Query 035316
Match_columns 68
No_of_seqs 102 out of 156
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 10:55:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035316.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035316hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02732 Probable NADH dehydro 99.9 3.3E-24 7.2E-29 149.6 6.8 67 2-68 5-72 (159)
2 KOG3382 NADH:ubiquinone oxidor 99.7 1.3E-17 2.9E-22 115.7 3.7 65 2-68 5-69 (151)
3 PRK08183 NADH dehydrogenase; V 99.6 9.7E-17 2.1E-21 109.3 3.1 41 17-63 2-43 (133)
4 COG3761 NADH:ubiquinone oxidor 99.0 3.9E-11 8.4E-16 80.8 -0.8 35 29-68 1-36 (118)
5 PRK06630 hypothetical protein; 99.0 2.3E-10 5E-15 75.4 1.6 24 40-63 6-30 (99)
6 PLN03095 NADH:ubiquinone oxido 98.8 4E-09 8.6E-14 70.7 2.7 24 45-68 9-32 (115)
7 PF05071 NDUFA12: NADH ubiquin 98.6 2.8E-08 6.2E-13 64.3 2.2 17 46-62 1-17 (105)
8 PF15613 WHIM2: WSTF, HB1, Itc 92.7 0.051 1.1E-06 30.2 0.8 14 47-60 3-16 (38)
9 PF03639 Glyco_hydro_81: Glyco 50.3 18 0.00038 30.1 3.0 40 28-67 411-460 (695)
10 cd01717 Sm_B The eukaryotic Sm 49.7 11 0.00023 22.8 1.3 16 46-61 25-40 (79)
11 cd06168 LSm9 The eukaryotic Sm 48.6 16 0.00035 22.3 2.0 18 46-63 25-42 (75)
12 PF11385 DUF3189: Protein of u 46.2 14 0.00031 25.3 1.6 14 47-60 53-66 (148)
13 PRK06842 fumarate hydratase; P 44.2 7.3 0.00016 28.0 -0.0 18 46-63 160-177 (185)
14 PHA02142 putative RNA ligase 43.8 36 0.00078 26.8 3.7 21 45-65 252-272 (366)
15 smart00651 Sm snRNP Sm protein 42.5 15 0.00033 20.7 1.1 18 46-63 23-40 (67)
16 PF06739 SBBP: Beta-propeller 42.1 18 0.00039 19.2 1.3 15 46-60 15-29 (38)
17 COG0708 XthA Exonuclease III [ 40.0 25 0.00054 26.4 2.2 32 4-35 178-209 (261)
18 KOG3382 NADH:ubiquinone oxidor 39.0 46 0.001 23.6 3.3 28 2-29 17-45 (151)
19 smart00604 MD MD domain. 38.8 18 0.00039 25.3 1.2 12 47-58 131-142 (145)
20 cd00600 Sm_like The eukaryotic 38.6 21 0.00046 19.7 1.3 18 46-63 21-38 (63)
21 cd01727 LSm8 The eukaryotic Sm 37.7 21 0.00045 21.3 1.2 18 46-63 24-41 (74)
22 PRK08228 L(+)-tartrate dehydra 36.6 11 0.00023 27.6 -0.2 18 46-63 165-182 (204)
23 TIGR00723 ttdB_fumA_fumB hydro 36.4 22 0.00048 25.2 1.4 15 47-61 154-168 (168)
24 PRK08395 fumarate hydratase; P 33.6 25 0.00055 24.8 1.3 15 46-60 148-162 (162)
25 PF01423 LSM: LSM domain ; In 33.4 23 0.00051 19.9 0.9 18 46-63 23-40 (67)
26 PRK06043 fumarate hydratase; P 31.8 22 0.00047 25.8 0.7 17 46-62 163-179 (192)
27 cd06900 lectin_VcfQ VcfQ bacte 31.6 23 0.0005 26.9 0.9 10 49-58 118-127 (255)
28 COG1838 FumA Tartrate dehydrat 30.3 26 0.00057 25.4 1.0 18 46-63 160-177 (184)
29 cd01729 LSm7 The eukaryotic Sm 30.1 33 0.00071 21.0 1.2 15 46-60 27-41 (81)
30 KOG0766 Predicted mitochondria 28.6 83 0.0018 24.3 3.4 38 2-39 37-74 (297)
31 PF05683 Fumerase_C: Fumarase 27.5 29 0.00063 25.4 0.8 17 46-62 187-203 (205)
32 cd01719 Sm_G The eukaryotic Sm 27.3 39 0.00086 20.2 1.2 18 46-63 25-42 (72)
