Query psy8637
Match_columns 216
No_of_seqs 131 out of 362
Neff 5.8
Searched_HMMs 46136
Date Fri Aug 16 23:56:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8637.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8637hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2732|consensus 100.0 2.7E-56 5.9E-61 407.7 17.4 196 11-210 6-206 (435)
2 PRK04036 DNA polymerase II sma 99.9 2.4E-24 5.3E-29 205.2 12.3 145 31-210 116-274 (504)
3 KOG3911|consensus 99.3 5.4E-13 1.2E-17 120.7 2.1 29 187-215 42-70 (378)
4 PF05997 Nop52: Nucleolar prot 99.2 2.8E-12 6E-17 110.7 1.3 26 190-215 36-61 (217)
5 COG1311 HYS2 Archaeal DNA poly 99.1 2E-11 4.3E-16 115.4 2.0 141 27-168 42-193 (481)
6 KOG3818|consensus 95.8 0.074 1.6E-06 50.9 9.9 128 11-171 96-245 (525)
7 cd04490 PolII_SU_OBF PolII_SU_ 91.9 0.45 9.6E-06 34.8 5.2 49 118-166 20-77 (79)
8 KOG1625|consensus 90.0 4 8.6E-05 40.4 11.1 72 73-164 243-320 (600)
9 COG5214 POL12 DNA polymerase a 86.7 0.95 2.1E-05 43.4 4.4 71 72-164 200-278 (581)
10 COG1311 HYS2 Archaeal DNA poly 77.1 14 0.00029 36.0 8.4 128 31-191 101-236 (481)
11 cd04491 SoSSB_OBF SoSSB_OBF: A 68.7 13 0.00027 26.6 4.8 35 118-152 26-63 (82)
12 PRK12366 replication factor A; 62.6 26 0.00056 35.1 7.1 80 65-160 177-260 (637)
13 cd04492 YhaM_OBF_like YhaM_OBF 60.6 22 0.00048 24.5 4.7 46 118-163 22-74 (83)
14 PF03100 CcmE: CcmE; InterPro 58.7 26 0.00057 27.8 5.3 47 118-164 74-121 (131)
15 cd04485 DnaE_OBF DnaE_OBF: A s 56.4 12 0.00027 25.4 2.8 38 117-154 21-63 (84)
16 cd04488 RecG_wedge_OBF RecG_we 55.9 19 0.00042 24.0 3.6 42 118-159 21-67 (75)
17 PF01336 tRNA_anti-codon: OB-f 54.1 12 0.00027 25.3 2.4 35 118-152 19-58 (75)
18 PRK06461 single-stranded DNA-b 53.7 34 0.00073 27.0 5.1 42 118-159 43-87 (129)
19 PRK13254 cytochrome c-type bio 53.1 42 0.0009 27.6 5.7 47 118-164 74-121 (148)
20 PRK06386 replication factor A; 53.1 28 0.00061 32.6 5.3 14 118-131 145-158 (358)
21 cd04320 AspRS_cyto_N AspRS_cyt 51.3 41 0.0009 24.9 5.1 36 118-153 20-66 (102)
22 cd04489 ExoVII_LU_OBF ExoVII_L 51.2 38 0.00082 23.4 4.6 46 118-163 20-75 (78)
23 PRK08402 replication factor A; 49.9 27 0.00059 32.6 4.6 77 62-160 61-152 (355)
24 cd04321 ScAspRS_mt_like_N ScAs 48.5 35 0.00075 24.7 4.2 43 118-160 20-77 (86)
25 PF08476 VD10_N: Viral D10 N-t 46.1 17 0.00038 24.2 2.0 17 117-133 21-37 (45)
26 cd04478 RPA2_DBD_D RPA2_DBD_D: 45.9 64 0.0014 23.3 5.3 44 117-160 18-70 (95)
27 PRK07217 replication factor A; 41.8 45 0.00098 30.7 4.7 76 62-159 71-150 (311)
28 PRK07211 replication factor A; 40.4 31 0.00068 33.7 3.6 38 118-155 308-347 (485)
29 cd04317 EcAspRS_like_N EcAspRS 36.3 1.5E+02 0.0032 23.1 6.3 35 118-152 34-75 (135)
30 PRK13150 cytochrome c-type bio 36.0 1.2E+02 0.0027 25.2 6.0 47 118-164 81-128 (159)
31 KOG1942|consensus 34.8 30 0.00065 32.5 2.3 38 85-133 169-206 (456)
32 PRK12366 replication factor A; 32.7 51 0.0011 33.1 3.8 35 118-152 438-474 (637)
33 cd04323 AsnRS_cyto_like_N AsnR 32.6 1.1E+02 0.0024 21.8 4.7 37 117-153 18-61 (84)
34 cd04475 RPA1_DBD_B RPA1_DBD_B: 31.3 65 0.0014 23.7 3.4 34 118-152 30-68 (101)
35 KOG1536|consensus 30.8 1.3E+02 0.0027 30.3 6.0 80 54-133 484-607 (649)
36 cd03524 RPA2_OBF_family RPA2_O 30.5 93 0.002 19.9 3.7 37 117-153 19-61 (75)
37 PRK14699 replication factor A; 28.9 86 0.0019 30.5 4.6 51 63-131 386-438 (484)
38 COG4898 Uncharacterized protei 28.9 28 0.00061 27.0 1.0 18 137-154 70-87 (115)
39 PRK15491 replication factor A; 28.1 77 0.0017 29.7 4.0 14 118-131 315-328 (374)
40 PF06138 Chordopox_E11: Chordo 27.2 44 0.00095 27.0 1.8 16 118-133 5-20 (130)
41 PRK13165 cytochrome c-type bio 26.9 2.2E+02 0.0047 23.8 6.0 47 118-164 81-128 (160)
42 cd04100 Asp_Lys_Asn_RS_N Asp_L 26.9 1.5E+02 0.0032 21.0 4.6 35 118-152 19-61 (85)
43 PF11325 DUF3127: Domain of un 26.3 1.5E+02 0.0032 22.1 4.4 24 140-164 2-28 (84)
44 PF07725 LRR_3: Leucine Rich R 26.1 18 0.0004 20.0 -0.3 13 189-201 7-19 (20)
45 PF04076 BOF: Bacterial OB fol 25.1 1.3E+02 0.0029 23.1 4.2 57 72-155 32-91 (103)
46 cd04483 hOBFC1_like hOBFC1_lik 25.1 1.9E+02 0.004 21.5 4.9 40 118-157 17-82 (92)
47 cd04318 EcAsnRS_like_N EcAsnRS 24.4 2.4E+02 0.0052 19.7 5.2 43 118-160 19-73 (82)
48 COG1905 NuoE NADH:ubiquinone o 24.1 1.2E+02 0.0026 25.4 3.9 54 138-197 81-152 (160)
49 TIGR00617 rpa1 replication fac 24.0 80 0.0017 31.5 3.4 35 118-152 341-379 (608)
50 PF09933 DUF2165: Predicted sm 23.6 44 0.00096 27.9 1.3 17 199-215 124-140 (160)
51 PF02197 RIIa: Regulatory subu 23.6 82 0.0018 19.8 2.3 18 29-46 20-37 (38)
52 PF06188 HrpE: HrpE/YscL/FliH 23.3 1.3E+02 0.0028 25.4 4.1 47 79-131 131-182 (191)
53 PRK07252 hypothetical protein; 23.2 3.6E+02 0.0079 21.0 6.9 59 134-200 48-109 (120)
54 PF09966 DUF2200: Uncharacteri 23.0 22 0.00048 28.0 -0.5 18 136-153 66-83 (111)
55 PRK03932 asnC asparaginyl-tRNA 22.7 3.1E+02 0.0067 26.2 7.0 48 118-165 36-98 (450)
56 cd04316 ND_PkAspRS_like_N ND_P 21.5 3.5E+02 0.0076 20.1 6.0 50 118-167 32-97 (108)
57 COG3097 Uncharacterized protei 20.4 2.5E+02 0.0055 21.7 4.7 70 125-202 18-89 (106)
58 PHA03001 putative virion core 20.2 1E+02 0.0022 25.0 2.7 17 118-134 5-21 (132)
59 PRK07218 replication factor A; 20.2 1.9E+02 0.0041 27.8 4.9 42 118-159 200-243 (423)
No 1
>KOG2732|consensus
Probab=100.00 E-value=2.7e-56 Score=407.67 Aligned_cols=196 Identities=38% Similarity=0.629 Sum_probs=178.0
Q ss_pred ccceecccCCCceeeCCcchhhhhHHHHHHHHHHHHHHHHHHHHhhcCCCcceeeeeecccCCCC-eEEEEEEEEeeCCC
Q psy8637 11 RPTADYKNLSQCFRLASKDYSKQFAHIYAVRLNKMRECLLARVSQKWGKSVSVLKLSDLNETDTE-ECVIIGTLFKHQQL 89 (216)
Q Consensus 11 R~~~~y~~~s~rF~l~~~~y~~QY~~iY~~RL~~Lr~~l~~~a~~kw~~~~~i~kll~l~~~~g~-~cvvIGTlyK~mkl 89 (216)
+....|+|.|++|+|..++|++||+|||++||++|||++.++|++|||++.+++++|++ +.++ +||||||+||+|++
T Consensus 6 ~~~~~~~n~s~~f~L~~~~y~~Qy~~iY~aRL~elRp~i~~~A~k~wg~~~~l~~~l~l--~~~~~~C~vVGTlfk~~~l 83 (435)
T KOG2732|consen 6 SLILNYENKSDRFRLSEKDYSRQYFHIYFARLKELRPRILELAQKKWGSGPPLKKQLDL--EKGKGECWVVGTLFKAMAL 83 (435)
T ss_pred eccccccccccceeeccchhHHHHHHHHHHHHHHhHHHHHHHHHhhcCCCCchhhheee--ccCCccEEEEEehhhhccc
Confidence 34457899999999999999999999999999999999999999999999999999999 4666 99999999999999
Q ss_pred CCchHHHHHhhhcCCCCCCCCCcCCCCCeEEEecCCCcEEEEec-cCCCCceeeeEEEEEeccCCCCcEEEEEEEe-cCC
Q psy8637 90 KPNILKEISEELKLVPQPQHTHFVSDSDELILEDELQRIPLHGN-IDIHNQVTGVVVAIKGTPVGNGKFKVSDVCY-ATP 167 (216)
Q Consensus 90 KPsIL~e~~~e~~~~~~~~~~~y~s~~D~l~LEDesgRI~L~G~-i~~~~lVTGvVvaV~G~~~~~G~F~V~di~~-~~~ 167 (216)
|||||||+++|+.++|++++++|.+++|+++||||+|||+|.|. ++...+||||||||+|++.++|.|.|+|+|| +.+
T Consensus 84 KPsIl~~v~~e~~~~p~~~~~~y~~ped~i~LEDe~grV~L~G~~i~~~~~vTGvvvavlG~~~e~G~F~VeDv~fp~~~ 163 (435)
T KOG2732|consen 84 KPSILDEVSNEHKVAPDPEESNYHSPEDEIVLEDESGRVRLEGSFISHAVLVTGVVVAVLGKEAEAGRFLVEDVLFPGSS 163 (435)
T ss_pred CcHHHHHHhhhhccCCCCcccccCCccceEEEecCCceEEEEeecccccceeeeEEEEEecccccCceEEEEEEeccCCC
Confidence 99999999999999999999999999999999999999999996 9999999999999999999999999999999 999
Q ss_pred CC-CCcccCCCCCCcceeecCCCCHH-HHHHHhhHHHhhhhhcCC
Q psy8637 168 VF-KPRTTLSNNENKYVNHVDAFTDD-DFIRLWEGLFFSMWMSDK 210 (216)
Q Consensus 168 pq-~p~~~~~~~~~~yv~lvsgl~~~-d~~~l~kgl~~~~w~~d~ 210 (216)
|| .|++...++ +||||||||++. +-+.+-.-.++.+||.+.
