Query 026093
Match_columns 243
No_of_seqs 203 out of 907
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 03:41:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026093.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026093hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01310 L7 60S ribosomal pro 100.0 5.7E-85 1.2E-89 575.6 26.3 233 11-243 1-235 (235)
2 KOG3184 60S ribosomal protein 100.0 7.1E-66 1.5E-70 454.0 18.6 234 9-243 1-235 (235)
3 cd01657 Ribosomal_L7_archeal_e 100.0 1.1E-63 2.4E-68 419.0 15.8 159 84-243 1-159 (159)
4 PRK06049 rpl30p 50S ribosomal 100.0 4.5E-62 9.7E-67 406.7 16.0 154 83-243 1-154 (154)
5 TIGR01309 L30P_arch 50S riboso 100.0 4.1E-60 8.9E-65 394.1 14.7 151 85-243 1-152 (152)
6 COG1841 RpmD Ribosomal protein 99.8 6E-20 1.3E-24 128.6 6.0 55 85-139 1-55 (55)
7 cd00355 Ribosomal_L30_like Rib 99.8 1.2E-18 2.6E-23 121.2 6.6 53 86-138 1-53 (53)
8 PF08079 Ribosomal_L30_N: Ribo 99.7 8.6E-18 1.9E-22 123.7 6.6 71 12-82 1-71 (71)
9 PF00327 Ribosomal_L30: Riboso 99.7 2.8E-17 6E-22 113.9 7.0 52 84-135 1-52 (52)
10 PRK05611 rpmD 50S ribosomal pr 99.7 3.2E-17 6.9E-22 116.6 6.5 55 85-139 4-58 (59)
11 TIGR01308 rpmD_bact ribosomal 99.7 1.9E-16 4.2E-21 111.1 6.3 54 86-139 2-55 (55)
12 cd01658 Ribosomal_L30 Ribosoma 99.6 5.8E-16 1.3E-20 108.3 6.2 54 85-138 1-54 (54)
13 KOG4799 Mitochondrial ribosoma 97.2 0.00082 1.8E-08 56.6 6.1 73 79-151 53-134 (182)
14 PF00571 CBS: CBS domain CBS d 46.6 31 0.00067 22.5 3.4 48 132-190 8-56 (57)
15 KOG0030 Myosin essential light 33.3 62 0.0013 27.2 3.8 46 138-192 103-152 (152)
16 TIGR03757 conj_TIGR03757 integ 32.5 70 0.0015 25.7 3.9 32 106-150 79-110 (113)
17 KOG1097 Adenine deaminase/aden 30.2 84 0.0018 30.5 4.6 54 88-141 244-298 (399)
18 PF14229 DUF4332: Domain of un 29.7 89 0.0019 24.9 4.1 81 95-187 2-82 (122)
19 PF01086 Clathrin_lg_ch: Clath 29.5 90 0.002 27.6 4.5 28 37-64 131-158 (225)
20 PF01849 NAC: NAC domain; Int 27.3 9.2 0.0002 26.6 -1.8 43 98-141 2-55 (58)
21 PF11372 DUF3173: Domain of un 24.9 74 0.0016 22.7 2.5 42 134-175 9-56 (59)
22 PF07511 DUF1525: Protein of u 24.2 1.1E+02 0.0024 24.5 3.7 33 106-151 78-110 (114)
23 COG4597 BatB ABC-type amino ac 24.1 58 0.0013 30.8 2.3 53 92-144 288-351 (397)
24 cd01321 ADGF Adenosine deamina 21.1 1.4E+02 0.0031 28.0 4.3 33 97-130 212-244 (345)
25 COG4957 Predicted transcriptio 20.6 28 0.0006 29.0 -0.5 24 179-210 77-101 (148)
No 1
>TIGR01310 L7 60S ribosomal protein L7, eukaryotic. Members of this family average ~ 250 residues in length, somewhat longer than the archaeal L30P/L7E homolog (~ 155 residues) and much longer than the related bacterial/organellar form (~ 60 residues).
Probab=100.00 E-value=5.7e-85 Score=575.58 Aligned_cols=233 Identities=62% Similarity=1.038 Sum_probs=228.6
Q ss_pred hHHHHhhhhHHHHHHHHHHHHHHHHHHHHhhhhhHhhhhHHHHHHHHHHHHHHHHHHHHHHhhCCCccCCCCeeEEEEee
Q 026093 11 ESVLKKKKREEEWALAKKQELEAAKKKKAETRKLIYNRTKQYAKEYDEEQKELIRLKREAKLKGGFYVNPEAKLLFIIRI 90 (243)
Q Consensus 11 E~llKKrk~~~~~~~~~~~~~~~~k~~~k~~rk~~~krae~~vkeyr~~erd~~r~kr~ak~~~~~~~~~e~kl~~Viri 90 (243)
|++|||||++++++..+++++.+.++.++++++.+|+|||+|+++|+++++|.+|++|+++++|++|+|++|+++|||||
T Consensus 1 e~llkkrk~~~~~~~~~~~~~~~~k~~~~~~k~~~fkr~e~~~~~y~~~e~d~~r~~r~~k~~~~~~~~~e~kl~fVIRi 80 (235)
T TIGR01310 1 ELLLKKRKARQELAVVRAKQAKAKKKRNKKKKKHYFKRAESFVHEYRKAERERIRLKRLAKKPGKFYVPAEHKLLFVIRI 80 (235)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhhcccCcCCCCCCeEEEEEEe
Confidence 78999999999999999999888888888999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhhccCeEEEcCCCHHHHHHHHHhhcccccCCccccCCCchHH
Q 026093 91 RGINAVDPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYGYPNLKSVRELIYKRGYGKLNKQRIALTDNSII 170 (243)
Q Consensus 91 rg~~~~~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~KRG~~k~~~~~~~ltdn~~i 170 (243)
||++++||++++||++|||+++|+|||+++||++.+||++|+|||||||||++||++||||||+++++|++||||||+||
T Consensus 81 rG~~~v~p~v~k~L~lLRL~~in~~Vfvk~~~~~~~ML~~VepYVt~G~p~l~tvr~Li~KRG~~k~~~~~v~Ltdn~ii 160 (235)
