Query 046604
Match_columns 134
No_of_seqs 118 out of 716
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 02:32:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046604.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046604hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5201 SKP1 SCF ubiquitin lig 100.0 5.3E-43 1.1E-47 245.8 12.1 128 3-132 3-157 (158)
2 KOG1724 SCF ubiquitin ligase, 100.0 8.7E-43 1.9E-47 255.5 11.3 129 2-132 5-162 (162)
3 PF01466 Skp1: Skp1 family, di 100.0 2.1E-29 4.6E-34 164.8 6.7 73 58-131 5-77 (78)
4 smart00512 Skp1 Found in Skp1 99.8 2.1E-21 4.5E-26 132.8 6.9 79 2-82 2-104 (104)
5 PF03931 Skp1_POZ: Skp1 family 99.6 6.2E-16 1.3E-20 96.8 3.4 51 3-54 2-61 (62)
6 KOG3473 RNA polymerase II tran 99.1 1.4E-10 3.1E-15 78.2 6.4 78 2-82 17-112 (112)
7 PF00651 BTB: BTB/POZ domain; 97.7 0.00032 6.9E-09 46.8 7.7 85 3-95 12-109 (111)
8 PHA02713 hypothetical protein; 97.4 0.0016 3.5E-08 56.2 10.1 93 3-106 27-132 (557)
9 PHA03098 kelch-like protein; P 97.4 0.0012 2.7E-08 55.9 8.8 89 4-101 12-109 (534)
10 smart00225 BTB Broad-Complex, 97.4 0.00055 1.2E-08 43.0 5.1 77 4-90 2-90 (90)
11 PHA02790 Kelch-like protein; P 96.2 0.019 4.1E-07 48.6 7.0 85 5-98 24-121 (480)
12 KOG4441 Proteins containing BT 95.3 0.067 1.5E-06 46.5 7.0 84 4-97 39-134 (571)
13 KOG2716 Polymerase delta-inter 94.9 0.17 3.7E-06 39.4 7.5 85 9-100 11-108 (230)
14 KOG3433 Protein involved in me 93.4 0.085 1.8E-06 39.7 3.0 38 74-116 161-200 (203)
15 COG5124 Protein predicted to b 93.2 0.089 1.9E-06 39.5 2.8 31 81-116 174-204 (209)
16 PF03962 Mnd1: Mnd1 family; I 83.4 1.4 3.1E-05 33.1 3.3 42 70-116 144-187 (188)
17 PF11822 DUF3342: Domain of un 80.8 1.6 3.5E-05 35.5 2.9 82 12-98 14-105 (317)
18 PF02214 BTB_2: BTB/POZ domain 79.6 1.7 3.8E-05 28.2 2.3 73 10-89 6-94 (94)
19 KOG0783 Uncharacterized conser 70.9 6.3 0.00014 36.5 4.1 101 4-107 713-825 (1267)
20 PF13921 Myb_DNA-bind_6: Myb-l 70.2 8.5 0.00018 22.7 3.5 34 90-123 20-60 (60)
21 PF15063 TC1: Thyroid cancer p 59.6 11 0.00023 24.5 2.5 33 91-123 28-60 (79)
22 PF10892 DUF2688: Protein of u 59.6 12 0.00026 22.9 2.6 25 102-126 30-56 (60)
23 PF12556 CobS_N: Cobaltochelat 59.1 5.7 0.00012 22.0 1.1 12 105-116 14-25 (36)
24 PF03656 Pam16: Pam16; InterP 58.3 9.1 0.0002 27.1 2.3 33 96-131 51-83 (127)
25 KOG4682 Uncharacterized conser 57.1 12 0.00025 31.9 3.0 48 66-116 139-186 (488)
26 cd00167 SANT 'SWI3, ADA2, N-Co 56.0 14 0.00031 19.6 2.5 20 91-110 23-42 (45)
27 PRK05365 malonic semialdehyde 54.6 9.1 0.0002 28.2 1.9 33 73-115 131-163 (195)
28 smart00717 SANT SANT SWI3, AD 52.9 17 0.00037 19.5 2.5 20 91-110 25-44 (49)
29 PF11978 MVP_shoulder: Shoulde 52.9 11 0.00024 26.4 2.0 41 74-114 37-90 (118)
30 KOG4350 Uncharacterized conser 52.3 73 0.0016 27.5 6.9 96 4-106 47-181 (620)
31 cd02148 Nitroreductase_5 Nitro 51.2 11 0.00023 27.6 1.8 33 73-115 124-156 (185)
32 PF11460 DUF3007: Protein of u 49.2 19 0.0004 24.7 2.5 24 101-127 79-102 (104)
33 PF13798 PCYCGC: Protein of un 49.1 27 0.00058 25.7 3.5 22 87-108 119-140 (158)
34 COG4957 Predicted transcriptio 47.0 18 0.00038 26.1 2.2 19 98-116 97-115 (148)
35 PF02519 Auxin_inducible: Auxi 46.3 26 0.00057 23.6 2.9 47 3-50 40-99 (100)
36 PRK11053 dihydropteridine redu 43.0 22 0.00049 26.5 2.5 36 70-115 147-183 (217)
37 TIGR02698 CopY_TcrY copper tra 42.9 88 0.0019 21.8 5.3 41 85-125 72-112 (130)
38 KOG3442 Uncharacterized conser 42.8 27 0.00058 24.8 2.6 31 98-131 54-84 (132)
39 PF08671 SinI: Anti-repressor 40.9 20 0.00044 19.0 1.4 13 98-110 15-27 (30)
40 PF00249 Myb_DNA-binding: Myb- 40.7 67 0.0015 18.0 4.8 36 69-109 8-44 (48)
41 cd02140 Nitroreductase_4 Nitro 40.6 19 0.00041 26.3 1.7 38 70-115 127-164 (192)
42 PF13518 HTH_28: Helix-turn-he 40.1 52 0.0011 18.3 3.2 21 92-112 5-25 (52)
43 cd05029 S-100A6 S-100A6: S-100 40.0 66 0.0014 20.8 4.1 44 82-125 9-58 (88)
44 TIGR03147 cyt_nit_nrfF cytochr 39.8 32 0.00068 24.4 2.6 18 92-109 65-83 (126)
45 PF02736 Myosin_N: Myosin N-te 38.3 27 0.00059 19.5 1.7 18 1-18 23-40 (42)
46 PF13384 HTH_23: Homeodomain-l 38.1 38 0.00083 18.9 2.4 17 97-113 15-31 (50)
47 PF05443 ROS_MUCR: ROS/MUCR tr 37.4 16 0.00035 26.0 0.9 17 99-115 94-110 (132)
48 TIGR01999 iscU FeS cluster ass 37.4 41 0.00089 23.2 2.9 36 74-109 51-87 (124)
49 TIGR03419 NifU_clost FeS clust 37.4 45 0.00098 22.9 3.1 37 73-109 46-83 (121)
50 PRK11325 scaffold protein; Pro 37.1 41 0.00089 23.4 2.9 37 73-109 52-89 (127)
51 KOG4244 Failed axon connection 35.4 40 0.00087 27.0 2.8 24 102-125 111-134 (281)
52 PF03883 DUF328: Protein of un 35.0 43 0.00092 25.9 2.9 41 84-124 25-65 (237)
53 PF01843 DIL: DIL domain; Int 34.4 22 0.00048 23.6 1.1 59 43-109 37-96 (105)
54 PF03750 DUF310: Protein of un 33.8 61 0.0013 22.3 3.3 34 80-114 8-43 (119)
55 PF09524 Phg_2220_C: Conserved 33.6 37 0.0008 21.8 2.0 63 11-81 10-73 (74)
56 COG3370 Uncharacterized protei 33.5 30 0.00064 24.1 1.6 28 66-96 52-79 (113)
57 PF03918 CcmH: Cytochrome C bi 32.9 41 0.00089 24.3 2.4 18 92-109 65-83 (148)
58 PF11103 DUF2887: Protein of u 32.6 60 0.0013 24.7 3.3 29 81-109 172-200 (200)
59 PF10507 DUF2453: Protein of u 32.6 1E+02 0.0022 21.3 4.2 46 84-131 34-87 (111)
60 PRK13696 hypothetical protein; 31.9 1.2E+02 0.0026 18.8 4.0 26 98-126 36-61 (62)
61 PF01592 NifU_N: NifU-like N t 31.7 60 0.0013 22.4 3.0 22 86-107 64-85 (126)
62 PRK10144 formate-dependent nit 30.4 55 0.0012 23.2 2.6 18 92-109 65-83 (126)
63 TIGR02476 BluB cob(II)yrinic a 29.8 44 0.00095 24.7 2.2 36 71-116 135-170 (205)
64 PF14098 SSPI: Small, acid-sol 29.4 64 0.0014 20.2 2.5 19 91-109 5-23 (65)
65 PLN03212 Transcription repress 29.2 85 0.0018 24.8 3.7 35 91-125 49-91 (249)
66 PRK09296 cysteine desufuration 29.2 1.1E+02 0.0023 21.9 4.0 30 89-118 81-118 (138)
67 PF09382 RQC: RQC domain; Int 28.1 77 0.0017 20.6 3.0 39 87-125 19-64 (106)
68 PF11399 DUF3192: Protein of u 27.7 64 0.0014 22.0 2.5 25 91-116 26-50 (102)
69 PF05871 ESCRT-II: ESCRT-II co 27.4 41 0.0009 24.1 1.6 14 43-56 26-39 (139)
70 PF09713 A_thal_3526: Plant pr 27.2 93 0.002 18.7 2.9 34 99-132 12-49 (54)
71 PF02796 HTH_7: Helix-turn-hel 27.0 91 0.002 17.4 2.7 16 97-112 19-34 (45)
72 PF00196 GerE: Bacterial regul 26.7 1.2E+02 0.0026 17.5 3.4 23 91-113 10-32 (58)
73 cd02144 iodotyrosine_dehalogen 26.7 58 0.0013 23.3 2.3 35 72-116 131-166 (193)
74 PF11165 DUF2949: Protein of u 26.6 1E+02 0.0022 18.8 3.0 10 43-52 49-58 (58)
75 COG4680 Uncharacterized protei 26.6 45 0.00097 22.5 1.5 17 99-115 35-51 (98)
76 cd06664 IscU_like Iron-sulfur 26.4 1.1E+02 0.0024 20.6 3.6 37 73-109 47-84 (123)
77 smart00421 HTH_LUXR helix_turn 26.4 1.1E+02 0.0023 16.7 3.1 18 96-113 15-32 (58)
78 PRK15019 CsdA-binding activato 26.3 1.2E+02 0.0025 22.0 3.8 29 90-118 92-128 (147)
79 TIGR03553 F420_FbiB_CTERM F420 26.2 48 0.001 24.0 1.8 17 100-116 149-165 (194)
80 COG2996 Predicted RNA-bindinin 25.9 42 0.00092 27.0 1.5 13 101-113 248-260 (287)
81 PF07671 DUF1601: Protein of u 25.0 80 0.0017 17.5 2.1 30 79-108 7-36 (37)
82 smart00385 CYCLIN domain prese 24.9 1.5E+02 0.0033 17.2 4.9 41 81-124 36-78 (83)
83 PF04355 SmpA_OmlA: SmpA / Oml 24.6 44 0.00095 20.4 1.2 21 93-113 9-29 (71)
84 TIGR03391 FeS_syn_CsdE cystein 24.4 1.4E+02 0.003 21.3 3.8 29 90-118 87-123 (138)
85 COG1710 Uncharacterized protei 24.3 56 0.0012 23.1 1.7 20 94-113 103-123 (139)
86 cd03370 NADH_oxidase NADPH_oxi 24.1 58 0.0013 22.8 1.9 19 97-115 112-131 (156)
87 PF14748 P5CR_dimer: Pyrroline 23.9 2E+02 0.0043 19.2 4.4 55 72-126 26-87 (107)
88 cd05295 MDH_like Malate dehydr 23.5 81 0.0018 27.0 2.9 26 103-128 79-104 (452)
89 PF01476 LysM: LysM domain; I 23.5 70 0.0015 17.2 1.8 23 89-112 8-31 (44)
90 COG0822 IscU NifU homolog invo 23.3 1.4E+02 0.003 21.6 3.7 36 74-109 54-90 (150)
91 TIGR01994 SUF_scaf_2 SUF syste 23.1 1.1E+02 0.0024 21.4 3.2 37 74-110 51-88 (137)
92 PRK14981 DNA-directed RNA poly 23.0 1.1E+02 0.0024 20.8 3.1 44 81-125 61-105 (112)
93 PF03131 bZIP_Maf: bZIP Maf tr 22.9 1E+02 0.0023 20.0 2.8 27 96-125 5-31 (92)
94 PF02657 SufE: Fe-S metabolism 22.3 2.1E+02 0.0045 19.8 4.4 33 82-118 69-108 (125)
95 PF09278 MerR-DNA-bind: MerR, 22.3 62 0.0013 19.2 1.5 17 98-114 13-29 (65)
96 PF05391 Lsm_interact: Lsm int 21.8 70 0.0015 15.6 1.3 12 98-109 8-19 (21)
97 KOG1665 AFH1-interacting prote 21.6 86 0.0019 24.8 2.4 40 43-89 64-103 (302)
98 PF05409 Peptidase_C30: Corona 21.5 1.1E+02 0.0023 24.8 2.9 51 66-120 215-265 (293)
99 PF06851 DUF1247: Protein of u 21.3 1.4E+02 0.003 21.7 3.3 34 78-112 100-134 (148)
100 cd02149 NfsB_like_nitroreducta 21.1 84 0.0018 22.0 2.2 17 98-114 112-128 (157)
101 PF08281 Sigma70_r4_2: Sigma-7 20.9 64 0.0014 18.3 1.3 18 96-113 23-40 (54)
102 cd02062 Nitro_FMN_reductase Pr 20.8 1.1E+02 0.0023 20.0 2.5 36 70-115 75-112 (122)
103 PF04282 DUF438: Family of unk 20.7 2.1E+02 0.0045 18.1 3.7 27 98-124 11-38 (71)
104 PF06056 Terminase_5: Putative 20.2 1.6E+02 0.0036 17.6 3.1 19 94-112 8-26 (58)
105 PF10584 Proteasome_A_N: Prote 20.0 24 0.00052 17.6 -0.6 16 4-19 5-20 (23)
No 1
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.3e-43 Score=245.82 Aligned_cols=128 Identities=33% Similarity=0.398 Sum_probs=119.5
Q ss_pred ceEEEeCCCCEEEecHHHHHH--HHhhccCCCCCC-CCceecc------hHHHHHHHHhcCCC-----------c-----
Q 046604 3 ENIFEDGGQQLFKVEEQGCSR--LCSHSSTSDGTS-EDMVVLQ------LPYIIKFCKAHGVS-----------K----- 57 (134)
Q Consensus 3 ~i~l~S~DG~~f~V~~~~~~~--~i~~~~le~~~~-~~~Ipl~------L~~Iie~c~~h~~~-----------k----- 57 (134)
+|.|+|+||++|+|+...|.. +|++| +.+.++ .-|||+| |.+|++||+||+.. |
T Consensus 3 ~i~l~s~dge~F~vd~~iAerSiLikN~-l~d~~~~n~p~p~pnVrSsvl~kv~ew~ehh~~s~sede~d~~~rks~p~D 81 (158)
T COG5201 3 MIELESIDGEIFRVDENIAERSILIKNM-LCDSTACNYPIPAPNVRSSVLMKVQEWMEHHTSSLSEDENDLEIRKSKPSD 81 (158)
T ss_pred ceEEEecCCcEEEehHHHHHHHHHHHHH-hccccccCCCCcccchhHHHHHHHHHHHHhccccCCCccChHhhhccCCcc
Confidence 689999999999999999999 99999 888765 3688888 99999999999875 1
Q ss_pred --ccccccCCChHHHHHHHHhhccccchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCCHHHHHHHHHhchhhhh
Q 046604 58 --ENEFGKGKSNDELKEMLLVADYLTIKDTLDYLAETLANRIKNKSVEYIRKFFGIENNFMPEEKEATRKEYELLRL 132 (134)
Q Consensus 58 --D~~F~~~~~~~~l~~Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~t~eee~~i~~e~~w~~~ 132 (134)
|+.|+++ |+++|++++.|||||+|++|+++||+.||.+|+||||+|||++|||++||||||+++||+||.|+++
T Consensus 82 ~wdr~Fm~v-DqemL~eI~laaNYL~ikpLLd~gCKivaemirgkSpeeir~tfni~ndfTpEEe~~irkEnEWaed 157 (158)
T COG5201 82 FWDRFFMEV-DQEMLLEICLAANYLEIKPLLDLGCKIVAEMIRGKSPEEIRETFNIENDFTPEEERRIRKENEWAED 157 (158)
T ss_pred HHHHHHHHh-hHHHHHHHHHhhccccchHHHHHHHHHHHHHHccCCHHHHHHHhCCCCCCCHHHHHHHHHhcccccc
Confidence 7788888 9999999999999999999999999999999999999999999999999999999999999999975
No 2
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.7e-43 Score=255.47 Aligned_cols=129 Identities=36% Similarity=0.504 Sum_probs=117.7
Q ss_pred CceEEEeCCCCEEEecHHHHHH--HHhhccCCCC-CCCC--ceecc------hHHHHHHHHhcCCC-----------c--
Q 046604 2 EENIFEDGGQQLFKVEEQGCSR--LCSHSSTSDG-TSED--MVVLQ------LPYIIKFCKAHGVS-----------K-- 57 (134)
Q Consensus 2 ~~i~l~S~DG~~f~V~~~~~~~--~i~~~~le~~-~~~~--~Ipl~------L~~Iie~c~~h~~~-----------k-- 57 (134)
..|+|+||||++|.|+.++|++ +|+++ +.+. +..+ +|||| |++||+||+||+.+ +
T Consensus 5 ~~ikL~SsDG~~f~ve~~~a~~s~~i~~~-~~~~~~~~~~~~IPl~nV~~~iL~kVIewC~~Hk~d~~~~~~~~~~~~~~ 83 (162)
T KOG1724|consen 5 KKIKLESSDGEIFEVEEEVARQSQTISAH-MIEDGCADENDPIPLPNVTSKILKKVIEWCKKHKDDDPANPEDKELPEET 83 (162)
T ss_pred CeEEEEccCCceeehhHHHHHHhHHHHHH-HHHcCCCccCCccccCccCHHHHHHHHHHHHHcccccccccccccccccC
Confidence 3689999999999999999999 87776 5543 3444 89999 99999999999964 1
Q ss_pred -----ccccccCCChHHHHHHHHhhccccchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCCHHHHHHHHHhchhhhh
Q 046604 58 -----ENEFGKGKSNDELKEMLLVADYLTIKDTLDYLAETLANRIKNKSVEYIRKFFGIENNFMPEEKEATRKEYELLRL 132 (134)
Q Consensus 58 -----D~~F~~~~~~~~l~~Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~t~eee~~i~~e~~w~~~ 132 (134)
|++|++. +...||+|+.|||||+|++|+++||+.||+|++||||+|+|..|||++|+||||+++++++|.|++.
