Query 038709
Match_columns 67
No_of_seqs 106 out of 850
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 02:34:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038709.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038709hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00018 AP2 DNA-binding domain 99.8 2.1E-20 4.5E-25 103.8 5.5 47 20-66 1-47 (61)
2 PHA00280 putative NHN endonucl 99.8 7.4E-20 1.6E-24 114.6 5.4 62 2-65 45-111 (121)
3 smart00380 AP2 DNA-binding dom 99.8 4.4E-19 9.5E-24 99.6 6.1 46 21-66 1-46 (64)
4 PF00847 AP2: AP2 domain; Int 99.5 7E-14 1.5E-18 75.8 4.7 47 20-66 1-51 (56)
5 PF14657 Integrase_AP2: AP2-li 90.0 1.4 3E-05 22.6 4.6 33 32-64 1-37 (46)
6 PHA02601 int integrase; Provis 84.9 1.6 3.6E-05 29.7 3.8 38 24-62 2-40 (333)
7 PF05036 SPOR: Sporulation rel 84.4 0.52 1.1E-05 25.3 1.0 22 42-63 42-63 (76)
8 PF08846 DUF1816: Domain of un 82.5 3.8 8.2E-05 23.4 4.0 30 32-61 9-38 (68)
9 PF08471 Ribonuc_red_2_N: Clas 82.3 1.3 2.9E-05 26.7 2.2 17 49-65 71-87 (93)
10 PF14112 DUF4284: Domain of un 80.9 1.1 2.3E-05 27.8 1.5 15 44-58 2-16 (122)
11 cd00801 INT_P4 Bacteriophage P 80.7 4.3 9.4E-05 27.3 4.6 34 30-63 9-44 (357)
12 PRK09692 integrase; Provisiona 80.6 6.7 0.00014 27.9 5.6 38 25-62 33-76 (413)
13 PF09954 DUF2188: Uncharacteri 78.3 5 0.00011 21.6 3.5 33 25-61 3-35 (62)
14 PF13356 DUF4102: Domain of un 75.2 9.6 0.00021 21.7 4.3 36 26-61 28-67 (89)
15 COG2185 Sbm Methylmalonyl-CoA 73.0 3 6.6E-05 26.9 2.0 18 44-61 42-59 (143)
16 PF13773 DUF4170: Domain of un 64.3 7.5 0.00016 22.3 2.2 20 46-65 27-46 (69)
17 PF14882 GHL12: Hypothetical g 60.9 6 0.00013 21.3 1.3 12 50-61 39-50 (53)
18 PF10729 CedA: Cell division a 60.7 25 0.00054 20.4 3.9 38 19-59 30-67 (80)
19 PF12286 DUF3622: Protein of u 57.8 17 0.00037 20.9 2.9 29 30-58 15-47 (71)
20 PF11132 SplA: Transcriptional 56.8 8.9 0.00019 22.3 1.6 15 49-63 58-72 (75)
21 PRK10927 essential cell divisi 53.1 26 0.00056 25.5 3.8 32 33-64 273-304 (319)
22 PF09003 Phage_integ_N: Bacter 49.5 40 0.00086 19.5 3.6 20 38-59 32-51 (75)
23 COG3087 FtsN Cell division pro 48.2 33 0.00071 24.3 3.7 21 44-64 229-249 (264)
24 cd08001 WGR_PARP1_like WGR dom 46.5 29 0.00062 20.5 2.8 20 45-64 56-75 (104)
25 COG3010 NanE Putative N-acetyl 45.9 17 0.00037 25.2 1.9 19 45-63 183-201 (229)
26 PF07978 NIPSNAP: NIPSNAP ; I 42.9 39 0.00085 18.9 3.0 33 30-64 36-68 (102)
27 PRK10113 cell division modulat 42.7 23 0.0005 20.5 1.9 37 20-59 31-67 (80)
28 PRK12757 cell division protein 42.7 46 0.001 23.4 3.7 31 34-64 211-241 (256)
29 PF14259 RRM_6: RNA recognitio 42.0 17 0.00037 19.0 1.2 15 49-63 44-58 (70)
30 PF07453 NUMOD1: NUMOD1 domain 41.4 16 0.00034 17.5 1.0 15 48-62 13-27 (37)
31 PF07494 Reg_prop: Two compone 40.9 11 0.00023 16.7 0.2 11 42-52 14-24 (24)
32 cd07997 WGR_PARP WGR domain of 40.8 44 0.00096 19.7 3.0 21 42-63 52-72 (102)
33 cd07996 WGR_MMR_like WGR domai 40.6 24 0.00052 19.3 1.7 15 50-64 48-62 (74)
34 COG0197 RplP Ribosomal protein 40.5 65 0.0014 20.9 3.9 31 32-65 95-125 (146)
35 cd00590 RRM RRM (RNA recogniti 39.8 21 0.00046 17.7 1.3 18 46-63 42-59 (74)
36 PF05406 WGR: WGR domain; Int 39.1 23 0.00049 19.9 1.5 16 49-64 50-65 (81)
37 PF00352 TBP: Transcription fa 38.7 75 0.0016 18.0 3.9 43 19-64 35-78 (86)
38 PF08178 GnsAB: GnsA/GnsB fami 38.5 13 0.00029 20.3 0.4 11 29-39 28-38 (54)
39 cd07994 WGR WGR domain. The WG 37.0 34 0.00074 19.1 2.0 15 50-64 48-62 (73)
40 cd08002 WGR_PARP3_like WGR dom 36.9 49 0.0011 19.7 2.8 22 42-63 49-70 (100)
41 PF13893 RRM_5: RNA recognitio 35.5 30 0.00064 17.5 1.5 13 50-62 27-39 (56)
42 PF06236 MelC1: Tyrosinase co- 35.2 18 0.0004 22.9 0.7 12 49-60 98-109 (125)
43 PF00076 RRM_1: RNA recognitio 34.5 27 0.00058 17.7 1.2 15 49-63 44-58 (70)
44 PRK09203 rplP 50S ribosomal pr 34.3 96 0.0021 19.6 3.9 31 31-65 91-122 (138)
45 smart00773 WGR Proposed nuclei 34.2 40 0.00086 18.9 2.0 15 50-64 54-68 (84)
46 TIGR02223 ftsN cell division p 33.8 55 0.0012 23.3 3.0 32 33-64 253-286 (298)
47 TIGR01164 rplP_bact ribosomal 33.6 1E+02 0.0022 19.1 4.0 31 31-65 90-121 (126)
48 PF00626 Gelsolin: Gelsolin re 32.7 54 0.0012 17.3 2.3 23 43-65 28-50 (76)
49 KOG1256 Long-chain acyl-CoA sy 32.6 25 0.00055 28.0 1.3 28 34-63 498-525 (691)
50 cd07998 WGR_DNA_ligase WGR dom 32.4 44 0.00096 19.3 2.0 35 30-64 25-63 (77)
51 smart00360 RRM RNA recognition 32.1 34 0.00073 16.7 1.4 15 49-63 43-57 (71)
52 PF14032 PknH_C: PknH-like ext 31.7 36 0.00078 21.4 1.7 18 47-64 86-103 (189)
53 smart00361 RRM_1 RNA recogniti 31.2 32 0.00068 18.5 1.2 14 50-63 43-56 (70)
54 smart00497 IENR1 Intron encode 31.0 33 0.00071 17.1 1.2 16 46-61 12-27 (53)
55 CHL00044 rpl16 ribosomal prote 30.9 1.2E+02 0.0025 19.1 3.9 31 31-65 91-122 (135)
56 PF07358 DUF1482: Protein of u 30.4 61 0.0013 17.9 2.2 24 42-65 14-37 (57)
57 PRK10545 nucleotide excision r 30.4 39 0.00085 23.9 1.8 17 44-60 241-257 (286)
58 PF03799 FtsQ: Cell division p 30.3 1.1E+02 0.0023 17.3 4.5 40 20-63 59-98 (117)
59 PRK10672 rare lipoprotein A; P 29.6 69 0.0015 23.7 3.0 20 44-63 327-346 (361)
60 PF07384 DUF1497: Protein of u 29.3 53 0.0011 17.9 1.8 17 48-64 1-17 (59)
61 PRK10905 cell division protein 28.1 57 0.0012 23.9 2.3 19 45-63 287-305 (328)
62 PF04131 NanE: Putative N-acet 27.2 45 0.00098 22.5 1.6 18 47-64 149-166 (192)
63 smart00362 RRM_2 RNA recogniti 26.4 48 0.001 16.1 1.4 16 48-63 43-58 (72)
64 TIGR00640 acid_CoA_mut_C methy 26.2 79 0.0017 19.5 2.5 19 44-62 32-50 (132)
65 PF09341 Pcc1: Transcription f 25.9 63 0.0014 17.8 1.9 13 51-63 9-21 (76)
66 KOG1176 Acyl-CoA synthetase [L 25.7 37 0.00079 26.0 1.1 27 35-63 380-406 (537)
67 COG4935 Regulatory P domain of 25.4 1.1E+02 0.0025 20.4 3.2 34 17-53 78-119 (177)
68 cd00283 GIY-YIG_Cterm GIYX(10- 24.3 49 0.0011 20.2 1.3 16 47-62 76-91 (113)
69 COG1022 FAA1 Long-chain acyl-C 24.1 40 0.00086 26.4 1.0 27 34-62 420-446 (613)
70 PF01693 Cauli_VI: Caulimoviru 23.5 49 0.0011 16.6 1.0 11 49-59 33-43 (44)
71 PRK11901 hypothetical protein; 23.4 71 0.0015 23.3 2.1 16 47-62 287-302 (327)
72 COG3831 Uncharacterized conser 23.3 72 0.0016 18.9 1.8 17 47-63 41-57 (85)
73 PF02249 MCR_alpha: Methyl-coe 23.2 29 0.00063 22.1 0.1 9 45-53 2-10 (127)
74 TIGR02717 AcCoA-syn-alpha acet 22.8 72 0.0016 23.5 2.1 20 48-67 427-446 (447)
75 PF10045 DUF2280: Uncharacteri 22.7 52 0.0011 20.2 1.2 15 48-62 16-30 (104)
76 TIGR00279 L10e ribosomal prote 22.3 1.6E+02 0.0034 19.6 3.5 32 31-65 120-153 (172)
77 PRK14887 KEOPS complex Pcc1-li 22.2 69 0.0015 18.6 1.6 15 50-64 11-25 (84)
78 PF08383 Maf_N: Maf N-terminal 21.6 65 0.0014 16.1 1.2 10 52-61 23-32 (35)
79 PF10003 DUF2244: Integral mem 21.4 1.4E+02 0.0031 18.5 3.0 23 41-63 113-135 (140)
80 PF02805 Ada_Zn_binding: Metal 20.5 44 0.00095 18.8 0.5 14 47-60 42-55 (66)
81 smart00703 NRF N-terminal doma 20.1 27 0.00059 20.7 -0.4 25 27-54 8-32 (110)
82 PF11821 DUF3341: Protein of u 20.1 88 0.0019 20.6 1.9 20 44-63 2-21 (173)
No 1
>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=99.82 E-value=2.1e-20 Score=103.83 Aligned_cols=47 Identities=60% Similarity=1.010 Sum_probs=43.2
Q ss_pred CceeeEEECCCCeEEEEEecCCCCceEEeCCCCcHHHHHHHHHHhhc
Q 038709 20 SRYLGVRRRPWGRYAAEIRNPRTKERHWLGTFDAAEEAAIAVYMMIL 66 (67)
Q Consensus 20 Sg~rGV~~~~~gkW~A~I~~~~~~k~~~LG~f~t~eeAa~Ayd~aa~ 66 (67)
|+|+||+++++|+|+|+|+++..|+.+|||+|+|+|||+.|||.|++
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~ 47 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAAL 47 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHH
Confidence 79999998888999999998544999999999999999999999875
No 2
>PHA00280 putative NHN endonuclease
Probab=99.80 E-value=7.4e-20 Score=114.64 Aligned_cols=62 Identities=15% Similarity=0.069 Sum_probs=53.6
Q ss_pred Ccccccc----cCCCCCCCCCCCceeeEEECC-CCeEEEEEecCCCCceEEeCCCCcHHHHHHHHHHhh
Q 038709 2 EKFPELL----YGNPKRSSRQSSRYLGVRRRP-WGRYAAEIRNPRTKERHWLGTFDAAEEAAIAVYMMI 65 (67)
Q Consensus 2 ~~~~~~~----~~n~~~~~~~~Sg~rGV~~~~-~gkW~A~I~~~~~~k~~~LG~f~t~eeAa~Ayd~aa 65 (67)
+||+.++ ++|.+.+++|+|||+||+|.+ .|||+|+|.+ +|+.++||+|+|+|+|+.||+++.
