Query psy15258
Match_columns 265
No_of_seqs 163 out of 274
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 16:23:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15258.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15258hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4071|consensus 100.0 2.4E-61 5.1E-66 416.9 13.5 174 1-178 3-176 (187)
2 COG5093 Uncharacterized conser 100.0 3.1E-48 6.6E-53 328.3 12.8 171 1-176 11-183 (185)
3 PTZ00362 hypothetical protein; 100.0 3.6E-43 7.8E-48 338.0 14.8 167 10-181 282-464 (479)
4 KOG4071|consensus 99.9 1.2E-23 2.6E-28 182.6 5.6 76 176-256 104-179 (187)
5 PF05916 Sld5: GINS complex pr 99.8 1.9E-18 4.1E-23 134.2 9.9 104 43-154 1-108 (108)
6 COG5093 Uncharacterized conser 99.6 2.2E-16 4.7E-21 134.6 5.6 70 175-250 113-182 (185)
7 PTZ00362 hypothetical protein; 99.4 4.8E-13 1E-17 130.2 9.6 96 143-248 360-456 (479)
8 KOG1106|consensus 97.3 0.0011 2.3E-08 58.3 7.7 98 9-109 21-118 (177)
9 PF05916 Sld5: GINS complex pr 94.7 0.052 1.1E-06 41.6 4.5 43 187-229 65-108 (108)
10 COG5138 Uncharacterized conser 93.8 0.12 2.7E-06 44.5 5.1 89 8-99 9-97 (168)
11 COG1711 DNA replication initia 75.4 11 0.00024 34.5 6.9 83 67-153 1-97 (223)
12 COG4218 MtrF Tetrahydromethano 35.8 40 0.00087 25.8 2.8 33 178-210 11-48 (73)
13 PF03233 Cauli_AT: Aphid trans 35.3 2.5E+02 0.0055 24.7 8.0 76 59-136 51-130 (163)
14 PTZ00095 40S ribosomal protein 34.0 26 0.00056 30.9 1.7 63 26-100 11-83 (169)
15 COG3248 Tsx Nucleoside-binding 31.3 23 0.00049 33.1 1.0 40 14-54 100-165 (284)
16 PRK09333 30S ribosomal protein 29.1 36 0.00079 29.4 1.8 40 49-100 16-59 (150)
17 PF11568 Med29: Mediator compl 29.1 1.2E+02 0.0026 26.2 5.0 58 185-246 6-64 (148)
18 COG3924 Predicted membrane pro 26.2 57 0.0012 25.2 2.2 34 66-101 17-53 (80)
19 PF10792 DUF2605: Protein of u 26.1 1.7E+02 0.0036 23.8 4.9 37 91-127 20-56 (98)
20 PF08542 Rep_fac_C: Replicatio 25.7 1.1E+02 0.0023 22.7 3.7 33 107-139 1-33 (89)
21 PF08690 GET2: GET complex sub 24.4 22 0.00047 33.9 -0.4 12 121-132 11-22 (302)
22 PF11198 DUF2857: Protein of u 23.6 3.7E+02 0.008 23.4 7.2 84 148-237 26-112 (180)
23 PF01090 Ribosomal_S19e: Ribos 22.6 39 0.00084 28.9 0.8 40 49-100 15-58 (139)
24 PRK13655 phosphoenolpyruvate c 22.2 65 0.0014 32.9 2.4 16 62-77 379-394 (494)
25 PF15614 WHIM3: WSTF, HB1, Itc 20.9 1.2E+02 0.0026 21.3 2.8 29 185-213 6-37 (46)
No 1
>KOG4071|consensus
Probab=100.00 E-value=2.4e-61 Score=416.91 Aligned_cols=174 Identities=48% Similarity=0.899 Sum_probs=167.8
Q ss_pred CChhhhhhhhcCceeEEeeCCccccccccccccccCCCCCCccchhHHHHHHhcccCcceeeCCCCCCHHHHHHHHHHhh
Q psy15258 1 MDPAEIEFIAEDQNVEIIPKFNHLNLIHLISGDVGPFRAGIPAKVPLWLAINLKQRQKCRLVLPTWMNLETLTEIKEEEK 80 (265)
Q Consensus 1 m~p~E~eFlAe~e~I~IvP~f~~~~~l~lI~g~~GPF~p~~p~~VPLWlAi~LKk~~kC~IvpP~WL~ve~L~~~l~~E~ 80 (265)
|+|+|++|+|++++|+|+|+|++ ++++||+|++|||.||.|++||||+|++||||++|+|+||.||+++.|+++++.|+
T Consensus 3 ~~peeiefia~~eli~I~P~~S~-~~l~li~~d~gp~~p~~~~rVpLWlAllLKkq~kc~Iv~P~wm~~~~L~~i~d~E~ 81 (187)
T KOG4071|consen 3 MSPEEIEFIAENELIEIIPNISM-DQLHLISGDIGPFNPGVPCRVPLWLALLLKKQNKCRIVPPEWMDVDELEKIRDVEK 81 (187)
T ss_pred CCHHHHHHHhcccceeeccCCcc-hhhhhhcCCCcccCCCCcceehHHHHHHHhhccCceEeCcccccHHHHHHHHHHhh
Confidence 79999999999999999999999 99999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCCccHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCcceecCCchHHHHHhhHHh
Q psy15258 81 KSRFFIKMPSDHYMEMSHIILDIGADDIPNVDLIRTLIKDIWDLRISKLRSSIDTFVKSGGGHATLNHLTQFEINSIRNI 160 (265)
Q Consensus 81 ~~~~Fs~LP~~hy~EiA~lLL~~a~dDi~~~~~ir~Li~DI~evR~~Klr~gl~~~~~~~~~~l~l~NLt~mEin~iR~f 160 (265)
.++.|++|| +||+|+|++|+++|.||||+.++||++|+||||+|++|+|+|++.|.. ..|+++||||+||||++|||
T Consensus 82 e~~tfs~lp-~~~~ela~lL~n~a~Ddi~~~eeiR~lV~DI~d~R~aKlr~s~~~f~~--~~hakldNltLmEiN~~rpf 158 (187)
T KOG4071|consen 82 ESETFSKLP-FYYFELATLLLNFARDDIPDIEEIRTLVKDIRDIRLAKLRTSLDSFNR--QAHAKLDNLTLMEINEIRPF 158 (187)
T ss_pred cccccccCC-hHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHHHHHHHhHHHHhh--HhhcCcccceeeeeccchHH
Confidence 988999999 899999999999999999999999999999999999999999999943 36999999999999999999
Q ss_pred HHHHHHHHhhhhcccccc
Q psy15258 161 LCDVLDTMSSLKDKQCDV 178 (265)
Q Consensus 161 ~~~amd~l~~l~~~~~~~ 178 (265)
++++||+++++++++.+.
