Query 016724
Match_columns 384
No_of_seqs 238 out of 803
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 09:25:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016724.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016724hhsearch_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 99.5 6.1E-15 1.3E-19 111.7 2.3 44 244-290 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.5 3.4E-14 7.3E-19 106.7 3.3 46 242-289 3-48 (52)
3 PF00320 GATA: GATA zinc finge 99.4 4.6E-14 9.9E-19 98.7 -0.5 35 245-279 1-35 (36)
4 KOG1601 GATA-4/5/6 transcripti 99.0 1.5E-10 3.3E-15 103.7 4.7 71 242-312 199-303 (340)
5 COG5641 GAT1 GATA Zn-finger-co 98.3 2.4E-07 5.2E-12 97.0 2.3 53 242-297 158-215 (498)
6 COG5641 GAT1 GATA Zn-finger-co 82.0 0.86 1.9E-05 48.8 2.2 44 242-288 297-341 (498)
7 KOG3554 Histone deacetylase co 80.3 1.2 2.6E-05 47.6 2.5 37 240-276 384-422 (693)
8 PF14803 Nudix_N_2: Nudix N-te 66.9 1.6 3.5E-05 30.6 -0.3 30 243-272 1-30 (34)
9 KOG0909 Peptide:N-glycanase [P 52.5 8.4 0.00018 41.1 1.8 52 243-312 162-224 (500)
10 PRK03988 translation initiatio 48.7 5.2 0.00011 36.0 -0.3 31 243-274 103-133 (138)
11 TIGR00311 aIF-2beta translatio 46.4 6.2 0.00013 35.4 -0.2 31 243-274 98-128 (133)
12 KOG3740 Uncharacterized conser 46.2 8.1 0.00018 42.7 0.6 48 239-286 459-509 (706)
13 PRK14892 putative transcriptio 44.7 11 0.00024 32.3 1.1 34 242-276 21-54 (99)
14 PRK13130 H/ACA RNA-protein com 43.9 21 0.00045 27.9 2.4 48 242-308 5-52 (56)
15 smart00653 eIF2B_5 domain pres 43.3 7 0.00015 33.9 -0.3 29 243-272 81-109 (110)
16 PF01783 Ribosomal_L32p: Ribos 42.0 11 0.00023 28.9 0.5 25 241-275 25-49 (56)
17 PF08271 TF_Zn_Ribbon: TFIIB z 40.3 7.9 0.00017 27.7 -0.4 30 244-276 2-31 (43)
18 PRK12336 translation initiatio 39.6 8.7 0.00019 36.3 -0.3 32 243-275 99-130 (201)
19 COG2816 NPY1 NTP pyrophosphohy 37.9 15 0.00032 37.0 0.9 30 242-275 111-140 (279)
20 PRK12286 rpmF 50S ribosomal pr 34.2 30 0.00065 26.9 1.9 25 241-274 26-50 (57)
21 PF04810 zf-Sec23_Sec24: Sec23 32.7 10 0.00022 27.0 -0.8 34 242-275 2-35 (40)
22 smart00105 ArfGap Putative GTP 32.6 34 0.00075 29.1 2.3 50 242-293 3-53 (112)
23 PF01873 eIF-5_eIF-2B: Domain 31.7 13 0.00028 32.9 -0.5 29 243-272 94-122 (125)
24 KOG1598 Transcription initiati 31.5 25 0.00054 38.2 1.4 65 243-311 1-67 (521)
25 TIGR00244 transcriptional regu 30.8 26 0.00057 32.2 1.3 34 243-276 1-40 (147)
26 PF13248 zf-ribbon_3: zinc-rib 30.8 30 0.00066 22.4 1.2 23 243-273 3-25 (26)
27 PF10083 DUF2321: Uncharacteri 30.7 31 0.00068 32.1 1.8 34 242-275 39-79 (158)
28 PF15468 DUF4636: Domain of un 29.4 40 0.00086 33.2 2.3 21 359-380 38-58 (243)
29 PF09297 zf-NADH-PPase: NADH p 28.6 13 0.00028 25.1 -0.8 29 242-274 3-31 (32)
30 TIGR01385 TFSII transcription 27.5 29 0.00063 35.0 1.1 36 239-275 255-297 (299)
31 PF07282 OrfB_Zn_ribbon: Putat 27.1 33 0.00072 26.3 1.1 31 241-275 27-57 (69)
32 PF09538 FYDLN_acid: Protein o 26.2 35 0.00076 29.6 1.2 15 261-275 6-20 (108)
33 PF01096 TFIIS_C: Transcriptio 26.0 14 0.0003 26.3 -1.0 32 244-275 2-39 (39)
34 PLN03114 ADP-ribosylation fact 25.7 53 0.0012 34.5 2.6 50 242-293 22-72 (395)
35 PF12760 Zn_Tnp_IS1595: Transp 25.6 32 0.00069 25.0 0.7 27 243-272 19-45 (46)
36 COG5347 GTPase-activating prot 25.4 34 0.00074 34.9 1.2 32 242-275 20-51 (319)
37 PRK00241 nudC NADH pyrophospha 24.7 31 0.00067 33.7 0.7 30 242-275 99-128 (256)
38 PF01412 ArfGap: Putative GTPa 24.3 34 0.00074 29.3 0.8 48 242-291 13-61 (116)
39 smart00778 Prim_Zn_Ribbon Zinc 23.4 50 0.0011 23.7 1.3 30 243-272 4-33 (37)
40 PRK00420 hypothetical protein; 23.1 38 0.00083 29.8 0.9 28 243-275 24-51 (112)
41 PHA02998 RNA polymerase subuni 21.9 38 0.00083 32.4 0.7 34 241-275 142-182 (195)
