Query 033900
Match_columns 109
No_of_seqs 144 out of 740
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 07:34:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033900.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033900hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05090 hypothetical protein; 99.9 4.6E-25 1E-29 153.1 9.4 77 29-106 1-83 (95)
2 PF02594 DUF167: Uncharacteris 99.9 5.8E-24 1.3E-28 142.3 7.3 69 38-106 2-77 (77)
3 PRK01310 hypothetical protein; 99.9 1.7E-23 3.7E-28 147.3 9.1 76 30-106 3-89 (104)
4 KOG3276 Uncharacterized conser 99.9 3E-23 6.6E-28 149.4 9.4 100 1-105 1-106 (125)
5 PRK00647 hypothetical protein; 99.9 3.4E-23 7.3E-28 144.3 8.3 70 37-106 3-78 (96)
6 PRK01530 hypothetical protein; 99.9 4.9E-23 1.1E-27 145.3 8.6 71 37-107 11-91 (105)
7 COG1872 Uncharacterized conser 99.9 9E-23 2E-27 143.6 7.2 77 29-106 3-87 (102)
8 TIGR00251 conserved hypothetic 99.9 7.3E-22 1.6E-26 135.2 8.7 70 33-106 2-79 (87)
9 PRK04021 hypothetical protein; 99.8 4.7E-21 1E-25 132.3 9.0 72 32-107 2-81 (92)
10 PF01187 MIF: Macrophage migra 91.5 0.78 1.7E-05 31.7 5.8 61 41-102 36-101 (114)
11 PF09581 Spore_III_AF: Stage I 89.5 0.98 2.1E-05 33.3 5.2 56 41-98 124-187 (188)
12 PTZ00397 macrophage migration 83.3 9.6 0.00021 26.1 7.2 60 41-101 38-102 (116)
13 KOG1759 Macrophage migration i 72.2 9 0.0002 27.8 4.5 58 41-99 37-99 (115)
14 PF08968 DUF1885: Domain of un 68.4 5.8 0.00013 29.3 2.9 29 60-89 81-114 (130)
15 PTZ00450 macrophage migration 65.9 4 8.7E-05 28.7 1.6 61 40-101 37-102 (113)
16 COG1451 Predicted metal-depend 64.8 15 0.00033 28.6 4.8 47 39-89 9-55 (223)
17 cd02552 PseudoU_synth_TruD_lik 53.3 20 0.00044 28.1 3.7 44 60-106 30-82 (232)
18 PF01361 Tautomerase: Tautomer 52.5 29 0.00062 20.8 3.6 25 78-102 21-45 (60)
19 cd02576 PseudoU_synth_ScPUS7 P 49.0 25 0.00055 29.0 3.8 43 61-106 29-80 (371)
20 PF04969 CS: CS domain; Inter 48.8 49 0.0011 19.8 4.3 37 32-69 5-43 (79)
21 cd00491 4Oxalocrotonate_Tautom 48.7 38 0.00083 19.8 3.7 25 77-101 20-44 (58)
22 TIGR00013 taut 4-oxalocrotonat 47.3 36 0.00078 20.3 3.5 26 76-101 20-45 (63)
23 PRK00745 4-oxalocrotonate taut 45.7 34 0.00075 20.4 3.2 25 77-101 21-45 (62)
24 cd02575 PseudoU_synth_EcTruD P 45.0 32 0.00069 27.6 3.7 44 59-105 23-75 (253)
25 PRK01964 4-oxalocrotonate taut 44.7 36 0.00079 20.7 3.2 26 76-101 20-45 (64)
26 PRK02220 4-oxalocrotonate taut 42.5 44 0.00095 19.9 3.3 24 77-100 21-44 (61)
27 cd02577 PSTD1 PSTD1: Pseudouri 40.7 38 0.00082 27.9 3.6 44 60-106 24-76 (319)
28 cd06406 PB1_P67 A PB1 domain i 40.7 33 0.00071 23.3 2.7 37 64-102 12-48 (80)
29 PF12685 SpoIIIAH: SpoIIIAH-li 40.6 62 0.0013 24.4 4.5 46 52-97 150-195 (196)
30 PRK02289 4-oxalocrotonate taut 39.3 60 0.0013 19.7 3.6 25 77-101 21-45 (60)
31 PF01142 TruD: tRNA pseudourid 39.2 59 0.0013 26.8 4.5 45 59-106 42-95 (378)
32 cd06463 p23_like Proteins cont 38.5 68 0.0015 19.2 3.8 33 38-70 6-38 (84)
33 COG0245 IspF 2C-methyl-D-eryth 38.4 37 0.00081 25.8 3.0 40 69-108 101-140 (159)
34 PF01187 MIF: Macrophage migra 38.1 68 0.0015 21.9 4.1 32 75-106 17-51 (114)
35 smart00760 Bac_DnaA_C Bacteria 37.6 16 0.00035 22.3 0.8 19 78-96 3-21 (60)
36 PF14552 Tautomerase_2: Tautom 37.3 43 0.00093 22.3 2.9 43 59-101 26-73 (82)
37 TIGR00094 tRNA_TruD_broad tRNA 34.3 59 0.0013 26.9 3.8 34 60-96 41-74 (387)
38 PRK00984 truD tRNA pseudouridi 34.3 55 0.0012 27.1 3.6 43 59-104 40-91 (341)
39 PF12116 SpoIIID: Stage III sp 32.9 15 0.00033 25.2 0.1 20 77-96 18-37 (82)
40 PF02738 Ald_Xan_dh_C2: Molybd 32.5 82 0.0018 27.1 4.5 41 59-99 328-368 (547)
41 PHA02564 V virion protein; Pro 31.7 52 0.0011 24.4 2.8 30 65-95 73-102 (141)
42 PRK01271 4-oxalocrotonate taut 30.6 83 0.0018 20.7 3.4 24 78-101 23-46 (76)
43 PF02542 YgbB: YgbB family; I 30.2 1E+02 0.0022 23.3 4.1 35 67-101 99-133 (157)
44 PF08299 Bac_DnaA_C: Bacterial 27.3 25 0.00055 22.4 0.4 19 78-96 3-21 (70)
45 KOG4079 Putative mitochondrial 27.1 45 0.00098 25.4 1.8 21 72-92 91-111 (169)
46 TIGR01215 minE cell division t 26.1 83 0.0018 21.0 2.8 24 77-100 42-65 (81)
47 cd00298 ACD_sHsps_p23-like Thi 25.8 1.4E+02 0.003 17.1 3.5 37 38-74 6-42 (80)
48 PF01257 2Fe-2S_thioredx: Thio 25.6 28 0.00061 25.1 0.4 20 77-96 30-49 (145)
49 PRK06290 aspartate aminotransf 25.4 89 0.0019 25.7 3.4 28 61-88 376-403 (410)
50 PF14804 Jag_N: Jag N-terminus 25.3 1.3E+02 0.0028 18.5 3.3 26 74-99 4-29 (52)
51 TIGR01958 nuoE_fam NADH-quinon 24.6 33 0.00072 24.8 0.7 20 77-96 33-52 (148)
52 cd06411 PB1_p51 The PB1 domain 24.2 1.7E+02 0.0038 19.7 4.1 37 63-101 7-43 (78)
53 PF03776 MinE: Septum formatio 24.2 1.3E+02 0.0029 19.3 3.4 24 77-100 31-54 (70)
54 PF05046 Img2: Mitochondrial l 23.9 2.1E+02 0.0045 19.0 4.4 65 28-107 2-73 (87)
55 PF10410 DnaB_bind: DnaB-helic 23.6 77 0.0017 18.6 2.1 22 74-95 38-59 (59)
56 PRK00084 ispF 2-C-methyl-D-ery 23.6 92 0.002 23.6 2.9 34 69-102 103-136 (159)
57 PF09098 Dehyd-heme_bind: Quin 23.4 56 0.0012 25.1 1.7 26 71-96 50-75 (167)
58 cd00554 MECDP_synthase MECDP_s 23.4 98 0.0021 23.2 3.0 33 71-103 102-134 (153)
59 PF06138 Chordopox_E11: Chordo 23.3 1.7E+02 0.0037 21.7 4.2 42 59-100 11-60 (130)
60 PRK00296 minE cell division to 23.2 1.1E+02 0.0025 20.6 3.1 26 75-100 41-66 (86)
61 PHA03001 putative virion core 23.2 1.9E+02 0.0042 21.4 4.4 42 59-100 11-59 (132)
62 PF00046 Homeobox: Homeobox do 23.1 40 0.00087 19.7 0.7 21 76-96 25-45 (57)
63 KOG0676 Actin and related prot 22.4 93 0.002 26.4 3.0 30 63-92 100-130 (372)
64 PRK07539 NADH dehydrogenase su 21.9 40 0.00087 24.5 0.7 20 77-96 39-58 (154)
65 PF00550 PP-binding: Phosphopa 21.8 69 0.0015 18.9 1.6 19 78-96 1-19 (67)
66 cd00086 homeodomain Homeodomai 21.3 38 0.00082 19.5 0.4 22 75-96 24-45 (59)
67 COG0770 MurF UDP-N-acetylmuram 21.2 39 0.00084 29.2 0.5 57 42-99 253-309 (451)
68 TIGR00151 ispF 2C-methyl-D-ery 21.1 1.1E+02 0.0024 23.0 2.9 34 69-102 100-133 (155)
69 COG3382 Solo B3/4 domain (OB-f 21.1 3.2E+02 0.0069 21.9 5.6 64 26-89 150-213 (229)
70 COG1905 NuoE NADH:ubiquinone o 20.8 63 0.0014 24.5 1.5 23 74-96 39-61 (160)
71 COG1942 Uncharacterized protei 20.6 1.8E+02 0.0038 18.9 3.4 40 63-102 4-47 (69)
72 cd06467 p23_NUDC_like p23_like 20.1 2.3E+02 0.005 17.5 4.0 36 32-68 3-39 (85)
73 PF08381 BRX: Transcription fa 20.1 1.6E+02 0.0035 18.9 3.1 22 30-52 5-26 (59)
No 1
>PRK05090 hypothetical protein; Validated
Probab=99.92 E-value=4.6e-25 Score=153.14 Aligned_cols=77 Identities=21% Similarity=0.320 Sum_probs=72.9
Q ss_pred CcceEeeCCCeEEEEEEEecCCCccccccccCCeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE------EEEeEE
Q 033900 29 PSCIRLVPPSSVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV------ESVQVF 102 (109)
Q Consensus 29 p~~i~~~~~g~v~L~V~VkP~Ak~~~I~g~~~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~------~~~~~~ 102 (109)
|.|+++.++ +++|+|+|+|+|++++|.++++++|+|+|+|||+|||||++|++|||+.|+||+|+|+ .|.|++
T Consensus 1 ~~~~~~~~~-~~~l~i~V~P~A~~~~i~~~~~~~lkv~v~ApPveGkAN~ali~~LAk~l~v~ks~I~i~~G~tsr~K~v 79 (95)
T PRK05090 1 MSAVTWDGD-GLVLRLYIQPKASRDQIVGLHGDELKVAITAPPVDGQANAHLLKFLAKQFRVAKSQVVIEKGELGRHKQV 79 (95)
T ss_pred CCceEEeCC-eEEEEEEEeeCCCcceeccccCCEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEEEecCCCCceEE
Confidence 578888775 8999999999999999999999999999999999999999999999999999999999 789999
Q ss_pred Eeec
Q 033900 103 FLNG 106 (109)
Q Consensus 103 ~~~g 106 (109)
.|.|
T Consensus 80 ~I~~ 83 (95)
T PRK05090 80 RIIN 83 (95)
T ss_pred EEcC
Confidence 9876
No 2
>PF02594 DUF167: Uncharacterised ACR, YggU family COG1872; InterPro: IPR003746 This entry describes proteins of unknown function. Structures for two of these proteins, YggU from Escherichia coli and MTH637 from the archaea Methanobacterium thermoautotrophicum, have been determined; they have a core 2-layer alpha/beta structure consisting of beta(2)-loop-alpha-beta(2)-alpha [, ].; PDB: 1YH5_A 1N91_A 1JRM_A.
