Query psy13866
Match_columns 201
No_of_seqs 27 out of 29
Neff 3.5
Searched_HMMs 46136
Date Fri Aug 16 22:24:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13866.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13866hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11277 Med24_N: Mediator com 100.0 3.8E-87 8.3E-92 662.8 18.7 197 1-201 413-609 (990)
2 PHA02135 hypothetical protein 90.4 0.25 5.5E-06 39.9 2.8 58 54-121 27-87 (122)
3 PF12469 DUF3692: CRISPR-assoc 73.3 2.5 5.4E-05 33.0 2.0 54 87-141 32-91 (117)
4 PF02607 B12-binding_2: B12 bi 72.5 10 0.00022 26.5 4.8 55 136-198 12-67 (79)
5 PF08689 Med5: Mediator comple 62.6 1.8E+02 0.0039 30.9 13.3 149 39-196 505-668 (989)
6 PF00428 Ribosomal_60s: 60s Ac 54.9 7.4 0.00016 29.0 1.4 45 6-50 1-45 (88)
7 PF00620 RhoGAP: RhoGAP domain 47.1 71 0.0015 24.4 5.8 55 139-198 26-81 (151)
8 TIGR03685 L21P_arch 50S riboso 45.0 38 0.00082 26.7 4.1 43 6-48 16-58 (105)
9 cd05832 Ribosomal_L12p Ribosom 44.7 33 0.00072 27.3 3.7 43 6-48 16-58 (106)
10 PF08125 Mannitol_dh_C: Mannit 44.1 19 0.00041 31.2 2.4 77 87-172 80-157 (245)
11 cd04411 Ribosomal_P1_P2_L12p R 41.9 51 0.0011 25.9 4.4 44 5-48 15-58 (105)
12 PF00482 T2SF: Type II secreti 41.0 47 0.001 23.4 3.7 61 3-66 9-72 (124)
13 cd05831 Ribosomal_P1 Ribosomal 37.6 44 0.00096 26.1 3.4 42 5-46 16-57 (103)
14 cd05833 Ribosomal_P2 Ribosomal 37.5 60 0.0013 25.7 4.1 46 4-49 15-60 (109)
15 PLN00138 large subunit ribosom 37.2 56 0.0012 26.1 4.0 42 5-46 16-57 (113)
16 PF02572 CobA_CobO_BtuR: ATP:c 36.8 27 0.00058 29.5 2.2 24 177-200 102-125 (172)
17 PRK03643 altronate oxidoreduct 34.2 51 0.0011 31.9 3.9 78 85-172 283-361 (471)
18 PTZ00373 60S Acidic ribosomal 34.2 72 0.0016 25.6 4.1 42 5-46 18-59 (112)
19 PF11848 DUF3368: Domain of un 33.1 29 0.00063 23.2 1.5 27 173-201 2-28 (48)
20 PF04282 DUF438: Family of unk 32.5 56 0.0012 24.3 3.0 46 145-199 3-56 (71)
21 PF11165 DUF2949: Protein of u 31.3 33 0.00071 24.7 1.6 17 183-199 38-54 (58)
22 PHA01806 hypothetical protein 29.3 1E+02 0.0022 27.4 4.5 55 89-152 23-77 (200)
23 cd00014 CH Calponin homology d 29.1 65 0.0014 23.0 2.9 62 90-152 32-103 (107)
24 PF10415 FumaraseC_C: Fumarase 28.9 60 0.0013 22.6 2.6 21 177-199 28-48 (55)
25 PF08831 MHCassoc_trimer: Clas 28.0 37 0.00079 25.7 1.4 12 114-125 45-56 (72)
26 PTZ00278 ARP2/3 complex subuni 25.4 27 0.00059 30.3 0.4 22 85-106 115-136 (174)
27 PRK06770 hypothetical protein; 25.0 66 0.0014 28.0 2.6 41 136-191 92-132 (180)
28 smart00845 GatB_Yqey GatB doma 25.0 1.4E+02 0.0031 23.8 4.5 26 174-199 41-66 (147)
29 PRK06402 rpl12p 50S ribosomal 24.9 1.1E+02 0.0023 24.5 3.6 41 6-46 16-56 (106)
30 PF08721 Tn7_Tnp_TnsA_C: TnsA 24.2 64 0.0014 22.2 2.0 31 6-36 41-71 (79)
31 PF05044 HPD: Homeo-prospero d 21.4 3.3E+02 0.0071 23.4 6.0 71 116-194 59-129 (158)
32 cd00159 RhoGAP RhoGAP: GTPase- 21.3 2.9E+02 0.0063 21.1 5.4 51 139-195 26-77 (169)
33 PF07511 DUF1525: Protein of u 20.0 2.1E+02 0.0045 23.0 4.4 41 139-189 41-82 (114)
No 1
>PF11277 Med24_N: Mediator complex subunit 24 N-terminal; InterPro: IPR021429 This subunit of the Mediator complex appears to be conserved only from insects to humans. It is essential for correct retinal development in fish. Subunit composition of the mediator contributes to the control of differentiation in the vertebrate CNS as there are divergent functions of the mediator subunits Crsp34/Med27, Trap100/Med24, and Crsp150/Med14 [].
