Query 041752
Match_columns 72
No_of_seqs 102 out of 896
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 10:15:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041752.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041752hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA00280 putative NHN endonucl 99.9 1.8E-22 4E-27 128.8 7.1 69 1-72 49-118 (121)
2 cd00018 AP2 DNA-binding domain 99.9 3.6E-22 7.8E-27 112.9 6.7 54 19-72 1-54 (61)
3 smart00380 AP2 DNA-binding dom 99.8 3.8E-21 8.1E-26 110.0 7.1 53 20-72 1-53 (64)
4 PF00847 AP2: AP2 domain; Int 99.5 2E-14 4.3E-19 79.4 6.2 52 19-70 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 92.8 0.76 1.6E-05 24.1 5.5 38 31-68 1-42 (46)
6 PHA02601 int integrase; Provis 87.2 1.2 2.7E-05 30.9 4.2 42 23-65 2-44 (333)
7 PF08846 DUF1816: Domain of un 86.5 2.3 5E-05 24.7 4.4 38 31-68 9-46 (68)
8 PF05036 SPOR: Sporulation rel 85.0 0.66 1.4E-05 25.4 1.6 25 40-64 41-65 (76)
9 PF13356 DUF4102: Domain of un 84.7 5.1 0.00011 23.3 5.4 43 25-67 28-74 (89)
10 PRK09692 integrase; Provisiona 82.0 6.5 0.00014 28.5 6.1 42 24-65 33-80 (413)
11 cd00801 INT_P4 Bacteriophage P 79.5 7.5 0.00016 26.6 5.5 38 30-67 10-49 (357)
12 PF08471 Ribonuc_red_2_N: Clas 77.5 3.3 7.1E-05 25.5 2.8 21 47-67 70-90 (93)
13 PF14112 DUF4284: Domain of un 73.3 2.6 5.7E-05 26.5 1.8 15 43-57 2-16 (122)
14 PF09003 Phage_integ_N: Bacter 62.3 21 0.00045 21.1 3.9 30 36-67 31-60 (75)
15 PF13773 DUF4170: Domain of un 62.0 9.1 0.0002 22.4 2.3 21 46-66 28-48 (69)
16 COG2185 Sbm Methylmalonyl-CoA 61.9 7.2 0.00016 25.6 2.1 17 43-59 42-58 (143)
17 PF09954 DUF2188: Uncharacteri 60.0 27 0.00057 19.0 4.5 39 24-66 3-41 (62)
18 COG0197 RplP Ribosomal protein 57.1 22 0.00048 23.5 3.8 34 32-68 96-129 (146)
19 PF12752 SUZ: SUZ domain; Int 56.5 18 0.00038 19.9 2.8 23 49-71 36-58 (59)
20 TIGR01164 rplP_bact ribosomal 52.8 41 0.0009 21.3 4.4 33 31-67 91-124 (126)
21 PF11453 DUF2950: Protein of u 50.8 16 0.00034 26.5 2.5 17 49-65 3-19 (271)
22 PRK09203 rplP 50S ribosomal pr 50.5 42 0.0009 21.6 4.2 33 31-67 92-125 (138)
23 PF14882 GHL12: Hypothetical g 46.5 15 0.00033 20.0 1.5 11 49-59 39-49 (53)
24 CHL00044 rpl16 ribosomal prote 45.5 45 0.00097 21.5 3.8 33 31-67 92-125 (135)
25 PF11132 SplA: Transcriptional 44.3 20 0.00044 21.2 1.9 15 48-62 58-72 (75)
26 PRK10927 essential cell divisi 40.2 63 0.0014 24.0 4.2 23 43-65 284-306 (319)
27 PF14032 PknH_C: PknH-like ext 39.2 25 0.00055 22.6 1.9 23 46-68 86-108 (189)
28 cd08001 WGR_PARP1_like WGR dom 36.4 79 0.0017 18.9 3.7 26 44-69 56-81 (104)
29 COG3010 NanE Putative N-acetyl 35.7 31 0.00068 24.4 2.0 19 45-63 184-202 (229)
30 cd07996 WGR_MMR_like WGR domai 35.2 48 0.001 18.3 2.5 17 49-65 48-64 (74)
31 PF08178 GnsAB: GnsA/GnsB fami 34.4 17 0.00037 20.3 0.4 13 26-38 26-38 (54)
32 COG3087 FtsN Cell division pro 33.5 83 0.0018 22.7 3.9 22 43-64 229-250 (264)
33 PF07494 Reg_prop: Two compone 32.9 13 0.00029 16.7 -0.1 8 44-51 17-24 (24)
34 KOG3422 Mitochondrial ribosoma 32.6 1.2E+02 0.0025 21.5 4.4 36 31-69 133-169 (221)
35 cd01433 Ribosomal_L16_L10e Rib 32.6 1.1E+02 0.0024 18.6 4.0 34 31-67 71-105 (112)
36 cd07997 WGR_PARP WGR domain of 32.2 71 0.0015 19.1 3.0 24 41-65 52-75 (102)
37 TIGR00279 L10e ribosomal prote 31.9 64 0.0014 21.9 3.0 34 31-67 121-156 (172)
38 PF00252 Ribosomal_L16: Riboso 31.6 1.2E+02 0.0025 19.2 4.0 34 32-68 92-126 (133)
39 PF14259 RRM_6: RNA recognitio 31.3 24 0.00052 18.7 0.7 18 47-64 43-60 (70)
40 PF07978 NIPSNAP: NIPSNAP ; I 30.9 84 0.0018 17.9 3.1 34 29-64 36-69 (102)
41 PF10729 CedA: Cell division a 30.8 1.2E+02 0.0026 17.9 4.1 37 19-58 31-67 (80)
42 PRK11901 hypothetical protein; 30.7 80 0.0017 23.5 3.5 16 47-62 288-303 (327)
43 PF12286 DUF3622: Protein of u 30.5 1.2E+02 0.0026 17.8 4.2 29 29-57 15-47 (71)
44 PRK12757 cell division protein 30.1 1.2E+02 0.0025 21.8 4.2 23 43-65 221-243 (256)
45 cd00590 RRM RRM (RNA recogniti 28.6 46 0.00099 16.7 1.6 19 45-63 42-60 (74)
46 TIGR00125 cyt_tran_rel cytidyl 28.3 71 0.0015 16.7 2.3 24 45-68 3-26 (66)
47 cd07998 WGR_DNA_ligase WGR dom 27.9 83 0.0018 18.5 2.7 36 29-64 25-64 (77)
48 PF05406 WGR: WGR domain; Int 27.8 67 0.0014 18.2 2.3 16 49-64 51-66 (81)
49 PF07453 NUMOD1: NUMOD1 domain 26.9 35 0.00077 16.5 0.8 15 47-61 13-27 (37)
50 PRK10672 rare lipoprotein A; P 26.8 90 0.0019 23.5 3.3 22 44-65 328-349 (361)
51 cd08002 WGR_PARP3_like WGR dom 26.5 91 0.002 18.9 2.8 26 41-66 49-74 (100)
52 TIGR02223 ftsN cell division p 26.5 93 0.002 22.6 3.2 23 43-65 266-288 (298)
53 cd03070 PDI_b_ERp44 PDIb famil 25.7 34 0.00073 20.6 0.7 28 41-68 15-43 (91)
54 PF07358 DUF1482: Protein of u 25.7 61 0.0013 18.2 1.7 24 42-65 15-38 (57)
55 cd07994 WGR WGR domain. The WG 25.3 1E+02 0.0022 17.4 2.7 17 49-65 48-64 (73)
56 PF06279 DUF1033: Protein of u 25.0 79 0.0017 20.2 2.4 23 47-69 27-49 (120)
57 PRK04199 rpl10e 50S ribosomal 24.1 1.1E+02 0.0025 20.6 3.1 34 31-67 121-156 (172)
58 smart00773 WGR Proposed nuclei 23.5 1.1E+02 0.0025 17.3 2.7 17 49-65 54-70 (84)
59 PF13893 RRM_5: RNA recognitio 23.5 68 0.0015 16.4 1.6 14 49-62 27-40 (56)
60 PF12434 Malate_DH: Malate deh 23.0 1.1E+02 0.0023 14.8 2.3 19 51-69 8-26 (28)
61 PF06236 MelC1: Tyrosinase co- 22.9 67 0.0015 20.7 1.8 12 48-59 98-109 (125)
62 PF07384 DUF1497: Protein of u 21.9 92 0.002 17.3 1.9 19 47-65 1-19 (59)
63 PF00076 RRM_1: RNA recognitio 21.4 87 0.0019 16.0 1.8 17 47-63 43-59 (70)
64 smart00360 RRM RNA recognition 21.2 73 0.0016 15.6 1.5 15 48-62 43-57 (71)
65 COG3266 DamX Uncharacterized p 20.9 1.4E+02 0.003 21.9 3.2 23 40-62 244-269 (292)
66 PF00352 TBP: Transcription fa 20.8 1.8E+02 0.004 16.6 5.6 46 19-67 36-82 (86)
67 COG3831 Uncharacterized conser 20.8 1.2E+02 0.0027 18.2 2.5 18 46-63 41-58 (85)
68 cd08355 Glo_EDI_BRP_like_14 Th 20.8 1.4E+02 0.0029 17.2 2.7 25 25-50 98-122 (122)
No 1
>PHA00280 putative NHN endonuclease
Probab=99.87 E-value=1.8e-22 Score=128.81 Aligned_cols=69 Identities=14% Similarity=0.178 Sum_probs=64.1
Q ss_pred CCcccccccccccCCCCCCCeeeeE-ECCCCcEEEEeecCCCceEEecCCCCCHHHHHHHHHHHHHhhcCCCC
Q 041752 1 LSSAKAEDSSYKAAHDEGTEKKTLR-ARPWGKWAAETRDRYKGICIWLGIFNITKEAARAYAEAAKHIRSNKA 72 (72)
Q Consensus 1 ~~~~~~n~~n~~~~~~~~s~~~GV~-~~~~gkw~A~i~~~~~~k~~~LG~f~t~eeAa~AYd~aa~~~~g~~A 72 (72)
++|.++|++|++..++|+|||+||+ ....|||+|+|. ++||.++||.|+++|+|+.||+ ++.+|||+||
T Consensus 49 ~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~--~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa 118 (121)
T PHA00280 49 LALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVT--AEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFA 118 (121)
T ss_pred hcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEE--ECCEEEEcCCCCCHHHHHHHHH-HHHHHhhccc
Confidence 4789999999999999999999998 567799999999 7999999999999999999997 7789999987
No 2
>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.
