Query 009712
Match_columns 528
No_of_seqs 161 out of 890
Neff 3.9
Searched_HMMs 46136
Date Thu Mar 28 16:26:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009712.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009712hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2206 Exosome 3'-5' exoribon 99.9 1.9E-22 4.2E-27 216.7 13.5 125 1-133 356-480 (687)
2 PRK10829 ribonuclease D; Provi 99.8 8.4E-19 1.8E-23 182.6 12.5 119 17-139 174-293 (373)
3 TIGR01388 rnd ribonuclease D. 99.8 2.7E-18 5.8E-23 177.8 11.7 118 17-139 170-289 (367)
4 PF00570 HRDC: HRDC domain Blo 99.6 8.2E-16 1.8E-20 122.1 6.6 68 59-126 1-68 (68)
5 smart00341 HRDC Helicase and R 99.6 3.5E-15 7.6E-20 121.5 9.5 77 57-133 2-78 (81)
6 COG0349 Rnd Ribonuclease D [Tr 99.5 3.4E-14 7.5E-19 147.6 11.2 114 17-134 170-283 (361)
7 TIGR01389 recQ ATP-dependent D 98.9 2.6E-09 5.7E-14 116.2 8.4 70 59-128 521-590 (591)
8 PRK11057 ATP-dependent DNA hel 98.3 2E-06 4.4E-11 94.8 8.4 74 58-131 531-604 (607)
9 PLN03137 ATP-dependent DNA hel 98.0 1.7E-05 3.7E-10 93.3 8.4 72 60-131 1029-1102(1195)
10 COG0514 RecQ Superfamily II DN 97.4 0.00024 5.1E-09 79.2 7.1 72 59-130 517-588 (590)
11 PF11408 Helicase_Sgs1: Sgs1 R 91.8 0.43 9.4E-06 41.2 5.7 55 62-116 8-62 (80)
12 COG1460 Uncharacterized protei 50.1 24 0.00051 32.7 4.1 47 85-131 66-113 (114)
13 PF03874 RNA_pol_Rpb4: RNA pol 40.6 95 0.0021 27.3 6.4 48 82-129 68-116 (117)
14 PRK14981 DNA-directed RNA poly 36.0 50 0.0011 29.9 3.9 46 85-130 65-111 (112)
15 COG2906 Bfd Bacterioferritin-a 24.3 1.9E+02 0.0041 24.4 5.1 44 85-128 9-54 (63)
16 cd06258 Peptidase_M3_like The 22.8 2.6E+02 0.0056 29.0 7.0 62 61-128 2-63 (365)
No 1
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=1.9e-22 Score=216.68 Aligned_cols=125 Identities=34% Similarity=0.537 Sum_probs=111.9
Q ss_pred ChhhhhcCCCCCCCCCCcHHHHHHHHHHHHHHHHhhccCChhHHHHhhhhccCCCCHHHHHHHHHHHHHHHHHHHHhCCC
Q 009712 1 MKIKLSSMPKESENSDTPLTEVYKRSYDVCRQLYEKELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDES 80 (528)
Q Consensus 1 MRneLi~~s~~s~~~~nlL~wVLerS~eLcLq~YEKe~~deesYlrIkG~~~~~Ls~rQLAVLRaL~eWRD~iAReeDeP 80 (528)
||.+|-+.++. ..-++.++..+|...|.++.+....|+.+...+. .+++.|+.||++|++|||.+||++|+|
T Consensus 356 lr~el~~~a~~-------~~~~~~~~~d~c~~~~~k~~~~~~sy~~v~~~q~-~ln~~q~~~l~~L~~wRd~iARaeDES 427 (687)
T KOG2206|consen 356 LRKELKRLAKG-------RAVTYSESRDMCTNGYKKKTFCTKSYLEVEDIQS-RLNSSQLDVLRALLRWRDFIARAEDES 427 (687)
T ss_pred HHHHHHHHhcc-------cccccchhhhhhhcceecccCCCcchHhHHHHHh-ccchhHHHHHHHHHHHHHHHHhhccCC
Confidence 56677666531 1123448999999999999999999999998875 599999999999999999999999999
Q ss_pred CCcccChHHHHHHHHhCCCCHHHHHhhhCCChhHHHhhHHHHHHHHHHHHhcc
Q 009712 81 TGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQNA 133 (528)
Q Consensus 81 p~yVLpDkaLLELAkq~PtS~~eLlrI~g~~~~~VRrhgdeILeIIr~A~elp 133 (528)
++|||||++|+.||+.+|.++..|++++...+++|++|...++.||+.|++..
