Query 031146
Match_columns 165
No_of_seqs 108 out of 351
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 09:53:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031146.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031146hhsearch_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 8.1E-73 1.7E-77 453.0 16.7 156 5-165 8-172 (172)
2 PF00838 TCTP: Translationally 100.0 1E-70 2.2E-75 439.2 12.3 154 5-162 8-165 (165)
3 KOG1727 Microtubule-binding pr 100.0 1.4E-63 2.9E-68 395.6 9.5 159 5-165 8-169 (169)
4 PF12095 DUF3571: Protein of u 62.6 20 0.00043 26.0 4.7 57 67-127 13-69 (83)
5 PF07523 Big_3: Bacterial Ig-l 57.5 4.4 9.6E-05 27.0 0.5 27 123-149 4-30 (67)
6 PF09230 DFF40: DNA fragmentat 52.9 19 0.0004 30.8 3.6 47 77-123 50-105 (230)
7 KOG2582 COP9 signalosome, subu 43.7 33 0.00072 31.5 4.0 73 78-154 294-371 (422)
8 KOG0907 Thioredoxin [Posttrans 33.1 26 0.00057 25.8 1.4 48 114-164 42-89 (106)
9 PF09142 TruB_C: tRNA Pseudour 32.5 32 0.0007 22.6 1.6 23 133-155 32-55 (56)
10 cd02957 Phd_like Phosducin (Ph 31.8 37 0.0008 24.3 2.0 42 116-161 47-88 (113)
11 cd06908 M14_AGBL4_like Peptida 29.2 39 0.00084 29.0 2.0 23 123-146 82-104 (261)
12 PF14679 FANCI_HD1: FANCI heli 28.9 12 0.00026 27.1 -1.0 29 102-130 33-62 (87)
13 KOG3222 Inosine triphosphate p 23.8 2.2E+02 0.0048 23.7 5.4 24 86-124 84-107 (195)
14 cd00717 URO-D Uroporphyrinogen 23.1 48 0.001 28.5 1.5 38 61-99 187-224 (335)
15 PF14659 Phage_int_SAM_3: Phag 21.7 2E+02 0.0044 17.4 5.4 29 81-109 22-55 (58)
16 PTZ00062 glutaredoxin; Provisi 21.6 1.8E+02 0.0039 23.9 4.6 42 111-163 35-76 (204)
17 TIGR03825 FliH_bacil flagellar 21.4 4.8E+02 0.01 21.8 7.2 64 80-144 157-226 (255)
18 KOG4709 Uncharacterized conser 21.4 1.4E+02 0.0031 25.1 3.8 24 71-95 24-47 (217)
19 PHA02278 thioredoxin-like prot 21.4 55 0.0012 23.7 1.3 14 149-162 72-85 (103)
20 TIGR01464 hemE uroporphyrinoge 21.3 54 0.0012 28.2 1.5 38 61-99 190-227 (338)
21 PF03992 ABM: Antibiotic biosy 21.2 2.3E+02 0.005 17.9 5.2 46 100-145 11-58 (78)
No 1
>PTZ00151 translationally controlled tumor-like protein; Provisional
Probab=100.00 E-value=8.1e-73 Score=453.03 Aligned_cols=156 Identities=38% Similarity=0.682 Sum_probs=148.8
Q ss_pred ccCCeeeccCCCce------EeeCCEEEEEEEEEEEeccccccCCCCCCCCCCCCCCCcccceEEeeeeeeccccccCCC
