Query 044476
Match_columns 376
No_of_seqs 78 out of 80
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 03:36:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044476.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044476hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09346 SMI1_KNR4: SMI1 / KNR 96.9 0.00058 1.3E-08 54.7 2.7 28 48-75 1-28 (130)
2 smart00860 SMI1_KNR4 SMI1 / KN 96.8 0.0011 2.4E-08 51.4 3.4 29 48-76 1-29 (129)
3 PF14567 SUKH_5: SMI1-KNR4 cel 96.2 0.0046 1E-07 54.9 3.5 45 32-76 2-49 (132)
4 PF14568 SUKH_6: SMI1-KNR4 cel 95.5 0.01 2.3E-07 48.0 2.6 25 51-75 1-25 (120)
5 COG4282 SMI1 Protein involved 91.5 0.2 4.3E-06 47.0 3.6 36 40-75 24-59 (191)
6 PF14433 SUKH-3: SUKH-3 immuni 66.6 86 0.0019 27.2 10.3 128 32-184 2-135 (142)
7 PF13559 DUF4129: Domain of un 50.4 23 0.0005 26.4 3.5 27 30-56 2-28 (72)
8 PF13340 DUF4096: Putative tra 50.4 25 0.00053 27.6 3.8 40 49-88 1-56 (75)
9 PF13271 DUF4062: Domain of un 42.6 16 0.00034 29.2 1.6 41 114-154 27-67 (83)
10 PF14399 Transpep_BrtH: NlpC/p 42.3 65 0.0014 30.7 6.0 99 28-157 1-105 (317)
11 PHA02591 hypothetical protein; 41.0 25 0.00055 29.6 2.6 24 302-325 50-73 (83)
12 PRK06130 3-hydroxybutyryl-CoA 40.2 43 0.00094 32.2 4.5 46 64-109 257-305 (311)
13 PF01522 Polysacc_deac_1: Poly 40.2 23 0.00049 28.6 2.2 76 19-102 4-86 (123)
14 cd08779 Death_PIDD Death Domai 39.8 26 0.00057 28.7 2.5 26 47-76 23-48 (86)
15 TIGR01926 peroxid_rel uncharac 38.7 25 0.00055 30.9 2.5 75 246-323 78-156 (177)
16 cd08503 PBP2_NikA_DppA_OppA_li 33.7 68 0.0015 32.2 4.9 35 126-160 424-459 (460)
17 cd08313 Death_TNFR1 Death doma 33.1 43 0.00092 27.6 2.7 15 48-62 22-36 (80)
18 PF11203 DUF2984: Protein of u 32.9 60 0.0013 27.3 3.7 52 28-90 38-89 (98)
19 PF02954 HTH_8: Bacterial regu 30.0 69 0.0015 22.6 3.1 27 299-325 6-32 (42)
20 PF00690 Cation_ATPase_N: Cati 29.4 30 0.00065 26.4 1.2 28 36-63 8-35 (69)
21 PF13560 HTH_31: Helix-turn-he 24.6 69 0.0015 23.9 2.4 24 302-325 5-28 (64)
22 PRK05087 D-alanine--poly(phosp 24.4 46 0.001 26.8 1.5 16 54-69 43-58 (78)
23 PRK12449 acyl carrier protein; 24.2 48 0.001 25.8 1.6 15 54-68 46-60 (80)
24 PF13384 HTH_23: Homeodomain-l 24.1 51 0.0011 23.2 1.6 19 307-325 13-31 (50)
25 TIGR01124 ilvA_2Cterm threonin 23.9 54 0.0012 34.8 2.3 53 22-75 365-439 (499)
26 COG4174 ABC-type uncharacteriz 23.6 88 0.0019 32.1 3.6 102 45-183 76-184 (364)
27 PF02796 HTH_7: Helix-turn-hel 23.1 63 0.0014 23.1 1.9 20 305-324 15-34 (45)
28 TIGR00677 fadh2_euk methylenet 23.0 1.4E+02 0.003 29.4 4.8 55 21-76 167-227 (281)
29 PRK07081 acyl carrier protein; 22.8 52 0.0011 26.5 1.6 16 54-69 42-57 (83)
30 PF04255 DUF433: Protein of un 22.6 78 0.0017 23.8 2.4 23 299-322 20-42 (56)
31 PF02513 Spin-Ssty: Spin/Ssty 22.5 41 0.00089 25.9 0.8 19 161-179 30-50 (50)
32 PRK07639 acyl carrier protein; 21.0 57 0.0012 26.6 1.4 16 54-69 47-62 (86)
33 TIGR00517 acyl_carrier acyl ca 21.0 61 0.0013 25.0 1.5 15 55-69 45-59 (77)
34 PF04760 IF2_N: Translation in 20.4 38 0.00081 24.9 0.2 34 31-64 17-54 (54)
35 PRK05350 acyl carrier protein; 20.2 62 0.0013 25.6 1.5 16 54-69 47-62 (82)
36 COG3357 Predicted transcriptio 20.2 1.6E+02 0.0034 25.6 3.9 49 250-313 5-53 (97)
No 1
>PF09346 SMI1_KNR4: SMI1 / KNR4 family (SUKH-1); InterPro: IPR018958 Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation [, ]. Yeast members of this family are involved in the regulation of cell wall assembly. Saccharomyces cerevisiae (Baker's yeast) protein KNR4 (SMI1) has a regulatory role in chitin deposition and in cell wall assembly []. It was originally identified as a regulator of chitin synthase expression (acting as a repressor) [] and of 1,3-beta-glucan synthase levels []. It was shown to localise in patches at presumptive bud sites in unbudded cells and at the incipient bud site during bud emergence []. KNR4 is believed to connect the PKC1-SLT2 MAPK pathway with cell proliferation. It has been shown to interact with BCK2, a gene involved in cell cycle progression in S. cerevisiae (forming a complex) to allow PKC1 to coordinate the cell cycle (cell proliferation) with cell wall integrity [, ]. PKC1 plays an essential role in cell wall integrity and cell proliferation through a bifurcated PKC1/mitogen-activated protein (MAP) kinase pathway. KNR4 also interacts with the tyrosine-tRNA synthetase protein encoded by TYS1 and is involved in sporulation process []. Note: previously reported evidence that KNR4 may interact with nuclear matrix-association region [] may be due to an artefact [].; PDB: 3D5P_A 2ICG_A.