T Consensus 428 ~~yVlpN~~ll~l~e~~P~~v~gl~~~ln~~~p~vkq~~~~~~~ii~~a~~~~ 480 (687)
T KOG2206|consen 428 VHYVLPNDQLLKLAEERPDTVDGLLGGLNRLSPLVKQNVMDFLYIIRSAGRGF 480 (687)
T ss_pred CceecccHHHHHHHHHCCccHHHHHHhccCCCHHHHHHHHHHHHHHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999999764
No 2
>PRK10829 ribonuclease D; Provisional
Probab=99.78 E-value=8.4e-19 Score=182.64 Aligned_cols=119 Identities=22% Similarity=0.271 Sum_probs=105.6
Q ss_pred CcHHHHHHHHHHHHHHHHhhccCChhHHHHhhhhccCCCCHHHHHHHHHHHHHHHHHHHHhCCCCCcccChHHHHHHHHh
Q 009712 17 TPLTEVYKRSYDVCRQLYEKELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQ 96 (528)
Q Consensus 17 nlL~wVLerS~eLcLq~YEKe~~deesYlrIkG~~~~~Ls~rQLAVLRaL~eWRD~iAReeDePp~yVLpDkaLLELAkq 96 (528)
.++.|++++|+.+|...+. ...++..|++|++. +.|+++||+||++|++|||++||.+|+|++|||+|++|++||++
T Consensus 174 g~~~w~~ee~~~l~~~~~~-~~~~~~~~~~ik~~--~~L~~~~lavl~~L~~WRe~~Ar~~d~p~~~Vl~d~~L~~lA~~ 250 (373)
T PRK10829 174 GWLPAALDECRLLCQRRQE-VLAPEEAYRDITNA--WQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHLWQVARY 250 (373)
T ss_pred CcHHHHHHHHHHHHhcccc-CCChHHHHHHhccc--cCCCHHHHHHHHHHHHHHHHHHHHhCCCcceecChHHHHHHHHh
Confidence 4899999999999986533 23345789999975 58999999999999999999999999999999999999999999
Q ss_pred CCCCHHHHHhhhCCChhHHHhhHHHHHHHHHHHHhccc-chHHH
Q 009712 97 LPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQNAA-NFEVI 139 (528)
Q Consensus 97 ~PtS~~eLlrI~g~~~~~VRrhgdeILeIIr~A~elp~-~~ps~ 139 (528)
+|++..+|.++ ++.+..+++|+++|+++|++|.+.+. .+|..
