Query 045340
Match_columns 136
No_of_seqs 143 out of 624
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 12:15:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045340.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045340hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1724 SCF ubiquitin ligase, 100.0 1.7E-36 3.8E-41 231.5 9.8 102 1-103 48-162 (162)
2 COG5201 SKP1 SCF ubiquitin lig 100.0 1.1E-35 2.4E-40 220.2 9.5 102 1-103 43-157 (158)
3 PF01466 Skp1: Skp1 family, di 100.0 4.6E-29 1E-33 169.3 7.8 73 30-103 6-78 (78)
4 smart00512 Skp1 Found in Skp1 99.4 4.5E-13 9.8E-18 94.5 5.3 52 1-53 46-104 (104)
5 KOG3473 RNA polymerase II tran 97.1 0.00056 1.2E-08 49.0 3.0 50 2-53 63-112 (112)
6 PF03931 Skp1_POZ: Skp1 family 96.9 0.00052 1.1E-08 44.2 1.5 19 1-19 42-60 (62)
7 PHA02713 hypothetical protein; 96.0 0.032 6.9E-07 49.7 7.7 63 1-78 71-133 (557)
8 smart00225 BTB Broad-Complex, 95.2 0.041 8.9E-07 34.9 4.2 47 2-61 44-90 (90)
9 PHA02790 Kelch-like protein; P 94.8 0.056 1.2E-06 47.1 5.3 54 3-69 68-121 (480)
10 KOG3433 Protein involved in me 94.5 0.056 1.2E-06 42.7 4.2 38 45-87 161-200 (203)
11 PHA03098 kelch-like protein; P 94.2 0.13 2.8E-06 44.8 6.2 55 5-72 55-109 (534)
12 COG5124 Protein predicted to b 93.9 0.059 1.3E-06 42.5 3.2 31 52-87 174-204 (209)
13 KOG4441 Proteins containing BT 93.3 0.16 3.6E-06 45.6 5.4 54 2-69 81-135 (571)
14 PF00651 BTB: BTB/POZ domain; 92.8 0.15 3.2E-06 34.5 3.4 29 38-66 81-109 (111)
15 PF03962 Mnd1: Mnd1 family; I 84.5 1.2 2.7E-05 34.7 3.5 41 42-87 145-187 (188)
16 KOG2716 Polymerase delta-inter 81.5 6.2 0.00014 32.0 6.5 35 37-71 74-108 (230)
17 PF03656 Pam16: Pam16; InterP 73.5 2.7 5.9E-05 31.1 2.1 36 66-104 50-85 (127)
18 PF13921 Myb_DNA-bind_6: Myb-l 66.4 10 0.00022 23.3 3.4 35 60-94 19-60 (60)
19 KOG4682 Uncharacterized conser 60.9 12 0.00025 33.3 3.8 47 37-86 139-185 (488)
20 PF00249 Myb_DNA-binding: Myb- 60.5 33 0.00071 20.2 4.8 36 40-80 8-44 (48)
21 cd00167 SANT 'SWI3, ADA2, N-Co 57.7 12 0.00025 20.7 2.3 21 61-81 22-42 (45)
22 smart00717 SANT SANT SWI3, AD 56.4 13 0.00027 20.8 2.4 21 61-81 24-44 (49)
23 PRK05365 malonic semialdehyde 56.0 9 0.00019 29.1 2.1 34 44-87 131-164 (195)
24 cd02148 Nitroreductase_5 Nitro 54.2 9.8 0.00021 28.6 2.0 34 44-87 124-157 (185)
25 KOG3442 Uncharacterized conser 53.3 14 0.0003 27.6 2.6 26 67-92 52-77 (132)
26 PF09713 A_thal_3526: Plant pr 50.8 28 0.00061 22.1 3.4 37 70-106 12-52 (54)
27 TIGR03147 cyt_nit_nrfF cytochr 50.8 15 0.00032 27.3 2.4 21 61-81 63-84 (126)
28 PRK11053 dihydropteridine redu 50.6 14 0.0003 28.5 2.4 35 42-86 148-183 (217)
29 PF08006 DUF1700: Protein of u 49.8 51 0.0011 24.8 5.4 41 47-92 16-57 (181)
30 PF12556 CobS_N: Cobaltochelat 49.3 10 0.00022 22.3 1.1 12 76-87 14-25 (36)
31 TIGR01999 iscU FeS cluster ass 47.7 21 0.00046 25.6 2.9 38 44-81 50-88 (124)
32 TIGR03419 NifU_clost FeS clust 46.8 24 0.00053 25.3 3.0 38 44-81 46-84 (121)
33 PRK11325 scaffold protein; Pro 46.5 22 0.00048 25.7 2.8 38 44-81 52-90 (127)
34 PF11978 MVP_shoulder: Shoulde 45.2 16 0.00034 26.9 1.8 28 44-71 36-63 (118)
35 PF13798 PCYCGC: Protein of un 44.9 31 0.00067 26.6 3.4 25 56-80 117-141 (158)
36 PF03918 CcmH: Cytochrome C bi 44.7 18 0.0004 27.2 2.2 19 62-80 64-83 (148)
37 cd08330 CARD_ASC_NALP1 Caspase 43.8 21 0.00045 24.1 2.1 62 72-135 16-81 (82)
38 COG1710 Uncharacterized protei 43.2 24 0.00052 26.3 2.5 21 63-83 101-122 (139)
39 PF01592 NifU_N: NifU-like N t 42.7 32 0.0007 24.6 3.2 22 58-79 65-86 (126)
40 PRK10144 formate-dependent nit 41.6 25 0.00054 26.1 2.4 20 62-81 64-84 (126)
41 COG4957 Predicted transcriptio 40.0 25 0.00054 26.7 2.2 18 70-87 98-115 (148)
42 cd02140 Nitroreductase_4 Nitro 37.2 24 0.00053 26.6 1.9 38 42-87 128-165 (192)
43 COG0822 IscU NifU homolog invo 36.8 55 0.0012 24.6 3.7 37 44-80 53-90 (150)
44 cd06664 IscU_like Iron-sulfur 36.6 58 0.0013 22.9 3.7 39 43-81 46-85 (123)
45 PF03750 DUF310: Protein of un 35.5 54 0.0012 23.5 3.3 34 51-85 8-43 (119)
46 TIGR02476 BluB cob(II)yrinic a 35.2 33 0.00072 26.2 2.4 38 41-88 134-171 (205)
47 cd02144 iodotyrosine_dehalogen 35.2 34 0.00074 25.3 2.4 36 43-88 131-167 (193)
48 PF13518 HTH_28: Helix-turn-he 34.3 64 0.0014 18.6 3.1 21 63-83 5-25 (52)
49 PF04355 SmpA_OmlA: SmpA / Oml 33.6 24 0.00053 22.4 1.2 21 64-84 9-29 (71)
50 PF14098 SSPI: Small, acid-sol 33.1 47 0.001 21.9 2.5 20 62-81 5-24 (65)
51 PF11460 DUF3007: Protein of u 32.6 40 0.00087 24.2 2.2 23 72-97 79-101 (104)
52 PF05443 ROS_MUCR: ROS/MUCR tr 32.3 22 0.00047 26.5 0.8 18 70-87 94-111 (132)
53 cd03370 NADH_oxidase NADPH_oxi 32.0 35 0.00075 24.8 1.9 20 67-86 111-131 (156)
54 PF13384 HTH_23: Homeodomain-l 31.8 49 0.0011 19.3 2.2 15 69-83 16-30 (50)
55 PF04255 DUF433: Protein of un 31.4 97 0.0021 19.1 3.7 27 63-92 23-50 (56)
56 TIGR01994 SUF_scaf_2 SUF syste 31.3 79 0.0017 23.1 3.7 37 45-81 51-88 (137)
57 TIGR02698 CopY_TcrY copper tra 30.7 1.8E+02 0.0039 20.9 5.5 56 56-111 72-128 (130)
58 KOG4244 Failed axon connection 30.0 52 0.0011 27.6 2.8 23 74-96 112-134 (281)
59 PF11103 DUF2887: Protein of u 29.6 76 0.0016 25.2 3.6 29 52-80 172-200 (200)
60 PF15063 TC1: Thyroid cancer p 29.5 55 0.0012 22.4 2.3 34 62-95 28-61 (79)
61 PF00196 GerE: Bacterial regul 28.8 70 0.0015 19.4 2.7 23 61-83 9-31 (58)
62 PF08671 SinI: Anti-repressor 28.7 43 0.00093 18.7 1.5 13 69-81 15-27 (30)
63 PF09382 RQC: RQC domain; Int 28.3 84 0.0018 21.2 3.3 37 58-94 19-62 (106)
64 PF03883 DUF328: Protein of un 28.2 52 0.0011 26.4 2.5 33 57-89 27-59 (237)
65 PF11399 DUF3192: Protein of u 27.7 63 0.0014 23.1 2.5 27 61-88 25-51 (102)
66 TIGR01044 rplV_bact ribosomal 27.6 67 0.0015 22.5 2.7 22 61-82 13-34 (103)
67 KOG4079 Putative mitochondrial 27.4 1.1E+02 0.0025 23.3 4.0 74 37-130 84-157 (169)
68 PF07671 DUF1601: Protein of u 27.3 68 0.0015 18.8 2.2 30 50-79 7-36 (37)
69 PLN03212 Transcription repress 27.2 80 0.0017 26.0 3.4 43 61-103 48-103 (249)
70 PF10892 DUF2688: Protein of u 27.2 68 0.0015 20.8 2.4 24 73-96 30-55 (60)
71 smart00421 HTH_LUXR helix_turn 26.6 96 0.0021 17.5 2.9 17 67-83 15-31 (58)
72 cd05029 S-100A6 S-100A6: S-100 26.1 1.6E+02 0.0034 19.8 4.2 45 53-97 9-59 (88)
73 TIGR03553 F420_FbiB_CTERM F420 25.9 26 0.00057 26.2 0.4 18 71-88 149-166 (194)
74 smart00385 CYCLIN domain prese 25.9 1.6E+02 0.0034 17.7 4.8 39 52-93 36-76 (83)
75 PF11822 DUF3342: Domain of un 25.4 24 0.00051 30.1 0.0 33 36-68 72-104 (317)
76 cd02138 Nitroreductase_2 Nitro 24.5 70 0.0015 23.8 2.5 38 41-88 108-145 (181)
77 cd02145 BluB Subfamily of the 24.1 53 0.0012 24.7 1.8 20 68-87 142-161 (196)
78 PF02796 HTH_7: Helix-turn-hel 24.0 1E+02 0.0022 18.0 2.7 16 68-83 19-34 (45)
79 PF14748 P5CR_dimer: Pyrroline 23.8 1.8E+02 0.0039 20.2 4.3 55 43-97 26-87 (107)
80 PF05397 Med15_fungi: Mediator 23.8 78 0.0017 22.7 2.5 19 81-99 24-42 (115)
81 PRK11548 outer membrane biogen 23.3 88 0.0019 22.1 2.7 23 62-84 41-63 (113)
82 TIGR02000 NifU_proper Fe-S clu 23.1 90 0.002 25.9 3.0 37 45-81 52-89 (290)
83 cd08329 CARD_BIRC2_BIRC3 Caspa 23.0 1.6E+02 0.0034 20.3 3.8 50 84-135 36-89 (94)
84 smart00497 IENR1 Intron encode 22.7 80 0.0017 18.4 2.1 26 41-72 17-42 (53)
85 KOG0027 Calmodulin and related 22.6 3E+02 0.0065 19.7 7.3 89 6-95 7-111 (151)
86 PF13010 pRN1_helical: Primase 22.4 45 0.00097 24.9 1.0 14 66-79 24-37 (135)
87 PF08281 Sigma70_r4_2: Sigma-7 22.1 60 0.0013 19.2 1.4 17 67-83 23-39 (54)
88 cd02062 Nitro_FMN_reductase Pr 21.4 1E+02 0.0023 20.6 2.7 37 41-87 75-113 (122)
89 PRK03094 hypothetical protein; 21.3 60 0.0013 22.2 1.4 14 67-80 62-75 (80)
90 PF13700 DUF4158: Domain of un 21.1 1.1E+02 0.0024 22.6 3.0 33 72-105 3-39 (166)
91 PF01726 LexA_DNA_bind: LexA D 21.0 1.9E+02 0.0042 18.4 3.7 33 55-87 10-42 (65)
92 KOG0743 AAA+-type ATPase [Post 20.8 81 0.0018 28.2 2.4 40 45-85 377-418 (457)
93 cd00336 Ribosomal_L22 Ribosoma 20.5 98 0.0021 21.4 2.4 21 62-82 16-36 (105)
94 PF15628 RRM_DME: RRM in Demet 20.3 85 0.0019 22.5 2.0 20 62-81 57-76 (103)
95 COG2219 PRI2 Eukaryotic-type D 20.3 2.1E+02 0.0045 24.6 4.8 61 60-120 262-327 (363)
