Query 029470
Match_columns 193
No_of_seqs 168 out of 356
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 13:25:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029470.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029470hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3389 NADH:ubiquinone oxidor 100.0 7.9E-53 1.7E-57 346.5 9.0 132 21-191 41-176 (178)
2 PF04800 ETC_C1_NDUFA4: ETC co 100.0 2.3E-48 4.9E-53 299.3 6.9 96 52-188 1-97 (101)
3 PF09954 DUF2188: Uncharacteri 79.2 1.5 3.3E-05 30.2 2.0 17 105-121 22-38 (62)
4 PF05573 NosL: NosL; InterPro 71.9 4.5 9.8E-05 32.5 3.2 51 71-122 76-135 (149)
5 PF08727 P3A: Poliovirus 3A pr 66.8 3.7 8.1E-05 29.5 1.5 15 112-126 30-44 (57)
6 PHA02552 4 head completion pro 64.7 5.8 0.00013 33.0 2.5 65 52-127 60-136 (151)
7 PRK05370 argininosuccinate syn 59.4 6.3 0.00014 38.1 2.1 40 106-145 164-207 (447)
8 COG1010 CobJ Precorrin-3B meth 52.1 16 0.00035 33.0 3.3 49 92-148 78-143 (249)
9 PF08722 Tn7_Tnp_TnsA_N: TnsA 50.8 16 0.00035 26.3 2.6 17 111-127 69-85 (88)
10 PRK12354 carbamate kinase; Rev 47.0 19 0.00042 33.0 3.1 29 107-135 125-153 (307)
11 COG3341 Predicted double-stran 45.8 15 0.00033 32.8 2.1 15 106-120 38-52 (225)
12 PF11360 DUF3110: Protein of u 45.5 17 0.00037 27.5 2.1 14 105-118 26-39 (86)
13 PF06194 Phage_Orf51: Phage Co 40.1 24 0.00052 27.0 2.1 23 104-126 50-72 (80)
14 PF07045 DUF1330: Protein of u 39.9 24 0.00051 24.4 2.0 14 105-118 43-56 (65)
15 PF08803 ydhR: Putative mono-o 39.7 16 0.00034 28.7 1.1 29 91-121 38-66 (97)
16 PF10075 PCI_Csn8: COP9 signal 39.5 20 0.00044 27.9 1.8 20 106-126 107-126 (143)
17 PF00331 Glyco_hydro_10: Glyco 39.0 28 0.00061 31.1 2.8 33 105-146 55-87 (320)
18 PRK04527 argininosuccinate syn 37.9 21 0.00047 33.8 2.0 21 107-127 150-170 (400)
19 PF02844 GARS_N: Phosphoribosy 36.9 29 0.00064 26.9 2.3 26 105-130 45-70 (100)
20 PF03462 PCRF: PCRF domain; I 34.4 29 0.00062 26.9 1.9 14 115-128 73-86 (115)
21 PLN00139 hypothetical protein; 33.3 59 0.0013 29.5 3.9 26 106-131 195-220 (320)
22 PRK11118 putative monooxygenas 31.7 51 0.0011 26.1 2.9 29 91-121 41-69 (100)
23 PF12518 DUF3721: Protein of u 31.3 43 0.00093 21.8 2.0 16 108-123 1-16 (34)
24 PF01071 GARS_A: Phosphoribosy 31.2 51 0.0011 28.3 3.0 28 105-132 20-48 (194)
25 KOG2854 Possible pfkB family c 30.8 27 0.00058 32.9 1.4 52 105-168 216-268 (343)
26 smart00156 PP2Ac Protein phosp 30.7 79 0.0017 27.8 4.2 39 83-128 176-217 (271)
27 PF01693 Cauli_VI: Caulimoviru 30.7 38 0.00082 22.0 1.7 13 105-117 32-44 (44)
28 PF13031 DUF3892: Protein of u 30.3 80 0.0017 22.9 3.5 23 106-128 28-50 (85)
29 PF05198 IF3_N: Translation in 30.2 65 0.0014 23.7 3.1 35 105-139 24-59 (76)
30 PF11360 DUF3110: Protein of u 29.3 63 0.0014 24.4 2.9 52 72-131 23-77 (86)
31 PRK05773 3,4-dihydroxy-2-butan 27.2 52 0.0011 28.9 2.5 18 109-126 191-208 (219)
32 PRK09411 carbamate kinase; Rev 26.6 68 0.0015 29.5 3.2 30 106-135 125-154 (297)
33 smart00633 Glyco_10 Glycosyl h 26.6 61 0.0013 27.6 2.7 34 105-147 12-45 (254)
34 PF02811 PHP: PHP domain; Int 26.4 39 0.00084 25.6 1.4 38 109-157 16-53 (175)
35 PF03108 DBD_Tnp_Mut: MuDR fam 26.3 97 0.0021 21.1 3.2 23 105-127 7-33 (67)
36 PRK00823 phhB pterin-4-alpha-c 26.3 60 0.0013 24.3 2.4 35 86-122 16-50 (97)
37 COG0108 RibB 3,4-dihydroxy-2-b 26.2 49 0.0011 29.1 2.1 19 109-127 172-190 (203)
38 KOG4748 Subunit of Golgi manno 25.2 44 0.00096 31.7 1.7 18 110-127 127-144 (364)
39 PRK12454 carbamate kinase-like 25.1 75 0.0016 29.3 3.2 28 107-134 134-162 (313)
40 PF05406 WGR: WGR domain; Int 24.5 56 0.0012 23.4 1.8 47 69-120 17-64 (81)
41 PF11823 DUF3343: Protein of u 24.4 87 0.0019 22.0 2.8 22 105-126 44-67 (73)
42 cd00913 PCD_DCoH_subfamily_a P 24.4 85 0.0018 22.5 2.7 30 90-121 1-30 (76)
43 TIGR01465 cobM_cbiF precorrin- 23.5 92 0.002 25.6 3.2 36 89-132 74-109 (229)
44 PRK06136 uroporphyrin-III C-me 23.4 38 0.00082 28.4 0.9 38 89-134 83-120 (249)
45 COG5470 Uncharacterized conser 23.4 67 0.0015 25.3 2.2 20 95-117 50-69 (96)
46 TIGR00269 conserved hypothetic 23.1 76 0.0017 24.0 2.4 22 105-126 6-27 (104)
47 cd00914 PCD_DCoH_subfamily_b P 23.1 75 0.0016 22.8 2.3 31 90-122 1-31 (76)
48 PF07862 Nif11: Nitrogen fixat 23.1 75 0.0016 20.7 2.1 19 108-126 26-44 (49)
49 cd01206 Homer Homer type EVH1 23.0 82 0.0018 25.4 2.6 32 87-120 63-102 (111)
50 PF14791 DNA_pol_B_thumb: DNA 22.6 8.7 0.00019 27.4 -2.7 26 88-126 2-27 (64)
51 PF14259 RRM_6: RNA recognitio 22.0 91 0.002 20.4 2.4 18 105-122 43-60 (70)
52 PF00568 WH1: WH1 domain; Int 21.9 76 0.0016 24.1 2.2 29 86-120 78-106 (111)
53 PF01329 Pterin_4a: Pterin 4 a 21.5 77 0.0017 23.6 2.1 31 86-120 15-46 (95)
54 PF14542 Acetyltransf_CG: GCN5 21.5 71 0.0015 23.0 1.9 16 111-126 44-59 (78)
55 smart00461 WH1 WASP homology r 21.5 75 0.0016 24.2 2.1 17 105-121 86-102 (106)
56 PF10566 Glyco_hydro_97: Glyco 21.3 84 0.0018 28.4 2.7 28 105-132 28-55 (273)
57 cd01207 Ena-Vasp Enabled-VASP- 21.1 68 0.0015 25.5 1.8 45 71-121 54-103 (111)
58 PF12745 HGTP_anticodon2: Anti 21.1 98 0.0021 27.7 3.1 19 109-127 44-62 (273)
59 PTZ00175 diphthine synthase; P 20.6 1.2E+02 0.0025 27.0 3.4 34 91-132 81-114 (270)
60 PRK11235 bifunctional antitoxi 20.4 24 0.00053 26.5 -0.8 55 105-163 7-61 (80)
61 cd07415 MPP_PP2A_PP4_PP6 PP2A, 20.2 1.6E+02 0.0035 26.3 4.2 39 83-128 191-231 (285)
62 TIGR02384 RelB_DinJ addiction 20.0 31 0.00067 25.6 -0.3 45 105-152 8-52 (83)
No 1
>KOG3389 consensus NADH:ubiquinone oxidoreductase, NDUFS4/18 kDa subunit [Energy production and conversion]
Probab=100.00 E-value=7.9e-53 Score=346.54 Aligned_cols=132 Identities=59% Similarity=1.081 Sum_probs=124.2
Q ss_pred CcccccCccc-ccc--cCCCccccccCCccccc-cceEEEecCCCCCCCCCCCCCCCcEEEcCCCCCCcCCCcCccCCCC
Q 029470 21 PFSRAFSADA-LVE--VKPGEIGMVSGIPEEHL-RRRVVIYTPARTATQQGSGKLGRWKINFMSTQKWENPLMGWTSTGD 96 (193)
Q Consensus 21 pl~r~Fs~Da-~~~--~~~ge~~~vSGiPee~~-~RrVrIY~PaK~AmQSG~~~t~~W~LeFe~~~rwenPLMGWTSS~D 96 (193)
-|+++|+.|+ ++| .+-++++.|+|+|+||+ .|+||||+|||++||||.+|+++|+|||+.+.+||||||||+|++|
T Consensus 41 rla~~~~~Dak~ve~d~kld~i~~v~GvPeeH~~sRkvrIf~PAR~~tQSg~gntkkWkiefd~r~rWENPLMGWtsTaD 120 (178)
T KOG3389|consen 41 RLARPFATDAKVVESDYKLDEIGKVSGVPEEHLDSRKVRIFSPARTATQSGSGNTKKWKIEFDSRLRWENPLMGWTSTAD 120 (178)
T ss_pred cccccccccceeEeehhhhcccccccCCChHHhcceeEEEecchhhhhhcccCCccceEEEecchhhccCccccccccCC
Confidence 3688999999 555 46788999999999999 5999999999999999999999999999999999999999999999
Q ss_pred ccCCcCCceeeeCCHHHHHHHHHHcCCeeEEcccccccceeeeccccCCCCCCCChhhhhhhhhcccccccCCCCCCCcc
Q 029470 97 PYANVGDAGLSFDSKEAAREFAERHGWEYVAAGDIFRTFCAITISHTTTPLTPHPKKEKRKKEMYETLVRKPHRPLLKVK 176 (193)
Q Consensus 97 plsqV~~~~L~F~SkE~AIaYAer~Gw~Y~V~~~~~~~~~~~~~sh~~~p~~~~~~~~~~~~~~~~~~v~~p~~~~~~~k 176 (193)
|++||+ +.|.|+|+|||++|||||||+|. |.+||.|++|+|
T Consensus 121 PlsNvg-m~L~F~tkEdA~sFaEkngW~yd--------------------------------------veep~~pk~K~K 161 (178)
