Query 033186
Match_columns 125
No_of_seqs 68 out of 70
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 10:52:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033186.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033186hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF15490 Ten1_2: Telomere-capp 100.0 1.1E-47 2.4E-52 280.6 14.4 112 6-119 2-118 (118)
2 PF08661 Rep_fac-A_3: Replicat 99.2 3.7E-10 8.1E-15 80.3 10.6 86 26-116 17-106 (109)
3 cd04479 RPA3 RPA3: A subfamily 98.9 1.7E-08 3.8E-13 71.3 10.6 81 26-115 14-97 (101)
4 PF12658 Ten1: Telomere cappin 98.6 1.6E-06 3.5E-11 63.9 11.1 103 4-110 6-124 (124)
5 cd04478 RPA2_DBD_D RPA2_DBD_D: 88.6 5.4 0.00012 26.6 8.1 75 30-105 2-85 (95)
6 PRK13254 cytochrome c-type bio 85.3 6.9 0.00015 29.6 7.7 95 11-111 37-138 (148)
7 PF03100 CcmE: CcmE; InterPro 84.9 13 0.00028 27.1 9.9 67 11-79 36-108 (131)
8 cd04322 LysRS_N LysRS_N: N-ter 75.9 16 0.00034 25.2 6.4 68 30-97 2-80 (108)
9 PRK05159 aspC aspartyl-tRNA sy 72.8 49 0.0011 28.7 10.0 82 12-97 5-97 (437)
10 PF03843 Slp: Outer membrane l 72.1 14 0.0003 28.1 5.8 75 8-83 16-107 (160)
11 PRK05813 single-stranded DNA-b 71.9 50 0.0011 26.5 9.6 79 11-95 50-140 (219)
12 PF01455 HupF_HypC: HupF/HypC 71.0 27 0.00058 23.0 6.3 42 32-75 5-46 (68)
13 PF09465 LBR_tudor: Lamin-B re 64.7 36 0.00078 22.1 6.1 25 33-57 24-49 (55)
14 TIGR00752 slp outer membrane l 52.0 1.1E+02 0.0025 23.9 8.0 81 13-95 35-140 (182)
15 TIGR00458 aspS_arch aspartyl-t 51.9 1.6E+02 0.0035 25.5 10.6 72 26-97 11-94 (428)
16 COG0186 RpsQ Ribosomal protein 48.5 29 0.00064 24.4 3.5 31 4-38 54-84 (87)
17 TIGR00499 lysS_bact lysyl-tRNA 47.5 2.1E+02 0.0045 25.5 10.1 71 26-96 52-133 (496)
18 cd04478 RPA2_DBD_D RPA2_DBD_D: 47.5 35 0.00077 22.5 3.8 25 21-45 45-69 (95)
19 PLN02502 lysyl-tRNA synthetase 47.0 2.3E+02 0.0049 25.8 10.6 71 26-96 107-190 (553)
20 PF10451 Stn1: Telomere regula 46.8 1.6E+02 0.0035 24.1 10.1 83 28-113 67-165 (256)
21 cd04483 hOBFC1_like hOBFC1_lik 46.8 30 0.00064 23.8 3.3 22 22-43 61-82 (92)
22 PF07866 DUF1653: Protein of u 46.6 30 0.00064 22.9 3.1 20 70-89 9-28 (64)
23 cd04486 YhcR_OBF_like YhcR_OBF 44.3 33 0.00071 22.9 3.2 24 22-45 43-66 (78)
24 cd04316 ND_PkAspRS_like_N ND_P 43.4 1.1E+02 0.0023 21.0 10.3 72 26-97 11-94 (108)
25 PF01336 tRNA_anti-codon: OB-f 42.7 78 0.0017 19.3 9.7 65 30-94 1-72 (75)
26 PRK00513 minC septum formation 41.5 55 0.0012 25.8 4.5 56 23-78 127-183 (214)
27 PRK13165 cytochrome c-type bio 41.0 1.7E+02 0.0036 22.6 8.7 70 11-80 37-116 (160)
28 PRK09507 cspE cold shock prote 41.0 1E+02 0.0022 20.0 7.4 45 31-75 3-52 (69)
29 TIGR00457 asnS asparaginyl-tRN 40.9 2.5E+02 0.0054 24.6 10.0 71 25-96 14-98 (453)
30 PF03088 Str_synth: Strictosid 40.1 26 0.00057 24.3 2.2 20 31-50 34-53 (89)
31 PRK15464 cold shock-like prote 39.0 98 0.0021 20.4 4.8 49 30-78 3-56 (70)
32 cd04317 EcAspRS_like_N EcAspRS 38.8 1.4E+02 0.0031 21.1 9.3 57 26-82 13-77 (135)
33 COG3065 Slp Starvation-inducib 37.4 2.1E+02 0.0046 22.8 8.4 80 13-95 40-145 (191)
34 PRK10943 cold shock-like prote 36.0 1.2E+02 0.0027 19.6 7.3 49 31-81 3-56 (69)
35 PF03775 MinC_C: Septum format 35.8 93 0.002 22.2 4.6 67 9-82 18-85 (105)
36 PF08863 YolD: YolD-like prote 35.0 1.3E+02 0.0028 19.6 5.1 36 26-61 52-88 (92)
37 PHA02783 uncharacterized prote 34.9 96 0.0021 23.8 4.7 58 19-76 91-167 (181)
38 cd04488 RecG_wedge_OBF RecG_we 33.4 56 0.0012 19.7 2.8 19 22-40 44-62 (75)
39 PRK13150 cytochrome c-type bio 32.5 2.3E+02 0.0051 21.8 8.4 71 11-81 37-117 (159)
40 PRK03359 putative electron tra 31.4 60 0.0013 26.5 3.4 51 54-115 2-52 (256)
41 PF13374 TPR_10: Tetratricopep 31.2 44 0.00094 17.9 1.8 19 102-120 22-40 (42)
42 COG0250 NusG Transcription ant 30.9 1.9E+02 0.004 22.4 5.9 41 23-63 123-175 (178)
43 cd01735 LSm12_N LSm12 belongs 30.4 1.4E+02 0.0031 19.4 4.4 34 32-65 19-60 (61)
44 PRK14699 replication factor A; 30.4 2.2E+02 0.0047 25.5 6.9 30 23-52 230-259 (484)
45 PRK04804 minC septum formation 30.2 1.6E+02 0.0035 23.2 5.5 55 23-77 139-194 (221)
46 PRK02983 lysS lysyl-tRNA synth 30.1 5.5E+02 0.012 25.4 10.8 70 25-94 649-729 (1094)
47 PRK00484 lysS lysyl-tRNA synth 29.9 4E+02 0.0086 23.7 10.3 71 26-96 53-133 (491)
48 PRK13159 cytochrome c-type bio 29.4 2.6E+02 0.0057 21.4 7.1 68 11-80 37-110 (155)
49 PF04189 Gcd10p: Gcd10p family 28.6 44 0.00095 28.0 2.2 37 4-43 2-42 (299)
50 PRK12445 lysyl-tRNA synthetase 28.2 4.4E+02 0.0095 23.6 10.7 72 26-97 64-146 (505)
51 PLN02221 asparaginyl-tRNA synt 27.7 4.6E+02 0.01 24.1 8.6 87 10-97 31-134 (572)
52 PF05606 DUF777: Borrelia burg 27.5 71 0.0015 25.3 3.0 41 26-66 30-71 (181)
53 PRK15463 cold shock-like prote 27.5 1.8E+02 0.0039 19.0 7.1 49 31-81 4-57 (70)
54 TIGR01222 minC septum site-det 27.3 1.1E+02 0.0025 23.9 4.2 56 23-78 137-193 (217)
55 COG1107 Archaea-specific RecJ- 27.1 2.2E+02 0.0048 26.9 6.5 85 25-119 211-304 (715)
56 PRK09890 cold shock protein Cs 26.5 1.9E+02 0.0041 18.8 7.7 46 31-76 4-54 (70)
57 PRK05610 rpsQ 30S ribosomal pr 25.8 1.3E+02 0.0029 20.6 3.8 29 4-36 52-80 (84)
58 PLN02850 aspartate-tRNA ligase 25.5 5E+02 0.011 23.4 10.4 84 10-97 68-169 (530)
59 PF14485 DUF4431: Domain of un 25.4 62 0.0013 20.0 1.9 19 25-43 17-35 (48)
60 cd00430 PLPDE_III_AR Type III 24.7 1.1E+02 0.0025 25.1 4.0 37 26-78 296-332 (367)
61 PF08922 DUF1905: Domain of un 24.5 36 0.00077 22.8 0.8 65 8-75 11-78 (80)
62 cd04458 CSP_CDS Cold-Shock Pro 24.2 1.8E+02 0.0039 17.9 4.9 46 33-78 2-52 (65)
63 cd04489 ExoVII_LU_OBF ExoVII_L 23.9 1.7E+02 0.0037 18.2 3.9 22 19-40 41-62 (78)
64 COG3218 ABC-type uncharacteriz 23.9 2.4E+02 0.0051 22.8 5.4 74 36-110 102-186 (205)
65 TIGR03635 S17_bact 30S ribosom 23.8 64 0.0014 21.5 1.9 20 3-22 46-65 (71)
66 PRK13992 minC septum formation 23.7 1.7E+02 0.0037 22.9 4.6 52 23-74 122-174 (205)
67 cd04492 YhaM_OBF_like YhaM_OBF 23.3 1.9E+02 0.0042 17.8 4.2 20 21-40 44-63 (83)
68 PRK10354 RNA chaperone/anti-te 23.2 2.2E+02 0.0047 18.4 7.5 48 32-81 5-57 (70)
69 PRK10694 acyl-CoA esterase; Pr 22.9 3E+02 0.0065 19.9 6.2 42 54-97 56-98 (133)
70 PRK03511 minC septum formation 21.9 1.9E+02 0.0041 23.1 4.5 57 23-79 147-204 (228)
71 cd04323 AsnRS_cyto_like_N AsnR 21.6 2.4E+02 0.0052 18.3 6.7 27 66-92 46-77 (84)
72 CHL00142 rps17 ribosomal prote 21.6 1.7E+02 0.0037 20.1 3.8 30 4-37 49-78 (84)
73 TIGR03170 flgA_cterm flagella 21.4 1.6E+02 0.0035 20.3 3.7 38 2-40 45-82 (122)
74 PF10726 DUF2518: Protein of f 20.7 26 0.00056 26.9 -0.6 63 38-105 75-138 (145)
75 PTZ00385 lysyl-tRNA synthetase 20.6 4.1E+02 0.0089 24.9 7.0 70 27-96 107-188 (659)
76 COG0832 UreB Urea amidohydrola 20.6 1.4E+02 0.003 21.8 3.2 23 54-76 21-43 (106)
No 1
>PF15490 Ten1_2: Telomere-capping, CST complex subunit
Probab=100.00 E-value=1.1e-47 Score=280.59 Aligned_cols=112 Identities=49% Similarity=0.690 Sum_probs=108.1
Q ss_pred CCCCeEEEccccccCCcccCCCCeEEEEEEeEeecccccEEEE----EeCCeEEEEecccccccccccCCEEEEEEEEee
Q 033186 6 IKSGALVNLTELHPSSQFYEEGASLRVTGKLQDYAVEAAMAII----ADGNAILKIDTQHLRDLSFRVGSIYQFIGELHI 81 (125)
Q Consensus 6 ~~~g~~v~l~El~~~~~~~~~g~sVR~~GrL~~yD~~~~~a~l----~~~g~~l~Vdt~~v~~~~~~igs~Yq~IGEl~~ 81 (125)
|+||+||+|||+ +++++++|+||||||||++||+++++|+| .+++++++|||++++||++++||+||||||+++
T Consensus 2 ~~~g~~~~l~Ev--s~~~~~~g~svR~~GrL~~yD~~~~~a~l~~~~~~~~~~l~V~t~~l~~~~~~~gslyq~iGEl~~ 79 (118)
T PF15490_consen 2 PKPGVYVFLWEV--SSGFVPEGKSVRTFGRLQSYDVATSRATLTAQHESDQHSLKVDTKLLEPFQARVGSLYQFIGELEH 79 (118)
T ss_pred CCCcEEEehHHh--cCccccCCCeEEEEEEEEEEeccCCEEEEEeeccCCCcEEEEEeeEccccccCCCCEEEEEEEEEE
Confidence 899999999998 88999999999999999999999999999 667789999999999999999999999999999
Q ss_pred e-cCCceeEEEEEEEeccCCCHHHHHHHHHHHHHHHhhh
Q 033186 82 Q-ADCEAILQARVGRNVDGLDLNLYRQSLQLLRQFQADR 119 (125)
Q Consensus 82 ~-~d~~~~lkARV~r~VDglDl~L~ekal~~~R~f~~~~ 119 (125)
+ +|++.+|+|||+|||||||++||++||++||||+++|
T Consensus 80 ~~~~~~~~L~ARV~r~VdG~Dl~Ly~~al~~rRkf~~~r 118 (118)
T PF15490_consen 80 QPQDGGIVLKARVLRCVDGMDLNLYEQALQERRKFLQER 118 (118)
T ss_pred EcCCCcEEEEEEEEEecCCcCHHHHHHHHHHHHHHhhcC
Confidence 9 6778899999999999999999999999999999986
No 2
>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=99.18 E-value=3.7e-10 Score=80.27 Aligned_cols=86 Identities=19% Similarity=0.346 Sum_probs=57.9
Q ss_pred CCCeEEEEEEeEeecccccEEEEEeCC-eEEEEecccccccccccCCEEEEEEEEeeecCCceeEEEEEEEec---cCCC
Q 033186 26 EGASLRVTGKLQDYAVEAAMAIIADGN-AILKIDTQHLRDLSFRVGSIYQFIGELHIQADCEAILQARVGRNV---DGLD 101 (125)
Q Consensus 26 ~g~sVR~~GrL~~yD~~~~~a~l~~~g-~~l~Vdt~~v~~~~~~igs~Yq~IGEl~~~~d~~~~lkARV~r~V---DglD 101 (125)
.|+.||++||+.+.++..+.|++.+.+ .+|.|. +.+|.+..++.+|||+|.+... ..++..+...++ |.+|
T Consensus 17 ~gk~VrivGkv~~~~~~g~~~~l~~~d~~~V~v~--l~~~~~~~~~~~vEviG~V~~~---~~~~~i~~~~~~~~g~~~D 91 (109)
T PF08661_consen 17 VGKTVRIVGKVESVDPDGGSATLSTSDGGQVTVS--LNPPSDEELSKYVEVIGKVNDD---GTVLSIRYFSFTDFGDDFD 91 (109)
T ss_dssp TTSEEEEEEEEEEE-TTSSEEEEE-TTS-EEEEE--ESS--SS---SEEEEEEEE-TT---S-EEEEEEEE---SSS---
T ss_pred CCCeEEEEEEEeeEcCCCCEEEEEcCCCCEEEEE--eCCCCCCCCCCEEEEEEEEcCC---CCceEEEEEEeccCCCCcC
Confidence 699999999999999999999999744 355544 4466778899999999999742 234466666666 9999
Q ss_pred HHHHHHHHHHHHHHH
Q 033186 102 LNLYRQSLQLLRQFQ 116 (125)
Q Consensus 102 l~L~ekal~~~R~f~ 116 (125)
+++|.++++..-+|-
T Consensus 92 ~~~y~~lv~l~~~~p 106 (109)
T PF08661_consen 92 MDLYNELVQLTHKFP 106 (109)
T ss_dssp HHHHHHHHHHHHHSG
T ss_pred HHHHHHHHHHHhhCC
Confidence 999999999987763
No 3
>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=98.93 E-value=1.7e-08 Score=71.27 Aligned_cols=81 Identities=22% Similarity=0.480 Sum_probs=62.5
Q ss_pred CCCeEEEEEEeEeecccccEEEEEeCCeEEEEecccccccccccCCEEEEEEEEeeecCCceeEEEEEEEec---cCCCH
Q 033186 26 EGASLRVTGKLQDYAVEAAMAIIADGNAILKIDTQHLRDLSFRVGSIYQFIGELHIQADCEAILQARVGRNV---DGLDL 102 (125)
Q Consensus 26 ~g~sVR~~GrL~~yD~~~~~a~l~~~g~~l~Vdt~~v~~~~~~igs~Yq~IGEl~~~~d~~~~lkARV~r~V---DglDl 102 (125)
.|+.||++||+.+.|.. ..+...++|..+.|... +|..+..+.+|||+|.+.- .+..|+.+++ |.+|+
T Consensus 14 ~gk~V~ivGkV~~~~~~-~~~~~~~Dg~~v~v~l~--~~~~~~~~~~vEViG~V~~------~~~I~~~~~~~~g~~~D~ 84 (101)
T cd04479 14 VGKTVRIVGKVEKVDGD-SLTLISSDGVNVTVELN--RPLDLPISGYVEVIGKVSP------DLTIRVLSYIDFGDDFDM 84 (101)
T ss_pred CCCEEEEEEEEEEecCC-eEEEEcCCCCEEEEEeC--CCCCcccCCEEEEEEEECC------CCeEEEEEEEECCCccCH
Confidence 58999999999999987 34444446556766644 4557899999999999973 2455666666 88999
Q ss_pred HHHHHHHHHHHHH
Q 033186 103 NLYRQSLQLLRQF 115 (125)
Q Consensus 103 ~L~ekal~~~R~f 115 (125)
++|.+.++..-+|
T Consensus 85 ~~yn~lv~l~~~~ 97 (101)
T cd04479 85 DLYNELVKLSHKF 97 (101)
T ss_pred HHHHHHHHHHhhC
Confidence 9999999987665
No 4
>PF12658 Ten1: Telomere capping, CST complex subunit; InterPro: IPR024222 Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex []. These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast, and a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localise at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. Two separate protein complexes are required for chromosome end protection in fission yeast. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF8_D 3KF6_B 3K0X_A.
