Query 035957
Match_columns 211
No_of_seqs 121 out of 222
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 08:00:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035957.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035957hhsearch_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 6E-36 1.3E-40 218.6 8.2 66 133-201 1-66 (66)
2 PF04844 Ovate: Transcriptiona 100.0 9.4E-33 2E-37 197.9 7.6 59 139-201 1-59 (59)
3 smart00544 MA3 Domain in DAP-5 76.0 5.5 0.00012 29.9 4.4 46 146-197 1-46 (113)
4 cd00982 gltB_C gltb_C. This do 57.6 9.4 0.0002 34.7 2.8 65 128-196 177-242 (251)
5 PF14551 MCM_N: MCM N-terminal 49.2 33 0.00071 25.5 4.2 54 146-200 18-74 (121)
6 PF02847 MA3: MA3 domain; Int 46.2 35 0.00075 25.4 3.9 42 146-193 1-42 (113)
7 PF04716 ETC_C1_NDUFA5: ETC co 46.0 12 0.00027 26.7 1.3 32 144-175 25-57 (57)
8 PRK10072 putative transcriptio 32.2 44 0.00096 25.9 2.6 21 139-159 3-23 (96)
9 PRK10548 flagellar biosynthesi 31.5 77 0.0017 25.7 3.9 55 143-201 11-73 (121)
10 COG0337 AroB 3-dehydroquinate 30.9 60 0.0013 31.1 3.7 51 138-190 169-219 (360)
11 PF05400 FliT: Flagellar prote 28.9 66 0.0014 22.4 2.8 16 164-179 8-23 (84)
12 KOG1497 COP9 signalosome, subu 27.4 85 0.0018 30.5 4.0 50 149-199 5-54 (399)
13 cd03154 TM4SF3_like_LEL Tetras 25.3 37 0.0008 24.7 1.0 38 138-175 7-46 (100)
14 cd03331 Macro_Poa1p_like_SNF2 22.2 1.8E+02 0.0039 24.2 4.7 38 142-179 102-151 (152)
15 PF02337 Gag_p10: Retroviral G 21.9 1.5E+02 0.0033 23.1 3.9 34 144-180 8-41 (90)
16 PF02979 NHase_alpha: Nitrile 21.9 1.5E+02 0.0032 26.2 4.3 48 143-194 5-53 (188)
17 PF15089 DUF4552: Domain of un 21.7 87 0.0019 30.6 3.0 48 54-101 241-290 (425)
18 TIGR02908 CoxD_Bacillus cytoch 21.2 98 0.0021 25.1 2.8 27 173-199 72-98 (110)
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=6e-36 Score=218.61 Aligned_cols=66 Identities=64% Similarity=0.975 Sum_probs=63.2
Q ss_pred EEEEeeCCChHHHHHHHHHHHHHHcCCCcccCChHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHcc
Q 035957 133 VAVKKYSPDPYQDFRCSMQEMIEARNLTDVMANCDFLHELLLCYLTLNPKHTHKFIISAFADILISLLS 201 (211)
Q Consensus 133 vAVvk~S~DPy~DFR~SM~EMI~a~~i~~~~~dwd~LeELL~cYL~LN~~~~H~~Iv~AF~Dl~~~L~s 201 (211)
|||+|+|.|||.|||+||+|||+++|+. .+|++|||||+|||+||+++||++|++||+|||++|++
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 6999999999999999999999999986 47999999999999999999999999999999999974
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=99.98 E-value=9.4e-33 Score=197.85 Aligned_cols=59 Identities=54% Similarity=0.914 Sum_probs=56.9
Q ss_pred CCChHHHHHHHHHHHHHHcCCCcccCChHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHcc
Q 035957 139 SPDPYQDFRCSMQEMIEARNLTDVMANCDFLHELLLCYLTLNPKHTHKFIISAFADILISLLS 201 (211)
Q Consensus 139 S~DPy~DFR~SM~EMI~a~~i~~~~~dwd~LeELL~cYL~LN~~~~H~~Iv~AF~Dl~~~L~s 201 (211)
|.|||+|||+||+|||+++|++ +|++|||||+|||+||+++||++||+||+|||++|++
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 6999999999999999999999999999999999975
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=76.03 E-value=5.5 Score=29.91 Aligned_cols=46 Identities=15% Similarity=0.211 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHcCCCcccCChHHHHHHHHHHHhcCCCCchHHHHHHHHHHHH
Q 035957 146 FRCSMQEMIEARNLTDVMANCDFLHELLLCYLTLNPKHTHKFIISAFADILI 197 (211)
Q Consensus 146 FR~SM~EMI~a~~i~~~~~dwd~LeELL~cYL~LN~~~~H~~Iv~AF~Dl~~ 197 (211)
||+.+...|++---. .+.+|...|...||.+++|+.++...+..+.
