Query 030941
Match_columns 168
No_of_seqs 114 out of 355
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 06:52:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030941.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030941hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00151 translationally contr 100.0 1.9E-78 4.2E-83 486.1 17.5 163 1-168 1-172 (172)
2 PF00838 TCTP: Translationally 100.0 2.2E-76 4.7E-81 472.6 12.8 161 1-165 1-165 (165)
3 KOG1727 Microtubule-binding pr 100.0 3.8E-68 8.2E-73 422.0 10.3 166 1-168 1-169 (169)
4 PF07523 Big_3: Bacterial Ig-l 58.0 4.4 9.5E-05 27.1 0.6 27 126-152 4-30 (67)
5 PF12095 DUF3571: Protein of u 53.8 34 0.00074 24.8 4.7 57 70-130 13-69 (83)
6 PF09230 DFF40: DNA fragmentat 53.5 18 0.00038 30.9 3.6 46 80-126 50-105 (230)
7 KOG2582 COP9 signalosome, subu 46.4 28 0.00061 32.0 4.0 51 103-157 319-371 (422)
8 KOG0907 Thioredoxin [Posttrans 34.8 24 0.00051 26.1 1.4 48 117-167 42-89 (106)
9 PF09142 TruB_C: tRNA Pseudour 33.7 30 0.00064 22.8 1.6 23 136-158 32-55 (56)
10 cd02957 Phd_like Phosducin (Ph 31.0 37 0.00081 24.3 2.0 42 118-163 46-87 (113)
11 cd06908 M14_AGBL4_like Peptida 31.0 34 0.00073 29.4 1.9 23 126-149 82-104 (261)
12 PTZ00062 glutaredoxin; Provisi 25.4 1.4E+02 0.0029 24.7 4.5 42 114-166 35-76 (204)
13 PF14679 FANCI_HD1: FANCI heli 22.7 20 0.00043 26.0 -0.8 29 105-133 33-62 (87)
14 PHA02278 thioredoxin-like prot 21.8 53 0.0011 23.8 1.3 13 152-164 72-84 (103)
15 TIGR03825 FliH_bacil flagellar 20.6 5.1E+02 0.011 21.7 7.2 64 83-147 157-226 (255)
16 PF14659 Phage_int_SAM_3: Phag 20.4 2.2E+02 0.0047 17.3 5.4 17 84-100 22-38 (58)
17 PF03992 ABM: Antibiotic biosy 20.1 2.4E+02 0.0053 17.8 5.1 46 103-148 11-58 (78)
18 KOG4709 Uncharacterized conser 20.0 1.6E+02 0.0034 24.9 3.8 23 74-97 24-46 (217)
No 1
>PTZ00151 translationally controlled tumor-like protein; Provisional
Probab=100.00 E-value=1.9e-78 Score=486.13 Aligned_cols=163 Identities=40% Similarity=0.710 Sum_probs=156.2
Q ss_pred CeEeeccCCCCeecccCCCce------EeeCCEEEEEEEEEEEeccccccCCCCCCCCCCCCCCCcccceEEEeeeeecc
Q 030941 1 MLVYQDLLTGDELLSDSFPYK------EIENGILWEVEGKWVVQGAVDVDIGANPSAEGADEDEGVDDQAVKVVDIVDTF 74 (168)
Q Consensus 1 MiiykDiisgDEm~SD~y~~~------~v~~~~~~eV~~k~v~~~~~~~diG~N~SaE~~e~~e~~~~~~~~vvdiV~~~ 74 (168)
||||||||||||||||+||++ ++ +|++|||+||+|+|+.++ ||+|||||+++ +|++++++++|||||+||
T Consensus 1 MiIykDi~tgDEm~SDsyk~~~~~~~~~~-~~~~yEV~~k~v~~~~~d--ig~n~saee~~-~e~~d~~~~~vvDIV~~f 76 (172)
T PTZ00151 1 MKVYKDVFTGDEVCSDSYKQLDPFGNAEF-SEIAFEVKSKKVIKGNED--YGIADNSEEGD-VEGVDADVETVIDIVDAF 76 (172)
