Query 027762
Match_columns 219
No_of_seqs 139 out of 241
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 14:47:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027762.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027762hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4011 Transcription initiati 100.0 6.9E-61 1.5E-65 432.8 11.0 189 12-219 15-223 (330)
2 PF04658 TAFII55_N: TAFII55 pr 100.0 4.2E-59 9.1E-64 390.1 13.8 141 19-162 1-161 (162)
3 cd08047 TAF7 TATA Binding Prot 100.0 1.6E-57 3.6E-62 378.7 13.1 148 20-169 1-162 (162)
4 COG5414 TATA-binding protein-a 100.0 3.7E-47 7.9E-52 343.6 3.4 162 11-179 64-241 (392)
5 PF03869 Arc: Arc-like DNA bin 58.5 6.9 0.00015 26.9 1.6 22 21-42 5-26 (50)
6 PF02767 DNA_pol3_beta_2: DNA 41.2 43 0.00093 25.7 3.9 45 27-78 68-112 (116)
7 KOG1180 Acyl-CoA synthetase [L 37.3 16 0.00035 37.3 1.1 42 61-102 483-525 (678)
8 PF14836 Ubiquitin_3: Ubiquiti 33.9 20 0.00043 27.9 0.9 28 126-158 12-39 (88)
9 PHA01513 mnt Mnt 31.2 40 0.00086 26.0 2.2 23 20-42 5-27 (82)
10 TIGR01624 LRP1_Cterm LRP1 C-te 29.4 54 0.0012 23.2 2.4 17 61-77 31-47 (50)
11 PRK13744 conjugal transfer pro 28.9 24 0.00053 26.5 0.6 14 116-129 17-30 (83)
12 TIGR00194 uvrC excinuclease AB 28.1 25 0.00054 35.4 0.7 63 73-137 373-442 (574)
13 PRK12582 acyl-CoA synthetase; 27.5 57 0.0012 31.6 3.0 16 87-102 447-462 (624)
14 PLN02330 4-coumarate--CoA liga 26.1 43 0.00093 31.5 1.9 40 61-102 388-427 (546)
15 PF05142 DUF702: Domain of unk 25.9 54 0.0012 28.0 2.3 17 62-78 133-149 (154)
16 PF09696 Ctf8: Ctf8; InterPro 25.6 2.2E+02 0.0047 22.9 5.6 31 58-88 54-85 (122)
17 PF08459 UvrC_HhH_N: UvrC Heli 24.9 8.5 0.00019 32.5 -2.7 62 75-137 4-72 (155)
18 KOG1176 Acyl-CoA synthetase [L 22.6 23 0.00049 35.3 -0.7 29 74-102 382-418 (537)
19 KOG1487 GTP-binding protein DR 22.5 1E+02 0.0022 29.3 3.6 45 64-108 95-145 (358)
20 PRK00558 uvrC excinuclease ABC 21.7 41 0.00088 33.9 0.9 64 73-137 374-444 (598)
21 PF11979 DUF3480: Domain of un 21.4 1.5E+02 0.0032 28.5 4.5 59 15-73 173-246 (356)
22 PRK14670 uvrC excinuclease ABC 21.1 37 0.00079 34.3 0.4 64 73-137 349-421 (574)
23 PRK01115 DNA polymerase slidin 20.7 2.3E+02 0.005 24.2 5.2 43 32-77 72-117 (247)
No 1
>KOG4011 consensus Transcription initiation factor TFIID, subunit TAF7 [Transcription]
Probab=100.00 E-value=6.9e-61 Score=432.85 Aligned_cols=189 Identities=39% Similarity=0.608 Sum_probs=163.8
Q ss_pred CCCCCCcccceeEEecCcchHHHHHHHHhcCCCCCCCCCceEEEecCCceEEEEECCeecceeeccCCeeeeeeeecCCc
Q 027762 12 NKFNRALMEEQFILRVPPSVAERIDRLLSENESSEEDKSLDLSFCEDGRSGTFVIGNDHFPVSLMDLPCVVESFKTYDDC 91 (219)
Q Consensus 12 ~~~~~p~iEeQfILRlPp~~A~~vr~~l~~~~~~~~~~~l~i~f~~D~R~~~v~i~~~~y~a~LVDLPcIVEs~KT~D~k 91 (219)
..+++|+||+||||||||+++.+++++++++. .+.+|+|.|++|+|+|+|+|||+.|+|+|||||||||||||+|+|
T Consensus 15 ~~ed~~e~EsqfILRvPp~~~~~v~~~~~~~~---~~~~l~i~~~~D~R~~vV~i~n~~l~akLvDLPtVvEs~KT~D~k 91 (330)
T KOG4011|consen 15 EAEDDPEMESQFILRVPPDIACRVDRAASEDG---DKDELSIKLKPDGRHAVVRINNQLLPAKLVDLPTVVESNKTLDNK 91 (330)
T ss_pred ccccchhhhhheeeecCHHHHHHHHHHhhccc---ccccceeeeccCCceeEEEECCEEccceeeccchhhhhhhccccc
Confidence 44888999999999999999999999988874 688999999999999999999999999999999999999999999
Q ss_pred ceEEeccccceEEecCC-----CCCCC-----------CcccccCCCCcccchhhhccccCCCCCChHHHHHHHHHHHHH
