Query 044883
Match_columns 180
No_of_seqs 36 out of 38
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 07:42:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044883.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044883hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1294 Apurinic/apyrimidinic 83.3 0.23 5E-06 44.7 -1.2 42 3-44 44-85 (335)
2 PF02064 MAS20: MAS20 protein 68.1 18 0.0004 28.5 5.8 66 30-97 56-121 (121)
3 PF02631 RecX: RecX family; I 61.2 32 0.0007 25.3 5.7 57 55-111 12-68 (121)
4 COG2137 OraA Uncharacterized p 51.9 37 0.00081 28.1 5.2 78 29-110 15-109 (174)
5 COG3656 Predicted periplasmic 43.0 9.4 0.0002 32.4 0.4 45 52-102 73-139 (172)
6 smart00300 ChSh Chromo Shadow 41.2 16 0.00035 25.2 1.3 21 49-69 41-61 (61)
7 TIGR00985 3a0801s04tom mitocho 40.0 1.2E+02 0.0027 24.8 6.4 63 29-91 82-145 (148)
8 PF02937 COX6C: Cytochrome c o 36.4 23 0.00049 25.9 1.5 23 82-104 50-72 (73)
9 cd00034 ChSh Chromo Shadow Dom 32.7 27 0.00058 23.7 1.3 20 49-68 35-54 (54)
10 PRK14136 recX recombination re 32.6 77 0.0017 29.0 4.5 53 57-111 199-251 (309)
11 PF01393 Chromo_shadow: Chromo 31.7 35 0.00076 23.5 1.8 21 48-68 37-57 (58)
12 KOG0736 Peroxisome assembly fa 30.1 1.1E+02 0.0025 31.9 5.7 123 31-158 548-690 (953)
13 PF08573 SAE2: DNA repair prot 29.8 38 0.00082 25.0 1.8 18 162-179 75-92 (93)
14 COG3461 Uncharacterized conser 28.7 71 0.0015 25.4 3.2 38 38-78 16-53 (103)
15 PF04049 APC8: Anaphase promot 28.4 45 0.00097 26.3 2.1 33 34-66 82-116 (142)
16 smart00515 eIF5C Domain at the 27.9 1.1E+02 0.0025 21.3 3.9 16 50-65 46-61 (83)
17 PF11848 DUF3368: Domain of un 27.9 58 0.0013 21.3 2.2 28 73-103 9-36 (48)
18 PF12066 DUF3546: Domain of un 27.4 83 0.0018 23.8 3.3 44 59-106 45-88 (110)
19 cd04444 DEP_PLEK2 DEP (Disheve 27.3 76 0.0016 25.1 3.1 44 66-109 31-74 (109)
20 PHA03278 envelope glycoprotein 26.6 13 0.00028 34.4 -1.4 14 5-18 173-186 (347)
21 PF00619 CARD: Caspase recruit 25.8 1.7E+02 0.0036 19.8 4.3 27 78-104 8-34 (85)
22 PRK11869 2-oxoacid ferredoxin 25.5 44 0.00095 29.4 1.7 28 40-67 181-212 (280)
23 PF13890 Rab3-GTPase_cat: Rab3 24.9 39 0.00084 28.2 1.2 27 36-62 70-97 (164)
24 KOG2297 Predicted translation 24.9 1.1E+02 0.0023 29.2 4.1 43 37-79 355-399 (412)
25 PF01621 Fusion_gly_K: Cell fu 24.7 15 0.00032 33.9 -1.4 14 5-18 173-186 (337)
26 PF02799 NMT_C: Myristoyl-CoA: 24.0 26 0.00056 29.8 -0.0 40 29-68 35-77 (190)
27 PRK05778 2-oxoglutarate ferred 23.8 65 0.0014 28.5 2.4 18 51-68 214-231 (301)
28 PF13145 Rotamase_2: PPIC-type 23.5 55 0.0012 22.1 1.6 12 53-64 2-13 (121)
29 PHA03275 envelope glycoprotein 22.9 17 0.00037 33.6 -1.4 14 5-18 171-184 (340)
30 COG2179 Predicted hydrolase of 22.5 27 0.00058 29.8 -0.2 64 35-99 29-107 (175)
31 cd08330 CARD_ASC_NALP1 Caspase 22.3 1.6E+02 0.0036 21.1 3.9 28 77-104 6-33 (82)
32 cd00927 Cyt_c_Oxidase_VIc Cyto 22.1 43 0.00093 24.7 0.8 22 83-104 49-70 (70)
33 PRK00117 recX recombination re 21.8 2.7E+02 0.0059 21.3 5.2 44 68-112 59-102 (157)
34 PF13309 HTH_22: HTH domain 21.4 59 0.0013 22.4 1.4 13 90-102 28-40 (64)
35 PRK12702 mannosyl-3-phosphogly 20.3 89 0.0019 28.4 2.6 48 7-74 114-161 (302)
No 1
>KOG1294 consensus Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair]
Probab=83.30 E-value=0.23 Score=44.71 Aligned_cols=42 Identities=24% Similarity=0.221 Sum_probs=39.6
Q ss_pred cceeeeeecccccccccccccCCCCCChhhhhhhhhhhhhhh
Q 044883 3 DAAVLHYTYTKFSDLTSRRDRCGCKPTKEDVRRCFMLEFDRA 44 (180)
Q Consensus 3 EaAVLHytY~kfsdltsRrdRCgCKPTkeDVkrCfmL~FDR~ 44 (180)
.+.||||++-++.+..+|...|-|++-.++++-|++.++|+.
