Query psy1312
Match_columns 213
No_of_seqs 144 out of 593
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 20:07:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1312.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1312hhsearch_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 5.3E-64 1.1E-68 435.8 20.0 184 30-213 1-235 (235)
2 KOG3184|consensus 100.0 2.7E-50 5.8E-55 349.9 14.6 185 28-213 1-235 (235)
3 PRK06049 rpl30p 50S ribosomal 100.0 3.9E-42 8.4E-47 282.7 9.8 112 102-213 1-154 (154)
4 TIGR01309 L30P_arch 50S riboso 100.0 8.1E-41 1.8E-45 274.3 9.3 109 104-213 1-152 (152)
5 cd01657 Ribosomal_L7_archeal_e 100.0 1.1E-40 2.4E-45 275.3 9.3 111 103-213 1-159 (159)
6 PF08079 Ribosomal_L30_N: Ribo 99.8 1.2E-18 2.7E-23 126.5 6.8 71 31-101 1-71 (71)
7 PF00327 Ribosomal_L30: Riboso 99.1 1E-10 2.3E-15 79.8 3.7 43 103-145 1-43 (52)
8 COG1841 RpmD Ribosomal protein 98.9 5.2E-10 1.1E-14 77.7 3.1 42 104-145 1-42 (55)
9 cd00355 Ribosomal_L30_like Rib 98.8 2.5E-09 5.4E-14 73.3 3.1 41 105-145 1-41 (53)
10 PRK05611 rpmD 50S ribosomal pr 98.5 9.3E-08 2E-12 67.2 3.9 42 104-145 4-45 (59)
11 cd01658 Ribosomal_L30 Ribosoma 98.5 1.2E-07 2.5E-12 65.5 3.4 41 105-145 2-42 (54)
12 TIGR01308 rpmD_bact ribosomal 98.4 2.4E-07 5.2E-12 64.3 3.4 41 105-145 2-42 (55)
13 KOG4799|consensus 70.6 14 0.0003 31.2 5.9 65 97-161 52-134 (182)
14 PLN03216 actin depolymerizing 68.3 8.2 0.00018 31.1 4.0 60 105-166 3-69 (141)
15 cd00013 ADF Actin depolymerisa 44.4 32 0.00069 26.4 3.6 52 114-166 4-62 (132)
16 KOG1736|consensus 42.4 30 0.00064 28.2 3.1 54 114-167 9-71 (143)
17 COG1253 TlyC Hemolysins and re 36.0 37 0.00079 32.1 3.2 39 119-160 290-328 (429)
18 PF01086 Clathrin_lg_ch: Clath 32.7 74 0.0016 27.7 4.4 48 29-83 111-158 (225)
19 COG4957 Predicted transcriptio 32.1 14 0.00029 30.5 -0.3 27 145-180 74-101 (148)
20 PRK11573 hypothetical protein; 31.5 46 0.00099 31.4 3.1 16 145-160 296-311 (413)
21 PTZ00152 cofilin/actin-depolym 29.9 94 0.002 24.6 4.2 70 113-185 5-84 (122)
22 PRK10318 hypothetical protein; 29.4 77 0.0017 25.5 3.6 58 120-183 27-98 (121)
23 KOG2962|consensus 28.6 3.8E+02 0.0081 24.4 8.1 23 25-50 172-194 (322)
24 PF02817 E3_binding: e3 bindin 25.9 1.5E+02 0.0033 18.8 3.9 33 113-156 3-38 (39)
25 TIGR03520 GldE gliding motilit 25.7 68 0.0015 30.2 3.2 15 146-160 297-311 (408)
26 PF03484 B5: tRNA synthetase B 24.8 75 0.0016 22.2 2.6 49 111-161 16-66 (70)
27 smart00874 B5 tRNA synthetase 23.1 1.6E+02 0.0035 20.1 4.0 49 111-161 16-67 (71)
28 KOG2292|consensus 21.6 42 0.00092 33.7 0.9 18 193-210 602-619 (751)
29 PF07946 DUF1682: Protein of u 21.3 4.8E+02 0.01 23.7 7.7 17 28-44 253-269 (321)
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=5.3e-64 Score=435.80 Aligned_cols=184 Identities=54% Similarity=0.936 Sum_probs=179.5
Q ss_pred hHHHHHHHhHHHHHHHHHHHHHHHHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCeeEEEEEe
Q psy1312 30 ESVLKKRKKRENSRIISLHKKLTALANRKKKTREIFIRAEKYVKAYRAKERDEIRLMREAKKRGNYYIPGEAKLAFVIRI 109 (213)
Q Consensus 30 E~lLKKrK~~~~~~~~~~~~~~~~k~~~k~~rk~~fkrae~yvkey~~~erd~~r~kR~akk~~~~yvp~e~kl~fVIRi 109 (213)
|++|||||++++++.++++++.+.+..++.+++.+|+|||+|+++|+++++|.+|++|+++++|++|+|++++|+|||||
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 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCHHHHHHHHhcCcccccceEEEecCcccc---------------------------------------------
Q psy1312 110 RGINRVAPKVRKTLQLLRLRQINNGIFVRLNKVSV--------------------------------------------- 144 (213)
Q Consensus 110 rG~~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~--------------------------------------------- 144 (213)
||++++||++++||++|||+++||||||++|++|.
