Query psy8360
Match_columns 152
No_of_seqs 110 out of 258
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 16:42:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8360.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8360hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3405|consensus 100.0 1.6E-36 3.5E-41 235.9 8.1 84 68-151 53-136 (136)
2 PLN00152 DNA-directed RNA poly 100.0 1.5E-34 3.2E-39 224.4 8.8 83 69-151 48-130 (130)
3 PRK01099 rpoK DNA-directed RNA 99.9 2.6E-25 5.7E-30 153.2 6.8 61 76-136 2-62 (62)
4 COG1758 RpoZ DNA-directed RNA 99.7 4.5E-18 9.7E-23 119.3 4.5 65 76-140 9-74 (74)
5 PF01192 RNA_pol_Rpb6: RNA pol 99.6 5.2E-16 1.1E-20 103.2 4.7 53 78-130 5-57 (57)
6 PRK00392 rpoZ DNA-directed RNA 99.3 7.7E-12 1.7E-16 85.4 5.1 49 82-131 15-63 (69)
7 TIGR00690 rpoZ DNA-directed RN 99.2 2.7E-11 5.7E-16 82.2 4.8 45 82-127 14-59 (59)
8 PF05320 Pox_RNA_Pol_19: Poxvi 82.8 1.2 2.7E-05 36.6 2.9 64 69-132 68-135 (167)
9 PF15192 TMEM213: TMEM213 fami 56.7 6.2 0.00013 29.2 1.2 25 2-26 22-63 (82)
10 PF15468 DUF4636: Domain of un 44.2 50 0.0011 28.8 4.9 84 4-97 28-132 (243)
11 PF15277 Sec3-PIP2_bind: Exocy 42.4 28 0.00061 25.2 2.8 27 126-152 20-49 (91)
12 CHL00191 ycf61 DNA-directed RN 35.4 55 0.0012 24.0 3.3 44 82-126 26-69 (76)
13 PF11669 WBP-1: WW domain-bind 22.5 41 0.00089 25.0 0.8 15 8-22 11-27 (102)
14 PF10429 Mtr2: Nuclear pore RN 21.2 17 0.00037 30.0 -1.5 18 13-30 122-139 (166)
No 1
>KOG3405|consensus
Probab=100.00 E-value=1.6e-36 Score=235.94 Aligned_cols=84 Identities=70% Similarity=1.043 Sum_probs=81.9
Q ss_pred ccccccccccCCCCcchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEEEEEcCCCcEEEEecccc
Q psy8360 68 KNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDEL 147 (152)
Q Consensus 68 k~i~d~~~~t~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIrR~lP~g~yEdw~l~eL 147 (152)
|.|++.+|+|.|++||||+|||+|+||+|||||||+||++++.+||+.||++||+|+||||+||||||||+||||+++||
T Consensus 53 ~~v~~s~R~TtpyMTKYErArvLGtRAlQIsm~APvmVeLegETdPL~IAmkEL~qkKIP~iIRRyLPDgSyEDW~vdEL 132 (136)
T KOG3405|consen 53 KAVPKSERKTTPYMTKYERARVLGTRALQISMNAPVMVELEGETDPLEIAMKELKQKKIPFIIRRYLPDGSYEDWSVDEL 132 (136)
T ss_pred ccccccccccCcchhHHHHHHhhhHHHHHHhcCCCeEEecCCCCCHHHHHHHHHhhccCceEEeeeCCCCCcccccccee
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceec
Q psy8360 148 KIID 151 (152)
Q Consensus 148 ~i~~ 151 (152)
++.|
T Consensus 133 iv~d 136 (136)
T KOG3405|consen 133 IVED 136 (136)
T ss_pred eccC
Confidence 9864
No 2
>PLN00152 DNA-directed RNA polymerase; Provisional
Probab=100.00 E-value=1.5e-34 Score=224.39 Aligned_cols=83 Identities=67% Similarity=1.072 Sum_probs=79.2
Q ss_pred cccccccccCCCCcchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEEEEEcCCCcEEEEeccccc
Q psy8360 69 NQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELK 148 (152)
Q Consensus 69 ~i~d~~~~t~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIrR~lP~g~yEdw~l~eL~ 148 (152)
......|+|+|+|||||+|||+|+||+|||||||++|++++.+||+.||++||.+|+|||+|||++|||+||+|+++||+
T Consensus 48 ~~~~~~R~T~p~lTkyErARIiG~RALQIsmgApvlV~~~g~tdPl~IA~~El~~~~iP~iVrR~lPdG~yEd~~v~EL~ 127 (130)
T PLN00152 48 EPVQRPRKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELI 127 (130)
T ss_pred cccccccccccchhHHHHHhhHhHHHHHHhcCCceEEccCCCcCHHHHHHHHHHcCCCCeEEEEECCCCCEEeeEeeeEe
Confidence 55677799999999999999999999999999999999987899999999999999999999999999999999999999
