Query psy8352
Match_columns 69
No_of_seqs 47 out of 49
Neff 2.8
Searched_HMMs 46136
Date Sat Aug 17 01:31:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8352.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8352hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3175|consensus 76.9 0.52 1.1E-05 37.8 -1.0 37 3-42 75-111 (366)
2 PF13221 DUF4029: Protein of u 75.7 2.1 4.5E-05 28.8 1.8 31 20-50 49-79 (96)
3 PF06371 Drf_GBD: Diaphanous G 72.2 2.3 5E-05 27.7 1.3 39 11-49 147-185 (187)
4 cd00020 ARM Armadillo/beta-cat 46.6 4 8.7E-05 23.5 -0.9 43 20-62 47-89 (120)
5 PRK03692 putative UDP-N-acetyl 40.3 19 0.00041 26.4 1.6 24 24-50 212-235 (243)
6 cd06533 Glyco_transf_WecG_TagA 37.7 16 0.00034 24.8 0.8 15 24-38 154-168 (171)
7 PF03808 Glyco_tran_WecB: Glyc 28.4 33 0.00072 23.1 1.2 14 24-37 156-169 (172)
8 TIGR00696 wecB_tagA_cpsF bacte 28.3 31 0.00067 24.0 1.0 13 24-36 155-167 (177)
9 PF00075 RNase_H: RNase H; In 27.1 38 0.00083 20.5 1.2 10 5-14 2-11 (132)
10 smart00328 BPI1 BPI/LBP/CETP N 25.5 1.3E+02 0.0028 21.0 3.7 34 23-65 142-175 (225)
11 PF08514 STAG: STAG domain ; 22.2 42 0.00091 22.0 0.7 16 22-37 46-61 (118)
12 PF05991 NYN_YacP: YacP-like N 21.7 33 0.00072 23.4 0.2 19 9-28 1-19 (166)
13 PF11842 DUF3362: Domain of un 21.3 70 0.0015 22.8 1.7 23 43-67 47-69 (150)
14 COG1758 RpoZ DNA-directed RNA 20.7 81 0.0018 19.1 1.7 46 21-67 3-55 (74)
15 PF04938 SIP1: Survival motor 20.4 92 0.002 21.8 2.2 27 22-48 169-206 (233)
16 PF03634 TCP: TCP family trans 20.4 58 0.0013 21.4 1.1 17 14-30 38-54 (138)
No 1
>KOG3175|consensus
Probab=76.94 E-value=0.52 Score=37.81 Aligned_cols=37 Identities=32% Similarity=0.390 Sum_probs=31.5
Q ss_pred ccceeeEEEecccccccCchhhhhHHHHhhcchhHHHHHH
Q psy8352 3 TLGQVMLYVDGMTGIMDHPPTVQWLYVLVASKFRLVIKTA 42 (69)
Q Consensus 3 Algqiml~VDGMngvi~h~~tvqwLY~L~~S~frlVvKta 42 (69)
+=.||.--+|||||+ +-|+||+..|+..++|.|-++=
T Consensus 75 ~k~~~~~~~~~~n~~---~~t~~~~~e~li~p~~nv~~~d 111 (366)
T KOG3175|consen 75 MKERILKIVTGFNGI---PFTIQRLCELLIDPRRNVTGTD 111 (366)
T ss_pred HHHhhhhhhhhccCC---CHHHHHHHHHhcCcccccCcch
Confidence 345777889999997 7899999999999999987653
No 2
>PF13221 DUF4029: Protein of unknown function (DUF4029)
Probab=75.68 E-value=2.1 Score=28.77 Aligned_cols=31 Identities=16% Similarity=0.324 Sum_probs=28.0
Q ss_pred CchhhhhHHHHhhcchhHHHHHHHhhhhhee
Q psy8352 20 HPPTVQWLYVLVASKFRLVIKTALKLLLIFV 50 (69)
Q Consensus 20 h~~tvqwLY~L~~S~frlVvKtaLkLLLVfv 50 (69)
-||..||++++..-|+..++-.+.-.-.|||
T Consensus 49 lnelf~wi~sf~l~k~gnivlq~icayivfv 79 (96)
T PF13221_consen 49 LNELFQWIHSFELMKLGNIVLQVICAYIVFV 79 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999988888886
No 3
>PF06371 Drf_GBD: Diaphanous GTPase-binding Domain; InterPro: IPR010473 Diaphanous-related formins (Drfs) are a family of formin homology (FH) proteins that act as effectors of Rho small GTPases during growth factor-induced cytoskeletal remodelling, stress fibre formation, and cell division []. Drf proteins are characterised by a variety of shared domains: an N-terminal GTPase-binding domain (GBD), formin-homology domains FH1, FH2 (IPR003104 from INTERPRO) and FH3 (IPR010472 from INTERPRO), and a C-terminal conserved Dia-autoregulatory domain (DAD) that binds