Query 035110
Match_columns 73
No_of_seqs 48 out of 50
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 09:17:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035110.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035110hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1763 Uncharacterized conser 99.7 1.1E-17 2.3E-22 130.3 4.3 62 7-71 219-280 (343)
2 COG5252 Uncharacterized conser 97.7 2.5E-05 5.4E-10 60.7 2.9 63 6-71 203-266 (299)
3 KOG4018 Uncharacterized conser 97.5 6.1E-05 1.3E-09 56.4 2.0 51 10-64 138-188 (215)
4 PF15086 UPF0542: Uncharacteri 89.3 0.88 1.9E-05 29.6 4.2 31 19-49 36-66 (74)
5 PF12602 FinO_N: Fertility inh 76.5 5.1 0.00011 26.0 3.7 32 15-46 36-69 (72)
6 PF00558 Vpu: Vpu protein; In 75.9 0.55 1.2E-05 30.7 -0.9 30 21-52 26-55 (81)
7 COG3657 Uncharacterized protei 69.2 12 0.00026 25.6 4.3 38 14-54 4-41 (100)
8 KOG3206 Alpha-tubulin folding 61.4 13 0.00029 28.6 3.7 12 20-31 110-121 (234)
9 PF09720 Unstab_antitox: Putat 60.7 7.9 0.00017 22.1 1.9 24 38-61 30-54 (54)
10 PF02604 PhdYeFM_antitox: Anti 53.9 31 0.00068 19.9 3.8 40 12-51 35-75 (75)
11 PF01372 Melittin: Melittin; 50.5 17 0.00037 19.5 2.0 14 19-32 13-26 (26)
12 TIGR02574 stabl_TIGR02574 puta 44.0 19 0.00041 21.4 1.7 24 39-62 34-58 (63)
13 KOG2335 tRNA-dihydrouridine sy 43.4 10 0.00023 30.5 0.7 22 50-72 225-247 (358)
14 KOG3088 Secretory carrier memb 42.9 76 0.0017 25.5 5.4 44 14-59 55-99 (313)
15 KOG1098 Putative SAM-dependent 40.8 68 0.0015 28.6 5.2 37 13-49 655-701 (780)
16 PF06945 DUF1289: Protein of u 37.9 67 0.0015 18.5 3.4 29 17-45 22-50 (51)
17 COG5011 Uncharacterized protei 37.3 47 0.001 25.6 3.3 39 14-59 121-160 (228)
18 PF03234 CDC37_N: Cdc37 N term 35.5 76 0.0016 23.0 4.0 22 14-35 21-42 (177)
19 PF10883 DUF2681: Protein of u 34.9 1E+02 0.0023 20.1 4.3 28 21-48 19-46 (87)
20 PF07897 DUF1675: Protein of u 34.8 80 0.0017 24.6 4.3 34 13-47 61-94 (284)
21 PF13275 S4_2: S4 domain; PDB: 33.6 27 0.00058 21.6 1.3 13 14-26 5-17 (65)
22 PF08763 Ca_chan_IQ: Voltage g 33.5 35 0.00076 19.3 1.6 18 18-35 15-32 (35)
23 PRK07952 DNA replication prote 30.8 1.4E+02 0.003 22.0 4.9 28 11-38 16-45 (244)
24 PF09069 EF-hand_3: EF-hand; 30.7 34 0.00074 22.3 1.5 16 13-28 60-75 (90)
25 PF04406 TP6A_N: Type IIB DNA 30.6 17 0.00037 21.6 0.1 22 48-70 22-43 (68)
26 TIGR00742 yjbN tRNA dihydrouri 29.9 25 0.00055 26.8 0.9 20 50-70 215-235 (318)
27 PRK00247 putative inner membra 29.5 68 0.0015 26.2 3.3 12 30-41 341-352 (429)
28 PF05178 Kri1: KRI1-like famil 28.3 59 0.0013 21.4 2.3 20 26-45 1-20 (101)
29 PRK11507 ribosome-associated p 27.9 27 0.00059 22.1 0.6 36 14-58 9-44 (70)
30 KOG4691 Uncharacterized conser 27.0 1.1E+02 0.0023 23.6 3.7 26 23-48 117-142 (227)
31 PF12220 U1snRNP70_N: U1 small 24.8 1.2E+02 0.0025 19.3 3.2 27 22-48 59-85 (94)
32 PF13904 DUF4207: Domain of un 24.6 1.4E+02 0.003 22.3 3.9 19 19-37 183-201 (264)
33 PF04673 Cyclase_polyket: Poly 24.5 24 0.00052 23.8 -0.1 12 53-64 25-36 (97)
34 cd04741 DHOD_1A_like Dihydroor 24.5 30 0.00065 25.7 0.4 24 47-70 261-285 (294)
35 PF14981 FAM165: FAM165 family 24.4 86 0.0019 19.1 2.3 19 25-44 30-48 (51)
36 cd02735 RNAP_I_Rpa1_C Largest 24.2 29 0.00064 26.7 0.3 17 7-23 18-34 (309)
37 smart00084 NMU Neuromedin U. N 23.7 38 0.00083 18.2 0.6 16 51-66 9-24 (26)
38 cd00165 S4 S4/Hsp/ tRNA synthe 22.6 1.1E+02 0.0023 16.0 2.3 13 48-60 23-35 (70)
39 PF10107 Endonuc_Holl: Endonuc 21.7 1.8E+02 0.0038 21.2 3.9 10 19-28 25-34 (156)
40 KOG3925 Uncharacterized conser 21.7 1.5E+02 0.0033 24.3 3.9 27 12-38 17-43 (371)
41 PF01527 HTH_Tnp_1: Transposas 21.4 75 0.0016 18.1 1.6 15 16-30 34-48 (76)
42 PF02035 Coagulin: Coagulin; 21.1 1.1E+02 0.0024 22.5 2.7 14 52-65 38-53 (174)
43 PF02699 YajC: Preprotein tran 21.1 56 0.0012 20.4 1.1 25 22-52 17-41 (82)
44 PHA00490 terminal protein 21.0 58 0.0013 25.4 1.4 13 17-29 52-64 (266)
45 KOG4819 Uncharacterized conser 20.9 2.9E+02 0.0062 19.1 4.6 32 18-49 34-65 (106)
46 PF07141 Phage_term_sma: Putat 20.7 1.2E+02 0.0026 22.3 2.9 17 13-29 39-55 (174)
47 cd07692 Ig_CD3_epsilon Immunog 20.2 47 0.001 20.7 0.6 19 52-70 2-20 (65)
48 PF14062 DUF4253: Domain of un 20.2 28 0.00061 22.9 -0.4 13 58-70 74-86 (111)
No 1
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=99.70 E-value=1.1e-17 Score=130.33 Aligned_cols=62 Identities=21% Similarity=0.428 Sum_probs=55.1
Q ss_pred cCCCCCCccccCHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhCccccccccccccCCcccccC
Q 035110 7 QQSEEPRGKSISQAQFVSWKRQKDADASARKEEAARKRAEDIAAGTVQMNGRELFLHEPWVFDNT 71 (73)
Q Consensus 7 ~~~~~p~~T~ITle~Fl~WKkrK~~Ek~ak~ae~~~kr~~d~~AG~~~MsGRElF~~~P~lfdd~ 71 (73)
-+.++||.||||+++|++||++|.+|+++++++..++|+ ++|+--|||||||+++|+||+|-
T Consensus 219 R~~L~~nlT~~T~e~F~~WKk~k~~er~~k~~~~~~~~k---~~gk~~~sGRElF~~~~dl~~dd 280 (343)
T KOG1763|consen 219 RAALGPNLTPLTEETFKAWKKRKIRERKEKLAAEKAERK---KVGKSNMSGRELFESNADLVNDD 280 (343)
T ss_pred HHhcCCCCccccHHHHHHHHHhhHHHHHHHHHHHHHHhh---hhccCCCchHHHHhhchhhccCc
Confidence 345899999999999999999999999999988888887 57763399999999999999985
No 2
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=97.71 E-value=2.5e-05 Score=60.66 Aligned_cols=63 Identities=17% Similarity=0.279 Sum_probs=46.7
Q ss_pred ccCCCCCCccccCHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhCccccccc-cccccCCcccccC
Q 035110 6 DQQSEEPRGKSISQAQFVSWKRQKDADASARKEEAARKRAEDIAAGTVQMNGR-ELFLHEPWVFDNT 71 (73)
Q Consensus 6 ~~~~~~p~~T~ITle~Fl~WKkrK~~Ek~ak~ae~~~kr~~d~~AG~~~MsGR-ElF~~~P~lfdd~ 71 (73)
+-++++++.||||.+.|-.||.-.+..... ++++++-++-.-|+--++|+ |+|+.+-++|-|.