33 TIGR02242 tail_TIGR02242 phage 26.9 1.3E+02 0.0029 20.0 3.9 47 2-56 75-123 (130)
34 cd01728 LSm1 The eukaryotic Sm 26.8 40 0.00087 20.4 1.2 17 46-62 27-43 (74)
35 cd01731 archaeal_Sm1 The archa 26.4 40 0.00086 19.5 1.1 18 46-63 25-42 (68)
36 PRK00737 small nuclear ribonuc 25.2 51 0.0011 19.5 1.5 17 46-62 29-45 (72)
37 KOG1775 U6 snRNA-associated Sm 21.6 15 0.00033 23.7 -1.4 26 37-62 16-48 (84)
38 PF14563 DUF4444: Domain of un 20.9 58 0.0013 18.6 1.1 10 45-54 11-20 (42)
No 1
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=99.90 E-value=3.3e-24 Score=149.60 Aligned_cols=67 Identities=73% Similarity=1.188 Sum_probs=63.2
Q ss_pred hHHHHHHHHHHhcHHHHHHHHHHcCchhhhcCCcccceeeeecCceEeeeeCCCceeeccCc-cccCC
Q 035316 2 AMKSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKLD-EQFGQ 68 (68)
Q Consensus 2 ~~~~~~~~i~~~G~~~fl~~l~~~G~~~tww~g~t~~t~~~~~~G~lVGeD~~GNkYYE~~~-~~~gr 68 (68)
+|+++|++|+++|++.|+++|+++||++||.||+|++|++|++.|+|||+|+|||||||+.+ ..+||
T Consensus 5 ~~~~~~~~~~~~G~~~~~~~l~~~g~~k~~~~g~t~gt~~~~~~G~lVG~D~~GNkYYE~~~~~~~gr 72 (159)
T PLN02732 5 VVKSALEAIREKGLGGFLRMLREEGYLRCLADGNLLQTKIHNIGATLVGVDKFGNKYYQKLGDTQYGR 72 (159)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHccchhhccCcceeeeEEEeeCcEEEEecCCCCeeeecCCCCCCCc
Confidence 68999999999999999999999999999999999999999999999999999999999874 56665
No 2
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=99.69 E-value=1.3e-17 Score=115.72 Aligned_cols=65 Identities=52% Similarity=0.841 Sum_probs=59.9
Q ss_pred hHHHHHHHHHHhcHHHHHHHHHHcCchhhhcCCcccceeeeecCceEeeeeCCCceeeccCccccCC
Q 035316 2 AMKSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKLDEQFGQ 68 (68)
Q Consensus 2 ~~~~~~~~i~~~G~~~fl~~l~~~G~~~tww~g~t~~t~~~~~~G~lVGeD~~GNkYYE~~~~~~gr 68 (68)
|.+++++.+...|+.+|+.+++++|.++|..+ +.+.|..|.+ |+|||+|+||||||||+++||||
T Consensus 5 ~~~s~~~~l~i~~l~k~~qmire~Gglr~~~~-k~yrtd~~ki-GTLVG~DkfGNkYyen~~~fygR 69 (151)
T KOG3382|consen 5 VAKSALEALGIKGLGKFMQMIREEGGLRCLLD-KLYRTDDHKI-GTLVGVDKFGNKYYENNDYFYGR 69 (151)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhhccHHHHHH-HHHhcccccc-eeeeeecccccchhcccceeccc
Confidence 56788999999999999999999999999998 7888877777 89999999999999999999998
No 3
>PRK08183 NADH dehydrogenase; Validated
Probab=99.64 E-value=9.7e-17 Score=109.28 Aligned_cols=41 Identities=32% Similarity=0.566 Sum_probs=37.3
Q ss_pred HHHHHHHHcCchhhhcCCcccceeeeec-CceEeeeeCCCceeeccCc
Q 035316 17 SFLRELKEEGFLRALLDGNLMQTKLHNR-GATLVGVDKFGNKYYQKLD 63 (68)
Q Consensus 17 ~fl~~l~~~G~~~tww~g~t~~t~~~~~-~G~lVGeD~~GNkYYE~~~ 63 (68)
++|.++ +|||+|+|++|+|+++ .|+|||+|++||||||+.+
T Consensus 2 ~~~~~i------f~ww~g~t~~t~~~~~r~g~lVG~D~~GNkYYE~~~ 43 (133)
T PRK08183 2 SFLLQI------FTWWNGQTLGTRFFTWRKGERVGEDEFGNVYYRTKG 43 (133)
T ss_pred cHHHHH------HHHhccCchhheeehhccCeEeEecCCCCeeeecCC
Confidence 466777 9999999999999999 5999999999999999766
No 4
>COG3761 NADH:ubiquinone oxidoreductase 17.2 kD subunit [Energy production and conversion]
