Query 029148
Match_columns 198
No_of_seqs 213 out of 508
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 08:16:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029148.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029148hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3165 Predicted nucleic-acid 100.0 2.3E-81 5E-86 510.5 13.4 193 1-194 1-193 (195)
2 KOG3164 Uncharacterized protei 100.0 6E-43 1.3E-47 296.4 11.9 138 52-191 13-153 (236)
3 COG1412 Uncharacterized protei 100.0 2.9E-41 6.2E-46 269.5 11.6 133 55-189 1-136 (136)
4 PF04900 Fcf1: Fcf1; InterPro 100.0 1.2E-31 2.7E-36 202.5 9.1 99 89-187 1-101 (101)
5 smart00670 PINc Large family o 98.5 5E-07 1.1E-11 66.9 7.0 93 67-164 1-111 (111)
6 PF13638 PIN_4: PIN domain; PD 98.2 1.9E-05 4.2E-10 60.9 10.4 101 67-177 1-132 (133)
7 PRK13764 ATPase; Provisional 97.8 3.5E-05 7.5E-10 74.9 6.4 115 66-187 2-139 (602)
8 TIGR00305 probable toxin-antit 97.2 0.0046 1E-07 46.9 10.1 96 66-163 1-112 (114)
9 PF01850 PIN: PIN domain; Int 96.9 0.0068 1.5E-07 44.6 8.1 99 67-167 1-120 (121)
10 TIGR00028 Mtu_PIN_fam Mycobact 96.8 0.0035 7.6E-08 47.9 6.0 104 67-175 2-137 (142)
11 PRK00124 hypothetical protein; 95.7 0.0094 2E-07 48.8 3.2 81 104-187 12-102 (151)
12 PF13470 PIN_3: PIN domain 95.7 0.11 2.4E-06 38.9 8.8 46 66-111 1-47 (119)
13 PF02639 DUF188: Uncharacteriz 94.9 0.026 5.6E-07 45.0 3.2 61 125-188 27-87 (130)
14 COG1848 Predicted nucleic acid 94.4 0.31 6.6E-06 37.8 8.1 100 66-165 1-131 (140)
15 COG1569 Predicted nucleic acid 93.8 0.56 1.2E-05 38.1 8.6 95 66-163 2-116 (142)
16 COG2402 Predicted nucleic acid 92.9 0.44 9.6E-06 38.3 6.7 95 67-161 2-123 (135)
17 COG4956 Integral membrane prot 90.7 0.38 8.3E-06 44.0 4.6 81 97-179 187-282 (356)
18 PRK12496 hypothetical protein; 89.8 2.1 4.5E-05 35.2 7.9 97 66-179 3-117 (164)
19 PF05991 NYN_YacP: YacP-like N 88.7 1.2 2.5E-05 36.5 5.6 42 134-176 74-119 (166)
20 PRK13725 plasmid maintenance p 88.6 3.9 8.6E-05 31.9 8.4 42 67-110 4-45 (132)
21 COG1487 VapC Predicted nucleic 86.6 4.2 9E-05 31.3 7.4 43 65-110 2-44 (133)
22 COG1671 Uncharacterized protei 85.3 1.4 2.9E-05 36.3 4.2 48 138-188 55-102 (150)
23 COG1656 Uncharacterized conser 77.1 9.8 0.00021 31.7 6.5 42 137-181 34-75 (165)
24 cd06167 LabA_like LabA_like pr 74.2 37 0.00081 26.0 10.3 107 66-180 4-132 (149)
25 PF14367 DUF4411: Domain of un 73.9 4.3 9.3E-05 32.9 3.6 46 68-113 2-52 (162)
26 PF01936 NYN: NYN domain; Int 72.5 29 0.00062 26.2 7.8 104 66-178 3-126 (146)
27 PF01927 Mut7-C: Mut7-C RNAse 71.6 8.6 0.00019 30.7 4.8 40 137-179 28-67 (147)
28 COG2405 Predicted nucleic acid 68.2 28 0.00062 28.6 7.1 100 67-177 2-112 (157)
29 COG4113 Predicted nucleic acid 62.9 69 0.0015 25.6 8.3 102 64-168 1-126 (134)
30 smart00500 SFM Splicing Factor 62.2 6.2 0.00013 25.9 1.8 23 157-180 1-23 (44)
31 COG1855 ATPase (PilT family) [ 59.9 52 0.0011 32.2 8.2 82 96-179 31-133 (604)
32 COG1875 NYN ribonuclease and A 56.7 15 0.00033 34.8 4.0 98 67-174 5-142 (436)
33 PF02739 5_3_exonuc_N: 5'-3' e 51.2 35 0.00076 27.9 5.0 43 135-179 106-152 (169)
34 PF09713 A_thal_3526: Plant pr 50.5 34 0.00074 23.4 4.0 47 72-119 3-51 (54)
35 PF13344 Hydrolase_6: Haloacid 49.9 41 0.00089 24.9 4.8 36 138-174 18-58 (101)
36 PF11977 RNase_Zc3h12a: Zc3h12 49.1 15 0.00032 29.4 2.5 23 137-160 88-110 (155)
37 PRK04358 hypothetical protein; 49.0 39 0.00086 29.4 5.1 107 44-176 87-198 (217)
38 COG0117 RibD Pyrimidine deamin 44.2 26 0.00056 28.7 3.1 46 128-175 74-126 (146)
39 COG1439 Predicted nucleic acid 43.0 1.2E+02 0.0026 25.6 6.9 99 66-179 8-128 (177)
40 cd00008 53EXOc 5'-3' exonuclea 42.7 79 0.0017 27.2 6.1 31 136-166 106-140 (240)
41 TIGR03875 RNA_lig_partner RNA 42.1 82 0.0018 27.2 6.0 105 44-176 83-194 (206)
42 COG1458 Predicted DNA-binding 41.3 70 0.0015 27.7 5.4 105 44-175 87-197 (221)
43 COG5573 Predicted nucleic-acid 40.2 31 0.00067 28.0 2.9 42 66-109 5-51 (142)
44 PF00462 Glutaredoxin: Glutare 38.7 26 0.00056 22.9 2.0 28 153-180 28-58 (60)
45 TIGR01589 A_thal_3526 uncharac 36.8 87 0.0019 21.7 4.4 48 72-119 6-54 (57)
46 PF10130 PIN_2: PIN domain; I 35.5 30 0.00065 27.4 2.2 91 68-163 1-116 (133)
47 KOG4127 Renal dipeptidase [Pos 33.5 1.5E+02 0.0033 28.1 6.7 116 54-180 194-342 (419)
48 COG1911 RPL30 Ribosomal protei 33.1 43 0.00093 25.8 2.6 45 140-184 25-74 (100)
49 COG0069 GltB Glutamate synthas 31.4 26 0.00056 33.9 1.4 26 141-166 411-438 (485)
50 COG0337 AroB 3-dehydroquinate 30.2 31 0.00068 32.1 1.7 16 60-75 155-170 (360)
51 PF02254 TrkA_N: TrkA-N domain 30.0 1.4E+02 0.0029 21.7 4.9 37 141-178 11-48 (116)
52 COG2082 CobH Precorrin isomera 28.6 2.4E+02 0.0052 24.4 6.7 111 60-180 65-188 (210)
53 KOG1475 Ribosomal protein RPL1 28.5 46 0.001 30.6 2.4 29 151-179 205-233 (363)
54 COG4634 Uncharacterized protei 27.7 1.2E+02 0.0026 23.8 4.3 39 139-179 36-76 (113)
55 PF08712 Nfu_N: Scaffold prote 27.3 1.2E+02 0.0025 22.2 4.1 34 158-191 35-68 (87)
56 PRK09482 flap endonuclease-lik 26.7 96 0.0021 27.4 4.1 42 133-176 102-147 (256)
57 TIGR02181 GRX_bact Glutaredoxi 26.7 99 0.0021 21.0 3.4 29 153-181 28-59 (79)
58 cd03418 GRX_GRXb_1_3_like Glut 26.7 69 0.0015 21.3 2.6 29 153-181 29-61 (75)
59 PF12813 XPG_I_2: XPG domain c 26.3 73 0.0016 27.7 3.2 26 137-163 28-53 (246)
60 PF08745 UPF0278: UPF0278 fami 25.2 66 0.0014 27.8 2.7 46 138-185 155-200 (205)
61 smart00475 53EXOc 5'-3' exonuc 25.2 1.2E+02 0.0026 26.6 4.4 33 135-167 104-140 (259)
62 COG5611 Predicted nucleic-acid 24.3 3.7E+02 0.0081 21.5 8.1 99 67-168 2-126 (130)
63 TIGR00411 redox_disulf_1 small 23.8 1.2E+02 0.0026 20.2 3.4 30 156-187 39-68 (82)
64 COG0695 GrxC Glutaredoxin and 23.1 1.3E+02 0.0027 21.4 3.5 29 152-180 29-62 (80)
65 cd08556 GDPD Glycerophosphodie 22.9 1.9E+02 0.0042 22.4 4.9 45 139-183 77-125 (189)
66 cd08568 GDPD_TmGDE_like Glycer 22.8 4.4E+02 0.0095 21.8 7.3 80 99-180 60-149 (226)
67 PRK13010 purU formyltetrahydro 22.7 2.6E+02 0.0057 24.9 6.2 42 138-180 105-150 (289)
68 cd01543 PBP1_XylR Ligand-bindi 22.5 3E+02 0.0065 22.5 6.2 40 140-180 40-80 (265)
69 cd00128 XPG Xeroderma pigmento 22.1 68 0.0015 28.4 2.3 36 137-177 149-184 (316)
70 PHA00439 exonuclease 21.7 93 0.002 28.1 3.1 32 134-165 116-152 (286)
71 PRK04358 hypothetical protein; 21.3 1E+02 0.0022 26.9 3.1 49 65-113 4-64 (217)
72 cd04888 ACT_PheB-BS C-terminal 20.5 2E+02 0.0042 19.1 3.9 25 153-177 45-74 (76)
73 TIGR02634 xylF D-xylose ABC tr 20.4 4.5E+02 0.0097 22.4 7.0 59 121-180 23-88 (302)
74 PF13407 Peripla_BP_4: Peripla 20.2 2.2E+02 0.0047 23.2 4.8 41 139-180 44-89 (257)
75 PHA02567 rnh RnaseH; Provision 20.0 1.1E+02 0.0024 27.9 3.2 40 135-175 127-170 (304)
No 1
>KOG3165 consensus Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only]
Probab=100.00 E-value=2.3e-81 Score=510.48 Aligned_cols=193 Identities=75% Similarity=1.228 Sum_probs=183.4
Q ss_pred CCccccchhhHHhhhccCccccccccccccCCCCcCCCCCCCCcccCCCchhhhHHhhhCCCCCeEEEeehHHHHHHHHc
Q 029148 1 MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQN 80 (198)
Q Consensus 1 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~fy~~n~~~~~PY~VLvDtNFl~~~i~~ 80 (198)
|||+|||||||.||+||+.+ .|++++++.+.++++.+.+..++++||+||++||+||++|+|||+|||||||||+|+++
T Consensus 1 mgk~kktrk~~~vk~~i~~k-~~~~~~dr~k~k~K~d~~~~~~~e~Pq~~s~lffqyn~~L~PPy~vivDTNFINfsi~~ 79 (195)
T KOG3165|consen 1 MGKAKKTRKFAVVKRMIKTK-QRLKKKDRVKNKEKKDENELLTREVPQVPSALFFQYNTTLGPPYHVIVDTNFINFSIQN 79 (195)
T ss_pred CCcccchHHHHHHHHHHHHH-HHHHHHHhhhcccCCCchhhhcccCcCcchhHHHhcccccCCCeEEEEecchhhHHHHh
Confidence 99999999999999999887 88888887665544444556899999999999999999999999999999999999999
Q ss_pred CCChHHhHHHhhcccceEeecHHHHHHHHHhhhhhHHHHHhccCCCeeeeecCCCCCCHHHHHHHHHhcCCeEEEEecCH
Q 029148 81 KLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDR 160 (198)
Q Consensus 81 kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k~~~Al~iak~~r~e~~~C~H~g~~aDdCIv~~v~~~~~yiVATnD~ 160 (198)
|+|++++||+||+++|+||||+|||+|||+||.+|+.||++|+||+|+|++|.|+|+||||||+++|.+|+||||||||+
T Consensus 80 KiDi~~gmmdcl~Ak~~pcitDCVmaELEkLg~kyrvALri~kDpr~eRL~C~HKGTYADDClv~RV~qHkCYIVAT~D~ 159 (195)
T KOG3165|consen 80 KIDLFEGMMDCLYAKCIPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVATNDR 159 (195)
T ss_pred HHHHHHHHHHHHHhccccchhHHHHHHHHHhcchhhhhhhhhcCCcccccccccCCcchhhHHHHHHhhcceEEEEeccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCccEEEEeCceEEEecCCCcccCC
Q 029148 161 DLKRRIRKVPGVPIMYITRHKYSIERLPEATVGG 194 (198)
Q Consensus 161 ~LrrrLRkipGVPIiyi~~~~~~lE~~s~~~~~~ 194 (198)
+|++|||+||||||||+.++++.||++|+++.||
T Consensus 160 dLK~RIrkIPGVPim~v~~hk~~IEr~pda~~g~ 193 (195)
T KOG3165|consen 160 DLKQRIRKIPGVPIMYVANHKYSIERLPDATLGG 193 (195)
T ss_pred HHHHHHhcCCCCceEEEecceeeeeeCCcccccC
Confidence 9999999999999999999999999999998443
No 2
>KOG3164 consensus Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=100.00 E-value=6e-43 Score=296.38 Aligned_cols=138 Identities=36% Similarity=0.637 Sum_probs=132.1
Q ss_pred hhhHHhhhCCCCCeEEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhhhHHHHHhccCCCeeeee
Q 029148 52 ALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLP 131 (198)
Q Consensus 52 ~~fy~~n~~~~~PY~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k~~~Al~iak~~r~e~~~ 131 (198)
-.||++|||||+|||||||++|+.++++++|++.++|.++|.+.++++||+|||.||+++|..+.+|+.+|+ +|+++.
