Query psy12551
Match_columns 66
No_of_seqs 101 out of 121
Neff 3.1
Searched_HMMs 46136
Date Fri Aug 16 22:15:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12551.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12551hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0985|consensus 99.9 2.9E-27 6.2E-32 201.0 1.1 59 5-65 792-850 (1666)
2 PF00658 PABP: Poly-adenylate 71.1 0.43 9.3E-06 29.4 -2.2 29 19-49 29-57 (72)
3 smart00517 PolyA C-terminal do 64.7 1.5 3.3E-05 26.9 -0.6 28 19-48 18-45 (64)
4 PF07499 RuvA_C: RuvA, C-termi 62.3 14 0.0003 20.4 3.0 37 27-63 4-42 (47)
5 KOG3449|consensus 50.1 21 0.00047 24.3 2.9 32 30-62 23-57 (112)
6 TIGR00299 conserved hypothetic 49.7 14 0.0003 29.1 2.2 24 28-51 14-37 (382)
7 cd03400 Band_7_1 A subgroup of 49.2 18 0.00039 22.4 2.3 54 6-61 20-77 (124)
8 COG1641 Uncharacterized conser 49.0 11 0.00023 30.4 1.5 28 25-52 12-39 (387)
9 PRK04194 hypothetical protein; 49.0 15 0.00032 28.9 2.3 24 28-51 16-39 (392)
10 PF03911 Sec61_beta: Sec61beta 46.0 8.2 0.00018 21.5 0.4 21 4-24 1-21 (41)
11 KOG2595|consensus 44.7 14 0.0003 29.9 1.5 31 32-62 265-295 (395)
12 PF09457 RBD-FIP: FIP domain ; 39.5 23 0.00051 20.5 1.6 16 40-55 27-42 (48)
13 PF12986 DUF3870: Domain of un 37.4 5.7 0.00012 25.5 -1.3 34 31-64 33-72 (96)
14 PLN00138 large subunit ribosom 36.9 21 0.00046 23.7 1.3 36 26-62 19-57 (113)
15 PF14383 VARLMGL: DUF761-assoc 35.4 18 0.00039 20.2 0.6 17 22-38 10-26 (34)
16 PF06029 AlkA_N: AlkA N-termin 34.3 33 0.00071 22.4 1.9 26 22-47 67-95 (116)
17 PF01969 DUF111: Protein of un 34.2 13 0.00029 29.0 0.0 26 27-52 12-37 (382)
18 COG4803 Predicted membrane pro 31.0 34 0.00074 24.9 1.6 26 26-51 89-114 (170)
19 PF05047 L51_S25_CI-B8: Mitoch 29.7 20 0.00044 19.6 0.2 21 12-35 19-39 (52)
20 PF09427 DUF2014: Domain of un 29.4 33 0.00071 26.3 1.4 29 22-50 119-147 (260)
21 PF12916 DUF3834: Protein of u 28.3 3.4 7.4E-05 30.5 -3.9 47 4-50 149-198 (201)
22 PF08973 TM1506: Domain of unk 27.9 16 0.00035 24.9 -0.4 16 51-66 106-121 (134)
23 cd05832 Ribosomal_L12p Ribosom 27.6 88 0.0019 20.7 3.1 34 29-63 21-57 (106)
24 PF11378 DUF3181: Protein of u 27.1 73 0.0016 20.8 2.5 22 28-50 34-55 (87)
25 KOG3036|consensus 26.0 40 0.00088 26.3 1.4 22 27-49 146-167 (293)
26 PF08850 DUF1820: Domain of un 24.7 31 0.00067 23.0 0.5 56 8-65 11-78 (100)
27 KOG4311|consensus 23.4 33 0.00072 27.3 0.5 10 37-46 212-221 (359)
28 cd02412 30S_S3_KH K homology R 23.2 31 0.00068 21.9 0.3 6 18-23 1-6 (109)
29 PF05585 DUF1758: Putative pep 22.0 50 0.0011 21.6 1.1 29 21-49 4-32 (164)
30 cd01896 DRG The developmentall 21.7 1.2E+02 0.0026 21.1 3.0 29 36-64 134-171 (233)
31 PF08142 AARP2CN: AARP2CN (NUC 21.6 68 0.0015 19.9 1.6 17 9-25 47-63 (85)
32 PF01551 Peptidase_M23: Peptid 21.6 43 0.00094 19.7 0.6 15 9-23 82-96 (96)
33 TIGR01639 P_fal_TIGR01639 Plas 20.8 1.3E+02 0.0028 17.5 2.6 23 38-60 10-32 (61)
34 TIGR03685 L21P_arch 50S riboso 20.5 1.5E+02 0.0032 19.3 3.0 35 28-63 20-57 (105)
35 COG1163 DRG Predicted GTPase [ 20.4 1.1E+02 0.0024 24.6 2.9 36 30-65 190-235 (365)
No 1
>KOG0985|consensus
Probab=99.93 E-value=2.9e-27 Score=200.99 Aligned_cols=59 Identities=63% Similarity=0.917 Sum_probs=58.3
Q ss_pred CCCCcceeeEeeceeecCCCCcchhhhhhhccCCCHHHHHHHHHHhccCCChhhhhhhccC
Q psy12551 5 SKSGLTYIPVVLRQSQVNPSRLPVVVGGLLDVDCSEDIIKNLILVVRGQFSTDELVEEDKI 65 (66)
Q Consensus 5 ~n~~~kyIEvYV~~qkVNP~~tP~VVG~LLDvdc~E~~Ik~LL~sV~~~~pideLVeEvE~ 65 (66)
+|+++||||+|| |||||+|||+|||+|||+|||||+||+||+||+|++|+||||+||||
T Consensus 792 rnn~~kyIE~yV--QkvNps~~p~VvG~LLD~dC~E~~ik~Li~~v~gq~~~deLv~EvEk 850 (1666)
T KOG0985|consen 792 RNNLQKYIEIYV--QKVNPSRTPQVVGALLDVDCSEDFIKNLILSVRGQFPVDELVEEVEK 850 (1666)
T ss_pred HhhHHHHHHHHH--hhcCCcccchhhhhhhcCCCcHHHHHHHHHHHhccCChHHHHHHHHh
Confidence 699999999999 99999999999999999999999999999999999999999999998
No 2
>PF00658 PABP: Poly-adenylate binding protein, unique domain; InterPro: IPR002004 The polyadenylate-binding protein (PABP) has a conserved C-terminal domain (PABC), which is also found in the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains (IPR000569 from INTERPRO) []. PABP recognises the 3' mRNA poly(A) tail and plays an essential role in eukaryotic translation initiation and mRNA stabilisation/degradation. PABC domains of PABP are peptide-binding domains that mediate PABP homo-oligomerisation and protein-protein interactions. In mammals, the PABC domain of PABP functions to recruit several different translation factors to the mRNA poly(A) tail [].; GO: 0003723 RNA binding; PDB: 3KUR_E 1JH4_A 2RQH_B 3KUI_A 3KUS_A 3KUJ_A 3KTR_A 2X04_A 3PTH_A 1JGN_A ....