Probab=99.00 E-value=3.9e-11 Score=80.81 Aligned_cols=35 Identities=31% Similarity=0.530 Sum_probs=29.7
Q ss_pred hhhcCCcccceeeeecCceEeeeeCCCceeecc-CccccCC
Q 035316 29 RALLDGNLMQTKLHNRGATLVGVDKFGNKYYQK-LDEQFGQ 68 (68)
Q Consensus 29 ~tww~g~t~~t~~~~~~G~lVGeD~~GNkYYE~-~~~~~gr 68 (68)
+|||| ++++|+|| +.||||||||.|||. +....||
T Consensus 1 ftWwn-qt~gTrfh----~kvGeDefgN~Yye~r~~ds~gr 36 (118)
T COG3761 1 FTWWN-QTFGTRFH----KKVGEDEFGNVYYEGRNIDSEGR 36 (118)
T ss_pred CchHH-hHHHHHHH----HhccchhccceeeeccCCccCCC
Confidence 48999 99999999 679999999999997 4455555
No 5
>PRK06630 hypothetical protein; Provisional
Probab=98.96 E-value=2.3e-10 Score=75.45 Aligned_cols=24 Identities=33% Similarity=0.465 Sum_probs=20.9
Q ss_pred eeeec-CceEeeeeCCCceeeccCc
Q 035316 40 KLHNR-GATLVGVDKFGNKYYQKLD 63 (68)
Q Consensus 40 ~~~~~-~G~lVGeD~~GNkYYE~~~ 63 (68)
+|+|+ .|+|||+|+|||+|||+.+
T Consensus 6 ~~~t~r~G~lVG~D~~GNkYYE~~~ 30 (99)
T PRK06630 6 KFFITFFHKKVGEDEFLNQYYESRN 30 (99)
T ss_pred hhhhhccCeEeEEeCCCChhcccCC
Confidence 57777 5999999999999999854
No 6
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=98.78 E-value=4e-09 Score=70.75 Aligned_cols=24 Identities=50% Similarity=0.847 Sum_probs=20.8
Q ss_pred CceEeeeeCCCceeeccCccccCC
Q 035316 45 GATLVGVDKFGNKYYQKLDEQFGQ 68 (68)
Q Consensus 45 ~G~lVGeD~~GNkYYE~~~~~~gr 68 (68)
.|+|||+|+|||||||+.++..||
T Consensus 9 ~g~lVG~D~~GNkYYE~~~~~~~r 32 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPSYQSGR 32 (115)
T ss_pred cceEeEEcCCCCeeeEcCCCCCCC
Confidence 699999999999999988766554
No 7
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=98.58 E-value=2.8e-08 Score=64.30 Aligned_cols=17 Identities=65% Similarity=1.161 Sum_probs=16.1
Q ss_pred ceEeeeeCCCceeeccC
Q 035316 46 ATLVGVDKFGNKYYQKL 62 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~ 62 (68)
|+|||+|++||+|||+.
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999999987
No 8
>PF15613 WHIM2: WSTF, HB1, Itc1p, MBD9 motif 2
Probab=92.73 E-value=0.051 Score=30.18 Aligned_cols=14 Identities=36% Similarity=0.935 Sum_probs=12.1
Q ss_pred eEeeeeCCCceeec
Q 035316 47 TLVGVDKFGNKYYQ 60 (68)
Q Consensus 47 ~lVGeD~~GNkYYE 60 (68)
+.+|.|.+||+||-
T Consensus 3 ~pLG~DR~~NrYww 16 (38)
T PF15613_consen 3 KPLGKDRYGNRYWW 16 (38)
T ss_pred ccccccCCCceEEE
Confidence 46899999999985
No 9
>PF03639 Glyco_hydro_81: Glycosyl hydrolase family 81 ; InterPro: IPR005200 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This is a family of eukaryotic beta-1,3-glucanases belonging to glycoside hydrolase family 81 (GH81 from CAZY).; GO: 0033903 endo-1,3(4)-beta-glucanase activity, 0016998 cell wall macromolecule catabolic process
Probab=50.34 E-value=18 Score=30.05 Aligned_cols=40 Identities=28% Similarity=0.463 Sum_probs=30.6
Q ss_pred hhhhcCCcccceeeeec--CceEeee--------eCCCceeeccCccccC
Q 035316 28 LRALLDGNLMQTKLHNR--GATLVGV--------DKFGNKYYQKLDEQFG 67 (68)
Q Consensus 28 ~~tww~g~t~~t~~~~~--~G~lVGe--------D~~GNkYYE~~~~~~g 67 (68)