Probab=99.87 E-value=3.6e-22 Score=112.95 Aligned_cols=54 Identities=50% Similarity=0.917 Sum_probs=49.8
Q ss_pred CCeeeeEECCCCcEEEEeecCCCceEEecCCCCCHHHHHHHHHHHHHhhcCCCC
Q 041752 19 TEKKTLRARPWGKWAAETRDRYKGICIWLGIFNITKEAARAYAEAAKHIRSNKA 72 (72)
Q Consensus 19 s~~~GV~~~~~gkw~A~i~~~~~~k~~~LG~f~t~eeAa~AYd~aa~~~~g~~A 72 (72)
|+|+||+++++|+|+|+|+++..|+.+|||+|+|+|||+.|||.+++++||.+|
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a 54 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSA 54 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCcc
Confidence 789999988889999999965559999999999999999999999999999764
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.85 E-value=3.8e-21 Score=109.97 Aligned_cols=53 Identities=51% Similarity=0.925 Sum_probs=49.8
Q ss_pred CeeeeEECCCCcEEEEeecCCCceEEecCCCCCHHHHHHHHHHHHHhhcCCCC
Q 041752 20 EKKTLRARPWGKWAAETRDRYKGICIWLGIFNITKEAARAYAEAAKHIRSNKA 72 (72)
Q Consensus 20 ~~~GV~~~~~gkw~A~i~~~~~~k~~~LG~f~t~eeAa~AYd~aa~~~~g~~A 72 (72)
.|+||+++++|+|+|+|+++..++.++||+|+|+|||+.|||.+++++||+++
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a 53 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSA 53 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCcc
Confidence 48999988899999999987799999999999999999999999999999764
No 4
>PF00847 AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-related genes transcriptional activator binds to the GCC-box pathogenesis-related promoter element and activates the plant's defence genes. Ethylene, chemically the simplest plant hormone, participates in a number of stress responses and developmental processes: e.g., fruit ripening, inhibition of stem and root elongation, promotion of seed germination and flowering, senescence of leaves and flowers, and sex determination []. DNA sequence elements that confer ethylene responsiveness have been shown to contain two 11bp GCC boxes, which are necessary and sufficient for transcriptional control by ethylene. Ethylene responsive element binding proteins (EREBPs) have now been identified in a variety of plants. The proteins share a similar domain of around 59 amino acids, which interacts directly with the GCC box in the ERE.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3IGM_A 3GCC_A 1GCC_A 2GCC_A.
Probab=99.55 E-value=2e-14 Score=79.38 Aligned_cols=52 Identities=27% Similarity=0.380 Sum_probs=45.4
Q ss_pred CCeeeeE-ECCCCcEEEEeecCC-C--ceEEecCCCCCHHHHHHHHHHHHHhhcCC
Q 041752 19 TEKKTLR-ARPWGKWAAETRDRY-K--GICIWLGIFNITKEAARAYAEAAKHIRSN 70 (72)
Q Consensus 19 s~~~GV~-~~~~gkw~A~i~~~~-~--~k~~~LG~f~t~eeAa~AYd~aa~~~~g~ 70 (72)
|+|+||+ ++..++|+|+|.++. + ++.++||.|++++||+.+++++++.++||
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSENGKRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCCTTEEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEcccCcccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 7899998 667899999999632 2 49999999999999999999999999986
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=92.79 E-value=0.76 Score=24.07 Aligned_cols=38 Identities=24% Similarity=0.237 Sum_probs=29.1
Q ss_pred cEEEEee--cCCCc--eEEecCCCCCHHHHHHHHHHHHHhhc
Q 041752 31 KWAAETR--DRYKG--ICIWLGIFNITKEAARAYAEAAKHIR 68 (72)
Q Consensus 31 kw~A~i~--~~~~~--k~~~LG~f~t~eeAa~AYd~aa~~~~ 68 (72)
+|...|. ++..| ++++-+-|.|..||..+...+...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5888883 44455 66678999999999999988776653
No 6
>PHA02601 int integrase; Provisional
Probab=87.20 E-value=1.2 Score=30.93 Aligned_cols=42 Identities=24% Similarity=0.170 Sum_probs=29.2
Q ss_pred eeEECCCCcEEEEeec-CCCceEEecCCCCCHHHHHHHHHHHHH
Q 041752 23 TLRARPWGKWAAETRD-RYKGICIWLGIFNITKEAARAYAEAAK 65 (72)
Q Consensus 23 GV~~~~~gkw~A~i~~-~~~~k~~~LG~f~t~eeAa~AYd~aa~ 65 (72)
+|.+.++|+|.+++.. ...|+++.. +|.|..||....+....
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~~-~f~tk~eA~~~~~~~~~ 44 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIRK-RFATKGEALAFENYTMA 44 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhhh-hhcCHHHHHHHHHHHHH
Confidence 4667788999999974 234776653 69999988765554433
No 7
>PF08846 DUF1816: Domain of unknown function (DUF1816); InterPro: IPR014945 Q4C9H3 from SWISSPROT is associated with the IPR008213 from INTERPRO domain suggesting this protein could have a role in phycobilisomes.
Probab=86.46 E-value=2.3 Score=24.70 Aligned_cols=38 Identities=18% Similarity=0.343 Sum_probs=29.0
Q ss_pred cEEEEeecCCCceEEecCCCCCHHHHHHHHHHHHHhhc
Q 041752 31 KWAAETRDRYKGICIWLGIFNITKEAARAYAEAAKHIR 68 (72)
Q Consensus 31 kw~A~i~~~~~~k~~~LG~f~t~eeAa~AYd~aa~~~~ 68 (72)
.|=++|....-.-..|-|-|+|.+||..+-.-....|-
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 37799986445578899999999999988765555443
No 8
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=84.97 E-value=0.66 Score=25.37 Aligned_cols=25 Identities=20% Similarity=0.131 Sum_probs=20.3
Q ss_pred CCceEEecCCCCCHHHHHHHHHHHH
Q 041752 40 YKGICIWLGIFNITKEAARAYAEAA 64 (72)
Q Consensus 40 ~~~k~~~LG~f~t~eeAa~AYd~aa 64 (72)
..--++.+|.|+|.+||..+.....
T Consensus 41 ~~~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 41 GPWYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp TTCEEEEECCECTCCHHHHHHHHHH
T ss_pred CceEEEEECCCCCHHHHHHHHHHHh
Confidence 4556788999999999998887665
No 9
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=84.68 E-value=5.1 Score=23.31 Aligned_cols=43 Identities=26% Similarity=0.170 Sum_probs=26.2
Q ss_pred EECCCCc--EEEEeecCCCceEEecCCCCC--HHHHHHHHHHHHHhh
Q 041752 25 RARPWGK--WAAETRDRYKGICIWLGIFNI--TKEAARAYAEAAKHI 67 (72)
Q Consensus 25 ~~~~~gk--w~A~i~~~~~~k~~~LG~f~t--~eeAa~AYd~aa~~~ 67 (72)
+-.++|. |..+.+.....+++-||.|++ ..||..........+
T Consensus 28 ~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 3446653 998887533445678999986 666665555444333
No 10
>PRK09692 integrase; Provisional
Probab=82.03 E-value=6.5 Score=28.47 Aligned_cols=42 Identities=17% Similarity=0.167 Sum_probs=27.0
Q ss_pred eEECCCCc--EEEEeecCCCceE--EecCCCC--CHHHHHHHHHHHHH
Q 041752 24 LRARPWGK--WAAETRDRYKGIC--IWLGIFN--ITKEAARAYAEAAK 65 (72)
Q Consensus 24 V~~~~~gk--w~A~i~~~~~~k~--~~LG~f~--t~eeAa~AYd~aa~ 65 (72)
|+-+++|. |..+-+.+.+|++ +-||.|+ |..||..+-.++..
