Query 041604
Match_columns 162
No_of_seqs 113 out of 607
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 08:53:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041604.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041604hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13165 cytochrome c-type bio 100.0 1.9E-43 4.1E-48 283.5 15.7 135 2-157 19-157 (160)
2 PRK13159 cytochrome c-type bio 100.0 2.7E-43 5.8E-48 281.5 15.8 126 2-151 19-144 (155)
3 PRK13150 cytochrome c-type bio 100.0 6.2E-43 1.3E-47 280.4 15.7 129 2-151 19-151 (159)
4 PRK13254 cytochrome c-type bio 100.0 5.1E-42 1.1E-46 271.4 15.7 126 2-151 19-144 (148)
5 PF03100 CcmE: CcmE; InterPro 100.0 6.2E-41 1.3E-45 257.8 12.2 115 1-138 17-131 (131)
6 COG2332 CcmE Cytochrome c-type 100.0 2.1E-40 4.5E-45 264.1 13.2 130 2-154 19-148 (153)
7 PF03843 Slp: Outer membrane l 95.3 0.065 1.4E-06 43.0 6.7 80 14-96 13-105 (160)
8 cd04482 RPA2_OBF_like RPA2_OBF 94.9 0.47 1E-05 34.5 9.6 55 40-96 2-62 (91)
9 PF13742 tRNA_anti_2: OB-fold 94.6 0.23 5E-06 36.4 7.4 58 35-95 20-82 (99)
10 PF01336 tRNA_anti-codon: OB-f 94.5 0.095 2.1E-06 34.4 4.8 55 39-96 1-59 (75)
11 cd04489 ExoVII_LU_OBF ExoVII_L 93.4 1.2 2.7E-05 29.9 8.6 55 38-95 1-59 (78)
12 cd04487 RecJ_OBF2_like RecJ_OB 93.3 0.78 1.7E-05 32.2 7.7 53 39-95 1-57 (73)
13 cd04488 RecG_wedge_OBF RecG_we 92.9 1.1 2.3E-05 29.0 7.5 40 56-95 17-59 (75)
14 PRK00286 xseA exodeoxyribonucl 92.5 2 4.4E-05 38.5 11.1 111 19-153 4-120 (438)
15 TIGR00752 slp outer membrane l 91.1 2.6 5.7E-05 34.9 9.5 69 22-96 35-118 (182)
16 cd04478 RPA2_DBD_D RPA2_DBD_D: 90.4 2.5 5.5E-05 29.6 7.7 54 39-96 2-62 (95)
17 COG1570 XseA Exonuclease VII, 90.3 2.6 5.7E-05 39.4 9.7 111 18-152 3-119 (440)
18 cd04490 PolII_SU_OBF PolII_SU_ 89.7 5.6 0.00012 28.1 9.1 54 39-95 2-61 (79)
19 TIGR00237 xseA exodeoxyribonuc 87.5 9.1 0.0002 34.9 11.1 93 37-153 18-114 (432)
20 cd04485 DnaE_OBF DnaE_OBF: A s 85.6 3.9 8.4E-05 26.7 5.8 56 41-96 2-62 (84)
21 PF15490 Ten1_2: Telomere-capp 82.4 12 0.00026 29.0 8.1 69 19-95 6-78 (118)
22 TIGR00457 asnS asparaginyl-tRN 81.2 30 0.00066 31.9 11.6 81 34-134 14-107 (453)
23 PF08661 Rep_fac-A_3: Replicat 80.8 20 0.00044 26.4 10.4 69 16-96 3-71 (109)
24 PF11736 DUF3299: Protein of u 79.0 14 0.00031 29.4 7.7 59 34-96 53-123 (146)
25 cd03524 RPA2_OBF_family RPA2_O 78.3 11 0.00023 23.3 5.7 39 57-95 17-60 (75)
26 cd04317 EcAspRS_like_N EcAspRS 77.2 20 0.00043 27.0 7.8 57 35-96 13-76 (135)
27 PF13567 DUF4131: Domain of un 76.6 22 0.00048 25.7 7.6 58 36-96 75-143 (176)
28 PRK04036 DNA polymerase II sma 75.6 25 0.00055 32.7 9.5 69 35-127 152-227 (504)
29 cd04492 YhaM_OBF_like YhaM_OBF 74.7 12 0.00025 24.8 5.3 39 57-95 19-60 (83)
30 PRK05159 aspC aspartyl-tRNA sy 70.6 55 0.0012 29.9 10.3 58 34-96 14-79 (437)
31 cd04483 hOBFC1_like hOBFC1_lik 69.1 40 0.00087 24.4 7.5 51 41-95 2-76 (92)
32 cd04484 polC_OBF polC_OBF: A s 68.2 39 0.00085 23.8 7.3 57 39-95 2-64 (82)
33 PLN02603 asparaginyl-tRNA synt 66.7 68 0.0015 30.9 10.4 82 34-135 105-198 (565)
34 PTZ00417 lysine-tRNA ligase; P 65.7 61 0.0013 31.3 9.9 71 21-95 112-199 (585)
35 PRK10917 ATP-dependent DNA hel 65.2 23 0.0005 34.0 7.0 61 35-96 58-122 (681)
36 cd04316 ND_PkAspRS_like_N ND_P 65.2 50 0.0011 23.9 11.7 57 35-96 11-76 (108)
37 cd04100 Asp_Lys_Asn_RS_N Asp_L 64.8 43 0.00094 23.0 7.8 54 38-96 1-62 (85)
38 TIGR00643 recG ATP-dependent D 64.6 50 0.0011 31.4 9.0 61 35-95 31-94 (630)
39 PRK03932 asnC asparaginyl-tRNA 64.4 87 0.0019 28.8 10.3 92 21-135 4-105 (450)
40 PRK02983 lysS lysyl-tRNA synth 63.4 1.5E+02 0.0033 30.7 12.6 65 22-95 641-715 (1094)
41 cd04474 RPA1_DBD_A RPA1_DBD_A: 61.9 35 0.00075 24.9 6.0 62 34-95 7-78 (104)
42 PLN02502 lysyl-tRNA synthetase 61.1 1.6E+02 0.0034 28.3 12.1 70 21-95 88-174 (553)
43 cd04322 LysRS_N LysRS_N: N-ter 60.5 62 0.0013 23.4 7.4 53 38-95 1-63 (108)
44 PF04076 BOF: Bacterial OB fol 59.5 57 0.0012 24.6 6.9 67 18-95 20-88 (103)
45 TIGR00499 lysS_bact lysyl-tRNA 59.4 1.5E+02 0.0033 27.8 11.0 70 21-95 32-117 (496)
46 cd04491 SoSSB_OBF SoSSB_OBF: A 58.9 55 0.0012 22.3 6.8 41 55-95 21-63 (82)
47 cd04320 AspRS_cyto_N AspRS_cyt 56.3 71 0.0015 22.8 11.3 55 38-96 1-66 (102)
48 PRK07373 DNA polymerase III su 55.6 55 0.0012 30.4 7.5 61 35-95 279-344 (449)
49 PRK00476 aspS aspartyl-tRNA sy 54.4 1.3E+02 0.0027 29.1 9.8 65 22-96 7-78 (588)
50 PLN02903 aminoacyl-tRNA ligase 54.2 1.9E+02 0.0041 28.5 11.1 57 34-95 70-134 (652)
51 PRK12445 lysyl-tRNA synthetase 53.0 1.9E+02 0.0041 27.3 10.6 56 36-95 65-129 (505)
52 COG1200 RecG RecG-like helicas 52.5 71 0.0015 31.7 7.9 62 35-96 59-123 (677)
53 TIGR00156 conserved hypothetic 48.1 1.4E+02 0.0029 23.6 7.7 66 20-96 45-112 (126)
54 KOG0554 Asparaginyl-tRNA synth 48.0 58 0.0012 30.8 6.3 57 34-95 18-77 (446)
55 COG0017 AsnS Aspartyl/asparagi 45.5 1E+02 0.0022 29.1 7.5 67 21-96 5-79 (435)
56 smart00276 GLECT Galectin. Gal 43.4 41 0.00088 25.2 3.9 23 74-96 1-23 (128)
57 cd04497 hPOT1_OB1_like hPOT1_O 42.4 1.5E+02 0.0033 22.6 8.7 69 19-93 2-80 (138)
58 PTZ00401 aspartyl-tRNA synthet 39.3 3.6E+02 0.0077 25.9 11.3 70 19-95 64-142 (550)
59 cd04323 AsnRS_cyto_like_N AsnR 39.2 1.3E+02 0.0028 20.7 8.5 54 38-96 1-61 (84)
60 PRK00484 lysS lysyl-tRNA synth 39.1 3.3E+02 0.0072 25.5 11.6 70 21-95 33-117 (491)
61 PRK09507 cspE cold shock prote 39.0 1.3E+02 0.0028 20.7 7.0 48 48-95 6-57 (69)
62 PRK10053 hypothetical protein; 38.6 2E+02 0.0043 22.8 7.4 63 22-95 51-115 (130)
63 PRK13480 3'-5' exoribonuclease 38.2 2.4E+02 0.0052 25.1 8.5 61 35-95 10-74 (314)
64 PLN02850 aspartate-tRNA ligase 37.9 2.4E+02 0.0053 26.8 8.9 68 19-95 68-146 (530)
65 cd04319 PhAsnRS_like_N PhAsnRS 37.9 1.5E+02 0.0033 21.2 8.4 55 38-96 1-62 (103)
66 cd00070 GLECT Galectin/galacto 37.9 60 0.0013 24.1 4.1 23 74-96 2-24 (127)
67 PF00337 Gal-bind_lectin: Gala 37.4 22 0.00047 26.4 1.6 23 74-96 2-24 (133)
68 PF10451 Stn1: Telomere regula 36.0 1.5E+02 0.0033 25.6 6.7 60 34-95 64-133 (256)
69 KOG3818 DNA polymerase epsilon 35.7 1.1E+02 0.0023 29.6 6.1 80 14-126 157-238 (525)
70 KOG2732 DNA polymerase delta, 35.6 89 0.0019 29.5 5.5 53 56-129 108-160 (435)
71 COG3065 Slp Starvation-inducib 35.0 1.6E+02 0.0036 25.0 6.5 59 33-96 50-123 (191)
72 PLN02221 asparaginyl-tRNA synt 34.3 1.7E+02 0.0036 28.4 7.3 71 21-95 33-112 (572)
73 PF12869 tRNA_anti-like: tRNA_ 34.3 55 0.0012 24.4 3.4 71 21-95 45-130 (144)
74 cd04486 YhcR_OBF_like YhcR_OBF 33.9 1.5E+02 0.0032 20.9 5.3 37 59-96 16-59 (78)
75 PRK06461 single-stranded DNA-b 33.5 2.2E+02 0.0047 21.7 8.1 57 37-93 15-76 (129)
76 PRK07459 single-stranded DNA-b 33.2 2.2E+02 0.0047 21.6 6.6 60 37-96 4-76 (121)
77 cd04321 ScAspRS_mt_like_N ScAs 32.8 1.7E+02 0.0037 20.3 7.8 55 38-96 1-62 (86)
78 KOG1625 DNA polymerase alpha-p 32.6 2E+02 0.0044 28.3 7.5 85 33-138 241-332 (600)
79 cd04479 RPA3 RPA3: A subfamily 32.4 2E+02 0.0043 21.0 11.3 62 20-96 4-66 (101)
80 TIGR00458 aspS_arch aspartyl-t 32.2 4E+02 0.0086 24.4 11.3 56 35-95 11-75 (428)
81 PRK12820 bifunctional aspartyl 31.1 5.5E+02 0.012 25.7 11.1 57 35-96 17-82 (706)
82 COG1665 Predicted nucleotidylt 30.9 1.1E+02 0.0023 27.9 5.0 58 36-96 231-291 (315)
83 COG3689 Predicted membrane pro 30.5 1.2E+02 0.0025 27.1 5.2 75 20-96 159-238 (271)
84 PRK05673 dnaE DNA polymerase I 30.5 2.3E+02 0.005 29.6 8.0 61 35-95 976-1041(1135)
85 PRK08182 single-stranded DNA-b 30.0 2.7E+02 0.0059 21.9 6.8 59 37-95 3-85 (148)
86 PLN03094 Substrate binding sub 29.8 1.8E+02 0.0038 26.7 6.4 58 18-80 117-185 (370)
87 PF11948 DUF3465: Protein of u 29.6 2.9E+02 0.0064 22.1 9.1 58 38-95 36-99 (131)
88 cd04318 EcAsnRS_like_N EcAsnRS 29.5 1.8E+02 0.004 19.7 6.9 54 38-96 1-62 (82)
89 PTZ00425 asparagine-tRNA ligas 26.0 2.4E+02 0.0053 27.4 6.9 58 34-95 79-145 (586)
90 PRK06293 single-stranded DNA-b 25.8 3E+02 0.0065 22.4 6.4 59 38-96 3-75 (161)
91 PRK06920 dnaE DNA polymerase I 25.5 2.4E+02 0.0051 29.6 7.1 61 35-95 942-1007(1107)
92 PRK00448 polC DNA polymerase I 24.1 6.9E+02 0.015 27.1 10.2 62 35-96 235-303 (1437)
93 PRK07772 single-stranded DNA-b 23.3 3.9E+02 0.0086 22.1 6.8 61 36-96 4-85 (186)
94 TIGR02922 conserved hypothetic 22.6 33 0.00071 24.6 0.3 28 68-95 25-56 (67)
95 TIGR03503 conserved hypothetic 22.5 6.2E+02 0.014 23.4 8.8 49 75-136 140-188 (374)
96 PF09558 DUF2375: Protein of u 22.4 42 0.0009 24.4 0.8 28 68-95 27-58 (71)
97 PF14584 DUF4446: Protein of u 21.6 3.4E+02 0.0073 21.7 5.9 72 37-146 78-150 (151)
98 PRK07374 dnaE DNA polymerase I 21.4 3E+02 0.0064 29.0 6.9 61 35-95 999-1064(1170)
99 KOG3206 Alpha-tubulin folding 20.6 1.2E+02 0.0025 26.6 3.2 47 68-135 165-211 (234)
100 PRK08763 single-stranded DNA-b 20.4 4.6E+02 0.0099 21.2 6.5 60 36-95 5-83 (164)
101 PF09144 YpM: Yersinia pseudot 20.4 25 0.00054 27.1 -0.7 8 124-131 109-116 (117)
102 TIGR00996 Mtu_fam_mce virulenc 20.1 2.7E+02 0.0059 23.2 5.4 47 15-66 31-80 (291)
No 1
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=100.00 E-value=1.9e-43 Score=283.49 Aligned_cols=135 Identities=34% Similarity=0.578 Sum_probs=121.9
Q ss_pred hhhHHHHHHHHhhcCeeeeeCHHHHHhhcCC----CCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCC
Q 041604 2 IAGFIVIVLNNFQDQLVFYVTPSEALEKYQS----NPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGS 77 (162)
Q Consensus 2 ia~~i~l~l~~~~~~~~yy~tpsE~~~~~~~----~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~ 77 (162)
++++++|++++|++|++||+||||+++..++ .+.+++|||+|+|++|||.|++++.+++|.|||+..+++|+|+|+
T Consensus 19 ~~~a~~L~l~al~~n~~yF~tPsev~~~~~~~~~~~~~g~~iRvgG~V~~GSi~r~~~~l~v~F~vtD~~~~v~V~Y~Gi 98 (160)
T PRK13165 19 LALTIGLVLYALRSNIDLFYTPGEILYGKRETQQKPEVGQRLRVGGMVMPGSVQRDPNSLKVSFTLYDAGGSVTVTYEGI 98 (160)
T ss_pred HHHHHHHHHHHHhhCccEEeCHHHHhccccccccccCCCCEEEEeeEEeCCcEEECCCCeEEEEEEEcCCeEEEEEEccc
Confidence 4567899999999999999999999986432 246899999999999999998888899999999999999999999
Q ss_pred CCCCCCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhHHHHhhh
Q 041604 78 LPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQQEE 157 (162)
Q Consensus 78 ~Pd~F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~~~~~~~ 157 (162)
+||+|+||++|||+|+|++ +|+|+|++|||||||||||+|++++|+++++.+......+
T Consensus 99 lPDlFrEG~gVVveG~~~~---------------------~g~F~A~~vLAKhdekYmPpEv~~al~~~~~~~~~~~~~~ 157 (160)
T PRK13165 99 LPDLFREGQGIVAQGVLEE---------------------GNHIEAKEVLAKHDENYTPPEVEEAMKKNHRRPAYSYKDK 157 (160)
T ss_pred CCccccCCCeEEEEEEECC---------------------CCeEEEEEEEecCCCCCCCHHHHHHHHhccCCCCcccccc
Confidence 9999999999999999985 6899999999999999999999999999888776654433
No 2
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=100.00 E-value=2.7e-43 Score=281.49 Aligned_cols=126 Identities=35% Similarity=0.562 Sum_probs=118.1
Q ss_pred hhhHHHHHHHHhhcCeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCCCCC
Q 041604 2 IAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDL 81 (162)
Q Consensus 2 ia~~i~l~l~~~~~~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~Pd~ 81 (162)
++++++|++++|++|++||+||||+.+... ..++.+||||+|++|||.|++++..++|.|||+..+++|+|+|++||+
T Consensus 19 ~~~a~~Lv~~al~~n~~yF~tpsEv~~~~~--~~~~~~RlGG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~GilPDl 96 (155)
T PRK13159 19 AALAVTLIVLALQRNMSYLFTPSQVRAGAA--AGYQQFRLGGMVKAGSIQRAADSLKVSFTVIDKNAATQVEYTGILPDL 96 (155)
T ss_pred HHHHHHHHHHHhhhCceEEECHHHHhcCCc--ccCCeEEEccEEecCcEEEcCCCcEEEEEEEcCCcEEEEEEccCCCcc
Confidence 567889999999999999999999998643 467999999999999999988888999999999999999999999999
Q ss_pred CCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhH
Q 041604 82 FREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLE 151 (162)
Q Consensus 82 F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~ 151 (162)
|+||++||++|+|+ +|+|+|++|||||||||||+|++++|++.+.|-.
T Consensus 97 FrEGqgVVaeG~~~----------------------~g~F~A~~vLAKHde~YmP~Ev~~al~~~~~~~~ 144 (155)
T PRK13159 97 FRDNQSVIANGRMQ----------------------GGRFVANEVLAKHDETYMPKELKDAMAEGHLGKP 144 (155)
T ss_pred ccCCCeEEEEEEEc----------------------CCEEEEeEEEecCCCcCCCHHHHHHHHhccccCC
Confidence 99999999999998 6899999999999999999999999999987754
No 3
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=100.00 E-value=6.2e-43 Score=280.37 Aligned_cols=129 Identities=35% Similarity=0.582 Sum_probs=117.1
Q ss_pred hhhHHHHHHHHhhcCeeeeeCHHHHHhhcC----CCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCC
Q 041604 2 IAGFIVIVLNNFQDQLVFYVTPSEALEKYQ----SNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGS 77 (162)
Q Consensus 2 ia~~i~l~l~~~~~~~~yy~tpsE~~~~~~----~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~ 77 (162)
++++++|++++|++|++||+||||+++... ..+.+++|||+|+|++|||.|.+++..++|.|||+..+|+|+|+|+
T Consensus 19 ~~~a~~Lvl~al~~n~~yF~tPsev~~~~~~~~~~~~~g~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~Gi 98 (159)
T PRK13150 19 LGLTTALVLYALRANIDLFYTPGEILYGKRETQQLPAVGQRLRVGGMVMPGSVRRDPDSLKVNFSLYDAEGSVTVSYEGI 98 (159)
T ss_pred HHHHHHHHHHHHhhCccEEeCHHHHhccccccccCcCCCCEEEEeeEEeCCcEEECCCCcEEEEEEEcCCcEEEEEEecc
Confidence 567889999999999999999999986431 1246899999999999999998888899999999999999999999
Q ss_pred CCCCCCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhH
Q 041604 78 LPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLE 151 (162)
Q Consensus 78 ~Pd~F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~ 151 (162)
+||+|+||++||++|+|++ +|+|+|++|||||||||||+|++++|++.++.-.