Q ss_pred eec
Q psy8360 149 IID 151 (152)
Q Consensus 149 i~~ 151 (152)
+.|
T Consensus 128 ~~~ 130 (130)
T PLN00152 128 VED 130 (130)
T ss_pred ecC
Confidence 875
No 3
>PRK01099 rpoK DNA-directed RNA polymerase subunit K; Provisional
Probab=99.92 E-value=2.6e-25 Score=153.16 Aligned_cols=61 Identities=48% Similarity=0.797 Sum_probs=58.1
Q ss_pred ccCCCCcchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEEEEEcCC
Q psy8360 76 KLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPD 136 (152)
Q Consensus 76 ~t~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIrR~lP~ 136 (152)
.++++|||||+||++|+||+||++||||+|+.+++.||++||++||++|+||++|+|++||
T Consensus 2 ~~~~~ltrfe~a~i~akRArQl~~Ga~~lv~~~~~~kPv~iAl~Ei~~gkI~~~v~r~~p~ 62 (62)
T PRK01099 2 MGPMKLTRFERARIIGARALQISMGAPVLIDIPESTDPLDIAEEEFKRGVLPITVKRPLPN 62 (62)
T ss_pred CCCcccCHHHHHHHHHHHHHHHHcCCCceecCCCCCCHHHHHHHHHHcCCCCeEeecCCCC
Confidence 3689999999999999999999999999999855899999999999999999999999997
No 4
>COG1758 RpoZ DNA-directed RNA polymerase, subunit K/omega [Transcription]
Probab=99.72 E-value=4.5e-18 Score=119.29 Aligned_cols=65 Identities=38% Similarity=0.444 Sum_probs=59.0
Q ss_pred ccCCCCcchhhhHHHHHHHHHHhcCCCceeeCCCC-CChHHHHHHHHHcCCccEEEEEEcCCCcEE
Q psy8360 76 KLNIKQIRYERARVLGTRALQIAMCAPVMVELEGE-TDPLQIAMKELKARKIPIIIRRYLPDNSYE 140 (152)
Q Consensus 76 ~t~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~-~dPv~IAl~EL~eGkIpiiIrR~lP~g~yE 140 (152)
-+....||||+|+++|+||+||++||+++++.+.. .||+.||++|+++|+||+.+.|..++++.+
T Consensus 9 l~~~~~~ryelv~~aa~RA~Ql~~ga~~~~~~~~~~~kpv~iAl~Ei~~g~i~~~i~~~~~~~~~~ 74 (74)
T COG1758 9 LLDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKIPIEILRELLIHSLQ 74 (74)
T ss_pred HHhhccCHHHHHHHHHHHHHHHHcCCCCccccccccCChHHHHHHHHHcCCCCcccchhhhccccC
Confidence 45678899999999999999999999999987643 899999999999999999999999998753
No 5
>PF01192 RNA_pol_Rpb6: RNA polymerase Rpb6 ; InterPro: IPR006110 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. A component of 14 to 18 kDa shared by all three forms of eukaryotic RNA polymerases and which has been sequenced in budding yeast (gene RPB6 or RPO26), in Schizosaccharomyces pombe (Fission yeast) (gene rpb6 or rpo15), in human and in African swine fever virus (ASFV) is evolutionary related to the archaebacterial subunit K (gene rpoK). The archaebacterial protein is colinear with the C-terminal part of the eukaryotic subunit. The structures of the omega subunit and RBP6, and the structures of the omega/beta' and RPB6/RPB1 interfaces, suggest a molecular mechanism for the function of omega and RPB6 in promoting RNAP assembly and/or stability. The conserved regions of omega and RPB6 form a compact structural domain that interacts simultaneously with conserved regions of the largest RNAP subunit and with the C-terminal tail following a conserved region of the largest RNAP subunit. The second half of the conserved region of omega and RPB6 forms an arc that projects away from the remainder of the structural domain and wraps over and around the C-terminal tail of the largest RNAP subunit, clamping it in a crevice, and threading the C-terminal tail of the largest RNAP subunit through the narrow gap between omega and RPB6 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_R 2Y0S_I 3HKZ_U 2PMZ_K 3M3Y_F 3HOX_F 3GTJ_F 4A3K_F 2VUM_F 3S14_F ....
