Query 042743
Match_columns 65
No_of_seqs 102 out of 115
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 08:59:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042743.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042743hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3473 RNA polymerase II tran 99.9 6.1E-25 1.3E-29 147.2 3.8 47 11-65 65-112 (112)
2 smart00512 Skp1 Found in Skp1 99.2 1.1E-11 2.4E-16 77.1 3.2 50 11-65 49-104 (104)
3 KOG1724 SCF ubiquitin ligase, 97.3 0.0003 6.6E-09 49.0 3.3 55 11-65 51-112 (162)
4 COG5201 SKP1 SCF ubiquitin lig 96.3 0.0035 7.6E-08 44.5 2.9 55 11-65 46-107 (158)
5 PF03931 Skp1_POZ: Skp1 family 93.6 0.035 7.7E-07 32.1 1.1 17 11-27 45-61 (62)
6 PF01466 Skp1: Skp1 family, di 93.4 0.059 1.3E-06 32.5 1.9 19 47-65 10-28 (78)
7 smart00225 BTB Broad-Complex, 90.8 0.27 5.9E-06 26.6 2.4 36 12-65 47-82 (90)
8 PHA03098 kelch-like protein; P 82.5 1.7 3.7E-05 32.8 3.3 19 47-65 72-90 (534)
9 PHA02713 hypothetical protein; 80.4 1.8 3.9E-05 34.0 2.9 35 11-65 74-108 (557)
10 PHA02790 Kelch-like protein; P 80.0 1.4 3E-05 33.7 2.1 18 47-64 87-104 (480)
11 PF00651 BTB: BTB/POZ domain; 69.3 2.5 5.5E-05 24.6 0.9 18 48-65 78-96 (111)
12 COG1334 FlaG Uncharacterized f 61.1 6 0.00013 26.9 1.7 48 11-59 53-107 (120)
13 PF09509 Hypoth_Ymh: Protein o 57.7 12 0.00026 24.6 2.6 41 16-64 77-122 (125)
14 PF06200 tify: tify domain; I 56.1 10 0.00022 20.8 1.8 19 43-61 16-35 (36)
15 cd00170 SEC14 Sec14p-like lipi 51.8 10 0.00022 22.5 1.4 21 2-23 125-145 (157)
16 PF10330 Stb3: Putative Sin3 b 50.7 16 0.00035 24.1 2.3 20 41-60 32-52 (92)
17 PF07784 DUF1622: Protein of u 46.5 9 0.0002 23.8 0.6 14 51-64 33-46 (77)
18 PF11420 Subtilosin_A: Bacteri 45.6 9.7 0.00021 21.2 0.6 11 40-50 16-26 (35)
19 PF00152 tRNA-synt_2: tRNA syn 45.4 19 0.0004 26.2 2.2 54 8-62 21-93 (335)
20 PF07818 HCNGP: HCNGP-like pro 39.5 17 0.00037 23.3 1.1 20 7-26 37-57 (96)
21 smart00025 Pumilio Pumilio-lik 39.4 18 0.00039 17.0 1.0 13 11-23 14-26 (36)
22 PRK10972 Z-ring-associated pro 38.6 19 0.00042 23.8 1.3 21 44-64 15-35 (109)
23 PRK08452 flagellar protein Fla 33.0 30 0.00065 23.3 1.5 13 47-59 99-111 (124)
24 PF00806 PUF: Pumilio-family R 26.9 31 0.00067 17.2 0.6 13 11-23 14-26 (35)
25 COG0837 Glk Glucokinase [Carbo 24.7 44 0.00095 26.2 1.3 24 9-32 262-289 (320)
26 PF03646 FlaG: FlaG protein; 24.4 39 0.00085 20.8 0.9 13 47-59 83-95 (107)
27 smart00516 SEC14 Domain in hom 24.4 58 0.0012 19.9 1.6 21 2-22 123-143 (158)
28 PF08356 EF_assoc_2: EF hand a 23.2 27 0.00058 22.4 -0.0 30 24-56 55-84 (89)
29 PRK08868 flagellar protein Fla 23.1 57 0.0012 22.8 1.5 13 47-59 117-129 (144)
30 cd00872 PI3Ka_I Phosphoinositi 22.9 44 0.00096 23.2 1.0 12 47-58 68-79 (171)
31 PRK07738 flagellar protein Fla 21.8 63 0.0014 21.6 1.5 14 47-60 92-105 (117)
No 1
>KOG3473 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin C [Transcription]
Probab=99.91 E-value=6.1e-25 Score=147.20 Aligned_cols=47 Identities=43% Similarity=0.641 Sum_probs=45.3
Q ss_pred eccchHHHHHHHh-hhhhcccCcccccccccCCCCCCCCChHHHHHHHHhhhhcCC
Q 042743 11 HASNDIDVGSEYF-EAVRFVNSLGSVMLSIWGKETDFHIEPELTLELMMAANYLHT 65 (65)
Q Consensus 11 ~~S~vLekV~eYl-Yk~rY~~s~~~~~~~~~~~iPeF~IppEiaLELLmAAdyLd~ 65 (65)
+.||+|+|||||| ||+||+|++ .++|+|+||||+|||||||||||+|
T Consensus 65 i~shiLeKvc~Yl~Yk~rY~~~s--------~eiPeF~IppemaleLL~aAn~Lec 112 (112)
T KOG3473|consen 65 IPSHILEKVCEYLAYKVRYTNSS--------TEIPEFDIPPEMALELLMAANYLEC 112 (112)
T ss_pred chHHHHHHHHHHhhheeeecccc--------ccCCCCCCCHHHHHHHHHHhhhhcC
Confidence 6799999999999 999999997 7999999999999999999999998
No 2
>smart00512 Skp1 Found in Skp1 protein family. Family of Skp1 (kinetochore protein required for cell cycle progression) and elongin C (subunit of RNA polymerase II transcription factor SIII) homologues.