T Consensus 251 ~P~~~~~L~~~-~~~~~~~r~~g~~ll~~i~~a~~~~~~~~P~~ 293 (373)
T PRK10829 251 MPGSLGELDSL-GLSGSEIRFHGKTLLALVAKAQALPEEALPPP 293 (373)
T ss_pred CCCCHHHHHhc-cCChHhHHhhHHHHHHHHHHHhcCCHhhCCCC
Confidence 99999999999 88889999999999999999998765 46544
No 3
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=99.76 E-value=2.7e-18 Score=177.84 Aligned_cols=118 Identities=25% Similarity=0.338 Sum_probs=105.3
Q ss_pred CcHHHHHHHHHHHHHHH-HhhccCChhHHHHhhhhccCCCCHHHHHHHHHHHHHHHHHHHHhCCCCCcccChHHHHHHHH
Q 009712 17 TPLTEVYKRSYDVCRQL-YEKELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAK 95 (528)
Q Consensus 17 nlL~wVLerS~eLcLq~-YEKe~~deesYlrIkG~~~~~Ls~rQLAVLRaL~eWRD~iAReeDePp~yVLpDkaLLELAk 95 (528)
+++.|+.++|..++... |. ..++..|++|++. +.|+++||+||++|++|||.+||++|+|++|||+|++|++||+
T Consensus 170 g~~~w~~ee~~~l~~~~~~~--~~~~~~~~~i~~~--~~l~~~~l~~l~~L~~wRe~~A~~~d~p~~~il~d~~l~~lA~ 245 (367)
T TIGR01388 170 GRLAWLEEECTLLTDRRTYV--VNPEDAWRDIKNA--WQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEALWELAR 245 (367)
T ss_pred CcHHHHHHHHHHHhccccCC--CChHHHHHHhccc--ccCCHHHHHHHHHHHHHHHHHHHHcCCCcceeeCHHHHHHHHH
Confidence 58999999999999865 33 3455689999974 5799999999999999999999999999999999999999999
Q ss_pred hCCCCHHHHHhhhCCChhHHHhhHHHHHHHHHHHHhccc-chHHH
Q 009712 96 QLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQNAA-NFEVI 139 (528)
Q Consensus 96 q~PtS~~eLlrI~g~~~~~VRrhgdeILeIIr~A~elp~-~~ps~ 139 (528)
++|+|..+|.++ ++.+..+++|+++|+++|++|.+.+. .+|..
T Consensus 246 ~~P~~~~~l~~~-~~~~~~~r~~~~~l~~~i~~a~~~~~~~~P~~ 289 (367)
T TIGR01388 246 QAPGNLTELASL-GPKGSEIRKHGDTLLALVKTALALPEDALPQA 289 (367)
T ss_pred hCCCCHHHHHhc-cCChHHHHhhHHHHHHHHHHHhhCCHhhCCCC
Confidence 999999999999 88889999999999999999988765 45554
No 4
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=99.62 E-value=8.2e-16 Score=122.11 Aligned_cols=68 Identities=35% Similarity=0.586 Sum_probs=62.6
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCcccChHHHHHHHHhCCCCHHHHHhhhCCChhHHHhhHHHHHHHH
Q 009712 59 QLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSII 126 (528)
Q Consensus 59 QLAVLRaL~eWRD~iAReeDePp~yVLpDkaLLELAkq~PtS~~eLlrI~g~~~~~VRrhgdeILeII 126 (528)
|++++++|++||+.+|++.|+++++||+|.+|.+||+.+|+|.++|.+|.|+....+++||++|+++|
T Consensus 1 q~~~~~~L~~~R~~~A~~~~~~~~~Il~~~~L~~ia~~~P~s~~~L~~i~g~~~~~~~~~g~~il~~I 68 (68)
T PF00570_consen 1 QLALLKALKEWREELAREEDVPPYRILSDEALLEIAKRLPTSIEELLQIPGMGKRKVRKYGDEILEII 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH--SSHHHHHTSTTCGHHHHHHCHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHcCcCcccccCHHHHHHHHHhCCCCHHHHHHccCCCHHHHHHHHHHHHhhC
Confidence 78999999999999999999999999999999999999999999999999999999999999999987
No 5