T ss_pred CeEEEecccCCeeeccccccccccccccc-CCEEEEEeeEEEEECCcc--ccCCCCccccc-ccccccccEEEEEeeecC
Confidence 999999999999999999998 55 579999999999998765 69999999853 688999999999999999
Q ss_pred ccccCCCCCHHHHHHHHHHHHHHhccCC---ChHHHHHHHHhHHHHHHHHHhcCCCcceeecCCCCCCceEEEEeccCCC
Q 030941 75 RLQEQPAFDKKQFVTYMKRFIKLLTPKL---SEERQEIFKKNIEGATKFLLSKLSDLQFFVGESMHDDGCLVFAYYKEGA 151 (168)
Q Consensus 75 ~Lqe~t~f~Kk~y~~yiK~Y~K~ik~kL---~~erv~~F~~~a~~~vK~il~nfkd~qFf~Gesmd~dgmv~l~~y~edg 151 (168)
|||| |+||||+|++|||+|||+|++|| +|+||+.|+++||++||+||+||+|||||+||||||||||||++|||||
T Consensus 77 rLqe-t~f~Kk~Y~~yiK~YmK~vk~~L~e~~pe~v~~Fk~~a~~~vK~il~~Fkd~qFf~GeSmd~dgmv~l~~Yredg 155 (172)
T PTZ00151 77 KLQS-TPFTKKEYSTYIKKYMQRIKAYLEEKNPDRVEKFKTNAQPFVKHILENFDDFEFYLGESLDCEAGLIYGYYKGEE 155 (172)
T ss_pred ccee-cCCCHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHhcCCceEeecCCCCCCccEEEEeecCCC
Confidence 9999 99999999999999999999999 5999999999999999999999999999999999999999999999999
Q ss_pred cceEEEEEccccceecC
Q 030941 152 TDPTFLYIADALKEVKC 168 (168)
Q Consensus 152 ~tP~~~f~KdGL~eeK~ 168 (168)
+||||+||||||+||||
T Consensus 156 ~tP~~~f~KdGL~eeK~ 172 (172)
T PTZ00151 156 LAPRFVYIKDGLKEERY 172 (172)
T ss_pred cceEEEEEcccceeecC
Confidence 99999999999999998
No 2
>PF00838 TCTP: Translationally controlled tumour protein; InterPro: IPR018105 Mammalian translationally controlled tumour protein (TCTP) (or P23) is a protein which has been found to be preferentially synthesised in cells during the early growth phase of some types of tumour [, ], but which is also expressed in normal cells. The physiological function of TCTP is still not known. It was first identified as a histamine-releasing factor, acting in IgE +-dependent allergic reactions. In addition, TCTP has been shown to bind to tubulin in the cytoskeleton, has a high affinity for calcium, is the binding target for the antimalarial compound artemisinin, and is induced in vitamin D-dependent apoptosis. TCTP production is thought to be controlled at the translational as well as the transcriptional level []. TCTP is a hydrophilic protein of 18 to 20 kD. TCTPs do not share significant sequence similarity with any other class of proteins. Recently, the structure of TCTP was determined and exhibited significant structural similarity to the human protein Mss4, which is a guanine nucleotide-free chaperone of the Rab protein []. Close homologues have been found in plants [], earthworm [], Caenorhabditis elegans (F52H2.11), Hydra, Saccharomyces cerevisiae (YKL056c) [] and Schizosaccharomyces pombe (SpAC1F12.02c).; PDB: 2KWB_A 2LOY_A 1TXJ_A 1H6Q_A 1H7Y_A 3P3K_A 1YZ1_C 3EBM_D 2HR9_A.