T Consensus 164 pq~~P~~~~~~~--~~i~lVSGL~l~~~~~~~~~l~~l~D~l~g~ 206 (435)
T KOG2732|consen 164 PQGKPRATLPSQ--RKIALVSGLDLGGGSKNLLRLELLVDWLRGQ 206 (435)
T ss_pred ccCCCCCcCCCC--CEEEEEeccccCCCcchhHHHHHHHHHHhcc
Confidence 99 777766655 899999999962 123333447888998653
No 2
>PRK04036 DNA polymerase II small subunit; Validated
Probab=99.91 E-value=2.4e-24 Score=205.23 Aligned_cols=145 Identities=19% Similarity=0.281 Sum_probs=114.8
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHhhcCCCcceeeeeecccC-CCCeEEEEEEEEeeCCCCCchHHHHHhhhcCCCCCCC
Q psy8637 31 SKQFAHIYAVRLNKMRECLLARVSQKWGKSVSVLKLSDLNET-DTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQH 109 (216)
Q Consensus 31 ~~QY~~iY~~RL~~Lr~~l~~~a~~kw~~~~~i~kll~l~~~-~g~~cvvIGTlyK~mklKPsIL~e~~~e~~~~~~~~~ 109 (216)
-+||+++|++||+.||+++..+++.+ ++.+|+++ + .+++|+|||||+ ++ +
T Consensus 116 ~~~~~~~y~~R~~~L~~~l~~~~~~~-----~i~~l~~~--~~~~~~~~viG~v~-~~----------~----------- 166 (504)
T PRK04036 116 VEDFVAYFRDRYEKLSKIIRGRVNHR-----PIESLKKL--KRGGEEVSIIGMVS-DI----------R----------- 166 (504)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcccc-----cHHHHhcC--ccCCceEEEEEEEE-Ee----------e-----------
Confidence 48999999999999999999999875 46789999 4 688999999997 22 1
Q ss_pred CCcCCCCC-eEEEecCCCcEEEEecc------C-CCCceeeeEEEEEeccCCCC-cEEEEEEEe-cCCCCCCcccCCCCC
Q psy8637 110 THFVSDSD-ELILEDELQRIPLHGNI------D-IHNQVTGVVVAIKGTPVGNG-KFKVSDVCY-ATPVFKPRTTLSNNE 179 (216)
Q Consensus 110 ~~y~s~~D-~l~LEDesgRI~L~G~i------~-~~~lVTGvVvaV~G~~~~~G-~F~V~di~~-~~~pq~p~~~~~~~~ 179 (216)
.+++++ .++|||+||||+|.|.. + .+.+|||+||||+|++.++| .|.|+|+|| +.||+.+++....+
T Consensus 167 --~~~~g~~~~~LED~sgrv~l~~~~~~~~~~~~~~~lvtg~vv~v~G~~~~~g~~f~v~~i~~p~~p~~~~~~~~~~~- 243 (504)
T PRK04036 167 --STKNGHKIVELEDTTGTFPVLIMKDREDLAELADELLLDEVIGVEGTLSGDGGLIFADEIIRPDVPRTKEPPTKDEK- 243 (504)
T ss_pred --cccCCceEEEEECCCCeEEEEeecchhhhhhhhhcccCceEEEEEEEEcCCCCEEEEEEEECCCCCccCCCCcCCCc-
Confidence 113344 78999999999999832 2 35799999999999999999 899999999 99988666544444
Q ss_pred CcceeecCCCCHHHH---HHHhhHHHhhhhhcCC
Q psy8637 180 NKYVNHVDAFTDDDF---IRLWEGLFFSMWMSDK 210 (216)
Q Consensus 180 ~~yv~lvsgl~~~d~---~~l~kgl~~~~w~~d~ 210 (216)
.++||+||+.+..- .+.| .-+..|+++.
T Consensus 244 -~~i~~ISDlHlgs~~~~~~~l--~~li~~L~g~ 274 (504)
T PRK04036 244 -VYAVFISDVHVGSKEFLEDAF--EKFIDWLNGE 274 (504)
T ss_pred -cEEEEEcccCCCCcchhHHHH--HHHHHHHhCC
Confidence 89999999986542 2333 3456788743
No 3
>KOG3911|consensus
Probab=99.31 E-value=5.4e-13 Score=120.74 Aligned_cols=29 Identities=59% Similarity=1.428 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHhhHHHhhhhhcCCCcccC
Q psy8637 187 DAFTDDDFIRLWEGLFFSMWMSDKPLIQK 215 (216)
Q Consensus 187 sgl~~~d~~~l~kgl~~~~w~~d~~~~q~ 215 (216)
+|++.+|++||||||||||||||||++||
T Consensus 42 ~~F~~~dflklWKGLfY~MWmqDkPllQe 70 (378)
T KOG3911|consen 42 EGFDQDDFLKLWKGLFYCMWMQDKPLLQE 70 (378)
T ss_pred cCCCHHHHHHHHHhhHHHHhhcCCchHHH
Confidence 57999999999999999999999999997
No 4
>PF05997 Nop52: Nucleolar protein,Nop52; InterPro: IPR010301 Nop52 is believed to be involved in the generation of 28S rRNA [].; GO: 0006364 rRNA processing, 0030688 preribosome, small subunit precursor
Probab=99.22 E-value=2.8e-12 Score=110.74 Aligned_cols=26 Identities=62% Similarity=1.366 Sum_probs=25.4
Q ss_pred CHHHHHHHhhHHHhhhhhcCCCcccC
Q psy8637 190 TDDDFIRLWEGLFFSMWMSDKPLIQK 215 (216)
Q Consensus 190 ~~~d~~~l~kgl~~~~w~~d~~~~q~ 215 (216)
+..|++||||||||||||||||++||
T Consensus 36 ~~~~~~kLWKGLfy~mWmsDkpl~Q~ 61 (217)
T PF05997_consen 36 TELDMLKLWKGLFYCMWMSDKPLVQE 61 (217)
T ss_pred CHHHHHHHHHHHHHHHHhcCCchhHH
Confidence 89999999999999999999999997
No 5
>COG1311 HYS2 Archaeal DNA polymerase II, small subunit/DNA polymerase delta, subunit B [DNA replication, recombination, and repair]
Probab=99.12 E-value=2e-11 Score=115.36 Aligned_cols=141 Identities=23% Similarity=0.316 Sum_probs=111.7
Q ss_pred CcchhhhhHHHHHHHH-HHHHHHHHHHHHhhcCCCcceeeeeecc---c-CCCCeEE-EEEEEEeeCCCCCchHHHHHhh
Q psy8637 27 SKDYSKQFAHIYAVRL-NKMRECLLARVSQKWGKSVSVLKLSDLN---E-TDTEECV-IIGTLFKHQQLKPNILKEISEE 100 (216)
Q Consensus 27 ~~~y~~QY~~iY~~RL-~~Lr~~l~~~a~~kw~~~~~i~kll~l~---~-~~g~~cv-vIGTlyK~mklKPsIL~e~~~e 100 (216)
.+.|..||+++|++|+ +.+|++...++.++|+......+.++++ + +....|+ +++-+.+.++-|++-|+++-++
T Consensus 42 ~~~y~~qy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ve~~~d~~~~s~~~g~vedf~~~f~~R~~kL~~ii~~ 121 (481)
T COG1311 42 KVDYIIQYASIYFARLLKALRPRIIKESVKRWPDKPVLERDLDVEYLPDVRGNSTCGGIVEDFVPYFRDRYEKLSRIIRE 121 (481)
T ss_pred HhccccccchHHHhhhhhhhccccchhhhhcccCccccccceeEEEccCcccccccceeHHHHHHHHHHHHHHHHHHHhc
Confidence 6899999999999999 9999999999999998754444444441 1 3455565 5777888889999999998776
Q ss_pred hcCCCC-CCCC-CcCCCCC-eEEEecCCCcEEEEec-cCCCCceeeeEEEEEeccCCCCcEEEEEEEe-cCCC
Q psy8637 101 LKLVPQ-PQHT-HFVSDSD-ELILEDELQRIPLHGN-IDIHNQVTGVVVAIKGTPVGNGKFKVSDVCY-ATPV 168 (216)
Q Consensus 101 ~~~~~~-~~~~-~y~s~~D-~l~LEDesgRI~L~G~-i~~~~lVTGvVvaV~G~~~~~G~F~V~di~~-~~~p 168 (216)
....+. .+.. .+-..+| ++++|+.++|....|. +-.-.-+||+|.+|+|...+.|+|.+ |+|+ ..-+
T Consensus 122 ~~~~~~~~~~~~~~~~g~dv~Iig~v~~~r~t~~gh~ii~~ed~tG~v~vvl~k~~e~~~~~~-dvl~d~vig 193 (481)
T COG1311 122 REEARYVSPIKKDLEGGSDVKIIGEVNDVRETKNGHFIISLEDTTGVVTVVLGKDREAGRFVV-DVLFDEVIG 193 (481)
T ss_pred cccCCCcchhhcccccCCCcEEEEEEccceeeecccEEEEcccccceEEEEeccchhhhhhHH-hhcCCcccc
Confidence 543322 1222 5566677 9999999999999997 66677999999999999999999999 9999 6544
No 6
>KOG3818|consensus
Probab=95.81 E-value=0.074 Score=50.89 Aligned_cols=128 Identities=19% Similarity=0.232 Sum_probs=83.6
Q ss_pred ccceecccCCCceeeCCc------chhhhhHHHHHHHHHHHHHHHHHH-------------HHhhcCCCcceeeeeeccc
Q psy8637 11 RPTADYKNLSQCFRLASK------DYSKQFAHIYAVRLNKMRECLLAR-------------VSQKWGKSVSVLKLSDLNE 71 (216)
Q Consensus 11 R~~~~y~~~s~rF~l~~~------~y~~QY~~iY~~RL~~Lr~~l~~~-------------a~~kw~~~~~i~kll~l~~ 71 (216)
=+...|...-.+|.++++ .-.+-.+++...|+..+..|+... |+.+-=.-.||..|+.-
T Consensus 96 ~prF~Yn~~~kkFvl~~k~~~~l~~~~~~ks~m~~~Ry~i~~qR~mR~e~Fq~pv~~s~~~~q~~~fklt~ienLL~t-- 173 (525)
T KOG3818|consen 96 LPRFDYNSDRKKFVLPNKPKPSLLADPSDKSDMFRQRYFIVKQRTMRNELFQPPVSGSGRCAQLKKFKLTPIENLLST-- 173 (525)
T ss_pred CCccccCchheEEEecCCCCccccCChHHHHHHHHHHHHHHHHHHHhhhccCCCccCCchhhhccccceeEHHHhhcc--
Confidence 345567776778988431 234677888888998888877662 11100000244445442
Q ss_pred CCCCeEEEEEEEEeeCCCCCchHHHHHhhhcCCCCCCCCCcCCCCCeEEEecCCCcEEEEec---cCCCCceeeeEEEEE
Q psy8637 72 TDTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHTHFVSDSDELILEDELQRIPLHGN---IDIHNQVTGVVVAIK 148 (216)
Q Consensus 72 ~~g~~cvvIGTlyK~mklKPsIL~e~~~e~~~~~~~~~~~y~s~~D~l~LEDesgRI~L~G~---i~~~~lVTGvVvaV~ 148 (216)
+..+..+|.|-|-+ -.++..+|||-||-|.|.-. .-...++.||.|-|-
T Consensus 174 ~~~~~~lvLGlLTq----------------------------~k~G~~~lEDpsgsVqlDlsqa~fh~glf~egC~VL~E 225 (525)
T KOG3818|consen 174 RALQSFLVLGLLTQ----------------------------LKEGKFHLEDPSGSVQLDLSQAKFHHGLFCEGCFVLVE 225 (525)
T ss_pred ccccceeeeehhhh----------------------------ccCCcEEEeCCCCcEEEeecccccccceeccceEEEEe
Confidence 34555666664321 12788999999999999643 445679999999999
Q ss_pred eccCCCCcEEEEEEEecCCCCCC
Q psy8637 149 GTPVGNGKFKVSDVCYATPVFKP 171 (216)
Q Consensus 149 G~~~~~G~F~V~di~~~~~pq~p 171 (216)
|.-.+ |.|+|..+- .||..+
T Consensus 226 G~f~~-~vf~V~~lg--~PP~E~ 245 (525)
T KOG3818|consen 226 GTFES-GVFHVNELG--FPPVER 245 (525)
T ss_pred eeeec-ceEEEeecc--CCCCCc
Confidence 98655 999999874 455443
No 7
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=91.85 E-value=0.45 Score=34.76 Aligned_cols=49 Identities=18% Similarity=0.235 Sum_probs=38.4
Q ss_pred eEEEecCCCcEEEEe--c-cC----CCCceeeeEEEEEeccCC-CCcEEEEEEEe-cC
Q psy8637 118 ELILEDELQRIPLHG--N-ID----IHNQVTGVVVAIKGTPVG-NGKFKVSDVCY-AT 166 (216)
Q Consensus 118 ~l~LEDesgRI~L~G--~-i~----~~~lVTGvVvaV~G~~~~-~G~F~V~di~~-~~ 166 (216)
.+-|||.+|++.+.- + .. .+.+..|.++.|.|.... ++.+.|+++++ +.
