Query 027552
Match_columns 222
No_of_seqs 132 out of 165
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 11:37:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027552.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027552hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11523 DUF3223: Protein of u 100.0 2E-32 4.3E-37 204.4 4.2 74 95-169 1-76 (76)
2 KOG3973 Uncharacterized conser 96.4 0.0033 7.2E-08 59.9 3.8 24 194-218 436-459 (465)
3 KOG3973 Uncharacterized conser 95.2 0.018 3.9E-07 55.1 3.6 16 198-213 435-450 (465)
4 KOG0921 Dosage compensation co 89.9 0.34 7.4E-06 51.5 4.0 6 116-121 1129-1134(1282)
5 PRK10590 ATP-dependent RNA hel 89.0 0.56 1.2E-05 44.4 4.5 15 107-121 278-292 (456)
6 COG4907 Predicted membrane pro 88.7 0.39 8.5E-06 47.6 3.2 15 165-179 553-567 (595)
7 KOG0105 Alternative splicing f 88.0 0.5 1.1E-05 42.2 3.2 24 198-221 89-112 (241)
8 KOG0116 RasGAP SH3 binding pro 86.1 0.95 2.1E-05 43.9 4.2 20 138-158 320-340 (419)
9 KOG0116 RasGAP SH3 binding pro 85.0 0.96 2.1E-05 43.9 3.7 8 138-145 291-298 (419)
10 PF12764 Gly-rich_Ago1: Glycin 82.2 1.7 3.8E-05 34.9 3.5 22 191-212 9-30 (104)
11 TIGR01659 sex-lethal sex-letha 80.7 14 0.0003 34.7 9.4 16 82-97 153-168 (346)
12 PRK10590 ATP-dependent RNA hel 80.5 2.2 4.8E-05 40.4 4.2 13 161-173 352-364 (456)
13 PLN03134 glycine-rich RNA-bind 79.4 22 0.00047 29.1 9.2 34 112-154 47-81 (144)
14 COG1512 Beta-propeller domains 76.1 3.5 7.6E-05 37.9 4.0 13 89-101 127-139 (271)
15 KOG3172 Small nuclear ribonucl 74.5 7.2 0.00016 31.9 4.9 38 126-164 34-71 (119)
16 PF15320 RAM: mRNA cap methyla 73.8 8.3 0.00018 29.6 4.9 21 159-179 12-32 (81)
17 COG4679 Phage-related protein 64.6 28 0.0006 28.6 6.4 57 112-173 30-91 (116)
18 PF12300 DUF3628: Protein of u 63.1 8 0.00017 33.6 3.2 8 186-193 55-62 (180)
19 PHA02131 hypothetical protein 58.5 7.8 0.00017 28.6 2.0 43 123-167 4-47 (70)
20 KOG0105 Alternative splicing f 50.6 50 0.0011 29.8 6.1 32 115-157 22-54 (241)
21 PF08897 DUF1841: Domain of un 48.0 31 0.00068 29.0 4.2 57 86-144 1-57 (137)
22 TIGR01659 sex-lethal sex-letha 47.0 26 0.00056 32.9 4.0 7 115-121 209-215 (346)
23 PTZ00034 40S ribosomal protein 46.9 35 0.00076 28.3 4.3 37 146-185 60-98 (124)
24 KOG2945 Predicted RNA-binding 46.5 17 0.00037 35.0 2.7 10 170-179 307-316 (365)
25 PLN03134 glycine-rich RNA-bind 43.3 25 0.00055 28.7 3.0 24 74-97 33-57 (144)
26 COG3860 Uncharacterized protei 41.7 18 0.00039 28.4 1.7 39 93-134 32-74 (89)
27 PF09349 OHCU_decarbox: OHCU d 37.2 57 0.0012 27.2 4.2 40 82-131 30-69 (159)
28 PF03859 CG-1: CG-1 domain; I 36.9 29 0.00064 28.5 2.4 27 130-157 74-105 (118)
29 PRK04537 ATP-dependent RNA hel 34.0 63 0.0014 32.1 4.6 15 108-122 291-305 (572)
30 KOG3172 Small nuclear ribonucl 33.5 41 0.00088 27.6 2.7 12 149-160 44-55 (119)
31 PF02084 Bindin: Bindin; Inte 32.0 46 0.001 30.4 3.0 43 89-132 103-148 (238)
32 PF07624 PSD2: Protein of unkn 30.6 71 0.0015 23.4 3.4 33 89-121 21-53 (76)
33 PHA02102 hypothetical protein 29.4 23 0.00049 26.7 0.5 30 130-160 29-66 (72)
34 KOG2945 Predicted RNA-binding 29.2 46 0.001 32.1 2.7 6 178-183 308-313 (365)
35 cd04880 ACT_AAAH-PDT-like ACT 29.1 2E+02 0.0044 20.0 5.5 44 131-174 23-66 (75)
36 PF01991 vATP-synt_E: ATP synt 28.0 1.1E+02 0.0024 25.1 4.5 66 109-174 120-187 (198)
37 PRK13798 putative OHCU decarbo 27.8 72 0.0016 27.1 3.4 41 81-131 38-78 (166)
38 PF05742 NRDE: NRDE protein; 25.7 2.2E+02 0.0047 25.6 6.2 72 83-158 162-247 (273)
39 KOG2716 Polymerase delta-inter 25.6 84 0.0018 28.4 3.5 15 94-108 56-70 (230)
40 TIGR02464 ribofla_fusion conse 24.8 58 0.0013 27.0 2.3 52 76-137 19-70 (153)
41 KOG0556 Aspartyl-tRNA syntheta 24.7 1.1E+02 0.0024 30.6 4.4 66 87-160 42-111 (533)
42 TIGR03180 UraD_2 OHCU decarbox 24.7 94 0.002 26.2 3.5 41 81-131 28-68 (158)
43 PF08719 DUF1768: Domain of un 24.4 36 0.00078 28.0 0.9 54 76-139 19-72 (157)
44 PF06356 DUF1064: Protein of u 23.0 88 0.0019 25.4 2.9 28 73-100 4-31 (118)
45 cd04905 ACT_CM-PDT C-terminal 22.3 2.2E+02 0.0048 20.2 4.7 44 131-174 25-68 (80)
46 KOG0339 ATP-dependent RNA heli 22.2 72 0.0016 32.9 2.7 18 84-101 473-490 (731)
47 PF02671 PAH: Paired amphipath 21.7 63 0.0014 21.3 1.5 35 91-127 3-38 (47)
48 PHA00370 III attachment protei 20.8 1.2E+02 0.0027 28.3 3.7 8 153-160 62-69 (297)
49 TIGR01648 hnRNP-R-Q heterogene 20.7 1E+02 0.0022 31.3 3.5 6 116-121 250-255 (578)
50 PF08818 DUF1801: Domain of un 20.0 1.2E+02 0.0027 22.3 3.0 43 113-157 6-48 (103)
No 1
>PF11523 DUF3223: Protein of unknown function (DUF3223); InterPro: IPR021602 This family of proteins has no known function. ; PDB: 2K0M_A.