Probab=96.94 E-value=0.00058 Score=54.74 Aligned_cols=28 Identities=21% Similarity=0.533 Sum_probs=20.9
Q ss_pred CCCHHHHHHHHHHcCccCCchHHHHHHh
Q 044476 48 GLNDAEFSDIESTFNFTFPPDLRSILRE 75 (376)
Q Consensus 48 GLSd~Ef~~IEa~fgF~FPpDlRa~L~~ 75 (376)
++|++||+.+|+++|++||+++|.||+.
T Consensus 1 p~t~~~I~~~E~~lg~~LP~~yk~fl~~ 28 (130)
T PF09346_consen 1 PATEEEIQELEEKLGVRLPDDYKEFLKE 28 (130)
T ss_dssp ---HHHHHHHHHHHTS---HHHHHHHH-
T ss_pred CCCHHHHHHHHHHhCCCCcHHHHHHHHh
Confidence 5899999999999999999999999995
No 2
>smart00860 SMI1_KNR4 SMI1 / KNR4 family. Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation.
Probab=96.84 E-value=0.0011 Score=51.36 Aligned_cols=29 Identities=17% Similarity=0.399 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHcCccCCchHHHHHHhc
Q 044476 48 GLNDAEFSDIESTFNFTFPPDLRSILREG 76 (376)
Q Consensus 48 GLSd~Ef~~IEa~fgF~FPpDlRa~L~~G 76 (376)
|.|++||.++|+.+|++||+|+|.||+.-
T Consensus 1 ~~s~~~i~~~e~~lg~~LP~~y~~f~~~~ 29 (129)
T smart00860 1 PASEEEIAELEKKLGIKLPEDYKEFLLLH 29 (129)
T ss_pred CCCHHHHHHHHHHHCCCCCHHHHHHHHHc
Confidence 57999999999999999999999999984
No 3
>PF14567 SUKH_5: SMI1-KNR4 cell-wall; PDB: 2PAG_A.
Probab=96.17 E-value=0.0046 Score=54.93 Aligned_cols=45 Identities=24% Similarity=0.561 Sum_probs=30.5
Q ss_pred HHHHHHHHhCC--cccCCC-CCHHHHHHHHHHcCccCCchHHHHHHhc
Q 044476 32 KNLIDHLKSLN--IPILPG-LNDAEFSDIESTFNFTFPPDLRSILREG 76 (376)
Q Consensus 32 ~~ii~~L~~~G--v~i~pG-LSd~Ef~~IEa~fgF~FPpDlRa~L~~G 76 (376)
..||+.|++.+ ++..-+ =|+++|..+|+..||.||+|+|+||...
T Consensus 2 ~~~i~~L~~~~e~~~~~l~lpd~e~I~~~Ee~L~i~lP~eyk~fL~~~ 49 (132)
T PF14567_consen 2 EDIIERLKELNEPVPVPLELPDDEQIVEAEEQLGISLPEEYKEFLLEA 49 (132)
T ss_dssp HHHHHHHHHH----SS------HHHHHHHHHHHT----HHHHHHHHHH
T ss_pred hHHHHHHHHhcCCccCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHC
Confidence 46899999954 555434 5899999999999999999999999986
No 4
>PF14568 SUKH_6: SMI1-KNR4 cell-wall; PDB: 2PRV_A.
Probab=95.47 E-value=0.01 Score=47.96 Aligned_cols=25 Identities=24% Similarity=0.585 Sum_probs=20.4
Q ss_pred HHHHHHHHHHcCccCCchHHHHHHh
Q 044476 51 DAEFSDIESTFNFTFPPDLRSILRE 75 (376)
Q Consensus 51 d~Ef~~IEa~fgF~FPpDlRa~L~~ 75 (376)
|++|..+|+++|++||.|+|.||..
T Consensus 1 ee~I~~~E~~Lg~~lP~~Yk~fL~~ 25 (120)
T PF14568_consen 1 EEEIEEAEKKLGVKLPEDYKEFLKE 25 (120)
T ss_dssp -HHHHHHHHHHTS---HHHHHHHHH
T ss_pred ChHHHHHHHHhCCCCCHHHHHHHHH
Confidence 6899999999999999999999997
No 5
>COG4282 SMI1 Protein involved in beta-1,3-glucan synthesis [Carbohydrate transport and metabolism]
Probab=91.48 E-value=0.2 Score=46.97 Aligned_cols=36 Identities=28% Similarity=0.401 Sum_probs=33.0
Q ss_pred hCCcccCCCCCHHHHHHHHHHcCccCCchHHHHHHh
Q 044476 40 SLNIPILPGLNDAEFSDIESTFNFTFPPDLRSILRE 75 (376)
Q Consensus 40 ~~Gv~i~pGLSd~Ef~~IEa~fgF~FPpDlRa~L~~ 75 (376)
.+-..+.||-|-..|+++|+.||.+||||.|+.|+.
