Query psy3660
Match_columns 144
No_of_seqs 188 out of 1105
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 22:24:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3660.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3660hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1278 CspC Cold shock protei 99.8 1.5E-20 3.3E-25 130.0 5.4 61 78-138 1-66 (67)
2 PRK09937 stationary phase/star 99.8 6.1E-20 1.3E-24 128.1 5.9 64 78-141 1-69 (74)
3 PRK14998 cold shock-like prote 99.8 8.9E-20 1.9E-24 126.9 6.0 65 78-142 1-70 (73)
4 TIGR02381 cspD cold shock doma 99.8 8.8E-20 1.9E-24 124.6 4.9 63 78-140 1-68 (68)
5 PRK09507 cspE cold shock prote 99.8 2.4E-19 5.2E-24 123.0 5.6 61 78-138 3-68 (69)
6 PRK15464 cold shock-like prote 99.8 2E-19 4.3E-24 124.5 5.1 58 79-136 5-67 (70)
7 PRK10943 cold shock-like prote 99.8 1.9E-19 4.1E-24 123.6 4.8 60 78-137 3-67 (69)
8 PRK15463 cold shock-like prote 99.8 1.9E-19 4.1E-24 124.2 4.9 58 79-136 5-67 (70)
9 PRK09890 cold shock protein Cs 99.8 5E-19 1.1E-23 121.7 5.9 60 79-138 5-69 (70)
10 PRK10354 RNA chaperone/anti-te 99.8 1.3E-18 2.9E-23 119.4 5.6 59 79-137 5-68 (70)
11 cd04458 CSP_CDS Cold-Shock Pro 99.6 2.3E-16 5E-21 104.8 4.7 58 79-136 1-63 (65)
12 PF00313 CSD: 'Cold-shock' DNA 99.6 2.7E-16 5.9E-21 104.7 4.4 60 79-138 1-65 (66)
13 KOG3070|consensus 99.2 1.5E-11 3.3E-16 102.0 5.3 65 72-136 50-123 (235)
14 smart00357 CSP Cold shock prot 98.4 3.7E-07 8E-12 58.2 3.3 46 80-128 1-46 (64)
15 PF08206 OB_RNB: Ribonuclease 96.6 0.0013 2.8E-08 43.3 1.9 39 81-121 1-40 (58)
16 PF14444 S1-like: S1-like 96.1 0.006 1.3E-07 41.5 2.9 45 78-132 3-47 (58)
17 PF07497 Rho_RNA_bind: Rho ter 95.0 0.02 4.4E-07 40.7 2.5 37 89-128 11-52 (78)
18 cd04459 Rho_CSD Rho_CSD: Rho p 94.5 0.02 4.4E-07 39.6 1.5 36 90-128 10-50 (68)
19 PRK11642 exoribonuclease R; Pr 89.4 0.5 1.1E-05 45.7 4.5 44 77-122 83-127 (813)
20 TIGR00358 3_prime_RNase VacB a 88.8 0.75 1.6E-05 43.1 5.0 43 77-121 15-59 (654)
21 PF00575 S1: S1 RNA binding do 84.3 1.3 2.8E-05 28.9 3.0 51 74-127 3-57 (74)
22 TIGR02062 RNase_B exoribonucle 83.9 1 2.3E-05 42.2 3.3 44 75-121 15-59 (639)
23 PRK05054 exoribonuclease II; P 82.8 1.2 2.6E-05 41.8 3.2 43 76-121 19-62 (644)
24 cd04461 S1_Rrp5_repeat_hs8_sc7 81.6 1.4 3.1E-05 29.8 2.5 54 73-129 12-69 (83)
25 cd05689 S1_RPS1_repeat_ec4 S1_ 80.0 4.7 0.0001 26.2 4.5 49 76-127 4-57 (72)
26 PRK12608 transcription termina 79.9 1.5 3.3E-05 39.2 2.7 50 74-128 14-68 (380)
27 cd05692 S1_RPS1_repeat_hs4 S1_ 79.4 2 4.4E-05 26.8 2.5 50 77-129 2-55 (69)
28 cd00164 S1_like S1_like: Ribos 78.0 2.3 4.9E-05 25.8 2.4 46 80-129 2-52 (65)
29 cd05698 S1_Rrp5_repeat_hs6_sc5 75.6 2.3 5E-05 27.4 2.0 49 77-128 2-54 (70)
30 cd04453 S1_RNase_E S1_RNase_E: 74.7 3.9 8.5E-05 28.7 3.1 53 73-127 5-65 (88)
31 cd05690 S1_RPS1_repeat_ec5 S1_ 74.2 4.9 0.00011 25.7 3.3 49 77-128 2-55 (69)
32 TIGR00767 rho transcription te 74.0 1.6 3.4E-05 39.6 1.1 46 78-128 50-100 (415)
33 cd05706 S1_Rrp5_repeat_sc10 S1 73.8 5 0.00011 26.1 3.3 51 75-129 3-58 (73)
34 cd05696 S1_Rrp5_repeat_hs4 S1_ 72.7 4.2 9.1E-05 27.0 2.7 49 77-128 2-56 (71)
35 smart00316 S1 Ribosomal protei 72.4 3.1 6.7E-05 25.6 1.9 50 76-128 3-56 (72)
36 PRK09376 rho transcription ter 71.1 2 4.3E-05 39.1 1.1 45 78-127 50-99 (416)
37 cd04472 S1_PNPase S1_PNPase: P 71.1 6.6 0.00014 24.6 3.3 49 77-128 2-54 (68)
38 COG1158 Rho Transcription term 69.9 2.2 4.8E-05 38.6 1.2 45 79-128 54-103 (422)
39 cd05704 S1_Rrp5_repeat_hs13 S1 69.5 9 0.0002 25.5 3.8 53 75-129 3-59 (72)
40 TIGR02063 RNase_R ribonuclease 69.2 4.3 9.4E-05 38.3 2.9 42 77-120 67-110 (709)
41 cd05686 S1_pNO40 S1_pNO40: pNO 66.2 8.1 0.00017 25.6 3.1 51 75-128 3-58 (73)
42 cd05694 S1_Rrp5_repeat_hs2_sc2 66.2 8.4 0.00018 26.1 3.2 50 74-128 3-53 (74)
43 cd05707 S1_Rrp5_repeat_sc11 S1 64.7 7.4 0.00016 25.1 2.6 49 77-128 2-54 (68)
44 COG4776 Rnb Exoribonuclease II 63.6 4.7 0.0001 38.0 2.0 35 74-111 17-51 (645)
45 PF13509 S1_2: S1 domain; PDB: 63.3 4 8.6E-05 26.9 1.1 50 78-134 4-53 (61)
46 PRK12678 transcription termina 60.2 4.5 9.8E-05 38.8 1.3 43 79-127 296-341 (672)
47 PRK07252 hypothetical protein; 59.1 12 0.00026 27.9 3.2 50 76-128 4-57 (120)
48 cd04471 S1_RNase_R S1_RNase_R: 58.4 19 0.00042 23.5 3.8 48 77-127 3-66 (83)
49 cd05691 S1_RPS1_repeat_ec6 S1_ 57.1 12 0.00026 23.9 2.5 49 77-128 2-54 (73)
50 cd04473 S1_RecJ_like S1_RecJ_l 56.4 19 0.00042 24.1 3.6 48 73-127 14-61 (77)
51 cd05705 S1_Rrp5_repeat_hs14 S1 54.5 16 0.00035 24.6 2.9 50 75-128 3-60 (74)
52 PRK08582 hypothetical protein; 53.6 25 0.00053 26.9 4.1 51 75-128 5-59 (139)
53 cd05697 S1_Rrp5_repeat_hs5 S1_ 53.5 13 0.00029 23.9 2.3 49 77-128 2-54 (69)
54 cd05687 S1_RPS1_repeat_ec1_hs1 52.7 15 0.00032 23.6 2.5 50 77-129 2-55 (70)
55 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 52.6 8.7 0.00019 25.9 1.4 52 75-129 6-65 (86)
56 cd05685 S1_Tex S1_Tex: The C-t 51.5 21 0.00044 22.1 2.9 49 77-128 2-54 (68)
57 cd05703 S1_Rrp5_repeat_hs12_sc 49.8 13 0.00027 24.9 1.8 49 77-128 2-56 (73)
58 COG0539 RpsA Ribosomal protein 48.0 20 0.00043 33.8 3.3 94 31-127 227-330 (541)
59 cd05684 S1_DHX8_helicase S1_DH 44.7 32 0.00069 22.8 3.2 47 77-126 2-56 (79)
60 TIGR02696 pppGpp_PNP guanosine 42.8 22 0.00047 34.6 2.8 52 73-127 645-704 (719)
61 cd04452 S1_IF2_alpha S1_IF2_al 42.0 41 0.00088 21.7 3.3 51 75-128 3-59 (76)
62 cd05702 S1_Rrp5_repeat_hs11_sc 41.6 30 0.00065 22.5 2.6 47 77-127 2-55 (70)
63 PF01551 Peptidase_M23: Peptid 41.5 21 0.00046 24.4 2.0 47 79-125 20-69 (96)
64 TIGR03591 polynuc_phos polyrib 40.0 25 0.00054 33.5 2.8 52 73-127 616-671 (684)
65 cd04465 S1_RPS1_repeat_ec2_hs2 39.3 28 0.00061 22.3 2.2 47 77-127 2-50 (67)
66 PRK11637 AmiB activator; Provi 38.9 23 0.00051 31.1 2.3 48 78-125 345-395 (428)
67 PHA02945 interferon resistance 38.4 86 0.0019 23.0 4.8 36 73-112 9-46 (88)
68 PRK08059 general stress protei 37.3 45 0.00097 24.6 3.3 52 74-128 6-61 (123)
69 PRK10871 nlpD lipoprotein NlpD 37.3 42 0.0009 29.5 3.5 55 78-132 235-295 (319)
70 PRK11824 polynucleotide phosph 34.4 49 0.0011 31.6 3.8 53 73-128 619-675 (693)
71 PF05606 DUF777: Borrelia burg 34.1 45 0.00098 27.3 3.0 45 79-125 36-80 (181)
72 PRK13806 rpsA 30S ribosomal pr 33.0 39 0.00085 30.6 2.8 55 72-129 289-348 (491)
73 cd05708 S1_Rrp5_repeat_sc12 S1 32.9 57 0.0012 20.8 2.9 49 76-127 3-56 (77)
74 cd05688 S1_RPS1_repeat_ec3 S1_ 31.8 60 0.0013 20.0 2.8 49 76-128 2-54 (68)
75 cd04454 S1_Rrp4_like S1_Rrp4_l 28.6 47 0.001 22.2 2.0 52 75-129 6-61 (82)
76 COG4942 Membrane-bound metallo 28.3 42 0.00091 30.7 2.1 53 78-130 337-394 (420)
77 COG2183 Tex Transcriptional ac 28.1 36 0.00079 33.5 1.8 53 73-128 656-712 (780)
78 PRK11649 putative peptidase; P 27.8 47 0.001 30.1 2.3 53 79-131 330-387 (439)
79 PLN00207 polyribonucleotide nu 27.6 50 0.0011 32.9 2.6 51 74-127 752-807 (891)
80 cd04455 S1_NusA S1_NusA: N-uti 27.2 70 0.0015 20.7 2.6 47 75-127 3-49 (67)
81 PRK05807 hypothetical protein; 27.2 64 0.0014 24.5 2.7 50 75-128 5-58 (136)
82 COG0539 RpsA Ribosomal protein 25.1 49 0.0011 31.2 2.0 51 72-126 189-243 (541)
83 PRK06299 rpsA 30S ribosomal pr 23.5 68 0.0015 29.2 2.6 53 73-128 371-428 (565)
84 PRK13806 rpsA 30S ribosomal pr 23.3 76 0.0017 28.8 2.9 53 73-128 200-256 (491)
85 COG1098 VacB Predicted RNA bin 23.3 47 0.001 25.9 1.3 47 76-126 6-57 (129)
86 PF01796 DUF35: DUF35 OB-fold 22.3 1.5E+02 0.0031 19.5 3.4 34 92-126 31-64 (68)
87 KOG0407|consensus 22.2 59 0.0013 25.2 1.7 16 100-115 24-39 (139)
88 TIGR00358 3_prime_RNase VacB a 22.0 1.2E+02 0.0025 28.7 3.9 51 75-128 572-638 (654)
89 cd05695 S1_Rrp5_repeat_hs3 S1_ 21.2 97 0.0021 20.1 2.4 49 77-128 2-52 (66)
90 TIGR00717 rpsA ribosomal prote 20.8 94 0.002 27.8 2.9 54 72-128 356-414 (516)
No 1
>COG1278 CspC Cold shock proteins [Transcription]
Probab=99.82 E-value=1.5e-20 Score=130.00 Aligned_cols=61 Identities=36% Similarity=0.499 Sum_probs=51.4
Q ss_pred ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceec-----eeeeCCccccccccee
Q psy3660 78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQIN-----KALQGSKTCNSCNISS 138 (144)
Q Consensus 78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~G-----d~V~g~kg~~a~~i~~ 138 (144)
|.+|+|||||..||||||+++++++|||||+|+|+...-..+..| ++++|.||.+|.||..