Probab=99.97 E-value=2e-32 Score=204.44 Aligned_cols=74 Identities=47% Similarity=0.910 Sum_probs=61.3
Q ss_pred HHHhhhcCCCCCCcChhh-HHHHHHHHhhCCCCcccccCCCceeEEeeeCCCCC-cceeEEEecCCCcccccHHHHh
Q 027552 95 FYKFLHFWPPNLNVNKYE-HMVLLDLLKKGHPEPDKKIGGGIQAFQVRYHPTYK-SRCFFLIREDETADDFSFRKCV 169 (222)
Q Consensus 95 Fr~IL~~y~~g~~L~e~D-~~vL~eLL~~yHPd~e~KIG~GI~~i~V~~hp~~~-sRCFfVvR~DGt~eDFSY~KCi 169 (222)
|+.|||+|++++.|+++| +.+|+.|| .|||+++.|||+||++|+|++||.|. ||||||||+|||.+||||+|||
T Consensus 1 ~k~iL~~y~~g~~l~~~d~~~~l~~ll-~~HP~~~~KiG~Gi~~i~V~~hp~~~~srCF~vvR~DGs~~DFSy~KCi 76 (76)
T PF11523_consen 1 FKRILHRYPDGERLSEEDEKSVLEALL-KYHPEAEEKIGCGIDHIMVRKHPEFKDSRCFFVVRTDGSEEDFSYRKCI 76 (76)
T ss_dssp HHHHHHHS-TTEE--HHH-HHHHHHHH-HTSTTHHHHHTT-EEEEEEEESSSS---EEEEEEETTS-EEE--GGGSS
T ss_pred ChhHHhhCCCcCCcCHHHHHHHHHHHH-HhCCcHHHhhcCCeeeEEEeecCCCCcceEEEEEEeCCCeeeeEhhhhC
Confidence 789999999999999998 67777777 59999999999999999999999997 9999999999999999999997
No 2
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=96.37 E-value=0.0033 Score=59.91 Aligned_cols=24 Identities=63% Similarity=1.282 Sum_probs=12.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCC
Q 027552 194 GGKGRGGGRGGHGHGKGGHGRGRGG 218 (222)
Q Consensus 194 g~~~~~~~~~~~~~~~~~~~~~~~~ 218 (222)
||+.++|||+|+|||+| +|+|||+
T Consensus 436 gggr~gggr~gggrgrg-ggggrg~ 459 (465)
T KOG3973|consen 436 GGGRDGGGRDGGGRGRG-GGGGRGG 459 (465)
T ss_pred CCCCCCCCCCCCCCCCC-CCCCCcc
Confidence 33334466666666554 3355544
No 3
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=95.22 E-value=0.018 Score=55.05 Aligned_cols=16 Identities=56% Similarity=1.168 Sum_probs=8.0
Q ss_pred CCCCCCCCCCCCCCCC
Q 027552 198 RGGGRGGHGHGKGGHG 213 (222)
Q Consensus 198 ~~~~~~~~~~~~~~~~ 213 (222)
.+|||+|+||++||||
T Consensus 435 ~gggr~gggr~gggrg 450 (465)
T KOG3973|consen 435 DGGGRDGGGRDGGGRG 450 (465)
T ss_pred CCCCCCCCCCCCCCCC
Confidence 4455555555554444
No 4
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=89.91 E-value=0.34 Score=51.48 Aligned_cols=6 Identities=33% Similarity=1.027 Sum_probs=2.6
Q ss_pred HHHHHh
Q 027552 116 LLDLLK 121 (222)
Q Consensus 116 L~eLL~ 121 (222)
|+.++.
T Consensus 1129 llnmiR 1134 (1282)
T KOG0921|consen 1129 LLNMIR 1134 (1282)
T ss_pred HHHHHH
Confidence 444443
No 5
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=89.03 E-value=0.56 Score=44.43 Aligned_cols=15 Identities=20% Similarity=0.051 Sum_probs=8.4
Q ss_pred CcChhhHHHHHHHHh
Q 027552 107 NVNKYEHMVLLDLLK 121 (222)
Q Consensus 107 ~L~e~D~~vL~eLL~ 121 (222)
.++..+...+++.|.
T Consensus 278 ~~~~~~R~~~l~~F~ 292 (456)
T PRK10590 278 NKSQGARTRALADFK 292 (456)
T ss_pred CCCHHHHHHHHHHHH
Confidence 345555555666664
No 6
>COG4907 Predicted membrane protein [Function unknown]
Probab=88.66 E-value=0.39 Score=47.64 Aligned_cols=15 Identities=0% Similarity=0.184 Sum_probs=6.6
Q ss_pred HHHHhhhcCCCchhh
Q 027552 165 FRKCVDHMLPLPEDM 179 (222)
Q Consensus 165 Y~KCi~~~~p~~~~~ 179 (222)
|.....++-+.++++
T Consensus 553 ysr~~~~~~raysa~ 567 (595)
T COG4907 553 YSRSFNNLNRAYSAI 567 (595)
T ss_pred hhhhhcccchhhhcc
Confidence 444444444444443
No 7
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=88.03 E-value=0.5 Score=42.24 Aligned_cols=24 Identities=50% Similarity=0.828 Sum_probs=14.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCC
Q 027552 198 RGGGRGGHGHGKGGHGRGRGGKSR 221 (222)
Q Consensus 198 ~~~~~~~~~~~~~~~~~~~~~~~~ 221 (222)
++|+++|+|+|++|+|+.||+.+|
T Consensus 89 ~~G~y~gggrgGgg~gg~rgppsr 112 (241)
T KOG0105|consen 89 RRGSYSGGGRGGGGGGGRRGPPSR 112 (241)
T ss_pred cccccCCCCCCCCCCCcccCCccc
Confidence 344455555666666666776665
No 8
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=86.08 E-value=0.95 Score=43.91 Aligned_cols=20 Identities=40% Similarity=0.610 Sum_probs=9.5
Q ss_pred EEeeeCCCCCcceeEEE-ecCC
Q 027552 138 FQVRYHPTYKSRCFFLI-REDE 158 (222)
Q Consensus 138 i~V~~hp~~~sRCFfVv-R~DG 158 (222)
|+|+. |.-...||-.| ..|.
T Consensus 320 I~vr~-~~~~~~~fgFV~f~~~ 340 (419)
T KOG0116|consen 320 IQVRS-PGGKNPCFGFVEFENA 340 (419)
T ss_pred eEEec-cCCCcCceEEEEEeec
Confidence 44444 33333388544 4443
No 9
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=85.03 E-value=0.96 Score=43.89 Aligned_cols=8 Identities=25% Similarity=0.372 Sum_probs=5.0
Q ss_pred EEeeeCCC
Q 027552 138 FQVRYHPT 145 (222)
Q Consensus 138 i~V~~hp~ 145 (222)
|.|..=|.
T Consensus 291 i~V~nlP~ 298 (419)
T KOG0116|consen 291 IFVKNLPP 298 (419)
T ss_pred eEeecCCC
Confidence 77776554
No 10
>PF12764 Gly-rich_Ago1: Glycine-rich region of argonaut; InterPro: IPR024357 This domain is found in the N terminus of some argonaut proteins. Argonaut (AGO) proteins are involved in RNA-mediated post-transcriptional gene silencing [].
