Query psy9606
Match_columns 356
No_of_seqs 194 out of 797
Neff 3.4
Searched_HMMs 46136
Date Sat Aug 17 00:05:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9606.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9606hhsearch_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 1.7E-15 3.7E-20 113.5 3.7 50 75-124 1-52 (54)
2 smart00401 ZnF_GATA zinc finge 99.5 2.4E-14 5.1E-19 106.3 3.6 47 72-118 2-50 (52)
3 PF00320 GATA: GATA zinc finge 99.3 3.5E-13 7.5E-18 93.4 2.0 35 76-110 1-36 (36)
4 KOG1601|consensus 98.8 5.4E-09 1.2E-13 90.4 3.5 52 73-124 199-251 (340)
5 COG5641 GAT1 GATA Zn-finger-co 98.7 3.4E-09 7.4E-14 108.9 2.4 56 70-125 155-216 (498)
6 COG5641 GAT1 GATA Zn-finger-co 91.6 0.075 1.6E-06 55.8 1.1 54 73-126 297-352 (498)
7 KOG3554|consensus 85.3 0.59 1.3E-05 49.5 2.5 38 72-109 385-425 (693)
8 KOG3740|consensus 79.6 0.74 1.6E-05 49.9 0.8 35 70-104 459-497 (706)
9 PF08271 TF_Zn_Ribbon: TFIIB z 74.9 1.3 2.9E-05 31.4 0.8 29 74-104 1-29 (43)
10 PF01412 ArfGap: Putative GTPa 63.6 6.5 0.00014 33.2 2.7 37 72-109 12-48 (116)
11 PRK03988 translation initiatio 59.2 3.5 7.6E-05 36.7 0.4 30 73-102 102-131 (138)
12 TIGR00311 aIF-2beta translatio 57.9 4 8.6E-05 36.2 0.5 30 73-102 97-126 (133)
13 PRK12286 rpmF 50S ribosomal pr 57.2 5.6 0.00012 30.6 1.1 27 70-104 24-50 (57)
14 PF11781 RRN7: RNA polymerase 56.2 6.4 0.00014 27.7 1.2 26 73-102 8-33 (36)
15 smart00653 eIF2B_5 domain pres 55.9 4.6 0.0001 34.7 0.5 29 74-102 81-109 (110)
16 PRK12336 translation initiatio 51.5 5.5 0.00012 37.1 0.3 30 73-102 98-127 (201)
17 smart00105 ArfGap Putative GTP 51.1 13 0.00029 31.2 2.5 36 73-109 3-38 (112)
18 COG5347 GTPase-activating prot 49.2 10 0.00022 38.1 1.8 29 72-101 19-47 (319)
19 PF01873 eIF-5_eIF-2B: Domain 46.9 9.5 0.00021 33.4 1.1 29 74-102 94-122 (125)
20 PRK00423 tfb transcription ini 46.6 11 0.00023 36.9 1.5 30 73-104 11-40 (310)
21 PF06677 Auto_anti-p27: Sjogre 45.2 11 0.00023 27.5 0.9 26 72-101 16-41 (41)
22 PF14803 Nudix_N_2: Nudix N-te 44.4 8.1 0.00018 27.1 0.2 26 74-102 1-30 (34)
23 PLN03106 TCP2 Protein TCP2; Pr 43.6 52 0.0011 34.4 5.7 56 221-278 361-423 (447)
24 PF01783 Ribosomal_L32p: Ribos 43.4 8.8 0.00019 29.1 0.3 24 72-103 25-48 (56)
25 PRK14892 putative transcriptio 42.3 10 0.00022 32.3 0.5 36 71-106 19-54 (99)
26 PRK01110 rpmF 50S ribosomal pr 41.3 12 0.00026 29.1 0.7 26 70-104 24-49 (60)
27 COG3529 Predicted nucleic-acid 41.0 7.7 0.00017 31.1 -0.4 33 72-104 9-42 (66)
28 COG1405 SUA7 Transcription ini 39.3 14 0.0003 36.5 1.0 29 74-104 2-30 (285)
29 PF09526 DUF2387: Probable met 37.4 14 0.00031 29.6 0.6 35 72-106 7-42 (71)
30 PLN03119 putative ADP-ribosyla 35.6 20 0.00042 39.3 1.5 30 71-101 21-50 (648)
31 PF09297 zf-NADH-PPase: NADH p 35.6 8.3 0.00018 25.8 -0.8 27 73-103 3-30 (32)
32 PLN03131 hypothetical protein; 34.4 21 0.00046 39.3 1.5 30 71-101 21-50 (705)
33 KOG1598|consensus 34.2 21 0.00045 38.4 1.4 29 74-104 1-29 (521)
34 COG2816 NPY1 NTP pyrophosphohy 34.0 15 0.00033 36.5 0.3 31 72-106 110-141 (279)
35 TIGR01031 rpmF_bact ribosomal 30.6 23 0.00049 27.1 0.7 27 70-104 23-49 (55)
36 PRK00420 hypothetical protein; 30.1 27 0.0006 30.4 1.2 29 72-104 22-50 (112)
37 PF04810 zf-Sec23_Sec24: Sec23 29.8 31 0.00067 24.4 1.3 30 73-102 2-32 (40)
38 PF04161 Arv1: Arv1-like famil 29.7 23 0.0005 32.8 0.8 28 74-101 1-31 (208)
39 smart00778 Prim_Zn_Ribbon Zinc 29.2 33 0.0007 24.6 1.3 28 74-101 4-32 (37)
40 TIGR03573 WbuX N-acetyl sugar 29.0 52 0.0011 32.6 3.1 32 73-106 1-33 (343)
41 PF13248 zf-ribbon_3: zinc-rib 28.9 32 0.0007 22.2 1.1 22 74-102 3-24 (26)
42 PF06689 zf-C4_ClpX: ClpX C4-t 28.8 24 0.00052 25.2 0.5 31 74-104 2-34 (41)
43 KOG0703|consensus 28.8 27 0.00057 35.0 1.0 28 73-101 25-52 (287)
44 PLN03114 ADP-ribosylation fact 28.8 34 0.00074 35.6 1.8 34 72-106 21-54 (395)
45 TIGR02443 conserved hypothetic 28.1 26 0.00057 27.7 0.7 33 72-104 8-41 (59)
46 PRK00085 recO DNA repair prote 27.1 35 0.00075 31.4 1.4 28 74-101 150-177 (247)
47 PF08047 His_leader: Histidine 26.5 34 0.00074 20.7 0.8 7 277-283 9-15 (16)
48 COG3952 Predicted membrane pro 26.0 16 0.00035 32.0 -0.9 21 86-107 76-96 (113)
49 COG1066 Sms Predicted ATP-depe 24.5 33 0.00071 36.3 0.9 28 72-106 6-33 (456)
50 KOG1597|consensus 24.3 40 0.00088 34.1 1.4 30 75-104 2-31 (308)
51 PRK11823 DNA repair protein Ra 23.4 39 0.00084 34.9 1.1 29 71-106 5-33 (446)
52 cd07172 NR_DBD_GR_PR DNA-bindi 22.4 66 0.0014 25.8 2.0 31 74-108 3-33 (78)
