Query 041802
Match_columns 223
No_of_seqs 136 out of 226
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 10:48:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041802.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041802hhsearch_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 1.1E-34 2.3E-39 213.4 7.9 65 131-195 1-66 (66)
2 PF04844 Ovate: Transcriptiona 100.0 1.3E-32 2.7E-37 198.5 7.5 59 137-195 1-59 (59)
3 smart00544 MA3 Domain in DAP-5 74.1 4.9 0.00011 30.5 3.7 46 144-191 1-46 (113)
4 PF02979 NHase_alpha: Nitrile 46.5 34 0.00074 30.4 4.4 48 141-188 5-53 (188)
5 cd00982 gltB_C gltb_C. This do 46.3 18 0.00038 33.2 2.7 59 129-190 180-242 (251)
6 PF08887 GAD-like: GAD-like do 45.8 6.7 0.00014 31.4 -0.1 46 146-191 34-93 (109)
7 PF14551 MCM_N: MCM N-terminal 40.9 49 0.0011 24.8 4.1 52 144-195 18-75 (121)
8 PF09388 SpoOE-like: Spo0E lik 40.5 71 0.0015 21.3 4.3 32 142-173 7-44 (45)
9 TIGR01323 nitrile_alph nitrile 38.4 55 0.0012 29.0 4.4 43 146-188 4-47 (185)
10 PF02847 MA3: MA3 domain; Int 36.7 44 0.00096 25.1 3.2 25 162-186 17-41 (113)
11 PF10273 WGG: Pre-rRNA-process 34.1 60 0.0013 24.6 3.5 37 136-172 28-64 (82)
12 PF04994 TfoX_C: TfoX C-termin 31.9 65 0.0014 24.3 3.4 31 146-176 13-45 (81)
13 PRK10072 putative transcriptio 31.3 79 0.0017 24.8 3.9 31 137-167 3-42 (96)
14 PF02211 NHase_beta: Nitrile h 26.6 2.1E+02 0.0045 25.7 6.2 57 139-197 67-123 (222)
15 smart00335 ANX Annexin repeats 23.9 1.5E+02 0.0033 19.4 3.8 36 157-192 13-52 (53)
16 PRK10548 flagellar biosynthesi 21.8 1.3E+02 0.0028 24.5 3.7 55 140-194 10-72 (121)
17 PF02337 Gag_p10: Retroviral G 20.8 1.5E+02 0.0032 23.3 3.7 33 142-174 8-41 (90)
18 PF05400 FliT: Flagellar prote 20.8 78 0.0017 22.3 2.0 23 151-173 1-23 (84)
19 TIGR02908 CoxD_Bacillus cytoch 20.1 1E+02 0.0022 25.2 2.7 27 167-193 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=1.1e-34 Score=213.40 Aligned_cols=65 Identities=52% Similarity=0.874 Sum_probs=62.9
Q ss_pred eEEEeeccChhHHHHHHHHHHHHHcCC-CChhhHHHHHHHHHHccCCCChhhHHHHHHHHHHHhhc
Q 041802 131 LVCSMESQDPYVDFKKSMVEMVEAHGL-KDWEDLEELLCWYLRMNGKSNHGYIVGAFVDLLVALAF 195 (223)
Q Consensus 131 vAV~~~S~DPy~DFR~SM~EMI~e~gi-~d~~dLeELL~cYL~LN~~~~H~~Iv~AF~dl~~~L~s 195 (223)
|||+|+|.|||.|||+||+|||+++|| .+|++|||||+|||+||+++||++|++||+|||++|++
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 VAVAKESDDPYEDFRRSMEEMIEERELEADWKELEELLACYLDLNPKKSHRFIVRAFVDILSALLS 66 (66)
T ss_pred CeeeeCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCchhhhHHHHHHHHHHHHHhC
Confidence 799999999999999999999999999 58999999999999999999999999999999999974
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=99.97 E-value=1.3e-32 Score=198.50 Aligned_cols=59 Identities=56% Similarity=0.993 Sum_probs=57.7