T KOG3389|consen 121 PLSNVG-MALAFDTKEDAKSFAEKNGWDYD--------------------------------------VEEPNTPKLKVK 161 (178)
T ss_pred cccccc-eeeeeccHHHHHHHHHHcCCccc--------------------------------------ccCCCCCccccc
Confidence 999996 69999999999999999999999 999999999999
Q ss_pred cccccCCCCCCCCCC
Q 029470 177 SYADNFKWKGPPKTD 191 (193)
Q Consensus 177 sya~nf~~~~~~~~~ 191 (193)
||+|||+|||.+..+
T Consensus 162 sYg~NFsWn~rtr~~ 176 (178)
T KOG3389|consen 162 SYGDNFSWNGRTRPE 176 (178)
T ss_pred cccccccccCCCCCC
Confidence 999999999988644
No 2
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=100.00 E-value=2.3e-48 Score=299.31 Aligned_cols=96 Identities=49% Similarity=0.987 Sum_probs=60.6
Q ss_pred ceEEEecCCCCCCCCCCCCCCCcEEEcCCCCCCcCCCcCccCCCCccCC-cCCceeeeCCHHHHHHHHHHcCCeeEEccc
Q 029470 52 RRVVIYTPARTATQQGSGKLGRWKINFMSTQKWENPLMGWTSTGDPYAN-VGDAGLSFDSKEAAREFAERHGWEYVAAGD 130 (193)
Q Consensus 52 RrVrIY~PaK~AmQSG~~~t~~W~LeFe~~~rwenPLMGWTSS~Dplsq-V~~~~L~F~SkE~AIaYAer~Gw~Y~V~~~ 130 (193)
|+||||+|+|+|||||.+++++|+|||+..++|+|||||||||+||++| | +|+|+|+|+||+|||+|||+|+
T Consensus 1 r~arIy~pak~amQSG~~~t~~W~lefe~~~~~~~PLMGWtss~D~~~q~v---~l~F~skE~Ai~yaer~G~~Y~---- 73 (101)
T PF04800_consen 1 RKARIYQPAKNAMQSGTANTKKWVLEFETRARWENPLMGWTSSGDPLSQSV---RLKFDSKEDAIAYAERNGWDYE---- 73 (101)
T ss_dssp -EEEEE--SS--STTTT-SS--EEEEEEESSS---TTT-SSSS--SEEE-C---EEEESSHHHHHHHHHHCT-EEE----
T ss_pred CeEEEeCCCCCCCCCCCCCCCCEEEeecCcCCcCCCccCCCCCCChhhCee---EeeeCCHHHHHHHHHHcCCeEE----
Confidence 6899999999999999999999999999889999999999999999998 7 9999999999999999999999
Q ss_pred ccccceeeeccccCCCCCCCChhhhhhhhhcccccccCCCCCCCcccccccCCCCCCC
Q 029470 131 IFRTFCAITISHTTTPLTPHPKKEKRKKEMYETLVRKPHRPLLKVKSYADNFKWKGPP 188 (193)
Q Consensus 131 ~~~~~~~~~~sh~~~p~~~~~~~~~~~~~~~~~~v~~p~~~~~~~ksya~nf~~~~~~ 188 (193)
|.+|+.+.+++|||+|||+|++..
T Consensus 74 ----------------------------------V~~p~~r~~~~ksY~dNF~~~r~~ 97 (101)
T PF04800_consen 74 ----------------------------------VEEPKKRKRRPKSYADNFSWNRRT 97 (101)
T ss_dssp ----------------------------------EE-STT------------------
T ss_pred ----------------------------------EeCCCCCcCCcccHHHhCCcCCCC
Confidence 999999999999999999999753
No 3
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=79.19 E-value=1.5 Score=30.16 Aligned_cols=17 Identities=35% Similarity=0.370 Sum_probs=14.4
Q ss_pred eeeeCCHHHHHHHHHHc
Q 029470 105 GLSFDSKEAAREFAERH 121 (193)
Q Consensus 105 ~L~F~SkE~AIaYAer~ 121 (193)
...|+|+++||++|++.
T Consensus 22 ~~~~~Tk~eAi~~Ar~~ 38 (62)
T PF09954_consen 22 SKTFDTKAEAIEAAREL 38 (62)
T ss_pred ccccCcHHHHHHHHHHH
Confidence 58899999999988753
No 4
>PF05573 NosL: NosL; InterPro: IPR008719 NosL is one of the accessory proteins of the nos (nitrous oxide reductase) gene cluster. NosL is a monomeric protein of 18,540 MW that specifically and stoichiometrically binds Cu(I). The copper ion in NosL is ligated by a Cys residue, and one Met and one His are thought to serve as the other ligands. It is possible that NosL is a copper chaperone involved in metallocentre assembly []. This entry also contains HTH-type transcriptional repressors, including YcnK. YcnK may act as a negative transcriptional regulator of YcnJ in the presence of copper and may use copper as a corepressor. The gene, ycnK, is significantly induced under copper-limiting conditions.; PDB: 2HQ3_A 2HPU_A.
Probab=71.89 E-value=4.5 Score=32.48 Aligned_cols=51 Identities=27% Similarity=0.575 Sum_probs=28.8
Q ss_pred CCCcEEEcCCCCCCcCCCc-CccCC--------CCccCCcCCceeeeCCHHHHHHHHHHcC
Q 029470 71 LGRWKINFMSTQKWENPLM-GWTST--------GDPYANVGDAGLSFDSKEAAREFAERHG 122 (193)
Q Consensus 71 t~~W~LeFe~~~rwenPLM-GWTSS--------~DplsqV~~~~L~F~SkE~AIaYAer~G 122 (193)
..-|+-||.. ..|.+|-- -|... +|-.+-++..-+-|.++++|.+|+++||
T Consensus 76 ~~~~V~D~~~-~~~~~p~~~~~Ida~~A~yV~gs~~~~pMg~~~~aF~~~~~A~~F~~~~G 135 (149)
T PF05573_consen 76 AAIYVTDYST-TDWDQPGDGEWIDAKKAYYVVGSDVRGPMGPDLIAFASKEDAEAFAKEHG 135 (149)
T ss_dssp EEEEEEES-T-S-TT-S---EEEEGGGSEEEEESSSS-TTS--EEEES-HHHHHHHHHHTE
T ss_pred cEEEEEeccc-ccccCCCCCceEEcceEEEEECCCcCCCCCCcccccCCHHHHHHHHHHcC
Confidence 3568888887 55555542 34332 2222222334688999999999999998
No 5
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=66.76 E-value=3.7 Score=29.55 Aligned_cols=15 Identities=33% Similarity=0.762 Sum_probs=11.0
Q ss_pred HHHHHHHHHcCCeeE
Q 029470 112 EAAREFAERHGWEYV 126 (193)
Q Consensus 112 E~AIaYAer~Gw~Y~ 126 (193)
++-++||+++||-..
T Consensus 30 ~eV~~YC~~~GWIip 44 (57)
T PF08727_consen 30 PEVREYCEEQGWIIP 44 (57)
T ss_dssp HHHHHHHHHHT--TT
T ss_pred HHHHHHHHHCCcccc
Confidence 558999999999655
No 6
>PHA02552 4 head completion protein; Provisional
Probab=64.69 E-value=5.8 Score=33.02 Aligned_cols=65 Identities=18% Similarity=0.260 Sum_probs=40.3
Q ss_pred ceEEEecCCCCC-CCCCCCCCCCcEEEcCCCCCCcCCCcCccCCCCccCCcCCceeeeC-----------CHHHHHHHHH
Q 029470 52 RRVVIYTPARTA-TQQGSGKLGRWKINFMSTQKWENPLMGWTSTGDPYANVGDAGLSFD-----------SKEAAREFAE 119 (193)
Q Consensus 52 RrVrIY~PaK~A-mQSG~~~t~~W~LeFe~~~rwenPLMGWTSS~DplsqV~~~~L~F~-----------SkE~AIaYAe 119 (193)
.++|.|-|.=-+ +..| ....+|.-+..+..+|.|- ..-|+.+ ...|. --++|.+||+
T Consensus 60 Gk~r~Y~PDFLV~~~dG----~~~lvEVKp~~~~~~p~~~--~~~~~~~-----~~~~~~~~~~w~~~~~K~~Aa~~~a~ 128 (151)
T PHA02552 60 GKRRRYFMDFYVKVDNG----QKFLIEVKPKKETQPPKKP--AKMTTAA-----KKRFINEVYTWSVNTDKWKAARALCE 128 (151)
T ss_pred CCeeeEcCcEEEEEeCC----CEEEEEEccHHHccCcccc--cccchhh-----hhhhhhhhhhHHHHHHHHHHHHHHHH
Confidence 457788887333 2233 4788898888777766442 1111110 12222 2378999999
Q ss_pred HcCCeeEE
Q 029470 120 RHGWEYVA 127 (193)
Q Consensus 120 r~Gw~Y~V 127 (193)
++||.|.|
T Consensus 129 ~~Gw~F~i 136 (151)
T PHA02552 129 KKGWKFKI 136 (151)
T ss_pred HcCCEEEE
Confidence 99999996
No 7
>PRK05370 argininosuccinate synthase; Validated
Probab=59.36 E-value=6.3 Score=38.05 Aligned_cols=40 Identities=15% Similarity=0.212 Sum_probs=28.1
Q ss_pred eeeCCHHHHHHHHHHcCCeeEEc--cccccc--ceeeeccccCC
Q 029470 106 LSFDSKEAAREFAERHGWEYVAA--GDIFRT--FCAITISHTTT 145 (193)
Q Consensus 106 L~F~SkE~AIaYAer~Gw~Y~V~--~~~~~~--~~~~~~sh~~~ 145 (193)
-.|.|+++.|+||++||++..+. .+++.. ||-++|.=--|
T Consensus 164 ~~f~sR~e~i~Ya~~hGIpv~~~~~~~ySiD~NLwg~S~Egg~L 207 (447)
T PRK05370 164 DELGGRAEMSEFLIAHGFDYKMSVEKAYSTDSNMLGATHEAKDL 207 (447)
T ss_pred cccCCHHHHHHHHHHcCCCCCccCCCCccCccChheeeeccccc
Confidence 46899999999999999997742 233322 66666655544
No 8
>COG1010 CobJ Precorrin-3B methylase [Coenzyme metabolism]
Probab=52.09 E-value=16 Score=33.03 Aligned_cols=49 Identities=31% Similarity=0.460 Sum_probs=35.4
Q ss_pred cCCCCccCCcCCceeeeCCHHHHHHHHHHcC---CeeEEc--------------ccccccceeeeccccCCCCC
Q 029470 92 TSTGDPYANVGDAGLSFDSKEAAREFAERHG---WEYVAA--------------GDIFRTFCAITISHTTTPLT 148 (193)
Q Consensus 92 TSS~DplsqV~~~~L~F~SkE~AIaYAer~G---w~Y~V~--------------~~~~~~~~~~~~sh~~~p~~ 148 (193)
.|||||- | |.=.-.+...++++| .+++|+ .+..--||+|++|-+.+|..