Probab=99.90 E-value=5.8e-24 Score=142.28 Aligned_cols=69 Identities=26% Similarity=0.515 Sum_probs=60.4
Q ss_pred CeEEEEEEEecCCCccccccccCC-eEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE------EEEeEEEeec
Q 033900 38 SSVSITIHAKPGSKSCSITDVSDE-AVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV------ESVQVFFLNG 106 (109)
Q Consensus 38 g~v~L~V~VkP~Ak~~~I~g~~~~-~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~------~~~~~~~~~g 106 (109)
++++|.|+|+|+|++++|.+++++ .|+|+|+|||+||+||+||++|||+.|+||+|+|+ .|.|++.|.|
T Consensus 2 ~~~~l~v~V~P~ak~~~i~~~~~~~~l~i~v~app~~GkAN~ali~~La~~l~v~ks~i~i~~G~~Sr~K~v~i~~ 77 (77)
T PF02594_consen 2 DGVILSVRVKPGAKRNAIVGVEGDGALKIRVTAPPVDGKANKALIRFLAKALGVPKSDIEIVSGHTSRNKVVRIEN 77 (77)
T ss_dssp TEEEEEEECEBSSSS-EEEEE-TTT-EEEEBSTTCCCCCHHHHHHHHHHHHCT--TTCEEECC-CCCSEEEEEEE-
T ss_pred CeEEEEEEEEeCCCccccccccCceEEEEEEecCCCcChhHHHHHHHHHHHhCCCcccEEEEecCCCCceEEEEeC
Confidence 589999999999999999999996 99999999999999999999999999999999999 7899998875
No 3
>PRK01310 hypothetical protein; Validated
Probab=99.90 E-value=1.7e-23 Score=147.27 Aligned_cols=76 Identities=18% Similarity=0.326 Sum_probs=69.9
Q ss_pred cceEeeCCCeEEEEEEEecCCCccccccccC-----CeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE------EE
Q 033900 30 SCIRLVPPSSVSITIHAKPGSKSCSITDVSD-----EAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV------ES 98 (109)
Q Consensus 30 ~~i~~~~~g~v~L~V~VkP~Ak~~~I~g~~~-----~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~------~~ 98 (109)
.+|++.++ +++|.|+|+|+|++++|.++++ +.|+|+|+|||+|||||+||++|||+.|+||+|+|+ .|
T Consensus 3 ~~~~~~~~-~~~i~v~V~P~A~~~~i~g~~~~~~g~~~lkv~v~apPv~GkAN~ali~~LA~~l~v~ks~I~iv~G~tsR 81 (104)
T PRK01310 3 EPWRYSAD-GLRLAVRLTPRGGRDAIDGIETLADGRAVLKVRVRAVPEGGEANRALIELLAKALGVPKSSVRLLSGATSR 81 (104)
T ss_pred CceEECCC-cEEEEEEEeeCCCcceeccccccCCCccEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEEEecCCCC
Confidence 46777776 8999999999999999999864 389999999999999999999999999999999999 78
Q ss_pred EeEEEeec
Q 033900 99 VQVFFLNG 106 (109)
Q Consensus 99 ~~~~~~~g 106 (109)
.|++.|.|
T Consensus 82 ~K~v~I~~ 89 (104)
T PRK01310 82 LKQLRIDG 89 (104)
T ss_pred ceEEEEeC
Confidence 99999987
No 4
>KOG3276 consensus Uncharacterized conserved protein, contains YggU domain [Function unknown]
Probab=99.89 E-value=3e-23 Score=149.39 Aligned_cols=100 Identities=44% Similarity=0.716 Sum_probs=91.4
Q ss_pred CCCcccCcccccCCCCccccCCCCCCCCCcceEeeCCCeEEEEEEEecCCCccccccccCCeEEEEEeCCCCCChhHHHH
Q 033900 1 MAPAKKGKSKAKSAGSTQSKIKTNDENLPSCIRLVPPSSVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAAL 80 (109)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~i~~~~~g~v~L~V~VkP~Ak~~~I~g~~~~~L~I~V~ApPvdGkAN~aL 80 (109)
|.|+++|++..+.+.++ .+...+|+||+.+..|.+.|.|+++|||++++|+++.++.+.|.|.|||.+|+||+||
T Consensus 1 i~pkk~g~s~k~~~t~~-----~~~~~~p~~i~~d~~g~V~i~IhakpgaK~s~It~v~~e~V~V~IaApp~eGeANaeL 75 (125)
T KOG3276|consen 1 VMPKKKGKSTKGAETSK-----VDDKPVPPCISVDTGGLVQIAIHAKPGAKQSAITDVGDEAVGVAIAAPPREGEANAEL 75 (125)
T ss_pred CccccccccccccccCC-----CccCCCCCceEecCCCeEEEEEEecCCccccceeeccccccceEEecCCccchhhHHH
Confidence 67999999999988874 5667788899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCceE------EEEeEEEee
Q 033900 81 LEYMSSLIHVSVGEFV------ESVQVFFLN 105 (109)
Q Consensus 81 i~~LAk~L~Vpks~I~------~~~~~~~~~ 105 (109)
++||++.||+++|+++ +|-|++.|.
T Consensus 76 l~ylskvLgLRksdv~ldkG~kSrsKvv~i~ 106 (125)
T KOG3276|consen 76 LEYLSKVLGLRKSDVTLDKGWKSRSKVVVIE 106 (125)
T ss_pred HHHHHHHhhhhhhheeecccccccceEEEEe
Confidence 9999999999999999 666666654
No 5
>PRK00647 hypothetical protein; Validated
Probab=99.89 E-value=3.4e-23 Score=144.29 Aligned_cols=70 Identities=11% Similarity=0.258 Sum_probs=66.0
Q ss_pred CCeEEEEEEEecCCCccccccccCCeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE------EEEeEEEeec
Q 033900 37 PSSVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV------ESVQVFFLNG 106 (109)
Q Consensus 37 ~g~v~L~V~VkP~Ak~~~I~g~~~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~------~~~~~~~~~g 106 (109)
++.+.|.|+|+|+|++++|.+++++.|+|+|+|||+|||||+||++|||+.|+||+|+|+ .|.|++.|.+
T Consensus 3 ~~~~~l~V~V~P~Ak~~~I~g~~~~~Lkvrv~ApPvdGKAN~ali~~LAk~l~vpks~I~Iv~G~tSr~K~v~i~~ 78 (96)
T PRK00647 3 EGFWILEVKVTPKARENKIVGFEGGILKVRVTEVPEKGKANDAVIALLAKFLSLPKRDVTLIAGETSRKKKVLLPR 78 (96)
T ss_pred CCcEEEEEEEeeCCCcceeccccCCEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEEEecCCCCceEEEECh
Confidence 357999999999999999999999999999999999999999999999999999999999 7888888754
No 6
>PRK01530 hypothetical protein; Reviewed
Probab=99.89 E-value=4.9e-23 Score=145.33 Aligned_cols=71 Identities=17% Similarity=0.336 Sum_probs=66.7
Q ss_pred CCeEEEEEEEecCCCcccccccc----CCeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE------EEEeEEEeec
Q 033900 37 PSSVSITIHAKPGSKSCSITDVS----DEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV------ESVQVFFLNG 106 (109)
Q Consensus 37 ~g~v~L~V~VkP~Ak~~~I~g~~----~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~------~~~~~~~~~g 106 (109)
.+++.|.|+|+|+|++++|.+++ ++.|+|+|+|||+|||||+||++|||+.|+||+|+|+ .|.|++.|.|
T Consensus 11 ~~gv~l~V~V~P~Akk~~i~g~~~~~~~~~Lki~v~ApPvdGkAN~ali~~LAk~l~v~ks~I~IvsG~tSR~K~i~I~g 90 (105)
T PRK01530 11 SHQALLNLKVKPNAKQNLISNFVIINNIPYLKLSIKAIPEQGKANEEIINYLAKEWKLSRSNIEIIKGHTHSLKTILIKN 90 (105)
T ss_pred CCcEEEEEEEeeCCCcccccceeccCCCCEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEEEecCCCCceEEEEeC
Confidence 35899999999999999999885 4799999999999999999999999999999999999 7999999988
Q ss_pred c
Q 033900 107 F 107 (109)
Q Consensus 107 ~ 107 (109)
.
T Consensus 91 ~ 91 (105)
T PRK01530 91 I 91 (105)
T ss_pred C
Confidence 5
No 7
>COG1872 Uncharacterized conserved protein [Function unknown]
Probab=99.88 E-value=9e-23 Score=143.56 Aligned_cols=77 Identities=22% Similarity=0.405 Sum_probs=71.1
Q ss_pred CcceEeeCCCeEEEEEEEecCCCccccccccCCe--EEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE------EEEe
Q 033900 29 PSCIRLVPPSSVSITIHAKPGSKSCSITDVSDEA--VGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV------ESVQ 100 (109)
Q Consensus 29 p~~i~~~~~g~v~L~V~VkP~Ak~~~I~g~~~~~--L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~------~~~~ 100 (109)
+.+++..++ ++.|+|+|+|+|+++.|.++++++ |+|+|++||++||||++|++|||+.|++|+|+|+ .|.|
T Consensus 3 ~~~~~~~~~-~~~l~V~V~P~a~~~~i~g~~~~~~~Lkv~i~apP~~GKAN~~li~~Lak~~~v~kS~V~ivsGetsR~K 81 (102)
T COG1872 3 ESAVKELDD-GVLLRVRVKPKAKRDSIVGLDEWRKRLKVRITAPPVDGKANEELIKFLAKTFGVPKSSVEIVSGETSRLK 81 (102)
T ss_pred hhhHhhcCC-ceEEEEEECCCCccCcccceecCcceEEEEEecCCCCcchhHHHHHHHHHHhCCCcccEEEEecCcccce
Confidence 456677776 899999999999999999998876 9999999999999999999999999999999999 7899
Q ss_pred EEEeec
Q 033900 101 VFFLNG 106 (109)
Q Consensus 101 ~~~~~g 106 (109)
++.|-|
T Consensus 82 ~v~i~~ 87 (102)
T COG1872 82 TVLIKN 87 (102)
T ss_pred EEEecC
Confidence 998876
No 8
>TIGR00251 conserved hypothetical protein TIGR00251.
Probab=99.87 E-value=7.3e-22 Score=135.18 Aligned_cols=70 Identities=23% Similarity=0.365 Sum_probs=64.8
Q ss_pred EeeCCCeEEEEEEEecCCCccccccccC--CeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE------EEEeEEEe
Q 033900 33 RLVPPSSVSITIHAKPGSKSCSITDVSD--EAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV------ESVQVFFL 104 (109)
Q Consensus 33 ~~~~~g~v~L~V~VkP~Ak~~~I~g~~~--~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~------~~~~~~~~ 104 (109)
++.++ +++|.|+|+|+|++++|.++++ +.|+|+|+|||+|||||+||++|||+.|+| +|+ .|.|++.|
T Consensus 2 ~~~~~-g~~l~v~V~P~A~~~~i~g~~~~~~~Lki~v~ApP~~GkAN~ali~~La~~l~v---~I~i~~G~tsR~K~v~I 77 (87)
T TIGR00251 2 RENDD-GLLIRIYVQPKASKDSIVGYNEWRKRVEVKIKAPPVEGKANRELIKFFGEIFGV---DVEIVSGELSRQKTIKI 77 (87)
T ss_pred eEeCC-eEEEEEEEeeCCCcceeccccCCCCeEEEEEecCCCCChHHHHHHHHHHHHhCc---eEEEEecCCCCceEEEE
Confidence 45554 8999999999999999999999 899999999999999999999999999999 676 78999999
Q ss_pred ec
Q 033900 105 NG 106 (109)
Q Consensus 105 ~g 106 (109)
.|
T Consensus 78 ~~ 79 (87)
T TIGR00251 78 IN 79 (87)
T ss_pred eC
Confidence 87
No 9
>PRK04021 hypothetical protein; Reviewed
Probab=99.85 E-value=4.7e-21 Score=132.27 Aligned_cols=72 Identities=24% Similarity=0.439 Sum_probs=65.2
Q ss_pred eEeeCCCeEEEEEEEecCCCccccccccC--CeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE------EEEeEEE
Q 033900 32 IRLVPPSSVSITIHAKPGSKSCSITDVSD--EAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV------ESVQVFF 103 (109)
Q Consensus 32 i~~~~~g~v~L~V~VkP~Ak~~~I~g~~~--~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~------~~~~~~~ 103 (109)
+++..+ ++.|.|+|+|+|++++|.++++ +.|+|+|+|||+||+||+||++|||+.|++ +|+ .|.|++.