+..|+.+++-.-.|..- -|.+|+. ..|||-||-|-.+.||
T Consensus 411 ~~~~f~~n~~~~~l~YD~~wgglis~~~~~~d~~~dfGn~~yNDHHfHYG 460 (695)
T PF03639_consen 411 LFDWFTGNTQKNPLVYDTTWGGLISSAYGSGDPNADFGNTYYNDHHFHYG 460 (695)
T ss_pred HHHHHhccCCCCccEeccccCeEEeccccCCCCccccCcccccccccchH
Confidence 47888888766666333 3889998 5899999998877776
No 10
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=49.71 E-value=11 Score=22.77 Aligned_cols=16 Identities=19% Similarity=0.220 Sum_probs=13.4
Q ss_pred ceEeeeeCCCceeecc
Q 035316 46 ATLVGVDKFGNKYYQK 61 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~ 61 (68)
|+|+|.|++.|-=-++
T Consensus 25 G~L~~~D~~~NlVL~~ 40 (79)
T cd01717 25 GQFLAFDKHMNLVLSD 40 (79)
T ss_pred EEEEEEcCccCEEcCC
Confidence 9999999999975443
No 11
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=48.58 E-value=16 Score=22.26 Aligned_cols=18 Identities=11% Similarity=0.058 Sum_probs=14.5
Q ss_pred ceEeeeeCCCceeeccCc
Q 035316 46 ATLVGVDKFGNKYYQKLD 63 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~~ 63 (68)
|+|.+.|+++|-=-++..
T Consensus 25 G~l~~~D~~~NivL~~~~ 42 (75)
T cd06168 25 GVFLCTDRDCNIILGSAQ 42 (75)
T ss_pred EEEEEEcCCCcEEecCcE
Confidence 999999999997655443
No 12
>PF11385 DUF3189: Protein of unknown function (DUF3189); InterPro: IPR021525 This family of proteins with unknown function appears to be restricted to Firmicutes
Probab=46.17 E-value=14 Score=25.30 Aligned_cols=14 Identities=36% Similarity=0.833 Sum_probs=12.1
Q ss_pred eEeeeeCCCceeec
Q 035316 47 TLVGVDKFGNKYYQ 60 (68)
Q Consensus 47 ~lVGeD~~GNkYYE 60 (68)
..+|+|++||.=|-
T Consensus 53 ~y~G~De~gn~VY~ 66 (148)
T PF11385_consen 53 IYMGTDEYGNEVYI 66 (148)
T ss_pred EEEEEcCCCCEEEE
Confidence 48999999998775
No 13
>PRK06842 fumarate hydratase; Provisional
Probab=44.21 E-value=7.3 Score=28.03 Aligned_cols=18 Identities=28% Similarity=0.373 Sum_probs=15.5
Q ss_pred ceEeeeeCCCceeeccCc
Q 035316 46 ATLVGVDKFGNKYYQKLD 63 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~~ 63 (68)
=-.|..|.+||..|+...
T Consensus 160 P~iV~iD~~Gn~ly~~~~ 177 (185)
T PRK06842 160 PVVVIIDSEGNNLYEIGQ 177 (185)
T ss_pred CEEEEEeCCCccHHHHhH
Confidence 568999999999999654
No 14
>PHA02142 putative RNA ligase
Probab=43.76 E-value=36 Score=26.81 Aligned_cols=21 Identities=14% Similarity=-0.029 Sum_probs=17.3
Q ss_pred CceEeeeeCCCceeeccCccc
Q 035316 45 GATLVGVDKFGNKYYQKLDEQ 65 (68)
Q Consensus 45 ~G~lVGeD~~GNkYYE~~~~~ 65 (68)
-|++||..-+||.||-....|
T Consensus 252 qGEl~Gp~IQ~N~~~~~~~~F 272 (366)
T PHA02142 252 QGELMGPGIQKNRENFDKYRI 272 (366)
T ss_pred EEEEecccccCccccCCCCce
Confidence 399999999999999854433
No 15
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=42.47 E-value=15 Score=20.68 Aligned_cols=18 Identities=33% Similarity=0.538 Sum_probs=15.3
Q ss_pred ceEeeeeCCCceeeccCc
Q 035316 46 ATLVGVDKFGNKYYQKLD 63 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~~ 63 (68)
|+|++.|++.|-.-++..
