Query 031072
Match_columns 166
No_of_seqs 109 out of 354
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 08:49:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031072.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031072hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04398 DUF538: Protein of un 100.0 1.3E-44 2.7E-49 274.1 7.4 108 30-140 1-110 (110)
2 PRK09455 rseB anti-sigma E fac 49.7 1.3E+02 0.0027 26.7 8.5 115 6-137 2-117 (319)
3 cd03697 EFTU_II EFTU_II: Elong 44.2 55 0.0012 22.9 4.5 35 79-115 15-53 (87)
4 cd03694 GTPBP_II Domain II of 32.2 96 0.0021 21.7 4.2 35 79-115 15-55 (87)
5 PF09949 DUF2183: Uncharacteri 31.4 25 0.00054 26.1 1.1 18 28-45 13-30 (100)
6 PRK12442 translation initiatio 31.1 1.3E+02 0.0029 22.2 4.8 55 56-126 18-72 (87)
7 PF07494 Reg_prop: Two compone 29.3 65 0.0014 17.6 2.3 19 45-63 2-21 (24)
8 PF07172 GRP: Glycine rich pro 28.5 31 0.00068 25.5 1.2 9 10-18 4-12 (95)
9 PF08300 HCV_NS5a_1a: Hepatiti 27.9 54 0.0012 22.9 2.1 17 79-96 27-43 (62)
10 cd03690 Tet_II Tet_II: This su 27.0 1.6E+02 0.0036 20.4 4.6 53 74-126 18-73 (85)
11 smart00540 LEM in nuclear memb 26.8 35 0.00077 22.0 1.0 19 27-45 7-25 (44)
12 PF07419 PilM: PilM; InterPro 26.2 88 0.0019 24.4 3.4 59 36-99 58-119 (136)
13 cd03700 eEF2_snRNP_like_II EF2 24.6 2.5E+02 0.0054 19.6 6.1 54 74-127 16-82 (93)
14 cd01215 Dab Disabled (Dab) Pho 24.4 2.4E+02 0.0051 22.5 5.5 38 95-132 48-85 (139)
15 PF14060 DUF4252: Domain of un 23.3 72 0.0016 24.2 2.4 28 12-39 4-32 (155)
16 PF14567 SUKH_5: SMI1-KNR4 cel 22.7 58 0.0013 25.6 1.7 31 31-61 74-107 (132)
17 KOG2455 Delta-1-pyrroline-5-ca 22.6 50 0.0011 31.6 1.5 16 30-45 241-256 (561)
18 cd03676 Nudix_hydrolase_3 Memb 20.5 74 0.0016 24.9 2.0 47 41-89 27-77 (180)
No 1
>PF04398 DUF538: Protein of unknown function, DUF538; InterPro: IPR007493 This family consists of several plant proteins of unknown function.; PDB: 1YDU_A.
