Query psy13278
Match_columns 174
No_of_seqs 137 out of 236
Neff 5.3
Searched_HMMs 46136
Date Sat Aug 17 00:40:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13278.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13278hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01843 DIL: DIL domain; Int 100.0 1.5E-30 3.2E-35 193.4 3.6 92 17-110 1-105 (105)
2 KOG1892|consensus 99.9 6.9E-24 1.5E-28 203.9 8.9 149 15-166 711-880 (1629)
3 COG5022 Myosin heavy chain [Cy 99.2 2.3E-11 4.9E-16 122.1 7.8 108 17-126 1284-1403(1463)
4 PF01843 DIL: DIL domain; Int 70.6 1.4 3E-05 32.3 0.0 34 16-49 60-94 (105)
5 smart00657 RPOL4c DNA-directed 51.2 89 0.0019 23.5 6.9 56 46-102 52-110 (118)
6 smart00546 CUE Domain that may 44.2 45 0.00097 20.4 3.6 27 78-104 3-29 (43)
7 PF12728 HTH_17: Helix-turn-he 44.1 33 0.00072 21.4 3.0 45 17-62 5-50 (51)
8 PF10281 Ish1: Putative stress 43.4 16 0.00035 22.2 1.4 13 52-64 6-18 (38)
9 PF06209 COBRA1: Cofactor of B 43.0 49 0.0011 31.3 5.1 61 85-146 406-466 (474)
10 PF02845 CUE: CUE domain; Int 41.7 54 0.0012 20.0 3.7 27 78-104 2-28 (42)
11 PF14893 PNMA: PNMA 40.0 31 0.00067 31.1 3.2 35 52-86 3-40 (331)
12 PF11338 DUF3140: Protein of u 35.2 55 0.0012 24.4 3.4 50 51-105 9-78 (92)
13 COG4973 XerC Site-specific rec 34.4 35 0.00075 30.2 2.5 77 17-98 186-278 (299)
14 PF07176 DUF1400: Alpha/beta h 34.1 1.4E+02 0.003 22.9 5.7 73 45-127 12-86 (127)
15 PF03874 RNA_pol_Rpb4: RNA pol 33.7 83 0.0018 23.1 4.3 50 52-101 59-111 (117)
16 PRK10945 gene expression modul 33.1 53 0.0011 23.5 2.9 29 70-98 11-42 (72)
17 TIGR01764 excise DNA binding d 32.1 64 0.0014 19.0 2.9 42 19-61 7-49 (49)
18 PHA02102 hypothetical protein 31.8 81 0.0018 22.2 3.6 44 14-62 6-49 (72)
19 PF01017 STAT_alpha: STAT prot 27.8 1.5E+02 0.0033 23.9 5.2 17 44-61 116-132 (182)
20 PRK10391 oriC-binding nucleoid 27.1 30 0.00065 24.6 0.8 25 69-93 5-32 (71)
21 PF05361 PP1_inhibitor: PKC-ac 26.7 1.4E+02 0.003 24.0 4.5 60 54-126 50-115 (144)
22 smart00335 ANX Annexin repeats 26.6 47 0.001 20.8 1.6 32 80-113 3-34 (53)
23 cd08336 DED_FADD Death Effecto 26.1 2.2E+02 0.0049 20.1 5.2 75 19-104 3-82 (82)
24 PF13808 DDE_Tnp_1_assoc: DDE_ 25.1 1.1E+02 0.0025 21.7 3.6 58 39-103 30-88 (90)
25 COG1535 EntB Isochorismate hyd 24.5 35 0.00075 28.9 0.8 78 46-128 55-141 (218)
26 PRK07539 NADH dehydrogenase su 24.5 1.5E+02 0.0033 23.2 4.5 73 52-126 7-102 (154)
27 KOG0098|consensus 23.6 55 0.0012 27.8 1.9 88 3-102 82-173 (216)
28 PF13625 Helicase_C_3: Helicas 23.6 1.7E+02 0.0036 21.9 4.4 38 87-129 51-88 (129)
29 PF09494 Slx4: Slx4 endonuclea 23.3 38 0.00083 22.9 0.7 14 51-64 46-59 (64)
30 KOG3242|consensus 22.3 1.9E+02 0.004 24.4 4.7 49 52-113 75-124 (208)
31 PF01335 DED: Death effector d 21.5 2E+02 0.0043 19.9 4.2 76 19-104 1-80 (84)
32 COG4496 Uncharacterized protei 21.1 2.9E+02 0.0062 20.8 5.0 38 94-131 47-86 (100)
33 PF02898 NO_synthase: Nitric o 20.0 82 0.0018 29.0 2.3 35 2-36 77-112 (372)
No 1
>PF01843 DIL: DIL domain; InterPro: IPR018444 Dilute encodes a novel type of myosin heavy chain, with a tail, or C-terminal, region that has elements of both type II (alpha-helical coiled-coil) and type I (non-coiled-coil) myosin heavy chains. The DIL non alpha-helical domain is found in dilute myosin heavy chain proteins and other myosins. In mouse the dilute protein may play a role in the elaboration, maintenance, or function of cellular processes of melanocytes and neurons []. The MYO2 protein of Saccharomyces cerevisiae is implicated in vectorial vesicle transport and is homologous to the dilute protein over practically its entire length [].; PDB: 3MMI_B 2F6H_X.
