Query 026027
Match_columns 244
No_of_seqs 209 out of 898
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 02:50:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026027.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026027hhsearch_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 1.3E-84 2.7E-89 573.9 26.4 233 12-244 1-235 (235)
2 KOG3184 60S ribosomal protein 100.0 2.2E-65 4.7E-70 451.4 18.6 234 10-244 1-235 (235)
3 cd01657 Ribosomal_L7_archeal_e 100.0 2E-63 4.3E-68 417.8 15.9 159 85-244 1-159 (159)
4 PRK06049 rpl30p 50S ribosomal 100.0 5.9E-62 1.3E-66 406.3 16.2 154 84-244 1-154 (154)
5 TIGR01309 L30P_arch 50S riboso 100.0 6.9E-60 1.5E-64 393.1 15.0 151 86-244 1-152 (152)
6 COG1841 RpmD Ribosomal protein 99.8 7.6E-20 1.6E-24 128.3 6.0 55 86-140 1-55 (55)
7 cd00355 Ribosomal_L30_like Rib 99.8 1.6E-18 3.5E-23 120.7 6.4 53 87-139 1-53 (53)
8 PF08079 Ribosomal_L30_N: Ribo 99.7 8E-18 1.7E-22 124.0 6.3 71 13-83 1-71 (71)
9 PRK05611 rpmD 50S ribosomal pr 99.7 3.5E-17 7.6E-22 116.5 6.8 56 86-141 4-59 (59)
10 PF00327 Ribosomal_L30: Riboso 99.7 4.9E-17 1.1E-21 112.7 7.1 52 85-136 1-52 (52)
11 TIGR01308 rpmD_bact ribosomal 99.7 2.3E-16 4.9E-21 110.9 6.4 54 87-140 2-55 (55)
12 cd01658 Ribosomal_L30 Ribosoma 99.6 6.8E-16 1.5E-20 108.0 6.0 54 86-139 1-54 (54)
13 KOG4799 Mitochondrial ribosoma 97.3 0.00054 1.2E-08 57.7 5.9 74 80-153 53-135 (182)
14 PF00571 CBS: CBS domain CBS d 42.0 40 0.00087 21.9 3.4 47 134-191 9-56 (57)
15 TIGR03757 conj_TIGR03757 integ 37.5 50 0.0011 26.6 3.7 33 106-151 78-110 (113)
16 KOG0030 Myosin essential light 33.8 61 0.0013 27.3 3.8 46 139-193 103-152 (152)
17 PF07511 DUF1525: Protein of u 28.5 82 0.0018 25.3 3.6 34 106-152 77-110 (114)
18 KOG1097 Adenine deaminase/aden 27.6 1.3E+02 0.0029 29.2 5.5 55 88-142 243-298 (399)
19 PF01849 NAC: NAC domain; Int 27.0 8.5 0.00018 26.8 -2.0 43 99-142 2-55 (58)
20 PF01086 Clathrin_lg_ch: Clath 24.0 1.3E+02 0.0027 26.7 4.4 26 40-65 133-158 (225)
21 PF11372 DUF3173: Domain of un 22.7 94 0.002 22.2 2.6 43 134-176 8-56 (59)
22 cd01321 ADGF Adenosine deamina 22.6 1.3E+02 0.0027 28.3 4.3 43 88-131 197-244 (345)
23 PF00289 CPSase_L_chain: Carba 20.3 4E+02 0.0087 20.7 6.1 71 98-172 14-92 (110)
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=1.3e-84 Score=573.94 Aligned_cols=233 Identities=60% Similarity=1.020 Sum_probs=228.7
Q ss_pred hHHHHhhhhHHHHHHHHHHHHHHHHHhhhhhhhhHHhhhHHHHHHHHHHHHHHHHHHHHHHhhCCCccCCCCeeEEEEEe
Q 026027 12 ESVLKKQKRNEEWALAKKQELETSKKNKLESRKLIYNRAKQYAKEFAEQEKVLIQLKREAKLKGGFYVDPEAKLLFIIRI 91 (244)
Q Consensus 12 E~~LKKrk~~~~~~~~~~~~~~~~k~~~~~~rk~~~krae~~vkeyr~~e~d~~r~kr~ak~~~~~~~~~e~kl~~Viri 91 (244)