T Consensus 44 ~~~~l~~r~~~~~~~g~~~~~~i~~~~i~~~~~~~~~~~~~~ 85 (335)
T KOG1294|consen 44 FAKVLHYRVEKLLKQGNRKVLNICPWDIAGLEACEKFSGDPE 85 (335)
T ss_pred hhhHHHHHHHHHHHhCCeeEeecCchhhhhhhhhhccccchh
Confidence 578999999999999999999999999999999999997776
No 2
>PF02064 MAS20: MAS20 protein import receptor; InterPro: IPR002056 Virtually all mitochondrial precursors are imported via the same mechanism []: precursors first bind to receptors on the mitochondrial surface, then insert into the translocation channel in the outer membrane. Many outer-membrane proteins participate in the early stages of import, four of which (MAS20, MAS22, MAS37 and MAS70) are components of the receptor. MAS20, which forms a subcomplex with MAS22, seems to interact with most or all mitochondrial precursors, suggesting that the protein binds directly to mitochondrial targeting sequences. The MAS37 and MAS70 components also form a subcomplex, the two subcomplexes possibly binding via their trans- membrane (TM) regions - the TM region of MAS70 promotes oligomerisation of attatched protein domains and shares sequence similarity with the TM region of MAS20 []. MAS20 is also known as TOM20.; GO: 0006605 protein targeting, 0006886 intracellular protein transport, 0005742 mitochondrial outer membrane translocase complex; PDB: 3AX3_A 3AWR_B 2V1S_A 3AX5_C 3AX2_C 1OM2_A 2V1T_B.
Probab=68.05 E-value=18 Score=28.46 Aligned_cols=66 Identities=17% Similarity=0.261 Sum_probs=52.4
Q ss_pred hhhhhhhhhhhhhhhHHHhhhcccHHHHHHHHhhhccccchHHHHHHHhhhhHhHhhhhHHHHHHHHh
Q 044883 30 KEDVRRCFMLEFDRAAFIIASTATEDEMLNWYREHVVWADKTLKKKLMMKGILTRIYAPMIINQGLRE 97 (180)
Q Consensus 30 keDVkrCfmL~FDR~AFIiast~teeem~~wy~erVvw~d~~~~~kLlrkGiltRiy~P~~ii~~lrE 97 (180)
.|+++++||-+...-==.++....++....+|+.-.|...+.--+..+.+.|=-.||.+ ||+.|-|
T Consensus 56 ~~~~e~~Fl~qV~lGE~L~~~G~~~~aa~hf~nAl~V~~qP~~LL~i~q~tlP~~vf~~--l~~~l~e 121 (121)
T PF02064_consen 56 PEEMERFFLQQVQLGEQLLAQGDYEEAAEHFYNALKVCPQPAELLQIYQKTLPPPVFEM--LVQKLPE 121 (121)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTSSSHHHHHHHHHHHS-HHHHHH--HHHTS--
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCHHHHHHHHHhhCCHHHHHH--HHHHcCC
Confidence 68899999998876544466666778899999999999999999999999998888887 6665543
No 3
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=61.23 E-value=32 Score=25.30 Aligned_cols=57 Identities=19% Similarity=0.246 Sum_probs=41.9
Q ss_pred HHHHHHHhhhccccchHHHHHHHhhhhHhHhhhhHHHHHHHHhhcchhHHHHhhccc
Q 044883 55 DEMLNWYREHVVWADKTLKKKLMMKGILTRIYAPMIINQGLRESGIYASVIASANTM 111 (180)
Q Consensus 55 eem~~wy~erVvw~d~~~~~kLlrkGiltRiy~P~~ii~~lrEsGVFss~i~sa~~~ 111 (180)
++.+.++.+.=.=+|...-...++.-+-.+-|.|..|.+.|++-||=..+|..+-..
T Consensus 12 ~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~~~I~~~L~~kGi~~~~i~~~l~~ 68 (121)
T PF02631_consen 12 EEVIDRLKELGYIDDERYAESYVRSRLRRKGKGPRRIRQKLKQKGIDREIIEEALEE 68 (121)
T ss_dssp HHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--HHHHHHHHHHTT--HHHHHHHHTC
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHhcccccccHHHHHHHHHHHCCChHHHHHHHHH
Confidence 344555555444499999999999999999999999999999999999999877663
No 4
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=51.87 E-value=37 Score=28.12 Aligned_cols=78 Identities=14% Similarity=0.156 Sum_probs=53.7
Q ss_pred ChhhhhhhhhhhhhhhHHHhhhcccHHHHHHH-----------------HhhhccccchHHHHHHHhhhhHhHhhhhHHH
Q 044883 29 TKEDVRRCFMLEFDRAAFIIASTATEDEMLNW-----------------YREHVVWADKTLKKKLMMKGILTRIYAPMII 91 (180)
Q Consensus 29 TkeDVkrCfmL~FDR~AFIiast~teeem~~w-----------------y~erVvw~d~~~~~kLlrkGiltRiy~P~~i 91 (180)
..+.+..|+-+.++..+ .-..|+.|+++- ..++=-=+|...-...++...-+. |.|..|
T Consensus 15 ~~~~~~~~~~~Al~~Ls---~R~rse~ELr~kL~k~~~~~~~Ie~Vi~~l~~~~~ldD~~fAe~~i~~r~~~g-~G~~rl 90 (174)
T COG2137 15 RSDQYAKGLNRALRLLS---RRDRSEKELRRKLAKKEFSEEIIEEVIDRLAEEGYLDDTRFAEAYIRSRSRKG-KGPARL 90 (174)
T ss_pred hHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhcc-cChHHH
Confidence 44556666655444442 225555555544 444444466666777777777788 999999
Q ss_pred HHHHHhhcchhHHHHhhcc
Q 044883 92 NQGLRESGIYASVIASANT 110 (180)
Q Consensus 92 i~~lrEsGVFss~i~sa~~ 110 (180)
.|.|++-||=..+|..|-.