T Consensus 1 ~~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~~g~kgp~A~nv~~ 66 (67)
T COG1278 1 MATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQGRKGPSAANVRA 66 (67)
T ss_pred CCcceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCcccCCCCEEEEEEecCCCCCceeEEEe
Confidence 468999999999999999999999999999999987643444444 5668899999999864
No 2
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=99.80 E-value=6.1e-20 Score=128.10 Aligned_cols=64 Identities=31% Similarity=0.508 Sum_probs=54.8
Q ss_pred ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccceeeec
Q psy3660 78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNISSVEL 141 (144)
Q Consensus 78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~~~~~ 141 (144)
|.+|+|||||..||||||+++++++|||||+++|+....+.++.||.| ++++|.+|.+|..++.
T Consensus 1 M~~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~~ 69 (74)
T PRK09937 1 MEKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIVPVEV 69 (74)
T ss_pred CCCeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCCceeeEEEECCc
Confidence 457999999999999999999999999999999987633667777655 7889999999987753
No 3
>PRK14998 cold shock-like protein CspD; Provisional
Probab=99.80 E-value=8.9e-20 Score=126.87 Aligned_cols=65 Identities=31% Similarity=0.492 Sum_probs=55.2
Q ss_pred ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccceeeecC
Q psy3660 78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNISSVELG 142 (144)
Q Consensus 78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~~~~~~ 142 (144)
|.+|+|||||..||||||+++++++|||||+++|+...-+.+..|+.| ++.+|.+|.+|..++.+
T Consensus 1 M~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~~~ 70 (73)
T PRK14998 1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIVPIEAE 70 (73)
T ss_pred CCCeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCCCCCCCEEEEEEEECCCCceeEEEEECccc
Confidence 458999999999999999999999999999999987633666666655 78899999999877654
No 4
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=99.79 E-value=8.8e-20 Score=124.60 Aligned_cols=63 Identities=27% Similarity=0.450 Sum_probs=53.0
Q ss_pred ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccceeee
Q psy3660 78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNISSVE 140 (144)
Q Consensus 78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~~~~ 140 (144)
|.+|+|||||..||||||.++++++|||||+++|+....+.++.||.| ++.+|.+|.+|+.++
T Consensus 1 m~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~ 68 (68)
T TIGR02381 1 MAIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGPKGAHATHIVPIE 68 (68)
T ss_pred CCCeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCCCCCCCEEEEEEEECCCCceeEEEEECC
Confidence 457999999999999999999999999999999987633666777766 678888998887653
No 5
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=99.78 E-value=2.4e-19 Score=123.00 Aligned_cols=61 Identities=33% Similarity=0.458 Sum_probs=51.7
Q ss_pred ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCccccccccee
Q psy3660 78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNISS 138 (144)
Q Consensus 78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~~ 138 (144)
..+|+|||||..||||||+++++++|||||+++|+...-+.++.||.| ++.+|.+|.+|..
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 68 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIA 68 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCCCCCCCEEEEEEEECCCCcccEEEEe
Confidence 468999999999999999999999999999999987633677777766 6677788887754
No 6
>PRK15464 cold shock-like protein CspH; Provisional
Probab=99.78 E-value=2e-19 Score=124.45 Aligned_cols=58 Identities=31% Similarity=0.465 Sum_probs=49.2
Q ss_pred cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccc
Q psy3660 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNI 136 (144)
Q Consensus 79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i 136 (144)
++|+|||||..||||||+++++++|||||+++|+...-+.++.||.| ++.+|.+|.+|
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~~~~kG~~A~~v 67 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 67 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEEECCCCceeEEE
Confidence 48999999999999999999999999999999987734467777766 56677777776
No 7
>PRK10943 cold shock-like protein CspC; Provisional
Probab=99.78 E-value=1.9e-19 Score=123.55 Aligned_cols=60 Identities=33% Similarity=0.432 Sum_probs=50.6
Q ss_pred ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccce
Q psy3660 78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNIS 137 (144)
Q Consensus 78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~ 137 (144)
+++|+|||||..||||||+++++++|||||+++|+....+.++.||.| ++.+|.+|.+|.
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~g~~A~~V~ 67 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVT 67 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEECCCCceeEEEE
Confidence 578999999999999999999999999999999987733667777766 667777777774
No 8
>PRK15463 cold shock-like protein CspF; Provisional
Probab=99.78 E-value=1.9e-19 Score=124.22 Aligned_cols=58 Identities=29% Similarity=0.398 Sum_probs=48.2
Q ss_pred cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccc
Q psy3660 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNI 136 (144)
Q Consensus 79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i 136 (144)
++|+|||||..||||||+++++++|||||+++|+....+.|+.||.| ++.+|.+|.+|
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~~~G~~A~~V 67 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 67 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEECCCCceeEEE
Confidence 48999999999999999999999999999999987655667777766 55556666555
No 9
>PRK09890 cold shock protein CspG; Provisional
Probab=99.77 E-value=5e-19 Score=121.73 Aligned_cols=60 Identities=35% Similarity=0.496 Sum_probs=50.9
Q ss_pred cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCccccccccee
Q psy3660 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNISS 138 (144)
Q Consensus 79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~~ 138 (144)
++|+|||||..||||||+++++++|||||+++|+....+.++.||.| ++.+|.+|.+|..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 69 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVT 69 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence 48999999999999999999999999999999987744667777766 6677888888753
No 10
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=99.75 E-value=1.3e-18 Score=119.36 Aligned_cols=59 Identities=36% Similarity=0.460 Sum_probs=49.7
Q ss_pred cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccce
Q psy3660 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNIS 137 (144)
Q Consensus 79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~ 137 (144)
++|+|||||..||||||.++++++|||||+++|+....+.++.||.| ++.+|.+|.+|.
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G~~A~~V~ 68 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVT 68 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCCceeEEEE
Confidence 38999999999999999999999999999999988744677888877 456666777664
No 11
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=99.64 E-value=2.3e-16 Score=104.80 Aligned_cols=58 Identities=36% Similarity=0.413 Sum_probs=48.8
Q ss_pred cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceeeeC-----Ccccccccc
Q psy3660 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQG-----SKTCNSCNI 136 (144)
Q Consensus 79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V~g-----~kg~~a~~i 136 (144)
.+|+|||||..||||||+++++++|||||++++.....+.++.||.|++ .+|.+|.+|
T Consensus 1 ~~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~~~g~~A~~V 63 (65)
T cd04458 1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNV 63 (65)
T ss_pred CcEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEECCCCCeEEEe
Confidence 3799999999999999999998899999999999875677888887755 555566555
No 12
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=99.63 E-value=2.7e-16 Score=104.74 Aligned_cols=60 Identities=33% Similarity=0.426 Sum_probs=48.4
Q ss_pred cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceeee-----CCccccccccee
Q psy3660 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQ-----GSKTCNSCNISS 138 (144)
Q Consensus 79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V~-----g~kg~~a~~i~~ 138 (144)
++|+||||+..||||||.++++++|||||++++....-+.+..||.|+ +.+|.+|.+|..
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~F~~~~~~~g~~A~~V~~ 65 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVEFEVEEGKKGPQAVNVRK 65 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEEEEEEECTTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccccccCCCCCEEEEEEEECCCCCEEEEEEC
Confidence 479999999999999999999999999999999888336777777775 566677776643
No 13
>KOG3070|consensus
Probab=99.21 E-value=1.5e-11 Score=102.01 Aligned_cols=65 Identities=31% Similarity=0.376 Sum_probs=50.7
Q ss_pred cccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeecccc----CC-----CccceeceeeeCCcccccccc
Q psy3660 72 RALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVI----MP-----KLISQINKALQGSKTCNSCNI 136 (144)
Q Consensus 72 r~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~----~~-----g~~p~~Gd~V~g~kg~~a~~i 136 (144)
+.......+|+|||||..+|||||.++|+.+|||||+++|.. .. .+....-+++.+.+|..|.++
T Consensus 50 ~~~~~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g~~a~~v 123 (235)
T KOG3070|consen 50 KKVQGARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKGTEAANV 123 (235)
T ss_pred cccccccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCccceeeee
Confidence 455667889999999999999999999999999999999988 21 122234467778888555554
No 14
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=98.37 E-value=3.7e-07 Score=58.21 Aligned_cols=46 Identities=37% Similarity=0.446 Sum_probs=35.1
Q ss_pred ccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceeeeCC
Q psy3660 80 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQGS 128 (144)
Q Consensus 80 ~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V~g~ 128 (144)
+|+|+|++ +|||||.+++...|+|||.+.++. ....+..||.|.+.