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 99999999999999999999999999999999998
Q ss_pred ----cccccccHHHHHHHHHhcCcchhhhhcCCCCeecCCCCCcccc--cccccccCCCCCCChHHHHHHHHhhC
Q psy1312 145 ----GKQNIICVEDLIHEVFTVGDNFKYASNALWPFKLNNPTGGWRK--KTIHYVEGGDFGNREDKINKLLRKMV 213 (213)
Q Consensus 145 ----G~~giiciEDliheI~~~g~~fk~v~~fl~pF~L~~P~~G~~~--~~~~~~~GG~~G~r~~~IN~LI~rM~ 213 (213)
|++||+||||||||||++|+||+++++|||||+||||++||+. +++||.+||++||||++||+||++|+
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 7899999999999999999999999999999999999999985 77999999999999999999999997
No 2
>KOG3184|consensus
Probab=100.00 E-value=2.7e-50 Score=349.90 Aligned_cols=185 Identities=55% Similarity=0.889 Sum_probs=181.7
Q ss_pred CchHHHHHHHhHHHHHHHHHHHHHHHHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCeeEEEE
Q psy1312 28 VPESVLKKRKKRENSRIISLHKKLTALANRKKKTREIFIRAEKYVKAYRAKERDEIRLMREAKKRGNYYIPGEAKLAFVI 107 (213)
Q Consensus 28 vpE~lLKKrK~~~~~~~~~~~~~~~~k~~~k~~rk~~fkrae~yvkey~~~erd~~r~kR~akk~~~~yvp~e~kl~fVI 107 (213)
+||++|| ||+++++++++++++.+.+..+++++...|+++++|.++|++++++.++++|.+++.+++|+|++++++|||
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 EecCCCCCCHHHHHHHHhcCcccccceEEEecCcccc-------------------------------------------
Q psy1312 108 RIRGINRVAPKVRKTLQLLRLRQINNGIFVRLNKVSV------------------------------------------- 144 (213)
Q Consensus 108 RirG~~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~------------------------------------------- 144 (213)
||+|+++++|+++++|++|||.+||+||||++|+++.
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 9999999999999999999999999999999999986
Q ss_pred -------cccccccHHHHHHHHHhcCcchhhhhcCCCCeecCCCCCcccccccccccCCCCCCChHHHHHHHHhhC
Q psy1312 145 -------GKQNIICVEDLIHEVFTVGDNFKYASNALWPFKLNNPTGGWRKKTIHYVEGGDFGNREDKINKLLRKMV 213 (213)
Q Consensus 145 -------G~~giiciEDliheI~~~g~~fk~v~~fl~pF~L~~P~~G~~~~~~~~~~GG~~G~r~~~IN~LI~rM~ 213 (213)
|++|++|+||++|+|+++|++|+++++|||||+|++|.+||..+..||.+||++||||+.||+|+++|+
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 789999999999999999999999999999999999999999988999999999999999999999996
No 3
>PRK06049 rpl30p 50S ribosomal protein L30P; Reviewed
Probab=100.00 E-value=3.9e-42 Score=282.68 Aligned_cols=112 Identities=30% Similarity=0.458 Sum_probs=108.3
Q ss_pred eeEEEEEecCCCCCCHHHHHHHHhcCcccccceEEEecCcccc-------------------------------------
Q psy1312 102 KLAFVIRIRGINRVAPKVRKTLQLLRLRQINNGIFVRLNKVSV------------------------------------- 144 (213)
Q Consensus 102 kl~fVIRirG~~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~------------------------------------- 144 (213)
.|+||+||||.++++|++++||++|||+++|+|||+++|+++.
T Consensus 1 ~~~~ViriRg~ig~~~~~r~tL~~LgL~ki~~~V~v~~tp~~~GML~kV~~~V~~ge~~~~tv~~Li~kRG~~~g~~~lt 80 (154)
T PRK06049 1 EMYAVIRIRGRVNVPRDIADTLKMLRLHRVNHCVLVPETPSYKGMLQKVKDYVTWGEIDADTLAELLRKRGRLEGNKKLT 80 (154)
T ss_pred CcEEEEEecCCCCCCHHHHHHHHHcCCCcCCCEEEEeCCHHHHHHHHhhhceeEEeeCchHHHHHHHHHhCcccCCCCCC
Confidence 4799999999999999999999999999999999999999998
Q ss_pred -----cccccccHHHHHHHHHhcCcchhhhhcCCCCeecCCCCCcccccccccccCCCCCCChHHHHHHHHhhC
Q psy1312 145 -----GKQNIICVEDLIHEVFTVGDNFKYASNALWPFKLNNPTGGWRKKTIHYVEGGDFGNREDKINKLLRKMV 213 (213)
Q Consensus 145 -----G~~giiciEDliheI~~~g~~fk~v~~fl~pF~L~~P~~G~~~~~~~~~~GG~~G~r~~~IN~LI~rM~ 213 (213)
..+||+|+|||||+||++|++|+++++|+|||+||||++||++++++|.+||++||||++||+||++|+
T Consensus 81 d~~i~e~~g~~~iedl~~~i~~~~~~fk~~~~~~~~FrL~pPr~G~~~~k~~~~~gG~~G~r~~~In~Li~rM~ 154 (154)
T PRK06049 81 DEYVKENTGYDSIEELAEALVEGEIKLKDLPGLKPVFRLHPPRGGFGGIKRPFKEGGELGYRGEKINELLRRMR 154 (154)
T ss_pred HHHHHHhcCCccHHHHHHHHHhCCCCHHHhhcccCceecCCcchhhhhcccccccCCCCCccHHHHHHHHHHhC
Confidence 258999999999999999999999999999999999999999888999999999999999999999996
No 4
>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=8.1e-41 Score=274.35 Aligned_cols=109 Identities=29% Similarity=0.458 Sum_probs=104.4
Q ss_pred EEEEEecCCCCCCHHHHHHHHhcCcccccceEEEecCcccc---------------------------------------
Q psy1312 104 AFVIRIRGINRVAPKVRKTLQLLRLRQINNGIFVRLNKVSV--------------------------------------- 144 (213)
Q Consensus 104 ~fVIRirG~~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~--------------------------------------- 144 (213)
++||||||.++++|++++||++|||+++|+|||+++|+++.