Probab=99.62 E-value=5.2e-16 Score=103.16 Aligned_cols=53 Identities=36% Similarity=0.468 Sum_probs=49.1
Q ss_pred CCCCcchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEE
Q psy8360 78 NIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIII 130 (152)
Q Consensus 78 ~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiI 130 (152)
....+||++++++|+||+||++||+|+++.+...+|+++|++||.+|+++|.|
T Consensus 5 ~~~~~rY~Lv~~~akRArql~~g~~~~~~~~~~~k~v~iAl~EI~~gki~~~i 57 (57)
T PF01192_consen 5 EKVDNRYELVILAAKRARQLSEGAPPLVEEDNEMKPVSIALEEIAEGKIKIEI 57 (57)
T ss_dssp HSSSSHHHHHHHHHHHHHHHHTTSTTSSSSSSSSSSSHHHHHHHHTTSSCEEE
T ss_pred hccCCHhHHHHHHHHHHHHHHcCcccccccccCCCcHHHHHHHHHcCCCCCcC
Confidence 45679999999999999999999999998775669999999999999999986
No 6
>PRK00392 rpoZ DNA-directed RNA polymerase subunit omega; Reviewed
Probab=99.26 E-value=7.7e-12 Score=85.41 Aligned_cols=49 Identities=29% Similarity=0.337 Sum_probs=45.1
Q ss_pred cchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEEE
Q psy8360 82 IRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIR 131 (152)
Q Consensus 82 TKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIr 131 (152)
+||+++.++++||+||+.|+++.++.. ..+|+.||++||.+|+|.+..-
T Consensus 15 ~ry~Lv~~aakRArql~~~~~~~~~~~-~~K~~~~Al~EI~~gki~~~~~ 63 (69)
T PRK00392 15 NRYELVLLAAKRARQLRAGAKPPVDKS-SDKPVVIALREIAEGKVTYEIL 63 (69)
T ss_pred CHHHHHHHHHHHHHHHHcCCCCCCCCc-CCChHHHHHHHHHcCCCceecc
Confidence 899999999999999999999997764 7799999999999999998764
No 7
>TIGR00690 rpoZ DNA-directed RNA polymerase, omega subunit. The trusted cutoff excludes archaeal homologs but captures some organellar sequences.
Probab=99.19 E-value=2.7e-11 Score=82.24 Aligned_cols=45 Identities=29% Similarity=0.393 Sum_probs=39.0
Q ss_pred cchhhhHHHHHHHHHHhcCC-CceeeCCCCCChHHHHHHHHHcCCcc
Q psy8360 82 IRYERARVLGTRALQIAMCA-PVMVELEGETDPLQIAMKELKARKIP 127 (152)
Q Consensus 82 TKYElARIIG~RAlQLs~GA-ppLVd~~~~~dPv~IAl~EL~eGkIp 127 (152)
+||+++.++++||+||+.|+ +++++.. +.+|+.||++||++|+|.
T Consensus 14 srY~Lv~~aakRArqL~~~~~~~~~~~~-~~Kp~~iAl~EIa~gkvs 59 (59)
T TIGR00690 14 SRYDLVLVAARRARQLQLKGTDPIVPEE-NDKPTVIALREIAAGLVS 59 (59)
T ss_pred CHhHHHHHHHHHHHHHHhCCCCCccCcc-cCchHHHHHHHHHcCCCC
Confidence 89999999999999999776 5555543 789999999999999973
No 8
>PF05320 Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymerase 19 kDa subunit; InterPro: IPR007984 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=82.78 E-value=1.2 Score=36.63 Aligned_cols=64 Identities=13% Similarity=0.197 Sum_probs=52.2
Q ss_pred cccccccccCCCCcchhhhHHHHHHHHHHhcCCCceeeC-CC---CCChHHHHHHHHHcCCccEEEEE
Q psy8360 69 NQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVEL-EG---ETDPLQIAMKELKARKIPIIIRR 132 (152)
Q Consensus 69 ~i~d~~~~t~~~lTKYElARIIG~RAlQLs~GAppLVd~-~~---~~dPv~IAl~EL~eGkIpiiIrR 132 (152)
+|..-++.+.-+++=||..=|+|.--.-|..|--|||.- .. ..+-+.|-++||.+|.-|++|..
