Query 014129
Match_columns 430
No_of_seqs 205 out of 334
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 02:07:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014129.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014129hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08585 DUF1767: Domain of un 99.8 1.2E-19 2.5E-24 150.2 5.4 86 12-100 1-89 (90)
2 KOG3683 Uncharacterized conser 99.8 3.8E-19 8.2E-24 184.4 5.9 115 91-210 1-117 (460)
3 PF05918 API5: Apoptosis inhib 96.9 0.00026 5.7E-09 76.7 0.0 24 407-430 531-554 (556)
4 PF05918 API5: Apoptosis inhib 94.9 0.0072 1.6E-07 65.9 0.0 21 410-430 530-550 (556)
5 KOG3428 Small nuclear ribonucl 92.6 0.06 1.3E-06 47.3 1.5 14 369-382 69-82 (109)
6 KOG3683 Uncharacterized conser 89.9 0.11 2.3E-06 55.6 0.5 64 107-171 154-221 (460)
7 cd04488 RecG_wedge_OBF RecG_we 88.0 1.1 2.5E-05 33.9 4.9 53 107-159 17-69 (75)
8 PF14619 SnAC: Snf2-ATP coupli 84.3 0.54 1.2E-05 38.3 1.4 24 317-342 51-74 (74)
9 PF04057 Rep-A_N: Replication 83.2 2 4.3E-05 36.9 4.5 59 81-146 18-78 (101)
10 cd04492 YhaM_OBF_like YhaM_OBF 83.0 3.7 7.9E-05 32.0 5.7 50 106-155 17-66 (83)
11 cd04487 RecJ_OBF2_like RecJ_OB 82.9 4.5 9.7E-05 32.8 6.2 56 110-165 17-73 (73)
12 PF01336 tRNA_anti-codon: OB-f 82.3 1 2.2E-05 34.5 2.2 59 107-165 15-75 (75)
13 cd04477 RPA1N RPA1N: A subfami 78.3 2.5 5.3E-05 36.2 3.4 58 81-146 17-76 (97)
14 cd04485 DnaE_OBF DnaE_OBF: A s 73.7 2.7 5.8E-05 32.3 2.3 55 107-161 18-73 (84)
15 KOG3973 Uncharacterized conser 72.3 3.4 7.3E-05 43.4 3.2 14 278-291 279-292 (465)
16 KOG3172 Small nuclear ribonucl 70.0 4.2 9.2E-05 36.0 2.8 14 319-332 23-36 (119)
17 cd04493 BRCA2DBD_OB1 BRCA2DBD_ 67.1 7.6 0.00016 33.9 3.8 56 81-146 4-61 (100)
18 KOG0921 Dosage compensation co 67.1 4.9 0.00011 46.9 3.3 24 197-220 1032-1055(1282)
19 cd04489 ExoVII_LU_OBF ExoVII_L 62.5 38 0.00082 26.4 6.8 44 108-151 17-61 (78)
20 cd03524 RPA2_OBF_family RPA2_O 59.7 31 0.00068 25.0 5.6 49 107-155 16-66 (75)
21 cd04478 RPA2_DBD_D RPA2_DBD_D: 58.3 27 0.00058 28.5 5.5 59 108-166 16-78 (95)
22 PRK10590 ATP-dependent RNA hel 55.9 17 0.00036 38.4 4.8 16 8-23 9-24 (456)
23 PF09103 BRCA-2_OB1: BRCA2, ol 55.9 6.6 0.00014 34.9 1.5 58 79-146 14-73 (118)
24 PF04774 HABP4_PAI-RBP1: Hyalu 54.7 6.8 0.00015 33.2 1.4 18 328-346 72-89 (106)
25 KOG3973 Uncharacterized conser 54.6 11 0.00025 39.6 3.1 9 419-427 449-457 (465)
26 PRK10590 ATP-dependent RNA hel 52.7 12 0.00025 39.6 3.0 17 360-376 351-367 (456)
27 cd04482 RPA2_OBF_like RPA2_OBF 51.4 39 0.00085 28.3 5.4 54 110-166 19-75 (91)
28 KOG2269 Serine/threonine prote 45.0 15 0.00031 39.3 2.2 42 337-378 50-94 (531)
29 KOG0116 RasGAP SH3 binding pro 39.2 24 0.00053 37.8 2.9 14 309-322 277-290 (419)
30 TIGR01648 hnRNP-R-Q heterogene 38.2 28 0.0006 38.8 3.2 16 296-311 276-291 (578)
31 cd04483 hOBFC1_like hOBFC1_lik 37.6 91 0.002 26.2 5.5 55 108-162 14-89 (92)
32 COG1200 RecG RecG-like helicas 36.9 61 0.0013 36.9 5.6 61 105-165 78-138 (677)
33 PF07076 DUF1344: Protein of u 36.5 40 0.00087 27.1 3.0 34 107-145 14-47 (61)
34 PTZ00034 40S ribosomal protein 36.5 29 0.00062 31.5 2.5 18 360-378 69-86 (124)
35 KOG2945 Predicted RNA-binding 35.0 31 0.00068 36.4 2.8 15 330-344 251-265 (365)
36 KOG2567 Uncharacterized conser 31.1 39 0.00084 32.3 2.5 21 337-357 85-106 (179)
37 KOG0921 Dosage compensation co 29.6 47 0.001 39.3 3.2 15 317-331 1158-1172(1282)
38 PRK13605 endoribonuclease SymE 29.4 58 0.0013 29.2 3.1 48 106-162 19-74 (113)
39 KOG4501 Transcription coactiva 28.9 43 0.00093 37.3 2.7 9 25-33 158-166 (707)
40 PF08845 SymE_toxin: Toxin Sym 28.0 60 0.0013 25.5 2.7 30 126-159 20-57 (57)
41 TIGR01648 hnRNP-R-Q heterogene 27.7 40 0.00087 37.6 2.3 6 204-209 186-191 (578)
42 TIGR00643 recG ATP-dependent D 26.7 98 0.0021 34.4 5.1 54 107-161 52-107 (630)
43 KOG3262 H/ACA small nucleolar 25.8 56 0.0012 31.8 2.6 7 374-380 134-140 (215)
44 KOG2567 Uncharacterized conser 25.0 47 0.001 31.7 1.9 10 406-415 148-157 (179)
45 KOG0116 RasGAP SH3 binding pro 25.0 57 0.0012 35.1 2.8 8 353-360 294-301 (419)
46 PF13742 tRNA_anti_2: OB-fold 24.5 2.2E+02 0.0048 24.0 5.8 52 107-158 38-93 (99)
47 PF03276 Gag_spuma: Spumavirus 24.4 60 0.0013 36.1 2.8 11 368-378 397-407 (582)
48 cd04491 SoSSB_OBF SoSSB_OBF: A 24.0 3.6E+02 0.0079 21.4 6.7 66 89-158 6-72 (82)
49 KOG2945 Predicted RNA-binding 22.9 66 0.0014 34.1 2.7 11 302-312 255-265 (365)
50 KOG2135 Proteins containing th 22.4 45 0.00097 36.5 1.4 10 86-95 65-74 (526)
51 COG1799 Uncharacterized protei 22.0 50 0.0011 31.4 1.5 40 135-174 117-159 (167)
52 cd04323 AsnRS_cyto_like_N AsnR 20.9 2.9E+02 0.0062 22.2 5.6 59 108-166 16-83 (84)
No 1
>PF08585 DUF1767: Domain of unknown function (DUF1767); InterPro: IPR013894 This domain is present in eukaryotic proteins of unknown function, and is sometimes found to the N terminus of ubiquitin-binding and nucleic acid-binding domains. ; PDB: 3NBI_A.