T TIGR01310 81 KGINGIPPKPRKVLRLLRLKQVHNGVFVKVNKATLQMLRIVEPYVAYGYPNLKSVRELIYKRGFAKINGQRVPLTDNTII 160 (235)
T ss_pred CCCCCCCHHHHHHHHHhCCCccceEEEEECCHHHHHHHHhcCCeEEEecCCHHHHHHHHHHhCceeeCCCeeeCChhHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhccCCcccHHHHHHHHHhcCCChhhhhcCCCCcccCCCCccccc--ccccccccCCCCCChhHHHHHHHhhC
Q 026093 171 EQALGQHGIICMEDLIHEILTVGPHFKEANNFLWPFKLKAPLGGLKK--KRNHYVEGGDAGNREDYINELIRRMN 243 (243)
Q Consensus 171 ee~lg~~gi~ciEdlv~ei~~~g~~f~~v~~fl~pF~L~~P~~G~~~--~k~~~~~gG~~G~r~~~In~li~rm~ 243 (243)
|++||++||+|+|||||||+|+|+||+++++|||||+||||+|||++ +++||.+||++||||++||+||++|+
T Consensus 161 E~~lg~~gi~ciEDliheI~t~g~~fk~i~~~L~PFrL~~Pr~G~~~~~~~~~~~egG~~G~r~~~IN~Li~rM~ 235 (235)
T TIGR01310 161 EQHLGKYGIICIEDLIHEIYTVGPHFKEVNNFLWPFKLSSPVKGFGKRKKVKHFKEGGDFGNREDAINELIRKMN 235 (235)
T ss_pred HHhhccCCcccHHHHHHHHHhCCCCHHHHhcCccCccCCCCcccccccCcccCcccCCCCCccHHHHHHHHHHhC
Confidence 99999999999999999999999999999999999999999999974 78999999999999999999999997
No 2
>KOG3184 consensus 60S ribosomal protein L7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.1e-66 Score=454.00 Aligned_cols=234 Identities=60% Similarity=1.002 Sum_probs=230.5
Q ss_pred CchHHHHhhhhHHHHHHHHHHHHHHHHHHHHhhhhhHhhhhHHHHHHHHHHHHHHHHHHHHHHhhCCCccCCCCeeEEEE
Q 026093 9 VPESVLKKKKREEEWALAKKQELEAAKKKKAETRKLIYNRTKQYAKEYDEEQKELIRLKREAKLKGGFYVNPEAKLLFII 88 (243)
Q Consensus 9 vpE~llKKrk~~~~~~~~~~~~~~~~k~~~k~~rk~~~krae~~vkeyr~~erd~~r~kr~ak~~~~~~~~~e~kl~~Vi 88 (243)
+||++|| ||+++++++.++++..+.+..+++++...++++|+|+++|++++++.++++|.+++++++|+|++++++||+
T Consensus 1 vPE~llk-rk~~~~~~~~~~~~~~~~k~~~k~~~~~~~~~~e~~~~~~~~~~r~~i~~~r~~~~~~~~~~~~e~~l~fvv 79 (235)
T KOG3184|consen 1 VPENLLK-RKAQAELATQALRKLLAKKEIRKKKRKLFLKKAKHYHKEYRQKYRTEIRMARIARKAGNFYVPAEPKLAFVI 79 (235)
T ss_pred Cchhhhh-hhhHHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHhhhhHHHHHHHHHhccccCcCccccccceee
Confidence 6999999 999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecccCCCCHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhhccCeEEEcCCCHHHHHHHHHhhcccc-cCCccccCCCc
Q 026093 89 RIRGINAVDPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYGYPNLKSVRELIYKRGYGK-LNKQRIALTDN 167 (243)
Q Consensus 89 rirg~~~~~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~KRG~~k-~~~~~~~ltdn 167 (243)
|++|+++++|+++++|++|+|.+||+||||+.|+++..||+.|+||||||+||++++++||||||+++ +++++|+||||
T Consensus 80 ri~gin~v~pk~~k~l~lLrL~~If~g~fVKlnk~~~~mLriVepYVa~G~pnlksv~elI~krG~~k~~~~k~i~ltdn 159 (235)
T KOG3184|consen 80 RIRGVNGVEPKSRKVLQLLRLKQIFNGTFVKLNKATVNMLRIVEPYIAWGYPNLKSVSELIYKRGYGKKIEKKRIPLTDN 159 (235)
T ss_pred ecccccccCchHHHHHHHHHhhccccceeEEechhhhhhHhhcccceeeccCcHHHHHHHHhhcccccccCCceeccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999995 99999999999
Q ss_pred hHHHhhhccCCcccHHHHHHHHHhcCCChhhhhcCCCCcccCCCCcccccccccccccCCCCCChhHHHHHHHhhC
Q 026093 168 SIIEQALGQHGIICMEDLIHEILTVGPHFKEANNFLWPFKLKAPLGGLKKKRNHYVEGGDAGNREDYINELIRRMN 243 (243)
Q Consensus 168 ~~iee~lg~~gi~ciEdlv~ei~~~g~~f~~v~~fl~pF~L~~P~~G~~~~k~~~~~gG~~G~r~~~In~li~rm~ 243 (243)
.++++++|++|++|+||++|+|+++|++|+++++|||||+|++|.+||..+..||.|||+.||||+.||+|+++|+
T Consensus 160 ~ii~~~lgk~~~i~~edl~hei~~vg~~fk~~n~fL~pf~l~~~~~~~~~k~~h~~e~g~~g~~~~~in~L~~~~~ 235 (235)
T KOG3184|consen 160 FLIERKLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPVAGHKTKFGHFKEGGTAGNRGEHINDLIRQLN 235 (235)
T ss_pred hHHHHhcCCcceeechhhhccccccchhHHHHhhccCceeccCcccchhhhccccccCCCCCchHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999999999888999999999999999999999996
No 3
>cd01657 Ribosomal_L7_archeal_euk Ribosomal protein L7, which is found in archaea and eukaryotes but not in prokaryotes, binds domain II of the 23S rRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L7 members have an N-terminal extension not found in the archeal L7 orthologs. L7 is closely related to the ribosomal L30 protein found in eukaryotes and prokaryotes.