T Consensus 2 ~~~~~~-~v~l~v~v~P~a~~~~i~g~~~~~~~lkv~v~apP~~GkAN~ali~~LAk~l~~---~I~I~~G~~sr~K~v~ 77 (92)
T PRK04021 2 LKETKE-GVILQVYVQPKAKENEIEGVDEWRGRLKVKIKAPPVKGKANKELVKFFSKLLGA---EVEIIRGETSREKDLL 77 (92)
T ss_pred eEEeCC-cEEEEEEEeeCCCcceEccccCCCCEEEEEEecCCCCChHHHHHHHHHHHHhCC---CEEEEecCCcCceEEE
Confidence 567675 8999999999999999998865 899999999999999999999999999998 465 7899999
Q ss_pred eecc
Q 033900 104 LNGF 107 (109)
Q Consensus 104 ~~g~ 107 (109)
|.|.
T Consensus 78 i~g~ 81 (92)
T PRK04021 78 VKGI 81 (92)
T ss_pred EecC
Confidence 9874
No 10
>PF01187 MIF: Macrophage migration inhibitory factor (MIF); InterPro: IPR001398 Macrophage migration inhibitory factor (MIF) is a key regulatory cytokine within innate and adaptive immune responses, capable of promoting and modulating the magnitude of the response []. MIF is released from T-cells and macrophages, and acts within the neuroendocrine system. MIF is capable of tautomerase activity, although its biological function has not been fully characterised. It is induced by glucocorticoid and is capable of overriding the anti-inflammatory actions of glucocorticoid []. MIF regulates cytokine secretion and the expression of receptors involved in the immune response. It can be taken up into target cells in order to interact with intracellular signalling molecules, inhibiting p53 function, and/or activating components of the mitogen-activated protein kinase and Jun-activation domain-binding protein-1 (Jab-1) []. MIF has been linked to various inflammatory diseases, such as rheumatoid arthritis and atherosclerosis []. The MIF homologue D-dopachrome tautomerase (4.1.1.84 from EC) is involved in detoxification through the conversion of dopaminechrome (and possibly norepinephrinechrome), the toxic quinine product of the neurotransmitter dopamine (and norepinephrine), to an indole derivative that can serve as a precursor to neuromelanin [, ].; PDB: 1UIZ_C 3FWT_A 1HFO_F 2WKB_D 3RF4_B 2OS5_A 3RF5_A 2XCZ_A 3FWU_A 3B64_A ....
Probab=91.47 E-value=0.78 Score=31.71 Aligned_cols=61 Identities=18% Similarity=0.265 Sum_probs=41.0
Q ss_pred EEEEEEecCCCccccccccCCeEEEEEeCCCC-CChhH----HHHHHHHHhhcCCCCCceEEEEeEE
Q 033900 41 SITIHAKPGSKSCSITDVSDEAVGVQIDAPAK-DGEAN----AALLEYMSSLIHVSVGEFVESVQVF 102 (109)
Q Consensus 41 ~L~V~VkP~Ak~~~I~g~~~~~L~I~V~ApPv-dGkAN----~aLi~~LAk~L~Vpks~I~~~~~~~ 102 (109)
.|-|.|+++..-. +.|-++...-+.|++--. +.+.| ++|.+||.+.||||+++|-+.|--+
T Consensus 36 ~i~V~v~~~~~m~-fgGs~~P~a~v~l~sig~~~~~~n~~~s~~i~~~l~~~LgIp~~Riyi~f~d~ 101 (114)
T PF01187_consen 36 YIMVTVEDGQRMS-FGGSDDPAAFVELKSIGGLDPEQNKKYSAAITEFLEEELGIPPDRIYINFHDL 101 (114)
T ss_dssp GEEEEEEESTEEE-ETTB-SS-EEEEEEESSSSSHHHHHHHHHHHHHHHHHHHT--GGGEEEEEEEE
T ss_pred hEEEEeeCCceEE-ECCCCCCEEEEEEEEccCCCHHHHHHHHHHHHHHHHHHhCCCcCceEEEEEEC
Confidence 5778888887664 445456666677766553 44444 6889999999999999999887644
No 11
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=89.54 E-value=0.98 Score=33.27 Aligned_cols=56 Identities=16% Similarity=0.304 Sum_probs=37.9
Q ss_pred EEEEEEecCCCcc--ccccccCCeEEEEE------eCCCCCChhHHHHHHHHHhhcCCCCCceEEE
Q 033900 41 SITIHAKPGSKSC--SITDVSDEAVGVQI------DAPAKDGEANAALLEYMSSLIHVSVGEFVES 98 (109)
Q Consensus 41 ~L~V~VkP~Ak~~--~I~g~~~~~L~I~V------~ApPvdGkAN~aLi~~LAk~L~Vpks~I~~~ 98 (109)
.|.|.+++..... ....+ +-+.|.+ ...+.+.+..++|.++||+.|||++++|+..
T Consensus 124 ~I~v~l~~~~~~~~~~~~~V--e~V~I~~~~~~~~~~~~~~~~~~~~i~~~la~~~~i~~~~I~V~ 187 (188)
T PF09581_consen 124 EIKVTLSEEEEQKEEAVEPV--EPVEIDIEKESDSSKSPEDSEEEEEIKQYLADFYGISPEQIKVY 187 (188)
T ss_pred EEEEEEcCCCccccccCCcc--cceEecccccccccccccchHHHHHHHHHHHHHhCCCHHHeEEe
Confidence 4667777754322 11112 3344444 4566777889999999999999999999865
No 12
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=83.30 E-value=9.6 Score=26.09 Aligned_cols=60 Identities=13% Similarity=0.044 Sum_probs=38.5
Q ss_pred EEEEEEecCCCccccccccCCeEEEEEeCCC-CCChhH----HHHHHHHHhhcCCCCCceEEEEeE
Q 033900 41 SITIHAKPGSKSCSITDVSDEAVGVQIDAPA-KDGEAN----AALLEYMSSLIHVSVGEFVESVQV 101 (109)
Q Consensus 41 ~L~V~VkP~Ak~~~I~g~~~~~L~I~V~ApP-vdGkAN----~aLi~~LAk~L~Vpks~I~~~~~~ 101 (109)
.+-|.+.|...-. +.+-++...-|+|+.-. ...+.| ++|.++|++.||||+.+|-+.+.-
T Consensus 38 ~~~v~~~~~~~m~-f~g~~~p~a~v~i~~~g~~~~e~k~~l~~~i~~~l~~~lgi~~~rv~I~f~~ 102 (116)
T PTZ00397 38 YIMSGYDYQKHMR-FGGSHDGCCFVRVTSIGGISRSNNSSIAAAITKILASHLKVKSERVYIEFKD 102 (116)
T ss_pred HEEEEEeCCceEE-ECCCCCceEEEEEEEecCCCHHHHHHHHHHHHHHHHHHhCcCcccEEEEEEE
Confidence 4555555554331 22445577777777433 333334 567788899999999999977654
No 13
>KOG1759 consensus Macrophage migration inhibitory factor [Defense mechanisms]
Probab=72.24 E-value=9 Score=27.75 Aligned_cols=58 Identities=10% Similarity=0.086 Sum_probs=38.9
Q ss_pred EEEEEEecCCCccccccccCC-----eEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceEEEE
Q 033900 41 SITIHAKPGSKSCSITDVSDE-----AVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVESV 99 (109)
Q Consensus 41 ~L~V~VkP~Ak~~~I~g~~~~-----~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~~~~ 99 (109)
+|.|++.++..- ...+.++- -..|..-.+-++.+=-++|.++|.+.|++++++|-++|
T Consensus 37 ~i~V~l~~~~~i-~fggt~eP~A~~~l~Sig~v~~~~N~~~sa~l~~il~~~L~l~~~rv~I~f 99 (115)
T KOG1759|consen 37 YIMVELAGGVRI-AFGGTTEPAAYASLKSIGGVGAIVNRSYSAALTEILEKELSLDPDRVYIKF 99 (115)
T ss_pred hEEEEecCCceE-eccCCCCccEEEEEEeccccChhHhHHHHHHHHHHHHHHhCCCCCeEEEEE
Confidence 477777777655 24444442 22344444555555567789999999999999998766
No 14
>PF08968 DUF1885: Domain of unknown function (DUF1885); InterPro: IPR015062 This family consists of hypothetical proteins produced by bacteria of the Bacillus genus. ; PDB: 1T6A_A.
Probab=68.38 E-value=5.8 Score=29.31 Aligned_cols=29 Identities=21% Similarity=0.440 Sum_probs=19.7
Q ss_pred CCeEEEEEeCCCC-----CChhHHHHHHHHHhhcC
Q 033900 60 DEAVGVQIDAPAK-----DGEANAALLEYMSSLIH 89 (109)
Q Consensus 60 ~~~L~I~V~ApPv-----dGkAN~aLi~~LAk~L~ 89 (109)
++.--|.|.=|+- .||||+ +|+|||+.|.
T Consensus 81 ~e~~~IQv~LP~~AThGDK~KANE-fckfLAk~l~ 114 (130)
T PF08968_consen 81 NEQSYIQVVLPDGATHGDKGKANE-FCKFLAKKLK 114 (130)
T ss_dssp TTEEEEEEE--TT--HHHHHHHHH-HHHHHHHHH-
T ss_pred CcceEEEEECCCCCccCcchhHHH-HHHHHHHHhh
Confidence 3455667776664 689995 8999999885
No 15
>PTZ00450 macrophage migration inhibitory factor-like protein; Provisional
Probab=65.95 E-value=4 Score=28.75 Aligned_cols=61 Identities=8% Similarity=0.031 Sum_probs=39.8
Q ss_pred EEEEEEEecCCCccccccccCCeEEEEEeC-----CCCCChhHHHHHHHHHhhcCCCCCceEEEEeE
Q 033900 40 VSITIHAKPGSKSCSITDVSDEAVGVQIDA-----PAKDGEANAALLEYMSSLIHVSVGEFVESVQV 101 (109)
Q Consensus 40 v~L~V~VkP~Ak~~~I~g~~~~~L~I~V~A-----pPvdGkAN~aLi~~LAk~L~Vpks~I~~~~~~ 101 (109)
-+|.|.+.|+..-. +.|-++..--+.|+. +....+-.++|+++|.+.||||+.+|-+.|-.
T Consensus 37 ~yvmV~~~~~~~m~-fgGs~~P~A~~~l~siG~~~~~~n~~~s~~i~~~l~~~LgIp~dRiYI~f~d 102 (113)
T PTZ00450 37 DFVMTAFSDSTPMS-FQGSTAPAAYVRVEAWGEYAPSKPKMMTPRITAAITKECGIPAERIYVFYYS 102 (113)
T ss_pred HHEEEEEeCCceEE-EcCCCCCEEEEEEEEecCcCHHHHHHHHHHHHHHHHHHcCCCcccEEEEEEc
Confidence 36778888876542 334344333333332 23344555778999999999999999987754
No 16
>COG1451 Predicted metal-dependent hydrolase [General function prediction only]
Probab=64.82 E-value=15 Score=28.65 Aligned_cols=47 Identities=13% Similarity=0.312 Sum_probs=36.7
Q ss_pred eEEEEEEEecCCCccccccccCCeEEEEEeCCCCCChhHHHHHHHHHhhcC
Q 033900 39 SVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSLIH 89 (109)
Q Consensus 39 ~v~L~V~VkP~Ak~~~I~g~~~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~ 89 (109)
+..+.|.+++++++..|.-..++ .|++.+|| +..++++..||.+..+
T Consensus 9 ~~~~~v~~~r~~r~~~i~i~~~~--~v~v~~P~--~~~~~~~~~fl~k~~~ 55 (223)
T COG1451 9 GLPLEVQVKRRAKRLTIRIPPGG--TVRVSVPP--GLSDEEVENFLAKKLG 55 (223)
T ss_pred CccEEEEEeecccceeEEecCCC--eEEEEeCC--CCCHHHHHHHHHHHHH
Confidence 68899999999999988755555 89999997 4556777777776554
No 17
>cd02552 PseudoU_synth_TruD_like PseudoU_synth_TruD_like: Pseudouridine synthase, TruD family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruD and Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD and S. cerevisiae Pus7 make psi13 in cytoplasmic tRNAs. In addition S. cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA) and psi35 in pre-tRNATyr. Psi35 in U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35.