53 PF09723 Zn-ribbon_8: Zinc rib 22.2 38 0.00083 24.1 0.6 29 74-102 6-34 (42)
54 PF12760 Zn_Tnp_IS1595: Transp 22.0 48 0.001 23.8 1.1 26 74-101 19-44 (46)
55 PF15396 FAM60A: Protein Famil 21.1 52 0.0011 31.8 1.4 17 96-112 51-67 (213)
56 PRK09727 his operon leader pep 21.0 46 0.001 22.2 0.7 11 276-286 8-18 (26)
57 KOG0818|consensus 20.5 65 0.0014 35.2 2.1 35 73-108 8-42 (669)
58 PF12773 DZR: Double zinc ribb 20.0 66 0.0014 22.9 1.4 12 73-84 12-23 (50)
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=99.56 E-value=1.7e-15 Score=113.49 Aligned_cols=50 Identities=52% Similarity=1.089 Sum_probs=43.4
Q ss_pred ccccCCCCCCcceeeCCCC-CcccchhhHHHHHhCCCCCCcccc-CCCCCCC
Q psy9606 75 TCTNCNTKVTTIWRRYPSG-EMVCNACGLYYRLHCRPRPVSMRR-DNIHPRK 124 (356)
Q Consensus 75 ~CsnCgTt~TP~WRRgp~G-~~LCNACGL~~k~~g~~RP~slkk-~~i~kRk 124 (356)
.|+||++++||+||+++.| .+|||||||||++++..||..++. ..++.++
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~~~~~~~~~ 52 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRKKDQIKRRN 52 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCccccccccc
Confidence 5999999999999999965 689999999999999999999877 4444443
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.48 E-value=2.4e-14 Score=106.32 Aligned_cols=47 Identities=51% Similarity=1.128 Sum_probs=42.3
Q ss_pred CCcccccCCCCCCcceeeCCCCC-cccchhhHHHHHhCCC-CCCccccC
Q psy9606 72 ADLTCTNCNTKVTTIWRRYPSGE-MVCNACGLYYRLHCRP-RPVSMRRD 118 (356)
Q Consensus 72 ~~~~CsnCgTt~TP~WRRgp~G~-~LCNACGL~~k~~g~~-RP~slkk~ 118 (356)
....|+||++++||+||+++.|. +|||||||||+++++. ||..+++.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~~~ 50 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLKKD 50 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCCCCccccccc
Confidence 35789999999999999999997 9999999999999988 88876554
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=99.34 E-value=3.5e-13 Score=93.39 Aligned_cols=35 Identities=51% Similarity=1.122 Sum_probs=28.2
Q ss_pred cccCCCCCCcceeeCCCCCc-ccchhhHHHHHhCCC
Q psy9606 76 CTNCNTKVTTIWRRYPSGEM-VCNACGLYYRLHCRP 110 (356)
Q Consensus 76 CsnCgTt~TP~WRRgp~G~~-LCNACGL~~k~~g~~ 110 (356)
|++|+|++||+||+++.|.. |||+||||+++++++
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~~ 36 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGKM 36 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS-
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCCC
Confidence 89999999999999999984 999999999998764
No 4
>KOG1601|consensus
Probab=98.75 E-value=5.4e-09 Score=90.45 Aligned_cols=52 Identities=42% Similarity=0.862 Sum_probs=46.9
Q ss_pred CcccccCCCCCCcceeeCCCC-CcccchhhHHHHHhCCCCCCccccCCCCCCC
Q psy9606 73 DLTCTNCNTKVTTIWRRYPSG-EMVCNACGLYYRLHCRPRPVSMRRDNIHPRK 124 (356)
Q Consensus 73 ~~~CsnCgTt~TP~WRRgp~G-~~LCNACGL~~k~~g~~RP~slkk~~i~kRk 124 (356)
...|.+|++++||+||+++.| +.+||||||+++++++.|++.+++..+.++.
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~~ 251 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPRN 251 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCccccccc
Confidence 589999999999999999999 7899999999999988888888877776665
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.75 E-value=3.4e-09 Score=108.94 Aligned_cols=56 Identities=46% Similarity=1.003 Sum_probs=51.2
Q ss_pred CCCCcccccCCCCCCcceeeCCC-----CCcccchhhHHHHHhCCCC-CCccccCCCCCCCC
Q psy9606 70 KRADLTCTNCNTKVTTIWRRYPS-----GEMVCNACGLYYRLHCRPR-PVSMRRDNIHPRKR 125 (356)
Q Consensus 70 ~~~~~~CsnCgTt~TP~WRRgp~-----G~~LCNACGL~~k~~g~~R-P~slkk~~i~kRkR 125 (356)
...+.+|.||.|+.||+|||+.. |.+||||||||++.++++| |+.++.+.+++|.+
T Consensus 155 s~~~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~~~ks~~~ 216 (498)
T COG5641 155 SNQPHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDSIKSRSS 216 (498)
T ss_pred ccccchhccccccCCccccccccccccCCccccccccccccccCCcCCCccccccccccccc
Confidence 33455999999999999999999 8899999999999999999 99999999988874
No 6
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=91.62 E-value=0.075 Score=55.78 Aligned_cols=54 Identities=26% Similarity=0.409 Sum_probs=43.2
Q ss_pred CcccccCCC-CCCcceeeCCC-CCcccchhhHHHHHhCCCCCCccccCCCCCCCCC
Q psy9606 73 DLTCTNCNT-KVTTIWRRYPS-GEMVCNACGLYYRLHCRPRPVSMRRDNIHPRKRR 126 (356)
Q Consensus 73 ~~~CsnCgT-t~TP~WRRgp~-G~~LCNACGL~~k~~g~~RP~slkk~~i~kRkRk 126 (356)
...|.+|.+ +.||.|||... .-++||+|+++.+..+.+||+..|-+...+|.+.