T Consensus 84 ~i~~WD~~Flk~-d~~tLfdli~AAnyLdi~gLl~~~ck~va~mikgktpeEir~~f~I~~d~t~eE~~~~~~e~~~~~~ 162 (162)
T KOG1724|consen 84 DIPEWDAEFLKV-DQGTLFDLILAANYLDIKGLLDLTCKTVANMIKGKTPEEIREIFNIENDETPEEEEAIRKENEWAFE 162 (162)
T ss_pred CccHHHHHHHhc-CHHHHHHHHHHhhhcccHHHHHHHHHHHHHHHccCCHHHHHHHcCCCCCCChhHHHHHhhccccccC
Confidence 8999995 9999999999999999999999999999999999999999999999999999999999999999974
No 3
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=99.96 E-value=2.1e-29 Score=164.81 Aligned_cols=73 Identities=51% Similarity=0.679 Sum_probs=64.6
Q ss_pred ccccccCCChHHHHHHHHhhccccchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCCHHHHHHHHHhchhhh
Q 046604 58 ENEFGKGKSNDELKEMLLVADYLTIKDTLDYLAETLANRIKNKSVEYIRKFFGIENNFMPEEKEATRKEYELLR 131 (134)
Q Consensus 58 D~~F~~~~~~~~l~~Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~t~eee~~i~~e~~w~~ 131 (134)
|++|++. +.+.|++|+.||+||+|++|+++||++||++++||||+|||++|||++|+|+||++++|+||+|++
T Consensus 5 D~~F~~~-~~~~L~~l~~AA~yL~I~~L~~~~~~~iA~~i~gks~eeir~~fgi~~d~t~eee~~i~~e~~w~~ 77 (78)
T PF01466_consen 5 DQEFLDV-DNDELFDLLNAANYLDIKGLLDLCCKYIANMIKGKSPEEIRKYFGIENDLTPEEEEEIRKENEWAF 77 (78)
T ss_dssp HHHHT-S--HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHTTS-HHHHHHHHT---TSSHHHHHHHHHHCCCTB
T ss_pred HHHHHHc-CHHHHHHHHHHHHHHcchHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHHHHcchhc
Confidence 7899966 999999999999999999999999999999999999999999999999999999999999999997
No 4
>smart00512 Skp1 Found in Skp1 protein family. Family of Skp1 (kinetochore protein required for cell cycle progression) and elongin C (subunit of RNA polymerase II transcription factor SIII) homologues.
Probab=99.85 E-value=2.1e-21 Score=132.82 Aligned_cols=79 Identities=24% Similarity=0.364 Sum_probs=70.2
Q ss_pred CceEEEeCCCCEEEecHHHHHH--HHhhccCCCCCCC----Cceecc------hHHHHHHHHhcCCCc------------
Q 046604 2 EENIFEDGGQQLFKVEEQGCSR--LCSHSSTSDGTSE----DMVVLQ------LPYIIKFCKAHGVSK------------ 57 (134)
Q Consensus 2 ~~i~l~S~DG~~f~V~~~~~~~--~i~~~~le~~~~~----~~Ipl~------L~~Iie~c~~h~~~k------------ 57 (134)
..|+|+|+||+.|.|++.+|++ ++++| +++.+.. .+||+| |++|++||+||+.+.
T Consensus 2 ~~v~L~S~Dg~~f~v~~~~a~~S~~i~~~-l~~~~~~~~~~~~Ipl~~v~~~~L~~Vi~yc~~h~~~~~~~~~~~~~~~w 80 (104)
T smart00512 2 KYIKLISSDGEVFEVEREVARQSKTIKAM-IEDLGVDDENNNPIPLPNVTSKILSKVIEYCEHHVDDPPSVADKDDIPTW 80 (104)
T ss_pred CeEEEEeCCCCEEEecHHHHHHHHHHHHH-HHccCcccCCCCCccCCCcCHHHHHHHHHHHHHcccCCCCccccccccHH
Confidence 4699999999999999999999 99999 9876532 489988 999999999998651
Q ss_pred ccccccCCChHHHHHHHHhhccccc
Q 046604 58 ENEFGKGKSNDELKEMLLVADYLTI 82 (134)
Q Consensus 58 D~~F~~~~~~~~l~~Li~AA~yL~I 82 (134)
|.+|++. +++.|++|+.||+||+|
T Consensus 81 D~~F~~~-d~~~l~dLl~AAnyL~I 104 (104)
T smart00512 81 DAEFLKI-DQETLFELILAANYLDI 104 (104)
T ss_pred HHHHHcC-CHHHHHHHHHHHHhhCC
Confidence 7899995 99999999999999997
No 5
>PF03931 Skp1_POZ: Skp1 family, tetramerisation domain; InterPro: IPR016073 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a POZ domain with a core structure consisting of beta(2)/alpha(2)/beta(2)/alpha(2) in two layers, alpha/beta. This domain is found at the N-terminal of SKP1 proteins [] as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1LM8_C 2XAI_E 1VCB_E 3ZRC_K 3ZRF_E 3DCG_B 2C9W_C 1LQB_B 2IZV_C 1HV2_A ....
Probab=99.60 E-value=6.2e-16 Score=96.79 Aligned_cols=51 Identities=22% Similarity=0.306 Sum_probs=46.5
Q ss_pred ceEEEeCCCCEEEecHHHHHH--HHhhccCCCCCCCC-ceecc------hHHHHHHHHhcC
Q 046604 3 ENIFEDGGQQLFKVEEQGCSR--LCSHSSTSDGTSED-MVVLQ------LPYIIKFCKAHG 54 (134)
Q Consensus 3 ~i~l~S~DG~~f~V~~~~~~~--~i~~~~le~~~~~~-~Ipl~------L~~Iie~c~~h~ 54 (134)
.|+|+|+||+.|.|++++|++ ++++| +++.+... +||+| |++|++||+||+
T Consensus 2 ~v~L~SsDg~~f~V~~~~a~~S~~i~~m-l~~~~~~~~~Ipl~~v~~~~L~kViewc~~H~ 61 (62)
T PF03931_consen 2 YVKLVSSDGQEFEVSREAAKQSKTIKNM-LEDLGDEDEPIPLPNVSSRILKKVIEWCEHHK 61 (62)
T ss_dssp EEEEEETTSEEEEEEHHHHTTSHHHHHH-HHCTCCCGTEEEETTS-HHHHHHHHHHHHHHH
T ss_pred EEEEEcCCCCEEEeeHHHHHHhHHHHHH-HhhhcccccccccCccCHHHHHHHHHHHHhcC
Confidence 589999999999999999999 99999 98876553 59998 999999999996
No 6
>KOG3473 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin C [Transcription]
Probab=99.14 E-value=1.4e-10 Score=78.23 Aligned_cols=78 Identities=14% Similarity=0.124 Sum_probs=62.1
Q ss_pred CceEEEeCCCCEEEecHHHHHH--HHhhccCCCCC-----CCCceecc------hHHHHHHHHhcCCCc-----cccccc
Q 046604 2 EENIFEDGGQQLFKVEEQGCSR--LCSHSSTSDGT-----SEDMVVLQ------LPYIIKFCKAHGVSK-----ENEFGK 63 (134)
Q Consensus 2 ~~i~l~S~DG~~f~V~~~~~~~--~i~~~~le~~~-----~~~~Ipl~------L~~Iie~c~~h~~~k-----D~~F~~ 63 (134)
+.|+|+|+||..|.+.+++|+. +||.| +.+.+ ..+.+-++ |+||.+|+.+....+ -.+| +
T Consensus 17 ~yVkLvS~Ddhefiikre~AmtSgTiram-l~gpg~~se~~~n~v~f~di~shiLeKvc~Yl~Yk~rY~~~s~eiPeF-~ 94 (112)
T KOG3473|consen 17 MYVKLVSSDDHEFIIKREHAMTSGTIRAM-LSGPGVFSEAEKNEVYFRDIPSHILEKVCEYLAYKVRYTNSSTEIPEF-D 94 (112)
T ss_pred hheEeecCCCcEEEEeehhhhhhhHHHHH-HcCCccccccccceEEeccchHHHHHHHHHHhhheeeeccccccCCCC-C
Confidence 5699999999999999999999 99999 88643 12444443 999999998744332 3465 5
Q ss_pred CCChHHHHHHHHhhccccc
Q 046604 64 GKSNDELKEMLLVADYLTI 82 (134)
Q Consensus 64 ~~~~~~l~~Li~AA~yL~I 82 (134)
. ..++.++|+.||+||++
T Consensus 95 I-ppemaleLL~aAn~Lec 112 (112)
T KOG3473|consen 95 I-PPEMALELLMAANYLEC 112 (112)
T ss_pred C-CHHHHHHHHHHhhhhcC
Confidence 5 89999999999999974
No 7
>PF00651 BTB: BTB/POZ domain; InterPro: IPR013069 The BTB (for BR-C, ttk and bab) [] or POZ (for Pox virus and Zinc finger) [] domain is present near the N terminus of a fraction of zinc finger (IPR007087 from INTERPRO) proteins and in proteins that contain the IPR006652 from INTERPRO motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation []. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule []. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [, , ]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.; GO: 0005515 protein binding; PDB: 3M5B_A 1R28_B 3LBZ_A 3E4U_F 3BIM_B 1R2B_A 1R29_A 2VPK_A 2YY9_B 3GA1_A ....
Probab=97.69 E-value=0.00032 Score=46.82 Aligned_cols=85 Identities=15% Similarity=0.172 Sum_probs=65.5
Q ss_pred ceEEEeCCCCEEEecHHHHHH---HHhhccCCCCC-CC---Cceecc------hHHHHHHHHhcCCCcccccccCCChHH
Q 046604 3 ENIFEDGGQQLFKVEEQGCSR---LCSHSSTSDGT-SE---DMVVLQ------LPYIIKFCKAHGVSKENEFGKGKSNDE 69 (134)
Q Consensus 3 ~i~l~S~DG~~f~V~~~~~~~---~i~~~~le~~~-~~---~~Ipl~------L~~Iie~c~~h~~~kD~~F~~~~~~~~ 69 (134)
.++|+..||+.|.|.+.+... .++++ +...+ .+ ..|+++ +..+++||.... +..-+.+.
T Consensus 12 D~~i~v~d~~~~~vhk~iL~~~S~~F~~~-~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~Y~~~-------~~~~~~~~ 83 (111)
T PF00651_consen 12 DVTIRVGDGKTFYVHKNILAARSPYFRNL-FEGSKFKESTVPEISLPDVSPEAFEAFLEYMYTGE-------IEINSDEN 83 (111)
T ss_dssp -EEEEETTTEEEEE-HHHHHHHBHHHHHH-HTTTTSTTSSEEEEEETTSCHHHHHHHHHHHHHSE-------EEEE-TTT
T ss_pred CEEEEECCCEEEeechhhhhccchhhhhc-ccccccccccccccccccccccccccccccccCCc-------ccCCHHHH
Confidence 478999999999999999977 99999 88763 22 246655 999999995422 11203677
Q ss_pred HHHHHHhhccccchhHHHHHHHHHHH
Q 046604 70 LKEMLLVADYLTIKDTLDYLAETLAN 95 (134)
Q Consensus 70 l~~Li~AA~yL~I~~Ll~l~~~~iA~ 95 (134)
+.+++.+|++++++.|.+.|+..+..
T Consensus 84 ~~~ll~lA~~~~~~~L~~~~~~~l~~ 109 (111)
T PF00651_consen 84 VEELLELADKLQIPELKKACEKFLQE 109 (111)
T ss_dssp HHHHHHHHHHTTBHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCcHHHHHHHHHHHHh
Confidence 99999999999999999999998854
No 8
>PHA02713 hypothetical protein; Provisional
Probab=97.40 E-value=0.0016 Score=56.17 Aligned_cols=93 Identities=17% Similarity=0.179 Sum_probs=72.8
Q ss_pred ceEEEeCCCCEEEecHHHHHH---HHhhccCCCCC----CCCceecc------hHHHHHHHHhcCCCcccccccCCChHH
Q 046604 3 ENIFEDGGQQLFKVEEQGCSR---LCSHSSTSDGT----SEDMVVLQ------LPYIIKFCKAHGVSKENEFGKGKSNDE 69 (134)
Q Consensus 3 ~i~l~S~DG~~f~V~~~~~~~---~i~~~~le~~~----~~~~Ipl~------L~~Iie~c~~h~~~kD~~F~~~~~~~~ 69 (134)
.|+|...+|+.|.+-+.+... .++.| +..+- ....|.|. |+.|++|+.... ++.+.
T Consensus 27 DV~L~v~~~~~f~~Hr~vLaa~S~YF~am-F~~~~~e~~~~~~v~l~~v~~~~~~~ll~y~Yt~~----------i~~~n 95 (557)
T PHA02713 27 DVIITIGDGEEIKAHKTILAAGSKYFRTL-FTTPMIIRDLVTRVNLQMFDKDAVKNIVQYLYNRH----------ISSMN 95 (557)
T ss_pred CEEEEeCCCCEEeehHHHHhhcCHHHHHH-hcCCchhhccCceEEeccCCHHHHHHHHHHhcCCC----------CCHHH
Confidence 478888779999999988876 88888 76531 12446554 999999998731 26678
Q ss_pred HHHHHHhhccccchhHHHHHHHHHHHHhcCCCHHHHH
Q 046604 70 LKEMLLVADYLTIKDTLDYLAETLANRIKNKSVEYIR 106 (134)
Q Consensus 70 l~~Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~eeir 106 (134)
+.+|+.||++|+|+.|.+.||.++...+.-.+-=+|+
T Consensus 96 v~~ll~aA~~lqi~~l~~~C~~~l~~~l~~~NCl~i~ 132 (557)
T PHA02713 96 VIDVLKCADYLLIDDLVTDCESYIKDYTNHDTCIYMY 132 (557)
T ss_pred HHHHHHHHHHHCHHHHHHHHHHHHHhhCCccchHHHH
Confidence 9999999999999999999999998877655544444
No 9
>PHA03098 kelch-like protein; Provisional
Probab=97.36 E-value=0.0012 Score=55.86 Aligned_cols=89 Identities=17% Similarity=0.219 Sum_probs=69.2
Q ss_pred eEEE-eCCCCEEEecHHHHHH---HHhhccCCCCCCCCceecc-----hHHHHHHHHhcCCCcccccccCCChHHHHHHH
Q 046604 4 NIFE-DGGQQLFKVEEQGCSR---LCSHSSTSDGTSEDMVVLQ-----LPYIIKFCKAHGVSKENEFGKGKSNDELKEML 74 (134)
Q Consensus 4 i~l~-S~DG~~f~V~~~~~~~---~i~~~~le~~~~~~~Ipl~-----L~~Iie~c~~h~~~kD~~F~~~~~~~~l~~Li 74 (134)
++|. +.+|+.|.+.+.++.. .++.| +..+-.+..|.++ ++.|++|+..-+ +.. +.+.+.+|+
T Consensus 12 v~l~~~~~~~~~~~Hk~vLaa~S~yF~~m-f~~~~~~~~i~l~~~~~~~~~~l~y~Ytg~-------~~i-~~~~~~~ll 82 (534)
T PHA03098 12 ESIIIVNGGGIIKVHKIILSSSSEYFKKM-FKNNFKENEINLNIDYDSFNEVIKYIYTGK-------INI-TSNNVKDIL 82 (534)
T ss_pred EEEEEEcCCEEEEeHHHHHHhhhHHHHHH-HhCCCCCceEEecCCHHHHHHHHHHhcCCc-------eEE-cHHHHHHHH
Confidence 4555 4689999999998776 88998 8764323445554 999999987743 333 677799999
Q ss_pred HhhccccchhHHHHHHHHHHHHhcCCC
Q 046604 75 LVADYLTIKDTLDYLAETLANRIKNKS 101 (134)
Q Consensus 75 ~AA~yL~I~~Ll~l~~~~iA~~i~gks 101 (134)
.||++|+++.|.+.|++++...+.-.+
T Consensus 83 ~~A~~l~~~~l~~~C~~~l~~~l~~~n 109 (534)
T PHA03098 83 SIANYLIIDFLINLCINYIIKIIDDNN 109 (534)
T ss_pred HHHHHhCcHHHHHHHHHHHHHhCCHhH
Confidence 999999999999999999987765443
No 10
>smart00225 BTB Broad-Complex, Tramtrack and Bric a brac. Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structures.