96 KOG0783 Uncharacterized conser 20.1 3.6E+02 0.0079 26.7 6.6 66 4-77 758-824 (1267)
97 TIGR01038 L22_arch ribosomal p 20.1 1.1E+02 0.0023 23.2 2.7 21 61-81 26-46 (150)
98 PRK10828 putative oxidoreducta 20.1 59 0.0013 24.4 1.3 36 42-87 116-153 (183)
No 1
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.7e-36 Score=231.54 Aligned_cols=102 Identities=37% Similarity=0.505 Sum_probs=92.4
Q ss_pred CCCCcHHHHHHHHHhhc-CCCCCCCC--------chHH----HhhccCCChhHHHHHHHhhhhhchHHHHHHHHHHHHHH
Q 045340 1 MDNNYSRWKSKGVRDCD-HSSTSDGT--------SEDM----VEFGKGKSNDELKEMLLVANYLNITEMLDYLTETLANR 67 (136)
Q Consensus 1 i~nV~s~~L~kViewC~-H~~~~~~~--------~~~l----~~Fl~~ld~~~L~~Li~AAnyL~I~~Ll~l~c~~IA~~ 67 (136)
|+||+|.||+|||+||+ |+++++.. ..++ ++|++ +|.++||+|+.|||||+|++|+++||++||+|
T Consensus 48 l~nV~~~iL~kVIewC~~Hk~d~~~~~~~~~~~~~~~i~~WD~~Flk-~d~~tLfdli~AAnyLdi~gLl~~~ck~va~m 126 (162)
T KOG1724|consen 48 LPNVTSKILKKVIEWCKKHKDDDPANPEDKELPEETDIPEWDAEFLK-VDQGTLFDLILAANYLDIKGLLDLTCKTVANM 126 (162)
T ss_pred cCccCHHHHHHHHHHHHHcccccccccccccccccCCccHHHHHHHh-cCHHHHHHHHHHhhhcccHHHHHHHHHHHHHH
Confidence 68999999999999999 99874311 1113 99999 49999999999999999999999999999999
Q ss_pred hcCCCHHHHHHHcCCCCCCCHHHHHHHhhhhchhhh
Q 045340 68 IKNKSVEYIRKFFRIENNFMPEEEEAARNDSTKISC 103 (136)
Q Consensus 68 ikgKt~eEIR~~fgI~~D~T~EEee~ir~en~w~~~ 103 (136)
+|||||+|||+.|||++|+||||++++|++|.|+++
T Consensus 127 ikgktpeEir~~f~I~~d~t~eE~~~~~~e~~~~~~ 162 (162)
T KOG1724|consen 127 IKGKTPEEIREIFNIENDETPEEEEAIRKENEWAFE 162 (162)
T ss_pred HccCCHHHHHHHcCCCCCCChhHHHHHhhccccccC
Confidence 999999999999999999999999999999999874
No 2
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-35 Score=220.17 Aligned_cols=102 Identities=33% Similarity=0.370 Sum_probs=91.0
Q ss_pred CCCCcHHHHHHHHHhhc-CCCCCCCCchH----------H--HhhccCCChhHHHHHHHhhhhhchHHHHHHHHHHHHHH
Q 045340 1 MDNNYSRWKSKGVRDCD-HSSTSDGTSED----------M--VEFGKGKSNDELKEMLLVANYLNITEMLDYLTETLANR 67 (136)
Q Consensus 1 i~nV~s~~L~kViewC~-H~~~~~~~~~~----------l--~~Fl~~ld~~~L~~Li~AAnyL~I~~Ll~l~c~~IA~~ 67 (136)
+|||.|.+|.||++||+ |++....++.+ . +.|+++ |+++|++++.|||||+|++|+++||+.||+|
T Consensus 43 ~pnVrSsvl~kv~ew~ehh~~s~sede~d~~~rks~p~D~wdr~Fm~v-DqemL~eI~laaNYL~ikpLLd~gCKivaem 121 (158)
T COG5201 43 APNVRSSVLMKVQEWMEHHTSSLSEDENDLEIRKSKPSDFWDRFFMEV-DQEMLLEICLAANYLEIKPLLDLGCKIVAEM 121 (158)
T ss_pred ccchhHHHHHHHHHHHHhccccCCCccChHhhhccCCccHHHHHHHHh-hHHHHHHHHHhhccccchHHHHHHHHHHHHH
Confidence 47999999999999999 76643222211 2 567787 9999999999999999999999999999999
Q ss_pred hcCCCHHHHHHHcCCCCCCCHHHHHHHhhhhchhhh
Q 045340 68 IKNKSVEYIRKFFRIENNFMPEEEEAARNDSTKISC 103 (136)
Q Consensus 68 ikgKt~eEIR~~fgI~~D~T~EEee~ir~en~w~~~ 103 (136)
|+||||+|||++|||+|||||||+++||+||.|+++
T Consensus 122 irgkSpeeir~tfni~ndfTpEEe~~irkEnEWaed 157 (158)
T COG5201 122 IRGKSPEEIRETFNIENDFTPEEERRIRKENEWAED 157 (158)
T ss_pred HccCCHHHHHHHhCCCCCCCHHHHHHHHHhcccccc
Confidence 999999999999999999999999999999999986
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=4.6e-29 Score=169.35 Aligned_cols=73 Identities=47% Similarity=0.601 Sum_probs=63.4
Q ss_pred HhhccCCChhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHhhhhchhhh
Q 045340 30 VEFGKGKSNDELKEMLLVANYLNITEMLDYLTETLANRIKNKSVEYIRKFFRIENNFMPEEEEAARNDSTKISC 103 (136)
Q Consensus 30 ~~Fl~~ld~~~L~~Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~D~T~EEee~ir~en~w~~~ 103 (136)
++|++. +.+.|++|+.||+||+|++|++++|++||++|+||||+|||++|||++|+|+||++++|++|+|+++
T Consensus 6 ~~F~~~-~~~~L~~l~~AA~yL~I~~L~~~~~~~iA~~i~gks~eeir~~fgi~~d~t~eee~~i~~e~~w~~~ 78 (78)
T PF01466_consen 6 QEFLDV-DNDELFDLLNAANYLDIKGLLDLCCKYIANMIKGKSPEEIRKYFGIENDLTPEEEEEIRKENEWAFE 78 (78)
T ss_dssp HHHT-S--HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHTTS-HHHHHHHHT---TSSHHHHHHHHHHCCCTB-
T ss_pred HHHHHc-CHHHHHHHHHHHHHHcchHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHHHHcchhcC
Confidence 689976 9999999999999999999999999999999999999999999999999999999999999999975
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=99.39 E-value=4.5e-13 Score=94.49 Aligned_cols=52 Identities=33% Similarity=0.463 Sum_probs=43.5
Q ss_pred CCCCcHHHHHHHHHhhc-CCCCCCCCc-----hHH-HhhccCCChhHHHHHHHhhhhhch
Q 045340 1 MDNNYSRWKSKGVRDCD-HSSTSDGTS-----EDM-VEFGKGKSNDELKEMLLVANYLNI 53 (136)
Q Consensus 1 i~nV~s~~L~kViewC~-H~~~~~~~~-----~~l-~~Fl~~ld~~~L~~Li~AAnyL~I 53 (136)
+++|+|.+|++|++||+ |+.++.... .++ .+|++. ++++|++|++|||||+|
T Consensus 46 l~~v~~~~L~~Vi~yc~~h~~~~~~~~~~~~~~~wD~~F~~~-d~~~l~dLl~AAnyL~I 104 (104)
T smart00512 46 LPNVTSKILSKVIEYCEHHVDDPPSVADKDDIPTWDAEFLKI-DQETLFELILAANYLDI 104 (104)
T ss_pred CCCcCHHHHHHHHHHHHHcccCCCCccccccccHHHHHHHcC-CHHHHHHHHHHHHhhCC
Confidence 58999999999999999 887653221 223 899995 99999999999999997
No 5
>KOG3473 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin C [Transcription]
Probab=97.05 E-value=0.00056 Score=49.04 Aligned_cols=50 Identities=22% Similarity=0.186 Sum_probs=35.9
Q ss_pred CCCcHHHHHHHHHhhcCCCCCCCCchHHHhhccCCChhHHHHHHHhhhhhch
Q 045340 2 DNNYSRWKSKGVRDCDHSSTSDGTSEDMVEFGKGKSNDELKEMLLVANYLNI 53 (136)
Q Consensus 2 ~nV~s~~L~kViewC~H~~~~~~~~~~l~~Fl~~ld~~~L~~Li~AAnyL~I 53 (136)
++++|.+|+||.+|..++-.=.....++-+| +. ..++.++|++|||||++
T Consensus 63 ~di~shiLeKvc~Yl~Yk~rY~~~s~eiPeF-~I-ppemaleLL~aAn~Lec 112 (112)
T KOG3473|consen 63 RDIPSHILEKVCEYLAYKVRYTNSSTEIPEF-DI-PPEMALELLMAANYLEC 112 (112)
T ss_pred ccchHHHHHHHHHHhhheeeeccccccCCCC-CC-CHHHHHHHHHHhhhhcC
Confidence 5789999999999998221101111234567 44 89999999999999974
No 6
>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=96.88 E-value=0.00052 Score=44.22 Aligned_cols=19 Identities=32% Similarity=0.407 Sum_probs=16.1
Q ss_pred CCCCcHHHHHHHHHhhcCC
Q 045340 1 MDNNYSRWKSKGVRDCDHS 19 (136)
Q Consensus 1 i~nV~s~~L~kViewC~H~ 19 (136)
+++|+|++|+||++||+|.
T Consensus 42 l~~v~~~~L~kViewc~~H 60 (62)
T PF03931_consen 42 LPNVSSRILKKVIEWCEHH 60 (62)
T ss_dssp ETTS-HHHHHHHHHHHHHH
T ss_pred cCccCHHHHHHHHHHHHhc
Confidence 5799999999999999864
No 7
>PHA02713 hypothetical protein; Provisional
Probab=95.96 E-value=0.032 Score=49.74 Aligned_cols=63 Identities=13% Similarity=0.114 Sum_probs=48.7
Q ss_pred CCCCcHHHHHHHHHhhcCCCCCCCCchHHHhhccCCChhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHH
Q 045340 1 MDNNYSRWKSKGVRDCDHSSTSDGTSEDMVEFGKGKSNDELKEMLLVANYLNITEMLDYLTETLANRIKNKSVEYIRK 78 (136)
Q Consensus 1 i~nV~s~~L~kViewC~H~~~~~~~~~~l~~Fl~~ld~~~L~~Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt~eEIR~ 78 (136)
|.+|+..+|+.|++|+.... ++.+.+.+|+.||++|+|+.|.+.||+.+.+.+.-.+-=+|+.
T Consensus 71 l~~v~~~~~~~ll~y~Yt~~---------------i~~~nv~~ll~aA~~lqi~~l~~~C~~~l~~~l~~~NCl~i~~ 133 (557)
T PHA02713 71 LQMFDKDAVKNIVQYLYNRH---------------ISSMNVIDVLKCADYLLIDDLVTDCESYIKDYTNHDTCIYMYH 133 (557)
T ss_pred eccCCHHHHHHHHHHhcCCC---------------CCHHHHHHHHHHHHHHCHHHHHHHHHHHHHhhCCccchHHHHH
Confidence 35678888888888877311 2455688999999999999999999999988877666666654
No 8
>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=95.16 E-value=0.041 Score=34.87 Aligned_cols=47 Identities=15% Similarity=0.174 Sum_probs=32.5
Q ss_pred CCCcHHHHHHHHHhhcCCCCCCCCchHHHhhccCCChhHHHHHHHhhhhhchHHHHHHHH
Q 045340 2 DNNYSRWKSKGVRDCDHSSTSDGTSEDMVEFGKGKSNDELKEMLLVANYLNITEMLDYLT 61 (136)
Q Consensus 2 ~nV~s~~L~kViewC~H~~~~~~~~~~l~~Fl~~ld~~~L~~Li~AAnyL~I~~Ll~l~c 61 (136)
++++..+++.+++|+.+..- . ++...+.+++.+|+++++++|.+.|+
T Consensus 44 ~~~~~~~f~~~l~~ly~~~~------------~-~~~~~~~~l~~~a~~~~~~~l~~~c~ 90 (90)
T smart00225 44 DDVSPEDFRALLEFLYTGKL------------D-LPEENVEELLELADYLQIPGLVELCE 90 (90)
T ss_pred cCCCHHHHHHHHHeecCcee------------e-cCHHHHHHHHHHHHHHCcHHHHhhhC
Confidence 45666666666666663211 1 13447889999999999999998763
No 9
>PHA02790 Kelch-like protein; Provisional
Probab=94.81 E-value=0.056 Score=47.11 Aligned_cols=54 Identities=4% Similarity=-0.102 Sum_probs=33.0
Q ss_pred CCcHHHHHHHHHhhcCCCCCCCCchHHHhhccCCChhHHHHHHHhhhhhchHHHHHHHHHHHHHHhc
Q 045340 3 NNYSRWKSKGVRDCDHSSTSDGTSEDMVEFGKGKSNDELKEMLLVANYLNITEMLDYLTETLANRIK 69 (136)
Q Consensus 3 nV~s~~L~kViewC~H~~~~~~~~~~l~~Fl~~ld~~~L~~Li~AAnyL~I~~Ll~l~c~~IA~~ik 69 (136)
+|+..+|+.|++|..-.. +. ++.+.+.+|+.||++|+|+.+.+.||+.+...|.