T Consensus 20 ~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~v~~~~~~l~~~~I~~~~~ 77 (79)
T cd04490 20 IVELEDTTGRITVLLTKDKEELFEEAEDILPDEVIGVSGTVSKDGGLIFADEIFRPDV 77 (79)
T ss_pred EEEEECCCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEEEecCCCEEEEEEeEcCCC
Confidence 889999999999973 2 33 356889999999999853 23688999987 54
No 8
>KOG1625|consensus
Probab=90.04 E-value=4 Score=40.36 Aligned_cols=72 Identities=18% Similarity=0.304 Sum_probs=49.7
Q ss_pred CCCeEEEEEEEEeeCCCCCchHHHHHhhhcCCCCCCCCCcCCCCCeEEEe----cCC-CcEEEEec-cCCCCceeeeEEE
Q psy8637 73 DTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHTHFVSDSDELILE----DEL-QRIPLHGN-IDIHNQVTGVVVA 146 (216)
Q Consensus 73 ~g~~cvvIGTlyK~mklKPsIL~e~~~e~~~~~~~~~~~y~s~~D~l~LE----Des-gRI~L~G~-i~~~~lVTGvVva 146 (216)
..+..+.+|-|-.+...- ..++ ++-.++|| |++ .||+|.-+ ++.-.+-.|=|||
T Consensus 243 Sq~~v~avG~I~~d~~~~------------------~~kl--n~~Sv~Less~e~~~g~~Vrldls~l~e~SiFPGQIVa 302 (600)
T KOG1625|consen 243 SQSSVYAVGQIVCDSTKD------------------NGKL--NEESVLLESSREDSSGVRVRLDLSRLKEYSIFPGQIVA 302 (600)
T ss_pred cccceEEEEEEecCCCCc------------------cccc--CccceEeeeccccCCCceEEeehhhccceeecCCcEEE
Confidence 567788999998774110 0011 12234554 443 37888877 8778899999999
Q ss_pred EEeccCCCCcEEEEEEEe
Q psy8637 147 IKGTPVGNGKFKVSDVCY 164 (216)
Q Consensus 147 V~G~~~~~G~F~V~di~~ 164 (216)
|+|.-...+.|.|+.|.-
T Consensus 303 vkG~N~~G~~l~v~ki~~ 320 (600)
T KOG1625|consen 303 VKGKNPTGEKLTVEKILP 320 (600)
T ss_pred EeeecCCCCeEEeeeecc
Confidence 999866677799998875
No 9
>COG5214 POL12 DNA polymerase alpha-primase complex, polymerase-associated subunit B [DNA replication, recombination, and repair]
Probab=86.65 E-value=0.95 Score=43.37 Aligned_cols=71 Identities=24% Similarity=0.385 Sum_probs=52.8
Q ss_pred CCCCeEEEEEEEEeeCCCCCchHHHHHhhhcCCCCCCCCCcCC--CCCeEEEecC-----CCcEEEEec-cCCCCceeee
Q psy8637 72 TDTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHTHFVS--DSDELILEDE-----LQRIPLHGN-IDIHNQVTGV 143 (216)
Q Consensus 72 ~~g~~cvvIGTlyK~mklKPsIL~e~~~e~~~~~~~~~~~y~s--~~D~l~LEDe-----sgRI~L~G~-i~~~~lVTGv 143 (216)
...+..+++|.+.-+. .+|-. +...++||-. .-||+|.-+ ++.-.+..|-
T Consensus 200 ~sqs~~y~vGrIv~~s----------------------~~~g~~Ln~eSv~lesSr~gg~gvrVRL~l~~l~~yS~FpGQ 257 (581)
T COG5214 200 VSQSSFYTVGRIVNPS----------------------TNFGHKLNSESVFLESSRDGGNGVRVRLNLAHLQRYSVFPGQ 257 (581)
T ss_pred cccCceEEEEEecCCC----------------------cccccccCcceeeeeeecccCCCeEEEeehhhcccccccccc
Confidence 4667788999875431 12222 2356788865 238888876 8878889999
Q ss_pred EEEEEeccCCCCcEEEEEEEe
Q psy8637 144 VVAIKGTPVGNGKFKVSDVCY 164 (216)
Q Consensus 144 VvaV~G~~~~~G~F~V~di~~ 164 (216)
||||+|.-.+.|.|.|+.|.-
T Consensus 258 IVavKGkN~~G~~ftv~~ilp 278 (581)
T COG5214 258 IVAVKGKNTDGGKFTVEAILP 278 (581)
T ss_pred EEEEecccCCCCeEEeeeeec
Confidence 999999988889999999985
No 10
>COG1311 HYS2 Archaeal DNA polymerase II, small subunit/DNA polymerase delta, subunit B [DNA replication, recombination, and repair]
Probab=77.08 E-value=14 Score=36.04 Aligned_cols=128 Identities=16% Similarity=0.273 Sum_probs=83.7
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHhhcCCCcceeeeeecccCCCCeEEEEEEEEeeCCCCCchHHHHHhhhcCCCCCCCC
Q psy8637 31 SKQFAHIYAVRLNKMRECLLARVSQKWGKSVSVLKLSDLNETDTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHT 110 (216)
Q Consensus 31 ~~QY~~iY~~RL~~Lr~~l~~~a~~kw~~~~~i~kll~l~~~~g~~cvvIGTlyK~mklKPsIL~e~~~e~~~~~~~~~~ 110 (216)
-.+|....+.|+.+|++.+.++...+|- .++.+ ++ +.|...-|||-+= ++... .+.
T Consensus 101 vedf~~~f~~R~~kL~~ii~~~~~~~~~--~~~~~--~~--~~g~dv~Iig~v~-----------~~r~t-------~~g 156 (481)
T COG1311 101 VEDFVPYFRDRYEKLSRIIREREEARYV--SPIKK--DL--EGGSDVKIIGEVN-----------DVRET-------KNG 156 (481)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccCCCc--chhhc--cc--ccCCCcEEEEEEc-----------cceee-------ecc
Confidence 5789999999999999999999888774 34444 55 3455566777541 11100 011
Q ss_pred CcCCCCCeEEEecCCCcEEEE-------eccCCCCceeeeEEEEEeccCCCCcEEEEEEEe-cCCCCCCcccCCCCCCcc
Q psy8637 111 HFVSDSDELILEDELQRIPLH-------GNIDIHNQVTGVVVAIKGTPVGNGKFKVSDVCY-ATPVFKPRTTLSNNENKY 182 (216)
Q Consensus 111 ~y~s~~D~l~LEDesgRI~L~-------G~i~~~~lVTGvVvaV~G~~~~~G~F~V~di~~-~~~pq~p~~~~~~~~~~y 182 (216)
.=.+-+||.+|.|... |..-. .++-..|+|+.|.....|. ....+.+ +.|- .-+... .+++-|
T Consensus 157 -----h~ii~~ed~tG~v~vvl~k~~e~~~~~~-dvl~d~vig~~g~~t~~~~-~a~~~~~p~Vpg-~~~~~~-~~e~v~ 227 (481)
T COG1311 157 -----HFIISLEDTTGVVTVVLGKDREAGRFVV-DVLFDEVIGVSGPVTPRSS-FADRIYLPDVPG-LSLNNT-GDERVY 227 (481)
T ss_pred -----cEEEEcccccceEEEEeccchhhhhhHH-hhcCCccccccCccCCccc-cCCcceeccCcc-ccCCCC-CCcceE
Confidence 1247799999999875 22112 5678999999999999998 5566665 5442 111111 122358
Q ss_pred eeecCCCCH
Q psy8637 183 VNHVDAFTD 191 (216)
Q Consensus 183 v~lvsgl~~ 191 (216)
++|+|..-.
T Consensus 228 v~~isDih~ 236 (481)
T COG1311 228 VALISDIHR 236 (481)
T ss_pred EEEEeeeec
Confidence 999987665
No 11
>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=68.72 E-value=13 Score=26.55 Aligned_cols=35 Identities=20% Similarity=0.165 Sum_probs=26.5
Q ss_pred eEEEecCCCcEEEE--eccCCCCceeeeEEEEE-eccC
Q psy8637 118 ELILEDELQRIPLH--GNIDIHNQVTGVVVAIK-GTPV 152 (216)
Q Consensus 118 ~l~LEDesgRI~L~--G~i~~~~lVTGvVvaV~-G~~~ 152 (216)
.+.|.|+||+|++. ++-....+-.|-|+.+. |...
