Query psy6459
Match_columns 66
No_of_seqs 15 out of 17
Neff 1.8
Searched_HMMs 46136
Date Fri Aug 16 18:25:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6459.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6459hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0249|consensus 83.2 0.63 1.4E-05 40.6 1.4 32 31-62 1-32 (916)
2 PF07707 BACK: BTB And C-termi 43.4 29 0.00063 19.6 2.4 32 33-64 55-86 (103)
3 PF14234 DUF4336: Domain of un 42.9 7.1 0.00015 29.6 -0.3 38 17-56 18-76 (285)
4 KOG4797|consensus 40.6 37 0.00079 23.8 3.0 25 33-57 64-89 (123)
5 PF10234 Cluap1: Clusterin-ass 37.6 57 0.0012 24.6 3.8 37 3-48 21-60 (267)
6 PF04458 DUF505: Protein of un 35.8 26 0.00056 29.5 1.9 20 33-52 284-304 (591)
7 PLN00061 photosystem II protei 34.4 42 0.00092 24.0 2.5 36 30-65 104-145 (150)
8 PF15421 Polysacc_deac_3: Puta 32.1 30 0.00064 28.3 1.6 19 1-19 377-395 (425)
9 TIGR03044 PS_II_psb27 photosys 31.9 48 0.001 23.2 2.5 36 30-65 84-124 (135)
10 PF04807 Gemini_AC4_5: Geminiv 30.9 22 0.00047 19.9 0.5 22 2-23 10-31 (33)
11 PF10189 DUF2356: Conserved pr 30.3 26 0.00056 26.2 1.0 57 4-62 165-221 (230)
12 PF00618 RasGEF_N: RasGEF N-te 28.0 92 0.002 18.2 2.9 15 39-53 75-89 (104)
13 PF04325 DUF465: Protein of un 27.6 72 0.0016 17.6 2.3 17 44-60 1-17 (49)
14 PHA02944 hypothetical protein; 26.1 96 0.0021 23.0 3.3 33 21-55 50-83 (180)
15 PF00046 Homeobox: Homeobox do 25.6 45 0.00097 17.7 1.2 25 39-63 10-34 (57)
16 PF01166 TSC22: TSC-22/dip/bun 24.7 30 0.00065 21.5 0.4 24 32-55 10-34 (59)
17 cd07597 BAR_SNX8 The Bin/Amphi 24.5 58 0.0013 23.0 1.9 20 37-56 125-144 (246)
18 smart00875 BACK BTB And C-term 24.5 1.2E+02 0.0025 16.6 2.8 50 3-52 23-74 (101)
19 TIGR01791 CM_archaeal chorisma 24.0 1.6E+02 0.0035 17.2 4.7 55 10-65 18-73 (83)
20 PF07304 SRA1: Steroid recepto 23.1 1E+02 0.0022 20.8 2.8 26 39-64 69-96 (157)
21 PF13326 PSII_Pbs27: Photosyst 22.8 74 0.0016 21.7 2.0 36 30-65 96-137 (145)
22 KOG2737|consensus 22.4 67 0.0015 26.8 2.1 22 33-54 199-231 (492)
23 PF02424 ApbE: ApbE family; I 20.9 2.2E+02 0.0048 20.0 4.2 44 5-48 1-46 (254)
24 PF08385 DHC_N1: Dynein heavy 20.8 2.9E+02 0.0063 20.5 4.9 47 4-50 4-57 (579)
25 PF08158 NUC130_3NT: NUC130/3N 20.7 54 0.0012 19.1 0.9 20 45-64 22-41 (52)
26 KOG3584|consensus 20.7 64 0.0014 25.9 1.6 16 37-52 331-346 (348)
27 PF11590 DNAPolymera_Pol: DNA 20.6 1.3E+02 0.0028 17.6 2.5 23 27-49 14-38 (41)
28 PF06371 Drf_GBD: Diaphanous G 20.4 2.2E+02 0.0048 17.8 3.7 27 31-57 127-153 (187)
29 PF02302 PTS_IIB: PTS system, 20.3 1.6E+02 0.0034 16.6 2.8 22 30-51 6-27 (90)
No 1
>KOG0249|consensus
Probab=83.24 E-value=0.63 Score=40.61 Aligned_cols=32 Identities=3% Similarity=-0.204 Sum_probs=29.1
Q ss_pred cCCchHHHHHHHHHHHHHHHhhHHhHhhhhhh
Q psy6459 31 QSGVSSEAEVLKALKSLFEHHKALDEKGKGTA 62 (66)
Q Consensus 31 ~~gvssEvEVLkALksLFeHHKaLDEKv~~~l 62 (66)
+.++++|+++.++.+++|+||+++|+++|...
