Query 045165
Match_columns 203
No_of_seqs 49 out of 51
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 10:29:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045165.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045165hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08285 DPM3: Dolichol-phosph 81.2 14 0.0003 28.3 8.0 85 61-151 4-91 (91)
2 PF06305 DUF1049: Protein of u 78.4 11 0.00024 25.9 6.3 49 97-145 18-68 (68)
3 COG4064 MtrG Tetrahydromethano 58.9 58 0.0013 24.3 6.6 44 38-81 15-67 (75)
4 PF14235 DUF4337: Domain of un 56.2 1.1E+02 0.0024 25.4 8.8 79 26-113 68-154 (157)
5 KOG4841 Dolichol-phosphate man 47.4 86 0.0019 24.4 6.2 73 73-151 20-95 (95)
6 PF11846 DUF3366: Domain of un 45.8 1.1E+02 0.0024 24.9 7.3 64 67-131 21-84 (193)
7 PF00957 Synaptobrevin: Synapt 42.1 69 0.0015 23.3 4.9 13 136-148 35-47 (89)
8 PRK01026 tetrahydromethanopter 41.3 57 0.0012 24.6 4.3 29 38-66 15-43 (77)
9 TIGR01149 mtrG N5-methyltetrah 40.8 61 0.0013 24.0 4.3 42 38-79 12-62 (70)
10 PF05804 KAP: Kinesin-associat 39.1 47 0.001 34.0 4.7 49 16-76 152-205 (708)
11 PF04210 MtrG: Tetrahydrometha 36.7 72 0.0016 23.7 4.1 42 38-79 12-62 (70)
12 PHA02686 hypothetical protein; 35.3 50 0.0011 27.3 3.4 40 114-157 97-136 (138)
13 PF07544 Med9: RNA polymerase 34.6 45 0.00097 24.7 2.9 40 22-61 43-82 (83)
14 PF10852 DUF2651: Protein of u 32.2 2.1E+02 0.0045 21.9 6.1 38 91-128 25-62 (82)
15 PF01544 CorA: CorA-like Mg2+ 31.6 2.9E+02 0.0064 23.2 7.8 87 27-114 188-287 (292)
16 PRK00888 ftsB cell division pr 31.5 2.1E+02 0.0046 22.1 6.3 29 118-146 27-62 (105)
17 PF08863 YolD: YolD-like prote 30.0 38 0.00082 24.3 1.8 34 27-61 2-35 (92)
18 KOG1318 Helix loop helix trans 28.5 5.6E+02 0.012 24.9 10.3 101 33-154 226-326 (411)
19 PF14015 DUF4231: Protein of u 28.2 2.5E+02 0.0053 20.7 12.7 25 95-119 49-73 (112)
20 PRK10884 SH3 domain-containing 25.9 3.6E+02 0.0079 23.3 7.4 45 37-81 145-192 (206)
21 PF11853 DUF3373: Protein of u 24.4 1.3E+02 0.0027 29.8 4.7 13 135-147 34-46 (489)
22 PF05745 CRPA: Chlamydia 15 kD 23.9 4.3E+02 0.0094 22.1 9.4 118 5-134 9-141 (150)
23 PF06103 DUF948: Bacterial pro 23.8 2.9E+02 0.0063 20.0 6.5 45 103-147 4-48 (90)
24 PF03311 Cornichon: Cornichon 23.5 3.8E+02 0.0083 21.3 7.3 36 58-104 44-79 (128)
25 PF07271 Cytadhesin_P30: Cytad 23.4 5.1E+02 0.011 23.9 8.1 53 89-141 62-116 (279)
26 COG1654 BirA Biotin operon rep 23.1 1.2E+02 0.0026 22.6 3.4 40 113-152 11-51 (79)
27 PF04340 DUF484: Protein of un 20.7 5.2E+02 0.011 21.9 7.4 52 32-83 41-92 (225)
28 PF08542 Rep_fac_C: Replicatio 20.2 2.4E+02 0.0053 19.9 4.5 32 40-71 58-89 (89)
No 1
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=81.20 E-value=14 Score=28.31 Aligned_cols=85 Identities=19% Similarity=0.285 Sum_probs=49.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCcccccccccchHHHhHHHHHHHHHHHHHHh---hhHhHHHHHHHHHHHHhhHHH
Q 045165 61 ITQLYMFFFVFHSIALILLFNASSNDPVEKSCRRSWIPSLCTLLCSLGLIWAVRYK---SDVESHLEKLLEREKEDGKLL 137 (203)
Q Consensus 61 i~qL~~ff~VFqGviLtav~~ss~~~~~~~~C~~wWiP~~LSLlaSl~~~~av~~K---~~~~~~~~~~l~~Ek~d~~~l 137 (203)
+.|....+.++=++-+.++...-...+.....--|+.|+-.=++-..-.++-|-+. ++++.+....|++|..++|
T Consensus 4 ~~~~l~~~~~l~~~w~~l~~~~~~~~~~~~~~ii~~lP~~~Lv~fG~Ysl~~lgy~v~tFnDcpeA~~eL~~eI~eAK-- 81 (91)
T PF08285_consen 4 LQQWLSALLLLSALWLALLLGLLPLPPEPQQEIIPYLPFYALVSFGCYSLFTLGYGVATFNDCPEAAKELQKEIKEAK-- 81 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCchhHHHHHHHhhHHHHHHHHHHHHHHHHHhhhccCCCHHHHHHHHHHHHHHH--
Confidence 45555555555555555554332111112346678889865554444444444443 6677777777777666665