Q 031146 5 CLGDELLSDSFPYK------EIENGILWEVEGKWVVQGAVDVDIGANPSAEGADEDEGVDDQAVKVVDIVDTFRLQEQPA 78 (165)
Q Consensus 5 itgDEm~SD~y~~~------~v~~~~~yeV~gk~v~~~~~d~~iG~N~saE~~e~~e~~~~~~~~vvDiV~~~~Lqe~t~ 78 (165)
|||||||||+||++ ++ +|++|||+||+|+|+.++ ||+|||||+++ +|++++++++|||||+|||||| |+
T Consensus 8 ~tgDEm~SDsyk~~~~~~~~~~-~~~~yEV~~k~v~~~~~d--ig~n~saee~~-~e~~d~~~~~vvDIV~~frLqe-t~ 82 (172)
T PTZ00151 8 FTGDEVCSDSYKQLDPFGNAEF-SEIAFEVKSKKVIKGNED--YGIADNSEEGD-VEGVDADVETVIDIVDAFKLQS-TP 82 (172)
T ss_pred ccCCeeeccccccccccccccc-CCEEEEEeeEEEEECCcc--ccCCCCccccc-ccccccccEEEEEeeecCccee-cC
Confidence 79999999999998 55 579999999999998765 69999999753 6889999999999999999999 99
Q ss_pred CCHHHHHHHHHHHHHHhccCC---ChHHHHHHHHhHHHHHHHHHhcCCCcceeeccCCCCCceEEEEeccCCCcceEEEE
Q 031146 79 FDKKQFVTYMKRFIKLLTPKL---SEERQEIFKKNIEGATKFLLSKLSDLQFFVGESMHDDGCLVFAYYKEGATDPTFLY 155 (165)
Q Consensus 79 f~Kk~y~~yiK~Y~K~ik~kL---~~erv~~F~~~a~~~vK~il~nfkd~qFy~Gesmd~dgmv~l~~y~edg~tP~~~f 155 (165)
||||+|++|||+|||+|++|| +|+||+.|+++||++||+||+||+|||||+||||||||||||++|||||+||||+|
T Consensus 83 f~Kk~Y~~yiK~YmK~vk~~L~e~~pe~v~~Fk~~a~~~vK~il~~Fkd~qFf~GeSmd~dgmv~l~~Yredg~tP~~~f 162 (172)
T PTZ00151 83 FTKKEYSTYIKKYMQRIKAYLEEKNPDRVEKFKTNAQPFVKHILENFDDFEFYLGESLDCEAGLIYGYYKGEELAPRFVY 162 (172)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHhcCCceEeecCCCCCCccEEEEeecCCCcceEEEE
Confidence 999999999999999999999 59999999999999999999999999999999999999999999999999999999
Q ss_pred EccccceecC
Q 031146 156 IADALKEVKC 165 (165)
Q Consensus 156 ~KdGL~eeK~ 165 (165)
|||||+||||
T Consensus 163 ~KdGL~eeK~ 172 (172)
T PTZ00151 163 IKDGLKEERY 172 (172)
T ss_pred EcccceeecC
Confidence 9999999998
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=1e-70 Score=439.21 Aligned_cols=154 Identities=44% Similarity=0.734 Sum_probs=141.5
Q ss_pred ccCCeeeccCCCceEeeCCEEEEEEEEEEEec-cccccCCCCCCCCCCCCCCCcccceEEeeeeeeccccccCCCCCHHH
Q 031146 5 CLGDELLSDSFPYKEIENGILWEVEGKWVVQG-AVDVDIGANPSAEGADEDEGVDDQAVKVVDIVDTFRLQEQPAFDKKQ 83 (165)
Q Consensus 5 itgDEm~SD~y~~~~v~~~~~yeV~gk~v~~~-~~d~~iG~N~saE~~e~~e~~~~~~~~vvDiV~~~~Lqe~t~f~Kk~ 83 (165)
|||||||||+||++++ +|++|||+||+|+++ .++++||||||||+++ +++++++++|||||+|||||| |+||||+
T Consensus 8 isgdEm~SD~y~~~~~-~~~~yeV~gk~vt~~~~d~~liG~N~SaE~~~--e~~~~~~~~viDiV~~~~L~e-t~f~Kk~ 83 (165)