Probab=82.22 E-value=1.7 Score=34.92 Aligned_cols=22 Identities=50% Similarity=0.955 Sum_probs=10.4
Q ss_pred CCCCCCCCCCCCCCCCCCCCCC
Q 027552 191 GGGGGKGRGGGRGGHGHGKGGH 212 (222)
Q Consensus 191 ~~~g~~~~~~~~~~~~~~~~~~ 212 (222)
||+|+..-.|||++.|+|++|+
T Consensus 9 rGRGgp~~qgG~~~yGggrgg~ 30 (104)
T PF12764_consen 9 RGRGGPPQQGGRPGYGGGRGGG 30 (104)
T ss_pred cCCCCCcccCCCCCCCCCCCCC
Confidence 3444444445555554444433
No 11
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=80.70 E-value=14 Score=34.73 Aligned_cols=16 Identities=19% Similarity=0.175 Sum_probs=11.6
Q ss_pred CcccCCHHHHHHHHHH
Q 027552 82 PKEFGSSIEMFDYFYK 97 (222)
Q Consensus 82 ~k~F~S~~ea~~yFr~ 97 (222)
-.+|.+..+|...+..
T Consensus 153 FVeF~~~e~A~~Ai~~ 168 (346)
T TIGR01659 153 FVDFGSEADSQRAIKN 168 (346)
T ss_pred EEEEccHHHHHHHHHH
Confidence 3568888888877754
No 12
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=80.55 E-value=2.2 Score=40.43 Aligned_cols=13 Identities=15% Similarity=0.511 Sum_probs=7.1
Q ss_pred ccccHHHHhhhcC
Q 027552 161 DDFSFRKCVDHML 173 (222)
Q Consensus 161 eDFSY~KCi~~~~ 173 (222)
.|..+.+.|..++
T Consensus 352 ~d~~~~~~ie~~l 364 (456)
T PRK10590 352 DEHKLLRDIEKLL 364 (456)
T ss_pred HHHHHHHHHHHHh
Confidence 3555556666553
No 13
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=79.43 E-value=22 Score=29.09 Aligned_cols=34 Identities=21% Similarity=0.286 Sum_probs=19.8
Q ss_pred hHHHHHHHHhhCCCCcccccCCCceeEEeeeCCCC-CcceeEEE
Q 027552 112 EHMVLLDLLKKGHPEPDKKIGGGIQAFQVRYHPTY-KSRCFFLI 154 (222)
Q Consensus 112 D~~vL~eLL~~yHPd~e~KIG~GI~~i~V~~hp~~-~sRCFfVv 154 (222)
....|.+++. +.| -|..|.|-..+.- .+++|-+|
T Consensus 47 te~~L~~~F~--------~~G-~I~~v~i~~d~~tg~~kGfaFV 81 (144)
T PLN03134 47 DDASLRDAFA--------HFG-DVVDAKVIVDRETGRSRGFGFV 81 (144)
T ss_pred CHHHHHHHHh--------cCC-CeEEEEEEecCCCCCcceEEEE
Confidence 3455888886 234 4788777665433 35655443
No 14
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=76.14 E-value=3.5 Score=37.90 Aligned_cols=13 Identities=0% Similarity=-0.243 Sum_probs=5.5
Q ss_pred HHHHHHHHHhhhc
Q 027552 89 IEMFDYFYKFLHF 101 (222)
Q Consensus 89 ~ea~~yFr~IL~~ 101 (222)
..+...+++.|.-
T Consensus 127 ~~a~~iIr~~i~P 139 (271)
T COG1512 127 AQAGRIIRETIAP 139 (271)
T ss_pred HHHHHHHHhhhCc
Confidence 3344444444433
No 15
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=74.52 E-value=7.2 Score=31.88 Aligned_cols=38 Identities=8% Similarity=0.038 Sum_probs=20.2
Q ss_pred CcccccCCCceeEEeeeCCCCCcceeEEEecCCCccccc
Q 027552 126 EPDKKIGGGIQAFQVRYHPTYKSRCFFLIREDETADDFS 164 (222)
Q Consensus 126 d~e~KIG~GI~~i~V~~hp~~~sRCFfVvR~DGt~eDFS 164 (222)
++++-+-|-++.|.|-.. +-...-.--|..-||..-|-
T Consensus 34 EaeDnmNcql~di~vT~~-dg~vs~le~V~IRGS~IRFl 71 (119)
T KOG3172|consen 34 EAEDNMNCQLRDITVTAR-DGRVSQLEQVFIRGSKIRFL 71 (119)
T ss_pred EeccccccEEEEEEEEcc-CCcceeeeeEEEecCeEEEE
Confidence 455667788888888763 22211122222336665553
No 16
>PF15320 RAM: mRNA cap methylation, RNMT-activating mini protein
Probab=73.78 E-value=8.3 Score=29.61 Aligned_cols=21 Identities=24% Similarity=0.369 Sum_probs=15.0
Q ss_pred CcccccHHHHhhhcCCCchhh
Q 027552 159 TADDFSFRKCVDHMLPLPEDM 179 (222)
Q Consensus 159 t~eDFSY~KCi~~~~p~~~~~ 179 (222)
|..|..|-+-++.-++.|.=+
T Consensus 12 Te~D~ey~~~~~~~~~~PPIV 32 (81)
T PF15320_consen 12 TEDDEEYMEYCKRPFPPPPIV 32 (81)
T ss_pred cccCHHHHHHHhCCCCCCCEe
Confidence 678999999888666544433
No 17
>COG4679 Phage-related protein [Function unknown]
Probab=64.63 E-value=28 Score=28.63 Aligned_cols=57 Identities=26% Similarity=0.471 Sum_probs=40.5
Q ss_pred hHHHHHHHHhhC-CCCcc---cccCCCceeEEeeeC-CCCCcceeEEEecCCCcccccHHHHhhhcC
Q 027552 112 EHMVLLDLLKKG-HPEPD---KKIGGGIQAFQVRYH-PTYKSRCFFLIREDETADDFSFRKCVDHML 173 (222)
Q Consensus 112 D~~vL~eLL~~y-HPd~e---~KIG~GI~~i~V~~h-p~~~sRCFfVvR~DGt~eDFSY~KCi~~~~ 173 (222)
+...-++++..+ ||... ..||.||.+|.|+.. |.| |-||++.-|+.. =..+|+.--.
T Consensus 30 ~~~~aL~~iq~~~~~~~~~~~~~~G~gv~El~i~~~~g~~--R~~y~~~~~~~v---yvLH~FqKKT 91 (116)
T COG4679 30 EFGYALDKIQAGGEPLDWKPVSTIGPGVKELRIRDARGIY--RVFYVAKFDEAV---YVLHCFQKKT 91 (116)
T ss_pred HHHHHHHHHHhcCCccccCCccccCCCeeEEEeeccCCce--EEEEEEEecceE---EeehhhHHhc
Confidence 677777888654 44433 789999999997764 444 999999999874 3456665433
No 18
>PF12300 DUF3628: Protein of unknown function (DUF3628); InterPro: IPR022077 Proteins in this entry are DEAD Box RhlB RNA Helicases found in Xanthomonadaceae bacteria.; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=63.13 E-value=8 Score=33.62 Aligned_cols=8 Identities=25% Similarity=0.489 Sum_probs=3.9
Q ss_pred ccCCCCCC
Q 027552 186 NKALGGGG 193 (222)
Q Consensus 186 ~~~gg~~~ 193 (222)
.++||+++
T Consensus 55 RRGggRsg 62 (180)
T PF12300_consen 55 RRGGGRSG 62 (180)
T ss_pred hhcCCCCC
Confidence 44555543
No 19
>PHA02131 hypothetical protein
Probab=58.52 E-value=7.8 Score=28.62 Aligned_cols=43 Identities=23% Similarity=0.481 Sum_probs=32.9
Q ss_pred CCCCcccccCCCce-eEEeeeCCCCCcceeEEEecCCCcccccHHH
Q 027552 123 GHPEPDKKIGGGIQ-AFQVRYHPTYKSRCFFLIREDETADDFSFRK 167 (222)
Q Consensus 123 yHPd~e~KIG~GI~-~i~V~~hp~~~sRCFfVvR~DGt~eDFSY~K 167 (222)
|||.--.|+- ||. .=+++-|-.|+-.|| |...||.+.|..|..