T Consensus 1 ~G~i~~~~--~g~gfv~~~~~~~~i~v~~~~~~~-~~~~~~~Gd~V~~~ 46 (64)
T smart00357 1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFK 46 (64)
T ss_pred CeEEEEEc--CCeeEEecCCCCccEEEEhHHhhc-CCCcCCCCCEEEEE
Confidence 58999998 799999998766799999998755 23445556666554
No 15
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=96.61 E-value=0.0013 Score=43.31 Aligned_cols=39 Identities=26% Similarity=0.439 Sum_probs=26.0
Q ss_pred cEEEEccCCCceeEecCCCCCCcEEEEeeccccC-CCcccee
Q psy3660 81 GKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM-PKLISQI 121 (144)
Q Consensus 81 GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~-~g~~p~~ 121 (144)
|+++. ..+||||+.+++.++||||....+... .|+++.+
T Consensus 1 G~~~~--~~~GfGFv~~~~~~~DifIp~~~l~~A~~gD~V~v 40 (58)
T PF08206_consen 1 GTLKI--HPKGFGFVIPDDGGEDIFIPPRNLNGAMDGDKVLV 40 (58)
T ss_dssp EEEEE---SSS-EEEEECT-TEEEEE-HHHHTTS-TT-EEEE
T ss_pred CEEEE--EcCCCEEEEECCCCCCEEECHHHHCCCCCCCEEEE
Confidence 44444 479999999999889999999998764 3555544
No 16
>PF14444 S1-like: S1-like
Probab=96.07 E-value=0.006 Score=41.46 Aligned_cols=45 Identities=22% Similarity=0.369 Sum_probs=35.8
Q ss_pred ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceeeeCCcccc
Q psy3660 78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQGSKTCN 132 (144)
Q Consensus 78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V~g~kg~~ 132 (144)
..+|.|..++ ..||||. +||||+.++++ |..|++||.|...-.+|
T Consensus 3 ~~~GvVTkl~--~~yG~ID-----e~vFF~~~vv~---G~~P~vGdrV~v~A~~n 47 (58)
T PF14444_consen 3 VFTGVVTKLC--DDYGFID-----EDVFFQTDVVK---GNVPKVGDRVLVEAIYN 47 (58)
T ss_pred eEEEEEEEEe--CCcceEc-----ccEEEEcccEe---cCCCccCCEEEEEEEeC
Confidence 3589999997 5799995 68999999966 67889999997654443
No 17
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=95.00 E-value=0.02 Score=40.68 Aligned_cols=37 Identities=19% Similarity=0.334 Sum_probs=24.8
Q ss_pred CCceeEecCC-----CCCCcEEEEeeccccCCCccceeceeeeCC
Q psy3660 89 SKGHGFITPD-----SGEPAVFVHISDYVIMPKLISQINKALQGS 128 (144)
Q Consensus 89 ~KGfGFI~~d-----~gg~DVFVHiSai~~~~g~~p~~Gd~V~g~ 128 (144)
.+||||+... .+.+||||-.+.|+.- + ++.||.|.|.
T Consensus 11 ~dGyGFLR~~~~~y~~~~~DvYVs~~qIrrf-~--LR~GD~V~G~ 52 (78)
T PF07497_consen 11 PDGYGFLRSPDNNYLPSPDDVYVSPSQIRRF-G--LRTGDLVEGQ 52 (78)
T ss_dssp TTS-EEEE-GGGTTS-STTSEEE-CCCCCCT-T----TTEEEEEE
T ss_pred CCCcEEeECCCcCCCCCCCCEEECHHHHHHc-C--CCCCCEEEEE
Confidence 4799999987 3568999999999876 3 5667777654
No 18
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=94.51 E-value=0.02 Score=39.60 Aligned_cols=36 Identities=19% Similarity=0.429 Sum_probs=28.5
Q ss_pred CceeEecCC-----CCCCcEEEEeeccccCCCccceeceeeeCC
Q psy3660 90 KGHGFITPD-----SGEPAVFVHISDYVIMPKLISQINKALQGS 128 (144)
Q Consensus 90 KGfGFI~~d-----~gg~DVFVHiSai~~~~g~~p~~Gd~V~g~ 128 (144)
+||||+... .+.+||||..+-|+.- + +..||.|.|.
T Consensus 10 ~g~GFLR~~~~~y~~~~~DvyVs~~~Irr~-~--LR~GD~V~G~ 50 (68)
T cd04459 10 DGFGFLRSSGYNYLPGPDDIYVSPSQIRRF-N--LRTGDTVVGQ 50 (68)
T ss_pred CCceEEecCCcCCCCCCCCEEECHHHHHHh-C--CCCCCEEEEE
Confidence 499999976 2568999999999887 4 5667888774
No 19
>PRK11642 exoribonuclease R; Provisional
Probab=89.41 E-value=0.5 Score=45.65 Aligned_cols=44 Identities=9% Similarity=0.160 Sum_probs=33.5
Q ss_pred cccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC-CCccceec
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM-PKLISQIN 122 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~-~g~~p~~G 122 (144)
..+.|+|+. ..+||||+.++++++||||.-..+... .||++.+-
T Consensus 83 ~~~~G~v~~--~~~GfgFv~~e~~~~difI~~~~l~~A~~GD~V~v~ 127 (813)
T PRK11642 83 DLLKGTVIG--HRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQ 127 (813)
T ss_pred ceEEEEEEE--CCCccEEEEECCCCCCEEEChHHHccCCCCCEEEEE
Confidence 357899996 679999999987678999988776543 36666543
No 20
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=88.77 E-value=0.75 Score=43.09 Aligned_cols=43 Identities=21% Similarity=0.403 Sum_probs=32.5
Q ss_pred cccccEEEEccCCCceeEecCCC-CCCcEEEEeeccccC-CCcccee
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDS-GEPAVFVHISDYVIM-PKLISQI 121 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~-gg~DVFVHiSai~~~-~g~~p~~ 121 (144)
....|++++ ..|||||+.+++ +++||||.-..+... .||++.+
T Consensus 15 ~~~~G~i~~--~~~gfgFv~~~~~~~~difI~~~~~~~a~~GD~V~v 59 (654)
T TIGR00358 15 DLVKGVVKA--HNKGFGFLRPDDDDKKDYFIPPPQMKKVMHGDLVEA 59 (654)
T ss_pred CeEEEEEEE--CCCccEEEEeCCCCCCcEEEchHHhCcCCCCCEEEE
Confidence 457899997 579999999986 368999987776442 3666644
No 21
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=84.29 E-value=1.3 Score=28.88 Aligned_cols=51 Identities=16% Similarity=0.208 Sum_probs=38.1
Q ss_pred cCCcccccEEEEccCCCceeEecCCCCCCcEEEEeecccc----CCCccceeceeeeC
Q psy3660 74 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVI----MPKLISQINKALQG 127 (144)
Q Consensus 74 ~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~----~~g~~p~~Gd~V~g 127 (144)
..++.+.|+|...+. +|++-.-+.+-+.|+|.+.+.. .+.....+||.|..
T Consensus 3 ~~G~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v 57 (74)
T PF00575_consen 3 KEGDIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRV 57 (74)
T ss_dssp STTSEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEE
T ss_pred CCCCEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEE
Confidence 457788999999876 5555544466899999999874 35677788887754
No 22
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=83.87 E-value=1 Score=42.23 Aligned_cols=44 Identities=23% Similarity=0.317 Sum_probs=32.0
Q ss_pred CCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC-CCcccee
Q psy3660 75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM-PKLISQI 121 (144)
Q Consensus 75 ~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~-~g~~p~~ 121 (144)
......|++++ ..|||||+..++ .+||||.-..+... .||++.+
T Consensus 15 ~~~~~~G~i~~--~~kGfgFv~~~~-~~difI~~~~l~~A~~GD~V~v 59 (639)
T TIGR02062 15 QTPRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKVMHGDKIIA 59 (639)
T ss_pred cCceEEEEEEE--CCCccEEEEECC-CCcEEEChHHHccCCCCCEEEE
Confidence 34567799997 679999996554 46999988876543 3666644
No 23
>PRK05054 exoribonuclease II; Provisional
Probab=82.83 E-value=1.2 Score=41.83 Aligned_cols=43 Identities=21% Similarity=0.301 Sum_probs=31.9
Q ss_pred CcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC-CCcccee
Q psy3660 76 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM-PKLISQI 121 (144)
Q Consensus 76 ~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~-~g~~p~~ 121 (144)
.....|++++ ..|||||+.+++ .+||||.-..+... .||++.+
T Consensus 19 ~~~~~G~~~~--~~~gfgFv~~~~-~~difI~~~~l~~a~~GD~V~v 62 (644)
T PRK05054 19 TPRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKVMHGDRIIA 62 (644)
T ss_pred CCeEEEEEEE--CCCccEEEEECC-CCcEEEChHHHccCCCCCEEEE
Confidence 3457799997 579999998754 46999988887543 3666644
No 24
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=81.62 E-value=1.4 Score=29.77 Aligned_cols=54 Identities=11% Similarity=0.015 Sum_probs=38.9
Q ss_pred ccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeCCc
Q psy3660 73 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQGSK 129 (144)
Q Consensus 73 ~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~k 129 (144)
+..+..+.|+|+.... ||++-.-.++-+.|+|++.+... +.+...+||.|....
T Consensus 12 ~~~G~i~~g~V~~v~~---~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV 69 (83)
T cd04461 12 LKPGMVVHGYVRNITP---YGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKV 69 (83)
T ss_pred CCCCCEEEEEEEEEee---ceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEE
Confidence 5567889999998764 77766654557999999998543 244457788876543
No 25
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=80.00 E-value=4.7 Score=26.19 Aligned_cols=49 Identities=14% Similarity=0.194 Sum_probs=33.3
Q ss_pred CcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC-----CCccceeceeeeC
Q psy3660 76 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM-----PKLISQINKALQG 127 (144)
Q Consensus 76 ~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~-----~g~~p~~Gd~V~g 127 (144)
+..+.|+|+... -||+...-+.+-+.|+|++.+... .++..++||.|.-
T Consensus 4 g~~~~g~V~~i~---~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v 57 (72)
T cd05689 4 GTRLFGKVTNLT---DYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEV 57 (72)
T ss_pred CCEEEEEEEEEE---eeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEE
Confidence 456889999864 488776544458999999998532 2334577777743
No 26
>PRK12608 transcription termination factor Rho; Provisional
Probab=79.95 E-value=1.5 Score=39.24 Aligned_cols=50 Identities=16% Similarity=0.240 Sum_probs=37.0
Q ss_pred cCCcccccEEEEccCCCceeEecCC-----CCCCcEEEEeeccccCCCccceeceeeeCC
Q psy3660 74 LQNPVETGKIKEFCRSKGHGFITPD-----SGEPAVFVHISDYVIMPKLISQINKALQGS 128 (144)
Q Consensus 74 ~~~~~~~GtVK~Fd~~KGfGFI~~d-----~gg~DVFVHiSai~~~~g~~p~~Gd~V~g~ 128 (144)
.+.....|.+--.. +||||+... .+.+||||..+.|+.. + +..||.|.+.
T Consensus 14 ~~~~~~~g~l~~~~--~g~gflr~~~~~~~~~~~d~yv~~~~i~~~-~--l~~Gd~V~~~ 68 (380)
T PRK12608 14 QSTEEVLGVLEILG--DGFGFLRSARRNYLPSPDDVFVPPALIRRF-N--LRTGDVVEGV 68 (380)
T ss_pred cCCCcceEEEEEcC--CCceEeecCccCCCCCCCCeeeCHHHHHHh-C--CCCCCEEEec
Confidence 34445678888765 499999985 3468999999999876 3 5667777664
No 27
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=79.40 E-value=2 Score=26.81 Aligned_cols=50 Identities=18% Similarity=0.161 Sum_probs=33.7
Q ss_pred cccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCC----CccceeceeeeCCc
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMP----KLISQINKALQGSK 129 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~----g~~p~~Gd~V~g~k 129 (144)
..+.|+|..... ||+.-.-+.+.+.|+|++.+.... ....++||.|....
T Consensus 2 ~~~~g~V~~i~~---~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v 55 (69)
T cd05692 2 SVVEGTVTRLKP---FGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKV 55 (69)
T ss_pred CEEEEEEEEEEe---eeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEE
Confidence 456788888653 676665555578999999986431 23457788876543
No 28
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=77.97 E-value=2.3 Score=25.81 Aligned_cols=46 Identities=22% Similarity=0.348 Sum_probs=31.3
Q ss_pred ccEEEEccCCCcee-EecCCCCCCcEEEEeeccccC----CCccceeceeeeCCc
Q psy3660 80 TGKIKEFCRSKGHG-FITPDSGEPAVFVHISDYVIM----PKLISQINKALQGSK 129 (144)
Q Consensus 80 ~GtVK~Fd~~KGfG-FI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~k 129 (144)
.|+|+... .+| |+..+ .+.+.|+|.+.+... .....+.||.|....