T Consensus 78 VSsGDpg--V------YgMA~lv~E~~~~~~~~~v~veVvPGvTA~~aaAa~lGAPL~hDF~~ISLSDlLtPwe 143 (249)
T COG1010 78 VSSGDPG--V------YGMAGLVLEAAEEEGWYDVDVEVVPGVTAALAAAARLGAPLGHDFCVISLSDLLTPWE 143 (249)
T ss_pred EeCCCcc--H------HHhHHHHHHHHHhcCCCCccEEEeCChHHHHHHHHHhCCCcccceEEEEhHhcCCcHH
Confidence 6899994 3 444566778888887 477774 23345599999999988753
No 9
>PF08722 Tn7_Tnp_TnsA_N: TnsA endonuclease N terminal; InterPro: IPR014833 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The N-terminal domain of TnsA is catalytic. ; PDB: 1F1Z_B 1T0F_B.
Probab=50.79 E-value=16 Score=26.33 Aligned_cols=17 Identities=29% Similarity=0.438 Sum_probs=12.6
Q ss_pred HHHHHHHHHHcCCeeEE
Q 029470 111 KEAAREFAERHGWEYVA 127 (193)
Q Consensus 111 kE~AIaYAer~Gw~Y~V 127 (193)
.+.|-.||+++||+|.|
T Consensus 69 ~~~~~~y~~~~g~~f~i 85 (88)
T PF08722_consen 69 LEIEREYWEEQGIPFRI 85 (88)
T ss_dssp HHHHHHHHHHCT--EEE
T ss_pred HHHHHHHHHHcCCeEEE
Confidence 35688999999999995
No 10
>PRK12354 carbamate kinase; Reviewed
Probab=47.03 E-value=19 Score=32.95 Aligned_cols=29 Identities=28% Similarity=0.558 Sum_probs=25.1
Q ss_pred eeCCHHHHHHHHHHcCCeeEEcccccccc
Q 029470 107 SFDSKEAAREFAERHGWEYVAAGDIFRTF 135 (193)
Q Consensus 107 ~F~SkE~AIaYAer~Gw~Y~V~~~~~~~~ 135 (193)
.|-|+|+|.+.++++||.+...+..+||.
T Consensus 125 ~~y~~~~a~~~~~e~g~~~~~dg~g~rrV 153 (307)
T PRK12354 125 PVYDEAEAERLAAEKGWTIKPDGDYFRRV 153 (307)
T ss_pred cccCHHHHHHHHHhcCCEEeecCCceEEE
Confidence 58899999999999999988777777753
No 11
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=45.79 E-value=15 Score=32.75 Aligned_cols=15 Identities=40% Similarity=0.496 Sum_probs=13.5
Q ss_pred eeeCCHHHHHHHHHH
Q 029470 106 LSFDSKEAAREFAER 120 (193)
Q Consensus 106 L~F~SkE~AIaYAer 120 (193)
=+|+|.|+|.+||+.
T Consensus 38 Ksf~s~EeA~a~~~g 52 (225)
T COG3341 38 KSFKSYEEAEAYCEG 52 (225)
T ss_pred cccccHHHHHHHhcc
Confidence 469999999999995
No 12
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=45.52 E-value=17 Score=27.48 Aligned_cols=14 Identities=29% Similarity=0.567 Sum_probs=10.9
Q ss_pred eeeeCCHHHHHHHH
Q 029470 105 GLSFDSKEAAREFA 118 (193)
Q Consensus 105 ~L~F~SkE~AIaYA 118 (193)
.|-|.+.+||.+||
T Consensus 26 Vl~FE~edDA~RYa 39 (86)
T PF11360_consen 26 VLMFEDEDDAERYA 39 (86)
T ss_pred EEEEccHHHHHHHH
Confidence 78888888887665
No 13
>PF06194 Phage_Orf51: Phage Conserved Open Reading Frame 51; InterPro: IPR009338 This entry is represented by the Staphylococcus phage PVL (bacteriophage phi-PVL), Orf51. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=40.10 E-value=24 Score=27.00 Aligned_cols=23 Identities=17% Similarity=0.382 Sum_probs=21.8
Q ss_pred ceeeeCCHHHHHHHHHHcCCeeE
Q 029470 104 AGLSFDSKEAAREFAERHGWEYV 126 (193)
Q Consensus 104 ~~L~F~SkE~AIaYAer~Gw~Y~ 126 (193)
....|+|+++-..|-+.+|+.|+
T Consensus 50 vKktFn~~~Ef~~Yi~~~~L~~e 72 (80)
T PF06194_consen 50 VKKTFNNKEEFENYIKQHELYFE 72 (80)
T ss_pred hhhhcCcHHHHHHHHHHcCCcee
Confidence 38999999999999999999998
No 14
>PF07045 DUF1330: Protein of unknown function (DUF1330); InterPro: IPR010753 This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.; PDB: 2FIU_B 3HHL_A 3DCA_D 3LO3_I.
Probab=39.90 E-value=24 Score=24.41 Aligned_cols=14 Identities=36% Similarity=0.432 Sum_probs=12.8
Q ss_pred eeeeCCHHHHHHHH
Q 029470 105 GLSFDSKEAAREFA 118 (193)
Q Consensus 105 ~L~F~SkE~AIaYA 118 (193)
-+.|+|.++|++|-
T Consensus 43 iieFPs~~aa~~~~ 56 (65)
T PF07045_consen 43 IIEFPSMEAAKAWY 56 (65)
T ss_dssp EEEESSHHHHHHHH
T ss_pred EEECCCHHHHHHHH
Confidence 89999999999874
No 15
>PF08803 ydhR: Putative mono-oxygenase ydhR; InterPro: IPR014910 YdhR is a homodimeric protein that comprises of a central four-stranded beta sheet and four surrounding alpha helices []. It shows structural homology to the ActVA-Orf6 and YgiN proteins which indicates it could be a mono-oxygenase. ; PDB: 1WD6_B 2HIQ_B 2ASY_B.
Probab=39.69 E-value=16 Score=28.69 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=22.9
Q ss_pred ccCCCCccCCcCCceeeeCCHHHHHHHHHHc
Q 029470 91 WTSTGDPYANVGDAGLSFDSKEAAREFAERH 121 (193)
Q Consensus 91 WTSS~DplsqV~~~~L~F~SkE~AIaYAer~ 121 (193)
||.+.++..- +| ..-|+|+++|.+|+++|
T Consensus 38 Wten~~t~ea-GG-iYLFe~e~~A~aY~~~h 66 (97)
T PF08803_consen 38 WTENEETGEA-GG-IYLFEDEASAEAYLEMH 66 (97)
T ss_dssp EEEETTTTEE-EE-EEEESSHHHHHHHHHHH
T ss_pred EEecCCCCcc-ce-EEEECCHHHHHHHHHHH
Confidence 7777776532 33 67899999999999998
No 16
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=39.52 E-value=20 Score=27.93 Aligned_cols=20 Identities=25% Similarity=0.611 Sum_probs=15.5
Q ss_pred eeeCCHHHHHHHHHHcCCeeE
Q 029470 106 LSFDSKEAAREFAERHGWEYV 126 (193)
Q Consensus 106 L~F~SkE~AIaYAer~Gw~Y~ 126 (193)
|-|+ .+++++||+++||.++
T Consensus 107 Lg~~-~~el~~~~~~~gW~~d 126 (143)
T PF10075_consen 107 LGLS-EEELEKFIKSRGWTVD 126 (143)
T ss_dssp TTS--HHHHHHHHHHHT-EE-
T ss_pred hCCC-HHHHHHHHHHcCCEEC
Confidence 5666 8999999999999998
No 17
>PF00331 Glyco_hydro_10: Glycosyl hydrolase family 10; InterPro: IPR001000 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 10 GH10 from CAZY comprises enzymes with a number of known activities; xylanase (3.2.1.8 from EC); endo-1,3-beta-xylanase (3.2.1.32 from EC); cellobiohydrolase (3.2.1.91 from EC). These enzymes were formerly known as cellulase family F. The microbial degradation of cellulose and xylans requires several types of enzymes such as endoglucanases (3.2.1.4 from EC), cellobiohydrolases (3.2.1.91 from EC) (exoglucanases), or xylanases (3.2.1.8 from EC) [, ]. Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family F [] or as the glycosyl hydrolases family 10 []. ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1UQZ_A 1UQY_A 1UR2_A 1UR1_A 2CNC_A 1OD8_A 1E0W_A 1E0V_A 1V0M_A 1E0X_B ....