Probab=99.20 E-value=1.1e-11 Score=77.15 Aligned_cols=50 Identities=28% Similarity=0.283 Sum_probs=41.5
Q ss_pred eccchHHHHHHHh-hhhhcccCcccccccccCCCCCCC-----CChHHHHHHHHhhhhcCC
Q 042743 11 HASNDIDVGSEYF-EAVRFVNSLGSVMLSIWGKETDFH-----IEPELTLELMMAANYLHT 65 (65)
Q Consensus 11 ~~S~vLekV~eYl-Yk~rY~~s~~~~~~~~~~~iPeF~-----IppEiaLELLmAAdyLd~ 65 (65)
+.|.+|++||+|+ |+..|.++.. ...++|+|+ ++++.++|||+|||||++
T Consensus 49 v~~~~L~~Vi~yc~~h~~~~~~~~-----~~~~~~~wD~~F~~~d~~~l~dLl~AAnyL~I 104 (104)
T smart00512 49 VTSKILSKVIEYCEHHVDDPPSVA-----DKDDIPTWDAEFLKIDQETLFELILAANYLDI 104 (104)
T ss_pred cCHHHHHHHHHHHHHcccCCCCcc-----ccccccHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence 6899999999999 8888876542 113578776 999999999999999986
No 3
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.26 E-value=0.0003 Score=48.96 Aligned_cols=55 Identities=16% Similarity=0.192 Sum_probs=36.3
Q ss_pred eccchHHHHHHHhhhhhcccCcc--cccccccCCCCCC-----CCChHHHHHHHHhhhhcCC
Q 042743 11 HASNDIDVGSEYFEAVRFVNSLG--SVMLSIWGKETDF-----HIEPELTLELMMAANYLHT 65 (65)
Q Consensus 11 ~~S~vLekV~eYlYk~rY~~s~~--~~~~~~~~~iPeF-----~IppEiaLELLmAAdyLd~ 65 (65)
.+|.+|.||++|.++|+-.+... +.......++|+. .++-..-.||+.|||||++
T Consensus 51 V~~~iL~kVIewC~~Hk~d~~~~~~~~~~~~~~~i~~WD~~Flk~d~~tLfdli~AAnyLdi 112 (162)
T KOG1724|consen 51 VTSKILKKVIEWCKKHKDDDPANPEDKELPEETDIPEWDAEFLKVDQGTLFDLILAANYLDI 112 (162)
T ss_pred cCHHHHHHHHHHHHHcccccccccccccccccCCccHHHHHHHhcCHHHHHHHHHHhhhccc
Confidence 57999999999997666432110 0000111235532 5888899999999999985
No 4
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=96.34 E-value=0.0035 Score=44.49 Aligned_cols=55 Identities=29% Similarity=0.319 Sum_probs=38.2
Q ss_pred eccchHHHHHHHhhhhhcccCcccccccccCCCC-CC------CCChHHHHHHHHhhhhcCC
Q 042743 11 HASNDIDVGSEYFEAVRFVNSLGSVMLSIWGKET-DF------HIEPELTLELMMAANYLHT 65 (65)
Q Consensus 11 ~~S~vLekV~eYlYk~rY~~s~~~~~~~~~~~iP-eF------~IppEiaLELLmAAdyLd~ 65 (65)
..|.||.||.+|+-.++-+++.+....++..--| || .++.|+-+|...|||||++
T Consensus 46 VrSsvl~kv~ew~ehh~~s~sede~d~~~rks~p~D~wdr~Fm~vDqemL~eI~laaNYL~i 107 (158)
T COG5201 46 VRSSVLMKVQEWMEHHTSSLSEDENDLEIRKSKPSDFWDRFFMEVDQEMLLEICLAANYLEI 107 (158)
T ss_pred hhHHHHHHHHHHHHhccccCCCccChHhhhccCCccHHHHHHHHhhHHHHHHHHHhhccccc
Confidence 4689999999999767767664322222221112 33 4889999999999999984
No 5
>PF03931 Skp1_POZ: Skp1 family, tetramerisation domain; InterPro: IPR016073 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a POZ domain with a core structure consisting of beta(2)/alpha(2)/beta(2)/alpha(2) in two layers, alpha/beta. This domain is found at the N-terminal of SKP1 proteins [] as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1LM8_C 2XAI_E 1VCB_E 3ZRC_K 3ZRF_E 3DCG_B 2C9W_C 1LQB_B 2IZV_C 1HV2_A ....