T PF00838_consen 8 ISGDEMFSDSYKIELV-DDVFYEVEGKMVTRTGIDDSLIGANPSAEEGE--EGTDDSVETVIDIVDNHRLQE-TSFDKKS 83 (165)
T ss_dssp TTTTEEEETTSCEEEG-CTTEEEEE--EEEEETTB-TTTSSS--SSSSS--SSSCCCECEEEHHHHHTTEEE-ECCHHHH
T ss_pred CCCCEecccCcccccc-CCEEEEEEEEEEeeccccccccccCcccccCc--cCCCCccEEccceeeccccee-ecccHHH
Confidence 7999999999999655 679999999999995 4577899999999865 889999999999999999999 9999999
Q ss_pred HHHHHHHHHHHhccCC---ChHHHHHHHHhHHHHHHHHHhcCCCcceeeccCCCCCceEEEEeccCCCcceEEEEEcccc
Q 031146 84 FVTYMKRFIKLLTPKL---SEERQEIFKKNIEGATKFLLSKLSDLQFFVGESMHDDGCLVFAYYKEGATDPTFLYIADAL 160 (165)
Q Consensus 84 y~~yiK~Y~K~ik~kL---~~erv~~F~~~a~~~vK~il~nfkd~qFy~Gesmd~dgmv~l~~y~edg~tP~~~f~KdGL 160 (165)
|++|||+|||+|++|| .|+||++|+++|+++||+||+||||||||+||||||||||||++|||||+||||+||||||
T Consensus 84 y~~yiK~Y~K~i~~kL~e~~~erv~~F~~~a~~~vK~il~nfkd~qFf~Gesm~~dgmv~l~~yredg~tP~~~f~KdGL 163 (165)
T PF00838_consen 84 YKAYIKDYMKKIKEKLEENGPERVKAFKKGAQEFVKKILANFKDYQFFTGESMDPDGMVALLNYREDGVTPYFIFFKDGL 163 (165)
T ss_dssp HHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHTGGGCEEEEETTCCTTS-EEEEEEETTSSSEEEEEEGGGE
T ss_pred HHHHHHHHHHHHHHHHhhhccchhhHHHHHhHHHHHHHHhhccccccccccccCCCCcEEEEEecCCCccEEEEEEcccc
Confidence 9999999999999999 7999999999999999999999999999999999999999999999999999999999999
Q ss_pred ce
Q 031146 161 KE 162 (165)
Q Consensus 161 ~e 162 (165)
+|
T Consensus 164 ~E 165 (165)
T PF00838_consen 164 KE 165 (165)
T ss_dssp EE
T ss_pred cC
Confidence 87
No 3
>KOG1727 consensus Microtubule-binding protein (translationally controlled tumor protein) [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=100.00 E-value=1.4e-63 Score=395.64 Aligned_cols=159 Identities=46% Similarity=0.753 Sum_probs=149.1
Q ss_pred ccCCeeeccCCCceEeeCCEEEEEEEEEEEecccc-ccCCCCCCCCCCCCCCCcccceEEeeeeeeccccccCCCCCHHH
Q 031146 5 CLGDELLSDSFPYKEIENGILWEVEGKWVVQGAVD-VDIGANPSAEGADEDEGVDDQAVKVVDIVDTFRLQEQPAFDKKQ 83 (165)
Q Consensus 5 itgDEm~SD~y~~~~v~~~~~yeV~gk~v~~~~~d-~~iG~N~saE~~e~~e~~~~~~~~vvDiV~~~~Lqe~t~f~Kk~ 83 (165)
||||||+||+||++++++ +||||+||+|+|+++| .+||+|||||++.+++++++++++|+|||++||||| +++.|++
T Consensus 8 ~t~del~sd~~~~k~i~~-l~~EvegK~vsr~~~D~~lig~NpSaE~~~edegte~~~~~~vdiV~~~rLqE-q~~~ke~ 85 (169)
T KOG1727|consen 8 ITGDELLSDSYPMKEVDD-LCYEVEGKMVTRTNGDDSLIGANPSAEEGAEDEGTEETVETVVDIVLNFRLQE-QSPFKER 85 (169)
