Query 035575
Match_columns 132
No_of_seqs 105 out of 220
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 04:11:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035575.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035575hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5431 Uncharacterized metal- 99.7 1.3E-17 2.8E-22 116.4 6.1 91 37-132 10-101 (117)
2 PF04434 SWIM: SWIM zinc finge 98.3 2.9E-07 6.3E-12 53.4 2.3 27 78-110 13-39 (40)
3 COG4279 Uncharacterized conser 97.4 0.0006 1.3E-08 54.6 7.2 89 31-129 24-172 (266)
4 COG4715 Uncharacterized conser 97.4 0.00052 1.1E-08 60.2 7.1 72 28-112 18-97 (587)
5 smart00575 ZnF_PMZ plant mutat 95.6 0.0093 2E-07 32.1 1.8 24 81-110 2-25 (28)
6 PRK13717 conjugal transfer pro 83.0 5.9 0.00013 28.8 6.2 48 5-53 53-101 (128)
7 PRK09334 30S ribosomal protein 79.8 8.2 0.00018 26.2 5.7 57 6-63 27-84 (86)
8 PLN03097 FHY3 Protein FAR-RED 75.4 5.5 0.00012 37.2 5.0 47 59-112 554-605 (846)
9 PF03297 Ribosomal_S25: S25 ri 74.8 13 0.00029 26.0 5.8 57 6-63 45-102 (105)
10 cd08325 CARD_CASP1-like Caspas 71.6 14 0.00031 24.4 5.1 44 3-46 13-56 (83)
11 COG4901 Ribosomal protein S25 71.4 16 0.00034 25.8 5.4 59 5-63 44-102 (107)
12 TIGR02744 TrbI_Ftype type-F co 71.1 21 0.00046 25.3 6.1 47 6-53 41-88 (112)
13 COG3355 Predicted transcriptio 61.6 54 0.0012 23.7 6.8 55 10-64 32-88 (126)
14 PRK11402 DNA-binding transcrip 60.7 30 0.00065 26.6 5.8 48 4-53 11-67 (241)
15 TIGR02404 trehalos_R_Bsub treh 59.7 30 0.00065 26.4 5.6 47 5-53 3-58 (233)
16 PRK14999 histidine utilization 59.0 34 0.00073 26.4 5.8 47 5-53 15-70 (241)
17 PF00392 GntR: Bacterial regul 57.2 42 0.00091 20.4 5.6 46 5-53 3-57 (64)
18 TIGR02325 C_P_lyase_phnF phosp 56.7 39 0.00086 25.6 5.8 47 5-53 11-66 (238)
19 PRK10079 phosphonate metabolis 54.8 51 0.0011 25.3 6.2 55 4-64 14-76 (241)
20 TIGR02018 his_ut_repres histid 53.8 51 0.0011 25.1 6.0 54 5-64 4-66 (230)
21 PRK09764 DNA-binding transcrip 50.9 78 0.0017 24.3 6.7 48 4-53 7-63 (240)
22 COG2188 PhnF Transcriptional r 50.9 62 0.0013 25.1 6.1 48 4-53 9-65 (236)
23 PF08221 HTH_9: RNA polymerase 46.9 62 0.0013 20.1 4.6 51 3-53 10-60 (62)
24 PRK06266 transcription initiat 46.6 76 0.0016 24.0 5.8 55 8-62 24-81 (178)
25 COG2905 Predicted signal-trans 44.9 78 0.0017 28.7 6.4 55 10-69 298-352 (610)
26 PF00619 CARD: Caspase recruit 42.7 77 0.0017 20.0 4.7 39 7-46 17-55 (85)
27 PF09012 FeoC: FeoC like trans 39.9 42 0.00091 20.9 3.0 46 9-54 3-49 (69)
28 PF00837 T4_deiodinase: Iodoth 39.4 1.9E+02 0.004 23.2 7.2 83 5-90 28-120 (237)
29 COG4175 ProV ABC-type proline/ 35.6 16 0.00034 31.1 0.6 45 28-72 9-67 (386)
30 PF08290 Hep_core_N: Hepatitis 35.3 15 0.00032 19.6 0.3 12 79-90 9-20 (27)
31 COG1675 TFA1 Transcription ini 34.9 1.6E+02 0.0034 22.5 6.0 58 9-66 21-83 (176)
32 PHA02902 putative IMV membrane 32.5 39 0.00084 21.9 1.9 17 19-35 52-68 (70)
33 PLN03081 pentatricopeptide (PP 32.3 2.2E+02 0.0048 25.3 7.4 76 6-87 592-696 (697)
34 PRK11830 dapD 2,3,4,5-tetrahyd 31.4 1.9E+02 0.004 23.5 6.2 45 1-53 1-47 (272)
35 cd08810 CARD_BCL10 Caspase act 30.8 1.5E+02 0.0032 19.8 4.7 39 6-45 16-54 (84)
36 PRK09990 DNA-binding transcrip 30.0 2.1E+02 0.0046 21.8 6.2 57 3-65 8-73 (251)
37 cd08329 CARD_BIRC2_BIRC3 Caspa 29.6 1.5E+02 0.0033 19.9 4.6 39 7-46 24-62 (94)
38 TIGR00373 conserved hypothetic 29.6 1.9E+02 0.0042 21.2 5.6 40 11-50 19-58 (158)
39 PF06543 Lac_bphage_repr: Lact 29.1 40 0.00086 20.5 1.5 21 18-38 28-48 (49)
40 PHA02681 ORF089 virion membran 29.1 46 0.00099 22.6 1.9 17 19-35 50-66 (92)
41 cd08326 CARD_CASP9 Caspase act 28.8 1.7E+02 0.0037 19.3 4.7 38 8-46 18-55 (84)
42 cd01671 CARD Caspase activatio 28.7 1.5E+02 0.0033 18.4 4.7 39 7-46 14-52 (80)
43 cd08814 DED_Caspase_10_repeat2 28.3 99 0.0021 20.4 3.4 26 10-35 40-65 (79)
44 PF09645 F-112: F-112 protein; 27.7 1E+02 0.0022 21.6 3.5 41 6-46 7-50 (110)
45 PRK10421 DNA-binding transcrip 27.1 2.3E+02 0.0051 21.7 6.0 59 3-64 3-67 (253)
46 cd08332 CARD_CASP2 Caspase act 26.8 1.9E+02 0.0042 19.2 4.7 38 8-46 22-59 (90)
47 PF02002 TFIIE_alpha: TFIIE al 26.5 56 0.0012 22.0 2.1 44 10-53 17-60 (105)
48 PRK03824 hypA hydrogenase nick 26.3 99 0.0021 22.2 3.4 49 1-49 4-56 (135)
49 PF02268 TFIIA_gamma_N: Transc 26.2 1.6E+02 0.0034 17.8 4.8 34 9-42 16-49 (49)
50 PRK14981 DNA-directed RNA poly 25.9 1.8E+02 0.004 20.2 4.7 41 7-47 51-91 (112)
51 PF02828 L27: L27 domain; Int 25.9 1.6E+02 0.0034 17.6 4.4 35 7-41 4-38 (56)
52 PF14338 Mrr_N: Mrr N-terminal 25.5 84 0.0018 20.6 2.8 54 9-67 23-83 (92)
53 PRK11523 DNA-binding transcrip 25.3 2.6E+02 0.0056 21.5 5.9 57 3-65 9-74 (253)
54 cd08330 CARD_ASC_NALP1 Caspase 24.3 2.1E+02 0.0046 18.6 4.8 39 7-46 16-54 (82)
55 PRK11534 DNA-binding transcrip 24.1 3.1E+02 0.0067 20.5 6.4 47 4-53 9-63 (224)
56 PRK15441 peptidyl-prolyl cis-t 24.0 91 0.002 20.5 2.7 34 34-67 59-92 (93)
57 cd08819 CARD_MDA5_2 Caspase ac 23.8 2.4E+02 0.0053 19.1 5.2 41 6-46 19-61 (88)
58 PRK04984 fatty acid metabolism 23.6 3.3E+02 0.0071 20.6 6.4 57 2-64 7-72 (239)
59 PF09677 TrbI_Ftype: Type-F co 22.6 2.8E+02 0.006 19.4 5.9 47 6-53 40-87 (111)
60 TIGR01889 Staph_reg_Sar staphy 22.3 2.5E+02 0.0055 18.8 5.8 31 35-65 58-89 (109)
61 TIGR03338 phnR_burk phosphonat 22.0 3.3E+02 0.0072 20.1 6.1 47 4-53 13-67 (212)
62 PF14954 LIX1: Limb expression 21.9 90 0.002 25.0 2.7 52 24-88 22-81 (252)
63 PF07305 DUF1454: Protein of u 21.6 1.9E+02 0.0042 22.5 4.3 56 21-76 123-184 (200)
64 TIGR03415 ABC_choXWV_ATP choli 20.2 35 0.00076 28.8 0.1 21 29-49 6-26 (382)
65 PRK10225 DNA-binding transcrip 20.2 3.8E+02 0.0082 20.6 5.9 57 3-65 10-75 (257)
No 1
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=99.71 E-value=1.3e-17 Score=116.44 Aligned_cols=91 Identities=19% Similarity=0.341 Sum_probs=80.1
Q ss_pred HHHHHHHHhc-CCeEEEeeCCCcceEEEEeccCCCCceeEEccCCCccCccchhhhhccCCCccchHHHHHHHHHHhCCe
Q 035575 37 IERATRIVDQ-RGVRRISGEPSGRSIFKVVGESRRKEEYLCFAENYCACYSFFYDIVNKGEQLCCKHQLAARLASALGAC 115 (132)
Q Consensus 37 l~~Al~lld~-~~V~~~~~~~s~r~~y~V~g~s~~~~~Y~v~~~~~CsC~~F~~~vl~~~~~~~CKHlLA~~la~~lg~~ 115 (132)
+.+|+..+.+ |+........+.-.+|++.|. .++|++ .++|||||+|..+|+.+|..+ |+|+++++.|...|++
T Consensus 10 llka~~v~g~~Grfv~l~l~~~~~~~fVyvG~---~rdYIl-~~gfCSCp~~~~svvl~Gk~~-C~Hi~glk~A~~~gk~ 84 (117)
T COG5431 10 LLKALLVFGKRGRFVFLYLKRSKVKFFVYVGK---ERDYIL-EGGFCSCPDFLGSVVLKGKSP-CAHIIGLKVAKITGKY 84 (117)
T ss_pred HhhHHHHhcccCcEEEEeeCCceEEEEEEEcc---ccceEE-EcCcccCHHHHhHhhhcCccc-chhhhheeeeeecCcE
Confidence 5677777776 888888766665669999998 789999 677999999999999999765 9999999999999999
Q ss_pred EEEEeCHHHHHHHHhcC
Q 035575 116 VEVNVSDEQLALLLAKL 132 (132)
Q Consensus 116 ~~~~v~d~~~~~ll~~~ 132 (132)
..+++...++.++|.|+
T Consensus 85 ~~I~~y~~d~~~Il~e~ 101 (117)
T COG5431 85 DYIDAYYVDYPDILREK 101 (117)
T ss_pred EEEEEecccHHHHHHHH
Confidence 99999999999999874
No 2
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=98.35 E-value=2.9e-07 Score=53.42 Aligned_cols=27 Identities=33% Similarity=0.550 Sum_probs=23.2
Q ss_pred cCCCccCccchhhhhccCCCccchHHHHHHHHH
Q 035575 78 AENYCACYSFFYDIVNKGEQLCCKHQLAARLAS 110 (132)
Q Consensus 78 ~~~~CsC~~F~~~vl~~~~~~~CKHlLA~~la~ 110 (132)
..++||||+|.+. ..+|||++|+.++.
