Query 042287
Match_columns 97
No_of_seqs 126 out of 161
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 04:45:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042287.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042287hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0009 Ubiquitin-like/40S rib 100.0 3.9E-36 8.4E-41 196.9 3.0 62 36-97 1-62 (62)
2 PF04758 Ribosomal_S30: Riboso 100.0 6.2E-34 1.3E-38 184.7 -3.1 59 38-96 1-59 (59)
3 PTZ00467 40S ribosomal protein 100.0 1.7E-32 3.7E-37 181.4 2.7 61 36-96 1-61 (66)
4 PRK09336 30S ribosomal protein 99.9 1.8E-25 3.8E-30 141.4 1.1 45 39-84 3-47 (50)
5 COG4919 Ribosomal protein S30 99.5 8.8E-16 1.9E-20 98.6 0.4 45 39-84 3-47 (54)
6 cd01793 Fubi Fubi ubiquitin-li 67.1 0.86 1.9E-05 28.4 -1.5 35 3-37 40-74 (74)
7 cd01810 ISG15_repeat2 ISG15 ub 49.8 2.4 5.2E-05 26.4 -1.6 36 2-37 39-74 (74)
8 cd01803 Ubiquitin Ubiquitin. U 28.0 8.3 0.00018 23.2 -1.7 30 4-33 43-72 (76)
9 cd01802 AN1_N ubiquitin-like d 26.0 11 0.00024 25.7 -1.5 35 3-37 69-103 (103)
10 PF03818 MadM: Malonate/sodium 20.4 48 0.0011 21.9 0.7 11 32-42 32-42 (60)
No 1
>KOG0009 consensus Ubiquitin-like/40S ribosomal S30 protein fusion [Translation, ribosomal structure and biogenesis; Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.9e-36 Score=196.89 Aligned_cols=62 Identities=79% Similarity=1.188 Sum_probs=60.8
Q ss_pred ccchhhhhhccCcccCCCccccccccccCCChhhhhhhhcccceeeceecCCccCCCCCCCC
Q 042287 36 MGKVHGSLARAGKVRGQTPKVAKQDKKKKPRGRAHKRMQYNRRFVTAVVGFGKKRGPNSSEK 97 (97)
Q Consensus 36 ~GKvHGSLarAGKVR~QTPKV~kqeKkK~~~gRak~R~qYnrRfvnv~~~~g~krgpN~~~~ 97 (97)
|||||||||+|||||+|||||++|||+|+++|||++|+||||||||++.+||+|++||+||.
T Consensus 1 ~gkvhgslarAGKVr~QTPKv~kqeK~kkk~GRa~~Rlqy~rR~vn~~~~~g~Kr~~N~~s~ 62 (62)
T KOG0009|consen 1 MGKVHGSLARAGKVRGQTPKVEKQEKKKKKRGRAKKRLQYNRRFVNVVFGVGGKRGPNPNSK 62 (62)
T ss_pred CCceeeehhhcccccccCCcchhhhhcccccchHHHHhhhheeeEEeeeccccccCCCCCCC
Confidence 89999999999999999999999999999999999999999999999999999999999984
No 2
>PF04758 Ribosomal_S30: Ribosomal protein S30; InterPro: IPR006846 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 entry is for the ribosomal protein S30.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_X 2XZM_X 3IZB_Z 3U5G_e 3U5C_e 3J16_E 3IZ6_Z.
