Query 001962
Match_columns 990
No_of_seqs 17 out of 19
Neff 1.9
Searched_HMMs 46136
Date Thu Mar 28 13:21:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001962.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001962hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07718 Coatamer_beta_C: Coat 97.0 0.0027 5.8E-08 61.9 8.3 95 589-690 43-137 (140)
2 KOG1058 Vesicle coat complex C 96.6 0.0059 1.3E-07 71.8 8.2 134 593-761 712-845 (948)
3 PF09066 B2-adapt-app_C: Beta2 59.7 8.8 0.00019 34.5 2.9 96 745-870 4-105 (114)
4 PF02296 Alpha_adaptin_C: Alph 53.5 37 0.0008 32.1 6.0 103 744-871 3-111 (113)
5 KOG3068 mRNA splicing factor [ 51.4 25 0.00054 38.1 5.1 106 860-972 147-257 (268)
6 TIGR02511 type_III_tyeA type I 50.9 23 0.00049 31.8 4.0 44 191-235 27-75 (79)
7 cd06902 lectin_ERGIC-53_ERGL E 47.8 14 0.0003 38.0 2.5 31 518-548 194-224 (225)
8 PF09059 TyeA: TyeA; InterPro 41.4 43 0.00093 31.1 4.3 47 187-234 25-76 (87)
9 KOG2894 Uncharacterized conser 40.3 30 0.00065 38.3 3.7 92 889-981 80-178 (331)
10 PLN03237 DNA topoisomerase 2; 38.0 30 0.00064 44.6 3.7 9 874-882 1151-1159(1465)
11 PHA03211 serine/threonine kina 34.8 57 0.0012 36.3 4.9 74 896-971 62-147 (461)
12 PRK04019 rplP0 acidic ribosoma 31.8 40 0.00086 36.6 3.0 25 618-644 23-47 (330)
13 PF04712 Radial_spoke: Radial 31.2 26 0.00056 40.2 1.6 26 494-522 16-41 (491)
14 PRK04019 rplP0 acidic ribosoma 29.4 24 0.00051 38.2 0.9 11 887-897 253-263 (330)
15 KOG2573 Ribosome biogenesis pr 26.2 37 0.0008 39.2 1.7 33 878-910 399-431 (498)
16 PF05308 Mito_fiss_reg: Mitoch 24.9 37 0.00081 36.2 1.4 27 172-199 3-29 (253)
17 cd05753 Ig2_FcgammaR_like Seco 24.8 37 0.0008 29.1 1.1 13 724-736 13-25 (83)
18 PF06964 Alpha-L-AF_C: Alpha-L 24.6 1.9E+02 0.0041 28.0 5.9 69 602-675 91-165 (177)
19 TIGR01874 cas_cas5a CRISPR-ass 22.3 30 0.00065 35.4 0.1 33 295-333 22-58 (172)
20 cd06901 lectin_VIP36_VIPL VIP3 22.0 68 0.0015 33.7 2.6 34 518-551 193-226 (248)
21 PF14807 AP4E_app_platf: Adapt 21.1 2.3E+02 0.005 27.1 5.5 100 745-876 2-101 (104)
22 PF02459 Adeno_terminal: Adeno 21.0 35 0.00076 40.2 0.3 21 652-672 88-108 (548)
23 KOG3980 RNA 3'-terminal phosph 20.1 53 0.0011 37.2 1.4 63 668-736 86-172 (361)
No 1
>PF07718 Coatamer_beta_C: Coatomer beta C-terminal region; InterPro: IPR011710 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C-terminal domain of the beta subunit from coatomer proteins (Beta-coat proteins). The C-terminal domain probably adapts the function of the N-terminal IPR002553 from INTERPRO domain. Coatomer protein complex I (COPI)-coated vesicles are involved in transport between the endoplasmic reticulum and the Golgi but also participate in transport from early to late endosomes within the endocytic pathway []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat
Probab=97.02 E-value=0.0027 Score=61.94 Aligned_cols=95 Identities=24% Similarity=0.314 Sum_probs=76.3
Q ss_pred ccCCceecccCCCCccEEEeeeeccCCCCeEEEEEEEecCCcccccceeeEEecceeeecccCchHHHHHhcccccCCce
Q 001962 589 KASPTAYTLTGSSDPCYVEAYHLADSSDGKITLHLKVLNLTELELNRVDIRVGLSGALYFMNGSPQAVRQLRNLVSQDPV 668 (990)
Q Consensus 589 k~pp~avtLSGSSDPCyVEAyHladP~~~RlTLHLKv~Nlte~eL~rvdvrVGL~GAL~fmDGs~QaVrqL~~L~sqdpv 668 (990)
+..-.-+.|||=|||+|+|||=. .|.+.|.|-+=+.|-|+.-|..+.++.--.|-|.+.|.-+ --+|...+-.