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=99.60 E-value=3.5e-15 Score=121.53 Aligned_cols=77 Identities=32% Similarity=0.534 Sum_probs=73.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCcccChHHHHHHHHhCCCCHHHHHhhhCCChhHHHhhHHHHHHHHHHHHhcc
Q 009712 57 AQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQNA 133 (528)
Q Consensus 57 ~rQLAVLRaL~eWRD~iAReeDePp~yVLpDkaLLELAkq~PtS~~eLlrI~g~~~~~VRrhgdeILeIIr~A~elp 133 (528)
++++++|++|+.||+.+|++.|+|+++||+|.+|++||+.+|+|..+|.++.++....+++|+..|+.+|+.+.+.+
T Consensus 2 ~~~~~~~~~L~~wR~~~A~~~~~~~~~I~~~~~L~~ia~~~P~~~~~L~~i~g~~~~~~~~~g~~~~~~i~~~~~~~ 78 (81)
T smart00341 2 ERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEASDSP 78 (81)
T ss_pred hHHHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 57899999999999999999999999999999999999999999999999999988999999999999999998764
No 6
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.53 E-value=3.4e-14 Score=147.60 Aligned_cols=114 Identities=23% Similarity=0.271 Sum_probs=102.8
Q ss_pred CcHHHHHHHHHHHHHHHHhhccCChhHHHHhhhhccCCCCHHHHHHHHHHHHHHHHHHHHhCCCCCcccChHHHHHHHHh
Q 009712 17 TPLTEVYKRSYDVCRQLYEKELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQ 96 (528)
Q Consensus 17 nlL~wVLerS~eLcLq~YEKe~~deesYlrIkG~~~~~Ls~rQLAVLRaL~eWRD~iAReeDePp~yVLpDkaLLELAkq 96 (528)
+++.|+.++|..+..+++.. ..+...|+++.. .+.+.+.++++++.|++|||++||.+|+|++|||+|+.|+++|+.
T Consensus 170 ~r~~~a~~ef~~l~~r~~~~-~~~~~~w~~i~~--a~~~~p~~la~l~~La~wRe~~Ar~rd~~~~~vl~de~i~~~a~~ 246 (361)
T COG0349 170 GRLEWAEDEFRLLPTRRTYK-VLPEDAWREIKI--AHSLDPRELAVLRELAAWREREARERDLARNFVLKDEALWELARY 246 (361)
T ss_pred CchHHHHHHHHHhhhccccc-cChHhHHHHhhh--hhcCChHHHHHHHHHHHHHHHHHHHhccccccccchhHHHHHHHh
Confidence 58999999999998875442 467889999986 368999999999999999999999999999999999999999999
Q ss_pred CCCCHHHHHhhhCCChhHHHhhHHHHHHHHHHHHhccc
Q 009712 97 LPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQNAA 134 (528)
Q Consensus 97 ~PtS~~eLlrI~g~~~~~VRrhgdeILeIIr~A~elp~ 134 (528)
+|++..+|..+..+.. .++.|+..|+.+|.+|...|.
T Consensus 247 ~P~~~~~l~~l~~~~~-~~~~~~~~l~~~~~~a~~~p~ 283 (361)
T COG0349 247 TPKNLKELDALGLIPK-ERRRHGKLLLALLANALASPE 283 (361)
T ss_pred CCCCHHHHHhccCCcc-cchhhhHHHHHHHHHHHhCch
Confidence 9999999999876555 889999999999999998875
No 7
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=98.91 E-value=2.6e-09 Score=116.25 Aligned_cols=70 Identities=23% Similarity=0.325 Sum_probs=67.2
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCcccChHHHHHHHHhCCCCHHHHHhhhCCChhHHHhhHHHHHHHHHH
Q 009712 59 QLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKN 128 (528)
Q Consensus 59 QLAVLRaL~eWRD~iAReeDePp~yVLpDkaLLELAkq~PtS~~eLlrI~g~~~~~VRrhgdeILeIIr~ 128 (528)
+.++|++|++||+++|++.|+|+++||+|.+|++||+.+|+|..+|.++.|+....+++||+.|+++|+.
