Query 018867
Match_columns 349
No_of_seqs 184 out of 458
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 04:42:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018867.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018867hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2753 Uncharacterized conser 100.0 1.2E-59 2.6E-64 437.7 26.5 320 6-343 1-325 (378)
2 KOG2908 26S proteasome regulat 100.0 1.1E-50 2.4E-55 379.5 23.9 305 32-348 14-342 (380)
3 KOG3250 COP9 signalosome, subu 99.4 8.3E-13 1.8E-17 117.6 5.8 112 223-343 26-141 (258)
4 PF01399 PCI: PCI domain; Int 98.7 4.4E-08 9.5E-13 78.4 6.6 85 257-342 1-90 (105)
5 smart00088 PINT motif in prote 96.8 0.0017 3.6E-08 50.5 4.4 50 292-342 3-54 (88)
6 smart00753 PAM PCI/PINT associ 96.8 0.0017 3.6E-08 50.5 4.4 50 292-342 3-54 (88)
7 KOG2581 26S proteasome regulat 96.5 0.68 1.5E-05 46.1 20.8 139 191-345 260-411 (493)
8 COG5187 RPN7 26S proteasome re 92.6 2.3 4.9E-05 40.9 12.0 188 133-329 149-346 (412)
9 PF14938 SNAP: Soluble NSF att 91.5 13 0.00027 35.1 17.0 139 136-280 114-259 (282)
10 KOG0687 26S proteasome regulat 90.9 17 0.00037 35.5 19.3 204 118-329 123-332 (393)
11 PF03399 SAC3_GANP: SAC3/GANP/ 89.5 2.7 5.8E-05 37.4 9.1 167 151-325 30-203 (204)
12 PF14938 SNAP: Soluble NSF att 81.5 48 0.001 31.2 18.0 217 37-265 54-276 (282)
13 COG5600 Transcription-associat 79.5 70 0.0015 31.9 20.8 200 114-328 145-365 (413)
14 KOG2688 Transcription-associat 72.4 28 0.0006 34.9 9.5 181 144-342 171-369 (394)
15 PF10075 PCI_Csn8: COP9 signal 71.2 15 0.00031 31.1 6.5 73 254-330 39-113 (143)
16 PF03979 Sigma70_r1_1: Sigma-7 69.0 5.3 0.00011 30.7 3.0 40 301-341 9-48 (82)
17 PF05369 MtmB: Monomethylamine 65.6 13 0.00028 37.3 5.5 69 17-107 382-450 (457)
18 PF10602 RPN7: 26S proteasome 64.0 1E+02 0.0022 27.1 14.8 95 133-232 70-167 (177)
19 PF13404 HTH_AsnC-type: AsnC-t 57.0 8.2 0.00018 25.8 1.8 21 312-332 15-35 (42)
20 PF04510 DUF577: Family of unk 56.5 1.4E+02 0.0031 26.4 10.0 52 48-108 39-90 (174)
21 KOG1463 26S proteasome regulat 53.0 2.4E+02 0.0053 28.0 22.0 277 38-332 48-363 (411)
22 KOG1861 Leucine permease trans 45.9 2.9E+02 0.0063 28.5 11.3 201 121-330 283-494 (540)
23 PF13424 TPR_12: Tetratricopep 45.9 1.1E+02 0.0024 22.0 7.3 68 137-205 6-73 (78)
24 PF09012 FeoC: FeoC like trans 45.8 10 0.00022 27.9 0.9 29 303-332 4-32 (69)
25 KOG1464 COP9 signalosome, subu 45.3 2.9E+02 0.0064 26.7 23.2 79 251-333 299-383 (440)
26 PF09339 HTH_IclR: IclR helix- 44.7 17 0.00036 25.0 1.9 32 300-331 4-35 (52)
27 PF08280 HTH_Mga: M protein tr 42.3 15 0.00032 26.3 1.3 48 294-345 3-51 (59)
28 smart00668 CTLH C-terminal to 42.2 1E+02 0.0023 21.0 5.8 49 258-306 4-52 (58)
29 PF04539 Sigma70_r3: Sigma-70 35.1 22 0.00047 26.4 1.3 28 312-339 18-46 (78)
30 TIGR03643 conserved hypothetic 35.0 36 0.00079 25.6 2.4 26 304-331 5-30 (72)
31 PF01603 B56: Protein phosphat 34.8 2.3E+02 0.0049 28.5 8.9 106 74-182 105-220 (409)
32 PF12840 HTH_20: Helix-turn-he 34.3 63 0.0014 22.8 3.6 32 312-343 22-55 (61)
33 TIGR02010 IscR iron-sulfur clu 32.9 87 0.0019 26.1 4.8 47 298-344 8-57 (135)
34 PF10985 DUF2805: Protein of u 32.8 41 0.00089 25.4 2.4 26 304-331 4-29 (73)
35 PF10668 Phage_terminase: Phag 32.7 27 0.00059 25.4 1.4 20 312-331 20-39 (60)
36 PF02082 Rrf2: Transcriptional 31.6 73 0.0016 24.1 3.8 44 301-344 11-57 (83)
37 PF08281 Sigma70_r4_2: Sigma-7 30.9 25 0.00054 24.1 1.0 20 313-332 25-44 (54)
38 PF11864 DUF3384: Domain of un 30.3 6E+02 0.013 25.8 11.3 18 37-54 376-393 (464)
39 PRK11920 rirA iron-responsive 30.0 76 0.0016 27.3 4.0 44 301-344 11-56 (153)
40 COG1654 BirA Biotin operon rep 29.5 84 0.0018 24.1 3.7 39 298-338 5-44 (79)
41 KOG1498 26S proteasome regulat 28.7 6.3E+02 0.014 25.6 15.7 61 98-160 91-155 (439)
42 KOG1840 Kinesin light chain [C 27.9 7.1E+02 0.015 25.9 15.8 57 148-205 421-477 (508)
43 TIGR02944 suf_reg_Xantho FeS a 27.9 88 0.0019 25.7 4.0 44 301-344 12-57 (130)
44 KOG2171 Karyopherin (importin) 27.2 9.9E+02 0.021 27.4 16.8 72 52-130 115-191 (1075)
45 cd00280 TRFH Telomeric Repeat 26.4 1E+02 0.0023 27.8 4.3 50 260-309 18-67 (200)
46 cd06445 ATase The DNA repair p 26.0 67 0.0015 24.3 2.6 18 312-329 15-32 (79)
47 PF03671 Ufm1: Ubiquitin fold 25.6 33 0.00072 25.9 0.8 22 4-25 19-40 (76)
48 PF03635 Vps35: Vacuolar prote 25.4 6.3E+02 0.014 27.8 10.8 160 73-238 451-650 (762)
49 PF04545 Sigma70_r4: Sigma-70, 25.2 40 0.00086 22.8 1.1 20 312-331 18-37 (50)
50 PF12397 U3snoRNP10: U3 small 24.7 3.7E+02 0.008 21.6 7.9 70 57-129 4-76 (121)
51 cd01766 Ufm1 Urm1-like ubiquit 24.1 53 0.0011 24.9 1.6 22 4-25 19-40 (82)
52 PRK10857 DNA-binding transcrip 23.3 1.6E+02 0.0034 25.7 4.9 47 298-344 8-57 (164)
53 PRK09191 two-component respons 23.2 1.8E+02 0.0038 26.2 5.5 21 312-332 102-122 (261)
54 TIGR00738 rrf2_super rrf2 fami 22.9 1.7E+02 0.0037 23.8 4.8 46 299-344 9-57 (132)
55 KOG1059 Vesicle coat complex A 22.0 6.4E+02 0.014 27.6 9.6 139 115-270 139-285 (877)
56 PF14764 SPG48: AP-5 complex s 21.5 7.3E+02 0.016 25.5 9.7 125 118-250 28-162 (459)
57 COG1017 Hmp Hemoglobin-like fl 21.1 5.2E+02 0.011 22.3 7.2 52 122-173 39-92 (150)
58 KOG2908 26S proteasome regulat 21.0 2E+02 0.0044 28.4 5.4 31 79-109 77-107 (380)
59 KOG0686 COP9 signalosome, subu 20.8 9.1E+02 0.02 24.7 10.6 83 257-340 306-393 (466)
60 PF08279 HTH_11: HTH domain; 20.6 90 0.002 21.3 2.3 30 301-331 2-32 (55)
No 1
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=100.00 E-value=1.2e-59 Score=437.68 Aligned_cols=320 Identities=38% Similarity=0.641 Sum_probs=292.1
Q ss_pred cCCCCchhHHHHHHHhHhhhhcCCCcccchhHHHHHHHHHHHHHcCCHHHHHHHHHHhhHHhhccCChhhHHHHHHHHHH
Q 018867 6 PTSEEDPALAVVRFTSELAWADAGPEAAEEQVNRLCLEAQESMVMGRWMDLASLMLTSADLMFSKVSDKDLECIFTVICN 85 (349)
Q Consensus 6 ~~~~e~~~~~~~~~~~~~~~~~~~~~~a~~e~~~~~~~~e~l~~~klwhqLt~~ll~~~~~~f~~~~~ke~E~~~n~li~ 85 (349)
+||+|+|+.+.+++..+++|.++|+..++|+.+ .+..+ |.-++.+..+++.++.+++. |+|++|+++|+|++
T Consensus 1 ~~~~e~P~f~dis~~~Ql~elr~yl~~~eaeis---~e~~~----kgl~~~l~~ii~~c~v~~k~-~ekdle~vlnsi~s 72 (378)
T KOG2753|consen 1 PTSEEVPVFADISFEEQLAELRAYLKKLEAEIS---EEASE----KGLEEDLLMIIEACDVLAKI-PEKDLECVLNSIVS 72 (378)
T ss_pred CCCccCceEEEecHHHHHHHHHHHHhhcCcccc---hhhhc----cCHHHHHHHHHHHhHHhhcC-CcchHHHHHHHHHH
Confidence 589999999999999999999999999999998 22222 43344444555556666654 89999999999999
Q ss_pred HhcCCCChhHHHHHHHHHHHHhhcCCCCC-hhhHHHHHHHHHhhccCC-chhHHHHHHHHHHHHcCCCcchhhhhHHhHH
Q 018867 86 LVTKPESLDEVHEMTKLISGKIIQQPNDK-PAMRLKILFNLYNLLENP-YSRFFVYMKALNLAVNGKVTEHIIPSFKKID 163 (349)
Q Consensus 86 l~~~~~~~~~~~~lv~~l~~~v~~~~~~~-~~~rl~~L~~Lfn~l~~~-~~r~~v~~~il~la~~~~~~~~l~~~l~~~~ 163 (349)
++...+ +++..++++.+|++++.+|.+. |.+|+++|++|||.++.+ +.|+.||++++++|.+++.+..+.+.++.++
T Consensus 73 Li~~~~-~e~~e~~v~a~~ekva~q~n~~~~~l~L~vLsnLfn~~d~~~~aR~~Vy~~lv~la~~~~~~~~i~~~lk~~~ 151 (378)
T KOG2753|consen 73 LIKNAP-PEKVEEMVKAICEKVAKQPNDKTASLRLQVLSNLFNGVDKPTPARYQVYMSLVTLAASCKLIEYIVPNLKQLD 151 (378)
T ss_pred HHHhCC-HHHhHHHHHHHHHHHhcCccCCCcccHHHHHHHHHhccCCCchHHHHHHHHHHHHHhhcceeeeecccHHHHH
Confidence 999885 9999999999999999998765 889999999999999975 5999999999999999999999999999999
Q ss_pred HHHhhcCCCHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHhcccCCCCCCChhHHHHHHHHHHHHHhcCCCeeeec-CC
Q 018867 164 SFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQCD-LL 242 (349)
Q Consensus 164 ~~L~~w~~~~~~~~~~y~~~a~~l~~~~~~~~~~y~~~l~yL~~~~~~~~~~~~e~~~~A~~li~~aL~~p~iy~f~-LL 242 (349)
+|+++|+++.+++|.+|++++++++.. +.-+++-+++..||+||+.+++ ++|++.|.+|++.|+.+|++|.|| |+
T Consensus 152 ~~lkew~~~vedqrel~r~v~~al~~~-k~~~~s~kvmt~lLgtyt~dna---s~AredA~rcV~~av~dP~~F~fD~Ll 227 (378)
T KOG2753|consen 152 DWLKEWNISVEDQRELLRAVHKALKDN-KSVDESSKVMTELLGTYTEDNA---SEAREDAMRCVVEAVKDPKIFLFDHLL 227 (378)
T ss_pred HHHHhCCCCHHHHHHHHHHHHHHHHhc-chhhhHHHHHHHHHHHhcccch---hHHHHHHHHHHHHHHcCCceeccchhc
Confidence 999999999999999999999999997 4478999999999999999885 689999999999999999999999 99
Q ss_pred CChhhhhcccCCCchhHHHHHHHHhcCChhhHHHHHhhChhhhhhcCCChHHHHHHHHHHHHhhhhhcCCCCcChHHHHh
Q 018867 243 DMPAIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQAGNSALLKSYGLVHEDCIAKMRLMSLVDLGSNESGQIPYGLIKD 322 (349)
Q Consensus 243 ~~p~v~~L~~~~~~~~l~~LL~if~~G~l~~y~~~~~~~~~~~~~~~l~~~~l~~KirLLtL~~La~~~~r~isy~~Ia~ 322 (349)
.+|+|++|+++ .+|+||.||.+|.+++|.+|.+.|++++.++|++++++.+||||||||+||+. +++|||.+|++
T Consensus 228 ~L~pV~qLE~d----~i~qLL~IF~s~~L~aYveF~~~N~~Fvqs~gl~~E~~~~KMRLLTlm~LA~e-s~eisy~~l~k 302 (378)
T KOG2753|consen 228 TLPPVKQLEGD----LIHQLLKIFVSGKLDAYVEFVAANSGFVQSQGLVHEQNMAKMRLLTLMSLAEE-SNEISYDTLAK 302 (378)
T ss_pred cCchHHHhccc----hHHHHHHHHHhcchHHHHHHHHhChHHHHHhcccHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHH
Confidence 99999999987 49999999999999999999999999999999999999999999999999984 89999999999
Q ss_pred hcCCCCchH--HHHHHhhcccee
Q 018867 323 TLQVYFLTF--LLLDLWYGLFVV 343 (349)
Q Consensus 323 ~l~i~~~ev--e~id~i~~~~~~ 343 (349)
.|+|.+||| |+||+|++++|-
T Consensus 303 ~LqI~edeVE~fVIdaI~aklV~ 325 (378)
T KOG2753|consen 303 ELQINEDEVELFVIDAIRAKLVE 325 (378)
T ss_pred HhccCHHHHHHHHHHHHHHHHHH
Confidence 999999987 689999999873
No 2
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-50 Score=379.53 Aligned_cols=305 Identities=14% Similarity=0.167 Sum_probs=263.5
Q ss_pred ccchhHHHHHHHHHHHHHcCCHHHHHHHHHHh-hHHhhccCChhhHHHHHHHHH-HHhcCCCChhHHHHHHHHHHHHhhc
Q 018867 32 AAEEQVNRLCLEAQESMVMGRWMDLASLMLTS-ADLMFSKVSDKDLECIFTVIC-NLVTKPESLDEVHEMTKLISGKIIQ 109 (349)
Q Consensus 32 ~a~~e~~~~~~~~e~l~~~klwhqLt~~ll~~-~~~~f~~~~~ke~E~~~n~li-~l~~~~~~~~~~~~lv~~l~~~v~~ 109 (349)
.|.|++...|..+++||++|+|||||.+++.+ .+++|.. ...+..+|..|+ .+-.++ || +++|+ ++.++.+
T Consensus 14 ~a~~~l~~ew~~leeLy~eKLW~QLt~~l~~fvd~~~f~~--~~~~l~lY~NFvsefe~kI-Np---lslve-i~l~~~~ 86 (380)
T KOG2908|consen 14 SANPSLAAEWDRLEELYEEKLWHQLTLALVDFVDDPPFQA--GDLLLQLYLNFVSEFETKI-NP---LSLVE-ILLVVSE 86 (380)
T ss_pred hcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcccccc--chHHHHHHHHHHHHHhhcc-Ch---HHHHH-HHHHHHH
Confidence 35688999999999999999999999999998 7777875 346678888777 555578 88 78888 6666776
Q ss_pred CCCCChhhHHHHHHHHHhhccC-CchhHHHHH--HHHHHHHcCCCcchhhhhHHhHHHHHhhc-CCCHHHHHHHHHHHHH
Q 018867 110 QPNDKPAMRLKILFNLYNLLEN-PYSRFFVYM--KALNLAVNGKVTEHIIPSFKKIDSFLKEW-NIDIKDKRALFLGIAN 185 (349)
Q Consensus 110 ~~~~~~~~rl~~L~~Lfn~l~~-~~~r~~v~~--~il~la~~~~~~~~l~~~l~~~~~~L~~w-~~~~~~~~~~y~~~a~ 185 (349)
+. .+....+++|..+-+.+.. +.+...+|+ .+..+--..|++..++..|++.++.+++. ++++.+|.+||++.+.