T Consensus 13 ~~~~CsC~~~~~~------~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 13 EQASCSCPYFQFR------GGPCKHIVAVLLAL 39 (40)
T ss_pred cccEeeCCCcccc------CCcchhHHHHHHhh
Confidence 5889999999964 67999999998864
No 3
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=97.42 E-value=0.0006 Score=54.61 Aligned_cols=89 Identities=22% Similarity=0.288 Sum_probs=60.0
Q ss_pred HhhChhHHHHHHHHhcCCeEEEeeCCCcceEEEEeccCC-----------------------------------CC----
Q 035575 31 FLFGKNIERATRIVDQRGVRRISGEPSGRSIFKVVGESR-----------------------------------RK---- 71 (132)
Q Consensus 31 ~lf~~~l~~Al~lld~~~V~~~~~~~s~r~~y~V~g~s~-----------------------------------~~---- 71 (132)
+.|+.|+.++....-+|.|+.+.. ..|+..-.|.|+-. .|
T Consensus 24 ~~d~gRlsRgr~YaR~GnV~si~i-~~g~V~A~VqGS~~~pY~vti~~~~~s~e~w~~vi~~ia~ka~~aakLL~gemP~ 102 (266)
T COG4279 24 FRDDGRLSRGRSYARNGNVTSIQI-LEGKVTALVQGSEEEPYVVTIGIPTFSKEQWREVIATIAQKANYAAKLLSGEMPE 102 (266)
T ss_pred hcccchHHHhHHHHhcCceEEEEe-ecceEEEEEecCCCCCeEEEEecCCCcHHHHHHHHHHHHhhhHHHHHHhcCCCCc
Confidence 456789999999999999999874 45677777777620 00
Q ss_pred --ceeEE------ccC------CCccCccchhhhhccCCCccchHHHHHHH--HHHhCC-----eEEEEeCHHHHHHHH
Q 035575 72 --EEYLC------FAE------NYCACYSFFYDIVNKGEQLCCKHQLAARL--ASALGA-----CVEVNVSDEQLALLL 129 (132)
Q Consensus 72 --~~Y~v------~~~------~~CsC~~F~~~vl~~~~~~~CKHlLA~~l--a~~lg~-----~~~~~v~d~~~~~ll 129 (132)
.+.++ ||. .-||||+++. +|||+-|+.+ |+.+.. ++-.-.+.+++...|
T Consensus 103 sIedvf~~~GL~LfP~t~~dl~~dCSCPD~an---------PCKHi~AvyY~lae~f~~dPflif~lRG~~k~eL~a~l 172 (266)
T COG4279 103 SIEDVFVGNGLSLFPFTLRDLSTDCSCPDYAN---------PCKHIAAVYYLLAEKFDEDPFLIFKLRGRNKEELLALL 172 (266)
T ss_pred hHHHHHHhcCcccCCCchhhcccccCCCCccc---------chHHHHHHHHHHHHHhccCCeeeeeecCCCHHHHHHHH
Confidence 01111 242 4699999983 7999999976 555542 344556777766655
No 4
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=97.40 E-value=0.00052 Score=60.25 Aligned_cols=72 Identities=19% Similarity=0.271 Sum_probs=54.4
Q ss_pred HHHHhhChh-HHHHHHHHhcCCeEEEeeCCCcceEEEEeccCCCCceeEE---c--c--CCCccCccchhhhhccCCCcc
Q 035575 28 ILHFLFGKN-IERATRIVDQRGVRRISGEPSGRSIFKVVGESRRKEEYLC---F--A--ENYCACYSFFYDIVNKGEQLC 99 (132)
Q Consensus 28 ~L~~lf~~~-l~~Al~lld~~~V~~~~~~~s~r~~y~V~g~s~~~~~Y~v---~--~--~~~CsC~~F~~~vl~~~~~~~ 99 (132)
.|..--+++ +.+.....+.|+|.+++ .+.+...-+|.|+ +.|.+ + + ..-||||. + ..+.
T Consensus 18 ~lr~~~d~r~~~kG~~y~e~G~V~~i~-~~g~~v~A~V~Gs----~~y~v~vtL~~~~~ss~CTCP~---~-----~~ga 84 (587)
T COG4715 18 DLRRWADARSFQKGEAYLEAGAVLKIT-IRGGTVRAVVEGS----RRYRVRVTLEGGALSSICTCPY---G-----GSGA 84 (587)
T ss_pred HHHHHhcchHhhhhHHHHhcCCceEEe-ecCCeEEEEEecc----ceeeEEEEeecCCcCceeeCCC---C-----CCcc
Confidence 444455555 67999999999999999 7888889999987 44554 2 1 57899995 2 1468
Q ss_pred chHHHHHHHHHHh
Q 035575 100 CKHQLAARLASAL 112 (132)
Q Consensus 100 CKHlLA~~la~~l 112 (132)
|||+.|+.+.-.-
T Consensus 85 CKH~VAvvl~~~~ 97 (587)
T COG4715 85 CKHVVAVVLEYLD 97 (587)
T ss_pred hHHHHHHHHHHhh
Confidence 9999999886543
No 5
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=95.58 E-value=0.0093 Score=32.09 Aligned_cols=24 Identities=33% Similarity=0.729 Sum_probs=19.6
Q ss_pred CccCccchhhhhccCCCccchHHHHHHHHH
Q 035575 81 YCACYSFFYDIVNKGEQLCCKHQLAARLAS 110 (132)
Q Consensus 81 ~CsC~~F~~~vl~~~~~~~CKHlLA~~la~ 110 (132)
.|||.-|... ..+|.|.+|+....
T Consensus 2 ~CsC~~~~~~------gipC~H~i~v~~~~ 25 (28)
T smart00575 2 TCSCRKFQLS------GIPCRHALAAAIHI 25 (28)
T ss_pred cccCCCcccC------CccHHHHHHHHHHh
Confidence 5999988865 68999999987543
No 6
>PRK13717 conjugal transfer protein TrbI; Provisional
Probab=83.03 E-value=5.9 Score=28.84 Aligned_cols=48 Identities=13% Similarity=0.189 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHh-cCCeEEEe
Q 035575 5 SLVAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVD-QRGVRRIS 53 (132)
Q Consensus 5 ~~v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld-~~~V~~~~ 53 (132)
.+..++..+++. ...+||+..++|..-|+..|.++|+-.. ++++..++
T Consensus 53 K~Tld~F~~Q~~-~~~lte~q~e~lt~rF~~aL~~~L~~yq~~H~~VILV 101 (128)
T PRK13717 53 KQTVDAFFDSAS-QKQLSEAQSKALSARFNTALEASLQAWQQKHHAVILV 101 (128)
T ss_pred HHHHHHHHHHHh-ccCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCEEEEe
Confidence 356788888887 6669999999999999999999999888 56777765
No 7
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=79.82 E-value=8.2 Score=26.20 Aligned_cols=57 Identities=14% Similarity=0.049 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhc-CCeEEEeeCCCcceEEE
Q 035575 6 LVAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQ-RGVRRISGEPSGRSIFK 63 (132)
Q Consensus 6 ~v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~-~~V~~~~~~~s~r~~y~ 63 (132)
...|.+.+++...+-+|+-.+..=..+=++...+||+-+++ |-|+.+. ..+.-.+|+
T Consensus 27 ~t~dkl~kEV~~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~-~~~~q~IYt 84 (86)
T PRK09334 27 ELLKRVAKEVKKEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYS-KNRRTPIYV 84 (86)
T ss_pred HHHHHHHHHhccCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEe-cCCCeEEec
Confidence 46788888888889999999988878888888999885555 5555554 555556664
No 8
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=75.37 E-value=5.5 Score=37.24 Aligned_cols=47 Identities=23% Similarity=0.502 Sum_probs=33.6
Q ss_pred ceEEEEeccCCCCceeEE-cc----CCCccCccchhhhhccCCCccchHHHHHHHHHHh
Q 035575 59 RSIFKVVGESRRKEEYLC-FA----ENYCACYSFFYDIVNKGEQLCCKHQLAARLASAL 112 (132)
Q Consensus 59 r~~y~V~g~s~~~~~Y~v-~~----~~~CsC~~F~~~vl~~~~~~~CKHlLA~~la~~l 112 (132)
...|.|.... ....|.| +. .-.|+|.-|.+. ..+|.|+|.|......
T Consensus 554 ~~~y~V~~~~-~~~~~~V~~d~~~~~v~CsC~kFE~~------GILCrHaLkVL~~~~v 605 (846)
T PLN03097 554 SITFRVQDFE-KNQDFTVTWNQTKLEVSCICRLFEYK------GYLCRHALVVLQMCQL 605 (846)
T ss_pred eEEEEEEEec-CCCcEEEEEecCCCeEEeeccCeecC------ccchhhHHHHHhhcCc
Confidence 4567776432 2457777 22 568999999976 6899999998876543
No 9
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 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 S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=74.82 E-value=13 Score=26.01 Aligned_cols=57 Identities=16% Similarity=0.194 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhc-CCeEEEeeCCCcceEEE
Q 035575 6 LVAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQ-RGVRRISGEPSGRSIFK 63 (132)
Q Consensus 6 ~v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~-~~V~~~~~~~s~r~~y~ 63 (132)
...|.+.+++..-+-+|+-.+..=..+=++...++|+-+.+ |-|..+. ..++-.+|.
