Query 043344
Match_columns 194
No_of_seqs 124 out of 227
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 04:06:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043344.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043344hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01568 A_thal_3678 uncharac 100.0 2.1E-36 4.6E-41 218.5 8.0 66 116-184 1-66 (66)
2 PF04844 Ovate: Transcriptiona 100.0 1.5E-33 3.3E-38 199.6 7.5 59 122-184 1-59 (59)
3 smart00544 MA3 Domain in DAP-5 80.7 3.3 7.2E-05 30.7 4.4 46 129-180 1-46 (113)
4 cd00982 gltB_C gltb_C. This do 59.5 7.4 0.00016 34.9 2.4 65 111-179 177-242 (251)
5 PF02847 MA3: MA3 domain; Int 53.6 24 0.00051 26.0 4.0 43 129-177 1-43 (113)
6 PF14551 MCM_N: MCM N-terminal 50.4 32 0.00069 25.3 4.2 54 129-183 18-74 (121)
7 PF04716 ETC_C1_NDUFA5: ETC co 46.5 12 0.00027 26.3 1.4 31 128-158 26-57 (57)
8 PRK10072 putative transcriptio 35.5 34 0.00074 26.2 2.4 20 123-142 4-23 (96)
9 PRK10548 flagellar biosynthesi 33.8 69 0.0015 25.6 4.0 56 126-185 11-74 (121)
10 COG0337 AroB 3-dehydroquinate 28.7 69 0.0015 30.3 3.7 50 122-173 170-219 (360)
11 KOG1497 COP9 signalosome, subu 26.3 89 0.0019 30.0 3.9 50 132-182 5-54 (399)
12 TIGR02908 CoxD_Bacillus cytoch 24.5 76 0.0016 25.4 2.7 27 156-182 72-98 (110)
13 PF09177 Syntaxin-6_N: Syntaxi 23.7 3.1E+02 0.0067 20.3 6.2 32 124-167 1-32 (97)
14 PF02847 MA3: MA3 domain; Int 23.4 2E+02 0.0043 21.0 4.7 54 128-182 32-85 (113)
15 cd03331 Macro_Poa1p_like_SNF2 23.3 1.6E+02 0.0034 24.2 4.5 38 125-162 102-151 (152)
16 PF05400 FliT: Flagellar prote 23.2 1E+02 0.0022 21.1 3.0 16 147-162 8-23 (84)
17 PF02979 NHase_alpha: Nitrile 22.5 1.1E+02 0.0025 26.6 3.6 47 127-177 6-53 (188)
18 smart00544 MA3 Domain in DAP-5 22.3 2.4E+02 0.0053 20.6 5.0 55 128-183 32-86 (113)
19 PF02337 Gag_p10: Retroviral G 20.6 1.8E+02 0.0039 22.3 4.0 34 127-163 8-41 (90)
20 cd03154 TM4SF3_like_LEL Tetras 20.3 42 0.00091 24.1 0.5 36 123-158 9-46 (100)
No 1
>TIGR01568 A_thal_3678 uncharacterized plant-specific domain TIGR01568. This model describes an uncharacterized domain of about 70 residues found exclusively in plants, generally toward the C-terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence.