T Consensus 1 ~~ViriRg~ig~~~~~r~tL~~LrL~ri~~~V~v~~tp~~~gML~kV~~yV~~ge~~~~tv~~Li~kRG~~~g~~~ltd~ 80 (152)
T TIGR01309 1 LAVIRIRGTVDVPRDIADTLEMLRLHRVNHCVLYPETPTYLGMLQKVKDYVTWGEIDEDTLELLIRKRGRLVGGDKVTDE 80 (152)
T ss_pred CeEEEecCcCCCCHHHHHHHHHcCCCcCCCEEEEeCCHHHHHHHHHhHhheeEecCCHHHHHHHHHHhccccCCCcCCHH
Confidence 58999999999999999999999999999999999999998
Q ss_pred ---cccccccHHHHHHHHHhcCcchhhhhcCCCCeecCCCCCccc-ccccccccCCCCCCChHHHHHHHHhhC
Q psy1312 145 ---GKQNIICVEDLIHEVFTVGDNFKYASNALWPFKLNNPTGGWR-KKTIHYVEGGDFGNREDKINKLLRKMV 213 (213)
Q Consensus 145 ---G~~giiciEDliheI~~~g~~fk~v~~fl~pF~L~~P~~G~~-~~~~~~~~GG~~G~r~~~IN~LI~rM~ 213 (213)
.++||+|+||||||||++|++|++++ |+|||+||||++||+ +++++|.+||++||||++||+||++|+
T Consensus 81 ~i~e~~g~~~iedl~~~i~~~~~~f~~~~-~~~~FrL~pPr~G~~~~~k~~~~~gG~~G~r~~~In~Li~rMi 152 (152)
T TIGR01309 81 YVKEVTGYESVDELAKALVEGEIKLSEAG-LKPVFRLHPPRKGFKGGIKTPYRDGGELGYRGEKINELLRRMR 152 (152)
T ss_pred HHHHHcCCccHHHHHHHHHcCCCCccccC-ccCceeCCCCCcccccccccccccCCCCcccHHHHHHHHHHhC
Confidence 25689999999999999999999996 999999999999998 688999999999999999999999996
No 5
>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-40 Score=275.34 Aligned_cols=111 Identities=55% Similarity=0.966 Sum_probs=106.8
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhcCcccccceEEEecCcccc--------------------------------------
Q psy1312 103 LAFVIRIRGINRVAPKVRKTLQLLRLRQINNGIFVRLNKVSV-------------------------------------- 144 (213)
Q Consensus 103 l~fVIRirG~~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~-------------------------------------- 144 (213)
|+||||+||..+++|++++||++|||+++|+|||+++|+++.
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 689999999999999999999999999999999999999998
Q ss_pred -------c---ccccccHHHHHHHHHhcCcchhhhhcCCCCeecCCCCCcccccccccccCCCCCCChHHHHHHHHhhC
Q psy1312 145 -------G---KQNIICVEDLIHEVFTVGDNFKYASNALWPFKLNNPTGGWRKKTIHYVEGGDFGNREDKINKLLRKMV 213 (213)
Q Consensus 145 -------G---~~giiciEDliheI~~~g~~fk~v~~fl~pF~L~~P~~G~~~~~~~~~~GG~~G~r~~~IN~LI~rM~ 213 (213)
. ++||+|+||||||||++|++|+++++|||||+||||++||++++++|++||++||||++||+||++|+
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 LTDNYLVEKTLKKGIICIEDLAHEIYTGGPNFKEVNNFLPPFRLHPPRGGFKGKKRHFSEGGELGYRGEDINELIRRMI 159 (159)
T ss_pred CChHHHHHHHcccCcccHHHHHHHHHhCccCHHHhhccCCCeECCCcccchhccccccccCCCCCccHHHHHHHHHHhC
Confidence 1 24999999999999999999999999999999999999999888999999999999999999999997
No 6
>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=99.76 E-value=1.2e-18 Score=126.47 Aligned_cols=71 Identities=59% Similarity=0.856 Sum_probs=64.6
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCCC
Q psy1312 31 SVLKKRKKRENSRIISLHKKLTALANRKKKTREIFIRAEKYVKAYRAKERDEIRLMREAKKRGNYYIPGEA 101 (213)
Q Consensus 31 ~lLKKrK~~~~~~~~~~~~~~~~k~~~k~~rk~~fkrae~yvkey~~~erd~~r~kR~akk~~~~yvp~e~ 101 (213)
||||||++++++++.++++..+.+..++.+++.+|+|||+|++||+++|+|+|+++|+|++.||||||+||
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 68999999999999999999999999999999999999999999999999999999999999999999987
No 7
>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=99.08 E-value=1e-10 Score=79.80 Aligned_cols=43 Identities=49% Similarity=0.670 Sum_probs=39.2
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhcCcccccceEEEecCccccc
Q psy1312 103 LAFVIRIRGINRVAPKVRKTLQLLRLRQINNGIFVRLNKVSVG 145 (213)
Q Consensus 103 l~fVIRirG~~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~G 145 (213)