T Consensus 91 ~qeL~qkGi~~~~Ie~aL~ 109 (174)
T COG2137 91 KQELKQKGIDDEIIEEALE 109 (174)
T ss_pred HHHHHHcCCCHHHHHHHHh
Confidence 9999999999999988776
No 5
>COG3656 Predicted periplasmic protein [Function unknown]
Probab=43.00 E-value=9.4 Score=32.40 Aligned_cols=45 Identities=29% Similarity=0.499 Sum_probs=35.8
Q ss_pred ccHHHHHHHHhh----------------------hccccchHHHHHHHhhhhHhHhhhhHHHHHHHHhhcchh
Q 044883 52 ATEDEMLNWYRE----------------------HVVWADKTLKKKLMMKGILTRIYAPMIINQGLRESGIYA 102 (180)
Q Consensus 52 ~teeem~~wy~e----------------------rVvw~d~~~~~kLlrkGiltRiy~P~~ii~~lrEsGVFs 102 (180)
.=-+||++|||. -++|..+.-++|||.-|-|. +.+..-||-|.|-
T Consensus 73 kWL~elRqWwRk~Gr~vs~p~dgVsgaTR~pG~y~l~~dg~k~~lk~lppG~Y~------lvVEa~REvGg~e 139 (172)
T COG3656 73 KWLEELRQWWRKNGRLVSTPIDGVSGATRNPGTYALAWDGKKDKLKLLPPGDYY------LVVEAGREVGGYE 139 (172)
T ss_pred hhHHHHHHHHHhcCeEEeccccccccCcCCCCceEEEecCccchhccCCCCcEE------EEEEeccccCCce
Confidence 345789999998 57899999999999999775 3566678887764
No 6
>smart00300 ChSh Chromo Shadow Domain.
Probab=41.17 E-value=16 Score=25.16 Aligned_cols=21 Identities=14% Similarity=0.515 Sum_probs=15.8
Q ss_pred hhcccHHHHHHHHhhhccccc
Q 044883 49 ASTATEDEMLNWYREHVVWAD 69 (180)
Q Consensus 49 ast~teeem~~wy~erVvw~d 69 (180)
|...-..-|.++|++|+.|++
T Consensus 41 ~~~k~P~~vI~FYE~~l~~~~ 61 (61)
T smart00300 41 ANVKCPQKVIRFYESHLTFQS 61 (61)
T ss_pred HHHHChHHHHHHHHHhCccCC
Confidence 334445568999999999974
No 7
>TIGR00985 3a0801s04tom mitochondrial import receptor subunit translocase of outer membrane 20 kDa subunit.
Probab=40.00 E-value=1.2e+02 Score=24.79 Aligned_cols=63 Identities=13% Similarity=0.245 Sum_probs=51.6
Q ss_pred ChhhhhhhhhhhhhhhHHHhhhc-ccHHHHHHHHhhhccccchHHHHHHHhhhhHhHhhhhHHH
Q 044883 29 TKEDVRRCFMLEFDRAAFIIAST-ATEDEMLNWYREHVVWADKTLKKKLMMKGILTRIYAPMII 91 (180)
Q Consensus 29 TkeDVkrCfmL~FDR~AFIiast-~teeem~~wy~erVvw~d~~~~~kLlrkGiltRiy~P~~i 91 (180)
..|+++++||-+.-.-==.++.. ..+|....+|+.-.|+..+.--+..+.+.|=-.||.+|+-
T Consensus 82 d~~e~E~~Fl~eV~~GE~L~~~g~~~~ega~hf~nAl~Vc~qP~~LL~iyq~tlP~~Vf~~lia 145 (148)
T TIGR00985 82 DPSEKEAFFLQEVQLGEELMAQGTNVDEGAVHFYNALKVYPQPQQLLSIYQQTLPEPIFRLMIA 145 (148)
T ss_pred CHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhCCCHHHHHHHHHhhCCHHHHHHHHh
Confidence 57789999998776543335554 6678899999999999999999999999999999996543
No 8
>PF02937 COX6C: Cytochrome c oxidase subunit VIc; InterPro: IPR004204 Cytochrome c oxidase, a 13 subunit complex, 1.9.3.1 from EC is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIc.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3AG4_I 2DYS_V 3ASO_I 2EIK_V 2EIM_I 1OCC_V 1V54_V 1OCO_V 3ASN_V 2EIL_I ....
Probab=36.41 E-value=23 Score=25.90 Aligned_cols=23 Identities=35% Similarity=0.612 Sum_probs=15.5
Q ss_pred HhHhhhhHHHHHHHHhhcchhHH
Q 044883 82 LTRIYAPMIINQGLRESGIYASV 104 (180)
Q Consensus 82 ltRiy~P~~ii~~lrEsGVFss~ 104 (180)
+-+=|-||.=...+++.|+|.|+
T Consensus 50 FYknYD~~k~fe~M~~~G~fqS~ 72 (73)
T PF02937_consen 50 FYKNYDPMKDFEEMRKAGIFQSV 72 (73)
T ss_dssp HHHT--HHHHHHHHHHTT--SS-
T ss_pred HHHccChHHHHHHHHhcCCcccC
Confidence 34568899999999999999986
No 9
>cd00034 ChSh Chromo Shadow Domain, found in association with N-terminal chromo (CHRromatin Organization MOdifier) domain; Chromo domains mediate the interaction of the heterochromatin with other heterochromatin proteins, thereby affecting chromatin structure (e.g. Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2)
Probab=32.70 E-value=27 Score=23.69 Aligned_cols=20 Identities=15% Similarity=0.398 Sum_probs=14.8
Q ss_pred hhcccHHHHHHHHhhhcccc
Q 044883 49 ASTATEDEMLNWYREHVVWA 68 (180)
Q Consensus 49 ast~teeem~~wy~erVvw~ 68 (180)
|...-..-|.++|++|+.|+
T Consensus 35 ~~~k~P~~vI~FYE~~l~~~ 54 (54)
T cd00034 35 LNVKCPLLVISFYEEHLTYN 54 (54)
T ss_pred HHhhCcHHHHHHHHHhcccC
Confidence 33444556899999999995
No 10
>PRK14136 recX recombination regulator RecX; Provisional
Probab=32.59 E-value=77 Score=28.99 Aligned_cols=53 Identities=11% Similarity=0.136 Sum_probs=34.7
Q ss_pred HHHHHhhhccccchHHHHHHHhhhhHhHhhhhHHHHHHHHhhcchhHHHHhhccc
Q 044883 57 MLNWYREHVVWADKTLKKKLMMKGILTRIYAPMIINQGLRESGIYASVIASANTM 111 (180)
Q Consensus 57 m~~wy~erVvw~d~~~~~kLlrkGiltRiy~P~~ii~~lrEsGVFss~i~sa~~~ 111 (180)
.+.++.+.=.-+|...-..+++. -. +-|.|+.|.+.|+.-||=.++|..+-..
