Query psy15596
Match_columns 149
No_of_seqs 71 out of 73
Neff 2.5
Searched_HMMs 46136
Date Fri Aug 16 16:38:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15596.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15596hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4385|consensus 100.0 1.9E-41 4E-46 305.4 8.5 104 37-140 173-283 (581)
2 KOG4385|consensus 97.0 5.5E-05 1.2E-09 70.2 -3.3 78 56-137 131-208 (581)
3 PF12756 zf-C2H2_2: C2H2 type 89.6 0.1 2.2E-06 34.5 0.0 62 72-133 3-73 (100)
4 PF00096 zf-C2H2: Zinc finger, 88.5 0.35 7.5E-06 25.7 1.6 19 72-90 4-22 (23)
5 PF13894 zf-C2H2_4: C2H2-type 85.4 0.95 2E-05 23.1 2.2 21 72-92 4-24 (24)
6 PF13912 zf-C2H2_6: C2H2-type 84.4 0.82 1.8E-05 25.1 1.8 21 73-93 6-26 (27)
7 PF05605 zf-Di19: Drought indu 78.8 2.5 5.5E-05 27.1 2.8 32 71-104 5-36 (54)
8 PF12874 zf-met: Zinc-finger o 73.3 2.8 6E-05 22.5 1.6 18 73-90 5-22 (25)
9 smart00355 ZnF_C2H2 zinc finge 72.9 4.8 0.0001 20.3 2.4 22 71-93 3-24 (26)
10 PHA00616 hypothetical protein 72.3 2.5 5.5E-05 27.8 1.5 26 71-96 4-29 (44)
11 PF04696 Pinin_SDK_memA: pinin 71.5 9.9 0.00021 29.0 4.8 48 81-128 13-60 (131)
12 COG4049 Uncharacterized protei 71.4 1.9 4.2E-05 30.8 0.9 26 69-94 18-43 (65)
13 smart00307 ILWEQ I/LWEQ domain 66.9 13 0.00027 31.0 4.8 28 101-129 168-195 (200)
14 PF12013 DUF3505: Protein of u 66.2 9 0.00019 27.4 3.4 41 53-93 67-109 (109)
15 TIGR00741 yfiA ribosomal subun 63.2 7.2 0.00016 26.5 2.4 18 107-124 76-93 (95)
16 PF12171 zf-C2H2_jaz: Zinc-fin 61.1 3.7 8.1E-05 22.9 0.6 19 72-90 5-23 (27)
17 PF12756 zf-C2H2_2: C2H2 type 60.9 9.6 0.00021 25.0 2.6 28 66-95 50-77 (100)
18 PRK15178 Vi polysaccharide exp 52.3 28 0.0006 32.0 4.9 31 99-129 278-308 (434)
19 KOG4377|consensus 51.4 7 0.00015 36.6 1.0 29 61-89 396-424 (480)
20 cd04776 HTH_GnyR Helix-Turn-He 51.0 78 0.0017 23.2 6.3 55 73-131 53-107 (118)
21 COG1544 Ribosome-associated pr 46.3 22 0.00048 26.8 2.8 19 107-125 78-96 (110)
22 TIGR02436 conserved hypothetic 43.5 49 0.0011 24.3 4.2 49 79-131 50-105 (111)
23 PRK10324 translation inhibitor 43.2 30 0.00064 25.6 3.0 19 107-125 76-94 (113)
24 PF01608 I_LWEQ: I/LWEQ domain 41.2 76 0.0017 25.4 5.2 21 109-129 127-147 (152)
25 PRK10470 ribosome hibernation 40.4 28 0.00061 24.2 2.4 18 107-124 76-93 (95)
26 smart00451 ZnF_U1 U1-like zinc 38.7 28 0.00061 19.6 1.9 19 73-91 8-26 (35)
27 KOG3608|consensus 35.1 21 0.00044 33.4 1.3 24 67-90 178-201 (467)
28 PF02482 Ribosomal_S30AE: Sigm 35.1 24 0.00051 23.8 1.3 18 107-124 78-95 (97)
29 PF13611 Peptidase_S76: Serine 34.9 20 0.00043 28.1 1.1 20 71-90 78-97 (121)
30 PF15372 DUF4600: Domain of un 34.3 88 0.0019 24.7 4.5 30 99-128 7-36 (129)
31 PF04780 DUF629: Protein of un 33.0 33 0.00072 31.9 2.3 27 72-98 61-87 (466)
32 PRK00846 hypothetical protein; 32.3 91 0.002 22.5 4.0 23 105-127 39-61 (77)
33 PF04968 CHORD: CHORD ; Inter 31.9 17 0.00038 25.4 0.3 29 58-86 26-54 (64)
34 smart00037 CNX Connexin homolo 30.4 10 0.00022 24.3 -1.0 17 71-87 16-32 (34)
35 PF15369 KIAA1328: Uncharacter 30.3 75 0.0016 28.7 4.0 24 103-128 284-307 (328)
36 PF06348 DUF1059: Protein of u 29.0 56 0.0012 21.7 2.3 27 72-98 11-43 (57)
37 KOG3915|consensus 28.7 64 0.0014 31.2 3.4 19 71-89 192-212 (641)
38 TIGR02218 phg_TIGR02218 phage 28.0 24 0.00053 29.4 0.5 19 62-80 171-191 (229)
39 cd00552 RaiA RaiA ("ribosome-a 26.1 45 0.00097 22.4 1.5 16 107-122 78-93 (93)
40 PF08900 DUF1845: Domain of un 25.7 3.8E+02 0.0082 22.0 7.3 50 80-129 41-91 (217)
41 PRK12275 hypothetical protein; 24.1 1.6E+02 0.0034 21.2 4.1 46 80-129 58-110 (116)
42 cd04777 HTH_MerR-like_sg1 Heli 23.9 2.3E+02 0.0049 20.0 4.8 60 68-130 48-107 (107)
43 PF12925 APP_E2: E2 domain of 23.4 1.1E+02 0.0024 25.5 3.6 20 107-126 81-100 (193)
44 PF03262 Corona_6B_7B: Coronav 23.3 23 0.0005 30.2 -0.4 23 62-84 64-86 (209)
45 PRK07720 fliJ flagellar biosyn 23.1 3.2E+02 0.0069 20.2 6.1 41 79-129 67-107 (146)
46 cd00592 HTH_MerR-like Helix-Tu 22.7 1.9E+02 0.0042 19.7 4.2 46 73-126 54-99 (100)
47 COG3524 KpsE Capsule polysacch 22.2 1.5E+02 0.0033 27.3 4.4 28 99-126 215-242 (372)
48 KOG0980|consensus 20.9 1.7E+02 0.0037 30.0 4.9 30 99-129 944-973 (980)
49 COG5613 Uncharacterized conser 20.4 2.1E+02 0.0045 26.7 5.0 29 100-128 344-372 (400)
No 1
>KOG4385|consensus
Probab=100.00 E-value=1.9e-41 Score=305.44 Aligned_cols=104 Identities=57% Similarity=0.883 Sum_probs=94.3
Q ss_pred CCCCccccCCCC----ccccccccccc---ccccccCccccCCCCCccccCHHHHHHHhhhhCCCCCchHHHHHHHHHHH
Q psy15596 37 MGISRREWMNGD----DQKANESYAEK---VHFLFGHGVCKWPGCEAVCEDVQAFYKHLNKEHNLDDRSTAQARVQMQVV 109 (149)
Q Consensus 37 ~~~s~~~~~ng~----~~~~~~~~~~~---shpLy~hGvCkWPGCe~~~ed~~~FLkHLnseH~LDDrStAQcRVQmqVV 109 (149)
...++|...||+ ..|+|++++++ +||||+||+|||||||++|||+++||||||+||+|||||+||||||||||
T Consensus 173 ~~~nph~~~n~q~~~~~~r~ds~~~~~~~~shPl~~hgvckwpgcE~~~ed~~~flKhln~eh~lddrstaQcrvQmQVv 252 (581)
T KOG4385|consen 173 KVSNPHKVENGQHSVSSPRRDSSSMEEHPSSHPLYAHGVCKWPGCEAVCEDFGSFLKHLNTEHALDDRSTAQCRVQMQVV 252 (581)
T ss_pred cCCCcccccccccccccccchhhhhhcccccCCcccCCccCCCchhhhccchHHHHHhhccccccchhhhHHHHHHHHHH
Confidence 344558999999 57888888775 99999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccCcccCcch
Q psy15596 110 SQLELQLQKERDRLQAMMLHLHMTKQQSQTV 140 (149)
Q Consensus 110 qqLE~QL~kEkeRLqAMm~HL~m~~~~~~~~ 140 (149)
|+||.||.||||||+|||+||+|+.....+.
