Query 035652
Match_columns 71
No_of_seqs 108 out of 154
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 05:00:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035652.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035652hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3344 40s ribosomal protein 99.5 3.1E-15 6.6E-20 106.4 2.3 39 1-40 73-112 (150)
2 PTZ00034 40S ribosomal protein 99.3 8.4E-13 1.8E-17 91.4 2.5 26 1-26 74-99 (124)
3 PF03501 S10_plectin: Plectin/ 99.2 2.9E-12 6.3E-17 85.2 0.2 24 1-24 71-94 (95)
4 COG5045 Ribosomal protein S10E 98.5 3.2E-08 6.9E-13 67.5 1.4 30 1-31 73-102 (105)
5 PF14756 Pdase_C33_assoc: Pept 77.3 0.55 1.2E-05 33.8 -0.7 21 2-22 17-37 (147)
6 KOG0366 Protein geranylgeranyl 37.9 7.7 0.00017 31.1 -0.8 20 35-54 229-248 (329)
7 cd03071 PDI_b'_NRX PDIb' famil 36.8 18 0.0004 25.3 1.0 13 2-14 69-81 (116)
8 PF08790 zf-LYAR: LYAR-type C2 32.8 21 0.00046 19.2 0.7 15 49-63 8-22 (28)
9 COG5029 CAL1 Prenyltransferase 22.2 36 0.00078 27.5 0.5 18 37-54 244-261 (342)
10 cd01236 PH_outspread Outspread 21.1 72 0.0016 20.7 1.7 29 40-69 52-80 (104)
11 PF14567 SUKH_5: SMI1-KNR4 cel 21.1 45 0.00097 23.0 0.7 15 2-17 76-90 (132)
No 1
>KOG3344 consensus 40s ribosomal protein s10 [Translation, ribosomal structure and biogenesis]
Probab=99.53 E-value=3.1e-15 Score=106.44 Aligned_cols=39 Identities=59% Similarity=1.018 Sum_probs=35.8
Q ss_pred ChhhhhhhCCCCCCchhhhhcccCCCCCCCCC-CCCCCCch
Q 035652 1 IEFLRGYLNLPSEIVPATLKKQAKPAGGRPFG-GPGGDRPR 40 (71)
Q Consensus 1 IeYLR~YLhLP~EIVPaTLkr~~r~~t~Rpr~-g~~gerp~ 40 (71)
|||||+|||||+|||||||++ ++|+++||++ |.++.+|+
T Consensus 73 i~yLR~YLhLP~EiVpaTl~~-~rP~~~rpr~~g~e~~~p~ 112 (150)
T KOG3344|consen 73 IEYLREYLHLPPEIVPATLKR-SRPETGRPRPPGLEGRGPA 112 (150)
T ss_pred HHHHHHHhcCCcccccchhhc-cCCCCCCCCCCCCCCCCcc
Confidence 799999999999999999999 5888889988 88888885
No 2
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=99.31 E-value=8.4e-13 Score=91.38 Aligned_cols=26 Identities=50% Similarity=0.844 Sum_probs=23.7
Q ss_pred ChhhhhhhCCCCCCchhhhhcccCCC
Q 035652 1 IEFLRGYLNLPSEIVPATLKKQAKPA 26 (71)
Q Consensus 1 IeYLR~YLhLP~EIVPaTLkr~~r~~ 26 (71)
|||||+|||||+||||+||++++++.
T Consensus 74 ieyLR~yL~LP~eivP~T~k~~~~~~ 99 (124)
T PTZ00034 74 IEYLRTYLHLPPDVFPATHKKKSVNF 99 (124)
T ss_pred HHHHHHHhCCCcccCchhhcccccCc
Confidence 79999999999999999999986654
No 3
>PF03501 S10_plectin: Plectin/S10 domain; InterPro: IPR005326 This presumed domain is found at the N terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.; PDB: 2XZM_7 2XZN_7 3U5C_K 3U5G_K.