T Consensus 199 VIerLke~gYLDDeRFAesyVr~-R~-~kkGp~rIrqELrQKGId~eLIEqALee 251 (309)
T PRK14136 199 LLDALEREGWLSDARFAESLVHR-RA-SRVGSARIVSELKRHAVGDALVESVGAQ 251 (309)
T ss_pred HHHHHHHcCCcCHHHHHHHHHHH-Hh-hchhHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 34444444344555555555543 22 3388999999999999999999876553
No 11
>PF01393 Chromo_shadow: Chromo shadow domain Web page maintained by Rein Aasland; InterPro: IPR008251 Chromo shadow domain is distantly related to chromo domain. It is always found in association with a chromo domain. The CHROMO (CHRromatin Organization MOdifier) domain [, , , ] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting. Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain [], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1); and mammalian modifier 1 and modifier 2. The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigenand and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1.; GO: 0005634 nucleus; PDB: 3Q6S_C 2FMM_B 3P7J_B 1E0B_B 3I3C_A 1DZ1_B 1S4Z_A 3KUP_D.
Probab=31.71 E-value=35 Score=23.53 Aligned_cols=21 Identities=19% Similarity=0.521 Sum_probs=16.4
Q ss_pred hhhcccHHHHHHHHhhhcccc
Q 044883 48 IASTATEDEMLNWYREHVVWA 68 (180)
Q Consensus 48 iast~teeem~~wy~erVvw~ 68 (180)
+|..+-..-|.++|++|++|.
T Consensus 37 ~~~~k~Pq~vI~FYE~~l~f~ 57 (58)
T PF01393_consen 37 EANEKCPQKVIKFYESHLVFK 57 (58)
T ss_dssp HHHHHSHHHHHHHHHHTCEEE
T ss_pred HHHHHCcHHHHHHHHHHeeec
Confidence 444555667999999999995
No 12
>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]
Probab=30.10 E-value=1.1e+02 Score=31.89 Aligned_cols=123 Identities=19% Similarity=0.318 Sum_probs=69.1
Q ss_pred hhhhhhhhhhhhhhHHHhhhcccHHHHHHHHhhhccccchHHHHHHHhh--h--------hHhHhhhhHHHHHHHHhhcc
Q 044883 31 EDVRRCFMLEFDRAAFIIASTATEDEMLNWYREHVVWADKTLKKKLMMK--G--------ILTRIYAPMIINQGLRESGI 100 (180)
Q Consensus 31 eDVkrCfmL~FDR~AFIiast~teeem~~wy~erVvw~d~~~~~kLlrk--G--------iltRiy~P~~ii~~lrEsGV 100 (180)
-+++.||-.+|--. ..|..-+-+.++||-.|+.-|+.-...++.++ | +.+++ +..+.+..+++|.
T Consensus 548 ~~i~~~f~~ei~~~---~lse~qRl~iLq~y~~~~~~n~~v~~k~~a~~t~gfs~~~L~~l~~~~--s~~~~~~i~~~~l 622 (953)
T KOG0736|consen 548 ADIQSLFLHEIEVP---ALSEEQRLEILQWYLNHLPLNQDVNLKQLARKTSGFSFGDLEALVAHS--SLAAKTRIKNKGL 622 (953)
T ss_pred HHHHHhhhhhccCC---CCCHHHHHHHHHHHHhccccchHHHHHHHHHhcCCCCHHHHHHHhcCc--hHHHHHHHHhhcc
Confidence 47899998776544 33444444699999999998876665555554 2 22333 6667777777773
Q ss_pred -------hhHHHHhhcccccc---chhhhhhccccCccccccccccccccCCCchHHHHHHHHhhccc
Q 044883 101 -------YASVIASANTMLSK---DKILSSVESRNNTRESKSVNSSRKIGGFGQSQATARRVLEFIDD 158 (180)
Q Consensus 101 -------Fss~i~sa~~~~~k---~~~l~s~~~~~s~~~~~s~~~s~~~~~~~~sqat~RkiL~~~d~ 158 (180)
+...+-++-..+-. +|-++.+.++.|..--+.-+|.-+-..-+..+.+-..||+-++.
T Consensus 623 ~g~~~~~~~~~~~~~~~~l~~edf~kals~~~~~fs~aiGAPKIPnV~WdDVGGLeevK~eIldTIql 690 (953)
T KOG0736|consen 623 AGGLQEEDEGELCAAGFLLTEEDFDKALSRLQKEFSDAIGAPKIPNVSWDDVGGLEEVKTEILDTIQL 690 (953)
T ss_pred cccchhccccccccccceecHHHHHHHHHHHHHhhhhhcCCCCCCccchhcccCHHHHHHHHHHHhcC
Confidence 22333322222222 22233344444443333335554444555666666777776654
No 13
>PF08573 SAE2: DNA repair protein endonuclease SAE2/CtIP C-terminus; InterPro: IPR013882 SAE2 is a protein involved in repairing meiotic and mitotic double-strand breaks in DNA. It has been shown to negatively regulate DNA damage checkpoint signalling [, ]. SAE2 is homologous to the CtIP proteins in mammals and an homologous protein in plants. Crucial sequence motifs that are highly conserved are the CxxC and the RHR motifs in this C-terminal part of the protein []. It is now known to be an endonuclease. In budding yeast, genetic evidence suggests that the SAE2 protein is essential for the processing of hairpin DNA intermediates and meiotic double-strand breaks by Mre11/Rad50 complexes. SAE2 binds DNA and exhibits endonuclease activity on single-stranded DNA independently of Mre11/Rad50 complexes, but hairpin DNA structures are cleaved cooperatively in the presence of Mre11/Rad50 or Mre11/Rad50/Xrs2. Hairpin structures are not processed at the tip by SAE2 but rather at single-stranded DNA regions adjacent to the hairpin. The catalytic activities of SAE2 are important for its biological functions [].