Probab=53.35 E-value=20 Score=28.14 Aligned_cols=44 Identities=11% Similarity=0.111 Sum_probs=34.6
Q ss_pred CCeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE---------EEEeEEEeec
Q 033900 60 DEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV---------ESVQVFFLNG 106 (109)
Q Consensus 60 ~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~---------~~~~~~~~~g 106 (109)
++.+.+.|. -.|.-..++++.||+.|+|+.++|. +++|.|-|-+
T Consensus 30 G~~~~~~l~---K~~~~T~~a~~~la~~l~i~~~~i~yAG~KDk~AvT~Q~~sv~~ 82 (232)
T cd02552 30 GEYLHFTLY---KENKDTMEALREIAKALGVPPRDIGYAGTKDKRAVTTQRVSVHK 82 (232)
T ss_pred CCEEEEEEE---ECCCCHHHHHHHHHHHcCCCHHHEeEcccccCceeeEEEEEEEC
Confidence 456666665 3678899999999999999999998 7777766643
No 18
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=52.55 E-value=29 Score=20.77 Aligned_cols=25 Identities=4% Similarity=0.133 Sum_probs=19.8
Q ss_pred HHHHHHHHhhcCCCCCceEEEEeEE
Q 033900 78 AALLEYMSSLIHVSVGEFVESVQVF 102 (109)
Q Consensus 78 ~aLi~~LAk~L~Vpks~I~~~~~~~ 102 (109)
++|.+.+.+.||+|...|+..+.-+
T Consensus 21 ~~it~~~~~~lg~~~~~i~V~i~E~ 45 (60)
T PF01361_consen 21 EAITDAVVEVLGIPPERISVVIEEV 45 (60)
T ss_dssp HHHHHHHHHHHTS-GGGEEEEEEEE
T ss_pred HHHHHHHHHHhCcCCCeEEEEEEEE
Confidence 5677888999999999999777654
No 19
>cd02576 PseudoU_synth_ScPUS7 PseudoU_synth_ScPUS7: Pseudouridine synthase, TruD family. This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Saccharomyces cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA), psi13 in cytoplasmic tRNAs and psi35 in pre-tRNATyr. Psi35 in yeast U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35.
Probab=48.95 E-value=25 Score=28.99 Aligned_cols=43 Identities=14% Similarity=0.256 Sum_probs=33.8
Q ss_pred CeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE---------EEEeEEEeec
Q 033900 61 EAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV---------ESVQVFFLNG 106 (109)
Q Consensus 61 ~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~---------~~~~~~~~~g 106 (109)
+.+.+.+. -.|.-..+++..||+.|+|+.++|. +++|.+-|-+
T Consensus 29 ~y~~~~L~---K~~~~T~~ai~~lar~l~i~~~~i~~AG~KDk~AvT~Q~vsi~~ 80 (371)
T cd02576 29 DYLHFTLY---KENKDTMEAINKIAKLLRVKPSDFSYAGTKDKRAVTVQRVSVKK 80 (371)
T ss_pred CEEEEEEE---ECCCCHHHHHHHHHHHhCCChhheeecccccccceeEEEEEecC
Confidence 34555554 3577889999999999999999998 7888777654
No 20
>PF04969 CS: CS domain; InterPro: IPR017447 The function of the CS domain is unknown. The CS domain is sometimes found C-terminal to the CHORD domain (IPR007051 from INTERPRO) in metazoan proteins, but occurs separately from the CHORD domain in plants. This association is thought to be indicative of an functional interaction between CS and CHORD domains [].; PDB: 1WGV_A 2KMW_A 2O30_B 1WH0_A 1EJF_A 2RH0_B 1RL1_A 2CR0_A 1WFI_A 2XCM_D ....
Probab=48.82 E-value=49 Score=19.84 Aligned_cols=37 Identities=27% Similarity=0.333 Sum_probs=24.7
Q ss_pred eEeeCCCeEEEEEEEecCC--CccccccccCCeEEEEEeC
Q 033900 32 IRLVPPSSVSITIHAKPGS--KSCSITDVSDEAVGVQIDA 69 (109)
Q Consensus 32 i~~~~~g~v~L~V~VkP~A--k~~~I~g~~~~~L~I~V~A 69 (109)
|.+.. ..+.|.|.++|.- +.+--+.+.+..|.|.+..
T Consensus 5 W~Qt~-~~V~v~i~~~~~~~~~~dv~v~~~~~~l~v~~~~ 43 (79)
T PF04969_consen 5 WYQTD-DEVTVTIPVKPVDISKEDVKVDFTDTSLSVSIKS 43 (79)
T ss_dssp EEEES-SEEEEEEE-TTTTSSGGGEEEEEETTEEEEEEEE
T ss_pred EEECC-CEEEEEEEEcCCCCChHHeEEEEEeeEEEEEEEc
Confidence 34555 4899999998874 4444446778888888663
No 21
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=48.72 E-value=38 Score=19.76 Aligned_cols=25 Identities=12% Similarity=0.116 Sum_probs=20.5
Q ss_pred HHHHHHHHHhhcCCCCCceEEEEeE
Q 033900 77 NAALLEYMSSLIHVSVGEFVESVQV 101 (109)
Q Consensus 77 N~aLi~~LAk~L~Vpks~I~~~~~~ 101 (109)
-++|.+.|++.||++..+|...+..
T Consensus 20 ~~~i~~~l~~~~g~~~~~v~V~i~e 44 (58)
T cd00491 20 IERVTEAVSEILGAPEATIVVIIDE 44 (58)
T ss_pred HHHHHHHHHHHhCcCcccEEEEEEE
Confidence 4678889999999999999866543
No 22
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=47.27 E-value=36 Score=20.34 Aligned_cols=26 Identities=12% Similarity=0.119 Sum_probs=21.3
Q ss_pred hHHHHHHHHHhhcCCCCCceEEEEeE
Q 033900 76 ANAALLEYMSSLIHVSVGEFVESVQV 101 (109)
Q Consensus 76 AN~aLi~~LAk~L~Vpks~I~~~~~~ 101 (109)
--++|.+.|++.||+|..++...+..
T Consensus 20 l~~~it~~l~~~lg~~~~~v~V~i~e 45 (63)
T TIGR00013 20 LIEGVTEAMAETLGANLESIVVIIDE 45 (63)
T ss_pred HHHHHHHHHHHHhCCCcccEEEEEEE
Confidence 35678889999999999999976654
No 23
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=45.68 E-value=34 Score=20.42 Aligned_cols=25 Identities=0% Similarity=-0.154 Sum_probs=20.1
Q ss_pred HHHHHHHHHhhcCCCCCceEEEEeE
Q 033900 77 NAALLEYMSSLIHVSVGEFVESVQV 101 (109)
Q Consensus 77 N~aLi~~LAk~L~Vpks~I~~~~~~ 101 (109)
-++|.+.|.+.||+|..+|...+..
T Consensus 21 ~~~it~~l~~~~~~p~~~v~V~i~e 45 (62)
T PRK00745 21 VEEITRVTVETLGCPPESVDIIITD 45 (62)
T ss_pred HHHHHHHHHHHcCCChhHEEEEEEE
Confidence 3567788899999999999866654
No 24
>cd02575 PseudoU_synth_EcTruD PseudoU_synth_EcTruD: Pseudouridine synthase, TruD family. This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD makes the highly phylogenetically conserved psi13 in tRNAs.
Probab=45.01 E-value=32 Score=27.61 Aligned_cols=44 Identities=16% Similarity=0.185 Sum_probs=34.5
Q ss_pred cCCeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE---------EEEeEEEee
Q 033900 59 SDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV---------ESVQVFFLN 105 (109)
Q Consensus 59 ~~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~---------~~~~~~~~~ 105 (109)
.++.+.+.|. -.|.-..++++.||+.|+|+.++|. +++|.|-|-
T Consensus 23 ~Ge~l~~~l~---K~~~~T~~ai~~LAr~lgi~~~~igyAGlKDk~AvT~Q~~sv~ 75 (253)
T cd02575 23 EGEHLLLHIR---KTGLNTREVAKELAKALGVKERDVGYAGLKDRHAVTTQWFSVH 75 (253)
T ss_pred CCCEEEEEEE---ECCCCHHHHHHHHHHHhCCChhheeecccccCceeeEEEEEEE
Confidence 4566777765 3577889999999999999999997 666666553
No 25
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=44.72 E-value=36 Score=20.68 Aligned_cols=26 Identities=15% Similarity=0.045 Sum_probs=20.7
Q ss_pred hHHHHHHHHHhhcCCCCCceEEEEeE
Q 033900 76 ANAALLEYMSSLIHVSVGEFVESVQV 101 (109)
Q Consensus 76 AN~aLi~~LAk~L~Vpks~I~~~~~~ 101 (109)
--++|-+.|++.||+|..+|...+..
T Consensus 20 l~~~it~~l~~~lg~p~~~v~V~i~e 45 (64)
T PRK01964 20 LIREVTEAISATLDVPKERVRVIVNE 45 (64)
T ss_pred HHHHHHHHHHHHhCcChhhEEEEEEE
Confidence 34677888899999999999966543
No 26
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=42.54 E-value=44 Score=19.88 Aligned_cols=24 Identities=4% Similarity=-0.086 Sum_probs=19.4
Q ss_pred HHHHHHHHHhhcCCCCCceEEEEe
Q 033900 77 NAALLEYMSSLIHVSVGEFVESVQ 100 (109)
Q Consensus 77 N~aLi~~LAk~L~Vpks~I~~~~~ 100 (109)
-++|-+.|++.||+|..+|...+.
T Consensus 21 ~~~it~~l~~~~~~p~~~v~V~i~ 44 (61)
T PRK02220 21 VKDVTAAVSKNTGAPAEHIHVIIN 44 (61)
T ss_pred HHHHHHHHHHHhCcChhhEEEEEE
Confidence 467778889999999999986553
No 27
>cd02577 PSTD1 PSTD1: Pseudouridine synthase, a subgroup of the TruD family. This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD.
Probab=40.74 E-value=38 Score=27.85 Aligned_cols=44 Identities=7% Similarity=0.005 Sum_probs=33.7
Q ss_pred CCeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE---------EEEeEEEeec
Q 033900 60 DEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV---------ESVQVFFLNG 106 (109)
Q Consensus 60 ~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~---------~~~~~~~~~g 106 (109)
++.+.+.+. -.|.-..+++..||+.|+|+.++|. .++|.+-|-+
T Consensus 24 g~y~~f~l~---K~n~dT~~ai~~lar~l~i~~~~i~~AG~KDk~AvT~Q~vsv~~ 76 (319)
T cd02577 24 GKYLIYLLE---KKNWDTLDAVRRIAKALGISRKRIGYAGTKDKHAVTTQYISIFD 76 (319)
T ss_pred CCEEEEEEE---ECCCCHHHHHHHHHHHhCCChhheeeccccccccceEEEEEeec
Confidence 455555554 3577788999999999999999998 7777776644
No 28
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=40.72 E-value=33 Score=23.26 Aligned_cols=37 Identities=24% Similarity=0.242 Sum_probs=29.4
Q ss_pred EEEEeCCCCCChhHHHHHHHHHhhcCCCCCceEEEEeEE
Q 033900 64 GVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVESVQVF 102 (109)
Q Consensus 64 ~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~~~~~~~ 102 (109)
.|.|+.|+ |-.=..|.+.|++.|++|...+.++|+.-
T Consensus 12 tIaIrvp~--~~~y~~L~~ki~~kLkl~~e~i~LsYkde 48 (80)
T cd06406 12 TVAIQVAR--GLSYATLLQKISSKLELPAEHITLSYKSE 48 (80)
T ss_pred EEEEEcCC--CCCHHHHHHHHHHHhCCCchhcEEEeccC
Confidence 45555554 55567899999999999999999999853
No 29
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=40.57 E-value=62 Score=24.36 Aligned_cols=46 Identities=13% Similarity=0.177 Sum_probs=34.1
Q ss_pred ccccccccCCeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceEE
Q 033900 52 SCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVE 97 (109)
Q Consensus 52 ~~~I~g~~~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~~ 97 (109)
.++++-++++.+.|-|.++=..-+-=..+++.+.+.+||+..+|++
T Consensus 150 ~davv~~~~~~v~VvV~~~~L~~~~~~~I~diV~~~~~v~~~~I~V 195 (196)
T PF12685_consen 150 EDAVVFIEDDSVDVVVKADKLSDAEAAQIIDIVMRETGVPAENISV 195 (196)
T ss_dssp SEEEEE-SSSEEEEEEE-S---HHHHHHHHHHHHHHHC-STSEEEE
T ss_pred CceEEEeeCCEEEEEEeCCCCCHHHHHHHHHHHHHHhCCCcCeEEe
Confidence 4567777889999999998877777778999999999999999975
No 30
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=39.32 E-value=60 Score=19.70 Aligned_cols=25 Identities=8% Similarity=0.022 Sum_probs=20.7
Q ss_pred HHHHHHHHHhhcCCCCCceEEEEeE
Q 033900 77 NAALLEYMSSLIHVSVGEFVESVQV 101 (109)
Q Consensus 77 N~aLi~~LAk~L~Vpks~I~~~~~~ 101 (109)
-++|-+.+++.|++|...|+..+.-
T Consensus 21 ~~~it~a~~~~~~~p~~~v~V~i~e 45 (60)
T PRK02289 21 AREVTEVVSRIAKAPKEAIHVFIND 45 (60)
T ss_pred HHHHHHHHHHHhCcCcceEEEEEEE
Confidence 4678889999999999999966643
No 31
>PF01142 TruD: tRNA pseudouridine synthase D (TruD); InterPro: IPR001656 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. Pseudouridine synthase TruD modifies uracil-13 in tRNA []. TruD belongs to a recently identified and large family of pseudouridine synthases present in all kingdoms of life []. TruD folds into a V-shaped molecule with an RNA-binding cleft formed between its two domains: a catalytic domain and an insertion domain. The catalytic domain differs in sequence but is structurally very similar to the catalytic domain of other pseudouridine synthases. The insertion (or TRUD) domain displays a novel alpha/beta structure that forms a compact fold titled away from the catalytic domain to form a deep cleft in TruD which is lined with basic residues from each domain. The insertion domain is characterised by two conserved sequence motifs that form a part of the hydrophobic core, as well as by large insertions at several specific sites that are seen in many archaeal and eukaryotic homologues. The insertion domain is likely to be involved in substrate recognition and may represent a RNA binding module []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1SB7_B 1SI7_A 1SZW_B 1Z2Z_B.