Probab=100.00 E-value=1.3e-44 Score=274.07 Aligned_cols=108 Identities=36% Similarity=0.654 Sum_probs=81.3
Q ss_pred cHHHHHHhCCCCCCCCCCCceeeEeCCC-ceEEEEEcCceEEEec-ceEEEccEEEEEEecCeeeccccceEEEEEeecc
Q 031072 30 SLKNLLESRGLPGGLFPENVKSYNLDQN-GRLEVYLEGPCMAKFD-TRVLFDSVVRANLSYGGLVGLEGLTQEELFLWLP 107 (166)
Q Consensus 30 ta~elL~~~gLP~GLLP~~V~~Y~l~~t-G~f~V~l~~~C~~~f~-~~v~Y~~~ItG~i~~GkI~~L~GVk~K~lf~Wv~ 107 (166)
||||+|++||||+||||++|++|++|++ |+|||+|+++|+|+|+ +.|+|+++|||+|++|+|++|+|||+|++|+|++
T Consensus 1 tayelL~~~glP~GLLP~~v~~y~l~~~tG~f~v~l~~~C~~~~~~~~v~Y~~~ItG~i~~g~i~~L~GVk~k~l~~W~~ 80 (110)
T PF04398_consen 1 TAYELLEEYGLPRGLLPLGVTEYGLNRDTGFFWVKLKSPCEFRFEGYLVSYDSEITGYIEKGKIKNLTGVKVKELFLWVP 80 (110)
T ss_dssp --HHHHHHHS-TT-TTTSSS-EEEE-TTT-SEEEE-SS-EEEESTTSEEEE-SEEEEEE-SS-EEEEES-EEE-SSSEES
T ss_pred CHHHhHHHcCCCCCcCCCCceEEEEecCCcEEEEEecCCEEEEEEEEEEEEcCeEEEEECCCcCccccCEEEEEEEEEee
Confidence 7999999999999999999999999965 9999999999999998 4999999999999999999999999999999999
Q ss_pred eeEEEecCCCCCeEEEEEceeeeeecccccCCC
Q 031072 108 VKGIIVNDPSSGLILIDIGLARKQLSLSLFEDP 140 (166)
Q Consensus 108 V~eI~vd~~~~~~I~F~vG~isksFP~s~F~~~ 140 (166)
|+||.+ ++++|+|++|.++++||+++|+++
T Consensus 81 v~~i~~---~~~~i~F~~g~~s~sfp~~~F~~s 110 (110)
T PF04398_consen 81 VTEISV---DGDKIYFKVGGISKSFPVSAFEES 110 (110)
T ss_dssp ---BEE----SSSEE-TTSSSS----TTTTSS-
T ss_pred EEEEEE---cCCEEEEEEeeEeccCCHHHhccC
Confidence 999999 479999999999999999999985
No 2
>PRK09455 rseB anti-sigma E factor; Provisional
Probab=49.71 E-value=1.3e+02 Score=26.73 Aligned_cols=115 Identities=13% Similarity=0.074 Sum_probs=59.7
Q ss_pred hhhhHHHHHHHHHHHhhccCCCC-CcHHHHHHhCCCCCCCCCCCceeeEeCCCceEEEEEcCceEEEecceEEEccEEEE
Q 031072 6 TLTQKSIFILLLTLSLLLPLTAT-SSLKNLLESRGLPGGLFPENVKSYNLDQNGRLEVYLEGPCMAKFDTRVLFDSVVRA 84 (166)
Q Consensus 6 ~l~~~~~~~~ll~~~~~~~~~~~-~ta~elL~~~gLP~GLLP~~V~~Y~l~~tG~f~V~l~~~C~~~f~~~v~Y~~~ItG 84 (166)
+.+++++++++.+|+++.++++. .++.++|++++ +-...-++ .|.|.....+. ++ ..+|--.+.+
T Consensus 2 ~~~~~~~~~l~~~l~~~~~~~~~~~~a~~~L~~M~-------~A~~~lnY--~g~fV~~~~~~----i~-s~ri~H~~~~ 67 (319)
T PRK09455 2 KQLWFAVSLLTGSLLFSANASAQPLSSGALLQQMN-------EASQSLNY--ELSFINITKQG----IE-SLRYRHARLD 67 (319)
