Query 008811
Match_columns 552
No_of_seqs 253 out of 1625
Neff 4.9
Searched_HMMs 46136
Date Thu Mar 28 16:52:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008811.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008811hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.0 1.9E-09 4.2E-14 85.4 8.9 58 13-70 1-62 (62)
2 COG2608 CopZ Copper chaperone 98.9 6.4E-09 1.4E-13 86.0 9.3 65 10-74 2-70 (71)
3 KOG1603 Copper chaperone [Inor 98.8 2E-08 4.4E-13 83.3 8.9 68 8-75 3-71 (73)
4 KOG4656 Copper chaperone for s 98.5 4.1E-07 8.8E-12 89.4 10.2 82 11-97 8-89 (247)
5 PLN02957 copper, zinc superoxi 98.0 2.9E-05 6.3E-10 78.2 10.6 75 6-80 2-76 (238)
6 PRK10671 copA copper exporting 97.6 0.00016 3.6E-09 84.4 8.3 64 10-75 3-67 (834)
7 TIGR00003 copper ion binding p 97.6 0.00077 1.7E-08 49.1 8.8 62 10-71 2-67 (68)
8 COG2217 ZntA Cation transport 97.4 0.00043 9.4E-09 79.7 8.0 63 10-73 2-69 (713)
9 KOG0207 Cation transport ATPas 97.2 0.00097 2.1E-08 77.5 8.0 88 10-97 146-239 (951)
10 KOG0207 Cation transport ATPas 96.6 0.0046 1E-07 72.1 7.5 69 10-78 69-141 (951)
11 PRK10671 copA copper exporting 96.2 0.018 3.9E-07 67.6 9.6 65 11-75 100-165 (834)
12 PRK11033 zntA zinc/cadmium/mer 95.1 0.052 1.1E-06 63.2 7.9 66 9-74 52-119 (741)
13 PF06524 NOA36: NOA36 protein; 94.3 0.031 6.7E-07 57.3 2.9 10 18-27 39-48 (314)
14 PF06524 NOA36: NOA36 protein; 94.0 0.035 7.5E-07 57.0 2.6 9 19-27 99-107 (314)
15 KOG1832 HIV-1 Vpr-binding prot 93.5 0.035 7.7E-07 64.8 1.8 6 19-24 1215-1220(1516)
16 TIGR02052 MerP mercuric transp 92.0 1.8 3.8E-05 34.8 9.5 63 11-73 24-90 (92)
17 PRK13748 putative mercuric red 90.0 1.7 3.8E-05 48.4 10.0 66 13-78 3-71 (561)
18 cd00371 HMA Heavy-metal-associ 87.8 5.1 0.00011 25.9 7.6 52 18-69 7-60 (63)
19 PF05764 YL1: YL1 nuclear prot 85.2 0.76 1.6E-05 46.7 3.3 10 186-195 35-44 (240)
20 PF11705 RNA_pol_3_Rpc31: DNA- 81.7 1.1 2.3E-05 45.3 2.7 6 29-34 63-68 (233)
21 KOG1991 Nuclear transport rece 80.9 0.95 2.1E-05 53.9 2.2 18 19-36 744-761 (1010)
22 PF12253 CAF1A: Chromatin asse 79.9 2 4.4E-05 36.8 3.3 19 173-191 31-49 (77)
23 KOG3241 Uncharacterized conser 78.0 1.5 3.2E-05 43.2 2.2 13 19-31 44-56 (227)
24 KOG1991 Nuclear transport rece 76.4 1.5 3.2E-05 52.3 2.0 6 63-68 809-814 (1010)
25 COG1888 Uncharacterized protei 75.8 12 0.00026 33.2 6.9 65 8-72 4-77 (97)
26 PTZ00415 transmission-blocking 72.4 2.3 5.1E-05 53.4 2.4 9 182-190 150-158 (2849)
27 PF02680 DUF211: Uncharacteriz 71.0 24 0.00052 31.5 7.8 63 9-72 4-75 (95)
28 KOG2023 Nuclear transport rece 70.2 2.3 5E-05 49.2 1.6 20 20-39 95-114 (885)
29 PF02724 CDC45: CDC45-like pro 68.7 3.6 7.7E-05 47.5 2.8 27 12-38 2-29 (622)
30 KOG4369 RTK signaling protein 65.5 5.4 0.00012 48.8 3.4 15 476-490 2067-2081(2131)
31 KOG0772 Uncharacterized conser 65.1 4.2 9.1E-05 45.8 2.3 7 64-70 44-50 (641)
32 KOG4364 Chromatin assembly fac 63.1 6.1 0.00013 45.7 3.1 21 18-38 366-386 (811)
33 PF01883 DUF59: Domain of unkn 63.1 13 0.00029 30.2 4.4 33 10-42 34-72 (72)
34 PF02724 CDC45: CDC45-like pro 60.3 6.2 0.00013 45.6 2.6 21 11-31 27-48 (622)
35 PRK14054 methionine sulfoxide 60.2 21 0.00047 34.9 5.9 28 21-48 10-37 (172)
36 cd04908 ACT_Bt0572_1 N-termina 59.6 57 0.0012 25.8 7.4 61 13-73 3-66 (66)
37 PRK10553 assembly protein for 59.2 48 0.001 29.0 7.3 47 21-67 16-63 (87)
38 cd04883 ACT_AcuB C-terminal AC 58.8 63 0.0014 25.5 7.6 59 13-71 3-68 (72)
39 PF03344 Daxx: Daxx Family; I 57.3 3.5 7.5E-05 48.3 0.0 9 59-67 300-308 (713)
40 KOG2038 CAATT-binding transcri 57.0 5.8 0.00013 46.7 1.7 21 21-41 594-614 (988)
41 PF08777 RRM_3: RNA binding mo 57.0 35 0.00076 30.5 6.3 56 12-67 2-60 (105)
42 PF01206 TusA: Sulfurtransfera 54.5 23 0.00049 28.6 4.4 55 13-76 2-59 (70)
43 PF14492 EFG_II: Elongation Fa 53.9 43 0.00093 27.9 6.0 62 11-72 5-72 (75)
44 KOG3540 Beta amyloid precursor 53.7 11 0.00023 42.4 2.9 8 57-64 80-87 (615)
45 PF14283 DUF4366: Domain of un 51.4 9.3 0.0002 38.7 1.9 16 53-68 103-118 (218)
46 PRK00058 methionine sulfoxide 50.1 35 0.00076 34.6 5.7 29 20-48 51-79 (213)
47 KOG3648 Golgi apparatus protei 50.1 19 0.00041 41.8 4.2 17 142-158 68-84 (1179)
48 PF11702 DUF3295: Protein of u 49.3 9.7 0.00021 42.9 1.9 12 535-547 489-500 (507)
49 PF05086 Dicty_REP: Dictyostel 47.2 9.3 0.0002 44.9 1.3 6 12-17 748-753 (911)
50 PF14437 MafB19-deam: MafB19-l 45.6 40 0.00087 32.3 5.1 40 10-50 100-141 (146)
51 cd04906 ACT_ThrD-I_1 First of 45.5 1.6E+02 0.0034 24.8 8.3 62 13-75 3-73 (85)
52 PRK05528 methionine sulfoxide 44.7 58 0.0013 31.4 6.1 29 21-49 8-36 (156)
53 PF03927 NapD: NapD protein; 44.4 91 0.002 26.5 6.6 46 21-67 14-60 (79)
54 PF09849 DUF2076: Uncharacteri 42.9 26 0.00056 36.2 3.6 16 24-39 6-21 (247)
55 PF09580 Spore_YhcN_YlaJ: Spor 42.6 73 0.0016 30.3 6.5 33 20-52 73-105 (177)
56 PTZ00007 (NAP-L) nucleosome as 42.3 23 0.00051 38.1 3.3 8 30-37 124-131 (337)
57 KOG0296 Angio-associated migra 42.0 12 0.00026 40.6 1.1 6 263-268 99-104 (399)
58 PRK12766 50S ribosomal protein 41.2 9.8 0.00021 38.9 0.3 7 63-69 18-24 (232)
59 PF13732 DUF4162: Domain of un 40.1 84 0.0018 25.9 5.7 48 31-79 26-74 (84)
60 KOG4369 RTK signaling protein 39.2 32 0.00069 42.6 4.0 7 93-99 1772-1778(2131)
61 cd02410 archeal_CPSF_KH The ar 38.9 2.3E+02 0.005 27.3 9.0 58 21-78 52-116 (145)
62 PRK13014 methionine sulfoxide 38.2 53 0.0011 32.6 4.8 28 21-48 15-42 (186)
63 KOG2548 SWAP mRNA splicing reg 37.7 22 0.00047 40.4 2.3 17 55-71 77-93 (653)
64 KOG3064 RNA-binding nuclear pr 37.0 13 0.00028 38.7 0.4 11 39-49 50-60 (303)
65 COG3076 Uncharacterized protei 36.5 18 0.00038 33.4 1.1 8 66-73 52-59 (135)
66 PF09849 DUF2076: Uncharacteri 36.4 35 0.00075 35.3 3.4 17 20-36 25-41 (247)
67 PTZ00482 membrane-attack compl 34.6 23 0.0005 42.4 2.0 12 31-42 16-27 (844)
68 PF01625 PMSR: Peptide methion 34.0 1.1E+02 0.0025 29.3 6.2 27 21-47 7-33 (155)
69 TIGR03406 FeS_long_SufT probab 33.7 46 0.001 32.6 3.6 34 11-44 114-153 (174)
70 PF06752 E_Pc_C: Enhancer of P 33.7 45 0.00098 34.1 3.6 16 142-157 13-28 (230)
71 PRK11018 hypothetical protein; 33.5 1.3E+02 0.0029 25.2 5.9 55 12-75 9-66 (78)
72 PF11491 DUF3213: Protein of u 33.1 53 0.0011 28.9 3.4 52 21-72 10-64 (88)
73 TIGR02945 SUF_assoc FeS assemb 32.5 32 0.00069 29.8 2.1 35 11-45 38-78 (99)
74 TIGR02300 FYDLN_acid conserved 31.9 34 0.00073 32.2 2.2 6 19-24 28-33 (129)
75 PRK07334 threonine dehydratase 31.9 1.5E+02 0.0033 32.1 7.6 64 12-75 327-403 (403)
76 KOG3064 RNA-binding nuclear pr 31.6 24 0.00052 36.8 1.3 10 40-49 41-50 (303)
77 KOG0127 Nucleolar protein fibr 31.2 22 0.00047 40.6 1.0 12 24-35 57-68 (678)
78 cd04909 ACT_PDH-BS C-terminal 30.8 1.8E+02 0.004 22.7 6.1 59 13-71 3-69 (69)
79 PRK11200 grxA glutaredoxin 1; 30.0 1E+02 0.0022 25.5 4.7 26 18-44 9-38 (85)
80 TIGR02159 PA_CoA_Oxy4 phenylac 29.5 60 0.0013 30.9 3.5 57 11-69 26-88 (146)
81 PRK02048 4-hydroxy-3-methylbut 29.2 50 0.0011 38.3 3.4 27 14-40 514-551 (611)
82 KOG4364 Chromatin assembly fac 29.0 38 0.00083 39.5 2.4 12 182-193 518-529 (811)
83 PRK05550 bifunctional methioni 28.6 1.1E+02 0.0025 32.2 5.7 30 20-49 133-162 (283)
84 cd03418 GRX_GRXb_1_3_like Glut 28.1 2.3E+02 0.0049 22.3 6.3 22 15-38 5-26 (75)
85 TIGR00377 ant_ant_sig anti-ant 27.6 3.7E+02 0.008 22.7 7.9 66 11-78 13-85 (108)
86 cd04888 ACT_PheB-BS C-terminal 27.0 1.5E+02 0.0033 23.4 5.1 31 12-42 43-74 (76)
87 cd03421 SirA_like_N SirA_like_ 26.8 1.5E+02 0.0032 23.7 4.9 51 15-75 3-56 (67)
88 cd04885 ACT_ThrD-I Tandem C-te 26.2 2.4E+02 0.0051 22.5 6.0 57 15-71 2-66 (68)
89 KOG3671 Actin regulatory prote 26.2 31 0.00067 39.0 1.1 16 19-34 36-51 (569)
90 TIGR01617 arsC_related transcr 25.9 1E+02 0.0022 27.5 4.2 44 18-69 7-50 (117)
91 PRK11670 antiporter inner memb 25.7 1.6E+02 0.0034 31.9 6.3 68 11-78 48-146 (369)
92 KOG3555 Ca2+-binding proteogly 25.2 53 0.0012 35.8 2.6 14 86-100 210-223 (434)
93 cd02066 GRX_family Glutaredoxi 24.6 1.4E+02 0.0031 22.5 4.4 21 14-35 4-24 (72)
94 KOG0699 Serine/threonine prote 24.5 43 0.00094 36.7 1.8 57 11-67 50-114 (542)
95 KOG4032 Uncharacterized conser 24.0 58 0.0013 32.4 2.4 14 55-68 61-74 (184)
96 PRK10026 arsenate reductase; P 23.8 1.7E+02 0.0036 27.8 5.4 51 11-69 3-53 (141)
97 cd03036 ArsC_like Arsenate Red 23.8 1.7E+02 0.0038 25.9 5.3 44 18-69 7-50 (111)
98 KOG0127 Nucleolar protein fibr 22.5 55 0.0012 37.5 2.2 11 59-69 133-143 (678)
99 TIGR00119 acolac_sm acetolacta 22.3 7.1E+02 0.015 24.0 9.4 61 11-72 44-112 (157)
100 TIGR03675 arCOG00543 arCOG0054 22.1 4E+02 0.0086 31.2 9.0 59 20-78 68-133 (630)
101 KOG2393 Transcription initiati 22.1 60 0.0013 37.0 2.4 33 189-222 278-310 (555)
102 PTZ00248 eukaryotic translatio 22.1 53 0.0012 35.2 1.9 16 18-33 191-208 (319)
103 TIGR02190 GlrX-dom Glutaredoxi 22.1 1.6E+02 0.0035 24.1 4.4 31 11-43 9-39 (79)
104 KOG3411 40S ribosomal protein 22.0 66 0.0014 30.5 2.2 48 19-66 92-140 (143)
105 PF10991 DUF2815: Protein of u 21.5 36 0.00079 33.6 0.5 8 58-65 45-52 (181)
106 TIGR02886 spore_II_AA anti-sig 21.2 4.5E+02 0.0097 22.3 7.2 67 11-78 9-81 (106)
107 COG2151 PaaD Predicted metal-s 21.1 1.2E+02 0.0027 27.7 3.7 33 12-44 51-89 (111)
108 cd03032 ArsC_Spx Arsenate Redu 21.0 1.7E+02 0.0038 26.0 4.7 42 18-67 8-49 (115)
109 PLN02925 4-hydroxy-3-methylbut 20.9 92 0.002 36.8 3.6 25 14-38 630-665 (733)
110 PRK00694 4-hydroxy-3-methylbut 20.7 75 0.0016 36.7 2.8 26 14-39 506-542 (606)
111 cd04884 ACT_CBS C-terminal ACT 20.7 3.2E+02 0.007 21.7 5.8 60 14-74 2-72 (72)
112 PRK01655 spxA transcriptional 20.7 1.4E+02 0.003 27.5 4.1 46 14-67 4-49 (131)
113 PF11111 CENP-M: Centromere pr 20.6 4.1E+02 0.0088 26.4 7.4 56 10-71 66-130 (176)
114 PF05046 Img2: Mitochondrial l 20.4 4.4E+02 0.0095 22.8 6.9 58 11-69 29-87 (87)
115 KOG1274 WD40 repeat protein [G 20.2 72 0.0016 38.4 2.6 47 175-221 319-388 (933)
116 PRK14440 acylphosphatase; Prov 20.1 4.2E+02 0.009 23.0 6.7 57 10-67 3-64 (90)
117 cd03029 GRX_hybridPRX5 Glutare 20.1 1.9E+02 0.0041 23.0 4.4 29 13-43 4-32 (72)
No 1
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.01 E-value=1.9e-09 Score=85.36 Aligned_cols=58 Identities=40% Similarity=0.647 Sum_probs=53.4
Q ss_pred EEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEec---CCHHHHHHHHHHcCCc
Q 008811 13 VLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGN---VDPAILIKKLEKLGKH 70 (552)
Q Consensus 13 ~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~---idpeeII~aI~KaGf~ 70 (552)
+|+|. |+|.+|+.+|+++|.+++||.+++||+.+.+++|+.. +++++|+++|+++||+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGYE 62 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTSE
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCcC
Confidence 58897 9999999999999999999999999999999999833 5679999999999985
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.92 E-value=6.4e-09 Score=86.02 Aligned_cols=65 Identities=37% Similarity=0.615 Sum_probs=58.2
Q ss_pred cEEEEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE--e-cCCHHHHHHHHHHcCCceEEc
Q 008811 10 QSCVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT--G-NVDPAILIKKLEKLGKHAELW 74 (552)
Q Consensus 10 qkv~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~--g-~idpeeII~aI~KaGf~Ael~ 74 (552)
.+++|+|+ |+|.+|+.+|+++|.+++||.+++|++...+++|+ . .++.++|+++|+++||.+..+
T Consensus 2 ~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~~ 70 (71)
T COG2608 2 MKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEEI 70 (71)
T ss_pred ceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeeec
Confidence 46789999 99999999999999999999999999999666665 4 579999999999999998764
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.82 E-value=2e-08 Score=83.32 Aligned_cols=68 Identities=54% Similarity=0.983 Sum_probs=62.5
Q ss_pred CccEEEEEEecccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcC-CceEEcC
Q 008811 8 KLQSCVLRVNVDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGNVDPAILIKKLEKLG-KHAELWG 75 (552)
Q Consensus 8 ~~qkv~LkV~m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~idpeeII~aI~KaG-f~Ael~~ 75 (552)
...+++++|.|+|..|+.+|++.|+.++||++++++....+|+|.+.+++..|++.|++.+ .++++|.
