Query psy9696
Match_columns 96
No_of_seqs 106 out of 168
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 17:16:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9696.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9696hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2229|consensus 100.0 6.5E-36 1.4E-40 248.5 10.0 96 1-96 32-127 (616)
2 PF08158 NUC130_3NT: NUC130/3N 98.8 2.8E-09 6E-14 65.3 2.6 22 1-22 31-52 (52)
3 PF12717 Cnd1: non-SMC mitotic 82.8 15 0.00032 26.2 8.6 87 2-95 1-89 (178)
4 cd07347 harmonin_N_like N-term 71.8 14 0.00031 24.1 5.0 38 1-40 16-53 (78)
5 PF12830 Nipped-B_C: Sister ch 70.2 15 0.00032 26.7 5.3 47 2-48 21-67 (187)
6 PF13646 HEAT_2: HEAT repeats; 67.9 24 0.00052 21.2 5.3 63 2-82 13-75 (88)
7 PF01602 Adaptin_N: Adaptin N 54.8 69 0.0015 25.6 7.0 83 2-90 353-435 (526)
8 cd07355 HN_L-delphilin-R2_like 52.2 24 0.00052 23.5 3.3 39 1-41 16-54 (80)
9 PF10835 DUF2573: Protein of u 48.3 15 0.00034 24.4 2.0 18 48-65 63-80 (82)
10 PF13646 HEAT_2: HEAT repeats; 46.5 62 0.0014 19.3 7.0 54 28-93 1-55 (88)
11 PF12717 Cnd1: non-SMC mitotic 46.0 1.1E+02 0.0023 21.7 8.2 79 2-80 38-140 (178)
12 PF06685 DUF1186: Protein of u 44.8 46 0.00099 25.9 4.4 56 5-60 129-184 (249)
13 PF05997 Nop52: Nucleolar prot 41.5 17 0.00037 27.3 1.6 30 25-54 187-217 (217)
14 cd07358 harmonin_N_like_1 Doma 34.2 1.1E+02 0.0024 20.2 4.3 46 6-60 21-66 (78)
15 KOG1243|consensus 32.8 1.7E+02 0.0036 26.4 6.4 63 27-93 331-393 (690)
16 PRK13800 putative oxidoreducta 32.7 2.3E+02 0.005 25.5 7.4 74 2-92 820-893 (897)
17 KOG2256|consensus 32.7 2.6E+02 0.0056 25.2 7.5 72 4-78 443-567 (661)
18 PF14075 UBN_AB: Ubinuclein co 32.0 2.3E+02 0.0049 21.5 7.1 59 19-78 28-100 (214)
19 PF10189 DUF2356: Conserved pr 31.5 94 0.002 24.2 4.2 41 3-49 182-224 (230)
20 smart00638 LPD_N Lipoprotein N 29.5 93 0.002 25.9 4.2 73 2-78 493-573 (574)
21 cd07357 HN_L-whirlin_R2_like S 28.5 69 0.0015 21.3 2.7 22 19-40 33-54 (81)
22 KOG1078|consensus 28.2 1.3E+02 0.0029 27.7 5.2 44 7-50 41-88 (865)
23 PF05496 RuvB_N: Holliday junc 26.5 38 0.00082 26.4 1.3 18 64-81 111-128 (233)
24 COG5162 Transcription initiati 26.0 2.6E+02 0.0055 21.3 5.6 50 15-64 81-142 (197)
25 PF01347 Vitellogenin_N: Lipop 25.6 1.4E+02 0.0031 24.8 4.6 44 2-50 573-617 (618)
26 PF04286 DUF445: Protein of un 24.9 3.1E+02 0.0067 20.8 6.9 32 3-34 36-67 (367)
27 PF08717 nsp8: nsp8 replicase; 24.9 59 0.0013 24.9 2.1 19 62-80 79-97 (199)
28 PF12926 MOZART2: Mitotic-spin 24.7 56 0.0012 22.0 1.7 38 16-55 17-54 (88)
29 cd00020 ARM Armadillo/beta-cat 24.5 1.7E+02 0.0038 17.7 5.8 91 3-94 21-116 (120)
30 PF08103 Antimicrobial_8: Uper 24.4 72 0.0016 15.4 1.6 12 46-57 5-16 (17)
31 PTZ00200 cysteine proteinase; 23.8 2E+02 0.0043 24.2 5.2 59 1-59 91-162 (448)
32 PF04155 Ground-like: Ground-l 23.8 1.2E+02 0.0027 18.8 3.1 16 36-51 5-20 (76)
33 PF09802 Sec66: Preprotein tra 23.5 1.7E+02 0.0036 22.1 4.3 51 22-72 42-105 (190)
34 KOG1248|consensus 23.1 2.5E+02 0.0054 26.9 6.0 50 2-51 530-598 (1176)
35 PF09733 VEFS-Box: VEFS-Box of 22.5 1.4E+02 0.003 21.3 3.5 28 3-30 109-136 (140)
36 PF03140 DUF247: Plant protein 22.0 3.9E+02 0.0084 21.4 6.4 65 15-83 308-377 (391)
37 PF06798 PrkA: PrkA serine pro 21.5 3.9E+02 0.0085 20.7 7.7 74 4-77 41-128 (254)
38 PF01602 Adaptin_N: Adaptin N 21.0 3.7E+02 0.0081 21.4 6.1 84 5-95 95-178 (526)
39 COG1583 CRISPR system related 20.8 93 0.002 24.5 2.5 23 66-88 19-41 (240)
40 PF11838 ERAP1_C: ERAP1-like C 20.8 3.6E+02 0.0078 20.0 9.1 58 1-58 33-91 (324)
41 PF10552 ORF6C: ORF6C domain; 20.5 1E+02 0.0022 20.7 2.4 18 39-56 63-80 (116)
42 PF02985 HEAT: HEAT repeat; I 20.4 1.4E+02 0.003 15.1 3.5 25 27-51 1-25 (31)
No 1
>KOG2229|consensus
Probab=100.00 E-value=6.5e-36 Score=248.52 Aligned_cols=96 Identities=58% Similarity=0.852 Sum_probs=95.1
Q ss_pred CCchHHHHHHHHHHHHHhCCCCChhhhHHHhhhhccCCChhHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhcc
Q psy9696 1 MAKGSSDTFCKALILLRNKGLLTPIDLLPLFFGLLRCPDKPLRKFLETHIITDIKNINAKHKNAKLNTTLQNFMYEMLKD 80 (96)
Q Consensus 1 l~p~lR~~lv~aLilLRnk~~i~~~~lL~~~f~Ll~~~dK~LR~~l~~~IvsdIk~~N~k~kn~klNr~lQ~~lf~ml~d 80 (96)
|||++|++||+||||||||++|+|++||++|||||+|+||.+|+++|+|||+|||++|+++||+|+|+++|+|||+||++
T Consensus 32 lp~~Lr~~i~~~LiLLrNk~~i~~~~LL~lff~l~~~~dk~lRkllythiv~~Ikn~n~~~kn~klnkslq~~~fsml~~ 111 (616)
T KOG2229|consen 32 LPPELREKIVKALILLRNKNLIVAEDLLELFFPLLRCGDKNLRKLLYTHIVTTIKNINKKHKNDKLNKSLQAFMFSMLDQ 111 (616)
T ss_pred CCHHHHHHHHHHHHHHhccCcCCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHhC
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHhhhC
Q psy9696 81 SNHRAAKMSLSIMVHL 96 (96)
Q Consensus 81 ~~~~~Ak~al~v~~eL 96 (96)
+++++|+||+++||||
T Consensus 112 ~d~~~ak~a~~~~~eL 127 (616)
T KOG2229|consen 112 SDSTAAKMALDTMIEL 127 (616)
T ss_pred CCchhHHHHHHHHHHH
Confidence 9999999999999997
No 2
>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=98.81 E-value=2.8e-09 Score=65.28 Aligned_cols=22 Identities=45% Similarity=0.591 Sum_probs=21.2
Q ss_pred CCchHHHHHHHHHHHHHhCCCC
Q psy9696 1 MAKGSSDTFCKALILLRNKGLL 22 (96)
Q Consensus 1 l~p~lR~~lv~aLilLRnk~~i 22 (96)
|+||+|+++|+|||+|||||+|
T Consensus 31 L~p~lR~~lv~aLiLLRnK~~I 52 (52)
T PF08158_consen 31 LDPDLRMKLVKALILLRNKDLI 52 (52)
T ss_pred CCHHHHHHHHHHHHHHHccCCC
Confidence 7999999999999999999987
No 3
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=82.83 E-value=15 Score=26.20 Aligned_cols=87 Identities=22% Similarity=0.171 Sum_probs=58.5
Q ss_pred CchHHHHHHHHHHHH--HhCCCCChhhhHHHhhhhccCCChhHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhc
Q psy9696 2 AKGSSDTFCKALILL--RNKGLLTPIDLLPLFFGLLRCPDKPLRKFLETHIITDIKNINAKHKNAKLNTTLQNFMYEMLK 79 (96)
Q Consensus 2 ~p~lR~~lv~aLilL--Rnk~~i~~~~lL~~~f~Ll~~~dK~LR~~l~~~IvsdIk~~N~k~kn~klNr~lQ~~lf~ml~ 79 (96)
||..|..++-++-=| |=-+++ +..++.++..++-+|..+|+.....+..-|.+=-.|-|++ -+..++ ..+.