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d~n~~~~~~ 352 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPNSKRSNA 352 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCcccccccCCCCChhhhhhhh
Confidence 457888877 78888887754 4689999999999999999998877766555544
No 7
>KOG3554|consensus
Probab=85.26 E-value=0.59 Score=49.54 Aligned_cols=38 Identities=21% Similarity=0.600 Sum_probs=31.4
Q ss_pred CCcccccCCCCCCcceee-CCCC-C-cccchhhHHHHHhCC
Q psy9606 72 ADLTCTNCNTKVTTIWRR-YPSG-E-MVCNACGLYYRLHCR 109 (356)
Q Consensus 72 ~~~~CsnCgTt~TP~WRR-gp~G-~-~LCNACGL~~k~~g~ 109 (356)
..+.|.+|+|+++-.|-. |+-+ + .||-.|-+|||+++.
T Consensus 385 ~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygG 425 (693)
T KOG3554|consen 385 DGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGG 425 (693)
T ss_pred CCCcccccccccccceeccCCCCccchhhHHHHHHHHHhcC
Confidence 467999999999999864 5555 4 799999999999874
No 8
>KOG3740|consensus
Probab=79.64 E-value=0.74 Score=49.94 Aligned_cols=35 Identities=26% Similarity=0.651 Sum_probs=30.3
Q ss_pred CCCCcccccCCCCCCcceeeCCCC----CcccchhhHHH
Q psy9606 70 KRADLTCTNCNTKVTTIWRRYPSG----EMVCNACGLYY 104 (356)
Q Consensus 70 ~~~~~~CsnCgTt~TP~WRRgp~G----~~LCNACGL~~ 104 (356)
...+..|..|.|..||.|+.-+.+ +++|.+|-.-.
T Consensus 459 a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSn 497 (706)
T KOG3740|consen 459 ATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSN 497 (706)
T ss_pred cCCchhhhhcccccccccccccccCcchHHHHHhhhhhc
Confidence 456899999999999999999888 68999996543
No 9
>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=74.93 E-value=1.3 Score=31.37 Aligned_cols=29 Identities=38% Similarity=0.950 Sum_probs=20.4
Q ss_pred cccccCCCCCCcceeeCCCCCcccchhhHHH
Q psy9606 74 LTCTNCNTKVTTIWRRYPSGEMVCNACGLYY 104 (356)
Q Consensus 74 ~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~ 104 (356)
..|.+|+.+. ..+ ....|..+|..||+-.
T Consensus 1 m~Cp~Cg~~~-~~~-D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKE-IVF-DPERGELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSE-EEE-ETTTTEEEETTT-BBE
T ss_pred CCCcCCcCCc-eEE-cCCCCeEECCCCCCEe
Confidence 3699999977 343 2456889999999743
No 10
>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=63.62 E-value=6.5 Score=33.17 Aligned_cols=37 Identities=19% Similarity=0.468 Sum_probs=26.4
Q ss_pred CCcccccCCCCCCcceeeCCCCCcccchhhHHHHHhCC
Q psy9606 72 ADLTCTNCNTKVTTIWRRYPSGEMVCNACGLYYRLHCR 109 (356)
Q Consensus 72 ~~~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~k~~g~ 109 (356)
....|.+|+... |.|-.-.-|-.||-.|.-..|..++
T Consensus 12 ~N~~CaDCg~~~-p~w~s~~~GiflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 12 GNKVCADCGAPN-PTWASLNYGIFLCLECAGIHRSLGV 48 (116)
T ss_dssp TCTB-TTT-SBS---EEETTTTEEE-HHHHHHHHHHTT
T ss_pred CcCcCCCCCCCC-CCEEEeecChhhhHHHHHHHHHhcc
Confidence 348999999555 4999999999999999888877763
No 11
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=59.22 E-value=3.5 Score=36.69 Aligned_cols=30 Identities=23% Similarity=0.531 Sum_probs=22.6
Q ss_pred CcccccCCCCCCcceeeCCCCCcccchhhH
Q psy9606 73 DLTCTNCNTKVTTIWRRYPSGEMVCNACGL 102 (356)
Q Consensus 73 ~~~CsnCgTt~TP~WRRgp~G~~LCNACGL 102 (356)
--.|..|+..+|-+-+++..=...|+|||-
T Consensus 102 yVlC~~C~spdT~l~k~~r~~~l~C~ACGa 131 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIWVLKCEACGA 131 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeEEEEcccCCC
Confidence 468999999999986642211358999986
No 12
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=57.87 E-value=4 Score=36.16 Aligned_cols=30 Identities=30% Similarity=0.604 Sum_probs=22.4
Q ss_pred CcccccCCCCCCcceeeCCCCCcccchhhH
Q psy9606 73 DLTCTNCNTKVTTIWRRYPSGEMVCNACGL 102 (356)
Q Consensus 73 ~~~CsnCgTt~TP~WRRgp~G~~LCNACGL 102 (356)
--.|..|+..+|-+-+.+..=...|+|||-
T Consensus 97 yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa 126 (133)
T TIGR00311 97 YVICRECNRPDTRIIKEGRVSLLKCEACGA 126 (133)
T ss_pred eEECCCCCCCCcEEEEeCCeEEEecccCCC
Confidence 368999999999987643211258999986
No 13
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=57.17 E-value=5.6 Score=30.62 Aligned_cols=27 Identities=30% Similarity=0.719 Sum_probs=20.6
Q ss_pred CCCCcccccCCCCCCcceeeCCCCCcccchhhHHH
Q psy9606 70 KRADLTCTNCNTKVTTIWRRYPSGEMVCNACGLYY 104 (356)
Q Consensus 70 ~~~~~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~ 104 (356)
......|.+||...-| ..+|..||+|.