Probab=97.35 E-value=0.00055 Score=42.96 Aligned_cols=77 Identities=17% Similarity=0.204 Sum_probs=58.6
Q ss_pred eEEEeCCCCEEEecHHHHHH---HHhhccCCCCC---CCCceecc------hHHHHHHHHhcCCCcccccccCCChHHHH
Q 046604 4 NIFEDGGQQLFKVEEQGCSR---LCSHSSTSDGT---SEDMVVLQ------LPYIIKFCKAHGVSKENEFGKGKSNDELK 71 (134)
Q Consensus 4 i~l~S~DG~~f~V~~~~~~~---~i~~~~le~~~---~~~~Ipl~------L~~Iie~c~~h~~~kD~~F~~~~~~~~l~ 71 (134)
+++ ..+|+.|.+.+..+.. .++.| +.... ....|+++ ++.+++|+.... +.. +...+.
T Consensus 2 v~i-~v~~~~~~~h~~iL~~~s~~f~~~-~~~~~~~~~~~~i~l~~~~~~~f~~~l~~ly~~~-------~~~-~~~~~~ 71 (90)
T smart00225 2 VTL-VVGGKKFKAHKAVLAACSPYFKAL-FSGDFKESKKSEIYLDDVSPEDFRALLEFLYTGK-------LDL-PEENVE 71 (90)
T ss_pred eEE-EECCEEEehHHHHHhhcCHHHHHH-HcCCCccCCCCEEEecCCCHHHHHHHHHeecCce-------eec-CHHHHH
Confidence 344 5577999999988887 88888 87653 23456665 999999988643 223 455889
Q ss_pred HHHHhhccccchhHHHHHH
Q 046604 72 EMLLVADYLTIKDTLDYLA 90 (134)
Q Consensus 72 ~Li~AA~yL~I~~Ll~l~~ 90 (134)
+++.+|+++++++|.+.|+
T Consensus 72 ~l~~~a~~~~~~~l~~~c~ 90 (90)
T smart00225 72 ELLELADYLQIPGLVELCE 90 (90)
T ss_pred HHHHHHHHHCcHHHHhhhC
Confidence 9999999999999998874
No 11
>PHA02790 Kelch-like protein; Provisional
Probab=96.16 E-value=0.019 Score=48.56 Aligned_cols=85 Identities=7% Similarity=-0.010 Sum_probs=61.9
Q ss_pred EEEeCCCCEEEecHHHHHH---HHhhccCCCCCC--CC--ce---ecc---hHHHHHHHHhcCCCcccccccCCChHHHH
Q 046604 5 IFEDGGQQLFKVEEQGCSR---LCSHSSTSDGTS--ED--MV---VLQ---LPYIIKFCKAHGVSKENEFGKGKSNDELK 71 (134)
Q Consensus 5 ~l~S~DG~~f~V~~~~~~~---~i~~~~le~~~~--~~--~I---pl~---L~~Iie~c~~h~~~kD~~F~~~~~~~~l~ 71 (134)
.+..--|+.|.+-+.+... .++.| +..+-. .. .+ .++ |+.|++|+..-+ +.. +.+.+.
T Consensus 24 ~~~~~~~~~~~~HR~VLAa~S~YFraM-F~~~~~Es~~~v~~~~~~v~~~~l~~lldy~YTg~-------l~i-t~~nV~ 94 (480)
T PHA02790 24 TIIEAIGGNIIVNSTILKKLSPYFRTH-LRQKYTKNKDPVTRVCLDLDIHSLTSIVIYSYTGK-------VYI-DSHNVV 94 (480)
T ss_pred eEEEEcCcEEeeehhhhhhcCHHHHHH-hcCCccccccceEEEecCcCHHHHHHHHHhheeee-------EEE-ecccHH
Confidence 3445568899998887655 88888 754311 11 12 233 999999985533 344 667799
Q ss_pred HHHHhhccccchhHHHHHHHHHHHHhc
Q 046604 72 EMLLVADYLTIKDTLDYLAETLANRIK 98 (134)
Q Consensus 72 ~Li~AA~yL~I~~Ll~l~~~~iA~~i~ 98 (134)
+|+.||++|+|+.+.+.||+++...+.
T Consensus 95 ~ll~aA~~Lqi~~v~~~C~~fL~~~l~ 121 (480)
T PHA02790 95 NLLRASILTSVEFIIYTCINFILRDFR 121 (480)
T ss_pred HHHHHHHHhChHHHHHHHHHHHHhhCC
Confidence 999999999999999999998876654
No 12
>KOG4441 consensus Proteins containing BTB/POZ and Kelch domains, involved in regulatory/signal transduction processes [Signal transduction mechanisms; General function prediction only]
Probab=95.27 E-value=0.067 Score=46.51 Aligned_cols=84 Identities=18% Similarity=0.237 Sum_probs=61.6
Q ss_pred eEEEeCCCCEEEecHHHHHH---HHhhccCCCCC---CCCceecc------hHHHHHHHHhcCCCcccccccCCChHHHH
Q 046604 4 NIFEDGGQQLFKVEEQGCSR---LCSHSSTSDGT---SEDMVVLQ------LPYIIKFCKAHGVSKENEFGKGKSNDELK 71 (134)
Q Consensus 4 i~l~S~DG~~f~V~~~~~~~---~i~~~~le~~~---~~~~Ipl~------L~~Iie~c~~h~~~kD~~F~~~~~~~~l~ 71 (134)
+.|.-.+ +.|..-+.+... .++.| +..+- ....|.+. |..+++|+...+ +.. +.+.+-
T Consensus 39 v~L~v~~-~~~~aHR~VLAa~S~YFraM-Ft~~l~e~~~~~i~l~~v~~~~l~~ll~y~Yt~~-------i~i-~~~nVq 108 (571)
T KOG4441|consen 39 VTLLVGD-REFPAHRVVLAACSPYFRAM-FTSGLKESKQKEINLEGVDPETLELLLDYAYTGK-------LEI-SEDNVQ 108 (571)
T ss_pred EEEEECC-eeechHHHHHHhccHHHHHH-hcCCcccccceEEEEecCCHHHHHHHHHHhhcce-------EEe-chHhHH
Confidence 3444444 777777666655 88888 76431 12445543 999999988755 455 788899
Q ss_pred HHHHhhccccchhHHHHHHHHHHHHh
Q 046604 72 EMLLVADYLTIKDTLDYLAETLANRI 97 (134)
Q Consensus 72 ~Li~AA~yL~I~~Ll~l~~~~iA~~i 97 (134)
+|+.||++|+|+++.+.||..+...+
T Consensus 109 ~ll~aA~~lQi~~v~~~C~~fL~~~l 134 (571)
T KOG4441|consen 109 ELLEAASLLQIPEVVDACCEFLESQL 134 (571)
T ss_pred HHHHHHHHhhhHHHHHHHHHHHHhcC
Confidence 99999999999999999998776543
No 13
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=94.86 E-value=0.17 Score=39.37 Aligned_cols=85 Identities=16% Similarity=0.271 Sum_probs=66.0
Q ss_pred CCCCEEEecHHHHHH---HHhhccCCCCC-----CCCceecc-----hHHHHHHHHhcCCCcccccccCCChHHHHHHHH
Q 046604 9 GGQQLFKVEEQGCSR---LCSHSSTSDGT-----SEDMVVLQ-----LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLL 75 (134)
Q Consensus 9 ~DG~~f~V~~~~~~~---~i~~~~le~~~-----~~~~Ipl~-----L~~Iie~c~~h~~~kD~~F~~~~~~~~l~~Li~ 75 (134)
-.|..|.-+...... .++.| ++..- ..+.|=+. +..|+.|++.-. -.+.. +...|-+|+.
T Consensus 11 vGG~~F~Tsk~TLtk~dg~fk~m-~e~~i~~~~d~s~~IFIDRSpKHF~~ILNfmRdGd-----v~LPe-~~kel~El~~ 83 (230)
T KOG2716|consen 11 VGGTIFKTSKSTLTKFDGFFKTM-LETDIPVEKDESGCIFIDRSPKHFDTILNFMRDGD-----VDLPE-SEKELKELLR 83 (230)
T ss_pred cCCeEEEeehhhhhhhhhHHHHH-hhcCCccccCCcCcEEecCChhHHHHHHHhhhccc-----ccCcc-chHHHHHHHH
Confidence 358889888888877 88888 87541 11345333 999999998422 11666 7889999999
Q ss_pred hhccccchhHHHHHHHHHHHHhcCC
Q 046604 76 VADYLTIKDTLDYLAETLANRIKNK 100 (134)
Q Consensus 76 AA~yL~I~~Ll~l~~~~iA~~i~gk 100 (134)
-|.|..+++|.++|..+++..+.+.
T Consensus 84 EA~fYlL~~Lv~~C~~~i~~~~~~~ 108 (230)
T KOG2716|consen 84 EAEFYLLDGLVELCQSAIARLIRGY 108 (230)
T ss_pred HHHHhhHHHHHHHHHHHhhhcccCc
Confidence 9999999999999999999997764
No 14
>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.36 E-value=0.085 Score=39.70 Aligned_cols=38 Identities=32% Similarity=0.370 Sum_probs=29.4
Q ss_pred HHhhccc--cchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCC
Q 046604 74 LLVADYL--TIKDTLDYLAETLANRIKNKSVEYIRKFFGIENNFM 116 (134)
Q Consensus 74 i~AA~yL--~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~t 116 (134)
..|||.- +|--|.+++|+.. |.-+.+||+.||||+||.
T Consensus 161 ~eaanrwtDnI~il~dy~~rkf-----~~e~nqi~~~fgIPed~d 200 (203)
T KOG3433|consen 161 AEAANRWTDNIFILIDYLYRKF-----GLEPNQIRKEFGIPEDFD 200 (203)
T ss_pred HHHHhhhhhhHHHHHHHHHHhc-----CCCHHHHhHhcCCCcccc
Confidence 3444432 6777888888664 899999999999999974
No 15
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=93.16 E-value=0.089 Score=39.50 Aligned_cols=31 Identities=35% Similarity=0.494 Sum_probs=24.4
Q ss_pred cchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCC
Q 046604 81 TIKDTLDYLAETLANRIKNKSVEYIRKFFGIENNFM 116 (134)
Q Consensus 81 ~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~t 116 (134)
+|.-|.++.|+.. +..|+|||+.||||+|+.
T Consensus 174 nI~ilidy~c~kf-----~~~~~qir~~fgIPedld 204 (209)
T COG5124 174 NIEILIDYLCKKF-----FLKPEQIRKEFGIPEDLD 204 (209)
T ss_pred hHHHHHHHHHHHc-----CCCHHHHHHhcCCCcchh
Confidence 4566677666543 788999999999999874
No 16
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=83.44 E-value=1.4 Score=33.05 Aligned_cols=42 Identities=31% Similarity=0.309 Sum_probs=29.8
Q ss_pred HHHHHHhhccc--cchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCC
Q 046604 70 LKEMLLVADYL--TIKDTLDYLAETLANRIKNKSVEYIRKFFGIENNFM 116 (134)
Q Consensus 70 l~~Li~AA~yL--~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~t 116 (134)
+.....||+.- ||-.|..++++. .|.+.+++|+.||||+||.
T Consensus 144 ~~~~~~~anrwTDNI~~l~~~~~~k-----~~~~~~~i~k~f~Ip~d~d 187 (188)
T PF03962_consen 144 IKIAKEAANRWTDNIFSLKSYLKKK-----FGMDEEDIRKEFGIPEDFD 187 (188)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHh-----cCCCHHHHHHHcCCccccC
Confidence 34444566654 566666666653 4999999999999999974
No 17
>PF11822 DUF3342: Domain of unknown function (DUF3342); InterPro: IPR021777 This family of proteins are functionally uncharacterised. This family is found in bacteria. This presumed domain is typically between 170 to 303 amino acids in length. The N-terminal half of this family is a BTB-like domain.
Probab=80.76 E-value=1.6 Score=35.52 Aligned_cols=82 Identities=6% Similarity=0.071 Sum_probs=51.5
Q ss_pred CEEEecHHHHHH---HHhhccCCC---CCC-CCceecc---hHHHHHHHHhcCCCcccccccCCChHHHHHHHHhhcccc
Q 046604 12 QLFKVEEQGCSR---LCSHSSTSD---GTS-EDMVVLQ---LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVADYLT 81 (134)
Q Consensus 12 ~~f~V~~~~~~~---~i~~~~le~---~~~-~~~Ipl~---L~~Iie~c~~h~~~kD~~F~~~~~~~~l~~Li~AA~yL~ 81 (134)
+.|..+...... .+++. +.. .+. .++|++. =-.|++|+=.|-..+... ++.+.+..++.-|+||+
T Consensus 14 rdF~C~~~lL~~~M~YF~~~-l~~~~~~~~~~~~idisVhCDv~iF~WLm~yv~~~~p~----l~~~NvvsIliSS~FL~ 88 (317)
T PF11822_consen 14 RDFTCPRDLLVSEMRYFAEY-LSRYINDSQRWEEIDISVHCDVHIFEWLMRYVKGEPPS----LTPSNVVSILISSEFLQ 88 (317)
T ss_pred eeeeccHHHHHHhhHHHHHH-HhhcccccCcCCCcceEEecChhHHHHHHHHhhcCCCc----CCcCcEEEeEehhhhhc
Confidence 467777777755 67776 632 111 2444444 122555554443322222 26777889999999999
Q ss_pred chhHHHHHHHHHHHHhc
Q 046604 82 IKDTLDYLAETLANRIK 98 (134)
Q Consensus 82 I~~Ll~l~~~~iA~~i~ 98 (134)
|++|++.|-.++...+.
T Consensus 89 M~~Lve~cl~y~~~~~~ 105 (317)
T PF11822_consen 89 MESLVEECLQYCHDHMS 105 (317)
T ss_pred cHHHHHHHHHHHHHhHH
Confidence 99999999888755443
No 18
>PF02214 BTB_2: BTB/POZ domain; InterPro: IPR003131 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. The Kv family can be divided into several subfamilies on the basis of sequence similarity and function. Four of these subfamilies, Kv1 (Shaker), Kv2 (Shab), Kv3 (Shaw) and Kv4 (Shal), consist of pore-forming alpha subunits that associate with different types of beta subunit. Each alpha subunit comprises six hydrophobic TM domains with a P-domain between the fifth and sixth, which partially resides in the membrane. The fourth TM domain has positively charged residues at every third residue and acts as a voltage sensor, which triggers the conformational change that opens the channel pore in response to a displacement in membrane potential []. More recently, 4 new electrically-silent alpha subunits have been cloned: Kv5 (KCNF), Kv6 (KCNG), Kv8 and Kv9 (KCNS). These subunits do not themselves possess any functional activity, but appear to form heteromeric channels with Kv2 subunits, and thus modulate Shab channel activity []. When highly expressed, they inhibit channel activity, but at lower levels show more specific modulatory actions. The N-terminal, cytoplasmic tetramerization domain (T1) of voltage-gated potassium channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels []. This domain is found in a subset of a larger group of proteins that contain the BTB/POZ domain.; GO: 0005249 voltage-gated potassium channel activity, 0006813 potassium ion transport, 0008076 voltage-gated potassium channel complex, 0016020 membrane; PDB: 1NN7_A 3KVT_A 1EXB_E 1QDV_A 1DSX_E 1QDW_F 3LUT_B 3LNM_B 2A79_B 3DRY_C ....
Probab=79.63 E-value=1.7 Score=28.20 Aligned_cols=73 Identities=15% Similarity=0.262 Sum_probs=47.4
Q ss_pred CCCEEEecHHHHHH----HHhhccCCCC------CCCCceecc-----hHHHHHHHHhcCCCcccccccCCChHHHHHHH
Q 046604 10 GQQLFKVEEQGCSR----LCSHSSTSDG------TSEDMVVLQ-----LPYIIKFCKAHGVSKENEFGKGKSNDELKEML 74 (134)
Q Consensus 10 DG~~f~V~~~~~~~----~i~~~~le~~------~~~~~Ipl~-----L~~Iie~c~~h~~~kD~~F~~~~~~~~l~~Li 74 (134)
.|+.|.++.+.+.. .+..| +... .....+=+. ++.|+.|++.. . . +..-+...+..+.