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~ 80 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRS 80 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHH
Confidence 34456664 9998865445555 5799999 67776665544433
No 11
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=79.49 E-value=7.5 Score=26.64 Aligned_cols=38 Identities=24% Similarity=0.181 Sum_probs=25.5
Q ss_pred CcEEEEeecCCCceEEecCCCC--CHHHHHHHHHHHHHhh
Q 041752 30 GKWAAETRDRYKGICIWLGIFN--ITKEAARAYAEAAKHI 67 (72)
Q Consensus 30 gkw~A~i~~~~~~k~~~LG~f~--t~eeAa~AYd~aa~~~ 67 (72)
+.|..+++.....+++.||+|+ +.++|.....+....+
T Consensus 10 ~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 3599998853333456799996 6777777766654444
No 12
>PF08471 Ribonuc_red_2_N: Class II vitamin B12-dependent ribonucleotide reductase; InterPro: IPR013678 This domain is found to the N terminus of the ribonucleotide reductase barrel domain (IPR000788 from INTERPRO). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine) []. ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0050897 cobalt ion binding, 0055114 oxidation-reduction process
Probab=77.49 E-value=3.3 Score=25.53 Aligned_cols=21 Identities=24% Similarity=0.331 Sum_probs=17.7
Q ss_pred cCCCCCHHHHHHHHHHHHHhh
Q 041752 47 LGIFNITKEAARAYAEAAKHI 67 (72)
Q Consensus 47 LG~f~t~eeAa~AYd~aa~~~ 67 (72)
-|+|+|+|+|..=||...-.|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 499999999999999866543
No 13
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=73.34 E-value=2.6 Score=26.49 Aligned_cols=15 Identities=33% Similarity=0.818 Sum_probs=12.0
Q ss_pred eEEecCCCCCHHHHH
Q 041752 43 ICIWLGIFNITKEAA 57 (72)
Q Consensus 43 k~~~LG~f~t~eeAa 57 (72)
..+|||+|.|.+|=-
T Consensus 2 VsiWiG~f~s~~el~ 16 (122)
T PF14112_consen 2 VSIWIGNFKSEDELE 16 (122)
T ss_pred eEEEEecCCCHHHHH
Confidence 469999999987743
No 14
>PF09003 Phage_integ_N: Bacteriophage lambda integrase, N-terminal domain ; InterPro: IPR015094 The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage []. ; GO: 0003677 DNA binding, 0008907 integrase activity, 0015074 DNA integration; PDB: 1Z1G_B 1Z1B_A 2WCC_3 1KJK_A.
Probab=62.33 E-value=21 Score=21.07 Aligned_cols=30 Identities=30% Similarity=0.158 Sum_probs=17.8
Q ss_pred eecCCCceEEecCCCCCHHHHHHHHHHHHHhh
Q 041752 36 TRDRYKGICIWLGIFNITKEAARAYAEAAKHI 67 (72)
Q Consensus 36 i~~~~~~k~~~LG~f~t~eeAa~AYd~aa~~~ 67 (72)
-++|..|+.+.||+ +.+||...=-+|-..+
T Consensus 31 Yr~P~tGk~~~LG~--d~~~Ai~~A~eaN~~i 60 (75)
T PF09003_consen 31 YRNPITGKEHGLGT--DRAEAIAQAIEANLRI 60 (75)
T ss_dssp EE-TTTS-EEEEES---HHHHHHHHHHHHHHH
T ss_pred EecCCCCceeeCCC--CHHHHHHHHHHHHHHH
Confidence 34678999999999 6666655544443333
No 15
>PF13773 DUF4170: Domain of unknown function (DUF4170)
Probab=61.99 E-value=9.1 Score=22.37 Aligned_cols=21 Identities=29% Similarity=0.325 Sum_probs=18.0
Q ss_pred ecCCCCCHHHHHHHHHHHHHh
Q 041752 46 WLGIFNITKEAARAYAEAAKH 66 (72)
Q Consensus 46 ~LG~f~t~eeAa~AYd~aa~~ 66 (72)
.+|.|++-++|..|..+.|.+
T Consensus 28 iVG~fp~y~~A~~aWrakAq~ 48 (69)
T PF13773_consen 28 IVGIFPDYASAYAAWRAKAQR 48 (69)
T ss_pred EEecCCChHHHHHHHHHHHhC
Confidence 479999999999999887653
No 16
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=61.92 E-value=7.2 Score=25.65 Aligned_cols=17 Identities=47% Similarity=0.642 Sum_probs=14.5
Q ss_pred eEEecCCCCCHHHHHHH
Q 041752 43 ICIWLGIFNITKEAARA 59 (72)
Q Consensus 43 k~~~LG~f~t~eeAa~A 59 (72)
.=+++|.|.|+||++.+
T Consensus 42 eVi~~g~~~tp~e~v~a 58 (143)
T COG2185 42 EVINLGLFQTPEEAVRA 58 (143)
T ss_pred eEEecCCcCCHHHHHHH
Confidence 34689999999999876
No 17
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=60.01 E-value=27 Score=19.01 Aligned_cols=39 Identities=31% Similarity=0.334 Sum_probs=25.5
Q ss_pred eEECCCCcEEEEeecCCCceEEecCCCCCHHHHHHHHHHHHHh
Q 041752 24 LRARPWGKWAAETRDRYKGICIWLGIFNITKEAARAYAEAAKH 66 (72)
Q Consensus 24 V~~~~~gkw~A~i~~~~~~k~~~LG~f~t~eeAa~AYd~aa~~ 66 (72)
|..+..+.|..... |..--..+|+|-+||..+=...+..
T Consensus 3 V~p~~~~~W~v~~e----g~~ra~~~~~Tk~eAi~~Ar~~a~~ 41 (62)
T PF09954_consen 3 VVPREDGGWAVKKE----GAKRASKTFDTKAEAIEAARELAKN 41 (62)
T ss_pred EEecCCCCceEEeC----CCcccccccCcHHHHHHHHHHHHHh
Confidence 33455688998875 2222369999999987765544443
No 18
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=57.10 E-value=22 Score=23.49 Aligned_cols=34 Identities=24% Similarity=0.233 Sum_probs=28.4
Q ss_pred EEEEeecCCCceEEecCCCCCHHHHHHHHHHHHHhhc
Q 041752 32 WAAETRDRYKGICIWLGIFNITKEAARAYAEAAKHIR 68 (72)
Q Consensus 32 w~A~i~~~~~~k~~~LG~f~t~eeAa~AYd~aa~~~~ 68 (72)
|.|+|. -|+-++-=..++++.|..|...|+.+|=
T Consensus 96 waArVk---pG~vlfei~g~~e~~A~EAlr~Aa~KLP 129 (146)
T COG0197 96 WAARVK---PGRVLFEIAGVPEELAREALRRAAAKLP 129 (146)
T ss_pred EEEEec---CCcEEEEEecCcHHHHHHHHHHHhhcCC
Confidence 999997 5777776677888889999999998873
No 19
>PF12752 SUZ: SUZ domain; InterPro: IPR024771 The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterised in the Caenorhabditis elegans protein SZY-20 where it has been shown to bind RNA and allow their localization to the centrosome [].
Probab=56.47 E-value=18 Score=19.92 Aligned_cols=23 Identities=26% Similarity=0.203 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHHHHHHHhhcCCC
Q 041752 49 IFNITKEAARAYAEAAKHIRSNK 71 (72)
Q Consensus 49 ~f~t~eeAa~AYd~aa~~~~g~~ 71 (72)
.-.|.||=..+|.+|...+||.+
T Consensus 36 ~~kSlEERE~eY~~AR~RIFg~~ 58 (59)
T PF12752_consen 36 PSKSLEEREAEYAEARARIFGSS 58 (59)
T ss_pred ccCCHHHHHHHHHHHHHHHhCCC
Confidence 34789999999999999999975
No 20
>TIGR01164 rplP_bact ribosomal protein L16, bacterial/organelle. This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10
Probab=52.85 E-value=41 Score=21.31 Aligned_cols=33 Identities=21% Similarity=0.249 Sum_probs=25.8
Q ss_pred cEEEEeecCCCceEE-ecCCCCCHHHHHHHHHHHHHhh
Q 041752 31 KWAAETRDRYKGICI-WLGIFNITKEAARAYAEAAKHI 67 (72)
Q Consensus 31 kw~A~i~~~~~~k~~-~LG~f~t~eeAa~AYd~aa~~~ 67 (72)
-|+|+|. .|..+ -++. .+++.|..|...++.+|
T Consensus 91 ~~varV~---~G~ilfEi~~-~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 91 YWVAVVK---PGKILFEIAG-VPEEVAREAFRLAASKL 124 (126)
T ss_pred EEEEEEC---CCCEEEEEeC-CCHHHHHHHHHHHHhcC
Confidence 4999997 45555 4655 89999999999888775
No 21
>PF11453 DUF2950: Protein of unknown function (DUF2950); InterPro: IPR021556 This is a bacterial family of uncharacterised proteins.
Probab=50.81 E-value=16 Score=26.49 Aligned_cols=17 Identities=29% Similarity=0.427 Sum_probs=14.4
Q ss_pred CCCCHHHHHHHHHHHHH
Q 041752 49 IFNITKEAARAYAEAAK 65 (72)
Q Consensus 49 ~f~t~eeAa~AYd~aa~ 65 (72)
.|+|+|+|+.|.-.|..
