Query 025994
Match_columns 245
No_of_seqs 162 out of 375
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 02:26:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025994.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025994hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05712 MRG: MRG; InterPro: 100.0 6.5E-50 1.4E-54 343.4 13.4 159 71-229 16-194 (194)
2 KOG3001 Dosage compensation re 100.0 1.1E-38 2.5E-43 297.6 10.4 167 76-242 217-390 (391)
3 PLN00104 MYST -like histone ac 92.4 0.038 8.3E-07 53.3 0.0 16 2-17 97-112 (450)
4 cd04402 RhoGAP_ARHGAP20 RhoGAP 68.9 59 0.0013 27.5 9.7 141 82-228 14-191 (192)
5 cd04404 RhoGAP-p50rhoGAP RhoGA 63.2 68 0.0015 27.0 9.0 137 82-225 22-195 (195)
6 smart00340 HALZ homeobox assoc 55.9 5.9 0.00013 26.0 0.9 16 19-34 17-32 (44)
7 PF06543 Lac_bphage_repr: Lact 55.3 3.8 8.3E-05 27.5 -0.1 19 6-25 19-37 (49)
8 PF13495 Phage_int_SAM_4: Phag 45.3 36 0.00078 24.1 3.8 44 108-152 38-81 (85)
9 PF02899 Phage_int_SAM_1: Phag 43.9 1.1E+02 0.0024 21.3 8.8 82 117-219 1-82 (84)
10 PF15136 UPF0449: Uncharacteri 41.8 18 0.0004 27.9 1.8 20 104-123 7-26 (97)
11 PF11390 FdsD: NADH-dependant 38.2 46 0.001 23.4 3.3 33 181-213 1-33 (61)
12 PRK14752 delta-hemolysin; Prov 38.0 54 0.0012 21.1 3.2 37 182-224 5-41 (44)
13 cd04390 RhoGAP_ARHGAP22_24_25 33.3 3E+02 0.0064 23.2 11.4 19 207-225 181-199 (199)
14 PF05372 Delta_lysin: Delta ly 31.1 86 0.0019 18.0 2.9 21 204-224 3-23 (25)
15 KOG2573 Ribosome biogenesis pr 29.8 1.3E+02 0.0027 29.3 5.7 78 81-162 69-146 (498)
16 PF10496 Syntaxin-18_N: SNARE- 28.8 51 0.0011 24.2 2.4 24 203-226 45-68 (87)
17 PRK00236 xerC site-specific ty 25.5 4.1E+02 0.0089 22.4 9.1 88 109-220 2-92 (297)
18 TIGR03248 galactar-dH20 galact 25.4 1.1E+02 0.0024 30.4 4.6 49 172-234 305-353 (507)
19 cd00024 CHROMO Chromatin organ 24.1 28 0.00061 22.6 0.2 18 2-19 28-45 (55)
20 PF09539 DUF2385: Protein of u 22.6 81 0.0018 24.3 2.5 41 172-212 8-58 (96)
21 KOG1556 26S proteasome regulat 21.6 1.3E+02 0.0028 27.4 3.9 45 175-219 169-215 (309)
22 cd04392 RhoGAP_ARHGAP19 RhoGAP 21.3 94 0.002 26.8 3.0 36 191-226 162-197 (208)
23 PF04295 GD_AH_C: D-galactarat 20.7 1.6E+02 0.0035 28.3 4.6 49 172-234 196-244 (396)
No 1
>PF05712 MRG: MRG; InterPro: IPR008676 This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation [, ].; GO: 0005634 nucleus; PDB: 2AQL_A 2F5J_A 2LKM_B 2Y0N_D.
Probab=100.00 E-value=6.5e-50 Score=343.35 Aligned_cols=159 Identities=48% Similarity=0.752 Sum_probs=126.9
Q ss_pred cccCCCcceEEeCChhHHHHHHHHHHhhhhCCceeeCCCCCCHHHHHHHHHHhhcccC--Cch-----hhhHHHHHHHHH
Q 025994 71 NGLQMENFVNIQIPPPLKKQLVDDCEFITHLGKLVKLPRTPNVDDILEKYCDYRSKKD--GLV-----ADSTGEIVKGLR 143 (245)
Q Consensus 71 ~~~~~~~~i~i~iP~~Lk~~LvdD~e~Itk~~~L~~LP~~~tV~~IL~~y~~~~~~~~--~~~-----~~~~~e~~~Gl~ 143 (245)
++....++++|+||..||.+|||||++|+++++|++|||++||++||++|+++..... ... ...+.|+++||+
T Consensus 16 ~~~~~~~~~~i~lP~~Lk~~LvdD~~~I~~~~~l~~LP~~~~V~~IL~~y~~~~~~~~~~~~~~~~~~~~~~~e~~~Gl~ 95 (194)
T PF05712_consen 16 DDSEEEPEIKIELPEELKKILVDDWELITKEKKLVKLPAKPSVDDILEDYVESFADSDDSEEESAEQERDLLKEVADGLR 95 (194)
T ss_dssp --------------HHHHHHHHHHHHHHHTS-EEE-SS-SSBHHHHHHHHHHHHHHCHCSS---THH--HHHHHHHHHHH
T ss_pred cccccCceEEEECCHHHHHHHHHHHHHHHcCCceeeCCCCCCHHHHHHHHHHHHhhcccCcchhHHHHHHHHHHHHHHHH
Confidence 3445668899999999999999999999999999999999999999999999987432 111 146899999999
Q ss_pred HHHhhhcCccCCChhhHhhHHHhhhcC------------CCCCcccchHHHHHHHhhhHHHhhhccCCHHHHHHHHHHHH