42 COG5349 Uncharacterized protei 21.8 42 0.00091 30.2 0.9 33 241-276 20-52 (126)
43 PF12773 DZR: Double zinc ribb 21.2 50 0.0011 23.8 1.0 29 242-275 12-40 (50)
44 PF09723 Zn-ribbon_8: Zinc rib 21.0 29 0.00062 24.9 -0.3 28 244-272 7-34 (42)
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=99.50 E-value=6.1e-15 Score=111.74 Aligned_cols=44 Identities=45% Similarity=0.942 Sum_probs=39.6
Q ss_pred ccccCCCCCCCCcCCCCCCChhhhhhhhhhhhcCCCCCCCCCCCCCC
Q 016724 244 KCMHCEITKTPQWRAGPMGPKTLCNACGVRYKSGRLFPEYRPAASPT 290 (384)
Q Consensus 244 ~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk~~rl~p~~RP~~spt 290 (384)
.|+||++++||+||+||.|..+||||||+||+++ +..||+..+.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~---~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKH---GVMRPLSKRK 44 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhc---CCCCCcccCc
Confidence 4999999999999999988899999999999954 4889988763
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.46 E-value=3.4e-14 Score=106.73 Aligned_cols=46 Identities=50% Similarity=0.949 Sum_probs=39.1
Q ss_pred CcccccCCCCCCCCcCCCCCCChhhhhhhhhhhhcCCCCCCCCCCCCC
Q 016724 242 VRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYKSGRLFPEYRPAASP 289 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk~~rl~p~~RP~~sp 289 (384)
.+.|.||++++||+||+||.|..+||||||++|++.+.. +||...+
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~--~rp~~~~ 48 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL--KRPLSLK 48 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC--CCccccc
Confidence 578999999999999999999889999999999964433 4666654
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=99.38 E-value=4.6e-14 Score=98.71 Aligned_cols=35 Identities=57% Similarity=1.169 Sum_probs=27.9
Q ss_pred cccCCCCCCCCcCCCCCCChhhhhhhhhhhhcCCC
Q 016724 245 CMHCEITKTPQWRAGPMGPKTLCNACGVRYKSGRL 279 (384)
Q Consensus 245 C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk~~rl 279 (384)
|.||++++||+||+||.|..+||||||++|++++.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 89999999999999999988899999999998654
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=99.05 E-value=1.5e-10 Score=103.72 Aligned_cols=71 Identities=61% Similarity=1.135 Sum_probs=61.5
Q ss_pred CcccccCCCCCCCCcCCCCCCChhhhhhhhhhhhcC---CCCCCCCCCCCCC--------------ccCCcccc------
Q 016724 242 VRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYKSG---RLFPEYRPAASPT--------------FVPSLHSN------ 298 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk~~---rl~p~~RP~~spt--------------f~~~~hsn------ 298 (384)
...|.+|++++||+||+++.|.+.+|||||++|+++ +.++.++...+++ +....|.+
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPRNVSPKGSGAVKGRTFTKSLHSNSAQLLL 278 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCccccccccCCCccccccCCCCCcccccchhhhhh
Confidence 579999999999999999999999999999999998 7888889888887 55566666
Q ss_pred -----------chhHHHHHhhhcCC
Q 016724 299 -----------SHKKVVEMRNKNCQ 312 (384)
Q Consensus 299 -----------~hrkv~~~R~~~~~ 312 (384)
.+.++.++++.+.+
T Consensus 279 ~~~~~~~~~~~~~~~~~~~~r~~~~ 303 (340)
T KOG1601|consen 279 APSKSEPPLLSSHQRVAEVRRYRES 303 (340)
T ss_pred hhcccCccccccchHHHHHhhccCc
Confidence 67888888887764
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.31 E-value=2.4e-07 Score=96.98 Aligned_cols=53 Identities=34% Similarity=0.597 Sum_probs=45.3
Q ss_pred CcccccCCCCCCCCcCCCCCC----ChhhhhhhhhhhhcCCCCCCCC-CCCCCCccCCccc
Q 016724 242 VRKCMHCEITKTPQWRAGPMG----PKTLCNACGVRYKSGRLFPEYR-PAASPTFVPSLHS 297 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G----~~~LCNACGl~yk~~rl~p~~R-P~~sptf~~~~hs 297 (384)
...|.+|.++.||+|||+..+ .-.||||||++|+ +|+..| |.++++.+..-|.