T ss_pred ccCchhcccchhHHHHHh-hhheeeceeccccCccchhcccCccccccccCCcchhheeeeeeeeeeecccc-cchHHHH
Confidence 799999999999999976 9999999999998665 469999999997568999999999999999999999 4555999
Q ss_pred HHHHHHHHHHHhccCCChHHHHHHHHhHHHHHHHHHh-cCCCcceeeccCCCCCceEEEEeccCCC-cceEEEEEccccc
Q 031146 84 FVTYMKRFIKLLTPKLSEERQEIFKKNIEGATKFLLS-KLSDLQFFVGESMHDDGCLVFAYYKEGA-TDPTFLYIADALK 161 (165)
Q Consensus 84 y~~yiK~Y~K~ik~kL~~erv~~F~~~a~~~vK~il~-nfkd~qFy~Gesmd~dgmv~l~~y~edg-~tP~~~f~KdGL~ 161 (165)
|++|||+|||+|++||++++++.|+++++.++|.++. ||||||||+||||||||||||++||||| +||+|+||||||+
T Consensus 86 ~k~yik~ymK~v~~klee~~~~~f~k~~~~a~q~~h~anFKnyqFFIGEnMnpdgmVal~~YRedg~~~P~~~ffk~gl~ 165 (169)
T KOG1727|consen 86 FKAYIKGYMKAVKAKLEEEDVDVFKKNIQGAEKIKHIANFKNYQFFIGENMNPDGMVALLDYREDGGVTPYMIFFKDGLE 165 (169)
T ss_pred HHHHHHHHHHHhhhhhhhhhhhhhhhccchHHHHHHhhccccceeeecccCCCCceEEEeeeecCCCcCceEEEeccCcc
Confidence 9999999999999999889999999999999997776 9999999999999999999999999966 9999999999999
Q ss_pred eecC
Q 031146 162 EVKC 165 (165)
Q Consensus 162 eeK~ 165 (165)
+|||
T Consensus 166 ~ekc 169 (169)
T KOG1727|consen 166 EEKC 169 (169)
T ss_pred cccC
Confidence 9998
No 4
>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=62.55 E-value=20 Score=26.01 Aligned_cols=57 Identities=16% Similarity=0.298 Sum_probs=36.7
Q ss_pred eeeccccccCCCCCHHHHHHHHHHHHHHhccCCChHHHHHHHHhHHHHHHHHHhcCCCcce
Q 031146 67 IVDTFRLQEQPAFDKKQFVTYMKRFIKLLTPKLSEERQEIFKKNIEGATKFLLSKLSDLQF 127 (165)
Q Consensus 67 iV~~~~Lqe~t~f~Kk~y~~yiK~Y~K~ik~kL~~erv~~F~~~a~~~vK~il~nfkd~qF 127 (165)
||+-..--| .-.|+.+...++|.++.. ...| |..++.| ....+++++++.++=++++
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-PPDLAKF-SSVEEQAQYLLDTACELEI 69 (83)
T ss_dssp EEEESSS-S-EEE-HHHHHHHHHHHHHH-TTTS--HHHHH----HHHHHHHHHHH---EEE
T ss_pred EEecCCCCc-ccCCHHHHHHHHHHHHHc-CCCC-CHHHHhC-CCHHHHHHHHHHhceeeec
Confidence 344444444 234999999999999999 6666 6777777 5566888999999998887
No 5
>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=57.50 E-value=4.4 Score=26.99 Aligned_cols=27 Identities=30% Similarity=0.650 Sum_probs=17.8
Q ss_pred CCcceeeccCCCCCceEEEEeccCCCc
Q 031146 123 SDLQFFVGESMHDDGCLVFAYYKEGAT 149 (165)
Q Consensus 123 kd~qFy~Gesmd~dgmv~l~~y~edg~ 149 (165)
++-.++.||++||+|+++-..|.++..