Q 025994 144 CYFDKALPIMLLYKSEREQYEDSMAAD------------VSPSSVYGAEHLLRLFVKLPELLVHAKIEEETLTLLQHKLV 211 (245)
Q Consensus 144 ~yFn~~L~~~LLY~~ER~Qy~~~~~~~------------~~~S~~YG~~HLLRL~vkLP~ll~~t~~d~~~~~~l~~~l~ 211 (245)
.|||++||.+|||++||+||.+++... .+||++||++|||||||+||+||+.++|++.+++.|..+++
T Consensus 96 ~yFn~~L~~~LLY~~Er~Qy~~~~~~~~~~~~~~~~~~~~~ps~~YG~~HLLRL~vkLPell~~~~~~~~~~~~l~~~l~ 175 (194)
T PF05712_consen 96 DYFNKALGSQLLYKFERPQYDELLKKHATRDDSPPDEPGFRPSDIYGAIHLLRLFVKLPELLSSTNMDEESINILLEHLQ 175 (194)
T ss_dssp HHHHHHCCCCTS-GGGHHHHHHHHHHS---------STTS-HHHC-BHHHHHHHHHHHHHHHCCCGGCHHHHHHHHHHHH
T ss_pred HHHHHHhccccCcHHHHHHHHHHHHhcccchhccccCCCCCHHhhccHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHH
Confidence 999999999999999999999998653 49999999999999999999999999999999999999999
Q ss_pred HHHHHHHHchhhhcc-ccC
Q 025994 212 DLLKFLQKHQSTFFL-SRY 229 (245)
Q Consensus 212 ~fl~fL~~n~~~~f~-~~Y 229 (245)
+||+||++|.++||. ++|
T Consensus 176 ~fl~fL~~n~~~~f~~~~y 194 (194)
T PF05712_consen 176 DFLKFLEKNSEEYFSEEDY 194 (194)
T ss_dssp HHHHHHHHTHHHHS-GGGE
T ss_pred HHHHHHHHHHHHhCCcccC
Confidence 999999999999999 666
No 2
>KOG3001 consensus Dosage compensation regulatory complex/histone acetyltransferase complex, subunit MSL-3/MRG15/EAF3, and related CHROMO domain-containing proteins [Chromatin structure and dynamics; Transcription]
Probab=100.00 E-value=1.1e-38 Score=297.61 Aligned_cols=167 Identities=41% Similarity=0.628 Sum_probs=148.3
Q ss_pred CcceEEeCChhHHHHHHHHHHhhhhCCceeeCCCCCCHHHHHHHHHHhhcccC--Cc-hhhhHHHHHHHHHHHHhhhcCc
Q 025994 76 ENFVNIQIPPPLKKQLVDDCEFITHLGKLVKLPRTPNVDDILEKYCDYRSKKD--GL-VADSTGEIVKGLRCYFDKALPI 152 (245)
Q Consensus 76 ~~~i~i~iP~~Lk~~LvdD~e~Itk~~~L~~LP~~~tV~~IL~~y~~~~~~~~--~~-~~~~~~e~~~Gl~~yFn~~L~~ 152 (245)
.+++.+.||..|+..|+|||+.+++..+++.+|+..+|+.|+..|........ +. ....+.+...|++.|||.+||.
T Consensus 217 ~~~v~~~l~~~~~~~l~dd~~~vt~~~~~~~~~~~~~~e~~~~~~~~~~k~~~~~~~~~~~~~~~~~~g~~~yfn~~lG~ 296 (391)
T KOG3001|consen 217 TVEVKLSLPQELKRSLVDDWDSVTEVDSLAELPQDVTVEQILKKYGFSEKKASGLSNSKEPEVLEVAAGLKRYFNGQLGV 296 (391)
T ss_pred cccccccCchhhcccccchhhhhhhhhhhhcccCCchhhhhhhhhhHhhhhccccccccccccccccccceeeecccchh
Confidence 45789999999999999999999999999999999999999999987665322 11 1223345559999999999999
Q ss_pred cCCChhhHhhHHHhhhcCC---CCCcccchHHHHHHHhhhHHHhhhccCCHHHHHHHHHHHHHHHHHHHHchhhhcc-cc
Q 025994 153 MLLYKSEREQYEDSMAADV---SPSSVYGAEHLLRLFVKLPELLVHAKIEEETLTLLQHKLVDLLKFLQKHQSTFFL-SR 228 (245)
Q Consensus 153 ~LLY~~ER~Qy~~~~~~~~---~~S~~YG~~HLLRL~vkLP~ll~~t~~d~~~~~~l~~~l~~fl~fL~~n~~~~f~-~~ 228 (245)
+|||++||.||.+++.+.. +||++|||+|||||||+||+||.++.|+.++++.|..++++|++||.+|...||. ++
T Consensus 297 ~llyk~Er~qy~~~~~~~~~Ds~~s~vyGa~HLlRLfvKLpe~l~~~~~~~~~l~~Ll~~~~~flk~L~~~~~~~f~~s~ 376 (391)
T KOG3001|consen 297 MLLYKFERLQYAEVVAKYPKDSPPSNVYGAEHLLRLFVKLPEILKYTPMDEKSLALLLRHRKDFLKYLRKNSASFFSSSD 376 (391)
T ss_pred hhhhhhhhHHHHHHHhcCCCCCCcccchhHHHHHHHHhHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 9999999999999986433 4999999999999999999999999999999999999999999999999977887 99
Q ss_pred CCCCCHHHHHhccc
Q 025994 229 YHSAEDVETSANKQ 242 (245)
Q Consensus 229 Y~~~~~~Y~~~a~~ 242 (245)
|.+++++|.+.+.|
T Consensus 377 y~~~~~e~~~~~~~ 390 (391)
T KOG3001|consen 377 YSNASPEYSSSSLP 390 (391)
T ss_pred hhhhchhhhhcccC
Confidence 99999999998765
No 3
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=92.38 E-value=0.038 Score=53.29 Aligned_cols=16 Identities=31% Similarity=0.497 Sum_probs=15.2
Q ss_pred CCCCCcccccccCCCC
Q 025994 2 REAGSWDEWVGVHRLM 17 (245)