Probab=99.96 E-value=1.5e-30 Score=193.42 Aligned_cols=92 Identities=33% Similarity=0.467 Sum_probs=81.0
Q ss_pred HHHHHHHHHHh--hhhhHHhhhccccccccccccccchhHHHHHHhhcCc------h----HhhhhhhcccC-ChhHHHH
Q psy13278 17 KVASQLLQARK--TQEDVNTVCEMCNKMSTNQVRAVSTSQVRDLNRIKSV------H----KVASQLLQARK-TQEDVNT 83 (174)
Q Consensus 17 q~fsQLf~~i~--~fNdl~s~~~lCs~~~G~QIr~~Nls~LEeW~~~~~l------h----iQa~~LLQ~~K-t~~D~~~ 83 (174)
|+|+|||+|++ .||+++.++++|+|.+|+||++ |++.||+||+++|+ | +||++|||++| +.+|++.
T Consensus 1 Q~f~qlf~~i~~~~fN~ll~~~~~~~~~~g~qi~~-nls~l~~W~~~~~l~~~~~~~l~~l~Qa~~lL~~~k~~~~d~~~ 79 (105)
T PF01843_consen 1 QLFSQLFHYINASLFNSLLLRRKYCSWSKGVQIRY-NLSELEDWARSHGLEEAAEEHLQPLSQAANLLQLRKSTLQDWDS 79 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHCHSS-B-HHHHHHHHH-HHHHHHHCCCCTTSTTH-HHHCHHHHHHHHHCCC--SSHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHCCCCccccccHHHHHH-HHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhcCcchhHHHH
Confidence 78999999996 8999999999999999999999 99999999999999 1 99999999999 8999999
Q ss_pred HHHHhccCCHHHHHHHHHhcCCCCCCC
Q psy13278 84 VCEMCNKMSTNQIIKLLNLYTPADDYE 110 (174)
Q Consensus 84 i~~~C~~L~~~Qi~klL~~Y~P~~~~E 110 (174)
++++|++||+.||++||++|+| ++||
T Consensus 80 ~~~~c~~Ln~~Qi~~iL~~Y~~-~~~e 105 (105)
T PF01843_consen 80 LRETCPSLNPAQIRKILSNYQP-DDYE 105 (105)
T ss_dssp HCCCTTTS-HHHHHHHHCCB----TTS
T ss_pred HHHHcccCCHHHHHHHHHhCCC-cCCC
Confidence 9999999999999999999998 8876
No 2
>KOG1892|consensus
Probab=99.90 E-value=6.9e-24 Score=203.94 Aligned_cols=149 Identities=17% Similarity=0.251 Sum_probs=130.2
Q ss_pred HHHHHHHHHHHHh--hhhhHHhh--hccccccccccccccchhHHHHHHhhcCc------h----HhhhhhhcccC-Chh
Q psy13278 15 VHKVASQLLQARK--TQEDVNTV--CEMCNKMSTNQVRAVSTSQVRDLNRIKSV------H----KVASQLLQARK-TQE 79 (174)
Q Consensus 15 v~q~fsQLf~~i~--~fNdl~s~--~~lCs~~~G~QIr~~Nls~LEeW~~~~~l------h----iQa~~LLQ~~K-t~~ 79 (174)
.||+|+||||||+ +||.|++. ..+|+..||.-|++ .+..||.||+++|+ | +|||+||++.| .++
T Consensus 711 TIQLfsqLfH~iN~~~FN~lVt~~~s~~cs~~wGk~~~~-rl~~ie~waErqGlElAAdCHL~ri~Qaa~lL~~~K~a~d 789 (1629)
T KOG1892|consen 711 TIQLFSQLFHFINMWLFNRLVTDPDSGLCSHYWGKIIRQ-RLGHIEAWAERQGLELAADCHLSRIVQAATLLTMDKYAPD 789 (1629)
T ss_pred HHHHHHHHHHHHHHHHhhhhcccCchhhhhhhHHHHHHH-HHHHHHHHHHHhcchHhhhccHHHHHHHHHHHhccccChh
Confidence 3999999999996 89999998 89999999999999 99999999999999 3 99999999999 899
Q ss_pred HHHHHHHHhccCCHHHHHHHHHhcCCCCCCCCCCCHHHHHHHHHHHhh------CCCCcccchhcccCcccccccccCCC
Q psy13278 80 DVNTVCEMCNKMSTNQIIKLLNLYTPADDYEERISQSFIHLIQEKLKE------RPQSEQSTLLMDTKFNFSVRFPFSAS 153 (174)
Q Consensus 80 D~~~i~~~C~~L~~~Qi~klL~~Y~P~~~~E~~ip~~~i~~v~~~~~~------r~~~~~~~l~~D~~~~~p~~~pf~ps 153 (174)
|+..|.+.|++||+.|+++||+.|+| +++|+++|.++++.|...... |.|+...++.++.....|+.+|-.-.