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 577777777655211 2588899999999988777777766555443
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=57.62 E-value=9.4 Score=34.66 Aligned_cols=65 Identities=26% Similarity=0.341 Sum_probs=46.6
Q ss_pred CcCCcEEEEeeCCChHHHHHHH-HHHHHHHcCCCcccCChHHHHHHHHHHHhcCCCCchHHHHHHHHHHH
Q 035957 128 PLNGGVAVKKYSPDPYQDFRCS-MQEMIEARNLTDVMANCDFLHELLLCYLTLNPKHTHKFIISAFADIL 196 (211)
Q Consensus 128 ~~~~svAVvk~S~DPy~DFR~S-M~EMI~a~~i~~~~~dwd~LeELL~cYL~LN~~~~H~~Iv~AF~Dl~ 196 (211)
-..++++++. ||-.+|.+- -.|||+-..+.+ ..||++|++||..|+..-..+..+.|+.-|.+..
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 3456677765 676777542 236776444532 3578999999999999999999999998886543
No 5
>PF14551 MCM_N: MCM N-terminal domain; PDB: 2VL6_C 3F9V_A 1LTL_E.
Probab=49.18 E-value=33 Score=25.51 Aligned_cols=54 Identities=22% Similarity=0.286 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHcCCCcccCChHHHHH---HHHHHHhcCCCCchHHHHHHHHHHHHHHc
Q 035957 146 FRCSMQEMIEARNLTDVMANCDFLHE---LLLCYLTLNPKHTHKFIISAFADILISLL 200 (211)
Q Consensus 146 FR~SM~EMI~a~~i~~~~~dwd~LeE---LL~cYL~LN~~~~H~~Iv~AF~Dl~~~L~ 200 (211)
+++.+.+|+.... ..-..||++|.+ =|.-.|.-|+.++..++-+|..+++..+.
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 4667777777632 223368888876 78899999999999999999999998764
No 6
>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=46.25 E-value=35 Score=25.38 Aligned_cols=42 Identities=12% Similarity=0.169 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHcCCCcccCChHHHHHHHHHHHhcCCCCchHHHHHHHH
Q 035957 146 FRCSMQEMIEARNLTDVMANCDFLHELLLCYLTLNPKHTHKFIISAFA 193 (211)
Q Consensus 146 FR~SM~EMI~a~~i~~~~~dwd~LeELL~cYL~LN~~~~H~~Iv~AF~ 193 (211)
||+.+...|.+.--. .+.+|...|-..||.+.+|..++...+
T Consensus 1 ~rk~i~~~l~ey~~~------~d~~ea~~~l~el~~~~~~~~vv~~~l 42 (113)
T PF02847_consen 1 LRKKIFSILMEYFSS------GDVDEAVECLKELKLPSQHHEVVKVIL 42 (113)
T ss_dssp HHHHHHHHHHHHHHH------T-HHHHHHHHHHTT-GGGHHHHHHHHH
T ss_pred ChHHHHHHHHHHhcC------CCHHHHHHHHHHhCCCccHHHHHHHHH
Confidence 566666666554211 146666666666766655555554443
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=46.03 E-value=12 Score=26.65 Aligned_cols=32 Identities=9% Similarity=0.295 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHc-CCCcccCChHHHHHHHHH
Q 035957 144 QDFRCSMQEMIEAR-NLTDVMANCDFLHELLLC 175 (211)
Q Consensus 144 ~DFR~SM~EMI~a~-~i~~~~~dwd~LeELL~c 175 (211)
..+|++.++++..+ .+.....||+.+|+.+.|
T Consensus 25 a~YR~~tE~it~~Rl~iv~~~~d~~~iE~~i~c 57 (57)
T PF04716_consen 25 AAYRQYTEAITKHRLKIVEEEEDIEKIEKKIGC 57 (57)
T ss_pred cHHHHHHHHHHHHHHHHHHccccHHHHHHHhCc
Confidence 35899999998876 444445789999999887
No 8
>PRK10072 putative transcriptional regulator; Provisional
Probab=32.18 E-value=44 Score=25.94 Aligned_cols=21 Identities=14% Similarity=0.297 Sum_probs=18.5
Q ss_pred CCChHHHHHHHHHHHHHHcCC
Q 035957 139 SPDPYQDFRCSMQEMIEARNL 159 (211)
Q Consensus 139 S~DPy~DFR~SM~EMI~a~~i 159 (211)
=.||..|..+||.|||+++|-
T Consensus 3 ~~~~~~~l~~~~~~~~~~~~~ 23 (96)
T PRK10072 3 YKDPMFELLSSLEQIVFKDET 23 (96)
T ss_pred cCCHHHHHHHHHHHHHHhcCC
Confidence 369999999999999997773
No 9
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=31.48 E-value=77 Score=25.66 Aligned_cols=55 Identities=18% Similarity=0.233 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHcCCCcccCChHHHHHHHHHHHhc------C--CCCchHHHHHHHHHHHHHHcc
Q 035957 143 YQDFRCSMQEMIEARNLTDVMANCDFLHELLLCYLTL------N--PKHTHKFIISAFADILISLLS 201 (211)
Q Consensus 143 y~DFR~SM~EMI~a~~i~~~~~dwd~LeELL~cYL~L------N--~~~~H~~Iv~AF~Dl~~~L~s 201 (211)
|..--..-++|+++-.- ++||.|=+|-..|+.+ + +......+-+.+.+++..++.