T ss_pred chHHHHHHHHHHhhcccccccccccCHHHHHHHHH-------HHHHhCCe--EEEEEEEeCCe----EE-EEEEEEEEeC
Confidence 44555555444455555555544 46889998864 22222222 36665543332 11 2244444667
Q ss_pred EEecCeeeccccceEEEEEeecceeEEEecCCCCCeEEEEEceeeeeeccccc
Q 031072 85 NLSYGGLVGLEGLTQEELFLWLPVKGIIVNDPSSGLILIDIGLARKQLSLSLF 137 (166)
Q Consensus 85 ~i~~GkI~~L~GVk~K~lf~Wv~V~eI~vd~~~~~~I~F~vG~isksFP~s~F 137 (166)
.-+.-++..|+|-.-.++-.-=.|+-+ .|+...+.-+...+...||.-.+
T Consensus 68 ~~e~erL~~LdG~~rEviR~~d~V~~~---~p~~~~~~l~~~~~~~~fP~~l~ 117 (319)
T PRK09455 68 NKPLAQLLQMDGPRREIIQRGNEISYF---EPGLEPFTLNGDHIVDSLPSLIY 117 (319)
T ss_pred CEEEEEEEecCCCceEEEEECCEEEEE---ecCCceEEEecccccccCccccc
Confidence 778889999999887765332222222 23333343333335555665444
No 3
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=44.24 E-value=55 Score=22.86 Aligned_cols=35 Identities=26% Similarity=0.243 Sum_probs=24.1
Q ss_pred ccEEEEEEecCeeeccccceEEEE----EeecceeEEEecC
Q 031072 79 DSVVRANLSYGGLVGLEGLTQEEL----FLWLPVKGIIVND 115 (166)
Q Consensus 79 ~~~ItG~i~~GkI~~L~GVk~K~l----f~Wv~V~eI~vd~ 115 (166)
.+.++|+|+.|+|+ .|-++..+ .....|..|.+.+
T Consensus 15 G~vv~G~v~~G~v~--~gd~v~~~p~~~~~~~~V~si~~~~ 53 (87)
T cd03697 15 GTVVTGRIERGTIK--VGDEVEIVGFGETLKTTVTGIEMFR 53 (87)
T ss_pred EEEEEEEECCCCCc--cCCEEEEeCCCCCceEEEEEEEECC
Confidence 35799999999998 45444443 3456677777654
No 4
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=32.24 E-value=96 Score=21.69 Aligned_cols=35 Identities=31% Similarity=0.165 Sum_probs=24.8
Q ss_pred ccEEEEEEecCeeeccccceEEEE------EeecceeEEEecC
Q 031072 79 DSVVRANLSYGGLVGLEGLTQEEL------FLWLPVKGIIVND 115 (166)
Q Consensus 79 ~~~ItG~i~~GkI~~L~GVk~K~l------f~Wv~V~eI~vd~ 115 (166)
.+.|+|+++.|.++ .|-++..+ +....|..|++++
T Consensus 15 GtVv~G~v~~G~v~--~g~~v~~~P~~~g~~~~~~V~sI~~~~ 55 (87)
T cd03694 15 GTVVGGTVSKGVIR--LGDTLLLGPDQDGSFRPVTVKSIHRNR 55 (87)
T ss_pred ceEEEEEEecCEEe--CCCEEEECCCCCCCEeEEEEEEEEECC
Confidence 57899999999999 45454432 2467788887654
No 5
>PF09949 DUF2183: Uncharacterized conserved protein (DUF2183); InterPro: IPR019236 This domain, found in various bacterial and fungal proteins, has no known function.