T Consensus 99 lPDlFrEG~gVVveG~~~~---------------------~g~F~A~evLAKhdekYmPpEv~~al~~~~~~~~ 151 (159)
T PRK13150 99 LPDLFREGQGVVVQGTLEK---------------------GNHVLAHEVLAKHDENYTPPEVEKAMQENHRRPQ 151 (159)
T ss_pred CCccccCCCeEEEEEEECC---------------------CCEEEEeEEEeCCCCCCCCHHHHHHHHHhCCCCc
Confidence 9999999999999999985 6999999999999999999999999988776543
No 4
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=100.00 E-value=5.1e-42 Score=271.41 Aligned_cols=126 Identities=45% Similarity=0.706 Sum_probs=117.3
Q ss_pred hhhHHHHHHHHhhcCeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCCCCC
Q 041604 2 IAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDL 81 (162)
Q Consensus 2 ia~~i~l~l~~~~~~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~Pd~ 81 (162)
++++++|++++|++|++||+||||+.+.. .+.++.|||+|+|++||+.+. ++..++|.|+|+..+|+|+|+|++||+
T Consensus 19 ~~~~~~L~~~a~~~~~~yf~tpse~~~~~--~~~g~~vrvgG~V~~gSi~~~-~~~~~~F~ltD~~~~i~V~Y~G~lPd~ 95 (148)
T PRK13254 19 LGLAVALVLYALRQNIVFFYTPSEVAEGE--APAGRRFRLGGLVEKGSVQRG-DGLTVRFVVTDGNATVPVVYTGILPDL 95 (148)
T ss_pred HHHHHHHHHHHHHhCCceeeCHHHHhcCC--ccCCCeEEEeEEEecCcEEeC-CCCEEEEEEEeCCeEEEEEECCCCCcc
Confidence 56788999999999999999999998864 257999999999999999997 788999999999999999999999999
Q ss_pred CCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhH
Q 041604 82 FREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLE 151 (162)
Q Consensus 82 F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~ 151 (162)
|+||++|||+|+|++ +|+|+|++||+||||||||+|+++++++.++|.+
T Consensus 96 F~eg~~VVv~G~~~~---------------------~g~F~A~~vLaKc~skY~p~ev~~~~~~~~~~~~ 144 (148)
T PRK13254 96 FREGQGVVAEGRLQD---------------------GGVFVADEVLAKHDENYMPKEVADALKKAGVWKD 144 (148)
T ss_pred ccCCCEEEEEEEECC---------------------CCeEEEEEEEecCCCCCCCHHHHHHHHHhccccC
Confidence 999999999999985 6799999999999999999999999999887754
No 5
>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=100.00 E-value=6.2e-41 Score=257.85 Aligned_cols=115 Identities=48% Similarity=0.732 Sum_probs=79.9
Q ss_pred ChhhHHHHHHHHhhcCeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCCCC
Q 041604 1 CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPD 80 (162)
Q Consensus 1 ~ia~~i~l~l~~~~~~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~Pd 80 (162)
+|+++++|++++++++++||+||+|+++..+ ..++.+||+|+|++||++|+++++.++|.|+|+.++++|+|+|++||
T Consensus 17 ~i~~~~~l~~~~~~~~~~yy~t~se~~~~~~--~~~~~vrv~G~V~~gSv~~~~~~~~~~F~i~D~~~~i~V~Y~G~~Pd 94 (131)
T PF03100_consen 17 IIAAAIYLILYSFSDSAVYYLTPSELAAEPQ--KVGRKVRVGGLVVEGSVEYDPDGNTLTFTITDGGKEIPVVYTGPLPD 94 (131)
T ss_dssp ---------------SSS-EE-TTTTTTTST---TTSEEEEEEEEECTTEEE-TTSSEEEEEEE-SS-EEEEEEES--CT
T ss_pred HHHHHHHHHHHHhhccceEEcCHHHHhhccc--cCCceEEEeeEEccCCEEEcCCCCEEEEEEEECCcEEEEEECCCCCc
Confidence 4678899999999999999999999998764 48999999999999999999889999999999999999999999999
Q ss_pred CCCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChH
Q 041604 81 LFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQE 138 (162)
Q Consensus 81 ~F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~e 138 (162)
+|+||++|||+|+|.. +|+|+|++||+||||||||+|
T Consensus 95 ~F~eg~~VVv~G~~~~---------------------~g~F~A~~lL~KcpskY~p~e 131 (131)
T PF03100_consen 95 LFREGQGVVVEGRLGE---------------------DGVFEATELLAKCPSKYMPPE 131 (131)
T ss_dssp T--TTSEEEEEEEECC---------------------TSEEEEEEEEETS------HH
T ss_pred cccCCCeEEEEEEECC---------------------CCEEEEEEEEeCCCCCCCCCC
Confidence 9999999999999953 799999999999999999986
No 6
>COG2332 CcmE Cytochrome c-type biogenesis protein CcmE [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.1e-40 Score=264.12 Aligned_cols=130 Identities=44% Similarity=0.661 Sum_probs=121.1
Q ss_pred hhhHHHHHHHHhhcCeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCCCCC
Q 041604 2 IAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDL 81 (162)
Q Consensus 2 ia~~i~l~l~~~~~~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~Pd~ 81 (162)
|++++.|+|+++.+|+.||+||+|+.+.. ...++++|+||+|++||+++++++..++|+|+|...+++|.|+|+|||+
T Consensus 19 l~~a~~l~Lyal~~ni~~fy~Psel~~~~--~~~G~rlR~GGlV~~GSv~R~~~~~~v~F~vtD~~~~v~V~Y~GiLPDL 96 (153)
T COG2332 19 LALAVGLVLYALRSNIDYFYTPSELLEGK--VETGQRLRLGGLVEAGSVQRDPGSLKVSFVVTDGNKSVTVSYEGILPDL 96 (153)
T ss_pred HHHHHHHHHhhhccCceEEECHHHhcccc--ccCCcEEEEeeeEeeceEEecCCCcEEEEEEecCCceEEEEEeccCchh
Confidence 67788999999999999999999998764 3568999999999999999999999999999999999999999999999
Q ss_pred CCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhHHHH
Q 041604 82 FREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQ 154 (162)
Q Consensus 82 F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~~~~ 154 (162)
||||++||++|.|.. .++|+|++|||||||+|+|+|++++|++++.|+....
T Consensus 97 FREGQgVVa~G~~~~---------------------~~~f~A~~vLAKHdEnY~P~ev~~~mk~~~~~~~~~~ 148 (153)
T COG2332 97 FREGQGVVAEGQLQG---------------------GGVFEAKEVLAKHDENYTPPEVAKAMKKNGVWLGKAE 148 (153)
T ss_pred hhcCCeEEEEEEecC---------------------CCEEEeeehhhcCCcccCCHHHHHHhhhcCCcccccc
Confidence 999999999999973 4899999999999999999999999999999987443
No 7
>PF03843 Slp: Outer membrane lipoprotein Slp family; InterPro: IPR004658 Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli (which also contains a close paralog), Haemophilus influenzae and Pasteurella multocida and Vibrio cholerae. The known members of the family to date share a motif LX[GA]C near the N terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N terminus. Slp from E. coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation.; GO: 0019867 outer membrane
Probab=95.33 E-value=0.065 Score=42.98 Aligned_cols=80 Identities=21% Similarity=0.312 Sum_probs=57.3
Q ss_pred hcCeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEE---EEEEeC---------CeEEEEEEcCC-CCC
Q 041604 14 QDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME---FVVTDL---------VTDILVRYQGS-LPD 80 (162)
Q Consensus 14 ~~~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~---F~vtD~---------~~~i~V~Y~G~-~Pd 80 (162)
.+...--++++++++++. .+.|+.||+||.|.. +...++...++ |-|-.. ..+..|++.|- =|.
T Consensus 13 ~~~~~~~~~~~~v~~~p~-~~~G~~VrwGG~I~~--v~n~~~~T~leV~~~PLd~~grP~~~~~s~GRFla~~~gFLDP~ 89 (160)
T PF03843_consen 13 RDQVDPQPSFSQVRANPD-AYQGQQVRWGGVIVN--VRNLPDQTELEVVQYPLDSSGRPQTDDPSQGRFLARVPGFLDPA 89 (160)
T ss_pred cCCCCccCCHHHHHhChh-hcCCCEEEECCEEEE--EEECCCceEEEEEEccCCCCCCcCCCCCCCCEEEEEeCCCcCHH
Confidence 345566789999998875 578999999999973 44333333332 111111 25889999995 478
Q ss_pred CCCCCCeEEEEEEEcC
Q 041604 81 LFREGHSVVVEGFIKP 96 (162)
Q Consensus 81 ~F~eg~~VVveG~~~~ 96 (162)
.|++|+.|.|.|++..
T Consensus 90 ~y~~Gr~vTV~G~v~g 105 (160)
T PF03843_consen 90 IYAPGRLVTVVGTVTG 105 (160)
T ss_pred HcCCCCEEEEEEEecc
Confidence 9999999999999974
No 8
>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=94.91 E-value=0.47 Score=34.45 Aligned_cols=55 Identities=25% Similarity=0.414 Sum_probs=40.8
Q ss_pred EEeEEEecCcEEecCCCceEEEEEEeCCeEEE-EEEcCC-----CCCCCCCCCeEEEEEEEcC
Q 041604 40 RLGGLVLEGSVAHPASSSEMEFVVTDLVTDIL-VRYQGS-----LPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 40 rv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~-V~Y~G~-----~Pd~F~eg~~VVveG~~~~ 96 (162)
+|.|.|.. +.+...+.++-|.|.|....|. |.|... +....++|+.|+|.|.+..
T Consensus 2 ~v~GeVs~--~~~~~~sGH~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~v~~ 62 (91)
T cd04482 2 RVTGKVVE--EPRTIEGGHVFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGSVRP 62 (91)
T ss_pred EEEEEEeC--CeecCCCCCEEEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEEEEEec
Confidence 57787753 2232135689999999987776 466554 6678899999999999974
No 9
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=94.62 E-value=0.23 Score=36.44 Aligned_cols=58 Identities=17% Similarity=0.281 Sum_probs=44.7
Q ss_pred CCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEE-EcCC---CC-CCCCCCCeEEEEEEEc
Q 041604 35 SKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVR-YQGS---LP-DLFREGHSVVVEGFIK 95 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~-Y~G~---~P-d~F~eg~~VVveG~~~ 95 (162)
.-..+.|.|.|.. +... .+.++=|.|.|+...|... |... ++ ..+++|..|+|.|++.
T Consensus 20 ~~~~vwV~GEIs~--~~~~-~~gh~YftLkD~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~ 82 (99)
T PF13742_consen 20 PLPNVWVEGEISN--LKRH-SSGHVYFTLKDEEASISCVIFRSRARRIRGFDLKDGDKVLVRGRVS 82 (99)
T ss_pred CcCCEEEEEEEee--cEEC-CCceEEEEEEcCCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEE
Confidence 3479999999974 3332 4578999999999888655 4432 44 7899999999999985
No 10
>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=94.54 E-value=0.095 Score=34.43 Aligned_cols=55 Identities=22% Similarity=0.271 Sum_probs=43.9
Q ss_pred EEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcC----CCCCCCCCCCeEEEEEEEcC
Q 041604 39 FRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQG----SLPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 39 vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G----~~Pd~F~eg~~VVveG~~~~ 96 (162)
|+|.|.|..=+ . ..+..+.|.|.|+...+.+.+-. ...+.+++|..|.|.|+++.
T Consensus 1 V~v~G~V~~~~--~-~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~ 59 (75)
T PF01336_consen 1 VTVEGRVTSIR--R-SGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVRGKVKR 59 (75)
T ss_dssp EEEEEEEEEEE--E-EETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEEEEEEE
T ss_pred CEEEEEEEEEE--c-CCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEEEEEEE
Confidence 57889887322 2 34578899999999999999888 56678999999999999974
No 11
>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=93.38 E-value=1.2 Score=29.87 Aligned_cols=55 Identities=22% Similarity=0.257 Sum_probs=41.6
Q ss_pred cEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEc-C---CCCCCCCCCCeEEEEEEEc
Q 041604 38 KFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQ-G---SLPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 38 ~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~-G---~~Pd~F~eg~~VVveG~~~ 95 (162)
.++|.|.|..-.. ...+ ..-|.|.|....+.+..- . ...+.+.+|..|+++|+++
T Consensus 1 ~~~v~g~v~~i~~--tk~g-~~~~~L~D~~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g~v~ 59 (78)
T cd04489 1 RVWVEGEISNLKR--PSSG-HLYFTLKDEDASIRCVMWRSNARRLGFPLEEGMEVLVRGKVS 59 (78)
T ss_pred CEEEEEEEecCEE--CCCc-EEEEEEEeCCeEEEEEEEcchhhhCCCCCCCCCEEEEEEEEE
Confidence 3689999985333 2334 788999999888876443 3 4678999999999999997
No 12
>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=93.31 E-value=0.78 Score=32.17 Aligned_cols=53 Identities=17% Similarity=0.224 Sum_probs=40.2
Q ss_pred EEEeEEEecCcEEecCCCceEEEEEEeCCeEEEE-EEcC---CCCCCCCCCCeEEEEEEEc
Q 041604 39 FRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILV-RYQG---SLPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 39 vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V-~Y~G---~~Pd~F~eg~~VVveG~~~ 95 (162)
++|.|.|..-. + .+.++-|.|.|....|+. .|.+ .++...++|..|++.|+++
T Consensus 1 v~v~GeVs~~~--~--~~GHvyfsLkD~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~ 57 (73)
T cd04487 1 VHIEGEVVQIK--Q--TSGPTIFTLRDETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGEVE 57 (73)
T ss_pred CEEEEEEeccc--c--CCCCEEEEEEcCCEEEEEEEEchhccCCcCCCCCCCEEEEEEEEe
Confidence 46778776443 2 356799999999877765 4543 3677889999999999986
No 13
>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=92.94 E-value=1.1 Score=28.98 Aligned_cols=40 Identities=18% Similarity=0.265 Sum_probs=33.7
Q ss_pred CceEEEEEEeCCeEEEEEEcCC---CCCCCCCCCeEEEEEEEc
Q 041604 56 SSEMEFVVTDLVTDILVRYQGS---LPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 56 ~~~~~F~vtD~~~~i~V~Y~G~---~Pd~F~eg~~VVveG~~~ 95 (162)
...++|.+.|+...+.+++=+. +...|+.|..+.+.|++.
T Consensus 17 ~~~~~~~~~D~~g~i~~~~F~~~~~~~~~~~~G~~~~v~Gkv~ 59 (75)
T cd04488 17 RRRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVSGKVK 59 (75)
T ss_pred ccEEEEEEEcCCCEEEEEEECCCHHHHhcCCCCCEEEEEEEEe
Confidence 3579999999998888877653 456899999999999997
No 14
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=92.49 E-value=2 Score=38.54 Aligned_cols=111 Identities=21% Similarity=0.193 Sum_probs=73.9
Q ss_pred eeeCHHHHHhhcCCCC--CCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEE-EcC---CCCCCCCCCCeEEEEE
Q 041604 19 FYVTPSEALEKYQSNP--SKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVR-YQG---SLPDLFREGHSVVVEG 92 (162)
Q Consensus 19 yy~tpsE~~~~~~~~~--~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~-Y~G---~~Pd~F~eg~~VVveG 92 (162)
-++|+||+...-.... .-..|.|.|-|.. +.+. .+.++=|.|.|....|... |.+ .++-.+++|..|+|.|
T Consensus 4 ~~~svsel~~~ik~~le~~~~~v~v~gEis~--~~~~-~sGH~Yf~Lkd~~a~i~~~~~~~~~~~~~~~~~~G~~v~v~g 80 (438)
T PRK00286 4 KILSVSELNRYVKSLLERDLGQVWVRGEISN--FTRH-SSGHWYFTLKDEIAQIRCVMFKGSARRLKFKPEEGMKVLVRG 80 (438)
T ss_pred CcCcHHHHHHHHHHHHHhhCCcEEEEEEeCC--CeeC-CCCeEEEEEEcCCcEEEEEEEcChhhcCCCCCCCCCEEEEEE
Confidence 3688998874322100 1468999999864 3333 3558999999999888654 444 4667789999999999
Q ss_pred EEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhHHH
Q 041604 93 FIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQ 153 (162)
Q Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~~~ 153 (162)
++.- - ...|.=.|.+++|- ..+. .+.+...++.++.|++.
T Consensus 81 ~~~~--------------y--~~~g~~ql~v~~i~----~~g~-G~l~~~~~~lk~~L~~e 120 (438)
T PRK00286 81 KVSL--------------Y--EPRGDYQLIVEEIE----PAGI-GALAAAFEQLKEKLAAE 120 (438)
T ss_pred EEEE--------------E--CCCCCEEEEEEEee----eCCc-cHHHHHHHHHHHHHHHC
Confidence 9861 0 11123356677764 3455 67788888887777653
No 15
>TIGR00752 slp outer membrane lipoprotein, Slp family. Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli, which also contains a close paralog, Haemophilus influenzae and Pasteurella multocida and Vibrio cholera. The known members of the family to date share a motif LX[GA]C near the N-terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N-terminus. Slp from Escherichia coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation.
Probab=91.08 E-value=2.6 Score=34.90 Aligned_cols=69 Identities=19% Similarity=0.200 Sum_probs=47.7
Q ss_pred CHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEE-----eC---------CeEEEEEEcCC-CCCCCCCCC
Q 041604 22 TPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVT-----DL---------VTDILVRYQGS-LPDLFREGH 86 (162)
Q Consensus 22 tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vt-----D~---------~~~i~V~Y~G~-~Pd~F~eg~ 86 (162)
+.+++..+++ .+.++.+|+||.|.. +....+. .++.|. +. ..++.+..+|- =|..| +|+
T Consensus 35 ~~~~v~~~p~-~y~G~~Vr~GG~I~~--v~N~~~~--T~lEVv~~PLd~~grP~~~~~s~GRFla~~~gFLDP~~y-~Gr 108 (182)
T TIGR00752 35 SYVEVSPQPL-LYVGQTARFGGKVVN--VTNLANQ--TKLEIASLPLDSIAKPFVELQSDGRFIAYFNGFLDPVNL-RER 108 (182)
T ss_pred chHHHhhChh-hcCCCEEEECCEEEE--EEECCCc--eEEEEEEcccCCCCCcCCCCCCCCEEEEEeCCCcChhhc-CCC
Confidence 3677776554 467999999999973 4433333 333333 11 15788888985 57899 799
Q ss_pred eEEEEEEEcC
Q 041604 87 SVVVEGFIKP 96 (162)
Q Consensus 87 ~VVveG~~~~ 96 (162)
.|.|.|++..