T Consensus 68 kI~~iK~RYTRRiSLfEiTGIiaESyNLLqRGRlPLv~dlsdeT~k~n~L~vvi~EIeEg~CPIVIeK 135 (167)
T PF05320_consen 68 KISAIKKRYTRRISLFEITGIIAESYNLLQRGRLPLVSDLSDETLKDNILHVVIKEIEEGTCPIVIEK 135 (167)
T ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHccccccccccchHHHHHhHHHHHHHHHhcCCCcEEEee
Confidence 344555667778899999999999989999999999952 11 34568899999999999999986
No 9
>PF15192 TMEM213: TMEM213 family
Probab=56.72 E-value=6.2 Score=29.24 Aligned_cols=25 Identities=48% Similarity=1.192 Sum_probs=16.9
Q ss_pred CcccCCCce------eeecc-----------chhhhhhhhhc
Q psy8360 2 VSQCSNTDL------CCTYG-----------SWLGWAFTLLL 26 (152)
Q Consensus 2 ~~~~~~~~~------~~~~~-----------~~~~~~~~~~~ 26 (152)
.+||+|.|. ||..| .|--|..||++
T Consensus 22 le~c~~vDFCp~Aa~CC~~gvDeyGWIAAAVGWSLwFLTLIL 63 (82)
T PF15192_consen 22 LEQCPNVDFCPQAARCCHAGVDEYGWIAAAVGWSLWFLTLIL 63 (82)
T ss_pred hhcCCCcccchHHHHHhccCCchhhHHHHHHhHHHHHHHHHH
Confidence 468999886 46644 35567777765
No 10
>PF15468 DUF4636: Domain of unknown function (DUF4636)
Probab=44.17 E-value=50 Score=28.80 Aligned_cols=84 Identities=27% Similarity=0.360 Sum_probs=47.3
Q ss_pred ccCCCceeeeccchhhhhhhhhc-----------------ccCCCCCcccccccCCccchhcccCchhHHHHHhhhhhcc
Q psy8360 4 QCSNTDLCCTYGSWLGWAFTLLL-----------------DENAPTPSKANKWMGDLNLILGIKGERALVLILNHYMKVK 66 (152)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~-----------------de~~p~~~~~~~~~~~~n~~~~~~~~~~~i~~ln~~~~~~ 66 (152)
.|-..|.|-+-|+.|-|-|+.++ ||...++-..++-.-|+- |.--+..+ +.+.+..||
T Consensus 28 Ec~KDdsc~~iG~fLlWyfviilvLm~~~ras~Wmse~K~D~~sgts~s~ska~k~~s--~k~~sk~~---~wds~~~mK 102 (243)
T PF15468_consen 28 ECRKDDSCGAIGSFLLWYFVIILVLMFFSRASVWMSEKKKDEDSGTSASVSKASKDAS--CKRQSKDG---AWDSSQKMK 102 (243)
T ss_pred hhccCCccchhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhcccCCccccccccccchh--hhhhcccc---chhHHHHhh
Confidence 37888999999999999998764 666666555555444432 22222232 234444442
Q ss_pred cccccccccccCCCCcchhhhHHHH----HHHHHH
Q psy8360 67 SKNQIKNNNKLNIKQIRYERARVLG----TRALQI 97 (152)
Q Consensus 67 ~k~i~d~~~~t~~~lTKYElARIIG----~RAlQL 97 (152)
- ++...-+ ..|-=|.|-+-+ .||+|.
T Consensus 103 K---pKq~ql~--pvtdSEvalvnayleqRrar~~ 132 (243)
T PF15468_consen 103 K---PKQNQLS--PVTDSEVALVNAYLEQRRARRH 132 (243)
T ss_pred c---cccccCC--cccchHHHHHHHhHHHHHHHHH
Confidence 1 3333322 335556555554 566653
No 11
>PF15277 Sec3-PIP2_bind: Exocyst complex component SEC3 N-terminal PIP2 binding PH; PDB: 3HIE_D 3A58_E.