Probab=31.38 E-value=25 Score=26.14 Aligned_cols=18 Identities=28% Similarity=0.632 Sum_probs=15.2
Q ss_pred CCcHHHHHHhCCCCCCCC
Q 031072 28 TSSLKNLLESRGLPGGLF 45 (166)
Q Consensus 28 ~~ta~elL~~~gLP~GLL 45 (166)
.+...+.|+++|+|.|=+
T Consensus 13 y~~l~~Fl~~~~~P~G~~ 30 (100)
T PF09949_consen 13 YPFLRDFLRRNGFPAGPL 30 (100)
T ss_pred HHHHHHHHHhcCCCCCce
Confidence 377888999999999964
No 6
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=31.08 E-value=1.3e+02 Score=22.22 Aligned_cols=55 Identities=20% Similarity=0.147 Sum_probs=39.5
Q ss_pred CCceEEEEEcCceEEEecceEEEccEEEEEEecCeeeccccceEEEEEeecceeEEEecCCCCCeEEEEEc
Q 031072 56 QNGRLEVYLEGPCMAKFDTRVLFDSVVRANLSYGGLVGLEGLTQEELFLWLPVKGIIVNDPSSGLILIDIG 126 (166)
Q Consensus 56 ~tG~f~V~l~~~C~~~f~~~v~Y~~~ItG~i~~GkI~~L~GVk~K~lf~Wv~V~eI~vd~~~~~~I~F~vG 126 (166)
+++.|+|.|...+.. -+.|+|.+...+|+=+.|=+|++- +| + - |.+-|.|.|.--
T Consensus 18 p~~~frV~LenG~~v--------la~isGKmR~~rIrIl~GD~V~VE-~s-p-----Y-DltkGRIiyR~~ 72 (87)
T PRK12442 18 PDSRFRVTLENGVEV--------GAYASGRMRKHRIRILAGDRVTLE-LS-P-----Y-DLTKGRINFRHK 72 (87)
T ss_pred CCCEEEEEeCCCCEE--------EEEeccceeeeeEEecCCCEEEEE-EC-c-----c-cCCceeEEEEec
Confidence 467788877655433 267899999999999999999886 33 1 1 334577888763
No 7
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=29.27 E-value=65 Score=17.60 Aligned_cols=19 Identities=32% Similarity=0.447 Sum_probs=12.1
Q ss_pred CC-CCceeeEeCCCceEEEE
Q 031072 45 FP-ENVKSYNLDQNGRLEVY 63 (166)
Q Consensus 45 LP-~~V~~Y~l~~tG~f~V~ 63 (166)
|| ..|.+---|.+|.+||-
T Consensus 2 L~~n~I~~i~~D~~G~lWig 21 (24)
T PF07494_consen 2 LPNNNIYSIYEDSDGNLWIG 21 (24)
T ss_dssp BSSSCEEEEEE-TTSCEEEE
T ss_pred CCCCeEEEEEEcCCcCEEEE
Confidence 45 35666555778999983
No 8
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=28.47 E-value=31 Score=25.52 Aligned_cols=9 Identities=33% Similarity=0.460 Sum_probs=3.4
Q ss_pred HHHHHHHHH
Q 031072 10 KSIFILLLT 18 (166)
Q Consensus 10 ~~~~~~ll~ 18 (166)
|++++|.|+
T Consensus 4 K~~llL~l~ 12 (95)
T PF07172_consen 4 KAFLLLGLL 12 (95)
T ss_pred hHHHHHHHH
Confidence 333333333
No 9
>PF08300 HCV_NS5a_1a: Hepatitis C virus non-structural 5a zinc finger domain; InterPro: IPR013192 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 entry represents a zinc finger motif found in the non-structural 5a protein (NS5a) in Hepatitis C virus. The molecular function of NS5a is uncertain, but it is phosphorylated when expressed in mammalian cells. It is thought to interact with the dsRNA dependent (interferon inducible) kinase PKR, P19525 from SWISSPROT [, ]. This region corresponds to the N-terminal zinc binding domain (1a) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003968 RNA-directed RNA polymerase activity, 0004252 serine-type endopeptidase activity, 0008270 zinc ion binding, 0017111 nucleoside-triphosphatase activity, 0006355 regulation of transcription, DNA-dependent, 0006915 apoptosis, 0030683 evasion by virus of host immune response, 0005789 endoplasmic reticulum membrane, 0016021 integral to membrane; PDB: 1ZH1_B 3FQM_A 3FQQ_B.