T Consensus 24 dl~~~l~pgat~~di~~aE~dlg~tlPpdvResl~i 59 (191)
T COG4282 24 DLLPFLRPGATCGDIQRAEADLGRTLPPDVRESLAI 59 (191)
T ss_pred ccccccCCCccHHHHHHHHHHhcCcCChHHHHHHHh
Confidence 344789999999999999999999999999999987
No 6
>PF14433 SUKH-3: SUKH-3 immunity protein
Probab=66.61 E-value=86 Score=27.17 Aligned_cols=128 Identities=15% Similarity=0.162 Sum_probs=71.5
Q ss_pred HHHHHHHHhCCcccCCCCCHHHHHHHHHHcCccCCchHHHHHHh--cCCCCCCCCCCCCCCHHHHHHHHhhccccchhhc
Q 044476 32 KNLIDHLKSLNIPILPGLNDAEFSDIESTFNFTFPPDLRSILRE--GLPAGPAFPNWRSSSHQQLRILVKLPVLSLSKNV 109 (376)
Q Consensus 32 ~~ii~~L~~~Gv~i~pGLSd~Ef~~IEa~fgF~FPpDlRa~L~~--GLPvG~gFPdWR~~s~~~Lr~~L~~P~~gil~dV 109 (376)
++|++.|+++|-.=..-...+.+...=+..|+...|..+.||+. ||-+....|.-+..+.. .+.++-
T Consensus 2 ~~v~~~L~~aGW~~~R~idi~~~~~~~~~~g~~~~paa~~fL~efGgL~i~~~~~~~~~~~~~-----------~~~~~P 70 (142)
T PF14433_consen 2 EKVIELLRAAGWYEGRKIDISLWEKILEEEGYPVFPAAVEFLAEFGGLRINPSGPYGRQDAPS-----------DFDFDP 70 (142)
T ss_pred HHHHHHHHHcCCCCCcccCHHHHHHHHHhcCCCCCHHHHHHHHHcCCeEEeccCccccccCCc-----------eEEeCh
Confidence 57899999999553333444455544444599999999999998 88887666631111111 111111
Q ss_pred cccCCcccccCCCCCChhHHHHHHHHhhccCCceecc----cCCccccCCCCCCCCceEEEeCCCEEEEccchHHHHhh
Q 044476 110 SLNNFWSVSWGQRPQNNNDALSLIKKLLDKAPLLVPI----YRNCYVPSTPNMAGNPVFYIDTEEVRVLSFDLAGFFKQ 184 (376)
Q Consensus 110 e~n~fW~~sWG~RP~~~~eal~~Ar~~L~~aP~LVPI----ygHrYlPs~p~~aGnPVfSV~qtDIi~yG~DLadyf~r 184 (376)
.+...+ ...+.+..-.+. --=.|+|| .+|-.|-.+ .. .=||.++++...++|.|+-+.|.+
T Consensus 71 ~~~~~~---------~~~~~~~~~~~~--~~~~l~PiG~~~~~~~~l~id--e~-Grvy~~~~~~~~~lG~~~~~al~~ 135 (142)
T PF14433_consen 71 LEALGI---------HDAETLAELEEA--LGTKLFPIGEEHDGHAILAID--ES-GRVYGLDDTGLWYLGDDIDEALEN 135 (142)
T ss_pred hhhccc---------chHHHHHHHHHH--hCCcEEEEEEecCCCEEEEEe--CC-CCEEEecCCeeEEeCCCHHHHHHH
Confidence 111111 111111111111 23467786 233333333 22 458888888889999999988886
No 7
>PF13559 DUF4129: Domain of unknown function (DUF4129)
Probab=50.42 E-value=23 Score=26.44 Aligned_cols=27 Identities=22% Similarity=0.338 Sum_probs=23.0
Q ss_pred hHHHHHHHHHhCCcccCCCCCHHHHHH
Q 044476 30 YAKNLIDHLKSLNIPILPGLNDAEFSD 56 (376)
Q Consensus 30 ya~~ii~~L~~~Gv~i~pGLSd~Ef~~ 56 (376)
+...++..|+..|++..||.|..|+.+
T Consensus 2 ~y~~l~~~~~~~g~~~~~~~T~~E~~~ 28 (72)
T PF13559_consen 2 LYRALLRLLARRGIPRRPSETPREYAR 28 (72)
T ss_pred HHHHHHHHHHHcCCCCCCCcCHHHHHH
Confidence 356677899999999999999999864
No 8
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=50.37 E-value=25 Score=27.63 Aligned_cols=40 Identities=33% Similarity=0.469 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHcCccCCc------hHHHHHHhcCCC----------CCCCCCCCC
Q 044476 49 LNDAEFSDIESTFNFTFPP------DLRSILREGLPA----------GPAFPNWRS 88 (376)
Q Consensus 49 LSd~Ef~~IEa~fgF~FPp------DlRa~L~~GLPv----------G~gFPdWR~ 88 (376)
|||+|.+.||..|--.-+. |+|.++.+.+=+ +..|++|.+
T Consensus 1 lsD~~W~~i~p~lp~~~~~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg~~~t 56 (75)
T PF13340_consen 1 LSDEEWALIEPLLPPRKPRGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFGPWST 56 (75)
T ss_pred CCHHHHHHHHhhCCCCCCCCCCCccchHHHHhcccccceecceecccchhccCcCc
Confidence 7999999999999866665 899988775433 355888876
No 9
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=42.56 E-value=16 Score=29.20 Aligned_cols=41 Identities=20% Similarity=0.240 Sum_probs=31.7
Q ss_pred CcccccCCCCCChhHHHHHHHHhhccCCceecccCCccccC
Q 044476 114 FWSVSWGQRPQNNNDALSLIKKLLDKAPLLVPIYRNCYVPS 154 (376)
Q Consensus 114 fW~~sWG~RP~~~~eal~~Ar~~L~~aP~LVPIygHrYlPs 154 (376)
+.+..+..-|++.........+.++++..+|=|+|+||=-.
T Consensus 27 ~~~~~~e~~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~~ 67 (83)
T PF13271_consen 27 CEPVGMEFFPASDQSPLEICLKEVDECDIFILILGNRYGSV 67 (83)
T ss_pred CeeeeeeeecCCCCCHHHHHHHHHhhCCEEEEeeccccCCC
Confidence 33333333477778889999999999999999999999433
No 10
>PF14399 Transpep_BrtH: NlpC/p60-like transpeptidase
Probab=42.25 E-value=65 Score=30.72 Aligned_cols=99 Identities=21% Similarity=0.305 Sum_probs=63.6
Q ss_pred hhhHHHHHHHHHhCCcccCCCCCHHHHHHHHHHcCccCCc---hHHHHHHhcCCCCCCCCCCCCC--CHHHHHHHHhhcc
Q 044476 28 AAYAKNLIDHLKSLNIPILPGLNDAEFSDIESTFNFTFPP---DLRSILREGLPAGPAFPNWRSS--SHQQLRILVKLPV 102 (376)
Q Consensus 28 ~~ya~~ii~~L~~~Gv~i~pGLSd~Ef~~IEa~fgF~FPp---DlRa~L~~GLPvG~gFPdWR~~--s~~~Lr~~L~~P~ 102 (376)
.|+...+.+.|...|+.+ |+.=+=-+-.-+||.+=+ ..+. .+.+=|.. .-.++...+++.+
T Consensus 1 hC~~~~l~~ll~~~g~~~----~e~l~fglg~g~gf~y~~~~~~~~~----------~~~~~r~~~~~~~~~~~~lG~~~ 66 (317)
T PF14399_consen 1 HCESNALRDLLAHYGLPL----SEALIFGLGSGLGFSYLPFPDSNPP----------PLLGGRSPPDFEENLLERLGIKY 66 (317)
T ss_pred CchhHHHHHHHHhcCCCC----CHHHHHHHcCCcceEEEeccccCCC----------eeecCCCchHHHHHHHHHCCceE
Confidence 367788999999999887 555555577777876433 1111 12222332 1334444555543
Q ss_pred ccchhhccccCCcccccCCCCCChhHHHHHHHHhhccC-CceecccCCccccCCCC
Q 044476 103 LSLSKNVSLNNFWSVSWGQRPQNNNDALSLIKKLLDKA-PLLVPIYRNCYVPSTPN 157 (376)
Q Consensus 103 ~gil~dVe~n~fW~~sWG~RP~~~~eal~~Ar~~L~~a-P~LVPIygHrYlPs~p~ 157 (376)
. . . ...++++++...++.|.+- |++|. ..--|||=.|.