Probab=100.00 E-value=1.1e-63 Score=418.98 Aligned_cols=159 Identities=62% Similarity=0.987 Sum_probs=156.8
Q ss_pred eEEEEeecccCCCCHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhhccCeEEEcCCCHHHHHHHHHhhcccccCCcccc
Q 026093 84 LLFIIRIRGINAVDPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYGYPNLKSVRELIYKRGYGKLNKQRIA 163 (243)
Q Consensus 84 l~~Virirg~~~~~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~KRG~~k~~~~~~~ 163 (243)
++||+|+||.+|++|++++||++|||+++|+|||+++||+++|||++|+|||+|||||++||++||+|||+++++++++|
T Consensus 1 l~~Virirg~~g~~~~~r~tL~~LgL~k~~~~v~~~~t~~~~gmL~kV~~~V~~ge~~~~tv~~Li~kRG~~~~~~~~~~ 80 (159)
T cd01657 1 LYAVVRIRGIVGVPPKIRKTLQLLRLRRINNAVFVKLTKATIGMLKKVEPYVTWGEPNLETLRELIYKRGRLKGNGQRIP 80 (159)
T ss_pred CEEEEEecCcCCCCHHHHHHHHHcCCCcCCCEEEEeCCHHHHHHHHHhhhheEeccCcHHHHHHHHHHhCeecCCCeeee
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCchHHHhhhccCCcccHHHHHHHHHhcCCChhhhhcCCCCcccCCCCcccccccccccccCCCCCChhHHHHHHHhhC
Q 026093 164 LTDNSIIEQALGQHGIICMEDLIHEILTVGPHFKEANNFLWPFKLKAPLGGLKKKRNHYVEGGDAGNREDYINELIRRMN 243 (243)
Q Consensus 164 ltdn~~iee~lg~~gi~ciEdlv~ei~~~g~~f~~v~~fl~pF~L~~P~~G~~~~k~~~~~gG~~G~r~~~In~li~rm~ 243 (243)
||||+++|++| ++||+|+|||||||+++|+||+++++|+|||+||||++||++++++|++||++||||++||+||++|+
T Consensus 81 ltdn~iie~~l-~~gi~ciedlv~~i~~~~~~f~~~~~~l~pF~L~~P~~g~~~~~~~~~~gG~~G~r~~~In~Li~~m~ 159 (159)
T cd01657 81 LTDNYLVEKTL-KKGIICIEDLAHEIYTGGPNFKEVNNFLPPFRLHPPRGGFKGKKRHFSEGGELGYRGEDINELIRRMI 159 (159)
T ss_pred CChHHHHHHHc-ccCcccHHHHHHHHHhCccCHHHhhccCCCeECCCcccchhccccccccCCCCCccHHHHHHHHHHhC
Confidence 99999999999 99999999999999999999999999999999999999999888999999999999999999999997
No 4
>PRK06049 rpl30p 50S ribosomal protein L30P; Reviewed
Probab=100.00 E-value=4.5e-62 Score=406.66 Aligned_cols=154 Identities=32% Similarity=0.520 Sum_probs=147.9
Q ss_pred eeEEEEeecccCCCCHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhhccCeEEEcCCCHHHHHHHHHhhcccccCCccc
Q 026093 83 KLLFIIRIRGINAVDPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYGYPNLKSVRELIYKRGYGKLNKQRI 162 (243)
Q Consensus 83 kl~~Virirg~~~~~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~KRG~~k~~~~~~ 162 (243)
.++||+|+||.+|++|++++||++|||+++|++||+++||+++|||++|+|||+|||||++||++||||||+ ++|++
T Consensus 1 ~~~~ViriRg~ig~~~~~r~tL~~LgL~ki~~~V~v~~tp~~~GML~kV~~~V~~ge~~~~tv~~Li~kRG~--~~g~~- 77 (154)
T PRK06049 1 EMYAVIRIRGRVNVPRDIADTLKMLRLHRVNHCVLVPETPSYKGMLQKVKDYVTWGEIDADTLAELLRKRGR--LEGNK- 77 (154)
T ss_pred CcEEEEEecCCCCCCHHHHHHHHHcCCCcCCCEEEEeCCHHHHHHHHhhhceeEEeeCchHHHHHHHHHhCc--ccCCC-
Confidence 378999999999999999999999999999999999999999999999999999999999999999999999 45555
Q ss_pred cCCCchHHHhhhccCCcccHHHHHHHHHhcCCChhhhhcCCCCcccCCCCcccccccccccccCCCCCChhHHHHHHHhh
Q 026093 163 ALTDNSIIEQALGQHGIICMEDLIHEILTVGPHFKEANNFLWPFKLKAPLGGLKKKRNHYVEGGDAGNREDYINELIRRM 242 (243)
Q Consensus 163 ~ltdn~~iee~lg~~gi~ciEdlv~ei~~~g~~f~~v~~fl~pF~L~~P~~G~~~~k~~~~~gG~~G~r~~~In~li~rm 242 (243)
|||||+|+| + +||+|+|||||+|+++|++|+++++|+|||+||||+|||++++++|.+||++||||++||+||++|
T Consensus 78 ~ltd~~i~e-~---~g~~~iedl~~~i~~~~~~fk~~~~~~~~FrL~pPr~G~~~~k~~~~~gG~~G~r~~~In~Li~rM 153 (154)
T PRK06049 78 KLTDEYVKE-N---TGYDSIEELAEALVEGEIKLKDLPGLKPVFRLHPPRGGFGGIKRPFKEGGELGYRGEKINELLRRM 153 (154)
T ss_pred CCCHHHHHH-h---cCCccHHHHHHHHHhCCCCHHHhhcccCceecCCcchhhhhcccccccCCCCCccHHHHHHHHHHh
Confidence 999999877 4 599999999999999999999999999999999999999989999999999999999999999999
Q ss_pred C
Q 026093 243 N 243 (243)
Q Consensus 243 ~ 243 (243)
+
T Consensus 154 ~ 154 (154)
T PRK06049 154 R 154 (154)
T ss_pred C
Confidence 6
No 5
>TIGR01309 L30P_arch 50S ribosomal protein L30P, archaeal. This model represents the archaeal ribosomal protein similar to longer (~ 250 residue) eukaryotic 60S ribosomal protein L7 and to the much shorter (~ 60 residue) bacterial 50S ribosomal protein L30. Protein naming follows the SwissProt designation as L30P, while the gene symbol rpmD follows TIGR usage.