T Consensus 203 eR~~L~~~LTP~TeenFk~Wkd~~~~r~lk---q~ee~~s~Rk~~gr~~~~k~~e~FEt~~d~~~dd 266 (299)
T COG5252 203 ERQSLPEKLTPLTEENFKEWKDGRRLRILK---QKEEKESARKVKGRATGTKGVELFETRRDLFKDD 266 (299)
T ss_pred HhccCCCcCCcccHHHHHHhccchHHHHHH---HHHHHHhcccchhhhhhccchhhhhccccccccc
Confidence 456799999999999999999776655555 44455555444566556666 9999999988764
No 3
>KOG4018 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.47 E-value=6.1e-05 Score=56.45 Aligned_cols=51 Identities=20% Similarity=0.404 Sum_probs=36.3
Q ss_pred CCCCccccCHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhCccccccccccccC
Q 035110 10 EEPRGKSISQAQFVSWKRQKDADASARKEEAARKRAEDIAAGTVQMNGRELFLHE 64 (73)
Q Consensus 10 ~~p~~T~ITle~Fl~WKkrK~~Ek~ak~ae~~~kr~~d~~AG~~~MsGRElF~~~ 64 (73)
..+-.||||+++|+.||.+=+++... ...+++.+.++..-..+||.+|..+
T Consensus 138 ~kfhgt~VT~esfl~Wk~~fe~el~~----~~~k~~~~~~~~~~k~tgRQ~f~~d 188 (215)
T KOG4018|consen 138 KKFHGTPVTLESFLEWKLKFEEELLQ----IKAKVKKRLQALAKKLTGRQLFETD 188 (215)
T ss_pred ccccCCceehhhhHHHHHhhhhhhhh----hhhhhhhHHHHHhhhHHHHHHHHhc
Confidence 45669999999999999999998833 3333333344555567888888754
No 4
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=89.31 E-value=0.88 Score=29.60 Aligned_cols=31 Identities=29% Similarity=0.495 Sum_probs=26.1
Q ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHhh
Q 035110 19 QAQFVSWKRQKDADASARKEEAARKRAEDIA 49 (73)
Q Consensus 19 le~Fl~WKkrK~~Ek~ak~ae~~~kr~~d~~ 49 (73)
+.-|++||=.|..|+..+.....+||.+.|+
T Consensus 36 isa~lSwkLaK~ie~~ere~K~k~Kr~~~i~ 66 (74)
T PF15086_consen 36 ISAVLSWKLAKAIEKEEREKKKKAKRQANIA 66 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999888888888888874
No 5
>PF12602 FinO_N: Fertility inhibition protein N terminal; InterPro: IPR021065 This entry represents the N-terminal of the Fertility inhibition protein FinO, found in bacteria, and is typically between 62 and 102 amino acids in length. The FinOP (fertility inhibition) system of F-like plasmids consists of an antisense RNA (FinP) and a 22 kDa protein (FinO) which act in concert to prevent the translation of TraJ, the positive regulator of the transfer operon []. ; PDB: 1DVO_A.
Probab=76.54 E-value=5.1 Score=25.96 Aligned_cols=32 Identities=31% Similarity=0.495 Sum_probs=15.9
Q ss_pred cccCHHHHHHHHHhhH--HHHHHHHHHHHHHHHH
Q 035110 15 KSISQAQFVSWKRQKD--ADASARKEEAARKRAE 46 (73)
Q Consensus 15 T~ITle~Fl~WKkrK~--~Ek~ak~ae~~~kr~~ 46 (73)
+-|...+=-+||-+|. .|+.++.+|++.++..
T Consensus 36 kvvvV~tpPaWKvkKqkl~ekA~r~Ae~aarka~ 69 (72)
T PF12602_consen 36 KVVVVSTPPAWKVKKQKLDEKAAREAEAAARKAA 69 (72)
T ss_dssp ---------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred eEEEecCCchhhHHHHHHHHHHHHHHHHHHhccc
Confidence 4466677889986654 4677777777766653
No 6
>PF00558 Vpu: Vpu protein; InterPro: IPR008187 The Human immunodeficiency virus 1 (HIV-1) Vpu protein acts in the degradation of CD4 in the endoplasmic reticulum and in the enhancement of virion release from the plasma membrane of infected cells [].; GO: 0019076 release of virus from host; PDB: 2JPX_A 1PI8_A 2GOH_A 2GOF_A 1PI7_A 1PJE_A 1VPU_A 2K7Y_A.
Probab=75.94 E-value=0.55 Score=30.69 Aligned_cols=30 Identities=30% Similarity=0.512 Sum_probs=15.9
Q ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHHHhhhCc
Q 035110 21 QFVSWKRQKDADASARKEEAARKRAEDIAAGT 52 (73)
Q Consensus 21 ~Fl~WKkrK~~Ek~ak~ae~~~kr~~d~~AG~ 52 (73)
-|..||+.|+|.++.++-+--+.|++| ||+
T Consensus 26 v~ieYrk~~rqrkId~li~RIreraED--SGn 55 (81)
T PF00558_consen 26 VYIEYRKIKRQRKIDRLIERIRERAED--SGN 55 (81)
T ss_dssp H------------CHHHHHHHHCTTTC--CHC
T ss_pred HHHHHHHHHHHHhHHHHHHHHHccccc--CCC
Confidence 478899999999999999999999999 775
No 7
>COG3657 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=69.24 E-value=12 Score=25.56 Aligned_cols=38 Identities=13% Similarity=0.228 Sum_probs=28.1
Q ss_pred ccccCHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhCccc
Q 035110 14 GKSISQAQFVSWKRQKDADASARKEEAARKRAEDIAAGTVQ 54 (73)
Q Consensus 14 ~T~ITle~Fl~WKkrK~~Ek~ak~ae~~~kr~~d~~AG~~~ 54 (73)
.|....++|.+|-+.=+-.++. ++-.+|-.+++.|+.+
T Consensus 4 i~~~~~d~F~~W~~kLkD~~Ak---a~I~~Rl~rl~~GN~G 41 (100)
T COG3657 4 ITLKGTDTFSEWLKKLKDRRAK---AKIAARLDRLALGNFG 41 (100)
T ss_pred EeecchHHHHHHHHHHHhHHHH---HHHHHHHHHHhcCCCc
Confidence 4677889999998765444444 6677888888888744
No 8
>KOG3206 consensus Alpha-tubulin folding cofactor B [Posttranslational modification, protein turnover, chaperones]
Probab=61.39 E-value=13 Score=28.58 Aligned_cols=12 Identities=8% Similarity=0.205 Sum_probs=8.9
Q ss_pred HHHHHHHHhhHH
Q 035110 20 AQFVSWKRQKDA 31 (73)
Q Consensus 20 e~Fl~WKkrK~~ 31 (73)
+++++||++-.-
T Consensus 110 dSvr~~kk~~~~ 121 (234)
T KOG3206|consen 110 DSVRRFKKKHGY 121 (234)
T ss_pred HHHHHHHHHhcc
Confidence 567899987654
No 9
>PF09720 Unstab_antitox: Putative addiction module component; InterPro: IPR013406 This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilisation proteins (IPR007712 from INTERPRO). It is likely that this protein and its partner comprise some form of addiction module - a pair of genes consisting of a stable toxin and an unstable antitoxin which mediate programmed cell death [] - although these gene pairs are usually found on the bacterial main chromosome.