T Consensus 3 ~F~tPe~Aa~Al~~Av~ 19 (271)
T PF11453_consen 3 VFPTPEAAADALVDAVA 19 (271)
T ss_pred CCCCHHHHHHHHHHHHh
Confidence 69999999999977653
No 22
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=50.45 E-value=42 Score=21.63 Aligned_cols=33 Identities=21% Similarity=0.189 Sum_probs=26.1
Q ss_pred cEEEEeecCCCceEE-ecCCCCCHHHHHHHHHHHHHhh
Q 041752 31 KWAAETRDRYKGICI-WLGIFNITKEAARAYAEAAKHI 67 (72)
Q Consensus 31 kw~A~i~~~~~~k~~-~LG~f~t~eeAa~AYd~aa~~~ 67 (72)
-|+|+|. .|.-+ -++. .+.+.|..|...|+.+|
T Consensus 92 ~~varVk---~G~iifEi~~-~~~~~a~~al~~a~~KL 125 (138)
T PRK09203 92 YWVAVVK---PGRILFEIAG-VSEELAREALRLAAAKL 125 (138)
T ss_pred EEEEEEC---CCCEEEEEeC-CCHHHHHHHHHHHhccC
Confidence 4999997 45554 4666 89999999999998876
No 23
>PF14882 GHL12: Hypothetical glycosyl hydrolase 12
Probab=46.53 E-value=15 Score=20.02 Aligned_cols=11 Identities=27% Similarity=0.489 Sum_probs=9.3
Q ss_pred CCCCHHHHHHH
Q 041752 49 IFNITKEAARA 59 (72)
Q Consensus 49 ~f~t~eeAa~A 59 (72)
.|.|.+||..|
T Consensus 39 ~Y~t~~eA~~A 49 (53)
T PF14882_consen 39 FYPTYEEASKA 49 (53)
T ss_pred ccCCHHHHHHH
Confidence 48999999877
No 24
>CHL00044 rpl16 ribosomal protein L16
Probab=45.47 E-value=45 Score=21.46 Aligned_cols=33 Identities=24% Similarity=0.290 Sum_probs=24.9
Q ss_pred cEEEEeecCCCceEEe-cCCCCCHHHHHHHHHHHHHhh
Q 041752 31 KWAAETRDRYKGICIW-LGIFNITKEAARAYAEAAKHI 67 (72)
Q Consensus 31 kw~A~i~~~~~~k~~~-LG~f~t~eeAa~AYd~aa~~~ 67 (72)
-|+|.|. .|.-++ ++. .+++.|..|...++.+|
T Consensus 92 ~~va~V~---~G~ilfEi~g-~~~~~ak~al~~a~~KL 125 (135)
T CHL00044 92 YWVAVVK---PGRILYEMGG-VSETIARAAIKIAAYKM 125 (135)
T ss_pred EEEEEEC---CCcEEEEEeC-CCHHHHHHHHHHHhhcC
Confidence 3999998 455554 555 56689999999888876
No 25
>PF11132 SplA: Transcriptional regulator protein (SplA); InterPro: IPR022608 The SplA protein functions in trans as a negative regulator of the level of splB-lacZ expression in the developing forespore [].
Probab=44.28 E-value=20 Score=21.19 Aligned_cols=15 Identities=40% Similarity=0.656 Sum_probs=12.9
Q ss_pred CCCCCHHHHHHHHHH
Q 041752 48 GIFNITKEAARAYAE 62 (72)
Q Consensus 48 G~f~t~eeAa~AYd~ 62 (72)
-.|.|.+||.+||..
T Consensus 58 Avfss~~eAe~ay~~ 72 (75)
T PF11132_consen 58 AVFSSYEEAEQAYHE 72 (75)
T ss_pred hhhcCHHHHHHHHHH
Confidence 568999999999975
No 26
>PRK10927 essential cell division protein FtsN; Provisional
Probab=40.18 E-value=63 Score=23.97 Aligned_cols=23 Identities=9% Similarity=0.010 Sum_probs=18.8
Q ss_pred eEEecCCCCCHHHHHHHHHHHHH
Q 041752 43 ICIWLGIFNITKEAARAYAEAAK 65 (72)
Q Consensus 43 k~~~LG~f~t~eeAa~AYd~aa~ 65 (72)
.++.||-|.+.++|.++.+....
T Consensus 284 ~RVrVGPf~sr~eAe~a~~rLk~ 306 (319)
T PRK10927 284 NRVVIGPVKGKENADSTLNRLKM 306 (319)
T ss_pred EEEEeCCCCCHHHHHHHHHHHHH
Confidence 57789999999999998876543
No 27
>PF14032 PknH_C: PknH-like extracellular domain
Probab=39.16 E-value=25 Score=22.56 Aligned_cols=23 Identities=22% Similarity=0.226 Sum_probs=19.4
Q ss_pred ecCCCCCHHHHHHHHHHHHHhhc
Q 041752 46 WLGIFNITKEAARAYAEAAKHIR 68 (72)
Q Consensus 46 ~LG~f~t~eeAa~AYd~aa~~~~ 68 (72)
-++.|+++++|..+++..+..+.
T Consensus 86 aV~~fp~~~~A~~~f~~~~~~w~ 108 (189)
T PF14032_consen 86 AVVVFPSAAAAQAFFARLADQWR 108 (189)
T ss_pred EEEEeCCHHHHHHHHHHHHHHHH
Confidence 36899999999999998776653
No 28
>cd08001 WGR_PARP1_like WGR domain of poly(ADP-ribose) polymerase 1 and similar proteins. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent synthesis of ADP-ribose polymers and their addition to various nuclear proteins. Higher eukaryotes contain several PARPs and and there may be up to 17 human PARP-like proteins, with three of them (PARP-1, PARP-2, and PARP-3) containing a WGR domain. The synthesis of poly-ADP-ribose requires multiple enzymatic activities for initiation, trans-ADP-ribosylation, elongation, branching, and release of the polymer from the enzyme. This subfamily is composed of vertebrate PARP-1 and similar proteins, including Arabidopsis thaliana
Probab=36.45 E-value=79 Score=18.94 Aligned_cols=26 Identities=23% Similarity=0.124 Sum_probs=19.6
Q ss_pred EEecCCCCCHHHHHHHHHHHHHhhcC
Q 041752 44 CIWLGIFNITKEAARAYAEAAKHIRS 69 (72)
Q Consensus 44 ~~~LG~f~t~eeAa~AYd~aa~~~~g 69 (72)
..-+-.|++.++|..++++.-...-|
T Consensus 56 q~~~~~~~~~~~A~~~F~k~f~~KTg 81 (104)
T cd08001 56 GNKLEEFSSLEEAKMAFEELYEEKTG 81 (104)
T ss_pred ceEccCCCCHHHHHHHHHHHHHHHhC
Confidence 34467899999999999986655433
No 29
>COG3010 NanE Putative N-acetylmannosamine-6-phosphate epimerase [Carbohydrate transport and metabolism]
Probab=35.71 E-value=31 Score=24.38 Aligned_cols=19 Identities=26% Similarity=0.305 Sum_probs=15.8
Q ss_pred EecCCCCCHHHHHHHHHHH
Q 041752 45 IWLGIFNITKEAARAYAEA 63 (72)
Q Consensus 45 ~~LG~f~t~eeAa~AYd~a 63 (72)
|-=|.|+|++.|+.|++.-
T Consensus 184 IAEGr~~tP~~Ak~a~~~G 202 (229)
T COG3010 184 IAEGRYNTPEQAKKAIEIG 202 (229)
T ss_pred EeeCCCCCHHHHHHHHHhC
Confidence 4459999999999999853
No 30
>cd07996 WGR_MMR_like WGR domain of molybdate metabolism regulator and related proteins. The WGR domain is found in the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, as well as in various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain appears to occur in single-domain proteins and in a variety of domain architectures, together with ATP-dependent DNA ligase domains, WD40 repeats, leucine-rich repeats, and other domains. It has been proposed to function as a nucleic acid binding domain.
Probab=35.22 E-value=48 Score=18.35 Aligned_cols=17 Identities=24% Similarity=0.345 Sum_probs=13.9
Q ss_pred CCCCHHHHHHHHHHHHH
Q 041752 49 IFNITKEAARAYAEAAK 65 (72)
Q Consensus 49 ~f~t~eeAa~AYd~aa~ 65 (72)
.|+|.++|..++++...
T Consensus 48 ~~~s~~~A~~~~~k~~~ 64 (74)
T cd07996 48 TFDSEEEALKAAEKLIR 64 (74)
T ss_pred ECCCHHHHHHHHHHHHH
Confidence 38999999999987544
No 31
>PF08178 GnsAB: GnsA/GnsB family; InterPro: IPR012563 This family consists of the GnsA/GnsB family. GnsA and GnsB are multicopy suppressors of the secG null mutation. These proteins participate in the synthesis of phospholipids, suggesting the functional relationship between SecG and membrane phospholipids. Over expression of gnsA and gnsB causes a remarkable increase in the unsaturated fatty acid content. However, the gnsA-gnsB double null mutant exhibits no effect. Both proteins are predicted to possess a helix-turn-helix structure [].
Probab=34.41 E-value=17 Score=20.26 Aligned_cols=13 Identities=23% Similarity=0.095 Sum_probs=10.2
Q ss_pred ECCCCcEEEEeec
Q 041752 26 ARPWGKWAAETRD 38 (72)
Q Consensus 26 ~~~~gkw~A~i~~ 38 (72)
+.+-|+|+++|..