T Consensus 13 l~ff~~~fgfRePYQVLvD~tF~~a~~~~~i~l~~~i~r~l~~~vKL~tTqCvikele~~g~~l~ga~~iAK--~fe~~~ 90 (236)
T KOG3164|consen 13 LKFFSVNFGFREPYQVLVDGTFCQAALQQKIGLDEQIKRYLQGEVKLMTTQCVIKELEELGKDLYGAKGIAK--QFEIRN 90 (236)
T ss_pred eeeeeeccCccCceEEEehhHHHHHHHHhhhChHHHHHHHhcCCCeeeehHHHHHHHHHhCcchhhhHHHHH--HHhHhc
Confidence 469999999999999999999999999999999999999999999999999999999999999999999999 799999
Q ss_pred cCCCCC-CHHHHHHHHHhc--CCeEEEEecCHHHHHHHhcCCCccEEEEeCceEEEecCCCcc
Q 029148 132 CTHKGT-YADDCLVERVTQ--HKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLPEAT 191 (198)
Q Consensus 132 C~H~g~-~aDdCIv~~v~~--~~~yiVATnD~~LrrrLRkipGVPIiyi~~~~~~lE~~s~~~ 191 (198)
|+|+.. +|++||.++++. .++|||||||.+|++.||++||||+||+.++.++||.||+++
T Consensus 91 C~H~~~~s~seCl~svv~~~Nk~~YvvATQD~el~~kLr~~pgvPli~~~r~t~vld~~S~at 153 (236)
T KOG3164|consen 91 CNHKDARSPSECLRSVVRISNKHHYVVATQDQELRRKLRKEPGVPLIYLKRNTLVLDAPSQAT 153 (236)
T ss_pred CCCCCCCCHHHHHHHHHhccCCceEEEecCCHHHHHHHhcCCCCceEEEecceEEecCcchhh
Confidence 999643 899999999974 467999999999999999999999999999999999999998
No 3
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=100.00 E-value=2.9e-41 Score=269.47 Aligned_cols=133 Identities=46% Similarity=0.744 Sum_probs=123.5
Q ss_pred HHhhhCCCCCeEEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhhhHHHHH--hccCCCeeeeec
Q 029148 55 FTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR--IAKDPRFERLPC 132 (198)
Q Consensus 55 y~~n~~~~~PY~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k~~~Al~--iak~~r~e~~~C 132 (198)
|++|++|++||+||+|||||+++.++++|++++|+++++++++|+||+||++||++|+..++.+++ +|.. .+++++|
T Consensus 1 ~~~~~~~~~~~~VlvDTNfl~~~~q~~vdi~~~l~r~l~~~~~~~Ip~~Vi~EL~~l~~~~~~~~r~~ia~~-~~er~~~ 79 (136)
T COG1412 1 FQDNFGFRKPYQVLVDTNFLLYPYQFKVDIFEELERLLGAKYKPAIPSCVIRELEKLKRKHRGKARIAIALK-YAERLEC 79 (136)
T ss_pred CccccccCCceEEEecchHHHHHHHccCCHHHHHHHHhcccccccchHHHHHHHHHHHHhcCchHHHHHHHH-HhhccCc
Confidence 678999999999999999999999999999999999999999999999999999999998777666 4442 5888999
Q ss_pred CCCCCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeC-ceEEEecCCC
Q 029148 133 THKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITR-HKYSIERLPE 189 (198)
Q Consensus 133 ~H~g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~-~~~~lE~~s~ 189 (198)
.|.+++|||||.++|.+++||+|||||++|++|||+. |||+||+++ +.+.+|++++
T Consensus 80 ~~~~~~aDe~i~~~a~~~~~~iVaTnD~eLk~rlr~~-GIPvi~lr~r~~~~ie~~~~ 136 (136)
T COG1412 80 IHKGRYADECLLEAALKHGRYIVATNDKELKRRLREN-GIPVITLRQRKLLIIERLSD 136 (136)
T ss_pred cccCCChHHHHHHHHHHcCCEEEEeCCHHHHHHHHHc-CCCEEEEeCCeEEEeeCCCC
Confidence 9999999999999999999999999999999999996 999999995 5899998874
No 4
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=99.97 E-value=1.2e-31 Score=202.47 Aligned_cols=99 Identities=45% Similarity=0.813 Sum_probs=92.5
Q ss_pred HHhhcccceEeecHHHHHHHHHhhhhhHHHHHhccCCCeeeeecCCCCC--CHHHHHHHHHhcCCeEEEEecCHHHHHHH
Q 029148 89 MDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGT--YADDCLVERVTQHKCFIVATCDRDLKRRI 166 (198)
Q Consensus 89 ~~~L~~k~~~~iT~CVi~ELekLg~k~~~Al~iak~~r~e~~~C~H~g~--~aDdCIv~~v~~~~~yiVATnD~~LrrrL 166 (198)
+++|+++++|+||+||++||++||+.++.+..+|+...+++++|+|.+. +|||||++++++++.|||||||++||++|
T Consensus 1 ~~~L~~~~~~~vt~cVl~EL~~L~~~~~~~~~~a~~~~~~~~~c~h~~~~~~addci~~~~~~~~~~~VaT~D~~Lr~~l 80 (101)
T PF04900_consen 1 KKLLGGKVKPYVTQCVLEELESLGKKFKGALRIAKRKALERRKCNHKETPGSADDCILDLAGKNNKYIVATQDKELRRRL 80 (101)
T ss_pred CccccCccEEEecHHHHHHHHHhcccccchhhhhhchhhHhhcCCCCCCCcCHHHHHHHHhccCCeEEEEecCHHHHHHH
Confidence 3689999999999999999999999999999999954499999999965 99999999999887799999999999999
Q ss_pred hcCCCccEEEEeCceEEEecC
Q 029148 167 RKVPGVPIMYITRHKYSIERL 187 (198)
Q Consensus 167 RkipGVPIiyi~~~~~~lE~~ 187 (198)
|++|||||||+++++++||+|
T Consensus 81 r~~~GvPvi~l~~~~~~le~p 101 (101)
T PF04900_consen 81 RKIPGVPVIYLRRNVLILEPP 101 (101)
T ss_pred hcCCCCCEEEEECCEEEecCC
Confidence 988999999999999999987
No 5
>smart00670 PINc Large family of predicted nucleotide-binding domains. From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.
Probab=98.48 E-value=5e-07 Score=66.89 Aligned_cols=93 Identities=24% Similarity=0.255 Sum_probs=59.5
Q ss_pred EEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhh--hhHHHHHhcc----------CCC-eeeeecC
Q 029148 67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ--KYRVALRIAK----------DPR-FERLPCT 133 (198)
Q Consensus 67 VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~--k~~~Al~iak----------~~r-~e~~~C~ 133 (198)
+++|||+++..+.. ++.+. +...+..++||.+|++||..+.. .++.--.++. +.. +....+.
T Consensus 1 ~vlDTnvli~~~~~--~~~~~---~~~~~~~~~i~~~v~~El~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~ 75 (111)
T smart00670 1 VVLDTNVLIDGLIG--KALEK---LLEKKGEVYIPPTVLEELEYLAKLRSLKKLEELALEGKIKLKVLKEERKLEEEILE 75 (111)
T ss_pred CEeeHHHHHHHHHH--HHHHH---HHcCCCcEEECHHHHHHHHHHHHHHHHhhHHHHHHhcccccceeecCCCeEEEecc
Confidence 58999999998766 33333 33447889999999999999772 1111111111 000 1112233
Q ss_pred CCCC-----CHHHHHHHHHhcCCeEEEEecCHHHHH
Q 029148 134 HKGT-----YADDCLVERVTQHKCFIVATCDRDLKR 164 (198)
Q Consensus 134 H~g~-----~aDdCIv~~v~~~~~yiVATnD~~Lrr 164 (198)
+.+. ..|.+|+..+...++.+++|+|.+|++
T Consensus 76 ~~~~~~~~~~~D~~il~~a~~~~~~~lvT~D~~l~~ 111 (111)
T smart00670 76 RLSLKLELLPNDALILATAKELGNVVLVTNDRDLRR 111 (111)
T ss_pred cCChhhcCCCChHHHHHHHHHCCCCEEEeCCcccCC
Confidence 3222 368899999988756899999998863
No 6
>PF13638 PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_B 2WP8_J.
Probab=98.21 E-value=1.9e-05 Score=60.86 Aligned_cols=101 Identities=19% Similarity=0.262 Sum_probs=60.2
Q ss_pred EEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhh-----------hHHHHHhccC---CCeeeeec
Q 029148 67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK-----------YRVALRIAKD---PRFERLPC 132 (198)
Q Consensus 67 VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k-----------~~~Al~iak~---~r~e~~~C 132 (198)
+++|||+++... +.+.++ ....++||.+|+.||..+... .+.|.++... ..-..+..
T Consensus 1 ~V~DTnvll~~~-------~~l~~~--~~~~ivIP~~Vl~ELd~lk~~~~~~~~~~~~~ar~~~~~l~~~~~~~~~~i~~ 71 (133)
T PF13638_consen 1 YVLDTNVLLHHP-------DLLEKL--EQNKIVIPLTVLEELDRLKKSSRDRDRELRKRAREAIRWLEKLLKRGSRSIRV 71 (133)
T ss_dssp EEE-HHHHHHHH-------HHHHHH--SSSEEEEEHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHCT-TTEEE
T ss_pred CEeehhHHhCCh-------HHHhcc--ccCEEEechHHHHHHHHHhccccchhHHHHHHHHHHHHHHHHHHhcCCCeEec
Confidence 589999999763 223332 788899999999999887432 2334333321 00001111
Q ss_pred CCC-----------CCCHHHHHHHHHhc------CCeEEEEecCHHHHHHHhcCCCccEEEE
Q 029148 133 THK-----------GTYADDCLVERVTQ------HKCFIVATCDRDLKRRIRKVPGVPIMYI 177 (198)
Q Consensus 133 ~H~-----------g~~aDdCIv~~v~~------~~~yiVATnD~~LrrrLRkipGVPIiyi 177 (198)
... ....|+.|++.+.. ....++.|+|..|+-+++. -|||...+
T Consensus 72 q~~~~~~~~~~~~~~~~~D~~Il~~a~~~~~~~~~~~vvLvT~D~~l~~~A~~-~gi~~~~~ 132 (133)
T PF13638_consen 72 QTSDEEIDEDLNLDAQRNDDRILNCALYLQEENPGRKVVLVTNDKNLRLKARA-EGIPAVSY 132 (133)
T ss_dssp CTTTS-EES--S----HHHHHHHHHHHHHHHHCGCEEEEEEE--HHHHHHHHH-TT--EE--
T ss_pred chhhhhcchhhhccccccHHHHHHHHHHHHHhcCCCeEEEEeCCHHHHHHHhh-cccccccC
Confidence 111 12578888888742 3457999999999999999 79998865
No 7
>PRK13764 ATPase; Provisional
Probab=97.82 E-value=3.5e-05 Score=74.92 Aligned_cols=115 Identities=21% Similarity=0.218 Sum_probs=75.4
Q ss_pred EEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhh----hHHHHHhccC-------CCeeeeecCC
Q 029148 66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK----YRVALRIAKD-------PRFERLPCTH 134 (198)
Q Consensus 66 ~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k----~~~Al~iak~-------~r~e~~~C~H 134 (198)
.+++|||.|+.-- +.+.+..-+.-...++||.-|++||+.+... -+.|++.++. -.++..-.++
T Consensus 2 ~yVlDTSVIIDGr-----i~~~i~~g~~~~~~IiIP~~Vl~ELe~~A~~~r~~G~~gLeeL~~L~~l~~~g~i~ie~~~~ 76 (602)
T PRK13764 2 KIVPDTSVVIDGR-----VSELIEKGEYIGGTIIIPEAVVAELEAQANQGREIGFSGLEELKKLRELAEEGLIELEFVGE 76 (602)
T ss_pred eEEccceEEEech-----HHHHHHcCCccCCEEEeehHHHHHHHHHhhccchhhHHHHHHHHHHHHhhccCceEEEEecc
Confidence 4677777776531 2222222221245799999999999998653 2334444431 0121111111
Q ss_pred C----------CCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeCc-e-EEEecC
Q 029148 135 K----------GTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRH-K-YSIERL 187 (198)
Q Consensus 135 ~----------g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~~-~-~~lE~~ 187 (198)
. +...|+-|++++.+++ .++.|||..|+..++. -|||++|++.. . +.||..
T Consensus 77 ~p~~~~~~~~~~gevD~~I~~~A~~~~-~~lvT~D~~l~~~A~~-~GI~V~~l~~~~~~L~ie~~ 139 (602)
T PRK13764 77 RPTLEQIKLAKGGEIDALIREVAKELG-ATLVTSDRVQAEVARA-KGIDVIYLKPEREPLEIEKF 139 (602)
T ss_pred ccchhhcccccCCCHHHHHHHHHHHcC-CEEEeCCHHHHHHHHH-cCCEEEEeCCCCCccchHHH
Confidence 1 1468999999999887 5999999999999998 69999999985 3 567764
No 8
>TIGR00305 probable toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.
Probab=97.25 E-value=0.0046 Score=46.86 Aligned_cols=96 Identities=18% Similarity=0.119 Sum_probs=61.0
Q ss_pred EEEeehHHHHHHHHcCCChHHhHHH-hhcccceEeecHHHHHHH-HHhh-hhh---------HHHHHhccCCCeeeeecC
Q 029148 66 RVLVDTNFINFSIQNKLDLEKGMMD-CLYAKCTPCITDCVMAEL-EKLG-QKY---------RVALRIAKDPRFERLPCT 133 (198)
Q Consensus 66 ~VLvDtNFl~~~i~~kldl~~~L~~-~L~~k~~~~iT~CVi~EL-ekLg-~k~---------~~Al~iak~~r~e~~~C~ 133 (198)
+|++|||.++.++-.+-. ...+.+ +..+.+.++++..++.|+ +.|. +++ +..+..... .++...-.
T Consensus 1 rvvlDTNVli~all~~~~-~~~l~~~~~~~~~~~~~s~~~l~E~~~~l~~~~~~~~~~~~~~~~~l~~l~~-~~~~~~~~ 78 (114)
T TIGR00305 1 KVVIDTNVWISALIWKGL-PGKLIKLIIDNKIVNCTSVEILQEVEFVLLYPKLQKYFALETILEILLLLGE-KSTIINPN 78 (114)
T ss_pred CEEEEhHHHHHHHhCCCC-HHHHHHHHHhCCEEEEECHHHHHHHHHHHhhHhhhhhcCHHHHHHHHHHHHH-hcEEecCC
Confidence 489999999998877654 334443 356889999999999999 4443 111 111211111 22222211
Q ss_pred C----CCCCHHHHHHHHHhcCCeEEEEecCHHHH
Q 029148 134 H----KGTYADDCLVERVTQHKCFIVATCDRDLK 163 (198)
Q Consensus 134 H----~g~~aDdCIv~~v~~~~~yiVATnD~~Lr 163 (198)
. -..+.|+.+++.+...++=++.|.|++|-
T Consensus 79 ~~~~~~~D~~D~~~l~~A~~~~ad~iVT~Dkdll 112 (114)
T TIGR00305 79 PEFDDCRDKKDNKFLNTAYASKANALITGDTDLL 112 (114)
T ss_pred CCCCCCCCchhHHHHHHHHhcCCCEEEECCHHHh
Confidence 1 12356888889888777668889999874
No 9
>PF01850 PIN: PIN domain; InterPro: IPR002716 The PilT protein, N-terminal domain (PIN) is a compact domain of about 100 amino acids. The domain has two nearly invariant aspartates and forms a coiled-coil with other monomer units to polymerise a pilus fibre []. The function of the PIN domain is unknown but a role in signalling appears likely given the presence of this domain in some bacterial plasmid stability proteins and Dis3 from yeast that is implicated in mitotic control [].; PDB: 3TND_G 2H1O_B 2BSQ_B 2H1C_A 2FE1_A 3ZVK_C 1V8P_F 1V8O_C 3H87_A 1O4W_A ....
Probab=96.91 E-value=0.0068 Score=44.59 Aligned_cols=99 Identities=22% Similarity=0.273 Sum_probs=61.7
Q ss_pred EEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhh-----h---HHHHHhccCCCeeeeecCCC---
Q 029148 67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK-----Y---RVALRIAKDPRFERLPCTHK--- 135 (198)
Q Consensus 67 VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k-----~---~~Al~iak~~r~e~~~C~H~--- 135 (198)
|+||||++...+ ..=.-.+...+++.....++++.-++.|+-..-.+ . ....... .+.++.++.+..
T Consensus 1 i~lDTsili~~~-~~~~~~~~~~~~~~~~~~~~is~~~~~E~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~~~~~~~~ 78 (121)
T PF01850_consen 1 ILLDTSILIALL-RDEENHEKARELLERAIEIVISSLVLAELLYVLRRRSKQQKAIALLELLIL-LSNFNILPITSEVFE 78 (121)
T ss_dssp EEE-HHHHHHHH-SHSCHHHHHHHHHHTHSEEEEEHHHHHHHHHHHHHSHCHHHHHHHHHHHHH-HCTSEEEEBCHHHHH
T ss_pred EEEcChhhcccc-CCChhHHHHHHHHhcCCCEEEcHHHHHHHHHHhhhccccchhhhHHHHHHH-HhhhccccchhHHHH
Confidence 799999999988 33344456666666558899999999999776433 1 1111111 235666664321
Q ss_pred ---------CCCHHHHH-HHHHhcCCeEEEEecCHHHHHHHh
Q 029148 136 ---------GTYADDCL-VERVTQHKCFIVATCDRDLKRRIR 167 (198)
Q Consensus 136 ---------g~~aDdCI-v~~v~~~~~yiVATnD~~LrrrLR 167 (198)
+....||+ +..+..+++-+|.|+|+++++-.+
T Consensus 79 ~~~~~~~~~~~~~~Da~~~a~A~~~~~~~v~T~D~~f~~~a~ 120 (121)
T PF01850_consen 79 RAAELMRKYGLDFADALIAATAKENGAPLVVTFDKDFRKVAK 120 (121)
T ss_dssp HHHHHHHHHHSSHHHHHHHHHHHHHT-EEE-ESSHHHHHHHC
T ss_pred HHHHHHHhccCChhHHHHHHHHHHcCCEEEEECCcCHHhccC
Confidence 12445554 466777787788899999887543
No 10
>TIGR00028 Mtu_PIN_fam Mycobacterium tuberculosis PIN domain family. Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see Pfam pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis. Two more are now found in Synechococcus sp. WH8102. The specific function is unknown but may be in signal transduction.