Probab=93.60 E-value=0.035 Score=32.06 Aligned_cols=17 Identities=18% Similarity=0.094 Sum_probs=13.2
Q ss_pred eccchHHHHHHHhhhhh
Q 042743 11 HASNDIDVGSEYFEAVR 27 (65)
Q Consensus 11 ~~S~vLekV~eYlYk~r 27 (65)
+.|.+|+||+||+++++
T Consensus 45 v~~~~L~kViewc~~H~ 61 (62)
T PF03931_consen 45 VSSRILKKVIEWCEHHK 61 (62)
T ss_dssp S-HHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHhcC
Confidence 57999999999994444
No 6
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=93.41 E-value=0.059 Score=32.46 Aligned_cols=19 Identities=32% Similarity=0.587 Sum_probs=15.0
Q ss_pred CCChHHHHHHHHhhhhcCC
Q 042743 47 HIEPELTLELMMAANYLHT 65 (65)
Q Consensus 47 ~IppEiaLELLmAAdyLd~ 65 (65)
++..+.-++|+.||+||++
T Consensus 10 ~~~~~~L~~l~~AA~yL~I 28 (78)
T PF01466_consen 10 DVDNDELFDLLNAANYLDI 28 (78)
T ss_dssp -S-HHHHHHHHHHHHHHT-
T ss_pred HcCHHHHHHHHHHHHHHcc
Confidence 6678899999999999985
No 7
>smart00225 BTB Broad-Complex, Tramtrack and Bric a brac. Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structures.
Probab=90.79 E-value=0.27 Score=26.61 Aligned_cols=36 Identities=22% Similarity=0.311 Sum_probs=24.6
Q ss_pred ccchHHHHHHHhhhhhcccCcccccccccCCCCCCCCChHHHHHHHHhhhhcCC
Q 042743 12 ASNDIDVGSEYFEAVRFVNSLGSVMLSIWGKETDFHIEPELTLELMMAANYLHT 65 (65)
Q Consensus 12 ~S~vLekV~eYlYk~rY~~s~~~~~~~~~~~iPeF~IppEiaLELLmAAdyLd~ 65 (65)
.+..++.+++|+|.. +.+++++...+++.+|+++++
T Consensus 47 ~~~~f~~~l~~ly~~------------------~~~~~~~~~~~l~~~a~~~~~ 82 (90)
T smart00225 47 SPEDFRALLEFLYTG------------------KLDLPEENVEELLELADYLQI 82 (90)
T ss_pred CHHHHHHHHHeecCc------------------eeecCHHHHHHHHHHHHHHCc
Confidence 455666666666532 124566688999999999874
No 8
>PHA03098 kelch-like protein; Provisional
Probab=82.47 E-value=1.7 Score=32.75 Aligned_cols=19 Identities=26% Similarity=0.398 Sum_probs=16.3
Q ss_pred CCChHHHHHHHHhhhhcCC
Q 042743 47 HIEPELTLELMMAANYLHT 65 (65)
Q Consensus 47 ~IppEiaLELLmAAdyLd~ 65 (65)
+|..+.+.+||.|||+|+.