Probab=100.00 E-value=4.1e-60 Score=394.10 Aligned_cols=151 Identities=32% Similarity=0.488 Sum_probs=143.5
Q ss_pred EEEEeecccCCCCHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhhccCeEEEcCCCHHHHHHHHHhhcccccCCccccC
Q 026093 85 LFIIRIRGINAVDPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYGYPNLKSVRELIYKRGYGKLNKQRIAL 164 (243)
Q Consensus 85 ~~Virirg~~~~~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~KRG~~k~~~~~~~l 164 (243)
++|+|+||.+|++|++++||++|||+|+|+|||+++||+++|||++|+|||+|||||++||++||||||++. ++ .||
T Consensus 1 ~~ViriRg~ig~~~~~r~tL~~LrL~ri~~~V~v~~tp~~~gML~kV~~yV~~ge~~~~tv~~Li~kRG~~~-g~--~~l 77 (152)
T TIGR01309 1 LAVIRIRGTVDVPRDIADTLEMLRLHRVNHCVLYPETPTYLGMLQKVKDYVTWGEIDEDTLELLIRKRGRLV-GG--DKV 77 (152)
T ss_pred CeEEEecCcCCCCHHHHHHHHHcCCCcCCCEEEEeCCHHHHHHHHHhHhheeEecCCHHHHHHHHHHhcccc-CC--CcC
Confidence 589999999999999999999999999999999999999999999999999999999999999999999974 44 399
Q ss_pred CCchHHHhhhccCCcccHHHHHHHHHhcCCChhhhhcCCCCcccCCCCcccc-cccccccccCCCCCChhHHHHHHHhhC
Q 026093 165 TDNSIIEQALGQHGIICMEDLIHEILTVGPHFKEANNFLWPFKLKAPLGGLK-KKRNHYVEGGDAGNREDYINELIRRMN 243 (243)
Q Consensus 165 tdn~~iee~lg~~gi~ciEdlv~ei~~~g~~f~~v~~fl~pF~L~~P~~G~~-~~k~~~~~gG~~G~r~~~In~li~rm~ 243 (243)
|||+ |||+| ||+|+|||||||+++|++|++++ |+|||+||||++||+ +++++|.+||++||||++||+||++|+
T Consensus 78 td~~-i~e~~---g~~~iedl~~~i~~~~~~f~~~~-~~~~FrL~pPr~G~~~~~k~~~~~gG~~G~r~~~In~Li~rMi 152 (152)
T TIGR01309 78 TDEY-VKEVT---GYESVDELAKALVEGEIKLSEAG-LKPVFRLHPPRKGFKGGIKTPYRDGGELGYRGEKINELLRRMR 152 (152)
T ss_pred CHHH-HHHHc---CCccHHHHHHHHHcCCCCccccC-ccCceeCCCCCcccccccccccccCCCCcccHHHHHHHHHHhC
Confidence 9985 57777 79999999999999999999996 999999999999998 688999999999999999999999996
No 6
>COG1841 RpmD Ribosomal protein L30/L7E [Translation, ribosomal structure and biogenesis]
Probab=99.80 E-value=6e-20 Score=128.64 Aligned_cols=55 Identities=36% Similarity=0.432 Sum_probs=53.7
Q ss_pred EEEEeecccCCCCHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhhccCeEEEcC
Q 026093 85 LFIIRIRGINAVDPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYGY 139 (243)
Q Consensus 85 ~~Virirg~~~~~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G~ 139 (243)
++|+|+||.+|+||++++||++|||+++|++|++++||+++|||++|+|||+||+
T Consensus 1 ~~V~~iRs~ig~~~~~r~tl~~LgL~kin~~v~~~dtp~irGMi~kV~~lV~v~e 55 (55)
T COG1841 1 LKVTLIRSPIGRPPKIRKTLRLLGLRKINHTVIVEDTPAVRGMLNKVKHLVTVGE 55 (55)
T ss_pred CeEEEEeccCCCChHHHHHHHHhCCCccCCEEEEcCCHHHHHHHHHHHhheEecC
Confidence 4799999999999999999999999999999999999999999999999999996
No 7
>cd00355 Ribosomal_L30_like Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L30 members have N- and/or C-terminal extensions not found in their prokaryotic orthologs. L30 is closely related to the ribosomal L7 protein found in eukaryotes and archaea.
Probab=99.76 E-value=1.2e-18 Score=121.22 Aligned_cols=53 Identities=36% Similarity=0.514 Sum_probs=52.1
Q ss_pred EEEeecccCCCCHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhhccCeEEEc
Q 026093 86 FIIRIRGINAVDPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYG 138 (243)
Q Consensus 86 ~Virirg~~~~~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G 138 (243)
+|+|+||.+|.+|++++||++|||+++|++||+++||+++|||++|+|||+||
T Consensus 1 ~V~~irs~ig~~~~~~~tl~~LgL~k~~~~v~~~~tp~~~gml~kV~~lV~~~ 53 (53)
T cd00355 1 KVTRVRSLIGRPPKQRKTLKALGLRKINQTVFVKDTPSIRGMLRKVKHLVTVG 53 (53)
T ss_pred CEEEecCCCCCCHHHHHHHHHcCCCcCCCEEEEeCCHHHHHHHHhccceEEEC
Confidence 58999999999999999999999999999999999999999999999999998
No 8
>PF08079 Ribosomal_L30_N: Ribosomal L30 N-terminal domain; InterPro: IPR012988 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 presumed domain is found at the N terminus of Ribosomal L30 proteins and has been termed RL30NT or NUC018 [].; PDB: 3IZR_e 3O5H_G 3O58_G 3IZS_e 4A1A_V 4A17_V 4A1E_V 4A1C_V.