the GBD. This entry represents the GBD, which is a bifunctional autoinhibitory domain that interacts with and is regulated by activated Rho family members. Mammalian Drf3 contains a CRIB-like motif within its GBD for binding to Cdc42, which is required for Cdc42 to activate and guide Drf3 towards the cell cortex where it remodels the actin skeleton [].; GO: 0003779 actin binding, 0017048 Rho GTPase binding, 0030036 actin cytoskeleton organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=72.24 E-value=2.3 Score=27.72 Aligned_cols=39 Identities=23% Similarity=0.336 Sum_probs=32.9
Q ss_pred EecccccccCchhhhhHHHHhhcchhHHHHHHHhhhhhe
Q psy8352 11 VDGMTGIMDHPPTVQWLYVLVASKFRLVIKTALKLLLIF 49 (69)
Q Consensus 11 VDGMngvi~h~~tvqwLY~L~~S~frlVvKtaLkLLLVf 49 (69)
=.|+..+++|++.+..|-....|+.-.+-+.|+++|.++
T Consensus 147 ~~G~~~v~~~~~~v~~i~~~L~s~~~~~r~~~leiL~~l 185 (187)
T PF06371_consen 147 KYGLEAVLSHPDSVNLIALSLDSPNIKTRKLALEILAAL 185 (187)
T ss_dssp HHHHHHHHCSSSHHHHHHHT--TTSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCcHHHHHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 368899999999999999999999888999999998764
No 4
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=46.59 E-value=4 Score=23.52 Aligned_cols=43 Identities=23% Similarity=0.179 Sum_probs=33.0
Q ss_pred CchhhhhHHHHhhcchhHHHHHHHhhhhheeeeeccchHHHHH
Q psy8352 20 HPPTVQWLYVLVASKFRLVIKTALKLLLIFVEYVESNCFLLIQ 62 (69)
Q Consensus 20 h~~tvqwLY~L~~S~frlVvKtaLkLLLVfveY~EsN~~lli~ 62 (69)
..+.++.+-.+..++...+.+.|+..|--+.+..+.+...+++
T Consensus 47 ~~~~i~~l~~~l~~~~~~v~~~a~~~L~~l~~~~~~~~~~~~~ 89 (120)
T cd00020 47 EAGGLPALVQLLKSEDEEVVKAALWALRNLAAGPEDNKLIVLE 89 (120)
T ss_pred HCCChHHHHHHHhCCCHHHHHHHHHHHHHHccCcHHHHHHHHH
Confidence 3477888888888888889999999988888777665555443
No 5
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=40.27 E-value=19 Score=26.41 Aligned_cols=24 Identities=33% Similarity=0.836 Sum_probs=18.1
Q ss_pred hhhHHHHhhcchhHHHHHHHhhhhhee
Q psy8352 24 VQWLYVLVASKFRLVIKTALKLLLIFV 50 (69)
Q Consensus 24 vqwLY~L~~S~frlVvKtaLkLLLVfv 50 (69)
+.|||+|...|-|+ |.-+. +..|+
T Consensus 212 LEWlyRl~~EP~R~--~R~~~-~~~F~ 235 (243)
T PRK03692 212 LEWLYRLLSQPSRI--RRQLR-LLRYL 235 (243)
T ss_pred hHHHHHhHhCcHHH--HHHHH-HHHHH
Confidence 57999999999995 77665 34553
No 6
>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.
Probab=37.75 E-value=16 Score=24.78 Aligned_cols=15 Identities=40% Similarity=0.791 Sum_probs=12.8
Q ss_pred hhhHHHHhhcchhHH
Q psy8352 24 VQWLYVLVASKFRLV 38 (69)
Q Consensus 24 vqwLY~L~~S~frlV 38 (69)
+.|||++...|.||.
T Consensus 154 lEWlyRl~~eP~Rl~ 168 (171)
T cd06533 154 LEWLYRLLQEPRRLW 168 (171)
T ss_pred chhHHhhhhCcchhh
Confidence 469999999999863
No 7
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=28.41 E-value=33 Score=23.14 Aligned_cols=14 Identities=43% Similarity=0.907 Sum_probs=12.2
Q ss_pred hhhHHHHhhcchhH
Q psy8352 24 VQWLYVLVASKFRL 37 (69)
Q Consensus 24 vqwLY~L~~S~frl 37 (69)
+.|||++...|.|+
T Consensus 156 lEWlyRl~~eP~Rl 169 (172)
T PF03808_consen 156 LEWLYRLLQEPKRL 169 (172)
T ss_pred cHHHHHHHhChHhh
Confidence 57999999999886
No 8
>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family. The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.