T Consensus 45 ~~~~kl~kEV~~~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~-k~~~~~IYt 102 (105)
T PF03297_consen 45 ETYDKLLKEVPKMKLITPSVLSERLKINGSLARKALRELESKGLIKPVS-KHHRQRIYT 102 (105)
T ss_dssp HHHHHHHHHCTTSSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEEE-CCTTCEEEE
T ss_pred HHHHHHHHHhccCcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEEe-ccCCeEEEe
Confidence 46788888888889999999988888888888889766555 5666664 666666665
No 10
>cd08325 CARD_CASP1-like Caspase activation and recruitment domain found in Caspase-1 and related proteins. Caspase activation and recruitment domain (CARD) similar to those found in Caspase-1 (CASP1, ICE) and related proteins, including CARD-only proteins such as ICEBERG or CARD18, INCA (CARD17), CARD16 (COP1, PSEUDO-ICE), CARD8 (DACAR, NDPP1, TUCAN), and CARD12 (NLRC4), as well as ICE-like caspases such as CASP12, CASP5 (ICH-3) and CASP4 (TX, ICH-2). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. CASP1 plays a central role in the cellular response to a wide variety of microbial and non-microbial stimuli, being activated by the inflammasome or the pyroptosome. CARD8 binds itself and the initiator caspase-9, interfering with the binding of APAF-1 and suppressing caspase-9 activation. CARD12 is a Nod-like receptor (NLR) that plays an important role in the innate immune response to Gram-negative bacteria. Caspase-4 (CASP4), -5 (CASP5),
Probab=71.63 E-value=14 Score=24.42 Aligned_cols=44 Identities=11% Similarity=0.180 Sum_probs=35.8
Q ss_pred hhHHHHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhc
Q 035575 3 ASSLVAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQ 46 (132)
Q Consensus 3 ~~~~v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~ 46 (132)
+...+.+.+|+.+.+.+-++++-...+..--+.+..+|..|||.
T Consensus 13 l~~~~i~~llD~Ll~~~Vl~~~E~e~i~~~~~t~~dkar~Lid~ 56 (83)
T cd08325 13 VGKGVINGLLDDLLEKNVLNEEEMEKIKEENNTIMDKARVLVDS 56 (83)
T ss_pred hhHhhHHHHHHHHHHcCCCCHHHHHHHHhccCCHHHHHHHHHHH
Confidence 45668889999999999999998888876644567899888875
No 11
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=71.43 E-value=16 Score=25.77 Aligned_cols=59 Identities=17% Similarity=0.219 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhcCCeEEEeeCCCcceEEE
Q 035575 5 SLVAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQRGVRRISGEPSGRSIFK 63 (132)
Q Consensus 5 ~~v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~~~V~~~~~~~s~r~~y~ 63 (132)
..+.+.+.+++...+-+|+=.|..=+-|=++-...+|..+++..|......++.-.+|.
T Consensus 44 ee~~~ki~KEV~~~r~VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~lvsknrR~~IY~ 102 (107)
T COG4901 44 EELLDKIRKEVPRERVVTPYVLASRYGINGSVARIVLRHLEEEGVVQLVSKNRRQAIYT 102 (107)
T ss_pred HHHHHHHHHhcccceeecHHHHHHHhccchHHHHHHHHHHHhCCceeeeccCccceeee
Confidence 34566666777777889998888887787788899999999988888876665555654
No 12
>TIGR02744 TrbI_Ftype type-F conjugative transfer system protein TrbI. This protein is an essential component of the F-type conjugative transfer sytem for plasmid DNA transfer and has been shown to be localized to the periplasm.
Probab=71.14 E-value=21 Score=25.33 Aligned_cols=47 Identities=15% Similarity=0.128 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHh-cCCeEEEe
Q 035575 6 LVAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVD-QRGVRRIS 53 (132)
Q Consensus 6 ~v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld-~~~V~~~~ 53 (132)
...++..+++. .+.+||+..+++..-|+..+.++|+-.. ++++..++
T Consensus 41 ~tld~F~~q~~-~~~lte~q~~~~~~rF~~~L~~~L~~yq~~H~~vILv 88 (112)
T TIGR02744 41 QTLDAFFDSAS-QKKLSEAQQKALLGRFNALLEAELQAWQAQHHAIILV 88 (112)
T ss_pred HHHHHHHHHHh-hcCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCEEEEe
Confidence 45677788776 5669999999999999999999999877 46677765
No 13
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=61.63 E-value=54 Score=23.72 Aligned_cols=55 Identities=15% Similarity=0.106 Sum_probs=34.2
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHhhChhHHHHH-HHHhcCCeEEEeeC-CCcceEEEE
Q 035575 10 SVWKSIESTRSVTEDQLSILHFLFGKNIERAT-RIVDQRGVRRISGE-PSGRSIFKV 64 (132)
Q Consensus 10 ~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al-~lld~~~V~~~~~~-~s~r~~y~V 64 (132)
-.+.-+++.+.+|-|-+..--..=-+++.+|+ .|++.|-|.|-... +.||.-|.+
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY 88 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLY 88 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEE
Confidence 33443435777777766655555456788885 68888999887632 444544444
No 14
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=60.70 E-value=30 Score=26.58 Aligned_cols=48 Identities=13% Similarity=0.101 Sum_probs=33.3
Q ss_pred hHHHHHHHHHHHHhcC-----CCCHHHHHHHHHhhC---hhHHHHHHHHhc-CCeEEEe
Q 035575 4 SSLVAESVWKSIESTR-----SVTEDQLSILHFLFG---KNIERATRIVDQ-RGVRRIS 53 (132)
Q Consensus 4 ~~~v~~~~~~~i~~~~-----~ltd~~l~~L~~lf~---~~l~~Al~lld~-~~V~~~~ 53 (132)
-..|+++|.++|.+.. .|+.| ..|...|| .++.+|++.|.+ |-|.+..
T Consensus 11 y~qI~~~i~~~I~~G~~~~g~kLPsE--~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~ 67 (241)
T PRK11402 11 YATVRQRLLDDIAQGVYQAGQQIPTE--NELCTQYNVSRITIRKAISDLVADGVLIRWQ 67 (241)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCH--HHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 3578899999998632 34444 56777788 468999776554 7777764
No 15
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=59.73 E-value=30 Score=26.40 Aligned_cols=47 Identities=11% Similarity=0.252 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHhcC-----CCCHHHHHHHHHhhC---hhHHHHHHHHhc-CCeEEEe
Q 035575 5 SLVAESVWKSIESTR-----SVTEDQLSILHFLFG---KNIERATRIVDQ-RGVRRIS 53 (132)
Q Consensus 5 ~~v~~~~~~~i~~~~-----~ltd~~l~~L~~lf~---~~l~~Al~lld~-~~V~~~~ 53 (132)
..|++.|.++|.+.. .|+.| ..|..-|| .++.+|++.|.+ |-|.+..
T Consensus 3 ~qi~~~l~~~I~~g~~~~G~~LPsE--~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~ 58 (233)
T TIGR02404 3 EQIYQDLEQKITHGQYKEGDYLPSE--HELMDQYGASRETVRKALNLLTEAGYIQKIQ 58 (233)
T ss_pred HHHHHHHHHHHHhCCCCCCCCCcCH--HHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 468899999998632 34433 56777788 568999776655 6777654
No 16
>PRK14999 histidine utilization repressor; Provisional
Probab=58.96 E-value=34 Score=26.36 Aligned_cols=47 Identities=21% Similarity=0.299 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHhcC-----CCCHHHHHHHHHhhC---hhHHHHHHHHhc-CCeEEEe
Q 035575 5 SLVAESVWKSIESTR-----SVTEDQLSILHFLFG---KNIERATRIVDQ-RGVRRIS 53 (132)
Q Consensus 5 ~~v~~~~~~~i~~~~-----~ltd~~l~~L~~lf~---~~l~~Al~lld~-~~V~~~~ 53 (132)
..|++.|.++|.+.. .|+.| ..|...|| .++.+|++.|.+ |-|.+..
T Consensus 15 ~qi~~~i~~~I~~g~~~~G~~LPsE--~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~ 70 (241)
T PRK14999 15 ETVKQDICKKIAGGVWQPHDRIPSE--AELVAQYGFSRMTINRALRELTDEGWLVRLQ 70 (241)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCCCH--HHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 568888999998632 35322 45666677 568999876655 6676654
No 17
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=57.25 E-value=42 Score=20.43 Aligned_cols=46 Identities=20% Similarity=0.300 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHhcC-----CC-CHHHHHHHHHhhC---hhHHHHHHHHhcCCeEEEe
Q 035575 5 SLVAESVWKSIESTR-----SV-TEDQLSILHFLFG---KNIERATRIVDQRGVRRIS 53 (132)
Q Consensus 5 ~~v~~~~~~~i~~~~-----~l-td~~l~~L~~lf~---~~l~~Al~lld~~~V~~~~ 53 (132)
..|++.|.+.|.+.. .+ ++ ..|...|+ .++.+|+..+.+..+....
T Consensus 3 ~~i~~~l~~~I~~g~~~~g~~lps~---~~la~~~~vsr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 3 EQIYDQLRQAILSGRLPPGDRLPSE---RELAERYGVSRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp HHHHHHHHHHHHTTSS-TTSBE--H---HHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHHcCCCCCCCEeCCH---HHHHHHhccCCcHHHHHHHHHHHCCcEEEE
Confidence 467888888887643 34 44 44555555 5689998888876665553
No 18
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=56.69 E-value=39 Score=25.61 Aligned_cols=47 Identities=17% Similarity=0.215 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHhcC-----CCCHHHHHHHHHhhC---hhHHHHHHHHhc-CCeEEEe
Q 035575 5 SLVAESVWKSIESTR-----SVTEDQLSILHFLFG---KNIERATRIVDQ-RGVRRIS 53 (132)
Q Consensus 5 ~~v~~~~~~~i~~~~-----~ltd~~l~~L~~lf~---~~l~~Al~lld~-~~V~~~~ 53 (132)
..|++.|.++|.+.. .|+.| ..|..-|| .++.+|++.|.. |-|.+..