T Consensus 6 GG~~f~~~~~tL~~~~~s~l~~~-~~~~~~~~~~~~~~~~fiDRdp~~F~~IL~ylr~~-~----~-l~~~~~~~~~~l~ 78 (94)
T PF02214_consen 6 GGTIFETSRSTLTRYPDSLLARL-FSGERSDDYDDDDGEYFIDRDPELFEYILNYLRTG-G----K-LPIPDEICLEELL 78 (94)
T ss_dssp TTEEEEEEHHHHHTSTTSTTTSH-HHTGHGGGEETTTTEEEESS-HHHHHHHHHHHHHT-S----S-B---TTS-HHHHH
T ss_pred CCEEEEEcHHHHhhCCCChhhhH-HhhccccccCCccceEEeccChhhhhHHHHHHhhc-C----c-cCCCCchhHHHHH
Confidence 58999999999885 55555 5432 112334333 99999999984 1 1 2221355678999
Q ss_pred HhhccccchhH-HHHH
Q 046604 75 LVADYLTIKDT-LDYL 89 (134)
Q Consensus 75 ~AA~yL~I~~L-l~l~ 89 (134)
..|.|.+|++| ++.|
T Consensus 79 ~Ea~fy~l~~l~i~~c 94 (94)
T PF02214_consen 79 EEAEFYGLDELFIEDC 94 (94)
T ss_dssp HHHHHHT-HHHHBHHC
T ss_pred HHHHHcCCCccccCCC
Confidence 99999999998 6543
No 19
>KOG0783 consensus Uncharacterized conserved protein, contains ankyrin and BTB/POZ domains [Function unknown]
Probab=70.85 E-value=6.3 Score=36.46 Aligned_cols=101 Identities=16% Similarity=0.194 Sum_probs=67.7
Q ss_pred eEEEeCCCCEEEecHHHHHH---HHhhc----cCCCC-CCCCceecc---hHHHHHHHHhcCCCcccccccC-CChHHHH
Q 046604 4 NIFEDGGQQLFKVEEQGCSR---LCSHS----STSDG-TSEDMVVLQ---LPYIIKFCKAHGVSKENEFGKG-KSNDELK 71 (134)
Q Consensus 4 i~l~S~DG~~f~V~~~~~~~---~i~~~----~le~~-~~~~~Ipl~---L~~Iie~c~~h~~~kD~~F~~~-~~~~~l~ 71 (134)
..++.+||++|..-...... .+..| -++.+ .+-+..|+. |+-|+.|+..-. ..+|++. .+.+.+|
T Consensus 713 ~~i~~KDGkvl~aHkc~L~aRlEYF~smf~~~w~E~sS~t~~~~p~~~e~m~ivLdylYs~d---~~~~~k~~~~~dF~~ 789 (1267)
T KOG0783|consen 713 TVIKLKDGKVLKAHKCFLSARLEYFSSMFQFVWMESSSITVNLSPLTVEHMSIVLDYLYSDD---KVELFKDLKESDFMF 789 (1267)
T ss_pred EEEEecCCcCcccceeEeeeHHHHHHHHHHHHHhhhccceeecCcchHHHHHHHHHHHHccc---hHHHHhccchhhhhH
Confidence 34667799987765443322 33333 02322 222344544 999999986422 3356653 2567899
Q ss_pred HHHHhhccccchhHHHHHHHHHHHHhcCCCHHHHHH
Q 046604 72 EMLLVADYLTIKDTLDYLAETLANRIKNKSVEYIRK 107 (134)
Q Consensus 72 ~Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~eeir~ 107 (134)
+++..|+-|=|..|-++|-+.+-+.+.=|+...+-+
T Consensus 790 ~il~iaDqlli~~Lk~Ice~~ll~kl~lk~~~~lle 825 (1267)
T KOG0783|consen 790 EILSIADQLLILELKSICEQSLLRKLNLKTLPTLLE 825 (1267)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHhcccchHHHHH
Confidence 999999999999999999999999988887665554
No 20
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=70.19 E-value=8.5 Score=22.75 Aligned_cols=34 Identities=15% Similarity=0.221 Sum_probs=23.0
Q ss_pred HHHHHHHhcCCCHHHHHHHhCC------C-CCCCHHHHHHH
Q 046604 90 AETLANRIKNKSVEYIRKFFGI------E-NNFMPEEKEAT 123 (134)
Q Consensus 90 ~~~iA~~i~gks~eeir~~f~i------~-~d~t~eee~~i 123 (134)
=..||..+..+|+.+++..|.- . ..+|++|.+.+
T Consensus 20 W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 20 WKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred HHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 4578888844999999986542 2 24888887654
No 21
>PF15063 TC1: Thyroid cancer protein 1
Probab=59.64 E-value=11 Score=24.50 Aligned_cols=33 Identities=18% Similarity=0.320 Sum_probs=27.3
Q ss_pred HHHHHHhcCCCHHHHHHHhCCCCCCCHHHHHHH
Q 046604 91 ETLANRIKNKSVEYIRKFFGIENNFMPEEKEAT 123 (134)
Q Consensus 91 ~~iA~~i~gks~eeir~~f~i~~d~t~eee~~i 123 (134)
+.+|+.+.+-..++|++.|.-..|--.||-.++
T Consensus 28 kasaNIFe~vn~~qlqrLF~~sGD~kAEeRA~i 60 (79)
T PF15063_consen 28 KASANIFENVNLDQLQRLFQKSGDKKAEERARI 60 (79)
T ss_pred hhhhhhhhccCHHHHHHHHHHccchhHHHHHHH
Confidence 467888899999999999999988877776665
No 22
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=59.61 E-value=12 Score=22.87 Aligned_cols=25 Identities=24% Similarity=0.391 Sum_probs=19.6
Q ss_pred HHHHHHHhC-CCCC-CCHHHHHHHHHh
Q 046604 102 VEYIRKFFG-IENN-FMPEEKEATRKE 126 (134)
Q Consensus 102 ~eeir~~f~-i~~d-~t~eee~~i~~e 126 (134)
.+++|..|| |=.+ +||||..+|.+-
T Consensus 30 ad~lr~klG~IC~~CitpEE~~~I~e~ 56 (60)
T PF10892_consen 30 ADDLRVKLGGICGDCITPEEDREILEA 56 (60)
T ss_pred hHHHHHHHcchhhccCCHHHHHHHHHH
Confidence 678999887 4445 899999988653
No 23
>PF12556 CobS_N: Cobaltochelatase CobS subunit N terminal
Probab=59.11 E-value=5.7 Score=22.04 Aligned_cols=12 Identities=33% Similarity=0.908 Sum_probs=10.6
Q ss_pred HHHHhCCCCCCC
Q 046604 105 IRKFFGIENNFM 116 (134)
Q Consensus 105 ir~~f~i~~d~t 116 (134)
+|+.|||..|++
T Consensus 14 vre~FGiDsDm~ 25 (36)
T PF12556_consen 14 VREVFGIDSDMK 25 (36)
T ss_pred HHHhcCCCcCCe
Confidence 689999999975
No 24
>PF03656 Pam16: Pam16; InterPro: IPR005341 The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM) []. In Saccharomyces cerevisiae (Baker's yeast), Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane [].; PDB: 2GUZ_J.
Probab=58.35 E-value=9.1 Score=27.11 Aligned_cols=33 Identities=21% Similarity=0.387 Sum_probs=16.8
Q ss_pred HhcCCCHHHHHHHhCCCCCCCHHHHHHHHHhchhhh
Q 046604 96 RIKNKSVEYIRKFFGIENNFMPEEKEATRKEYELLR 131 (134)
Q Consensus 96 ~i~gks~eeir~~f~i~~d~t~eee~~i~~e~~w~~ 131 (134)
..+|+|++|-++.+|+++..++|+ |++.+.-+|
T Consensus 51 ~~~~Mtl~EA~~ILnv~~~~~~ee---I~k~y~~Lf 83 (127)
T PF03656_consen 51 NSKGMTLDEARQILNVKEELSREE---IQKRYKHLF 83 (127)
T ss_dssp ------HHHHHHHHT--G--SHHH---HHHHHHHHH
T ss_pred hcCCCCHHHHHHHcCCCCccCHHH---HHHHHHHHH
Confidence 346899999999999999777665 445554444
No 25
>KOG4682 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=57.05 E-value=12 Score=31.89 Aligned_cols=48 Identities=10% Similarity=0.170 Sum_probs=37.7
Q ss_pred ChHHHHHHHHhhccccchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCC
Q 046604 66 SNDELKEMLLVADYLTIKDTLDYLAETLANRIKNKSVEYIRKFFGIENNFM 116 (134)
Q Consensus 66 ~~~~l~~Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~t 116 (134)
+.+.+..++.||++|..++|.+-|...+-..+ ||+-+.+++....-+-
T Consensus 139 ~l~dv~gvlAaA~~lqldgl~qrC~evMie~l---spkta~~yYea~ckYg 186 (488)
T KOG4682|consen 139 KLSDVVGVLAAACLLQLDGLIQRCGEVMIETL---SPKTACGYYEAACKYG 186 (488)
T ss_pred cHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhc---ChhhhhHhhhhhhhhh
Confidence 78899999999999999999999998766554 4555666766665543
No 26
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=55.97 E-value=14 Score=19.58 Aligned_cols=20 Identities=15% Similarity=0.315 Sum_probs=16.5
Q ss_pred HHHHHHhcCCCHHHHHHHhC
Q 046604 91 ETLANRIKNKSVEYIRKFFG 110 (134)
Q Consensus 91 ~~iA~~i~gks~eeir~~f~ 110 (134)
..||..+.++|+.+++..+.
T Consensus 23 ~~Ia~~~~~rs~~~~~~~~~ 42 (45)
T cd00167 23 EKIAKELPGRTPKQCRERWR 42 (45)
T ss_pred HHHHhHcCCCCHHHHHHHHH
Confidence 57888888899999998763
No 27
>PRK05365 malonic semialdehyde reductase; Provisional
Probab=54.59 E-value=9.1 Score=28.19 Aligned_cols=33 Identities=12% Similarity=0.168 Sum_probs=25.8
Q ss_pred HHHhhccccchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCC
Q 046604 73 MLLVADYLTIKDTLDYLAETLANRIKNKSVEYIRKFFGIENNF 115 (134)
Q Consensus 73 Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~ 115 (134)
|+.||.-+++.. ..+.|-..+.+++.||+++++
T Consensus 131 l~LaA~~~Glgs----------~~~~g~~~~~v~~~l~ip~~~ 163 (195)
T PRK05365 131 LILAARALGLDA----------GPMSGFDAAAVDAEFFAGTTW 163 (195)
T ss_pred HHHHHHHcCCcc----------CCccccCHHHHHHHhCCCCCe
Confidence 788888888776 134567889999999999765
No 28
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=52.94 E-value=17 Score=19.53 Aligned_cols=20 Identities=20% Similarity=0.409 Sum_probs=16.5
Q ss_pred HHHHHHhcCCCHHHHHHHhC
Q 046604 91 ETLANRIKNKSVEYIRKFFG 110 (134)
Q Consensus 91 ~~iA~~i~gks~eeir~~f~ 110 (134)
..||..+.++|+.+++..|.
T Consensus 25 ~~Ia~~~~~rt~~~~~~~~~ 44 (49)
T smart00717 25 EKIAKELPGRTAEQCRERWN 44 (49)
T ss_pred HHHHHHcCCCCHHHHHHHHH
Confidence 56788888999999998764
No 29
>PF11978 MVP_shoulder: Shoulder domain; InterPro: IPR021870 This domain is found in the Major Vault Protein and has been called the shoulder domain []. This family includes two bacterial proteins A6FXE2 from SWISSPROT and A1ZGE7 from SWISSPROT. This suggests that some bacteria may possess vault particles. ; PDB: 2ZUO_G 2QZV_B 2ZV5_c 2ZV4_Y.
Probab=52.89 E-value=11 Score=26.37 Aligned_cols=41 Identities=27% Similarity=0.462 Sum_probs=31.4
Q ss_pred HHhhccccchhHHHHHHHHHHHHhcCC------------CHHHHHH-HhCCCCC
Q 046604 74 LLVADYLTIKDTLDYLAETLANRIKNK------------SVEYIRK-FFGIENN 114 (134)
Q Consensus 74 i~AA~yL~I~~Ll~l~~~~iA~~i~gk------------s~eeir~-~f~i~~d 114 (134)
-.|+....++..+..+|+++|++++|. |..-||+ .||....
T Consensus 37 ~~~~k~F~VpDFVGd~Ck~iaSRIR~aVa~~~Fd~FHknSa~iiR~aVFg~~~~ 90 (118)
T PF11978_consen 37 EDAAKLFSVPDFVGDACKAIASRIRGAVASVTFDDFHKNSARIIRQAVFGFDEN 90 (118)
T ss_dssp HHHHHTTSSTTHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHSTS---
T ss_pred hHHHHhcCCcchHHHHHHHHHHHHHHHHhcCcHHHHcccHHHHHHHHhcCCCCC
Confidence 378889999999999999999999874 3555665 7887653
No 30
>KOG4350 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=52.29 E-value=73 Score=27.46 Aligned_cols=96 Identities=13% Similarity=0.146 Sum_probs=59.2
Q ss_pred eEEEeCCCCEEEecHHHH--HH-HHhhccCCCCCC---CCceecc------hHHHHHHHHhcCCC----c----------
Q 046604 4 NIFEDGGQQLFKVEEQGC--SR-LCSHSSTSDGTS---EDMVVLQ------LPYIIKFCKAHGVS----K---------- 57 (134)
Q Consensus 4 i~l~S~DG~~f~V~~~~~--~~-~i~~~~le~~~~---~~~Ipl~------L~~Iie~c~~h~~~----k---------- 57 (134)
|+++-.| +.|..-+-+. +. .+|.| +=.+-. +..||+. ++.++.|...-+-. +
T Consensus 47 Vtfvve~-~rfpAHRvILAaRs~yFRAl-LYgGm~Es~q~~ipLq~t~~eAF~~lLrYiYtg~~~l~~~~ed~lld~Lsl 124 (620)
T KOG4350|consen 47 VTFVVED-TRFPAHRVILAARSSYFRAL-LYGGMQESHQQLIPLQETNSEAFRALLRYIYTGKIDLAGVEEDILLDYLSL 124 (620)
T ss_pred eEEEEec-cccchhhhhHHHHHHHHHHH-HhhhhhhhhhcccccccccHHHHHHHHHHHhhcceecccchHHHHHHHHHH
Confidence 4455444 5555544333 22 77777 644321 3567776 78888887664432 1
Q ss_pred ------------cccccc-CCChHHHHHHHHhhccccchhHHHHHHHHHHHHhcCCCHHHHH
Q 046604 58 ------------ENEFGK-GKSNDELKEMLLVADYLTIKDTLDYLAETLANRIKNKSVEYIR 106 (134)
Q Consensus 58 ------------D~~F~~-~~~~~~l~~Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~eeir 106 (134)
-.+|++ .+..+.++-++.||.+.+.+.|.++||.. ..+...++-
T Consensus 125 Ah~Ygf~~Le~aiSeYl~~iL~~~NvCmifdaA~ly~l~~Lt~~C~mf-----mDrnA~~lL 181 (620)
T KOG4350|consen 125 AHRYGFIQLETAISEYLKEILKNENVCMIFDAAYLYQLTDLTDYCMMF-----MDRNADQLL 181 (620)
T ss_pred HHhcCcHHHHHHHHHHHHHHHcccceeeeeeHHHHhcchHHHHHHHHH-----HhcCHHhhh
Confidence 123332 23566778888999999999999999954 456666654
No 31
>cd02148 Nitroreductase_5 Nitroreductase-like family 5. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=51.24 E-value=11 Score=27.55 Aligned_cols=33 Identities=12% Similarity=0.189 Sum_probs=25.5
Q ss_pred HHHhhccccchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCC
Q 046604 73 MLLVADYLTIKDTLDYLAETLANRIKNKSVEYIRKFFGIENNF 115 (134)
Q Consensus 73 Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~ 115 (134)
++.||.-|++.. ..+.|-..+.+++.||+++++
T Consensus 124 l~LaA~~lGlgs----------~~~~g~d~~~~~~~L~lp~~~ 156 (185)
T cd02148 124 FILAARALGLDA----------GPMSGFDAAAVDAEFFADTRW 156 (185)
T ss_pred HHHHHHHcCCCc----------CCCcccCHHHHHHHhCCCCCe
Confidence 777777777765 234577889999999999876
No 32
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=49.24 E-value=19 Score=24.73 Aligned_cols=24 Identities=33% Similarity=0.398 Sum_probs=17.2
Q ss_pred CHHHHHHHhCCCCCCCHHHHHHHHHhc
Q 046604 101 SVEYIRKFFGIENNFMPEEKEATRKEY 127 (134)
Q Consensus 101 s~eeir~~f~i~~d~t~eee~~i~~e~ 127 (134)
+.+++.+.|. .+||||.+++..|-
T Consensus 79 ~~~~lqkRle---~l~~eE~~~L~~ei 102 (104)
T PF11460_consen 79 TNEELQKRLE---ELSPEELEALQAEI 102 (104)
T ss_pred hHHHHHHHHH---hCCHHHHHHHHHHh
Confidence 4556777763 57899988888763
No 33
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=49.12 E-value=27 Score=25.74 Aligned_cols=22 Identities=23% Similarity=0.303 Sum_probs=16.0
Q ss_pred HHHHHHHHHHhcCCCHHHHHHH
Q 046604 87 DYLAETLANRIKNKSVEYIRKF 108 (134)
Q Consensus 87 ~l~~~~iA~~i~gks~eeir~~ 108 (134)
+.+...+...=+|||+.|||++
T Consensus 119 ~ia~~a~~~~~~Gks~~eIR~~ 140 (158)
T PF13798_consen 119 DIAVQAVQMYQEGKSPKEIRQY 140 (158)
T ss_pred HHHHHHHHHHHcCCCHHHHHHH
Confidence 4445555555679999999985
No 34
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=47.03 E-value=18 Score=26.14 Aligned_cols=19 Identities=11% Similarity=0.224 Sum_probs=17.1
Q ss_pred cCCCHHHHHHHhCCCCCCC
Q 046604 98 KNKSVEYIRKFFGIENNFM 116 (134)
Q Consensus 98 ~gks~eeir~~f~i~~d~t 116 (134)
-|.||+|-|..+|++.|+.