Probab=99.72 E-value=8.6e-18 Score=123.70 Aligned_cols=71 Identities=45% Similarity=0.728 Sum_probs=64.3
Q ss_pred HHHHhhhhHHHHHHHHHHHHHHHHHHHHhhhhhHhhhhHHHHHHHHHHHHHHHHHHHHHHhhCCCccCCCC
Q 026093 12 SVLKKKKREEEWALAKKQELEAAKKKKAETRKLIYNRTKQYAKEYDEEQKELIRLKREAKLKGGFYVNPEA 82 (243)
Q Consensus 12 ~llKKrk~~~~~~~~~~~~~~~~k~~~k~~rk~~~krae~~vkeyr~~erd~~r~kr~ak~~~~~~~~~e~ 82 (243)
||||||+++++++...+++..+.+...+.+++.+|+|||+|++||+++|+|+++|+|+|++.|+||||+||
T Consensus 1 s~LKKrK~~~~~~~~~~~~~~~~k~~~~~~r~~~~kRAekY~kEYr~~erd~Irl~R~Ak~~G~fyvpaEp 71 (71)
T PF08079_consen 1 SLLKKRKRNEKLKAKRAKKAAARKKKRKKKRKEIFKRAEKYVKEYRQKERDEIRLKREAKKAGNFYVPAEP 71 (71)
T ss_dssp CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCS-SEE----
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHccCccCCCCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999997
No 9
>PF00327 Ribosomal_L30: Ribosomal protein L30p/L7e; InterPro: IPR016082 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 [, ]. Ribosomal protein L30 is one of the proteins from the large ribosomal subunit. L30 belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups bacteria and archaea L30, yeast mitochondrial L33, and Drosophila melanogaster, Dictyostelium discoideum (Slime mold), fungal and mammalian L7 ribosomal proteins. L30 from bacteria are small proteins of about 60 residues, those from archaea are proteins of about 150 residues, and eukaryotic L7 are proteins of about 250 to 270 residues. This entry represents a domain with a ferredoxin-like fold, with a core structure consisting of core: beta-alpha-beta-alpha-beta. This domain is found in prokaryotic ribosomal protein L30 (short-chain member of the family), as well as in archaeal L30 (L30a) (long-chain member of the family), the later containing an additional C-terminal (sub)domain).; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3DF2_Y 3DF4_Y 3O5H_G 3O58_G 1S1I_F 3IZS_e 1M1K_X 1M90_X 1QVG_V 1YIT_W ....
Probab=99.71 E-value=2.8e-17 Score=113.88 Aligned_cols=52 Identities=40% Similarity=0.589 Sum_probs=48.9
Q ss_pred eEEEEeecccCCCCHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhhccCeE
Q 026093 84 LLFIIRIRGINAVDPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYV 135 (243)
Q Consensus 84 l~~Virirg~~~~~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V 135 (243)
++||+|+||.+|.+|++++||++|||+++|++||+++||+++|||++|+|||
T Consensus 1 ~l~V~~irs~~g~~~~~~~tl~~LgL~k~~~~v~~~~t~~~~gml~kV~~lV 52 (52)
T PF00327_consen 1 LLFVTRIRSPIGAPPKVRKTLKALGLRKINQAVFVKNTPSIRGMLKKVKHLV 52 (52)
T ss_dssp EEEEEESS-STTSSHHHHHHHHHTT-SSTTEEEEEESSHHHHHHHHHTGCGE
T ss_pred CEEEEEeCCCCCCCHHHHHHHHHcCCCcCCCEEEEECCHHHHHHHHHHHhhC
Confidence 5899999999999999999999999999999999999999999999999997
No 10
>PRK05611 rpmD 50S ribosomal protein L30; Reviewed
Probab=99.70 E-value=3.2e-17 Score=116.62 Aligned_cols=55 Identities=27% Similarity=0.297 Sum_probs=54.0
Q ss_pred EEEEeecccCCCCHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhhccCeEEEcC
Q 026093 85 LFIIRIRGINAVDPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYGY 139 (243)
Q Consensus 85 ~~Virirg~~~~~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G~ 139 (243)
++|+++||.+|.+|++++||++|||+++|++|++++||+++|||++|+|||+|.+
T Consensus 4 ~~I~~vRs~ig~~~~~r~tl~~LgL~k~~~~v~~~dtp~~rGmi~kV~~lV~vee 58 (59)
T PRK05611 4 LKITLVKSLIGRKPKQRATLRGLGLRKINSTVELEDTPAIRGMINKVSHLVKVEE 58 (59)
T ss_pred EEEEEeecCCCCCHHHHHHHHHcCCCcCCCEEEecCCHHHHHHHHHhHhhEEEEe
Confidence 7899999999999999999999999999999999999999999999999999986
No 11
>TIGR01308 rpmD_bact ribosomal protein L30, bacterial/organelle. This model describes bacterial (and organellar) 50S ribosomal protein L30. Homologous ribosomal proteins of the eukaryotic cytosol and of the archaea differ substantially in architecture, from bacterial L30 and also from each other, and are described by separate models.
Probab=99.66 E-value=1.9e-16 Score=111.10 Aligned_cols=54 Identities=28% Similarity=0.297 Sum_probs=52.3
Q ss_pred EEEeecccCCCCHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhhccCeEEEcC
Q 026093 86 FIIRIRGINAVDPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYGY 139 (243)
Q Consensus 86 ~Virirg~~~~~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G~ 139 (243)
.|+++||.+|.+|++++||++|||+++|++|+++|||+++|||++|+|||.+.+
T Consensus 2 kItlvrs~ig~~~~~r~tl~~LgL~k~~~~v~~~dtp~irGMi~kV~~lV~vee 55 (55)
T TIGR01308 2 KVTLVRSLIGRPKKQRKTLKALGLRKIGRQVVLEDNPAIRGMVNKVKHLVKVEE 55 (55)
T ss_pred EEEEEeCCCCCCHHHHHHHHHcCCCcCCCEEEecCCHHHHHHHHHhHheEEEeC
Confidence 589999999999999999999999999999999999999999999999999875
No 12
>cd01658 Ribosomal_L30 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L30 members have N- and/or C-terminal extensions not found in their prokaryotic orthologs. L30 is closely related to the ribosomal L7 protein found in eukaryotes and archaea.
