Query 030237
Match_columns 181
No_of_seqs 203 out of 832
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 10:40:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030237.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030237hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00202 ZnF_GATA Zinc finger D 99.6 1.1E-16 2.4E-21 108.3 4.1 44 91-136 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.6 4E-16 8.8E-21 104.7 3.6 47 89-137 3-50 (52)
3 PF00320 GATA: GATA zinc finge 99.5 3.2E-15 7E-20 93.3 1.2 35 92-128 1-35 (36)
4 PF06203 CCT: CCT motif; Inte 99.2 3.4E-12 7.3E-17 83.6 2.7 43 23-65 1-43 (45)
5 KOG1601 GATA-4/5/6 transcripti 98.8 4.3E-09 9.3E-14 85.5 3.3 52 89-142 199-250 (340)
6 COG5641 GAT1 GATA Zn-finger-co 98.7 1.3E-08 2.8E-13 95.2 4.0 54 87-143 156-215 (498)
7 PF09425 CCT_2: Divergent CCT 95.4 0.0091 2E-07 35.2 1.5 20 21-40 2-21 (27)
8 COG5641 GAT1 GATA Zn-finger-co 92.4 0.065 1.4E-06 50.8 1.5 53 87-140 295-347 (498)
9 KOG3554 Histone deacetylase co 89.7 1.9 4.2E-05 41.1 8.4 39 89-129 386-426 (693)
10 PF14803 Nudix_N_2: Nudix N-te 79.9 0.54 1.2E-05 29.0 -0.1 29 91-121 2-30 (34)
11 KOG1601 GATA-4/5/6 transcripti 72.3 1.1 2.4E-05 36.1 -0.2 41 20-60 290-330 (340)
12 PF01783 Ribosomal_L32p: Ribos 69.7 1.3 2.8E-05 29.9 -0.3 25 88-124 25-49 (56)
13 PF01412 ArfGap: Putative GTPa 66.5 5 0.00011 30.4 2.3 38 87-128 11-48 (116)
14 PRK12286 rpmF 50S ribosomal pr 61.6 3.3 7.1E-05 28.2 0.5 26 86-122 24-49 (57)
15 PF13248 zf-ribbon_3: zinc-rib 61.4 5.5 0.00012 22.6 1.3 23 89-121 2-24 (26)
16 PRK03988 translation initiatio 59.6 2.7 5.8E-05 33.5 -0.3 31 88-121 101-131 (138)
17 TIGR00311 aIF-2beta translatio 57.1 3.2 6.9E-05 32.8 -0.2 31 88-121 96-126 (133)
18 smart00653 eIF2B_5 domain pres 55.7 3.6 7.8E-05 31.5 -0.2 30 89-121 80-109 (110)
19 PF06677 Auto_anti-p27: Sjogre 55.4 5 0.00011 25.7 0.5 26 88-120 16-41 (41)
20 KOG1598 Transcription initiati 53.3 6.8 0.00015 37.6 1.2 32 90-126 1-32 (521)
21 smart00105 ArfGap Putative GTP 53.0 14 0.0003 27.8 2.7 37 88-128 2-38 (112)
22 PF08271 TF_Zn_Ribbon: TFIIB z 52.7 4.8 0.0001 25.3 0.1 28 91-123 2-29 (43)
23 PRK12336 translation initiatio 51.5 4.3 9.4E-05 34.0 -0.3 30 89-121 98-127 (201)
24 COG3952 Predicted membrane pro 50.6 4.4 9.6E-05 31.3 -0.4 20 104-125 76-95 (113)
25 PF13240 zinc_ribbon_2: zinc-r 49.9 9.9 0.00021 21.2 1.1 20 92-121 2-21 (23)
26 PF02701 zf-Dof: Dof domain, z 45.7 14 0.00031 25.8 1.6 46 88-135 4-52 (63)
27 TIGR01031 rpmF_bact ribosomal 45.5 7.7 0.00017 26.2 0.2 25 87-122 24-48 (55)
28 PRK14892 putative transcriptio 44.8 7.8 0.00017 29.3 0.2 36 87-125 19-54 (99)
29 PF06689 zf-C4_ClpX: ClpX C4-t 44.4 10 0.00023 23.8 0.7 32 90-122 2-33 (41)
30 PF01873 eIF-5_eIF-2B: Domain 43.6 7.7 0.00017 30.3 -0.0 29 90-121 94-122 (125)
31 PF13717 zinc_ribbon_4: zinc-r 42.1 5.8 0.00012 24.4 -0.7 33 90-123 3-35 (36)
32 PF09889 DUF2116: Uncharacteri 39.6 25 0.00055 24.2 2.1 30 88-127 2-32 (59)
33 COG3529 Predicted nucleic-acid 39.6 6.9 0.00015 27.5 -0.8 33 90-124 11-43 (66)
34 smart00834 CxxC_CXXC_SSSS Puta 38.5 11 0.00024 22.7 0.2 29 90-121 6-34 (41)
35 PRK00420 hypothetical protein; 37.0 16 0.00035 28.2 0.9 29 89-124 23-51 (112)
36 PRK01110 rpmF 50S ribosomal pr 36.7 13 0.00029 25.4 0.3 24 88-123 26-49 (60)
37 KOG1597 Transcription initiati 34.9 44 0.00095 30.1 3.3 32 91-126 2-34 (308)
38 KOG3740 Uncharacterized conser 34.6 17 0.00036 35.9 0.7 39 87-127 460-501 (706)
39 COG5349 Uncharacterized protei 33.9 17 0.00036 28.8 0.5 35 88-127 20-54 (126)
40 PF09297 zf-NADH-PPase: NADH p 33.7 16 0.00035 21.5 0.3 28 89-122 3-30 (32)
41 TIGR02098 MJ0042_CXXC MJ0042 f 33.4 7.7 0.00017 23.4 -1.2 33 90-123 3-35 (38)
42 PF09723 Zn-ribbon_8: Zinc rib 33.4 14 0.00031 23.2 0.0 29 90-121 6-34 (42)
43 PF12773 DZR: Double zinc ribb 32.2 30 0.00064 21.9 1.4 27 88-121 11-37 (50)
44 COG1645 Uncharacterized Zn-fin 31.8 17 0.00037 28.9 0.2 26 88-121 27-52 (131)
45 TIGR02605 CxxC_CxxC_SSSS putat 31.4 18 0.00038 23.2 0.2 29 90-121 6-34 (52)
46 PF07282 OrfB_Zn_ribbon: Putat 31.2 24 0.00053 23.7 0.9 29 89-123 28-56 (69)
47 KOG0706 Predicted GTPase-activ 30.6 25 0.00055 33.2 1.2 39 87-129 21-59 (454)
48 PRK05342 clpX ATP-dependent pr 30.3 29 0.00063 32.1 1.5 30 89-120 9-38 (412)
49 TIGR00416 sms DNA repair prote 30.1 21 0.00045 33.4 0.5 25 88-122 6-30 (454)
50 COG2331 Uncharacterized protei 29.3 20 0.00042 26.3 0.2 37 89-128 12-48 (82)
51 PF04810 zf-Sec23_Sec24: Sec23 29.1 24 0.00052 21.9 0.5 31 89-121 2-32 (40)
52 PF09526 DUF2387: Probable met 28.6 18 0.00038 25.7 -0.2 34 89-124 8-41 (71)
53 PF11781 RRN7: RNA polymerase 28.2 24 0.00051 21.8 0.4 26 89-121 8-33 (36)
54 PRK05978 hypothetical protein; 27.8 25 0.00054 28.4 0.6 34 88-126 32-65 (148)
55 TIGR03573 WbuX N-acetyl sugar 27.6 40 0.00087 30.1 1.9 32 90-125 2-33 (343)
56 PF14122 YokU: YokU-like prote 27.3 19 0.00042 26.7 -0.1 37 92-128 2-50 (87)
57 COG4260 Membrane protease subu 27.3 32 0.0007 31.1 1.2 29 88-121 314-342 (345)
58 PRK12496 hypothetical protein; 27.0 34 0.00074 27.7 1.2 33 88-128 126-158 (164)
59 COG5347 GTPase-activating prot 26.9 35 0.00077 30.8 1.4 37 88-128 19-55 (319)
60 PRK11823 DNA repair protein Ra 26.2 25 0.00055 32.6 0.4 25 88-122 6-30 (446)
61 COG2816 NPY1 NTP pyrophosphohy 25.7 26 0.00057 31.1 0.4 33 86-124 108-140 (279)
62 PLN03114 ADP-ribosylation fact 24.2 55 0.0012 30.4 2.1 37 88-128 21-57 (395)