Q 027762 92 ALVKTADIGQMIMVREP-----GDSTP-----------DAVEYRHGLTPPMRDARKRRFRREPDLNPELVQRVEKDLLNI 155 (219)
Q Consensus 92 ~~yKtaDIsQMLvV~~~-----~d~~p-----------~~~~~pHGLTPPmknVRkRRFRK~~~~~~~~Ie~VEkel~~L 155 (219)
+|||||||||||||+.+ .+..| ..|.|||||||||||||||||||+.+.++-++.+||++|.+|
T Consensus 92 ~lyKtADIsQMLvc~~~~~e~ie~~~p~~~~k~~~~k~k~y~y~HGiTPPmKnvRkRRFRK~~~kk~~e~~eVEkevkrL 171 (330)
T KOG4011|consen 92 TLYKTADISQMLVCTEDVEEGIEDEDPDAARKKAKEKEKKYIYPHGITPPMKNVRKRRFRKTKKKKPMEVPEVEKEVKRL 171 (330)
T ss_pred cceeecchheeEEEecCccccccccChhhHHHhhhhhhhceecccCCCcchhHHHHHHhhhccccCCCchHHHHHHHHHH
Confidence 99999999999999988 44555 579999999999999999999999876677999999999999
Q ss_pred hc-CcCccccceeeecccccccccccccCCCCCCCCCCCCCCccccc---cCCCCCCCCCCcccCCCC
Q 027762 156 MT-GATVENADPEVNEQEEEGDGNARHANRKDAPSPQLKQPDIAEAG---ANTGAPARSDSDESDDSM 219 (219)
Q Consensus 156 L~-~~~ae~v~~e~v~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~ 219 (219)
|. +..|..|.|++|+..+-+... ..+...+ -..++++||++-++||++
T Consensus 172 Lr~D~eA~Sv~~eiv~e~e~~~~~----------------~ei~~~~~~~~~~~~~~~~e~~~~dde~ 223 (330)
T KOG4011|consen 172 LRADNEAVSVRWEIVDEDETSPDL----------------EEIEEQGNKPGDGAEEDRSESGDRDDEE 223 (330)
T ss_pred HhhhhhhhhhheeeeccccCCcch----------------hhHHhhcCCCCCcccccccccccCcchh
Confidence 98 899999999999988642211 1111111 136778888888888864
No 2
>PF04658 TAFII55_N: TAFII55 protein conserved region; InterPro: IPR006751 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. TAFII55 binds to TAFII250 and inhibits its acetyltransferase activity. The exact role of TAFII55 is currently unknown. The conserved region is situated towards the N-terminal of the protein [].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005669 transcription factor TFIID complex
Probab=100.00 E-value=4.2e-59 Score=390.05 Aligned_cols=141 Identities=41% Similarity=0.726 Sum_probs=123.0
Q ss_pred ccceeEEecCc-chHHHHHHHHhcCCCCCCCCCceEEEecCCceEEEEECCeecceeeccCCeeeeeeeecCCcceEEec
Q 027762 19 MEEQFILRVPP-SVAERIDRLLSENESSEEDKSLDLSFCEDGRSGTFVIGNDHFPVSLMDLPCVVESFKTYDDCALVKTA 97 (219)
Q Consensus 19 iEeQfILRlPp-~~A~~vr~~l~~~~~~~~~~~l~i~f~~D~R~~~v~i~~~~y~a~LVDLPcIVEs~KT~D~k~~yKta 97 (219)
||+|||||||+ ++|++||++|++|.... ..+|+|+| .|+|+|+|+|+|+.|+|+|||||||||||||+|+++|||||
T Consensus 1 ~E~q~ILR~p~~~~ad~lr~~i~~~~~~~-~~~I~~~~-~d~R~~~v~i~~~~y~a~LvDLP~IvEs~KT~D~k~~yKta 78 (162)
T PF04658_consen 1 IEEQFILRLPPGEDADRLREAIEEGDINE-KLDIDFKF-KDGRRAVVRIGGQIYSAKLVDLPCIVESHKTLDKKNFYKTA 78 (162)
T ss_pred CcceEEEecCChhHHHHHHHHHHcCCCCC-CceEEEec-CCCCEEEEEECCEEcceEEeecCceeeEEeecccCeEEEEe
Confidence 79999999999 89999999999997532 12445555 69999999999999999999999999999999999999999
Q ss_pred cccceEEecCCCC------------------CCCCcccccCCCCcccchhhhccccCCCCCChHHHHHHHHHHHHHhc-C
Q 027762 98 DIGQMIMVREPGD------------------STPDAVEYRHGLTPPMRDARKRRFRREPDLNPELVQRVEKDLLNIMT-G 158 (219)
Q Consensus 98 DIsQMLvV~~~~d------------------~~p~~~~~pHGLTPPmknVRkRRFRK~~~~~~~~Ie~VEkel~~LL~-~ 158 (219)
||||||||+++.. ..+..|+|||||||||||||||||||+... ..+|++||+||.+||+ |
T Consensus 79 DI~QMLiv~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~hGiTPP~knvrkRRFRk~~~~-~~~i~~vE~ev~~LL~~D 157 (162)
T PF04658_consen 79 DISQMLIVYEPIEDEEEAKETDLKEKKKNKEKEDKKFEWPHGITPPMKNVRKRRFRKRKKK-YREIPEVEKEVKRLLRED 157 (162)