T Consensus 45 ~NLr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~~~~ 111 (121)
T PHA00280 45 DNLRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYRTRR 111 (121)
T ss_pred HHhhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHHHHH
Confidence 4555444 778888889999999999876 8999999996 999999999999999999998654
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.78 E-value=4.4e-19 Score=99.56 Aligned_cols=46 Identities=57% Similarity=1.018 Sum_probs=42.9
Q ss_pred ceeeEEECCCCeEEEEEecCCCCceEEeCCCCcHHHHHHHHHHhhc
Q 038709 21 RYLGVRRRPWGRYAAEIRNPRTKERHWLGTFDAAEEAAIAVYMMIL 66 (67)
Q Consensus 21 g~rGV~~~~~gkW~A~I~~~~~~k~~~LG~f~t~eeAa~Ayd~aa~ 66 (67)
.|+||+++++|+|+|+|+++.+++.++||+|+|+|||+.|||.|++
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~ 46 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAF 46 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHH
Confidence 4899998889999999999889999999999999999999999875
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=99.48 E-value=7e-14 Score=75.80 Aligned_cols=47 Identities=34% Similarity=0.379 Sum_probs=41.0
Q ss_pred CceeeEEECC-CCeEEEEEecCC-C--CceEEeCCCCcHHHHHHHHHHhhc
Q 038709 20 SRYLGVRRRP-WGRYAAEIRNPR-T--KERHWLGTFDAAEEAAIAVYMMIL 66 (67)
Q Consensus 20 Sg~rGV~~~~-~gkW~A~I~~~~-~--~k~~~LG~f~t~eeAa~Ayd~aa~ 66 (67)
|+|+||++++ .++|+|+|.++. + ++.++||.|+++|||+++++++++
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~~g~~k~f~~g~fg~~~eA~~~a~~~r~ 51 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSENGKRKRFSVGKFGFEEEAKRAAIEARK 51 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCCTTEEEEEEECCCCCHHHHHHHHHHHHH
T ss_pred CCcEEEEEcCCCCEEEEEEEEcccCcccEEEeCccCCCHHHHHHHHHHHHH
Confidence 7999999877 899999999732 2 499999999999999999998864
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=90.05 E-value=1.4 Score=22.63 Aligned_cols=33 Identities=15% Similarity=0.164 Sum_probs=24.6
Q ss_pred eEEEEEe--cCCCC--ceEEeCCCCcHHHHHHHHHHh
Q 038709 32 RYAAEIR--NPRTK--ERHWLGTFDAAEEAAIAVYMM 64 (67)
Q Consensus 32 kW~A~I~--~~~~~--k~~~LG~f~t~eeAa~Ayd~a 64 (67)
+|...|. ++..| ++++-+-|.|..||..+...+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~ 37 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKI 37 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHH
Confidence 5778883 44455 567888899999999887654
No 6
>PHA02601 int integrase; Provisional
Probab=84.85 E-value=1.6 Score=29.72 Aligned_cols=38 Identities=26% Similarity=0.249 Sum_probs=26.2
Q ss_pred eEEECCCCeEEEEEec-CCCCceEEeCCCCcHHHHHHHHH
Q 038709 24 GVRRRPWGRYAAEIRN-PRTKERHWLGTFDAAEEAAIAVY 62 (67)
Q Consensus 24 GV~~~~~gkW~A~I~~-~~~~k~~~LG~f~t~eeAa~Ayd 62 (67)
+|+..++|+|.+++.. ...|+++. .+|.|..||...-+
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~-~~f~tk~eA~~~~~ 40 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIR-KRFATKGEALAFEN 40 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhh-hhhcCHHHHHHHHH
Confidence 4555668899999984 22466664 36999988865443
No 7
>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=84.41 E-value=0.52 Score=25.34 Aligned_cols=22 Identities=32% Similarity=0.324 Sum_probs=18.2
Q ss_pred CCceEEeCCCCcHHHHHHHHHH
Q 038709 42 TKERHWLGTFDAAEEAAIAVYM 63 (67)
Q Consensus 42 ~~k~~~LG~f~t~eeAa~Ayd~ 63 (67)
.-.++.+|.|+|.+||..+...
T Consensus 42 ~~yrV~~G~f~~~~~A~~~~~~ 63 (76)
T PF05036_consen 42 PWYRVRVGPFSSREEAEAALRK 63 (76)
T ss_dssp TCEEEEECCECTCCHHHHHHHH
T ss_pred ceEEEEECCCCCHHHHHHHHHH
Confidence 4568999999999999887664
No 8
>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=82.53 E-value=3.8 Score=23.38 Aligned_cols=30 Identities=30% Similarity=0.469 Sum_probs=23.3
Q ss_pred eEEEEEecCCCCceEEeCCCCcHHHHHHHH
Q 038709 32 RYAAEIRNPRTKERHWLGTFDAAEEAAIAV 61 (67)
Q Consensus 32 kW~A~I~~~~~~k~~~LG~f~t~eeAa~Ay 61 (67)
.|=++|.-..-.-..|.|-|+|.+||..+-
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~ 38 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAAL 38 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHh
Confidence 577899863334677999999999998763
No 9
>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=82.32 E-value=1.3 Score=26.73 Aligned_cols=17 Identities=24% Similarity=0.274 Sum_probs=15.2
Q ss_pred CCCCcHHHHHHHHHHhh
Q 038709 49 GTFDAAEEAAIAVYMMI 65 (67)
Q Consensus 49 G~f~t~eeAa~Ayd~aa 65 (67)
|+|+|+|+|..=||+..
T Consensus 71 GYF~t~eDA~~FydEl~ 87 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELT 87 (93)
T ss_pred CCcCCHHHHHHHHHHHH
Confidence 99999999999999753
No 10
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=80.94 E-value=1.1 Score=27.75 Aligned_cols=15 Identities=27% Similarity=0.745 Sum_probs=12.2
Q ss_pred ceEEeCCCCcHHHHH
Q 038709 44 ERHWLGTFDAAEEAA 58 (67)
Q Consensus 44 k~~~LG~f~t~eeAa 58 (67)
..+|||+|+|.+|-.
T Consensus 2 VsiWiG~f~s~~el~ 16 (122)
T PF14112_consen 2 VSIWIGNFKSEDELE 16 (122)
T ss_pred eEEEEecCCCHHHHH
Confidence 368999999988754
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=80.73 E-value=4.3 Score=27.29 Aligned_cols=34 Identities=18% Similarity=0.145 Sum_probs=23.3
Q ss_pred CCeEEEEEecCCCCceEEeCCCC--cHHHHHHHHHH
Q 038709 30 WGRYAAEIRNPRTKERHWLGTFD--AAEEAAIAVYM 63 (67)
Q Consensus 30 ~gkW~A~I~~~~~~k~~~LG~f~--t~eeAa~Ayd~ 63 (67)
++.|..++.......++.||+|+ |.++|....++
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~ 44 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADE 44 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHH
Confidence 45799998874334567899996 66676665443
No 12
>PRK09692 integrase; Provisional
Probab=80.57 E-value=6.7 Score=27.87 Aligned_cols=38 Identities=18% Similarity=0.193 Sum_probs=24.5
Q ss_pred EEECCCC--eEEEEEecCCCCce--EEeCCCC--cHHHHHHHHH
Q 038709 25 VRRRPWG--RYAAEIRNPRTKER--HWLGTFD--AAEEAAIAVY 62 (67)
Q Consensus 25 V~~~~~g--kW~A~I~~~~~~k~--~~LG~f~--t~eeAa~Ayd 62 (67)
|+..++| .|..+.+.+.+|++ +-||.|+ |..||..+-.