Probab=99.97 E-value=6.2e-34 Score=184.68 Aligned_cols=59 Identities=78% Similarity=1.187 Sum_probs=54.0
Q ss_pred chhhhhhccCcccCCCccccccccccCCChhhhhhhhcccceeeceecCCccCCCCCCC
Q 042287 38 KVHGSLARAGKVRGQTPKVAKQDKKKKPRGRAHKRMQYNRRFVTAVVGFGKKRGPNSSE 96 (97)
Q Consensus 38 KvHGSLarAGKVR~QTPKV~kqeKkK~~~gRak~R~qYnrRfvnv~~~~g~krgpN~~~ 96 (97)
|||||||+|||||+||||||++||+|.++|||++|++||+||++++++||+|++||+||
T Consensus 1 KvHGSLarAGKVR~QTPKV~k~~k~k~~~gRak~R~~Y~rRfv~~~~~~g~k~~~N~~s 59 (59)
T PF04758_consen 1 KVHGSLARAGKVRGQTPKVEKQEKKKKPTGRAKKRIQYNRRFVNVVPTFGKKKGPNANS 59 (59)
T ss_dssp HHCCCCTTTTHHHHHSSSSS--HHHHHHHCHHHHHHHHHHHCSTTHHHSCTTTTTTS--
T ss_pred CcccchhhcccccccCCCcCccccccCCchhHHHHHhhhhheeeecccCCCccCCCCCC
Confidence 79999999999999999999999998999999999999999999999999999999986
No 3
>PTZ00467 40S ribosomal protein S30; Provisional
Probab=99.97 E-value=1.7e-32 Score=181.42 Aligned_cols=61 Identities=62% Similarity=0.927 Sum_probs=57.5
Q ss_pred ccchhhhhhccCcccCCCccccccccccCCChhhhhhhhcccceeeceecCCccCCCCCCC
Q 042287 36 MGKVHGSLARAGKVRGQTPKVAKQDKKKKPRGRAHKRMQYNRRFVTAVVGFGKKRGPNSSE 96 (97)
Q Consensus 36 ~GKvHGSLarAGKVR~QTPKV~kqeKkK~~~gRak~R~qYnrRfvnv~~~~g~krgpN~~~ 96 (97)
|||||||||+||||++|||||+++||+|.++|||++|+||||||+|++.+||+|+..|+++
T Consensus 1 mgKvHGSLarAGKVr~QTPkv~k~eKkk~~~gRA~~R~qYnrRfv~~~~~~g~kr~~~~~~ 61 (66)
T PTZ00467 1 MGKIHGSLARAGKVKNQTPKVAKQEKPKQPRGRALKRLKYTRRFLAKTVKPGEKVHMNKQP 61 (66)
T ss_pred CcchhhhhhhcccccCCCCCchhhhcccCCCchHHHHHHHHhhhhhccccCCcccccCCCC
Confidence 8999999999999999999999999999999999999999999999999999887666654
No 4
>PRK09336 30S ribosomal protein S30e; Provisional
Probab=99.90 E-value=1.8e-25 Score=141.38 Aligned_cols=45 Identities=47% Similarity=0.699 Sum_probs=41.8
Q ss_pred hhhhhhccCcccCCCccccccccccCCChhhhhhhhcccceeecee
Q 042287 39 VHGSLARAGKVRGQTPKVAKQDKKKKPRGRAHKRMQYNRRFVTAVV 84 (97)
Q Consensus 39 vHGSLarAGKVR~QTPKV~kqeKkK~~~gRak~R~qYnrRfvnv~~ 84 (97)
+|||||+|||||+|||||+++||+ +++|||++|++|||||+|+..
T Consensus 3 ~HGSLarAGKVr~qTPkv~k~ekk-k~~gra~~R~qynrRf~~~~~ 47 (50)
T PRK09336 3 SHGSLTKAGKVRSQTPKIPPKPKK-NEVPRVRNRREYERRVLKARQ 47 (50)
T ss_pred cchhhhhcccccCCCCCcchhhhc-cCCchhHHHHHHHHHHhhhhc
Confidence 899999999999999999999985 457999999999999999874
No 5
>COG4919 Ribosomal protein S30 [Translation, ribosomal structure and biogenesis]
Probab=99.54 E-value=8.8e-16 Score=98.56 Aligned_cols=45 Identities=44% Similarity=0.654 Sum_probs=41.5
Q ss_pred hhhhhhccCcccCCCccccccccccCCChhhhhhhhcccceeecee
Q 042287 39 VHGSLARAGKVRGQTPKVAKQDKKKKPRGRAHKRMQYNRRFVTAVV 84 (97)
Q Consensus 39 vHGSLarAGKVR~QTPKV~kqeKkK~~~gRak~R~qYnrRfvnv~~ 84 (97)
+||||++|||||+||||++.++| |+-++|.|+|..|.+|++.+..