|++|||||++++++.++++++.+.++.++++++.+|+|||+|+++|+++|+|.+|++|+++++|++|+|++|+++|||||
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 cCcCCCCHHHHHHHHHhCCCCcccEEEEecCHhhHHHHhhccCceEEecCCHHHHHHHHHhhcccccCCccccCCChhHH
Q 026027 92 RGINAIDPKTKKILQLLRLRQIFNGVFLKVNKATMNMLHRVEPYVTYGYPNLKSVRELIYKRGYGKLDKQRIALTDNSII 171 (244)
Q Consensus 92 rg~~~~~~~~~k~L~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~KRG~~k~~~~~~~ltdn~li 171 (244)
||++++||++++||++|||+++|+|||+++||++.+||++|+|||||||||++||++||||||+++++|+++|||||+||
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 HhhcccCCcccHHHHHHHHHhcCCChhhhhcCCCCcccCCCccccc--cccccccccCCCCCChhHHHHHHHhhC
Q 026027 172 EKALGKFGIICMEDLIHEIMTVGPHFKEANNFLWPFKLKAPLGGLK--KKRNHYVEGGDAGNRENYVNELIRRMN 244 (244)
Q Consensus 172 ee~lg~~gi~ciEdlv~eI~~~g~~f~~v~~fl~pF~L~~P~~G~~--~~~~~~~~gG~~G~rg~~In~Li~rM~ 244 (244)
|++||++||+|+|||||||+|+|+||+++++|||||+||||++||+ +++++|.+||++||||+.||+||++|+
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 9999999999999999999999999999999999999999999997 488999999999999999999999997
No 2
>KOG3184 consensus 60S ribosomal protein L7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.2e-65 Score=451.37 Aligned_cols=234 Identities=59% Similarity=0.999 Sum_probs=230.6
Q ss_pred CchHHHHhhhhHHHHHHHHHHHHHHHHHhhhhhhhhHHhhhHHHHHHHHHHHHHHHHHHHHHHhhCCCccCCCCeeEEEE
Q 026027 10 VPESVLKKQKRNEEWALAKKQELETSKKNKLESRKLIYNRAKQYAKEFAEQEKVLIQLKREAKLKGGFYVDPEAKLLFII 89 (244)
Q Consensus 10 vpE~~LKKrk~~~~~~~~~~~~~~~~k~~~~~~rk~~~krae~~vkeyr~~e~d~~r~kr~ak~~~~~~~~~e~kl~~Vi 89 (244)
+||++|| ||++++++..+++++.+.+..+++++...++++++|+++|++++++.++++|.+++++++|+|++++++|||
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 EecCcCCCCHHHHHHHHHhCCCCcccEEEEecCHhhHHHHhhccCceEEecCCHHHHHHHHHhhcccc-cCCccccCCCh
Q 026027 90 RIRGINAIDPKTKKILQLLRLRQIFNGVFLKVNKATMNMLHRVEPYVTYGYPNLKSVRELIYKRGYGK-LDKQRIALTDN 168 (244)
Q Consensus 90 rirg~~~~~~~~~k~L~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~KRG~~k-~~~~~~~ltdn 168 (244)
|++|+++++|+.+++|++|+|.++|+||||+.|+++..||+.|+||||||+||++++++||||||+++ ++++++|||||
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 99999999999999999999999999999999999999999999999999999999999999999994 99999999999
Q ss_pred hHHHhhcccCCcccHHHHHHHHHhcCCChhhhhcCCCCcccCCCccccccccccccccCCCCCChhHHHHHHHhhC
Q 026027 169 SIIEKALGKFGIICMEDLIHEIMTVGPHFKEANNFLWPFKLKAPLGGLKKKRNHYVEGGDAGNRENYVNELIRRMN 244 (244)
Q Consensus 169 ~liee~lg~~gi~ciEdlv~eI~~~g~~f~~v~~fl~pF~L~~P~~G~~~~~~~~~~gG~~G~rg~~In~Li~rM~ 244 (244)
.++++++|++|++|+||++|+|+++|++|+++++|||||+|++|.+||..+..||.+||+.||||+.||+|+++|+
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=2e-63 Score=417.82 Aligned_cols=159 Identities=61% Similarity=0.975 Sum_probs=156.8