T Consensus 43 skL~kv~QLTGfsDPvYaEA~v~--v~q~DIvLDvllvNqT~~tLqNl~vElat~gdLklve~p~-----~~tL~P~~~~ 115 (140)
T PF07718_consen 43 SKLNKVVQLTGFSDPVYAEAYVT--VHQYDIVLDVLLVNQTNETLQNLTVELATLGDLKLVERPQ-----PITLAPHGFA 115 (140)
T ss_pred hhhccEEecccCCCCeEEEEEEE--EEeeeEEEEEEEEeCChhhhhcEEEEEEecCCcEEccCCC-----ceeeCCCcEE
Confidence 34445689999999999999954 4677899999999999999999999999999999999764 3456667777
Q ss_pred eeeeEeeeecccccceeeeeee
Q 001962 669 ICSVTVGVSHFERCAFWVQVLY 690 (990)
Q Consensus 669 ~~svtvgVS~ferc~l~vQvLy 690 (990)
....++-||.=|-+-..-.|.|
T Consensus 116 ~i~~~iKVsStetGvIfG~I~Y 137 (140)
T PF07718_consen 116 RIKATIKVSSTETGVIFGNIVY 137 (140)
T ss_pred EEEEEEEEEeccCCEEEEEEEE
Confidence 7777888887776665555554
No 2
>KOG1058 consensus Vesicle coat complex COPI, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.58 E-value=0.0059 Score=71.83 Aligned_cols=134 Identities=27% Similarity=0.391 Sum_probs=105.1
Q ss_pred ceecccCCCCccEEEeeeeccCCCCeEEEEEEEecCCcccccceeeEEecceeeecccCchHHHHHhcccccCCceeeee
Q 001962 593 TAYTLTGSSDPCYVEAYHLADSSDGKITLHLKVLNLTELELNRVDIRVGLSGALYFMNGSPQAVRQLRNLVSQDPVICSV 672 (990)
Q Consensus 593 ~avtLSGSSDPCyVEAyHladP~~~RlTLHLKv~Nlte~eL~rvdvrVGL~GAL~fmDGs~QaVrqL~~L~sqdpv~~sv 672 (990)
+-+.|||=|||+|+|||--. +-+-|-|.+=++|-|+.-|....+...-.|-|-+.|-.+- -+|...|-+....
T Consensus 712 kV~QLtGfSDPVYaEAyv~v--nqyDIVLDvL~VNqT~~tLQNl~lelATlgdLKlve~p~p-----~~Laph~f~~ika 784 (948)
T KOG1058|consen 712 KVTQLTGFSDPVYAEAYVTV--NQYDIVLDVLLVNQTKETLQNLSLELATLGDLKLVERPTP-----FSLAPHDFVNIKA 784 (948)
T ss_pred ceeeccCCCCCeeeEEEeee--eeeeEEEEEEEecCChHHHhhheeeeeeccCceeeecCCC-----cccCcccceeEEE
Confidence 34679999999999999544 5677999999999999999999999999999999998654 3678888899999
Q ss_pred EeeeecccccceeeeeeeccccCCCCCCCCCCCccccchhHHhhhcccCCCCCCceEEeecccccccccccccCcCChhh
Q 001962 673 TVGVSHFERCAFWVQVLYYPFHGSGAIGDYEGDYAEEDPQIMRQKRSARPELGEPVILRCQPYKIPLTELLLPHKISPVE 752 (990)
Q Consensus 673 tvgVS~ferc~l~vQvLyyPf~Gs~G~g~~E~D~~~E~~~~~rqr~~~rpeygepViLRCqpYkIPLtELLlP~klSpve 752 (990)
||-||.=|.+=..-+|.|- |+ |+ +.|.+ -|+| +--+|-..+-+-|.++++.+
T Consensus 785 tvKVsStenGvIfGnIvY~---~~-~~-------a~~~~---------------~VvL--ndIhidImDYI~Pa~~~d~~ 836 (948)
T KOG1058|consen 785 TVKVSSTENGVIFGNIVYD---TS-EA-------ANDRN---------------VVVL--NDIHIDIMDYIKPAKCDDDE 836 (948)
T ss_pred EEEEeeccCcEEEEEEEec---Cc-cc-------cccce---------------EEEe--ccccccHHHhcCCCcCChHH
Confidence 9999988887776666652 22 21 22333 2333 34567778889999999999
Q ss_pred hhhhcCCCc
Q 001962 753 FFRLWPSLP 761 (990)
Q Consensus 753 FfRLWpsLP 761 (990)
|-..|.-|+
T Consensus 837 FRtmW~efE 845 (948)
T KOG1058|consen 837 FRTMWAEFE 845 (948)
T ss_pred HHHHHHHhh
Confidence 999997764
No 3
>PF09066 B2-adapt-app_C: Beta2-adaptin appendage, C-terminal sub-domain; InterPro: IPR015151 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents a subdomain of the appendage (ear) domain of beta-adaptin from AP clathrin adaptor complexes. This domain has a three-layer arrangement, alpha-beta-alpha, with a bifurcated antiparallel beta-sheet []. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15) []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1E42_B 2G30_A 2IV9_B 2IV8_A 3HS9_A 3H1Z_A.
Probab=59.67 E-value=8.8 Score=34.53 Aligned_cols=96 Identities=19% Similarity=0.208 Sum_probs=47.2
Q ss_pred cCcCChhhhhhhcCCCcceE--EEEEEEeeecCcchhhhh--hhcCCCccccccccccCCCcceeeceeeeeccc-hhh-
Q 001962 745 PHKISPVEFFRLWPSLPAIV--EYTGTYIYEGSGFKATAA--QQYGTSPFFSGLKSLSSKPFHIVCSHIIQAVAG-FQL- 818 (990)
Q Consensus 745 P~klSpveFfRLWpsLPAiv--e~tgay~yEG~G~kaa~a--a~~g~SP~lSGLkslSskPFH~vcshiLRtvag-FQ~- 818 (990)
.-+|++.+|-+.|.++|... +++...........+... +..++ +.+.+ |.+.+ ...