T Consensus 158 ~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~k---lhg~~r~P~t~ks~~~ks~~ 215 (498)
T COG5641 158 PHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLK---LHGSPRAPISLKSDSIKSRS 215 (498)
T ss_pred cchhccccccCCccccccccccccCCcccccccccccc---ccCCcCCCcccccccccccc
Confidence 348999999999999999993 3899999999999 999999 9999965554433
No 6
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=82.05 E-value=0.86 Score=48.76 Aligned_cols=44 Identities=30% Similarity=0.334 Sum_probs=34.2
Q ss_pred CcccccCCC-CCCCCcCCCCCCChhhhhhhhhhhhcCCCCCCCCCCCC
Q 016724 242 VRKCMHCEI-TKTPQWRAGPMGPKTLCNACGVRYKSGRLFPEYRPAAS 288 (384)
Q Consensus 242 ~~~C~~C~t-t~TP~WR~GP~G~~~LCNACGl~yk~~rl~p~~RP~~s 288 (384)
...|.+|++ +.||.||+...-.-++|||||.+.+ +...+||..-
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~---~~~~~~p~~p 341 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALK---PPGSKRPLLP 341 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccC---CcccccccCC
Confidence 567888887 7789998887776999999999998 5555555543
No 7
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=80.30 E-value=1.2 Score=47.60 Aligned_cols=37 Identities=32% Similarity=0.627 Sum_probs=31.8
Q ss_pred CCCcccccCCCCCCCCc--CCCCCCChhhhhhhhhhhhc
Q 016724 240 QAVRKCMHCEITKTPQW--RAGPMGPKTLCNACGVRYKS 276 (384)
Q Consensus 240 ~~~~~C~~C~tt~TP~W--R~GP~G~~~LCNACGl~yk~ 276 (384)
+.++.|-+|+|+..-+| .-+|.-.+.||--|=+||||
T Consensus 384 ~~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKK 422 (693)
T KOG3554|consen 384 QDGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKK 422 (693)
T ss_pred CCCCcccccccccccceeccCCCCccchhhHHHHHHHHH
Confidence 45789999999999999 44566667899999999998
No 8
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=66.87 E-value=1.6 Score=30.63 Aligned_cols=30 Identities=23% Similarity=0.528 Sum_probs=16.3
Q ss_pred cccccCCCCCCCCcCCCCCCChhhhhhhhh
Q 016724 243 RKCMHCEITKTPQWRAGPMGPKTLCNACGV 272 (384)
Q Consensus 243 ~~C~~C~tt~TP~WR~GP~G~~~LCNACGl 272 (384)
+.|.+||..-+-.=-.|..-.+.+|.+||-
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 369999988544344677777899999984
No 9
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=52.53 E-value=8.4 Score=41.10 Aligned_cols=52 Identities=29% Similarity=0.588 Sum_probs=36.7
Q ss_pred cccccCCCCC-CCCcCCCCCCCh----------hhhhhhhhhhhcCCCCCCCCCCCCCCccCCccccchhHHHHHhhhcC
Q 016724 243 RKCMHCEITK-TPQWRAGPMGPK----------TLCNACGVRYKSGRLFPEYRPAASPTFVPSLHSNSHKKVVEMRNKNC 311 (384)
Q Consensus 243 ~~C~~C~tt~-TP~WR~GP~G~~----------~LCNACGl~yk~~rl~p~~RP~~sptf~~~~hsn~hrkv~~~R~~~~ 311 (384)
-.|.+||..+ ++.=+.+|.+.. +.||+||---+ +|.| |...|.++.|+-+-
T Consensus 162 PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~R----FPRY--------------Ndp~kLLeTRkGRC 223 (500)
T KOG0909|consen 162 PPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETR----FPRY--------------NDPIKLLETRKGRC 223 (500)
T ss_pred CCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCccc----Cccc--------------CCHHHHHhhccCcc
Confidence 4799999887 555554554432 78999997666 5555 45588999988665
Q ss_pred C
Q 016724 312 Q 312 (384)
Q Consensus 312 ~ 312 (384)
+
T Consensus 224 G 224 (500)
T KOG0909|consen 224 G 224 (500)
T ss_pred c
Confidence 4
No 10
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=48.74 E-value=5.2 Score=36.04 Aligned_cols=31 Identities=26% Similarity=0.492 Sum_probs=23.6
Q ss_pred cccccCCCCCCCCcCCCCCCChhhhhhhhhhh
Q 016724 243 RKCMHCEITKTPQWRAGPMGPKTLCNACGVRY 274 (384)
Q Consensus 243 ~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~y 274 (384)
-.|..|+...|-+=+++-. --.-|+|||-..
T Consensus 103 VlC~~C~spdT~l~k~~r~-~~l~C~ACGa~~ 133 (138)
T PRK03988 103 VICPECGSPDTKLIKEGRI-WVLKCEACGAET 133 (138)
T ss_pred EECCCCCCCCcEEEEcCCe-EEEEcccCCCCC
Confidence 4799999999999775332 146899999654
No 11
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=46.35 E-value=6.2 Score=35.39 Aligned_cols=31 Identities=26% Similarity=0.518 Sum_probs=23.3
Q ss_pred cccccCCCCCCCCcCCCCCCChhhhhhhhhhh
Q 016724 243 RKCMHCEITKTPQWRAGPMGPKTLCNACGVRY 274 (384)
Q Consensus 243 ~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~y 274 (384)
-.|..|+-..|-+=+.+. ---.-|+|||-..