T Consensus 68 ~v~~~~l~~lldy~YTg~------------l~-it~~nV~~ll~aA~~Lqi~~v~~~C~~fL~~~l~ 121 (480)
T PHA02790 68 DLDIHSLTSIVIYSYTGK------------VY-IDSHNVVNLLRASILTSVEFIIYTCINFILRDFR 121 (480)
T ss_pred CcCHHHHHHHHHhheeee------------EE-EecccHHHHHHHHHHhChHHHHHHHHHHHHhhCC
Confidence 577777888887765111 11 1444566677777777777777777666655433
No 10
>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=94.55 E-value=0.056 Score=42.68 Aligned_cols=38 Identities=34% Similarity=0.404 Sum_probs=31.3
Q ss_pred HHhhhhh--chHHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCC
Q 045340 45 LLVANYL--NITEMLDYLTETLANRIKNKSVEYIRKFFRIENNFM 87 (136)
Q Consensus 45 i~AAnyL--~I~~Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~D~T 87 (136)
+.|||.- ||--|.+++|+.. |.-+.+||+.||||.||.
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 3455533 8889999999876 999999999999999984
No 11
>PHA03098 kelch-like protein; Provisional
Probab=94.20 E-value=0.13 Score=44.78 Aligned_cols=55 Identities=15% Similarity=0.185 Sum_probs=34.4
Q ss_pred cHHHHHHHHHhhcCCCCCCCCchHHHhhccCCChhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCC
Q 045340 5 YSRWKSKGVRDCDHSSTSDGTSEDMVEFGKGKSNDELKEMLLVANYLNITEMLDYLTETLANRIKNKS 72 (136)
Q Consensus 5 ~s~~L~kViewC~H~~~~~~~~~~l~~Fl~~ld~~~L~~Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt 72 (136)
+.++++.|++|..... +. ++.+.+.+|+.||++|+++.|.+.|++.+...+.-.+
T Consensus 55 ~~~~~~~~l~y~Ytg~------------~~-i~~~~~~~ll~~A~~l~~~~l~~~C~~~l~~~l~~~n 109 (534)
T PHA03098 55 DYDSFNEVIKYIYTGK------------IN-ITSNNVKDILSIANYLIIDFLINLCINYIIKIIDDNN 109 (534)
T ss_pred CHHHHHHHHHHhcCCc------------eE-EcHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhCCHhH
Confidence 5566666666655211 11 2455577777777777777777777777766654433
No 12
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=93.94 E-value=0.059 Score=42.48 Aligned_cols=31 Identities=35% Similarity=0.479 Sum_probs=27.6
Q ss_pred chHHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCC
Q 045340 52 NITEMLDYLTETLANRIKNKSVEYIRKFFRIENNFM 87 (136)
Q Consensus 52 ~I~~Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~D~T 87 (136)
+|.-|.++.|+.. |.-|+|||+.||||.|+.
T Consensus 174 nI~ilidy~c~kf-----~~~~~qir~~fgIPedld 204 (209)
T COG5124 174 NIEILIDYLCKKF-----FLKPEQIRKEFGIPEDLD 204 (209)
T ss_pred hHHHHHHHHHHHc-----CCCHHHHHHhcCCCcchh
Confidence 6888999999876 899999999999999874
No 13
>KOG4441 consensus Proteins containing BTB/POZ and Kelch domains, involved in regulatory/signal transduction processes [Signal transduction mechanisms; General function prediction only]
Probab=93.33 E-value=0.16 Score=45.61 Aligned_cols=54 Identities=20% Similarity=0.170 Sum_probs=39.2
Q ss_pred CCCcHHHHHHHHHhhc-CCCCCCCCchHHHhhccCCChhHHHHHHHhhhhhchHHHHHHHHHHHHHHhc
Q 045340 2 DNNYSRWKSKGVRDCD-HSSTSDGTSEDMVEFGKGKSNDELKEMLLVANYLNITEMLDYLTETLANRIK 69 (136)
Q Consensus 2 ~nV~s~~L~kViewC~-H~~~~~~~~~~l~~Fl~~ld~~~L~~Li~AAnyL~I~~Ll~l~c~~IA~~ik 69 (136)
.+|++.+|+.+++|+. .. +. ++.+..-+|+.||++|+|+++.+.||..+...+-
T Consensus 81 ~~v~~~~l~~ll~y~Yt~~-------------i~-i~~~nVq~ll~aA~~lQi~~v~~~C~~fL~~~l~ 135 (571)
T KOG4441|consen 81 EGVDPETLELLLDYAYTGK-------------LE-ISEDNVQELLEAASLLQIPEVVDACCEFLESQLD 135 (571)
T ss_pred ecCCHHHHHHHHHHhhcce-------------EE-echHhHHHHHHHHHHhhhHHHHHHHHHHHHhcCC
Confidence 4567777777777765 32 12 3667788889999999999999999988776543
No 14
>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=92.77 E-value=0.15 Score=34.51 Aligned_cols=29 Identities=24% Similarity=0.394 Sum_probs=26.1
Q ss_pred hhHHHHHHHhhhhhchHHHHHHHHHHHHH
Q 045340 38 NDELKEMLLVANYLNITEMLDYLTETLAN 66 (136)
Q Consensus 38 ~~~L~~Li~AAnyL~I~~Ll~l~c~~IA~ 66 (136)
.+.+.+++.+|++|+++.|.+.|++.+..
T Consensus 81 ~~~~~~ll~lA~~~~~~~L~~~~~~~l~~ 109 (111)
T PF00651_consen 81 DENVEELLELADKLQIPELKKACEKFLQE 109 (111)
T ss_dssp TTTHHHHHHHHHHTTBHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCcHHHHHHHHHHHHh
Confidence 66799999999999999999999998754
No 15
>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=84.47 E-value=1.2 Score=34.67 Aligned_cols=41 Identities=34% Similarity=0.315 Sum_probs=31.8
Q ss_pred HHHHHhhhhh--chHHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCC
Q 045340 42 KEMLLVANYL--NITEMLDYLTETLANRIKNKSVEYIRKFFRIENNFM 87 (136)
Q Consensus 42 ~~Li~AAnyL--~I~~Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~D~T 87 (136)
.....|||.- ||-.|..++++. -|.+.+++|+.||||+||.
T Consensus 145 ~~~~~~anrwTDNI~~l~~~~~~k-----~~~~~~~i~k~f~Ip~d~d 187 (188)
T PF03962_consen 145 KIAKEAANRWTDNIFSLKSYLKKK-----FGMDEEDIRKEFGIPEDFD 187 (188)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHh-----cCCCHHHHHHHcCCccccC
Confidence 3344477665 688888888775 3999999999999999984
No 16
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=81.46 E-value=6.2 Score=32.02 Aligned_cols=35 Identities=26% Similarity=0.411 Sum_probs=32.2
Q ss_pred ChhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCC
Q 045340 37 SNDELKEMLLVANYLNITEMLDYLTETLANRIKNK 71 (136)
Q Consensus 37 d~~~L~~Li~AAnyL~I~~Ll~l~c~~IA~~ikgK 71 (136)
+..+|-+|+.=|.|-.+.+|+++|..+++..+++.
T Consensus 74 ~~kel~El~~EA~fYlL~~Lv~~C~~~i~~~~~~~ 108 (230)
T KOG2716|consen 74 SEKELKELLREAEFYLLDGLVELCQSAIARLIRGY 108 (230)
T ss_pred chHHHHHHHHHHHHhhHHHHHHHHHHHhhhcccCc
Confidence 45689999999999999999999999999998875
No 17
>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=73.47 E-value=2.7 Score=31.11 Aligned_cols=36 Identities=11% Similarity=0.215 Sum_probs=17.9
Q ss_pred HHhcCCCHHHHHHHcCCCCCCCHHHHHHHhhhhchhhhc
Q 045340 66 NRIKNKSVEYIRKFFRIENNFMPEEEEAARNDSTKISCI 104 (136)
Q Consensus 66 ~~ikgKt~eEIR~~fgI~~D~T~EEee~ir~en~w~~~~ 104 (136)
...+|+|.+|-++++|+++..++|| |.+.+.-+++.
T Consensus 50 ~~~~~Mtl~EA~~ILnv~~~~~~ee---I~k~y~~Lf~~ 85 (127)
T PF03656_consen 50 SNSKGMTLDEARQILNVKEELSREE---IQKRYKHLFKA 85 (127)
T ss_dssp -------HHHHHHHHT--G--SHHH---HHHHHHHHHHH
T ss_pred hhcCCCCHHHHHHHcCCCCccCHHH---HHHHHHHHHhc
Confidence 3456999999999999999888765 44554444444
No 18
>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=66.41 E-value=10 Score=23.32 Aligned_cols=35 Identities=17% Similarity=0.254 Sum_probs=23.3
Q ss_pred HHHHHHHHhcCCCHHHHHHHcCC------C-CCCCHHHHHHH
Q 045340 60 LTETLANRIKNKSVEYIRKFFRI------E-NNFMPEEEEAA 94 (136)
Q Consensus 60 ~c~~IA~~ikgKt~eEIR~~fgI------~-~D~T~EEee~i 94 (136)
--..||..+..+|+.+++..|.- . ..+|+||.+.+
T Consensus 19 ~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 19 DWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp -HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 35788999944999999987653 1 24777776643
No 19
>KOG4682 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=60.88 E-value=12 Score=33.30 Aligned_cols=47 Identities=11% Similarity=0.229 Sum_probs=36.5
Q ss_pred ChhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCC
Q 045340 37 SNDELKEMLLVANYLNITEMLDYLTETLANRIKNKSVEYIRKFFRIENNF 86 (136)
Q Consensus 37 d~~~L~~Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~D~ 86 (136)
+.+.+..++.||.+|..+||++-|...+-..| +|+-+.+++....-+
T Consensus 139 ~l~dv~gvlAaA~~lqldgl~qrC~evMie~l---spkta~~yYea~ckY 185 (488)
T KOG4682|consen 139 KLSDVVGVLAAACLLQLDGLIQRCGEVMIETL---SPKTACGYYEAACKY 185 (488)
T ss_pred cHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhc---ChhhhhHhhhhhhhh
Confidence 77899999999999999999998887665444 555566676655544
No 20
>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=60.51 E-value=33 Score=20.20 Aligned_cols=36 Identities=14% Similarity=0.191 Sum_probs=25.2
Q ss_pred HHHHHHHhhhhhchHHHHHHHHHHHHHHhc-CCCHHHHHHHc
Q 045340 40 ELKEMLLVANYLNITEMLDYLTETLANRIK-NKSVEYIRKFF 80 (136)
Q Consensus 40 ~L~~Li~AAnyL~I~~Ll~l~c~~IA~~ik-gKt~eEIR~~f 80 (136)
+---|+.|..-++-. --+.||..+. |+|+.++|..|
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 5688999999 99999999876
No 21
>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=57.69 E-value=12 Score=20.70 Aligned_cols=21 Identities=19% Similarity=0.335 Sum_probs=17.7
Q ss_pred HHHHHHHhcCCCHHHHHHHcC
Q 045340 61 TETLANRIKNKSVEYIRKFFR 81 (136)
Q Consensus 61 c~~IA~~ikgKt~eEIR~~fg 81 (136)
-..||..+.++|+.+++..+.
T Consensus 22 w~~Ia~~~~~rs~~~~~~~~~ 42 (45)
T cd00167 22 WEKIAKELPGRTPKQCRERWR 42 (45)
T ss_pred HHHHHhHcCCCCHHHHHHHHH
Confidence 477888998999999998764
No 22
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=56.44 E-value=13 Score=20.83 Aligned_cols=21 Identities=19% Similarity=0.333 Sum_probs=17.6
Q ss_pred HHHHHHHhcCCCHHHHHHHcC
Q 045340 61 TETLANRIKNKSVEYIRKFFR 81 (136)
Q Consensus 61 c~~IA~~ikgKt~eEIR~~fg 81 (136)
-..||..+.++|+.+++..+.
T Consensus 24 w~~Ia~~~~~rt~~~~~~~~~ 44 (49)
T smart00717 24 WEKIAKELPGRTAEQCRERWN 44 (49)
T ss_pred HHHHHHHcCCCCHHHHHHHHH
Confidence 467888888999999998764
No 23
>PRK05365 malonic semialdehyde reductase; Provisional
Probab=56.05 E-value=9 Score=29.12 Aligned_cols=34 Identities=12% Similarity=0.149 Sum_probs=26.2
Q ss_pred HHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCC
Q 045340 44 MLLVANYLNITEMLDYLTETLANRIKNKSVEYIRKFFRIENNFM 87 (136)
Q Consensus 44 Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~D~T 87 (136)
|+.||..||+... .+.|-..+.+++.|||+.++.
T Consensus 131 l~LaA~~~Glgs~----------~~~g~~~~~v~~~l~ip~~~~ 164 (195)
T PRK05365 131 LILAARALGLDAG----------PMSGFDAAAVDAEFFAGTTWK 164 (195)
T ss_pred HHHHHHHcCCccC----------CccccCHHHHHHHhCCCCCee
Confidence 7778888877662 445778899999999987654
No 24
>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=54.22 E-value=9.8 Score=28.61 Aligned_cols=34 Identities=12% Similarity=0.205 Sum_probs=25.7
Q ss_pred HHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCC
Q 045340 44 MLLVANYLNITEMLDYLTETLANRIKNKSVEYIRKFFRIENNFM 87 (136)
Q Consensus 44 Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~D~T 87 (136)
|+.||.-||+.. ..|.|-..+++++.||+++++.