Probab=39.19 E-value=59 Score=26.79 Aligned_cols=45 Identities=9% Similarity=0.101 Sum_probs=34.2
Q ss_pred cCCeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE---------EEEeEEEeec
Q 033900 59 SDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV---------ESVQVFFLNG 106 (109)
Q Consensus 59 ~~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~---------~~~~~~~~~g 106 (109)
.++.+.+.+. -.|.-..+++..||+.|+|+.++|. +++|.+-|-+
T Consensus 42 ~g~~~~~~l~---K~~~~T~~a~~~ia~~l~i~~~~i~~aG~KDk~avT~Q~vsv~~ 95 (378)
T PF01142_consen 42 EGEYLVFTLE---KRNIDTMEAIRIIARKLGISPKDISYAGLKDKRAVTTQYVSVPR 95 (378)
T ss_dssp -SSEEEEEEE---EESS-HHHHHHHHHHHCTS-CCCEEESS---TTSEEEEEEEEET
T ss_pred CCCEEEEEEE---EcCCCHHHHHHHHHHHhCCChhhceeccccccceeEEEEEEEec
Confidence 4566666665 3688889999999999999999997 7888887754
No 32
>cd06463 p23_like Proteins containing this p23_like domain include p23 and its Saccharomyces cerevisiae (Sc) homolog Sba1. Both are co-chaperones for the heat shock protein (Hsp) 90. p23 binds Hsp90 and participates in the folding of a number of Hsp90 clients, including the progesterone receptor. p23 also has a passive chaperoning activity and in addition may participate in prostaglandin synthesis. Both p23 and Sba1p can regulate telomerase activity. This group includes domains similar to the C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1). Sgt1 interacts with multiple protein complexes and has the features of a co-chaperone. Human (h) Sgt1 interacts with both Hsp70 and Hsp90, and has been shown to bind Hsp90 through its CS domain. Saccharomyces cerevisiae (Sc) Sgt1 is a subunit of both core kinetochore and SCF (Skp1-Cul1-F-box) ubiquitin ligase complexes. Sgt1 is required for pathogen resistance in plants. This group also includes the p23_like domains of
Probab=38.48 E-value=68 Score=19.24 Aligned_cols=33 Identities=21% Similarity=0.246 Sum_probs=24.0
Q ss_pred CeEEEEEEEecCCCccccccccCCeEEEEEeCC
Q 033900 38 SSVSITIHAKPGSKSCSITDVSDEAVGVQIDAP 70 (109)
Q Consensus 38 g~v~L~V~VkP~Ak~~~I~g~~~~~L~I~V~Ap 70 (109)
..+.|.|.+....+.+--+.+.++.|.|++...
T Consensus 6 ~~v~i~v~~~~~~~~~~~v~~~~~~l~i~~~~~ 38 (84)
T cd06463 6 DEVTITIPLKDVTKKDVKVEFTPKSLTVSVKGG 38 (84)
T ss_pred cEEEEEEEcCCCCccceEEEEecCEEEEEeeCC
Confidence 378888888777655555567778888888753
No 33
>COG0245 IspF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Lipid metabolism]
Probab=38.44 E-value=37 Score=25.85 Aligned_cols=40 Identities=18% Similarity=0.169 Sum_probs=29.6
Q ss_pred CCCCCChhHHHHHHHHHhhcCCCCCceEEEEeEEEeeccC
Q 033900 69 APAKDGEANAALLEYMSSLIHVSVGEFVESVQVFFLNGFR 108 (109)
Q Consensus 69 ApPvdGkAN~aLi~~LAk~L~Vpks~I~~~~~~~~~~g~~ 108 (109)
+.|-=+===+++.+.||+.|+++.++|.+..++--==||.
T Consensus 101 ~~PK~~P~~~amr~~ia~~L~i~~~~invKatT~E~LGf~ 140 (159)
T COG0245 101 QRPKLGPYREAMRANIAELLGIPVDRINVKATTTEKLGFT 140 (159)
T ss_pred ecCcccchHHHHHHHHHHHhCCCchheEEEEeccCccccc
Confidence 4444445567899999999999999999777765444443
No 34
>PF01187 MIF: Macrophage migration inhibitory factor (MIF); InterPro: IPR001398 Macrophage migration inhibitory factor (MIF) is a key regulatory cytokine within innate and adaptive immune responses, capable of promoting and modulating the magnitude of the response []. MIF is released from T-cells and macrophages, and acts within the neuroendocrine system. MIF is capable of tautomerase activity, although its biological function has not been fully characterised. It is induced by glucocorticoid and is capable of overriding the anti-inflammatory actions of glucocorticoid []. MIF regulates cytokine secretion and the expression of receptors involved in the immune response. It can be taken up into target cells in order to interact with intracellular signalling molecules, inhibiting p53 function, and/or activating components of the mitogen-activated protein kinase and Jun-activation domain-binding protein-1 (Jab-1) []. MIF has been linked to various inflammatory diseases, such as rheumatoid arthritis and atherosclerosis []. The MIF homologue D-dopachrome tautomerase (4.1.1.84 from EC) is involved in detoxification through the conversion of dopaminechrome (and possibly norepinephrinechrome), the toxic quinine product of the neurotransmitter dopamine (and norepinephrine), to an indole derivative that can serve as a precursor to neuromelanin [, ].; PDB: 1UIZ_C 3FWT_A 1HFO_F 2WKB_D 3RF4_B 2OS5_A 3RF5_A 2XCZ_A 3FWU_A 3B64_A ....
Probab=38.11 E-value=68 Score=21.88 Aligned_cols=32 Identities=13% Similarity=0.169 Sum_probs=26.1
Q ss_pred hhHHHHHHHHHhhcCCCCCceEEEEe---EEEeec
Q 033900 75 EANAALLEYMSSLIHVSVGEFVESVQ---VFFLNG 106 (109)
Q Consensus 75 kAN~aLi~~LAk~L~Vpks~I~~~~~---~~~~~g 106 (109)
.--.+|.+++|+.||-|.+.|...+. .|++.|
T Consensus 17 ~f~~~ls~~va~~lgKpe~~i~V~v~~~~~m~fgG 51 (114)
T PF01187_consen 17 DFLKELSKLVAELLGKPESYIMVTVEDGQRMSFGG 51 (114)
T ss_dssp THHHHHHHHHHHHHTSTGGGEEEEEEESTEEEETT
T ss_pred HHHHHHHHHHHHHhCcchhhEEEEeeCCceEEECC
Confidence 45578999999999999999997764 377766
No 35
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=37.60 E-value=16 Score=22.35 Aligned_cols=19 Identities=11% Similarity=0.237 Sum_probs=17.1
Q ss_pred HHHHHHHHhhcCCCCCceE
Q 033900 78 AALLEYMSSLIHVSVGEFV 96 (109)
Q Consensus 78 ~aLi~~LAk~L~Vpks~I~ 96 (109)
++|++.+|+.|||+..+|.
T Consensus 3 ~~I~~~Va~~~~i~~~~i~ 21 (60)
T smart00760 3 EEIIEAVAEYFGVKPEDLK 21 (60)
T ss_pred HHHHHHHHHHhCCCHHHHh
Confidence 5789999999999998886
No 36
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=37.32 E-value=43 Score=22.25 Aligned_cols=43 Identities=21% Similarity=0.257 Sum_probs=24.4
Q ss_pred cCCeEEEEEeCC-CCCChhHHHHH----HHHHhhcCCCCCceEEEEeE
Q 033900 59 SDEAVGVQIDAP-AKDGEANAALL----EYMSSLIHVSVGEFVESVQV 101 (109)
Q Consensus 59 ~~~~L~I~V~Ap-PvdGkAN~aLi----~~LAk~L~Vpks~I~~~~~~ 101 (109)
.++.+-|.|+.- +..=++=++|. +.|++.+||++.+|.+.+..
T Consensus 26 s~~~v~I~It~~~gRs~e~K~~ly~~l~~~L~~~~gi~p~Dv~I~l~e 73 (82)
T PF14552_consen 26 SDDFVIIQITSGAGRSTEQKKALYRALAERLAEKLGIRPEDVMIVLVE 73 (82)
T ss_dssp -TT-EEEEEEECS---HHHHHHHHHHHHHHHHHHH---GGGEEEEEEE
T ss_pred CCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHcCCCHHHEEEEEEE
Confidence 457788888887 55555555554 55566679999999977653
No 37
>TIGR00094 tRNA_TruD_broad tRNA pseudouridine synthase, TruD family. MJ11364 is a strong partial match from 50 to 230 aa.
Probab=34.34 E-value=59 Score=26.93 Aligned_cols=34 Identities=15% Similarity=0.292 Sum_probs=29.5
Q ss_pred CCeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE
Q 033900 60 DEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV 96 (109)
Q Consensus 60 ~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~ 96 (109)
++.+.+.|.- .|.-..++++.||+.|+|+.++|.
T Consensus 41 g~~~~~~l~K---~~~~T~~a~~~iar~l~i~~~~i~ 74 (387)
T TIGR00094 41 GEFIHIRVEK---EGCNTLEVARVLAKFLGVSRREIG 74 (387)
T ss_pred CCEEEEEEEE---CCcCHHHHHHHHHHHhCCChhhee
Confidence 5677777764 788899999999999999999997
No 38
>PRK00984 truD tRNA pseudouridine synthase D; Reviewed
Probab=34.32 E-value=55 Score=27.07 Aligned_cols=43 Identities=19% Similarity=0.231 Sum_probs=33.8
Q ss_pred cCCeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceE---------EEEeEEEe
Q 033900 59 SDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFV---------ESVQVFFL 104 (109)
Q Consensus 59 ~~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~---------~~~~~~~~ 104 (109)
.++.+.+.|. -.|.-..+++..||+.|+|+.++|. +++|.|-|
T Consensus 40 ~G~~~~~~l~---K~~~~T~~~~~~lar~l~i~~~~i~yAG~KDk~AvT~Q~~si 91 (341)
T PRK00984 40 EGEHLLVRIR---KRGWNTLFVARALAKFLGISLRDVGYAGLKDRHAVTTQWFSI 91 (341)
T ss_pred CcCEEEEEEE---ECCCCHHHHHHHHHHHhCCChhheeecccCcCCeeeEEEEEE
Confidence 3456666665 3577889999999999999999997 66776665
No 39
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=32.89 E-value=15 Score=25.22 Aligned_cols=20 Identities=15% Similarity=0.101 Sum_probs=13.6
Q ss_pred HHHHHHHHHhhcCCCCCceE
Q 033900 77 NAALLEYMSSLIHVSVGEFV 96 (109)
Q Consensus 77 N~aLi~~LAk~L~Vpks~I~ 96 (109)
|.+-++-.|+.|||++|.|.