Probab=100.00 E-value=3.8e-87 Score=662.83 Aligned_cols=197 Identities=60% Similarity=0.915 Sum_probs=195.2
Q ss_pred CceeccccHHHHHHhhccccccchHHHHHHHHhhhccchHHHHHHHHHhhcchhHHHHHhcccccccccCCCCCCccccc
Q psy13866 1 VIICAEPTLARVLRTLDTEFSKIQDALLNVLSQVLNGKSFDLILAVAAVEGKLCTFVTKLIKFNECSKQSNPSDTSKTAQ 80 (201)
Q Consensus 1 ~IlrAEptl~~IlKtl~aD~sK~qe~Ll~~L~~mlsGkSfdlilAaAa~~GkLk~Fa~kLIk~NE~~K~~~~e~~~K~a~ 80 (201)
+|+||||||++|||||||||||+||+|++|||||+||||||+||||||+|||||+||+|||||||++||++||+ +|+|+
T Consensus 413 lIlRAE~tl~~IlKtl~ad~~k~~e~ll~vL~~mlsG~SfdlilAaAa~~GkLk~FaskLIk~Ne~~K~~~~e~-~K~a~ 491 (990)
T PF11277_consen 413 LILRAEPTLTGILKTLDADYSKSQEGLLGVLCQMLSGKSFDLILAAAAVTGKLKSFASKLIKCNEFSKQISGEG-SKSAQ 491 (990)
T ss_pred eEEecccHHHHHHHHhccccccchHHHHHHHHhhccCCcHHHHHHHHHHcccHHHHHHHHHhhccccccCCccc-cccch
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999 99999
Q ss_pred hhHhhhhHHHHHHHHHHHhhCcceEecCCCCChhHHHHHHHHHhcCCCCCChhhhhhccChhhHHHHHHhhccCcccccc
Q psy13866 81 TKVMLFDITFLMLCSIVQRYGSKVVFSENGGDSFFEKWVRDCMVEGGRPKPYKKMLDEKDQAGVDDLLRQFNSSDAEFKN 160 (201)
Q Consensus 81 ~ra~LFDiSFLmLc~IvQ~YGse~vl~~~~gdsFFe~Wv~~cm~e~~~~ksP~~~l~~~Dp~~Vd~Ll~~lns~~~efk~ 160 (201)
+||+||||||||||||+|+||+|+|++|+ |+|||||||++||+|++|++||++++++|||++||+||++||+|+ |||+
T Consensus 492 ~Ra~LFDiSFLMLc~i~q~YGsevvlse~-~~SfFe~Wv~~~m~e~~~~~sP~~~~~~~d~~~vd~ll~~l~~~~-~~k~ 569 (990)
T PF11277_consen 492 TRALLFDISFLMLCSIVQTYGSEVVLSEN-GDSFFEKWVRECMPEEGKSKSPDQPLALCDPAKVDSLLAQLNSSQ-EFKL 569 (990)
T ss_pred hHHHHHhhHHHHHHHHHHHcCCcEEECCC-CCcHHHHHHHHhcccccCCCChhhhhhccCchhHHHHHHHhcCcc-ccCc
Confidence 99999999999999999999999999987 999999999999999999999999999999999999999999999 9999
Q ss_pred CCCCchHHHhhchHHHHHHHHHHhhcCCCChHHHHHHhhcC
Q psy13866 161 CPKLNCYEICLNIPAVIYDVLGAWETSVLSSTDVKRILDAM 201 (201)
Q Consensus 161 ~~~~kW~eiC~nip~ai~evL~AwE~g~lS~~~VkrilD~l 201 (201)
+ ++||||||+||||+|+|||+|||+|+||.+|||||||||
T Consensus 570 ~-~~kW~eiC~~iP~~i~eiL~AwE~g~ls~~~Vk~ild~i 609 (990)
T PF11277_consen 570 S-QVKWHEICLNIPGAIKEILNAWENGTLSIEEVKRILDNI 609 (990)
T ss_pred c-cCcHHHHHHhhHHHHHHHHHHHHhCcccHHHHHHHHHHh
Confidence 9 999999999999999999999999999999999999986
No 2
>PHA02135 hypothetical protein
Probab=90.42 E-value=0.25 Score=39.86 Aligned_cols=58 Identities=29% Similarity=0.420 Sum_probs=45.3
Q ss_pred hHHHHHhc-ccccccccCC--CCCCccccchhHhhhhHHHHHHHHHHHhhCcceEecCCCCChhHHHHHHH
Q psy13866 54 CTFVTKLI-KFNECSKQSN--PSDTSKTAQTKVMLFDITFLMLCSIVQRYGSKVVFSENGGDSFFEKWVRD 121 (201)
Q Consensus 54 k~Fa~kLI-k~NE~~K~~~--~e~~~K~a~~ra~LFDiSFLmLc~IvQ~YGse~vl~~~~gdsFFe~Wv~~ 121 (201)
..||-|.| +|||...+.+ +-.|.|.-++..+|=|++=| +++|+||.|-- -=..||+++
T Consensus 27 ~~fa~kvi~~fn~nt~~~~~~~v~pm~~~ps~~yl~~m~rl---f~~~ry~~e~~-------~d~r~wc~~ 87 (122)
T PHA02135 27 AEFADKVISKFNDNTSNYPGISVPPMKGKPTMGYLGEMTRL---FFIQRYNKENN-------KDWRKWCRE 87 (122)
T ss_pred HHHHHHHHHHhccCCcCCCccccCccCCCCcchhhhcccHH---HHHHHhhhhhh-------hHHHHHHhc
Confidence 47999999 8999987766 34458888999999998866 57999998742 226788884
No 3
>PF12469 DUF3692: CRISPR-associated protein ; InterPro: IPR024615 This uncharacterised N-terminal domain family is typically between 101 and 138 amino acids in length. ; PDB: 3UNG_C 4DOZ_A 3UR3_C.
Probab=73.32 E-value=2.5 Score=33.00 Aligned_cols=54 Identities=15% Similarity=0.378 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHHhhCcceEecCC-CCChhHHHHHHHHHhc-----CCCCCChhhhhhccCh
Q psy13866 87 DITFLMLCSIVQRYGSKVVFSEN-GGDSFFEKWVRDCMVE-----GGRPKPYKKMLDEKDQ 141 (201)
Q Consensus 87 DiSFLmLc~IvQ~YGse~vl~~~-~gdsFFe~Wv~~cm~e-----~~~~ksP~~~l~~~Dp 141 (201)
.++.-.+-.+++.||.+.++.+. .++||+..|..+-... ..... |..++...+.
T Consensus 32 ~L~~~~~~~l~~~~g~~~ii~P~~~~np~~~~~l~~~~~~~~~~~~~~~~-Pnr~~a~~p~ 91 (117)
T PF12469_consen 32 YLAWAAIEELVERYGPDEIIFPSLRGNPFYDAWLLEEIQKDKDSEPRAGI-PNRFLAIVPG 91 (117)
T ss_dssp HHHHHHHHHHHHHT-GGGEEES--TT-HHHHHTT----GG---GGGSB----SEEEEEEET
T ss_pred HHHHHHHHHHHHHhCCCEEEeCCCCCCchHHHHHHHhhccccccccccCC-CceeeeecCc
Confidence 34555566789999999999994 6899999999866544 12222 5566555433
No 4
>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2.1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.
Probab=72.54 E-value=10 Score=26.47 Aligned_cols=55 Identities=15% Similarity=0.157 Sum_probs=40.5
Q ss_pred hhccChhhHHHHHHhhccCccccccCCCCchHHHhhc-hHHHHHHHHHHhhcCCCChHHHHHHh
Q psy13866 136 LDEKDQAGVDDLLRQFNSSDAEFKNCPKLNCYEICLN-IPAVIYDVLGAWETSVLSSTDVKRIL 198 (201)
Q Consensus 136 l~~~Dp~~Vd~Ll~~lns~~~efk~~~~~kW~eiC~n-ip~ai~evL~AwE~g~lS~~~Vkril 198 (201)
+...|+..++.++.+.-+.. ..-.++|.+ +..++++|=..|++|.++..++-...
