Query psy1283
Match_columns 123
No_of_seqs 108 out of 155
Neff 3.1
Searched_HMMs 46136
Date Fri Aug 16 20:54:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1283.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1283hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03153 TFIIA: Transcription 99.9 2E-22 4.3E-27 165.0 6.7 53 11-63 1-53 (375)
2 KOG2652|consensus 99.8 3.7E-21 8E-26 163.2 7.8 58 5-62 3-60 (348)
3 COG5149 TOA1 Transcription ini 99.7 3E-18 6.5E-23 142.0 6.0 59 5-63 2-60 (293)
4 PF10593 Z1: Z1 domain; Inter 42.1 1E+02 0.0022 24.8 6.2 44 7-50 37-80 (239)
5 PF05555 DUF762: Coxiella burn 41.0 27 0.00059 29.5 2.8 37 4-40 58-95 (248)
6 PTZ00098 phosphoethanolamine N 37.7 1.2E+02 0.0026 24.1 5.9 49 9-59 207-255 (263)
7 COG3514 Uncharacterized protei 37.0 28 0.00061 25.5 2.0 24 28-51 57-83 (93)
8 PF12294 DUF3626: Protein of u 36.9 38 0.00082 29.3 3.1 20 27-46 273-292 (297)
9 TIGR00064 ftsY signal recognit 36.4 89 0.0019 25.4 5.1 41 16-56 2-42 (272)
10 PRK05685 fliS flagellar protei 33.2 47 0.001 24.4 2.8 40 9-48 84-124 (132)
11 PF10968 DUF2770: Protein of u 32.9 45 0.00097 20.8 2.2 16 14-29 2-17 (36)
12 PF07345 DUF1476: Domain of un 27.7 36 0.00078 25.0 1.3 19 18-36 66-84 (103)
13 COG5467 Uncharacterized conser 27.5 41 0.00089 25.1 1.6 19 17-35 63-81 (104)
14 PF08358 Flexi_CP_N: Carlaviru 26.1 65 0.0014 21.1 2.2 24 38-61 2-25 (52)
15 PF05402 PqqD: Coenzyme PQQ sy 24.8 1.8E+02 0.0039 18.0 4.7 36 17-55 32-67 (68)
16 TIGR00208 fliS flagellar biosy 24.5 82 0.0018 22.9 2.7 38 10-49 81-121 (124)
17 cd08780 Death_TRADD Death Doma 24.5 54 0.0012 23.9 1.7 31 16-47 30-60 (90)
18 COG0571 Rnc dsRNA-specific rib 24.4 3.4E+02 0.0075 22.2 6.5 56 11-70 117-174 (235)
19 PF06992 Phage_lambda_P: Repli 23.5 2.8E+02 0.0062 23.1 6.0 68 14-82 37-106 (233)
20 PF01985 CRS1_YhbY: CRS1 / Yhb 22.6 99 0.0022 21.0 2.7 19 30-48 24-42 (84)
21 TIGR01425 SRP54_euk signal rec 22.5 2.7E+02 0.0059 24.8 6.0 49 10-58 20-68 (429)
22 PF08006 DUF1700: Protein of u 22.1 1.2E+02 0.0027 22.6 3.4 28 14-41 19-50 (181)
23 PF14384 DUF4415: Domain of un 22.0 1.1E+02 0.0024 19.9 2.7 20 32-51 34-56 (62)
24 PF06152 Phage_min_cap2: Phage 21.9 1.1E+02 0.0025 26.1 3.5 44 7-55 13-59 (361)
25 PF01152 Bac_globin: Bacterial 21.6 2.6E+02 0.0056 19.1 4.7 29 18-46 83-111 (120)
26 PF12296 HsbA: Hydrophobic sur 21.4 2.2E+02 0.0049 19.5 4.3 21 24-44 90-110 (124)
27 COG0541 Ffh Signal recognition 20.3 3.1E+02 0.0066 25.2 5.9 55 9-63 19-74 (451)
28 TIGR02698 CopY_TcrY copper tra 20.1 2.2E+02 0.0048 20.7 4.3 22 28-49 97-118 (130)
No 1
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=99.87 E-value=2e-22 Score=164.98 Aligned_cols=53 Identities=58% Similarity=0.865 Sum_probs=46.2
Q ss_pred HHHHHHHHHHHHhhHHHHHhcCCCHHHHHHHHHHHHHHHhhcCCCCCCchhhh
Q psy1283 11 KLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKLFGIGVGKLSKRKEW 63 (123)
Q Consensus 11 ~VY~~VIdDVI~~VReDFeeeGVDE~VLqELK~lWEsKL~qSgva~f~~~~~~ 63 (123)
+||++||+|||++||+||+|+||||+||+|||++||+||+++||++|+|+...