T Consensus 26 ~~~l~D~TG~i~~~~W~~~~~~~~~~G~vv~i~~~~v~ 63 (82)
T cd04491 26 SGLVGDETGTIRFTLWDEKAADDLEPGDVVRIENAYVR 63 (82)
T ss_pred EEEEECCCCEEEEEEECchhcccCCCCCEEEEEeEEEE
Confidence 68999999999997 33114567789899999 5543
No 12
>PRK12366 replication factor A; Reviewed
Probab=62.60 E-value=26 Score=35.10 Aligned_cols=80 Identities=18% Similarity=0.245 Sum_probs=47.3
Q ss_pred eeeecccCCCCeEEEEEEEEeeCCCCCchHHHHHhhhcCCCCCCCCCcCCCCCeEEEecCCCcEEEE--eccCCCCceee
Q psy8637 65 KLSDLNETDTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHTHFVSDSDELILEDELQRIPLH--GNIDIHNQVTG 142 (216)
Q Consensus 65 kll~l~~~~g~~cvvIGTlyK~mklKPsIL~e~~~e~~~~~~~~~~~y~s~~D~l~LEDesgRI~L~--G~i~~~~lVTG 142 (216)
+|-+| .+|..+-|+|+|..-.+.+. +.+..+ . ...-=.+.|-|+||+|+++ |+.-...+-.|
T Consensus 177 ~I~el--~~g~~v~v~G~V~~~~~~~~-----f~rkdg---~------~~~~r~~~l~D~TG~irvTlW~~~a~~~~~~g 240 (637)
T PRK12366 177 DIPEL--EPNLSATIEGEVTKAYPIKE-----FTRKDG---S------EGKLKSFILKDDTGSIRVTLWNDLTDIEVNKG 240 (637)
T ss_pred ccccc--CCCCeEEEEEEEEEccCcEE-----EEEcCC---C------eeEEEEEEEEcCCCcEEEEEEChhhcccCCCC
Confidence 45556 46777778888876544431 111000 0 0011269999999999998 55222246789
Q ss_pred eEEEEEeccCC--CCcEEEE
Q psy8637 143 VVVAIKGTPVG--NGKFKVS 160 (216)
Q Consensus 143 vVvaV~G~~~~--~G~F~V~ 160 (216)
-|++|.|...+ +|.++++
T Consensus 241 ~vv~i~g~~~~~~~~~~el~ 260 (637)
T PRK12366 241 DIVRVKGYVKQGYRTGLEIS 260 (637)
T ss_pred CEEEEEeEEecCcCCceEEE
Confidence 99999996433 2445544
No 13
>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=60.60 E-value=22 Score=24.48 Aligned_cols=46 Identities=24% Similarity=0.311 Sum_probs=33.1
Q ss_pred eEEEecCCCcEEEEe--c--cCCCCceeeeEEEEEeccCC-CC--cEEEEEEE
Q psy8637 118 ELILEDELQRIPLHG--N--IDIHNQVTGVVVAIKGTPVG-NG--KFKVSDVC 163 (216)
Q Consensus 118 ~l~LEDesgRI~L~G--~--i~~~~lVTGvVvaV~G~~~~-~G--~F~V~di~ 163 (216)
.+.|||.+|+|.+.- + -....+-.|.++-|.|.... +| .+.+.++.
T Consensus 22 ~~~l~D~tg~i~~~~f~~~~~~~~~l~~g~~v~v~G~v~~~~~~~~l~~~~i~ 74 (83)
T cd04492 22 ALTLQDKTGEIEAKLWDASEEDEEKFKPGDIVHVKGRVEEYRGRLQLKIQRIR 74 (83)
T ss_pred EEEEEcCCCeEEEEEcCCChhhHhhCCCCCEEEEEEEEEEeCCceeEEEEEEE
Confidence 689999999999873 1 11356788999999998864 44 35555655
No 14
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=58.74 E-value=26 Score=27.76 Aligned_cols=47 Identities=17% Similarity=0.173 Sum_probs=35.1
Q ss_pred eEEEecCCCcEEEEec-cCCCCceeeeEEEEEeccCCCCcEEEEEEEe
Q psy8637 118 ELILEDELQRIPLHGN-IDIHNQVTGVVVAIKGTPVGNGKFKVSDVCY 164 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~-i~~~~lVTGvVvaV~G~~~~~G~F~V~di~~ 164 (216)
.-.|.|...+|...=+ .-++.|--|.-|-|.|+..++|.|+.+++.-
T Consensus 74 ~F~i~D~~~~i~V~Y~G~~Pd~F~eg~~VVv~G~~~~~g~F~A~~lL~ 121 (131)
T PF03100_consen 74 TFTITDGGKEIPVVYTGPLPDLFREGQGVVVEGRLGEDGVFEATELLA 121 (131)
T ss_dssp EEEEE-SS-EEEEEEES--CTT--TTSEEEEEEEECCTSEEEEEEEEE
T ss_pred EEEEEECCcEEEEEECCCCCccccCCCeEEEEEEECCCCEEEEEEEEe
Confidence 5678999888887633 5578898899999999999999999999986
No 15
>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=56.41 E-value=12 Score=25.45 Aligned_cols=38 Identities=13% Similarity=-0.013 Sum_probs=28.9
Q ss_pred CeEEEecCCCcEEEEec---c--CCCCceeeeEEEEEeccCCC
Q psy8637 117 DELILEDELQRIPLHGN---I--DIHNQVTGVVVAIKGTPVGN 154 (216)
Q Consensus 117 D~l~LEDesgRI~L~G~---i--~~~~lVTGvVvaV~G~~~~~ 154 (216)
-.+-|+|.+|.+.+.-- . ....+..|.++.|.|.....
T Consensus 21 ~~~~l~D~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G~v~~~ 63 (84)
T cd04485 21 AFVTLEDLTGSIEVVVFPETYEKYRDLLKEDALLLVEGKVERR 63 (84)
T ss_pred EEEEEEeCCCeEEEEECHHHHHHHHHHhcCCCEEEEEEEEEec
Confidence 36789999999988631 1 24567889999999998753
No 16
>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=55.93 E-value=19 Score=24.02 Aligned_cols=42 Identities=17% Similarity=0.216 Sum_probs=30.9
Q ss_pred eEEEecCCCcEEEE--e-c-cCCCCceeeeEEEEEeccCCC-CcEEE
Q psy8637 118 ELILEDELQRIPLH--G-N-IDIHNQVTGVVVAIKGTPVGN-GKFKV 159 (216)
Q Consensus 118 ~l~LEDesgRI~L~--G-~-i~~~~lVTGvVvaV~G~~~~~-G~F~V 159 (216)
.+.+.|++|.|.+. + . -....+-.|..+.+.|..... |..++
T Consensus 21 ~~~~~D~~g~i~~~~F~~~~~~~~~~~~G~~~~v~Gkv~~~~~~~qi 67 (75)
T cd04488 21 KVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVSGKVKRFRGGLQI 67 (75)
T ss_pred EEEEEcCCCEEEEEEECCCHHHHhcCCCCCEEEEEEEEeecCCeeEE
Confidence 57899999999886 2 2 224568889999999998763 54444
No 17
>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=54.07 E-value=12 Score=25.30 Aligned_cols=35 Identities=20% Similarity=0.087 Sum_probs=27.0
Q ss_pred eEEEecCCCcEEEEec-----cCCCCceeeeEEEEEeccC
Q psy8637 118 ELILEDELQRIPLHGN-----IDIHNQVTGVVVAIKGTPV 152 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~-----i~~~~lVTGvVvaV~G~~~ 152 (216)
.+-|+|+||+|.+.-- -....+-.|-++.|.|...
T Consensus 19 ~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v~ 58 (75)
T PF01336_consen 19 FFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVRGKVK 58 (75)
T ss_dssp EEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEEEEEE
T ss_pred EEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEEEEEE
Confidence 5789999999999732 2345688999999999876
No 18
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=53.72 E-value=34 Score=27.04 Aligned_cols=42 Identities=26% Similarity=0.253 Sum_probs=28.5
Q ss_pred eEEEecCCCcEEEEec-cCCCCceeeeEEEEEe-ccCC-CCcEEE
Q psy8637 118 ELILEDELQRIPLHGN-IDIHNQVTGVVVAIKG-TPVG-NGKFKV 159 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~-i~~~~lVTGvVvaV~G-~~~~-~G~F~V 159 (216)
.+.|.|+||+|.++-= -....+-.|-||.|.| .+.. +|..++
T Consensus 43 ~~~l~D~TG~I~~tlW~~~a~~l~~GdvV~I~na~v~~f~G~lqL 87 (129)
T PRK06461 43 EAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTLYRGKVQL 87 (129)
T ss_pred EEEEECCCCEEEEEEeCCccccCCCCCEEEEECcEEeeeCCEEEE
Confidence 5899999999988731 2334566799999994 4332 565443
No 19
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=53.08 E-value=42 Score=27.57 Aligned_cols=47 Identities=19% Similarity=0.192 Sum_probs=40.0
Q ss_pred eEEEecCCCcEEEEec-cCCCCceeeeEEEEEeccCCCCcEEEEEEEe
Q psy8637 118 ELILEDELQRIPLHGN-IDIHNQVTGVVVAIKGTPVGNGKFKVSDVCY 164 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~-i~~~~lVTGvVvaV~G~~~~~G~F~V~di~~ 164 (216)
.-.|.|....|...=+ +-++.|--|.-|-+.|+..++|.|+.+++.-
T Consensus 74 ~F~ltD~~~~i~V~Y~G~lPd~F~eg~~VVv~G~~~~~g~F~A~~vLa 121 (148)
T PRK13254 74 RFVVTDGNATVPVVYTGILPDLFREGQGVVAEGRLQDGGVFVADEVLA 121 (148)
T ss_pred EEEEEeCCeEEEEEECCCCCccccCCCEEEEEEEECCCCeEEEEEEEe
Confidence 5678999888887644 5678899999999999999899999999987
No 20
>PRK06386 replication factor A; Reviewed
Probab=53.05 E-value=28 Score=32.61 Aligned_cols=14 Identities=21% Similarity=0.439 Sum_probs=13.1
Q ss_pred eEEEecCCCcEEEE
Q psy8637 118 ELILEDELQRIPLH 131 (216)
Q Consensus 118 ~l~LEDesgRI~L~ 131 (216)
..+|.||||||+++
T Consensus 145 sg~lgDeTGrIr~T 158 (358)
T PRK06386 145 QGYIEDDTARVRIS 158 (358)
T ss_pred EEEEEcCCCeEEEE
Confidence 68999999999997
No 21
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). 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 protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=51.26 E-value=41 Score=24.91 Aligned_cols=36 Identities=17% Similarity=0.055 Sum_probs=26.1
Q ss_pred eEEEecCCCcEEEEeccC-----------CCCceeeeEEEEEeccCC
Q psy8637 118 ELILEDELQRIPLHGNID-----------IHNQVTGVVVAIKGTPVG 153 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~i~-----------~~~lVTGvVvaV~G~~~~ 153 (216)
.+.|-|.+|.|.+.-+-+ ...+-.|.+|.|.|....
T Consensus 20 Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~ 66 (102)
T cd04320 20 FLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKK 66 (102)
T ss_pred EEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEEC
Confidence 578889999998865411 134667999999998654
No 22
>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=51.16 E-value=38 Score=23.39 Aligned_cols=46 Identities=20% Similarity=0.125 Sum_probs=33.8
Q ss_pred eEEEecCCCcEEEEe--c-c--CCCCceeeeEEEEEeccCCC---C--cEEEEEEE
Q psy8637 118 ELILEDELQRIPLHG--N-I--DIHNQVTGVVVAIKGTPVGN---G--KFKVSDVC 163 (216)
Q Consensus 118 ~l~LEDesgRI~L~G--~-i--~~~~lVTGvVvaV~G~~~~~---G--~F~V~di~ 163 (216)
.+-|||.+|++.+.- + . ....+..|.+|-|.|....+ | .+.|+++.