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 345688999999999999998876443
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=52.85 E-value=19 Score=30.76 Aligned_cols=47 Identities=11% Similarity=0.176 Sum_probs=28.9
Q ss_pred CCC-CHHHHHHH-----HHHHHHHhccCC--C-hHHHHHHHHhHHHHHHHHHhcCC
Q 031146 77 PAF-DKKQFVTY-----MKRFIKLLTPKL--S-EERQEIFKKNIEGATKFLLSKLS 123 (165)
Q Consensus 77 t~f-~Kk~y~~y-----iK~Y~K~ik~kL--~-~erv~~F~~~a~~~vK~il~nfk 123 (165)
+.| ||.+|+.| |.+|++++++.+ . ..+...--..+-+.+...|...+
T Consensus 50 ~rfktK~~yM~~~~qsRIRgY~~k~~~~~~~~~~~~ar~~~~~~l~~~~~~Lk~~~ 105 (230)
T PF09230_consen 50 SRFKTKSEYMRYRCQSRIRGYFYKVKEYLSKVQNAKAREEYLRVLESFRQKLKSDK 105 (230)
T ss_dssp TT--BHHHHHHHHHHHHHHHHHHHHHGGGGGS--TTTHHHHHHHHHHHHHHHHHGG
T ss_pred hhhccHHHHHhhhHHHhHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHHhcCC
Confidence 577 89999876 999999999998 1 22332222333344455555444
No 7
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=43.73 E-value=33 Score=31.54 Aligned_cols=73 Identities=19% Similarity=0.263 Sum_probs=51.9
Q ss_pred CCCHHHHHHHHHHHHHHhccCC---ChHHHHH--HHHhHHHHHHHHHhcCCCcceeeccCCCCCceEEEEeccCCCcceE
Q 031146 78 AFDKKQFVTYMKRFIKLLTPKL---SEERQEI--FKKNIEGATKFLLSKLSDLQFFVGESMHDDGCLVFAYYKEGATDPT 152 (165)
Q Consensus 78 ~f~Kk~y~~yiK~Y~K~ik~kL---~~erv~~--F~~~a~~~vK~il~nfkd~qFy~Gesmd~dgmv~l~~y~edg~tP~ 152 (165)
+|-|-.-..|=|.=++++.... +=+.++. +.+.+++.-|.|+..|+|=+.|+--+ |||.+..=.++-..|-
T Consensus 294 ~l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~Ilqmie~~~i~a~iN----G~v~f~~n~e~~~Spe 369 (422)
T KOG2582|consen 294 GLAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKYILQMIEDGEIFASIN----GMVFFTDNPEKYNSPE 369 (422)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHHHHHHhccCceEEEec----ceEEEecCcccCCCHH
Confidence 3434333334444444444433 5677777 99999999999999999999998765 9999987777777776
Q ss_pred EE
Q 031146 153 FL 154 (165)
Q Consensus 153 ~~ 154 (165)
|.