T Consensus 1 ~~~vR~n~i~~l~DL~~r~~~~v--e~~~~~l~~~L~D~~~~VR~~al~~Ls~Li~~d~ik~k~~----l~~~~l-~~l~ 73 (178)
T PF12717_consen 1 DPSVRNNAIIALGDLCIRYPNLV--EPYLPNLYKCLRDEDPLVRKTALLVLSHLILEDMIKVKGQ----LFSRIL-KLLV 73 (178)
T ss_pred CHHHHHHHHHHHHHHHHhCcHHH--HhHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCceeehhh----hhHHHH-HHHc
Confidence 578888888887733 333333 4568899999999999999988777777776544444433 124454 3457
Q ss_pred cCCHHHHHHHHHHhhh
Q psy9696 80 DSNHRAAKMSLSIMVH 95 (96)
Q Consensus 80 d~~~~~Ak~al~v~~e 95 (96)
|+++....-|.....|
T Consensus 74 D~~~~Ir~~A~~~~~e 89 (178)
T PF12717_consen 74 DENPEIRSLARSFFSE 89 (178)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 8888777777666554
No 4
>cd07347 harmonin_N_like N-terminal protein-binding module of harmonin and similar domains. This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain is found in either one or two copies. Harmonin contains a single copy, which is found at its N-terminus and binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. Whirlin contains two copies of the harmonin_N_like domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected.
Probab=71.82 E-value=14 Score=24.11 Aligned_cols=38 Identities=18% Similarity=0.274 Sum_probs=34.2
Q ss_pred CCchHHHHHHHHHHHHHhCCCCChhhhHHHhhhhccCCCh
Q psy9696 1 MAKGSSDTFCKALILLRNKGLLTPIDLLPLFFGLLRCPDK 40 (96)
Q Consensus 1 l~p~lR~~lv~aLilLRnk~~i~~~~lL~~~f~Ll~~~dK 40 (96)
|++.-|.+++.+|=--...+ +.++|...+|+++..+.|
T Consensus 16 L~~~Er~~~~~~L~~Y~~~~--~Vd~LV~~L~~vLdtPaK 53 (78)
T cd07347 16 LTDAEREQVTRALERYHQER--NVDDLVRDLYLVLDTPAK 53 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHcCcHhH
Confidence 45667999999999999998 999999999999999887
No 5
>PF12830 Nipped-B_C: Sister chromatid cohesion C-terminus
Probab=70.20 E-value=15 Score=26.67 Aligned_cols=47 Identities=19% Similarity=0.300 Sum_probs=40.8
Q ss_pred CchHHHHHHHHHHHHHhCCCCChhhhHHHhhhhccCCChhHHHHHHH
Q psy9696 2 AKGSSDTFCKALILLRNKGLLTPIDLLPLFFGLLRCPDKPLRKFLET 48 (96)
Q Consensus 2 ~p~lR~~lv~aLilLRnk~~i~~~~lL~~~f~Ll~~~dK~LR~~l~~ 48 (96)
+++.|..-++-+-+.-+.|++.|..-.|++.-|...+++.+|+..+.
T Consensus 21 ~~~vr~~Al~~l~~il~qGLvnP~~cvp~lIAL~ts~~~~ir~~A~~ 67 (187)
T PF12830_consen 21 DDSVRLAALQVLELILRQGLVNPKQCVPTLIALETSPNPSIRSRAYQ 67 (187)
T ss_pred CHHHHHHHHHHHHHHHhcCCCChHHHHhHhhhhhCCCChHHHHHHHH
Confidence 35678888888888889999999999999999999999999986643
No 6
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=67.86 E-value=24 Score=21.17 Aligned_cols=63 Identities=17% Similarity=0.215 Sum_probs=43.5
Q ss_pred CchHHHHHHHHHHHHHhCCCCChhhhHHHhhhhccCCChhHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhccC
Q psy9696 2 AKGSSDTFCKALILLRNKGLLTPIDLLPLFFGLLRCPDKPLRKFLETHIITDIKNINAKHKNAKLNTTLQNFMYEMLKDS 81 (96)
Q Consensus 2 ~p~lR~~lv~aLilLRnk~~i~~~~lL~~~f~Ll~~~dK~LR~~l~~~IvsdIk~~N~k~kn~klNr~lQ~~lf~ml~d~ 81 (96)
+|..|...+.+|- -+...+.++.+.+++.-+|..+|......+- .+. +......+..+++++
T Consensus 13 ~~~vr~~a~~~L~------~~~~~~~~~~L~~~l~d~~~~vr~~a~~aL~----~i~--------~~~~~~~L~~~l~~~ 74 (88)
T PF13646_consen 13 DPQVRAEAARALG------ELGDPEAIPALIELLKDEDPMVRRAAARALG----RIG--------DPEAIPALIKLLQDD 74 (88)
T ss_dssp SHHHHHHHHHHHH------CCTHHHHHHHHHHHHTSSSHHHHHHHHHHHH----CCH--------HHHTHHHHHHHHTC-
T ss_pred CHHHHHHHHHHHH------HcCCHhHHHHHHHHHcCCCHHHHHHHHHHHH----HhC--------CHHHHHHHHHHHcCC
Confidence 4678888777777 3346689999999999888988888776654 221 233445667777665
Q ss_pred C
Q psy9696 82 N 82 (96)
Q Consensus 82 ~ 82 (96)
+
T Consensus 75 ~ 75 (88)
T PF13646_consen 75 D 75 (88)
T ss_dssp S
T ss_pred C
Confidence 3
No 7
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=54.80 E-value=69 Score=25.61 Aligned_cols=83 Identities=16% Similarity=0.057 Sum_probs=55.5
Q ss_pred CchHHHHHHHHHHHHHhCCCCChhhhHHHhhhhccCCChhHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhccC
Q psy9696 2 AKGSSDTFCKALILLRNKGLLTPIDLLPLFFGLLRCPDKPLRKFLETHIITDIKNINAKHKNAKLNTTLQNFMYEMLKDS 81 (96)
Q Consensus 2 ~p~lR~~lv~aLilLRnk~~i~~~~lL~~~f~Ll~~~dK~LR~~l~~~IvsdIk~~N~k~kn~klNr~lQ~~lf~ml~d~ 81 (96)
+++.|..+++++.-+-.+..-++...++++++++...+......+...|..=+.+- +..-..+=..++..+.+-
T Consensus 353 d~~~~~~~i~~I~~la~~~~~~~~~~v~~l~~ll~~~~~~~~~~~~~~i~~ll~~~------~~~~~~~l~~L~~~l~~~ 426 (526)
T PF01602_consen 353 DPDFRRELIKAIGDLAEKFPPDAEWYVDTLLKLLEISGDYVSNEIINVIRDLLSNN------PELREKILKKLIELLEDI 426 (526)
T ss_dssp -HHHHHHHHHHHHHHHHHHGSSHHHHHHHHHHHHHCTGGGCHCHHHHHHHHHHHHS------TTTHHHHHHHHHHHHTSS
T ss_pred chhhhhhHHHHHHHHHhccCchHHHHHHHHHHhhhhccccccchHHHHHHHHhhcC------hhhhHHHHHHHHHHHHHh
Confidence 56789999999999999998888999999999999888777666655555544331 111122233346776664
Q ss_pred CHHHHHHHH
Q psy9696 82 NHRAAKMSL 90 (96)
Q Consensus 82 ~~~~Ak~al 90 (96)
.+..++++.
T Consensus 427 ~~~~~~~~~ 435 (526)
T PF01602_consen 427 SSPEALAAA 435 (526)
T ss_dssp SSHHHHHHH
T ss_pred hHHHHHHHH
Confidence 333444443
No 8
>cd07355 HN_L-delphilin-R2_like Second harmonin_N_like domain (repeat 2) of L-delphilin, and related domains. This subgroup contains the second of two harmonin_N_like domains of an alternatively spliced longer variant of mouse delphilin (L-delphilin), and related domains. Delphilin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds the glutamate receptor delta-2 (GRID2) subunit and the monocarboxylate transporter 2 at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain in L-delphilin follows the second PDZ protein-binding domain, PDZ2; it is also found in the shorter C-terminal isoforms (S-delphilin/delphilin alpha and delphilin beta). It is a putative protein-binding module based on its sequence similarity to the harmonin N-domain. The first harmonin_N_like domain of L-delphilin belongs to a different subgroup and is missing from S-delphilin.