T Consensus 1 kvY~~VI~dVI~~vr~dF~~~Gvde~vL~eLk~~We~KL~qs~v~~~~~d~~~ 53 (375)
T PF03153_consen 1 KVYESVIDDVINNVREDFEEEGVDEQVLQELKQLWESKLSQSGVADFPWDPPP 53 (375)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHH-SS--TTGGGG
T ss_pred CcHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcCCccCCCCccc
Confidence 69999999999999999999999999999999999999999999999999753
No 2
>KOG2652|consensus
Probab=99.84 E-value=3.7e-21 Score=163.22 Aligned_cols=58 Identities=50% Similarity=0.822 Sum_probs=56.7
Q ss_pred CCcchHHHHHHHHHHHHHhhHHHHHhcCCCHHHHHHHHHHHHHHHhhcCCCCCCchhh
Q psy1283 5 PQSLTMKLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKLFGIGVGKLSKRKE 62 (123)
Q Consensus 5 sN~~V~~VY~~VIdDVI~~VReDFeeeGVDE~VLqELK~lWEsKL~qSgva~f~~~~~ 62 (123)
|++.|++||++||+|||++||++|+++||||+||.|||++||+||.++|++.|+|+.+
T Consensus 3 ~~~~v~kvY~~VIeDVI~~vRe~F~~~GiDeqvL~eLk~lWe~Kl~qs~~~~~~~d~~ 60 (348)
T KOG2652|consen 3 STNTVSKVYESVIEDVINNVREDFLENGIDEQVLSELKNLWETKLIQSGVATFPWDRE 60 (348)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHHHHhhcccccCcccc
Confidence 5999999999999999999999999999999999999999999999999999999985
No 3
>COG5149 TOA1 Transcription initiation factor IIA, large chain [Transcription]
Probab=99.73 E-value=3e-18 Score=141.96 Aligned_cols=59 Identities=34% Similarity=0.666 Sum_probs=57.6
Q ss_pred CCcchHHHHHHHHHHHHHhhHHHHHhcCCCHHHHHHHHHHHHHHHhhcCCCCCCchhhh
Q psy1283 5 PQSLTMKLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKLFGIGVGKLSKRKEW 63 (123)
Q Consensus 5 sN~~V~~VY~~VIdDVI~~VReDFeeeGVDE~VLqELK~lWEsKL~qSgva~f~~~~~~ 63 (123)
||+.|+.||+.||.|||+++|.||++.|||+++|+|||.+||+||.+++|+.|||++.|
T Consensus 2 sns~~~~vy~~vi~~vi~~~r~dfe~~gvdd~tlrelqnlwq~kl~~t~vatf~w~~~f 60 (293)
T COG5149 2 SNSIVGEVYHHVILDVIANSRSDFEENGVDDATLRELQNLWQSKLVATDVATFPWAQAF 60 (293)
T ss_pred CcchhhHHHHHHHHHHHHHhhhHHHhcCccHHHHHHHHHHHHHhhhhheeeecchhhcC
Confidence 79999999999999999999999999999999999999999999999999999999965
No 4
>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases. This domain is found associated with a helicase domain of superfamily type II [].
Probab=42.08 E-value=1e+02 Score=24.82 Aligned_cols=44 Identities=23% Similarity=0.367 Sum_probs=36.3
Q ss_pred cchHHHHHHHHHHHHHhhHHHHHhcCCCHHHHHHHHHHHHHHHh
Q psy1283 7 SLTMKLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKLF 50 (123)
Q Consensus 7 ~~V~~VY~~VIdDVI~~VReDFeeeGVDE~VLqELK~lWEsKL~ 50 (123)
..+-+-+...|++.++..+.+.....-+...+.+|+.+|++-..
T Consensus 37 ~~~h~~~~~~I~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~ 80 (239)
T PF10593_consen 37 VDVHEQVADWIEEYLNELKKALRYNDDDPEELNELRELWEEDFE 80 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCcchhHHHHHHHHHHHHhh
Confidence 44557778888999999999988887777669999999998776
No 5
>PF05555 DUF762: Coxiella burnetii protein of unknown function (DUF762); InterPro: IPR008481 This family consists several of several uncharacterised proteins from the bacterium Coxiella burnetii. C. burnetii is the causative agent of the Q fever disease.