T Consensus 26 rk~~Gke~sei~~ 38 (54)
T PF08178_consen 26 RKKTGKEVSEIEF 38 (54)
T ss_pred ccccCceeeeeee
Confidence 3566999999974
No 32
>COG3087 FtsN Cell division protein [Cell division and chromosome partitioning]
Probab=33.47 E-value=83 Score=22.75 Aligned_cols=22 Identities=23% Similarity=0.306 Sum_probs=17.9
Q ss_pred eEEecCCCCCHHHHHHHHHHHH
Q 041752 43 ICIWLGIFNITKEAARAYAEAA 64 (72)
Q Consensus 43 k~~~LG~f~t~eeAa~AYd~aa 64 (72)
.++.||.|++.++|..|-++..
T Consensus 229 yRV~vGP~n~~~~a~~aq~rLk 250 (264)
T COG3087 229 YRVRVGPFNSKADAVKAQKRLK 250 (264)
T ss_pred EEEEecCCCcHHHHHHHHHHHH
Confidence 4677899999999999877643
No 33
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=32.90 E-value=13 Score=16.70 Aligned_cols=8 Identities=38% Similarity=1.369 Sum_probs=5.3
Q ss_pred EEecCCCC
Q 041752 44 CIWLGIFN 51 (72)
Q Consensus 44 ~~~LG~f~ 51 (72)
.+|+||++
T Consensus 17 ~lWigT~~ 24 (24)
T PF07494_consen 17 NLWIGTYN 24 (24)
T ss_dssp CEEEEETS
T ss_pred CEEEEeCC
Confidence 67777763
No 34
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=32.64 E-value=1.2e+02 Score=21.45 Aligned_cols=36 Identities=25% Similarity=0.308 Sum_probs=27.9
Q ss_pred cEEEEeecCCCceEE-ecCCCCCHHHHHHHHHHHHHhhcC
Q 041752 31 KWAAETRDRYKGICI-WLGIFNITKEAARAYAEAAKHIRS 69 (72)
Q Consensus 31 kw~A~i~~~~~~k~~-~LG~f~t~eeAa~AYd~aa~~~~g 69 (72)
.|+|.|. .|+-+ -+|---+.+||..|.+.||.++-+
T Consensus 133 ~wva~V~---~GrIl~EmgG~~~~~~Ar~al~~aa~klp~ 169 (221)
T KOG3422|consen 133 HWVARVK---AGRILFEMGGDVEEEEARQALLQAAHKLPF 169 (221)
T ss_pred eeEEEec---CCcEEEEeCCcccHHHHHHHHHHHHhcCCc
Confidence 4999997 44444 466658999999999999988744
No 35
>cd01433 Ribosomal_L16_L10e Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.
Probab=32.57 E-value=1.1e+02 Score=18.57 Aligned_cols=34 Identities=24% Similarity=0.278 Sum_probs=25.1
Q ss_pred cEEEEeecCCCceEE-ecCCCCCHHHHHHHHHHHHHhh
Q 041752 31 KWAAETRDRYKGICI-WLGIFNITKEAARAYAEAAKHI 67 (72)
Q Consensus 31 kw~A~i~~~~~~k~~-~LG~f~t~eeAa~AYd~aa~~~ 67 (72)
.|.|+|. .|..+ -++..+..+.|..|...++.++
T Consensus 71 ~~~a~v~---~G~iifEi~~~~~~~~~~~alk~a~~Kl 105 (112)
T cd01433 71 GWVARVK---PGQILFEVRGVPEEEVAKEALRRAAKKL 105 (112)
T ss_pred EEEEEEC---CCCEEEEEeCcCcHHHHHHHHHHhhccC
Confidence 4999997 45554 4555555899999988888776
No 36
>cd07997 WGR_PARP WGR domain of poly(ADP-ribose) polymerases. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent synthesis of ADP-ribose polymers and their addition to various nuclear proteins and histones. Higher eukaryotes contain several PARPs and there may be up to 17 human PARP-like proteins, with three of them (PARP-1, PARP-2, and PARP-3) containing a WGR domain. The synthesis of poly-ADP-ribose requires multiple enzymatic activities for initiation, trans-ADP-ribosylation, elongation, branching, and release of the polymer from the enzyme. Poly-ADP-ribosylation was thought to be a reversible post-translational covalent modification that serves as a regulator
Probab=32.22 E-value=71 Score=19.11 Aligned_cols=24 Identities=17% Similarity=0.252 Sum_probs=16.6
Q ss_pred CceEEecCCCCCHHHHHHHHHHHHH
Q 041752 41 KGICIWLGIFNITKEAARAYAEAAK 65 (72)
Q Consensus 41 ~~k~~~LG~f~t~eeAa~AYd~aa~ 65 (72)
.|.... =.|.++++|..++.+.-.
T Consensus 52 ~Gq~~~-~~~~~~~~A~~~F~k~f~ 75 (102)
T cd07997 52 RGQSQL-TPFGSLESAIKEFEKKFK 75 (102)
T ss_pred cCceee-cCCCCHHHHHHHHHHHHH
Confidence 444443 348889999999987443
No 37
>TIGR00279 L10e ribosomal protein L10.e. L10.e is distantly related to eubacterial ribosomal protein L16.
Probab=31.94 E-value=64 Score=21.86 Aligned_cols=34 Identities=24% Similarity=0.037 Sum_probs=25.6
Q ss_pred cEEEEeecCCCceEEecC--CCCCHHHHHHHHHHHHHhh
Q 041752 31 KWAAETRDRYKGICIWLG--IFNITKEAARAYAEAAKHI 67 (72)
Q Consensus 31 kw~A~i~~~~~~k~~~LG--~f~t~eeAa~AYd~aa~~~ 67 (72)
-|+|+|. .|..++-- .-++.+.|..|...|+.+|
T Consensus 121 ~wvArVk---~Gqiifei~~~~~~~~~AkeAlr~A~~KL 156 (172)
T TIGR00279 121 GTAARVK---IGQKIFSVWTKPSNFDVAKEALRRAAMKF 156 (172)
T ss_pred EEEEEEC---cCCEEEEEEeecCCHHHHHHHHHHHhccC
Confidence 3999997 56666533 3348899999999988876
No 38
>PF00252 Ribosomal_L16: Ribosomal protein L16p/L10e; InterPro: IPR016180 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a structural domain with an alpha/beta-hammerhead fold, where the beta-hammerhead motif is similar to that in barrel-sandwich hybrids. Domains of this structure can be found in ribosomal proteins L10e and L16. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 2ZJR_J 1Y69_K 3DLL_J 2ZJQ_J 2ZJP_J 3PIO_J 3CF5_J 3PIP_J 2ZKR_h 3J11_O ....
Probab=31.57 E-value=1.2e+02 Score=19.24 Aligned_cols=34 Identities=32% Similarity=0.385 Sum_probs=26.5
Q ss_pred EEEEeecCCCceEE-ecCCCCCHHHHHHHHHHHHHhhc
Q 041752 32 WAAETRDRYKGICI-WLGIFNITKEAARAYAEAAKHIR 68 (72)
Q Consensus 32 w~A~i~~~~~~k~~-~LG~f~t~eeAa~AYd~aa~~~~ 68 (72)
|+|.|. .|.-+ -++..-+.++|-.|...++.+|=
T Consensus 92 ~~a~V~---~G~iifEi~~~v~~~~a~~alk~a~~KLP 126 (133)
T PF00252_consen 92 WVARVK---PGQIIFEIGGKVNEEEAKEALKRAAKKLP 126 (133)
T ss_dssp EEEEES---TTEEEEEEESGSCHHHHHHHHHHHHHTSS
T ss_pred EEEEEC---CCcEEEEECCcCCHHHHHHHHHHHHhhCC
Confidence 999997 55554 47664589999999999988773
No 39
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=31.35 E-value=24 Score=18.72 Aligned_cols=18 Identities=22% Similarity=0.200 Sum_probs=14.4
Q ss_pred cCCCCCHHHHHHHHHHHH
Q 041752 47 LGIFNITKEAARAYAEAA 64 (72)
Q Consensus 47 LG~f~t~eeAa~AYd~aa 64 (72)
+=.|.|+++|.+|++..-
T Consensus 43 ~v~f~~~~~a~~al~~~~ 60 (70)
T PF14259_consen 43 FVEFSSEEDAKRALELLN 60 (70)
T ss_dssp EEEESSHHHHHHHHHHHT
T ss_pred EEEeCCHHHHHHHHHHCC
Confidence 346899999999988754
No 40
>PF07978 NIPSNAP: NIPSNAP ; InterPro: IPR012577 Members of this family include many hypothetical proteins. It also includes members of the NIPSNAP family, which have putative roles in vesicular transport []. This domain is often found in duplicate.; PDB: 1VQY_D 2AP6_H.
Probab=30.94 E-value=84 Score=17.87 Aligned_cols=34 Identities=15% Similarity=0.143 Sum_probs=25.2
Q ss_pred CCcEEEEeecCCCceEEecCCCCCHHHHHHHHHHHH
Q 041752 29 WGKWAAETRDRYKGICIWLGIFNITKEAARAYAEAA 64 (72)
Q Consensus 29 ~gkw~A~i~~~~~~k~~~LG~f~t~eeAa~AYd~aa 64 (72)
-|-|..++.. ...-+||=.|++.++-.+..+++.