Probab=100.00 E-value=2.1e-36 Score=218.45 Aligned_cols=66 Identities=61% Similarity=1.062 Sum_probs=63.1
Q ss_pred EEEeccCCCcHHHHHHHHHHHHHhcCCCCcCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHHHHhcC
Q 043344 116 VAVPTDSPDPYVDFRRSMQEMVEARDLFDVKANWDCLHELLLCYLALNPKTTHKFIISAFADLLVSLMS 184 (194)
Q Consensus 116 vAV~k~S~DPy~DFR~SM~EMI~e~~l~~~~~dw~~LeELL~cYL~LN~~~~H~~Iv~AF~Dl~~~L~s 184 (194)
|||+|+|.|||.|||+||+|||+++|+. .+|++|||||+|||+||+++||++|++||+|||++|++
T Consensus 1 vAv~k~S~DPy~DFr~SM~EMI~~~~i~---~~w~~LeeLL~cYL~LN~~~~H~~Iv~AF~dl~~~L~~ 66 (66)
T TIGR01568 1 VAVAKESDDPYEDFRRSMEEMIEERELE---ADWKELEELLACYLDLNPKKSHRFIVRAFVDILSALLS 66 (66)
T ss_pred CeeeeCCCChHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHHHHhCCchhhhHHHHHHHHHHHHHhC
Confidence 6999999999999999999999999985 36999999999999999999999999999999999974
No 2
>PF04844 Ovate: Transcriptional repressor, ovate; InterPro: IPR006458 This group of sequences contain an uncharacterised domain of about 70 residues found exclusively in plants, generally toward the C terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana (Mouse-ear cress). Other regions of these proteins tend to consist largely of low-complexity sequence. Function is not known.
Probab=100.00 E-value=1.5e-33 Score=199.59 Aligned_cols=59 Identities=56% Similarity=0.969 Sum_probs=56.8
Q ss_pred CCCcHHHHHHHHHHHHHhcCCCCcCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHHHHhcC
Q 043344 122 SPDPYVDFRRSMQEMVEARDLFDVKANWDCLHELLLCYLALNPKTTHKFIISAFADLLVSLMS 184 (194)
Q Consensus 122 S~DPy~DFR~SM~EMI~e~~l~~~~~dw~~LeELL~cYL~LN~~~~H~~Iv~AF~Dl~~~L~s 184 (194)
|.|||+|||+||+|||+++|++ +|++|||||+|||+||+++||++||+||+|||.+|++
T Consensus 1 S~DP~~DFr~SM~EMI~~~~i~----~~~~LeeLL~cYL~LN~~~~H~~Iv~aF~dv~~~l~s 59 (59)
T PF04844_consen 1 SSDPYEDFRESMVEMIEENGIR----DWDDLEELLACYLSLNSPEHHKFIVEAFVDVWVELFS 59 (59)
T ss_pred CCCHHHHHHHHHHHHHHHcCCC----CHHHHHHHHHHHHHhCChhhhhHHHHHHHHHHHHHhC
Confidence 7899999999999999999997 4999999999999999999999999999999999975
No 3
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=80.73 E-value=3.3 Score=30.72 Aligned_cols=46 Identities=13% Similarity=0.202 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhcCCCCcCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHHH
Q 043344 129 FRRSMQEMVEARDLFDVKANWDCLHELLLCYLALNPKTTHKFIISAFADLLV 180 (194)
Q Consensus 129 FR~SM~EMI~e~~l~~~~~dw~~LeELL~cYL~LN~~~~H~~Iv~AF~Dl~~ 180 (194)
||+.+...|++---. .+.+|...|.+.||.+.+|+.++...+..+.
T Consensus 1 ~~k~i~~~l~ey~~~------~D~~ea~~~l~~L~~~~~~~~vv~~~i~~~l 46 (113)
T smart00544 1 LKKKIFLIIEEYLSS------GDTDEAVHCLLELKLPEQHHEVVKVLLTCAL 46 (113)
T ss_pred ChhHHHHHHHHHHHc------CCHHHHHHHHHHhCCCcchHHHHHHHHHHHH
Confidence 567777776654221 2578888888888877777776666555544
No 4
>cd00982 gltB_C gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the transfer of ammonia and electrons among three distinct active centers that carry out L-Gln hydrolysis, conversion of 2-oxoglutarate into L-Glu, and electron uptake from a donor. These catalytic sites appear to occur in other domains within the protein, and not the domain in this CD. This particular domain has no known function, but it likely has a structural role as it interacts with the amidotransferase and FMN-binding domains of gltS.