T Consensus 72 ~i~~~~~~~ll~~A~~l~~ 90 (534)
T PHA03098 72 NITSNNVKDILSIANYLII 90 (534)
T ss_pred EEcHHHHHHHHHHHHHhCc
Confidence 5678889999999999873
No 9
>PHA02713 hypothetical protein; Provisional
Probab=80.35 E-value=1.8 Score=34.00 Aligned_cols=35 Identities=17% Similarity=0.313 Sum_probs=27.2
Q ss_pred eccchHHHHHHHhhhhhcccCcccccccccCCCCCCCCChHHHHHHHHhhhhcCC
Q 042743 11 HASNDIDVGSEYFEAVRFVNSLGSVMLSIWGKETDFHIEPELTLELMMAANYLHT 65 (65)
Q Consensus 11 ~~S~vLekV~eYlYk~rY~~s~~~~~~~~~~~iPeF~IppEiaLELLmAAdyLd~ 65 (65)
+...+++.+++|+|.- +|.++.+.+||.|||+|++
T Consensus 74 v~~~~~~~ll~y~Yt~--------------------~i~~~nv~~ll~aA~~lqi 108 (557)
T PHA02713 74 FDKDAVKNIVQYLYNR--------------------HISSMNVIDVLKCADYLLI 108 (557)
T ss_pred CCHHHHHHHHHHhcCC--------------------CCCHHHHHHHHHHHHHHCH
Confidence 4567888888888751 1567889999999999973
No 10
>PHA02790 Kelch-like protein; Provisional
Probab=80.01 E-value=1.4 Score=33.72 Aligned_cols=18 Identities=17% Similarity=0.174 Sum_probs=13.8
Q ss_pred CCChHHHHHHHHhhhhcC
Q 042743 47 HIEPELTLELMMAANYLH 64 (65)
Q Consensus 47 ~IppEiaLELLmAAdyLd 64 (65)
.|..+.+.+||.||++|+
T Consensus 87 ~it~~nV~~ll~aA~~Lq 104 (480)
T PHA02790 87 YIDSHNVVNLLRASILTS 104 (480)
T ss_pred EEecccHHHHHHHHHHhC
Confidence 355567888999999886
No 11
>PF00651 BTB: BTB/POZ domain; InterPro: IPR013069 The BTB (for BR-C, ttk and bab) [] or POZ (for Pox virus and Zinc finger) [] domain is present near the N terminus of a fraction of zinc finger (IPR007087 from INTERPRO) proteins and in proteins that contain the IPR006652 from INTERPRO motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation []. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule []. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [, , ]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.; GO: 0005515 protein binding; PDB: 3M5B_A 1R28_B 3LBZ_A 3E4U_F 3BIM_B 1R2B_A 1R29_A 2VPK_A 2YY9_B 3GA1_A ....
Probab=69.32 E-value=2.5 Score=24.60 Aligned_cols=18 Identities=33% Similarity=0.303 Sum_probs=13.8
Q ss_pred CC-hHHHHHHHHhhhhcCC
Q 042743 48 IE-PELTLELMMAANYLHT 65 (65)
Q Consensus 48 Ip-pEiaLELLmAAdyLd~ 65 (65)
|+ .+.+.++|..|+++++
T Consensus 78 ~~~~~~~~~ll~lA~~~~~ 96 (111)
T PF00651_consen 78 INSDENVEELLELADKLQI 96 (111)
T ss_dssp EE-TTTHHHHHHHHHHTTB
T ss_pred CCHHHHHHHHHHHHHHhCc
Confidence 55 7778888888888763
No 12
>COG1334 FlaG Uncharacterized flagellar protein FlaG [Cell motility and secretion]
Probab=61.09 E-value=6 Score=26.86 Aligned_cols=48 Identities=27% Similarity=0.375 Sum_probs=27.4
Q ss_pred eccchHHHHHHHh-hhhhc--ccCcccccccc----cCCCCCCCCChHHHHHHHHh
Q 042743 11 HASNDIDVGSEYF-EAVRF--VNSLGSVMLSI----WGKETDFHIEPELTLELMMA 59 (65)
Q Consensus 11 ~~S~vLekV~eYl-Yk~rY--~~s~~~~~~~~----~~~iPeF~IppEiaLELLmA 59 (65)
+.+..|.+.++++ =..+| .+..+.+--++ .+++=. +||||.+|||+.+
T Consensus 53 ~~v~~ink~~k~~nt~l~F~~dd~lg~~vVkI~d~~TgeVIR-qIPpee~L~l~~r 107 (120)
T COG1334 53 LIVEDINKLLKSLNTHLNFSYDDELGELVVKIIDKDTGEVIR-QIPPEEALELAAR 107 (120)
T ss_pred HHHHHHHHHHHhhcCceEEEEecccCcEEEEEEECCCCcchh-hCChHHHHHHHHH
Confidence 3455677888888 44444 33332211111 122222 7999999999865
No 13
>PF09509 Hypoth_Ymh: Protein of unknown function (Hypoth_ymh); InterPro: IPR012654 This entry consists of a relatively rare prokaryotic protein family (about 8 occurrences per 200 genomes). Genes for members of this family appear to be associated variously with phage and plasmid regions, restriction system loci, transposons, and housekeeping genes. Their function is unknown.