T Consensus 36 vG~~~~~~G~--~~~~~~l~~y~~~~~r~~~~~a~~ 69 (102)
T PF07978_consen 36 VGYWVTEVGP--LNQVVHLWSYDDLAAREEAREALY 69 (102)
T ss_dssp EEEEEEEESB--SSEEEEEEEES-HHHHHHHHHHHH
T ss_pred eEEEEeccCC--CceEEEEEEcCCHHHHHHHHHHHH
Confidence 3679999983 678889999999877777666543
No 41
>PF10729 CedA: Cell division activator CedA; InterPro: IPR019666 CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet [, ]. ; GO: 0003677 DNA binding, 0051301 cell division; PDB: 2BN8_A 2D35_A.
Probab=30.83 E-value=1.2e+02 Score=17.91 Aligned_cols=37 Identities=16% Similarity=0.090 Sum_probs=22.1
Q ss_pred CCeeeeEECCCCcEEEEeecCCCceEEecCCCCCHHHHHH
Q 041752 19 TEKKTLRARPWGKWAAETRDRYKGICIWLGIFNITKEAAR 58 (72)
Q Consensus 19 s~~~GV~~~~~gkw~A~i~~~~~~k~~~LG~f~t~eeAa~ 58 (72)
-+|+-|. .-.|||+|.+-. ...-.---.|..+|.|-+
T Consensus 31 dgfrdvw-~lrgkyvafvl~--ge~f~rsp~fs~pesaqr 67 (80)
T PF10729_consen 31 DGFRDVW-QLRGKYVAFVLM--GEHFRRSPAFSVPESAQR 67 (80)
T ss_dssp TTECCEC-CCCCEEEEEEES--SS-EEE---BSSHHHHHH
T ss_pred cccccee-eeccceEEEEEe--cchhccCCCcCCcHHHHH
Confidence 5788884 344999999873 333333467888877654
No 42
>PRK11901 hypothetical protein; Reviewed
Probab=30.68 E-value=80 Score=23.51 Aligned_cols=16 Identities=38% Similarity=0.420 Sum_probs=14.0
Q ss_pred cCCCCCHHHHHHHHHH
Q 041752 47 LGIFNITKEAARAYAE 62 (72)
Q Consensus 47 LG~f~t~eeAa~AYd~ 62 (72)
.|.|++.+||..|-..
T Consensus 288 yG~Y~Sr~eAk~Ai~s 303 (327)
T PRK11901 288 SGNYASSAEAKRAIAT 303 (327)
T ss_pred ecCcCCHHHHHHHHHh
Confidence 5999999999998765
No 43
>PF12286 DUF3622: Protein of unknown function (DUF3622); InterPro: IPR022069 This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif.
Probab=30.48 E-value=1.2e+02 Score=17.78 Aligned_cols=29 Identities=24% Similarity=0.240 Sum_probs=17.7
Q ss_pred CCcEEEEeecCCCceEEec----CCCCCHHHHH
Q 041752 29 WGKWAAETRDRYKGICIWL----GIFNITKEAA 57 (72)
Q Consensus 29 ~gkw~A~i~~~~~~k~~~L----G~f~t~eeAa 57 (72)
.+.|.|+|.--+..++.-+ --|+|++||-
T Consensus 15 ~~~W~aEItR~vTsrkTvVSK~~~GF~SEaeAq 47 (71)
T PF12286_consen 15 RNGWTAEITRRVTSRKTVVSKRQDGFASEAEAQ 47 (71)
T ss_pred CCceeeeeeeeecCceeEEEecccCcccHHHHH
Confidence 4689999974333322222 4589988864
No 44
>PRK12757 cell division protein FtsN; Provisional
Probab=30.13 E-value=1.2e+02 Score=21.84 Aligned_cols=23 Identities=17% Similarity=0.174 Sum_probs=19.4
Q ss_pred eEEecCCCCCHHHHHHHHHHHHH
Q 041752 43 ICIWLGIFNITKEAARAYAEAAK 65 (72)
Q Consensus 43 k~~~LG~f~t~eeAa~AYd~aa~ 65 (72)
.|+.||-|.+.++|..+-++...
T Consensus 221 yRVrVGPf~sr~~A~~~~~rLk~ 243 (256)
T PRK12757 221 NRVVLGPYNSKAAADKMLQRLKG 243 (256)
T ss_pred EEEEeCCCCCHHHHHHHHHHHHH
Confidence 57889999999999999887654
No 45
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=28.63 E-value=46 Score=16.65 Aligned_cols=19 Identities=16% Similarity=0.135 Sum_probs=14.4
Q ss_pred EecCCCCCHHHHHHHHHHH
Q 041752 45 IWLGIFNITKEAARAYAEA 63 (72)
Q Consensus 45 ~~LG~f~t~eeAa~AYd~a 63 (72)
..+=.|.+.++|..|.+..
T Consensus 42 ~~~v~f~s~~~a~~a~~~~ 60 (74)
T cd00590 42 FAFVEFEDEEDAEKALEAL 60 (74)
T ss_pred EEEEEECCHHHHHHHHHHh
Confidence 3445689999999998754
No 46
>TIGR00125 cyt_tran_rel cytidyltransferase-related domain. Protein families that contain at least one copy of this domain include citrate lyase ligase, pantoate-beta-alanine ligase, glycerol-3-phosphate cytidyltransferase, ADP-heptose synthase, phosphocholine cytidylyltransferase, lipopolysaccharide core biosynthesis protein KdtB, the bifunctional protein NadR, and a number whose function is unknown. Many of these proteins are known to use CTP or ATP and release pyrophosphate.
Probab=28.28 E-value=71 Score=16.74 Aligned_cols=24 Identities=25% Similarity=0.310 Sum_probs=19.1
Q ss_pred EecCCCCCHHHHHHHHHHHHHhhc
Q 041752 45 IWLGIFNITKEAARAYAEAAKHIR 68 (72)
Q Consensus 45 ~~LG~f~t~eeAa~AYd~aa~~~~ 68 (72)
+..|+||-....+...-..+.++.
T Consensus 3 ~~~G~Fdp~H~GH~~~l~~a~~~~ 26 (66)
T TIGR00125 3 IFVGTFDPFHLGHLDLLERAKELF 26 (66)
T ss_pred EEcCccCCCCHHHHHHHHHHHHhC
Confidence 568999999888888887776654
No 47
>cd07998 WGR_DNA_ligase WGR domain of bacterial DNA ligases. The WGR domain is found in a small family of predicted bacterial DNA ligases. It has been called WGR after the most conserved central motif of the domain. The domain typically occurs in together with an ATP-dependent DNA ligase domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain.
Probab=27.92 E-value=83 Score=18.54 Aligned_cols=36 Identities=8% Similarity=0.009 Sum_probs=21.9
Q ss_pred CCcEEEEeecCCCceEEec----CCCCCHHHHHHHHHHHH
Q 041752 29 WGKWAAETRDRYKGICIWL----GIFNITKEAARAYAEAA 64 (72)
Q Consensus 29 ~gkw~A~i~~~~~~k~~~L----G~f~t~eeAa~AYd~aa 64 (72)
.+.|...|+....|...-. ..|+++++|.++++...
T Consensus 25 d~g~~v~~~yGR~Gt~gq~~tkt~~~~~~~~A~k~~~Klv 64 (77)
T cd07998 25 DDGYVVNFRYGRRGSALREGTKTVAPVTLEAAEKIFDKLV 64 (77)
T ss_pred CCceEEEEEEccccCCcccccccCCCCCHHHHHHHHHHHH
Confidence 3455555554444443322 35689999999999743
No 48
>PF05406 WGR: WGR domain; InterPro: IPR008893 This domain is named after the most conserved central motif of the domain. It is found in a variety of polyA polymerases as well as the Escherichia coli molybdate metabolism regulator P33345 from SWISSPROT and other proteins of unknown function.The domain is found in isolation in proteins such as Q9JN21 from SWISSPROT and is between 70 and 80 residues in length. ; PDB: 2EOC_A 2RA8_A 4DQY_C 2CR9_A.
Probab=27.77 E-value=67 Score=18.24 Aligned_cols=16 Identities=19% Similarity=0.347 Sum_probs=13.8
Q ss_pred CCCCHHHHHHHHHHHH
Q 041752 49 IFNITKEAARAYAEAA 64 (72)
Q Consensus 49 ~f~t~eeAa~AYd~aa 64 (72)
.|++++||..++++.-
T Consensus 51 ~f~s~~eA~~~f~~~~ 66 (81)
T PF05406_consen 51 PFDSEEEAIKEFEKLF 66 (81)
T ss_dssp EESSHHHHHHHHHHHH
T ss_pred eCCCHHHHHHHHHHHH
Confidence 7899999999998743
No 49
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=26.87 E-value=35 Score=16.51 Aligned_cols=15 Identities=33% Similarity=0.463 Sum_probs=13.1
Q ss_pred cCCCCCHHHHHHHHH
Q 041752 47 LGIFNITKEAARAYA 61 (72)
Q Consensus 47 LG~f~t~eeAa~AYd 61 (72)
+..|++..||++...