Probab=100.00 E-value=2.2e-76 Score=472.65 Aligned_cols=161 Identities=44% Similarity=0.774 Sum_probs=148.5
Q ss_pred CeEeeccCCCCeecccCCCceEeeCCEEEEEEEEEEEec-cccccCCCCCCCCCCCCCCCcccceEEEeeeeeccccccC
Q 030941 1 MLVYQDLLTGDELLSDSFPYKEIENGILWEVEGKWVVQG-AVDVDIGANPSAEGADEDEGVDDQAVKVVDIVDTFRLQEQ 79 (168)
Q Consensus 1 MiiykDiisgDEm~SD~y~~~~v~~~~~~eV~~k~v~~~-~~~~diG~N~SaE~~e~~e~~~~~~~~vvdiV~~~~Lqe~ 79 (168)
||||||||||||||||+||++++ +|+||||+||+|+++ .++.+||||||||+++ +++++++++|||||+||||||
T Consensus 1 MiiykDiisgdEm~SD~y~~~~~-~~~~yeV~gk~vt~~~~d~~liG~N~SaE~~~--e~~~~~~~~viDiV~~~~L~e- 76 (165)
T PF00838_consen 1 MIIYKDIISGDEMFSDSYKIELV-DDVFYEVEGKMVTRTGIDDSLIGANPSAEEGE--EGTDDSVETVIDIVDNHRLQE- 76 (165)
T ss_dssp EEEEEETTTTTEEEETTSCEEEG-CTTEEEEE--EEEEETTB-TTTSSS--SSSSS--SSSCCCECEEEHHHHHTTEEE-
T ss_pred CeEEeccCCCCEecccCcccccc-CCEEEEEEEEEEeeccccccccccCcccccCc--cCCCCccEEccceeeccccee-
Confidence 99999999999999999999555 689999999999995 4567899999999875 889999999999999999999
Q ss_pred CCCCHHHHHHHHHHHHHHhccCC---ChHHHHHHHHhHHHHHHHHHhcCCCcceeecCCCCCCceEEEEeccCCCcceEE
Q 030941 80 PAFDKKQFVTYMKRFIKLLTPKL---SEERQEIFKKNIEGATKFLLSKLSDLQFFVGESMHDDGCLVFAYYKEGATDPTF 156 (168)
Q Consensus 80 t~f~Kk~y~~yiK~Y~K~ik~kL---~~erv~~F~~~a~~~vK~il~nfkd~qFf~Gesmd~dgmv~l~~y~edg~tP~~ 156 (168)
|+||||+|++|||+|||+|++|| +|+||++|+++|+++||+||+||||||||+||||||||||||++|||||+||||
T Consensus 77 t~f~Kk~y~~yiK~Y~K~i~~kL~e~~~erv~~F~~~a~~~vK~il~nfkd~qFf~Gesm~~dgmv~l~~yredg~tP~~ 156 (165)
T PF00838_consen 77 TSFDKKSYKAYIKDYMKKIKEKLEENGPERVKAFKKGAQEFVKKILANFKDYQFFTGESMDPDGMVALLNYREDGVTPYF 156 (165)
T ss_dssp ECCHHHHHHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHTGGGCEEEEETTCCTTS-EEEEEEETTSSSEEE
T ss_pred ecccHHHHHHHHHHHHHHHHHHHhhhccchhhHHHHHhHHHHHHHHhhccccccccccccCCCCcEEEEEecCCCccEEE
Confidence 99999999999999999999999 799999999999999999999999999999999999999999999999999999
Q ss_pred EEEccccce
Q 030941 157 LYIADALKE 165 (168)
Q Consensus 157 ~f~KdGL~e 165 (168)
+||||||+|
T Consensus 157 ~f~KdGL~E 165 (165)
T PF00838_consen 157 IFFKDGLKE 165 (165)
T ss_dssp EEEGGGEEE
T ss_pred EEEcccccC
Confidence 999999987
No 3
>KOG1727 consensus Microtubule-binding protein (translationally controlled tumor protein) [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=100.00 E-value=3.8e-68 Score=421.99 Aligned_cols=166 Identities=47% Similarity=0.793 Sum_probs=155.9
Q ss_pred CeEeeccCCCCeecccCCCceEeeCCEEEEEEEEEEEecccc-ccCCCCCCCCCCCCCCCcccceEEEeeeeeccccccC
Q 030941 1 MLVYQDLLTGDELLSDSFPYKEIENGILWEVEGKWVVQGAVD-VDIGANPSAEGADEDEGVDDQAVKVVDIVDTFRLQEQ 79 (168)
Q Consensus 1 MiiykDiisgDEm~SD~y~~~~v~~~~~~eV~~k~v~~~~~~-~diG~N~SaE~~e~~e~~~~~~~~vvdiV~~~~Lqe~ 79 (168)
|+||+||||||||+||+||++++++ +||||+||+|+|+++| .+||+|||||++.+++++++++++|+|||+||||||