Probab=96.81 E-value=0.0035 Score=47.89 Aligned_cols=104 Identities=17% Similarity=0.162 Sum_probs=56.2
Q ss_pred EEeehHHHHHHHHcCCChHHhHHHhhc---ccceEeecHHHHHHHHHh-hhh-----------hHHHHHhc-cCCCeeee
Q 029148 67 VLVDTNFINFSIQNKLDLEKGMMDCLY---AKCTPCITDCVMAELEKL-GQK-----------YRVALRIA-KDPRFERL 130 (198)
Q Consensus 67 VLvDtNFl~~~i~~kldl~~~L~~~L~---~k~~~~iT~CVi~ELekL-g~k-----------~~~Al~ia-k~~r~e~~ 130 (198)
+++|||++++.+...=...+...+.+. ....++++.-|+.|+... ... ....++-. ..+.+...
T Consensus 2 i~lDTnvli~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vl~E~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 81 (142)
T TIGR00028 2 LLLDVNVLLAAVNRDHPHHDAARAWLDRFAAGGDWATCPLTLAGFVRLLTNPRVLPAPLSPAEAIAVVAAFLATPRHRLL 81 (142)
T ss_pred ccchhhHHHHhcCCCCcchHHHHHHHHHHhcCCCceechhhhhhheeeeccCCcCCCCCCHHHHHHHHHHHHhCCCeeec
Confidence 689999999988654322223333332 344567788999998552 211 11112111 11112111
Q ss_pred ec--------------CC-CCC-CHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEE
Q 029148 131 PC--------------TH-KGT-YADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIM 175 (198)
Q Consensus 131 ~C--------------~H-~g~-~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIi 175 (198)
.- .. .+. ++|..|+..+..+++ .+.|.|+++ .+.+|+.++
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~D~~i~a~A~~~~~-~lvT~D~~f----~~~~~~~i~ 137 (142)
T TIGR00028 82 WPGPRHLAVLRGLADPVIAGGRLVTDAHLAALAREHGA-ELVTFDRGF----ARFAGIRWR 137 (142)
T ss_pred CCCcchHHHHHHHHHHhccCCCCchHHHHHHHHHHcCC-EEEecCCCc----cccCCCeee
Confidence 11 00 112 455556678888876 555999864 456777765
No 11
>PRK00124 hypothetical protein; Validated
Probab=95.72 E-value=0.0094 Score=48.79 Aligned_cols=81 Identities=15% Similarity=0.160 Sum_probs=58.2
Q ss_pred HHHHHHHhhhhhHHHHHhcc-------CC---CeeeeecCCCCCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCcc
Q 029148 104 VMAELEKLGQKYRVALRIAK-------DP---RFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVP 173 (198)
Q Consensus 104 Vi~ELekLg~k~~~Al~iak-------~~---r~e~~~C~H~g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVP 173 (198)
|.+|+.+++.++..-+-+.- .| ..+.+-.+.....||+-|++.+.+.. +|.|||-.|-.++-. .|.-
T Consensus 12 Vk~~i~r~a~r~~i~v~~Vas~n~~~~~~~~~~v~~v~V~~g~D~AD~~Iv~~~~~gD--iVIT~Di~LAa~~l~-Kga~ 88 (151)
T PRK00124 12 VKDIIIRVAERHGIPVTLVASFNHFLRVPYSPFIRTVYVDAGFDAADNEIVQLAEKGD--IVITQDYGLAALALE-KGAI 88 (151)
T ss_pred HHHHHHHHHHHHCCeEEEEEeCCcccCCCCCCceEEEEeCCCCChHHHHHHHhCCCCC--EEEeCCHHHHHHHHH-CCCE
Confidence 88899988877643322211 11 12223333333479999999998886 999999999999999 7999
Q ss_pred EEEEeCceEEEecC
Q 029148 174 IMYITRHKYSIERL 187 (198)
Q Consensus 174 Iiyi~~~~~~lE~~ 187 (198)
+|.-++..|.=|.+
T Consensus 89 vl~prG~~yt~~nI 102 (151)
T PRK00124 89 VLNPRGYIYTNDNI 102 (151)
T ss_pred EECCCCcCCCHHHH
Confidence 99999888766554
No 12
>PF13470 PIN_3: PIN domain
Probab=95.70 E-value=0.11 Score=38.93 Aligned_cols=46 Identities=22% Similarity=0.363 Sum_probs=36.0
Q ss_pred EEEeehHHHHHHHHcCCChHHhHHHhh-cccceEeecHHHHHHHHHh
Q 029148 66 RVLVDTNFINFSIQNKLDLEKGMMDCL-YAKCTPCITDCVMAELEKL 111 (198)
Q Consensus 66 ~VLvDtNFl~~~i~~kldl~~~L~~~L-~~k~~~~iT~CVi~ELekL 111 (198)
+|++|||.++.++-..=.....+.+.+ .+.+.++++.-++.|++..
T Consensus 1 RVvlDTNVli~~ll~~~~~~~~l~~~~~~~~~~~~~s~~~l~E~~~v 47 (119)
T PF13470_consen 1 RVVLDTNVLISALLSREPAARKLLDLAEDGRIELYISPEILDELERV 47 (119)
T ss_pred CEEEEechhHHHHhCCCchHHHHHHHHHcCCCeEEecHHHHHHHHHH
Confidence 589999999998875543444454444 6889999999999999864
No 13
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=94.90 E-value=0.026 Score=44.96 Aligned_cols=61 Identities=21% Similarity=0.211 Sum_probs=51.7
Q ss_pred CCeeeeecCCCCCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeCceEEEecCC
Q 029148 125 PRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLP 188 (198)
Q Consensus 125 ~r~e~~~C~H~g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~~~~~lE~~s 188 (198)
+..+.+-|+.....||.-|++.+.+.. +|.|||-.|-.++-. .|+.+|.-++..|.-|.+.
T Consensus 27 ~~~~~i~Vd~g~DaaD~~I~~~~~~gD--iVITqDigLA~~~l~-Kga~vl~~rG~~yt~~nI~ 87 (130)
T PF02639_consen 27 PYVEMIVVDSGFDAADFYIVNHAKPGD--IVITQDIGLASLLLA-KGAYVLNPRGKEYTKENID 87 (130)
T ss_pred CCeEEEEECCCCChHHHHHHHcCCCCC--EEEECCHHHHHHHHH-CCCEEECCCCCCCCHHHHH
Confidence 456666677666689999999999887 999999999999998 7999999999888777653
No 14
>COG1848 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=94.37 E-value=0.31 Score=37.83 Aligned_cols=100 Identities=20% Similarity=0.283 Sum_probs=58.9
Q ss_pred EEEeehHHHHHHHHcCC----ChHHhHHHhhcccceEeecHHHHHHHHHhhhh----h--HHHHHhc----cCCCe----
Q 029148 66 RVLVDTNFINFSIQNKL----DLEKGMMDCLYAKCTPCITDCVMAELEKLGQK----Y--RVALRIA----KDPRF---- 127 (198)
Q Consensus 66 ~VLvDtNFl~~~i~~kl----dl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k----~--~~Al~ia----k~~r~---- 127 (198)
.+++|||++.+.+-..- ...+.+.....+....+++.-|+.|+-.+-.+ + ..+.... ..+.+
T Consensus 1 ~i~~Dtnvlv~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~v~~e~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (140)
T COG1848 1 MIVIDTNVLVYALFRDHPHHDRARELLERLEAGDIRVYTPELVLAELLRVLTRRRRPLSLAEAIEVVAALLALPRFELLL 80 (140)
T ss_pred CeeeehHHHHHHHHccChhHHHHHHHHHHHhcCCCceeecHHHHHHHHHHHhhcccCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 37899999999887763 23455555666677899999999999665332 1 1111111 00011
Q ss_pred eeee--cC----------CCCCCHHHHHH-HHHhcCCeEEEEecCHHHHHH
Q 029148 128 ERLP--CT----------HKGTYADDCLV-ERVTQHKCFIVATCDRDLKRR 165 (198)
Q Consensus 128 e~~~--C~----------H~g~~aDdCIv-~~v~~~~~yiVATnD~~Lrrr 165 (198)
+.++ .. +.+-.+.|||. ..+..++.--++|.|+++++-
T Consensus 81 ~~~~~~~~~~~~a~~~~~~~~l~~~DAl~lA~a~~~gi~~i~T~D~df~~~ 131 (140)
T COG1848 81 DILEVTAEAYRLAAALALKYGLLPNDALLLATAKRYGIKAIATFDEDFARV 131 (140)
T ss_pred hcccchHHHHHHHHHHHHHcCCCCcHHHHHHHHHHcCcceeeecchhhhhc
Confidence 1110 00 11123566655 566666667899999977763
No 15
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=93.77 E-value=0.56 Score=38.13 Aligned_cols=95 Identities=25% Similarity=0.288 Sum_probs=63.8
Q ss_pred EEEeehHHHHHHHHcCCChHHhHHHhhc-ccceEeecHHHHHHHHH-hhh-hhH------------HHHH-----hccCC
Q 029148 66 RVLVDTNFINFSIQNKLDLEKGMMDCLY-AKCTPCITDCVMAELEK-LGQ-KYR------------VALR-----IAKDP 125 (198)
Q Consensus 66 ~VLvDtNFl~~~i~~kldl~~~L~~~L~-~k~~~~iT~CVi~ELek-Lg~-k~~------------~Al~-----iak~~ 125 (198)
+|++|||-++.++=.+=.+...+.+++. .+...|++.-.++||+. ++. +++ .++. ++-.|
T Consensus 2 kVViDTNV~isaLi~p~Gl~~~l~~ll~~~~i~n~tS~eil~El~~v~~~pKl~k~l~~e~~~~~v~~l~~~~~~i~I~p 81 (142)
T COG1569 2 KVVIDTNVWISALISPGGLPGELISLLIKEKIENYTSEEILDELEEVLSYPKLKKYLPLEVLGELVLVLFESVSLIAINP 81 (142)
T ss_pred eEEEEhhHHHHHHhCCCCCcHHHHHHHhhCceEEEecHHHHHHHHHHHhhHHHHhhcchHHHHHHHHHHHHhheeEeecc
Confidence 7999999999998887766667776665 56889999999999943 331 211 0111 11112
Q ss_pred CeeeeecCCCCCCHHHHHHHHHhcCCeEEEEecCHHHH
Q 029148 126 RFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLK 163 (198)
Q Consensus 126 r~e~~~C~H~g~~aDdCIv~~v~~~~~yiVATnD~~Lr 163 (198)
.++...|. .+-|.-++++|-..+..++.|-|.+|-
T Consensus 82 ~~~f~~~R---Dp~Dn~~L~~A~~~kA~~lvTgD~dLL 116 (142)
T COG1569 82 LEKFNICR---DPKDNKLLALAYESKADYLVTGDQDLL 116 (142)
T ss_pred cccccccC---CchHHHHHHHHHhccCCEEEEcchhhh
Confidence 22222342 245778899998877779999999774
No 16
>COG2402 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=92.88 E-value=0.44 Score=38.26 Aligned_cols=95 Identities=18% Similarity=0.156 Sum_probs=55.0
Q ss_pred EEeehHHHHHHHHcCCChHHhHHHhhcccc-----eEeecHHHHHHHHHhhhh-hHHHH----HhccCCCeeeeecCC--
Q 029148 67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKC-----TPCITDCVMAELEKLGQK-YRVAL----RIAKDPRFERLPCTH-- 134 (198)
Q Consensus 67 VLvDtNFl~~~i~~kldl~~~L~~~L~~k~-----~~~iT~CVi~ELekLg~k-~~~Al----~iak~~r~e~~~C~H-- 134 (198)
|||||||+.+....+=.--+.-..++.+.. .+++++|++.|.--|.++ +..|. ..+....+.+..|.-
T Consensus 2 v~vDT~~~~a~~~~~d~~H~~a~~~~~~~~~~~~~~~~~~~~v~~e~~~l~k~r~~~aa~~l~~~i~~~~~~~~~~~t~~ 81 (135)
T COG2402 2 VLVDTSVLLALFDKRDKNHEAAVQLFVSLADNKFRRLVVSDHVLDETLTLLKKRVVDAAAFLLEALEEGALEIFESVTEE 81 (135)
T ss_pred EEEechHHHHHHhchhhhHHHHHHHHhhcccCccceEEEeeeeHHHHHHHHHHhhhhHHHHHHHHhccCceEEEecccHH
Confidence 899999998876655443333333444433 789999999999988652 22221 122223455555542
Q ss_pred --------------CCCC-HHHHHHHHHhcCCeEEEEecCHH
Q 029148 135 --------------KGTY-ADDCLVERVTQHKCFIVATCDRD 161 (198)
Q Consensus 135 --------------~g~~-aDdCIv~~v~~~~~yiVATnD~~ 161 (198)
.+-+ +|-|.+-++.+.++-=+-|.|.+
T Consensus 82 ~~~~a~~~~k~~d~~~~df~Da~~~ala~k~g~~~ilSfD~d 123 (135)
T COG2402 82 LEEAAEAVFKRQDDLGLDFVDATSVALAEKLGILKILSFDSD 123 (135)
T ss_pred HHHHHHHHHHhhcccCCCHHHHHHHHHHHHcCCCcEEEeccc
Confidence 2223 44444455566665556677664
No 17
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=90.70 E-value=0.38 Score=43.95 Aligned_cols=81 Identities=22% Similarity=0.241 Sum_probs=55.7
Q ss_pred eEeecHHHHHHHHHhhhh--------hHHHHHhccC------CCeeeeecCCCC-CCHHHHHHHHHhcCCeEEEEecCHH
Q 029148 97 TPCITDCVMAELEKLGQK--------YRVALRIAKD------PRFERLPCTHKG-TYADDCLVERVTQHKCFIVATCDRD 161 (198)
Q Consensus 97 ~~~iT~CVi~ELekLg~k--------~~~Al~iak~------~r~e~~~C~H~g-~~aDdCIv~~v~~~~~yiVATnD~~ 161 (198)
.++||+-|++||..++.. -|..|.+.-. ++.+...-+-.. ...|.-|+.+++..+ -.|.|||-+
T Consensus 187 ~iiiP~FVL~ELQ~iADssD~lKR~RGRRGLdILn~iqk~~~~~v~I~~~Df~di~eVD~KLvklAk~~~-g~lvTND~N 265 (356)
T COG4956 187 TIIIPQFVLLELQHIADSSDDLKRNRGRRGLDILNEIQKEDPIQVEIYEGDFEDIPEVDSKLVKLAKVTG-GKLVTNDFN 265 (356)
T ss_pred eEeeeHHHHHHHHHHhhccchhhhhcccchhHHHHHHHhhCCCcEEEccCCccchhhHHHHHHHHHHHhC-CEEEeccCc
Confidence 589999999999999642 2445555421 123333322111 147889999999876 599999999
Q ss_pred HHHHHhcCCCccEEEEeC
Q 029148 162 LKRRIRKVPGVPIMYITR 179 (198)
Q Consensus 162 LrrrLRkipGVPIiyi~~ 179 (198)
|-+=.. +-|||++.++.