Probab=98.55 E-value=1.6e-06 Score=63.91 Aligned_cols=103 Identities=19% Similarity=0.298 Sum_probs=77.7
Q ss_pred CCCCCCeEEEccccccCCcccCCCCeEEEEEEeEeecccccEEEEEeCC------e--EEEEecccc-ccc---ccccCC
Q 033186 4 SAIKSGALVNLTELHPSSQFYEEGASLRVTGKLQDYAVEAAMAIIADGN------A--ILKIDTQHL-RDL---SFRVGS 71 (125)
Q Consensus 4 ~~~~~g~~v~l~El~~~~~~~~~g~sVR~~GrL~~yD~~~~~a~l~~~g------~--~l~Vdt~~v-~~~---~~~igs 71 (125)
..|.|-..+++.||. ..+.|.-||.+|-+.+||..++.-+|.++- + ++.||-+++ +.. ..++|.
T Consensus 6 ~gP~~~~l~fl~~l~----s~~~g~KVRfLgcV~~Y~~~~~~L~l~h~~p~~~~~~~~~v~VdI~~vL~tv~~~~~rvG~ 81 (124)
T PF12658_consen 6 LGPSPSQLLFLSQLP----SCSPGDKVRFLGCVSSYDTSTGTLTLEHNYPRENDSQPSSVSVDINLVLETVSSEELRVGE 81 (124)
T ss_dssp S-GGGHCCH-CCGGG----CTTCTEEEEEEEEEEEEECCCTEEEEEETCCC---S----EEEE-TTTTTTS-GGGGSTT-
T ss_pred CCCcchhHhCccccc----cCCCCCEEEEEEEEeEEecCccEEEEeecCCCCcCCCCceEEEEHHHHhhhcCccceecce
Confidence 456666777777643 356699999999999999999999999942 2 588998884 554 799999
Q ss_pred EEEEEEEEeeec----CCceeEEEEEEEeccCCCHHHHHHHHH
Q 033186 72 IYQFIGELHIQA----DCEAILQARVGRNVDGLDLNLYRQSLQ 110 (125)
Q Consensus 72 ~Yq~IGEl~~~~----d~~~~lkARV~r~VDglDl~L~ekal~ 110 (125)
++-++|-+.... +..+.++|=.+.-+.++|+.-|+++++
T Consensus 82 WvNV~Gy~~~~~~~~~~~~v~Vqai~i~~ag~~dl~~ye~~l~ 124 (124)
T PF12658_consen 82 WVNVVGYIRGEKPSQTQSPVYVQAIMIWSAGPIDLGEYEESLQ 124 (124)
T ss_dssp EEEEEEEEECTT--------EEEEEEEEE-TCGGHHHHHHHHH
T ss_pred EEEEEEEecccccccccccceEEEEEEEecCchhhhhhhcccC
Confidence 999999998865 345679999999999999999999985
No 5
>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=88.65 E-value=5.4 Score=26.58 Aligned_cols=75 Identities=13% Similarity=0.187 Sum_probs=51.2
Q ss_pred EEEEEEeEeecccccEEEEEe--CCeEEE----Eeccc---ccccccccCCEEEEEEEEeeecCCceeEEEEEEEeccCC
Q 033186 30 LRVTGKLQDYAVEAAMAIIAD--GNAILK----IDTQH---LRDLSFRVGSIYQFIGELHIQADCEAILQARVGRNVDGL 100 (125)
Q Consensus 30 VR~~GrL~~yD~~~~~a~l~~--~g~~l~----Vdt~~---v~~~~~~igs~Yq~IGEl~~~~d~~~~lkARV~r~VDgl 100 (125)
|+++|.+.+++......+++- +..++. -+... -..-.++.|..+.+.|.+.... +...+++.-.+.++..
T Consensus 2 v~~vG~V~~~~~~~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~~~-g~~ql~i~~i~~v~d~ 80 (95)
T cd04478 2 VTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSFQ-GKKSIMAFSIRPVTDF 80 (95)
T ss_pred EEEEEEEEeeeEcccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEcccC-CeeEEEEEEEEEeCCc
Confidence 789999999998876666554 222333 22221 0122589999999999997653 4568888888888877
Q ss_pred CHHHH
Q 033186 101 DLNLY 105 (125)
Q Consensus 101 Dl~L~ 105 (125)
|-=.|
T Consensus 81 ne~~~ 85 (95)
T cd04478 81 NEVTY 85 (95)
T ss_pred cHHHH
Confidence 75444
No 6
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=85.26 E-value=6.9 Score=29.64 Aligned_cols=95 Identities=16% Similarity=0.189 Sum_probs=61.4
Q ss_pred EEEccccccCCcccCCCCeEEEEEEeEe----ec-ccccEEEEEeCCeEEEEecccccccccccCCEEEEEEEEeeecCC
Q 033186 11 LVNLTELHPSSQFYEEGASLRVTGKLQD----YA-VEAAMAIIADGNAILKIDTQHLRDLSFRVGSIYQFIGELHIQADC 85 (125)
Q Consensus 11 ~v~l~El~~~~~~~~~g~sVR~~GrL~~----yD-~~~~~a~l~~~g~~l~Vdt~~v~~~~~~igs~Yq~IGEl~~~~d~ 85 (125)
++++.|+..... ..|+.||+.|.+.. ++ ...-+=+|++++..+.|.-.-+-|-.|+=|.-.-+.|.+.. +
T Consensus 37 f~tpse~~~~~~--~~g~~vrvgG~V~~gSi~~~~~~~~~F~ltD~~~~i~V~Y~G~lPd~F~eg~~VVv~G~~~~--~- 111 (148)
T PRK13254 37 FYTPSEVAEGEA--PAGRRFRLGGLVEKGSVQRGDGLTVRFVVTDGNATVPVVYTGILPDLFREGQGVVAEGRLQD--G- 111 (148)
T ss_pred eeCHHHHhcCCc--cCCCeEEEeEEEecCcEEeCCCCEEEEEEEeCCeEEEEEECCCCCccccCCCEEEEEEEECC--C-
Confidence 566778755432 68999999999974 42 22234456677778888888777777999999999999853 2
Q ss_pred ceeEEEE--EEEeccCCCHHHHHHHHHH
Q 033186 86 EAILQAR--VGRNVDGLDLNLYRQSLQL 111 (125)
Q Consensus 86 ~~~lkAR--V~r~VDglDl~L~ekal~~ 111 (125)
....|. +.+|=+.---+-...+++.
T Consensus 112 -g~F~A~~vLaKc~skY~p~ev~~~~~~ 138 (148)
T PRK13254 112 -GVFVADEVLAKHDENYMPKEVADALKK 138 (148)
T ss_pred -CeEEEEEEEecCCCCCCCHHHHHHHHH
Confidence 233333 2344444433444444443
No 7
>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=84.93 E-value=13 Score=27.14 Aligned_cols=67 Identities=24% Similarity=0.288 Sum_probs=46.0
Q ss_pred EEEccccccCCcccCCCCeEEEEEEeE----eeccccc--EEEEEeCCeEEEEecccccccccccCCEEEEEEEE
Q 033186 11 LVNLTELHPSSQFYEEGASLRVTGKLQ----DYAVEAA--MAIIADGNAILKIDTQHLRDLSFRVGSIYQFIGEL 79 (125)
Q Consensus 11 ~v~l~El~~~~~~~~~g~sVR~~GrL~----~yD~~~~--~a~l~~~g~~l~Vdt~~v~~~~~~igs~Yq~IGEl 79 (125)
++++.|+..... +.|+.||+-|.+. .||++.. +=+|++++..+.|--+-..|-.|+-|.---+.|.+
T Consensus 36 y~t~se~~~~~~--~~~~~vrv~G~V~~gSv~~~~~~~~~~F~i~D~~~~i~V~Y~G~~Pd~F~eg~~VVv~G~~ 108 (131)
T PF03100_consen 36 YLTPSELAAEPQ--KVGRKVRVGGLVVEGSVEYDPDGNTLTFTITDGGKEIPVVYTGPLPDLFREGQGVVVEGRL 108 (131)
T ss_dssp EE-TTTTTTTST---TTSEEEEEEEEECTTEEE-TTSSEEEEEEE-SS-EEEEEEES--CTT--TTSEEEEEEEE
T ss_pred EcCHHHHhhccc--cCCceEEEeeEEccCCEEEcCCCCEEEEEEEECCcEEEEEECCCCCccccCCCeEEEEEEE
Confidence 577888876654 4899999999998 5764443 34455677788888888878789999999999998
No 8
>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=75.89 E-value=16 Score=25.22 Aligned_cols=68 Identities=12% Similarity=0.193 Sum_probs=41.1
Q ss_pred EEEEEEeEeecccccEE--EEEeCCe--EEEEecccccc--c----c-cccCCEEEEEEEEeeecCCceeEEEEEEEec
Q 033186 30 LRVTGKLQDYAVEAAMA--IIADGNA--ILKIDTQHLRD--L----S-FRVGSIYQFIGELHIQADCEAILQARVGRNV 97 (125)
Q Consensus 30 VR~~GrL~~yD~~~~~a--~l~~~g~--~l~Vdt~~v~~--~----~-~~igs~Yq~IGEl~~~~d~~~~lkARV~r~V 97 (125)
|++-|++++.=...+.+ .|.+++. ++.++.....+ | . +++|+...+.|++...+.++..+.|.-..++
T Consensus 2 v~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~~~~il 80 (108)
T cd04322 2 VSVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVKEFTLL 80 (108)
T ss_pred EEEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeCEeEEe
Confidence 45556665554444332 2223333 55555443222 1 3 8999999999999887777777777666555
No 9
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=72.85 E-value=49 Score=28.69 Aligned_cols=82 Identities=11% Similarity=0.164 Sum_probs=53.7
Q ss_pred EEccccccCCcccCCCCeEEEEEEeEeecccccE--EEEEeCCe--EEEEecccccc-----cccccCCEEEEEEEEeee
Q 033186 12 VNLTELHPSSQFYEEGASLRVTGKLQDYAVEAAM--AIIADGNA--ILKIDTQHLRD-----LSFRVGSIYQFIGELHIQ 82 (125)
Q Consensus 12 v~l~El~~~~~~~~~g~sVR~~GrL~~yD~~~~~--a~l~~~g~--~l~Vdt~~v~~-----~~~~igs~Yq~IGEl~~~ 82 (125)
+.+.||.+.. .|+.|++-|++.+.=...+. +.|.+++. ++.++.+.+++ -.+.+|+...+-|.+...
