Query 039507
Match_columns 108
No_of_seqs 101 out of 986
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 10:22:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039507.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039507hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05670 DUF814: Domain of unk 100.0 2.8E-34 6E-39 188.7 9.4 87 2-92 3-90 (90)
2 COG1293 Predicted RNA-binding 100.0 3.8E-31 8.2E-36 219.8 9.6 102 2-108 445-547 (564)
3 KOG3272 Predicted coiled-coil 99.9 3.1E-21 6.6E-26 141.4 9.1 106 3-108 10-115 (207)
4 KOG2030 Predicted RNA-binding 99.8 1.8E-20 3.9E-25 159.1 9.7 101 2-107 500-607 (911)
5 KOG0407 40S ribosomal protein 85.2 0.79 1.7E-05 31.7 2.3 61 11-71 5-73 (139)
6 PF02639 DUF188: Uncharacteriz 60.7 41 0.00089 23.3 5.9 53 5-63 28-89 (130)
7 PRK12756 phospho-2-dehydro-3-d 53.1 59 0.0013 26.4 6.3 49 31-86 219-267 (348)
8 PRK12822 phospho-2-dehydro-3-d 53.0 61 0.0013 26.4 6.4 50 30-86 219-268 (356)
9 KOG0536 Flavohemoprotein b5+b5 45.6 20 0.00043 25.5 2.3 19 18-36 72-90 (145)
10 COG0722 AroG 3-deoxy-D-arabino 40.6 53 0.0011 26.7 4.2 49 32-86 221-269 (351)
11 COG1598 Predicted nuclease of 37.7 29 0.00063 21.4 2.0 20 26-45 12-31 (73)
12 PF08111 Pea-VEAacid: Pea-VEAa 35.7 13 0.00029 16.3 0.1 6 37-42 4-9 (15)
13 PF09941 DUF2173: Uncharacteri 35.5 82 0.0018 21.4 4.0 36 36-71 8-47 (108)
14 PRK04203 rpl1P 50S ribosomal p 32.8 1.4E+02 0.003 22.2 5.2 49 55-103 2-51 (215)
15 PRK09261 phospho-2-dehydro-3-d 32.6 2.7E+02 0.0059 22.6 8.1 49 30-84 219-267 (349)
16 COG1671 Uncharacterized protei 30.6 1.6E+02 0.0034 21.2 5.0 48 10-64 50-105 (150)
17 PRK00124 hypothetical protein; 27.9 2.2E+02 0.0048 20.3 5.4 54 8-70 47-110 (151)
18 PRK09750 hypothetical protein; 25.6 84 0.0018 19.3 2.5 23 86-108 6-28 (64)
19 PF06672 DUF1175: Protein of u 25.5 94 0.002 23.7 3.2 32 9-47 127-160 (216)
20 PF00282 Pyridoxal_deC: Pyrido 23.8 34 0.00073 27.4 0.6 22 19-40 214-235 (373)
21 PF00313 CSD: 'Cold-shock' DNA 23.2 44 0.00096 19.6 0.9 14 27-40 23-36 (66)
22 PF02056 Glyco_hydro_4: Family 23.0 1.3E+02 0.0027 22.1 3.5 43 33-85 22-64 (183)
23 PF05677 DUF818: Chlamydia CHL 22.8 1.7E+02 0.0036 24.1 4.4 65 7-71 139-205 (365)
24 cd04458 CSP_CDS Cold-Shock Pro 22.7 42 0.00092 19.6 0.8 14 27-40 23-36 (65)
25 PLN02590 probable tyrosine dec 22.6 31 0.00066 29.4 0.2 25 19-43 307-331 (539)
26 COG0078 ArgF Ornithine carbamo 21.2 99 0.0022 24.8 2.8 32 18-61 253-284 (310)
27 cd04862 PaeLigD_Pol_like PaeLi 20.3 2.9E+02 0.0063 21.0 5.1 52 30-87 134-198 (227)
No 1
>PF05670 DUF814: Domain of unknown function (DUF814); InterPro: IPR008532 This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from O34693 from SWISSPROT where the N-terminal region is involved in this activity []. Hence the activity of this C-terminal domain is unknown. This domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.