Probab=57.73 E-value=12 Score=24.63 Aligned_cols=41 Identities=22% Similarity=0.179 Sum_probs=27.3
Q ss_pred HHHHHHHh---hhhhcccCcccccccccCCCCC--CCCChHHHHHHHHhhhhcC
Q 042743 16 IDVGSEYF---EAVRFVNSLGSVMLSIWGKETD--FHIEPELTLELMMAANYLH 64 (65)
Q Consensus 16 LekV~eYl---Yk~rY~~s~~~~~~~~~~~iPe--F~IppEiaLELLmAAdyLd 64 (65)
.++....| .-.-|+|.. .--|. .++.++.|||+|+.|.||.
T Consensus 77 eq~G~~~L~~G~~~~~RNp~--------aH~~~~~~~~~~~dale~L~~~S~l~ 122 (125)
T PF09509_consen 77 EQKGFMNLFKGIFGAFRNPR--------AHEPRIEWPDTEQDALEILSLASLLH 122 (125)
T ss_pred HHHHHHHHHHHHHHHcCCcc--------ccCCcccCCCCHHHHHHHHHHHHHHH
Confidence 34555555 334456654 23444 3499999999999999974
No 14
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=56.13 E-value=10 Score=20.83 Aligned_cols=19 Identities=26% Similarity=0.483 Sum_probs=14.5
Q ss_pred CCCCC-CChHHHHHHHHhhh
Q 042743 43 ETDFH-IEPELTLELMMAAN 61 (65)
Q Consensus 43 iPeF~-IppEiaLELLmAAd 61 (65)
+-=|+ +||+.|-|+|.-|.
T Consensus 16 V~Vfd~v~~~Ka~~im~lA~ 35 (36)
T PF06200_consen 16 VCVFDDVPPDKAQEIMLLAS 35 (36)
T ss_pred EEEeCCCCHHHHHHHHHHhc
Confidence 33455 99999999998764
No 15
>cd00170 SEC14 Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=51.77 E-value=10 Score=22.53 Aligned_cols=21 Identities=38% Similarity=0.578 Sum_probs=13.3
Q ss_pred ccccceEEeeccchHHHHHHHh
Q 042743 2 KKTRKKVIFHASNDIDVGSEYF 23 (65)
Q Consensus 2 ~~~~~~~~~~~S~vLekV~eYl 23 (65)
+++|+||.++.+. ++...+|+
T Consensus 125 ~~~~~ki~~~~~~-~~~L~~~i 145 (157)
T cd00170 125 EKTRKKIVFLGSD-KEELLKYI 145 (157)
T ss_pred HhhhhhEEEecCC-HHHHHhhC
Confidence 3567777777776 55555544
No 16
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=50.75 E-value=16 Score=24.08 Aligned_cols=20 Identities=30% Similarity=0.454 Sum_probs=18.6
Q ss_pred CCCCCC-CCChHHHHHHHHhh
Q 042743 41 GKETDF-HIEPELTLELMMAA 60 (65)
Q Consensus 41 ~~iPeF-~IppEiaLELLmAA 60 (65)
.++|-| +|||.-+--|.|+|
T Consensus 32 ~~vPgF~~ls~sKqRRLi~~A 52 (92)
T PF10330_consen 32 TSVPGFSDLSPSKQRRLIMAA 52 (92)
T ss_pred ccCCCcccCCHHHHHHHHHHH
Confidence 589999 79999999999998
No 17
>PF07784 DUF1622: Protein of unknown function (DUF1622); InterPro: IPR012427 This is a family of 14 highly conserved sequences, from hypothetical proteins expressed by both bacterial and archaeal species.
Probab=46.47 E-value=9 Score=23.79 Aligned_cols=14 Identities=43% Similarity=0.624 Sum_probs=11.6
Q ss_pred HHHHHHHHhhhhcC
Q 042743 51 ELTLELMMAANYLH 64 (65)
Q Consensus 51 EiaLELLmAAdyLd 64 (65)
-++||.++|||-+.