T Consensus 159 l~~~l~~~~ki~~~s~~~ 176 (187)
T KOG4071|consen 159 LTEALDHGRKIRQTSKDQ 176 (187)
T ss_pred HHHHHHHHHHHhhhhhhc
Confidence 999999999999766533
No 2
>COG5093 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.1e-48 Score=328.29 Aligned_cols=171 Identities=29% Similarity=0.524 Sum_probs=163.6
Q ss_pred CChhhhhhhhcCceeEEeeCCcccccccccc-ccccCCCCCCccchhHHHHHHhcccCcceeeCCCCCCHHHHHHHHHHh
Q psy15258 1 MDPAEIEFIAEDQNVEIIPKFNHLNLIHLIS-GDVGPFRAGIPAKVPLWLAINLKQRQKCRLVLPTWMNLETLTEIKEEE 79 (265)
Q Consensus 1 m~p~E~eFlAe~e~I~IvP~f~~~~~l~lI~-g~~GPF~p~~p~~VPLWlAi~LKk~~kC~IvpP~WL~ve~L~~~l~~E 79 (265)
++|+|+.|+|++|+|.|+|..++ +.+.|++ .+|+|+.|...++||||+|+.|||+++|+|++|.||+++.|+..++.|
T Consensus 11 fSPEEi~fia~nE~i~I~P~~t~-~qlrL~~~~t~p~m~p~~~~rvpLw~ALlLKkqn~c~Iv~P~wl~~~~L~~~i~~e 89 (185)
T COG5093 11 FSPEEILFIAYNELIEIEPMTTI-PQLRLLERATYPPMMPLDIARVPLWAALLLKKQNMCKIVLPSWLQLESLKMSIDVE 89 (185)
T ss_pred CCHHHHHHHhcccceeeeccccc-chhhhhhhhcCCCCCCchhhhhHHHHHHHHHhcccccccChhHhhHHHHHhhhhHH
Confidence 48999999999999999999999 8899999 599999999999999999999999999999999999999999988888
Q ss_pred hc-cCCCCCCCCccHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCcceecCCchHHHHHhhH
Q psy15258 80 KK-SRFFIKMPSDHYMEMSHIILDIGADDIPNVDLIRTLIKDIWDLRISKLRSSIDTFVKSGGGHATLNHLTQFEINSIR 158 (265)
Q Consensus 80 ~~-~~~Fs~LP~~hy~EiA~lLL~~a~dDi~~~~~ir~Li~DI~evR~~Klr~gl~~~~~~~~~~l~l~NLt~mEin~iR 158 (265)
+. .+.||.+| |||++.|+.||+.|.||+.+.+++|..|+||+++|++|.++|++.+ |+.++++||||+||||+||
T Consensus 90 ~~~~d~fSelp-~~wl~lA~~Lln~~~ddvediee~r~iv~dirEiRq~K~lkGlk~l---ne~~L~ldNl~l~EiNEir 165 (185)
T COG5093 90 IEKADEFSELP-PYWLPLATELLNENCDDVEDIEESRMIVEDIREIRQAKTLKGLKCL---NEKALNLDNLTLFEINEIR 165 (185)
T ss_pred HhcccccccCC-chHHHHHHHHHHhccchHhHHHHHHHHHHHHHHHHHHHHHhhHhhh---hhhhcCccccchhhhhhhH
Confidence 76 89999999 9999999999999999999999999999999999999999999875 8999999999999999999
Q ss_pred HhHHHHHHHHhhhhcccc
Q psy15258 159 NILCDVLDTMSSLKDKQC 176 (265)
Q Consensus 159 ~f~~~amd~l~~l~~~~~ 176 (265)
|++.++||.++++.+.+.
T Consensus 166 p~i~e~md~~R~I~~~s~ 183 (185)
T COG5093 166 PLILESMDVGRRIEDLSK 183 (185)
T ss_pred HHHHHHHHHHHHHHhhhh
Confidence 999999999999987654
No 3
>PTZ00362 hypothetical protein; Provisional
Probab=100.00 E-value=3.6e-43 Score=337.97 Aligned_cols=167 Identities=18% Similarity=0.301 Sum_probs=144.2
Q ss_pred hcCceeEEeeCCcccc-ccccccc-cccCCCCCCccchhHHHHHHhcccCcceeeCCCCCCHHHHHHHHHHh-hccCCCC
Q psy15258 10 AEDQNVEIIPKFNHLN-LIHLISG-DVGPFRAGIPAKVPLWLAINLKQRQKCRLVLPTWMNLETLTEIKEEE-KKSRFFI 86 (265)
Q Consensus 10 Ae~e~I~IvP~f~~~~-~l~lI~g-~~GPF~p~~p~~VPLWlAi~LKk~~kC~IvpP~WL~ve~L~~~l~~E-~~~~~Fs 86 (265)
|-+|+|-|--....|. .+.+|+| ++|||+||.|++||||||++||++++|+|+||.||+++.|++++++| ++++.|+
T Consensus 282 al~eLvVvKalvDip~~~L~lI~G~digpfkag~~~~VPLWLAi~LKq~~KC~IvpP~Wm~ie~Lk~I~eeE~~~~~~Ft 361 (479)
T PTZ00362 282 ALDELVVVKALVDIPYIDLSEIEGFDFKEMKSGERQWLPIYIAKELSHFGLVTVEFPFWFYIKNLKNIYEREFEDQNELT 361 (479)
T ss_pred HhcceEEEEEecCCCCCcceeeeccccCCcCCCCeeEEeeeehhhhcccCceEEeCcccccHHHHHHHHHHHhhCccccc
Confidence 5567777754444411 2378999 99999999999999999999999999999999999999999999999 7789999
Q ss_pred CCCCccHHHHHHHHHhc-------CCCCCCC------hHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCcceecCCchHHH
Q psy15258 87 KMPSDHYMEMSHIILDI-------GADDIPN------VDLIRTLIKDIWDLRISKLRSSIDTFVKSGGGHATLNHLTQFE 153 (265)
Q Consensus 87 ~LP~~hy~EiA~lLL~~-------a~dDi~~------~~~ir~Li~DI~evR~~Klr~gl~~~~~~~~~~l~l~NLt~mE 153 (265)
+||++||+|||++||++ |+||+++ +++||++|+|||++|++|+|+|++.+ ...+.|++++|||.||
T Consensus 362 ~LP~p~y~EIa~lLl~~~~F~~~~a~edi~~~d~~~~~~kVR~LIeDIrd~R~~KIr~~Le~~-~~~ss~i~LdNLslmE 440 (479)
T PTZ00362 362 DLPSPYFFEISSMFLENNIFKKVTPIETIGQRTVYKYISKVAGLVEDIRYKRLKKIMNHLENQ-DVHSSIIYIDNLQISE 440 (479)
T ss_pred cCCchhHHHHHHHHHhcccccccCChhhcccccccccHHHHHHHHHHHHHHHHHHHHHHHHhc-cccccEEEECCccHHH
Confidence 99977999999999999 7777666 69999999999999999999999997 3446899999999999
Q ss_pred HHhhHHhHHHHHHHHhhhhccccccccc
Q psy15258 154 INSIRNILCDVLDTMSSLKDKQCDVDVT 181 (265)
Q Consensus 154 in~iR~f~~~amd~l~~l~~~~~~~d~~ 181 (265)
++.+|+ +|+.+.+.....+..+-+
T Consensus 441 i~~Vn~----~Ls~f~k~d~~~~~~~~~ 464 (479)