T Consensus 4 yhpqhiakvn-gitkvdmirgh~~~g~~c~-imfk~~~v~dctfk~ 47 (70)
T PHA02131 4 YHPQHIAKVN-GITKVDMIRGHYRFGISCW-IMFKNDQVIDCTFKN 47 (70)
T ss_pred cchhHhhhhc-CceEEEEeccceecceEEE-EEEcCCCEEEeeecC
Confidence 8998777774 653 446777888888885 778999999987754
No 20
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=50.62 E-value=50 Score=29.84 Aligned_cols=32 Identities=28% Similarity=0.502 Sum_probs=19.0
Q ss_pred HHHHHHhhCCCCcccccCCCceeEEeeeCCCCCcceeEEEe-cC
Q 027552 115 VLLDLLKKGHPEPDKKIGGGIQAFQVRYHPTYKSRCFFLIR-ED 157 (222)
Q Consensus 115 vL~eLL~~yHPd~e~KIG~GI~~i~V~~hp~~~sRCFfVvR-~D 157 (222)
.|++|+.+ .| -|..|.+.+.| ...||-.|. .|
T Consensus 22 eieDlFyK--------yg-~i~~ieLK~r~--g~ppfafVeFEd 54 (241)
T KOG0105|consen 22 EIEDLFYK--------YG-RIREIELKNRP--GPPPFAFVEFED 54 (241)
T ss_pred cHHHHHhh--------hc-ceEEEEeccCC--CCCCeeEEEecC
Confidence 47888864 43 48888877633 445554443 44
No 21
>PF08897 DUF1841: Domain of unknown function (DUF1841); InterPro: IPR014993 This group of proteins are functionally uncharacterised.
Probab=47.96 E-value=31 Score=28.99 Aligned_cols=57 Identities=18% Similarity=0.293 Sum_probs=41.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCCCcChhhHHHHHHHHhhCCCCcccccCCCceeEEeeeCC
Q 027552 86 GSSIEMFDYFYKFLHFWPPNLNVNKYEHMVLLDLLKKGHPEPDKKIGGGIQAFQVRYHP 144 (222)
Q Consensus 86 ~S~~ea~~yFr~IL~~y~~g~~L~e~D~~vL~eLL~~yHPd~e~KIG~GI~~i~V~~hp 144 (222)
+|..+++.+|...-.++..+..|+.-|...+ .++. -||++..-+-..=.++.-.+.|
T Consensus 1 psr~~~R~ff~~~w~K~~~~~~L~~lE~~a~-~~i~-~HPEYh~~l~~~e~~l~~dy~p 57 (137)
T PF08897_consen 1 PSRDQVRRFFCDAWRKYRAGEPLTPLEQIAA-DVIE-EHPEYHALLDDPERALARDYSP 57 (137)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHH-HHHH-HCcchHHHHhCHHHHhhccCCc
Confidence 4788999999999999999999999776644 4553 6999986664322233334433
No 22
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=46.99 E-value=26 Score=32.92 Aligned_cols=7 Identities=14% Similarity=0.107 Sum_probs=4.5
Q ss_pred HHHHHHh
Q 027552 115 VLLDLLK 121 (222)
Q Consensus 115 vL~eLL~ 121 (222)
.|.+++.
T Consensus 209 ~L~~~F~ 215 (346)
T TIGR01659 209 QLDTIFG 215 (346)
T ss_pred HHHHHHH
Confidence 4667775
No 23
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=46.93 E-value=35 Score=28.33 Aligned_cols=37 Identities=22% Similarity=0.348 Sum_probs=19.0
Q ss_pred CCcceeEEEecCCCcccccHHHHhhhcCCC--chhhcccccc
Q 027552 146 YKSRCFFLIREDETADDFSFRKCVDHMLPL--PEDMKVKSDA 185 (222)
Q Consensus 146 ~~sRCFfVvR~DGt~eDFSY~KCi~~~~p~--~~~~~~k~~~ 185 (222)
|.+|+||..-+|- -..|-...-++.+. |+.++.....
T Consensus 60 f~WrhyYw~LT~e---GieyLR~yL~LP~eivP~T~k~~~~~ 98 (124)
T PTZ00034 60 FAWQHYYYYLTDE---GIEYLRTYLHLPPDVFPATHKKKSVN 98 (124)
T ss_pred EeeEEEEEEEchH---HHHHHHHHhCCCcccCchhhcccccC
Confidence 5666665555542 24565555555542 5555544443
No 24
>KOG2945 consensus Predicted RNA-binding protein [General function prediction only]
Probab=46.46 E-value=17 Score=35.01 Aligned_cols=10 Identities=10% Similarity=0.321 Sum_probs=4.8
Q ss_pred hhcCCCchhh
Q 027552 170 DHMLPLPEDM 179 (222)
Q Consensus 170 ~~~~p~~~~~ 179 (222)
.+++..|++.
T Consensus 307 ~~vf~k~~n~ 316 (365)
T KOG2945|consen 307 INVFDKPANF 316 (365)
T ss_pred hheeeccccc
Confidence 4455554443
No 25
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=43.32 E-value=25 Score=28.68 Aligned_cols=24 Identities=17% Similarity=0.212 Sum_probs=14.0
Q ss_pred CCCceeeCCccc-CCHHHHHHHHHH
Q 027552 74 GSGRVKLGPKEF-GSSIEMFDYFYK 97 (222)
Q Consensus 74 ~~kPV~LG~k~F-~S~~ea~~yFr~ 97 (222)
....|-|+...| .|..+++++|..
T Consensus 33 ~~~~lfVgnL~~~~te~~L~~~F~~ 57 (144)
T PLN03134 33 MSTKLFIGGLSWGTDDASLRDAFAH 57 (144)
T ss_pred CCCEEEEeCCCCCCCHHHHHHHHhc
Confidence 344566665553 455677777764
No 26
>COG3860 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.70 E-value=18 Score=28.40 Aligned_cols=39 Identities=18% Similarity=0.201 Sum_probs=27.8
Q ss_pred HHHHHhhhcCCCCCCcChhhHHHHHHHHhhCCCCcc----cccCCC
Q 027552 93 DYFYKFLHFWPPNLNVNKYEHMVLLDLLKKGHPEPD----KKIGGG 134 (222)
Q Consensus 93 ~yFr~IL~~y~~g~~L~e~D~~vL~eLL~~yHPd~e----~KIG~G 134 (222)
-.++-||....++..-++.+ +-.+|.+||||+. +-|++|
T Consensus 32 ivLk~ll~~fe~~r~YsEke---VN~ii~ryh~DyaTvRReli~~~ 74 (89)
T COG3860 32 IVLKHLLKNFENERQYSEKE---VNLIIKRYHPDYATVRRELIEYG 74 (89)
T ss_pred hhHHHHHhhcccccccCHHH---HHHHHHHhCchHHHHHHHHHHcc
Confidence 34667788888877777765 5567778999986 556665
No 27
>PF09349 OHCU_decarbox: OHCU decarboxylase; InterPro: IPR018020 The proteins in this entry are OHCU decarboxylase, an enzyme of the purine catabolism that catalyses the conversion of OHCU into S(+)-allantoin []; it is the third step of the conversion of uric acid (a purine derivative) to allantoin. Step one is catalysed by urate oxidase (IPR002042 from INTERPRO) and step two is catalysed by hydroxyisourate hydrolase (IPR000895 from INTERPRO). ; PDB: 3O7I_B 3O7H_B 3O7J_A 3O7K_A 2Q37_A 2O70_B 2O73_C 2O74_C 2O8I_A.