Q Consensus 2 ~~~~~WDeWV~e~r~l 17 (245)
|||++|||||+.+||-
T Consensus 97 g~nrRlDEWV~~~rLd 112 (450)
T PLN00104 97 EFNRRLDEWVKLEQLD 112 (450)
T ss_pred cCCccHhhccCHhhcc
Confidence 8999999999999994
No 4
>cd04402 RhoGAP_ARHGAP20 RhoGAP_ARHGAP20: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP20-like proteins. ArhGAP20, also known as KIAA1391 and RA-RhoGAP, contains a RhoGAP, a RA, and a PH domain, and ANXL repeats. ArhGAP20 is activated by Rap1 and induces inactivation of Rho, which in turn leads to neurite outgrowth. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=68.92 E-value=59 Score=27.48 Aligned_cols=141 Identities=16% Similarity=0.196 Sum_probs=67.5
Q ss_pred eCChhHHHHHHH-HHHhhhhCCceeeCCCCCCHHHHHHHHHHhhcccCCchhhhHHHHHHHHHHHHhhhcCccCCChhhH
Q 025994 82 QIPPPLKKQLVD-DCEFITHLGKLVKLPRTPNVDDILEKYCDYRSKKDGLVADSTGEIVKGLRCYFDKALPIMLLYKSER 160 (245)
Q Consensus 82 ~iP~~Lk~~Lvd-D~e~Itk~~~L~~LP~~~tV~~IL~~y~~~~~~~~~~~~~~~~e~~~Gl~~yFn~~L~~~LLY~~ER 160 (245)
.+|..+..++.. +..-....| ++++|...+.-+-+...++.-...+ -....+..++..|+.||...=...+=+.
T Consensus 14 ~vP~~i~~~i~~l~~~g~~~eG-iFR~~g~~~~i~~l~~~~~~~~~~~-~~~~~~~~va~~lK~flreLpepLi~~~--- 88 (192)
T cd04402 14 NLPKPILDMLSLLYQKGPSTEG-IFRRSANAKACKELKEKLNSGVEVD-LKAEPVLLLASVLKDFLRNIPGSLLSSD--- 88 (192)
T ss_pred CCCHHHHHHHHHHHHhCCCCCC-eeeCCCcHHHHHHHHHHHhCCCCCC-CccCCHHHHHHHHHHHHHhCCCccCCHH---
Confidence 477666554432 111122233 7888877663333333333221111 1112345567777777776544333221
Q ss_pred hhHHHhhh------------------cCCCCCcccchHHHHHHHhhhHHHhhhccCCHHHHHH-----------------
Q 025994 161 EQYEDSMA------------------ADVSPSSVYGAEHLLRLFVKLPELLVHAKIEEETLTL----------------- 205 (245)
Q Consensus 161 ~Qy~~~~~------------------~~~~~S~~YG~~HLLRL~vkLP~ll~~t~~d~~~~~~----------------- 205 (245)
.|..++. ...+.+...=..||+++|.++-.-=..+.|+...+..
T Consensus 89 -~~~~~~~~~~~~~~~~~i~~l~~~i~~LP~~n~~~L~~l~~~L~~V~~~~~~NkM~~~nLAi~faP~l~~~~~~~~~~~ 167 (192)
T cd04402 89 -LYEEWMSALDQENEEEKIAELQRLLDKLPRPNVLLLKHLICVLHNISQNSETNKMDAFNLAVCIAPSLLWPPASSELQN 167 (192)
T ss_pred -HHHHHHHHHccCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHhccccCCCHHHhhhhccccccCCCCccHHHH
Confidence 2222211 1123333344445555555443322234444433321
Q ss_pred -HHHHHHHHHHHHHHchhhhcccc
Q 025994 206 -LQHKLVDLLKFLQKHQSTFFLSR 228 (245)
Q Consensus 206 -l~~~l~~fl~fL~~n~~~~f~~~ 228 (245)
-...+..++.||-.|.+..|..|
T Consensus 168 ~~~~~~~~~~~~LI~~~~~IF~~~ 191 (192)
T cd04402 168 EDLKKVTSLVQFLIENCQEIFGED 191 (192)
T ss_pred HHHHhhhHHHHHHHHhHHHhCCCC
Confidence 12456889999999999988754
No 5
>cd04404 RhoGAP-p50rhoGAP RhoGAP-p50rhoGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p50RhoGAP-like proteins; p50RhoGAP, also known as RhoGAP-1, contains a C-terminal RhoGAP domain and an N-terminal Sec14 domain which binds phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). It is ubiquitously expressed and preferentially active on Cdc42. This subgroup also contains closely related ARHGAP8. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=63.21 E-value=68 Score=27.02 Aligned_cols=137 Identities=17% Similarity=0.255 Sum_probs=65.3
Q ss_pred eCChhHHHHHHHHH-HhhhhCCceeeCCCCCC-HHHHHHHHHHhhcccCCchh-hhHHHHHHHHHHHHhhhcCccCCChh
Q 025994 82 QIPPPLKKQLVDDC-EFITHLGKLVKLPRTPN-VDDILEKYCDYRSKKDGLVA-DSTGEIVKGLRCYFDKALPIMLLYKS 158 (245)
Q Consensus 82 ~iP~~Lk~~LvdD~-e~Itk~~~L~~LP~~~t-V~~IL~~y~~~~~~~~~~~~-~~~~e~~~Gl~~yFn~~L~~~LLY~~ 158 (245)
.+|..|..++..=. .-+... -++++|...+ |+++.+.|-+.... .... ..+..++.-|+.||... +.-|+-.