Probab=41.03 E-value=27 Score=29.46 Aligned_cols=37 Identities=27% Similarity=0.291 Sum_probs=31.5
Q ss_pred CCCcchHHHHHHHHHHHHHhhHHHHHhcC-CCHHHHHH
Q psy1283 4 TPQSLTMKLYQAVIADVINNVKEAFQEEG-VDEQVLQE 40 (123)
Q Consensus 4 ~sN~~V~~VY~~VIdDVI~~VReDFeeeG-VDE~VLqE 40 (123)
+||+...++=..=|+++|..|...|--+| .|+.+++=
T Consensus 58 ~S~~~Lpkl~i~~i~~sIk~v~n~FKk~GLkde~i~nY 95 (248)
T PF05555_consen 58 RSNRDLPKLPIPNIDNSIKYVKNEFKKHGLKDENISNY 95 (248)
T ss_pred cccCCCccCchhHHHHHHHHHHHHHHHhccchHHHHHH
Confidence 56777778888889999999999999999 78888774
No 6
>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional
Probab=37.72 E-value=1.2e+02 Score=24.13 Aligned_cols=49 Identities=20% Similarity=0.218 Sum_probs=35.7
Q ss_pred hHHHHHHHHHHHHHhhHHHHHhcCCCHHHHHHHHHHHHHHHhhcCCCCCCc
Q psy1283 9 TMKLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKLFGIGVGKLSK 59 (123)
Q Consensus 9 V~~VY~~VIdDVI~~VReDFeeeGVDE~VLqELK~lWEsKL~qSgva~f~~ 59 (123)
....|..+.+.+ ..-|++|.+. +.+..++.+...|+.++...+.-...|
T Consensus 207 ~~~~~~~~~~~~-~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~w 255 (263)
T PTZ00098 207 WLELLQVELKKL-EEKKEEFLKL-YSEKEYNSLKDGWTRKIKDTKRKLQKW 255 (263)
T ss_pred HHHHHHHHHHHH-HHhHHHHHHh-cCHHHHHHHHHHHHHHHHHhhcccccc
Confidence 345566555444 4448888876 899999999999999998777655554
No 7
>COG3514 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.97 E-value=28 Score=25.55 Aligned_cols=24 Identities=17% Similarity=0.483 Sum_probs=19.1
Q ss_pred HHhcCCCHHHHHHHHH---HHHHHHhh
Q psy1283 28 FQEEGVDEQVLQELKH---IWEAKLFG 51 (123)
Q Consensus 28 FeeeGVDE~VLqELK~---lWEsKL~q 51 (123)
+..--||.+||+-+|. +||+++.+
T Consensus 57 ~vslRiDaDVle~fra~GkGwQtRiN~ 83 (93)
T COG3514 57 LVSLRIDADVLEKFRAGGKGWQTRINA 83 (93)
T ss_pred eeeeEecHHHHHHHHcCCccHHHHHHH
Confidence 3444589999999995 79999875
No 8
>PF12294 DUF3626: Protein of unknown function (DUF3626); InterPro: IPR022074 This family of proteins is found in bacteria. Proteins in this family are typically between 294 and 374 amino acids in length.
Probab=36.89 E-value=38 Score=29.32 Aligned_cols=20 Identities=45% Similarity=0.853 Sum_probs=18.0
Q ss_pred HHHhcCCCHHHHHHHHHHHH
Q psy1283 27 AFQEEGVDEQVLQELKHIWE 46 (123)
Q Consensus 27 DFeeeGVDE~VLqELK~lWE 46 (123)
...|.|--..|||+||.+|-
T Consensus 273 ~w~d~G~~~~~lQ~LK~LWH 292 (297)
T PF12294_consen 273 AWSDRGTYAEVLQELKLLWH 292 (297)
T ss_pred HHhhcCcHHHHHHHHHHHHH
Confidence 47888999999999999995
No 9
>TIGR00064 ftsY signal recognition particle-docking protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.
Probab=36.39 E-value=89 Score=25.40 Aligned_cols=41 Identities=20% Similarity=0.247 Sum_probs=32.8
Q ss_pred HHHHHHHhhHHHHHhcCCCHHHHHHHHHHHHHHHhhcCCCC
Q psy1283 16 VIADVINNVKEAFQEEGVDEQVLQELKHIWEAKLFGIGVGK 56 (123)
Q Consensus 16 VIdDVI~~VReDFeeeGVDE~VLqELK~lWEsKL~qSgva~ 56 (123)
+|+++++.++..+.+.||+..+-++|-..=++++...+...