Probab=99.78 E-value=1.2e-19 Score=150.25 Aligned_cols=86 Identities=34% Similarity=0.584 Sum_probs=65.8
Q ss_pred HHHHHHCCceeCchHHHHHHHH-HHhhcCCCCChhHHHHHHHHHHHHhhhhhcCCCCCCCcc--ccccccCCceEEEEee
Q 014129 12 IKALRSRGWCFGNIQEVTAIIA-INSALIDDKDPRKVADSTESELLNTDLKSIGGKSLPDPT--RKFSHIQGPIVLQVAS 88 (430)
Q Consensus 12 ~~~L~~~Gw~L~~~eWLk~Cv~-i~~~~~~~~~~~~~~~~V~~qlL~sDLr~ig~~~LP~~~--~k~~~L~Gp~VLQI~~ 88 (430)
++.|+++||||++ +||++|++ ++.+.+. +...+.+.|+.+||++||++++.++||+++ .+..+|+||+||||++
T Consensus 1 ~~~L~~~g~~l~~-~wl~~c~~~~~~~~~~--~~~~~~~~v~~~~L~sDL~~~~~~~LP~~i~~~~~~~l~gp~vlQV~~ 77 (90)
T PF08585_consen 1 MEWLNKRGWHLSP-EWLEECVEYLQQEHPG--DLEELAEEVYEQLLNSDLRDSGSPSLPDDIASQKKTTLPGPVVLQVNS 77 (90)
T ss_dssp HHHHHHH-----H-HHHHHHHHHHHHHHT----HHHHHHHHHHHHHTS-HHHH----S-TTTTT-SEEEEEEEEEEEEEE
T ss_pred ChHHHhcCCCcCH-HHHHHHHHHHHHhcCC--CHHHHHHHHHHHHHHchhhhccCCCCCcchhhCCccEeCCCEEEEEee
Confidence 3689999999997 89999999 7777765 568999999999999999999999999988 3578899999999999
Q ss_pred eeecccchhhhh
Q 014129 89 VRDISRSSIEEF 100 (430)
Q Consensus 89 I~DIs~s~~~q~ 100 (430)
|+|||+|+++|+
T Consensus 78 i~dIs~s~~~q~ 89 (90)
T PF08585_consen 78 IRDISASAYSQL 89 (90)
T ss_dssp EEESHHHHHHHH
T ss_pred eeecccChHhhc
Confidence 999999999886
No 2
>KOG3683 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.76 E-value=3.8e-19 Score=184.44 Aligned_cols=115 Identities=30% Similarity=0.415 Sum_probs=100.7
Q ss_pred ecccchhhhhcc--CCCCCceEEEEEecCceEEEEeecccCCCCCCCCCCCceEEEeCCceEeeeEEEEeCCcEEEeccc
Q 014129 91 DISRSSIEEFSG--NPGSNRLLKLVLTDGHIEITAIEYSHIPSIPYDVVPGTKVRLENKVPVHSGIVCLNPNVVTVLGGV 168 (430)
Q Consensus 91 DIs~s~~~q~~~--~~~~~RmLKL~LTDG~~~i~AiE~~pI~~Lsl~tpPGtKIlLkg~v~vrrGvLLL~p~Nv~VLGG~ 168 (430)
|++.+..+++.+ ...+.+||+|.||||+..|+|+||.+|+.|.++++|||||++.+.+.|+.|+|||.+.||.||||.
T Consensus 1 n~~~~~~~e~~~~~~~~~s~ml~l~LtDg~~si~a~el~~~pql~~~~~pgtkIl~~g~vd~~~g~LlL~~~nv~~lgg~ 80 (460)
T KOG3683|consen 1 NQATPRSTETQNQGVSKPSILLQLQLTDGHNSIHALELQTIPQLVSDLPPGTKILFTGKVDIKAGFLLLDQSNVRFLGGM 80 (460)
T ss_pred CcccccccccccccccccchhhhhhhhcccccceeeecccccceeeccCCCCceEEeechhhccceeEecccceeeeccc
Confidence 566677666543 334456999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHhhhhhhhcccccCCCCCCCCCCCCCCCCccCCCC
Q 014129 169 VASLHEEWQMNRKYSVFSRSSLRPSQESGGGGPPPFEKFQIG 210 (430)
Q Consensus 169 Ve~L~e~W~~~r~l~~~~r~~~~~~~~~~~~gPPpFvpf~~~ 210 (430)
|++|+++|.+++.+.++.+....+ ..++|+|++|+..
T Consensus 81 Ve~l~e~~~ie~sl~k~~~~~~~v-----~~~~p~~~~~g~~ 117 (460)
T KOG3683|consen 81 VEALIEKWEIEISLAKQLGSKNKV-----EKLIPGAIGFGRK 117 (460)
T ss_pred hHHHHHHHHHHHHHHHhcccccch-----hccCccccccCcc
Confidence 999999999999999998754433 4479999999874
No 3
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=96.85 E-value=0.00026 Score=76.71 Aligned_cols=24 Identities=63% Similarity=1.111 Sum_probs=0.0
Q ss_pred CCcCCCCCCCCCCCCCCCCCCCCC
Q 014129 407 GTENRGRGRGRGRRKGRGRGRGRG 430 (430)
Q Consensus 407 ~grgrgRGRGrgr~~~~~~~~~~~ 430 (430)
+||||||||||++|+|||||+|||
T Consensus 531 ~~~g~gr~rg~~~ggg~grg~~r~ 554 (556)
T PF05918_consen 531 RGRGGGRGRGRRSGGGRGRGRGRG 554 (556)
T ss_dssp ------------------------
T ss_pred CCCCCCCCCCCCCCCCCCCccccc
Confidence 444555555544444555555555
No 4
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=94.90 E-value=0.0072 Score=65.86 Aligned_cols=21 Identities=67% Similarity=1.267 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCC
Q 014129 410 NRGRGRGRGRRKGRGRGRGRG 430 (430)
Q Consensus 410 grgRGRGrgr~~~~~~~~~~~ 430 (430)
+|||||||||||++|+|||||
T Consensus 530 ~~~~g~gr~rg~~~ggg~grg 550 (556)
T PF05918_consen 530 GRGRGGGRGRGRRSGGGRGRG 550 (556)
T ss_dssp ---------------------
T ss_pred CCCCCCCCCCCCCCCCCCCCc
Confidence 445555555555555566665
No 5
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=92.63 E-value=0.06 Score=47.26 Aligned_cols=14 Identities=21% Similarity=0.349 Sum_probs=10.2
Q ss_pred hhhcCCcccccccC
Q 014129 369 LQNQLDLEDSHEQS 382 (430)
Q Consensus 369 lq~qldle~~~~~~ 382 (430)
+++.++++.-|+.+
T Consensus 69 lpD~l~ld~Llvd~ 82 (109)
T KOG3428|consen 69 LPDSLNLDTLLVDD 82 (109)
T ss_pred ccCCcCcceeeeeh
Confidence 56778888877655
No 6
>KOG3683 consensus Uncharacterized conserved protein [Function unknown]
Probab=89.94 E-value=0.11 Score=55.62 Aligned_cols=64 Identities=30% Similarity=0.353 Sum_probs=54.3
Q ss_pred CceEEEEEecCceEEEEeecccCCCCCCCCCCC---ceEEEeCCceEeeeEEEEeCCcEEEec-ccchh
Q 014129 107 NRLLKLVLTDGHIEITAIEYSHIPSIPYDVVPG---TKVRLENKVPVHSGIVCLNPNVVTVLG-GVVAS 171 (430)
Q Consensus 107 ~RmLKL~LTDG~~~i~AiE~~pI~~Lsl~tpPG---tKIlLkg~v~vrrGvLLL~p~Nv~VLG-G~Ve~ 171 (430)
.+++...+-+|.+..++++.+.|+.+.+..+|| ||+++.+ +...+|.++|.+.+++.|| |.|..