T Consensus 521 ~~~l~~~L~~wR~~~A~~~~~p~~~If~d~~L~~ia~~~P~~~~~l~~i~gv~~~k~~~~G~~~l~~i~~ 590 (591)
T TIGR01389 521 DNALFEALRELRKEQADEQNVPPYVIFSDSTLREMAEKRPATLNALLKIKGVGQNKLDRYGEAFLEVIRE 590 (591)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhCCCCCCHHHHHHHHHHHHHHHHh
Confidence 4499999999999999999999999999999999999999999999999998999999999999999975
No 8
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=98.27 E-value=2e-06 Score=94.81 Aligned_cols=74 Identities=26% Similarity=0.387 Sum_probs=70.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCcccChHHHHHHHHhCCCCHHHHHhhhCCChhHHHhhHHHHHHHHHHHHh
Q 009712 58 QQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQ 131 (528)
Q Consensus 58 rQLAVLRaL~eWRD~iAReeDePp~yVLpDkaLLELAkq~PtS~~eLlrI~g~~~~~VRrhgdeILeIIr~A~e 131 (528)
..-.++.+|..||.++|++.++|++.||+|.+|.+||+.+|+|..+|.+|.|+....+.+||..++++|+...+
T Consensus 531 ~~~~l~~~Lr~~R~~~a~~~~~~~~~if~d~tL~~ia~~~P~t~~~l~~i~Gvg~~K~~~yg~~~l~~i~~~~~ 604 (607)
T PRK11057 531 YDRKLFAKLRKLRKSIADEENIPPYVVFNDATLIEMAEQMPITASEMLSVNGVGQRKLERFGKPFMALIRAHVD 604 (607)
T ss_pred chHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45679999999999999999999999999999999999999999999999999999999999999999988764
No 9
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=97.96 E-value=1.7e-05 Score=93.28 Aligned_cols=72 Identities=19% Similarity=0.315 Sum_probs=67.8
Q ss_pred HHHHHHHHHHHHHHHHH--hCCCCCcccChHHHHHHHHhCCCCHHHHHhhhCCChhHHHhhHHHHHHHHHHHHh
Q 009712 60 LAVVAGLCEWRDVIARA--DDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQ 131 (528)
Q Consensus 60 LAVLRaL~eWRD~iARe--eDePp~yVLpDkaLLELAkq~PtS~~eLlrI~g~~~~~VRrhgdeILeIIr~A~e 131 (528)
-.++.+|..||..+|++ +++|++.||+|.+|.+||+.+|+|..+|.+|.|+....+.+||..+|++|+..+.
T Consensus 1029 ~~Lfe~Lr~lR~elA~e~~~~vppyvIFsD~TL~eIA~~~P~T~~eLl~I~GVG~~KlekYG~~fL~vI~~~~~ 1102 (1195)
T PLN03137 1029 AILYTALRKLRTALVKEAGDGVMAYHIFGNATLQQISKRIPRTKEELLEINGLGKAKVSKYGDRLLETIESTIN 1102 (1195)
T ss_pred HHHHHHHHHHHHHHHHhhhcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCccHHHHHHHHHHHHHHHHHHHH
Confidence 35999999999999999 6999999999999999999999999999999999999999999999999987653
No 10
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=97.45 E-value=0.00024 Score=79.23 Aligned_cols=72 Identities=24% Similarity=0.311 Sum_probs=68.1
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCcccChHHHHHHHHhCCCCHHHHHhhhCCChhHHHhhHHHHHHHHHHHH
Q 009712 59 QLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSM 130 (528)
Q Consensus 59 QLAVLRaL~eWRD~iAReeDePp~yVLpDkaLLELAkq~PtS~~eLlrI~g~~~~~VRrhgdeILeIIr~A~ 130 (528)
...++.+|..||-++|.+.|+||.-|++|.+|.++|+.+|.+..+|..+.|.....+.+|+..++++|++..