T Consensus 2 ~~~~~~~~l~~~L~~~dv~~~~~~~i~~~~~~~~~~~~~~~ 42 (272)
T TIGR00064 2 DDEDFFEELEEILLESDVGYEVVEKIIEALKKELKGKKVKD 42 (272)
T ss_pred ccHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHhhccCCC
Confidence 57889999999999999999999988777666666555443
No 10
>PRK05685 fliS flagellar protein FliS; Validated
Probab=33.17 E-value=47 Score=24.36 Aligned_cols=40 Identities=23% Similarity=0.418 Sum_probs=26.9
Q ss_pred hHHHHHHHHHHHHHh-hHHHHHhcCCCHHHHHHHHHHHHHH
Q psy1283 9 TMKLYQAVIADVINN-VKEAFQEEGVDEQVLQELKHIWEAK 48 (123)
Q Consensus 9 V~~VY~~VIdDVI~~-VReDFeeeGVDE~VLqELK~lWEsK 48 (123)
..++|..++...... ++.|.+.-.--..+|.+|+..|+.=
T Consensus 84 L~~LY~y~~~~L~~A~~~~d~~~l~ev~~il~~LreaW~~i 124 (132)
T PRK05685 84 LSALYDYMIRRLLEANLRNDVQAIDEVEGLLREIKEAWKQI 124 (132)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence 358999999888654 3333333333356899999999873
No 11
>PF10968 DUF2770: Protein of unknown function (DUF2770); InterPro: IPR024494 Members in this family of proteins from Enterobacteria are annotated as YceO; however, currently no function is known.
Probab=32.94 E-value=45 Score=20.81 Aligned_cols=16 Identities=25% Similarity=0.482 Sum_probs=12.6
Q ss_pred HHHHHHHHHhhHHHHH
Q psy1283 14 QAVIADVINNVKEAFQ 29 (123)
Q Consensus 14 ~~VIdDVI~~VReDFe 29 (123)
+.++.-+||+||+.|.
T Consensus 2 ~rl~~~~inNiReHlm 17 (36)
T PF10968_consen 2 RRLFHYLINNIREHLM 17 (36)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 4566778999999985
No 12
>PF07345 DUF1476: Domain of unknown function (DUF1476); InterPro: IPR009945 This family consists of several hypothetical bacterial proteins of around 100 residues in length. Members of this family are found in Bradyrhizobium, Rhizobium, Brucella and Caulobacter species. The function of this family is unknown.; PDB: 2KZC_A 2LL0_A.
Probab=27.74 E-value=36 Score=25.02 Aligned_cols=19 Identities=32% Similarity=0.573 Sum_probs=14.2
Q ss_pred HHHHHhhHHHHHhcCCCHH
Q psy1283 18 ADVINNVKEAFQEEGVDEQ 36 (123)
Q Consensus 18 dDVI~~VReDFeeeGVDE~ 36 (123)
+||++.|+.||...||+.+
T Consensus 66 edv~~kv~~DL~a~gv~~~ 84 (103)
T PF07345_consen 66 EDVLRKVRADLAAAGVDVS 84 (103)
T ss_dssp THHHHHHHHHHTTTS----
T ss_pred HHHHHHHHHHHHHccCCCC
Confidence 6899999999999996543
No 13
>COG5467 Uncharacterized conserved protein [Function unknown]
Probab=27.46 E-value=41 Score=25.09 Aligned_cols=19 Identities=32% Similarity=0.511 Sum_probs=13.4
Q ss_pred HHHHHHhhHHHHHhcCCCH
Q psy1283 17 IADVINNVKEAFQEEGVDE 35 (123)
Q Consensus 17 IdDVI~~VReDFeeeGVDE 35 (123)
-+||.+.||.||...||..
T Consensus 63 deDV~RKv~~D~daAGVs~ 81 (104)
T COG5467 63 DEDVFRKVREDLDAAGVST 81 (104)
T ss_pred cHHHHHHHHHhcccccccc
Confidence 3577777777777777643
No 14
>PF08358 Flexi_CP_N: Carlavirus coat; InterPro: IPR013569 This domain is found together with the viral coat protein domain (IPR000052 from INTERPRO) in coat/capsid proteins of the plant infecting Carlavirus. It is required for genome encapsidation by forming ribonucleoprotein complexes along with TGB1 helicase and viral RNA. The N- and the C terminus of this coat protein can be exposed on the surface of the virus particle. The central core sequence may be important in maintaining correct tertiary structure of the coat protein and/or play a role in the interaction with the viral RNA. Coat proteins are often used to distinguish between Carlavirus isolates. In the coat protein amino acid sequences of definitive and tentative species of carlaviruses, there is a region of seven amino acids (GLGVPTE) that are conserved []. The complete coat protein (CP) sequences of 29 Indian Chrysanthemum virus B (CVB) isolates were highly heterogeneous, sharing nucleotide sequence identities of 74-98% [, ].