Q ss_pred eEEEEEecCcCCCCHHHHHHHHHhCCCCcccEEEEecCHhhHHHHhhccCceEEecCCHHHHHHHHHhhcccccCCcccc
Q 026027 85 LLFIIRIRGINAIDPKTKKILQLLRLRQIFNGVFLKVNKATMNMLHRVEPYVTYGYPNLKSVRELIYKRGYGKLDKQRIA 164 (244)
Q Consensus 85 l~~Virirg~~~~~~~~~k~L~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~KRG~~k~~~~~~~ 164 (244)
++||+|+||.+|++|++++||++|||+++|+|||+++||+++|||++|+|||+|||||++||++||+|||+++++++++|
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 CCChhHHHhhcccCCcccHHHHHHHHHhcCCChhhhhcCCCCcccCCCccccccccccccccCCCCCChhHHHHHHHhhC
Q 026027 165 LTDNSIIEKALGKFGIICMEDLIHEIMTVGPHFKEANNFLWPFKLKAPLGGLKKKRNHYVEGGDAGNRENYVNELIRRMN 244 (244)
Q Consensus 165 ltdn~liee~lg~~gi~ciEdlv~eI~~~g~~f~~v~~fl~pF~L~~P~~G~~~~~~~~~~gG~~G~rg~~In~Li~rM~ 244 (244)
||||+++|++| ++||+|+|||||||+++|++|+++++|+|||+||||++||++++++|++||++||||++||+||++|+
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=5.9e-62 Score=406.30 Aligned_cols=154 Identities=31% Similarity=0.514 Sum_probs=147.8
Q ss_pred eeEEEEEecCcCCCCHHHHHHHHHhCCCCcccEEEEecCHhhHHHHhhccCceEEecCCHHHHHHHHHhhcccccCCccc
Q 026027 84 KLLFIIRIRGINAIDPKTKKILQLLRLRQIFNGVFLKVNKATMNMLHRVEPYVTYGYPNLKSVRELIYKRGYGKLDKQRI 163 (244)
Q Consensus 84 kl~~Virirg~~~~~~~~~k~L~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~KRG~~k~~~~~~ 163 (244)
.++||+|+||.+|++|++++||++|||+++|++||+++||+++|||++|+|||+|||||++||++||||||+ +.|++
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 cCCChhHHHhhcccCCcccHHHHHHHHHhcCCChhhhhcCCCCcccCCCccccccccccccccCCCCCChhHHHHHHHhh
Q 026027 164 ALTDNSIIEKALGKFGIICMEDLIHEIMTVGPHFKEANNFLWPFKLKAPLGGLKKKRNHYVEGGDAGNRENYVNELIRRM 243 (244)
Q Consensus 164 ~ltdn~liee~lg~~gi~ciEdlv~eI~~~g~~f~~v~~fl~pF~L~~P~~G~~~~~~~~~~gG~~G~rg~~In~Li~rM 243 (244)
|||||+|+| + +||+|+|||||+|+++|++|+++++|+|||+||||++||++++++|.+||++||||++||+||++|
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 999999977 4 579999999999999999999999999999999999999999999999999999999999999999
Q ss_pred C
Q 026027 244 N 244 (244)
Q Consensus 244 ~ 244 (244)
+
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=6.9e-60 Score=393.10 Aligned_cols=151 Identities=30% Similarity=0.487 Sum_probs=143.4
Q ss_pred EEEEEecCcCCCCHHHHHHHHHhCCCCcccEEEEecCHhhHHHHhhccCceEEecCCHHHHHHHHHhhcccccCCccccC
Q 026027 86 LFIIRIRGINAIDPKTKKILQLLRLRQIFNGVFLKVNKATMNMLHRVEPYVTYGYPNLKSVRELIYKRGYGKLDKQRIAL 165 (244)
Q Consensus 86 ~~Virirg~~~~~~~~~k~L~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~KRG~~k~~~~~~~l 165 (244)
++|+|+||.+|++|++++||++|||+|+|+|||+++||+++|||++|+|||+|||||++||++||||||++. ++. ||
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-GGD--KV 77 (152)
T ss_pred CeEEEecCcCCCCHHHHHHHHHcCCCcCCCEEEEeCCHHHHHHHHHhHhheeEecCCHHHHHHHHHHhcccc-CCC--cC