T Consensus 3 ~~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 3 PIKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred CccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEec
Confidence 3567889999999999999999999999999999999999999998899999999999987 7777764
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.55 E-value=4.1e-07 Score=89.35 Aligned_cols=82 Identities=30% Similarity=0.464 Sum_probs=71.7
Q ss_pred EEEEEEecccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcCCceEEcCCCCCCCchhhHHHHH
Q 008811 11 SCVLRVNVDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGNVDPAILIKKLEKLGKHAELWGPQKGSSNSNYQNLLN 90 (552)
Q Consensus 11 kv~LkV~m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~idpeeII~aI~KaGf~Ael~~~~~~~~~~~~~~~l~ 90 (552)
+++|.|.|+|.+|+..|+..|..++||.+|+|+++...|+|++.+.+.+|+.+|+.+|.+|+|.....+. ...+.
T Consensus 8 ~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G~ps-----aval~ 82 (247)
T KOG4656|consen 8 EAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAGKPS-----AVALL 82 (247)
T ss_pred eEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCCchh-----HHHHH
Confidence 5789999999999999999999999999999999999999999999999999999999999999887762 22345
Q ss_pred HHHhhcc
Q 008811 91 NQFKNMM 97 (552)
Q Consensus 91 ~q~k~l~ 97 (552)
.++..+.
T Consensus 83 at~a~~~ 89 (247)
T KOG4656|consen 83 ATVAKYT 89 (247)
T ss_pred HHHHHhc
Confidence 5555555
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.04 E-value=2.9e-05 Score=78.20 Aligned_cols=75 Identities=27% Similarity=0.443 Sum_probs=66.3
Q ss_pred ccCccEEEEEEecccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcCCceEEcCCCCCC
Q 008811 6 FMKLQSCVLRVNVDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGNVDPAILIKKLEKLGKHAELWGPQKGS 80 (552)
Q Consensus 6 ~l~~qkv~LkV~m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~idpeeII~aI~KaGf~Ael~~~~~~~ 80 (552)
+|...+++|.|.|+|..|+.+|+++|.++++|..+.+++...+++|+..+..++|+.+|++++|.++++.....+
T Consensus 2 ~~~~~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 2 ALPELLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQGDPE 76 (238)
T ss_pred CCCcEEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCCCcc
Confidence 466677888888999999999999999999999999999999999986678889999999999999988775543
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.57 E-value=0.00016 Score=84.36 Aligned_cols=64 Identities=25% Similarity=0.455 Sum_probs=56.9
Q ss_pred cEEEEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcCCceEEcC
Q 008811 10 QSCVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGNVDPAILIKKLEKLGKHAELWG 75 (552)
Q Consensus 10 qkv~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~idpeeII~aI~KaGf~Ael~~ 75 (552)
++++|+|+ |+|.+|+.+|+++|.++++|..++|++. +++|+..++.+.|+++|+++||++++.+
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 46789999 9999999999999999999999999984 4566666789999999999999998764
No 7
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.55 E-value=0.00077 Score=49.08 Aligned_cols=62 Identities=21% Similarity=0.407 Sum_probs=50.9
Q ss_pred cEEEEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEe---cCCHHHHHHHHHHcCCce
Q 008811 10 QSCVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTG---NVDPAILIKKLEKLGKHA 71 (552)
Q Consensus 10 qkv~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g---~idpeeII~aI~KaGf~A 71 (552)
+++.|.|. ++|..|..+|++.|..+++|..+.+++...++.|.. .+....++..++..+|.+
T Consensus 2 ~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 2 QKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYEV 67 (68)
T ss_pred cEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCCc
Confidence 35678898 899999999999999999999999999998888762 346777777777777754
No 8
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.35 E-value=0.00043 Score=79.73 Aligned_cols=63 Identities=32% Similarity=0.573 Sum_probs=56.0
Q ss_pred cEEEEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEe---cCC-HHHHHHHHHHcCCceEE
Q 008811 10 QSCVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTG---NVD-PAILIKKLEKLGKHAEL 73 (552)
Q Consensus 10 qkv~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g---~id-peeII~aI~KaGf~Ael 73 (552)
.+++|.|+ |+|..|+.+|| +|++++||..++||+.+++++|.. .++ .++++.+|++++|.++.
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 35679999 99999999999 999999999999999999999872 345 78999999999998765
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.16 E-value=0.00097 Score=77.54 Aligned_cols=88 Identities=20% Similarity=0.309 Sum_probs=70.3
Q ss_pred cEEEEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE---ecCCHHHHHHHHHHcCCceEEcCCCCCCCc--h
Q 008811 10 QSCVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT---GNVDPAILIKKLEKLGKHAELWGPQKGSSN--S 83 (552)
Q Consensus 10 qkv~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~---g~idpeeII~aI~KaGf~Ael~~~~~~~~~--~ 83 (552)
.+++|.|. ++|..|+.+|++.|.++.+|.+++|++.+.++.|. ..+.+.+|++.|++.+|.+.+..-...... -
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~~~~~~~~~~l 225 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRPYGDTTFKNSL 225 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeeeccccchhhhh
Confidence 57889999 89999999999999999999999999999999887 458999999999999999877653332221 1
Q ss_pred hhHHHHHHHHhhcc
Q 008811 84 NYQNLLNNQFKNMM 97 (552)
Q Consensus 84 ~~~~~l~~q~k~l~ 97 (552)
....++++|++.+.
T Consensus 226 ~~~~ei~~w~~~fl 239 (951)
T KOG0207|consen 226 KHKEEIRKWKRPFL 239 (951)
T ss_pred hhhhHHHhcchHHH
Confidence 12345666666655
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.60 E-value=0.0046 Score=72.15 Aligned_cols=69 Identities=33% Similarity=0.561 Sum_probs=62.4
Q ss_pred cEEEEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE---ecCCHHHHHHHHHHcCCceEEcCCCC
Q 008811 10 QSCVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT---GNVDPAILIKKLEKLGKHAELWGPQK 78 (552)
Q Consensus 10 qkv~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~---g~idpeeII~aI~KaGf~Ael~~~~~ 78 (552)
.++.|+|+ |+|..|+..|++.|++++||.++.|.+..++++|. ..++++.+.+.+++++|.+++++...
T Consensus 69 ~~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~~~ 141 (951)
T KOG0207|consen 69 SKCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIESVN 141 (951)
T ss_pred ceeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhccc
Confidence 37889999 99999999999999999999999999999999987 45799999999999999999876544
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.21 E-value=0.018 Score=67.58 Aligned_cols=65 Identities=28% Similarity=0.486 Sum_probs=56.8
Q ss_pred EEEEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcCCceEEcC
Q 008811 11 SCVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGNVDPAILIKKLEKLGKHAELWG 75 (552)
Q Consensus 11 kv~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~idpeeII~aI~KaGf~Ael~~ 75 (552)
+++|.|. ++|..|+.+|++.|.++++|..+.+++.+.++.|....++++|.+.|++++|.+.++.
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~~~ 165 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEAIE 165 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCccccc
Confidence 5678888 8999999999999999999999999999988888755678888889999999876554
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=95.13 E-value=0.052 Score=63.19 Aligned_cols=66 Identities=24% Similarity=0.313 Sum_probs=54.0
Q ss_pred ccEEEEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEe-cCCHHHHHHHHHHcCCceEEc
Q 008811 9 LQSCVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTG-NVDPAILIKKLEKLGKHAELW 74 (552)
Q Consensus 9 ~qkv~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g-~idpeeII~aI~KaGf~Ael~ 74 (552)
..+++++|. ++|..|..+|++.|.++++|..+.+++.+.++.|.. ....+++...+++++|.+..+
T Consensus 52 ~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~~~ 119 (741)
T PRK11033 52 GTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLRDE 119 (741)
T ss_pred CceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccccccc
Confidence 346678888 899999999999999999999999999998887762 112367778888999987654
No 13
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=94.29 E-value=0.031 Score=57.32 Aligned_cols=10 Identities=40% Similarity=1.185 Sum_probs=4.8
Q ss_pred cccHHHHHHH
Q 008811 18 VDCDGCKQKV 27 (552)
Q Consensus 18 m~C~gCa~KI 27 (552)
|.|+.|..+-
T Consensus 39 MeCdkC~r~Q 48 (314)
T PF06524_consen 39 MECDKCQRKQ 48 (314)
T ss_pred ccchhhhhhc
Confidence 3455554443
No 14
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=94.04 E-value=0.035 Score=57.00 Aligned_cols=9 Identities=44% Similarity=0.726 Sum_probs=4.5
Q ss_pred ccHHHHHHH
Q 008811 19 DCDGCKQKV 27 (552)
Q Consensus 19 ~C~gCa~KI 27 (552)
.|+.|..-|
T Consensus 99 iCDfCEawv 107 (314)
T PF06524_consen 99 ICDFCEAWV 107 (314)
T ss_pred hhccchhhe
Confidence 455554444
No 15
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=93.52 E-value=0.035 Score=64.76 Aligned_cols=6 Identities=17% Similarity=0.578 Sum_probs=2.4
Q ss_pred ccHHHH
Q 008811 19 DCDGCK 24 (552)
Q Consensus 19 ~C~gCa 24 (552)
+|..|.
T Consensus 1215 T~~~l~ 1220 (1516)
T KOG1832|consen 1215 TCSPLQ 1220 (1516)
T ss_pred cCcHHH
Confidence 344443
No 16
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=92.00 E-value=1.8 Score=34.78 Aligned_cols=63 Identities=25% Similarity=0.412 Sum_probs=46.4
Q ss_pred EEEEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE--e-cCCHHHHHHHHHHcCCceEE
Q 008811 11 SCVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT--G-NVDPAILIKKLEKLGKHAEL 73 (552)
Q Consensus 11 kv~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~--g-~idpeeII~aI~KaGf~Ael 73 (552)
++.+.+. +.|..|...++..+...++|..+.+.+...++.+. . ......+...++++++.+++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 4456666 78999999999999999998888888777765554 1 24555565666777777654
No 17
>PRK13748 putative mercuric reductase; Provisional
Probab=89.98 E-value=1.7 Score=48.36 Aligned_cols=66 Identities=29% Similarity=0.511 Sum_probs=51.6
Q ss_pred EEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEe--cCCHHHHHHHHHHcCCceEEcCCCC
Q 008811 13 VLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTG--NVDPAILIKKLEKLGKHAELWGPQK 78 (552)
Q Consensus 13 ~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g--~idpeeII~aI~KaGf~Ael~~~~~ 78 (552)
.+.+. ++|..|..+++..+..+++|..+.+++....+.+.. ....+.+...++.+++.++++....