Probab=26.15 E-value=65 Score=21.12 Aligned_cols=24 Identities=17% Similarity=0.081 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHhhcCCCCCCchh
Q psy1283 38 LQELKHIWEAKLFGIGVGKLSKRK 61 (123)
Q Consensus 38 LqELK~lWEsKL~qSgva~f~~~~ 61 (123)
|+.|+..+.+.+.++.+....++.
T Consensus 2 l~~L~e~l~~~~~~~~v~N~~fE~ 25 (52)
T PF08358_consen 2 LDKLKEFLRKNRTASNVTNPGFEI 25 (52)
T ss_pred HHHHHHHHHhcccCCccccccccc
Confidence 567888888888888888766654
No 15
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=24.83 E-value=1.8e+02 Score=17.99 Aligned_cols=36 Identities=17% Similarity=0.295 Sum_probs=18.9
Q ss_pred HHHHHHhhHHHHHhcCCCHHHHHHHHHHHHHHHhhcCCC
Q psy1283 17 IADVINNVKEAFQEEGVDEQVLQELKHIWEAKLFGIGVG 55 (123)
Q Consensus 17 IdDVI~~VReDFeeeGVDE~VLqELK~lWEsKL~qSgva 55 (123)
++++++.+.+.| +++...+.+=-..+-..|.+.|.+
T Consensus 32 ~~ei~~~l~~~y---~~~~~~~~~dv~~fl~~L~~~glI 67 (68)
T PF05402_consen 32 VEEIVDALAEEY---DVDPEEAEEDVEEFLEQLREKGLI 67 (68)
T ss_dssp HHHHHHHHHHHT---T--HHHHHHHHHHHHHHHHHTT--
T ss_pred HHHHHHHHHHHc---CCCHHHHHHHHHHHHHHHHHCcCc
Confidence 566777777776 667665544333455555555543
No 16
>TIGR00208 fliS flagellar biosynthetic protein FliS. The function of this protein in flagellar biosynthesis is unknown, but appears to be regulatory. The member of this family in Vibrio parahaemolyticus is designated FlaJ (creating a synonym for FliS) and was shown essential for flagellin biosynthesis.
Probab=24.49 E-value=82 Score=22.95 Aligned_cols=38 Identities=11% Similarity=0.322 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHhhHH-HHHhcCCC--HHHHHHHHHHHHHHH
Q psy1283 10 MKLYQAVIADVINNVKE-AFQEEGVD--EQVLQELKHIWEAKL 49 (123)
Q Consensus 10 ~~VY~~VIdDVI~~VRe-DFeeeGVD--E~VLqELK~lWEsKL 49 (123)
..+|..++......... |-+ -+| ..+|.+|+..|+.=+
T Consensus 81 ~~LY~y~~~~L~~An~~~d~~--~l~ev~~~l~~Lr~aW~e~~ 121 (124)
T TIGR00208 81 GALYDYMYRRLVQANIKNDTS--KLAEVEGYVRDFRDAWKEAI 121 (124)
T ss_pred HHHHHHHHHHHHHHHhhCCHH--HHHHHHHHHHHHHHHHHHHh
Confidence 48999999888544332 221 233 356999999998644
No 17
>cd08780 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into s
Probab=24.46 E-value=54 Score=23.94 Aligned_cols=31 Identities=26% Similarity=0.400 Sum_probs=26.2
Q ss_pred HHHHHHHhhHHHHHhcCCCHHHHHHHHHHHHH
Q psy1283 16 VIADVINNVKEAFQEEGVDEQVLQELKHIWEA 47 (123)
Q Consensus 16 VIdDVI~~VReDFeeeGVDE~VLqELK~lWEs 47 (123)
+=|..|+++..++..+|..|+|.|-|++ |..