T PTZ00362 441 TYCVNQ----LLSVFFQYDKNLNSLTNS 464 (479)
T ss_pred HHHHHH----HHHHHHHhcccccccccc
Confidence 999999 556666666666665555
No 4
>KOG4071|consensus
Probab=99.89 E-value=1.2e-23 Score=182.55 Aligned_cols=76 Identities=39% Similarity=0.649 Sum_probs=71.4
Q ss_pred cccccccccChHHHHHHHHHHHHHHHHHHHhhHHHHHhcCCcccccCCcchHHHHhhhhhHHHHHHHHhhhhccccCccc
Q psy15258 176 CDVDVTLQLNVDLIRTLIKDIWDLRISKLRSSIDTFVKSGGGHATLNHLTQFEINSIRNILCDVLDTMSSLKDKQCDVDV 255 (265)
Q Consensus 176 ~~~d~~~~~~~~~ir~li~Di~d~R~~Klr~~~~~f~~~~~~h~~ldnlt~mEin~irpf~~~~m~~l~~~~~~~~~~~~ 255 (265)
+++||+ ++++||++||||||+|+||+|+|++.|+++ +|||+||||+||||++|||++++||++++++++..+++.
T Consensus 104 a~Ddi~---~~eeiR~lV~DI~d~R~aKlr~s~~~f~~~--~hakldNltLmEiN~~rpfl~~~l~~~~ki~~~s~~~~~ 178 (187)
T KOG4071|consen 104 ARDDIP---DIEEIRTLVKDIRDIRLAKLRTSLDSFNRQ--AHAKLDNLTLMEINEIRPFLTEALDHGRKIRQTSKDQQE 178 (187)
T ss_pred ccccch---hHHHHHHHHHHHHHHHHHHHHHhHHHHhhH--hhcCcccceeeeeccchHHHHHHHHHHHHHhhhhhhccc
Confidence 788999 999999999999999999999999999755 899999999999999999999999999999998877776
Q ss_pred c
Q psy15258 256 T 256 (265)
Q Consensus 256 ~ 256 (265)
+
T Consensus 179 ~ 179 (187)
T KOG4071|consen 179 E 179 (187)
T ss_pred c
Confidence 5
No 5
>PF05916 Sld5: GINS complex protein; InterPro: IPR021151 DNA replication in eukaryotes results from a highly coordinated interaction between proteins, often as part of protein complexes, and the DNA template. One of the key early steps leading to DNA replication is formation of the pre- replication complex, or pre-RC. The pre-RC is formed by the sequential binding of the origin recognition complex (ORC), Cdc6 and Cdt1 proteins, and the MCM complex. Activation of the pre-RC into the initiation complex (IC) is achieved via the action of S-phase kinases, eventually leading to the loading of the replication machinery. Recently, a novel replication complex, GINS (for Go, Ichi, Nii, and San; five, one, two, and three in Japanese), has been identified [, ]. The precise function of GINS is not known. However, genetic and two-hybrid interactions indicate that it mediates the loading of the enzymatic replication machinery at a step after the action of the S-phase kinases []. Furthermore, GINS may be a part of the replication machinery itself, since it is found associated with replicating DNA [, ]. Electron microscopy of GINS shows that it forms a ring-like structure [], reminiscent of the structure of PCNA [], the DNA polymerase delta replication clamp.This observation, coupled with the observed interactions for GINS, indicates that the complex may represent the replication clamp for DNA polymerase epsilon []. The GINS complex is essential for initiation of DNA replication in Xenopus egg extracts []. This 100 kDa stable complex includes Sld5, Psf1, Psf2, and Psf3. Homologues of these components are found also in other eukaryotes. ; PDB: 2EHO_L 2E9X_G 2Q9Q_H 3ANW_B.
Probab=99.77 E-value=1.9e-18 Score=134.15 Aligned_cols=104 Identities=27% Similarity=0.522 Sum_probs=89.9
Q ss_pred cchhHHHHHHhcccCcceeeCCCCCCHHHHHHHHHHhhcc---CCCCCCCCccHHHHHHHHHhcCCCCCCChHHHHHHHH
Q psy15258 43 AKVPLWLAINLKQRQKCRLVLPTWMNLETLTEIKEEEKKS---RFFIKMPSDHYMEMSHIILDIGADDIPNVDLIRTLIK 119 (265)
Q Consensus 43 ~~VPLWlAi~LKk~~kC~IvpP~WL~ve~L~~~l~~E~~~---~~Fs~LP~~hy~EiA~lLL~~a~dDi~~~~~ir~Li~ 119 (265)
++||+|+|..|++++.|+|.+|+|++++++..+..+|++. ..|+++| +||+|.+.+++..+ +.++.++.
T Consensus 1 v~lP~w~a~~L~~~~~~~i~~p~~~~~~~~~~l~~e~~~~~~~~~l~~l~-~~f~~~~~~l~~~~-------~~ik~~l~ 72 (108)
T PF05916_consen 1 VELPLWLAKELKKRNLVEIQPPDWFSIEYLNALEAEEKNNSNKVDLSKLP-PYFYELGEMLLELL-------ERIKRLLR 72 (108)
T ss_dssp EEEEHHHHHHHHHTTSEEEE-TCCHCHHHHHHHHHHHCCCS-HCSCCTSS-TTHHHHHHHHHHHH-------HHHHHHHH
T ss_pred CcCCcchHHHHHHcCCeeecCcHhhhHHHHHHHHhhhccccchhhhhcCC-hHHHHHHHHHHHHH-------HHHHHHHH
Confidence 5799999999999999999999999999966666666653 5999999 89999999999988 89999999
Q ss_pred HHHHHHHHHHHHhHHHHH-hcCCcceecCCchHHHH
Q psy15258 120 DIWDLRISKLRSSIDTFV-KSGGGHATLNHLTQFEI 154 (265)
Q Consensus 120 DI~evR~~Klr~gl~~~~-~~~~~~l~l~NLt~mEi 154 (265)
+++..|..||+++..... ..+.....++|||.+|.