T Consensus 20 ~~~L~D~~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g~v~~~~~~~~~~l~v~~i~ 75 (78)
T cd04489 20 YFTLKDEDASIRCVMWRSNARRLGFPLEEGMEVLVRGKVSFYEPRGGYQLIVEEIE 75 (78)
T ss_pred EEEEEeCCeEEEEEEEcchhhhCCCCCCCCCEEEEEEEEEEECCCCEEEEEEEEEE
Confidence 578999999998862 2 2 24678899999999987732 3 57777764
No 23
>PRK08402 replication factor A; Reviewed
Probab=49.93 E-value=27 Score=32.60 Aligned_cols=77 Identities=17% Similarity=0.316 Sum_probs=48.2
Q ss_pred ceeeeeecccCCCC-eEEEEEEEEeeCCCCCchHHHHHhhhcCCCCCCCCCcCCCCC------eEEEecCCCcEEEE--e
Q psy8637 62 SVLKLSDLNETDTE-ECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHTHFVSDSD------ELILEDELQRIPLH--G 132 (216)
Q Consensus 62 ~i~kll~l~~~~g~-~cvvIGTlyK~mklKPsIL~e~~~e~~~~~~~~~~~y~s~~D------~l~LEDesgRI~L~--G 132 (216)
+..+|.|| .+|. .+-++|.|-.....| .|...+. .+.|.|+||+|+++ |
T Consensus 61 ~~~kI~dl--~~g~~~V~v~~rVl~~~~~r--------------------~f~rrdG~~~~V~~i~l~DeTG~ir~TlW~ 118 (355)
T PRK08402 61 PLMHISDL--VPGMRGVNIVGRVLRKYPPR--------------------EYTKKDGSTGRVASLIIYDDTGRARVVLWD 118 (355)
T ss_pred CccCHHHc--cCCCceeeEEEEEEEccCCc--------------------eeeccCCCcceEEEEEEEcCCCeEEEEEec
Confidence 35677888 4664 577888887443322 2221111 38999999999997 3
Q ss_pred c-cC--CCCceeeeEEEEEeccC-C--CCcEEEE
Q psy8637 133 N-ID--IHNQVTGVVVAIKGTPV-G--NGKFKVS 160 (216)
Q Consensus 133 ~-i~--~~~lVTGvVvaV~G~~~-~--~G~F~V~ 160 (216)
+ .+ ...+=.|-|++|.|.-. + +|.++++
T Consensus 119 ~~a~~~~~~l~~Gdvi~I~~a~V~e~~~G~~eLs 152 (355)
T PRK08402 119 AKVAKYYNKINVGDVIKVIDAQVRESLSGLPELH 152 (355)
T ss_pred hhhhhhcccCCCCCEEEEECCEEeecCCCcEEEE
Confidence 3 22 13477899999985443 3 5666665
No 24
>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal 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 protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for
Probab=48.51 E-value=35 Score=24.72 Aligned_cols=43 Identities=14% Similarity=0.078 Sum_probs=28.8
Q ss_pred eEEEecCCC-cEEEEecc------CCCCceeeeEEEEEeccCCC--------CcEEEE
Q psy8637 118 ELILEDELQ-RIPLHGNI------DIHNQVTGVVVAIKGTPVGN--------GKFKVS 160 (216)
Q Consensus 118 ~l~LEDesg-RI~L~G~i------~~~~lVTGvVvaV~G~~~~~--------G~F~V~ 160 (216)
.+.|-|.+| ++.++-+- ....+=+|.+|+|.|..... |.|++.
T Consensus 20 Fi~LrD~~g~~iQvv~~~~~~~~~~~~~l~~~s~V~V~G~v~~~~~~~~~~~~~~Ei~ 77 (86)
T cd04321 20 FADLRDPNGDIIQLVSTAKKDAFSLLKSITAESPVQVRGKLQLKEAKSSEKNDEWELV 77 (86)
T ss_pred EEEEECCCCCEEEEEECCCHHHHHHHhcCCCCcEEEEEEEEEeCCCcCCCCCCCEEEE
Confidence 577889999 68876421 11346689999999976532 666653
No 25
>PF08476 VD10_N: Viral D10 N-terminal; InterPro: IPR013683 This domain is found on the N terminus of the viral protein D10 (VD10) and the related MutT motif proteins []. The VD10 protein is probably essential for virus replication [] and is often found to the N terminus of a NUDIX hydrolase domain. Previous studies indicated that the vaccinia virus D10 protein, which is conserved in all sequenced poxviruses, participates in the rapid turnover of host and viral mRNAs. D10 contains a motif present in the family of Nudix/MutT enzymes, a subset of which has been shown to enhance mRNA turnover in eukaryotic cells through cleavage of the 5' cap (m7GpppNm-). The D10 protein possesses an intrinsic activity that liberates m7GDP from capped RNA substrates. Furthermore, point mutations in the Nudix/MutT motif abolished decapping activity. D10 has a strong affinity for capped RNA substrates of lengths of 24-309 nt were decapped efficiently. The poxviruses represent the only virus family shown to encode a Nudix hydrolase-decapping enzyme. The activity of the decapping and capping enzymes, accelerate mRNA turnover and helps to eliminate competing host mRNAs allowing stage-specific synthesis of viral proteins [].; GO: 0016791 phosphatase activity
Probab=46.14 E-value=17 Score=24.16 Aligned_cols=17 Identities=35% Similarity=0.499 Sum_probs=14.6
Q ss_pred CeEEEecCCCcEEEEec
Q psy8637 117 DELILEDELQRIPLHGN 133 (216)
Q Consensus 117 D~l~LEDesgRI~L~G~ 133 (216)
-.+++.|.+|||.++|-
T Consensus 21 ktyi~~Dd~QrI~aT~F 37 (45)
T PF08476_consen 21 KTYIFSDDSQRITATGF 37 (45)
T ss_pred CcEEEecCCeEEEEeeh
Confidence 35789999999999984
No 26
>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=45.92 E-value=64 Score=23.30 Aligned_cols=44 Identities=16% Similarity=0.228 Sum_probs=32.0
Q ss_pred CeEEEecCCCcEEEE----ecc----CCCCceeeeEEEEEeccCC-CCcEEEE
Q psy8637 117 DELILEDELQRIPLH----GNI----DIHNQVTGVVVAIKGTPVG-NGKFKVS 160 (216)
Q Consensus 117 D~l~LEDesgRI~L~----G~i----~~~~lVTGvVvaV~G~~~~-~G~F~V~ 160 (216)
-.+-|+|.||+|... ++- +...+-.|.++.|.|.... +|.-.+.
T Consensus 18 ~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~~~g~~ql~ 70 (95)
T cd04478 18 ITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIM 70 (95)
T ss_pred EEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEcccCCeeEEE
Confidence 368899999998875 211 3556788999999999875 4555544
No 27
>PRK07217 replication factor A; Reviewed
Probab=41.79 E-value=45 Score=30.75 Aligned_cols=76 Identities=16% Similarity=0.265 Sum_probs=46.1
Q ss_pred ceeeeeecccCCCCeEEEEEEEEeeCCCCCchHHHHHhhhcCCCCCCCCCcCCCCCeEEEecCCCcEEEEe--ccCCCCc
Q psy8637 62 SVLKLSDLNETDTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHTHFVSDSDELILEDELQRIPLHG--NIDIHNQ 139 (216)
Q Consensus 62 ~i~kll~l~~~~g~~cvvIGTlyK~mklKPsIL~e~~~e~~~~~~~~~~~y~s~~D~l~LEDesgRI~L~G--~i~~~~l 139 (216)
+..+|.||. ..++.+-|.|.|.-.-+ |+ .+.-.+ .=+|+||||||+++- +-+...+
T Consensus 71 ~~~kI~Di~-~~~~~VsV~aKVl~l~e--~~--------------~~si~q-----vGllgDETG~IkfT~W~~s~~~~l 128 (311)
T PRK07217 71 ELVNIADID-EPEQWVDVTAKVVQLWE--PS--------------SDSIAQ-----VGLLGDETGTIKFTKWAKSDLPEL 128 (311)
T ss_pred CceeeeecC-CCCCcEEEEEEEEEecC--CC--------------CCceEE-----EEEEEcCCceEEEEEccCCCCCcc
Confidence 455788885 35666779999885432 11 000111 127999999999983 2233445
Q ss_pred eeeeEEEEEeccCC--CCcEEE
Q psy8637 140 VTGVVVAIKGTPVG--NGKFKV 159 (216)
Q Consensus 140 VTGvVvaV~G~~~~--~G~F~V 159 (216)
--|-++-+.+.... +|.+.|
T Consensus 129 eeGd~~rI~na~v~ey~G~~~l 150 (311)
T PRK07217 129 EEGKSYLLKNVVTDEYQGRFSV 150 (311)
T ss_pred cCCCEEEEEeEEEeeECCEEEE
Confidence 66777777766543 455544
No 28
>PRK07211 replication factor A; Reviewed
Probab=40.39 E-value=31 Score=33.65 Aligned_cols=38 Identities=16% Similarity=0.219 Sum_probs=29.4
Q ss_pred eEEEecCCCcEEEE--eccCCCCceeeeEEEEEeccCCCC
Q psy8637 118 ELILEDELQRIPLH--GNIDIHNQVTGVVVAIKGTPVGNG 155 (216)
Q Consensus 118 ~l~LEDesgRI~L~--G~i~~~~lVTGvVvaV~G~~~~~G 155 (216)
.+.|-|+||||+++ |+.-...+-.|-+|+|.|....+|
T Consensus 308 ~l~l~D~TG~IrvTLWg~~A~~~i~~GdvV~Ikg~~V~dg 347 (485)
T PRK07211 308 NVRIQDDTGDIRVALWGEKADLDIGPGDEVVAADVEIQDG 347 (485)
T ss_pred EEEEEcCCCcEEEEEeCccccCCCCCCCEEEEEccEEEec
Confidence 59999999999998 552122477899999999666555
No 29
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. 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, wh
Probab=36.26 E-value=1.5e+02 Score=23.06 Aligned_cols=35 Identities=11% Similarity=0.022 Sum_probs=24.0
Q ss_pred eEEEecCCCcEEEEec--c-----CCCCceeeeEEEEEeccC
Q psy8637 118 ELILEDELQRIPLHGN--I-----DIHNQVTGVVVAIKGTPV 152 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~--i-----~~~~lVTGvVvaV~G~~~ 152 (216)
.+.|-|.+|.+.++-+ . ....+-.|.+|.|.|...