Confidence 589999999999999999999999999999999999999999999999999999999999999999999974 443 99
Q ss_pred CChhHHHhhcccCCcccHHHHHHHHHhcCCChhhhhcCCCCcccCCCccccc-cccccccccCCCCCChhHHHHHHHhhC
Q 026027 166 TDNSIIEKALGKFGIICMEDLIHEIMTVGPHFKEANNFLWPFKLKAPLGGLK-KKRNHYVEGGDAGNRENYVNELIRRMN 244 (244)
Q Consensus 166 tdn~liee~lg~~gi~ciEdlv~eI~~~g~~f~~v~~fl~pF~L~~P~~G~~-~~~~~~~~gG~~G~rg~~In~Li~rM~ 244 (244)
|||+ |||+| ||+|+|||||||+++|++|++++ |+|||+||||++||+ +++++|.+||++||||++||+||++|+
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 59999999999999999999996 999999999999998 799999999999999999999999996
No 6
>COG1841 RpmD Ribosomal protein L30/L7E [Translation, ribosomal structure and biogenesis]
Probab=99.80 E-value=7.6e-20 Score=128.26 Aligned_cols=55 Identities=36% Similarity=0.433 Sum_probs=53.7
Q ss_pred EEEEEecCcCCCCHHHHHHHHHhCCCCcccEEEEecCHhhHHHHhhccCceEEec
Q 026027 86 LFIIRIRGINAIDPKTKKILQLLRLRQIFNGVFLKVNKATMNMLHRVEPYVTYGY 140 (244)
Q Consensus 86 ~~Virirg~~~~~~~~~k~L~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V~~G~ 140 (244)
++|+|+||.+|++|++++||++|||+++|++|+++|||+++|||++|+|||+||+
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=99.75 E-value=1.6e-18 Score=120.71 Aligned_cols=53 Identities=36% Similarity=0.515 Sum_probs=52.0
Q ss_pred EEEEecCcCCCCHHHHHHHHHhCCCCcccEEEEecCHhhHHHHhhccCceEEe
Q 026027 87 FIIRIRGINAIDPKTKKILQLLRLRQIFNGVFLKVNKATMNMLHRVEPYVTYG 139 (244)
Q Consensus 87 ~Virirg~~~~~~~~~k~L~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V~~G 139 (244)
+|+|+||.+|.+|++++||++|||+++|++||+++||+++|||++|+|||+||
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 58999999999999999999999999999999999999999999999999997
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=8e-18 Score=123.99 Aligned_cols=71 Identities=44% Similarity=0.674 Sum_probs=64.3
Q ss_pred HHHHhhhhHHHHHHHHHHHHHHHHHhhhhhhhhHHhhhHHHHHHHHHHHHHHHHHHHHHHhhCCCccCCCC
Q 026027 13 SVLKKQKRNEEWALAKKQELETSKKNKLESRKLIYNRAKQYAKEFAEQEKVLIQLKREAKLKGGFYVDPEA 83 (244)
Q Consensus 13 ~~LKKrk~~~~~~~~~~~~~~~~k~~~~~~rk~~~krae~~vkeyr~~e~d~~r~kr~ak~~~~~~~~~e~ 83 (244)
||||||+++++++..++++....+...+.+++.+|+|||+|++||+++|+|+++++|+|++.|+||||+||
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
>PRK05611 rpmD 50S ribosomal protein L30; Reviewed
Probab=99.70 E-value=3.5e-17 Score=116.51 Aligned_cols=56 Identities=27% Similarity=0.281 Sum_probs=54.5
Q ss_pred EEEEEecCcCCCCHHHHHHHHHhCCCCcccEEEEecCHhhHHHHhhccCceEEecC
Q 026027 86 LFIIRIRGINAIDPKTKKILQLLRLRQIFNGVFLKVNKATMNMLHRVEPYVTYGYP 141 (244)
Q Consensus 86 ~~Virirg~~~~~~~~~k~L~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V~~G~p 141 (244)
++|+++||.+|.+|++++||++|||+++|++|++++||+++|||++|+|||+|.+.