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~~~~~ 71 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLADAPP 71 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeeccCccc
Confidence 35566 799999999999999999998888888888766652 2456667677788888887776643
No 18
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=87.79 E-value=5.1 Score=25.91 Aligned_cols=52 Identities=42% Similarity=0.733 Sum_probs=34.1
Q ss_pred cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEec--CCHHHHHHHHHHcCC
Q 008811 18 VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGN--VDPAILIKKLEKLGK 69 (552)
Q Consensus 18 m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~--idpeeII~aI~KaGf 69 (552)
+.|..|...++..+..+.+|....+.+....+.+... .....+...++..++
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 (63)
T cd00371 7 MTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIEDAGY 60 (63)
T ss_pred eEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHHHcCC
Confidence 6799999999999988888877777766665554421 244444344444433
No 19
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=85.22 E-value=0.76 Score=46.74 Aligned_cols=10 Identities=50% Similarity=0.926 Sum_probs=4.1
Q ss_pred CCCCCCCCCC
Q 008811 186 IEDDFDDEEF 195 (552)
Q Consensus 186 ~~~~~~dd~~ 195 (552)
|.++++|+||
T Consensus 35 f~Eee~D~ef 44 (240)
T PF05764_consen 35 FQEEEDDEEF 44 (240)
T ss_pred ccccCCCccc
Confidence 3444444433
No 20
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=81.72 E-value=1.1 Score=45.29 Aligned_cols=6 Identities=17% Similarity=0.302 Sum_probs=2.3
Q ss_pred HHHhcC
Q 008811 29 KVLRKI 34 (552)
Q Consensus 29 kaL~kI 34 (552)
..++..
T Consensus 63 ~~~~~s 68 (233)
T PF11705_consen 63 ERMRDS 68 (233)
T ss_pred HHHHhC
Confidence 334433
No 21
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=80.86 E-value=0.95 Score=53.89 Aligned_cols=18 Identities=17% Similarity=0.523 Sum_probs=8.5
Q ss_pred ccHHHHHHHHHHHhcCCC
Q 008811 19 DCDGCKQKVKKVLRKIDG 36 (552)
Q Consensus 19 ~C~gCa~KIekaL~kIeG 36 (552)
.|.+-...++-++....|
T Consensus 744 d~~~a~kLle~iiL~~kg 761 (1010)
T KOG1991|consen 744 DCESACKLLEVIILNCKG 761 (1010)
T ss_pred HHHHHHHHHHHHHHHhcC
Confidence 344333355555555555
No 22
>PF12253 CAF1A: Chromatin assembly factor 1 subunit A; InterPro: IPR022043 The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A []. The A domain is uniquely required for the progression of S phase in mouse cells [], independent of its ability to promote histone deposition [] but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints [].
Probab=79.87 E-value=2 Score=36.78 Aligned_cols=19 Identities=21% Similarity=0.081 Sum_probs=9.4
Q ss_pred cCcccccCCCCCCCCCCCC
Q 008811 173 QHNKDQKHGKFNTIEDDFD 191 (552)
Q Consensus 173 ~~~~~~k~~k~~~~~~~~~ 191 (552)
|..++.....+....++|.
T Consensus 31 P~~~d~~~lDYdyDSd~EW 49 (77)
T PF12253_consen 31 PFAKDLPNLDYDYDSDDEW 49 (77)
T ss_pred cccccccccceecCCcccc
Confidence 3344445555555555444
No 23
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=78.04 E-value=1.5 Score=43.22 Aligned_cols=13 Identities=23% Similarity=0.598 Sum_probs=8.9
Q ss_pred ccHHHHHHHHHHH
Q 008811 19 DCDGCKQKVKKVL 31 (552)
Q Consensus 19 ~C~gCa~KIekaL 31 (552)
-|..|...|+=.+
T Consensus 44 VCqRCkEqieWk~ 56 (227)
T KOG3241|consen 44 VCQRCKEQIEWKR 56 (227)
T ss_pred HHHHHHHHHHHHH
Confidence 5888877775443
No 24
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=76.36 E-value=1.5 Score=52.32 Aligned_cols=6 Identities=50% Similarity=0.628 Sum_probs=2.3
Q ss_pred HHHHcC
Q 008811 63 KLEKLG 68 (552)
Q Consensus 63 aI~KaG 68 (552)
.|+..+
T Consensus 809 iLe~~~ 814 (1010)
T KOG1991|consen 809 ILENQG 814 (1010)
T ss_pred HHHHcC
Confidence 333333
No 25
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=75.77 E-value=12 Score=33.24 Aligned_cols=65 Identities=28% Similarity=0.326 Sum_probs=40.9
Q ss_pred CccEEEEEEe-cccHHHHHHHHHHHhcCCCeeEEEE-----ecCC--cEEEEE-ecCCHHHHHHHHHHcCCceE
Q 008811 8 KLQSCVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNV-----DVEQ--GKVTVT-GNVDPAILIKKLEKLGKHAE 72 (552)
Q Consensus 8 ~~qkv~LkV~-m~C~gCa~KIekaL~kIeGV~sV~V-----dla~--~kVtV~-g~idpeeII~aI~KaGf~Ae 72 (552)
..++++|.|. .+..-.--.+.+.|++++||..|+| |.++ -+++|+ ..++.++|.+.|++.|-.++
T Consensus 4 ~iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IH 77 (97)
T COG1888 4 GIRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIH 77 (97)
T ss_pred cceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeee
Confidence 3456777776 4422233355566788877655543 3333 334555 45899999999999986543
No 26
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=72.42 E-value=2.3 Score=53.36 Aligned_cols=9 Identities=33% Similarity=0.350 Sum_probs=3.7
Q ss_pred CCCCCCCCC
Q 008811 182 KFNTIEDDF 190 (552)
Q Consensus 182 k~~~~~~~~ 190 (552)
.|+..+|||
T Consensus 150 ~~~~d~~~~ 158 (2849)
T PTZ00415 150 NFVIDDDDE 158 (2849)
T ss_pred ccccCCccc
Confidence 354443333
No 27
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=71.05 E-value=24 Score=31.53 Aligned_cols=63 Identities=25% Similarity=0.392 Sum_probs=41.5
Q ss_pred ccEEEEEEe-cccHHHHHHHHHHHhcCCCeeEEEEec-----CCcEE--EEEe-cCCHHHHHHHHHHcCCceE
Q 008811 9 LQSCVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDV-----EQGKV--TVTG-NVDPAILIKKLEKLGKHAE 72 (552)
Q Consensus 9 ~qkv~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdl-----a~~kV--tV~g-~idpeeII~aI~KaGf~Ae 72 (552)
.+|++|.|- .+-+.-. .+.+.|.++++|..|++.+ .+..+ +|++ .++.++|.++|++.|-.++
T Consensus 4 irRlVLDVlKP~~p~i~-e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IH 75 (95)
T PF02680_consen 4 IRRLVLDVLKPHEPSIV-ELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIH 75 (95)
T ss_dssp EEEEEEEEEEESSS-HH-HHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEE
T ss_pred eeEEEEEeecCCCCCHH-HHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEE
Confidence 456777776 4555544 5677899999987776543 33333 3444 4899999999999986544
No 28
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=70.19 E-value=2.3 Score=49.19 Aligned_cols=20 Identities=15% Similarity=0.223 Sum_probs=8.0
Q ss_pred cHHHHHHHHHHHhcCCCeeE
Q 008811 20 CDGCKQKVKKVLRKIDGVYS 39 (552)
Q Consensus 20 C~gCa~KIekaL~kIeGV~s 39 (552)
|-.|.-..+..++.+-||..
T Consensus 95 ~l~~lgd~~~lIr~tvGivI 114 (885)
T KOG2023|consen 95 CLHGLGDASPLIRATVGIVI 114 (885)
T ss_pred HHhhccCchHHHHhhhhhee
Confidence 33333333344444444433
No 29
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=68.72 E-value=3.6 Score=47.47 Aligned_cols=27 Identities=26% Similarity=0.359 Sum_probs=19.3
Q ss_pred EEEEEeccc-HHHHHHHHHHHhcCCCee
Q 008811 12 CVLRVNVDC-DGCKQKVKKVLRKIDGVY 38 (552)
Q Consensus 12 v~LkV~m~C-~gCa~KIekaL~kIeGV~ 38 (552)
|.|-|...| .-|+.+|-+.|-+-+.|.
T Consensus 2 Vli~v~~dvDalcA~kiL~~Llk~d~I~ 29 (622)
T PF02724_consen 2 VLILVALDVDALCACKILTSLLKSDNIQ 29 (622)
T ss_pred EEEEEcCChHHHHHHHHHHHHHHhcCCC
Confidence 344555544 678999988888888774
No 30
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=65.51 E-value=5.4 Score=48.76 Aligned_cols=15 Identities=40% Similarity=0.512 Sum_probs=7.1
Q ss_pred cCCCCCCCCchhhHH
Q 008811 476 YGAMGPGTNPYNQQQ 490 (552)
Q Consensus 476 ~~g~~~~~~~~~qq~ 490 (552)
|.-+..-.||-.+||
T Consensus 2067 ~~n~~s~~n~s~~qq 2081 (2131)
T KOG4369|consen 2067 LGNASSTTNPSRTQQ 2081 (2131)
T ss_pred hcccCCCCCccHHHH
Confidence 344443456655544
No 31
>KOG0772 consensus Uncharacterized conserved protein, contains WD40 repeat [Function unknown]
Probab=65.09 E-value=4.2 Score=45.78 Aligned_cols=7 Identities=14% Similarity=0.140 Sum_probs=3.1
Q ss_pred HHHcCCc
Q 008811 64 LEKLGKH 70 (552)
Q Consensus 64 I~KaGf~ 70 (552)
|+.+-+.
T Consensus 44 i~~~~~~ 50 (641)
T KOG0772|consen 44 ISDLQFT 50 (641)
T ss_pred hhhcccc
Confidence 4444443
No 32
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=63.12 E-value=6.1 Score=45.70 Aligned_cols=21 Identities=19% Similarity=0.376 Sum_probs=13.0
Q ss_pred cccHHHHHHHHHHHhcCCCee
Q 008811 18 VDCDGCKQKVKKVLRKIDGVY 38 (552)
Q Consensus 18 m~C~gCa~KIekaL~kIeGV~ 38 (552)
..|-.-+..|.+.+.++.--.
T Consensus 366 ~rkkr~~aei~Kffqk~~~k~ 386 (811)
T KOG4364|consen 366 LRKKRHEAEIGKFFQKIDNKF 386 (811)
T ss_pred HHHHHHHHHHHhhhccccccc
Confidence 356666667777777665443
No 33
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=63.09 E-value=13 Score=30.16 Aligned_cols=33 Identities=18% Similarity=0.503 Sum_probs=22.2
Q ss_pred cEEEEEEecccHHH------HHHHHHHHhcCCCeeEEEE
Q 008811 10 QSCVLRVNVDCDGC------KQKVKKVLRKIDGVYSTNV 42 (552)
Q Consensus 10 qkv~LkV~m~C~gC------a~KIekaL~kIeGV~sV~V 42 (552)
.+++|.|.+.++.| ...|+++|..+++|.+|+|
T Consensus 34 ~~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 34 GKVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp CEEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred CEEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 45666666555555 5678889999999988876
No 34
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=60.27 E-value=6.2 Score=45.58 Aligned_cols=21 Identities=10% Similarity=-0.032 Sum_probs=10.9
Q ss_pred EEEEEEe-cccHHHHHHHHHHH
Q 008811 11 SCVLRVN-VDCDGCKQKVKKVL 31 (552)
Q Consensus 11 kv~LkV~-m~C~gCa~KIekaL 31 (552)
-+.|+|. +.+..+..++-..+
T Consensus 27 ~I~~~l~PV~gy~el~~~~~~~ 48 (622)
T PF02724_consen 27 NIQYSLVPVSGYSELERAYEEL 48 (622)
T ss_pred CCCeeEEEeCCHHHHHHHHHHH
Confidence 3455555 55555555554444
No 35
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=60.15 E-value=21 Score=34.85 Aligned_cols=28 Identities=29% Similarity=0.507 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEecCCcE
Q 008811 21 DGCKQKVKKVLRKIDGVYSTNVDVEQGK 48 (552)
Q Consensus 21 ~gCa~KIekaL~kIeGV~sV~Vdla~~k 48 (552)
.+|-+-+|..+.+|+||.+++|-++.+.
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~ 37 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGH 37 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCC
Confidence 6888889999999999999999888774
No 36
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=59.63 E-value=57 Score=25.83 Aligned_cols=61 Identities=16% Similarity=0.095 Sum_probs=37.9
Q ss_pred EEEEe-cccHHHHHHHHHHHhcCCC-eeEEEEecCCcEEEEE-ecCCHHHHHHHHHHcCCceEE
Q 008811 13 VLRVN-VDCDGCKQKVKKVLRKIDG-VYSTNVDVEQGKVTVT-GNVDPAILIKKLEKLGKHAEL 73 (552)
Q Consensus 13 ~LkV~-m~C~gCa~KIekaL~kIeG-V~sV~Vdla~~kVtV~-g~idpeeII~aI~KaGf~Ael 73 (552)
+|.|. -+.++--.+|-++|.+-.- |.++.+.....++++. ...+++.+++.|+++||++.+
T Consensus 3 ri~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~~~~~~~rl~~~~~~~~~~~L~~~G~~v~~ 66 (66)
T cd04908 3 QLSVFLENKPGRLAAVTEILSEAGINIRALSIADTSEFGILRLIVSDPDKAKEALKEAGFAVKL 66 (66)
T ss_pred EEEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEecCCCCEEEEEECCHHHHHHHHHHCCCEEEC
Confidence 34555 3667777788888766533 4444443332333333 225677999999999998753
No 37
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=59.22 E-value=48 Score=29.00 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE-ecCCHHHHHHHHHHc
Q 008811 21 DGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT-GNVDPAILIKKLEKL 67 (552)
Q Consensus 21 ~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~-g~idpeeII~aI~Ka 67 (552)
+.-...|.+.|..++++.-...+...+|+.|+ ...+.+.+++.|..+
T Consensus 16 Pe~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~~I 63 (87)
T PRK10553 16 SERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIESV 63 (87)
T ss_pred hHHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHHHH
Confidence 55577899999999999888887777888766 444666666655543
No 38
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=58.80 E-value=63 Score=25.48 Aligned_cols=59 Identities=17% Similarity=0.303 Sum_probs=35.2
Q ss_pred EEEEec-ccHHHHHHHHHHHhcCC-CeeEEEEecC--CcE--EEEE-ecCCHHHHHHHHHHcCCce
Q 008811 13 VLRVNV-DCDGCKQKVKKVLRKID-GVYSTNVDVE--QGK--VTVT-GNVDPAILIKKLEKLGKHA 71 (552)
Q Consensus 13 ~LkV~m-~C~gCa~KIekaL~kIe-GV~sV~Vdla--~~k--VtV~-g~idpeeII~aI~KaGf~A 71 (552)
+|.|.+ ..++...+|...|.+.. .|.++.+... ... ++|. ...+.+.+++.|++.||.+
T Consensus 3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L~~~G~~v 68 (72)
T cd04883 3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNPRPIIEDLRRAGYEV 68 (72)
T ss_pred EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCHHHHHHHHHHCCCee
Confidence 355553 55666677777776653 3555544332 122 3333 2246779999999999965
No 39
>PF03344 Daxx: Daxx Family; InterPro: IPR005012 Daxx is a ubiquitously expressed protein that functions, in part, as a transcriptional co-repressor through its interaction with a growing number of nuclear, DNA-associated proteins. Human Daxx contains four structural domains commonly found in transcriptional regulatory proteins: two predicted paired amphipathic helices, an acid-rich domain and a Ser/Pro/Thr (SPT)-rich domain. The post-translational modification status of the SPT-domain of hDaxx regulates its association with transcription factors such as Pax3 and ETS-1, effectively bringing hDaxx to sites of active transcription. Through its presence at the site of active transcription, hDaxx could then be able to associate with acetylated histones present in the nucleosomes and Dek that is associated with chromatin. Through its association with the SPT-domain of hDaxx, histone deacetylases may also be brought to the site of active transcription. As a consequence, nucleosomes in the vicinity of the site of active transcription will have the histone tails deacetylated, allowing the deactylated tail to bind to DNA, thereby leading to an inactive chromatin structure and transcriptional repression []. The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis as a component of nuclear promyelocytic leukemia protein (PML) oncogenic domains (PODS). Daxx associates with PODs through a direct interaction with PML, a critical component of PODs. The interaction is a dynamic, cell cycle regulated event and is dependent on the post-translational modification of PML by the small ubiquitin-related modifier SUMO-1. ; PDB: 2KZS_A 2KZU_A.