T ss_pred ccceeEEEeccCCCcccccccccccccccccccccccCCCCCCChhhhhHHHhhhccCccc-cccHHHHHHHHHHHHhcc
Confidence 9999999998721 124578999999999999999999999653 5999999999999998 4
Q ss_pred cCcc
Q 027762 159 ATVE 162 (219)
Q Consensus 159 ~~ae 162 (219)
..|+
T Consensus 158 ~~A~ 161 (162)
T PF04658_consen 158 AEAV 161 (162)
T ss_pred hhhc
Confidence 5443
No 3
>cd08047 TAF7 TATA Binding Protein (TBP) Associated Factor 7 (TAF7) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 7 (TAF7) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving
Probab=100.00 E-value=1.6e-57 Score=378.71 Aligned_cols=148 Identities=44% Similarity=0.757 Sum_probs=130.3
Q ss_pred cceeEEecCcchHHHHHHHHhcCCCCCCCCCceEEEecCCceEEEEECCeecceeeccCCeeeeeeeecCCcceEEeccc
Q 027762 20 EEQFILRVPPSVAERIDRLLSENESSEEDKSLDLSFCEDGRSGTFVIGNDHFPVSLMDLPCVVESFKTYDDCALVKTADI 99 (219)
Q Consensus 20 EeQfILRlPp~~A~~vr~~l~~~~~~~~~~~l~i~f~~D~R~~~v~i~~~~y~a~LVDLPcIVEs~KT~D~k~~yKtaDI 99 (219)
|+||||||||++|++||++|++|..+.. .+.+.+..|+|+|+|+|+|+.|+|+|||||||||||||||+++|||||||
T Consensus 1 E~q~ILR~p~~~a~~vr~~i~~~~~~~~--~~~~~~~~d~R~~~v~v~~~~y~a~LvdLPtiiEs~KT~D~k~~yKtaDI 78 (162)
T cd08047 1 EEQFILRLPPDVADRLRKAIEEGDSNEK--LLSITLFEDSRRAVVRINGQKYPAKLVDLPTIIESHKTLDKKNLYKTADI 78 (162)
T ss_pred CCeEEEEcCcHHHHHHHHHHHcCCCccc--ccccccCCCCcEEEEEECCEEcceEEeecCceeeeeeccccCceEEecCh
Confidence 7999999999999999999999964321 13455667999999999999999999999999999999999999999999
Q ss_pred cceEEecCCCCCC-------------CCcccccCCCCcccchhhhccccCCCCCChHHHHHHHHHHHHHhc-CcCccccc
Q 027762 100 GQMIMVREPGDST-------------PDAVEYRHGLTPPMRDARKRRFRREPDLNPELVQRVEKDLLNIMT-GATVENAD 165 (219)
Q Consensus 100 sQMLvV~~~~d~~-------------p~~~~~pHGLTPPmknVRkRRFRK~~~~~~~~Ie~VEkel~~LL~-~~~ae~v~ 165 (219)
||||+|+++.+.. +..|+|||||||||+|||+|||||+......++++||++|.+||+ +..|..+.
T Consensus 79 ~QMliv~~~~~~~~~~~~~~~~~~~~~~~~~~~hGLTPP~~~vrkRrfrk~~~~~~~~i~~vEkev~~ll~~d~~a~~~~ 158 (162)
T cd08047 79 SQMLIVYEPDDSEKEAKEAKLDKKDKPKKFEYPHGLTPPMKNVRKRRFRKTPSKKIAEIEEVEKEVKRLLKEDTEAVSVE 158 (162)
T ss_pred hhEEEEecCCCchhhhhhccccccccccccccCCCCCcCchhhhhcccccccccccchHHHHHHHHHHHHHhhhhhccee
Confidence 9999999886531 467899999999999999999999976666679999999999998 57777777
Q ss_pred eeee
Q 027762 166 PEVN 169 (219)
Q Consensus 166 ~e~v 169 (219)
+|++
T Consensus 159 ~e~~ 162 (162)
T cd08047 159 YEVI 162 (162)
T ss_pred eeeC
Confidence 7763
No 4
>COG5414 TATA-binding protein-associated factor [Transcription]
Probab=100.00 E-value=3.7e-47 Score=343.62 Aligned_cols=162 Identities=30% Similarity=0.499 Sum_probs=144.4
Q ss_pred CCCCCCCcccceeEEecCcch-HHHHHHHHhcCCCCCCCCCceEEEecCCceEEEEECCeecceeeccCCeeeeeeeecC
Q 027762 11 GNKFNRALMEEQFILRVPPSV-AERIDRLLSENESSEEDKSLDLSFCEDGRSGTFVIGNDHFPVSLMDLPCVVESFKTYD 89 (219)
Q Consensus 11 ~~~~~~p~iEeQfILRlPp~~-A~~vr~~l~~~~~~~~~~~l~i~f~~D~R~~~v~i~~~~y~a~LVDLPcIVEs~KT~D 89 (219)
+.-++||+||+|||||+||++ +++|++++.+| .+.+|+|+|+ |.|+++|++||+.|+|+||||||||||.||+|
T Consensus 64 SD~EdD~~iE~q~ILRl~p~~~~e~V~~~~esG----~~s~I~ik~k-d~R~aVvt~N~~~Y~ailVdLPciIEsnKS~D 138 (392)
T COG5414 64 SDIEDDPLIEQQFILRLHPSIQIEHVVDLGESG----DYSGITIKIK-DDRSAVVTHNNKKYPAILVDLPCIIESNKSMD 138 (392)
T ss_pred ccccccchhhhceeeecCCccchHHHHHHhhcC----CccCceEEec-cCceEEEEECCcccceeEeecceeEecccccc
Confidence 445789999999999999985 89999999997 5778999999 89999999999999999999999999999999