T Consensus 790 di~~l~stCfkLNSLQ~~alLq~~~~-~~~e~~~p~dlvd~v~r~AE~~ADeLtr~DGreV~LEEspeL~LpfLlP~DGy 868 (1629)
T KOG1892|consen 790 DIPNLNSTCFKLNSLQLQALLQNYHC-APDEPFIPTDLVDNVVRVAENTADELTRSDGREVQLEESPELQLPFLLPEDGY 868 (1629)
T ss_pred hHHhhccchhhcchHHHHHHHhcCCC-CCCCCCCchHHHHHHHHHHHhhhhHhhhccCceeecccCcccccceeecCCCc
Confidence 99999999999999999999999997 999999999999999888763 34555667889999999999986543
Q ss_pred cccccccccCCCC
Q psy13278 154 NIQLEHIEIPDVL 166 (174)
Q Consensus 154 ~~~le~~~iP~~l 166 (174)
+...-.= ||..|
T Consensus 869 scdvvR~-iP~GL 880 (1629)
T KOG1892|consen 869 SCDVVRN-IPNGL 880 (1629)
T ss_pred eeeeecc-CChhH
Confidence 3332222 56554
No 3
>COG5022 Myosin heavy chain [Cytoskeleton]
Probab=99.21 E-value=2.3e-11 Score=122.05 Aligned_cols=108 Identities=19% Similarity=0.260 Sum_probs=98.1
Q ss_pred HHHHHHHHHHh--hhhhHHhhhccccccccccccccchhHHHHHHhhcCch---------HhhhhhhcccC-ChhHHHHH
Q psy13278 17 KVASQLLQARK--TQEDVNTVCEMCNKMSTNQVRAVSTSQVRDLNRIKSVH---------KVASQLLQARK-TQEDVNTV 84 (174)
Q Consensus 17 q~fsQLf~~i~--~fNdl~s~~~lCs~~~G~QIr~~Nls~LEeW~~~~~lh---------iQa~~LLQ~~K-t~~D~~~i 84 (174)
..+.+++++++ +||.+.+++.-.+|+.|-++.+ |.+++++||+.+|++ +||++.+|.+| ++++++++
T Consensus 1284 ~~i~~~~~~~~~~~~n~L~~~~~~~~~k~~~~~~~-n~~~~~~w~~~~~i~~~~~~l~~l~q~~k~~~~~~~dl~~~~~~ 1362 (1463)
T COG5022 1284 ATINSLLQYINVGLFNALRTKASSLRWKSATEVNY-NSEELDDWCREFEISDVDEELEELIQAVKVLQLLKDDLNKLDEL 1362 (1463)
T ss_pred HHHHhHhhhcchhhhhhhhcccCccchhhcccccc-cchhhhHHHHhhcccchHHHHHHHHhhhhhhhhhhCCHHHHHHH
Confidence 35667777774 8999999999999999999999 999999999999992 99999999999 99999999
Q ss_pred HHHhccCCHHHHHHHHHhcCCCCCCCCCCCHHHHHHHHHHHh
Q psy13278 85 CEMCNKMSTNQIIKLLNLYTPADDYEERISQSFIHLIQEKLK 126 (174)
Q Consensus 85 ~~~C~~L~~~Qi~klL~~Y~P~~~~E~~ip~~~i~~v~~~~~ 126 (174)
.++|.+|++.|+++|+..|.| .++|.++|.++..++.+...