T Consensus 87 ~~-~D~~~al~~Le~i~~~~~~~~e~~av~~~~t~~~r~~L~i~DLk~~kk~ldd~~~~ld~~~~v~~~Vh~~fY~lssq 165 (380)
T KOG2908|consen 87 QI-SDKDEALEFLEKIIEKLKEYKEPDAVIYILTEIARLKLEINDLKEIKKLLDDLKSMLDSLDGVTSNVHSSFYSLSSQ 165 (380)
T ss_pred Hh-ccHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhcccCCChhhhhhHHHHHHH
Confidence 64 4688899999999998875 333444444 23333337889999999999999999998 7777799999999999
Q ss_pred HHHHhccChHHHHHHHHHHhcccCCCCCCChhHHHHHHHHHHHHHhcCCCeeeec-CCCChhhhhcccCCCchhHHHHHH
Q 018867 186 VLKESRSSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQCD-LLDMPAIGQLENDAKYASVYQLLK 264 (349)
Q Consensus 186 ~l~~~~~~~~~~y~~~l~yL~~~~~~~~~~~~e~~~~A~~li~~aL~~p~iy~f~-LL~~p~v~~L~~~~~~~~l~~LL~ 264 (349)
||+. .|+++.||+.+|+||+|.+.++.+ .+|.++.|+.++.+||+|+++|||| ||.||++.+|+|| ++.||+++|.
T Consensus 166 Yyk~-~~d~a~yYr~~L~YL~~~d~~~l~-~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT-~~eWL~dll~ 242 (380)
T KOG2908|consen 166 YYKK-IGDFASYYRHALLYLGCSDIDDLS-ESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGT-NREWLKDLLI 242 (380)
T ss_pred HHHH-HHhHHHHHHHHHHHhccccccccC-HHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCC-cHHHHHHHHH
Confidence 9999 599999999999999999988866 5889999999999999999999999 9999999999997 7999999999
Q ss_pred HHhcCChhhHHHHHhhChhhhhhcCCChHHHHHHHHHHHHhhhh-hcC--CCCcChHHHHhhcCCCCchHHH--------
Q 018867 265 IFLTQRLDGYLEFQAGNSALLKSYGLVHEDCIAKMRLMSLVDLG-SNE--SGQIPYGLIKDTLQVYFLTFLL-------- 333 (349)
Q Consensus 265 if~~G~l~~y~~~~~~~~~~~~~~~l~~~~l~~KirLLtL~~La-~~~--~r~isy~~Ia~~l~i~~~eve~-------- 333 (349)
+|+.||+..|++.+..+.+ ++.++-+++.+++||||||||+++ ++| .|.+||++||++++||.+|||+
T Consensus 243 Afn~Gdl~~f~~l~~~~~~-~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~eVE~LVMKAlsl 321 (380)
T KOG2908|consen 243 AFNSGDLKRFESLKGVWGK-QPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIPNKEVELLVMKALSL 321 (380)
T ss_pred HhccCCHHHHHHHHHHhcc-CchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence 9999999999999887765 555666799999999999999999 674 9999999999999999999986
Q ss_pred ------HHHhhccceeEEEEe
Q 018867 334 ------LDLWYGLFVVNVLQV 348 (349)
Q Consensus 334 ------id~i~~~~~~~~~~~ 348 (349)
||++-+.+-++|||-
T Consensus 322 gLikG~Idqv~~~v~~swvqP 342 (380)
T KOG2908|consen 322 GLIKGSIDQVEGVVYMSWVQP 342 (380)
T ss_pred cceeeeecccccEEEEecccc
Confidence 888888899999984
No 3
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.36 E-value=8.3e-13 Score=117.60 Aligned_cols=112 Identities=20% Similarity=0.268 Sum_probs=95.7
Q ss_pred HHHHHHHHhcCCCeeeec-CCCChhhhhcccCCCchhHHHHHHHHhcCChhhHHHHHhhChhhhhhcCCChHHHHHHHHH
Q 018867 223 AVRTIIEFVKSPDMFQCD-LLDMPAIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQAGNSALLKSYGLVHEDCIAKMRL 301 (349)
Q Consensus 223 A~~li~~aL~~p~iy~f~-LL~~p~v~~L~~~~~~~~l~~LL~if~~G~l~~y~~~~~~~~~~~~~~~l~~~~l~~KirL 301 (349)
-..+|..|+.+|++|.|+ |+.+|+|.+|.++ .++..++||.+|++|++.||..-. .-++++ ......|++-
T Consensus 26 l~~lIsqale~P~vf~F~ELl~l~nv~qlae~-~dsa~lrlL~lFa~Gt~~Dy~aea----~rlp~L---s~~q~~kLk~ 97 (258)
T KOG3250|consen 26 LEELISQALEAPGVFVFGELLILPNVVQLAEP-IDSAYLRLLELFAYGTYRDYSAEA----LRLPKL---SLAQLNKLKH 97 (258)
T ss_pred HHHHHHHHhcCCCeeeHHHHHhhhhHHHHccc-ccHHHHHHHHHHhcCchhhhhhhh----hcCCCC---CHHHHHhhhc
Confidence 457899999999999998 9999999999876 689999999999999999996532 234444 4568899999
Q ss_pred HHHhhhhhcCCCCcChHHHHhhcCCCCc---hHHHHHHhhcccee
Q 018867 302 MSLVDLGSNESGQIPYGLIKDTLQVYFL---TFLLLDLWYGLFVV 343 (349)
Q Consensus 302 LtL~~La~~~~r~isy~~Ia~~l~i~~~---eve~id~i~~~~~~ 343 (349)
++.+++|+. .+.|||..+.+.+.+..- |..+|+|||++++.
T Consensus 98 ltV~slas~-~k~lpy~~Ll~~l~~~nvrelEd~iieamya~Ilr 141 (258)
T KOG3250|consen 98 LTVVSLASF-EKCLPYLVLLRLLPSRNVRELEDLIIEAMYADILR 141 (258)
T ss_pred ceehhhhhh-chhhhHHHHHhhccCCchhHHHHHHHHHHHHHHHH
Confidence 999999987 899999999999988753 56789999998764
No 4
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=98.68 E-value=4.4e-08 Score=78.36 Aligned_cols=85 Identities=25% Similarity=0.275 Sum_probs=72.2
Q ss_pred hhHHHHHHHHhcCChhhHHHHHhhC-hhhhhhcCCC--hHHHHHHHHHHHHhhhhhcCCCCcChHHHHhhcCCCCchH--
Q 018867 257 ASVYQLLKIFLTQRLDGYLEFQAGN-SALLKSYGLV--HEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQVYFLTF-- 331 (349)
Q Consensus 257 ~~l~~LL~if~~G~l~~y~~~~~~~-~~~~~~~~l~--~~~l~~KirLLtL~~La~~~~r~isy~~Ia~~l~i~~~ev-- 331 (349)
+|+.+|+++|.+|++.+|.++.+.+ +.++.+.++. .+.+.+|+|..+|..++.. -+.+++++||+.++++.+++
T Consensus 1 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~-y~~i~~~~ia~~l~~~~~~vE~ 79 (105)
T PF01399_consen 1 PPYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKP-YSSISISEIAKALQLSEEEVES 79 (105)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC--SEEEHHHHHHHHTCCHHHHHH
T ss_pred CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHH-hcccchHHHHHHhccchHHHHH
Confidence 4899999999999999999999988 6666655543 4899999999999999974 78999999999999999986
Q ss_pred HHHHHhhccce
Q 018867 332 LLLDLWYGLFV 342 (349)
Q Consensus 332 e~id~i~~~~~ 342 (349)
+++++|+.|.+
T Consensus 80 ~l~~~I~~~~i 90 (105)
T PF01399_consen 80 ILIDLISNGLI 90 (105)
T ss_dssp HHHHHHHTTSS
T ss_pred HHHHHHHCCCE
Confidence 47888888875
No 5
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=96.82 E-value=0.0017 Score=50.48 Aligned_cols=50 Identities=18% Similarity=0.125 Sum_probs=43.8
Q ss_pred hHHHHHHHHHHHHhhhhhcCCCCcChHHHHhhcCCCCchH--HHHHHhhccce
Q 018867 292 HEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQVYFLTF--LLLDLWYGLFV 342 (349)
Q Consensus 292 ~~~l~~KirLLtL~~La~~~~r~isy~~Ia~~l~i~~~ev--e~id~i~~~~~ 342 (349)
.+.+.+|+|..++.++++. .+.|+|++|++.++++.+++ +++++|+.|.+
T Consensus 3 ~~~l~~~~~~~~l~~l~~~-y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l 54 (88)
T smart00088 3 VERLQRKIRLTNLLQLSEP-YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEI 54 (88)
T ss_pred HHHHHHHHHHHHHHHHhHH-hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCe
Confidence 4679999999999999975 78999999999999999875 57888888865
No 6
>smart00753 PAM PCI/PINT associated module.
Probab=96.82 E-value=0.0017 Score=50.48 Aligned_cols=50 Identities=18% Similarity=0.125 Sum_probs=43.8
Q ss_pred hHHHHHHHHHHHHhhhhhcCCCCcChHHHHhhcCCCCchH--HHHHHhhccce
Q 018867 292 HEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQVYFLTF--LLLDLWYGLFV 342 (349)
Q Consensus 292 ~~~l~~KirLLtL~~La~~~~r~isy~~Ia~~l~i~~~ev--e~id~i~~~~~ 342 (349)
.+.+.+|+|..++.++++. .+.|+|++|++.++++.+++ +++++|+.|.+
T Consensus 3 ~~~l~~~~~~~~l~~l~~~-y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l 54 (88)
T smart00753 3 VERLQRKIRLTNLLQLSEP-YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEI 54 (88)
T ss_pred HHHHHHHHHHHHHHHHhHH-hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCe
Confidence 4679999999999999975 78999999999999999875 57888888865
No 7
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=96.54 E-value=0.68 Score=46.09 Aligned_cols=139 Identities=12% Similarity=0.117 Sum_probs=89.5
Q ss_pred ccChHHHHHHHHHHhcccCCCCCCChhHHHHHHHH--HHHHHhcCCCeeeecCCCChhhh-hcccCCCchhHHHHHHHHh
Q 018867 191 RSSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVR--TIIEFVKSPDMFQCDLLDMPAIG-QLENDAKYASVYQLLKIFL 267 (349)
Q Consensus 191 ~~~~~~~y~~~l~yL~~~~~~~~~~~~e~~~~A~~--li~~aL~~p~iy~f~LL~~p~v~-~L~~~~~~~~l~~LL~if~ 267 (349)
+.+|..+-++++..+.--+...+. . .++...+ +++.-|.||-- .-..+..|+++ +| .+.|+|=++.-
T Consensus 260 qldYssA~~~~~qa~rkapq~~al--G-f~q~v~k~~ivv~ll~geiP-ers~F~Qp~~~ksL------~~Yf~Lt~AVr 329 (493)
T KOG2581|consen 260 QLDYSSALEYFLQALRKAPQHAAL--G-FRQQVNKLMIVVELLLGEIP-ERSVFRQPGMRKSL------RPYFKLTQAVR 329 (493)
T ss_pred hcchhHHHHHHHHHHHhCcchhhh--h-HHHHHHHHHHHHHHHcCCCc-chhhhcCccHHHHH------HHHHHHHHHHH
Confidence 367788888877777765543221 1 2222323 34455555521 11234566663 55 37999999999
Q ss_pred cCChhhHHHHHhhChhhhhhcC-------CChHHHHHHHHHHHHhhhhhcCCCCcChHHHHhhcCCCCch-HHH--HHHh
Q 018867 268 TQRLDGYLEFQAGNSALLKSYG-------LVHEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQVYFLT-FLL--LDLW 337 (349)
Q Consensus 268 ~G~l~~y~~~~~~~~~~~~~~~-------l~~~~l~~KirLLtL~~La~~~~r~isy~~Ia~~l~i~~~e-ve~--id~i 337 (349)
.||++.|..-..++...+..-| |.+...+.=||.++ ++ =..||+.+||+.|++..+| +|. =.||
T Consensus 330 ~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~IS---ls---YSRISl~DIA~kL~l~Seed~EyiVakAI 403 (493)
T KOG2581|consen 330 LGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKIS---LS---YSRISLQDIAKKLGLNSEEDAEYIVAKAI 403 (493)
T ss_pred HhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhhee---ee---eeeccHHHHHHHhcCCCchhHHHHHHHHH
Confidence 9999999998888766444422 24555555566543 34 2349999999999998876 664 5789
Q ss_pred hccceeEE
Q 018867 338 YGLFVVNV 345 (349)
Q Consensus 338 ~~~~~~~~ 345 (349)
+-|++-.-
T Consensus 404 RDGvIea~ 411 (493)
T KOG2581|consen 404 RDGVIEAK 411 (493)
T ss_pred Hhccceee
Confidence 99987653
No 8
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=92.60 E-value=2.3 Score=40.85 Aligned_cols=188 Identities=15% Similarity=0.163 Sum_probs=118.5
Q ss_pred chhHHHHHHHHHHHHcCCCcchhhhhHHhHHHHHhhcCCCHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHhcccCCCC
Q 018867 133 YSRFFVYMKALNLAVNGKVTEHIIPSFKKIDSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGED 212 (349)
Q Consensus 133 ~~r~~v~~~il~la~~~~~~~~l~~~l~~~~~~L~~w~~~~~~~~~~y~~~a~~l~~~~~~~~~~y~~~l~yL~~~~~~~ 212 (349)
..+..||+.++.++--.|+...+...++.++..++ .+.+=++|.=|.+-.-.++-+.+++.++-..+..-|+||+...