Q ss_pred CcceEEeccccceEE----ecCCCCCC------CCcccccCCCCcccchhhhccccCCCCCChHHHHHHHHHHHHHhc-C
Q 027762 90 DCALVKTADIGQMIM----VREPGDST------PDAVEYRHGLTPPMRDARKRRFRREPDLNPELVQRVEKDLLNIMT-G 158 (219)
Q Consensus 90 ~k~~yKtaDIsQMLv----V~~~~d~~------p~~~~~pHGLTPPmknVRkRRFRK~~~~~~~~Ie~VEkel~~LL~-~ 158 (219)
+|++||+|||||||| |+.+.... ...|.|+|||||||+|||.|||||+ .++.+|+.||++|.+||+ +
T Consensus 139 ~k~~~K~aDisqmlvA~E~v~hensflN~~lk~~~~y~y~hGlspPl~~Vr~rRFRkk--~s~~eIe~VEk~Vd~LL~~D 216 (392)
T COG5414 139 SKQHYKVADISQMLVALEAVYHENSFLNKHLKKEREYYYLHGLSPPLKYVRARRFRKK--SSKIEIEEVEKKVDDLLEKD 216 (392)
T ss_pred hhhhHhHhhHHHHHHHHhhhcccchhhHHHHHHHhhhhccccCCchhHHHHHHHHHhh--cCcchHHHHHHHHHHHHHHh
Confidence 999999999999999 44432222 1268999999999999999999999 778889999999999998 8
Q ss_pred cCccccceeeecccc----cccccc
Q 027762 159 ATVENADPEVNEQEE----EGDGNA 179 (219)
Q Consensus 159 ~~ae~v~~e~v~~~e----~~~~~~ 179 (219)
..|+.|.++++++.+ +-.++|
T Consensus 217 ~~Aesvs~~l~d~~elAR~~~vs~~ 241 (392)
T COG5414 217 MKAESVSVVLKDEKELARQERVSSW 241 (392)
T ss_pred hhhhhhHHHHHhHHHHhhhhhhhhh
Confidence 999999999999987 345555
No 5
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=58.50 E-value=6.9 Score=26.94 Aligned_cols=22 Identities=36% Similarity=0.603 Sum_probs=17.7
Q ss_pred ceeEEecCcchHHHHHHHHhcC
Q 027762 21 EQFILRVPPSVAERIDRLLSEN 42 (219)
Q Consensus 21 eQfILRlPp~~A~~vr~~l~~~ 42 (219)
.||-||||.++.+.|+..=...
T Consensus 5 ~~f~lRlP~~l~~~lk~~A~~~ 26 (50)
T PF03869_consen 5 PQFNLRLPEELKEKLKERAEEN 26 (50)
T ss_dssp EEEEEECEHHHHHHHHHHHHHT
T ss_pred CceeeECCHHHHHHHHHHHHHh
Confidence 5999999999999988654443
No 6
>PF02767 DNA_pol3_beta_2: DNA polymerase III beta subunit, central domain; InterPro: IPR022637 This entry describes the central domain of the beta chain of DNA polymerase III. This is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication from an RNA primer, nucleotide triphosphate (dNTP) residues being added to the 5'-end of the growing DNA chain.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 3T0P_B 3P16_A 3RB9_B 2AWA_C 1VPK_A 2AVT_B 2XUR_B 3Q4K_A 3BEP_A 3D1G_A ....
Probab=41.19 E-value=43 Score=25.70 Aligned_cols=45 Identities=22% Similarity=0.424 Sum_probs=33.7
Q ss_pred cCcchHHHHHHHHhcCCCCCCCCCceEEEecCCceEEEEECCeecceeeccC
Q 027762 27 VPPSVAERIDRLLSENESSEEDKSLDLSFCEDGRSGTFVIGNDHFPVSLMDL 78 (219)
Q Consensus 27 lPp~~A~~vr~~l~~~~~~~~~~~l~i~f~~D~R~~~v~i~~~~y~a~LVDL 78 (219)
+|...+..|.+++... ...+.|.+. +.++.|.+++..+..+|+|-
T Consensus 68 Ip~k~l~~l~k~l~~~-----~~~v~i~~~--~~~i~f~~~~~~~~srli~g 112 (116)
T PF02767_consen 68 IPAKALKELKKLLSDE-----DEEVEISIS--DNQIIFKFDNIEITSRLIDG 112 (116)
T ss_dssp EEHHHHHHHHHHSSTT-----SSEEEEEEE--SSEEEEEESSEEEEEE-BSS
T ss_pred EechHHHHHhhhcccC-----CceEEEEEc--CCEEEEEECCEEEEEEEecc
Confidence 4666777888877662 235777765 78899999999999999874
No 7
>KOG1180 consensus Acyl-CoA synthetase [Lipid transport and metabolism]
Probab=37.32 E-value=16 Score=37.35 Aligned_cols=42 Identities=24% Similarity=0.391 Sum_probs=28.4
Q ss_pred eEEEEECCeecceeeccCC-eeeeeeeecCCcceEEeccccce
Q 027762 61 SGTFVIGNDHFPVSLMDLP-CVVESFKTYDDCALVKTADIGQM 102 (219)
Q Consensus 61 ~~~v~i~~~~y~a~LVDLP-cIVEs~KT~D~k~~yKtaDIsQM 102 (219)
+|.+.|+|.....=-+.=| -.=|+++..|.+.||+||||++.