Probab=37.24 E-value=57 Score=27.16 Aligned_cols=40 Identities=15% Similarity=0.192 Sum_probs=28.8
Q ss_pred CcccCCHHHHHHHHHHhhhcCCCCCCcChhhHHHHHHHHhhCCCCccccc
Q 027552 82 PKEFGSSIEMFDYFYKFLHFWPPNLNVNKYEHMVLLDLLKKGHPEPDKKI 131 (222)
Q Consensus 82 ~k~F~S~~ea~~yFr~IL~~y~~g~~L~e~D~~vL~eLL~~yHPd~e~KI 131 (222)
.+.|.|..+|...+..++..+. ...++++|. .||+...+.
T Consensus 30 ~rPf~s~~~L~~a~~~~~~~~~---------~~~~~~~l~-aHP~lg~~~ 69 (159)
T PF09349_consen 30 ARPFASVDALIAAADEAVRSLS---------EEDKLEALR-AHPRLGERA 69 (159)
T ss_dssp GGS-SSHHHHHHHHHHHHHCS----------HHHHHHHHH-TS--TTSHH
T ss_pred cCCCCCHHHHHHHHHHHHHhCC---------HHHHHHHHH-hCccccccc
Confidence 5789999999999999998855 334777884 999876653
No 28
>PF03859 CG-1: CG-1 domain; InterPro: IPR005559 CG-1 domains are highly conserved domains of about 130 amino-acid residues containing a predicted bipartite NLS and named after a partial cDNA clone isolated from parsley encoding a sequence-specific DNA-binding protein []. CG-1 domains are associated with CAMTA proteins (for CAlModulin -binding Transcription Activator) that are transcription factors containing a calmodulin-binding domain and ankyrins [].; GO: 0005516 calmodulin binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=36.92 E-value=29 Score=28.53 Aligned_cols=27 Identities=33% Similarity=0.988 Sum_probs=19.7
Q ss_pred ccCCCceeEEeee-----CCCCCcceeEEEecC
Q 027552 130 KIGGGIQAFQVRY-----HPTYKSRCFFLIRED 157 (222)
Q Consensus 130 KIG~GI~~i~V~~-----hp~~~sRCFfVvR~D 157 (222)
|+| ||..|..-+ .|.|.-||||++..+
T Consensus 74 Kv~-~~e~l~~~Yah~~~~~~F~RR~Ywll~~~ 105 (118)
T PF03859_consen 74 KVG-GVEVLNCYYAHSEDNPTFHRRCYWLLDPP 105 (118)
T ss_pred ccC-ceeeeEEEEEeeccCCCeeeEEEEccCCC
Confidence 454 566666554 488999999998754
No 29
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=34.03 E-value=63 Score=32.12 Aligned_cols=15 Identities=27% Similarity=0.344 Sum_probs=9.1
Q ss_pred cChhhHHHHHHHHhh
Q 027552 108 VNKYEHMVLLDLLKK 122 (222)
Q Consensus 108 L~e~D~~vL~eLL~~ 122 (222)
++..+...+++.|.+
T Consensus 291 l~~~eR~~il~~Fr~ 305 (572)
T PRK04537 291 VPQKKRESLLNRFQK 305 (572)
T ss_pred CCHHHHHHHHHHHHc
Confidence 455566666766653
No 30
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=33.52 E-value=41 Score=27.58 Aligned_cols=12 Identities=17% Similarity=0.144 Sum_probs=5.6
Q ss_pred ceeEEEecCCCc
Q 027552 149 RCFFLIREDETA 160 (222)
Q Consensus 149 RCFfVvR~DGt~ 160 (222)
+-..|.-.||.+
T Consensus 44 ~di~vT~~dg~v 55 (119)
T KOG3172|consen 44 RDITVTARDGRV 55 (119)
T ss_pred EEEEEEccCCcc
Confidence 334444555543
No 31
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=32.01 E-value=46 Score=30.40 Aligned_cols=43 Identities=26% Similarity=0.302 Sum_probs=34.6
Q ss_pred HHHHHHHHHhhhcCCCCCCc--Ch-hhHHHHHHHHhhCCCCcccccC
Q 027552 89 IEMFDYFYKFLHFWPPNLNV--NK-YEHMVLLDLLKKGHPEPDKKIG 132 (222)
Q Consensus 89 ~ea~~yFr~IL~~y~~g~~L--~e-~D~~vL~eLL~~yHPd~e~KIG 132 (222)
.++++-+|.+|-..+.+.+| |+ ||.-+|+--| +||...-.-||
T Consensus 103 AKvm~~ikavLgaTKiDLPVDINDPYDlGLLLRhL-RHHSNLLAnIg 148 (238)
T PF02084_consen 103 AKVMEDIKAVLGATKIDLPVDINDPYDLGLLLRHL-RHHSNLLANIG 148 (238)
T ss_pred HHHHHHHHHHhcccccccccccCChhhHHHHHHHH-HHHHHHHhhcC
Confidence 34788899999998888775 44 4898888888 49999888887
No 32
>PF07624 PSD2: Protein of unknown function (DUF1585); InterPro: IPR011478 This entry represents a conserved region at the C terminus of a family of cytochrome-like proteins found in bacteria such as Rhodopirellula baltica and Solibacter usitatus. These proteins also contain IPR013036 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=30.56 E-value=71 Score=23.44 Aligned_cols=33 Identities=6% Similarity=0.009 Sum_probs=25.0
Q ss_pred HHHHHHHHHhhhcCCCCCCcChhhHHHHHHHHh
Q 027552 89 IEMFDYFYKFLHFWPPNLNVNKYEHMVLLDLLK 121 (222)
Q Consensus 89 ~ea~~yFr~IL~~y~~g~~L~e~D~~vL~eLL~ 121 (222)
.++..+|..-|-.|..+-.++..|...|..++.