Probab=29.78 E-value=38 Score=25.02 Aligned_cols=18 Identities=28% Similarity=0.447 Sum_probs=14.0
Q ss_pred cCCCCCCCCCCCCCCCCC
Q 044883 162 TLAIPPESPPGPDDLNID 179 (180)
Q Consensus 162 ~~AvPP~SPPg~~~~~~~ 179 (180)
..-.||.||||+=+.++-
T Consensus 75 ~~~~rp~TPpGfW~~dFP 92 (93)
T PF08573_consen 75 YRYARPSTPPGFWDIDFP 92 (93)
T ss_pred CCCCCCCCCCCCcCCCCC
Confidence 355899999999777653
No 14
>COG3461 Uncharacterized conserved protein [Function unknown]
Probab=28.66 E-value=71 Score=25.36 Aligned_cols=38 Identities=24% Similarity=0.341 Sum_probs=29.8
Q ss_pred hhhhhhhHHHhhhcccHHHHHHHHhhhccccchHHHHHHHh
Q 044883 38 MLEFDRAAFIIASTATEDEMLNWYREHVVWADKTLKKKLMM 78 (180)
Q Consensus 38 mL~FDR~AFIiast~teeem~~wy~erVvw~d~~~~~kLlr 78 (180)
+-+|-|+ +-|..-|-|-.-||.+|++=+-+....+.|.
T Consensus 16 irdf~Ra---~~SLiEEiEA~~wY~qR~~~tKD~~~r~Ime 53 (103)
T COG3461 16 IRDFSRA---RQSLIEEIEAMMWYDQRADATKDEDLRAIME 53 (103)
T ss_pred HHHHHHH---HHHHHHHHHHHHHHHHHhhccccHhHHHHHH
Confidence 4578888 8898888898899999998776665555543
No 15
>PF04049 APC8: Anaphase promoting complex subunit 8 / Cdc23 ; InterPro: IPR007192 The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8). This entry is for CDC23.; GO: 0030071 regulation of mitotic metaphase/anaphase transition, 0005680 anaphase-promoting complex
Probab=28.36 E-value=45 Score=26.28 Aligned_cols=33 Identities=24% Similarity=0.470 Sum_probs=20.8
Q ss_pred hhhh-hhhhhhhHHHhhhccc-HHHHHHHHhhhcc
Q 044883 34 RRCF-MLEFDRAAFIIASTAT-EDEMLNWYREHVV 66 (180)
Q Consensus 34 krCf-mL~FDR~AFIiast~t-eeem~~wy~erVv 66 (180)
|-+| .-||||+||++-...+ ..-|++.|-.-+-
T Consensus 82 ksyFD~kEy~RaA~~L~~~~s~~~~FL~lYs~YLa 116 (142)
T PF04049_consen 82 KSYFDCKEYDRAAHVLKDCKSPKALFLRLYSRYLA 116 (142)
T ss_pred HHHhchhHHHHHHHHHccCCCchHHHHHHHHHHHH
Confidence 3444 2489999999988553 3336666654433
No 16
>smart00515 eIF5C Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5.
Probab=27.93 E-value=1.1e+02 Score=21.28 Aligned_cols=16 Identities=31% Similarity=0.800 Sum_probs=13.0
Q ss_pred hcccHHHHHHHHhhhc
Q 044883 50 STATEDEMLNWYREHV 65 (180)
Q Consensus 50 st~teeem~~wy~erV 65 (180)
...+||.+++||.+..
T Consensus 46 dileEe~il~W~~~~~ 61 (83)
T smart00515 46 DILEEEAILKWYEKAV 61 (83)
T ss_pred ccccHHHHHHHHHcCC
Confidence 3568889999999874
No 17
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=27.90 E-value=58 Score=21.31 Aligned_cols=28 Identities=14% Similarity=0.246 Sum_probs=20.5
Q ss_pred HHHHHhhhhHhHhhhhHHHHHHHHhhcchhH
Q 044883 73 KKKLMMKGILTRIYAPMIINQGLRESGIYAS 103 (180)
Q Consensus 73 ~~kLlrkGiltRiy~P~~ii~~lrEsGVFss 103 (180)
-....++|+++.+ .-+++.|+++|.|-|
T Consensus 9 L~~Ak~~GlI~~~---~~~l~~l~~~g~~is 36 (48)
T PF11848_consen 9 LLLAKRRGLISEV---KPLLDRLQQAGFRIS 36 (48)
T ss_pred HHHHHHcCChhhH---HHHHHHHHHcCcccC
Confidence 4566788999833 337889999998854
No 18
>PF12066 DUF3546: Domain of unknown function (DUF3546); InterPro: IPR021933 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 93 to 114 amino acids in length. This domain has two completely conserved Y residues that may be functionally important. ; PDB: 3AX1_A.
Probab=27.38 E-value=83 Score=23.83 Aligned_cols=44 Identities=18% Similarity=0.149 Sum_probs=24.8
Q ss_pred HHHhhhccccchHHHHHHHhhhhHhHhhhhHHHHHHHHhhcchhHHHH
Q 044883 59 NWYREHVVWADKTLKKKLMMKGILTRIYAPMIINQGLRESGIYASVIA 106 (180)
Q Consensus 59 ~wy~erVvw~d~~~~~kLlrkGiltRiy~P~~ii~~lrEsGVFss~i~ 106 (180)
.||+|+-............+.+...|+- ..-.+.++|.|..+--
T Consensus 45 eWFreKY~P~~~~~~~~~~~~~~~~~~~----~F~~~l~~G~~d~~~l 88 (110)
T PF12066_consen 45 EWFREKYHPEELDKRREERKEFRKGRAD----VFMEDLESGKFDEVSL 88 (110)
T ss_dssp HHHHHHH-HHHHHHHHHHHHHHHHHHHH----HHHHHHHTT-------
T ss_pred HHHHHhcCcHhhHHHHHHHHHHHHHHHH----HHHHHHHCCCCccccc
Confidence 4999999777766666666666655553 3445678999987643
No 19
>cd04444 DEP_PLEK2 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in pleckstrin 2-like proteins. Pleckstrin 2 is found in a wide variety of cell types, which suggest a more general role in signaling than pleckstrin 1. Pleckstrin-like proteins contain a central DEP domain, flanked by 2 PH (pleckstrin homology) domains.