Probab=27.89 E-value=54 Score=22.93 Aligned_cols=17 Identities=18% Similarity=0.476 Sum_probs=13.1
Q ss_pred ccEEEEEEecCeeecccc
Q 031072 79 DSVVRANLSYGGLVGLEG 96 (166)
Q Consensus 79 ~~~ItG~i~~GkI~~L~G 96 (166)
..+|+|.|+.|+|+ +.|
T Consensus 27 Ga~ItGhVknG~mr-i~g 43 (62)
T PF08300_consen 27 GAVITGHVKNGSMR-IYG 43 (62)
T ss_dssp S-EEEEEEETTEEE-EE-
T ss_pred CCEEeEEEeCCeEE-Eec
Confidence 57899999999998 555
No 10
>cd03690 Tet_II Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=27.05 E-value=1.6e+02 Score=20.39 Aligned_cols=53 Identities=17% Similarity=0.197 Sum_probs=36.1
Q ss_pred ceEEEccEEEEEEecCeeeccc-c--ceEEEEEeecceeEEEecCCCCCeEEEEEc
Q 031072 74 TRVLFDSVVRANLSYGGLVGLE-G--LTQEELFLWLPVKGIIVNDPSSGLILIDIG 126 (166)
Q Consensus 74 ~~v~Y~~~ItG~i~~GkI~~L~-G--Vk~K~lf~Wv~V~eI~vd~~~~~~I~F~vG 126 (166)
-++.|..-.+|.|..|..-... + .+++.++.+..-....++....|.|-=-.|
T Consensus 18 G~la~~RV~sG~l~~g~~v~~~~~~~~~v~~l~~~~g~~~~~v~~~~aGdI~ai~g 73 (85)
T cd03690 18 ERLAYLRLYSGTLRLRDSVRVNREEKIKITELRVFNNGEVVTADTVTAGDIAILTG 73 (85)
T ss_pred CeEEEEEEccCEEcCCCEEEeCCCcEEEeceeEEEeCCCeEECcEECCCCEEEEEC
Confidence 3678888888999888544322 2 456678888777777777766777654444
No 11
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=26.83 E-value=35 Score=22.04 Aligned_cols=19 Identities=32% Similarity=0.553 Sum_probs=15.0
Q ss_pred CCCcHHHHHHhCCCCCCCC
Q 031072 27 ATSSLKNLLESRGLPGGLF 45 (166)
Q Consensus 27 ~~~ta~elL~~~gLP~GLL 45 (166)
++.-+.+.|.+||+|.|=+
T Consensus 7 Sd~eL~~~L~~~G~~~gPI 25 (44)
T smart00540 7 SDAELRAELKQYGLPPGPI 25 (44)
T ss_pred CHHHHHHHHHHcCCCCCCc
Confidence 3466788999999999844
No 12
>PF07419 PilM: PilM; InterPro: IPR009987 This entry contains the bacterial protein PilM (approximately 150 residues long). PilM is an inner membrane protein that has been predicted to function as a component of the pilin transport apparatus and thin-pilus basal body [].; PDB: 3EOI_A 3HG9_A.
Probab=26.24 E-value=88 Score=24.39 Aligned_cols=59 Identities=24% Similarity=0.307 Sum_probs=39.6
Q ss_pred HhCCCCCCCCC-CCceeeEeCCCceEEEEEcCceEEEec--ceEEEccEEEEEEecCeeeccccceE
Q 031072 36 ESRGLPGGLFP-ENVKSYNLDQNGRLEVYLEGPCMAKFD--TRVLFDSVVRANLSYGGLVGLEGLTQ 99 (166)
Q Consensus 36 ~~~gLP~GLLP-~~V~~Y~l~~tG~f~V~l~~~C~~~f~--~~v~Y~~~ItG~i~~GkI~~L~GVk~ 99 (166)
.+.|||. .| .++..|. +.|..||+.+.++.. +. ...+=++-.-|.++.|++....|-..