T Consensus 1 ~~~e~qel~~~~~~e~~~~~~q~a~~ttr~~e 32 (916)
T KOG0249|consen 1 MTIELQELLEKQQHEQAQSKEQLAPLTTRVPE 32 (916)
T ss_pred CccchHHHHHHHHHHHhhcccccCCCcCCcHH
Confidence 35789999999999999999999999998765
No 2
>PF07707 BACK: BTB And C-terminal Kelch; InterPro: IPR011705 This domain is found associated with (IPR000210 from INTERPRO) and (IPR006652 from INTERPRO). BTB (broad-complex, tramtrack and bric a brac) is a Kelch related domain, also known as the POZ domain []. BTB proteins are divided into subgroups depending on what domain lies at the C terminus. Despite the divergence in sequences, the BTB fold is highly conserved. BTB-Kelch proteins have Kelch repeats that form a beta-propeller that can interact with actin filaments []. BTB and C-terminal Kelch (BACK) together constitute a novel conserved domain, which is thought to have a possible role in substrate orientation in Cullin3-based E3 ligase complexes. Four domains, namely the BTB domain, a kelch domain, a BACK domain, and an intervening region (IVR) make up the aryl hydrocarbon receptor (AHR); a ligand-activated transcription factor []. This entry represents the domain associated with BTB and Kelch.; PDB: 3HVE_A 2EQX_A 3I3N_A 4AP2_A 4APF_A.
Probab=43.42 E-value=29 Score=19.57 Aligned_cols=32 Identities=25% Similarity=0.310 Sum_probs=23.1
Q ss_pred CchHHHHHHHHHHHHHHHhhHHhHhhhhhhhh
Q psy6459 33 GVSSEAEVLKALKSLFEHHKALDEKGKGTAFQ 64 (66)
Q Consensus 33 gvssEvEVLkALksLFeHHKaLDEKv~~~l~~ 64 (66)
.+.+|.+|+.|+..-.+|...-.++.-..++.
T Consensus 55 ~v~~E~~v~~av~~W~~~~~~~r~~~~~~Ll~ 86 (103)
T PF07707_consen 55 NVSSEDDVFEAVLRWLKHNPENREEHLKELLS 86 (103)
T ss_dssp -ECTCCCHHHHHHHHHHCTHHHHTTTHHHHHC
T ss_pred ccccHHHHHHHHHHHHHhCHHHHHHHHHHHHH
Confidence 37899999999999999987744444444443
No 3
>PF14234 DUF4336: Domain of unknown function (DUF4336)
Probab=42.92 E-value=7.1 Score=29.57 Aligned_cols=38 Identities=29% Similarity=0.333 Sum_probs=27.9
Q ss_pred hhhHHHHHHHhhh-----ccCCchHHHHHHHHHHHH----------------HHHhhHHhH
Q psy6459 17 RSLRSTVVKRQAQ-----NQSGVSSEAEVLKALKSL----------------FEHHKALDE 56 (66)
Q Consensus 17 ~Slr~Tv~krqa~-----s~~gvssEvEVLkALksL----------------FeHHKaLDE 56 (66)
-+.||||+|=... ||-..+.| +..++++| +|||.-+.+
T Consensus 18 v~~RMTVVrL~~G~L~VhSPvapT~e--l~~~l~~L~~~~G~VkyIVaPn~~lEH~lfl~~ 76 (285)
T PF14234_consen 18 VPTRMTVVRLSDGGLWVHSPVAPTPE--LKAELDELEAQHGPVKYIVAPNKGLEHHLFLGP 76 (285)
T ss_pred ecceEEEEEECCCCEEEECCCCCCHH--HHHHHHHHhccCCceeEEEcCCcchhHHHhHHH
Confidence 4679999998876 66666665 45666766 889887654
No 4
>KOG4797|consensus
Probab=40.57 E-value=37 Score=23.82 Aligned_cols=25 Identities=40% Similarity=0.585 Sum_probs=20.6
Q ss_pred CchHHHHHHHH-HHHHHHHhhHHhHh
Q psy6459 33 GVSSEAEVLKA-LKSLFEHHKALDEK 57 (66)
Q Consensus 33 gvssEvEVLkA-LksLFeHHKaLDEK 57 (66)
.|..||||||- ++.|-+|..+|.+.
T Consensus 64 AVREEVe~Lk~qI~eL~er~~~Le~E 89 (123)
T KOG4797|consen 64 AVREEVEVLKEQIRELEERNSALERE 89 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 58899999995 67888888888764
No 5
>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].