T Consensus 266 LnKVae-~qgV~vLNIND 282 (356)
T COG4956 266 LNKVAE-LQGVQVLNIND 282 (356)
T ss_pred HHHHHh-hcCCceecHHH
Confidence 976554 47999998764
No 18
>PRK12496 hypothetical protein; Provisional
Probab=89.84 E-value=2.1 Score=35.23 Aligned_cols=97 Identities=13% Similarity=0.086 Sum_probs=62.1
Q ss_pred EEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhhhHHHHHhccC-CCeeeeecCC----------
Q 029148 66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKD-PRFERLPCTH---------- 134 (198)
Q Consensus 66 ~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k~~~Al~iak~-~r~e~~~C~H---------- 134 (198)
.+++||+.+++-.. .+++ .++||.-|++|+..-... ..+..+.. ..++...=+.
T Consensus 3 ~~VlDtS~~I~~~~-----------~~~~--~i~tp~~V~~Ev~d~~~~--~~~~~l~~~~~i~v~~p~~~~i~~v~~~a 67 (164)
T PRK12496 3 IKVLDASAFIHGYN-----------PEDG--EHYTTPSVVEEVKDKESR--LILESAISAGKLKILEPSPESIEKVEEAA 67 (164)
T ss_pred EEEEEChHHHccch-----------hhCC--CEEecHHHHHHHhCHHHH--HHHHHhcccCCeEEECCCHHHHHHHHHHH
Confidence 47999999986422 1233 479999999999873322 22222221 0122221110
Q ss_pred --CC-----CCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeC
Q 029148 135 --KG-----TYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITR 179 (198)
Q Consensus 135 --~g-----~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~ 179 (198)
.| ..+|.-++.++.+.+ ..+.|.|..+++-++. -|++++.+++
T Consensus 68 ~~tgd~~~Ls~~D~~~iaLA~el~-~~lvtDD~~~~~vA~~-lgi~v~~~~~ 117 (164)
T PRK12496 68 IKTGDLMRLSNTDIEVLALALELN-GTLYTDDYGIQNVAKK-LNIKFENIKT 117 (164)
T ss_pred HhcCCccccchhhHHHHHHHHHhC-CcEECcHHHHHHHHHH-cCCeEecccc
Confidence 01 135666777777766 4899999999999998 6999999883
No 19
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=88.71 E-value=1.2 Score=36.52 Aligned_cols=42 Identities=29% Similarity=0.423 Sum_probs=33.7
Q ss_pred CCCCCHHHHHHHHHhc----CCeEEEEecCHHHHHHHhcCCCccEEE
Q 029148 134 HKGTYADDCLVERVTQ----HKCFIVATCDRDLKRRIRKVPGVPIMY 176 (198)
Q Consensus 134 H~g~~aDdCIv~~v~~----~~~yiVATnD~~LrrrLRkipGVPIiy 176 (198)
..|..||+.|.+++.. +...+|+|.|..+++.++. -|.-.|.
T Consensus 74 ~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~-~GA~~is 119 (166)
T PF05991_consen 74 KEGETADDYIERLVRELKNRPRQVTVVTSDREIQRAARG-RGAKRIS 119 (166)
T ss_pred CCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhh-CCCEEEc
Confidence 3456899999999964 3467999999999999988 5765554
No 20
>PRK13725 plasmid maintenance protein; Provisional
Probab=88.61 E-value=3.9 Score=31.90 Aligned_cols=42 Identities=29% Similarity=0.445 Sum_probs=29.1
Q ss_pred EEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHH
Q 029148 67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEK 110 (198)
Q Consensus 67 VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELek 110 (198)
.|+|||.+.+.++.+-.......+ . ..-.++|+.-++.||..
T Consensus 4 yLLDTni~i~~~~~~~~~v~~~~~-~-~~~~~~iS~It~~EL~~ 45 (132)
T PRK13725 4 FMLDTNICIFTIKNKPEHVRERFN-L-NTGRMCISSVTLMELIY 45 (132)
T ss_pred hhhhHHHHHHHHhCCcHHHHHHHh-C-CCcceeehHHHHHHHHH
Confidence 589999999998866433222222 1 23458899999999975
No 21
>COG1487 VapC Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=86.58 E-value=4.2 Score=31.30 Aligned_cols=43 Identities=19% Similarity=0.073 Sum_probs=29.1
Q ss_pred eEEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHH
Q 029148 65 YRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEK 110 (198)
Q Consensus 65 Y~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELek 110 (198)
...++|||.+.......-.-. +...+.. ...+++.-++.||..
T Consensus 2 ~~~llDTnv~i~l~~~~~~~~--~~~~~~~-~~~~~s~it~~El~~ 44 (133)
T COG1487 2 MMYLLDTSVIIALLRGEPKEL--LELRLAE-FEIYLSSITVAELLL 44 (133)
T ss_pred CceeeeHHHHHHHHhcCChHH--HHHHHhc-CCeeecHHHHHHHHH
Confidence 357999999999877655432 1112222 567889899999864
No 22
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=85.33 E-value=1.4 Score=36.26 Aligned_cols=48 Identities=23% Similarity=0.311 Sum_probs=42.4
Q ss_pred CHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeCceEEEecCC
Q 029148 138 YADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLP 188 (198)
Q Consensus 138 ~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~~~~~lE~~s 188 (198)
-||+-|++++.... +|.|+|-.|-.++-. .|+-+|.=++..|.-|.+.
T Consensus 55 aaD~~Iv~~a~~gD--lVVT~Di~LA~~ll~-kg~~v~~prGr~y~~~nI~ 102 (150)
T COG1671 55 AADDWIVNLAEKGD--LVVTADIPLASLLLD-KGAAVLNPRGRLYTEENIG 102 (150)
T ss_pred hHHHHHHHhCCCCC--EEEECchHHHHHHHh-cCCEEECCCCcccCHhHHH
Confidence 58999999998876 999999999999999 7999998888888777654
No 23
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=77.15 E-value=9.8 Score=31.72 Aligned_cols=42 Identities=26% Similarity=0.367 Sum_probs=36.5
Q ss_pred CCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeCce
Q 029148 137 TYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHK 181 (198)
Q Consensus 137 ~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~~~ 181 (198)
.+.|+=|+.++.++++ |+-|-|++|-+|. + -|++.||+..+.
T Consensus 34 ~~~d~~i~~i~~~e~r-IllTRDr~L~~r~-k-~g~~~i~i~~~s 75 (165)
T COG1656 34 NESDDEIILIAKKEGR-ILLTRDRELYKRA-K-LGIKAILIRSDS 75 (165)
T ss_pred cCCcHHHHHHHhcCCe-EEEeccHHHHHHh-h-ccCceEEEeCCC
Confidence 4678889999988875 9999999999999 6 699999999864
No 24
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=74.18 E-value=37 Score=26.02 Aligned_cols=107 Identities=17% Similarity=0.159 Sum_probs=57.6
Q ss_pred EEEeehHHHHHHHHcC----CChHHhHHHhhcc----cceEeecHHHHHHHHHhhhhhHHHHHhccCCCeeeeecCC---
Q 029148 66 RVLVDTNFINFSIQNK----LDLEKGMMDCLYA----KCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTH--- 134 (198)
Q Consensus 66 ~VLvDtNFl~~~i~~k----ldl~~~L~~~L~~----k~~~~iT~CVi~ELekLg~k~~~Al~iak~~r~e~~~C~H--- 134 (198)
-|++|++-+..+.... +|+...+..+... ..+.|.....-... ..+..+|+-. .++......
T Consensus 4 ~ifiD~~Nl~~~~~~~~~~~~d~~~l~~~~~~~~~~~~~r~y~~~~~~~~~----~~~~~~L~~~---g~~~~~~~~~~~ 76 (149)
T cd06167 4 AVFIDGENLYYSLRDLGGKRFDYRKLLEFLRDGGEIVLARAYGNWTSPERQ----RGFLDALRRL---GFEPIQKPLRTR 76 (149)
T ss_pred EEEEeHHHHHHHHHHhcCCCcCHHHHHHHHHhCCeEEEEEEEEecCCchhH----HHHHHHHHHC---CcEEEEEcceec
Confidence 5899999998887774 7876555544421 22333222211000 1122333222 244443332
Q ss_pred --CCCCHHHHHH----HHHhc--CCeEEEEecCHHHH---HHHhcCCCccEEEEeCc
Q 029148 135 --KGTYADDCLV----ERVTQ--HKCFIVATCDRDLK---RRIRKVPGVPIMYITRH 180 (198)
Q Consensus 135 --~g~~aDdCIv----~~v~~--~~~yiVATnD~~Lr---rrLRkipGVPIiyi~~~ 180 (198)
....+|-.|. +.+.+ -.+++++|.|.++- ++||+ -|..|+-+.-.
T Consensus 77 ~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i~~lr~-~G~~V~v~~~~ 132 (149)
T cd06167 77 GSGKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPLVERLRE-LGKRVIVVGFE 132 (149)
T ss_pred CCcccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHHHHHHHH-cCCEEEEEccC
Confidence 1123443332 22222 46799999999765 77888 59888877654
No 25
>PF14367 DUF4411: Domain of unknown function (DUF4411)
Probab=73.95 E-value=4.3 Score=32.95 Aligned_cols=46 Identities=26% Similarity=0.224 Sum_probs=34.0
Q ss_pred EeehHHHHHHHHc--CCChHHhHHHhhcc---cceEeecHHHHHHHHHhhh
Q 029148 68 LVDTNFINFSIQN--KLDLEKGMMDCLYA---KCTPCITDCVMAELEKLGQ 113 (198)
Q Consensus 68 LvDtNFl~~~i~~--kldl~~~L~~~L~~---k~~~~iT~CVi~ELekLg~ 113 (198)
|+|||.++.+... ..|+..++=+-|.. .-.+++++.|.+||+.-+.
T Consensus 2 llDtN~~I~a~~~yY~~d~~p~fW~~L~~~~~~g~i~~~~~V~~El~~~~d 52 (162)
T PF14367_consen 2 LLDTNVFIQAWNRYYPFDIFPSFWDWLEQLIESGRIISPDEVYDELERGDD 52 (162)
T ss_pred ccchHHHHHHHHhcCCchHHHHHHHHHHHHHhCCeEeehHHHHHHHhhCCh
Confidence 6999999877654 56777655555443 4578999999999996543
No 26
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=72.51 E-value=29 Score=26.20 Aligned_cols=104 Identities=14% Similarity=0.186 Sum_probs=45.4
Q ss_pred EEEeehHHHHHHHH-cCCChHHhHHHhhcc----cceEeecHHHHHHHHHhhhhhHHHHHhccCCCeeeeecCC------
Q 029148 66 RVLVDTNFINFSIQ-NKLDLEKGMMDCLYA----KCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTH------ 134 (198)
Q Consensus 66 ~VLvDtNFl~~~i~-~kldl~~~L~~~L~~----k~~~~iT~CVi~ELekLg~k~~~Al~iak~~r~e~~~C~H------ 134 (198)
-|++|.+-+..+.. ..+|+...+..+... ....|.. .-..-...+..+|+-. .+....+..
T Consensus 3 avfvD~eN~~~~~~~~~~~~~~l~~~i~~~~~~~~~~~y~~-----~~~~~~~~~~~~L~~~---g~~v~~~~~~~~~~~ 74 (146)
T PF01936_consen 3 AVFVDGENLYIPLKRWDIDFERLLEEIRKYGPLVRIRAYGN-----WDDPNQKSFQEALQRA---GIKVRHFPLRKRGGG 74 (146)
T ss_dssp EEEEEHHHHHHHHHSS-B-HHHHHHHHTTTEEEEEEEEEE---------HHHHHHHHHHHHH---T-EEEE------S--
T ss_pred EEEEEhHhCchhhCCCCCCHHHHHHHHHhcCCeEEEEEEee-----ccccchhhHHHHHHhC---eeeEEeeeccccccc
Confidence 48899999999876 236775555543332 1222333 1111112233333332 243333322
Q ss_pred CCCCHHHHHH-HH---H--hcCCeEEEEecCHHHH---HHHhcCCCccEEEEe
Q 029148 135 KGTYADDCLV-ER---V--TQHKCFIVATCDRDLK---RRIRKVPGVPIMYIT 178 (198)
Q Consensus 135 ~g~~aDdCIv-~~---v--~~~~~yiVATnD~~Lr---rrLRkipGVPIiyi~ 178 (198)
....+|-.|. ++ + .....++++|.|.++. ++||+ .|..|.-+.
T Consensus 75 ~k~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~v~~l~~-~g~~V~v~~ 126 (146)
T PF01936_consen 75 GKKGVDVALAVDILELAYENPPDTIVLVSGDSDFAPLVRKLRE-RGKRVIVVG 126 (146)
T ss_dssp -S---HHHHHHHHHHHG--GG-SEEEEE---GGGHHHHHHHHH-H--EEEEEE
T ss_pred ccCCcHHHHHHHHHHHhhccCCCEEEEEECcHHHHHHHHHHHH-cCCEEEEEE
Confidence 1123444442 22 2 2347799999999765 67776 788877766
No 27
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=71.58 E-value=8.6 Score=30.67 Aligned_cols=40 Identities=33% Similarity=0.436 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeC
Q 029148 137 TYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITR 179 (198)
Q Consensus 137 ~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~ 179 (198)
...|+-|++++.+.++ |+-|.|++|.++.....+ ++++..
T Consensus 28 ~~~D~~il~~A~~e~R-illTrd~~l~~~~~~~~~--~~li~~ 67 (147)
T PF01927_consen 28 DIDDDEILELAREEGR-ILLTRDRDLLKRRRVSGG--VILIRS 67 (147)
T ss_pred CCChHHHHHHhhhCCe-EEEECCHHHHHHhhccCC--EEEEcC
Confidence 3579999999988775 999999999999998545 666644
No 28
>COG2405 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=68.16 E-value=28 Score=28.64 Aligned_cols=100 Identities=19% Similarity=0.125 Sum_probs=61.2
Q ss_pred EEeehHHH-HHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhhhHHHHHhccCCCeeeeecC-C---------C
Q 029148 67 VLVDTNFI-NFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCT-H---------K 135 (198)
Q Consensus 67 VLvDtNFl-~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k~~~Al~iak~~r~e~~~C~-H---------~ 135 (198)
|+.||+-| +.+.-.++++..++- . ..+||.-|-+|++-....- ...+.-.-++.+.-. | -
T Consensus 2 vvsdts~i~nla~ig~i~ll~~~y----e--~viip~~v~~E~~~~~~s~---~~~~~l~~iei~~~~n~~lv~~lre~L 72 (157)
T COG2405 2 VVSDTSPIINLANIGEIDLLHALY----E--KVIIPEQVAEEFEFGVNSG---VLPALLGWIEILRLKNRDLVNLLREKL 72 (157)
T ss_pred eeecchhHHHHHhcchhhHHHHHh----h--cccCCchHHHHHHHhhccc---ccccccCceEEeccCcHHHHHHHHHhc
Confidence 67888766 555444677665543 3 3689999999999876532 111110022322211 1 0
Q ss_pred CCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEE
Q 029148 136 GTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYI 177 (198)
Q Consensus 136 g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi 177 (198)
+..-.+||. ++.+.++-.+.+.|++=|+-..+ -|+||+-.