T Consensus 98 VlC~~C~sPdT~l~k~~r-~~~l~C~ACGa~~ 128 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGR-VSLLKCEACGAKA 128 (133)
T ss_pred EECCCCCCCCcEEEEeCC-eEEEecccCCCCC
Confidence 479999999999887532 1135899999654
No 12
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.24 E-value=8.1 Score=42.70 Aligned_cols=48 Identities=19% Similarity=0.405 Sum_probs=34.9
Q ss_pred CCCCcccccCCCCCCCCcCCCCCC---ChhhhhhhhhhhhcCCCCCCCCCC
Q 016724 239 TQAVRKCMHCEITKTPQWRAGPMG---PKTLCNACGVRYKSGRLFPEYRPA 286 (384)
Q Consensus 239 ~~~~~~C~~C~tt~TP~WR~GP~G---~~~LCNACGl~yk~~rl~p~~RP~ 286 (384)
....-.|..|.|.-||.|+.-+.+ .+.+|.+|----.|+.+--+..+.
T Consensus 459 a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnqkkAlK~ehT~r 509 (706)
T KOG3740|consen 459 ATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQKKALKVEHTNR 509 (706)
T ss_pred cCCchhhhhcccccccccccccccCcchHHHHHhhhhhcccccccccchHH
Confidence 345678999999999999887766 468999997655554444443333
No 13
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=44.69 E-value=11 Score=32.31 Aligned_cols=34 Identities=15% Similarity=0.263 Sum_probs=22.1
Q ss_pred CcccccCCCCCCCCcCCCCCCChhhhhhhhhhhhc
Q 016724 242 VRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYKS 276 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk~ 276 (384)
.-.|.+|+...-+.=+. -......|..||.|+.+
T Consensus 21 ~f~CP~Cge~~v~v~~~-k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 21 IFECPRCGKVSISVKIK-KNIAIITCGNCGLYTEF 54 (99)
T ss_pred EeECCCCCCeEeeeecC-CCcceEECCCCCCccCE
Confidence 35799999533221111 13447999999999874
No 14
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=43.94 E-value=21 Score=27.86 Aligned_cols=48 Identities=27% Similarity=0.640 Sum_probs=30.4
Q ss_pred CcccccCCCCCCCCcCCCCCCChhhhhhhhhhhhcCCCCCCCCCCCCCCccCCccccchhHHHHHhh
Q 016724 242 VRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYKSGRLFPEYRPAASPTFVPSLHSNSHKKVVEMRN 308 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk~~rl~p~~RP~~sptf~~~~hsn~hrkv~~~R~ 308 (384)
.+.|..||+.+- +..|-.||.... .+.-+.|.+.---..+|..++.|.
T Consensus 5 mr~C~~CgvYTL----------k~~CP~CG~~t~---------~~~P~rfSp~D~y~~yR~~~kk~~ 52 (56)
T PRK13130 5 IRKCPKCGVYTL----------KEICPVCGGKTK---------NPHPPRFSPEDKYGKYRRALKKRR 52 (56)
T ss_pred ceECCCCCCEEc----------cccCcCCCCCCC---------CCCCCCCCCCCccHHHHHHHHHHh
Confidence 467888888765 457888886644 233455666655555666666554
No 15
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=43.30 E-value=7 Score=33.94 Aligned_cols=29 Identities=24% Similarity=0.456 Sum_probs=22.2
Q ss_pred cccccCCCCCCCCcCCCCCCChhhhhhhhh
Q 016724 243 RKCMHCEITKTPQWRAGPMGPKTLCNACGV 272 (384)
Q Consensus 243 ~~C~~C~tt~TP~WR~GP~G~~~LCNACGl 272 (384)
-.|..|+...|-+=+.+..= -.-|+|||-
T Consensus 81 VlC~~C~spdT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeE-EEEccccCC
Confidence 47999999999998873211 356999995
No 16
>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=42.03 E-value=11 Score=28.91 Aligned_cols=25 Identities=40% Similarity=0.956 Sum_probs=18.3
Q ss_pred CCcccccCCCCCCCCcCCCCCCChhhhhhhhhhhh
Q 016724 241 AVRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYK 275 (384)
Q Consensus 241 ~~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk 275 (384)
....|.+||...- +..+|.+|| +|+
T Consensus 25 ~l~~c~~cg~~~~---------~H~vc~~cG-~y~ 49 (56)
T PF01783_consen 25 NLVKCPNCGEPKL---------PHRVCPSCG-YYK 49 (56)
T ss_dssp SEEESSSSSSEES---------TTSBCTTTB-BSS
T ss_pred ceeeeccCCCEec---------ccEeeCCCC-eEC
Confidence 3468999996432 378999999 555
No 17
>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=40.32 E-value=7.9 Score=27.69 Aligned_cols=30 Identities=23% Similarity=0.634 Sum_probs=18.0
Q ss_pred ccccCCCCCCCCcCCCCCCChhhhhhhhhhhhc
Q 016724 244 KCMHCEITKTPQWRAGPMGPKTLCNACGVRYKS 276 (384)
Q Consensus 244 ~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk~ 276 (384)
+|.+|+.+. -.+- -..| ..+|..||+-..-
T Consensus 2 ~Cp~Cg~~~-~~~D-~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE-IVFD-PERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE-EEEE-TTTT-EEEETTT-BBEE-
T ss_pred CCcCCcCCc-eEEc-CCCC-eEECCCCCCEeec
Confidence 688888866 2222 2344 7789999876553
No 18