T Consensus 21 ~~~~~~~~~kl~~YAlGR~~~~~D~~~i~~i~~ 53 (76)
T PF07624_consen 21 DQFARCFAEKLLTYALGRPLEFSDRCEIDRIVE 53 (76)
T ss_pred HHHHHHHHHHHHHHHcCCCCCcchHHHHHHHHH
Confidence 334444555577899999999999988888886
No 33
>PHA02102 hypothetical protein
Probab=29.45 E-value=23 Score=26.67 Aligned_cols=30 Identities=30% Similarity=0.658 Sum_probs=19.7
Q ss_pred ccCCCcee-EEeeeCCCC-Cccee------EEEecCCCc
Q 027552 130 KIGGGIQA-FQVRYHPTY-KSRCF------FLIREDETA 160 (222)
Q Consensus 130 KIG~GI~~-i~V~~hp~~-~sRCF------fVvR~DGt~ 160 (222)
-.|.-|+. =.|++ .+| +|.|| |++|+||++
T Consensus 29 ~yGvein~~nev~f-~DWLsSSCYGEg~eaF~~~SDGsv 66 (72)
T PHA02102 29 DYGVEINDDNEVRF-EDWLSSSCYGEGGEAFVARSDGSV 66 (72)
T ss_pred ccceeeCCCCcEeH-HHhhcccccccccceeeeccCCcE
Confidence 34444433 45555 456 69998 899999985
No 34
>KOG2945 consensus Predicted RNA-binding protein [General function prediction only]
Probab=29.18 E-value=46 Score=32.12 Aligned_cols=6 Identities=17% Similarity=0.069 Sum_probs=2.3
Q ss_pred hhcccc
Q 027552 178 DMKVKS 183 (222)
Q Consensus 178 ~~~~k~ 183 (222)
..|.++
T Consensus 308 ~vf~k~ 313 (365)
T KOG2945|consen 308 NVFDKP 313 (365)
T ss_pred heeecc
Confidence 334333
No 35
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=29.14 E-value=2e+02 Score=20.02 Aligned_cols=44 Identities=11% Similarity=0.119 Sum_probs=31.4
Q ss_pred cCCCceeEEeeeCCCCCcceeEEEecCCCcccccHHHHhhhcCC
Q 027552 131 IGGGIQAFQVRYHPTYKSRCFFLIREDETADDFSFRKCVDHMLP 174 (222)
Q Consensus 131 IG~GI~~i~V~~hp~~~sRCFfVvR~DGt~eDFSY~KCi~~~~p 174 (222)
-|.-|.+|+-+..+.-...+.|+++.+|...+-++.+.++.+-.
T Consensus 23 ~~vni~~I~Srp~~~~~~~~~f~id~~~~~~~~~~~~~l~~l~~ 66 (75)
T cd04880 23 RGINLTKIESRPSRKGLWEYEFFVDFEGHIDDPDVKEALEELKR 66 (75)
T ss_pred CCCCEEEEEeeecCCCCceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 34557777655444335788899999998888888888876644
No 36
>PF01991 vATP-synt_E: ATP synthase (E/31 kDa) subunit; InterPro: IPR002842 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit E from the V1 and A1 complexes of V- and A-ATPases, respectively. Subunit E appears to form a tight interaction with subunit G in the F0 complex, which together may act as stators to prevent certain subunits from rotating with the central rotary element, much in the same way as the F0 complex subunit B does in F-ATPases []. In addition to its key role in stator structure, subunit E appears to have a role in mediating interactions with putative regulatory subunits []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 3LG8_A 2KK7_A 4DT0_A 2DM9_A 2DMA_A 3V6I_A 3K5B_A 3J0J_L 2KZ9_A.
Probab=28.00 E-value=1.1e+02 Score=25.10 Aligned_cols=66 Identities=21% Similarity=0.185 Sum_probs=36.7
Q ss_pred ChhhHHHHHHHHhhCCCCcccccCCCceeEEeee-CCCCCcceeEEEecCCC-cccccHHHHhhhcCC
Q 027552 109 NKYEHMVLLDLLKKGHPEPDKKIGGGIQAFQVRY-HPTYKSRCFFLIREDET-ADDFSFRKCVDHMLP 174 (222)
Q Consensus 109 ~e~D~~vL~eLL~~yHPd~e~KIG~GI~~i~V~~-hp~~~sRCFfVvR~DGt-~eDFSY~KCi~~~~p 174 (222)
+..|..++.++|......+..+++.....+.+.. -|.--+-+|.|...||+ ..||||...+..+.+
T Consensus 120 ~~~D~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GG~il~~~dg~i~vd~T~e~~l~~~~~ 187 (198)
T PF01991_consen 120 NKKDLELVKEILKRIKKELKSKAGKDSVEVSVDSDYLIDIIGGFILESEDGKIRVDNTFESRLERLKE 187 (198)
T ss_dssp CCHHHHCCHCCHCCCCCCHCCCSSTTTEEEEE-T---BSSSSEEEEECSSSSCEEEEEHHHHHHHCHH
T ss_pred ccchHHHHHHHHHHHHHHHHHHhCCCcceeecCccccCCccceEEEEECCCCEEEECCHHHHHHHHHH
Confidence 4556666665554333443333333322222222 01123568999989986 789999988876653
No 37
>PRK13798 putative OHCU decarboxylase; Provisional
Probab=27.85 E-value=72 Score=27.09 Aligned_cols=41 Identities=15% Similarity=0.152 Sum_probs=32.5
Q ss_pred CCcccCCHHHHHHHHHHhhhcCCCCCCcChhhHHHHHHHHhhCCCCccccc
Q 027552 81 GPKEFGSSIEMFDYFYKFLHFWPPNLNVNKYEHMVLLDLLKKGHPEPDKKI 131 (222)
Q Consensus 81 G~k~F~S~~ea~~yFr~IL~~y~~g~~L~e~D~~vL~eLL~~yHPd~e~KI 131 (222)
..+.|.|..++...+..++..+.. . .++++|. .||+...+.
T Consensus 38 ~~RPf~s~~~L~~a~~~~~~~~~~------~---~~~~~l~-~HP~lg~~~ 78 (166)
T PRK13798 38 AARPFADHDALLAAADEALAGLSE------A---DIDEALA-GHPRIGERP 78 (166)
T ss_pred HcCCCCCHHHHHHHHHHHHHcCCH------H---HHHHHHH-hCCcccCcc
Confidence 457799999999999999988543 2 3777884 999987665
No 38
>PF05742 NRDE: NRDE protein; InterPro: IPR008551 This family is found in eukaryotes, prokaryotes and viruses and has no known function. P54797 from SWISSPROT has been found to be expressed during early embryogenesis in Mus sp [].
Probab=25.67 E-value=2.2e+02 Score=25.57 Aligned_cols=72 Identities=19% Similarity=0.241 Sum_probs=44.9
Q ss_pred cccCCHHHHHHHHHHhhhcCCCCCCcChhh-HHHHHHHHhhC---CCCcc-cccCCC---------ceeEEeeeCCCCCc
Q 027552 83 KEFGSSIEMFDYFYKFLHFWPPNLNVNKYE-HMVLLDLLKKG---HPEPD-KKIGGG---------IQAFQVRYHPTYKS 148 (222)
Q Consensus 83 k~F~S~~ea~~yFr~IL~~y~~g~~L~e~D-~~vL~eLL~~y---HPd~e-~KIG~G---------I~~i~V~~hp~~~s 148 (222)
..|+.....+..|..+|..... ++.++ ...|.+||... .|+.. ...|.+ +.+|.|. .+.|+|
T Consensus 162 ~pWpKv~~gk~~l~~~~~~~~~---~~~~~l~~~l~~~L~~~~~~~~d~~l~~~g~~~~~~~~~~~lssifi~-~~~YGT 237 (273)
T PF05742_consen 162 TPWPKVERGKQLLEEILEQSNE---SSEEELIEELFELLSDDTQCAPDEQLPDTGIGLPELERPINLSSIFIR-GPYYGT 237 (273)
T ss_pred CCccchhHHHHHHHHHHhcccC---CCHHHHHHHHHHHhcCCCcCCChhHccccCCCcchhhhhccccccccc-CCCccC
Confidence 5677788899999999994332 34333 46688888633 23332 233443 3345555 377898
Q ss_pred ceeEEEecCC
Q 027552 149 RCFFLIREDE 158 (222)
Q Consensus 149 RCFfVvR~DG 158 (222)
||=-||..|.