Probab=57.31 E-value=3.5 Score=48.34 Aligned_cols=9 Identities=22% Similarity=0.257 Sum_probs=0.0
Q ss_pred HHHHHHHHc
Q 008811 59 ILIKKLEKL 67 (552)
Q Consensus 59 eII~aI~Ka 67 (552)
+|+..|+++
T Consensus 300 Dvl~~v~~~ 308 (713)
T PF03344_consen 300 DVLQCVEKA 308 (713)
T ss_dssp ---------
T ss_pred ccccccccc
Confidence 344444433
No 40
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=57.00 E-value=5.8 Score=46.67 Aligned_cols=21 Identities=10% Similarity=-0.012 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHhcCCCeeEEE
Q 008811 21 DGCKQKVKKVLRKIDGVYSTN 41 (552)
Q Consensus 21 ~gCa~KIekaL~kIeGV~sV~ 41 (552)
++|--.|.++|...+.+++.-
T Consensus 594 ~G~l~Llsel~Karp~l~~lv 614 (988)
T KOG2038|consen 594 CGILFLLSELLKARPTLRKLV 614 (988)
T ss_pred HhHHHHHHHHHHhcchHHHHh
Confidence 456666666666666654443
No 41
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=56.98 E-value=35 Score=30.47 Aligned_cols=56 Identities=13% Similarity=0.233 Sum_probs=33.0
Q ss_pred EEEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE--ecCCHHHHHHHHHHc
Q 008811 12 CVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT--GNVDPAILIKKLEKL 67 (552)
Q Consensus 12 v~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~--g~idpeeII~aI~Ka 67 (552)
++|+|. ++-+.|...|+.+|+.+..|..|++..-.....|. .......+++++...
T Consensus 2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhc
Confidence 456777 55455588999999999999999998877777776 334577777877766
No 42
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=54.46 E-value=23 Score=28.55 Aligned_cols=55 Identities=16% Similarity=0.089 Sum_probs=38.1
Q ss_pred EEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE--ecCCHHHHHHHHHHcCCceEEcCC
Q 008811 13 VLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT--GNVDPAILIKKLEKLGKHAELWGP 76 (552)
Q Consensus 13 ~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~--g~idpeeII~aI~KaGf~Ael~~~ 76 (552)
+|.+. ..|+...-+++++|.+++.= ..++|. .....+.|...+++.|+.+..+..
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~g~~~~~~~~ 59 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEENGYEVVEVEE 59 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTEEEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHCCCEEEEEEE
Confidence 35555 58999999999999997332 233333 334678899999999998655543
No 43
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=53.94 E-value=43 Score=27.89 Aligned_cols=62 Identities=19% Similarity=0.397 Sum_probs=41.2
Q ss_pred EEEEEEecccHHHHHHHHHHHhcC---CCeeEEEEecCCcEEEEE--ecCCHHHHHHHHHH-cCCceE
Q 008811 11 SCVLRVNVDCDGCKQKVKKVLRKI---DGVYSTNVDVEQGKVTVT--GNVDPAILIKKLEK-LGKHAE 72 (552)
Q Consensus 11 kv~LkV~m~C~gCa~KIekaL~kI---eGV~sV~Vdla~~kVtV~--g~idpeeII~aI~K-aGf~Ae 72 (552)
.+.+.|...-..-..++.++|.+| +-...+.+|..++.+.|. +.+..+.+++.|++ .+.+++
T Consensus 5 v~~~~i~p~~~~d~~kl~~aL~~l~~eDP~l~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~ 72 (75)
T PF14492_consen 5 VLSVAIEPKNKEDEPKLSEALQKLSEEDPSLRVERDEETGELILSGMGELHLEVLLERLKRRFGVEVE 72 (75)
T ss_dssp SEEEEEEESSHHHHHHHHHHHHHHHHH-TTSEEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEE
T ss_pred eEEEEEEECCHhHHHHHHHHHHHHHhcCCeEEEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeE
Confidence 345666644455566666666665 334578888888888887 67888889998875 344433
No 44
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=53.74 E-value=11 Score=42.37 Aligned_cols=8 Identities=25% Similarity=0.646 Sum_probs=3.0
Q ss_pred HHHHHHHH
Q 008811 57 PAILIKKL 64 (552)
Q Consensus 57 peeII~aI 64 (552)
|+..|..|
T Consensus 80 PelqitnV 87 (615)
T KOG3540|consen 80 PELQITNV 87 (615)
T ss_pred hHHHHHHH
Confidence 33333333
No 45
>PF14283 DUF4366: Domain of unknown function (DUF4366)
Probab=51.45 E-value=9.3 Score=38.69 Aligned_cols=16 Identities=31% Similarity=0.327 Sum_probs=11.6
Q ss_pred ecCCHHHHHHHHHHcC
Q 008811 53 GNVDPAILIKKLEKLG 68 (552)
Q Consensus 53 g~idpeeII~aI~KaG 68 (552)
..++.++|++++.+..
T Consensus 103 n~VdE~DLl~l~e~~~ 118 (218)
T PF14283_consen 103 NQVDEADLLALMEEEE 118 (218)
T ss_pred ccCCHHHHHHHHhccC
Confidence 5578888888887554
No 46
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=50.12 E-value=35 Score=34.58 Aligned_cols=29 Identities=31% Similarity=0.505 Sum_probs=25.2
Q ss_pred cHHHHHHHHHHHhcCCCeeEEEEecCCcE
Q 008811 20 CDGCKQKVKKVLRKIDGVYSTNVDVEQGK 48 (552)
Q Consensus 20 C~gCa~KIekaL~kIeGV~sV~Vdla~~k 48 (552)
-.+|-+-+|..+.+|+||.+++|-++.+.
T Consensus 51 agGCFWg~E~~F~~l~GV~~t~vGYagG~ 79 (213)
T PRK00058 51 GMGCFWGAERLFWQLPGVYSTAVGYAGGY 79 (213)
T ss_pred EccCcchhHHHHhcCCCEEEEEeeecCCC
Confidence 36888889999999999999999888763
No 47
>KOG3648 consensus Golgi apparatus protein (cysteine-rich fibroblast growth factor receptor) [Intracellular trafficking, secretion, and vesicular transport]
Probab=50.06 E-value=19 Score=41.85 Aligned_cols=17 Identities=65% Similarity=0.497 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHHHHHH
Q 008811 142 QLQQLQQLQAQQMMQQQ 158 (552)
Q Consensus 142 q~qq~qq~q~qQ~qQ~q 158 (552)
|.-|+||||+||+||++
T Consensus 68 ~~~~~~~~~~~~~~~~~ 84 (1179)
T KOG3648|consen 68 QSSQLQQQQQQQQQQQQ 84 (1179)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 44445555544444433
No 48
>PF11702 DUF3295: Protein of unknown function (DUF3295); InterPro: IPR021711 This family is conserved in fungi but the function is not known.
Probab=49.34 E-value=9.7 Score=42.91 Aligned_cols=12 Identities=25% Similarity=0.556 Sum_probs=8.1
Q ss_pred CCCCCCCCCCCCC
Q 008811 535 DHYTHYFSDENAN 547 (552)
Q Consensus 535 ~~~~~~Fsden~~ 547 (552)
-+++||| |+-++
T Consensus 489 ~swn~yf-~~~~~ 500 (507)
T PF11702_consen 489 SSWNQYF-DYGPW 500 (507)
T ss_pred cchhhhh-ccCCc
Confidence 4678999 66443
No 49
>PF05086 Dicty_REP: Dictyostelium (Slime Mold) REP protein; InterPro: IPR007778 This family consists of REP proteins from a number of Dictyostelium species (Slime molds). REP protein is probably involved in transcription regulation and control of DNA replication, specifically the amplification of plasmid at low copy numbers. The formation of homomultimers may be required for their regulatory activity [].
Probab=47.24 E-value=9.3 Score=44.92 Aligned_cols=6 Identities=17% Similarity=1.243 Sum_probs=2.6
Q ss_pred EEEEEe
Q 008811 12 CVLRVN 17 (552)
Q Consensus 12 v~LkV~ 17 (552)
|.++|.
T Consensus 748 CLikIt 753 (911)
T PF05086_consen 748 CLIKIT 753 (911)
T ss_pred ceeEee
Confidence 444444
No 50
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=45.57 E-value=40 Score=32.33 Aligned_cols=40 Identities=25% Similarity=0.424 Sum_probs=30.0
Q ss_pred cEEEEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecC-CcEEE
Q 008811 10 QSCVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVE-QGKVT 50 (552)
Q Consensus 10 qkv~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla-~~kVt 50 (552)
..+++.|. -.|..|..-|...++++ |+.+++|... ++++.
T Consensus 100 ~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~ 141 (146)
T PF14437_consen 100 RSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVY 141 (146)
T ss_pred CeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEE
Confidence 45678888 78999999998888776 7777777665 55443
No 51
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=45.52 E-value=1.6e+02 Score=24.83 Aligned_cols=62 Identities=16% Similarity=0.197 Sum_probs=39.1
Q ss_pred EEEEec-ccHHHHHHHHHHHhcCCCeeEEEEec---CCcEEEEE-e----cCCHHHHHHHHHHcCCceEEcC
Q 008811 13 VLRVNV-DCDGCKQKVKKVLRKIDGVYSTNVDV---EQGKVTVT-G----NVDPAILIKKLEKLGKHAELWG 75 (552)
Q Consensus 13 ~LkV~m-~C~gCa~KIekaL~kIeGV~sV~Vdl---a~~kVtV~-g----~idpeeII~aI~KaGf~Ael~~ 75 (552)
+|.|.+ .-++--.++-.+|. -..|..+..+. ....+.|. . ..+.++|++.|++.||.++...
T Consensus 3 vl~v~ipD~PG~L~~ll~~l~-~anI~~~~y~~~~~~~~~v~i~ie~~~~~~~~~~i~~~L~~~G~~~~~~~ 73 (85)
T cd04906 3 LLAVTIPERPGSFKKFCELIG-PRNITEFNYRYADEKDAHIFVGVSVANGAEELAELLEDLKSAGYEVVDLS 73 (85)
T ss_pred EEEEecCCCCcHHHHHHHHhC-CCceeEEEEEccCCCeeEEEEEEEeCCcHHHHHHHHHHHHHCCCCeEECC
Confidence 466774 56776777777777 34565555544 23334332 2 2347788999999999877644
No 52
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=44.72 E-value=58 Score=31.44 Aligned_cols=29 Identities=24% Similarity=0.512 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEecCCcEE
Q 008811 21 DGCKQKVKKVLRKIDGVYSTNVDVEQGKV 49 (552)
Q Consensus 21 ~gCa~KIekaL~kIeGV~sV~Vdla~~kV 49 (552)
.+|-+-+|..+.+++||.+++|-++.+.+
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~ 36 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRT 36 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCC
Confidence 67888889999999999999998887744
No 53
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=44.40 E-value=91 Score=26.49 Aligned_cols=46 Identities=24% Similarity=0.312 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE-ecCCHHHHHHHHHHc
Q 008811 21 DGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT-GNVDPAILIKKLEKL 67 (552)
Q Consensus 21 ~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~-g~idpeeII~aI~Ka 67 (552)
+.-...|+++|..+++|.-..++.. +++.|+ ...+.+++.+.|.++
T Consensus 14 p~~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~i 60 (79)
T PF03927_consen 14 PERLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDAI 60 (79)
T ss_dssp CCCHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHHH
T ss_pred chhHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHHH
Confidence 4456789999999999977777766 677655 445677777777654
No 54
>PF09849 DUF2076: Uncharacterized protein conserved in bacteria (DUF2076); InterPro: IPR018648 This family of hypothetical prokaryotic proteins has no known function but includes putative perimplasmic ligand-binding sensor proteins.
Probab=42.91 E-value=26 Score=36.24 Aligned_cols=16 Identities=6% Similarity=0.304 Sum_probs=10.8
Q ss_pred HHHHHHHHhcCCCeeE
Q 008811 24 KQKVKKVLRKIDGVYS 39 (552)
Q Consensus 24 a~KIekaL~kIeGV~s 39 (552)
...|+.+|.+|..++.
T Consensus 6 ~qLI~~lf~RL~~ae~ 21 (247)
T PF09849_consen 6 RQLIDDLFSRLKQAEA 21 (247)
T ss_pred HHHHHHHHHHHHhccC
Confidence 4677777777766643
No 55
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=42.58 E-value=73 Score=30.28 Aligned_cols=33 Identities=18% Similarity=0.281 Sum_probs=28.0
Q ss_pred cHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE
Q 008811 20 CDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT 52 (552)
Q Consensus 20 C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~ 52 (552)
-..-+.+|.+.|.++++|..+.|-.....|.|.