T Consensus 1 mliy~di~t~del~sd~~~~k~i~~-l~~EvegK~vsr~~~D~~lig~NpSaE~~~edegte~~~~~~vdiV~~~rLqE- 78 (169)
T KOG1727|consen 1 MLIYKDIITGDELLSDSYPMKEVDD-LCYEVEGKMVTRTNGDDSLIGANPSAEEGAEDEGTEETVETVVDIVLNFRLQE- 78 (169)
T ss_pred CceeeccccCchhcccchhHHHHHh-hhheeeceeccccCccchhcccCccccccccCCcchhheeeeeeeeeeecccc-
Confidence 8999999999999999999999976 9999999999999665 469999999997558999999999999999999999
Q ss_pred CCCCHHHHHHHHHHHHHHhccCCChHHHHHHHHhHHHHHHHHHh-cCCCcceeecCCCCCCceEEEEeccCCC-cceEEE
Q 030941 80 PAFDKKQFVTYMKRFIKLLTPKLSEERQEIFKKNIEGATKFLLS-KLSDLQFFVGESMHDDGCLVFAYYKEGA-TDPTFL 157 (168)
Q Consensus 80 t~f~Kk~y~~yiK~Y~K~ik~kL~~erv~~F~~~a~~~vK~il~-nfkd~qFf~Gesmd~dgmv~l~~y~edg-~tP~~~ 157 (168)
++++|++|++|||+|||+|++||+++++..|++++++++|.++. ||||||||+||||||||||||++||||| +||+|+
T Consensus 79 q~~~ke~~k~yik~ymK~v~~klee~~~~~f~k~~~~a~q~~h~anFKnyqFFIGEnMnpdgmVal~~YRedg~~~P~~~ 158 (169)
T KOG1727|consen 79 QSPFKERFKAYIKGYMKAVKAKLEEEDVDVFKKNIQGAEKIKHIANFKNYQFFIGENMNPDGMVALLDYREDGGVTPYMI 158 (169)
T ss_pred cchHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhccchHHHHHHhhccccceeeecccCCCCceEEEeeeecCCCcCceEE
Confidence 55559999999999999999999889999999999988887766 9999999999999999999999999966 999999
Q ss_pred EEccccceecC
Q 030941 158 YIADALKEVKC 168 (168)
Q Consensus 158 f~KdGL~eeK~ 168 (168)
||||||++|||
T Consensus 159 ffk~gl~~ekc 169 (169)
T KOG1727|consen 159 FFKDGLEEEKC 169 (169)
T ss_pred EeccCcccccC
Confidence 99999999998
No 4
>PF07523 Big_3: Bacterial Ig-like domain (group 3); InterPro: IPR011080 This entry represents bacterial domains with an Ig-like fold. These domains are found in a variety of bacterial surface proteins.; PDB: 2L7Y_A 2KPN_A.
Probab=58.05 E-value=4.4 Score=27.06 Aligned_cols=27 Identities=30% Similarity=0.650 Sum_probs=17.9
Q ss_pred CCcceeecCCCCCCceEEEEeccCCCc
Q 030941 126 SDLQFFVGESMHDDGCLVFAYYKEGAT 152 (168)
Q Consensus 126 kd~qFf~Gesmd~dgmv~l~~y~edg~ 152 (168)
++-.++.||++||+|+++-..|.++..
T Consensus 4 ~kt~y~~Ge~~d~~~~~v~at~~dG~~ 30 (67)
T PF07523_consen 4 KKTTYYVGEKFDPTGLFVTATYSDGTS 30 (67)
T ss_dssp S-EEEETTT---HHCHEEEEEETTS-E
T ss_pred ccCEEECCCCcCccCCEEEEEEcCCCE
Confidence 345688999999999999988876543
No 5
>PF12095 DUF3571: Protein of unknown function (DUF3571); InterPro: IPR021954 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 85 to 97 amino acids in length. ; PDB: 2KRX_A.
Probab=53.81 E-value=34 Score=24.79 Aligned_cols=57 Identities=16% Similarity=0.298 Sum_probs=36.5
Q ss_pred eeeccccccCCCCCHHHHHHHHHHHHHHhccCCChHHHHHHHHhHHHHHHHHHhcCCCcce
Q 030941 70 IVDTFRLQEQPAFDKKQFVTYMKRFIKLLTPKLSEERQEIFKKNIEGATKFLLSKLSDLQF 130 (168)
Q Consensus 70 iV~~~~Lqe~t~f~Kk~y~~yiK~Y~K~ik~kL~~erv~~F~~~a~~~vK~il~nfkd~qF 130 (168)
||+-..--| .-.|+.+...++|.++.. ...| |..++.|. ...+++++++.++=++++
T Consensus 13 VvLEp~~~E-qflt~~Ell~~Lk~~L~~-~~~L-P~dL~~~~-s~~~qa~~Lldt~CeLei 69 (83)