T Consensus 30 l~d~~ID~I~~~y~r~gL~EqvyQ~L~~-W~~ 60 (90)
T cd08780 30 LRDPAIDNLAYEYDREGLYEQAYQLLRR-FIQ 60 (90)
T ss_pred cchhHHHHHHhhcccccHHHHHHHHHHH-HHH
Confidence 4567899999999999999999997764 754
No 18
>COG0571 Rnc dsRNA-specific ribonuclease [Transcription]
Probab=24.35 E-value=3.4e+02 Score=22.20 Aligned_cols=56 Identities=11% Similarity=0.172 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHhhHHHHHhcCCCHHHHHHHHHHHHHHHhhcCCCC--CCchhhhhhHhhhc
Q psy1283 11 KLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKLFGIGVGK--LSKRKEWMSKCYRS 70 (123)
Q Consensus 11 ~VY~~VIdDVI~~VReDFeeeGVDE~VLqELK~lWEsKL~qSgva~--f~~~~~~~~~~~~~ 70 (123)
+++..+++-+|.+ -|+|.| -+.+-.=+.+.|..++.+.+... ..++...++..+++
T Consensus 117 silaD~~EAligA---iylD~g-~~~~~~~i~~l~~~~~~~~~~~~~~~D~Kt~LQe~~q~~ 174 (235)
T COG0571 117 SILADAFEALIGA---IYLDSG-LEAARKFILKLFLPRLEEIDAGDQFKDPKTRLQELLQAQ 174 (235)
T ss_pred hHHHHHHHHHHHH---HHHhCC-hHHHHHHHHHHHHHHHhhccccccccChhHHHHHHHHhc
Confidence 3444444444443 378888 56667777889999999888887 55666555554444
No 19
>PF06992 Phage_lambda_P: Replication protein P; InterPro: IPR009731 This family consists of several Bacteriophage lambda replication protein P like proteins. The bacteriophage lambda P protein promoters replication of the phage chromosome by recruiting a key component of the cellular replication machinery to the viral origin. Specifically, P protein delivers one or more molecules of Escherichia coli DnaB helicase to a nucleoprotein structure formed by the lambda O initiator at the lambda replication origin [].; GO: 0006270 DNA-dependent DNA replication initiation
Probab=23.46 E-value=2.8e+02 Score=23.14 Aligned_cols=68 Identities=19% Similarity=0.277 Sum_probs=47.5
Q ss_pred HHHHHHHHHhhHHHHHh--cCCCHHHHHHHHHHHHHHHhhcCCCCCCchhhhhhHhhhccCCCCCCCCCCC
Q psy1283 14 QAVIADVINNVKEAFQE--EGVDEQVLQELKHIWEAKLFGIGVGKLSKRKEWMSKCYRSSNISGRPSLSGN 82 (123)
Q Consensus 14 ~~VIdDVI~~VReDFee--eGVDE~VLqELK~lWEsKL~qSgva~f~~~~~~~~~~~~~~~~~g~p~~~~n 82 (123)
..+||.+-+..+..|-- .--|+..+++.|+.|-.-+.+.|+.+..-=..=| ..-|.+...=-||+|.=
T Consensus 37 ~~~vd~lF~~L~aifPa~~a~~~~~~~~~aKr~Wi~~f~engI~t~eQv~~Gm-~~aR~~~spF~PS~GqF 106 (233)
T PF06992_consen 37 AKLVDRLFRQLKAIFPAWRANPDQEELNEAKRQWIKAFAENGITTMEQVRAGM-RRARASESPFWPSPGQF 106 (233)
T ss_pred HHHHHHHHHHHHHhCchhccCCCHHHHHHHHHHHHHHHHHcCCCcHHHHHHHH-HHHHhcCCCCCCChhHH
Confidence 36888888888888864 2368888999999999999999998643211112 33366666566666643
No 20
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=22.65 E-value=99 Score=20.98 Aligned_cols=19 Identities=21% Similarity=0.522 Sum_probs=15.6
Q ss_pred hcCCCHHHHHHHHHHHHHH
Q psy1283 30 EEGVDEQVLQELKHIWEAK 48 (123)
Q Consensus 30 eeGVDE~VLqELK~lWEsK 48 (123)
-.|+.+.+++++...|+..
T Consensus 24 k~Glt~~vi~~i~~~l~~~ 42 (84)
T PF01985_consen 24 KNGLTDGVIEEIDDALEKH 42 (84)
T ss_dssp TTSS-HHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHhC
Confidence 3689999999999999874
No 21
>TIGR01425 SRP54_euk signal recognition particle protein SRP54. This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.
Probab=22.53 E-value=2.7e+02 Score=24.80 Aligned_cols=49 Identities=10% Similarity=0.135 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHhhHHHHHhcCCCHHHHHHHHHHHHHHHhhcCCCCCC
Q psy1283 10 MKLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKLFGIGVGKLS 58 (123)
Q Consensus 10 ~~VY~~VIdDVI~~VReDFeeeGVDE~VLqELK~lWEsKL~qSgva~f~ 58 (123)
+.+-+.-|+++++.++..+.+.+|+..+..++...=++++....+..+.