Probab=28.34 E-value=31 Score=24.02 Aligned_cols=13 Identities=38% Similarity=0.940 Sum_probs=12.0
Q ss_pred hhhHHHHhhcchh
Q psy8352 24 VQWLYVLVASKFR 36 (69)
Q Consensus 24 vqwLY~L~~S~fr 36 (69)
+.|||.|...|.|
T Consensus 155 LEWlyRl~~eP~R 167 (177)
T TIGR00696 155 LEWLYRLRMEPWR 167 (177)
T ss_pred chHHHHhhhCcHH
Confidence 5799999999999
No 9
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=27.08 E-value=38 Score=20.45 Aligned_cols=10 Identities=30% Similarity=0.826 Sum_probs=7.5
Q ss_pred ceeeEEEecc
Q psy8352 5 GQVMLYVDGM 14 (69)
Q Consensus 5 gqiml~VDGM 14 (69)
.++.+|+||=
T Consensus 2 ~~~~iytDgS 11 (132)
T PF00075_consen 2 KAIIIYTDGS 11 (132)
T ss_dssp TSEEEEEEEE
T ss_pred CcEEEEEeCC
Confidence 3678888886
No 10
>smart00328 BPI1 BPI/LBP/CETP N-terminal domain. Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) N-terminal domain
Probab=25.48 E-value=1.3e+02 Score=20.96 Aligned_cols=34 Identities=21% Similarity=0.366 Sum_probs=25.8
Q ss_pred hhhhHHHHhhcchhHHHHHHHhhhhheeeeeccchHHHHHHHH
Q psy8352 23 TVQWLYVLVASKFRLVIKTALKLLLIFVEYVESNCFLLIQAVH 65 (69)
Q Consensus 23 tvqwLY~L~~S~frlVvKtaLkLLLVfveY~EsN~~lli~Av~ 65 (69)
...|||.+....+.--+|.+|+=.+ ||.+-+++.
T Consensus 142 ~~swl~n~f~~~i~~~i~~~l~~~I---------C~~i~~~i~ 175 (225)
T smart00328 142 VLGWLINLFRKFIENTLRNVLEGQI---------CPVIDSAVS 175 (225)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHH
Confidence 6899999988777777777776544 777777764
No 11
>PF08514 STAG: STAG domain ; InterPro: IPR013721 STAG domain proteins are subunits of cohesin complex - a protein complex required for sister chromatid cohesion in eukaryotes. The STAG domain is present in Schizosaccharomyces pombe (Fission yeast) mitotic cohesin Psc3, and the meiosis specific cohesin Rec11. Many organisms express a meiosis-specific STAG protein, for example, mice and humans have a meiosis specific variant called STAG3, although budding yeast does not have a meiosis specific version [].
Probab=22.19 E-value=42 Score=22.03 Aligned_cols=16 Identities=38% Similarity=0.615 Sum_probs=12.9
Q ss_pred hhhhhHHHHhhcchhH
Q psy8352 22 PTVQWLYVLVASKFRL 37 (69)
Q Consensus 22 ~tvqwLY~L~~S~frl 37 (69)
..+.||-+|++|+.|-
T Consensus 46 ~l~~wl~~lS~S~~R~ 61 (118)
T PF08514_consen 46 NLISWLTALSSSKVRP 61 (118)
T ss_pred HHHHHHHHhccCCcee
Confidence 5789999999996543
No 12
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=21.73 E-value=33 Score=23.41 Aligned_cols=19 Identities=26% Similarity=0.490 Sum_probs=13.0
Q ss_pred EEEecccccccCchhhhhHH
Q psy8352 9 LYVDGMTGIMDHPPTVQWLY 28 (69)
Q Consensus 9 l~VDGMngvi~h~~tvqwLY 28 (69)
|.|||+| ||.+.+-+.++.
T Consensus 1 LlIDGYN-li~~~~~l~~~~ 19 (166)
T PF05991_consen 1 LLIDGYN-LIHAWPELRSLA 19 (166)
T ss_pred CeEcchh-hhCCCHHHHhhc
Confidence 5799999 455555566655
No 13
>PF11842 DUF3362: Domain of unknown function (DUF3362); InterPro: IPR024560 This domain tends to occur to the C terminus of a radical SAM domain (PF04055 from PFAM) in members of the uncharacterised protein family UPF0313. Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Evidence exists that these proteins generate a radical species by reductive cleavage of S:-adenosylmethionine (SAM) through an unusual Fe-S centre [, ].