T PF12095_consen 13 VVLEPGQPE-QFLTPEELLEKLKEWLQN-QDDL-PPDLAKFS-SVEEQAQYLLDTACELEI 69 (83)
T ss_dssp EEEESSS-S-EEE-HHHHHHHHHHHHHH-TTTS--HHHHH----HHHHHHHHHHH---EEE
T ss_pred EEecCCCCc-ccCCHHHHHHHHHHHHHc-CCCC-CHHHHhCC-CHHHHHHHHHHhceeeec
Confidence 444444444 233999999999999999 6666 66777774 456888999999998887
No 6
>PF09230 DFF40: DNA fragmentation factor 40 kDa; InterPro: IPR015311 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. DNA fragmentation factor (DFF) is a complex of the DNase DFF40 (CAD) and its chaperone/inhibitor DFF45 (ICAD-L). In its inactive form, DFF is a heterodimer composed of a 45kDa chaperone inhibitor subunit (DFF45 or ICAD), and a 40kDa latent endonuclease subunit (DFF40 or CAD). Upon caspase-3 cleavage of DFF45, DFF40 forms active endonuclease homo-oligomers. It is activated during apoptosis to induce DNA fragmentation. DNA binding by DFF is mediated by the nuclease subunit, which can also form stable DNA complexes after release from DFF [, ]. The nuclease subunit is inhibited in DNA cleavage but not in DNA binding []. DFF45 can also be cleaved and inactivated by caspase-7 but not by caspase-6 and caspase-8. The cleaved DFF45 fragments dissociate from DFF40, allowing DFF40 to oligomerise, forming a large complex that cleaves DNA by introducing double strand breaks. Histone H1 confers DNA binding ability to DFF and stimulates the nuclease activity of DFF40 [].; GO: 0016787 hydrolase activity, 0006309 DNA fragmentation involved in apoptotic nuclear change, 0005634 nucleus, 0005737 cytoplasm; PDB: 1V0D_A.
Probab=53.45 E-value=18 Score=30.92 Aligned_cols=46 Identities=13% Similarity=0.287 Sum_probs=28.7
Q ss_pred CCC-CHHHHHHH-----HHHHHHHhccCC----ChHHHHHHHHhHHHHHHHHHhcCC
Q 030941 80 PAF-DKKQFVTY-----MKRFIKLLTPKL----SEERQEIFKKNIEGATKFLLSKLS 126 (168)
Q Consensus 80 t~f-~Kk~y~~y-----iK~Y~K~ik~kL----~~erv~~F~~~a~~~vK~il~nfk 126 (168)
+.| ||.+|+.| |++|++++++.+ +|.--+.+. .+-+.+...|...+
T Consensus 50 ~rfktK~~yM~~~~qsRIRgY~~k~~~~~~~~~~~~ar~~~~-~~l~~~~~~Lk~~~ 105 (230)
T PF09230_consen 50 SRFKTKSEYMRYRCQSRIRGYFYKVKEYLSKVQNAKAREEYL-RVLESFRQKLKSDK 105 (230)
T ss_dssp TT--BHHHHHHHHHHHHHHHHHHHHHGGGGGS--TTTHHHHH-HHHHHHHHHHHHGG
T ss_pred hhhccHHHHHhhhHHHhHHHHHHHHHHHHHhccCHHHHHHHH-HHHHHHHHHHhcCC
Confidence 577 89999876 999999999998 232223333 33344555555444
No 7
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=46.44 E-value=28 Score=31.99 Aligned_cols=51 Identities=18% Similarity=0.237 Sum_probs=42.9
Q ss_pred ChHHHHH--HHHhHHHHHHHHHhcCCCcceeecCCCCCCceEEEEeccCCCcceEEE
Q 030941 103 SEERQEI--FKKNIEGATKFLLSKLSDLQFFVGESMHDDGCLVFAYYKEGATDPTFL 157 (168)
Q Consensus 103 ~~erv~~--F~~~a~~~vK~il~nfkd~qFf~Gesmd~dgmv~l~~y~edg~tP~~~ 157 (168)
+-+.++. +.+.+|+.-|.|+..|+|=+.|+--+ |||.+..=.++-..|-|.