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~ 76 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRA 76 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHH
Confidence 4455644 59999875444554 6799999 6666655433
No 13
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=78.35 E-value=5 Score=21.61 Aligned_cols=33 Identities=33% Similarity=0.319 Sum_probs=22.2
Q ss_pred EEECCCCeEEEEEecCCCCceEEeCCCCcHHHHHHHH
Q 038709 25 VRRRPWGRYAAEIRNPRTKERHWLGTFDAAEEAAIAV 61 (67)
Q Consensus 25 V~~~~~gkW~A~I~~~~~~k~~~LG~f~t~eeAa~Ay 61 (67)
|..+..+.|...... +.+. ..+|+|.+||..+=
T Consensus 3 V~p~~~~~W~v~~eg--~~ra--~~~~~Tk~eAi~~A 35 (62)
T PF09954_consen 3 VVPREDGGWAVKKEG--AKRA--SKTFDTKAEAIEAA 35 (62)
T ss_pred EEecCCCCceEEeCC--Cccc--ccccCcHHHHHHHH
Confidence 333446889988773 2222 58999999987653
No 14
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=75.20 E-value=9.6 Score=21.72 Aligned_cols=36 Identities=22% Similarity=0.224 Sum_probs=22.9
Q ss_pred EECCC--CeEEEEEecCCCCceEEeCCCCc--HHHHHHHH
Q 038709 26 RRRPW--GRYAAEIRNPRTKERHWLGTFDA--AEEAAIAV 61 (67)
Q Consensus 26 ~~~~~--gkW~A~I~~~~~~k~~~LG~f~t--~eeAa~Ay 61 (67)
+..++ ..|..+.......+++-||.|++ ++||....
T Consensus 28 ~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a 67 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKA 67 (89)
T ss_dssp EE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHH
Confidence 44554 46999988633336789999986 55554443
No 15
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=72.98 E-value=3 Score=26.90 Aligned_cols=18 Identities=44% Similarity=0.440 Sum_probs=15.2
Q ss_pred ceEEeCCCCcHHHHHHHH
Q 038709 44 ERHWLGTFDAAEEAAIAV 61 (67)
Q Consensus 44 k~~~LG~f~t~eeAa~Ay 61 (67)
.=+++|.|.|+|||+++=
T Consensus 42 eVi~~g~~~tp~e~v~aA 59 (143)
T COG2185 42 EVINLGLFQTPEEAVRAA 59 (143)
T ss_pred eEEecCCcCCHHHHHHHH
Confidence 457999999999998863
No 16
>PF13773 DUF4170: Domain of unknown function (DUF4170)
Probab=64.28 E-value=7.5 Score=22.30 Aligned_cols=20 Identities=20% Similarity=0.084 Sum_probs=17.0
Q ss_pred EEeCCCCcHHHHHHHHHHhh
Q 038709 46 HWLGTFDAAEEAAIAVYMMI 65 (67)
Q Consensus 46 ~~LG~f~t~eeAa~Ayd~aa 65 (67)
-.+|-|++-++|..|..+.|
T Consensus 27 diVG~fp~y~~A~~aWrakA 46 (69)
T PF13773_consen 27 DIVGIFPDYASAYAAWRAKA 46 (69)
T ss_pred eEEecCCChHHHHHHHHHHH
Confidence 35799999999999988765
No 17
>PF14882 GHL12: Hypothetical glycosyl hydrolase 12
Probab=60.93 E-value=6 Score=21.28 Aligned_cols=12 Identities=33% Similarity=0.326 Sum_probs=9.8
Q ss_pred CCCcHHHHHHHH
Q 038709 50 TFDAAEEAAIAV 61 (67)
Q Consensus 50 ~f~t~eeAa~Ay 61 (67)
.|.|.+||..|-
T Consensus 39 ~Y~t~~eA~~Aa 50 (53)
T PF14882_consen 39 FYPTYEEASKAA 50 (53)
T ss_pred ccCCHHHHHHHH
Confidence 388999998873
No 18
>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=60.70 E-value=25 Score=20.40 Aligned_cols=38 Identities=18% Similarity=0.174 Sum_probs=23.8
Q ss_pred CCceeeEEECCCCeEEEEEecCCCCceEEeCCCCcHHHHHH
Q 038709 19 SSRYLGVRRRPWGRYAAEIRNPRTKERHWLGTFDAAEEAAI 59 (67)
Q Consensus 19 ~Sg~rGV~~~~~gkW~A~I~~~~~~k~~~LG~f~t~eeAa~ 59 (67)
--||+-|+ .-.|||+|-+-. +..-.---.|..+|.|.+
T Consensus 30 ~dgfrdvw-~lrgkyvafvl~--ge~f~rsp~fs~pesaqr 67 (80)
T PF10729_consen 30 MDGFRDVW-QLRGKYVAFVLM--GEHFRRSPAFSVPESAQR 67 (80)
T ss_dssp TTTECCEC-CCCCEEEEEEES--SS-EEE---BSSHHHHHH
T ss_pred ccccccee-eeccceEEEEEe--cchhccCCCcCCcHHHHH
Confidence 35788885 345999999985 233333467888888765
No 19
>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=57.80 E-value=17 Score=20.93 Aligned_cols=29 Identities=24% Similarity=0.311 Sum_probs=19.0
Q ss_pred CCeEEEEEecCCCCceEEe----CCCCcHHHHH
Q 038709 30 WGRYAAEIRNPRTKERHWL----GTFDAAEEAA 58 (67)
Q Consensus 30 ~gkW~A~I~~~~~~k~~~L----G~f~t~eeAa 58 (67)
.+-|.|+|.-....++.-+ --|+|++||.
T Consensus 15 ~~~W~aEItR~vTsrkTvVSK~~~GF~SEaeAq 47 (71)
T PF12286_consen 15 RNGWTAEITRRVTSRKTVVSKRQDGFASEAEAQ 47 (71)
T ss_pred CCceeeeeeeeecCceeEEEecccCcccHHHHH
Confidence 5789999985443332222 3599998875
No 20
>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=56.80 E-value=8.9 Score=22.31 Aligned_cols=15 Identities=33% Similarity=0.262 Sum_probs=12.9
Q ss_pred CCCCcHHHHHHHHHH
Q 038709 49 GTFDAAEEAAIAVYM 63 (67)
Q Consensus 49 G~f~t~eeAa~Ayd~ 63 (67)
-.|.|.|||.+||..
T Consensus 58 Avfss~~eAe~ay~~ 72 (75)
T PF11132_consen 58 AVFSSYEEAEQAYHE 72 (75)
T ss_pred hhhcCHHHHHHHHHH
Confidence 468999999999975
No 21
>PRK10927 essential cell division protein FtsN; Provisional
Probab=53.14 E-value=26 Score=25.51 Aligned_cols=32 Identities=16% Similarity=0.255 Sum_probs=22.0
Q ss_pred EEEEEecCCCCceEEeCCCCcHHHHHHHHHHh
Q 038709 33 YAAEIRNPRTKERHWLGTFDAAEEAAIAVYMM 64 (67)
Q Consensus 33 W~A~I~~~~~~k~~~LG~f~t~eeAa~Ayd~a 64 (67)
+.|+|.....=.||.||-|.+.++|.++.+..
T Consensus 273 ~~A~I~~~g~~~RVrVGPf~sr~eAe~a~~rL 304 (319)
T PRK10927 273 FDSKITTNNGWNRVVIGPVKGKENADSTLNRL 304 (319)
T ss_pred CeeEEccCCcEEEEEeCCCCCHHHHHHHHHHH
Confidence 34555432122588899999999998888764
No 22
>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=49.54 E-value=40 Score=19.50 Aligned_cols=20 Identities=50% Similarity=0.589 Sum_probs=12.8
Q ss_pred ecCCCCceEEeCCCCcHHHHHH
Q 038709 38 RNPRTKERHWLGTFDAAEEAAI 59 (67)
Q Consensus 38 ~~~~~~k~~~LG~f~t~eeAa~ 59 (67)
++|..|+.+.||+ +.+||..
T Consensus 32 r~P~tGk~~~LG~--d~~~Ai~ 51 (75)
T PF09003_consen 32 RNPITGKEHGLGT--DRAEAIA 51 (75)
T ss_dssp E-TTTS-EEEEES---HHHHHH
T ss_pred ecCCCCceeeCCC--CHHHHHH
Confidence 3667999999999 5555544
No 23
>COG3087 FtsN Cell division protein [Cell division and chromosome partitioning]
Probab=48.16 E-value=33 Score=24.34 Aligned_cols=21 Identities=24% Similarity=0.316 Sum_probs=18.3
Q ss_pred ceEEeCCCCcHHHHHHHHHHh
Q 038709 44 ERHWLGTFDAAEEAAIAVYMM 64 (67)
Q Consensus 44 k~~~LG~f~t~eeAa~Ayd~a 64 (67)
.|+-||.|++.++|..|-++.
T Consensus 229 yRV~vGP~n~~~~a~~aq~rL 249 (264)
T COG3087 229 YRVRVGPFNSKADAVKAQKRL 249 (264)
T ss_pred EEEEecCCCcHHHHHHHHHHH
Confidence 588899999999999987764
No 24
>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=46.54 E-value=29 Score=20.53 Aligned_cols=20 Identities=30% Similarity=0.327 Sum_probs=16.1
Q ss_pred eEEeCCCCcHHHHHHHHHHh
Q 038709 45 RHWLGTFDAAEEAAIAVYMM 64 (67)
Q Consensus 45 ~~~LG~f~t~eeAa~Ayd~a 64 (67)
..-+-.|+|+++|..+++..
T Consensus 56 q~~~~~~~~~~~A~~~F~k~ 75 (104)
T cd08001 56 GNKLEEFSSLEEAKMAFEEL 75 (104)
T ss_pred ceEccCCCCHHHHHHHHHHH
Confidence 44567899999999999863
No 25
>COG3010 NanE Putative N-acetylmannosamine-6-phosphate epimerase [Carbohydrate transport and metabolism]
Probab=45.86 E-value=17 Score=25.23 Aligned_cols=19 Identities=21% Similarity=0.256 Sum_probs=15.8
Q ss_pred eEEeCCCCcHHHHHHHHHH
Q 038709 45 RHWLGTFDAAEEAAIAVYM 63 (67)
Q Consensus 45 ~~~LG~f~t~eeAa~Ayd~ 63 (67)
-+-=|.|+|||.|+.|++.