T Consensus 24 ~~~l~~C~~CG~~~~~--------H~vC~~CG~Y~ 50 (57)
T PRK12286 24 APGLVECPNCGEPKLP--------HRVCPSCGYYK 50 (57)
T ss_pred CCcceECCCCCCccCC--------eEECCCCCcCC
Confidence 4445679999987766 46999999764
No 14
>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=56.20 E-value=6.4 Score=27.70 Aligned_cols=26 Identities=27% Similarity=0.805 Sum_probs=21.8
Q ss_pred CcccccCCCCCCcceeeCCCCCcccchhhH
Q psy9606 73 DLTCTNCNTKVTTIWRRYPSGEMVCNACGL 102 (356)
Q Consensus 73 ~~~CsnCgTt~TP~WRRgp~G~~LCNACGL 102 (356)
...|..|+.. |-...+|...|..||-
T Consensus 8 ~~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CCcCCCCCCe----EeEccCCEEEhhhCce
Confidence 3569999987 7778889999999985
No 15
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=55.90 E-value=4.6 Score=34.65 Aligned_cols=29 Identities=24% Similarity=0.560 Sum_probs=21.8
Q ss_pred cccccCCCCCCcceeeCCCCCcccchhhH
Q psy9606 74 LTCTNCNTKVTTIWRRYPSGEMVCNACGL 102 (356)
Q Consensus 74 ~~CsnCgTt~TP~WRRgp~G~~LCNACGL 102 (356)
-.|..|+..+|-+-+.+..=...|+|||-
T Consensus 81 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 68999999999987652211257999983
No 16
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=51.48 E-value=5.5 Score=37.09 Aligned_cols=30 Identities=23% Similarity=0.531 Sum_probs=22.5
Q ss_pred CcccccCCCCCCcceeeCCCCCcccchhhH
Q psy9606 73 DLTCTNCNTKVTTIWRRYPSGEMVCNACGL 102 (356)
Q Consensus 73 ~~~CsnCgTt~TP~WRRgp~G~~LCNACGL 102 (356)
--.|..|+..+|-+-+.+..=...|+|||-
T Consensus 98 yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa 127 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDRVLMLRCDACGA 127 (201)
T ss_pred eEECCCCCCCCcEEEEcCCeEEEEcccCCC
Confidence 368999999999987653211258999987
No 17
>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=51.08 E-value=13 Score=31.20 Aligned_cols=36 Identities=19% Similarity=0.462 Sum_probs=30.3
Q ss_pred CcccccCCCCCCcceeeCCCCCcccchhhHHHHHhCC
Q psy9606 73 DLTCTNCNTKVTTIWRRYPSGEMVCNACGLYYRLHCR 109 (356)
Q Consensus 73 ~~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~k~~g~ 109 (356)
...|.+|+. .-|.|-.-.-|-.||-.|.-..|..+.
T Consensus 3 N~~CaDC~~-~~p~w~s~~~GifvC~~CsgiHR~lg~ 38 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLGVFLCIECSGIHRSLGV 38 (112)
T ss_pred CCcccCCCC-CCCCcEEeccceeEhHHhHHHHHhcCC
Confidence 368999998 559999999999999999887777664
No 18
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=49.25 E-value=10 Score=38.11 Aligned_cols=29 Identities=21% Similarity=0.720 Sum_probs=26.7
Q ss_pred CCcccccCCCCCCcceeeCCCCCcccchhh
Q psy9606 72 ADLTCTNCNTKVTTIWRRYPSGEMVCNACG 101 (356)
Q Consensus 72 ~~~~CsnCgTt~TP~WRRgp~G~~LCNACG 101 (356)
....|..|++.. |+|-.-.-|-.||--|.
T Consensus 19 ~Nk~CaDCga~~-P~W~S~nlGvfiCi~Ca 47 (319)
T COG5347 19 SNKKCADCGAPN-PTWASVNLGVFLCIDCA 47 (319)
T ss_pred ccCccccCCCCC-CceEecccCeEEEeecc
Confidence 458999999999 99999999999999994
No 19
>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=46.87 E-value=9.5 Score=33.38 Aligned_cols=29 Identities=24% Similarity=0.537 Sum_probs=22.8
Q ss_pred cccccCCCCCCcceeeCCCCCcccchhhH
Q psy9606 74 LTCTNCNTKVTTIWRRYPSGEMVCNACGL 102 (356)
Q Consensus 74 ~~CsnCgTt~TP~WRRgp~G~~LCNACGL 102 (356)
-.|..|+..+|-+-+.+..=...|+|||-
T Consensus 94 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred EEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 57999999999987773333469999983
No 20
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=46.60 E-value=11 Score=36.93 Aligned_cols=30 Identities=40% Similarity=1.020 Sum_probs=22.0
Q ss_pred CcccccCCCCCCcceeeCCCCCcccchhhHHH
Q psy9606 73 DLTCTNCNTKVTTIWRRYPSGEMVCNACGLYY 104 (356)
Q Consensus 73 ~~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~ 104 (356)
...|.+|+.+ .-... -..|.++|..||+-.
T Consensus 11 ~~~Cp~Cg~~-~iv~d-~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 11 KLVCPECGSD-KLIYD-YERGEIVCADCGLVI 40 (310)
T ss_pred CCcCcCCCCC-CeeEE-CCCCeEeecccCCcc
Confidence 4689999963 23343 468999999999844
No 21
>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=45.24 E-value=11 Score=27.47 Aligned_cols=26 Identities=35% Similarity=0.897 Sum_probs=20.5
Q ss_pred CCcccccCCCCCCcceeeCCCCCcccchhh
Q psy9606 72 ADLTCTNCNTKVTTIWRRYPSGEMVCNACG 101 (356)
Q Consensus 72 ~~~~CsnCgTt~TP~WRRgp~G~~LCNACG 101 (356)
....|..|+ +|+-| ..+|+++|-.|+
T Consensus 16 L~~~Cp~C~---~PL~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCPDCG---TPLMR-DKDGKIYCVSCG 41 (41)
T ss_pred hcCccCCCC---CeeEE-ecCCCEECCCCC
Confidence 346798994 89888 567889999985
No 22
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=44.42 E-value=8.1 Score=27.05 Aligned_cols=26 Identities=46% Similarity=1.100 Sum_probs=12.6
Q ss_pred cccccCCCCCCcceeeCCCC---C-cccchhhH
Q psy9606 74 LTCTNCNTKVTTIWRRYPSG---E-MVCNACGL 102 (356)
Q Consensus 74 ~~CsnCgTt~TP~WRRgp~G---~-~LCNACGL 102 (356)
..|.+||...+ ++-++| . .+|.+||.