T Consensus 2 ~g~V~~v~---~~g~~v~l~-~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v 52 (65)
T cd00164 2 TGKVVSIT---KFGVFVELE-DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKV 52 (65)
T ss_pred EEEEEEEE---eeeEEEEec-CCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEE
Confidence 57888876 345 44444 447899999998653 245678888886554
No 29
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=75.61 E-value=2.3 Score=27.43 Aligned_cols=49 Identities=14% Similarity=0.116 Sum_probs=32.8
Q ss_pred cccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeCC
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQGS 128 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~ 128 (144)
..+.|+|+...+ ||..-.-.++-+.|+|++.+... +....++||.+...
T Consensus 2 ~~~~g~V~~v~~---~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~ 54 (70)
T cd05698 2 LKTHGTIVKVKP---NGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVK 54 (70)
T ss_pred CEEEEEEEEEec---CcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEE
Confidence 457889988753 55555444447899999998532 34446788877654
No 30
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=74.71 E-value=3.9 Score=28.73 Aligned_cols=53 Identities=13% Similarity=0.212 Sum_probs=35.4
Q ss_pred ccCCcccccEEEEccCCCcee-EecCCCCCCcEEEEeecccc-------CCCccceeceeeeC
Q psy3660 73 ALQNPVETGKIKEFCRSKGHG-FITPDSGEPAVFVHISDYVI-------MPKLISQINKALQG 127 (144)
Q Consensus 73 ~~~~~~~~GtVK~Fd~~KGfG-FI~~d~gg~DVFVHiSai~~-------~~g~~p~~Gd~V~g 127 (144)
...+..+.|+|+.....- +| |+...+ +.+.|+|++.+.. ...+.++.||.|.-
T Consensus 5 ~~~G~iy~g~V~~i~~~~-~GaFV~l~~-g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~V 65 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGL-QAAFVDIGL-GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILV 65 (88)
T ss_pred CCCCCEEEEEEEEeccCC-cEEEEEeCC-CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEE
Confidence 346778999999985421 34 555554 4799999999843 22445677777643
No 31
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=74.20 E-value=4.9 Score=25.66 Aligned_cols=49 Identities=29% Similarity=0.362 Sum_probs=32.9
Q ss_pred cccccEEEEccCCCceeEecCCCCCCcEEEEeecccc-C----CCccceeceeeeCC
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVI-M----PKLISQINKALQGS 128 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~-~----~g~~p~~Gd~V~g~ 128 (144)
..+.|+|+... -||+...-+.+-+.++|++.+.. . +.+..++||.|.-.
T Consensus 2 ~~~~g~V~~i~---~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~ 55 (69)
T cd05690 2 TVVSGKIKSIT---DFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAV 55 (69)
T ss_pred CEEEEEEEEEE---eeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEE
Confidence 35678888864 47777654455889999999862 2 13345778877543
No 32
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=73.95 E-value=1.6 Score=39.61 Aligned_cols=46 Identities=17% Similarity=0.389 Sum_probs=33.9
Q ss_pred ccccEEEEccCCCceeEecCC-----CCCCcEEEEeeccccCCCccceeceeeeCC
Q psy3660 78 VETGKIKEFCRSKGHGFITPD-----SGEPAVFVHISDYVIMPKLISQINKALQGS 128 (144)
Q Consensus 78 ~~~GtVK~Fd~~KGfGFI~~d-----~gg~DVFVHiSai~~~~g~~p~~Gd~V~g~ 128 (144)
...|.+--.. .||||+... .+.+||||-.+.|+.- + +..||.|.|.
T Consensus 50 ~~~g~le~~~--~g~gflr~~~~~~~~~~~d~yvs~~~i~~~-~--lr~gd~v~g~ 100 (415)
T TIGR00767 50 FGEGVLEILP--DGFGFLRSPDSSYLPGPDDIYVSPSQIRRF-N--LRTGDTIEGQ 100 (415)
T ss_pred EEEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhc-C--CCCCCEEEEE
Confidence 4567766544 499999985 3568999999999876 3 4567777764
No 33
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=73.77 E-value=5 Score=26.13 Aligned_cols=51 Identities=8% Similarity=0.006 Sum_probs=34.5
Q ss_pred CCcccccEEEEccCCCceeEe-cCCCCCCcEEEEeeccccC----CCccceeceeeeCCc
Q psy3660 75 QNPVETGKIKEFCRSKGHGFI-TPDSGEPAVFVHISDYVIM----PKLISQINKALQGSK 129 (144)
Q Consensus 75 ~~~~~~GtVK~Fd~~KGfGFI-~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~k 129 (144)
.+..+.|+|+.... +|.+ ..+. +-+.|+|++++... ......+||.|+...
T Consensus 3 ~G~iv~g~V~~v~~---~gi~v~l~~-~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V 58 (73)
T cd05706 3 VGDILPGRVTKVND---RYVLVQLGN-KVTGPSFITDALDDYSEALPYKFKKNDIVRACV 58 (73)
T ss_pred CCCEEEEEEEEEeC---CeEEEEeCC-CcEEEEEhhhccCccccccccccCCCCEEEEEE
Confidence 45678899998743 4544 4444 47899999998643 234467888886644
No 34
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=72.69 E-value=4.2 Score=27.04 Aligned_cols=49 Identities=16% Similarity=0.025 Sum_probs=31.9
Q ss_pred cccc-cEEEEccCCCceeE-ecCCCCCCcEEEEeeccccC----CCccceeceeeeCC
Q psy3660 77 PVET-GKIKEFCRSKGHGF-ITPDSGEPAVFVHISDYVIM----PKLISQINKALQGS 128 (144)
Q Consensus 77 ~~~~-GtVK~Fd~~KGfGF-I~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~ 128 (144)
+.++ |+|+.-.. -||. +...+ +-+-|+|++.+... .....++||.+...
T Consensus 2 ~v~~~g~V~~v~~--~~G~~V~l~~-gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~k 56 (71)
T cd05696 2 AVVDSVKVTKVEP--DLGAVFELKD-GLLGFVHISHLSDDKVPSDTGPFKAGTTHKAR 56 (71)
T ss_pred cEeeeeEEEEEcc--CceEEEEeCC-CCEEEEEHHHCCcchhcCcccccCCCCEEEEE
Confidence 3455 88888642 3555 55555 47899999988432 24556888887654
No 35
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=72.42 E-value=3.1 Score=25.64 Aligned_cols=50 Identities=12% Similarity=0.138 Sum_probs=34.4
Q ss_pred CcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCC----CccceeceeeeCC
Q psy3660 76 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMP----KLISQINKALQGS 128 (144)
Q Consensus 76 ~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~----g~~p~~Gd~V~g~ 128 (144)
+..+.|+|+..+. +|++-.-+.+-..|+|.+.+.... ....+.||.+...
T Consensus 3 G~~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~ 56 (72)
T smart00316 3 GDVVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVK 56 (72)
T ss_pred CCEEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEE
Confidence 5678899999876 555554444578999999987652 2345778877554
No 36
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=71.10 E-value=2 Score=39.07 Aligned_cols=45 Identities=18% Similarity=0.389 Sum_probs=32.2
Q ss_pred ccccEEEEccCCCceeEecCCC-----CCCcEEEEeeccccCCCccceeceeeeC
Q psy3660 78 VETGKIKEFCRSKGHGFITPDS-----GEPAVFVHISDYVIMPKLISQINKALQG 127 (144)
Q Consensus 78 ~~~GtVK~Fd~~KGfGFI~~d~-----gg~DVFVHiSai~~~~g~~p~~Gd~V~g 127 (144)
...|.+--.. .||||+...+ +.+||||-.+.|+.- + +..||.|.|
T Consensus 50 ~~~g~le~~~--~g~gflr~~~~~y~~~~~d~yvs~~~ir~~-~--lr~gd~v~g 99 (416)
T PRK09376 50 FGEGVLEILP--DGFGFLRSPDANYLPGPDDIYVSPSQIRRF-N--LRTGDTVEG 99 (416)
T ss_pred EEEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhc-C--CCCCCEEEE
Confidence 4567766554 4999999853 348999999998876 3 455666665
No 37
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=71.08 E-value=6.6 Score=24.65 Aligned_cols=49 Identities=14% Similarity=0.129 Sum_probs=33.6
Q ss_pred cccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCC----CccceeceeeeCC
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMP----KLISQINKALQGS 128 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~----g~~p~~Gd~V~g~ 128 (144)
..+.|+|..... ||+...-..+.+.|+|++.+.... .+..+.||.|...
T Consensus 2 ~~~~g~V~~v~~---~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~ 54 (68)
T cd04472 2 KIYEGKVVKIKD---FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVK 54 (68)
T ss_pred CEEEEEEEEEEE---eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEE
Confidence 356788888764 887776444579999999986542 2345778877544
No 38
>COG1158 Rho Transcription termination factor [Transcription]
Probab=69.95 E-value=2.2 Score=38.60 Aligned_cols=45 Identities=18% Similarity=0.393 Sum_probs=31.9
Q ss_pred cccEEEEccCCCceeEecCCC-----CCCcEEEEeeccccCCCccceeceeeeCC
Q psy3660 79 ETGKIKEFCRSKGHGFITPDS-----GEPAVFVHISDYVIMPKLISQINKALQGS 128 (144)
Q Consensus 79 ~~GtVK~Fd~~KGfGFI~~d~-----gg~DVFVHiSai~~~~g~~p~~Gd~V~g~ 128 (144)
..|+.--.. .||||+...+ +.+||||--|.|+.- + +..||.|+|.
T Consensus 54 ~~GvLeil~--dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf-~--LrtGD~v~G~ 103 (422)
T COG1158 54 GDGVLEILP--DGFGFLRSADSSYLPGPDDIYVSPSQIRRF-N--LRTGDTVEGK 103 (422)
T ss_pred eeeEEEecc--CCcceeecCccccCCCCCceEECHHHHhhc-c--CccCCEEeee
Confidence 345655543 7999999866 458999999998875 2 4556666553
No 39
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=69.53 E-value=9 Score=25.48 Aligned_cols=53 Identities=11% Similarity=-0.042 Sum_probs=34.1
Q ss_pred CCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCC----CccceeceeeeCCc
Q psy3660 75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMP----KLISQINKALQGSK 129 (144)
Q Consensus 75 ~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~----g~~p~~Gd~V~g~k 129 (144)
.+..+.|+|+.-... ||.+..-..+.+-|+|++.+.... .+..++||.|....
T Consensus 3 ~G~iv~G~V~~i~~~--~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV 59 (72)
T cd05704 3 EGAVTLGMVTKVIPH--SGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCI 59 (72)
T ss_pred CCCEEEEEEEEeeCC--cEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEE
Confidence 466788999986433 444444344579999999985432 23357788775543
No 40
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=69.23 E-value=4.3 Score=38.26 Aligned_cols=42 Identities=19% Similarity=0.324 Sum_probs=29.8
Q ss_pred cccccEEEEccCCCceeEecCCC-CCCcEEEEeecccc-CCCccce
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDS-GEPAVFVHISDYVI-MPKLISQ 120 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~-gg~DVFVHiSai~~-~~g~~p~ 120 (144)
..+.|+++. ..+||||+.+++ ...|+||.-..+.. ..|+++.
T Consensus 67 ~~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~~a~~GD~Vl 110 (709)
T TIGR02063 67 KLVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMNGAMHGDRVL 110 (709)
T ss_pred CeEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhCcCCCCCEEE
Confidence 357799986 578999999876 45799997666543 2355543
No 41
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=66.20 E-value=8.1 Score=25.59 Aligned_cols=51 Identities=12% Similarity=0.109 Sum_probs=34.2
Q ss_pred CCcccccEEEEccCCCceeEecCCCC-CCcEEEEeeccccCC----CccceeceeeeCC
Q psy3660 75 QNPVETGKIKEFCRSKGHGFITPDSG-EPAVFVHISDYVIMP----KLISQINKALQGS 128 (144)
Q Consensus 75 ~~~~~~GtVK~Fd~~KGfGFI~~d~g-g~DVFVHiSai~~~~----g~~p~~Gd~V~g~ 128 (144)
.+..+.|+|+...+ ||+...-++ ..+.|+|++.+.... .+..++||.|.-.