T Consensus 67 ~-------~----~-----~~~~~~~~~~~l~~~l~~g~pv~~~-~D~~~lpy~~~ 105 (317)
T PF14399_consen 67 E-------W----R-----EFSSPDEAWEELKEALDAGRPVIVW-VDMYYLPYRPN 105 (317)
T ss_pred E-------E----E-----ecCCHHHHHHHHHHHHhCCCceEEE-eccccCCCCcc
Confidence 3 1 1 1256899999999999988 99999 77788887665
No 11
>PHA02591 hypothetical protein; Provisional
Probab=41.00 E-value=25 Score=29.56 Aligned_cols=24 Identities=21% Similarity=0.297 Sum_probs=20.8
Q ss_pred HHHHHHHhcCCChHHHHHHhccCC
Q 044476 302 LLSLVLLRAGWSKEDVVYSLNLQD 325 (376)
Q Consensus 302 ~~S~sL~rAGWS~eDV~eal~~~~ 325 (376)
-+...|++-|.|.++|++.||++.
T Consensus 50 ~vA~eL~eqGlSqeqIA~~LGVsq 73 (83)
T PHA02591 50 SVTHELARKGFTVEKIASLLGVSV 73 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCH
Confidence 355689999999999999999875
No 12
>PRK06130 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=40.18 E-value=43 Score=32.17 Aligned_cols=46 Identities=15% Similarity=0.270 Sum_probs=33.3
Q ss_pred cCCchHHHHHHh---cCCCCCCCCCCCCCCHHHHHHHHhhccccchhhc
Q 044476 64 TFPPDLRSILRE---GLPAGPAFPNWRSSSHQQLRILVKLPVLSLSKNV 109 (376)
Q Consensus 64 ~FPpDlRa~L~~---GLPvG~gFPdWR~~s~~~Lr~~L~~P~~gil~dV 109 (376)
..++-++..+.. |.-.|.|||+|.+..+..++...+..+..++..+
T Consensus 257 ~~~~~l~~~~~~g~~G~~~g~gfy~y~~~~~~~~~~~~~~~~~~~~~~~ 305 (311)
T PRK06130 257 TPSPLLEEKVEAGELGAKSGQGFYAWPPERREEVLADKSAALVEVRAWL 305 (311)
T ss_pred CCCHHHHHHHHcCCccccCCCcCccCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 345556776654 5577899999998888888887777766665443
No 13
>PF01522 Polysacc_deac_1: Polysaccharide deacetylase; InterPro: IPR002509 This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase []. It also includes chitin deacetylase from yeast [], and endoxylanases which hydrolyses glucosidic bonds in xylan [].; GO: 0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, 0005975 carbohydrate metabolic process; PDB: 2IW0_A 2CC0_B 2VYO_A 2J13_A 2C71_A 2C79_A 1W1A_1 1W1B_1 1W17_A 1NY1_B ....
Probab=40.17 E-value=23 Score=28.60 Aligned_cols=76 Identities=22% Similarity=0.282 Sum_probs=51.4
Q ss_pred CCccceeec----hhhHHHHHHHHHhCCcccCCCCCHHHHHHHHHHcCccCCchHHHHHHhcCCCCC---CCCCCCCCCH
Q 044476 19 TTKLVCFSY----AAYAKNLIDHLKSLNIPILPGLNDAEFSDIESTFNFTFPPDLRSILREGLPAGP---AFPNWRSSSH 91 (376)
Q Consensus 19 ~~r~~~~Sf----~~ya~~ii~~L~~~Gv~i~pGLSd~Ef~~IEa~fgF~FPpDlRa~L~~GLPvG~---gFPdWR~~s~ 91 (376)
+++.+.++| ..+...+++.|++.|++..=.++-.-++.- |..+|.+.+.|.-+|. .-+++...+.
T Consensus 4 ~~~~v~ltfDdg~~~~~~~~~~~l~~~~i~at~fv~~~~~~~~--------~~~l~~l~~~G~ei~~H~~~H~~~~~~~~ 75 (123)
T PF01522_consen 4 PKKSVALTFDDGYRDNYDRLLPLLKKYGIPATFFVIGSWVERY--------PDQLRELAAAGHEIGNHGWSHPNLSTLSP 75 (123)
T ss_dssp TSSEEEEEEESHCHTHHHHHHHHHHHTT--EEEEE-HHHHHHH--------HHHHHHHHHTT-EEEEE-SSSSCGGGS-H
T ss_pred CCCEEEEEEecCchhhHHHHHHHHHhcccceeeeecccccccc--------cccchhHHHHHHHHHhcCCcccccccCCH
Confidence 455677776 467899999999999887777777754433 8899999999999873 3556656667
Q ss_pred HHHHHHHhhcc
Q 044476 92 QQLRILVKLPV 102 (376)
Q Consensus 92 ~~Lr~~L~~P~ 102 (376)
++++..|..-.