T Consensus 11 ~~i~~~l~~~I~~g~~~~G~~LPsE--~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~ 66 (238)
T TIGR02325 11 RQIADKIEQEIAAGHLRAGDYLPAE--MQLAERFGVNRHTVRRAIAALVERGLLRAEQ 66 (238)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCcCH--HHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 568888999998632 34333 46677777 568999876655 6677654
No 19
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=54.81 E-value=51 Score=25.33 Aligned_cols=55 Identities=13% Similarity=0.176 Sum_probs=35.7
Q ss_pred hHHHHHHHHHHHHhc----CCCCHHHHHHHHHhhC---hhHHHHHHHHh-cCCeEEEeeCCCcceEEEE
Q 035575 4 SSLVAESVWKSIEST----RSVTEDQLSILHFLFG---KNIERATRIVD-QRGVRRISGEPSGRSIFKV 64 (132)
Q Consensus 4 ~~~v~~~~~~~i~~~----~~ltd~~l~~L~~lf~---~~l~~Al~lld-~~~V~~~~~~~s~r~~y~V 64 (132)
-..|++.|.++|.+. ..|+.| ..|...|| .++.+|++.|. +|-|.+.. |++.|+.
T Consensus 14 Y~qi~~~L~~~I~~~~~~G~~LPsE--~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~----G~GtfV~ 76 (241)
T PRK10079 14 YQEIAAKLEQELRQHYRCGDYLPAE--QQLAARYEVNRHTLRRAIDQLVEKGWVQRRQ----GVGVLVL 76 (241)
T ss_pred HHHHHHHHHHHHhcccCCCCcCCCH--HHHHHHHCCCHHHHHHHHHHHHHCCCEEEec----CCEEEEe
Confidence 357888899888741 234433 56777888 46899976555 57777664 3555543
No 20
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=53.77 E-value=51 Score=25.10 Aligned_cols=54 Identities=19% Similarity=0.296 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHhcC-----CCCHHHHHHHHHhhC---hhHHHHHHHHhc-CCeEEEeeCCCcceEEEE
Q 035575 5 SLVAESVWKSIESTR-----SVTEDQLSILHFLFG---KNIERATRIVDQ-RGVRRISGEPSGRSIFKV 64 (132)
Q Consensus 5 ~~v~~~~~~~i~~~~-----~ltd~~l~~L~~lf~---~~l~~Al~lld~-~~V~~~~~~~s~r~~y~V 64 (132)
..|++.|.++|.+.. .|+.| ..|...|| .++.+|++.|.+ |-|.+.. |++.|+.
T Consensus 4 ~qi~~~l~~~I~~g~~~~g~~LPsE--~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~----G~GtfV~ 66 (230)
T TIGR02018 4 QRIKQDILERIRSGEWPPGHRIPSE--HELVAQYGCSRMTVNRALRELTDAGLLERRQ----GVGTFVA 66 (230)
T ss_pred HHHHHHHHHHHHhCCCCCCCcCcCH--HHHHHHHCCCHHHHHHHHHHHHHCCCEEEec----CCEEEEc
Confidence 468889999998632 34222 45666777 568999876655 6676664 3445543
No 21
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=50.93 E-value=78 Score=24.32 Aligned_cols=48 Identities=19% Similarity=0.297 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHHHhcC-----CCCHHHHHHHHHhhC---hhHHHHHHHHhc-CCeEEEe
Q 035575 4 SSLVAESVWKSIESTR-----SVTEDQLSILHFLFG---KNIERATRIVDQ-RGVRRIS 53 (132)
Q Consensus 4 ~~~v~~~~~~~i~~~~-----~ltd~~l~~L~~lf~---~~l~~Al~lld~-~~V~~~~ 53 (132)
-..|++.|.++|.+.. .|+.| ..|...|| .++.+|++.|.+ |-|.+..
T Consensus 7 y~qi~~~L~~~I~~g~~~~G~~LPsE--~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~ 63 (240)
T PRK09764 7 YRQIADRIREQIARGELKPGDALPTE--SALQTEFGVSRVTVRQALRQLVEQQILESIQ 63 (240)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCH--HHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 3578888888888632 45322 34556666 568999876665 6677654
No 22
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=50.92 E-value=62 Score=25.08 Aligned_cols=48 Identities=21% Similarity=0.236 Sum_probs=34.1
Q ss_pred hHHHHHHHHHHHHhcC-----CCCHHHHHHHHHhhC---hhHHHHHHHHhc-CCeEEEe
Q 035575 4 SSLVAESVWKSIESTR-----SVTEDQLSILHFLFG---KNIERATRIVDQ-RGVRRIS 53 (132)
Q Consensus 4 ~~~v~~~~~~~i~~~~-----~ltd~~l~~L~~lf~---~~l~~Al~lld~-~~V~~~~ 53 (132)
-..|+++|.++|.+.. .|+.| ..|..-|| -++.+|++.|.+ |-|.+..
T Consensus 9 Y~qI~~~i~~~I~~G~~~~G~~LPsE--~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~ 65 (236)
T COG2188 9 YQQIAEDIRQRIESGELPPGDKLPSE--RELAEQFGVSRMTVRKALDELVEEGLIVRRQ 65 (236)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCCCCH--HHHHHHHCCcHHHHHHHHHHHHHCCcEEEEe
Confidence 3578899999998632 45555 56777888 468999876655 7777765
No 23
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=46.86 E-value=62 Score=20.07 Aligned_cols=51 Identities=14% Similarity=0.032 Sum_probs=37.1
Q ss_pred hhHHHHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhcCCeEEEe
Q 035575 3 ASSLVAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQRGVRRIS 53 (132)
Q Consensus 3 ~~~~v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~~~V~~~~ 53 (132)
.+..++..+...+.+.+.+|=..+.....+=++.+.+|+-.+-+.++..|.
T Consensus 10 ~fG~~~~~V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y~ 60 (62)
T PF08221_consen 10 HFGEIVAKVGEVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQYF 60 (62)
T ss_dssp HHHHHHHHHHHHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HcChHHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCeeee
Confidence 456677777888888888887777777776666789999888887777664
No 24
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=46.61 E-value=76 Score=23.96 Aligned_cols=55 Identities=9% Similarity=0.067 Sum_probs=38.6
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhcCCeEEEee---CCCcceEE
Q 035575 8 AESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQRGVRRISG---EPSGRSIF 62 (132)
Q Consensus 8 ~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~~~V~~~~~---~~s~r~~y 62 (132)
+..+++.+...+.+||+.|+.+..+=.+.+.+.|..+.+.+...+.. ..+||..|
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y 81 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTY 81 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEE
Confidence 45677777777899999999998887788888877666655444332 24565444
No 25
>COG2905 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]
Probab=44.91 E-value=78 Score=28.66 Aligned_cols=55 Identities=20% Similarity=0.233 Sum_probs=37.4
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhcCCeEEEeeCCCcceEEEEeccCC
Q 035575 10 SVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQRGVRRISGEPSGRSIFKVVGESR 69 (132)
Q Consensus 10 ~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~~~V~~~~~~~s~r~~y~V~g~s~ 69 (132)
.++..+-+++.-+..+...+..+...-+.+|++++... ....| -...|+|.||++
T Consensus 298 ~~~s~L~~~gv~~~~i~~lit~i~d~lv~r~leL~~~~----~g~~p-v~fcfvvmGS~G 352 (610)
T COG2905 298 DSLSTLVSRGVRTEFISELITEINDQLVQRALELVEPE----FGAEP-VPFCFVVMGSEG 352 (610)
T ss_pred HHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHhhhh----hcCCC-CceEEEEEccCC
Confidence 34444555676677777777788777789999999763 22122 357888889864
No 26
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=42.70 E-value=77 Score=20.01 Aligned_cols=39 Identities=13% Similarity=0.198 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhc
Q 035575 7 VAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQ 46 (132)
Q Consensus 7 v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~ 46 (132)
..+.+++.+-+.+-+|++....+.. -+.+-.++-.|+|-
T Consensus 17 ~~~~ild~L~~~~vlt~~e~e~I~~-~~t~~~k~~~LLd~ 55 (85)
T PF00619_consen 17 DLDDILDHLLSRGVLTEEEYEEIRS-EPTRQDKARKLLDI 55 (85)
T ss_dssp HHHHHHHHHHHTTSSSHHHHHHHHT-SSSHHHHHHHHHHH
T ss_pred cHHHHHHHHHHCCCCCHHHHHHHHc-cCChHHHHHHHHHH
Confidence 3677888888899999999999998 55566667666653
No 27
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=39.93 E-value=42 Score=20.94 Aligned_cols=46 Identities=9% Similarity=0.068 Sum_probs=27.0
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHh-cCCeEEEee
Q 035575 9 ESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVD-QRGVRRISG 54 (132)
Q Consensus 9 ~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld-~~~V~~~~~ 54 (132)
.+|.+-|++.+.+|-..|..-..+=++.+..-|+.+. +|+|.++..