T Consensus 4 ~~I~~vRs~ig~~~~~r~tl~~LgL~k~~~~v~~~dtp~~rGmi~kV~~lV~vee~ 59 (59)
T PRK05611 4 LKITLVKSLIGRKPKQRATLRGLGLRKINSTVELEDTPAIRGMINKVSHLVKVEEV 59 (59)
T ss_pred EEEEEeecCCCCCHHHHHHHHHcCCCcCCCEEEecCCHHHHHHHHHhHhhEEEEeC
Confidence 88999999999999999999999999999999999999999999999999999863
No 10
>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=99.70 E-value=4.9e-17 Score=112.74 Aligned_cols=52 Identities=40% Similarity=0.586 Sum_probs=48.9
Q ss_pred eEEEEEecCcCCCCHHHHHHHHHhCCCCcccEEEEecCHhhHHHHhhccCce
Q 026027 85 LLFIIRIRGINAIDPKTKKILQLLRLRQIFNGVFLKVNKATMNMLHRVEPYV 136 (244)
Q Consensus 85 l~~Virirg~~~~~~~~~k~L~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V 136 (244)
+++|+|+||.+|.+|++++||++|||+++|++||+++||+++|||++|+|||
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 5899999999999999999999999999999999999999999999999998
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=99.65 E-value=2.3e-16 Score=110.87 Aligned_cols=54 Identities=28% Similarity=0.298 Sum_probs=52.4
Q ss_pred EEEEecCcCCCCHHHHHHHHHhCCCCcccEEEEecCHhhHHHHhhccCceEEec
Q 026027 87 FIIRIRGINAIDPKTKKILQLLRLRQIFNGVFLKVNKATMNMLHRVEPYVTYGY 140 (244)
Q Consensus 87 ~Virirg~~~~~~~~~k~L~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V~~G~ 140 (244)
.|+++||.+|.+|++++||++|||+++|++|+++|||+++|||++|+|||.+.+
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=99.62 E-value=6.8e-16 Score=108.03 Aligned_cols=54 Identities=22% Similarity=0.266 Sum_probs=51.8
Q ss_pred EEEEEecCcCCCCHHHHHHHHHhCCCCcccEEEEecCHhhHHHHhhccCceEEe
Q 026027 86 LFIIRIRGINAIDPKTKKILQLLRLRQIFNGVFLKVNKATMNMLHRVEPYVTYG 139 (244)
Q Consensus 86 ~~Virirg~~~~~~~~~k~L~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V~~G 139 (244)
+.|+++||.+|.+|++++||++|||+++|++|++++||+++|||++|+|||.|.
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=97.30 E-value=0.00054 Score=57.74 Aligned_cols=74 Identities=18% Similarity=0.186 Sum_probs=66.5
Q ss_pred CCC-CeeEEEEEecCcCCCCHHHHHHHHHhCCCCccc-EEEEecCHhhHHHHhhccCceE-------EecCCHHHHHHHH
Q 026027 80 DPE-AKLLFIIRIRGINAIDPKTKKILQLLRLRQIFN-GVFLKVNKATMNMLHRVEPYVT-------YGYPNLKSVRELI 150 (244)
Q Consensus 80 ~~e-~kl~~Virirg~~~~~~~~~k~L~~LrL~ki~~-~vfv~~~~~~~gmL~~V~~~V~-------~G~p~~~tv~~Li 150 (244)
|.+ ++|..|.||++..+.|..-.+++++|||....+ -.++++.|++-.-|.+|+|+|. +|+|..+.|+..+
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 579999999999999999999999999999988 8889999999999999999986 5999999999987
Q ss_pred Hhh
Q 026027 151 YKR 153 (244)
Q Consensus 151 ~KR 153 (244)
.|.