Probab=38.97 E-value=28 Score=31.06 Aligned_cols=33 Identities=24% Similarity=0.423 Sum_probs=26.4
Q ss_pred eeeeCCHHHHHHHHHHcCCeeEEcccccccceeeeccccCCC
Q 029470 105 GLSFDSKEAAREFAERHGWEYVAAGDIFRTFCAITISHTTTP 146 (193)
Q Consensus 105 ~L~F~SkE~AIaYAer~Gw~Y~V~~~~~~~~~~~~~sh~~~p 146 (193)
+..|++.++.++||+++|+... |-+-+-|.-+|
T Consensus 55 ~~~~~~~D~~~~~a~~~g~~vr---------GH~LvW~~~~P 87 (320)
T PF00331_consen 55 RFNFESADAILDWARENGIKVR---------GHTLVWHSQTP 87 (320)
T ss_dssp BEE-HHHHHHHHHHHHTT-EEE---------EEEEEESSSS-
T ss_pred ccCccchhHHHHHHHhcCccee---------eeeEEEccccc
Confidence 5899999999999999999999 67777787666
No 18
>PRK04527 argininosuccinate synthase; Provisional
Probab=37.85 E-value=21 Score=33.79 Aligned_cols=21 Identities=14% Similarity=0.325 Sum_probs=18.4
Q ss_pred eeCCHHHHHHHHHHcCCeeEE
Q 029470 107 SFDSKEAAREFAERHGWEYVA 127 (193)
Q Consensus 107 ~F~SkE~AIaYAer~Gw~Y~V 127 (193)
+++++++.|+||++|||+..+
T Consensus 150 k~~~R~~~i~ya~~~gipv~~ 170 (400)
T PRK04527 150 HTQTRAYEQKYLEERGFGVRA 170 (400)
T ss_pred ccccHHHHHHHHHHcCCCCCC
Confidence 347999999999999998874
No 19
>PF02844 GARS_N: Phosphoribosylglycinamide synthetase, N domain; InterPro: IPR020562 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) [] catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide: ATP + 5-phosphoribosylamine + glycine = ADP + Pi + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART. This entry represents the N-domain, which is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (IPR005481 from INTERPRO).; GO: 0004637 phosphoribosylamine-glycine ligase activity, 0009113 purine base biosynthetic process; PDB: 3MJF_A 2XD4_A 2XCL_A 2IP4_A 2YW2_B 2YYA_A 3LP8_A 1VKZ_A 2YS6_A 2YRX_A ....
Probab=36.87 E-value=29 Score=26.94 Aligned_cols=26 Identities=19% Similarity=0.368 Sum_probs=20.3
Q ss_pred eeeeCCHHHHHHHHHHcCCeeEEccc
Q 029470 105 GLSFDSKEAAREFAERHGWEYVAAGD 130 (193)
Q Consensus 105 ~L~F~SkE~AIaYAer~Gw~Y~V~~~ 130 (193)
.+...+.++-++||+++++++.|+|+
T Consensus 45 ~~~~~d~~~l~~~a~~~~idlvvvGP 70 (100)
T PF02844_consen 45 PIDITDPEELADFAKENKIDLVVVGP 70 (100)
T ss_dssp -S-TT-HHHHHHHHHHTTESEEEESS
T ss_pred CCCCCCHHHHHHHHHHcCCCEEEECC
Confidence 35678899999999999999997654
No 20
>PF03462 PCRF: PCRF domain; InterPro: IPR005139 This domain is found in peptide chain release factors. Peptide chain release factors are important for protein synthesis since they direct the termination of translation in response to the peptide chain termination codons UAG and UAA. These are structurally distinct but both contain the PCRF domain [].; GO: 0016149 translation release factor activity, codon specific, 0006415 translational termination, 0005737 cytoplasm; PDB: 3D5A_X 3D5C_X 3MR8_V 3MS0_V 3F1G_X 3F1E_X 1ZBT_A 2IHR_1 2X9R_Y 2X9T_Y ....
Probab=34.43 E-value=29 Score=26.86 Aligned_cols=14 Identities=36% Similarity=0.862 Sum_probs=11.2
Q ss_pred HHHHHHcCCeeEEc
Q 029470 115 REFAERHGWEYVAA 128 (193)
Q Consensus 115 IaYAer~Gw~Y~V~ 128 (193)
..||+++||+|+|.
T Consensus 73 ~~~a~~~gw~~~~l 86 (115)
T PF03462_consen 73 QRYAERRGWKVEVL 86 (115)
T ss_dssp HHHHHHTT-EEEEE
T ss_pred HHHHHHcCCEEEEE
Confidence 48999999999963
No 21
>PLN00139 hypothetical protein; Provisional
Probab=33.30 E-value=59 Score=29.49 Aligned_cols=26 Identities=15% Similarity=0.041 Sum_probs=22.2
Q ss_pred eeeCCHHHHHHHHHHcCCeeEEcccc
Q 029470 106 LSFDSKEAAREFAERHGWEYVAAGDI 131 (193)
Q Consensus 106 L~F~SkE~AIaYAer~Gw~Y~V~~~~ 131 (193)
..-++++++.+||.++|++|+-.+|.
T Consensus 195 F~t~d~~eve~~~~~~g~~~eW~~dg 220 (320)
T PLN00139 195 FGTSDKAEAERRAKALGMDMEWLPNG 220 (320)
T ss_pred hCCCCHHHHHHHHHHcCCeEEEcCCC
Confidence 44578999999999999999986664
No 22
>PRK11118 putative monooxygenase; Provisional
Probab=31.66 E-value=51 Score=26.13 Aligned_cols=29 Identities=21% Similarity=0.428 Sum_probs=22.7
Q ss_pred ccCCCCccCCcCCceeeeCCHHHHHHHHHHc
Q 029470 91 WTSTGDPYANVGDAGLSFDSKEAAREFAERH 121 (193)
Q Consensus 91 WTSS~DplsqV~~~~L~F~SkE~AIaYAer~ 121 (193)
||.+.++.. .|--.-|++.++|-+|.++|
T Consensus 41 WTen~~t~e--aGGiYlF~~e~~a~aYl~mH 69 (100)
T PRK11118 41 WTENEKTQE--AGGIYLFEDEASAEAYLEMH 69 (100)
T ss_pred eecCCCCcc--cceEEEECCHHHHHHHHHHH
Confidence 777776653 23378899999999999986
No 23
>PF12518 DUF3721: Protein of unknown function; InterPro: IPR022196 This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length. There is a conserved WMPC sequence motif. There are two completely conserved residues (A and C) that may be functionally important.
Probab=31.29 E-value=43 Score=21.83 Aligned_cols=16 Identities=25% Similarity=0.368 Sum_probs=14.1
Q ss_pred eCCHHHHHHHHHHcCC
Q 029470 108 FDSKEAAREFAERHGW 123 (193)
Q Consensus 108 F~SkE~AIaYAer~Gw 123 (193)
|+|+++|.+=|.+.|-
T Consensus 1 y~tk~eAe~~A~~~GC 16 (34)
T PF12518_consen 1 YPTKAEAEKRAKELGC 16 (34)
T ss_pred CCcHHHHHHHHHHcCC
Confidence 7899999999998774
No 24
>PF01071 GARS_A: Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; InterPro: IPR020561 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) [] catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide: ATP + 5-phosphoribosylamine + glycine = ADP + Pi + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART. This entry represents the A-domain of the enzyme, and is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase.; PDB: 1GSO_A 3LP8_A 2IP4_A 1VKZ_A 2QK4_A 2XD4_A 2XCL_A 3MJF_A 2YRW_A 2YS6_A ....
Probab=31.17 E-value=51 Score=28.27 Aligned_cols=28 Identities=32% Similarity=0.450 Sum_probs=23.9
Q ss_pred eeeeCCHHHHHHHHHHcCCee-EEccccc
Q 029470 105 GLSFDSKEAAREFAERHGWEY-VAAGDIF 132 (193)
Q Consensus 105 ~L~F~SkE~AIaYAer~Gw~Y-~V~~~~~ 132 (193)
--.|.+.++|++|.++++..+ .|..|..
T Consensus 20 ~~~f~~~~~A~~~l~~~~~p~~ViKadGl 48 (194)
T PF01071_consen 20 YKVFTDYEEALEYLEEQGYPYVVIKADGL 48 (194)
T ss_dssp EEEESSHHHHHHHHHHHSSSEEEEEESSS
T ss_pred eeEECCHHHHHHHHHhcCCCceEEccCCC
Confidence 467999999999999999999 7665554
No 25
>KOG2854 consensus Possible pfkB family carbohydrate kinase [Carbohydrate transport and metabolism]
Probab=30.81 E-value=27 Score=32.91 Aligned_cols=52 Identities=29% Similarity=0.484 Sum_probs=33.8
Q ss_pred eeeeCCHHHHHHHHHHcCCeeEEcccccccceeeeccccCCCCCCCChhh-hhhhhhcccccccC
Q 029470 105 GLSFDSKEAAREFAERHGWEYVAAGDIFRTFCAITISHTTTPLTPHPKKE-KRKKEMYETLVRKP 168 (193)
Q Consensus 105 ~L~F~SkE~AIaYAer~Gw~Y~V~~~~~~~~~~~~~sh~~~p~~~~~~~~-~~~~~~~~~~v~~p 168 (193)
-+-|.+.+||.+||+.+||+-.-+.++- +++.--||.- +|.+-.+-||-.+|
T Consensus 216 DiifgNe~EA~af~~~~~~~t~dv~eia------------~~~~~~~k~~~~~~r~vvit~g~~~ 268 (343)
T KOG2854|consen 216 DIIFGNEDEAAAFARAHGWETKDVKEIA------------LKLSALPKVNGTRPRTVVITQGPDP 268 (343)
T ss_pred eEEEcCHHHHHHHHHhhCCcccchHHHh------------hHhhccccccccccceEEEccCCCc
Confidence 6889999999999999999876322222 3444456665 44444555554333
No 26
>smart00156 PP2Ac Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, that includes PP1, PP2A and PP2B (calcineurin) family members.
Probab=30.71 E-value=79 Score=27.79 Aligned_cols=39 Identities=21% Similarity=0.500 Sum_probs=27.4
Q ss_pred CCcCC---CcCccCCCCccCCcCCceeeeCCHHHHHHHHHHcCCeeEEc
Q 029470 83 KWENP---LMGWTSTGDPYANVGDAGLSFDSKEAAREFAERHGWEYVAA 128 (193)
Q Consensus 83 rwenP---LMGWTSS~DplsqV~~~~L~F~SkE~AIaYAer~Gw~Y~V~ 128 (193)
-|.|| .-||..| +. . ....|. .+++.+|++++|+.+.|+
T Consensus 176 lWsDP~~~~~~~~~~--~R-g---~g~~fg-~~~~~~Fl~~n~l~~iiR 217 (271)
T smart00156 176 LWSDPDQPVDGFQPS--IR-G---ASYYFG-PDAVDEFLKKNNLKLIIR 217 (271)
T ss_pred eecCCCcccCCCccC--CC-C---CccccC-HHHHHHHHHHCCCeEEEe
Confidence 57777 4566554 22 2 256775 688889999999999864
No 27
>PF01693 Cauli_VI: Caulimovirus viroplasmin; InterPro: IPR011320 This entry represents the N-terminal domain of RNase HI, which has a 3-layer alpha/beta/alpha structure []. This domain is lacking in retroviral and prokaryotic enzymes, but shows a striking structural similarity to the ribosomal protein L9 N-terminal domain, and may function as a regulatory RNA-binding module. However, the topology of this domain differs from structures of known RNA binding domains such as the double-stranded RNA binding domain (dsRBD), the hnRNP K homology (KH) domain and the RNP motif. Eukaryotic RNases HI possess either one or two copies of this small N-terminal domain, in addition to the well-conserved catalytic RNase H domain. RNase HI belongs to the family of ribonuclease H enzymes that recognise RNA:DNA hybrids and degrade the RNA component. ; PDB: 1QHK_A 3BSU_C.