T Consensus 154 ~~~I~~~s~~~~t~~~~~~~~~~p~~~~s~~~g~~~tk~~~~~-~~~~rgr~~ld~~~~~~l~~~~v~k 221 (460)
T KOG3683|consen 154 CRLILKDSNSGETKTFAFEPESIPQSPLSEPPGERRTKALVPG-PLEGRGRLILDKNNLKKLGEGRVEK 221 (460)
T ss_pred HHHHHHHhccCccceeecccccCCCcccCCCCCccccccccCC-ccccccceeccCCCccccccccccc
Confidence 366666777778999999999999999999999 9999988 6778888999999999998 56544
No 7
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=88.02 E-value=1.1 Score=33.86 Aligned_cols=53 Identities=30% Similarity=0.456 Sum_probs=40.5
Q ss_pred CceEEEEEecCceEEEEeecccCCCCCCCCCCCceEEEeCCceEeeeEEEEeC
Q 014129 107 NRLLKLVLTDGHIEITAIEYSHIPSIPYDVVPGTKVRLENKVPVHSGIVCLNP 159 (430)
Q Consensus 107 ~RmLKL~LTDG~~~i~AiE~~pI~~Lsl~tpPGtKIlLkg~v~vrrGvLLL~p 159 (430)
+.+|++.|+|+...|.++=+..-+.+.-.+.+|.++.|.|.+...+|.+-|..
T Consensus 17 ~~~~~~~~~D~~g~i~~~~F~~~~~~~~~~~~G~~~~v~Gkv~~~~~~~qi~~ 69 (75)
T cd04488 17 RRRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVSGKVKRFRGGLQIVH 69 (75)
T ss_pred ccEEEEEEEcCCCEEEEEEECCCHHHHhcCCCCCEEEEEEEEeecCCeeEEeC
Confidence 45899999999988888777644445445899999999998877777664433
No 8
>PF14619 SnAC: Snf2-ATP coupling, chromatin remodelling complex
Probab=84.33 E-value=0.54 Score=38.33 Aligned_cols=24 Identities=29% Similarity=0.473 Sum_probs=22.2
Q ss_pred cCCCCCCCCCCCCCCCCCccCHHHHH
Q 014129 317 RHSRGRRYRGKGKEEEPAVFTLEEWE 342 (430)
Q Consensus 317 ~~~rg~~~rg~~~~ed~~~~t~~eWe 342 (430)
-+|||.|.|+.-.|+| .||++||+
T Consensus 51 ~~grG~R~RK~V~Y~D--~LTEeQwL 74 (74)
T PF14619_consen 51 EYGRGKRERKEVSYDD--GLTEEQWL 74 (74)
T ss_pred hcccccccccccccCC--CCCHHHhC
Confidence 4799999999999999 99999995
No 9
>PF04057 Rep-A_N: Replication factor-A protein 1, N-terminal domain; InterPro: IPR007199 Replication factor-a protein 1 (RPA1) forms a multiprotein complex with RPA2 and RPA3 that binds single-stranded DNA and functions in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian Virus 40 origin of replication [].; GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus; PDB: 1EWI_A 2B3G_A 2B29_A.
Probab=83.22 E-value=2 Score=36.92 Aligned_cols=59 Identities=27% Similarity=0.436 Sum_probs=40.2
Q ss_pred ceEEEEeeeeecccchhhhhccCCCCCceEEEEEecCceEEEEeecccCCCCCC--CCCCCceEEEeC
Q 014129 81 PIVLQVASVRDISRSSIEEFSGNPGSNRLLKLVLTDGHIEITAIEYSHIPSIPY--DVVPGTKVRLEN 146 (430)
Q Consensus 81 p~VLQI~~I~DIs~s~~~q~~~~~~~~RmLKL~LTDG~~~i~AiE~~pI~~Lsl--~tpPGtKIlLkg 146 (430)
.-||||..++-|... ......-+||.|+||...+.||--..+..+-. .+.-|+=|.|+.
T Consensus 18 ~pvlQVl~~k~i~~~-------~~~~~~RyR~~lSDG~~~~~amLatqln~lv~~g~l~~~siirl~~ 78 (101)
T PF04057_consen 18 NPVLQVLNIKKINSK-------QGGGSDRYRLVLSDGVHSIQAMLATQLNHLVESGELQKGSIIRLKQ 78 (101)
T ss_dssp -TEEEEEEEEEE-----------TTS--EEEEEEESSSEEEEEEESGGGHHHHHTTSSSTT-EEEEEE
T ss_pred CcEEEEEeeEEccCC-------CCCCCceEEEEEEChHHHHHHHhHHHhHHHHhcCCcccCCEEEEeE
Confidence 678999999998764 12334569999999999999997766655422 377788888874
No 10
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=82.97 E-value=3.7 Score=32.03 Aligned_cols=50 Identities=24% Similarity=0.242 Sum_probs=37.7
Q ss_pred CCceEEEEEecCceEEEEeecccCCCCCCCCCCCceEEEeCCceEeeeEE
Q 014129 106 SNRLLKLVLTDGHIEITAIEYSHIPSIPYDVVPGTKVRLENKVPVHSGIV 155 (430)
Q Consensus 106 ~~RmLKL~LTDG~~~i~AiE~~pI~~Lsl~tpPGtKIlLkg~v~vrrGvL 155 (430)
.++++.+.|.|+.-.+.++=|...+.+...+.+|..|+|.|.+...+|-+
T Consensus 17 g~~~~~~~l~D~tg~i~~~~f~~~~~~~~~l~~g~~v~v~G~v~~~~~~~ 66 (83)
T cd04492 17 GKPYLALTLQDKTGEIEAKLWDASEEDEEKFKPGDIVHVKGRVEEYRGRL 66 (83)
T ss_pred CCcEEEEEEEcCCCeEEEEEcCCChhhHhhCCCCCEEEEEEEEEEeCCce
Confidence 34799999999998888777764545544589999999998776555533
No 11
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=82.90 E-value=4.5 Score=32.76 Aligned_cols=56 Identities=20% Similarity=0.205 Sum_probs=43.9
Q ss_pred EEEEEecCceEEEEeecccCC-CCCCCCCCCceEEEeCCceEeeeEEEEeCCcEEEe
Q 014129 110 LKLVLTDGHIEITAIEYSHIP-SIPYDVVPGTKVRLENKVPVHSGIVCLNPNVVTVL 165 (430)
Q Consensus 110 LKL~LTDG~~~i~AiE~~pI~-~Lsl~tpPGtKIlLkg~v~vrrGvLLL~p~Nv~VL 165 (430)
+-|+|.|+...+.++=|++.. .+...+.+|.+|.+.|.+.+.+|-+-|.-..++||
T Consensus 17 vyfsLkD~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~~~~G~~ql~v~~i~~~ 73 (73)
T cd04487 17 TIFTLRDETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGEVEPRDGQLQIEVESLEVL 73 (73)
T ss_pred EEEEEEcCCEEEEEEEEchhccCCcCCCCCCCEEEEEEEEecCCeEEEEEEeeEEEC
Confidence 678889988666666666543 35556899999999999888999998888777775
No 12
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=82.34 E-value=1 Score=34.53 Aligned_cols=59 Identities=20% Similarity=0.276 Sum_probs=44.8
Q ss_pred CceEEEEEecCceEEEEeecc-cCCCCCCCCCCCceEEEeCCceEeeeE-EEEeCCcEEEe
Q 014129 107 NRLLKLVLTDGHIEITAIEYS-HIPSIPYDVVPGTKVRLENKVPVHSGI-VCLNPNVVTVL 165 (430)
Q Consensus 107 ~RmLKL~LTDG~~~i~AiE~~-pI~~Lsl~tpPGtKIlLkg~v~vrrGv-LLL~p~Nv~VL 165 (430)
..++.++|+||.-.+.++=+. ....+...+.+|+-|.+.|.+...++- +-|...++++|
T Consensus 15 ~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~~~~~~~~l~~~~i~~l 75 (75)
T PF01336_consen 15 GKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVRGKVKRYNGGELELIVPKIEIL 75 (75)
T ss_dssp TTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEEEEEEEETTSSEEEEEEEEEEE
T ss_pred CCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEEEEEEEECCccEEEEECEEEEC
Confidence 478999999999887777666 444444468999999999988888776 77777777665
No 13
>cd04477 RPA1N RPA1N: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA1N is known to specifically interact with the p53 tumor suppressor, DNA polymerase alpha, and transcription factors. In addition to RPA1N, RPA1 contains three other OB folds: ssDNA-binding domain (DBD)-A, DBD-B, and DBD-C.