T Consensus 1363 ~~~~~~l~~~~~~~L~~~y~~-~~~e~~l~ke~~~~~~a~~~ 1403 (1463)
T COG5022 1363 LDACYSLNPAEIQNLKSRYDP-ADKENNLPKEILKKIEALLI 1403 (1463)
T ss_pred HHHHHhcCHHHHHHHHHhhhh-hcccCCChHHHHHHHhhhhh
Confidence 999999999999999999997 89999999999966655553
No 4
>PF01843 DIL: DIL domain; InterPro: IPR018444 Dilute encodes a novel type of myosin heavy chain, with a tail, or C-terminal, region that has elements of both type II (alpha-helical coiled-coil) and type I (non-coiled-coil) myosin heavy chains. The DIL non alpha-helical domain is found in dilute myosin heavy chain proteins and other myosins. In mouse the dilute protein may play a role in the elaboration, maintenance, or function of cellular processes of melanocytes and neurons []. The MYO2 protein of Saccharomyces cerevisiae is implicated in vectorial vesicle transport and is homologous to the dilute protein over practically its entire length [].; PDB: 3MMI_B 2F6H_X.
Probab=70.60 E-value=1.4 Score=32.26 Aligned_cols=34 Identities=35% Similarity=0.526 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHh-hhhhHHhhhccccccccccccc
Q psy13278 16 HKVASQLLQARK-TQEDVNTVCEMCNKMSTNQVRA 49 (174)
Q Consensus 16 ~q~fsQLf~~i~-~fNdl~s~~~lCs~~~G~QIr~ 49 (174)
..++++||+..| ++.|+..+++.|..+++.||+.
T Consensus 60 l~Qa~~lL~~~k~~~~d~~~~~~~c~~Ln~~Qi~~ 94 (105)
T PF01843_consen 60 LSQAANLLQLRKSTLQDWDSLRETCPSLNPAQIRK 94 (105)
T ss_dssp HHHHHHHCCC--SSHHHHHHHCCCTTTS-HHHHHH
T ss_pred HHHHHHHHHhcCcchhHHHHHHHHcccCCHHHHHH
Confidence 456777777655 7999999999999999999987
No 5
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=51.18 E-value=89 Score=23.51 Aligned_cols=56 Identities=23% Similarity=0.275 Sum_probs=43.0
Q ss_pred cccccchhHHHHHHhhcCch-HhhhhhhcccC-ChhHHHHHHHHhc-cCCHHHHHHHHHh
Q psy13278 46 QVRAVSTSQVRDLNRIKSVH-KVASQLLQARK-TQEDVNTVCEMCN-KMSTNQIIKLLNL 102 (174)
Q Consensus 46 QIr~~Nls~LEeW~~~~~lh-iQa~~LLQ~~K-t~~D~~~i~~~C~-~L~~~Qi~klL~~ 102 (174)
+=+. .++.+.+=++..|+| .+.+++.=++- +.+.+..|.+.|. +++..|+.+||..
T Consensus 52 ~~~e-~i~~~~~~L~~~~L~k~E~~~i~Nl~P~s~~E~~~lI~sl~~r~~ee~l~~iL~~ 110 (118)
T smart00657 52 KNRE-IVRAVRTLLKSKKLHKFEIAQLGNLRPETAEEAQLLIPSLEERIDEEELEELLDD 110 (118)
T ss_pred CCHH-HHHHHHHHHHhcCCCHHHHHHHhCCCCCCHHHHHHHhhhhhccCCHHHHHHHHHH
Confidence 3344 566677777778886 77777776755 9999999999996 8999999988853
No 6
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=44.20 E-value=45 Score=20.42 Aligned_cols=27 Identities=15% Similarity=0.261 Sum_probs=24.4
Q ss_pred hhHHHHHHHHhccCCHHHHHHHHHhcC
Q psy13278 78 QEDVNTVCEMCNKMSTNQIIKLLNLYT 104 (174)
Q Consensus 78 ~~D~~~i~~~C~~L~~~Qi~klL~~Y~ 104 (174)
.+.++.+.++.+.+...+|++.|..+.