Probab=37.58 E-value=57 Score=24.59 Aligned_cols=37 Identities=22% Similarity=0.304 Sum_probs=26.4
Q ss_pred hhHHHHHHHHhhhhhhhHHHHHHHhhhccCCchHH---HHHHHHHHHHH
Q psy6459 3 LLLEHLEALVSRHERSLRSTVVKRQAQNQSGVSSE---AEVLKALKSLF 48 (66)
Q Consensus 3 llLehlE~Lvsrhe~Slr~Tv~krqa~s~~gvssE---vEVLkALksLF 48 (66)
|.-|=|.|||-||+|.. .-|+++++| |..+|+.-.+|
T Consensus 21 LVAeiL~WLv~rydP~~---------~i~~~i~tE~dRV~Fik~v~~~~ 60 (267)
T PF10234_consen 21 LVAEILRWLVKRYDPDA---------DIPGDIDTEQDRVFFIKSVAEFM 60 (267)
T ss_pred HHHHHHHHHHHHcCCCC---------CCCCcCCcHHHHHHHHHHHHHHH
Confidence 44577899999999976 356778776 55666655444
No 6
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=35.78 E-value=26 Score=29.55 Aligned_cols=20 Identities=40% Similarity=0.717 Sum_probs=17.8
Q ss_pred Cch-HHHHHHHHHHHHHHHhh
Q psy6459 33 GVS-SEAEVLKALKSLFEHHK 52 (66)
Q Consensus 33 gvs-sEvEVLkALksLFeHHK 52 (66)
.++ .|+||||+++.|+++|+
T Consensus 284 ~le~~E~evLk~I~~lwkk~e 304 (591)
T PF04458_consen 284 ALEEDEVEVLKAIDHLWKKHE 304 (591)
T ss_pred ecchhHHHHHHHHHHHHhhcc
Confidence 556 69999999999999987
No 7
>PLN00061 photosystem II protein Psb27; Provisional
Probab=34.44 E-value=42 Score=23.98 Aligned_cols=36 Identities=25% Similarity=0.211 Sum_probs=30.2
Q ss_pred ccCCchHHHHHHHHHHHHHHHhhH------HhHhhhhhhhhc
Q psy6459 30 NQSGVSSEAEVLKALKSLFEHHKA------LDEKGKGTAFQK 65 (66)
Q Consensus 30 s~~gvssEvEVLkALksLFeHHKa------LDEKv~~~l~~~ 65 (66)
+-+|.+|=..+=+||.+|=.|-+. |.||+|+++-|.
T Consensus 104 ~V~gl~SfttMqtALnsLAghYssyGpnrPLPe~lK~Rll~E 145 (150)
T PLN00061 104 TVAEEESYVELEKAIRSLASFYSKAGPSAPLPEDVKSEILDD 145 (150)
T ss_pred cccccchHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHH
Confidence 446889988888999999999876 589999998764
No 8
>PF15421 Polysacc_deac_3: Putative polysaccharide deacetylase; PDB: 4DWE_A.
Probab=32.05 E-value=30 Score=28.34 Aligned_cols=19 Identities=37% Similarity=0.403 Sum_probs=16.4
Q ss_pred ChhhHHHHHHHHhhhhhhh
Q psy6459 1 MVLLLEHLEALVSRHERSL 19 (66)
Q Consensus 1 mrllLehlE~Lvsrhe~Sl 19 (66)
++.|+||.|..|.|||.+-
T Consensus 377 r~~L~Eha~~fV~~yEa~~ 395 (425)
T PF15421_consen 377 RKYLVEHAEHFVERYEADP 395 (425)
T ss_dssp -TTHHHHHHHHHHHHHHST
T ss_pred HHHHHHHHHHHHHHHhcCc
Confidence 4789999999999999865
No 9
>TIGR03044 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.
Probab=31.93 E-value=48 Score=23.16 Aligned_cols=36 Identities=36% Similarity=0.308 Sum_probs=31.2
Q ss_pred ccCCchHHHHHHHHHHHHHHHhhH-----HhHhhhhhhhhc
Q psy6459 30 NQSGVSSEAEVLKALKSLFEHHKA-----LDEKGKGTAFQK 65 (66)
Q Consensus 30 s~~gvssEvEVLkALksLFeHHKa-----LDEKv~~~l~~~ 65 (66)
.-+|.+|=..+=.||.+|=-|-.. |.||+|+|+.|.
T Consensus 84 ~v~g~~SFttm~TALNsLAGHY~sy~~rPlPeklk~Rl~~E 124 (135)
T TIGR03044 84 RVNGLSSFTTMQTALNSLAGHYKSYANRPLPEKLKERLEKE 124 (135)
T ss_pred CcCCcccHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHH
Confidence 346999988899999999999876 999999999874
No 10
>PF04807 Gemini_AC4_5: Geminivirus AC4/5 conserved region; InterPro: IPR006892 This entry represents a conserved domain found in Gemini virus AC4 and AC5 proteins [].