Q ss_pred HHHHHHHHhhccCC
Q 045165 138 AKCVEELKKKGVEF 151 (203)
Q Consensus 138 ~~~I~eLk~kG~~F 151 (203)
.+||.||.+|
T Consensus 82 ----~dLr~kGv~~ 91 (91)
T PF08285_consen 82 ----ADLRKKGVDV 91 (91)
T ss_pred ----HHHHHcCCCC
Confidence 4788888764
No 2
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=78.40 E-value=11 Score=25.93 Aligned_cols=49 Identities=22% Similarity=0.285 Sum_probs=34.3
Q ss_pred hHHHhHHHHH--HHHHHHHHHhhhHhHHHHHHHHHHHHhhHHHHHHHHHHH
Q 045165 97 IPSLCTLLCS--LGLIWAVRYKSDVESHLEKLLEREKEDGKLLAKCVEELK 145 (203)
Q Consensus 97 iP~~LSLlaS--l~~~~av~~K~~~~~~~~~~l~~Ek~d~~~l~~~I~eLk 145 (203)
.|..+-++.+ ++.+.|...-.-.+++..+++.+-+.+.+.+.+.+++||
T Consensus 18 ~pl~l~il~~f~~G~llg~l~~~~~~~~~r~~~~~~~k~l~~le~e~~~lr 68 (68)
T PF06305_consen 18 LPLGLLILIAFLLGALLGWLLSLPSRLRLRRRIRRLRKELKKLEKELEQLR 68 (68)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 5555444443 445667777777788888888887777777777777765
No 3
>COG4064 MtrG Tetrahydromethanopterin S-methyltransferase, subunit G [Coenzyme metabolism]
Probab=58.88 E-value=58 Score=24.33 Aligned_cols=44 Identities=16% Similarity=0.222 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHH---------HHHHHHHHHHHHHHh
Q 045165 38 KEEELILNRIALKETQIDSVRKEITQLYM---------FFFVFHSIALILLFN 81 (203)
Q Consensus 38 kee~l~~~Ri~~ke~r~~s~~~Ei~qL~~---------ff~VFqGviLtav~~ 81 (203)
.+.+-+.+|.+..|++.+....|.||.+| .|=..-|++|.++..
T Consensus 15 ~dfne~~kRLdeieekvef~~~Ev~Qr~GkkiGRDIGILYGlVIGlil~~i~~ 67 (75)
T COG4064 15 DDFNEIHKRLDEIEEKVEFVNGEVYQRIGKKIGRDIGILYGLVIGLILCMIYI 67 (75)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHH
Confidence 35677889999999999999999999985 566667777766643
No 4
>PF14235 DUF4337: Domain of unknown function (DUF4337)
Probab=56.23 E-value=1.1e+02 Score=25.36 Aligned_cols=79 Identities=13% Similarity=0.176 Sum_probs=40.9
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH-------HHHHHHHH-HHHHHHHHhhcCCCcccccccccch
Q 045165 26 TPTHKLLLKQWLKEEELILNRIALKETQIDSVRKEITQL-------YMFFFVFH-SIALILLFNASSNDPVEKSCRRSWI 97 (203)
Q Consensus 26 s~~h~llLk~W~kee~l~~~Ri~~ke~r~~s~~~Ei~qL-------~~ff~VFq-GviLtav~~ss~~~~~~~~C~~wWi 97 (203)
.+......+.|++|.+...+..+..|++-+....|-=.. --.=-.|| +++|.+++.-+ +++|+
T Consensus 68 ~~~~~~~i~~Y~~~~~~~~~e~~~l~~~A~~~e~~~d~~~~~~~~f~~a~~~lQIaI~Lasit~Lt---------~~~~l 138 (157)
T PF14235_consen 68 RAAYQKKIARYKKEKARYKSEAEELEAKAKEAEAESDHALHHHHRFDLAVALLQIAIVLASITALT---------KKKWL 138 (157)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcccchhHHHHHHHHHHHHHHHHHHHH---------HhHHH
Confidence 455566667777776666666666655543333222111 12222334 45555664443 46776
Q ss_pred HHHhHHHHHHHHHHHH
Q 045165 98 PSLCTLLCSLGLIWAV 113 (203)
Q Consensus 98 P~~LSLlaSl~~~~av 113 (203)
...--.++.+++++++
T Consensus 139 ~~~~~~~g~~G~~~~~ 154 (157)
T PF14235_consen 139 WYASLGLGAVGVAFFV 154 (157)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 6665555555555443
No 5
>KOG4841 consensus Dolichol-phosphate mannosyltransferase, subunit 3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=47.36 E-value=86 Score=24.39 Aligned_cols=73 Identities=14% Similarity=0.151 Sum_probs=44.2
Q ss_pred HHHHHHHHhhcCCCcccccccccchHHHhHHHHHHHHHHHHHHh---hhHhHHHHHHHHHHHHhhHHHHHHHHHHHhhcc
Q 045165 73 SIALILLFNASSNDPVEKSCRRSWIPSLCTLLCSLGLIWAVRYK---SDVESHLEKLLEREKEDGKLLAKCVEELKKKGV 149 (203)
Q Consensus 73 GviLtav~~ss~~~~~~~~C~~wWiP~~LSLlaSl~~~~av~~K---~~~~~~~~~~l~~Ek~d~~~l~~~I~eLk~kG~ 149 (203)
+.+.++|...-..-+..++|.+-.-|+.+-+.+..-.+.-|-+. ++++.+....|..|..++| .+||+||.