T Consensus 22 ~iP~il~~~i~~l~~~g~~~e-GIFR~~g~~~~i~~l~~~~~~~~~~--~~~~~~d~~~va~~LK~~lr~L-p~pLi~~- 96 (195)
T cd04404 22 PIPPVVRETVEYLQAHALTTE-GIFRRSANTQVVKEVQQKYNMGEPV--DFDQYEDVHLPAVILKTFLREL-PEPLLTF- 96 (195)
T ss_pred CCChHHHHHHHHHHHcCCCCC-CeeeCCCcHHHHHHHHHHHhCCCCC--CcccccCHHHHHHHHHHHHHhC-CCccCCH-
Confidence 47776655432211 123222 3788887654 44444444221110 1111 12344566688888764 3333321
Q ss_pred hHhhHHHhhh-----------------cCCCCCcccchHHHHHHHhhhHHHhhhccCCHHHHHH----------------
Q 025994 159 EREQYEDSMA-----------------ADVSPSSVYGAEHLLRLFVKLPELLVHAKIEEETLTL---------------- 205 (245)
Q Consensus 159 ER~Qy~~~~~-----------------~~~~~S~~YG~~HLLRL~vkLP~ll~~t~~d~~~~~~---------------- 205 (245)
| .|..++. ...++....=..+|+++|.++-.--....|+...+..
T Consensus 97 ~--~~~~l~~~~~~~~~~~~~~~~~~i~~LP~~n~~~L~~L~~~l~~i~~~s~~NkM~~~nLa~vfaP~l~~~~~~~~~l 174 (195)
T cd04404 97 D--LYDDIVGFLNVDKEERVERVKQLLQTLPEENYQVLKYLIKFLVQVSAHSDQNKMTNSNLAVVFGPNLLWAKDASMSL 174 (195)
T ss_pred H--HHHHHHHHHcCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhcccccCCCHhHhheeeeccccCCCCcccCH
Confidence 1 2222221 1123344444555666665543332334455544432
Q ss_pred -HHHHHHHHHHHHHHchhhhc
Q 025994 206 -LQHKLVDLLKFLQKHQSTFF 225 (245)
Q Consensus 206 -l~~~l~~fl~fL~~n~~~~f 225 (245)
=...++.|++||-.|.++.|
T Consensus 175 ~~~~~~~~~~~~LI~~~~~iF 195 (195)
T cd04404 175 SAINPINTFTKFLLDHQDEIF 195 (195)
T ss_pred HHHHHHHHHHHHHHHhHHhhC
Confidence 12346789999999988766
No 6
>smart00340 HALZ homeobox associated leucin zipper.
Probab=55.89 E-value=5.9 Score=25.98 Aligned_cols=16 Identities=38% Similarity=0.275 Sum_probs=13.8
Q ss_pred CCHHHHhhchhHHhhh
Q 025994 19 DTEANRHRQPVFTKKR 34 (245)
Q Consensus 19 ~~eeN~~~qk~L~~~~ 34 (245)
.|+||+.+|+++++-.
T Consensus 17 LteeNrRL~ke~~eLr 32 (44)
T smart00340 17 LTEENRRLQKEVQELR 32 (44)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5899999999998755
No 7
>PF06543 Lac_bphage_repr: Lactococcus bacteriophage repressor; InterPro: IPR009498 This entry represents the C terminus of various Lactococcus bacteriophage repressor proteins.
Probab=55.30 E-value=3.8 Score=27.53 Aligned_cols=19 Identities=26% Similarity=0.665 Sum_probs=12.2
Q ss_pred CcccccccCCCCCCCHHHHh
Q 025994 6 SWDEWVGVHRLMKDTEANRH 25 (245)
Q Consensus 6 ~WDeWV~e~r~lk~~eeN~~ 25 (245)
.||+||+.+- ...|++-.+
T Consensus 19 dWd~wvSf~G-rPltdevK~ 37 (49)
T PF06543_consen 19 DWDKWVSFDG-RPLTDEVKE 37 (49)
T ss_pred chHHheeeCC-eeCCHHHHH
Confidence 4999999853 244555543
No 8
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=45.28 E-value=36 Score=24.09 Aligned_cols=44 Identities=27% Similarity=0.515 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHHHHhhcccCCchhhhHHHHHHHHHHHHhhhcCc
Q 025994 108 PRTPNVDDILEKYCDYRSKKDGLVADSTGEIVKGLRCYFDKALPI 152 (245)
Q Consensus 108 P~~~tV~~IL~~y~~~~~~~~~~~~~~~~e~~~Gl~~yFn~~L~~ 152 (245)
|...|.++| .+|+.+.....+-....++-...+|+.+|+.+++.