T Consensus 319 sL~dIA~~vQLa~~qevek~Ilqmie~~~i~a~iN----G~v~f~~n~e~~~SpeM~ 371 (422)
T KOG2582|consen 319 SLSDIASRVQLASAQEVEKYILQMIEDGEIFASIN----GMVFFTDNPEKYNSPEMH 371 (422)
T ss_pred hHHHHHHHHHhcchHHHHHHHHHHhccCceEEEec----ceEEEecCcccCCCHHHH
Confidence 5667777 99999999999999999999998765 999998777777777654
No 8
>KOG0907 consensus Thioredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=34.77 E-value=24 Score=26.10 Aligned_cols=48 Identities=19% Similarity=0.097 Sum_probs=27.7
Q ss_pred HHHHHHhcCCCcceeecCCCCCCceEEEEeccCCCcceEEEEEccccceec
Q 030941 117 ATKFLLSKLSDLQFFVGESMHDDGCLVFAYYKEGATDPTFLYIADALKEVK 167 (168)
Q Consensus 117 ~vK~il~nfkd~qFf~Gesmd~dgmv~l~~y~edg~tP~~~f~KdGL~eeK 167 (168)
.+..+-..+.|-.|+.= |.|-..-+++=-+--..|+|.|||+|-+..+
T Consensus 42 ~~~~La~~y~~v~Flkv---dvde~~~~~~~~~V~~~PTf~f~k~g~~~~~ 89 (106)
T KOG0907|consen 42 KFEKLAEKYPDVVFLKV---DVDELEEVAKEFNVKAMPTFVFYKGGEEVDE 89 (106)
T ss_pred HHHHHHHHCCCCEEEEE---ecccCHhHHHhcCceEeeEEEEEECCEEEEE
Confidence 44555567788666632 3332111221112346999999999987665
No 9
>PF09142 TruB_C: tRNA Pseudouridine synthase II, C terminal; InterPro: IPR015225 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. The C-terminal domain adopts a secondary structure consisting of a four-stranded beta sheet and one alpha helix, similar to that found in PUA domains. It is predominantly involved in RNA-binding, being mostly found in tRNA pseudouridine synthase B (TruB) []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1SGV_B.
Probab=33.72 E-value=30 Score=22.82 Aligned_cols=23 Identities=17% Similarity=0.436 Sum_probs=17.0
Q ss_pred CCCCc-eEEEEeccCCCcceEEEE
Q 030941 136 MHDDG-CLVFAYYKEGATDPTFLY 158 (168)
Q Consensus 136 md~dg-mv~l~~y~edg~tP~~~f 158 (168)
++||| +|||+.-+.+...|..+|
T Consensus 32 ~~pdG~lvAL~~~~g~~~rp~~Vf 55 (56)
T PF09142_consen 32 FAPDGRLVALLEERGGRARPVVVF 55 (56)
T ss_dssp E-TTS-EEEEEEEETTEEEEEEES
T ss_pred ECCCCcEEEEEEccCCcEeEEEee
Confidence 47887 788887777777888775
No 10
>cd02957 Phd_like Phosducin (Phd)-like family; composed of Phd and Phd-like proteins (PhLP), characterized as cytosolic regulators of G protein functions. Phd and PhLPs specifically bind G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane and impeding G protein-mediated signal transduction by inhibiting the formation of a functional G protein trimer (G protein alphabetagamma). Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-te
Probab=31.04 E-value=37 Score=24.35 Aligned_cols=42 Identities=17% Similarity=0.251 Sum_probs=24.6
Q ss_pred HHHHHhcCCCcceeecCCCCCCceEEEEeccCCCcceEEEEEcccc
Q 030941 118 TKFLLSKLSDLQFFVGESMHDDGCLVFAYYKEGATDPTFLYIADAL 163 (168)
Q Consensus 118 vK~il~nfkd~qFf~Gesmd~dgmv~l~~y~edg~tP~~~f~KdGL 163 (168)
+..+...+.+..|+. +|.+-. .+..--.=..+|++++|++|=
T Consensus 46 l~~la~~~~~v~f~~---vd~~~~-~l~~~~~i~~~Pt~~~f~~G~ 87 (113)
T cd02957 46 LEELAAKYPETKFVK---INAEKA-FLVNYLDIKVLPTLLVYKNGE 87 (113)
T ss_pred HHHHHHHCCCcEEEE---EEchhh-HHHHhcCCCcCCEEEEEECCE
Confidence 344444566667763 444433 444322224699999999984
No 11
>cd06908 M14_AGBL4_like Peptidase M14-like domain of ATP/GTP binding protein_like (AGBL)-4, and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This eukaryotic subgroup includes the human AGBL4 and the mouse cytosolic carboxypeptidase (CCP)-6. ATP/GTP binding protein (AGTPBP-1/Nna1)-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Mutations in AGTPBP-1/Nna1 cause Purkinje cell degeneration (pcd). AGTPBP-1/Nna1 however does not belong to this subgroup. AGTPBP-1/Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal
Probab=30.97 E-value=34 Score=29.39 Aligned_cols=23 Identities=22% Similarity=0.434 Sum_probs=18.8
Q ss_pred CCcceeecCCCCCCceEEEEeccC
Q 030941 126 SDLQFFVGESMHDDGCLVFAYYKE 149 (168)
Q Consensus 126 kd~qFf~Gesmd~dgmv~l~~y~e 149 (168)
+++.||+=+.|||||.+ +.+||-
T Consensus 82 ~~~~~~IvP~~NPDGv~-~gn~R~ 104 (261)
T cd06908 82 EHLVFKIVPMLNPDGVF-LGNYRC 104 (261)
T ss_pred HhCcEEEEeeecCccee-ecCCcC
Confidence 55779999999999977 567765
No 12
>PTZ00062 glutaredoxin; Provisional
Probab=25.35 E-value=1.4e+02 Score=24.73 Aligned_cols=42 Identities=12% Similarity=0.151 Sum_probs=28.2
Q ss_pred HHHHHHHHHhcCCCcceeecCCCCCCceEEEEeccCCCcceEEEEEcccccee
Q 030941 114 IEGATKFLLSKLSDLQFFVGESMHDDGCLVFAYYKEGATDPTFLYIADALKEV 166 (168)
Q Consensus 114 a~~~vK~il~nfkd~qFf~Gesmd~dgmv~l~~y~edg~tP~~~f~KdGL~ee 166 (168)
+...+..|...|.+++|+.=+ .| | +--..|+|+||++|-.-.