Probab=100.00 E-value=2.8e-34 Score=188.71 Aligned_cols=87 Identities=36% Similarity=0.543 Sum_probs=79.1
Q ss_pred CccCCeEEEEeCChHHHHHH-HHhcCCCceEEeecCCCccEEEEEcCCCCCCCCCCHHHHHHHHHHHHhhccccCCccce
Q 039507 2 PEAGDYTIFMGLDKYENEEL-IKYGFPEDIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNI 80 (108)
Q Consensus 2 ~s~~g~~i~vGrn~~eNe~L-~k~~~~~D~w~H~~~~pG~hviir~~~~~~~~~~~~~~l~~AA~laa~ySkk~~~~~~v 80 (108)
+|++|++|+||||++|||.| +++++++|||||++++||||||||++.+ +.++++|++||.||++||+.++...++
T Consensus 3 ~s~~g~~i~vGrn~~eNe~L~~k~~~~~D~wfH~~~~pg~hvil~~~~~----~~~~~~l~~AA~laa~~Ska~~~~~~v 78 (90)
T PF05670_consen 3 ISSDGFKIIVGRNAKENEMLTKKYARPNDLWFHADDFPGPHVILRNNPG----DEPPPTLQEAAQLAASYSKAWKKGEKV 78 (90)
T ss_pred EecCCeEEEEeCCHHHHHHHHHHhhhhcceeEeccCCCCCEEEEECCCC----ccchHHHHHHHHHHHHhCHhhccCCCe
Confidence 68999999999999999999 8999999999999999999999999865 344459999999999999326778889
Q ss_pred EEEEEecCceec
Q 039507 81 DVVYTPWANLKK 92 (108)
Q Consensus 81 ~V~yt~~k~V~k 92 (108)
+|+||++++|+|
T Consensus 79 ~V~yt~~k~v~K 90 (90)
T PF05670_consen 79 EVDYTQGKYVKK 90 (90)
T ss_pred EEEEeehHhccC
Confidence 999999999987
No 2
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=99.97 E-value=3.8e-31 Score=219.84 Aligned_cols=102 Identities=26% Similarity=0.410 Sum_probs=96.9
Q ss_pred CccCCeEEEEeCChHHHHHH-HHhcCCCceEEeecCCCccEEEEEcCCCCCCCCCCHHHHHHHHHHHHhhccccCCccce
Q 039507 2 PEAGDYTIFMGLDKYENEEL-IKYGFPEDIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNI 80 (108)
Q Consensus 2 ~s~~g~~i~vGrn~~eNe~L-~k~~~~~D~w~H~~~~pG~hviir~~~~~~~~~~~~~~l~~AA~laa~ySkk~~~~~~v 80 (108)
+|++|++|++|||+.|||.| .++++++|+|||++++|||||||++++. ++++++|.+||.|||+|| ++|.++.+
T Consensus 445 ~ss~Gf~vi~Grna~qNe~l~~k~~~~~DlwfHa~~~~gshvvik~~~~----~~~e~ti~eAA~~Aa~~S-ka~~~~~v 519 (564)
T COG1293 445 VSSDGFLVIGGRNAKQNEELVKKYAEKDDLWFHADDIPGSHVVIKTEGK----EPSEETILEAAQLAASYS-KAWKSGLV 519 (564)
T ss_pred eccCCeEEEEecCcccchHHHHhhcccCcEEEEccCCCCCeEEEeCCCC----CCChHHHHHHHHHHHHhc-hHhhcCCC
Confidence 68999999999999999999 8999999999999999999999998632 899999999999999999 59999999
Q ss_pred EEEEEecCceecCCCCCcceEEEecCCC
Q 039507 81 DVVYTPWANLKKTASMDVGQVGFHNPKM 108 (108)
Q Consensus 81 ~V~yt~~k~V~k~~~~~~G~V~~~~~k~ 108 (108)
+|+||.+++|.++++++||+|+|++.+|
T Consensus 520 ~vd~t~vk~vqv~K~a~~G~vl~~g~~~ 547 (564)
T COG1293 520 PVDYTWVKPVQVPKGAKSGEVLYKGQKT 547 (564)
T ss_pred ceEEEEEcccccCCCCCCceEEecCcEE
Confidence 9999999999999999999999998875
No 3
>KOG3272 consensus Predicted coiled-coil protein [General function prediction only]
Probab=99.85 E-value=3.1e-21 Score=141.41 Aligned_cols=106 Identities=77% Similarity=1.246 Sum_probs=99.9
Q ss_pred ccCCeEEEEeCChHHHHHHHHhcCCCceEEeecCCCccEEEEEcCCCCCCCCCCHHHHHHHHHHHHhhccccCCccceEE
Q 039507 3 EAGDYTIFMGLDKYENEELIKYGFPEDIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDV 82 (108)
Q Consensus 3 s~~g~~i~vGrn~~eNe~L~k~~~~~D~w~H~~~~pG~hviir~~~~~~~~~~~~~~l~~AA~laa~ySkk~~~~~~v~V 82 (108)
+...+.|++|++..+|+.|+++..++|.|||+.+..+|||+|+..++++++++|++.|.+||+||...|-.+.+.++|+|
T Consensus 10 t~~~~~i~mg~dk~en~~lIk~g~~e~Vwfhv~~~sS~hvyl~l~~~qtiddip~~vL~DC~QLvKaNSIQG~Kmnnv~V 89 (207)
T KOG3272|consen 10 TEPPYMIYMGKDKFENEELIKWGWPEDVWFHVDKLSSAHVYLRLREGQTIDDIPEFVLEDCAQLVKANSIQGNKMNNVEV 89 (207)