T Consensus 23 G~L~~~D~~~NlvL~~~~ 40 (67)
T smart00651 23 GTLKGFDQFMNLVLEDVE 40 (67)
T ss_pred EEEEEECccccEEEccEE
Confidence 999999999998876543
No 16
>PF06739 SBBP: Beta-propeller repeat; InterPro: IPR010620 This family is related to IPR001680 from INTERPRO and is likely to also form a beta-propeller. SBBP stands for Seven Bladed Beta Propeller.
Probab=42.06 E-value=18 Score=19.21 Aligned_cols=15 Identities=33% Similarity=0.452 Sum_probs=12.8
Q ss_pred ceEeeeeCCCceeec
Q 035316 46 ATLVGVDKFGNKYYQ 60 (68)
Q Consensus 46 G~lVGeD~~GNkYYE 60 (68)
+.=|..|..||.|--
T Consensus 15 ~~~IavD~~GNiYv~ 29 (38)
T PF06739_consen 15 GNGIAVDSNGNIYVT 29 (38)
T ss_pred EEEEEECCCCCEEEE
Confidence 667899999999965
No 17
>COG0708 XthA Exonuclease III [DNA replication, recombination, and repair]
Probab=40.00 E-value=25 Score=26.41 Aligned_cols=32 Identities=13% Similarity=0.102 Sum_probs=28.2
Q ss_pred HHHHHHHHHhcHHHHHHHHHHcCchhhhcCCc
Q 035316 4 KSALKSIRERGLGSFLRELKEEGFLRALLDGN 35 (68)
Q Consensus 4 ~~~~~~i~~~G~~~fl~~l~~~G~~~tww~g~ 35 (68)
|..+..+.+.|+-..+|++.-++...|||+-.
T Consensus 178 R~~~~~ll~~G~~D~~R~~~p~~~~YTwW~YR 209 (261)
T COG0708 178 RAWFRRLLNAGFVDTFRLFHPEPEKYTWWDYR 209 (261)
T ss_pred HHHHHHHHHcchhhhhHhhCCCCCcccccccc
Confidence 67788999999999999999999989999743
No 18
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=38.98 E-value=46 Score=23.56 Aligned_cols=28 Identities=25% Similarity=0.368 Sum_probs=23.0
Q ss_pred hHHHHHHHHHHh-cHHHHHHHHHHcCchh
Q 035316 2 AMKSALKSIRER-GLGSFLRELKEEGFLR 29 (68)
Q Consensus 2 ~~~~~~~~i~~~-G~~~fl~~l~~~G~~~ 29 (68)
.+.+.++.|++. |++..++.+....+.+
T Consensus 17 ~l~k~~qmire~Gglr~~~~k~yrtd~~k 45 (151)
T KOG3382|consen 17 GLGKFMQMIREEGGLRCLLDKLYRTDDHK 45 (151)
T ss_pred HHHHHHHHHHhhccHHHHHHHHHhccccc
Confidence 467899999999 8899999887776644
No 19
>smart00604 MD MD domain.
Probab=38.80 E-value=18 Score=25.28 Aligned_cols=12 Identities=33% Similarity=0.626 Sum_probs=10.5
Q ss_pred eEeeeeCCCcee
Q 035316 47 TLVGVDKFGNKY 58 (68)
Q Consensus 47 ~lVGeD~~GNkY 58 (68)
.++|+|++||.|
T Consensus 131 ~i~G~D~~G~~F 142 (145)
T smart00604 131 LIDGVDENGYNF 142 (145)
T ss_pred EEEeecCCCcee
Confidence 478999999987
No 20
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=38.58 E-value=21 Score=19.69 Aligned_cols=18 Identities=28% Similarity=0.455 Sum_probs=14.9
Q ss_pred ceEeeeeCCCceeeccCc
Q 035316 46 ATLVGVDKFGNKYYQKLD 63 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~~ 63 (68)
|++++.|++.|---++..
T Consensus 21 G~L~~~D~~~Ni~L~~~~ 38 (63)
T cd00600 21 GVLVAFDKYMNLVLDDVE 38 (63)
T ss_pred EEEEEECCCCCEEECCEE
Confidence 999999999998766543
No 21
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=37.75 E-value=21 Score=21.27 Aligned_cols=18 Identities=28% Similarity=0.289 Sum_probs=15.0
Q ss_pred ceEeeeeCCCceeeccCc
Q 035316 46 ATLVGVDKFGNKYYQKLD 63 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~~ 63 (68)
|+|.|.|++.|--=++..