Q ss_pred ccChhHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHccCCCChhhHHHHHHHHHHHhhc
Q 041802 137 SQDPYVDFKKSMVEMVEAHGLKDWEDLEELLCWYLRMNGKSNHGYIVGAFVDLLVALAF 195 (223)
Q Consensus 137 S~DPy~DFR~SM~EMI~e~gi~d~~dLeELL~cYL~LN~~~~H~~Iv~AF~dl~~~L~s 195 (223)
|.|||+|||+||+|||+++||++|++|||||+|||+||+++||++|++||+|||.+|++
T Consensus 1 S~DP~~DFr~SM~EMI~~~~i~~~~~LeeLL~cYL~LN~~~~H~~Iv~aF~dv~~~l~s 59 (59)
T PF04844_consen 1 SSDPYEDFRESMVEMIEENGIRDWDDLEELLACYLSLNSPEHHKFIVEAFVDVWVELFS 59 (59)
T ss_pred CCCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCChhhhhHHHHHHHHHHHHHhC
Confidence 78999999999999999999999999999999999999999999999999999999974
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=74.09 E-value=4.9 Score=30.51 Aligned_cols=46 Identities=17% Similarity=0.215 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHcCCCChhhHHHHHHHHHHccCCCChhhHHHHHHHHHH
Q 041802 144 FKKSMVEMVEAHGLKDWEDLEELLCWYLRMNGKSNHGYIVGAFVDLLV 191 (223)
Q Consensus 144 FR~SM~EMI~e~gi~d~~dLeELL~cYL~LN~~~~H~~Iv~AF~dl~~ 191 (223)
||+.+...|.+-- .-.|.+|...|.+.||.+.+|+.++..-+..+.
T Consensus 1 ~~k~i~~~l~ey~--~~~D~~ea~~~l~~L~~~~~~~~vv~~~i~~~l 46 (113)
T smart00544 1 LKKKIFLIIEEYL--SSGDTDEAVHCLLELKLPEQHHEVVKVLLTCAL 46 (113)
T ss_pred ChhHHHHHHHHHH--HcCCHHHHHHHHHHhCCCcchHHHHHHHHHHHH
Confidence 4556666555421 224777888888888877777776666555444
No 4
>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=46.48 E-value=34 Score=30.39 Aligned_cols=48 Identities=10% Similarity=0.194 Sum_probs=39.1
Q ss_pred hHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHc-cCCCChhhHHHHHHH
Q 041802 141 YVDFKKSMVEMVEAHGLKDWEDLEELLCWYLRM-NGKSNHGYIVGAFVD 188 (223)
Q Consensus 141 y~DFR~SM~EMI~e~gi~d~~dLeELL~cYL~L-N~~~~H~~Iv~AF~d 188 (223)
+..-.+-++++..|+|+.+.+++++++..|-+. ++..--++|-+|.+|
T Consensus 5 ~~~~~~al~~ll~ekg~~~~~~~~~~~~~~~~~~~P~~GarvVArAW~D 53 (188)
T PF02979_consen 5 IAARVRALESLLIEKGLITPAEVDRIIETYESRVGPRNGARVVARAWTD 53 (188)
T ss_dssp HHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTSSHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhccCccccceeehhhhCC
Confidence 344456789999999999999999999999998 777777888888776
No 5
>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=46.31 E-value=18 Score=33.22 Aligned_cols=59 Identities=27% Similarity=0.325 Sum_probs=44.0
Q ss_pred CceEEEeeccChhHHHHH-HHHHHHHHcCCC---ChhhHHHHHHHHHHccCCCChhhHHHHHHHHH
Q 041802 129 ESLVCSMESQDPYVDFKK-SMVEMVEAHGLK---DWEDLEELLCWYLRMNGKSNHGYIVGAFVDLL 190 (223)
Q Consensus 129 ~svAV~~~S~DPy~DFR~-SM~EMI~e~gi~---d~~dLeELL~cYL~LN~~~~H~~Iv~AF~dl~ 190 (223)
++++++. ||..+|.+ --.+||.-..+. |+.+|++||..|+..-..+..+.|+.-|.+..