T Consensus 20 l~~~~~vt~~l~~Leeplscl~~y~P~~~~l~~G~Ya~~tv~Y~VATfnDc~eA~veL~~~IkEAr------~~L~rkg~ 93 (95)
T KOG4841|consen 20 LSTWVAVTTGLLGLEEPLSCLEVYWPLYLLLSAGCYALGTVGYRVATFNDCEEAAVELQSQIKEAR------ADLARKGL 93 (95)
T ss_pred HHHHHHHHHHHccCcccHHHHHhhhHHHHHHHHHhHhhhhheeeeeccCCcHHHHHHHHHHHHHHH------HHHHHccC
Confidence 44555555333333457889999999977666555555556555 4555666665655544444 46777776
Q ss_pred CC
Q 045165 150 EF 151 (203)
Q Consensus 150 ~F 151 (203)
.|
T Consensus 94 ri 95 (95)
T KOG4841|consen 94 RI 95 (95)
T ss_pred CC
Confidence 43
No 6
>PF11846 DUF3366: Domain of unknown function (DUF3366); InterPro: IPR021797 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 200 amino acids in length.
Probab=45.82 E-value=1.1e+02 Score=24.95 Aligned_cols=64 Identities=13% Similarity=-0.061 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHhhcCCCcccccccccchHHHhHHHHHHHHHHHHHHhhhHhHHHHHHHHHHH
Q 045165 67 FFFVFHSIALILLFNASSNDPVEKSCRRSWIPSLCTLLCSLGLIWAVRYKSDVESHLEKLLEREK 131 (203)
Q Consensus 67 ff~VFqGviLtav~~ss~~~~~~~~C~~wWiP~~LSLlaSl~~~~av~~K~~~~~~~~~~l~~Ek 131 (203)
.|+.||.+++.++.-...+.+ .......+.+..+..++.++.++++..-..+|...+..-..|+
T Consensus 21 ~ysyfl~~~~l~Lg~~~~~~~-~~~~~~~~~~~~l~~~~~l~~l~~~~~~~~~~~~~~~l~~~~~ 84 (193)
T PF11846_consen 21 WYSYFLWPFALLLGLLPDPAR-RLRRIPRSLAFALRAAALLIALAALGFMLTDYHTNEQLTRFER 84 (193)
T ss_pred HHHHHHHHHHHHHHHHhcccc-cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 377788777666655432111 1112223333444444445555555555556655544434443
No 7
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain []. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins []. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.; GO: 0016192 vesicle-mediated transport, 0016021 integral to membrane; PDB: 3EGX_C 2NUP_C 3EGD_C 2NUT_C 1IOU_A 1H8M_A 3B5N_A 3ZYM_A 2NPS_A 1SFC_E ....
Probab=42.14 E-value=69 Score=23.26 Aligned_cols=13 Identities=31% Similarity=0.309 Sum_probs=5.9
Q ss_pred HHHHHHHHHHhhc
Q 045165 136 LLAKCVEELKKKG 148 (203)
Q Consensus 136 ~l~~~I~eLk~kG 148 (203)
.|...-++|....
T Consensus 35 ~L~~kt~~L~~~a 47 (89)
T PF00957_consen 35 ELEDKTEELSDNA 47 (89)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHh
Confidence 3444445554443
No 8
>PRK01026 tetrahydromethanopterin S-methyltransferase subunit G; Provisional
Probab=41.30 E-value=57 Score=24.58 Aligned_cols=29 Identities=24% Similarity=0.180 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 045165 38 KEEELILNRIALKETQIDSVRKEITQLYM 66 (203)
Q Consensus 38 kee~l~~~Ri~~ke~r~~s~~~Ei~qL~~ 66 (203)
++.+-+.+|.+..|.+++....|+||-+|
T Consensus 15 ~d~~~i~~rLD~iEeKVEftn~Ei~Qr~G 43 (77)
T PRK01026 15 KDFKEIQKRLDEIEEKVEFTNAEIFQRIG 43 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45677888999999999999999999763
No 9
>TIGR01149 mtrG N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit G. coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.