T Consensus 4 d~~~~~~~F~~~W~sl~~~~~~e~~~~~~~~~~~~~~i~~~L~~~nI---------------~~iA~---~~~~~~~~~~ 65 (114)
T PF09066_consen 4 DGSMDPEEFQEMWKSLPDSNQQELSIQLNASVPSPDAIEEKLQANNI---------------FTIAS---GKVDNGQKFF 65 (114)
T ss_dssp T----HHHHHHHHHHS-GGG--EEEEEETT----HHHHHHHHHCTT----------------EEEEE---EECTT-EEEE
T ss_pred CCccCHHHHHHHHHhCCcccceEEEEeccccCCcHHHHHHHHHHCCE---------------EEEec---CCCCccccEE
Confidence 46799999999999999998 555544411111111111 33333 22222 33442 433
Q ss_pred hhhhhccccceeeEEEeeeccccccccCCCcceeeEEEEEEEcCCccchhhc
Q 001962 819 CYAAKTWYGGFVGMMIFGASEVSRNVDLGDETTTMMCKFVVRASDSSITKEI 870 (990)
Q Consensus 819 CyAAkTW~GDfVgMmiFGaSevs~nvDLGdet~tMvCkFvvRASsasi~~eI 870 (990)
.|++++=-|.++++=+--....+ .|++-+|+++.++..-+
T Consensus 66 y~s~~~~~~~~fL~El~~~~~~~------------~~~v~vK~~~~~~~~~f 105 (114)
T PF09066_consen 66 YFSAKTTNGIWFLVELTIDPGSP------------SVKVTVKSENPEMAPLF 105 (114)
T ss_dssp EEEEEBTTS-EEEEEEEE-TT-S------------SEEEEEEESSCCCHHHH
T ss_pred EEEEEcCCCcEEEEEEEEcCCCc------------cEEEEEecCCHHHHHHH
Confidence 46777776776654333222221 46888999998765544
No 4
>PF02296 Alpha_adaptin_C: Alpha adaptin AP2, C-terminal domain; InterPro: IPR003164 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. AP adaptor alpha-adaptin can be divided into a trunk domain and the C-terminal appendage domain (or ear domain), separated by a linker region. The C-terminal appendage domain regulates translocation of endocytic accessory proteins to the bud site []. This entry represents a subdomain of the appendage (ear) domain of alpha-adaptin from AP clathrin adaptor complexes. This domain has a three-layer arrangement, alpha-beta-alpha, with a bifurcated antiparallel beta-sheet []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1KYF_A 1B9K_A 1QTS_A 1KYU_A 2VJ0_A 1KY6_A 1W80_A 3HS8_A 1KYD_A 1QTP_A ....
Probab=53.47 E-value=37 Score=32.06 Aligned_cols=103 Identities=22% Similarity=0.326 Sum_probs=53.8
Q ss_pred ccCcCChhhhhhhcCCCcce-EEEEEEEe--eecCcchhhhhh--hcCC-CccccccccccCCCcceeeceeeeeccchh
Q 001962 744 LPHKISPVEFFRLWPSLPAI-VEYTGTYI--YEGSGFKATAAQ--QYGT-SPFFSGLKSLSSKPFHIVCSHIIQAVAGFQ 817 (990)
Q Consensus 744 lP~klSpveFfRLWpsLPAi-ve~tgay~--yEG~G~kaa~aa--~~g~-SP~lSGLkslSskPFH~vcshiLRtvagFQ 817 (990)
-|..+++.+||.=|-.|..- -|..-.+. ..+.....+..+ ..|. -..+ +.+...|--.|+.=+++|-++=+
T Consensus 3 ~p~~l~~~~Ff~RWkql~~~~~E~Q~vf~~~~~~~~~~~~~~~~~l~g~~~~vl---~~vDpnp~n~v~Agi~~t~~~g~ 79 (113)
T PF02296_consen 3 EPTTLSSEDFFQRWKQLGGPPQEAQEVFKLKDAKRPMDLESIRRKLEGFGFAVL---DGVDPNPNNIVGAGIFHTKSSGN 79 (113)
T ss_dssp EE----HHHHHHHHTTT-SGGGEEEEEEE----SS---HHHHHHHHHHHTSEEE---TSSSSSTTSEEEEEEEE-S-S-E
T ss_pred CCccCCHHHHHHHHHhccCCccccEEEEcccccCCcccHHHHHHHHhcCCeEec---CCCCCCcccEEEEEEEEecCCCc
Confidence 48999999999999999421 23222222 233333333332 1111 1133 44577888999999999973322
Q ss_pred hhhhhhccccceeeEEEeeeccccccccCCCcceeeEEEEEEEcCCccchhhcc
Q 001962 818 LCYAAKTWYGGFVGMMIFGASEVSRNVDLGDETTTMMCKFVVRASDSSITKEIG 871 (990)
Q Consensus 818 ~CyAAkTW~GDfVgMmiFGaSevs~nvDLGdet~tMvCkFvvRASsasi~~eI~ 871 (990)
+|-+ -.-|. |-|-+ +|++.+|++++.+...|.
T Consensus 80 ------------~gcL--lRlE~--n~~~~------~~RlTvRst~~~vs~~l~ 111 (113)
T PF02296_consen 80 ------------VGCL--LRLEP--NQDAK------MFRLTVRSTDPSVSKALC 111 (113)
T ss_dssp ------------EEEE--EEEEE--ETTTT------EEEEEEEESSHHHHHHHH
T ss_pred ------------EEEE--EEEeE--CCcCC------eEEEEEEECChhHHHHHh
Confidence 2221 12333 23333 889999999998887664
No 5
>KOG3068 consensus mRNA splicing factor [RNA processing and modification]
Probab=51.41 E-value=25 Score=38.12 Aligned_cols=106 Identities=27% Similarity=0.385 Sum_probs=62.1
Q ss_pred EcCCccchhhcccchhhhhhhhccCccccccchhhhhhhHHHHHHHHHHHHHhhhcCCCCCCCCchhhhh-----hhhhH
Q 001962 860 RASDSSITKEIGSDLQGWLDDLTDGGVEYMPEDEVKASAAERLRISMERIALLKAARPKKTPKTDEEEEN-----EVEEE 934 (990)
Q Consensus 860 RASsasi~~eI~sDlq~WLdDLTD~~vr~~~e~eV~~aaaEklkrsme~~al~ka~~~~~~p~~~~~ee~-----e~~~~ 934 (990)
|.+-+++++.|++.--|.+||- ||.+.-+ |...... -..++.|--++.|+++..+.- +|++|+ +++++
T Consensus 147 rk~rael~k~iDa~yfgY~dde-dg~L~~l-E~~~E~~---~~~~~v~ew~~~k~ar~~~~~--~deee~~~~~l~~~~~ 219 (268)
T KOG3068|consen 147 RKTRAELMKRIDAEYFGYLDDE-DGVLEPL-EAKIESK---NRERIVEEWRIEKQARKGPVE--EDEEEEEIYPLEEDEE 219 (268)
T ss_pred cchHHHHHHhhhHHHccccccc-chhhhHH-HHHHHHH---HHHHHHHHHHHHHHHhcCCcc--chhhhhhhhhcccchh
Confidence 5566788888999999999864 3444321 1111111 234566667778887644432 333332 12333
Q ss_pred HHHhhcccccCcccCCCCCCCccccCCHHHHHHHHHHH
Q 001962 935 EEDKKKNKEDGEEDGKAKGPSTLSKLTAEEAEHLALQA 972 (990)
Q Consensus 935 ~~~~kk~~~~~~e~~~~kgpstl~~~t~ee~eh~alq~ 972 (990)
+..+..+.+...|+++++--...--||-.||||+-||.