T Consensus 73 ~~~~~R~~KI~~~~~~~~~~~~~~~~~~~~Ls~~Er 108 (108)
T PF05916_consen 73 DYLRIRLKKILSLAWHLLSGNDDPQEILENLSEEER 108 (108)
T ss_dssp HHHHHHHHHHHHHHCHHHHHCTTCHHHHTTS-HHHH
T ss_pred HHHHHHHHHHHHHHHHhccccCCcHHHHccCCHhhC
Confidence 999999999999988762 34556778999999984
No 6
>COG5093 Uncharacterized conserved protein [Function unknown]
Probab=99.64 E-value=2.2e-16 Score=134.62 Aligned_cols=70 Identities=26% Similarity=0.429 Sum_probs=65.3
Q ss_pred ccccccccccChHHHHHHHHHHHHHHHHHHHhhHHHHHhcCCcccccCCcchHHHHhhhhhHHHHHHHHhhhhccc
Q psy15258 175 QCDVDVTLQLNVDLIRTLIKDIWDLRISKLRSSIDTFVKSGGGHATLNHLTQFEINSIRNILCDVLDTMSSLKDKQ 250 (265)
Q Consensus 175 ~~~~d~~~~~~~~~ir~li~Di~d~R~~Klr~~~~~f~~~~~~h~~ldnlt~mEin~irpf~~~~m~~l~~~~~~~ 250 (265)
.|-+||- |++++|.+|+||+++|++|.++|++.. ||+|+++||||+||||++|||+..+||.++++++.-
T Consensus 113 ~~~ddve---diee~r~iv~dirEiRq~K~lkGlk~l---ne~~L~ldNl~l~EiNEirp~i~e~md~~R~I~~~s 182 (185)
T COG5093 113 ENCDDVE---DIEESRMIVEDIREIRQAKTLKGLKCL---NEKALNLDNLTLFEINEIRPLILESMDVGRRIEDLS 182 (185)
T ss_pred hccchHh---HHHHHHHHHHHHHHHHHHHHHhhHhhh---hhhhcCccccchhhhhhhHHHHHHHHHHHHHHHhhh
Confidence 4566777 899999999999999999999999996 999999999999999999999999999999998753
No 7
>PTZ00362 hypothetical protein; Provisional
Probab=99.42 E-value=4.8e-13 Score=130.16 Aligned_cols=96 Identities=15% Similarity=0.188 Sum_probs=70.5
Q ss_pred ceecCCchHHHHHhhHHhHHHH-HHHHhhhhccccccccccccChHHHHHHHHHHHHHHHHHHHhhHHHHHhcCCccccc
Q psy15258 143 HATLNHLTQFEINSIRNILCDV-LDTMSSLKDKQCDVDVTLQLNVDLIRTLIKDIWDLRISKLRSSIDTFVKSGGGHATL 221 (265)
Q Consensus 143 ~l~l~NLt~mEin~iR~f~~~a-md~l~~l~~~~~~~d~~~~~~~~~ir~li~Di~d~R~~Klr~~~~~f~~~~~~h~~l 221 (265)
.-.|.+=-.|||..+ |+..+ +........-...++++ .+++||++||||||+|++|+|+|+++|- .+++|++|
T Consensus 360 Ft~LP~p~y~EIa~l--Ll~~~~F~~~~a~edi~~~d~~~---~~~kVR~LIeDIrd~R~~KIr~~Le~~~-~~ss~i~L 433 (479)
T PTZ00362 360 LTDLPSPYFFEISSM--FLENNIFKKVTPIETIGQRTVYK---YISKVAGLVEDIRYKRLKKIMNHLENQD-VHSSIIYI 433 (479)
T ss_pred cccCCchhHHHHHHH--HHhcccccccCChhhcccccccc---cHHHHHHHHHHHHHHHHHHHHHHHHhcc-ccccEEEE
Confidence 345665566888876 55431 11111111122345666 6899999999999999999999999983 45799999
Q ss_pred CCcchHHHHhhhhhHHHHHHHHhhhhc
Q psy15258 222 NHLTQFEINSIRNILCDVLDTMSSLKD 248 (265)
Q Consensus 222 dnlt~mEin~irpf~~~~m~~l~~~~~ 248 (265)
||||+||++.||| +|+.+.+++.
T Consensus 434 dNLslmEi~~Vn~----~Ls~f~k~d~ 456 (479)
T PTZ00362 434 DNLQISETYCVNQ----LLSVFFQYDK 456 (479)
T ss_pred CCccHHHHHHHHH----HHHHHHHhcc
Confidence 9999999999999 7888888743
No 8
>KOG1106|consensus
Probab=97.27 E-value=0.0011 Score=58.27 Aligned_cols=98 Identities=14% Similarity=0.255 Sum_probs=76.3
Q ss_pred hhcCceeEEeeCCccccccccccccccCCCCCCccchhHHHHHHhcccCcceeeCCCCCCHHHHHHHHHHhhccCCCCCC
Q psy15258 9 IAEDQNVEIIPKFNHLNLIHLISGDVGPFRAGIPAKVPLWLAINLKQRQKCRLVLPTWMNLETLTEIKEEEKKSRFFIKM 88 (265)
Q Consensus 9 lAe~e~I~IvP~f~~~~~l~lI~g~~GPF~p~~p~~VPLWlAi~LKk~~kC~IvpP~WL~ve~L~~~l~~E~~~~~Fs~L 88 (265)
+|..+.|...-...+ ..+-+++..--+..+|..|.+|+|+|-.|+..+--.|.+|+-++. ..++.++.+-+.-.+..+
T Consensus 21 la~~~ki~ct~e~~i-~~lgfl~~~~~~~~~g~kVelP~wl~~~L~~~~~~si~lP~~fs~-~~rn~i~Adp~~vdL~s~ 98 (177)
T KOG1106|consen 21 LASGEKIPCTFETKI-PNLGFLQAPPRELPAGRKVELPYWLAEELAINQFVSILLPDIFSE-KVRNVIKADPNKVDLRSL 98 (177)
T ss_pred HhcCCcccceeeecC-CCCCccCCCcccCCCCCcccchHHHHHHHhhccceeecCchHHHH-HHHHHHhcCcceeecccc
Confidence 566666555555555 555556655667789999999999999999999999999998875 455666777777788888
Q ss_pred CCccHHHHHHHHHhcCCCCCC
Q psy15258 89 PSDHYMEMSHIILDIGADDIP 109 (265)
Q Consensus 89 P~~hy~EiA~lLL~~a~dDi~ 109 (265)
- +||++.+..|+-.-+++-.