Probab=40.80 E-value=61 Score=24.04 Aligned_cols=42 Identities=19% Similarity=0.298 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHH---------HHHHHHHHHHHHH
Q 045165 38 KEEELILNRIALKETQIDSVRKEITQLYM---------FFFVFHSIALILL 79 (203)
Q Consensus 38 kee~l~~~Ri~~ke~r~~s~~~Ei~qL~~---------ff~VFqGviLtav 79 (203)
++.+-+..|.+..|.+++....|+||-.| .|=+.=|+++-.+
T Consensus 12 ~d~~~i~~rLd~iEeKVEf~~~E~~Qr~Gkk~GRDiGIlYG~viGlli~~~ 62 (70)
T TIGR01149 12 DEFNEVMKRLDEIEEKVEFVNGEVAQRIGKKVGRDIGILYGLVIGLILFLI 62 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhhHHHHHHHHHHHHHHHHH
Confidence 45667788999999999999999999763 4555555554433
No 10
>PF05804 KAP: Kinesin-associated protein (KAP)
Probab=39.06 E-value=47 Score=34.00 Aligned_cols=49 Identities=31% Similarity=0.390 Sum_probs=39.8
Q ss_pred CCccccccccCchHHHHH-----HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Q 045165 16 PPHPLHQIAETPTHKLLL-----KQWLKEEELILNRIALKETQIDSVRKEITQLYMFFFVFHSIAL 76 (203)
Q Consensus 16 ~~~pL~eIa~s~~h~llL-----k~W~kee~l~~~Ri~~ke~r~~s~~~Ei~qL~~ff~VFqGviL 76 (203)
...+|.++..|+++.-+| ++|+|.-++..+.+. ||.-..-|+=||+++.
T Consensus 152 ~~~NL~~l~~ne~l~~aL~RvLred~~ks~~l~tnI~~------------iF~~fS~f~~fH~~l~ 205 (708)
T PF05804_consen 152 NPENLEELVQNETLMSALARVLREDWKKSVELATNIIY------------IFFCFSNFSQFHPILA 205 (708)
T ss_pred CcchHHHHHHhHHHHHHHHHHHHHHhhhhHHHHHHHHH------------HHHHHHhHHHHHHHHH
Confidence 345677777777777655 789999999988887 9999999999999875
No 11
>PF04210 MtrG: Tetrahydromethanopterin S-methyltransferase, subunit G ; InterPro: IPR005866 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane
Probab=36.66 E-value=72 Score=23.68 Aligned_cols=42 Identities=14% Similarity=0.252 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHH---------HHHHHHHHHHHHH
Q 045165 38 KEEELILNRIALKETQIDSVRKEITQLYM---------FFFVFHSIALILL 79 (203)
Q Consensus 38 kee~l~~~Ri~~ke~r~~s~~~Ei~qL~~---------ff~VFqGviLtav 79 (203)
++.+-+..|.+..|++++....|+||-.| .|=+.=|+++..+
T Consensus 12 ~~~~~i~~rLd~iEeKvEf~~~Ei~Qr~GkkiGRDiGIlYG~v~Glii~~~ 62 (70)
T PF04210_consen 12 DDFNEIMKRLDEIEEKVEFTNAEIAQRAGKKIGRDIGILYGLVIGLIIFII 62 (70)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHhHHhhhHHHHHHHHHHHHHHHHH
Confidence 45677888999999999999999999763 4545555554433
No 12
>PHA02686 hypothetical protein; Provisional
Probab=35.27 E-value=50 Score=27.28 Aligned_cols=40 Identities=20% Similarity=0.406 Sum_probs=30.7
Q ss_pred HHhhhHhHHHHHHHHHHHHhhHHHHHHHHHHHhhccCCCchhhh
Q 045165 114 RYKSDVESHLEKLLEREKEDGKLLAKCVEELKKKGVEFDLLKEV 157 (203)
Q Consensus 114 ~~K~~~~~~~~~~l~~Ek~d~~~l~~~I~eLk~kG~~F~lsKe~ 157 (203)
.-|.+++.++. +++.-.+.|.+.+++++.+|++|-|-|++
T Consensus 97 s~k~R~~~Rv~----~N~KK~~~l~r~~k~~~drgiD~~FIkda 136 (138)
T PHA02686 97 RGKARAALRVC----RNREKVHRLARLLRDAESRGADFAFIRAA 136 (138)
T ss_pred cHHHHHHHHHH----hhHHHHHHHHHHHHHHHHcCCCHHHHHHh
Confidence 34566777766 44445678999999999999999987764
No 13
>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=34.59 E-value=45 Score=24.68 Aligned_cols=40 Identities=18% Similarity=0.211 Sum_probs=32.5
Q ss_pred ccccCchHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 045165 22 QIAETPTHKLLLKQWLKEEELILNRIALKETQIDSVRKEI 61 (203)
Q Consensus 22 eIa~s~~h~llLk~W~kee~l~~~Ri~~ke~r~~s~~~Ei 61 (203)
.|.+.|+.-.-.++|+.+-.-+..+++.|+..+...++.+
T Consensus 43 ~i~~lpgi~~s~eeq~~~i~~Le~~i~~k~~~L~~~~~~~ 82 (83)
T PF07544_consen 43 AIRELPGIDRSVEEQEEEIEELEEQIRKKREVLQKFKERV 82 (83)
T ss_pred HHHhCCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3455666666679999999999999999999998888764
No 14
>PF10852 DUF2651: Protein of unknown function (DUF2651) ; InterPro: IPR020258 This entry contains transmembrane proteins with no known function.