T Consensus 253 qqlE~ql~ke~erlqamm~hl~~~~s~~k~~ 283 (581)
T KOG4385|consen 253 QQLEIQLSKESERLQAMMAHLAMKPSEPKAS 283 (581)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcccCCCccc
Confidence 9999999999999999999999977544443
No 2
>KOG4385|consensus
Probab=96.98 E-value=5.5e-05 Score=70.24 Aligned_cols=78 Identities=10% Similarity=0.028 Sum_probs=71.1
Q ss_pred ccccccccccCccccCCCCCccccCHHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCcc
Q psy15596 56 YAEKVHFLFGHGVCKWPGCEAVCEDVQAFYKHLNKEHNLDDRSTAQARVQMQVVSQLELQLQKERDRLQAMMLHLHMTKQ 135 (149)
Q Consensus 56 ~~~~shpLy~hGvCkWPGCe~~~ed~~~FLkHLnseH~LDDrStAQcRVQmqVVqqLE~QL~kEkeRLqAMm~HL~m~~~ 135 (149)
+|.+.+-||.+|+|.||+|+. |.+-..|..|+.++|...+.+++--+ +.|...|..+..+|.++.+|+.|+++.+.
T Consensus 131 ~pt~~~~lw~e~~~a~psed~-~~~~l~ltt~~~~s~~ps~~s~~~np---h~~~n~q~~~~~~r~ds~~~~~~~~shPl 206 (581)
T KOG4385|consen 131 SPTPLQGLWKEGTPAHPSEDP-KHSGLDLTTTEASSTEPSKTSKVSNP---HKVENGQHSVSSPRRDSSSMEEHPSSHPL 206 (581)
T ss_pred CCccHHHHhhccccCCcCCCc-cccceeeeecchhccCccccccCCCc---ccccccccccccccchhhhhhcccccCCc
Confidence 345678899999999999999 99999999999999999999999888 78899999999999999999999998875
Q ss_pred cC
Q psy15596 136 QS 137 (149)
Q Consensus 136 ~~ 137 (149)
-+
T Consensus 207 ~~ 208 (581)
T KOG4385|consen 207 YA 208 (581)
T ss_pred cc
Confidence 44
No 3
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=89.60 E-value=0.1 Score=34.51 Aligned_cols=62 Identities=15% Similarity=0.234 Sum_probs=8.4
Q ss_pred CCCCccccCHHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHhhccC
Q psy15596 72 PGCEAVCEDVQAFYKHLNKEHNLDDRSTAQARVQMQVVSQLELQLQK---------ERDRLQAMMLHLHMT 133 (149)
Q Consensus 72 PGCe~~~ed~~~FLkHLnseH~LDDrStAQcRVQmqVVqqLE~QL~k---------EkeRLqAMm~HL~m~ 133 (149)
+-|+..|.+..++++||...|.++-.....+.....++..+..++.. .-.-..+++.|+.-+
T Consensus 3 ~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 3 LFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ----------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 35999999999999999999999876555555666677776655532 223466677777643
No 4
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=88.50 E-value=0.35 Score=25.70 Aligned_cols=19 Identities=16% Similarity=0.438 Sum_probs=17.7
Q ss_pred CCCCccccCHHHHHHHhhh
Q psy15596 72 PGCEAVCEDVQAFYKHLNK 90 (149)
Q Consensus 72 PGCe~~~ed~~~FLkHLns 90 (149)
|.|++.|.+...|.+|+..
T Consensus 4 ~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 4 PICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp TTTTEEESSHHHHHHHHHH
T ss_pred CCCCCccCCHHHHHHHHhH
Confidence 5899999999999999986
No 5
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=85.40 E-value=0.95 Score=23.13 Aligned_cols=21 Identities=19% Similarity=0.450 Sum_probs=17.9
Q ss_pred CCCCccccCHHHHHHHhhhhC
Q psy15596 72 PGCEAVCEDVQAFYKHLNKEH 92 (149)
Q Consensus 72 PGCe~~~ed~~~FLkHLnseH 92 (149)
|-|++.|.+..++.+|+.+.|
T Consensus 4 ~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 4 PICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp SSTS-EESSHHHHHHHHHHHS
T ss_pred cCCCCcCCcHHHHHHHHHhhC
Confidence 459999999999999999876
No 6
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=84.44 E-value=0.82 Score=25.10 Aligned_cols=21 Identities=14% Similarity=0.311 Sum_probs=18.2
Q ss_pred CCCccccCHHHHHHHhhhhCC
Q psy15596 73 GCEAVCEDVQAFYKHLNKEHN 93 (149)
Q Consensus 73 GCe~~~ed~~~FLkHLnseH~ 93 (149)
-|++.|.+..+|++|+..-|.