T Consensus 180 gG~iyv~---~~~~~~~~~~n~~~V~~~~l~~~~d~~~l~~ll~~h~~~t~s~~a~~iL~~~~~~~ 242 (251)
T cd00982 180 GGVAYVL---DEDGDFEKKVNHEMVDLERLEDAEDEEQLKELIEEHVEYTGSEKAKEILANWEAYL 242 (251)
T ss_pred CCEEEEE---CCcCChhhhcCHhhEeeccCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHhHHHHh
Confidence 5566664 67677764 334676654454 78899999999999999999999998886543
No 6
>PF08887 GAD-like: GAD-like domain; InterPro: IPR014983 This domain is functionally uncharacterised, but it appears to be distantly related to the GAD domain IPR004115 from INTERPRO.
Probab=45.76 E-value=6.7 Score=31.43 Aligned_cols=46 Identities=24% Similarity=0.294 Sum_probs=38.6
Q ss_pred HHHHHHHHHcCC----------CChhhHHHHHHHHHH----ccCCCChhhHHHHHHHHHH
Q 041802 146 KSMVEMVEAHGL----------KDWEDLEELLCWYLR----MNGKSNHGYIVGAFVDLLV 191 (223)
Q Consensus 146 ~SM~EMI~e~gi----------~d~~dLeELL~cYL~----LN~~~~H~~Iv~AF~dl~~ 191 (223)
+.+.+.-.++|. .++++.+++|..++. .+.+.+|.+...||.||++
T Consensus 34 ~~Ll~~W~~~G~g~~~dG~f~~vnP~dy~~vl~~~~~~~~~~~~~~~~~ia~tAFGdl~~ 93 (109)
T PF08887_consen 34 DELLEYWKEYGFGGYGDGLFWLVNPDDYEDVLDEWLGGTPLFDPDNYIPIARTAFGDLYV 93 (109)
T ss_pred HHHHHHHHHcCCchhcCcEEEEECHHHHHHHHHHHhcCCccccCceEEEEEEcccccEEE
Confidence 466777777763 589999999999996 7889999999999999863
No 7
>PF14551 MCM_N: MCM N-terminal domain; PDB: 2VL6_C 3F9V_A 1LTL_E.
Probab=40.94 E-value=49 Score=24.82 Aligned_cols=52 Identities=21% Similarity=0.176 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHcC---CCChhhHHH---HHHHHHHccCCCChhhHHHHHHHHHHHhhc
Q 041802 144 FKKSMVEMVEAHG---LKDWEDLEE---LLCWYLRMNGKSNHGYIVGAFVDLLVALAF 195 (223)
Q Consensus 144 FR~SM~EMI~e~g---i~d~~dLeE---LL~cYL~LN~~~~H~~Iv~AF~dl~~~L~s 195 (223)
+++.+.+|+..+. ..||++|.+ =|+-.|.-|+.++..++-+|..+++..+..
T Consensus 18 Y~~~l~~~~~~~~~~l~Vd~~dL~~f~~~L~~~l~~~P~~~l~~~~~a~~~~~~~~~~ 75 (121)
T PF14551_consen 18 YMDQLREMIQRNKKSLYVDLDDLREFDPDLAEALIENPYRYLPLFEEALKEVVKELFP 75 (121)
T ss_dssp CHHHHHHHHHHT-SCEEEEHHHHHHH-HHHHHHHHHCCCCCHHHHHHHHHHCHHTT--
T ss_pred HHHHHHHHHHcCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 4567777777644 258888866 789999999999999999999999987653
No 8
>PF09388 SpoOE-like: Spo0E like sporulation regulatory protein; InterPro: IPR018540 Spore formation is an extreme response to starvation and can also be a component of disease transmission. Sporulation is controlled by an expanded two-component system where starvation signals result in sensor kinase activation and phosphorylation of the master sporulation response regulator Spo0A. Phosphatases such as Spo0E dephosphorylate Spo0A thereby inhibiting sporulation. This is a family of Spo0E-like phosphatases. The structure of a Bacillus anthracis member of this family has revealed an anti-parallel alpha-helical structure []. ; PDB: 2BZB_B 2C0S_A.