Probab=60.72 E-value=7.9 Score=22.06 Aligned_cols=24 Identities=17% Similarity=0.246 Sum_probs=18.9
Q ss_pred HHHHHHHHHHhhhCc-ccccccccc
Q 035110 38 EEAARKRAEDIAAGT-VQMNGRELF 61 (73)
Q Consensus 38 ae~~~kr~~d~~AG~-~~MsGRElF 61 (73)
.++.++|-++|.+|+ ..+++-|+|
T Consensus 30 ~~el~rR~~~~~~G~~~~i~~eev~ 54 (54)
T PF09720_consen 30 KEELERRLAEYESGKVQGIPWEEVK 54 (54)
T ss_pred HHHHHHHHHHHHcCCCCCCcHHHhC
Confidence 366778888999998 668887776
No 10
>PF02604 PhdYeFM_antitox: Antitoxin Phd_YefM, type II toxin-antitoxin system; InterPro: IPR006442 This entry is represented by Bacteriophage P1, prevent-host-death protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins is characterised by a region of about 55 amino acids toward the N-terminal end of bacterial proteins which are themselves only 85 amino acids, or thereabouts, in length. The best-characterised member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (IPR006440 from INTERPRO) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family. ; PDB: 3DBO_A 2ODK_B 3G5O_D 2A6Q_B 3D55_C 3OEI_E 3CTO_C 3K33_D 3KH2_F 3HS2_C ....
Probab=53.86 E-value=31 Score=19.88 Aligned_cols=40 Identities=23% Similarity=0.309 Sum_probs=28.5
Q ss_pred CCccccCHHHHHHHHH-hhHHHHHHHHHHHHHHHHHHhhhC
Q 035110 12 PRGKSISQAQFVSWKR-QKDADASARKEEAARKRAEDIAAG 51 (73)
Q Consensus 12 p~~T~ITle~Fl~WKk-rK~~Ek~ak~ae~~~kr~~d~~AG 51 (73)
|...=|+.+.|.++.+ ...........+...+..+.|++|
T Consensus 35 ~~~vli~~~~ye~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (75)
T PF02604_consen 35 PVAVLISVEDYERLQELTEELLQAQTAAEALEESGEEIEAG 75 (75)
T ss_dssp EEEEEEEHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHC-
T ss_pred CCeecccHHHHHHHHHHHHHHHHHHHHHHHHHhChhhhhcC
Confidence 3455588899999999 666666666667777777777776
No 11
>PF01372 Melittin: Melittin; InterPro: IPR002116 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: Api m 3. Melittin is the principal protein component of the venom of the honeybee, Apis mellifera. It inhibits protein kinase C, Ca2+/calmodulin-dependent protein kinase II, myosin light chain kinase and Na+/K+-ATPase (synaptosomal membrane) and is a cell membrane lytic factor. Melittin is a small peptide with no disulphide bridge; the N-terminal part of the molecule is predominantly hydrophobic and the C-terminal part is hydrophilic and strongly basic. The molecular mechanisms underlying the various effects of melittin on membranes have not been completely defined and much of the evidence indicates that different molecular mechanisms may underlie different actions of the peptide []. Extensive work with melittin has shown that the venom has multiple effects, probably, as a result of its interaction with negatively changed phospholipids. It inhibits well known transport pumps such as the Na+-K+-ATPase and the H+-K+-ATPase. Melittin increases the permeability of cell membranes to ions, particularly Na+ and indirectly Ca2+, because of the Na+-Ca2+-exchange. This effect results in marked morphological and functional changes, particularly in excitable tissues such as cardiac myocytes. In some other tissues, e.g., cornea, not only Na+ but Cl- permeability is also increased by melittin. Similar effects to melittin on H+-K+-ATPase have been found with the synthetic amphipathic polypeptide Trp-3 []. The study of melittin in model membranes has been useful for the development of methodology for determination of membrane protein structures. A molecular dynamics simulation of melittin in a hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer was carried out. The effect of melittin on the surrounding membrane was localised to its immediate vicinity, and its asymmetry with respect to the two layers may be a result of the fact that it is not fully transmembranal. Melittin's hydrophilic C terminus anchors it at the extracellular interface, leaving the N terminus "loose" in the lower layer of the membrane [].; GO: 0004860 protein kinase inhibitor activity, 0005576 extracellular region; PDB: 3QRX_B 2MLT_A 1BH1_A.
Probab=50.48 E-value=17 Score=19.54 Aligned_cols=14 Identities=21% Similarity=0.598 Sum_probs=10.7
Q ss_pred HHHHHHHHHhhHHH
Q 035110 19 QAQFVSWKRQKDAD 32 (73)
Q Consensus 19 le~Fl~WKkrK~~E 32 (73)
|-+..+|-|+|+++
T Consensus 13 LP~lISWIK~kr~~ 26 (26)
T PF01372_consen 13 LPTLISWIKNKRQQ 26 (26)
T ss_dssp HHHHHHHHHHHHH-
T ss_pred ChHHHHHHHHHhcC
Confidence 45678999999875
No 12
>TIGR02574 stabl_TIGR02574 putative addiction module component, TIGR02574 family. Members of this family are bacterial proteins, typically are about 75 amino acids long, always found as part of a pair (at least) of two small genes. The other in the pair always belongs to a subfamily of the larger family pfam05016 (although not necessarily scoring above the designated cutoff), which contains plasmid stabilization proteins. It is likely that this protein and its pfam05016 member partner comprise some form of addiction module, although these gene pairs usually are found on the bacterial main chromosome.
Probab=44.03 E-value=19 Score=21.38 Aligned_cols=24 Identities=17% Similarity=0.059 Sum_probs=19.2
Q ss_pred HHHHHHHHHhhhCc-cccccccccc
Q 035110 39 EAARKRAEDIAAGT-VQMNGRELFL 62 (73)
Q Consensus 39 e~~~kr~~d~~AG~-~~MsGRElF~ 62 (73)
++.++|.+.|.+|+ ..+++-|+|.