T Consensus 109 ~VTVvG~i~G 118 (182)
T TIGR00752 109 YVTVGGQIAG 118 (182)
T ss_pred EEEEEEEecc
Confidence 9999999974
No 16
>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=90.41 E-value=2.5 Score=29.62 Aligned_cols=54 Identities=28% Similarity=0.286 Sum_probs=43.1
Q ss_pred EEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCC-------CCCCCCCCCeEEEEEEEcC
Q 041604 39 FRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGS-------LPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 39 vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~-------~Pd~F~eg~~VVveG~~~~ 96 (162)
|++-|+|.. ++.. +..++|.|.|+...|++.+-.. ..+.|++|.-|-|.|++..
T Consensus 2 v~~vG~V~~--~~~~--~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~ 62 (95)
T cd04478 2 VTLVGVVRN--VEEQ--STNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKS 62 (95)
T ss_pred EEEEEEEEe--eeEc--ccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEcc
Confidence 788899973 4433 4689999999988898888653 3556999999999999974
No 17
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=90.27 E-value=2.6 Score=39.36 Aligned_cols=111 Identities=22% Similarity=0.174 Sum_probs=69.3
Q ss_pred eeeeCHHHHHhhcCCCC--CCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEE-EEEEcCC---CCCCCCCCCeEEEE
Q 041604 18 VFYVTPSEALEKYQSNP--SKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDI-LVRYQGS---LPDLFREGHSVVVE 91 (162)
Q Consensus 18 ~yy~tpsE~~~~~~~~~--~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i-~V~Y~G~---~Pd~F~eg~~VVve 91 (162)
..|+||||+...-..-. .=..|.|.|-+. .+...+++ ++=|.+.|....| -|.|.|. ++-.-+||..|+|.
T Consensus 3 ~~~~sVSeln~~ik~llE~~~~~V~v~GEIS--n~t~~~sg-H~YFtLKD~~A~i~c~mf~~~~~~l~f~p~eG~~V~v~ 79 (440)
T COG1570 3 EKILSVSELNDYIKRLLERDLGQVWVRGEIS--NFTRPASG-HLYFTLKDERAQIRCVMFKGNNRRLKFRPEEGMQVLVR 79 (440)
T ss_pred CCeecHHHHHHHHHHHHHhcCCeEEEEEEec--CCccCCCc-cEEEEEccCCceEEEEEEcCcccccCCCccCCCEEEEE
Confidence 36899999875321100 125688888885 35544555 9999999999877 4667774 44445799999999
Q ss_pred EEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhHH
Q 041604 92 GFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEE 152 (162)
Q Consensus 92 G~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~~ 152 (162)
|++.- -+.+|+-.+.++.|- -+--.....++++.++.|..
T Consensus 80 G~is~----------------Y~~rG~YQi~~~~~~-----p~G~G~L~~~~E~lK~kL~a 119 (440)
T COG1570 80 GKISL----------------YEPRGDYQIVAESME-----PAGLGALYLAFEQLKAKLAA 119 (440)
T ss_pred EEEEE----------------EcCCCceEEEEecCC-----cCChhHHHHHHHHHHHHHHh
Confidence 99841 111234445555542 22333456666777666654
No 18
>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=89.68 E-value=5.6 Score=28.12 Aligned_cols=54 Identities=13% Similarity=0.099 Sum_probs=39.6
Q ss_pred EEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCC------CCCCCCCCCeEEEEEEEc
Q 041604 39 FRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGS------LPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 39 vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~------~Pd~F~eg~~VVveG~~~ 95 (162)
+++.|+|..=. ....+.. .|.|.|....+.|..-.. .-+.+.++..|+++|+++
T Consensus 2 v~i~GiI~~v~--~TK~g~~-~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~v~ 61 (79)
T cd04490 2 VSIIGMVNDVR--STKNGHR-IVELEDTTGRITVLLTKDKEELFEEAEDILPDEVIGVSGTVS 61 (79)
T ss_pred EEEEEEEeEEE--EcCCCCE-EEEEECCCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEEEe
Confidence 68899997433 3334555 999999988887765542 234677899999999996
No 19
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=87.50 E-value=9.1 Score=34.93 Aligned_cols=93 Identities=19% Similarity=0.203 Sum_probs=63.7
Q ss_pred CcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEE-EEEcC---CCCCCCCCCCeEEEEEEEcCchhhhhhccccccccc
Q 041604 37 NKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDIL-VRYQG---SLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSE 112 (162)
Q Consensus 37 ~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~-V~Y~G---~~Pd~F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~ 112 (162)
..+.|.|-|.. +.+. .+.++-|.|.|....|+ |.|.+ .++-.+++|..|+|.|++.-
T Consensus 18 ~~v~V~GEisn--~~~~-~sGH~YFtLkD~~a~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~~---------------- 78 (432)
T TIGR00237 18 LQVWIQGEISN--FTQP-VSGHWYFTLKDENAQVRCVMFRGNNNRLKFRPQNGQQVLVRGGISV---------------- 78 (432)
T ss_pred CcEEEEEEecC--CeeC-CCceEEEEEEcCCcEEEEEEEcChhhCCCCCCCCCCEEEEEEEEEE----------------
Confidence 48999999974 3333 34589999999987775 45555 46777899999999999851
Q ss_pred cccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhHHH
Q 041604 113 NARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQ 153 (162)
Q Consensus 113 ~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~~~ 153 (162)
-+..|.=.|.+++|- |. + -.+.+.+.++.++.|+..
T Consensus 79 y~~~G~~ql~v~~i~---~~-G-~G~l~~~~~~lk~~L~~e 114 (432)
T TIGR00237 79 YEPRGDYQIICFEMQ---PA-G-EGLLQLAYEQLKEKLAAE 114 (432)
T ss_pred ECCCCcEEEEEEEec---cC-C-hHHHHHHHHHHHHHHHHC
Confidence 111223456677775 33 3 446677777777776643
No 20
>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=85.56 E-value=3.9 Score=26.65 Aligned_cols=56 Identities=23% Similarity=0.254 Sum_probs=38.8
Q ss_pred EeEEEecCcEEecCCC-ceEEEEEEeCCeEEEEEEcC-C---CCCCCCCCCeEEEEEEEcC
Q 041604 41 LGGLVLEGSVAHPASS-SEMEFVVTDLVTDILVRYQG-S---LPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 41 v~G~V~~gSv~~~~~~-~~~~F~vtD~~~~i~V~Y~G-~---~Pd~F~eg~~VVveG~~~~ 96 (162)
+.|+|..=.......+ .-+.|.+.|....+.+.+=. . ..+.+.+|..|++.|+++.
T Consensus 2 i~g~v~~~~~~~~k~g~~~~~~~l~D~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G~v~~ 62 (84)
T cd04485 2 VAGLVTSVRRRRTKKGKRMAFVTLEDLTGSIEVVVFPETYEKYRDLLKEDALLLVEGKVER 62 (84)
T ss_pred EEEEEEEeEEEEcCCCCEEEEEEEEeCCCeEEEEECHHHHHHHHHHhcCCCEEEEEEEEEe
Confidence 5677754333332222 35889999998888777653 2 3567899999999999973
No 21
>PF15490 Ten1_2: Telomere-capping, CST complex subunit
Probab=82.44 E-value=12 Score=29.01 Aligned_cols=69 Identities=16% Similarity=0.010 Sum_probs=53.8
Q ss_pred eeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEE----EeCCeEEEEEEcCCCCCCCCCCCeEEEEEEE
Q 041604 19 FYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVV----TDLVTDILVRYQGSLPDLFREGHSVVVEGFI 94 (162)
Q Consensus 19 yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~v----tD~~~~i~V~Y~G~~Pd~F~eg~~VVveG~~ 94 (162)
-|+++.|+.. + ..+.+..+|+-|.+. .++.. .-..+| .|....+.|.-+=.-|..|+-|.-..+.|-+
T Consensus 6 ~~~~l~Evs~-~-~~~~g~svR~~GrL~----~yD~~--~~~a~l~~~~~~~~~~l~V~t~~l~~~~~~~gslyq~iGEl 77 (118)
T PF15490_consen 6 VYVFLWEVSS-G-FVPEGKSVRTFGRLQ----SYDVA--TSRATLTAQHESDQHSLKVDTKLLEPFQARVGSLYQFIGEL 77 (118)
T ss_pred EEEehHHhcC-c-cccCCCeEEEEEEEE----EEecc--CCEEEEEeeccCCCcEEEEEeeEccccccCCCCEEEEEEEE
Confidence 4889999833 2 257899999999997 24332 344667 7777888888777888899999999999999
Q ss_pred c
Q 041604 95 K 95 (162)
Q Consensus 95 ~ 95 (162)
.
T Consensus 78 ~ 78 (118)
T PF15490_consen 78 E 78 (118)
T ss_pred E
Confidence 7
No 22
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=81.24 E-value=30 Score=31.87 Aligned_cols=81 Identities=17% Similarity=0.253 Sum_probs=52.8
Q ss_pred CCCCcEEEeEEEecCcEEecCCCceEEEE-EEeCC--eEEEEEEcCCCCC-------CCCCCCeEEEEEEEcCchhhhhh
Q 041604 34 PSKNKFRLGGLVLEGSVAHPASSSEMEFV-VTDLV--TDILVRYQGSLPD-------LFREGHSVVVEGFIKPITEEIKN 103 (162)
Q Consensus 34 ~~~~~vrv~G~V~~gSv~~~~~~~~~~F~-vtD~~--~~i~V~Y~G~~Pd-------~F~eg~~VVveG~~~~~~~~~~~ 103 (162)
..++.|+|.|+|. ++. . ...+.|. |.|+. ..+.|......++ .+..|..|-|+|.+...
T Consensus 14 ~~g~~v~v~Gwv~--~~R-~--~~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~gs~V~v~G~v~~~------ 82 (453)
T TIGR00457 14 FVGDEVTVSGWVR--TKR-S--SKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVES------ 82 (453)
T ss_pred cCCCEEEEEEEeE--EEE-c--CCCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCCcEEEEEEEEEcC------
Confidence 3578999999996 343 2 2345664 56666 6888888765332 36889999999999731
Q ss_pred ccccccccccccCCCCeEEEe--EEeecCC-CCC
Q 041604 104 VKSEKSVSENARSRDCFFSAT--DVLAKHD-EKY 134 (162)
Q Consensus 104 ~~~~~~~~~~~~~~dg~F~A~--~lLaKcp-skY 134 (162)
+. +.++-...++ +||.||+ ..|
T Consensus 83 --------~~-~~~~~El~~~~i~vl~~~~~~~~ 107 (453)
T TIGR00457 83 --------PG-KGQPVELQVKKIEVVGEAEPDDY 107 (453)
T ss_pred --------CC-CCCCEEEEEeEEEEEecCCccCC
Confidence 00 1123345555 6899997 444
No 23
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=80.78 E-value=20 Score=26.41 Aligned_cols=69 Identities=14% Similarity=-0.006 Sum_probs=39.5
Q ss_pred CeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCCCCCCCCCCeEEEEEEEc
Q 041604 16 QLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 16 ~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~Pd~F~eg~~VVveG~~~ 95 (162)
.....++++.|.+ +.++.|||-|.|.. .++++..+...-+|+ ..+.|...... .+..+.-|-|.|+..
T Consensus 3 ~~~pRVn~~~L~~-----~~gk~VrivGkv~~----~~~~g~~~~l~~~d~-~~V~v~l~~~~--~~~~~~~vEviG~V~ 70 (109)
T PF08661_consen 3 APTPRVNGSMLSQ-----FVGKTVRIVGKVES----VDPDGGSATLSTSDG-GQVTVSLNPPS--DEELSKYVEVIGKVN 70 (109)
T ss_dssp S--EEE-GGGGGG-----GTTSEEEEEEEEEE----E-TTSSEEEEE-TTS--EEEEEESS----SS---SEEEEEEEE-
T ss_pred CCcceECHHHHHh-----hCCCeEEEEEEEee----EcCCCCEEEEEcCCC-CEEEEEeCCCC--CCCCCCEEEEEEEEc
Confidence 3456778877754 47999999999962 233344433333354 47777776544 345688999999998
Q ss_pred C
Q 041604 96 P 96 (162)
Q Consensus 96 ~ 96 (162)
+
T Consensus 71 ~ 71 (109)
T PF08661_consen 71 D 71 (109)
T ss_dssp T
T ss_pred C
Confidence 6
No 24
>PF11736 DUF3299: Protein of unknown function (DUF3299); InterPro: IPR021727 This is a family of bacterial proteins of unknown function.
Probab=79.02 E-value=14 Score=29.43 Aligned_cols=59 Identities=19% Similarity=0.224 Sum_probs=43.1
Q ss_pred CCCCcEEEeEEEecCcEEecCCCceEEEEEEeC------------CeEEEEEEcCCCCCCCCCCCeEEEEEEEcC
Q 041604 34 PSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDL------------VTDILVRYQGSLPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 34 ~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~------------~~~i~V~Y~G~~Pd~F~eg~~VVveG~~~~ 96 (162)
..|+.|||.|.+.+= +. .++...+|.|+-- +.-|.|++...+|-. .--..|.|+|+|.-
T Consensus 53 L~Gk~V~i~Gf~vPl--e~-~~~~v~eFlLvP~~gaC~h~PpPppNqiV~V~~~~~~~~~-~~~~pv~V~G~l~~ 123 (146)
T PF11736_consen 53 LDGKQVRIPGFMVPL--EQ-EEGKVTEFLLVPYFGACIHVPPPPPNQIVHVKMPKPIPVD-SLYDPVWVEGTLKV 123 (146)
T ss_pred hCCCEEEEeeEEEee--cc-CCCcEEEEEEeccCCcCcCCCCCCCccEEEEEeCCCcccc-ccceeEEEEEEEEe
Confidence 468999999999863 32 2345678988854 267899999876654 22358999999973
No 25
>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=78.35 E-value=11 Score=23.32 Aligned_cols=39 Identities=33% Similarity=0.512 Sum_probs=32.1
Q ss_pred ceEEEEEEeCC-eEEEEEEcCCCC----CCCCCCCeEEEEEEEc
Q 041604 57 SEMEFVVTDLV-TDILVRYQGSLP----DLFREGHSVVVEGFIK 95 (162)
Q Consensus 57 ~~~~F~vtD~~-~~i~V~Y~G~~P----d~F~eg~~VVveG~~~ 95 (162)
....|.|.|.. ..+.+..-.... +.+++|..+.++|+++
T Consensus 17 ~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~g~v~ 60 (75)
T cd03524 17 KVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIKGKVK 60 (75)
T ss_pred eEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEEEEEE
Confidence 46889999998 888877766543 4579999999999997
No 26
>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=77.16 E-value=20 Score=26.98 Aligned_cols=57 Identities=16% Similarity=0.228 Sum_probs=40.5
Q ss_pred CCCcEEEeEEEecCcEEecCCCceEEEE-EEeCCeEEEEEEcCCCCC------CCCCCCeEEEEEEEcC
Q 041604 35 SKNKFRLGGLVLEGSVAHPASSSEMEFV-VTDLVTDILVRYQGSLPD------LFREGHSVVVEGFIKP 96 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F~-vtD~~~~i~V~Y~G~~Pd------~F~eg~~VVveG~~~~ 96 (162)
.++.|+|.|+|.. +.. .+. +.|. |.|+...+.|.+.....+ ..+.|..|.|+|.+..
T Consensus 13 ~g~~V~i~Gwv~~--~R~--~gk-~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~ 76 (135)
T cd04317 13 VGQEVTLCGWVQR--RRD--HGG-LIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRA 76 (135)
T ss_pred CCCEEEEEEeEeh--hcc--cCC-EEEEEEecCCeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEEC
Confidence 5778999999963 322 233 6665 556667888888654333 4678999999999973
No 27
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=76.57 E-value=22 Score=25.67 Aligned_cols=58 Identities=17% Similarity=0.182 Sum_probs=38.6
Q ss_pred CCcEEEeEEEecCcEEecCCCceEEEEEEe-----CC------eEEEEEEcCCCCCCCCCCCeEEEEEEEcC
Q 041604 36 KNKFRLGGLVLEGSVAHPASSSEMEFVVTD-----LV------TDILVRYQGSLPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 36 ~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD-----~~------~~i~V~Y~G~~Pd~F~eg~~VVveG~~~~ 96 (162)
++.+.+.|.|..-.- . ++...+|.+.. .. ..+.+.....-...++.|+.+.++|++.|
T Consensus 75 ~~~~~v~g~V~~~~~-~--~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~Gd~i~~~g~l~~ 143 (176)
T PF13567_consen 75 GKEVTVQGTVESVPQ-I--DGRGQRFTLRVERVLAGGNWIPVSGKILLYLPKDSQPRLQPGDRIRVRGKLKP 143 (176)
T ss_pred CceEEEEEEEccccc-c--cCceEEEEEEEEEeeccccccccceeeEEEeccccccccCCCCEEEEEEEEec
Confidence 778999998853222 2 23345777651 11 45555555554446899999999999987
No 28
>PRK04036 DNA polymerase II small subunit; Validated
Probab=75.55 E-value=25 Score=32.74 Aligned_cols=69 Identities=16% Similarity=0.202 Sum_probs=51.5
Q ss_pred CCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCC------CCCCCCCCCeEEEEEEEcCchhhhhhccccc
Q 041604 35 SKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGS------LPDLFREGHSVVVEGFIKPITEEIKNVKSEK 108 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~------~Pd~F~eg~~VVveG~~~~~~~~~~~~~~~~ 108 (162)
.+..+-|-|+|.+ +.... .....+.|.|...++++...-. +++.|-.|.-|-|+|++.+
T Consensus 152 ~~~~~~viG~v~~--~~~~~-~g~~~~~LED~sgrv~l~~~~~~~~~~~~~~~lvtg~vv~v~G~~~~------------ 216 (504)
T PRK04036 152 GGEEVSIIGMVSD--IRSTK-NGHKIVELEDTTGTFPVLIMKDREDLAELADELLLDEVIGVEGTLSG------------ 216 (504)
T ss_pred CCceEEEEEEEEE--eeccc-CCceEEEEECCCCeEEEEeecchhhhhhhhhcccCceEEEEEEEEcC------------
Confidence 4578899999952 33222 2234699999999999886422 3567899999999999974
Q ss_pred cccccccCCCC-eEEEeEEe
Q 041604 109 SVSENARSRDC-FFSATDVL 127 (162)
Q Consensus 109 ~~~~~~~~~dg-~F~A~~lL 127 (162)
+| .|.+++|.