Probab=30.71 E-value=38 Score=22.01 Aligned_cols=13 Identities=46% Similarity=0.636 Sum_probs=11.8
Q ss_pred eeeeCCHHHHHHH
Q 029470 105 GLSFDSKEAAREF 117 (193)
Q Consensus 105 ~L~F~SkE~AIaY 117 (193)
..+|+|.|+|.+|
T Consensus 32 ~k~F~t~~eA~~~ 44 (44)
T PF01693_consen 32 YKSFKTREEAEEF 44 (44)
T ss_dssp EEEESSHHHHHHH
T ss_pred ECCcCCHHHHhhC
Confidence 6899999999986
No 28
>PF13031 DUF3892: Protein of unknown function (DUF3892)
Probab=30.26 E-value=80 Score=22.89 Aligned_cols=23 Identities=22% Similarity=0.284 Sum_probs=19.3
Q ss_pred eeeCCHHHHHHHHHHcCCeeEEc
Q 029470 106 LSFDSKEAAREFAERHGWEYVAA 128 (193)
Q Consensus 106 L~F~SkE~AIaYAer~Gw~Y~V~ 128 (193)
+-.-|+++||+++|+..|.|.|.
T Consensus 28 ~~~~s~~~~i~~ie~g~~~~yv~ 50 (85)
T PF13031_consen 28 PWKYSREEAIAWIENGKWSFYVE 50 (85)
T ss_pred cccccHHHHHHHHHcCCceEEeC
Confidence 44558999999999988999965
No 29
>PF05198 IF3_N: Translation initiation factor IF-3, N-terminal domain; InterPro: IPR019814 Initiation factor 3 (IF-3) (gene infC) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consist of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit []. The chloroplast initiation factor IF-3(chl) is a protein that enhances the poly(A,U,G)-dependent binding of the initiator tRNA to chloroplast ribosomal 30s subunits in which the central section is evolutionary related to the sequence of bacterial IF-3 []. ; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1TIF_A.
Probab=30.22 E-value=65 Score=23.70 Aligned_cols=35 Identities=23% Similarity=0.281 Sum_probs=23.5
Q ss_pred eeeeCCHHHHHHHHHHcCCeeEEccccccc-ceeee
Q 029470 105 GLSFDSKEAAREFAERHGWEYVAAGDIFRT-FCAIT 139 (193)
Q Consensus 105 ~L~F~SkE~AIaYAer~Gw~Y~V~~~~~~~-~~~~~ 139 (193)
.+-.=+.++|++-|++.|++-..+.+--.- .|+|.
T Consensus 24 ~lGv~~~~eAl~~A~~~~lDLV~v~~~~~PPVcKi~ 59 (76)
T PF05198_consen 24 QLGVMSLREALRLAKEKGLDLVEVSPNADPPVCKIM 59 (76)
T ss_dssp EEEEEEHHHHHHHHHHTT-EEEEEETTSSS-EEEEE
T ss_pred EeceEEHHHHHHHHHHcCCcEEEEcCCCCCCeEEEe
Confidence 344557899999999999999865433222 55554
No 30
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=29.32 E-value=63 Score=24.44 Aligned_cols=52 Identities=17% Similarity=0.196 Sum_probs=32.7
Q ss_pred CCcEEEcCCC---CCCcCCCcCccCCCCccCCcCCceeeeCCHHHHHHHHHHcCCeeEEcccc
Q 029470 72 GRWKINFMST---QKWENPLMGWTSTGDPYANVGDAGLSFDSKEAAREFAERHGWEYVAAGDI 131 (193)
Q Consensus 72 ~~W~LeFe~~---~rwenPLMGWTSS~DplsqV~~~~L~F~SkE~AIaYAer~Gw~Y~V~~~~ 131 (193)
+.=+|=|+.. .|+-.=|-. .++|.- .+.-=..++-+.||+.+|..|+|+...
T Consensus 23 ~~~Vl~FE~edDA~RYa~lLEA---qd~~~p-----~Ve~id~~~i~~fC~~~gy~~~iv~~g 77 (86)
T PF11360_consen 23 RNVVLMFEDEDDAERYAGLLEA---QDFPDP-----TVEEIDPEEIEEFCRSAGYEYEIVPPG 77 (86)
T ss_pred CCEEEEEccHHHHHHHHHHHHh---cCCCCC-----CeEEECHHHHHHHHHHCCceEEEECCC
Confidence 4556777764 355555522 223322 244456788999999999999965443
No 31
>PRK05773 3,4-dihydroxy-2-butanone 4-phosphate synthase; Validated
Probab=27.20 E-value=52 Score=28.93 Aligned_cols=18 Identities=39% Similarity=0.501 Sum_probs=16.4
Q ss_pred CCHHHHHHHHHHcCCeeE
Q 029470 109 DSKEAAREFAERHGWEYV 126 (193)
Q Consensus 109 ~SkE~AIaYAer~Gw~Y~ 126 (193)
-++++|++||++||+.+.
T Consensus 191 ~~~~~~~~fA~~~~l~~i 208 (219)
T PRK05773 191 LSKEKAKKIAKNLGFPLV 208 (219)
T ss_pred cCHHHHHHHHHHcCCcEE
Confidence 379999999999999996
No 32
>PRK09411 carbamate kinase; Reviewed
Probab=26.64 E-value=68 Score=29.46 Aligned_cols=30 Identities=17% Similarity=0.319 Sum_probs=26.3
Q ss_pred eeeCCHHHHHHHHHHcCCeeEEcccccccc
Q 029470 106 LSFDSKEAAREFAERHGWEYVAAGDIFRTF 135 (193)
Q Consensus 106 L~F~SkE~AIaYAer~Gw~Y~V~~~~~~~~ 135 (193)
=.|-|+|+|-+.++++||.+...|+.+||.
T Consensus 125 G~~y~~e~a~~l~~e~g~~~~~dg~g~rrV 154 (297)
T PRK09411 125 GPVYQPEEQEALEAAYGWQMKRDGKYLRRV 154 (297)
T ss_pred CCccCHHHHHHHHHhcCCEEEecCCceEEE
Confidence 468999999999999999999888888864
No 33
>smart00633 Glyco_10 Glycosyl hydrolase family 10.
Probab=26.61 E-value=61 Score=27.60 Aligned_cols=34 Identities=24% Similarity=0.358 Sum_probs=27.0
Q ss_pred eeeeCCHHHHHHHHHHcCCeeEEcccccccceeeeccccCCCC
Q 029470 105 GLSFDSKEAAREFAERHGWEYVAAGDIFRTFCAITISHTTTPL 147 (193)
Q Consensus 105 ~L~F~SkE~AIaYAer~Gw~Y~V~~~~~~~~~~~~~sh~~~p~ 147 (193)
+..|...++++++|+++|+... |-+.+-|..+|.
T Consensus 12 ~~n~~~~D~~~~~a~~~gi~v~---------gH~l~W~~~~P~ 45 (254)
T smart00633 12 QFNFSGADAIVNFAKENGIKVR---------GHTLVWHSQTPD 45 (254)
T ss_pred ccChHHHHHHHHHHHHCCCEEE---------EEEEeecccCCH
Confidence 5789999999999999999987 444456666664
No 34
>PF02811 PHP: PHP domain; InterPro: IPR004013 The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. This family is often associated with an N-terminal region IPR003141 from INTERPRO.; GO: 0003824 catalytic activity; PDB: 2WJE_A 3QY8_A 2WJD_A 2WJF_A 1PB0_B 1M68_A 1M65_A 3E38_B 2W9M_A 3E0F_A ....