Probab=52.22 E-value=24 Score=23.45 Aligned_cols=39 Identities=18% Similarity=0.083 Sum_probs=31.4
Q ss_pred CCchHHHHHHHHHHHHHhCCCCChhhhHHHhhhhccCCChh
Q psy9696 1 MAKGSSDTFCKALILLRNKGLLTPIDLLPLFFGLLRCPDKP 41 (96)
Q Consensus 1 l~p~lR~~lv~aLilLRnk~~i~~~~lL~~~f~Ll~~~dK~ 41 (96)
|+|+-|..+|+||---+... +..+|+.-.||.+-.++|.
T Consensus 16 Lt~~ER~~i~qaL~~y~~~R--nvd~Li~~v~pVLDtPaK~ 54 (80)
T cd07355 16 LTPPERYGIKKALEDYFQHR--NIDTLIVDVYPVLDTPAKQ 54 (80)
T ss_pred CCHHHHHHHHHHHHHHHHhc--cHHHHHhhhhhhcCCHHHH
Confidence 57899999999998776554 3567888899999888874
No 9
>PF10835 DUF2573: Protein of unknown function (DUF2573); InterPro: IPR020393 This entry contains proteins with no known function.
Probab=48.28 E-value=15 Score=24.43 Aligned_cols=18 Identities=33% Similarity=0.654 Sum_probs=14.3
Q ss_pred HHHHHHHHHHhhhhhhhH
Q psy9696 48 THIITDIKNINAKHKNAK 65 (96)
Q Consensus 48 ~~IvsdIk~~N~k~kn~k 65 (96)
+.|+.+||.+|..+|+.+
T Consensus 63 k~li~~Ik~lNe~~r~~~ 80 (82)
T PF10835_consen 63 KELIEEIKQLNEAHRANK 80 (82)
T ss_pred HHHHHHHHHHHHHHHhhc
Confidence 356889999999988654
No 10
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=46.50 E-value=62 Score=19.26 Aligned_cols=54 Identities=19% Similarity=0.303 Sum_probs=36.3
Q ss_pred HHHhhhhc-cCCChhHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhccCCHHHHHHHHHHh
Q psy9696 28 LPLFFGLL-RCPDKPLRKFLETHIITDIKNINAKHKNAKLNTTLQNFMYEMLKDSNHRAAKMSLSIM 93 (96)
Q Consensus 28 L~~~f~Ll-~~~dK~LR~~l~~~IvsdIk~~N~k~kn~klNr~lQ~~lf~ml~d~~~~~Ak~al~v~ 93 (96)
++.+++.+ .-+|+.+|.....-+- +. . ...+...+..+++|+++.....|...+
T Consensus 1 i~~L~~~l~~~~~~~vr~~a~~~L~----~~----~----~~~~~~~L~~~l~d~~~~vr~~a~~aL 55 (88)
T PF13646_consen 1 IPALLQLLQNDPDPQVRAEAARALG----EL----G----DPEAIPALIELLKDEDPMVRRAAARAL 55 (88)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHH----CC----T----HHHHHHHHHHHHTSSSHHHHHHHHHHH
T ss_pred CHHHHHHHhcCCCHHHHHHHHHHHH----Hc----C----CHhHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 45677777 7888999976555444 11 1 225677888999999987666665544
No 11
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=45.96 E-value=1.1e+02 Score=21.73 Aligned_cols=79 Identities=13% Similarity=0.122 Sum_probs=57.1
Q ss_pred CchHHHHHHHHHHHHHhCCCCChhhhH-HHhhhhccCCChhHHH----------------HHHHHHHHHHHHHhhh----
Q psy9696 2 AKGSSDTFCKALILLRNKGLLTPIDLL-PLFFGLLRCPDKPLRK----------------FLETHIITDIKNINAK---- 60 (96)
Q Consensus 2 ~p~lR~~lv~aLilLRnk~~i~~~~lL-~~~f~Ll~~~dK~LR~----------------~l~~~IvsdIk~~N~k---- 60 (96)
+|..|++-+..|.-|-..|.+-+..-+ .-+..++.=+|..+|+ .+|++++.-|-.+|..
T Consensus 38 ~~~VR~~al~~Ls~Li~~d~ik~k~~l~~~~l~~l~D~~~~Ir~~A~~~~~e~~~~~~~~~i~~~~~e~i~~l~~~~~~~ 117 (178)
T PF12717_consen 38 DPLVRKTALLVLSHLILEDMIKVKGQLFSRILKLLVDENPEIRSLARSFFSELLKKRNPNIIYNNFPELISSLNNCYEHP 117 (178)
T ss_pred CHHHHHHHHHHHHHHHHcCceeehhhhhHHHHHHHcCCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHhCccccc
Confidence 578899988888888889999888766 6666666545555554 4666677777777764
Q ss_pred ---hhhhHHHHHHHHHHHHHhcc
Q psy9696 61 ---HKNAKLNTTLQNFMYEMLKD 80 (96)
Q Consensus 61 ---~kn~klNr~lQ~~lf~ml~d 80 (96)
..+.+-.+.+=.||+..+++
T Consensus 118 ~~~~~~~~~~~~I~~fll~~i~~ 140 (178)
T PF12717_consen 118 VYGPLSREKRKKIYKFLLDFIDK 140 (178)
T ss_pred cccccCHHHHHHHHHHHHHHcCc
Confidence 34566677788888888873
No 12
>PF06685 DUF1186: Protein of unknown function (DUF1186); InterPro: IPR010602 This family consists of several hypothetical bacterial proteins of around 250 residues in length and is found in several Chlamydia and Anabaena species. The function of this family is unknown.
Probab=44.76 E-value=46 Score=25.94 Aligned_cols=56 Identities=20% Similarity=0.237 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHhCCCCChhhhHHHhhhhccCCChhHHHHHHHHHHHHHHHHhhh
Q psy9696 5 SSDTFCKALILLRNKGLLTPIDLLPLFFGLLRCPDKPLRKFLETHIITDIKNINAK 60 (96)
Q Consensus 5 lR~~lv~aLilLRnk~~i~~~~lL~~~f~Ll~~~dK~LR~~l~~~IvsdIk~~N~k 60 (96)
.|...+.||.-+-..|.++-+++.+.|-+++...=+.=.+++...+|+++=.++.+
T Consensus 129 vR~aa~~aL~~l~~~~~~~Re~vi~~f~~ll~~~l~~~~~~~~~~Lv~~~~dL~~~ 184 (249)
T PF06685_consen 129 VRMAAISALAFLVHEGPISREEVIQYFRELLNYFLERNPSFLWGSLVADICDLYPE 184 (249)
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHhcCHH
Confidence 58899999999999999999999999999986533333666888888887555544
No 13
>PF05997 Nop52: Nucleolar protein,Nop52; InterPro: IPR010301 Nop52 is believed to be involved in the generation of 28S rRNA [].; GO: 0006364 rRNA processing, 0030688 preribosome, small subunit precursor
Probab=41.50 E-value=17 Score=27.29 Aligned_cols=30 Identities=37% Similarity=0.589 Sum_probs=23.0
Q ss_pred hhhHHHhhhhc-cCCChhHHHHHHHHHHHHH
Q psy9696 25 IDLLPLFFGLL-RCPDKPLRKFLETHIITDI 54 (96)
Q Consensus 25 ~~lL~~~f~Ll-~~~dK~LR~~l~~~IvsdI 54 (96)
..+++-|+.++ .++||.+|+.+.+.|..+|
T Consensus 187 ~~ll~PF~~~~~~s~~k~l~~~i~~~Vf~~l 217 (217)
T PF05997_consen 187 LLLLEPFVKLLAKSPDKVLRKRIKESVFEPL 217 (217)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHhcCCC
Confidence 35666677776 6899999999999887653
No 14
>cd07358 harmonin_N_like_1 Domains similar to the N-terminal protein-binding module of harmonin. This domain is a putative protein-binding module based on its sequence similarity to the N-terminal domain of harmonin. Harmonin (not belonging to this group) is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein, which organizes the Usher protein network of the inner ear and the retina. This domain is also related to domains found in several other PDZ domain-containing scaffold proteins which organize supramolecular complexes. This subgroup is comprised of uncharacterized PDZ-containing proteins including a protein designated Bos taurus PDZ containing 7 which has an N-terminal PDZ domain and a C-terminal harmonin_N_like domain; however the characterized human PDZ containing 7 containing two PDZ domains does not appear to contain a harmonin_N_like domain.