T Consensus 99 ~-phFY~fg~kl~~l~s~~~l 118 (177)
T KOG1106|consen 99 C-PHFYEFGMKLLPLDSGENL 118 (177)
T ss_pred c-cHHHHHHHHHhhcccCcch
Confidence 7 8999999999987776544
No 9
>PF05916 Sld5: GINS complex protein; InterPro: IPR021151 DNA replication in eukaryotes results from a highly coordinated interaction between proteins, often as part of protein complexes, and the DNA template. One of the key early steps leading to DNA replication is formation of the pre- replication complex, or pre-RC. The pre-RC is formed by the sequential binding of the origin recognition complex (ORC), Cdc6 and Cdt1 proteins, and the MCM complex. Activation of the pre-RC into the initiation complex (IC) is achieved via the action of S-phase kinases, eventually leading to the loading of the replication machinery. Recently, a novel replication complex, GINS (for Go, Ichi, Nii, and San; five, one, two, and three in Japanese), has been identified [, ]. The precise function of GINS is not known. However, genetic and two-hybrid interactions indicate that it mediates the loading of the enzymatic replication machinery at a step after the action of the S-phase kinases []. Furthermore, GINS may be a part of the replication machinery itself, since it is found associated with replicating DNA [, ]. Electron microscopy of GINS shows that it forms a ring-like structure [], reminiscent of the structure of PCNA [], the DNA polymerase delta replication clamp.This observation, coupled with the observed interactions for GINS, indicates that the complex may represent the replication clamp for DNA polymerase epsilon []. The GINS complex is essential for initiation of DNA replication in Xenopus egg extracts []. This 100 kDa stable complex includes Sld5, Psf1, Psf2, and Psf3. Homologues of these components are found also in other eukaryotes. ; PDB: 2EHO_L 2E9X_G 2Q9Q_H 3ANW_B.
Probab=94.74 E-value=0.052 Score=41.58 Aligned_cols=43 Identities=21% Similarity=0.319 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHH-hcCCcccccCCcchHHH
Q psy15258 187 DLIRTLIKDIWDLRISKLRSSIDTFV-KSGGGHATLNHLTQFEI 229 (265)
Q Consensus 187 ~~ir~li~Di~d~R~~Klr~~~~~f~-~~~~~h~~ldnlt~mEi 229 (265)
+.++.++.|+++.|..|++.++..+. ..+.++..++|||.+|.
T Consensus 65 ~~ik~~l~~~~~~R~~KI~~~~~~~~~~~~~~~~~~~~Ls~~Er 108 (108)
T PF05916_consen 65 ERIKRLLRDYLRIRLKKILSLAWHLLSGNDDPQEILENLSEEER 108 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCHHHHHCTTCHHHHTTS-HHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccccCCcHHHHccCCHhhC
Confidence 77889999999999999999999973 34666679999999994
No 10
>COG5138 Uncharacterized conserved protein [Function unknown]
Probab=93.78 E-value=0.12 Score=44.45 Aligned_cols=89 Identities=12% Similarity=0.149 Sum_probs=60.5
Q ss_pred hhhcCceeEEeeCCccccccccccccccCCCCCCccchhHHHHHHhcccCcceeeCCCCCCHHHHHHHHHHhhccCCCCC
Q psy15258 8 FIAEDQNVEIIPKFNHLNLIHLISGDVGPFRAGIPAKVPLWLAINLKQRQKCRLVLPTWMNLETLTEIKEEEKKSRFFIK 87 (265)
Q Consensus 8 FlAe~e~I~IvP~f~~~~~l~lI~g~~GPF~p~~p~~VPLWlAi~LKk~~kC~IvpP~WL~ve~L~~~l~~E~~~~~Fs~ 87 (265)
-++++..|...-..+. +.+-+++..=.|.--|.++++|+|||-.|-...-..+.+|..++-.-+.++...=.. -..-.
T Consensus 9 iL~~~s~ipctf~~~I-pglG~l~~~gr~~p~n~kvelP~wLa~~Lainsfv~~l~p~~fs~~v~naika~P~t-vdlrs 86 (168)
T COG5138 9 ILLGESRIPCTFKHKI-PGLGFLGPRGRILPENRKVELPYWLASFLAINSFVCELGPGFFSESVLNAIKAKPST-VDLRS 86 (168)
T ss_pred HhcCCCccceeeEeec-CCcccCCCCCcccCCCCeeechHHHHHHHHHhhhHHhcCcchHHHHHHHHHhcCCce-eehhh
Confidence 3566766666666666 566556655556777899999999999999887888999999987766665443322 23334
Q ss_pred CCCccHHHHHHH
Q psy15258 88 MPSDHYMEMSHI 99 (265)
Q Consensus 88 LP~~hy~EiA~l 99 (265)
+- +||+-.|..