T Consensus 34 ~el~~R~~~~~~g~~~~i~~eev~~ 58 (63)
T TIGR02574 34 AELDRRLADYKADPSKASPWEEVRA 58 (63)
T ss_pred HHHHHHHHHHHcCCcCCCCHHHHHH
Confidence 66778888999998 6688887774
No 13
>KOG2335 consensus tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=43.44 E-value=10 Score=30.51 Aligned_cols=22 Identities=32% Similarity=0.422 Sum_probs=17.6
Q ss_pred hCc-cccccccccccCCcccccCC
Q 035110 50 AGT-VQMNGRELFLHEPWVFDNTH 72 (73)
Q Consensus 50 AG~-~~MsGRElF~~~P~lfdd~~ 72 (73)
.|. -+||||-| ++||++|.+..
T Consensus 225 tG~dGVM~argl-L~NPa~F~~~~ 247 (358)
T KOG2335|consen 225 TGADGVMSARGL-LYNPALFLTAG 247 (358)
T ss_pred hCCceEEecchh-hcCchhhccCC
Confidence 676 56999988 69999997644
No 14
>KOG3088 consensus Secretory carrier membrane protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=42.90 E-value=76 Score=25.46 Aligned_cols=44 Identities=18% Similarity=0.159 Sum_probs=22.9
Q ss_pred ccccCHHHHHHHHH-hhHHHHHHHHHHHHHHHHHHhhhCcccccccc
Q 035110 14 GKSISQAQFVSWKR-QKDADASARKEEAARKRAEDIAAGTVQMNGRE 59 (73)
Q Consensus 14 ~T~ITle~Fl~WKk-rK~~Ek~ak~ae~~~kr~~d~~AG~~~MsGRE 59 (73)
.|.+.-+..++=++ .|+||+-.|+|++-+||+..+ ++ .+|.+|+
T Consensus 55 ~~~~a~~~~~kq~eL~~rqeEL~Rke~ELdRREr~~-a~-~g~~~~~ 99 (313)
T KOG3088|consen 55 PSTQAKDLAKKQAELLKKQEELRRKEQELDRRERAL-AR-AGIVIRE 99 (313)
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH-hh-ccCcccc
Confidence 35666777754443 344455555555554444443 33 5666664
No 15
>KOG1098 consensus Putative SAM-dependent rRNA methyltransferase SPB1 [RNA processing and modification; General function prediction only]
Probab=40.79 E-value=68 Score=28.55 Aligned_cols=37 Identities=30% Similarity=0.539 Sum_probs=31.4
Q ss_pred CccccCHHHHHHHHHh----------hHHHHHHHHHHHHHHHHHHhh
Q 035110 13 RGKSISQAQFVSWKRQ----------KDADASARKEEAARKRAEDIA 49 (73)
Q Consensus 13 ~~T~ITle~Fl~WKkr----------K~~Ek~ak~ae~~~kr~~d~~ 49 (73)
..+|||-+.-...+++ |-+|..+|+...|.+|.+.++
T Consensus 655 ~~kPvtKe~v~a~rer~keiNARPiKKVaEAkARKkrra~kRLek~k 701 (780)
T KOG1098|consen 655 KQKPVTKEEVAAYRERMKEINARPIKKVAEAKARKKRRAQKRLEKVK 701 (780)
T ss_pred CCCCCCHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999888877 788888888888888888873
No 16
>PF06945 DUF1289: Protein of unknown function (DUF1289); InterPro: IPR010710 This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N terminus. The function of this family is unknown.
Probab=37.93 E-value=67 Score=18.51 Aligned_cols=29 Identities=21% Similarity=0.308 Sum_probs=23.3
Q ss_pred cCHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 035110 17 ISQAQFVSWKRQKDADASARKEEAARKRA 45 (73)
Q Consensus 17 ITle~Fl~WKkrK~~Ek~ak~ae~~~kr~ 45 (73)
-|++.-..|+...+.++.+=.++..++++
T Consensus 22 RT~dEI~~W~~~s~~er~~i~~~l~~R~~ 50 (51)
T PF06945_consen 22 RTLDEIRDWKSMSDDERRAILARLRARRA 50 (51)
T ss_pred CcHHHHHHHhhCCHHHHHHHHHHHHHHhc
Confidence 48999999999999998886666665543
No 17
>COG5011 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.32 E-value=47 Score=25.57 Aligned_cols=39 Identities=18% Similarity=0.169 Sum_probs=28.7
Q ss_pred ccccCHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhCc-ccccccc
Q 035110 14 GKSISQAQFVSWKRQKDADASARKEEAARKRAEDIAAGT-VQMNGRE 59 (73)
Q Consensus 14 ~T~ITle~Fl~WKkrK~~Ek~ak~ae~~~kr~~d~~AG~-~~MsGRE 59 (73)
..|+||.++..|+.++-++..-= =+.-+++|+ +-+++|.
T Consensus 121 e~pv~ltq~i~ki~kila~~esL-------lekttksgKkv~i~~~~ 160 (228)
T COG5011 121 ESPVSLTQWIEKIIKILAENESL-------LEKTTKSGKKVNINLRV 160 (228)
T ss_pred cCcccHHHHHHHHHHHhhhHHHH-------HHHhhccCcEEEeehHH
Confidence 45799999999998887666541 123357897 8899885
No 18
>PF03234 CDC37_N: Cdc37 N terminal kinase binding; InterPro: IPR013855 In Saccharomyces cerevisiae (Baker's yeast), cell division control protein Cdc37 is required for the productive formation of Cdc28-cyclin complexes. Cdc37 may be a kinase targeting subunit of Hsp90 [].
Probab=35.50 E-value=76 Score=22.96 Aligned_cols=22 Identities=18% Similarity=0.418 Sum_probs=16.8
Q ss_pred ccccCHHHHHHHHHhhHHHHHH
Q 035110 14 GKSISQAQFVSWKRQKDADASA 35 (73)
Q Consensus 14 ~T~ITle~Fl~WKkrK~~Ek~a 35 (73)
...|.-.+|..||.+-+-|+-.
T Consensus 21 HPniD~~S~~rwk~~~~~e~~~ 42 (177)
T PF03234_consen 21 HPNIDKRSLFRWKHQARHERRE 42 (177)
T ss_pred CCCCChHHHHhHHHHHHHHHHH
Confidence 4458999999999987655544
No 19
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=34.94 E-value=1e+02 Score=20.14 Aligned_cols=28 Identities=14% Similarity=0.351 Sum_probs=19.8
Q ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHHHh
Q 035110 21 QFVSWKRQKDADASARKEEAARKRAEDI 48 (73)
Q Consensus 21 ~Fl~WKkrK~~Ek~ak~ae~~~kr~~d~ 48 (73)
-|+.||-+|..++.+++.++.+.-+..+
T Consensus 19 ~y~~~k~~ka~~~~~kL~~en~qlk~Ek 46 (87)
T PF10883_consen 19 AYLWWKVKKAKKQNAKLQKENEQLKTEK 46 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4778888888888777766665555544
No 20
>PF07897 DUF1675: Protein of unknown function (DUF1675); InterPro: IPR012463 The members of this family are sequences derived from hypothetical plant proteins of unknown function. One member of this family (Q9SFV5 from SWISSPROT) is annotated as a putative RNA-binding protein, but no evidence was found to support this.