T Consensus 97 ~gmTPd~YR~KW~LP~dYP 115 (148)
T COG4957 97 YGLTPDEYRAKWGLPPDYP 115 (148)
T ss_pred cCCCHHHHHHhcCCCCCCC
Confidence 4899999999999999964
No 35
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=46.30 E-value=26 Score=23.59 Aligned_cols=47 Identities=9% Similarity=0.058 Sum_probs=32.2
Q ss_pred ceEEEeCC-CCEEEecHHHHHH-HHhhccCCCC----C--CCCceecc-----hHHHHHHH
Q 046604 3 ENIFEDGG-QQLFKVEEQGCSR-LCSHSSTSDG----T--SEDMVVLQ-----LPYIIKFC 50 (134)
Q Consensus 3 ~i~l~S~D-G~~f~V~~~~~~~-~i~~~~le~~----~--~~~~Ipl~-----L~~Iie~c 50 (134)
.+.+...+ .+.|.|+...+.+ +++.+ |+.. | .+.+|-+| ++.|+..+
T Consensus 40 ~~~VyVG~~~~Rfvvp~~~L~hp~f~~L-L~~aeeEfG~~~~G~l~iPC~~~~Fe~~l~~l 99 (100)
T PF02519_consen 40 HFAVYVGEERRRFVVPVSYLNHPLFQEL-LEQAEEEFGFDQDGPLTIPCDVVLFEHLLWLL 99 (100)
T ss_pred eEEEEeCccceEEEechHHcCchhHHHH-HHHHhhhcCcCCCCcEEeeCCHHHHHHHHHHh
Confidence 34455555 8999999999999 88877 7543 2 23567777 66666543
No 36
>PRK11053 dihydropteridine reductase; Provisional
Probab=43.00 E-value=22 Score=26.50 Aligned_cols=36 Identities=28% Similarity=0.375 Sum_probs=24.9
Q ss_pred HHHHHHhhccccchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCC-CC
Q 046604 70 LKEMLLVADYLTIKDTLDYLAETLANRIKNKSVEYIRKFFGIEN-NF 115 (134)
Q Consensus 70 l~~Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~-d~ 115 (134)
+..|+.||.-|++..- .+.|-.++.+++.|||++ ++
T Consensus 147 ~~~lmLaA~~~Glgs~----------~i~g~~~~~v~~~l~ip~~~~ 183 (217)
T PRK11053 147 LGNLLLGAAALGIDAT----------PIEGFDAAILDAEFGLREKGL 183 (217)
T ss_pred HHHHHHHHHHcCCCCC----------CcCCcCHHHHHHHhCCCCcCc
Confidence 3456666666666542 345678999999999985 44
No 37
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=42.89 E-value=88 Score=21.76 Aligned_cols=41 Identities=20% Similarity=0.162 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCCHHHHHHHHH
Q 046604 85 TLDYLAETLANRIKNKSVEYIRKFFGIENNFMPEEKEATRK 125 (134)
Q Consensus 85 Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~t~eee~~i~~ 125 (134)
.+....+.+.+.+.|-|+..+-..|--.+.+|+||.+++++
T Consensus 72 ~~~~~~~~~~~~~f~gs~~~ll~~l~~~~~ls~eele~L~~ 112 (130)
T TIGR02698 72 AVENAAQELFSRICSRKVGAVIADLIEESPLSQTDIEKLEK 112 (130)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHH
Confidence 33444556666666777777666664456799999999986
No 38
>KOG3442 consensus Uncharacterized conserved protein [Function unknown]
Probab=42.80 E-value=27 Score=24.83 Aligned_cols=31 Identities=19% Similarity=0.320 Sum_probs=22.8
Q ss_pred cCCCHHHHHHHhCCCCCCCHHHHHHHHHhchhhh
Q 046604 98 KNKSVEYIRKFFGIENNFMPEEKEATRKEYELLR 131 (134)
Q Consensus 98 ~gks~eeir~~f~i~~d~t~eee~~i~~e~~w~~ 131 (134)
.|.|.+|-++.+||++++++|| |.+-+.-+|
T Consensus 54 ~~iTlqEa~qILnV~~~ln~ee---i~k~yehLF 84 (132)
T KOG3442|consen 54 GKITLQEAQQILNVKEPLNREE---IEKRYEHLF 84 (132)
T ss_pred ccccHHHHhhHhCCCCCCCHHH---HHHHHHHHH
Confidence 4578999999999999877665 444455444
No 39
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=40.91 E-value=20 Score=18.97 Aligned_cols=13 Identities=38% Similarity=0.460 Sum_probs=9.3
Q ss_pred cCCCHHHHHHHhC
Q 046604 98 KNKSVEYIRKFFG 110 (134)
Q Consensus 98 ~gks~eeir~~f~ 110 (134)
.|-|.+|+|+++.
T Consensus 15 ~Gls~eeir~FL~ 27 (30)
T PF08671_consen 15 SGLSKEEIREFLE 27 (30)
T ss_dssp TT--HHHHHHHHH
T ss_pred cCCCHHHHHHHHH
Confidence 6999999999873
No 40
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=40.74 E-value=67 Score=17.98 Aligned_cols=36 Identities=14% Similarity=0.178 Sum_probs=24.2
Q ss_pred HHHHHHHhhccccchhHHHHHHHHHHHHhc-CCCHHHHHHHh
Q 046604 69 ELKEMLLVADYLTIKDTLDYLAETLANRIK-NKSVEYIRKFF 109 (134)
Q Consensus 69 ~l~~Li~AA~yL~I~~Ll~l~~~~iA~~i~-gks~eeir~~f 109 (134)
+---|+.|..-++-. -=..||..+. |+|+.++|..|
T Consensus 8 E~~~l~~~v~~~g~~-----~W~~Ia~~~~~~Rt~~qc~~~~ 44 (48)
T PF00249_consen 8 EDEKLLEAVKKYGKD-----NWKKIAKRMPGGRTAKQCRSRY 44 (48)
T ss_dssp HHHHHHHHHHHSTTT-----HHHHHHHHHSSSSTHHHHHHHH
T ss_pred HHHHHHHHHHHhCCc-----HHHHHHHHcCCCCCHHHHHHHH
Confidence 333444444444444 3467888888 99999999876
No 41
>cd02140 Nitroreductase_4 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=40.59 E-value=19 Score=26.34 Aligned_cols=38 Identities=16% Similarity=0.052 Sum_probs=24.7
Q ss_pred HHHHHHhhccccchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCC
Q 046604 70 LKEMLLVADYLTIKDTLDYLAETLANRIKNKSVEYIRKFFGIENNF 115 (134)
Q Consensus 70 l~~Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~ 115 (134)
+-.|+.||.-+++-.-+.. ......+.+|+.|||++++
T Consensus 127 ~~nl~LaA~~~GlGs~~~~--------~~~~~~~~v~~~l~ip~~~ 164 (192)
T cd02140 127 QIAVWTALAAEGIGANLQH--------YNPLIDEEVAKKWNIPSNW 164 (192)
T ss_pred HHHHHHHHHhCCCcccHHH--------hCccCCHHHHHhcCCCccc
Confidence 3577788888887762110 0012358999999999875
No 42
>PF13518 HTH_28: Helix-turn-helix domain
Probab=40.05 E-value=52 Score=18.30 Aligned_cols=21 Identities=29% Similarity=0.403 Sum_probs=16.8
Q ss_pred HHHHHhcCCCHHHHHHHhCCC
Q 046604 92 TLANRIKNKSVEYIRKFFGIE 112 (134)
Q Consensus 92 ~iA~~i~gks~eeir~~f~i~ 112 (134)
.|.....|.|..++.+.|||.
T Consensus 5 iv~~~~~g~s~~~~a~~~gis 25 (52)
T PF13518_consen 5 IVELYLEGESVREIAREFGIS 25 (52)
T ss_pred HHHHHHcCCCHHHHHHHHCCC
Confidence 344456799999999999994
No 43
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=40.05 E-value=66 Score=20.78 Aligned_cols=44 Identities=14% Similarity=0.083 Sum_probs=24.7
Q ss_pred chhHHHHHHHHHHHHh-cC-CCHHHHHHHhC----CCCCCCHHHHHHHHH
Q 046604 82 IKDTLDYLAETLANRI-KN-KSVEYIRKFFG----IENNFMPEEKEATRK 125 (134)
Q Consensus 82 I~~Ll~l~~~~iA~~i-~g-ks~eeir~~f~----i~~d~t~eee~~i~~ 125 (134)
|..|+.+..++.++-- +| -|.+|+|+++. +-+.+|++|-+++.+
T Consensus 9 ~~~~i~~F~~y~~~~~~~g~Is~~EL~~~l~~~~~lg~k~t~~ev~~m~~ 58 (88)
T cd05029 9 IGLLVAIFHKYSGREGDKNTLSKKELKELIQKELTIGSKLQDAEIAKLME 58 (88)
T ss_pred HHHHHHHHHHHHccCCCCCEECHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence 3455555566655321 23 36777777773 344467776666544
No 44
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=39.78 E-value=32 Score=24.39 Aligned_cols=18 Identities=22% Similarity=0.322 Sum_probs=13.8
Q ss_pred HHHHHh-cCCCHHHHHHHh
Q 046604 92 TLANRI-KNKSVEYIRKFF 109 (134)
Q Consensus 92 ~iA~~i-~gks~eeir~~f 109 (134)
.|..++ .|+|.+||+++|
T Consensus 65 ~Vr~~i~~G~Sd~eI~~~~ 83 (126)
T TIGR03147 65 EVYSMVNEGKSNQQIIDFM 83 (126)
T ss_pred HHHHHHHcCCCHHHHHHHH
Confidence 455555 599999999876
No 45
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=38.30 E-value=27 Score=19.52 Aligned_cols=18 Identities=6% Similarity=0.110 Sum_probs=14.8
Q ss_pred CCceEEEeCCCCEEEecH
Q 046604 1 NEENIFEDGGQQLFKVEE 18 (134)
Q Consensus 1 ~~~i~l~S~DG~~f~V~~ 18 (134)
++.+++++.||+...|++
T Consensus 23 g~~vtV~~~~G~~~tv~~ 40 (42)
T PF02736_consen 23 GDKVTVKTEDGKEVTVKK 40 (42)
T ss_dssp SSEEEEEETTTEEEEEEG
T ss_pred CCEEEEEECCCCEEEeCC
Confidence 457899999999988865
No 46
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=38.12 E-value=38 Score=18.94 Aligned_cols=17 Identities=24% Similarity=0.282 Sum_probs=11.6
Q ss_pred hcCCCHHHHHHHhCCCC
Q 046604 97 IKNKSVEYIRKFFGIEN 113 (134)
Q Consensus 97 i~gks~eeir~~f~i~~ 113 (134)
..|+|..+|-+.||++.
T Consensus 15 ~~G~s~~~ia~~lgvs~ 31 (50)
T PF13384_consen 15 REGWSIREIAKRLGVSR 31 (50)
T ss_dssp HHT--HHHHHHHHTS-H
T ss_pred HCCCCHHHHHHHHCcCH
Confidence 34999999999999873
No 47
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=37.44 E-value=16 Score=26.00 Aligned_cols=17 Identities=18% Similarity=0.389 Sum_probs=12.6
Q ss_pred CCCHHHHHHHhCCCCCC
Q 046604 99 NKSVEYIRKFFGIENNF 115 (134)
Q Consensus 99 gks~eeir~~f~i~~d~ 115 (134)
|.||+|=|+.||++.|+
T Consensus 94 gltp~eYR~kwGlp~dy 110 (132)
T PF05443_consen 94 GLTPEEYRAKWGLPKDY 110 (132)
T ss_dssp -S-HHHHHHHTT-GGG-
T ss_pred CCCHHHHHHHhCcCCCC
Confidence 99999999999999985
No 48
>TIGR01999 iscU FeS cluster assembly scaffold IscU. This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms.
Probab=37.43 E-value=41 Score=23.23 Aligned_cols=36 Identities=22% Similarity=0.081 Sum_probs=22.5
Q ss_pred HHhhccccchhHHHHHH-HHHHHHhcCCCHHHHHHHh
Q 046604 74 LLVADYLTIKDTLDYLA-ETLANRIKNKSVEYIRKFF 109 (134)
Q Consensus 74 i~AA~yL~I~~Ll~l~~-~~iA~~i~gks~eeir~~f 109 (134)
+.-+.|-.-=.-...+| ..++.+++|||.+|.+..-
T Consensus 51 I~d~~f~~~GC~~s~Asas~~~e~i~Gktl~ea~~i~ 87 (124)
T TIGR01999 51 IEDAKFKTFGCGSAIASSSLATELIKGKSLEEALKIK 87 (124)
T ss_pred EEEEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHhcc
Confidence 33444444434444444 5668889999999988753
No 49
>TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not.
Probab=37.35 E-value=45 Score=22.95 Aligned_cols=37 Identities=14% Similarity=0.106 Sum_probs=23.6
Q ss_pred HHHhhccccchhHHHHHH-HHHHHHhcCCCHHHHHHHh
Q 046604 73 MLLVADYLTIKDTLDYLA-ETLANRIKNKSVEYIRKFF 109 (134)
Q Consensus 73 Li~AA~yL~I~~Ll~l~~-~~iA~~i~gks~eeir~~f 109 (134)
.+.-+.|-.-=.-...+| ..++.++.|||++|..+.-
T Consensus 46 ~I~d~~f~~~GC~is~Asas~~~e~i~Gk~l~ea~~i~ 83 (121)
T TIGR03419 46 IIKDVKFKTFGCGAAIASSSMATEMIKGKTLEEAWELT 83 (121)
T ss_pred EEEEEEEEEeccHHHHHHHHHHHHHHcCCCHHHHHHhh
Confidence 344445554444444444 4558889999999977653
No 50
>PRK11325 scaffold protein; Provisional
Probab=37.06 E-value=41 Score=23.40 Aligned_cols=37 Identities=11% Similarity=0.064 Sum_probs=23.1
Q ss_pred HHHhhccccchhHHHHHH-HHHHHHhcCCCHHHHHHHh
Q 046604 73 MLLVADYLTIKDTLDYLA-ETLANRIKNKSVEYIRKFF 109 (134)
Q Consensus 73 Li~AA~yL~I~~Ll~l~~-~~iA~~i~gks~eeir~~f 109 (134)
.+.-+.|-.-=.-...+| ..++.+++|||++|.+.+-
T Consensus 52 ~I~d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~ 89 (127)
T PRK11325 52 IIEDAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIK 89 (127)
T ss_pred eEEEEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcC
Confidence 344444444444444444 4557889999999988753
No 51
>KOG4244 consensus Failed axon connections (fax) protein/glutathione S-transferase-like protein [Signal transduction mechanisms]
Probab=35.41 E-value=40 Score=27.02 Aligned_cols=24 Identities=25% Similarity=0.527 Sum_probs=20.1
Q ss_pred HHHHHHHhCCCCCCCHHHHHHHHH
Q 046604 102 VEYIRKFFGIENNFMPEEKEATRK 125 (134)
Q Consensus 102 ~eeir~~f~i~~d~t~eee~~i~~ 125 (134)
...+|+.|++++++++||+.+-+.
T Consensus 111 ~~~L~~hf~~~~~L~~e~~a~s~A 134 (281)
T KOG4244|consen 111 EDRLRKHFKIPDDLSAEQRAQSRA 134 (281)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHH
Confidence 356889999999999999887654
No 52
>PF03883 DUF328: Protein of unknown function (DUF328); InterPro: IPR005583 The members of this family are functionally uncharacterised. They are about 250 amino acids in length.
Probab=35.05 E-value=43 Score=25.92 Aligned_cols=41 Identities=20% Similarity=0.248 Sum_probs=29.7
Q ss_pred hHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCCHHHHHHHH
Q 046604 84 DTLDYLAETLANRIKNKSVEYIRKFFGIENNFMPEEKEATR 124 (134)
Q Consensus 84 ~Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~t~eee~~i~ 124 (134)
+.+.-..+.++..++..|++|+++.|++...+..+.-++.+
T Consensus 25 p~f~~~~~~l~~~L~~~s~~el~~l~~is~~la~~~~~~~~ 65 (237)
T PF03883_consen 25 PEFLEKTEELLEALKSLSEEELKKLMKISDKLAEENYQRNQ 65 (237)
T ss_pred cChHHHHHHHHHHHHhcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 33444566778888999999999999999876555544443
No 53
>PF01843 DIL: DIL domain; InterPro: IPR018444 Dilute encodes a novel type of myosin heavy chain, with a tail, or C-terminal, region that has elements of both type II (alpha-helical coiled-coil) and type I (non-coiled-coil) myosin heavy chains. The DIL non alpha-helical domain is found in dilute myosin heavy chain proteins and other myosins. In mouse the dilute protein may play a role in the elaboration, maintenance, or function of cellular processes of melanocytes and neurons []. The MYO2 protein of Saccharomyces cerevisiae is implicated in vectorial vesicle transport and is homologous to the dilute protein over practically its entire length [].; PDB: 3MMI_B 2F6H_X.
Probab=34.45 E-value=22 Score=23.55 Aligned_cols=59 Identities=20% Similarity=0.369 Sum_probs=34.9
Q ss_pred hHHHHHHHHhcCCCcccccccCCChHHHHHHHHhhccccchh-HHHHHHHHHHHHhcCCCHHHHHHHh
Q 046604 43 LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVADYLTIKD-TLDYLAETLANRIKNKSVEYIRKFF 109 (134)
Q Consensus 43 L~~Iie~c~~h~~~kD~~F~~~~~~~~l~~Li~AA~yL~I~~-Ll~l~~~~iA~~i~gks~eeir~~f 109 (134)
|..+-+||+.|.-. ..-.+.+-.+..||+.|.++. .++ --..+-...-.-||.+|++.+
T Consensus 37 ls~l~~W~~~~~l~-------~~~~~~l~~l~Qa~~lL~~~k~~~~-d~~~~~~~c~~Ln~~Qi~~iL 96 (105)
T PF01843_consen 37 LSELEDWARSHGLE-------EAAEEHLQPLSQAANLLQLRKSTLQ-DWDSLRETCPSLNPAQIRKIL 96 (105)
T ss_dssp HHHHHHCCCCTTST-------TH-HHHCHHHHHHHHHCCC--SSHH-HHHHHCCCTTTS-HHHHHHHH
T ss_pred HHHHHHHHHhcccc-------hhHHHHHHHHHHHHHHHHhcCcchh-HHHHHHHHcccCCHHHHHHHH
Confidence 88999999987742 102577888999999999942 222 222222222345666666654
No 54
>PF03750 DUF310: Protein of unknown function (DUF310); InterPro: IPR010149 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents the C-terminal domain of a minor family of CRISPR-associated proteins. These proteins are found adjacent to a characteristic short, palindromic repeat cluster termed CRISPR, a probable mobile DNA element.