T Consensus 483 rGEI~i~G~~vt~gY~kn~ekT~e~ft~~~G~~WF~TGDIGe~ 525 (678)
T KOG1180|consen 483 RGEILIGGPNVTMGYYKNEEKTKEDFTVEDGQRWFRTGDIGEF 525 (678)
T ss_pred CceEEecCCccChhhhCChhhhhhhceecCCcEEEecccccee
Confidence 8888888755432111111 13477888899999999999874
No 8
>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A.
Probab=33.94 E-value=20 Score=27.86 Aligned_cols=28 Identities=14% Similarity=0.375 Sum_probs=22.8
Q ss_pred cchhhhccccCCCCCChHHHHHHHHHHHHHhcC
Q 027762 126 MRDARKRRFRREPDLNPELVQRVEKDLLNIMTG 158 (219)
Q Consensus 126 mknVRkRRFRK~~~~~~~~Ie~VEkel~~LL~~ 158 (219)
|.++..+.|.|+ +.|..||+++.+++.-
T Consensus 12 l~~~~t~~FSk~-----DTI~~v~~~~rklf~i 39 (88)
T PF14836_consen 12 LQSVLTKQFSKT-----DTIGFVEKEMRKLFNI 39 (88)
T ss_dssp CCEEEEEEE-TT-----SBHHHHHHHHHHHCT-
T ss_pred cccHhHhhcccc-----ChHHHHHHHHHHHhCC
Confidence 678888999998 7788999999999874
No 9
>PHA01513 mnt Mnt
Probab=31.23 E-value=40 Score=25.98 Aligned_cols=23 Identities=30% Similarity=0.541 Sum_probs=17.7
Q ss_pred cceeEEecCcchHHHHHHHHhcC
Q 027762 20 EEQFILRVPPSVAERIDRLLSEN 42 (219)
Q Consensus 20 EeQfILRlPp~~A~~vr~~l~~~ 42 (219)
.-||-||||.++-+.|+..-..+
T Consensus 5 ~~qf~LRLP~eLk~rL~~aA~~n 27 (82)
T PHA01513 5 DPQFNLRLPYELKEKLKQRAKAN 27 (82)
T ss_pred CcceeeeCCHHHHHHHHHHHHHh
Confidence 35899999999988887654443
No 10
>TIGR01624 LRP1_Cterm LRP1 C-terminal domain. This model represents a tightly conserved small domain found in LRP1 and related plant proteins. This family also contains a well-conserved putative zinc finger domain (TIGR01623). The rest of the sequence of most members consists of highly divergent, low-complexity sequence.
Probab=29.38 E-value=54 Score=23.17 Aligned_cols=17 Identities=35% Similarity=0.401 Sum_probs=15.1
Q ss_pred eEEEEECCeecceeecc
Q 027762 61 SGTFVIGNDHFPVSLMD 77 (219)
Q Consensus 61 ~~~v~i~~~~y~a~LVD 77 (219)
...|.|+|..|.|.|.|
T Consensus 31 Qt~V~IgGHvFkGiLyD 47 (50)
T TIGR01624 31 QATVTIGGHVFKGFLHD 47 (50)
T ss_pred EEEEEECceEEeeEEec
Confidence 35799999999999987
No 11
>PRK13744 conjugal transfer protein TrbG; Provisional
Probab=28.93 E-value=24 Score=26.53 Aligned_cols=14 Identities=43% Similarity=0.930 Sum_probs=12.0
Q ss_pred ccccCCCCcccchh
Q 027762 116 VEYRHGLTPPMRDA 129 (219)
Q Consensus 116 ~~~pHGLTPPmknV 129 (219)
+.|-.||||||-.|
T Consensus 17 vlyesgitpplcev 30 (83)
T PRK13744 17 VLYESGITPPLCEV 30 (83)
T ss_pred EeeecCCCCccccc
Confidence 57889999999766
No 12
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=28.12 E-value=25 Score=35.39 Aligned_cols=63 Identities=25% Similarity=0.470 Sum_probs=48.6
Q ss_pred eeeccCCeeeeeeeecCCcceEEeccccceEEecCCCCCCCCcc-cc-cCCCCcc-----cchhhhccccCC
Q 027762 73 VSLMDLPCVVESFKTYDDCALVKTADIGQMIMVREPGDSTPDAV-EY-RHGLTPP-----MRDARKRRFRRE 137 (219)
Q Consensus 73 a~LVDLPcIVEs~KT~D~k~~yKtaDIsQMLvV~~~~d~~p~~~-~~-pHGLTPP-----mknVRkRRFRK~ 137 (219)
+.++.|+++ ...-.+|..++.=|.=|+-| ||++.+.+....| .| -++++.| |+-|-.|||++.