T Consensus 33 ~lgLEfllaAdIl~ 46 (77)
T PF07784_consen 33 LLGLEFLLAADILR 46 (77)
T ss_pred HHHHHHHHHHHHHH
Confidence 36899999999774
No 18
>PF11420 Subtilosin_A: Bacteriocin subtilosin A; InterPro: IPR021539 Subtilosin A is a bacteriocin from Bacillus subtilis.The protein has a cyclized peptide backbone and forms three cross-liks between the sulphurs of Cys13, Cys7 and Cys4 and the alpha-positions of Phe22,Thr28 and Phe31 []. ; PDB: 1PXQ_A.
Probab=45.60 E-value=9.7 Score=21.25 Aligned_cols=11 Identities=36% Similarity=0.386 Sum_probs=3.8
Q ss_pred cCCCCCCCCCh
Q 042743 40 WGKETDFHIEP 50 (65)
Q Consensus 40 ~~~iPeF~Ipp 50 (65)
++.+|||+|..
T Consensus 16 dgpipdfeia~ 26 (35)
T PF11420_consen 16 DGPIPDFEIAG 26 (35)
T ss_dssp TTT---S--S-
T ss_pred cCCCCcchhhh
Confidence 47999999864
No 19
>PF00152 tRNA-synt_2: tRNA synthetases class II (D, K and N) ; InterPro: IPR004364 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry includes the asparagine, aspartic acid and lysine tRNA synthetases.; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 1N9W_B 1BBU_A 1BBW_A 4EX5_B 3E9I_A 3E9H_C 3A74_C 1NNH_A 3M4P_C 3M4Q_B ....
Probab=45.37 E-value=19 Score=26.21 Aligned_cols=54 Identities=20% Similarity=0.271 Sum_probs=32.7
Q ss_pred EEeeccchHHHHHHHhhhhhcccCcccccccccCC---CCCC----------------CCChHHHHHHHHhhhh
Q 042743 8 VIFHASNDIDVGSEYFEAVRFVNSLGSVMLSIWGK---ETDF----------------HIEPELTLELMMAANY 62 (65)
Q Consensus 8 ~~~~~S~vLekV~eYlYk~rY~~s~~~~~~~~~~~---iPeF----------------~IppEiaLELLmAAdy 62 (65)
++-+-|.+++.+-+||++..|..-.. .++..... .-.| .+-|++.+++|+++++
T Consensus 21 ~~~~rs~i~~~ir~ff~~~~f~Ev~t-P~l~~~~~~~~~~~F~v~~~~~~~~~~~~~L~~Spql~~k~ll~~g~ 93 (335)
T PF00152_consen 21 ILRIRSAILQAIREFFDKRGFIEVDT-PILTSSTCEGGAEPFSVDSEPGKYFGEPAYLTQSPQLYLKRLLAAGL 93 (335)
T ss_dssp HHHHHHHHHHHHHHHHHHTT-EEE----SEESSSSSSSSCSEEEEESTTEETTEEEEE-SSSHHHHHHHHHTTH
T ss_pred HHHHHHHHHHHHHHHHHhCCceEEcC-ceeeccccCccccccccccchhhhcccceecCcChHHHHhhhccccc
Confidence 34456889999999998888754321 11111111 1233 3569999999999874
No 20
>PF07818 HCNGP: HCNGP-like protein; InterPro: IPR012479 This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP (Q02614 from SWISSPROT). This protein is localised to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.
Probab=39.55 E-value=17 Score=23.26 Aligned_cols=20 Identities=15% Similarity=0.165 Sum_probs=16.3
Q ss_pred eEEeeccchHHHHHHHh-hhh
Q 042743 7 KVIFHASNDIDVGSEYF-EAV 26 (65)
Q Consensus 7 ~~~~~~S~vLekV~eYl-Yk~ 26 (65)
.-=|.|+++++|+++|+ =..
T Consensus 37 s~~frNP~i~ekLi~~~~Ide 57 (96)
T PF07818_consen 37 SKSFRNPSILEKLIEFFGIDE 57 (96)
T ss_pred ccccCChHHHHHHHHHcCCCc
Confidence 34589999999999999 443
No 21
>smart00025 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA.
Probab=39.43 E-value=18 Score=17.05 Aligned_cols=13 Identities=8% Similarity=-0.215 Sum_probs=10.7
Q ss_pred eccchHHHHHHHh
Q 042743 11 HASNDIDVGSEYF 23 (65)
Q Consensus 11 ~~S~vLekV~eYl 23 (65)
++|+++++++++.