T Consensus 24 G~L~~~D~~~NlvL~~~~ 41 (74)
T cd01727 24 GTLKGFDQATNLILDDSH 41 (74)
T ss_pred EEEEEEccccCEEccceE
Confidence 999999999998766543
No 22
>PRK08228 L(+)-tartrate dehydratase subunit beta; Validated
Probab=36.62 E-value=11 Score=27.63 Aligned_cols=18 Identities=22% Similarity=0.558 Sum_probs=14.9
Q ss_pred ceEeeeeCCCceeeccCc
Q 035316 46 ATLVGVDKFGNKYYQKLD 63 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~~ 63 (68)
=-+|..|.+||..|+...
T Consensus 165 P~iV~iD~~Gn~ly~~~~ 182 (204)
T PRK08228 165 PLIVSIDTHGNNLFEENK 182 (204)
T ss_pred ceEEEEECCCccHHHHHH
Confidence 348999999999998654
No 23
>TIGR00723 ttdB_fumA_fumB hydro-lyases, Fe-S type, tartrate/fumarate subfamily, beta region. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase. This model represents a subset of closely related proteins or modules, including the E. coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of archaeal proteins in this subfamily has not been established.
Probab=36.41 E-value=22 Score=25.19 Aligned_cols=15 Identities=33% Similarity=0.711 Sum_probs=13.1
Q ss_pred eEeeeeCCCceeecc
Q 035316 47 TLVGVDKFGNKYYQK 61 (68)
Q Consensus 47 ~lVGeD~~GNkYYE~ 61 (68)
-.|..|..||..|+.
T Consensus 154 liV~iDs~Gn~ly~~ 168 (168)
T TIGR00723 154 LIVAIDSHGNSIFQE 168 (168)
T ss_pred EEEEEECCCCccccC
Confidence 489999999999973
No 24
>PRK08395 fumarate hydratase; Provisional
Probab=33.61 E-value=25 Score=24.75 Aligned_cols=15 Identities=33% Similarity=0.618 Sum_probs=13.1
Q ss_pred ceEeeeeCCCceeec
Q 035316 46 ATLVGVDKFGNKYYQ 60 (68)
Q Consensus 46 G~lVGeD~~GNkYYE 60 (68)
=-.|..|..||..|+
T Consensus 148 P~iV~iDs~Gn~ly~ 162 (162)
T PRK08395 148 PLLVAIDSKGRSLYR 162 (162)
T ss_pred cEEEEEeCCCCcccC
Confidence 458999999999885
No 25
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=33.39 E-value=23 Score=19.94 Aligned_cols=18 Identities=33% Similarity=0.440 Sum_probs=14.5
Q ss_pred ceEeeeeCCCceeeccCc
Q 035316 46 ATLVGVDKFGNKYYQKLD 63 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~~ 63 (68)
|++++.|++.|---++..
T Consensus 23 G~L~~~D~~~Nl~L~~~~ 40 (67)
T PF01423_consen 23 GTLVSFDQFMNLVLSDVT 40 (67)
T ss_dssp EEEEEEETTEEEEEEEEE
T ss_pred EEEEEeechheEEeeeEE
Confidence 999999999997665433
No 26
>PRK06043 fumarate hydratase; Provisional
Probab=31.85 E-value=22 Score=25.82 Aligned_cols=17 Identities=35% Similarity=0.741 Sum_probs=14.3
Q ss_pred ceEeeeeCCCceeeccC
Q 035316 46 ATLVGVDKFGNKYYQKL 62 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~ 62 (68)
=-+|..|..||..||..
T Consensus 163 P~iV~iD~~Gn~ly~~~ 179 (192)
T PRK06043 163 PLIVGIDAKGNDLYSEV 179 (192)
T ss_pred ceEEEEeCCCccHHHHH
Confidence 34899999999999853
No 27
>cd06900 lectin_VcfQ VcfQ bacterial pilus biogenesis protein, lectin domain. This family includes bacterial proteins homologous to the VcfQ (also known as MshQ) bacterial pilus biogenesis protein. VcfQ is encoded by the vcfQ gene of the type IV pilus gene cluster of Vibrio cholerae and is essential for type IV pilus assembly. VcfQ has a Laminin G-like domain as well as an L-type lectin domain.
Probab=31.56 E-value=23 Score=26.92 Aligned_cols=10 Identities=40% Similarity=0.923 Sum_probs=8.8
Q ss_pred eeeeCCCcee
Q 035316 49 VGVDKFGNKY 58 (68)
Q Consensus 49 VGeD~~GNkY 58 (68)
||.|||||-.