T ss_pred CCCCeeEEEeecccchhHHHHcCCccceEEEeecccccceeeeecCCCCcccccHHHHHHHHHHHHhcccccccccceeE
Confidence 44589999999999999999999999999999999999999999998889999999999999999999976778999999
Q ss_pred EEEecCceecCCCCCcceEEEecCCC
Q 039507 83 VYTPWANLKKTASMDVGQVGFHNPKM 108 (108)
Q Consensus 83 ~yt~~k~V~k~~~~~~G~V~~~~~k~ 108 (108)
.||.+.|++|.+++.+|+|.++..|+
T Consensus 90 vYT~w~NLKKt~~M~~Gqv~fh~~k~ 115 (207)
T KOG3272|consen 90 VYTPWSNLKKTADMDVGQVGFHSTKQ 115 (207)
T ss_pred EechhHhhcccCCCCcccccchhhhh
Confidence 99999999999999999999987663
No 4
>KOG2030 consensus Predicted RNA-binding protein [General function prediction only]
Probab=99.83 E-value=1.8e-20 Score=159.08 Aligned_cols=101 Identities=24% Similarity=0.318 Sum_probs=86.6
Q ss_pred CccCCeEEEEeCChHHHHHH-HHhcCCCceEEeecCCCcc-EEEEEcCCCCCCCCCCHHHHHHHHHHHHhhccccCCccc
Q 039507 2 PEAGDYTIFMGLDKYENEEL-IKYGFPEDIWFHVDKMSSA-HVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNN 79 (108)
Q Consensus 2 ~s~~g~~i~vGrn~~eNe~L-~k~~~~~D~w~H~~~~pG~-hviir~~~~~~~~~~~~~~l~~AA~laa~ySkk~~~~~~ 79 (108)
|||+||+|+.|||++|||.| .+|++|+|||||++ ++|+ ||||+|++.+ ++|+.+|++||.+|.+|| +||...-
T Consensus 500 iSSEg~LVi~GrdaqQnEllvkky~~~~DiY~had-~~gaSsviIkN~~~~---eipp~TL~eAg~ma~~~S-~aWdakv 574 (911)
T KOG2030|consen 500 ISSEGYLVIGGRDAQQNELLVKKYLEPGDIYVHAD-LHGASSVIIKNPPKT---EIPPKTLEEAGSMALCYS-KAWDAKV 574 (911)
T ss_pred EecCcEEEEcCCChhhhhHHHHhhCCCCCeEEecc-cCCCceEEEeCCCCC---CCChhhHHHHHHHHhHHh-hhhcccc
Confidence 79999999999999999999 69999999999995 6655 9999997765 999999999999999999 5975433
Q ss_pred e-EEEEEecCceecCCC----CCcceEEEecCC
Q 039507 80 I-DVVYTPWANLKKTAS----MDVGQVGFHNPK 107 (108)
Q Consensus 80 v-~V~yt~~k~V~k~~~----~~~G~V~~~~~k 107 (108)
| ++-|+..++|+|..+ .+-|.+.+++.|
T Consensus 575 vssaWwv~~dqVSKtaptgeyL~~GSFmIrgkk 607 (911)
T KOG2030|consen 575 VSSAWWVYPDQVSKTAPTGEYLPTGSFMIRGKK 607 (911)
T ss_pred cccceEEecccccccCCCCccccccceEEeccc
Confidence 2 344999999999766 577888887765
No 5
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=85.19 E-value=0.79 Score=31.70 Aligned_cols=61 Identities=25% Similarity=0.280 Sum_probs=44.3
Q ss_pred EeCChHHHHHHH----HhcCCCceEEeecCCCccEEEEEcCCCC----CCCCCCHHHHHHHHHHHHhhc
Q 039507 11 MGLDKYENEELI----KYGFPEDIWFHVDKMSSAHVYLRLHKGQ----TIDDISEGVLEDCAQLVKANS 71 (108)
Q Consensus 11 vGrn~~eNe~L~----k~~~~~D~w~H~~~~pG~hviir~~~~~----~~~~~~~~~l~~AA~laa~yS 71 (108)
+|--.++++.++ -++..+|-|+|+-|+.|.-.|+|-..+. .-+|-++-.-+.||+=+|.-+
T Consensus 5 lg~q~~e~~~vfgvahi~asfndtfvhitdlsg~eti~rvtggmkvkadrdesspyaamlaaqdva~kc 73 (139)
T KOG0407|consen 5 LGPQVREGEQVFGVAHIFASFNDTFVHVTDLSGKETIVRVTGGMKVKADRDESSPYAAMLAAQDVAAKC 73 (139)
T ss_pred ccchhcccceeeeEEEEEeecccceEEEeccCCceEEEEecCCeEEecccccCChHHHHHHHHHHHHHH
Confidence 455667778775 3678999999999999999999976543 112556666666776666655
No 6
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=60.75 E-value=41 Score=23.28 Aligned_cols=53 Identities=13% Similarity=0.142 Sum_probs=35.1
Q ss_pred CCeEEEEeCChHHHHHH-HHhcCCCceEEeecCCC--------ccEEEEEcCCCCCCCCCCHHHHHHH
Q 039507 5 GDYTIFMGLDKYENEEL-IKYGFPEDIWFHVDKMS--------SAHVYLRLHKGQTIDDISEGVLEDC 63 (108)
Q Consensus 5 ~g~~i~vGrn~~eNe~L-~k~~~~~D~w~H~~~~p--------G~hviir~~~~~~~~~~~~~~l~~A 63 (108)
...+|+|+.....-|.- ...++++|+.. ++|+| |+.|| ++.|. .++++.|.+.