T Consensus 87 I~-~hff~lA~K 97 (168)
T COG5138 87 IC-PHFFYLAEK 97 (168)
T ss_pred cc-hHHHHHHHH
Confidence 43 466666543
No 11
>COG1711 DNA replication initiation complex subunit, GINS family [Replication, recombination, and repair]
Probab=75.38 E-value=11 Score=34.54 Aligned_cols=83 Identities=22% Similarity=0.288 Sum_probs=59.7
Q ss_pred CCHHHHHHHHHHhhccCCCCCCCCccHHHHHHHHH---hcCC-----CCCCC------hHHHHHHHHHHHHHHHHHHHHh
Q psy15258 67 MNLETLTEIKEEEKKSRFFIKMPSDHYMEMSHIIL---DIGA-----DDIPN------VDLIRTLIKDIWDLRISKLRSS 132 (265)
Q Consensus 67 L~ve~L~~~l~~E~~~~~Fs~LP~~hy~EiA~lLL---~~a~-----dDi~~------~~~ir~Li~DI~evR~~Klr~g 132 (265)
|.++.|+.++..|+.+.+++.++--+|.+++..+= ..+. .|+.. -+.+.+..+-|...|..|+-+-
T Consensus 1 m~i~eLR~~~~kErS~~~L~~Id~dFY~~v~~~I~eLe~~~~~~~~~~D~e~~~~~~~~et~~~~~r~ifqrR~~Kiv~~ 80 (223)
T COG1711 1 MDIEELRRALYKERSQDGLTEIDEDFYRDVRSFIKELEDEAGRAEEARDIEKYLLTDRIETAKSDARSIFQRRYGKIVSR 80 (223)
T ss_pred CCHHHHHHHHHHHhhhhhhhhcCHHHHHHHHHHHHHHHHHhhccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999999999999668888877642 2232 33332 2366677788999999999864
Q ss_pred HHHHHhcCCcceecCCchHHH
Q psy15258 133 IDTFVKSGGGHATLNHLTQFE 153 (265)
Q Consensus 133 l~~~~~~~~~~l~l~NLt~mE 153 (265)
... +...-.+.|||.-|
T Consensus 81 A~~----~~~~~~~~~Lt~eE 97 (223)
T COG1711 81 AIY----DVPGETISNLTPEE 97 (223)
T ss_pred HHH----hccccchhcCCHHH
Confidence 322 22233488999877
No 12
>COG4218 MtrF Tetrahydromethanopterin S-methyltransferase, subunit F [Coenzyme metabolism]
Probab=35.80 E-value=40 Score=25.76 Aligned_cols=33 Identities=27% Similarity=0.364 Sum_probs=25.6
Q ss_pred cccccccChHHHHHHHHHHHHH-----HHHHHHhhHHH
Q psy15258 178 VDVTLQLNVDLIRTLIKDIWDL-----RISKLRSSIDT 210 (265)
Q Consensus 178 ~d~~~~~~~~~ir~li~Di~d~-----R~~Klr~~~~~ 210 (265)
+.++..+|.+.|.+.|+||++. |-+||-.|+..
T Consensus 11 i~~snkpn~~~id~yVediryr~qligRd~rL~sGl~s 48 (73)
T COG4218 11 IGASNKPNTDRIDTYVEDIRYRSQLIGRDARLYSGLNS 48 (73)
T ss_pred ccccCCCChhHHHHHHHHHHHHHHhhcccchhhhhhhh
Confidence 4445556999999999999985 66777777754
No 13
>PF03233 Cauli_AT: Aphid transmission protein; InterPro: IPR004917 This protein is found in various caulimoviruses. It codes for an 18 kDa protein (PII), which is dispensable for infection but which is required for aphid transmission of the virus []. This protein interacts with the PIII protein []. ; GO: 0019089 transmission of virus
Probab=35.34 E-value=2.5e+02 Score=24.69 Aligned_cols=76 Identities=24% Similarity=0.349 Sum_probs=54.2
Q ss_pred ceeeCCCCCCHHHHHHHHHHhhc-cCCCCCCCCc--cHHHHHHHHHhcCCCCCCCh-HHHHHHHHHHHHHHHHHHHHhHH
Q psy15258 59 CRLVLPTWMNLETLTEIKEEEKK-SRFFIKMPSD--HYMEMSHIILDIGADDIPNV-DLIRTLIKDIWDLRISKLRSSID 134 (265)
Q Consensus 59 C~IvpP~WL~ve~L~~~l~~E~~-~~~Fs~LP~~--hy~EiA~lLL~~a~dDi~~~-~~ir~Li~DI~evR~~Klr~gl~ 134 (265)
=.|+.=-||.+.+|...+-.|+. +++++.=|.+ -|+--+.-.|....+|.... +++.+ ++++-+ |..||.+...
T Consensus 51 N~i~~r~~l~~~kl~sylGleKD~Se~~S~~K~Pf~~~~k~~~~ifkegg~d~~k~~~~l~~-L~e~sn-ki~kLe~~~k 128 (163)
T PF03233_consen 51 NEIVGRNWLKLSKLLSYLGLEKDPSEGLSKSKSPFESFFKDLSKIFKEGGGDKQKQLKLLPT-LEEISN-KIRKLETEVK 128 (163)
T ss_pred HHHHHHHHHHHHHHHHHhccccCCccccccCCCcHHHHHHHHHHHHHhcCCchhhHHHHHHH-HHHHHH-HHHHHHHHHH
Confidence 35777789999999999999987 6777754444 77777777888887777654 45554 444544 7777777665
Q ss_pred HH
Q psy15258 135 TF 136 (265)
Q Consensus 135 ~~ 136 (265)
.+
T Consensus 129 ~L 130 (163)
T PF03233_consen 129 KL 130 (163)
T ss_pred hH
Confidence 54
No 14
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=34.04 E-value=26 Score=30.93 Aligned_cols=63 Identities=16% Similarity=0.252 Sum_probs=38.4
Q ss_pred ccccccccccCCCCCCc-cchhHH-----HHHHhcccCcceeeCCCCCCHHHHHHHHHHhhccCCCCCCC----CccHHH
Q psy15258 26 LIHLISGDVGPFRAGIP-AKVPLW-----LAINLKQRQKCRLVLPTWMNLETLTEIKEEEKKSRFFIKMP----SDHYME 95 (265)
Q Consensus 26 ~l~lI~g~~GPF~p~~p-~~VPLW-----lAi~LKk~~kC~IvpP~WL~ve~L~~~l~~E~~~~~Fs~LP----~~hy~E 95 (265)
++..|++.+|=++++.. -.||-+ +|-+||+.+ +|.+|+|.++- + +..+-++| .|+|.-
T Consensus 11 ~~~~~~~~~~~~~~~~tvkDVpa~~fI~~~A~~LK~~g--ki~~P~W~d~v--K--------Tg~~KElaP~d~DW~YiR 78 (169)
T PTZ00095 11 KIKRIGKPVPYRRKNATLKDVSPWRFIKAFAQHFKLEG--KIFVPKCTEIV--K--------TSHGRELAPQNPDWYYIR 78 (169)
T ss_pred HHHHhcCCCCcccCCCceeeCCHHHHHHHHHHHHHHcC--CCCCCcchhhh--c--------ccccccCCCCCccHHHHH
Confidence 44556666665566654 457776 577888554 79999995442 2 22333333 367777
Q ss_pred HHHHH
Q psy15258 96 MSHII 100 (265)
Q Consensus 96 iA~lL 100 (265)
.|.+|
T Consensus 79 aASil 83 (169)
T PTZ00095 79 CAAVL 83 (169)
T ss_pred HHHHH
Confidence 66655
No 15
>COG3248 Tsx Nucleoside-binding outer membrane protein [Cell envelope biogenesis, outer membrane]
Probab=31.34 E-value=23 Score=33.14 Aligned_cols=40 Identities=25% Similarity=0.517 Sum_probs=29.5
Q ss_pred eeEEeeCCccccccccccccccCCC--------------------------CCCccchhHHHHHHhc
Q psy15258 14 NVEIIPKFNHLNLIHLISGDVGPFR--------------------------AGIPAKVPLWLAINLK 54 (265)
Q Consensus 14 ~I~IvP~f~~~~~l~lI~g~~GPF~--------------------------p~~p~~VPLWlAi~LK 54 (265)
--+|.|||++ +++.-..-+||||+ ||.-+.+|+-.-+.|.