Probab=21.31 E-value=70 Score=22.77 Aligned_cols=23 Identities=26% Similarity=0.244 Sum_probs=18.4
Q ss_pred HhhhhheeeeeccchHHHHHHHHhh
Q psy8352 43 LKLLLIFVEYVESNCFLLIQAVHAI 67 (69)
Q Consensus 43 LkLLLVfveY~EsN~~lli~Av~~v 67 (69)
=|.||-| +...|++++.+|....
T Consensus 47 qkAll~Y--~~PeN~~lvreAL~~~ 69 (150)
T PF11842_consen 47 QKALLRY--HDPENWPLVREALKKM 69 (150)
T ss_pred HHHHHhh--cChhhHHHHHHHHHHh
Confidence 3567777 7889999999998753
No 14
>COG1758 RpoZ DNA-directed RNA polymerase, subunit K/omega [Transcription]
Probab=20.68 E-value=81 Score=19.15 Aligned_cols=46 Identities=30% Similarity=0.325 Sum_probs=28.1
Q ss_pred chhhhhHHHHhhcchhHHH---HHHHhhhhhe---eeeeccc-hHHHHHHHHhh
Q psy8352 21 PPTVQWLYVLVASKFRLVI---KTALKLLLIF---VEYVESN-CFLLIQAVHAI 67 (69)
Q Consensus 21 ~~tvqwLY~L~~S~frlVv---KtaLkLLLVf---veY~EsN-~~lli~Av~~v 67 (69)
+.+++-+.....|+|++|+ |.|+.+---- ++ .+.| -..+..|.+.+
T Consensus 3 ~~~~~~l~~~~~~ryelv~~aa~RA~Ql~~ga~~~~~-~~~~~~kpv~iAl~Ei 55 (74)
T COG1758 3 RPTIEDLLDKVGNRYELVVVAAKRARQLAAGAPPLVD-DEENKDKPVVIALREI 55 (74)
T ss_pred ccCHHHHHhhccCHHHHHHHHHHHHHHHHcCCCCccc-cccccCChHHHHHHHH
Confidence 3578889999999998875 6666664321 11 2233 44455565544
No 15
>PF04938 SIP1: Survival motor neuron (SMN) interacting protein 1 (SIP1); PDB: 3S6N_2.
Probab=20.42 E-value=92 Score=21.76 Aligned_cols=27 Identities=37% Similarity=0.562 Sum_probs=21.3
Q ss_pred hhhhhHHHHhh-----------cchhHHHHHHHhhhhh
Q psy8352 22 PTVQWLYVLVA-----------SKFRLVIKTALKLLLI 48 (69)
Q Consensus 22 ~tvqwLY~L~~-----------S~frlVvKtaLkLLLV 48 (69)
..-||||.|.. |--|-++|...++---
T Consensus 169 ~~~~WlyaLLa~ld~pL~~d~~s~LR~LaR~C~~lR~~ 206 (233)
T PF04938_consen 169 NLSQWLYALLARLDKPLDADTCSSLRSLARKCAKLRAK 206 (233)
T ss_dssp HHHHHHHHHHHH--SS--HHHHHHHHHHHHHHHHHGGG
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 47899999974 5678889988887654
No 16
>PF03634 TCP: TCP family transcription factor; InterPro: IPR005333 The TCP transcription factor family was named after: teosinte branched 1 (tb1, Zea mays (Maize)) [], cycloidea (cyc) (Antirrhinum majus) (Garden snapdragon) [] and PCF in rice (Oryza sativa) [, ]. The TCP proteins code for structurally related proteins implicated in the evolution of key morphological traits []. However, the biochemical function of CYC and TB1 proteins remains to be demonstrated. One of the conserved regions is predicted to form a non-canonical basic-Helix-Loop-Helix (bHLP) structure. This domain is also found in two rice DNA-binding proteins, PCF1 and PCF2, where it has been shown to be involved in DNA-binding and dimerization. This family of transcription factors are exclusive to higher plants. They can be divided into two groups, TCP-C and TCP-P, that appear to have separated following an early gene duplication event []. This duplication event may have led to functional divergence and it has been proposed that that the TCP-P subfamily are transcriptional repressors, while the TPC-C subfamily are transcription activators [].
Probab=20.40 E-value=58 Score=21.39 Aligned_cols=17 Identities=35% Similarity=0.604 Sum_probs=14.4
Q ss_pred ccccccCchhhhhHHHH
Q psy8352 14 MTGIMDHPPTVQWLYVL 30 (69)
Q Consensus 14 Mngvi~h~~tvqwLY~L 30 (69)
|-|.-.-..||.||.+-
T Consensus 38 mLGfDKaSKTveWLL~k 54 (138)
T PF03634_consen 38 MLGFDKASKTVEWLLTK 54 (138)
T ss_pred HhcCCCCCchHHHHHHh
Confidence 67888889999999854
Done!