Probab=34.21 E-value=1.1e+02 Score=20.22 Aligned_cols=46 Identities=20% Similarity=0.320 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhCCCCChhhhHHHhhhhccCCChhHHHHHHHHHHHHHHHHhhh
Q psy9696 6 SDTFCKALILLRNKGLLTPIDLLPLFFGLLRCPDKPLRKFLETHIITDIKNINAK 60 (96)
Q Consensus 6 R~~lv~aLilLRnk~~i~~~~lL~~~f~Ll~~~dK~LR~~l~~~IvsdIk~~N~k 60 (96)
+.++..-+---+..| +.++|..-+|.+|..+.|-+ .++|||.+=..
T Consensus 21 ~~t~~~~~~~Y~~~G--~VE~LV~~Ll~iLd~p~Kll-------LL~eIR~~v~p 66 (78)
T cd07358 21 ALAVLRHCSRYVHEG--GVEDLVRPLLAILDRPEKLL-------LLRDIRSVVTP 66 (78)
T ss_pred HHHHHHhHHHHhcCC--CHHHHHHHHHHHHccHHHHH-------HHHHHHhcCCH
Confidence 344444444445455 88899999999999999887 77888765443
No 15
>KOG1243|consensus
Probab=32.83 E-value=1.7e+02 Score=26.43 Aligned_cols=63 Identities=22% Similarity=0.371 Sum_probs=42.9
Q ss_pred hHHHhhhhccCCChhHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhccCCHHHHHHHHHHh
Q psy9696 27 LLPLFFGLLRCPDKPLRKFLETHIITDIKNINAKHKNAKLNTTLQNFMYEMLKDSNHRAAKMSLSIM 93 (96)
Q Consensus 27 lL~~~f~Ll~~~dK~LR~~l~~~IvsdIk~~N~k~kn~klNr~lQ~~lf~ml~d~~~~~Ak~al~v~ 93 (96)
+.|++.+||..+|...|-.|.+||-.=|..+-... +|..+=.-+-.-+.|.|+..--..+..|
T Consensus 331 i~p~l~kLF~~~Dr~iR~~LL~~i~~~i~~Lt~~~----~~d~I~phv~~G~~DTn~~Lre~Tlksm 393 (690)
T KOG1243|consen 331 IIPVLLKLFKSPDRQIRLLLLQYIEKYIDHLTKQI----LNDQIFPHVALGFLDTNATLREQTLKSM 393 (690)
T ss_pred hhhhHHHHhcCcchHHHHHHHHhHHHHhhhcCHHh----hcchhHHHHHhhcccCCHHHHHHHHHHH
Confidence 89999999999999999999999999998886543 4444333333333566664333333333
No 16
>PRK13800 putative oxidoreductase/HEAT repeat-containing protein; Provisional
Probab=32.71 E-value=2.3e+02 Score=25.46 Aligned_cols=74 Identities=15% Similarity=0.065 Sum_probs=49.9
Q ss_pred CchHHHHHHHHHHHHHhCCCCChhhhHHHhhhhccCCChhHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhccC
Q psy9696 2 AKGSSDTFCKALILLRNKGLLTPIDLLPLFFGLLRCPDKPLRKFLETHIITDIKNINAKHKNAKLNTTLQNFMYEMLKDS 81 (96)
Q Consensus 2 ~p~lR~~lv~aLilLRnk~~i~~~~lL~~~f~Ll~~~dK~LR~~l~~~IvsdIk~~N~k~kn~klNr~lQ~~lf~ml~d~ 81 (96)
++.+|..-++||-. +.+.+-++.+.+++.-+|..+|+..-..+.. + +.....+..+-..++|+
T Consensus 820 d~~VR~~Aa~aL~~------l~~~~a~~~L~~~L~D~~~~VR~~A~~aL~~-~----------~~~~~a~~~L~~al~D~ 882 (897)
T PRK13800 820 AWQVRQGAARALAG------AAADVAVPALVEALTDPHLDVRKAAVLALTR-W----------PGDPAARDALTTALTDS 882 (897)
T ss_pred ChHHHHHHHHHHHh------ccccchHHHHHHHhcCCCHHHHHHHHHHHhc-c----------CCCHHHHHHHHHHHhCC
Confidence 45688888888853 4556677888888888888888766554433 1 22445677777888888
Q ss_pred CHHHHHHHHHH
Q psy9696 82 NHRAAKMSLSI 92 (96)
Q Consensus 82 ~~~~Ak~al~v 92 (96)
++.+.+.|...
T Consensus 883 d~~Vr~~A~~a 893 (897)
T PRK13800 883 DADVRAYARRA 893 (897)
T ss_pred CHHHHHHHHHH
Confidence 87555554443
No 17
>KOG2256|consensus
Probab=32.67 E-value=2.6e+02 Score=25.18 Aligned_cols=72 Identities=24% Similarity=0.369 Sum_probs=48.0
Q ss_pred hHHHHHHHHHHHHHh-CCCCChhhhHHHhhhhcc-----------------------CCChhHHHHHHH-----H-----
Q psy9696 4 GSSDTFCKALILLRN-KGLLTPIDLLPLFFGLLR-----------------------CPDKPLRKFLET-----H----- 49 (96)
Q Consensus 4 ~lR~~lv~aLilLRn-k~~i~~~~lL~~~f~Ll~-----------------------~~dK~LR~~l~~-----~----- 49 (96)
.+|..++++|+.|-. -|+--| +++++++++. |+...|+.-.|+ +
T Consensus 443 PLRlhcir~Li~Ls~ssg~fIP--i~~ll~Eml~~~~~nrkp~~~~~k~~D~~~~Lk~sk~~L~sk~yq~~~ieqv~~lL 520 (661)
T KOG2256|consen 443 PLRLHCIRSLISLSRSSGTFIP--LSPLLVEMLKSVTFNRKPKASSVKPIDFDSTLKLSKRYLRSKAYQDGVIEQVIELL 520 (661)
T ss_pred hHHHHHHHHHHHHHhhcCceee--cHHHHHHHHHHhhccCCccccccCCCCeeEEeecCHHHhccHHHHHHHHHHHHHHH
Confidence 589999999998865 554333 4555666664 222223333332 2
Q ss_pred -------------------HHHHHHHHhhhhhhhHHHHHHHHHHHHHh
Q psy9696 50 -------------------IITDIKNINAKHKNAKLNTTLQNFMYEML 78 (96)
Q Consensus 50 -------------------IvsdIk~~N~k~kn~klNr~lQ~~lf~ml 78 (96)
+|.-+|+.-..+||.++||.+++|+ +-|
T Consensus 521 ~ey~a~~s~~IaFPELv~p~i~rLk~f~k~skn~~~~r~v~~li-~kl 567 (661)
T KOG2256|consen 521 LEYFALFSKSIAFPELVLPVIMRLKSFLKESKNGNYKRVVKQLI-EKL 567 (661)
T ss_pred HHHHHHHhccCCchhhhHHHHHHHHHHHHHhccHHHHHHHHHHH-HHH
Confidence 3455689999999999999999996 444
No 18
>PF14075 UBN_AB: Ubinuclein conserved middle domain
Probab=32.03 E-value=2.3e+02 Score=21.52 Aligned_cols=59 Identities=20% Similarity=0.357 Sum_probs=38.3
Q ss_pred CCCCChhhhHHHhhhh---ccCCChhHHHHHHHHHHH-----------HHHHHhhhhhhhHHHHHHHHHHHHHh
Q psy9696 19 KGLLTPIDLLPLFFGL---LRCPDKPLRKFLETHIIT-----------DIKNINAKHKNAKLNTTLQNFMYEML 78 (96)
Q Consensus 19 k~~i~~~~lL~~~f~L---l~~~dK~LR~~l~~~Ivs-----------dIk~~N~k~kn~klNr~lQ~~lf~ml 78 (96)
|.-.=+.++-++++.+ .++.+.+.|..+|+|+-+ -+|++..+.-.++++-.+|.+ -.++
T Consensus 28 K~kff~~~vn~lLL~ie~~~~~~~~~~R~~vy~hL~~~lPc~K~tL~kr~KkL~~~~~~~~l~e~L~KL-k~aI 100 (214)
T PF14075_consen 28 KKKFFTSEVNPLLLDIELQCRELNPSVRSAVYSHLESFLPCNKDTLLKRAKKLRLKEQDDRLKEPLQKL-KEAI 100 (214)
T ss_pred ccccCCHHHHHHHHHHHHHHHHcCchhhHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHhhhHHHHHHHH-HHHH
Confidence 4434445566666666 367779999999999865 346666666666666666654 3333
No 19
>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=31.46 E-value=94 Score=24.25 Aligned_cols=41 Identities=22% Similarity=0.357 Sum_probs=30.6
Q ss_pred chHHHHHHHHHHHHHhCCCCChhhhHHHhhhhccCC--ChhHHHHHHHH
Q psy9696 3 KGSSDTFCKALILLRNKGLLTPIDLLPLFFGLLRCP--DKPLRKFLETH 49 (96)
Q Consensus 3 p~lR~~lv~aLilLRnk~~i~~~~lL~~~f~Ll~~~--dK~LR~~l~~~ 49 (96)
...|..+-.|+=.+..||++.+.+ +++.++ |+.||+.+.+.