T Consensus 100 fmei~PR~S~-dklTgaDlSFGPvkevy~A~~ye~d~gd~ka~~~s~~~mGlG~Di~~p~f~~~~LN 165 (284)
T COG3248 100 FMEIEPRFSI-DKLTGADLSFGPVKEVYFANNYEYDMGDNKAGRQSTWYMGLGTDIDTPLFMSLSLN 165 (284)
T ss_pred eEEeccceee-ccccccccccccceeEEEeceeEEcCCcccccceeeEEeccCcccccCCcceEEEE
Confidence 3589999999 98765555799986 4566677777766665
No 16
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=29.12 E-value=36 Score=29.43 Aligned_cols=40 Identities=23% Similarity=0.381 Sum_probs=23.8
Q ss_pred HHHHhcccCcceeeCCCCCCHHHHHHHHHHhhccCCCCCCC----CccHHHHHHHH
Q psy15258 49 LAINLKQRQKCRLVLPTWMNLETLTEIKEEEKKSRFFIKMP----SDHYMEMSHII 100 (265)
Q Consensus 49 lAi~LKk~~kC~IvpP~WL~ve~L~~~l~~E~~~~~Fs~LP----~~hy~EiA~lL 100 (265)
+|-+||+. -+|.+|+|.++ .+ +..+-++| .|+|.--|.+|
T Consensus 16 ~A~~LK~~--~ki~~P~W~~~--vK--------Tg~~kE~~P~~~DW~Y~R~AsIl 59 (150)
T PRK09333 16 LAEYLKNV--DEIKPPEWAAF--VK--------TGVHKERPPEQEDWWYVRAASIL 59 (150)
T ss_pred HHHHHHhc--CCcCCCcchhh--hc--------ccccccCCCCCCchHHHHHHHHH
Confidence 57788854 47999999543 22 23344444 25666655554
No 17
>PF11568 Med29: Mediator complex subunit 29; InterPro: IPR021018 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med29, along with Med11 and Med28, in mammals, is part of the core head-region of the complex. Med29 is the apparent orthologue of the Drosophila melanogaster Intersex protein, which interacts directly with, and functions as a transcriptional coactivator for, the DNA-binding transcription factor Doublesex, so it is likely that mammalian Med29 serves as a target for one or more DNA-binding transcriptional activators []. ; GO: 0016592 mediator complex
Probab=29.07 E-value=1.2e+02 Score=26.17 Aligned_cols=58 Identities=7% Similarity=0.115 Sum_probs=40.8
Q ss_pred ChHHHHHHHHHHHHHHHHHHHhhHHHHHhcCCcccccCCcchH-HHHhhhhhHHHHHHHHhhh
Q psy15258 185 NVDLIRTLIKDIWDLRISKLRSSIDTFVKSGGGHATLNHLTQF-EINSIRNILCDVLDTMSSL 246 (265)
Q Consensus 185 ~~~~ir~li~Di~d~R~~Klr~~~~~f~~~~~~h~~ldnlt~m-Ein~irpf~~~~m~~l~~~ 246 (265)
+++-+|+||.+|+|-=..=++.+...|- ++. -+||.+.- =.+.-+|=|-+.|..+|.+
T Consensus 6 ~I~kvK~Lv~~LreSl~~~~k~AA~~l~-qn~---~~D~g~~~~~~d~~~~RFdK~lEeFysi 64 (148)
T PF11568_consen 6 PISKVKSLVGPLRESLSNLMKTAAQNLQ-QNS---LVDNGTRGKSSDEPVPRFDKNLEEFYSI 64 (148)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-Hhc---ccccccccccccCcHHHHHHHHHHHHHH
Confidence 5789999999999999999999999984 222 36776431 1233556666666666544
No 18
>COG3924 Predicted membrane protein [Function unknown]
Probab=26.22 E-value=57 Score=25.23 Aligned_cols=34 Identities=24% Similarity=0.281 Sum_probs=22.5
Q ss_pred CCCHHHHHHHHHHh---hccCCCCCCCCccHHHHHHHHH
Q psy15258 66 WMNLETLTEIKEEE---KKSRFFIKMPSDHYMEMSHIIL 101 (265)
Q Consensus 66 WL~ve~L~~~l~~E---~~~~~Fs~LP~~hy~EiA~lLL 101 (265)
||++-||--.+-.- .+.++|+.+| +|||.|-+++
T Consensus 17 gLtllYl~gW~v~AYlp~~t~G~~gfP--~WFE~aCi~l 53 (80)
T COG3924 17 GLTLLYLAGWLVAAYLPGNTPGFTGFP--LWFEMACILL 53 (80)
T ss_pred HHHHHHHHHHHHHHhCCCCCCCCCCCh--HHHHHHHHHH
Confidence 34444444433332 3578999998 8999998765
No 19
>PF10792 DUF2605: Protein of unknown function (DUF2605); InterPro: IPR019728 This entry represents a protein conserved in Cyanobacteria. The function is not known.
Probab=26.08 E-value=1.7e+02 Score=23.75 Aligned_cols=37 Identities=8% Similarity=0.097 Sum_probs=29.8
Q ss_pred ccHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHH
Q psy15258 91 DHYMEMSHIILDIGADDIPNVDLIRTLIKDIWDLRIS 127 (265)
Q Consensus 91 ~hy~EiA~lLL~~a~dDi~~~~~ir~Li~DI~evR~~ 127 (265)
.|||+=|.-||+.+++++-++++=..|+.-+.+.++.
T Consensus 20 ~yWF~Rs~~LLe~e~~~fls~~eQ~~Ll~Rv~qaq~e 56 (98)
T PF10792_consen 20 QYWFSRSRELLETEPISFLSPEEQSDLLERVKQAQQE 56 (98)
T ss_pred HHHHHHHHHHHhcCCcccCCHHHHHHHHHHHHHHHHH
Confidence 4999999999999999998887777777666555443
No 20
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=25.69 E-value=1.1e+02 Score=22.74 Aligned_cols=33 Identities=12% Similarity=0.282 Sum_probs=26.9
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHhHHHHHhc
Q psy15258 107 DIPNVDLIRTLIKDIWDLRISKLRSSIDTFVKS 139 (265)
Q Consensus 107 Di~~~~~ir~Li~DI~evR~~Klr~gl~~~~~~ 139 (265)
|.|.++.|+.+++.+..-...+++..+..++..