T Consensus 58 ~~L~lp~--~~~~~i~~~i--~~Gr~yVw~~~~pgL-~~aL~~~s~~S~l~G~~~~G~L~~~~g~~~ 119 (136)
T PF07419_consen 58 SQLGLPP--NPDPRISNVI--SNGRLYVWMPEQPGL-YAALREQSRGSALVGRVQNGRLVDPSGTDM 119 (136)
T ss_dssp CCCTS-S---SSTTEEEEE--CTTEEEEEECS-TTH-HHHHHHCTTT-EEEEEECTTCEEETTTEEE
T ss_pred HHcCCCC--CCchhhheee--eCCeEEEEeCCCchH-HHHHHHhcCCceEEEEecCCEEECCCCCCc
Confidence 4668998 55 4787777 479999999887721 11 22344577889999999999998553
No 13
>cd03700 eEF2_snRNP_like_II EF2_snRNP_like_II: this subfamily represents domain II of elongation factor (EF) EF-2 found eukaryotes and archaea and, the C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This translocation step is catalyzed by EF-2_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p.
Probab=24.64 E-value=2.5e+02 Score=19.62 Aligned_cols=54 Identities=22% Similarity=0.290 Sum_probs=38.8
Q ss_pred ceEEEccEEEEEEecCeeeccc-------------cceEEEEEeecceeEEEecCCCCCeEEEEEce
Q 031072 74 TRVLFDSVVRANLSYGGLVGLE-------------GLTQEELFLWLPVKGIIVNDPSSGLILIDIGL 127 (166)
Q Consensus 74 ~~v~Y~~~ItG~i~~GkI~~L~-------------GVk~K~lf~Wv~V~eI~vd~~~~~~I~F~vG~ 127 (166)
..+.|.+-.+|.++.|.--... ..+++.++.+..-..+.++...+|+|.--.|.
T Consensus 16 g~la~~RV~sGtl~~g~~v~~~~~~~~~~~~~~~~~~~v~~l~~~~g~~~~~v~~a~aGdIv~i~g~ 82 (93)
T cd03700 16 GFIAFGRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYREPVDEVPAGNIVLIVGL 82 (93)
T ss_pred EEEEEEEEeeCeEeCCCEEEEECCCCCCCccCcEEEEEEeEEEEEcCCCEEEccccCCCCEEEEECC
Confidence 4677888888888887543222 26677888888888888888778888766654
No 14
>cd01215 Dab Disabled (Dab) Phosphotyrosine-binding domain. Disabled (Dab) Phosphotyrosine-binding domain. Dab is a cystosolic adaptor protein, which binds to the cytoplasmic tails of lipoprotein receptors, such as ApoER2 and VLDLR, via its PTB domain. The dab PTB domain has a preference for unphosphorylated tyrosine within an NPxY motif. Additionally, the Dab PTB domain, which is structurally similar to PH domains, binds to phosphatidlyinositol phosphate 4,5 bisphosphate in a manner characteristic of phosphoinositide binding PH domains.
Probab=24.41 E-value=2.4e+02 Score=22.47 Aligned_cols=38 Identities=24% Similarity=0.367 Sum_probs=29.3
Q ss_pred ccceEEEEEeecceeEEEecCCCCCeEEEEEceeeeee
Q 031072 95 EGLTQEELFLWLPVKGIIVNDPSSGLILIDIGLARKQL 132 (166)
Q Consensus 95 ~GVk~K~lf~Wv~V~eI~vd~~~~~~I~F~vG~isksF 132 (166)
+|-+-+...+|+++.+|.|-|+.++.+..+-.+-.=||
T Consensus 48 ~~~kk~kV~L~IS~dGi~v~D~~T~~ll~~~~i~rISf 85 (139)
T cd01215 48 AGAHKTRITLQINIDGIKVLDEKTGAVLHHHPVHRISF 85 (139)
T ss_pred hccccceEEEEEccCCEEEEcCCCCcEEEeeceeeEEE
Confidence 55677778899999999999888888777776633333
No 15
>PF14060 DUF4252: Domain of unknown function (DUF4252)
Probab=23.26 E-value=72 Score=24.24 Aligned_cols=28 Identities=32% Similarity=0.446 Sum_probs=15.8
Q ss_pred HHHHHHHHHhhccCC-CCCcHHHHHHhCC
Q 031072 12 IFILLLTLSLLLPLT-ATSSLKNLLESRG 39 (166)
Q Consensus 12 ~~~~ll~~~~~~~~~-~~~ta~elL~~~g 39 (166)
+++++|+++...+.+ ..+++..++++|.