T Consensus 217 ---------~g~~f~v~~i~ 227 (504)
T PRK04036 217 ---------DGGLIFADEII 227 (504)
T ss_pred ---------CCCEEEEEEEE
Confidence 56 89999987
No 29
>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=74.72 E-value=12 Score=24.77 Aligned_cols=39 Identities=18% Similarity=0.319 Sum_probs=32.6
Q ss_pred ceEEEEEEeCCeEEEEEEcCCCC---CCCCCCCeEEEEEEEc
Q 041604 57 SEMEFVVTDLVTDILVRYQGSLP---DLFREGHSVVVEGFIK 95 (162)
Q Consensus 57 ~~~~F~vtD~~~~i~V~Y~G~~P---d~F~eg~~VVveG~~~ 95 (162)
.-+.|.|.|....+.+.+-+..| +.+++|..|++.|+++
T Consensus 19 ~~~~~~l~D~tg~i~~~~f~~~~~~~~~l~~g~~v~v~G~v~ 60 (83)
T cd04492 19 PYLALTLQDKTGEIEAKLWDASEEDEEKFKPGDIVHVKGRVE 60 (83)
T ss_pred cEEEEEEEcCCCeEEEEEcCCChhhHhhCCCCCEEEEEEEEE
Confidence 46889999998888888876444 4689999999999997
No 30
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=70.60 E-value=55 Score=29.87 Aligned_cols=58 Identities=19% Similarity=0.274 Sum_probs=41.3
Q ss_pred CCCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCCC-CC------CCCCCCeEEEEEEEcC
Q 041604 34 PSKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGSL-PD------LFREGHSVVVEGFIKP 96 (162)
Q Consensus 34 ~~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~~-Pd------~F~eg~~VVveG~~~~ 96 (162)
..+++|+|.|+|. ++ +. .+ .+.| +|.|+...+.+..+... |+ .+..|..|-|+|++..
T Consensus 14 ~~g~~V~i~GrV~--~~-R~-~g-k~~Fl~LrD~~g~iQ~v~~~~~~~~~~~~~~~L~~gs~V~v~G~v~~ 79 (437)
T PRK05159 14 LDGEEVTLAGWVH--EI-RD-LG-GIAFLILRDRSGIIQVVVKKKVDEELFETIKKLKRESVVSVTGTVKA 79 (437)
T ss_pred hCCCEEEEEEEeE--ee-ec-CC-CeEEEEEEcCCcEEEEEEeCCccHHHHHHHhCCCCCcEEEEEEEEEc
Confidence 3588999999996 23 22 23 4555 56777778888887531 32 4678999999999974
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=69.13 E-value=40 Score=24.43 Aligned_cols=51 Identities=22% Similarity=0.193 Sum_probs=37.8
Q ss_pred EeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCC------------------------CCCCCCCCeEEEEEEEc
Q 041604 41 LGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSL------------------------PDLFREGHSVVVEGFIK 95 (162)
Q Consensus 41 v~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~------------------------Pd~F~eg~~VVveG~~~ 95 (162)
|-|.|. |+... ..-+.|.|-|+...|.+.+=... .+.|+.|.-|-|.|++.
T Consensus 2 ivG~V~--sv~~~--~~~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV~G~i~ 76 (92)
T cd04483 2 ILGTVV--SRRER--ETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVRGSIR 76 (92)
T ss_pred eEEEEE--EEEec--CCeEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEEEEEEe
Confidence 567775 34433 46799999999888887775432 23489999999999997
No 32
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=68.17 E-value=39 Score=23.81 Aligned_cols=57 Identities=21% Similarity=0.262 Sum_probs=36.3
Q ss_pred EEEeEEEecCcE-EecCCCceEEEEEEeCCeEEEEEEcC-CCC---CCCC-CCCeEEEEEEEc
Q 041604 39 FRLGGLVLEGSV-AHPASSSEMEFVVTDLVTDILVRYQG-SLP---DLFR-EGHSVVVEGFIK 95 (162)
Q Consensus 39 vrv~G~V~~gSv-~~~~~~~~~~F~vtD~~~~i~V~Y~G-~~P---d~F~-eg~~VVveG~~~ 95 (162)
+.|.|.|-.=.. ....+..-++|.|||....|.+..=. ..+ +..+ +|..|.+.|.+.
T Consensus 2 v~i~G~Vf~~e~re~k~g~~i~~~~itD~t~Si~~K~F~~~~~~~~~~ik~~G~~v~v~G~v~ 64 (82)
T cd04484 2 VVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLRKDEKDKEELKSKGDWVRVRGKVQ 64 (82)
T ss_pred EEEEEEEEEEEEEEecCCCEEEEEEEEcCCCCEEEEEeccCChhHHhhcccCCCEEEEEEEEE
Confidence 567887742111 11223556789999987655443322 222 4567 999999999975
No 33
>PLN02603 asparaginyl-tRNA synthetase
Probab=66.74 E-value=68 Score=30.87 Aligned_cols=82 Identities=18% Similarity=0.271 Sum_probs=52.5
Q ss_pred CCCCcEEEeEEEecCcEEecCCCceEEEEEE-eCC--eEEEEEEcCCCCC-------CCCCCCeEEEEEEEcCchhhhhh
Q 041604 34 PSKNKFRLGGLVLEGSVAHPASSSEMEFVVT-DLV--TDILVRYQGSLPD-------LFREGHSVVVEGFIKPITEEIKN 103 (162)
Q Consensus 34 ~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vt-D~~--~~i~V~Y~G~~Pd-------~F~eg~~VVveG~~~~~~~~~~~ 103 (162)
..+++|+|.|+|. ++.. ...+.|... |+. ..|.|+.+..... .+.-|..|.|+|.+...
T Consensus 105 ~~g~~V~v~GwV~--~iR~---~g~~~Fi~l~Dgs~~~~lQ~v~~~~~~~~~~l~~~~l~~gs~V~V~G~v~~~------ 173 (565)
T PLN02603 105 RVGKTLNVMGWVR--TLRA---QSSVTFIEVNDGSCLSNMQCVMTPDAEGYDQVESGLITTGASVLVQGTVVSS------ 173 (565)
T ss_pred cCCCEEEEEEEEE--EEEe---CCCeEEEEEECCCCCEeEEEEEECcHHHHHHHhhcCCCCCCEEEEEEEEEec------
Confidence 4588999999997 4432 235777655 544 3688888654321 26789999999999631
Q ss_pred ccccccccccccCCCCeEEEe--EEeecCCCCCC
Q 041604 104 VKSEKSVSENARSRDCFFSAT--DVLAKHDEKYM 135 (162)
Q Consensus 104 ~~~~~~~~~~~~~~dg~F~A~--~lLaKcpskY~ 135 (162)
. .. ..+=.+.++ +||.+|+..|-
T Consensus 174 ---~-----~~-~~~~EL~v~~i~vlg~a~~~~P 198 (565)
T PLN02603 174 ---Q-----GG-KQKVELKVSKIVVVGKSDPSYP 198 (565)
T ss_pred ---C-----CC-CccEEEEEeEEEEEECCCCCCC
Confidence 0 00 001234455 46999987774
No 34
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=65.68 E-value=61 Score=31.31 Aligned_cols=71 Identities=24% Similarity=0.286 Sum_probs=45.5
Q ss_pred eCHHHHHhhcCCC-----CCCCcEEEeEEEecCcEEecCCCceEEEEEE-eCCeEEEEEEc----CCCCC-------CCC
Q 041604 21 VTPSEALEKYQSN-----PSKNKFRLGGLVLEGSVAHPASSSEMEFVVT-DLVTDILVRYQ----GSLPD-------LFR 83 (162)
Q Consensus 21 ~tpsE~~~~~~~~-----~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vt-D~~~~i~V~Y~----G~~Pd-------~F~ 83 (162)
.+..|+.+..... ..+..++|.|+|. ++ |. .+..+.|... |....|.|... |...+ .+.
T Consensus 112 ~~~~~~~~~~~~~~~~~~~~~~~v~v~Grv~--~~-R~-~G~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~~l~ 187 (585)
T PTZ00417 112 ITVPEFVEKYQDLASGEHLEDTILNVTGRIM--RV-SA-SGQKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYDKIR 187 (585)
T ss_pred cCHHHHHHHhhccCccccccCCeEEEEEEEE--ee-ec-CCCCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHhcCC
Confidence 4567777654311 1234599999996 23 22 2335777666 88888888886 22122 356
Q ss_pred CCCeEEEEEEEc
Q 041604 84 EGHSVVVEGFIK 95 (162)
Q Consensus 84 eg~~VVveG~~~ 95 (162)
-|+.|-|+|...
T Consensus 188 ~Gd~V~V~G~~~ 199 (585)
T PTZ00417 188 RGDIVGIVGFPG 199 (585)
T ss_pred CCCEEEEEeEEc
Confidence 699999999976
No 35
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=65.20 E-value=23 Score=34.03 Aligned_cols=61 Identities=23% Similarity=0.337 Sum_probs=44.9
Q ss_pred CCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEc--C--CCCCCCCCCCeEEEEEEEcC
Q 041604 35 SKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQ--G--SLPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~--G--~~Pd~F~eg~~VVveG~~~~ 96 (162)
.+..+.+.|.|..-..... ....+++.+.|+...+.++|= + -+...|+.|..++|.|+++.
T Consensus 58 ~g~~vtv~g~V~~~~~~~~-~~~~~~v~l~D~tg~i~l~~F~~n~~~~~~~l~~G~~~~v~Gkv~~ 122 (681)
T PRK10917 58 PGEKVTVEGEVLSAEVVFG-KRRRLTVTVSDGTGNLTLRFFNFNQPYLKKQLKVGKRVAVYGKVKR 122 (681)
T ss_pred CCCEEEEEEEEEEEEEccC-CceEEEEEEEECCeEEEEEEEccCcHHHHhhCCCCCEEEEEEEEEe
Confidence 4779999998864333222 345789999998866766555 2 24678999999999999973
No 36
>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=65.19 E-value=50 Score=23.94 Aligned_cols=57 Identities=16% Similarity=0.254 Sum_probs=39.0
Q ss_pred CCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCCC-C-C------CCCCCCeEEEEEEEcC
Q 041604 35 SKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGSL-P-D------LFREGHSVVVEGFIKP 96 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~~-P-d------~F~eg~~VVveG~~~~ 96 (162)
.++.++|.|+|.. +.. .+. +.| .|.|....+.+.+.... | + ....|..|-|+|.+..
T Consensus 11 ~g~~V~v~Gwv~~--~R~--~g~-~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~ 76 (108)
T cd04316 11 DGEEVTVAGWVHE--IRD--LGG-IKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKA 76 (108)
T ss_pred CCCEEEEEEEEEe--eec--cCC-eEEEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEe
Confidence 5788999999963 322 233 565 45666677888776432 2 2 3567999999999973
No 37
>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=64.82 E-value=43 Score=23.05 Aligned_cols=54 Identities=20% Similarity=0.172 Sum_probs=37.4
Q ss_pred cEEEeEEEecCcEEecCCCceEEEE-EEeCCeEEEEEEcCCCCC-------CCCCCCeEEEEEEEcC
Q 041604 38 KFRLGGLVLEGSVAHPASSSEMEFV-VTDLVTDILVRYQGSLPD-------LFREGHSVVVEGFIKP 96 (162)
Q Consensus 38 ~vrv~G~V~~gSv~~~~~~~~~~F~-vtD~~~~i~V~Y~G~~Pd-------~F~eg~~VVveG~~~~ 96 (162)
+++|.|+|. ++.. .+. +.|. |.|+...+.+.+.....+ ....|..|.|+|.+..
T Consensus 1 ~V~i~Gwv~--~~R~--~g~-~~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~ 62 (85)
T cd04100 1 EVTLAGWVH--SRRD--HGG-LIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVK 62 (85)
T ss_pred CEEEEEEEe--hhcc--CCC-EEEEEEEeCCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEE
Confidence 478999996 2322 233 6664 567778888887754332 5678999999999973
No 38
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=64.55 E-value=50 Score=31.37 Aligned_cols=61 Identities=21% Similarity=0.281 Sum_probs=44.6
Q ss_pred CCCcEEEeEEEecCcEEecCCCceEEEEEEe-CCeEEEEEEcCC--CCCCCCCCCeEEEEEEEc
Q 041604 35 SKNKFRLGGLVLEGSVAHPASSSEMEFVVTD-LVTDILVRYQGS--LPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD-~~~~i~V~Y~G~--~Pd~F~eg~~VVveG~~~ 95 (162)
.|..+.|.|.|.............+++.+.| +...+.++|=.. +...|..|..+++.|++.
T Consensus 31 ~g~~~~~~~~v~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~F~~~~~~~~~~~g~~~~~~Gk~~ 94 (630)
T TIGR00643 31 PGERATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKLELRFFNRAFLKKKFKVGSKVVVYGKVK 94 (630)
T ss_pred CCCEEEEEEEEEEeEeccCCCCceEEEEEEECCCCEEEEEEECCHHHHhhCCCCCEEEEEEEEE
Confidence 5779999999875222111223469999999 887777666552 457899999999999996
No 39
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=64.43 E-value=87 Score=28.80 Aligned_cols=92 Identities=17% Similarity=0.227 Sum_probs=53.8
Q ss_pred eCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEE-EEeCCeEEEEEEcC-CCCCC------CCCCCeEEEEE
Q 041604 21 VTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFV-VTDLVTDILVRYQG-SLPDL------FREGHSVVVEG 92 (162)
Q Consensus 21 ~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~-vtD~~~~i~V~Y~G-~~Pd~------F~eg~~VVveG 92 (162)
.+..+++.. ...++.|+|.|+|. ++... ..+.|. |.|+...+.|...- .-+++ +..|..|-|+|
T Consensus 4 ~~~~~~~~~---~~~~~~V~i~G~v~--~~R~~---g~~~Fi~lrD~~g~iq~~~~~~~~~~~~~~~~~l~~~s~v~v~G 75 (450)
T PRK03932 4 VSIKDILKG---KYVGQEVTVRGWVR--TKRDS---GKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTGSSVIVTG 75 (450)
T ss_pred EEHHHhccc---ccCCCEEEEEEEEE--EEEeC---CCeEEEEEECCCCcEEEEEEcCCChHHHHHHhcCCCCcEEEEEE
Confidence 345666532 24688999999996 34322 345664 56665555444331 12232 57899999999
Q ss_pred EEcCchhhhhhccccccccccccCCCCeEEEeE--EeecCCCCCC
Q 041604 93 FIKPITEEIKNVKSEKSVSENARSRDCFFSATD--VLAKHDEKYM 135 (162)
Q Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~--lLaKcpskY~ 135 (162)
.+... . . ..++=...+++ ||.||+..|-
T Consensus 76 ~v~~~---------~-----~-~~~~~el~~~~i~vl~~~~~~~p 105 (450)
T PRK03932 76 TVVES---------P-----R-AGQGYELQATKIEVIGEDPEDYP 105 (450)
T ss_pred EEEcC---------C-----C-CCCCEEEEEEEEEEccCCCCCCC
Confidence 99741 0 0 00123455664 6888876665
No 40
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=63.36 E-value=1.5e+02 Score=30.73 Aligned_cols=65 Identities=26% Similarity=0.356 Sum_probs=44.2
Q ss_pred CHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCC-CC-C-------CCCCCCeEEEE
Q 041604 22 TPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGS-LP-D-------LFREGHSVVVE 91 (162)
Q Consensus 22 tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~-~P-d-------~F~eg~~VVve 91 (162)
+..|+.+. ..+++|+|.|+|.. + ++ .+ .+.| .|.|....|.|..+.. ++ + ....|+.|-|+
T Consensus 641 ~~~~~~~~----~~~~~V~v~Grv~~--~-R~-~G-~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~ 711 (1094)
T PRK02983 641 TVAEALDA----PTGEEVSVSGRVLR--I-RD-YG-GVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVT 711 (1094)
T ss_pred CHHHHHHh----cCCCEEEEEEEEEE--E-ee-CC-CeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEE
Confidence 46676654 35778999999962 3 32 23 4555 5677778888877643 22 1 25689999999
Q ss_pred EEEc
Q 041604 92 GFIK 95 (162)
Q Consensus 92 G~~~ 95 (162)
|++.
T Consensus 712 G~v~ 715 (1094)
T PRK02983 712 GTMG 715 (1094)
T ss_pred EEEE
Confidence 9997
No 41
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, 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-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. 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 funct
Probab=61.93 E-value=35 Score=24.87 Aligned_cols=62 Identities=16% Similarity=0.170 Sum_probs=44.3
Q ss_pred CCCCcEEEeEEEec-CcEEec----CCCceEEEEEEeC-CeEEEEEEcCCC----CCCCCCCCeEEEEEEEc
Q 041604 34 PSKNKFRLGGLVLE-GSVAHP----ASSSEMEFVVTDL-VTDILVRYQGSL----PDLFREGHSVVVEGFIK 95 (162)
Q Consensus 34 ~~~~~vrv~G~V~~-gSv~~~----~~~~~~~F~vtD~-~~~i~V~Y~G~~----Pd~F~eg~~VVveG~~~ 95 (162)
+....+++.|.|.. +.+..- .++..+.|.|.|. +..|.+..-+.. =+.+++|+.+.+.+.--
T Consensus 7 p~~~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~~V 78 (104)
T cd04474 7 PYQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYISKGSV 78 (104)
T ss_pred CCCCcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCEEEEEEehHHHHHhhcccccccEEEEeccEE
Confidence 34568999999963 333321 1366789999999 789988877643 34888999998887654
No 42
>PLN02502 lysyl-tRNA synthetase
Probab=61.09 E-value=1.6e+02 Score=28.29 Aligned_cols=70 Identities=23% Similarity=0.210 Sum_probs=44.8
Q ss_pred eCHHHHHhhcCC-----CCCCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCC-CCC----------CCC
Q 041604 21 VTPSEALEKYQS-----NPSKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGS-LPD----------LFR 83 (162)
Q Consensus 21 ~tpsE~~~~~~~-----~~~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~-~Pd----------~F~ 83 (162)
.+..++.+++.. ...+..|+|.|+|.. + |. .+ .+.| .|.|+...|.|..... +++ .+.
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~V~v~GrV~~--~-R~-~G-k~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~ 162 (553)
T PLN02502 88 HTAPELQEKYGSLENGEELEDVSVSVAGRIMA--K-RA-FG-KLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVD 162 (553)
T ss_pred ccHHHHHHHhhccccccccCCCEEEEEEEEEE--E-ec-CC-CeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCC
Confidence 455666655321 124678999999962 3 22 23 3455 6778777888776533 221 356
Q ss_pred CCCeEEEEEEEc
Q 041604 84 EGHSVVVEGFIK 95 (162)
Q Consensus 84 eg~~VVveG~~~ 95 (162)
-|..|-|+|.+.
T Consensus 163 ~gdiV~V~G~~~ 174 (553)
T PLN02502 163 RGDIVGVTGTPG 174 (553)
T ss_pred CCcEEEEEEEEE
Confidence 899999999996
No 43
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b 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. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=60.54 E-value=62 Score=23.40 Aligned_cols=53 Identities=15% Similarity=0.159 Sum_probs=36.8
Q ss_pred cEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCCC--CCC-------CCCCCeEEEEEEEc
Q 041604 38 KFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGSL--PDL-------FREGHSVVVEGFIK 95 (162)
Q Consensus 38 ~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~~--Pd~-------F~eg~~VVveG~~~ 95 (162)
.++|.|+|.. +. .. +. +.| .|.|+...+.+.+.... |.. +..|..|.|+|++.