T Consensus 3 ~g~~~~g~V~~i~~---fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vk 58 (73)
T cd05686 3 LYQIFKGEVASVTE---YGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVK 58 (73)
T ss_pred CCCEEEEEEEEEEe---eeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEE
Confidence 45678899998764 776554333 358999999985542 3334778877543
No 42
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=66.15 E-value=8.4 Score=26.11 Aligned_cols=50 Identities=16% Similarity=0.145 Sum_probs=35.4
Q ss_pred cCCcccccEEEEccCCCceeEecCCC-CCCcEEEEeeccccCCCccceeceeeeCC
Q psy3660 74 LQNPVETGKIKEFCRSKGHGFITPDS-GEPAVFVHISDYVIMPKLISQINKALQGS 128 (144)
Q Consensus 74 ~~~~~~~GtVK~Fd~~KGfGFI~~d~-gg~DVFVHiSai~~~~g~~p~~Gd~V~g~ 128 (144)
.++...+|+|+... -||++-.-. ++=+-|+|.+++... ....+||.+...
T Consensus 3 ~~G~~v~g~V~si~---d~G~~v~~g~~gv~Gfl~~~~~~~~--~~~~~Gq~v~~~ 53 (74)
T cd05694 3 VEGMVLSGCVSSVE---DHGYILDIGIPGTTGFLPKKDAGNF--SKLKVGQLLLCV 53 (74)
T ss_pred CCCCEEEEEEEEEe---CCEEEEEeCCCCcEEEEEHHHCCcc--cccCCCCEEEEE
Confidence 34667899999875 478766543 345899999998764 556777776443
No 43
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=64.67 E-value=7.4 Score=25.10 Aligned_cols=49 Identities=16% Similarity=0.161 Sum_probs=32.0
Q ss_pred cccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeCC
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQGS 128 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~ 128 (144)
..+.|+|+... .+|.+-.-.++-+.|+|++.+... ++....+||.|+..
T Consensus 2 ~~v~g~V~~v~---~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~ 54 (68)
T cd05707 2 DVVRGFVKNIA---NNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGK 54 (68)
T ss_pred CEEEEEEEEEE---CccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEE
Confidence 35678888864 355544433447899999987432 34556788887653
No 44
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=63.60 E-value=4.7 Score=37.95 Aligned_cols=35 Identities=29% Similarity=0.494 Sum_probs=25.9
Q ss_pred cCCcccccEEEEccCCCceeEecCCCCCCcEEEEeecc
Q psy3660 74 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDY 111 (144)
Q Consensus 74 ~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai 111 (144)
.+.+...|+||. .+|||||+..|.- +.+|+-=-.+
T Consensus 17 ~~~prvEGvVK~--tekgfGFLEvD~q-kSYFIpPp~M 51 (645)
T COG4776 17 SQTPRVEGVVKA--TEKGFGFLEVDAQ-KSYFIPPPQM 51 (645)
T ss_pred hcCcccceeeee--ccccceeEEEcCc-cccccCCHHH
Confidence 456788999998 7899999999854 4566544333
No 45
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=63.30 E-value=4 Score=26.85 Aligned_cols=50 Identities=12% Similarity=0.088 Sum_probs=27.1
Q ss_pred ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceeeeCCcccccc
Q psy3660 78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQGSKTCNSC 134 (144)
Q Consensus 78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V~g~kg~~a~ 134 (144)
..+.+|+..+ .+|+.-.++.+++||++.+.+... +++||.|..=.+.+..
T Consensus 4 ~~~L~V~~~~---~~g~fL~~~~~~~vlLp~~e~~~~----~~~Gd~v~VFvY~D~~ 53 (61)
T PF13509_consen 4 INTLKVVDKN---EFGYFLDDGEGKEVLLPKSEVPEP----LKVGDEVEVFVYLDKE 53 (61)
T ss_dssp -----EEEE----SSEEEEEETT-EEEEEEGGG----------TTSEEEEEEEE-TT
T ss_pred CcceEEEEEe---CCEEEEECCCCCEEEechHHcCCC----CCCCCEEEEEEEECCC
Confidence 4456777765 477776666668999999987633 6888888766655543
No 46
>PRK12678 transcription termination factor Rho; Provisional
Probab=60.17 E-value=4.5 Score=38.83 Aligned_cols=43 Identities=16% Similarity=0.297 Sum_probs=31.6
Q ss_pred cccEEEEccCCCceeEecCC---CCCCcEEEEeeccccCCCccceeceeeeC
Q psy3660 79 ETGKIKEFCRSKGHGFITPD---SGEPAVFVHISDYVIMPKLISQINKALQG 127 (144)
Q Consensus 79 ~~GtVK~Fd~~KGfGFI~~d---~gg~DVFVHiSai~~~~g~~p~~Gd~V~g 127 (144)
..|++--. .||||+... .+..||||..+.|+.. + +..||.|.|
T Consensus 296 ~~GiLdi~---dg~gFlR~~~y~~~~~Dvyvs~~qirr~-~--Lr~Gd~v~G 341 (672)
T PRK12678 296 VAGILDVL---DNYAFVRTSGYLPGPNDVYVSMNQVRKN-G--LRKGDAVTG 341 (672)
T ss_pred eeEEEEec---CCeeEeeCCCCCCCCCCeeeCHHHHHHc-C--CCCCCEEEE
Confidence 45666655 499999976 3568999999999876 3 455666665
No 47
>PRK07252 hypothetical protein; Provisional
Probab=59.11 E-value=12 Score=27.94 Aligned_cols=50 Identities=12% Similarity=0.090 Sum_probs=36.0
Q ss_pred CcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeCC
Q psy3660 76 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQGS 128 (144)
Q Consensus 76 ~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~ 128 (144)
+..+.|+|..... ||++..-.++-+.|+|++.+... ......+||.|...
T Consensus 4 G~iv~G~V~~V~~---~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~Vk 57 (120)
T PRK07252 4 GDKLKGTITGIKP---YGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQ 57 (120)
T ss_pred CCEEEEEEEEEeC---cEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEE
Confidence 5678899998753 78777655557999999998542 24556788877543
No 48
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=58.36 E-value=19 Score=23.50 Aligned_cols=48 Identities=13% Similarity=0.076 Sum_probs=30.4
Q ss_pred cccccEEEEccCCCceeEecCCCC-CCcEEEEeeccccC---------------CCccceeceeeeC
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSG-EPAVFVHISDYVIM---------------PKLISQINKALQG 127 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~g-g~DVFVHiSai~~~---------------~g~~p~~Gd~V~g 127 (144)
..+.|+|..... ||+...-.. +-+-|+|++++... .++..+.||.|.-
T Consensus 3 ~~~~g~V~~v~~---~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v 66 (83)
T cd04471 3 EEFDGVISGVTS---FGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKV 66 (83)
T ss_pred CEEEEEEEeEEe---eeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEE
Confidence 456778877643 677665443 46789999987532 1345577777743
No 49
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=57.10 E-value=12 Score=23.94 Aligned_cols=49 Identities=12% Similarity=0.133 Sum_probs=32.7
Q ss_pred cccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCC----CccceeceeeeCC
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMP----KLISQINKALQGS 128 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~----g~~p~~Gd~V~g~ 128 (144)
..+.|+|+... .+|++-.-..+-+.|+|++.+.... ....++||.+...
T Consensus 2 ~~v~g~V~~v~---~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~ 54 (73)
T cd05691 2 SIVTGKVTEVD---AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAK 54 (73)
T ss_pred CEEEEEEEEEE---CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEE
Confidence 34678888874 4665555444478999999876532 3445788888664
No 50
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=56.37 E-value=19 Score=24.11 Aligned_cols=48 Identities=10% Similarity=0.082 Sum_probs=34.7
Q ss_pred ccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceeeeC
Q psy3660 73 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQG 127 (144)
Q Consensus 73 ~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V~g 127 (144)
...+..+.|+|.... -||+...-+.+.+.|+|.+.+.. ..+.||.+..
T Consensus 14 ~~~G~~~~g~V~~i~---~~G~fV~l~~~~~Glv~~se~~~----~~~iGd~v~v 61 (77)
T cd04473 14 LEVGKLYKGKVNGVA---KYGVFVDLNDHVRGLIHRSNLLR----DYEVGDEVIV 61 (77)
T ss_pred CCCCCEEEEEEEeEe---cceEEEEECCCcEEEEEchhccC----cCCCCCEEEE
Confidence 456778899999864 47777665555899999999753 3667776644
No 51
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=54.45 E-value=16 Score=24.61 Aligned_cols=50 Identities=14% Similarity=0.082 Sum_probs=33.8
Q ss_pred CCcccccEEEEccCCCcee-EecCCCCCCcEEEEeeccccCC-------CccceeceeeeCC
Q psy3660 75 QNPVETGKIKEFCRSKGHG-FITPDSGEPAVFVHISDYVIMP-------KLISQINKALQGS 128 (144)
Q Consensus 75 ~~~~~~GtVK~Fd~~KGfG-FI~~d~gg~DVFVHiSai~~~~-------g~~p~~Gd~V~g~ 128 (144)
.+....|+|+... -|| |+.... +-+.|+|++++.... .+...+||.|...
T Consensus 3 ~G~~V~g~V~~i~---~~G~fV~l~~-~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~k 60 (74)
T cd05705 3 EGQLLRGYVSSVT---KQGVFFRLSS-SIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAK 60 (74)
T ss_pred CCCEEEEEEEEEe---CCcEEEEeCC-CCEEEEEHHHccCccccChhhHhcccCCCCEEEEE
Confidence 4667899999975 344 445443 578999988875532 2455888888653
No 52
>PRK08582 hypothetical protein; Provisional
Probab=53.64 E-value=25 Score=26.89 Aligned_cols=51 Identities=14% Similarity=0.088 Sum_probs=35.4
Q ss_pred CCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeCC
Q psy3660 75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQGS 128 (144)
Q Consensus 75 ~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~ 128 (144)
.+..+.|+|+... .||+...-+.+.+.+||++.+... ....+.+||.|...
T Consensus 5 vG~iv~G~V~~I~---~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~Vkvk 59 (139)
T PRK08582 5 VGSKLQGKVTGIT---NFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVK 59 (139)
T ss_pred CCCEEEEEEEEEE---CCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEE
Confidence 4667889999864 477665544457899999998532 23556778877554
No 53
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=53.50 E-value=13 Score=23.95 Aligned_cols=49 Identities=14% Similarity=0.089 Sum_probs=33.2
Q ss_pred cccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeCC
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQGS 128 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~ 128 (144)
..+.|+|+... -||.+-.-+.+-+.|+|++.+... +....+.||.+...
T Consensus 2 ~~v~g~V~~v~---~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~ 54 (69)
T cd05697 2 QVVKGTIRKLR---PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCR 54 (69)
T ss_pred CEEEEEEEEEe---ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEE
Confidence 45788999875 367665544457899999887543 24456778877543
No 54
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=52.69 E-value=15 Score=23.61 Aligned_cols=50 Identities=6% Similarity=0.026 Sum_probs=32.8
Q ss_pred cccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeCCc
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQGSK 129 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~k 129 (144)
..+.|+|...... .=|+.. ..+.+.|+|.+.+... +.+..++||.+....