Probab=33.77 E-value=61 Score=22.30 Aligned_cols=34 Identities=26% Similarity=0.478 Sum_probs=22.1
Q ss_pred ccchhHHHHHHHHHHHHhc--CCCHHHHHHHhCCCCC
Q 046604 80 LTIKDTLDYLAETLANRIK--NKSVEYIRKFFGIENN 114 (134)
Q Consensus 80 L~I~~Ll~l~~~~iA~~i~--gks~eeir~~f~i~~d 114 (134)
++++.|.+.+.+ +|..++ +-|+.|||++|+--..
T Consensus 8 ~~~~~~~~~Ae~-~~k~l~~~~lttsQlRkf~~~v~~ 43 (119)
T PF03750_consen 8 LDIELLVDYAEK-IAKELKKNKLTTSQLRKFYDEVKR 43 (119)
T ss_pred cCHHHHHHHHHH-HHHHHHhCCCCHHHHHHHHHHHHH
Confidence 445555555554 444444 4799999999986544
No 55
>PF09524 Phg_2220_C: Conserved phage C-terminus (Phg_2220_C); InterPro: IPR011741 This entry is represented by the C-terminal domain of Bacteriophage r1t, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Probab=33.59 E-value=37 Score=21.77 Aligned_cols=63 Identities=17% Similarity=0.188 Sum_probs=38.2
Q ss_pred CCEEEecHHHHHHHHhhccCCCCCCCCceecc-hHHHHHHHHhcCCCcccccccCCChHHHHHHHHhhcccc
Q 046604 11 QQLFKVEEQGCSRLCSHSSTSDGTSEDMVVLQ-LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVADYLT 81 (134)
Q Consensus 11 G~~f~V~~~~~~~~i~~~~le~~~~~~~Ipl~-L~~Iie~c~~h~~~kD~~F~~~~~~~~l~~Li~AA~yL~ 81 (134)
|..|..+.......|+.. +.++- .+. +.+||++.-.+..+ |..+-+.+.+++||. -.=..||+
T Consensus 10 g~~f~~~~~~~~~~I~aR-l~eG~-----t~edf~~VID~k~~~W~~-~~~m~~YLRP~TLF~-~kFe~YLn 73 (74)
T PF09524_consen 10 GKKFKSNTKSTKKLIKAR-LNEGY-----TLEDFKKVIDNKVAEWKG-DPKMEKYLRPETLFG-SKFESYLN 73 (74)
T ss_pred cCccCCCcHHHHHHHHHH-HHCCC-----CHHHHHHHHHHHHHHHCC-CHHHHHhcCchhhhH-HhHHHHcc
Confidence 556665444444456555 55432 333 89999998776554 444445557788887 66666654
No 56
>COG3370 Uncharacterized protein conserved in archaea [Function unknown]
Probab=33.49 E-value=30 Score=24.06 Aligned_cols=28 Identities=21% Similarity=0.235 Sum_probs=23.4
Q ss_pred ChHHHHHHHHhhccccchhHHHHHHHHHHHH
Q 046604 66 SNDELKEMLLVADYLTIKDTLDYLAETLANR 96 (134)
Q Consensus 66 ~~~~l~~Li~AA~yL~I~~Ll~l~~~~iA~~ 96 (134)
++...+..+..+..+++++ ++|+.+|+.
T Consensus 52 ~~~~~l~~l~~~~s~g~~p---~AC~~va~~ 79 (113)
T COG3370 52 NDGDSLKMLQELRSLGIKP---LACKVVAEN 79 (113)
T ss_pred cchHHHHHHHHHHHcCCcc---hHHHHHHHh
Confidence 4566689999999999998 589999975
No 57
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=32.93 E-value=41 Score=24.28 Aligned_cols=18 Identities=28% Similarity=0.433 Sum_probs=11.1
Q ss_pred HHHHHh-cCCCHHHHHHHh
Q 046604 92 TLANRI-KNKSVEYIRKFF 109 (134)
Q Consensus 92 ~iA~~i-~gks~eeir~~f 109 (134)
.|..++ .|+|.+||+++|
T Consensus 65 ~I~~~l~~G~s~~eI~~~~ 83 (148)
T PF03918_consen 65 EIREMLAEGKSDEEIIDYF 83 (148)
T ss_dssp HHHHHHHHT--HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHH
Confidence 344444 699999999865
No 58
>PF11103 DUF2887: Protein of unknown function (DUF2887); InterPro: IPR022573 This bacterial group of proteins has no known function.
Probab=32.62 E-value=60 Score=24.71 Aligned_cols=29 Identities=17% Similarity=0.279 Sum_probs=25.2
Q ss_pred cchhHHHHHHHHHHHHhcCCCHHHHHHHh
Q 046604 81 TIKDTLDYLAETLANRIKNKSVEYIRKFF 109 (134)
Q Consensus 81 ~I~~Ll~l~~~~iA~~i~gks~eeir~~f 109 (134)
.=..++++.-..+..++..+|.+||.+||
T Consensus 172 ~~~~lleLIEtIlvyKfp~lSreEIeaMl 200 (200)
T PF11103_consen 172 QQRELLELIETILVYKFPQLSREEIEAML 200 (200)
T ss_pred HHHHHHHHHHHHHHHHccccCHHHHHHhC
Confidence 35678888888999999999999999987
No 59
>PF10507 DUF2453: Protein of unknown function (DUF2453); InterPro: IPR019537 The function of these transmembrane protein is not known.
Probab=32.60 E-value=1e+02 Score=21.35 Aligned_cols=46 Identities=15% Similarity=0.252 Sum_probs=32.1
Q ss_pred hHHHHHHHHHHHHhcC-------CCHHHHHHHhCCCCC-CCHHHHHHHHHhchhhh
Q 046604 84 DTLDYLAETLANRIKN-------KSVEYIRKFFGIENN-FMPEEKEATRKEYELLR 131 (134)
Q Consensus 84 ~Ll~l~~~~iA~~i~g-------ks~eeir~~f~i~~d-~t~eee~~i~~e~~w~~ 131 (134)
++--++++.+.+.+++ -..|.+.+..|++.. +|++|.+. +..+|+.
T Consensus 34 giStmAAAalGN~vSDv~Gi~~~~~vE~~~~rlg~~~P~Lt~~Q~~~--~~~r~a~ 87 (111)
T PF10507_consen 34 GISTMAAAALGNLVSDVAGIGLGGYVERLAQRLGLKAPVLTPAQLNS--RSTRWAS 87 (111)
T ss_pred hHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhCCCCCCCCHHHHhC--hHHHHHH
Confidence 3445677777777664 469999999999884 99988653 4455543
No 60
>PRK13696 hypothetical protein; Provisional
Probab=31.94 E-value=1.2e+02 Score=18.83 Aligned_cols=26 Identities=38% Similarity=0.539 Sum_probs=19.4
Q ss_pred cCCCHHHHHHHhCCCCCCCHHHHHHHHHh
Q 046604 98 KNKSVEYIRKFFGIENNFMPEEKEATRKE 126 (134)
Q Consensus 98 ~gks~eeir~~f~i~~d~t~eee~~i~~e 126 (134)
+..+...+.++||+-+ +||-++++++
T Consensus 36 ~~~~~~~l~~~~Gil~---dee~~e~~~~ 61 (62)
T PRK13696 36 KKGNLDKLMKAFGILS---EEEAEELKKE 61 (62)
T ss_pred hhccHHHHHHHHCCCC---HHHHHHHHhh
Confidence 3456889999999975 4676777664
No 61
>PF01592 NifU_N: NifU-like N terminal domain; InterPro: IPR002871 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the N-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal and a C-terminal domain (IPR001075 from INTERPRO) []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 3LVL_A 4EB5_C 4EB7_C 1WFZ_A 2Z7E_C 2AZH_A 1XJS_A 1Q48_A 1R9P_A 2KQK_A ....
Probab=31.70 E-value=60 Score=22.36 Aligned_cols=22 Identities=27% Similarity=0.138 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHhcCCCHHHHHH
Q 046604 86 LDYLAETLANRIKNKSVEYIRK 107 (134)
Q Consensus 86 l~l~~~~iA~~i~gks~eeir~ 107 (134)
.-.++..++.+++|||.+|+.+
T Consensus 64 ~~Asas~~~~~i~gk~l~ea~~ 85 (126)
T PF01592_consen 64 SIASASMMCELIKGKTLEEALK 85 (126)
T ss_dssp HHHHHHHHHHHHTTSBHHHHHC
T ss_pred HHHHHHHHHHHHcCCCHHHHHH
Confidence 3445567788899999888853
No 62
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=30.36 E-value=55 Score=23.16 Aligned_cols=18 Identities=17% Similarity=0.152 Sum_probs=13.5
Q ss_pred HHHHHh-cCCCHHHHHHHh
Q 046604 92 TLANRI-KNKSVEYIRKFF 109 (134)
Q Consensus 92 ~iA~~i-~gks~eeir~~f 109 (134)
.|..++ .|+|.+||+.+|
T Consensus 65 ~Vr~~i~~G~sd~eI~~~~ 83 (126)
T PRK10144 65 QVYSMVAEGKSEVEIIGWM 83 (126)
T ss_pred HHHHHHHcCCCHHHHHHHH
Confidence 455554 599999999876
No 63
>TIGR02476 BluB cob(II)yrinic acid a,c-diamide reductase. The BluB protein is related to the nitroreductase family (pfam0881), and is found to substitute for the FldA cobalt reductase in aerobic species (by phylogenetic profiling). BluB is also found to be preceded by B12 promoter elements elements. The gene in R. capsulatus has been shown to be essential for cobalamin biosynthesis.
Probab=29.76 E-value=44 Score=24.70 Aligned_cols=36 Identities=11% Similarity=0.234 Sum_probs=24.6
Q ss_pred HHHHHhhccccchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCC
Q 046604 71 KEMLLVADYLTIKDTLDYLAETLANRIKNKSVEYIRKFFGIENNFM 116 (134)
Q Consensus 71 ~~Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~t 116 (134)
-.++.||..+++-.- .+.+-..+.+++.|||+.+.+
T Consensus 135 ~nl~LaA~~~GlGs~----------~~~~~~~~~v~~~L~lp~~~~ 170 (205)
T TIGR02476 135 QNLWLAARAEGLGVG----------WVSILDPDAVRRLLGVPEGWR 170 (205)
T ss_pred HHHHHHHHHCCCcce----------eecccChHHHHHHhCcCCCce
Confidence 466777777776642 123456789999999997754
No 64
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=29.38 E-value=64 Score=20.23 Aligned_cols=19 Identities=16% Similarity=0.331 Sum_probs=15.0
Q ss_pred HHHHHHhcCCCHHHHHHHh
Q 046604 91 ETLANRIKNKSVEYIRKFF 109 (134)
Q Consensus 91 ~~iA~~i~gks~eeir~~f 109 (134)
++|-..++|+|.+|++.+-
T Consensus 5 ~AI~~nv~g~s~~el~~~I 23 (65)
T PF14098_consen 5 QAIIHNVKGSSKEELKDTI 23 (65)
T ss_pred HHHHHHccCCCHHHHHHHH
Confidence 3566677999999999864
No 65
>PLN03212 Transcription repressor MYB5; Provisional
Probab=29.23 E-value=85 Score=24.82 Aligned_cols=35 Identities=11% Similarity=0.171 Sum_probs=26.7
Q ss_pred HHHHHHh-cCCCHHHHHHHhC------CCC-CCCHHHHHHHHH
Q 046604 91 ETLANRI-KNKSVEYIRKFFG------IEN-NFMPEEKEATRK 125 (134)
Q Consensus 91 ~~iA~~i-~gks~eeir~~f~------i~~-d~t~eee~~i~~ 125 (134)
..||..+ .|+|..+.|+.+. |.. .||+||.+.|.+
T Consensus 49 ~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLle 91 (249)
T PLN03212 49 RSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILR 91 (249)
T ss_pred HHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHH
Confidence 4577776 4899999999774 655 599999887654
No 66
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=29.19 E-value=1.1e+02 Score=21.88 Aligned_cols=30 Identities=10% Similarity=0.138 Sum_probs=20.4
Q ss_pred HHHHHHHHhcCCCHHHHHH--------HhCCCCCCCHH
Q 046604 89 LAETLANRIKNKSVEYIRK--------FFGIENNFMPE 118 (134)
Q Consensus 89 ~~~~iA~~i~gks~eeir~--------~f~i~~d~t~e 118 (134)
.+..+...+.|+||+||.+ -+|+..-+||-
T Consensus 81 l~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSps 118 (138)
T PRK09296 81 LIAVVFILYQQMTPQDIVNFDVRPWFEKLALTQHLTPS 118 (138)
T ss_pred HHHHHHHHHcCCCHHHHHhCChHHHHHHcCcccccCcc
Confidence 3444555678999999875 34677666653
No 67
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=28.10 E-value=77 Score=20.62 Aligned_cols=39 Identities=13% Similarity=0.308 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhcCCCHHHHHH-------HhCCCCCCCHHHHHHHHH
Q 046604 87 DYLAETLANRIKNKSVEYIRK-------FFGIENNFMPEEKEATRK 125 (134)
Q Consensus 87 ~l~~~~iA~~i~gks~eeir~-------~f~i~~d~t~eee~~i~~ 125 (134)
.++...+++.++|.....+++ .||+-.+++..+.+++=.
T Consensus 19 ~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~ 64 (106)
T PF09382_consen 19 RFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIR 64 (106)
T ss_dssp -S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHH
T ss_pred cccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHH
Confidence 577888999999988888776 499999999888877643
No 68
>PF11399 DUF3192: Protein of unknown function (DUF3192); InterPro: IPR021534 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed.
Probab=27.71 E-value=64 Score=22.03 Aligned_cols=25 Identities=16% Similarity=0.271 Sum_probs=20.7
Q ss_pred HHHHHHhcCCCHHHHHHHhCCCCCCC
Q 046604 91 ETLANRIKNKSVEYIRKFFGIENNFM 116 (134)
Q Consensus 91 ~~iA~~i~gks~eeir~~f~i~~d~t 116 (134)
+.||..--|.|-++++..+|-| |||
T Consensus 26 ~~i~~L~lg~s~~~V~~~lG~p-dfs 50 (102)
T PF11399_consen 26 QNIAKLSLGMSKDQVIALLGTP-DFS 50 (102)
T ss_pred HHHHhcCCCCCHHHHHHHhCCC-Cch
Confidence 4667776799999999999998 465
No 69
>PF05871 ESCRT-II: ESCRT-II complex subunit; InterPro: IPR008570 This entry represents the vps25 subunit (vacuolar protein sorting-associated protein 25) of the endosome-associated complex ESCRT-II (Endosomal Sorting Complexes Required for Transport protein II). ESCRT (ESCRT-I, -II, -III) complexes orchestrate efficient sorting of ubiquitinated transmembrane receptors to lysosomes via multivesicular bodies (MVBs) []. ESCRT-II recruits the transport machinery for protein sorting at MVB []. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. ESCRT-II transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo []. ESCRT-II is a trilobal complex composed of two copies of vps25, one copy of vps22 and the C-terminal region of vps36. The crystal structure of vps25 revealed two winged-helix domains, the N-terminal domain of vps25 interacting with vps22 and vps35 [].; PDB: 1W7P_B 1U5T_D 1XB4_D 3HTU_E 3CUQ_C 2ZME_D.
Probab=27.42 E-value=41 Score=24.06 Aligned_cols=14 Identities=21% Similarity=0.672 Sum_probs=11.2
Q ss_pred hHHHHHHHHhcCCC
Q 046604 43 LPYIIKFCKAHGVS 56 (134)
Q Consensus 43 L~~Iie~c~~h~~~ 56 (134)
-..|+.||+||+-.
T Consensus 26 ~~lIl~y~~~~k~~ 39 (139)
T PF05871_consen 26 SDLILDYCRHHKIF 39 (139)
T ss_dssp HHHHHHHHHHTT-S
T ss_pred HHHHHHHHHHhcee
Confidence 56799999999876
No 70
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=27.18 E-value=93 Score=18.72 Aligned_cols=34 Identities=21% Similarity=-0.010 Sum_probs=26.5
Q ss_pred CCCHHHHHH----HhCCCCCCCHHHHHHHHHhchhhhh
Q 046604 99 NKSVEYIRK----FFGIENNFMPEEKEATRKEYELLRL 132 (134)
Q Consensus 99 gks~eeir~----~f~i~~d~t~eee~~i~~e~~w~~~ 132 (134)
.+|.+|+-. -.||+..+|.-=..++++||+=.|.
T Consensus 12 yMsk~E~v~~L~~~a~I~P~~T~~VW~~Le~eN~eFF~ 49 (54)
T PF09713_consen 12 YMSKEECVRALQKQANIEPVFTSTVWQKLEKENPEFFK 49 (54)
T ss_pred cCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHCHHHHH
Confidence 466666554 4589999999999999999986654
No 71
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=27.03 E-value=91 Score=17.35 Aligned_cols=16 Identities=31% Similarity=0.478 Sum_probs=11.4
Q ss_pred hcCCCHHHHHHHhCCC
Q 046604 97 IKNKSVEYIRKFFGIE 112 (134)
Q Consensus 97 i~gks~eeir~~f~i~ 112 (134)
-.|.|..+|-+.|||.