Probab=32.25 E-value=2.1e+02 Score=21.87 Aligned_cols=38 Identities=16% Similarity=0.024 Sum_probs=31.8
Q ss_pred cccccchHHHhHHHHHHHHHHHHHHhhhHhHHHHHHHH
Q 045165 91 SCRRSWIPSLCTLLCSLGLIWAVRYKSDVESHLEKLLE 128 (203)
Q Consensus 91 ~C~~wWiP~~LSLlaSl~~~~av~~K~~~~~~~~~~l~ 128 (203)
-++|||++-.++++.|+..-+-+.....-+|-.-+.+-
T Consensus 25 l~k~~yimPivtf~i~Lil~~t~fn~SFf~WvvvYT~~ 62 (82)
T PF10852_consen 25 LFKKVYIMPIVTFAISLILTFTLFNPSFFFWVVVYTIF 62 (82)
T ss_pred hcceeehHHHHHHHHHHHHHHHhhChHHHHHHHHHHHH
Confidence 49999999999999999888888888888887766543
No 15
>PF01544 CorA: CorA-like Mg2+ transporter protein; InterPro: IPR002523 The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli [, ]. CorA is virtually ubiquitous in the Bacteria and Archaea. There are also eukaryotic relatives of this protein. Transporter ZntB mediates efflux of zinc ions [].; GO: 0046873 metal ion transmembrane transporter activity, 0030001 metal ion transport, 0055085 transmembrane transport, 0016020 membrane; PDB: 2HN1_A 3NWI_D 3NVO_B 3CK6_A 2IUB_E 2BBJ_E 2HN2_A 2BBH_A.
Probab=31.56 E-value=2.9e+02 Score=23.22 Aligned_cols=87 Identities=10% Similarity=0.037 Sum_probs=37.5
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH-----------HHHHHH-HHHH-HHHHHHHHHHhhcCCCccccccc
Q 045165 27 PTHKLLLKQWLKEEELILNRIALKETQIDSVRKE-----------ITQLYM-FFFV-FHSIALILLFNASSNDPVEKSCR 93 (203)
Q Consensus 27 ~~h~llLk~W~kee~l~~~Ri~~ke~r~~s~~~E-----------i~qL~~-ff~V-FqGviLtav~~ss~~~~~~~~C~ 93 (203)
+..+..++.=..+-+.+.++++....+++++.+. +.+... .=.| ...-+++.++.-|... ....=.
T Consensus 188 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~n~~m~~LT~~t~iflPlt~i~g~fGMN~~~-~p~~~~ 266 (292)
T PF01544_consen 188 DEDKEYLRDLLDRIERLLERAESLRERLESLQDLYQSKLSNRQNRVMKVLTIVTAIFLPLTFITGIFGMNFKG-MPELDW 266 (292)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHTTSTTS-SS----SSSS
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCccC-CCccCC
Confidence 3444445555555555666666666655555443 322221 1122 2223334444433321 122346
Q ss_pred ccchHHHhHHHHHHHHHHHHH
Q 045165 94 RSWIPSLCTLLCSLGLIWAVR 114 (203)
Q Consensus 94 ~wWiP~~LSLlaSl~~~~av~ 114 (203)
+||.++.+.+...++..+++.
T Consensus 267 ~~g~~~~~~~~~~~~~~~~~~ 287 (292)
T PF01544_consen 267 PYGYFFVIILGLMILVAILLY 287 (292)
T ss_dssp SS-SHHH--HHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHHHHHHH
Confidence 777777754444444444443
No 16
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=31.50 E-value=2.1e+02 Score=22.08 Aligned_cols=29 Identities=10% Similarity=0.090 Sum_probs=16.1
Q ss_pred hHhHHHHHHHHHHHHhh-------HHHHHHHHHHHh
Q 045165 118 DVESHLEKLLEREKEDG-------KLLAKCVEELKK 146 (203)
Q Consensus 118 ~~~~~~~~~l~~Ek~d~-------~~l~~~I~eLk~ 146 (203)
..|..+.++++.-+... +.|.+.|..|+.