T Consensus 28 ~~~~i~Vd~g~DaaD~~I~~~~~~gDiVI-TqDigLA~~~l~Kga~vl--~~rG~---~yt~~nI~~~ 89 (130)
T PF02639_consen 28 YVEMIVVDSGFDAADFYIVNHAKPGDIVI-TQDIGLASLLLAKGAYVL--NPRGK---EYTKENIDEL 89 (130)
T ss_pred CeEEEEECCCCChHHHHHHHcCCCCCEEE-ECCHHHHHHHHHCCCEEE--CCCCC---CCCHHHHHHH
Confidence 34566665544444444 68899999988 55887 55555 44554 7898888654
No 7
>PRK12756 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional
Probab=53.07 E-value=59 Score=26.42 Aligned_cols=49 Identities=8% Similarity=0.143 Sum_probs=34.2
Q ss_pred EEeecCCCccEEEEEcCCCCCCCCCCHHHHHHHHHHHHhhccccCCccceEEEEEe
Q 039507 31 WFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVYTP 86 (108)
Q Consensus 31 w~H~~~~pG~hviir~~~~~~~~~~~~~~l~~AA~laa~ySkk~~~~~~v~V~yt~ 86 (108)
.+++.+=|-+|+|||+..+. +.+.+.+..|+..-. ++.-...+-||...
T Consensus 219 iv~T~GN~~~HvILRGg~~P---NY~~~~v~~a~~~l~----~~~l~~~imVDcSH 267 (348)
T PRK12756 219 IYQTSGNPYGHIIMRGGKKP---NYHAEDIAAACDTLR----EFDLPEHLVVDFSH 267 (348)
T ss_pred EEEcCCCCCeEEEeeCCCCC---CCCHHHHHHHHHHHH----HCCCCCcEEEECCC
Confidence 46788889999999986543 788888888876655 23334556666443
No 8
>PRK12822 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional
Probab=52.99 E-value=61 Score=26.44 Aligned_cols=50 Identities=10% Similarity=0.088 Sum_probs=34.6
Q ss_pred eEEeecCCCccEEEEEcCCCCCCCCCCHHHHHHHHHHHHhhccccCCccceEEEEEe
Q 039507 30 IWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVYTP 86 (108)
Q Consensus 30 ~w~H~~~~pG~hviir~~~~~~~~~~~~~~l~~AA~laa~ySkk~~~~~~v~V~yt~ 86 (108)
..+++.+=|-+|+|||+..+. +.+.+.+..|...-.. +.-...+-||...
T Consensus 219 aiv~T~GN~~~HvILRGg~~P---NY~~~~v~~a~~~l~~----~~l~~~vmVDcSH 268 (356)
T PRK12822 219 STLLSDGNPHGHIILRGGREP---NYGLSDVTKASKLLHD----EGLNHRLIIDCSH 268 (356)
T ss_pred EEEEcCCCCCceEEEeCCCCC---CCCHHHHHHHHHHHHH----CCCCCcEEEECCC
Confidence 457778889999999986432 6778888888876653 3233556666443
No 9
>KOG0536 consensus Flavohemoprotein b5+b5R [Energy production and conversion]
Probab=45.63 E-value=20 Score=25.54 Aligned_cols=19 Identities=32% Similarity=0.504 Sum_probs=16.0
Q ss_pred HHHHHHhcCCCceEEeecC
Q 039507 18 NEELIKYGFPEDIWFHVDK 36 (108)
Q Consensus 18 Ne~L~k~~~~~D~w~H~~~ 36 (108)
-++|.++.+++|+|+++++
T Consensus 72 ~~El~KH~~~dDcW~~i~G 90 (145)
T KOG0536|consen 72 AEELKKHNKKDDCWIAIRG 90 (145)
T ss_pred HHHHHhhCCccceEEEEcC
Confidence 3567899999999999874
No 10
>COG0722 AroG 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]
Probab=40.55 E-value=53 Score=26.67 Aligned_cols=49 Identities=10% Similarity=0.098 Sum_probs=31.6
Q ss_pred EeecCCCccEEEEEcCCCCCCCCCCHHHHHHHHHHHHhhccccCCccceEEEEEe
Q 039507 32 FHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVYTP 86 (108)
Q Consensus 32 ~H~~~~pG~hviir~~~~~~~~~~~~~~l~~AA~laa~ySkk~~~~~~v~V~yt~ 86 (108)
+++.+-|=+|||+|+..+. .+.+.+.+.+|+..-.. +.-...+=|++..