T Consensus 183 vIAEGr~~tP~~Ak~a~~~ 201 (229)
T COG3010 183 VIAEGRYNTPEQAKKAIEI 201 (229)
T ss_pred EEeeCCCCCHHHHHHHHHh
Confidence 3455889999999999985
No 26
>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=42.93 E-value=39 Score=18.95 Aligned_cols=33 Identities=15% Similarity=0.149 Sum_probs=25.4
Q ss_pred CCeEEEEEecCCCCceEEeCCCCcHHHHHHHHHHh
Q 038709 30 WGRYAAEIRNPRTKERHWLGTFDAAEEAAIAVYMM 64 (67)
Q Consensus 30 ~gkW~A~I~~~~~~k~~~LG~f~t~eeAa~Ayd~a 64 (67)
.|-|.+++.. ...-+||=.|++.++-.++.+++
T Consensus 36 vG~~~~~~G~--~~~~~~l~~y~~~~~r~~~~~a~ 68 (102)
T PF07978_consen 36 VGYWVTEVGP--LNQVVHLWSYDDLAAREEAREAL 68 (102)
T ss_dssp EEEEEEEESB--SSEEEEEEEES-HHHHHHHHHHH
T ss_pred eEEEEeccCC--CceEEEEEEcCCHHHHHHHHHHH
Confidence 4789999885 67888999999988877776654
No 27
>PRK10113 cell division modulator; Provisional
Probab=42.72 E-value=23 Score=20.51 Aligned_cols=37 Identities=19% Similarity=0.142 Sum_probs=24.1
Q ss_pred CceeeEEECCCCeEEEEEecCCCCceEEeCCCCcHHHHHH
Q 038709 20 SRYLGVRRRPWGRYAAEIRNPRTKERHWLGTFDAAEEAAI 59 (67)
Q Consensus 20 Sg~rGV~~~~~gkW~A~I~~~~~~k~~~LG~f~t~eeAa~ 59 (67)
-+|+-|+.- .|||+|-+... ..-----.|..+|.|.+
T Consensus 31 d~frDVW~L-rGKYVAFvl~g--e~FrRSPaFs~PEsAQR 67 (80)
T PRK10113 31 DSFRDVWML-RGKYVAFVLMG--ESFLRSPAFSVPESAQR 67 (80)
T ss_pred cchhhhhee-ccceEEEEEec--hhhccCCccCCcHHHHH
Confidence 567777533 49999998852 22122367888888765
No 28
>PRK12757 cell division protein FtsN; Provisional
Probab=42.66 E-value=46 Score=23.39 Aligned_cols=31 Identities=16% Similarity=0.204 Sum_probs=21.9
Q ss_pred EEEEecCCCCceEEeCCCCcHHHHHHHHHHh
Q 038709 34 AAEIRNPRTKERHWLGTFDAAEEAAIAVYMM 64 (67)
Q Consensus 34 ~A~I~~~~~~k~~~LG~f~t~eeAa~Ayd~a 64 (67)
.++|....+=.||.+|-|.|.++|..+-+..
T Consensus 211 ~a~I~~~gg~yRVrVGPf~sr~~A~~~~~rL 241 (256)
T PRK12757 211 ESRITTGGGWNRVVLGPYNSKAAADKMLQRL 241 (256)
T ss_pred ceEEeecCCEEEEEeCCCCCHHHHHHHHHHH
Confidence 4555542223588999999999998887754
No 29
>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=42.04 E-value=17 Score=18.96 Aligned_cols=15 Identities=27% Similarity=0.344 Sum_probs=12.4
Q ss_pred CCCCcHHHHHHHHHH
Q 038709 49 GTFDAAEEAAIAVYM 63 (67)
Q Consensus 49 G~f~t~eeAa~Ayd~ 63 (67)
=.|.|+++|.+|.+.
T Consensus 44 v~f~~~~~a~~al~~ 58 (70)
T PF14259_consen 44 VEFSSEEDAKRALEL 58 (70)
T ss_dssp EEESSHHHHHHHHHH
T ss_pred EEeCCHHHHHHHHHH
Confidence 358999999999875
No 30
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=41.38 E-value=16 Score=17.51 Aligned_cols=15 Identities=33% Similarity=0.383 Sum_probs=13.1
Q ss_pred eCCCCcHHHHHHHHH
Q 038709 48 LGTFDAAEEAAIAVY 62 (67)
Q Consensus 48 LG~f~t~eeAa~Ayd 62 (67)
+..|+|..||++...
T Consensus 13 i~~F~Si~eAa~~l~ 27 (37)
T PF07453_consen 13 IKSFDSIREAARYLG 27 (37)
T ss_pred EEEEcCHHHHHHHhC
Confidence 589999999999864
No 31
>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=40.86 E-value=11 Score=16.74 Aligned_cols=11 Identities=27% Similarity=0.999 Sum_probs=7.6
Q ss_pred CCceEEeCCCC
Q 038709 42 TKERHWLGTFD 52 (67)
Q Consensus 42 ~~k~~~LG~f~ 52 (67)
....+|+||+.
T Consensus 14 ~~G~lWigT~~ 24 (24)
T PF07494_consen 14 SDGNLWIGTYN 24 (24)
T ss_dssp TTSCEEEEETS
T ss_pred CCcCEEEEeCC
Confidence 44578888863
No 32
>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=40.75 E-value=44 Score=19.66 Aligned_cols=21 Identities=19% Similarity=0.172 Sum_probs=14.8
Q ss_pred CCceEEeCCCCcHHHHHHHHHH
Q 038709 42 TKERHWLGTFDAAEEAAIAVYM 63 (67)
Q Consensus 42 ~~k~~~LG~f~t~eeAa~Ayd~ 63 (67)
.|... +=.|.|+++|..++..
T Consensus 52 ~Gq~~-~~~~~~~~~A~~~F~k 72 (102)
T cd07997 52 RGQSQ-LTPFGSLESAIKEFEK 72 (102)
T ss_pred cCcee-ecCCCCHHHHHHHHHH
Confidence 34443 3448889999999875
No 33
>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=40.64 E-value=24 Score=19.25 Aligned_cols=15 Identities=47% Similarity=0.507 Sum_probs=12.6
Q ss_pred CCCcHHHHHHHHHHh
Q 038709 50 TFDAAEEAAIAVYMM 64 (67)
Q Consensus 50 ~f~t~eeAa~Ayd~a 64 (67)
.|+|+++|..++++.
T Consensus 48 ~~~s~~~A~~~~~k~ 62 (74)
T cd07996 48 TFDSEEEALKAAEKL 62 (74)
T ss_pred ECCCHHHHHHHHHHH
Confidence 488999999998864
No 34
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=40.48 E-value=65 Score=20.90 Aligned_cols=31 Identities=16% Similarity=-0.032 Sum_probs=25.0
Q ss_pred eEEEEEecCCCCceEEeCCCCcHHHHHHHHHHhh
Q 038709 32 RYAAEIRNPRTKERHWLGTFDAAEEAAIAVYMMI 65 (67)
Q Consensus 32 kW~A~I~~~~~~k~~~LG~f~t~eeAa~Ayd~aa 65 (67)
-|.|+|.. |+-++-=..+++|.|..|...|+
T Consensus 95 gwaArVkp---G~vlfei~g~~e~~A~EAlr~Aa 125 (146)
T COG0197 95 GWAARVKP---GRVLFEIAGVPEELAREALRRAA 125 (146)
T ss_pred EEEEEecC---CcEEEEEecCcHHHHHHHHHHHh
Confidence 49999994 77777667788888999988776
No 35
>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=39.80 E-value=21 Score=17.68 Aligned_cols=18 Identities=22% Similarity=0.218 Sum_probs=13.9
Q ss_pred EEeCCCCcHHHHHHHHHH
Q 038709 46 HWLGTFDAAEEAAIAVYM 63 (67)
Q Consensus 46 ~~LG~f~t~eeAa~Ayd~ 63 (67)
..+=.|.|+++|..|.+.
T Consensus 42 ~~~v~f~s~~~a~~a~~~ 59 (74)
T cd00590 42 FAFVEFEDEEDAEKALEA 59 (74)
T ss_pred EEEEEECCHHHHHHHHHH
Confidence 444468999999999875
No 36
>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=39.07 E-value=23 Score=19.89 Aligned_cols=16 Identities=31% Similarity=0.362 Sum_probs=13.4
Q ss_pred CCCCcHHHHHHHHHHh
Q 038709 49 GTFDAAEEAAIAVYMM 64 (67)
Q Consensus 49 G~f~t~eeAa~Ayd~a 64 (67)
=.|+|++||..++++.
T Consensus 50 ~~f~s~~eA~~~f~~~ 65 (81)
T PF05406_consen 50 KPFDSEEEAIKEFEKL 65 (81)
T ss_dssp EEESSHHHHHHHHHHH
T ss_pred EeCCCHHHHHHHHHHH
Confidence 3789999999998763
No 37
>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=38.70 E-value=75 Score=17.97 Aligned_cols=43 Identities=21% Similarity=0.184 Sum_probs=30.0
Q ss_pred CCceeeEEECC-CCeEEEEEecCCCCceEEeCCCCcHHHHHHHHHHh
Q 038709 19 SSRYLGVRRRP-WGRYAAEIRNPRTKERHWLGTFDAAEEAAIAVYMM 64 (67)
Q Consensus 19 ~Sg~rGV~~~~-~gkW~A~I~~~~~~k~~~LG~f~t~eeAa~Ayd~a 64 (67)
...|.||..+- .-+-.+.|.. .|+-+..|. .|+|||..|.+..
T Consensus 35 Pe~fpgl~~r~~~p~~t~~IF~--sGki~itGa-ks~~~~~~a~~~i 78 (86)
T PF00352_consen 35 PERFPGLIYRLRNPKATVLIFS--SGKIVITGA-KSEEEAKKAIEKI 78 (86)
T ss_dssp TTTESSEEEEETTTTEEEEEET--TSEEEEEEE-SSHHHHHHHHHHH
T ss_pred eccCCeEEEeecCCcEEEEEEc--CCEEEEEec-CCHHHHHHHHHHH
Confidence 34788876554 3466677774 888887775 6788888887753
No 38
>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=38.51 E-value=13 Score=20.30 Aligned_cols=11 Identities=27% Similarity=0.263 Sum_probs=9.4
Q ss_pred CCCeEEEEEec
Q 038709 29 PWGRYAAEIRN 39 (67)
Q Consensus 29 ~~gkW~A~I~~ 39 (67)
+.|+|+++|..