Probab=99.19 E-value=2.9e-12 Score=85.19 Aligned_cols=24 Identities=71% Similarity=1.144 Sum_probs=17.4
Q ss_pred ChhhhhhhCCCCCCchhhhhcccC
Q 035652 1 IEFLRGYLNLPSEIVPATLKKQAK 24 (71)
Q Consensus 1 IeYLR~YLhLP~EIVPaTLkr~~r 24 (71)
|||||+|||||+|||||||+++++
T Consensus 71 IeyLR~yL~LP~eivPaTlk~~~~ 94 (95)
T PF03501_consen 71 IEYLREYLHLPAEIVPATLKKSRR 94 (95)
T ss_dssp HHHHHHHC-SSTT--TCCCS-S--
T ss_pred HHHHHHHhCCChhhCcHHhccccC
Confidence 799999999999999999998744
No 4
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=98.53 E-value=3.2e-08 Score=67.45 Aligned_cols=30 Identities=47% Similarity=0.739 Sum_probs=24.6
Q ss_pred ChhhhhhhCCCCCCchhhhhcccCCCCCCCC
Q 035652 1 IEFLRGYLNLPSEIVPATLKKQAKPAGGRPF 31 (71)
Q Consensus 1 IeYLR~YLhLP~EIVPaTLkr~~r~~t~Rpr 31 (71)
+||||+||+||+|+||+|.+++.++ ++||.
T Consensus 73 veyLREyL~lp~e~Vp~t~~~~v~p-t~rp~ 102 (105)
T COG5045 73 VEYLREYLVLPDEGVPSTEAPAVSP-TQRPQ 102 (105)
T ss_pred HHHHHHHhcCccccCccccccccCc-ccCCC
Confidence 4899999999999999999987444 35554
No 5
>PF14756 Pdase_C33_assoc: Peptidase_C33-associated domain
Probab=77.34 E-value=0.55 Score=33.76 Aligned_cols=21 Identities=33% Similarity=0.629 Sum_probs=17.4
Q ss_pred hhhhhhhCCCCCCchhhhhcc
Q 035652 2 EFLRGYLNLPSEIVPATLKKQ 22 (71)
Q Consensus 2 eYLR~YLhLP~EIVPaTLkr~ 22 (71)
+-|-+-.|||+.++||.|-.-
T Consensus 17 drla~vmhlps~~ipaalaem 37 (147)
T PF14756_consen 17 DRLAEVMHLPSSVIPAALAEM 37 (147)
T ss_pred HHHHHHhcCccchhHHHHHHh
Confidence 457788999999999998653
No 6
>KOG0366 consensus Protein geranylgeranyltransferase type II, beta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=37.88 E-value=7.7 Score=31.08 Aligned_cols=20 Identities=30% Similarity=0.464 Sum_probs=17.2
Q ss_pred CCCCchhhhcceeeeEeecc
Q 035652 35 GGDRPRIFLSLCQVIFFLSS 54 (71)
Q Consensus 35 ~gerp~r~~~~~~~~~~~~~ 54 (71)
=..||...-|.||+-|+|||
T Consensus 229 LNGRpeKlpDVCYSwWvlsS 248 (329)
T KOG0366|consen 229 LNGRPEKLPDVCYSWWVLSS 248 (329)
T ss_pred CCCCcccCcchhhHHHHHhH
Confidence 33678888999999999998
No 7
>cd03071 PDI_b'_NRX PDIb' family, NRX subgroup, redox inactive TRX-like domain b'; composed of vertebrate nucleoredoxins (NRX). NRX is a 400-amino acid nuclear protein with one redox active TRX domain followed by one redox inactive TRX-like domain homologous to the b' domain of PDI. In vitro studies show that NRX has thiol oxidoreductase activity and that it may be involved in the redox regulation of transcription, in a manner different from that of TRX or glutaredoxin. NRX enhances the activation of NF-kB by TNFalpha, as well as PMA-1 induced AP-1 and FK-induced CREB activation. Mouse NRX transcripts are expressed in all adult tissues but is restricted to the nervous system and limb buds in embryos. The mouse NRX gene is implicated in streptozotocin-induced diabetes. Similar to PDI, the b' domain of NRX is likely involved in substrate recognition.