T Consensus 35 m~~vl~~l~~~~~~~~F~~V~---~d-------~-~V~~vPtfv~~~~g~~i~ 76 (204)
T PTZ00062 35 LMDVCNALVEDFPSLEFYVVN---LA-------D-ANNEYGVFEFYQNSQLIN 76 (204)
T ss_pred HHHHHHHHHHHCCCcEEEEEc---cc-------c-CcccceEEEEEECCEEEe
Confidence 344556666678999997643 33 2 223589999999996543
No 13
>PF14679 FANCI_HD1: FANCI helical domain 1; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=22.66 E-value=20 Score=26.02 Aligned_cols=29 Identities=21% Similarity=0.212 Sum_probs=23.5
Q ss_pred HHHHHHHHhHHHHHHH-HHhcCCCcceeec
Q 030941 105 ERQEIFKKNIEGATKF-LLSKLSDLQFFVG 133 (168)
Q Consensus 105 erv~~F~~~a~~~vK~-il~nfkd~qFf~G 133 (168)
.|+.+|...+.+.+|. |+.+|+|+|+-.|
T Consensus 33 arI~Rfeeqvfd~Lk~~i~k~~kd~~~~~~ 62 (87)
T PF14679_consen 33 ARIQRFEEQVFDFLKAAIVKSFKDDQKQQG 62 (87)
T ss_dssp TTSGGGHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4677899999999995 6689999988554
No 14
>PHA02278 thioredoxin-like protein
Probab=21.80 E-value=53 Score=23.84 Aligned_cols=13 Identities=15% Similarity=0.266 Sum_probs=10.9
Q ss_pred cceEEEEEccccc
Q 030941 152 TDPTFLYIADALK 164 (168)
Q Consensus 152 ~tP~~~f~KdGL~ 164 (168)
..|++++||+|=.
T Consensus 72 ~iPT~i~fk~G~~ 84 (103)
T PHA02278 72 STPVLIGYKDGQL 84 (103)
T ss_pred cccEEEEEECCEE
Confidence 4899999999943
No 15
>TIGR03825 FliH_bacil flagellar assembly protein FliH. This bacillus clade of FliH proteins is not found by the Pfam FliH model pfam02108, but is closely related to the sequences identified by that model. Sequences identified by this model are observed in flagellar operons in an analogous position relative to other flagellar operon genes.