T Consensus 118 iGlDEyGNFs 127 (255)
T cd06900 118 IGLDEYGNFS 127 (255)
T ss_pred EEEecccccc
Confidence 8999999954
No 28
>COG1838 FumA Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain [Energy production and conversion]
Probab=30.29 E-value=26 Score=25.41 Aligned_cols=18 Identities=22% Similarity=0.436 Sum_probs=15.2
Q ss_pred ceEeeeeCCCceeeccCc
Q 035316 46 ATLVGVDKFGNKYYQKLD 63 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~~ 63 (68)
-..|..|..||.+|+...
T Consensus 160 PliV~iDs~Gn~~~~~~~ 177 (184)
T COG1838 160 PLIVAIDSKGNSLFKEGP 177 (184)
T ss_pred cEEEEEeCCCcChhhhcc
Confidence 458999999999998654
No 29
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=30.11 E-value=33 Score=21.00 Aligned_cols=15 Identities=27% Similarity=0.290 Sum_probs=12.6
Q ss_pred ceEeeeeCCCceeec
Q 035316 46 ATLVGVDKFGNKYYQ 60 (68)
Q Consensus 46 G~lVGeD~~GNkYYE 60 (68)
|+|.|-|+|-|-=-+
T Consensus 27 G~L~~~D~~mNlvL~ 41 (81)
T cd01729 27 GILKGYDQLLNLVLD 41 (81)
T ss_pred EEEEEEcCcccEEec
Confidence 999999999996443
No 30
>KOG0766 consensus Predicted mitochondrial carrier protein [Energy production and conversion]
Probab=28.55 E-value=83 Score=24.34 Aligned_cols=38 Identities=24% Similarity=0.315 Sum_probs=32.3
Q ss_pred hHHHHHHHHHHhcHHHHHHHHHHcCchhhhcCCcccce
Q 035316 2 AMKSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQT 39 (68)
Q Consensus 2 ~~~~~~~~i~~~G~~~fl~~l~~~G~~~tww~g~t~~t 39 (68)
+++--+++.++.|+.+-++++..++.+.-.|+|-....
T Consensus 37 LLKTR~Qq~qr~~l~k~l~~iv~~~s~l~LWkGtlPSi 74 (297)
T KOG0766|consen 37 LLKTRLQQLQRVGLLKVLLKIVRTESLLGLWKGTLPSI 74 (297)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHhccchHHhhcccchhh
Confidence 45667899999999999999999999999999976543
No 31
>PF05683 Fumerase_C: Fumarase C-terminus; InterPro: IPR004647 This entry represents various Fe-S type hydro-lyases, including the beta subunit from both L-tartrate dehydratase (TtdB; EC:4.2.1.32) and class 2 fumarate hydratase (FumC; (4.2.1.2 from EC) []. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see IPR000362 from INTERPRO). Proteins in this group represent a subset of closely related proteins or modules, including the Escherichia coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of the archaeal proteins in this group is unknown.; GO: 0016836 hydro-lyase activity; PDB: 2ISB_A.
Probab=27.52 E-value=29 Score=25.36 Aligned_cols=17 Identities=29% Similarity=0.716 Sum_probs=10.5
Q ss_pred ceEeeeeCCCceeeccC
Q 035316 46 ATLVGVDKFGNKYYQKL 62 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~ 62 (68)
=..|..|.+||..|+..
T Consensus 187 P~iVaiD~~G~~ly~~~ 203 (205)
T PF05683_consen 187 PLIVAIDSHGNSLYEEV 203 (205)
T ss_dssp EEEEEE-TTS-BTT---
T ss_pred CEEEEEeCCCCchhhcc
Confidence 35899999999999864
No 32
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=27.26 E-value=39 Score=20.18 Aligned_cols=18 Identities=28% Similarity=0.263 Sum_probs=15.3
Q ss_pred ceEeeeeCCCceeeccCc
Q 035316 46 ATLVGVDKFGNKYYQKLD 63 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~~ 63 (68)
|+|+|-|++-|---++..
T Consensus 25 G~L~~~D~~mNlvL~~~~ 42 (72)
T cd01719 25 GILRGFDPFMNLVLDDAV 42 (72)
T ss_pred EEEEEEcccccEEeccEE
Confidence 999999999998776543
No 33
>TIGR02242 tail_TIGR02242 phage tail protein domain. This model describes a region of sequence similarity shared by a number of uncharacterized proteins in bacterial genomes, including Geobacter sulfurreducens PCA, Mesorhizobium loti, Streptomyces coelicolor A3(2), Gloeobacter violaceus PCC 7421, and Myxococcus xanthus. In all cases, the genomic region resembles a phage tail region, based on tentative identifications of neighboring genes. A region of this domain resembles a region of TIGR01634, another phage tail protein model.