T Consensus 238 RssTvIlvd~ 247 (273)
T PF05742_consen 238 RSSTVILVDR 247 (273)
T ss_pred eeEEEEEEec
Confidence 8877666554
No 39
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=25.62 E-value=84 Score=28.44 Aligned_cols=15 Identities=20% Similarity=0.091 Sum_probs=11.6
Q ss_pred HHHHhhhcCCCCCCc
Q 027552 94 YFYKFLHFWPPNLNV 108 (222)
Q Consensus 94 yFr~IL~~y~~g~~L 108 (222)
||--|||...+|+..
T Consensus 56 HF~~ILNfmRdGdv~ 70 (230)
T KOG2716|consen 56 HFDTILNFMRDGDVD 70 (230)
T ss_pred HHHHHHHhhhccccc
Confidence 777888888877765
No 40
>TIGR02464 ribofla_fusion conserved hypothetical protein, ribA/ribD-fused. This model describes a sequence region that occurs in at least three different polypeptide contexts. It is found fused to GTP cyclohydrolase II, the RibA of riboflavin biosynthesis (TIGR00505), as in Vibrio vulnificus. It is found fused to riboflavin biosynthesis protein RibD (TIGR00326) in rice and Arabidopsis. It occurs as a standalone protein in a number of bacterial species in varied contexts, including single gene operons and bacteriophage genomes. The member from E. coli currently is named YbiA. The function(s) of members of this family is unknown.
Probab=24.80 E-value=58 Score=27.03 Aligned_cols=52 Identities=15% Similarity=0.213 Sum_probs=35.6
Q ss_pred CceeeCCcccCCHHHHHHHHHHhhhcCCCCCCcChhhHHHHHHHHhhCCCCcccccCCCcee
Q 027552 76 GRVKLGPKEFGSSIEMFDYFYKFLHFWPPNLNVNKYEHMVLLDLLKKGHPEPDKKIGGGIQA 137 (222)
Q Consensus 76 kPV~LG~k~F~S~~ea~~yFr~IL~~y~~g~~L~e~D~~vL~eLL~~yHPd~e~KIG~GI~~ 137 (222)
-||.|.+..|+|..+.+.+.+..|-. |......++.--+|....++|.-++.
T Consensus 19 ~~f~~~g~~y~s~Ehy~qa~K~~~~~----------d~~~~~~I~~~~sp~~ak~lgr~~~~ 70 (153)
T TIGR02464 19 SPFTVDGVTFPTSEHYYMAQKARLFG----------DEEIAEEILEAKTPEEAKRLGRKVRG 70 (153)
T ss_pred CCeEECCEEeCCHHHHHHHhchhcCC----------CHHHHHHHHhCCCHHHHHHHhCcccC
Confidence 38999999999999999988887522 12334445544466666777766544
No 41
>KOG0556 consensus Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=24.71 E-value=1.1e+02 Score=30.64 Aligned_cols=66 Identities=20% Similarity=0.170 Sum_probs=42.6
Q ss_pred CHHHHHHHHHHhhhcCCCCCCcChh--hHHHHHHHHhhCCCCcccccCCCceeEEeeeCCCC--CcceeEEEecCCCc
Q 027552 87 SSIEMFDYFYKFLHFWPPNLNVNKY--EHMVLLDLLKKGHPEPDKKIGGGIQAFQVRYHPTY--KSRCFFLIREDETA 160 (222)
Q Consensus 87 S~~ea~~yFr~IL~~y~~g~~L~e~--D~~vL~eLL~~yHPd~e~KIG~GI~~i~V~~hp~~--~sRCFfVvR~DGt~ 160 (222)
+..++.+|+...+..++..+--+.. .+..+.+|-. .+......|.-+.|.+- +..||+|.|.-++.
T Consensus 42 ~~~~~ed~~~~~yg~~~l~~s~~~~~~~~~~v~dl~~--------~~~~~~V~vRgrVhtsr~~GK~~FlvLRq~~~t 111 (533)
T KOG0556|consen 42 REAEAEDYAKERYGDLSLIQSQSKEGRELTDVSDLDE--------SNDGSEVLVRGRVHTSRLKGKLCFLVLRQQGST 111 (533)
T ss_pred hhhhhhhHHhhhcCcccccccccccccceeehhhhhh--------hcCCceEEEEEEEeeccccceEEEEEEeccCce
Confidence 3367888888888887765432222 2223444432 34446777877888665 48999999998865
No 42
>TIGR03180 UraD_2 OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model. This model is a separate (but related) clade from that represented by TIGR3164. This model places a second homolog in streptomyces species which (are not in the vicinity of other urate catabolism associated genes) below the trusted cutoff.
Probab=24.71 E-value=94 Score=26.17 Aligned_cols=41 Identities=20% Similarity=0.250 Sum_probs=32.0
Q ss_pred CCcccCCHHHHHHHHHHhhhcCCCCCCcChhhHHHHHHHHhhCCCCccccc
Q 027552 81 GPKEFGSSIEMFDYFYKFLHFWPPNLNVNKYEHMVLLDLLKKGHPEPDKKI 131 (222)
Q Consensus 81 G~k~F~S~~ea~~yFr~IL~~y~~g~~L~e~D~~vL~eLL~~yHPd~e~KI 131 (222)
..+.|.|..++...+..++..+.. . .++++|. .||+...+.
T Consensus 28 ~~RPf~s~~~L~~a~~~~~~~~~~------~---~~~~~l~-~HP~lg~~~ 68 (158)
T TIGR03180 28 AARPFASAEALLAAADQAWQNLSE------Q---DLFEALA-GHPRIGEKP 68 (158)
T ss_pred HcCCCCCHHHHHHHHHHHHHcCCH------H---HHHHHHH-hCCcccCcc
Confidence 357799999999999999988543 2 3778884 999976554
No 43
>PF08719 DUF1768: Domain of unknown function (DUF1768); InterPro: IPR012816 This entry describes a sequence region that occurs in at least three different polypeptide contexts. It is found fused to GTP cyclohydrolase II, the RibA of riboflavin biosynthesis (IPR000926 from INTERPRO), as in Vibrio vulnificus. It is found fused to riboflavin biosynthesis protein RibD (IPR004794 from INTERPRO) in rice and Arabidopsis. It occurs as a standalone protein in a number of bacterial species in varied contexts, including single gene operons and bacteriophage genomes. The member from Escherichia coli currently is named YbiA. The function(s) of members of this family is unknown.; PDB: 2B3W_A.
Probab=24.36 E-value=36 Score=28.05 Aligned_cols=54 Identities=13% Similarity=0.180 Sum_probs=30.4
Q ss_pred CceeeCCcccCCHHHHHHHHHHhhhcCCCCCCcChhhHHHHHHHHhhCCCCcccccCCCceeEE
Q 027552 76 GRVKLGPKEFGSSIEMFDYFYKFLHFWPPNLNVNKYEHMVLLDLLKKGHPEPDKKIGGGIQAFQ 139 (222)
Q Consensus 76 kPV~LG~k~F~S~~ea~~yFr~IL~~y~~g~~L~e~D~~vL~eLL~~yHPd~e~KIG~GI~~i~ 139 (222)
-||.+.+..|+|..+++.+.+.++-. +......++...+|....++|.-+..+.