T Consensus 11 Yq~I~~lS~~ML~aA~~----g~Wd~Li~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~lL~~IL~ 73 (121)
T PRK10548 11 WQQILTLSQSMLRLATE----GQWDELIEQEVAYVQAVEEIAHLTIPPDISTVMQEQLRPMLRQILD 73 (121)
T ss_pred HHHHHHHHHHHHHHHHH----CCHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHH
Confidence 66666777889887643 5799999999999875 2 233456677777777766543
No 10
>COG0337 AroB 3-dehydroquinate synthetase [Amino acid transport and metabolism]
Probab=30.94 E-value=60 Score=31.07 Aligned_cols=51 Identities=27% Similarity=0.393 Sum_probs=37.3
Q ss_pred eCCChHHHHHHHHHHHHHHcCCCcccCChHHHHHHHHHHHhcCCCCchHHHHH
Q 035957 138 YSPDPYQDFRCSMQEMIEARNLTDVMANCDFLHELLLCYLTLNPKHTHKFIIS 190 (211)
Q Consensus 138 ~S~DPy~DFR~SM~EMI~a~~i~~~~~dwd~LeELL~cYL~LN~~~~H~~Iv~ 190 (211)
-..=|.++||.=|.|+|.--=|.+. .-|++||+-+.+.++++. ....+|.+
T Consensus 169 L~TLp~re~~~G~AEvIK~g~I~D~-~~f~~Le~~~~~l~~~~~-~l~~~I~r 219 (360)
T COG0337 169 LKTLPPRELRAGMAEVIKYGLIADP-EFFDWLEENLDALLALDP-ALEELIAR 219 (360)
T ss_pred hccCCHHHHHHhHHHHHHHhhhcCH-HHHHHHHHHHHHHHhcch-HHHHHHHH
Confidence 3678999999999999987767653 357888887777776665 34555543
No 11
>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=28.86 E-value=66 Score=22.42 Aligned_cols=16 Identities=31% Similarity=0.210 Sum_probs=12.1
Q ss_pred CChHHHHHHHHHHHhc
Q 035957 164 ANCDFLHELLLCYLTL 179 (211)
Q Consensus 164 ~dwd~LeELL~cYL~L 179 (211)
+||+.|.+|+..|-.+
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 4799999999887553
No 12
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=27.41 E-value=85 Score=30.48 Aligned_cols=50 Identities=18% Similarity=0.121 Sum_probs=36.8
Q ss_pred HHHHHHHHcCCCcccCChHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHH
Q 035957 149 SMQEMIEARNLTDVMANCDFLHELLLCYLTLNPKHTHKFIISAFADILISL 199 (211)
Q Consensus 149 SM~EMI~a~~i~~~~~dwd~LeELL~cYL~LN~~~~H~~Iv~AF~Dl~~~L 199 (211)
-|+||+...-.++.+...+-+++||.-||..|..+. --++++|+|.+++.
T Consensus 5 r~eev~~~~~~g~hk~~~~qyr~~l~~~lt~~~~el-~e~~k~~id~~~~~ 54 (399)
T KOG1497|consen 5 RSEEVVLIFAEGDHKDQAEQYRQLLAKVLTNNGMEL-LEALKRFIDAIVNE 54 (399)
T ss_pred HHHHHHHHHhcCchhhHHHHHHHHHHHHhccchHHH-HHHHHHHHHHHHcC
Confidence 467777766554445556789999999999997644 34678899988764
No 13
>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=25.29 E-value=37 Score=24.68 Aligned_cols=38 Identities=13% Similarity=0.280 Sum_probs=23.9
Q ss_pred eCCChHHHHHHHHHHHHHHcCCCc--ccCChHHHHHHHHH
Q 035957 138 YSPDPYQDFRCSMQEMIEARNLTD--VMANCDFLHELLLC 175 (211)
Q Consensus 138 ~S~DPy~DFR~SM~EMI~a~~i~~--~~~dwd~LeELL~c 175 (211)
+-..-...+++.|.++|...+-.+ ...-|+.||+-|.|
T Consensus 7 ~r~~i~~~i~~~~~~~i~~y~~~~~~~~~~~d~lQ~~l~C 46 (100)
T cd03154 7 YKPKIENELKEKNTKLLSLLGQNAKSVKKSLEKFQKELKC 46 (100)
T ss_pred eHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCC
Confidence 334456677888888887643321 11248888887776
No 14
>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=22.16 E-value=1.8e+02 Score=24.18 Aligned_cols=38 Identities=13% Similarity=0.084 Sum_probs=27.5
Q ss_pred hHHHHHHHHHHHHHHc---C-------CCc--ccCChHHHHHHHHHHHhc
Q 035957 142 PYQDFRCSMQEMIEAR---N-------LTD--VMANCDFLHELLLCYLTL 179 (211)
Q Consensus 142 Py~DFR~SM~EMI~a~---~-------i~~--~~~dwd~LeELL~cYL~L 179 (211)
=|.++++.|.|+-... + |.. ..++|+..|+||.-||..