T Consensus 220 ~~~E~~~~~~~~ed~~~~f~~hV~vPtqqdiE~~Ller 257 (268)
T KOG3068|consen 220 DVIEEQESEVIGEDGRPKFIAHVPVPTQQDIEEMLLER 257 (268)
T ss_pred hHHHHHHhhhccccccccceeeccCCCHHHHHHHHHHH
Confidence 44444444445566666655566689999999988874
No 6
>TIGR02511 type_III_tyeA type III secretion effector delivery regulator, TyeA family. Members of this family include both small proteins, about 90 amino acids, in which this model covers the whole, and longer proteins of about 360 residues which match in the C-terminal region. The longer proteins (HrpJ) have N-terminal regions that match Pfam model pfam07201. Members of this family belong to bacterial type III secretion systems, and include TyeA from the well-studied Yersinia systems. TyeA appears involved in calcium-responsive regulation of the delivery of type III effectors.
Probab=50.87 E-value=23 Score=31.76 Aligned_cols=44 Identities=25% Similarity=0.370 Sum_probs=36.3
Q ss_pred HHhhhccccchhhHHHHHHHHHHHhhcc-----cccchhHHHHHHHhhhh
Q 001962 191 VVTNLHLLDLHLQVSLFRRLLLMVRNLR-----AESDRMHALACICRTAL 235 (990)
Q Consensus 191 vv~nl~lldlh~qvslfkrlllmvrnlr-----ae~drmhalacicrtal 235 (990)
+++-+.+-|.+.|+.+|+++..++|+|. -+-.|+++|.| ||.++
T Consensus 27 l~~~l~~~~~~~qv~fl~~l~~l~~~lP~~lf~D~eqR~~~L~~-~~~~~ 75 (79)
T TIGR02511 27 LANALGLPELEHRVAFLQGLKRLLRLLPIALFSDEEQRQNLLQA-LQEAI 75 (79)
T ss_pred HHHHccCccHHHHHHHHHHHHHHHHHCCHHHhCCHHHHHHHHHH-HHHHH
Confidence 5666788899999999999999999985 46789999997 45543
No 7
>cd06902 lectin_ERGIC-53_ERGL ERGIC-53 and ERGL type 1 transmembrane proteins, N-terminal lectin domain. ERGIC-53 and ERGL, N-terminal carbohydrate recognition domain. ERGIC-53 and ERGL are eukaryotic mannose-binding type 1 transmembrane proteins of the early secretory pathway that transport newly synthesized glycoproteins from the endoplasmic reticulum (ER) to the ER-Golgi intermediate compartment (ERGIC). ERGIC-53 and ERGL have an N-terminal lectin-like carbohydrate recognition domain (represented by this alignment model) as well as a C-terminal transmembrane domain. ERGIC-53 functions as a 'cargo receptor' to facilitate the export of glycoproteins with different characteristics from the ER, while the ERGIC-53-like protein (ERGL) which may act as a regulator of ERGIC-53. In mammals, ERGIC-53 forms a complex with MCFD2 (multi-coagulation factor deficiency 2) which then recruits blood coagulation factors V and VIII. Mutations in either MCFD2 or ERGIC-53 cause a mild form of inherite
Probab=47.82 E-value=14 Score=38.04 Aligned_cols=31 Identities=23% Similarity=0.290 Sum_probs=28.5
Q ss_pred cCCCCcccccccccCCCccccceeEEEeecc
Q 001962 518 SHPENKWACVNEARGDYPFSHHKLTVQFYEA 548 (990)
Q Consensus 518 ~hp~~kw~g~~~a~gdypfshhkltvq~~e~ 548 (990)
.-|.+.+.|++.+||+++=+|.=|++++|+.
T Consensus 194 ~LP~~~yfGiSA~Tg~l~d~hDIls~~~~sl 224 (225)
T cd06902 194 VLPPNGYFGVSAATGGLADDHDVLSFLTFSL 224 (225)
T ss_pred eCCCCCEEEEEecCCCCCCcEeEEEEEEecc
Confidence 4688999999999999999999999999964
No 8
>PF09059 TyeA: TyeA; InterPro: IPR015144 This domain is composed of two pairs of parallel alpha-helices, and interacts with the bacterial protein YopN via hydrophobic residues located on the helices. Association of TyeA with the C terminus of YopN is accompanied by conformational changes in both polypeptides that create order out of disorder: the resulting structure then serves as an impediment to type III secretion of YopN []. ; PDB: 1XL3_D.