Probab=99.63 E-value=5.8e-16 Score=108.27 Aligned_cols=54 Identities=22% Similarity=0.266 Sum_probs=51.8
Q ss_pred EEEEeecccCCCCHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhhccCeEEEc
Q 026093 85 LFIIRIRGINAVDPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYG 138 (243)
Q Consensus 85 ~~Virirg~~~~~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G 138 (243)
+.|+++||.+|.+|++++||++|||+++|++|++++||+++|||++|+|||.|.
T Consensus 1 ~~i~~iRs~ig~~~~~r~tl~~LgL~k~~~~v~~~~tp~~~Gml~kV~~lV~ve 54 (54)
T cd01658 1 LKITLVKSLIGRPKKQRATLKALGLKKINQTVVHKDTPSIRGMINKVKHLVKVE 54 (54)
T ss_pred CEEEEEeCCCCCCHHHHHHHHHcCCCcCCCEEEecCCHHHHHHHHHHhheEEeC
Confidence 368999999999999999999999999999999999999999999999999874
No 13
>KOG4799 consensus Mitochondrial ribosomal protein L30 [Translation, ribosomal structure and biogenesis]
Probab=97.22 E-value=0.00082 Score=56.63 Aligned_cols=73 Identities=18% Similarity=0.190 Sum_probs=65.4
Q ss_pred CCC-CeeEEEEeecccCCCCHHHHHHHHHhCCCcccc-eEEEeCCHhhHHHHhhccCeEE-------EcCCCHHHHHHHH
Q 026093 79 NPE-AKLLFIIRIRGINAVDPKTKKILQLLRLRQIFN-GVFLKVNKATLNMLHRVEPYVT-------YGYPNLKSVRELI 149 (243)
Q Consensus 79 ~~e-~kl~~Virirg~~~~~~~~~k~L~~L~L~ki~~-~v~v~~~~~~~gmL~~V~~~V~-------~G~p~~~tv~~Li 149 (243)
|.+ .+|..|.||++..+.|..-++++++|||....+ --++++.|++-.-|.+|+|+|. +|+|..+.|+..+
T Consensus 53 P~~p~KL~~v~rik~t~~~PyWek~iik~lGld~k~t~~qV~kNip~vNakLwkIKHLI~~~pv~fp~gePte~di~~t~ 132 (182)
T KOG4799|consen 53 PQNPHKLHIVTRIKSTRRRPYWEKDIIKMLGLDKKHTRPQVHKNIPSVNAKLWKIKHLIRLRPVEFPGGEPTEDDISSTS 132 (182)
T ss_pred CCCccceEEEEEeccccCCcchHHHHHHHhCcccccCCceEeecccchhhHHHHhhheeEEEeeccCCCCCchhhhhhhh
Confidence 444 468999999999999999999999999999988 7788999999999999999986 5999999999887
Q ss_pred Hh
Q 026093 150 YK 151 (243)
Q Consensus 150 ~K 151 (243)
.|
T Consensus 133 Lk 134 (182)
T KOG4799|consen 133 LK 134 (182)
T ss_pred hc
Confidence 54
No 14
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=46.63 E-value=31 Score=22.46 Aligned_cols=48 Identities=29% Similarity=0.517 Sum_probs=33.9
Q ss_pred cCeEEEcCCCHHHHHHHHHhhcccccCCccccCCCchHHHhhhccC-CcccHHHHHHHHH
Q 026093 132 EPYVTYGYPNLKSVRELIYKRGYGKLNKQRIALTDNSIIEQALGQH-GIICMEDLIHEIL 190 (243)
Q Consensus 132 ~~~V~~G~p~~~tv~~Li~KRG~~k~~~~~~~ltdn~~iee~lg~~-gi~ciEdlv~ei~ 190 (243)
.+.+.-..-++..+-+++.+.+. ..+|+.|+. |++ |+++..||++.+.
T Consensus 8 ~~~~v~~~~~l~~~~~~~~~~~~-----~~~~V~d~~------~~~~G~is~~dl~~~l~ 56 (57)
T PF00571_consen 8 PPITVSPDDSLEEALEIMRKNGI-----SRLPVVDED------GKLVGIISRSDLLKALL 56 (57)
T ss_dssp SSEEEETTSBHHHHHHHHHHHTS-----SEEEEESTT------SBEEEEEEHHHHHHHHH
T ss_pred CCEEEcCcCcHHHHHHHHHHcCC-----cEEEEEecC------CEEEEEEEHHHHHhhhh
Confidence 34444555677778888888775 446877654 343 9999999999875
No 15
>KOG0030 consensus Myosin essential light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=33.32 E-value=62 Score=27.22 Aligned_cols=46 Identities=28% Similarity=0.437 Sum_probs=31.0
Q ss_pred cCCCHHHHHHHHHhhcccccCCccccCCCchHHHhhh-cc---CCcccHHHHHHHHHhc
Q 026093 138 GYPNLKSVRELIYKRGYGKLNKQRIALTDNSIIEQAL-GQ---HGIICMEDLIHEILTV 192 (243)
Q Consensus 138 G~p~~~tv~~Li~KRG~~k~~~~~~~ltdn~~iee~l-g~---~gi~ciEdlv~ei~~~ 192 (243)
|.+...-+|-++.+-|- .||+..+ ++.| |. .|.+..|+||+.|.++
T Consensus 103 G~i~~aeLRhvLttlGe--------kl~eeEV-e~Llag~eD~nG~i~YE~fVk~i~~g 152 (152)
T KOG0030|consen 103 GTIMGAELRHVLTTLGE--------KLTEEEV-EELLAGQEDSNGCINYEAFVKHIMSG 152 (152)
T ss_pred cceeHHHHHHHHHHHHh--------hccHHHH-HHHHccccccCCcCcHHHHHHHHhcC
Confidence 44555556666665553 5888777 5565 43 3888999999998753
No 16
>TIGR03757 conj_TIGR03757 integrating conjugative element protein, PFL_4709 family. Members of this protein belong to extended genomic regions that appear to be spread by conjugative transfer.