T Consensus 13 i~~F~Si~eAa~~l~ 27 (37)
T PF07453_consen 13 IKSFDSIREAARYLG 27 (37)
T ss_pred EEEEcCHHHHHHHhC
Confidence 589999999999864
No 50
>PRK10672 rare lipoprotein A; Provisional
Probab=26.83 E-value=90 Score=23.53 Aligned_cols=22 Identities=18% Similarity=0.199 Sum_probs=14.7
Q ss_pred EEecCCCCCHHHHHHHHHHHHH
Q 041752 44 CIWLGIFNITKEAARAYAEAAK 65 (72)
Q Consensus 44 ~~~LG~f~t~eeAa~AYd~aa~ 65 (72)
|+.||-|.+.++|..+.++...
T Consensus 328 RVrLGPF~sr~eA~kl~~rLk~ 349 (361)
T PRK10672 328 RVQLGPFASRQQASALQQRLQT 349 (361)
T ss_pred EEEeCCCCCHHHHHHHHHHHHh
Confidence 5667777777777776665544
No 51
>cd08002 WGR_PARP3_like WGR domain of poly(ADP-ribose) polymerase 3 and similar proteins. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent synthesis of ADP-ribose polymers and their addition to various nuclear proteins. Higher eukaryotes contain several PARPs and and there may be up to 17 human PARP-like proteins, with three of them (PARP-1, PARP-2, and PARP-3) containing a WGR domain. The synthesis of poly-ADP-ribose requires multiple enzymatic activities for initiation, trans-ADP-ribosylation, elongation, branching, and release of the polymer from the enzyme. This subfamily is composed of human PARP-3 and similar proteins, including Arabidopsis thaliana PARP-
Probab=26.50 E-value=91 Score=18.86 Aligned_cols=26 Identities=19% Similarity=0.252 Sum_probs=18.0
Q ss_pred CceEEecCCCCCHHHHHHHHHHHHHh
Q 041752 41 KGICIWLGIFNITKEAARAYAEAAKH 66 (72)
Q Consensus 41 ~~k~~~LG~f~t~eeAa~AYd~aa~~ 66 (72)
.|.....+.+++.++|..++...-..
T Consensus 49 ~Gq~~~~~~~~~l~~A~~~F~k~F~~ 74 (100)
T cd08002 49 KGQNKLKGPWDSLEGAIKDFEKKFKD 74 (100)
T ss_pred cCcceeccCCCCHHHHHHHHHHHHHH
Confidence 35555556667799999999875433
No 52
>TIGR02223 ftsN cell division protein FtsN. FtsN is a poorly conserved protein active in cell division in a number of Proteobacteria. The N-terminal 30 residue region tends to by Lys/Arg-rich, and is followed by a membrane-spanning region. This is followed by an acidic low-complexity region of variable length and a well-conserved C-terminal domain of two tandem regions matched by Pfam model pfam05036 (Sporulation related repeat), found in several cell division and sporulation proteins. The role of FtsN as a suppressor for other cell division mutations is poorly understood; it may involve cell wall hydrolysis.
Probab=26.49 E-value=93 Score=22.59 Aligned_cols=23 Identities=9% Similarity=0.122 Sum_probs=19.2
Q ss_pred eEEecCCCCCHHHHHHHHHHHHH
Q 041752 43 ICIWLGIFNITKEAARAYAEAAK 65 (72)
Q Consensus 43 k~~~LG~f~t~eeAa~AYd~aa~ 65 (72)
.||.||-|.+.++|..+-+....
T Consensus 266 yRV~vGPf~sr~~A~~~~~~Lk~ 288 (298)
T TIGR02223 266 YRVVSGPYKNKDDAEKDLNKLKV 288 (298)
T ss_pred EEEEeCCCCCHHHHHHHHHHHHH
Confidence 57889999999999998876554
No 53
>cd03070 PDI_b_ERp44 PDIb family, ERp44 subfamily, first redox inactive TRX-like domain b; ERp44 is an endoplasmic reticulum (ER)-resident protein, induced during stress, involved in thiol-mediated ER retention. It contains an N-terminal TRX domain with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. Through the formation of reversible mixed disulfides, ERp44 mediates the ER localization of Ero1alpha, a protein that oxidizes protein disulfide isomerases into their active form. ERp44 also prevents the secretion of unassembled cargo protein with unpaired cysteines. ERp44 also modulates the activity of inositol 1,4,5-triphosphate type I receptor (IP3R1), an intracellular channel protein that mediates calcium release from the ER to the cytosol. Similar to PDI, the b domain of ERp44 is likely involved in binding to substrates.
Probab=25.71 E-value=34 Score=20.65 Aligned_cols=28 Identities=14% Similarity=0.285 Sum_probs=21.5
Q ss_pred CceEEecCCCCCHH-HHHHHHHHHHHhhc
Q 041752 41 KGICIWLGIFNITK-EAARAYAEAAKHIR 68 (72)
Q Consensus 41 ~~k~~~LG~f~t~e-eAa~AYd~aa~~~~ 68 (72)
..++..||+|++.+ .....|.++|..|+
T Consensus 15 ~~kr~iIgYF~~~~~~eY~~f~kvA~~lr 43 (91)
T cd03070 15 RSKRNIIGYFESKDSDEYDNFRKVANILR 43 (91)
T ss_pred cCCceEEEEEcCCCChhHHHHHHHHHHHh
Confidence 57888899998866 56677777777664
No 54
>PF07358 DUF1482: Protein of unknown function (DUF1482); InterPro: IPR009954 This family consists of several Enterobacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=25.68 E-value=61 Score=18.21 Aligned_cols=24 Identities=13% Similarity=0.171 Sum_probs=18.6
Q ss_pred ceEEecCCCCCHHHHHHHHHHHHH
Q 041752 42 GICIWLGIFNITKEAARAYAEAAK 65 (72)
Q Consensus 42 ~k~~~LG~f~t~eeAa~AYd~aa~ 65 (72)
-..+.+|.|+|.++.-.|-+...+
T Consensus 15 ~~d~v~gvy~se~~C~~a~~eQki 38 (57)
T PF07358_consen 15 CEDVVVGVYDSEQQCLAAADEQKI 38 (57)
T ss_pred CeEEEeecccCHHHHHHHHHhccC
Confidence 356789999999999888665443
No 55
>cd07994 WGR WGR domain. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs) as well as the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, a small family of bacterial DNA ligases, and various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain occurs in single-domain proteins and in a variety of domain architectures, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain.
Probab=25.34 E-value=1e+02 Score=17.41 Aligned_cols=17 Identities=12% Similarity=0.145 Sum_probs=14.0
Q ss_pred CCCCHHHHHHHHHHHHH
Q 041752 49 IFNITKEAARAYAEAAK 65 (72)
Q Consensus 49 ~f~t~eeAa~AYd~aa~ 65 (72)
.|+++++|..++++...
T Consensus 48 ~~~s~~~A~~~f~kl~~ 64 (73)
T cd07994 48 QMPSKEEAEEHFMKLYE 64 (73)
T ss_pred cCCCHHHHHHHHHHHHH
Confidence 48999999999997543
No 56
>PF06279 DUF1033: Protein of unknown function (DUF1033); InterPro: IPR010434 This family consists of several hypothetical bacterial proteins. Many of the sequences in this family are annotated as putative DNA binding proteins but the function of this family is unknown.
Probab=24.96 E-value=79 Score=20.25 Aligned_cols=23 Identities=17% Similarity=0.234 Sum_probs=19.1
Q ss_pred cCCCCCHHHHHHHHHHHHHhhcC
Q 041752 47 LGIFNITKEAARAYAEAAKHIRS 69 (72)
Q Consensus 47 LG~f~t~eeAa~AYd~aa~~~~g 69 (72)
.=.|++.+||-..|.....++..
T Consensus 27 ~~~F~~~eeAl~~Y~~~~~~~~~ 49 (120)
T PF06279_consen 27 EKEFDNYEEALKYYKKLWQKLKE 49 (120)
T ss_pred hhhcCCHHHHHHHHHHHHHHHHH
Confidence 35799999999999988777653
No 57
>PRK04199 rpl10e 50S ribosomal protein L10e; Reviewed
Probab=24.13 E-value=1.1e+02 Score=20.62 Aligned_cols=34 Identities=26% Similarity=0.125 Sum_probs=25.7
Q ss_pred cEEEEeecCCCceEEecC--CCCCHHHHHHHHHHHHHhh
Q 041752 31 KWAAETRDRYKGICIWLG--IFNITKEAARAYAEAAKHI 67 (72)
Q Consensus 31 kw~A~i~~~~~~k~~~LG--~f~t~eeAa~AYd~aa~~~ 67 (72)
-|+|.|. .|..++-= .-.+.+.|..|...|+.+|
T Consensus 121 ~wva~Vk---~G~ilfei~~~~~~~~~akeAlr~a~~KL 156 (172)
T PRK04199 121 GTAARVE---KGQKIFTVRVNPEHLEAAKEALRRAAMKL 156 (172)
T ss_pred EEEEEEC---cCCEEEEEEecCCCHHHHHHHHHHhhccC
Confidence 4999997 56666533 3458899999999988876
No 58
>smart00773 WGR Proposed nucleic acid binding domain. This domain is named after its most conserved central motif. It is found in a variety of polyA polymerases as well as in molybdate metabolism regulators (e.g. in E.coli) and other proteins of unknown function. The domain is found in isolation in some proteins and is between 70 and 80 residues in length. It is proposed that it may be a nucleic acid binding domain.