Probab=41.37 E-value=43 Score=31.15 Aligned_cols=47 Identities=21% Similarity=0.345 Sum_probs=37.1
Q ss_pred HHHHHHhhhccccchhhHHHHHHHHHHHhhcccc-----cchhHHHHHHHhhh
Q 001962 187 IVRAVVTNLHLLDLHLQVSLFRRLLLMVRNLRAE-----SDRMHALACICRTA 234 (990)
Q Consensus 187 ivravv~nl~lldlh~qvslfkrlllmvrnlrae-----~drmhalacicrta 234 (990)
=+..+.+.+.+.|...|+..|+++..++|.+.++ -.|++-|++ |..|
T Consensus 25 ~i~~l~~~~~~~d~e~qI~Flrel~~l~r~~Pv~vF~D~EqR~~vL~a-~Q~a 76 (87)
T PF09059_consen 25 QIERLAEALGLPDIEQQILFLRELKELFRLMPVDVFNDEEQRQNVLDA-VQEA 76 (87)
T ss_dssp HHHHHHHCT--SSHHHHHHHHHHHHHHHHTS-GGGSS-HHHHHHHHHH-HHHH
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHHHHHCcHHhcCCHHHHHHHHHH-HHHH
Confidence 3678899999999999999999999999999876 478988876 4444
No 9
>KOG2894 consensus Uncharacterized conserved protein XAP-5 [Function unknown]
Probab=40.33 E-value=30 Score=38.34 Aligned_cols=92 Identities=18% Similarity=0.230 Sum_probs=45.2
Q ss_pred ccchhhhhhh--HHHHHHHHHHHHHhhhcCCCCCCCCc---hhhhhhhhhHHHHhh-cccccCcccCCCCCCCccccCCH
Q 001962 889 MPEDEVKASA--AERLRISMERIALLKAARPKKTPKTD---EEEENEVEEEEEDKK-KNKEDGEEDGKAKGPSTLSKLTA 962 (990)
Q Consensus 889 ~~e~eV~~aa--aEklkrsme~~al~ka~~~~~~p~~~---~~ee~e~~~~~~~~k-k~~~~~~e~~~~kgpstl~~~t~ 962 (990)
+.++|-+++- -.+.++--+-.++.|.-.......++ =-+++|++|+|.+++ ...+.+.-...|.- .|-+.|..
T Consensus 80 VreRekqlak~~~~k~q~k~~e~~~eKe~K~~kkr~~s~LSFa~DdEededD~~~k~~~~Kk~klGKdP~V-DTSFLPDr 158 (331)
T KOG2894|consen 80 VREREKQLAKKKLSKTQQKKRELAREKEEKKEKKRQISRLSFALDDEEDEDDAEEKSIPLKKGKLGKDPDV-DTSFLPDR 158 (331)
T ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccchhhcchhhhhcCCCCCc-ccccCCch
Confidence 4555555555 33444444445555544333322222 112222222233333 33333333344433 34455554
Q ss_pred H-HHHHHHHHHHHHHHHHHH
Q 001962 963 E-EAEHLALQAAVLQEWHMR 981 (990)
Q Consensus 963 e-e~eh~alq~avl~ew~~~ 981 (990)
| |.|-+++..-+-|||.+-
T Consensus 159 EREeeEnr~RE~L~~eW~~~ 178 (331)
T KOG2894|consen 159 EREEEENRLREELRQEWEAK 178 (331)
T ss_pred hhHHHHHHHHHHHHHHHHHH
Confidence 4 788899999999999764
No 10
>PLN03237 DNA topoisomerase 2; Provisional
Probab=38.02 E-value=30 Score=44.65 Aligned_cols=9 Identities=44% Similarity=0.781 Sum_probs=6.4
Q ss_pred hhhhhhhhc
Q 001962 874 LQGWLDDLT 882 (990)
Q Consensus 874 lq~WLdDLT 882 (990)
.+-|++||.
T Consensus 1151 ~~lW~~DLd 1159 (1465)
T PLN03237 1151 KSLWLKDLD 1159 (1465)
T ss_pred HHHHHHHHH
Confidence 456888884
No 11
>PHA03211 serine/threonine kinase US3; Provisional
Probab=34.83 E-value=57 Score=36.34 Aligned_cols=74 Identities=24% Similarity=0.312 Sum_probs=43.0
Q ss_pred hhhHHHHHHHHHHHHHhhhcCCCCCCCCchhhhhhhhhHHHHhhcccccCcc------------cCCCCCCCccccCCHH
Q 001962 896 ASAAERLRISMERIALLKAARPKKTPKTDEEEENEVEEEEEDKKKNKEDGEE------------DGKAKGPSTLSKLTAE 963 (990)
Q Consensus 896 ~aaaEklkrsme~~al~ka~~~~~~p~~~~~ee~e~~~~~~~~kk~~~~~~e------------~~~~kgpstl~~~t~e 963 (990)
...|++|-..-|.+|++...+..|.. .+++++++++++.++-+..+++.+ ...+-||+.-..+|++
T Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~ 139 (461)
T PHA03211 62 RDEAARLCQIQELLAEMRSSEEYPDS--GAEAEDDDDDDAPDDVAYPDEYAEDDFLPGDGAPDHDPAPCGPAPPGGLTPE 139 (461)
T ss_pred hhHHHHHHHHHHHHHHHhccCCCCCC--ChhhhccCCCCCccccCCCCCCCCcceecCCCCCCCCCCCCCCCCCCCCChh
Confidence 46789999999999999976654432 222233333232233233333221 2223456667778899
Q ss_pred HHHHHHHH
Q 001962 964 EAEHLALQ 971 (990)
Q Consensus 964 e~eh~alq 971 (990)
+.+++.-+
T Consensus 140 ~l~~~~~~ 147 (461)
T PHA03211 140 ELERLDRE 147 (461)
T ss_pred hhhhhhhh
Confidence 98876544
No 12
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=31.84 E-value=40 Score=36.58 Aligned_cols=25 Identities=20% Similarity=0.314 Sum_probs=13.7
Q ss_pred eEEEEEEEecCCcccccceeeEEecce
Q 001962 618 KITLHLKVLNLTELELNRVDIRVGLSG 644 (990)
Q Consensus 618 RlTLHLKv~Nlte~eL~rvdvrVGL~G 644 (990)
...+.+...|+|...|. ++|--|.|
T Consensus 23 ~~v~iv~~~gl~~~ql~--~lR~~lr~ 47 (330)