T Consensus 3 ~~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 3 QEIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 4566777777777755554443333345666666554 588998874
No 28
>PF00837 T4_deiodinase: Iodothyronine deiodinase; InterPro: IPR000643 Iodothyronine deiodinase (1.97.1.10 from EC) (DI) [] is the vertebrate enzyme responsible for the deiodination of the prohormone thyroxine (T4 or 3,5,3',5'-tetraiodothyronine) into the biologically active hormone T3 (3,5,3'-triiodothyronine) and of T3 into the inactive metabolite T2 (3,3'-diiodothyronine). All known DI are proteins of about 250 residues that contain a selenocysteine at their active site. Three types of DI are known, type II is essential for providing the brain with the appropriate levels of T3 during the critical period of development, and type III is essential for the regulation of thyroid hormone inactivation during embryological development.; GO: 0004800 thyroxine 5'-deiodinase activity, 0055114 oxidation-reduction process
Probab=39.38 E-value=1.9e+02 Score=23.21 Aligned_cols=83 Identities=13% Similarity=0.237 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHH---HHHhcCCeEEEeeCCCcceEEEEeccCC-------CCcee
Q 035575 5 SLVAESVWKSIESTRSVTEDQLSILHFLFGKNIERAT---RIVDQRGVRRISGEPSGRSIFKVVGESR-------RKEEY 74 (132)
Q Consensus 5 ~~v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al---~lld~~~V~~~~~~~s~r~~y~V~g~s~-------~~~~Y 74 (132)
+.+.+.++...+++..+.-+... .+|.-...++. ..+|-++-.+....--+-.+..+.|... +|..=
T Consensus 28 ~~i~k~il~~~~~nP~f~~edw~---t~fT~~~lk~vw~~~~ldl~~~a~~G~~APns~vv~l~g~~~~~ildf~~g~RP 104 (237)
T PF00837_consen 28 LCIRKKILLMLEKNPSFCYEDWG---TFFTLESLKAVWKVMWLDLFKEAKLGGPAPNSPVVTLDGQRSCRILDFAKGNRP 104 (237)
T ss_pred HHHHHHHHHhhccCCCCChhHhh---hhhhHHHHHHHHHHHHHHcccceeCCCCCCCCceEeeCCCcceeHHHhccCCCC
Confidence 45667777777666666444444 33332222221 1122222222221111235556665530 23344
Q ss_pred EEccCCCccCccchhh
Q 035575 75 LCFAENYCACYSFFYD 90 (132)
Q Consensus 75 ~v~~~~~CsC~~F~~~ 90 (132)
+|+.-.-||||-|..+
T Consensus 105 LVlnFGS~TCPpF~~~ 120 (237)
T PF00837_consen 105 LVLNFGSCTCPPFMAK 120 (237)
T ss_pred eEEEcccccchHHHHH
Confidence 5556678999999854
No 29
>COG4175 ProV ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]
Probab=35.63 E-value=16 Score=31.10 Aligned_cols=45 Identities=27% Similarity=0.338 Sum_probs=30.3
Q ss_pred HHHHhhChhHHHHHHHHhcCCeEEEeeCCC--------------cceEEEEeccCCCCc
Q 035575 28 ILHFLFGKNIERATRIVDQRGVRRISGEPS--------------GRSIFKVVGESRRKE 72 (132)
Q Consensus 28 ~L~~lf~~~l~~Al~lld~~~V~~~~~~~s--------------~r~~y~V~g~s~~~~ 72 (132)
-++.+||++..+|++++++|+=+.-..+.+ .=.+|++.|-|+.|+
T Consensus 9 nv~kiFG~~~~~a~~~~~~G~~k~ei~~~tg~vvGv~~~sl~v~~GeIfViMGLSGSGK 67 (386)
T COG4175 9 NVYKIFGKNPKRALKLLDQGKSKAEILKKTGLVVGVNDASLDVEEGEIFVIMGLSGSGK 67 (386)
T ss_pred cceeecccCHHHHHHHHHcCCcHHHHHHhhCcEEeeccceeeecCCeEEEEEecCCCCH
Confidence 467899999999999999986432111111 136888887665443
No 30
>PF08290 Hep_core_N: Hepatitis core protein, putative zinc finger; InterPro: IPR013195 This entry represent a short region found at the N terminus of some viral capsid (HBcAg) proteins from various Hepatitis B virus (HBV), which is a major human pathogen. The conservation of four Cys residues suggests that this region acts as a zinc binding domain. Hepatitis virus is composed of an outer envelope of host-derived lipid containing the surface proteins, and an inner protein capsid that contains genomic DNA. The capsid is composed of a single polypeptide, HBcAg, also known as the core antigen. The capsid has a 5-helical fold, where two long helices form a hairpin that dimerises into a 4-helical bundle []; this fold is unusual for icosahedral viruses. The monomer fold is stabilised by a hydrophobic core that is highly conserved among human viral variants. The capsid is assembled from dimers via interactions involving a highly conserved arginine-rich region near the C terminus. This viral capsid acts as a core antigen, the major immunodominant region lying at the tips of the alpha-helical hairpins that form spikes on the capsid surface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005198 structural molecule activity, 0009405 pathogenesis
Probab=35.30 E-value=15 Score=19.61 Aligned_cols=12 Identities=17% Similarity=0.304 Sum_probs=8.9
Q ss_pred CCCccCccchhh
Q 035575 79 ENYCACYSFFYD 90 (132)
Q Consensus 79 ~~~CsC~~F~~~ 90 (132)
.-.||||.++-.
T Consensus 9 iiscscpt~qas 20 (27)
T PF08290_consen 9 IISCSCPTVQAS 20 (27)
T ss_pred eeeccCCcchhh
Confidence 447999988743
No 31
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=34.90 E-value=1.6e+02 Score=22.48 Aligned_cols=58 Identities=16% Similarity=0.143 Sum_probs=42.9
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhcCCeEEEee---CCCc--ceEEEEec
Q 035575 9 ESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQRGVRRISG---EPSG--RSIFKVVG 66 (132)
Q Consensus 9 ~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~~~V~~~~~---~~s~--r~~y~V~g 66 (132)
-.+++.+...+.+||+-+..+..+=...+.+.|.++-+.++..|.. .++| +..|.+..
T Consensus 21 ~~v~~~l~~kge~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~~~~~~~y~w~~~~ 83 (176)
T COG1675 21 VLVVDALLEKGELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDEESGWEEYTWYINY 83 (176)
T ss_pred hHHHHHHHhcCCcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCCCcEEEEEEech
Confidence 5566667767789999988887777778999999998888776653 2334 56666664
No 32
>PHA02902 putative IMV membrane protein; Provisional
Probab=32.51 E-value=39 Score=21.90 Aligned_cols=17 Identities=41% Similarity=0.479 Sum_probs=14.5
Q ss_pred CCCCHHHHHHHHHhhCh
Q 035575 19 RSVTEDQLSILHFLFGK 35 (132)
Q Consensus 19 ~~ltd~~l~~L~~lf~~ 35 (132)
.++|||+..+||.++..
T Consensus 52 D~lTpDQirAlHrlvT~ 68 (70)
T PHA02902 52 DSLTPDQIKALHRLVSL 68 (70)
T ss_pred ccCCHHHHHHHHHHHhc
Confidence 47999999999998754
No 33
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=32.30 E-value=2.2e+02 Score=25.34 Aligned_cols=76 Identities=16% Similarity=0.257 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHhcCCCC----------HHHHHHHHHhhChhHHHHHHHHhc--CCeEEEeeCC-----------------
Q 035575 6 LVAESVWKSIESTRSVT----------EDQLSILHFLFGKNIERATRIVDQ--RGVRRISGEP----------------- 56 (132)
Q Consensus 6 ~v~~~~~~~i~~~~~lt----------d~~l~~L~~lf~~~l~~Al~lld~--~~V~~~~~~~----------------- 56 (132)
...+.+..++.+.+-.+ ++.-..+.....+++.=|..|+.. |...++. ++
T Consensus 592 ~~l~~l~~~~~~~gy~~~~~~~~~~~~~~~~~~~~~~hsekla~a~~l~~~~~~~~i~i~-knlr~c~dch~~~k~~s~~ 670 (697)
T PLN03081 592 QKLDELMKEISEYGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQIT-QSHRICKDCHKVIKFIALV 670 (697)
T ss_pred HHHHHHHHHHHHcCCCCCcchhhccccHHHHHHHHHhccHHHHHHhhCccCCCCCeEEEe-cCCEECCCchhhHHHHhhh
Confidence 35567777777765333 333344444555678778888875 3333332 22
Q ss_pred CcceEEEEeccCCCCceeEEccCCCccCccc
Q 035575 57 SGRSIFKVVGESRRKEEYLCFAENYCACYSF 87 (132)
Q Consensus 57 s~r~~y~V~g~s~~~~~Y~v~~~~~CsC~~F 87 (132)
.||. .+|.. ...+-.|....|||.+|
T Consensus 671 ~~r~-i~~rd----~~rfh~f~~g~csc~d~ 696 (697)
T PLN03081 671 TKRE-IVVRD----ASRFHHFKLGKCSCGDY 696 (697)
T ss_pred cceE-EEEec----CCccccCCCCccccccc
Confidence 2343 23332 23455567889999987
No 34
>PRK11830 dapD 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional
Probab=31.45 E-value=1.9e+02 Score=23.49 Aligned_cols=45 Identities=16% Similarity=0.299 Sum_probs=30.5
Q ss_pred CchhHHHHHHHHHHHHhc--CCCCHHHHHHHHHhhChhHHHHHHHHhcCCeEEEe
Q 035575 1 MSASSLVAESVWKSIEST--RSVTEDQLSILHFLFGKNIERATRIVDQRGVRRIS 53 (132)
Q Consensus 1 ~~~~~~v~~~~~~~i~~~--~~ltd~~l~~L~~lf~~~l~~Al~lld~~~V~~~~ 53 (132)
|.-+....|+.|++-.+- ...+.+. -..+..++++||+|+++--.
T Consensus 1 ~~~~~~~i~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~l~~g~~r~a~ 47 (272)
T PRK11830 1 MSQLQKIIEEAWERRAELTPATADTEV--------REAVEEVIDLLDSGELRVAE 47 (272)
T ss_pred ChHHHHHHHHHHHhHhhCCccCCCHHH--------HHHHHHHHHHhcCCCeEEEe
Confidence 566778888888876652 2222332 23468899999999988765
No 35
>cd08810 CARD_BCL10 Caspase activation and recruitment domain of B-cell lymphoma 10. Caspase activation and recruitment domain (CARD) similar to that found in BCL10 (B-cell lymphoma 10). BCL10 and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1) are the integral components of CBM signalosomes. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. Both CARMA1 and CARD9 associate with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. 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 asso
Probab=30.82 E-value=1.5e+02 Score=19.83 Aligned_cols=39 Identities=18% Similarity=0.325 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHh
Q 035575 6 LVAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVD 45 (132)
Q Consensus 6 ~v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld 45 (132)
..++.+++-+.+.+-+|++....+.. .+.+-.+|-.|+|
T Consensus 16 L~~~~l~d~L~s~~ILt~~d~EeI~~-~~t~~~qa~~LLd 54 (84)
T cd08810 16 IIADRHFDYLRSKRILTRDDCEEISC-RTTSRKQAGKLLD 54 (84)
T ss_pred hcHHHHHHHHHHcCCCCHHHHHHHhc-cCCcHHHHHHHHH
Confidence 34677888889999999999888877 5555667766555
No 36
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=29.97 E-value=2.1e+02 Score=21.85 Aligned_cols=57 Identities=21% Similarity=0.309 Sum_probs=37.3
Q ss_pred hhHHHHHHHHHHHHhcC-----CC-CHHHHHHHHHhhC---hhHHHHHHHHhcCCeEEEeeCCCcceEEEEe
Q 035575 3 ASSLVAESVWKSIESTR-----SV-TEDQLSILHFLFG---KNIERATRIVDQRGVRRISGEPSGRSIFKVV 65 (132)
Q Consensus 3 ~~~~v~~~~~~~i~~~~-----~l-td~~l~~L~~lf~---~~l~~Al~lld~~~V~~~~~~~s~r~~y~V~ 65 (132)
+...|.+.|.+.|.+.. .| ++ ..|...|| .++..|+..+....+..+.+ |++.|+-.