Probab=23.53 E-value=1.1e+02 Score=17.32 Aligned_cols=17 Identities=18% Similarity=0.387 Sum_probs=14.4
Q ss_pred CCCCHHHHHHHHHHHHH
Q 041752 49 IFNITKEAARAYAEAAK 65 (72)
Q Consensus 49 ~f~t~eeAa~AYd~aa~ 65 (72)
.|++.++|..++++.-.
T Consensus 54 ~~~s~~~A~~~f~k~~~ 70 (84)
T smart00773 54 TFDSLEDAIKEFEKLFK 70 (84)
T ss_pred cCCCHHHHHHHHHHHHH
Confidence 68999999999997544
No 59
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=23.53 E-value=68 Score=16.36 Aligned_cols=14 Identities=21% Similarity=0.344 Sum_probs=11.3
Q ss_pred CCCCHHHHHHHHHH
Q 041752 49 IFNITKEAARAYAE 62 (72)
Q Consensus 49 ~f~t~eeAa~AYd~ 62 (72)
.|++.++|..|...
T Consensus 27 ~f~~~~~A~~a~~~ 40 (56)
T PF13893_consen 27 EFASVEDAQKAIEQ 40 (56)
T ss_dssp EESSHHHHHHHHHH
T ss_pred EECCHHHHHHHHHH
Confidence 58999999988654
No 60
>PF12434 Malate_DH: Malate dehydrogenase enzyme
Probab=23.02 E-value=1.1e+02 Score=14.80 Aligned_cols=19 Identities=11% Similarity=0.106 Sum_probs=14.1
Q ss_pred CCHHHHHHHHHHHHHhhcC
Q 041752 51 NITKEAARAYAEAAKHIRS 69 (72)
Q Consensus 51 ~t~eeAa~AYd~aa~~~~g 69 (72)
|..++...+...||+.||-
T Consensus 8 d~~~~~r~~lR~AALeYHe 26 (28)
T PF12434_consen 8 DNKEDKRAQLRQAALEYHE 26 (28)
T ss_pred cchHHHHHHHHHHHHHhcc
Confidence 3457777788888988874
No 61
>PF06236 MelC1: Tyrosinase co-factor MelC1; InterPro: IPR010928 This family consists of several tyrosinase co-factor MELC1 proteins from a number of Streptomyces species. The melanin operon (melC) of Streptomyces antibioticus contains two genes, melC1 and melC2 (apotyrosinase). It is thought that MelC1 forms a transient binary complex with the downstream apotyrosinase MelC2 to facilitate the incorporation of copper ion and the secretion of tyrosinase indicating that MelC1 is a chaperone for the apotyrosinase MelC2 [].; GO: 0005507 copper ion binding, 0042438 melanin biosynthetic process; PDB: 1WX4_B 2ZWD_B 2ZMZ_B 1WX2_B 1WX5_D 3AWX_B 3AWS_B 2ZMY_B 3AX0_B 2ZWG_B ....
Probab=22.95 E-value=67 Score=20.75 Aligned_cols=12 Identities=42% Similarity=0.404 Sum_probs=9.7
Q ss_pred CCCCCHHHHHHH
Q 041752 48 GIFNITKEAARA 59 (72)
Q Consensus 48 G~f~t~eeAa~A 59 (72)
-.|+|+-||++|
T Consensus 98 e~~pTpl~aARA 109 (125)
T PF06236_consen 98 ESYPTPLEAARA 109 (125)
T ss_dssp EEESSHHHHHHH
T ss_pred cCCCCHHHHHHH
Confidence 467999999886
No 62
>PF07384 DUF1497: Protein of unknown function (DUF1497); InterPro: IPR009972 This entry is represented by Bacteriophage r1t, Orf17. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins of around 59 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this organism. The function of this family is unknown.
Probab=21.92 E-value=92 Score=17.26 Aligned_cols=19 Identities=26% Similarity=0.417 Sum_probs=14.6
Q ss_pred cCCCCCHHHHHHHHHHHHH
Q 041752 47 LGIFNITKEAARAYAEAAK 65 (72)
Q Consensus 47 LG~f~t~eeAa~AYd~aa~ 65 (72)
.|+||+..||.+.-..|..
T Consensus 1 mgyyd~~nearrisklas~ 19 (59)
T PF07384_consen 1 MGYYDKRNEARRISKLASQ 19 (59)
T ss_pred CCcccchhHHHHHHHHHhc
Confidence 4899999999887665543
No 63
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=21.40 E-value=87 Score=15.98 Aligned_cols=17 Identities=24% Similarity=0.311 Sum_probs=13.2
Q ss_pred cCCCCCHHHHHHHHHHH
Q 041752 47 LGIFNITKEAARAYAEA 63 (72)
Q Consensus 47 LG~f~t~eeAa~AYd~a 63 (72)
.=.|++.++|..|.+..
T Consensus 43 ~V~F~~~~~a~~a~~~l 59 (70)
T PF00076_consen 43 FVEFESEEDAEKALEEL 59 (70)
T ss_dssp EEEESSHHHHHHHHHHH
T ss_pred EEEEcCHHHHHHHHHHc
Confidence 34689999999987754
No 64
>smart00360 RRM RNA recognition motif.
Probab=21.21 E-value=73 Score=15.62 Aligned_cols=15 Identities=20% Similarity=0.255 Sum_probs=11.6
Q ss_pred CCCCCHHHHHHHHHH
Q 041752 48 GIFNITKEAARAYAE 62 (72)
Q Consensus 48 G~f~t~eeAa~AYd~ 62 (72)
=.|.+.++|..|.+.
T Consensus 43 v~f~~~~~a~~a~~~ 57 (71)
T smart00360 43 VEFESEEDAEKALEA 57 (71)
T ss_pred EEeCCHHHHHHHHHH
Confidence 357999999988653
No 65
>COG3266 DamX Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.90 E-value=1.4e+02 Score=21.94 Aligned_cols=23 Identities=22% Similarity=0.281 Sum_probs=17.6
Q ss_pred CCceEEe---cCCCCCHHHHHHHHHH
Q 041752 40 YKGICIW---LGIFNITKEAARAYAE 62 (72)
Q Consensus 40 ~~~k~~~---LG~f~t~eeAa~AYd~ 62 (72)
.+|+..| -|.|.|.+||..|-..
T Consensus 244 rnG~pWYvv~~G~YatrqeA~~Avst 269 (292)
T COG3266 244 RNGKPWYVVVYGNYATRQEAKAAVST 269 (292)
T ss_pred cCCceeEEEEecCcccHHHHHHHHhh
Confidence 4665554 4999999999988654
No 66
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=20.83 E-value=1.8e+02 Score=16.63 Aligned_cols=46 Identities=15% Similarity=-0.009 Sum_probs=32.9
Q ss_pred CCeeeeE-ECCCCcEEEEeecCCCceEEecCCCCCHHHHHHHHHHHHHhh
Q 041752 19 TEKKTLR-ARPWGKWAAETRDRYKGICIWLGIFNITKEAARAYAEAAKHI 67 (72)
Q Consensus 19 s~~~GV~-~~~~gkw~A~i~~~~~~k~~~LG~f~t~eeAa~AYd~aa~~~ 67 (72)
..|.||. +-..-+-.+.|. ..|+-+..|. .+.||+..|.+.....+
T Consensus 36 e~fpgl~~r~~~p~~t~~IF--~sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 36 ERFPGLIYRLRNPKATVLIF--SSGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTESSEEEEETTTTEEEEEE--TTSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred ccCCeEEEeecCCcEEEEEE--cCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 3677875 333335666776 7898888875 68899999988877655
No 67
>COG3831 Uncharacterized conserved protein [Function unknown]
Probab=20.78 E-value=1.2e+02 Score=18.25 Aligned_cols=18 Identities=17% Similarity=0.196 Sum_probs=14.1
Q ss_pred ecCCCCCHHHHHHHHHHH
Q 041752 46 WLGIFNITKEAARAYAEA 63 (72)
Q Consensus 46 ~LG~f~t~eeAa~AYd~a 63 (72)
-+=+|++.++|..++...
T Consensus 41 ~~k~F~~~~~a~~~~~kL 58 (85)
T COG3831 41 QIKSFDDSADAEKAALKL 58 (85)
T ss_pred eeeeCCCHHHHHHHHHHH
Confidence 356799999998887753
No 68
>cd08355 Glo_EDI_BRP_like_14 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins.
Probab=20.77 E-value=1.4e+02 Score=17.15 Aligned_cols=25 Identities=24% Similarity=0.456 Sum_probs=18.4
Q ss_pred EECCCCcEEEEeecCCCceEEecCCC
Q 041752 25 RARPWGKWAAETRDRYKGICIWLGIF 50 (72)
Q Consensus 25 ~~~~~gkw~A~i~~~~~~k~~~LG~f 50 (72)
...++|...+.++|| .|..+.|++|
T Consensus 98 ~~~~~g~~~~~~~DP-dG~~~~l~~~ 122 (122)
T cd08355 98 TDTPYGSREFTARDP-EGNLWTFGTY 122 (122)
T ss_pred cccCCCcEEEEEECC-CCCEEEEecC
Confidence 345677777889996 8888877765
Done!