T PRK04019 23 PVVGIVDLEGIPARQLQ--EIRRKLRG 47 (330)
T ss_pred CEEEEEEcCCCCHHHHH--HHHHHHHc
Confidence 34455666677766555 44444444
No 13
>PF04712 Radial_spoke: Radial spokehead-like protein
Probab=31.23 E-value=26 Score=40.16 Aligned_cols=26 Identities=23% Similarity=0.405 Sum_probs=17.7
Q ss_pred cchhhhhhhhhhhHHHHHHHHhhccCCCC
Q 001962 494 NSTLADSVNKHQCRLILQRIKYASSHPEN 522 (990)
Q Consensus 494 ~~~ladsv~khqcrlilq~~ky~~~hp~~ 522 (990)
++.-.+|+-.|-|++|.+ .+..+|+|
T Consensus 16 s~~~G~sLYdHL~~vL~k---IL~ErP~n 41 (491)
T PF04712_consen 16 SNKSGDSLYDHLSDVLTK---ILDERPEN 41 (491)
T ss_pred cCCCCCcHHHHHHHHHHH---HHHhCCCc
Confidence 445567788888888874 34567766
No 14
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=29.40 E-value=24 Score=38.25 Aligned_cols=11 Identities=0% Similarity=0.027 Sum_probs=5.6
Q ss_pred ccccchhhhhh
Q 001962 887 EYMPEDEVKAS 897 (990)
Q Consensus 887 r~~~e~eV~~a 897 (990)
-|+.++.++..
T Consensus 253 ~~~t~e~~~~i 263 (330)
T PRK04019 253 GIVTPETADDI 263 (330)
T ss_pred CCCChhhHHHH
Confidence 45555555443
No 15
>KOG2573 consensus Ribosome biogenesis protein - Nop56p/Sik1p [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=26.17 E-value=37 Score=39.25 Aligned_cols=33 Identities=15% Similarity=0.303 Sum_probs=20.2
Q ss_pred hhhhccCccccccchhhhhhhHHHHHHHHHHHH
Q 001962 878 LDDLTDGGVEYMPEDEVKASAAERLRISMERIA 910 (990)
Q Consensus 878 LdDLTD~~vr~~~e~eV~~aaaEklkrsme~~a 910 (990)
|...++.-++|+.-.++-.---.-.++.||++.
T Consensus 399 Lr~qVEeRL~fy~tg~~p~kn~~vmkea~e~~~ 431 (498)
T KOG2573|consen 399 LREQVEERLEFYETGEAPRKNSDVMKEAMEAYN 431 (498)
T ss_pred HHHHHHHHHHhhhcCCccchhhHHHHHHHHHhc
Confidence 444555566666655555555556777788765
No 16
>PF05308 Mito_fiss_reg: Mitochondrial fission regulator; InterPro: IPR007972 This family consists of several uncharacterised eukaryotic proteins of unknown function.
Probab=24.95 E-value=37 Score=36.22 Aligned_cols=27 Identities=44% Similarity=0.744 Sum_probs=23.3
Q ss_pred HhhccccccchhHHHHHHHHHhhhcccc
Q 001962 172 LTLWDRQEFSSARESIVRAVVTNLHLLD 199 (990)
Q Consensus 172 ltlwdrqef~~~resivravv~nl~lld 199 (990)
+-+|..++|.+.| ||||-+=|||-|--
T Consensus 3 ~~~w~~K~yGs~R-SIVR~IGt~LPL~p 29 (253)
T PF05308_consen 3 LPIWSNKPYGSSR-SIVRRIGTNLPLKP 29 (253)
T ss_pred cccccCCCCcchH-HHHHHHhccCCCCC
Confidence 3469999999996 89999999998764
No 17
>cd05753 Ig2_FcgammaR_like Second immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs) and similar proteins. Ig2_FcgammaR_like: domain similar to the second immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs). Interactions between IgG and FcgammaR are important to the initiation of cellular and humoral response. IgG binding to FcgammaR leads to a cascade of signals and ultimately to functions such as antibody-dependent-cellular-cytotoxicity (ADCC), endocytosis, phagocytosis, release of inflammatory mediators, etc. FcgammaR has two Ig-like domains. This group also contains FcepsilonRI, which binds IgE with high affinity.
Probab=24.77 E-value=37 Score=29.08 Aligned_cols=13 Identities=54% Similarity=1.203 Sum_probs=10.7
Q ss_pred CCCceEEeecccc
Q 001962 724 LGEPVILRCQPYK 736 (990)
Q Consensus 724 ygepViLRCqpYk 736 (990)
-|++|+|||+..+
T Consensus 13 ~G~~vtL~C~~~~ 25 (83)
T cd05753 13 EGEPLVLRCHGWK 25 (83)
T ss_pred CCCCEEEEeeCCC
Confidence 4889999999743
No 18
>PF06964 Alpha-L-AF_C: Alpha-L-arabinofuranosidase C-terminus; InterPro: IPR010720 This entry represents the C terminus (approximately 200 residues) of bacterial and eukaryotic alpha-L-arabinofuranosidase (3.2.1.55 from EC). This catalyses the hydrolysis of non-reducing terminal alpha-L-arabinofuranosidic linkages in L-arabinose-containing polysaccharides [].; GO: 0046556 alpha-N-arabinofuranosidase activity, 0046373 L-arabinose metabolic process; PDB: 3FW6_A 3II1_A 3S2C_K 1QW9_A 1PZ3_B 1PZ2_B 1QW8_A 3UG4_A 3UG3_A 4ATW_B ....