T Consensus 149 g~KiDv~l~kiRlg~~y~d~~vV~e~lE~~~~~iE--kGgDWeRrNRyK~Y~Gi~~m~~RnFkeAa~Ll~d~l~tF~S~E 226 (412)
T COG5187 149 GLKIDVFLCKIRLGLIYGDRKVVEESLEVADDIIE--KGGDWERRNRYKVYKGIFKMMRRNFKEAAILLSDILPTFESSE 226 (412)
T ss_pred ccchhhHHHHHHHHHhhccHHHHHHHHHHHHHHHH--hCCCHHhhhhHHHHHHHHHHHHHhhHHHHHHHHHHhccccccc
Confidence 45788999999999888998899999998888887 4555566666677666666655778899999999999998776
Q ss_pred CCChhHHHHHHHHHHHHHhcCCCeeee-c-CCCChhhhhccc-CCCchhHHHHHHHHhcCChh-hHHHHH----hhC-hh
Q 018867 213 AHTMDEAKEEAVRTIIEFVKSPDMFQC-D-LLDMPAIGQLEN-DAKYASVYQLLKIFLTQRLD-GYLEFQ----AGN-SA 283 (349)
Q Consensus 213 ~~~~~e~~~~A~~li~~aL~~p~iy~f-~-LL~~p~v~~L~~-~~~~~~l~~LL~if~~G~l~-~y~~~~----~~~-~~ 283 (349)
..+-+.+...|.-+ .+++-+.. +. . +++.|-|-.+=+ ++.-+.+.+|...+-.-|+. .|.... +.- +.
T Consensus 227 l~sY~~~vrYa~~~--Gl~~leR~-diktki~dspevl~vi~~~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d 303 (412)
T COG5187 227 LISYSRAVRYAIFC--GLLRLERR-DIKTKILDSPEVLDVIGSSEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDD 303 (412)
T ss_pred cccHHHHHHHHHHh--hhheeehh-hhhhhhcCCHHHHHhccchhhhhhHHHHHHHHHHhccchhhHHHHHHHHhhccch
Confidence 54333332222222 22333222 33 3 777886644333 33344566666655555555 332222 111 11
Q ss_pred -hhhhcCCChHHHHHHHHHHHHhhhhhcCCCCcChHHHHhhcCCCCc
Q 018867 284 -LLKSYGLVHEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQVYFL 329 (349)
Q Consensus 284 -~~~~~~l~~~~l~~KirLLtL~~La~~~~r~isy~~Ia~~l~i~~~ 329 (349)
++ |-..+...+-||.=.-+.+-.. -|.++.+-.|++.+++.+
T Consensus 304 ~fl---~rh~d~fvREMRrrvYaQlLES-Yr~lsl~sMA~tFgVSV~ 346 (412)
T COG5187 304 VFL---GRHVDLFVREMRRRVYAQLLES-YRLLSLESMAQTFGVSVE 346 (412)
T ss_pred HHH---HHHHHHHHHHHHHHHHHHHHHH-HHHhhHHHHHHHhCccHH
Confidence 22 2235666677877777777732 567888888888888754
No 9
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=91.46 E-value=13 Score=35.13 Aligned_cols=139 Identities=12% Similarity=0.126 Sum_probs=82.7
Q ss_pred HHHHHHHHHHHHcC-CCcchhhhhHHhHHHHHhhcCCCHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHhcccCCCCCC
Q 018867 136 FFVYMKALNLAVNG-KVTEHIIPSFKKIDSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGEDAH 214 (349)
Q Consensus 136 ~~v~~~il~la~~~-~~~~~l~~~l~~~~~~L~~w~~~~~~~~~~y~~~a~~l~~~~~~~~~~y~~~l~yL~~~~~~~~~ 214 (349)
..++..+.++.... ++.+.......+.-.+...-+ .+.....++..++..+-.. +++.++....-+....+...+..
T Consensus 114 A~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l-~~y~~A~~~~e~~~~~~l~~~l~ 191 (282)
T PF14938_consen 114 AKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARL-GRYEEAIEIYEEVAKKCLENNLL 191 (282)
T ss_dssp HHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHT-T-HHHHHHHHHHHHHTCCCHCTT
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHhhccccc
Confidence 44455555555555 566666666666655665445 6677788888888888875 77777777766655444332222
Q ss_pred ChhHHHHHHHHHHHHHhcCCCeee----ec-CC-CChhhhhcccCCCchhHHHHHHHHhcCChhhHHHHHhh
Q 018867 215 TMDEAKEEAVRTIIEFVKSPDMFQ----CD-LL-DMPAIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQAG 280 (349)
Q Consensus 215 ~~~e~~~~A~~li~~aL~~p~iy~----f~-LL-~~p~v~~L~~~~~~~~l~~LL~if~~G~l~~y~~~~~~ 280 (349)
.-.+++.....++--|..++.-. |+ .. ..|.. .+|.++.-+.+|+.+|..||.+.|..-...
T Consensus 192 -~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F---~~s~E~~~~~~l~~A~~~~D~e~f~~av~~ 259 (282)
T PF14938_consen 192 -KYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSF---ASSREYKFLEDLLEAYEEGDVEAFTEAVAE 259 (282)
T ss_dssp -GHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTS---TTSHHHHHHHHHHHHHHTT-CCCHHHHCHH
T ss_pred -chhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCC---CCcHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 23466666777766665544322 22 11 12322 335567889999999999999999765433
No 10
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=90.86 E-value=17 Score=35.53 Aligned_cols=204 Identities=15% Similarity=0.119 Sum_probs=133.1
Q ss_pred HHHHHHHHHhhccCCchhHHHHHHHHHHHHcCCCcchhhhhHHhHHHHHhhcCCCHHHHHHHHHHHHHHHHHhccChHHH
Q 018867 118 RLKILFNLYNLLENPYSRFFVYMKALNLAVNGKVTEHIIPSFKKIDSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDS 197 (349)
Q Consensus 118 rl~~L~~Lfn~l~~~~~r~~v~~~il~la~~~~~~~~l~~~l~~~~~~L~~w~~~~~~~~~~y~~~a~~l~~~~~~~~~~ 197 (349)
.++.+...|..--.-..|..|+..++.++--.++.+.+...++.+++.++ .+.+=++|.=|++---.|.-+-++++++
T Consensus 123 a~~~~~~t~~ktvs~g~kiDVvf~~iRlglfy~D~~lV~~~iekak~liE--~GgDWeRrNRlKvY~Gly~msvR~Fk~A 200 (393)
T KOG0687|consen 123 ALEALRKTYEKTVSLGHKIDVVFYKIRLGLFYLDHDLVTESIEKAKSLIE--EGGDWERRNRLKVYQGLYCMSVRNFKEA 200 (393)
T ss_pred HHHHHHHHHHHHhhcccchhhHHHHHHHHHhhccHHHHHHHHHHHHHHHH--hCCChhhhhhHHHHHHHHHHHHHhHHHH
Confidence 34444444443222246888888899999888999999999999998887 3444445544555544454444678899
Q ss_pred HHHHHHHhcccCCCCCCChhHHHHHHHHHHHHHhcCCCeeeec-CCCChhhhh-cccCCCchhHHHHHHHHhcCChhhHH
Q 018867 198 FKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQCD-LLDMPAIGQ-LENDAKYASVYQLLKIFLTQRLDGYL 275 (349)
Q Consensus 198 y~~~l~yL~~~~~~~~~~~~e~~~~A~~li~~aL~~p~iy~f~-LL~~p~v~~-L~~~~~~~~l~~LL~if~~G~l~~y~ 275 (349)
-...+.-++||+.-...+-+....-++-++.-+|--|++ =. ++..|-|.. |.+ -+.+.+++..+-.-++++|-
T Consensus 201 a~Lfld~vsTFtS~El~~Y~~~v~Ytv~~g~i~leR~dl--ktKVi~~~Evl~vl~~---l~~~~q~l~SLY~C~Y~~Ff 275 (393)
T KOG0687|consen 201 ADLFLDSVSTFTSYELMSYETFVRYTVITGLIALERVDL--KTKVIKCPEVLEVLHK---LPSVSQLLNSLYECDYSDFF 275 (393)
T ss_pred HHHHHHHcccccceecccHHHHHHHHHHHhhheeccchH--HhhhcCcHHHHHHhhc---CchHHHHHHHHHhccHHHHH
Confidence 999999999998766543344444444444444433322 14 777787754 432 45788888888887887774
Q ss_pred HHH-hhChhhhhh---cCCChHHHHHHHHHHHHhhhhhcCCCCcChHHHHhhcCCCCc
Q 018867 276 EFQ-AGNSALLKS---YGLVHEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQVYFL 329 (349)
Q Consensus 276 ~~~-~~~~~~~~~---~~l~~~~l~~KirLLtL~~La~~~~r~isy~~Ia~~l~i~~~ 329 (349)
.-. .-....++. ++-.-....+-||.-+-..+-.. =|.++.+-.|++.||+.+
T Consensus 276 ~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLES-Yrsl~l~~MA~aFgVSVe 332 (393)
T KOG0687|consen 276 NDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLES-YRSLTLESMAKAFGVSVE 332 (393)
T ss_pred HHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHhCchHH
Confidence 332 111111111 12225677889999999998843 679999999999999964
No 11
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=89.45 E-value=2.7 Score=37.45 Aligned_cols=167 Identities=14% Similarity=0.160 Sum_probs=91.3
Q ss_pred CcchhhhhHHhHHHHHhhcCCCHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHhcccCCC--CCCChhHHHHHHHHHHH
Q 018867 151 VTEHIIPSFKKIDSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGE--DAHTMDEAKEEAVRTII 228 (349)
Q Consensus 151 ~~~~l~~~l~~~~~~L~~w~~~~~~~~~~y~~~a~~l~~~~~~~~~~y~~~l~yL~~~~~~--~~~~~~e~~~~A~~li~ 228 (349)
..+.+...+..+..=+.-.++..+....+|..++..+-.. ++..++-+.+.....+|+.- ..+...+..=.+..+..
T Consensus 30 ~y~fi~drlRsiRqDl~vQ~~~~~~~i~v~E~~ar~~i~~-~d~~qf~~c~~~L~~lY~~~~~~~~~~~~~ef~~y~lL~ 108 (204)
T PF03399_consen 30 DYNFIWDRLRSIRQDLTVQNIENDFAIKVYERIARFAIES-GDLEQFNQCLSQLKELYDDLRDLPPSPNEAEFIAYYLLY 108 (204)
T ss_dssp HHHHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHT---TTHHHHHHHHHHH
T ss_pred hhHHHHHHhHHHHhhHHHHhcCCHHHHHHHHHHHHHHhhc-CCHHHHHHHHHHHHHHHHhhccCCCCCCHHHHHHHHHHH
Confidence 3445555555555545555777777888888888777664 44444444444434444331 11111333334555554
Q ss_pred HHhcCCCeeee--cCCCChhhhhcccCCCchhHHHHHHHHhcCChhhHHHHH--hhChhhhhhcCCChHHHHHHHHHHHH
Q 018867 229 EFVKSPDMFQC--DLLDMPAIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQ--AGNSALLKSYGLVHEDCIAKMRLMSL 304 (349)
Q Consensus 229 ~aL~~p~iy~f--~LL~~p~v~~L~~~~~~~~l~~LL~if~~G~l~~y~~~~--~~~~~~~~~~~l~~~~l~~KirLLtL 304 (349)
....++ .=.| .+..+|. .+.+++.-.-..++..++..|++..|-... ++.|.....+ -+....+||.-+|
T Consensus 109 ~l~~~~-~~~~~~~l~~l~~--~~~~~~~i~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~l---~~~~~~~iR~~al 182 (204)
T PF03399_consen 109 LLCQNN-IPDFHMELELLPS--EILSSPYIQFALELCRALMEGNYVRFFRLYRSKSAPYLFACL---MERFFNRIRLRAL 182 (204)
T ss_dssp TT-T----THHHHHHTTS-H--HHHTSHHHHHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHHH---HGGGHHHHHHHHH
T ss_pred HHHccc-chHHHHHHHHCch--hhhcCHHHHHHHHHHHHHHcCCHHHHHHHHhccCCChHHHHH---HHHHHHHHHHHHH
Confidence 333442 2233 2444442 233443345667888999999999998877 4445443332 3347789999999
Q ss_pred hhhhhcCCCC-cChHHHHhhcC
Q 018867 305 VDLGSNESGQ-IPYGLIKDTLQ 325 (349)
Q Consensus 305 ~~La~~~~r~-isy~~Ia~~l~ 325 (349)
-.++.. -+. +|-+.+++-|+
T Consensus 183 ~~i~~a-y~~~i~l~~l~~~L~ 203 (204)
T PF03399_consen 183 QSISKA-YRSSIPLSFLAELLG 203 (204)
T ss_dssp HHHHHH-S-T-EEHHHHHHHTT
T ss_pred HHHHHH-cCCCCCHHHHHHHcC
Confidence 999954 444 99999888664
No 12
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=81.49 E-value=48 Score=31.19 Aligned_cols=217 Identities=14% Similarity=0.048 Sum_probs=119.8
Q ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHhhHHhhccCChhhHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHhhcCCCCChh
Q 018867 37 VNRLCLEAQESMVMGRWMDLASLMLTSADLMFSKVSDKDLECIFTVICNLVTKPESLDEVHEMTKLISGKIIQQPNDKPA 116 (349)
Q Consensus 37 ~~~~~~~~e~l~~~klwhqLt~~ll~~~~~~f~~~~~ke~E~~~n~li~l~~~~~~~~~~~~lv~~l~~~v~~~~~~~~~ 116 (349)
...-+.++-+++.+.....-..+.+..+..++.+....+....|.--+.+....+++..+..+...+++..... ..++.
T Consensus 54 A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye~~-~~d~e 132 (282)
T PF14938_consen 54 AAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKKGDPDEAIECYEKAIEIYREAGRFSQAAKCLKELAEIYEEQ-LGDYE 132 (282)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHCCT-T--HH
T ss_pred hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHH-cCCHH
Confidence 33667777777765544444444445566666665545667777877777777777877777777777654332 13455
Q ss_pred hHHHHHH---HHHhhccCCchhHHHHHHHHHHHHcCCCcchhhhhHHhHHHHHhhcCCC-HHHHHHHHHHHHHHHHHhcc
Q 018867 117 MRLKILF---NLYNLLENPYSRFFVYMKALNLAVNGKVTEHIIPSFKKIDSFLKEWNID-IKDKRALFLGIANVLKESRS 192 (349)
Q Consensus 117 ~rl~~L~---~Lfn~l~~~~~r~~v~~~il~la~~~~~~~~l~~~l~~~~~~L~~w~~~-~~~~~~~y~~~a~~l~~~~~ 192 (349)
..+.... .+|..-+.+.....++..+..+..+.+.++.....++++-...-+-++. ...++.++.++.=++. .|
T Consensus 133 ~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~--~~ 210 (282)
T PF14938_consen 133 KAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLA--MG 210 (282)
T ss_dssp HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHH--TT
T ss_pred HHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHH--cC
Confidence 5555544 3444433334567888888899889998887777777654432222332 3445555555554444 37
Q ss_pred ChHHHHHHHHHHhcccCCCCCCChhHHHHHHHHHHHHHhcCCCeeee-c-CCCChhhhhcccCCCchhHHHHHHH
Q 018867 193 SSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQC-D-LLDMPAIGQLENDAKYASVYQLLKI 265 (349)
Q Consensus 193 ~~~~~y~~~l~yL~~~~~~~~~~~~e~~~~A~~li~~aL~~p~iy~f-~-LL~~p~v~~L~~~~~~~~l~~LL~i 265 (349)
|...+-+..-+|.+-.+. -.. ..|. . ...-++.|....+.=.| + +-..+.+..| .+|...+|-.