T Consensus 73 ~~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 73 RQQLADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 455688999999999999999998888888765
No 56
>PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional
Probab=42.30 E-value=23 Score=38.13 Aligned_cols=8 Identities=13% Similarity=0.472 Sum_probs=3.3
Q ss_pred HHhcCCCe
Q 008811 30 VLRKIDGV 37 (552)
Q Consensus 30 aL~kIeGV 37 (552)
+|.-|..|
T Consensus 124 iL~~L~dI 131 (337)
T PTZ00007 124 ILSYLSDI 131 (337)
T ss_pred HHHhhCce
Confidence 34444444
No 57
>KOG0296 consensus Angio-associated migratory cell protein (contains WD40 repeats) [Function unknown]
Probab=41.98 E-value=12 Score=40.60 Aligned_cols=6 Identities=33% Similarity=0.418 Sum_probs=2.2
Q ss_pred CccccC
Q 008811 263 PFEMMG 268 (552)
Q Consensus 263 p~~m~g 268 (552)
+....+
T Consensus 99 ~~eltg 104 (399)
T KOG0296|consen 99 AGELTG 104 (399)
T ss_pred eeEecC
Confidence 333333
No 58
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=41.25 E-value=9.8 Score=38.94 Aligned_cols=7 Identities=29% Similarity=0.349 Sum_probs=2.9
Q ss_pred HHHHcCC
Q 008811 63 KLEKLGK 69 (552)
Q Consensus 63 aI~KaGf 69 (552)
+|.++||
T Consensus 18 kLl~~GF 24 (232)
T PRK12766 18 ALREAGF 24 (232)
T ss_pred HHHHcCC
Confidence 3334444
No 59
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=40.12 E-value=84 Score=25.87 Aligned_cols=48 Identities=17% Similarity=0.243 Sum_probs=33.6
Q ss_pred HhcCCCeeEEEEecCC-cEEEEEecCCHHHHHHHHHHcCCceEEcCCCCC
Q 008811 31 LRKIDGVYSTNVDVEQ-GKVTVTGNVDPAILIKKLEKLGKHAELWGPQKG 79 (552)
Q Consensus 31 L~kIeGV~sV~Vdla~-~kVtV~g~idpeeII~aI~KaGf~Ael~~~~~~ 79 (552)
|..+++|..+...... -++.|....+..+|+..|...+. +.-.+..++
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~f~~~~P 74 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDEETANELLQELIEKGI-IRSFEEEEP 74 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHHhCCC-eeEEEEcCC
Confidence 8888999988865433 33444455678889999999888 665555444
No 60
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=39.17 E-value=32 Score=42.63 Aligned_cols=7 Identities=0% Similarity=0.074 Sum_probs=3.4
Q ss_pred Hhhcccc
Q 008811 93 FKNMMNF 99 (552)
Q Consensus 93 ~k~l~~~ 99 (552)
+..|+||
T Consensus 1772 ~sql~i~ 1778 (2131)
T KOG4369|consen 1772 ISQLLIN 1778 (2131)
T ss_pred hhhheee
Confidence 4455534
No 61
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=38.92 E-value=2.3e+02 Score=27.26 Aligned_cols=58 Identities=10% Similarity=0.165 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEec-------CCHHHHHHHHHHcCCceEEcCCCC
Q 008811 21 DGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGN-------VDPAILIKKLEKLGKHAELWGPQK 78 (552)
Q Consensus 21 ~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~-------idpeeII~aI~KaGf~Ael~~~~~ 78 (552)
......|++++-+-.+|..+.++..++.|+|+.. ..-..+.+.+.++|+..++.-...
T Consensus 52 e~A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 52 EEAIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred HHHHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 4445566776766679999999999999988722 234445666678999888865443
No 62
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=38.19 E-value=53 Score=32.61 Aligned_cols=28 Identities=29% Similarity=0.451 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEecCCcE
Q 008811 21 DGCKQKVKKVLRKIDGVYSTNVDVEQGK 48 (552)
Q Consensus 21 ~gCa~KIekaL~kIeGV~sV~Vdla~~k 48 (552)
.+|-+-+|..+.+|+||.+++|-++.+.
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~ 42 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGH 42 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCC
Confidence 6788888999999999999999888774
No 63
>KOG2548 consensus SWAP mRNA splicing regulator [RNA processing and modification]
Probab=37.68 E-value=22 Score=40.35 Aligned_cols=17 Identities=6% Similarity=0.196 Sum_probs=9.6
Q ss_pred CCHHHHHHHHHHcCCce
Q 008811 55 VDPAILIKKLEKLGKHA 71 (552)
Q Consensus 55 idpeeII~aI~KaGf~A 71 (552)
++...++..|..+++..
T Consensus 77 FDvRAhLdhi~~vd~t~ 93 (653)
T KOG2548|consen 77 FDVRAHLDHIPEVDSTS 93 (653)
T ss_pred hhhHhhhccCCccCCCc
Confidence 45555666666555543
No 64
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=37.03 E-value=13 Score=38.70 Aligned_cols=11 Identities=27% Similarity=0.347 Sum_probs=4.3
Q ss_pred EEEEecCCcEE
Q 008811 39 STNVDVEQGKV 49 (552)
Q Consensus 39 sV~Vdla~~kV 49 (552)
.++|-...+.+
T Consensus 50 YATVre~~g~~ 60 (303)
T KOG3064|consen 50 YATVREENGVL 60 (303)
T ss_pred ceeEeecCCEE
Confidence 33443344433
No 65
>COG3076 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.51 E-value=18 Score=33.35 Aligned_cols=8 Identities=38% Similarity=0.389 Sum_probs=4.9
Q ss_pred HcCCceEE
Q 008811 66 KLGKHAEL 73 (552)
Q Consensus 66 KaGf~Ael 73 (552)
|+||.+..
T Consensus 52 K~GyEV~e 59 (135)
T COG3076 52 KLGYEVTE 59 (135)
T ss_pred hhcceecc
Confidence 66776543
No 66
>PF09849 DUF2076: Uncharacterized protein conserved in bacteria (DUF2076); InterPro: IPR018648 This family of hypothetical prokaryotic proteins has no known function but includes putative perimplasmic ligand-binding sensor proteins.
Probab=36.38 E-value=35 Score=35.30 Aligned_cols=17 Identities=6% Similarity=0.053 Sum_probs=8.6
Q ss_pred cHHHHHHHHHHHhcCCC
Q 008811 20 CDGCKQKVKKVLRKIDG 36 (552)
Q Consensus 20 C~gCa~KIekaL~kIeG 36 (552)
.......|...|.+-+.
T Consensus 25 D~eAe~lI~~~~~~qP~ 41 (247)
T PF09849_consen 25 DPEAEALIAQALARQPD 41 (247)
T ss_pred CHHHHHHHHHHHHhCCc
Confidence 34445555555555543
No 67
>PTZ00482 membrane-attack complex/perforin (MACPF) Superfamily; Provisional
Probab=34.60 E-value=23 Score=42.43 Aligned_cols=12 Identities=33% Similarity=0.110 Sum_probs=4.8
Q ss_pred HhcCCCeeEEEE
Q 008811 31 LRKIDGVYSTNV 42 (552)
Q Consensus 31 L~kIeGV~sV~V 42 (552)
|-.++-|..+++
T Consensus 16 ~~~~~~~~~~~~ 27 (844)
T PTZ00482 16 LYEIPFVGSLRL 27 (844)
T ss_pred hhccccceeeee
Confidence 334444433333
No 68
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=33.98 E-value=1.1e+02 Score=29.30 Aligned_cols=27 Identities=37% Similarity=0.608 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEecCCc
Q 008811 21 DGCKQKVKKVLRKIDGVYSTNVDVEQG 47 (552)
Q Consensus 21 ~gCa~KIekaL~kIeGV~sV~Vdla~~ 47 (552)
.+|-+-++..+.+++||.+++|-++.+
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG 33 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGG 33 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESS
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCC
Confidence 578888999999999999999887766
No 69
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=33.74 E-value=46 Score=32.58 Aligned_cols=34 Identities=15% Similarity=0.368 Sum_probs=23.5
Q ss_pred EEEEEEecccHHH------HHHHHHHHhcCCCeeEEEEec
Q 008811 11 SCVLRVNVDCDGC------KQKVKKVLRKIDGVYSTNVDV 44 (552)
Q Consensus 11 kv~LkV~m~C~gC------a~KIekaL~kIeGV~sV~Vdl 44 (552)
++.|.+.+.++.| +..|+.+|..+++|.+|+|++
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 4556665444444 355888899999998888765
No 70
>PF06752 E_Pc_C: Enhancer of Polycomb C-terminus; InterPro: IPR009607 This entry represents the C terminus of eukaryotic enhancer of polycomb proteins, which have roles in heterochromatin formation []. This family contains several conserved motifs.
Probab=33.72 E-value=45 Score=34.14 Aligned_cols=16 Identities=44% Similarity=0.416 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHHHHHH
Q 008811 142 QLQQLQQLQAQQMMQQ 157 (552)
Q Consensus 142 q~qq~qq~q~qQ~qQ~ 157 (552)
|..++|.||+-|+||+
T Consensus 13 QL~~MQkQQLaqiqqq 28 (230)
T PF06752_consen 13 QLVLMQKQQLAQIQQQ 28 (230)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3333444333344333
No 71
>PRK11018 hypothetical protein; Provisional
Probab=33.52 E-value=1.3e+02 Score=25.24 Aligned_cols=55 Identities=9% Similarity=-0.093 Sum_probs=38.9
Q ss_pred EEEEEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE--ecCCHHHHHHHHHHcCCceEEcC
Q 008811 12 CVLRVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT--GNVDPAILIKKLEKLGKHAELWG 75 (552)
Q Consensus 12 v~LkV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~--g~idpeeII~aI~KaGf~Ael~~ 75 (552)
++|.+. ..|+.-.-+.+++|.++.--. .++|. ...+.+.|...+++.|+.+....
T Consensus 9 ~~lD~rG~~CP~Pvl~~kk~l~~l~~G~---------~L~V~~d~~~a~~di~~~~~~~G~~v~~~~ 66 (78)
T PRK11018 9 YRLDMVGEPCPYPAVATLEALPQLKKGE---------ILEVVSDCPQSINNIPLDARNHGYTVLDIQ 66 (78)
T ss_pred eeEECCCCcCCHHHHHHHHHHHhCCCCC---------EEEEEeCCccHHHHHHHHHHHcCCEEEEEE
Confidence 456666 699999999999999885322 22222 23466778888999999875443
No 72
>PF11491 DUF3213: Protein of unknown function (DUF3213) ; InterPro: IPR021583 The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold []. ; PDB: 2F40_A.
Probab=33.06 E-value=53 Score=28.86 Aligned_cols=52 Identities=15% Similarity=0.088 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE---ecCCHHHHHHHHHHcCCceE
Q 008811 21 DGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT---GNVDPAILIKKLEKLGKHAE 72 (552)
Q Consensus 21 ~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~---g~idpeeII~aI~KaGf~Ae 72 (552)
+-.+..+.=.|++.+.|++|-||--.....|. ..++.++|+++|++....++
T Consensus 10 ~eeA~~~QYeLsk~~~vyRvFiNgYar~g~VifDe~kl~~e~lL~~le~~kpEVi 64 (88)
T PF11491_consen 10 PEEAMVKQYELSKNEAVYRVFINGYARNGFVIFDESKLSKEELLEMLEEFKPEVI 64 (88)
T ss_dssp TTTTHHHHHTTTTTTTB------TTSS--EEE--B-S-SHHHH---HHHTTT-SS
T ss_pred HHHHHHHHHHhhcccceeeeeecccccceEEEECcccCCHHHHHHHHHhcChhhe
Confidence 34455667779999999999999777666665 45799999999999877643
No 73
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=32.51 E-value=32 Score=29.77 Aligned_cols=35 Identities=20% Similarity=0.416 Sum_probs=23.3
Q ss_pred EEEEEEec---ccHHH---HHHHHHHHhcCCCeeEEEEecC
Q 008811 11 SCVLRVNV---DCDGC---KQKVKKVLRKIDGVYSTNVDVE 45 (552)
Q Consensus 11 kv~LkV~m---~C~gC---a~KIekaL~kIeGV~sV~Vdla 45 (552)
++.+.|.+ +|..+ ...|+.+|..+++|.+++|++.
T Consensus 38 ~v~i~l~l~~p~~~~~~~l~~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 38 HVDIQMTLTAPNCPVAGSMPGEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred eEEEEEEECCCCCChHHHHHHHHHHHHHhCCCCceEEEEEE
Confidence 44455553 45444 3457888999999988888754
No 74
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=31.92 E-value=34 Score=32.19 Aligned_cols=6 Identities=0% Similarity=-0.501 Sum_probs=2.7
Q ss_pred ccHHHH
Q 008811 19 DCDGCK 24 (552)
Q Consensus 19 ~C~gCa 24 (552)
.|+.|.
T Consensus 28 vcP~cg 33 (129)
T TIGR02300 28 VSPYTG 33 (129)
T ss_pred cCCCcC
Confidence 444443
No 75
>PRK07334 threonine dehydratase; Provisional
Probab=31.88 E-value=1.5e+02 Score=32.14 Aligned_cols=64 Identities=17% Similarity=0.182 Sum_probs=39.0
Q ss_pred EEEEEe-cccHHHHHHHHHHHhcCC-CeeEEEEecC-----CcEEEEE------ecCCHHHHHHHHHHcCCceEEcC
Q 008811 12 CVLRVN-VDCDGCKQKVKKVLRKID-GVYSTNVDVE-----QGKVTVT------GNVDPAILIKKLEKLGKHAELWG 75 (552)
Q Consensus 12 v~LkV~-m~C~gCa~KIekaL~kIe-GV~sV~Vdla-----~~kVtV~------g~idpeeII~aI~KaGf~Ael~~ 75 (552)
++|.|. ..-..-...|-++|++.. .|.++++... ...++|. .....+.|++.|++.+|.+++++
T Consensus 327 v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~~~L~~vi~~Lr~~g~~~~~~~ 403 (403)
T PRK07334 327 ARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDAAHLQEVIAALRAAGFEARLVE 403 (403)
T ss_pred EEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCHHHHHHHHHHHHHcCCeeEeCC
Confidence 567776 456666777777776652 2455554322 2343332 12345578889999999988753
No 76
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=31.62 E-value=24 Score=36.82 Aligned_cols=10 Identities=0% Similarity=0.209 Sum_probs=4.4
Q ss_pred EEEecCCcEE
Q 008811 40 TNVDVEQGKV 49 (552)
Q Consensus 40 V~Vdla~~kV 49 (552)
.++-++++++
T Consensus 41 ~SCPLANSrY 50 (303)
T KOG3064|consen 41 SSCPLANSRY 50 (303)
T ss_pred ccCcCccccc
Confidence 3344444444
No 77
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=31.17 E-value=22 Score=40.60 Aligned_cols=12 Identities=17% Similarity=0.495 Sum_probs=5.4
Q ss_pred HHHHHHHHhcCC
Q 008811 24 KQKVKKVLRKID 35 (552)
Q Consensus 24 a~KIekaL~kIe 35 (552)
..-++++|..+.