T Consensus 3 sHGSLTKAGKVR~QTPkipaK~k-kn~~PR~rNr~~Y~~Rv~ka~s 47 (54)
T COG4919 3 SHGSLTKAGKVRKQTPKIPAKQK-KNYPPRLRNRLKYQVRVEKAAS 47 (54)
T ss_pred CccccccccchhccCCCCCcccc-ccCChhHHHHHHHHHHHHHHHh
Confidence 69999999999999999998887 5889999999999999988764
No 6
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=67.13 E-value=0.86 Score=28.42 Aligned_cols=35 Identities=14% Similarity=0.028 Sum_probs=27.5
Q ss_pred ccccCCCCCCCcccchhhhhhhhhhhhHhhhhccc
Q 042287 3 TLDSCCLPQFGRERVSQQQQQQQRPTRLLKRSAMG 37 (97)
Q Consensus 3 ~l~s~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~G 37 (97)
.|...|-++.|+..++++.-......++..++++|
T Consensus 40 ~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~~~l~GG 74 (74)
T cd01793 40 VLLLAGVPLEDDATLGQCGVEELCTLEVAGRLLGG 74 (74)
T ss_pred EEEECCeECCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence 56677888999999999887776777777777765
No 7
>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=49.81 E-value=2.4 Score=26.36 Aligned_cols=36 Identities=11% Similarity=-0.061 Sum_probs=25.5
Q ss_pred cccccCCCCCCCcccchhhhhhhhhhhhHhhhhccc
Q 042287 2 LTLDSCCLPQFGRERVSQQQQQQQRPTRLLKRSAMG 37 (97)
Q Consensus 2 ~~l~s~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~G 37 (97)
+.|...|-++.|+..++++.-.......+..++++|
T Consensus 39 q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~~l~gg 74 (74)
T cd01810 39 FWLSFEGRPMEDEHPLGEYGLKPGCTVFMNLRLRGG 74 (74)
T ss_pred eEEEECCEECCCCCCHHHcCCCCCCEEEEEEEccCC
Confidence 356677888888888888877666666665555544
No 8
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=28.05 E-value=8.3 Score=23.16 Aligned_cols=30 Identities=17% Similarity=0.035 Sum_probs=14.8
Q ss_pred cccCCCCCCCcccchhhhhhhhhhhhHhhh
Q 042287 4 LDSCCLPQFGRERVSQQQQQQQRPTRLLKR 33 (97)
Q Consensus 4 l~s~~~~~~~~~~~s~~~~~~~~~~~~~~~ 33 (97)
|...|-.+.|+..++++.-..-...++..+
T Consensus 43 L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~ 72 (76)
T cd01803 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72 (76)
T ss_pred EEECCEECCCCCcHHHcCCCCCCEEEEEEE
Confidence 444555566666666555444333333333
No 9
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=26.01 E-value=11 Score=25.69 Aligned_cols=35 Identities=9% Similarity=-0.088 Sum_probs=21.2
Q ss_pred ccccCCCCCCCcccchhhhhhhhhhhhHhhhhccc
Q 042287 3 TLDSCCLPQFGRERVSQQQQQQQRPTRLLKRSAMG 37 (97)
Q Consensus 3 ~l~s~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~G 37 (97)
.|...|-.+.|+..+++..-..-....+..++.+|
T Consensus 69 rLi~~Gk~L~D~~tL~dy~I~~~stL~l~~~l~GG 103 (103)
T cd01802 69 HLIWNNMELEDEYCLNDYNISEGCTLKLVLAMRGG 103 (103)
T ss_pred EEEECCEECCCCCcHHHcCCCCCCEEEEEEecCCC
Confidence 45666777777777777665544445544454443
No 10
>PF03818 MadM: Malonate/sodium symporter MadM subunit; InterPro: IPR018402 The MSS family includes the monobasic malonate:Na+ symporter of Malonomonas rubra. It consists of two integral membrane proteins, MadL and MadM.The transporter is believed to catalyze the electroneutral reversible uptake of H+-malonate with one Na+, and both subunits have been shown to be essential for activity.
Probab=20.37 E-value=48 Score=21.86 Aligned_cols=11 Identities=45% Similarity=0.906 Sum_probs=9.3
Q ss_pred hhhcccchhhh
Q 042287 32 KRSAMGKVHGS 42 (97)
Q Consensus 32 ~~~~~GKvHGS 42 (97)
.++--|++|||
T Consensus 32 ~~LT~GrihGS 42 (60)
T PF03818_consen 32 KKLTRGRIHGS 42 (60)
T ss_pred HHHhCCCcchH
Confidence 36778999999
Done!