T Consensus 211 D~v~A~~~~~~~~~~~~~-F~~-s~E~-~-~~~~l~~A~~~~D~e~f~~av~~~d~~~~l-----d~w~~~~l~~ 276 (282)
T PF14938_consen 211 DYVAARKALERYCSQDPS-FAS-SREY-K-FLEDLLEAYEEGDVEAFTEAVAEYDSISRL-----DNWKTKMLLK 276 (282)
T ss_dssp -HHHHHHHHHHHGTTSTT-STT-SHHH-H-HHHHHHHHHHTT-CCCHHHHCHHHTTSS--------HHHHHHHHH
T ss_pred CHHHHHHHHHHHHhhCCC-CCC-cHHH-H-HHHHHHHHHHhCCHHHHHHHHHHHcccCcc-----HHHHHHHHHH
Confidence 776676666667654322 111 1332 3 44555567766555344 2 4444444444 3477766643
No 13
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=79.53 E-value=70 Score=31.91 Aligned_cols=200 Identities=15% Similarity=0.112 Sum_probs=110.3
Q ss_pred ChhhHHHHHHHHHhhccC---C---chh----HHHHHHHHHHHHcCCCcchhhhhHHhHHHHHhhcCCC-----HHHHHH
Q 018867 114 KPAMRLKILFNLYNLLEN---P---YSR----FFVYMKALNLAVNGKVTEHIIPSFKKIDSFLKEWNID-----IKDKRA 178 (349)
Q Consensus 114 ~~~~rl~~L~~Lfn~l~~---~---~~r----~~v~~~il~la~~~~~~~~l~~~l~~~~~~L~~w~~~-----~~~~~~ 178 (349)
.-+.+-+.+.-.||..-+ + +.+ +.+-..+..+--+.+..+.+...++..+. .+--+++ ..+.=+
T Consensus 145 ~l~~~sr~l~R~Fn~il~dR~p~ln~skk~g~y~iaNlL~~iY~Rl~~~~l~~n~lka~~~-vs~~Di~~~~~sq~v~f~ 223 (413)
T COG5600 145 NLSKISRLLTRMFNSILNDRSPALNPSKKVGLYYIANLLFQIYLRLGRFKLCENFLKASKE-VSMPDISEYQKSQVVVFH 223 (413)
T ss_pred hHHHHHHHHHHHHHHhcCCcCccCChhhHHHHHHHHHHHHHHHHHhccHHHHHHHHHhccc-ccccccchhhhcceeehh
Confidence 344556777777875532 1 122 11112233444466666666666553222 1101222 223346
Q ss_pred HHHHHHHHHHHhccChHHHHHHHHHHhcccCCCCCCChhHHHHHHHHHHHHHhcCCCeeeecCCCChhhhhcccCCCchh
Q 018867 179 LFLGIANVLKESRSSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQCDLLDMPAIGQLENDAKYAS 258 (349)
Q Consensus 179 ~y~~~a~~l~~~~~~~~~~y~~~l~yL~~~~~~~~~~~~e~~~~A~~li~~aL~~p~iy~f~LL~~p~v~~L~~~~~~~~ 258 (349)
||+-+.-.+.. ..++.+..+-.-+++|-.... -..+..+-=.+..+|.-.+.+ |-..-|+..+.-+.
T Consensus 224 YYLG~~~l~~e--n~heA~~~L~~aFl~c~~l~~----~n~~rIl~~~ipt~Llv~~~~-------Ptk~~L~r~~~~s~ 290 (413)
T COG5600 224 YYLGIYYLLNE--NFHEAFLHLNEAFLQCPWLIT----RNRKRILPYYIPTSLLVNKFP-------PTKDLLERFKRCSV 290 (413)
T ss_pred hHHHHHHHHHH--hHHHHHHHHHHHHHhChhhhh----cchheehhHHhhHHHHhCCCC-------CchHHHHhccccch
Confidence 67776666654 233444444455777755321 122233444455555444432 33345555422445
Q ss_pred HHHHHHHHhcCChhhHHHHHhhChhhhhhcCCChHHHHHHHHHHHHhhhhhc------CCCCcChHHHHhhcCCCC
Q 018867 259 VYQLLKIFLTQRLDGYLEFQAGNSALLKSYGLVHEDCIAKMRLMSLVDLGSN------ESGQIPYGLIKDTLQVYF 328 (349)
Q Consensus 259 l~~LL~if~~G~l~~y~~~~~~~~~~~~~~~l~~~~l~~KirLLtL~~La~~------~~r~isy~~Ia~~l~i~~ 328 (349)
+--|.++.-+|++++|....+.|..++.+.|+ .-.+..+.++++.=.|..+ .+..+|++-+-.+++++.
T Consensus 291 ~~~LvkavrsGni~~~~~~l~~ner~~~~~~l-~ltl~~~~~~V~~RNL~rk~w~~~~~qsrlp~sil~~~~qls~ 365 (413)
T COG5600 291 YSPLVKAVRSGNIEDFDLALSRNERKFAKRGL-YLTLLAHYPLVCFRNLFRKIWRLHGKQSRLPLSILLIVLQLSA 365 (413)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHhHHHHHHcch-HHHHHhhccHHHHHHHHHHHHhhccccccCcHHHHHHHHHccC
Confidence 66788999999999999999999988887776 3456777788887777743 133456665555555543
No 14
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=72.40 E-value=28 Score=34.88 Aligned_cols=181 Identities=13% Similarity=0.039 Sum_probs=106.2
Q ss_pred HHHHcCCCcchhhhhHHh---HHHHHhhcCCCHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHhcccCCCCCCChhHHH
Q 018867 144 NLAVNGKVTEHIIPSFKK---IDSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGEDAHTMDEAK 220 (349)
Q Consensus 144 ~la~~~~~~~~l~~~l~~---~~~~L~~w~~~~~~~~~~y~~~a~~l~~~~~~~~~~y~~~l~yL~~~~~~~~~~~~e~~ 220 (349)
++-.+.+....+++.+.. ..+|...|..+.-+.-.+|.-....+.. ++..++..+.......+..-. ...+
T Consensus 171 ~Iyfri~~~~L~k~l~ra~~~~~~~~~~~~l~~~v~y~YylGr~a~~~~---d~~~A~~~L~~af~~cp~~~~---~n~~ 244 (394)
T KOG2688|consen 171 QIYFRIEKLLLCKNLIRAFDQSGSDISDFPLAQLVVYHYYLGRYAMFES---DFLNAFLQLNEAFRLCPDLLL---KNKR 244 (394)
T ss_pred HHHHHHhhHHHhHHHHHHhhccccchhhcccccceeeeeeeeeehhhhh---hHHHHHHHHHHHHHhCcHHHH---hhhh
Confidence 444455555555555543 3356677777777777777664443432 234444444433222222111 1111
Q ss_pred HHHHHHHHHHhcCCCeeeecCCC-ChhhhhcccCCCchhHHHHHHHHhcCChhhHHHHHhhChhhhhhcCCChHHHHHHH
Q 018867 221 EEAVRTIIEFVKSPDMFQCDLLD-MPAIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQAGNSALLKSYGLVHEDCIAKM 299 (349)
Q Consensus 221 ~~A~~li~~aL~~p~iy~f~LL~-~p~v~~L~~~~~~~~l~~LL~if~~G~l~~y~~~~~~~~~~~~~~~l~~~~l~~Ki 299 (349)
-...-++.-.+ ++. +|-..-|+.- .-..+-.|+++.-.|++..|....+.|..++-..|+- -...|.
T Consensus 245 ~iliylip~~~---------llg~~Pt~~lL~~~-~~~~~~~lv~aVr~Gnl~~f~~al~~~E~~f~~~gi~--l~l~~l 312 (394)
T KOG2688|consen 245 LILIYLIPTGL---------LLGRIPTKELLDFY-TLDKYSPLVQAVRSGNLRLFDLALADNERFFIRSGIY--LTLEKL 312 (394)
T ss_pred hHHHHHhHHHH---------HhccCcchhhHhHh-hHHhHHHHHHHHHhccHHHHHHHHhhhHHHHHHhccH--HHhhhh
Confidence 11111111111 222 3555555432 1336777899999999999999999999988887763 244569
Q ss_pred HHHHHhhhhhc------CCCCcChHHHHhhcCCCC------chHHH--HHHhhccce
Q 018867 300 RLMSLVDLGSN------ESGQIPYGLIKDTLQVYF------LTFLL--LDLWYGLFV 342 (349)
Q Consensus 300 rLLtL~~La~~------~~r~isy~~Ia~~l~i~~------~eve~--id~i~~~~~ 342 (349)
++++.-.|.++ ....+|++.+-.+++... +|||- -+.|+.|.+
T Consensus 313 ~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~~~~~deveciLa~lI~~G~i 369 (394)
T KOG2688|consen 313 PLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVTDVDLDEVECILANLIDLGRI 369 (394)
T ss_pred hHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCCCCchhhHHHHHHhhhhhccc
Confidence 99999988865 257899999999988765 45653 355666543
No 15
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=71.18 E-value=15 Score=31.07 Aligned_cols=73 Identities=10% Similarity=0.058 Sum_probs=45.3
Q ss_pred CCchhHHHHHHHHhcCChhhHHHHHhhC--hhhhhhcCCChHHHHHHHHHHHHhhhhhcCCCCcChHHHHhhcCCCCch
Q 018867 254 AKYASVYQLLKIFLTQRLDGYLEFQAGN--SALLKSYGLVHEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQVYFLT 330 (349)
Q Consensus 254 ~~~~~l~~LL~if~~G~l~~y~~~~~~~--~~~~~~~~l~~~~l~~KirLLtL~~La~~~~r~isy~~Ia~~l~i~~~e 330 (349)
++-..+..|.+.+-.|++.+|-...+++ +..+..+ .+.+..++|-=.+-.+.+. -+.|+-+++++-||++.+|
T Consensus 39 ~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~---v~~~~~~iR~~i~~~i~~a-Y~sIs~~~la~~Lg~~~~e 113 (143)
T PF10075_consen 39 PEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPF---VPGFEDTIRERIAHLISKA-YSSISLSDLAEMLGLSEEE 113 (143)
T ss_dssp TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHT---STTHHHHHHHHHHHHHHHH--SEE-HHHHHHHTTS-HHH
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHH---HHHHHHHHHHHHHHHHHHH-HhHcCHHHHHHHhCCCHHH
Confidence 4455778899999999999998766554 2223322 3445666665554444432 4689999999999999444
No 16
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=69.04 E-value=5.3 Score=30.69 Aligned_cols=40 Identities=25% Similarity=0.349 Sum_probs=25.7
Q ss_pred HHHHhhhhhcCCCCcChHHHHhhcCCCCchHHHHHHhhccc
Q 018867 301 LMSLVDLGSNESGQIPYGLIKDTLQVYFLTFLLLDLWYGLF 341 (349)
Q Consensus 301 LLtL~~La~~~~r~isy~~Ia~~l~i~~~eve~id~i~~~~ 341 (349)
+-.|+..+++ .+.|||++|.++|.=.....+-|+.|+..|
T Consensus 9 i~~Li~~gK~-~G~lT~~eI~~~L~~~~~~~e~id~i~~~L 48 (82)
T PF03979_consen 9 IKKLIEKGKK-KGYLTYDEINDALPEDDLDPEQIDEIYDTL 48 (82)
T ss_dssp HHHHHHHHHH-HSS-BHHHHHHH-S-S---HHHHHHHHHHH
T ss_pred HHHHHHHHhh-cCcCCHHHHHHHcCccCCCHHHHHHHHHHH
Confidence 3447777754 578999999999985555667788887655
No 17
>PF05369 MtmB: Monomethylamine methyltransferase MtmB; InterPro: IPR008031 Monomethylamine methyltransferase of the archaebacterium Methanosarcina barkeri contains a novel amino acid, pyrrolysine, encoded by the termination codon UAG []. The structure of the enzyme reveals a homohexamer comprised of individual subunits with a TIM barrel fold. MtmB initiates the metabolism of monomethylamine by catalysing the transfer of the methyl group from monomethylamine to the corrinoid cofactor of MtmC.; GO: 0008168 methyltransferase activity
Probab=65.56 E-value=13 Score=37.30 Aligned_cols=69 Identities=20% Similarity=0.203 Sum_probs=50.8
Q ss_pred HHHHhHhhhhcCCCcccchhHHHHHHHHHHHHHcCCHHHHHHHHHHhhHHhhccCChhhHHHHHHHHHHHhcCCCChhHH
Q 018867 17 VRFTSELAWADAGPEAAEEQVNRLCLEAQESMVMGRWMDLASLMLTSADLMFSKVSDKDLECIFTVICNLVTKPESLDEV 96 (349)
Q Consensus 17 ~~~~~~~~~~~~~~~~a~~e~~~~~~~~e~l~~~klwhqLt~~ll~~~~~~f~~~~~ke~E~~~n~li~l~~~~~~~~~~ 96 (349)
+||++|.+.+-+|-+++ +.+.++..+=.+|+++. + +....|+|+.+|++-- +++.++.
T Consensus 382 arfmaEva~a~a~~~ls--evN~i~~~i~~~Ye~~~---------~------~~p~Gk~F~EcYdv~t-----~~Pt~EY 439 (457)
T PF05369_consen 382 ARFMAEVARAVAGMDLS--EVNDILDKIVAKYEKNY---------S------SAPKGKPFQECYDVNT-----MQPTDEY 439 (457)
T ss_pred HHHHHHHHHHHhcccHH--HHHHHHHHHHHHhhhcc---------c------cCCCCCChHHHhcccc-----cCCcHHH
Confidence 69999999998887777 78888888888888642 1 1224799999988543 5567778
Q ss_pred HHHHHHHHHHh
Q 018867 97 HEMTKLISGKI 107 (349)
Q Consensus 97 ~~lv~~l~~~v 107 (349)
.++-+....++
T Consensus 440 ~~~Y~~~~k~l 450 (457)
T PF05369_consen 440 MNVYDKAKKEL 450 (457)
T ss_pred HHHHHHHHHHH
Confidence 77777665544
No 18
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=64.03 E-value=1e+02 Score=27.09 Aligned_cols=95 Identities=11% Similarity=0.090 Sum_probs=61.1
Q ss_pred chhHHHHHHHHHHHHcCCCcchhhhhHHhHHHHHhhcCCCHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHhcccCC--
Q 018867 133 YSRFFVYMKALNLAVNGKVTEHIIPSFKKIDSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSG-- 210 (349)
Q Consensus 133 ~~r~~v~~~il~la~~~~~~~~l~~~l~~~~~~L~~w~~~~~~~~~~y~~~a~~l~~~~~~~~~~y~~~l~yL~~~~~-- 210 (349)
..+..+++.++.++-..++...+...+.+++..++. .++.+++.=+.+..-.+.-..++|..+-+..+.-+.+|+.