Probab=78.26 E-value=2.5 Score=36.23 Aligned_cols=58 Identities=24% Similarity=0.389 Sum_probs=42.2
Q ss_pred ceEEEEeeeeecccchhhhhccCCCCCceEEEEEecCceEEEEeecccCCCCCC--CCCCCceEEEeC
Q 014129 81 PIVLQVASVRDISRSSIEEFSGNPGSNRLLKLVLTDGHIEITAIEYSHIPSIPY--DVVPGTKVRLEN 146 (430)
Q Consensus 81 p~VLQI~~I~DIs~s~~~q~~~~~~~~RmLKL~LTDG~~~i~AiE~~pI~~Lsl--~tpPGtKIlLkg 146 (430)
+-||||..++=|.... +.. .=+|+.|+||...+.||=-..+..+-. .+..|+=|.|+.
T Consensus 17 ~PvlQv~~ik~i~~~~-------~~~-~RyRi~lSDG~~~~~amLatqln~~v~~g~l~~~sIirl~~ 76 (97)
T cd04477 17 KPVLQVLNIKKIDSSN-------GSS-ERYRILLSDGVYYVQAMLATQLNPLVESGQLQRGSIIRLKR 76 (97)
T ss_pred CCEEEEEEEEEccCCC-------CCc-ceEEEEEEChhHHHHHHHhhhhhhHHhcCCccCCcEEEECe
Confidence 5788999998886532 112 348999999998888886655555432 388899998863
No 14
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=73.72 E-value=2.7 Score=32.32 Aligned_cols=55 Identities=16% Similarity=0.110 Sum_probs=38.1
Q ss_pred CceEEEEEecCceEEEEeecccC-CCCCCCCCCCceEEEeCCceEeeeEEEEeCCc
Q 014129 107 NRLLKLVLTDGHIEITAIEYSHI-PSIPYDVVPGTKVRLENKVPVHSGIVCLNPNV 161 (430)
Q Consensus 107 ~RmLKL~LTDG~~~i~AiE~~pI-~~Lsl~tpPGtKIlLkg~v~vrrGvLLL~p~N 161 (430)
++|+.++|.|+.-.+.++=|... ..+.-.+.+|+.+.|.|.+...+|-+-|.-..
T Consensus 18 ~~~~~~~l~D~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G~v~~~~~~~~l~~~~ 73 (84)
T cd04485 18 KRMAFVTLEDLTGSIEVVVFPETYEKYRDLLKEDALLLVEGKVERRDGGLRLIAER 73 (84)
T ss_pred CEEEEEEEEeCCCeEEEEECHHHHHHHHHHhcCCCEEEEEEEEEecCCceEEEeec
Confidence 46999999999977777666422 12333488999999999776655655444333
No 15
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=72.33 E-value=3.4 Score=43.38 Aligned_cols=14 Identities=21% Similarity=0.276 Sum_probs=9.8
Q ss_pred cCCCCCCCCcchhh
Q 014129 278 EDPSSSQARPKEVV 291 (430)
Q Consensus 278 ~~~~~~~~~~~~v~ 291 (430)
+|-||.+.|++-++
T Consensus 279 ~ktSS~~~Re~Tas 292 (465)
T KOG3973|consen 279 QKTSSMDRRERTAS 292 (465)
T ss_pred Hhhcccchhhhhhh
Confidence 56778888777654
No 16
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=69.99 E-value=4.2 Score=35.96 Aligned_cols=14 Identities=50% Similarity=0.665 Sum_probs=8.1
Q ss_pred CCCCCCCCCCCCCC
Q 014129 319 SRGRRYRGKGKEEE 332 (430)
Q Consensus 319 ~rg~~~rg~~~~ed 332 (430)
..|.=+||+..|-|
T Consensus 23 ~tGe~YRGkliEae 36 (119)
T KOG3172|consen 23 KTGEVYRGKLIEAE 36 (119)
T ss_pred cCCceeeeeeEEec
Confidence 44556777775443
No 17
>cd04493 BRCA2DBD_OB1 BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA). BRCA2DBD OB1 binds DNA weakly.
Probab=67.10 E-value=7.6 Score=33.92 Aligned_cols=56 Identities=25% Similarity=0.272 Sum_probs=40.9
Q ss_pred ceEEEEeeeeecccchhhhhccCCCCCceEEEEEecCceEEEEeecccCCCCCCC--CCCCceEEEeC
Q 014129 81 PIVLQVASVRDISRSSIEEFSGNPGSNRLLKLVLTDGHIEITAIEYSHIPSIPYD--VVPGTKVRLEN 146 (430)
Q Consensus 81 p~VLQI~~I~DIs~s~~~q~~~~~~~~RmLKL~LTDG~~~i~AiE~~pI~~Lsl~--tpPGtKIlLkg 146 (430)
++||=|.+|..-.. ..+-+-.|+||||--.|.|.=-.++..+--. +..|+||.|.|
T Consensus 4 ~mVL~Vs~I~~~~~----------~~~~~~~lEltDGWYsi~a~lD~~L~~~l~~gkl~vGqKL~i~G 61 (100)
T cd04493 4 LMVLCVSGINSEER----------LSPHMPIIELTDGWYSIRAQLDPPLTNLVRKGKLRVGQKLRICG 61 (100)
T ss_pred eEEEEEEEEeeccC----------CCCcccEEEEecCeEEEEEEeCHHHHHHHHcCCeecccEEEEEC
Confidence 56666666655443 1234668999999999999877777665322 89999999987
No 18
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=67.05 E-value=4.9 Score=46.89 Aligned_cols=24 Identities=17% Similarity=0.185 Sum_probs=18.3
Q ss_pred CCCCCCCCccCCCCCCcccccccC
Q 014129 197 GGGGPPPFEKFQIGAPSHQLAQRG 220 (430)
Q Consensus 197 ~~~gPPpFvpf~~~a~~r~~~~~~ 220 (430)
+-.=|-||.=|+-.-.+|+.+.-+
T Consensus 1032 dM~fPsPFFVFGEKIRTRAIS~K~ 1055 (1282)
T KOG0921|consen 1032 EMDFPSPFFVFGEKIRTRAISCKQ 1055 (1282)
T ss_pred ccCCCCceeeechhhhhheecccC
Confidence 455688888888888888877664
No 19
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=62.49 E-value=38 Score=26.39 Aligned_cols=44 Identities=18% Similarity=0.281 Sum_probs=34.6
Q ss_pred ceEEEEEecCceEEEEeeccc-CCCCCCCCCCCceEEEeCCceEe
Q 014129 108 RLLKLVLTDGHIEITAIEYSH-IPSIPYDVVPGTKVRLENKVPVH 151 (430)
Q Consensus 108 RmLKL~LTDG~~~i~AiE~~p-I~~Lsl~tpPGtKIlLkg~v~vr 151 (430)
.|.-++|.|+...+.++=|.. ...+...+.+|..|++++.+...