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 1 221 136899999999999864
No 15
>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=21.89 E-value=1.5e+02 Score=23.07 Aligned_cols=34 Identities=15% Similarity=0.196 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHcCCCcccCChHHHHHHHHHHHhcC
Q 035957 144 QDFRCSMQEMIEARNLTDVMANCDFLHELLLCYLTLN 180 (211)
Q Consensus 144 ~DFR~SM~EMI~a~~i~~~~~dwd~LeELL~cYL~LN 180 (211)
.=|...|.+|+.++||. ..|++|.+++.---..|
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 34888999999999986 34677777765444444
No 16
>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=21.87 E-value=1.5e+02 Score=26.23 Aligned_cols=48 Identities=10% Similarity=0.252 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHcCCCcccCChHHHHHHHHHHHhc-CCCCchHHHHHHHHH
Q 035957 143 YQDFRCSMQEMIEARNLTDVMANCDFLHELLLCYLTL-NPKHTHKFIISAFAD 194 (211)
Q Consensus 143 y~DFR~SM~EMI~a~~i~~~~~dwd~LeELL~cYL~L-N~~~~H~~Iv~AF~D 194 (211)
+.---+-++++..++|+.+. +++++++..|-.. .++.--++|-+|.+|
T Consensus 5 ~~~~~~al~~ll~ekg~~~~----~~~~~~~~~~~~~~~P~~GarvVArAW~D 53 (188)
T PF02979_consen 5 IAARVRALESLLIEKGLITP----AEVDRIIETYESRVGPRNGARVVARAWTD 53 (188)
T ss_dssp HHHHHHHHHHHHHHTTSS-H----HHHHHHHHHHHHTSSHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHcCCCCH----HHHHHHHHHHHhccCccccceeehhhhCC
Confidence 34445678999999999753 6999999999998 777788888898877
No 17
>PF15089 DUF4552: Domain of unknown function (DUF4552)
Probab=21.74 E-value=87 Score=30.62 Aligned_cols=48 Identities=31% Similarity=0.296 Sum_probs=26.7
Q ss_pred hccccCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCch-hhhhccccccc
Q 035957 54 SLYDQSSDFSTSKSL-TPSTDDYFSSDTEADTVSPPDF-TTIFASQRFFF 101 (211)
Q Consensus 54 sly~~~~~~~~~~s~-t~s~~s~~ss~~d~~~~~~~d~-~~~~~S~RfFf 101 (211)
-+|++++-.+.+.|. ...|+|+|||+++-.++..+.+ -.+=.|.|.+.
T Consensus 241 KiyldSSqSSQstSYSPRpTdScFSSSsem~SEdEDQi~qqiEdSnr~~i 290 (425)
T PF15089_consen 241 KIYLDSSQSSQSTSYSPRPTDSCFSSSSEMPSEDEDQILQQIEDSNRRSI 290 (425)
T ss_pred ceeecccccccCCCCCCCCCcccccCCccCCccchhhhhhhhcccccccc
Confidence 358887766666666 3455678888876443333333 22223555444
No 18
>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=21.23 E-value=98 Score=25.14 Aligned_cols=27 Identities=7% Similarity=0.277 Sum_probs=22.4
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHH
Q 035957 173 LLCYLTLNPKHTHKFIISAFADILISL 199 (211)
Q Consensus 173 L~cYL~LN~~~~H~~Iv~AF~Dl~~~L 199 (211)
|.|||.+|.+.+...++-.|.-+.+++
T Consensus 72 L~yFLHm~~k~~~~~~~~if~gi~va~ 98 (110)
T TIGR02908 72 LYYFMHMKDKGHEVPAQFIYGGVFVTM 98 (110)
T ss_pred HHHheeeCCCccchHHHHHHHHHHHHH
Confidence 678999999999888888888777765
Done!