T Consensus 14 ~g~~viqk~l~~~ 26 (36)
T smart00025 14 YGNRVVQKLLEHA 26 (36)
T ss_pred hhhHHHHHHHHHC
Confidence 4688999998886
No 22
>PRK10972 Z-ring-associated protein; Provisional
Probab=38.59 E-value=19 Score=23.78 Aligned_cols=21 Identities=29% Similarity=0.199 Sum_probs=18.2
Q ss_pred CCCCCChHHHHHHHHhhhhcC
Q 042743 44 TDFHIEPELTLELMMAANYLH 64 (65)
Q Consensus 44 PeF~IppEiaLELLmAAdyLd 64 (65)
=.+.-||+.--.|+.||++||
T Consensus 15 y~v~Cp~~e~~~L~~AA~~Ld 35 (109)
T PRK10972 15 LRVNCPPEQRDALNQAAEDLN 35 (109)
T ss_pred eEecCChhHHHHHHHHHHHHH
Confidence 345679999999999999997
No 23
>PRK08452 flagellar protein FlaG; Provisional
Probab=33.03 E-value=30 Score=23.29 Aligned_cols=13 Identities=31% Similarity=0.355 Sum_probs=11.3
Q ss_pred CCChHHHHHHHHh
Q 042743 47 HIEPELTLELMMA 59 (65)
Q Consensus 47 ~IppEiaLELLmA 59 (65)
+||||.+|+|+.+
T Consensus 99 qIP~Ee~L~l~~~ 111 (124)
T PRK08452 99 EIPSKEAIELMEY 111 (124)
T ss_pred eCCCHHHHHHHHH
Confidence 6999999998754
No 24
>PF00806 PUF: Pumilio-family RNA binding repeat; InterPro: IPR001313 The drosophila pumilio gene codes for an unusual protein that binds through the Puf domain that usually occurs as a tandem repeat of eight domains. The FBF-2 protein of Caenorhabditis elegans also has a Puf domain. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs [, ]. The same type of repetitive domain has been found in in a number of other proteins from all eukaryotic kingdoms. The Puf proteins characterised to date have been reported to bind to 3'-untranslated region (UTR) sequences encompassing a so-called UGUR tetranucleotide motif and thereby to repress gene expression by affecting mRNA translation or stability. In Saccharomyces cerevisiae (Baker's yeast), five proteins, termed Puf1p to Puf5p, bear six to eight Puf repeats []. Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. This suggests the existence of an extensive network of RNA-protein interactions that coordinate the post-transcriptional fate of large sets of cytotopically and functionally related RNAs through each stage of its lifecycle.; GO: 0003723 RNA binding; PDB: 3BX2_A 4DZS_B 3BX3_B 3BWT_A 3GVT_B 3GVO_A 1IB2_A 3Q0N_A 2YJY_A 1M8Z_A ....
Probab=26.92 E-value=31 Score=17.19 Aligned_cols=13 Identities=8% Similarity=-0.197 Sum_probs=10.4
Q ss_pred eccchHHHHHHHh
Q 042743 11 HASNDIDVGSEYF 23 (65)
Q Consensus 11 ~~S~vLekV~eYl 23 (65)
.+++|++|++|..
T Consensus 14 ~Gn~VvQk~le~~ 26 (35)
T PF00806_consen 14 YGNYVVQKCLEHA 26 (35)
T ss_dssp THHHHHHHHHHHS
T ss_pred ccCHHHHHHHHHC
Confidence 3688999999875
No 25
>COG0837 Glk Glucokinase [Carbohydrate transport and metabolism]
Probab=24.68 E-value=44 Score=26.25 Aligned_cols=24 Identities=17% Similarity=0.084 Sum_probs=21.5
Q ss_pred EeeccchHHHHHHHh----hhhhcccCc
Q 042743 9 IFHASNDIDVGSEYF----EAVRFVNSL 32 (65)
Q Consensus 9 ~~~~S~vLekV~eYl----Yk~rY~~s~ 32 (65)
+|+++-|+.|++++| |..+|++..
T Consensus 262 VyiaGGI~pril~~l~~s~Fr~~FedKG 289 (320)
T COG0837 262 VYIAGGIVPRILEALKASGFRARFEDKG 289 (320)
T ss_pred EEEcCCchHhHHHHHhcchHHHHhhhcC
Confidence 689999999999999 888888873
No 26
>PF03646 FlaG: FlaG protein; InterPro: IPR005186 Although these proteins are known to be important for flagellar their exact function is unknown.; PDB: 2HC5_A.