T Consensus 73 d~GEa~aIA-LA~e~~ad~Ll~Ddr~aR~~A~~-lgL~V~Gt 112 (157)
T COG2405 73 DKGEAEAIA-LALELKADLLLMDDRDARNVAKS-LGLKVTGT 112 (157)
T ss_pred ccchHHHHH-HHHHcCCCeeeeccHHHHHHHHH-cCCeeeeh
Confidence 122345553 55566766999999998888888 79998754
No 29
>COG4113 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=62.93 E-value=69 Score=25.58 Aligned_cols=102 Identities=16% Similarity=0.090 Sum_probs=57.4
Q ss_pred CeEEEeehHHHHHHHHcCCC--hHHhHHHhhcccceEeecHHHHHHHHHhhhh-------hHHHHHhccCCCeeeeecCC
Q 029148 64 PYRVLVDTNFINFSIQNKLD--LEKGMMDCLYAKCTPCITDCVMAELEKLGQK-------YRVALRIAKDPRFERLPCTH 134 (198)
Q Consensus 64 PY~VLvDtNFl~~~i~~kld--l~~~L~~~L~~k~~~~iT~CVi~ELekLg~k-------~~~Al~iak~~r~e~~~C~H 134 (198)
|..+++|++++..-+-.--+ ........-....-.+.--+|..-+.++... ...++...+ ++....-.+
T Consensus 1 ~~~~vvDaSa~i~~~v~e~~~~~~~~~~~~~~~~~~~l~~~Ev~~~~~k~~~~~~l~~~~~~~~~~~l~--~l~v~~~~~ 78 (134)
T COG4113 1 MEMIVVDASALVKLLVREENSDAVALRLKAEELHAPDLAIGEVANALWKLVVRVELSVEEALAALKLLR--RLAVTRVPL 78 (134)
T ss_pred CcEEEeeHHHHHHHHhccccchHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH--hCCceecCC
Confidence 35689999999776544443 2233333222222223444555555555443 234444444 343333222
Q ss_pred CC---------------CCHHHHHHHHHhcCCeEEEEecCHHHHHHHhc
Q 029148 135 KG---------------TYADDCLVERVTQHKCFIVATCDRDLKRRIRK 168 (198)
Q Consensus 135 ~g---------------~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRk 168 (198)
.+ +..|---+.++...++ .+-|+|+.|-+..++
T Consensus 79 ~~~ll~~A~~i~~~~~lt~YDA~yialAe~~g~-~l~T~D~rL~~~~~~ 126 (134)
T COG4113 79 SEELLERAWEIALKYSLTVYDALYIALAERLGL-ELVTADKRLARKAKK 126 (134)
T ss_pred cHHHHHHHHHHHHhcCccHHHHHHHHHHHHcCC-eEEeCCHHHHHHhhh
Confidence 22 2345556777777776 899999999999887
No 30
>smart00500 SFM Splicing Factor Motif, present in Prp18 and Pr04.
Probab=62.22 E-value=6.2 Score=25.93 Aligned_cols=23 Identities=30% Similarity=0.504 Sum_probs=20.2
Q ss_pred ecCHHHHHHHhcCCCccEEEEeCc
Q 029148 157 TCDRDLKRRIRKVPGVPIMYITRH 180 (198)
Q Consensus 157 TnD~~LrrrLRkipGVPIiyi~~~ 180 (198)
|.|.+++++||. -|=||.++..+
T Consensus 1 ~~d~eV~~~LR~-lgePi~lFGE~ 23 (44)
T smart00500 1 LPDSEVIRRLRE-LGEPITLFGED 23 (44)
T ss_pred CCHHHHHHHHHH-cCCCeeecCCC
Confidence 689999999999 69999998754
No 31
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=59.85 E-value=52 Score=32.23 Aligned_cols=82 Identities=21% Similarity=0.270 Sum_probs=52.8
Q ss_pred ceEeecHHHHHHHHHhhhh-----------hHHHHHhccCCCeeeeecCC----------CCCCHHHHHHHHHhcCCeEE
Q 029148 96 CTPCITDCVMAELEKLGQK-----------YRVALRIAKDPRFERLPCTH----------KGTYADDCLVERVTQHKCFI 154 (198)
Q Consensus 96 ~~~~iT~CVi~ELekLg~k-----------~~~Al~iak~~r~e~~~C~H----------~g~~aDdCIv~~v~~~~~yi 154 (198)
...+|+..|++||+..+.. .+.-..++.+-.+++.--+. ++.-.|.-|-+.+.+++ ++
T Consensus 31 ~~viipeAvvsele~qAn~Gr~~G~~gLeEL~kL~~l~~~g~i~~~~~gerp~~~~Ik~ak~GEid~miR~vA~e~~-a~ 109 (604)
T COG1855 31 ATVIIPEAVVSELEAQANRGREIGFAGLEELKKLRDLADEGKIELEFVGERPTLEEIKRAKSGEIDAMIREVALEYG-AT 109 (604)
T ss_pred cEEEeeHHHHHHHHHHhccchhhhhhHHHHHHHHHHHHhcCcEEEEEEeccCchhhhcccccccHHHHHHHHHHHhC-cE
Confidence 4689999999999987442 22223343321122221111 12346777788888888 69
Q ss_pred EEecCHHHHHHHhcCCCccEEEEeC
Q 029148 155 VATCDRDLKRRIRKVPGVPIMYITR 179 (198)
Q Consensus 155 VATnD~~LrrrLRkipGVPIiyi~~ 179 (198)
..|.|+-= +.+-...|+-+.|+..
T Consensus 110 lVTsD~vQ-~~va~a~Giev~yl~p 133 (604)
T COG1855 110 LVTSDRVQ-RDVARAKGIEVEYLEP 133 (604)
T ss_pred EEechHHH-HHHHHhcCceEEEeCC
Confidence 99999854 4444458999999987
No 32
>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]
Probab=56.72 E-value=15 Score=34.76 Aligned_cols=98 Identities=18% Similarity=0.308 Sum_probs=60.6
Q ss_pred EEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhh-------hhhHHHHHhccCCC---------e---
Q 029148 67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLG-------QKYRVALRIAKDPR---------F--- 127 (198)
Q Consensus 67 VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg-------~k~~~Al~iak~~r---------~--- 127 (198)
-++|||-|++ |. ..+-. ..+-..+||--|++||+++. ...|.|++....-+ +
T Consensus 5 yVLDTnVLi~------DP-~Alf~--F~eh~VvIP~~VlEELd~~Kr~~~evgrnAR~a~r~ld~L~~~~~~l~~giPl~ 75 (436)
T COG1875 5 YVLDTNVLIH------DP-TALFR--FEEHDVVIPMVVIEELDATKRGHSEIGRNARQASRLLDELRNEHGRLKAGIPLG 75 (436)
T ss_pred EEEecceeee------Cc-HHHhc--ccccceEeeehHHHHHHhhcccchhhHHHHHHHHHHHHHHHhhcCCccCCcccC
Confidence 4789998876 23 23222 24557899999999999963 34666666543211 0
Q ss_pred -----eeeecCCCC----------CCHHHHHHHHHh----cC--CeEEEEecCHHHHHHHhcCCCccE
Q 029148 128 -----ERLPCTHKG----------TYADDCLVERVT----QH--KCFIVATCDRDLKRRIRKVPGVPI 174 (198)
Q Consensus 128 -----e~~~C~H~g----------~~aDdCIv~~v~----~~--~~yiVATnD~~LrrrLRkipGVPI 174 (198)
-++.-+|.. ...|.-|++.+. ++ ...+..|-|-.+|=+.+. -|++-
T Consensus 76 ~~G~~l~iel~~~~~~~~~~~~~~~~~DnrIL~~~~~L~~~~~~~~VvLVSKDi~~RvkA~a-~Gl~A 142 (436)
T COG1875 76 NKGGTLHVELNHQNSTKLPNGFREGVNDNRILAVVLNLQEEEPGRRVVLVSKDINLRVKASA-LGLAA 142 (436)
T ss_pred CCCCeEEEEEeccCccccccccccccchHHHHHHHHHHHhcCCCCcEEEEECCccceeehhh-cCccH
Confidence 011122321 146777777664 22 358999999999888887 57763
No 33
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=51.21 E-value=35 Score=27.89 Aligned_cols=43 Identities=21% Similarity=0.322 Sum_probs=30.5
Q ss_pred CCCCHHHHHHHHHhc---C-CeEEEEecCHHHHHHHhcCCCccEEEEeC
Q 029148 135 KGTYADDCLVERVTQ---H-KCFIVATCDRDLKRRIRKVPGVPIMYITR 179 (198)
Q Consensus 135 ~g~~aDdCIv~~v~~---~-~~yiVATnD~~LrrrLRkipGVPIiyi~~ 179 (198)
.|--|||+|-.++.. + ...+|.|.|+||.+-+.. .+-|..+..
T Consensus 106 ~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~--~~~V~~~~~ 152 (169)
T PF02739_consen 106 PGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDE--NVNVYLLDP 152 (169)
T ss_dssp TTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS---TSEEEEET
T ss_pred CCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCC--CceEEEeec
Confidence 466799999988863 2 457999999999998886 455555554
No 34
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=50.55 E-value=34 Score=23.43 Aligned_cols=47 Identities=28% Similarity=0.308 Sum_probs=35.9
Q ss_pred HHHHHHHHcCCChHHhHHHhh--cccceEeecHHHHHHHHHhhhhhHHHH
Q 029148 72 NFINFSIQNKLDLEKGMMDCL--YAKCTPCITDCVMAELEKLGQKYRVAL 119 (198)
Q Consensus 72 NFl~~~i~~kldl~~~L~~~L--~~k~~~~iT~CVi~ELekLg~k~~~Al 119 (198)
|-|=.|++..++-.+-+. .| .+++.|.+|.-|..+|++=.+.+-.|.
T Consensus 3 ~lIErCl~~yMsk~E~v~-~L~~~a~I~P~~T~~VW~~Le~eN~eFF~aY 51 (54)
T PF09713_consen 3 NLIERCLQLYMSKEECVR-ALQKQANIEPVFTSTVWQKLEKENPEFFKAY 51 (54)
T ss_pred hHHHHHHHHcCCHHHHHH-HHHHHcCCChHHHHHHHHHHHHHCHHHHHHh
Confidence 345667888888755444 55 578999999999999999888875553
No 35
>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A ....
Probab=49.87 E-value=41 Score=24.90 Aligned_cols=36 Identities=19% Similarity=0.331 Sum_probs=29.2
Q ss_pred CHHHHHHHHHhcCCeEEEEecC-----HHHHHHHhcCCCccE
Q 029148 138 YADDCLVERVTQHKCFIVATCD-----RDLKRRIRKVPGVPI 174 (198)
Q Consensus 138 ~aDdCIv~~v~~~~~yiVATnD-----~~LrrrLRkipGVPI 174 (198)
.|.++|-.+-..+..+++.||. .++.++|++ -|+++
T Consensus 18 ga~e~l~~L~~~g~~~~~lTNns~~s~~~~~~~L~~-~Gi~~ 58 (101)
T PF13344_consen 18 GAVEALDALRERGKPVVFLTNNSSRSREEYAKKLKK-LGIPV 58 (101)
T ss_dssp THHHHHHHHHHTTSEEEEEES-SSS-HHHHHHHHHH-TTTT-
T ss_pred CHHHHHHHHHHcCCCEEEEeCCCCCCHHHHHHHHHh-cCcCC
Confidence 5888988888887889999998 489999988 69884
No 36
>PF11977 RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domain; InterPro: IPR021869 This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes []. It has been suggested that this domain belongs to the PIN domain superfamily []. ; PDB: 3V33_A 3V34_B 3V32_B.
Probab=49.09 E-value=15 Score=29.41 Aligned_cols=23 Identities=17% Similarity=0.446 Sum_probs=15.2
Q ss_pred CCHHHHHHHHHhcCCeEEEEecCH
Q 029148 137 TYADDCLVERVTQHKCFIVATCDR 160 (198)
Q Consensus 137 ~~aDdCIv~~v~~~~~yiVATnD~ 160 (198)
+|+|-.|+++|.+++. +|.|||+
T Consensus 88 ~ydD~~il~~A~~~~a-~IVSND~ 110 (155)
T PF11977_consen 88 NYDDRYILYYAEEKDA-VIVSNDR 110 (155)
T ss_dssp B-HHHHHHHHHHHTT--EEE-S--
T ss_pred ccchHHHHHHHHHcCC-EEEeCch
Confidence 3799999999999886 5559997
No 37
>PRK04358 hypothetical protein; Provisional
Probab=48.97 E-value=39 Score=29.36 Aligned_cols=107 Identities=17% Similarity=0.242 Sum_probs=64.4
Q ss_pred cccCCCchhhhHHhhhCCCCCeEEEeehHHHHHHHHcCCChHHhHH-Hhhcc---cceEeecHHHHHHH-HHhhhhhHHH
Q 029148 44 RNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMM-DCLYA---KCTPCITDCVMAEL-EKLGQKYRVA 118 (198)
Q Consensus 44 ~~~~~~~s~~fy~~n~~~~~PY~VLvDtNFl~~~i~~kldl~~~L~-~~L~~---k~~~~iT~CVi~EL-ekLg~k~~~A 118 (198)
|+--++|+..||.|-.-.|. =+..++.+-|.-. +.-.. ...--+..-++.++ .+|-.+||.|
T Consensus 87 ry~v~IPA~i~ye~I~~mR~-------------RInkGLRVAEeavrea~~~~~~~~~~~~~~~~v~~~I~~lRekYReA 153 (217)
T PRK04358 87 RYEIKIPAEIFYEYIEDMRE-------------RINKGLRVAEEAVREAALECYDLSKEEIEREVVGKIISKLREKYREA 153 (217)
T ss_pred ceeeeccHHHHHHHHHHHHH-------------HHhcchHHHHHHHHHHHhhhccccccchhhhhHHHHHHHHHHHHHHH
Confidence 34457888999887554443 2344555543322 21100 00001222223333 4456789999
Q ss_pred HHhccCCCeeeeecCCCCCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEE
Q 029148 119 LRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMY 176 (198)
Q Consensus 119 l~iak~~r~e~~~C~H~g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiy 176 (198)
++-. +-...+|--++.++.+.+ .+|.|.|..+++.+.+ -||.++.
T Consensus 154 lr~G-----------~ldS~~DidvlaLA~ELd-a~lvTdD~giqn~A~~-LGI~~~~ 198 (217)
T PRK04358 154 LRKG-----------ILDSAEDLDVLLLAKELD-AAVVSADEGIRKWAER-LGLRFVD 198 (217)
T ss_pred HHcC-----------cccchhhHHHHHHHHHhC-CEEEeCCHHHHHHHHH-cCCeeec
Confidence 7443 233457888888988876 7999999999999999 5988764
No 38
>COG0117 RibD Pyrimidine deaminase [Coenzyme metabolism]
Probab=44.22 E-value=26 Score=28.72 Aligned_cols=46 Identities=24% Similarity=0.428 Sum_probs=30.4
Q ss_pred eeeecCCCCCCHHHHHHHHHhc-CCeEEEEecCHHH------HHHHhcCCCccEE
Q 029148 128 ERLPCTHKGTYADDCLVERVTQ-HKCFIVATCDRDL------KRRIRKVPGVPIM 175 (198)
Q Consensus 128 e~~~C~H~g~~aDdCIv~~v~~-~~~yiVATnD~~L------rrrLRkipGVPIi 175 (198)
..-+|+|.|. .--|--.++.. -...+||+.|++- -.+||+ .||.|-
T Consensus 74 TLEPCsH~Gr-TPPC~~ali~agi~rVvva~~DPnp~Vag~G~~~L~~-aGi~V~ 126 (146)
T COG0117 74 TLEPCSHYGR-TPPCADALIKAGVARVVVAMLDPNPLVAGGGLARLRA-AGIEVE 126 (146)
T ss_pred EecCcccCCC-CcchHHHHHHhCCCEEEEEecCCCccccCchHHHHHH-cCCeEE
Confidence 3457999886 22354444433 2468999999984 278888 787653
No 39
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=42.96 E-value=1.2e+02 Score=25.65 Aligned_cols=99 Identities=16% Similarity=0.134 Sum_probs=63.9
Q ss_pred EEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhhhH--HHHHhccCCCeeeeecCCC--------
Q 029148 66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYR--VALRIAKDPRFERLPCTHK-------- 135 (198)
Q Consensus 66 ~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k~~--~Al~iak~~r~e~~~C~H~-------- 135 (198)
..++||+.++.. ++++ .+.+. .|+|.-|++|++.-..++. .++..+ ++....+++.