T Consensus 373 ~~~l~L~~~-~rIE~fDiSh~~G~~~V~sm-Vvf~~G~~~k~~YR~f~i~~~~~~dDya~m~Evl~RR~~r~ 442 (574)
T TIGR00194 373 ASLLNLPKI-KRIEIFDISHIDGSQTVGSM-VVFEDGKPLKASYRRYNINSITGGDDYAAMREVLRRRYSSI 442 (574)
T ss_pred HHHhCcCCC-CEEEEEECCccCCCcceEEE-EEEeCCccChhhCCeeecCCCCCCCHHHHHHHHHHHHHhhh
Confidence 578899988 88899999999999999999 6777777765443 12 2245554 888999999773
No 13
>PRK12582 acyl-CoA synthetase; Provisional
Probab=27.46 E-value=57 Score=31.62 Aligned_cols=16 Identities=13% Similarity=0.436 Sum_probs=12.5
Q ss_pred ecCCcceEEeccccce
Q 027762 87 TYDDCALVKTADIGQM 102 (219)
Q Consensus 87 T~D~k~~yKtaDIsQM 102 (219)
.++...||+|||++.+
T Consensus 447 ~f~~dgw~~TGDlg~~ 462 (624)
T PRK12582 447 AFDEEGFYRLGDAARF 462 (624)
T ss_pred hcCccCCccccceEEe
Confidence 4555679999999876
No 14
>PLN02330 4-coumarate--CoA ligase-like 1
Probab=26.12 E-value=43 Score=31.51 Aligned_cols=40 Identities=18% Similarity=0.228 Sum_probs=21.8
Q ss_pred eEEEEECCeecceeeccCCeeeeeeeecCCcceEEeccccce
Q 027762 61 SGTFVIGNDHFPVSLMDLPCVVESFKTYDDCALVKTADIGQM 102 (219)
Q Consensus 61 ~~~v~i~~~~y~a~LVDLPcIVEs~KT~D~k~~yKtaDIsQM 102 (219)
.|.+.+.|.....-.++-|.-. .+++|...||+|||++.+
T Consensus 388 ~Gel~v~g~~~~~gy~~~~~~~--~~~~~~~g~~~TGD~~~~ 427 (546)
T PLN02330 388 PGELCVRSQCVMQGYYNNKEET--DRTIDEDGWLHTGDIGYI 427 (546)
T ss_pred ceEEEEecchhhhhhccCccch--hhhccCCCceecccEEEE
Confidence 3555555433322223333222 245677789999998754
No 15
>PF05142 DUF702: Domain of unknown function (DUF702) ; InterPro: IPR007818 This is a family of plant proteins of unknown function.
Probab=25.88 E-value=54 Score=28.05 Aligned_cols=17 Identities=29% Similarity=0.296 Sum_probs=15.3
Q ss_pred EEEEECCeecceeeccC
Q 027762 62 GTFVIGNDHFPVSLMDL 78 (219)
Q Consensus 62 ~~v~i~~~~y~a~LVDL 78 (219)
.+|.|+|..|.|.|.|-
T Consensus 133 TaV~IGGHVFKGiLYDq 149 (154)
T PF05142_consen 133 TAVNIGGHVFKGILYDQ 149 (154)
T ss_pred EeEEECCEEeeeeeecc
Confidence 47999999999999983
No 16
>PF09696 Ctf8: Ctf8; InterPro: IPR018607 Ctf8 (chromosome transmissions fidelity 8) is a component of the Ctf18 RFC-like complex which is a DNA clamp loader involved in sister chromatid cohesion.
Probab=25.58 E-value=2.2e+02 Score=22.87 Aligned_cols=31 Identities=13% Similarity=0.131 Sum_probs=27.2
Q ss_pred CCceEEEEEC-CeecceeeccCCeeeeeeeec
Q 027762 58 DGRSGTFVIG-NDHFPVSLMDLPCVVESFKTY 88 (219)
Q Consensus 58 D~R~~~v~i~-~~~y~a~LVDLPcIVEs~KT~ 88 (219)
++.++.++|| ++.+.|+.+.|+.=+=.++--
T Consensus 54 ~~~~~~L~IG~~q~L~Gkv~kL~kPLaVLrk~ 85 (122)
T PF09696_consen 54 WMKRVTLYIGKHQRLEGKVVKLKKPLAVLRKR 85 (122)
T ss_pred CCCeEEEEECCCEEEEEEEeccCCCEEEEEEc
Confidence 6889999999 999999999999877777554
No 17
>PF08459 UvrC_HhH_N: UvrC Helix-hairpin-helix N-terminal; InterPro: IPR001162 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. Proteins that contain the UvrC homology region 1, IPR000305 from INTERPRO, are listed below: Prokaryotic UvrC proteins. Bacteriophage T4 END2 protein. Small subunit of ribonucleotide reductase enzyme. T4 TEV1 protein. Endonuclease specific to the thymidylate synthase (td) gene splice junction. Found in putative intron-homing endonucleases encoded by group I introns of fungi and phage. Mycobacterium hypothetical protein Y002. Exonuclease by similarity. Bacillus subtilis hypothetical protein YURQ. ; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3C65_A 2NRZ_A 2NRR_A 2NRX_A 2NRV_A 2NRT_A 2NRW_A.