T Consensus 517 ~~~lf~~lr~~r~~~a~~~~vp~~vif~d~tl~~ma~~~p~~~~~~~~i~gvg~~k~~~yg~~fl~~i~~~~ 588 (590)
T COG0514 517 DRDLFERLRALRKEIADEENVPPYVVFSDATLKEMAEKQPQSADELLSINGVGEAKLERYGQAFLAVIQAHA 588 (590)
T ss_pred cHHHHHHHHHHHHHhhhhhcCCceEEecchHHHHHHHHcCCCHHHHHHhcCCcccchhhccHHHHHHHHHhc
Confidence 456999999999999999999999999999999999999999999999999988999999999999998754
No 11
>PF11408 Helicase_Sgs1: Sgs1 RecQ helicase; InterPro: IPR022758 RecQ helicases unwind DNA in an ATP-dependent manner. Sgs1 has a HRDC (helicase and RNaseD C-terminal) domain which modulates the helicase function via auxiliary contacts to DNA []. The proteins matching this entry are restricted to fungi (Saccharomycetaceae). ; PDB: 1D8B_A.
Probab=91.77 E-value=0.43 Score=41.19 Aligned_cols=55 Identities=16% Similarity=0.215 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHHHhCCCCCcccChHHHHHHHHhCCCCHHHHHhhhCCChhHHH
Q 009712 62 VVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIE 116 (528)
Q Consensus 62 VLRaL~eWRD~iAReeDePp~yVLpDkaLLELAkq~PtS~~eLlrI~g~~~~~VR 116 (528)
.+..|.+-|-.++.+.+-|..-.|+|.+|-.||..+|+|..++.++.+....+.+
T Consensus 8 aY~~Lr~~~~~~~~~~n~p~~~f~sd~~LKk~A~~LP~te~eF~~l~g~~~~~~~ 62 (80)
T PF11408_consen 8 AYEKLREISINLSNRMNPPNDNFMSDTILKKMATKLPTTEEEFSKLVGINEQQRK 62 (80)
T ss_dssp HHHHHHHHHHHHHHSSSS--S-SS-HHHHHHHHHH---SHHHHGGGS---HHHHH
T ss_pred HHHHHHHHHHHHhhccCCCccccCCHHHHHHHHHHCCCCHHHHHHhcCCcHHHHH
Confidence 5678888899999999999999999999999999999999999999987666643
No 12
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=50.09 E-value=24 Score=32.66 Aligned_cols=47 Identities=19% Similarity=0.409 Sum_probs=38.3
Q ss_pred cChHHHHHHHHhCCCCHHHHHhhhCC-ChhHHHhhHHHHHHHHHHHHh
Q 009712 85 LPNRTLIEIAKQLPTTAAKLRRLLKS-KHSYIERYMGPVLSIIKNSMQ 131 (528)
Q Consensus 85 LpDkaLLELAkq~PtS~~eLlrI~g~-~~~~VRrhgdeILeIIr~A~e 131 (528)
|+......||--+|+|..+|+.|.-. .........+.|+++|.+++.
T Consensus 66 ~~e~~avkIadI~P~t~~ElRsIla~e~~~~s~E~l~~Ildiv~Ky~~ 113 (114)
T COG1460 66 MSEKIAVKIADIMPRTPDELRSILAKERVMLSDEELDKILDIVDKYRE 113 (114)
T ss_pred ccHHHHHHHHHhCCCCHHHHHHHHHHccCCCCHHHHHHHHHHHHHHhc
Confidence 68999999999999999999998743 233346788899999988753
No 13
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=40.61 E-value=95 Score=27.31 Aligned_cols=48 Identities=23% Similarity=0.417 Sum_probs=35.3
Q ss_pred CcccChHHHHHHHHhCCCCHHHHHhhhCCCh-hHHHhhHHHHHHHHHHH
Q 009712 82 GYVLPNRTLIEIAKQLPTTAAKLRRLLKSKH-SYIERYMGPVLSIIKNS 129 (528)
Q Consensus 82 ~yVLpDkaLLELAkq~PtS~~eLlrI~g~~~-~~VRrhgdeILeIIr~A 129 (528)
.|-|....++.|+..+|++..+|..|..... ++-....+.||++|...