T Consensus 5 ~~~~~l~~~~----~g~~V~i~GrV~~~R~~gk~~Fl~LrD~~g~iQ~v~~~~~~~~~~~~~~~L~~gs~V~v~G~v~~~ 80 (437)
T PRK05159 5 HLTSELTPEL----DGEEVTLAGWVHEIRDLGGIAFLILRDRSGIIQVVVKKKVDEELFETIKKLKRESVVSVTGTVKAN 80 (437)
T ss_pred eEhhhCChhh----CCCEEEEEEEeEeeecCCCeEEEEEEcCCcEEEEEEeCCccHHHHHHHhCCCCCcEEEEEEEEEcC
Confidence 3455554443 58999999999988655443 55656554 55565443222 158999999999999876
Q ss_pred cC--CceeEEEEEEEec
Q 033186 83 AD--CEAILQARVGRNV 97 (125)
Q Consensus 83 ~d--~~~~lkARV~r~V 97 (125)
+. ++..|++.=++++
T Consensus 81 ~~~~~~~el~~~~i~vl 97 (437)
T PRK05159 81 PKAPGGVEVIPEEIEVL 97 (437)
T ss_pred CCCCCCEEEEEeEEEEE
Confidence 53 5567777444444
No 10
>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=72.12 E-value=14 Score=28.09 Aligned_cols=75 Identities=9% Similarity=0.115 Sum_probs=57.8
Q ss_pred CCeEEEccccccCCcccCCCCeEEEEEEeEeecccccEEEEEe-----------------CCeEEEEecccccccccccC
Q 033186 8 SGALVNLTELHPSSQFYEEGASLRVTGKLQDYAVEAAMAIIAD-----------------GNAILKIDTQHLRDLSFRVG 70 (125)
Q Consensus 8 ~g~~v~l~El~~~~~~~~~g~sVR~~GrL~~yD~~~~~a~l~~-----------------~g~~l~Vdt~~v~~~~~~ig 70 (125)
+...+.+.++..+.. .-+|+.||.=|++..-....+...|+- .|..+..-..|+.|.-+.-|
T Consensus 16 ~~~~~~~~~v~~~p~-~~~G~~VrwGG~I~~v~n~~~~T~leV~~~PLd~~grP~~~~~s~GRFla~~~gFLDP~~y~~G 94 (160)
T PF03843_consen 16 VDPQPSFSQVRANPD-AYQGQQVRWGGVIVNVRNLPDQTELEVVQYPLDSSGRPQTDDPSQGRFLARVPGFLDPAIYAPG 94 (160)
T ss_pred CCccCCHHHHHhChh-hcCCCEEEECCEEEEEEECCCceEEEEEEccCCCCCCcCCCCCCCCEEEEEeCCCcCHHHcCCC
Confidence 445566777666643 456999999999999998888887773 23255566677999999999
Q ss_pred CEEEEEEEEeeec
Q 033186 71 SIYQFIGELHIQA 83 (125)
Q Consensus 71 s~Yq~IGEl~~~~ 83 (125)
....++|.+...+
T Consensus 95 r~vTV~G~v~g~~ 107 (160)
T PF03843_consen 95 RLVTVVGTVTGME 107 (160)
T ss_pred CEEEEEEEecceE
Confidence 9999999998754
No 11
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=71.90 E-value=50 Score=26.49 Aligned_cols=79 Identities=15% Similarity=0.084 Sum_probs=45.7
Q ss_pred EEEccc-cccCCcccCCCCeEEEEEEeEeeccc---ccEEEEEeCCeEEE-EecccccccccccC-CEEEEEEEEeeec-
Q 033186 11 LVNLTE-LHPSSQFYEEGASLRVTGKLQDYAVE---AAMAIIADGNAILK-IDTQHLRDLSFRVG-SIYQFIGELHIQA- 83 (125)
Q Consensus 11 ~v~l~E-l~~~~~~~~~g~sVR~~GrL~~yD~~---~~~a~l~~~g~~l~-Vdt~~v~~~~~~ig-s~Yq~IGEl~~~~- 83 (125)
.+++|| |....+ +..|..|-|.|+|.||+-. ..+-++ +|. -+.+++++-+-.-+ ....++|-|-.+|
T Consensus 50 ~v~v~~rlae~~~-l~kG~~v~VeGqlrsy~~~~~G~~R~vl-----~V~a~~i~~l~~~~~~~~~N~V~LiGrL~~DPe 123 (219)
T PRK05813 50 PVTVSERLLAGMD-LKVGTLVIVEGQLRSYNKFIDGKNRLIL-----TVFARNIEYCDERSDIKNPNEIFLDGYICKEPV 123 (219)
T ss_pred EEEEEhhhhhhhc-ccCCCEEEEEEEEEEeccCCCCcEEEEE-----EEEEEEEEEccCCCccCCccEEEEEEEccCCCe
Confidence 356666 555555 8899999999999999543 233333 222 13344544321122 3456889887764
Q ss_pred -----CCceeEEEEEEE
Q 033186 84 -----DCEAILQARVGR 95 (125)
Q Consensus 84 -----d~~~~lkARV~r 95 (125)
++..+...++..
T Consensus 124 lR~t~~G~~va~f~lAv 140 (219)
T PRK05813 124 YRTTPFGREIADLLLAV 140 (219)
T ss_pred EEECCCCCEEEEEEEEE
Confidence 333455555543
No 12
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=70.96 E-value=27 Score=23.04 Aligned_cols=42 Identities=17% Similarity=0.347 Sum_probs=32.5
Q ss_pred EEEEeEeecccccEEEEEeCCeEEEEecccccccccccCCEEEE
Q 033186 32 VTGKLQDYAVEAAMAIIADGNAILKIDTQHLRDLSFRVGSIYQF 75 (125)
Q Consensus 32 ~~GrL~~yD~~~~~a~l~~~g~~l~Vdt~~v~~~~~~igs~Yq~ 75 (125)
+=||+.+.|...+.|++..+|..-.|++.++++ .++|.+..+
T Consensus 5 iP~~Vv~v~~~~~~A~v~~~G~~~~V~~~lv~~--v~~Gd~VLV 46 (68)
T PF01455_consen 5 IPGRVVEVDEDGGMAVVDFGGVRREVSLALVPD--VKVGDYVLV 46 (68)
T ss_dssp EEEEEEEEETTTTEEEEEETTEEEEEEGTTCTS--B-TT-EEEE
T ss_pred ccEEEEEEeCCCCEEEEEcCCcEEEEEEEEeCC--CCCCCEEEE
Confidence 346777778889999999999888899999996 677776543
No 13
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=64.67 E-value=36 Score=22.06 Aligned_cols=25 Identities=16% Similarity=0.267 Sum_probs=20.3
Q ss_pred EEEeEeecccccEEEEEe-CCeEEEE
Q 033186 33 TGKLQDYAVEAAMAIIAD-GNAILKI 57 (125)
Q Consensus 33 ~GrL~~yD~~~~~a~l~~-~g~~l~V 57 (125)
=|++.+||..+.+.++.+ +|.++.+
T Consensus 24 e~kV~~~d~~~~~y~V~Y~DGtel~l 49 (55)
T PF09465_consen 24 EGKVLSYDSKSDRYTVLYEDGTELEL 49 (55)
T ss_dssp EEEEEEEETTTTEEEEEETTS-EEEE
T ss_pred EEEEEEecccCceEEEEEcCCCEEEe
Confidence 489999999999999999 5556554
No 14
>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=51.99 E-value=1.1e+02 Score=23.88 Aligned_cols=81 Identities=16% Similarity=0.156 Sum_probs=57.9
Q ss_pred EccccccCCcccCCCCeEEEEEEeEeecccccEEEEEe-----------------CCeEEEEecccccccccccCCEEEE
Q 033186 13 NLTELHPSSQFYEEGASLRVTGKLQDYAVEAAMAIIAD-----------------GNAILKIDTQHLRDLSFRVGSIYQF 75 (125)
Q Consensus 13 ~l~El~~~~~~~~~g~sVR~~GrL~~yD~~~~~a~l~~-----------------~g~~l~Vdt~~v~~~~~~igs~Yq~ 75 (125)
.+.++... +..-.|+.||.=|++-+-....+...|+- .|..+..-.-|+.|..++ |.+..|
T Consensus 35 ~~~~v~~~-p~~y~G~~Vr~GG~I~~v~N~~~~T~lEVv~~PLd~~grP~~~~~s~GRFla~~~gFLDP~~y~-Gr~VTV 112 (182)
T TIGR00752 35 SYVEVSPQ-PLLYVGQTARFGGKVVNVTNLANQTKLEIASLPLDSIAKPFVELQSDGRFIAYFNGFLDPVNLR-ERYVTV 112 (182)
T ss_pred chHHHhhC-hhhcCCCEEEECCEEEEEEECCCceEEEEEEcccCCCCCcCCCCCCCCEEEEEeCCCcChhhcC-CCEEEE
Confidence 45666533 44557999999999999999888887773 222444566679998885 999999
Q ss_pred EEEEeeecCC--------ceeEEEEEEE
Q 033186 76 IGELHIQADC--------EAILQARVGR 95 (125)
Q Consensus 76 IGEl~~~~d~--------~~~lkARV~r 95 (125)
+|.+...+.+ -.+++|..+.
T Consensus 113 vG~i~G~e~gkIGe~~Y~yPvv~~~~~~ 140 (182)
T TIGR00752 113 GGQIAGTEKGKIEQAPYTFPVVQADGYR 140 (182)
T ss_pred EEEecceEEeeeCCCcceeEEEEeeeEE
Confidence 9999876532 2256666543
No 15
>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=51.93 E-value=1.6e+02 Score=25.54 Aligned_cols=72 Identities=8% Similarity=0.154 Sum_probs=49.1
Q ss_pred CCCeEEEEEEeEeecccccE--EEEEeCCe--EEEEecccccc------cccccCCEEEEEEEEeeec--CCceeEEEEE
Q 033186 26 EGASLRVTGKLQDYAVEAAM--AIIADGNA--ILKIDTQHLRD------LSFRVGSIYQFIGELHIQA--DCEAILQARV 93 (125)
Q Consensus 26 ~g~sVR~~GrL~~yD~~~~~--a~l~~~g~--~l~Vdt~~v~~------~~~~igs~Yq~IGEl~~~~--d~~~~lkARV 93 (125)
.|+.|++-|++.+.=...+. ++|.+++. ++.++.+.+++ -.+.+||..++-|.+...+ .++..+.+.=
T Consensus 11 ~g~~v~i~G~v~~~R~~g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~~~~~~~~~el~~~~ 90 (428)
T TIGR00458 11 DGQEVTFMGWVHEIRDLGGLIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLESVVAVRGIVKIKEKAPGGFEIIPTK 90 (428)
T ss_pred CCCEEEEEEEEEEEecCCCcEEEEEEeCCeeEEEEEECCcCCHHHHHHHhCCCCCcEEEEEEEEEecCCCCCcEEEEEeE
Confidence 58999999999988777654 45555554 44454443432 1478999999999998643 3556776665
Q ss_pred EEec
Q 033186 94 GRNV 97 (125)
Q Consensus 94 ~r~V 97 (125)
+.++
T Consensus 91 i~vl 94 (428)
T TIGR00458 91 IEVI 94 (428)
T ss_pred EEEE
Confidence 5544
No 16
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=48.54 E-value=29 Score=24.36 Aligned_cols=31 Identities=23% Similarity=0.360 Sum_probs=25.6
Q ss_pred CCCCCCeEEEccccccCCcccCCCCeEEEEEEeEe
Q 033186 4 SAIKSGALVNLTELHPSSQFYEEGASLRVTGKLQD 38 (125)
Q Consensus 4 ~~~~~g~~v~l~El~~~~~~~~~g~sVR~~GrL~~ 38 (125)
...+.|+.|++.|.+|-|. .++-|+.+.++.
T Consensus 54 ~~~k~GD~V~I~EtRPLSK----tK~~~vv~i~~~ 84 (87)
T COG0186 54 NEAKVGDIVRIAETRPLSK----TKRFVVVEIVEK 84 (87)
T ss_pred ccCCCCCEEEEEEccccCC----cceEEEEEEeee
Confidence 4578999999999999986 788888877653
No 17
>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=47.51 E-value=2.1e+02 Score=25.52 Aligned_cols=71 Identities=11% Similarity=0.155 Sum_probs=48.9
Q ss_pred CCCeEEEEEEeEeecccc--cEEEEEeCCe--EEEEecccccc-----c--ccccCCEEEEEEEEeeecCCceeEEEEEE
Q 033186 26 EGASLRVTGKLQDYAVEA--AMAIIADGNA--ILKIDTQHLRD-----L--SFRVGSIYQFIGELHIQADCEAILQARVG 94 (125)
Q Consensus 26 ~g~sVR~~GrL~~yD~~~--~~a~l~~~g~--~l~Vdt~~v~~-----~--~~~igs~Yq~IGEl~~~~d~~~~lkARV~ 94 (125)
.|+.|++-|++.+.=... ..+.|.+++. ++.++...+.+ + .+.+|+...+.|.+...+.++..++|.=.
T Consensus 52 ~~~~v~v~Grv~~~R~~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~~gelel~~~~i 131 (496)
T TIGR00499 52 KNIEVSIAGRIMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTKTGELSVHVTEL 131 (496)
T ss_pred CCCEEEEEEEEEEEecCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECCCCcEEEEeeEE
Confidence 388999999999988554 3555555443 66666554432 1 26899999999999876666666666544
Q ss_pred Ee
Q 033186 95 RN 96 (125)
Q Consensus 95 r~ 96 (125)
+.
T Consensus 132 ~i 133 (496)
T TIGR00499 132 QI 133 (496)
T ss_pred EE
Confidence 43
No 18
>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=47.49 E-value=35 Score=22.51 Aligned_cols=25 Identities=28% Similarity=0.478 Sum_probs=19.7
Q ss_pred CcccCCCCeEEEEEEeEeecccccE
Q 033186 21 SQFYEEGASLRVTGKLQDYAVEAAM 45 (125)
Q Consensus 21 ~~~~~~g~sVR~~GrL~~yD~~~~~ 45 (125)
...++.|.-||+.|++..|.-..+.
T Consensus 45 ~~~~~~g~~v~v~G~v~~~~g~~ql 69 (95)
T cd04478 45 VEPIEEGTYVRVFGNLKSFQGKKSI 69 (95)
T ss_pred ccccccCCEEEEEEEEcccCCeeEE
Confidence 3568889999999999999844333
No 19
>PLN02502 lysyl-tRNA synthetase
Probab=47.01 E-value=2.3e+02 Score=25.84 Aligned_cols=71 Identities=17% Similarity=0.111 Sum_probs=47.8
Q ss_pred CCCeEEEEEEeEeeccccc--EEEEEeCCe--EEEEecccccc----c-----ccccCCEEEEEEEEeeecCCceeEEEE
Q 033186 26 EGASLRVTGKLQDYAVEAA--MAIIADGNA--ILKIDTQHLRD----L-----SFRVGSIYQFIGELHIQADCEAILQAR 92 (125)
Q Consensus 26 ~g~sVR~~GrL~~yD~~~~--~a~l~~~g~--~l~Vdt~~v~~----~-----~~~igs~Yq~IGEl~~~~d~~~~lkAR 92 (125)
.|+.|++-|++.+.=...+ .+.|.+++. ++.+..+.+.+ | .+.+|+...+.|.+...+.++..+.|.