Probab=30.86 E-value=22 Score=19.90 Aligned_cols=22 Identities=27% Similarity=0.247 Sum_probs=17.6
Q ss_pred hhhHHHHHHHHhhhhhhhHHHH
Q psy6459 2 VLLLEHLEALVSRHERSLRSTV 23 (66)
Q Consensus 2 rllLehlE~Lvsrhe~Slr~Tv 23 (66)
+|..+|.|.|-.=+-++-|.||
T Consensus 10 ~liVkHvk~l~KIl~~~~rsti 31 (33)
T PF04807_consen 10 GLIVKHVKHLTKILWFICRSTI 31 (33)
T ss_pred cchhHHHHHHHHHhhhcccCcC
Confidence 5788999999888877777664
No 11
>PF10189 DUF2356: Conserved protein (DUF2356); InterPro: IPR019333 The Integrator complex is involved in small nuclear RNA (snRNA) U1 and U2 transcription, and in their 3'-box-dependent processing. This complex associates with the C-terminal domain of RNA polymerase II largest subunit and is recruited to the U1 and U2 snRNAs genes []. This entry represents subunit 3 of this complex. The function of this subunit is unknown.
Probab=30.30 E-value=26 Score=26.18 Aligned_cols=57 Identities=23% Similarity=0.286 Sum_probs=36.1
Q ss_pred hHHHHHHHHhhhhhhhHHHHHHHhhhccCCchHHHHHHHHHHHHHHHhhHHhHhhhhhh
Q psy6459 4 LLEHLEALVSRHERSLRSTVVKRQAQNQSGVSSEAEVLKALKSLFEHHKALDEKGKGTA 62 (66)
Q Consensus 4 lLehlE~Lvsrhe~Slr~Tv~krqa~s~~gvssEvEVLkALksLFeHHKaLDEKv~~~l 62 (66)
|||-|=.++..+.++++-.+.+--.++- .+=.|--|..-|--||+++ .||+++|+.+
T Consensus 165 LLeFL~~~v~~~~p~~~~~I~~gV~~a~-~~i~~k~vv~sl~~l~~~~-~ld~~lre~l 221 (230)
T PF10189_consen 165 LLEFLCRIVENFDPPRRDRIRRGVRNAF-RTIVEKGVVPSLSPLFDNP-KLDPELRELL 221 (230)
T ss_pred HHHHHHHHHHHhCccHHHHHHHHHHHHH-HHHHHcCCcCChHHhcCCc-ccCHHHHHHH
Confidence 6777778888888886554433111111 2222334556678899997 5788888765
No 12
>PF00618 RasGEF_N: RasGEF N-terminal motif; InterPro: IPR000651 The crystal structure of the guanine nucleotide exchange factor (GEF) region of human Sos1 complexes with Ras has been solved []. The structure consists of two distinct alpha helical structural domains: the N-terminal domain which seems to have a purely structural role and the C-terminal domain which is sufficient for catalytic activity and contains all residues that interact with Ras. A main feature of the catalytic domain is the protrusion of a helical hairpin important for the nucleotide-exchange mechanism. The N-terminal domain is likely to be important for the stability and correct placement of the hairpin structure. This entry represents a domain found in several GEF for Ras-like small GTPases which lies N-terminal to the RasGef (Cdc25-like) domain. ; GO: 0005085 guanyl-nucleotide exchange factor activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3CF6_E 2BYV_E 1NVW_S 1BKD_S 1XDV_A 2II0_A 1NVU_S 1NVX_S 1NVV_S 1XD4_B ....
Probab=28.00 E-value=92 Score=18.17 Aligned_cols=15 Identities=33% Similarity=0.357 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHhhH
Q psy6459 39 EVLKALKSLFEHHKA 53 (66)
Q Consensus 39 EVLkALksLFeHHKa 53 (66)
-|+++++...+.+..
T Consensus 75 rv~~~l~~Wi~~~~~ 89 (104)
T PF00618_consen 75 RVLNVLKYWIENYPD 89 (104)
T ss_dssp HHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHChH
Confidence 588888888887765
No 13
>PF04325 DUF465: Protein of unknown function (DUF465); InterPro: IPR007420 Family members are found in small bacterial proteins, and also in the heavy chains of eukaryotic myosin and kinesin, C-terminal of the motor domain. Members of this family may form coiled coil structures.; PDB: 1ZHC_A.