T Consensus 68 ~~~L~~~E~~qi~Nl~P~~~~El~~ii~~~~~r~~ee~l~~iL~~v~~~ 116 (117)
T PF03874_consen 68 KFGLTEFEILQIINLRPTTAVELRAIIESLESRFSEEDLEEILDLVSKY 116 (117)
T ss_dssp TSTS-HHHHHHHHHH--SSHHHHHHHSTTGTTTSTHHHHHHHHHHHHHH
T ss_pred cccCCHHHHHHHhcCCCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHHh
Confidence 4449999999999999999999999875433 44467788888888753
No 14
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=36.02 E-value=50 Score=29.85 Aligned_cols=46 Identities=24% Similarity=0.412 Sum_probs=37.4
Q ss_pred cChHHHHHHHHhCCCCHHHHHhhhCCC-hhHHHhhHHHHHHHHHHHH
Q 009712 85 LPNRTLIEIAKQLPTTAAKLRRLLKSK-HSYIERYMGPVLSIIKNSM 130 (528)
Q Consensus 85 LpDkaLLELAkq~PtS~~eLlrI~g~~-~~~VRrhgdeILeIIr~A~ 130 (528)
|.....+.||.-+|.|.++|+.+...- ........++||++|...+
T Consensus 65 l~e~~a~~I~nL~P~~~dElrai~~~~~~~~~~e~l~~ILd~l~k~~ 111 (112)
T PRK14981 65 MKEKTAVKIADILPETRDELRAIFAKERYTLSPEELDEILDIVKKYR 111 (112)
T ss_pred CCHHHHHHHHhcCCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHHhh
Confidence 689999999999999999999987543 3445778888998887653
No 15
>COG2906 Bfd Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]
Probab=24.27 E-value=1.9e+02 Score=24.35 Aligned_cols=44 Identities=23% Similarity=0.159 Sum_probs=32.4
Q ss_pred cChHHHHHHHHhCCCCHHHHHhhhCCChh--HHHhhHHHHHHHHHH
Q 009712 85 LPNRTLIEIAKQLPTTAAKLRRLLKSKHS--YIERYMGPVLSIIKN 128 (528)
Q Consensus 85 LpDkaLLELAkq~PtS~~eLlrI~g~~~~--~VRrhgdeILeIIr~ 128 (528)
++|+.|-+.+.+-|+|+.+|.+..|.... .=.+.+.+||+-...
T Consensus 9 VtD~~Ir~av~~g~tt~~el~~~~gvGs~CGkC~~~Arevl~e~~~ 54 (63)
T COG2906 9 VTDKQIREAVAQGATTLKELRRFTGVGSQCGKCVRAAREVLEEALA 54 (63)
T ss_pred ccHHHHHHHHHHcCCCHHHHHHHcCcccchHHHHHHHHHHHHHHHH
Confidence 58999999999999999999998875443 224556566544433
No 16
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=22.83 E-value=2.6e+02 Score=29.03 Aligned_cols=62 Identities=16% Similarity=0.206 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCcccChHHHHHHHHhCCCCHHHHHhhhCCChhHHHhhHHHHHHHHHH
Q 009712 61 AVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKN 128 (528)
Q Consensus 61 AVLRaL~eWRD~iAReeDePp~yVLpDkaLLELAkq~PtS~~eLlrI~g~~~~~VRrhgdeILeIIr~ 128 (528)
.+|.+|..-|.++|+..+ | .+..=+.|..+++.+++.+..+..-....++...+.+++.+++
T Consensus 2 ~~l~~lv~lr~e~A~~lG----y--~~~~d~~l~~~~~~~~e~v~~f~~~l~~~~~p~~~~~~~~l~~ 63 (365)
T cd06258 2 ALLEELVSLRNQLARLLG----Y--ENFADYKLALQEAKSPETVEGFFEELKRKLRPLLAKLREEISA 63 (365)
T ss_pred hHHHHHHHHHHHHHHHcC----C--CCHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999996 4 7777788888888888888877654555555555555554443
Done!