T Consensus 12 l~~~d~~~~~~~~~~~l~~g--------~~~~~i~~~~l~p~m~~iG~~w~~~~~~v~~e~~as 67 (79)
T PF02607_consen 12 LLAGDEEEAEALLEEALAQG--------YPPEDIIEEILMPAMEEIGELWEEGEISVAQEHLAS 67 (79)
T ss_dssp HHTT-CCHHHHHHHHHHHCS--------SSTTHHHHHTHHHHHHHHHHHHHTTSS-HHHHHHHH
T ss_pred HHhCCHHHHHHHHHHHHHcC--------CCHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHHHH
Confidence 55678888888888875331 225678887 77889999999999999998875543
No 5
>PF08689 Med5: Mediator complex subunit Med5; InterPro: IPR014801 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents the Med5 subunit of the Mediator complex in fungi. Deletion of the MED5 gene leads to increased transcription of nuclear genes encoding components of the oxidative phosphorylation machinery, and decreased transcription of mitochondrial genes encoding components of the same machinery []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=62.63 E-value=1.8e+02 Score=30.94 Aligned_cols=149 Identities=17% Similarity=0.245 Sum_probs=88.3
Q ss_pred hHHHHHHHHHhhcchhHHHHHhcccc-cccccCCCCCCccccchhHhhhhHHHHHHHHHHHhhCcce---EecCC---C-
Q psy13866 39 SFDLILAVAAVEGKLCTFVTKLIKFN-ECSKQSNPSDTSKTAQTKVMLFDITFLMLCSIVQRYGSKV---VFSEN---G- 110 (201)
Q Consensus 39 SfdlilAaAa~~GkLk~Fa~kLIk~N-E~~K~~~~e~~~K~a~~ra~LFDiSFLmLc~IvQ~YGse~---vl~~~---~- 110 (201)
++|.||-=- +-..+...|++|= +.. ....|+ .-..|.--.=|=...|++-.++++|+-.. .+... .
T Consensus 505 sld~il~~~----~P~~iL~pL~~~l~d~~-~~~ded-~~e~q~~y~~Fg~ilL~i~~~~~~y~l~~~d~~~~~s~~~s~ 578 (989)
T PF08689_consen 505 SLDIILLFV----SPQSILEPLCDFLDDSW-FDYDED-QGEYQPVYSEFGSILLLIIAIVYRYNLSLSDLALENSGINSP 578 (989)
T ss_pred HHHHHHHhC----CHHHHHHHHHHHHhhhc-CCCCcC-CCcccHHHHHHHHHHHHHHHHHHHcCCcHHHHhhhcccccCc
Confidence 666665422 2455666666554 322 224445 44567777888889999999999999865 22211 1
Q ss_pred CChhHHHHHH--HHHhcCCCCCChhhhhhccChhhHHHHHHhhc--c--Ccc-ccccCCCCchHHHhhchHHHHHHHHHH
Q psy13866 111 GDSFFEKWVR--DCMVEGGRPKPYKKMLDEKDQAGVDDLLRQFN--S--SDA-EFKNCPKLNCYEICLNIPAVIYDVLGA 183 (201)
Q Consensus 111 gdsFFe~Wv~--~cm~e~~~~ksP~~~l~~~Dp~~Vd~Ll~~ln--s--~~~-efk~~~~~kW~eiC~nip~ai~evL~A 183 (201)
.++|+.+=.. .-+.. +....|..-+..-+-+.+..-|..|= . |=+ |+..+ +..+++...||-+.++.+.|
T Consensus 579 ~~sf~~~l~~~~~~~~~-~~~~~~~~~l~~~~~~~l~~Wi~aLFd~~n~giSDdLm~s--~~pk~~y~LiP~if~Qsi~A 655 (989)
T PF08689_consen 579 SDSFYSRLCFVLDLLTR-GSSSEPDDELSENSNNLLGGWINALFDAENGGISDDLMKS--CSPKQFYKLIPTIFKQSILA 655 (989)
T ss_pred chhhhhccchHHHHhcC-CccccChhhhhHHHHHHHHHHHHHHHhccCCCCcHHHHhc--CCHHHHHHHHHHHHHHHHHH
Confidence 1565443222 11111 11111222222233445556666663 2 212 44433 67999999999999999999
Q ss_pred hhcCCCChHHHHH
Q psy13866 184 WETSVLSSTDVKR 196 (201)
Q Consensus 184 wE~g~lS~~~Vkr 196 (201)
-|.|.|..+.++-
T Consensus 656 ~~~G~id~~~L~~ 668 (989)
T PF08689_consen 656 CEAGKIDFETLKN 668 (989)
T ss_pred HHcCCcCHHHHcc
Confidence 9999997776653
No 6
>PF00428 Ribosomal_60s: 60s Acidic ribosomal protein; InterPro: IPR001813 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The 60S acidic ribosomal protein plays an important role in the elongation step of protein synthesis. This family includes archaebacterial L12, eukaryotic P0, P1 and P2 []. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Alt a 6, Alt a 12, Cla h 3, Cla h 4 and Cla h 12.; GO: 0003735 structural constituent of ribosome, 0006414 translational elongation, 0005622 intracellular, 0005840 ribosome; PDB: 3A1Y_C 3N2D_B 2LBF_A 3IZS_t 3IZR_t 1S4J_A 2JDL_C 2W1O_B 1S4H_A 2ZKR_g.
Probab=54.90 E-value=7.4 Score=28.99 Aligned_cols=45 Identities=20% Similarity=0.383 Sum_probs=35.8
Q ss_pred cccHHHHHHhhccccccchHHHHHHHHhhhccchHHHHHHHHHhh
Q psy13866 6 EPTLARVLRTLDTEFSKIQDALLNVLSQVLNGKSFDLILAVAAVE 50 (201)
Q Consensus 6 Eptl~~IlKtl~aD~sK~qe~Ll~~L~~mlsGkSfdlilAaAa~~ 50 (201)
+||-.+|-+.+.+=+.++...++.++...|.|+..+=+|+.+...
T Consensus 1 ~pT~~~i~~vl~aag~~v~~~~~~~~~~~l~~~~i~~li~~~~~~ 45 (88)
T PF00428_consen 1 EPTAENIKKVLKAAGVEVEAIWLELFAKALEGKDIKELIANGSAG 45 (88)
T ss_dssp S-SCCCHHHHHHHHTHHHHHHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHhCCchhHHHHHHHHHHHcCCcHHHHHhccccc
Confidence 577777777777666677888999999999999999998866544
No 7
>PF00620 RhoGAP: RhoGAP domain; InterPro: IPR000198 Members of the Rho family of small G proteins transduce signals from plasma-membrane receptors and control cell adhesion, motility and shape by actin cytoskeleton formation. Like all other GTPases, Rho proteins act as molecular switches, with an active GTP-bound form and an inactive GDP-bound form. The active conformation is promoted by guanine-nucleotide exchange factors, and the inactive state by GTPase-activating proteins (GAPs) which stimulate the intrinsic GTPase activity of small G proteins. This entry is a Rho/Rac/Cdc42-like GAP domain, that is found in a wide variety of large, multi-functional proteins []. A number of structure are known for this family [, , ]. The domain is composed of seven alpha helices. This domain is also known as the breakpoint cluster region-homology (BH) domain.; GO: 0007165 signal transduction, 0005622 intracellular; PDB: 1RGP_A 1AM4_B 1GRN_B 2NGR_B 1OW3_A 1TX4_A 3BYI_B 1XA6_A 3FK2_B 1F7C_A ....