T Consensus 182 ~~I~~gV~~a~~~i~~k~vv~sl~------~l~~~~~ld~~lre~lr~~ 224 (230)
T PF10189_consen 182 DRIRRGVRNAFRTIVEKGVVPSLS------PLFDNPKLDPELRELLRET 224 (230)
T ss_pred HHHHHHHHHHHHHHHHcCCcCChH------HhcCCcccCHHHHHHHHHH
Confidence 345777888999999999987654 455555 89998877553
No 20
>smart00638 LPD_N Lipoprotein N-terminal Domain.
Probab=29.55 E-value=93 Score=25.88 Aligned_cols=73 Identities=12% Similarity=0.123 Sum_probs=46.6
Q ss_pred CchHHHHHHHHHHHHHhCCCCChhhhHHHhhhhcc--CCChhHHHHHHHHHHHH------HHHHhhhhhhhHHHHHHHHH
Q psy9696 2 AKGSSDTFCKALILLRNKGLLTPIDLLPLFFGLLR--CPDKPLRKFLETHIITD------IKNINAKHKNAKLNTTLQNF 73 (96)
Q Consensus 2 ~p~lR~~lv~aLilLRnk~~i~~~~lL~~~f~Ll~--~~dK~LR~~l~~~Ivsd------Ik~~N~k~kn~klNr~lQ~~ 73 (96)
++.+|...+.||-.+.. -.|...-+.+++++. ..|-++|-.-|.-++.. +.++=..-..++ |.-|-+|
T Consensus 493 ~~~iR~~Av~Alr~~a~---~~p~~v~~~l~~i~~n~~e~~EvRiaA~~~lm~t~P~~~~l~~ia~~l~~E~-~~QV~sf 568 (574)
T smart00638 493 STFIRLAAILALRNLAK---RDPRKVQEVLLPIYLNRAEPPEVRMAAVLVLMETKPSVALLQRIAELLNKEP-NLQVASF 568 (574)
T ss_pred CHHHHHHHHHHHHHHHH---hCchHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCCHHHHHHHHHHHhhcC-cHHHHHH
Confidence 56788888888875543 347788888888874 55678888777666543 333333322222 6667777
Q ss_pred HHHHh
Q psy9696 74 MYEML 78 (96)
Q Consensus 74 lf~ml 78 (96)
.++.|
T Consensus 569 v~S~l 573 (574)
T smart00638 569 VYSHI 573 (574)
T ss_pred hHHhh
Confidence 77665
No 21
>cd07357 HN_L-whirlin_R2_like Second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains. This subgroup contains the second of two harmonin_N_like domains found in the long isoform of whirlin, and related domains. Whirlin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds various components of the Usher protein network of the inner ear and the retina: erythrocyte protein p55, usherin, VlGR1, and myosin XVa. The long isoform of whirlin contains two harmonin_N_like domains, and three PDZ protein-binding domains, PDZ1-3. The short whirlin isoform, derived from an alternative start ATG, lacks the first harmonin_N_like domain but has in common with the long isoform, this second harmonin_N_like domain (designated repeat 2, included in this subgroup) and PDZ3. This second harmonin_N_like domain is a putative protein-binding module based on its sequence similarity to the harmonin N-domain.
Probab=28.55 E-value=69 Score=21.32 Aligned_cols=22 Identities=27% Similarity=0.398 Sum_probs=19.8
Q ss_pred CCCCChhhhHHHhhhhccCCCh
Q psy9696 19 KGLLTPIDLLPLFFGLLRCPDK 40 (96)
Q Consensus 19 k~~i~~~~lL~~~f~Ll~~~dK 40 (96)
.|=|+++.+..-+|+||..+.|
T Consensus 33 ~~~~tVealV~aL~elLnt~~K 54 (81)
T cd07357 33 SGHISVDALVMALFELLNTHEK 54 (81)
T ss_pred cCCCCHHHHHHHHHHHhccHHH
Confidence 4678999999999999999998
No 22
>KOG1078|consensus
Probab=28.25 E-value=1.3e+02 Score=27.67 Aligned_cols=44 Identities=25% Similarity=0.443 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHhCC-CCChhhhHHHhhhh---ccCCChhHHHHHHHHH
Q psy9696 7 DTFCKALILLRNKG-LLTPIDLLPLFFGL---LRCPDKPLRKFLETHI 50 (96)
Q Consensus 7 ~~lv~aLilLRnk~-~i~~~~lL~~~f~L---l~~~dK~LR~~l~~~I 50 (96)
..+..-|.-|-|.| -++-.+.-++||.+ |...|+.||+.+|..|
T Consensus 41 ~~~lskllyll~qge~~~~~eate~ff~~tKlfQskd~~LRr~vYl~I 88 (865)
T KOG1078|consen 41 RHILSKLLYLLNQGEHFGETEATELFFAITKLFQSKDVSLRRMVYLAI 88 (865)
T ss_pred HHHHHHHHHHHhcccccchhhHHHHHHHHHHHHhhcCHHHHHHHHHHH
Confidence 34566677777888 88888899999965 7899999999999876
No 23
>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.
Probab=26.52 E-value=38 Score=26.39 Aligned_cols=18 Identities=22% Similarity=0.447 Sum_probs=14.5
Q ss_pred hHHHHHHHHHHHHHhccC
Q psy9696 64 AKLNTTLQNFMYEMLKDS 81 (96)
Q Consensus 64 ~klNr~lQ~~lf~ml~d~ 81 (96)
|++|+.+|-+||..++|.
T Consensus 111 HRlnk~~qe~LlpamEd~ 128 (233)
T PF05496_consen 111 HRLNKAQQEILLPAMEDG 128 (233)
T ss_dssp CC--HHHHHHHHHHHHCS
T ss_pred hhccHHHHHHHHHHhccC
Confidence 789999999999999874
No 24
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=26.03 E-value=2.6e+02 Score=21.28 Aligned_cols=50 Identities=22% Similarity=0.305 Sum_probs=35.4
Q ss_pred HHHhCCCCChhhhHHHhhhh--ccCCC---hhHHHHHHHHHHHHHH-------HHhhhhhhh
Q psy9696 15 LLRNKGLLTPIDLLPLFFGL--LRCPD---KPLRKFLETHIITDIK-------NINAKHKNA 64 (96)
Q Consensus 15 lLRnk~~i~~~~lL~~~f~L--l~~~d---K~LR~~l~~~IvsdIk-------~~N~k~kn~ 64 (96)
.+-.-.-|-|+.++.-+++. |.|.| |.|=.++-+..|+||- +++....|.
T Consensus 81 ~mDsy~PliPd~v~DYyl~k~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna 142 (197)
T COG5162 81 NMDSYTPLIPDSVTDYYLEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNA 142 (197)
T ss_pred hcccCCCCccHHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 33444456678889999988 78989 6666677889999983 555554444
No 25
>PF01347 Vitellogenin_N: Lipoprotein amino terminal region; InterPro: IPR001747 This entry represents a conserved region found in several lipid transport proteins, including vitellogenin, microsomal triglyceride transfer protein and apolipoprotein B-100 []. Vitellinogen precursors provide the major egg yolk proteins that are a source of nutrients during early development of oviparous vertebrates and invertebrates. Vitellinogen precursors are multi-domain apolipoproteins that are cleaved into distinct yolk proteins. Different vitellinogen precursors exist, which are composed of variable combinations of yolk protein components; however, the cleavage sites are conserved. In vertebrates, a complete vitellinogen is composed of an N-terminal signal peptide for export, followed by four regions that can be cleaved into yolk proteins: lipovitellin-1, phosvitin, lipovitellin-2, and a von Willebrand factor type D domain (YGP40) [, ]. Microsomal triglyceride transfer protein (MTTP) is an endoplasmic reticulum lipid transfer protein involved in the biosynthesis and lipid loading of apolipoprotein B. MTTP is also involved in the late stage of CD1d trafficking in the lysosomal compartment, CD1d being the MHC I-like lipid antigen presenting molecule []. Apolipoprotein B can exist in two forms: B-100 and B-48. Apoliporotein B-100 is present on several lipoproteins, including very low-density lipoproteins (VLDL), intermediate density lipoproteins (IDL) and low density lipoproteins (LDL), and can assemble VLDL particles in the liver []. Apolipoprotein B-100 has been linked to the development of atherosclerosis.; GO: 0005319 lipid transporter activity, 0006869 lipid transport; PDB: 1LSH_A.