T Consensus 28 ~~Gke~sei~~ 38 (54)
T PF08178_consen 28 KTGKEVSEIEF 38 (54)
T ss_pred ccCceeeeeee
Confidence 47999999985
No 39
>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=37.01 E-value=34 Score=19.09 Aligned_cols=15 Identities=20% Similarity=0.202 Sum_probs=12.9
Q ss_pred CCCcHHHHHHHHHHh
Q 038709 50 TFDAAEEAAIAVYMM 64 (67)
Q Consensus 50 ~f~t~eeAa~Ayd~a 64 (67)
.|+|+++|..+++..
T Consensus 48 ~~~s~~~A~~~f~kl 62 (73)
T cd07994 48 QMPSKEEAEEHFMKL 62 (73)
T ss_pred cCCCHHHHHHHHHHH
Confidence 589999999999864
No 40
>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=36.87 E-value=49 Score=19.69 Aligned_cols=22 Identities=18% Similarity=0.179 Sum_probs=15.7
Q ss_pred CCceEEeCCCCcHHHHHHHHHH
Q 038709 42 TKERHWLGTFDAAEEAAIAVYM 63 (67)
Q Consensus 42 ~~k~~~LG~f~t~eeAa~Ayd~ 63 (67)
.|.....+.+++.++|..++..
T Consensus 49 ~Gq~~~~~~~~~l~~A~~~F~k 70 (100)
T cd08002 49 KGQNKLKGPWDSLEGAIKDFEK 70 (100)
T ss_pred cCcceeccCCCCHHHHHHHHHH
Confidence 3444455666779999999875
No 41
>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=35.51 E-value=30 Score=17.49 Aligned_cols=13 Identities=31% Similarity=0.437 Sum_probs=10.9
Q ss_pred CCCcHHHHHHHHH
Q 038709 50 TFDAAEEAAIAVY 62 (67)
Q Consensus 50 ~f~t~eeAa~Ayd 62 (67)
.|+|+|+|..|..
T Consensus 27 ~f~~~~~A~~a~~ 39 (56)
T PF13893_consen 27 EFASVEDAQKAIE 39 (56)
T ss_dssp EESSHHHHHHHHH
T ss_pred EECCHHHHHHHHH
Confidence 4899999998865
No 42
>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=35.21 E-value=18 Score=22.91 Aligned_cols=12 Identities=33% Similarity=0.324 Sum_probs=9.3
Q ss_pred CCCCcHHHHHHH
Q 038709 49 GTFDAAEEAAIA 60 (67)
Q Consensus 49 G~f~t~eeAa~A 60 (67)
-.|+|+-||++|
T Consensus 98 e~~pTpl~aARA 109 (125)
T PF06236_consen 98 ESYPTPLEAARA 109 (125)
T ss_dssp EEESSHHHHHHH
T ss_pred cCCCCHHHHHHH
Confidence 457898888876
No 43
>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=34.50 E-value=27 Score=17.73 Aligned_cols=15 Identities=27% Similarity=0.302 Sum_probs=12.2
Q ss_pred CCCCcHHHHHHHHHH
Q 038709 49 GTFDAAEEAAIAVYM 63 (67)
Q Consensus 49 G~f~t~eeAa~Ayd~ 63 (67)
=.|++.++|..|.+.
T Consensus 44 V~F~~~~~a~~a~~~ 58 (70)
T PF00076_consen 44 VEFESEEDAEKALEE 58 (70)
T ss_dssp EEESSHHHHHHHHHH
T ss_pred EEEcCHHHHHHHHHH
Confidence 358999999998764
No 44
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=34.26 E-value=96 Score=19.57 Aligned_cols=31 Identities=13% Similarity=0.021 Sum_probs=23.5
Q ss_pred CeEEEEEecCCCCceE-EeCCCCcHHHHHHHHHHhh
Q 038709 31 GRYAAEIRNPRTKERH-WLGTFDAAEEAAIAVYMMI 65 (67)
Q Consensus 31 gkW~A~I~~~~~~k~~-~LG~f~t~eeAa~Ayd~aa 65 (67)
.-|.|+|.. |+-+ -++. .+++.|..|...|+
T Consensus 91 ~~~varVk~---G~iifEi~~-~~~~~a~~al~~a~ 122 (138)
T PRK09203 91 EYWVAVVKP---GRILFEIAG-VSEELAREALRLAA 122 (138)
T ss_pred cEEEEEECC---CCEEEEEeC-CCHHHHHHHHHHHh
Confidence 459999994 5544 4555 88999999988775
No 45
>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=34.17 E-value=40 Score=18.94 Aligned_cols=15 Identities=33% Similarity=0.417 Sum_probs=13.1
Q ss_pred CCCcHHHHHHHHHHh
Q 038709 50 TFDAAEEAAIAVYMM 64 (67)
Q Consensus 50 ~f~t~eeAa~Ayd~a 64 (67)
.|+|+++|..+++..
T Consensus 54 ~~~s~~~A~~~f~k~ 68 (84)
T smart00773 54 TFDSLEDAIKEFEKL 68 (84)
T ss_pred cCCCHHHHHHHHHHH
Confidence 689999999999864
No 46
>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=33.85 E-value=55 Score=23.32 Aligned_cols=32 Identities=13% Similarity=0.172 Sum_probs=22.1
Q ss_pred EEEEEecCCC--CceEEeCCCCcHHHHHHHHHHh
Q 038709 33 YAAEIRNPRT--KERHWLGTFDAAEEAAIAVYMM 64 (67)
Q Consensus 33 W~A~I~~~~~--~k~~~LG~f~t~eeAa~Ayd~a 64 (67)
+.+.|....+ -.||.+|-|.+.++|..+-+..
T Consensus 253 ~~~~i~~~~g~~~yRV~vGPf~sr~~A~~~~~~L 286 (298)
T TIGR02223 253 ISSKITTTDGGKWYRVVSGPYKNKDDAEKDLNKL 286 (298)
T ss_pred CceEEEecCCceEEEEEeCCCCCHHHHHHHHHHH
Confidence 3455553222 2588999999999998887654
No 47
>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=33.60 E-value=1e+02 Score=19.11 Aligned_cols=31 Identities=13% Similarity=0.012 Sum_probs=23.3
Q ss_pred CeEEEEEecCCCCceE-EeCCCCcHHHHHHHHHHhh
Q 038709 31 GRYAAEIRNPRTKERH-WLGTFDAAEEAAIAVYMMI 65 (67)
Q Consensus 31 gkW~A~I~~~~~~k~~-~LG~f~t~eeAa~Ayd~aa 65 (67)
.-|+|+|.. |+-+ -++. .+++.|..|...|+
T Consensus 90 ~~~varV~~---G~ilfEi~~-~~~~~a~~al~~a~ 121 (126)
T TIGR01164 90 EYWVAVVKP---GKILFEIAG-VPEEVAREAFRLAA 121 (126)
T ss_pred CEEEEEECC---CCEEEEEeC-CCHHHHHHHHHHHH
Confidence 459999994 5554 4555 89999999988765
No 48
>PF00626 Gelsolin: Gelsolin repeat; InterPro: IPR007123 Gelsolin is a cytoplasmic, calcium-regulated, actin-modulating protein that binds to the barbed ends of actin filaments, preventing monomer exchange (end-blocking or capping) []. It can promote nucleation (the assembly of monomers into filaments), as well as sever existing filaments. In addition, this protein binds with high affinity to fibronectin. Plasma gelsolin and cytoplasmic gelsolin are derived from a single gene by alternate initiation sites and differential splicing. Sequence comparisons indicate an evolutionary relationship between gelsolin, villin, fragmin and severin []. Six large repeating segments occur in gelsolin and villin, and 3 similar segments in severin and fragmin. While the multiple repeats have yet to be related to any known function of the actin-severing proteins, the superfamily appears to have evolved from an ancestral sequence of 120 to 130 amino acid residues [].; PDB: 3FG6_F 1RGI_G 2FGH_A 1D0N_B 3EGD_B 2NUP_B 2NUT_B 3EGX_B 1JHW_A 1J72_A ....
Probab=32.72 E-value=54 Score=17.33 Aligned_cols=23 Identities=26% Similarity=0.375 Sum_probs=18.5
Q ss_pred CceEEeCCCCcHHHHHHHHHHhh
Q 038709 43 KERHWLGTFDAAEEAAIAVYMMI 65 (67)
Q Consensus 43 ~k~~~LG~f~t~eeAa~Ayd~aa 65 (67)
.-.+|+|.-.+.+|-..|.+.|.
T Consensus 28 ~i~vW~G~~~~~~e~~~a~~~a~ 50 (76)
T PF00626_consen 28 EIFVWVGKKSSPEEKAFAAQLAQ 50 (76)
T ss_dssp EEEEEEHTTSHHHHHHHHHHHHH
T ss_pred CcEEEEeccCCHHHHHHHHHHHH
Confidence 44679999999999888877664
No 49
>KOG1256 consensus Long-chain acyl-CoA synthetases (AMP-forming) [Lipid transport and metabolism]
Probab=32.55 E-value=25 Score=28.00 Aligned_cols=28 Identities=21% Similarity=0.267 Sum_probs=25.1
Q ss_pred EEEEecCCCCceEEeCCCCcHHHHHHHHHH
Q 038709 34 AAEIRNPRTKERHWLGTFDAAEEAAIAVYM 63 (67)
Q Consensus 34 ~A~I~~~~~~k~~~LG~f~t~eeAa~Ayd~ 63 (67)
..||.+ .|..++-|+|.++|+-+.|.|.
T Consensus 498 ~GEIci--rG~~Vf~GYyK~p~~T~e~ide 525 (691)
T KOG1256|consen 498 KGEICV--RGPNVFMGYYKDPEKTAEAIDE 525 (691)
T ss_pred cceEEE--ecchhceeccCChHHHhhhhcc
Confidence 678886 8999999999999999999874
No 50
>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=32.43 E-value=44 Score=19.34 Aligned_cols=35 Identities=14% Similarity=-0.054 Sum_probs=21.7
Q ss_pred CCeEEEEEecCCCCceEEe----CCCCcHHHHHHHHHHh
Q 038709 30 WGRYAAEIRNPRTKERHWL----GTFDAAEEAAIAVYMM 64 (67)
Q Consensus 30 ~gkW~A~I~~~~~~k~~~L----G~f~t~eeAa~Ayd~a 64 (67)
.+-|..-|+....|...-. .+|.|+|+|.++++..