Probab=47.10 E-value=71 Score=24.37 Aligned_cols=55 Identities=9% Similarity=0.196 Sum_probs=41.2
Q ss_pred cChhhHHHHHHhhccCcccc-ccCCCCchHHHhhchHHHHHHHHHHhhcCCCChHHHHHHh
Q psy13866 139 KDQAGVDDLLRQFNSSDAEF-KNCPKLNCYEICLNIPAVIYDVLGAWETSVLSSTDVKRIL 198 (201)
Q Consensus 139 ~Dp~~Vd~Ll~~lns~~~ef-k~~~~~kW~eiC~nip~ai~evL~AwE~g~lS~~~Vkril 198 (201)
.+.++++.+...++++.... ... ....|++| ++++..|.....+.++.+..+.++
T Consensus 26 g~~~~~~~l~~~~~~~~~~~~~~~-~~~~~~va----~~lK~~L~~lp~pli~~~~~~~~~ 81 (151)
T PF00620_consen 26 GSSSEVQELRNKIDSGEPPNENLE-NYDVHDVA----SLLKRFLRELPEPLIPSELYDKFI 81 (151)
T ss_dssp --HHHHHHHHHHHHTTTTCSTTGT-TSTHHHHH----HHHHHHHHHSSSTSTTHHHHHHHH
T ss_pred CCHHHHHHHHHHHHhhhccccccc-ccChhhcc----ccceeeeeccccchhhhhHHHHHh
Confidence 58899999999999888321 333 56688887 677888888888899888777766
No 8
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=45.04 E-value=38 Score=26.67 Aligned_cols=43 Identities=19% Similarity=0.228 Sum_probs=37.0
Q ss_pred cccHHHHHHhhccccccchHHHHHHHHhhhccchHHHHHHHHH
Q psy13866 6 EPTLARVLRTLDTEFSKIQDALLNVLSQVLNGKSFDLILAVAA 48 (201)
Q Consensus 6 Eptl~~IlKtl~aD~sK~qe~Ll~~L~~mlsGkSfdlilAaAa 48 (201)
+||-.+|-+.|++=..++.+.++..|...|.|+.++-+++.++
T Consensus 16 ~iT~e~I~~IL~AAGv~ve~~~~~~la~~L~gk~i~eli~~~~ 58 (105)
T TIGR03685 16 EINEENLKAVLEAAGVEVDEARVKALVAALEGVNIEEAIKKAA 58 (105)
T ss_pred CCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHhhh
Confidence 7888899999987667788889999999999999999986544
No 9
>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=44.67 E-value=33 Score=27.29 Aligned_cols=43 Identities=19% Similarity=0.206 Sum_probs=36.9
Q ss_pred cccHHHHHHhhccccccchHHHHHHHHhhhccchHHHHHHHHH
Q psy13866 6 EPTLARVLRTLDTEFSKIQDALLNVLSQVLNGKSFDLILAVAA 48 (201)
Q Consensus 6 Eptl~~IlKtl~aD~sK~qe~Ll~~L~~mlsGkSfdlilAaAa 48 (201)
+||-.+|-+-|.+=..++.+.+...|..-|.|+.+|-+++.++
T Consensus 16 eITae~I~~IL~AAGveVd~~~~~ala~aL~gkdIeElIa~~~ 58 (106)
T cd05832 16 EINEENLKKVLEAAGIEVDEARVKALVAALEEVNIDEAIKKAA 58 (106)
T ss_pred CCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHhcc
Confidence 7888888888887666788889999999999999999987544
No 10
>PF08125 Mannitol_dh_C: Mannitol dehydrogenase C-terminal domain; InterPro: IPR013118 Long-chain mannitol dehydrogenases are a group of secondary alcohol dehydrogenases that differ from other alcohol or polyol dehydrogenases in that they do not utilise Zn(2+) or other metal cofactors and do not contain a conserved catalytic tyrosine residue. The proteins in this family that have been studied are monomeric enzymes of ~54 kDa and include: Mannitol-1-phosphate 5-dehydrogenase (1.1.1.17 from EC) [] Mannitol 2-dehydrogenase (1.1.1.67 from EC) [] D-arabinitol 4-dehydrogenase (1.1.1.11 from EC) [] Altronate oxidoreductase (1.1.1.58 from EC) D-mannonate oxidoreductase (1.1.1.57 from EC) These enzymes are mostly found in bacteria, though they are also present in some fungal species. This entry represents the C-terminal substrate-binding domain of long-chain mannitol dehydrogenases. This domain is primarily alpha-helical in nature, being composed of eleven helices and a small beta hairpin []. Most of the residues implicated in substrate binding are located within this region, and a conserved lysine residue is thought to act as a proton acceptor during catalysis.; GO: 0016491 oxidoreductase activity, 0050662 coenzyme binding, 0055114 oxidation-reduction process; PDB: 3H2Z_A 1M2W_A 1LJ8_A.
Probab=44.07 E-value=19 Score=31.18 Aligned_cols=77 Identities=22% Similarity=0.159 Sum_probs=51.1
Q ss_pred hHHHHHHHHHHHhhCcceEecCCCCChhHHHHHHHHHhcCCCCCChhhhhhccCh-hhHHHHHHhhccCccccccCCCCc
Q psy13866 87 DITFLMLCSIVQRYGSKVVFSENGGDSFFEKWVRDCMVEGGRPKPYKKMLDEKDQ-AGVDDLLRQFNSSDAEFKNCPKLN 165 (201)
Q Consensus 87 DiSFLmLc~IvQ~YGse~vl~~~~gdsFFe~Wv~~cm~e~~~~ksP~~~l~~~Dp-~~Vd~Ll~~lns~~~efk~~~~~k 165 (201)
--+=-+++++-+..|.+.|=.-- .|+.+.++++..|-|...+.-+.. ...|. +=.+.++.+|.|+. + .=+
T Consensus 80 Ng~Ht~lAylG~l~G~~tV~ea~-~d~~i~~~v~~~~~ee~~p~l~~~--~~~dl~~y~~~~l~RF~Np~--i----~d~ 150 (245)
T PF08125_consen 80 NGSHTALAYLGYLAGYETVHEAM-ADPEIRAFVRRLMEEEIAPLLPKY--PGEDLEAYADKVLERFSNPY--I----KDT 150 (245)
T ss_dssp HHHHHHHHHHHHHCT--BHHHHH-TSHHHHHHHHHHHHHCCHHHHHHH--TCHHHHHHHHHHHHHHT-ST--T------B
T ss_pred ccHHHHHHHHHHhcCccChHHhh-CchHHHHHHHHHHHHHHHhhcCCc--chhhHHHHHHHHHHhcCCCC--C----CCc
Confidence 33445788999999999876655 799999999999999986543222 22333 23677888888775 2 234
Q ss_pred hHHHhhc
Q psy13866 166 CYEICLN 172 (201)
Q Consensus 166 W~eiC~n 172 (201)
+..||.|
T Consensus 151 ~~rIa~d 157 (245)
T PF08125_consen 151 LERIARD 157 (245)
T ss_dssp HHHHCTT
T ss_pred HHHHhhh
Confidence 7777777
No 11
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=41.85 E-value=51 Score=25.88 Aligned_cols=44 Identities=20% Similarity=0.301 Sum_probs=37.8
Q ss_pred ccccHHHHHHhhccccccchHHHHHHHHhhhccchHHHHHHHHH
Q psy13866 5 AEPTLARVLRTLDTEFSKIQDALLNVLSQVLNGKSFDLILAVAA 48 (201)
Q Consensus 5 AEptl~~IlKtl~aD~sK~qe~Ll~~L~~mlsGkSfdlilAaAa 48 (201)
.|||-.+|-|.|.+--.++.+.++..+..-|.|+..+=+++...