Probab=34.80 E-value=80 Score=24.58 Aligned_cols=34 Identities=35% Similarity=0.586 Sum_probs=25.0
Q ss_pred CccccCHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 035110 13 RGKSISQAQFVSWKRQKDADASARKEEAARKRAED 47 (73)
Q Consensus 13 ~~T~ITle~Fl~WKkrK~~Ek~ak~ae~~~kr~~d 47 (73)
.++.++-++=..|+|||..+ ..+..|+.++|-++
T Consensus 61 RTsSLP~etEee~~Krke~q-~~~r~eakrkr~e~ 94 (284)
T PF07897_consen 61 RTSSLPTETEEEWRKRKEMQ-SLRRLEAKRKRSEK 94 (284)
T ss_pred cccCCChHHHHHHHHHHHHH-HHHHHHHHHHHHHh
Confidence 46778888889999999887 44455666666665
No 21
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=33.61 E-value=27 Score=21.61 Aligned_cols=13 Identities=15% Similarity=0.210 Sum_probs=7.5
Q ss_pred ccccCHHHHHHHH
Q 035110 14 GKSISQAQFVSWK 26 (73)
Q Consensus 14 ~T~ITle~Fl~WK 26 (73)
.-+|+|.+||+|-
T Consensus 5 ~e~I~L~qlLK~~ 17 (65)
T PF13275_consen 5 TEYITLGQLLKLA 17 (65)
T ss_dssp -S---HHHHHHHH
T ss_pred CCcEEHHHHHhHc
Confidence 4579999999884
No 22
>PF08763 Ca_chan_IQ: Voltage gated calcium channel IQ domain; InterPro: IPR014873 Ca2+ ions are unique in that they not only carry charge but they are also the most widely used of diffusible second messengers. Voltage-dependent Ca2+ channels (VDCC) are a family of molecules that allow cells to couple electrical activity to intracellular Ca2+ signalling. The opening and closing of these channels by depolarizing stimuli, such as action potentials, allows Ca2+ ions to enter neurons down a steep electrochemical gradient, producing transient intracellular Ca2+ signals. Many of the processes that occur in neurons, including transmitter release, gene transcription and metabolism are controlled by Ca2+ influx occurring simultaneously at different cellular locales. The pore is formed by the alpha-1 subunit which incorporates the conduction pore, the voltage sensor and gating apparatus, and the known sites of channel regulation by second messengers, drugs, and toxins []. The activity of this pore is modulated by 4 tightly-coupled subunits: an intracellular beta subunit; a transmembrane gamma subunit; and a disulphide-linked complex of alpha-2 and delta subunits, which are proteolytically cleaved from the same gene product. Properties of the protein including gating voltage-dependence, G protein modulation and kinase susceptibility can be influenced by these subunits. Voltage-gated calcium channels are classified as T, L, N, P, Q and R, and are distinguished by their sensitivity to pharmacological blocks, single-channel conductance kinetics, and voltage-dependence. On the basis of their voltage activation properties, the voltage-gated calcium classes can be further divided into two broad groups: the low (T-type) and high (L, N, P, Q and R-type) threshold-activated channels. The voltage-gated calcium channel alpha 1 subunit contains an IQ domain, named for its isoleucine-glutamine (IQ) motif, which interacts with hydrophobic pockets of Ca2+/calmodulin []. The interaction regulates two self-regulatory calcium dependent feedback mechanisms, calcium dependent inactivation (CDI), and calcium-dependent facilitation (CDF). ; PDB: 3OXQ_F 2F3Z_B 3G43_E 2F3Y_B 2BE6_D 3DVM_B 3BXK_D 2VAY_B 3DVK_B 3BXL_B ....
Probab=33.52 E-value=35 Score=19.30 Aligned_cols=18 Identities=22% Similarity=0.436 Sum_probs=12.1
Q ss_pred CHHHHHHHHHhhHHHHHH
Q 035110 18 SQAQFVSWKRQKDADASA 35 (73)
Q Consensus 18 Tle~Fl~WKkrK~~Ek~a 35 (73)
=.|-|..||++|.++...
T Consensus 15 I~dyfr~~K~rk~~~~~~ 32 (35)
T PF08763_consen 15 IQDYFRQFKKRKEQEQQE 32 (35)
T ss_dssp HHHHHHHHHHHHHHT---
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 357788999999876544
No 23
>PRK07952 DNA replication protein DnaC; Validated
Probab=30.81 E-value=1.4e+02 Score=21.97 Aligned_cols=28 Identities=18% Similarity=0.319 Sum_probs=20.5
Q ss_pred CCCccc--cCHHHHHHHHHhhHHHHHHHHH
Q 035110 11 EPRGKS--ISQAQFVSWKRQKDADASARKE 38 (73)
Q Consensus 11 ~p~~T~--ITle~Fl~WKkrK~~Ek~ak~a 38 (73)
++++.| -|-+.+++|.......+.....
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ 45 (244)
T PRK07952 16 PAHIKPAFKTGEELLAWQKEQGRIRSAALE 45 (244)
T ss_pred cccCCCCcCCHHHHHHHHHHHhHHHHHHHH
Confidence 445666 6899999999887777666443
No 24
>PF09069 EF-hand_3: EF-hand; InterPro: IPR015154 Like other EF hand domains, this domain forms a helix-loop-helix motif, though since it does not contain the canonical pattern of calcium binding residues found in many EF hand domains, it does not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (IPR001202 from INTERPRO), enhancing dystroglycan binding []. ; PDB: 1EG3_A 1EG4_A.
Probab=30.67 E-value=34 Score=22.32 Aligned_cols=16 Identities=25% Similarity=0.567 Sum_probs=10.6
Q ss_pred CccccCHHHHHHHHHh
Q 035110 13 RGKSISQAQFVSWKRQ 28 (73)
Q Consensus 13 ~~T~ITle~Fl~WKkr 28 (73)
....|+++.|+.|=..
T Consensus 60 ~~~~I~~~~Fl~wl~~ 75 (90)
T PF09069_consen 60 LSPKITENQFLDWLMS 75 (90)
T ss_dssp T-S-B-HHHHHHHHHT
T ss_pred CCCccCHHHHHHHHHh
Confidence 3677999999999653
No 25
>PF04406 TP6A_N: Type IIB DNA topoisomerase; InterPro: IPR013049 This entry represents the N-terminal domain found in Spo11, a meiotic recombination protein found in eukaryotes, and in subunit A of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea [, ]. These two types of proteins share structural homology. Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination through the formation of DNA double-strand breaks by a type II DNA topoisomerase-like activity. Spo11 acts in conjunction with several other proteins, including Rec102 in yeast, to bring about meiotic recombination []. DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. They can be divided into two classes: type I enzymes (5.99.1.2 from EC, topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC, topoisomerases II, IV and VI) break double-strand DNA []. Topoisomerase VI is a type IIB enzymes that assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003824 catalytic activity, 0005524 ATP binding, 0006259 DNA metabolic process, 0005694 chromosome; PDB: 1D3Y_B 2ZBK_A 2Q2E_A.
Probab=30.64 E-value=17 Score=21.62 Aligned_cols=22 Identities=9% Similarity=0.345 Sum_probs=15.2
Q ss_pred hhhCccccccccccccCCccccc
Q 035110 48 IAAGTVQMNGRELFLHEPWVFDN 70 (73)
Q Consensus 48 ~~AG~~~MsGRElF~~~P~lfdd 70 (73)
+..|+ ..+=||||=.+|+||.+
T Consensus 22 l~~~~-~~T~RdiYY~~~~lF~~ 43 (68)
T PF04406_consen 22 LQNNK-TSTKRDIYYRNVSLFKS 43 (68)
T ss_dssp HHTT---EEHHHHHHHCSCS-SS
T ss_pred HHcCC-ccchHHHHHhchhhccC
Confidence 34444 34889999999999975
No 26
>TIGR00742 yjbN tRNA dihydrouridine synthase A. Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase.