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=39.59 E-value=8.7 Score=36.32 Aligned_cols=32 Identities=22% Similarity=0.436 Sum_probs=24.5
Q ss_pred cccccCCCCCCCCcCCCCCCChhhhhhhhhhhh
Q 016724 243 RKCMHCEITKTPQWRAGPMGPKTLCNACGVRYK 275 (384)
Q Consensus 243 ~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk 275 (384)
-.|..|+-..|-+=+.+. ---.-|+|||-..-
T Consensus 99 V~C~~C~~pdT~l~k~~~-~~~l~C~aCGa~~~ 130 (201)
T PRK12336 99 VICSECGLPDTRLVKEDR-VLMLRCDACGAHRP 130 (201)
T ss_pred EECCCCCCCCcEEEEcCC-eEEEEcccCCCCcc
Confidence 479999999999977632 11358999998765
No 19
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=37.86 E-value=15 Score=36.99 Aligned_cols=30 Identities=27% Similarity=0.506 Sum_probs=23.5
Q ss_pred CcccccCCCCCCCCcCCCCCCChhhhhhhhhhhh
Q 016724 242 VRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYK 275 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk 275 (384)
.+.|.+||+.+.+. ..|-+.+|+.||.++-
T Consensus 111 ~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~f 140 (279)
T COG2816 111 HRFCGRCGTKTYPR----EGGWARVCPKCGHEHF 140 (279)
T ss_pred CcCCCCCCCcCccc----cCceeeeCCCCCCccC
Confidence 47899999988774 3466789999998753
No 20
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=34.16 E-value=30 Score=26.86 Aligned_cols=25 Identities=28% Similarity=0.752 Sum_probs=19.3
Q ss_pred CCcccccCCCCCCCCcCCCCCCChhhhhhhhhhh
Q 016724 241 AVRKCMHCEITKTPQWRAGPMGPKTLCNACGVRY 274 (384)
Q Consensus 241 ~~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~y 274 (384)
..-.|.+||...-| ..+|..||.|-
T Consensus 26 ~l~~C~~CG~~~~~---------H~vC~~CG~Y~ 50 (57)
T PRK12286 26 GLVECPNCGEPKLP---------HRVCPSCGYYK 50 (57)
T ss_pred cceECCCCCCccCC---------eEECCCCCcCC
Confidence 34579999987755 78999999543
No 21
>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=32.70 E-value=10 Score=27.02 Aligned_cols=34 Identities=24% Similarity=0.522 Sum_probs=21.8
Q ss_pred CcccccCCCCCCCCcCCCCCCChhhhhhhhhhhh
Q 016724 242 VRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYK 275 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk 275 (384)
..+|.+|++---|.=+-...|..-.||-||..-.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~ 35 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNP 35 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--EEE
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCCcCC
Confidence 3589999999999877777887889999997543
No 22
>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=32.64 E-value=34 Score=29.14 Aligned_cols=50 Identities=24% Similarity=0.509 Sum_probs=37.7
Q ss_pred CcccccCCCCCCCCcCCCCCCChhhhhhhhhhhhcCCCC-CCCCCCCCCCccC
Q 016724 242 VRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYKSGRLF-PEYRPAASPTFVP 293 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk~~rl~-p~~RP~~sptf~~ 293 (384)
.+.|.+|+. .-|+|=.=..| -.+|-.|.-..+.-+.| ...|.++|-+|..
T Consensus 3 N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~lg~his~VkSl~md~w~~ 53 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSLGVHISKVRSLTLDTWTE 53 (112)
T ss_pred CCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhcCCCcCeeeecccCCCCH
Confidence 468999998 55999888889 99999998888853333 3467777765543
No 23
>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=31.66 E-value=13 Score=32.95 Aligned_cols=29 Identities=28% Similarity=0.534 Sum_probs=23.4
Q ss_pred cccccCCCCCCCCcCCCCCCChhhhhhhhh
Q 016724 243 RKCMHCEITKTPQWRAGPMGPKTLCNACGV 272 (384)
Q Consensus 243 ~~C~~C~tt~TP~WR~GP~G~~~LCNACGl 272 (384)
-.|..|+...|-+=+++..= -.-|+|||-
T Consensus 94 VlC~~C~spdT~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCC-EEEETTTSC
T ss_pred EEcCCCCCCccEEEEcCCEE-EEEecccCC
Confidence 46999999999988774433 678999995
No 24
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=31.51 E-value=25 Score=38.22 Aligned_cols=65 Identities=25% Similarity=0.400 Sum_probs=35.7
Q ss_pred cccccCCCCCCCCcCCCCCCChhhhhhhhhhhhcCCCCCCC--CCCCCCCccCCccccchhHHHHHhhhcC
Q 016724 243 RKCMHCEITKTPQWRAGPMGPKTLCNACGVRYKSGRLFPEY--RPAASPTFVPSLHSNSHKKVVEMRNKNC 311 (384)
Q Consensus 243 ~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk~~rl~p~~--RP~~sptf~~~~hsn~hrkv~~~R~~~~ 311 (384)
+.|.||+.+. +. |+--.| ...|+|||.-.......-+. --.++.+|+...-+.... +++.|-++.