T Consensus 15 ~~~ta~~I~~IL~aaGveVe~~~~~~~~~aLaGk~V~eli~~g~ 58 (105)
T cd04411 15 KELTEDKIKELLSAAGAEIEPERVKLFLSALNGKNIDEVISKGK 58 (105)
T ss_pred CCCCHHHHHHHHHHcCCCcCHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 46999999999997667888889999999999999999886543
No 12
>PF00482 T2SF: Type II secretion system (T2SS), protein F; InterPro: IPR018076 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) [], have been found to be evolutionary related. These are proteins of about 400 amino acids that are highly hydrophobic and which are thought to be integral protein of the inner membrane. Proteins with this domain form a platform for the type II secretion machinery, as well as the type IV pili and the archaeal flagellae [].; PDB: 2VMA_A 3C1Q_A 2VMB_B 2WHN_B.
Probab=40.95 E-value=47 Score=23.43 Aligned_cols=61 Identities=23% Similarity=0.371 Sum_probs=40.6
Q ss_pred eeccccHHHHHHhhc--cccccchHHHHHHHHhhhccchHHHHHHHHHhhc-chhHHHHHhcccccc
Q psy13866 3 ICAEPTLARVLRTLD--TEFSKIQDALLNVLSQVLNGKSFDLILAVAAVEG-KLCTFVTKLIKFNEC 66 (201)
Q Consensus 3 lrAEptl~~IlKtl~--aD~sK~qe~Ll~~L~~mlsGkSfdlilAaAa~~G-kLk~Fa~kLIk~NE~ 66 (201)
+++..|+.+.++.+. .++....+.+-.+...+-.|.+++--+. -+| .+..|+..+++--+.
T Consensus 9 l~sG~~l~~al~~~~~~~~~~~l~~~~~~~~~~l~~G~~~~~al~---~~~~~~~~~~~~~~~~~~~ 72 (124)
T PF00482_consen 9 LKSGIPLSEALEILAEESDSGPLREELQKIRRRLRNGGSLEEALE---RTGSEFPDFVASLIQAGES 72 (124)
T ss_dssp HHCT--HHHHHHHHCCC-SSHHHHHHHHHHHHHHHTT--HHHHHC---TSTTTS-HHHHHHHHHHHH
T ss_pred HHcCCCHHHHHHHHHhHcCCHHHHHHHHHHHHHHHcCCCHHHHHH---HhcccCchHHHHHHHHHhh
Confidence 577889999999988 3356677888899999999998875555 444 677777777765543
No 13
>cd05831 Ribosomal_P1 Ribosomal protein P1. This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and
Probab=37.61 E-value=44 Score=26.07 Aligned_cols=42 Identities=17% Similarity=0.189 Sum_probs=36.0
Q ss_pred ccccHHHHHHhhccccccchHHHHHHHHhhhccchHHHHHHH
Q psy13866 5 AEPTLARVLRTLDTEFSKIQDALLNVLSQVLNGKSFDLILAV 46 (201)
Q Consensus 5 AEptl~~IlKtl~aD~sK~qe~Ll~~L~~mlsGkSfdlilAa 46 (201)
.+||-.+|-|.|.+-=.++.+.++..+...|.||+++=+++.
T Consensus 16 ~~~Tae~I~~ilkAaGveve~~~~~~f~~~L~gk~i~elIa~ 57 (103)
T cd05831 16 IEITADNINALLKAAGVNVEPYWPGLFAKALEGKDIKDLLSN 57 (103)
T ss_pred CCCCHHHHHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHhhc
Confidence 478999999999875567778899999999999999888864
No 14
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=37.51 E-value=60 Score=25.73 Aligned_cols=46 Identities=26% Similarity=0.330 Sum_probs=38.2
Q ss_pred eccccHHHHHHhhccccccchHHHHHHHHhhhccchHHHHHHHHHh
Q psy13866 4 CAEPTLARVLRTLDTEFSKIQDALLNVLSQVLNGKSFDLILAVAAV 49 (201)
Q Consensus 4 rAEptl~~IlKtl~aD~sK~qe~Ll~~L~~mlsGkSfdlilAaAa~ 49 (201)
+++||-.+|-|.|++=-.++...++..|.--|.||+++=+++....
T Consensus 15 ~~~pTa~dI~~IL~AaGveVe~~~~~lf~~~L~GKdi~eLIa~g~~ 60 (109)
T cd05833 15 NASPSAADVKKILGSVGVEVDDEKLNKVISELEGKDVEELIAAGKE 60 (109)
T ss_pred CCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHh
Confidence 3589999999999964467778899999999999999988876443
No 15
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=37.23 E-value=56 Score=26.11 Aligned_cols=42 Identities=17% Similarity=0.241 Sum_probs=35.7
Q ss_pred ccccHHHHHHhhccccccchHHHHHHHHhhhccchHHHHHHH
Q psy13866 5 AEPTLARVLRTLDTEFSKIQDALLNVLSQVLNGKSFDLILAV 46 (201)
Q Consensus 5 AEptl~~IlKtl~aD~sK~qe~Ll~~L~~mlsGkSfdlilAa 46 (201)
.+||-.+|-|.|++==.++.+.++..|..-|.||+++=+++.
T Consensus 16 ~~pta~dI~~IL~AaGvevd~~~~~~f~~~L~gK~i~eLIa~ 57 (113)
T PLN00138 16 TCPSAEDLKDILGSVGADADDDRIELLLSEVKGKDITELIAS 57 (113)
T ss_pred CCCCHHHHHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHHHh
Confidence 579999999999864457778899999999999999988863
No 16
>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2.5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.
Probab=36.79 E-value=27 Score=29.53 Aligned_cols=24 Identities=21% Similarity=0.291 Sum_probs=20.5
Q ss_pred HHHHHHHhhcCCCChHHHHHHhhc
Q psy13866 177 IYDVLGAWETSVLSSTDVKRILDA 200 (201)
Q Consensus 177 i~evL~AwE~g~lS~~~VkrilD~ 200 (201)
+-||+.|+..|.|+.+||.+++++
T Consensus 102 LDEi~~a~~~gll~~~~v~~~l~~ 125 (172)
T PF02572_consen 102 LDEINYAVDYGLLSEEEVLDLLEN 125 (172)
T ss_dssp EETHHHHHHTTSS-HHHHHHHHHT
T ss_pred EcchHHHhHCCCccHHHHHHHHHc
Confidence 358999999999999999999875
No 17
>PRK03643 altronate oxidoreductase; Provisional
Probab=34.21 E-value=51 Score=31.87 Aligned_cols=78 Identities=19% Similarity=0.205 Sum_probs=54.6
Q ss_pred hhhHHHHHHHHHHHhhCcceEecCCCCChhHHHHHHHHHhcCCCCCChhhhhhccChhh-HHHHHHhhccCccccccCCC
Q psy13866 85 LFDITFLMLCSIVQRYGSKVVFSENGGDSFFEKWVRDCMVEGGRPKPYKKMLDEKDQAG-VDDLLRQFNSSDAEFKNCPK 163 (201)
Q Consensus 85 LFDiSFLmLc~IvQ~YGse~vl~~~~gdsFFe~Wv~~cm~e~~~~ksP~~~l~~~Dp~~-Vd~Ll~~lns~~~efk~~~~ 163 (201)
+.--+=-+++++-+.+|.+.|-.-- .|+.+..+++..|.|+.-|.=+ ....|+.. ++.++.+|.|+- + .