T Consensus 70 ~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~--~~d~~~~nrlk~~~gL~~l~~r~f~~AA~~fl~~~~t~~~~~ 147 (177)
T PF10602_consen 70 GHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEK--GGDWERRNRLKVYEGLANLAQRDFKEAAELFLDSLSTFTSLQ 147 (177)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhc--cchHHHHHHHHHHHHHHHHHhchHHHHHHHHHccCcCCCCCc
Confidence 456777777888888889999999999999999985 3333333323333333333346677777777777777764
Q ss_pred -CCCCChhHHHHHHHHHHHHHhc
Q 018867 211 -EDAHTMDEAKEEAVRTIIEFVK 232 (349)
Q Consensus 211 -~~~~~~~e~~~~A~~li~~aL~ 232 (349)
....+ ..+.|+=.++.||.
T Consensus 148 ~~el~s---~~d~a~Y~~l~aLa 167 (177)
T PF10602_consen 148 YTELIS---YNDFAIYGGLCALA 167 (177)
T ss_pred hhhhcC---HHHHHHHHHHHHHH
Confidence 33322 44556666665553
No 19
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=57.01 E-value=8.2 Score=25.80 Aligned_cols=21 Identities=19% Similarity=0.230 Sum_probs=15.5
Q ss_pred CCCcChHHHHhhcCCCCchHH
Q 018867 312 SGQIPYGLIKDTLQVYFLTFL 332 (349)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eve 332 (349)
+...||.+||+.+|++...|.
T Consensus 15 d~r~s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 15 DGRRSYAELAEELGLSESTVR 35 (42)
T ss_dssp -TTS-HHHHHHHHTS-HHHHH
T ss_pred cCCccHHHHHHHHCcCHHHHH
Confidence 466899999999999987764
No 20
>PF04510 DUF577: Family of unknown function (DUF577); InterPro: IPR007598 This is a family of Arabidopsis thaliana (Mouse-ear cress) proteins. Many of these members contain a repeated region.
Probab=56.48 E-value=1.4e+02 Score=26.40 Aligned_cols=52 Identities=15% Similarity=0.215 Sum_probs=34.6
Q ss_pred HHcCCHHHHHHHHHHhhHHhhccCChhhHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHhh
Q 018867 48 MVMGRWMDLASLMLTSADLMFSKVSDKDLECIFTVICNLVTKPESLDEVHEMTKLISGKII 108 (349)
Q Consensus 48 ~~~klwhqLt~~ll~~~~~~f~~~~~ke~E~~~n~li~l~~~~~~~~~~~~lv~~l~~~v~ 108 (349)
+.++.|++|-.=|++ .+.++++..|.+|+.+-..+ ..+-+.++.++|..++.
T Consensus 39 ~~~~~W~eL~d~Ils--------~~~~e~~kA~~IF~~L~~~l-~~efl~~~~~~L~~~~~ 90 (174)
T PF04510_consen 39 LQEGGWDELSDCILS--------LSENEPVKAFHIFICLPMPL-YGEFLIPFMENLLPEIS 90 (174)
T ss_pred cCCCCchhHHHHHHH--------hhccchHHHHHHHHhCCchh-hhhHHHHHHHHHHHHHH
Confidence 467889999843333 24678899999998666454 44555566666666554
No 21
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=52.97 E-value=2.4e+02 Score=27.97 Aligned_cols=277 Identities=13% Similarity=0.111 Sum_probs=137.4
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHhhHHhhccCChhhHHHHHHHHHHHhcCCCC-hhHHHHHHHHHHHHhhcCCCCChh
Q 018867 38 NRLCLEAQESMVMGRWMDLASLMLTSADLMFSKVSDKDLECIFTVICNLVTKPES-LDEVHEMTKLISGKIIQQPNDKPA 116 (349)
Q Consensus 38 ~~~~~~~e~l~~~klwhqLt~~ll~~~~~~f~~~~~ke~E~~~n~li~l~~~~~~-~~~~~~lv~~l~~~v~~~~~~~~~ 116 (349)
..-..++-++|.++.-+.-...++++..+++...+-.-.-.+.-.++..+.++++ .+....+|....+=.+++ .+.-
T Consensus 48 E~~Ilel~~ll~~~~~~~~lr~li~~~Rpf~~~v~KakaaKlvR~Lvd~~~~~~~~~~~~i~l~~~cIeWA~~e--kRtF 125 (411)
T KOG1463|consen 48 EQSILELGDLLAKEGDAEELRDLITSLRPFLSSVSKAKAAKLVRSLVDMFLKIDDGTGDQIELCTECIEWAKRE--KRTF 125 (411)
T ss_pred HHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCCCCcchHHHHHHHHHHHHHHH--hHHH
Confidence 3344455555555554555556677777887755433334444555555555432 233345666555433332 2333
Q ss_pred hHHHH---HHHHHhhccCCchhHHHHHHHHHHHH-----------------------cCCCcchhhhhHHhHHHHHhhcC
Q 018867 117 MRLKI---LFNLYNLLENPYSRFFVYMKALNLAV-----------------------NGKVTEHIIPSFKKIDSFLKEWN 170 (349)
Q Consensus 117 ~rl~~---L~~Lfn~l~~~~~r~~v~~~il~la~-----------------------~~~~~~~l~~~l~~~~~~L~~w~ 170 (349)
+|.+. |-.|||.... +.. .+..+-.+++ +.+++...+..|.....--+..-
T Consensus 126 LRq~Learli~Ly~d~~~-Yte--AlaL~~~L~rElKKlDDK~lLvev~llESK~y~~l~Nl~KakasLTsART~AnaiY 202 (411)
T KOG1463|consen 126 LRQSLEARLIRLYNDTKR-YTE--ALALINDLLRELKKLDDKILLVEVHLLESKAYHALRNLPKAKASLTSARTTANAIY 202 (411)
T ss_pred HHHHHHHHHHHHHHhhHH-HHH--HHHHHHHHHHHHHhcccccceeeehhhhhHHHHHHhcchhHHHHHHHHHHhhcccc
Confidence 33221 2223332110 000 0000111111 12223333444444444444455
Q ss_pred CCHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHhcccCCCCCCChhHHHHHHHHHHHHHhcCCCeee----ec-CCCCh
Q 018867 171 IDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQ----CD-LLDMP 245 (349)
Q Consensus 171 ~~~~~~~~~y~~~a~~l~~~~~~~~~~y~~~l~yL~~~~~~~~~~~~e~~~~A~~li~~aL~~p~iy~----f~-LL~~p 245 (349)
++|..++.+=....-++-. .++|..+|.+....+..|+.-+.. .. |......-|+..-+.| .+ |+.-.
T Consensus 203 cpPqlQa~lDLqSGIlha~-ekDykTafSYFyEAfEgf~s~~~~--v~----A~~sLKYMlLcKIMln~~ddv~~lls~K 275 (411)
T KOG1463|consen 203 CPPQLQATLDLQSGILHAA-EKDYKTAFSYFYEAFEGFDSLDDD--VK----ALTSLKYMLLCKIMLNLPDDVAALLSAK 275 (411)
T ss_pred cCHHHHHHHHHhccceeec-ccccchHHHHHHHHHccccccCCc--HH----HHHHHHHHHHHHHHhcCHHHHHHHHhhH
Confidence 6677677765555444444 367888999888888888664321 12 2222222222222222 32 44433
Q ss_pred hhhhcccCCCchhHHHHHHHHhcCChhhHHHHHhhChhhhhhcCCC-------hHHHHHHHHHHHHhhhhhcCCCCcChH
Q 018867 246 AIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQAGNSALLKSYGLV-------HEDCIAKMRLMSLVDLGSNESGQIPYG 318 (349)
Q Consensus 246 ~v~~L~~~~~~~~l~~LL~if~~G~l~~y~~~~~~~~~~~~~~~l~-------~~~l~~KirLLtL~~La~~~~r~isy~ 318 (349)
..-...| +.-..+...=++|...++.+|+...+.++.-+.+=.+. .+.+..| -|+.+. .|-..+-.+
T Consensus 276 ~~l~y~g-~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEk----nl~riI-EPyS~Vei~ 349 (411)
T KOG1463|consen 276 LALKYAG-RDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEK----NLCRII-EPYSRVEIS 349 (411)
T ss_pred HHHhccC-cchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHH----hHHHHc-CchhhhhHH
Confidence 3322333 24556677778899999999988777765533321000 2222222 122222 255556777
Q ss_pred HHHhhcCCCCchHH
Q 018867 319 LIKDTLQVYFLTFL 332 (349)
Q Consensus 319 ~Ia~~l~i~~~eve 332 (349)
-||+-.|++..+||
T Consensus 350 hIA~~IGl~~~~VE 363 (411)
T KOG1463|consen 350 HIAEVIGLDVPQVE 363 (411)
T ss_pred HHHHHHCCCcHHHH
Confidence 89999999999988
No 22
>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]
Probab=45.94 E-value=2.9e+02 Score=28.51 Aligned_cols=201 Identities=15% Similarity=0.077 Sum_probs=114.5
Q ss_pred HHHHHHhhccC-C---chh-HHHHHHHHHHHH-c---CCCcchhhhhHHhHHHHHhhcCCCHHHHHHHHHHHHHHHHHhc
Q 018867 121 ILFNLYNLLEN-P---YSR-FFVYMKALNLAV-N---GKVTEHIIPSFKKIDSFLKEWNIDIKDKRALFLGIANVLKESR 191 (349)
Q Consensus 121 ~L~~Lfn~l~~-~---~~r-~~v~~~il~la~-~---~~~~~~l~~~l~~~~~~L~~w~~~~~~~~~~y~~~a~~l~~~~ 191 (349)
-|.-=|.+|.. | ..| ..|+.+.+.+.+ + ..+...+..+++.+..=|.=..+-.+-...+|..-|..--+ +
T Consensus 283 ~lEKsyLRLTsAPdPstVRP~~VL~ksL~~vkdk~k~~~~Y~y~CdQ~KSiRQDLTVQ~IrneFTveVYEtHARIALE-k 361 (540)
T KOG1861|consen 283 ELEKSYLRLTSAPDPSTVRPLEVLKKSLCLVKDKWKAKANYAYLCDQFKSIRQDLTVQRIRNEFTVEVYETHARIALE-K 361 (540)
T ss_pred hHHHhHhhhccCCCccccCCHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhhhhhhheeccceeeeeehhhhHHHHh-c
Confidence 34445555543 2 223 667777776665 2 23566777777776666654455555556667777766666 5
Q ss_pred cChHHHHHHHHHHhcccCCCCCCChhHHHHHHHHHHHHHhcCCCeeeec-CCCChhh-hhcccCCCchhHHHHHHHHhcC
Q 018867 192 SSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQCD-LLDMPAI-GQLENDAKYASVYQLLKIFLTQ 269 (349)
Q Consensus 192 ~~~~~~y~~~l~yL~~~~~~~~~~~~e~~~~A~~li~~aL~~p~iy~f~-LL~~p~v-~~L~~~~~~~~l~~LL~if~~G 269 (349)
||..+|=++....-.-|.. ..+ .....=.|+++.-.-+..... | +-.+..+ ..++.++--.-.+++=.+...|
T Consensus 362 GD~~EfNQCQtQLk~LY~e-gip-g~~~EF~AYriLY~i~tkN~~---di~sll~~lt~E~ked~~V~hAL~vR~A~~~G 436 (540)
T KOG1861|consen 362 GDLEEFNQCQTQLKALYSE-GIP-GAYLEFTAYRILYYIFTKNYP---DILSLLRDLTEEDKEDEAVAHALEVRSAVTLG 436 (540)
T ss_pred CCHHHHHHHHHHHHHHHcc-CCC-CchhhHHHHHHHHHHHhcCch---HHHHHHHhccHhhccCHHHHHHHHHHHHHHhc
Confidence 8888876655443333311 111 111223466665444433322 2 1112222 1222221122345666788899
Q ss_pred ChhhHHHHHhhChhhhhhcCCChHHHHHHHHHHHHhhhhhcCCCCcChHHHHhhcCCCCch
Q 018867 270 RLDGYLEFQAGNSALLKSYGLVHEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQVYFLT 330 (349)
Q Consensus 270 ~l~~y~~~~~~~~~~~~~~~l~~~~l~~KirLLtL~~La~~~~r~isy~~Ia~~l~i~~~e 330 (349)
++..|-.+...-|..-.-+ .+.-..+.|..+|.=||..-.-+||++=|++.+....-|
T Consensus 437 NY~kFFrLY~~AP~M~~yL---mdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~e 494 (540)
T KOG1861|consen 437 NYHKFFRLYLTAPNMSGYL---MDLFLERERKKALTIICKSYRPTITVDFIASELAFDSME 494 (540)
T ss_pred cHHHHHHHHhhcccchhHH---HHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchHH
Confidence 9999887766555421112 456788999999999995423499999999988776644
No 23
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=45.90 E-value=1.1e+02 Score=22.01 Aligned_cols=68 Identities=9% Similarity=0.084 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHcCCCcchhhhhHHhHHHHHhhcCCCHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHh
Q 018867 137 FVYMKALNLAVNGKVTEHIIPSFKKIDSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYL 205 (349)
Q Consensus 137 ~v~~~il~la~~~~~~~~l~~~l~~~~~~L~~w~~~~~~~~~~y~~~a~~l~~~~~~~~~~y~~~l~yL 205 (349)
.+|..+..+-...|..+...+.+++.-+.....+-+.......|..++..+... |+++++..+..+.+
T Consensus 6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~-g~~~~A~~~~~~al 73 (78)
T PF13424_consen 6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRL-GDYEEALEYYQKAL 73 (78)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHT-THHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHH
Confidence 444445555567777877777777666665555555556788899999999985 87777666655443
No 24
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=45.77 E-value=10 Score=27.93 Aligned_cols=29 Identities=7% Similarity=0.078 Sum_probs=19.8
Q ss_pred HHhhhhhcCCCCcChHHHHhhcCCCCchHH
Q 018867 303 SLVDLGSNESGQIPYGLIKDTLQVYFLTFL 332 (349)
Q Consensus 303 tL~~La~~~~r~isy~~Ia~~l~i~~~eve 332 (349)
.|-+.... ++.+|+++||..++++.+.++
T Consensus 4 ~i~~~l~~-~~~~S~~eLa~~~~~s~~~ve 32 (69)
T PF09012_consen 4 EIRDYLRE-RGRVSLAELAREFGISPEAVE 32 (69)
T ss_dssp HHHHHHHH-S-SEEHHHHHHHTT--HHHHH
T ss_pred HHHHHHHH-cCCcCHHHHHHHHCcCHHHHH
Confidence 34444433 688999999999999999875
No 25
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=45.35 E-value=2.9e+02 Score=26.69 Aligned_cols=79 Identities=16% Similarity=0.195 Sum_probs=60.9
Q ss_pred ccCCCchhHHHHHHHHhcCChhhHHHHHhhCh------hhhhhcCCChHHHHHHHHHHHHhhhhhcCCCCcChHHHHhhc
Q 018867 251 ENDAKYASVYQLLKIFLTQRLDGYLEFQAGNS------ALLKSYGLVHEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTL 324 (349)
Q Consensus 251 ~~~~~~~~l~~LL~if~~G~l~~y~~~~~~~~------~~~~~~~l~~~~l~~KirLLtL~~La~~~~r~isy~~Ia~~l 324 (349)
+++|+--..-+|+.++-..|+.+|+...++|. .++.++ .+.+.++||--.|+.|.. |-..|...=|+++|
T Consensus 299 KNdPEIlAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh---~EdLl~niRTQVLlkLIk-PYt~i~Ipfis~~L 374 (440)
T KOG1464|consen 299 KNDPEILAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREH---IEDLLRNIRTQVLLKLIK-PYTNIGIPFISKEL 374 (440)
T ss_pred CCCHHHHHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHH---HHHHHHHHHHHHHHHHhc-cccccCchhhHhhc
Confidence 44555556778999999999999999988773 355555 788999999999999995 32333444499999
Q ss_pred CCCCchHHH
Q 018867 325 QVYFLTFLL 333 (349)
Q Consensus 325 ~i~~~eve~ 333 (349)
+|++.||+.