T Consensus 1 ~v~v~GwV~~--~R-~~-g~-~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~ 63 (108)
T cd04322 1 EVSVAGRIMS--KR-GS-GK-LSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPF 63 (108)
T ss_pred CEEEEEEEEE--Ee-cC-CC-eEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEE
Confidence 3789999973 33 22 33 555 57788888888886432 332 56799999999997
No 44
>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=59.48 E-value=57 Score=24.58 Aligned_cols=67 Identities=13% Similarity=0.218 Sum_probs=42.3
Q ss_pred eeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCC--CCCCCCCCCeEEEEEEEc
Q 041604 18 VFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGS--LPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 18 ~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~--~Pd~F~eg~~VVveG~~~ 95 (162)
.--.|+++++.. ..+..|.|.|.+.. .+. .. .|...|...+|.|.=... .+....+...|-+.|.++
T Consensus 20 ~~~~TV~~a~~~----~Dd~~V~L~G~Iv~-~l~----~d--~Y~F~D~TG~I~VeId~~~w~g~~vt~~~~Vri~GeVD 88 (103)
T PF04076_consen 20 ATVTTVAQAKNA----KDDTPVTLEGNIVK-QLG----DD--KYLFRDATGEIEVEIDDDVWRGQTVTPDDKVRISGEVD 88 (103)
T ss_dssp -----HHHHTTS-----SSEEEEEEEEEEE-EEE----TT--EEEEEETTEEEEEE--GGGSTT----TTSEEEEEEEEE
T ss_pred cCeEeHHHHhhC----cCCCeEEEEEEEEE-Eec----CC--EEEEECCCCcEEEEEChhhcCCcccCCCCEEEEEEEEe
Confidence 445789998764 46789999998863 232 22 377789999999986654 455677889999999998
No 45
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=59.42 E-value=1.5e+02 Score=27.82 Aligned_cols=70 Identities=19% Similarity=0.317 Sum_probs=45.8
Q ss_pred eCHHHHHhhcCC------CCCCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEc-CCCCC--------CCCC
Q 041604 21 VTPSEALEKYQS------NPSKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQ-GSLPD--------LFRE 84 (162)
Q Consensus 21 ~tpsE~~~~~~~------~~~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~-G~~Pd--------~F~e 84 (162)
.+..++.++... ...++.|+|.|+|.. +. . .+ .+.| .|.|....|.+... +.+++ .+.-
T Consensus 32 ~~~~~~~~~~~~~~~~~~~~~~~~v~v~Grv~~--~R-~-~g-k~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~ 106 (496)
T TIGR00499 32 HSSQEFQEEYADLSNEELEDKNIEVSIAGRIMA--RR-S-MG-KATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDL 106 (496)
T ss_pred cCHHHHHHHhhccCccchhcCCCEEEEEEEEEE--Ee-c-CC-CeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCC
Confidence 566777665431 012567999999972 32 2 23 3555 57787777877665 33432 3578
Q ss_pred CCeEEEEEEEc
Q 041604 85 GHSVVVEGFIK 95 (162)
Q Consensus 85 g~~VVveG~~~ 95 (162)
|..|-|+|++.
T Consensus 107 gd~V~v~G~~~ 117 (496)
T TIGR00499 107 GDIIGVTGYPF 117 (496)
T ss_pred CCEEEEEEEEE
Confidence 99999999996
No 46
>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=58.87 E-value=55 Score=22.34 Aligned_cols=41 Identities=17% Similarity=0.191 Sum_probs=32.6
Q ss_pred CCceEEEEEEeCCeEEEEEEcCCC-CCCCCCCCeEEEE-EEEc
Q 041604 55 SSSEMEFVVTDLVTDILVRYQGSL-PDLFREGHSVVVE-GFIK 95 (162)
Q Consensus 55 ~~~~~~F~vtD~~~~i~V~Y~G~~-Pd~F~eg~~VVve-G~~~ 95 (162)
.+.-+.+.|.|....|++.+=+.. .+.+++|.-|.++ |+..
T Consensus 21 ~~~~~~~~l~D~TG~i~~~~W~~~~~~~~~~G~vv~i~~~~v~ 63 (82)
T cd04491 21 EGKVQSGLVGDETGTIRFTLWDEKAADDLEPGDVVRIENAYVR 63 (82)
T ss_pred eeEEEEEEEECCCCEEEEEEECchhcccCCCCCEEEEEeEEEE
Confidence 345677888888778888887765 6789999999999 7775
No 47
>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=56.31 E-value=71 Score=22.78 Aligned_cols=55 Identities=18% Similarity=0.164 Sum_probs=37.4
Q ss_pred cEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCCC----CC------CCCCCCeEEEEEEEcC
Q 041604 38 KFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGSL----PD------LFREGHSVVVEGFIKP 96 (162)
Q Consensus 38 ~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~~----Pd------~F~eg~~VVveG~~~~ 96 (162)
.|+|.|+|.. + |. .+..+.| .|.|....+.+.+.... ++ .++.|..|-|+|.+..
T Consensus 1 ~V~i~Gwv~~--~-R~-~g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~ 66 (102)
T cd04320 1 EVLIRARVHT--S-RA-QGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKK 66 (102)
T ss_pred CEEEEEEEEE--e-ec-CCCceEEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEEC
Confidence 4789999962 2 22 2324666 45677788999997542 22 3577999999999973
No 48
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=55.61 E-value=55 Score=30.44 Aligned_cols=61 Identities=15% Similarity=0.142 Sum_probs=40.8
Q ss_pred CCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEc-C---CCCCCCCCCCeEEEEEEEc
Q 041604 35 SKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQ-G---SLPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~-G---~~Pd~F~eg~~VVveG~~~ 95 (162)
.+..++|.|+|..=.......+..|.| ++.|....+.++.= . ..-+.+.++..++++|+++
T Consensus 279 ~~~~v~vaG~I~~ik~~~TKkG~~maf~~leD~tG~ie~vvFp~~y~~~~~~l~~~~~v~v~G~v~ 344 (449)
T PRK07373 279 EKTKVSAVVMLNEVKKIVTKKGDPMAFLQLEDLSGQSEAVVFPKSYERISELLQVDARLIIWGKVD 344 (449)
T ss_pred CCCEEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHHHHHHHHHHhccCCEEEEEEEEE
Confidence 467899999997533333334556665 56787777766532 1 1223577899999999997
No 49
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=54.40 E-value=1.3e+02 Score=29.06 Aligned_cols=65 Identities=17% Similarity=0.172 Sum_probs=44.2
Q ss_pred CHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCCCCCC------CCCCCeEEEEEEE
Q 041604 22 TPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGSLPDL------FREGHSVVVEGFI 94 (162)
Q Consensus 22 tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~~Pd~------F~eg~~VVveG~~ 94 (162)
+..++... ..+++|+|.|+|.. +.. .+ .+.| .|.|....+.|..+.. ++. .+.|..|-|+|.+
T Consensus 7 ~~~~l~~~----~~g~~V~l~GwV~~--~R~--~g-~l~Fi~LrD~~g~iQ~v~~~~-~~~~~~~~~l~~es~V~V~G~v 76 (588)
T PRK00476 7 YCGELRES----HVGQTVTLCGWVHR--RRD--HG-GLIFIDLRDREGIVQVVFDPD-AEAFEVAESLRSEYVIQVTGTV 76 (588)
T ss_pred eHHHhhHH----hCCCEEEEEEEEEE--EEe--CC-CeEEEEEEeCCceEEEEEeCC-HHHHHHHhCCCCCCEEEEEEEE
Confidence 34566543 35789999999962 332 23 4555 5667777788887653 433 5669999999999
Q ss_pred cC
Q 041604 95 KP 96 (162)
Q Consensus 95 ~~ 96 (162)
..
T Consensus 77 ~~ 78 (588)
T PRK00476 77 RA 78 (588)
T ss_pred Ee
Confidence 73
No 50
>PLN02903 aminoacyl-tRNA ligase
Probab=54.18 E-value=1.9e+02 Score=28.54 Aligned_cols=57 Identities=23% Similarity=0.251 Sum_probs=40.3
Q ss_pred CCCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCC-CCC------CCCCCCeEEEEEEEc
Q 041604 34 PSKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGS-LPD------LFREGHSVVVEGFIK 95 (162)
Q Consensus 34 ~~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~-~Pd------~F~eg~~VVveG~~~ 95 (162)
..+++|+|.|+|.. + |+- + .+.| .|.|....+.|+.... .++ ..+.+..|-|+|.+.
T Consensus 70 ~~gk~V~l~GWV~~--~-R~~-G-~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~L~~esvV~V~G~V~ 134 (652)
T PLN02903 70 DVGSRVTLCGWVDL--H-RDM-G-GLTFLDVRDHTGIVQVVTLPDEFPEAHRTANRLRNEYVVAVEGTVR 134 (652)
T ss_pred hCCCEEEEEEEEEE--E-ecC-C-CcEEEEEEcCCccEEEEEeCCccHHHHHHHhcCCCCCEEEEEEEEE
Confidence 36789999999962 3 332 3 3555 5667767788887643 343 467899999999996
No 51
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=53.01 E-value=1.9e+02 Score=27.34 Aligned_cols=56 Identities=14% Similarity=0.162 Sum_probs=37.9
Q ss_pred CCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEc-CCCC-C-------CCCCCCeEEEEEEEc
Q 041604 36 KNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQ-GSLP-D-------LFREGHSVVVEGFIK 95 (162)
Q Consensus 36 ~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~-G~~P-d-------~F~eg~~VVveG~~~ 95 (162)
+..|+|.|+|. ++. . .+...=+.|.|....|.|... +.++ + .+.-|..|-|+|.+.
T Consensus 65 ~~~v~v~Grv~--~~R-~-~Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~ 129 (505)
T PRK12445 65 NIEVSVAGRMM--TRR-I-MGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLF 129 (505)
T ss_pred CCEEEEEEEEE--EEe-c-CCCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEE
Confidence 55799999996 232 2 233333467788778887765 3333 2 356799999999996
No 52
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=52.49 E-value=71 Score=31.75 Aligned_cols=62 Identities=16% Similarity=0.184 Sum_probs=46.3
Q ss_pred CCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcC---CCCCCCCCCCeEEEEEEEcC
Q 041604 35 SKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQG---SLPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G---~~Pd~F~eg~~VVveG~~~~ 96 (162)
.|..+.+.|.|..=..........++|.+.|+...+..+|=. -+...|+.|..|++.|+++.
T Consensus 59 ~g~~vti~g~V~~~~~~~~~~~~~l~v~~~d~~~~l~l~fFn~~~~l~~~~~~G~~v~v~Gk~~~ 123 (677)
T COG1200 59 PGEIVTIEGTVLSHEKFPFGKRKLLKVTLSDGTGVLTLVFFNFPAYLKKKLKVGERVIVYGKVKR 123 (677)
T ss_pred CCceEEEEEEEEeeeccCCCCCceEEEEEecCcEEEEEEEECccHHHHhhCCCCCEEEEEEEEee
Confidence 567899999996322221234678999999988777655443 46889999999999999984
No 53
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=48.11 E-value=1.4e+02 Score=23.59 Aligned_cols=66 Identities=15% Similarity=0.127 Sum_probs=46.4
Q ss_pred eeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCC--CCCCCCCCCeEEEEEEEcC
Q 041604 20 YVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGS--LPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 20 y~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~--~Pd~F~eg~~VVveG~~~~ 96 (162)
..|+++++.. ..+..|.|.|.+.. .+ +. =.|...|...+|.|.-.-. -.....++..|-+.|.++.
T Consensus 45 ~~tV~~a~~~----~Ddt~V~L~G~Iv~-~l----~~--d~Y~F~D~TG~I~VeId~~~w~G~~v~p~d~V~I~GeVDk 112 (126)
T TIGR00156 45 KMTVDFAKSM----HDGASVTLRGNIIS-HI----GD--DRYVFRDKSGEINVVIPAAVWNGREVQPKDMVNISGSLDK 112 (126)
T ss_pred eEeHHHHhhC----CCCCEEEEEEEEEE-Ee----CC--ceEEEECCCCCEEEEECHHHcCCCcCCCCCEEEEEEEECC
Confidence 4678888764 35789999998852 12 12 2377789988888876432 2335677999999999983
No 54
>KOG0554 consensus Asparaginyl-tRNA synthetase (mitochondrial) [Translation, ribosomal structure and biogenesis]
Probab=48.04 E-value=58 Score=30.80 Aligned_cols=57 Identities=21% Similarity=0.345 Sum_probs=43.6
Q ss_pred CCCCcEEEeEEEecCcEEecCCCceEEEEEEeCC---eEEEEEEcCCCCCCCCCCCeEEEEEEEc
Q 041604 34 PSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLV---TDILVRYQGSLPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 34 ~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~---~~i~V~Y~G~~Pd~F~eg~~VVveG~~~ 95 (162)
..+.+++++|+|+ |+... ..+.|...+.+ ..+.|+-.-..-...+-|..|.++|.+.
T Consensus 18 ~~g~~~~i~GWvK--svr~~---~~~~Fl~i~DGs~~~~lQvVv~~~~~q~la~Gt~i~~~g~l~ 77 (446)
T KOG0554|consen 18 RAGDTISIGGWVK--SVRKL---KKVTFLDINDGSCPSPLQVVVDSEQSQLLATGTCISAEGVLK 77 (446)
T ss_pred CCCCceeecchhh--hcccc---cceEEEEecCCCCCcceEEEechHHhhhccccceEEEEeeEE
Confidence 4789999999998 44432 23666665544 6788887776777888999999999997
No 55
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=45.50 E-value=1e+02 Score=29.05 Aligned_cols=67 Identities=21% Similarity=0.207 Sum_probs=45.4
Q ss_pred eCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEE-eCCeEEEEEEcC--CCCCCC-----CCCCeEEEEE
Q 041604 21 VTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVT-DLVTDILVRYQG--SLPDLF-----REGHSVVVEG 92 (162)
Q Consensus 21 ~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vt-D~~~~i~V~Y~G--~~Pd~F-----~eg~~VVveG 92 (162)
.+..++... ..++.|+|.|+|.. .+ +...+.|.+. |+...+.+++.. .-++.| .-+..|.|+|
T Consensus 5 ~~i~di~~~----~~~~~V~v~GWV~~---~R--~~g~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~~L~~es~v~V~G 75 (435)
T COG0017 5 TYIKDIKPH----VGGQEVTVRGWVHN---KR--DLGKIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLESSVVVTG 75 (435)
T ss_pred eeHHhhhcc----CCCcEEEEEEEeee---ec--ccCCeEEEEEEcCCcEEEEEEECCCCcHHHhhhhcCCCccEEEEEE
Confidence 455666553 23489999999963 12 2345888755 666678888863 344555 4789999999
Q ss_pred EEcC
Q 041604 93 FIKP 96 (162)
Q Consensus 93 ~~~~ 96 (162)
.+..
T Consensus 76 ~v~~ 79 (435)
T COG0017 76 IVKA 79 (435)
T ss_pred EEEc
Confidence 9973
No 56
>smart00276 GLECT Galectin. Galectin - galactose-binding lectin
Probab=43.43 E-value=41 Score=25.17 Aligned_cols=23 Identities=22% Similarity=0.616 Sum_probs=20.7
Q ss_pred EcCCCCCCCCCCCeEEEEEEEcC
Q 041604 74 YQGSLPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 74 Y~G~~Pd~F~eg~~VVveG~~~~ 96 (162)
|...+|..|+.|..+++.|+..+
T Consensus 1 ~~~~lp~~l~~G~~i~i~G~~~~ 23 (128)
T smart00276 1 FTLPIPGGLKPGQTLTVRGIVLP 23 (128)
T ss_pred CcccCCCCCCCCCEEEEEEEECC
Confidence 56789999999999999999975
No 57
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=42.42 E-value=1.5e+02 Score=22.59 Aligned_cols=69 Identities=19% Similarity=0.297 Sum_probs=49.3
Q ss_pred eeeCHHHHHhhcCCCCCCCcEEEeEEEecCc-EEec-CCCceEEEEEEeCC----eEEEEEEcCC----CCCCCCCCCeE
Q 041604 19 FYVTPSEALEKYQSNPSKNKFRLGGLVLEGS-VAHP-ASSSEMEFVVTDLV----TDILVRYQGS----LPDLFREGHSV 88 (162)
Q Consensus 19 yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gS-v~~~-~~~~~~~F~vtD~~----~~i~V~Y~G~----~Pd~F~eg~~V 88 (162)
+|+..++|... .+..+-|-|.|..-+ ..+. ...-.++|.|+|.. ..+.|.|=+. ||.. ..|+.|
T Consensus 2 ~f~~i~~~~~~-----~~~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~v-~~GDVI 75 (138)
T cd04497 2 KYTPLSSALKE-----SGGSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLANSDGLTVKLFRPNEESLPIV-KVGDII 75 (138)
T ss_pred ceEeHHHHHhc-----cCCeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCCCCcEEEEEECCChhhCCCC-CCCCEE
Confidence 47777887652 578999999997433 2322 23467889999974 5688887664 7877 999988
Q ss_pred EEEEE
Q 041604 89 VVEGF 93 (162)
Q Consensus 89 VveG~ 93 (162)
.+.+.
T Consensus 76 ll~~~ 80 (138)
T cd04497 76 LLRRV 80 (138)
T ss_pred EEEEE
Confidence 87764
No 58
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=39.25 E-value=3.6e+02 Score=25.93 Aligned_cols=70 Identities=11% Similarity=0.077 Sum_probs=47.0
Q ss_pred eeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEc--CCCCC-------CCCCCCeEE
Q 041604 19 FYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQ--GSLPD-------LFREGHSVV 89 (162)
Q Consensus 19 yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~--G~~Pd-------~F~eg~~VV 89 (162)
-|..+.++... ...++.|+|.|+|.. + |. .+..+=+.|.|....|.+... +..++ ....|..|-
T Consensus 64 ~~~~i~~l~~~---~~~g~~V~v~Grv~~--~-R~-~Gk~~Fl~LRd~~~~iQ~v~~~~~~~~~~~~~~~~~l~~esiV~ 136 (550)
T PTZ00401 64 TFIPVAVLSKP---ELVDKTVLIRARVST--T-RK-KGKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQIPTESIVD 136 (550)
T ss_pred ceEEHHHCCcc---ccCCCEEEEEEEEEE--E-ec-CCCeEEEEEEeCCcCEEEEEECCCccCHHHHHHHhcCCCCCEEE
Confidence 47788888643 236889999999962 2 22 233333456777778877763 23443 367899999
Q ss_pred EEEEEc
Q 041604 90 VEGFIK 95 (162)
Q Consensus 90 veG~~~ 95 (162)
|+|.+.
T Consensus 137 V~G~v~ 142 (550)
T PTZ00401 137 VEATVC 142 (550)
T ss_pred EEEEEE
Confidence 999987
No 59
>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=39.19 E-value=1.3e+02 Score=20.73 Aligned_cols=54 Identities=20% Similarity=0.235 Sum_probs=36.2
Q ss_pred cEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCCCCC------CCCCCCeEEEEEEEcC
Q 041604 38 KFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGSLPD------LFREGHSVVVEGFIKP 96 (162)
Q Consensus 38 ~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~~Pd------~F~eg~~VVveG~~~~ 96 (162)
+++|.|+|.. + +.. + .+.| .|.|....+.+.+....+. ....|..|-|+|.+..