T Consensus 18 ~~aTVR~~Ak~FGvSKSTVH 37 (82)
T PF12116_consen 18 TKATVRQAAKVFGVSKSTVH 37 (82)
T ss_dssp H---HHHHHHHHTS-HHHHH
T ss_pred cccHHHHHHHHHCCcHHHHH
Confidence 56678899999999999763
No 40
>PF02738 Ald_Xan_dh_C2: Molybdopterin-binding domain of aldehyde dehydrogenase; InterPro: IPR008274 Aldehyde oxidase (1.2.3.1 from EC) catalyses the conversion of an aldehyde in the presence of oxygen and water to an acid and hydrogen peroxide. The enzyme is a homodimer, and requires FAD, molybdenum and two 2FE-2S clusters as cofactors. Xanthine dehydrogenase (1.1.1.204 from EC) catalyses the hydrogenation of xanthine to urate, and also requires FAD, molybdenum and two 2FE-2S clusters as cofactors. This activity is often found in a bifunctional enzyme with xanthine oxidase (1.1.3.22 from EC) activity too. The enzyme can be converted from the dehydrogenase form to the oxidase form irreversibly by proteolysis or reversibly through oxidation of sulphydryl groups.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3NVZ_C 3NVY_C 1FO4_B 3NRZ_L 3AM9_A 3B9J_C 3AX7_B 3NVW_L 3BDJ_A 3ETR_N ....
Probab=32.53 E-value=82 Score=27.05 Aligned_cols=41 Identities=12% Similarity=0.081 Sum_probs=31.6
Q ss_pred cCCeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceEEEE
Q 033900 59 SDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVESV 99 (109)
Q Consensus 59 ~~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~~~~ 99 (109)
.++.+.|.+...+.--=....+...+|+.||||.++|+...
T Consensus 328 ~DG~v~v~~~~~e~GqG~~T~~~qiaAe~Lgi~~~~V~v~~ 368 (547)
T PF02738_consen 328 PDGSVTVYTGGVEMGQGSRTALAQIAAEELGIPPEDVRVVS 368 (547)
T ss_dssp TTS-EEEEES--BSSSSHHHHHHHHHHHHHTS-GGGEEEEE
T ss_pred eCCCEEEEEecccCCcchhhhHHHHHHHHhCCChhhEEEEe
Confidence 46889999888877767888999999999999999999653
No 41
>PHA02564 V virion protein; Provisional
Probab=31.74 E-value=52 Score=24.38 Aligned_cols=30 Identities=13% Similarity=0.126 Sum_probs=24.1
Q ss_pred EEEeCCCCCChhHHHHHHHHHhhcCCCCCce
Q 033900 65 VQIDAPAKDGEANAALLEYMSSLIHVSVGEF 95 (109)
Q Consensus 65 I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I 95 (109)
|.-=|||.|+. -++-+.++|+.+||++.+.
T Consensus 73 I~rwAP~~ENn-T~aYi~~Vs~~~GV~~~~~ 102 (141)
T PHA02564 73 IARWAPSNEND-TRAYATAVANAMGVPPQAG 102 (141)
T ss_pred HHhcCCCCCCC-HHHHHHHHHHHHCCCCCCc
Confidence 34468888753 6789999999999998875
No 42
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=30.60 E-value=83 Score=20.71 Aligned_cols=24 Identities=8% Similarity=0.086 Sum_probs=20.4
Q ss_pred HHHHHHHHhhcCCCCCceEEEEeE
Q 033900 78 AALLEYMSSLIHVSVGEFVESVQV 101 (109)
Q Consensus 78 ~aLi~~LAk~L~Vpks~I~~~~~~ 101 (109)
+++-+.+++.||.+...|+..+.-
T Consensus 23 ~~iT~a~~~~lg~~~e~v~V~I~e 46 (76)
T PRK01271 23 ADITDVIIRHLNSKDSSISIALQQ 46 (76)
T ss_pred HHHHHHHHHHhCcCcceEEEEEEE
Confidence 578889999999999999977654
No 43
>PF02542 YgbB: YgbB family; InterPro: IPR003526 MECDP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate) synthetase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis, isoprenoids being essential in all organisms. Isoprenoids can also be synthesized through the mevalonate pathway. The non-mevolante route is used by many bacteria and human pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum. This route appears to involve seven enzymes. MECDP synthetase catalyses the intramolecular attack by a phosphate group on a diphosphate, with cytidine monophosphate (CMP) acting as the leaving group to give the cyclic diphosphate product MEDCP. The enzyme is a trimer with three active sites shared between adjacent copies of the protein. The enzyme also has two metal binding sites, the metals playing key roles in catalysis[]. A number of proteins from eukaryotes and prokaryotes share this common N-terminal signature and appear to be involved in terpenoid biosynthesis. The YgbB protein is a putative enzyme of this type [].; GO: 0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity, 0016114 terpenoid biosynthetic process; PDB: 3T80_B 3GHZ_A 2PMP_A 3F6M_A 3FPI_A 3RE3_A 1T0A_C 1W57_A 1W55_A 3B6N_A ....
Probab=30.18 E-value=1e+02 Score=23.31 Aligned_cols=35 Identities=14% Similarity=0.126 Sum_probs=27.5
Q ss_pred EeCCCCCChhHHHHHHHHHhhcCCCCCceEEEEeE
Q 033900 67 IDAPAKDGEANAALLEYMSSLIHVSVGEFVESVQV 101 (109)
Q Consensus 67 V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~~~~~~ 101 (109)
+.+.|.=+.-=+++.+.||+.|+++.++|.+..++
T Consensus 99 i~e~PKi~p~~~~m~~~la~~L~~~~~~V~iKatT 133 (157)
T PF02542_consen 99 IAERPKISPYRPAMRENLAKLLGIPPDRVNIKATT 133 (157)
T ss_dssp ESSSSTTGGGHHHHHHHHHHHHTS-GGGEEEEEE-
T ss_pred EcCCCccHHHHHHHHHHHHHHhCCCcceEEEEEec
Confidence 44556667777899999999999999999977665
No 44
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=27.27 E-value=25 Score=22.38 Aligned_cols=19 Identities=21% Similarity=0.337 Sum_probs=14.8
Q ss_pred HHHHHHHHhhcCCCCCceE
Q 033900 78 AALLEYMSSLIHVSVGEFV 96 (109)
Q Consensus 78 ~aLi~~LAk~L~Vpks~I~ 96 (109)
+++++.+|+.|||+..+|.
T Consensus 3 ~~Ii~~Va~~~~v~~~~i~ 21 (70)
T PF08299_consen 3 EDIIEAVAEYFGVSVEDIR 21 (70)
T ss_dssp HHHHHHHHHHTT--HHHHH
T ss_pred HHHHHHHHHHHCCCHHHHh
Confidence 5789999999999988876
No 45
>KOG4079 consensus Putative mitochondrial ribosomal protein mRpS25 [Translation, ribosomal structure and biogenesis]
Probab=27.15 E-value=45 Score=25.39 Aligned_cols=21 Identities=10% Similarity=0.131 Sum_probs=18.5
Q ss_pred CCChhHHHHHHHHHhhcCCCC
Q 033900 72 KDGEANAALLEYMSSLIHVSV 92 (109)
Q Consensus 72 vdGkAN~aLi~~LAk~L~Vpk 92 (109)
.||+-|+++++.|++.||-..
T Consensus 91 ld~~~r~eI~~hl~K~lGKte 111 (169)
T KOG4079|consen 91 LDGMKREEIEKHLAKTLGKTE 111 (169)
T ss_pred cccccHHHHHHHHHHHhCccH
Confidence 589999999999999998543
No 46
>TIGR01215 minE cell division topological specificity factor MinE. This protein is involved in the process of cell division. This protein prevents the proteins MinC and MinD to inhibit cell division at internal sites, but allows inhibiton at polar sites. This allows for correct cell division at the proper sites.
Probab=26.10 E-value=83 Score=20.97 Aligned_cols=24 Identities=17% Similarity=0.259 Sum_probs=20.9
Q ss_pred HHHHHHHHHhhcCCCCCceEEEEe
Q 033900 77 NAALLEYMSSLIHVSVGEFVESVQ 100 (109)
Q Consensus 77 N~aLi~~LAk~L~Vpks~I~~~~~ 100 (109)
=++|++.+++++.|....|+..+.
T Consensus 42 k~dil~VIskY~~id~~~v~v~l~ 65 (81)
T TIGR01215 42 RKEILEVISKYVEIDPEMVEVSLE 65 (81)
T ss_pred HHHHHHHHHHheecchHhEEEEEE
Confidence 368999999999999999997665
No 47
>cd00298 ACD_sHsps_p23-like This domain family includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this family is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind
Probab=25.76 E-value=1.4e+02 Score=17.12 Aligned_cols=37 Identities=14% Similarity=0.145 Sum_probs=26.2
Q ss_pred CeEEEEEEEecCCCccccccccCCeEEEEEeCCCCCC
Q 033900 38 SSVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDG 74 (109)
Q Consensus 38 g~v~L~V~VkP~Ak~~~I~g~~~~~L~I~V~ApPvdG 74 (109)
+.+.|.|.+..-...+--+.+.++.|.|+....+.+.
T Consensus 6 ~~v~i~i~~~~~~~~~i~v~~~~~~l~v~~~~~~~~~ 42 (80)
T cd00298 6 DEVVVTVDLPGVKKEDIKVEVEDNVLTISGKREEEEE 42 (80)
T ss_pred CEEEEEEECCCCCHHHeEEEEECCEEEEEEEEcCCCc
Confidence 4788888887766454444667788888888776654
No 48
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=25.62 E-value=28 Score=25.06 Aligned_cols=20 Identities=15% Similarity=0.195 Sum_probs=16.3
Q ss_pred HHHHHHHHHhhcCCCCCceE
Q 033900 77 NAALLEYMSSLIHVSVGEFV 96 (109)
Q Consensus 77 N~aLi~~LAk~L~Vpks~I~ 96 (109)
-++.++++|+.|+|+.++|.
T Consensus 30 ~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 30 PEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp -HHHHHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHHHHHCCCHHHHH
Confidence 46789999999999999886
No 49
>PRK06290 aspartate aminotransferase; Provisional
Probab=25.42 E-value=89 Score=25.70 Aligned_cols=28 Identities=21% Similarity=0.279 Sum_probs=26.4
Q ss_pred CeEEEEEeCCCCCChhHHHHHHHHHhhc
Q 033900 61 EAVGVQIDAPAKDGEANAALLEYMSSLI 88 (109)
Q Consensus 61 ~~L~I~V~ApPvdGkAN~aLi~~LAk~L 88 (109)
+.|+|.+..++.+-+-|+++++-|++.|
T Consensus 376 ~~lRi~~~~~~~~~~~~~~~~~~l~~~~ 403 (410)
T PRK06290 376 HFLRFSVTFEAKDEEEEDRILEEIKRRL 403 (410)
T ss_pred CeEEEEEEcccccccchhHHHHHHHHHH
Confidence 6899999999999999999999999887
No 50
>PF14804 Jag_N: Jag N-terminus; PDB: 3GKU_B.
Probab=25.31 E-value=1.3e+02 Score=18.45 Aligned_cols=26 Identities=19% Similarity=0.141 Sum_probs=17.1
Q ss_pred ChhHHHHHHHHHhhcCCCCCceEEEE
Q 033900 74 GEANAALLEYMSSLIHVSVGEFVESV 99 (109)
Q Consensus 74 GkAN~aLi~~LAk~L~Vpks~I~~~~ 99 (109)
|+-=++.++--++.|++++.+++.-+
T Consensus 4 gkt~eeAi~~A~~~l~~~~~~~~~eV 29 (52)
T PF14804_consen 4 GKTVEEAIEKALKELGVPREELEYEV 29 (52)
T ss_dssp ESSHHHHHHHHHHHTT--GGGEEEEE
T ss_pred ECCHHHHHHHHHHHhCCChHHEEEEE
Confidence 33445677777889999999998444
No 51
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=24.62 E-value=33 Score=24.76 Aligned_cols=20 Identities=0% Similarity=0.009 Sum_probs=17.8
Q ss_pred HHHHHHHHHhhcCCCCCceE
Q 033900 77 NAALLEYMSSLIHVSVGEFV 96 (109)
Q Consensus 77 N~aLi~~LAk~L~Vpks~I~ 96 (109)
-++.++++|+.||||.++|.
T Consensus 33 ~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 33 TPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred CHHHHHHHHHHhCcCHHHHH
Confidence 46789999999999999987
No 52
>cd06411 PB1_p51 The PB1 domain is present in the p51 protein, a homolog of the p67 protein. p51 plays an important role in NADPH oxidase activation during phagosytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain mo
Probab=24.20 E-value=1.7e+02 Score=19.69 Aligned_cols=37 Identities=19% Similarity=0.176 Sum_probs=28.3
Q ss_pred EEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceEEEEeE
Q 033900 63 VGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVESVQV 101 (109)
Q Consensus 63 L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~~~~~~ 101 (109)
+.|.|..|| |..=..|...||+.|.++.+.+.++|+.