T Consensus 8 ~~~~v~~~i~~~I~~g~l~pG~~LPsE---~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~---~~G~~V~~ 73 (251)
T PRK09990 8 IADVVAERIERLIVDGVLKVGQALPSE---RRLCEKLGFSRSALREGLTVLRGRGIIETAQ---GRGSFVAR 73 (251)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCcCH---HHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC---CCeeEEec
Confidence 45567777777777533 34 33 35666677 56899999998877777652 35555543
No 37
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interac
Probab=29.61 E-value=1.5e+02 Score=19.94 Aligned_cols=39 Identities=15% Similarity=0.243 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhc
Q 035575 7 VAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQ 46 (132)
Q Consensus 7 v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~ 46 (132)
+++.+++.+-+.+.+|++-...+..- +.+-.+|-.|+|-
T Consensus 24 ~v~~ilD~Ll~~~Vlt~ee~e~I~~~-~t~~~qAr~Lld~ 62 (94)
T cd08329 24 SVLPILDSLLSANVITEQEYDVIKQK-TQTPLQARELIDT 62 (94)
T ss_pred hhHHHHHHHHHcCCCCHHHHHHHHcC-CChHHHHHHHHHH
Confidence 46778888888999999988887663 2335888888875
No 38
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=29.61 E-value=1.9e+02 Score=21.22 Aligned_cols=40 Identities=15% Similarity=0.146 Sum_probs=29.2
Q ss_pred HHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhcCCeE
Q 035575 11 VWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQRGVR 50 (132)
Q Consensus 11 ~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~~~V~ 50 (132)
+++.+-..+.+|||.++.+.-+=.+.+.+++..+-+.+..
T Consensus 19 Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv 58 (158)
T TIGR00373 19 VLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLA 58 (158)
T ss_pred HHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 4455555778999999998888667788887666665544
No 39
>PF06543 Lac_bphage_repr: Lactococcus bacteriophage repressor; InterPro: IPR009498 This entry represents the C terminus of various Lactococcus bacteriophage repressor proteins.
Probab=29.10 E-value=40 Score=20.50 Aligned_cols=21 Identities=29% Similarity=0.654 Sum_probs=18.2
Q ss_pred cCCCCHHHHHHHHHhhChhHH
Q 035575 18 TRSVTEDQLSILHFLFGKNIE 38 (132)
Q Consensus 18 ~~~ltd~~l~~L~~lf~~~l~ 38 (132)
.+.|||+.-.++..+||.++.
T Consensus 28 GrPltdevK~a~k~i~~~~l~ 48 (49)
T PF06543_consen 28 GRPLTDEVKEAMKLIFGKRLE 48 (49)
T ss_pred CeeCCHHHHHHHHHHHhhhcc
Confidence 458999999999999998763
No 40
>PHA02681 ORF089 virion membrane protein; Provisional
Probab=29.10 E-value=46 Score=22.64 Aligned_cols=17 Identities=29% Similarity=0.464 Sum_probs=14.8
Q ss_pred CCCCHHHHHHHHHhhCh
Q 035575 19 RSVTEDQLSILHFLFGK 35 (132)
Q Consensus 19 ~~ltd~~l~~L~~lf~~ 35 (132)
.++|||+..+||.++-.
T Consensus 50 D~lTpDQVrAlHRlvTs 66 (92)
T PHA02681 50 DKMTDDQVRAFHALVTS 66 (92)
T ss_pred ccCCHHHHHHHHHHHhC
Confidence 47999999999999864
No 41
>cd08326 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9. Caspase activation and recruitment domain (CARD) similar to that found in caspase-9 (CASP9, MCH6, APAF3), which interacts with the CARD of apoptotic protease-activating factor 1 (APAF-1). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-9 is the initiator caspase associated with the intrinsic or mitochondrial pathway of apoptosis, induced by many pro-apoptotic signals. Together with APAF-1, it forms the heptameric 'apoptosome' in response to the release of cytochrome c from mitochondria. Activated caspase-9 cleaves and activates downstream effector caspases, like caspase-3, caspase-6, and caspase-7, resulting in apoptosis. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apopt
Probab=28.78 E-value=1.7e+02 Score=19.32 Aligned_cols=38 Identities=16% Similarity=0.314 Sum_probs=28.6
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhc
Q 035575 8 AESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQ 46 (132)
Q Consensus 8 ~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~ 46 (132)
++.+++-+-+++.+|++....+.. -+.+-.+|..|+|-
T Consensus 18 ~~~v~~~L~~~~Vlt~~~~e~I~~-~~tr~~q~~~LLd~ 55 (84)
T cd08326 18 PKYLWDHLLSRGVFTPDMIEEIQA-AGSRRDQARQLLID 55 (84)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHc-CCCHHHHHHHHHHH
Confidence 466788888899999999888876 45566777766654
No 42
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and 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 PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=28.66 E-value=1.5e+02 Score=18.41 Aligned_cols=39 Identities=18% Similarity=0.215 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhc
Q 035575 7 VAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQ 46 (132)
Q Consensus 7 v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~ 46 (132)
-.+.+++.+.+.+-+|++....+...-. +-.++-.++|.
T Consensus 14 ~~~~il~~L~~~~vlt~~e~~~i~~~~~-~~~k~~~Lld~ 52 (80)
T cd01671 14 DVEDVLDHLLSDGVLTEEEYEKIRSEST-RQDKARKLLDI 52 (80)
T ss_pred cHHHHHHHHHHcCCCCHHHHHHHHcCCC-hHHHHHHHHHH
Confidence 4567888888899999999999887544 55666666654
No 43
>cd08814 DED_Caspase_10_repeat2 Death Effector Domain, repeat 2, of Caspase-10. Death effector domain (DED) found in Caspase-10, repeat 2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-10 is an initiator of death receptor mediated apoptosis. Together with FADD, caspase-8 and the pseudo-caspase c-FLIP, it forms the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. It contains two N-terminal DED domains and a C-terminal caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. 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 m
Probab=28.33 E-value=99 Score=20.43 Aligned_cols=26 Identities=27% Similarity=0.335 Sum_probs=22.6
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHhhCh
Q 035575 10 SVWKSIESTRSVTEDQLSILHFLFGK 35 (132)
Q Consensus 10 ~~~~~i~~~~~ltd~~l~~L~~lf~~ 35 (132)
+||..+++.+.++++.+..|..+|.+
T Consensus 40 dlf~~LEk~~~L~~dnl~~L~~il~~ 65 (79)
T cd08814 40 SLLAFLEKQNLLTENNLTILEDICKT 65 (79)
T ss_pred HHHHHHHhcCCCCCccHHHHHHHHHH
Confidence 67888888899999999999988884
No 44
>PF09645 F-112: F-112 protein; InterPro: IPR018601 This entry is represented by Sulfolobus virus-like particle SSV1, p11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2VQC_A.
Probab=27.65 E-value=1e+02 Score=21.55 Aligned_cols=41 Identities=17% Similarity=0.243 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHhhChh---HHHHHHHHhc
Q 035575 6 LVAESVWKSIESTRSVTEDQLSILHFLFGKN---IERATRIVDQ 46 (132)
Q Consensus 6 ~v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~---l~~Al~lld~ 46 (132)
.+|+.+++.+.+.+++|-+...+...+-+++ +.++++.+=+
T Consensus 7 q~A~~l~kiLq~K~Eit~eDIlaqfeIS~s~Ay~I~~~lr~iCe 50 (110)
T PF09645_consen 7 QMAEILYKILQEKKEITLEDILAQFEISYSRAYNIQRVLRKICE 50 (110)
T ss_dssp HHHHHHHHHHHHHSEE-HHHHHHHH---HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCcCcHHHHHHHhccchhhhhHHHHHHHHHHH
Confidence 7899999999999999988877777776665 4666665533
No 45
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=27.15 E-value=2.3e+02 Score=21.71 Aligned_cols=59 Identities=24% Similarity=0.209 Sum_probs=37.3
Q ss_pred hhHHHHHHHHHHHHhcCCCCHHHH---HHHHHhhC---hhHHHHHHHHhcCCeEEEeeCCCcceEEEE
Q 035575 3 ASSLVAESVWKSIESTRSVTEDQL---SILHFLFG---KNIERATRIVDQRGVRRISGEPSGRSIFKV 64 (132)
Q Consensus 3 ~~~~v~~~~~~~i~~~~~ltd~~l---~~L~~lf~---~~l~~Al~lld~~~V~~~~~~~s~r~~y~V 64 (132)
+...|++.|.+.|.+..--+.+.| ..|...|| .++..|+..++...+....+ |++.|+-
T Consensus 3 l~~~v~~~L~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~---~~G~~V~ 67 (253)
T PRK10421 3 LSDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRR---GGGTFIR 67 (253)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC---CCeEEEe
Confidence 346778888888875431111222 35667778 45899999999987777652 3455543
No 46
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. 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 PYRIN and
Probab=26.79 E-value=1.9e+02 Score=19.19 Aligned_cols=38 Identities=3% Similarity=0.054 Sum_probs=28.1
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhc
Q 035575 8 AESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQ 46 (132)
Q Consensus 8 ~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~ 46 (132)
++.+++.+-+.+.+|++....+... +.+..++..|+|-
T Consensus 22 ~~~v~~~L~~~gvlt~~~~~~I~~~-~t~~~k~~~Lld~ 59 (90)
T cd08332 22 LDELLIHLLQKDILTDSMAESIMAK-PTSFSQNVALLNL 59 (90)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHcC-CCcHHHHHHHHHH
Confidence 5667888888999999998888763 3456677666654
No 47
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=26.55 E-value=56 Score=21.98 Aligned_cols=44 Identities=11% Similarity=0.126 Sum_probs=28.9
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhcCCeEEEe
Q 035575 10 SVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQRGVRRIS 53 (132)
Q Consensus 10 ~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~~~V~~~~ 53 (132)
.++..|...+.++||.+..+..+=++.+.+.+.-+.+.++..+.