T Consensus 19 ~~G~si~~IA~~~gvs 34 (45)
T PF02796_consen 19 AEGMSIAEIAKQFGVS 34 (45)
T ss_dssp HTT--HHHHHHHTTS-
T ss_pred HCCCCHHHHHHHHCcC
Confidence 4689999999999986
No 72
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=26.74 E-value=1.2e+02 Score=17.54 Aligned_cols=23 Identities=26% Similarity=0.210 Sum_probs=16.1
Q ss_pred HHHHHHhcCCCHHHHHHHhCCCC
Q 046604 91 ETLANRIKNKSVEYIRKFFGIEN 113 (134)
Q Consensus 91 ~~iA~~i~gks~eeir~~f~i~~ 113 (134)
+.+.-+..|+|+.||-..+|++.
T Consensus 10 ~vl~~l~~G~~~~eIA~~l~is~ 32 (58)
T PF00196_consen 10 EVLRLLAQGMSNKEIAEELGISE 32 (58)
T ss_dssp HHHHHHHTTS-HHHHHHHHTSHH
T ss_pred HHHHHHHhcCCcchhHHhcCcch
Confidence 44555668899988888888763
No 73
>cd02144 iodotyrosine_dehalogenase Iodotyrosine dehalogenase catalyzes the removal of iodine from the 3, 5 positions of L-tyosine in thyroid, liver and kidney, using NADPH as electron donor. This enzyme is a homolog of the nitroreductase family. These enzymes are usually homodimers.
Probab=26.71 E-value=58 Score=23.34 Aligned_cols=35 Identities=11% Similarity=0.193 Sum_probs=24.5
Q ss_pred HHHHhhccccchhHHHHHHHHHHHHhcCCCH-HHHHHHhCCCCCCC
Q 046604 72 EMLLVADYLTIKDTLDYLAETLANRIKNKSV-EYIRKFFGIENNFM 116 (134)
Q Consensus 72 ~Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~-eeir~~f~i~~d~t 116 (134)
.++.||.-+++... .+.+... +.+|+.|||+++..
T Consensus 131 ~l~LaA~~~Glgs~----------~~~~~~~~~~v~~~l~ip~~~~ 166 (193)
T cd02144 131 LLLAALQNAGLGTV----------TTTPLNMGPFLRRLLGRPANEK 166 (193)
T ss_pred HHHHHHHHCCCcee----------ecCCcchhHHHHHHhCCCCCCc
Confidence 47778888887761 1234344 89999999998654
No 74
>PF11165 DUF2949: Protein of unknown function (DUF2949); InterPro: IPR021336 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=26.60 E-value=1e+02 Score=18.81 Aligned_cols=10 Identities=20% Similarity=0.338 Sum_probs=8.7
Q ss_pred hHHHHHHHHh
Q 046604 43 LPYIIKFCKA 52 (134)
Q Consensus 43 L~~Iie~c~~ 52 (134)
|.+|++|+++
T Consensus 49 L~~i~DWl~~ 58 (58)
T PF11165_consen 49 LDQIFDWLEN 58 (58)
T ss_pred HHHHHHHHhC
Confidence 9999999864
No 75
>COG4680 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.59 E-value=45 Score=22.48 Aligned_cols=17 Identities=29% Similarity=0.274 Sum_probs=14.4
Q ss_pred CCCHHHHHHHhCCCCCC
Q 046604 99 NKSVEYIRKFFGIENNF 115 (134)
Q Consensus 99 gks~eeir~~f~i~~d~ 115 (134)
=++|++|+.+||..+++
T Consensus 35 w~~P~diK~~f~~d~~~ 51 (98)
T COG4680 35 WKKPEDIKSVFPLDNFK 51 (98)
T ss_pred cCCHHHHHHhcCcccce
Confidence 48999999999977764
No 76
>cd06664 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.
Probab=26.39 E-value=1.1e+02 Score=20.61 Aligned_cols=37 Identities=16% Similarity=0.205 Sum_probs=23.8
Q ss_pred HHHhhccccchhHHHHHH-HHHHHHhcCCCHHHHHHHh
Q 046604 73 MLLVADYLTIKDTLDYLA-ETLANRIKNKSVEYIRKFF 109 (134)
Q Consensus 73 Li~AA~yL~I~~Ll~l~~-~~iA~~i~gks~eeir~~f 109 (134)
.+..+.|-.-=...-.+| ..++.+++|||.+|...+.
T Consensus 47 ~I~d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~ 84 (123)
T cd06664 47 RITDAKFQGFGCAISIASASLLTELIKGKTLDEALKLL 84 (123)
T ss_pred EEEEEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHH
Confidence 444455544444444444 4557888999999998755
No 77
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=26.38 E-value=1.1e+02 Score=16.70 Aligned_cols=18 Identities=17% Similarity=0.176 Sum_probs=14.0
Q ss_pred HhcCCCHHHHHHHhCCCC
Q 046604 96 RIKNKSVEYIRKFFGIEN 113 (134)
Q Consensus 96 ~i~gks~eeir~~f~i~~ 113 (134)
...|+|..+|-+.+|++.
T Consensus 15 ~~~g~s~~eia~~l~is~ 32 (58)
T smart00421 15 LAEGLTNKEIAERLGISE 32 (58)
T ss_pred HHcCCCHHHHHHHHCCCH
Confidence 346888888888888864
No 78
>PRK15019 CsdA-binding activator; Provisional
Probab=26.26 E-value=1.2e+02 Score=21.98 Aligned_cols=29 Identities=10% Similarity=0.250 Sum_probs=19.7
Q ss_pred HHHHHHHhcCCCHHHHHH--------HhCCCCCCCHH
Q 046604 90 AETLANRIKNKSVEYIRK--------FFGIENNFMPE 118 (134)
Q Consensus 90 ~~~iA~~i~gks~eeir~--------~f~i~~d~t~e 118 (134)
+..+...+.|+||+||.+ -+|+..-+||-
T Consensus 92 ~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSps 128 (147)
T PRK15019 92 LAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSAS 128 (147)
T ss_pred HHHHHHHHcCCCHHHHHhcCHHHHHHHCCchhhcCcc
Confidence 344455568999999975 34677666653
No 79
>TIGR03553 F420_FbiB_CTERM F420 biosynthesis protein FbiB, C-terminal domain. Coenzyme F420 differs between the Archaea and the Actinobacteria, where the numbers of glutamate residues attached are 2 (Archaea) or 5-6 (Mycobacterium). The enzyme in the Archaea is homologous to the N-terminal domain of FbiB from Mycobacterium bovis, and is responsible for glutamate ligation. Therefore it seems likely that the C-terminal domain of FbiB, modeled by this alignment, is involved in additional glutamate ligation.
Probab=26.20 E-value=48 Score=24.03 Aligned_cols=17 Identities=6% Similarity=0.216 Sum_probs=14.0
Q ss_pred CCHHHHHHHhCCCCCCC
Q 046604 100 KSVEYIRKFFGIENNFM 116 (134)
Q Consensus 100 ks~eeir~~f~i~~d~t 116 (134)
...+.+|+.|||+.++.
T Consensus 149 ~~~~~v~~~l~lp~~~~ 165 (194)
T TIGR03553 149 FAADVVRAELDLPADWE 165 (194)
T ss_pred cCHHHHHHHhCcCCCce
Confidence 45789999999998753
No 80
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=25.89 E-value=42 Score=26.97 Aligned_cols=13 Identities=46% Similarity=0.613 Sum_probs=11.9
Q ss_pred CHHHHHHHhCCCC
Q 046604 101 SVEYIRKFFGIEN 113 (134)
Q Consensus 101 s~eeir~~f~i~~ 113 (134)
|||+|++.||++.
T Consensus 248 sPEdIk~~FgiSK 260 (287)
T COG2996 248 SPEDIKATFGISK 260 (287)
T ss_pred CHHHHHHHhCcCH
Confidence 6999999999975
No 81
>PF07671 DUF1601: Protein of unknown function (DUF1601); InterPro: IPR011632 This repeat is found in a small number of proteins and is apparently limited to Coxiella burnetii.
Probab=25.05 E-value=80 Score=17.48 Aligned_cols=30 Identities=17% Similarity=0.174 Sum_probs=23.5
Q ss_pred cccchhHHHHHHHHHHHHhcCCCHHHHHHH
Q 046604 79 YLTIKDTLDYLAETLANRIKNKSVEYIRKF 108 (134)
Q Consensus 79 yL~I~~Ll~l~~~~iA~~i~gks~eeir~~ 108 (134)
||.-.+|-+....+|+..+..-+|++|-..
T Consensus 7 ~l~~q~L~~~L~~aV~~~a~~Fn~QeiaNt 36 (37)
T PF07671_consen 7 YLEEQRLSDRLLDAVRRNAEQFNPQEIANT 36 (37)
T ss_pred hhhhccchHHHHHHHHHHHHHcCHHHHhhc
Confidence 567778888888888888888888887543
No 82
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=24.90 E-value=1.5e+02 Score=17.21 Aligned_cols=41 Identities=17% Similarity=0.118 Sum_probs=26.1
Q ss_pred cchhHHHHHHHHHHHHhcC--CCHHHHHHHhCCCCCCCHHHHHHHH
Q 046604 81 TIKDTLDYLAETLANRIKN--KSVEYIRKFFGIENNFMPEEKEATR 124 (134)
Q Consensus 81 ~I~~Ll~l~~~~iA~~i~g--ks~eeir~~f~i~~d~t~eee~~i~ 124 (134)
.-+.++-.+|=.+|.++.+ .+..++..+.|. +|.++-.+..
T Consensus 36 ~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~---~~~~~i~~~~ 78 (83)
T smart00385 36 YSPSLIAAAALYLAAKTEEIPPWTKELVHYTGY---FTEEEILRME 78 (83)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC---CCHHHHHHHH
Confidence 3445666677788888776 356677777666 5666555443
No 83
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=24.58 E-value=44 Score=20.39 Aligned_cols=21 Identities=19% Similarity=0.293 Sum_probs=15.5
Q ss_pred HHHHhcCCCHHHHHHHhCCCC
Q 046604 93 LANRIKNKSVEYIRKFFGIEN 113 (134)
Q Consensus 93 iA~~i~gks~eeir~~f~i~~ 113 (134)
++..-.|+|.+|++..+|-|.
T Consensus 9 ~~~i~~GmTk~qV~~lLG~P~ 29 (71)
T PF04355_consen 9 LAQIKPGMTKDQVRALLGSPS 29 (71)
T ss_dssp HTTT-TTSBHHHHHHHHTS-S
T ss_pred HHhhcCCCCHHHHHHhcCCCC
Confidence 344446999999999999875
No 84
>TIGR03391 FeS_syn_CsdE cysteine desulfurase, sulfur acceptor subunit CsdE. Members of this protein family are CsdE, formerly called YgdK. This protein, found as a paralog to SufE in Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, works together and physically interacts with CsdA (a paralog of SufS). CsdA has cysteine desulfurase activity that is enhanced by this protein (CsdE), in which Cys-61 (numbered as in E. coli) is a sulfur acceptor site. This gene pair, although involved in FeS cluster biosynthesis, is not found next to other such genes as are its paralogs from the Suf or Isc systems.
Probab=24.36 E-value=1.4e+02 Score=21.29 Aligned_cols=29 Identities=14% Similarity=0.238 Sum_probs=19.0
Q ss_pred HHHHHHHhcCCCHHHHHH--------HhCCCCCCCHH
Q 046604 90 AETLANRIKNKSVEYIRK--------FFGIENNFMPE 118 (134)
Q Consensus 90 ~~~iA~~i~gks~eeir~--------~f~i~~d~t~e 118 (134)
+..+...+.|+||+||.+ .+|+..-+||-
T Consensus 87 ~alL~~~~~g~tp~eI~~~d~~~~~~~lGL~~~LSps 123 (138)
T TIGR03391 87 LAVLLTAVEGKTPEQLLAQDPLALFDELGLRAQLSAS 123 (138)
T ss_pred HHHHHHHHcCCCHHHHHHCCHHHHHHHcCchhccCcc
Confidence 334445568999999874 34666666653
No 85
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.35 E-value=56 Score=23.14 Aligned_cols=20 Identities=25% Similarity=0.252 Sum_probs=16.1
Q ss_pred HHHh-cCCCHHHHHHHhCCCC
Q 046604 94 ANRI-KNKSVEYIRKFFGIEN 113 (134)
Q Consensus 94 A~~i-~gks~eeir~~f~i~~ 113 (134)
-.++ +||+|.||.+.+||+=
T Consensus 103 ~emlr~gk~preIsk~lGIpi 123 (139)
T COG1710 103 REMLRNGKTPREISKDLGIPI 123 (139)
T ss_pred HHHHHcCCCHHHHHHhhCCch
Confidence 3344 5999999999999973
No 86
>cd03370 NADH_oxidase NADPH_oxidase. Nitroreductase family containing NADH oxidase and other, uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=24.11 E-value=58 Score=22.81 Aligned_cols=19 Identities=11% Similarity=0.261 Sum_probs=15.2
Q ss_pred hcCCCHHHHHHHhCCCC-CC
Q 046604 97 IKNKSVEYIRKFFGIEN-NF 115 (134)
Q Consensus 97 i~gks~eeir~~f~i~~-d~ 115 (134)
+.|...+.+++.||++. +.
T Consensus 112 i~~~~~~~v~~~l~l~~~~~ 131 (156)
T cd03370 112 MTGFDEEKVKEALGLPGRDR 131 (156)
T ss_pred CcCcCHHHHHHHhCcCCcCc
Confidence 44677899999999996 53
No 87
>PF14748 P5CR_dimer: Pyrroline-5-carboxylate reductase dimerisation; PDB: 2RCY_D 3TRI_A 2IZZ_B 2GR9_B 2GRA_B 2GER_C 1YQG_A 2AG8_A 3GT0_A 2AMF_E ....
Probab=23.86 E-value=2e+02 Score=19.20 Aligned_cols=55 Identities=11% Similarity=-0.060 Sum_probs=33.5
Q ss_pred HHHHhhccccchh-----HHHHHHHHHHHHhc--CCCHHHHHHHhCCCCCCCHHHHHHHHHh
Q 046604 72 EMLLVADYLTIKD-----TLDYLAETLANRIK--NKSVEYIRKFFGIENNFMPEEKEATRKE 126 (134)
Q Consensus 72 ~Li~AA~yL~I~~-----Ll~l~~~~iA~~i~--gks~eeir~~f~i~~d~t~eee~~i~~e 126 (134)
.++.||-..++++ |.--+..-.|.++. +++|+++|+..--|.-.|.+-.+.+++.
T Consensus 26 al~~a~v~~Gl~~~~A~~lv~~t~~G~a~ll~~~~~~~~~l~~~v~tPgG~T~~gl~~L~~~ 87 (107)
T PF14748_consen 26 ALADAAVAQGLPREEARKLVAQTFIGAAKLLEESGRSPAELRDEVTTPGGTTIAGLEVLEKG 87 (107)
T ss_dssp HHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHCSS-HHHHHHHHS-TTSHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHccCCCHHHHhhhccCCCCcHHHHHHHHHHC
Confidence 3444444444432 23333444455554 6899999999999999998888877765
No 88
>cd05295 MDH_like Malate dehydrogenase-like. These MDH-like proteins are related to other groups in the MDH family but do not have conserved substrate and cofactor binding residues. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subgroup are uncharacterized MDH-like proteins from animals. They are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Probab=23.55 E-value=81 Score=27.01 Aligned_cols=26 Identities=31% Similarity=0.579 Sum_probs=20.1
Q ss_pred HHHHHHhCCCCCCCHHHHHHHHHhch
Q 046604 103 EYIRKFFGIENNFMPEEKEATRKEYE 128 (134)
Q Consensus 103 eeir~~f~i~~d~t~eee~~i~~e~~ 128 (134)
|...-|||++..++.|++..|.+||.
T Consensus 79 e~~~~yyg~~s~m~~~~~~~i~~en~ 104 (452)
T cd05295 79 EYAESYYGITSSMMSEEMTVIAEENL 104 (452)
T ss_pred HHHHHHhCccccccHHHHHHHHHHhH
Confidence 45556888888888888888888874
No 89
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=23.53 E-value=70 Score=17.15 Aligned_cols=23 Identities=22% Similarity=0.247 Sum_probs=13.5
Q ss_pred HHHHHHHHhcCCCHHHHHHHh-CCC
Q 046604 89 LAETLANRIKNKSVEYIRKFF-GIE 112 (134)
Q Consensus 89 ~~~~iA~~i~gks~eeir~~f-~i~ 112 (134)
+|..||.+. |.|.++|++.- ++.
T Consensus 8 tl~~IA~~~-~~~~~~l~~~N~~~~ 31 (44)
T PF01476_consen 8 TLWSIAKRY-GISVDELMELNPNID 31 (44)
T ss_dssp -HHHHHHHT-TS-HHHHHHHCCTTH
T ss_pred cHHHHHhhh-hhhHhHHHHhcCCCC
Confidence 455666664 77777777765 443
No 90
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=23.29 E-value=1.4e+02 Score=21.58 Aligned_cols=36 Identities=11% Similarity=0.146 Sum_probs=21.1
Q ss_pred HHhhccccchhHHHHH-HHHHHHHhcCCCHHHHHHHh
Q 046604 74 LLVADYLTIKDTLDYL-AETLANRIKNKSVEYIRKFF 109 (134)
Q Consensus 74 i~AA~yL~I~~Ll~l~-~~~iA~~i~gks~eeir~~f 109 (134)
+..|-|...=.=...+ +..+..+++|||.+|.++.-
T Consensus 54 I~d~~F~~~GC~is~ASss~~te~v~Gkti~EAl~i~ 90 (150)
T COG0822 54 IEDAKFKGFGCAISIASSSMMTELVKGKTLDEALKIT 90 (150)
T ss_pred EEEEEeeecCcHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 3334444433333333 34557778999999988754
No 91
>TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family. Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.