T Consensus 8 ~~vlDtsa~I~g---~~~~------~~~g~--~yttp~Vv~Eikd~~s~~~~e~~~~~~---~~kv~~P~~e~vk~V~e~ 73 (177)
T COG1439 8 LYVLDTSAFING---KIPL------LLDGR--LYTTPSVVEEIKDRESRSLLELLLESG---KVKVAEPSTEYVKEVREA 73 (177)
T ss_pred eEEecchhhccC---CCCc------ccCCc--ccccHHHHHHHhchhhhHHHHHHhhhc---CeeEecCCHHHHHHHHHH
Confidence 467888887653 4443 22333 5788899999997766533 333333 3555556551
Q ss_pred ----C-----CCHHHHHHHHHhcCC---eEEEEecCHHHHHHHhcCCCccEEEEeC
Q 029148 136 ----G-----TYADDCLVERVTQHK---CFIVATCDRDLKRRIRKVPGVPIMYITR 179 (198)
Q Consensus 136 ----g-----~~aDdCIv~~v~~~~---~yiVATnD~~LrrrLRkipGVPIiyi~~ 179 (198)
| +.+|--++.++-+.+ ..+++|-|-.+..=+.+ -|+-++++.-
T Consensus 74 a~~tgd~~~LS~tDi~VlalAlel~~~~~v~l~TdDysvQNVa~~-Lgi~~~~~~~ 128 (177)
T COG1439 74 AKKTGDLGNLSPTDIEVLALALELGEEVQVALATDDYSVQNVALQ-LGLNVRSISY 128 (177)
T ss_pred HHhhCcccccChhhHHHHHHHHhhccccceeEEecchHHHHHHHH-hCceEEeeec
Confidence 1 145655666665433 36999999999999998 6999987443
No 40
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=42.73 E-value=79 Score=27.15 Aligned_cols=31 Identities=23% Similarity=0.310 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHHhc----CCeEEEEecCHHHHHHH
Q 029148 136 GTYADDCLVERVTQ----HKCFIVATCDRDLKRRI 166 (198)
Q Consensus 136 g~~aDdCIv~~v~~----~~~yiVATnD~~LrrrL 166 (198)
|--|||.|-.++.+ ...++|+|.|+||..-+
T Consensus 106 ~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~ 140 (240)
T cd00008 106 GYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLV 140 (240)
T ss_pred CcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhC
Confidence 45799999988853 34679999999999766
No 41
>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family. This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.
Probab=42.07 E-value=82 Score=27.22 Aligned_cols=105 Identities=17% Similarity=0.244 Sum_probs=63.2
Q ss_pred cccCCCchhhhHHhhhCCCCCeEEEeehHHHHHHHHcCCChHHhH-HHhhcccc-----eEeecHHHHHHH-HHhhhhhH
Q 029148 44 RNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGM-MDCLYAKC-----TPCITDCVMAEL-EKLGQKYR 116 (198)
Q Consensus 44 ~~~~~~~s~~fy~~n~~~~~PY~VLvDtNFl~~~i~~kldl~~~L-~~~L~~k~-----~~~iT~CVi~EL-ekLg~k~~ 116 (198)
|+--++|+..||.|-.-.|. =+..++.+-|.- .+...... ...-+. +.++ .+|-.+||
T Consensus 83 rye~~IPA~i~ye~I~e~R~-------------RInkGLRVAEe~vrea~~~~~~~~~~~~~~~~--~~~~I~~lRekYR 147 (206)
T TIGR03875 83 RYEVKIPAEIFYEYIEEVRE-------------RIDKGLRVAEEHVREAALAGDEISAEHEKKEE--VGKIIRKLREKYR 147 (206)
T ss_pred eeeeeccHHHHHHHHHHHHH-------------HHhcchhHHHHHHHHHhhcccchhcccccccc--HHHHHHHHHHHHH
Confidence 34457889999987655443 244555555332 22111000 000011 2322 44557899
Q ss_pred HHHHhccCCCeeeeecCCCCCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEE
Q 029148 117 VALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMY 176 (198)
Q Consensus 117 ~Al~iak~~r~e~~~C~H~g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiy 176 (198)
.|++-.- + ...+|--++-++.+.+ ..|.|.|-.+++.+.+ -|+.++.
T Consensus 148 eAlR~Gi------L-----dS~~DidvlaLA~ELd-a~lvTdD~giqn~A~~-Lgi~~~~ 194 (206)
T TIGR03875 148 EALRKGI------L-----DSAEDLDVLLLAKELD-AAVVSADEGIRKWAER-LGLRFVD 194 (206)
T ss_pred HHHHccc------c-----CchhhHHHHHHHHHcC-cEEEeCcHHHHHHHHH-cCCeeec
Confidence 9975432 1 2346778888888876 6999999999999999 5887653
No 42
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=41.26 E-value=70 Score=27.75 Aligned_cols=105 Identities=20% Similarity=0.310 Sum_probs=59.3
Q ss_pred cccCCCchhhhHHhhhCCCCCeEEEeehHHHHHHHHcCCChHHh-HHHhhcccceEeecHHHHHH-----HHHhhhhhHH
Q 029148 44 RNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKG-MMDCLYAKCTPCITDCVMAE-----LEKLGQKYRV 117 (198)
Q Consensus 44 ~~~~~~~s~~fy~~n~~~~~PY~VLvDtNFl~~~i~~kldl~~~-L~~~L~~k~~~~iT~CVi~E-----LekLg~k~~~ 117 (198)
|+--++||.+||.|-..+|+- +..++.+-+. +.+... .|-.+...-++.| ..+|-.+||.
T Consensus 87 ryevkiPa~ifyeyV~diR~R-------------inkGlRvAE~~i~eA~~-~~~~~~~~~i~~e~igk~I~~lR~KYR~ 152 (221)
T COG1458 87 RYEVKIPAAIFYEYVEDIRER-------------INKGLRVAEEAIREASI-ECYELEKEEIIREVVGKIIRKLREKYRE 152 (221)
T ss_pred ceeecCcHHHHHHHHHHHHHH-------------HHhhhhhHHHHHHHHHH-HHHHhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 455589999999987666542 2334433322 111110 0111111222222 2445567888
Q ss_pred HHHhccCCCeeeeecCCCCCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEE
Q 029148 118 ALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIM 175 (198)
Q Consensus 118 Al~iak~~r~e~~~C~H~g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIi 175 (198)
|++-.- +. .-+|=-++=++.+-+ ..|.+.|..+++...+ -|+-.+
T Consensus 153 alR~Gi------LD-----SapDlDvLLLAkELd-aavVssD~Gir~WAe~-LGlrfv 197 (221)
T COG1458 153 ALRKGI------LD-----SAPDLDVLLLAKELD-AAVVSSDEGIRTWAEK-LGLRFV 197 (221)
T ss_pred HHHhcc------cc-----ccchhHHHHHHHHhC-ceEEecchhHHHHHHH-hCCeee
Confidence 875442 21 123545556777777 5889999999999999 587654
No 43
>COG5573 Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only]
Probab=40.24 E-value=31 Score=28.04 Aligned_cols=42 Identities=17% Similarity=0.235 Sum_probs=31.3
Q ss_pred EEEeehHHHHHHHHcCCC-----hHHhHHHhhcccceEeecHHHHHHHH
Q 029148 66 RVLVDTNFINFSIQNKLD-----LEKGMMDCLYAKCTPCITDCVMAELE 109 (198)
Q Consensus 66 ~VLvDtNFl~~~i~~kld-----l~~~L~~~L~~k~~~~iT~CVi~ELe 109 (198)
...+|||.+++++.++-+ +.+.|.+.+.. ..+|+.-|++|+-
T Consensus 5 ~~flDsNI~iYa~~~~~~~~kr~~a~~L~~a~~~--~~VVs~QVl~Et~ 51 (142)
T COG5573 5 PAFLDSNILIYALDNNAGEKKRDAAEVLEQALGH--TYVVSVQVLNETC 51 (142)
T ss_pred hhhhccchhhhhhcccchhhHHHHHHHHHHhcCc--eEEEehHHHHHHH
Confidence 356899999998877654 44556665554 3799999999984
No 44
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=38.70 E-value=26 Score=22.87 Aligned_cols=28 Identities=14% Similarity=0.351 Sum_probs=19.8
Q ss_pred EEEEecCHHHHHHHhcC---CCccEEEEeCc
Q 029148 153 FIVATCDRDLKRRIRKV---PGVPIMYITRH 180 (198)
Q Consensus 153 yiVATnD~~LrrrLRki---pGVPIiyi~~~ 180 (198)
++=.+.|.++++.+++. .++|.+++.+.
T Consensus 28 ~~dv~~~~~~~~~l~~~~g~~~~P~v~i~g~ 58 (60)
T PF00462_consen 28 EVDVDEDEEAREELKELSGVRTVPQVFIDGK 58 (60)
T ss_dssp EEEGGGSHHHHHHHHHHHSSSSSSEEEETTE
T ss_pred EcccccchhHHHHHHHHcCCCccCEEEECCE
Confidence 44556666777777653 88999999654
No 45
>TIGR01589 A_thal_3526 uncharacterized plant-specific domain TIGR01589. This model represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa.
Probab=36.85 E-value=87 Score=21.71 Aligned_cols=48 Identities=25% Similarity=0.165 Sum_probs=35.4
Q ss_pred HHHHHHHHcCCChHHhHHHhh-cccceEeecHHHHHHHHHhhhhhHHHH
Q 029148 72 NFINFSIQNKLDLEKGMMDCL-YAKCTPCITDCVMAELEKLGQKYRVAL 119 (198)
Q Consensus 72 NFl~~~i~~kldl~~~L~~~L-~~k~~~~iT~CVi~ELekLg~k~~~Al 119 (198)
|.|=.|++.-++..+-+.-+. .+++.|.+|.-|..+|++=.+++-.|.
T Consensus 6 ~lIE~Cl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~LekeN~eFF~aY 54 (57)
T TIGR01589 6 NRIETCIQGYMSKEETVSFLFENAGISPKFTRFVWYLLEKENADFFRCY 54 (57)
T ss_pred HHHHHHHHHHCCHHHHHHHHHHHcCCCchhHHHHHHHHHHHHHHHHHHH
Confidence 445567777777755554333 378999999999999999888876553
No 46
>PF10130 PIN_2: PIN domain; InterPro: IPR019298 This entry represents a set of bacterial and archaeal proteins that are predicted to be RNases (from similarities to 5'-exonucleases).
Probab=35.52 E-value=30 Score=27.43 Aligned_cols=91 Identities=21% Similarity=0.162 Sum_probs=51.4
Q ss_pred EeehHHHHHHHHc-CCChHHhHHHhhcccceEeecHHHHHHHHHhhhh-----------hHHHHHhccCCCeeeeecCC-
Q 029148 68 LVDTNFINFSIQN-KLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK-----------YRVALRIAKDPRFERLPCTH- 134 (198)
Q Consensus 68 LvDtNFl~~~i~~-kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k-----------~~~Al~iak~~r~e~~~C~H- 134 (198)
+||||.++.++-. +.-. .+ -.......+++|+-++.|+++-.++ ....+.+... +++.++=+-
T Consensus 1 VvDaNIl~Sall~~~~~~--~~-~~~~~~~~f~~p~~~~~Ei~kh~~~I~~k~~l~~~~~~~~l~~l~~-~I~iv~~~~~ 76 (133)
T PF10130_consen 1 VVDANILFSALLGKRSRT--RI-LLVEPRIEFFAPDYALEEIEKHLPKIAKKSKLSEEELEEVLNILFS-RIKIVPEEIY 76 (133)
T ss_pred CccHHHHHHHHHccCcce--ee-eecccchheeccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh-heEEecHHHh
Confidence 5899999998653 2211 11 1234567899999999999886542 2233333332 232222000
Q ss_pred -----------CCCCH-HHHHHHHHhcCCeEEEEecCHHHH
Q 029148 135 -----------KGTYA-DDCLVERVTQHKCFIVATCDRDLK 163 (198)
Q Consensus 135 -----------~g~~a-DdCIv~~v~~~~~yiVATnD~~Lr 163 (198)
...++ |-=.+.++-+.+| -+=|+|++|.
T Consensus 77 ~~~~~~A~~~~~~~D~~D~p~vALaL~l~~-~IWT~Dkdl~ 116 (133)
T PF10130_consen 77 SENIEEAREIIRDRDPDDWPFVALALQLNA-PIWTEDKDLF 116 (133)
T ss_pred HHHHHHHHHHhcCCCcchHHHHHHHHHcCC-CeecCcHHHH
Confidence 00112 2224455556666 8899999995
No 47
>KOG4127 consensus Renal dipeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=33.52 E-value=1.5e+02 Score=28.07 Aligned_cols=116 Identities=21% Similarity=0.319 Sum_probs=66.5
Q ss_pred hHHhhhCCCCCeEEEeehHHHHHHHHcCCChH---HhHHHhhcccceEeecHHHHHHHHHhhh----------hhHHHHH
Q 029148 54 FFTHNTALGPPYRVLVDTNFINFSIQNKLDLE---KGMMDCLYAKCTPCITDCVMAELEKLGQ----------KYRVALR 120 (198)
Q Consensus 54 fy~~n~~~~~PY~VLvDtNFl~~~i~~kldl~---~~L~~~L~~k~~~~iT~CVi~ELekLg~----------k~~~Al~ 120 (198)
||+.---+-. +.-=+||-|.-.+...-.+-. ..|.. .-+-|+.|+.+||. -.+.||+
T Consensus 194 fY~LG~Rylt-LTh~C~tpwA~a~~~~~~~~~~~~~gLs~---------FG~~vV~EMNRLGMmVDLShvS~atm~~aL~ 263 (419)
T KOG4127|consen 194 FYSLGVRYLT-LTHTCDTPWADAAIVDYHDGENNIGGLSP---------FGQKVVFEMNRLGMMVDLSHVSDATMRDALE 263 (419)
T ss_pred HHHhhhhhee-eeeccCCCchhhhhhcccCcCcccCCccH---------HHHHHHHHHhhhhheeehhhcCHHHHHHHHH
Confidence 6654333222 233478888777764322211 11211 23467899999986 2578999
Q ss_pred hccCCCeee-----eecCCCCCCHHHHHHHHHhcCCeEEE--------EecCH-------HHHHHHhcCCCccEEEEeCc
Q 029148 121 IAKDPRFER-----LPCTHKGTYADDCLVERVTQHKCFIV--------ATCDR-------DLKRRIRKVPGVPIMYITRH 180 (198)
Q Consensus 121 iak~~r~e~-----~~C~H~g~~aDdCIv~~v~~~~~yiV--------ATnD~-------~LrrrLRkipGVPIiyi~~~ 180 (198)
..+.|-+=- --|+|.-.-+ |-|++++.+++-.+. .-+|+ +-...+|++.|+--|-+.++
T Consensus 264 vS~APVIFSHSsA~~vcns~rNVP-DdVL~llk~NgGvVMVnfy~~~isc~~~A~v~~v~~Hi~hIr~VaG~~hIGlGg~ 342 (419)
T KOG4127|consen 264 VSRAPVIFSHSSAYSVCNSSRNVP-DDVLQLLKENGGVVMVNFYPGFISCSDRATVSDVADHINHIRAVAGIDHIGLGGD 342 (419)
T ss_pred hhcCceEeecccHHHHhcCccCCc-HHHHHHHhhcCCEEEEEeecccccCCCcccHHHHHHHHHHHHHhhccceeeccCC
Confidence 988765411 1277753334 456666665432222 23333 44568899999988888775
No 48
>COG1911 RPL30 Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]
Probab=33.12 E-value=43 Score=25.76 Aligned_cols=45 Identities=11% Similarity=0.113 Sum_probs=30.7
Q ss_pred HHHHHHHH-hcCCeEEEEecCHHHHHHHh----cCCCccEEEEeCceEEE
Q 029148 140 DDCLVERV-TQHKCFIVATCDRDLKRRIR----KVPGVPIMYITRHKYSI 184 (198)
Q Consensus 140 DdCIv~~v-~~~~~yiVATnD~~LrrrLR----kipGVPIiyi~~~~~~l 184 (198)
..-|..+- ++.++.|||.|-+..++.-- +..|+||+++.+....|
T Consensus 25 k~tiK~lk~gkaKliiiAsN~P~~~k~~ieyYAkLs~ipV~~y~Gt~~eL 74 (100)
T COG1911 25 KRTIKSLKLGKAKLIIIASNCPKELKEDIEYYAKLSDIPVYVYEGTSVEL 74 (100)
T ss_pred HHHHHHHHcCCCcEEEEecCCCHHHHHHHHHHHHHcCCcEEEecCCceeH
Confidence 34444443 35678899999886665543 45699999999876654
No 49
>COG0069 GltB Glutamate synthase domain 2 [Amino acid transport and metabolism]
Probab=31.38 E-value=26 Score=33.91 Aligned_cols=26 Identities=35% Similarity=0.710 Sum_probs=17.0
Q ss_pred HHHHHHHh-cCCe-EEEEecCHHHHHHH
Q 029148 141 DCLVERVT-QHKC-FIVATCDRDLKRRI 166 (198)
Q Consensus 141 dCIv~~v~-~~~~-yiVATnD~~LrrrL 166 (198)
-||.-++= -+.| .=|||||++||+|+
T Consensus 411 GCim~r~CH~~tCp~GIaTqdp~Lrkrl 438 (485)
T COG0069 411 GCIMCRVCHTGTCPVGIATQDPELRKRL 438 (485)
T ss_pred hhHhhhhccCCCCCceeeecCHHHHhhc
Confidence 45543332 2335 34999999999996
No 50
>COG0337 AroB 3-dehydroquinate synthetase [Amino acid transport and metabolism]
Probab=30.21 E-value=31 Score=32.09 Aligned_cols=16 Identities=44% Similarity=0.742 Sum_probs=14.4
Q ss_pred CCCCCeEEEeehHHHH
Q 029148 60 ALGPPYRVLVDTNFIN 75 (198)
Q Consensus 60 ~~~~PY~VLvDtNFl~ 75 (198)
.|.+|+-||+|+.||.