T Consensus 6 ~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 6 ECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp TTTEEESSHHHHHHHHCTTTT
T ss_pred ccCCccCChhHHHHHhHHhcC
Confidence 599999999999999976554
No 7
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=78.83 E-value=2.5 Score=27.14 Aligned_cols=32 Identities=16% Similarity=0.318 Sum_probs=25.5
Q ss_pred CCCCCccccCHHHHHHHhhhhCCCCCchHHHHHH
Q psy15596 71 WPGCEAVCEDVQAFYKHLNKEHNLDDRSTAQARV 104 (149)
Q Consensus 71 WPGCe~~~ed~~~FLkHLnseH~LDDrStAQcRV 104 (149)
=|-|++ --|..+|++|+..+|..|.+ ..-|-+
T Consensus 5 CP~C~~-~~~~~~L~~H~~~~H~~~~~-~v~CPi 36 (54)
T PF05605_consen 5 CPYCGK-GFSESSLVEHCEDEHRSESK-NVVCPI 36 (54)
T ss_pred CCCCCC-ccCHHHHHHHHHhHCcCCCC-CccCCC
Confidence 377999 56789999999999999877 355544
No 8
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=73.35 E-value=2.8 Score=22.54 Aligned_cols=18 Identities=17% Similarity=0.342 Sum_probs=16.4
Q ss_pred CCCccccCHHHHHHHhhh
Q psy15596 73 GCEAVCEDVQAFYKHLNK 90 (149)
Q Consensus 73 GCe~~~ed~~~FLkHLns 90 (149)
=|++.|.+..+|..|+++
T Consensus 5 ~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 5 ICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp TTTEEESSHHHHHHHHTT
T ss_pred CCCCCcCCHHHHHHHHCc
Confidence 389999999999999985
No 9
>smart00355 ZnF_C2H2 zinc finger.
Probab=72.90 E-value=4.8 Score=20.32 Aligned_cols=22 Identities=27% Similarity=0.563 Sum_probs=18.4
Q ss_pred CCCCCccccCHHHHHHHhhhhCC
Q psy15596 71 WPGCEAVCEDVQAFYKHLNKEHN 93 (149)
Q Consensus 71 WPGCe~~~ed~~~FLkHLnseH~ 93 (149)
.+-|++.|.+..+|..|+. .|.
T Consensus 3 C~~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 3 CPECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCcchhCCHHHHHHHHH-Hhc
Confidence 3559999999999999997 554
No 10
>PHA00616 hypothetical protein
Probab=72.34 E-value=2.5 Score=27.84 Aligned_cols=26 Identities=15% Similarity=0.304 Sum_probs=23.2
Q ss_pred CCCCCccccCHHHHHHHhhhhCCCCC
Q psy15596 71 WPGCEAVCEDVQAFYKHLNKEHNLDD 96 (149)
Q Consensus 71 WPGCe~~~ed~~~FLkHLnseH~LDD 96 (149)
=|=|++.|-...++.+|+++.|.-|+
T Consensus 4 C~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 4 CLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred cchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 36799999999999999999998765
No 11
>PF04696 Pinin_SDK_memA: pinin/SDK/memA/ protein conserved region; InterPro: IPR006786 This conserved region is located adjacent and C-terminal to a N-terminal pinin/SKD domain IPR006787 from INTERPRO. Members of this family have very varied localisations within the eukaryotic cell. Pinin is known to localise at the desmosomes and is implicated in anchoring intermediate filaments to the desmosomal plaque []. SDK2/3 is a dynamically localised nuclear protein thought to be involved in modulation of alternative pre-mRNA splicing []. MemA is a tumour marker preferentially expressed in human melanoma cell lines. A common feature of the members of this family is that they may all participate in regulating protein-protein interactions [].
Probab=71.53 E-value=9.9 Score=28.95 Aligned_cols=48 Identities=19% Similarity=0.304 Sum_probs=38.4
Q ss_pred HHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy15596 81 VQAFYKHLNKEHNLDDRSTAQARVQMQVVSQLELQLQKERDRLQAMML 128 (149)
Q Consensus 81 ~~~FLkHLnseH~LDDrStAQcRVQmqVVqqLE~QL~kEkeRLqAMm~ 128 (149)
|+.++-+|+.-=.-+++.++|-.=+.+|-+.||.++..|++.|..-..
T Consensus 13 FG~LlGTL~kf~~e~~k~~~~~~rR~eie~rleek~~~e~e~l~~~~~ 60 (131)
T PF04696_consen 13 FGGLLGTLQKFKKEEEKKTEQQKRRAEIEKRLEEKLKEEKEELRKERR 60 (131)
T ss_pred HHHHHHHHHHHHHhHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 677788887666556777888888899999999999988888876554
No 12
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=71.44 E-value=1.9 Score=30.76 Aligned_cols=26 Identities=27% Similarity=0.594 Sum_probs=23.3
Q ss_pred ccCCCCCccccCHHHHHHHhhhhCCC
Q psy15596 69 CKWPGCEAVCEDVQAFYKHLNKEHNL 94 (149)
Q Consensus 69 CkWPGCe~~~ed~~~FLkHLnseH~L 94 (149)
-+-|-|+++|.+-.++++|.|..|..
T Consensus 18 lrCPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 18 LRCPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred eeCCchhHHHHHhHHHHHHhhHHhhh
Confidence 46699999999999999999999863
No 13
>smart00307 ILWEQ I/LWEQ domain. Thought to possess an F-actin binding function.
Probab=66.89 E-value=13 Score=31.01 Aligned_cols=28 Identities=21% Similarity=0.424 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy15596 101 QARVQMQVVSQLELQLQKERDRLQAMMLH 129 (149)
Q Consensus 101 QcRVQmqVVqqLE~QL~kEkeRLqAMm~H 129 (149)
...-|.+|+ .||..|.++|.||..|-.+
T Consensus 168 emE~Qv~IL-~lE~~L~~ar~~L~~lRk~ 195 (200)
T smart00307 168 EMEQQVEIL-KLENELEAARKKLAEIRKQ 195 (200)
T ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHHH
Confidence 344455666 8999999999999998765
No 14
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=66.17 E-value=9 Score=27.38 Aligned_cols=41 Identities=22% Similarity=0.293 Sum_probs=34.4
Q ss_pred cccccccccccccCccc--cCCCCCccccCHHHHHHHhhhhCC
Q psy15596 53 NESYAEKVHFLFGHGVC--KWPGCEAVCEDVQAFYKHLNKEHN 93 (149)
Q Consensus 53 ~~~~~~~shpLy~hGvC--kWPGCe~~~ed~~~FLkHLnseH~ 93 (149)
+.+.|-+.=|.|.+-.| .+++|.-++.+....-+|+..+|.