T Consensus 34 Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~ 75 (135)
T cd04317 34 FIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVR 75 (135)
T ss_pred EEEEecCCeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEE
Confidence 5678888888877642 1 113467888888888655
No 30
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=35.95 E-value=1.2e+02 Score=25.24 Aligned_cols=47 Identities=17% Similarity=0.075 Sum_probs=40.7
Q ss_pred eEEEecCCCcEEEEec-cCCCCceeeeEEEEEeccCCCCcEEEEEEEe
Q psy8637 118 ELILEDELQRIPLHGN-IDIHNQVTGVVVAIKGTPVGNGKFKVSDVCY 164 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~-i~~~~lVTGvVvaV~G~~~~~G~F~V~di~~ 164 (216)
...+.|....|..+-. +-++.|--|.-|-+.|+..++|.|+...+.-
T Consensus 81 ~F~vtD~~~~v~V~Y~GilPDlFrEG~gVVveG~~~~~g~F~A~evLA 128 (159)
T PRK13150 81 NFSLYDAEGSVTVSYEGILPDLFREGQGVVVQGTLEKGNHVLAHEVLA 128 (159)
T ss_pred EEEEEcCCcEEEEEEeccCCccccCCCeEEEEEEECCCCEEEEeEEEe
Confidence 4577898888888755 7788899999999999999999999999986
No 31
>KOG1942|consensus
Probab=34.81 E-value=30 Score=32.45 Aligned_cols=38 Identities=24% Similarity=0.343 Sum_probs=32.5
Q ss_pred eeCCCCCchHHHHHhhhcCCCCCCCCCcCCCCCeEEEecCCCcEEEEec
Q psy8637 85 KHQQLKPNILKEISEELKLVPQPQHTHFVSDSDELILEDELQRIPLHGN 133 (216)
Q Consensus 85 K~mklKPsIL~e~~~e~~~~~~~~~~~y~s~~D~l~LEDesgRI~L~G~ 133 (216)
|+.||-|||.+.+.++.- +..|.+|+|-.||-|+=+|-
T Consensus 169 KqLkLdPsiyesi~kerv-----------~~GDViYIEaNsGavKrvGR 206 (456)
T KOG1942|consen 169 KQLKLDPSIYESIQKERV-----------EVGDVIYIEANSGAVKRVGR 206 (456)
T ss_pred ceeccChHHHHHHHHhhh-----------ccCcEEEEEeccchhhcccc
Confidence 778999999999998752 33899999999999998874
No 32
>PRK12366 replication factor A; Reviewed
Probab=32.70 E-value=51 Score=33.06 Aligned_cols=35 Identities=20% Similarity=0.108 Sum_probs=24.8
Q ss_pred eEEEecCCCcEEEE--eccCCCCceeeeEEEEEeccC
Q psy8637 118 ELILEDELQRIPLH--GNIDIHNQVTGVVVAIKGTPV 152 (216)
Q Consensus 118 ~l~LEDesgRI~L~--G~i~~~~lVTGvVvaV~G~~~ 152 (216)
.++|.|+||+|+|+ |+.-...+-.|-|+++.|...
T Consensus 438 ~i~l~D~TG~I~vtlWg~~a~~~~~~G~vi~i~~~~V 474 (637)
T PRK12366 438 NIELADGTGSIRLTLWDDDAEIEIKEGDAIKILHPYV 474 (637)
T ss_pred EEEEEeCCCEEEEEEeccccccCCCCCCEEEEEeeEE
Confidence 58999999999998 541112345688888887554
No 33
>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=32.62 E-value=1.1e+02 Score=21.77 Aligned_cols=37 Identities=16% Similarity=0.103 Sum_probs=25.8
Q ss_pred CeEEEecCCCcEEEEec--c-----CCCCceeeeEEEEEeccCC
Q psy8637 117 DELILEDELQRIPLHGN--I-----DIHNQVTGVVVAIKGTPVG 153 (216)
Q Consensus 117 D~l~LEDesgRI~L~G~--i-----~~~~lVTGvVvaV~G~~~~ 153 (216)
-.+.|-|.+|.+.+.-+ . ....+-+|.+|.|.|.+..
T Consensus 18 ~Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~v~~ 61 (84)
T cd04323 18 MFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEVKE 61 (84)
T ss_pred EEEEEEcCCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEEEEE
Confidence 35778899998887643 1 1134668999999997653
No 34
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, 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). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=31.30 E-value=65 Score=23.68 Aligned_cols=34 Identities=35% Similarity=0.453 Sum_probs=22.7
Q ss_pred eEEEecCCC-cEEEE--ec-c-CCCCceeeeEEEEEeccC
Q psy8637 118 ELILEDELQ-RIPLH--GN-I-DIHNQVTGVVVAIKGTPV 152 (216)
Q Consensus 118 ~l~LEDesg-RI~L~--G~-i-~~~~lVTGvVvaV~G~~~ 152 (216)
.+.|.|+|+ .|.++ |+ - ...... |.|+++.|.-.
T Consensus 30 ~v~i~D~t~~~i~vtLWg~~a~~~~~~~-~~vv~~~~~~i 68 (101)
T cd04475 30 EITLVDESGHSVELTLWGEQAELFDGSE-NPVIAIKGVKV 68 (101)
T ss_pred EEEEEeCCCCEEEEEEEHHHhhhcccCC-CCEEEEEeeEE
Confidence 689999999 66665 55 1 111112 99999999544
No 35
>KOG1536|consensus
Probab=30.85 E-value=1.3e+02 Score=30.30 Aligned_cols=80 Identities=21% Similarity=0.300 Sum_probs=53.0
Q ss_pred HhhcCCCcceeeeeec------cc-CCCCeEEEEEEEEeeCCCCCch-----HHHHHhhhcCCCCCCC------------
Q psy8637 54 SQKWGKSVSVLKLSDL------NE-TDTEECVIIGTLFKHQQLKPNI-----LKEISEELKLVPQPQH------------ 109 (216)
Q Consensus 54 ~~kw~~~~~i~kll~l------~~-~~g~~cvvIGTlyK~mklKPsI-----L~e~~~e~~~~~~~~~------------ 109 (216)
.-||+++..+...+.+ .. ....-|+.||.=+--...+|.+ |+|++++++..-.+-+
T Consensus 484 rIKWPNDlY~~~~lKvgGiLv~st~r~n~f~v~iGCGiNVtN~~PT~cLN~ll~~~n~e~~~~~l~~k~EkLiA~~~n~f 563 (649)
T KOG1536|consen 484 RIKWPNDLYVNGYLKVGGILVTSTYRSNKFNVSIGCGINVTNDGPTTCLNDLLDEMNEERNLLHLAIKAEKLIAAVFNKF 563 (649)
T ss_pred eeecCccceeeeccccceEEEEeeecCceEEEEEeeeeEecCCCCceeHHHHHHhhchhhccccchhhHHHHHHHHHHHH
Confidence 3489887655443333 11 3566799999999999999964 7777777654211100
Q ss_pred --------------------CCcCCCCCeEEEecCCCcEEEEec
Q psy8637 110 --------------------THFVSDSDELILEDELQRIPLHGN 133 (216)
Q Consensus 110 --------------------~~y~s~~D~l~LEDesgRI~L~G~ 133 (216)
.-+.+..-++.|+|-..+|...|.
T Consensus 564 e~~~k~f~d~G~~silp~YYeyWLHS~Q~V~L~d~~e~vii~~~ 607 (649)
T KOG1536|consen 564 EKYFKLFMDQGPKSILPLYYEYWLHSNQRVILEDKGEAVIIGGT 607 (649)
T ss_pred HHHHHHHHhhCHHhHhHHHHHHHhccCcEEeccCCCcceEEeee
Confidence 123556778999999988888775
No 36
>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=30.47 E-value=93 Score=19.91 Aligned_cols=37 Identities=24% Similarity=0.093 Sum_probs=27.6
Q ss_pred CeEEEecCC-CcEEEEec---cC--CCCceeeeEEEEEeccCC
Q psy8637 117 DELILEDEL-QRIPLHGN---ID--IHNQVTGVVVAIKGTPVG 153 (216)
Q Consensus 117 D~l~LEDes-gRI~L~G~---i~--~~~lVTGvVvaV~G~~~~ 153 (216)
-.+-|+|.+ +.+.+.-- .. ...+-.|.++.|.|....
T Consensus 19 ~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~g~v~~ 61 (75)
T cd03524 19 LIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIKGKVKK 61 (75)
T ss_pred EEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEEEEEEe
Confidence 468899999 99988632 11 245788999999998863
No 37
>PRK14699 replication factor A; Provisional
Probab=28.92 E-value=86 Score=30.52 Aligned_cols=51 Identities=24% Similarity=0.337 Sum_probs=34.1
Q ss_pred eeeeeecccCCCCeEEEEEEEEeeCCCCCchHHHHHhhhcCCCCCCCCCcCCC--CCeEEEecCCCcEEEE
Q psy8637 63 VLKLSDLNETDTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHTHFVSD--SDELILEDELQRIPLH 131 (216)
Q Consensus 63 i~kll~l~~~~g~~cvvIGTlyK~mklKPsIL~e~~~e~~~~~~~~~~~y~s~--~D~l~LEDesgRI~L~ 131 (216)
..+|.+| +.+..+=|+|+|..-.+.+ ++.+..+ ++ -=.++|.|+||+|+|+
T Consensus 386 ~~~I~di--e~~~~vdV~G~V~~v~~~~-----~~~~~~g-----------~~~~vr~i~l~D~TG~Ir~t 438 (484)
T PRK14699 386 FTDIADI--IPGESYSVQGKVSEIGELR-----EFEREDG-----------TENVVANLQLKDETGSIRLT 438 (484)
T ss_pred cccHHHc--cCCCeeEEEEEEEEcCCcc-----eEEecCC-----------CEEEEEEEEEEcCCCeEEEE
Confidence 3457777 5788899999998776544 2221100 11 1269999999999997
No 38
>COG4898 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.90 E-value=28 Score=27.02 Aligned_cols=18 Identities=17% Similarity=0.490 Sum_probs=14.1
Q ss_pred CCceeeeEEEEEeccCCC
Q psy8637 137 HNQVTGVVVAIKGTPVGN 154 (216)
Q Consensus 137 ~~lVTGvVvaV~G~~~~~ 154 (216)
..++||++|||+=.|.++
T Consensus 70 rslITGvICGvRvEEI~D 87 (115)
T COG4898 70 RSLITGVICGVRVEEIDD 87 (115)
T ss_pred hhhhcceeeeeehhhhcc
Confidence 458999999998766553
No 39
>PRK15491 replication factor A; Provisional
Probab=28.15 E-value=77 Score=29.70 Aligned_cols=14 Identities=21% Similarity=0.475 Sum_probs=13.0
Q ss_pred eEEEecCCCcEEEE
Q psy8637 118 ELILEDELQRIPLH 131 (216)
Q Consensus 118 ~l~LEDesgRI~L~ 131 (216)
.++|.|+||||+++
T Consensus 315 ~i~l~D~Tg~Ir~t 328 (374)
T PRK15491 315 NIYVSDDTGRIRIA 328 (374)
T ss_pred eEEEEeCCCcEEEE
Confidence 58999999999998
No 40
>PF06138 Chordopox_E11: Chordopoxvirus E11 protein; InterPro: IPR009201 This group represents a virion core protein, vaccinia E11L type.
Probab=27.19 E-value=44 Score=27.04 Aligned_cols=16 Identities=25% Similarity=0.441 Sum_probs=14.0
Q ss_pred eEEEecCCCcEEEEec
Q psy8637 118 ELILEDELQRIPLHGN 133 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~ 133 (216)
.+|||-++|||+|.-.