Probab=71.12 E-value=0.43 Score=29.36 Aligned_cols=29 Identities=28% Similarity=0.381 Sum_probs=22.6
Q ss_pred eecCCCCcchhhhhhhccCCCHHHHHHHHHH
Q psy12551 19 SQVNPSRLPVVVGGLLDVDCSEDIIKNLILV 49 (66)
Q Consensus 19 qkVNP~~tP~VVG~LLDvdc~E~~Ik~LL~s 49 (66)
+..+|..+|.+-|-|||.|-+| +-+||.+
T Consensus 29 ~~~~p~~A~KITGMLLe~~~~e--ll~ll~~ 57 (72)
T PF00658_consen 29 QAIYPELAGKITGMLLEMDNSE--LLHLLED 57 (72)
T ss_dssp HHHTHHHHHHHHHHHTTSCHHH--HHHHHHT
T ss_pred HHhCcchhHHHHHHHhcCCHHH--HHHHhCC
Confidence 5788999999999999987544 5566654
No 3
>smart00517 PolyA C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. Involved in homodimerisation (either directly or indirectly)
Probab=64.69 E-value=1.5 Score=26.85 Aligned_cols=28 Identities=29% Similarity=0.440 Sum_probs=22.1
Q ss_pred eecCCCCcchhhhhhhccCCCHHHHHHHHH
Q psy12551 19 SQVNPSRLPVVVGGLLDVDCSEDIIKNLIL 48 (66)
Q Consensus 19 qkVNP~~tP~VVG~LLDvdc~E~~Ik~LL~ 48 (66)
++..|.-++.|-|-||++|-+| |-+||.
T Consensus 18 ~~~~p~~A~KITGMLLEmd~~e--ll~lle 45 (64)
T smart00517 18 QALEPELAGKITGMLLEMDNSE--LLHLLE 45 (64)
T ss_pred HhhCcccCCcCeeeeeCCCHHH--HHHHhc
Confidence 6788999999999999998755 334443
No 4
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=62.29 E-value=14 Score=20.40 Aligned_cols=37 Identities=11% Similarity=0.244 Sum_probs=30.0
Q ss_pred chhhhhhhccCCCHHHHHHHHHHh--ccCCChhhhhhhc
Q psy12551 27 PVVVGGLLDVDCSEDIIKNLILVV--RGQFSTDELVEED 63 (66)
Q Consensus 27 P~VVG~LLDvdc~E~~Ik~LL~sV--~~~~pideLVeEv 63 (66)
..++.+|+-+.=++.-+...+..+ ....++++++.+.
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~~~~~~~~~e~~ik~a 42 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKLLEKPGMDVEELIKQA 42 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHHHHSTTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhhcCCCCCHHHHHHHH
Confidence 468899999999999999999999 5788899988763
No 5
>KOG3449|consensus
Probab=50.07 E-value=21 Score=24.32 Aligned_cols=32 Identities=16% Similarity=0.458 Sum_probs=24.9
Q ss_pred hhhhhc---cCCCHHHHHHHHHHhccCCChhhhhhh
Q psy12551 30 VGGLLD---VDCSEDIIKNLILVVRGQFSTDELVEE 62 (66)
Q Consensus 30 VG~LLD---vdc~E~~Ik~LL~sV~~~~pideLVeE 62 (66)
|-.+|+ .+++.+.|..+|..+.|. .|+||+.+
T Consensus 23 ikkIl~sVG~E~d~e~i~~visel~GK-~i~ElIA~ 57 (112)
T KOG3449|consen 23 IKKILESVGAEIDDERINLVLSELKGK-DIEELIAA 57 (112)
T ss_pred HHHHHHHhCcccCHHHHHHHHHHhcCC-CHHHHHHH
Confidence 445555 788888888888888887 88888864
No 6
>TIGR00299 conserved hypothetical protein TIGR00299. Members of this family are found in the Archaea and in several different bacteria lineages. The function in unknown and the genomic context is not well conserved.