T Consensus 221 v~T~GNp~~HvILRGG~~~--PNYda~~v~~~~~~l~~----~gl~~~lmID~SH 269 (351)
T COG0722 221 VETSGNPDGHVILRGGKKG--PNYDAASVAAACEQLEK----AGLPPRLMIDCSH 269 (351)
T ss_pred EEccCCCCceEEecCCCCC--CCCCHHHHHHHHHHHHH----cCCCCeEEEeccC
Confidence 4567788889999987543 26778888777765542 3333455555443
No 11
>COG1598 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]
Probab=37.66 E-value=29 Score=21.39 Aligned_cols=20 Identities=10% Similarity=-0.072 Sum_probs=16.9
Q ss_pred CCCceEEeecCCCccEEEEE
Q 039507 26 FPEDIWFHVDKMSSAHVYLR 45 (108)
Q Consensus 26 ~~~D~w~H~~~~pG~hviir 45 (108)
..+.||.++.++||+|...+
T Consensus 12 ~dg~y~~~~Pdlpgc~s~G~ 31 (73)
T COG1598 12 EDGGYVASVPDLPGCHSQGE 31 (73)
T ss_pred CCCCEEEEeCCCCCccccCC
Confidence 67889999999999987433
No 12
>PF08111 Pea-VEAacid: Pea-VEAacid family; InterPro: IPR012593 This family consists of the PEA-VEAacid neuropeptides family. These neuropeptides are isolated from the abdominal perisympathetic organs of the American cockroach. These peptides are found together with Pea-YLS-amide and Pea-SKNacid, giving a unique neuropeptide pattern in abdominal perisympathetic organs. The functions of these neuropeptides are unknown [].; GO: 0005184 neuropeptide hormone activity, 0007218 neuropeptide signaling pathway, 0005576 extracellular region
Probab=35.68 E-value=13 Score=16.35 Aligned_cols=6 Identities=33% Similarity=0.595 Sum_probs=4.4
Q ss_pred CCccEE
Q 039507 37 MSSAHV 42 (108)
Q Consensus 37 ~pG~hv 42 (108)
.||+||
T Consensus 4 tpgshv 9 (15)
T PF08111_consen 4 TPGSHV 9 (15)
T ss_pred cCccch
Confidence 478886
No 13
>PF09941 DUF2173: Uncharacterized conserved protein (DUF2173); InterPro: IPR018685 This family of various hypothetical prokaryotic proteins has no known function.
Probab=35.51 E-value=82 Score=21.36 Aligned_cols=36 Identities=19% Similarity=0.311 Sum_probs=24.8
Q ss_pred CCCccEEEEEcC-CCCCC---CCCCHHHHHHHHHHHHhhc
Q 039507 36 KMSSAHVYLRLH-KGQTI---DDISEGVLEDCAQLVKANS 71 (108)
Q Consensus 36 ~~pG~hviir~~-~~~~~---~~~~~~~l~~AA~laa~yS 71 (108)
.+||.....+=. .++.. .++|++..+.+|.+|+.+-
T Consensus 8 ~lpGv~AAg~Fs~~G~l~e~~G~l~~~~a~m~A~mc~An~ 47 (108)
T PF09941_consen 8 KLPGVVAAGEFSDDGKLVEYKGELDEEMAEMLAKMCAANT 47 (108)
T ss_pred cCCCeEEEEEECCCCeEEeeecCCCHHHHHHHHHHHHHHH
Confidence 578876655422 33211 1799999999999999765
No 14
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=32.81 E-value=1.4e+02 Score=22.23 Aligned_cols=49 Identities=14% Similarity=0.162 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHHhhccccCCccceEEEEEecC-ceecCCCCCcceEEE
Q 039507 55 ISEGVLEDCAQLVKANSIQGNKVNNIDVVYTPWA-NLKKTASMDVGQVGF 103 (108)
Q Consensus 55 ~~~~~l~~AA~laa~ySkk~~~~~~v~V~yt~~k-~V~k~~~~~~G~V~~ 103 (108)
++.+.+.+|-.++..++++.+..+.|++..+... ..+|+...-.|.|.+
T Consensus 2 ~~~~~~~eai~~~k~~~~~~kf~esvel~v~Lk~id~~k~~~~irg~i~L 51 (215)
T PRK04203 2 MDREKIEEAVKEALEEAPKRNFTQSVDLIVNLKDIDLKKPENRIDEEVVL 51 (215)
T ss_pred CcHHHHHHHHHHHHHhcccCCCCceEEEEEEecCCCCCccCceeeEEEEC
Confidence 3678899999999987545667889999987732 333433333555544
No 15
>PRK09261 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated
Probab=32.61 E-value=2.7e+02 Score=22.62 Aligned_cols=49 Identities=10% Similarity=0.064 Sum_probs=34.5
Q ss_pred eEEeecCCCccEEEEEcCCCCCCCCCCHHHHHHHHHHHHhhccccCCccceEEEE
Q 039507 30 IWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVY 84 (108)
Q Consensus 30 ~w~H~~~~pG~hviir~~~~~~~~~~~~~~l~~AA~laa~ySkk~~~~~~v~V~y 84 (108)
.++++.+=|-.|+|+|+.... .+.+.++|..|+..... ..-...|=||.