T Consensus 5 NIfLEsd~grvkl~~~ 20 (130)
T PF06138_consen 5 NIFLESDSGRVKLRYE 20 (130)
T ss_pred EEEEeccCceeEEEEe
Confidence 4899999999999754
No 41
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=26.93 E-value=2.2e+02 Score=23.83 Aligned_cols=47 Identities=13% Similarity=0.053 Sum_probs=40.1
Q ss_pred eEEEecCCCcEEEEec-cCCCCceeeeEEEEEeccCCCCcEEEEEEEe
Q psy8637 118 ELILEDELQRIPLHGN-IDIHNQVTGVVVAIKGTPVGNGKFKVSDVCY 164 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~-i~~~~lVTGvVvaV~G~~~~~G~F~V~di~~ 164 (216)
...+-|....|...-. +-++.|--|.-|-+.|+..++|.|....+.-
T Consensus 81 ~F~vtD~~~~v~V~Y~GilPDlFrEG~gVVveG~~~~~g~F~A~~vLA 128 (160)
T PRK13165 81 SFTLYDAGGSVTVTYEGILPDLFREGQGIVAQGVLEEGNHIEAKEVLA 128 (160)
T ss_pred EEEEEcCCeEEEEEEcccCCccccCCCeEEEEEEECCCCeEEEEEEEe
Confidence 4567788888888755 7788999999999999999999999999986
No 42
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). 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 protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=26.92 E-value=1.5e+02 Score=21.00 Aligned_cols=35 Identities=26% Similarity=0.218 Sum_probs=24.6
Q ss_pred eEEEecCCCcEEEEec---cC-----CCCceeeeEEEEEeccC
Q psy8637 118 ELILEDELQRIPLHGN---ID-----IHNQVTGVVVAIKGTPV 152 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~---i~-----~~~lVTGvVvaV~G~~~ 152 (216)
.+.|-|.+|.+.+.-+ .+ ...+-.|.+|.|.|...
T Consensus 19 Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~ 61 (85)
T cd04100 19 FIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVV 61 (85)
T ss_pred EEEEEeCCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEE
Confidence 4678899999988643 11 23567788888888654
No 43
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=26.26 E-value=1.5e+02 Score=22.15 Aligned_cols=24 Identities=21% Similarity=0.437 Sum_probs=19.8
Q ss_pred eeeeEEEEEecc---CCCCcEEEEEEEe
Q psy8637 140 VTGVVVAIKGTP---VGNGKFKVSDVCY 164 (216)
Q Consensus 140 VTGvVvaV~G~~---~~~G~F~V~di~~ 164 (216)
+||.|++++... .++| |.-.+++.
T Consensus 2 i~Gkii~~l~~~~g~s~~G-w~Kre~Vl 28 (84)
T PF11325_consen 2 ITGKIIKVLPEQQGVSKNG-WKKREFVL 28 (84)
T ss_pred cccEEEEEecCcccCcCCC-cEEEEEEE
Confidence 589999998654 4588 99999998
No 44
>PF07725 LRR_3: Leucine Rich Repeat; InterPro: IPR011713 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. This entry includes some LRRs that fail to be detected by the IPR001611 from INTERPRO model.
Probab=26.11 E-value=18 Score=19.98 Aligned_cols=13 Identities=31% Similarity=0.823 Sum_probs=8.9
Q ss_pred CCHHHHHHHhhHH
Q psy8637 189 FTDDDFIRLWEGL 201 (216)
Q Consensus 189 l~~~d~~~l~kgl 201 (216)
+..+.+.|||.|.
T Consensus 7 m~~S~lekLW~G~ 19 (20)
T PF07725_consen 7 MPYSKLEKLWEGV 19 (20)
T ss_pred CCCCChHHhcCcc
Confidence 3345678899883
No 45
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=25.15 E-value=1.3e+02 Score=23.08 Aligned_cols=57 Identities=16% Similarity=0.177 Sum_probs=36.4
Q ss_pred CCCCeEEEEEEEEeeCCCCCchHHHHHhhhcCCCCCCCCCcCCCCCeEEEecCCCcEEEEec---cCCCCceeeeEEEEE
Q psy8637 72 TDTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHTHFVSDSDELILEDELQRIPLHGN---IDIHNQVTGVVVAIK 148 (216)
Q Consensus 72 ~~g~~cvvIGTlyK~mklKPsIL~e~~~e~~~~~~~~~~~y~s~~D~l~LEDesgRI~L~G~---i~~~~lVTGvVvaV~ 148 (216)
..+..+.+-|.|-++. .+|.+.+-|.||+|.+.-+ -....+-.+.-|-+.
T Consensus 32 ~Dd~~V~L~G~Iv~~l---------------------------~~d~Y~F~D~TG~I~VeId~~~w~g~~vt~~~~Vri~ 84 (103)
T PF04076_consen 32 KDDTPVTLEGNIVKQL---------------------------GDDKYLFRDATGEIEVEIDDDVWRGQTVTPDDKVRIS 84 (103)
T ss_dssp -SSEEEEEEEEEEEEE---------------------------ETTEEEEEETTEEEEEE--GGGSTT----TTSEEEEE
T ss_pred cCCCeEEEEEEEEEEe---------------------------cCCEEEEECCCCcEEEEEChhhcCCcccCCCCEEEEE
Confidence 4677788888888762 1788899999999999743 222334445566777
Q ss_pred eccCCCC
Q psy8637 149 GTPVGNG 155 (216)
Q Consensus 149 G~~~~~G 155 (216)
|.+..++
T Consensus 85 GeVDk~~ 91 (103)
T PF04076_consen 85 GEVDKDW 91 (103)
T ss_dssp EEEEEET
T ss_pred EEEeCCC
Confidence 8766443
No 46
>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=25.10 E-value=1.9e+02 Score=21.46 Aligned_cols=40 Identities=10% Similarity=0.061 Sum_probs=27.8
Q ss_pred eEEEecCCCcEEEEecc-------------------------CCCCceeeeEEEEEeccCC-CCcE
Q psy8637 118 ELILEDELQRIPLHGNI-------------------------DIHNQVTGVVVAIKGTPVG-NGKF 157 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~i-------------------------~~~~lVTGvVvaV~G~~~~-~G~F 157 (216)
.+-|.|.||.|...-=. ....+-.|.++-|.|+... .|.-
T Consensus 17 ~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV~G~i~~frg~~ 82 (92)
T cd04483 17 SFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVRGSIRTYRGER 82 (92)
T ss_pred EEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEEEEEEeccCCee
Confidence 57889999988775211 2334788999999998764 4443
No 47
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. 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 protein synthesis, whereas the other exclusively with mitochondrial
Probab=24.45 E-value=2.4e+02 Score=19.73 Aligned_cols=43 Identities=19% Similarity=0.268 Sum_probs=28.0
Q ss_pred eEEEecCCC--cEEEEec---c---CCCCceeeeEEEEEeccCC----CCcEEEE
Q psy8637 118 ELILEDELQ--RIPLHGN---I---DIHNQVTGVVVAIKGTPVG----NGKFKVS 160 (216)
Q Consensus 118 ~l~LEDesg--RI~L~G~---i---~~~~lVTGvVvaV~G~~~~----~G~F~V~ 160 (216)
.+.|-|.++ .+.++-+ . ....+=+|.+|.|.|.... .|.|++.
T Consensus 19 Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~~~~~El~ 73 (82)
T cd04318 19 FIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGAKQPFELQ 73 (82)
T ss_pred EEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEEeCCCCCCCEEEE
Confidence 466779888 4887643 1 1235668999999997543 2556664
No 48
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=24.15 E-value=1.2e+02 Score=25.39 Aligned_cols=54 Identities=19% Similarity=0.328 Sum_probs=37.0
Q ss_pred CceeeeEEEEEec-----------------cCCCCcEEEEEEEe-cCCCCCCcccCCCCCCcceeecCCCCHHHHHHH
Q psy8637 138 NQVTGVVVAIKGT-----------------PVGNGKFKVSDVCY-ATPVFKPRTTLSNNENKYVNHVDAFTDDDFIRL 197 (216)
Q Consensus 138 ~lVTGvVvaV~G~-----------------~~~~G~F~V~di~~-~~~pq~p~~~~~~~~~~yv~lvsgl~~~d~~~l 197 (216)
.++||++|.+.|. .+++|.|.++.+.+ |.--+-|.-..+.+ ..++++.+-+.+|
T Consensus 81 ~VC~~t~C~l~Gs~~l~~~l~~~lgi~~gett~DG~ftl~~v~ClGaC~~AP~vmind~------~~~~lt~e~l~ei 152 (160)
T COG1905 81 RVCTGTACHLKGSEALLKALEKKLGIKPGETTADGKFTLEPVECLGACGQAPVVMINDD------VYGRLTPEKLEEI 152 (160)
T ss_pred EEeCCcHHhhcChHHHHHHHHHHhCCCCCCcCCCCeEEEeeeeeecccccCCEEEECCc------hhccCCHHHHHHH
Confidence 4677888887764 47899999999999 86665555444433 2355776666555
No 49
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.99 E-value=80 Score=31.54 Aligned_cols=35 Identities=26% Similarity=0.435 Sum_probs=24.5
Q ss_pred eEEEecCCCc-EEEE--ec-cCCCCceeeeEEEEEeccC
Q psy8637 118 ELILEDELQR-IPLH--GN-IDIHNQVTGVVVAIKGTPV 152 (216)
Q Consensus 118 ~l~LEDesgR-I~L~--G~-i~~~~lVTGvVvaV~G~~~ 152 (216)
.+.|.|+||+ |+|+ |+ -..-..-.|.|||+.|...
T Consensus 341 ~i~L~D~sg~sI~vTLWG~~A~~~~~~~~~Vva~kg~~V 379 (608)
T TIGR00617 341 DITLVDDSGKSVRVTLWGDDATKFDVSVQPVIAIKGVRV 379 (608)
T ss_pred EEEEEeCCCCEEEEEEEhhhhhhcCCCCCCEEEEEeEEE
Confidence 6999999995 6665 66 2112244688999998654
No 50
>PF09933 DUF2165: Predicted small integral membrane protein (DUF2165); InterPro: IPR018681 This family of various hypothetical prokaryotic proteins has no known function.
Probab=23.63 E-value=44 Score=27.86 Aligned_cols=17 Identities=35% Similarity=0.534 Sum_probs=13.9
Q ss_pred hHHHhhhhhcCCCcccC
Q psy8637 199 EGLFFSMWMSDKPLIQK 215 (216)
Q Consensus 199 kgl~~~~w~~d~~~~q~ 215 (216)
.|.+|.||+|.-...|+
T Consensus 124 GGeWF~MWqs~~wngq~ 140 (160)
T PF09933_consen 124 GGEWFGMWQSQEWNGQE 140 (160)
T ss_pred HHHHHHHHHccccCCcH
Confidence 68899999998776664
No 51
>PF02197 RIIa: Regulatory subunit of type II PKA R-subunit; InterPro: IPR003117 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In the absence of cAMP, Protein Kinase A (PKA) exists as an equimolar tetramer of regulatory (R) and catalytic (C) subunits []. In addition to its role as an inhibitor of the C subunit, the R subunit anchors the holoenzyme to specific intracellular locations and prevents the C subunit from entering the nucleus. All R subunits have a conserved domain structure consisting of the N-terminal dimerization domain, inhibitory region, cAMP-binding domain A and cAMP-binding domain B. R subunits interact with C subunits primarily through the inhibitory site. The cAMP-binding domains show extensive sequence similarity and bind cAMP cooperatively. Two types of regulatory (R) subunits exist - types I and I - which differ in molecular weight, sequence, autophosphorylation cabaility, cellular location and tissue distribution. Types I and II were further sub-divided into alpha and beta subtypes, based mainly on sequence similarity. This entry represents types I-alpha, I-beta, II-alpha and II-beta regulatory subunits of PKA proteins. These subunits contain the dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).; GO: 0008603 cAMP-dependent protein kinase regulator activity, 0007165 signal transduction; PDB: 2IZY_E 1R2A_A 1L6E_A 2IZX_B 2KYG_A 2EZW_B 3IM4_B 3IM3_A 4F9K_C 2HWN_B ....