T Consensus 57 ~ED~qrA~~e~~ 68 (678)
T KOG0127|consen 57 EEDVQRALAETE 68 (678)
T ss_pred HhHHHHHHHHhh
Confidence 344444444443
No 78
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=30.78 E-value=1.8e+02 Score=22.74 Aligned_cols=59 Identities=19% Similarity=0.164 Sum_probs=34.2
Q ss_pred EEEEec-ccHHHHHHHHHHHhcCCC-eeEEEEecC----CcEEEEEe--cCCHHHHHHHHHHcCCce
Q 008811 13 VLRVNV-DCDGCKQKVKKVLRKIDG-VYSTNVDVE----QGKVTVTG--NVDPAILIKKLEKLGKHA 71 (552)
Q Consensus 13 ~LkV~m-~C~gCa~KIekaL~kIeG-V~sV~Vdla----~~kVtV~g--~idpeeII~aI~KaGf~A 71 (552)
.|.|.+ .-++...+|.+.|.+..- |.++.+... ...+.|.- ..+.+++++.|+++||++
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~~~~~~~~~~i~v~~~~~~~~~~~~L~~~G~~v 69 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEIREGIGGILRISFKTQEDRERAKEILKEAGYEV 69 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEeecCCcEEEEEEECCHHHHHHHHHHHHHcCCcC
Confidence 355553 456677778887766532 334433221 22333332 236788999999999863
No 79
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=30.02 E-value=1e+02 Score=25.54 Aligned_cols=26 Identities=27% Similarity=0.500 Sum_probs=17.3
Q ss_pred cccHHHHHHHHHHHhcC----CCeeEEEEec
Q 008811 18 VDCDGCKQKVKKVLRKI----DGVYSTNVDV 44 (552)
Q Consensus 18 m~C~gCa~KIekaL~kI----eGV~sV~Vdl 44 (552)
-.|+.|. ++++.|.++ .+|....+|.
T Consensus 9 ~~C~~C~-~a~~~L~~l~~~~~~i~~~~idi 38 (85)
T PRK11200 9 PGCPYCV-RAKELAEKLSEERDDFDYRYVDI 38 (85)
T ss_pred CCChhHH-HHHHHHHhhcccccCCcEEEEEC
Confidence 5899998 666777775 4555444444
No 80
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=29.48 E-value=60 Score=30.91 Aligned_cols=57 Identities=21% Similarity=0.350 Sum_probs=30.7
Q ss_pred EEEEEEecccHHH------HHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcCC
Q 008811 11 SCVLRVNVDCDGC------KQKVKKVLRKIDGVYSTNVDVEQGKVTVTGNVDPAILIKKLEKLGK 69 (552)
Q Consensus 11 kv~LkV~m~C~gC------a~KIekaL~kIeGV~sV~Vdla~~kVtV~g~idpeeII~aI~KaGf 69 (552)
++++.|.++.+.| ...|+++|..+ ||..|+|++.-..+.-+.-+ .++-.++|+..|.
T Consensus 26 ~V~VtIt~Ty~gcpa~e~L~~~I~~aL~~~-Gv~~V~V~i~~~p~Wt~d~i-t~~gr~~l~~~gi 88 (146)
T TIGR02159 26 GVVVKFTPTYSGCPALEVIRQDIRDAVRAL-GVEVVEVSTSLDPPWTTDWI-TEDAREKLREYGI 88 (146)
T ss_pred EEEEEEEeCCCCCchHHHHHHHHHHHHHhc-CCCeEEEeEeeCCCCChHHC-CHHHHHHHHhcCc
Confidence 4556666544444 34577778876 88777775432222211112 2334667766664
No 81
>PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional
Probab=29.15 E-value=50 Score=38.29 Aligned_cols=27 Identities=19% Similarity=0.591 Sum_probs=19.2
Q ss_pred EEEe-cccHHH----------HHHHHHHHhcCCCeeEE
Q 008811 14 LRVN-VDCDGC----------KQKVKKVLRKIDGVYST 40 (552)
Q Consensus 14 LkV~-m~C~gC----------a~KIekaL~kIeGV~sV 40 (552)
.|.+ ++|++| ..+|+++...|+||...
T Consensus 514 sKTEyISCPsCGRTLfDLq~tta~Ik~~t~HLkGlkI~ 551 (611)
T PRK02048 514 SKTEYISCPGCGRTLYDLQSTIARIKEATSHLKGLKIG 551 (611)
T ss_pred ccceEEECCCCCcchhhHHHHHHHHHHHhCCCCCceEE
Confidence 3445 799999 45677778888887543
No 82
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=28.97 E-value=38 Score=39.51 Aligned_cols=12 Identities=17% Similarity=0.211 Sum_probs=5.0
Q ss_pred CCCCCCCCCCCC
Q 008811 182 KFNTIEDDFDDE 193 (552)
Q Consensus 182 k~~~~~~~~~dd 193 (552)
++.+..|+|+++
T Consensus 518 DYEVdSDeEWEE 529 (811)
T KOG4364|consen 518 DYEVDSDEEWEE 529 (811)
T ss_pred cccccCcccccc
Confidence 344444444433
No 83
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=28.63 E-value=1.1e+02 Score=32.24 Aligned_cols=30 Identities=27% Similarity=0.447 Sum_probs=25.8
Q ss_pred cHHHHHHHHHHHhcCCCeeEEEEecCCcEE
Q 008811 20 CDGCKQKVKKVLRKIDGVYSTNVDVEQGKV 49 (552)
Q Consensus 20 C~gCa~KIekaL~kIeGV~sV~Vdla~~kV 49 (552)
-.+|-+-+|..+.+++||.+++|-++.+.+
T Consensus 133 agGCFWg~E~~F~~~~GV~~t~vGYagG~~ 162 (283)
T PRK05550 133 AGGCFWGVEYYFKKLPGVLSVESGYTGGDT 162 (283)
T ss_pred ecCCchhhhhhHhhCcCEEEEEEeeCCCCC
Confidence 478888999999999999999998887743
No 84
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=28.07 E-value=2.3e+02 Score=22.34 Aligned_cols=22 Identities=32% Similarity=0.537 Sum_probs=14.6
Q ss_pred EEecccHHHHHHHHHHHhcCCCee
Q 008811 15 RVNVDCDGCKQKVKKVLRKIDGVY 38 (552)
Q Consensus 15 kV~m~C~gCa~KIekaL~kIeGV~ 38 (552)
...-.|+.|. ++++.|.++ +|.
T Consensus 5 y~~~~Cp~C~-~ak~~L~~~-~i~ 26 (75)
T cd03418 5 YTKPNCPYCV-RAKALLDKK-GVD 26 (75)
T ss_pred EeCCCChHHH-HHHHHHHHC-CCc
Confidence 3335899998 667777764 443
No 85
>TIGR00377 ant_ant_sig anti-anti-sigma factor. This superfamily includes small (105-125 residue) proteins related to SpoIIAA of Bacillus subtilis, an anti-anti-sigma factor. SpoIIAA can bind to and inhibit the anti-sigma F factor SpoIIAB. Also, it can be phosphorylated by SpoIIAB on a Ser residue at position 59 of the seed alignment. A similar arrangement is inferred for RsbV, an anti-anti-sigma factor for sigma B. This Ser is fairly well conserved within a motif resembling MXS[STA]G[VIL]X[VIL][VILF] among homologous known or predicted anti-anti-sigma factors. Regions similar to SpoIIAA and apparently homologous, but differing considerably near the phosphorlated Ser of SpoIIAA, appear in a single copy in several longer proteins.
Probab=27.63 E-value=3.7e+02 Score=22.68 Aligned_cols=66 Identities=15% Similarity=0.155 Sum_probs=36.5
Q ss_pred EEEEEEe--c---ccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE--ecCCHHHHHHHHHHcCCceEEcCCCC
Q 008811 11 SCVLRVN--V---DCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT--GNVDPAILIKKLEKLGKHAELWGPQK 78 (552)
Q Consensus 11 kv~LkV~--m---~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~--g~idpeeII~aI~KaGf~Ael~~~~~ 78 (552)
.++|++. + .+..+...+..++.. +.+..+.+|+..-. .|. +......+++.+++.+..+.++....
T Consensus 13 ~~vi~~~G~l~~~~~~~~~~~l~~~~~~-~~~~~vvidls~v~-~iDssgl~~L~~~~~~~~~~~~~~~l~~~~~ 85 (108)
T TIGR00377 13 VVIVRLSGELDAHTAPLLREKVTPAAER-TGPRPIVLDLEDLE-FMDSSGLGVLLGRYKQVRRVGGQLVLVSVSP 85 (108)
T ss_pred EEEEEEecccccccHHHHHHHHHHHHHh-cCCCeEEEECCCCe-EEccccHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence 3455665 3 566666666666554 46667778765422 222 22234444555666677766666433
No 86
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=27.02 E-value=1.5e+02 Score=23.43 Aligned_cols=31 Identities=19% Similarity=0.322 Sum_probs=21.6
Q ss_pred EEEEEecccHH-HHHHHHHHHhcCCCeeEEEE
Q 008811 12 CVLRVNVDCDG-CKQKVKKVLRKIDGVYSTNV 42 (552)
Q Consensus 12 v~LkV~m~C~g-Ca~KIekaL~kIeGV~sV~V 42 (552)
+.|.|+..-.. ....|-+.|+++++|.+|.+
T Consensus 43 i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 43 VTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 44444444443 67788888999999988875
No 87
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=26.81 E-value=1.5e+02 Score=23.74 Aligned_cols=51 Identities=20% Similarity=0.249 Sum_probs=34.5
Q ss_pred EEe-cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE--ecCCHHHHHHHHHHcCCceEEcC
Q 008811 15 RVN-VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT--GNVDPAILIKKLEKLGKHAELWG 75 (552)
Q Consensus 15 kV~-m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~--g~idpeeII~aI~KaGf~Ael~~ 75 (552)
.+. ..|+.-.-+++++| ++..- ..++|. ...+.+.|...+++.||.+++..
T Consensus 3 D~rG~~CP~P~l~~k~al-~~~~g---------~~l~v~~d~~~s~~~i~~~~~~~G~~~~~~~ 56 (67)
T cd03421 3 DARGLACPQPVIKTKKAL-ELEAG---------GEIEVLVDNEVAKENVSRFAESRGYEVSVEE 56 (67)
T ss_pred ccCCCCCCHHHHHHHHHH-hcCCC---------CEEEEEEcChhHHHHHHHHHHHcCCEEEEEe
Confidence 344 58999999999999 55321 223332 33456788889999999985544
No 88
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=26.24 E-value=2.4e+02 Score=22.53 Aligned_cols=57 Identities=23% Similarity=0.238 Sum_probs=32.9
Q ss_pred EEec-ccHHHHHHHHHHHhcCCCeeEEEEecC---CcEEEEE----ecCCHHHHHHHHHHcCCce
Q 008811 15 RVNV-DCDGCKQKVKKVLRKIDGVYSTNVDVE---QGKVTVT----GNVDPAILIKKLEKLGKHA 71 (552)
Q Consensus 15 kV~m-~C~gCa~KIekaL~kIeGV~sV~Vdla---~~kVtV~----g~idpeeII~aI~KaGf~A 71 (552)
+|.+ ..++--.++-++|..-.-|..+..+.. ...|+|. .....++|+++|++.||.+
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~~~nI~~~~~~~~~~~~~~v~v~ie~~~~~~~~~i~~~L~~~G~~~ 66 (68)
T cd04885 2 AVTFPERPGALKKFLELLGPPRNITEFHYRNQGGDEARVLVGIQVPDREDLAELKERLEALGYPY 66 (68)
T ss_pred EEECCCCCCHHHHHHHHhCCCCcEEEEEEEcCCCCceEEEEEEEeCCHHHHHHHHHHHHHcCCCc
Confidence 3443 566666677777765223444444431 2233332 2246677899999999975
No 89
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=26.18 E-value=31 Score=39.02 Aligned_cols=16 Identities=13% Similarity=0.324 Sum_probs=7.3
Q ss_pred ccHHHHHHHHHHHhcC
Q 008811 19 DCDGCKQKVKKVLRKI 34 (552)
Q Consensus 19 ~C~gCa~KIekaL~kI 34 (552)
.|-.-...|.+++...
T Consensus 36 ~~~~l~aAVVqLY~a~ 51 (569)
T KOG3671|consen 36 KCKTLAAAVVQLYKAY 51 (569)
T ss_pred chhhHHHHHHHHHhhc
Confidence 4444444455544443
No 90
>TIGR01617 arsC_related transcriptional regulator, Spx/MgsR family. This model represents a portion of the proteins within the larger set covered by Pfam model pfam03960. That larger family includes a glutaredoxin-dependent arsenate reductase (TIGR00014). Characterized members of this family include Spx and MgsR from Bacillus subtili. Spx is a global regulator for response to thiol-specific oxidative stress. It interacts with RNA polymerase. MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B.
Probab=25.91 E-value=1e+02 Score=27.49 Aligned_cols=44 Identities=20% Similarity=0.388 Sum_probs=27.4
Q ss_pred cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcCC
Q 008811 18 VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGNVDPAILIKKLEKLGK 69 (552)
Q Consensus 18 m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~idpeeII~aI~KaGf 69 (552)
-.|+.|.. +++.|.+. +|.-..+++.. ...+.++|.+.++.++.
T Consensus 7 ~~C~~c~k-a~~~L~~~-~i~~~~idi~~------~~~~~~el~~l~~~~~~ 50 (117)
T TIGR01617 7 PNCTTCKK-ARRWLEAN-GIEYQFIDIGE------DGPTREELLDILSLLED 50 (117)
T ss_pred CCCHHHHH-HHHHHHHc-CCceEEEecCC------ChhhHHHHHHHHHHcCC
Confidence 58999984 45666653 55444444432 23456778888887774
No 91
>PRK11670 antiporter inner membrane protein; Provisional
Probab=25.71 E-value=1.6e+02 Score=31.92 Aligned_cols=68 Identities=13% Similarity=0.181 Sum_probs=39.8
Q ss_pred EEEEEEec---ccHHH---HHHHHHHHhcCCCeeEEEEecCC------------------cEEEEE------ec-CCHHH
Q 008811 11 SCVLRVNV---DCDGC---KQKVKKVLRKIDGVYSTNVDVEQ------------------GKVTVT------GN-VDPAI 59 (552)
Q Consensus 11 kv~LkV~m---~C~gC---a~KIekaL~kIeGV~sV~Vdla~------------------~kVtV~------g~-idpee 59 (552)
++.|.|.+ .|+.- ...|+++|..+++|.+++|.+.. ..++|. +. +....