T Consensus 38 ~~~it~~~i-~~y~~~l~~~~~~s~~T~~~~~~~l~~ff~~~~~~ 81 (85)
T PF13495_consen 38 PDEITPEDI-EQYLNYLQNERGLSPSTINQYLSALRSFFRWLLER 81 (85)
T ss_dssp GGG--HHHH-HHHHHHHHTTT---HHHHHHHHHHHHHHHHCTSS-
T ss_pred cchhHHHHH-HHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHcC
Confidence 556677776 68988887433334445677899999999998764
No 9
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=43.88 E-value=1.1e+02 Score=21.28 Aligned_cols=82 Identities=15% Similarity=0.263 Sum_probs=44.6
Q ss_pred HHHHHHhhcccCCchhhhHHHHHHHHHHHHhhhcCccCCChhhHhhHHHhhhcCCCCCcccchHHHHHHHhhhHHHhhhc
Q 025994 117 LEKYCDYRSKKDGLVADSTGEIVKGLRCYFDKALPIMLLYKSEREQYEDSMAADVSPSSVYGAEHLLRLFVKLPELLVHA 196 (245)
Q Consensus 117 L~~y~~~~~~~~~~~~~~~~e~~~Gl~~yFn~~L~~~LLY~~ER~Qy~~~~~~~~~~S~~YG~~HLLRL~vkLP~ll~~t 196 (245)
|++|..+.....+.....+......|+.+++.+-.. ....+.++ ...|+...+. -+...
T Consensus 1 i~~f~~~l~~~~~ls~~T~~~Y~~~l~~f~~~~~~~----------------~~~~~~~i-~~~~v~~f~~----~~~~~ 59 (84)
T PF02899_consen 1 IERFLRYLEQERGLSPNTIRSYRRDLRRFIRWLEEH----------------GIIDWEDI-TEEDVRDFLE----YLAKE 59 (84)
T ss_dssp HHHHHHHHHHTTTS-HHHHHHHHHHHHHHHHHHHHT----------------TS-CGGG---HHHHHHHHH----HHHCT
T ss_pred CHHHHHHHHHccCCcHHHHHHHHHHHHHHHHhhhhh----------------hhhhhhhh-hhHHHHHHHH----HHHcc
Confidence 567888876544333444555555565555442210 11223333 3444443333 23334
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHH
Q 025994 197 KIEEETLTLLQHKLVDLLKFLQK 219 (245)
Q Consensus 197 ~~d~~~~~~l~~~l~~fl~fL~~ 219 (245)
...+.+++..+..|..|.+|+.+
T Consensus 60 ~~s~~T~~~~~~alr~f~~~l~~ 82 (84)
T PF02899_consen 60 GLSPSTINRRLSALRAFFRFLYR 82 (84)
T ss_dssp T--HHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHH
Confidence 47888999999999999999975
No 10
>PF15136 UPF0449: Uncharacterised protein family UPF0449
Probab=41.81 E-value=18 Score=27.89 Aligned_cols=20 Identities=35% Similarity=0.501 Sum_probs=15.4
Q ss_pred eeeCCCCCCHHHHHHHHHHh
Q 025994 104 LVKLPRTPNVDDILEKYCDY 123 (245)
Q Consensus 104 L~~LP~~~tV~~IL~~y~~~ 123 (245)
|..=|..|||++||+|-...
T Consensus 7 LPtRP~PPTvEqILEDv~~A 26 (97)
T PF15136_consen 7 LPTRPEPPTVEQILEDVRGA 26 (97)
T ss_pred CCCCCCCCCHHHHHHHHhcC
Confidence 44456779999999997654
No 11
>PF11390 FdsD: NADH-dependant formate dehydrogenase delta subunit FdsD; InterPro: IPR021074 FdsD is the delta subunit of the enzyme formate dehydrogenase. This subunit may play a role in maintaining the quaternary structure by means of electrostatic interactions with the other subunits []. The delta subunit is not involved in the active centre of the enzyme [].