Probab=36.81 E-value=18 Score=25.27 Aligned_cols=13 Identities=46% Similarity=0.769 Sum_probs=10.9
Q ss_pred hhhhhhhCCCCCC
Q 035652 2 EFLRGYLNLPSEI 14 (71)
Q Consensus 2 eYLR~YLhLP~EI 14 (71)
+.||+|+|||.+.
T Consensus 69 dsLRDf~nL~d~~ 81 (116)
T cd03071 69 DSLRDYTNLPEAA 81 (116)
T ss_pred HHHHHhcCCCccC
Confidence 5799999999654
No 8
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=32.84 E-value=21 Score=19.25 Aligned_cols=15 Identities=27% Similarity=0.554 Sum_probs=7.9
Q ss_pred eEeecccceeeeeee
Q 035652 49 IFFLSSDYVAHSYCL 63 (71)
Q Consensus 49 ~~~~~~~~~~~~~~~ 63 (71)
+-|-..+|.+|+-|+
T Consensus 8 ~~F~~~~y~~Ht~CI 22 (28)
T PF08790_consen 8 KDFDGDSYKSHTSCI 22 (28)
T ss_dssp EEEEGGGTTT-----
T ss_pred CCcCcCCcCCCCccc
Confidence 356789999999996
No 9
>COG5029 CAL1 Prenyltransferase, beta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=22.19 E-value=36 Score=27.51 Aligned_cols=18 Identities=28% Similarity=0.525 Sum_probs=16.0
Q ss_pred CCchhhhcceeeeEeecc
Q 035652 37 DRPRIFLSLCQVIFFLSS 54 (71)
Q Consensus 37 erp~r~~~~~~~~~~~~~ 54 (71)
.|+-.+-|-||+-|++||
T Consensus 244 GR~nKl~D~CYs~WvlsS 261 (342)
T COG5029 244 GRSNKLVDTCYSFWVLSS 261 (342)
T ss_pred CCcccCccchhhhhhcch
Confidence 567788899999999998
No 10
>cd01236 PH_outspread Outspread Pleckstrin homology (PH) domain. Outspread Pleckstrin homology (PH) domain. Outspread contains two PH domains and a C-terminal coiled-coil region. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=21.10 E-value=72 Score=20.74 Aligned_cols=29 Identities=17% Similarity=0.368 Sum_probs=19.4
Q ss_pred hhhhcceeeeEeecccceeeeeeeeccCCC
Q 035652 40 RIFLSLCQVIFFLSSDYVAHSYCLNITTPE 69 (71)
Q Consensus 40 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 (71)
-++++.|.++- -+.|...+.+|+.|.||+
T Consensus 52 ~IdL~~~~~V~-~~~~~~~~~~~f~I~tp~ 80 (104)
T cd01236 52 TIDMNQCTDVV-DAEARTGQKFSICILTPD 80 (104)
T ss_pred EEEccceEEEe-ecccccCCccEEEEECCC
Confidence 46777887644 122344567899999996
No 11
>PF14567 SUKH_5: SMI1-KNR4 cell-wall; PDB: 2PAG_A.
Probab=21.06 E-value=45 Score=23.05 Aligned_cols=15 Identities=33% Similarity=0.674 Sum_probs=10.7
Q ss_pred hhhhhhhCCCCCCchh
Q 035652 2 EFLRGYLNLPSEIVPA 17 (71)
Q Consensus 2 eYLR~YLhLP~EIVPa 17 (71)
.++|+ .|||.+.||-
T Consensus 76 ~~ar~-~glP~~~ipi 90 (132)
T PF14567_consen 76 ADARS-IGLPRELIPI 90 (132)
T ss_dssp HHHHH-HT--TTSEEE
T ss_pred HHHHH-cCCChhheeE
Confidence 47888 9999999985
Done!