T Consensus 67 ~~~~Pi~gLp~~~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 67 DPSPPIPGLPVYDGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCCcCCCCCCCCCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 44445455588988899 999999999999999999999984
No 15
>TIGR00741 yfiA ribosomal subunit interface protein. The member of this family from E. coli is now recognized as a protein at the interace between ribosomal large and small subunits, with about 1/3 as many copies per cell as the number of ribosomes.
Probab=63.16 E-value=7.2 Score=26.54 Aligned_cols=18 Identities=28% Similarity=0.464 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy15596 107 QVVSQLELQLQKERDRLQ 124 (149)
Q Consensus 107 qVVqqLE~QL~kEkeRLq 124 (149)
.+++.||.||.++|+|+.
T Consensus 76 ~a~~klerql~k~k~k~~ 93 (95)
T TIGR00741 76 LAIDKLERQLRKLKEKRK 93 (95)
T ss_pred HHHHHHHHHHHHHHhhhh
Confidence 478999999999999985
No 16
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=61.08 E-value=3.7 Score=22.93 Aligned_cols=19 Identities=11% Similarity=0.389 Sum_probs=17.1
Q ss_pred CCCCccccCHHHHHHHhhh
Q psy15596 72 PGCEAVCEDVQAFYKHLNK 90 (149)
Q Consensus 72 PGCe~~~ed~~~FLkHLns 90 (149)
+-|++.|.+-.+|..|+++
T Consensus 5 ~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 5 DACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp TTTTBBBSSHHHHHCCTTS
T ss_pred ccCCCCcCCHHHHHHHHcc
Confidence 3599999999999999986
No 17
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=60.86 E-value=9.6 Score=25.00 Aligned_cols=28 Identities=21% Similarity=0.470 Sum_probs=21.8
Q ss_pred CccccCCCCCccccCHHHHHHHhhhhCCCC
Q psy15596 66 HGVCKWPGCEAVCEDVQAFYKHLNKEHNLD 95 (149)
Q Consensus 66 hGvCkWPGCe~~~ed~~~FLkHLnseH~LD 95 (149)
.-.| +-|.+.|.+..++.+|+++.+...
T Consensus 50 ~~~C--~~C~~~f~s~~~l~~Hm~~~~H~~ 77 (100)
T PF12756_consen 50 SFRC--PYCNKTFRSREALQEHMRSKHHKK 77 (100)
T ss_dssp SEEB--SSSS-EESSHHHHHHHHHHTTTTC
T ss_pred CCCC--CccCCCCcCHHHHHHHHcCccCCC
Confidence 3456 459999999999999999876554
No 18
>PRK15178 Vi polysaccharide export inner membrane protein VexD; Provisional
Probab=52.30 E-value=28 Score=32.00 Aligned_cols=31 Identities=16% Similarity=0.317 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy15596 99 TAQARVQMQVVSQLELQLQKERDRLQAMMLH 129 (149)
Q Consensus 99 tAQcRVQmqVVqqLE~QL~kEkeRLqAMm~H 129 (149)
.+|...|+++|..||.||..++-+|.+|+.-
T Consensus 278 ~~~a~~~~~lI~~Le~qLa~~~aeL~~L~~~ 308 (434)
T PRK15178 278 KETITAIYQLIAGFETQLAEAKAEYAQLMVN 308 (434)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4566678899999999999999999999765
No 19
>KOG4377|consensus
Probab=51.39 E-value=7 Score=36.63 Aligned_cols=29 Identities=28% Similarity=0.362 Sum_probs=23.6
Q ss_pred cccccCccccCCCCCccccCHHHHHHHhh
Q psy15596 61 HFLFGHGVCKWPGCEAVCEDVQAFYKHLN 89 (149)
Q Consensus 61 hpLy~hGvCkWPGCe~~~ed~~~FLkHLn 89 (149)
.-.+.|+.|.|+|||..+-+..+-..|-.
T Consensus 396 s~~cnhfhc~r~Gc~~tl~s~sqm~shkr 424 (480)
T KOG4377|consen 396 SGICNHFHCDRLGCEATLYSVSQMASHKR 424 (480)
T ss_pred ccceeeeeecccCCceEEEehhhhhhhhh
Confidence 34577999999999999999888877643
No 20
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=51.01 E-value=78 Score=23.24 Aligned_cols=55 Identities=11% Similarity=0.198 Sum_probs=37.8
Q ss_pred CCCccccCHHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy15596 73 GCEAVCEDVQAFYKHLNKEHNLDDRSTAQARVQMQVVSQLELQLQKERDRLQAMMLHLH 131 (149)
Q Consensus 73 GCe~~~ed~~~FLkHLnseH~LDDrStAQcRVQmqVVqqLE~QL~kEkeRLqAMm~HL~ 131 (149)
..+...++...|+.-.. .++.+.++|+-+.+++..=-..|..++++|+++...|.
T Consensus 53 ~~G~~L~~I~~~l~~~~----~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~L~ 107 (118)
T cd04776 53 RLGFSLEEIRELLDLYD----PPGGNRKQLEKMLEKIEKRRAELEQQRRDIDAALAELD 107 (118)
T ss_pred HCCCCHHHHHHHHHhhc----cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556667777775433 34455677877777777777777888888888887764
No 21
>COG1544 Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]
Probab=46.27 E-value=22 Score=26.78 Aligned_cols=19 Identities=32% Similarity=0.599 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy15596 107 QVVSQLELQLQKERDRLQA 125 (149)
Q Consensus 107 qVVqqLE~QL~kEkeRLqA 125 (149)
.++..||.||.|-|+|+..
T Consensus 78 ~a~dKLerqlrK~K~K~~~ 96 (110)
T COG1544 78 LAIDKLERQLRKHKEKLKD 96 (110)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 4789999999999999985
No 22
>TIGR02436 conserved hypothetical protein TIGR02436. This family consists of a few small, well-conserved proteins found so far in Bacteroides thetaiotaomicron VPI-5482, Nostoc sp. PCC 7120, Clostridium tetani E88, Chlorobium tepidum TLS, and Prevotella ruminicola 23. The function is unknown.
Probab=43.54 E-value=49 Score=24.26 Aligned_cols=49 Identities=12% Similarity=0.183 Sum_probs=38.6
Q ss_pred cCHHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHhhc
Q psy15596 79 EDVQAFYKHLNKEHNLDDRSTAQARVQMQVVSQLE-------LQLQKERDRLQAMMLHLH 131 (149)
Q Consensus 79 ed~~~FLkHLnseH~LDDrStAQcRVQmqVVqqLE-------~QL~kEkeRLqAMm~HL~ 131 (149)
.+..+|+++|+ .--.|.++++.|..+...+. ..|..|-+.|.+|..-+.