Probab=23.10 E-value=1.1e+02 Score=21.44 Aligned_cols=37 Identities=14% Similarity=0.091 Sum_probs=23.8
Q ss_pred HHhhccccchhHHHHHH-HHHHHHhcCCCHHHHHHHhC
Q 046604 74 LLVADYLTIKDTLDYLA-ETLANRIKNKSVEYIRKFFG 110 (134)
Q Consensus 74 i~AA~yL~I~~Ll~l~~-~~iA~~i~gks~eeir~~f~ 110 (134)
+..+.|-.--.-...+| -.++.++.|||.+|+.....
T Consensus 51 I~d~~f~~~GCais~Asas~~~e~i~Gk~~~ea~~l~~ 88 (137)
T TIGR01994 51 IEDIAFEGEGCSISQASASMMTELIKGKTVEEALSLVE 88 (137)
T ss_pred EEEEEEEecccHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 44444444444444444 45688899999999987653
No 92
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=22.97 E-value=1.1e+02 Score=20.83 Aligned_cols=44 Identities=18% Similarity=0.274 Sum_probs=30.4
Q ss_pred cchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCC-CCCHHHHHHHHH
Q 046604 81 TIKDTLDYLAETLANRIKNKSVEYIRKFFGIEN-NFMPEEKEATRK 125 (134)
Q Consensus 81 ~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~-d~t~eee~~i~~ 125 (134)
++..|-+-....||+. .=.|++|+|..|.-.. -+++|+.++|-+
T Consensus 61 ~~~~l~e~~a~~I~nL-~P~~~dElrai~~~~~~~~~~e~l~~ILd 105 (112)
T PRK14981 61 ELEKMKEKTAVKIADI-LPETRDELRAIFAKERYTLSPEELDEILD 105 (112)
T ss_pred HccCCCHHHHHHHHhc-CCCCHHHHHHHHHHhccCCCHHHHHHHHH
Confidence 3334445555566654 5689999999987663 488888888754
No 93
>PF03131 bZIP_Maf: bZIP Maf transcription factor; InterPro: IPR004826 There are several different types of Maf transcription factors with different roles in the cell. MafG and MafH are small Mafs which lack a putative transactivation domain. They behave as transcriptional repressors when they dimerize among themselves. However they also serve as transcriptional activators by dimerizing with other (usually larger) basic-zipper proteins and recruiting them to specific DNA-binding sites. Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerization and DNA binding property. Neural retina-specific leucine zipper proteins also belong to this family. Together with the basic region, the Maf extended homology region (EHR), conserved only within the Maf family, defines the DNA binding specific to Mafs. This structure enables Mafs to make a broader area of contact with DNA and to recognise longer DNA sequences. In particular, the two residues at the beginning of helix H2 are positioned to recognise the flanking region []. Small Maf proteins heterodimerize with Fos and may act as competitive repressors of the NF2-E2 transcription factor. In mouse, Maf1 may play an early role in axial patterning. Defects in these proteins are a cause of autosomal dominant retinitis pigmentosa. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2KZ5_A 3A5T_A 1K1V_A 1SKN_P 2WT7_B 2WTY_B.
Probab=22.91 E-value=1e+02 Score=20.04 Aligned_cols=27 Identities=11% Similarity=0.249 Sum_probs=19.9
Q ss_pred HhcCCCHHHHHHHhCCCCCCCHHHHHHHHH
Q 046604 96 RIKNKSVEYIRKFFGIENNFMPEEKEATRK 125 (134)
Q Consensus 96 ~i~gks~eeir~~f~i~~d~t~eee~~i~~ 125 (134)
.+...|++|+..++ ..+|+++...++.
T Consensus 5 eL~~m~v~efn~~L---~~lt~~q~~~lK~ 31 (92)
T PF03131_consen 5 ELVSMSVREFNRLL---RGLTEEQIAELKQ 31 (92)
T ss_dssp HHHHS-HHHHHHHC---TTS-HHHHHHHHH
T ss_pred HHhhCCHHHHHHHH---HcCCHHHHHHHHH
Confidence 35567899999988 7799999888765
No 94
>PF02657 SufE: Fe-S metabolism associated domain; InterPro: IPR003808 This entry represents the core domain of SufE and related proteins. This domain of SufE shows strong structural similarity to IscU, and the sulfur-acceptor site in SufE coincides with the location of the cysteine residues mediating Fe-S cluster assembly in IscU. Thus, a conserved core structure is implicated in mediating the interactions of both SufE and IscU with the mutually homologous cysteine desulfurase enzymes present in their respective operons [].; PDB: 1MZG_B 1WLO_A 3G0M_A 1NI7_A.
Probab=22.30 E-value=2.1e+02 Score=19.83 Aligned_cols=33 Identities=24% Similarity=0.405 Sum_probs=22.1
Q ss_pred chhHHHHHHHHHHHHhcCCCHHHHHH-------HhCCCCCCCHH
Q 046604 82 IKDTLDYLAETLANRIKNKSVEYIRK-------FFGIENNFMPE 118 (134)
Q Consensus 82 I~~Ll~l~~~~iA~~i~gks~eeir~-------~f~i~~d~t~e 118 (134)
+++|+.+.++ .++|+||+||.. .+|+...+||-
T Consensus 69 vkGl~all~~----~~~g~t~~eI~~~~~~fl~~lgl~~~Ls~s 108 (125)
T PF02657_consen 69 VKGLLALLLE----VLNGQTPEEILAFDPDFLEQLGLSQHLSPS 108 (125)
T ss_dssp HHHHHHHHHH----HTTT-BHHHHHHS-THHHHHHTSCCCSTHH
T ss_pred HHHHHHHHHH----HHcCCCHHHHHhCCHHHHHHcCcccccCch
Confidence 4444444443 458999999986 57888888875
No 95
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=22.30 E-value=62 Score=19.15 Aligned_cols=17 Identities=24% Similarity=0.315 Sum_probs=13.0
Q ss_pred cCCCHHHHHHHhCCCCC
Q 046604 98 KNKSVEYIRKFFGIENN 114 (134)
Q Consensus 98 ~gks~eeir~~f~i~~d 114 (134)
-|.|.+|||+++.+..+
T Consensus 13 lGfsL~eI~~~l~l~~~ 29 (65)
T PF09278_consen 13 LGFSLEEIRELLELYDQ 29 (65)
T ss_dssp TT--HHHHHHHHHHCCS
T ss_pred cCCCHHHHHHHHhccCC
Confidence 49999999999988775
No 96
>PF05391 Lsm_interact: Lsm interaction motif; InterPro: IPR008669 This short motif is found at the C terminus of Prp24 proteins and probably interacts with the Lsm proteins to promote U4/U6 formation [].
Probab=21.83 E-value=70 Score=15.57 Aligned_cols=12 Identities=50% Similarity=0.636 Sum_probs=9.5
Q ss_pred cCCCHHHHHHHh
Q 046604 98 KNKSVEYIRKFF 109 (134)
Q Consensus 98 ~gks~eeir~~f 109 (134)
.-||-++.|++|
T Consensus 8 ~p~SNddFrkmf 19 (21)
T PF05391_consen 8 KPKSNDDFRKMF 19 (21)
T ss_pred CccchHHHHHHH
Confidence 357888999987
No 97
>KOG1665 consensus AFH1-interacting protein FIP2, contains BTB/POZ domain and pentapeptide repeats [General function prediction only]
Probab=21.63 E-value=86 Score=24.84 Aligned_cols=40 Identities=18% Similarity=0.184 Sum_probs=32.8
Q ss_pred hHHHHHHHHhcCCCcccccccCCChHHHHHHHHhhccccchhHHHHH
Q 046604 43 LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVADYLTIKDTLDYL 89 (134)
Q Consensus 43 L~~Iie~c~~h~~~kD~~F~~~~~~~~l~~Li~AA~yL~I~~Ll~l~ 89 (134)
++-|+.|+.+- +|.-. ++-.++.++.+|.|.+|-+|.+-.
T Consensus 64 FepIlNyLr~G------q~~~~-s~i~~lgvLeeArff~i~sL~~hl 103 (302)
T KOG1665|consen 64 FEPILNYLRDG------QIPSL-SDIDCLGVLEEARFFQILSLKDHL 103 (302)
T ss_pred hHHHHHHHhcC------ceeec-CCccHHHHHHHhhHHhhHhHHhHH
Confidence 99999998763 45444 777899999999999999988754
No 98
>PF05409 Peptidase_C30: Coronavirus endopeptidase C30; InterPro: IPR008740 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases correspond to MEROPS peptidase family C30 (clan PA(C)). These peptidases are related to serine endopeptidases of family S1 and are restricted to RNA viruses, where they are involved in viral polyprotein processing during replication [, , ]. This entry represents the CoV M-pro which comprises three domains. Domains I and II are six-stranded antiparallel beta barrels and together resemble the architecture of chymotrypsin and of picornaviruses 3C proteinases. The substrate-binding site is located in a cleft between these two domains. The catalytic site is situated at the centre of the cleft. A long loop connects domain II to the C-terminal domain (domain III). This latter domain, a globular cluster of five helices, has been implicated in the proteolytic activity of M-pro. In the active site of M-pro, Cys and His form a catalytic dyad. In contrast to serine proteinases and other cysteine proteinases, which have a catalytic triad, there is no third catalytic residue present [, , , ]. ; GO: 0019082 viral protein processing; PDB: 2VJ1_B 2K7X_A 2Q6D_B 2Q6F_A 1P9U_E 1LVO_B 2AMP_B 1P9S_A 2ZU2_A 3D23_A ....
Probab=21.47 E-value=1.1e+02 Score=24.81 Aligned_cols=51 Identities=22% Similarity=0.331 Sum_probs=32.8
Q ss_pred ChHHHHHHHHhhccccchhHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCCHHHH
Q 046604 66 SNDELKEMLLVADYLTIKDTLDYLAETLANRIKNKSVEYIRKFFGIENNFMPEEK 120 (134)
Q Consensus 66 ~~~~l~~Li~AA~yL~I~~Ll~l~~~~iA~~i~gks~eeir~~f~i~~d~t~eee 120 (134)
..+..++.+.|..=..+.+|+...-+ +..-..|++ |--...+++||||++-
T Consensus 215 ~~~~~~~~Laa~TgVsV~rlLaaI~~-L~~g~~G~~---IlG~~~ledE~Tp~~V 265 (293)
T PF05409_consen 215 SSDDAFDMLAAKTGVSVERLLAAIQR-LHKGFGGRT---ILGSCSLEDEFTPEMV 265 (293)
T ss_dssp SHHHHHHHHHHHHT--HHHHHHHHHH-HHHTTTTT----BTTBSS--TSS-HHHH
T ss_pred chhhHHHHHHHHhCCcHHHHHHHHHH-HhcCCCCCc---ccccccccccCCHHHH
Confidence 67788999999999999999876655 555555665 3334457778888863
No 99
>PF06851 DUF1247: Protein of unknown function (DUF1247); InterPro: IPR009657 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf2; it is a family of uncharacterised viral proteins.
Probab=21.34 E-value=1.4e+02 Score=21.68 Aligned_cols=34 Identities=15% Similarity=0.297 Sum_probs=25.1
Q ss_pred ccccchhHHHHHHHHHHHHhcC-CCHHHHHHHhCCC
Q 046604 78 DYLTIKDTLDYLAETLANRIKN-KSVEYIRKFFGIE 112 (134)
Q Consensus 78 ~yL~I~~Ll~l~~~~iA~~i~g-ks~eeir~~f~i~ 112 (134)
.||..+. ....++.+-..+.| .|..++-..+|-+
T Consensus 100 ~yLs~~~-wk~~a~~~l~dLTgF~s~~~LL~~Yny~ 134 (148)
T PF06851_consen 100 TYLSVDF-WKITAKRVLRDLTGFESLKDLLTHYNYE 134 (148)
T ss_pred HHHcccc-cHHHHHHHHHHhhCcccHHHHHHHcCCC
Confidence 4555544 66777777777777 7899999988876
No 100
>cd02149 NfsB_like_nitroreductase NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family includes FRase I in Vibrio fischeri, wihich reduces FMN into FMNH2 as part of the bioluminescent reaction. The family also includes oxygen-insensitive nitroreductases that use NADH or NADPH as an electron donor in the ping pong bi bi mechanism. This type of nitroreductase can be used in cancer chemotherapy to activate a range of prodrugs.
Probab=21.14 E-value=84 Score=21.96 Aligned_cols=17 Identities=6% Similarity=0.304 Sum_probs=13.8
Q ss_pred cCCCHHHHHHHhCCCCC
Q 046604 98 KNKSVEYIRKFFGIENN 114 (134)
Q Consensus 98 ~gks~eeir~~f~i~~d 114 (134)
.|...+++++.||++++
T Consensus 112 ~~~~~~~v~~~l~l~~~ 128 (157)
T cd02149 112 EGFDPAKLDEILGLDEK 128 (157)
T ss_pred cCcCHHHHHHHhCCCcc
Confidence 35678999999999863
No 101
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=20.87 E-value=64 Score=18.28 Aligned_cols=18 Identities=22% Similarity=0.324 Sum_probs=11.5
Q ss_pred HhcCCCHHHHHHHhCCCC
Q 046604 96 RIKNKSVEYIRKFFGIEN 113 (134)
Q Consensus 96 ~i~gks~eeir~~f~i~~ 113 (134)
.+.|+|.+||-+.+|++.
T Consensus 23 ~~~g~s~~eIa~~l~~s~ 40 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGISE 40 (54)
T ss_dssp HTS---HHHHHHHCTS-H
T ss_pred HHHCcCHHHHHHHHCcCH
Confidence 357999999999999874
No 102
>cd02062 Nitro_FMN_reductase Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are described as NAD(P)H:FMN oxidoreductases, oxygen-insensitive nitroreductase, flavin reductase P, dihydropteridine reductase, NADH oxidase or NADH dehydrogenase.
Probab=20.75 E-value=1.1e+02 Score=19.97 Aligned_cols=36 Identities=25% Similarity=0.409 Sum_probs=23.7
Q ss_pred HHHHHHhhccccchhHHHHHHHHHHHHhcCCC--HHHHHHHhCCCCCC
Q 046604 70 LKEMLLVADYLTIKDTLDYLAETLANRIKNKS--VEYIRKFFGIENNF 115 (134)
Q Consensus 70 l~~Li~AA~yL~I~~Ll~l~~~~iA~~i~gks--~eeir~~f~i~~d~ 115 (134)
...++.+|..+++.. ..+.|-. .+++++.||++++.
T Consensus 75 ~~~l~l~a~~~Glg~----------~~~~~~~~~~~~~~~~l~l~~~~ 112 (122)
T cd02062 75 AQNILLAAHALGLGS----------CWIGGLDLVEEELRELLGIPEGY 112 (122)
T ss_pred HHHHHHHHHHcCCCc----------hhcCCcccchHHHHHHhCcCCCc
Confidence 346666666666544 1334444 89999999999764
No 103
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=20.68 E-value=2.1e+02 Score=18.13 Aligned_cols=27 Identities=15% Similarity=0.160 Sum_probs=15.3
Q ss_pred cCCCHHHHHHHhCC-CCCCCHHHHHHHH
Q 046604 98 KNKSVEYIRKFFGI-ENNFMPEEKEATR 124 (134)
Q Consensus 98 ~gks~eeir~~f~i-~~d~t~eee~~i~ 124 (134)
.|.+++++|+.|.= =.+.+|.|-..++
T Consensus 11 ~G~~~e~vk~~F~~~~~~Vs~~EI~~~E 38 (71)
T PF04282_consen 11 EGEDPEEVKEEFKKLFSDVSASEISAAE 38 (71)
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 57777777776652 2234555544443
No 104
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=20.17 E-value=1.6e+02 Score=17.59 Aligned_cols=19 Identities=16% Similarity=0.233 Sum_probs=16.2
Q ss_pred HHHhcCCCHHHHHHHhCCC
Q 046604 94 ANRIKNKSVEYIRKFFGIE 112 (134)
Q Consensus 94 A~~i~gks~eeir~~f~i~ 112 (134)
.-.++|-++.||-+.+|++
T Consensus 8 ~LY~~G~~~~eIA~~Lg~~ 26 (58)
T PF06056_consen 8 SLYLQGWSIKEIAEELGVP 26 (58)
T ss_pred HHHHcCCCHHHHHHHHCCC
Confidence 3446899999999999998
No 105
>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....
Probab=20.01 E-value=24 Score=17.57 Aligned_cols=16 Identities=25% Similarity=0.139 Sum_probs=12.5
Q ss_pred eEEEeCCCCEEEecHH
Q 046604 4 NIFEDGGQQLFKVEEQ 19 (134)
Q Consensus 4 i~l~S~DG~~f~V~~~ 19 (134)
+++-|.||..|+|+..
T Consensus 5 ~t~FSp~Grl~QVEYA 20 (23)
T PF10584_consen 5 ITTFSPDGRLFQVEYA 20 (23)
T ss_dssp TTSBBTTSSBHHHHHH
T ss_pred ceeECCCCeEEeeEee
Confidence 4566899999998764
Done!