T Consensus 124 l~LaA~~lGlgs----------~~~~g~d~~~~~~~L~lp~~~~ 157 (185)
T cd02148 124 FILAARALGLDA----------GPMSGFDAAAVDAEFFADTRWR 157 (185)
T ss_pred HHHHHHHcCCCc----------CCCcccCHHHHHHHhCCCCCeE
Confidence 777777777665 2455778899999999997764
No 25
>KOG3442 consensus Uncharacterized conserved protein [Function unknown]
Probab=53.31 E-value=14 Score=27.60 Aligned_cols=26 Identities=12% Similarity=0.178 Sum_probs=21.0
Q ss_pred HhcCCCHHHHHHHcCCCCCCCHHHHH
Q 045340 67 RIKNKSVEYIRKFFRIENNFMPEEEE 92 (136)
Q Consensus 67 ~ikgKt~eEIR~~fgI~~D~T~EEee 92 (136)
..-|.|.+|-++++||.+++++||.+
T Consensus 52 ~~~~iTlqEa~qILnV~~~ln~eei~ 77 (132)
T KOG3442|consen 52 SNGKITLQEAQQILNVKEPLNREEIE 77 (132)
T ss_pred ccccccHHHHhhHhCCCCCCCHHHHH
Confidence 33568999999999999988877544
No 26
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=50.78 E-value=28 Score=22.14 Aligned_cols=37 Identities=14% Similarity=0.084 Sum_probs=29.7
Q ss_pred CCCHHHHHHHc----CCCCCCCHHHHHHHhhhhchhhhccc
Q 045340 70 NKSVEYIRKFF----RIENNFMPEEEEAARNDSTKISCIFL 106 (136)
Q Consensus 70 gKt~eEIR~~f----gI~~D~T~EEee~ir~en~w~~~~~~ 106 (136)
.+|.+|+-..+ ||+..+|.-=..+++++|+=.|.+|.
T Consensus 12 yMsk~E~v~~L~~~a~I~P~~T~~VW~~Le~eN~eFF~aY~ 52 (54)
T PF09713_consen 12 YMSKEECVRALQKQANIEPVFTSTVWQKLEKENPEFFKAYY 52 (54)
T ss_pred cCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHCHHHHHHhh
Confidence 56766665554 89999998889999999998888764
No 27
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=50.78 E-value=15 Score=27.25 Aligned_cols=21 Identities=19% Similarity=0.270 Sum_probs=15.7
Q ss_pred HHHHHHHhc-CCCHHHHHHHcC
Q 045340 61 TETLANRIK-NKSVEYIRKFFR 81 (136)
Q Consensus 61 c~~IA~~ik-gKt~eEIR~~fg 81 (136)
-+.|..+++ |+|.+||+++|-
T Consensus 63 R~~Vr~~i~~G~Sd~eI~~~~v 84 (126)
T TIGR03147 63 RHEVYSMVNEGKSNQQIIDFMT 84 (126)
T ss_pred HHHHHHHHHcCCCHHHHHHHHH
Confidence 355666666 999999998863
No 28
>PRK11053 dihydropteridine reductase; Provisional
Probab=50.63 E-value=14 Score=28.51 Aligned_cols=35 Identities=20% Similarity=0.259 Sum_probs=24.1
Q ss_pred HHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHcCCCC-CC
Q 045340 42 KEMLLVANYLNITEMLDYLTETLANRIKNKSVEYIRKFFRIEN-NF 86 (136)
Q Consensus 42 ~~Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~-D~ 86 (136)
-.|+.||.-||+... .|.|-.++.+++.|||+. ++
T Consensus 148 ~~lmLaA~~~Glgs~----------~i~g~~~~~v~~~l~ip~~~~ 183 (217)
T PRK11053 148 GNLLLGAAALGIDAT----------PIEGFDAAILDAEFGLREKGL 183 (217)
T ss_pred HHHHHHHHHcCCCCC----------CcCCcCHHHHHHHhCCCCcCc
Confidence 355556666665543 455778999999999984 45
No 29
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=49.82 E-value=51 Score=24.83 Aligned_cols=41 Identities=24% Similarity=0.186 Sum_probs=31.4
Q ss_pred hhhhhchHHHHHHHHHHHHHHhc-CCCHHHHHHHcCCCCCCCHHHHH
Q 045340 47 VANYLNITEMLDYLTETLANRIK-NKSVEYIRKFFRIENNFMPEEEE 92 (136)
Q Consensus 47 AAnyL~I~~Ll~l~c~~IA~~ik-gKt~eEIR~~fgI~~D~T~EEee 92 (136)
.-..=+.+..++.-..++.+... |+|-||+-+-+| ||+|.+
T Consensus 16 ~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG-----~P~~iA 57 (181)
T PF08006_consen 16 KLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELG-----SPKEIA 57 (181)
T ss_pred cCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcC-----CHHHHH
Confidence 33445677788888889988665 999999999999 566553
No 30
>PF12556 CobS_N: Cobaltochelatase CobS subunit N terminal
Probab=49.33 E-value=10 Score=22.28 Aligned_cols=12 Identities=25% Similarity=0.697 Sum_probs=10.7
Q ss_pred HHHHcCCCCCCC
Q 045340 76 IRKFFRIENNFM 87 (136)
Q Consensus 76 IR~~fgI~~D~T 87 (136)
+|+.|||..|++
T Consensus 14 vre~FGiDsDm~ 25 (36)
T PF12556_consen 14 VREVFGIDSDMK 25 (36)
T ss_pred HHHhcCCCcCCe
Confidence 699999999976
No 31
>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=47.65 E-value=21 Score=25.64 Aligned_cols=38 Identities=18% Similarity=0.071 Sum_probs=25.3
Q ss_pred HHHhhhhhchHHHHHHHH-HHHHHHhcCCCHHHHHHHcC
Q 045340 44 MLLVANYLNITEMLDYLT-ETLANRIKNKSVEYIRKFFR 81 (136)
Q Consensus 44 Li~AAnyL~I~~Ll~l~c-~~IA~~ikgKt~eEIR~~fg 81 (136)
.|.-+.|-.-=.-.-.+| ..++.+++|||.+|.+.+-+
T Consensus 50 ~I~d~~f~~~GC~~s~Asas~~~e~i~Gktl~ea~~i~~ 88 (124)
T TIGR01999 50 IIEDAKFKTFGCGSAIASSSLATELIKGKSLEEALKIKN 88 (124)
T ss_pred eEEEEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHhccH
Confidence 444455554444444444 56688999999999997754
No 32
>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=46.81 E-value=24 Score=25.26 Aligned_cols=38 Identities=11% Similarity=0.075 Sum_probs=25.2
Q ss_pred HHHhhhhhchHHHHHHHH-HHHHHHhcCCCHHHHHHHcC
Q 045340 44 MLLVANYLNITEMLDYLT-ETLANRIKNKSVEYIRKFFR 81 (136)
Q Consensus 44 Li~AAnyL~I~~Ll~l~c-~~IA~~ikgKt~eEIR~~fg 81 (136)
.|.-+.|-.-=.-+-.+| ..++.+++|||++|..++-.
T Consensus 46 ~I~d~~f~~~GC~is~Asas~~~e~i~Gk~l~ea~~i~~ 84 (121)
T TIGR03419 46 IIKDVKFKTFGCGAAIASSSMATEMIKGKTLEEAWELTN 84 (121)
T ss_pred EEEEEEEEEeccHHHHHHHHHHHHHHcCCCHHHHHHhhh
Confidence 444455555544444444 45588999999999887743
No 33
>PRK11325 scaffold protein; Provisional
Probab=46.46 E-value=22 Score=25.73 Aligned_cols=38 Identities=8% Similarity=0.034 Sum_probs=25.4
Q ss_pred HHHhhhhhchHHHHHHHH-HHHHHHhcCCCHHHHHHHcC
Q 045340 44 MLLVANYLNITEMLDYLT-ETLANRIKNKSVEYIRKFFR 81 (136)
Q Consensus 44 Li~AAnyL~I~~Ll~l~c-~~IA~~ikgKt~eEIR~~fg 81 (136)
.|.-+.|-.-=.-.-.+| ..++.+++|||++|.+++-+
T Consensus 52 ~I~d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~~ 90 (127)
T PRK11325 52 IIEDAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKN 90 (127)
T ss_pred eEEEEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcCH
Confidence 444555555544444444 45588999999999997744
No 34
>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=45.21 E-value=16 Score=26.91 Aligned_cols=28 Identities=14% Similarity=0.254 Sum_probs=24.9
Q ss_pred HHHhhhhhchHHHHHHHHHHHHHHhcCC
Q 045340 44 MLLVANYLNITEMLDYLTETLANRIKNK 71 (136)
Q Consensus 44 Li~AAnyL~I~~Ll~l~c~~IA~~ikgK 71 (136)
--.|+....++.-+-.+|+.||++|+|.
T Consensus 36 ~~~~~k~F~VpDFVGd~Ck~iaSRIR~a 63 (118)
T PF11978_consen 36 PEDAAKLFSVPDFVGDACKAIASRIRGA 63 (118)
T ss_dssp HHHHHHTTSSTTHHHHHHHHHHHHHHHH
T ss_pred hhHHHHhcCCcchHHHHHHHHHHHHHHH
Confidence 3478889999999999999999999985
No 35
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=44.95 E-value=31 Score=26.60 Aligned_cols=25 Identities=24% Similarity=0.320 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHc
Q 045340 56 MLDYLTETLANRIKNKSVEYIRKFF 80 (136)
Q Consensus 56 Ll~l~c~~IA~~ikgKt~eEIR~~f 80 (136)
-++.+-+.+...=+|||+.|||+.-
T Consensus 117 Cl~ia~~a~~~~~~Gks~~eIR~~I 141 (158)
T PF13798_consen 117 CLDIAVQAVQMYQEGKSPKEIRQYI 141 (158)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 3455666666677799999999763
No 36
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=44.71 E-value=18 Score=27.18 Aligned_cols=19 Identities=26% Similarity=0.389 Sum_probs=11.5
Q ss_pred HHHHHHhc-CCCHHHHHHHc
Q 045340 62 ETLANRIK-NKSVEYIRKFF 80 (136)
Q Consensus 62 ~~IA~~ik-gKt~eEIR~~f 80 (136)
+.|..++. |+|.+||+++|
T Consensus 64 ~~I~~~l~~G~s~~eI~~~~ 83 (148)
T PF03918_consen 64 REIREMLAEGKSDEEIIDYF 83 (148)
T ss_dssp HHHHHHHHHT--HHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHH
Confidence 34444444 99999999876
No 37
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=43.76 E-value=21 Score=24.07 Aligned_cols=62 Identities=16% Similarity=0.145 Sum_probs=35.3
Q ss_pred CHHHHHHHcCCCCCCCHHHHHHHhhhhchhhhcccccccchhhccCCchhhhhhc----ccchhhhhc
Q 045340 72 SVEYIRKFFRIENNFMPEEEEAARNDSTKISCIFLSGFCPILAFLGPGCFERCRL----IPKHAVQDL 135 (136)
Q Consensus 72 t~eEIR~~fgI~~D~T~EEee~ir~en~w~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~ 135 (136)
+++.|-..+-=..-+|+||.+.|+.++.--.-|. ....+|+.-||.||..-+- ..+|+++|+
T Consensus 16 ~v~~ilD~L~~~~Vit~e~~~~I~a~~T~~~kar--~Lld~l~~kG~~A~~~F~~~L~e~~p~L~~~L 81 (82)
T cd08330 16 NVDPILDKLHGKKVITQEQYSEVRAEKTNQEKMR--KLFSFVRSWGASCKDIFYQILREEEPYLVEDL 81 (82)
T ss_pred hHHHHHHHHHHCCCCCHHHHHHHHcCCCcHHHHH--HHHHHHHccCHHHHHHHHHHHHHhChHHHhHc
Confidence 3444444444344578888888877655333332 3344677777777654322 556666664
No 38
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=43.19 E-value=24 Score=26.33 Aligned_cols=21 Identities=19% Similarity=0.235 Sum_probs=17.5
Q ss_pred HHHHHhc-CCCHHHHHHHcCCC
Q 045340 63 TLANRIK-NKSVEYIRKFFRIE 83 (136)
Q Consensus 63 ~IA~~ik-gKt~eEIR~~fgI~ 83 (136)
.|-.|++ ||+|.||.+.+||+
T Consensus 101 ~i~emlr~gk~preIsk~lGIp 122 (139)
T COG1710 101 RIREMLRNGKTPREISKDLGIP 122 (139)
T ss_pred HHHHHHHcCCCHHHHHHhhCCc
Confidence 4555666 89999999999998
No 39
>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=42.72 E-value=32 Score=24.63 Aligned_cols=22 Identities=23% Similarity=0.158 Sum_probs=16.9
Q ss_pred HHHHHHHHHHhcCCCHHHHHHH
Q 045340 58 DYLTETLANRIKNKSVEYIRKF 79 (136)
Q Consensus 58 ~l~c~~IA~~ikgKt~eEIR~~ 79 (136)
-.++..++.+++|||.+|+.++
T Consensus 65 ~Asas~~~~~i~gk~l~ea~~i 86 (126)
T PF01592_consen 65 IASASMMCELIKGKTLEEALKI 86 (126)
T ss_dssp HHHHHHHHHHHTTSBHHHHHCH
T ss_pred HHHHHHHHHHHcCCCHHHHHHH
Confidence 3455677889999999998653
No 40
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=41.63 E-value=25 Score=26.06 Aligned_cols=20 Identities=15% Similarity=0.114 Sum_probs=14.9
Q ss_pred HHHHHHhc-CCCHHHHHHHcC
Q 045340 62 ETLANRIK-NKSVEYIRKFFR 81 (136)
Q Consensus 62 ~~IA~~ik-gKt~eEIR~~fg 81 (136)
..|..+++ |+|.+||+++|-
T Consensus 64 ~~Vr~~i~~G~sd~eI~~~~v 84 (126)
T PRK10144 64 HQVYSMVAEGKSEVEIIGWMT 84 (126)
T ss_pred HHHHHHHHcCCCHHHHHHHHH
Confidence 45556555 999999998763
No 41
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=40.04 E-value=25 Score=26.67 Aligned_cols=18 Identities=6% Similarity=0.135 Sum_probs=17.0
Q ss_pred CCCHHHHHHHcCCCCCCC
Q 045340 70 NKSVEYIRKFFRIENNFM 87 (136)
Q Consensus 70 gKt~eEIR~~fgI~~D~T 87 (136)
|+||+|-|.-+|++.|+.