T Consensus 107 ~~~~V~v~GrV~~~R~~Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~~gelel~~~ 186 (553)
T PLN02502 107 EDVSVSVAGRIMAKRAFGKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTKKGELSIFPT 186 (553)
T ss_pred CCCEEEEEEEEEEEecCCCeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecCCCCEEEEEe
Confidence 5889999999998866654 445555544 55555444321 2 378999999999988766666666655
Q ss_pred EEEe
Q 033186 93 VGRN 96 (125)
Q Consensus 93 V~r~ 96 (125)
=+++
T Consensus 187 ~i~v 190 (553)
T PLN02502 187 SFEV 190 (553)
T ss_pred EEEE
Confidence 4433
No 20
>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=46.83 E-value=1.6e+02 Score=24.10 Aligned_cols=83 Identities=12% Similarity=0.181 Sum_probs=52.6
Q ss_pred CeEEEEEEeEeeccc----ccEEEEEe---CCe-EEE--Eecc----cccccccccCCEEEEEEEEeeecCCceeEEEEE
Q 033186 28 ASLRVTGKLQDYAVE----AAMAIIAD---GNA-ILK--IDTQ----HLRDLSFRVGSIYQFIGELHIQADCEAILQARV 93 (125)
Q Consensus 28 ~sVR~~GrL~~yD~~----~~~a~l~~---~g~-~l~--Vdt~----~v~~~~~~igs~Yq~IGEl~~~~d~~~~lkARV 93 (125)
+.||+.|++.+++-- ..+.+++- .|+ .+. +.-+ .--++..-+|++.++.|.+.. +...+++..
T Consensus 67 ~~v~i~G~Vv~~~~~~~~~~~~~~l~iDD~Sg~~~i~~~~~~~~~~~~~l~~~~~~G~~V~VkG~vsr---~~~ql~ve~ 143 (256)
T PF10451_consen 67 RWVRIVGVVVGIDYKWIENEDRIILTIDDSSGANTIECKCSKSSYLSMGLPINDLIGKVVEVKGTVSR---NERQLDVER 143 (256)
T ss_dssp -EEEEEEEEEEEEEEE-BBTCEEEEEEE-SSCS-EEEEEEEHHHHHCCCHHCTT-TT-EEEEEEEEES---SSEEEEEEE
T ss_pred EEEEEEEEEEEEEEEeecccceEEEEEeCCCCceeEEEEEEcccccccCCCccCCCCcEEEEEEEEcc---CcEEEEEEE
Confidence 579999999999854 45555543 222 333 2222 111233349999999999983 456899999
Q ss_pred EEeccCCCHH--HHHHHHHHHH
Q 033186 94 GRNVDGLDLN--LYRQSLQLLR 113 (125)
Q Consensus 94 ~r~VDglDl~--L~ekal~~~R 113 (125)
+..+++++.. ..+++++-|+
T Consensus 144 i~~~~~l~~Ei~fW~~~~~~R~ 165 (256)
T PF10451_consen 144 IELVRDLNAEIEFWKERMRFRK 165 (256)
T ss_dssp EEEETSCCHHHHHHHHHHHHHH
T ss_pred EEccCChHHHHHHHHHHHHHHH
Confidence 9989988854 4556666654
No 21
>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=46.81 E-value=30 Score=23.77 Aligned_cols=22 Identities=36% Similarity=0.554 Sum_probs=18.5
Q ss_pred cccCCCCeEEEEEEeEeecccc
Q 033186 22 QFYEEGASLRVTGKLQDYAVEA 43 (125)
Q Consensus 22 ~~~~~g~sVR~~GrL~~yD~~~ 43 (125)
+.+..|.-||+.|++..|.-..
T Consensus 61 ~~i~~G~vvrV~G~i~~frg~~ 82 (92)
T cd04483 61 KVLEIGDLLRVRGSIRTYRGER 82 (92)
T ss_pred cccCCCCEEEEEEEEeccCCee
Confidence 4588999999999999997533
No 22
>PF07866 DUF1653: Protein of unknown function (DUF1653); InterPro: IPR023387 This entry represents the structural domain found in DUF1653, a protein family of unknown function. ; PDB: 3BE3_B.
Probab=46.59 E-value=30 Score=22.89 Aligned_cols=20 Identities=20% Similarity=0.488 Sum_probs=15.8
Q ss_pred CCEEEEEEEEeeecCCceeE
Q 033186 70 GSIYQFIGELHIQADCEAIL 89 (125)
Q Consensus 70 gs~Yq~IGEl~~~~d~~~~l 89 (125)
|.+|++||...+.++.+.++
T Consensus 9 G~~Y~Vl~~A~hsEt~E~~V 28 (64)
T PF07866_consen 9 GGLYEVLGVARHSETEEEMV 28 (64)
T ss_dssp S-EEEEEEEEEETTTTEEEE
T ss_pred CCeEEEEEEEEeCCCCccEE
Confidence 89999999999988776543
No 23
>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=44.26 E-value=33 Score=22.88 Aligned_cols=24 Identities=25% Similarity=0.318 Sum_probs=19.5
Q ss_pred cccCCCCeEEEEEEeEeecccccE
Q 033186 22 QFYEEGASLRVTGKLQDYAVEAAM 45 (125)
Q Consensus 22 ~~~~~g~sVR~~GrL~~yD~~~~~ 45 (125)
..+..|..||+.|++..|.-.+++
T Consensus 43 ~~~~~Gd~V~vtG~v~ey~g~tql 66 (78)
T cd04486 43 ADVAVGDLVRVTGTVTEYYGLTQL 66 (78)
T ss_pred CCCCCCCEEEEEEEEEeeCCeEEE
Confidence 356789999999999999875443
No 24
>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=43.44 E-value=1.1e+02 Score=21.04 Aligned_cols=72 Identities=8% Similarity=0.154 Sum_probs=45.7
Q ss_pred CCCeEEEEEEeEeecccccEEEEE--eCCe--EEEEecccccc------cccccCCEEEEEEEEeeecC--CceeEEEEE
Q 033186 26 EGASLRVTGKLQDYAVEAAMAIIA--DGNA--ILKIDTQHLRD------LSFRVGSIYQFIGELHIQAD--CEAILQARV 93 (125)
Q Consensus 26 ~g~sVR~~GrL~~yD~~~~~a~l~--~~g~--~l~Vdt~~v~~------~~~~igs~Yq~IGEl~~~~d--~~~~lkARV 93 (125)
.|+.|++-|++..--...+.+=+. +++. ++.++.+..++ ..+..|+...+.|++...+. ++..+.+.=
T Consensus 11 ~g~~V~v~Gwv~~~R~~g~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~Ei~~~~ 90 (108)
T cd04316 11 DGEEVTVAGWVHEIRDLGGIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPKAPNGVEIIPEE 90 (108)
T ss_pred CCCEEEEEEEEEeeeccCCeEEEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCCCCCCEEEEEeE
Confidence 589999999999877666544333 3333 55555443221 14789999999999887543 245555544
Q ss_pred EEec
Q 033186 94 GRNV 97 (125)
Q Consensus 94 ~r~V 97 (125)
++++
T Consensus 91 i~il 94 (108)
T cd04316 91 IEVL 94 (108)
T ss_pred EEEE
Confidence 4333
No 25
>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=42.66 E-value=78 Score=19.25 Aligned_cols=65 Identities=14% Similarity=0.196 Sum_probs=40.8
Q ss_pred EEEEEEeEee-cccccEE--EEEeCCeEEEEeccc--ccc--cccccCCEEEEEEEEeeecCCceeEEEEEE
Q 033186 30 LRVTGKLQDY-AVEAAMA--IIADGNAILKIDTQH--LRD--LSFRVGSIYQFIGELHIQADCEAILQARVG 94 (125)
Q Consensus 30 VR~~GrL~~y-D~~~~~a--~l~~~g~~l~Vdt~~--v~~--~~~~igs~Yq~IGEl~~~~d~~~~lkARV~ 94 (125)
|.+-|++.+. ......+ +|.++..++.+-... ... -.++.|+.+.+-|++...++++..|.+--+
T Consensus 1 V~v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~~~~~~~~l~~~~i 72 (75)
T PF01336_consen 1 VTVEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVRGKVKRYNGGELELIVPKI 72 (75)
T ss_dssp EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEEEEEEEETTSSEEEEEEEE
T ss_pred CEEEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEEEEEEEECCccEEEEECEE
Confidence 5778888888 4444444 444555555533332 111 258999999999999987666576665433
No 26
>PRK00513 minC septum formation inhibitor; Reviewed
Probab=41.46 E-value=55 Score=25.75 Aligned_cols=56 Identities=13% Similarity=0.101 Sum_probs=43.9
Q ss_pred ccCCCCeEEEEEEeEeecccccEEEEEeCCe-EEEEecccccccccccCCEEEEEEE
Q 033186 23 FYEEGASLRVTGKLQDYAVEAAMAIIADGNA-ILKIDTQHLRDLSFRVGSIYQFIGE 78 (125)
Q Consensus 23 ~~~~g~sVR~~GrL~~yD~~~~~a~l~~~g~-~l~Vdt~~v~~~~~~igs~Yq~IGE 78 (125)
.+-+|..|+--|-+.-|=.-.++|.--++|+ .-.|....++|-+++|+..|...-+
T Consensus 127 dVn~GAev~A~GnI~V~G~lrG~~~AG~~G~~~A~I~a~~l~~~~lrIa~~~~~~~d 183 (214)
T PRK00513 127 DVNPGGEVIAGGNIIVLGALRGIAHAGATGNKEAVIAALQLEPTQLRIADVIARAPE 183 (214)
T ss_pred cCCCCCEEEeCCCEEEEEEeccEEEECCCCCCceEEEEccCCccEEEECcEEEeCcc
Confidence 4556777888888888877788888777665 6777788889999999999987544
No 27
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=40.99 E-value=1.7e+02 Score=22.63 Aligned_cols=70 Identities=19% Similarity=0.156 Sum_probs=48.7
Q ss_pred EEEccccccCCc----ccCCCCeEEEEEEeE--eeccccc----EEEEEeCCeEEEEecccccccccccCCEEEEEEEEe
Q 033186 11 LVNLTELHPSSQ----FYEEGASLRVTGKLQ--DYAVEAA----MAIIADGNAILKIDTQHLRDLSFRVGSIYQFIGELH 80 (125)
Q Consensus 11 ~v~l~El~~~~~----~~~~g~sVR~~GrL~--~yD~~~~----~a~l~~~g~~l~Vdt~~v~~~~~~igs~Yq~IGEl~ 80 (125)
++++.|+..... ..+.|+.+|+-|.++ |..-... .=+|+++...+.|.-+=+-|-.|+=|.-.-+.|.+.
T Consensus 37 F~tPsev~~~~~~~~~~~~~g~~iRvgG~V~~GSi~r~~~~l~v~F~vtD~~~~v~V~Y~GilPDlFrEG~gVVveG~~~ 116 (160)
T PRK13165 37 FYTPGEILYGKRETQQKPEVGQRLRVGGMVMPGSVQRDPNSLKVSFTLYDAGGSVTVTYEGILPDLFREGQGIVAQGVLE 116 (160)
T ss_pred EeCHHHHhccccccccccCCCCEEEEeeEEeCCcEEECCCCeEEEEEEEcCCeEEEEEEcccCCccccCCCeEEEEEEEC
Confidence 466777654321 146899999999998 4443333 334445556888877776676699999999999985
No 28
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=40.96 E-value=1e+02 Score=20.04 Aligned_cols=45 Identities=9% Similarity=0.241 Sum_probs=36.4
Q ss_pred EEEEEeEeecccccEEEEEeCC--eEEEEeccccccc---ccccCCEEEE
Q 033186 31 RVTGKLQDYAVEAAMAIIADGN--AILKIDTQHLRDL---SFRVGSIYQF 75 (125)
Q Consensus 31 R~~GrL~~yD~~~~~a~l~~~g--~~l~Vdt~~v~~~---~~~igs~Yq~ 75 (125)
|..|+++.||.+.+-.-|..++ ..+.+.-+.++.. .++.|...+|
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f 52 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEF 52 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCCCCCCCEEEE
Confidence 6789999999999999998733 4777877777652 4899999988
No 29
>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=40.94 E-value=2.5e+02 Score=24.62 Aligned_cols=71 Identities=17% Similarity=0.137 Sum_probs=46.3
Q ss_pred CCCCeEEEEEEeEeeccccc--EEEEEeCC--e--EEEEecccccc------cccccCCEEEEEEEEeeec--CCceeEE
Q 033186 25 EEGASLRVTGKLQDYAVEAA--MAIIADGN--A--ILKIDTQHLRD------LSFRVGSIYQFIGELHIQA--DCEAILQ 90 (125)
Q Consensus 25 ~~g~sVR~~GrL~~yD~~~~--~a~l~~~g--~--~l~Vdt~~v~~------~~~~igs~Yq~IGEl~~~~--d~~~~lk 90 (125)
..|+.|++.|++++.-...+ .+.|.+++ . ++.++.. ..+ -.+..|+...+-|++...+ .++..|.
T Consensus 14 ~~g~~v~v~Gwv~~~R~~~~~~F~~lrD~~~~g~iQ~v~~~~-~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~~~~~El~ 92 (453)
T TIGR00457 14 FVGDEVTVSGWVRTKRSSKKIIFLELNDGSSLGPIQAVINGE-DNPYLFQLLKSLTTGSSVSVTGKVVESPGKGQPVELQ 92 (453)
T ss_pred cCCCEEEEEEEeEEEEcCCCeEEEEEECCCCCccEEEEEeCC-cChHHHHHHHcCCCCcEEEEEEEEEcCCCCCCCEEEE
Confidence 45899999999999885544 35555554 2 6656554 211 1589999999999987642 3345555
Q ss_pred EEEEEe
Q 033186 91 ARVGRN 96 (125)
Q Consensus 91 ARV~r~ 96 (125)
+.=.++
T Consensus 93 ~~~i~v 98 (453)
T TIGR00457 93 VKKIEV 98 (453)
T ss_pred EeEEEE
Confidence 543333
No 30
>PF03088 Str_synth: Strictosidine synthase; InterPro: IPR018119 This entry represents a conserved region found in strictosidine synthase (4.3.3.2 from EC), a key enzyme in alkaloid biosynthesis. It catalyses the Pictet-Spengler stereospecific condensation of tryptamine with secologanin to form strictosidine []. The structure of the native enzyme from the Indian medicinal plant Rauvolfia serpentina (Serpentwood) (Devilpepper) represents the first example of a six-bladed four-stranded beta-propeller fold from the plant kingdom [].; GO: 0016844 strictosidine synthase activity, 0009058 biosynthetic process; PDB: 2FPB_A 2V91_B 2FP8_A 3V1S_B 2FPC_A 2VAQ_A 2FP9_B.
Probab=40.10 E-value=26 Score=24.27 Aligned_cols=20 Identities=25% Similarity=0.315 Sum_probs=14.8
Q ss_pred EEEEEeEeecccccEEEEEe
Q 033186 31 RVTGKLQDYAVEAAMAIIAD 50 (125)
Q Consensus 31 R~~GrL~~yD~~~~~a~l~~ 50 (125)
+-.|||..||+.++.+++-.