T Consensus 2 ~iv~g~V~~i~~~--~~~v~l-~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i 55 (70)
T cd05687 2 DIVKGTVVSVDDD--EVLVDI-GYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYV 55 (70)
T ss_pred CEEEEEEEEEeCC--EEEEEe-CCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEE
Confidence 4578999987542 334444 3346899999998543 244567888876553
No 55
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=52.63 E-value=8.7 Score=25.90 Aligned_cols=52 Identities=8% Similarity=0.014 Sum_probs=33.6
Q ss_pred CCcccccEEEEccCCCceeEecCCCCCCcEEEEeecccc----C----CCccceeceeeeCCc
Q psy3660 75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVI----M----PKLISQINKALQGSK 129 (144)
Q Consensus 75 ~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~----~----~g~~p~~Gd~V~g~k 129 (144)
.+..+.|+|..-. .+|+...-+.+-+-|+|++.+.. . ....+++||.+....
T Consensus 6 ~GdiV~g~V~~i~---~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V 65 (86)
T cd05789 6 VGDVVIGRVTEVG---FKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEV 65 (86)
T ss_pred CCCEEEEEEEEEC---CCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEE
Confidence 5667889999864 34444443444789999999853 1 122468888876544
No 56
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=51.52 E-value=21 Score=22.09 Aligned_cols=49 Identities=12% Similarity=0.086 Sum_probs=30.9
Q ss_pred cccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCC----CccceeceeeeCC
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMP----KLISQINKALQGS 128 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~----g~~p~~Gd~V~g~ 128 (144)
..+.|+|+... .||+...-..+.+.|+|.+.+.... ....+.||.|...
T Consensus 2 ~~~~g~V~~i~---~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~ 54 (68)
T cd05685 2 MVLEGVVTNVT---DFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVK 54 (68)
T ss_pred CEEEEEEEEEe---cccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEE
Confidence 34678888764 3565544444578999999885431 2245778877543
No 57
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=49.83 E-value=13 Score=24.95 Aligned_cols=49 Identities=16% Similarity=0.164 Sum_probs=32.9
Q ss_pred cccccEEEEccCCCceeEecCCCCCCcEEEEeecccc------CCCccceeceeeeCC
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVI------MPKLISQINKALQGS 128 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~------~~g~~p~~Gd~V~g~ 128 (144)
..++|+|+...+ ..=|+...+ +=+-|+|++++.. .+.....+||.|++.
T Consensus 2 ~~V~g~V~~i~~--~g~~V~l~~-~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~k 56 (73)
T cd05703 2 QEVTGFVNNVSK--EFVWLTISP-DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAK 56 (73)
T ss_pred CEEEEEEEEEeC--CEEEEEeCC-CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEE
Confidence 356899999853 223566654 3689999998742 234556888988765
No 58
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=48.05 E-value=20 Score=33.76 Aligned_cols=94 Identities=13% Similarity=0.176 Sum_probs=63.0
Q ss_pred CCcCCCCccccCCceeEEEeeeeecccCCCCCCC-----Cccc-ccccccCCcccccEEEEccCCCceeEecCCCCCCcE
Q psy3660 31 NTLSLPSPIITRRTRTESMDFKATAQRSKGSKEQ-----PNFL-ISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAV 104 (144)
Q Consensus 31 ~~~~~p~~~~t~Rgrq~s~vl~i~~~~~~~~~~~-----~~~~-~~~r~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DV 104 (144)
....-|+-++.-.-..-+.|++++...--..... ..|. +..+...+....|+|..+-. ||.+..-..|=+-
T Consensus 227 ~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~---~GafVei~~GvEG 303 (541)
T COG0539 227 KRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTD---YGAFVEIEEGVEG 303 (541)
T ss_pred cccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEeec---CcEEEEecCCccc
Confidence 3455677777777788888888886554433322 1122 24556778899999999865 7766555555789
Q ss_pred EEEeeccc----cCCCccceeceeeeC
Q psy3660 105 FVHISDYV----IMPKLISQINKALQG 127 (144)
Q Consensus 105 FVHiSai~----~~~g~~p~~Gd~V~g 127 (144)
|||+|.+. ..|...+.+||.|.-
T Consensus 304 lvhvSEisw~~~~~P~evv~~Gq~V~V 330 (541)
T COG0539 304 LVHVSEISWTKKNVPSEVVKVGQEVEV 330 (541)
T ss_pred eeechhhcccccCCHHHhcccCCEEEE
Confidence 99999752 235666788887743
No 59
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=44.69 E-value=32 Score=22.76 Aligned_cols=47 Identities=17% Similarity=0.258 Sum_probs=29.2
Q ss_pred cccccEEEEccCCCceeEecCCC---CCCcEEEEeeccccCC-----Cccceeceeee
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDS---GEPAVFVHISDYVIMP-----KLISQINKALQ 126 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~---gg~DVFVHiSai~~~~-----g~~p~~Gd~V~ 126 (144)
..+.|+|+... -||+...-+ .+.+.|+|++.+.... ....++||.|.
T Consensus 2 ~~~~g~V~~v~---~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~ 56 (79)
T cd05684 2 KIYKGKVTSIM---DFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVK 56 (79)
T ss_pred CEEEEEEEEEE---eeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEE
Confidence 35678888764 366655433 2478999999985431 22346777664
No 60
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=42.76 E-value=22 Score=34.57 Aligned_cols=52 Identities=12% Similarity=0.011 Sum_probs=37.3
Q ss_pred ccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccc--------cCCCccceeceeeeC
Q psy3660 73 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYV--------IMPKLISQINKALQG 127 (144)
Q Consensus 73 ~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~--------~~~g~~p~~Gd~V~g 127 (144)
...+..++|+|+..- -||....-..+.+-|||+|.|. .+..+.+++||.|..
T Consensus 645 ~~vG~i~~GkV~~I~---dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~V 704 (719)
T TIGR02696 645 PEVGERFLGTVVKTT---AFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQV 704 (719)
T ss_pred CCCCCEEEEEEEEEE---CceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEE
Confidence 457889999999875 4887665445689999999773 122445677887754
No 61
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=42.00 E-value=41 Score=21.68 Aligned_cols=51 Identities=8% Similarity=0.076 Sum_probs=34.3
Q ss_pred CCcccccEEEEccCCCceeEecCCC--CCCcEEEEeeccccCC----CccceeceeeeCC
Q psy3660 75 QNPVETGKIKEFCRSKGHGFITPDS--GEPAVFVHISDYVIMP----KLISQINKALQGS 128 (144)
Q Consensus 75 ~~~~~~GtVK~Fd~~KGfGFI~~d~--gg~DVFVHiSai~~~~----g~~p~~Gd~V~g~ 128 (144)
.+..+.|+|+... .||++..-. .+-+.|+|++.+.... .+...+||.|...
T Consensus 3 ~G~~~~g~V~~v~---~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vk 59 (76)
T cd04452 3 EGELVVVTVKSIA---DMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVK 59 (76)
T ss_pred CCCEEEEEEEEEE---ccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEE
Confidence 3567889998874 477765432 2468999999986542 2335788877654
No 62
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=41.55 E-value=30 Score=22.46 Aligned_cols=47 Identities=13% Similarity=0.108 Sum_probs=30.3
Q ss_pred cccccEEEEccCCCcee-EecCCCCCCcEEEEeeccccC------CCccceeceeeeC
Q psy3660 77 PVETGKIKEFCRSKGHG-FITPDSGEPAVFVHISDYVIM------PKLISQINKALQG 127 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfG-FI~~d~gg~DVFVHiSai~~~------~g~~p~~Gd~V~g 127 (144)
..+.|+|+.... +| |+..+. +-+.++|++++... +....++||.|..
T Consensus 2 ~iV~g~V~~i~~---~gi~v~l~~-~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~ 55 (70)
T cd05702 2 DLVKAKVKSVKP---TQLNVQLAD-NVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKA 55 (70)
T ss_pred CEEEEEEEEEEC---CcEEEEeCC-CcEEEEEHHHhccccccccChhHhCCCCCEEEE
Confidence 456788888754 33 444444 47899999998543 1233577887754
No 63
>PF01551 Peptidase_M23: Peptidase family M23; InterPro: IPR016047 Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.; PDB: 3IT5_A 3IT7_B 2GU1_A 3NYY_A 2HSI_B 3SLU_B 3UZ0_D 3TUF_B 1QWY_A 2B44_B ....
Probab=41.55 E-value=21 Score=24.40 Aligned_cols=47 Identities=15% Similarity=0.165 Sum_probs=31.6
Q ss_pred cccEEEEccCCCceeEecC---CCCCCcEEEEeeccccCCCccceeceee
Q psy3660 79 ETGKIKEFCRSKGHGFITP---DSGEPAVFVHISDYVIMPKLISQINKAL 125 (144)
Q Consensus 79 ~~GtVK~Fd~~KGfGFI~~---d~gg~DVFVHiSai~~~~g~~p~~Gd~V 125 (144)
..|+|......+++|.... .++-.-+|.|+..+.-..|+.++.||.+
T Consensus 20 ~~G~V~~~~~~~~~g~~V~i~~~~g~~~~y~~l~~~~v~~G~~V~~G~~I 69 (96)
T PF01551_consen 20 ADGKVVFVGEDPGYGNYVIIQHGNGYITVYGHLDSVSVKVGDRVKAGQVI 69 (96)
T ss_dssp SSEEEEEEEEETTTEEEEEEEETTSEEEEEEEESEESS-TTSEE-TTCEE
T ss_pred ccEEEEEEEeccCCccEEEEEeCCcCCEEEeccccccceecccccCCCEE
Confidence 4689988887766665443 2222457888888766678888888876
No 64
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=39.99 E-value=25 Score=33.51 Aligned_cols=52 Identities=13% Similarity=0.073 Sum_probs=37.9
Q ss_pred ccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeC
Q psy3660 73 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQG 127 (144)
Q Consensus 73 ~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g 127 (144)
...+..+.|+|+... .||....-..+.+-|+|+|.+... ..+..++||.|..
T Consensus 616 ~~~G~i~~G~V~~I~---~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~V 671 (684)
T TIGR03591 616 PEVGKIYEGKVVRIM---DFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKV 671 (684)
T ss_pred cccCcEEEEEEEEEe---CCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEE
Confidence 456889999999985 478766544458999999998443 2455677887754
No 65
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=39.26 E-value=28 Score=22.29 Aligned_cols=47 Identities=21% Similarity=0.224 Sum_probs=29.5
Q ss_pred cccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCc--cceeceeeeC
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKL--ISQINKALQG 127 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~--~p~~Gd~V~g 127 (144)
..++|+|+.... +|++..- ++-+.|+|.+.+....-. .-.+||.+..