T Consensus 17 ~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 17 RILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp HHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEE
T ss_pred HHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEE
Confidence 45666666788999999999888778898888777776665554
No 48
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.31 E-value=99 Score=22.23 Aligned_cols=49 Identities=12% Similarity=0.015 Sum_probs=31.8
Q ss_pred CchhHHHHHHHHHHHHhcC--CCCHH--HHHHHHHhhChhHHHHHHHHhcCCe
Q 035575 1 MSASSLVAESVWKSIESTR--SVTED--QLSILHFLFGKNIERATRIVDQRGV 49 (132)
Q Consensus 1 ~~~~~~v~~~~~~~i~~~~--~ltd~--~l~~L~~lf~~~l~~Al~lld~~~V 49 (132)
|++..++++.+.+..++.+ .++.- .+..|..+.++.+..|++.+.+|.+
T Consensus 4 ~si~~~i~~~v~~~A~~~g~~~V~~V~l~IG~ls~V~pe~L~fafe~l~~gt~ 56 (135)
T PRK03824 4 WALAEAIVRTVIDYAQKEGASKVKALKVVLGELQDVDKEIVEFALNELLKGTI 56 (135)
T ss_pred HHHHHHHHHHHHHHHHHcCCchhHhHHhhHhhhhhhhHHHHHHHHHHHHcCCc
Confidence 3455566666555444433 22222 2356888888999999999999875
No 49
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 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 alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=26.17 E-value=1.6e+02 Score=17.82 Aligned_cols=34 Identities=15% Similarity=0.112 Sum_probs=25.1
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHH
Q 035575 9 ESVWKSIESTRSVTEDQLSILHFLFGKNIERATR 42 (132)
Q Consensus 9 ~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~ 42 (132)
.+-++++-+++.++|++-...-.-|...+.+||+
T Consensus 16 ~dtLDeli~~~~I~p~La~kVL~~FDksi~~~L~ 49 (49)
T PF02268_consen 16 TDTLDELIQEGKITPQLAMKVLEQFDKSINEALS 49 (49)
T ss_dssp HHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHhC
Confidence 3344555668889999999998999888877764
No 50
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=25.90 E-value=1.8e+02 Score=20.19 Aligned_cols=41 Identities=10% Similarity=0.097 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhcC
Q 035575 7 VAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQR 47 (132)
Q Consensus 7 v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~~ 47 (132)
=+.++..+|.+.+.++++....|..+.|.+...+..++-+-
T Consensus 51 ~a~elve~L~~~~~l~e~~a~~I~nL~P~~~dElrai~~~~ 91 (112)
T PRK14981 51 DAEELVEELLELEKMKEKTAVKIADILPETRDELRAIFAKE 91 (112)
T ss_pred HHHHHHHHHHHccCCCHHHHHHHHhcCCCCHHHHHHHHHHh
Confidence 34566667766666788888888888888776666666543
No 51
>PF02828 L27: L27 domain; InterPro: IPR014775 The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7, as well as some protein kinases and human MPP2 protein.; PDB: 1ZL8_B 1VA8_A 3LRA_A 3UIT_A 1Y74_D 1RSO_B.
Probab=25.86 E-value=1.6e+02 Score=17.62 Aligned_cols=35 Identities=14% Similarity=0.116 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHH
Q 035575 7 VAESVWKSIESTRSVTEDQLSILHFLFGKNIERAT 41 (132)
Q Consensus 7 v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al 41 (132)
-+-+++.+|......+.+-...|..++.+...+|+
T Consensus 4 ~~~e~L~~L~~~~~~~~~~~~eL~~lL~~p~~~aL 38 (56)
T PF02828_consen 4 RVLELLEELQSLSSASQEDAQELQQLLQSPHFQAL 38 (56)
T ss_dssp HHHHHHHHHHHHTSSTHHHHHHHHHHHHSHHHHHH
T ss_pred HHHHHHHHHHhccCCChHHHHHHHHHHcCHHHHHH
Confidence 45667788887776666779999999998765554
No 52
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=25.52 E-value=84 Score=20.65 Aligned_cols=54 Identities=13% Similarity=0.295 Sum_probs=33.5
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHH------hhChhHHHHHHHH-hcCCeEEEeeCCCcceEEEEecc
Q 035575 9 ESVWKSIESTRSVTEDQLSILHF------LFGKNIERATRIV-DQRGVRRISGEPSGRSIFKVVGE 67 (132)
Q Consensus 9 ~~~~~~i~~~~~ltd~~l~~L~~------lf~~~l~~Al~ll-d~~~V~~~~~~~s~r~~y~V~g~ 67 (132)
.++.+.+.+.-.+||+....... .|..++.=|+.-+ ..|-|.+ | .|.+|.+...
T Consensus 23 ~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~----~-~rG~~~iT~~ 83 (92)
T PF14338_consen 23 KEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIER----P-KRGIWRITEK 83 (92)
T ss_pred HHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccC----C-CCCceEECHh
Confidence 46667777767788887776543 5666665554433 3455533 2 2888888643
No 53
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=25.30 E-value=2.6e+02 Score=21.46 Aligned_cols=57 Identities=16% Similarity=0.155 Sum_probs=37.4
Q ss_pred hhHHHHHHHHHHHHhcC-----CCC-HHHHHHHHHhhC---hhHHHHHHHHhcCCeEEEeeCCCcceEEEEe
Q 035575 3 ASSLVAESVWKSIESTR-----SVT-EDQLSILHFLFG---KNIERATRIVDQRGVRRISGEPSGRSIFKVV 65 (132)
Q Consensus 3 ~~~~v~~~~~~~i~~~~-----~lt-d~~l~~L~~lf~---~~l~~Al~lld~~~V~~~~~~~s~r~~y~V~ 65 (132)
+...|.+.|.+.|.+.. .|+ +. .|..-|| .++..|+..+....+....+ |++.|+..
T Consensus 9 ~~~~v~~~l~~~I~~g~l~pG~~LpsE~---eLae~~gVSRtpVREAL~~L~~eGlV~~~~---~~G~~V~~ 74 (253)
T PRK11523 9 LYQQLAAELKERIEQGVYLVGDKLPAER---FIADEKNVSRTVVREAIIMLEVEGYVEVRK---GSGIHVVS 74 (253)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCCCCCHH---HHHHHHCCCHHHHHHHHHHHHHCCCEEEec---CCeeEEec
Confidence 45667788888887543 343 33 4666677 56899999998877766642 35665553
No 54
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. 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 PYRIN and DED (Death Effector Domain). They se
Probab=24.32 E-value=2.1e+02 Score=18.63 Aligned_cols=39 Identities=13% Similarity=0.238 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhc
Q 035575 7 VAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQ 46 (132)
Q Consensus 7 v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~ 46 (132)
.++.+++.+-+.+.+|++....+.. -+.+-.+|-.|++-
T Consensus 16 ~v~~ilD~L~~~~Vit~e~~~~I~a-~~T~~~kar~Lld~ 54 (82)
T cd08330 16 NVDPILDKLHGKKVITQEQYSEVRA-EKTNQEKMRKLFSF 54 (82)
T ss_pred hHHHHHHHHHHCCCCCHHHHHHHHc-CCCcHHHHHHHHHH
Confidence 4677888888889999998887766 22345666666653
No 55
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=24.13 E-value=3.1e+02 Score=20.50 Aligned_cols=47 Identities=6% Similarity=-0.038 Sum_probs=31.4
Q ss_pred hHHHHHHHHHHHHhc-----CCCCHHHHHHHHHhhC---hhHHHHHHHHhcCCeEEEe
Q 035575 4 SSLVAESVWKSIEST-----RSVTEDQLSILHFLFG---KNIERATRIVDQRGVRRIS 53 (132)
Q Consensus 4 ~~~v~~~~~~~i~~~-----~~ltd~~l~~L~~lf~---~~l~~Al~lld~~~V~~~~ 53 (132)
...|.+.|.+.|-+. ..|++. .|..-|| ..+..|+..+....+....
T Consensus 9 ~~~vy~~i~~~I~~g~l~pG~~L~e~---eLae~lgVSRtpVREAL~~L~~eGlv~~~ 63 (224)
T PRK11534 9 ALDGYRWLKNDIIRGNFQPDEKLRMS---LLTSRYALGVGPLREALSQLVAERLVTVV 63 (224)
T ss_pred hHHHHHHHHHHHHhCCCCCCCcCCHH---HHHHHHCCChHHHHHHHHHHHHCCCEEEe
Confidence 344556666666542 256654 5777777 4589999999887776664
No 56
>PRK15441 peptidyl-prolyl cis-trans isomerase C; Provisional
Probab=24.02 E-value=91 Score=20.48 Aligned_cols=34 Identities=12% Similarity=-0.053 Sum_probs=24.6
Q ss_pred ChhHHHHHHHHhcCCeEEEeeCCCcceEEEEecc
Q 035575 34 GKNIERATRIVDQRGVRRISGEPSGRSIFKVVGE 67 (132)
Q Consensus 34 ~~~l~~Al~lld~~~V~~~~~~~s~r~~y~V~g~ 67 (132)
++.+.+|+.-++.|.|+....++.|-.+..|.+.
T Consensus 59 ~~~f~~a~~~l~~G~vs~Pi~t~~G~hIlkv~~r 92 (93)
T PRK15441 59 VPAFDKVVFSCPVLEPTGPLHTQFGYHIIKVLYR 92 (93)
T ss_pred CHHHHHHHHhCCCCCcCCcEEcCCEEEEEEEEec
Confidence 5668889888999998776656666666666543
No 57
>cd08819 CARD_MDA5_2 Caspase activation and recruitment domain found in MDA5, second repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protei
Probab=23.77 E-value=2.4e+02 Score=19.14 Aligned_cols=41 Identities=12% Similarity=0.085 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHh--hChhHHHHHHHHhc
Q 035575 6 LVAESVWKSIESTRSVTEDQLSILHFL--FGKNIERATRIVDQ 46 (132)
Q Consensus 6 ~v~~~~~~~i~~~~~ltd~~l~~L~~l--f~~~l~~Al~lld~ 46 (132)
..+.+++..+-+.+-+|++....+..- -+.+-..|.+|+++
T Consensus 19 L~~~~v~d~ll~~~ilT~~d~e~I~aa~~~~g~~~~ar~LL~~ 61 (88)
T cd08819 19 MKTRDVCDKCLEQGLLTEEDRNRIEAATENHGNESGARELLKR 61 (88)
T ss_pred hhHHHHHHHHHhcCCCCHHHHHHHHHhccccCcHHHHHHHHHH
Confidence 456788888888999999999999886 44456777777765
No 58
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=23.63 E-value=3.3e+02 Score=20.57 Aligned_cols=57 Identities=21% Similarity=0.248 Sum_probs=36.6
Q ss_pred chhHHHHHHHHHHHHhcC-----CC-CHHHHHHHHHhhC---hhHHHHHHHHhcCCeEEEeeCCCcceEEEE
Q 035575 2 SASSLVAESVWKSIESTR-----SV-TEDQLSILHFLFG---KNIERATRIVDQRGVRRISGEPSGRSIFKV 64 (132)
Q Consensus 2 ~~~~~v~~~~~~~i~~~~-----~l-td~~l~~L~~lf~---~~l~~Al~lld~~~V~~~~~~~s~r~~y~V 64 (132)
+....+.+.|.+.|.+.. .| |+. .|..-|| .++..|+..+....+....+ |++.|+.