Probab=27.60 E-value=72 Score=17.58 Aligned_cols=17 Identities=35% Similarity=0.573 Sum_probs=13.3
Q ss_pred HHHHHHHhhHHhHhhhh
Q psy6459 44 LKSLFEHHKALDEKGKG 60 (66)
Q Consensus 44 LksLFeHHKaLDEKv~~ 60 (66)
+..||+=|.+||.+++.
T Consensus 1 f~~L~~~h~~Ld~~I~~ 17 (49)
T PF04325_consen 1 FARLFEEHHELDKEIHR 17 (49)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHH
Confidence 45788889999988753
No 14
>PHA02944 hypothetical protein; Provisional
Probab=26.13 E-value=96 Score=22.95 Aligned_cols=33 Identities=30% Similarity=0.397 Sum_probs=23.1
Q ss_pred HHHHHHhhhccCCchHHHHHHHHHH-HHHHHhhHHh
Q psy6459 21 STVVKRQAQNQSGVSSEAEVLKALK-SLFEHHKALD 55 (66)
Q Consensus 21 ~Tv~krqa~s~~gvssEvEVLkALk-sLFeHHKaLD 55 (66)
-.|+.|-++..+-...+ |.||++ |+|||--+--
T Consensus 50 k~vL~R~~~Aka~lPed--VvKaaiesv~ehv~aa~ 83 (180)
T PHA02944 50 KEVLRRIAQAKADLPED--VIKAAIESVAEHILSAS 83 (180)
T ss_pred HHHHHHHHHccCCCcHH--HHHHHHHHHHHHHHHHH
Confidence 34667777776666654 679977 9999976543
No 15
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=25.62 E-value=45 Score=17.65 Aligned_cols=25 Identities=20% Similarity=0.274 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHhhHHhHhhhhhhh
Q psy6459 39 EVLKALKSLFEHHKALDEKGKGTAF 63 (66)
Q Consensus 39 EVLkALksLFeHHKaLDEKv~~~l~ 63 (66)
+.++.|...|+.....|...++.|-
T Consensus 10 ~q~~~L~~~f~~~~~p~~~~~~~la 34 (57)
T PF00046_consen 10 EQLKVLEEYFQENPYPSKEEREELA 34 (57)
T ss_dssp HHHHHHHHHHHHSSSCHHHHHHHHH
T ss_pred HHHHHHHHHHHHhcccccccccccc
Confidence 4567788888887777777666654
No 16
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=24.73 E-value=30 Score=21.52 Aligned_cols=24 Identities=38% Similarity=0.481 Sum_probs=15.6
Q ss_pred CCchHHHHHHHH-HHHHHHHhhHHh
Q psy6459 32 SGVSSEAEVLKA-LKSLFEHHKALD 55 (66)
Q Consensus 32 ~gvssEvEVLkA-LksLFeHHKaLD 55 (66)
-.|..||||||. ++.|.+.-..|.
T Consensus 10 ~AVrEEVevLK~~I~eL~~~n~~Le 34 (59)
T PF01166_consen 10 YAVREEVEVLKEQIAELEERNSQLE 34 (59)
T ss_dssp GT-TTSHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 368899999985 455655555544
No 17
>cd07597 BAR_SNX8 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 8. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX8 and the yeast counterpart Mvp1p are involved in sorting and delivery of late-Golgi proteins, such as carboxypeptidase Y, to vacuoles. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=24.48 E-value=58 Score=23.01 Aligned_cols=20 Identities=35% Similarity=0.655 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHhhHHhH
Q psy6459 37 EAEVLKALKSLFEHHKALDE 56 (66)
Q Consensus 37 EvEVLkALksLFeHHKaLDE 56 (66)
=+++|.|+|.||+=|+-+.-
T Consensus 125 ~~d~l~S~r~lf~R~~k~~~ 144 (246)
T cd07597 125 QLDLLVSLRDLFERHEKLSL 144 (246)
T ss_pred HHHHHHHHHHHHHHHHhccc
Confidence 35788899999996664433
No 18
>smart00875 BACK BTB And C-terminal Kelch. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues.
Probab=24.48 E-value=1.2e+02 Score=16.60 Aligned_cols=50 Identities=20% Similarity=0.258 Sum_probs=28.7
Q ss_pred hhHHHHHHHHhhhhh-hhHHHHHHHhhhcc-CCchHHHHHHHHHHHHHHHhh
Q psy6459 3 LLLEHLEALVSRHER-SLRSTVVKRQAQNQ-SGVSSEAEVLKALKSLFEHHK 52 (66)
Q Consensus 3 llLehlE~Lvsrhe~-Slr~Tv~krqa~s~-~gvssEvEVLkALksLFeHHK 52 (66)
.+.+|++.+++.-+. .|-...+..--.++ -.|.+|.+|+.|+..-.+|..