Probab=32.48 E-value=70 Score=25.66 Aligned_cols=32 Identities=28% Similarity=0.321 Sum_probs=25.2
Q ss_pred HhCCCcccceEEEeCCHhhHHHHhhccCeEEEcCCCHHHHHHHHH
Q 026093 106 LLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYGYPNLKSVRELIY 150 (243)
Q Consensus 106 ~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~ 150 (243)
.||++++=-.||= ..||.||++|...-..++.
T Consensus 79 ~lGi~k~PAVV~D-------------~~~VVYG~~DV~~A~~~~~ 110 (113)
T TIGR03757 79 QLGVTKIPAVVVD-------------RRYVVYGETDVARALALIQ 110 (113)
T ss_pred HcCCccCCEEEEc-------------CCeEEecCccHHHHHHHHH
Confidence 5888887766663 5699999999988877765
No 17
>KOG1097 consensus Adenine deaminase/adenosine deaminase [Nucleotide transport and metabolism]
Probab=30.20 E-value=84 Score=30.53 Aligned_cols=54 Identities=20% Similarity=0.165 Sum_probs=44.4
Q ss_pred EeecccC-CCCHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhhccCeEEEcCCC
Q 026093 88 IRIRGIN-AVDPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYGYPN 141 (243)
Q Consensus 88 irirg~~-~~~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G~p~ 141 (243)
+-.-|-. |-+..++..|.+||..||+||.++-..|...++++.-.=.++..-.|
T Consensus 244 t~HaGE~~~~~~~v~~~LD~l~~~RIGHG~~l~~dp~L~~~~k~~nI~lEiCP~S 298 (399)
T KOG1097|consen 244 TFHAGETNGGASVVKNALDLLGTERIGHGYFLTKDPELINLLKSRNIALEICPIS 298 (399)
T ss_pred EEEccccCCChHHHHHHHHhhCCccccCceeccCCHHHHHHHHhcCceEEEccch
Confidence 3445655 68889999999999999999999999999999998877666665444
No 18
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=29.67 E-value=89 Score=24.87 Aligned_cols=81 Identities=11% Similarity=0.057 Sum_probs=55.5
Q ss_pred CCCHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhhccCeEEEcCCCHHHHHHHHHhhcccccCCccccCCCchHHHhhh
Q 026093 95 AVDPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYGYPNLKSVRELIYKRGYGKLNKQRIALTDNSIIEQAL 174 (243)
Q Consensus 95 ~~~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~KRG~~k~~~~~~~ltdn~~iee~l 174 (243)
|+.+....-|...|+.-..+-.-.-.++..+..|- .=+..|..+|.++..---...+.| |.-.+-. .|
T Consensus 2 gi~~~~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La------~~~~i~~~~l~~w~~~AdL~ri~g--i~~~~a~----LL 69 (122)
T PF14229_consen 2 GIGPKEAAKLKAAGIKTTGDLLEAGDTPLGRKALA------KKLGISERNLLKWVNQADLMRIPG--IGPQYAE----LL 69 (122)
T ss_pred CCCHHHHHHHHHcCCCcHHHHHHcCCCHHHHHHHH------HhcCCCHHHHHHHHhHHHhhhcCC--CCHHHHH----HH
Confidence 67788888889999887777776777777775554 234578888888865555555554 2222333 34
Q ss_pred ccCCcccHHHHHH
Q 026093 175 GQHGIICMEDLIH 187 (243)
Q Consensus 175 g~~gi~ciEdlv~ 187 (243)
-+-||.|++||++
T Consensus 70 ~~AGv~Tv~~LA~ 82 (122)
T PF14229_consen 70 EHAGVDTVEELAQ 82 (122)
T ss_pred HHhCcCcHHHHHh
Confidence 4569999999976
No 19
>PF01086 Clathrin_lg_ch: Clathrin light chain; InterPro: IPR000996 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 [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents clathrin light chains, which are more divergent in sequence than the heavy chains []. In higher eukaryotes, two genes encode distinct but related light chains, each of which can yield two separate forms via alternative splicing. In yeast there is a single light chain whose sequence is only distantly related to that of higher eukaryotes. Clathrin light chains have a conserved acidic N-terminal domain, a central coiled-coil domain and a conserved C-terminal domain. 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, 0030130 clathrin coat of trans-Golgi network vesicle, 0030132 clathrin coat of coated pit; PDB: 3LVG_E 3LVH_D.
Probab=29.48 E-value=90 Score=27.60 Aligned_cols=28 Identities=18% Similarity=0.309 Sum_probs=16.4
Q ss_pred HHHhhhhhHhhhhHHHHHHHHHHHHHHH
Q 026093 37 KKAETRKLIYNRTKQYAKEYDEEQKELI 64 (243)
Q Consensus 37 ~~k~~rk~~~krae~~vkeyr~~erd~~ 64 (243)
..++++..+...|++++.++.......+
T Consensus 131 ~e~~kk~e~~~~A~k~lddfY~~~~~k~ 158 (225)
T PF01086_consen 131 EEEEKKEEIKEKAKKELDDFYENRNEKK 158 (225)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344455666677777777665544443
No 20
>PF01849 NAC: NAC domain; InterPro: IPR002715 Nascent polypeptide-associated complex (NAC) is among the first ribosome-associated entities to bind the nascent polypeptide after peptide bond formation. The nascent polypeptide-associated complex (NAC) of yeast functions in the targeting process of ribosomes to the ER membrane []. NAC may prevent binding of ribosome nascent chains (RNCs) without a signal sequence to yeast membranes.; PDB: 3MCE_D 3MCB_A 3LKX_B 1TR8_B.
Probab=27.29 E-value=9.2 Score=26.57 Aligned_cols=43 Identities=28% Similarity=0.365 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCCcccc-----------eEEEeCCHhhHHHHhhccCeEEEcCCC
Q 026093 98 PKTKKILQLLRLRQIFN-----------GVFLKVNKATLNMLHRVEPYVTYGYPN 141 (243)
Q Consensus 98 ~~~~k~L~~L~L~ki~~-----------~v~v~~~~~~~gmL~~V~~~V~~G~p~ 141 (243)
.+.++.|+.|||..+.. .+|+=++|.+. ...-...|+..|+|.