T Consensus 4 i~~l~l~~~~~~~~aq~~~~~~~~~~~~~ 32 (155)
T PF14060_consen 4 ILILLLLLACLASCAQQGQSLQKYFDKYS 32 (155)
T ss_pred HHHHHHHHHHHHHhcccchhHHHHHHHhC
Confidence 444444444444444 4577778877654
No 16
>PF14567 SUKH_5: SMI1-KNR4 cell-wall; PDB: 2PAG_A.
Probab=22.67 E-value=58 Score=25.60 Aligned_cols=31 Identities=35% Similarity=0.500 Sum_probs=18.1
Q ss_pred HHHHHHhCCCCCCCCCC--Ccee-eEeCCCceEE
Q 031072 31 LKNLLESRGLPGGLFPE--NVKS-YNLDQNGRLE 61 (166)
Q Consensus 31 a~elL~~~gLP~GLLP~--~V~~-Y~l~~tG~f~ 61 (166)
+..-+.+.|+|+-++|- ...+ |-++++|.+.
T Consensus 74 ~~~~ar~~glP~~~ipice~~~~yYcl~~~g~V~ 107 (132)
T PF14567_consen 74 VTADARSIGLPRELIPICEDGGDYYCLDQEGEVV 107 (132)
T ss_dssp HHHHHHHHT--TTSEEEEEETTEEEEE-TTS-EE
T ss_pred HHHHHHHcCCChhheeEEecCCcEEEEeCCCeEE
Confidence 33445678999999993 3444 7778888743
No 17
>KOG2455 consensus Delta-1-pyrroline-5-carboxylate dehydrogenase [Amino acid transport and metabolism]
Probab=22.57 E-value=50 Score=31.57 Aligned_cols=16 Identities=31% Similarity=0.667 Sum_probs=14.4
Q ss_pred cHHHHHHhCCCCCCCC
Q 031072 30 SLKNLLESRGLPGGLF 45 (166)
Q Consensus 30 ta~elL~~~gLP~GLL 45 (166)
-+|++|+|-|||.|.+
T Consensus 241 ii~~il~EAGlP~Gvi 256 (561)
T KOG2455|consen 241 IIYRILREAGLPPGVI 256 (561)
T ss_pred HHHHHHHHcCCCccce
Confidence 4689999999999987
No 18
>cd03676 Nudix_hydrolase_3 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate spe
Probab=20.48 E-value=74 Score=24.87 Aligned_cols=47 Identities=26% Similarity=0.352 Sum_probs=31.4
Q ss_pred CCCCCCCCce--eeEeCCC--ceEEEEEcCceEEEecceEEEccEEEEEEecC
Q 031072 41 PGGLFPENVK--SYNLDQN--GRLEVYLEGPCMAKFDTRVLFDSVVRANLSYG 89 (166)
Q Consensus 41 P~GLLP~~V~--~Y~l~~t--G~f~V~l~~~C~~~f~~~v~Y~~~ItG~i~~G 89 (166)
+.|+.-..|. .|..|.+ |.+|+...+.....+.- .+|..+.|.++.|
T Consensus 27 ~~g~~h~~v~~~~~~~~~~~~~~l~lqrRs~~K~~~Pg--~wd~~~~G~v~~g 77 (180)
T cd03676 27 LFGLVTYGVHLNGYVRDEDGGLRIWIPRRSPTKATWPG--MLDNLVAGGLGHG 77 (180)
T ss_pred cCCceEEEEEEEEEEEcCCCCeEEEEEeccCCCCCCCC--ceeeecccCCCCC
Confidence 3444444433 5677765 89999887776554543 6888889998876
Done!