T Consensus 34 ~~~GRll~ydp~t~~~~vl~ 53 (89)
T PF03088_consen 34 RPTGRLLRYDPSTKETTVLL 53 (89)
T ss_dssp ---EEEEEEETTTTEEEEEE
T ss_pred CCCcCEEEEECCCCeEEEeh
Confidence 44799999999999886654
No 31
>PRK15464 cold shock-like protein CspH; Provisional
Probab=39.01 E-value=98 Score=20.39 Aligned_cols=49 Identities=10% Similarity=0.186 Sum_probs=37.1
Q ss_pred EEEEEEeEeecccccEEEEEeCC--eEEEEeccccccc---ccccCCEEEEEEE
Q 033186 30 LRVTGKLQDYAVEAAMAIIADGN--AILKIDTQHLRDL---SFRVGSIYQFIGE 78 (125)
Q Consensus 30 VR~~GrL~~yD~~~~~a~l~~~g--~~l~Vdt~~v~~~---~~~igs~Yq~IGE 78 (125)
.|..|+++.||.+.+-.=|+.++ ..|-|..+.+.+. .++.|...+|-=+
T Consensus 3 ~~~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~ 56 (70)
T PRK15464 3 RKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRV 56 (70)
T ss_pred ccceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEE
Confidence 35689999999999999887633 4777777777542 5889988887443
No 32
>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=38.78 E-value=1.4e+02 Score=21.14 Aligned_cols=57 Identities=16% Similarity=0.194 Sum_probs=38.4
Q ss_pred CCCeEEEEEEeEeecccccE--EEEEeCCe--EEEEeccccc---c-cccccCCEEEEEEEEeee
Q 033186 26 EGASLRVTGKLQDYAVEAAM--AIIADGNA--ILKIDTQHLR---D-LSFRVGSIYQFIGELHIQ 82 (125)
Q Consensus 26 ~g~sVR~~GrL~~yD~~~~~--a~l~~~g~--~l~Vdt~~v~---~-~~~~igs~Yq~IGEl~~~ 82 (125)
.|+.|++.|++...-...+. ..|.+++. ++.+..+... . ..+..|+...+-|.+...
T Consensus 13 ~g~~V~i~Gwv~~~R~~gk~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~ 77 (135)
T cd04317 13 VGQEVTLCGWVQRRRDHGGLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRAR 77 (135)
T ss_pred CCCEEEEEEeEehhcccCCEEEEEEecCCeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEECC
Confidence 48899999999987666543 33433333 5555444322 1 158899999999998864
No 33
>COG3065 Slp Starvation-inducible outer membrane lipoprotein [Cell envelope biogenesis, outer membrane]
Probab=37.44 E-value=2.1e+02 Score=22.84 Aligned_cols=80 Identities=16% Similarity=0.182 Sum_probs=56.6
Q ss_pred EccccccCCcccCCCCeEEEEEEeEeecccccEEEEEe-----------------CCeEEEEe-cccccccccccCCEEE
Q 033186 13 NLTELHPSSQFYEEGASLRVTGKLQDYAVEAAMAIIAD-----------------GNAILKID-TQHLRDLSFRVGSIYQ 74 (125)
Q Consensus 13 ~l~El~~~~~~~~~g~sVR~~GrL~~yD~~~~~a~l~~-----------------~g~~l~Vd-t~~v~~~~~~igs~Yq 74 (125)
.+.+++.- +..-.|+++|.=||+..--...++..++- +| ++..+ .-|++|..++ |.+..
T Consensus 40 s~~~~~~~-~~~~~gq~aR~GGkVvnv~n~~~rTrlEi~slPldS~arP~l~~~~qG-RfiAy~~GFlDPv~~~-gr~vT 116 (191)
T COG3065 40 SLVRVMSQ-PQLYVGQQARFGGKVVNVINQKGRTRLEIASLPLDSGARPDLEAESQG-RFIAYVNGFLDPVNFR-GRLVT 116 (191)
T ss_pred heeeeccC-CcccccceeeeCcEEEEEecCCCcEEEEEEeeccCcccCCCcCCCCCc-eEEEEcccccChhhhc-CcEEE
Confidence 34443332 55668999999999999988888887763 22 33333 3468888999 99999
Q ss_pred EEEEEeeecCC--------ceeEEEEEEE
Q 033186 75 FIGELHIQADC--------EAILQARVGR 95 (125)
Q Consensus 75 ~IGEl~~~~d~--------~~~lkARV~r 95 (125)
|+|.+...+++ -.+++|-.++
T Consensus 117 v~G~i~g~E~GkIg~~~Y~~pvv~a~gy~ 145 (191)
T COG3065 117 VVGTIAGTEDGKIGQVPYKFPVVQATGYK 145 (191)
T ss_pred EEeeeccccCCccccccccceEEeeeeEE
Confidence 99999887643 3467775543
No 34
>PRK10943 cold shock-like protein CspC; Provisional
Probab=35.97 E-value=1.2e+02 Score=19.62 Aligned_cols=49 Identities=10% Similarity=0.250 Sum_probs=38.9
Q ss_pred EEEEEeEeecccccEEEEEeC--CeEEEEeccccccc---ccccCCEEEEEEEEee
Q 033186 31 RVTGKLQDYAVEAAMAIIADG--NAILKIDTQHLRDL---SFRVGSIYQFIGELHI 81 (125)
Q Consensus 31 R~~GrL~~yD~~~~~a~l~~~--g~~l~Vdt~~v~~~---~~~igs~Yq~IGEl~~ 81 (125)
|..|++..||.+.+-.-|+.+ +..|.+.-+.++.. .++.|...+| ++..
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f--~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEF--EIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEE--EEEE
Confidence 678999999999999998863 34788888887653 4789999888 4444
No 35
>PF03775 MinC_C: Septum formation inhibitor MinC, C-terminal domain; InterPro: IPR005526 In Escherichia coli, three Min proteins (MinC, MinD and MinE) negatively regulate FtsZ assembly at the cell poles in order to ensure the Z-ring only assembles at cell midpoint. MinC inhibits formation of the Z-ring by preventing FtsZ assembly. MinD binds to MinC near the cell poles, sequestering MinC away from the cell midpoint so the Z-ring can form there. MinC is an oligomer, probably a dimer, that consists of two domains: the N-terminal domain is responsible for FtsZ inhibition, while the C-terminal domain is responsible for binding to MinD and to a component of the division septum [, ].; GO: 0000902 cell morphogenesis; PDB: 1HF2_C.
Probab=35.77 E-value=93 Score=22.18 Aligned_cols=67 Identities=16% Similarity=0.157 Sum_probs=33.1
Q ss_pred CeEEEccccccCCcccCCCCeEEEEEEeEeecccccEEEEEeCCe-EEEEecccccccccccCCEEEEEEEEeee
Q 033186 9 GALVNLTELHPSSQFYEEGASLRVTGKLQDYAVEAAMAIIADGNA-ILKIDTQHLRDLSFRVGSIYQFIGELHIQ 82 (125)
Q Consensus 9 g~~v~l~El~~~~~~~~~g~sVR~~GrL~~yD~~~~~a~l~~~g~-~l~Vdt~~v~~~~~~igs~Yq~IGEl~~~ 82 (125)
|.++.+-.++ +|..|+--|.+.-|-.-.++|.--++|+ .-.|-...+.|-+++++..|...-+++..
T Consensus 18 gdvvilGdVn-------~GA~V~A~GnI~V~G~l~G~v~AG~~g~~~a~I~a~~~~~~~i~Ia~~~~~~~~~~~~ 85 (105)
T PF03775_consen 18 GDVVILGDVN-------PGAEVIAGGNIHVYGRLRGRVHAGAPGNEDAFIFALSFDPEQIRIAGIIARAPDLPKE 85 (105)
T ss_dssp SEEEESS-B--------TT-EEEESS-EEEEEEE-SEEEE-TTT-TT-EEEEEEE--SEEEETTEEE--------
T ss_pred CCEEEEccCC-------CCCEEEECCCEEEEEecCCEEEeCCCCCCCCEEEEccCCCCEEEECCEEEeCcccccc
Confidence 5566665544 4555666666666655667776665554 44555666678899999999988886543
No 36
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=34.99 E-value=1.3e+02 Score=19.60 Aligned_cols=36 Identities=19% Similarity=0.186 Sum_probs=28.9
Q ss_pred CCCeEEEEEEeEeecccccEEEEEe-CCeEEEEeccc
Q 033186 26 EGASLRVTGKLQDYAVEAAMAIIAD-GNAILKIDTQH 61 (125)
Q Consensus 26 ~g~sVR~~GrL~~yD~~~~~a~l~~-~g~~l~Vdt~~ 61 (125)
.|.-..+.|.+..+|.....-.+.. ++....+.+..
T Consensus 52 ~g~~~~~~G~I~~id~~~~~l~~~~~~~~~~~I~~~~ 88 (92)
T PF08863_consen 52 DGYYQSVTGTIHKIDEINRTLKLKDEDGETEKIPFDD 88 (92)
T ss_pred CCeeEEEEEEEEEEcCCCCEEEEEeCCCCEEEEEhhh
Confidence 6889999999999999999999988 44455555543
No 37
>PHA02783 uncharacterized protein; Provisional
Probab=34.87 E-value=96 Score=23.76 Aligned_cols=58 Identities=26% Similarity=0.344 Sum_probs=39.6
Q ss_pred cCCcccCCCCeEEEEEEeEe-eccc---------ccEEEEEeCCe---------EEEEecccccccccccCCEEEEE
Q 033186 19 PSSQFYEEGASLRVTGKLQD-YAVE---------AAMAIIADGNA---------ILKIDTQHLRDLSFRVGSIYQFI 76 (125)
Q Consensus 19 ~~~~~~~~g~sVR~~GrL~~-yD~~---------~~~a~l~~~g~---------~l~Vdt~~v~~~~~~igs~Yq~I 76 (125)
+||--...|.++|+--||.+ ||-. .-.-.|++.|. ++.-|..+++-..+++||.|.|=
T Consensus 91 dsstiqrrghtcristklschydkhpyihkyegderqysitaegkcykgikyeismmnddtllrkhtlkigstyifd 167 (181)
T PHA02783 91 DSSTIQRRGHTCRISTKLSCHYDKHPYIHKYEGDERQYSITAEGKCYKGIKYEISMMNDDTLLRKHTLKIGSTYIFD 167 (181)
T ss_pred cchhhhhcCceEEeeeeeeeeccCCcceeeccCcceeEEEeecceeecceeEEEEEecchhhhhhheeecccEEEEe
Confidence 34555668999999999854 5543 34445565553 34456667777789999999883
No 38
>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=33.36 E-value=56 Score=19.66 Aligned_cols=19 Identities=26% Similarity=0.590 Sum_probs=16.8
Q ss_pred cccCCCCeEEEEEEeEeec
Q 033186 22 QFYEEGASLRVTGKLQDYA 40 (125)
Q Consensus 22 ~~~~~g~sVR~~GrL~~yD 40 (125)
..++.|..+.+.|++..|.
T Consensus 44 ~~~~~G~~~~v~Gkv~~~~ 62 (75)
T cd04488 44 KQLPPGTRVRVSGKVKRFR 62 (75)
T ss_pred hcCCCCCEEEEEEEEeecC
Confidence 4688999999999999985
No 39
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=32.53 E-value=2.3e+02 Score=21.82 Aligned_cols=71 Identities=18% Similarity=0.169 Sum_probs=47.7
Q ss_pred EEEccccccCC----cccCCCCeEEEEEEeE--eeccccc----EEEEEeCCeEEEEecccccccccccCCEEEEEEEEe
Q 033186 11 LVNLTELHPSS----QFYEEGASLRVTGKLQ--DYAVEAA----MAIIADGNAILKIDTQHLRDLSFRVGSIYQFIGELH 80 (125)
Q Consensus 11 ~v~l~El~~~~----~~~~~g~sVR~~GrL~--~yD~~~~----~a~l~~~g~~l~Vdt~~v~~~~~~igs~Yq~IGEl~ 80 (125)
++++.|+.... +..+.|+.+|+-|.++ |..-... .=+|+++...|.|.-+=+-|-.|+=|.-.-+.|.+.
T Consensus 37 F~tPsev~~~~~~~~~~~~~g~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~GilPDlFrEG~gVVveG~~~ 116 (159)
T PRK13150 37 FYTPGEILYGKRETQQLPAVGQRLRVGGMVMPGSVRRDPDSLKVNFSLYDAEGSVTVSYEGILPDLFREGQGVVVQGTLE 116 (159)
T ss_pred EeCHHHHhccccccccCcCCCCEEEEeeEEeCCcEEECCCCcEEEEEEEcCCcEEEEEEeccCCccccCCCeEEEEEEEC
Confidence 45667764321 2245799999999998 4433222 223444555888877776676699999999999985
Q ss_pred e
Q 033186 81 I 81 (125)
Q Consensus 81 ~ 81 (125)
.
T Consensus 117 ~ 117 (159)
T PRK13150 117 K 117 (159)
T ss_pred C
Confidence 3
No 40
>PRK03359 putative electron transfer flavoprotein FixA; Reviewed
Probab=31.45 E-value=60 Score=26.48 Aligned_cols=51 Identities=14% Similarity=0.131 Sum_probs=36.4
Q ss_pred EEEEecccccccccccCCEEEEEEEEeeecCCceeEEEEEEEeccCCCHHHHHHHHHHHHHH
Q 033186 54 ILKIDTQHLRDLSFRVGSIYQFIGELHIQADCEAILQARVGRNVDGLDLNLYRQSLQLLRQF 115 (125)
Q Consensus 54 ~l~Vdt~~v~~~~~~igs~Yq~IGEl~~~~d~~~~lkARV~r~VDglDl~L~ekal~~~R~f 115 (125)
.|.||.++|.+- -++...+.+....+..+-..++-.|.+.+|.||+++-++
T Consensus 2 ~IvVcvKqVPD~-----------~~~~~~~~~~~l~r~~~~~~iN~~D~~AlE~Alrlke~~ 52 (256)
T PRK03359 2 KIITCYKCVPDE-----------QDIAVNNADGSLDFSKADAKISQYDLNAIEAACQLKQQA 52 (256)
T ss_pred EEEEEEEECcCC-----------cceEEeCCCCeEEcCCCccccChhhHHHHHHHHHHhhhc
Confidence 367888988762 122333333445567777788999999999999999875
No 41
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=31.25 E-value=44 Score=17.86 Aligned_cols=19 Identities=16% Similarity=0.333 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHHHHHhhhc
Q 033186 102 LNLYRQSLQLLRQFQADRM 120 (125)
Q Consensus 102 l~L~ekal~~~R~f~~~~~ 120 (125)
++++++++..+++.+...+
T Consensus 22 ~~~~~~al~~~~~~~G~~H 40 (42)
T PF13374_consen 22 LELLEEALEIRERLLGPDH 40 (42)
T ss_dssp HHHHHHHHHHH--------
T ss_pred hHHHHHHHHHHHHHhcccc
Confidence 4678899999888766543
No 42
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=30.87 E-value=1.9e+02 Score=22.39 Aligned_cols=41 Identities=12% Similarity=0.277 Sum_probs=28.5
Q ss_pred ccCCCCeEEE--------EEEeEeecccccEEEEEeC--C--eEEEEeccccc
Q 033186 23 FYEEGASLRV--------TGKLQDYAVEAAMAIIADG--N--AILKIDTQHLR 63 (125)
Q Consensus 23 ~~~~g~sVR~--------~GrL~~yD~~~~~a~l~~~--g--~~l~Vdt~~v~ 63 (125)
.+..|..||+ .|++...|.+.++.++.-. | .++.+++.+++
T Consensus 123 ~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~ifgr~tPVel~~~qVe 175 (178)
T COG0250 123 DFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVELEFDQVE 175 (178)
T ss_pred cCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEEeCCceEEEEehhhEE
Confidence 3445555555 4899999999988887752 2 27777777765
No 43
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=30.36 E-value=1.4e+02 Score=19.43 Aligned_cols=34 Identities=15% Similarity=0.323 Sum_probs=23.9
Q ss_pred EEEEeEeecccccEEEEEeCC--------eEEEEeccccccc
Q 033186 32 VTGKLQDYAVEAAMAIIADGN--------AILKIDTQHLRDL 65 (125)
Q Consensus 32 ~~GrL~~yD~~~~~a~l~~~g--------~~l~Vdt~~v~~~ 65 (125)
+-|.+-.||..+...+|.+.+ +--.|++.++.++
T Consensus 19 ieGEV~afD~~tk~lIlk~~s~~~~~~~~dv~ivnls~~~dv 60 (61)
T cd01735 19 LQGEVVAFDYPSKMLILKCPSSSGKPNHADILLVNLSYVSEV 60 (61)
T ss_pred EEEEEEEecCCCcEEEEECccccCCCCcceEEEEEhhhEEec
Confidence 359999999999999997422 1333666666554
No 44
>PRK14699 replication factor A; Provisional
Probab=30.36 E-value=2.2e+02 Score=25.50 Aligned_cols=30 Identities=13% Similarity=0.091 Sum_probs=16.7
Q ss_pred ccCCCCeEEEEEEeEeecccccEEEEEeCC
Q 033186 23 FYEEGASLRVTGKLQDYAVEAAMAIIADGN 52 (125)
Q Consensus 23 ~~~~g~sVR~~GrL~~yD~~~~~a~l~~~g 52 (125)
.+.+|.+||+.+....-+--.+...|..+.