T Consensus 219 ~~i~t~GN~~~hlilRGg~~~--pNy~~~~i~~~~~~l~k----~~l~~~v~VD~ 267 (349)
T PRK09261 219 AIVSTTGNPDCHVILRGGNKG--PNYDAESVAEAKERLEK----AGLPPRIMIDC 267 (349)
T ss_pred EEEECCCCCCEEEEECCCCCC--CCCCHHHHHHHHHHHHH----cCCCCCEEEEC
Confidence 567788889999999986332 26788999888877663 33345565553
No 16
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.62 E-value=1.6e+02 Score=21.20 Aligned_cols=48 Identities=15% Similarity=0.142 Sum_probs=32.4
Q ss_pred EEeCChHHHHHHHHhcCCCceEEeecCCC--------ccEEEEEcCCCCCCCCCCHHHHHHHH
Q 039507 10 FMGLDKYENEELIKYGFPEDIWFHVDKMS--------SAHVYLRLHKGQTIDDISEGVLEDCA 64 (108)
Q Consensus 10 ~vGrn~~eNe~L~k~~~~~D~w~H~~~~p--------G~hviir~~~~~~~~~~~~~~l~~AA 64 (108)
--|.++.++..+ .+++++|+.... |+| |+.|+ ++.|. -.++++|.++-
T Consensus 50 ~~g~DaaD~~Iv-~~a~~gDlVVT~-Di~LA~~ll~kg~~v~--~prGr---~y~~~nI~~~L 105 (150)
T COG1671 50 DAGFDAADDWIV-NLAEKGDLVVTA-DIPLASLLLDKGAAVL--NPRGR---LYTEENIGERL 105 (150)
T ss_pred cCCcchHHHHHH-HhCCCCCEEEEC-chHHHHHHHhcCCEEE--CCCCc---ccCHhHHHHHH
Confidence 347777776654 789999999855 788 33333 44443 67888887653
No 17
>PRK00124 hypothetical protein; Validated
Probab=27.88 E-value=2.2e+02 Score=20.29 Aligned_cols=54 Identities=20% Similarity=0.351 Sum_probs=35.0
Q ss_pred EEEE--eCChHHHHHHHHhcCCCceEEeecCCC--------ccEEEEEcCCCCCCCCCCHHHHHHHHHHHHhh
Q 039507 8 TIFM--GLDKYENEELIKYGFPEDIWFHVDKMS--------SAHVYLRLHKGQTIDDISEGVLEDCAQLVKAN 70 (108)
Q Consensus 8 ~i~v--Grn~~eNe~L~k~~~~~D~w~H~~~~p--------G~hviir~~~~~~~~~~~~~~l~~AA~laa~y 70 (108)
.|+| |.++.++ .|...+.++|+... +|+| |++|| ++.|. ..+++.|.+. |+.+|
T Consensus 47 ~v~V~~g~D~AD~-~Iv~~~~~gDiVIT-~Di~LAa~~l~Kga~vl--~prG~---~yt~~nI~~~--L~~R~ 110 (151)
T PRK00124 47 TVYVDAGFDAADN-EIVQLAEKGDIVIT-QDYGLAALALEKGAIVL--NPRGY---IYTNDNIDQL--LAMRD 110 (151)
T ss_pred EEEeCCCCChHHH-HHHHhCCCCCEEEe-CCHHHHHHHHHCCCEEE--CCCCc---CCCHHHHHHH--HHHHH
Confidence 4667 5566554 34578999999985 4787 45555 44454 7899888654 44443
No 18
>PRK09750 hypothetical protein; Provisional
Probab=25.57 E-value=84 Score=19.30 Aligned_cols=23 Identities=13% Similarity=0.180 Sum_probs=18.4
Q ss_pred ecCceecCCCCCcceEEEecCCC
Q 039507 86 PWANLKKTASMDVGQVGFHNPKM 108 (108)
Q Consensus 86 ~~k~V~k~~~~~~G~V~~~~~k~ 108 (108)
----+.|+.|.+.-.++|++++|
T Consensus 6 I~Ati~KpGg~P~~W~r~s~~~m 28 (64)
T PRK09750 6 ITATIEKEGGTPTNWTRYSKSKL 28 (64)
T ss_pred EEEEEECCCCCccceeEecCCcC
Confidence 33457888889999999999887
No 19
>PF06672 DUF1175: Protein of unknown function (DUF1175); InterPro: IPR009558 This family consists of several hypothetical bacterial proteins of around 210 residues in length. The function of this family is unknown.
Probab=25.48 E-value=94 Score=23.65 Aligned_cols=32 Identities=22% Similarity=0.422 Sum_probs=20.8
Q ss_pred EEEeCChHHHHHHHHhcCCCceEEeecCCCc-c-EEEEEcC
Q 039507 9 IFMGLDKYENEELIKYGFPEDIWFHVDKMSS-A-HVYLRLH 47 (108)
Q Consensus 9 i~vGrn~~eNe~L~k~~~~~D~w~H~~~~pG-~-hviir~~ 47 (108)
.+|||+ +..|+|+||.|--++-++ + |+.|-..