T Consensus 20 ~~l~e~~i~~~l~ei~~aLleaDV~~~vv~~~~~~v~~~~~~~~~~~~~ 68 (429)
T TIGR01425 20 TVIDEEVLNAMLKEICTALLESDVNIKLVRQLRENIKKAINLEEMASGL 68 (429)
T ss_pred CccCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHhcccccccc
Confidence 3566788999999999999999999999999999888887766665543
No 22
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=22.07 E-value=1.2e+02 Score=22.64 Aligned_cols=28 Identities=21% Similarity=0.520 Sum_probs=21.6
Q ss_pred HHHHHHHHHhhHHHHHhcCC----CHHHHHHH
Q psy1283 14 QAVIADVINNVKEAFQEEGV----DEQVLQEL 41 (123)
Q Consensus 14 ~~VIdDVI~~VReDFeeeGV----DE~VLqEL 41 (123)
++-++|.++--++.|+|.+- +|++.+||
T Consensus 19 ~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~L 50 (181)
T PF08006_consen 19 EEEREEILEYYEEYFDDAGEEGKSEEEIIAEL 50 (181)
T ss_pred HHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHc
Confidence 45678889999999987653 57888876
No 23
>PF14384 DUF4415: Domain of unknown function (DUF4415)
Probab=21.95 E-value=1.1e+02 Score=19.90 Aligned_cols=20 Identities=20% Similarity=0.312 Sum_probs=15.3
Q ss_pred CCCHHHHHHHHH---HHHHHHhh
Q psy1283 32 GVDEQVLQELKH---IWEAKLFG 51 (123)
Q Consensus 32 GVDE~VLqELK~---lWEsKL~q 51 (123)
-+|.+||+-+|. +||+++.+
T Consensus 34 rld~dVl~~fka~G~gyQtriN~ 56 (62)
T PF14384_consen 34 RLDPDVLEWFKAQGKGYQTRINE 56 (62)
T ss_pred EeCHHHHHHHHHHChhHHHHHHH
Confidence 368888888885 69988764
No 24
>PF06152 Phage_min_cap2: Phage minor capsid protein 2; InterPro: IPR009319 This entry is represented by Bacteriophage A118, Gp4, the minor capsid protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=21.92 E-value=1.1e+02 Score=26.13 Aligned_cols=44 Identities=20% Similarity=0.440 Sum_probs=33.0
Q ss_pred cchHHHHHHHHHHHHHhhHHHHHhcCCC--HHHHHHHHHHHHH-HHhhcCCC
Q psy1283 7 SLTMKLYQAVIADVINNVKEAFQEEGVD--EQVLQELKHIWEA-KLFGIGVG 55 (123)
Q Consensus 7 ~~V~~VY~~VIdDVI~~VReDFeeeGVD--E~VLqELK~lWEs-KL~qSgva 55 (123)
..+..+|...-++.|..+..-|...|.. .++.+ ||- ||.+.|..
T Consensus 13 ~~i~~ly~~lE~~i~~~i~rri~~~~~~~~~~~~~-----WQ~~kL~~lg~~ 59 (361)
T PF06152_consen 13 DQIVDLYQELEQEIIADIIRRIKKHGYILGTNTAD-----WQIEKLQELGML 59 (361)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCccCCCCHHH-----HHHHHHHHHHHH
Confidence 4577999999999999988888887765 44443 765 77777754
No 25
>PF01152 Bac_globin: Bacterial-like globin; InterPro: IPR001486 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry represents a group of haemoglobin-like proteins found in eubacteria, cyanobacteria, protozoa, algae and plants, but not in animals or yeast. These proteins have a truncated 2-over-2 rather than the canonical 3-over-3 alpha-helical sandwich fold []. This entry includes: HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress []. Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment []. HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism []. Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide []. ; GO: 0019825 oxygen binding, 0015671 oxygen transport; PDB: 2BKM_B 1UVY_A 1DLW_A 2XYK_B 2IG3_A 2GKM_B 1S61_A 1S56_B 1RTE_B 2GLN_A ....