T Consensus 23 ~i~~nf~~~~~~~~f~~L~~~~l~~iL~~d~l~v~~E~~v~~av~~W~~~~~ 74 (101)
T smart00875 23 FILKNFLEVAQSEEFLELSLEQLLSLLSSDDLNVPSEEEVFEAVLRWVKHDP 74 (101)
T ss_pred HHHHHHHHHhcCcHHhcCCHHHHHHHhCcccCCCCCHHHHHHHHHHHHHCCH
Confidence 456777776553121 11112222222232 245679999999999888886
No 19
>TIGR01791 CM_archaeal chorismate mutase, archaeal type. This model represents a clade of archaeal chorismate mutases. Chorismate mutase catalyzes the conversion of chorismate into prephenate which is subsequently converted into either phenylalanine or tyrosine. In Sulfolobus this gene is found as a fusion with prephenate dehydrogenase (although the non-TIGR annotation contains a typographical error indicating it as a dehydratase) which is the next enzyme in the tyrosine biosynthesis pathway. The Archaeoglobus gene contains an N-terminal prephenate dehydrogenase domain and a C-terminal prephenate dehydratase domain followed by a regulatory amino acid-binding ACT domain. The Thermoplasma volcanium gene is adjacent to prephenate dehydratase.
Probab=23.97 E-value=1.6e+02 Score=17.19 Aligned_cols=55 Identities=15% Similarity=0.100 Sum_probs=36.3
Q ss_pred HHHhhhhhhhHHHHHHHhhhccCCc-hHHHHHHHHHHHHHHHhhHHhHhhhhhhhhc
Q psy6459 10 ALVSRHERSLRSTVVKRQAQNQSGV-SSEAEVLKALKSLFEHHKALDEKGKGTAFQK 65 (66)
Q Consensus 10 ~Lvsrhe~Slr~Tv~krqa~s~~gv-ssEvEVLkALksLFeHHKaLDEKv~~~l~~~ 65 (66)
-|.-|..-+-+..-.|...+.|--- ..|-+|+..+..+-+. ..+|+..-..+|+.
T Consensus 18 Ll~~R~~l~~~i~~~K~~~g~~i~d~~RE~~v~~~~~~~~~~-~~l~~~~i~~if~~ 73 (83)
T TIGR01791 18 LIEKRIKIARKIGEIKHNNGLPITDEEREERVIERLRNTARN-LGLDVLKLKEIFEI 73 (83)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHh-cCCCHHHHHHHHHH
Confidence 3444555555666667766555333 3499999998877765 35888877778764
No 20
>PF07304 SRA1: Steroid receptor RNA activator (SRA1); InterPro: IPR009917 This entry consists of several hypothetical mammalian steroid receptor RNA activator proteins. The SRA-RNAs encode stable proteins that are widely expressed and upregulated in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA. This domain is also found at the C terminus of Sec31, a component of the coat protein complex II (COPII, which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). COPII has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. ; PDB: 2YRU_A.
Probab=23.12 E-value=1e+02 Score=20.84 Aligned_cols=26 Identities=27% Similarity=0.368 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHhhH--HhHhhhhhhhh
Q psy6459 39 EVLKALKSLFEHHKA--LDEKGKGTAFQ 64 (66)
Q Consensus 39 EVLkALksLFeHHKa--LDEKv~~~l~~ 64 (66)
++=|.|.-||+|-+. |..-|.++|++
T Consensus 69 D~~KRL~iLfd~ln~g~Ls~~v~~~L~~ 96 (157)
T PF07304_consen 69 DIEKRLNILFDHLNNGKLSKPVVDKLHQ 96 (157)
T ss_dssp HHHHHHHHHHHHHHHT-S-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHH
Confidence 788999999999874 77777777654
No 21
>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A.
Probab=22.77 E-value=74 Score=21.66 Aligned_cols=36 Identities=31% Similarity=0.332 Sum_probs=27.7
Q ss_pred ccCCchHHHHHHHHHHHHHHHhh------HHhHhhhhhhhhc
Q psy6459 30 NQSGVSSEAEVLKALKSLFEHHK------ALDEKGKGTAFQK 65 (66)
Q Consensus 30 s~~gvssEvEVLkALksLFeHHK------aLDEKv~~~l~~~ 65 (66)
+-.|-.|=..+=.||.+|=.|.. .|.+|+|+++.+.