T Consensus 48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avN 127 (369)
T PRK11670 48 TLHIELVMPFVWNSAFEELKEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVN 127 (369)
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHH
Confidence 44555553 34332 45688999999998777654432 122233 11 23444
Q ss_pred HHHHHHHcCCceEEcCCCC
Q 008811 60 LIKKLEKLGKHAELWGPQK 78 (552)
Q Consensus 60 II~aI~KaGf~Ael~~~~~ 78 (552)
|..+|.+.|+++-++..+.
T Consensus 128 LA~aLA~~G~rVlLID~D~ 146 (369)
T PRK11670 128 LALALAAEGAKVGILDADI 146 (369)
T ss_pred HHHHHHHCCCcEEEEeCCC
Confidence 6667778888887765544
No 92
>KOG3555 consensus Ca2+-binding proteoglycan Testican [General function prediction only]
Probab=25.18 E-value=53 Score=35.77 Aligned_cols=14 Identities=29% Similarity=0.349 Sum_probs=10.9
Q ss_pred HHHHHHHHhhccccc
Q 008811 86 QNLLNNQFKNMMNFE 100 (552)
Q Consensus 86 ~~~l~~q~k~l~~~~ 100 (552)
.++|+.||+.|. -+
T Consensus 210 g~RL~dWF~~lh-e~ 223 (434)
T KOG3555|consen 210 GNRLRDWFKALH-ED 223 (434)
T ss_pred HHHHHHHHHHHH-hh
Confidence 446889999988 55
No 93
>cd02066 GRX_family Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including human GRX1 and GRX2, as well as E. coli GRX1 and GRX3, which
Probab=24.55 E-value=1.4e+02 Score=22.45 Aligned_cols=21 Identities=24% Similarity=0.585 Sum_probs=14.5
Q ss_pred EEEecccHHHHHHHHHHHhcCC
Q 008811 14 LRVNVDCDGCKQKVKKVLRKID 35 (552)
Q Consensus 14 LkV~m~C~gCa~KIekaL~kIe 35 (552)
+...-.|+.|. +++..|.++.
T Consensus 4 ly~~~~Cp~C~-~~~~~L~~~~ 24 (72)
T cd02066 4 VFSKSTCPYCK-RAKRLLESLG 24 (72)
T ss_pred EEECCCCHHHH-HHHHHHHHcC
Confidence 33345799998 6777777664
No 94
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=24.51 E-value=43 Score=36.74 Aligned_cols=57 Identities=14% Similarity=0.151 Sum_probs=30.3
Q ss_pred EEEEEEe-cc-----cHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE--ecCCHHHHHHHHHHc
Q 008811 11 SCVLRVN-VD-----CDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT--GNVDPAILIKKLEKL 67 (552)
Q Consensus 11 kv~LkV~-m~-----C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~--g~idpeeII~aI~Ka 67 (552)
+..|.|. .| --.|+.++...|..++-...-.|-.+..+++|. ..+..++++..|..+
T Consensus 50 t~mF~VYDGHGG~EVa~yca~kLPdflK~~k~yk~g~~~~aL~~AFl~fD~~l~~ee~~keLk~i 114 (542)
T KOG0699|consen 50 THMFGVYDGHGGTEVAKYCAAKLPDFLKERKFYKAGDVAEALQKAFLDFDDFLRAEESMKELKDI 114 (542)
T ss_pred ceEEEEecCCCcHHHHHHHHHhhhHHHHhHHhhhcccHHHHHHHHHhchhhhhcCHHHHHHHHHH
Confidence 4557776 44 346788887777776554433333333333332 334455555555544
No 95
>KOG4032 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.97 E-value=58 Score=32.36 Aligned_cols=14 Identities=21% Similarity=0.052 Sum_probs=8.6
Q ss_pred CCHHHHHHHHHHcC
Q 008811 55 VDPAILIKKLEKLG 68 (552)
Q Consensus 55 idpeeII~aI~KaG 68 (552)
+...+|.+.|..+.
T Consensus 61 V~~~eieE~L~~~l 74 (184)
T KOG4032|consen 61 VKAREIEELLLELL 74 (184)
T ss_pred hhHHHHHHHHHHHH
Confidence 55666666666554
No 96
>PRK10026 arsenate reductase; Provisional
Probab=23.84 E-value=1.7e+02 Score=27.76 Aligned_cols=51 Identities=16% Similarity=0.277 Sum_probs=29.7
Q ss_pred EEEEEEecccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcCC
Q 008811 11 SCVLRVNVDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGNVDPAILIKKLEKLGK 69 (552)
Q Consensus 11 kv~LkV~m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~idpeeII~aI~KaGf 69 (552)
.++|...-.|+.|...+ +.|... +|.-..+++.. ...+.++|...|++.+.
T Consensus 3 ~i~iY~~p~Cst~RKA~-~wL~~~-gi~~~~~d~~~------~ppt~~eL~~~l~~~g~ 53 (141)
T PRK10026 3 NITIYHNPACGTSRNTL-EMIRNS-GTEPTIIHYLE------TPPTRDELVKLIADMGI 53 (141)
T ss_pred EEEEEeCCCCHHHHHHH-HHHHHC-CCCcEEEeeeC------CCcCHHHHHHHHHhCCC
Confidence 34444456999998544 444433 44433333322 34577778888877775
No 97
>cd03036 ArsC_like Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX) function as protein disulfide oxidoreductases, altering the redox state of target proteins via the reversible oxidation of the active site dithiol. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via GRX, through a single catalytic cysteine.
Probab=23.83 E-value=1.7e+02 Score=25.89 Aligned_cols=44 Identities=34% Similarity=0.445 Sum_probs=25.0
Q ss_pred cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcCC
Q 008811 18 VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGNVDPAILIKKLEKLGK 69 (552)
Q Consensus 18 m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~idpeeII~aI~KaGf 69 (552)
-.|+.|.. +++.|.+. +|.-..+++... ..+.++|.+.+.+++.
T Consensus 7 ~~C~~c~k-a~~~L~~~-~i~~~~idi~~~------~~~~~el~~~~~~~~~ 50 (111)
T cd03036 7 PKCSTCRK-AKKWLDEH-GVDYTAIDIVEE------PPSKEELKKWLEKSGL 50 (111)
T ss_pred CCCHHHHH-HHHHHHHc-CCceEEecccCC------cccHHHHHHHHHHcCC
Confidence 58999984 45666653 554444444332 2345566666665553
No 98
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=22.54 E-value=55 Score=37.54 Aligned_cols=11 Identities=27% Similarity=0.365 Sum_probs=4.2
Q ss_pred HHHHHHHHcCC
Q 008811 59 ILIKKLEKLGK 69 (552)
Q Consensus 59 eII~aI~KaGf 69 (552)
+|...+...|+
T Consensus 133 dLk~vFs~~G~ 143 (678)
T KOG0127|consen 133 DLKNVFSNFGK 143 (678)
T ss_pred HHHHHHhhcce
Confidence 33333333343
No 99
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=22.31 E-value=7.1e+02 Score=23.98 Aligned_cols=61 Identities=16% Similarity=0.067 Sum_probs=37.1
Q ss_pred EEEEEEecccHHHHHHHHHHHhcCCCeeEEEEecCCcEE-----EEE---ecCCHHHHHHHHHHcCCceE
Q 008811 11 SCVLRVNVDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKV-----TVT---GNVDPAILIKKLEKLGKHAE 72 (552)
Q Consensus 11 kv~LkV~m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kV-----tV~---g~idpeeII~aI~KaGf~Ae 72 (552)
+++|.|.. .+.....|.+.|+++-.|.+|..-.....+ .|. ...+-.+|.+.++.....+.
T Consensus 44 riti~V~~-d~~~i~qi~kQl~Kli~V~~V~~~~~~~~v~rEl~LiKv~~~~~~r~~i~~i~~~f~a~iv 112 (157)
T TIGR00119 44 RMTIVVVG-DDKVLEQITKQLNKLVDVIKVSDLTESAIVERELCLVKVSAPGEGRDEIIRLTNIFRGRIV 112 (157)
T ss_pred EEEEEEEC-CHHHHHHHHHHHhcCccEEEEEecCCCcceeeEEEEEEEECCccCHHHHHHHHHHhCCEEE
Confidence 34555543 588889999999999999888763333222 222 12345566666665544433
No 100
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=22.12 E-value=4e+02 Score=31.20 Aligned_cols=59 Identities=14% Similarity=0.180 Sum_probs=42.5
Q ss_pred cHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEec-------CCHHHHHHHHHHcCCceEEcCCCC
Q 008811 20 CDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGN-------VDPAILIKKLEKLGKHAELWGPQK 78 (552)
Q Consensus 20 C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~-------idpeeII~aI~KaGf~Ael~~~~~ 78 (552)
-.....+|++++-+..+|..+.++..++.|.|+.. .....+.+.++++++..+++-...
T Consensus 68 ~~~~~~~i~~~~~~~~~~~~~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 68 PEEAIEKIKEIVPEEAGITDIYFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred HHHHHHHHHHhCCCcCCceeEEecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 34455677777777789999999999999988722 244455666778899888765443
No 101
>KOG2393 consensus Transcription initiation factor IIF, large subunit (RAP74) [Transcription]
Probab=22.10 E-value=60 Score=37.02 Aligned_cols=33 Identities=33% Similarity=0.452 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCC
Q 008811 189 DFDDEEFDDDFDEDDFDDYDDEDDEEFGHGHHLP 222 (552)
Q Consensus 189 ~~~dd~~ddd~dddddddddd~ddd~~dd~~~dp 222 (552)
+-||+.+++++|.|+++.+-|+|++ |-|+...|
T Consensus 278 d~Dd~a~eesdd~d~e~~E~DYdee-~addEE~P 310 (555)
T KOG2393|consen 278 DVDDEAFEESDDGDNEGRELDYDEE-SADDEEAP 310 (555)
T ss_pred CCcccccccCCCccccccccccccc-cCCccccc
No 102
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=22.08 E-value=53 Score=35.21 Aligned_cols=16 Identities=31% Similarity=0.376 Sum_probs=8.1
Q ss_pred cccHHH--HHHHHHHHhc
Q 008811 18 VDCDGC--KQKVKKVLRK 33 (552)
Q Consensus 18 m~C~gC--a~KIekaL~k 33 (552)
++|..+ ..+|+++|.+
T Consensus 191 l~c~~~dGIe~IK~aL~~ 208 (319)
T PTZ00248 191 VSCFDYEGIDAVKEALIA 208 (319)
T ss_pred EEeCCCchHHHHHHHHHH
Confidence 455443 4555555544
No 103
>TIGR02190 GlrX-dom Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain.
Probab=22.07 E-value=1.6e+02 Score=24.11 Aligned_cols=31 Identities=26% Similarity=0.378 Sum_probs=19.4
Q ss_pred EEEEEEecccHHHHHHHHHHHhcCCCeeEEEEe
Q 008811 11 SCVLRVNVDCDGCKQKVKKVLRKIDGVYSTNVD 43 (552)
Q Consensus 11 kv~LkV~m~C~gCa~KIekaL~kIeGV~sV~Vd 43 (552)
+++|...-.|+.|. ++++.|..+ +|.-..++
T Consensus 9 ~V~ly~~~~Cp~C~-~ak~~L~~~-gi~y~~id 39 (79)
T TIGR02190 9 SVVVFTKPGCPFCA-KAKATLKEK-GYDFEEIP 39 (79)
T ss_pred CEEEEECCCCHhHH-HHHHHHHHc-CCCcEEEE
Confidence 44444446899998 677777754 55443333
No 104
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=21.99 E-value=66 Score=30.51 Aligned_cols=48 Identities=19% Similarity=0.309 Sum_probs=27.6
Q ss_pred ccHHHHHHHHHHHhcCCCeeEEEEecCCcE-EEEEecCCHHHHHHHHHH
Q 008811 19 DCDGCKQKVKKVLRKIDGVYSTNVDVEQGK-VTVTGNVDPAILIKKLEK 66 (552)
Q Consensus 19 ~C~gCa~KIekaL~kIeGV~sV~Vdla~~k-VtV~g~idpeeII~aI~K 66 (552)
+|.+.-...+++|+.|+.+.-|+.+....+ ++-.+..+++.|+..|+.
T Consensus 92 ~~~as~~i~rkvlQ~Le~~~~ve~hp~gGR~lt~~GqrdldrIa~~i~~ 140 (143)
T KOG3411|consen 92 FCDASGGIARKVLQALEKMGIVEKHPKGGRRLTEQGQRDLDRIAGQIRE 140 (143)
T ss_pred hhccccHHHHHHHHHHHhCCceeeCCCCcceeCcccchhHHHHHHHHHh
Confidence 455444455555555555555566555433 333366778888777764
No 105
>PF10991 DUF2815: Protein of unknown function (DUF2815); InterPro: IPR022595 This entry is represented by Bacteriophage APSE-1, protein 50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.47 E-value=36 Score=33.58 Aligned_cols=8 Identities=25% Similarity=0.331 Sum_probs=3.5
Q ss_pred HHHHHHHH
Q 008811 58 AILIKKLE 65 (552)
Q Consensus 58 eeII~aI~ 65 (552)
+.|.++|+
T Consensus 45 ~~I~~Ai~ 52 (181)
T PF10991_consen 45 AAIKAAIE 52 (181)
T ss_pred HHHHHHHH
Confidence 34444443
No 106
>TIGR02886 spore_II_AA anti-sigma F factor antagonist. The anti-sigma F factor antagonist, also called stage II sporulation protein AA, is a protein universal among endospore-forming bacteria, all of which belong to the Firmcutes
Probab=21.23 E-value=4.5e+02 Score=22.32 Aligned_cols=67 Identities=9% Similarity=0.129 Sum_probs=37.1
Q ss_pred EEEEEEe--c---ccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE-ecCCHHHHHHHHHHcCCceEEcCCCC
Q 008811 11 SCVLRVN--V---DCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT-GNVDPAILIKKLEKLGKHAELWGPQK 78 (552)
Q Consensus 11 kv~LkV~--m---~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~-g~idpeeII~aI~KaGf~Ael~~~~~ 78 (552)
.++++|. + ++......+..++.. ..+..+.+|+..-...=+ +......++..+++.+..+.++....