Probab=27.27 E-value=76 Score=25.05 Aligned_cols=44 Identities=11% Similarity=0.094 Sum_probs=30.9
Q ss_pred cccchHHHHHHHhhhhHhHhhhhHHHHHHHHhhcchhHHHHhhc
Q 044883 66 VWADKTLKKKLMMKGILTRIYAPMIINQGLRESGIYASVIASAN 109 (180)
Q Consensus 66 vw~d~~~~~kLlrkGiltRiy~P~~ii~~lrEsGVFss~i~sa~ 109 (180)
+...++++.=|+..|...-=.....|-|.|++.|+|..|..-+.
T Consensus 31 CF~Gse~VDWLv~~~~~i~R~EAv~l~q~Lmd~gli~hV~~~s~ 74 (109)
T cd04444 31 TFLGSALVDWLISNSFAASRLEAVTLASMLMEENFLRPVGVRSM 74 (109)
T ss_pred cccchHHHHHHHHCCCCCCHHHHHHHHHHHHhCCchhhHHHHhh
Confidence 45566666677777654333445568899999999999986443
No 20
>PHA03278 envelope glycoprotein K; Provisional
Probab=26.60 E-value=13 Score=34.43 Aligned_cols=14 Identities=50% Similarity=0.802 Sum_probs=12.2
Q ss_pred eeeeeecccccccc
Q 044883 5 AVLHYTYTKFSDLT 18 (180)
Q Consensus 5 AVLHytY~kfsdlt 18 (180)
-+|||+||||++|-
T Consensus 173 ~~L~~~YTK~arlm 186 (347)
T PHA03278 173 TLLHCTYTKMARLM 186 (347)
T ss_pred HHhcCChHHHHHHH
Confidence 47999999999885
No 21
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=25.85 E-value=1.7e+02 Score=19.76 Aligned_cols=27 Identities=11% Similarity=0.060 Sum_probs=20.8
Q ss_pred hhhhHhHhhhhHHHHHHHHhhcchhHH
Q 044883 78 MKGILTRIYAPMIINQGLRESGIYASV 104 (180)
Q Consensus 78 rkGiltRiy~P~~ii~~lrEsGVFss~ 104 (180)
|.-|+..|..|.-|+..|.+.|||+.-
T Consensus 8 r~~Lv~~l~~~~~ild~L~~~~vlt~~ 34 (85)
T PF00619_consen 8 RQELVEDLDDLDDILDHLLSRGVLTEE 34 (85)
T ss_dssp HHHHHHHSSHHHHHHHHHHHTTSSSHH
T ss_pred HHHHHHHhCcHHHHHHHHHHCCCCCHH
Confidence 444556666788899999999999864
No 22
>PRK11869 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional
Probab=25.54 E-value=44 Score=29.36 Aligned_cols=28 Identities=18% Similarity=0.382 Sum_probs=19.1
Q ss_pred hhhhhHHHhhh----cccHHHHHHHHhhhccc
Q 044883 40 EFDRAAFIIAS----TATEDEMLNWYREHVVW 67 (180)
Q Consensus 40 ~FDR~AFIias----t~teeem~~wy~erVvw 67 (180)
+.+..+||..- |-....|..||++|++|
T Consensus 181 ~~~Gp~lIeV~~pC~~~~~~~~~~~~~~~~~~ 212 (280)
T PRK11869 181 KHKGLAIVDIFQPCVSFNKVNTYQWYRENTYY 212 (280)
T ss_pred hCCCCEEEEEECCCCCCCccchHHHHHhhccc
Confidence 45566665443 33334699999999999
No 23
>PF13890 Rab3-GTPase_cat: Rab3 GTPase-activating protein catalytic subunit
Probab=24.91 E-value=39 Score=28.19 Aligned_cols=27 Identities=26% Similarity=0.418 Sum_probs=22.9
Q ss_pred hhhhhhhhhHHHhhh-cccHHHHHHHHh
Q 044883 36 CFMLEFDRAAFIIAS-TATEDEMLNWYR 62 (180)
Q Consensus 36 CfmL~FDR~AFIias-t~teeem~~wy~ 62 (180)
|-.|-=|..||..|+ .+--|+|-+||-
T Consensus 70 s~~LlSDM~aFKAANpg~vfeDFVRW~S 97 (164)
T PF13890_consen 70 SASLLSDMQAFKAANPGCVFEDFVRWYS 97 (164)
T ss_pred HHHHHHHHHHHHhcCCCcchHhhhhccC
Confidence 345667999999999 888899999995
No 24
>KOG2297 consensus Predicted translation factor, contains W2 domain [Translation, ribosomal structure and biogenesis]
Probab=24.86 E-value=1.1e+02 Score=29.23 Aligned_cols=43 Identities=33% Similarity=0.542 Sum_probs=34.9
Q ss_pred hhhhhhhh--HHHhhhcccHHHHHHHHhhhccccchHHHHHHHhh
Q 044883 37 FMLEFDRA--AFIIASTATEDEMLNWYREHVVWADKTLKKKLMMK 79 (180)
Q Consensus 37 fmL~FDR~--AFIiast~teeem~~wy~erVvw~d~~~~~kLlrk 79 (180)
||-.|-.. .|-=|..-+||.+++||++--|--++.+-++-|++
T Consensus 355 fMKaFqkiV~lfYk~dVLsEe~IL~Wyk~gh~~KGk~~Fleqmkk 399 (412)
T KOG2297|consen 355 FMKAFQKIVVLFYKADVLSEETILKWYKEGHVAKGKSVFLEQMKK 399 (412)
T ss_pred HHHHHHHHHHHHHHHHhhhhHHHHHHHHhccccccHHHHHHHHHH
Confidence 77777764 35567789999999999998888888888877775
No 25
>PF01621 Fusion_gly_K: Cell fusion glycoprotein K; InterPro: IPR002567 Human herpesvirus 1 (HHV-1) (Human herpes simplex virus 1) glycoprotein K (gK) plays an essential role in viral replication and cell fusion. gK is a very hydrophobic membrane protein that contains a signal sequence and several hydrophobic regions. gK contains three transmembrane domains (amino acids 125-139, 226-239, and 311-325) and another hydrophobic domain (amino acids 241-265), which is relatively less hydrophobic and much longer compared with the transmembrane sequences located in the extracellular loop. The domains may interact with each other to form a complex tertiary structure that is critical for the biological function of gK [].; GO: 0007155 cell adhesion, 0016020 membrane
Probab=24.72 E-value=15 Score=33.90 Aligned_cols=14 Identities=43% Similarity=0.802 Sum_probs=12.3
Q ss_pred eeeeeecccccccc
Q 044883 5 AVLHYTYTKFSDLT 18 (180)
Q Consensus 5 AVLHytY~kfsdlt 18 (180)
.+|||+||||++|.