Probab=40.45 E-value=71 Score=21.32 Aligned_cols=32 Identities=28% Similarity=0.575 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHcCCCChh------hHHHHHHHHHHc
Q 041802 142 VDFKKSMVEMVEAHGLKDWE------DLEELLCWYLRM 173 (223)
Q Consensus 142 ~DFR~SM~EMI~e~gi~d~~------dLeELL~cYL~L 173 (223)
+.-|+-|.+++...|+.|.+ .|-+|+..|..+
T Consensus 7 e~~R~~L~~~~~~~~l~~~~vl~~Sq~LD~lI~~y~~~ 44 (45)
T PF09388_consen 7 EELRQELNELAEKKGLTDPEVLELSQELDKLINEYQKL 44 (45)
T ss_dssp HHHHHHHHHHHHHCCTTCHHHHHHHHHHHHHHHHHHCH
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhhh
Confidence 34688999999999998876 677888888654
No 9
>TIGR01323 nitrile_alph nitrile hydratase, alpha subunit. This model describes both iron- and cobalt-containing nitrile hydratase alpha chains. It excludes the thiocyanate hydrolase gamma subunit of Thiobacillus thioparus, a sequence that appears to have evolved from within the family of nitrile hydratase alpha subunits but which differs by several indels and a more rapid accumulation of point mutations.
Probab=38.37 E-value=55 Score=29.03 Aligned_cols=43 Identities=19% Similarity=0.333 Sum_probs=35.9
Q ss_pred HHHHHHHHHcCCCChhhHHHHHHHHHH-ccCCCChhhHHHHHHH
Q 041802 146 KSMVEMVEAHGLKDWEDLEELLCWYLR-MNGKSNHGYIVGAFVD 188 (223)
Q Consensus 146 ~SM~EMI~e~gi~d~~dLeELL~cYL~-LN~~~~H~~Iv~AF~d 188 (223)
+-++++..++|+.+.+++++++..|-+ ..+..=-++|-+|.+|
T Consensus 4 ~Ale~ll~eKGli~~~~id~~i~~~~~~~gP~nGA~vVArAW~D 47 (185)
T TIGR01323 4 KALEQVLKSKGLIPEGAVDQLTSLYENEWGPENGAKVVAKAWVD 47 (185)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHhccCCcchhhhhhHHhcC
Confidence 457899999999999999999999999 5666666777777665
No 10
>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=36.72 E-value=44 Score=25.05 Aligned_cols=25 Identities=20% Similarity=0.236 Sum_probs=12.5
Q ss_pred hHHHHHHHHHHccCCCChhhHHHHH
Q 041802 162 DLEELLCWYLRMNGKSNHGYIVGAF 186 (223)
Q Consensus 162 dLeELL~cYL~LN~~~~H~~Iv~AF 186 (223)
|.+|...|-..||.+.+|..++...
T Consensus 17 d~~ea~~~l~el~~~~~~~~vv~~~ 41 (113)
T PF02847_consen 17 DVDEAVECLKELKLPSQHHEVVKVI 41 (113)
T ss_dssp -HHHHHHHHHHTT-GGGHHHHHHHH
T ss_pred CHHHHHHHHHHhCCCccHHHHHHHH
Confidence 5555555556666555555544433
No 11
>PF10273 WGG: Pre-rRNA-processing protein TSR2; InterPro: IPR019398 The pre-rRNA-processing protein TSR2 is required for 20S pre-rRNA processing []. This family contains a distinctive WGG motif.
Probab=34.07 E-value=60 Score=24.55 Aligned_cols=37 Identities=22% Similarity=0.206 Sum_probs=29.4
Q ss_pred eccChhHHHHHHHHHHHHHcCCCChhhHHHHHHHHHH
Q 041802 136 ESQDPYVDFKKSMVEMVEAHGLKDWEDLEELLCWYLR 172 (223)
Q Consensus 136 ~S~DPy~DFR~SM~EMI~e~gi~d~~dLeELL~cYL~ 172 (223)
+|.+-...|...+.+++..+.-.+.++||++|.-||.