T Consensus 133 Lk~ 135 (182)
T KOG4799|consen 133 LKP 135 (182)
T ss_pred hcc
Confidence 654
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=41.95 E-value=40 Score=21.94 Aligned_cols=47 Identities=30% Similarity=0.562 Sum_probs=32.5
Q ss_pred CceEEecCCHHHHHHHHHhhcccccCCccccCCChhHHHhhcccC-CcccHHHHHHHHH
Q 026027 134 PYVTYGYPNLKSVRELIYKRGYGKLDKQRIALTDNSIIEKALGKF-GIICMEDLIHEIM 191 (244)
Q Consensus 134 ~~V~~G~p~~~tv~~Li~KRG~~k~~~~~~~ltdn~liee~lg~~-gi~ciEdlv~eI~ 191 (244)
+.+.-..-++..+-+++.+.+. ..+|+.|+. |++ |+++..||++.+.
T Consensus 9 ~~~v~~~~~l~~~~~~~~~~~~-----~~~~V~d~~------~~~~G~is~~dl~~~l~ 56 (57)
T PF00571_consen 9 PITVSPDDSLEEALEIMRKNGI-----SRLPVVDED------GKLVGIISRSDLLKALL 56 (57)
T ss_dssp SEEEETTSBHHHHHHHHHHHTS-----SEEEEESTT------SBEEEEEEHHHHHHHHH
T ss_pred CEEEcCcCcHHHHHHHHHHcCC-----cEEEEEecC------CEEEEEEEHHHHHhhhh
Confidence 3334445567777788887774 346777654 443 7999999999875
No 15
>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=37.54 E-value=50 Score=26.56 Aligned_cols=33 Identities=27% Similarity=0.284 Sum_probs=25.6
Q ss_pred HHhCCCCcccEEEEecCHhhHHHHhhccCceEEecCCHHHHHHHHH
Q 026027 106 QLLRLRQIFNGVFLKVNKATMNMLHRVEPYVTYGYPNLKSVRELIY 151 (244)
Q Consensus 106 ~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~ 151 (244)
..||++++=-.||= ..||.||++|......++.
T Consensus 78 w~lGi~k~PAVV~D-------------~~~VVYG~~DV~~A~~~~~ 110 (113)
T TIGR03757 78 WQLGVTKIPAVVVD-------------RRYVVYGETDVARALALIQ 110 (113)
T ss_pred HHcCCccCCEEEEc-------------CCeEEecCccHHHHHHHHH
Confidence 36888887666663 5699999999998877765
No 16
>KOG0030 consensus Myosin essential light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=33.79 E-value=61 Score=27.31 Aligned_cols=46 Identities=28% Similarity=0.405 Sum_probs=32.4
Q ss_pred ecCCHHHHHHHHHhhcccccCCccccCCChhHHHhhc-cc---CCcccHHHHHHHHHhc
Q 026027 139 GYPNLKSVRELIYKRGYGKLDKQRIALTDNSIIEKAL-GK---FGIICMEDLIHEIMTV 193 (244)
Q Consensus 139 G~p~~~tv~~Li~KRG~~k~~~~~~~ltdn~liee~l-g~---~gi~ciEdlv~eI~~~ 193 (244)
|.+...-+|-+|.+-|- .||+..+ ++.| |. .|-+..|+||+.|.++
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 55666667777766664 5788777 5555 43 4889999999999764
No 17
>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=28.45 E-value=82 Score=25.31 Aligned_cols=34 Identities=24% Similarity=0.269 Sum_probs=27.0
Q ss_pred HHhCCCCcccEEEEecCHhhHHHHhhccCceEEecCCHHHHHHHHHh
Q 026027 106 QLLRLRQIFNGVFLKVNKATMNMLHRVEPYVTYGYPNLKSVRELIYK 152 (244)
Q Consensus 106 ~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V~~G~p~~~tv~~Li~K 152 (244)
..||++++=-.||= .-||.||++|..-...++..