++||+||||..+.+|++++||++|||+++|++||+++|+++.|
T Consensus 1 ~l~V~~irs~~g~~~~~~~tl~~LgL~k~~~~v~~~~t~~~~g 43 (52)
T PF00327_consen 1 LLFVTRIRSPIGAPPKVRKTLKALGLRKINQAVFVKNTPSIRG 43 (52)
T ss_dssp EEEEEESS-STTSSHHHHHHHHHTT-SSTTEEEEEESSHHHHH
T ss_pred CEEEEEeCCCCCCCHHHHHHHHHcCCCcCCCEEEEECCHHHHH
Confidence 5899999999999999999999999999999999999998875
No 8
>COG1841 RpmD Ribosomal protein L30/L7E [Translation, ribosomal structure and biogenesis]
Probab=98.95 E-value=5.2e-10 Score=77.68 Aligned_cols=42 Identities=40% Similarity=0.473 Sum_probs=40.4
Q ss_pred EEEEEecCCCCCCHHHHHHHHhcCcccccceEEEecCccccc
Q psy1312 104 AFVIRIRGINRVAPKVRKTLQLLRLRQINNGIFVRLNKVSVG 145 (213)
Q Consensus 104 ~fVIRirG~~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~G 145 (213)
++|+|+||..|.+|++++||++|||+++|++|+++.|+++.|
T Consensus 1 ~~V~~iRs~ig~~~~~r~tl~~LgL~kin~~v~~~dtp~irG 42 (55)
T COG1841 1 LKVTLIRSPIGRPPKIRKTLRLLGLRKINHTVIVEDTPAVRG 42 (55)
T ss_pred CeEEEEeccCCCChHHHHHHHHhCCCccCCEEEEcCCHHHHH
Confidence 479999999999999999999999999999999999999986
No 9
>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=98.83 E-value=2.5e-09 Score=73.31 Aligned_cols=41 Identities=41% Similarity=0.555 Sum_probs=39.6
Q ss_pred EEEEecCCCCCCHHHHHHHHhcCcccccceEEEecCccccc
Q psy1312 105 FVIRIRGINRVAPKVRKTLQLLRLRQINNGIFVRLNKVSVG 145 (213)
Q Consensus 105 fVIRirG~~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~G 145 (213)
+|+|+||..+.+|++++||+.|||+++|++||+++|+++.|
T Consensus 1 ~V~~irs~ig~~~~~~~tl~~LgL~k~~~~v~~~~tp~~~g 41 (53)
T cd00355 1 KVTRVRSLIGRPPKQRKTLKALGLRKINQTVFVKDTPSIRG 41 (53)
T ss_pred CEEEecCCCCCCHHHHHHHHHcCCCcCCCEEEEeCCHHHHH
Confidence 58999999999999999999999999999999999999986
No 10
>PRK05611 rpmD 50S ribosomal protein L30; Reviewed
Probab=98.53 E-value=9.3e-08 Score=67.21 Aligned_cols=42 Identities=26% Similarity=0.294 Sum_probs=40.9
Q ss_pred EEEEEecCCCCCCHHHHHHHHhcCcccccceEEEecCccccc
Q psy1312 104 AFVIRIRGINRVAPKVRKTLQLLRLRQINNGIFVRLNKVSVG 145 (213)
Q Consensus 104 ~fVIRirG~~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~G 145 (213)
+.|+++||..|.+|++++||+.|||+++|++|++++|+++.|
T Consensus 4 ~~I~~vRs~ig~~~~~r~tl~~LgL~k~~~~v~~~dtp~~rG 45 (59)
T PRK05611 4 LKITLVKSLIGRKPKQRATLRGLGLRKINSTVELEDTPAIRG 45 (59)
T ss_pred EEEEEeecCCCCCHHHHHHHHHcCCCcCCCEEEecCCHHHHH
Confidence 789999999999999999999999999999999999999986
No 11
>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=98.49 E-value=1.2e-07 Score=65.52 Aligned_cols=41 Identities=22% Similarity=0.269 Sum_probs=39.4
Q ss_pred EEEEecCCCCCCHHHHHHHHhcCcccccceEEEecCccccc
Q psy1312 105 FVIRIRGINRVAPKVRKTLQLLRLRQINNGIFVRLNKVSVG 145 (213)
Q Consensus 105 fVIRirG~~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~G 145 (213)
-|.++||..|.+|++++||+.|||+++|++|++++|+++.|
T Consensus 2 ~i~~iRs~ig~~~~~r~tl~~LgL~k~~~~v~~~~tp~~~G 42 (54)
T cd01658 2 KITLVKSLIGRPKKQRATLKALGLKKINQTVVHKDTPSIRG 42 (54)
T ss_pred EEEEEeCCCCCCHHHHHHHHHcCCCcCCCEEEecCCHHHHH
Confidence 58899999999999999999999999999999999999986
No 12
>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=98.41 E-value=2.4e-07 Score=64.27 Aligned_cols=41 Identities=32% Similarity=0.351 Sum_probs=39.2
Q ss_pred EEEEecCCCCCCHHHHHHHHhcCcccccceEEEecCccccc
Q psy1312 105 FVIRIRGINRVAPKVRKTLQLLRLRQINNGIFVRLNKVSVG 145 (213)
Q Consensus 105 fVIRirG~~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~G 145 (213)
-|+++||..|.+|+.++||+.|||+++|++|++++||++.|