T Consensus 375 nv~~~dV~~ 383 (440)
T KOG1464|consen 375 NVPEADVES 383 (440)
T ss_pred CCCHHHHHH
Confidence 999998863
No 26
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=44.68 E-value=17 Score=25.04 Aligned_cols=32 Identities=16% Similarity=0.211 Sum_probs=23.7
Q ss_pred HHHHHhhhhhcCCCCcChHHHHhhcCCCCchH
Q 018867 300 RLMSLVDLGSNESGQIPYGLIKDTLQVYFLTF 331 (349)
Q Consensus 300 rLLtL~~La~~~~r~isy~~Ia~~l~i~~~ev 331 (349)
|-+.+++...+..+.++..+|++.+++|..-+
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv 35 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTV 35 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHH
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHH
Confidence 56777777754355689999999999997654
No 27
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=42.30 E-value=15 Score=26.27 Aligned_cols=48 Identities=17% Similarity=0.160 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhhhhhcCCCCcChHHHHhhcCCCCchH-HHHHHhhccceeEE
Q 018867 294 DCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQVYFLTF-LLLDLWYGLFVVNV 345 (349)
Q Consensus 294 ~l~~KirLLtL~~La~~~~r~isy~~Ia~~l~i~~~ev-e~id~i~~~~~~~~ 345 (349)
...+|++||.++-= ++.+++.+||+.++++.--+ -.|+.+..-+--.|
T Consensus 3 ~i~rq~~Ll~~L~~----~~~~~~~ela~~l~~S~rti~~~i~~L~~~f~~~~ 51 (59)
T PF08280_consen 3 DIKRQLKLLELLLK----NKWITLKELAKKLNISERTIKNDINELNEFFPENI 51 (59)
T ss_dssp HHHHHHHHHHHHHH----HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT--TCC
T ss_pred hHHHHHHHHHHHHc----CCCCcHHHHHHHHCCCHHHHHHHHHHHHHHhhhhc
Confidence 35566666665543 46899999999999997653 34555554443333
No 28
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=42.24 E-value=1e+02 Score=20.98 Aligned_cols=49 Identities=18% Similarity=0.162 Sum_probs=32.8
Q ss_pred hHHHHHHHHhcCChhhHHHHHhhChhhhhhcCCChHHHHHHHHHHHHhh
Q 018867 258 SVYQLLKIFLTQRLDGYLEFQAGNSALLKSYGLVHEDCIAKMRLMSLVD 306 (349)
Q Consensus 258 ~l~~LL~if~~G~l~~y~~~~~~~~~~~~~~~l~~~~l~~KirLLtL~~ 306 (349)
....+.+.+..|+++.-.++...+...+...+-+-.+..++-+.+-|++
T Consensus 4 ~~~~i~~~i~~g~~~~a~~~~~~~~~~l~~~~~~l~f~L~~q~~lell~ 52 (58)
T smart00668 4 ERKRIRELILKGDWDEALEWLSSLKPPLLERNSKLEFELRKQKFLELVR 52 (58)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHcCHHHhccCCCchhHHHHHHHHHHHH
Confidence 4567888999999999999988875544433334455555555555543
No 29
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=35.05 E-value=22 Score=26.44 Aligned_cols=28 Identities=14% Similarity=-0.006 Sum_probs=19.7
Q ss_pred CCCcChHHHHhhcCCCCchHH-HHHHhhc
Q 018867 312 SGQIPYGLIKDTLQVYFLTFL-LLDLWYG 339 (349)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eve-~id~i~~ 339 (349)
+|.-+-.+||+.++++.++|. ++.+.+.
T Consensus 18 gr~Pt~eEiA~~lgis~~~v~~~l~~~~~ 46 (78)
T PF04539_consen 18 GREPTDEEIAEELGISVEEVRELLQASRR 46 (78)
T ss_dssp SS--BHHHHHHHHTS-HHHHHHHHHHHSC
T ss_pred CCCCCHHHHHHHHcccHHHHHHHHHhCCC
Confidence 789999999999999999974 4444443
No 30
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=35.02 E-value=36 Score=25.62 Aligned_cols=26 Identities=8% Similarity=0.267 Sum_probs=20.5
Q ss_pred HhhhhhcCCCCcChHHHHhhcCCCCchH
Q 018867 304 LVDLGSNESGQIPYGLIKDTLQVYFLTF 331 (349)
Q Consensus 304 L~~La~~~~r~isy~~Ia~~l~i~~~ev 331 (349)
+++||=. .|+ ||+.|....|+++.||
T Consensus 5 iIeMAwe-DRt-pFeaI~~~fGL~E~eV 30 (72)
T TIGR03643 5 IIEMAWE-DRT-PFEAIEQQFGLSEKEV 30 (72)
T ss_pred HHHHHHc-cCC-CHHHHHHHHCCCHHHH
Confidence 6788832 344 9999999999998775
No 31
>PF01603 B56: Protein phosphatase 2A regulatory B subunit (B56 family); InterPro: IPR002554 Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits, this family is called the B56 family [].; GO: 0008601 protein phosphatase type 2A regulator activity, 0007165 signal transduction, 0000159 protein phosphatase type 2A complex; PDB: 2NYM_B 2NYL_B 2IAE_E 2NPP_B 3FGA_B 2JAK_A.
Probab=34.80 E-value=2.3e+02 Score=28.50 Aligned_cols=106 Identities=11% Similarity=0.250 Sum_probs=65.3
Q ss_pred hhHHHHHHHHHHHhcCCCChh---HH-HHHHHHHHHHhhcCCCCChhhH---HHHHHHHHhhccC--CchhHHHHHHHHH
Q 018867 74 KDLECIFTVICNLVTKPESLD---EV-HEMTKLISGKIIQQPNDKPAMR---LKILFNLYNLLEN--PYSRFFVYMKALN 144 (349)
Q Consensus 74 ke~E~~~n~li~l~~~~~~~~---~~-~~lv~~l~~~v~~~~~~~~~~r---l~~L~~Lfn~l~~--~~~r~~v~~~il~ 144 (349)
.-+.-+|.+|..++...+... -. .+++..|..-+ .+ .++..| ..+|-.+|..++. +..|-.+...+.+
T Consensus 105 pHL~~vY~il~~~i~~~~~~~~~~~i~~~fi~~Ll~l~-~S--~D~rER~~lk~~l~~iy~k~~~~r~~Ir~~i~~~~~~ 181 (409)
T PF01603_consen 105 PHLQLVYEILLRFIESPPFDPAKKYIDQKFIKKLLELF-DS--PDPRERDYLKTILHRIYGKFPNLRSFIRKSINNIFYR 181 (409)
T ss_dssp HHHHHHHHHHHHHHTSTT--CCTTTS-HHHHHHHHHTT-TS--STHHHHHHHHHHHHHHHHH-TTTHHHHHHHHHHHHHH
T ss_pred HhHHHHHHHHHHHHHCccccHHHHHcCHHHHHHHHHHc-CC--CCHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 345677888887776542211 01 23666666533 33 356665 3677888887764 3456666666777
Q ss_pred HHHcCCCcchhhhhHHhHHHHHhhcCCCH-HHHHHHHHH
Q 018867 145 LAVNGKVTEHIIPSFKKIDSFLKEWNIDI-KDKRALFLG 182 (349)
Q Consensus 145 la~~~~~~~~l~~~l~~~~~~L~~w~~~~-~~~~~~y~~ 182 (349)
+.........+.+.|+-+.+.++.+.++. ++|..++..
T Consensus 182 fi~e~~~~~gI~elLeil~sii~gf~~plk~eh~~fl~~ 220 (409)
T PF01603_consen 182 FIYETERHNGIAELLEILGSIINGFAVPLKEEHKQFLRK 220 (409)
T ss_dssp HHHTTS--STHHHHHHHHHHHHTT--SS--HHHHHHHHH
T ss_pred HhcCcccccCHHHHHHHHHHHHhccCCCCcHHHHHHHHH
Confidence 77788888899999999999999886654 667777744
No 32
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=34.33 E-value=63 Score=22.84 Aligned_cols=32 Identities=13% Similarity=0.105 Sum_probs=24.3
Q ss_pred CCCcChHHHHhhcCCCCchH-HHHHHh-hcccee
Q 018867 312 SGQIPYGLIKDTLQVYFLTF-LLLDLW-YGLFVV 343 (349)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~ev-e~id~i-~~~~~~ 343 (349)
++.++..+|++.++++...+ .|+... .+|+|.
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~ 55 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVSYHLKKLEEAGLIE 55 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 57899999999999998875 667766 456654
No 33
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=32.94 E-value=87 Score=26.05 Aligned_cols=47 Identities=19% Similarity=0.291 Sum_probs=33.2
Q ss_pred HHHHHHHhhhhhc-CCCCcChHHHHhhcCCCCchHH-HH-HHhhccceeE
Q 018867 298 KMRLMSLVDLGSN-ESGQIPYGLIKDTLQVYFLTFL-LL-DLWYGLFVVN 344 (349)
Q Consensus 298 KirLLtL~~La~~-~~r~isy~~Ia~~l~i~~~eve-~i-d~i~~~~~~~ 344 (349)
+.-+.+++.||.+ .++.+|-++||+.++||..-++ ++ .-.++|+|.+
T Consensus 8 ~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s 57 (135)
T TIGR02010 8 RYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKS 57 (135)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence 3446677788843 2457999999999999988754 23 3456677765
No 34
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=32.82 E-value=41 Score=25.43 Aligned_cols=26 Identities=8% Similarity=0.244 Sum_probs=20.3
Q ss_pred HhhhhhcCCCCcChHHHHhhcCCCCchH
Q 018867 304 LVDLGSNESGQIPYGLIKDTLQVYFLTF 331 (349)
Q Consensus 304 L~~La~~~~r~isy~~Ia~~l~i~~~ev 331 (349)
+++||=. .| .||+.|....|+++.||
T Consensus 4 iIeMAwe-DR-tpFeaI~~qfGl~E~eV 29 (73)
T PF10985_consen 4 IIEMAWE-DR-TPFEAIERQFGLSEKEV 29 (73)
T ss_pred HHHHHHc-cC-CCHHHHHHHHCCCHHHH
Confidence 5788832 34 49999999999997765
No 35
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=32.75 E-value=27 Score=25.40 Aligned_cols=20 Identities=30% Similarity=0.263 Sum_probs=17.8
Q ss_pred CCCcChHHHHhhcCCCCchH
Q 018867 312 SGQIPYGLIKDTLQVYFLTF 331 (349)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~ev 331 (349)
++.+++.+||+.|+|++..|
T Consensus 20 ~g~i~lkdIA~~Lgvs~~tI 39 (60)
T PF10668_consen 20 NGKIKLKDIAEKLGVSESTI 39 (60)
T ss_pred CCCccHHHHHHHHCCCHHHH
Confidence 68999999999999998654
No 36
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=31.57 E-value=73 Score=24.07 Aligned_cols=44 Identities=16% Similarity=0.104 Sum_probs=27.4
Q ss_pred HHHHhhhhhcC-CCCcChHHHHhhcCCCCchHH-HH-HHhhccceeE
Q 018867 301 LMSLVDLGSNE-SGQIPYGLIKDTLQVYFLTFL-LL-DLWYGLFVVN 344 (349)
Q Consensus 301 LLtL~~La~~~-~r~isy~~Ia~~l~i~~~eve-~i-d~i~~~~~~~ 344 (349)
+-.|+.|+..+ .+.++-++||+.+++|..-+. ++ .-.++|+|.+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s 57 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIES 57 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEe
Confidence 44455566432 345999999999999998753 33 3345666544
No 37
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=30.89 E-value=25 Score=24.08 Aligned_cols=20 Identities=20% Similarity=0.182 Sum_probs=13.7
Q ss_pred CCcChHHHHhhcCCCCchHH
Q 018867 313 GQIPYGLIKDTLQVYFLTFL 332 (349)
Q Consensus 313 r~isy~~Ia~~l~i~~~eve 332 (349)
...||++||+.++++...|.
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~ 44 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVK 44 (54)
T ss_dssp S---HHHHHHHCTS-HHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHH
Confidence 45899999999999987654
No 38
>PF11864 DUF3384: Domain of unknown function (DUF3384); InterPro: IPR024584 This entry represents the N-terminal domain of tuberin which is functionally uncharacterised.