T Consensus 25 d~g~~v~~~yGR~Gt~gq~~tkt~~~~~~~~A~k~~~Kl 63 (77)
T cd07998 25 DDGYVVNFRYGRRGSALREGTKTVAPVTLEAAEKIFDKL 63 (77)
T ss_pred CCceEEEEEEccccCCcccccccCCCCCHHHHHHHHHHH
Confidence 3455555555444443322 3558999999999864
No 51
>smart00360 RRM RNA recognition motif.
Probab=32.10 E-value=34 Score=16.65 Aligned_cols=15 Identities=27% Similarity=0.330 Sum_probs=11.7
Q ss_pred CCCCcHHHHHHHHHH
Q 038709 49 GTFDAAEEAAIAVYM 63 (67)
Q Consensus 49 G~f~t~eeAa~Ayd~ 63 (67)
=+|.|.++|..|.+.
T Consensus 43 v~f~~~~~a~~a~~~ 57 (71)
T smart00360 43 VEFESEEDAEKALEA 57 (71)
T ss_pred EEeCCHHHHHHHHHH
Confidence 358999999988754
No 52
>PF14032 PknH_C: PknH-like extracellular domain
Probab=31.72 E-value=36 Score=21.42 Aligned_cols=18 Identities=17% Similarity=0.054 Sum_probs=15.5
Q ss_pred EeCCCCcHHHHHHHHHHh
Q 038709 47 WLGTFDAAEEAAIAVYMM 64 (67)
Q Consensus 47 ~LG~f~t~eeAa~Ayd~a 64 (67)
-++.|+|+++|..+++..
T Consensus 86 aV~~fp~~~~A~~~f~~~ 103 (189)
T PF14032_consen 86 AVVVFPSAAAAQAFFARL 103 (189)
T ss_pred EEEEeCCHHHHHHHHHHH
Confidence 458899999999999864
No 53
>smart00361 RRM_1 RNA recognition motif.
Probab=31.24 E-value=32 Score=18.47 Aligned_cols=14 Identities=43% Similarity=0.544 Sum_probs=11.8
Q ss_pred CCCcHHHHHHHHHH
Q 038709 50 TFDAAEEAAIAVYM 63 (67)
Q Consensus 50 ~f~t~eeAa~Ayd~ 63 (67)
+|.+.++|..|...
T Consensus 43 ~f~~~~dA~~A~~~ 56 (70)
T smart00361 43 TFERSEDAARAIVD 56 (70)
T ss_pred EECCHHHHHHHHHH
Confidence 68999999998764
No 54
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=31.00 E-value=33 Score=17.15 Aligned_cols=16 Identities=31% Similarity=0.499 Sum_probs=12.9
Q ss_pred EEeCCCCcHHHHHHHH
Q 038709 46 HWLGTFDAAEEAAIAV 61 (67)
Q Consensus 46 ~~LG~f~t~eeAa~Ay 61 (67)
..+..|+|..||++..
T Consensus 12 ~~i~~f~S~~eAa~~l 27 (53)
T smart00497 12 NLIGEFSSIREAAKYL 27 (53)
T ss_pred CEEEEecCHHHHHHHh
Confidence 3556999999999874
No 55
>CHL00044 rpl16 ribosomal protein L16
Probab=30.91 E-value=1.2e+02 Score=19.14 Aligned_cols=31 Identities=13% Similarity=0.075 Sum_probs=21.7
Q ss_pred CeEEEEEecCCCCceE-EeCCCCcHHHHHHHHHHhh
Q 038709 31 GRYAAEIRNPRTKERH-WLGTFDAAEEAAIAVYMMI 65 (67)
Q Consensus 31 gkW~A~I~~~~~~k~~-~LG~f~t~eeAa~Ayd~aa 65 (67)
.-|.|.|.. |+-+ -++. .+++.|..|...|+
T Consensus 91 ~~~va~V~~---G~ilfEi~g-~~~~~ak~al~~a~ 122 (135)
T CHL00044 91 EYWVAVVKP---GRILYEMGG-VSETIARAAIKIAA 122 (135)
T ss_pred cEEEEEECC---CcEEEEEeC-CCHHHHHHHHHHHh
Confidence 359999994 5554 4554 56688888887765
No 56
>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=30.43 E-value=61 Score=17.89 Aligned_cols=24 Identities=17% Similarity=0.163 Sum_probs=19.0
Q ss_pred CCceEEeCCCCcHHHHHHHHHHhh
Q 038709 42 TKERHWLGTFDAAEEAAIAVYMMI 65 (67)
Q Consensus 42 ~~k~~~LG~f~t~eeAa~Ayd~aa 65 (67)
.-..+.+|.|+|.++.-.|-+...
T Consensus 14 ~~~d~v~gvy~se~~C~~a~~eQk 37 (57)
T PF07358_consen 14 ECEDVVVGVYDSEQQCLAAADEQK 37 (57)
T ss_pred CCeEEEeecccCHHHHHHHHHhcc
Confidence 346788999999999888876543
No 57
>PRK10545 nucleotide excision repair endonuclease; Provisional
Probab=30.42 E-value=39 Score=23.92 Aligned_cols=17 Identities=41% Similarity=0.691 Sum_probs=13.0
Q ss_pred ceEEeCCCCcHHHHHHH
Q 038709 44 ERHWLGTFDAAEEAAIA 60 (67)
Q Consensus 44 k~~~LG~f~t~eeAa~A 60 (67)
.=.||||++|.+|+...
T Consensus 241 ~W~~lg~~~~~~~~~~l 257 (286)
T PRK10545 241 NWLWLGAVNSLEEAATL 257 (286)
T ss_pred ceEEecccCCHHHHHHH
Confidence 33579999999988543
No 58
>PF03799 FtsQ: Cell division protein FtsQ; InterPro: IPR005548 FtsQ is one of several cell division proteins. FtsQ interacts with other Fts proteins, reviewed in []. The precise function of FtsQ is unknown.; PDB: 2VH1_B 2VH2_B 2ALJ_A 1YR1_A.
Probab=30.29 E-value=1.1e+02 Score=17.27 Aligned_cols=40 Identities=18% Similarity=0.155 Sum_probs=27.3
Q ss_pred CceeeEEECCCCeEEEEEecCCCCceEEeCCCCcHHHHHHHHHH
Q 038709 20 SRYLGVRRRPWGRYAAEIRNPRTKERHWLGTFDAAEEAAIAVYM 63 (67)
Q Consensus 20 Sg~rGV~~~~~gkW~A~I~~~~~~k~~~LG~f~t~eeAa~Ayd~ 63 (67)
+...-|...+.+.|...+. +|..+.+|.-+ .++....|..
T Consensus 59 ~~i~~i~~~~~~~~~l~l~---dg~~V~lg~~~-~~~kl~~~~~ 98 (117)
T PF03799_consen 59 SQISEISYDPRGSWTLYLD---DGVEVKLGRSD-LAEKLQRLVK 98 (117)
T ss_dssp HS-SEEEEETTSCEEEE-S---SS-EEEEESST-HHHHHHHHHH
T ss_pred ceeeEEEECCCCeEEEEEC---CCcEEEEcCcC-HHHHHHHHHH
Confidence 4455677777677998887 69999999997 6666655543
No 59
>PRK10672 rare lipoprotein A; Provisional
Probab=29.60 E-value=69 Score=23.67 Aligned_cols=20 Identities=25% Similarity=0.255 Sum_probs=13.6
Q ss_pred ceEEeCCCCcHHHHHHHHHH
Q 038709 44 ERHWLGTFDAAEEAAIAVYM 63 (67)
Q Consensus 44 k~~~LG~f~t~eeAa~Ayd~ 63 (67)
.|+.||-|.+.++|..+.++
T Consensus 327 YRVrLGPF~sr~eA~kl~~r 346 (361)
T PRK10672 327 YRVQLGPFASRQQASALQQR 346 (361)
T ss_pred EEEEeCCCCCHHHHHHHHHH
Confidence 36677777777777766554
No 60
>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=29.31 E-value=53 Score=17.90 Aligned_cols=17 Identities=24% Similarity=0.362 Sum_probs=13.2
Q ss_pred eCCCCcHHHHHHHHHHh
Q 038709 48 LGTFDAAEEAAIAVYMM 64 (67)
Q Consensus 48 LG~f~t~eeAa~Ayd~a 64 (67)
+|+||+..||.+.-..|
T Consensus 1 mgyyd~~nearriskla 17 (59)
T PF07384_consen 1 MGYYDKRNEARRISKLA 17 (59)
T ss_pred CCcccchhHHHHHHHHH
Confidence 48999999998865443
No 61
>PRK10905 cell division protein DamX; Validated
Probab=28.12 E-value=57 Score=23.86 Aligned_cols=19 Identities=32% Similarity=0.240 Sum_probs=15.5
Q ss_pred eEEeCCCCcHHHHHHHHHH
Q 038709 45 RHWLGTFDAAEEAAIAVYM 63 (67)
Q Consensus 45 ~~~LG~f~t~eeAa~Ayd~ 63 (67)
.+..|.|.|.+||.+|-..
T Consensus 287 VV~yG~YaSraeAk~Aiak 305 (328)
T PRK10905 287 VLVSGVYASKEEAKRAVST 305 (328)
T ss_pred EEEecCCCCHHHHHHHHHH
Confidence 4567999999999998543
No 62
>PF04131 NanE: Putative N-acetylmannosamine-6-phosphate epimerase; InterPro: IPR007260 This family represents a putative ManNAc-6-P-to-GlcNAc-6P epimerase in the N-acetylmannosamine (ManNAc) utilization pathway found mainly in pathogenic bacteria for the reaction: N-acyl-D-glucosamine 6-phosphate = N-acyl-D-mannosamine 6-phosphate It is probably encoded by the yhcJ gene [].; GO: 0047465 N-acylglucosamine-6-phosphate 2-epimerase activity, 0006051 N-acetylmannosamine metabolic process; PDB: 1Y0E_B 3IGS_A 1YXY_A 3Q58_B.