T Consensus 17 g~~~~~L~D~~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g~v~~~ 61 (78)
T cd04489 17 GHLYFTLKDEDASIRCVMWRSNARRLGFPLEEGMEVLVRGKVSFY 61 (78)
T ss_pred cEEEEEEEeCCeEEEEEEEcchhhhCCCCCCCCCEEEEEEEEEEE
Confidence 399999999997777766654 44455568999999999987765
No 20
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=59.67 E-value=31 Score=25.05 Aligned_cols=49 Identities=22% Similarity=0.333 Sum_probs=33.1
Q ss_pred CceEEEEEecCc-eEEEEeecccCCC-CCCCCCCCceEEEeCCceEeeeEE
Q 014129 107 NRLLKLVLTDGH-IEITAIEYSHIPS-IPYDVVPGTKVRLENKVPVHSGIV 155 (430)
Q Consensus 107 ~RmLKL~LTDG~-~~i~AiE~~pI~~-Lsl~tpPGtKIlLkg~v~vrrGvL 155 (430)
+.++.|.|+|+. ..+.++=+..... ....+.+|..|.+.+.+...+|.+
T Consensus 16 ~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~g~v~~~~~~~ 66 (75)
T cd03524 16 GKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIKGKVKKFRGRL 66 (75)
T ss_pred CeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEEEEEEecCCeE
Confidence 468999999988 7777666654322 223488899999987665444433
No 21
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=58.31 E-value=27 Score=28.53 Aligned_cols=59 Identities=14% Similarity=0.114 Sum_probs=46.9
Q ss_pred ceEEEEEecCceEEEEeecccCCC----CCCCCCCCceEEEeCCceEeeeEEEEeCCcEEEec
Q 014129 108 RLLKLVLTDGHIEITAIEYSHIPS----IPYDVVPGTKVRLENKVPVHSGIVCLNPNVVTVLG 166 (430)
Q Consensus 108 RmLKL~LTDG~~~i~AiE~~pI~~----Lsl~tpPGtKIlLkg~v~vrrGvLLL~p~Nv~VLG 166 (430)
.-+.++|.||.-+|.|+-+..-+. ....+.+|+-|.+.|.+..-+|-+-|.-..+..+-
T Consensus 16 ~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~~~g~~ql~i~~i~~v~ 78 (95)
T cd04478 16 TNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVT 78 (95)
T ss_pred cEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEcccCCeeEEEEEEEEEeC
Confidence 448899999998888888765542 33458899999999988888898888877777654
No 22
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=55.88 E-value=17 Score=38.42 Aligned_cols=16 Identities=13% Similarity=0.368 Sum_probs=11.5
Q ss_pred HHHHHHHHHHCCceeC
Q 014129 8 TEAVIKALRSRGWCFG 23 (430)
Q Consensus 8 ~~~l~~~L~~~Gw~L~ 23 (430)
...|.+.|.+.||.--
T Consensus 9 ~~~l~~~l~~~g~~~p 24 (456)
T PRK10590 9 SPDILRAVAEQGYREP 24 (456)
T ss_pred CHHHHHHHHHCCCCCC
Confidence 4678888888888443
No 23
>PF09103 BRCA-2_OB1: BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; InterPro: IPR015187 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome []. ; GO: 0000724 double-strand break repair via homologous recombination; PDB: 1IYJ_D 1MIU_A.
Probab=55.87 E-value=6.6 Score=34.91 Aligned_cols=58 Identities=29% Similarity=0.333 Sum_probs=27.1
Q ss_pred CCceEEEEeeeeecccchhhhhccCCCCCceEEEEEecCceEEEEeecccCCCCCC--CCCCCceEEEeC
Q 014129 79 QGPIVLQVASVRDISRSSIEEFSGNPGSNRLLKLVLTDGHIEITAIEYSHIPSIPY--DVVPGTKVRLEN 146 (430)
Q Consensus 79 ~Gp~VLQI~~I~DIs~s~~~q~~~~~~~~RmLKL~LTDG~~~i~AiE~~pI~~Lsl--~tpPGtKIlLkg 146 (430)
..|+||=|.+| +. ......-...|+||||--.|.|.=-.++..+-- .+..|+||.|.|
T Consensus 14 ~~~mVL~Vs~i---~~-------~~~~~~~~~~lelTDGWY~Ika~lD~~L~~~l~~gki~vG~KL~v~G 73 (118)
T PF09103_consen 14 SKPMVLCVSSI---SS-------SDNDSPESAILELTDGWYSIKAQLDPPLTRLLRKGKIRVGQKLRVCG 73 (118)
T ss_dssp B-SEEEEEEE-----------------------EEEE-SS-EEEE---HHHHHHHHTT-S-TT-EEEESS
T ss_pred CCcEEEEEEEE---cc-------CCCCCCccCEEEEecCCEEEEEEeCHHHHHHHHhCCccCCccEEEEC
Confidence 44777777776 11 111223467899999999999875444443322 378899999988
No 24
>PF04774 HABP4_PAI-RBP1: Hyaluronan / mRNA binding family; InterPro: IPR006861 This entry includes the HABP4 protein family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan []. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability []. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Hyaluronan/mRNA-binding protein may be involved in nuclear functions such as the remodeling of chromatin and the regulation of transcription [, ].
Probab=54.72 E-value=6.8 Score=33.20 Aligned_cols=18 Identities=39% Similarity=0.490 Sum_probs=13.9
Q ss_pred CCCCCCCccCHHHHHhhhc
Q 014129 328 GKEEEPAVFTLEEWEKRKA 346 (430)
Q Consensus 328 ~~~ed~~~~t~~eWek~~~ 346 (430)
..++++..|||||| |...