T Consensus 96 ~v~g~~Sf~~m~tAln~LaghY~s~g~raPlP~k~k~rll~e 137 (145)
T PF13326_consen 96 SVSGLPSFTTMYTALNALAGHYSSYGNRAPLPEKLKERLLKE 137 (145)
T ss_dssp HCCTSHHHHHHHHHHHHHHHHCHHHTTS-S--HHHHHHHHHH
T ss_pred CcCCcchHHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHH
Confidence 44588887777799999999986 4899999998764
No 22
>KOG2737|consensus
Probab=22.43 E-value=67 Score=26.83 Aligned_cols=22 Identities=55% Similarity=0.720 Sum_probs=16.4
Q ss_pred CchHH--HHHHHH---------HHHHHHHhhHH
Q psy6459 33 GVSSE--AEVLKA---------LKSLFEHHKAL 54 (66)
Q Consensus 33 gvssE--vEVLkA---------LksLFeHHKaL 54 (66)
-+||| ++|+|| +.|||+||-..
T Consensus 199 kISseaH~~vM~~~~pg~~Eyq~eslF~hh~y~ 231 (492)
T KOG2737|consen 199 KISSEAHIEVMRAVRPGMKEYQLESLFLHHSYS 231 (492)
T ss_pred hhccHHHHHHHHhCCchHhHHhHHHHHHHhhhc
Confidence 35664 788987 57999999753
No 23
>PF02424 ApbE: ApbE family; InterPro: IPR003374 This prokaryotic family of lipoproteins are related to ApbE, from Salmonella typhimurium. ApbE is involved in thiamine synthesis []. More specifically is may be involved in the conversion of aminoimidazole ribotide (AIR) to 4-amino-5-hydroxymethyl-2-methyl pyrimidine (HMP) during the biosynthesis of the pyrimidine moiety of thiamine.; PDB: 2O34_B 2O18_C 1VRM_A 3PND_D.
Probab=20.92 E-value=2.2e+02 Score=19.96 Aligned_cols=44 Identities=25% Similarity=0.270 Sum_probs=24.0
Q ss_pred HHHHHHHHhhhhhhhHHHHHHHhhh-ccCCchHHH-HHHHHHHHHH
Q psy6459 5 LEHLEALVSRHERSLRSTVVKRQAQ-NQSGVSSEA-EVLKALKSLF 48 (66)
Q Consensus 5 LehlE~Lvsrhe~Slr~Tv~krqa~-s~~gvssEv-EVLkALksLF 48 (66)
++++|...|||.+.=-....-|++. .+--||.|+ ++|+.-..++
T Consensus 1 ~~~le~~~S~~~~~SeisrlN~~~~~~~v~v~~e~~~ll~~a~~~~ 46 (254)
T PF02424_consen 1 IDRLERKLSRYRPDSEISRLNRAAGGQPVEVSPELYELLELALEIS 46 (254)
T ss_dssp HHHHHHHH-SSSTTSHHHHHHHS-S-S-EEE-HHHHHHHHHHHHHH
T ss_pred ChhHHhhhCCCCCcCHHHHHhcCCCCCcEeCCHHHHHHHHHHHHHH
Confidence 5789999999987543344444443 344667764 5555544443
No 24
>PF08385 DHC_N1: Dynein heavy chain, N-terminal region 1; InterPro: IPR013594 Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit []. The region featured in this family includes the sequences implicated in mediating these interactions []. It is thought to be flexible and not to adopt a rigid conformation [].
Probab=20.85 E-value=2.9e+02 Score=20.50 Aligned_cols=47 Identities=21% Similarity=0.388 Sum_probs=36.0
Q ss_pred hHHHHHHHHhhhhhhhHHHHHHHhhhcc---CCchHHHHHHH----HHHHHHHH
Q psy6459 4 LLEHLEALVSRHERSLRSTVVKRQAQNQ---SGVSSEAEVLK----ALKSLFEH 50 (66)
Q Consensus 4 lLehlE~Lvsrhe~Slr~Tv~krqa~s~---~gvssEvEVLk----ALksLFeH 50 (66)
++..||..|...-+.++..+.......+ +|...|++--+ +|.+|.+.
T Consensus 4 ~~~~le~~v~~W~~qI~~vl~~~~~~~~~~~~~p~~Ei~fW~~r~~~L~~i~~Q 57 (579)
T PF08385_consen 4 FLNSLESIVIQWIKQIQKVLSLSSDPRSGDNPGPLDEIEFWRSREENLSSIYEQ 57 (579)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCcccccCCCCChHHHHHHHHHHHHHHHHHHHH
Confidence 6789999999999999888776666666 78889998654 45555543
No 25
>PF08158 NUC130_3NT: NUC130/3NT domain; InterPro: IPR012977 This N-terminal domain is found in a novel nucleolar protein family defined by NUC130/133 [].