T Consensus 230 ~l~~Gd~v~I~~a~vr~~~~~~~~el~~~~ 259 (484)
T PRK14699 230 QIEYGDTVELINAYARENAFTQKVELQVGN 259 (484)
T ss_pred ccCCCCEEEEecceEeecccCCceEEEecC
Confidence 478899999885533211112455555543
No 45
>PRK04804 minC septum formation inhibitor; Reviewed
Probab=30.22 E-value=1.6e+02 Score=23.25 Aligned_cols=55 Identities=16% Similarity=0.148 Sum_probs=41.6
Q ss_pred ccCCCCeEEEEEEeEeecccccEEEEEeCCe-EEEEecccccccccccCCEEEEEE
Q 033186 23 FYEEGASLRVTGKLQDYAVEAAMAIIADGNA-ILKIDTQHLRDLSFRVGSIYQFIG 77 (125)
Q Consensus 23 ~~~~g~sVR~~GrL~~yD~~~~~a~l~~~g~-~l~Vdt~~v~~~~~~igs~Yq~IG 77 (125)
.|-+|..|.--|-++-|=.-.++|.--+.|+ .=.|-...++|-+++|+.+|...=
T Consensus 139 dVn~GAEViA~GnI~V~G~LrG~a~AG~~Gd~~A~I~a~~l~~elv~Iag~y~~~e 194 (221)
T PRK04804 139 AVSNGAEVIADGSIHIYGTLRGRAIAGASGDKEAVIICHSLEAELVSIAGQYWLSE 194 (221)
T ss_pred cCCCCCEEEeCCCEEEEEEeccEEEecCCCCCccEEEeccCCccEEEECCEEEecc
Confidence 3445666777777777777788888888665 666777778899999999998763
No 46
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=30.10 E-value=5.5e+02 Score=25.40 Aligned_cols=70 Identities=14% Similarity=0.225 Sum_probs=48.3
Q ss_pred CCCCeEEEEEEeEeecccc--cEEEEEeCCe--EEEEecccccc-----c--ccccCCEEEEEEEEeeecCCceeEEEEE
Q 033186 25 EEGASLRVTGKLQDYAVEA--AMAIIADGNA--ILKIDTQHLRD-----L--SFRVGSIYQFIGELHIQADCEAILQARV 93 (125)
Q Consensus 25 ~~g~sVR~~GrL~~yD~~~--~~a~l~~~g~--~l~Vdt~~v~~-----~--~~~igs~Yq~IGEl~~~~d~~~~lkARV 93 (125)
..|+.|++-|++.+.=... ..++|.+++. ++.++.+.+.+ + .+.+|+...+-|.+...+.++..+.|.=
T Consensus 649 ~~~~~V~v~Grv~~~R~~G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~G~v~~t~~ge~ei~~~~ 728 (1094)
T PRK02983 649 PTGEEVSVSGRVLRIRDYGGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMGTSRNGTLSLLVTS 728 (1094)
T ss_pred cCCCEEEEEEEEEEEeeCCCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEEcCCCCEEEEEeE
Confidence 4688999999999876554 3455555544 66676655432 1 3689999999999987766666665543
Q ss_pred E
Q 033186 94 G 94 (125)
Q Consensus 94 ~ 94 (125)
.
T Consensus 729 i 729 (1094)
T PRK02983 729 W 729 (1094)
T ss_pred E
Confidence 3
No 47
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=29.93 E-value=4e+02 Score=23.67 Aligned_cols=71 Identities=20% Similarity=0.238 Sum_probs=47.3
Q ss_pred CCCeEEEEEEeEeeccccc--EEEEEeCCe--EEEEecccccc--c----ccccCCEEEEEEEEeeecCCceeEEEEEEE
Q 033186 26 EGASLRVTGKLQDYAVEAA--MAIIADGNA--ILKIDTQHLRD--L----SFRVGSIYQFIGELHIQADCEAILQARVGR 95 (125)
Q Consensus 26 ~g~sVR~~GrL~~yD~~~~--~a~l~~~g~--~l~Vdt~~v~~--~----~~~igs~Yq~IGEl~~~~d~~~~lkARV~r 95 (125)
+++.|++-|++.+.=...+ .+.|.+++. ++.++...+.+ + .+.+|+...+.|.+...+.++..|.|.=++
T Consensus 53 ~~~~v~v~G~v~~~R~~g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~t~~ge~el~~~~~~ 132 (491)
T PRK00484 53 LEIEVSVAGRVMLKRVMGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDLGDIIGVEGTLFKTKTGELSVKATELT 132 (491)
T ss_pred cCcEEEEEEEEEEEecCCceEEEEEEcCCccEEEEEECCcCCHHHHHHHhcCCCCCEEEEEEEEEEcCCCcEEEEEeEEE
Confidence 3578999999998865543 445555443 66666544332 1 478999999999998766566666554444
Q ss_pred e
Q 033186 96 N 96 (125)
Q Consensus 96 ~ 96 (125)
.
T Consensus 133 v 133 (491)
T PRK00484 133 L 133 (491)
T ss_pred E
Confidence 3
No 48
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=29.37 E-value=2.6e+02 Score=21.45 Aligned_cols=68 Identities=15% Similarity=0.160 Sum_probs=47.4
Q ss_pred EEEccccccCCcccCCCCeEEEEEEeE--eeccccc----EEEEEeCCeEEEEecccccccccccCCEEEEEEEEe
Q 033186 11 LVNLTELHPSSQFYEEGASLRVTGKLQ--DYAVEAA----MAIIADGNAILKIDTQHLRDLSFRVGSIYQFIGELH 80 (125)
Q Consensus 11 ~v~l~El~~~~~~~~~g~sVR~~GrL~--~yD~~~~----~a~l~~~g~~l~Vdt~~v~~~~~~igs~Yq~IGEl~ 80 (125)
++++.|+.... -+.++.+|+-|.++ |..-..+ +=+|+++...+.|..+=+-|--|+=|.=.-..|.+.
T Consensus 37 F~tpsEv~~~~--~~~~~~~RlGG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~GilPDlFrEGqgVVaeG~~~ 110 (155)
T PRK13159 37 LFTPSQVRAGA--AAGYQQFRLGGMVKAGSIQRAADSLKVSFTVIDKNAATQVEYTGILPDLFRDNQSVIANGRMQ 110 (155)
T ss_pred EECHHHHhcCC--cccCCeEEEccEEecCcEEEcCCCcEEEEEEEcCCcEEEEEEccCCCccccCCCeEEEEEEEc
Confidence 45677765532 46789999999987 4333322 334445556888887766666689999999999985
No 49
>PF04189 Gcd10p: Gcd10p family; InterPro: IPR007316 eIF-3 is a multisubunit complex that stimulates translation initiation in vitro at several different steps. This family corresponds to the gamma subunit of eIF3 [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation
Probab=28.55 E-value=44 Score=28.03 Aligned_cols=37 Identities=24% Similarity=0.408 Sum_probs=28.4
Q ss_pred CCCCCCeEEEccccccCCc----ccCCCCeEEEEEEeEeecccc
Q 033186 4 SAIKSGALVNLTELHPSSQ----FYEEGASLRVTGKLQDYAVEA 43 (125)
Q Consensus 4 ~~~~~g~~v~l~El~~~~~----~~~~g~sVR~~GrL~~yD~~~ 43 (125)
+.|++|.+|.|+. |+.. .+..+++|+ +||..+|....
T Consensus 2 ~~I~~gd~Vil~~--~~~~~k~v~l~~~~~i~-lGK~~sf~~~~ 42 (299)
T PF04189_consen 2 SIIQEGDYVILRL--PSGNMKIVKLKPNKTIS-LGKFGSFPLND 42 (299)
T ss_pred CCcCCCCEEEEEc--CCCcEEEEEECCCCEEE-ecCCCcccHHH
Confidence 5799999999983 5532 466888888 89998887665
No 50
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=28.25 E-value=4.4e+02 Score=23.61 Aligned_cols=72 Identities=15% Similarity=0.218 Sum_probs=48.4
Q ss_pred CCCeEEEEEEeEeecccc--cEEEEEeCCe--EEEEeccccc-c-----c-ccccCCEEEEEEEEeeecCCceeEEEEEE
Q 033186 26 EGASLRVTGKLQDYAVEA--AMAIIADGNA--ILKIDTQHLR-D-----L-SFRVGSIYQFIGELHIQADCEAILQARVG 94 (125)
Q Consensus 26 ~g~sVR~~GrL~~yD~~~--~~a~l~~~g~--~l~Vdt~~v~-~-----~-~~~igs~Yq~IGEl~~~~d~~~~lkARV~ 94 (125)
.|+.|++-|++.+.=... ..+.|.+++. ++.+.-..+. + + .+.+|+...+-|.+-..+.++..|+|.=+
T Consensus 64 ~~~~v~v~Grv~~~R~~Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~~gelel~~~~~ 143 (505)
T PRK12445 64 LNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTEL 143 (505)
T ss_pred CCCEEEEEEEEEEEecCCCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecCCCcEEEEEeEE
Confidence 478899999999886654 4555656544 5555433332 1 1 47899999999999876666666666544
Q ss_pred Eec
Q 033186 95 RNV 97 (125)
Q Consensus 95 r~V 97 (125)
+.+
T Consensus 144 ~ll 146 (505)
T PRK12445 144 RLL 146 (505)
T ss_pred EEE
Confidence 443
No 51
>PLN02221 asparaginyl-tRNA synthetase
Probab=27.65 E-value=4.6e+02 Score=24.06 Aligned_cols=87 Identities=17% Similarity=0.198 Sum_probs=56.4
Q ss_pred eEEEccccccC--CcccCCCCeEEEEEEeEeeccccc----EEEEEeCC----eEEEEeccccccc--ccccCCEEEEEE
Q 033186 10 ALVNLTELHPS--SQFYEEGASLRVTGKLQDYAVEAA----MAIIADGN----AILKIDTQHLRDL--SFRVGSIYQFIG 77 (125)
Q Consensus 10 ~~v~l~El~~~--~~~~~~g~sVR~~GrL~~yD~~~~----~a~l~~~g----~~l~Vdt~~v~~~--~~~igs~Yq~IG 77 (125)
.-++++++..+ ++.-..|+.|++-|.+++.=...+ ...|.+++ -++.++.. .... .+..+|..++.|
T Consensus 31 ~~~~~~~~~~~~~~~~~~~g~~V~I~GWV~~iR~~Gk~~i~Fl~LRDgs~~g~iQvVv~~~-~~~~~~~L~~ES~V~V~G 109 (572)
T PLN02221 31 DRVLIRSILDRPDGGAGLAGQKVRIGGWVKTGREQGKGTFAFLEVNDGSCPANLQVMVDSS-LYDLSTLVATGTCVTVDG 109 (572)
T ss_pred CceEHHHHhccccCChhcCCCEEEEEEEEEehhhCCCceEEEEEEeCCcccccEEEEEcCc-hhhHHhcCCCceEEEEEE
Confidence 45678887533 344557999999999999977653 34444554 15556543 1111 368999999999
Q ss_pred EEeeecC-----CceeEEEEEEEec
Q 033186 78 ELHIQAD-----CEAILQARVGRNV 97 (125)
Q Consensus 78 El~~~~d-----~~~~lkARV~r~V 97 (125)
.+...+. ++..|.+.=+.++
T Consensus 110 ~V~~~~~~~~~~~~iEl~v~~i~vl 134 (572)
T PLN02221 110 VLKVPPEGKGTKQKIELSVEKVIDV 134 (572)
T ss_pred EEEeCCccCCCCccEEEEEeEEEEE
Confidence 9976541 2567777655444
No 52
>PF05606 DUF777: Borrelia burgdorferi protein of unknown function (DUF777); InterPro: IPR008495 This family consists of several hypothetical proteins of unknown function, found in Borrelia burgdorferi and Borrelia garinii.
Probab=27.53 E-value=71 Score=25.28 Aligned_cols=41 Identities=12% Similarity=0.265 Sum_probs=29.9
Q ss_pred CCCeEEEEEEeEeecccccEEEEEeCCe-EEEEecccccccc
Q 033186 26 EGASLRVTGKLQDYAVEAAMAIIADGNA-ILKIDTQHLRDLS 66 (125)
Q Consensus 26 ~g~sVR~~GrL~~yD~~~~~a~l~~~g~-~l~Vdt~~v~~~~ 66 (125)
.+.-+=.+|.+++||-+++.|+++-.-. -+.+.|+.+..+.