T Consensus 370 M~ 371 (422)
T KOG2582|consen 370 MH 371 (422)
T ss_pred HH
Confidence 54
No 8
>KOG0907 consensus Thioredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=33.10 E-value=26 Score=25.82 Aligned_cols=48 Identities=19% Similarity=0.097 Sum_probs=27.7
Q ss_pred HHHHHHhcCCCcceeeccCCCCCceEEEEeccCCCcceEEEEEccccceec
Q 031146 114 ATKFLLSKLSDLQFFVGESMHDDGCLVFAYYKEGATDPTFLYIADALKEVK 164 (165)
Q Consensus 114 ~vK~il~nfkd~qFy~Gesmd~dgmv~l~~y~edg~tP~~~f~KdGL~eeK 164 (165)
.+..+-..+.|-.|+.= |.|-..-+++=-+--..|+|.|||+|-+..+
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 44555567788777642 2222111221112346999999999987765
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=32.45 E-value=32 Score=22.64 Aligned_cols=23 Identities=17% Similarity=0.436 Sum_probs=17.0
Q ss_pred CCCCc-eEEEEeccCCCcceEEEE
Q 031146 133 MHDDG-CLVFAYYKEGATDPTFLY 155 (165)
Q Consensus 133 md~dg-mv~l~~y~edg~tP~~~f 155 (165)
++||| +|||+.-+.+...|..+|
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 788887777778888775
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=31.76 E-value=37 Score=24.31 Aligned_cols=42 Identities=17% Similarity=0.245 Sum_probs=24.3
Q ss_pred HHHHhcCCCcceeeccCCCCCceEEEEeccCCCcceEEEEEccccc
Q 031146 116 KFLLSKLSDLQFFVGESMHDDGCLVFAYYKEGATDPTFLYIADALK 161 (165)
Q Consensus 116 K~il~nfkd~qFy~Gesmd~dgmv~l~~y~edg~tP~~~f~KdGL~ 161 (165)
..+...+.+..|+. +|.+-. .+..-..=..+|++++|++|=.
T Consensus 47 ~~la~~~~~v~f~~---vd~~~~-~l~~~~~i~~~Pt~~~f~~G~~ 88 (113)
T cd02957 47 EELAAKYPETKFVK---INAEKA-FLVNYLDIKVLPTLLVYKNGEL 88 (113)
T ss_pred HHHHHHCCCcEEEE---EEchhh-HHHHhcCCCcCCEEEEEECCEE
Confidence 33444566667764 444433 4443222346999999999843
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=29.23 E-value=39 Score=28.97 Aligned_cols=23 Identities=22% Similarity=0.434 Sum_probs=18.9
Q ss_pred CCcceeeccCCCCCceEEEEeccC
Q 031146 123 SDLQFFVGESMHDDGCLVFAYYKE 146 (165)
Q Consensus 123 kd~qFy~Gesmd~dgmv~l~~y~e 146 (165)
+++.||+=+.|||||.+ +.+||-
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
>PF14679 FANCI_HD1: FANCI helical domain 1; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=28.92 E-value=12 Score=27.12 Aligned_cols=29 Identities=21% Similarity=0.212 Sum_probs=24.0
Q ss_pred HHHHHHHHhHHHHHHH-HHhcCCCcceeec
Q 031146 102 ERQEIFKKNIEGATKF-LLSKLSDLQFFVG 130 (165)
Q Consensus 102 erv~~F~~~a~~~vK~-il~nfkd~qFy~G 130 (165)
.|+.+|...+.+++|. |+.+|+|+|+-.|
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 4677899999999996 6789999988654
No 13
>KOG3222 consensus Inosine triphosphate pyrophosphatase [Nucleotide transport and metabolism]
Probab=23.81 E-value=2.2e+02 Score=23.69 Aligned_cols=24 Identities=38% Similarity=0.627 Sum_probs=16.7
Q ss_pred HHHHHHHHHhccCCChHHHHHHHHhHHHHHHHHHhcCCC
Q 031146 86 TYMKRFIKLLTPKLSEERQEIFKKNIEGATKFLLSKLSD 124 (165)
Q Consensus 86 ~yiK~Y~K~ik~kL~~erv~~F~~~a~~~vK~il~nfkd 124 (165)
.|||.|+|++.. +-+-.+|+.|.|
T Consensus 84 pYiKwFLk~lg~---------------egl~~~l~~~~~ 107 (195)
T KOG3222|consen 84 PYIKWFLKKLGP---------------EGLHEMLSKFEN 107 (195)
T ss_pred HHHHHHHHHhCc---------------HHHHHHHHhhCC
Confidence 488888887765 445567777776
No 14
>cd00717 URO-D Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction is located at the branching point of the tetrapyrrole biosynthetic pathway, leading to the biosynthesis of heme, chlorophyll or bacteriochlorophyll. URO-D deficiency is responsible for the human genetic diseases familial porphyria cutanea tarda (fPCT) and hepatoerythropoietic porphyria (HEP).