63 PF12553 DUF3742: Protein of u 24.2 29 0.00062 23.5 0.2 10 103-112 34-43 (54)
64 PRK00423 tfb transcription ini 23.8 38 0.00082 29.9 1.0 31 88-123 10-40 (310)
65 smart00778 Prim_Zn_Ribbon Zinc 23.5 46 0.001 20.8 1.1 28 90-120 4-32 (37)
66 cd01121 Sms Sms (bacterial rad 23.3 32 0.0007 31.3 0.5 22 91-122 2-23 (372)
67 PF15396 FAM60A: Protein Famil 22.7 52 0.0011 28.2 1.6 18 114-131 50-67 (213)
68 PHA00626 hypothetical protein 21.9 30 0.00064 23.9 -0.0 31 91-126 2-36 (59)
69 KOG0703 Predicted GTPase-activ 21.8 40 0.00087 30.1 0.8 30 88-121 24-53 (287)
70 COG0846 SIR2 NAD-dependent pro 21.0 42 0.00092 29.1 0.7 33 87-122 120-155 (250)
71 TIGR02443 conserved hypothetic 20.1 31 0.00067 23.9 -0.3 31 90-122 10-40 (59)
No 1
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.65 E-value=1.1e-16 Score=108.33 Aligned_cols=44 Identities=52% Similarity=1.258 Sum_probs=41.7
Q ss_pred cccccccCCCCCCccccCCCCCCccchhhhHHHHhcCCCCCCCccc
Q 030237 91 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGALRDLGKKM 136 (181)
Q Consensus 91 ~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~~~~r~~~~~~ 136 (181)
.|+||+++ .||+||+||.|..+|||||||||++++..||+.+..
T Consensus 1 ~C~~C~~~--~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTT--TTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRK 44 (54)
T ss_pred CCCCCCCC--CCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCc
Confidence 59999997 999999999888999999999999999999999876
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.61 E-value=4e-16 Score=104.68 Aligned_cols=47 Identities=51% Similarity=1.120 Sum_probs=43.3
Q ss_pred CccccccccCCCCCCccccCCCCCCccchhhhHHHHhcCCC-CCCCcccc
Q 030237 89 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGAL-RDLGKKME 137 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~~~~-r~~~~~~~ 137 (181)
...|+||+++ .||+||+||.|++.|||||||||++++.+ ||+.+.++
T Consensus 3 ~~~C~~C~~~--~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~~~ 50 (52)
T smart00401 3 GRSCSNCGTT--ETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLKKD 50 (52)
T ss_pred CCCcCCCCCC--CCCccccCCCCCCcEeecccHHHHHcCCCCCccccccc
Confidence 5789999997 99999999999989999999999999998 88877664
No 3
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.51 E-value=3.2e-15 Score=93.30 Aligned_cols=35 Identities=54% Similarity=1.288 Sum_probs=28.6
Q ss_pred ccccccCCCCCCccccCCCCCCccchhhhHHHHhcCC
Q 030237 92 CTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 128 (181)
Q Consensus 92 C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~~~ 128 (181)
|+||+++ .||+||++|.|..+|||+|||||+++++
T Consensus 1 C~~C~tt--~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTT--ETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--S--T-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCC--CCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 8999998 8999999999998899999999999986
No 4
>PF06203 CCT: CCT motif; InterPro: IPR010402 The CCT (CONSTANS, CO-like, and TOC1) domain is a highly conserved basic module of ~43 amino acids, which is found near the C terminus of plant proteins often involved in light signal transduction. The CCT domain is found in association with other domains, such as the B-box zinc finger, the GATA-type zinc finger, the ZIM motif or the response regulatory domain. The CCT domain contains a putative nuclear localisation signal within the second half of the CCT motif and has been shown to be involved in nuclear localization and probably also has a role in protein-protein interaction [].; GO: 0005515 protein binding
Probab=99.25 E-value=3.4e-12 Score=83.61 Aligned_cols=43 Identities=47% Similarity=0.779 Sum_probs=41.1
Q ss_pred HHHHHHHHHhhhhhhcccceeeehhhHHHHHHhhhhhcccccc
Q 030237 23 RAASLDRFRQKRKERCFDKKVRYSVRQEVALRMQRNKGQFTSA 65 (181)
Q Consensus 23 r~a~~~r~rekr~~r~f~K~~rY~~Rqe~A~r~~RekGqfss~ 65 (181)
|.++|.||+|||++|+|+|+|+|++|+.+|+.++|.+|+|++.
T Consensus 1 R~~~l~Ry~~Kr~~R~f~kkirY~~Rk~~A~~R~RvkGRFvk~ 43 (45)
T PF06203_consen 1 REEKLQRYREKRKRRNFEKKIRYESRKAVADKRPRVKGRFVKK 43 (45)
T ss_pred CHHHHHHHHHHHHhhcccccCCcchHHHHHhhCCccCCcccCC
Confidence 6789999999999999999999999999999999999999964
No 5
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.77 E-value=4.3e-09 Score=85.52 Aligned_cols=52 Identities=44% Similarity=0.898 Sum_probs=45.6
Q ss_pred CccccccccCCCCCCccccCCCCCCccchhhhHHHHhcCCCCCCCccccCCCCC
Q 030237 89 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGALRDLGKKMEDQPLT 142 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~~~~r~~~~~~~~~~~~ 142 (181)
...|.+|+++ .||+||+++.|..++||||||++++++..|++.+.+......
T Consensus 199 ~~~c~~~~~~--~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~ 250 (340)
T KOG1601|consen 199 LRQCSNCGTT--KTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPR 250 (340)
T ss_pred CcccCCCCCC--CCcceecCCCCCccccccchhhhhhcCccccccccCcccccc
Confidence 5899999997 999999999998899999999999999888888877555433
No 6
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.68 E-value=1.3e-08 Score=95.16 Aligned_cols=54 Identities=35% Similarity=0.696 Sum_probs=47.5
Q ss_pred CCCccccccccCCCCCCccccCCC-----CCCccchhhhHHHHhcCCCC-CCCccccCCCCCC
Q 030237 87 PSETSCTHCGISSKSTPMMRRGPS-----GPRSLCNACGLFWANKGALR-DLGKKMEDQPLTP 143 (181)
Q Consensus 87 ~~~~~C~nC~~~~~~Tp~wRrgp~-----G~~~LCNaCGl~~~~~~~~r-~~~~~~~~~~~~~ 143 (181)
....+|.||.++ .||+|||+.. |. +||||||||++.||.+| |++++..-+....