T Consensus 1 ~~C~~C~~s~-fe-~d~a~g-~~~C~~CG~v~E~~~ivsev~F~e~~~G~~v~~~~~g~~~-s~e~r~~t~ 67 (521)
T KOG1598|consen 1 MVCKNCGGSN-FE-RDEATG-NLYCTACGTVLEYNNIVAEVTFVEGAQGQFVRVGQSGAGS-SLESREKTI 67 (521)
T ss_pred CcCCCCCCCC-cc-cccccC-CceeccccceeeccceeEEeeeecccceeEEeccccCCcc-chHHHHHHH
Confidence 4799999864 22 233456 89999999977654432211 001566665543222211 555555554
No 25
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=30.80 E-value=26 Score=32.21 Aligned_cols=34 Identities=24% Similarity=0.481 Sum_probs=25.9
Q ss_pred cccccCCCCCCCCc--CCCCCC----Chhhhhhhhhhhhc
Q 016724 243 RKCMHCEITKTPQW--RAGPMG----PKTLCNACGVRYKS 276 (384)
Q Consensus 243 ~~C~~C~tt~TP~W--R~GP~G----~~~LCNACGl~yk~ 276 (384)
++|..|+...|-.- |...+| ..--|.+||.+|-.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTT 40 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTT 40 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccce
Confidence 47999999888775 555565 23689999999875
No 26
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=30.77 E-value=30 Score=22.44 Aligned_cols=23 Identities=26% Similarity=0.788 Sum_probs=14.1
Q ss_pred cccccCCCCCCCCcCCCCCCChhhhhhhhhh
Q 016724 243 RKCMHCEITKTPQWRAGPMGPKTLCNACGVR 273 (384)
Q Consensus 243 ~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~ 273 (384)
+.|.+||....+. ...|..||..
T Consensus 3 ~~Cp~Cg~~~~~~--------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPD--------AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcc--------cccChhhCCC
Confidence 4678888754332 4467777753
No 27
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=30.71 E-value=31 Score=32.13 Aligned_cols=34 Identities=21% Similarity=0.658 Sum_probs=25.1
Q ss_pred CcccccCCCCCCCCcCC-------CCCCChhhhhhhhhhhh
Q 016724 242 VRKCMHCEITKTPQWRA-------GPMGPKTLCNACGVRYK 275 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~-------GP~G~~~LCNACGl~yk 275 (384)
...|.+|++..--.|-- ++.-....|+.||..|-
T Consensus 39 I~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 39 ITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred HHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCc
Confidence 45799999887666632 44556689999999884
No 28
>PF15468 DUF4636: Domain of unknown function (DUF4636)
Probab=29.44 E-value=40 Score=33.17 Aligned_cols=21 Identities=33% Similarity=0.531 Sum_probs=14.7
Q ss_pred hhHHHHHHHHHHHHHHHhhhcc
Q 016724 359 FRSLLFAYCYFISLFICFLYRD 380 (384)
Q Consensus 359 ~~~~~~~~~~~~~~~~~~~~~~ 380 (384)
+-+.||-|| .|.|+|||+||-
T Consensus 38 iG~fLlWyf-viilvLm~~~ra 58 (243)
T PF15468_consen 38 IGSFLLWYF-VIILVLMFFSRA 58 (243)
T ss_pred hhhHHHHHH-HHHHHHHHHHHH
Confidence 445666655 566789999984
No 29
>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=28.59 E-value=13 Score=25.08 Aligned_cols=29 Identities=28% Similarity=0.482 Sum_probs=16.1
Q ss_pred CcccccCCCCCCCCcCCCCCCChhhhhhhhhhh
Q 016724 242 VRKCMHCEITKTPQWRAGPMGPKTLCNACGVRY 274 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~y 274 (384)
.+.|..||....+.. .|....|.+||..+
T Consensus 3 ~rfC~~CG~~t~~~~----~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAP----GGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BEEE-S----SSS-EEESSSS-EE
T ss_pred CcccCcCCccccCCC----CcCEeECCCCcCEe
Confidence 367999998776543 35578899998753
No 30
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=27.53 E-value=29 Score=34.97 Aligned_cols=36 Identities=25% Similarity=0.581 Sum_probs=26.1
Q ss_pred CCCCcccccCCCCCCCCc----CCCCCCCh---hhhhhhhhhhh
Q 016724 239 TQAVRKCMHCEITKTPQW----RAGPMGPK---TLCNACGVRYK 275 (384)
Q Consensus 239 ~~~~~~C~~C~tt~TP~W----R~GP~G~~---~LCNACGl~yk 275 (384)
......|..|+-..+-.| |...++ - ..|..||-+|+
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEp-mT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEP-MTTFVTCEECGNRWK 297 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCC-CeEEEEcCCCCCeee
Confidence 345679999998876555 444444 3 48999999987
No 31
>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=27.08 E-value=33 Score=26.28 Aligned_cols=31 Identities=19% Similarity=0.494 Sum_probs=23.4
Q ss_pred CCcccccCCCCCCCCcCCCCCCChhhhhhhhhhhh
Q 016724 241 AVRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYK 275 (384)
Q Consensus 241 ~~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk 275 (384)
....|..||....- ...+....|..||..+.