T Consensus 76 ~~~~~ei~~~~ 86 (123)
T PF01522_consen 76 EELRREIERSR 86 (123)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 77666555443
No 14
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, 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
Probab=39.77 E-value=26 Score=28.66 Aligned_cols=26 Identities=23% Similarity=0.206 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHHHHcCccCCchHHHHHHhc
Q 044476 47 PGLNDAEFSDIESTFNFTFPPDLRSILREG 76 (376)
Q Consensus 47 pGLSd~Ef~~IEa~fgF~FPpDlRa~L~~G 76 (376)
=|||+.+|+.||..| |.|++.--..+
T Consensus 23 LGlse~~Id~Ie~~~----~~dl~eq~~~m 48 (86)
T cd08779 23 LGLSYRELQRIKYNN----RDDLDEQIFDM 48 (86)
T ss_pred cCCCHHHHHHHHHHC----ccCHHHHHHHH
Confidence 389999999999998 66766544433
No 15
>TIGR01926 peroxid_rel uncharacterized peroxidase-related enzyme. This protein family with length of about 200 amino acids. One member, from Myxococcus xanthus, is a selenoprotein, with an otherwise conserved Cys replaced by Sec. This family is drawn narrowly enough to suggest that These proteins contain a domain described by TIGR00778, with a CxxCxxxHxxxxxxxG motif. Some members of that family are known to act as peroxidases or correlate with resistance to oxidative stress.
Probab=38.71 E-value=25 Score=30.91 Aligned_cols=75 Identities=13% Similarity=0.005 Sum_probs=40.6
Q ss_pred hhhhHHHHHHHHHhCCCCchhhhhhhhcccCCCCCcccccccCCccccchhhhhhhHHHH----HHHhcCCChHHHHHHh
Q 044476 246 LECCMDEVFWRLRDGGWREEEVREMMMVVDCHDDPTSEVQLVGDRTGRGSVERHVRLLSL----VLLRAGWSKEDVVYSL 321 (376)
Q Consensus 246 l~~yld~~~~~LR~GGW~E~ev~EM~~~~~~~~~e~~~~~~~~d~~~~~~l~~~vd~~S~----sL~rAGWS~eDV~eal 321 (376)
-.-|++-=...++..|-++++++.+-.-..+...+.++.++ -+-.+.+..+-...++ .|+++|||.++|+|..
T Consensus 78 c~yc~~~H~~~~~~~g~~~~~~~ai~~~~~~~~~~~~e~a~---l~~a~~~~~~~~~v~~~~~~~l~~~g~s~~eivel~ 154 (177)
T TIGR01926 78 CVYCAAVHGAALRQLSGDPDLADAVAVNFRDADLSPRERAM---LDFAVKLTATPAKVNEADFAALRAAGFSDLDILDLI 154 (177)
T ss_pred CHHHHHHHHHHHHHhcCCHHHHHHHHhCcccCCCCHHHHHH---HHHHHHHhhCcccCCHHHHHHHHHcCCCHHHHHHHH
Confidence 35577776778888888888887766322111111011110 0000222222222333 5889999999999876
Q ss_pred cc
Q 044476 322 NL 323 (376)
Q Consensus 322 ~~ 323 (376)
..
T Consensus 155 ~~ 156 (177)
T TIGR01926 155 HS 156 (177)
T ss_pred HH
Confidence 43
No 16
>cd08503 PBP2_NikA_DppA_OppA_like_17 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=33.67 E-value=68 Score=32.23 Aligned_cols=35 Identities=11% Similarity=0.433 Sum_probs=23.9
Q ss_pred hhHHHHHHHHhhcc-CCceecccCCccccCCCCCCC
Q 044476 126 NNDALSLIKKLLDK-APLLVPIYRNCYVPSTPNMAG 160 (376)
Q Consensus 126 ~~eal~~Ar~~L~~-aP~LVPIygHrYlPs~p~~aG 160 (376)
..++.+.+.+.|.. +|.++|+|.+.++...+...|
T Consensus 424 r~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~v~g 459 (460)
T cd08503 424 RKELYAEMQQILHDEGGIIIPYFRSYLDAHSDKVKG 459 (460)
T ss_pred HHHHHHHHHHHHHhcCCeEeEeecchhhhccccccC
Confidence 44455555666554 899999999977766665543
No 17
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. 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 CARD (Caspase activation a
Probab=33.07 E-value=43 Score=27.56 Aligned_cols=15 Identities=33% Similarity=0.561 Sum_probs=13.5
Q ss_pred CCCHHHHHHHHHHcC
Q 044476 48 GLNDAEFSDIESTFN 62 (376)
Q Consensus 48 GLSd~Ef~~IEa~fg 62 (376)
||||.+|+.||..+.
T Consensus 22 Glse~~Id~ie~~~~ 36 (80)
T cd08313 22 GLSDNEIERVELDHR 36 (80)
T ss_pred CCCHHHHHHHHHhCC
Confidence 899999999998773
No 18
>PF11203 DUF2984: Protein of unknown function (DUF2984); InterPro: IPR021368 This entry represents the transmembrane protein EccE found in the Actinobacteria, which are part of type VII secretion system (T7SS) [].