T Consensus 156 ~~~~vc~Nc~t~--stPlwrR~~~~~s~~~n-~lcnaCgl~~klhg~~r~P~t~ks~~~ks~~ 215 (498)
T COG5641 156 NQPHVCSNCKTT--STPLWRRASSESSLPGN-NLCNACGLYLKLHGSPRAPISLKSDSIKSRS 215 (498)
T ss_pred cccchhcccccc--CCccccccccccccCCc-cccccccccccccCCcCCCcccccccccccc
Confidence 344599999998 9999999999 65 99999999999999999 9999987766555
No 7
>PF09425 CCT_2: Divergent CCT motif; InterPro: IPR018467 The short CCT (CO, COL, TOC1) motif is found in a number of plant proteins, including Constans (CO), Constans-like (COL) and TOC1. The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif []. The CCT motif is found in the Arabidopsis circadian rhythm protein TOC1, an autoregulatory response regulator homologue the controls the photoperiodic flowering through its clock function []. ; GO: 0005515 protein binding; PDB: 3OGK_V 3OGL_S 3OGM_W.
Probab=95.43 E-value=0.0091 Score=35.24 Aligned_cols=20 Identities=50% Similarity=0.610 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHhhhhhhccc
Q 030237 21 PQRAASLDRFRQKRKERCFD 40 (181)
Q Consensus 21 ~~r~a~~~r~rekr~~r~f~ 40 (181)
-.|.+||.||.||||+|.+.
T Consensus 2 ~aRK~SLqRFLeKRK~R~~~ 21 (27)
T PF09425_consen 2 IARKASLQRFLEKRKDRLAA 21 (27)
T ss_dssp ----HHHHHHHHHH------
T ss_pred chHHHHHHHHHHHHHHhhcc
Confidence 35889999999999999775
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=92.37 E-value=0.065 Score=50.76 Aligned_cols=53 Identities=28% Similarity=0.360 Sum_probs=44.4
Q ss_pred CCCccccccccCCCCCCccccCCCCCCccchhhhHHHHhcCCCCCCCccccCCC
Q 030237 87 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGALRDLGKKMEDQP 140 (181)
Q Consensus 87 ~~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~~~~r~~~~~~~~~~ 140 (181)
+....|.+|++. ..||.||+...-.-++||+||++.+.++..+|+.++.+...
T Consensus 295 ps~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d~n~ 347 (498)
T COG5641 295 PSDKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPNS 347 (498)
T ss_pred hhhcCccccccc-ccCcccccccccccccccccccccCCcccccccCCCCChhh
Confidence 456789999975 58999999887777999999999999999999998765444
No 9
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=89.68 E-value=1.9 Score=41.11 Aligned_cols=39 Identities=23% Similarity=0.604 Sum_probs=31.1
Q ss_pred CccccccccCCCCCCcc--ccCCCCCCccchhhhHHHHhcCCC
Q 030237 89 ETSCTHCGISSKSTPMM--RRGPSGPRSLCNACGLFWANKGAL 129 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~w--Rrgp~G~~~LCNaCGl~~~~~~~~ 129 (181)
.+.|.+|+++ +.-+| |-+|.-...||-.|=+||++.|.+
T Consensus 386 g~~CEsC~tt--qs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 386 GRACESCYTT--QSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCcccccccc--cccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 6799999998 66666 455555568999999999998753
No 10
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=79.85 E-value=0.54 Score=28.97 Aligned_cols=29 Identities=31% Similarity=0.731 Sum_probs=14.7
Q ss_pred cccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 91 SCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 91 ~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
.|.+||.. .+..-=.|.+-.+.+|.+||.
T Consensus 2 fC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGP--LERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B---EEE--TT-SS-EEEETTTTE
T ss_pred ccccccCh--hhhhcCCCCCccceECCCCCC
Confidence 58999985 222222455666789999984
No 11
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=72.29 E-value=1.1 Score=36.09 Aligned_cols=41 Identities=41% Similarity=0.637 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHhhhhhhcccceeeehhhHHHHHHhhhhhc
Q 030237 20 QPQRAASLDRFRQKRKERCFDKKVRYSVRQEVALRMQRNKG 60 (181)
Q Consensus 20 ~~~r~a~~~r~rekr~~r~f~K~~rY~~Rqe~A~r~~RekG 60 (181)
...|.+.+.||++++..+.|++.++|..++..+..+++-++
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 57899999999999999999999999999998888877655
No 12
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=69.71 E-value=1.3 Score=29.86 Aligned_cols=25 Identities=28% Similarity=0.945 Sum_probs=18.5
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhHHHH
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 124 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~ 124 (181)
....|.+||.. .-++.+|..|| ||+
T Consensus 25 ~l~~c~~cg~~-----------~~~H~vc~~cG-~y~ 49 (56)
T PF01783_consen 25 NLVKCPNCGEP-----------KLPHRVCPSCG-YYK 49 (56)
T ss_dssp SEEESSSSSSE-----------ESTTSBCTTTB-BSS
T ss_pred ceeeeccCCCE-----------ecccEeeCCCC-eEC
Confidence 56789999974 23468999999 443
No 13
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=66.45 E-value=5 Score=30.38 Aligned_cols=38 Identities=26% Similarity=0.556 Sum_probs=27.8
Q ss_pred CCCccccccccCCCCCCccccCCCCCCccchhhhHHHHhcCC
Q 030237 87 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 128 (181)
Q Consensus 87 ~~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~~~ 128 (181)
+....|+.|+. .-|.|-.=.-| ..||-.|.-..+..|+
T Consensus 11 ~~N~~CaDCg~---~~p~w~s~~~G-iflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 11 PGNKVCADCGA---PNPTWASLNYG-IFLCLECAGIHRSLGV 48 (116)
T ss_dssp TTCTB-TTT-S---BS--EEETTTT-EEE-HHHHHHHHHHTT
T ss_pred cCcCcCCCCCC---CCCCEEEeecC-hhhhHHHHHHHHHhcc
Confidence 45789999997 68899999999 4999999988888774
No 14
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=61.58 E-value=3.3 Score=28.22 Aligned_cols=26 Identities=31% Similarity=1.007 Sum_probs=19.4
Q ss_pred CCCCccccccccCCCCCCccccCCCCCCccchhhhHH
Q 030237 86 SPSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 122 (181)
Q Consensus 86 ~~~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~ 122 (181)
.+....|.+||.. .- ++.+|..||.|
T Consensus 24 ~~~l~~C~~CG~~--~~---------~H~vC~~CG~Y 49 (57)
T PRK12286 24 APGLVECPNCGEP--KL---------PHRVCPSCGYY 49 (57)
T ss_pred CCcceECCCCCCc--cC---------CeEECCCCCcC
Confidence 3456789999985 22 25899999965
No 15
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=61.37 E-value=5.5 Score=22.63 Aligned_cols=23 Identities=30% Similarity=0.803 Sum_probs=15.4
Q ss_pred CccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 89 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
...|.+||.. -+.+. .+|..||-