Probab=59.55 E-value=7.4 Score=34.88 Aligned_cols=65 Identities=25% Similarity=0.259 Sum_probs=46.5
Q ss_pred cccceEEEeccCCCcHHHHHHH-HHHHHHhcCCCCcCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHH
Q 043344 111 CVRDSVAVPTDSPDPYVDFRRS-MQEMVEARDLFDVKANWDCLHELLLCYLALNPKTTHKFIISAFADLL 179 (194)
Q Consensus 111 ~~~~svAV~k~S~DPy~DFR~S-M~EMI~e~~l~~~~~dw~~LeELL~cYL~LN~~~~H~~Iv~AF~Dl~ 179 (194)
.-.++++++. ||-.+|.+- -.+||.-..+.+ ..||++|++||..|+..-..+..+.||.-|.+..
T Consensus 177 GM~gG~iyv~---~~~~~~~~~~n~~~V~~~~l~~-~~d~~~l~~ll~~h~~~t~s~~a~~iL~~~~~~~ 242 (251)
T cd00982 177 GMSGGVAYVL---DEDGDFEKKVNHEMVDLERLED-AEDEEQLKELIEEHVEYTGSEKAKEILANWEAYL 242 (251)
T ss_pred CCCCCEEEEE---CCcCChhhhcCHhhEeeccCCC-HHHHHHHHHHHHHHHHHHCCHHHHHHHHhHHHHh
Confidence 3456666664 676777542 336776444531 2479999999999999999999999998886543
No 5
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=53.61 E-value=24 Score=25.96 Aligned_cols=43 Identities=12% Similarity=0.200 Sum_probs=21.2
Q ss_pred HHHHHHHHHHhcCCCCcCCChHHHHHHHHHHHHcCCCCChHHHHHHHHH
Q 043344 129 FRRSMQEMVEARDLFDVKANWDCLHELLLCYLALNPKTTHKFIISAFAD 177 (194)
Q Consensus 129 FR~SM~EMI~e~~l~~~~~dw~~LeELL~cYL~LN~~~~H~~Iv~AF~D 177 (194)
||+.+...|.+---. .+.+|...|-..||.+.+|..++...+.
T Consensus 1 ~rk~i~~~l~ey~~~------~d~~ea~~~l~el~~~~~~~~vv~~~l~ 43 (113)
T PF02847_consen 1 LRKKIFSILMEYFSS------GDVDEAVECLKELKLPSQHHEVVKVILE 43 (113)
T ss_dssp HHHHHHHHHHHHHHH------T-HHHHHHHHHHTT-GGGHHHHHHHHHH
T ss_pred ChHHHHHHHHHHhcC------CCHHHHHHHHHHhCCCccHHHHHHHHHH
Confidence 455555555543211 1456666666666655555555444433
No 6
>PF14551 MCM_N: MCM N-terminal domain; PDB: 2VL6_C 3F9V_A 1LTL_E.
Probab=50.45 E-value=32 Score=25.26 Aligned_cols=54 Identities=20% Similarity=0.263 Sum_probs=41.0
Q ss_pred HHHHHHHHHHhcCCCCcCCChHHHHH---HHHHHHHcCCCCChHHHHHHHHHHHHHhc
Q 043344 129 FRRSMQEMVEARDLFDVKANWDCLHE---LLLCYLALNPKTTHKFIISAFADLLVSLM 183 (194)
Q Consensus 129 FR~SM~EMI~e~~l~~~~~dw~~LeE---LL~cYL~LN~~~~H~~Iv~AF~Dl~~~L~ 183 (194)
+++.+.+|+.... .....||++|.+ =|.-.|.-|+.++..++-+|..+++..+.