Probab=32.94 E-value=60 Score=27.28 Aligned_cols=52 Identities=25% Similarity=0.396 Sum_probs=37.1
Q ss_pred hhhHHHHHHHHHhCCcccCCCCCHHHHHHHHHHcCccCCchHHHHHHhcCCCCCCCCCCCCCC
Q 044476 28 AAYAKNLIDHLKSLNIPILPGLNDAEFSDIESTFNFTFPPDLRSILREGLPAGPAFPNWRSSS 90 (376)
Q Consensus 28 ~~ya~~ii~~L~~~Gv~i~pGLSd~Ef~~IEa~fgF~FPpDlRa~L~~GLPvG~gFPdWR~~s 90 (376)
..-+..|.++|++.|+.-.+ |+..|+..+-.....-.+++- .+.|-.|++++
T Consensus 38 ~~a~~Rla~~L~~~G~~a~~-l~a~el~~~~~~~~~~~~~~~----------~E~W~~~~~~~ 89 (98)
T PF11203_consen 38 AAAARRLADRLREAGIRARV-LTADELPAALAALADGLPPAP----------RETWRGWRGGG 89 (98)
T ss_pred HHHHHHHHHHHHHCCCCcee-cChhhhHHHHHHhhccCCCCC----------CCCcceEeeCC
Confidence 45678899999999999888 899898776554443333322 67788887753
No 19
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=30.01 E-value=69 Score=22.61 Aligned_cols=27 Identities=19% Similarity=0.219 Sum_probs=21.9
Q ss_pred hhhHHHHHHHhcCCChHHHHHHhccCC
Q 044476 299 HVRLLSLVLLRAGWSKEDVVYSLNLQD 325 (376)
Q Consensus 299 ~vd~~S~sL~rAGWS~eDV~eal~~~~ 325 (376)
.-+.+...|.+.||+...++..||+.-
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~Lgisr 32 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLLGISR 32 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHTS-H
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHCCCH
Confidence 456788899999999999999999863
No 20
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=29.41 E-value=30 Score=26.41 Aligned_cols=28 Identities=25% Similarity=0.355 Sum_probs=22.7
Q ss_pred HHHHhCCcccCCCCCHHHHHHHHHHcCc
Q 044476 36 DHLKSLNIPILPGLNDAEFSDIESTFNF 63 (376)
Q Consensus 36 ~~L~~~Gv~i~pGLSd~Ef~~IEa~fgF 63 (376)
+.++..++...-|||++|.++--++||-
T Consensus 8 ~v~~~l~t~~~~GLs~~ev~~r~~~~G~ 35 (69)
T PF00690_consen 8 EVLKRLNTSSSQGLSSEEVEERRKKYGP 35 (69)
T ss_dssp HHHHHHTTBTSSBBTHHHHHHHHHHHSS
T ss_pred HHHHHHCcCCCCCCCHHHHHHHHHhccc
Confidence 3344446788999999999999999994
No 21
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=24.56 E-value=69 Score=23.88 Aligned_cols=24 Identities=25% Similarity=0.279 Sum_probs=17.5
Q ss_pred HHHHHHHhcCCChHHHHHHhccCC
Q 044476 302 LLSLVLLRAGWSKEDVVYSLNLQD 325 (376)
Q Consensus 302 ~~S~sL~rAGWS~eDV~eal~~~~ 325 (376)
++-..-+++|||.++|++.+|...
T Consensus 5 ~lr~~R~~~gls~~~lA~~~g~s~ 28 (64)
T PF13560_consen 5 RLRRLRERAGLSQAQLADRLGVSQ 28 (64)
T ss_dssp HHHHHHHCHTS-HHHHHHHHTS-H
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCH
Confidence 444555678999999999999765
No 22
>PRK05087 D-alanine--poly(phosphoribitol) ligase subunit 2; Validated
Probab=24.38 E-value=46 Score=26.84 Aligned_cols=16 Identities=19% Similarity=0.511 Sum_probs=13.7
Q ss_pred HHHHHHHcCccCCchH
Q 044476 54 FSDIESTFNFTFPPDL 69 (376)
Q Consensus 54 f~~IEa~fgF~FPpDl 69 (376)
+..+|..||+++|++-
T Consensus 43 i~~lE~~fgi~i~~~e 58 (78)
T PRK05087 43 LVELENRFDIEVPVSE 58 (78)
T ss_pred HHHHHHHhCCccChHh
Confidence 4678999999999874
No 23
>PRK12449 acyl carrier protein; Provisional
Probab=24.24 E-value=48 Score=25.80 Aligned_cols=15 Identities=20% Similarity=0.643 Sum_probs=12.9
Q ss_pred HHHHHHHcCccCCch
Q 044476 54 FSDIESTFNFTFPPD 68 (376)
Q Consensus 54 f~~IEa~fgF~FPpD 68 (376)
+..+|.+||+.+|++
T Consensus 46 i~~lE~~f~i~i~~~ 60 (80)
T PRK12449 46 IINVEDEFHIAIPDE 60 (80)
T ss_pred HHHHHHHhCCCCCHH
Confidence 357999999999986
No 24
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.09 E-value=51 Score=23.25 Aligned_cols=19 Identities=37% Similarity=0.767 Sum_probs=12.8
Q ss_pred HHhcCCChHHHHHHhccCC
Q 044476 307 LLRAGWSKEDVVYSLNLQD 325 (376)
Q Consensus 307 L~rAGWS~eDV~eal~~~~ 325 (376)
|...|||..+|+..||..-
T Consensus 13 l~~~G~s~~~ia~~lgvs~ 31 (50)
T PF13384_consen 13 LLREGWSIREIAKRLGVSR 31 (50)
T ss_dssp HHHHT--HHHHHHHHTS-H
T ss_pred HHHCCCCHHHHHHHHCcCH
Confidence 4445999999999999753
No 25
>TIGR01124 ilvA_2Cterm threonine ammonia-lyase, biosynthetic, long form. Forms scoring between the trusted and noise cutoff tend to branch with this subgroup of threonine ammonia-lyase phylogenetically but have only a single copy of the C-terminal domain.
Probab=23.85 E-value=54 Score=34.81 Aligned_cols=53 Identities=19% Similarity=0.404 Sum_probs=41.9
Q ss_pred cceeech----hhHHHHHHHHHhCCcccCCCCCHHHHHHH---------------HHHcCccCCch---HHHHHHh
Q 044476 22 LVCFSYA----AYAKNLIDHLKSLNIPILPGLNDAEFSDI---------------ESTFNFTFPPD---LRSILRE 75 (376)
Q Consensus 22 ~~~~Sf~----~ya~~ii~~L~~~Gv~i~pGLSd~Ef~~I---------------Ea~fgF~FPpD---lRa~L~~ 75 (376)
++++.+. .-..+|++.|++.|.++.- |||.|+.+. |..|-|+||.- ||.||..