Probab=25.59 E-value=1.4e+02 Score=24.82 Aligned_cols=44 Identities=20% Similarity=0.252 Sum_probs=0.0
Q ss_pred CchHHHHHHHHHHHHHhCCCCChhhhHHHhhhhc-cCCChhHHHHHHHHH
Q psy9696 2 AKGSSDTFCKALILLRNKGLLTPIDLLPLFFGLL-RCPDKPLRKFLETHI 50 (96)
Q Consensus 2 ~p~lR~~lv~aLilLRnk~~i~~~~lL~~~f~Ll-~~~dK~LR~~l~~~I 50 (96)
++|+|.+-+ +++++.+- +...++.+...+ .-++.++++++|+||
T Consensus 573 ~~EvRiaA~--~~lm~~~P---~~~~l~~i~~~l~~E~~~QV~sfv~S~L 617 (618)
T PF01347_consen 573 DPEVRIAAY--LILMRCNP---SPSVLQRIAQSLWNEPSNQVASFVYSHL 617 (618)
T ss_dssp -HHHHHHHH--HHHHHT------HHHHHHHHHHHTT-S-HHHHHHHHHHH
T ss_pred ChhHHHHHH--HHHHhcCC---CHHHHHHHHHHHhhCchHHHHHHHHHhc
No 26
>PF04286 DUF445: Protein of unknown function (DUF445); InterPro: IPR007383 This entry contains proteins of unknown function. They are predicted to be transmembrane proteins with 2 or 3 TM domains.
Probab=24.93 E-value=3.1e+02 Score=20.76 Aligned_cols=32 Identities=13% Similarity=0.119 Sum_probs=27.5
Q ss_pred chHHHHHHHHHHHHHhCCCCChhhhHHHhhhh
Q psy9696 3 KGSSDTFCKALILLRNKGLLTPIDLLPLFFGL 34 (96)
Q Consensus 3 p~lR~~lv~aLilLRnk~~i~~~~lL~~~f~L 34 (96)
|.-|..+..++.-+..+++++++.+..-+-..
T Consensus 36 p~~r~~~~~~~~~~v~~~ll~~~~i~~~l~~~ 67 (367)
T PF04286_consen 36 PKNRERIAESIGEMVENELLTPETIRRKLESE 67 (367)
T ss_pred cccHHHHHHHHHHHHHHHCCCHHHHHHHHhcc
Confidence 66799999999999999999999887765543
No 27
>PF08717 nsp8: nsp8 replicase; InterPro: IPR014829 Viral Nsp8 (non structural protein 8) forms a hexadecameric supercomplex with Nsp7 that adopts a hollow cylinder-like structure []. The dimensions of the central channel and positive electrostatic properties of the cylinder imply that it confers processivity on RNA-dependent RNA polymerase []. ; GO: 0004197 cysteine-type endopeptidase activity, 0008242 omega peptidase activity, 0016740 transferase activity; PDB: 2AHM_F 3UB0_D.
Probab=24.87 E-value=59 Score=24.93 Aligned_cols=19 Identities=16% Similarity=0.572 Sum_probs=15.7
Q ss_pred hhhHHHHHHHHHHHHHhcc
Q psy9696 62 KNAKLNTTLQNFMYEMLKD 80 (96)
Q Consensus 62 kn~klNr~lQ~~lf~ml~d 80 (96)
|-.|+=..+|+.||.||+.
T Consensus 79 rksKvvSam~amLF~MLrr 97 (199)
T PF08717_consen 79 RKSKVVSAMHAMLFGMLRR 97 (199)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHH
Confidence 3357889999999999965
No 28
>PF12926 MOZART2: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR024332 The MOZART2 family of proteins (also known as FAM128 and Mitotic-spindle organizing protein 2) operate as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBGCP nomenclature cannot be used for it. The exact function of MOZART2 is not clear [].
Probab=24.72 E-value=56 Score=22.02 Aligned_cols=38 Identities=18% Similarity=0.308 Sum_probs=31.3
Q ss_pred HHhCCCCChhhhHHHhhhhccCCChhHHHHHHHHHHHHHH
Q psy9696 16 LRNKGLLTPIDLLPLFFGLLRCPDKPLRKFLETHIITDIK 55 (96)
Q Consensus 16 LRnk~~i~~~~lL~~~f~Ll~~~dK~LR~~l~~~IvsdIk 55 (96)
+|.|+++++++. -+|+|-....=.+..-+|++|+.-+|
T Consensus 17 ~~rk~~Ls~eE~--EL~ELa~~AGv~~dp~VFriildLL~ 54 (88)
T PF12926_consen 17 LRRKKVLSAEEV--ELYELAQLAGVPMDPEVFRIILDLLR 54 (88)
T ss_pred HHHHhccCHHHH--HHHHHHHHhCCCcChHHHHHHHHHHH
Confidence 488999999987 67888887788888889998886664
No 29
>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=24.52 E-value=1.7e+02 Score=17.72 Aligned_cols=91 Identities=16% Similarity=0.075 Sum_probs=44.8
Q ss_pred chHHHHHHHHHHHHHhCC-----CCChhhhHHHhhhhccCCChhHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHH
Q psy9696 3 KGSSDTFCKALILLRNKG-----LLTPIDLLPLFFGLLRCPDKPLRKFLETHIITDIKNINAKHKNAKLNTTLQNFMYEM 77 (96)
Q Consensus 3 p~lR~~lv~aLilLRnk~-----~i~~~~lL~~~f~Ll~~~dK~LR~~l~~~IvsdIk~~N~k~kn~klNr~lQ~~lf~m 77 (96)
++.|..-+.+|.-+-... .+-....++.+.+++..+|..+|......+-+=...-. .....-.+.-+-..+-..
T Consensus 21 ~~~~~~a~~~l~~l~~~~~~~~~~~~~~~~i~~l~~~l~~~~~~v~~~a~~~L~~l~~~~~-~~~~~~~~~g~l~~l~~~ 99 (120)
T cd00020 21 ENVQREAAWALSNLSAGNNDNIQAVVEAGGLPALVQLLKSEDEEVVKAALWALRNLAAGPE-DNKLIVLEAGGVPKLVNL 99 (120)
T ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHCCChHHHHHHHhCCCHHHHHHHHHHHHHHccCcH-HHHHHHHHCCChHHHHHH
Confidence 456666666666554331 11123678888888888887777644333222221110 001111112234455566
Q ss_pred hccCCHHHHHHHHHHhh
Q psy9696 78 LKDSNHRAAKMSLSIMV 94 (96)
Q Consensus 78 l~d~~~~~Ak~al~v~~ 94 (96)
+++++......|..++.
T Consensus 100 l~~~~~~~~~~a~~~l~ 116 (120)
T cd00020 100 LDSSNEDIQKNATGALS 116 (120)
T ss_pred HhcCCHHHHHHHHHHHH
Confidence 66666555555554443
No 30
>PF08103 Antimicrobial_8: Uperin family; InterPro: IPR012527 This family consists of the uperin family of antimicrobial peptides. Uperin is a wide-spectrum antibiotic peptide isolated from the Australian toadlet, Uperoleia mjobergii. Being only 17 amino acid residues long, it is smaller than most other wide-spectrum antibiotic peptides isolated from amphibians. Uperin adopts a well-defined amphipathic alpha-helix with distinct hydrophilic and hydrophobic faces [].; GO: 0005576 extracellular region
Probab=24.42 E-value=72 Score=15.38 Aligned_cols=12 Identities=33% Similarity=0.454 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHH
Q psy9696 46 LETHIITDIKNI 57 (96)
Q Consensus 46 l~~~IvsdIk~~ 57 (96)
+|+.|++-|||.