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~ 29 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEANN 29 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcC
Confidence 467889999999999999999999877
No 7
>PF12728 HTH_17: Helix-turn-helix domain
Probab=44.08 E-value=33 Score=21.37 Aligned_cols=45 Identities=16% Similarity=-0.009 Sum_probs=31.6
Q ss_pred HHHHHHHHHH-hhhhhHHhhhccccccccccccccchhHHHHHHhhc
Q psy13278 17 KVASQLLQAR-KTQEDVNTVCEMCNKMSTNQVRAVSTSQVRDLNRIK 62 (174)
Q Consensus 17 q~fsQLf~~i-~~fNdl~s~~~lCs~~~G~QIr~~Nls~LEeW~~~~ 62 (174)
+.++++|..- .++..+.....+=....|-+.++ +-+.|++|.+++
T Consensus 5 ~e~a~~l~is~~tv~~~~~~g~i~~~~~g~~~~~-~~~~l~~~~~~~ 50 (51)
T PF12728_consen 5 KEAAELLGISRSTVYRWIRQGKIPPFKIGRKWRI-PKSDLDRWLERR 50 (51)
T ss_pred HHHHHHHCcCHHHHHHHHHcCCCCeEEeCCEEEE-eHHHHHHHHHhC
Confidence 3455666633 36777776666633358888888 999999999875
No 8
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=43.36 E-value=16 Score=22.19 Aligned_cols=13 Identities=8% Similarity=0.243 Sum_probs=11.6
Q ss_pred hhHHHHHHhhcCc
Q psy13278 52 TSQVRDLNRIKSV 64 (174)
Q Consensus 52 ls~LEeW~~~~~l 64 (174)
-+.|++|+++||+
T Consensus 6 ~~~L~~wL~~~gi 18 (38)
T PF10281_consen 6 DSDLKSWLKSHGI 18 (38)
T ss_pred HHHHHHHHHHcCC
Confidence 4789999999998
No 9
>PF06209 COBRA1: Cofactor of BRCA1 (COBRA1); InterPro: IPR010405 This family consists of several cofactor of BRCA1 (COBRA1) like proteins. It is thought that COBRA1 along with BRCA1 is involved in chromatin unfolding. COBRA1 is recruited to the chromosome site by the first BRCT repeat of BRCA1, and is itself sufficient to induce chromatin unfolding. BRCA1 mutations that enhance chromatin unfolding also increase its affinity for, and recruitment of, COBRA1. It is thought that that reorganisation of higher levels of chromatin structure is an important regulated step in BRCA1-mediated nuclear functions [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=42.96 E-value=49 Score=31.28 Aligned_cols=61 Identities=8% Similarity=0.200 Sum_probs=38.5
Q ss_pred HHHhccCCHHHHHHHHHhcCCCCCCCCCCCHHHHHHHHHHHhhCCCCcccchhcccCccccc
Q psy13278 85 CEMCNKMSTNQIIKLLNLYTPADDYEERISQSFIHLIQEKLKERPQSEQSTLLMDTKFNFSV 146 (174)
Q Consensus 85 ~~~C~~L~~~Qi~klL~~Y~P~~~~E~~ip~~~i~~v~~~~~~r~~~~~~~l~~D~~~~~p~ 146 (174)
...|.+|.+.++..|++.+.|.....+.+ .+.-+.+++++++....-+....++.....|+
T Consensus 406 ~~~h~kl~~~~l~~L~k~L~Pt~~~~e~~-~~~y~~L~~ki~~~~~~~~~~~~~~~~~~~~l 466 (474)
T PF06209_consen 406 WYLHHKLPPARLETLMKALEPTSQHSEAV-KELYSKLVDKINSYQKPTPPMAEESPSLDSPL 466 (474)
T ss_pred HHHhccCCHHHHHHHHHHhCCCcchhHHH-HHHHHHHHHHHhccCCCCCCCCCCCCcccCCC
Confidence 36889999999999999999966655533 35666666666653221122233444444444
No 10
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=41.74 E-value=54 Score=20.03 Aligned_cols=27 Identities=22% Similarity=0.252 Sum_probs=23.4
Q ss_pred hhHHHHHHHHhccCCHHHHHHHHHhcC
Q psy13278 78 QEDVNTVCEMCNKMSTNQIIKLLNLYT 104 (174)
Q Consensus 78 ~~D~~~i~~~C~~L~~~Qi~klL~~Y~ 104 (174)
.+.++.+.++-+.++...|.+.|..+.
