHHHHHHHHHH
Confidence 478999999999999999853
No 12
>smart00212 UBCc Ubiquitin-conjugating enzyme E2, catalytic domain homologues. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. This pathway functions in regulating many fundamental processes required for cell viability.TSG101 is one of several UBC homologues that lacks this active site cysteine.
Probab=27.07 E-value=2.5e+02 Score=23.27 Aligned_cols=47 Identities=11% Similarity=0.089 Sum_probs=29.5
Q ss_pred CceeEEEEEEcCCCCCccccceeeeEEEEeCCCCC-CCceeEeecCCeEE
Q psy11123 149 STHKWTVYVRNCESNPESIVRHIAHVKFMLHESYA-PNNVVIVRKAPFKI 197 (285)
Q Consensus 149 ~THkWtVYVR~~~~e~edls~~IkKVtF~LHpSF~-pnp~rvV~~PPFeV 197 (285)
....|.+.+.|+.+.+ --...+ ++++.+.+.|- ..|.+.+..++|+-
T Consensus 27 ~~~~w~~~i~gp~~~~-y~g~~f-~~~l~~p~~yP~~pP~v~f~~~i~Hp 74 (145)
T smart00212 27 NLLEWTGTIVGPPGTP-YEGGIF-KLTIEFPPDYPFKPPKVKFITKIYHP 74 (145)
T ss_pred ChheEEEEEEcCCCCC-cCCcEE-EEEEECCcccCCCCCEEEEeCCceEe
Confidence 6899999999876654 111222 78888899993 12444455554443
No 13
>PF11559 ADIP: Afadin- and alpha -actinin-Binding; InterPro: IPR021622 This family is found in mammals where it is localised at cell-cell adherens junctions [], and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.
Probab=26.25 E-value=92 Score=26.26 Aligned_cols=31 Identities=16% Similarity=0.119 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHhhhhhHHHHHHHHHH
Q psy11123 21 SKVRDYLLREISTETAFLESQAVRLSDELNE 51 (285)
Q Consensus 21 ~ki~~ii~~ef~~E~~~ke~e~~~Id~rl~~ 51 (285)
+....-++.++..||..|+.|++...+||.+
T Consensus 121 k~~~~~~~tq~~~e~rkke~E~~kLk~rL~q 151 (151)
T PF11559_consen 121 KNQLQQRKTQYEHELRKKEREIEKLKERLNQ 151 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3445667889999999999999999998853
No 14
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=23.05 E-value=1.3e+02 Score=23.45 Aligned_cols=44 Identities=14% Similarity=0.209 Sum_probs=31.1
Q ss_pred hHHHHHHHHHH--HHHHHHHhhhhhHHHHHHHHHHHHHHHHHhhhh
Q psy11123 19 DESKVRDYLLR--EISTETAFLESQAVRLSDELNETLRLFRALKRS 62 (285)
Q Consensus 19 ~~~ki~~ii~~--ef~~E~~~ke~e~~~Id~rl~~~~~~l~~Lr~~ 62 (285)
.+++.++.|+. ..++=+...+.+|....+++..=+.+|.++|.-
T Consensus 36 Klq~ar~~i~~lpgi~~s~eeq~~~i~~Le~~i~~k~~~L~~~~~~ 81 (83)
T PF07544_consen 36 KLQKARAAIRELPGIDRSVEEQEEEIEELEEQIRKKREVLQKFKER 81 (83)
T ss_pred HHHHHHHHHHhCCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45666666654 244445667778888888888888888888753
No 15
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=22.24 E-value=3.4e+02 Score=21.55 Aligned_cols=45 Identities=22% Similarity=0.149 Sum_probs=40.3
Q ss_pred chhHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHhhh
Q psy11123 17 TLDESKVRDYLLREISTETAFLESQAVRLSDELNETLRLFRALKR 61 (285)
Q Consensus 17 ~~~~~ki~~ii~~ef~~E~~~ke~e~~~Id~rl~~~~~~l~~Lr~ 61 (285)
..++++....-+.++..|+...+..|..+-+|+..++.--++|+.
T Consensus 7 ~~d~e~~~~e~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~ 51 (80)
T PF10224_consen 7 SEDIEKLEKEEKEELIQEILELQDSLEALSDRVEEVKEENEKLES 51 (80)
T ss_pred hHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356677888889999999999999999999999999999999984
No 16
>PF05308 Mito_fiss_reg: Mitochondrial fission regulator; InterPro: IPR007972 This family consists of several uncharacterised eukaryotic proteins of unknown function.