Probab=26.45 E-value=39 Score=25.63 Aligned_cols=38 Identities=29% Similarity=0.287 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHcCCeeEEcccccccceeeeccccCCCCCCCChhhhhh
Q 029470 109 DSKEAAREFAERHGWEYVAAGDIFRTFCAITISHTTTPLTPHPKKEKRK 157 (193)
Q Consensus 109 ~SkE~AIaYAer~Gw~Y~V~~~~~~~~~~~~~sh~~~p~~~~~~~~~~~ 157 (193)
.+.|+.|+.|+++|++.. +.-.||.+...+...++-++
T Consensus 16 ~~~~e~v~~A~~~Gl~~i-----------~iTDH~~~~~~~~~~~~~~~ 53 (175)
T PF02811_consen 16 DSPEEYVEQAKEKGLDAI-----------AITDHNNFAGYPDFYKEAKK 53 (175)
T ss_dssp SSHHHHHHHHHHTTESEE-----------EEEEETTTTTHHHHHHHHHH
T ss_pred CCHHHHHHHHHHcCCCEE-----------EEcCCcccccchHHHHHHHh
Confidence 388999999999999988 45578888887776666554
No 35
>PF03108 DBD_Tnp_Mut: MuDR family transposase; InterPro: IPR004332 The plant MuDR transposase domain is present in plant proteins that are presumed to be the transposases for Mutator transposable elements [, ]. The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=26.35 E-value=97 Score=21.15 Aligned_cols=23 Identities=43% Similarity=0.780 Sum_probs=19.6
Q ss_pred eeeeCCHHHH----HHHHHHcCCeeEE
Q 029470 105 GLSFDSKEAA----REFAERHGWEYVA 127 (193)
Q Consensus 105 ~L~F~SkE~A----IaYAer~Gw~Y~V 127 (193)
.+.|+|+++. ..||-+++.+|.|
T Consensus 7 G~~F~~~~e~k~av~~yai~~~~~~~v 33 (67)
T PF03108_consen 7 GQTFPSKEEFKEAVREYAIKNGFEFKV 33 (67)
T ss_pred CCEECCHHHHHHHHHHHHHhcCcEEEE
Confidence 7899999876 4689999999995
No 36
>PRK00823 phhB pterin-4-alpha-carbinolamine dehydratase; Validated
Probab=26.28 E-value=60 Score=24.33 Aligned_cols=35 Identities=31% Similarity=0.477 Sum_probs=25.0
Q ss_pred CCCcCccCCCCccCCcCCceeeeCCHHHHHHHHHHcC
Q 029470 86 NPLMGWTSTGDPYANVGDAGLSFDSKEAAREFAERHG 122 (193)
Q Consensus 86 nPLMGWTSS~DplsqV~~~~L~F~SkE~AIaYAer~G 122 (193)
..|-||.-..|+.. +. ...+|++-.+|++|+.+-+
T Consensus 16 ~~l~gW~~~~~~~~-l~-r~f~f~~f~~a~~f~~~Va 50 (97)
T PRK00823 16 PQLPGWTLVGDRDA-IE-RTFKFKNFNEAFAFMNRVA 50 (97)
T ss_pred hcCCCCeEeCCcCe-EE-EEEEeCCHHHHHHHHHHHH
Confidence 45679988877431 21 2789999999999877644
No 37
>COG0108 RibB 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]
Probab=26.15 E-value=49 Score=29.07 Aligned_cols=19 Identities=26% Similarity=0.434 Sum_probs=16.6
Q ss_pred CCHHHHHHHHHHcCCeeEE
Q 029470 109 DSKEAAREFAERHGWEYVA 127 (193)
Q Consensus 109 ~SkE~AIaYAer~Gw~Y~V 127 (193)
..++++++||++||+.+.=
T Consensus 172 ar~~~~~~fa~~h~l~~it 190 (203)
T COG0108 172 ARLPELEEFAKEHGLPVIT 190 (203)
T ss_pred cChHHHHHHHHHcCCcEEE
Confidence 4678999999999999983
No 38
>KOG4748 consensus Subunit of Golgi mannosyltransferase complex [Carbohydrate transport and metabolism; Cell wall/membrane/envelope biogenesis]
Probab=25.16 E-value=44 Score=31.67 Aligned_cols=18 Identities=33% Similarity=0.641 Sum_probs=16.0
Q ss_pred CHHHHHHHHHHcCCeeEE
Q 029470 110 SKEAAREFAERHGWEYVA 127 (193)
Q Consensus 110 SkE~AIaYAer~Gw~Y~V 127 (193)
+-+-=|+||++||+++++
T Consensus 127 ~ikNridYA~rHgy~~~~ 144 (364)
T KOG4748|consen 127 SIKNRIDYARRHGYEFEY 144 (364)
T ss_pred HHHhHHHHHHHhCCeEEE
Confidence 677789999999999994
No 39
>PRK12454 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed
Probab=25.08 E-value=75 Score=29.27 Aligned_cols=28 Identities=29% Similarity=0.569 Sum_probs=22.4
Q ss_pred eeCCHHHHHHHHHHcCCeeEEc-cccccc
Q 029470 107 SFDSKEAAREFAERHGWEYVAA-GDIFRT 134 (193)
Q Consensus 107 ~F~SkE~AIaYAer~Gw~Y~V~-~~~~~~ 134 (193)
.|-|+|+|.+.++++||.|.-. |..|||
T Consensus 134 ~~y~~~~a~~~~~~~g~~~~~d~g~g~Rr 162 (313)
T PRK12454 134 PFYDEEEAKKLAKEKGWIVKEDAGRGWRR 162 (313)
T ss_pred CCcCHHHHHHHHHHcCCEEEEcCCCceEE
Confidence 4889999999999999977643 455664
No 40
>PF05406 WGR: WGR domain; InterPro: IPR008893 This domain is named after the most conserved central motif of the domain. It is found in a variety of polyA polymerases as well as the Escherichia coli molybdate metabolism regulator P33345 from SWISSPROT and other proteins of unknown function.The domain is found in isolation in proteins such as Q9JN21 from SWISSPROT and is between 70 and 80 residues in length. ; PDB: 2EOC_A 2RA8_A 4DQY_C 2CR9_A.
Probab=24.53 E-value=56 Score=23.38 Aligned_cols=47 Identities=19% Similarity=0.223 Sum_probs=26.4
Q ss_pred CCCCCcEEEcCCCCCCc-CCCcCccCCCCccCCcCCceeeeCCHHHHHHHHHH
Q 029470 69 GKLGRWKINFMSTQKWE-NPLMGWTSTGDPYANVGDAGLSFDSKEAAREFAER 120 (193)
Q Consensus 69 ~~t~~W~LeFe~~~rwe-nPLMGWTSS~DplsqV~~~~L~F~SkE~AIaYAer 120 (193)
+..+.|.|+..+...|. --==|-.++. ...+ .-.|+|.|+|++..++
T Consensus 17 n~~kfY~iql~~~~~~~v~~~wGRiG~~-gq~~----~~~f~s~~eA~~~f~~ 64 (81)
T PF05406_consen 17 NSNKFYRIQLLPDLEWVVFRRWGRIGSK-GQTR----IKPFDSEEEAIKEFEK 64 (81)
T ss_dssp TEEEEEEEEEEEETTEEEEEEEEETTSS-EEEE----EEEESSHHHHHHHHHH
T ss_pred CcEEEEEEEEEeCCCeEEEEEECCCCCc-CcEE----EEeCCCHHHHHHHHHH
Confidence 33466777775432000 0001334444 4444 4699999999998765
No 41
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=24.45 E-value=87 Score=21.99 Aligned_cols=22 Identities=36% Similarity=0.613 Sum_probs=17.9
Q ss_pred eeee--CCHHHHHHHHHHcCCeeE
Q 029470 105 GLSF--DSKEAAREFAERHGWEYV 126 (193)
Q Consensus 105 ~L~F--~SkE~AIaYAer~Gw~Y~ 126 (193)
.|+| +..|.++++.+++|+.|+
T Consensus 44 al~~~~~d~~~i~~~l~~~~i~~~ 67 (73)
T PF11823_consen 44 ALRFEPEDLEKIKEILEENGIEYE 67 (73)
T ss_pred EEEEChhhHHHHHHHHHHCCCCee
Confidence 3444 678899999999999988
No 42
>cd00913 PCD_DCoH_subfamily_a PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein).
Probab=24.37 E-value=85 Score=22.46 Aligned_cols=30 Identities=23% Similarity=0.396 Sum_probs=21.5
Q ss_pred CccCCCCccCCcCCceeeeCCHHHHHHHHHHc
Q 029470 90 GWTSTGDPYANVGDAGLSFDSKEAAREFAERH 121 (193)
Q Consensus 90 GWTSS~DplsqV~~~~L~F~SkE~AIaYAer~ 121 (193)
||.-..|+.. +. .+..|.+-.+|++|+.+-
T Consensus 1 gW~~~~~~~~-l~-r~f~f~~f~~a~~f~~~v 30 (76)
T cd00913 1 GWELADDGLK-LE-RTFRFKNFVEALEFVNAV 30 (76)
T ss_pred CCcCcCCCCe-EE-EEEEcCCHHHHHHHHHHH
Confidence 7887776521 11 278899999999997763
No 43
>TIGR01465 cobM_cbiF precorrin-4 C11-methyltransferase. This model represents precorrin-4 C11-methyltransferase, one of two methyltransferases commonly referred to as precorrin-3 methylase (the other is precorrin-3B C17-methyltransferase, EC 2.1.1.131). This enzyme participates in the pathway toward the biosynthesis of cobalamin and related products.
Probab=23.54 E-value=92 Score=25.63 Aligned_cols=36 Identities=19% Similarity=0.261 Sum_probs=27.4
Q ss_pred cCccCCCCccCCcCCceeeeCCHHHHHHHHHHcCCeeEEccccc
Q 029470 89 MGWTSTGDPYANVGDAGLSFDSKEAAREFAERHGWEYVAAGDIF 132 (193)
Q Consensus 89 MGWTSS~DplsqV~~~~L~F~SkE~AIaYAer~Gw~Y~V~~~~~ 132 (193)
...-.+|||+ -|.+--.-+.+++++|++++|.+.+.
T Consensus 74 V~~L~~GDP~--------~~~~~~~l~~~~~~~g~~veviPGiS 109 (229)
T TIGR01465 74 VVRLHTGDPS--------IYGAIAEQMQLLEALGIPYEVVPGVS 109 (229)
T ss_pred EEEEeCcCcc--------ccccHHHHHHHHHHCCCCEEEECChh
Confidence 4556789995 46777788888999999999975544
No 44
>PRK06136 uroporphyrin-III C-methyltransferase; Reviewed
Probab=23.43 E-value=38 Score=28.35 Aligned_cols=38 Identities=24% Similarity=0.293 Sum_probs=29.0
Q ss_pred cCccCCCCccCCcCCceeeeCCHHHHHHHHHHcCCeeEEccccccc
Q 029470 89 MGWTSTGDPYANVGDAGLSFDSKEAAREFAERHGWEYVAAGDIFRT 134 (193)
Q Consensus 89 MGWTSS~DplsqV~~~~L~F~SkE~AIaYAer~Gw~Y~V~~~~~~~ 134 (193)
...-.+|||. -|.+-..-+.+++++|++++|++.+.--
T Consensus 83 V~~l~~GDP~--------~ys~~~~l~~~l~~~~~~veviPGISS~ 120 (249)
T PRK06136 83 VVRLKGGDPF--------VFGRGGEELEALEAAGIPYEVVPGITAA 120 (249)
T ss_pred EEEEeCCCch--------hhhcHHHHHHHHHHCCCCEEEEcCccHH
Confidence 3456789985 3777777888899999999998776543
No 45
>COG5470 Uncharacterized conserved protein [Function unknown]
Probab=23.36 E-value=67 Score=25.33 Aligned_cols=20 Identities=45% Similarity=0.486 Sum_probs=16.4
Q ss_pred CCccCCcCCceeeeCCHHHHHHH
Q 029470 95 GDPYANVGDAGLSFDSKEAAREF 117 (193)
Q Consensus 95 ~DplsqV~~~~L~F~SkE~AIaY 117 (193)
.||-.+| .+.|+|.|.|.++
T Consensus 50 w~ptr~v---viEFps~~~ar~~ 69 (96)
T COG5470 50 WRPTRNV---VIEFPSLEAARDC 69 (96)
T ss_pred CCcccEE---EEEcCCHHHHHHH
Confidence 4666666 8999999999876
No 46
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=23.15 E-value=76 Score=24.03 Aligned_cols=22 Identities=9% Similarity=0.015 Sum_probs=19.7
Q ss_pred eeeeCCHHHHHHHHHHcCCeeE
Q 029470 105 GLSFDSKEAAREFAERHGWEYV 126 (193)
Q Consensus 105 ~L~F~SkE~AIaYAer~Gw~Y~ 126 (193)
-|.|-+.++-+.||..+|++|.