T Consensus 50 ~s~~df~~fl~----ia~gs~~E~~~~L~la~~~~~l~~~~~~~l~~e~~ei~~~L~~li 105 (111)
T TIGR02436 50 ESTADFIHKLS----IALKEGSETEYWIRLLIQTELIPENRYESIKGDCLELLKILAATV 105 (111)
T ss_pred CCHHHHHHHHH----HHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 47788999998 55688999999998887764 456788888888876654
No 23
>PRK10324 translation inhibitor protein RaiA; Provisional
Probab=43.24 E-value=30 Score=25.55 Aligned_cols=19 Identities=32% Similarity=0.466 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy15596 107 QVVSQLELQLQKERDRLQA 125 (149)
Q Consensus 107 qVVqqLE~QL~kEkeRLqA 125 (149)
.+++.||.||.+-|+|+.+
T Consensus 76 ~a~dklerQLrK~K~k~~~ 94 (113)
T PRK10324 76 ELINKLERQLNKLQHKGEA 94 (113)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 5899999999999999954
No 24
>PF01608 I_LWEQ: I/LWEQ domain; InterPro: IPR002558 I/LWEQ domains bind to actin. It has been shown that the I/LWEQ domains from mouse talin P26039 from SWISSPROT and yeast Sla2p P33338 from SWISSPROT interact with F-actin []. The domain has four conserved blocks, the name of the domain is derived from the initial conserved amino acid of each of the four blocks []. I/LWEQ domains can be placed into four major groups based on sequence similarity: Metazoan talin. Dictyostelium discoideum (Slime mould) TalA/TalB P54633 from SWISSPROT and SLA110. Metazoan Hip1p O00291 from SWISSPROT. Saccharomyces cerevisiae Sla2p P33338 from SWISSPROT. ; GO: 0003779 actin binding; PDB: 2QDQ_A 2JSW_A 1R0D_B.
Probab=41.19 E-value=76 Score=25.44 Aligned_cols=21 Identities=29% Similarity=0.453 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q psy15596 109 VSQLELQLQKERDRLQAMMLH 129 (149)
Q Consensus 109 VqqLE~QL~kEkeRLqAMm~H 129 (149)
|=.||..|.+||.||..|-.+
T Consensus 127 iL~lE~eLe~ar~kL~~lRk~ 147 (152)
T PF01608_consen 127 ILKLEKELEKARKKLAELRKA 147 (152)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 557999999999999998765
No 25
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=40.40 E-value=28 Score=24.18 Aligned_cols=18 Identities=33% Similarity=0.623 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy15596 107 QVVSQLELQLQKERDRLQ 124 (149)
Q Consensus 107 qVVqqLE~QL~kEkeRLq 124 (149)
.+++.||.||.+-|+|+.
T Consensus 76 ~a~~klerqL~k~k~k~~ 93 (95)
T PRK10470 76 GLIDKLARQLTKHKDKLK 93 (95)
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 478999999999999985
No 26
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=38.65 E-value=28 Score=19.62 Aligned_cols=19 Identities=21% Similarity=0.302 Sum_probs=16.5
Q ss_pred CCCccccCHHHHHHHhhhh
Q psy15596 73 GCEAVCEDVQAFYKHLNKE 91 (149)
Q Consensus 73 GCe~~~ed~~~FLkHLnse 91 (149)
=|.+.|.+..++..|+++.
T Consensus 8 ~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 8 LCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred ccCCccCCHHHHHHHHChH
Confidence 4899999999999999864
No 27
>KOG3608|consensus
Probab=35.13 E-value=21 Score=33.41 Aligned_cols=24 Identities=17% Similarity=0.555 Sum_probs=21.8
Q ss_pred ccccCCCCCccccCHHHHHHHhhh
Q psy15596 67 GVCKWPGCEAVCEDVQAFYKHLNK 90 (149)
Q Consensus 67 GvCkWPGCe~~~ed~~~FLkHLns 90 (149)
-+|+|-||-+.+++-..+.+|+.+
T Consensus 178 ~~C~W~~Ct~~~~~k~~LreH~r~ 201 (467)
T KOG3608|consen 178 TMCNWAMCTKHMGNKYRLREHIRT 201 (467)
T ss_pred eeccchhhhhhhccHHHHHHHHHh
Confidence 379999999999999999999874
No 28
>PF02482 Ribosomal_S30AE: Sigma 54 modulation protein / S30EA ribosomal protein; InterPro: IPR003489 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 [, ]. This family contains the sigma-54 modulation protein family and the S30Ae family of ribosomal proteins which includes the light-repressed protein (lrtA) [].; GO: 0005488 binding, 0044238 primary metabolic process; PDB: 1L4S_A 1VOX_a 1VOV_a 3V2E_Y 3V2C_Y 1N3G_A 1VOS_a 1VOZ_a 1VOQ_a 1IMU_A ....
Probab=35.11 E-value=24 Score=23.84 Aligned_cols=18 Identities=33% Similarity=0.586 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy15596 107 QVVSQLELQLQKERDRLQ 124 (149)
Q Consensus 107 qVVqqLE~QL~kEkeRLq 124 (149)
.++..||.||.+.++|++
T Consensus 78 ~a~dkl~rql~k~k~k~~ 95 (97)
T PF02482_consen 78 EAFDKLERQLRKYKEKLR 95 (97)
T ss_dssp HHHHHHHHHHHHHHHCCC
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 478999999999999864
No 29
>PF13611 Peptidase_S76: Serine peptidase of plant viral polyprotein, P1
Probab=34.88 E-value=20 Score=28.07 Aligned_cols=20 Identities=20% Similarity=0.375 Sum_probs=18.5
Q ss_pred CCCCCccccCHHHHHHHhhh
Q psy15596 71 WPGCEAVCEDVQAFYKHLNK 90 (149)
Q Consensus 71 WPGCe~~~ed~~~FLkHLns 90 (149)
|-||+-++++...||+|+|.
T Consensus 78 ~d~~~Dm~p~~r~fl~h~n~ 97 (121)
T PF13611_consen 78 KDGEDDMYPEDRSFLEHYNA 97 (121)
T ss_pred cCcccCCCHHHHHHHhcccc
Confidence 66999999999999999995
No 30
>PF15372 DUF4600: Domain of unknown function (DUF4600)
Probab=34.26 E-value=88 Score=24.75 Aligned_cols=30 Identities=20% Similarity=0.282 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy15596 99 TAQARVQMQVVSQLELQLQKERDRLQAMML 128 (149)
Q Consensus 99 tAQcRVQmqVVqqLE~QL~kEkeRLqAMm~ 128 (149)
+.+-..|+++..|||.|+.-.++++..+..