T Consensus 1 ~V~v~Gwv~~--~-R~~-g-~~~Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~v~~ 61 (84)
T cd04323 1 RVKVFGWVHR--L-RSQ-K-KLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEVKE 61 (84)
T ss_pred CEEEEEEEEE--E-ecC-C-CcEEEEEEcCCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEEEEE
Confidence 4789999962 3 222 2 4555 5667777888888754322 3456999999999973
No 60
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=39.09 E-value=3.3e+02 Score=25.50 Aligned_cols=70 Identities=19% Similarity=0.207 Sum_probs=45.0
Q ss_pred eCHHHHHhhcCCC------CCCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCC-CC-C------CCCCC
Q 041604 21 VTPSEALEKYQSN------PSKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGS-LP-D------LFREG 85 (162)
Q Consensus 21 ~tpsE~~~~~~~~------~~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~-~P-d------~F~eg 85 (162)
.+..++..+.... ..+..|+|.|+|. ++ |. .+ .+.| .|.|....|.|..... ++ + .+..|
T Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~v~v~G~v~--~~-R~-~g-~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~g 107 (491)
T PRK00484 33 HTAAELRAKYDDKEKEELEELEIEVSVAGRVM--LK-RV-MG-KASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDLG 107 (491)
T ss_pred cCHHHHHHHhccccchhhcccCcEEEEEEEEE--EE-ec-CC-ceEEEEEEcCCccEEEEEECCcCCHHHHHHHhcCCCC
Confidence 4566776553210 1136799999996 23 32 23 4555 5677777888888643 32 2 25789
Q ss_pred CeEEEEEEEc
Q 041604 86 HSVVVEGFIK 95 (162)
Q Consensus 86 ~~VVveG~~~ 95 (162)
..|-|+|++.
T Consensus 108 ~~v~v~G~v~ 117 (491)
T PRK00484 108 DIIGVEGTLF 117 (491)
T ss_pred CEEEEEEEEE
Confidence 9999999997
No 61
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=39.05 E-value=1.3e+02 Score=20.73 Aligned_cols=48 Identities=21% Similarity=0.245 Sum_probs=34.6
Q ss_pred CcEEecCCCceEEEEEEeCC-eEEEEEEcCCCCCC---CCCCCeEEEEEEEc
Q 041604 48 GSVAHPASSSEMEFVVTDLV-TDILVRYQGSLPDL---FREGHSVVVEGFIK 95 (162)
Q Consensus 48 gSv~~~~~~~~~~F~vtD~~-~~i~V~Y~G~~Pd~---F~eg~~VVveG~~~ 95 (162)
|.|+|=.+...+=|.-.|.. .++-|+++...++. .++|+.|..+=.-.
T Consensus 6 G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~ 57 (69)
T PRK09507 6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNG 57 (69)
T ss_pred eEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCCCCCCCEEEEEEEEC
Confidence 34444334467889887665 79999999987754 68899998876665
No 62
>PRK10053 hypothetical protein; Provisional
Probab=38.56 E-value=2e+02 Score=22.75 Aligned_cols=63 Identities=14% Similarity=0.152 Sum_probs=44.6
Q ss_pred CHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCC--CCCCCCCCCeEEEEEEEc
Q 041604 22 TPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGS--LPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 22 tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~--~Pd~F~eg~~VVveG~~~ 95 (162)
|+++++.. ..+..|.|.|.++. ++. + =.|...|...+|.|.-.-. ......+...|.+.|.++
T Consensus 51 tV~~a~~~----~Dd~~V~L~G~Iv~-~lg----~--d~Y~F~D~tG~I~VeID~~~w~G~~v~p~~kV~I~GevD 115 (130)
T PRK10053 51 TVEQAKTM----HDGATVSLRGNLID-HKG----D--DRYVFRDKSGEINVIIPAAVFDGREVQPDQMININGSLD 115 (130)
T ss_pred EHHHhhcC----cCCCeEEEEEEEEE-EeC----C--ceEEEECCCCcEEEEeCHHHcCCCcCCCCCEEEEEEEEC
Confidence 56666553 35789999998853 222 2 2367789988888876542 444678899999999998
No 63
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=38.23 E-value=2.4e+02 Score=25.07 Aligned_cols=61 Identities=15% Similarity=0.127 Sum_probs=46.6
Q ss_pred CCCcEEEeEEEecCcEEecC-CCceEEEEEEeCCeEEEEEEcCCCCC---CCCCCCeEEEEEEEc
Q 041604 35 SKNKFRLGGLVLEGSVAHPA-SSSEMEFVVTDLVTDILVRYQGSLPD---LFREGHSVVVEGFIK 95 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~-~~~~~~F~vtD~~~~i~V~Y~G~~Pd---~F~eg~~VVveG~~~ 95 (162)
.+.+|..-.+|..-.+.... +..-+.|++.|...+|.-.+=...++ .|++|.-|-|+|+..
T Consensus 10 ~g~~v~~~~lv~~~~~~~~knG~~yl~l~l~D~tG~I~ak~W~~~~~~~~~~~~g~vv~v~G~v~ 74 (314)
T PRK13480 10 VGEQVDHFLLIKSATKGVASNGKPFLTLILQDKSGDIEAKLWDVSPEDEATYVPETIVHVKGDII 74 (314)
T ss_pred CCCEeeEEEEEEEceeeecCCCCeEEEEEEEcCCcEEEEEeCCCChhhHhhcCCCCEEEEEEEEE
Confidence 35667766777765655443 34589999999998998888765544 599999999999996
No 64
>PLN02850 aspartate-tRNA ligase
Probab=37.94 E-value=2.4e+02 Score=26.79 Aligned_cols=68 Identities=16% Similarity=0.114 Sum_probs=47.1
Q ss_pred eeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCCC---C-C------CCCCCCe
Q 041604 19 FYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGSL---P-D------LFREGHS 87 (162)
Q Consensus 19 yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~~---P-d------~F~eg~~ 87 (162)
-+..+.++... ..++.|+|.|+|.. + |. .+. +.| +|.|....|.++..... + + .+..|..
T Consensus 68 ~~~~i~~l~~~----~~g~~V~v~Grv~~--~-R~-~gk-~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~~~~~~~l~~es~ 138 (530)
T PLN02850 68 EWTDVSDLGEE----LAGSEVLIRGRVHT--I-RG-KGK-SAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQLSRESV 138 (530)
T ss_pred eEeEhhhcchh----hCCCEEEEEEEEEE--E-cc-CCC-eEEEEEEeCCcCEEEEEECCccccCHHHHHHHhCCCCCCE
Confidence 36777887553 46889999999962 2 32 233 565 45677788888876542 2 1 3577999
Q ss_pred EEEEEEEc
Q 041604 88 VVVEGFIK 95 (162)
Q Consensus 88 VVveG~~~ 95 (162)
|-|+|++.
T Consensus 139 V~V~G~v~ 146 (530)
T PLN02850 139 VDVEGVVS 146 (530)
T ss_pred EEEEEEEE
Confidence 99999997
No 65
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal 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.
Probab=37.91 E-value=1.5e+02 Score=21.21 Aligned_cols=55 Identities=24% Similarity=0.278 Sum_probs=36.4
Q ss_pred cEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCC-CC------CCCCCCeEEEEEEEcC
Q 041604 38 KFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSL-PD------LFREGHSVVVEGFIKP 96 (162)
Q Consensus 38 ~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~-Pd------~F~eg~~VVveG~~~~ 96 (162)
+++|.|+|.. +.. .+...=+.|.|+...+.+.+.... ++ ....|..|-|+|.+..
T Consensus 1 ~V~v~Gwv~~--~R~--~gk~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~ 62 (103)
T cd04319 1 KVTLAGWVYR--KRE--VGKKAFIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKA 62 (103)
T ss_pred CEEEEEEEEe--EEc--CCCeEEEEEecCCeeEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEE
Confidence 4789999962 322 233333456777778888886543 22 3467999999999973
No 66
>cd00070 GLECT Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation.
Probab=37.90 E-value=60 Score=24.07 Aligned_cols=23 Identities=30% Similarity=0.625 Sum_probs=20.9
Q ss_pred EcCCCCCCCCCCCeEEEEEEEcC
Q 041604 74 YQGSLPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 74 Y~G~~Pd~F~eg~~VVveG~~~~ 96 (162)
|.+.+|..|+.|+.+++.|+..+
T Consensus 2 ~~~~l~~~l~~G~~i~i~G~~~~ 24 (127)
T cd00070 2 YKLPLPGGLKPGSTLTVKGRVLP 24 (127)
T ss_pred cccccCCCCcCCCEEEEEEEECC
Confidence 67889989999999999999975
No 67
>PF00337 Gal-bind_lectin: Galactoside-binding lectin; InterPro: IPR001079 Galectins (also known as galaptins or S-lectin) are a family of proteins defined by having at least one characteristic carbohydrate recognition domain (CRD) with an affinity for beta-galactosides and sharing certain sequence elements. Members of the galectins family are found in mammals, birds, amphibians, fish, nematodes, sponges, and some fungi. Galectins are known to carry out intra- and extracellular functions through glycoconjugate-mediated recogntion. From the cytosol they may be secreted by non-classical pathways, but they may also be targeted to the nucleus or specific sub-cytosolic sites. Within the same peptide chain some galectins have a CRD with only a few additional amino acids, whereas others have two CRDs joined by a link peptide, and one (galectin-3) has one CRD joined to a different type of domain [, ]. The galectin carbohydrate recognition domain (CRD) is a beta-sandwich of about 135 amino acid. The two sheets are slightly bent with 6 strands forming the concave side and 5 strands forming the convex side. The concave side forms a groove in which carbohydrate is bound, and which is long enough to hold about a linear tetrasaccharide [, ].; GO: 0005529 sugar binding; PDB: 2WSU_B 2WT0_A 2WT1_A 2WT2_B 2WSV_A 1HLC_A 2ZGQ_A 3M3Q_B 1WW5_C 3M3E_A ....
Probab=37.44 E-value=22 Score=26.37 Aligned_cols=23 Identities=26% Similarity=0.687 Sum_probs=21.1
Q ss_pred EcCCCCCCCCCCCeEEEEEEEcC
Q 041604 74 YQGSLPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 74 Y~G~~Pd~F~eg~~VVveG~~~~ 96 (162)
|.+.+|..|+.|+.+++.|+..+
T Consensus 2 f~~~l~~~l~~G~~i~i~G~~~~ 24 (133)
T PF00337_consen 2 FTARLPGGLSPGDSIIIRGTVPP 24 (133)
T ss_dssp EEEEETTEEETTEEEEEEEEEBT
T ss_pred ceEEcCCCCCCCcEEEEEEEECC
Confidence 77889999999999999999974
No 68
>PF10451 Stn1: Telomere regulation protein Stn1; InterPro: IPR018856 The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA. Structural profiling has predicted an OB-fold []. This entry represents the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF6_A 3KF8_A.
Probab=35.99 E-value=1.5e+02 Score=25.65 Aligned_cols=60 Identities=20% Similarity=0.236 Sum_probs=37.1
Q ss_pred CCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCe--EEEEEEcCC--------CCCCCCCCCeEEEEEEEc
Q 041604 34 PSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVT--DILVRYQGS--------LPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 34 ~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~--~i~V~Y~G~--------~Pd~F~eg~~VVveG~~~ 95 (162)
.+=+.|||.|.|+.=...+-....-+-|.|-|... .|.+.-... ++++ -|.-|-|.|.+.
T Consensus 64 hPI~~v~i~G~Vv~~~~~~~~~~~~~~l~iDD~Sg~~~i~~~~~~~~~~~~~l~~~~~--~G~~V~VkG~vs 133 (256)
T PF10451_consen 64 HPIRWVRIVGVVVGIDYKWIENEDRIILTIDDSSGANTIECKCSKSSYLSMGLPINDL--IGKVVEVKGTVS 133 (256)
T ss_dssp EEE-EEEEEEEEEEEEEEE-BBTCEEEEEEE-SSCS-EEEEEEEHHHHHCCCHHCTT---TT-EEEEEEEEE
T ss_pred cccEEEEEEEEEEEEEEEeecccceEEEEEeCCCCceeEEEEEEcccccccCCCccCC--CCcEEEEEEEEc
Confidence 35579999999984333322223456677777654 676665532 4555 899999999997
No 69
>KOG3818 consensus DNA polymerase epsilon, subunit B [Replication, recombination and repair]
Probab=35.66 E-value=1.1e+02 Score=29.56 Aligned_cols=80 Identities=25% Similarity=0.326 Sum_probs=57.1
Q ss_pred hcCeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCC--CCCCCCCCeEEEE
Q 041604 14 QDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSL--PDLFREGHSVVVE 91 (162)
Q Consensus 14 ~~~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~--Pd~F~eg~~VVve 91 (162)
++...|-+||-|-+-.. ...+.+-|-|++.. . .+=.|.|.|....+.+...++. -.+|-||--|.||
T Consensus 157 ~q~~~fklt~ienLL~t---~~~~~~lvLGlLTq-----~---k~G~~~lEDpsgsVqlDlsqa~fh~glf~egC~VL~E 225 (525)
T KOG3818|consen 157 AQLKKFKLTPIENLLST---RALQSFLVLGLLTQ-----L---KEGKFHLEDPSGSVQLDLSQAKFHHGLFCEGCFVLVE 225 (525)
T ss_pred hhccccceeEHHHhhcc---ccccceeeeehhhh-----c---cCCcEEEeCCCCcEEEeecccccccceeccceEEEEe
Confidence 34455668888865432 24677888888731 1 1224888898888888887732 2489999999999
Q ss_pred EEEcCchhhhhhccccccccccccCCCCeEEEeEE
Q 041604 92 GFIKPITEEIKNVKSEKSVSENARSRDCFFSATDV 126 (162)
Q Consensus 92 G~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~l 126 (162)
|.|. +|+|+-+.+
T Consensus 226 G~f~----------------------~~vf~V~~l 238 (525)
T KOG3818|consen 226 GTFE----------------------SGVFHVNEL 238 (525)
T ss_pred eeee----------------------cceEEEeec
Confidence 9997 689998876
No 70
>KOG2732 consensus DNA polymerase delta, regulatory subunit 55 [Replication, recombination and repair]
Probab=35.59 E-value=89 Score=29.52 Aligned_cols=53 Identities=25% Similarity=0.121 Sum_probs=44.4
Q ss_pred CceEEEEEEeCCeEEEEEEcCCCCCCCCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeec
Q 041604 56 SSEMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAK 129 (162)
Q Consensus 56 ~~~~~F~vtD~~~~i~V~Y~G~~Pd~F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaK 129 (162)
+.+-+..+.|+..+|+....-+-++.+.-|.-|-|-|++.. +|+|.+++|+==
T Consensus 108 ~ped~i~LEDe~grV~L~G~~i~~~~~vTGvvvavlG~~~e---------------------~G~F~VeDv~fp 160 (435)
T KOG2732|consen 108 SPEDEIVLEDESGRVRLEGSFISHAVLVTGVVVAVLGKEAE---------------------AGRFLVEDVLFP 160 (435)
T ss_pred CccceEEEecCCceEEEEeecccccceeeeEEEEEeccccc---------------------CceEEEEEEecc
Confidence 34558999999888888777788889999999999999984 799999999853
No 71
>COG3065 Slp Starvation-inducible outer membrane lipoprotein [Cell envelope biogenesis, outer membrane]
Probab=35.04 E-value=1.6e+02 Score=24.97 Aligned_cols=59 Identities=24% Similarity=0.255 Sum_probs=40.9
Q ss_pred CCCCCcEEEeEEEecCcEEecCCCceEEEEEEeC----C----------eEEEEEEcC-CCCCCCCCCCeEEEEEEEcC
Q 041604 33 NPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDL----V----------TDILVRYQG-SLPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 33 ~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~----~----------~~i~V~Y~G-~~Pd~F~eg~~VVveG~~~~ 96 (162)
...++.+|+||.|..=+. ..+..+|.|... . .++-...+| .=|-+|+ |+-|.|.|++.+
T Consensus 50 ~~~gq~aR~GGkVvnv~n----~~~rTrlEi~slPldS~arP~l~~~~qGRfiAy~~GFlDPv~~~-gr~vTv~G~i~g 123 (191)
T COG3065 50 LYVGQQARFGGKVVNVIN----QKGRTRLEIASLPLDSGARPDLEAESQGRFIAYVNGFLDPVNFR-GRLVTVVGTIAG 123 (191)
T ss_pred ccccceeeeCcEEEEEec----CCCcEEEEEEeeccCcccCCCcCCCCCceEEEEcccccChhhhc-CcEEEEEeeecc
Confidence 356899999999974332 335677777633 1 244444455 4588999 999999999974
No 72
>PLN02221 asparaginyl-tRNA synthetase
Probab=34.35 E-value=1.7e+02 Score=28.36 Aligned_cols=71 Identities=27% Similarity=0.364 Sum_probs=46.2
Q ss_pred eCHHHHHhh--cCCCCCCCcEEEeEEEecCcEEecCCCc-eEEEEEE-eCC--eEEEEEEcCCCCC---CCCCCCeEEEE
Q 041604 21 VTPSEALEK--YQSNPSKNKFRLGGLVLEGSVAHPASSS-EMEFVVT-DLV--TDILVRYQGSLPD---LFREGHSVVVE 91 (162)
Q Consensus 21 ~tpsE~~~~--~~~~~~~~~vrv~G~V~~gSv~~~~~~~-~~~F~vt-D~~--~~i~V~Y~G~~Pd---~F~eg~~VVve 91 (162)
++.-+++.. ......++.|+|.|||.. +. . .+. .+.|.+. |+. ..|.|++....++ ....+..|-|+
T Consensus 33 ~~~~~~~~~~~~~~~~~g~~V~I~GWV~~--iR-~-~Gk~~i~Fl~LRDgs~~g~iQvVv~~~~~~~~~~L~~ES~V~V~ 108 (572)
T PLN02221 33 VLIRSILDRPDGGAGLAGQKVRIGGWVKT--GR-E-QGKGTFAFLEVNDGSCPANLQVMVDSSLYDLSTLVATGTCVTVD 108 (572)
T ss_pred eEHHHHhccccCChhcCCCEEEEEEEEEe--hh-h-CCCceEEEEEEeCCcccccEEEEEcCchhhHHhcCCCceEEEEE
Confidence 456666522 112346889999999973 32 2 232 4677654 554 4788888755442 45789999999
Q ss_pred EEEc
Q 041604 92 GFIK 95 (162)
Q Consensus 92 G~~~ 95 (162)
|.+.
T Consensus 109 G~V~ 112 (572)
T PLN02221 109 GVLK 112 (572)
T ss_pred EEEE
Confidence 9996
No 73
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=34.33 E-value=55 Score=24.37 Aligned_cols=71 Identities=15% Similarity=0.311 Sum_probs=34.7
Q ss_pred eCHHHHHhhcCCC-------CCCCcEEEeEEEecCcEEecCCCceEEEEEEeC-C--eEEEEEEcCCC---CCC--CCCC
Q 041604 21 VTPSEALEKYQSN-------PSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDL-V--TDILVRYQGSL---PDL--FREG 85 (162)
Q Consensus 21 ~tpsE~~~~~~~~-------~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~-~--~~i~V~Y~G~~---Pd~--F~eg 85 (162)
+|..++.+.+.++ +.++.++|.|.|. +|.... +... |.+.+. . ..+...+.-.- +.. ++.|
T Consensus 45 ~sa~~L~~~y~~N~~~A~~kY~gK~i~vtG~V~--~I~~~~-~~~~-~~~~~~~~~~~~v~~~~~~~~~~~~~~~~l~~G 120 (144)
T PF12869_consen 45 VSAEELYKDYKDNEVAADKKYKGKIIEVTGTVS--SIDKGF-GDNY-VVLLGTENGFAGVQCYFSNDQEKRASVAKLKKG 120 (144)
T ss_dssp EEHHHHHHHHHH-HHHHHHHHTT-EEEEEEEEE--EEEE-S-TT-E-EEEEE-TT-S-S--EEEEEEGGGHHHHHH--TT
T ss_pred ecHHHHHHHHHhCHHHHHhhcCCCEEEEEEEEE--EEEEcC-CCcE-EEEccCCCCceeEEEEEccchhhhhhHhcCCCC
Confidence 5555655443212 4689999999996 465432 2233 444444 2 23333332211 123 8999
Q ss_pred CeEEEEEEEc
Q 041604 86 HSVVVEGFIK 95 (162)
Q Consensus 86 ~~VVveG~~~ 95 (162)
+.|.+.|.+.