Probab=21.83 E-value=1.1e+02 Score=28.96 Aligned_cols=37 Identities=16% Similarity=0.244 Sum_probs=27.0
Q ss_pred ccccccccCCCCchhHHHHHHHHHHHHHHHHHhhhhhHHHHH
Q psy11123 5 GERNDVTTHPSPTLDESKVRDYLLREISTETAFLESQAVRLS 46 (285)
Q Consensus 5 ~~~~~~~~~~a~~~~~~ki~~ii~~ef~~E~~~ke~e~~~Id 46 (285)
++........|.+++++||. +++.||+.+..||+.|=
T Consensus 106 ~~~~~~~~~~~~~~AlqKIs-----ALEdELs~LRaQIA~IV 142 (253)
T PF05308_consen 106 NEPRKQSDLPANEAALQKIS-----ALEDELSRLRAQIAKIV 142 (253)
T ss_pred CccccccccCCCHHHHHHHH-----HHHHHHHHHHHHHHHHH
Confidence 34344456778889999995 46788888888888764
No 17
>cd00089 HR1 Protein kinase C-related kinase homology region 1 domain; also known as the ACC (antiparallel coiled-coil) finger domain or Rho-binding domain. Found in vertebrate PRK1 and yeast PKC1 protein kinases C; those found in rhophilin bind RhoGTP; those in PRK1 bind RhoA and RhoB. Rho family members function as molecular switches, cycling between inactive and active forms, controlling a variety of cellular processes. HR1 repeats often occur in tandem repeat arrangments, seperated by a short linker region.
Probab=21.29 E-value=3.5e+02 Score=20.08 Aligned_cols=45 Identities=20% Similarity=0.161 Sum_probs=34.2
Q ss_pred hHHHHHHHHHHHHHHHHHhhhh---------------hHHHHHHHHHHHHHHHHHhhhhh
Q psy11123 19 DESKVRDYLLREISTETAFLES---------------QAVRLSDELNETLRLFRALKRSV 63 (285)
Q Consensus 19 ~~~ki~~ii~~ef~~E~~~ke~---------------e~~~Id~rl~~~~~~l~~Lr~~i 63 (285)
.++.--+-|+.+++.|+..++. -+...++.|..+.+-++.||..+
T Consensus 6 ~~~~~l~~L~~~l~~E~~~r~Gaenm~~~~~~~~~~~~~~~~~~~l~es~~ki~~Lr~~L 65 (72)
T cd00089 6 KLQSRLERLEKELSIELKVKEGAENLLRLYSDEKKKKLLAEAEQMLRESKQKLELLKMQL 65 (72)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455556677888888776542 37788999999999999999776
No 18
>PF04508 Pox_A_type_inc: Viral A-type inclusion protein repeat ; InterPro: IPR007596 The repeat is found in the A-type inclusion protein of the Poxvirus family [].; GO: 0016032 viral reproduction
Probab=20.59 E-value=89 Score=19.53 Aligned_cols=22 Identities=27% Similarity=0.306 Sum_probs=17.0
Q ss_pred HHHHhhhhhHHHHHHHHHHHHH
Q psy11123 33 TETAFLESQAVRLSDELNETLR 54 (285)
Q Consensus 33 ~E~~~ke~e~~~Id~rl~~~~~ 54 (285)
+||..+...|..++.+|..|++
T Consensus 1 ~E~~rlr~rI~dLer~L~~C~~ 22 (23)
T PF04508_consen 1 REMNRLRNRISDLERQLSECRR 22 (23)
T ss_pred ChHHHHHHHHHHHHHHHHHHhc
Confidence 3677778888888888887765
No 19
>PRK09737 EcoKI restriction-modification system protein HsdS; Provisional
Probab=20.57 E-value=2e+02 Score=27.59 Aligned_cols=44 Identities=18% Similarity=0.239 Sum_probs=33.9
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHhhhhhhhhhhccc
Q psy11123 28 LREISTETAFLESQAVRLSDELNETLRLFRALKRSVVTQYYATN 71 (285)
Q Consensus 28 ~~ef~~E~~~ke~e~~~Id~rl~~~~~~l~~Lr~~iv~~yy~~~ 71 (285)
.++|...++.....++.|.+.+.+.+..|+.||.+++...|.-.
T Consensus 375 Q~kI~~~l~~l~~~~d~i~~~~~~~l~~L~~lKqslLqk~ftG~ 418 (461)
T PRK09737 375 QAEIVRRVEQLFAYADTIEKQVNNALARVNNLTQSILAKAFRGE 418 (461)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCc
Confidence 34455555566666777888888899999999999999998643
No 20
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=20.49 E-value=2.2e+02 Score=25.70 Aligned_cols=47 Identities=11% Similarity=0.195 Sum_probs=27.4
Q ss_pred chhHHHHHHHHH----------HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHhhhhh
Q psy11123 17 TLDESKVRDYLL----------REISTETAFLESQAVRLSDELNETLRLFRALKRSV 63 (285)
Q Consensus 17 ~~~~~ki~~ii~----------~ef~~E~~~ke~e~~~Id~rl~~~~~~l~~Lr~~i 63 (285)
+....+|..+|. .+...|+..++..+..|.+++.+.++-++.+|.-+
T Consensus 37 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~r~~~l~~~i~~~~~~i~~~r~~l 93 (302)
T PF10186_consen 37 EELRRRIEEILESDSNGQLLEIQQLKREIEELRERLERLRERIERLRKRIEQKRERL 93 (302)
T ss_pred HHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556777776 34455666666666666666665555555555433
Done!