T Consensus 77 w~lgi~k~PAVVfD-------------~~~VVYG~tDV~~A~~~~~~ 110 (114)
T PF07511_consen 77 WSLGITKYPAVVFD-------------DRYVVYGETDVARALARIEQ 110 (114)
T ss_pred HHhCccccCEEEEc-------------CCeEEecccHHHHHHHHHHH
Confidence 36888887766663 67999999999988888765
No 18
>KOG1097 consensus Adenine deaminase/adenosine deaminase [Nucleotide transport and metabolism]
Probab=27.59 E-value=1.3e+02 Score=29.19 Aligned_cols=55 Identities=20% Similarity=0.170 Sum_probs=44.6
Q ss_pred EEEecCcC-CCCHHHHHHHHHhCCCCcccEEEEecCHhhHHHHhhccCceEEecCC
Q 026027 88 IIRIRGIN-AIDPKTKKILQLLRLRQIFNGVFLKVNKATMNMLHRVEPYVTYGYPN 142 (244)
Q Consensus 88 Virirg~~-~~~~~~~k~L~~LrL~ki~~~vfv~~~~~~~gmL~~V~~~V~~G~p~ 142 (244)
.+-+-|-. +-+..++..|.+||..||+||.++-..|..+++++.-.=.++..-.|
T Consensus 243 ~t~HaGE~~~~~~~v~~~LD~l~~~RIGHG~~l~~dp~L~~~~k~~nI~lEiCP~S 298 (399)
T KOG1097|consen 243 LTFHAGETNGGASVVKNALDLLGTERIGHGYFLTKDPELINLLKSRNIALEICPIS 298 (399)
T ss_pred EEEEccccCCChHHHHHHHHhhCCccccCceeccCCHHHHHHHHhcCceEEEccch
Confidence 34556766 68899999999999999999999999999999998766555554433
No 19
>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=27.01 E-value=8.5 Score=26.78 Aligned_cols=43 Identities=28% Similarity=0.386 Sum_probs=25.2
Q ss_pred HHHHHHHHHhCCCCccc-----------EEEEecCHhhHHHHhhccCceEEecCC
Q 026027 99 PKTKKILQLLRLRQIFN-----------GVFLKVNKATMNMLHRVEPYVTYGYPN 142 (244)
Q Consensus 99 ~~~~k~L~~LrL~ki~~-----------~vfv~~~~~~~gmL~~V~~~V~~G~p~ 142 (244)
.+.++.|+.|||..+.. .+|+=++|.+.. ..-...|+..|+|.
T Consensus 2 kk~~~~l~klgl~~i~~i~eV~i~~~dg~~~~~~~P~V~~-~~~~~tyvV~G~~~ 55 (58)
T PF01849_consen 2 KKLQKMLKKLGLKEIPGIEEVTIRKDDGTVFVFNNPEVQK-SPGSNTYVVFGEAE 55 (58)
T ss_dssp ------GHHCT-EEETTEEEEEEEETTTEEEEEESEEEEE-ETTCCEEEEESEEE
T ss_pred HHHHHHHHHcCCcccCCcEEEEEEECCceEEEEcCCeEEE-cCCCCEEEEEeeeE
Confidence 45678888888877632 567777888772 23367888888875
No 20
>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=24.04 E-value=1.3e+02 Score=26.71 Aligned_cols=26 Identities=23% Similarity=0.234 Sum_probs=15.0
Q ss_pred hhhhhhHHhhhHHHHHHHHHHHHHHH
Q 026027 40 LESRKLIYNRAKQYAKEFAEQEKVLI 65 (244)
Q Consensus 40 ~~~rk~~~krae~~vkeyr~~e~d~~ 65 (244)
.+++..+...|++++.++.......+
T Consensus 133 ~~kk~e~~~~A~k~lddfY~~~~~k~ 158 (225)
T PF01086_consen 133 EEKKEEIKEKAKKELDDFYENRNEKK 158 (225)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445566667777766665444443
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=22.69 E-value=94 Score=22.16 Aligned_cols=43 Identities=19% Similarity=0.492 Sum_probs=30.5
Q ss_pred CceEEecCCHH------HHHHHHHhhcccccCCccccCCChhHHHhhcc
Q 026027 134 PYVTYGYPNLK------SVRELIYKRGYGKLDKQRIALTDNSIIEKALG 176 (244)
Q Consensus 134 ~~V~~G~p~~~------tv~~Li~KRG~~k~~~~~~~ltdn~liee~lg 176 (244)
+++.-|+|.-. -.++++-++|+..-+++++-.-.-.+|||.||
T Consensus 8 dLi~lGf~~~tA~~IIrqAK~~lV~~G~~~Y~nkRlg~VP~~~VEeiLG 56 (59)
T PF11372_consen 8 DLIELGFSESTARDIIRQAKALLVQKGFSFYNNKRLGRVPASAVEEILG 56 (59)
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHHHcCCCcccCCccCcccHHHHHHHHC
Confidence 34555666543 23467778999999998876666778899887
No 22
>cd01321 ADGF Adenosine deaminase-related growth factors (ADGF), a novel family of secreted growth-factors with sequence similarty to adenosine deaminase.