T Consensus 2 kItlvrs~ig~~~~~r~tl~~LgL~k~~~~v~~~dtp~irG 42 (55)
T TIGR01308 2 KVTLVRSLIGRPKKQRKTLKALGLRKIGRQVVLEDNPAIRG 42 (55)
T ss_pred EEEEEeCCCCCCHHHHHHHHHcCCCcCCCEEEecCCHHHHH
Confidence 47899999999999999999999999999999999999986
No 13
>KOG4799|consensus
Probab=70.57 E-value=14 Score=31.24 Aligned_cols=65 Identities=15% Similarity=0.093 Sum_probs=51.7
Q ss_pred cCCC-CeeEEEEEecCCCCCCHHHHHHHHhcCcccccc-eEEEecCcccc----------------cccccccHHHHHHH
Q psy1312 97 IPGE-AKLAFVIRIRGINRVAPKVRKTLQLLRLRQINN-GIFVRLNKVSV----------------GKQNIICVEDLIHE 158 (213)
Q Consensus 97 vp~e-~kl~fVIRirG~~~v~~~v~k~L~lLrL~~in~-~vfvk~n~~t~----------------G~~giiciEDlihe 158 (213)
.|.+ +||..|-||+...+-|..-.+++.+|+|....+ -..+++.+++. =.+|.-.-+|+-|-
T Consensus 52 ~P~~p~KL~~v~rik~t~~~PyWek~iik~lGld~k~t~~qV~kNip~vNakLwkIKHLI~~~pv~fp~gePte~di~~t 131 (182)
T KOG4799|consen 52 GPQNPHKLHIVTRIKSTRRRPYWEKDIIKMLGLDKKHTRPQVHKNIPSVNAKLWKIKHLIRLRPVEFPGGEPTEDDISST 131 (182)
T ss_pred CCCCccceEEEEEeccccCCcchHHHHHHHhCcccccCCceEeecccchhhHHHHhhheeEEEeeccCCCCCchhhhhhh
Confidence 3444 589999999999999999999999999999998 77888888776 13456666777776
Q ss_pred HHh
Q psy1312 159 VFT 161 (213)
Q Consensus 159 I~~ 161 (213)
++.
T Consensus 132 ~Lk 134 (182)
T KOG4799|consen 132 SLK 134 (182)
T ss_pred hhc
Confidence 653
No 14
>PLN03216 actin depolymerizing factor; Provisional
Probab=68.31 E-value=8.2 Score=31.14 Aligned_cols=60 Identities=15% Similarity=0.279 Sum_probs=45.1
Q ss_pred EEEEecCCCCCCHHHHHHHHhcCcccccceEEEecCcccc-------cccccccHHHHHHHHHhcCcch
Q psy1312 105 FVIRIRGINRVAPKVRKTLQLLRLRQINNGIFVRLNKVSV-------GKQNIICVEDLIHEVFTVGDNF 166 (213)
Q Consensus 105 fVIRirG~~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~-------G~~giiciEDliheI~~~g~~f 166 (213)
|-+-.-| ..+++++..+++.|++.+.+..+.++.+.... |..|. +.+||+..+-..++.|
T Consensus 3 ~~m~~SG-i~v~~~c~~~f~~lk~~k~~r~iifkI~~~~~~ivv~~~~~~~~-~~~d~~~~L~~~~~rY 69 (141)
T PLN03216 3 FKMATTG-MWVTDECKNSFMEMKWKKVHRYIVFKIDEKSRKVTVDKVGGPGE-SYDDLAASLPTDDCRY 69 (141)
T ss_pred ceecCCC-CeeCHHHHHHHHHHHhCCCceEEEEEEcCCCCEEEEEecCCCCC-CHHHHHHhCCCCCCeE
Confidence 3333335 37999999999999999999999999997643 32333 7899999887655544
No 15
>cd00013 ADF Actin depolymerisation factor/cofilin -like domains; present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Probab=44.43 E-value=32 Score=26.44 Aligned_cols=52 Identities=10% Similarity=0.271 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHhcCcccccceEEEecCccc--c-----cccccccHHHHHHHHHhcCcch
Q psy1312 114 RVAPKVRKTLQLLRLRQINNGIFVRLNKVS--V-----GKQNIICVEDLIHEVFTVGDNF 166 (213)
Q Consensus 114 ~v~~~v~k~L~lLrL~~in~~vfvk~n~~t--~-----G~~giiciEDliheI~~~g~~f 166 (213)
.+++++.+.++.|+..+..+.|.+..+... + |..| .+++||+.++-...+.|
T Consensus 4 ~i~~e~~~a~~~~~~~~~~~~vi~~i~~~~~~i~~~~~~~~~-~~~~~l~~~l~~~~~~y 62 (132)
T cd00013 4 KVSDECKEAFEELKSGKKTRWIIFKIDDDKKEIVVEKTGEGG-ESFDEFVEELPEDECRY 62 (132)
T ss_pred eECHHHHHHHHHHHhCCceeEEEEEEcCCCCEEEEEecCCCC-CCHHHHHHhCCcCCceE
Confidence 688999999999999866777777777633 2 3322 47999999887666644
No 16
>KOG1736|consensus
Probab=42.41 E-value=30 Score=28.22 Aligned_cols=54 Identities=22% Similarity=0.378 Sum_probs=43.7
Q ss_pred CCCHHHHHHHHhcCcc---cccceEEEecCcccc------cccccccHHHHHHHHHhcCcchh
Q psy1312 114 RVAPKVRKTLQLLRLR---QINNGIFVRLNKVSV------GKQNIICVEDLIHEVFTVGDNFK 167 (213)
Q Consensus 114 ~v~~~v~k~L~lLrL~---~in~~vfvk~n~~t~------G~~giiciEDliheI~~~g~~fk 167 (213)