Probab=29.91 E-value=25 Score=26.78 Aligned_cols=20 Identities=30% Similarity=0.549 Sum_probs=16.2
Q ss_pred hCc-cccccccccccCCccccc
Q 035110 50 AGT-VQMNGRELFLHEPWVFDN 70 (73)
Q Consensus 50 AG~-~~MsGRElF~~~P~lfdd 70 (73)
+|- ..|.||.++. |||+|..
T Consensus 215 ~g~dgVMigRgal~-nP~if~~ 235 (318)
T TIGR00742 215 SHVDGVMVGREAYE-NPYLLAN 235 (318)
T ss_pred hCCCEEEECHHHHh-CCHHHHH
Confidence 364 7799999988 8999963
No 27
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=29.52 E-value=68 Score=26.24 Aligned_cols=12 Identities=25% Similarity=0.307 Sum_probs=4.5
Q ss_pred HHHHHHHHHHHH
Q 035110 30 DADASARKEEAA 41 (73)
Q Consensus 30 ~~Ek~ak~ae~~ 41 (73)
.++|..|++...
T Consensus 341 ~~~k~~~k~~~~ 352 (429)
T PRK00247 341 NEAKARKKEIAQ 352 (429)
T ss_pred HHHHHHHHHHHH
Confidence 333333333333
No 28
>PF05178 Kri1: KRI1-like family; InterPro: IPR018034 The Kri1 protein is also known as KRR1-interacting protein 1. The Saccharomyces cerevisiae member of this family is found to be required for the assembly of preribosomal 40S subunits in the nucleolus []. KRR1 is highly expressed in dividing cells and its expression ceases almost completely when cells enter the stationary phase.
Probab=28.28 E-value=59 Score=21.42 Aligned_cols=20 Identities=25% Similarity=0.468 Sum_probs=12.6
Q ss_pred HHhhHHHHHHHHHHHHHHHH
Q 035110 26 KRQKDADASARKEEAARKRA 45 (73)
Q Consensus 26 KkrK~~Ek~ak~ae~~~kr~ 45 (73)
|.||.+|+..|.++..+.+.
T Consensus 1 KeRK~~Ek~~k~eElkrlK~ 20 (101)
T PF05178_consen 1 KERKEEEKQEKEEELKRLKN 20 (101)
T ss_pred CcHHHHHHHHHHHHHHHHHH
Confidence 45677777776666655443
No 29
>PRK11507 ribosome-associated protein; Provisional
Probab=27.93 E-value=27 Score=22.11 Aligned_cols=36 Identities=14% Similarity=0.285 Sum_probs=21.6
Q ss_pred ccccCHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhCccccccc
Q 035110 14 GKSISQAQFVSWKRQKDADASARKEEAARKRAEDIAAGTVQMNGR 58 (73)
Q Consensus 14 ~T~ITle~Fl~WKkrK~~Ek~ak~ae~~~kr~~d~~AG~~~MsGR 58 (73)
.-.|+|.+||+|---=.- =-.-+.-|+.|.|.+||-
T Consensus 9 ~e~I~L~QlLK~~~~v~S---------GG~AK~~I~eg~V~VNGe 44 (70)
T PRK11507 9 HPHVELCDLLKLEGWSES---------GAQAKIAIAEGQVKVDGA 44 (70)
T ss_pred CCeEEHHHHHhhhCcccC---------hHHHHHHHHcCceEECCE
Confidence 345999999998532111 111123367888888874
No 30
>KOG4691 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.03 E-value=1.1e+02 Score=23.64 Aligned_cols=26 Identities=19% Similarity=0.178 Sum_probs=20.4
Q ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHh
Q 035110 23 VSWKRQKDADASARKEEAARKRAEDI 48 (73)
Q Consensus 23 l~WKkrK~~Ek~ak~ae~~~kr~~d~ 48 (73)
-+|-.++.+++++++++.++.+...|
T Consensus 117 ~a~N~~~~~~R~~Rla~~~~E~~~~i 142 (227)
T KOG4691|consen 117 QAENRRLHELRIARLAQEEREQEQRI 142 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46778888888888888887777666
No 31
>PF12220 U1snRNP70_N: U1 small nuclear ribonucleoprotein of 70kDa MW N terminal; InterPro: IPR022023 This domain is found in eukaryotes. This domain is about 90 amino acids in length. This domain is found associated with PF00076 from PFAM. This domain is part of U1 snRNP, which is the pre-mRNA binding protein of the penta-snRNP spliceosome complex. It extends over a distance of 180 A from its RNA binding domain, wraps around the core domain of U1 snRNP consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition.
Probab=24.78 E-value=1.2e+02 Score=19.29 Aligned_cols=27 Identities=15% Similarity=0.282 Sum_probs=15.1
Q ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHHh
Q 035110 22 FVSWKRQKDADASARKEEAARKRAEDI 48 (73)
Q Consensus 22 Fl~WKkrK~~Ek~ak~ae~~~kr~~d~ 48 (73)
+..|..++..++..|++..+++-++.+
T Consensus 59 ~et~~e~~~r~~~ek~~~~~~~l~~~l 85 (94)
T PF12220_consen 59 TETKEERRERKRKEKKEKNEEKLEEEL 85 (94)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345666666666555555555555443
No 32
>PF13904 DUF4207: Domain of unknown function (DUF4207)
Probab=24.63 E-value=1.4e+02 Score=22.30 Aligned_cols=19 Identities=16% Similarity=0.699 Sum_probs=14.0
Q ss_pred HHHHHHHHHhhHHHHHHHH
Q 035110 19 QAQFVSWKRQKDADASARK 37 (73)
Q Consensus 19 le~Fl~WKkrK~~Ek~ak~ 37 (73)
..-|-.|.++|.++...++
T Consensus 183 ~~~~q~W~~kK~~e~~~~r 201 (264)
T PF13904_consen 183 KQRYQEWERKKKEEQQQKR 201 (264)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4579999988887766553
No 33
>PF04673 Cyclase_polyket: Polyketide synthesis cyclase; InterPro: IPR006765 Aromatic polyketides are assembled by a type II (iterative) polyketide synthase in bacteria. Iterative type II polyketide synthases produce polyketide chains of variable but defined length from a specific starter unit and a number of extender units. They also specify the initial regiospecific folding and cyclization pattern of nascent polyketides either through the action of a cyclase (CYC) subunit or through the combined action of site-specific ketoreductase and CYC subunits. Additional CYCs and other modifications may be necessary to produce linear aromatic polyketides. This family represents a number of cyclases involved in polyketide synthesis in a number of actinobacterial species. TcmI (P39890 from SWISSPROT) catalyses an aromatic rearrangement in the biosynthetic pathaway of tetracenomycin C from Streptomyces coelicolor. The protein is a homodimer where each subunit forms a beta-alpha-beta fold belonging to the ferrodoxin fold superfamily []. Four strands of antiparallel sheets and a layer of alpha helices create a cavity which was proposed to be the active site. This structure shows strong topological similarity to a polyketide monoxygenase (Q53908 from SWISSPROT) from S. coelicolor which functions in the actinorhodin biosynthesic pathway []. It was suggested, therefore, that this fold is well suited to serve as a framework for rearrangements and chemical modification of polyaromatic substrates.; GO: 0030639 polyketide biosynthetic process; PDB: 1TUW_A.