T Consensus 155 aF~qP~aVi~D~~~L~ 170 (360)
T COG0337 155 AFYQPKAVLIDTDFLK 170 (360)
T ss_pred cccCCcEEEEchHHhc
Confidence 6889999999999984
No 51
>PF02254 TrkA_N: TrkA-N domain; InterPro: IPR003148 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the N-terminal subdomain of RCK.; GO: 0006813 potassium ion transport; PDB: 3L4B_E 1LSS_C 3LLV_A 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A 2AEJ_A 3RBZ_A ....
Probab=29.97 E-value=1.4e+02 Score=21.65 Aligned_cols=37 Identities=19% Similarity=0.328 Sum_probs=27.1
Q ss_pred HHHHHHHhcCC-eEEEEecCHHHHHHHhcCCCccEEEEe
Q 029148 141 DCLVERVTQHK-CFIVATCDRDLKRRIRKVPGVPIMYIT 178 (198)
Q Consensus 141 dCIv~~v~~~~-~yiVATnD~~LrrrLRkipGVPIiyi~ 178 (198)
..|++...+.+ .++|.+.|++..+.++. .|+++++-.
T Consensus 11 ~~i~~~L~~~~~~vvvid~d~~~~~~~~~-~~~~~i~gd 48 (116)
T PF02254_consen 11 REIAEQLKEGGIDVVVIDRDPERVEELRE-EGVEVIYGD 48 (116)
T ss_dssp HHHHHHHHHTTSEEEEEESSHHHHHHHHH-TTSEEEES-
T ss_pred HHHHHHHHhCCCEEEEEECCcHHHHHHHh-ccccccccc
Confidence 34444444444 69999999999999999 798877744
No 52
>COG2082 CobH Precorrin isomerase [Coenzyme metabolism]
Probab=28.64 E-value=2.4e+02 Score=24.40 Aligned_cols=111 Identities=22% Similarity=0.242 Sum_probs=70.5
Q ss_pred CCCCCeEEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhhhHHH--HHhccCCCee---eeecCC
Q 029148 60 ALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVA--LRIAKDPRFE---RLPCTH 134 (198)
Q Consensus 60 ~~~~PY~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k~~~A--l~iak~~r~e---~~~C~H 134 (198)
+|+..=.|++|+|.+..-+....- ..++ ++.+++-+--..||-+--...|.+ ++++.. ++. .+--++
T Consensus 65 AL~~g~~Iv~Dv~MV~aGI~~~~l------~~~~-~v~c~i~d~~~~e~a~~~g~Trsaa~~~~~~~-~~~~~~ivvIGN 136 (210)
T COG2082 65 ALKAGCPIVVDVNMVAAGITRRRL------PALN-PVICYVDDPRVAELAKEEGITRSAAGMRLAAE-RGEGGAIVVIGN 136 (210)
T ss_pred HHHcCCcEEEccHHHHHhcccccc------cccC-cEEEEecCcchHHHHHhhCchHHHHHHHHHHH-hcCCceEEEEeC
Confidence 677888999999999987655432 2345 788888888888876532222322 222221 221 111112
Q ss_pred CCCCHHHHHHHHHhcC---CeEEEEe-----cCHHHHHHHhcCCCccEEEEeCc
Q 029148 135 KGTYADDCLVERVTQH---KCFIVAT-----CDRDLKRRIRKVPGVPIMYITRH 180 (198)
Q Consensus 135 ~g~~aDdCIv~~v~~~---~~yiVAT-----nD~~LrrrLRkipGVPIiyi~~~ 180 (198)
...|-.-+++++.+. -.++|++ +=.+-|+.|++ -+||-|.+++.
T Consensus 137 -APTAL~~l~elie~~~~~palvIg~PVGFv~AaesKe~L~~-~~iP~itv~G~ 188 (210)
T COG2082 137 -APTALFELLELIEEGGIKPALVIGVPVGFVGAAESKEALRE-SPIPYITVRGR 188 (210)
T ss_pred -CHHHHHHHHHHHHccCCCCcEEEEcCCcccchHHHHHHHHh-CCCCeEEEecC
Confidence 124566667777652 2467765 67899999999 56999999875
No 53
>KOG1475 consensus Ribosomal protein RPL1/RPL2/RL4L4 [RNA processing and modification]
Probab=28.51 E-value=46 Score=30.61 Aligned_cols=29 Identities=28% Similarity=0.552 Sum_probs=26.4
Q ss_pred CeEEEEecCHHHHHHHhcCCCccEEEEeC
Q 029148 151 KCFIVATCDRDLKRRIRKVPGVPIMYITR 179 (198)
Q Consensus 151 ~~yiVATnD~~LrrrLRkipGVPIiyi~~ 179 (198)
+-+||-++|.+.-+-+|.||||-+|.+.+
T Consensus 205 GPlVVy~Ed~~ivkAFRNIpGV~~~nV~~ 233 (363)
T KOG1475|consen 205 GPLVVYNEDNGIVKAFRNIPGVELMNVER 233 (363)
T ss_pred CCEEEEecCcchhhhhcCCCcceeechhh
Confidence 45899999999999999999999998765
No 54
>COG4634 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.73 E-value=1.2e+02 Score=23.80 Aligned_cols=39 Identities=21% Similarity=0.261 Sum_probs=31.3
Q ss_pred HHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCcc--EEEEeC
Q 029148 139 ADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVP--IMYITR 179 (198)
Q Consensus 139 aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVP--Iiyi~~ 179 (198)
.|.=|.+.+..++ +++.|.|.|.-..... -|-| |+.++-
T Consensus 36 ~D~EI~a~A~~~~-~iivTkDsDF~~la~~-~G~Ppki~wLr~ 76 (113)
T COG4634 36 TDIEIWAYARRNN-RIIVTKDSDFADLALT-LGSPPKIVWLRC 76 (113)
T ss_pred ccHHHHHHHHhcC-cEEEEcCccHHHHHHH-cCCCCeEEEEEe
Confidence 4888889998877 7999999999887777 5887 666553
No 55
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=27.31 E-value=1.2e+02 Score=22.22 Aligned_cols=34 Identities=24% Similarity=0.476 Sum_probs=27.9
Q ss_pred cCHHHHHHHhcCCCccEEEEeCceEEEecCCCcc
Q 029148 158 CDRDLKRRIRKVPGVPIMYITRHKYSIERLPEAT 191 (198)
Q Consensus 158 nD~~LrrrLRkipGVPIiyi~~~~~~lE~~s~~~ 191 (198)
.+..|-++|-.|+||--+|+..+-+.+++-+++.
T Consensus 35 ~~spLA~~Lf~i~gV~~Vf~~~dfItVtK~~~~~ 68 (87)
T PF08712_consen 35 SDSPLAQALFAIPGVKSVFIGDDFITVTKNPDAD 68 (87)
T ss_dssp TS-HHHHHHHTSTTEEEEEEETTEEEEEE-TTS-
T ss_pred ccCHHHHHhcCCCCEeEEEEECCEEEEeeCCCCC
Confidence 3567999999999999999999999999987653
No 56
>PRK09482 flap endonuclease-like protein; Provisional
Probab=26.75 E-value=96 Score=27.37 Aligned_cols=42 Identities=17% Similarity=0.239 Sum_probs=29.7
Q ss_pred CCCCCCHHHHHHHHHhc----CCeEEEEecCHHHHHHHhcCCCccEEE
Q 029148 133 THKGTYADDCLVERVTQ----HKCFIVATCDRDLKRRIRKVPGVPIMY 176 (198)
Q Consensus 133 ~H~g~~aDdCIv~~v~~----~~~yiVATnD~~LrrrLRkipGVPIiy 176 (198)
.+.|--|||.|-.++.+ ....+++|.|+||.+-+. ++|-+..
T Consensus 102 ~~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~--~~v~~~~ 147 (256)
T PRK09482 102 HADGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQLLS--PTIQIRD 147 (256)
T ss_pred ccCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccccCC--CCeEEEe
Confidence 34455799998888753 335789999999977665 4555543
No 57
>TIGR02181 GRX_bact Glutaredoxin, GrxC family. This family of glutaredoxins includes the E. coli protein GrxC (Grx3) which appears to have a secondary role in reducing ribonucleotide reductase (in the absence of GrxA) possibly indicating a role in the reduction of other protein disulfides.
Probab=26.73 E-value=99 Score=21.01 Aligned_cols=29 Identities=21% Similarity=0.263 Sum_probs=21.2
Q ss_pred EEEEecCHHHHHHHhc---CCCccEEEEeCce
Q 029148 153 FIVATCDRDLKRRIRK---VPGVPIMYITRHK 181 (198)
Q Consensus 153 yiVATnD~~LrrrLRk---ipGVPIiyi~~~~ 181 (198)
++-.+.|.+.+..+.+ ..+||+|++.+..
T Consensus 28 ~~di~~~~~~~~~~~~~~g~~~vP~i~i~g~~ 59 (79)
T TIGR02181 28 EIRVDGDPALRDEMMQRSGRRTVPQIFIGDVH 59 (79)
T ss_pred EEEecCCHHHHHHHHHHhCCCCcCEEEECCEE
Confidence 4556778878777764 3679999998753
No 58
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=26.65 E-value=69 Score=21.34 Aligned_cols=29 Identities=21% Similarity=0.244 Sum_probs=19.9
Q ss_pred EEEEecCHHHHHHHhcC---C-CccEEEEeCce
Q 029148 153 FIVATCDRDLKRRIRKV---P-GVPIMYITRHK 181 (198)
Q Consensus 153 yiVATnD~~LrrrLRki---p-GVPIiyi~~~~ 181 (198)
++-.++|.+++..+++. . +||.+++.+..
T Consensus 29 ~i~i~~~~~~~~~~~~~~~~~~~vP~v~i~g~~ 61 (75)
T cd03418 29 EIDVDGDPALREEMINRSGGRRTVPQIFIGDVH 61 (75)
T ss_pred EEECCCCHHHHHHHHHHhCCCCccCEEEECCEE
Confidence 45556777777776532 3 89999998753
No 59
>PF12813 XPG_I_2: XPG domain containing
Probab=26.28 E-value=73 Score=27.69 Aligned_cols=26 Identities=27% Similarity=0.217 Sum_probs=22.8
Q ss_pred CCHHHHHHHHHhcCCeEEEEecCHHHH
Q 029148 137 TYADDCLVERVTQHKCFIVATCDRDLK 163 (198)
Q Consensus 137 ~~aDdCIv~~v~~~~~yiVATnD~~Lr 163 (198)
.-||.=+..+|.+++| .|.|+|-||-
T Consensus 28 ~EAD~~~A~~A~~~~~-~VLt~DSDf~ 53 (246)
T PF12813_consen 28 GEADRECAALARKWGC-PVLTNDSDFL 53 (246)
T ss_pred ccchHHHHHHHHHcCC-eEEccCCCEE
Confidence 3689999999999998 9999999874
No 60
>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains. Members of the UPF0278 family are uncharacterised and about 200 amino acids in length.; PDB: 2LCQ_A.
Probab=25.25 E-value=66 Score=27.75 Aligned_cols=46 Identities=13% Similarity=0.095 Sum_probs=24.3
Q ss_pred CHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeCceEEEe
Q 029148 138 YADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIE 185 (198)
Q Consensus 138 ~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~~~~~lE 185 (198)
-+|=-++-++.+.+ ..|.|+|..+++...+ -||-+|--..=.-.||
T Consensus 155 ~~D~dvl~LA~El~-a~lvt~D~gi~~~A~~-lGi~~i~~~~F~~~Le 200 (205)
T PF08745_consen 155 REDIDVLLLALELD-AVLVTDDYGIQNWAEK-LGIRFIDARDFPRMLE 200 (205)
T ss_dssp HHHHHHHHHHHHHT---EE---HHHHHHHHH-TT--EE----------
T ss_pred hHhHHHHHHHHHcC-CEEEeCCHhHHHHHHH-CCCEEEeccccccccc
Confidence 46777888888877 5999999999999999 6988765444333333
No 61
>smart00475 53EXOc 5'-3' exonuclease.
Probab=25.18 E-value=1.2e+02 Score=26.61 Aligned_cols=33 Identities=21% Similarity=0.278 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHHHhc----CCeEEEEecCHHHHHHHh
Q 029148 135 KGTYADDCLVERVTQ----HKCFIVATCDRDLKRRIR 167 (198)
Q Consensus 135 ~g~~aDdCIv~~v~~----~~~yiVATnD~~LrrrLR 167 (198)
.|--|||.|-.++.+ ....+|+|.|+||..-+.
T Consensus 104 ~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~ 140 (259)
T smart00475 104 EGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVS 140 (259)
T ss_pred CCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCC
Confidence 445799999888864 245799999999998764
No 62
>COG5611 Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only]
Probab=24.34 E-value=3.7e+02 Score=21.49 Aligned_cols=99 Identities=23% Similarity=0.233 Sum_probs=62.1
Q ss_pred EEeehHHHHHHHH--cCCC-hHHhHHHhhcccceEeecHHHHHHHHH-hhhhh-------HHHHH-hccCCCeeeeecCC
Q 029148 67 VLVDTNFINFSIQ--NKLD-LEKGMMDCLYAKCTPCITDCVMAELEK-LGQKY-------RVALR-IAKDPRFERLPCTH 134 (198)
Q Consensus 67 VLvDtNFl~~~i~--~kld-l~~~L~~~L~~k~~~~iT~CVi~ELek-Lg~k~-------~~Al~-iak~~r~e~~~C~H 134 (198)
|.+|||.|..-+. .++. ..+|+-+-+.-+.+.+|++-|+-|+-. |...| ...+. +..+..| .-+|
T Consensus 2 ig~DTnvL~r~l~eddkvq~ka~Q~f~~~s~~~k~fI~~~vliE~V~vL~~~y~~~rE~i~~VIetll~~~~f---~V~~ 78 (130)
T COG5611 2 IGLDTNVLLRFLSEDDKVQTKAEQFFEELSQKGKLFIPEEVLIELVYVLEHGYKWEREDIYEVIETLLNDELF---NVEL 78 (130)
T ss_pred ccchhHHHHHHHhhhhhHHHHHHHHHHhcCcCCCccchHHHHHHHHHHHHhcchhhHHHHHHHHHHHhccccc---eecc
Confidence 5799999966543 3333 245666667777899999999999854 32222 22233 4443233 2345
Q ss_pred CC-------------CCHHHHHHHHHhc-CCeEEEEecCHHHHHHHhc
Q 029148 135 KG-------------TYADDCLVERVTQ-HKCFIVATCDRDLKRRIRK 168 (198)
Q Consensus 135 ~g-------------~~aDdCIv~~v~~-~~~yiVATnD~~LrrrLRk 168 (198)
++ ..-.|||+..-++ .+|==+.|-|+.+.+...+
T Consensus 79 ~d~i~~A~~~Y~k~kadF~D~li~~~g~~~g~~e~vTFdk~~~~~~~~ 126 (130)
T COG5611 79 KDFIREAIKLYSKRKADFLDCLISVKGKKMGIKEVVTFDKRFKKLGFK 126 (130)
T ss_pred hHHHHHHHHHHHhccccHHHHHHHhhhhhcCceeeEeecHHHHHHhhh
Confidence 42 1346898877554 5666789999998876543
No 63
>TIGR00411 redox_disulf_1 small redox-active disulfide protein 1. This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.