.++++.++-++.+|++ -.|-|..+++.+.+. .....|++|+|+.++-.-.|.|-
T Consensus 9 ~i~~et~~ki~kFR~r~k~t~~~A~imKidK~~~eiV~d~Eeld~is~eEladeLpe~~PRFv 71 (143)
T KOG1736|consen 9 KIGTETREKIRKFRFRTKETSNAAIIMKIDKDSYEIVLDEEELDEISPEELADELPERQPRFV 71 (143)
T ss_pred EeCHHHHHHHHHhhhhhccccceeEEEEecCCceEeecCHHHhccCChHHHHhhccccCCcEE
Confidence 5788999999999998 456778889998876 35567899999999987777773
No 17
>COG1253 TlyC Hemolysins and related proteins containing CBS domains [General function prediction only]
Probab=35.95 E-value=37 Score=32.07 Aligned_cols=39 Identities=23% Similarity=0.401 Sum_probs=25.2
Q ss_pred HHHHHHhcCcccccceEEEecCcccccccccccHHHHHHHHH
Q psy1312 119 VRKTLQLLRLRQINNGIFVRLNKVSVGKQNIICVEDLIHEVF 160 (213)
Q Consensus 119 v~k~L~lLrL~~in~~vfvk~n~~t~G~~giiciEDliheI~ 160 (213)
+.+.|+.||-.+.+-|+.+..-- |-.|++++||++.+|+
T Consensus 290 ~~~lL~~~r~~~~hmAiVvDEyG---~~~GlVTleDIiEeIv 328 (429)
T COG1253 290 LSDLLEEFREERTHMAIVVDEYG---GVEGLVTLEDIIEEIV 328 (429)
T ss_pred HHHHHHHHHHhCCeEEEEEEcCC---CeEEEeEHHHHHHHHh
Confidence 34555555555555555544432 4558999999999995
No 18
>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=32.72 E-value=74 Score=27.67 Aligned_cols=48 Identities=19% Similarity=0.189 Sum_probs=25.2
Q ss_pred chHHHHHHHhHHHHHHHHHHHHHHHHHHHhhhhhHHHHhhHHHHHHHHHHHHHHH
Q psy1312 29 PESVLKKRKKRENSRIISLHKKLTALANRKKKTREIFIRAEKYVKAYRAKERDEI 83 (213)
Q Consensus 29 pE~lLKKrK~~~~~~~~~~~~~~~~k~~~k~~rk~~fkrae~yvkey~~~erd~~ 83 (213)
||.|-+ |+.++..+..++-....+++..+...|++|+.++.......+
T Consensus 111 ~e~ire-------Wre~~~~~i~ekD~~e~~kk~e~~~~A~k~lddfY~~~~~k~ 158 (225)
T PF01086_consen 111 PEAIRE-------WREERDKRIEEKDAEEEEKKEEIKEKAKKELDDFYENRNEKK 158 (225)
T ss_dssp TTHHHH-------HHHHHTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666654 333333333333333445555666677777777665554443
No 19
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=32.08 E-value=14 Score=30.50 Aligned_cols=27 Identities=37% Similarity=0.613 Sum_probs=21.8
Q ss_pred cccccccHHHHHHHHHhcCcchhhhhcCCCC-eecCC
Q psy1312 145 GKQNIICVEDLIHEVFTVGDNFKYASNALWP-FKLNN 180 (213)
Q Consensus 145 G~~giiciEDliheI~~~g~~fk~v~~fl~p-F~L~~ 180 (213)
-+| |||+|| |..|+.+...|.. |-|+|
T Consensus 74 pD~-IicLED--------GkkfKSLKRHL~t~~gmTP 101 (148)
T COG4957 74 PDY-IICLED--------GKKFKSLKRHLTTHYGLTP 101 (148)
T ss_pred CCe-EEEecc--------CcchHHHHHHHhcccCCCH
Confidence 445 899996 8999999988887 77776
No 20
>PRK11573 hypothetical protein; Provisional
Probab=31.55 E-value=46 Score=31.44 Aligned_cols=16 Identities=31% Similarity=0.646 Sum_probs=13.9
Q ss_pred cccccccHHHHHHHHH
Q psy1312 145 GKQNIICVEDLIHEVF 160 (213)
Q Consensus 145 G~~giiciEDliheI~ 160 (213)
|--|++++||++.||+
T Consensus 296 ~~~GiVTleDilEeiv 311 (413)
T PRK11573 296 DIQGLVTVEDILEEIV 311 (413)
T ss_pred CeEEEeeHHHHHHHHh
Confidence 4568999999999996
No 21
>PTZ00152 cofilin/actin-depolymerizing factor 1-like protein; Provisional
Probab=29.93 E-value=94 Score=24.58 Aligned_cols=70 Identities=11% Similarity=0.151 Sum_probs=47.7
Q ss_pred CCCCHHHHHHHHhcCcccccceEEEecCcccc-----cccccccHHHHHHHHHhcC---cchhhhhcC--CCCeecCCCC
Q psy1312 113 NRVAPKVRKTLQLLRLRQINNGIFVRLNKVSV-----GKQNIICVEDLIHEVFTVG---DNFKYASNA--LWPFKLNNPT 182 (213)
Q Consensus 113 ~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~-----G~~giiciEDliheI~~~g---~~fk~v~~f--l~pF~L~~P~ 182 (213)
..+++++...++.|++.+.+..+.++.+...+ |.. .+.+||+..|-..+ +.|--. .+ .+.|=.-.|.