Probab=20.58 E-value=5.1e+02 Score=21.66 Aligned_cols=64 Identities=17% Similarity=0.306 Sum_probs=47.3
Q ss_pred CHHHHHHHHHHHHHHhccC--C----ChHHHHHHHHhHHHHHHHHHhcCCCcceeecCCCCCCceEEEEec
Q 030941 83 DKKQFVTYMKRFIKLLTPK--L----SEERQEIFKKNIEGATKFLLSKLSDLQFFVGESMHDDGCLVFAYY 147 (168)
Q Consensus 83 ~Kk~y~~yiK~Y~K~ik~k--L----~~erv~~F~~~a~~~vK~il~nfkd~qFf~Gesmd~dgmv~l~~y 147 (168)
++......++..+..+... + +|+..+...... +.+...++....|.++-.+++.+.|+++=.++
T Consensus 157 ~~e~i~~lv~~al~~l~~~~~i~I~v~p~d~~~v~~~~-~~l~~~~~~~~~i~i~~D~~l~~GgcvIEt~~ 226 (255)
T TIGR03825 157 DKNAFQALVRQVLSEVREFDEVSIYVHPHWYERVAAQK-DELQSILPACEHLAVYPDEKLPDGGCYVETNF 226 (255)
T ss_pred CHHHHHHHHHHHHHhccCCCcEEEEECHHHHHHHHHhH-HHHHhhcCCCCceEEEeCCCCCCCCeEEEcCC
Confidence 4566788888888888752 2 888877666543 45566677778899999999999888875543
No 16
>PF14659 Phage_int_SAM_3: Phage integrase, N-terminal SAM-like domain; PDB: 2KD1_A 2KOB_A 2KHQ_A 3LYS_E 2KIW_A 2KKP_A.
Probab=20.40 E-value=2.2e+02 Score=17.32 Aligned_cols=17 Identities=18% Similarity=0.153 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHHHHhcc
Q 030941 84 KKQFVTYMKRFIKLLTP 100 (168)
Q Consensus 84 Kk~y~~yiK~Y~K~ik~ 100 (168)
...|+..++.++...-+
T Consensus 22 ~~~y~~~~~~~i~p~~g 38 (58)
T PF14659_consen 22 YKNYKSIIKNHILPYFG 38 (58)
T ss_dssp HHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHC
Confidence 34445555554443333
No 17
>PF03992 ABM: Antibiotic biosynthesis monooxygenase; InterPro: IPR007138 This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species, which can carry out oxygenation without the assistance of any of the prosthetic groups, metal ions or cofactors normally associated with activation of molecular oxygen. The structure of ActVA-Orf6 monooxygenase from Streptomyces coelicolor (Q53908 from SWISSPROT), which is involved in actinorhodin biosynthesis, reveals a dimeric alpha+beta barrel topology []. There is also a conserved histidine that is likely to be an active site residue. In S. coelicolor SCO1909 (Q9X9W3 from SWISSPROT) this domain occurs as a repeat. This domain is also found in protein LsrG, involved in the degradation of quorum-sensing molecule autoinducer-2 [], and in several uncharacterised proteins.; PDB: 1X7V_A 3F44_A 4DN9_B 1N5T_B 1LQ9_A 1N5Q_B 1N5V_A 1N5S_A 2GFF_B 3BM7_A ....
Probab=20.09 E-value=2.4e+02 Score=17.79 Aligned_cols=46 Identities=11% Similarity=0.175 Sum_probs=29.9
Q ss_pred ChHHHHHHHHhHHHHHHHHHhcCCCc-ceeecCCC-CCCceEEEEecc
Q 030941 103 SEERQEIFKKNIEGATKFLLSKLSDL-QFFVGESM-HDDGCLVFAYYK 148 (168)
Q Consensus 103 ~~erv~~F~~~a~~~vK~il~nfkd~-qFf~Gesm-d~dgmv~l~~y~ 148 (168)
.|++.+.|...+++.+..++.+...+ .+....+. ||+-.+.+-.|+
T Consensus 11 ~~~~~~~f~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~W~ 58 (78)
T PF03992_consen 11 KPGKEEEFLAAFQELAEATLRKEPGCLSYELYRSLDDPNRYVIVERWE 58 (78)
T ss_dssp ETTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEESSSTTEEEEEEEES
T ss_pred CcchHHHHHHHHHHHHHHHHhcCCCcEEEEEEEecCCCCEEEEEEEEC
Confidence 68888999999999999888777752 22233333 344444444454
No 18
>KOG4709 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.03 E-value=1.6e+02 Score=24.88 Aligned_cols=23 Identities=26% Similarity=0.309 Sum_probs=18.3
Q ss_pred cccccCCCCCHHHHHHHHHHHHHH
Q 030941 74 FRLQEQPAFDKKQFVTYMKRFIKL 97 (168)
Q Consensus 74 ~~Lqe~t~f~Kk~y~~yiK~Y~K~ 97 (168)
+++-+ .+||++.-+.|+-+|=|.
T Consensus 24 ~~~le-vsFDeekrkdylTGFHKR 46 (217)
T KOG4709|consen 24 RPRLE-VSFDEEKRKDYLTGFHKR 46 (217)
T ss_pred cCcee-EeecHHHHHHHHHHHHHH
Confidence 45556 799999999999988664
Done!