T Consensus 30 ~NiFI~rIG~iK~F~~~tQe~iVti~e~e~LeI~T~nISN~~ 71 (181)
T PF05606_consen 30 SNIFICRIGTIKSFKFQTQEGIVTIPEYEDLEIHTKNISNIN 71 (181)
T ss_pred hcEEEEEEeeeeecccccceEEEEeecccCceEEeeecccce
Confidence 4555667899999999999999986332 4666666666544
No 53
>PRK15463 cold shock-like protein CspF; Provisional
Probab=27.48 E-value=1.8e+02 Score=18.96 Aligned_cols=49 Identities=12% Similarity=0.190 Sum_probs=38.0
Q ss_pred EEEEEeEeecccccEEEEEeCC--eEEEEecccccc---cccccCCEEEEEEEEee
Q 033186 31 RVTGKLQDYAVEAAMAIIADGN--AILKIDTQHLRD---LSFRVGSIYQFIGELHI 81 (125)
Q Consensus 31 R~~GrL~~yD~~~~~a~l~~~g--~~l~Vdt~~v~~---~~~~igs~Yq~IGEl~~ 81 (125)
|..|+++.||.+.+-.-|+.++ ..|-|..+.++. -.++.|...+| ++..
T Consensus 4 ~~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f--~v~~ 57 (70)
T PRK15463 4 KMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEF--CRIN 57 (70)
T ss_pred cceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEE--EEEE
Confidence 4579999999999999888733 478888777754 35899999988 4544
No 54
>TIGR01222 minC septum site-determining protein MinC. The minC protein assists in correct placement of the septum for cell division by inhibiting septum formation at other sites. Homologs from Deinocoocus, Synechocystis PCC 6803, and Helicobacter pylori do not hit the full length of the model and score between the trusted and noise cutoffs.
Probab=27.35 E-value=1.1e+02 Score=23.88 Aligned_cols=56 Identities=14% Similarity=0.172 Sum_probs=42.6
Q ss_pred ccCCCCeEEEEEEeEeecccccEEEEEeCCe-EEEEecccccccccccCCEEEEEEE
Q 033186 23 FYEEGASLRVTGKLQDYAVEAAMAIIADGNA-ILKIDTQHLRDLSFRVGSIYQFIGE 78 (125)
Q Consensus 23 ~~~~g~sVR~~GrL~~yD~~~~~a~l~~~g~-~l~Vdt~~v~~~~~~igs~Yq~IGE 78 (125)
.+-+|..|+--|-++-|=.-.++|.--++|+ .=.|-...++|-+.+|+..|...-+
T Consensus 137 ~Vn~GAeViA~GnI~V~G~LrG~a~AG~~Gd~~A~I~a~~l~ae~v~Iag~~~~~~~ 193 (217)
T TIGR01222 137 NVNAGAEVLADGNIHVYGKLRGRALAGANGDTSAVIFALDLQAELISIAGRYKVSDD 193 (217)
T ss_pred CCCCCCEEEeCCCEEEEEEeccEEEcCCCCCCCcEEEeccCCccEEEECCEEEeCCC
Confidence 4556777777777777777788888777665 6667777788989999999986443
No 55
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=27.12 E-value=2.2e+02 Score=26.89 Aligned_cols=85 Identities=13% Similarity=0.223 Sum_probs=53.4
Q ss_pred CCCCeEEEEEEeEeecccccEEEEEe--CCeEEEEecccccc----c-ccccCCEEEEEEEEeeecCCceeEEEEEEEec
Q 033186 25 EEGASLRVTGKLQDYAVEAAMAIIAD--GNAILKIDTQHLRD----L-SFRVGSIYQFIGELHIQADCEAILQARVGRNV 97 (125)
Q Consensus 25 ~~g~sVR~~GrL~~yD~~~~~a~l~~--~g~~l~Vdt~~v~~----~-~~~igs~Yq~IGEl~~~~d~~~~lkARV~r~V 97 (125)
..|++||+-|.+.-.-.+++=.+.+- +...+ =.+.|.+| . ..++|.+.++||++....+ .|+.
T Consensus 211 ~ig~tV~I~GeV~qikqT~GPTVFtltDetg~i-~aAAFe~aGvRAyP~IevGdiV~ViG~V~~r~g---~lQi------ 280 (715)
T COG1107 211 MIGKTVRIEGEVTQIKQTSGPTVFTLTDETGAI-WAAAFEEAGVRAYPEIEVGDIVEVIGEVTRRDG---RLQI------ 280 (715)
T ss_pred hcCceEEEEEEEEEEEEcCCCEEEEEecCCCce-ehhhhccCCcccCCCCCCCceEEEEEEEeecCC---cEEE------
Confidence 46999999999998888876555443 33233 33444433 3 3899999999999987532 2222
Q ss_pred cCCCHHHH--HHHHHHHHHHHhhh
Q 033186 98 DGLDLNLY--RQSLQLLRQFQADR 119 (125)
Q Consensus 98 DglDl~L~--ekal~~~R~f~~~~ 119 (125)
+=+++..+ .+|.+.||+-.+..
T Consensus 281 E~~~me~L~G~ea~eVr~rid~al 304 (715)
T COG1107 281 EIEAMEKLTGDEAAEVRKRIDEAL 304 (715)
T ss_pred eehhhHHhhCchHHHHHHHHHHHH
Confidence 22333333 35666666665544
No 56
>PRK09890 cold shock protein CspG; Provisional
Probab=26.48 E-value=1.9e+02 Score=18.78 Aligned_cols=46 Identities=9% Similarity=0.213 Sum_probs=36.0
Q ss_pred EEEEEeEeecccccEEEEEeCC--eEEEEeccccccc---ccccCCEEEEE
Q 033186 31 RVTGKLQDYAVEAAMAIIADGN--AILKIDTQHLRDL---SFRVGSIYQFI 76 (125)
Q Consensus 31 R~~GrL~~yD~~~~~a~l~~~g--~~l~Vdt~~v~~~---~~~igs~Yq~I 76 (125)
|..|++..||.+.+-.-|+.++ ..|.+.-+.+..- .++.|...+|.
T Consensus 4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~ 54 (70)
T PRK09890 4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFS 54 (70)
T ss_pred cceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEE
Confidence 4579999999999999888743 4677777766542 47899999993
No 57
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=25.76 E-value=1.3e+02 Score=20.62 Aligned_cols=29 Identities=24% Similarity=0.353 Sum_probs=21.8
Q ss_pred CCCCCCeEEEccccccCCcccCCCCeEEEEEEe
Q 033186 4 SAIKSGALVNLTELHPSSQFYEEGASLRVTGKL 36 (125)
Q Consensus 4 ~~~~~g~~v~l~El~~~~~~~~~g~sVR~~GrL 36 (125)
...+.|++|.+.|.+|-|. .++-++...+
T Consensus 52 n~~k~GD~V~I~e~rPlSK----~K~~~v~~i~ 80 (84)
T PRK05610 52 NEAKIGDVVRIMETRPLSK----TKRWRLVEIV 80 (84)
T ss_pred CCCCCCCEEEEEEcccCCC----CEEEEEEEEE
Confidence 4678999999999999984 4555555444
No 58
>PLN02850 aspartate-tRNA ligase
Probab=25.48 E-value=5e+02 Score=23.40 Aligned_cols=84 Identities=11% Similarity=0.150 Sum_probs=53.4
Q ss_pred eEEEccccccCCcccCCCCeEEEEEEeEeecccccEE--EEEeCCe--EEEEeccc--ccc------cccccCCEEEEEE
Q 033186 10 ALVNLTELHPSSQFYEEGASLRVTGKLQDYAVEAAMA--IIADGNA--ILKIDTQH--LRD------LSFRVGSIYQFIG 77 (125)
Q Consensus 10 ~~v~l~El~~~~~~~~~g~sVR~~GrL~~yD~~~~~a--~l~~~g~--~l~Vdt~~--v~~------~~~~igs~Yq~IG 77 (125)
....+.||-++ ..|+.|++-|+++..=...+.+ +|.+++. ++.+..+. +.+ -.+..||...+-|
T Consensus 68 ~~~~i~~l~~~----~~g~~V~v~Grv~~~R~~gk~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G 143 (530)
T PLN02850 68 EWTDVSDLGEE----LAGSEVLIRGRVHTIRGKGKSAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQLSRESVVDVEG 143 (530)
T ss_pred eEeEhhhcchh----hCCCEEEEEEEEEEEccCCCeEEEEEEeCCcCEEEEEECCccccCHHHHHHHhCCCCCCEEEEEE
Confidence 45666666443 3599999999999988877654 4444443 44454332 221 1589999999999
Q ss_pred EEeeec------CCceeEEEEEEEec
Q 033186 78 ELHIQA------DCEAILQARVGRNV 97 (125)
Q Consensus 78 El~~~~------d~~~~lkARV~r~V 97 (125)
.+...+ ..+..|.+.=+.++
T Consensus 144 ~v~~~~~~~~~~t~~~El~~~~i~vl 169 (530)
T PLN02850 144 VVSVPKKPVKGTTQQVEIQVRKIYCV 169 (530)
T ss_pred EEEccCcCCCCCCccEEEEEeEEEEE
Confidence 997421 22456666555554
No 59
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=25.39 E-value=62 Score=20.01 Aligned_cols=19 Identities=32% Similarity=0.263 Sum_probs=14.7
Q ss_pred CCCCeEEEEEEeEeecccc
Q 033186 25 EEGASLRVTGKLQDYAVEA 43 (125)
Q Consensus 25 ~~g~sVR~~GrL~~yD~~~ 43 (125)
-.||.|+|.|+|-......
T Consensus 17 ~~Gk~V~V~G~l~~a~t~h 35 (48)
T PF14485_consen 17 LLGKRVSVTGKLFHAHTGH 35 (48)
T ss_pred hcCCeEEEEEEEeeccCcc
Confidence 3699999999997665443
No 60
>cd00430 PLPDE_III_AR Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase. This family includes predominantly bacterial alanine racemases (AR), some serine racemases (SerRac), and putative bifunctional enzymes containing N-terminal UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase (murF) and C-terminal AR domains. These proteins are fold type III PLP-dependent enzymes that play essential roles in peptidoglycan biosynthesis. AR catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. SerRac converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. murF catalyzes the addition of D-Ala-D-Ala to UDPMurNAc-tripeptide, the final step in the synthesis of the cytoplasmic precursor of bacterial cell wall peptidoglycan. Members of this family contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with activ
Probab=24.72 E-value=1.1e+02 Score=25.06 Aligned_cols=37 Identities=16% Similarity=0.340 Sum_probs=28.3
Q ss_pred CCCeEEEEEEeEeecccccEEEEEeCCeEEEEecccccccccccCCEEEEEEE
Q 033186 26 EGASLRVTGKLQDYAVEAAMAIIADGNAILKIDTQHLRDLSFRVGSIYQFIGE 78 (125)
Q Consensus 26 ~g~sVR~~GrL~~yD~~~~~a~l~~~g~~l~Vdt~~v~~~~~~igs~Yq~IGE 78 (125)
.|+.++++|+++ .+.+.||.+.++ ..++|....|+|+
T Consensus 296 ~~~~~~ivG~v~--------------mD~~~vdv~~~~--~~~~GD~v~l~g~ 332 (367)
T cd00430 296 RGKRAPIVGRVC--------------MDQTMVDVTDIP--DVKVGDEVVLFGR 332 (367)
T ss_pred CCEEcceeceee--------------ccEEEEECCCCC--CCCCCCEEEEEcC
Confidence 678888888875 236777776664 5789999999998
No 61
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=24.45 E-value=36 Score=22.81 Aligned_cols=65 Identities=12% Similarity=0.188 Sum_probs=35.6
Q ss_pred CCeEEEccccccCCcccCCC--CeEEEEEEeEeecccccEEEEEeCCe-EEEEecccccccccccCCEEEE
Q 033186 8 SGALVNLTELHPSSQFYEEG--ASLRVTGKLQDYAVEAAMAIIADGNA-ILKIDTQHLRDLSFRVGSIYQF 75 (125)
Q Consensus 8 ~g~~v~l~El~~~~~~~~~g--~sVR~~GrL~~yD~~~~~a~l~~~g~-~l~Vdt~~v~~~~~~igs~Yq~ 75 (125)
+..+|.+.+ +.+..+..+ +++||.|++-.+.-.++++- .-+|. -|-|+...-.....+.|....+
T Consensus 11 ~~~fv~vP~--~v~~~l~~~~~g~v~V~~tI~g~~~~~sl~p-~g~G~~~Lpv~~~vRk~~g~~~Gd~V~v 78 (80)
T PF08922_consen 11 GWTFVEVPF--DVAEELGEGGWGRVPVRGTIDGHPWRTSLFP-MGNGGYILPVKAAVRKAIGKEAGDTVEV 78 (80)
T ss_dssp S-EEEE--S---HHHHH--S--S-EEEEEEETTEEEEEEEEE-SSTT-EEEEE-HHHHHHHT--TTSEEEE
T ss_pred ceEEEEeCH--HHHHHhccccCCceEEEEEECCEEEEEEEEE-CCCCCEEEEEcHHHHHHcCCCCCCEEEE
Confidence 445666665 566778888 99999999988777665544 23343 5557776655556666665543
No 62
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=24.25 E-value=1.8e+02 Score=17.86 Aligned_cols=46 Identities=20% Similarity=0.228 Sum_probs=36.4
Q ss_pred EEEeEeecccccEEEEEeCC--eEEEEeccccccc---ccccCCEEEEEEE
Q 033186 33 TGKLQDYAVEAAMAIIADGN--AILKIDTQHLRDL---SFRVGSIYQFIGE 78 (125)
Q Consensus 33 ~GrL~~yD~~~~~a~l~~~g--~~l~Vdt~~v~~~---~~~igs~Yq~IGE 78 (125)
.|+++.||.+.+-.-|..++ ..+.+..+.+... .++.|....|-=+
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~ 52 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELE 52 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEE
Confidence 58999999999999999854 5777777777653 5899998888433
No 63
>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=23.93 E-value=1.7e+02 Score=18.18 Aligned_cols=22 Identities=32% Similarity=0.338 Sum_probs=18.2
Q ss_pred cCCcccCCCCeEEEEEEeEeec
Q 033186 19 PSSQFYEEGASLRVTGKLQDYA 40 (125)
Q Consensus 19 ~~~~~~~~g~sVR~~GrL~~yD 40 (125)
.....+++|..|-+.|+++.|+
T Consensus 41 ~~~~~l~~g~~v~v~g~v~~~~ 62 (78)
T cd04489 41 RLGFPLEEGMEVLVRGKVSFYE 62 (78)
T ss_pred hCCCCCCCCCEEEEEEEEEEEC
Confidence 3346788999999999999875
No 64
>COG3218 ABC-type uncharacterized transport system, auxiliary component [General function prediction only]
Probab=23.90 E-value=2.4e+02 Score=22.83 Aligned_cols=74 Identities=18% Similarity=0.192 Sum_probs=48.6
Q ss_pred eEeecccccEEEEEeCCeEEEEecccccc---cccc--cC---CEEEEEEEEeeecCCceeEEEEEEEec---cCCCHHH
Q 033186 36 LQDYAVEAAMAIIADGNAILKIDTQHLRD---LSFR--VG---SIYQFIGELHIQADCEAILQARVGRNV---DGLDLNL 104 (125)
Q Consensus 36 L~~yD~~~~~a~l~~~g~~l~Vdt~~v~~---~~~~--ig---s~Yq~IGEl~~~~d~~~~lkARV~r~V---DglDl~L 104 (125)
++.|+.+..++.+...|..+.+|.++..+ |..+ -| ...++-+.+... .++-+..-|+++.. ||-+...