T Consensus 1 kfC~~CG~~l~---~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLE---RRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-E---EE--TT-SS-EEEETTTTE
T ss_pred CccccccChhh---hhcCCCCCccceECCCCCC
Confidence 36999998743 233433 2 69999985
No 23
>PLN03106 TCP2 Protein TCP2; Provisional
Probab=43.55 E-value=52 Score=34.43 Aligned_cols=56 Identities=34% Similarity=0.530 Sum_probs=39.6
Q ss_pred eehhhhhhhccccCCcccCCCCCCCCC-----ccccc--cCCccccCCccccccCCCCCCCCCCC
Q psy9606 221 ISLHSFISASLHHAPFNVGAPGGNSPP-----SHYAL--NLSPLCEDNLPLNLAAGPPAEHSHHH 278 (356)
Q Consensus 221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (356)
..|---||..| +-||-|.--.||++ -|+-- .-+|+-..|||+-+.|.|.++|.|+|
T Consensus 361 ynLnfsiSSg~--~gfNRGtLQSNS~sh~s~~~~lqr~sts~~~dgsn~pF~~gaa~~~~~~~~~ 423 (447)
T PLN03106 361 FNLNFTISSGL--AGFNRGTLQSNSTSHQSLLPHLQRFSTSEPIDGSNVPFFFGAAPAENHHHNH 423 (447)
T ss_pred cceeeEeeccc--ccccccccccCCCcccccchHHHhhccCCCCCCCccceeecccchhhccccc
Confidence 34444566666 89999999999976 23221 12488888999999998888765553
No 24
>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=43.39 E-value=8.8 Score=29.06 Aligned_cols=24 Identities=33% Similarity=0.847 Sum_probs=17.4
Q ss_pred CCcccccCCCCCCcceeeCCCCCcccchhhHH
Q psy9606 72 ADLTCTNCNTKVTTIWRRYPSGEMVCNACGLY 103 (356)
Q Consensus 72 ~~~~CsnCgTt~TP~WRRgp~G~~LCNACGL~ 103 (356)
....|.+||...-| +.+|..||.|
T Consensus 25 ~l~~c~~cg~~~~~--------H~vc~~cG~y 48 (56)
T PF01783_consen 25 NLVKCPNCGEPKLP--------HRVCPSCGYY 48 (56)
T ss_dssp SEEESSSSSSEEST--------TSBCTTTBBS
T ss_pred ceeeeccCCCEecc--------cEeeCCCCeE
Confidence 55789999964433 3699999943
No 25
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=42.34 E-value=10 Score=32.28 Aligned_cols=36 Identities=19% Similarity=0.522 Sum_probs=22.5
Q ss_pred CCCcccccCCCCCCcceeeCCCCCcccchhhHHHHH
Q psy9606 71 RADLTCTNCNTKVTTIWRRYPSGEMVCNACGLYYRL 106 (356)
Q Consensus 71 ~~~~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~k~ 106 (356)
.....|.+|+...-+.=+...-++..|-.||+|+-.
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 345789999953322211112346899999998733
No 26
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=41.35 E-value=12 Score=29.05 Aligned_cols=26 Identities=12% Similarity=-0.078 Sum_probs=19.3
Q ss_pred CCCCcccccCCCCCCcceeeCCCCCcccchhhHHH
Q psy9606 70 KRADLTCTNCNTKVTTIWRRYPSGEMVCNACGLYY 104 (356)
Q Consensus 70 ~~~~~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~ 104 (356)
......|.+||+..-|- .+|. ||.|.
T Consensus 24 ~~~~~~c~~cg~~~~pH--------~vc~-cG~Y~ 49 (60)
T PRK01110 24 APTLSVDKTTGEYHLPH--------HVSP-KGYYK 49 (60)
T ss_pred CCceeEcCCCCceeccc--------eecC-CcccC
Confidence 33457899999877664 4899 99764
No 27
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=40.99 E-value=7.7 Score=31.09 Aligned_cols=33 Identities=27% Similarity=0.599 Sum_probs=25.4
Q ss_pred CCcccccCCCCCCcc-eeeCCCCCcccchhhHHH
Q psy9606 72 ADLTCTNCNTKVTTI-WRRYPSGEMVCNACGLYY 104 (356)
Q Consensus 72 ~~~~CsnCgTt~TP~-WRRgp~G~~LCNACGL~~ 104 (356)
..-.|-.|.+..|-. ||.+.--..-|.+||...
T Consensus 9 AGA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 9 AGAVCPACQAQDTLAMWRENNVEIVECVKCGHHM 42 (66)
T ss_pred ccCCCcccchhhHHHHHHhcCCceEehhhcchHh
Confidence 457899999999985 655544457999999866
No 28
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=39.28 E-value=14 Score=36.47 Aligned_cols=29 Identities=38% Similarity=0.982 Sum_probs=20.8
Q ss_pred cccccCCCCCCcceeeCCCCCcccchhhHHH
Q psy9606 74 LTCTNCNTKVTTIWRRYPSGEMVCNACGLYY 104 (356)
Q Consensus 74 ~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~ 104 (356)
..|.+|+.+ .-.| .-..|+.+|-.||+-.
T Consensus 2 ~~CpeCg~~-~~~~-d~~~ge~VC~~CG~Vi 30 (285)
T COG1405 2 MSCPECGST-NIIT-DYERGEIVCADCGLVL 30 (285)
T ss_pred CCCCCCCCc-ccee-eccCCeEEeccCCEEe
Confidence 579999988 2222 2246889999999854
No 29
>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=37.39 E-value=14 Score=29.62 Aligned_cols=35 Identities=29% Similarity=0.490 Sum_probs=27.0
Q ss_pred CCcccccCCCCCCcceeeCCCCC-cccchhhHHHHH
Q psy9606 72 ADLTCTNCNTKVTTIWRRYPSGE-MVCNACGLYYRL 106 (356)
Q Consensus 72 ~~~~CsnCgTt~TP~WRRgp~G~-~LCNACGL~~k~ 106 (356)
..-.|-.|.+..|-+|.+...-+ .-|-+||.....
T Consensus 7 AGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQ 42 (71)
T ss_pred cCccCCCCcCccEEEEEEeCCceEEEecCCCCeecc
Confidence 45789999999999766655554 699999985543
No 30
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=35.64 E-value=20 Score=39.26 Aligned_cols=30 Identities=27% Similarity=0.482 Sum_probs=25.6
Q ss_pred CCCcccccCCCCCCcceeeCCCCCcccchhh
Q psy9606 71 RADLTCTNCNTKVTTIWRRYPSGEMVCNACG 101 (356)
Q Consensus 71 ~~~~~CsnCgTt~TP~WRRgp~G~~LCNACG 101 (356)
.....|.+|+... |.|---..|-.+|-.|.
T Consensus 21 PgNk~CADCgs~~-P~WASiNlGIFICi~CS 50 (648)
T PLN03119 21 PPNRRCINCNSLG-PQYVCTTFWTFVCMACS 50 (648)
T ss_pred cCCCccccCCCCC-CCceeeccceEEeccch
Confidence 3458999999866 99999999999999993
No 31
>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=35.56 E-value=8.3 Score=25.85 Aligned_cols=27 Identities=26% Similarity=0.668 Sum_probs=15.8
Q ss_pred CcccccCCCCCCcceeeCCCC-CcccchhhHH
Q psy9606 73 DLTCTNCNTKVTTIWRRYPSG-EMVCNACGLY 103 (356)
Q Consensus 73 ~~~CsnCgTt~TP~WRRgp~G-~~LCNACGL~ 103 (356)
-+.|..||....+. +.| ..+|.+||..