T Consensus 283 lLNg~Ht~lAylG~L~G~~tV~eam-~dp~i~~~v~~~~~eei~p~l~---~~~~dl~~Y~~~ll~RF~Np~--i----~ 352 (471)
T PRK03643 283 ILNGAHTALVPVAYLAGLDTVGEAM-EDAEIGAFVEKAIYEEIIPVLD---LPEDELESFAEAVLDRFRNPF--I----K 352 (471)
T ss_pred hccHHHHHHHHHHHHcCcchHHHHH-CCHHHHHHHHHHHHHhccccCC---CChhhHHHHHHHHHHHcCCCC--C----C
Confidence 3344555788999999998876655 6999999999999998654321 22245544 888999998876 2 2
Q ss_pred CchHHHhhc
Q psy13866 164 LNCYEICLN 172 (201)
Q Consensus 164 ~kW~eiC~n 172 (201)
=++..||++
T Consensus 353 h~l~rIa~d 361 (471)
T PRK03643 353 HQLLSIALN 361 (471)
T ss_pred CCHHHHHhC
Confidence 335666655
No 18
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=34.20 E-value=72 Score=25.63 Aligned_cols=42 Identities=24% Similarity=0.358 Sum_probs=35.8
Q ss_pred ccccHHHHHHhhccccccchHHHHHHHHhhhccchHHHHHHH
Q psy13866 5 AEPTLARVLRTLDTEFSKIQDALLNVLSQVLNGKSFDLILAV 46 (201)
Q Consensus 5 AEptl~~IlKtl~aD~sK~qe~Ll~~L~~mlsGkSfdlilAa 46 (201)
.+||-.+|-|-|++=-.++.+.++..|..-|.||+++=+++.
T Consensus 18 ~~pTaddI~kIL~AaGveVd~~~~~l~~~~L~GKdI~ELIa~ 59 (112)
T PTZ00373 18 ENPTKKEVKNVLSAVNADVEDDVLDNFFKSLEGKTPHELIAA 59 (112)
T ss_pred CCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHH
Confidence 469999999999864457778899999999999999999874
No 19
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=33.08 E-value=29 Score=23.24 Aligned_cols=27 Identities=26% Similarity=0.353 Sum_probs=21.3
Q ss_pred hHHHHHHHHHHhhcCCCChHHHHHHhhcC
Q psy13866 173 IPAVIYDVLGAWETSVLSSTDVKRILDAM 201 (201)
Q Consensus 173 ip~ai~evL~AwE~g~lS~~~VkrilD~l 201 (201)
+-|.+--++.|.++|.|+ +++..+|.|
T Consensus 2 v~GTlGiL~~Ak~~GlI~--~~~~~l~~l 28 (48)
T PF11848_consen 2 VTGTLGILLLAKRRGLIS--EVKPLLDRL 28 (48)
T ss_pred ceehHHHHHHHHHcCChh--hHHHHHHHH
Confidence 346677889999999999 888777753
No 20
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=32.45 E-value=56 Score=24.29 Aligned_cols=46 Identities=9% Similarity=0.389 Sum_probs=28.5
Q ss_pred HHHHHhhccCccccccC--------CCCchHHHhhchHHHHHHHHHHhhcCCCChHHHHHHhh
Q psy13866 145 DDLLRQFNSSDAEFKNC--------PKLNCYEICLNIPAVIYDVLGAWETSVLSSTDVKRILD 199 (201)
Q Consensus 145 d~Ll~~lns~~~efk~~--------~~~kW~eiC~nip~ai~evL~AwE~g~lS~~~VkrilD 199 (201)
-++|.+|+.|+ ++... .++.-.| |+.+=++++. .| ++.+||+|+||
T Consensus 3 K~ii~~Lh~G~-~~e~vk~~F~~~~~~Vs~~E----I~~~Eq~Li~---eG-~~~eeiq~LCd 56 (71)
T PF04282_consen 3 KEIIKRLHEGE-DPEEVKEEFKKLFSDVSASE----ISAAEQELIQ---EG-MPVEEIQKLCD 56 (71)
T ss_pred HHHHHHHhCCC-CHHHHHHHHHHHHCCCCHHH----HHHHHHHHHH---cC-CCHHHHHHHhH
Confidence 35666676665 22221 0233444 4566677665 55 99999999998
No 21
>PF11165 DUF2949: Protein of unknown function (DUF2949); InterPro: IPR021336 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=31.34 E-value=33 Score=24.73 Aligned_cols=17 Identities=18% Similarity=0.638 Sum_probs=16.0
Q ss_pred HhhcCCCChHHHHHHhh
Q psy13866 183 AWETSVLSSTDVKRILD 199 (201)
Q Consensus 183 AwE~g~lS~~~VkrilD 199 (201)
=|..|.|+.+.+.+|+|
T Consensus 38 LWqyGLItL~QL~~i~D 54 (58)
T PF11165_consen 38 LWQYGLITLEQLDQIFD 54 (58)
T ss_pred HHHhccccHHHHHHHHH
Confidence 39999999999999998
No 22
>PHA01806 hypothetical protein
Probab=29.26 E-value=1e+02 Score=27.37 Aligned_cols=55 Identities=20% Similarity=0.149 Sum_probs=44.5
Q ss_pred HHHHHHHHHHhhCcceEecCCCCChhHHHHHHHHHhcCCCCCChhhhhhccChhhHHHHHHhhc
Q psy13866 89 TFLMLCSIVQRYGSKVVFSENGGDSFFEKWVRDCMVEGGRPKPYKKMLDEKDQAGVDDLLRQFN 152 (201)
Q Consensus 89 SFLmLc~IvQ~YGse~vl~~~~gdsFFe~Wv~~cm~e~~~~ksP~~~l~~~Dp~~Vd~Ll~~ln 152 (201)
--|-+++-.|.+|.++-+..+ .||+.+..+ .+++-+-......|..++.|..+|.