T Consensus 2 ~~~Cp~Cg~~---------~~~~~-~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAE---------IDPDA-KFCPNCGA 24 (26)
T ss_pred cCCCcccCCc---------CCccc-ccChhhCC
Confidence 3578888874 23343 68888885
No 16
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=59.62 E-value=2.7 Score=33.48 Aligned_cols=31 Identities=29% Similarity=0.652 Sum_probs=23.1
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
.--.|..|+.+ .|-+-+.+-.- -.-|+|||-
T Consensus 101 ~yVlC~~C~sp--dT~l~k~~r~~-~l~C~ACGa 131 (138)
T PRK03988 101 EYVICPECGSP--DTKLIKEGRIW-VLKCEACGA 131 (138)
T ss_pred hcEECCCCCCC--CcEEEEcCCeE-EEEcccCCC
Confidence 34689999998 88887753322 368999995
No 17
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=57.08 E-value=3.2 Score=32.84 Aligned_cols=31 Identities=26% Similarity=0.622 Sum_probs=22.5
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
.--.|..|+.+ .|-+-+.+.-- -.-|+|||-
T Consensus 96 ~yVlC~~C~sP--dT~l~k~~r~~-~l~C~ACGa 126 (133)
T TIGR00311 96 KYVICRECNRP--DTRIIKEGRVS-LLKCEACGA 126 (133)
T ss_pred heEECCCCCCC--CcEEEEeCCeE-EEecccCCC
Confidence 34689999998 88887753221 257999996
No 18
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=55.66 E-value=3.6 Score=31.52 Aligned_cols=30 Identities=27% Similarity=0.571 Sum_probs=22.1
Q ss_pred CccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 89 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
--.|..|+.+ .|-+-+.+..- -.-|+|||-
T Consensus 80 yVlC~~C~sp--dT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGSP--DTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred cEECCCCCCC--CcEEEEeCCeE-EEEccccCC
Confidence 3689999998 88888763222 245999994
No 19
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=55.38 E-value=5 Score=25.65 Aligned_cols=26 Identities=38% Similarity=1.091 Sum_probs=19.1
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhh
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 120 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCG 120 (181)
....|..|++ |++| ..+| +.+|-+|+
T Consensus 16 L~~~Cp~C~~-----PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCPDCGT-----PLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred hcCccCCCCC-----eeEE-ecCC-CEECCCCC
Confidence 3467888864 8999 3456 58999985
No 20
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=53.32 E-value=6.8 Score=37.60 Aligned_cols=32 Identities=28% Similarity=0.566 Sum_probs=22.4
Q ss_pred ccccccccCCCCCCccccCCCCCCccchhhhHHHHhc
Q 030237 90 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANK 126 (181)
Q Consensus 90 ~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~ 126 (181)
..|.|||. +.+.-+ --.|. ..|++||...-..
T Consensus 1 ~~C~~C~~---s~fe~d-~a~g~-~~C~~CG~v~E~~ 32 (521)
T KOG1598|consen 1 MVCKNCGG---SNFERD-EATGN-LYCTACGTVLEYN 32 (521)
T ss_pred CcCCCCCC---CCcccc-cccCC-ceeccccceeecc
Confidence 36999998 466633 34554 8999999855443
No 21
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=52.95 E-value=14 Score=27.80 Aligned_cols=37 Identities=24% Similarity=0.500 Sum_probs=31.3
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhHHHHhcCC
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 128 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~~~ 128 (181)
....|+.|+. .-|.|=.-.-| ..||-.|.-..+..|+
T Consensus 2 ~N~~CaDC~~---~~p~w~s~~~G-ifvC~~CsgiHR~lg~ 38 (112)
T smart00105 2 GNKKCFDCGA---PNPTWASVNLG-VFLCIECSGIHRSLGV 38 (112)
T ss_pred CCCcccCCCC---CCCCcEEeccc-eeEhHHhHHHHHhcCC
Confidence 3678999998 56999998889 4999999988888775
No 22
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=52.65 E-value=4.8 Score=25.27 Aligned_cols=28 Identities=29% Similarity=0.789 Sum_probs=17.0
Q ss_pred cccccccCCCCCCccccCCCCCCccchhhhHHH
Q 030237 91 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 123 (181)
Q Consensus 91 ~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~ 123 (181)
.|.+|+.+ . .--..-.| ..+|..||+-+
T Consensus 2 ~Cp~Cg~~--~--~~~D~~~g-~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSK--E--IVFDPERG-ELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSS--E--EEEETTTT-EEEETTT-BBE
T ss_pred CCcCCcCC--c--eEEcCCCC-eEECCCCCCEe
Confidence 58889884 2 22233345 47999999744
No 23
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=51.54 E-value=4.3 Score=33.95 Aligned_cols=30 Identities=27% Similarity=0.674 Sum_probs=22.7
Q ss_pred CccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 89 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
--.|..|+.+ .|-+-+.+..- -.-|+|||-
T Consensus 98 yV~C~~C~~p--dT~l~k~~~~~-~l~C~aCGa 127 (201)
T PRK12336 98 YVICSECGLP--DTRLVKEDRVL-MLRCDACGA 127 (201)
T ss_pred eEECCCCCCC--CcEEEEcCCeE-EEEcccCCC
Confidence 4689999998 88887764222 257999997
No 24
>COG3952 Predicted membrane protein [Function unknown]
Probab=50.57 E-value=4.4 Score=31.30 Aligned_cols=20 Identities=40% Similarity=0.579 Sum_probs=15.6
Q ss_pred ccccCCCCCCccchhhhHHHHh
Q 030237 104 MMRRGPSGPRSLCNACGLFWAN 125 (181)
Q Consensus 104 ~wRrgp~G~~~LCNaCGl~~~~ 125 (181)
+||.+|-+ .||++|||+-..
T Consensus 76 i~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHhcchHH--HHHHhhhHHHHH
Confidence 46777777 699999998653
No 25
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=49.94 E-value=9.9 Score=21.20 Aligned_cols=20 Identities=30% Similarity=0.923 Sum_probs=11.5
Q ss_pred ccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 92 CTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 92 C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
|.+||.. -+++. .+|..||.
T Consensus 2 Cp~CG~~---------~~~~~-~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAE---------IEDDA-KFCPNCGT 21 (23)
T ss_pred CcccCCC---------CCCcC-cchhhhCC
Confidence 6677763 22343 56777764
No 26
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=45.73 E-value=14 Score=25.85 Aligned_cols=46 Identities=26% Similarity=0.660 Sum_probs=31.4
Q ss_pred CCccccccccCCCCCCccc---cCCCCCCccchhhhHHHHhcCCCCCCCcc
Q 030237 88 SETSCTHCGISSKSTPMMR---RGPSGPRSLCNACGLFWANKGALRDLGKK 135 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wR---rgp~G~~~LCNaCGl~~~~~~~~r~~~~~ 135 (181)
....|..|..+ .|=.-= -...-|+.+|-+|-.||-..|.+|.++..