T Consensus 98 gmTPd~YR~KW~LP~dYP 115 (148)
T COG4957 98 GLTPDEYRAKWGLPPDYP 115 (148)
T ss_pred CCCHHHHHHhcCCCCCCC
Confidence 899999999999999975
No 42
>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=37.18 E-value=24 Score=26.59 Aligned_cols=38 Identities=16% Similarity=0.051 Sum_probs=22.4
Q ss_pred HHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCC
Q 045340 42 KEMLLVANYLNITEMLDYLTETLANRIKNKSVEYIRKFFRIENNFM 87 (136)
Q Consensus 42 ~~Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~D~T 87 (136)
-.|+.||.-+|+-..+... .....+.+|+.|||++|++
T Consensus 128 ~nl~LaA~~~GlGs~~~~~--------~~~~~~~v~~~l~ip~~~~ 165 (192)
T cd02140 128 IAVWTALAAEGIGANLQHY--------NPLIDEEVAKKWNIPSNWK 165 (192)
T ss_pred HHHHHHHHhCCCcccHHHh--------CccCCHHHHHhcCCCccce
Confidence 4556666666665421100 0123489999999997764
No 43
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=36.79 E-value=55 Score=24.62 Aligned_cols=37 Identities=11% Similarity=0.159 Sum_probs=23.5
Q ss_pred HHHhhhhhchHHHHHH-HHHHHHHHhcCCCHHHHHHHc
Q 045340 44 MLLVANYLNITEMLDY-LTETLANRIKNKSVEYIRKFF 80 (136)
Q Consensus 44 Li~AAnyL~I~~Ll~l-~c~~IA~~ikgKt~eEIR~~f 80 (136)
.+..|.|...=.=+-. ++..+..+++|||.+|..++-
T Consensus 53 ~I~d~~F~~~GC~is~ASss~~te~v~Gkti~EAl~i~ 90 (150)
T COG0822 53 VIEDAKFKGFGCAISIASSSMMTELVKGKTLDEALKIT 90 (150)
T ss_pred EEEEEEeeecCcHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 3444445444433333 345567899999999998876
No 44
>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=36.58 E-value=58 Score=22.87 Aligned_cols=39 Identities=15% Similarity=0.199 Sum_probs=25.3
Q ss_pred HHHHhhhhhchHHHHHHHH-HHHHHHhcCCCHHHHHHHcC
Q 045340 43 EMLLVANYLNITEMLDYLT-ETLANRIKNKSVEYIRKFFR 81 (136)
Q Consensus 43 ~Li~AAnyL~I~~Ll~l~c-~~IA~~ikgKt~eEIR~~fg 81 (136)
+.+..+.|-.-=..+-.+| ..++++++|||.+|...+.+
T Consensus 46 ~~I~d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~~ 85 (123)
T cd06664 46 GRITDAKFQGFGCAISIASASLLTELIKGKTLDEALKLLN 85 (123)
T ss_pred CEEEEEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHHH
Confidence 3444455544444444444 45588999999999998664
No 45
>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=35.47 E-value=54 Score=23.51 Aligned_cols=34 Identities=26% Similarity=0.534 Sum_probs=22.8
Q ss_pred hchHHHHHHHHHHHHHHhc--CCCHHHHHHHcCCCCC
Q 045340 51 LNITEMLDYLTETLANRIK--NKSVEYIRKFFRIENN 85 (136)
Q Consensus 51 L~I~~Ll~l~c~~IA~~ik--gKt~eEIR~~fgI~~D 85 (136)
++++.|.+.+.+ +|..++ +-|+.|||++|+--..
T Consensus 8 ~~~~~~~~~Ae~-~~k~l~~~~lttsQlRkf~~~v~~ 43 (119)
T PF03750_consen 8 LDIELLVDYAEK-IAKELKKNKLTTSQLRKFYDEVKR 43 (119)
T ss_pred cCHHHHHHHHHH-HHHHHHhCCCCHHHHHHHHHHHHH
Confidence 455666665554 445555 4899999999985443
No 46
>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=35.23 E-value=33 Score=26.16 Aligned_cols=38 Identities=8% Similarity=0.166 Sum_probs=26.1
Q ss_pred HHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCH
Q 045340 41 LKEMLLVANYLNITEMLDYLTETLANRIKNKSVEYIRKFFRIENNFMP 88 (136)
Q Consensus 41 L~~Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~D~T~ 88 (136)
+-.|+.||..||+-.. .+.|-..+++++.|||+.++++
T Consensus 134 ~~nl~LaA~~~GlGs~----------~~~~~~~~~v~~~L~lp~~~~~ 171 (205)
T TIGR02476 134 IQNLWLAARAEGLGVG----------WVSILDPDAVRRLLGVPEGWRL 171 (205)
T ss_pred HHHHHHHHHHCCCcce----------eecccChHHHHHHhCcCCCceE
Confidence 3466777777777642 2234457899999999987653
No 47
>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=35.22 E-value=34 Score=25.27 Aligned_cols=36 Identities=8% Similarity=0.122 Sum_probs=24.5
Q ss_pred HHHHhhhhhchHHHHHHHHHHHHHHhcCCCH-HHHHHHcCCCCCCCH
Q 045340 43 EMLLVANYLNITEMLDYLTETLANRIKNKSV-EYIRKFFRIENNFMP 88 (136)
Q Consensus 43 ~Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt~-eEIR~~fgI~~D~T~ 88 (136)
.|+.||.-||+... .+.|-.. +.+|+.|||++++.+
T Consensus 131 ~l~LaA~~~Glgs~----------~~~~~~~~~~v~~~l~ip~~~~~ 167 (193)
T cd02144 131 LLLAALQNAGLGTV----------TTTPLNMGPFLRRLLGRPANEKL 167 (193)
T ss_pred HHHHHHHHCCCcee----------ecCCcchhHHHHHHhCCCCCCce
Confidence 37777777777652 1234344 899999999987644
No 48
>PF13518 HTH_28: Helix-turn-helix domain
Probab=34.33 E-value=64 Score=18.62 Aligned_cols=21 Identities=24% Similarity=0.282 Sum_probs=17.2
Q ss_pred HHHHHhcCCCHHHHHHHcCCC
Q 045340 63 TLANRIKNKSVEYIRKFFRIE 83 (136)
Q Consensus 63 ~IA~~ikgKt~eEIR~~fgI~ 83 (136)
.|.....|.|..++.+.|||.
T Consensus 5 iv~~~~~g~s~~~~a~~~gis 25 (52)
T PF13518_consen 5 IVELYLEGESVREIAREFGIS 25 (52)
T ss_pred HHHHHHcCCCHHHHHHHHCCC
Confidence 455566799999999999994
No 49
>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=33.63 E-value=24 Score=22.44 Aligned_cols=21 Identities=14% Similarity=0.173 Sum_probs=15.5
Q ss_pred HHHHhcCCCHHHHHHHcCCCC
Q 045340 64 LANRIKNKSVEYIRKFFRIEN 84 (136)
Q Consensus 64 IA~~ikgKt~eEIR~~fgI~~ 84 (136)
++..-.|+|.+|++.++|-|.
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 444445999999999999774
No 50
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=33.07 E-value=47 Score=21.94 Aligned_cols=20 Identities=15% Similarity=0.321 Sum_probs=16.0
Q ss_pred HHHHHHhcCCCHHHHHHHcC
Q 045340 62 ETLANRIKNKSVEYIRKFFR 81 (136)
Q Consensus 62 ~~IA~~ikgKt~eEIR~~fg 81 (136)
++|-..++|+|.+|++.+-.
T Consensus 5 ~AI~~nv~g~s~~el~~~I~ 24 (65)
T PF14098_consen 5 QAIIHNVKGSSKEELKDTIE 24 (65)
T ss_pred HHHHHHccCCCHHHHHHHHH
Confidence 46677889999999998753
No 51
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=32.56 E-value=40 Score=24.25 Aligned_cols=23 Identities=30% Similarity=0.423 Sum_probs=15.0
Q ss_pred CHHHHHHHcCCCCCCCHHHHHHHhhh
Q 045340 72 SVEYIRKFFRIENNFMPEEEEAARND 97 (136)
Q Consensus 72 t~eEIR~~fgI~~D~T~EEee~ir~e 97 (136)
+.+||.+.|. .+||||.+++.+|
T Consensus 79 ~~~~lqkRle---~l~~eE~~~L~~e 101 (104)
T PF11460_consen 79 TNEELQKRLE---ELSPEELEALQAE 101 (104)
T ss_pred hHHHHHHHHH---hCCHHHHHHHHHH
Confidence 4455666664 5688887777655
No 52
>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=32.25 E-value=22 Score=26.51 Aligned_cols=18 Identities=11% Similarity=0.183 Sum_probs=12.6
Q ss_pred CCCHHHHHHHcCCCCCCC
Q 045340 70 NKSVEYIRKFFRIENNFM 87 (136)
Q Consensus 70 gKt~eEIR~~fgI~~D~T 87 (136)
|.||+|=|+.||++.|+.
T Consensus 94 gltp~eYR~kwGlp~dyp 111 (132)
T PF05443_consen 94 GLTPEEYRAKWGLPKDYP 111 (132)
T ss_dssp -S-HHHHHHHTT-GGG--
T ss_pred CCCHHHHHHHhCcCCCCc
Confidence 999999999999999863
No 53
>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=32.00 E-value=35 Score=24.76 Aligned_cols=20 Identities=5% Similarity=0.107 Sum_probs=15.7
Q ss_pred HhcCCCHHHHHHHcCCCC-CC
Q 045340 67 RIKNKSVEYIRKFFRIEN-NF 86 (136)
Q Consensus 67 ~ikgKt~eEIR~~fgI~~-D~ 86 (136)
.+.|...+.+++.||++. ++
T Consensus 111 ~i~~~~~~~v~~~l~l~~~~~ 131 (156)
T cd03370 111 PMTGFDEEKVKEALGLPGRDR 131 (156)
T ss_pred cCcCcCHHHHHHHhCcCCcCc
Confidence 445678899999999986 54
No 54
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=31.83 E-value=49 Score=19.26 Aligned_cols=15 Identities=20% Similarity=0.198 Sum_probs=11.0
Q ss_pred cCCCHHHHHHHcCCC
Q 045340 69 KNKSVEYIRKFFRIE 83 (136)
Q Consensus 69 kgKt~eEIR~~fgI~ 83 (136)
.|+|..+|.+.||++
T Consensus 16 ~G~s~~~ia~~lgvs 30 (50)
T PF13384_consen 16 EGWSIREIAKRLGVS 30 (50)
T ss_dssp HT--HHHHHHHHTS-
T ss_pred CCCCHHHHHHHHCcC
Confidence 499999999999987
No 55
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=31.40 E-value=97 Score=19.09 Aligned_cols=27 Identities=15% Similarity=0.145 Sum_probs=14.9
Q ss_pred HHHHH-hcCCCHHHHHHHcCCCCCCCHHHHH
Q 045340 63 TLANR-IKNKSVEYIRKFFRIENNFMPEEEE 92 (136)
Q Consensus 63 ~IA~~-ikgKt~eEIR~~fgI~~D~T~EEee 92 (136)
.|+.+ -.|.|++||.+-|. ++|+++..