Probab=49.73 E-value=14 Score=29.11 Aligned_cols=24 Identities=13% Similarity=0.357 Sum_probs=21.6
Q ss_pred hhhhhhhccCCCHHHHHHHHHHhc
Q psy12551 28 VVVGGLLDVDCSEDIIKNLILVVR 51 (66)
Q Consensus 28 ~VVG~LLDvdc~E~~Ik~LL~sV~ 51 (66)
+.+|+|||+..|.+.++..|.++.
T Consensus 14 M~lgALldlG~~~~~l~~~l~~l~ 37 (382)
T TIGR00299 14 MCLGALIDAGVPLEYLMEVLKPLG 37 (382)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhCC
Confidence 578999999999999999999774
No 7
>cd03400 Band_7_1 A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions. Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins. Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins. Prokaryotic H
Probab=49.18 E-value=18 Score=22.39 Aligned_cols=54 Identities=20% Similarity=0.391 Sum_probs=35.9
Q ss_pred CCCcceeeEeeceeecCCCCcchhhhhhhccCCCHHHHHH----HHHHhccCCChhhhhh
Q psy12551 6 KSGLTYIPVVLRQSQVNPSRLPVVVGGLLDVDCSEDIIKN----LILVVRGQFSTDELVE 61 (66)
Q Consensus 6 n~~~kyIEvYV~~qkVNP~~tP~VVG~LLDvdc~E~~Ik~----LL~sV~~~~pideLVe 61 (66)
.++.=-++++| +-+|+|.+++.+.-.+ ..+-.+.+|+. .+.++.|...+++++.
T Consensus 20 D~~~v~vd~~v-~y~V~~~~~~~~~~~~-~~~~~~~~i~~~~~~~lR~~~~~~~~~e~i~ 77 (124)
T cd03400 20 EGLSINADVSV-QYRINPNKAAAVHSKL-GTDYARKIVRPTFRSLVREVTGRYTAEQIYS 77 (124)
T ss_pred CCCEEEEEEEE-EEEEChhhHHHHHHHh-CcchhheeechhHHHHHHHHhcCCCHHHHhh
Confidence 34444567787 5689999999887654 22223334444 4666778999999874
No 8
>COG1641 Uncharacterized conserved protein [Function unknown]
Probab=48.99 E-value=11 Score=30.40 Aligned_cols=28 Identities=14% Similarity=0.382 Sum_probs=24.2
Q ss_pred CcchhhhhhhccCCCHHHHHHHHHHhcc
Q psy12551 25 RLPVVVGGLLDVDCSEDIIKNLILVVRG 52 (66)
Q Consensus 25 ~tP~VVG~LLDvdc~E~~Ik~LL~sV~~ 52 (66)
.-=+++|+|+|+..|.++|++.+..+..
T Consensus 12 SGDM~LgaLidlGv~~e~~~e~v~~l~~ 39 (387)
T COG1641 12 SGDMILGALIDLGVDPEYLKEVVEALGP 39 (387)
T ss_pred chhhHHHHHHHcCCCHHHHHHHHHhcCc
Confidence 3447899999999999999999988765
No 9
>PRK04194 hypothetical protein; Provisional
Probab=48.97 E-value=15 Score=28.93 Aligned_cols=24 Identities=17% Similarity=0.393 Sum_probs=21.8
Q ss_pred hhhhhhhccCCCHHHHHHHHHHhc
Q psy12551 28 VVVGGLLDVDCSEDIIKNLILVVR 51 (66)
Q Consensus 28 ~VVG~LLDvdc~E~~Ik~LL~sV~ 51 (66)
..+|+|||+..|.+.|+..|.++.
T Consensus 16 M~lgALldlG~~~~~l~~~l~~l~ 39 (392)
T PRK04194 16 MLLGALLDLGVDLEYLEAELAKLG 39 (392)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhcC
Confidence 578999999999999999999774
No 10
>PF03911 Sec61_beta: Sec61beta family; InterPro: IPR005609 This family consists of Sec61 subunit beta and homologues like archaeal SecG. This subunit is a component of the Sec61/SecYEG protein secretory system.; PDB: 2WWA_C 2WW9_C 3BO0_C 3KCR_C 3BO1_C 2YXR_C 3DKN_C 2YXQ_C 1RH5_C 1RHZ_C ....
Probab=46.04 E-value=8.2 Score=21.45 Aligned_cols=21 Identities=24% Similarity=0.243 Sum_probs=6.0
Q ss_pred CCCCCcceeeEeeceeecCCC
Q psy12551 4 SSKSGLTYIPVVLRQSQVNPS 24 (66)
Q Consensus 4 ~~n~~~kyIEvYV~~qkVNP~ 24 (66)
|++++.||-|-.-.|-|++|.