T Consensus 5 i~v~de~~~~f~~lk~~k~~r~iifkI~~~~Ivv~~~~~~--~~~~e~~~~L~~~~~~~crY~vy-d~~~klvFI~w~Pd 81 (122)
T PTZ00152 5 IRVNDNCVTEFNNMKIRKTCRWIIFVIENCEIIIHSKGAT--TTLTELVGSIDKNDKIQCAYVVF-DAVNKIHFFMYARE 81 (122)
T ss_pred cCcCHHHHHHHHHHhcCCcceEEEEEEcCcEEEEEecCCC--CCHHHHHHhccccCCCCceEEEE-ccCCCEEEEEECCC
Confidence 37899999999999999888899998875333 332 37899999987655 433211 11 2456566666
Q ss_pred Ccc
Q psy1312 183 GGW 185 (213)
Q Consensus 183 ~G~ 185 (213)
+.=
T Consensus 82 ~a~ 84 (122)
T PTZ00152 82 SSN 84 (122)
T ss_pred CCC
Confidence 543
No 22
>PRK10318 hypothetical protein; Provisional
Probab=29.38 E-value=77 Score=25.47 Aligned_cols=58 Identities=24% Similarity=0.253 Sum_probs=40.0
Q ss_pred HHHHHhcCcccccceEEEecCcccc--------------cccccccHHHHHHHHHhcCcchhhhhcCCCCeecCCCCC
Q psy1312 120 RKTLQLLRLRQINNGIFVRLNKVSV--------------GKQNIICVEDLIHEVFTVGDNFKYASNALWPFKLNNPTG 183 (213)
Q Consensus 120 ~k~L~lLrL~~in~~vfvk~n~~t~--------------G~~giiciEDliheI~~~g~~fk~v~~fl~pF~L~~P~~ 183 (213)
+.+=.|+.+-+.-+|+|+++....- ++--|-+.||+|..+.+-.. ++ --||....|.+
T Consensus 27 ~ei~~L~~~~~~s~c~FiRNG~~h~~~eA~~HLr~K~~~~k~~i~taE~FI~~~ASkSs----~S--GkpY~V~c~~~ 98 (121)
T PRK10318 27 RINAMLEGLAQKKDCTFVRNGDEHTCKEAVSHLRLKLGNTRNRIDTAEQFIDKVASSSS----IS--GKPYIVKCPGK 98 (121)
T ss_pred HHHHHHHHHHhcCCCEEEECCCcCCHHHHHHHHHHHHHhccCccccHHHHHHHHhhhcc----cC--CCCeEEEcCCC
Confidence 4455566665777999999998877 34458899999999975432 11 24677766653
No 23
>KOG2962|consensus
Probab=28.58 E-value=3.8e+02 Score=24.35 Aligned_cols=23 Identities=22% Similarity=0.271 Sum_probs=15.7
Q ss_pred CCCCchHHHHHHHhHHHHHHHHHHHH
Q psy1312 25 LPVVPESVLKKRKKRENSRIISLHKK 50 (213)
Q Consensus 25 l~~vpE~lLKKrK~~~~~~~~~~~~~ 50 (213)
-|.+||.+ |++++...+++.+..
T Consensus 172 KPkIPEai---RrN~E~ME~EkTKlL 194 (322)
T KOG2962|consen 172 KPKIPEAI---RRNFELMEAEKTKLL 194 (322)
T ss_pred CCCChHHH---HHhHHHHHHHhhhhH
Confidence 36789998 777777666555433
No 24
>PF02817 E3_binding: e3 binding domain; InterPro: IPR004167 A small domain of the E2 subunit of 2-oxo-acid dehydrogenases that is responsible for the binding of the E3 subunit. Proteins containing this domain include the branched-chain alpha-keto acid dehydrogenase complex of bacteria, which catalyses the overall conversion of alpha-keto acids to acyl-CoA and carbon dioxide; and the E-3 binding protein of eukaryotic pyruvate dehydrogenase.; GO: 0016746 transferase activity, transferring acyl groups, 0008152 metabolic process; PDB: 1BBL_A 1W4H_A 1BAL_A 2WXC_A 2BTH_A 2BTG_A 2CYU_A 2EQ7_C 2EQ8_C 3RNM_E ....