T Consensus 4 ~~~~CPRC~S~--nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvg 52 (63)
T PF02701_consen 4 QPLPCPRCDST--NTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVG 52 (63)
T ss_pred cCCCCCCcCCC--CCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccC
Confidence 35678888865 332100 01234578999999999999999988654
No 27
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=45.46 E-value=7.7 Score=26.15 Aligned_cols=25 Identities=32% Similarity=0.947 Sum_probs=18.5
Q ss_pred CCCccccccccCCCCCCccccCCCCCCccchhhhHH
Q 030237 87 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 122 (181)
Q Consensus 87 ~~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~ 122 (181)
+....|.+||.. --++-+|-.||.|
T Consensus 24 p~l~~C~~cG~~-----------~~~H~vc~~cG~Y 48 (55)
T TIGR01031 24 PTLVVCPNCGEF-----------KLPHRVCPSCGYY 48 (55)
T ss_pred CcceECCCCCCc-----------ccCeeECCccCeE
Confidence 456789999974 2335899999954
No 28
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=44.83 E-value=7.8 Score=29.27 Aligned_cols=36 Identities=25% Similarity=0.517 Sum_probs=23.6
Q ss_pred CCCccccccccCCCCCCccccCCCCCCccchhhhHHHHh
Q 030237 87 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWAN 125 (181)
Q Consensus 87 ~~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~ 125 (181)
+....|.+|+.. ..+. ..+-..++..|-.||.|+..
T Consensus 19 pt~f~CP~Cge~--~v~v-~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGKV--SISV-KIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCCe--Eeee-ecCCCcceEECCCCCCccCE
Confidence 346789999952 2221 12223557899999999765
No 29
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=44.41 E-value=10 Score=23.84 Aligned_cols=32 Identities=25% Similarity=0.675 Sum_probs=20.2
Q ss_pred ccccccccCCCCCCccccCCCCCCccchhhhHH
Q 030237 90 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 122 (181)
Q Consensus 90 ~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~ 122 (181)
..|+-||.+....-..=.||.+ ...|+.|-..
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHH
Confidence 5799999986655555588877 4899999754
No 30
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=43.57 E-value=7.7 Score=30.30 Aligned_cols=29 Identities=31% Similarity=0.699 Sum_probs=23.0
Q ss_pred ccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 90 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 90 ~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
-.|..|+.+ .|-+-+.+..- -.-|+|||-
T Consensus 94 VlC~~C~sp--dT~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSP--DTELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SSCTSTSSS--SEEEEEETTCC-EEEETTTSC
T ss_pred EEcCCCCCC--ccEEEEcCCEE-EEEecccCC
Confidence 689999998 88887775444 478999994
No 31
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=42.11 E-value=5.8 Score=24.38 Aligned_cols=33 Identities=21% Similarity=0.594 Sum_probs=24.1
Q ss_pred ccccccccCCCCCCccccCCCCCCccchhhhHHH
Q 030237 90 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 123 (181)
Q Consensus 90 ~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~ 123 (181)
..|.+|++. -..+...-.+.|....|-.||-.|
T Consensus 3 i~Cp~C~~~-y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAK-YEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCE-EeCCHHHCCCCCcEEECCCCCCEe
Confidence 468888885 566667777777778888887654
No 32
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=39.61 E-value=25 Score=24.17 Aligned_cols=30 Identities=23% Similarity=0.654 Sum_probs=22.2
Q ss_pred CCccccccccCCCCCCccccCCCCCCccc-hhhhHHHHhcC
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLC-NACGLFWANKG 127 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LC-NaCGl~~~~~~ 127 (181)
..+.|.+||.+ - |.. +.+| ..|+--|.++.
T Consensus 2 ~HkHC~~CG~~---I------p~~-~~fCS~~C~~~~~k~q 32 (59)
T PF09889_consen 2 PHKHCPVCGKP---I------PPD-ESFCSPKCREEYRKRQ 32 (59)
T ss_pred CCCcCCcCCCc---C------Ccc-hhhhCHHHHHHHHHHH
Confidence 35789999985 2 223 5899 69999888764
No 33
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=39.55 E-value=6.9 Score=27.46 Aligned_cols=33 Identities=24% Similarity=0.408 Sum_probs=25.9
Q ss_pred ccccccccCCCCCCccccCCCCCCccchhhhHHHH
Q 030237 90 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 124 (181)
Q Consensus 90 ~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~ 124 (181)
..|..|.+- .|-+||+-..-+..-|-+||...+
T Consensus 11 A~CP~C~~~--Dtl~mW~En~ve~vECV~CG~~~~ 43 (66)
T COG3529 11 AVCPACQAQ--DTLAMWRENNVEIVECVKCGHHMR 43 (66)
T ss_pred CCCcccchh--hHHHHHHhcCCceEehhhcchHhh
Confidence 579999985 777777766666789999998653
No 34
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=38.47 E-value=11 Score=22.69 Aligned_cols=29 Identities=24% Similarity=0.678 Sum_probs=18.4
Q ss_pred ccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 90 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 90 ~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
-.|..||. .-..|..-.++....|-.||-
T Consensus 6 y~C~~Cg~---~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGH---TFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCC---EEEEEEecCCCCCCCCCCCCC
Confidence 46888887 334444433355577888887
No 35
>PRK00420 hypothetical protein; Validated
Probab=37.00 E-value=16 Score=28.20 Aligned_cols=29 Identities=24% Similarity=0.756 Sum_probs=21.9
Q ss_pred CccccccccCCCCCCccccCCCCCCccchhhhHHHH
Q 030237 89 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 124 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~ 124 (181)
...|..||+ |+.|- ..| ..+|-.||-.+.
T Consensus 23 ~~~CP~Cg~-----pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCGL-----PLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCCC-----cceec-CCC-ceECCCCCCeee
Confidence 467988986 67774 456 499999998654
No 36
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=36.66 E-value=13 Score=25.44 Aligned_cols=24 Identities=13% Similarity=0.101 Sum_probs=17.2
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhHHH
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 123 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~ 123 (181)
....|.+||.. . -++.+|- ||.|.
T Consensus 26 ~~~~c~~cg~~--~---------~pH~vc~-cG~Y~ 49 (60)
T PRK01110 26 TLSVDKTTGEY--H---------LPHHVSP-KGYYK 49 (60)
T ss_pred ceeEcCCCCce--e---------ccceecC-CcccC
Confidence 46789999985 2 2357899 99653
No 37
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=34.89 E-value=44 Score=30.15 Aligned_cols=32 Identities=22% Similarity=0.766 Sum_probs=23.6
Q ss_pred cccccccCCCCCC-ccccCCCCCCccchhhhHHHHhc
Q 030237 91 SCTHCGISSKSTP-MMRRGPSGPRSLCNACGLFWANK 126 (181)
Q Consensus 91 ~C~nC~~~~~~Tp-~wRrgp~G~~~LCNaCGl~~~~~ 126 (181)
.|..|... ++ +.=+--.|. ++|-.|||-+..|
T Consensus 2 ~c~~C~~~---~~~~V~d~~~gd-tvC~~CGlVl~~r 34 (308)
T KOG1597|consen 2 TCPDCKRH---PENLVEDHSAGD-TVCSECGLVLEDR 34 (308)
T ss_pred CCCCCCCC---CCCeeeeccCCc-eecccCCeeeccc
Confidence 58888873 33 666666775 9999999976554
No 38
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.62 E-value=17 Score=35.92 Aligned_cols=39 Identities=21% Similarity=0.428 Sum_probs=31.0
Q ss_pred CCCccccccccCCCCCCccccCCCC---CCccchhhhHHHHhcC
Q 030237 87 PSETSCTHCGISSKSTPMMRRGPSG---PRSLCNACGLFWANKG 127 (181)
Q Consensus 87 ~~~~~C~nC~~~~~~Tp~wRrgp~G---~~~LCNaCGl~~~~~~ 127 (181)
.+...|..|.+- .||.|+.-+.+ .+.+|.+|----.++-
T Consensus 460 ~~P~~caqcktd--ftp~wk~ekstq~d~~i~cE~cvtSnqkkA 501 (706)
T KOG3740|consen 460 TEPYACAQCKTD--FTPAWKKEKSTQADAAIVCENCVTSNQKKA 501 (706)
T ss_pred CCchhhhhcccc--cccccccccccCcchHHHHHhhhhhccccc
Confidence 457889999994 99999998888 3489999987555543
No 39
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.89 E-value=17 Score=28.78 Aligned_cols=35 Identities=29% Similarity=0.589 Sum_probs=23.6
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhHHHHhcC
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKG 127 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~~ 127 (181)
..-+|-+||-- =+.| |=-...+-|.|||+-|-.+.