Probab=24.42 E-value=39 Score=20.85 Aligned_cols=13 Identities=38% Similarity=0.508 Sum_probs=10.1
Q ss_pred CCChHHHHHHHHh
Q 042743 47 HIEPELTLELMMA 59 (65)
Q Consensus 47 ~IppEiaLELLmA 59 (65)
+||||.+|+|...
T Consensus 83 qIP~Ee~l~l~~~ 95 (107)
T PF03646_consen 83 QIPPEELLDLAKR 95 (107)
T ss_dssp EE-HHHHHHHHHH
T ss_pred eCCcHHHHHHHHH
Confidence 6999999998754
No 27
>smart00516 SEC14 Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=24.36 E-value=58 Score=19.90 Aligned_cols=21 Identities=33% Similarity=0.468 Sum_probs=12.3
Q ss_pred ccccceEEeeccchHHHHHHH
Q 042743 2 KKTRKKVIFHASNDIDVGSEY 22 (65)
Q Consensus 2 ~~~~~~~~~~~S~vLekV~eY 22 (65)
+++|+|+.++.+.-.+...+|
T Consensus 123 ~~~~~ki~~~~~~~~~~L~~~ 143 (158)
T smart00516 123 EKTREKIRFVGNDSKEELLEY 143 (158)
T ss_pred hhhhccEEEeCCCCHHHHHhh
Confidence 356777777776444444443
No 28
>PF08356 EF_assoc_2: EF hand associated; InterPro: IPR013567 This region predominantly appears near EF-hands (IPR002048 from INTERPRO) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
Probab=23.15 E-value=27 Score=22.38 Aligned_cols=30 Identities=20% Similarity=0.233 Sum_probs=20.3
Q ss_pred hhhhcccCcccccccccCCCCCCCCChHHHHHH
Q 042743 24 EAVRFVNSLGSVMLSIWGKETDFHIEPELTLEL 56 (65)
Q Consensus 24 Yk~rY~~s~~~~~~~~~~~iPeF~IppEiaLEL 56 (65)
=+..|.|+.. ++++-=-|.|++||.-..||
T Consensus 55 R~FgY~d~L~---L~d~~l~p~l~v~~~~svEL 84 (89)
T PF08356_consen 55 RKFGYDDDLS---LSDDFLYPKLDVPPDQSVEL 84 (89)
T ss_pred HHcCCCCcce---eccccCCCCccCCCCCeeec
Confidence 4667888752 23322367899999988876
No 29
>PRK08868 flagellar protein FlaG; Provisional
Probab=23.07 E-value=57 Score=22.76 Aligned_cols=13 Identities=31% Similarity=0.363 Sum_probs=11.3
Q ss_pred CCChHHHHHHHHh
Q 042743 47 HIEPELTLELMMA 59 (65)
Q Consensus 47 ~IppEiaLELLmA 59 (65)
+||||.+|+|+.+
T Consensus 117 QIP~Ee~L~la~~ 129 (144)
T PRK08868 117 QIPDEEMLEVLRR 129 (144)
T ss_pred eCCCHHHHHHHHH
Confidence 7999999999854
No 30
>cd00872 PI3Ka_I Phosphoinositide 3-kinase (PI3K) class I, accessory domain ; PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. In general, PI3K class I prefer phosphoinositol (4,5)-bisphosphate as a substrate. Mammalian members interact with active Ras. They form heterodimers with adapter molecules linking them to different signaling pathways.
Probab=22.91 E-value=44 Score=23.23 Aligned_cols=12 Identities=42% Similarity=0.728 Sum_probs=10.6
Q ss_pred CCChHHHHHHHH
Q 042743 47 HIEPELTLELMM 58 (65)
Q Consensus 47 ~IppEiaLELLm 58 (65)
+|+|+.|||||-
T Consensus 68 ~i~~~~aLeLL~ 79 (171)
T cd00872 68 KLKPEQALELLD 79 (171)
T ss_pred CCCHHHHHHHCC
Confidence 489999999985
No 31
>PRK07738 flagellar protein FlaG; Provisional
Probab=21.81 E-value=63 Score=21.62 Aligned_cols=14 Identities=29% Similarity=0.468 Sum_probs=11.8
Q ss_pred CCChHHHHHHHHhh
Q 042743 47 HIEPELTLELMMAA 60 (65)
Q Consensus 47 ~IppEiaLELLmAA 60 (65)
+||||.+|+++.+-
T Consensus 92 QIPpEe~L~l~~~m 105 (117)
T PRK07738 92 EIPPKKLLDMYAAM 105 (117)
T ss_pred eCCCHHHHHHHHHH
Confidence 69999999998653
Done!