T Consensus 28 ~s~~K~~~l~~~i~~~f~~~~~~~~~~le~~L~~~m~ 64 (82)
T PF10273_consen 28 DSQEKADWLAEVIVDWFTENKDPDADDLEDFLEDIMD 64 (82)
T ss_pred cHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 3566677788888888888766679999999998883
No 12
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=31.86 E-value=65 Score=24.31 Aligned_cols=31 Identities=32% Similarity=0.473 Sum_probs=24.5
Q ss_pred HHHHHHHHHcCCCChhhHHHH--HHHHHHccCC
Q 041802 146 KSMVEMVEAHGLKDWEDLEEL--LCWYLRMNGK 176 (223)
Q Consensus 146 ~SM~EMI~e~gi~d~~dLeEL--L~cYL~LN~~ 176 (223)
.-|++|..+-||.+.++|+++ -.||+.|...
T Consensus 13 ~~~e~~L~~vGI~t~~~L~~~Ga~~a~~~Lk~~ 45 (81)
T PF04994_consen 13 PKSERMLAKVGIHTVEDLRELGAVEAYLRLKAS 45 (81)
T ss_dssp HHHHHHHHHTT--SHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHhCHHHHHHHHHHH
Confidence 458899999999999999998 6789888644
No 13
>PRK10072 putative transcriptional regulator; Provisional
Probab=31.34 E-value=79 Score=24.76 Aligned_cols=31 Identities=19% Similarity=0.379 Sum_probs=23.7
Q ss_pred ccChhHHHHHHHHHHHHHcCC---C------ChhhHHHHH
Q 041802 137 SQDPYVDFKKSMVEMVEAHGL---K------DWEDLEELL 167 (223)
Q Consensus 137 S~DPy~DFR~SM~EMI~e~gi---~------d~~dLeELL 167 (223)
=.||..|..++|.|||+++|- + ...++++|.
T Consensus 3 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~eik~LR 42 (96)
T PRK10072 3 YKDPMFELLSSLEQIVFKDETQKITLTQKTTSFTEFEQLR 42 (96)
T ss_pred cCCHHHHHHHHHHHHHHhcCCccceeecccCChHHHHHHH
Confidence 369999999999999998772 1 455666663
No 14
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their 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 they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=26.58 E-value=2.1e+02 Score=25.72 Aligned_cols=57 Identities=16% Similarity=0.202 Sum_probs=33.4
Q ss_pred ChhHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHccCCCChhhHHHHHHHHHHHhhcCC
Q 041802 139 DPYVDFKKSMVEMVEAHGLKDWEDLEELLCWYLRMNGKSNHGYIVGAFVDLLVALAFAN 197 (223)
Q Consensus 139 DPy~DFR~SM~EMI~e~gi~d~~dLeELL~cYL~LN~~~~H~~Iv~AF~dl~~~L~s~~ 197 (223)
+=|+-....|+.|++++|+.+.++|++...-....=.+..++ .+.| .++-..|..+.
T Consensus 67 ~YYe~Wl~ale~lLvekG~it~~EL~ar~~~~~~~~~~~~~~-~~~a-~~v~~~l~~G~ 123 (222)
T PF02211_consen 67 SYYERWLAALEKLLVEKGVITAEELDARAGEWARPAAPTPRR-VLPA-DQVAAALARGD 123 (222)
T ss_dssp -HHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHH-TT---S-----HH-HHHHHHHHH--
T ss_pred cHHHHHHHHHHHHHHHcCCCCHHHHHHHHhhhhcccCCCCcc-cCcH-HHHHHHhhcCC
Confidence 348889999999999999999999999844444443333333 3444 44445555443
No 15
>smart00335 ANX Annexin repeats.
Probab=23.86 E-value=1.5e+02 Score=19.39 Aligned_cols=36 Identities=25% Similarity=0.276 Sum_probs=29.2
Q ss_pred CCChhhHHHHHHHHHHccCCCChhhHHHH----HHHHHHH
Q 041802 157 LKDWEDLEELLCWYLRMNGKSNHGYIVGA----FVDLLVA 192 (223)
Q Consensus 157 i~d~~dLeELL~cYL~LN~~~~H~~Iv~A----F~dl~~~ 192 (223)
-+...+++++...|..+..+..++.|-.. |.++++.