T Consensus 27 TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCccCccccccc----ccccceEEcCCCCCEEC
Confidence 45689999987654 44555789999998765
No 32
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=26.17 E-value=35 Score=29.65 Aligned_cols=15 Identities=33% Similarity=1.039 Sum_probs=9.0
Q ss_pred CCChhhhhhhhhhhh
Q 016724 261 MGPKTLCNACGVRYK 275 (384)
Q Consensus 261 ~G~~~LCNACGl~yk 275 (384)
.|.|-+|..||.+|-
T Consensus 6 lGtKR~Cp~CG~kFY 20 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFY 20 (108)
T ss_pred cCCcccCCCCcchhc
Confidence 355666666666554
No 33
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=26.03 E-value=14 Score=26.27 Aligned_cols=32 Identities=25% Similarity=0.620 Sum_probs=18.9
Q ss_pred ccccCCCCCCCCc----CCCCCCCh--hhhhhhhhhhh
Q 016724 244 KCMHCEITKTPQW----RAGPMGPK--TLCNACGVRYK 275 (384)
Q Consensus 244 ~C~~C~tt~TP~W----R~GP~G~~--~LCNACGl~yk 275 (384)
.|..|+-.++-.| |.+.++.- ..|..||-+|+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 4778887764443 66666622 46888987764
No 34
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=25.66 E-value=53 Score=34.50 Aligned_cols=50 Identities=20% Similarity=0.464 Sum_probs=37.4
Q ss_pred CcccccCCCCCCCCcCCCCCCChhhhhhhhhhhhcCCCC-CCCCCCCCCCccC
Q 016724 242 VRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYKSGRLF-PEYRPAASPTFVP 293 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk~~rl~-p~~RP~~sptf~~ 293 (384)
.+.|..|+... |+|=.=..| -.||-.|.=..+.-+.| ...|.++|-+|..
T Consensus 22 Nk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRsLGvHISfVRSltLD~Ws~ 72 (395)
T PLN03114 22 NKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRSLGVHISFVRSTNLDSWSS 72 (395)
T ss_pred CCcCccCCCCC-CCceeeccc-eeehhhhhHhhccCCCCCceeecccCCCCCH
Confidence 47899999765 999998999 99999997776643332 3567777766543
No 35
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=25.65 E-value=32 Score=24.96 Aligned_cols=27 Identities=30% Similarity=0.502 Sum_probs=19.8
Q ss_pred cccccCCCCCCCCcCCCCCCChhhhhhhhh
Q 016724 243 RKCMHCEITKTPQWRAGPMGPKTLCNACGV 272 (384)
Q Consensus 243 ~~C~~C~tt~TP~WR~GP~G~~~LCNACGl 272 (384)
..|.+||.+ ..-|.++ .+ ..-|++|+.
T Consensus 19 ~~CP~Cg~~-~~~~~~~-~~-~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-KHYRLKT-RG-RYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-eeEEeCC-CC-eEECCCCCC
Confidence 469999998 5555554 34 788999974
No 36
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=25.43 E-value=34 Score=34.91 Aligned_cols=32 Identities=28% Similarity=0.718 Sum_probs=28.1
Q ss_pred CcccccCCCCCCCCcCCCCCCChhhhhhhhhhhh
Q 016724 242 VRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYK 275 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk 275 (384)
.+.|..|+... |+|=.=..| -.||=-|.=-.+
T Consensus 20 Nk~CaDCga~~-P~W~S~nlG-vfiCi~CagvHR 51 (319)
T COG5347 20 NKKCADCGAPN-PTWASVNLG-VFLCIDCAGVHR 51 (319)
T ss_pred cCccccCCCCC-CceEecccC-eEEEeecchhhh
Confidence 57899999999 999999999 999999965444
No 37
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=24.69 E-value=31 Score=33.65 Aligned_cols=30 Identities=30% Similarity=0.497 Sum_probs=22.0
Q ss_pred CcccccCCCCCCCCcCCCCCCChhhhhhhhhhhh
Q 016724 242 VRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYK 275 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk 275 (384)
.+.|.+||...... ..|....|.+||..+-
T Consensus 99 ~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 99 HRFCGYCGHPMHPS----KTEWAMLCPHCRERYY 128 (256)
T ss_pred CccccccCCCCeec----CCceeEECCCCCCEEC
Confidence 46899999976542 3566788999996543
No 38
>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=24.33 E-value=34 Score=29.29 Aligned_cols=48 Identities=19% Similarity=0.441 Sum_probs=28.3
Q ss_pred CcccccCCCCCCCCcCCCCCCChhhhhhhhhhhhcCCC-CCCCCCCCCCCc