T Consensus 365 ~v~vgie~~~~~~~~~l~~~L~~~Gy~~~d-ls~ne~~k~h~r~~~g~~~~~~~~e~~~~~~fperpgaL~~Fl~~ 439 (499)
T TIGR01124 365 HIFVGVQLSNPQERQEILARLNDGGYSVVD-LTDDELAKLHVRYMVGGRPPHVENERLYSFEFPERPGALLRFLNT 439 (499)
T ss_pred EEEEEEEeCCHHHHHHHHHHHHHcCCCeEE-CCCCHHHHHHHHhccCCCCCCCCCceEEEEeCCCCccHHHHHHHh
Confidence 4555554 4567999999999966654 499999976 77899999977 9999994
No 26
>COG4174 ABC-type uncharacterized transport system, permease component [General function prediction only]
Probab=23.55 E-value=88 Score=32.10 Aligned_cols=102 Identities=26% Similarity=0.378 Sum_probs=63.8
Q ss_pred cCCCCCHHHHHHHHHHcCccCCchHHHHHHhc----CCCCCCCCCCCCCCHHHHHHHHhhccccchhhccccCCcccc--
Q 044476 45 ILPGLNDAEFSDIESTFNFTFPPDLRSILREG----LPAGPAFPNWRSSSHQQLRILVKLPVLSLSKNVSLNNFWSVS-- 118 (376)
Q Consensus 45 i~pGLSd~Ef~~IEa~fgF~FPpDlRa~L~~G----LPvG~gFPdWR~~s~~~Lr~~L~~P~~gil~dVe~n~fW~~s-- 118 (376)
=..||..+-++.||+.|||.=||--|-+++.. .-.|+.|. |+.+--.|-+ =++|+. |.- .+|..-
T Consensus 76 g~~GlDpe~i~~i~~~~GFDKp~~eR~~~Ml~~y~rfDfGeS~f--r~~~VidLI~-eklPVS-----iSl-Glw~tli~ 146 (364)
T COG4174 76 GAQGLDPELIAEIEKQYGFDKPPLERYFLMLWDYARFDFGESFF--RDASVIDLIK-EKLPVS-----ISL-GLWSTLII 146 (364)
T ss_pred cccCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhccccHHhh--cCChHHHHHH-HhCCcE-----EEh-HHHHHHHH
Confidence 35789999999999999999999999998864 44566666 6654332221 134542 222 244310
Q ss_pred c-CCCCCChhHHHHHHHHhhccCCceecccCCccccCCCCCCCCceEEEeCCCEEEEccchHHHHh
Q 044476 119 W-GQRPQNNNDALSLIKKLLDKAPLLVPIYRNCYVPSTPNMAGNPVFYIDTEEVRVLSFDLAGFFK 183 (376)
Q Consensus 119 W-G~RP~~~~eal~~Ar~~L~~aP~LVPIygHrYlPs~p~~aGnPVfSV~qtDIi~yG~DLadyf~ 183 (376)
. =.-|-...+|+ .. +-.|-||.+-||..|+-+-.|+-
T Consensus 147 YliSIPLGI~KAv---------------------------~~-gs~fDvwsS~viiigyAiP~Flf 184 (364)
T COG4174 147 YLISIPLGIRKAV---------------------------RN-GSRFDVWSSAVIIIGYAIPAFLF 184 (364)
T ss_pred HHHhcchhHHHHH---------------------------hC-CCcceeeeeeeEEEecccHHHHH
Confidence 0 00112221111 12 34589999999999999999874
No 27
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=23.08 E-value=63 Score=23.10 Aligned_cols=20 Identities=15% Similarity=0.227 Sum_probs=15.0
Q ss_pred HHHHhcCCChHHHHHHhccC
Q 044476 305 LVLLRAGWSKEDVVYSLNLQ 324 (376)
Q Consensus 305 ~sL~rAGWS~eDV~eal~~~ 324 (376)
..|+..|.|..+|+..||..
T Consensus 15 ~~l~~~G~si~~IA~~~gvs 34 (45)
T PF02796_consen 15 KELYAEGMSIAEIAKQFGVS 34 (45)
T ss_dssp HHHHHTT--HHHHHHHTTS-
T ss_pred HHHHHCCCCHHHHHHHHCcC
Confidence 45889999999999999874
No 28
>TIGR00677 fadh2_euk methylenetetrahydrofolate reductase, eukaryotic type. This protein is an FAD-containing flavoprotein.
Probab=23.04 E-value=1.4e+02 Score=29.42 Aligned_cols=55 Identities=16% Similarity=0.330 Sum_probs=42.7
Q ss_pred ccceeechhhHHHHHHHHHhCC--cccCCCCC----HHHHHHHHHHcCccCCchHHHHHHhc
Q 044476 21 KLVCFSYAAYAKNLIDHLKSLN--IPILPGLN----DAEFSDIESTFNFTFPPDLRSILREG 76 (376)
Q Consensus 21 r~~~~Sf~~ya~~ii~~L~~~G--v~i~pGLS----d~Ef~~IEa~fgF~FPpDlRa~L~~G 76 (376)
.+.+|....|. ..++.+++.| ++|-||+. -..+.++.+..|+.+|.+++..|...
T Consensus 167 TQ~~Fd~~~~~-~f~~~~~~~gi~~PIi~GI~pi~s~~~~~~~~~~~Gi~vP~~l~~~l~~~ 227 (281)
T TIGR00677 167 TQLFYDVDNFL-KFVNDCRAIGIDCPIVPGIMPINNYASFLRRAKWSKTKIPQEIMSRLEPI 227 (281)
T ss_pred ccceecHHHHH-HHHHHHHHcCCCCCEEeeccccCCHHHHHHHHhcCCCCCCHHHHHHHHhc
Confidence 45667766654 6778888885 89999974 45677787789999999999999874
No 29
>PRK07081 acyl carrier protein; Provisional
Probab=22.83 E-value=52 Score=26.52 Aligned_cols=16 Identities=25% Similarity=0.654 Sum_probs=13.6
Q ss_pred HHHHHHHcCccCCchH
Q 044476 54 FSDIESTFNFTFPPDL 69 (376)
Q Consensus 54 f~~IEa~fgF~FPpDl 69 (376)
+..||.+||+.+|++.
T Consensus 42 i~~lE~~f~I~i~~~~ 57 (83)
T PRK07081 42 MLAIEDAFDIEIPDEM 57 (83)
T ss_pred HHHHHHHhCCcCCHHH
Confidence 4579999999999984
No 30
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=22.64 E-value=78 Score=23.82 Aligned_cols=23 Identities=30% Similarity=0.257 Sum_probs=16.5
Q ss_pred hhhHHHHHHHhcCCChHHHHHHhc
Q 044476 299 HVRLLSLVLLRAGWSKEDVVYSLN 322 (376)
Q Consensus 299 ~vd~~S~sL~rAGWS~eDV~eal~ 322 (376)
.|+.+-..+ ++|||.|||++.+.