T Consensus 27 ~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 27 LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 45666666666444443 455555555554
No 17
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=29.96 E-value=38 Score=24.34 Aligned_cols=34 Identities=26% Similarity=0.521 Sum_probs=23.8
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 045165 27 PTHKLLLKQWLKEEELILNRIALKETQIDSVRKEI 61 (203)
Q Consensus 27 ~~h~llLk~W~kee~l~~~Ri~~ke~r~~s~~~Ei 61 (203)
|.|+..|+.|.++.+...+.. .-|.+++.+.+-+
T Consensus 2 PEH~e~L~~~~~e~~k~~kp~-Lde~~leei~~~l 35 (92)
T PF08863_consen 2 PEHKEALRELIKEQNKVEKPE-LDEQQLEEINEKL 35 (92)
T ss_pred ChHHHHHHHHHHHhcccCCCC-CcHHHHHHHHHHH
Confidence 899999999999998886443 3345555444443
No 18
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=28.47 E-value=5.6e+02 Score=24.88 Aligned_cols=101 Identities=18% Similarity=0.123 Sum_probs=70.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccccccccchHHHhHHHHHHHHHHH
Q 045165 33 LKQWLKEEELILNRIALKETQIDSVRKEITQLYMFFFVFHSIALILLFNASSNDPVEKSCRRSWIPSLCTLLCSLGLIWA 112 (203)
Q Consensus 33 Lk~W~kee~l~~~Ri~~ke~r~~s~~~Ei~qL~~ff~VFqGviLtav~~ss~~~~~~~~C~~wWiP~~LSLlaSl~~~~a 112 (203)
-+.|+|......+-|| +-|.+++.+-|.+|-- +|--++.. =-+|=. -=.|-+|+=++--
T Consensus 226 ~~~rdr~Krd~HNeVE--RRRR~nIN~~IkeLg~-----------liP~~~~~------~~~~nK--gtILk~s~dYIr~ 284 (411)
T KOG1318|consen 226 ALERDRRKRDNHNEVE--RRRRENINDRIKELGQ-----------LIPKCNSE------DMKSNK--GTILKASCDYIRE 284 (411)
T ss_pred hhHHHHHHHhhhhHHH--HHHHHHHHHHHHHHHH-----------hCCCCCcc------hhhccc--chhhHHHHHHHHH
Confidence 4678888888888888 4577888888988753 23222211 112222 1234566778888
Q ss_pred HHHhhhHhHHHHHHHHHHHHhhHHHHHHHHHHHhhccCCCch
Q 045165 113 VRYKSDVESHLEKLLEREKEDGKLLAKCVEELKKKGVEFDLL 154 (203)
Q Consensus 113 v~~K~~~~~~~~~~l~~Ek~d~~~l~~~I~eLk~kG~~F~ls 154 (203)
++....+..+++.+.++-..+.+.|.++|+||+++-..-+..
T Consensus 285 Lqq~~q~~~E~~~rqk~le~~n~~L~~rieeLk~~~~~~~~~ 326 (411)
T KOG1318|consen 285 LQQTLQRARELENRQKKLESTNQELALRIEELKSEAGRHGLQ 326 (411)
T ss_pred HHHHHHHHHHHHhhhhHHHhHHHHHHHHHHHHHHHHHHhcCc
Confidence 888888888888888777788899999999999986555543
No 19
>PF14015 DUF4231: Protein of unknown function (DUF4231)
Probab=28.18 E-value=2.5e+02 Score=20.71 Aligned_cols=25 Identities=24% Similarity=0.286 Sum_probs=10.9
Q ss_pred cchHHHhHHHHHHHHHHHHHHhhhH
Q 045165 95 SWIPSLCTLLCSLGLIWAVRYKSDV 119 (203)
Q Consensus 95 wWiP~~LSLlaSl~~~~av~~K~~~ 119 (203)
+|.+.+.+++.+++++.+....+.+
T Consensus 49 ~~~~~~~~~l~~~~~~~~~~~~~~~ 73 (112)
T PF14015_consen 49 SWLKLVAAILSALAAILASLAAFFR 73 (112)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3444444444444444444444433
No 20
>PRK10884 SH3 domain-containing protein; Provisional
Probab=25.93 E-value=3.6e+02 Score=23.33 Aligned_cols=45 Identities=16% Similarity=0.074 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHHhhhHHHHHH---HHHHHHHHHHHHHHHHHHHh
Q 045165 37 LKEEELILNRIALKETQIDSVRKEI---TQLYMFFFVFHSIALILLFN 81 (203)
Q Consensus 37 ~kee~l~~~Ri~~ke~r~~s~~~Ei---~qL~~ff~VFqGviLtav~~ 81 (203)
+++-.....+++..+.+.++.++++ +.++|...+|=|++|.++.-
T Consensus 145 ~~~l~~~~~~~~~l~~~~~~~~~~~~~~wf~~Gg~v~~~GlllGlilp 192 (206)
T PRK10884 145 KNQLIVAQKKVDAANLQLDDKQRTIIMQWFMYGGGVAGIGLLLGLLLP 192 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhc
Confidence 3334445555555555666665543 56789999999999998843
No 21
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=24.38 E-value=1.3e+02 Score=29.78 Aligned_cols=13 Identities=46% Similarity=0.557 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHhh
Q 045165 135 KLLAKCVEELKKK 147 (203)
Q Consensus 135 ~~l~~~I~eLk~k 147 (203)
+.|.+.+++||.+
T Consensus 34 e~L~kql~~Lk~q 46 (489)
T PF11853_consen 34 EALKKQLEELKAQ 46 (489)
T ss_pred HHHHHHHHHHHHh
Confidence 4466666666665
No 22