T Consensus 3 ~rfC~~CG~~t~~~----~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA----PGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-----SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCC----CCcCEeECCCCcCE
Confidence 37899999988776 234 3699999874
No 32
>PLN03131 hypothetical protein; Provisional
Probab=34.37 E-value=21 Score=39.30 Aligned_cols=30 Identities=20% Similarity=0.466 Sum_probs=25.4
Q ss_pred CCCcccccCCCCCCcceeeCCCCCcccchhh
Q psy9606 71 RADLTCTNCNTKVTTIWRRYPSGEMVCNACG 101 (356)
Q Consensus 71 ~~~~~CsnCgTt~TP~WRRgp~G~~LCNACG 101 (356)
.....|.+|+.. -|.|-.-..|-.||-.|.
T Consensus 21 PgNk~CADCga~-~P~WASiNlGIFICi~CS 50 (705)
T PLN03131 21 PPNRRCINCNSL-GPQFVCTNFWTFICMTCS 50 (705)
T ss_pred cCCCccccCCCC-CCCeeEeccceEEchhch
Confidence 345899999975 499999899999999994
No 33
>KOG1598|consensus
Probab=34.19 E-value=21 Score=38.36 Aligned_cols=29 Identities=31% Similarity=0.775 Sum_probs=20.5
Q ss_pred cccccCCCCCCcceeeCCCCCcccchhhHHH
Q psy9606 74 LTCTNCNTKVTTIWRRYPSGEMVCNACGLYY 104 (356)
Q Consensus 74 ~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~ 104 (356)
+.|.||+.++=- |+-..|...|++||.-.
T Consensus 1 ~~C~~C~~s~fe--~d~a~g~~~C~~CG~v~ 29 (521)
T KOG1598|consen 1 MVCKNCGGSNFE--RDEATGNLYCTACGTVL 29 (521)
T ss_pred CcCCCCCCCCcc--cccccCCceecccccee
Confidence 469999876533 23356888999999743
No 34
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=33.96 E-value=15 Score=36.51 Aligned_cols=31 Identities=29% Similarity=0.489 Sum_probs=24.2
Q ss_pred CCcccccCCCCCCcceeeCCCC-CcccchhhHHHHH
Q psy9606 72 ADLTCTNCNTKVTTIWRRYPSG-EMVCNACGLYYRL 106 (356)
Q Consensus 72 ~~~~CsnCgTt~TP~WRRgp~G-~~LCNACGL~~k~ 106 (356)
.-+.|..||++..+. ..| ..+|+.||..++.
T Consensus 110 ~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 110 SHRFCGRCGTKTYPR----EGGWARVCPKCGHEHFP 141 (279)
T ss_pred hCcCCCCCCCcCccc----cCceeeeCCCCCCccCC
Confidence 458999999999886 233 4799999987654
No 35
>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=30.59 E-value=23 Score=27.06 Aligned_cols=27 Identities=30% Similarity=0.656 Sum_probs=19.4
Q ss_pred CCCCcccccCCCCCCcceeeCCCCCcccchhhHHH
Q psy9606 70 KRADLTCTNCNTKVTTIWRRYPSGEMVCNACGLYY 104 (356)
Q Consensus 70 ~~~~~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~ 104 (356)
......|.+||...-|= .+|-.||.|-
T Consensus 23 ~p~l~~C~~cG~~~~~H--------~vc~~cG~Y~ 49 (55)
T TIGR01031 23 APTLVVCPNCGEFKLPH--------RVCPSCGYYK 49 (55)
T ss_pred CCcceECCCCCCcccCe--------eECCccCeEC
Confidence 34456799999865543 5999999653
No 36
>PRK00420 hypothetical protein; Validated
Probab=30.07 E-value=27 Score=30.38 Aligned_cols=29 Identities=28% Similarity=0.659 Sum_probs=22.1
Q ss_pred CCcccccCCCCCCcceeeCCCCCcccchhhHHH
Q psy9606 72 ADLTCTNCNTKVTTIWRRYPSGEMVCNACGLYY 104 (356)
Q Consensus 72 ~~~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~ 104 (356)
....|..|| +|+.|- .+|+.+|-.||-.+
T Consensus 22 l~~~CP~Cg---~pLf~l-k~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 22 LSKHCPVCG---LPLFEL-KDGEVVCPVHGKVY 50 (112)
T ss_pred ccCCCCCCC---Ccceec-CCCceECCCCCCee
Confidence 347899999 566653 67889999999754
No 37
>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=29.78 E-value=31 Score=24.36 Aligned_cols=30 Identities=23% Similarity=0.668 Sum_probs=17.9
Q ss_pred CcccccCCCCCCcceeeCCCCC-cccchhhH
Q psy9606 73 DLTCTNCNTKVTTIWRRYPSGE-MVCNACGL 102 (356)
Q Consensus 73 ~~~CsnCgTt~TP~WRRgp~G~-~LCNACGL 102 (356)
+.+|..|++-.-|-=+-+..|+ -.||-|+.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCC
Confidence 5789999999988655566666 49999986
No 38
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=29.74 E-value=23 Score=32.83 Aligned_cols=28 Identities=32% Similarity=1.015 Sum_probs=23.4
Q ss_pred cccccCCCCCCcceeeCCCCC---cccchhh
Q psy9606 74 LTCTNCNTKVTTIWRRYPSGE---MVCNACG 101 (356)
Q Consensus 74 ~~CsnCgTt~TP~WRRgp~G~---~LCNACG 101 (356)
..|.+||.....++|+-..|. +.|..|+
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~ 31 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCG 31 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccC
Confidence 479999999998999876663 6899997
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=29.23 E-value=33 Score=24.57 Aligned_cols=28 Identities=25% Similarity=0.583 Sum_probs=21.0
Q ss_pred cccccCCCCCCcceee-CCCCCcccchhh
Q psy9606 74 LTCTNCNTKVTTIWRR-YPSGEMVCNACG 101 (356)
Q Consensus 74 ~~CsnCgTt~TP~WRR-gp~G~~LCNACG 101 (356)
..|-.|+.+..=.|.. ...|..+|+.|+
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg 32 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCG 32 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCC
Confidence 5799999887777653 334668999996
No 40
>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=28.97 E-value=52 Score=32.62 Aligned_cols=32 Identities=25% Similarity=0.371 Sum_probs=21.9
Q ss_pred CcccccCCCCCCc-ceeeCCCCCcccchhhHHHHH
Q psy9606 73 DLTCTNCNTKVTT-IWRRYPSGEMVCNACGLYYRL 106 (356)
Q Consensus 73 ~~~CsnCgTt~TP-~WRRgp~G~~LCNACGL~~k~ 106 (356)
+..|..|.-.+|- .-.=+.+| +||+|-.+.++
T Consensus 1 ~~~C~~C~~~~t~p~i~fd~~G--vC~~C~~~~~~ 33 (343)
T TIGR03573 1 MKFCKRCVMPTTRPGITFDEDG--VCSACRNFEEK 33 (343)
T ss_pred CCcCCCCCCCCCCCCeeECCCC--CchhhhhHHhh
Confidence 3689999776654 33334555 89999887754
No 41
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=28.88 E-value=32 Score=22.21 Aligned_cols=22 Identities=27% Similarity=0.892 Sum_probs=15.7
Q ss_pred cccccCCCCCCcceeeCCCCCcccchhhH
Q psy9606 74 LTCTNCNTKVTTIWRRYPSGEMVCNACGL 102 (356)
Q Consensus 74 ~~CsnCgTt~TP~WRRgp~G~~LCNACGL 102 (356)
..|.+|++...+ +...|-.||-
T Consensus 3 ~~Cp~Cg~~~~~-------~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDP-------DAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCc-------ccccChhhCC
Confidence 679999985433 4467888874
No 42
>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=28.82 E-value=24 Score=25.23 Aligned_cols=31 Identities=23% Similarity=0.549 Sum_probs=19.4
Q ss_pred cccccCCCCCCccee--eCCCCCcccchhhHHH
Q psy9606 74 LTCTNCNTKVTTIWR--RYPSGEMVCNACGLYY 104 (356)
Q Consensus 74 ~~CsnCgTt~TP~WR--Rgp~G~~LCNACGL~~ 104 (356)
..|+-||.+++..-+ .|+.|...|+.|...-
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~ 34 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVEQA 34 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHHHH
Confidence 579999998886532 6776778999997543
No 43
>KOG0703|consensus
Probab=28.82 E-value=27 Score=34.99 Aligned_cols=28 Identities=25% Similarity=0.839 Sum_probs=25.5
Q ss_pred CcccccCCCCCCcceeeCCCCCcccchhh
Q psy9606 73 DLTCTNCNTKVTTIWRRYPSGEMVCNACG 101 (356)
Q Consensus 73 ~~~CsnCgTt~TP~WRRgp~G~~LCNACG 101 (356)
...|+.|++. .|.|..-.-|--+|--|.