T Consensus 23 ~al~v~~~l~~~g~~aYlVGG--------~VRD~Llgr-~~kDiDivt~~~~pe~v~~L~~klG 77 (200)
T PHA01806 23 ALLLRLYSDARHSEGVALAGG--------AARDLMHGA-EPKDIDIALYGMDDRQAELLIGCIL 77 (200)
T ss_pred HHHHHHHHHHHCCcEEEEECc--------hHHHHHcCC-CCCceEEEccCCCHHHHHHHHHHhC
Confidence 345678999999999999888 899999876 5665444455789999999999886
No 23
>cd00014 CH Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
Probab=29.05 E-value=65 Score=23.03 Aligned_cols=62 Identities=11% Similarity=0.121 Sum_probs=43.2
Q ss_pred HHHHHHHHHhhCcceEecCC----------CCChhHHHHHHHHHhcCCCCCChhhhhhccChhhHHHHHHhhc
Q psy13866 90 FLMLCSIVQRYGSKVVFSEN----------GGDSFFEKWVRDCMVEGGRPKPYKKMLDEKDQAGVDDLLRQFN 152 (201)
Q Consensus 90 FLmLc~IvQ~YGse~vl~~~----------~gdsFFe~Wv~~cm~e~~~~ksP~~~l~~~Dp~~Vd~Ll~~ln 152 (201)
-..||.+++.|....+-... +.-.+|-+|+++.=+... ..+|+++..+.|+..|=.+|.+|.
T Consensus 32 G~~L~~Ll~~~~p~~~~~~~~~~~~~~~~~~Ni~~~l~~~~~~gi~~~-~~~~~Dl~~~~n~~~vl~~l~~l~ 103 (107)
T cd00014 32 GIALCKLLNSLSPDLIDKKKINPLSRFKRLENINLALNFAEKLGVPVV-NFDAEDLVEDGDEKLVLGLLWSLI 103 (107)
T ss_pred hHHHHHHHHHHCccccccccccccchhhHHHHHHHHHHHHHHcCCcee-ccCHHHHhhCCCceeeHHHHHHHH
Confidence 56799999998776642221 235677778887433333 477888888888888888887764
No 24
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=28.88 E-value=60 Score=22.60 Aligned_cols=21 Identities=24% Similarity=0.525 Sum_probs=16.2
Q ss_pred HHHHHHHhhcCCCChHHHHHHhh
Q psy13866 177 IYDVLGAWETSVLSSTDVKRILD 199 (201)
Q Consensus 177 i~evL~AwE~g~lS~~~VkrilD 199 (201)
|+|+.. |.|.+|.+++.++||
T Consensus 28 vre~v~--~~g~lt~ee~d~ll~ 48 (55)
T PF10415_consen 28 VREVVL--EEGLLTEEELDELLD 48 (55)
T ss_dssp HHHHHH--HTTSS-HHHHHHHTS
T ss_pred HHHHHH--HcCCCCHHHHHHHcC
Confidence 455554 789999999999987
No 25
>PF08831 MHCassoc_trimer: Class II MHC-associated invariant chain trimerisation domain; InterPro: IPR011988 This entry represents the trimerisation domain of the MHC class II-associated invariant chain (Ii). Ii plays a critical role in the assembly of the MHC, as well as in MHC II antigen processing by stabilising peptide-free class II alpha/beta heterodimers in a complex soon after their synthesis and directing transport of the complex from the endoplasmic reticulum to compartments where peptide loading of class II takes place []. In antigen-presenting cells (APCs), loading of MHC II molecules with peptides is regulated by Ii, which blocks MHC II antigen-binding sites in pre-endosomal compartments []. Several molecules then act upon MHC II molecules in endosomes to facilitate peptide loading: Ii-degrading proteases, the peptide exchange factor, human leukocyte antigen-DM (HLA-DM), and its modulator, HLA-DO (DO). The Invariant chain contains a single transmembrane domain. Ii first assembles into a trimer and then associates with three class II alpha/beta MHC heterodimers. Although the membrane-proximal region of the Ii luminal domain is structurally disordered, the C-terminal segment of the luminal domain is largely alpha-helical and contains a major interaction site for the Ii trimer []. More information about these proteins can be found at Protein of the Month: MHC [].; GO: 0042289 MHC class II protein binding, 0006886 intracellular protein transport, 0006955 immune response, 0019882 antigen processing and presentation, 0016020 membrane; PDB: 1IIE_C.
Probab=28.04 E-value=37 Score=25.68 Aligned_cols=12 Identities=25% Similarity=0.692 Sum_probs=9.7
Q ss_pred hHHHHHHHHHhc
Q psy13866 114 FFEKWVRDCMVE 125 (201)
Q Consensus 114 FFe~Wv~~cm~e 125 (201)
=||.|++.|+.=
T Consensus 45 ~FEsWM~~WLlF 56 (72)
T PF08831_consen 45 SFESWMHQWLLF 56 (72)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 389999999753
No 26
>PTZ00278 ARP2/3 complex subunit; Provisional
Probab=25.42 E-value=27 Score=30.26 Aligned_cols=22 Identities=18% Similarity=0.224 Sum_probs=18.8
Q ss_pred hhhHHHHHHHHHHHhhCcceEe
Q psy13866 85 LFDITFLMLCSIVQRYGSKVVF 106 (201)
Q Consensus 85 LFDiSFLmLc~IvQ~YGse~vl 106 (201)
-+|||||..-+-+..||++-.+
T Consensus 115 GYDISFLItn~H~e~m~k~kLi 136 (174)
T PTZ00278 115 GYDISFLITNFHTENMFKHKLI 136 (174)
T ss_pred CCChhhhhhhhhHHHHHHHHHH
Confidence 5899999999999999877543
No 27
>PRK06770 hypothetical protein; Provisional
Probab=25.05 E-value=66 Score=28.04 Aligned_cols=41 Identities=27% Similarity=0.361 Sum_probs=32.3
Q ss_pred hhccChhhHHHHHHhhccCccccccCCCCchHHHhhchHHHHHHHHHHhhcCCCCh
Q psy13866 136 LDEKDQAGVDDLLRQFNSSDAEFKNCPKLNCYEICLNIPAVIYDVLGAWETSVLSS 191 (201)
Q Consensus 136 l~~~Dp~~Vd~Ll~~lns~~~efk~~~~~kW~eiC~nip~ai~evL~AwE~g~lS~ 191 (201)
...+.|..++.|+..+++++.+-|. -..+||..|.+|--|.
T Consensus 92 ~~~mT~enI~~l~~~i~~sn~~~k~---------------~yl~IL~RW~~GDFS~ 132 (180)
T PRK06770 92 FIEMTQENIEKLKDIINSSNFVQKE---------------ELLAILERWEKGDFSK 132 (180)
T ss_pred eEecCHHHHHHHHHHHhccchhhHH---------------HHHHHHHHHhcCCcch
Confidence 5568999999999999977633332 3678999999998764
No 28
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=25.01 E-value=1.4e+02 Score=23.77 Aligned_cols=26 Identities=23% Similarity=0.383 Sum_probs=15.1
Q ss_pred HHHHHHHHHHhhcCCCChHHHHHHhh
Q psy13866 174 PAVIYDVLGAWETSVLSSTDVKRILD 199 (201)
Q Consensus 174 p~ai~evL~AwE~g~lS~~~VkrilD 199 (201)
|.-+-+++..-++|.||.+..|.++.