Q 016724 242 VRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYKSGRL-FPEYRPAASPTF 291 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk~~rl-~p~~RP~~sptf 291 (384)
.+.|.+|+... |.|-.=..| -.||-.|.-.++.=+. +-..+-++|-+|
T Consensus 13 N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~lg~~is~VkSi~~d~w 61 (116)
T PF01412_consen 13 NKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRSLGVHISRVKSITMDNW 61 (116)
T ss_dssp CTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHHHTTTT--EEETTTS--
T ss_pred cCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHHhcccchhccccccCCC
Confidence 47899999554 699988899 9999999988876222 234455555433
No 39
>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=23.36 E-value=50 Score=23.71 Aligned_cols=30 Identities=17% Similarity=0.432 Sum_probs=20.9
Q ss_pred cccccCCCCCCCCcCCCCCCChhhhhhhhh
Q 016724 243 RKCMHCEITKTPQWRAGPMGPKTLCNACGV 272 (384)
Q Consensus 243 ~~C~~C~tt~TP~WR~GP~G~~~LCNACGl 272 (384)
..|-.|+....=.|..........|+.||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 368999988777775533222789999974
No 40
>PRK00420 hypothetical protein; Validated
Probab=23.10 E-value=38 Score=29.77 Aligned_cols=28 Identities=25% Similarity=0.626 Sum_probs=22.2
Q ss_pred cccccCCCCCCCCcCCCCCCChhhhhhhhhhhh
Q 016724 243 RKCMHCEITKTPQWRAGPMGPKTLCNACGVRYK 275 (384)
Q Consensus 243 ~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk 275 (384)
..|..|| +|+.|- ..| +..|-+||..+.
T Consensus 24 ~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCG---LPLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCC---Ccceec-CCC-ceECCCCCCeee
Confidence 5688888 677774 356 899999999877
No 41
>PHA02998 RNA polymerase subunit; Provisional
Probab=21.91 E-value=38 Score=32.40 Aligned_cols=34 Identities=24% Similarity=0.468 Sum_probs=27.8
Q ss_pred CCcccccCCCCCCCCc----CCCCCCChh---hhhhhhhhhh
Q 016724 241 AVRKCMHCEITKTPQW----RAGPMGPKT---LCNACGVRYK 275 (384)
Q Consensus 241 ~~~~C~~C~tt~TP~W----R~GP~G~~~---LCNACGl~yk 275 (384)
....|..|+-..+--| |.+.++ .| .|-.||-+|+
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEP-mT~FYkC~~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEP-PLVRHACRDCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCC-ceEEEEcCCCCCccC
Confidence 4568999998887765 777777 54 8999999998
No 42
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.80 E-value=42 Score=30.23 Aligned_cols=33 Identities=24% Similarity=0.521 Sum_probs=22.2
Q ss_pred CCcccccCCCCCCCCcCCCCCCChhhhhhhhhhhhc
Q 016724 241 AVRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYKS 276 (384)
Q Consensus 241 ~~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk~ 276 (384)
...+|-+||--+ -=+|=.-....|.|||+.|-.
T Consensus 20 l~grCP~CGeGr---LF~gFLK~~p~C~aCG~dyg~ 52 (126)
T COG5349 20 LRGRCPRCGEGR---LFRGFLKVVPACEACGLDYGF 52 (126)
T ss_pred hcCCCCCCCCch---hhhhhcccCchhhhccccccC
Confidence 445899999532 122333346799999999973
No 43
>PF12773 DZR: Double zinc ribbon
Probab=21.18 E-value=50 Score=23.79 Aligned_cols=29 Identities=28% Similarity=0.669 Sum_probs=19.8
Q ss_pred CcccccCCCCCCCCcCCCCCCChhhhhhhhhhhh
Q 016724 242 VRKCMHCEITKTPQWRAGPMGPKTLCNACGVRYK 275 (384)
Q Consensus 242 ~~~C~~C~tt~TP~WR~GP~G~~~LCNACGl~yk 275 (384)
.+.|.+||+.-. ........|..||-...
T Consensus 12 ~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 12 AKFCPHCGTPLP-----PPDQSKKICPNCGAENP 40 (50)
T ss_pred ccCChhhcCChh-----hccCCCCCCcCCcCCCc
Confidence 567888888777 33444567888887544
No 44
>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=21.00 E-value=29 Score=24.94 Aligned_cols=28 Identities=18% Similarity=0.413 Sum_probs=17.8
Q ss_pred ccccCCCCCCCCcCCCCCCChhhhhhhhh
Q 016724 244 KCMHCEITKTPQWRAGPMGPKTLCNACGV 272 (384)
Q Consensus 244 ~C~~C~tt~TP~WR~GP~G~~~LCNACGl 272 (384)
+|..||..-+-...-.. .....|-+||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 68888866554443333 44678888886
Done!