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~ 28 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANN 28 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTT
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcC
Confidence 467899999999999999999998876
No 11
>PF14893 PNMA: PNMA
Probab=39.96 E-value=31 Score=31.05 Aligned_cols=35 Identities=14% Similarity=0.160 Sum_probs=20.3
Q ss_pred hhHHHHHHhhcCch-HhhhhhhcccC--ChhHHHHHHH
Q psy13278 52 TSQVRDLNRIKSVH-KVASQLLQARK--TQEDVNTVCE 86 (174)
Q Consensus 52 ls~LEeW~~~~~lh-iQa~~LLQ~~K--t~~D~~~i~~ 86 (174)
++-||||||..|+. .-+.-++-++- +.+++++..+
T Consensus 3 ~~lL~dWCr~m~~~~~r~lLv~giP~dc~~~ei~e~l~ 40 (331)
T PF14893_consen 3 LALLEDWCRGMGVDPQRALLVLGIPEDCEEAEIEEALQ 40 (331)
T ss_pred hHHHHHHHHhcCcChhhhheeecCCCCCCHHHHHHHHH
Confidence 67899999999983 22222333333 4455555443
No 12
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=35.21 E-value=55 Score=24.36 Aligned_cols=50 Identities=20% Similarity=0.348 Sum_probs=32.7
Q ss_pred chhHHHHHHhhcCc--------------h---HhhhhhhcccC---ChhHHHHHHHHhccCCHHHHHHHHHhcCC
Q psy13278 51 STSQVRDLNRIKSV--------------H---KVASQLLQARK---TQEDVNTVCEMCNKMSTNQIIKLLNLYTP 105 (174)
Q Consensus 51 Nls~LEeW~~~~~l--------------h---iQa~~LLQ~~K---t~~D~~~i~~~C~~L~~~Qi~klL~~Y~P 105 (174)
.-.+||+|++...- | .....+|+-+| |.+|++.+..+... |...+.+=.|
T Consensus 9 t~~EL~~WL~t~~S~~~g~~~~~~es~Gh~sGRrIv~IL~K~k~dltddD~~hMrkVV~y-----v~rhlaq~~p 78 (92)
T PF11338_consen 9 TPAELEDWLRTDESKSVGEKKDGGESVGHESGRRIVEILRKRKTDLTDDDYEHMRKVVGY-----VKRHLAQGEP 78 (92)
T ss_pred CHHHHHHHHcCccccccccCCCCCcccCcchhhHHHHHHhcCcccCCHHHHHHHHHHHHH-----HHHHHhccCC
Confidence 45689999985432 2 77777888777 77888877766432 4444444445
No 13
>COG4973 XerC Site-specific recombinase XerC [DNA replication, recombination, and repair]
Probab=34.35 E-value=35 Score=30.16 Aligned_cols=77 Identities=16% Similarity=0.244 Sum_probs=54.8
Q ss_pred HHHHHHHHHHh---h---hhhHHhhhccccccccccccccchhHHHHHHhhcCc----------hHhhhhhhcccCChhH
Q psy13278 17 KVASQLLQARK---T---QEDVNTVCEMCNKMSTNQVRAVSTSQVRDLNRIKSV----------HKVASQLLQARKTQED 80 (174)
Q Consensus 17 q~fsQLf~~i~---~---fNdl~s~~~lCs~~~G~QIr~~Nls~LEeW~~~~~l----------hiQa~~LLQ~~Kt~~D 80 (174)
+....|=+|.+ . ..+.+....+-.+.+.-+|.+ ++++|.-++|+ |-=|+++|+.-.++.-
T Consensus 186 ~A~~al~~WL~lR~~~a~~d~AlF~s~~G~Ris~R~iQk----R~~~wgikqg~~~HvhPH~LRHSFAtHmLesSgDLRa 261 (299)
T COG4973 186 KAVEALEHWLALRGLFASEDDALFLSRLGKRISARAIQK----RLAQWGIKQGLNSHVHPHKLRHSFATHMLESSGDLRA 261 (299)
T ss_pred HHHHHHHHHHhhhhccCCCCceeeecccCCcccHHHHHH----HHHHHHHhccccccCChHHHHHHHHHHHHHhcccHHH
Confidence 34444555652 2 334455667777888888888 99999999999 3779999997766666
Q ss_pred HHHHHHHhccCCHHHHHH
Q psy13278 81 VNTVCEMCNKMSTNQIIK 98 (174)
Q Consensus 81 ~~~i~~~C~~L~~~Qi~k 98 (174)
++++..- .+|++.||+.
T Consensus 262 VQELLGH-anlsTTQIYT 278 (299)
T COG4973 262 VQELLGH-ANLSTTQIYT 278 (299)
T ss_pred HHHHhcc-cccchhhhhh
Confidence 7777765 6777778753
No 14
>PF07176 DUF1400: Alpha/beta hydrolase of unknown function (DUF1400); InterPro: IPR010802 This domain is specific to cyanobacterial proteins, its function and the function of the proteins it is associated with, are uncharacterised.
Probab=34.06 E-value=1.4e+02 Score=22.87 Aligned_cols=73 Identities=10% Similarity=0.160 Sum_probs=50.0
Q ss_pred ccccccchhHHHHHHhhcCchHhhhhhhcc-cC-ChhHHHHHHHHhccCCHHHHHHHHHhcCCCCCCCCCCCHHHHHHHH
Q psy13278 45 NQVRAVSTSQVRDLNRIKSVHKVASQLLQA-RK-TQEDVNTVCEMCNKMSTNQIIKLLNLYTPADDYEERISQSFIHLIQ 122 (174)
Q Consensus 45 ~QIr~~Nls~LEeW~~~~~lhiQa~~LLQ~-~K-t~~D~~~i~~~C~~L~~~Qi~klL~~Y~P~~~~E~~ip~~~i~~v~ 122 (174)
+++ .|.++.||.|++.-.+.-+.+.+++. .. ..+.+..+...-..+++..+.++| |+ +.-..+++.+.