T Consensus 127 ~fvgrd-------l~~A~pGDL~Ff~~~d~~~pfHlMI~~g 160 (216)
T PF06672_consen 127 RFVGRD-------LEQARPGDLLFFHQGDDQMPFHLMIWVG 160 (216)
T ss_pred eeccch-------hhhcCCCcEEEecCCCCCcceEEEEEEc
Confidence 567777 567999996554444455 3 7766653
No 20
>PF00282 Pyridoxal_deC: Pyridoxal-dependent decarboxylase conserved domain; InterPro: IPR002129 Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). Pyridoxal 5'-phosphate (PLP) is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination [, , ]. PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors []. Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy []. PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalysed reactions, enzymatic and non-enzymatic []. A number of pyridoxal-dependent decarboxylases share regions of sequence similarity, particularly in the vicinity of a conserved lysine residue, which provides the attachment site for the pyridoxal-phosphate (PLP) group [, ]. Among these enzymes are aromatic-L-amino-acid decarboxylase (L-dopa decarboxylase or tryptophan decarboxylase), which catalyses the decarboxylation of tryptophan to tryptamine []; tyrosine decarboxylase, which converts tyrosine into tyramine; and histidine decarboxylase, which catalyses the decarboxylation of histidine to histamine []. These enzymes belong to the group II decarboxylases [, ].; GO: 0016831 carboxy-lyase activity, 0030170 pyridoxal phosphate binding, 0019752 carboxylic acid metabolic process; PDB: 3MC6_A 1XEY_A 1ES0_B 2OKK_A 2JIS_B 2QMA_A 3MAF_B 3MAD_B 3MAU_A 3MBB_A ....
Probab=23.80 E-value=34 Score=27.38 Aligned_cols=22 Identities=32% Similarity=0.519 Sum_probs=15.7
Q ss_pred HHHHHhcCCCceEEeecCCCcc
Q 039507 19 EELIKYGFPEDIWFHVDKMSSA 40 (108)
Q Consensus 19 e~L~k~~~~~D~w~H~~~~pG~ 40 (108)
+.|.++++..++|||++..=|.
T Consensus 214 ~~i~~i~~~~~~wlHVDaA~gg 235 (373)
T PF00282_consen 214 EEIADICEKYNIWLHVDAAYGG 235 (373)
T ss_dssp HHHHHHHHHCT-EEEEEETTGG
T ss_pred HHHhhhccccceeeeecccccc
Confidence 3456778889999999865554
No 21
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=23.21 E-value=44 Score=19.60 Aligned_cols=14 Identities=43% Similarity=0.869 Sum_probs=11.2
Q ss_pred CCceEEeecCCCcc
Q 039507 27 PEDIWFHVDKMSSA 40 (108)
Q Consensus 27 ~~D~w~H~~~~pG~ 40 (108)
..|+|||..++.+.
T Consensus 23 ~~diFfh~s~~~~~ 36 (66)
T PF00313_consen 23 GEDIFFHISDLSGN 36 (66)
T ss_dssp SSEEEEEGGGBCSS
T ss_pred ceeEEecccccccc
Confidence 34899999988864
No 22
>PF02056 Glyco_hydro_4: Family 4 glycosyl hydrolase; InterPro: IPR001088 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 4 GH4 from CAZY comprises enzymes with several known activities; 6-phospho-beta-glucosidase (3.2.1.86 from EC); 6-phospho-alpha-glucosidase (3.2.1.122 from EC); alpha-galactosidase (3.2.1.22 from EC). 6-phospho-alpha-glucosidase requires both NAD(H) and divalent metal (Mn2+, Fe2+, Co2+, or Ni2+) for activity [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1U8X_X 1S6Y_A 3FEF_B 1VJT_A 1UP4_A 1UP6_C 1UP7_E 1OBB_A.
Probab=23.01 E-value=1.3e+02 Score=22.09 Aligned_cols=43 Identities=23% Similarity=0.264 Sum_probs=31.7
Q ss_pred eecCCCccEEEEEcCCCCCCCCCCHHHHHHHHHHHHhhccccCCccceEEEEE
Q 039507 33 HVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVYT 85 (108)
Q Consensus 33 H~~~~pG~hviir~~~~~~~~~~~~~~l~~AA~laa~ySkk~~~~~~v~V~yt 85 (108)
+..++++.++.+- +++++.|+....+|.++-+ . ....+.|..|
T Consensus 22 ~~~~l~~~ei~L~--------Did~~RL~~~~~~~~~~~~-~-~~~~~~v~~t 64 (183)
T PF02056_consen 22 RTEELSGSEIVLM--------DIDEERLEIVERLARRMVE-E-AGADLKVEAT 64 (183)
T ss_dssp CTTTSTEEEEEEE---------SCHHHHHHHHHHHHHHHH-H-CTTSSEEEEE
T ss_pred cCccCCCcEEEEE--------cCCHHHHHHHHHHHHHHHH-h-cCCCeEEEEe
Confidence 4567888899888 6899999999999999984 4 2334555544
No 23
>PF05677 DUF818: Chlamydia CHLPS protein (DUF818); InterPro: IPR008536 This family of unknown function includes several Chlamydia CHLPS proteins and Legionella SidB proteins.