T Consensus 7 ktRYEtQ~E~N~QLekqi~~l~~kiek~r~ 36 (129)
T PF15372_consen 7 KTRYETQLELNDQLEKQIIILREKIEKIRG 36 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 345678999999999999999999987643
No 31
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=32.96 E-value=33 Score=31.95 Aligned_cols=27 Identities=22% Similarity=0.500 Sum_probs=24.2
Q ss_pred CCCCccccCHHHHHHHhhhhCCCCCch
Q psy15596 72 PGCEAVCEDVQAFYKHLNKEHNLDDRS 98 (149)
Q Consensus 72 PGCe~~~ed~~~FLkHLnseH~LDDrS 98 (149)
|-|++.|-|..+|+.|+-.+|.-+-..
T Consensus 61 p~CskkF~d~~~~~~H~~~eH~~~l~P 87 (466)
T PF04780_consen 61 PRCSKKFSDAESCLSHMEQEHPAGLKP 87 (466)
T ss_pred CcccceeCCHHHHHHHHHHhhhhhcCh
Confidence 559999999999999999999987654
No 32
>PRK00846 hypothetical protein; Provisional
Probab=32.28 E-value=91 Score=22.54 Aligned_cols=23 Identities=4% Similarity=-0.096 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy15596 105 QMQVVSQLELQLQKERDRLQAMM 127 (149)
Q Consensus 105 QmqVVqqLE~QL~kEkeRLqAMm 127 (149)
|.+++..|..||..=++||.+|.
T Consensus 39 qq~~I~~L~~ql~~L~~rL~~~~ 61 (77)
T PRK00846 39 ARLTGARNAELIRHLLEDLGKVR 61 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 66778888888888888888887
No 33
>PF04968 CHORD: CHORD ; InterPro: IPR007051 Cysteine- and histidine-rich domains (CHORDs) are 60-amino acid modules that bind two zinc ions. They are usually arranged in tandem and are found in all tested eukaryotes, with the exception of yeast, where they are involved in processes ranging from pressure sensing in the heart to maintenance of diploidy in fungi, and exhibit distinct protein-protein interaction specificity. Six cysteine and two histidine residues are invariant within the CHORD domain. Three other residues are also invariant and some positions are confined to positive, negative, or aromatic amino acids [, ]. Silencing of the Caenorhabditis elegansCHORD-containing gene results in semisterility and embryo lethality, suggesting an essential function of the wild-type gene in nematode development. The CHORD domain is sometimes found N-terminal to the CS domain, IPR007052 from INTERPRO, in metazoan proteins, but occurs separately from the CS domain in plants. This association is thought to be indicative of an functional interaction between CS and CHORD domains []. ; PDB: 2XCM_E 2YRT_A.
Probab=31.95 E-value=17 Score=25.39 Aligned_cols=29 Identities=24% Similarity=0.495 Sum_probs=25.3
Q ss_pred ccccccccCccccCCCCCccccCHHHHHH
Q psy15596 58 EKVHFLFGHGVCKWPGCEAVCEDVQAFYK 86 (149)
Q Consensus 58 ~~shpLy~hGvCkWPGCe~~~ed~~~FLk 86 (149)
-+..|.|..|+=.|-=|.+..-||.+||+
T Consensus 26 HpG~PvFHeg~K~WsCC~~k~~dF~~Fl~ 54 (64)
T PF04968_consen 26 HPGPPVFHEGMKGWSCCKKKVSDFDEFLK 54 (64)
T ss_dssp BSS-EEEETTEEEETTTTEEESSHHHHTT
T ss_pred cCCCceecCCceEEecCCCEeeCHHHHhc
Confidence 34678999999999999999999999985
No 34
>smart00037 CNX Connexin homologues. Connexin channels participate in the regulation of signaling between developing and differentiated cell types.
Probab=30.42 E-value=10 Score=24.25 Aligned_cols=17 Identities=47% Similarity=0.800 Sum_probs=11.9
Q ss_pred CCCCCccccCHHHHHHH
Q psy15596 71 WPGCEAVCEDVQAFYKH 87 (149)
Q Consensus 71 WPGCe~~~ed~~~FLkH 87 (149)
=|||+.+|-|.-.=|.|
T Consensus 16 QPGC~nvCyD~~fPiSh 32 (34)
T smart00037 16 QPGCENVCYDQAFPISH 32 (34)
T ss_pred CCCccceeccccccCcc
Confidence 49999999875443333
No 35
>PF15369 KIAA1328: Uncharacterised protein KIAA1328
Probab=30.27 E-value=75 Score=28.73 Aligned_cols=24 Identities=33% Similarity=0.585 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy15596 103 RVQMQVVSQLELQLQKERDRLQAMML 128 (149)
Q Consensus 103 RVQmqVVqqLE~QL~kEkeRLqAMm~ 128 (149)
|-|.=++|.|| |..||||||+.-+
T Consensus 284 rRqqLlLQKme--LEiEkERLQ~lLa 307 (328)
T PF15369_consen 284 RRQQLLLQKME--LEIEKERLQHLLA 307 (328)
T ss_pred HHHHHHHHHHH--HHHHHHHHHHHHH
Confidence 34444566664 6789999998765
No 36
>PF06348 DUF1059: Protein of unknown function (DUF1059); InterPro: IPR009409 This entry consists of short hypothetical archaeal and bacterial proteins of unknown function.
Probab=28.98 E-value=56 Score=21.72 Aligned_cols=27 Identities=22% Similarity=0.481 Sum_probs=21.7
Q ss_pred CCCCccccC------HHHHHHHhhhhCCCCCch
Q psy15596 72 PGCEAVCED------VQAFYKHLNKEHNLDDRS 98 (149)
Q Consensus 72 PGCe~~~ed------~~~FLkHLnseH~LDDrS 98 (149)
|||+..+.- +..+..|...+|..++-+
T Consensus 11 ~~C~~~~~a~tedEll~~~~~Ha~~~Hg~~~~~ 43 (57)
T PF06348_consen 11 PDCGFVIRAETEDELLEAVVEHAREVHGMTEIP 43 (57)
T ss_pred CCCCeEEeeCCHHHHHHHHHHHHHHhcCCccCC
Confidence 889887754 567889999999998743
No 37
>KOG3915|consensus
Probab=28.72 E-value=64 Score=31.24 Aligned_cols=19 Identities=42% Similarity=0.833 Sum_probs=15.6
Q ss_pred CCCCCcccc--CHHHHHHHhh
Q psy15596 71 WPGCEAVCE--DVQAFYKHLN 89 (149)
Q Consensus 71 WPGCe~~~e--d~~~FLkHLn 89 (149)
--|||.+|- -|+-|||||-
T Consensus 192 i~g~emiCLPQafdlFLKhlV 212 (641)
T KOG3915|consen 192 IEGCELICLPQAFDLFLKHLV 212 (641)
T ss_pred ecCceEEecHHHHHHHHHHHh
Confidence 369999995 4889999984
No 38
>TIGR02218 phg_TIGR02218 phage conserved hypothetical protein BR0599. This model describes a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions.