T Consensus 72 ~~eee~k~mTLdE~-k~~q 89 (106)
T PF04774_consen 72 PEEEEEKEMTLDEY-KALQ 89 (106)
T ss_pred cccccccccCHHHH-HHHH
Confidence 45778899999999 5543
No 25
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=54.61 E-value=11 Score=39.62 Aligned_cols=9 Identities=56% Similarity=1.070 Sum_probs=3.6
Q ss_pred CCCCCCCCC
Q 014129 419 RRKGRGRGR 427 (430)
Q Consensus 419 r~~~~~~~~ 427 (430)
||||.|.||
T Consensus 449 rgrgggggr 457 (465)
T KOG3973|consen 449 RGRGGGGGR 457 (465)
T ss_pred CCCCCCCCC
Confidence 444433333
No 26
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=52.72 E-value=12 Score=39.60 Aligned_cols=17 Identities=18% Similarity=0.327 Sum_probs=10.3
Q ss_pred CchHHHHHHhhhcCCcc
Q 014129 360 SNDEDLAWQLQNQLDLE 376 (430)
Q Consensus 360 ~~de~la~qlq~qldle 376 (430)
..|..+.+.+++.++.+
T Consensus 351 ~~d~~~~~~ie~~l~~~ 367 (456)
T PRK10590 351 VDEHKLLRDIEKLLKKE 367 (456)
T ss_pred HHHHHHHHHHHHHhcCC
Confidence 34666666677665544
No 27
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=51.39 E-value=39 Score=28.29 Aligned_cols=54 Identities=22% Similarity=0.340 Sum_probs=37.1
Q ss_pred EEEEEecCceEEEEeeccc---CCCCCCCCCCCceEEEeCCceEeeeEEEEeCCcEEEec
Q 014129 110 LKLVLTDGHIEITAIEYSH---IPSIPYDVVPGTKVRLENKVPVHSGIVCLNPNVVTVLG 166 (430)
Q Consensus 110 LKL~LTDG~~~i~AiE~~p---I~~Lsl~tpPGtKIlLkg~v~vrrGvLLL~p~Nv~VLG 166 (430)
+-|+|.|....+.++=|++ ...+...+.+|-+|.+.|.+.+.. -|.-+.++++|
T Consensus 19 ~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~v~~y~---ql~ve~l~~~g 75 (91)
T cd04482 19 VFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGSVRPGT---TLNLEKLRVIR 75 (91)
T ss_pred EEEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEEEEEecCC---EEEEEEEEECC
Confidence 5688889876665555555 346666799999999999766665 34444555544
No 28
>KOG2269 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=45.01 E-value=15 Score=39.27 Aligned_cols=42 Identities=29% Similarity=0.227 Sum_probs=31.4
Q ss_pred CHHHHHhhhc--CC-CCCccCCCCCCCchHHHHHHhhhcCCcccc
Q 014129 337 TLEEWEKRKA--GA-KPFVNHKLPDTSNDEDLAWQLQNQLDLEDS 378 (430)
Q Consensus 337 t~~eWek~~~--~~-~~~~~~~~~d~~~de~la~qlq~qldle~~ 378 (430)
.+|||+--+. .+ -+++.+...++++|+++|-.||.+||-|--
T Consensus 50 ~~Ee~~~~~~l~~~eG~~v~d~qlp~~sD~~vAq~LQ~~fDrEyd 94 (531)
T KOG2269|consen 50 KLEEERYMKQLDQMEGDSVSDDQLPINSDEEVAQALQRHFDREYD 94 (531)
T ss_pred hHHHHHHHHHHHHhcCCccccccCCCCcHHHHHHHHHHHhhhhhh
Confidence 4556654322 22 248889999999999999999999997754
No 29
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=39.20 E-value=24 Score=37.81 Aligned_cols=14 Identities=21% Similarity=0.147 Sum_probs=5.8
Q ss_pred hcCCCccCcCCCCC
Q 014129 309 MSTSNQDNRHSRGR 322 (430)
Q Consensus 309 ~~~~~~~~~~~rg~ 322 (430)
++.++++.++-.++
T Consensus 277 ~n~~~~~~~~~~~~ 290 (419)
T KOG0116|consen 277 GNSNNQEPRADGLG 290 (419)
T ss_pred cccCCcceeecccc
Confidence 33444444444443
No 30
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=38.23 E-value=28 Score=38.82 Aligned_cols=16 Identities=6% Similarity=0.300 Sum_probs=11.7
Q ss_pred CccHHHHHHHHHHhcC
Q 014129 296 VQNQAASQKLLQKMST 311 (430)
Q Consensus 296 ~qn~aaaqkllq~~~~ 311 (430)
-.+..+|+|.+..|+.
T Consensus 276 F~s~e~A~kAi~~lnG 291 (578)
T TIGR01648 276 FEDREDAVKAMDELNG 291 (578)
T ss_pred eCCHHHHHHHHHHhCC
Confidence 3457888888888854
No 31
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=37.57 E-value=91 Score=26.25 Aligned_cols=55 Identities=15% Similarity=0.230 Sum_probs=38.9
Q ss_pred ceEEEEEecCceEEEEeecccCC---------------------CCCCCCCCCceEEEeCCceEeeeEEEEeCCcE
Q 014129 108 RLLKLVLTDGHIEITAIEYSHIP---------------------SIPYDVVPGTKVRLENKVPVHSGIVCLNPNVV 162 (430)
Q Consensus 108 RmLKL~LTDG~~~i~AiE~~pI~---------------------~Lsl~tpPGtKIlLkg~v~vrrGvLLL~p~Nv 162 (430)
.-+.|+|-||.-.|-+.=+..-+ ...-.+.+|.-|.|+|.+..-+|.+-|+-+.+
T Consensus 14 ~~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV~G~i~~frg~~ql~i~~~ 89 (92)
T cd04483 14 TFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVRGSIRTYRGEREINASVV 89 (92)
T ss_pred CeEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEEEEEEeccCCeeEEEEEEE
Confidence 45889999999666666554332 12224789999999998888888877765544
No 32
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=36.87 E-value=61 Score=36.89 Aligned_cols=61 Identities=23% Similarity=0.275 Sum_probs=47.5
Q ss_pred CCCceEEEEEecCceEEEEeecccCCCCCCCCCCCceEEEeCCceEeeeEEEEeCCcEEEe
Q 014129 105 GSNRLLKLVLTDGHIEITAIEYSHIPSIPYDVVPGTKVRLENKVPVHSGIVCLNPNVVTVL 165 (430)
Q Consensus 105 ~~~RmLKL~LTDG~~~i~AiE~~pI~~Lsl~tpPGtKIlLkg~v~vrrGvLLL~p~Nv~VL 165 (430)
+.+.+|++.++||...+...=|..=..|.-.++.|+++.+.|++.-.+|.+-+..-.+.++
T Consensus 78 ~~~~~l~v~~~d~~~~l~l~fFn~~~~l~~~~~~G~~v~v~Gk~~~~~~~~~~~hpe~~~~ 138 (677)
T COG1200 78 GKRKLLKVTLSDGTGVLTLVFFNFPAYLKKKLKVGERVIVYGKVKRFKGGLQITHPEYIVN 138 (677)
T ss_pred CCCceEEEEEecCcEEEEEEEECccHHHHhhCCCCCEEEEEEEEeeccCceEEEcceEEec
Confidence 4568999999999988877766655577767999999999998887776665555555554
No 33
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=36.50 E-value=40 Score=27.11 Aligned_cols=34 Identities=24% Similarity=0.327 Sum_probs=26.0
Q ss_pred CceEEEEEecCceEEEEeecccCCCCCCCCCCCceEEEe
Q 014129 107 NRLLKLVLTDGHIEITAIEYSHIPSIPYDVVPGTKVRLE 145 (430)
Q Consensus 107 ~RmLKL~LTDG~~~i~AiE~~pI~~Lsl~tpPGtKIlLk 145 (430)
+-++.|+|.||++.-..-|+. + -.+.||-||+|.
T Consensus 14 ~~~~titLdDGksy~lp~ef~-~----~~L~~G~kV~V~ 47 (61)
T PF07076_consen 14 PETMTITLDDGKSYKLPEEFD-F----DGLKPGMKVVVF 47 (61)
T ss_pred CCceEEEecCCCEEECCCccc-c----cccCCCCEEEEE
Confidence 357889999999877666654 1 138899999986
No 34
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=36.48 E-value=29 Score=31.52 Aligned_cols=18 Identities=28% Similarity=0.370 Sum_probs=11.6
Q ss_pred CchHHHHHHhhhcCCcccc
Q 014129 360 SNDEDLAWQLQNQLDLEDS 378 (430)
Q Consensus 360 ~~de~la~qlq~qldle~~ 378 (430)
+.||-+. -|-+-|+|-..
T Consensus 69 LT~eGie-yLR~yL~LP~e 86 (124)
T PTZ00034 69 LTDEGIE-YLRTYLHLPPD 86 (124)
T ss_pred EchHHHH-HHHHHhCCCcc
Confidence 5566654 36677888766
No 35
>KOG2945 consensus Predicted RNA-binding protein [General function prediction only]
Probab=34.96 E-value=31 Score=36.42 Aligned_cols=15 Identities=33% Similarity=0.364 Sum_probs=10.0
Q ss_pred CCCCCccCHHHHHhh
Q 014129 330 EEEPAVFTLEEWEKR 344 (430)
Q Consensus 330 ~ed~~~~t~~eWek~ 344 (430)
++..--||+|||-..