Probab=23.06 E-value=48 Score=28.47 Aligned_cols=38 Identities=13% Similarity=0.234 Sum_probs=26.9
Q ss_pred eEEeeeeeeccccccCCCCCHHHHHHHHHHHHHHhccCC
Q 031146 61 AVKVVDIVDTFRLQEQPAFDKKQFVTYMKRFIKLLTPKL 99 (165)
Q Consensus 61 ~~~vvDiV~~~~Lqe~t~f~Kk~y~~yiK~Y~K~ik~kL 99 (165)
.+.|+|++.-+.-.. .-++.+.|..|++.|+|+|.+.+
T Consensus 187 ieaGad~i~i~d~~~-~~lsp~~f~ef~~P~~k~i~~~i 224 (335)
T cd00717 187 IEAGAQAVQIFDSWA-GALSPEDFEEFVLPYLKRIIEEV 224 (335)
T ss_pred HHhCCCEEEEeCccc-ccCCHHHHHHHHHHHHHHHHHHH
Confidence 445777664343333 35689999999999999988765
No 15
>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=21.67 E-value=2e+02 Score=17.44 Aligned_cols=29 Identities=14% Similarity=0.119 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHhccCC-----ChHHHHHHHH
Q 031146 81 KKQFVTYMKRFIKLLTPKL-----SEERQEIFKK 109 (165)
Q Consensus 81 Kk~y~~yiK~Y~K~ik~kL-----~~erv~~F~~ 109 (165)
...|...++.++...-++. .|..+..|..
T Consensus 22 ~~~y~~~~~~~i~p~~g~~~i~~It~~~i~~~~~ 55 (58)
T PF14659_consen 22 YKNYKSIIKNHILPYFGNKKIKDITPRDIQNFIN 55 (58)
T ss_dssp HHHHHHHHHHHHHHHTTSSBGGG--HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCcCcHHHCCHHHHHHHHH
Confidence 3445555555544443333 4455544443
No 16
>PTZ00062 glutaredoxin; Provisional
Probab=21.65 E-value=1.8e+02 Score=23.95 Aligned_cols=42 Identities=12% Similarity=0.151 Sum_probs=28.1
Q ss_pred HHHHHHHHHhcCCCcceeeccCCCCCceEEEEeccCCCcceEEEEEcccccee
Q 031146 111 IEGATKFLLSKLSDLQFFVGESMHDDGCLVFAYYKEGATDPTFLYIADALKEV 163 (165)
Q Consensus 111 a~~~vK~il~nfkd~qFy~Gesmd~dgmv~l~~y~edg~tP~~~f~KdGL~ee 163 (165)
+...+..|.+.|.+++|+.=+ .| | +--..|+|+||++|-.-.
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 334455666678999997653 33 2 233589999999996544
No 17
>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=21.42 E-value=4.8e+02 Score=21.78 Aligned_cols=64 Identities=17% Similarity=0.306 Sum_probs=47.6
Q ss_pred CHHHHHHHHHHHHHHhccC--C----ChHHHHHHHHhHHHHHHHHHhcCCCcceeeccCCCCCceEEEEec
Q 031146 80 DKKQFVTYMKRFIKLLTPK--L----SEERQEIFKKNIEGATKFLLSKLSDLQFFVGESMHDDGCLVFAYY 144 (165)
Q Consensus 80 ~Kk~y~~yiK~Y~K~ik~k--L----~~erv~~F~~~a~~~vK~il~nfkd~qFy~Gesmd~dgmv~l~~y 144 (165)
++......|+..+..+... + +|+..+...... +.+...++....|.++-.+++.+.|+++=.++
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 4566788889999888752 2 888887766544 45566677778899999999999888875543
No 18
>KOG4709 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.39 E-value=1.4e+02 Score=25.15 Aligned_cols=24 Identities=25% Similarity=0.267 Sum_probs=18.9
Q ss_pred cccccCCCCCHHHHHHHHHHHHHHh
Q 031146 71 FRLQEQPAFDKKQFVTYMKRFIKLL 95 (165)
Q Consensus 71 ~~Lqe~t~f~Kk~y~~yiK~Y~K~i 95 (165)
+++-+ .+||++.-+.|+-+|=|.=
T Consensus 24 ~~~le-vsFDeekrkdylTGFHKRK 47 (217)
T KOG4709|consen 24 RPRLE-VSFDEEKRKDYLTGFHKRK 47 (217)
T ss_pred cCcee-EeecHHHHHHHHHHHHHHH
Confidence 55666 7999999999998887653
No 19
>PHA02278 thioredoxin-like protein
Probab=21.36 E-value=55 Score=23.72 Aligned_cols=14 Identities=14% Similarity=0.202 Sum_probs=11.3
Q ss_pred cceEEEEEccccce
Q 031146 149 TDPTFLYIADALKE 162 (165)
Q Consensus 149 ~tP~~~f~KdGL~e 162 (165)
-.|++++||+|=..