Probab=27.22 E-value=45 Score=22.53 Aligned_cols=18 Identities=28% Similarity=0.207 Sum_probs=13.1
Q ss_pred EeCCCCcHHHHHHHHHHh
Q 038709 47 WLGTFDAAEEAAIAVYMM 64 (67)
Q Consensus 47 ~LG~f~t~eeAa~Ayd~a 64 (67)
-=|.+.|||+|++|.+.-
T Consensus 149 aEGri~tpe~a~~al~~G 166 (192)
T PF04131_consen 149 AEGRIHTPEQAAKALELG 166 (192)
T ss_dssp EESS--SHHHHHHHHHTT
T ss_pred ecCCCCCHHHHHHHHhcC
Confidence 348899999999998863
No 63
>smart00362 RRM_2 RNA recognition motif.
Probab=26.45 E-value=48 Score=16.15 Aligned_cols=16 Identities=25% Similarity=0.378 Sum_probs=11.7
Q ss_pred eCCCCcHHHHHHHHHH
Q 038709 48 LGTFDAAEEAAIAVYM 63 (67)
Q Consensus 48 LG~f~t~eeAa~Ayd~ 63 (67)
+=+|.+.++|..|...
T Consensus 43 ~v~f~~~~~a~~a~~~ 58 (72)
T smart00362 43 FVEFESEEDAEKAIEA 58 (72)
T ss_pred EEEeCCHHHHHHHHHH
Confidence 3458889999888653
No 64
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=26.18 E-value=79 Score=19.54 Aligned_cols=19 Identities=21% Similarity=0.093 Sum_probs=15.2
Q ss_pred ceEEeCCCCcHHHHHHHHH
Q 038709 44 ERHWLGTFDAAEEAAIAVY 62 (67)
Q Consensus 44 k~~~LG~f~t~eeAa~Ayd 62 (67)
.=+.||.|.|+|+...+..
T Consensus 32 eVi~lg~~~s~e~~v~aa~ 50 (132)
T TIGR00640 32 DVDVGPLFQTPEEIARQAV 50 (132)
T ss_pred EEEECCCCCCHHHHHHHHH
Confidence 3468999999999887754
No 65
>PF09341 Pcc1: Transcription factor Pcc1; InterPro: IPR015419 Pcc1 is a proposed transcription factor involved in the expression of genes regulated by alpha-factor and galactose; component of the EKC/KEOPS protein complex with Kae1, Gon7, Bud32, and Cgi121; related to human cancer-testis antigens [].; PDB: 2BNR_C 2P5W_C 3KLA_C 2F54_C 2P5E_C 2F53_C 3ENO_E 3ENC_B.
Probab=25.95 E-value=63 Score=17.79 Aligned_cols=13 Identities=31% Similarity=0.434 Sum_probs=10.6
Q ss_pred CCcHHHHHHHHHH
Q 038709 51 FDAAEEAAIAVYM 63 (67)
Q Consensus 51 f~t~eeAa~Ayd~ 63 (67)
|+|+++|..+|..
T Consensus 9 f~s~~~A~ii~~s 21 (76)
T PF09341_consen 9 FESEEKAEIIYRS 21 (76)
T ss_dssp -SSHHHHHHHHHH
T ss_pred eCCHHHHHHHHHH
Confidence 8999999999875
No 66
>KOG1176 consensus Acyl-CoA synthetase [Lipid transport and metabolism]
Probab=25.74 E-value=37 Score=26.02 Aligned_cols=27 Identities=19% Similarity=0.043 Sum_probs=23.4
Q ss_pred EEEecCCCCceEEeCCCCcHHHHHHHHHH
Q 038709 35 AEIRNPRTKERHWLGTFDAAEEAAIAVYM 63 (67)
Q Consensus 35 A~I~~~~~~k~~~LG~f~t~eeAa~Ayd~ 63 (67)
.||.+ .|..+|.|+|.++|+-+++.|.
T Consensus 380 GEI~v--rg~~imkGY~~NpeaT~~~~~~ 406 (537)
T KOG1176|consen 380 GEICV--RGPQVMKGYLKNPEATKEAFDD 406 (537)
T ss_pred eEEEE--ECcccchhhcCChHHHHhhccc
Confidence 78886 8999999999999998877663
No 67
>COG4935 Regulatory P domain of the subtilisin-like proprotein convertases and other proteases [Posttranslational modification, protein turnover, chaperones]
Probab=25.41 E-value=1.1e+02 Score=20.43 Aligned_cols=34 Identities=24% Similarity=0.322 Sum_probs=22.7
Q ss_pred CCCCceeeEEE--------CCCCeEEEEEecCCCCceEEeCCCCc
Q 038709 17 RQSSRYLGVRR--------RPWGRYAAEIRNPRTKERHWLGTFDA 53 (67)
Q Consensus 17 ~~~Sg~rGV~~--------~~~gkW~A~I~~~~~~k~~~LG~f~t 53 (67)
...-+|..++. ++.|.|.=+|.+...| ++|+|.+
T Consensus 78 ~~~q~~~~~s~~l~~~~ge~~~G~W~L~V~D~~~g---~~Gtf~s 119 (177)
T COG4935 78 DDSQGYNDQSFMLVQLWGERAEGNWRLEVQDLAGG---HTGTFHS 119 (177)
T ss_pred cccceeeeeeeeeeeeccCCCCceEEEEEEecCCC---ceeEEEE
Confidence 34556666543 3479999999986666 4477765
No 68
>cd00283 GIY-YIG_Cterm GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing endonucleases promote the mobility of intron or intein by recognizing and cleaving a homologous allele that lacks the sequence. They catalyze a double-strand break in the DNA near the insertion site of that element to facilitate homing at that site. Class I homing endonucleases are sorted into four families based on the presence of these motifs in their respective N-termini: LAGLIDADG, His-Cys box, HNH, and GIY-YIG. This CD contains several but not all members of the GIY-YIG family. The C-terminus of GIY-YIG is a DNA-binding domain which is separated from the N-terminus by a long, flexible linker. The DNA-binding domain consists of a minor-groove binding alpha-helix, and a helix-turn-helix. Some also contain a zinc finger (i.e. I-TevI) which is not required for DNA binding or catalysis, but is a component of the linker and directs the catalytic domain to cleave the homing sit
Probab=24.26 E-value=49 Score=20.19 Aligned_cols=16 Identities=38% Similarity=0.617 Sum_probs=14.0
Q ss_pred EeCCCCcHHHHHHHHH
Q 038709 47 WLGTFDAAEEAAIAVY 62 (67)
Q Consensus 47 ~LG~f~t~eeAa~Ayd 62 (67)
+++.|+|.-||++...
T Consensus 76 ~i~~F~S~~EAar~lg 91 (113)
T cd00283 76 YIGIFDSTTEAARFLK 91 (113)
T ss_pred CeEEeCCHHHHHHHHC
Confidence 7899999999999753
No 69
>COG1022 FAA1 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]
Probab=24.11 E-value=40 Score=26.36 Aligned_cols=27 Identities=22% Similarity=0.145 Sum_probs=23.8
Q ss_pred EEEEecCCCCceEEeCCCCcHHHHHHHHH
Q 038709 34 AAEIRNPRTKERHWLGTFDAAEEAAIAVY 62 (67)
Q Consensus 34 ~A~I~~~~~~k~~~LG~f~t~eeAa~Ayd 62 (67)
.-||.+ .|..+..|+|..+|+-+.|+|
T Consensus 420 ~GEilV--RG~~Vm~GYyk~pe~Taeaf~ 446 (613)
T COG1022 420 DGEILV--RGPNVMKGYYKNPEATAEAFT 446 (613)
T ss_pred CceEEE--ecchhcchhcCChHHHhhhcc
Confidence 567775 789999999999999999987
No 70
>PF01693 Cauli_VI: Caulimovirus viroplasmin; InterPro: IPR011320 This entry represents the N-terminal domain of RNase HI, which has a 3-layer alpha/beta/alpha structure []. This domain is lacking in retroviral and prokaryotic enzymes, but shows a striking structural similarity to the ribosomal protein L9 N-terminal domain, and may function as a regulatory RNA-binding module. However, the topology of this domain differs from structures of known RNA binding domains such as the double-stranded RNA binding domain (dsRBD), the hnRNP K homology (KH) domain and the RNP motif. Eukaryotic RNases HI possess either one or two copies of this small N-terminal domain, in addition to the well-conserved catalytic RNase H domain. RNase HI belongs to the family of ribonuclease H enzymes that recognise RNA:DNA hybrids and degrade the RNA component. ; PDB: 1QHK_A 3BSU_C.
Probab=23.47 E-value=49 Score=16.57 Aligned_cols=11 Identities=36% Similarity=0.450 Sum_probs=8.3
Q ss_pred CCCCcHHHHHH
Q 038709 49 GTFDAAEEAAI 59 (67)
Q Consensus 49 G~f~t~eeAa~ 59 (67)
-.|+|.|||..
T Consensus 33 k~F~t~~eA~~ 43 (44)
T PF01693_consen 33 KSFKTREEAEE 43 (44)
T ss_dssp EEESSHHHHHH
T ss_pred CCcCCHHHHhh
Confidence 56788888864
No 71
>PRK11901 hypothetical protein; Reviewed
Probab=23.41 E-value=71 Score=23.34 Aligned_cols=16 Identities=25% Similarity=0.333 Sum_probs=13.5
Q ss_pred EeCCCCcHHHHHHHHH
Q 038709 47 WLGTFDAAEEAAIAVY 62 (67)
Q Consensus 47 ~LG~f~t~eeAa~Ayd 62 (67)
..|.|+|.+||..|-.
T Consensus 287 vyG~Y~Sr~eAk~Ai~ 302 (327)
T PRK11901 287 VSGNYASSAEAKRAIA 302 (327)
T ss_pred EecCcCCHHHHHHHHH
Confidence 3599999999998854
No 72
>COG3831 Uncharacterized conserved protein [Function unknown]
Probab=23.34 E-value=72 Score=18.93 Aligned_cols=17 Identities=24% Similarity=0.337 Sum_probs=13.8
Q ss_pred EeCCCCcHHHHHHHHHH
Q 038709 47 WLGTFDAAEEAAIAVYM 63 (67)
Q Consensus 47 ~LG~f~t~eeAa~Ayd~ 63 (67)
-+=+|++.++|..++..