T Consensus 23 ~i~~~~~~G~s~eeI~~~yp---~Lt~~~i~ 50 (56)
T PF04255_consen 23 DILDLLAAGESPEEIAEDYP---SLTLEDIR 50 (56)
T ss_dssp HHHHHHHTT--HHHHHHHST---T--HHHHH
T ss_pred HHHHHHHcCCCHHHHHHHCC---CCCHHHHH
Confidence 34443 45999999999886 35566543
No 56
>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=31.26 E-value=79 Score=23.08 Aligned_cols=37 Identities=14% Similarity=0.095 Sum_probs=24.6
Q ss_pred HHhhhhhchHHHHHHHH-HHHHHHhcCCCHHHHHHHcC
Q 045340 45 LLVANYLNITEMLDYLT-ETLANRIKNKSVEYIRKFFR 81 (136)
Q Consensus 45 i~AAnyL~I~~Ll~l~c-~~IA~~ikgKt~eEIR~~fg 81 (136)
|..+.|-.--.-+-.+| ..++++++|||.+|+..+.+
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 44444544444444444 55688999999999987764
No 57
>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=30.73 E-value=1.8e+02 Score=20.95 Aligned_cols=56 Identities=18% Similarity=0.103 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHhhh-hchhhhcccccccc
Q 045340 56 MLDYLTETLANRIKNKSVEYIRKFFRIENNFMPEEEEAARND-STKISCIFLSGFCP 111 (136)
Q Consensus 56 Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~D~T~EEee~ir~e-n~w~~~~~~~~~~~ 111 (136)
......+.+.+.+-|-++..+-..|--.+++|+||.+++++- ..|..-+-.+--|+
T Consensus 72 ~~~~~~~~~~~~~f~gs~~~ll~~l~~~~~ls~eele~L~~li~~~~~~~~~~~~~~ 128 (130)
T TIGR02698 72 AVENAAQELFSRICSRKVGAVIADLIEESPLSQTDIEKLEKLLSEKKSTAVEEVPCN 128 (130)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHHHHHhcccCCCccccCC
Confidence 344445556665556666665555533567999999999864 33443343444443
No 58
>KOG4244 consensus Failed axon connections (fax) protein/glutathione S-transferase-like protein [Signal transduction mechanisms]
Probab=29.96 E-value=52 Score=27.58 Aligned_cols=23 Identities=26% Similarity=0.595 Sum_probs=19.2
Q ss_pred HHHHHHcCCCCCCCHHHHHHHhh
Q 045340 74 EYIRKFFRIENNFMPEEEEAARN 96 (136)
Q Consensus 74 eEIR~~fgI~~D~T~EEee~ir~ 96 (136)
..+|+.|++++++++||++.-|.
T Consensus 112 ~~L~~hf~~~~~L~~e~~a~s~A 134 (281)
T KOG4244|consen 112 DRLRKHFKIPDDLSAEQRAQSRA 134 (281)
T ss_pred HHHHHHcCCCCCCCHHHHHHHHH
Confidence 46789999999999999987653
No 59
>PF11103 DUF2887: Protein of unknown function (DUF2887); InterPro: IPR022573 This bacterial group of proteins has no known function.
Probab=29.65 E-value=76 Score=25.19 Aligned_cols=29 Identities=21% Similarity=0.310 Sum_probs=25.9
Q ss_pred chHHHHHHHHHHHHHHhcCCCHHHHHHHc
Q 045340 52 NITEMLDYLTETLANRIKNKSVEYIRKFF 80 (136)
Q Consensus 52 ~I~~Ll~l~c~~IA~~ikgKt~eEIR~~f 80 (136)
.=..|+++.-..+..+...+|.|||.+||
T Consensus 172 ~~~~lleLIEtIlvyKfp~lSreEIeaMl 200 (200)
T PF11103_consen 172 QQRELLELIETILVYKFPQLSREEIEAML 200 (200)
T ss_pred HHHHHHHHHHHHHHHHccccCHHHHHHhC
Confidence 45678999999999999999999999987
No 60
>PF15063 TC1: Thyroid cancer protein 1
Probab=29.46 E-value=55 Score=22.42 Aligned_cols=34 Identities=18% Similarity=0.287 Sum_probs=25.0
Q ss_pred HHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHh
Q 045340 62 ETLANRIKNKSVEYIRKFFRIENNFMPEEEEAAR 95 (136)
Q Consensus 62 ~~IA~~ikgKt~eEIR~~fgI~~D~T~EEee~ir 95 (136)
+.+||...+-+-++++..|.-..|--.||-+++-
T Consensus 28 kasaNIFe~vn~~qlqrLF~~sGD~kAEeRA~iI 61 (79)
T PF15063_consen 28 KASANIFENVNLDQLQRLFQKSGDKKAEERARII 61 (79)
T ss_pred hhhhhhhhccCHHHHHHHHHHccchhHHHHHHHH
Confidence 5567778888888888888877777766666553
No 61
>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=28.83 E-value=70 Score=19.38 Aligned_cols=23 Identities=22% Similarity=0.069 Sum_probs=17.4
Q ss_pred HHHHHHHhcCCCHHHHHHHcCCC
Q 045340 61 TETLANRIKNKSVEYIRKFFRIE 83 (136)
Q Consensus 61 c~~IA~~ikgKt~eEIR~~fgI~ 83 (136)
.+.+.-+..|+|+.||-+.+||.
T Consensus 9 ~~vl~~l~~G~~~~eIA~~l~is 31 (58)
T PF00196_consen 9 LEVLRLLAQGMSNKEIAEELGIS 31 (58)
T ss_dssp HHHHHHHHTTS-HHHHHHHHTSH
T ss_pred HHHHHHHHhcCCcchhHHhcCcc
Confidence 34556677899999999999976
No 62
>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=28.71 E-value=43 Score=18.74 Aligned_cols=13 Identities=38% Similarity=0.491 Sum_probs=9.1
Q ss_pred cCCCHHHHHHHcC
Q 045340 69 KNKSVEYIRKFFR 81 (136)
Q Consensus 69 kgKt~eEIR~~fg 81 (136)
.|-|.+|+|+++.
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 4999999999874
No 63
>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=28.29 E-value=84 Score=21.17 Aligned_cols=37 Identities=11% Similarity=0.236 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhcCCCHHHHHHH-------cCCCCCCCHHHHHHH
Q 045340 58 DYLTETLANRIKNKSVEYIRKF-------FRIENNFMPEEEEAA 94 (136)
Q Consensus 58 ~l~c~~IA~~ikgKt~eEIR~~-------fgI~~D~T~EEee~i 94 (136)
.++...+++.++|.....|++. ||+-.+++..+.+++
T Consensus 19 ~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~l 62 (106)
T PF09382_consen 19 RFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERL 62 (106)
T ss_dssp -S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHH
T ss_pred cccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHH
Confidence 5778889999999988888764 999999999888776
No 64
>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=28.15 E-value=52 Score=26.36 Aligned_cols=33 Identities=27% Similarity=0.354 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCHH
Q 045340 57 LDYLTETLANRIKNKSVEYIRKFFRIENNFMPE 89 (136)
Q Consensus 57 l~l~c~~IA~~ikgKt~eEIR~~fgI~~D~T~E 89 (136)
+.-..+.+++.++..|++|+++.|+|...+..+
T Consensus 27 f~~~~~~l~~~L~~~s~~el~~l~~is~~la~~ 59 (237)
T PF03883_consen 27 FLEKTEELLEALKSLSEEELKKLMKISDKLAEE 59 (237)
T ss_pred hHHHHHHHHHHHHhcCHHHHHHHHCCCHHHHHH
Confidence 334567788888999999999999998655443
No 65
>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=27.74 E-value=63 Score=23.15 Aligned_cols=27 Identities=11% Similarity=0.149 Sum_probs=21.7
Q ss_pred HHHHHHHhcCCCHHHHHHHcCCCCCCCH
Q 045340 61 TETLANRIKNKSVEYIRKFFRIENNFMP 88 (136)
Q Consensus 61 c~~IA~~ikgKt~eEIR~~fgI~~D~T~ 88 (136)
-+.||..--|+|.++++..+|-| |||.
T Consensus 25 r~~i~~L~lg~s~~~V~~~lG~p-dfsE 51 (102)
T PF11399_consen 25 RQNIAKLSLGMSKDQVIALLGTP-DFSE 51 (102)
T ss_pred HHHHHhcCCCCCHHHHHHHhCCC-Cchh
Confidence 45677777799999999999977 6663
No 66
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=27.60 E-value=67 Score=22.51 Aligned_cols=22 Identities=27% Similarity=0.372 Sum_probs=18.9
Q ss_pred HHHHHHHhcCCCHHHHHHHcCC
Q 045340 61 TETLANRIKNKSVEYIRKFFRI 82 (136)
Q Consensus 61 c~~IA~~ikgKt~eEIR~~fgI 82 (136)
...||+.|+||+.++-..++..
T Consensus 13 ~~~va~~IrG~~v~~A~~~L~f 34 (103)
T TIGR01044 13 ARLVADLIRGKSVSQALDILRF 34 (103)
T ss_pred HHHHHHHHcCCcHHHHHHHHhh
Confidence 3578999999999999988883
No 67
>KOG4079 consensus Putative mitochondrial ribosomal protein mRpS25 [Translation, ribosomal structure and biogenesis]
Probab=27.42 E-value=1.1e+02 Score=23.33 Aligned_cols=74 Identities=20% Similarity=0.101 Sum_probs=44.5
Q ss_pred ChhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHhhhhchhhhcccccccchhhcc
Q 045340 37 SNDELKEMLLVANYLNITEMLDYLTETLANRIKNKSVEYIRKFFRIENNFMPEEEEAARNDSTKISCIFLSGFCPILAFL 116 (136)
Q Consensus 37 d~~~L~~Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~D~T~EEee~ir~en~w~~~~~~~~~~~~~~~~ 116 (136)
..+.|+||-. .+=+.+.+...+.+ |||-|.+| .||++++.+.|+--|..+..-+|=-=---
T Consensus 84 Gr~vL~Dld~----~~r~eI~~hl~K~l-----GKtee~lr----------~Ee~ek~~k~nPAnFG~~c~R~CiCEv~G 144 (169)
T KOG4079|consen 84 GREVLFDLDG----MKREEIEKHLAKTL-----GKTEEVLR----------REELEKIAKLNPANFGSKCERQCICEVQG 144 (169)
T ss_pred cceEEEEccc----ccHHHHHHHHHHHh-----CccHHHHh----------HHHHHHHhhcChhhhcccccceEEEecCC
Confidence 3456666532 22234444444433 89888887 68889999999977776666554332244
Q ss_pred CCchhhhhhcccch
Q 045340 117 GPGCFERCRLIPKH 130 (136)
Q Consensus 117 ~~~~~~~~~~~~~~ 130 (136)
|.-|.-.+++ |+|
T Consensus 145 QvPCpglvpl-P~~ 157 (169)
T KOG4079|consen 145 QVPCPGLVPL-PQC 157 (169)
T ss_pred cCCCCccccC-chH
Confidence 5556666654 444
No 68
>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=27.35 E-value=68 Score=18.78 Aligned_cols=30 Identities=17% Similarity=0.221 Sum_probs=24.5
Q ss_pred hhchHHHHHHHHHHHHHHhcCCCHHHHHHH
Q 045340 50 YLNITEMLDYLTETLANRIKNKSVEYIRKF 79 (136)
Q Consensus 50 yL~I~~Ll~l~c~~IA~~ikgKt~eEIR~~ 79 (136)
||.-++|-+.....|+..+..-+|++|-.+
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 677888888888999988888888887654
No 69
>PLN03212 Transcription repressor MYB5; Provisional
Probab=27.18 E-value=80 Score=26.05 Aligned_cols=43 Identities=12% Similarity=0.065 Sum_probs=31.5
Q ss_pred HHHHHHHh-cCCCHHHHHHHcC------CCC-CCCHHHHHHHhh-----hhchhhh
Q 045340 61 TETLANRI-KNKSVEYIRKFFR------IEN-NFMPEEEEAARN-----DSTKISC 103 (136)
Q Consensus 61 c~~IA~~i-kgKt~eEIR~~fg------I~~-D~T~EEee~ir~-----en~w~~~ 103 (136)
-..||.++ .|+|+.+.|+.+. |.. .+|+||.+.|.+ .+.|..=
T Consensus 48 W~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~GnKWs~I 103 (249)
T PLN03212 48 WRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNRWSLI 103 (249)
T ss_pred HHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhccccHHHH
Confidence 46688877 4899999999884 655 599998876543 3567553
No 70
>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=27.18 E-value=68 Score=20.79 Aligned_cols=24 Identities=21% Similarity=0.325 Sum_probs=17.5
Q ss_pred HHHHHHHcC-CCCC-CCHHHHHHHhh
Q 045340 73 VEYIRKFFR-IENN-FMPEEEEAARN 96 (136)
Q Consensus 73 ~eEIR~~fg-I~~D-~T~EEee~ir~ 96 (136)
.+++|+-|| |=.| +||||..+|.+
T Consensus 30 ad~lr~klG~IC~~CitpEE~~~I~e 55 (60)
T PF10892_consen 30 ADDLRVKLGGICGDCITPEEDREILE 55 (60)
T ss_pred hHHHHHHHcchhhccCCHHHHHHHHH
Confidence 467888887 4445 89999888754
No 71
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=26.56 E-value=96 Score=17.52 Aligned_cols=17 Identities=12% Similarity=0.020 Sum_probs=14.4
Q ss_pred HhcCCCHHHHHHHcCCC
Q 045340 67 RIKNKSVEYIRKFFRIE 83 (136)