T Consensus 2 ~iv~g~V~~v~~---~G~~v~l-~g~~gfip~s~~~~~~~~~~~~~vG~~i~~ 50 (67)
T cd04465 2 EIVEGKVTEKVK---GGLIVDI-EGVRAFLPASQVDLRPVEDLDEYVGKELKF 50 (67)
T ss_pred CEEEEEEEEEEC---CeEEEEE-CCEEEEEEHHHCCCcccCChHHhCCCEEEE
Confidence 457889999864 5555555 457899999988643211 1135666543
No 66
>PRK11637 AmiB activator; Provisional
Probab=38.86 E-value=23 Score=31.13 Aligned_cols=48 Identities=8% Similarity=0.185 Sum_probs=34.6
Q ss_pred ccccEEEEccCCCceeE-ecCCCCCC--cEEEEeeccccCCCccceeceee
Q psy3660 78 VETGKIKEFCRSKGHGF-ITPDSGEP--AVFVHISDYVIMPKLISQINKAL 125 (144)
Q Consensus 78 ~~~GtVK~Fd~~KGfGF-I~~d~gg~--DVFVHiSai~~~~g~~p~~Gd~V 125 (144)
...|+|.+-+..+|||- |..++++. -+|-|.+.+.-..|+.+.-||.+
T Consensus 345 ~~~G~V~~~~~~~~~G~~vii~hg~g~~t~Y~~~~~~~v~~G~~V~~G~~i 395 (428)
T PRK11637 345 IADGRVLLADWLQGYGLVVVVEHGKGDMSLYGYNQSALVSVGAQVRAGQPI 395 (428)
T ss_pred cCCeEEEEeeccCCcccEEEEEeCCCcEEEccCCCcCCCCCcCEECCCCeE
Confidence 45799998888899994 44455533 35557777766678888888876
No 67
>PHA02945 interferon resistance protein; Provisional
Probab=38.45 E-value=86 Score=22.96 Aligned_cols=36 Identities=19% Similarity=0.130 Sum_probs=26.2
Q ss_pred ccCCcccccEEEEccCCCceeE-ecCCC-CCCcEEEEeeccc
Q psy3660 73 ALQNPVETGKIKEFCRSKGHGF-ITPDS-GEPAVFVHISDYV 112 (144)
Q Consensus 73 ~~~~~~~~GtVK~Fd~~KGfGF-I~~d~-gg~DVFVHiSai~ 112 (144)
...++...|+|+. +.||+ +..++ ++.+.|+|++.+.
T Consensus 9 P~~GelvigtV~~----~d~ga~v~L~EY~g~eg~i~~seve 46 (88)
T PHA02945 9 PNVGDVLKGKVYE----NGYALYIDLFDYPHSEAILAESVQM 46 (88)
T ss_pred CCCCcEEEEEEEe----cCceEEEEecccCCcEEEEEeehhh
Confidence 3567889999998 45664 55555 4679999999663
No 68
>PRK08059 general stress protein 13; Validated
Probab=37.28 E-value=45 Score=24.58 Aligned_cols=52 Identities=19% Similarity=0.128 Sum_probs=35.5
Q ss_pred cCCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCC----CccceeceeeeCC
Q psy3660 74 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMP----KLISQINKALQGS 128 (144)
Q Consensus 74 ~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~----g~~p~~Gd~V~g~ 128 (144)
..+..+.|+|..... ||+...-+.+-+.|+|++.+.... .....+||.|...
T Consensus 6 k~G~iv~G~V~~i~~---~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vk 61 (123)
T PRK08059 6 EVGSVVTGKVTGIQP---YGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVK 61 (123)
T ss_pred CCCCEEEEEEEEEec---ceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEE
Confidence 346788999988754 777666555578999999874421 2345777777543
No 69
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=37.25 E-value=42 Score=29.52 Aligned_cols=55 Identities=11% Similarity=0.179 Sum_probs=36.8
Q ss_pred ccccEEEEccC-CCceeEec-CC--CCCCcEEEEeeccccCCCccceeceee--eCCcccc
Q psy3660 78 VETGKIKEFCR-SKGHGFIT-PD--SGEPAVFVHISDYVIMPKLISQINKAL--QGSKTCN 132 (144)
Q Consensus 78 ~~~GtVK~Fd~-~KGfGFI~-~d--~gg~DVFVHiSai~~~~g~~p~~Gd~V--~g~kg~~ 132 (144)
...|+|.+-.. .+|||-+. .+ ++-.-+|-|...+.-.+|+.++-||.+ .|..|..
T Consensus 235 aa~G~Vv~ag~~~~gyGn~ViI~H~~g~~S~Yahl~~i~Vk~Gq~V~~Gq~Ig~~G~tg~~ 295 (319)
T PRK10871 235 TADGRVVYAGNALRGYGNLIIIKHNDDYLSAYAHNDTMLVREQQEVKAGQKIATMGSTGTS 295 (319)
T ss_pred ccCeEEEEEeeccCCcceEEEEEeCCceEEEeeCCCccccCCcCEECCCCeEEeEcCCCCC
Confidence 34699988754 58888533 33 333457888888877779999999977 4444443
No 70
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=34.39 E-value=49 Score=31.59 Aligned_cols=53 Identities=13% Similarity=0.073 Sum_probs=39.1
Q ss_pred ccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeCC
Q psy3660 73 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQGS 128 (144)
Q Consensus 73 ~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~ 128 (144)
...+..+.|+|+... -||+...-..+.+-++|++.+... ..+..++||.|...
T Consensus 619 ~~vG~v~~G~V~~I~---~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~Vk 675 (693)
T PRK11824 619 PEVGEIYEGKVVRIV---DFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVK 675 (693)
T ss_pred CcCCeEEEEEEEEEE---CCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEE
Confidence 456789999999975 488777644568999999998543 34556888887643
No 71
>PF05606 DUF777: Borrelia burgdorferi protein of unknown function (DUF777); InterPro: IPR008495 This family consists of several hypothetical proteins of unknown function, found in Borrelia burgdorferi and Borrelia garinii.
Probab=34.13 E-value=45 Score=27.34 Aligned_cols=45 Identities=18% Similarity=0.205 Sum_probs=35.1
Q ss_pred cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee
Q psy3660 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL 125 (144)
Q Consensus 79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V 125 (144)
.-|+||.|+....-|.++-.+- +|+=+|-..|..- ...+..||.|
T Consensus 36 rIG~iK~F~~~tQe~iVti~e~-e~LeI~T~nISN~-~leLs~~D~V 80 (181)
T PF05606_consen 36 RIGTIKSFKFQTQEGIVTIPEY-EDLEIHTKNISNI-NLELSKGDEV 80 (181)
T ss_pred EEeeeeecccccceEEEEeecc-cCceEEeeecccc-eeEecCCCEE
Confidence 4699999999999999998776 7888888887665 4455555554
No 72
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=33.00 E-value=39 Score=30.64 Aligned_cols=55 Identities=18% Similarity=0.132 Sum_probs=39.2
Q ss_pred cccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeecccc-----CCCccceeceeeeCCc
Q psy3660 72 RALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVI-----MPKLISQINKALQGSK 129 (144)
Q Consensus 72 r~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~-----~~g~~p~~Gd~V~g~k 129 (144)
....+..+.|+|+... -||+...-..+-+.|+|++.+.. .+...+++||.|....
T Consensus 289 ~~~~G~~v~G~V~~v~---~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkV 348 (491)
T PRK13806 289 RLKAGDKVTGKVVRLA---PFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKI 348 (491)
T ss_pred cCCCCCEEEEEEEEEe---CceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEE
Confidence 4567889999999874 48877554445789999998753 2245578888886543
No 73
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=32.85 E-value=57 Score=20.83 Aligned_cols=49 Identities=8% Similarity=0.082 Sum_probs=33.0
Q ss_pred CcccccEEEEccCCCceeEecCCC-CCCcEEEEeeccccCC----CccceeceeeeC
Q psy3660 76 NPVETGKIKEFCRSKGHGFITPDS-GEPAVFVHISDYVIMP----KLISQINKALQG 127 (144)
Q Consensus 76 ~~~~~GtVK~Fd~~KGfGFI~~d~-gg~DVFVHiSai~~~~----g~~p~~Gd~V~g 127 (144)
+..+.|+|+... .+|++..-. .+-+.|+|++.+.... .....+||.|..
T Consensus 3 g~~v~g~V~~i~---~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v 56 (77)
T cd05708 3 GQKIDGTVRRVE---DYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRA 56 (77)
T ss_pred CCEEEEEEEEEE---cceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEE
Confidence 456788998874 466665543 3568999999986532 234577887754
No 74
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=31.75 E-value=60 Score=20.03 Aligned_cols=49 Identities=18% Similarity=0.243 Sum_probs=31.6
Q ss_pred CcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeCC
Q psy3660 76 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQGS 128 (144)
Q Consensus 76 ~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~ 128 (144)
+..+.|+|...+. +|++..-+ +-+.|+|.+.+... +++..+.||.|...
T Consensus 2 g~~~~g~V~~v~~---~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~ 54 (68)
T cd05688 2 GDVVEGTVKSITD---FGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVK 54 (68)
T ss_pred CCEEEEEEEEEEe---eeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEE
Confidence 4567888888764 55554433 46899999987532 23445788877543
No 75
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=28.61 E-value=47 Score=22.15 Aligned_cols=52 Identities=8% Similarity=-0.087 Sum_probs=32.8
Q ss_pred CCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCC----CccceeceeeeCCc
Q psy3660 75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMP----KLISQINKALQGSK 129 (144)
Q Consensus 75 ~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~----g~~p~~Gd~V~g~k 129 (144)
.+....|+|..... .|++-.-...-+.|+|++++.... .....+||.+....
T Consensus 6 ~GdiV~G~V~~v~~---~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V 61 (82)
T cd04454 6 VGDIVIGIVTEVNS---RFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKV 61 (82)
T ss_pred CCCEEEEEEEEEcC---CEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEE
Confidence 45677888888743 333333334468999999985431 34468888776544
No 76
>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]
Probab=28.34 E-value=42 Score=30.75 Aligned_cols=53 Identities=15% Similarity=0.274 Sum_probs=40.4
Q ss_pred ccccEEEEccCCCceeEecC-CCCCCc--EEEEeeccccCCCccceeceee--eCCcc
Q psy3660 78 VETGKIKEFCRSKGHGFITP-DSGEPA--VFVHISDYVIMPKLISQINKAL--QGSKT 130 (144)
Q Consensus 78 ~~~GtVK~Fd~~KGfGFI~~-d~gg~D--VFVHiSai~~~~g~~p~~Gd~V--~g~kg 130 (144)
...|+|.+=+.-+|||.+.. |.|+.+ ||=+...|.-++|..+.-|+.| .|..|
T Consensus 337 ~AdG~VvyA~~l~GYG~vvIldhG~gy~slyg~~~~i~v~~G~~V~AGepIa~~G~sg 394 (420)
T COG4942 337 IADGRVVYADWLRGYGLVVILDHGGGYHSLYGGNQSILVNPGQFVKAGEPIALVGSSG 394 (420)
T ss_pred ecCceEEechhhccCceEEEEEcCCccEEEecccceeeecCCCEeecCCchhhccCCC
Confidence 34699999999999999875 666555 5666667777789999888866 55553
No 77
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=28.10 E-value=36 Score=33.45 Aligned_cols=53 Identities=15% Similarity=0.203 Sum_probs=39.3
Q ss_pred ccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeecc----ccCCCccceeceeeeCC
Q psy3660 73 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDY----VIMPKLISQINKALQGS 128 (144)
Q Consensus 73 ~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai----~~~~g~~p~~Gd~V~g~ 128 (144)
+..+....|+|+..- -||-+..-+-..|..||+|.+ ...|...+++||+|...