T Consensus 12 ~~~-si~V~dLe~fa~tG~~~~~L~~~~~ll~~~~~~~lr~~L~~~~~~~~~~~~~lL--~S-------~~G~~lL~~lg 81 (127)
T PF07176_consen 12 FQR-SISVSDLETFAETGEISPELAFYLNLLSPQQRQQLRELLNTPIPIDPVFLSQLL--NS-------PIGERLLDQLG 81 (127)
T ss_pred cee-eeeHHHHHHHHHcCCCCHHHHHHHHhcCHhhHHHHHHHHcCCCCCCHHHHHHHh--CC-------hHHHHHHHHHH
Confidence 344 45899999999986554555556665 23 566666677777889999999998 33 34455666666
Q ss_pred HHHhh
Q psy13278 123 EKLKE 127 (174)
Q Consensus 123 ~~~~~ 127 (174)
+.++.
T Consensus 82 ~vi~~ 86 (127)
T PF07176_consen 82 KVIRT 86 (127)
T ss_pred HHhcC
Confidence 66643
No 15
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=33.73 E-value=83 Score=23.08 Aligned_cols=50 Identities=14% Similarity=0.238 Sum_probs=35.2
Q ss_pred hhHHHHHHhhcCch-HhhhhhhcccC-ChhHHHHHHHHhc-cCCHHHHHHHHH
Q psy13278 52 TSQVRDLNRIKSVH-KVASQLLQARK-TQEDVNTVCEMCN-KMSTNQIIKLLN 101 (174)
Q Consensus 52 ls~LEeW~~~~~lh-iQa~~LLQ~~K-t~~D~~~i~~~C~-~L~~~Qi~klL~ 101 (174)
+..+.+=++..|++ .++++++=++- +.+++..|.+-|. .++..++.+||.
T Consensus 59 ~~~l~~~L~~~~L~~~E~~qi~Nl~P~~~~El~~ii~~~~~r~~ee~l~~iL~ 111 (117)
T PF03874_consen 59 IKELREELKKFGLTEFEILQIINLRPTTAVELRAIIESLESRFSEEDLEEILD 111 (117)
T ss_dssp HHHHHHHHTTSTS-HHHHHHHHHH--SSHHHHHHHSTTGTTTSTHHHHHHHHH
T ss_pred HHHHHHHHhcccCCHHHHHHHhcCCCCCHHHHHHHHHHhccCCCHHHHHHHHH
Confidence 44455555566674 67777776655 8999999998888 588888888875
No 16
>PRK10945 gene expression modulator; Provisional
Probab=33.13 E-value=53 Score=23.46 Aligned_cols=29 Identities=21% Similarity=0.329 Sum_probs=22.9
Q ss_pred hhhcccC--ChhHHHHHHH-HhccCCHHHHHH
Q psy13278 70 QLLQARK--TQEDVNTVCE-MCNKMSTNQIIK 98 (174)
Q Consensus 70 ~LLQ~~K--t~~D~~~i~~-~C~~L~~~Qi~k 98 (174)
.|+|.|| +.+.++.+.+ .+++|+...+..
T Consensus 11 yL~~fRrcss~eTLEkvie~~~~~L~~~E~~~ 42 (72)
T PRK10945 11 YLMRLRRCQTIDTLERVIEKNKYELSDDELAV 42 (72)
T ss_pred HHHHHHhcCcHHHHHHHHHHhhccCCHHHHHH
Confidence 4788999 7888888884 889999865553
No 17
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=32.14 E-value=64 Score=19.05 Aligned_cols=42 Identities=14% Similarity=0.045 Sum_probs=27.1
Q ss_pred HHHHHHHH-hhhhhHHhhhccccccccccccccchhHHHHHHhh
Q psy13278 19 ASQLLQAR-KTQEDVNTVCEMCNKMSTNQVRAVSTSQVRDLNRI 61 (174)
Q Consensus 19 fsQLf~~i-~~fNdl~s~~~lCs~~~G~QIr~~Nls~LEeW~~~ 61 (174)
++.+|..- .++..+.....+-....|-..++ +-+.|++|.++
T Consensus 7 ~a~~lgis~~ti~~~~~~g~i~~~~~g~~~~~-~~~~l~~~~~~ 49 (49)
T TIGR01764 7 AAEYLGVSKDTVYRLIHEGELPAYRVGRHYRI-PREDVDEYLEQ 49 (49)
T ss_pred HHHHHCCCHHHHHHHHHcCCCCeEEeCCeEEE-eHHHHHHHHhC
Confidence 44555532 26666665555555555767666 99999999863
No 18
>PHA02102 hypothetical protein
Probab=31.83 E-value=81 Score=22.22 Aligned_cols=44 Identities=11% Similarity=0.067 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHHhhhhhHHhhhccccccccccccccchhHHHHHHhhc
Q psy13278 14 SVHKVASQLLQARKTQEDVNTVCEMCNKMSTNQVRAVSTSQVRDLNRIK 62 (174)
Q Consensus 14 ~v~q~fsQLf~~i~~fNdl~s~~~lCs~~~G~QIr~~Nls~LEeW~~~~ 62 (174)
-...-+-+|-...+-.+|+.+-.+ .|++|.--|=-++++|..+.