Probab=30.32 E-value=6e+02 Score=25.84 Aligned_cols=18 Identities=6% Similarity=-0.016 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHHcCCHH
Q 018867 37 VNRLCLEAQESMVMGRWM 54 (349)
Q Consensus 37 ~~~~~~~~e~l~~~klwh 54 (349)
+..++..+|.+|+++..+
T Consensus 376 ~~~l~~~ie~L~~~~~~~ 393 (464)
T PF11864_consen 376 LHSLLSSIESLYEQHDFN 393 (464)
T ss_pred HHHHHHHHHHHHhCCCcC
Confidence 344444455555554433
No 39
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=30.05 E-value=76 Score=27.27 Aligned_cols=44 Identities=18% Similarity=0.046 Sum_probs=30.3
Q ss_pred HHHHhhhhhcCCCCcChHHHHhhcCCCCchHH--HHHHhhccceeE
Q 018867 301 LMSLVDLGSNESGQIPYGLIKDTLQVYFLTFL--LLDLWYGLFVVN 344 (349)
Q Consensus 301 LLtL~~La~~~~r~isy~~Ia~~l~i~~~eve--~id~i~~~~~~~ 344 (349)
+-+|+.||..+++.++-++||+..+||..=++ +-.-.++|+|.+
T Consensus 11 lr~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S 56 (153)
T PRK11920 11 IRMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVET 56 (153)
T ss_pred HHHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 45666777443556899999999999986432 334556677655
No 40
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=29.47 E-value=84 Score=24.13 Aligned_cols=39 Identities=10% Similarity=0.021 Sum_probs=29.6
Q ss_pred HHHHHHHhhhhhcCCCCcChHHHHhhcCCCCchHH-HHHHhh
Q 018867 298 KMRLMSLVDLGSNESGQIPYGLIKDTLQVYFLTFL-LLDLWY 338 (349)
Q Consensus 298 KirLLtL~~La~~~~r~isy~~Ia~~l~i~~~eve-~id~i~ 338 (349)
+.+++-+..+++ .+-+|=++|+++|+++..-|| +|++.+
T Consensus 5 ~~~~~~ll~~~~--~~~~SGe~La~~LgiSRtaVwK~Iq~Lr 44 (79)
T COG1654 5 SQMLLLLLLLLT--GNFVSGEKLAEELGISRTAVWKHIQQLR 44 (79)
T ss_pred HHHHHHHHHHcC--CCcccHHHHHHHHCccHHHHHHHHHHHH
Confidence 455555666665 467899999999999999987 577665
No 41
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=28.70 E-value=6.3e+02 Score=25.59 Aligned_cols=61 Identities=10% Similarity=-0.009 Sum_probs=39.4
Q ss_pred HHHHHHHHHhhcCCCCChhhHHHHHHHHHhhccC----CchhHHHHHHHHHHHHcCCCcchhhhhHH
Q 018867 98 EMTKLISGKIIQQPNDKPAMRLKILFNLYNLLEN----PYSRFFVYMKALNLAVNGKVTEHIIPSFK 160 (349)
Q Consensus 98 ~lv~~l~~~v~~~~~~~~~~rl~~L~~Lfn~l~~----~~~r~~v~~~il~la~~~~~~~~l~~~l~ 160 (349)
.++...++-+... .+-..+++++.+|-+--.. .-.|+++-.-+.+.-...|+.......+-
T Consensus 91 ~Mvq~~~~y~~~~--~d~~~k~~li~tLr~VtegkIyvEvERarlTk~L~~ike~~Gdi~~Aa~il~ 155 (439)
T KOG1498|consen 91 SMVQQAMTYIDGT--PDLETKIKLIETLRTVTEGKIYVEVERARLTKMLAKIKEEQGDIAEAADILC 155 (439)
T ss_pred HHHHHHHHhccCC--CCchhHHHHHHHHHHhhcCceEEeehHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 3666566544332 3567788888888775543 24688877777777777887765555443
No 42
>KOG1840 consensus Kinesin light chain [Cytoskeleton]
Probab=27.91 E-value=7.1e+02 Score=25.95 Aligned_cols=57 Identities=18% Similarity=0.172 Sum_probs=44.2
Q ss_pred cCCCcchhhhhHHhHHHHHhhcCCCHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHh
Q 018867 148 NGKVTEHIIPSFKKIDSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYL 205 (349)
Q Consensus 148 ~~~~~~~l~~~l~~~~~~L~~w~~~~~~~~~~y~~~a~~l~~~~~~~~~~y~~~l~yL 205 (349)
+.+........+.+...|+...+.+....-.-|+..+..|+.+ |+++.+..+...-+
T Consensus 421 ~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~-g~~e~a~~~~~~~~ 477 (508)
T KOG1840|consen 421 ELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQ-GNYEAAEELEEKVL 477 (508)
T ss_pred HhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHc-ccHHHHHHHHHHHH
Confidence 4555666667777888889888888777778889999999996 88888877766655
No 43
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=27.89 E-value=88 Score=25.66 Aligned_cols=44 Identities=18% Similarity=0.123 Sum_probs=28.5
Q ss_pred HHHHhhhhhcCCCCcChHHHHhhcCCCCchHH-HHHH-hhccceeE
Q 018867 301 LMSLVDLGSNESGQIPYGLIKDTLQVYFLTFL-LLDL-WYGLFVVN 344 (349)
Q Consensus 301 LLtL~~La~~~~r~isy~~Ia~~l~i~~~eve-~id~-i~~~~~~~ 344 (349)
+.+|+.|+..+++.+|..+|++.+++|..-++ ++.. .++|+|.+
T Consensus 12 l~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~ 57 (130)
T TIGR02944 12 TLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS 57 (130)
T ss_pred HHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 33445555433567999999999999987653 3333 45666654
No 44
>KOG2171 consensus Karyopherin (importin) beta 3 [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.25 E-value=9.9e+02 Score=27.38 Aligned_cols=72 Identities=15% Similarity=0.282 Sum_probs=41.9
Q ss_pred CHHHHHHHHHHhhHHhhccCChhhHHHHHHHHHHHhcCCCChhH-H-HHHHHHHHHHhhcCCCCChhhH---HHHHHHHH
Q 018867 52 RWMDLASLMLTSADLMFSKVSDKDLECIFTVICNLVTKPESLDE-V-HEMTKLISGKIIQQPNDKPAMR---LKILFNLY 126 (349)
Q Consensus 52 lwhqLt~~ll~~~~~~f~~~~~ke~E~~~n~li~l~~~~~~~~~-~-~~lv~~l~~~v~~~~~~~~~~r---l~~L~~Lf 126 (349)
.|.+|..-|.. +.+..+++..|..+-++-++...+++..+ . ..+..-|.+.+... +.+ .| ++.++...
T Consensus 115 ~WPell~~L~q----~~~S~~~~~rE~al~il~s~~~~~~~~~~~~~~~l~~lf~q~~~d~--s~~-vr~~a~rA~~a~~ 187 (1075)
T KOG2171|consen 115 KWPELLQFLFQ----STKSPNPSLRESALLILSSLPETFGNTLQPHLDDLLRLFSQTMTDP--SSP-VRVAAVRALGAFA 187 (1075)
T ss_pred chHHHHHHHHH----HhcCCCcchhHHHHHHHHhhhhhhccccchhHHHHHHHHHHhccCC--cch-HHHHHHHHHHHHH
Confidence 79999876666 55554566678888888877777765532 1 22444344444332 233 44 45555555
Q ss_pred hhcc
Q 018867 127 NLLE 130 (349)
Q Consensus 127 n~l~ 130 (349)
--++
T Consensus 188 ~~~~ 191 (1075)
T KOG2171|consen 188 EYLE 191 (1075)
T ss_pred HHhc
Confidence 5554
No 45
>cd00280 TRFH Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains.
Probab=26.44 E-value=1e+02 Score=27.75 Aligned_cols=50 Identities=14% Similarity=0.140 Sum_probs=35.5
Q ss_pred HHHHHHHhcCChhhHHHHHhhChhhhhhcCCChHHHHHHHHHHHHhhhhh
Q 018867 260 YQLLKIFLTQRLDGYLEFQAGNSALLKSYGLVHEDCIAKMRLMSLVDLGS 309 (349)
Q Consensus 260 ~~LL~if~~G~l~~y~~~~~~~~~~~~~~~l~~~~l~~KirLLtL~~La~ 309 (349)
+.+..+|-.|+..+|..+.+.-..++...---......|+|++.+++=..
T Consensus 18 ~~~c~aFR~~r~~dFr~~rdi~e~ll~~~~~~~a~~~k~l~i~QfLsRI~ 67 (200)
T cd00280 18 HSACRAFREGRYEDFRRTRDIAEALLVGPLKLTATQLKTLRIMQFLSRIA 67 (200)
T ss_pred HHHHHHHHccChHHHHHHHHHHHHHHhccccccccchhHhHHHHHHHHHH
Confidence 45788999999999998876555544332112456779999998877653
No 46
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=25.96 E-value=67 Score=24.26 Aligned_cols=18 Identities=17% Similarity=0.065 Sum_probs=16.1
Q ss_pred CCCcChHHHHhhcCCCCc
Q 018867 312 SGQIPYGLIKDTLQVYFL 329 (349)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~ 329 (349)
.+..||.+||+.++.|..
T Consensus 15 G~v~TYg~iA~~~g~p~~ 32 (79)
T cd06445 15 GEVTTYGQIAKLAGTPKA 32 (79)
T ss_pred CCcCcHHHHHHHHCCCCc
Confidence 789999999999999843
No 47
>PF03671 Ufm1: Ubiquitin fold modifier 1 protein; InterPro: IPR005375 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin-like molecules (UBLs) can be divided into two subclasses: type-1 UBLs, which ligate to target proteins in a manner similar, but not identical, to the ubiquitylation pathway, such as SUMO, NEDD8, and UCRP/ISG15, and type-2 UBLs (also called UDPs, ubiquitin-domain proteins), which contain ubiquitin-like structure embedded in a variety of different classes of large proteins with apparently distinct functions, such as Rad23, Elongin B, Scythe, Parkin, and HOIL-1. This entry represents Ufm1 (ubiquitin-fold modifier), which is a ubiquitin-like protein with structural similarities to ubiquitin [, ]. Ufm1 is one of a number of ubiquitin-like modifiers that conjugate to target proteins in cells through Uba5 (E1) and Ufc1 (E2). The Ufm1-system is conserved in metazoa and plants, suggesting it has a potential role in multicellular organisms []. Human Ufm1 is synthesized as a precursor consisting of 85 amino-acid residues. Prior to activation by Uba5, the extra amino acids at the C-terminal region of Ufm1 are removed to expose Gly, which is necessary for conjugation to target molecule(s). C-terminal processing of Ufm1 requires two specific cysteine peptidases (IPR012462 from INTERPRO): UfSP1 and UfSP2; both peptidases are also able to release Ufm1 from Ufm1-conjugated cellular proteins. UfSP2 is present in most, if not all, of multi-cellular organisms including plant, nematode, fly, and mammal, whereas UfSP1 is not present in plants and nematodes []. For further information on ubiquitin, please see Protein of the Month [].; PDB: 1J0G_A 1WXS_A 1L7Y_A.
Probab=25.56 E-value=33 Score=25.89 Aligned_cols=22 Identities=36% Similarity=0.489 Sum_probs=19.0
Q ss_pred cccCCCCchhHHHHHHHhHhhh
Q 018867 4 VVPTSEEDPALAVVRFTSELAW 25 (349)
Q Consensus 4 ~~~~~~e~~~~~~~~~~~~~~~ 25 (349)
++...|+-|+.+|.||.||-+.
T Consensus 19 v~sVPE~apftaVlkfaAeeF~ 40 (76)
T PF03671_consen 19 VISVPEEAPFTAVLKFAAEEFK 40 (76)
T ss_dssp EEEEETTSBHHHHHHHHHHHTT
T ss_pred EEecCCCCchHHHHHHHHHHcC
Confidence 5567789999999999999876
No 48
>PF03635 Vps35: Vacuolar protein sorting-associated protein 35 ; InterPro: IPR005378 The movement of lipid and protein components between intracellular organelles requires the regulated interactions of many molecules. Vacuolar protein sorting-associated protein (Vps)5 is a yeast protein that is a subunit of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. Sorting nexin (SNX) 1 and SNX2 are its mammalian orthologs []. To carry out its biological functions, Vps5 forms the retromer complex with at least four other proteins: Vps17, Vps26, Vps29, and Vps35.Vps35 contains a central region of weaker sequence similarity, thought to indicate the presence of at least three domains [].; PDB: 2R17_C.
Probab=25.41 E-value=6.3e+02 Score=27.76 Aligned_cols=160 Identities=19% Similarity=0.246 Sum_probs=78.3
Q ss_pred hhhHHHHHHHHHHHhcCCCCh-hH----------H---HHHHHHHHHHhhcCCCCChhhHHHHHHHHHhhccC-Cchh--
Q 018867 73 DKDLECIFTVICNLVTKPESL-DE----------V---HEMTKLISGKIIQQPNDKPAMRLKILFNLYNLLEN-PYSR-- 135 (349)
Q Consensus 73 ~ke~E~~~n~li~l~~~~~~~-~~----------~---~~lv~~l~~~v~~~~~~~~~~rl~~L~~Lfn~l~~-~~~r-- 135 (349)
..+++.+|.++-.++..-++. .. . ...+.++.--+ . .+++..-.++|..+.+.+.. .+.|
T Consensus 451 ~e~v~~ll~li~pLi~d~~d~~~~~~~~~~~~eef~eeQ~~varliHLi-~--~~D~d~~~~iL~~~rk~~~~Gg~~ri~ 527 (762)
T PF03635_consen 451 PEEVDNLLELISPLIKDQDDQPSSEPDLKEDSEEFAEEQELVARLIHLI-R--SDDPDQQFEILNIARKHFGNGGPKRIR 527 (762)
T ss_dssp ----------------------------------TCCCHHHHHHHHHHC-T--TSSHHHHHHHHHHHHHHHCTT-SSSHH
T ss_pred HHHHHHHHHHHHHHhhCCCCCCCccccccCchHHHHHHHHHHHHHHHHh-c--CCCHHHHHHHHHHHHHHHHhCCCceee
Confidence 467899998888887632211 00 0 11222243222 3 35788899999999998875 2222
Q ss_pred ---HHHHHHHHHHHHcCCC-----------------cchhhhhHHhHHHHHhhc-CCC--HHHHHHHHHHHHHHHHHhcc
Q 018867 136 ---FFVYMKALNLAVNGKV-----------------TEHIIPSFKKIDSFLKEW-NID--IKDKRALFLGIANVLKESRS 192 (349)
Q Consensus 136 ---~~v~~~il~la~~~~~-----------------~~~l~~~l~~~~~~L~~w-~~~--~~~~~~~y~~~a~~l~~~~~ 192 (349)
..+-...++++++... -..++..++.+-+.++.. +.. ++..=++|..+|...+.. +
T Consensus 528 ~TlP~LIf~~lkL~r~~~~~~~~~~~~~~~~~~~~~~~~~~kifkfi~~~i~~L~~~~~~~~lalkL~Lq~A~~AD~~-~ 606 (762)
T PF03635_consen 528 YTLPPLIFAALKLARRIKDLKQKYPNNAIKDDDEDWEKKCKKIFKFIHQCISALYQIHPSSELALKLYLQAAIVADQC-G 606 (762)
T ss_dssp HHCHHHHHHHHHHHHHHHCCC---------CT-TTHHHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHHHH--
T ss_pred eeHHHHHHHHHHHHHHHHHhhccchhhccccchhhHHHHHHHHHHHHHHHHHHHHhccCchhhhHHHHHHHHHHHHhh-C
Confidence 1122224455542111 123345555555555554 333 477888999999988886 6
Q ss_pred ChHHHHHHHHHHhcccCCCCCCChhHHHHHHHHHHHHHhcCCCeee
Q 018867 193 SSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQ 238 (349)
Q Consensus 193 ~~~~~y~~~l~yL~~~~~~~~~~~~e~~~~A~~li~~aL~~p~iy~ 238 (349)
-.+-+|.|....+..|+.+ .+ .+.++-.|...++.+|..-..|.
T Consensus 607 ~e~iaYEFf~QAf~iYEE~-Is-DSk~Q~~aL~~ii~tL~~~r~~~ 650 (762)
T PF03635_consen 607 LEEIAYEFFSQAFTIYEEE-IS-DSKAQFQALTLIIGTLQKTRSFS 650 (762)
T ss_dssp -TTHHHHHHHHHHHHHHHH----SHHHHHHHHHHHHHHHCC-----
T ss_pred cHHHHHHHHHHHHHHHHhh-cc-chHHHHHHHHHHHHHHHHhcCCC
Confidence 5566999999988888653 22 25667789999999997666553
No 49
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=25.18 E-value=40 Score=22.78 Aligned_cols=20 Identities=15% Similarity=0.041 Sum_probs=16.3
Q ss_pred CCCcChHHHHhhcCCCCchH
Q 018867 312 SGQIPYGLIKDTLQVYFLTF 331 (349)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~ev 331 (349)
....||++||+.++++...|
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V 37 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTV 37 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHH
Confidence 35789999999999998765
No 50
>PF12397 U3snoRNP10: U3 small nucleolar RNA-associated protein 10 ; InterPro: IPR022125 This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with PF08146 from PFAM. This family is the protein associated with U3 snoRNA which is involved in the processing of pre-rRNA.