T Consensus 5 ~~rKivs~iKNv 16 (17)
T PF08103_consen 5 AIRKIVSVIKNV 16 (17)
T ss_pred HHHHHHHHHHhc
Confidence 567788888864
No 31
>PTZ00200 cysteine proteinase; Provisional
Probab=23.84 E-value=2e+02 Score=24.17 Aligned_cols=59 Identities=17% Similarity=0.190 Sum_probs=45.1
Q ss_pred CCchHHHHHHHHHHHHHhCCCCChhhhHHH----hhhhc-----cCC-C---hhHHHHHHHHHHHHHHHHhh
Q psy9696 1 MAKGSSDTFCKALILLRNKGLLTPIDLLPL----FFGLL-----RCP-D---KPLRKFLETHIITDIKNINA 59 (96)
Q Consensus 1 l~p~lR~~lv~aLilLRnk~~i~~~~lL~~----~f~Ll-----~~~-d---K~LR~~l~~~IvsdIk~~N~ 59 (96)
|+|+.|.+.+..|+.|.++|.|+...-++. -|+-+ +.. + ..-|..+|..=+..|+.-|.
T Consensus 91 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~e~e~~~~F~~f~~ky~K~Y~~~~E~~~R~~iF~~Nl~~I~~hN~ 162 (448)
T PTZ00200 91 LDKSKRDSYVDELTRLFKDGYISDDPKLEFEVYLEFEEFNKKYNRKHATHAERLNRFLTFRNNYLEVKSHKG 162 (448)
T ss_pred cChhHHHHHHHHHHHHhhCCCcCCCccchHHHHHHHHHHHHHhCCcCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 578999999999999999999998765542 23333 121 2 55788899999999998884
No 32
>PF04155 Ground-like: Ground-like domain; InterPro: IPR007284 This group of proteins contain one or more copies of the ground-like domain, which are specific to Caenorhabditis elegans and Caenorhabditis briggsae. It has been proposed that the ground-like domain containing proteins may bind and modulate the activity of Patched-like membrane molecules, reminiscent of the modulating activities of neuropeptides [].
Probab=23.83 E-value=1.2e+02 Score=18.76 Aligned_cols=16 Identities=25% Similarity=0.607 Sum_probs=14.7
Q ss_pred cCCChhHHHHHHHHHH
Q psy9696 36 RCPDKPLRKFLETHII 51 (96)
Q Consensus 36 ~~~dK~LR~~l~~~Iv 51 (96)
.|.|+.||+.+-++|.
T Consensus 5 ~Cn~~~L~~ii~~~~~ 20 (76)
T PF04155_consen 5 KCNSEELRKIILKNMK 20 (76)
T ss_pred ccCCHHHHHHHHHHhc
Confidence 5889999999999998
No 33
>PF09802 Sec66: Preprotein translocase subunit Sec66; InterPro: IPR018624 Members of this family of proteins are a component of the heterotetrameric Sec62/63 complex composed of SEC62, SEC63, SEC66 and SEC72. The Sec62/63 complex associates with the Sec61 complex to form the Sec complex. Sec 66 is involved in SRP-independent post-translational translocation across the endoplasmic reticulum and functions together with the Sec61 complex and KAR2 in a channel-forming translocon complex. Furthermore, Sec66 is also required for growth at elevated temperatures [, , , ].
Probab=23.51 E-value=1.7e+02 Score=22.14 Aligned_cols=51 Identities=25% Similarity=0.366 Sum_probs=35.7
Q ss_pred CChhhhHHHhhhhccC------------CChhHHHHHHHHHHHHHHHHhhhhhh-hHHHHHHHH
Q psy9696 22 LTPIDLLPLFFGLLRC------------PDKPLRKFLETHIITDIKNINAKHKN-AKLNTTLQN 72 (96)
Q Consensus 22 i~~~~lL~~~f~Ll~~------------~dK~LR~~l~~~IvsdIk~~N~k~kn-~klNr~lQ~ 72 (96)
-++..--.++|.|... +||-|+.-|.+--+-||+++.+=+.+ +.+|+-+|+
T Consensus 42 F~~~~~rdiY~sL~~~~~~~~~~k~~k~~e~VLKAALLrRavedIrR~~klre~k~~l~~L~q~ 105 (190)
T PF09802_consen 42 FPEHLQRDIYLSLLHMEDPPASEKKPKVPEKVLKAALLRRAVEDIRRIIKLREDKPALNKLYQN 105 (190)
T ss_pred CCchhHHHHHHHHHhccCCccccccCCCcHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHC
Confidence 3344445667777644 66899999999999999998765443 455655554
No 34
>KOG1248|consensus
Probab=23.11 E-value=2.5e+02 Score=26.93 Aligned_cols=50 Identities=20% Similarity=0.264 Sum_probs=36.0
Q ss_pred CchHHHHHHHHHHHHHhCCC-----------C--ChhhhHHHhhhhccC------CChhHHHHHHHHHH
Q psy9696 2 AKGSSDTFCKALILLRNKGL-----------L--TPIDLLPLFFGLLRC------PDKPLRKFLETHII 51 (96)
Q Consensus 2 ~p~lR~~lv~aLilLRnk~~-----------i--~~~~lL~~~f~Ll~~------~dK~LR~~l~~~Iv 51 (96)
.||+|.++|.||-.|-+.+. + ++...||.+|..+.- .+...|+.....|.
T Consensus 530 ~~elr~~Ic~sL~~Lv~~n~~~~~a~e~~e~~s~~AknfL~~lfn~ytq~~~~~~~~l~~~~~~L~~i~ 598 (1176)
T KOG1248|consen 530 RPELRETICNSLRMLVEQNKPSSDAAENKEVLSNDAKNFLPRLFNVYTQTVAAGRKILASRSTVLEIIR 598 (1176)
T ss_pred chHhHHHHHHHHHHHHHcCCCcchHHHHHHHHhhhhhHHHHHHHHHhcCCCccccccHHHHHHHHHHHH
Confidence 47999999999999999974 1 123589999999852 23556666555555
No 35
>PF09733 VEFS-Box: VEFS-Box of polycomb protein; InterPro: IPR019135 The VEFS-Box is found in the the C-terminal region of the VRN2, EMF2, FIS2, and Su(z)12 polycomb proteins. This domain is characterised by an acidic cluster and a tryptophan/methionine-rich sequence, the acidic-W/M domain []. In some proteins the VEFS-Box is associated with a zinc-finger domain located roughly 100 residues towards the N terminus. These proteins are part of the polycomb cluster of proteins which control HOX gene transcription as it functions in heterochromatin-mediated repression [].
Probab=22.52 E-value=1.4e+02 Score=21.31 Aligned_cols=28 Identities=25% Similarity=0.184 Sum_probs=24.4
Q ss_pred chHHHHHHHHHHHHHhCCCCChhhhHHH
Q psy9696 3 KGSSDTFCKALILLRNKGLLTPIDLLPL 30 (96)
Q Consensus 3 p~lR~~lv~aLilLRnk~~i~~~~lL~~ 30 (96)
|.++..++.=++-|.+.|+|++.++-+.
T Consensus 109 ~~l~~~f~lHl~~L~d~glLd~~~i~~c 136 (140)
T PF09733_consen 109 PNLRREFLLHLINLWDFGLLDARTIDEC 136 (140)
T ss_pred hhHHHHHHHHHHHHHHcCCCCHHHHHHH
Confidence 5788889999999999999999887654
No 36
>PF03140 DUF247: Plant protein of unknown function; InterPro: IPR004158 The function of the plant proteins constituting this family is unknown.
Probab=21.96 E-value=3.9e+02 Score=21.36 Aligned_cols=65 Identities=17% Similarity=0.225 Sum_probs=42.6
Q ss_pred HHHhCCCCCh-----hhhHHHhhhhccCCChhHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhccCCH
Q psy9696 15 LLRNKGLLTP-----IDLLPLFFGLLRCPDKPLRKFLETHIITDIKNINAKHKNAKLNTTLQNFMYEMLKDSNH 83 (96)
Q Consensus 15 lLRnk~~i~~-----~~lL~~~f~Ll~~~dK~LR~~l~~~IvsdIk~~N~k~kn~klNr~lQ~~lf~ml~d~~~ 83 (96)
+||.||+|.. ++..++|=.|=..-.-.....-|..++.|+..-. +.+.|+-...+..+-...+-.
T Consensus 308 lL~~kgIi~~~l~~d~eva~~F~~L~~~v~~~~~~~~~~~v~~~l~~~~----~~~~~~~~a~l~~~yf~~pw~ 377 (391)
T PF03140_consen 308 LLRRKGIIVNWLGSDEEVAKLFNGLCKGVVFDVDDSYYSDVCEDLNKYY----QSRWNRWWAWLRRKYFSNPWT 377 (391)
T ss_pred HHHhCCeEecCCCCcHHHHHHHHHHhccCCCCCccHHHHHHHHHHHHHh----cChHHHHHHHHhhhhcCCcHH
Confidence 7899999865 5677777666443333344577888888876644 336677777776666666533
No 37
>PF06798 PrkA: PrkA serine protein kinase C-terminal domain; InterPro: IPR010650 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry is found at the C terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length. PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.