T Consensus 173 ~~L~~pYTK~arlm 186 (337)
T PF01621_consen 173 VLLKYPYTKMARLM 186 (337)
T ss_pred HHhcCChHHHHHHH
Confidence 47999999999885
No 26
>PF02799 NMT_C: Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain; InterPro: IPR022677 Myristoyl-CoA:protein N-myristoyltransferase (2.3.1.97 from EC) (Nmt) [] is the enzyme responsible for transferring a myristate group on the N-terminal glycine of a number of cellular eukaryotics and viral proteins. Nmt is a monomeric protein of about 50 to 60kDa whose sequence appears to be well conserved. The N and C-terminal domains of NMT are structurally similar, each adopting an acyl-CoA N-acyltransferase-like fold. This entry represents the C-terminal region.; GO: 0004379 glycylpeptide N-tetradecanoyltransferase activity; PDB: 2P6G_B 2P6F_F 2P6E_A 1IIC_A 1IID_A 2NMT_A 2WUU_A 1IYL_B 1NMT_B 1IYK_A ....
Probab=23.96 E-value=26 Score=29.77 Aligned_cols=40 Identities=28% Similarity=0.501 Sum_probs=26.9
Q ss_pred Chhhhhhhhhhhhh-hhHHHhhhcccHHHHHHHH--hhhcccc
Q 044883 29 TKEDVRRCFMLEFD-RAAFIIASTATEDEMLNWY--REHVVWA 68 (180)
Q Consensus 29 TkeDVkrCfmL~FD-R~AFIiast~teeem~~wy--~erVvw~ 68 (180)
+++||..+.-|=-+ -.-|-++-.-|+||+.+|+ ++.|||+
T Consensus 35 ~~~Dv~~v~~Ll~~yl~~f~l~~~fs~eev~Hw~lp~~~Vv~s 77 (190)
T PF02799_consen 35 EEKDVPQVTKLLNKYLKKFDLAPVFSEEEVKHWFLPRKNVVYS 77 (190)
T ss_dssp -GGGHHHHHHHHHHHHTTSSEEEE--HHHHHHHHS-BTTTEEE
T ss_pred chhhHHHHHHHHHHHHHhcccccccCHHHHHhhcccCCCeEEE
Confidence 78899888654221 1136688888999999999 7888875
No 27
>PRK05778 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Validated
Probab=23.78 E-value=65 Score=28.47 Aligned_cols=18 Identities=22% Similarity=0.318 Sum_probs=15.4
Q ss_pred cccHHHHHHHHhhhcccc
Q 044883 51 TATEDEMLNWYREHVVWA 68 (180)
Q Consensus 51 t~teeem~~wy~erVvw~ 68 (180)
..+-.+|++||+||++.-
T Consensus 214 ~~~~~~~~~~~~~~~~~~ 231 (301)
T PRK05778 214 TKSPAYMREYYKKRVYKL 231 (301)
T ss_pred ccCHHHHHHHHHhhcEEc
Confidence 467789999999999876
No 28
>PF13145 Rotamase_2: PPIC-type PPIASE domain; PDB: 3NRK_A 2KGJ_A.
Probab=23.46 E-value=55 Score=22.15 Aligned_cols=12 Identities=42% Similarity=0.828 Sum_probs=9.3
Q ss_pred cHHHHHHHHhhh
Q 044883 53 TEDEMLNWYREH 64 (180)
Q Consensus 53 teeem~~wy~er 64 (180)
|++|++.||++|
T Consensus 2 te~el~~yY~~n 13 (121)
T PF13145_consen 2 TEEELRAYYEEN 13 (121)
T ss_dssp -HHHHHHHHHH-
T ss_pred CHHHHHHHHHHH
Confidence 789999999984
No 29
>PHA03275 envelope glycoprotein K; Provisional
Probab=22.93 E-value=17 Score=33.64 Aligned_cols=14 Identities=43% Similarity=0.615 Sum_probs=12.2
Q ss_pred eeeeeecccccccc
Q 044883 5 AVLHYTYTKFSDLT 18 (180)
Q Consensus 5 AVLHytY~kfsdlt 18 (180)
-+|||+||||++|.