Probab=24.66 E-value=3.7e+02 Score=21.57 Aligned_cols=70 Identities=17% Similarity=0.131 Sum_probs=39.8
Q ss_pred HHHHHHhhHHhhccCChhhH-HHHHHHHHHHhcCCCChhHHHHHHHHHHHHhhcCCCC-Ch-hhHHHHHHHHHhhc
Q 018867 57 ASLMLTSADLMFSKVSDKDL-ECIFTVICNLVTKPESLDEVHEMTKLISGKIIQQPND-KP-AMRLKILFNLYNLL 129 (349)
Q Consensus 57 t~~ll~~~~~~f~~~~~ke~-E~~~n~li~l~~~~~~~~~~~~lv~~l~~~v~~~~~~-~~-~~rl~~L~~Lfn~l 129 (349)
...++.+....+...+..|+ -+.|-++..+..+.+=.+ ++++.+.+.+...... .. ...+-.|..++..-
T Consensus 4 l~~lLP~l~~~L~~s~~~d~~~a~ymIl~~La~k~~L~~---~~l~~l~~~i~~~~~~~~~~~~~l~~L~~l~q~q 76 (121)
T PF12397_consen 4 LPRLLPFLLKGLKSSSSPDLQAAAYMILSVLASKVPLSD---EVLNALMESILKNWTQETVQRQALICLIVLCQSQ 76 (121)
T ss_pred HHHHHHHHHHHHccCCcHHHHHHHHHHHHHHHhhcCCcH---HHHHHHHHHHHhccccchhHHHHHHHHHHHHHcc
Confidence 34455555556664445677 888888888888764332 3344444444443322 23 45566677777544
No 51
>cd01766 Ufm1 Urm1-like ubiquitin domain. Ufm1 (ubiquitin-fold modifier 1) is a post-translational UBL (ubiquitin-like) modifier with a tertiary structure similar to that of ubiquitin. Ufm1 is initially expressed as a precursor which undergoes C-terminal cleavage to expose a conserved glycine residue that is required for the conjugation reactions involving Ufm1.
Probab=24.06 E-value=53 Score=24.94 Aligned_cols=22 Identities=32% Similarity=0.422 Sum_probs=19.2
Q ss_pred cccCCCCchhHHHHHHHhHhhh
Q 018867 4 VVPTSEEDPALAVVRFTSELAW 25 (349)
Q Consensus 4 ~~~~~~e~~~~~~~~~~~~~~~ 25 (349)
++...|+-||-||.+|.||-+.
T Consensus 19 vlsVpE~aPftAvlkfaAEeFk 40 (82)
T cd01766 19 VLSVPESTPFTAVLKFAAEEFK 40 (82)
T ss_pred EEeccccCchHHHHHHHHHhcC
Confidence 4567889999999999999886
No 52
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=23.32 E-value=1.6e+02 Score=25.66 Aligned_cols=47 Identities=17% Similarity=0.281 Sum_probs=32.1
Q ss_pred HHHHHHHhhhhhc-CCCCcChHHHHhhcCCCCchHH--HHHHhhccceeE
Q 018867 298 KMRLMSLVDLGSN-ESGQIPYGLIKDTLQVYFLTFL--LLDLWYGLFVVN 344 (349)
Q Consensus 298 KirLLtL~~La~~-~~r~isy~~Ia~~l~i~~~eve--~id~i~~~~~~~ 344 (349)
..-|.+++.||.. +.+.+|=++||+.+++|..=++ +-.--++|+|.+
T Consensus 8 ~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s 57 (164)
T PRK10857 8 RYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSS 57 (164)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 3456666777743 3567999999999999987542 334456777664
No 53
>PRK09191 two-component response regulator; Provisional
Probab=23.25 E-value=1.8e+02 Score=26.23 Aligned_cols=21 Identities=10% Similarity=-0.202 Sum_probs=17.5
Q ss_pred CCCcChHHHHhhcCCCCchHH
Q 018867 312 SGQIPYGLIKDTLQVYFLTFL 332 (349)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eve 332 (349)
-..+||+|||+.++++..-|.
T Consensus 102 ~~~~s~~eIA~~l~~s~~tV~ 122 (261)
T PRK09191 102 LEGFSVEEAAEILGVDPAEAE 122 (261)
T ss_pred HhcCCHHHHHHHHCCCHHHHH
Confidence 347899999999999987653
No 54
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=22.92 E-value=1.7e+02 Score=23.76 Aligned_cols=46 Identities=22% Similarity=0.206 Sum_probs=29.5
Q ss_pred HHHHHHhhhhhcC-CCCcChHHHHhhcCCCCchHH-HHH-HhhccceeE
Q 018867 299 MRLMSLVDLGSNE-SGQIPYGLIKDTLQVYFLTFL-LLD-LWYGLFVVN 344 (349)
Q Consensus 299 irLLtL~~La~~~-~r~isy~~Ia~~l~i~~~eve-~id-~i~~~~~~~ 344 (349)
..|..++.++..+ ...+|-++||+.+++|..-+. +++ -.++|+|++
T Consensus 9 ~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~ 57 (132)
T TIGR00738 9 YALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVES 57 (132)
T ss_pred HHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 3444455555322 448999999999999988764 333 345566654
No 55
>KOG1059 consensus Vesicle coat complex AP-3, delta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.96 E-value=6.4e+02 Score=27.64 Aligned_cols=139 Identities=17% Similarity=0.221 Sum_probs=75.6
Q ss_pred hhhHHHHHHHHHhhccC--CchhHHHHHHHHHHHHcCCCcchhhhhHHhHHHHHhhcCCCHHHHHHHHHHHHHHHHHhcc
Q 018867 115 PAMRLKILFNLYNLLEN--PYSRFFVYMKALNLAVNGKVTEHIIPSFKKIDSFLKEWNIDIKDKRALFLGIANVLKESRS 192 (349)
Q Consensus 115 ~~~rl~~L~~Lfn~l~~--~~~r~~v~~~il~la~~~~~~~~l~~~l~~~~~~L~~w~~~~~~~~~~y~~~a~~l~~~~~ 192 (349)
|.++--+-..+|+.++. |+.|-+.-+.+..+.- +=.+.+++.+..+.+-|+ +-++.+..+--.++++.-++...
T Consensus 139 pdLARDLa~Dv~tLL~sskpYvRKkAIl~lykvFL--kYPeAlr~~FprL~EkLe--DpDp~V~SAAV~VICELArKnPk 214 (877)
T KOG1059|consen 139 PDLARDLADDVFTLLNSSKPYVRKKAILLLYKVFL--KYPEALRPCFPRLVEKLE--DPDPSVVSAAVSVICELARKNPQ 214 (877)
T ss_pred chhhHHHHHHHHHHHhcCchHHHHHHHHHHHHHHH--hhhHhHhhhHHHHHHhcc--CCCchHHHHHHHHHHHHHhhCCc
Confidence 44444555778888875 4444221111111111 125778888888877777 77888888888999998886544
Q ss_pred ChH----HHHHHHHHHhcccCCCCCCChhHHHHHHHHHHHHHh-cCCCeeeec-CCCChhhhhcccCCCchhHHHHHHHH
Q 018867 193 SSK----DSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFV-KSPDMFQCD-LLDMPAIGQLENDAKYASVYQLLKIF 266 (349)
Q Consensus 193 ~~~----~~y~~~l~yL~~~~~~~~~~~~e~~~~A~~li~~aL-~~p~iy~f~-LL~~p~v~~L~~~~~~~~l~~LL~if 266 (349)
+|- .||+.+. |.+..=. ..+++.-+= +.|--=..| =|.-|...-+++|..-+-+|+=+...
T Consensus 215 nyL~LAP~ffkllt----tSsNNWm---------LIKiiKLF~aLtplEPRLgKKLieplt~li~sT~AmSLlYECvNTV 281 (877)
T KOG1059|consen 215 NYLQLAPLFYKLLV----TSSNNWV---------LIKLLKLFAALTPLEPRLGKKLIEPITELMESTVAMSLLYECVNTV 281 (877)
T ss_pred ccccccHHHHHHHh----ccCCCee---------hHHHHHHHhhccccCchhhhhhhhHHHHHHHhhHHHHHHHHHHHHh
Confidence 442 2444433 3322111 233333211 111111234 23234444556554456788888888
Q ss_pred hcCC
Q 018867 267 LTQR 270 (349)
Q Consensus 267 ~~G~ 270 (349)
.+|+
T Consensus 282 Va~s 285 (877)
T KOG1059|consen 282 VAVS 285 (877)
T ss_pred eeeh
Confidence 8884
No 56
>PF14764 SPG48: AP-5 complex subunit, vesicle trafficking
Probab=21.52 E-value=7.3e+02 Score=25.54 Aligned_cols=125 Identities=21% Similarity=0.174 Sum_probs=72.8
Q ss_pred HHHHHHHHHhhccCCchhHHHHHHHHHHHHcCCCc--chhhhhHH-hHHHHHhhcCCC---HHHHHHHHHHHHHHHHHhc
Q 018867 118 RLKILFNLYNLLENPYSRFFVYMKALNLAVNGKVT--EHIIPSFK-KIDSFLKEWNID---IKDKRALFLGIANVLKESR 191 (349)
Q Consensus 118 rl~~L~~Lfn~l~~~~~r~~v~~~il~la~~~~~~--~~l~~~l~-~~~~~L~~w~~~---~~~~~~~y~~~a~~l~~~~ 191 (349)
.+..+..+|+++..+....++++.++++--.+|.. -...+.++ -..+.+.+-=-+ .-+--.|.+...+.+....
T Consensus 28 ~~p~ik~l~~R~~~~~~~~~~lL~i~qFfL~hge~~~~d~e~~~~~~F~~~l~~~f~dp~lA~e~~~F~~~N~~~L~~~~ 107 (459)
T PF14764_consen 28 VFPCIKRLFGRLASDLSSARVLLPIAQFFLNHGEAAAVDSEPVLQHFFTSVLSRLFHDPFLAFETLQFCRDNLKLLCSNT 107 (459)
T ss_pred HHHHHHHHHHHHhcCccchHHHHHHHHHHHccChHhhcChHHHHHHHHHHhhHHhcCChHHHHHHHHHHHHHHHHHcccc
Confidence 45677888887765555678888899888877754 22223332 111122222111 2334445555555555433
Q ss_pred cChHHHHHHHHHHhcccCCCCCCChhHHHHHHHHHHHHHhcCCCeee--ec-CCCChhhh-hc
Q 018867 192 SSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQ--CD-LLDMPAIG-QL 250 (349)
Q Consensus 192 ~~~~~~y~~~l~yL~~~~~~~~~~~~e~~~~A~~li~~aL~~p~iy~--f~-LL~~p~v~-~L 250 (349)
+-+..|+-+++|+|+-.+..- .+| =++ +.=++.+|+.+- |- ||++|.+. +|
T Consensus 108 ~~~~~~FP~llK~lAWn~~~l---~~e----Fv~-LLP~Li~~~Ta~EvlH~LLDLPcLtaaL 162 (459)
T PF14764_consen 108 SIFPQYFPNLLKFLAWNSPSL---VSE----FVD-LLPALISPGTAVEVLHSLLDLPCLTAAL 162 (459)
T ss_pred chHhHhchHHHHHHHcCcHHH---HHH----HHH-HhHHHcCCCcHHHHHHHHHhHHHHHHHH
Confidence 556789999999999754311 111 223 334677888765 55 88999873 44
No 57
>COG1017 Hmp Hemoglobin-like flavoprotein [Energy production and conversion]
Probab=21.11 E-value=5.2e+02 Score=22.29 Aligned_cols=52 Identities=19% Similarity=0.158 Sum_probs=36.7
Q ss_pred HHHHHhhccCC--chhHHHHHHHHHHHHcCCCcchhhhhHHhHHHHHhhcCCCH
Q 018867 122 LFNLYNLLENP--YSRFFVYMKALNLAVNGKVTEHIIPSFKKIDSFLKEWNIDI 173 (349)
Q Consensus 122 L~~Lfn~l~~~--~~r~~v~~~il~la~~~~~~~~l~~~l~~~~~~L~~w~~~~ 173 (349)
|.++||+-... .++--+..+++.+|+.-++++.+.+.++.+..-=-+.++-+
T Consensus 39 l~niFN~~nQ~~G~Q~~aLA~ai~ayA~nIdnl~~l~~~v~rIa~KHvsl~I~p 92 (150)
T COG1017 39 LKNIFNMANQKNGDQPKALANAILAYAKNIDNLEALLPVVERIAHKHVSLQIKP 92 (150)
T ss_pred HHHHHhHhhhcccccHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhcCCCh
Confidence 34788876642 45566677899999999999999998887655444455543
No 58
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=21.01 E-value=2e+02 Score=28.42 Aligned_cols=31 Identities=16% Similarity=0.214 Sum_probs=24.6
Q ss_pred HHHHHHHHhcCCCChhHHHHHHHHHHHHhhc
Q 018867 79 IFTVICNLVTKPESLDEVHEMTKLISGKIIQ 109 (349)
Q Consensus 79 ~~n~li~l~~~~~~~~~~~~lv~~l~~~v~~ 109 (349)
...++++++.++.++++++++++++.+++..
T Consensus 77 lvei~l~~~~~~~D~~~al~~Le~i~~~~~~ 107 (380)
T KOG2908|consen 77 LVEILLVVSEQISDKDEALEFLEKIIEKLKE 107 (380)
T ss_pred HHHHHHHHHHHhccHHHHHHHHHHHHHHHHh
Confidence 3346777788887899999999999988765
No 59
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=20.80 E-value=9.1e+02 Score=24.65 Aligned_cols=83 Identities=14% Similarity=0.122 Sum_probs=58.7
Q ss_pred hhHHHHHHHHhcCChhhHHHHHhhC-hhhhhhc--CCChHHHHHHHHHHHHhhhhhcCCCCcChHHHHhhcCCCCch--H
Q 018867 257 ASVYQLLKIFLTQRLDGYLEFQAGN-SALLKSY--GLVHEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQVYFLT--F 331 (349)
Q Consensus 257 ~~l~~LL~if~~G~l~~y~~~~~~~-~~~~~~~--~l~~~~l~~KirLLtL~~La~~~~r~isy~~Ia~~l~i~~~e--v 331 (349)
+.+.++|..|.++.+..-.....+. |.++=+. .=+.+.+-.|||-=+|+.--+ |-..++++.+|.+.+.+... -
T Consensus 306 Pqlr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~-py~s~~m~~mA~af~~sv~~le~ 384 (466)
T KOG0686|consen 306 PQLREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLS-PYSSADMSKMAEAFNTSVAILES 384 (466)
T ss_pred hHHHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcC-ccccchHHHHHHHhcccHHHHHH
Confidence 4788999999999988877666554 3222111 113678889999888888765 46689999999999999864 4
Q ss_pred HHHHHhhcc
Q 018867 332 LLLDLWYGL 340 (349)
Q Consensus 332 e~id~i~~~ 340 (349)
++..-|-.|
T Consensus 385 ~l~~LI~~~ 393 (466)
T KOG0686|consen 385 ELLELILEG 393 (466)
T ss_pred HHHHHHHcc
Confidence 455555444
No 60
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=20.56 E-value=90 Score=21.27 Aligned_cols=30 Identities=17% Similarity=0.088 Sum_probs=19.9
Q ss_pred HHHHhhhh-hcCCCCcChHHHHhhcCCCCchH
Q 018867 301 LMSLVDLG-SNESGQIPYGLIKDTLQVYFLTF 331 (349)
Q Consensus 301 LLtL~~La-~~~~r~isy~~Ia~~l~i~~~ev 331 (349)
+..++.+- .. +..+|-++||+.++|+.--|
T Consensus 2 ~~~il~~L~~~-~~~it~~eLa~~l~vS~rTi 32 (55)
T PF08279_consen 2 QKQILKLLLES-KEPITAKELAEELGVSRRTI 32 (55)
T ss_dssp HHHHHHHHHHT-TTSBEHHHHHHHCTS-HHHH
T ss_pred HHHHHHHHHHc-CCCcCHHHHHHHhCCCHHHH
Confidence 34444444 33 34599999999999997654
Done!