T Consensus 102 ~~aFe~sg~~~gl~~~g~gL~aDy~l~~dlr~FE~~y~~~~~~A~Iei~v~Ll~~-~n~~v~A~r~F~a~~pv~g~~~~a 180 (205)
T COG3218 102 VQAFEDSGRFAGLGRPGSGLAADYQLILDLRAFEIQYVTGAPTAVIEISVRLLND-RNGTVRASRVFRASQPVDGKGNAA 180 (205)
T ss_pred HHHHhhcCceeeccCCCccceeeeeeeehhhhhhhhccCCCceEEEEEEEEEecc-CCCcEEEEEEEEEeecccCCCcHH
Confidence 56677788888888777788888888555 3333 23 334445555443 23345566777765 9999988
Q ss_pred HHHHHH
Q 033186 105 YRQSLQ 110 (125)
Q Consensus 105 ~ekal~ 110 (125)
+-+|++
T Consensus 181 ~v~A~d 186 (205)
T COG3218 181 VVKAFD 186 (205)
T ss_pred HHHHHH
Confidence 888875
No 65
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=23.79 E-value=64 Score=21.50 Aligned_cols=20 Identities=30% Similarity=0.484 Sum_probs=16.8
Q ss_pred CCCCCCCeEEEccccccCCc
Q 033186 3 SSAIKSGALVNLTELHPSSQ 22 (125)
Q Consensus 3 ~~~~~~g~~v~l~El~~~~~ 22 (125)
....+.|+.|.+.|..|-|.
T Consensus 46 ~~~~k~GD~V~I~ecrPlSK 65 (71)
T TIGR03635 46 NNECKVGDVVRIIETRPLSK 65 (71)
T ss_pred CCCCCCCCEEEEEEcCCcCC
Confidence 34678999999999999873
No 66
>PRK13992 minC septum formation inhibitor; Provisional
Probab=23.66 E-value=1.7e+02 Score=22.91 Aligned_cols=52 Identities=10% Similarity=0.105 Sum_probs=39.8
Q ss_pred ccCCCCeEEEEEEeEeecccccEEEEEeCCe-EEEEecccccccccccCCEEE
Q 033186 23 FYEEGASLRVTGKLQDYAVEAAMAIIADGNA-ILKIDTQHLRDLSFRVGSIYQ 74 (125)
Q Consensus 23 ~~~~g~sVR~~GrL~~yD~~~~~a~l~~~g~-~l~Vdt~~v~~~~~~igs~Yq 74 (125)
.+-+|..|.--|-++-|=.-.++|.--++|+ .=.|-...++|-+++|+.+|.
T Consensus 122 dVn~GAeViA~GnI~V~G~LrG~a~AGa~Gd~~A~I~a~~l~p~~l~IA~~~~ 174 (205)
T PRK13992 122 NVHKGAEILAGGSVVIFGKAQGIVRAGLNEGEQSVIAALSLQTSLIQISGFIT 174 (205)
T ss_pred cCCCCCEEEeCCCEEEEEEeccEEEeCCCCCCceEEEEccCCccEEEECcEEe
Confidence 4556777777777777777788888877664 556667778899999999995
No 67
>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=23.25 E-value=1.9e+02 Score=17.78 Aligned_cols=20 Identities=20% Similarity=0.625 Sum_probs=16.8
Q ss_pred CcccCCCCeEEEEEEeEeec
Q 033186 21 SQFYEEGASLRVTGKLQDYA 40 (125)
Q Consensus 21 ~~~~~~g~sVR~~GrL~~yD 40 (125)
...+++|..|.+.|++..|+
T Consensus 44 ~~~l~~g~~v~v~G~v~~~~ 63 (83)
T cd04492 44 EEKFKPGDIVHVKGRVEEYR 63 (83)
T ss_pred HhhCCCCCEEEEEEEEEEeC
Confidence 35788999999999998764
No 68
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=23.17 E-value=2.2e+02 Score=18.38 Aligned_cols=48 Identities=13% Similarity=0.247 Sum_probs=37.2
Q ss_pred EEEEeEeecccccEEEEEeCC--eEEEEeccccccc---ccccCCEEEEEEEEee
Q 033186 32 VTGKLQDYAVEAAMAIIADGN--AILKIDTQHLRDL---SFRVGSIYQFIGELHI 81 (125)
Q Consensus 32 ~~GrL~~yD~~~~~a~l~~~g--~~l~Vdt~~v~~~---~~~igs~Yq~IGEl~~ 81 (125)
..|+++.||.+.+-.-|..++ ..+.+.-+.++.. .++.|...+| ++..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f--~~~~ 57 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSF--TIES 57 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEE--EEEE
Confidence 479999999999999998733 4677777777653 4899999998 4444
No 69
>PRK10694 acyl-CoA esterase; Provisional
Probab=22.90 E-value=3e+02 Score=19.87 Aligned_cols=42 Identities=12% Similarity=0.146 Sum_probs=32.6
Q ss_pred EEEEec-ccccccccccCCEEEEEEEEeeecCCceeEEEEEEEec
Q 033186 54 ILKIDT-QHLRDLSFRVGSIYQFIGELHIQADCEAILQARVGRNV 97 (125)
Q Consensus 54 ~l~Vdt-~~v~~~~~~igs~Yq~IGEl~~~~d~~~~lkARV~r~V 97 (125)
.+.+|. .|.. |.++|.+-.+-+++..-......+.++++...
T Consensus 56 tv~vd~i~F~~--Pv~~Gd~l~~~a~V~~~g~sS~~v~v~v~~~~ 98 (133)
T PRK10694 56 TVRVEGMTFLR--PVAVGDVVCCYARCVKTGTTSISINIEVWVKK 98 (133)
T ss_pred EEEECceEECC--CcccCcEEEEEEEEEEccCceEEEEEEEEEee
Confidence 445666 7787 56899999999999887777778888887643
No 70
>PRK03511 minC septum formation inhibitor; Reviewed
Probab=21.86 E-value=1.9e+02 Score=23.13 Aligned_cols=57 Identities=18% Similarity=0.241 Sum_probs=43.1
Q ss_pred ccCCCCeEEEEEEeEeecccccEEEEEeCCe-EEEEecccccccccccCCEEEEEEEE
Q 033186 23 FYEEGASLRVTGKLQDYAVEAAMAIIADGNA-ILKIDTQHLRDLSFRVGSIYQFIGEL 79 (125)
Q Consensus 23 ~~~~g~sVR~~GrL~~yD~~~~~a~l~~~g~-~l~Vdt~~v~~~~~~igs~Yq~IGEl 79 (125)
.|-+|.-|---|-++-|=.-.++|.--++|+ +=.|-...++|-+++|+.+|..+-.+
T Consensus 147 ~Vn~GAEViA~GnI~V~G~LrG~a~AG~~Gd~~A~Ifa~~l~aelvsIAg~y~~~e~~ 204 (228)
T PRK03511 147 HVSAGAELIADGNIHVYGMMRGRALAGASGDRECQIFCTHLMAELVSIAGQYWLSDQI 204 (228)
T ss_pred cCCCCCEEEeCCCEEEEEEeccEEEecCCCCCccEEEeccCCccEEEEcCEEeecccC
Confidence 3455666666666777777778887777665 66777778889999999999988864
No 71
>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=21.65 E-value=2.4e+02 Score=18.26 Aligned_cols=27 Identities=22% Similarity=0.148 Sum_probs=19.4
Q ss_pred ccccCCEEEEEEEEeeecC-----CceeEEEE
Q 033186 66 SFRVGSIYQFIGELHIQAD-----CEAILQAR 92 (125)
Q Consensus 66 ~~~igs~Yq~IGEl~~~~d-----~~~~lkAR 92 (125)
.+..|+..++-|++...+. ++.++++.
T Consensus 46 ~l~~es~V~V~G~v~~~~~~~~~~~~~Ei~~~ 77 (84)
T cd04323 46 SLTQESSVEVTGEVKEDPRAKQAPGGYELQVD 77 (84)
T ss_pred cCCCcCEEEEEEEEEECCcccCCCCCEEEEEE
Confidence 4789999999999987532 23455554
No 72
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=21.60 E-value=1.7e+02 Score=20.14 Aligned_cols=30 Identities=20% Similarity=0.192 Sum_probs=22.7
Q ss_pred CCCCCCeEEEccccccCCcccCCCCeEEEEEEeE
Q 033186 4 SAIKSGALVNLTELHPSSQFYEEGASLRVTGKLQ 37 (125)
Q Consensus 4 ~~~~~g~~v~l~El~~~~~~~~~g~sVR~~GrL~ 37 (125)
...+-|++|.+.|.+|-|. -++-++...++
T Consensus 49 n~~~~GD~V~I~e~RPlSK----tK~~~v~~i~~ 78 (84)
T CHL00142 49 NECNIGDQVLIEETRPLSK----TKRWILKEILS 78 (84)
T ss_pred CCCCCCCEEEEEEcCCCCC----cEEEEEEEEEE
Confidence 4678999999999999985 55666665543
No 73
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=21.43 E-value=1.6e+02 Score=20.33 Aligned_cols=38 Identities=16% Similarity=0.322 Sum_probs=24.3
Q ss_pred CCCCCCCCeEEEccccccCCcccCCCCeEEEEEEeEeec
Q 033186 2 ASSAIKSGALVNLTELHPSSQFYEEGASLRVTGKLQDYA 40 (125)
Q Consensus 2 ~~~~~~~g~~v~l~El~~~~~~~~~g~sVR~~GrL~~yD 40 (125)
+...+.+|.+++.+.|.+. ..++.|..|.++=+--.+.
T Consensus 45 a~r~i~~G~~i~~~~l~~~-~~V~~G~~V~i~~~~~~~~ 82 (122)
T TIGR03170 45 AKRPLRAGQPLTANMLRPP-WLVKRGDTVTVIARGGGLS 82 (122)
T ss_pred eecccCCCCeeChHhcCCc-cEEcCCCEEEEEEecCCEE
Confidence 3456777888877777654 5677777777654443333
No 74
>PF10726 DUF2518: Protein of function (DUF2518); InterPro: IPR019664 This entry contains the Ycf51 protein family, which is conserved in Cyanobacteria. The function is not known.
Probab=20.66 E-value=26 Score=26.88 Aligned_cols=63 Identities=22% Similarity=0.145 Sum_probs=39.1
Q ss_pred eecccccEEEEEeCCeEEEEecccccccccccCCEEEEEEEEeeecCCceeEEEEEEEec-cCCCHHHH
Q 033186 38 DYAVEAAMAIIADGNAILKIDTQHLRDLSFRVGSIYQFIGELHIQADCEAILQARVGRNV-DGLDLNLY 105 (125)
Q Consensus 38 ~yD~~~~~a~l~~~g~~l~Vdt~~v~~~~~~igs~Yq~IGEl~~~~d~~~~lkARV~r~V-DglDl~L~ 105 (125)
-||...+++++.... .+..+.+||---|.-+.+-=-|-... |+...++||...-. ||++.++|
T Consensus 75 VyDnG~~~vVi~v~~---~i~~~~leaTL~QaA~nL~s~GR~~~--~~~~~IR~R~l~h~~~GvS~Pl~ 138 (145)
T PF10726_consen 75 VYDNGADQVVIAVPP---DITPEALEATLEQAASNLFSGGRSGR--DNQVTIRARTLIHPEPGVSKPLY 138 (145)
T ss_pred EEECCCcEEEEEcCC---CCCHHHHHHHHHHHHHhccccCccCC--CCeEEEEEEEeEcCCCCCccceE
Confidence 588888888887655 23334455522333333333444333 56678889888776 88888765
No 75
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=20.60 E-value=4.1e+02 Score=24.95 Aligned_cols=70 Identities=19% Similarity=0.104 Sum_probs=45.6
Q ss_pred CCeEEEEEEeEeeccccc--EEEEEeCCe--EEEEecccc-cc-------cccccCCEEEEEEEEeeecCCceeEEEEEE
Q 033186 27 GASLRVTGKLQDYAVEAA--MAIIADGNA--ILKIDTQHL-RD-------LSFRVGSIYQFIGELHIQADCEAILQARVG 94 (125)
Q Consensus 27 g~sVR~~GrL~~yD~~~~--~a~l~~~g~--~l~Vdt~~v-~~-------~~~~igs~Yq~IGEl~~~~d~~~~lkARV~ 94 (125)
.+.|++-|++...=...+ .+.|.+.+. ++.++...+ .+ ..+.+|+...+-|.+...+.++..+.|.=+
T Consensus 107 ~~~V~vaGrV~~~R~~Gk~~F~~LrD~~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~v~~t~~GeleI~~~~i 186 (659)
T PTZ00385 107 QATVRVAGRVTSVRDIGKIIFVTIRSNGNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADGVPCRMQRGELSVAASRM 186 (659)
T ss_pred CCEEEEEEEEEeeeccCCeEEEEEEECCceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEEEEEecCCceEEEEeeEE
Confidence 556999999988766544 445555443 666654432 22 147899999999998876666666655444
Q ss_pred Ee
Q 033186 95 RN 96 (125)
Q Consensus 95 r~ 96 (125)
+.
T Consensus 187 ~l 188 (659)
T PTZ00385 187 LI 188 (659)
T ss_pred EE
Confidence 33
No 76
>COG0832 UreB Urea amidohydrolase (urease) beta subunit [Amino acid transport and metabolism]
Probab=20.57 E-value=1.4e+02 Score=21.81 Aligned_cols=23 Identities=26% Similarity=0.528 Sum_probs=16.5
Q ss_pred EEEEecccccccccccCCEEEEE
Q 033186 54 ILKIDTQHLRDLSFRVGSIYQFI 76 (125)
Q Consensus 54 ~l~Vdt~~v~~~~~~igs~Yq~I 76 (125)
..++.-.+-.|=|.|+||.|.|.
T Consensus 21 ~~~i~V~NtGDRPIQVGSHfHF~ 43 (106)
T COG0832 21 TVTIEVANTGDRPIQVGSHFHFF 43 (106)
T ss_pred ceEEEEeecCCCceEeecceeeh
Confidence 44455555567788999999885
Done!