T Consensus 20 ~v~~i~~~~-~~G~s~eeI~~~yp 42 (56)
T PF04255_consen 20 PVRDILDLL-AAGESPEEIAEDYP 42 (56)
T ss_dssp BHHHHHHHH-HTT--HHHHHHHST
T ss_pred cHHHHHHHH-HcCCCHHHHHHHCC
Confidence 456666666 99999999999875
No 31
>PF02513 Spin-Ssty: Spin/Ssty Family; InterPro: IPR003671 Spindlin (Spin) and Ssty were first identified for their involvement in gametogenesis. Spindlin was identified as a maternal transcript present in the unfertilised egg and early embryo, and was subsequently shown to interact with the spindle apparatus during oogenesis, and may therefore be important for mitosis []. In addition, spindlin appears to be a target for cell cycle-dependent phosphorylation, and as such may play a role in cell cycle regulation during the transition from gamete to embryo []. Ssty is a multi-copy, Y-linked spermatogenesis-specific transcript that appears to be required for normal spermatogenesis []. Ssty may play an analogous role to spindlin in sperm cells, namely during the transition from sperm cells to early embryo, and in mitosis.; GO: 0007276 gamete generation; PDB: 2NS2_A.
Probab=22.51 E-value=41 Score=25.88 Aligned_cols=19 Identities=21% Similarity=0.665 Sum_probs=15.7
Q ss_pred Cc-eEEE-eCCCEEEEccchH
Q 044476 161 NP-VFYI-DTEEVRVLSFDLA 179 (376)
Q Consensus 161 nP-VfSV-~qtDIi~yG~DLa 179 (376)
|| +|+| |+.|..+|+.+|.
T Consensus 30 ~ps~y~Ikyd~d~~iY~y~L~ 50 (50)
T PF02513_consen 30 KPSLYYIKYDGDDHIYVYELV 50 (50)
T ss_dssp STTEEEEEETTESBEEEEECH
T ss_pred CCcEEEEEECCCcEEEEEEeC
Confidence 45 8888 8899999998873
No 32
>PRK07639 acyl carrier protein; Provisional
Probab=21.03 E-value=57 Score=26.59 Aligned_cols=16 Identities=25% Similarity=0.312 Sum_probs=13.5
Q ss_pred HHHHHHHcCccCCchH
Q 044476 54 FSDIESTFNFTFPPDL 69 (376)
Q Consensus 54 f~~IEa~fgF~FPpDl 69 (376)
+..+|.+||+++|++-
T Consensus 47 v~~lE~~fgi~i~d~~ 62 (86)
T PRK07639 47 IVYIEMDVKLCVPEDE 62 (86)
T ss_pred HHHHHHHHCCccCHHH
Confidence 4569999999999873
No 33
>TIGR00517 acyl_carrier acyl carrier protein. S (Ser) at position 37 in the seed alignment, in the motif DSLD, is the phosphopantetheine attachment site.
Probab=20.97 E-value=61 Score=25.02 Aligned_cols=15 Identities=20% Similarity=0.505 Sum_probs=13.2
Q ss_pred HHHHHHcCccCCchH
Q 044476 55 SDIESTFNFTFPPDL 69 (376)
Q Consensus 55 ~~IEa~fgF~FPpDl 69 (376)
..||.+||+.+|++.
T Consensus 45 ~~lE~~f~i~i~~~~ 59 (77)
T TIGR00517 45 MALEEEFDIEIPDEE 59 (77)
T ss_pred HHHHHHHCCCCCHHH
Confidence 469999999999885
No 34
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=20.39 E-value=38 Score=24.94 Aligned_cols=34 Identities=32% Similarity=0.456 Sum_probs=24.5
Q ss_pred HHHHHHHH-HhCCcc---cCCCCCHHHHHHHHHHcCcc
Q 044476 31 AKNLIDHL-KSLNIP---ILPGLNDAEFSDIESTFNFT 64 (376)
Q Consensus 31 a~~ii~~L-~~~Gv~---i~pGLSd~Ef~~IEa~fgF~ 64 (376)
++.||+.| ++.|+. ..--|++++...|-+.||+.
T Consensus 17 ~~~ii~~l~~~~Gi~~~~~~~~ld~e~~~~i~~~~~~k 54 (54)
T PF04760_consen 17 SKEIIKKLFKELGIMVKSINSSLDEEEAELIAEEFGVK 54 (54)
T ss_dssp HHHHHHHH-HHHTS---SSSS-EETTGGGHHHHHH---
T ss_pred HHHHHHHHHHhCCcCcCCCCCcCCHHHHHHHHHHhCcC
Confidence 57899999 558866 66789999999999999874
No 35
>PRK05350 acyl carrier protein; Provisional
Probab=20.24 E-value=62 Score=25.60 Aligned_cols=16 Identities=6% Similarity=0.121 Sum_probs=13.3
Q ss_pred HHHHHHHcCccCCchH
Q 044476 54 FSDIESTFNFTFPPDL 69 (376)
Q Consensus 54 f~~IEa~fgF~FPpDl 69 (376)
+..+|.+||+.||++.
T Consensus 47 i~~lE~~fgI~i~~~~ 62 (82)
T PRK05350 47 VVHLQKLTGKKIKPEE 62 (82)
T ss_pred HHHHHHHHCCccCHHH
Confidence 3569999999999864
No 36
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=20.16 E-value=1.6e+02 Score=25.60 Aligned_cols=49 Identities=16% Similarity=0.214 Sum_probs=35.8
Q ss_pred HHHHHHHHHhCCCCchhhhhhhhcccCCCCCcccccccCCccccchhhhhhhHHHHHHHhcCCC
Q 044476 250 MDEVFWRLRDGGWREEEVREMMMVVDCHDDPTSEVQLVGDRTGRGSVERHVRLLSLVLLRAGWS 313 (376)
Q Consensus 250 ld~~~~~LR~GGW~E~ev~EM~~~~~~~~~e~~~~~~~~d~~~~~~l~~~vd~~S~sL~rAGWS 313 (376)
-|+|.+.|++-- .--+|+|++.+-..+ .+ ..+.-|+.-++.+|+|.|--
T Consensus 5 rEkii~lL~e~~-eplt~~ei~~~~~~~-~~-------------~~v~~~L~hiak~lkr~g~~ 53 (97)
T COG3357 5 REKIISLLLESD-EPLTVAEIFELLNGE-KE-------------KEVYDHLEHIAKSLKRKGKR 53 (97)
T ss_pred HHHHHHHHHcCC-CcchHHHHHHHHcCC-ch-------------HHHHHHHHHHHHHHHhCCce
Confidence 478888888876 667788887665532 11 24567889999999999964
Done!