T Consensus 6 PL~~v~E~ei~~ya~~~~lp~~ 27 (104)
T TIGR00269 6 PLRYIPEKEVVLYAFLNELKVH 27 (104)
T ss_pred ccccCCHHHHHHHHHHcCCCcC
Confidence 4677889999999999999998
No 47
>cd00914 PCD_DCoH_subfamily_b PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon
Probab=23.14 E-value=75 Score=22.78 Aligned_cols=31 Identities=26% Similarity=0.402 Sum_probs=22.1
Q ss_pred CccCCCCccCCcCCceeeeCCHHHHHHHHHHcC
Q 029470 90 GWTSTGDPYANVGDAGLSFDSKEAAREFAERHG 122 (193)
Q Consensus 90 GWTSS~DplsqV~~~~L~F~SkE~AIaYAer~G 122 (193)
||.-..|+.. +. .+.+|+|-.+|++|..+-+
T Consensus 1 gW~~~~~~~~-l~-r~f~f~~f~~a~~f~~~va 31 (76)
T cd00914 1 GWTLVDGRDA-IH-KSFKFKDFNEAFGFMTRVA 31 (76)
T ss_pred CCeEeCCCCe-EE-EEEEeCCHHHHHHHHHHHH
Confidence 7877776531 11 3799999999999987643
No 48
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=23.07 E-value=75 Score=20.71 Aligned_cols=19 Identities=16% Similarity=0.440 Sum_probs=17.1
Q ss_pred eCCHHHHHHHHHHcCCeeE
Q 029470 108 FDSKEAAREFAERHGWEYV 126 (193)
Q Consensus 108 F~SkE~AIaYAer~Gw~Y~ 126 (193)
..|.|+-|++|+.+|+.|.
T Consensus 26 ~~~~~e~~~lA~~~Gy~ft 44 (49)
T PF07862_consen 26 CQNPEEVVALAREAGYDFT 44 (49)
T ss_pred cCCHHHHHHHHHHcCCCCC
Confidence 4599999999999999987
No 49
>cd01206 Homer Homer type EVH1 domain. Homer type EVH1 domain. Homer is a synaptic scaffolding protein, involved in neuronal signaling. It contains an EVH1 domain, which binds to both neurotransmitter receptors, such as the metabotropic glutamate receptor (mGluR) and to other scaffolding proteins via PPXXF motifs, in order to target them to the synaptic junction. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=23.03 E-value=82 Score=25.43 Aligned_cols=32 Identities=44% Similarity=0.659 Sum_probs=22.6
Q ss_pred CCcCccCCC-------CccC-CcCCceeeeCCHHHHHHHHHH
Q 029470 87 PLMGWTSTG-------DPYA-NVGDAGLSFDSKEAAREFAER 120 (193)
Q Consensus 87 PLMGWTSS~-------Dpls-qV~~~~L~F~SkE~AIaYAer 120 (193)
|=|+++.+. |+.+ +| -.|.|.|+|||-.|+++
T Consensus 63 ~~~~y~kas~~FhQWrD~R~~tV--yGLnF~Sk~ea~~F~~~ 102 (111)
T cd01206 63 PNMTFTKTSQKFGQWADSRANTV--YGLGFSSEQQLTKFAEK 102 (111)
T ss_pred CCcceeeccccccccccccccee--eecccCCHHHHHHHHHH
Confidence 445555543 5553 45 36999999999999976
No 50
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=22.62 E-value=8.7 Score=27.38 Aligned_cols=26 Identities=19% Similarity=0.447 Sum_probs=19.3
Q ss_pred CcCccCCCCccCCcCCceeeeCCHHHHHHHHHHcCCeeE
Q 029470 88 LMGWTSTGDPYANVGDAGLSFDSKEAAREFAERHGWEYV 126 (193)
Q Consensus 88 LMGWTSS~DplsqV~~~~L~F~SkE~AIaYAer~Gw~Y~ 126 (193)
|.+||||.+-...+ -.+|.++||...
T Consensus 2 ll~~TGs~~fnr~l-------------R~~A~~~g~~L~ 27 (64)
T PF14791_consen 2 LLYFTGSKEFNRDL-------------RQYAKKKGMKLS 27 (64)
T ss_dssp HHHHHS-HHHHHHH-------------HHHHHHTTEEEE
T ss_pred cccccCCHHHHHHH-------------HHHHHHcCCeeC
Confidence 56899988876554 468999998877
No 51
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=22.04 E-value=91 Score=20.44 Aligned_cols=18 Identities=28% Similarity=0.241 Sum_probs=16.7
Q ss_pred eeeeCCHHHHHHHHHHcC
Q 029470 105 GLSFDSKEAAREFAERHG 122 (193)
Q Consensus 105 ~L~F~SkE~AIaYAer~G 122 (193)
-+.|.|.|+|...++.++
T Consensus 43 ~v~f~~~~~a~~al~~~~ 60 (70)
T PF14259_consen 43 FVEFSSEEDAKRALELLN 60 (70)
T ss_dssp EEEESSHHHHHHHHHHHT
T ss_pred EEEeCCHHHHHHHHHHCC
Confidence 699999999999999887
No 52
>PF00568 WH1: WH1 domain; InterPro: IPR000697 The EVH1 (WH1, RanBP1-WASP) domain is found in multi-domain proteins implicated in a diverse range of signalling, nuclear transport and cytoskeletal events. This domain of around 115 amino acids is present in species ranging from yeast to mammals. Many EVH1-containing proteins associate with actin-based structures and play a role in cytoskeletal organisation. EVH1 domains recognise and bind the proline-rich motif FPPPP with low-affinity, further interactions then form between flanking residues [][]. WASP family proteins contain a EVH1 (WH1) in their N-terminals which bind proline-rich sequences in the WASP interacting protein. Proteins of the RanBP1 family contain a WH1 domain in their N-terminal region, which seems to bind a different sequence motif present in the C-terminal part of RanGTP protein [,]. Tertiary structure of the WH1 domain of the Mena protein revealed structure similarities with the pleckstrin homology (PH) domain. The overall fold consists of a compact parallel beta-sandwich, closed along one edge by a long alpha-helix. A highly conserved cluster of three surface-exposed aromatic side-chains forms the recognition site for the molecules target ligands. [].; GO: 0005515 protein binding; PDB: 1I2H_A 1DDV_A 1DDW_A 1EGX_A 3SYX_A 1TJ6_B 1XOD_B 1EVH_A 1I7A_B 2JP2_A ....
Probab=21.92 E-value=76 Score=24.08 Aligned_cols=29 Identities=24% Similarity=0.359 Sum_probs=20.6
Q ss_pred CCCcCccCCCCccCCcCCceeeeCCHHHHHHHHHH
Q 029470 86 NPLMGWTSTGDPYANVGDAGLSFDSKEAAREFAER 120 (193)
Q Consensus 86 nPLMGWTSS~DplsqV~~~~L~F~SkE~AIaYAer 120 (193)
+=+.-|.+. ...+ .|.|.|.+||-.|+++
T Consensus 78 ~~Fh~f~~~---~~~~---GLnF~se~eA~~F~~~ 106 (111)
T PF00568_consen 78 PFFHQFEDD---DCVY---GLNFASEEEADQFYKK 106 (111)
T ss_dssp SSEEEEEET---TCEE---EEEESSHHHHHHHHHH
T ss_pred CcEEEEEeC---CeEE---EEecCCHHHHHHHHHH
Confidence 344555543 2244 7999999999999975
No 53
>PF01329 Pterin_4a: Pterin 4 alpha carbinolamine dehydratase; InterPro: IPR001533 DCoH is the dimerisation cofactor of hepatocyte nuclear factor 1 (HNF-1) that functions as both a transcriptional coactivator and a pterin dehydratase []. X-ray crystallographic studies have shown that the ligand binds at four sites per tetrameric enzyme, with little apparent conformational change in the protein.; GO: 0008124 4-alpha-hydroxytetrahydrobiopterin dehydratase activity, 0006729 tetrahydrobiopterin biosynthetic process; PDB: 2V6T_B 2V6U_A 2V6S_B 2EBB_A 1USM_A 1F93_B 1DCP_C 1DCH_E 3HXA_E 1DCO_C ....
Probab=21.53 E-value=77 Score=23.62 Aligned_cols=31 Identities=29% Similarity=0.518 Sum_probs=22.6
Q ss_pred CCCcCccCCC-CccCCcCCceeeeCCHHHHHHHHHH
Q 029470 86 NPLMGWTSTG-DPYANVGDAGLSFDSKEAAREFAER 120 (193)
Q Consensus 86 nPLMGWTSS~-DplsqV~~~~L~F~SkE~AIaYAer 120 (193)
..|-||.-.+ .-+.. ...|++-..|++|..+
T Consensus 15 ~~l~~W~~~~~~~l~r----~f~f~~f~~a~~f~~~ 46 (95)
T PF01329_consen 15 AELPGWKLDGGGRLER----TFKFKDFAEAVEFVNR 46 (95)
T ss_dssp HTSTTSEEETSSEEEE----EEE-SSHHHHHHHHHH
T ss_pred hcCcCCEECCCCcEEE----EEEeCCHHHHHHHHHH
Confidence 3577999888 44433 7999999999998754
No 54
>PF14542 Acetyltransf_CG: GCN5-related N-acetyl-transferase; PDB: 2H5M_A 2Q44_A 1XMT_A 2Q4Y_A 2IL4_A 2EVN_A 1R57_A.
Probab=21.53 E-value=71 Score=22.95 Aligned_cols=16 Identities=38% Similarity=0.545 Sum_probs=13.7
Q ss_pred HHHHHHHHHHcCCeeE
Q 029470 111 KEAAREFAERHGWEYV 126 (193)
Q Consensus 111 kE~AIaYAer~Gw~Y~ 126 (193)
-++|++||+++|+...
T Consensus 44 ~~~~l~~a~~~~~kv~ 59 (78)
T PF14542_consen 44 VEAALDYARENGLKVV 59 (78)
T ss_dssp HHHHHHHHHHTT-EEE
T ss_pred HHHHHHHHHHCCCEEE
Confidence 4799999999999988
No 55
>smart00461 WH1 WASP homology region 1. Region of the Wiskott-Aldrich syndrome protein (WASp) that contains point mutations in the majority of patients with WAS. Unknown function. Ena-like WH1 domains bind polyproline-containing peptides, and that Homer contains a WH1 domain.