T Consensus 9 ~~vi~l~G~L~f~~~~~~~~~l~~~~~~-~~~~~vilDls~v~~iDssgi~~L~~~~~~~~~~g~~l~l~~~~~ 81 (106)
T TIGR02886 9 VLIVRLSGELDHHTAERVRRKIDDAIER-RPIKHLILNLKNVTFMDSSGLGVILGRYKKIKNEGGEVIVCNVSP 81 (106)
T ss_pred EEEEEEecccchhhHHHHHHHHHHHHHh-CCCCEEEEECCCCcEecchHHHHHHHHHHHHHHcCCEEEEEeCCH
Confidence 4566776 2 444445555544432 346667777654322211 22344556667777888888777544
No 107
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=21.10 E-value=1.2e+02 Score=27.73 Aligned_cols=33 Identities=24% Similarity=0.566 Sum_probs=23.3
Q ss_pred EEEEEecccHHH------HHHHHHHHhcCCCeeEEEEec
Q 008811 12 CVLRVNVDCDGC------KQKVKKVLRKIDGVYSTNVDV 44 (552)
Q Consensus 12 v~LkV~m~C~gC------a~KIekaL~kIeGV~sV~Vdl 44 (552)
+.+++.++.+.| ...|+.+|..+++|..++|++
T Consensus 51 v~v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 51 VKVKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred EEEEEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEEE
Confidence 444444444444 677899999999998888764
No 108
>cd03032 ArsC_Spx Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex formation between RNAP and certain transcriptional activator proteins like ResD and ComA. In response to oxidative stress, Spx can also activate transcription, making it a general regulator that exerts both positive and negative control over transcription initiation. Spx has been shown to exert redox-sensitive transcriptional control over genes like trxA (TRX) and trxB (TRX reductase), genes that function in thiol homeostasis. This redox-sensitive activity is dependent on the presence of a CXXC motif, present in some members of the Spx subfamily, that acts as a thiol/disulfide switch. Spx has also been shown to repress genes in a sulfate-dependent manner independent of the presence of the CXXC motif.
Probab=21.04 E-value=1.7e+02 Score=25.96 Aligned_cols=42 Identities=14% Similarity=0.222 Sum_probs=25.1
Q ss_pred cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHc
Q 008811 18 VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGNVDPAILIKKLEKL 67 (552)
Q Consensus 18 m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~idpeeII~aI~Ka 67 (552)
-.|+.|.. +++.|... +|....+++.... .+.++|.+.++.+
T Consensus 8 ~~C~~c~k-a~~~L~~~-gi~~~~idi~~~~------~~~~el~~~~~~~ 49 (115)
T cd03032 8 PSCSSCRK-AKQWLEEH-QIPFEERNLFKQP------LTKEELKEILSLT 49 (115)
T ss_pred CCCHHHHH-HHHHHHHC-CCceEEEecCCCc------chHHHHHHHHHHh
Confidence 58999985 66666654 5655555543332 3455566666555
No 109
>PLN02925 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
Probab=20.93 E-value=92 Score=36.84 Aligned_cols=25 Identities=20% Similarity=0.595 Sum_probs=18.5
Q ss_pred EEEe-cccHHH----------HHHHHHHHhcCCCee
Q 008811 14 LRVN-VDCDGC----------KQKVKKVLRKIDGVY 38 (552)
Q Consensus 14 LkV~-m~C~gC----------a~KIekaL~kIeGV~ 38 (552)
++.+ +.|++| ..+|++....++||.
T Consensus 630 ~kte~isCPgCGRT~~dlq~~~~~I~~~~~hl~Gvk 665 (733)
T PLN02925 630 TKTEYVSCPSCGRTLFDLQEVSAEIREKTSHLPGVS 665 (733)
T ss_pred cCCeEEECCCCCCccccHHHHHHHHHHHhhcCCCce
Confidence 3444 699999 457777788888874
No 110
>PRK00694 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated
Probab=20.73 E-value=75 Score=36.74 Aligned_cols=26 Identities=19% Similarity=0.716 Sum_probs=18.2
Q ss_pred EEEe-cccHHH----------HHHHHHHHhcCCCeeE
Q 008811 14 LRVN-VDCDGC----------KQKVKKVLRKIDGVYS 39 (552)
Q Consensus 14 LkV~-m~C~gC----------a~KIekaL~kIeGV~s 39 (552)
.|.+ ++|++| ..+|++....|+++..
T Consensus 506 sKte~isCP~CgRtlfdlq~t~~~i~~~t~Hl~g~kI 542 (606)
T PRK00694 506 VKTEYISCPGCGRTLFDLLEVTQRIRERTQHLPGLKI 542 (606)
T ss_pred ccceEEECCCCCceeehHHHHHHHHHHHhccCCCceE
Confidence 3444 799999 5667777777777643
No 111
>cd04884 ACT_CBS C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This CD includes the C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This protein has two N-terminal tandem CBS domains and a single C-terminal ACT domain. The CBS domain is found in a wide range of proteins, often in tandem arrangements and together with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.69 E-value=3.2e+02 Score=21.73 Aligned_cols=60 Identities=20% Similarity=0.226 Sum_probs=35.6
Q ss_pred EEEe-cccHHHHHHHHHHHhcCCC-eeEEEEecC-----CcEEEEE--ecC--CHHHHHHHHHHcCCceEEc
Q 008811 14 LRVN-VDCDGCKQKVKKVLRKIDG-VYSTNVDVE-----QGKVTVT--GNV--DPAILIKKLEKLGKHAELW 74 (552)
Q Consensus 14 LkV~-m~C~gCa~KIekaL~kIeG-V~sV~Vdla-----~~kVtV~--g~i--dpeeII~aI~KaGf~Ael~ 74 (552)
|.|. -.+++--.+|-.+|.+... |.++.+... ...+.|. .+. ..++|+++|++. |++..|
T Consensus 2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~~~~~~~~~~~v~v~~e~~~~~~~i~~~L~~~-~~~~~~ 72 (72)
T cd04884 2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFEDAPDGMRRVFIRVTPMDRSKENELIEELKAK-FTVVYW 72 (72)
T ss_pred EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccccCCCCccEEEEEEEEecchHHHHHHHHHhCc-ccEEeC
Confidence 4455 3778888888888888754 444443332 1223333 211 235788888777 877654
No 112
>PRK01655 spxA transcriptional regulator Spx; Reviewed
Probab=20.69 E-value=1.4e+02 Score=27.48 Aligned_cols=46 Identities=17% Similarity=0.228 Sum_probs=26.1
Q ss_pred EEEecccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHc
Q 008811 14 LRVNVDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVTGNVDPAILIKKLEKL 67 (552)
Q Consensus 14 LkV~m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~g~idpeeII~aI~Ka 67 (552)
|...-.|+.|. ++++.|... +|....+++... ..+.++|.+.|+.+
T Consensus 4 iY~~~~C~~C~-ka~~~L~~~-gi~~~~idi~~~------~~~~~eL~~~l~~~ 49 (131)
T PRK01655 4 LFTSPSCTSCR-KAKAWLEEH-DIPFTERNIFSS------PLTIDEIKQILRMT 49 (131)
T ss_pred EEeCCCChHHH-HHHHHHHHc-CCCcEEeeccCC------hhhHHHHHHHHHHh
Confidence 33336899998 455666554 665555544332 23455566666655
No 113
>PF11111 CENP-M: Centromere protein M (CENP-M); InterPro: IPR020987 The prime candidate for specifying centromere identity is the array of nucleosomes assembles associated with CENP-A []. CENP-A recruits a nucleosome associated complex (CENP-A-NAC complex) comprised of CENP-M which this entry represents, along with two other proteins []. Assembly of the CENP-A NAC at centromeres is partly dependent on CENP-M. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival [].
Probab=20.56 E-value=4.1e+02 Score=26.41 Aligned_cols=56 Identities=21% Similarity=0.208 Sum_probs=36.8
Q ss_pred cEEEEEEecccHHHHHHHHHHHhcCCCeeEEEEecCCcEE-EEE--------ecCCHHHHHHHHHHcCCce
Q 008811 10 QSCVLRVNVDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKV-TVT--------GNVDPAILIKKLEKLGKHA 71 (552)
Q Consensus 10 qkv~LkV~m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kV-tV~--------g~idpeeII~aI~KaGf~A 71 (552)
.-++|-|++++..|-..||+.|..++ +++-.++| .|. -.+++.+|++...+....+
T Consensus 66 DlIVFvinl~sk~SL~~ve~SL~~vd------~~fflGKVCfl~t~a~~~~~~sv~~~~V~kla~~y~~pl 130 (176)
T PF11111_consen 66 DLIVFVINLHSKYSLQSVEASLSHVD------PSFFLGKVCFLATNAGRESHCSVHPNEVRKLAATYNSPL 130 (176)
T ss_pred EEEEEEEecCCcccHHHHHHHHhhCC------hhhhccceEEEEcCCCcccccccCHHHHHHHHHHhCCCE
Confidence 34667777899999999999999654 33444444 332 1256777776666655554
No 114
>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=20.41 E-value=4.4e+02 Score=22.79 Aligned_cols=58 Identities=17% Similarity=0.214 Sum_probs=39.8
Q ss_pred EEEEEEecccHHHHHHHHHHHhcCCC-eeEEEEecCCcEEEEEecCCHHHHHHHHHHcCC
Q 008811 11 SCVLRVNVDCDGCKQKVKKVLRKIDG-VYSTNVDVEQGKVTVTGNVDPAILIKKLEKLGK 69 (552)
Q Consensus 11 kv~LkV~m~C~gCa~KIekaL~kIeG-V~sV~Vdla~~kVtV~g~idpeeII~aI~KaGf 69 (552)
|+.=+|+..-..|+..++..|..... -..+.|+..+..|.|.+. ..++|.+-|.+.||
T Consensus 29 T~IrkI~GD~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~-~~~~Vk~wL~~~GF 87 (87)
T PF05046_consen 29 TVIRKIEGDIWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGD-HVEEVKKWLLEKGF 87 (87)
T ss_pred EEEEeecCCHHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCc-cHHHHHHHHHHCcC
Confidence 34445556667777788887766543 235677888888888876 36677777777665
No 115
>KOG1274 consensus WD40 repeat protein [General function prediction only]
Probab=20.22 E-value=72 Score=38.44 Aligned_cols=47 Identities=30% Similarity=0.283 Sum_probs=0.0
Q ss_pred cccccCCCCCCCCCCCCCCC-----------CCCCCCCCCCCCCC------------CCCccccCCCCCC
Q 008811 175 NKDQKHGKFNTIEDDFDDEE-----------FDDDFDEDDFDDYD------------DEDDEEFGHGHHL 221 (552)
Q Consensus 175 ~~~~k~~k~~~~~~~~~dd~-----------~ddd~ddddddddd------------d~ddd~~dd~~~d 221 (552)
.+...+.++.+.+.+.+|++ ++|+-|+++|||++ ++|+++++|+..+
T Consensus 319 ~k~~~~~l~~Dd~~~~~d~~~~~~~~~s~~~~~~~~d~a~~Ed~~t~~~~lrk~~~~~eD~~d~~e~~~~ 388 (933)
T KOG1274|consen 319 EKKRNSGLDVDDEVDLEDDEGNDDINKSEKLDSDINDEANEEDEFTSHDGLRKRKYNFEDEEDFDEDDNG 388 (933)
T ss_pred ccCCCcCcccchhhcccccccccccccchhhccccccccccccccccccchhhhcccccCccchhhhccc
No 116
>PRK14440 acylphosphatase; Provisional
Probab=20.13 E-value=4.2e+02 Score=23.02 Aligned_cols=57 Identities=19% Similarity=0.290 Sum_probs=36.1
Q ss_pred cEEEEEEe--cccHHHHHHHHHHHhcCCCeeEEEEecCCcEEEEE--e-cCCHHHHHHHHHHc
Q 008811 10 QSCVLRVN--VDCDGCKQKVKKVLRKIDGVYSTNVDVEQGKVTVT--G-NVDPAILIKKLEKL 67 (552)
Q Consensus 10 qkv~LkV~--m~C~gCa~KIekaL~kIeGV~sV~Vdla~~kVtV~--g-~idpeeII~aI~Ka 67 (552)
.+++|.|. ..+......+.+...++ ++.-..-|+...+|+|. + ....+++++.|++.
T Consensus 3 ~~~~~~v~G~VQGVGFR~~v~~~A~~~-gl~G~V~N~~dG~Vei~~~G~~~~v~~f~~~l~~g 64 (90)
T PRK14440 3 KRMYARVYGLVQGVGFRKFVQIHAIRL-GIKGYAKNLPDGSVEVVAEGYEEALSKLLERIKQG 64 (90)
T ss_pred EEEEEEEEEeEeccCchHHHHHHHHHc-CCEEEEEECCCCCEEEEEEcCHHHHHHHHHHHhhC
Confidence 45677777 46667777776666655 35455567777777765 3 23456677777753
No 117
>cd03029 GRX_hybridPRX5 Glutaredoxin (GRX) family, PRX5 hybrid subfamily; composed of hybrid proteins containing peroxiredoxin (PRX) and GRX domains, which is found in some pathogenic bacteria and cyanobacteria. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins. PRX-GRX hybrid proteins from Haemophilus influenza and Neisseria meningitis exhibit GSH-dependent peroxidase activity. The flow of reducing equivalents in the catalytic cycle of the hybrid protein goes from NADPH - GSH reductase - GSH - GRX domain of hybrid - PRX domain of hybrid - peroxide substrate.
Probab=20.12 E-value=1.9e+02 Score=22.98 Aligned_cols=29 Identities=21% Similarity=0.395 Sum_probs=17.5
Q ss_pred EEEEecccHHHHHHHHHHHhcCCCeeEEEEe
Q 008811 13 VLRVNVDCDGCKQKVKKVLRKIDGVYSTNVD 43 (552)
Q Consensus 13 ~LkV~m~C~gCa~KIekaL~kIeGV~sV~Vd 43 (552)
+|...-.|+.|. +++++|..+ +|.-..++
T Consensus 4 ~lys~~~Cp~C~-~ak~~L~~~-~i~~~~~~ 32 (72)
T cd03029 4 SLFTKPGCPFCA-RAKAALQEN-GISYEEIP 32 (72)
T ss_pred EEEECCCCHHHH-HHHHHHHHc-CCCcEEEE
Confidence 333335899998 567777764 45433333
Done!