Probab=24.55 E-value=1.9e+02 Score=27.99 Aligned_cols=69 Identities=26% Similarity=0.387 Sum_probs=44.7
Q ss_pred CccEEEeeeeccCCCCeEEEEEEEecCCcccccceeeEE-e----cceeeecccC-chHHHHHhcccccCCceeeeeEee
Q 001962 602 DPCYVEAYHLADSSDGKITLHLKVLNLTELELNRVDIRV-G----LSGALYFMNG-SPQAVRQLRNLVSQDPVICSVTVG 675 (990)
Q Consensus 602 DPCyVEAyHladP~~~RlTLHLKv~Nlte~eL~rvdvrV-G----L~GAL~fmDG-s~QaVrqL~~L~sqdpv~~svtvg 675 (990)
.++|+-|+. |.+.+. |.||+.|.+..+.. +++.+ | -.|-++.+-| ++.+...+.+...=-|+...++..
T Consensus 91 ~~l~~~As~--d~~~~~--l~v~vVN~~~~~~~-v~l~l~g~~~~~~a~~~~Ltg~~~~a~Nt~~~p~~V~p~~~~~~~~ 165 (177)
T PF06964_consen 91 PPLDVSASR--DEDGGE--LYVKVVNRSSEPQT-VTLNLQGFSPAATATVTTLTGDDPDAENTFENPENVVPVTSTVSAE 165 (177)
T ss_dssp ESEEEEEEE--ETTTTE--EEEEEEE-SSSBEE-EEEEETTSTS-EEEEEEEEETSSTT-B-CSSSTTSSEEEEEEEEEE
T ss_pred ccEEEEEEE--ECCCCE--EEEEEEECCCCCEE-EEEEEcCCCCCceEEEEEEECCCcccccCCCCCCEEEEEEeeEEec
Confidence 788888888 555554 66799999877544 55555 3 2345677777 678888777777666776666544
No 19
>TIGR01874 cas_cas5a CRISPR-associated protein Cas5, Apern subtype. This model represents a minor family of CRISPR-associated (Cas) protein. These proteins are found adjacent to a characteristic short, palidromic repeat cluster termed CRISPR, a probable mobile DNA element. This family belongs to a set of several Cas proteins, one each for a number of different CRISPR/Cas subtypes, that share a region of N-terminal sequence similarity modeled by TIGR02593. The family is designated Cas5a, for CRISPR-associated protein Cas5, Apern subtype.
Probab=22.30 E-value=30 Score=35.35 Aligned_cols=33 Identities=48% Similarity=0.677 Sum_probs=23.9
Q ss_pred ccCCcccccCCCCccccccccccCCCCcccc----ccchhhhh
Q 001962 295 SLPLPEQKNSGMESRVIGALAYGTGYGALNW----TEPALEVV 333 (990)
Q Consensus 295 s~plp~~k~~g~esrvigalaygt~~ga~~w----t~~alevv 333 (990)
|+|||.- |-|||||+||.--|+.+| .++|++-+
T Consensus 22 s~pLPpp------STl~Gal~~g~~~~~~~~g~~~~~~~~~~~ 58 (172)
T TIGR01874 22 SLPLPPP------STLIGALSYGKYLLGDTKGGKAGSPALKIV 58 (172)
T ss_pred CCCCCCh------HHHHHHHHhhhhhhccccccccCchhhhhh
Confidence 6888865 679999999887766665 34555444
No 20
>cd06901 lectin_VIP36_VIPL VIP36 and VIPL type 1 transmembrane proteins, lectin domain. The vesicular integral protein of 36 kDa (VIP36) is a type 1 transmembrane protein of the mammalian early secretory pathway that acts as a cargo receptor transporting high mannose type glycoproteins between the Golgi and the endoplasmic reticulum (ER). Lectins of the early secretory pathway are involved in the selective transport of newly synthesized glycoproteins from the ER to the ER-Golgi intermediate compartment (ERGIC). The most prominent cycling lectin is the mannose-binding type1 membrane protein ERGIC-53, which functions as a cargo receptor to facilitate export of glycoproteins from the ER. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the "front face" and a flat six-stranded beta-sheet referred to as the "back face". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded she
Probab=21.98 E-value=68 Score=33.73 Aligned_cols=34 Identities=21% Similarity=0.353 Sum_probs=30.2
Q ss_pred cCCCCcccccccccCCCccccceeEEEeeccccc
Q 001962 518 SHPENKWACVNEARGDYPFSHHKLTVQFYEASGA 551 (990)
Q Consensus 518 ~hp~~kw~g~~~a~gdypfshhkltvq~~e~saa 551 (990)
.-|.+.+.|++.+||+++=+|==++|++|+....
T Consensus 193 ~LP~~~yfGiSA~Tg~~sd~hdIlsv~~~~l~~~ 226 (248)
T cd06901 193 RLPTGYYFGASAATGDLSDNHDIISMKLYELDVE 226 (248)
T ss_pred ecCCCCEEEEEecCCCCCCcEEEEEEEEecCccc
Confidence 4688899999999999998888999999997654
No 21
>PF14807 AP4E_app_platf: Adaptin AP4 complex epsilon appendage platform
Probab=21.05 E-value=2.3e+02 Score=27.09 Aligned_cols=100 Identities=23% Similarity=0.198 Sum_probs=61.4
Q ss_pred cCcCChhhhhhhcCCCcceEEEEEEEeeecCcchhhhhhhcCCCccccccccccCCCcceeeceeeeeccchhhhhhhhc
Q 001962 745 PHKISPVEFFRLWPSLPAIVEYTGTYIYEGSGFKATAAQQYGTSPFFSGLKSLSSKPFHIVCSHIIQAVAGFQLCYAAKT 824 (990)
Q Consensus 745 P~klSpveFfRLWpsLPAive~tgay~yEG~G~kaa~aa~~g~SP~lSGLkslSskPFH~vcshiLRtvagFQ~CyAAkT 824 (990)
|-.||-.||=-+|.+++.-.+.+.. -.++.+-.-.... +... ..||-|. +| |-..=+|++.