Probab=22.79 E-value=1.7e+02 Score=24.07 Aligned_cols=65 Identities=14% Similarity=-0.023 Sum_probs=41.0
Q ss_pred eEEEEeCChHHHHHHHHhcCCCceEEeecCCCccEEEEEcCCCC--CCCCCCHHHHHHHHHHHHhhc
Q 039507 7 YTIFMGLDKYENEELIKYGFPEDIWFHVDKMSSAHVYLRLHKGQ--TIDDISEGVLEDCAQLVKANS 71 (108)
Q Consensus 7 ~~i~vGrn~~eNe~L~k~~~~~D~w~H~~~~pG~hviir~~~~~--~~~~~~~~~l~~AA~laa~yS 71 (108)
..++.+=|...=|.+.-+-..+|.|+-....-|++|++-|-+|- +...++.++|..+++.+++|=
T Consensus 139 WiL~s~GNg~~~E~~~~~~~~~~~~~~~ak~~~aNvl~fNYpGVg~S~G~~s~~dLv~~~~a~v~yL 205 (365)
T PF05677_consen 139 WILVSNGNGECYENRAMLDYKDDWIQRFAKELGANVLVFNYPGVGSSTGPPSRKDLVKDYQACVRYL 205 (365)
T ss_pred EEEEEcCChHHhhhhhhhccccHHHHHHHHHcCCcEEEECCCccccCCCCCCHHHHHHHHHHHHHHH
Confidence 33444444443333211223455666666777888888876532 233688999999999999987
No 24
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=22.74 E-value=42 Score=19.62 Aligned_cols=14 Identities=21% Similarity=0.615 Sum_probs=11.3
Q ss_pred CCceEEeecCCCcc
Q 039507 27 PEDIWFHVDKMSSA 40 (108)
Q Consensus 27 ~~D~w~H~~~~pG~ 40 (108)
..|+|||..++.+.
T Consensus 23 g~diffh~~~~~~~ 36 (65)
T cd04458 23 GEDVFVHISALEGD 36 (65)
T ss_pred CcCEEEEhhHhhcc
Confidence 67999999887753
No 25
>PLN02590 probable tyrosine decarboxylase
Probab=22.59 E-value=31 Score=29.37 Aligned_cols=25 Identities=24% Similarity=0.333 Sum_probs=17.5
Q ss_pred HHHHHhcCCCceEEeecCCCccEEE
Q 039507 19 EELIKYGFPEDIWFHVDKMSSAHVY 43 (108)
Q Consensus 19 e~L~k~~~~~D~w~H~~~~pG~hvi 43 (108)
+.|-+.++..++|||++..=|.-++
T Consensus 307 ~~Ia~i~~~~g~WlHVDaA~GG~al 331 (539)
T PLN02590 307 VPLGNIAKKYGIWLHVDAAYAGNAC 331 (539)
T ss_pred HHHHHHHHHhCCeEEEecchhhhhh
Confidence 3455677889999999865554443
No 26
>COG0078 ArgF Ornithine carbamoyltransferase [Amino acid transport and metabolism]
Probab=21.19 E-value=99 Score=24.77 Aligned_cols=32 Identities=31% Similarity=0.711 Sum_probs=24.5
Q ss_pred HHHHHHhcCCCceEEeecCCCccEEEEEcCCCCCCCCCCHHHHH
Q 039507 18 NEELIKYGFPEDIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLE 61 (108)
Q Consensus 18 Ne~L~k~~~~~D~w~H~~~~pG~hviir~~~~~~~~~~~~~~l~ 61 (108)
|++|...+.++-+++|. .|.-| |. |+++++++
T Consensus 253 n~~lm~~a~~~~ifmHC--LPA~r-------G~---EVTdeV~d 284 (310)
T COG0078 253 NEELMALAGPDAIFMHC--LPAHR-------GE---EVTDEVFE 284 (310)
T ss_pred CHHHHhhcCCCeEEEeC--CCCCC-------CC---ccCHHHhC
Confidence 77888889998899998 67544 22 78888773
No 27
>cd04862 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nu
Probab=20.34 E-value=2.9e+02 Score=21.05 Aligned_cols=52 Identities=15% Similarity=0.116 Sum_probs=33.0
Q ss_pred eEEeecCCCccEEEEEcCCCCCCCCCC-HHHHHHHHHHHHhh------------ccccCCccceEEEEEec
Q 039507 30 IWFHVDKMSSAHVYLRLHKGQTIDDIS-EGVLEDCAQLVKAN------------SIQGNKVNNIDVVYTPW 87 (108)
Q Consensus 30 ~w~H~~~~pG~hviir~~~~~~~~~~~-~~~l~~AA~laa~y------------Skk~~~~~~v~V~yt~~ 87 (108)
-|.-+.+-.|-||++.-.+ ..+ +++-..|-.||..- +| ++-.++|=|||.|-
T Consensus 134 ~~~KTSG~kGlHV~vPl~~-----~~~~~~~r~fa~~lA~~l~~~~P~~~t~~~~k-~~R~gkvfiDylqN 198 (227)
T cd04862 134 SFVKTSGGKGLHVVVPLAP-----RAGWDEVKAFAKALAQHLARTNPDRFVATMGK-AKRVGKIFIDYLRN 198 (227)
T ss_pred cceEccCCCeEEEEEEcCC-----CCCHHHHHHHHHHHHHHHHHHCchhhhHHhhH-HhCCCcEEEECccC
Confidence 4666778888999999865 345 44444444444332 22 33467888888774
Done!