Probab=24.88 E-value=8.5 Score=32.46 Aligned_cols=62 Identities=24% Similarity=0.452 Sum_probs=38.0
Q ss_pred eccCCeeeeeeeecCCcceEEeccccceEEecCCCCCCCCcc-ccc-CCCCcc-----cchhhhccccCC
Q 027762 75 LMDLPCVVESFKTYDDCALVKTADIGQMIMVREPGDSTPDAV-EYR-HGLTPP-----MRDARKRRFRRE 137 (219)
Q Consensus 75 LVDLPcIVEs~KT~D~k~~yKtaDIsQMLvV~~~~d~~p~~~-~~p-HGLTPP-----mknVRkRRFRK~ 137 (219)
++.||.+..-.--+|..++.-+.=|+-| ||++.+.+....| .|. .+.+.+ |+-|-.|||++.
T Consensus 4 ~L~L~~~P~rIE~fDiSh~~G~~~Vgs~-Vvf~~G~~~k~~YR~f~i~~~~~~dDy~~M~Evl~RR~~~~ 72 (155)
T PF08459_consen 4 LLGLPKLPRRIECFDISHIQGSDTVGSM-VVFENGKPDKSEYRRFNIKTVDGGDDYAAMREVLTRRFKRL 72 (155)
T ss_dssp HCTSSS--SEEEEEEEEECTTTCEEEEE-EEEETTEE-GGG-EEEEEE--STT-HHHHHHHHHHHHHCCC
T ss_pred hhCCCCCCCEEEEEECcccCCcccEEEE-EEEECCccChhhCceEecCCCCCCcHHHHHHHHHHHHHhcc
Confidence 4556655555555789999888889888 6666666554433 121 234444 888889999875
No 18
>KOG1176 consensus Acyl-CoA synthetase [Lipid transport and metabolism]
Probab=22.62 E-value=23 Score=35.30 Aligned_cols=29 Identities=24% Similarity=0.473 Sum_probs=20.5
Q ss_pred eeccCCeeeeee--------eecCCcceEEeccccce
Q 027762 74 SLMDLPCVVESF--------KTYDDCALVKTADIGQM 102 (219)
Q Consensus 74 ~LVDLPcIVEs~--------KT~D~k~~yKtaDIsQM 102 (219)
..+.-|+|...| .++|+..||+|||||=+
T Consensus 382 I~vrg~~imkGY~~NpeaT~~~~~~~GW~~TGDiGy~ 418 (537)
T KOG1176|consen 382 ICVRGPQVMKGYLKNPEATKEAFDDDGWFHTGDLGYF 418 (537)
T ss_pred EEEECcccchhhcCChHHHHhhcccCCccccCceEEE
Confidence 445555565554 38888899999999743
No 19
>KOG1487 consensus GTP-binding protein DRG1 (ODN superfamily) [Signal transduction mechanisms]
Probab=22.54 E-value=1e+02 Score=29.27 Aligned_cols=45 Identities=18% Similarity=0.242 Sum_probs=33.9
Q ss_pred EEECCee-cce---eeccCCeeeeeeeecC--CcceEEeccccceEEecCC
Q 027762 64 FVIGNDH-FPV---SLMDLPCVVESFKTYD--DCALVKTADIGQMIMVREP 108 (219)
Q Consensus 64 v~i~~~~-y~a---~LVDLPcIVEs~KT~D--~k~~yKtaDIsQMLvV~~~ 108 (219)
.+|.|.. |.| -|.|||-|||.-|-=- .++..-+|--|.+|++.-+
T Consensus 95 ~~vpG~~~y~gaKiqlldlpgiiegakdgkgrg~qviavartcnli~~vld 145 (358)
T KOG1487|consen 95 TTVPGVIRYKGAKIQLLDLPGIIEGAKDGKGRGKQVIAVARTCNLIFIVLD 145 (358)
T ss_pred EEecceEeccccceeeecCcchhcccccCCCCccEEEEEeecccEEEEEee
Confidence 4566665 654 6899999999998544 3679999999998876543
No 20
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=21.72 E-value=41 Score=33.93 Aligned_cols=64 Identities=28% Similarity=0.418 Sum_probs=45.3
Q ss_pred eeeccCCeeeeeeeecCCcceEEeccccceEEecCCCCCCCCcc-cc-cCCCCcc-----cchhhhccccCC
Q 027762 73 VSLMDLPCVVESFKTYDDCALVKTADIGQMIMVREPGDSTPDAV-EY-RHGLTPP-----MRDARKRRFRRE 137 (219)
Q Consensus 73 a~LVDLPcIVEs~KT~D~k~~yKtaDIsQMLvV~~~~d~~p~~~-~~-pHGLTPP-----mknVRkRRFRK~ 137 (219)
+.++.||......--+|..++.=+.=|+-| ||++.+.+....| .| -+++++| |+-|-.|||++-
T Consensus 374 ~~~l~l~~~p~rIE~fDiSh~~G~~~V~sm-Vvf~~G~~~k~~YR~f~i~~~~~~dDya~m~Evl~RR~~~~ 444 (598)
T PRK00558 374 AELLGLPEPPYRIECFDISHIQGTATVASM-VVFEDGGPDKSEYRRYNIKGVTGGDDYAAMREVLTRRYSRL 444 (598)
T ss_pred HHHhCCCCCCCEEEEEECCccCCCcceEEE-EEEECCccChhhCCeeecCCCCCCCHHHHHHHHHHHHhhcc
Confidence 466777655555556799999999999999 6777777765443 12 2245555 889999999874
No 21
>PF11979 DUF3480: Domain of unknown function (DUF3480); InterPro: IPR022557 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 350 to 362 amino acids in length. This domain is found C-terminal to PF01363 from PFAM.