T Consensus 1 Ssagl~r~y~ed~~giki~P~ 21 (41)
T PF03911_consen 1 SSAGLLRYYEEDAPGIKIDPK 21 (41)
T ss_dssp ------------S-SS-BSCC
T ss_pred CCCcceeeeeccCCcceeCCe
Confidence 788999999999988899985
No 11
>KOG2595|consensus
Probab=44.71 E-value=14 Score=29.87 Aligned_cols=31 Identities=23% Similarity=0.561 Sum_probs=28.2
Q ss_pred hhhccCCCHHHHHHHHHHhccCCChhhhhhh
Q psy12551 32 GLLDVDCSEDIIKNLILVVRGQFSTDELVEE 62 (66)
Q Consensus 32 ~LLDvdc~E~~Ik~LL~sV~~~~pideLVeE 62 (66)
..|++|||-.+...||..+....|+|+|+.+
T Consensus 265 eIl~~~~dms~~H~lLs~iPq~lp~d~lik~ 295 (395)
T KOG2595|consen 265 EILKCDCDMSLLHGLLSTIPQDLPYDTLIKE 295 (395)
T ss_pred HHHHHHhhhHHHHHHHHhCccccCHHHHHHH
Confidence 3678999999999999999999999999876
No 12
>PF09457 RBD-FIP: FIP domain ; InterPro: IPR019018 The Rab11 GTPase regulates recycling of internalized plasma membrane receptors and is essential for completion of cytokinesis. A family of Rab11 interacting proteins (FIPs) that conserve a C-terminal Rab-binding domain (RBD) selectively recognise the active form of Rab11. FIPs are diverse in sequence length and composition toward their N-termini, presumably a feature that underpins their specific roles in Rab11-mediated vesicle trafficking. They have been divided into three subfamilies (classe I, II, and III)on the basis of domain architecture. Class I FIPs comprises a subfamily of three proteins (Rip11/pp75/FIP5, Rab-coupling protein (RCP), and FIP2) that possess an N- terminal C2 domain, localize to recycling endosomes, and regulate plasma membrane recycling. The class II subfamily consists of two proteins (FIP3/eferin/arfophilin and FIP4) with tandem EF hands and a proline-rich region. Class II FIPs localize to recycling endosomes, the trans-Golgi network, and have been implicated in the regulation of membrane trafficking during cytokinesis. The class III subfamily consists of a single protein, FIP1, which does not contain obvious homology domains or motifs other than the FIP-RBD [, , , ]. The FIP-RBD domain is also found in Rab6-interacting protein Erc1/Elks. Erc1 is the regulatory subunit of the IKK complex and probably recruits IkappaBalpha/NFKBIA to the complex []. It may be involved in the organisation of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. It may also be involved in vesicle trafficking at the CAZ, as well as in Rab-6 regulated endosomes to Golgi transport []. The FIB-RBD domain consists of an N-terminal long alpha-helix, followed by a 90 degrees bend at a conserved proline residue, a 3(10) helix and a C-terminal short beta-strand, adopting an "L" shape. The long alpha-helix forms a parallel coiled-coil homodimer that symmetrically interacts with two Rab11 molecules on both sides, forming a quaternary Rab11-(FIP)2-Rab11 complex. The Rab11-interacting region of FIP-RBD is confined to the C-terminal 24 amino acids, which cover the C-terminal half of the long alpha-helix and the short beta-strand [, , , ]. This entry represents the FIP-RBD domain.; PDB: 2HV8_E 2D7C_D 2K6S_B 2GZD_D 2GZH_B.
Probab=39.49 E-value=23 Score=20.52 Aligned_cols=16 Identities=44% Similarity=0.507 Sum_probs=13.1
Q ss_pred HHHHHHHHHHhccCCC
Q psy12551 40 EDIIKNLILVVRGQFS 55 (66)
Q Consensus 40 E~~Ik~LL~sV~~~~p 55 (66)
|+||.+||..|....|
T Consensus 27 e~YiD~LL~rVmE~~P 42 (48)
T PF09457_consen 27 EDYIDNLLVRVMEQTP 42 (48)
T ss_dssp HHHHHHHHHHHHCC-G
T ss_pred HHHHHHHHHHHHHhCc
Confidence 7899999999977666
No 13
>PF12986 DUF3870: Domain of unknown function (DUF3870); InterPro: IPR024617 This domain is found in the C-terminal region of the putative pore-forming toxin YP_001301288.1 from Bacteroides vulgatus ATCC3 [, ], suggesting that the domain may have a lytic function.; PDB: 3KOG_A.
Probab=37.41 E-value=5.7 Score=25.52 Aligned_cols=34 Identities=26% Similarity=0.476 Sum_probs=13.9
Q ss_pred hhhhccCCC------HHHHHHHHHHhccCCChhhhhhhcc
Q psy12551 31 GGLLDVDCS------EDIIKNLILVVRGQFSTDELVEEDK 64 (66)
Q Consensus 31 G~LLDvdc~------E~~Ik~LL~sV~~~~pideLVeEvE 64 (66)
|..+|.||+ .+||++|+..-.=.--.++|++|++
T Consensus 33 g~Ivda~ct~~~~lt~~FI~~l~~G~~l~~~~~~l~~~i~ 72 (96)
T PF12986_consen 33 GKIVDADCTLTTELTREFIRSLFVGKNLTDDEEELEKEIE 72 (96)
T ss_dssp EEEE---S--HH------HHHHHHHT-SEEEEEEEEE-EE
T ss_pred CEEEEEEeeeehhhhHHHHHHHHcccccccchHHHHHHHH
Confidence 445688886 5779999854321111456666554