Probab=21.52 E-value=75 Score=24.20 Aligned_cols=17 Identities=41% Similarity=0.780 Sum_probs=15.3
Q ss_pred eeeeCCHHHHHHHHHHc
Q 029470 105 GLSFDSKEAAREFAERH 121 (193)
Q Consensus 105 ~L~F~SkE~AIaYAer~ 121 (193)
.|.|.|.+||-+|.++.
T Consensus 86 GLnF~se~EA~~F~~~v 102 (106)
T smart00461 86 GLNFASEEEAKKFRKKV 102 (106)
T ss_pred EeecCCHHHHHHHHHHH
Confidence 79999999999998863
No 56
>PF10566 Glyco_hydro_97: Glycoside hydrolase 97 ; InterPro: IPR019563 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This is the 97th family of glycosidases, in this case bacterial. The central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, most probably form two additional non-catalytic domains with as yet unknown functions. The non-catalytic domains of glycosidases from the alpha-galactosidase and alpha-glucosidase superfamilies are also predominantly composed of beta-strands, and at least some of these domains are involved in oligomerisation and carbohydrate binding. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands []. ; PDB: 2JKP_A 2JKE_A 2D73_B 2ZQ0_B 2JKA_A 3A24_A.
Probab=21.28 E-value=84 Score=28.38 Aligned_cols=28 Identities=25% Similarity=0.418 Sum_probs=23.0
Q ss_pred eeeeCCHHHHHHHHHHcCCeeEEccccc
Q 029470 105 GLSFDSKEAAREFAERHGWEYVAAGDIF 132 (193)
Q Consensus 105 ~L~F~SkE~AIaYAer~Gw~Y~V~~~~~ 132 (193)
.+.+++...=|+||.++||+|.++...-
T Consensus 28 g~~t~~~k~yIDfAa~~G~eYvlvD~GW 55 (273)
T PF10566_consen 28 GATTETQKRYIDFAAEMGIEYVLVDAGW 55 (273)
T ss_dssp SSSHHHHHHHHHHHHHTT-SEEEEBTTC
T ss_pred CCCHHHHHHHHHHHHHcCCCEEEecccc
Confidence 4678888899999999999999876655
No 57
>cd01207 Ena-Vasp Enabled-VASP-type homology (EVH1) domain. Enabled-VASP-type homology (EVH1) domain. The EVH1 domain binds to other proteins at proline rich sequences. It is found in proteins involved in cytoskeletal reorganization such as Enabled and VASP. Ena-VASP type EVH1 domains specifically recognize FPPPP motifs in the focal adhesion proteins zyxin and vinculin, and the ActA surface protein of Listeria monocytogenes. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=21.11 E-value=68 Score=25.49 Aligned_cols=45 Identities=27% Similarity=0.294 Sum_probs=27.1
Q ss_pred CCCcEEEcCCCC-----CCcCCCcCccCCCCccCCcCCceeeeCCHHHHHHHHHHc
Q 029470 71 LGRWKINFMSTQ-----KWENPLMGWTSTGDPYANVGDAGLSFDSKEAAREFAERH 121 (193)
Q Consensus 71 t~~W~LeFe~~~-----rwenPLMGWTSS~DplsqV~~~~L~F~SkE~AIaYAer~ 121 (193)
.+..+||.+-.. +-.-.+.=|.+. ..+. .|.|.|+|||-+|.+..
T Consensus 54 ~~~~v~e~~l~~~l~y~k~~p~Fh~w~~~---~~v~---GLnF~Se~eA~~F~~~v 103 (111)
T cd01207 54 DHQVVINCAIVKGLKYNQATPTFHQWRDA---RQVY---GLNFGSKEDATMFASAM 103 (111)
T ss_pred CCcEEEEEEecCCceeeecCCcceeeecC---CeEE---eeccCCHHHHHHHHHHH
Confidence 356677776431 111223334332 3444 79999999999998753
No 58
>PF12745 HGTP_anticodon2: Anticodon binding domain of tRNAs; InterPro: IPR024435 This is an anticodon binding domain, found largely on Gcn2 proteins which bind tRNA to down regulate translation in certain stress situations [].; GO: 0000049 tRNA binding
Probab=21.10 E-value=98 Score=27.69 Aligned_cols=19 Identities=16% Similarity=0.461 Sum_probs=17.8
Q ss_pred CCHHHHHHHHHHcCCeeEE
Q 029470 109 DSKEAAREFAERHGWEYVA 127 (193)
Q Consensus 109 ~SkE~AIaYAer~Gw~Y~V 127 (193)
.|.||.+.+|..+|+.|.|
T Consensus 44 ~S~Eel~~~~~~~gi~wiV 62 (273)
T PF12745_consen 44 PSQEELQSYCREDGISWIV 62 (273)
T ss_pred CCHHHHHHHHHHCCCCEEE
Confidence 5999999999999999995
No 59
>PTZ00175 diphthine synthase; Provisional
Probab=20.55 E-value=1.2e+02 Score=27.05 Aligned_cols=34 Identities=18% Similarity=0.243 Sum_probs=26.5
Q ss_pred ccCCCCccCCcCCceeeeCCHHHHHHHHHHcCCeeEEccccc
Q 029470 91 WTSTGDPYANVGDAGLSFDSKEAAREFAERHGWEYVAAGDIF 132 (193)
Q Consensus 91 WTSS~DplsqV~~~~L~F~SkE~AIaYAer~Gw~Y~V~~~~~ 132 (193)
--.+|||+ -|.+--+=+..|+++|++++|++.+.
T Consensus 81 ~L~~GDP~--------i~~t~~~l~~~~~~~gi~vevIPGvS 114 (270)
T PTZ00175 81 FLVVGDPF--------CATTHTDLYLRAKKKGIEVEVIHNAS 114 (270)
T ss_pred EEECCCCC--------ccCCHHHHHHHHHHCCCcEEEECCcC
Confidence 45578985 47777777889999999999987443
No 60
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=20.43 E-value=24 Score=26.50 Aligned_cols=55 Identities=15% Similarity=0.154 Sum_probs=44.7
Q ss_pred eeeeCCHHHHHHHHHHcCCeeEEcccccccceeeeccccCCCCCCCChhhhhhhhhccc
Q 029470 105 GLSFDSKEAAREFAERHGWEYVAAGDIFRTFCAITISHTTTPLTPHPKKEKRKKEMYET 163 (193)
Q Consensus 105 ~L~F~SkE~AIaYAer~Gw~Y~V~~~~~~~~~~~~~sh~~~p~~~~~~~~~~~~~~~~~ 163 (193)
++.=+.|++|.+-|++.|++-. +.++-|.+-+..|+-+|-.+-+--+. .++.++.
T Consensus 7 RiD~~lK~~A~~vl~~lGls~S---~Ai~~fl~qi~~~~~iPF~~~~~s~e-d~~~l~~ 61 (80)
T PRK11235 7 RVDDELKARAYAVLEKLGVTPS---EALRLLLQYVAENGRLPFKTVLLSDE-DAALLET 61 (80)
T ss_pred EeCHHHHHHHHHHHHHhCCCHH---HHHHHHHHHHHHhCCCCCCCCCCCHH-HHHHHHH
Confidence 6777789999999999999988 78888999999999999987665553 4455544
No 61
>cd07415 MPP_PP2A_PP4_PP6 PP2A, PP4, and PP6 phosphoprotein phosphatases, metallophosphatase domain. PP2A-like family of phosphoprotein phosphatases (PPP's) including PP4 and PP6. PP2A (Protein phosphatase 2A) is a critical regulator of many cellular activities. PP2A comprises about 1% of total cellular proteins. PP2A, together with protein phosphatase 1 (PP1), accounts for more than 90% of all serine/threonine phosphatase activities in most cells and tissues. The PP2A subunit in addition to having a catalytic domain homologous to PP1, has a unique C-terminal tail, containing a motif that is conserved in the catalytic subunits of all PP2A-like phosphatases including PP4 and PP6, and has an important role in PP2A regulation. The PP2A-like family of phosphatases all share a similar heterotrimeric architecture, that includes: a 65kDa scaffolding subunit (A), a 36kDa catalytic subunit (C), and one of 18 regulatory subunits (B). The PPP (phosphoprotein phosphatase) family, to which PP2
Probab=20.22 E-value=1.6e+02 Score=26.29 Aligned_cols=39 Identities=28% Similarity=0.705 Sum_probs=26.6
Q ss_pred CCcCCC--cCccCCCCccCCcCCceeeeCCHHHHHHHHHHcCCeeEEc
Q 029470 83 KWENPL--MGWTSTGDPYANVGDAGLSFDSKEAAREFAERHGWEYVAA 128 (193)
Q Consensus 83 rwenPL--MGWTSS~DplsqV~~~~L~F~SkE~AIaYAer~Gw~Y~V~ 128 (193)
-|.||. .||..| + . +....|. .+++.+|++++|+++.|+
T Consensus 191 lWsDP~~~~~~~~~--~-R---g~g~~fg-~~~~~~Fl~~n~l~~iiR 231 (285)
T cd07415 191 LWSDPDDIEGWGIS--P-R---GAGYLFG-QDVVEEFNHNNGLTLICR 231 (285)
T ss_pred EecCCCccCCCCcC--C-C---CCccccC-HHHHHHHHHHCCCeEEEE
Confidence 566665 355433 1 2 2356676 789999999999999964
No 62
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=20.03 E-value=31 Score=25.58 Aligned_cols=45 Identities=18% Similarity=0.149 Sum_probs=38.4
Q ss_pred eeeeCCHHHHHHHHHHcCCeeEEcccccccceeeeccccCCCCCCCCh
Q 029470 105 GLSFDSKEAAREFAERHGWEYVAAGDIFRTFCAITISHTTTPLTPHPK 152 (193)
Q Consensus 105 ~L~F~SkE~AIaYAer~Gw~Y~V~~~~~~~~~~~~~sh~~~p~~~~~~ 152 (193)
++.=+.|++|.+-|++.|++.. +.++-|++=+..|.-+|-.+-..
T Consensus 8 Rvd~~lK~~a~~i~~~lGl~~s---~ai~~fl~qvv~~~~lPF~~~~~ 52 (83)
T TIGR02384 8 RIDEELKKEAYAVFEELGLTPS---TAIRMFLKQVIREQGLPFDLRLP 52 (83)
T ss_pred eeCHHHHHHHHHHHHHhCCCHH---HHHHHHHHHHHHhCCCCCCcCCC
Confidence 5555679999999999999988 88888999999999999776643
Done!