Probab=23.60 E-value=82 Score=19.76 Aligned_cols=18 Identities=44% Similarity=0.438 Sum_probs=13.9
Q ss_pred chhhhhHHHHHHHHHHHH
Q psy8637 29 DYSKQFAHIYAVRLNKMR 46 (216)
Q Consensus 29 ~y~~QY~~iY~~RL~~Lr 46 (216)
.---|||.-||.||.+-|
T Consensus 20 ~Di~~F~a~yF~~L~~~R 37 (38)
T PF02197_consen 20 DDILQFAADYFEKLEKQR 37 (38)
T ss_dssp S-HHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHhh
Confidence 334699999999998765
No 52
>PF06188 HrpE: HrpE/YscL/FliH and V-type ATPase subunit E; InterPro: IPR009335 This family consists of several bacterial HrpE proteins, which are believed to function on the type III secretion system, specifically the secretion of HrpZ (harpinPss) []. This family also includes V-type proton ATPase subunit E proteins. This subunit appears to form a tight interaction with subunit G in the F0 complex. Subunits E and G may act together as stators to prevent certain subunits from rotating with the central rotary element []. PF01991 from PFAM also contains V-type ATPase subunit E proteins. There is an evolutionary link between type III secretion systems and membrane-associated proton translocating ATPases [].
Probab=23.28 E-value=1.3e+02 Score=25.44 Aligned_cols=47 Identities=28% Similarity=0.275 Sum_probs=33.0
Q ss_pred EEEEEEeeCCCCCchHHHHHhhhcCCCCCCCCCcCC-----CCCeEEEecCCCcEEEE
Q psy8637 79 IIGTLFKHQQLKPNILKEISEELKLVPQPQHTHFVS-----DSDELILEDELQRIPLH 131 (216)
Q Consensus 79 vIGTlyK~mklKPsIL~e~~~e~~~~~~~~~~~y~s-----~~D~l~LEDesgRI~L~ 131 (216)
..|||+.+ |+-+++++.-....+ ...-... +.|.+.|+..+|+..|.
T Consensus 131 ~~~tL~~h----P~~~~~V~~~L~~~~--~~~w~l~~D~sl~~~~l~L~t~~G~~~l~ 182 (191)
T PF06188_consen 131 SEATLRCH----PDQLEEVAAWLAEHP--ALHWQLQADESLAPDQLKLETANGEFRLD 182 (191)
T ss_pred cceEEEEC----HHHHHHHHHHHHhCC--CcceeeccCCCCCCCceEEEcCCCcEEEC
Confidence 78999999 999999976543222 1111222 24799999999999885
No 53
>PRK07252 hypothetical protein; Provisional
Probab=23.17 E-value=3.6e+02 Score=20.96 Aligned_cols=59 Identities=20% Similarity=0.331 Sum_probs=33.6
Q ss_pred cCCCCceeeeEEEEEeccCCCCc--EEEEEEEecCCCCCCcccCCCCCCcceeecCCC-CHHHHHHHhhH
Q psy8637 134 IDIHNQVTGVVVAIKGTPVGNGK--FKVSDVCYATPVFKPRTTLSNNENKYVNHVDAF-TDDDFIRLWEG 200 (216)
Q Consensus 134 i~~~~lVTGvVvaV~G~~~~~G~--F~V~di~~~~~pq~p~~~~~~~~~~yv~lvsgl-~~~d~~~l~kg 200 (216)
+.....|+..|+.+- .+.|. |...++....++++++...+.+ . +.+|+ ++.|+|++|+-
T Consensus 48 ~~vGD~V~VkI~~iD---~~~~ri~lSlk~~~~~~~~~~~~~~~~~~--~---~~~~~~~~~~~~~~~~~ 109 (120)
T PRK07252 48 LKVGEEVLVQVVDFD---EYTGKASLSLRTLEEEKQHFPHRHRFSNS--R---HKIGFKPLEEQLPIWIE 109 (120)
T ss_pred cCCCCEEEEEEEEEe---CCCCEEEEEEeecccCccccCcccccccc--c---ccCCchhHHHHHHHHHH
Confidence 556677777777664 22444 4444554422334544443332 2 55665 48999999974
No 54
>PF09966 DUF2200: Uncharacterized protein conserved in bacteria (DUF2200); InterPro: IPR014580 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3C9P_A.
Probab=22.99 E-value=22 Score=27.96 Aligned_cols=18 Identities=17% Similarity=0.381 Sum_probs=10.9
Q ss_pred CCCceeeeEEEEEeccCC
Q psy8637 136 IHNQVTGVVVAIKGTPVG 153 (216)
Q Consensus 136 ~~~lVTGvVvaV~G~~~~ 153 (216)
...++||+||||+=.+.+
T Consensus 66 ~~~lItGvICGvrvEeIe 83 (111)
T PF09966_consen 66 NRSLITGVICGVRVEEIE 83 (111)
T ss_dssp GGGG--SEETTEEGGG--
T ss_pred cHHHhcCcccceeeeecc
Confidence 356999999999866544
No 55
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=22.70 E-value=3.1e+02 Score=26.22 Aligned_cols=48 Identities=25% Similarity=0.205 Sum_probs=32.7
Q ss_pred eEEEecCCCcEEEEeccC--------CCCceeeeEEEEEeccCCC----Cc--EEEEEEEe-c
Q psy8637 118 ELILEDELQRIPLHGNID--------IHNQVTGVVVAIKGTPVGN----GK--FKVSDVCY-A 165 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~i~--------~~~lVTGvVvaV~G~~~~~----G~--F~V~di~~-~ 165 (216)
.+.|.|.+|+|.+.-..+ ...+-+|-+|+|.|..... |. ..|+++-. +
T Consensus 36 Fi~lrD~~g~iq~~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~~~~~~~~~el~~~~i~vl~ 98 (450)
T PRK03932 36 FLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTGSSVIVTGTVVESPRAGQGYELQATKIEVIG 98 (450)
T ss_pred EEEEECCCCcEEEEEEcCCChHHHHHHhcCCCCcEEEEEEEEEcCCCCCCCEEEEEEEEEEcc
Confidence 578899999987754311 1347789999999977642 33 55667766 5
No 56
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation 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. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=21.48 E-value=3.5e+02 Score=20.11 Aligned_cols=50 Identities=12% Similarity=0.203 Sum_probs=31.1
Q ss_pred eEEEecCCCcEEEEec---c------CCCCceeeeEEEEEeccCC----CCcEE--EEEEEe-cCC
Q psy8637 118 ELILEDELQRIPLHGN---I------DIHNQVTGVVVAIKGTPVG----NGKFK--VSDVCY-ATP 167 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~---i------~~~~lVTGvVvaV~G~~~~----~G~F~--V~di~~-~~~ 167 (216)
.+.|-|.+|.+.++-. . ....+-.|.+|.|.|.... .+.|+ |+++-. +.+
T Consensus 32 Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~Ei~~~~i~il~~~ 97 (108)
T cd04316 32 FVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPKAPNGVEIIPEEIEVLSEA 97 (108)
T ss_pred EEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCCCCCCEEEEEeEEEEEeCC
Confidence 5677888888877532 1 1234678899999996543 23454 566655 533
No 57
>COG3097 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.40 E-value=2.5e+02 Score=21.70 Aligned_cols=70 Identities=11% Similarity=0.097 Sum_probs=42.0
Q ss_pred CCcEEEEec-cCCCCceeeeEEEEEeccCCCCcEEEEEEEe-cCCCCCCcccCCCCCCcceeecCCCCHHHHHHHhhHHH
Q psy8637 125 LQRIPLHGN-IDIHNQVTGVVVAIKGTPVGNGKFKVSDVCY-ATPVFKPRTTLSNNENKYVNHVDAFTDDDFIRLWEGLF 202 (216)
Q Consensus 125 sgRI~L~G~-i~~~~lVTGvVvaV~G~~~~~G~F~V~di~~-~~~pq~p~~~~~~~~~~yv~lvsgl~~~d~~~l~kgl~ 202 (216)
+||=.++-- -.-+++++|-|+.| |+..+++.|.-.++.- .+-- +-.++ ..-|=--.+++.++.++-++.|
T Consensus 18 agrKTITIRD~SEShf~~g~vlrV-~r~Ed~~~fc~I~vl~vspvt---ld~l~----e~HAeQEnm~L~eLk~vI~eIY 89 (106)
T COG3097 18 AGRKTITIRDKSESHFKPGDVLRV-GRFEDDRYFCTIEVLAVSPVT---LDELT----EKHAEQENMTLPELKKVIAEIY 89 (106)
T ss_pred CCCceEEEeccchhcCCCCCEEEE-EEecCCcEEEEEEEEEeccEe---hhhhh----hhhhhhhcCCcHHHHHHHHHHC
Confidence 455555433 34578999999999 4556778888777774 3110 11111 1111224677888888888776
No 58
>PHA03001 putative virion core protein; Provisional
Probab=20.23 E-value=1e+02 Score=24.97 Aligned_cols=17 Identities=24% Similarity=0.331 Sum_probs=14.6
Q ss_pred eEEEecCCCcEEEEecc
Q psy8637 118 ELILEDELQRIPLHGNI 134 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~i 134 (216)
.+|||-++|||+|.-..
T Consensus 5 NIfLEsd~grvkl~~~~ 21 (132)
T PHA03001 5 NIFLETDAGRVKLAIEN 21 (132)
T ss_pred EEEEeccCCceEEEEcC
Confidence 48999999999998653
No 59
>PRK07218 replication factor A; Provisional
Probab=20.15 E-value=1.9e+02 Score=27.79 Aligned_cols=42 Identities=24% Similarity=0.273 Sum_probs=26.9
Q ss_pred eEEEecCCCcEEEEeccCCCCceeeeEEEEEeccCC--CCcEEE
Q psy8637 118 ELILEDELQRIPLHGNIDIHNQVTGVVVAIKGTPVG--NGKFKV 159 (216)
Q Consensus 118 ~l~LEDesgRI~L~G~i~~~~lVTGvVvaV~G~~~~--~G~F~V 159 (216)
..+|.|+||||+++-=-+...+--|-++-|.|.... +|.+++
T Consensus 200 ~giigDeTG~Ir~tlW~~~~~l~~Gd~v~I~na~v~e~~G~~el 243 (423)
T PRK07218 200 SGVLADETGRLPFTDWDPLPEIEIGASIRIEDAYVREFRGVPSV 243 (423)
T ss_pred EEEEECCCceEEEEEecccccCCCCCEEEEeeeEEeccCCeEEE
Confidence 468999999999983111224556777777775443 355444
Done!