T Consensus 7 fTVai~v~~--g~~y~~L~~~ls~kL~l~~~~~~LSY~~ 43 (78)
T cd06411 7 FTVALRAPR--GADVSSLRALLSQALPQQAQRGQLSYRA 43 (78)
T ss_pred EEEEEEccC--CCCHHHHHHHHHHHhcCChhhcEEEecC
Confidence 455566655 4455688999999999999999998864
No 53
>PF03776 MinE: Septum formation topological specificity factor MinE; InterPro: IPR005527 Cytokinesis needs to be regulated spatially in order to ensure that it occurs between the daughter genomes. In prokaryotes such as Escherichia coli, cytokinesis is initiated by FtsZ, a tubulin-like protein that assembles into a ring structure at the cell centre called the Z ring. A fundamental problem in prokaryotic cell biology is to understand how the midcell division site is identified. Two major negative regulatory systems are known to be involved in preventing Z-ring assembly at all sites except the midcell. One of these systems, called nucleoid occlusion, blocks Z-ring assembly in the area occupied by an unsegregated nucleoid until a critical stage in chromosome replication or segregation is reached. The other system consists of three proteins, MinC, MinD and MinE, which prevent assembly of Z rings in regions of the cell not covered by the nucleoid, such as the cell poles. MinC is an inhibitor of FtsZ polymerisation, resulting in the inhibition of Z ring assembly in the cell; MinD greatly enhances the inhibitory effects of MinC in vivo; and MinE antagonizes the effects of MinC and MinD []. MinE is a small bifunctional protein. The amino terminus of MinE is required to interact with MinD, while the carboxyl terminus is required for `topological specificity' - that is, the ability of MinE to antagonise MinCD inhibition of Z rings at the midcell position but not at the poles.; GO: 0032955 regulation of barrier septum formation, 0051301 cell division; PDB: 2KXO_A 3MCD_B 3KU7_A 3R9J_C 3R9I_E 1EV0_B.
Probab=24.18 E-value=1.3e+02 Score=19.27 Aligned_cols=24 Identities=13% Similarity=0.301 Sum_probs=18.1
Q ss_pred HHHHHHHHHhhcCCCCCceEEEEe
Q 033900 77 NAALLEYMSSLIHVSVGEFVESVQ 100 (109)
Q Consensus 77 N~aLi~~LAk~L~Vpks~I~~~~~ 100 (109)
=++|++.+++++.|...+|+..+.
T Consensus 31 k~eil~viskYv~i~~~~v~v~l~ 54 (70)
T PF03776_consen 31 KKEILEVISKYVEIDEEDVEVQLE 54 (70)
T ss_dssp HHHHHHHHHHHS---CCCEEEEEE
T ss_pred HHHHHHHHHhheecCcccEEEEEE
Confidence 368999999999999999997765
No 54
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=23.89 E-value=2.1e+02 Score=19.03 Aligned_cols=65 Identities=17% Similarity=0.205 Sum_probs=39.1
Q ss_pred CCcceEeeCCCeEEEEEEEecC--CCccccccccCCeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCC-----ceEEEEe
Q 033900 28 LPSCIRLVPPSSVSITIHAKPG--SKSCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVG-----EFVESVQ 100 (109)
Q Consensus 28 ~p~~i~~~~~g~v~L~V~VkP~--Ak~~~I~g~~~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks-----~I~~~~~ 100 (109)
+|=++.....+.+-+-.+.+.+ ...+.|-.+++|. .+|.+-|.+.|+.... +|....+
T Consensus 2 lpY~V~Rt~~~~LPVY~~~k~~g~~~~T~IrkI~GD~---------------~aL~~dL~~~l~~~~~~~~~~~V~~~~g 66 (87)
T PF05046_consen 2 LPYFVRRTKSGNLPVYLDIKNGGNRKITVIRKIEGDI---------------WALKKDLRKFLGEKPKKKIDVRVNELTG 66 (87)
T ss_pred CCeEEeecCCCcccEEEEEeCCCcEeEEEEEeecCCH---------------HHHHHHHHHHhhhhcCCCcceEEeecCC
Confidence 4555566555544444445552 2234455566654 5778888888865543 5667778
Q ss_pred EEEeecc
Q 033900 101 VFFLNGF 107 (109)
Q Consensus 101 ~~~~~g~ 107 (109)
++.|-|-
T Consensus 67 ~i~IkG~ 73 (87)
T PF05046_consen 67 HIEIKGD 73 (87)
T ss_pred EEEEcCc
Confidence 8888774
No 55
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=23.64 E-value=77 Score=18.57 Aligned_cols=22 Identities=5% Similarity=0.064 Sum_probs=15.1
Q ss_pred ChhHHHHHHHHHhhcCCCCCce
Q 033900 74 GEANAALLEYMSSLIHVSVGEF 95 (109)
Q Consensus 74 GkAN~aLi~~LAk~L~Vpks~I 95 (109)
+-.-+..++.||+.+||+..++
T Consensus 38 ~i~r~~y~~~la~~~~i~~~~L 59 (59)
T PF10410_consen 38 PIERELYIRELAERLGISEDAL 59 (59)
T ss_dssp HHHHHHHHHHHHHHCT-SSTT-
T ss_pred HHHHHHHHHHHHHHhCcCcccC
Confidence 3344677889999999987754
No 56
>PRK00084 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed
Probab=23.60 E-value=92 Score=23.56 Aligned_cols=34 Identities=3% Similarity=-0.014 Sum_probs=27.4
Q ss_pred CCCCCChhHHHHHHHHHhhcCCCCCceEEEEeEE
Q 033900 69 APAKDGEANAALLEYMSSLIHVSVGEFVESVQVF 102 (109)
Q Consensus 69 ApPvdGkAN~aLi~~LAk~L~Vpks~I~~~~~~~ 102 (109)
+.|.=+-==+++.+.||+.|+++.++|.+..++-
T Consensus 103 e~PKi~p~~~~m~~~la~~L~i~~~~V~iKatT~ 136 (159)
T PRK00084 103 QRPKMAPHIEEMRANIAEDLGIPLDDVNVKATTT 136 (159)
T ss_pred CCCcchHHHHHHHHHHHHHhCCCcceEEEEEecC
Confidence 4465566668899999999999999999777663
No 57
>PF09098 Dehyd-heme_bind: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding; InterPro: IPR015182 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the dihaem cytochrome c domain of the QHNDH alpha subunit. The domain contain two cysteine residues that are involved in thioether linkages to haem []. ; PDB: 1PBY_A 1JJU_A 1JMZ_A 1JMX_A.
Probab=23.42 E-value=56 Score=25.09 Aligned_cols=26 Identities=15% Similarity=0.235 Sum_probs=16.3
Q ss_pred CCCChhHHHHHHHHHhhcCCCCCceE
Q 033900 71 AKDGEANAALLEYMSSLIHVSVGEFV 96 (109)
Q Consensus 71 PvdGkAN~aLi~~LAk~L~Vpks~I~ 96 (109)
+..-..=++|++|||+..|+.++...
T Consensus 50 ~Is~eer~avVkYLAd~~GLap~Et~ 75 (167)
T PF09098_consen 50 PISPEERRAVVKYLADTQGLAPSETA 75 (167)
T ss_dssp ---HHHHHHHHHHHHHHT---CGGCT
T ss_pred CCCHHHHHHHHHHHHHccCCCchhhc
Confidence 34445567999999999999988754
No 58
>cd00554 MECDP_synthase MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis. This pathway is present in bacteria, plants and some protozoa but is distinct from that used by mammals and Archaea. MECDP_synthase forms a homotrimer, carrying three active sites, each of which is formed in a cleft between pairs of subunits.
Probab=23.35 E-value=98 Score=23.24 Aligned_cols=33 Identities=9% Similarity=0.009 Sum_probs=27.9
Q ss_pred CCCChhHHHHHHHHHhhcCCCCCceEEEEeEEE
Q 033900 71 AKDGEANAALLEYMSSLIHVSVGEFVESVQVFF 103 (109)
Q Consensus 71 PvdGkAN~aLi~~LAk~L~Vpks~I~~~~~~~~ 103 (109)
|.=+-==+++.+.||+.|+++..+|.+..++--
T Consensus 102 PKi~p~~~~m~~~ls~~L~~~~~~V~iKatT~E 134 (153)
T cd00554 102 PKISPYREAMRANLAELLGIPPSRVNIKATTTE 134 (153)
T ss_pred CcchHHHHHHHHHHHHHhCCCCceEEEEEecCC
Confidence 666667788999999999999999998877643
No 59
>PF06138 Chordopox_E11: Chordopoxvirus E11 protein; InterPro: IPR009201 This group represents a virion core protein, vaccinia E11L type.
Probab=23.29 E-value=1.7e+02 Score=21.65 Aligned_cols=42 Identities=19% Similarity=0.282 Sum_probs=29.6
Q ss_pred cCCeEEEEEeCCC--------CCChhHHHHHHHHHhhcCCCCCceEEEEe
Q 033900 59 SDEAVGVQIDAPA--------KDGEANAALLEYMSSLIHVSVGEFVESVQ 100 (109)
Q Consensus 59 ~~~~L~I~V~ApP--------vdGkAN~aLi~~LAk~L~Vpks~I~~~~~ 100 (109)
+.+.+++++..|+ .--+|=+..+..|.+.+.|.+|...+.++
T Consensus 11 d~grvkl~~~~~~~~c~~~~~~~~~Av~~Fl~~L~kyI~veeStFylvvr 60 (130)
T PF06138_consen 11 DSGRVKLRYEEPDCKCARTGCEARRAVKHFLSVLKKYIDVEESTFYLVVR 60 (130)
T ss_pred cCceeEEEEeCCCcccccccchHHHHHHHHHHHHHhhEEecccEEEEEEe
Confidence 3467777777766 22345556677788899999999886665
No 60
>PRK00296 minE cell division topological specificity factor MinE; Reviewed
Probab=23.20 E-value=1.1e+02 Score=20.59 Aligned_cols=26 Identities=8% Similarity=0.270 Sum_probs=21.2
Q ss_pred hhHHHHHHHHHhhcCCCCCceEEEEe
Q 033900 75 EANAALLEYMSSLIHVSVGEFVESVQ 100 (109)
Q Consensus 75 kAN~aLi~~LAk~L~Vpks~I~~~~~ 100 (109)
.==++|++.+++++.|...+|+..+.
T Consensus 41 ~lk~dIl~VIsKY~~Id~~~v~i~l~ 66 (86)
T PRK00296 41 QLRKEILEVIAKYVQIDPDKVSVQLD 66 (86)
T ss_pred HHHHHHHHHHHHheecChhhEEEEEE
Confidence 33468999999999999999986553
No 61
>PHA03001 putative virion core protein; Provisional
Probab=23.20 E-value=1.9e+02 Score=21.45 Aligned_cols=42 Identities=26% Similarity=0.396 Sum_probs=29.5
Q ss_pred cCCeEEEEEeCCC----CCC---hhHHHHHHHHHhhcCCCCCceEEEEe
Q 033900 59 SDEAVGVQIDAPA----KDG---EANAALLEYMSSLIHVSVGEFVESVQ 100 (109)
Q Consensus 59 ~~~~L~I~V~ApP----vdG---kAN~aLi~~LAk~L~Vpks~I~~~~~ 100 (109)
+.+.+++++..|| .+. +|=+..++.|.+.++|.+|...+.++
T Consensus 11 d~grvkl~~~~~~~~~~~~~~~~ka~~~fl~~L~kYi~v~eStFylvvr 59 (132)
T PHA03001 11 DAGRVKLAIENPDKVCATKAEMRKAINKFLELLKKYIHVDKSTFYLVVK 59 (132)
T ss_pred cCCceEEEEcCCCccccccchHHHHHHHHHHHHHhhEEecccEEEEEEe
Confidence 3467777777665 334 45556677778889999998886554
No 62
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=23.14 E-value=40 Score=19.72 Aligned_cols=21 Identities=5% Similarity=-0.001 Sum_probs=17.2
Q ss_pred hHHHHHHHHHhhcCCCCCceE
Q 033900 76 ANAALLEYMSSLIHVSVGEFV 96 (109)
Q Consensus 76 AN~aLi~~LAk~L~Vpks~I~ 96 (109)
-+.+-++.||..|||+..+|.