No 14
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=36.88 E-value=21 Score=23.69 Aligned_cols=36 Identities=25% Similarity=0.345 Sum_probs=26.6
Q ss_pred cchhhhhhhc---cCCCHHHHHHHHHHhccCCChhhhhhh
Q psy12551 26 LPVVVGGLLD---VDCSEDIIKNLILVVRGQFSTDELVEE 62 (66)
Q Consensus 26 tP~VVG~LLD---vdc~E~~Ik~LL~sV~~~~pideLVeE 62 (66)
|..-|-++|+ ++++++.++.++..+.+ -+|+||+.+
T Consensus 19 ta~dI~~IL~AaGvevd~~~~~~f~~~L~g-K~i~eLIa~ 57 (113)
T PLN00138 19 SAEDLKDILGSVGADADDDRIELLLSEVKG-KDITELIAS 57 (113)
T ss_pred CHHHHHHHHHHcCCcccHHHHHHHHHHHcC-CCHHHHHHh
Confidence 3445666666 78888888888888865 678888864
No 15
>PF14383 VARLMGL: DUF761-associated sequence motif
Probab=35.35 E-value=18 Score=20.16 Aligned_cols=17 Identities=35% Similarity=0.522 Sum_probs=13.7
Q ss_pred CCCCcchhhhhhhccCC
Q psy12551 22 NPSRLPVVVGGLLDVDC 38 (66)
Q Consensus 22 NP~~tP~VVG~LLDvdc 38 (66)
...|+|.||+.|.-+|-
T Consensus 10 ~~~r~P~vvarLMGld~ 26 (34)
T PF14383_consen 10 PGTRAPGVVARLMGLDS 26 (34)
T ss_pred ccccChhHHHHHhcccc
Confidence 35789999999987763
No 16
>PF06029 AlkA_N: AlkA N-terminal domain; InterPro: IPR010316 This domain is found at the N terminus of bacterial AlkA 3.2.2.21 from EC. AlkA (3-methyladenine-DNA glycosylase II) is a base excision repair glycosylase from Escherichia coli. It removes a variety of alkylated bases from DNA, primarily by removing alkylation damage from duplex and single stranded DNA. AlkA flips a 1-azaribose abasic nucleotide out of DNA. This produces a 66 degrees bend in the DNA and a marked widening of the minor groove []. This groove is a large hydrophobic cleft, which is unusually rich in aromatic residues. AlkA recognises electron-deficient methylated bases through pi-donor/acceptor interactions involving the electron-rich aromatic cleft. AlkA is similar in fold and active site location to the bifunctional glycosylase/lyase endonuclease III. This suggests that the two may use similar mechanisms for base excision []. The structural analysis of the AlkA and AlkA-hypoxanthine structures indicate that free hypoxanthine binding in the active site may inhibit glycosylase activity [].; GO: 0003905 alkylbase DNA N-glycosylase activity; PDB: 1MPG_B 3CWS_D 3CW7_C 3CWA_B 3D4V_A 3CWT_C 3CWU_B 3OGD_A 3CVS_C 1PVS_A ....
Probab=34.32 E-value=33 Score=22.38 Aligned_cols=26 Identities=27% Similarity=0.503 Sum_probs=18.3
Q ss_pred CCCCcchhh---hhhhccCCCHHHHHHHH
Q psy12551 22 NPSRLPVVV---GGLLDVDCSEDIIKNLI 47 (66)
Q Consensus 22 NP~~tP~VV---G~LLDvdc~E~~Ik~LL 47 (66)
....++.++ -.|||+|||-..|..-|
T Consensus 67 ~~~~l~~~~~rvRrlfDLdaDp~~I~~~L 95 (116)
T PF06029_consen 67 DLRDLPAVIARVRRLFDLDADPQAIEAHL 95 (116)
T ss_dssp GGGGHHHHHHHHHHHTTTT--HHHHHHHH
T ss_pred cHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence 344556666 56899999999999888
No 17
>PF01969 DUF111: Protein of unknown function DUF111; InterPro: IPR002822 The proteins in this family have no known function.; PDB: 3C19_A.
Probab=34.17 E-value=13 Score=28.98 Aligned_cols=26 Identities=15% Similarity=0.341 Sum_probs=0.0
Q ss_pred chhhhhhhccCCCHHHHHHHHHHhcc
Q psy12551 27 PVVVGGLLDVDCSEDIIKNLILVVRG 52 (66)
Q Consensus 27 P~VVG~LLDvdc~E~~Ik~LL~sV~~ 52 (66)
-+.+|+|||+..|.+.++..|.++..
T Consensus 12 DM~lgALldlG~~~~~l~~~l~~l~l 37 (382)
T PF01969_consen 12 DMLLGALLDLGVDPEALEEALEKLGL 37 (382)
T ss_dssp --------------------------
T ss_pred cccccccccccccccccccccccccc
Confidence 46799999999999999999988753
No 18
>COG4803 Predicted membrane protein [Function unknown]
Probab=30.98 E-value=34 Score=24.86 Aligned_cols=26 Identities=31% Similarity=0.415 Sum_probs=21.4
Q ss_pred cchhhhhhhccCCCHHHHHHHHHHhc
Q psy12551 26 LPVVVGGLLDVDCSEDIIKNLILVVR 51 (66)
Q Consensus 26 tP~VVG~LLDvdc~E~~Ik~LL~sV~ 51 (66)
+-..=|+|-|+.-|.||||.|=.++.
T Consensus 89 ~GAl~g~l~DvGIdDdFik~l~~ti~ 114 (170)
T COG4803 89 SGALSGSLTDVGIDDDFIKELGETIQ 114 (170)
T ss_pred hhhhccceeecCcCHHHHHHHHhhcC
Confidence 44556789999999999999987773
No 19
>PF05047 L51_S25_CI-B8: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain ; InterPro: IPR007741 Proteins containing this domain are located in the mitochondrion and include ribosomal protein L51, and S25. This domain is also found in mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) 1.6.5.3 from EC. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.; PDB: 1S3A_A.