Probab=24.50 E-value=24 Score=23.79 Aligned_cols=12 Identities=25% Similarity=0.434 Sum_probs=9.0
Q ss_pred cccccccccccC
Q 035110 53 VQMNGRELFLHE 64 (73)
Q Consensus 53 ~~MsGRElF~~~ 64 (73)
+++++|.||.|+
T Consensus 25 ~Gv~rR~Lf~~~ 36 (97)
T PF04673_consen 25 MGVRRRSLFSFH 36 (97)
T ss_dssp HT--EEEEEEET
T ss_pred hCccceeEeeeC
Confidence 789999999986
No 34
>cd04741 DHOD_1A_like Dihydroorotate dehydrogenase (DHOD) class 1A FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.
Probab=24.49 E-value=30 Score=25.70 Aligned_cols=24 Identities=29% Similarity=0.218 Sum_probs=20.5
Q ss_pred HhhhCc-cccccccccccCCccccc
Q 035110 47 DIAAGT-VQMNGRELFLHEPWVFDN 70 (73)
Q Consensus 47 d~~AG~-~~MsGRElF~~~P~lfdd 70 (73)
-|.||. .+|.|+-++..+||+|.+
T Consensus 261 ~l~aGA~~Vqv~ta~~~~gp~~~~~ 285 (294)
T cd04741 261 MRLAGASAVQVGTALGKEGPKVFAR 285 (294)
T ss_pred HHHcCCCceeEchhhhhcCchHHHH
Confidence 346896 899999999999999965
No 35
>PF14981 FAM165: FAM165 family
Probab=24.41 E-value=86 Score=19.12 Aligned_cols=19 Identities=21% Similarity=0.396 Sum_probs=8.9
Q ss_pred HHHhhHHHHHHHHHHHHHHH
Q 035110 25 WKRQKDADASARKEEAARKR 44 (73)
Q Consensus 25 WKkrK~~Ek~ak~ae~~~kr 44 (73)
|.+++.+++..+. +++++|
T Consensus 30 yQ~krlEak~~k~-~aekk~ 48 (51)
T PF14981_consen 30 YQRKRLEAKLKKL-EAEKKK 48 (51)
T ss_pred HHHHHHHHHHHHH-HHHHHh
Confidence 5555555554443 444443
No 36
>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain. RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=24.23 E-value=29 Score=26.72 Aligned_cols=17 Identities=18% Similarity=0.151 Sum_probs=12.8
Q ss_pred cCCCCCCccccCHHHHH
Q 035110 7 QQSEEPRGKSISQAQFV 23 (73)
Q Consensus 7 ~~~~~p~~T~ITle~Fl 23 (73)
.|+-|.-.|.|||.||-
T Consensus 18 AQSIGEPsTQMTLnTFH 34 (309)
T cd02735 18 AQSIGEPSTQMTLNTFH 34 (309)
T ss_pred hhccCCccccccccccc
Confidence 35667778889999883
No 37
>smart00084 NMU Neuromedin U. Neuromedin U (NmU) is a vertebrate peptide which stimulates uterine smooth muscle contraction and causes selective vasoconstriction. Like most other active peptides, it is proteolytically processed from a larger precursor protein. The mature peptides are 8 (NmU-8) to 25 (NmU-25) residues long and C- terminally amidated. The sequence of the C-terminal extremity of NmU is extremely well conserved in mammals, birds and amphibians.
Probab=23.74 E-value=38 Score=18.19 Aligned_cols=16 Identities=31% Similarity=0.636 Sum_probs=12.3
Q ss_pred CccccccccccccCCc
Q 035110 51 GTVQMNGRELFLHEPW 66 (73)
Q Consensus 51 G~~~MsGRElF~~~P~ 66 (73)
|-+++-+|--|+|+|-
T Consensus 9 gp~~~qsrgyFLfRPR 24 (26)
T smart00084 9 GPIASQSRGYFLFRPR 24 (26)
T ss_pred CccccccCceEEeccC
Confidence 4456678889999994
No 38
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=22.60 E-value=1.1e+02 Score=15.99 Aligned_cols=13 Identities=38% Similarity=0.654 Sum_probs=10.4
Q ss_pred hhhCccccccccc
Q 035110 48 IAAGTVQMNGREL 60 (73)
Q Consensus 48 ~~AG~~~MsGREl 60 (73)
|.+|.+.+||+-+
T Consensus 23 i~~g~V~vn~~~~ 35 (70)
T cd00165 23 IKHGHVLVNGKVV 35 (70)
T ss_pred HHcCCEEECCEEc
Confidence 5688899999865
No 39
>PF10107 Endonuc_Holl: Endonuclease related to archaeal Holliday junction resolvase; InterPro: IPR019287 This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Probab=21.71 E-value=1.8e+02 Score=21.20 Aligned_cols=10 Identities=20% Similarity=0.836 Sum_probs=7.2
Q ss_pred HHHHHHHHHh
Q 035110 19 QAQFVSWKRQ 28 (73)
Q Consensus 19 le~Fl~WKkr 28 (73)
.+.|.+|+++
T Consensus 25 ~~~fe~wr~~ 34 (156)
T PF10107_consen 25 RELFEQWRQR 34 (156)
T ss_pred HHHHHHHHHh
Confidence 3568889666
No 40
>KOG3925 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.65 E-value=1.5e+02 Score=24.28 Aligned_cols=27 Identities=19% Similarity=0.288 Sum_probs=20.7
Q ss_pred CCccccCHHHHHHHHHhhHHHHHHHHH
Q 035110 12 PRGKSISQAQFVSWKRQKDADASARKE 38 (73)
Q Consensus 12 p~~T~ITle~Fl~WKkrK~~Ek~ak~a 38 (73)
...+.++.|+=++||..|.+++..+.+
T Consensus 17 ~k~~~~~~eek~~~~~~~k~~klk~e~ 43 (371)
T KOG3925|consen 17 HKWKQQKKEEKKKWKVKKKEKKLKKEE 43 (371)
T ss_pred hhhhhhChHHHHHHHhhhHHHHHHHHH
Confidence 456788999999999888877665443
No 41
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=21.45 E-value=75 Score=18.10 Aligned_cols=15 Identities=27% Similarity=0.649 Sum_probs=11.5
Q ss_pred ccCHHHHHHHHHhhH
Q 035110 16 SISQAQFVSWKRQKD 30 (73)
Q Consensus 16 ~ITle~Fl~WKkrK~ 30 (73)
-|+..+|..|+++=+
T Consensus 34 gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 34 GISPSTLYNWRKQYR 48 (76)
T ss_dssp TS-HHHHHHHHHHHH
T ss_pred ccccccccHHHHHHh
Confidence 478999999998754
No 42
>PF02035 Coagulin: Coagulin; InterPro: IPR000275 Coagulogen is a gel-forming protein of hemolymph that hinders the spread of invaders by immobilising them [, ]. The protein contains a single 175- residue polypeptide chain; this is cleaved after Arg-18 and Arg-46 by a clotting enzyme contained in the hemocyte and activated by a bacterial endotoxin (lipopolysaccharide). Cleavage releases two chains of coagulin, A and B, linked by two disulphide bonds, together with the peptide C [, ]. Gel formation results from interlinking of coagulin molecules. Secondary structure prediction suggests the C peptide forms an alpha- helix, which is released during the proteolytic conversion of coagulogen to coagulin gel []. The beta-sheet structure and 16 half-cystines found in the molecule appear to yield a compact protein stable to acid and heat. Mammalian blood coagulation is based on the proteolytically induced polymerisation of fibrinogens. Initially, fibrin monomers noncovalently interact with each other. The resulting homopolymers are further stabilised when the plasma transglutaminase (TGase) intermolecularly cross-links epsilon-(gamma-glutamyl)lysine bonds. In crustaceans, hemolymph coagulation depends on the TGase-mediated cross-linking of specific plasma-clotting proteins, but without the proteolytic cascade. In horseshoe crabs, the proteolytic coagulation cascade triggered by lipopolysaccharides and beta-1,3-glucans leads to the conversion of coagulogen into coagulin, resulting in noncovalent coagulin homopolymers through head-to-tail interaction. Horseshoe crab TGase, however, does not cross-link coagulins intermolecularly. Recently, we found that coagulins are cross-linked on hemocyte cell surface proteins called proxins. This indicates that a cross-linking reaction at the final stage of hemolymph coagulation is an important innate immune system of horseshoe crabs [].; GO: 0042381 hemolymph coagulation, 0005576 extracellular region; PDB: 1AOC_A.