Probab=21.38 E-value=1.5e+02 Score=28.55 Aligned_cols=59 Identities=17% Similarity=0.357 Sum_probs=40.9
Q ss_pred CCCcccceeEEecCcchHHHHHHHHhcCCCC--------CCC---CCceEEEecCCceEE----EEECCeecce
Q 027762 15 NRALMEEQFILRVPPSVAERIDRLLSENESS--------EED---KSLDLSFCEDGRSGT----FVIGNDHFPV 73 (219)
Q Consensus 15 ~~p~iEeQfILRlPp~~A~~vr~~l~~~~~~--------~~~---~~l~i~f~~D~R~~~----v~i~~~~y~a 73 (219)
...-+|....+|++++--+.||++|++...- +.. ..+.|+|..+...+. --|+|+.+.+
T Consensus 173 KsSIVEDGlmVQi~~e~m~~Lr~ALr~~kDf~I~cg~~d~~~~~~e~V~i~Wv~~d~~~n~gv~SpIDg~sleg 246 (356)
T PF11979_consen 173 KSSIVEDGLMVQITPETMESLRQALREMKDFTITCGKVDAEDSQVEYVDIQWVDDDENFNKGVISPIDGKSLEG 246 (356)
T ss_pred cceEEeeeeEEEecHHHHHHHHHHHHhCCCeEEecCCcccccccccEEEEEEecCCcccCCCcccCCCCceecC
Confidence 3456899999999999999999999987520 111 247788875544432 2366777754
No 22
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=21.14 E-value=37 Score=34.30 Aligned_cols=64 Identities=13% Similarity=0.299 Sum_probs=44.5
Q ss_pred eeeccCCeeeeeeeecCCcceEEeccccceEEecCCCCCCCCcc-ccc-CCCCcc-------cchhhhccccCC
Q 027762 73 VSLMDLPCVVESFKTYDDCALVKTADIGQMIMVREPGDSTPDAV-EYR-HGLTPP-------MRDARKRRFRRE 137 (219)
Q Consensus 73 a~LVDLPcIVEs~KT~D~k~~yKtaDIsQMLvV~~~~d~~p~~~-~~p-HGLTPP-------mknVRkRRFRK~ 137 (219)
+.++.||+.-...-.+|..++.=|.=|+-| ||++.+.+..+.| .|. .|++.+ |+-|-.|||++.
T Consensus 349 ~~~L~L~~~p~rIE~fDiSh~~G~~~V~sm-Vvf~~G~~~k~~YRkf~ik~~~~~~~DD~a~M~Evl~RR~~r~ 421 (574)
T PRK14670 349 KIILEMDKLPKTIEGFDIAHLNGQKTVASL-VTFKMGKPFKDGYRVYKINSLLKGEIDDFKAIKEVISRRYSKL 421 (574)
T ss_pred HHHhCcCCCCCeEEEEECCccCCCCceEEE-EEEECCccChhhCCeeeccCCCCCCCCHHHHHHHHHHHHHhhc
Confidence 467777765555666799999999999999 6666677665443 121 234333 889999999873
No 23
>PRK01115 DNA polymerase sliding clamp; Validated
Probab=20.69 E-value=2.3e+02 Score=24.22 Aligned_cols=43 Identities=21% Similarity=0.464 Sum_probs=28.3
Q ss_pred HHHHHHHHhcCCCCCCCCCceEEEecCCceEEEEECC---eecceeecc
Q 027762 32 AERIDRLLSENESSEEDKSLDLSFCEDGRSGTFVIGN---DHFPVSLMD 77 (219)
Q Consensus 32 A~~vr~~l~~~~~~~~~~~l~i~f~~D~R~~~v~i~~---~~y~a~LVD 77 (219)
+..|.++++.-. .++.+.|.+..++.+..|.+++ ..|..+|+|
T Consensus 72 l~~l~~il~~~~---~~~~v~i~~~~~~~~l~~~~~~~~~~~~~~~Lie 117 (247)
T PRK01115 72 LEDLKKILKRAK---KGDKLELELDEEENKLKITFGGEKTREFSLPLLD 117 (247)
T ss_pred HHHHHHHHhhCC---CCCEEEEEEcCCCCEEEEEEecCcEEEEEEEeec
Confidence 345555554421 2345778876567899999998 777777665
Done!