T Consensus 7 ~~~~~~~~~l~~~I~~g~l~pG~~LPsE~---eLae~~gVSRt~VReAL~~L~~eGlv~~~~---g~G~~V~ 72 (239)
T PRK04984 7 SPAGFAEEYIIESIWNNRFPPGSILPAER---ELSELIGVTRTTLREVLQRLARDGWLTIQH---GKPTKVN 72 (239)
T ss_pred CHHHHHHHHHHHHHHcCCCCCCCcCCCHH---HHHHHHCCCHHHHHHHHHHHHHCCCEEEeC---CCeeEeC
Confidence 345677888888887643 35 343 4666677 56899998888866665542 3455553
No 59
>PF09677 TrbI_Ftype: Type-F conjugative transfer system protein (TrbI_Ftype); InterPro: IPR014115 This entry represents TrbI, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm [, ].
Probab=22.62 E-value=2.8e+02 Score=19.39 Aligned_cols=47 Identities=15% Similarity=0.132 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHhhChhHHHHHHHHhc-CCeEEEe
Q 035575 6 LVAESVWKSIESTRSVTEDQLSILHFLFGKNIERATRIVDQ-RGVRRIS 53 (132)
Q Consensus 6 ~v~~~~~~~i~~~~~ltd~~l~~L~~lf~~~l~~Al~lld~-~~V~~~~ 53 (132)
.++++..++.. ...+||+...++..-|...+.+++.-..+ +++..++
T Consensus 40 ~tv~~f~~~~a-~~~lt~~q~~a~t~~F~~aL~~~L~~~~~~h~~vILv 87 (111)
T PF09677_consen 40 GTVDEFVQQLA-RSSLTPEQVEALTQRFMQALEASLAEYQAEHHVVILV 87 (111)
T ss_pred HHHHHHHHHHh-ccCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCeEEEe
Confidence 45566666655 45689999999999999999999988755 5566554
No 60
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=22.26 E-value=2.5e+02 Score=18.79 Aligned_cols=31 Identities=6% Similarity=0.183 Sum_probs=19.0
Q ss_pred hhHHHHHH-HHhcCCeEEEeeCCCcceEEEEe
Q 035575 35 KNIERATR-IVDQRGVRRISGEPSGRSIFKVV 65 (132)
Q Consensus 35 ~~l~~Al~-lld~~~V~~~~~~~s~r~~y~V~ 65 (132)
+++.++++ |.++|-|.+.....+.|..+..-
T Consensus 58 stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~l 89 (109)
T TIGR01889 58 SALVKIIKKLSKKGYLSKERSEDDERKVIISI 89 (109)
T ss_pred HHHHHHHHHHHHCCCEeccCCcccCCeEEEEE
Confidence 45666654 44557788887545556666654
No 61
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=22.00 E-value=3.3e+02 Score=20.06 Aligned_cols=47 Identities=21% Similarity=0.330 Sum_probs=32.6
Q ss_pred hHHHHHHHHHHHHhc-----CCCCHHHHHHHHHhhC---hhHHHHHHHHhcCCeEEEe
Q 035575 4 SSLVAESVWKSIEST-----RSVTEDQLSILHFLFG---KNIERATRIVDQRGVRRIS 53 (132)
Q Consensus 4 ~~~v~~~~~~~i~~~-----~~ltd~~l~~L~~lf~---~~l~~Al~lld~~~V~~~~ 53 (132)
...|.+.|.+.|-+. ..|++. .|..-|| .++..|+..+....+..+.
T Consensus 13 ~~~v~~~l~~~I~~g~l~pG~~L~e~---~La~~lgVSRtpVReAL~~L~~eGlv~~~ 67 (212)
T TIGR03338 13 TTLVQDEIERAILSGELPPGAKLNES---DIAARLGVSRGPVREAFRALEEAGLVRNE 67 (212)
T ss_pred HHHHHHHHHHHHHcCCCCCCCEecHH---HHHHHhCCChHHHHHHHHHHHHCCCEEEe
Confidence 456677777777653 256554 5666677 5689999999887777664
No 62
>PF14954 LIX1: Limb expression 1
Probab=21.94 E-value=90 Score=24.99 Aligned_cols=52 Identities=13% Similarity=0.340 Sum_probs=27.2
Q ss_pred HHHHHHHHhhChhHHHHHHHHhcCCeEEEeeCCCcceEEEEeccCCCCceeEE---cc-----CCCccCccch
Q 035575 24 DQLSILHFLFGKNIERATRIVDQRGVRRISGEPSGRSIFKVVGESRRKEEYLC---FA-----ENYCACYSFF 88 (132)
Q Consensus 24 ~~l~~L~~lf~~~l~~Al~lld~~~V~~~~~~~s~r~~y~V~g~s~~~~~Y~v---~~-----~~~CsC~~F~ 88 (132)
....+|+.++...-.+..+ +..+. -.+|+-.-+ ++..|+| +| ++|+.||+-+
T Consensus 22 nvV~~LqeFWq~Kq~r~a~-~~~~~----------lv~YEs~ps--~~ppyVcyVTLPGGSCFGnfq~C~tkA 81 (252)
T PF14954_consen 22 NVVEALQEFWQMKQSRGAD-LKSEA----------LVVYESVPS--PSPPYVCYVTLPGGSCFGNFQNCPTKA 81 (252)
T ss_pred hHHHHHHHHHHHHHhcccc-CCCCC----------eeeeeccCC--CCCCeEEEEeCCCCCccCccccCCcHH
Confidence 3456676666433322222 22333 344444433 3556665 55 6889999765
No 63
>PF07305 DUF1454: Protein of unknown function (DUF1454); InterPro: IPR009918 This family consists of several Enterobacterial sequences of around 200 residues in length, which are often known as YiiQ proteins. The function of this family is unknown.
Probab=21.59 E-value=1.9e+02 Score=22.53 Aligned_cols=56 Identities=11% Similarity=0.191 Sum_probs=41.8
Q ss_pred CCHHHHHHHHHhhChh------HHHHHHHHhcCCeEEEeeCCCcceEEEEeccCCCCceeEE
Q 035575 21 VTEDQLSILHFLFGKN------IERATRIVDQRGVRRISGEPSGRSIFKVVGESRRKEEYLC 76 (132)
Q Consensus 21 ltd~~l~~L~~lf~~~------l~~Al~lld~~~V~~~~~~~s~r~~y~V~g~s~~~~~Y~v 76 (132)
+-.+-..+|-..|.|+ ..+.-.++.+|+-.+|....-|.--|+|..++.+|-++-|
T Consensus 123 ~a~~YmaAl~r~F~Ptls~eQs~~kl~~lL~~gk~~~yy~q~~GAiRYVvad~gekglTFAV 184 (200)
T PF07305_consen 123 LAIEYMAALMRQFEPTLSPEQSQEKLQKLLTKGKGSRYYSQTEGAIRYVVADNGEKGLTFAV 184 (200)
T ss_pred HHHHHHHHHHHHcCCcCCHHHHHHHHHHHHHcCCCCcceeeccCceEEEEecCCCceeEEEe
Confidence 4455667788888875 4566788999999998878888888999866545556655
No 64
>TIGR03415 ABC_choXWV_ATP choline ABC transporter, ATP-binding protein. Members of this protein family are the ATP-binding subunit of a three-protein transporter. This family belongs, more broadly, to the family of proline and glycine-betaine transporters, but members have been identified by direct characterization and by bioinformatic means as choline transporters. Many species have several closely-related members of this family, probably with variable abilities to act additionally on related quaternary amines.
Probab=20.18 E-value=35 Score=28.81 Aligned_cols=21 Identities=24% Similarity=0.431 Sum_probs=18.0
Q ss_pred HHHhhChhHHHHHHHHhcCCe
Q 035575 29 LHFLFGKNIERATRIVDQRGV 49 (132)
Q Consensus 29 L~~lf~~~l~~Al~lld~~~V 49 (132)
|..+||++-.+|++++++|.=
T Consensus 6 ~~k~fg~~~~~~~~~~~~g~~ 26 (382)
T TIGR03415 6 VDVVFGDQPAEALALLDQGKT 26 (382)
T ss_pred eEEeeCCCHHHHHHHHHcCCC
Confidence 556899999999999998864
No 65
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=20.18 E-value=3.8e+02 Score=20.56 Aligned_cols=57 Identities=14% Similarity=0.214 Sum_probs=37.2
Q ss_pred hhHHHHHHHHHHHHhcC-----CC-CHHHHHHHHHhhC---hhHHHHHHHHhcCCeEEEeeCCCcceEEEEe
Q 035575 3 ASSLVAESVWKSIESTR-----SV-TEDQLSILHFLFG---KNIERATRIVDQRGVRRISGEPSGRSIFKVV 65 (132)
Q Consensus 3 ~~~~v~~~~~~~i~~~~-----~l-td~~l~~L~~lf~---~~l~~Al~lld~~~V~~~~~~~s~r~~y~V~ 65 (132)
+...|.++|.+.|.+.. .| ++. .|..-|| .++..|+..+....+....+ |++.|+..
T Consensus 10 ~~~~v~~~l~~~I~~g~l~pG~~LpsE~---eLa~~~gVSRtpVREAL~~L~~eGlV~~~~---~~G~~V~~ 75 (257)
T PRK10225 10 PYQEVGAMIRDLIIKTPYNPGERLPPER---EIAEMLDVTRTVVREALIMLEIKGLVEVRR---GAGIYVLD 75 (257)
T ss_pred HHHHHHHHHHHHHHhCCCCCCCcCcCHH---HHHHHhCCCHHHHHHHHHHHHHCCCEEEec---CCEEEEeC
Confidence 34567777777777532 34 233 5666677 56899999998877776642 36666654
Done!