Probab=21.48 E-value=3.9e+02 Score=20.68 Aligned_cols=74 Identities=14% Similarity=0.179 Sum_probs=50.5
Q ss_pred hHHHHHHHHHHHHHhCCCCChhhhHHHhhhhccCCC--------------hhHHHHHHHHHHHHHHHHhhhhhhhHHHHH
Q psy9696 4 GSSDTFCKALILLRNKGLLTPIDLLPLFFGLLRCPD--------------KPLRKFLETHIITDIKNINAKHKNAKLNTT 69 (96)
Q Consensus 4 ~lR~~lv~aLilLRnk~~i~~~~lL~~~f~Ll~~~d--------------K~LR~~l~~~IvsdIk~~N~k~kn~klNr~ 69 (96)
..+..|-.++.-....+.|+|.++|..+.+-+.-++ +.+|+.....|-++|+.+=.-+--+..-+.
T Consensus 41 ~~~~~ls~a~~~~~~~~~i~p~~vl~~L~~~l~~~~~i~~e~~~~y~~~l~~v~~~Y~~~v~~EV~~A~~~~~ee~~~~l 120 (254)
T PF06798_consen 41 FVIKILSNALSSDSEEDCINPLDVLNELEEGLKDHPSISEEERERYLEFLKSVRKEYDERVEKEVQEAFYYSYEEQIQNL 120 (254)
T ss_pred HHHHHHHHHHHhCcccceecHHHHHHHHHHHhhcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHH
Confidence 456777788888889999999999999999886422 335555566666667666553333445556
Q ss_pred HHHHHHHH
Q psy9696 70 LQNFMYEM 77 (96)
Q Consensus 70 lQ~~lf~m 77 (96)
++|-++..
T Consensus 121 ~~nYl~~v 128 (254)
T PF06798_consen 121 FENYLDHV 128 (254)
T ss_pred HHHHHHHH
Confidence 66666554
No 38
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=21.00 E-value=3.7e+02 Score=21.42 Aligned_cols=84 Identities=17% Similarity=0.203 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHhCCCCChhhhHHHhhhhccCCChhHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhccCCHH
Q psy9696 5 SSDTFCKALILLRNKGLLTPIDLLPLFFGLLRCPDKPLRKFLETHIITDIKNINAKHKNAKLNTTLQNFMYEMLKDSNHR 84 (96)
Q Consensus 5 lR~~lv~aLilLRnk~~i~~~~lL~~~f~Ll~~~dK~LR~~l~~~IvsdIk~~N~k~kn~klNr~lQ~~lf~ml~d~~~~ 84 (96)
.|---++++--+++.+++ ..+.+...+++.-++..+|+...-.+..=.+.. .+ -+...+-..+..++.|+++.
T Consensus 95 ~~~lAL~~l~~i~~~~~~--~~l~~~v~~ll~~~~~~VRk~A~~~l~~i~~~~----p~-~~~~~~~~~l~~lL~d~~~~ 167 (526)
T PF01602_consen 95 IRGLALRTLSNIRTPEMA--EPLIPDVIKLLSDPSPYVRKKAALALLKIYRKD----PD-LVEDELIPKLKQLLSDKDPS 167 (526)
T ss_dssp HHHHHHHHHHHH-SHHHH--HHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHC----HC-CHHGGHHHHHHHHTTHSSHH
T ss_pred HHHHHHhhhhhhcccchh--hHHHHHHHHHhcCCchHHHHHHHHHHHHHhccC----HH-HHHHHHHHHHhhhccCCcch
Confidence 344444444444444433 235556666666666666665544444444331 11 11111445556666777766
Q ss_pred HHHHHHHHhhh
Q psy9696 85 AAKMSLSIMVH 95 (96)
Q Consensus 85 ~Ak~al~v~~e 95 (96)
+...|+.++.|
T Consensus 168 V~~~a~~~l~~ 178 (526)
T PF01602_consen 168 VVSAALSLLSE 178 (526)
T ss_dssp HHHHHHHHHHH
T ss_pred hHHHHHHHHHH
Confidence 65556555543
No 39
>COG1583 CRISPR system related protein, RAMP superfamily [Defense mechanisms]
Probab=20.77 E-value=93 Score=24.46 Aligned_cols=23 Identities=39% Similarity=0.595 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHhccCCHHHHHH
Q psy9696 66 LNTTLQNFMYEMLKDSNHRAAKM 88 (96)
Q Consensus 66 lNr~lQ~~lf~ml~d~~~~~Ak~ 88 (96)
-+..+|+++|++|.+.+|.-|+.
T Consensus 19 ~~y~l~s~Iy~~l~~~~~~~a~~ 41 (240)
T COG1583 19 YQYDLQSFIYSALKSANPNLAKF 41 (240)
T ss_pred hhHHHHHHHHHHHHhhChhHHHH
Confidence 46789999999999988866653
No 40
>PF11838 ERAP1_C: ERAP1-like C-terminal domain; InterPro: IPR024571 This entry represents the uncharacterised C-terminal domain of zinc metallopeptidases belonging to MEROPS peptidase family M1 (aminopeptidase N, clan MA), with a single member characterised in Streptomyces lividans: aminopeptidase G []. The rest of the members of this family are identified as aminopeptidase N of the actinomycete-type. The spectrum of activity may differ somewhat from the aminopeptidase N clade of Escherichia coli and most other proteobacteria, which are well separated phylogenetically within the M1 family. ; PDB: 3MDJ_A 2YD0_A 3QNF_C 3RJO_A 1Z5H_A 3Q7J_A 1Z1W_A 3SE6_B.
Probab=20.76 E-value=3.6e+02 Score=19.99 Aligned_cols=58 Identities=16% Similarity=0.089 Sum_probs=42.3
Q ss_pred CCchHHHHHHHHHHHHHhCCCCChhhhHHHhhhh-ccCCChhHHHHHHHHHHHHHHHHh
Q psy9696 1 MAKGSSDTFCKALILLRNKGLLTPIDLLPLFFGL-LRCPDKPLRKFLETHIITDIKNIN 58 (96)
Q Consensus 1 l~p~lR~~lv~aLilLRnk~~i~~~~lL~~~f~L-l~~~dK~LR~~l~~~IvsdIk~~N 58 (96)
++|..|-.++..+.-+-+-|.++..+.++++.-+ -.-+|-..-+.+.+++-+-.+.+.
T Consensus 33 l~~~~R~~ll~D~~al~~~g~~~~~~~l~l~~~~~~~E~~~~vw~~~~~~l~~l~~~l~ 91 (324)
T PF11838_consen 33 LSPLDRAQLLDDLFALARAGRLSYSDFLDLLEYLLPNETDYVVWSTALSNLSSLRNRLY 91 (324)
T ss_dssp S-HHHHHHHHHHHHHHHHTTSS-HHHHHHHHGGG-GT--SHHHHHHHHHHHHHHHHHHC
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhccCCCchHHHHHHHHHHHHHHHHHH
Confidence 4788899999999999999999999999999999 566676666666655555443444
No 41
>PF10552 ORF6C: ORF6C domain; InterPro: IPR018878 This entry represents the carboxy-terminal domain from ORF6 (Q9B012 from SWISSPROT), an antirepressor protein from Lactococcus phage bIL285 [].
Probab=20.49 E-value=1e+02 Score=20.68 Aligned_cols=18 Identities=39% Similarity=0.565 Sum_probs=15.6
Q ss_pred ChhHHHHHHHHHHHHHHH
Q psy9696 39 DKPLRKFLETHIITDIKN 56 (96)
Q Consensus 39 dK~LR~~l~~~IvsdIk~ 56 (96)
++.+|+.+|+.|-+|+|+
T Consensus 63 ~~~~~~k~f~~i~~~lk~ 80 (116)
T PF10552_consen 63 DKSFRRKLFSDIYRDLKR 80 (116)
T ss_pred hhHHhHHHHHHHHHHHHH
Confidence 456999999999999975
No 42
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=20.40 E-value=1.4e+02 Score=15.12 Aligned_cols=25 Identities=28% Similarity=0.466 Sum_probs=17.8
Q ss_pred hHHHhhhhccCCChhHHHHHHHHHH
Q psy9696 27 LLPLFFGLLRCPDKPLRKFLETHII 51 (96)
Q Consensus 27 lL~~~f~Ll~~~dK~LR~~l~~~Iv 51 (96)
++|.+++++.=++...|......+.
T Consensus 1 llp~l~~~l~D~~~~VR~~a~~~l~ 25 (31)
T PF02985_consen 1 LLPILLQLLNDPSPEVRQAAAECLG 25 (31)
T ss_dssp HHHHHHHHHT-SSHHHHHHHHHHHH
T ss_pred CHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 5788888888888888887655543
Done!