T Consensus 41 ~~k~F~~~~~a~~~~~k 57 (85)
T COG3831 41 QIKSFDDSADAEKAALK 57 (85)
T ss_pred eeeeCCCHHHHHHHHHH
Confidence 45679999999888765
No 73
>PF02249 MCR_alpha: Methyl-coenzyme M reductase alpha subunit, C-terminal domain; InterPro: IPR009047 Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterosulphide CoM-S-S-CoB (2.8.4.1 from EC), the final step in methane biosynthesis. This reaction proceeds under anaerobic conditions by methanogenic Archaea [], and requires a nickel-porphinoid prosthetic group, coenzyme F430, which is in the EPR-detectable Ni(I) oxidation state in the active enzyme. Studies on a catalytically inactive enzyme aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. The binding of coenzyme M appears to induce specific conformational changes that suggests a molecular mechanism by which the enzyme ensures that methyl-coenzyme M enters the substrate channel prior to coenzyme B, as required by the active-site geometry []. MCR is a hexamer composed of 2 alpha, 2 beta, and 2 gamma subunits with two identical nickel porphinoid active sites, which form two long active site channels with F430 embedded at the bottom [, ]. This entry represents the C-terminal domain of the alpha subunit, which is comprised of an all-alpha multi-helical bundle. ; GO: 0050524 coenzyme-B sulfoethylthiotransferase activity, 0015948 methanogenesis; PDB: 3SQG_A 1HBU_D 3M2V_D 3POT_A 3M2U_A 1HBN_A 1HBO_A 3M30_A 3M2R_A 3M1V_A ....
Probab=23.24 E-value=29 Score=22.09 Aligned_cols=9 Identities=33% Similarity=1.066 Sum_probs=7.6
Q ss_pred eEEeCCCCc
Q 038709 45 RHWLGTFDA 53 (67)
Q Consensus 45 ~~~LG~f~t 53 (67)
.||||+|.|
T Consensus 2 qiwlgsyms 10 (127)
T PF02249_consen 2 QIWLGSYMS 10 (127)
T ss_dssp CCCCCCCTS
T ss_pred ceeEccccc
Confidence 589999987
No 74
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain. Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. In reference, one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff.
Probab=22.79 E-value=72 Score=23.54 Aligned_cols=20 Identities=20% Similarity=0.310 Sum_probs=16.5
Q ss_pred eCCCCcHHHHHHHHHHhhcC
Q 038709 48 LGTFDAAEEAAIAVYMMILY 67 (67)
Q Consensus 48 LG~f~t~eeAa~Ayd~aa~~ 67 (67)
+-.|+|+|+|++|+.....|
T Consensus 427 ip~f~~p~~A~~al~~~~~~ 446 (447)
T TIGR02717 427 IPNYTFPERAVKALSALYRY 446 (447)
T ss_pred CCccCCHHHHHHHHHHHHhh
Confidence 68999999999998766543
No 75
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.70 E-value=52 Score=20.24 Aligned_cols=15 Identities=47% Similarity=0.532 Sum_probs=12.8
Q ss_pred eCCCCcHHHHHHHHH
Q 038709 48 LGTFDAAEEAAIAVY 62 (67)
Q Consensus 48 LG~f~t~eeAa~Ayd 62 (67)
|-+||||.+.+.|..
T Consensus 16 LAcfdTPs~v~~aVk 30 (104)
T PF10045_consen 16 LACFDTPSEVAEAVK 30 (104)
T ss_pred HHhhCCHHHHHHHHH
Confidence 678999999988865
No 76
>TIGR00279 L10e ribosomal protein L10.e. L10.e is distantly related to eubacterial ribosomal protein L16.
Probab=22.29 E-value=1.6e+02 Score=19.59 Aligned_cols=32 Identities=13% Similarity=-0.049 Sum_probs=22.8
Q ss_pred CeEEEEEecCCCCceEEeCCCC--cHHHHHHHHHHhh
Q 038709 31 GRYAAEIRNPRTKERHWLGTFD--AAEEAAIAVYMMI 65 (67)
Q Consensus 31 gkW~A~I~~~~~~k~~~LG~f~--t~eeAa~Ayd~aa 65 (67)
.-|.|.|. .|+.++--.-. +.+.|..|...|+
T Consensus 120 ~~wvArVk---~Gqiifei~~~~~~~~~AkeAlr~A~ 153 (172)
T TIGR00279 120 VGTAARVK---IGQKIFSVWTKPSNFDVAKEALRRAA 153 (172)
T ss_pred cEEEEEEC---cCCEEEEEEeecCCHHHHHHHHHHHh
Confidence 46999999 46666544334 7888888887764
No 77
>PRK14887 KEOPS complex Pcc1-like subunit; Provisional
Probab=22.24 E-value=69 Score=18.56 Aligned_cols=15 Identities=27% Similarity=0.368 Sum_probs=12.7
Q ss_pred CCCcHHHHHHHHHHh
Q 038709 50 TFDAAEEAAIAVYMM 64 (67)
Q Consensus 50 ~f~t~eeAa~Ayd~a 64 (67)
.|+|++.|..+|..-
T Consensus 11 ~f~s~~~A~iiy~sl 25 (84)
T PRK14887 11 EFETEERARIIYRSV 25 (84)
T ss_pred EECCHHHHHHHHHHh
Confidence 489999999999864
No 78
>PF08383 Maf_N: Maf N-terminal region; InterPro: IPR013592 This region is found in various leucine zipper transcription factors of the Maf family. These are implicated in the regulation of insulin gene expression [], in erythroid differentiation [], and in differentiation of the neuroretina [].
Probab=21.58 E-value=65 Score=16.11 Aligned_cols=10 Identities=30% Similarity=0.242 Sum_probs=7.6
Q ss_pred CcHHHHHHHH
Q 038709 52 DAAEEAAIAV 61 (67)
Q Consensus 52 ~t~eeAa~Ay 61 (67)
=|+|||..|-
T Consensus 23 LtpEDAvEaL 32 (35)
T PF08383_consen 23 LTPEDAVEAL 32 (35)
T ss_pred CCHHHHHHHH
Confidence 4789998774
No 79
>PF10003 DUF2244: Integral membrane protein (DUF2244); InterPro: IPR019253 This entry consists of various bacterial putative membrane proteins with no known function.
Probab=21.37 E-value=1.4e+02 Score=18.51 Aligned_cols=23 Identities=17% Similarity=0.063 Sum_probs=19.6
Q ss_pred CCCceEEeCCCCcHHHHHHHHHH
Q 038709 41 RTKERHWLGTFDAAEEAAIAVYM 63 (67)
Q Consensus 41 ~~~k~~~LG~f~t~eeAa~Ayd~ 63 (67)
..|+++-+|.|=++||-..-+++
T Consensus 113 ~~g~~veiG~fL~~~eR~~la~~ 135 (140)
T PF10003_consen 113 SRGREVEIGRFLNPEEREELARE 135 (140)
T ss_pred ECCEEEEEccCCCHHHHHHHHHH
Confidence 47999999999999998776654
No 80
>PF02805 Ada_Zn_binding: Metal binding domain of Ada; InterPro: IPR004026 The Escherichia coli Ada protein repairs O6-methylguanine residues and methyl phosphotriesters in DNA by direct transfer of the methyl group to a cysteine residue. This domain contains four conserved cysteines that form a zinc binding site [, ]. One of these cysteines is a methyl group acceptor. The methylated domain can then specifically bind to the ada box on a DNA duplex [].; GO: 0003677 DNA binding, 0008168 methyltransferase activity, 0008270 zinc ion binding, 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent; PDB: 1WPK_A 1ZGW_A 1EYF_A 1ADN_A 1U8B_A.
Probab=20.53 E-value=44 Score=18.76 Aligned_cols=14 Identities=50% Similarity=0.456 Sum_probs=10.3
Q ss_pred EeCCCCcHHHHHHH
Q 038709 47 WLGTFDAAEEAAIA 60 (67)
Q Consensus 47 ~LG~f~t~eeAa~A 60 (67)
.+-.|+|++||..|
T Consensus 42 nv~ff~s~~eA~~a 55 (66)
T PF02805_consen 42 NVVFFDSAEEAEAA 55 (66)
T ss_dssp CEEEESSHHHHHHT
T ss_pred eeEeeCCHHHHHHc
Confidence 33558999999764
No 81
>smart00703 NRF N-terminal domain in C. elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4). Also present in several other worm and fly proteins.
Probab=20.13 E-value=27 Score=20.69 Aligned_cols=25 Identities=20% Similarity=0.804 Sum_probs=18.8
Q ss_pred ECCCCeEEEEEecCCCCceEEeCCCCcH
Q 038709 27 RRPWGRYAAEIRNPRTKERHWLGTFDAA 54 (67)
Q Consensus 27 ~~~~gkW~A~I~~~~~~k~~~LG~f~t~ 54 (67)
.+.+||.-+-|. .|..+|||.|+.=
T Consensus 8 ~Da~Gk~psGll---~Gn~~~lG~ydeC 32 (110)
T smart00703 8 LDAWGKFPSGLL---EGNNLWLGSYEEC 32 (110)
T ss_pred ecccCCCCCeEE---EeecCcccCHHHH
Confidence 456788877776 5778999999863
No 82
>PF11821 DUF3341: Protein of unknown function (DUF3341); InterPro: IPR021776 This family of proteins are functionally uncharacterised. This family is found in bacteria. Proteins in this family are about 170 amino acids in length.
Probab=20.09 E-value=88 Score=20.61 Aligned_cols=20 Identities=25% Similarity=0.197 Sum_probs=15.5
Q ss_pred ceEEeCCCCcHHHHHHHHHH
Q 038709 44 ERHWLGTFDAAEEAAIAVYM 63 (67)
Q Consensus 44 k~~~LG~f~t~eeAa~Ayd~ 63 (67)
++..||.|+|+|+...|-.+
T Consensus 2 ~~gl~a~F~~~~~l~~A~~~ 21 (173)
T PF11821_consen 2 KYGLLAEFDDPEALLHAARK 21 (173)
T ss_pred CceEEEEECCHHHHHHHHHH
Confidence 45678999999988777554
Done!