>PF05745 CRPA: Chlamydia 15 kDa cysteine-rich outer membrane protein (CRPA); InterPro: IPR008436 Chlamydia is a genus of bacteria, which causes the most common bacterial sexually transmitted diseases. They are obligate intracellular bacterial pathogens. Members of this genus lack a peptidoglycan layer, but as a substitute, it has been proposed that they have several cysteine rich membrane proteins. This includes the major outer membrane protein (MOMP). These form disulphide bonds to provide rigidity to the cell wall. The alignment of the amino acid sequences of the MOMP from various serovars of Chlamydia show that they have between seven and ten cysteine residues; seven of which are highly conserved []. The MOMP has been the focus of efforts to produce a vaccine for Chlamydia trachomatis []. The 15 kDa cysteine-rich protein in this entry is a multi-pass outer membrane protein. They are associated with the differentiation of reticulate bodies (RBs) into elementary bodies (EBs) []. They immunolocalise to the inclusion membrane, which is the membrane that surrounds the intracellular parasite. These proteins are recognised by CD8+ T cells in both human and mouse infections, suggesting they gain access to the host cytoplasm.; GO: 0019867 outer membrane
Probab=23.89 E-value=4.3e+02 Score=22.09 Aligned_cols=118 Identities=17% Similarity=0.168 Sum_probs=69.3
Q ss_pred CCCCCCcCCCCC----CccccccccCchHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH----HHHHHHHHHHHHH
Q 045165 5 QGTKPSIMEPKP----PHPLHQIAETPTHKLLLKQWLKEEELILNRIALKETQIDSVRKEITQ----LYMFFFVFHSIAL 76 (203)
Q Consensus 5 ~~~~~~~~~~~~----~~pL~eIa~s~~h~llLk~W~kee~l~~~Ri~~ke~r~~s~~~Ei~q----L~~ff~VFqGviL 76 (203)
.++-.|+++... ...+.....++++...+--|-|+.-.=--|.. .=+++.+|| ++|.++|.-|+.|
T Consensus 9 ~~sv~~iv~~~~~s~~~~~~~~~~~~vtlvn~~lgw~r~~ii~pir~S------kiv~SrAfqItl~VlGiiLviagl~l 82 (150)
T PF05745_consen 9 GSSVTPIVQPIASSGSDQVIQNETVQVTLVNSVLGWCREKIIDPIRNS------KIVQSRAFQITLVVLGIILVIAGLAL 82 (150)
T ss_pred CCcccccccccccccHhHHhhccccCcchhhhhhhhHHHhhcChhHHH------HHhhhhhhhhhHHHHHHHHHHHHHHH
Confidence 344455555533 34445556678888888889865422111111 112333555 3599999999999
Q ss_pred HHHHhhcCCCccccccccc--chHHHhHHHHHHHHHHHH-----HHhhhHhHHHHHHHHHHHHhh
Q 045165 77 ILLFNASSNDPVEKSCRRS--WIPSLCTLLCSLGLIWAV-----RYKSDVESHLEKLLEREKEDG 134 (203)
Q Consensus 77 tav~~ss~~~~~~~~C~~w--WiP~~LSLlaSl~~~~av-----~~K~~~~~~~~~~l~~Ek~d~ 134 (203)
+-+.|+.... +-- =||..+.+.-=+++.+.. ..|.+.|.++....++..+|.
T Consensus 83 ~fil~~~lg~------naf~~~IPAviGlvkll~ts~~m~~~Cs~EKw~lck~~l~t~EDilDdG 141 (150)
T PF05745_consen 83 TFILHSQLGN------NAFLFIIPAVIGLVKLLITSLCMEESCSPEKWKLCKRWLGTLEDILDDG 141 (150)
T ss_pred HhhehhhhcC------ccchhhHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhhccc
Confidence 9999986432 222 358888877666665553 344555555555555544444
No 23
>PF06103 DUF948: Bacterial protein of unknown function (DUF948); InterPro: IPR009293 This family consists of bacterial sequences several of which are thought to be general stress proteins.
Probab=23.80 E-value=2.9e+02 Score=20.02 Aligned_cols=45 Identities=20% Similarity=0.280 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHhhhHhHHHHHHHHHHHHhhHHHHHHHHHHHhh
Q 045165 103 LLCSLGLIWAVRYKSDVESHLEKLLEREKEDGKLLAKCVEELKKK 147 (203)
Q Consensus 103 LlaSl~~~~av~~K~~~~~~~~~~l~~Ek~d~~~l~~~I~eLk~k 147 (203)
+++++++++.+.+-.....++.+.+++=....+.+.+.++++...
T Consensus 4 lI~Aiaf~vLvi~l~~~l~~l~~~l~~~~~ti~~l~~~~~~i~~e 48 (90)
T PF06103_consen 4 LIAAIAFAVLVIFLIKVLKKLKKTLDEVNKTIDTLQEQVDPITKE 48 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 567777777788887788888777777666666666666555533
No 24
>PF03311 Cornichon: Cornichon protein; InterPro: IPR003377 The drosophila cornichon protein (gene: cni) [] is required in the germline for dorsal-ventral signalling. The dorsal-ventral pattern formation involves a reorganisation of the microtubule network correlated with the movement of the oocyte nucleus, and depending on the initial correct establishment of the anterior-posterior axis via a signal from the oocyte produced by cornichon and gurken and received by torpedo protein in the follicle cells. The biochemical function of the cornichon protein is currently not known. It is a protein of 144 residues that seems to contain three transmembrane regions. ; GO: 0035556 intracellular signal transduction, 0016020 membrane
Probab=23.54 E-value=3.8e+02 Score=21.33 Aligned_cols=36 Identities=17% Similarity=0.297 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccccccccchHHHhHHH
Q 045165 58 RKEITQLYMFFFVFHSIALILLFNASSNDPVEKSCRRSWIPSLCTLL 104 (203)
Q Consensus 58 ~~Ei~qL~~ff~VFqGviLtav~~ss~~~~~~~~C~~wWiP~~LSLl 104 (203)
.|.+=+++-.-.+.||+..... -+..||+++++++.