T Consensus 2 kk~~~~l~klgl~~i~~i~eV~i~~~dg~~~~~~~P~V~-~~~~~~tyvV~G~~~ 55 (58)
T PF01849_consen 2 KKLQKMLKKLGLKEIPGIEEVTIRKDDGTVFVFNNPEVQ-KSPGSNTYVVFGEAE 55 (58)
T ss_dssp ------GHHCT-EEETTEEEEEEEETTTEEEEEESEEEE-EETTCCEEEEESEEE
T ss_pred HHHHHHHHHcCCcccCCcEEEEEEECCceEEEEcCCeEE-EcCCCCEEEEEeeeE
Confidence 46788888888877732 56667778877 222367888888875
No 21
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=24.93 E-value=74 Score=22.68 Aligned_cols=42 Identities=21% Similarity=0.526 Sum_probs=29.6
Q ss_pred eEEEcCCCHH------HHHHHHHhhcccccCCccccCCCchHHHhhhc
Q 026093 134 YVTYGYPNLK------SVRELIYKRGYGKLNKQRIALTDNSIIEQALG 175 (243)
Q Consensus 134 ~V~~G~p~~~------tv~~Li~KRG~~k~~~~~~~ltdn~~iee~lg 175 (243)
++..|+|.-. -.++++-++|+..-+++|+-.---.+|||.||
T Consensus 9 Li~lGf~~~tA~~IIrqAK~~lV~~G~~~Y~nkRlg~VP~~~VEeiLG 56 (59)
T PF11372_consen 9 LIELGFSESTARDIIRQAKALLVQKGFSFYNNKRLGRVPASAVEEILG 56 (59)
T ss_pred HHHcCCCHHHHHHHHHHHHHHHHHcCCCcccCCccCcccHHHHHHHHC
Confidence 3445666532 23466778999999998877767778898885
No 22
>PF07511 DUF1525: Protein of unknown function (DUF1525); InterPro: IPR011090 This family of proteins is restricted to the Gammaproteobacteria. Members belong to extended genomic regions that appear to be spread by conjugative transfer.
Probab=24.23 E-value=1.1e+02 Score=24.48 Aligned_cols=33 Identities=24% Similarity=0.304 Sum_probs=26.7
Q ss_pred HhCCCcccceEEEeCCHhhHHHHhhccCeEEEcCCCHHHHHHHHHh
Q 026093 106 LLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYGYPNLKSVRELIYK 151 (243)
Q Consensus 106 ~L~L~ki~~~v~v~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~K 151 (243)
.||++++=-.||= .-||.||++|..-...++..
T Consensus 78 ~lgi~k~PAVVfD-------------~~~VVYG~tDV~~A~~~~~~ 110 (114)
T PF07511_consen 78 SLGITKYPAVVFD-------------DRYVVYGETDVARALARIEQ 110 (114)
T ss_pred HhCccccCEEEEc-------------CCeEEecccHHHHHHHHHHH
Confidence 6788887776663 67999999999988888765
No 23
>COG4597 BatB ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]
Probab=24.06 E-value=58 Score=30.82 Aligned_cols=53 Identities=25% Similarity=0.377 Sum_probs=42.0
Q ss_pred ccCCCCHHHHHHHHHhCCCcccce-----------EEEeCCHhhHHHHhhccCeEEEcCCCHHH
Q 026093 92 GINAVDPKTKKILQLLRLRQIFNG-----------VFLKVNKATLNMLHRVEPYVTYGYPNLKS 144 (243)
Q Consensus 92 g~~~~~~~~~k~L~~L~L~ki~~~-----------v~v~~~~~~~gmL~~V~~~V~~G~p~~~t 144 (243)
|+.++|..+-..-..|||+.--.. ++=+.|.++.++.+.-.--++.||||+-.
T Consensus 288 GI~~VskGQtEAa~sLGL~~~~t~RlVivPQAlRiIIPPLTSQYLNLtKNSSLAiAIGYpDlv~ 351 (397)
T COG4597 288 GIQAVSKGQTEAARSLGLRSSLTLRLVIVPQALRIIIPPLTSQYLNLTKNSSLAIAIGYPDLVA 351 (397)
T ss_pred hhcccCcccHHHHHhcCCCCcceEEEEEecccceeecCcccHHHHhhcccchhhhhcCCCceEE
Confidence 677899999999999999865443 23357788888888888889999999753
No 24
>cd01321 ADGF Adenosine deaminase-related growth factors (ADGF), a novel family of secreted growth-factors with sequence similarty to adenosine deaminase.
Probab=21.13 E-value=1.4e+02 Score=27.95 Aligned_cols=33 Identities=21% Similarity=0.345 Sum_probs=28.6
Q ss_pred CHHHHHHHHHhCCCcccceEEEeCCHhhHHHHhh
Q 026093 97 DPKTKKILQLLRLRQIFNGVFLKVNKATLNMLHR 130 (243)
Q Consensus 97 ~~~~~k~L~~L~L~ki~~~v~v~~~~~~~gmL~~ 130 (243)
+..+.++| .||-.||.||+.+..+|....+|+.
T Consensus 212 ~~~v~~al-~lg~~RIGHG~~~~~dp~ll~~l~~ 244 (345)
T cd01321 212 DENLVDAL-LLNTKRIGHGFALPKHPLLMDLVKK 244 (345)
T ss_pred hhHHHHHH-HhCCCcCccccccCcCHHHHHHHHH
Confidence 45788899 6999999999999999988887764
No 25
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=20.63 E-value=28 Score=29.02 Aligned_cols=24 Identities=42% Similarity=0.783 Sum_probs=20.4
Q ss_pred cccHHHHHHHHHhcCCChhhhhcCCCC-cccCC
Q 026093 179 IICMEDLIHEILTVGPHFKEANNFLWP-FKLKA 210 (243)
Q Consensus 179 i~ciEdlv~ei~~~g~~f~~v~~fl~p-F~L~~ 210 (243)
|+|+|| |..|+.+.+.|-. |-|+|
T Consensus 77 IicLED--------GkkfKSLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLED--------GKKFKSLKRHLTTHYGLTP 101 (148)
T ss_pred EEEecc--------CcchHHHHHHHhcccCCCH
Confidence 679987 8999999888876 88876
Done!