T Consensus 18 Y~~~l~~~~~~~~-~~l~Vd~~dL~~f~~~L~~~l~~~P~~~l~~~~~a~~~~~~~~~ 74 (121)
T PF14551_consen 18 YMDQLREMIQRNK-KSLYVDLDDLREFDPDLAEALIENPYRYLPLFEEALKEVVKELF 74 (121)
T ss_dssp CHHHHHHHHHHT--SCEEEEHHHHHHH-HHHHHHHHHCCCCCHHHHHHHHHHCHHTT-
T ss_pred HHHHHHHHHHcCC-CEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4566777776532 223457888876 78899999999999999999999998764
No 7
>PF04716 ETC_C1_NDUFA5: ETC complex I subunit conserved region; InterPro: IPR006806 This is a family of eukaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC) (1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 29.9 kDa protein. The conserved region is found at the N terminus of the member proteins [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022904 respiratory electron transport chain, 0005743 mitochondrial inner membrane
Probab=46.48 E-value=12 Score=26.31 Aligned_cols=31 Identities=10% Similarity=0.385 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHhc-CCCCcCCChHHHHHHHHH
Q 043344 128 DFRRSMQEMVEAR-DLFDVKANWDCLHELLLC 158 (194)
Q Consensus 128 DFR~SM~EMI~e~-~l~~~~~dw~~LeELL~c 158 (194)
.+|++.++++..+ .+.....|++.+|+.+.|
T Consensus 26 ~YR~~tE~it~~Rl~iv~~~~d~~~iE~~i~c 57 (57)
T PF04716_consen 26 AYRQYTEAITKHRLKIVEEEEDIEKIEKKIGC 57 (57)
T ss_pred HHHHHHHHHHHHHHHHHHccccHHHHHHHhCc
Confidence 5899999998776 443335689999999987
No 8
>PRK10072 putative transcriptional regulator; Provisional
Probab=35.54 E-value=34 Score=26.21 Aligned_cols=20 Identities=20% Similarity=0.418 Sum_probs=18.1
Q ss_pred CCcHHHHHHHHHHHHHhcCC
Q 043344 123 PDPYVDFRRSMQEMVEARDL 142 (194)
Q Consensus 123 ~DPy~DFR~SM~EMI~e~~l 142 (194)
.||..|..+||.|||+++|-
T Consensus 4 ~~~~~~l~~~~~~~~~~~~~ 23 (96)
T PRK10072 4 KDPMFELLSSLEQIVFKDET 23 (96)
T ss_pred CCHHHHHHHHHHHHHHhcCC
Confidence 59999999999999997773
No 9
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=33.78 E-value=69 Score=25.58 Aligned_cols=56 Identities=16% Similarity=0.281 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHhcCCCCcCCChHHHHHHHHHHHHc------C--CCCChHHHHHHHHHHHHHhcCC
Q 043344 126 YVDFRRSMQEMVEARDLFDVKANWDCLHELLLCYLAL------N--PKTTHKFIISAFADLLVSLMSP 185 (194)
Q Consensus 126 y~DFR~SM~EMI~e~~l~~~~~dw~~LeELL~cYL~L------N--~~~~H~~Iv~AF~Dl~~~L~s~ 185 (194)
|..--..-.+|+++-.- ++||.|=+|-..|+.+ + +......+.+.+++++..++.+
T Consensus 11 Yq~I~~lS~~ML~aA~~----g~Wd~Li~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~lL~~IL~n 74 (121)
T PRK10548 11 WQQILTLSQSMLRLATE----GQWDELIEQEVAYVQAVEEIAHLTIPPDISTVMQEQLRPMLRQILDN 74 (121)
T ss_pred HHHHHHHHHHHHHHHHH----CCHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 66677778889886654 5799999999999875 2 2345666777888887776543
No 10