T Consensus 44 c~~lN~lv~pE~~~h~~l~~l~-----------ll~g~w~~~llnlP 79 (128)
T PF03311_consen 44 CSRLNPLVLPEYIIHGFLCLLF-----------LLTGHWFLFLLNLP 79 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHH
Confidence 4456678888888898876655 26789999998877
No 25
>PF07271 Cytadhesin_P30: Cytadhesin P30/P32; InterPro: IPR009896 This family consists of several Mycoplasma species specific Cytadhesin P32 and P30 proteins. P30 has been found to be membrane associated and localised on the tip organelle. It is thought that it is important in cytadherence and virulence [].; GO: 0007157 heterophilic cell-cell adhesion, 0009405 pathogenesis, 0016021 integral to membrane
Probab=23.42 E-value=5.1e+02 Score=23.91 Aligned_cols=53 Identities=21% Similarity=0.206 Sum_probs=27.4
Q ss_pred cccccccchHHHhHHH--HHHHHHHHHHHhhhHhHHHHHHHHHHHHhhHHHHHHH
Q 045165 89 EKSCRRSWIPSLCTLL--CSLGLIWAVRYKSDVESHLEKLLEREKEDGKLLAKCV 141 (203)
Q Consensus 89 ~~~C~~wWiP~~LSLl--aSl~~~~av~~K~~~~~~~~~~l~~Ek~d~~~l~~~I 141 (203)
.++-.-||||-+=+.. -.++++.||-.-.-.|.+=++.+=+|++..+-++...
T Consensus 62 ~i~~~~W~~P~v~~~~G~~~v~liLgl~ig~p~~krkek~~iee~e~~~q~~e~~ 116 (279)
T PF07271_consen 62 PITEQSWFIPVVGGSAGLLAVALILGLAIGIPIYKRKEKRMIEEKEEHEQLAEQL 116 (279)
T ss_pred ecccccceeeeccchhhHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHHH
Confidence 4567889999732211 1233344444444444444555555666555444333
No 26
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=23.11 E-value=1.2e+02 Score=22.57 Aligned_cols=40 Identities=15% Similarity=0.145 Sum_probs=29.1
Q ss_pred HHHhhhHhHHHHHHHHHHHHhh-HHHHHHHHHHHhhccCCC
Q 045165 113 VRYKSDVESHLEKLLEREKEDG-KLLAKCVEELKKKGVEFD 152 (203)
Q Consensus 113 v~~K~~~~~~~~~~l~~Ek~d~-~~l~~~I~eLk~kG~~F~ 152 (203)
+.......+.-...|.++.+-. .++-++|++||..|..++
T Consensus 11 ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~ 51 (79)
T COG1654 11 LLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIE 51 (79)
T ss_pred HHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceE
Confidence 3344444455566677777744 689999999999999877
No 27
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=20.73 E-value=5.2e+02 Score=21.87 Aligned_cols=52 Identities=19% Similarity=0.180 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 045165 32 LLKQWLKEEELILNRIALKETQIDSVRKEITQLYMFFFVFHSIALILLFNAS 83 (203)
Q Consensus 32 lLk~W~kee~l~~~Ri~~ke~r~~s~~~Ei~qL~~ff~VFqGviLtav~~ss 83 (203)
...+=++.-..+-.|+...|.|++.+-..+.+=-..|-.+|.+.+.++...+
T Consensus 41 avSL~erQ~~~LR~~~~~L~~~l~~Li~~Ar~Ne~~~~~~~~l~l~LL~a~s 92 (225)
T PF04340_consen 41 AVSLVERQLERLRERNRQLEEQLEELIENARENEAIFQRLHRLVLALLAARS 92 (225)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--S
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 3444444444444444444444444444444444778999999999986554
No 28
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=20.17 E-value=2.4e+02 Score=19.88 Aligned_cols=32 Identities=28% Similarity=0.260 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Q 045165 40 EELILNRIALKETQIDSVRKEITQLYMFFFVF 71 (203)
Q Consensus 40 e~l~~~Ri~~ke~r~~s~~~Ei~qL~~ff~VF 71 (203)
...+.+++..-|.|+...-+|.+||.++..-|
T Consensus 58 k~~i~~~la~~e~rl~~G~~e~lQl~alva~~ 89 (89)
T PF08542_consen 58 KAEILKILAEIEYRLSDGASEILQLEALVAAF 89 (89)
T ss_dssp HHHHHHHHHHHHHHHHTTC-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhHHHHCCCCHHHHHHHHHhhC
Confidence 34677888999999999999999999886544
Done!