T Consensus 121 ~~Vti~G~~~ 130 (144)
T PF12869_consen 121 QKVTIKGICT 130 (144)
T ss_dssp SEEEEEEE--
T ss_pred CEEEEEEEEE
Confidence 9999999997
No 74
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=33.87 E-value=1.5e+02 Score=20.87 Aligned_cols=37 Identities=24% Similarity=0.266 Sum_probs=27.0
Q ss_pred EEEEEEeCC-------eEEEEEEcCCCCCCCCCCCeEEEEEEEcC
Q 041604 59 MEFVVTDLV-------TDILVRYQGSLPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 59 ~~F~vtD~~-------~~i~V~Y~G~~Pd~F~eg~~VVveG~~~~ 96 (162)
--|.|.|.. .+=-.+|.+. +...+.|+.|.|+|+..+
T Consensus 16 ~GffiQd~~~d~~~~ts~gifV~~~~-~~~~~~Gd~V~vtG~v~e 59 (78)
T cd04486 16 GGFYIQDEDGDGDPATSEGIFVYTGS-GADVAVGDLVRVTGTVTE 59 (78)
T ss_pred CEEEEEcCCCCCCCcccceEEEecCC-CCCCCCCCEEEEEEEEEe
Confidence 358899873 1224445555 888899999999999973
No 75
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=33.50 E-value=2.2e+02 Score=21.71 Aligned_cols=57 Identities=21% Similarity=0.234 Sum_probs=42.0
Q ss_pred CcEEEeEEEec----CcEEecCC-CceEEEEEEeCCeEEEEEEcCCCCCCCCCCCeEEEEEE
Q 041604 37 NKFRLGGLVLE----GSVAHPAS-SSEMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGF 93 (162)
Q Consensus 37 ~~vrv~G~V~~----gSv~~~~~-~~~~~F~vtD~~~~i~V~Y~G~~Pd~F~eg~~VVveG~ 93 (162)
..|.+.+.|.. -.+....+ ..-+...|.|....|++..=+..-+.|++|+.|-+.+-
T Consensus 15 ~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG~I~~tlW~~~a~~l~~GdvV~I~na 76 (129)
T PRK06461 15 ERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENA 76 (129)
T ss_pred CceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCEEEEEEeCCccccCCCCCEEEEECc
Confidence 68999999972 22333322 22556788898888998888877788999999999943
No 76
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=33.21 E-value=2.2e+02 Score=21.62 Aligned_cols=60 Identities=17% Similarity=0.102 Sum_probs=40.9
Q ss_pred CcEEEeEEEecCc-EEecCCC-ceEEEEEEeC-------CeEEEEEEcCC----CCCCCCCCCeEEEEEEEcC
Q 041604 37 NKFRLGGLVLEGS-VAHPASS-SEMEFVVTDL-------VTDILVRYQGS----LPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 37 ~~vrv~G~V~~gS-v~~~~~~-~~~~F~vtD~-------~~~i~V~Y~G~----~Pd~F~eg~~VVveG~~~~ 96 (162)
++|.|.|.|.... +.+.+++ .-++|.|.-. ..=++|..=|. +=+..+.|..|.|+|++..
T Consensus 4 N~v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~ 76 (121)
T PRK07459 4 NSVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITGSLKF 76 (121)
T ss_pred cEEEEEEEccCCCEEEEcCCCCEEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEEEEEe
Confidence 5788999887664 3343333 5678988743 23456666554 3446789999999999973
No 77
>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=32.80 E-value=1.7e+02 Score=20.33 Aligned_cols=55 Identities=16% Similarity=0.116 Sum_probs=36.0
Q ss_pred cEEEeEEEecCcEEecCCCceEEEEE-EeCCe-EEEEEEcCCCC-----CCCCCCCeEEEEEEEcC
Q 041604 38 KFRLGGLVLEGSVAHPASSSEMEFVV-TDLVT-DILVRYQGSLP-----DLFREGHSVVVEGFIKP 96 (162)
Q Consensus 38 ~vrv~G~V~~gSv~~~~~~~~~~F~v-tD~~~-~i~V~Y~G~~P-----d~F~eg~~VVveG~~~~ 96 (162)
+++|.|+|.. + |.. +..+.|.. .|+.. .+.|.++...+ .....|..|.|+|.+..
T Consensus 1 ~V~v~Gwv~~--~-R~~-~~~~~Fi~LrD~~g~~iQvv~~~~~~~~~~~~~l~~~s~V~V~G~v~~ 62 (86)
T cd04321 1 KVTLNGWIDR--K-PRI-VKKLSFADLRDPNGDIIQLVSTAKKDAFSLLKSITAESPVQVRGKLQL 62 (86)
T ss_pred CEEEEEeEee--E-eCC-CCceEEEEEECCCCCEEEEEECCCHHHHHHHhcCCCCcEEEEEEEEEe
Confidence 4789999963 3 221 23477754 55555 58898865321 13567999999999973
No 78
>KOG1625 consensus DNA polymerase alpha-primase complex, polymerase-associated subunit B [Replication, recombination and repair]
Probab=32.61 E-value=2e+02 Score=28.26 Aligned_cols=85 Identities=14% Similarity=0.089 Sum_probs=56.2
Q ss_pred CCCCCcEEEeEEEecCcEEecCC-CceEEEEEE---eC-CeEEEEEEcCCCCCCCCCCCeEEEEEEEcCchhhhhhcccc
Q 041604 33 NPSKNKFRLGGLVLEGSVAHPAS-SSEMEFVVT---DL-VTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSE 107 (162)
Q Consensus 33 ~~~~~~vrv~G~V~~gSv~~~~~-~~~~~F~vt---D~-~~~i~V~Y~G~~Pd~F~eg~~VVveG~~~~~~~~~~~~~~~ 107 (162)
.++...|-.-|++...+-..+.- +.+..+-.. |+ +..+++-+.-..--.+-.|+.|.|+|+-..
T Consensus 241 ~~Sq~~v~avG~I~~d~~~~~~kln~~Sv~Less~e~~~g~~Vrldls~l~e~SiFPGQIVavkG~N~~----------- 309 (600)
T KOG1625|consen 241 IPSQSSVYAVGQIVCDSTKDNGKLNEESVLLESSREDSSGVRVRLDLSRLKEYSIFPGQIVAVKGKNPT----------- 309 (600)
T ss_pred cccccceEEEEEEecCCCCcccccCccceEeeeccccCCCceEEeehhhccceeecCCcEEEEeeecCC-----------
Confidence 34667899999998766433321 111222222 22 367888887777777889999999999863
Q ss_pred ccccccccCCCCeEEEeEEeec--CCCCCCChH
Q 041604 108 KSVSENARSRDCFFSATDVLAK--HDEKYMPQE 138 (162)
Q Consensus 108 ~~~~~~~~~~dg~F~A~~lLaK--cpskY~p~e 138 (162)
++.|.|++|+-- -|..+.|-+
T Consensus 310 ----------G~~l~v~ki~~~~plp~~~~~~q 332 (600)
T KOG1625|consen 310 ----------GEKLTVEKILPIPPLPIPVQPLQ 332 (600)
T ss_pred ----------CCeEEeeeeccCCCCCCCcCchh
Confidence 689999999854 344566543
No 79
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest 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). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=32.39 E-value=2e+02 Score=21.01 Aligned_cols=62 Identities=15% Similarity=0.106 Sum_probs=42.0
Q ss_pred eeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCC-eEEEEEEcCCCCCCCCCCCeEEEEEEEcC
Q 041604 20 YVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLV-TDILVRYQGSLPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 20 y~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~-~~i~V~Y~G~~Pd~F~eg~~VVveG~~~~ 96 (162)
.++.+-|.+ +.++.||+-|.|.. .++ . .|.+.+.. ..+.|.-+. |.....+.-|=|.|+..+
T Consensus 4 rVn~~~L~~-----f~gk~V~ivGkV~~----~~~--~--~~~~~~~Dg~~v~v~l~~--~~~~~~~~~vEViG~V~~ 66 (101)
T cd04479 4 RINGAMLSQ-----FVGKTVRIVGKVEK----VDG--D--SLTLISSDGVNVTVELNR--PLDLPISGYVEVIGKVSP 66 (101)
T ss_pred eeCHHHHHh-----hCCCEEEEEEEEEE----ecC--C--eEEEEcCCCCEEEEEeCC--CCCcccCCEEEEEEEECC
Confidence 455554433 57899999999962 222 2 46666655 588887664 334567778999999985
No 80
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=32.16 E-value=4e+02 Score=24.38 Aligned_cols=56 Identities=16% Similarity=0.224 Sum_probs=39.1
Q ss_pred CCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCC-C-CC------CCCCCCeEEEEEEEc
Q 041604 35 SKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGS-L-PD------LFREGHSVVVEGFIK 95 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~-~-Pd------~F~eg~~VVveG~~~ 95 (162)
.++.|+|.|+|. ++. . .+. +.| .|.|....|.|..... . ++ .+..|..|.|+|.+.
T Consensus 11 ~g~~v~i~G~v~--~~R-~-~g~-~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~ 75 (428)
T TIGR00458 11 DGQEVTFMGWVH--EIR-D-LGG-LIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLESVVAVRGIVK 75 (428)
T ss_pred CCCEEEEEEEEE--EEe-c-CCC-cEEEEEEeCCeeEEEEEECCcCCHHHHHHHhCCCCCcEEEEEEEEE
Confidence 578999999996 232 2 233 555 5677777888877643 2 23 356799999999997
No 81
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=31.10 E-value=5.5e+02 Score=25.67 Aligned_cols=57 Identities=19% Similarity=0.234 Sum_probs=40.1
Q ss_pred CCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCCC--CC------CCCCCCeEEEEEEEcC
Q 041604 35 SKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGSL--PD------LFREGHSVVVEGFIKP 96 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~~--Pd------~F~eg~~VVveG~~~~ 96 (162)
.++.|+|.|+|.. + |.- + .+.| .|.|....+.|...... ++ ..+.+..|-|+|.+..
T Consensus 17 ~g~~V~l~GWV~~--~-R~~-G-~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~~L~~EsvV~V~G~v~~ 82 (706)
T PRK12820 17 TGREVCLAGWVDA--F-RDH-G-ELLFIHLRDRNGFIQAVFSPEAAPADVYELAASLRAEFCVALQGEVQK 82 (706)
T ss_pred CCCEEEEEEEEEE--E-EcC-C-CcEEEEEEeCCccEEEEEeCCcCCHHHHHHHhcCCCCCEEEEEeEEec
Confidence 5789999999962 3 322 3 3565 56677778888886432 22 4677999999999973
No 82
>COG1665 Predicted nucleotidyltransferase [General function prediction only]
Probab=30.91 E-value=1.1e+02 Score=27.85 Aligned_cols=58 Identities=22% Similarity=0.280 Sum_probs=44.3
Q ss_pred CCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEE---EEEEcCCCCCCCCCCCeEEEEEEEcC
Q 041604 36 KNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDI---LVRYQGSLPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 36 ~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i---~V~Y~G~~Pd~F~eg~~VVveG~~~~ 96 (162)
..++++.+.|...+..-+ ..-.+.|.|.+-.- -|.|++.---.-.+|..|++.|.+..
T Consensus 231 ~gkvki~a~V~dd~~Afd---yPa~y~Ve~~n~~~v~eVvSythtyagQaf~ge~IearG~Le~ 291 (315)
T COG1665 231 IGKVKIEAEVLDDSEAFD---YPAVYKVEDVNIDNVSEVVSYTHTYAGQAFEGERIEARGKLEE 291 (315)
T ss_pred eeeEEEEEEEcCchhhcc---CCceeEeccccccchheeEEEeeeEehhccCCcEEEEEeeeee
Confidence 468899999988887765 23557777765322 68888887777789999999999973
No 83
>COG3689 Predicted membrane protein [Function unknown]
Probab=30.55 E-value=1.2e+02 Score=27.09 Aligned_cols=75 Identities=15% Similarity=0.205 Sum_probs=46.0
Q ss_pred eeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCC-----eEEEEEEcCCCCCCCCCCCeEEEEEEE
Q 041604 20 YVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLV-----TDILVRYQGSLPDLFREGHSVVVEGFI 94 (162)
Q Consensus 20 y~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~-----~~i~V~Y~G~~Pd~F~eg~~VVveG~~ 94 (162)
|+..-|.+..+-+...|+++.+.|.|-.+..-.+..---.||-|+--. --+.|.-. --+.+.+...+.|+|+|
T Consensus 159 yl~~m~~iy~~pdef~Gk~Ie~tGFVy~~~~~~~N~lflaRFgiicC~ADa~vygl~v~~~--~~~~y~ndtWltvkGtl 236 (271)
T COG3689 159 YLDTMEEIYNYPDEFAGKKIEFTGFVYNDESFPKNYLFLARFGIICCAADAGVYGLLVELD--NQTDYKNDTWLTVKGTL 236 (271)
T ss_pred HHHHHHHHhcCchhhcCceEEEEEEEECCCCCCcceeehhhhheeeeeccceeEEEEEEcc--ccccCCCCceEEEEeEE
Confidence 333334333333357899999999997533222222334577777432 45566543 44567788889999999
Q ss_pred cC
Q 041604 95 KP 96 (162)
Q Consensus 95 ~~ 96 (162)
..
T Consensus 237 ~~ 238 (271)
T COG3689 237 SS 238 (271)
T ss_pred Ee
Confidence 73
No 84
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=30.51 E-value=2.3e+02 Score=29.61 Aligned_cols=61 Identities=25% Similarity=0.308 Sum_probs=41.7
Q ss_pred CCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcC----CCCCCCCCCCeEEEEEEEc
Q 041604 35 SKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQG----SLPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G----~~Pd~F~eg~~VVveG~~~ 95 (162)
.++.+++.|+|..=.......+..+.| +|.|....+.+..=. ..-+.+.+|..|.|+|+++
T Consensus 976 ~g~~V~v~G~I~~vk~~~TKkG~~mafltLeD~TG~iEvviFp~~ye~~~~~L~~g~iV~V~GkVe 1041 (1135)
T PRK05673 976 GGSVVTVAGLVVSVRRRVTKRGNKMAIVTLEDLSGRIEVMLFSEALEKYRDLLEEDRIVVVKGQVS 1041 (1135)
T ss_pred cCceEEEEEEEEEEEecccCCCCeEEEEEEEeCCCcEEEEECHHHHHHHHHHhccCCEEEEEEEEE
Confidence 467899999998544444444555655 577877777665432 1223578999999999997
No 85
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=30.00 E-value=2.7e+02 Score=21.90 Aligned_cols=59 Identities=17% Similarity=0.093 Sum_probs=39.9
Q ss_pred CcEEEeEEEecCc-EEecCCCc-----eEEEEEEeC-------C-------eEEEEEEcC----CCCCCCCCCCeEEEEE
Q 041604 37 NKFRLGGLVLEGS-VAHPASSS-----EMEFVVTDL-------V-------TDILVRYQG----SLPDLFREGHSVVVEG 92 (162)
Q Consensus 37 ~~vrv~G~V~~gS-v~~~~~~~-----~~~F~vtD~-------~-------~~i~V~Y~G----~~Pd~F~eg~~VVveG 92 (162)
+.|.|.|.|.... +.+.+++. .++|.|.-. + .-++|..=| .+...++.|..|.|+|
T Consensus 3 N~V~LiGrLg~DPElr~t~~G~~~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae~v~~~l~KG~~V~V~G 82 (148)
T PRK08182 3 THFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLVEG 82 (148)
T ss_pred cEEEEEEECCCCCeEEECCCCCeeeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHHHHHHhcCCCCEEEEEE
Confidence 4788888886554 33444454 577888411 1 235677666 3667789999999999
Q ss_pred EEc
Q 041604 93 FIK 95 (162)
Q Consensus 93 ~~~ 95 (162)
++.
T Consensus 83 rL~ 85 (148)
T PRK08182 83 RME 85 (148)
T ss_pred EEE
Confidence 996
No 86
>PLN03094 Substrate binding subunit of ER-derived-lipid transporter; Provisional
Probab=29.81 E-value=1.8e+02 Score=26.70 Aligned_cols=58 Identities=16% Similarity=0.157 Sum_probs=34.9
Q ss_pred eeee--CHHHHHhhcCCCCCCCcEEEeEEEecCcEE---ecCCCceEEEEEEeCC------eEEEEEEcCCCCC
Q 041604 18 VFYV--TPSEALEKYQSNPSKNKFRLGGLVLEGSVA---HPASSSEMEFVVTDLV------TDILVRYQGSLPD 80 (162)
Q Consensus 18 ~yy~--tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~---~~~~~~~~~F~vtD~~------~~i~V~Y~G~~Pd 80 (162)
.|++ .+.++-. -..+..||+.|.-+ |.|. -++..-.++|.|.|.. ....|...|.+-+
T Consensus 117 ~Y~~~a~F~~a~G----L~~Gs~Vr~~GV~V-G~V~~I~l~~~~V~V~~~I~~~~~~Ip~ds~A~I~~~gLLG~ 185 (370)
T PLN03094 117 KYQAVFEFPQACG----ICVGTPVRIRGVTV-GNVVRVRPSLEKIDVVVEVEDDKIVIPRNSLVEVNQSGLIME 185 (370)
T ss_pred eEEEEEecCCCCC----CCCCCceEEcCEEe-eEEEEEEecCCeEEEEEEEecCceecCCCCEEEEeeCCcccc
Confidence 4555 3455432 35788999999543 4443 3444557778886432 4666777777653
No 87
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=29.65 E-value=2.9e+02 Score=22.07 Aligned_cols=58 Identities=19% Similarity=0.230 Sum_probs=38.4
Q ss_pred cEEE--eEEEecCcEEecCCCceEEEEEEeC-CeEEEEEEcCCC-CC--CCCCCCeEEEEEEEc
Q 041604 38 KFRL--GGLVLEGSVAHPASSSEMEFVVTDL-VTDILVRYQGSL-PD--LFREGHSVVVEGFIK 95 (162)
Q Consensus 38 ~vrv--~G~V~~gSv~~~~~~~~~~F~vtD~-~~~i~V~Y~G~~-Pd--~F~eg~~VVveG~~~ 95 (162)
.++| .|.|..=.-.....+..-+|.|.=. +.+|.|.++=.+ |. ..++|+.|-+-|.|.