T Consensus 251 e~~~~~~tlde~k~l 265 (365)
T KOG2945|consen 251 EEKVKEMTLDEMKAL 265 (365)
T ss_pred hhhhhhhhhhHHHHH
Confidence 444556888888654
No 36
>KOG2567 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.08 E-value=39 Score=32.25 Aligned_cols=21 Identities=29% Similarity=0.651 Sum_probs=11.4
Q ss_pred CHHHHHhhhcCCCC-CccCCCC
Q 014129 337 TLEEWEKRKAGAKP-FVNHKLP 357 (430)
Q Consensus 337 t~~eWek~~~~~~~-~~~~~~~ 357 (430)
+.|-||-.-.|--| .+.-+++
T Consensus 85 v~d~W~p~~eGl~pl~vtRhVp 106 (179)
T KOG2567|consen 85 VEDVWEPTEEGLEPLEVTRHVP 106 (179)
T ss_pred hhhcccccccCccceEEeeccc
Confidence 45678777556544 3333343
No 37
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=29.63 E-value=47 Score=39.33 Aligned_cols=15 Identities=13% Similarity=0.091 Sum_probs=6.5
Q ss_pred cCCCCCCCCCCCCCC
Q 014129 317 RHSRGRRYRGKGKEE 331 (430)
Q Consensus 317 ~~~rg~~~rg~~~~e 331 (430)
+|+-|-+-.+...+|
T Consensus 1158 rygDGp~PPKmaryD 1172 (1282)
T KOG0921|consen 1158 RYGDGPGPPKMARYD 1172 (1282)
T ss_pred cccCCCCCccccccc
Confidence 444444433333444
No 38
>PRK13605 endoribonuclease SymE; Provisional
Probab=29.41 E-value=58 Score=29.18 Aligned_cols=48 Identities=29% Similarity=0.445 Sum_probs=33.8
Q ss_pred CCceEEEEEecCceEEEEeecccCCCCCC--------CCCCCceEEEeCCceEeeeEEEEeCCcE
Q 014129 106 SNRLLKLVLTDGHIEITAIEYSHIPSIPY--------DVVPGTKVRLENKVPVHSGIVCLNPNVV 162 (430)
Q Consensus 106 ~~RmLKL~LTDG~~~i~AiE~~pI~~Lsl--------~tpPGtKIlLkg~v~vrrGvLLL~p~Nv 162 (430)
..|-|++-..-... .|.++|.|++ ++..|++|.| .|..|.|+|++.+=
T Consensus 19 t~R~~TVgY~~~~~-----~~~~~PaI~LkG~WLeeAGF~tG~~V~V----~V~~G~LVIt~~~~ 74 (113)
T PRK13605 19 NNRQLTVSYASRYP-----DYSRIPAITLKGQWLEAAGFATGTAVDV----RVMEGCIVLTAQPP 74 (113)
T ss_pred CceeEEEEeccCCC-----CCCCCCceeECchhHHhhCCCCCCeEEE----EEeCCEEEEEeCCC
Confidence 34656664332221 4788999887 4788999875 78999999998874
No 39
>KOG4501 consensus Transcription coactivator complex, P100 component [Transcription]
Probab=28.93 E-value=43 Score=37.33 Aligned_cols=9 Identities=0% Similarity=0.084 Sum_probs=5.7
Q ss_pred hHHHHHHHH
Q 014129 25 IQEVTAIIA 33 (430)
Q Consensus 25 ~eWLk~Cv~ 33 (430)
++.|+-||.
T Consensus 158 p~lldllV~ 166 (707)
T KOG4501|consen 158 PELLDLLVR 166 (707)
T ss_pred HHHHHHHHH
Confidence 566666666
No 40
>PF08845 SymE_toxin: Toxin SymE, type I toxin-antitoxin system; InterPro: IPR014944 This entry represents a SOS-induced gene whose product shows homology to the antitoxin MazE (SymE), the coding region contains a cis-encoded antisense RNA. The small antisense RNA and the gene have the all the hallmarks of a toxin-antitoxin module. The synthesis of the SymE is tightly repressed at multiple levels; at the transcriptional level by the LexA repressor, at the level of mRNA stability and translation by the SymR RNA and at the level of protein stability by the Lon protease. SymE co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased RNA degradation. These properties are shared with several RNA endonuclease toxins of toxin-antitoxin modules. It seems probable that the SymE protein represents an evolutionary derivative of a toxin containing the AbrB fold, whose representatives are typically antitoxins. The SymE promoted cleavage of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions []. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0016070 RNA metabolic process, 0005737 cytoplasm
Probab=27.97 E-value=60 Score=25.49 Aligned_cols=30 Identities=27% Similarity=0.576 Sum_probs=22.3
Q ss_pred cccCCCCCC--------CCCCCceEEEeCCceEeeeEEEEeC
Q 014129 126 YSHIPSIPY--------DVVPGTKVRLENKVPVHSGIVCLNP 159 (430)
Q Consensus 126 ~~pI~~Lsl--------~tpPGtKIlLkg~v~vrrGvLLL~p 159 (430)
|+++|.|.+ .+.+|++|.| .|..|.|+++|
T Consensus 20 ~~~~p~i~L~G~WL~~aGF~~G~~v~V----~v~~g~lvIt~ 57 (57)
T PF08845_consen 20 YRPVPEIRLKGKWLEEAGFTIGDPVKV----RVMPGCLVITP 57 (57)
T ss_pred cccCceEEEchhhhHHhCCCCCCEEEE----EEECCEEEEeC
Confidence 345666665 5789999875 67889998876
No 41
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=27.73 E-value=40 Score=37.58 Aligned_cols=6 Identities=17% Similarity=0.628 Sum_probs=3.4
Q ss_pred CccCCC
Q 014129 204 FEKFQI 209 (430)
Q Consensus 204 Fvpf~~ 209 (430)
||.|..
T Consensus 186 FVeF~s 191 (578)
T TIGR01648 186 FVEYES 191 (578)
T ss_pred EEEcCC
Confidence 566654
No 42
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=26.66 E-value=98 Score=34.42 Aligned_cols=54 Identities=22% Similarity=0.253 Sum_probs=40.7
Q ss_pred CceEEEEEec-CceEEEEeecccCCCCCCCCCCCceEEEeCCceEeeeEE-EEeCCc
Q 014129 107 NRLLKLVLTD-GHIEITAIEYSHIPSIPYDVVPGTKVRLENKVPVHSGIV-CLNPNV 161 (430)
Q Consensus 107 ~RmLKL~LTD-G~~~i~AiE~~pI~~Lsl~tpPGtKIlLkg~v~vrrGvL-LL~p~N 161 (430)
++++++.|+| |...+..+=|. -+.+.-.+++|+++++.|++...+|-+ |-.|+-
T Consensus 52 ~~~~~~~~~d~~~~~~~~~~F~-~~~~~~~~~~g~~~~~~Gk~~~~~~~~~~~~p~~ 107 (630)
T TIGR00643 52 RKVLKLRLKDGGYKKLELRFFN-RAFLKKKFKVGSKVVVYGKVKSSKFKAYLIHPEF 107 (630)
T ss_pred CceEEEEEEECCCCEEEEEEEC-CHHHHhhCCCCCEEEEEEEEEeeCCEEEEECCEE
Confidence 4589999999 88777766664 445555699999999999888766654 555554
No 43
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=25.82 E-value=56 Score=31.82 Aligned_cols=7 Identities=14% Similarity=0.026 Sum_probs=2.9
Q ss_pred Ccccccc
Q 014129 374 DLEDSHE 380 (430)
Q Consensus 374 dle~~~~ 380 (430)
-|+-|+-
T Consensus 134 Pl~RFLP 140 (215)
T KOG3262|consen 134 PLDRFLP 140 (215)
T ss_pred cHhhcCC
Confidence 3444443
No 44
>KOG2567 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.00 E-value=47 Score=31.67 Aligned_cols=10 Identities=60% Similarity=1.056 Sum_probs=4.7
Q ss_pred CCCcCCCCCC
Q 014129 406 HGTENRGRGR 415 (430)
Q Consensus 406 ~~grgrgRGR 415 (430)
-++||+||||
T Consensus 148 ~g~r~~gr~r 157 (179)
T KOG2567|consen 148 LGGRGRGRGR 157 (179)
T ss_pred CCCCCcCccc
Confidence 3444444444
No 45
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=24.99 E-value=57 Score=35.06 Aligned_cols=8 Identities=25% Similarity=0.501 Sum_probs=3.1
Q ss_pred cCCCCCCC
Q 014129 353 NHKLPDTS 360 (430)
Q Consensus 353 ~~~~~d~~ 360 (430)
++-++|++
T Consensus 294 ~nlP~da~ 301 (419)
T KOG0116|consen 294 KNLPPDAT 301 (419)
T ss_pred ecCCCCCC
Confidence 33334443
No 46
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=24.52 E-value=2.2e+02 Score=24.04 Aligned_cols=52 Identities=21% Similarity=0.359 Sum_probs=37.8
Q ss_pred CceEEEEEecCceEEEEeeccc-CCCCC-CCCCCCceEEEeCCceE--eeeEEEEe
Q 014129 107 NRLLKLVLTDGHIEITAIEYSH-IPSIP-YDVVPGTKVRLENKVPV--HSGIVCLN 158 (430)
Q Consensus 107 ~RmLKL~LTDG~~~i~AiE~~p-I~~Ls-l~tpPGtKIlLkg~v~v--rrGvLLL~ 158 (430)
..-+-|+|.|+..++.++=+.. ...|. ..+..|.||++.+.+.+ .+|-+-|.