T Consensus 25 N~~CADC~a~-~P~WaSwnlGvFiC~~C~ 52 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWASWNLGVFICLRCA 52 (287)
T ss_pred cCcccccCCC-CCCeEEeecCeEEEeecc
Confidence 5899999999 999999889988999994
No 44
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=28.81 E-value=34 Score=35.58 Aligned_cols=34 Identities=26% Similarity=0.621 Sum_probs=27.3
Q ss_pred CCcccccCCCCCCcceeeCCCCCcccchhhHHHHH
Q psy9606 72 ADLTCTNCNTKVTTIWRRYPSGEMVCNACGLYYRL 106 (356)
Q Consensus 72 ~~~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~k~ 106 (356)
....|..|+... |.|-.-..|-.||..|.=..|.
T Consensus 21 gNk~CaDCga~n-PtWASvn~GIFLCl~CSGVHRs 54 (395)
T PLN03114 21 DNKICFDCNAKN-PTWASVTYGIFLCIDCSAVHRS 54 (395)
T ss_pred CCCcCccCCCCC-CCceeeccceeehhhhhHhhcc
Confidence 347899999864 9999999999999999544433
No 45
>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=28.08 E-value=26 Score=27.68 Aligned_cols=33 Identities=24% Similarity=0.443 Sum_probs=25.0
Q ss_pred CCcccccCCCCCCcceeeCCCCC-cccchhhHHH
Q psy9606 72 ADLTCTNCNTKVTTIWRRYPSGE-MVCNACGLYY 104 (356)
Q Consensus 72 ~~~~CsnCgTt~TP~WRRgp~G~-~LCNACGL~~ 104 (356)
..-.|-.|.+..|-+|.+...-+ .-|-.||...
T Consensus 8 AGA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 8 AGAVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 45789999999999755443333 7999999854
No 46
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=27.13 E-value=35 Score=31.37 Aligned_cols=28 Identities=25% Similarity=0.568 Sum_probs=24.2
Q ss_pred cccccCCCCCCcceeeCCCCCcccchhh
Q psy9606 74 LTCTNCNTKVTTIWRRYPSGEMVCNACG 101 (356)
Q Consensus 74 ~~CsnCgTt~TP~WRRgp~G~~LCNACG 101 (356)
..|..||+.....|-.-.+|..+|..|+
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccCCccccccc
Confidence 5899999988777777788889999996
No 47
>PF08047 His_leader: Histidine operon leader peptide; InterPro: IPR012565 This family consists of the leader peptide of the histidine (his) operon. The his operon contains all the genes necessary for histidine biosynthesis. The region corresponding to the untranslated 5'-end of the transcript, named the his leader region, displays the typical features of the T box transcriptional attenuation mechanism which is involved in the regulation of many amino acid biosynthetic operons [].; GO: 0000105 histidine biosynthetic process
Probab=26.49 E-value=34 Score=20.70 Aligned_cols=7 Identities=71% Similarity=1.365 Sum_probs=2.9
Q ss_pred CCCCCCC
Q psy9606 277 HHSHHHH 283 (356)
Q Consensus 277 ~~~~~~~ 283 (356)
||.|||-
T Consensus 9 hhhhhhp 15 (16)
T PF08047_consen 9 HHHHHHP 15 (16)
T ss_pred cccccCC
Confidence 3444443
No 48
>COG3952 Predicted membrane protein [Function unknown]
Probab=25.98 E-value=16 Score=32.05 Aligned_cols=21 Identities=38% Similarity=0.651 Sum_probs=14.9
Q ss_pred ceeeCCCCCcccchhhHHHHHh
Q psy9606 86 IWRRYPSGEMVCNACGLYYRLH 107 (356)
Q Consensus 86 ~WRRgp~G~~LCNACGL~~k~~ 107 (356)
+||+++-+ .+|++|||+-...
T Consensus 76 i~~~DpV~-Vl~~~~glF~~l~ 96 (113)
T COG3952 76 IRRQDPVF-VLGQACGLFIYLR 96 (113)
T ss_pred HHhcchHH-HHHHhhhHHHHHH
Confidence 35555554 6999999987553
No 49
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=24.49 E-value=33 Score=36.35 Aligned_cols=28 Identities=32% Similarity=0.903 Sum_probs=20.8
Q ss_pred CCcccccCCCCCCcceeeCCCCCcccchhhHHHHH
Q psy9606 72 ADLTCTNCNTKVTTIWRRYPSGEMVCNACGLYYRL 106 (356)
Q Consensus 72 ~~~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~k~ 106 (356)
....|.+||+. .|.| .| -|..||-|--.