T Consensus 19 ~~~~~~g~~y~s~Ehy~qa~K~~~~~----------d~~~~~~I~~~~~p~~~k~l~r~~~~~~ 72 (157)
T PF08719_consen 19 CPFEIDGITYPSVEHYYQAQKFIDFN----------DREIAEKILAAKSPKEAKKLGRKVKNFD 72 (157)
T ss_dssp --EEETTEEESSHHHHHHHHHB--HH----------HHH---HHHH---HHHHHHHH--SS--S
T ss_pred CceEECCEEECcHHHHHHHHhccccc----------chhHHHHHHHCCCHHHHHHHhccccccc
Confidence 48999999999999999988877632 4444555665456666677776655443
No 44
>PF06356 DUF1064: Protein of unknown function (DUF1064); InterPro: IPR009414 This entry is represented by Bacteriophage 92, Orf34. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins whose functions have not been experimentally determined. Computational analysis involving sequence, predicted strucutre and genomic context suggests that these proteins may be endonucleases which function in phage genome segregation, or the repair of double-stranded breaks introduced during either this process or DNA replication [].
Probab=22.96 E-value=88 Score=25.43 Aligned_cols=28 Identities=18% Similarity=0.058 Sum_probs=22.8
Q ss_pred cCCCceeeCCcccCCHHHHHHHHHHhhh
Q 027552 73 NGSGRVKLGPKEFGSSIEMFDYFYKFLH 100 (222)
Q Consensus 73 ~~~kPV~LG~k~F~S~~ea~~yFr~IL~ 100 (222)
=.++.|++.+..|.|+.++.-|..-.|.
T Consensus 4 Y~~kK~~~dGi~FDSk~Ea~~Y~~Lk~~ 31 (118)
T PF06356_consen 4 YNNKKTTIDGIKFDSKKEAEYYQELKLL 31 (118)
T ss_pred cCcEEEEECCeEEccHHHHHHHHHHHHh
Confidence 3567899999999999999888765553
No 45
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=22.32 E-value=2.2e+02 Score=20.17 Aligned_cols=44 Identities=11% Similarity=0.112 Sum_probs=30.8
Q ss_pred cCCCceeEEeeeCCCCCcceeEEEecCCCcccccHHHHhhhcCC
Q 027552 131 IGGGIQAFQVRYHPTYKSRCFFLIREDETADDFSFRKCVDHMLP 174 (222)
Q Consensus 131 IG~GI~~i~V~~hp~~~sRCFfVvR~DGt~eDFSY~KCi~~~~p 174 (222)
-|.-|.+|..+.+..-...+.|.|..++...+-.+.+.++.+-.
T Consensus 25 ~~ini~~i~s~p~~~~~~~~~f~vd~~~~~~~~~~~~~l~~l~~ 68 (80)
T cd04905 25 RGINLTKIESRPSKGGLWEYVFFIDFEGHIEDPNVAEALEELKR 68 (80)
T ss_pred CCcCEEEEEEEEcCCCCceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 44567888777665545778888888987667777777765544
No 46
>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=22.22 E-value=72 Score=32.91 Aligned_cols=18 Identities=11% Similarity=-0.051 Sum_probs=10.9
Q ss_pred ccCCHHHHHHHHHHhhhc
Q 027552 84 EFGSSIEMFDYFYKFLHF 101 (222)
Q Consensus 84 ~F~S~~ea~~yFr~IL~~ 101 (222)
.|.|+++-..-+..+|.-
T Consensus 473 ifVTKk~~~e~i~a~Lkl 490 (731)
T KOG0339|consen 473 IFVTKKADAEEIAANLKL 490 (731)
T ss_pred EEEeccCCHHHHHHHhcc
Confidence 477776666666666544
No 47
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=21.67 E-value=63 Score=21.27 Aligned_cols=35 Identities=26% Similarity=0.505 Sum_probs=23.3
Q ss_pred HHHHHHHhhhcCCCCCCcChhh-HHHHHHHHhhCCCCc
Q 027552 91 MFDYFYKFLHFWPPNLNVNKYE-HMVLLDLLKKGHPEP 127 (222)
Q Consensus 91 a~~yFr~IL~~y~~g~~L~e~D-~~vL~eLL~~yHPd~ 127 (222)
...-|..+|+.|.. ..++..+ ...+..|| ..||+.
T Consensus 3 ~Y~~FL~il~~y~~-~~~~~~~v~~~v~~Ll-~~hpdL 38 (47)
T PF02671_consen 3 VYNEFLKILNDYKK-GRISRSEVIEEVSELL-RGHPDL 38 (47)
T ss_dssp HHHHHHHHHHHHHC-TCSCHHHHHHHHHHHT-TT-HHH
T ss_pred HHHHHHHHHHHHHh-cCCCHHHHHHHHHHHH-ccCHHH
Confidence 45668888888888 5566555 45566677 489874
No 48
>PHA00370 III attachment protein
Probab=20.79 E-value=1.2e+02 Score=28.34 Aligned_cols=8 Identities=25% Similarity=0.401 Sum_probs=4.4
Q ss_pred EEecCCCc
Q 027552 153 LIREDETA 160 (222)
Q Consensus 153 VvR~DGt~ 160 (222)
|--.|||+
T Consensus 62 V~~~dgTv 69 (297)
T PHA00370 62 VCQNDGTV 69 (297)
T ss_pred EecCCCCe
Confidence 33466765
No 49
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=20.74 E-value=1e+02 Score=31.30 Aligned_cols=6 Identities=0% Similarity=0.030 Sum_probs=2.5
Q ss_pred HHHHHh
Q 027552 116 LLDLLK 121 (222)
Q Consensus 116 L~eLL~ 121 (222)
|.++|.
T Consensus 250 L~~~F~ 255 (578)
T TIGR01648 250 IEKSFS 255 (578)
T ss_pred HHHHHH
Confidence 444443
No 50
>PF08818 DUF1801: Domain of unknown function (DU1801); InterPro: IPR014922 This large entry of bacterial proteins is uncharacterised. They contain a presumed domain about 110 amino acids in length. ; PDB: 2KL4_A 2OC6_B 2I8D_B.
Probab=20.02 E-value=1.2e+02 Score=22.32 Aligned_cols=43 Identities=19% Similarity=0.222 Sum_probs=29.8
Q ss_pred HHHHHHHHhhCCCCcccccCCCceeEEeeeCCCCCcceeEEEecC
Q 027552 113 HMVLLDLLKKGHPEPDKKIGGGIQAFQVRYHPTYKSRCFFLIRED 157 (222)
Q Consensus 113 ~~vL~eLL~~yHPd~e~KIG~GI~~i~V~~hp~~~sRCFfVvR~D 157 (222)
...|.+|+...+|+.++.|..|+=+|.+.-+. ..-|+|-..++
T Consensus 6 ~~~lr~li~~~~P~~~e~ikwg~P~y~~~g~~--~~~~~~~~~k~ 48 (103)
T PF08818_consen 6 LEELRELILEAAPDLEEVIKWGMPAYYYDGKG--GPFCGFSAFKN 48 (103)
T ss_dssp HHHHHHHHHHHSTTSEEEEETTEEEEEETTE----EEEEEEE-SS
T ss_pred HHHHHHHHHHhCcChhheeecceeEEEECCce--EEEEEEEecCC
Confidence 45688888889999999999998777763321 24566666555
Done!