T Consensus 20 l~grCP~CGeG----rLF~-gFLK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 20 LRGRCPRCGEG----RLFR-GFLKVVPACEACGLDYGFAD 54 (126)
T ss_pred hcCCCCCCCCc----hhhh-hhcccCchhhhccccccCCc
Confidence 35689999963 2333 33334579999999886654
No 40
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=33.66 E-value=16 Score=21.46 Aligned_cols=28 Identities=29% Similarity=0.689 Sum_probs=14.9
Q ss_pred CccccccccCCCCCCccccCCCCCCccchhhhHH
Q 030237 89 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 122 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~ 122 (181)
.+.|..||.. .. ..+.|....|..||..
T Consensus 3 ~rfC~~CG~~--t~----~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAP--TK----PAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--B--EE----E-SSSS-EEESSSS-E
T ss_pred CcccCcCCcc--cc----CCCCcCEeECCCCcCE
Confidence 4679999985 22 2445666899999874
No 41
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=33.39 E-value=7.7 Score=23.41 Aligned_cols=33 Identities=27% Similarity=0.690 Sum_probs=18.2
Q ss_pred ccccccccCCCCCCccccCCCCCCccchhhhHHH
Q 030237 90 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 123 (181)
Q Consensus 90 ~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~ 123 (181)
..|.+|++. -.-+...-+..|....|-.||..|
T Consensus 3 ~~CP~C~~~-~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTS-FRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCE-EEeCHHHcCCCCCEEECCCCCCEE
Confidence 457777774 223333334445456777777543
No 42
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=33.38 E-value=14 Score=23.17 Aligned_cols=29 Identities=21% Similarity=0.538 Sum_probs=16.8
Q ss_pred ccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 90 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 90 ~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
-+|..||.. --.++..-+.....|-.||-
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHE---FEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCE---EEEEEEcCCCCCCcCCCCCC
Confidence 467888852 33333333344578888875
No 43
>PF12773 DZR: Double zinc ribbon
Probab=32.18 E-value=30 Score=21.88 Aligned_cols=27 Identities=30% Similarity=0.864 Sum_probs=13.7
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
....|.+||+. .. .+......|..||-
T Consensus 11 ~~~fC~~CG~~--l~-----~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 11 DAKFCPHCGTP--LP-----PPDQSKKICPNCGA 37 (50)
T ss_pred cccCChhhcCC--hh-----hccCCCCCCcCCcC
Confidence 35667777764 11 22222356666665
No 44
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=31.83 E-value=17 Score=28.91 Aligned_cols=26 Identities=35% Similarity=1.025 Sum_probs=21.4
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
....|.-||+ |++| -+|. .+|--||.
T Consensus 27 L~~hCp~Cg~-----PLF~--KdG~-v~CPvC~~ 52 (131)
T COG1645 27 LAKHCPKCGT-----PLFR--KDGE-VFCPVCGY 52 (131)
T ss_pred HHhhCcccCC-----ccee--eCCe-EECCCCCc
Confidence 4568999986 8999 6784 99999995
No 45
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=31.37 E-value=18 Score=23.19 Aligned_cols=29 Identities=28% Similarity=0.686 Sum_probs=19.0
Q ss_pred ccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 90 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 90 ~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
-.|.+|+. ..-.|+.--+.....|-.||-
T Consensus 6 y~C~~Cg~---~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGH---RFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCC---EeEEEEecCCCCCCCCCCCCC
Confidence 46888887 344666533333467888886
No 46
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=31.18 E-value=24 Score=23.74 Aligned_cols=29 Identities=31% Similarity=0.681 Sum_probs=19.9
Q ss_pred CccccccccCCCCCCccccCCCCCCccchhhhHHH
Q 030237 89 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 123 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~ 123 (181)
...|+.||..... ...+....|..||..+
T Consensus 28 Sq~C~~CG~~~~~------~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRNKK------RRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCccccccc------ccccceEEcCCCCCEE
Confidence 4679999996222 3344457999999853
No 47
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=30.60 E-value=25 Score=33.21 Aligned_cols=39 Identities=26% Similarity=0.497 Sum_probs=33.0
Q ss_pred CCCccccccccCCCCCCccccCCCCCCccchhhhHHHHhcCCC
Q 030237 87 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGAL 129 (181)
Q Consensus 87 ~~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~~~~ 129 (181)
+...+|..|+. .-|-|=.-+.| ..||--|---.+.-|++
T Consensus 21 ~~NKvCFDCgA---knPtWaSVTYG-IFLCiDCSAvHRnLGVH 59 (454)
T KOG0706|consen 21 SENKVCFDCGA---KNPTWASVTYG-IFLCIDCSAVHRNLGVH 59 (454)
T ss_pred CCCceecccCC---CCCCceeecce-EEEEEecchhhhccccc
Confidence 46799999998 79999999999 59999998766666653
No 48
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=30.28 E-value=29 Score=32.07 Aligned_cols=30 Identities=27% Similarity=0.628 Sum_probs=24.6
Q ss_pred CccccccccCCCCCCccccCCCCCCccchhhh
Q 030237 89 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 120 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCG 120 (181)
...|+.||.+...+...-.||.. ..|+.|-
T Consensus 9 ~~~CSFCGr~~~ev~~li~g~~~--~IC~~Ci 38 (412)
T PRK05342 9 LLYCSFCGKSQHEVRKLIAGPGV--YICDECI 38 (412)
T ss_pred ccccCCCCCChhhccccccCCCC--cccchHH
Confidence 45899999997788888888743 7999993
No 49
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=30.08 E-value=21 Score=33.36 Aligned_cols=25 Identities=40% Similarity=0.982 Sum_probs=17.2
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhHH
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 122 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~ 122 (181)
....|.+||. .+|.|- | .|.+||-+
T Consensus 6 ~~y~C~~Cg~---~~~~~~----g---~Cp~C~~w 30 (454)
T TIGR00416 6 SKFVCQHCGA---DSPKWQ----G---KCPACHAW 30 (454)
T ss_pred CeEECCcCCC---CCcccc----E---ECcCCCCc
Confidence 3578999998 566652 2 58888763
No 50
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.26 E-value=20 Score=26.30 Aligned_cols=37 Identities=24% Similarity=0.473 Sum_probs=24.4
Q ss_pred CccccccccCCCCCCccccCCCCCCccchhhhHHHHhcCC
Q 030237 89 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 128 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~~~ 128 (181)
.-.|.+|+-.-+....++..|. +-|.+||-.+++--.
T Consensus 12 ~Y~c~~cg~~~dvvq~~~ddpl---t~ce~c~a~~kk~l~ 48 (82)
T COG2331 12 SYECTECGNRFDVVQAMTDDPL---TTCEECGARLKKLLN 48 (82)
T ss_pred EEeecccchHHHHHHhcccCcc---ccChhhChHHHHhhc
Confidence 3579999984333444555554 579999987765433
No 51
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=29.14 E-value=24 Score=21.92 Aligned_cols=31 Identities=26% Similarity=0.634 Sum_probs=19.4
Q ss_pred CccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 89 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
..+|.+|++= .-|...-...|..-.|+-|+.