>COG0337 AroB 3-dehydroquinate synthetase [Amino acid transport and metabolism]
Probab=28.70 E-value=69 Score=30.26 Aligned_cols=50 Identities=28% Similarity=0.358 Sum_probs=35.9
Q ss_pred CCCcHHHHHHHHHHHHHhcCCCCcCCChHHHHHHHHHHHHcCCCCChHHHHH
Q 043344 122 SPDPYVDFRRSMQEMVEARDLFDVKANWDCLHELLLCYLALNPKTTHKFIIS 173 (194)
Q Consensus 122 S~DPy~DFR~SM~EMI~e~~l~~~~~dw~~LeELL~cYL~LN~~~~H~~Iv~ 173 (194)
..=|.++||.=|.|+|.-.-|.|. .-|++||+-+.+.++++. ...++|.+
T Consensus 170 ~TLp~re~~~G~AEvIK~g~I~D~-~~f~~Le~~~~~l~~~~~-~l~~~I~r 219 (360)
T COG0337 170 KTLPPRELRAGMAEVIKYGLIADP-EFFDWLEENLDALLALDP-ALEELIAR 219 (360)
T ss_pred ccCCHHHHHHhHHHHHHHhhhcCH-HHHHHHHHHHHHHHhcch-HHHHHHHH
Confidence 567999999999999987777653 347788887777776655 34444443
No 11
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=26.34 E-value=89 Score=29.96 Aligned_cols=50 Identities=22% Similarity=0.086 Sum_probs=35.0
Q ss_pred HHHHHHHhcCCCCcCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHHHHh
Q 043344 132 SMQEMVEARDLFDVKANWDCLHELLLCYLALNPKTTHKFIISAFADLLVSL 182 (194)
Q Consensus 132 SM~EMI~e~~l~~~~~dw~~LeELL~cYL~LN~~~~H~~Iv~AF~Dl~~~L 182 (194)
-|+||+...-..+-+...+.+++||.-||..|..+.- -++++|+|.|++.
T Consensus 5 r~eev~~~~~~g~hk~~~~qyr~~l~~~lt~~~~el~-e~~k~~id~~~~~ 54 (399)
T KOG1497|consen 5 RSEEVVLIFAEGDHKDQAEQYRQLLAKVLTNNGMELL-EALKRFIDAIVNE 54 (399)
T ss_pred HHHHHHHHHhcCchhhHHHHHHHHHHHHhccchHHHH-HHHHHHHHHHHcC
Confidence 3667766553333344477899999999999976443 4678899988764
No 12
>TIGR02908 CoxD_Bacillus cytochrome c oxidase, subunit IVB. This model represents a small clade of cytochrome oxidase subunit IV's found in the Bacilli.
Probab=24.50 E-value=76 Score=25.41 Aligned_cols=27 Identities=11% Similarity=0.262 Sum_probs=22.1
Q ss_pred HHHHHHcCCCCChHHHHHHHHHHHHHh
Q 043344 156 LLCYLALNPKTTHKFIISAFADLLVSL 182 (194)
Q Consensus 156 L~cYL~LN~~~~H~~Iv~AF~Dl~~~L 182 (194)
|.|||.+|.+.+...++=.|.-+.+++
T Consensus 72 L~yFLHm~~k~~~~~~~~if~gi~va~ 98 (110)
T TIGR02908 72 LYYFMHMKDKGHEVPAQFIYGGVFVTM 98 (110)
T ss_pred HHHheeeCCCccchHHHHHHHHHHHHH
Confidence 578999999988888888887777654
No 13
>PF09177 Syntaxin-6_N: Syntaxin 6, N-terminal; InterPro: IPR015260 Members of this entry, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport []. ; GO: 0048193 Golgi vesicle transport, 0016020 membrane; PDB: 1LVF_B 2C5I_T 2C5J_A 2C5K_T 4DND_A.
Probab=23.72 E-value=3.1e+02 Score=20.30 Aligned_cols=32 Identities=22% Similarity=0.397 Sum_probs=24.0
Q ss_pred CcHHHHHHHHHHHHHhcCCCCcCCChHHHHHHHHHHHHcCCCCC
Q 043344 124 DPYVDFRRSMQEMVEARDLFDVKANWDCLHELLLCYLALNPKTT 167 (194)
Q Consensus 124 DPy~DFR~SM~EMI~e~~l~~~~~dw~~LeELL~cYL~LN~~~~ 167 (194)
|||-.+++-.++.|. .|+.|+.-|+.+.....