Q Consensus 67 ~ikgKt~eEIR~~fgI~ 83 (136)
...|+|..+|-+.+|++
T Consensus 15 ~~~g~s~~eia~~l~is 31 (58)
T smart00421 15 LAEGLTNKEIAERLGIS 31 (58)
T ss_pred HHcCCCHHHHHHHHCCC
Confidence 45799999999999986
No 72
>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=26.10 E-value=1.6e+02 Score=19.78 Aligned_cols=45 Identities=16% Similarity=0.171 Sum_probs=29.6
Q ss_pred hHHHHHHHHHHHHHHh-cC-CCHHHHHHHcC----CCCCCCHHHHHHHhhh
Q 045340 53 ITEMLDYLTETLANRI-KN-KSVEYIRKFFR----IENNFMPEEEEAARND 97 (136)
Q Consensus 53 I~~Ll~l~c~~IA~~i-kg-Kt~eEIR~~fg----I~~D~T~EEee~ir~e 97 (136)
|..|+..-.++.++-= +| -|.+|+|+++. .....|++|.+++-++
T Consensus 9 ~~~~i~~F~~y~~~~~~~g~Is~~EL~~~l~~~~~lg~k~t~~ev~~m~~~ 59 (88)
T cd05029 9 IGLLVAIFHKYSGREGDKNTLSKKELKELIQKELTIGSKLQDAEIAKLMED 59 (88)
T ss_pred HHHHHHHHHHHHccCCCCCEECHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence 5566777777776322 44 48899998883 4455788877776443
No 73
>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=25.95 E-value=26 Score=26.21 Aligned_cols=18 Identities=11% Similarity=0.337 Sum_probs=14.5
Q ss_pred CCHHHHHHHcCCCCCCCH
Q 045340 71 KSVEYIRKFFRIENNFMP 88 (136)
Q Consensus 71 Kt~eEIR~~fgI~~D~T~ 88 (136)
-..+.+|+.|||+.++.+
T Consensus 149 ~~~~~v~~~l~lp~~~~~ 166 (194)
T TIGR03553 149 FAADVVRAELDLPADWEP 166 (194)
T ss_pred cCHHHHHHHhCcCCCceE
Confidence 457899999999987653
No 74
>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=25.90 E-value=1.6e+02 Score=17.69 Aligned_cols=39 Identities=13% Similarity=0.070 Sum_probs=25.3
Q ss_pred chHHHHHHHHHHHHHHhcCC--CHHHHHHHcCCCCCCCHHHHHH
Q 045340 52 NITEMLDYLTETLANRIKNK--SVEYIRKFFRIENNFMPEEEEA 93 (136)
Q Consensus 52 ~I~~Ll~l~c~~IA~~ikgK--t~eEIR~~fgI~~D~T~EEee~ 93 (136)
.=+.++-.+|=.+|.++.|. +..++....|. +|.++..+
T Consensus 36 ~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~---~~~~~i~~ 76 (83)
T smart00385 36 YSPSLIAAAALYLAAKTEEIPPWTKELVHYTGY---FTEEEILR 76 (83)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC---CCHHHHHH
Confidence 34556667777788888773 56677766665 56665443
No 75
>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=25.42 E-value=24 Score=30.06 Aligned_cols=33 Identities=6% Similarity=0.279 Sum_probs=27.0
Q ss_pred CChhHHHHHHHhhhhhchHHHHHHHHHHHHHHh
Q 045340 36 KSNDELKEMLLVANYLNITEMLDYLTETLANRI 68 (136)
Q Consensus 36 ld~~~L~~Li~AAnyL~I~~Ll~l~c~~IA~~i 68 (136)
++.+....++..|+||++++|++.|-.++...+
T Consensus 72 l~~~NvvsIliSS~FL~M~~Lve~cl~y~~~~~ 104 (317)
T PF11822_consen 72 LTPSNVVSILISSEFLQMESLVEECLQYCHDHM 104 (317)
T ss_pred CCcCcEEEeEehhhhhccHHHHHHHHHHHHHhH
Confidence 356677889999999999999998888875443
No 76
>cd02138 Nitroreductase_2 Nitroreductase-like family 2. 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=24.51 E-value=70 Score=23.78 Aligned_cols=38 Identities=11% Similarity=0.193 Sum_probs=25.2
Q ss_pred HHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCH
Q 045340 41 LKEMLLVANYLNITEMLDYLTETLANRIKNKSVEYIRKFFRIENNFMP 88 (136)
Q Consensus 41 L~~Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~D~T~ 88 (136)
+-.|+.||.-||+... .+.|-..+++++.||++++..+
T Consensus 108 ~~nl~Laa~~lGlgt~----------~~~~~~~~~l~~~l~l~~~~~~ 145 (181)
T cd02138 108 WGNLALQATAMGLAAH----------QMGGFDADKAREELNIPEDYEV 145 (181)
T ss_pred HHHHHHHHHHcCcccc----------eecCcCHHHHHHHhCCCCCceE
Confidence 3456666666665532 3346678899999999977544
No 77
>cd02145 BluB Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD(P)H as electron donor and often use FMN as a cofactor.
Probab=24.10 E-value=53 Score=24.67 Aligned_cols=20 Identities=10% Similarity=0.243 Sum_probs=15.7
Q ss_pred hcCCCHHHHHHHcCCCCCCC
Q 045340 68 IKNKSVEYIRKFFRIENNFM 87 (136)
Q Consensus 68 ikgKt~eEIR~~fgI~~D~T 87 (136)
+.|-..+++++.||++.++.
T Consensus 142 ~~~~~~~~v~~~l~lp~~~~ 161 (196)
T cd02145 142 VSILDPEALARLLGIPEDWE 161 (196)
T ss_pred ecccChHHHHHHcCcCCCcE
Confidence 34567899999999997754
No 78
>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=24.04 E-value=1e+02 Score=17.97 Aligned_cols=16 Identities=25% Similarity=0.320 Sum_probs=11.4
Q ss_pred hcCCCHHHHHHHcCCC
Q 045340 68 IKNKSVEYIRKFFRIE 83 (136)
Q Consensus 68 ikgKt~eEIR~~fgI~ 83 (136)
-.|.|+.+|-+.|||.
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 3589999999999986
No 79
>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=23.82 E-value=1.8e+02 Score=20.19 Aligned_cols=55 Identities=9% Similarity=-0.020 Sum_probs=36.3
Q ss_pred HHHHhhhhhchHH-----HHHHHHHHHHHHhc--CCCHHHHHHHcCCCCCCCHHHHHHHhhh
Q 045340 43 EMLLVANYLNITE-----MLDYLTETLANRIK--NKSVEYIRKFFRIENNFMPEEEEAARND 97 (136)
Q Consensus 43 ~Li~AAnyL~I~~-----Ll~l~c~~IA~~ik--gKt~eEIR~~fgI~~D~T~EEee~ir~e 97 (136)
.|+.|+-..+|+. |+-.+..-.|.++. +++|+++|+..-.|.-.|.+-.+.+++.
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 5566666666643 44444455566666 6899999999999999998877777655
No 80
>PF05397 Med15_fungi: Mediator complex subunit 15; InterPro: IPR008626 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family represents subunit 15 of the Mediator complex in fungi. It contains Saccharomyces cerevisiae GAL11 (Med15) protein. Gal11 (Med15) and Sin4 (Med16) proteins are S. cerevisiae global transcription factors that regulate transcription of a variety of genes, both positively and negatively. Gal11, in a major part, functions in the activation of transcription, whereas Sin4 has an opposite role [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=23.80 E-value=78 Score=22.74 Aligned_cols=19 Identities=32% Similarity=0.513 Sum_probs=15.1
Q ss_pred CCCCCCCHHHHHHHhhhhc
Q 045340 81 RIENNFMPEEEEAARNDST 99 (136)
Q Consensus 81 gI~~D~T~EEee~ir~en~ 99 (136)
.|++++||||.+.+++.-.
T Consensus 24 ~v~~~ls~eeK~~i~~~l~ 42 (115)
T PF05397_consen 24 PVTNSLSPEEKAAIRQQLQ 42 (115)
T ss_pred cccccCCHHHHHHHHHHHH
Confidence 4778899999999987543
No 81
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=23.34 E-value=88 Score=22.10 Aligned_cols=23 Identities=4% Similarity=-0.077 Sum_probs=18.6
Q ss_pred HHHHHHhcCCCHHHHHHHcCCCC
Q 045340 62 ETLANRIKNKSVEYIRKFFRIEN 84 (136)
Q Consensus 62 ~~IA~~ikgKt~eEIR~~fgI~~ 84 (136)
..++..-.|+|.+|++..+|-|.
T Consensus 41 ~~l~~l~~GmTk~qV~~lLGtP~ 63 (113)
T PRK11548 41 NDVAKIHVGMTQQQVAYTLGTPM 63 (113)
T ss_pred HHHHHhcCCCCHHHHHHHcCCCc
Confidence 44566667999999999999874
No 82
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=23.07 E-value=90 Score=25.94 Aligned_cols=37 Identities=14% Similarity=0.095 Sum_probs=23.4
Q ss_pred HHhhhhhchHHHHHHH-HHHHHHHhcCCCHHHHHHHcC
Q 045340 45 LLVANYLNITEMLDYL-TETLANRIKNKSVEYIRKFFR 81 (136)
Q Consensus 45 i~AAnyL~I~~Ll~l~-c~~IA~~ikgKt~eEIR~~fg 81 (136)
|.-+.|-..=.-.-.+ +..++.+++|||++|..++-+
T Consensus 52 I~d~~F~~~GCais~ASAs~~~eli~Gktv~ea~~i~~ 89 (290)
T TIGR02000 52 IVDAGFQTFGCGSAIASSSALTEMIKGLTLDEALKVSN 89 (290)
T ss_pred EEEEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHHhhH
Confidence 4444454443334444 455688999999999776643
No 83
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interac
Probab=23.03 E-value=1.6e+02 Score=20.28 Aligned_cols=50 Identities=14% Similarity=0.052 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHhhhhchhhhcccccccchhhccCCchhhhhh----cccchhhhhc
Q 045340 84 NNFMPEEEEAARNDSTKISCIFLSGFCPILAFLGPGCFERCR----LIPKHAVQDL 135 (136)
Q Consensus 84 ~D~T~EEee~ir~en~w~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~ 135 (136)
+-+|.+|.+.|+.++.-..-+. .....|+.-||.+|..-+ -.+.|+.+|+
T Consensus 36 ~Vlt~ee~e~I~~~~t~~~qAr--~Lld~l~~KG~~A~~~F~~~L~e~~~~L~~~L 89 (94)
T cd08329 36 NVITEQEYDVIKQKTQTPLQAR--ELIDTVLVKGNAAAEVFRNCLKKNDPVLYRDL 89 (94)
T ss_pred CCCCHHHHHHHHcCCChHHHHH--HHHHHHHhhhHHHHHHHHHHHHhcCHhHHHHH
Confidence 3466666666665544322221 223355555555544322 2455666554
No 84
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=22.71 E-value=80 Score=18.41 Aligned_cols=26 Identities=15% Similarity=0.317 Sum_probs=18.1
Q ss_pred HHHHHHhhhhhchHHHHHHHHHHHHHHhcCCC
Q 045340 41 LKEMLLVANYLNITEMLDYLTETLANRIKNKS 72 (136)
Q Consensus 41 L~~Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt 72 (136)
.-.+..||.+|++ .-..|+..++|+.
T Consensus 17 f~S~~eAa~~lg~------~~~~I~~~~~~~~ 42 (53)
T smart00497 17 FSSIREAAKYLGI------SHSSISKYLNTGK 42 (53)
T ss_pred ecCHHHHHHHhCC------CHHHHHHHHhCCC
Confidence 3457789999998 3456666677653
No 85
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=22.60 E-value=3e+02 Score=19.75 Aligned_cols=89 Identities=15% Similarity=0.262 Sum_probs=57.2
Q ss_pred HHHHHHHHHhhc-CCCCCCCCchHH----HhhccCCChhHHHHHHHhhh-----hhchHHHHHHHHHHHHHHhcC-CCHH
Q 045340 6 SRWKSKGVRDCD-HSSTSDGTSEDM----VEFGKGKSNDELKEMLLVAN-----YLNITEMLDYLTETLANRIKN-KSVE 74 (136)
Q Consensus 6 s~~L~kViewC~-H~~~~~~~~~~l----~~Fl~~ld~~~L~~Li~AAn-----yL~I~~Ll~l~c~~IA~~ikg-Kt~e 74 (136)
..-|+.+++.+. +.+. .-..+++ ..+-......++.+++...+ .++...++.+..+.....-.. .+.+
T Consensus 7 ~~el~~~F~~fD~d~~G-~i~~~el~~~lr~lg~~~t~~el~~~~~~~D~dg~g~I~~~eF~~l~~~~~~~~~~~~~~~~ 85 (151)
T KOG0027|consen 7 ILELKEAFQLFDKDGDG-KISVEELGAVLRSLGQNPTEEELRDLIKEIDLDGDGTIDFEEFLDLMEKLGEEKTDEEASSE 85 (151)
T ss_pred HHHHHHHHHHHCCCCCC-cccHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCCCCeEcHHHHHHHHHhhhcccccccccHH
Confidence 345778888887 4432 1122334 22222225678888888887 688999988888776554444 3677
Q ss_pred HHHHHcCCCC-C----CCHHHHHHHh
Q 045340 75 YIRKFFRIEN-N----FMPEEEEAAR 95 (136)
Q Consensus 75 EIR~~fgI~~-D----~T~EEee~ir 95 (136)
++|+.|.+-+ | .|.+|...+-
T Consensus 86 el~eaF~~fD~d~~G~Is~~el~~~l 111 (151)
T KOG0027|consen 86 ELKEAFRVFDKDGDGFISASELKKVL 111 (151)
T ss_pred HHHHHHHHHccCCCCcCcHHHHHHHH
Confidence 8998888644 3 6777776653
No 86
>PF13010 pRN1_helical: Primase helical domain; PDB: 1RO0_A 1RNI_A 1RO2_A 3M1M_A.