T Consensus 2 p~rC~~C~ay--lNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAY--LNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--B--S-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCCE--ECCcceEcCCCCEEECcCCCC
Confidence 4579999984 778888888887789999986
No 52
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=28.61 E-value=18 Score=25.72 Aligned_cols=34 Identities=26% Similarity=0.403 Sum_probs=26.6
Q ss_pred CccccccccCCCCCCccccCCCCCCccchhhhHHHH
Q 030237 89 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 124 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~ 124 (181)
...|-.|... .|-+|++...-...-|-+||..-.
T Consensus 8 Ga~CP~C~~~--D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 8 GAVCPKCQAM--DTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred CccCCCCcCc--cEEEEEEeCCceEEEecCCCCeec
Confidence 3579999996 777777766677789999998543
No 53
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=28.23 E-value=24 Score=21.77 Aligned_cols=26 Identities=27% Similarity=0.666 Sum_probs=20.0
Q ss_pred CccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 89 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 89 ~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
...|..|+. . |-...+| ...|..||-
T Consensus 8 ~~~C~~C~~---~---~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGS---R---WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CCcCCCCCC---e---EeEccCC-EEEhhhCce
Confidence 356999997 2 7777788 599999984
No 54
>PRK05978 hypothetical protein; Provisional
Probab=27.80 E-value=25 Score=28.39 Aligned_cols=34 Identities=26% Similarity=0.569 Sum_probs=23.8
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhHHHHhc
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANK 126 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~ 126 (181)
...+|-+||. -.+++ +-..-..-|.+||+-|..+
T Consensus 32 l~grCP~CG~----G~LF~-g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 32 FRGRCPACGE----GKLFR-AFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred HcCcCCCCCC----Ccccc-cccccCCCccccCCccccC
Confidence 3468999995 45555 3344468899999977655
No 55
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=27.65 E-value=40 Score=30.07 Aligned_cols=32 Identities=25% Similarity=0.620 Sum_probs=25.1
Q ss_pred ccccccccCCCCCCccccCCCCCCccchhhhHHHHh
Q 030237 90 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWAN 125 (181)
Q Consensus 90 ~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~ 125 (181)
..|..|.-+ .+.|--.-+.+| +||+|--+-.+
T Consensus 2 ~~C~~C~~~-~t~p~i~fd~~G---vC~~C~~~~~~ 33 (343)
T TIGR03573 2 KFCKRCVMP-TTRPGITFDEDG---VCSACRNFEEK 33 (343)
T ss_pred CcCCCCCCC-CCCCCeeECCCC---CchhhhhHHhh
Confidence 479999997 566766677666 89999997654
No 56
>PF14122 YokU: YokU-like protein
Probab=27.30 E-value=19 Score=26.72 Aligned_cols=37 Identities=24% Similarity=0.761 Sum_probs=23.9
Q ss_pred ccccccC---CCCCCccccCCCCCC---------ccchhhhHHHHhcCC
Q 030237 92 CTHCGIS---SKSTPMMRRGPSGPR---------SLCNACGLFWANKGA 128 (181)
Q Consensus 92 C~nC~~~---~~~Tp~wRrgp~G~~---------~LCNaCGl~~~~~~~ 128 (181)
|..|+.. +..+...|.=|+|.+ ..|+.||+-|....+
T Consensus 2 C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~d~v 50 (87)
T PF14122_consen 2 CEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQDDEV 50 (87)
T ss_pred cccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEehhHH
Confidence 7777763 123444555666653 589999998876654
No 57
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=27.25 E-value=32 Score=31.13 Aligned_cols=29 Identities=28% Similarity=0.629 Sum_probs=20.6
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
....|.|||.. .|+- -+.|.--+|-+||-
T Consensus 314 k~nfc~ncG~~--~t~~---~~ng~a~fcp~cgq 342 (345)
T COG4260 314 KLNFCLNCGCG--TTAD---FDNGKAKFCPECGQ 342 (345)
T ss_pred ccccccccCcc--cccC---CccchhhhChhhcC
Confidence 34578999965 6664 34566679999985
No 58
>PRK12496 hypothetical protein; Provisional
Probab=26.99 E-value=34 Score=27.67 Aligned_cols=33 Identities=21% Similarity=0.397 Sum_probs=23.6
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhHHHHhcCC
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 128 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~~~ 128 (181)
...+|..|+. ..+. ++.+ ..|.-||...+++..
T Consensus 126 w~~~C~gC~~---~~~~---~~~~--~~C~~CG~~~~r~~~ 158 (164)
T PRK12496 126 WRKVCKGCKK---KYPE---DYPD--DVCEICGSPVKRKMV 158 (164)
T ss_pred eeEECCCCCc---cccC---CCCC--CcCCCCCChhhhcch
Confidence 4578999997 4443 3333 589999998877765
No 59
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=26.92 E-value=35 Score=30.76 Aligned_cols=37 Identities=27% Similarity=0.535 Sum_probs=30.0
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhHHHHhcCC
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 128 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~~~ 128 (181)
....|+.|+.+ . |.|=.=.-| ..||--|-=-.+.-|+
T Consensus 19 ~Nk~CaDCga~--~-P~W~S~nlG-vfiCi~CagvHRsLGv 55 (319)
T COG5347 19 SNKKCADCGAP--N-PTWASVNLG-VFLCIDCAGVHRSLGV 55 (319)
T ss_pred ccCccccCCCC--C-CceEecccC-eEEEeecchhhhcccc
Confidence 46889999996 5 999999999 4999999765555553
No 60
>PRK11823 DNA repair protein RadA; Provisional
Probab=26.20 E-value=25 Score=32.64 Aligned_cols=25 Identities=32% Similarity=0.906 Sum_probs=17.5
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhHH
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 122 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~ 122 (181)
...+|.+||. .++.|. | .|.+||-+
T Consensus 6 ~~y~C~~Cg~---~~~~~~----g---~Cp~C~~w 30 (446)
T PRK11823 6 TAYVCQECGA---ESPKWL----G---RCPECGAW 30 (446)
T ss_pred CeEECCcCCC---CCcccC----e---eCcCCCCc
Confidence 3578999998 566663 2 58888763
No 61
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=25.73 E-value=26 Score=31.15 Aligned_cols=33 Identities=27% Similarity=0.541 Sum_probs=23.9
Q ss_pred CCCCccccccccCCCCCCccccCCCCCCccchhhhHHHH
Q 030237 86 SPSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 124 (181)
Q Consensus 86 ~~~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~ 124 (181)
-...+.|..||+. ..| ...|-+.+|+.||..+.