Probab=38.18 E-value=46 Score=23.43 Aligned_cols=33 Identities=12% Similarity=0.256 Sum_probs=27.8
Q ss_pred HHHHHHhhhHHHhhhccCCHHHHHHHHHHHHHH
Q 025994 181 HLLRLFVKLPELLVHAKIEEETLTLLQHKLVDL 213 (245)
Q Consensus 181 HLLRL~vkLP~ll~~t~~d~~~~~~l~~~l~~f 213 (245)
||.||--.+-..+...+-.++.+.-+..||+.|
T Consensus 1 ~LI~MANQIa~ff~~~p~~~~a~~~va~Hi~kF 33 (61)
T PF11390_consen 1 KLIKMANQIAAFFESYPPEEEAVEGVANHIKKF 33 (61)
T ss_pred CHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHh
Confidence 688898888999888877778888888888776
No 12
>PRK14752 delta-hemolysin; Provisional
Probab=37.97 E-value=54 Score=21.11 Aligned_cols=37 Identities=22% Similarity=0.432 Sum_probs=25.2
Q ss_pred HHHHHhhhHHHhhhccCCHHHHHHHHHHHHHHHHHHHHchhhh
Q 025994 182 LLRLFVKLPELLVHAKIEEETLTLLQHKLVDLLKFLQKHQSTF 224 (245)
Q Consensus 182 LLRL~vkLP~ll~~t~~d~~~~~~l~~~l~~fl~fL~~n~~~~ 224 (245)
.||.|.-+.+=.-. +..-+...+.+|++|+-+...+|
T Consensus 5 ilrifilikegvis------ma~dii~tig~~vk~ii~tv~kf 41 (44)
T PRK14752 5 ILRIFILIKEGVIS------MAQDIISTIGDLVKWIIDTVNKF 41 (44)
T ss_pred HHHHHHHHHHhHHH------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 57888765543322 22457788999999998877654
No 13
>cd04390 RhoGAP_ARHGAP22_24_25 RhoGAP_ARHGAP22_24_25: GTPase-activator protein (GAP) domain for Rho-like GTPases found in ARHGAP22, 24 and 25-like proteins; longer isoforms of these proteins contain an additional N-terminal pleckstrin homology (PH) domain. ARHGAP25 (KIA0053) has been identified as a GAP for Rac1 and Cdc42. Short isoforms (without the PH domain) of ARHGAP24, called RC-GAP72 and p73RhoGAP, and of ARHGAP22, called p68RacGAP, has been shown to be involved in angiogenesis and endothelial cell capillary formation. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the r
Probab=33.29 E-value=3e+02 Score=23.21 Aligned_cols=19 Identities=11% Similarity=0.382 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHchhhhc
Q 025994 207 QHKLVDLLKFLQKHQSTFF 225 (245)
Q Consensus 207 ~~~l~~fl~fL~~n~~~~f 225 (245)
...++.++++|-+|.+.+|
T Consensus 181 ~~~~~~~~~~lI~~~~~~F 199 (199)
T cd04390 181 TPQIQQLMTVMISKHEPLF 199 (199)
T ss_pred cHHHHHHHHHHHHhhhhcC
Confidence 3446778888888887766
No 14
>PF05372 Delta_lysin: Delta lysin family; InterPro: IPR008034 Delta-lysin is a 26 amino acid, hemolytic peptide toxin secreted by Staphylococcus aureus. It is thought that delta-toxin forms an amphipathic helix upon binding to lipid bilayers []. The precise mode of action of delta-lysis is unclear.; GO: 0019836 hemolysis by symbiont of host erythrocytes, 0005576 extracellular region; PDB: 2KAM_A 2DTB_A 1DTC_A.
Probab=31.12 E-value=86 Score=18.03 Aligned_cols=21 Identities=14% Similarity=0.289 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHchhhh
Q 025994 204 TLLQHKLVDLLKFLQKHQSTF 224 (245)
Q Consensus 204 ~~l~~~l~~fl~fL~~n~~~~ 224 (245)
.-|.+.+.+|++|+.+...+|
T Consensus 3 ~DIisTIgdfvKlI~~TV~KF 23 (25)
T PF05372_consen 3 ADIISTIGDFVKLIIETVKKF 23 (25)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHHh
Confidence 347788999999998877655
No 15
>KOG2573 consensus Ribosome biogenesis protein - Nop56p/Sik1p [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=29.84 E-value=1.3e+02 Score=29.31 Aligned_cols=78 Identities=15% Similarity=0.070 Sum_probs=48.6
Q ss_pred EeCChhHHHHHHHHHHhhhhCCceeeCCCCCCHHHHHHHHHHhhcccCCchhhhHHHHHHHHHHHHhhhcCccCCChhhH
Q 025994 81 IQIPPPLKKQLVDDCEFITHLGKLVKLPRTPNVDDILEKYCDYRSKKDGLVADSTGEIVKGLRCYFDKALPIMLLYKSER 160 (245)
Q Consensus 81 i~iP~~Lk~~LvdD~e~Itk~~~L~~LP~~~tV~~IL~~y~~~~~~~~~~~~~~~~e~~~Gl~~yFn~~L~~~LLY~~ER 160 (245)
=.+++.|+..|..-.--+.+.+....+--..=-..|-+.+-... -.....+.|+++|+|..|++.+...==|..|+
T Consensus 69 G~~~edLr~fLe~nlpK~kkkk~sLgi~d~kLg~~i~E~~~~i~----c~~~~~~~ellRGvR~hf~kl~K~L~~~d~~k 144 (498)
T KOG2573|consen 69 GVVHEDLRSFLELNLPKVKKKKVSLGIGDSKLGISIKEAFPKIP----CQSNEVVQELLRGVRKHFDKLMKGLDPGDLEK 144 (498)
T ss_pred ccccHHHHHHHHhhChhhhcCceeeccCcchhhhHHHhhccCcc----cccchhHHHHHHHHHHHHHHHHccCCCccHHH
Confidence 35788999999887666633332222211111122333321000 11234778999999999999999888899999
Q ss_pred hh
Q 025994 161 EQ 162 (245)
Q Consensus 161 ~Q 162 (245)
.|
T Consensus 145 aq 146 (498)
T KOG2573|consen 145 AQ 146 (498)
T ss_pred HH
Confidence 99
No 16
>PF10496 Syntaxin-18_N: SNARE-complex protein Syntaxin-18 N-terminus ; InterPro: IPR019529 This is the conserved N-terminal of Syntaxin-18. Syntaxin-18 is found in the SNARE complex of the endoplasmic reticulum and functions in the trafficking between the ER intermediate compartment and the cis-Golgi vesicle. In particular, the N-terminal region is important for the formation of ER aggregates []. More specifically, syntaxin-18 is involved in endoplasmic reticulum-mediated phagocytosis, presumably by regulating the specific and direct fusion of the ER with the plasma or phagosomal membranes [].