Probab=21.07 E-value=1.1e+02 Score=22.50 Aligned_cols=14 Identities=36% Similarity=0.800 Sum_probs=9.2
Q ss_pred ccccccc--cccccCC
Q 035110 52 TVQMNGR--ELFLHEP 65 (73)
Q Consensus 52 ~~~MsGR--ElF~~~P 65 (73)
..++||| .||.++|
T Consensus 38 e~~vsgrgfs~f~~hp 53 (174)
T PF02035_consen 38 ESGVSGRGFSIFSHHP 53 (174)
T ss_dssp CC-SSTTTCGGCCCSH
T ss_pred hcCccccceeeecCCh
Confidence 3567777 5788887
No 43
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=21.06 E-value=56 Score=20.36 Aligned_cols=25 Identities=16% Similarity=0.310 Sum_probs=10.3
Q ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHHhhhCc
Q 035110 22 FVSWKRQKDADASARKEEAARKRAEDIAAGT 52 (73)
Q Consensus 22 Fl~WKkrK~~Ek~ak~ae~~~kr~~d~~AG~ 52 (73)
|+.|+.+|.++++. ++-.+.++.|.
T Consensus 17 f~~~rpqkk~~k~~------~~m~~~Lk~Gd 41 (82)
T PF02699_consen 17 FLMIRPQKKQQKEH------QEMLASLKPGD 41 (82)
T ss_dssp HHTHHHHHHHHHHH------TTGGG------
T ss_pred hheecHHHHHHHHH------HHHHHcCCCCC
Confidence 66777666544433 33445567785
No 44
>PHA00490 terminal protein
Probab=20.95 E-value=58 Score=25.42 Aligned_cols=13 Identities=31% Similarity=0.787 Sum_probs=10.9
Q ss_pred cCHHHHHHHHHhh
Q 035110 17 ISQAQFVSWKRQK 29 (73)
Q Consensus 17 ITle~Fl~WKkrK 29 (73)
-|-++|-+||++-
T Consensus 52 ~treqFN~wK~~a 64 (266)
T PHA00490 52 KTREQFNAWKKRA 64 (266)
T ss_pred hhHHHHHHHHHHH
Confidence 4789999999874
No 45
>KOG4819 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.90 E-value=2.9e+02 Score=19.09 Aligned_cols=32 Identities=19% Similarity=0.229 Sum_probs=18.5
Q ss_pred CHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhh
Q 035110 18 SQAQFVSWKRQKDADASARKEEAARKRAEDIA 49 (73)
Q Consensus 18 Tle~Fl~WKkrK~~Ek~ak~ae~~~kr~~d~~ 49 (73)
-.+..+.=++.|++++.+..++..+.|.+-++
T Consensus 34 k~~~~~~~~qeK~a~k~~Ere~~r~~R~e~~~ 65 (106)
T KOG4819|consen 34 KPEIRNMKRQEKAAQKAAEREKVRADRDEQVK 65 (106)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 35666666666666666655554445555443
No 46
>PF07141 Phage_term_sma: Putative bacteriophage terminase small subunit; InterPro: IPR010789 This entry is represented by Bacteriophage 712, Gp1; it is a family of uncharacterised viral proteins. This family consists of several putative Lactococcus bacteriophage terminase small subunit proteins. The exact function of this family is unknown.
Probab=20.71 E-value=1.2e+02 Score=22.31 Aligned_cols=17 Identities=29% Similarity=0.610 Sum_probs=14.3
Q ss_pred CccccCHHHHHHHHHhh
Q 035110 13 RGKSISQAQFVSWKRQK 29 (73)
Q Consensus 13 ~~T~ITle~Fl~WKkrK 29 (73)
+.-.|+--+|..|+.-|
T Consensus 39 ~~L~isrKtFyeWrdtk 55 (174)
T PF07141_consen 39 TSLHISRKTFYEWRDTK 55 (174)
T ss_pred HHHhccHHHHHHHHhhh
Confidence 34568899999999988
No 47
>cd07692 Ig_CD3_epsilon Immunoglobulin (Ig)-like domain of CD3 epsilon chain. Ig_CD3_epsilon; immunoglobulin (Ig)-like domain of CD3 epsilon chain. CD3 is a T cell surface receptor that is associated with alpha/beta T cell receptors (TCRs). The CD3 complex consists of one gamma, one delta, two epsilon, and two zeta chains. The CD3 subunits form heterodimers as gamma/epsilon, delta/epsilon, and zeta/zeta. The gamma, delta, and epsilon chains each contain an extracellular Ig domain, whereas the extracellular domains of the zeta chains are very small and have unknown structure. The CD3 domain participates in intracellular signalling once the TCR has bound an MHC/antigen complex.
Probab=20.22 E-value=47 Score=20.68 Aligned_cols=19 Identities=21% Similarity=0.336 Sum_probs=15.6
Q ss_pred ccccccccccccCCccccc
Q 035110 52 TVQMNGRELFLHEPWVFDN 70 (73)
Q Consensus 52 ~~~MsGRElF~~~P~lfdd 70 (73)
.|.+||..|.+-+|...++
T Consensus 2 ~VsisGTtVtlTCP~~~~~ 20 (65)
T cd07692 2 KVSISGTTVTVTCPLSGDD 20 (65)
T ss_pred eEEEeccEEEEECCCCCCC
Confidence 5789999999999976543
No 48
>PF14062 DUF4253: Domain of unknown function (DUF4253)
Probab=20.22 E-value=28 Score=22.90 Aligned_cols=13 Identities=23% Similarity=0.332 Sum_probs=10.9
Q ss_pred ccccccCCccccc
Q 035110 58 RELFLHEPWVFDN 70 (73)
Q Consensus 58 RElF~~~P~lfdd 70 (73)
+|+|.|+|++++.
T Consensus 74 ~E~y~fCpD~v~q 86 (111)
T PF14062_consen 74 AEHYAFCPDIVDQ 86 (111)
T ss_pred HHHHHhCccHHhc
Confidence 4689999998876
Done!