T Consensus 41 ~~~l~~li~lv~~g~It~~~ak~vl~ 66 (147)
T smart00845 41 PEHLAELLKLIEDGTISGKIAKEVLE 66 (147)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHH
Confidence 44555666666666666666555554
No 29
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=24.88 E-value=1.1e+02 Score=24.47 Aligned_cols=41 Identities=12% Similarity=0.172 Sum_probs=34.7
Q ss_pred cccHHHHHHhhccccccchHHHHHHHHhhhccchHHHHHHH
Q psy13866 6 EPTLARVLRTLDTEFSKIQDALLNVLSQVLNGKSFDLILAV 46 (201)
Q Consensus 6 Eptl~~IlKtl~aD~sK~qe~Ll~~L~~mlsGkSfdlilAa 46 (201)
+||-.+|-|.|++=-.++.+.++..|..-|.|+..+=+++-
T Consensus 16 ~it~e~I~~IL~AAGveVee~~~k~~v~aL~GkdIeElI~~ 56 (106)
T PRK06402 16 EINEDNLKKVLEAAGVEVDEARVKALVAALEDVNIEEAIKK 56 (106)
T ss_pred CCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHh
Confidence 78888888888864457778899999999999999988863
No 30
>PF08721 Tn7_Tnp_TnsA_C: TnsA endonuclease C terminal; InterPro: IPR014832 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The C-terminal domain of TnsA binds DNA. ; PDB: 1F1Z_B 1T0F_B.
Probab=24.16 E-value=64 Score=22.18 Aligned_cols=31 Identities=19% Similarity=0.340 Sum_probs=21.6
Q ss_pred cccHHHHHHhhccccccchHHHHHHHHhhhc
Q psy13866 6 EPTLARVLRTLDTEFSKIQDALLNVLSQVLN 36 (201)
Q Consensus 6 Eptl~~IlKtl~aD~sK~qe~Ll~~L~~mls 36 (201)
+-|+..+++.+|.+|.-.+...+..+-|++.
T Consensus 41 ~~tl~~l~~~~d~~~~l~~g~~L~~l~~LiA 71 (79)
T PF08721_consen 41 TMTLRDLCKELDKDYELEPGTALPLLRHLIA 71 (79)
T ss_dssp TSBHHHHHHHHHHHCT--TTHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHhcCCCcCChHHHHHHHHh
Confidence 4578888888888877666667777777764
No 31
>PF05044 HPD: Homeo-prospero domain; InterPro: IPR007738 The homeobox gene Prox1 is expressed in a subpopulation of endothelial cells that, after budding from veins, gives rise to the mammalian lymphatic system []. Prox1 has been found to be an early specific marker for the developing liver and pancreas in the mammalian foregut endoderm []. This family contains an atypical homeobox domain.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2LMD_A 1XPX_A 1MIJ_A.
Probab=21.44 E-value=3.3e+02 Score=23.43 Aligned_cols=71 Identities=15% Similarity=0.186 Sum_probs=49.6
Q ss_pred HHHHHHHHhcCCCCCChhhhhhccChhhHHHHHHhhccCccccccCCCCchHHHhhchHHHHHHHHHHhhcCCCChHHH
Q psy13866 116 EKWVRDCMVEGGRPKPYKKMLDEKDQAGVDDLLRQFNSSDAEFKNCPKLNCYEICLNIPAVIYDVLGAWETSVLSSTDV 194 (201)
Q Consensus 116 e~Wv~~cm~e~~~~ksP~~~l~~~Dp~~Vd~Ll~~lns~~~efk~~~~~kW~eiC~nip~ai~evL~AwE~g~lS~~~V 194 (201)
|+|+|++..|+.+. ++++.-.-|.+....|=.++|.+. +|... ..--.-+-..++|...|-..|-=+...-
T Consensus 59 EK~ARqa~~eGv~~--~~~l~V~rdsELfr~LN~HYNk~N-~~evP-----~~Fl~v~~~tLrEFf~AI~~gkD~dpsW 129 (158)
T PF05044_consen 59 EKFARQAVSEGVKN--ADDLRVTRDSELFRVLNMHYNKNN-DFEVP-----DRFLEVVQITLREFFNAIQAGKDSDPSW 129 (158)
T ss_dssp HHHHHHHHHHT-S---GGGSSSS-TTCHHHHHHHHHHTT--STT-------HHHHHHHHHHHHHHHHHHHCTCCCSTCC
T ss_pred HHHHHHHHHccCCc--HHHeeeccchHHHHHHHhhcccCC-CccCc-----hhHHHHHHHHHHHHHHHHHcCCCCCccc
Confidence 89999999998754 678888889999999999999888 77643 3334445566778888877776554433
No 32
>cd00159 RhoGAP RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins.
Probab=21.28 E-value=2.9e+02 Score=21.10 Aligned_cols=51 Identities=6% Similarity=0.191 Sum_probs=24.7
Q ss_pred cChhhHHHHHHhhccCcccc-ccCCCCchHHHhhchHHHHHHHHHHhhcCCCChHHHH
Q psy13866 139 KDQAGVDDLLRQFNSSDAEF-KNCPKLNCYEICLNIPAVIYDVLGAWETSVLSSTDVK 195 (201)
Q Consensus 139 ~Dp~~Vd~Ll~~lns~~~ef-k~~~~~kW~eiC~nip~ai~evL~AwE~g~lS~~~Vk 195 (201)
.+...++.|...++++. .. ... +...|++| ++++..|..=..+.|+.+-.+
T Consensus 26 g~~~~~~~l~~~~~~~~-~~~~~~-~~~~~~va----~~lK~~l~~Lp~pli~~~~~~ 77 (169)
T cd00159 26 GSASKIEELKKKFDRGE-DIDDLE-DYDVHDVA----SLLKLYLRELPEPLIPFELYD 77 (169)
T ss_pred CcHHHHHHHHHHHhcCC-CCcccc-ccCHHHHH----HHHHHHHHcCCCccCCHHHHH
Confidence 34555666666666665 22 222 34455555 344444444444445444333
No 33
>PF07511 DUF1525: Protein of unknown function (DUF1525); InterPro: IPR011090 This family of proteins is restricted to the Gammaproteobacteria. Members belong to extended genomic regions that appear to be spread by conjugative transfer.
Probab=20.01 E-value=2.1e+02 Score=23.04 Aligned_cols=41 Identities=20% Similarity=0.345 Sum_probs=32.4
Q ss_pred cChhhHHHHHHh-hccCccccccCCCCchHHHhhchHHHHHHHHHHhhcCCC
Q psy13866 139 KDQAGVDDLLRQ-FNSSDAEFKNCPKLNCYEICLNIPAVIYDVLGAWETSVL 189 (201)
Q Consensus 139 ~Dp~~Vd~Ll~~-lns~~~efk~~~~~kW~eiC~nip~ai~evL~AwE~g~l 189 (201)
.||...+....+ |++++ |.+.=--|-.+-+-+..||..|.=
T Consensus 41 adp~qA~~~~~~rl~s~~----------~~~~q~~L~~Ayqgv~~Aw~lgi~ 82 (114)
T PF07511_consen 41 ADPQQAEAQARQRLQSPD----------WQQLQQQLAQAYQGVVDAWSLGIT 82 (114)
T ss_pred CChHHHHHHHHHHHcCcc----------HHHHHHHHHHHHHHHHHHHHhCcc
Confidence 377777776644 45665 888889999999999999999963
Done!