Probab=29.67 E-value=20 Score=19.56 Aligned_cols=21 Identities=14% Similarity=0.354 Sum_probs=12.5
Q ss_pred eeEeeceeecCCCCcchhhhhhhc
Q psy12551 12 IPVVLRQSQVNPSRLPVVVGGLLD 35 (66)
Q Consensus 12 IEvYV~~qkVNP~~tP~VVG~LLD 35 (66)
++++| ++ ++...|.++|...+
T Consensus 19 v~~~v--~~-~~~~~P~~~~~y~~ 39 (52)
T PF05047_consen 19 VQFEV--RR-RRGRHPFLTAEYLN 39 (52)
T ss_dssp --EEE--E----SSS-EEEEEESS
T ss_pred cEEEE--EE-CCCCCCEEEEEEcC
Confidence 68888 66 88999999987765
No 20
>PF09427 DUF2014: Domain of unknown function (DUF2014) ; InterPro: IPR019006 This domain is found at the C-terminal of a family of ER membrane bound transcription factors called sterol regulatory element binding proteins (SREBP).
Probab=29.45 E-value=33 Score=26.28 Aligned_cols=29 Identities=24% Similarity=0.516 Sum_probs=25.0
Q ss_pred CCCCcchhhhhhhccCCCHHHHHHHHHHh
Q psy12551 22 NPSRLPVVVGGLLDVDCSEDIIKNLILVV 50 (66)
Q Consensus 22 NP~~tP~VVG~LLDvdc~E~~Ik~LL~sV 50 (66)
.+...|.=..+||+.||||-+.-++++-.
T Consensus 119 ~~d~LP~HLa~Lle~dcDdVl~d~iiQRa 147 (260)
T PF09427_consen 119 HDDALPEHLAALLEQDCDDVLTDDIIQRA 147 (260)
T ss_pred CcccchHHHHHHHhcccchhccHHHHHHH
Confidence 45678999999999999999988888765
No 21
>PF12916 DUF3834: Protein of unknown function (DUF3834); InterPro: IPR024533 This family is likely to be related to solute-binding lipo-proteins.; PDB: 3MST_A.
Probab=28.29 E-value=3.4 Score=30.48 Aligned_cols=47 Identities=13% Similarity=0.136 Sum_probs=34.7
Q ss_pred CCCCCcceeeEeece---eecCCCCcchhhhhhhccCCCHHHHHHHHHHh
Q psy12551 4 SSKSGLTYIPVVLRQ---SQVNPSRLPVVVGGLLDVDCSEDIIKNLILVV 50 (66)
Q Consensus 4 ~~n~~~kyIEvYV~~---qkVNP~~tP~VVG~LLDvdc~E~~Ik~LL~sV 50 (66)
++++...||++|-.| .|-||..+...|...|-.--+++||++++...
T Consensus 149 v~~~~~~fi~aY~~GI~~~r~dpe~sA~yI~~~lpi~~~~~fi~~ii~~~ 198 (201)
T PF12916_consen 149 VNGDPDYFISAYEEGIDLIREDPEGSAEYIASKLPIYYPREFIENIIKNS 198 (201)
T ss_dssp ESS--HHHHHHHHHHHHHHHH-HHHHHHHHHHH-HSSS-HHHHHHHGGG-
T ss_pred hcCChHHHHHHHHHHHHHHHhChhhHHHHHHhcCCccCCHHHHHHHHhhh
Confidence 356677889999633 57799999999999999999999999998654
No 22
>PF08973 TM1506: Domain of unknown function (DUF1893); InterPro: IPR015067 This family consist of hypothetical bacterial proteins. ; PDB: 1VK9_A.
Probab=27.86 E-value=16 Score=24.89 Aligned_cols=16 Identities=31% Similarity=0.362 Sum_probs=10.2
Q ss_pred ccCCChhhhhhhccCC
Q psy12551 51 RGQFSTDELVEEDKIP 66 (66)
Q Consensus 51 ~~~~pideLVeEvE~~ 66 (66)
.|+||++.+|.++|-|
T Consensus 106 tg~CP~E~~v~~~~d~ 121 (134)
T PF08973_consen 106 TGMCPMETLVLEVEDP 121 (134)
T ss_dssp SSB-HHHHHHHT---H
T ss_pred CCCCcHHHHHHccCCH
Confidence 4889999999988754
No 23
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=27.62 E-value=88 Score=20.72 Aligned_cols=34 Identities=18% Similarity=0.386 Sum_probs=25.3
Q ss_pred hhhhhhc---cCCCHHHHHHHHHHhccCCChhhhhhhc
Q psy12551 29 VVGGLLD---VDCSEDIIKNLILVVRGQFSTDELVEED 63 (66)
Q Consensus 29 VVG~LLD---vdc~E~~Ik~LL~sV~~~~pideLVeEv 63 (66)
-|..+|. +++++..++.|...+.+ ..|++|+.++
T Consensus 21 ~I~~IL~AAGveVd~~~~~ala~aL~g-kdIeElIa~~ 57 (106)
T cd05832 21 NLKKVLEAAGIEVDEARVKALVAALEE-VNIDEAIKKA 57 (106)
T ss_pred HHHHHHHHhCCcccHHHHHHHHHHHcC-CCHHHHHHhc
Confidence 3444444 88889998888888866 7888888754
No 24
>PF11378 DUF3181: Protein of unknown function (DUF3181); InterPro: IPR021518 This family of proteins has no known function.