T Consensus 2 Pl~isTeeFG~~W~s~~~e~k~~l~---~~~~~t~~~~l~~----l~~~------l~lh~Ve--vI----g~E~I~A~~l 62 (104)
T PF14807_consen 2 PLQISTEEFGQLWLSFSNERKQNLP---SSSQRTLPEFLQR----LQQK------LRLHVVE--VI----GNEGIFACQL 62 (104)
T ss_pred CccccHHHHHHHHHcCCCeEEEecc---ccCcCCHHHHHHH----HHHh------cCceEEE--Ee----Cccceeeeec
Confidence 7789999999999999988877765 2222111111100 1111 2335543 22 2255567777
Q ss_pred cccceeeEEEeeeccccccccCCCcceeeEEEEEEEcCCccchhhcccchhh
Q 001962 825 WYGGFVGMMIFGASEVSRNVDLGDETTTMMCKFVVRASDSSITKEIGSDLQG 876 (990)
Q Consensus 825 W~GDfVgMmiFGaSevs~nvDLGdet~tMvCkFvvRASsasi~~eI~sDlq~ 876 (990)
--++.+.|+=...... .-.+.+|++|....+.|-.+.|.
T Consensus 63 l~~~~~~L~H~~~~~~-------------~l~l~vrs~~~~l~d~ll~~~~~ 101 (104)
T PF14807_consen 63 LNSSPVCLLHCRVNAG-------------TLDLWVRSSDSPLTDCLLYQCQK 101 (104)
T ss_pred cCCCCeEEEEEEecCC-------------eEEEEEEcCCCCcHHHHHHHHHH
Confidence 7777754443333222 34889999999999999887765
No 22
>PF02459 Adeno_terminal: Adenoviral DNA terminal protein; InterPro: IPR003391 The genome of adenovirus contains a protein covalently bound to the 5' end of each strand of the linear DNA molecule []. Since adenovirus DNA replication is initiated at the termini of the DNA molecule it has been proposed that the terminal protein serves as the primer for initiation of replication. However, the priming function now appears to reside in the precursor form of the terminal protein (pTP) found on the 5' ends of nascent DNA strands replicated in vitro [, ] and as a component of DNA-protein complexes isolated from virions of the protease-deficient adenovirus serotype 2 (Ad2) mutant tsl. The pTP is encoded by the leftward-transcribed strand of the viral genome and comprises part of a transcription unit that also encodes the single-strand DNA binding protein [].; GO: 0003677 DNA binding, 0006260 DNA replication
Probab=21.00 E-value=35 Score=40.22 Aligned_cols=21 Identities=10% Similarity=0.330 Sum_probs=12.2
Q ss_pred chHHHHHhcccccCCceeeee
Q 001962 652 SPQAVRQLRNLVSQDPVICSV 672 (990)
Q Consensus 652 s~QaVrqL~~L~sqdpv~~sv 672 (990)
......|+++....|-|..|+
T Consensus 88 F~etl~qiQqaIL~dRIvADL 108 (548)
T PF02459_consen 88 FEETLTQIQQAILADRIVADL 108 (548)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 455566666666655555544
No 23
>KOG3980 consensus RNA 3'-terminal phosphate cyclase [RNA processing and modification]
Probab=20.08 E-value=53 Score=37.16 Aligned_cols=63 Identities=25% Similarity=0.419 Sum_probs=43.9
Q ss_pred eeeeeEeeeecccccceeee--eeeccccCCC------CCCCCCCCccccc------h----------hHHhhhcccCCC
Q 001962 668 VICSVTVGVSHFERCAFWVQ--VLYYPFHGSG------AIGDYEGDYAEED------P----------QIMRQKRSARPE 723 (990)
Q Consensus 668 v~~svtvgVS~ferc~l~vQ--vLyyPf~Gs~------G~g~~E~D~~~E~------~----------~~~rqr~~~rpe 723 (990)
+.|+++-+++-| .| +.-+||.++- |....++|..+|. | .++-|||.+.|+
T Consensus 86 ~dc~t~~~I~y~------leplL~l~pF~k~P~~i~lkGvTN~~~~p~VD~ik~~~lpvlkkFgv~~~elki~kRG~~P~ 159 (361)
T KOG3980|consen 86 HDCPTARSIGYF------LEPLLPLCPFAKSPLRITLKGVTNSDGDPSVDYIKAVLLPVLKKFGVNDEELKIQKRGFAPE 159 (361)
T ss_pred EeccCccceeee------hhhHHhhhcccCCCeEEEEecccCCCCCcchHHHHHHHHHHHHHhCcCcceEEEEecccCCC
Confidence 567777777766 77 4457898875 5334445544443 1 123478999999
Q ss_pred CCCceEEeecccc
Q 001962 724 LGEPVILRCQPYK 736 (990)
Q Consensus 724 ygepViLRCqpYk 736 (990)
=|+.|+++|+|-|
T Consensus 160 GgGeV~f~~~~~k 172 (361)
T KOG3980|consen 160 GGGEVVFTVPVVK 172 (361)
T ss_pred CCcEEEEEcCccc
Confidence 9999999999877
Done!