T Consensus 13 ~rs~~~~~~i~~~Y~~~~~~~L~~~i~~e~sG~~~~~l~~ 52 (53)
T smart00335 13 SRSNAQLQAIKQAYKKRYGKDLEDDIKSETSGDFEKLLLA 52 (53)
T ss_pred cCCHHHHHHHHHHHHHHhCccHHHHHHHhcChHHHHHHHh
Confidence 36788999999999999999999998875 5555543
No 16
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=21.83 E-value=1.3e+02 Score=24.51 Aligned_cols=55 Identities=11% Similarity=0.134 Sum_probs=41.2
Q ss_pred hhHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHcc--------CCCChhhHHHHHHHHHHHhh
Q 041802 140 PYVDFKKSMVEMVEAHGLKDWEDLEELLCWYLRMN--------GKSNHGYIVGAFVDLLVALA 194 (223)
Q Consensus 140 Py~DFR~SM~EMI~e~gi~d~~dLeELL~cYL~LN--------~~~~H~~Iv~AF~dl~~~L~ 194 (223)
=|..--..-.+|++.-.-.+||.|=+|-..|+.+= +......+.+.+.+++..+.
T Consensus 10 ~Yq~I~~lS~~ML~aA~~g~Wd~Li~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~lL~~IL 72 (121)
T PRK10548 10 AWQQILTLSQSMLRLATEGQWDELIEQEVAYVQAVEEIAHLTIPPDISTVMQEQLRPMLRQIL 72 (121)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHH
Confidence 47777788899999988999999999999998651 22345556666666666543
No 17
>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=20.81 E-value=1.5e+02 Score=23.28 Aligned_cols=33 Identities=15% Similarity=0.301 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHcCC-CChhhHHHHHHHHHHcc
Q 041802 142 VDFKKSMVEMVEAHGL-KDWEDLEELLCWYLRMN 174 (223)
Q Consensus 142 ~DFR~SM~EMI~e~gi-~d~~dLeELL~cYL~LN 174 (223)
.=|...|.+|+.++|| ..+++|.+++.-=...|
T Consensus 8 ~~fv~~Lk~lLk~rGi~v~~~~L~~f~~~i~~~~ 41 (90)
T PF02337_consen 8 QPFVSILKHLLKERGIRVKKKDLINFLSFIDKVC 41 (90)
T ss_dssp HHHHHHHHHHHHCCT----HHHHHHHHHHHHHHT
T ss_pred hHHHHHHHHHHHHcCeeecHHHHHHHHHHHHHhC
Confidence 3588899999999998 57888888776544444
No 18
>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=20.76 E-value=78 Score=22.27 Aligned_cols=23 Identities=48% Similarity=0.651 Sum_probs=16.2
Q ss_pred HHHHcCCCChhhHHHHHHHHHHc
Q 041802 151 MVEAHGLKDWEDLEELLCWYLRM 173 (223)
Q Consensus 151 MI~e~gi~d~~dLeELL~cYL~L 173 (223)
|+..-.-.||+.|.+|+..|-.|
T Consensus 1 ml~aa~~~dWe~l~~l~~~R~~l 23 (84)
T PF05400_consen 1 MLEAAEAGDWEELEELLDERQEL 23 (84)
T ss_dssp HHHHHHCT-HHHHHHHHHHHHHH
T ss_pred ChHHHhhCcHHHHHHHHHHHHHH
Confidence 44444467999999999988654
No 19
>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=20.13 E-value=1e+02 Score=25.25 Aligned_cols=27 Identities=15% Similarity=0.301 Sum_probs=22.7
Q ss_pred HHHHHHccCCCChhhHHHHHHHHHHHh
Q 041802 167 LCWYLRMNGKSNHGYIVGAFVDLLVAL 193 (223)
Q Consensus 167 L~cYL~LN~~~~H~~Iv~AF~dl~~~L 193 (223)
|.|||.+|.+.+...++=.|.-+.+++
T Consensus 72 L~yFLHm~~k~~~~~~~~if~gi~va~ 98 (110)
T TIGR02908 72 LYYFMHMKDKGHEVPAQFIYGGVFVTM 98 (110)
T ss_pred HHHheeeCCCccchHHHHHHHHHHHHH
Confidence 679999999999998888888777665
Done!