Probab=27.14 E-value=73 Score=20.75 Aligned_cols=22 Identities=27% Similarity=0.366 Sum_probs=19.6
Q ss_pred hhhhhhhccCCCHHHHHHHHHHh
Q psy12551 28 VVVGGLLDVDCSEDIIKNLILVV 50 (66)
Q Consensus 28 ~VVG~LLDvdc~E~~Ik~LL~sV 50 (66)
..++.+||-+ +|+-+.++|.+|
T Consensus 34 ~~~~~~l~~~-~e~~v~~~L~~i 55 (87)
T PF11378_consen 34 EECYPLLDQG-SEDAVRQILEAI 55 (87)
T ss_pred HHHHHhhcCC-cHHHHHHHHHcC
Confidence 4577899999 999999999998
No 25
>KOG3036|consensus
Probab=25.98 E-value=40 Score=26.31 Aligned_cols=22 Identities=32% Similarity=0.449 Sum_probs=18.1
Q ss_pred chhhhhhhccCCCHHHHHHHHHH
Q psy12551 27 PVVVGGLLDVDCSEDIIKNLILV 49 (66)
Q Consensus 27 P~VVG~LLDvdc~E~~Ik~LL~s 49 (66)
=.|||+|+..|=+| +|+.|+.+
T Consensus 146 LGVIgaLvk~dd~e-Vi~fLl~T 167 (293)
T KOG3036|consen 146 LGVIGALVKNDDQE-VIRFLLTT 167 (293)
T ss_pred HHHHHHHHhcCcHH-HHHHHHHh
Confidence 36999999998777 88888865
No 26
>PF08850 DUF1820: Domain of unknown function (DUF1820); InterPro: IPR014949 This protein includes small functionally uncharacterised proteins of around 100 amino acids in length.
Probab=24.72 E-value=31 Score=22.99 Aligned_cols=56 Identities=21% Similarity=0.176 Sum_probs=38.4
Q ss_pred CcceeeEeeceeecCCCCcch--hhhhh-hc------cCCCHHHHHHHHHHh-ccCCChhhh--hhhccC
Q psy12551 8 GLTYIPVVLRQSQVNPSRLPV--VVGGL-LD------VDCSEDIIKNLILVV-RGQFSTDEL--VEEDKI 65 (66)
Q Consensus 8 ~~kyIEvYV~~qkVNP~~tP~--VVG~L-LD------vdc~E~~Ik~LL~sV-~~~~pideL--VeEvE~ 65 (66)
.-+..|+|+ ..|+++..=. -|+.| +| +|=+|+-+|+....| |..+|+-.+ ++|||+
T Consensus 11 ~~kvyelyA--r~v~~s~l~GFieIed~vF~e~s~lvVDP~eEkLk~EF~~V~r~~iPm~~IiRIDeV~k 78 (100)
T PF08850_consen 11 QGKVYELYA--RSVYQSDLYGFIEIEDFVFGERSSLVVDPSEEKLKNEFAGVKRSYIPMHSIIRIDEVEK 78 (100)
T ss_pred CCEEEEEEE--EEecCCCceeEEEeEEEEEcCcceEEECCchHHHHHHhcCceEEEEeeeeEEEEEEecc
Confidence 446789999 9999988531 12222 22 789999999999998 577776654 345543
No 27
>KOG4311|consensus
Probab=23.38 E-value=33 Score=27.27 Aligned_cols=10 Identities=40% Similarity=0.720 Sum_probs=7.3
Q ss_pred CCCHHHHHHH
Q psy12551 37 DCSEDIIKNL 46 (66)
Q Consensus 37 dc~E~~Ik~L 46 (66)
|||+|-|+-|
T Consensus 212 DCD~D~l~f~ 221 (359)
T KOG4311|consen 212 DCDRDSLIFL 221 (359)
T ss_pred ccCccceEEE
Confidence 8888876644
No 28
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=23.17 E-value=31 Score=21.91 Aligned_cols=6 Identities=50% Similarity=0.861 Sum_probs=2.6
Q ss_pred eeecCC
Q psy12551 18 QSQVNP 23 (66)
Q Consensus 18 ~qkVNP 23 (66)
||||||
T Consensus 1 GqKv~P 6 (109)
T cd02412 1 GQKVNP 6 (109)
T ss_pred CCccCC
Confidence 344444
No 29
>PF05585 DUF1758: Putative peptidase (DUF1758); InterPro: IPR008737 This is a family of nematode proteins of unknown function []. However, it seems likely that these proteins act as aspartic peptidases.
Probab=21.98 E-value=50 Score=21.56 Aligned_cols=29 Identities=24% Similarity=0.296 Sum_probs=23.8
Q ss_pred cCCCCcchhhhhhhccCCCHHHHHHHHHH
Q psy12551 21 VNPSRLPVVVGGLLDVDCSEDIIKNLILV 49 (66)
Q Consensus 21 VNP~~tP~VVG~LLDvdc~E~~Ik~LL~s 49 (66)
.||.....-+=.|||..++-.||.+=+..
T Consensus 4 ~n~~g~~~~~~~LlDsGSq~SfIt~~la~ 32 (164)
T PF05585_consen 4 FNPNGNQVEARALLDSGSQRSFITESLAN 32 (164)
T ss_pred ECCCCCEEEEEEEEecCCchhHHhHHHHH
Confidence 58888877788899999999999875443
No 30
>cd01896 DRG The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding.