Probab=28.84 E-value=51 Score=24.21 Aligned_cols=24 Identities=17% Similarity=0.310 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHchhhhcc
Q 025994 203 LTLLQHKLVDLLKFLQKHQSTFFL 226 (245)
Q Consensus 203 ~~~l~~~l~~fl~fL~~n~~~~f~ 226 (245)
...|..+|..|.+||..+...|-.
T Consensus 45 A~~i~~~I~~L~~fL~~iR~~YL~ 68 (87)
T PF10496_consen 45 AYRILSHITSLRKFLKSIRKAYLS 68 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 357999999999999999986655
No 17
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=25.50 E-value=4.1e+02 Score=22.40 Aligned_cols=88 Identities=13% Similarity=0.235 Sum_probs=45.6
Q ss_pred CCCCHHHHHHHHHHhhcccCCchhhhHHH---HHHHHHHHHhhhcCccCCChhhHhhHHHhhhcCCCCCcccchHHHHHH
Q 025994 109 RTPNVDDILEKYCDYRSKKDGLVADSTGE---IVKGLRCYFDKALPIMLLYKSEREQYEDSMAADVSPSSVYGAEHLLRL 185 (245)
Q Consensus 109 ~~~tV~~IL~~y~~~~~~~~~~~~~~~~e---~~~Gl~~yFn~~L~~~LLY~~ER~Qy~~~~~~~~~~S~~YG~~HLLRL 185 (245)
+.+|+.+++++|+++.............. .+.-+..|+...-+ . ..+++ ...|+..+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~s~~T~~~~~~~~~~~~~~~~~~~~----~---------------~~~~i-~~~~i~~~ 61 (297)
T PRK00236 2 ADADLPAALEAFLEYLRVERGLSPHTLRAYRRDLRAFLAFLEEHGI----S---------------SLQDL-DAADLRSF 61 (297)
T ss_pred CCchHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHcCC----C---------------chhhC-CHHHHHHH
Confidence 45799999999999775432111112222 22333344432111 0 01111 23444443
Q ss_pred HhhhHHHhhhccCCHHHHHHHHHHHHHHHHHHHHc
Q 025994 186 FVKLPELLVHAKIEEETLTLLQHKLVDLLKFLQKH 220 (245)
Q Consensus 186 ~vkLP~ll~~t~~d~~~~~~l~~~l~~fl~fL~~n 220 (245)
+-.+- ...+...+++.....|..|+.|+.++
T Consensus 62 ~~~~~----~~~~~~~t~~~~~~~l~~~~~~a~~~ 92 (297)
T PRK00236 62 LARRR----RQGLSARSLARRLSALRSFYRWLVRR 92 (297)
T ss_pred HHHHH----hcccChhHHHHHHHHHHHHHHHHHhc
Confidence 33321 12345567777888899999998765
No 18
>TIGR03248 galactar-dH20 galactarate dehydratase. Galactarate dehydratase converts D-galactarate to 5-dehydro-4-deoxyglucarate which is subsequently acted on by GarL, tartronate semialdehyde reductase and glycerate kinase (, GenProp0714).
Probab=25.36 E-value=1.1e+02 Score=30.45 Aligned_cols=49 Identities=18% Similarity=0.118 Sum_probs=36.6
Q ss_pred CCCcccchHHHHHHHhhhHHHhhhccCCHHHHHHHHHHHHHHHHHHHHchhhhccccCCCCCH
Q 025994 172 SPSSVYGAEHLLRLFVKLPELLVHAKIEEETLTLLQHKLVDLLKFLQKHQSTFFLSRYHSAED 234 (245)
Q Consensus 172 ~~S~~YG~~HLLRL~vkLP~ll~~t~~d~~~~~~l~~~l~~fl~fL~~n~~~~f~~~Y~~~~~ 234 (245)
.-.++||+||+|-= ---+++....|...++.|-+|...+-..+ |.++||
T Consensus 305 Et~E~~GaE~iL~~----------Ra~~~ev~~k~~~~i~~~~~y~~~~g~~~----~~nPSp 353 (507)
T TIGR03248 305 EVTEVRDAIHLLTP----------RAETAEVAKALVREMDWYDRYLARGQADR----SANTTP 353 (507)
T ss_pred CCcceeChHHHHHh----------hhCCHHHHHHHHHHHHHHHHHHHHcCCCc----cCCCCc
Confidence 67889999998632 23477777888889999999888876644 556555
No 19
>cd00024 CHROMO Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain.
Probab=24.06 E-value=28 Score=22.60 Aligned_cols=18 Identities=22% Similarity=0.090 Sum_probs=15.5
Q ss_pred CCCCCcccccccCCCCCC
Q 025994 2 REAGSWDEWVGVHRLMKD 19 (245)
Q Consensus 2 ~~~~~WDeWV~e~r~lk~ 19 (245)
||+...|+|++++.|...
T Consensus 28 g~~~~~~tWe~~~~l~~~ 45 (55)
T cd00024 28 GYSYSEDTWEPEENLEDC 45 (55)
T ss_pred CCCCccCccccHHHhCch
Confidence 788889999999998854
No 20
>PF09539 DUF2385: Protein of unknown function (DUF2385); InterPro: IPR012645 Members of this uncharacterised protein family are found in a number of alphaproteobacteria, including root nodule bacteria, Brucella suis, Caulobacter crescentus (Caulobacter vibrioides), and Rhodopseudomonas palustris. Conserved residues include two well-separated cysteines, suggesting a disulphide bond. The function is unknown.