T Consensus 25 p~~~~~~~la~~l~l~~~~V~ 45 (57)
T PF00046_consen 25 PSKEEREELAKELGLTERQVK 45 (57)
T ss_dssp CHHHHHHHHHHHHTSSHHHHH
T ss_pred ccccccccccccccccccccc
Confidence 456778999999999988774
No 63
>KOG0676 consensus Actin and related proteins [Cytoskeleton]
Probab=22.40 E-value=93 Score=26.45 Aligned_cols=30 Identities=23% Similarity=0.244 Sum_probs=24.5
Q ss_pred EEEEEeCCCCCChhHHHHHH-HHHhhcCCCC
Q 033900 63 VGVQIDAPAKDGEANAALLE-YMSSLIHVSV 92 (109)
Q Consensus 63 L~I~V~ApPvdGkAN~aLi~-~LAk~L~Vpk 92 (109)
--|-+++||-+.+||+|.+. +|=+.|+||-
T Consensus 100 ~pvllte~pl~p~~nREk~tqi~FE~fnvpa 130 (372)
T KOG0676|consen 100 HPVLLTEPPLNPKANREKLTQIMFETFNVPA 130 (372)
T ss_pred CceEeecCCCCchHhHHHHHHHhhhhcCccH
Confidence 46789999999999998776 7777777764
No 64
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=21.87 E-value=40 Score=24.53 Aligned_cols=20 Identities=5% Similarity=0.084 Sum_probs=17.7
Q ss_pred HHHHHHHHHhhcCCCCCceE
Q 033900 77 NAALLEYMSSLIHVSVGEFV 96 (109)
Q Consensus 77 N~aLi~~LAk~L~Vpks~I~ 96 (109)
-++.++++|+.||||.++|.
T Consensus 39 p~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 39 PDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred CHHHHHHHHHHhCcCHHHHH
Confidence 35789999999999999987
No 65
>PF00550 PP-binding: Phosphopantetheine attachment site; InterPro: IPR006163 Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups []. The amino-terminal region of the ACP proteins is well defined and consists of alpha four helices arranged in a right-handed bundle held together by interhelical hydrophobic interactions. The Asp-Ser-Leu (DSL)motif is conserved in all of the ACP sequences, and the 4'-PP prosthetic group is covalently linked via a phosphodiester bond to the serine residue. The DSL sequence is present at the amino terminus of helix II, a domain of the protein referred to as the recognition helix and which is responsible for the interaction of ACPs with the enzymes of type II fatty acid synthesis [].; GO: 0048037 cofactor binding; PDB: 3EJB_E 3EJE_G 1L0I_A 2FHS_C 3EJD_E 2FAE_B 2FAD_B 2FAC_B 2K94_A 1ACP_A ....
Probab=21.83 E-value=69 Score=18.88 Aligned_cols=19 Identities=21% Similarity=0.256 Sum_probs=15.2
Q ss_pred HHHHHHHHhhcCCCCCceE
Q 033900 78 AALLEYMSSLIHVSVGEFV 96 (109)
Q Consensus 78 ~aLi~~LAk~L~Vpks~I~ 96 (109)
++|++.+++.|+++..+|.
T Consensus 1 e~l~~~~~~~l~~~~~~i~ 19 (67)
T PF00550_consen 1 EQLREIIAEVLGVDPEEID 19 (67)
T ss_dssp HHHHHHHHHHHTSSGGCTS
T ss_pred CHHHHHHHHHHCcCHhhCC
Confidence 4688899999998877764
No 66
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=21.34 E-value=38 Score=19.54 Aligned_cols=22 Identities=5% Similarity=-0.044 Sum_probs=17.7
Q ss_pred hhHHHHHHHHHhhcCCCCCceE
Q 033900 75 EANAALLEYMSSLIHVSVGEFV 96 (109)
Q Consensus 75 kAN~aLi~~LAk~L~Vpks~I~ 96 (109)
.-+.+-+..||+.+|++.++|.
T Consensus 24 ~P~~~~~~~la~~~~l~~~qV~ 45 (59)
T cd00086 24 YPSREEREELAKELGLTERQVK 45 (59)
T ss_pred CCCHHHHHHHHHHHCcCHHHHH
Confidence 3456778999999999988875
No 67
>COG0770 MurF UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]
Probab=21.16 E-value=39 Score=29.15 Aligned_cols=57 Identities=14% Similarity=0.263 Sum_probs=44.8
Q ss_pred EEEEEecCCCccccccccCCeEEEEEeCCCCCChhHHHHHHHHHhhcCCCCCceEEEE
Q 033900 42 ITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVESV 99 (109)
Q Consensus 42 L~V~VkP~Ak~~~I~g~~~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~Vpks~I~~~~ 99 (109)
-.++..+....-.+ ...+..+.+.+.-|+...-.|..+.-.+|..+|++..+|...+
T Consensus 253 ~~i~~~~~~~~f~~-~~~~~~~~~~l~~~G~hn~~NalaA~a~a~~lG~~~e~i~~~L 309 (451)
T COG0770 253 TNIHLDEEGSSFTL-DIEGGEAEFELPLPGRHNVTNALAAAALALELGLDLEEIAAGL 309 (451)
T ss_pred EEEEEcCCceEEEE-EecCceEEEEecCCcHhHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 34677777743333 3456778999999999999999999999999999998887333
No 68
>TIGR00151 ispF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. Members of this protein family are 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, the IspF protein of the deoxyxylulose (non-mevalonate) pathway of IPP biosynthesis. This protein occurs as an IspDF bifunctional fusion protein in about 20 percent of bacterial genomes.
Probab=21.09 E-value=1.1e+02 Score=23.05 Aligned_cols=34 Identities=12% Similarity=0.044 Sum_probs=27.8
Q ss_pred CCCCCChhHHHHHHHHHhhcCCCCCceEEEEeEE
Q 033900 69 APAKDGEANAALLEYMSSLIHVSVGEFVESVQVF 102 (109)
Q Consensus 69 ApPvdGkAN~aLi~~LAk~L~Vpks~I~~~~~~~ 102 (109)
+.|.=+.==+++.+.||+.|+++..+|.+..++-
T Consensus 100 e~PKi~p~~~~m~~~la~~L~~~~~~V~iKatT~ 133 (155)
T TIGR00151 100 QRPKLLPHIPAMRENIAELLGIPLDSVNVKATTT 133 (155)
T ss_pred CCCcchHHHHHHHHHHHHHhCCCcceEEEEEecC
Confidence 3466666678899999999999999999877763
No 69
>COG3382 Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]
Probab=21.07 E-value=3.2e+02 Score=21.93 Aligned_cols=64 Identities=16% Similarity=0.128 Sum_probs=51.2
Q ss_pred CCCCcceEeeCCCeEEEEEEEecCCCccccccccCCeEEEEEeCCCCCChhHHHHHHHHHhhcC
Q 033900 26 ENLPSCIRLVPPSSVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSLIH 89 (109)
Q Consensus 26 ~~~p~~i~~~~~g~v~L~V~VkP~Ak~~~I~g~~~~~L~I~V~ApPvdGkAN~aLi~~LAk~L~ 89 (109)
..+|.-+.+.++.|...+++.-=.+.++.|..-+...|-|-=.-|.++...=.++++.|++.|.
T Consensus 150 ~~~~geiv~~Dd~G~~~r~~~~Rds~rT~vt~~Tk~~l~I~e~vp~~~~~~l~~a~~~l~~~l~ 213 (229)
T COG3382 150 PPLEGEIVLVDDEGAFCRRWNWRDSVRTMVTESTKNVLLIAEGVPGVEVEDLVEALDSLADLLE 213 (229)
T ss_pred CCCCCcEEEEcCCCCeeeecccccceeeehhhccceEEEEEecCCCccHHHHHHHHHHHHHHHH
Confidence 4566777777777888888888889999988767777777777777788888888888888774
No 70
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=20.84 E-value=63 Score=24.47 Aligned_cols=23 Identities=9% Similarity=0.186 Sum_probs=19.4
Q ss_pred ChhHHHHHHHHHhhcCCCCCceE
Q 033900 74 GEANAALLEYMSSLIHVSVGEFV 96 (109)
Q Consensus 74 GkAN~aLi~~LAk~L~Vpks~I~ 96 (109)
|---.+.+.++|+.||+|.+.|.
T Consensus 39 G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 39 GWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred CCCCHHHHHHHHHHhCCCHHHhe
Confidence 33346789999999999999998
No 71
>COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]
Probab=20.58 E-value=1.8e+02 Score=18.91 Aligned_cols=40 Identities=10% Similarity=0.091 Sum_probs=25.9
Q ss_pred EEEEEeCC-CCCC-hhH--HHHHHHHHhhcCCCCCceEEEEeEE
Q 033900 63 VGVQIDAP-AKDG-EAN--AALLEYMSSLIHVSVGEFVESVQVF 102 (109)
Q Consensus 63 L~I~V~Ap-PvdG-kAN--~aLi~~LAk~L~Vpks~I~~~~~~~ 102 (109)
+.|++... +.+. |+. ++|-+.+++.||.+++.|..-+..+
T Consensus 4 v~Ik~~~g~~~~~~K~~la~~vT~~~~~~lg~~~~~i~Viieev 47 (69)
T COG1942 4 VNIKLFEGRLDEEQKAELAAEVTEVTVETLGKDPSAIHVIIEEV 47 (69)
T ss_pred EEEEecCCCCCHHHHHHHHHHHHHHHHHHhCCCcccEEEEEEec
Confidence 45566542 2222 332 4567788999999999998666543
No 72
>cd06467 p23_NUDC_like p23_like domain of NUD (nuclear distribution) C and similar proteins. Aspergillus nidulas (An) NUDC is needed for nuclear movement. AnNUDC is localized at the hyphal cortex, and binds NUDF at spindle pole bodies (SPBs) and in the cytoplasm at different stages in the cell cycle. At the SPBs it is part of the dynein molecular motor/NUDF complex that regulates microtubule dynamics. Mammalian(m) NUDC associates both with the dynein complex and also with an anti-inflammatory enzyme, platelet activating factor acetylhydrolase I, PAF-AH(I) complex, through binding mNUDF, the regulatory beta subunit of PAF-AH(I). mNUDC is important for cell proliferation both in normal and tumor tissues. Its expression is elevated in various cell types undergoing mitosis or stimulated to proliferate, with high expression levels observed in leukemic cells and tumors. For a leukemic cell line, human NUDC was shown to activate the thrombopoietin (TPO) receptor (Mpl) by binding to its ext
Probab=20.14 E-value=2.3e+02 Score=17.53 Aligned_cols=36 Identities=19% Similarity=0.304 Sum_probs=24.6
Q ss_pred eEeeCCCeEEEEEEEecCCCcccc-ccccCCeEEEEEe
Q 033900 32 IRLVPPSSVSITIHAKPGSKSCSI-TDVSDEAVGVQID 68 (109)
Q Consensus 32 i~~~~~g~v~L~V~VkP~Ak~~~I-~g~~~~~L~I~V~ 68 (109)
|.+..+ .+.|.|.+.++.....+ +.+.++.|.|++.
T Consensus 3 W~Qt~~-~V~i~i~~~~~~~~~dv~v~~~~~~l~v~~~ 39 (85)
T cd06467 3 WTQTLD-EVTVTIPLPEGTKSKDVKVEITPKHLKVGVK 39 (85)
T ss_pred EEeeCC-EEEEEEECCCCCcceeEEEEEEcCEEEEEEC
Confidence 345554 78888888777555444 3466788888885
No 73
>PF08381 BRX: Transcription factor regulating root and shoot growth via Pin3; InterPro: IPR013591 This is a short domain, approximately 35 residues in length that is found near the C terminus in a number of plant proteins, being repeated in some members. It is found in Brevis radix-like proteins. These may act as a regulator of cell proliferation and elongation in the root []. It is also found in proteins annotated as involved in disease resistance and in the regulation of chromosome condensation, which also contain other domains with varied functions, such as TIR (IPR000157 from INTERPRO) and FYVE (IPR000306 from INTERPRO) respectively.
Probab=20.06 E-value=1.6e+02 Score=18.90 Aligned_cols=22 Identities=23% Similarity=0.326 Sum_probs=18.3
Q ss_pred cceEeeCCCeEEEEEEEecCCCc
Q 033900 30 SCIRLVPPSSVSITIHAKPGSKS 52 (109)
Q Consensus 30 ~~i~~~~~g~v~L~V~VkP~Ak~ 52 (109)
.|+.+..+ ||.|.+.+.|+..+
T Consensus 5 Ewveq~Ep-GVyiTl~~~p~G~~ 26 (59)
T PF08381_consen 5 EWVEQDEP-GVYITLVSLPDGGN 26 (59)
T ss_pred cEEEeeCC-eeEEEEEECCCCCe
Confidence 68888887 89999999997643
Done!