T Consensus 1 ~~p~~~~i~~i~~~~~~~~~~~~~~~~~~l~~~ 33 (89)
T PF08542_consen 1 DWPPPEVIEEILESCLNGDFKEARKKLYELLVE 33 (89)
T ss_dssp TS--HHHHHHHHHHHHHTCHHHHHHHHHHHHHT
T ss_pred CCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHHc
Confidence 568899999999999999999999998887653
No 21
>PF08690 GET2: GET complex subunit GET2; InterPro: IPR014802 This family corresponds to the GET complex subunit GET2. The GET complex is involved in the retrieval of ER resident proteins from the Golgi []. ; PDB: 3SJD_D 3ZS9_C.
Probab=24.36 E-value=22 Score=33.87 Aligned_cols=12 Identities=17% Similarity=0.274 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHh
Q psy15258 121 IWDLRISKLRSS 132 (265)
Q Consensus 121 I~evR~~Klr~g 132 (265)
+||.|++|+++|
T Consensus 11 rRERReAKi~~G 22 (302)
T PF08690_consen 11 RRERREAKIKAG 22 (302)
T ss_dssp HHHHHHHHHHCC
T ss_pred HHHHHHHHHHCC
Confidence 589999999875
No 22
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=23.59 E-value=3.7e+02 Score=23.44 Aligned_cols=84 Identities=18% Similarity=0.264 Sum_probs=58.7
Q ss_pred CchHHHHHhhHHhHHHHHHHHhhhhccccccccccccChHHHHHHHHHHHHHHHHHHHhhHHHHHhcCCccc---ccCCc
Q psy15258 148 HLTQFEINSIRNILCDVLDTMSSLKDKQCDVDVTLQLNVDLIRTLIKDIWDLRISKLRSSIDTFVKSGGGHA---TLNHL 224 (265)
Q Consensus 148 NLt~mEin~iR~f~~~amd~l~~l~~~~~~~d~~~~~~~~~ir~li~Di~d~R~~Klr~~~~~f~~~~~~h~---~ldnl 224 (265)
+++.-|++.++..-. +.++.|..+ ...-++++.|.+.++.++.-..+.+. -..-++.+++.|+|-. ++=++
T Consensus 26 G~~~eel~~L~~ls~---~~l~~L~~~-~v~~~~i~in~~~l~~~L~~~~~~~~--~~~~idr~L~lGAS~~mm~~~FGl 99 (180)
T PF11198_consen 26 GFSPEELDALQQLSL---DDLHYLANS-SVSFVSISINHDVLWRLLEQARREQQ--EQQLIDRALRLGASIEMMQRLFGL 99 (180)
T ss_pred CCCHHHHHHHhCCCH---HHHHHHhcC-CcceeeeeeCHHHHHHHHHHHHHHHH--HHHHHHHHHHcCCCHHHHHHHHCC
Confidence 566777777766543 344444322 22244566789999999999987766 4455777887787766 77889
Q ss_pred chHHHHhhhhhHH
Q psy15258 225 TQFEINSIRNILC 237 (265)
Q Consensus 225 t~mEin~irpf~~ 237 (265)
|.-|+..-|-++.
T Consensus 100 s~~ev~~rR~llg 112 (180)
T PF11198_consen 100 SSAEVAARRRLLG 112 (180)
T ss_pred CHHHHHHHHHHhC
Confidence 9999999887763
No 23
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=22.61 E-value=39 Score=28.88 Aligned_cols=40 Identities=23% Similarity=0.406 Sum_probs=24.6
Q ss_pred HHHHhcccCcceeeCCCCCCHHHHHHHHHHhhccCCCCCCCC----ccHHHHHHHH
Q psy15258 49 LAINLKQRQKCRLVLPTWMNLETLTEIKEEEKKSRFFIKMPS----DHYMEMSHII 100 (265)
Q Consensus 49 lAi~LKk~~kC~IvpP~WL~ve~L~~~l~~E~~~~~Fs~LP~----~hy~EiA~lL 100 (265)
+|-+||+.+ .|.+|+|.++- .+..+-++|+ |+|.--|.+|
T Consensus 15 ~A~~LK~~g--ki~~P~w~d~v----------KTg~~kE~~P~~~DW~Y~RaASil 58 (139)
T PF01090_consen 15 LAEFLKKSG--KIEPPEWADIV----------KTGSHKELAPYDPDWWYIRAASIL 58 (139)
T ss_dssp HHHHHTCSS--TS--TSCGGGT----------SSSSS-SSTTCHHTHHHHHHHHHH
T ss_pred HHHHHHHcC--CcCCcchHHHH----------hhcccccCCCCCCCeeeeeHHHHH
Confidence 688999884 69999996542 2445556663 5666666554
No 24
>PRK13655 phosphoenolpyruvate carboxylase; Provisional
Probab=22.18 E-value=65 Score=32.92 Aligned_cols=16 Identities=19% Similarity=0.353 Sum_probs=11.7
Q ss_pred eCCCCCCHHHHHHHHH
Q psy15258 62 VLPTWMNLETLTEIKE 77 (265)
Q Consensus 62 vpP~WL~ve~L~~~l~ 77 (265)
+||.||.+...-+...
T Consensus 379 ~~P~wlG~g~aL~~~~ 394 (494)
T PRK13655 379 LPPELIGAGRLLELAK 394 (494)
T ss_pred CChHHHhHHHHHHHHH
Confidence 7999999986544333
No 25
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=20.86 E-value=1.2e+02 Score=21.30 Aligned_cols=29 Identities=28% Similarity=0.367 Sum_probs=24.3
Q ss_pred ChHHHHHHHH---HHHHHHHHHHHhhHHHHHh
Q psy15258 185 NVDLIRTLIK---DIWDLRISKLRSSIDTFVK 213 (265)
Q Consensus 185 ~~~~ir~li~---Di~d~R~~Klr~~~~~f~~ 213 (265)
+.+++..|++ |-|-+|-.||++.++++.+
T Consensus 6 ~~e~ld~L~~aL~~prG~RE~~L~~~L~~~~k 37 (46)
T PF15614_consen 6 DPEELDELLKALENPRGKRESKLKKELDKHRK 37 (46)
T ss_pred CHHHHHHHHHHHcCcccHhHHHHHHHHHHHhc
Confidence 5678888887 6699999999999999853
Done!