Probab=26.91 E-value=1.3e+02 Score=19.98 Aligned_cols=47 Identities=34% Similarity=0.349 Sum_probs=28.5
Q ss_pred hHHHHHHHHHHhcHHHHHHHHHHcCchhhhcCCcccceeeeec--CceEeeeeCCCc
Q 035316 2 AMKSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNR--GATLVGVDKFGN 56 (68)
Q Consensus 2 ~~~~~~~~i~~~G~~~fl~~l~~~G~~~tww~g~t~~t~~~~~--~G~lVGeD~~GN 56 (68)
+|++++...+.+|=+..++++.+. .-|... .+..+ ..+.+|+|.+|-
T Consensus 75 ~I~~a~~l~r~rGT~~gLr~~l~~------~~G~~~--~i~E~f~~~~~~~~~~~~~ 123 (130)
T TIGR02242 75 LVARAADIYRQRGTRLGLRELLRL------YLGIEP--RIVEPFASDTLVGEDEFGV 123 (130)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHH------hcCCCc--EEeeehhcccccccccccc
Confidence 577888888888877777777442 111111 22222 266668888774
No 34
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=26.76 E-value=40 Score=20.45 Aligned_cols=17 Identities=29% Similarity=0.366 Sum_probs=14.3
Q ss_pred ceEeeeeCCCceeeccC
Q 035316 46 ATLVGVDKFGNKYYQKL 62 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~ 62 (68)
|+|.|-|+|+|---++.
T Consensus 27 G~L~~fD~~~NlvL~d~ 43 (74)
T cd01728 27 GILRSFDQFANLVLQDT 43 (74)
T ss_pred EEEEEECCcccEEecce
Confidence 99999999999766544
No 35
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=26.36 E-value=40 Score=19.54 Aligned_cols=18 Identities=17% Similarity=0.165 Sum_probs=15.2
Q ss_pred ceEeeeeCCCceeeccCc
Q 035316 46 ATLVGVDKFGNKYYQKLD 63 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~~ 63 (68)
|+|.|.|++-|---++..
T Consensus 25 G~L~~~D~~mNlvL~~~~ 42 (68)
T cd01731 25 GRLKSYDQHMNLVLEDAE 42 (68)
T ss_pred EEEEEECCcceEEEeeEE
Confidence 999999999998776543
No 36
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=25.24 E-value=51 Score=19.47 Aligned_cols=17 Identities=24% Similarity=0.169 Sum_probs=14.4
Q ss_pred ceEeeeeCCCceeeccC
Q 035316 46 ATLVGVDKFGNKYYQKL 62 (68)
Q Consensus 46 G~lVGeD~~GNkYYE~~ 62 (68)
|+|+|.|++=|---++.
T Consensus 29 G~L~~~D~~mNlvL~d~ 45 (72)
T PRK00737 29 GELQGYDIHMNLVLDNA 45 (72)
T ss_pred EEEEEEcccceeEEeeE
Confidence 99999999999776654
No 37
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=21.61 E-value=15 Score=23.70 Aligned_cols=26 Identities=31% Similarity=0.446 Sum_probs=18.4
Q ss_pred cceeeeec--C-----ceEeeeeCCCceeeccC
Q 035316 37 MQTKLHNR--G-----ATLVGVDKFGNKYYQKL 62 (68)
Q Consensus 37 ~~t~~~~~--~-----G~lVGeD~~GNkYYE~~ 62 (68)
++.++|.. + |+|||-|.|=|---|+.
T Consensus 16 Igski~iimksdkE~~GtL~GFDd~VNmvLeDv 48 (84)
T KOG1775|consen 16 IGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDV 48 (84)
T ss_pred cCceEEEEEccCceeeeEEechHHHHHHHHHhh
Confidence 44556554 1 99999999988766643
No 38
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=20.94 E-value=58 Score=18.64 Aligned_cols=10 Identities=40% Similarity=0.571 Sum_probs=7.5
Q ss_pred CceEeeeeCC
Q 035316 45 GATLVGVDKF 54 (68)
Q Consensus 45 ~G~lVGeD~~ 54 (68)
.|+++|.||.
T Consensus 11 tGtFlGvDE~ 20 (42)
T PF14563_consen 11 TGTFLGVDED 20 (42)
T ss_dssp EEEEEEE-TT
T ss_pred ceeEEeeccc
Confidence 3999999984
Done!