Probab=23.76 E-value=1.2e+02 Score=20.23 Aligned_cols=30 Identities=10% Similarity=0.053 Sum_probs=19.9
Q ss_pred EecCHHHHHHHhcCCCccEEEEeCceEEEecC
Q 029148 156 ATCDRDLKRRIRKVPGVPIMYITRHKYSIERL 187 (198)
Q Consensus 156 ATnD~~LrrrLRkipGVPIiyi~~~~~~lE~~ 187 (198)
..+|+++-++.. +.|+|.+++ ++...+...
T Consensus 39 ~~~~~~~~~~~~-v~~vPt~~~-~g~~~~~G~ 68 (82)
T TIGR00411 39 VMENPQKAMEYG-IMAVPAIVI-NGDVEFIGA 68 (82)
T ss_pred CccCHHHHHHcC-CccCCEEEE-CCEEEEecC
Confidence 346777776654 589999998 444455443
No 64
>COG0695 GrxC Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones]
Probab=23.13 E-value=1.3e+02 Score=21.39 Aligned_cols=29 Identities=17% Similarity=0.249 Sum_probs=22.6
Q ss_pred eEEEEecCH--HHHHHHhcC---CCccEEEEeCc
Q 029148 152 CFIVATCDR--DLKRRIRKV---PGVPIMYITRH 180 (198)
Q Consensus 152 ~yiVATnD~--~LrrrLRki---pGVPIiyi~~~ 180 (198)
.++..+.|. +.+..+++. ..||+|++.+.
T Consensus 29 ~~i~~~~~~~~~~~~~~~~~~g~~tvP~I~i~~~ 62 (80)
T COG0695 29 EEIDVDDDEPEEAREMVKRGKGQRTVPQIFIGGK 62 (80)
T ss_pred EEEEecCCcHHHHHHHHHHhCCCCCcCEEEECCE
Confidence 367777777 777777765 57999999985
No 65
>cd08556 GDPD Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins. The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which lacks the GDPD-I region. Members in this family mainly consist of a large family of prokaryotic and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), and a number of uncharacterized homologs. Sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria are also included in this family. GDPD plays an essential role in glycerol metabolism and catalyzes the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcoho
Probab=22.94 E-value=1.9e+02 Score=22.44 Aligned_cols=45 Identities=16% Similarity=0.287 Sum_probs=34.9
Q ss_pred HHHHHHHHHhcC---CeEEEEecCHHHHHHHhcC-CCccEEEEeCceEE
Q 029148 139 ADDCLVERVTQH---KCFIVATCDRDLKRRIRKV-PGVPIMYITRHKYS 183 (198)
Q Consensus 139 aDdCIv~~v~~~---~~yiVATnD~~LrrrLRki-pGVPIiyi~~~~~~ 183 (198)
.-+.+++++.++ ++.++.+-|.+..+++++. |++|+.++..+...
T Consensus 77 ~~~~l~~~i~~~~~~~~v~i~s~~~~~l~~~~~~~p~~~~~~~~~~~~~ 125 (189)
T cd08556 77 LEAKVAELLREYGLEERVVVSSFDHEALRALKELDPEVPTGLLVDKPPL 125 (189)
T ss_pred HHHHHHHHHHHcCCcCCEEEEeCCHHHHHHHHHhCCCCcEEEEeecCcc
Confidence 456677777663 5689999999999999975 99999998875433
No 66
>cd08568 GDPD_TmGDE_like Glycerophosphodiester phosphodiesterase domain of Thermotoga maritime and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermotoga maritime glycerophosphodiester phosphodiesterase (TmGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. TmGDE exists as a monomer that might be the biologically relevant form.
Probab=22.85 E-value=4.4e+02 Score=21.78 Aligned_cols=80 Identities=19% Similarity=0.224 Sum_probs=53.5
Q ss_pred eecHHHHHHHHHhh------hhhHHHHHhccCCCeeeeecCCCCCCHHHHHHHHHhcC---CeEEEEecCHHHHHHHhc-
Q 029148 99 CITDCVMAELEKLG------QKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQH---KCFIVATCDRDLKRRIRK- 168 (198)
Q Consensus 99 ~iT~CVi~ELekLg------~k~~~Al~iak~~r~e~~~C~H~g~~aDdCIv~~v~~~---~~yiVATnD~~LrrrLRk- 168 (198)
.|.+.-++||.+|. +.+...|..+.+ +. .+.++-|....-+-+++++.++ +..+|.+-|.+.-+++|+
T Consensus 60 ~v~~~t~~eL~~l~~~g~~iPtL~evl~~~~~-~~-~l~iEiK~~~~~~~~~~~l~~~~~~~~v~i~SF~~~~l~~~~~~ 137 (226)
T cd08568 60 KVKELTYKELKKLHPGGELIPTLEEVFRALPN-DA-IINVEIKDIDAVEPVLEIVEKFNALDRVIFSSFNHDALRELRKL 137 (226)
T ss_pred eeecCCHHHHhhCCCCCCcCCCHHHHHHhcCC-Cc-EEEEEECCccHHHHHHHHHHHcCCCCcEEEEECCHHHHHHHHHh
Confidence 46677778888772 235566666653 11 2444555444456677777653 357999999999999987
Q ss_pred CCCccEEEEeCc
Q 029148 169 VPGVPIMYITRH 180 (198)
Q Consensus 169 ipGVPIiyi~~~ 180 (198)
-|.+|+.++...
T Consensus 138 ~p~~~~~~l~~~ 149 (226)
T cd08568 138 DPDAKVGLLIGE 149 (226)
T ss_pred CCCCcEEEEeec
Confidence 599999988743
No 67
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=22.75 E-value=2.6e+02 Score=24.93 Aligned_cols=42 Identities=12% Similarity=0.050 Sum_probs=31.3
Q ss_pred CHHHHHHHHHhcC----CeEEEEecCHHHHHHHhcCCCccEEEEeCc
Q 029148 138 YADDCLVERVTQH----KCFIVATCDRDLKRRIRKVPGVPIMYITRH 180 (198)
Q Consensus 138 ~aDdCIv~~v~~~----~~yiVATnD~~LrrrLRkipGVPIiyi~~~ 180 (198)
+--..|++.+... ....|.||.+++..++++ .|||+.++...
T Consensus 105 ~nl~al~~~~~~~~l~~~i~~visn~~~~~~~A~~-~gIp~~~~~~~ 150 (289)
T PRK13010 105 HCLNDLLYRWRMGELDMDIVGIISNHPDLQPLAVQ-HDIPFHHLPVT 150 (289)
T ss_pred ccHHHHHHHHHCCCCCcEEEEEEECChhHHHHHHH-cCCCEEEeCCC
Confidence 3355666666542 345788999999999998 79999998654
No 68
>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=22.51 E-value=3e+02 Score=22.48 Aligned_cols=40 Identities=15% Similarity=0.239 Sum_probs=26.7
Q ss_pred HHHHHHHHhcC-CeEEEEecCHHHHHHHhcCCCccEEEEeCc
Q 029148 140 DDCLVERVTQH-KCFIVATCDRDLKRRIRKVPGVPIMYITRH 180 (198)
Q Consensus 140 DdCIv~~v~~~-~~yiVATnD~~LrrrLRkipGVPIiyi~~~ 180 (198)
.+++-.+.... .-.|+.+.|.++.+.+.. .|+|++++.+.
T Consensus 40 ~~~~~~l~~~~vdGiI~~~~~~~~~~~l~~-~~~PvV~~~~~ 80 (265)
T cd01543 40 QEPLRWLKDWQGDGIIARIDDPEMAEALQK-LGIPVVDVSGS 80 (265)
T ss_pred hhhhhhccccccceEEEECCCHHHHHHHhh-CCCCEEEEeCc
Confidence 45554443321 225666777778788887 69999999875
No 69
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=22.12 E-value=68 Score=28.42 Aligned_cols=36 Identities=22% Similarity=0.097 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEE
Q 029148 137 TYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYI 177 (198)
Q Consensus 137 ~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi 177 (198)
..||+.+..++.+..++.|+|+|.|+-. -|.|.++.
T Consensus 149 ~EAdaq~a~l~~~g~v~~i~S~DsD~l~-----fg~~~vi~ 184 (316)
T cd00128 149 YEAEAQCAYLAKKGLVDAIITEDSDLLL-----FGAPRVYR 184 (316)
T ss_pred cCHHHHHHHHHhCCCeeEEEecCCCeee-----ecCceEEE
Confidence 3699999999888777899999999765 36666554
No 70
>PHA00439 exonuclease
Probab=21.74 E-value=93 Score=28.07 Aligned_cols=32 Identities=25% Similarity=0.345 Sum_probs=24.1
Q ss_pred CCCCCHHHHHHHHHhc---CC--eEEEEecCHHHHHH
Q 029148 134 HKGTYADDCLVERVTQ---HK--CFIVATCDRDLKRR 165 (198)
Q Consensus 134 H~g~~aDdCIv~~v~~---~~--~yiVATnD~~Lrrr 165 (198)
..|--|||+|-.++++ .+ ..+|+|.|+||.+-
T Consensus 116 ~~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~QL 152 (286)
T PHA00439 116 EPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTI 152 (286)
T ss_pred eCCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhhc
Confidence 3456799999888753 22 46899999998875
No 71
>PRK04358 hypothetical protein; Provisional
Probab=21.27 E-value=1e+02 Score=26.85 Aligned_cols=49 Identities=22% Similarity=0.240 Sum_probs=32.3
Q ss_pred eEEEeehHHHHHH-HHc--C-CChHHhHHHhhc----c----cceEeecHHHHHHHHHhhh
Q 029148 65 YRVLVDTNFINFS-IQN--K-LDLEKGMMDCLY----A----KCTPCITDCVMAELEKLGQ 113 (198)
Q Consensus 65 Y~VLvDtNFl~~~-i~~--k-ldl~~~L~~~L~----~----k~~~~iT~CVi~ELekLg~ 113 (198)
-+.++||+.+..+ +.. + =|+.+.+...|. + ...+|+|..|.+||...-.
T Consensus 4 qrfVLDTS~fT~p~vr~~fg~e~l~ea~~~~l~Lia~arl~l~is~YmPpSVy~El~~f~~ 64 (217)
T PRK04358 4 QRFVLDTSAFTDPDVREQFGVEDLEEAVEKFLDLIARARLKLGISCYMPPSVYKELRGFLE 64 (217)
T ss_pred eEEEeeccccCCHHHHHHcCCCCHHHHHHHHHHHHHHhhhccCceEEcCHHHHHHHHHHHH
Confidence 3678999877332 233 3 245555555443 2 5678999999999998744
No 72
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.50 E-value=2e+02 Score=19.09 Aligned_cols=25 Identities=20% Similarity=0.375 Sum_probs=19.0
Q ss_pred EEEEecCHH-----HHHHHhcCCCccEEEE
Q 029148 153 FIVATCDRD-----LKRRIRKVPGVPIMYI 177 (198)
Q Consensus 153 yiVATnD~~-----LrrrLRkipGVPIiyi 177 (198)
+.|.+.|.+ |.++||++|||.=+++
T Consensus 45 ~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 45 ISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 567777765 6789999999976654
No 73
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein. Members of this family are periplasmic (when in Gram-negative bacteria) binding proteins for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter.
Probab=20.37 E-value=4.5e+02 Score=22.42 Aligned_cols=59 Identities=7% Similarity=0.125 Sum_probs=34.6
Q ss_pred hccCCCeeeeecCCCCCC--HHHHHHHHHhcC-CeEEEEecCH----HHHHHHhcCCCccEEEEeCc
Q 029148 121 IAKDPRFERLPCTHKGTY--ADDCLVERVTQH-KCFIVATCDR----DLKRRIRKVPGVPIMYITRH 180 (198)
Q Consensus 121 iak~~r~e~~~C~H~g~~--aDdCIv~~v~~~-~~yiVATnD~----~LrrrLRkipGVPIiyi~~~ 180 (198)
.|++..++.+-|++.+.. ..+.|-.+..+. ...|++..|. +.-+++++ .|+|++.+.+.
T Consensus 23 ~a~~~g~~v~~~~~~~~~~~q~~~i~~l~~~~vDgIIi~~~~~~~~~~~l~~~~~-~~iPvV~~d~~ 88 (302)
T TIGR02634 23 AAESLGAKVFVQSANGNEAKQISQIENLIARGVDVLVIIPQNGQVLSNAVQEAKD-EGIKVVAYDRL 88 (302)
T ss_pred HHHhcCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhHHHHHHHHHHH-CCCeEEEecCc
Confidence 344434666667664432 235555555442 4467776663 44456677 79999999763
No 74
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=20.23 E-value=2.2e+02 Score=23.15 Aligned_cols=41 Identities=15% Similarity=0.356 Sum_probs=28.5
Q ss_pred HHHHHHHHHhcC-CeEEEEecCH----HHHHHHhcCCCccEEEEeCc
Q 029148 139 ADDCLVERVTQH-KCFIVATCDR----DLKRRIRKVPGVPIMYITRH 180 (198)
Q Consensus 139 aDdCIv~~v~~~-~~yiVATnD~----~LrrrLRkipGVPIiyi~~~ 180 (198)
..++|-+.+.++ ...||.+.|. ++-+++.. .||||+.+.+.
T Consensus 44 q~~~i~~~i~~~~d~Iiv~~~~~~~~~~~l~~~~~-~gIpvv~~d~~ 89 (257)
T PF13407_consen 44 QIEQIEQAISQGVDGIIVSPVDPDSLAPFLEKAKA-AGIPVVTVDSD 89 (257)
T ss_dssp HHHHHHHHHHTTESEEEEESSSTTTTHHHHHHHHH-TTSEEEEESST
T ss_pred HHHHHHHHHHhcCCEEEecCCCHHHHHHHHHHHhh-cCceEEEEecc
Confidence 345666666554 4456776775 56677887 79999998776
No 75
>PHA02567 rnh RnaseH; Provisional
Probab=20.04 E-value=1.1e+02 Score=27.92 Aligned_cols=40 Identities=20% Similarity=0.307 Sum_probs=29.8
Q ss_pred CCCCHHHHHHHHHhc----CCeEEEEecCHHHHHHHhcCCCccEE
Q 029148 135 KGTYADDCLVERVTQ----HKCFIVATCDRDLKRRIRKVPGVPIM 175 (198)
Q Consensus 135 ~g~~aDdCIv~~v~~----~~~yiVATnD~~LrrrLRkipGVPIi 175 (198)
.|--|||.|-.++++ ....+|+|.|++|.+-+.. +||-+.
T Consensus 127 ~g~EADDvIgTLA~k~~~~g~~VvIvS~DKDl~QLv~~-~~v~~~ 170 (304)
T PHA02567 127 DKAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQLHKY-PGVKQW 170 (304)
T ss_pred CCccHHHHHHHHHHHHHhCCCcEEEEeCCCChhhccCC-CCeEEe
Confidence 455799999888753 2357999999999988864 566544
Done!