T Consensus 1 DPF~~v~~ev~~sl~------------~l~~~~~~~~~~~~~~~ 32 (97)
T PF09177_consen 1 DPFFVVKDEVQSSLD------------RLESLYRRWQRLRSDTS 32 (97)
T ss_dssp -HHHHHHHHHHHHHH------------HHHHHHHHHHHHTTHCC
T ss_pred CCcHHHHHHHHHHHH------------HHHHHHHHHHHhcccCC
Confidence 899999988877763 57888888888876554
No 14
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=23.38 E-value=2e+02 Score=20.97 Aligned_cols=54 Identities=20% Similarity=0.198 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHhcCCCCcCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHHHHh
Q 043344 128 DFRRSMQEMVEARDLFDVKANWDCLHELLLCYLALNPKTTHKFIISAFADLLVSL 182 (194)
Q Consensus 128 DFR~SM~EMI~e~~l~~~~~dw~~LeELL~cYL~LN~~~~H~~Iv~AF~Dl~~~L 182 (194)
+|...++.+|....+...+ .+..+=-.|..+|.-...-.-..|..+|.+++..|
T Consensus 32 ~~~~~vv~~~l~~~le~~~-~~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~l 85 (113)
T PF02847_consen 32 SQHHEVVKVILECALEEKK-SYREYYSKLLSHLCKRKLISKEQFQEGFEDLLESL 85 (113)
T ss_dssp GGHHHHHHHHHHHHHTSSH-HHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHhhccH-HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhHh
Confidence 4555555555555554311 23444455555666677788888999999887765
No 15
>cd03331 Macro_Poa1p_like_SNF2 Macro domain, Poa1p_like family, SNF2 subfamily. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. Members of this subfamily contain a C-terminal macro domain that show similarity to the yeast protein Poa1p, reported to be a phosphatase specific for Appr-1"-p, a tRNA splicing metabolite. In addition, they also contain an SNF2 domain, defined by the presence of seven
Probab=23.34 E-value=1.6e+02 Score=24.23 Aligned_cols=38 Identities=18% Similarity=0.268 Sum_probs=27.6
Q ss_pred cHHHHHHHHHHHHHhc---C-------CCC--cCCChHHHHHHHHHHHHc
Q 043344 125 PYVDFRRSMQEMVEAR---D-------LFD--VKANWDCLHELLLCYLAL 162 (194)
Q Consensus 125 Py~DFR~SM~EMI~e~---~-------l~~--~~~dw~~LeELL~cYL~L 162 (194)
=|.++++.|.++-... + |.- ..++|+..|+||.-||.+
T Consensus 102 ~~~aL~~~L~~~~~~a~~~~~sVhmPrIg~Gl~g~~W~~~E~li~k~l~~ 151 (152)
T cd03331 102 KLSALEKGLKKIYFAAKQKSASVHLPRIGHSTKSFNWYGTERLIRKYLAT 151 (152)
T ss_pred CHHHHHHHHHHHHHHHHcCCCEEEeCCCCCCCCCCCHHHHHHHHHHHhcc
Confidence 3789999999877521 1 211 246899999999999864
No 16
>PF05400 FliT: Flagellar protein FliT; InterPro: IPR008622 This entry represents the bacterial flagellar FliT family of dual-function proteins. Together with FlgN, FliT has been proposed to act as a substrate-specific export chaperone, facilitating the incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum []. FliT has also been shown to act as a transcriptional regulator in Salmonella typhimurium [].; GO: 0019861 flagellum; PDB: 3A7M_A 3H3M_B 3NKZ_C 2G42_A 2FZT_B.