Probab=22.44 E-value=45 Score=24.90 Aligned_cols=14 Identities=50% Similarity=0.643 Sum_probs=5.7
Q ss_pred HHhcCCCHHHHHHH
Q 045340 66 NRIKNKSVEYIRKF 79 (136)
Q Consensus 66 ~~ikgKt~eEIR~~ 79 (136)
++.+|||+|.||.-
T Consensus 24 drfkGKtveair~e 37 (135)
T PF13010_consen 24 DRFKGKTVEAIREE 37 (135)
T ss_dssp -------HHHHHHH
T ss_pred ccccCchHHHHHHH
Confidence 46789999999953
No 87
>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=22.11 E-value=60 Score=19.17 Aligned_cols=17 Identities=18% Similarity=0.176 Sum_probs=11.2
Q ss_pred HhcCCCHHHHHHHcCCC
Q 045340 67 RIKNKSVEYIRKFFRIE 83 (136)
Q Consensus 67 ~ikgKt~eEIR~~fgI~ 83 (136)
.+.|+|..||-+.+|++
T Consensus 23 ~~~g~s~~eIa~~l~~s 39 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGIS 39 (54)
T ss_dssp HTS---HHHHHHHCTS-
T ss_pred HHHCcCHHHHHHHHCcC
Confidence 56799999999999976
No 88
>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=21.38 E-value=1e+02 Score=20.59 Aligned_cols=37 Identities=22% Similarity=0.337 Sum_probs=23.8
Q ss_pred HHHHHHhhhhhchHHHHHHHHHHHHHHhcCCC--HHHHHHHcCCCCCCC
Q 045340 41 LKEMLLVANYLNITEMLDYLTETLANRIKNKS--VEYIRKFFRIENNFM 87 (136)
Q Consensus 41 L~~Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt--~eEIR~~fgI~~D~T 87 (136)
...|+.+|..+++... .+.|-. .+++++.||++.+..
T Consensus 75 ~~~l~l~a~~~Glg~~----------~~~~~~~~~~~~~~~l~l~~~~~ 113 (122)
T cd02062 75 AQNILLAAHALGLGSC----------WIGGLDLVEEELRELLGIPEGYE 113 (122)
T ss_pred HHHHHHHHHHcCCCch----------hcCCcccchHHHHHHhCcCCCcE
Confidence 3455666666665432 334444 899999999997643
No 89
>PRK03094 hypothetical protein; Provisional
Probab=21.32 E-value=60 Score=22.23 Aligned_cols=14 Identities=7% Similarity=-0.002 Sum_probs=11.1
Q ss_pred HhcCCCHHHHHHHc
Q 045340 67 RIKNKSVEYIRKFF 80 (136)
Q Consensus 67 ~ikgKt~eEIR~~f 80 (136)
-..|||+|||.+..
T Consensus 62 ~A~G~TaeEI~~~v 75 (80)
T PRK03094 62 TASGLTADEICQQV 75 (80)
T ss_pred EcCCCCHHHHHHHH
Confidence 34699999998765
No 90
>PF13700 DUF4158: Domain of unknown function (DUF4158)
Probab=21.10 E-value=1.1e+02 Score=22.63 Aligned_cols=33 Identities=18% Similarity=0.074 Sum_probs=24.1
Q ss_pred CHHHHHHHcCCCCCCCHHHHHHH----hhhhchhhhcc
Q 045340 72 SVEYIRKFFRIENNFMPEEEEAA----RNDSTKISCIF 105 (136)
Q Consensus 72 t~eEIR~~fgI~~D~T~EEee~i----r~en~w~~~~~ 105 (136)
|++|..+++++|. ||++|.... ..|-.|+....
T Consensus 3 s~~e~~~l~~~P~-l~~~el~~~ftLs~~d~~~i~~~r 39 (166)
T PF13700_consen 3 SEEEREALYSLPR-LSEEELIRYFTLSPEDLELINSRR 39 (166)
T ss_pred CHHHHHHhcCCCC-CCHHHHHHHhCCCHHHHHHHhccc
Confidence 7889999999998 888777654 34555666543
No 91
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=20.97 E-value=1.9e+02 Score=18.45 Aligned_cols=33 Identities=15% Similarity=0.255 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCC
Q 045340 55 EMLDYLTETLANRIKNKSVEYIRKFFRIENNFM 87 (136)
Q Consensus 55 ~Ll~l~c~~IA~~ikgKt~eEIR~~fgI~~D~T 87 (136)
..++..++++...-..-|..||.+.||+.+--|
T Consensus 10 ~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~t 42 (65)
T PF01726_consen 10 EVLEFIREYIEENGYPPTVREIAEALGLKSTST 42 (65)
T ss_dssp HHHHHHHHHHHHHSS---HHHHHHHHTSSSHHH
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHH
Confidence 456777777777655678899999999984433
No 92
>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=20.78 E-value=81 Score=28.22 Aligned_cols=40 Identities=23% Similarity=0.293 Sum_probs=28.8
Q ss_pred HHhhhhhchHHHHHHHHHHHHHHhcCC--CHHHHHHHcCCCCC
Q 045340 45 LLVANYLNITEMLDYLTETLANRIKNK--SVEYIRKFFRIENN 85 (136)
Q Consensus 45 i~AAnyL~I~~Ll~l~c~~IA~~ikgK--t~eEIR~~fgI~~D 85 (136)
.+|+|||+++. =.-.+..|...+.|- ||.|+.+.|--..+
T Consensus 377 ~La~nYL~~~~-~h~L~~eie~l~~~~~~tPA~V~e~lm~~~~ 418 (457)
T KOG0743|consen 377 TLASNYLGIEE-DHRLFDEIERLIEETEVTPAQVAEELMKNKN 418 (457)
T ss_pred HHHHHhcCCCC-CcchhHHHHHHhhcCccCHHHHHHHHhhccc
Confidence 46899999976 333455666677774 89999988876654
No 93
>cd00336 Ribosomal_L22 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.
Probab=20.51 E-value=98 Score=21.35 Aligned_cols=21 Identities=19% Similarity=0.162 Sum_probs=17.3
Q ss_pred HHHHHHhcCCCHHHHHHHcCC
Q 045340 62 ETLANRIKNKSVEYIRKFFRI 82 (136)
Q Consensus 62 ~~IA~~ikgKt~eEIR~~fgI 82 (136)
..+|+.|+|++.++-..++.-
T Consensus 16 ~~v~~~Irg~~v~~A~~~L~~ 36 (105)
T cd00336 16 RLVARLIRGMSVDEALAQLEF 36 (105)
T ss_pred HHHHHHHcCCcHHHHHHHHHh
Confidence 568999999999997777664
No 94
>PF15628 RRM_DME: RRM in Demeter
Probab=20.27 E-value=85 Score=22.53 Aligned_cols=20 Identities=20% Similarity=0.293 Sum_probs=16.8
Q ss_pred HHHHHHhcCCCHHHHHHHcC
Q 045340 62 ETLANRIKNKSVEYIRKFFR 81 (136)
Q Consensus 62 ~~IA~~ikgKt~eEIR~~fg 81 (136)
-.|+...||+|.+||.+.|-
T Consensus 57 tsv~SIfrGls~~eIq~cF~ 76 (103)
T PF15628_consen 57 TSVSSIFRGLSREEIQQCFW 76 (103)
T ss_pred CcHHHHhcccCHHHHHHHHh
Confidence 35778889999999998885
No 95
>COG2219 PRI2 Eukaryotic-type DNA primase, large subunit [DNA replication, recombination, and repair]
Probab=20.25 E-value=2.1e+02 Score=24.64 Aligned_cols=61 Identities=20% Similarity=0.193 Sum_probs=38.4
Q ss_pred HHHHHHHHhc--CCCHHHHHHHcCCCCCCCHHH-HHHHhhhhc--hhhhcccccccchhhccCCch
Q 045340 60 LTETLANRIK--NKSVEYIRKFFRIENNFMPEE-EEAARNDST--KISCIFLSGFCPILAFLGPGC 120 (136)
Q Consensus 60 ~c~~IA~~ik--gKt~eEIR~~fgI~~D~T~EE-ee~ir~en~--w~~~~~~~~~~~~~~~~~~~~ 120 (136)
+-..++.-+. |.+++|++++|....||..+= .-+||.-.. =--+-|+.+.|.+..+++-.|
T Consensus 262 ~R~al~sFL~~ig~~~deiv~~fr~~pdFdee~tryqirHi~G~~~~~~ey~~p~C~~m~~~g~lC 327 (363)
T COG2219 262 ARFALTSFLSNIGLSVDEIVELFRNSPDFDEEITRYQIRHIIGEEGNRTEYTPPSCDTMRSYGHLC 327 (363)
T ss_pred HHHHHHHHHHhcCCChhHHHHHhccCCCcchhhhhhhhheeecccCCCCCCCCCCchhHhhcCCcc
Confidence 3345555554 899999999999999986543 224444322 112334556788888777455
No 96
>KOG0783 consensus Uncharacterized conserved protein, contains ankyrin and BTB/POZ domains [Function unknown]
Probab=20.14 E-value=3.6e+02 Score=26.71 Aligned_cols=66 Identities=20% Similarity=0.130 Sum_probs=40.1
Q ss_pred CcHHHHHHHHHhhcCCCCCCCCchHHHhhccCC-ChhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHH
Q 045340 4 NYSRWKSKGVRDCDHSSTSDGTSEDMVEFGKGK-SNDELKEMLLVANYLNITEMLDYLTETLANRIKNKSVEYIR 77 (136)
Q Consensus 4 V~s~~L~kViewC~H~~~~~~~~~~l~~Fl~~l-d~~~L~~Li~AAnyL~I~~Ll~l~c~~IA~~ikgKt~eEIR 77 (136)
++++.|+-|+.|..-.+. .+|++.. ..+.+|+++..|+-|=|..|-+.|-+.+-+++.=|+..+|-
T Consensus 758 ~~~e~m~ivLdylYs~d~--------~~~~k~~~~~dF~~~il~iaDqlli~~Lk~Ice~~ll~kl~lk~~~~ll 824 (1267)
T KOG0783|consen 758 LTVEHMSIVLDYLYSDDK--------VELFKDLKESDFMFEILSIADQLLILELKSICEQSLLRKLNLKTLPTLL 824 (1267)
T ss_pred chHHHHHHHHHHHHccch--------HHHHhccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchHHHH
Confidence 346777777777651111 3344432 34557777777777777777777777777777666655443
No 97
>TIGR01038 L22_arch ribosomal protein L22(archaeal)/L17(eukaryotic/archaeal). This model describes the ribosomal protein of the eukaryotic cytosol and of the Archaea, variously designated as L17, L22, and L23. The corresponding bacterial homolog, described by a separate model, is designated L22.
Probab=20.10 E-value=1.1e+02 Score=23.24 Aligned_cols=21 Identities=19% Similarity=0.392 Sum_probs=18.1
Q ss_pred HHHHHHHhcCCCHHHHHHHcC
Q 045340 61 TETLANRIKNKSVEYIRKFFR 81 (136)
Q Consensus 61 c~~IA~~ikgKt~eEIR~~fg 81 (136)
+..||+.|+||+.++-..++.
T Consensus 26 ~r~va~~IrG~~v~~A~~~L~ 46 (150)
T TIGR01038 26 ARETARAIRGMELDKARKYLE 46 (150)
T ss_pred HHHHHHHHcCCcHHHHHHHHH
Confidence 467899999999999888886
No 98
>PRK10828 putative oxidoreductase; Provisional
Probab=20.06 E-value=59 Score=24.40 Aligned_cols=36 Identities=11% Similarity=0.087 Sum_probs=22.1
Q ss_pred HHHHHhhhhhchHHHHHHHHHHHHHHhcC--CCHHHHHHHcCCCCCCC
Q 045340 42 KEMLLVANYLNITEMLDYLTETLANRIKN--KSVEYIRKFFRIENNFM 87 (136)
Q Consensus 42 ~~Li~AAnyL~I~~Ll~l~c~~IA~~ikg--Kt~eEIR~~fgI~~D~T 87 (136)
-.|+.||.-+|+-+..- .| ...+++|+.|||+.++.
T Consensus 116 ~nl~LaA~a~GlGs~w~----------~~~~~~~~~~~~~L~ip~~~~ 153 (183)
T PRK10828 116 MAMQMAAVAQGFNGIWR----------SGAWTESPVVREAFGCREQDK 153 (183)
T ss_pred HHHHHHHHHCCCCeEee----------cCCCccCHHHHHHcCCCCCCE
Confidence 35556666666643321 12 24578999999997753
Done!