Probab=28.02 E-value=24 Score=29.38 Aligned_cols=19 Identities=26% Similarity=0.676 Sum_probs=15.9
Q ss_pred ccccCccccC--CCCCccccC
Q psy15596 62 FLFGHGVCKW--PGCEAVCED 80 (149)
Q Consensus 62 pLy~hGvCkW--PGCe~~~ed 80 (149)
.-|..|+-+| |||++-|+.
T Consensus 171 g~f~~G~l~~~~~GCDk~~~T 191 (229)
T TIGR02218 171 GWFSRGRLEWTGAGCDKRFAT 191 (229)
T ss_pred ccccccEEEEeCCCCCCChhH
Confidence 4588999999 999998765
No 39
>cd00552 RaiA RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).
Probab=26.11 E-value=45 Score=22.45 Aligned_cols=16 Identities=38% Similarity=0.544 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHH
Q psy15596 107 QVVSQLELQLQKERDR 122 (149)
Q Consensus 107 qVVqqLE~QL~kEkeR 122 (149)
..++.||.||.+.|+|
T Consensus 78 ~a~~kl~rqL~k~k~k 93 (93)
T cd00552 78 LAVDKLERQLRKYKEK 93 (93)
T ss_pred HHHHHHHHHHHHhccC
Confidence 4778999999988865
No 40
>PF08900 DUF1845: Domain of unknown function (DUF1845); InterPro: IPR014996 Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=25.73 E-value=3.8e+02 Score=22.02 Aligned_cols=50 Identities=14% Similarity=0.203 Sum_probs=43.7
Q ss_pred CHHHHHHHhhhhCCCCCchHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHh
Q psy15596 80 DVQAFYKHLNKEHNLDDRSTAQARVQM-QVVSQLELQLQKERDRLQAMMLH 129 (149)
Q Consensus 80 d~~~FLkHLnseH~LDDrStAQcRVQm-qVVqqLE~QL~kEkeRLqAMm~H 129 (149)
.|-+-++-++.+-.-||-=.-+..+++ +.+..+..+|+.+.++|.++++.
T Consensus 41 ~~~~~~~~i~~~a~~DdPyAD~~L~~iEe~i~~~~~~l~~~~~~l~~~l~~ 91 (217)
T PF08900_consen 41 GFASRLNRIWRDARQDDPYADWWLLRIEEKINEARQELQELIARLDALLAE 91 (217)
T ss_pred HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455667788889999999999999998 68899999999999999999988
No 41
>PRK12275 hypothetical protein; Reviewed
Probab=24.15 E-value=1.6e+02 Score=21.18 Aligned_cols=46 Identities=20% Similarity=0.270 Sum_probs=35.6
Q ss_pred CHHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHh
Q psy15596 80 DVQAFYKHLNKEHNLDDRSTAQARVQMQVVSQLE-------LQLQKERDRLQAMMLH 129 (149)
Q Consensus 80 d~~~FLkHLnseH~LDDrStAQcRVQmqVVqqLE-------~QL~kEkeRLqAMm~H 129 (149)
+..+|+++|+ --..|.+.++.|..+...++ .+|..|-+.+.+|..-
T Consensus 58 s~~~~~~~l~----ia~~s~~E~~~~L~la~~~~~i~~~~~~~l~~~~~ei~kml~~ 110 (116)
T PRK12275 58 SKKDFIRFLY----IALGSLAELETQLYIAKELGYITKEQYESILQEYDEIAKMLNG 110 (116)
T ss_pred CHHHHHHHHH----HHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5778999998 45678999999999888774 4567778888877643
No 42
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.93 E-value=2.3e+02 Score=20.02 Aligned_cols=60 Identities=13% Similarity=0.171 Sum_probs=36.9
Q ss_pred cccCCCCCccccCHHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy15596 68 VCKWPGCEAVCEDVQAFYKHLNKEHNLDDRSTAQARVQMQVVSQLELQLQKERDRLQAMMLHL 130 (149)
Q Consensus 68 vCkWPGCe~~~ed~~~FLkHLnseH~LDDrStAQcRVQmqVVqqLE~QL~kEkeRLqAMm~HL 130 (149)
....=.++...++...|+.-.+. -++.+...|....+++.+-..+|..+.++|+.+.++|
T Consensus 48 I~~lr~~G~sL~eI~~~l~~~~~---~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l 107 (107)
T cd04777 48 ILELKGLGFSLIEIQKIFSYKRL---TKSRTHEDQDYYKSFLKNKKDELEKEIEDLKKAIQKL 107 (107)
T ss_pred HHHHHHCCCCHHHHHHHHHhccc---ccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 33344456677888888754221 1223334455555666666667788888999888765
No 43
>PF12925 APP_E2: E2 domain of amyloid precursor protein; InterPro: IPR024329 Amyloid-beta precursor protein (APP, or A4) is associated with Alzheimer's disease (AD), because one of its breakdown products, amyloid-beta (A-beta), aggregates to form amyloid or senile plaques [, ]. Mutations in APP or in proteins that process APP have been linked with early-onset, familial AD. Individuals with Down's syndrome carry an extra copy of chromosome 21, which contains the APP gene, and almost invariably develop amyloid plaques and Alzheimer's symptoms. APP is important for the neurogenesis and neuronal regeneration, either through the intact protein, or through its many breakdown products []. APP consists of a large N-terminal extracellular region containing heparin-binding and copper-binding sites, a short hydrophobic transmembrane domain, and a short C-terminal intracellular domain. The N-terminal region is similar in structure to cysteine-rich growth factors and appears to function as a cell surface receptor, contributing to neurite growth, neuronal adhesion, axonogenesis and cell mobility []. APP acts as a kinesin I membrane receptor to mediate the axonal transport of beta-secretase and presenilin 1. The N-terminal domain can regulate neurite outgrowth through its binding to heparin and collagen I and IV, which are components of the extracellular matrix. APP is also coupled to apoptosis-inducing pathways, and is involved in copper homeostasis/oxidative stress through copper ion reduction, where copper-metallated APP induces neuronal death []. The C-terminal intracellular domain appears to be involved in transcription regulation through protein-protein interactions. APP can promote transcription activation through binding to APBB1/Tip60, and may bind to the adaptor protein FE65 to transactivate a wide variety of different promoters. APP can be processed by different sets of enzymes: In the non-amyloidogenic (non-plaque-forming) pathway, APP is cleaved by alpha-secretase to yield a soluble N-terminal sAPP-alpha (neuroprotective) and a membrane-bound CTF-alpha. CTF-alpha is broken-down by presenilin-containing gamma-secretase to yield soluble p3 and membrane-bound AICD (nuclear signalling). In the amyloidogenic pathway (plaque-forming), APP is broken down by beta-secretase to yield soluble sAPP-beta and membrane-bound CTF-beta. CTF-beta is broken down by gamma-secretase to yield soluble amyloid-beta and membrane-bound AICD. Amyloid-beta is required for neuronal function, but can aggregate to form amyloid plaques that seem to disrupt brain cells by clogging points of cell-cell contact. The E2 domain is the largest of the conserved domains in the amyloidogenic glycoproteins. The structure of E2 consists of two coiled-coil sub-structures connected through a continuous helix, and bears an unexpected resemblance to the spectrin family of protein structures. E2 can reversibly dimerise in solution, and the dimerisation occurs along the longest dimension of the molecule in an antiparallel orientation, which enables the N-terminal substructure of one monomer to pack against the C-terminal substructure of a second monomer. The high degree of conservation of residues at the putative dimer interface suggests that the E2 dimer observed in the crystal could be physiologically relevant. Heparin sulphate proteoglycans, the putative ligands for the precursor present in extracellular matrix, bind to E2 at a conserved and positively charged site near the dimer interface [].; PDB: 3K6B_A 3K66_A 1TKN_A 3NYL_A 3NYJ_A 3UMH_A 3UMK_A 3UMI_A 3QMK_B 3PMR_B ....