T Consensus 656 Lk~Gm~leg~Vrnv~---~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~ 712 (780)
T COG2183 656 LKPGMILEGTVRNVV---DFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVK 712 (780)
T ss_pred ccCCCEEEEEEEEee---eccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEE
Confidence 556778899999764 466665555668999999995 44567788999988543
No 78
>PRK11649 putative peptidase; Provisional
Probab=27.79 E-value=47 Score=30.09 Aligned_cols=53 Identities=15% Similarity=0.262 Sum_probs=37.1
Q ss_pred cccEEEEccCCCceeE-ecCCCC--CCcEEEEeeccccCCCccceeceee--eCCccc
Q psy3660 79 ETGKIKEFCRSKGHGF-ITPDSG--EPAVFVHISDYVIMPKLISQINKAL--QGSKTC 131 (144)
Q Consensus 79 ~~GtVK~Fd~~KGfGF-I~~d~g--g~DVFVHiSai~~~~g~~p~~Gd~V--~g~kg~ 131 (144)
..|+|..-...+|||- |...++ -.-+|.|.+.+.-..|++++-||.+ .|.-|+
T Consensus 330 ~dG~V~~~~~~~~~G~~v~I~Hg~~y~t~Y~hLs~~~v~~Gq~V~~Gq~IG~vG~tG~ 387 (439)
T PRK11649 330 GDGEVVVAKRSGAAGNYVAIRHGRQYTTRYMHLRKLLVKPGQKVKRGDRIALSGNTGR 387 (439)
T ss_pred cCcEEEEEEEEcCCceEEEEECCCceEEEecccCcccCCCcCEECCCCeEEEEcCCCC
Confidence 4688887777778883 333333 3468899999877779999988875 455444
No 79
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=27.57 E-value=50 Score=32.94 Aligned_cols=51 Identities=14% Similarity=0.107 Sum_probs=34.3
Q ss_pred cCCccc-ccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeC
Q psy3660 74 LQNPVE-TGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQG 127 (144)
Q Consensus 74 ~~~~~~-~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g 127 (144)
..+..+ .|+|+... -||+...-..+.+.|||+|.|... ..+..++||.|..
T Consensus 752 ~vG~iy~~g~V~~I~---~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~V 807 (891)
T PLN00207 752 TVGDIYRNCEIKSIA---PYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDV 807 (891)
T ss_pred CCCcEEECcEEEEEe---ccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEE
Confidence 366777 46999864 488765444458999999998543 2345577877744
No 80
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=27.24 E-value=70 Score=20.73 Aligned_cols=47 Identities=11% Similarity=0.138 Sum_probs=31.4
Q ss_pred CCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceeeeC
Q psy3660 75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQG 127 (144)
Q Consensus 75 ~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V~g 127 (144)
.+..++|+|...+. ++=|+... +-+.|++.+.+... +..++||.|..
T Consensus 3 ~g~iV~G~V~~~~~--~~~~vdig--~~eg~lp~~e~~~~--~~~~~Gd~v~v 49 (67)
T cd04455 3 EGEIVTGIVKRVDR--GNVIVDLG--KVEAILPKKEQIPG--ESYRPGDRIKA 49 (67)
T ss_pred CCCEEEEEEEEEcC--CCEEEEcC--CeEEEeeHHHCCCC--CcCCCCCEEEE
Confidence 46678999999875 22344442 36789999988643 45577776643
No 81
>PRK05807 hypothetical protein; Provisional
Probab=27.21 E-value=64 Score=24.46 Aligned_cols=50 Identities=12% Similarity=0.110 Sum_probs=33.9
Q ss_pred CCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeCC
Q psy3660 75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQGS 128 (144)
Q Consensus 75 ~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~ 128 (144)
.+..+.|+|.-.. .||+...-+ +...+||++.+... ..+.+.+||.|...
T Consensus 5 vG~vv~G~Vt~i~---~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~Vk 58 (136)
T PRK05807 5 AGSILEGTVVNIT---NFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVK 58 (136)
T ss_pred CCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEE
Confidence 3667889999864 466655543 46899999997532 23446778877654
No 82
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=25.08 E-value=49 Score=31.20 Aligned_cols=51 Identities=16% Similarity=0.219 Sum_probs=38.3
Q ss_pred cccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeecccc----CCCccceeceeee
Q psy3660 72 RALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVI----MPKLISQINKALQ 126 (144)
Q Consensus 72 r~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~----~~g~~p~~Gd~V~ 126 (144)
.+..+..+.|+|+...+ ||-.-.=. |=|-+||+|.+.. .|.+.+++||.|.
T Consensus 189 ~l~~G~vV~G~V~~It~---~GafVdig-GvdGLlHiseiS~~rv~~P~~vvkvGd~Vk 243 (541)
T COG0539 189 KLEVGEVVEGVVKNITD---YGAFVDIG-GVDGLLHISEISWKRVDHPSEVVKVGDEVK 243 (541)
T ss_pred cCCCCceEEEEEEEeec---CcEEEEec-CeeeEEehhhccccccCCHHHhcccCCEEE
Confidence 36788899999999876 77554433 3799999999743 4567778888774
No 83
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=23.52 E-value=68 Score=29.18 Aligned_cols=53 Identities=19% Similarity=0.176 Sum_probs=37.1
Q ss_pred ccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeecccc-----CCCccceeceeeeCC
Q psy3660 73 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVI-----MPKLISQINKALQGS 128 (144)
Q Consensus 73 ~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~-----~~g~~p~~Gd~V~g~ 128 (144)
...+..+.|+|+... .+|+.-.-+.+-+.|+|++++.. ......++||.|...
T Consensus 371 ~~~G~~v~g~V~~v~---~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~ 428 (565)
T PRK06299 371 YPVGDVVEGKVKNIT---DFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAV 428 (565)
T ss_pred CCCCCEEEEEEEEEe---cceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEE
Confidence 346788999999964 46765544435799999999752 234556888888653
No 84
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=23.29 E-value=76 Score=28.81 Aligned_cols=53 Identities=13% Similarity=0.152 Sum_probs=35.9
Q ss_pred ccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeCC
Q psy3660 73 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQGS 128 (144)
Q Consensus 73 ~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~ 128 (144)
...+..+.|+|+.... ||..-.-.++-+.|+|++.+... +.....+||.|...
T Consensus 200 l~~G~iv~G~V~~v~~---~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vk 256 (491)
T PRK13806 200 VKEGDVVEGTVTRLAP---FGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVK 256 (491)
T ss_pred CCCCCEEEEEEEEEeC---CeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEE
Confidence 5677889999999743 55444333457899999997542 23445678877554
No 85
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=23.26 E-value=47 Score=25.92 Aligned_cols=47 Identities=19% Similarity=0.229 Sum_probs=30.3
Q ss_pred CcccccEEEEccCCCcee-EecCCCCCCcEEEEeeccccC----CCccceeceeee
Q psy3660 76 NPVETGKIKEFCRSKGHG-FITPDSGEPAVFVHISDYVIM----PKLISQINKALQ 126 (144)
Q Consensus 76 ~~~~~GtVK~Fd~~KGfG-FI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~ 126 (144)
+...+|+|.-- +-|| |+..++ ++.-+||||.|... =.+.+.+||.|+
T Consensus 6 G~~l~GkItgI---~~yGAFV~l~~-g~tGLVHISEIa~~fVkdI~d~L~vG~eV~ 57 (129)
T COG1098 6 GSKLKGKITGI---TPYGAFVELEG-GKTGLVHISEIADGFVKDIHDHLKVGQEVK 57 (129)
T ss_pred cceEEEEEEee---EecceEEEecC-CCcceEEehHhhhhhHHhHHHHhcCCCEEE
Confidence 44567777643 3466 555554 57899999996442 256677777764
No 86
>PF01796 DUF35: DUF35 OB-fold domain; InterPro: IPR002878 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is approximately 70 amino acids long. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain and a C-terminal OB fold domain represented in this entry. OB-folds are frequently found to bind nucleic acids suggesting this domain might bind to DNA or RNA.
Probab=22.34 E-value=1.5e+02 Score=19.46 Aligned_cols=34 Identities=15% Similarity=0.040 Sum_probs=22.4
Q ss_pred eeEecCCCCCCcEEEEeeccccCCCccceeceeee
Q psy3660 92 HGFITPDSGEPAVFVHISDYVIMPKLISQINKALQ 126 (144)
Q Consensus 92 fGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V~ 126 (144)
+|.|..|+ |-.++-++.+.....-+.+.+|+.|+
T Consensus 31 v~~V~lde-g~rv~~~i~~~~~~~~~~l~iG~~V~ 64 (68)
T PF01796_consen 31 VAIVELDE-GVRVMARIVDVDPEDPDELRIGMRVR 64 (68)
T ss_pred EEEEEeCC-CCEEEEEEecCCCCCcccCCCCCEEE
Confidence 46666654 46788888876544344567888875
No 87
>KOG0407|consensus
Probab=22.17 E-value=59 Score=25.25 Aligned_cols=16 Identities=25% Similarity=0.285 Sum_probs=12.4
Q ss_pred CCCcEEEEeeccccCC
Q psy3660 100 GEPAVFVHISDYVIMP 115 (144)
Q Consensus 100 gg~DVFVHiSai~~~~ 115 (144)
.-.|-|||++++...+
T Consensus 24 sfndtfvhitdlsg~e 39 (139)
T KOG0407|consen 24 SFNDTFVHVTDLSGKE 39 (139)
T ss_pred ecccceEEEeccCCce
Confidence 3468999999987663
No 88
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=22.03 E-value=1.2e+02 Score=28.71 Aligned_cols=51 Identities=18% Similarity=0.201 Sum_probs=35.4
Q ss_pred CCcccccEEEEccCCCceeE-ecCCCCCCcEEEEeeccccC---------------CCccceeceeeeCC
Q psy3660 75 QNPVETGKIKEFCRSKGHGF-ITPDSGEPAVFVHISDYVIM---------------PKLISQINKALQGS 128 (144)
Q Consensus 75 ~~~~~~GtVK~Fd~~KGfGF-I~~d~gg~DVFVHiSai~~~---------------~g~~p~~Gd~V~g~ 128 (144)
.+..+.|+|..... ||+ +..++.+-+.+||++++... .+...++||.|...
T Consensus 572 iG~~~~g~I~~v~~---~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vk 638 (654)
T TIGR00358 572 VGTEFSGEISSVTR---FGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVK 638 (654)
T ss_pred CCcEEEEEEEeEEc---CcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEE
Confidence 46778999998643 555 66666668999999987532 13556777777543
No 89
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.21 E-value=97 Score=20.09 Aligned_cols=49 Identities=12% Similarity=0.007 Sum_probs=30.5
Q ss_pred cccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC--CCccceeceeeeCC
Q psy3660 77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM--PKLISQINKALQGS 128 (144)
Q Consensus 77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~--~g~~p~~Gd~V~g~ 128 (144)
....|+|+.-. .+| =|+...+ +=+-|+|++.+... ..+..++||.+...
T Consensus 2 ~~V~g~V~~i~-~~G-~~v~l~~-~v~g~v~~~~l~~~~~~~~~~~~G~~i~~k 52 (66)
T cd05695 2 MLVNARVKKVL-SNG-LILDFLS-SFTGTVDFLHLDPEKSSKSTYKEGQKVRAR 52 (66)
T ss_pred CEEEEEEEEEe-CCc-EEEEEcC-CceEEEEHHHcCCccCcccCcCCCCEEEEE
Confidence 35678888875 333 2344444 46899999988532 13456777777554
No 90
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=20.76 E-value=94 Score=27.76 Aligned_cols=54 Identities=19% Similarity=0.222 Sum_probs=36.1
Q ss_pred cccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeecccc-----CCCccceeceeeeCC
Q psy3660 72 RALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVI-----MPKLISQINKALQGS 128 (144)
Q Consensus 72 r~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~-----~~g~~p~~Gd~V~g~ 128 (144)
....+....|+|+.. .-||+.-.-+.+-+.|+|++++.. .+....++||.|...
T Consensus 356 ~~~~G~~v~g~V~~v---~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~ 414 (516)
T TIGR00717 356 KHPVGDRVTGKIKKI---TDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAV 414 (516)
T ss_pred hCCCCCEEEEEEEEE---ecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEE
Confidence 345688999999985 345655544446899999998742 123456777776543
Done!