Probab=21.73 E-value=1.2e+02 Score=21.08 Aligned_cols=29 Identities=21% Similarity=0.350 Sum_probs=24.2
Q ss_pred cCCCHHHHHHHHHHh---------ccCCChhhhhhhcc
Q psy12551 36 VDCSEDIIKNLILVV---------RGQFSTDELVEEDK 64 (66)
Q Consensus 36 vdc~E~~Ik~LL~sV---------~~~~pideLVeEvE 64 (66)
.+++|+.++.+|... ++.+.+|+|.+.++
T Consensus 134 ~~~~~~~v~~~l~~~~i~~~~v~~~~~~~~~~~~~~~~ 171 (233)
T cd01896 134 TKLDEKTIKAILREYKIHNADVLIREDITVDDLIDVIE 171 (233)
T ss_pred CCCCHHHHHHHHHHhCeeeEEEEEccCCCHHHHHHHHh
Confidence 357999999999876 57788999988776
No 31
>PF08142 AARP2CN: AARP2CN (NUC121) domain; InterPro: IPR012948 This domain is the central domain of AARP2 (asparagine and aspartate rich protein 2). It is weakly similar to the GTP-binding domain of elongation factor TU []. PfAARP2 is an antigen from Plasmodium falciparum of 150 kDa, which is encoded by a unique gene on chromosome 1 []. The central region of Pfaarp2 contains blocks of repetitions encoding asparagine and aspartate residues. ; GO: 0042254 ribosome biogenesis, 0005634 nucleus
Probab=21.60 E-value=68 Score=19.85 Aligned_cols=17 Identities=12% Similarity=0.036 Sum_probs=13.8
Q ss_pred cceeeEeeceeecCCCC
Q psy12551 9 LTYIPVVLRQSQVNPSR 25 (66)
Q Consensus 9 ~kyIEvYV~~qkVNP~~ 25 (66)
.=.++.||||...|+.+
T Consensus 47 ~l~v~GyvRG~~l~~n~ 63 (85)
T PF08142_consen 47 TLKVYGYVRGSPLSVNQ 63 (85)
T ss_pred EEEEEEEEccccccCCC
Confidence 45789999999988854
No 32
>PF01551 Peptidase_M23: Peptidase family M23; InterPro: IPR016047 Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.; PDB: 3IT5_A 3IT7_B 2GU1_A 3NYY_A 2HSI_B 3SLU_B 3UZ0_D 3TUF_B 1QWY_A 2B44_B ....
Probab=21.57 E-value=43 Score=19.73 Aligned_cols=15 Identities=20% Similarity=0.122 Sum_probs=10.8
Q ss_pred cceeeEeeceeecCC
Q psy12551 9 LTYIPVVLRQSQVNP 23 (66)
Q Consensus 9 ~kyIEvYV~~qkVNP 23 (66)
.=++|+|..++.+||
T Consensus 82 hlhf~v~~~~~~vdP 96 (96)
T PF01551_consen 82 HLHFEVRKNGQYVDP 96 (96)
T ss_dssp EEEEEEEETTEEE-H
T ss_pred EEEEEEEECCEEcCc
Confidence 346788888888887
No 33
>TIGR01639 P_fal_TIGR01639 Plasmodium falciparum uncharacterized domain TIGR01639. This model represents a conserved sequence region of about 60 amino acids found in over 40 predicted proteins of Plasmodium falciparum. It is not found elsewhere, including closely related species such as Plasmodium yoelii. No member of this family is characterized.
Probab=20.84 E-value=1.3e+02 Score=17.51 Aligned_cols=23 Identities=13% Similarity=0.228 Sum_probs=19.5
Q ss_pred CCHHHHHHHHHHhccCCChhhhh
Q psy12551 38 CSEDIIKNLILVVRGQFSTDELV 60 (66)
Q Consensus 38 c~E~~Ik~LL~sV~~~~pideLV 60 (66)
-+|+-|..+|.++++..|..++.
T Consensus 10 lTeEEl~~~i~~L~~~~~~~dm~ 32 (61)
T TIGR01639 10 LSKEELNELINSLDEIPNRNDML 32 (61)
T ss_pred ccHHHHHHHHHhhcCCCCHHHHH
Confidence 46788899999999999988864
No 34
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=20.46 E-value=1.5e+02 Score=19.34 Aligned_cols=35 Identities=20% Similarity=0.426 Sum_probs=24.6
Q ss_pred hhhhhhhc---cCCCHHHHHHHHHHhccCCChhhhhhhc
Q psy12551 28 VVVGGLLD---VDCSEDIIKNLILVVRGQFSTDELVEED 63 (66)
Q Consensus 28 ~VVG~LLD---vdc~E~~Ik~LL~sV~~~~pideLVeEv 63 (66)
.-|..+|. +++++..++.|...+.+ ..+++|+..+
T Consensus 20 e~I~~IL~AAGv~ve~~~~~~la~~L~g-k~i~eli~~~ 57 (105)
T TIGR03685 20 ENLKAVLEAAGVEVDEARVKALVAALEG-VNIEEAIKKA 57 (105)
T ss_pred HHHHHHHHHhCCcccHHHHHHHHHHHcC-CCHHHHHHhh
Confidence 33444444 78888888888888876 6788887653
No 35
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=20.41 E-value=1.1e+02 Score=24.57 Aligned_cols=36 Identities=17% Similarity=0.308 Sum_probs=28.2
Q ss_pred hhhhhccC-CCHHHHHHHHHHh---------ccCCChhhhhhhccC
Q psy12551 30 VGGLLDVD-CSEDIIKNLILVV---------RGQFSTDELVEEDKI 65 (66)
Q Consensus 30 VG~LLDvd-c~E~~Ik~LL~sV---------~~~~pideLVeEvE~ 65 (66)
|.+.-.++ +||+.|+.+|..- ++.+.+|++++-++.
T Consensus 190 i~~t~~l~~~d~~~ir~iL~Ey~I~nA~V~Ir~dvTlDd~id~l~~ 235 (365)
T COG1163 190 INGTGPLTHLDEDTVRAILREYRIHNADVLIREDVTLDDLIDALEG 235 (365)
T ss_pred EecccccccCCHHHHHHHHHHhCcccceEEEecCCcHHHHHHHHhh
Confidence 34445564 9999999999874 788999999987653
Done!