T Consensus 38 ~gh~YftLkD~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~~y~~~G~~sl~ 93 (99)
T PF13742_consen 38 SGHVYFTLKDEEASISCVIFRSRARRIRGFDLKDGDKVLVRGRVSFYEPRGSLSLI 93 (99)
T ss_pred CceEEEEEEcCCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEEEECCCcEEEEE
Confidence 3568899999998877777653 34455 56899999999987664 45655444
No 47
>PF03276 Gag_spuma: Spumavirus gag protein; InterPro: IPR004957 The Spumavirus gag protein is a core viral polyprotein that undergoes specific enzymatic cleavages in vivo to yield the mature protein.; GO: 0019028 viral capsid
Probab=24.36 E-value=60 Score=36.08 Aligned_cols=11 Identities=36% Similarity=0.546 Sum_probs=5.4
Q ss_pred HhhhcCCcccc
Q 014129 368 QLQNQLDLEDS 378 (430)
Q Consensus 368 qlq~qldle~~ 378 (430)
-+|-.||.|-.
T Consensus 397 ~~Q~rLDq~~~ 407 (582)
T PF03276_consen 397 AMQQRLDQEPD 407 (582)
T ss_pred HHHHHhhcccc
Confidence 34555555443
No 48
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=24.04 E-value=3.6e+02 Score=21.37 Aligned_cols=66 Identities=21% Similarity=0.203 Sum_probs=42.3
Q ss_pred eeecccchhhhhccCCCCCceEEEEEecCceEEEEeecccCCCCCCCCCCCceEEEe-CCceEeeeEEEEe
Q 014129 89 VRDISRSSIEEFSGNPGSNRLLKLVLTDGHIEITAIEYSHIPSIPYDVVPGTKVRLE-NKVPVHSGIVCLN 158 (430)
Q Consensus 89 I~DIs~s~~~q~~~~~~~~RmLKL~LTDG~~~i~AiE~~pI~~Lsl~tpPGtKIlLk-g~v~vrrGvLLL~ 158 (430)
|.+|+.++.-. ......+++.+.|.|..-+|.+.-+..-. ...+.+|.-|.|. +.+...+|.+=|.
T Consensus 6 V~~~~~~~~~~--~~g~~~~~~~~~l~D~TG~i~~~~W~~~~--~~~~~~G~vv~i~~~~v~~~~g~~ql~ 72 (82)
T cd04491 6 VLSISEPREFT--RDGSEGKVQSGLVGDETGTIRFTLWDEKA--ADDLEPGDVVRIENAYVREFNGRLELS 72 (82)
T ss_pred EEEccCCeEec--cCCCeeEEEEEEEECCCCEEEEEEECchh--cccCCCCCEEEEEeEEEEecCCcEEEE
Confidence 44555544322 23345689999999998777776665433 2347899988888 4455556666554
No 49
>KOG2945 consensus Predicted RNA-binding protein [General function prediction only]
Probab=22.91 E-value=66 Score=34.08 Aligned_cols=11 Identities=18% Similarity=0.247 Sum_probs=6.3
Q ss_pred HHHHHHHhcCC
Q 014129 302 SQKLLQKMSTS 312 (430)
Q Consensus 302 aqkllq~~~~~ 312 (430)
=+++|..|.+-
T Consensus 255 ~~~tlde~k~l 265 (365)
T KOG2945|consen 255 KEMTLDEMKAL 265 (365)
T ss_pred hhhhhhHHHHH
Confidence 35666666543
No 50
>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]
Probab=22.40 E-value=45 Score=36.51 Aligned_cols=10 Identities=30% Similarity=0.285 Sum_probs=4.5
Q ss_pred Eeeeeecccc
Q 014129 86 VASVRDISRS 95 (430)
Q Consensus 86 I~~I~DIs~s 95 (430)
|+++.|...+
T Consensus 65 v~K~fda~~e 74 (526)
T KOG2135|consen 65 VDKLFDALRE 74 (526)
T ss_pred HHHHHHhhcc
Confidence 3444444443
No 51
>COG1799 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.96 E-value=50 Score=31.37 Aligned_cols=40 Identities=33% Similarity=0.512 Sum_probs=30.9
Q ss_pred CCCCCceEEEeCCc-eEeeeEEEEeCCcEEEec--ccchhHHH
Q 014129 135 DVVPGTKVRLENKV-PVHSGIVCLNPNVVTVLG--GVVASLHE 174 (430)
Q Consensus 135 ~tpPGtKIlLkg~v-~vrrGvLLL~p~Nv~VLG--G~Ve~L~e 174 (430)
+..-|+--.|.|.+ .|-..|+||+|+||.|.| |...++.+
T Consensus 117 DFlaG~~~al~G~~qkVg~~ifL~tP~nv~Vs~~~~~~~e~~~ 159 (167)
T COG1799 117 DFLAGAVFALRGSIQKVGSKIFLLTPSNVDVSGEGGRIPELDQ 159 (167)
T ss_pred HHhcchhhhhcccHHhhcceeEEecccceeeecccccCchhhh
Confidence 45667777777764 488999999999999985 56666655
No 52
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with
Probab=20.87 E-value=2.9e+02 Score=22.18 Aligned_cols=59 Identities=17% Similarity=0.254 Sum_probs=35.3
Q ss_pred ceEEEEEecCceEEEEeecccCCC-CC--CCCCCCceEEEeCCceEeeeE------EEEeCCcEEEec
Q 014129 108 RLLKLVLTDGHIEITAIEYSHIPS-IP--YDVVPGTKVRLENKVPVHSGI------VCLNPNVVTVLG 166 (430)
Q Consensus 108 RmLKL~LTDG~~~i~AiE~~pI~~-Ls--l~tpPGtKIlLkg~v~vrrGv------LLL~p~Nv~VLG 166 (430)
.+.-+.|.||...++++-...... +. ..+++|+=|.++|.+.-...- +=|..+++.+||
T Consensus 16 ~~~Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~Ei~~~~i~vl~ 83 (84)
T cd04323 16 KLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEVKEDPRAKQAPGGYELQVDYLEIIG 83 (84)
T ss_pred CcEEEEEEcCCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEEEEECCcccCCCCCEEEEEEEEEEEc
Confidence 467789999997787765432111 11 248899999998844332221 344445555554
Done!