T Consensus 36 ~~qv~g~G~V~~vLpdd~~GsrHQ~Fiv~l~~g~tllIahNIDlaprip~l~~GD~V~f~GeYe 99 (131)
T PF11948_consen 36 DVQVSGCGTVVKVLPDDNKGSRHQRFIVRLSSGQTLLIAHNIDLAPRIPWLQKGDQVEFYGEYE 99 (131)
T ss_pred CeeEeccEEEEEECcccCCCCcceEEEEEeCCCCEEEEEeccCccccCcCcCCCCEEEEEEEEE
Confidence 4455 5566432222223456778888754 589999998433 43 578999999999996
No 88
>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=29.53 E-value=1.8e+02 Score=19.69 Aligned_cols=54 Identities=26% Similarity=0.334 Sum_probs=36.9
Q ss_pred cEEEeEEEecCcEEecCCCceEEEEEE-eCCe--EEEEEEcCCCC-----CCCCCCCeEEEEEEEcC
Q 041604 38 KFRLGGLVLEGSVAHPASSSEMEFVVT-DLVT--DILVRYQGSLP-----DLFREGHSVVVEGFIKP 96 (162)
Q Consensus 38 ~vrv~G~V~~gSv~~~~~~~~~~F~vt-D~~~--~i~V~Y~G~~P-----d~F~eg~~VVveG~~~~ 96 (162)
.++|.|+|. ++. . ...+.|... |+.. .+.+.+..... .....|..|-|+|.+..
T Consensus 1 ~v~v~Gwv~--~~R-~--~g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~ 62 (82)
T cd04318 1 EVTVNGWVR--SVR-D--SKKISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLVK 62 (82)
T ss_pred CEEEEEeEE--EEE-c--CCcEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEEe
Confidence 378999996 232 2 235778766 7654 58888865422 24578999999999873
No 89
>PTZ00425 asparagine-tRNA ligase; Provisional
Probab=25.98 E-value=2.4e+02 Score=27.44 Aligned_cols=58 Identities=14% Similarity=0.064 Sum_probs=38.4
Q ss_pred CCCCcEEEeEEEecCcEEecCCCceEEEEEE-eCC--eEEEEEEcCCCCCC------CCCCCeEEEEEEEc
Q 041604 34 PSKNKFRLGGLVLEGSVAHPASSSEMEFVVT-DLV--TDILVRYQGSLPDL------FREGHSVVVEGFIK 95 (162)
Q Consensus 34 ~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vt-D~~--~~i~V~Y~G~~Pd~------F~eg~~VVveG~~~ 95 (162)
..++.|+|.|||.. +. .-.+..+.|... |+. ..+.|++... +.. ...|..|.|+|++.
T Consensus 79 ~~g~~Vtl~GWv~~--iR-~~g~~~~~Fv~lrDgsg~~~iQiVv~~~-~~~~~~l~~l~~gs~v~v~G~v~ 145 (586)
T PTZ00425 79 YIDQIITVCGWSKA--VR-KQGGGRFCFVNLNDGSCHLNLQIIVDQS-IENYEKLLKCGVGCCFRFTGKLI 145 (586)
T ss_pred cCCCEEEEEEEEee--hh-hcCCceEEEEEEECCCCCcceEEEECCc-hHHHHHHhcCCCccEEEEEEEEE
Confidence 45789999999962 32 222225778765 443 2578887643 223 35699999999997
No 90
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=25.76 E-value=3e+02 Score=22.38 Aligned_cols=59 Identities=12% Similarity=0.084 Sum_probs=38.3
Q ss_pred cEEEeEEEecCcEE-ecC-CCceEEEEEEeC--------CeEEEEEEcCC----CCCCCCCCCeEEEEEEEcC
Q 041604 38 KFRLGGLVLEGSVA-HPA-SSSEMEFVVTDL--------VTDILVRYQGS----LPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 38 ~vrv~G~V~~gSv~-~~~-~~~~~~F~vtD~--------~~~i~V~Y~G~----~Pd~F~eg~~VVveG~~~~ 96 (162)
.|.|.|.|....-. +.+ +...+.|.|.-. ..=++|..=|. +...++.|..|.|+|++..
T Consensus 3 ~V~LiGrLg~DPElR~t~sG~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~yL~KG~~V~VeGrL~~ 75 (161)
T PRK06293 3 FGYIVGRLGADPEERMTSKGKRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPYLKKGSGVIVAGEMSP 75 (161)
T ss_pred EEEEEEEecCCCeEEEcCCCCEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHhCCCCCEEEEEEEEEe
Confidence 67888887655433 333 334567888732 12455655553 4556899999999999973
No 91
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=25.53 E-value=2.4e+02 Score=29.57 Aligned_cols=61 Identities=21% Similarity=0.236 Sum_probs=41.5
Q ss_pred CCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcC----CCCCCCCCCCeEEEEEEEc
Q 041604 35 SKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQG----SLPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G----~~Pd~F~eg~~VVveG~~~ 95 (162)
.++.++|.|+|..-...+...+..|.| ++.|....+.|..-. ..-+.+.+|..++|+|+++
T Consensus 942 ~~~~v~v~g~i~~~~~~~tk~g~~maf~~leD~tg~~e~~vFp~~y~~~~~~l~~~~~~~v~G~v~ 1007 (1107)
T PRK06920 942 KKKVQRAIVYITSVKVIRTKKGQKMAFITFCDQNDEMEAVVFPETYIHFSDKLQEGAIVLVDGTIE 1007 (1107)
T ss_pred CCCEEEEEEEEEEeEeecCCCCCeEEEEEEeeCCCcEEEEECHHHHHHHHHHhccCCEEEEEEEEE
Confidence 366899999998544444455566765 556666666665321 1234577899999999997
No 92
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=24.06 E-value=6.9e+02 Score=27.13 Aligned_cols=62 Identities=19% Similarity=0.310 Sum_probs=40.5
Q ss_pred CCCcEEEeEEEecCcE-EecCCCceEEEEEEeCCeEEEE--EEcCC----CCCCCCCCCeEEEEEEEcC
Q 041604 35 SKNKFRLGGLVLEGSV-AHPASSSEMEFVVTDLVTDILV--RYQGS----LPDLFREGHSVVVEGFIKP 96 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv-~~~~~~~~~~F~vtD~~~~i~V--~Y~G~----~Pd~F~eg~~VVveG~~~~ 96 (162)
..+.|.|.|.|-.=.. ....+..-++|.|||....|.| ..... .-+.++.|..|.|.|.+.-
T Consensus 235 ~~~~v~i~G~if~~e~~~~k~~~~~~~~~~td~~~s~~~k~f~~~~~~~~~~~~~~~g~~v~~~g~~~~ 303 (1437)
T PRK00448 235 EERRVVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSRDKEDLKKFDEIKKGDWVKVRGSVQN 303 (1437)
T ss_pred cCCeEEEEEEEEEEEEEeccCCCEEEEEEEEcCCCCEEEEEEecCcchhHHHhcCCCCCEEEEEEEEec
Confidence 3568999998853222 1222345678999998755544 33221 1256899999999999963
No 93
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=23.30 E-value=3.9e+02 Score=22.10 Aligned_cols=61 Identities=15% Similarity=0.181 Sum_probs=41.4
Q ss_pred CCcEEEeEEEecCcEE-ecCCC-ceEEEEEEeCC---------------eEEEEEEcCC----CCCCCCCCCeEEEEEEE
Q 041604 36 KNKFRLGGLVLEGSVA-HPASS-SEMEFVVTDLV---------------TDILVRYQGS----LPDLFREGHSVVVEGFI 94 (162)
Q Consensus 36 ~~~vrv~G~V~~gSv~-~~~~~-~~~~F~vtD~~---------------~~i~V~Y~G~----~Pd~F~eg~~VVveG~~ 94 (162)
...|.|.|.+...... +.+++ ..++|.|.-.. .-++|.+=+. +-..++.|..|+|+|+|
T Consensus 4 ~~~VtLiGrL~~DPElR~t~sG~~va~FrVAv~~r~~~~~~g~~~d~~t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~GrL 83 (186)
T PRK07772 4 DTTITVVGNLTADPELRFTPSGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVTGRL 83 (186)
T ss_pred cCEEEEEEEeCCCCeEEEcCCCCEEEEEEEEecCcceecCCCcEeccCceEEEEEEecHHHHHHHHhcCCCCEEEEEEEE
Confidence 4578899988765543 33333 45678887321 1456766664 55678999999999999
Q ss_pred cC
Q 041604 95 KP 96 (162)
Q Consensus 95 ~~ 96 (162)
..
T Consensus 84 ~~ 85 (186)
T PRK07772 84 KQ 85 (186)
T ss_pred Ec
Confidence 74
No 94
>TIGR02922 conserved hypothetical protein TIGR02922. Two members of this family are found in Colwellia psychrerythraea 34H and one each in various other species of Colwellia and Shewanella. One member from C. psychrerythraea is of special interest because it is preceded by the same cis-regulatory site as a number of genes that have the PEP-CTERM domain described by TIGR02595.
Probab=22.62 E-value=33 Score=24.60 Aligned_cols=28 Identities=32% Similarity=0.598 Sum_probs=21.2
Q ss_pred eEEEEEEcC--CCCCCCCCCCeEE--EEEEEc
Q 041604 68 TDILVRYQG--SLPDLFREGHSVV--VEGFIK 95 (162)
Q Consensus 68 ~~i~V~Y~G--~~Pd~F~eg~~VV--veG~~~ 95 (162)
+.++|.-.| .+|..||.|.++| +||.++
T Consensus 25 ~~~~i~~~GrvmiPqeFkrGKsIiAV~EGe~~ 56 (67)
T TIGR02922 25 QSFPVNESGRVMIPQEFKRGKSIIAVCEGEIT 56 (67)
T ss_pred cCCCccccccEEcchHHcCCCeEEEEEeccee
Confidence 456666666 5899999999875 678775
No 95
>TIGR03503 conserved hypothetical protein TIGR03503. This set of conserved hypothetical protein has a phylogenetic range that closely matches that of TIGR03501, a putative C-terminal protein targeting signal.
Probab=22.52 E-value=6.2e+02 Score=23.42 Aligned_cols=49 Identities=20% Similarity=0.239 Sum_probs=31.7
Q ss_pred cCCCCCCCCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCC
Q 041604 75 QGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMP 136 (162)
Q Consensus 75 ~G~~Pd~F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p 136 (162)
+..--++|+.+..| -|.|.+.++.+ .++.+||+|.+.--|.--|-+|+.
T Consensus 140 ~~~~~e~~~~~~~v--vg~f~DdG~g~-----------DE~p~DGvFT~~l~l~~~~G~Y~~ 188 (374)
T TIGR03503 140 NNAEDENFGADPIV--VGEFEDDGEGL-----------DERPGDGIFTGEFNLDVAPGEYRP 188 (374)
T ss_pred CCccccccccCCEE--EEeeccCCccC-----------CCCCCCceEEEEeeccCCCceEEE
Confidence 34445578777754 45665443333 234569999998877777888875
No 96
>PF09558 DUF2375: Protein of unknown function (DUF2375); InterPro: IPR014271 Two members of this family are found in Colwellia psychrerythraea (strain 34H / ATCC BAA-681) and one each in various other species of Colwellia and Shewanella. One member from C. psychrerythraea is of special interest because it is preceded by the same cis-regulatory site as a number of genes that have the PEP-CTERM domain described by IPR013424 from INTERPRO.
Probab=22.42 E-value=42 Score=24.36 Aligned_cols=28 Identities=39% Similarity=0.668 Sum_probs=20.6
Q ss_pred eEEEEEEcC--CCCCCCCCCCeEE--EEEEEc
Q 041604 68 TDILVRYQG--SLPDLFREGHSVV--VEGFIK 95 (162)
Q Consensus 68 ~~i~V~Y~G--~~Pd~F~eg~~VV--veG~~~ 95 (162)
+.+++.-.| .+|.-||+|.++| +||.++
T Consensus 27 ~~~~~~~~grv~iP~~Fr~GKsIiAVleGe~~ 58 (71)
T PF09558_consen 27 TGLPVSESGRVMIPQSFRRGKSIIAVLEGECK 58 (71)
T ss_pred cCCccccCccEEChHHHcCCceEEEEEcCcee
Confidence 355666666 4899999999875 577765
No 97
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=21.62 E-value=3.4e+02 Score=21.74 Aligned_cols=72 Identities=17% Similarity=0.195 Sum_probs=44.7
Q ss_pred CcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCCCCCCCCCCeEEEEEEEcCchhhhhhccccccccccccC
Q 041604 37 NKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARS 116 (162)
Q Consensus 37 ~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~Pd~F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~ 116 (162)
..++=-|.|.=+... .-+..++|.+.=.+ .+|.+||+++-+..
T Consensus 78 ~~~~kvgvvRYnAF~--dmGg~LSFslAlLD---------------~~~nGvVltsI~~R-------------------- 120 (151)
T PF14584_consen 78 NCVQKVGVVRYNAFE--DMGGDLSFSLALLD---------------DNNNGVVLTSIHSR-------------------- 120 (151)
T ss_pred hccceEEEEEccCcc--cccccceeeeEEEe---------------CCCCEEEEEeeecC--------------------
Confidence 345555555433332 24566777665211 46889999999974
Q ss_pred CCCeEEEeEEeecCCCCCC-ChHHHHHHHHh
Q 041604 117 RDCFFSATDVLAKHDEKYM-PQEVAAAIEKN 146 (162)
Q Consensus 117 ~dg~F~A~~lLaKcpskY~-p~eva~~~~~~ 146 (162)
++.+.--+=+.+=-|.|. .+|-.++++++
T Consensus 121 -e~s~~YaK~I~~G~S~~~LS~EE~eal~~A 150 (151)
T PF14584_consen 121 -EESRTYAKPIVNGQSSYPLSEEEKEALEKA 150 (151)
T ss_pred -CCcEEEEEEecCCcccccCCHHHHHHHHHh
Confidence 455554455556677788 77878888664
No 98
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=21.44 E-value=3e+02 Score=29.05 Aligned_cols=61 Identities=15% Similarity=0.098 Sum_probs=40.9
Q ss_pred CCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEc-C---CCCCCCCCCCeEEEEEEEc
Q 041604 35 SKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQ-G---SLPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~-G---~~Pd~F~eg~~VVveG~~~ 95 (162)
.+..++|.|+|..-.......+..|.| ++.|....+.|+-- . ..-+.+++|..++|+|+++
T Consensus 999 ~~~~v~v~g~i~~~k~~~Tk~G~~maf~~leD~tg~~e~vvFp~~y~~~~~~l~~~~~~~v~g~v~ 1064 (1170)
T PRK07374 999 DKAKVSAIAMIPEMKQVTTRKGDRMAILQLEDLTGSCEAVVFPKSYERLSDHLMTDTRLLVWAKVD 1064 (1170)
T ss_pred CCCEEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHHHHHHHHHHhccCCEEEEEEEEE
Confidence 467899999997544333445556765 55677666655432 1 1223578899999999997
No 99
>KOG3206 consensus Alpha-tubulin folding cofactor B [Posttranslational modification, protein turnover, chaperones]
Probab=20.64 E-value=1.2e+02 Score=26.55 Aligned_cols=47 Identities=26% Similarity=0.323 Sum_probs=34.4
Q ss_pred eEEEEEEcCCCCCCCCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCC
Q 041604 68 TDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYM 135 (162)
Q Consensus 68 ~~i~V~Y~G~~Pd~F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~ 135 (162)
.+=.|+|.|++| |++|..|=|+ |+. -| --.||.|....+. -|+-+|-
T Consensus 165 Rrg~vrYvG~~~--~k~G~wiGVe--ydE---pl-------------GKnDGsv~G~ryF-~c~p~yG 211 (234)
T KOG3206|consen 165 RRGTVRYVGPLE--FKPGYWIGVE--YDE---PL-------------GKNDGSVNGKRYF-ECAPKYG 211 (234)
T ss_pred cceEEEEecccC--CCCceEEEEe--cCC---cc-------------ccCCCcccceEee-ecCCccC
Confidence 466799999999 9999988775 431 11 1117888888887 7888884
No 100
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=20.44 E-value=4.6e+02 Score=21.22 Aligned_cols=60 Identities=20% Similarity=0.233 Sum_probs=40.5
Q ss_pred CCcEEEeEEEecCc-EEecCC-CceEEEEEEeCC-------------eEEEEEEcCC----CCCCCCCCCeEEEEEEEc
Q 041604 36 KNKFRLGGLVLEGS-VAHPAS-SSEMEFVVTDLV-------------TDILVRYQGS----LPDLFREGHSVVVEGFIK 95 (162)
Q Consensus 36 ~~~vrv~G~V~~gS-v~~~~~-~~~~~F~vtD~~-------------~~i~V~Y~G~----~Pd~F~eg~~VVveG~~~ 95 (162)
=+++.|.|.|.... +.+.++ ...+.|.|.-.. .-++|..-|. +-+..+.|..|.|+|++.
T Consensus 5 ~Nkv~LiGrLg~DPelr~t~~G~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae~v~~~L~KGs~V~VeGrL~ 83 (164)
T PRK08763 5 INKVILVGNLGNDPDIKYTQSGMTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGEIAGEYLRKGSQCYIEGSIR 83 (164)
T ss_pred ceEEEEEEEecCCCeEEEcCCCCeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHHHHHHhcCCCCEEEEEEEEE
Confidence 46889999886553 444443 355778887321 1256666564 445689999999999997
No 101
>PF09144 YpM: Yersinia pseudotuberculosis mitogen; InterPro: IPR015227 Members of this family of Yersinia pseudotuberculosis mitogens adopt a sandwich structure consisting of nine strands in two beta sheets, in a jelly-roll topology. As with other superantigens, they are able to excessively activate T cells by binding to the T cell receptor []. ; PDB: 1PM4_B 1POQ_A.
Probab=20.39 E-value=25 Score=27.07 Aligned_cols=8 Identities=50% Similarity=0.588 Sum_probs=4.9
Q ss_pred eEEeecCC
Q 041604 124 TDVLAKHD 131 (162)
Q Consensus 124 ~~lLaKcp 131 (162)
.++|+|||
T Consensus 109 sdvl~kcp 116 (117)
T PF09144_consen 109 SDVLMKCP 116 (117)
T ss_dssp GGBSSS--
T ss_pred cchhhcCC
Confidence 47999998
No 102
>TIGR00996 Mtu_fam_mce virulence factor Mce family protein. Members of this paralogous family are found as six tandem homologous proteins in the same orientation per cassette, in four separate cassettes in Mycobacterium tuberculosis. The six members of each cassette represent six subfamilies. One subfamily includes the protein mce (mycobacterial cell entry), a virulence protein required for invasion of non-phagocytic cells.
Probab=20.13 E-value=2.7e+02 Score=23.23 Aligned_cols=47 Identities=19% Similarity=0.255 Sum_probs=29.6
Q ss_pred cCeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcE---EecCCCceEEEEEEeC
Q 041604 15 DQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSV---AHPASSSEMEFVVTDL 66 (162)
Q Consensus 15 ~~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv---~~~~~~~~~~F~vtD~ 66 (162)
+...|+..+.++.. -..+..|++.|. .-|.| ..+++.-.++|.|.+.
T Consensus 31 ~~~~~~~~f~~~~G----L~~g~~V~~~Gv-~VG~V~~i~~~~~~v~v~~~i~~~ 80 (291)
T TIGR00996 31 GTYTVYAYFTDAGG----LYPGSKVRVRGV-PVGKVTAISLPGNGARVTFSLDRG 80 (291)
T ss_pred CCeEEEEEECCCcC----CCCCCceEEcce-EEEEEEEEEecCCEEEEEEEecCC
Confidence 35667777777632 357889999993 33544 3444555666776554
Done!