Probab=25.87 E-value=1.5e+02 Score=18.80 Aligned_cols=33 Identities=27% Similarity=0.350 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHHhcCcccccceEEEecCcccc---cccccccHHHHH
Q psy1312 113 NRVAPKVRKTLQLLRLRQINNGIFVRLNKVSV---GKQNIICVEDLI 156 (213)
Q Consensus 113 ~~v~~~v~k~L~lLrL~~in~~vfvk~n~~t~---G~~giiciEDli 156 (213)
...+|-++++++.+++. .+.+ |..|-|+-+|+-
T Consensus 3 i~asP~ar~la~e~gid-----------l~~v~gtG~~GrI~k~Dv~ 38 (39)
T PF02817_consen 3 IKASPAARKLAAELGID-----------LSQVKGTGPGGRITKEDVL 38 (39)
T ss_dssp CCCSHHHHHHHHHTT-------------GGGSSSSSTTSBBCHHHHH
T ss_pred cccCHHHHHHHHHcCCC-----------cccccccCCCCcEeHHHhh
Confidence 45799999999998873 2222 788999999985
No 25
>TIGR03520 GldE gliding motility-associated protein GldE. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. GldE was discovered because of its adjacency to GldD in F. johnsonii. Overexpression of GldE partially supresses the effects of a GldB point mutant suggesting that GldB and GldE interact. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility and in fact some do not appear to express the gliding phenotype.
Probab=25.70 E-value=68 Score=30.16 Aligned_cols=15 Identities=27% Similarity=0.671 Sum_probs=13.3
Q ss_pred ccccccHHHHHHHHH
Q psy1312 146 KQNIICVEDLIHEVF 160 (213)
Q Consensus 146 ~~giiciEDliheI~ 160 (213)
--||+++|||+.+|+
T Consensus 297 ~~GiVT~eDileeiv 311 (408)
T TIGR03520 297 TSGLVTLEDIIEEIV 311 (408)
T ss_pred EEEEEEHHHHHHHHh
Confidence 458999999999995
No 26
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=24.79 E-value=75 Score=22.22 Aligned_cols=49 Identities=24% Similarity=0.285 Sum_probs=30.4
Q ss_pred CCCCCCHHHHHHHHhcCccccc-ceEEEecC-cccccccccccHHHHHHHHHh
Q psy1312 111 GINRVAPKVRKTLQLLRLRQIN-NGIFVRLN-KVSVGKQNIICVEDLIHEVFT 161 (213)
Q Consensus 111 G~~~v~~~v~k~L~lLrL~~in-~~vfvk~n-~~t~G~~giiciEDliheI~~ 161 (213)
|..--..++.++|..|++.-.. .+-.+.++ |+.+ +.|..-+||+.||+.
T Consensus 16 G~~i~~~~i~~~L~~lg~~~~~~~~~~~~v~vP~~R--~Di~~~~DliEEiaR 66 (70)
T PF03484_consen 16 GIDISPEEIIKILKRLGFKVEKIDGDTLEVTVPSYR--FDIEHEEDLIEEIAR 66 (70)
T ss_dssp TS---HHHHHHHHHHTT-EEEE-CTTEEEEEEETTS--TT-SSHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHCCCEEEECCCCEEEEEcCCCc--CCcCcccHHHHHHHH
Confidence 4433457788999999987665 33333333 3333 678899999999964
No 27
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=23.12 E-value=1.6e+02 Score=20.10 Aligned_cols=49 Identities=20% Similarity=0.195 Sum_probs=31.0
Q ss_pred CCCCCCHHHHHHHHhcCcccccc---eEEEecCcccccccccccHHHHHHHHHh
Q psy1312 111 GINRVAPKVRKTLQLLRLRQINN---GIFVRLNKVSVGKQNIICVEDLIHEVFT 161 (213)
Q Consensus 111 G~~~v~~~v~k~L~lLrL~~in~---~vfvk~n~~t~G~~giiciEDliheI~~ 161 (213)
|..--+.++.++|..|++.-..+ +.+--.-|+++ +.|.+..|||.||+-
T Consensus 16 G~~i~~~ei~~~L~~lg~~~~~~~~~~~~~v~~P~~R--~Di~~~~DliEei~r 67 (71)
T smart00874 16 GLDLSAEEIEEILKRLGFEVEVSGDDDTLEVTVPSYR--FDILIEADLIEEVAR 67 (71)
T ss_pred CCCCCHHHHHHHHHHCCCeEEecCCCCeEEEECCCCc--cccCcccHHHHHHHH
Confidence 44333457899999999865432 22211123333 578899999999964
No 28
>KOG2292|consensus
Probab=21.62 E-value=42 Score=33.70 Aligned_cols=18 Identities=44% Similarity=0.652 Sum_probs=15.5
Q ss_pred ccCCCCCCChHHHHHHHH
Q psy1312 193 VEGGDFGNREDKINKLLR 210 (213)
Q Consensus 193 ~~GG~~G~r~~~IN~LI~ 210 (213)
.-||..||.+|+||.++.
T Consensus 602 IFGG~iGYssDDINKFLW 619 (751)
T KOG2292|consen 602 IFGGLIGYSSDDINKFLW 619 (751)
T ss_pred EecccccCCcchhhhhhe
Confidence 349999999999999863
No 29
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=21.28 E-value=4.8e+02 Score=23.69 Aligned_cols=17 Identities=35% Similarity=0.474 Sum_probs=10.4
Q ss_pred CchHHHHHHHhHHHHHH
Q psy1312 28 VPESVLKKRKKRENSRI 44 (213)
Q Consensus 28 vpE~lLKKrK~~~~~~~ 44 (213)
-||++.|=.|.+++...
T Consensus 253 ~~e~~~K~~k~R~~~~~ 269 (321)
T PF07946_consen 253 SPEAKKKAKKNREEEEE 269 (321)
T ss_pred CHHHHHHHHHHHHHHHH
Confidence 36776666666655554
Done!