T Consensus 171 ~~L~~~YTK~arll 184 (340)
T PHA03275 171 TVLKTPYTKLARLL 184 (340)
T ss_pred HHhcCChHHHHHHH
Confidence 47999999999885
No 30
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=22.53 E-value=27 Score=29.78 Aligned_cols=64 Identities=20% Similarity=0.356 Sum_probs=39.3
Q ss_pred hhhhhhhhhhHHHhhh-cccHHHHHHHHhh--------hccccchHHHHHHHhh--h--hHhHhhhhH--HHHHHHHhhc
Q 044883 35 RCFMLEFDRAAFIIAS-TATEDEMLNWYRE--------HVVWADKTLKKKLMMK--G--ILTRIYAPM--IINQGLRESG 99 (180)
Q Consensus 35 rCfmL~FDR~AFIias-t~teeem~~wy~e--------rVvw~d~~~~~kLlrk--G--iltRiy~P~--~ii~~lrEsG 99 (180)
+|+++|+|-+. |-+. ---.+|++.|+.| -||=|.++-+.+.... | .+.|..-|| .+-++|+|-+
T Consensus 29 kgvi~DlDNTL-v~wd~~~~tpe~~~W~~e~k~~gi~v~vvSNn~e~RV~~~~~~l~v~fi~~A~KP~~~~fr~Al~~m~ 107 (175)
T COG2179 29 KGVILDLDNTL-VPWDNPDATPELRAWLAELKEAGIKVVVVSNNKESRVARAAEKLGVPFIYRAKKPFGRAFRRALKEMN 107 (175)
T ss_pred cEEEEeccCce-ecccCCCCCHHHHHHHHHHHhcCCEEEEEeCCCHHHHHhhhhhcCCceeecccCccHHHHHHHHHHcC
Confidence 79999999992 2222 4556789999988 4566766666653332 2 233444443 4556666554
No 31
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=22.25 E-value=1.6e+02 Score=21.11 Aligned_cols=28 Identities=11% Similarity=0.097 Sum_probs=22.9
Q ss_pred HhhhhHhHhhhhHHHHHHHHhhcchhHH
Q 044883 77 MMKGILTRIYAPMIINQGLRESGIYASV 104 (180)
Q Consensus 77 lrkGiltRiy~P~~ii~~lrEsGVFss~ 104 (180)
-|.-|+.|+-...-|+..|.+.||++.-
T Consensus 6 ~r~~Li~~v~~v~~ilD~L~~~~Vit~e 33 (82)
T cd08330 6 HREALIARVTNVDPILDKLHGKKVITQE 33 (82)
T ss_pred HHHHHHHHHhhHHHHHHHHHHCCCCCHH
Confidence 4566788888888899999999998754
No 32
>cd00927 Cyt_c_Oxidase_VIc Cytochrome c oxidase subunit VIc. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. The VIc subunit is found only in eukaryotes and its specific function remains unclear. It has been reported that the relative concentrations of some nuclear encoded CcO subunits, including subunit VIc, compared to those of the mitochondrial encoded subunits, are altered significantly during the progression of prostate cancer.
Probab=22.13 E-value=43 Score=24.72 Aligned_cols=22 Identities=23% Similarity=0.460 Sum_probs=18.8
Q ss_pred hHhhhhHHHHHHHHhhcchhHH
Q 044883 83 TRIYAPMIINQGLRESGIYASV 104 (180)
Q Consensus 83 tRiy~P~~ii~~lrEsGVFss~ 104 (180)
-+=|-||-=-..+|+.|+|.|+
T Consensus 49 YknYD~~kdFerM~~~G~f~S~ 70 (70)
T cd00927 49 YKTYDAMKDFERMRKAGLFQSC 70 (70)
T ss_pred HHccChHHHHHHHHHcCCcccC
Confidence 3557899999999999999885
No 33
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=21.79 E-value=2.7e+02 Score=21.26 Aligned_cols=44 Identities=25% Similarity=0.383 Sum_probs=32.8
Q ss_pred cchHHHHHHHhhhhHhHhhhhHHHHHHHHhhcchhHHHHhhcccc
Q 044883 68 ADKTLKKKLMMKGILTRIYAPMIINQGLRESGIYASVIASANTML 112 (180)
Q Consensus 68 ~d~~~~~kLlrkGiltRiy~P~~ii~~lrEsGVFss~i~sa~~~~ 112 (180)
+|...-.++++.- -.+-+.|..|.+.|+.-||=..+|..+-..+
T Consensus 59 dD~~~a~~~~~~~-~~~~~g~~~I~~~L~~kGi~~~~I~~~l~~~ 102 (157)
T PRK00117 59 DDERFAESFVRSR-ARKGYGPRRIRQELRQKGVDREIIEEALAEL 102 (157)
T ss_pred CHHHHHHHHHHHH-HhCCchHHHHHHHHHHcCCCHHHHHHHHHHc
Confidence 4555555555554 3466899999999999999999998876644
No 34
>PF13309 HTH_22: HTH domain
Probab=21.37 E-value=59 Score=22.39 Aligned_cols=13 Identities=38% Similarity=0.514 Sum_probs=11.6
Q ss_pred HHHHHHHhhcchh
Q 044883 90 IINQGLRESGIYA 102 (180)
Q Consensus 90 ~ii~~lrEsGVFs 102 (180)
-||+.|.+.|+|.
T Consensus 28 ~iV~~L~~~G~F~ 40 (64)
T PF13309_consen 28 EIVRQLYEKGIFL 40 (64)
T ss_pred HHHHHHHHCCCcc
Confidence 4899999999995
No 35
>PRK12702 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=20.30 E-value=89 Score=28.38 Aligned_cols=48 Identities=17% Similarity=0.234 Sum_probs=32.8
Q ss_pred eeeecccccccccccccCCCCCChhhhhhhhhhhhhhhHHHhhhcccHHHHHHHHhhhccccchHHHH
Q 044883 7 LHYTYTKFSDLTSRRDRCGCKPTKEDVRRCFMLEFDRAAFIIASTATEDEMLNWYREHVVWADKTLKK 74 (180)
Q Consensus 7 LHytY~kfsdltsRrdRCgCKPTkeDVkrCfmL~FDR~AFIiast~teeem~~wy~erVvw~d~~~~~ 74 (180)
+||.|+.|+|+ |.++|-+.-=|.-+.+ +-.+.|-|-|-++|.+.+..+
T Consensus 114 ~~~~f~gF~d~-----------t~~ei~~~TGL~~~~A---------~~A~~Re~SEp~~w~~~~~~~ 161 (302)
T PRK12702 114 SHLDLIGFGDW-----------TASELAAATGIPLEEA---------ERAQKREYSEIFSYSGDPARL 161 (302)
T ss_pred hCCCceehhhC-----------CHHHHHHHhCcCHHHH---------HHHHhccCCcceEecCCHHHH
Confidence 57888888888 5667665554443333 334788999999998865433
Done!