Probab=21.60 E-value=2.6e+02 Score=19.11 Aligned_cols=29 Identities=31% Similarity=0.410 Sum_probs=20.2
Q ss_pred HHHHHhhHHHHHhcCCCHHHHHHHHHHHH
Q psy1283 18 ADVINNVKEAFQEEGVDEQVLQELKHIWE 46 (123)
Q Consensus 18 dDVI~~VReDFeeeGVDE~VLqELK~lWE 46 (123)
+-.+...++.+++.|+++...+++-+..+
T Consensus 83 ~~~~~~~~~al~~~~v~~~~~~~~~~~~~ 111 (120)
T PF01152_consen 83 DRWLELLKQALDELGVPEELIDELLARLE 111 (120)
T ss_dssp HHHHHHHHHHHHHTTCTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34566777778888888887777665443
No 26
>PF12296 HsbA: Hydrophobic surface binding protein A; InterPro: IPR021054 Hydrophobic surface binding proteins are typically between 171 to 275 amino acids in length. Although the HsbA amino acid sequence suggests that HsbA may be hydrophilic, HsbA adsorbed to hydrophobic PBSA (Polybutylene succinate-co-adipate) surfaces in the presence of NaCl or CaCl2. When HsbA was adsorbed on the hydrophobic PBSA surfaces, it promoted PBSA degradation via the CutL1 polyesterase. CutL1 interacts directly with HsbA attached to the hydrophobic QCM electrode surface. These results suggest that when HsbA is adsorbed onto the PBSA surface, it recruits CutL1, and that when CutL1 is accumulated on the PBSA surface, it stimulates PBSA degradation []. This entry is also characterised by a antigenic cell wall galactomannoprotein in Aspergillus fumigatus, which is a protein of 284 amino acid residues. It contains a serine- and threonine-rich region for O glycosylation, a signal peptide, and a putative glycosylphosphatidyl inositol attachment signal sequence. Ultrastructural analysis showed that the protein is present in the cell walls of hyphae and conidia []. ; PDB: 3L1N_A.
Probab=21.44 E-value=2.2e+02 Score=19.48 Aligned_cols=21 Identities=29% Similarity=0.439 Sum_probs=17.3
Q ss_pred hHHHHHhcCCCHHHHHHHHHH
Q psy1283 24 VKEAFQEEGVDEQVLQELKHI 44 (123)
Q Consensus 24 VReDFeeeGVDE~VLqELK~l 44 (123)
=+..|+..|+...|+..|+.+
T Consensus 90 Kk~~f~~~g~~~~v~~~L~~l 110 (124)
T PF12296_consen 90 KKPAFDAAGLCSVVRADLQDL 110 (124)
T ss_dssp THHHHHHTT-HHHHHHHHHHH
T ss_pred hHHHHHHcCCcHHHHHHHHHH
Confidence 367899999999999999875
No 27
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=20.34 E-value=3.1e+02 Score=25.18 Aligned_cols=55 Identities=13% Similarity=0.258 Sum_probs=47.6
Q ss_pred hHHHHHHHHHHHHHhhHHHHHhcCCCHHHHHHHHHHHHHHHhhcCCCCCC-chhhh
Q psy1283 9 TMKLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKLFGIGVGKLS-KRKEW 63 (123)
Q Consensus 9 V~~VY~~VIdDVI~~VReDFeeeGVDE~VLqELK~lWEsKL~qSgva~f~-~~~~~ 63 (123)
.+++++.-|+++++.||-...+.-|.-.|..++.+.=++|.....+...- +.+.+
T Consensus 19 ~~~i~E~~i~e~~reir~ALLeADVnl~vVk~fi~~ikera~g~ev~~~l~p~q~~ 74 (451)
T COG0541 19 KGRITEKDVKEALREIRRALLEADVNLKVVKDFIKRIKERALGEEVPKGLTPGQQF 74 (451)
T ss_pred CCcCCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhccccCCCCCCHHHHH
Confidence 35788999999999999999999999999999999999999999888644 44443
No 28
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=20.14 E-value=2.2e+02 Score=20.68 Aligned_cols=22 Identities=14% Similarity=0.318 Sum_probs=18.3
Q ss_pred HHhcCCCHHHHHHHHHHHHHHH
Q psy1283 28 FQEEGVDEQVLQELKHIWEAKL 49 (123)
Q Consensus 28 FeeeGVDE~VLqELK~lWEsKL 49 (123)
+.++.+++.-|++|+++++++-
T Consensus 97 ~~~~~ls~eele~L~~li~~~~ 118 (130)
T TIGR02698 97 IEESPLSQTDIEKLEKLLSEKK 118 (130)
T ss_pred HhcCCCCHHHHHHHHHHHHhcc
Confidence 4567799999999999887764
Done!