Probab=23.37 E-value=1.1e+02 Score=25.52 Aligned_cols=20 Identities=30% Similarity=0.391 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy15596 107 QVVSQLELQLQKERDRLQAM 126 (149)
Q Consensus 107 qVVqqLE~QL~kEkeRLqAM 126 (149)
+.|+.||.+-..||++|.++
T Consensus 81 ~~v~aLE~e~~~er~qL~~~ 100 (193)
T PF12925_consen 81 KTVQALEQEAAAERQQLVET 100 (193)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 68999999999999998764
No 44
>PF03262 Corona_6B_7B: Coronavirus 6B/7B protein; InterPro: IPR004945 The function of the Coronavirus 6B and 7B proteins is not known.
Probab=23.34 E-value=23 Score=30.18 Aligned_cols=23 Identities=26% Similarity=0.473 Sum_probs=17.0
Q ss_pred ccccCccccCCCCCccccCHHHH
Q psy15596 62 FLFGHGVCKWPGCEAVCEDVQAF 84 (149)
Q Consensus 62 pLy~hGvCkWPGCe~~~ed~~~F 84 (149)
-...+-.|.|||-...-.|..+|
T Consensus 64 ~~ieGf~CtwPGf~~~a~DHiDf 86 (209)
T PF03262_consen 64 ESIEGFNCTWPGFQNPAHDHIDF 86 (209)
T ss_pred ccccceeccCCCcccccccceeE
Confidence 34566789999999877776554
No 45
>PRK07720 fliJ flagellar biosynthesis chaperone; Validated
Probab=23.10 E-value=3.2e+02 Score=20.22 Aligned_cols=41 Identities=17% Similarity=0.205 Sum_probs=30.8
Q ss_pred cCHHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy15596 79 EDVQAFYKHLNKEHNLDDRSTAQARVQMQVVSQLELQLQKERDRLQAMMLH 129 (149)
Q Consensus 79 ed~~~FLkHLnseH~LDDrStAQcRVQmqVVqqLE~QL~kEkeRLqAMm~H 129 (149)
-.+..||..|. ....-|.+.|.+++..+..-++.+...+..
T Consensus 67 ~~~~~fl~~L~----------~~i~~q~~~v~~~~~~ve~~r~~~~ea~~~ 107 (146)
T PRK07720 67 RHYQQFVTNLE----------RTIDHYQLLVMQAREQMNRKQQDLTEKNIE 107 (146)
T ss_pred HHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677888876 456678889999999988888777766554
No 46
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.75 E-value=1.9e+02 Score=19.71 Aligned_cols=46 Identities=13% Similarity=0.221 Sum_probs=33.6
Q ss_pred CCCccccCHHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy15596 73 GCEAVCEDVQAFYKHLNKEHNLDDRSTAQARVQMQVVSQLELQLQKERDRLQAM 126 (149)
Q Consensus 73 GCe~~~ed~~~FLkHLnseH~LDDrStAQcRVQmqVVqqLE~QL~kEkeRLqAM 126 (149)
.++...++...++..+..+. + |.-+.+++..--.+|..+.+.|.+|
T Consensus 54 ~~g~~~~~i~~~l~~~~~~~-----~---~~~~~~~~~~~~~~l~~~~~~l~~~ 99 (100)
T cd00592 54 ELGLSLKEIRELLDARDEEL-----S---LAALLALLDEKLAELEEKIARLEAL 99 (100)
T ss_pred HcCCCHHHHHHHHhcccccc-----h---HHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 35667788888887655322 2 7777888888888888888888876
No 47
>COG3524 KpsE Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]
Probab=22.20 E-value=1.5e+02 Score=27.29 Aligned_cols=28 Identities=43% Similarity=0.481 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy15596 99 TAQARVQMQVVSQLELQLQKERDRLQAM 126 (149)
Q Consensus 99 tAQcRVQmqVVqqLE~QL~kEkeRLqAM 126 (149)
.+|..|||.+|.+||..|.+=-..|.-.
T Consensus 215 ~~qaevq~~Lvs~Le~eL~~iqaqL~tv 242 (372)
T COG3524 215 KAQAEVQMSLVSKLEDELIVIQAQLDTV 242 (372)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999887655555433
No 48
>KOG0980|consensus
Probab=20.87 E-value=1.7e+02 Score=30.03 Aligned_cols=30 Identities=37% Similarity=0.482 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy15596 99 TAQARVQMQVVSQLELQLQKERDRLQAMMLH 129 (149)
Q Consensus 99 tAQcRVQmqVVqqLE~QL~kEkeRLqAMm~H 129 (149)
++....|-+|+ .||.-|..||.||.+|..+
T Consensus 944 ~~EME~QVkvL-eLEq~L~~eR~rL~elRK~ 973 (980)
T KOG0980|consen 944 TQEMEQQVKVL-ELEQSLQAERARLGELRKQ 973 (980)
T ss_pred HHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH
Confidence 34445555555 5899999999999999654
No 49
>COG5613 Uncharacterized conserved protein [Function unknown]
Probab=20.38 E-value=2.1e+02 Score=26.68 Aligned_cols=29 Identities=21% Similarity=0.287 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy15596 100 AQARVQMQVVSQLELQLQKERDRLQAMML 128 (149)
Q Consensus 100 AQcRVQmqVVqqLE~QL~kEkeRLqAMm~ 128 (149)
+|.+-=.-+.++|+.+|..|.+|++..|.
T Consensus 344 ad~~~Lq~iierlkeelk~e~e~~qe~me 372 (400)
T COG5613 344 ADVQNLQRIIERLKEELKLELEKAQEEME 372 (400)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333335788999999999999987654
Done!