Probab=42.43 E-value=28 Score=25.19 Aligned_cols=27 Identities=30% Similarity=0.535 Sum_probs=18.4
Q ss_pred ccEEEEEEcCCCcEEE---EeccccceecC
Q psy8360 126 IPIIIRRYLPDNSYED---WGIDELKIIDR 152 (152)
Q Consensus 126 IpiiIrR~lP~g~yEd---w~l~eL~i~~~ 152 (152)
+-+...|..++|+|+. |+|+||..||+
T Consensus 20 v~l~k~K~~~~g~f~i~ktW~L~eL~~I~~ 49 (91)
T PF15277_consen 20 VRLHKVKQNDNGSFQIGKTWDLDELKAIDG 49 (91)
T ss_dssp EEEEEEEE-CCS-EEEEEEEEGGG--EEEE
T ss_pred EEEEEEEecCCCcEEEeeEEehhhceeeee
Confidence 5667788899998765 99999998873
No 12
>CHL00191 ycf61 DNA-directed RNA polymerase subunit omega; Provisional
Probab=35.36 E-value=55 Score=24.02 Aligned_cols=44 Identities=16% Similarity=0.095 Sum_probs=34.2
Q ss_pred cchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCc
Q psy8360 82 IRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKI 126 (152)
Q Consensus 82 TKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkI 126 (152)
.||-...=+|.||+|--.-..--++- ...+|+--|+-|...-.-
T Consensus 26 NRY~iTvqVAnRAKrrRyed~d~~d~-~~~KPv~RAIiEMsDEl~ 69 (76)
T CHL00191 26 NRYKITIQVANRAKRRRYEDIDIIND-PSIKPIIRAILEMVDEIN 69 (76)
T ss_pred cceeehHHHHHHHHHhhhhccccccc-ccccHHHHHHHHHhcccc
Confidence 58999999999999987666444442 278999999999876543
No 13
>PF11669 WBP-1: WW domain-binding protein 1; InterPro: IPR021684 This family of proteins represents WBP-1, a ligand of the WW domain of Yes-associated protein. This protein has a proline-rich domain. WBP-1 does not bind to the SH3 domain [].
Probab=22.48 E-value=41 Score=24.98 Aligned_cols=15 Identities=33% Similarity=1.054 Sum_probs=7.9
Q ss_pred Cceeeec--cchhhhhh
Q psy8360 8 TDLCCTY--GSWLGWAF 22 (152)
Q Consensus 8 ~~~~~~~--~~~~~~~~ 22 (152)
.+.||+| ..|.-|++
T Consensus 11 ~~~CC~~~~~~w~FWlv 27 (102)
T PF11669_consen 11 ESGCCSYYYELWYFWLV 27 (102)
T ss_pred CCCcchhhHHHHHHHHH
Confidence 4578874 33444443
No 14
>PF10429 Mtr2: Nuclear pore RNA shuttling protein Mtr2; InterPro: IPR019488 Mtr2 is a monomeric, dual-action, RNA-shuttle protein found in yeasts. Transport across the nuclear-cytoplasmic membrane is via the macro-molecular membrane-spanning nuclear pore complex, NPC. The pore is lined by a subset of NPC members called nucleoporins that present FG (Phe-Gly) receptors, characteristically GLFG and FXFG motifs, for shuttling RNAs and proteins. RNA cargo is bound to soluble transport proteins (nuclear export factors) such as Mex67 in yeasts, and TAP in metazoa, which pass along the pore by binding to successive FG receptors. Mtr2 when bound to Mex67 maximises this FG-binding. Mtr2 also acts independently of Mex67 in transporting the large ribosomal RNA subunit through the pore []. ; PDB: 1Q40_A 1Q42_A 1OF5_B.
Probab=21.21 E-value=17 Score=29.99 Aligned_cols=18 Identities=33% Similarity=0.744 Sum_probs=12.7
Q ss_pred eccchhhhhhhhhcccCC
Q psy8360 13 TYGSWLGWAFTLLLDENA 30 (152)
Q Consensus 13 ~~~~~~~~~~~~~~de~~ 30 (152)
-+|||.|--..|++||.-
T Consensus 122 ~wgs~fGvsl~lvvDe~i 139 (166)
T PF10429_consen 122 LWGSYFGVSLQLVVDERI 139 (166)
T ss_dssp -B---EEEEEEEEEECGC
T ss_pred CcccccceeEEEEEechh
Confidence 489999999999999964
Done!