Probab=23.19 E-value=1e+02 Score=21.11 Aligned_cols=16 Identities=38% Similarity=0.547 Sum_probs=12.1
Q ss_pred CChHHHHHHHHHHHHc
Q 043344 147 ANWDCLHELLLCYLAL 162 (194)
Q Consensus 147 ~dw~~LeELL~cYL~L 162 (194)
+||+.|.+|+..|-.|
T Consensus 8 ~dWe~l~~l~~~R~~l 23 (84)
T PF05400_consen 8 GDWEELEELLDERQEL 23 (84)
T ss_dssp T-HHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHH
Confidence 4799999999887543
No 17
>PF02979 NHase_alpha: Nitrile hydratase, alpha chain; InterPro: IPR004232 Nitrile hydratases (4.2.1.84 from EC) are bacterial enzymes that catalyse the hydration of nitrile compounds to the corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and are normally active as a tetramer, alpha(2)beta(2). Nitrile hydratases contain either a non-haem iron or a non-corrinoid cobalt centre, both types sharing a highly conserved peptide sequence in the alpha subunit (CXLCSC) that provides all the residues involved in coordinating the metal ion. Each type of nitrile hydratase specifically incorporated its metal with the help of activator proteins encoded by flanking regions of the nitrile hydratase genes that are necessary for metal insertion. The Fe-containing enzyme is photo-regulated: in the dark the enzyme is inactivated due to the association of nitric oxide (NO) to the iron, while in the light the enzyme is active by photo-dissociation of NO. The NO is held in place by a claw setting formed through specific oxygen atoms in two modified cysteines and a serine residue in the active site [, ]. The cobalt-containing enzyme is unaffected by NO, but was shown to undergo a similar effect with carbon monoxide [, ]. Fe- and cobalt-containing enzymes also display different inhibition patterns with nitrophenols. Thiocyanate hydrolase (SCNase) is a cobalt-containing metalloenzyme with a cysteine-sulphinic acid ligand that hydrolyses thiocyanate to carbonyl sulphide and ammonia []. The two enzymes, nitrile hydratase and SCNase, are homologous over regions corresponding to almost the entire coding regions of the genes: the beta and alpha subunits of thiocyanate hydrolase were homologous to the amino- and carboxyl-terminal halves of the beta subunit of nitrile hydratase, and the gamma subunit of thiocyanate hydrolase was homologous to the alpha subunit of nitrile hydratase []. This entry represents the structural domain of the alpha subunit of both iron- and cobalt-containing nitrile hydratases; the alpha subunit is a duplication of two structural repeats, each consisting of 4 layers, alpha/beta/beta/alpha []. This structure is also found in the related protein, the gamma subunit of thiocyanate hydrolase (SCNase).; GO: 0003824 catalytic activity, 0046914 transition metal ion binding, 0006807 nitrogen compound metabolic process; PDB: 2DPP_A 3HHT_A 1V29_A 2ZZD_I 2DXC_F 2DXB_F 2DD5_C 2DD4_C 2ZPH_A 2CYZ_A ....