T Consensus 6 t~f~C~~CG~~-s~KW----~G--kCp~Cg~Wns~ 33 (456)
T COG1066 6 TAFVCQECGYV-SPKW----LG--KCPACGAWNTL 33 (456)
T ss_pred cEEEcccCCCC-Cccc----cc--cCCCCCCccce
Confidence 45899999975 6788 35 39999976543
No 50
>KOG1597|consensus
Probab=24.31 E-value=40 Score=34.09 Aligned_cols=30 Identities=30% Similarity=0.808 Sum_probs=23.7
Q ss_pred ccccCCCCCCcceeeCCCCCcccchhhHHH
Q psy9606 75 TCTNCNTKVTTIWRRYPSGEMVCNACGLYY 104 (356)
Q Consensus 75 ~CsnCgTt~TP~WRRgp~G~~LCNACGL~~ 104 (356)
.|..|....-.+--.-..|.++|-.|||-+
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl 31 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLVL 31 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCeee
Confidence 589997765566666677889999999965
No 51
>PRK11823 DNA repair protein RadA; Provisional
Probab=23.37 E-value=39 Score=34.86 Aligned_cols=29 Identities=28% Similarity=0.906 Sum_probs=20.0
Q ss_pred CCCcccccCCCCCCcceeeCCCCCcccchhhHHHHH
Q psy9606 71 RADLTCTNCNTKVTTIWRRYPSGEMVCNACGLYYRL 106 (356)
Q Consensus 71 ~~~~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~k~ 106 (356)
+....|.+||.+... |. | .|.+|+-|--.
T Consensus 5 ~~~y~C~~Cg~~~~~-~~----g--~Cp~C~~w~t~ 33 (446)
T PRK11823 5 KTAYVCQECGAESPK-WL----G--RCPECGAWNTL 33 (446)
T ss_pred CCeEECCcCCCCCcc-cC----e--eCcCCCCccce
Confidence 445899999986544 41 2 49999876633
No 52
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=22.45 E-value=66 Score=25.80 Aligned_cols=31 Identities=16% Similarity=0.626 Sum_probs=21.9
Q ss_pred cccccCCCCCCcceeeCCCCCcccchhhHHHHHhC
Q psy9606 74 LTCTNCNTKVTTIWRRYPSGEMVCNACGLYYRLHC 108 (356)
Q Consensus 74 ~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~k~~g 108 (356)
..|.-|+...+-.+ -|...|+||..++++.-
T Consensus 3 ~~C~VCg~~a~g~h----yGv~sC~aC~~FFRR~v 33 (78)
T cd07172 3 KICLVCSDEASGCH----YGVLTCGSCKVFFKRAV 33 (78)
T ss_pred CCCeecCCcCcceE----ECceeehhhHHhHHHHe
Confidence 46888986544432 35678999999997743
No 53
>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=22.23 E-value=38 Score=24.07 Aligned_cols=29 Identities=17% Similarity=0.535 Sum_probs=19.7
Q ss_pred cccccCCCCCCcceeeCCCCCcccchhhH
Q psy9606 74 LTCTNCNTKVTTIWRRYPSGEMVCNACGL 102 (356)
Q Consensus 74 ~~CsnCgTt~TP~WRRgp~G~~LCNACGL 102 (356)
..|..||..-+-+..-.......|-.||-
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 57889987766655444433468999875
No 54
>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=22.01 E-value=48 Score=23.78 Aligned_cols=26 Identities=23% Similarity=0.695 Sum_probs=19.0
Q ss_pred cccccCCCCCCcceeeCCCCCcccchhh
Q psy9606 74 LTCTNCNTKVTTIWRRYPSGEMVCNACG 101 (356)
Q Consensus 74 ~~CsnCgTt~TP~WRRgp~G~~LCNACG 101 (356)
.+|..|+.+ ...|-++ .+...|++|+
T Consensus 19 ~~CP~Cg~~-~~~~~~~-~~~~~C~~C~ 44 (46)
T PF12760_consen 19 FVCPHCGST-KHYRLKT-RGRYRCKACR 44 (46)
T ss_pred CCCCCCCCe-eeEEeCC-CCeEECCCCC
Confidence 679999998 4444444 5667999996
No 55
>PF15396 FAM60A: Protein Family FAM60A
Probab=21.05 E-value=52 Score=31.78 Aligned_cols=17 Identities=35% Similarity=0.704 Sum_probs=13.3
Q ss_pred ccchhhHHHHHhCCCCC
Q psy9606 96 VCNACGLYYRLHCRPRP 112 (356)
Q Consensus 96 LCNACGL~~k~~g~~RP 112 (356)
+||||-|..++.++.-+
T Consensus 51 ICNACVLLVKRwKKLP~ 67 (213)
T PF15396_consen 51 ICNACVLLVKRWKKLPP 67 (213)
T ss_pred hhHHHHHHHHHHhhCCC
Confidence 79999999988665443
No 56
>PRK09727 his operon leader peptide; Provisional
Probab=21.02 E-value=46 Score=22.22 Aligned_cols=11 Identities=64% Similarity=1.186 Sum_probs=6.1
Q ss_pred CCCCCCCCCCC
Q psy9606 276 HHHSHHHHDSG 286 (356)
Q Consensus 276 ~~~~~~~~~~~ 286 (356)
|||.|||-|..
T Consensus 8 hhhhhhhpd~~ 18 (26)
T PRK09727 8 HHHHHHHPDXX 18 (26)
T ss_pred ccccccCCCcc
Confidence 55555665543
No 57
>KOG0818|consensus
Probab=20.47 E-value=65 Score=35.16 Aligned_cols=35 Identities=20% Similarity=0.559 Sum_probs=28.1
Q ss_pred CcccccCCCCCCcceeeCCCCCcccchhhHHHHHhC
Q psy9606 73 DLTCTNCNTKVTTIWRRYPSGEMVCNACGLYYRLHC 108 (356)
Q Consensus 73 ~~~CsnCgTt~TP~WRRgp~G~~LCNACGL~~k~~g 108 (356)
..+|..|+.. -|.|..-.-|-.||..|.-+.+-.|
T Consensus 8 ~evC~DC~~~-dp~WASvnrGt~lC~eCcsvHrsLG 42 (669)
T KOG0818|consen 8 SEVCADCSGP-DPSWASVNRGTFLCDECCSVHRSLG 42 (669)
T ss_pred hhhhcccCCC-CCcceeecCceEehHhhhHHHhhhc
Confidence 4789999876 4889999999999999976665544
No 58
>PF12773 DZR: Double zinc ribbon
Probab=20.02 E-value=66 Score=22.87 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=7.2
Q ss_pred CcccccCCCCCC
Q psy9606 73 DLTCTNCNTKVT 84 (356)
Q Consensus 73 ~~~CsnCgTt~T 84 (356)
...|.+||+...
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 356666666555
Done!