T Consensus 72 ~iPT~i~fk~G~~v 85 (103)
T PHA02278 72 STPVLIGYKDGQLV 85 (103)
T ss_pred cccEEEEEECCEEE
Confidence 48999999999443
No 20
>TIGR01464 hemE uroporphyrinogen decarboxylase. This model represents uroporphyrinogen decarboxylase (HemE), which converts uroporphyrinogen III to coproporphyrinogen III. This step takes the pathway toward protoporphyrin IX, a common precursor of both heme and chlorophyll, rather than toward precorrin 2 and its products.
Probab=21.29 E-value=54 Score=28.21 Aligned_cols=38 Identities=13% Similarity=0.245 Sum_probs=26.9
Q ss_pred eEEeeeeeeccccccCCCCCHHHHHHHHHHHHHHhccCC
Q 031146 61 AVKVVDIVDTFRLQEQPAFDKKQFVTYMKRFIKLLTPKL 99 (165)
Q Consensus 61 ~~~vvDiV~~~~Lqe~t~f~Kk~y~~yiK~Y~K~ik~kL 99 (165)
.+.|+|++.-+.-.. .-++.+.|..|++.|+|+|.+.+
T Consensus 190 ~eaGad~i~i~d~~~-~~lsp~~f~ef~~p~~k~i~~~i 227 (338)
T TIGR01464 190 VKAGAQAVQIFDSWA-GALSPEDFEEFVLPYLKKIIEEV 227 (338)
T ss_pred HHcCCCEEEEECCcc-ccCCHHHHHHHHHHHHHHHHHHH
Confidence 345666655443333 45689999999999999988765
No 21
>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=21.16 E-value=2.3e+02 Score=17.88 Aligned_cols=46 Identities=11% Similarity=0.175 Sum_probs=30.5
Q ss_pred ChHHHHHHHHhHHHHHHHHHhcCCCc-ceeeccCC-CCCceEEEEecc
Q 031146 100 SEERQEIFKKNIEGATKFLLSKLSDL-QFFVGESM-HDDGCLVFAYYK 145 (165)
Q Consensus 100 ~~erv~~F~~~a~~~vK~il~nfkd~-qFy~Gesm-d~dgmv~l~~y~ 145 (165)
.|++.+.|...++..+..++.+...+ .+....+. ||+-.+.+-.|+
T Consensus 11 ~~~~~~~f~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~W~ 58 (78)
T PF03992_consen 11 KPGKEEEFLAAFQELAEATLRKEPGCLSYELYRSLDDPNRYVIVERWE 58 (78)
T ss_dssp ETTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEESSSTTEEEEEEEES
T ss_pred CcchHHHHHHHHHHHHHHHHhcCCCcEEEEEEEecCCCCEEEEEEEEC
Confidence 68888999999999999998777752 22333433 344455555554
Done!