Probab=22.55 E-value=81 Score=24.31 Aligned_cols=41 Identities=22% Similarity=0.224 Sum_probs=30.9
Q ss_pred CCCcccchHHHHHHHhh----------hHHHhhhccCCHHHHHHHHHHHHH
Q 025994 172 SPSSVYGAEHLLRLFVK----------LPELLVHAKIEEETLTLLQHKLVD 212 (245)
Q Consensus 172 ~~S~~YG~~HLLRL~vk----------LP~ll~~t~~d~~~~~~l~~~l~~ 212 (245)
+.|+|-|+.|.||-+.. |-+||.....++.-...|...++.
T Consensus 8 rLAeiLGalHyLR~LCg~~~~~~WR~~M~~Ll~~E~p~~~rR~rl~~aFN~ 58 (96)
T PF09539_consen 8 RLAEILGALHYLRNLCGGNEDQYWRDRMQALLDAEAPDEARRARLIAAFNR 58 (96)
T ss_pred HHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 56889999999999986 666787777777666666665443
No 21
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=21.57 E-value=1.3e+02 Score=27.36 Aligned_cols=45 Identities=29% Similarity=0.356 Sum_probs=25.1
Q ss_pred cccchHHHHHHHhh--hHHHhhhccCCHHHHHHHHHHHHHHHHHHHH
Q 025994 175 SVYGAEHLLRLFVK--LPELLVHAKIEEETLTLLQHKLVDLLKFLQK 219 (245)
Q Consensus 175 ~~YG~~HLLRL~vk--LP~ll~~t~~d~~~~~~l~~~l~~fl~fL~~ 219 (245)
+--|++||||=+-- ...|-..-+---.++.-|...+.+.-.||.+
T Consensus 169 EEvGVEHLlRDikd~t~gtla~rit~ql~sLkgl~~~L~eI~~YL~~ 215 (309)
T KOG1556|consen 169 EEVGVEHLLRDIKDTTVGTLATRITNQLMSLKGLQSRLREIRSYLDK 215 (309)
T ss_pred HHhhHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34699999997642 1111111111223455567777777777765
No 22
>cd04392 RhoGAP_ARHGAP19 RhoGAP_ARHGAP19: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP19-like proteins. The function of ArhGAP19 is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=21.30 E-value=94 Score=26.77 Aligned_cols=36 Identities=25% Similarity=0.424 Sum_probs=23.6
Q ss_pred HHhhhccCCHHHHHHHHHHHHHHHHHHHHchhhhcc
Q 025994 191 ELLVHAKIEEETLTLLQHKLVDLLKFLQKHQSTFFL 226 (245)
Q Consensus 191 ~ll~~t~~d~~~~~~l~~~l~~fl~fL~~n~~~~f~ 226 (245)
.|+.....+...+..-...+..++.||-+|.++.|.
T Consensus 162 ~Ll~~~~~~~~~~~~~~~~~~~iv~~lI~~~~~iF~ 197 (208)
T cd04392 162 HLICPRNLTPEDLHENAQKLNSIVTFMIKHSQKLFK 197 (208)
T ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 333333344443333345678999999999999997
No 23
>PF04295 GD_AH_C: D-galactarate dehydratase / Altronate hydrolase, C terminus; InterPro: IPR007392 This domain is found at the C terminus of D-galactarate dehydratase (4.2.1.42 from EC) which is thought to catalyse the reaction D-galactarate = 5-keto-4-deoxy-D-glucarate + H2O, [] and altronate hydrolase (altronic acid hydratase, 4.2.1.7 from EC), which catalyses D-altronate = 2-keto-2-deoxygluconate + H2O []. As purified, both enzymes are catalytically inactive in the absence of added Fe2+, Mn2+, and beta-mercaptoethanol. Synergistic activation of altronate hydrolase activity is seen in the presence of both iron and manganese ions, suggesting that the enzyme may have two ion binding sites. Mn2+ appears to be part of the enzyme active centre, but the function of the single bound Fe2+ ion is unknown. The hydratase has no Fe-S core []. The N-terminal is represented by IPR007389 from INTERPRO.; GO: 0016836 hydro-lyase activity
Probab=20.75 E-value=1.6e+02 Score=28.35 Aligned_cols=49 Identities=14% Similarity=0.191 Sum_probs=35.9
Q ss_pred CCCcccchHHHHHHHhhhHHHhhhccCCHHHHHHHHHHHHHHHHHHHHchhhhccccCCCCCH
Q 025994 172 SPSSVYGAEHLLRLFVKLPELLVHAKIEEETLTLLQHKLVDLLKFLQKHQSTFFLSRYHSAED 234 (245)
Q Consensus 172 ~~S~~YG~~HLLRL~vkLP~ll~~t~~d~~~~~~l~~~l~~fl~fL~~n~~~~f~~~Y~~~~~ 234 (245)
.-.++||+||+|-= --.+++....|...++.|-+|+..+-..+ |.+++|
T Consensus 196 Et~El~GaE~~l~~----------Ra~~~ev~~k~~~~i~~~~~~~~~~g~~~----~~nPSp 244 (396)
T PF04295_consen 196 ETPELIGAEHILAR----------RAVNPEVADKILALINWFEDYAKSHGQDI----GGNPSP 244 (396)
T ss_pred cCccccCHHHHHHH----------HhCCHHHHHHHHHHHHHHHHHHHHhCCCc----CCCcCC
Confidence 67899999998632 23477777888888999988888776544 445544
Done!