Probab=20.74 E-value=54 Score=19.10 Aligned_cols=20 Identities=25% Similarity=0.273 Sum_probs=16.3
Q ss_pred HHHHHHhhHHhHhhhhhhhh
Q psy6459 45 KSLFEHHKALDEKGKGTAFQ 64 (66)
Q Consensus 45 ksLFeHHKaLDEKv~~~l~~ 64 (66)
..|=+||..||..+|..+.+
T Consensus 22 ~lL~~~~~~L~p~lR~~lv~ 41 (52)
T PF08158_consen 22 DLLRNHHTVLDPDLRMKLVK 41 (52)
T ss_pred HHHHhccccCCHHHHHHHHH
Confidence 34668999999999998765
No 26
>KOG3584|consensus
Probab=20.70 E-value=64 Score=25.90 Aligned_cols=16 Identities=44% Similarity=0.544 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHhh
Q psy6459 37 EAEVLKALKSLFEHHK 52 (66)
Q Consensus 37 EvEVLkALksLFeHHK 52 (66)
=||=||+||.||-|-+
T Consensus 331 LIEELKtLKeLYc~k~ 346 (348)
T KOG3584|consen 331 LIEELKTLKELYCHKS 346 (348)
T ss_pred HHHHHHHHHHHhhccc
Confidence 4888999999998854
No 27
>PF11590 DNAPolymera_Pol: DNA polymerase catalytic subunit Pol; InterPro: IPR021639 This family of proteins represents the catalytic subunit, Pol, of the Herpes simplex virus DNA polymerase. Pol binds UL42, making up the DNA polymerase. UL42 is a processivity subunit which binds to the C-terminal of Pol in a similar way that the cell cycle regulator p21 binds to PCNA []. ; GO: 0003887 DNA-directed DNA polymerase activity, 0004523 ribonuclease H activity; PDB: 1DML_H.
Probab=20.59 E-value=1.3e+02 Score=17.62 Aligned_cols=23 Identities=26% Similarity=0.455 Sum_probs=14.4
Q ss_pred hhhccCCchH--HHHHHHHHHHHHH
Q psy6459 27 QAQNQSGVSS--EAEVLKALKSLFE 49 (66)
Q Consensus 27 qa~s~~gvss--EvEVLkALksLFe 49 (66)
...+++|+++ |.|-.+.|..-|+
T Consensus 14 ~i~~g~g~~~~~eeEt~qkL~~AF~ 38 (41)
T PF11590_consen 14 TIGSGAGLPSSEEEETRQKLRRAFD 38 (41)
T ss_dssp EECTTS------HHHHHHHHHHHHH
T ss_pred HhccCccccchhhHHHHHHHHHHHH
Confidence 4457888776 8899988887664
No 28
>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=20.38 E-value=2.2e+02 Score=17.81 Aligned_cols=27 Identities=26% Similarity=0.444 Sum_probs=20.7
Q ss_pred cCCchHHHHHHHHHHHHHHHhhHHhHh
Q psy6459 31 QSGVSSEAEVLKALKSLFEHHKALDEK 57 (66)
Q Consensus 31 ~~gvssEvEVLkALksLFeHHKaLDEK 57 (66)
..-..-|.++|+.+|.|..+.-.++.=
T Consensus 127 ~~~~~~~~~~l~Clkal~n~~~G~~~v 153 (187)
T PF06371_consen 127 EEDIDIEHECLRCLKALMNTKYGLEAV 153 (187)
T ss_dssp TTCHHHHHHHHHHHHHHTSSHHHHHHH
T ss_pred chhHHHHHHHHHHHHHHHccHHHHHHH
Confidence 344566899999999999988766643
No 29
>PF02302 PTS_IIB: PTS system, Lactose/Cellobiose specific IIB subunit; InterPro: IPR003501 The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This signature is often found downstream of IPR003352 from INTERPRO.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TVM_A 2WY2_D 1IIB_A 2WWV_D 1H9C_A 1E2B_A 2L2Q_A 2KYR_A 3CZC_A 3NBM_A ....
Probab=20.33 E-value=1.6e+02 Score=16.59 Aligned_cols=22 Identities=18% Similarity=0.262 Sum_probs=16.9
Q ss_pred ccCCchHHHHHHHHHHHHHHHh
Q psy6459 30 NQSGVSSEAEVLKALKSLFEHH 51 (66)
Q Consensus 30 s~~gvssEvEVLkALksLFeHH 51 (66)
+++|++|=.-+-.+++..++-+
T Consensus 6 C~~Gi~TS~~~~~~i~~~~~~~ 27 (90)
T PF02302_consen 6 CGSGIGTSLMVANKIKKALKEL 27 (90)
T ss_dssp ESSSSHHHHHHHHHHHHHHHHT
T ss_pred CCChHHHHHHHHHHHHHHHHhc
Confidence 7899999887777888766543
Done!