Probab=22.63 E-value=1.3e+02 Score=28.32 Aligned_cols=43 Identities=21% Similarity=0.273 Sum_probs=33.2
Q ss_pred EEEecCcCC-----CCHHHHHHHHHhCCCCcccEEEEecCHhhHHHHhh
Q 026027 88 IIRIRGINA-----IDPKTKKILQLLRLRQIFNGVFLKVNKATMNMLHR 131 (244)
Q Consensus 88 Virirg~~~-----~~~~~~k~L~~LrL~ki~~~vfv~~~~~~~gmL~~ 131 (244)
++-+-|-.+ .+..+.+.| .||-.||+||+.+..+|....+|+.
T Consensus 197 ~t~HAGE~~~~~~~~~~~v~~al-~lg~~RIGHG~~~~~dp~ll~~l~~ 244 (345)
T cd01321 197 FFFHAGETNGDGTETDENLVDAL-LLNTKRIGHGFALPKHPLLMDLVKK 244 (345)
T ss_pred eEeecCCCcCCCCCChhHHHHHH-HhCCCcCccccccCcCHHHHHHHHH
Confidence 444556443 245788889 6999999999999999988887764
No 23
>PF00289 CPSase_L_chain: Carbamoyl-phosphate synthase L chain, N-terminal domain; InterPro: IPR005481 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the N-terminal domain of the large subunit of carbamoyl phosphate synthase. This domain can also be found in certain other related proteins. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VA7_A 3OUU_A 3OUZ_B 1W96_B 1W93_A 1ULZ_A 3HB9_C 3HO8_A 3BG5_C 3HBL_A ....
Probab=20.27 E-value=4e+02 Score=20.73 Aligned_cols=71 Identities=15% Similarity=0.190 Sum_probs=44.7
Q ss_pred CHHHHHHHHHhCCCCcccEEEEecCHhhH-HHHhhccCceEEe-------cCCHHHHHHHHHhhcccccCCccccCCChh
Q 026027 98 DPKTKKILQLLRLRQIFNGVFLKVNKATM-NMLHRVEPYVTYG-------YPNLKSVRELIYKRGYGKLDKQRIALTDNS 169 (244)
Q Consensus 98 ~~~~~k~L~~LrL~ki~~~vfv~~~~~~~-gmL~~V~~~V~~G-------~p~~~tv~~Li~KRG~~k~~~~~~~ltdn~ 169 (244)
.-.+-++++.||. .+|.+-.+|.+. .........+..+ |.|.+.|-+.+.+-|..-+-+..-.|+.|.
T Consensus 14 a~r~~ra~r~~Gi----~tv~v~s~~d~~s~~~~~ad~~~~~~~~~~~~~yl~~e~I~~ia~~~g~~~i~pGyg~lse~~ 89 (110)
T PF00289_consen 14 AVRIIRALRELGI----ETVAVNSNPDTVSTHVDMADEAYFEPPGPSPESYLNIEAIIDIARKEGADAIHPGYGFLSENA 89 (110)
T ss_dssp HHHHHHHHHHTTS----EEEEEEEGGGTTGHHHHHSSEEEEEESSSGGGTTTSHHHHHHHHHHTTESEEESTSSTTTTHH
T ss_pred HHHHHHHHHHhCC----cceeccCchhcccccccccccceecCcchhhhhhccHHHHhhHhhhhcCcccccccchhHHHH
Confidence 4455667777765 566666666654 4555555555555 589999999999998654433334555444
Q ss_pred HHH
Q 026027 170 IIE 172 (244)
Q Consensus 170 lie 172 (244)
-..
T Consensus 90 ~fa 92 (110)
T PF00289_consen 90 EFA 92 (110)
T ss_dssp HHH
T ss_pred HHH
Confidence 333
Done!