T Consensus 108 ~~~~RFCg~CG~~--~~~----~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 108 YRSHRFCGRCGTK--TYP----REGGWARVCPKCGHEHF 140 (279)
T ss_pred HhhCcCCCCCCCc--Ccc----ccCceeeeCCCCCCccC
Confidence 3567899999995 333 33455689999998663
No 62
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=24.21 E-value=55 Score=30.42 Aligned_cols=37 Identities=22% Similarity=0.449 Sum_probs=29.9
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhHHHHhcCC
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 128 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~~~~~~ 128 (181)
....|..|+. .-|.|=.-.-|- .||-.|.=..+..|+
T Consensus 21 gNk~CaDCga---~nPtWASvn~GI-FLCl~CSGVHRsLGv 57 (395)
T PLN03114 21 DNKICFDCNA---KNPTWASVTYGI-FLCIDCSAVHRSLGV 57 (395)
T ss_pred CCCcCccCCC---CCCCceeeccce-eehhhhhHhhccCCC
Confidence 4688999998 569999999994 999999776665554
No 63
>PF12553 DUF3742: Protein of unknown function (DUF3742); InterPro: IPR022213 This domain family is found in bacteria, and is approximately 50 amino acids in length. There is a single completely conserved residue Y that may be functionally important.
Probab=24.18 E-value=29 Score=23.46 Aligned_cols=10 Identities=50% Similarity=0.926 Sum_probs=9.2
Q ss_pred CccccCCCCC
Q 030237 103 PMMRRGPSGP 112 (181)
Q Consensus 103 p~wRrgp~G~ 112 (181)
|+||.||.|-
T Consensus 34 ~E~R~G~~Gf 43 (54)
T PF12553_consen 34 PEWREGPAGF 43 (54)
T ss_pred HhheecCCCc
Confidence 8999999985
No 64
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=23.76 E-value=38 Score=29.89 Aligned_cols=31 Identities=26% Similarity=0.680 Sum_probs=18.5
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhHHH
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 123 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~~ 123 (181)
....|.+||.+ +..-.-..|. .+|..||+-.
T Consensus 10 ~~~~Cp~Cg~~----~iv~d~~~Ge-~vC~~CG~Vl 40 (310)
T PRK00423 10 EKLVCPECGSD----KLIYDYERGE-IVCADCGLVI 40 (310)
T ss_pred cCCcCcCCCCC----CeeEECCCCe-EeecccCCcc
Confidence 34568888852 2222234564 7888888844
No 65
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=23.53 E-value=46 Score=20.76 Aligned_cols=28 Identities=29% Similarity=0.673 Sum_probs=16.1
Q ss_pred ccccccccCCCCCCccccC-CCCCCccchhhh
Q 030237 90 TSCTHCGISSKSTPMMRRG-PSGPRSLCNACG 120 (181)
Q Consensus 90 ~~C~nC~~~~~~Tp~wRrg-p~G~~~LCNaCG 120 (181)
..|..|+-+ ..-.|..- ..| ..+|+.||
T Consensus 4 ~pCP~CGG~--DrFr~~d~~g~G-~~~C~~Cg 32 (37)
T smart00778 4 GPCPNCGGS--DRFRFDDKDGRG-TWFCSVCG 32 (37)
T ss_pred cCCCCCCCc--cccccccCCCCc-CEEeCCCC
Confidence 457788775 33334432 224 37888886
No 66
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=23.35 E-value=32 Score=31.29 Aligned_cols=22 Identities=36% Similarity=1.019 Sum_probs=15.4
Q ss_pred cccccccCCCCCCccccCCCCCCccchhhhHH
Q 030237 91 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 122 (181)
Q Consensus 91 ~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~ 122 (181)
.|.+||. .+|.|. | -|.+||-+
T Consensus 2 ~c~~cg~---~~~~~~----g---~cp~c~~w 23 (372)
T cd01121 2 VCSECGY---VSPKWL----G---KCPECGEW 23 (372)
T ss_pred CCCCCCC---CCCCcc----E---ECcCCCCc
Confidence 6888888 677763 3 57777763
No 67
>PF15396 FAM60A: Protein Family FAM60A
Probab=22.66 E-value=52 Score=28.21 Aligned_cols=18 Identities=33% Similarity=0.549 Sum_probs=13.8
Q ss_pred ccchhhhHHHHhcCCCCC
Q 030237 114 SLCNACGLFWANKGALRD 131 (181)
Q Consensus 114 ~LCNaCGl~~~~~~~~r~ 131 (181)
.+||||=|+.++-.++++
T Consensus 50 eICNACVLLVKRwKKLP~ 67 (213)
T PF15396_consen 50 EICNACVLLVKRWKKLPP 67 (213)
T ss_pred hhhHHHHHHHHHHhhCCC
Confidence 599999999888654443
No 68
>PHA00626 hypothetical protein
Probab=21.91 E-value=30 Score=23.94 Aligned_cols=31 Identities=32% Similarity=0.709 Sum_probs=20.8
Q ss_pred cccccccCCCCCCccc----cCCCCCCccchhhhHHHHhc
Q 030237 91 SCTHCGISSKSTPMMR----RGPSGPRSLCNACGLFWANK 126 (181)
Q Consensus 91 ~C~nC~~~~~~Tp~wR----rgp~G~~~LCNaCGl~~~~~ 126 (181)
.|.+||.. + ..| +++.. .+.|.-||.++-+.
T Consensus 2 ~CP~CGS~---~-Ivrcg~cr~~sn-rYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSG---N-IAKEKTMRGWSD-DYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCc---e-eeeeceecccCc-ceEcCCCCCeechh
Confidence 58888873 1 113 35566 49999999987653
No 69
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=21.85 E-value=40 Score=30.13 Aligned_cols=30 Identities=23% Similarity=0.517 Sum_probs=25.5
Q ss_pred CCccccccccCCCCCCccccCCCCCCccchhhhH
Q 030237 88 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 121 (181)
Q Consensus 88 ~~~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl 121 (181)
....|+.|++ ..|.|-.=.-| ..+|-.|-=
T Consensus 24 ~N~~CADC~a---~~P~WaSwnlG-vFiC~~C~g 53 (287)
T KOG0703|consen 24 DNKVCADCGA---KGPRWASWNLG-VFICLRCAG 53 (287)
T ss_pred ccCcccccCC---CCCCeEEeecC-eEEEeeccc
Confidence 4789999999 69999998889 499988754
No 70
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=20.96 E-value=42 Score=29.14 Aligned_cols=33 Identities=21% Similarity=0.357 Sum_probs=21.2
Q ss_pred CCCccccccccCCCCCCccc--c-CCCCCCccchhhhHH
Q 030237 87 PSETSCTHCGISSKSTPMMR--R-GPSGPRSLCNACGLF 122 (181)
Q Consensus 87 ~~~~~C~nC~~~~~~Tp~wR--r-gp~G~~~LCNaCGl~ 122 (181)
.....|..|+. .++.|. + -..+.-+.|..||-+
T Consensus 120 l~~~~C~~C~~---~~~~~~~~~~~~~~~~p~C~~Cg~~ 155 (250)
T COG0846 120 LKRVRCSKCGN---QYYDEDVIKFIEDGLIPRCPKCGGP 155 (250)
T ss_pred eeeeEeCCCcC---ccchhhhhhhcccCCCCcCccCCCc
Confidence 35678999997 344333 2 223334789999985
No 71
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=20.12 E-value=31 Score=23.91 Aligned_cols=31 Identities=23% Similarity=0.432 Sum_probs=22.8
Q ss_pred ccccccccCCCCCCccccCCCCCCccchhhhHH
Q 030237 90 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 122 (181)
Q Consensus 90 ~~C~nC~~~~~~Tp~wRrgp~G~~~LCNaCGl~ 122 (181)
..|..|..- .|-.|++...-...-|-.||..
T Consensus 10 A~CP~C~~~--Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQ--DTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred ccCCCCcCc--cEEEEEEeCCceEEEeccCCCc
Confidence 579999996 6666555555556899999973
Done!