Probab=22.45 E-value=1.1e+02 Score=26.59 Aligned_cols=47 Identities=13% Similarity=0.291 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHhcCCCCcCCChHHHHHHHHHHHHc-CCCCChHHHHHHHHH
Q 043344 127 VDFRRSMQEMVEARDLFDVKANWDCLHELLLCYLAL-NPKTTHKFIISAFAD 177 (194)
Q Consensus 127 ~DFR~SM~EMI~e~~l~~~~~dw~~LeELL~cYL~L-N~~~~H~~Iv~AF~D 177 (194)
.---+-++++..++|+.. .+++++++..|-.. .++.--++|-+|.+|
T Consensus 6 ~~~~~al~~ll~ekg~~~----~~~~~~~~~~~~~~~~P~~GarvVArAW~D 53 (188)
T PF02979_consen 6 AARVRALESLLIEKGLIT----PAEVDRIIETYESRVGPRNGARVVARAWTD 53 (188)
T ss_dssp HHHHHHHHHHHHHTTSS-----HHHHHHHHHHHHHTSSHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHcCCCC----HHHHHHHHHHHHhccCccccceeehhhhCC
Confidence 344567899999999965 67999999999998 777778888888877
No 18
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=22.30 E-value=2.4e+02 Score=20.63 Aligned_cols=55 Identities=15% Similarity=0.107 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHhcCCCCcCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHHHHhc
Q 043344 128 DFRRSMQEMVEARDLFDVKANWDCLHELLLCYLALNPKTTHKFIISAFADLLVSLM 183 (194)
Q Consensus 128 DFR~SM~EMI~e~~l~~~~~dw~~LeELL~cYL~LN~~~~H~~Iv~AF~Dl~~~L~ 183 (194)
+|+.-.+.++....+.......+..-.||. .|.-...-....+..+|.+++..|-
T Consensus 32 ~~~~~vv~~~i~~~le~~~~~~~~~~~Ll~-~L~~~~~~~~~~~~~~f~~~~~~l~ 86 (113)
T smart00544 32 EQHHEVVKVLLTCALEEKRTYREMYSVLLS-RLCQANVISTKQFEKGFWRLLEDIE 86 (113)
T ss_pred cchHHHHHHHHHHHHcCCccHHHHHHHHHH-HHHHcCCcCHHHHHHHHHHHHhhCh
Confidence 355556666655555331123445555555 5554557888889999999887654
No 19
>PF02337 Gag_p10: Retroviral GAG p10 protein; InterPro: IPR003322 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from beta-retroviruses such as Mason-Pfizer monkey virus (MPMV) (Simian Mason-Pfizer virus) and Mouse mammary tumor virus (MMTV) [, ]. This entry also identifies matrix proteins from several eukaryotic endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 2F77_X 2F76_X.
Probab=20.57 E-value=1.8e+02 Score=22.33 Aligned_cols=34 Identities=12% Similarity=0.111 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHhcCCCCcCCChHHHHHHHHHHHHcC
Q 043344 127 VDFRRSMQEMVEARDLFDVKANWDCLHELLLCYLALN 163 (194)
Q Consensus 127 ~DFR~SM~EMI~e~~l~~~~~dw~~LeELL~cYL~LN 163 (194)
.=|...|..|+.++||. ..|++|.+++.---..|
T Consensus 8 ~~fv~~Lk~lLk~rGi~---v~~~~L~~f~~~i~~~~ 41 (90)
T PF02337_consen 8 QPFVSILKHLLKERGIR---VKKKDLINFLSFIDKVC 41 (90)
T ss_dssp HHHHHHHHHHHHCCT-------HHHHHHHHHHHHHHT
T ss_pred hHHHHHHHHHHHHcCee---ecHHHHHHHHHHHHHhC
Confidence 34889999999999996 33777777766444444
No 20
>cd03154 TM4SF3_like_LEL Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF3_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". This subfamily contaions transmembrane 4 superfamily 3 (TM4SF3) or D6.1a and related proteins. D6.1a associates with alpha6beta4 integrin and supports cell motility, it has been ascribed a role in tumor progression and metastasis.
Probab=20.26 E-value=42 Score=24.06 Aligned_cols=36 Identities=14% Similarity=0.243 Sum_probs=22.6
Q ss_pred CCcHHHHHHHHHHHHHhcCCC--CcCCChHHHHHHHHH
Q 043344 123 PDPYVDFRRSMQEMVEARDLF--DVKANWDCLHELLLC 158 (194)
Q Consensus 123 ~DPy~DFR~SM~EMI~e~~l~--~~~~dw~~LeELL~c 158 (194)
..-...+++.|.++|...+-. +...-|+.||+-|.|
T Consensus 9 ~~i~~~i~~~~~~~i~~y~~~~~~~~~~~d~lQ~~l~C 46 (100)
T cd03154 9 PKIENELKEKNTKLLSLLGQNAKSVKKSLEKFQKELKC 46 (100)
T ss_pred HHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCC
Confidence 345567788888888764332 111237888887776
Done!