T Consensus 6 eLvekA~eLqkLl~eV~dlAse~~-----yGvein~~nev~f~DWLsSS 49 (72)
T PHA02102 6 ELVEKALELQKLLKEVKDLASEQD-----YGVEINDDNEVRFEDWLSSS 49 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhc-----cceeeCCCCcEeHHHhhccc
Confidence 334445565555567788887776 79999877888999999763
No 19
>PF01017 STAT_alpha: STAT protein, all-alpha domain; InterPro: IPR013800 The STAT protein (Signal Transducers and Activators of Transcription) family contains transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors, hence they act as signal transducers in the cytoplasm and transcription activators in the nucleus []. Binding of these factors to cell-surface receptors leads to receptor autophosphorylation at a tyrosine, the phosphotyrosine being recognised by the STAT SH2 domain, which mediates the recruitment of STAT proteins from the cytosol and their association with the activated receptor. The STAT proteins are then activated by phosphorylation via members of the JAK family of protein kinases, causing them to dimerise and translocated to the nucleus, where they bind to specific promoter sequences in target genes. In mammals, STATs comprise a family of seven structurally and functionally related proteins: Stat1, Stat2, Stat3, Stat4, Stat5a and Stat5b, Stat6. STAT proteins play a critical role in regulating innate and acquired host immune responses. Dysregulation of at least two STAT signalling cascades (i.e. Stat3 and Stat5) is associated with cellular transformation. Signalling through the JAK/STAT pathway is initiated when a cytokine binds to its corresponding receptor. This leads to conformational changes in the cytoplasmic portion of the receptor, initiating activation of receptor associated members of the JAK family of kinases. The JAKs, in turn, mediate phosphorylation at the specific receptor tyrosine residues, which then serve as docking sites for STATs and other signalling molecules. Once recruited to the receptor, STATs also become phosphorylated by JAKs, on a single tyrosine residue. Activated STATs dissociate from the receptor, dimerise, translocate to the nucleus and bind to members of the GAS (gamma activated site) family of enhancers. The seven STAT proteins identified in mammals range in size from 750 and 850 amino acids. The chromosomal distribution of these STATs, as well as the identification of STATs in more primitive eukaryotes, suggest that this family arose from a single primordial gene. STATs share structurally and functionally conserved domains including: an N-terminal domain that strengthens interactions between STAT dimers on adjacent DNA-binding sites; a coiled-coil STAT domain that is implicated in protein-protein interactions; a DNA-binding domain with an immunoglobulin-like fold similar to p53 tumour suppressor protein; an EF-hand-like linker domain connecting the DNA-binding and SH2 domains; an SH2 domain (IPR000980 from INTERPRO) that acts as a phosphorylation-dependent switch to control receptor recognition and DNA-binding; and a C-terminal transactivation domain []. The crystal structure of the N terminus of Stat4 reveals a dimer. The interface of this dimer is formed by a ring-shaped element consisting of five short helices. Several studies suggest that this N-terminal dimerisation promotes cooperativity of binding to tandem GAS elements and with the transcriptional coactivator CBP/p300. This entry represents the all-alpha helical domain, which consists of four long helices arranged in a bundle with a left-handed twist (coiled-coil), which in turn forms a right-handed superhelix.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0004871 signal transducer activity, 0006355 regulation of transcription, DNA-dependent, 0007165 signal transduction, 0005634 nucleus; PDB: 1YVL_A 1BF5_A 3CWG_B 1BG1_A 1Y1U_B.
Probab=27.83 E-value=1.5e+02 Score=23.88 Aligned_cols=17 Identities=12% Similarity=0.075 Sum_probs=9.7
Q ss_pred cccccccchhHHHHHHhh
Q psy13278 44 TNQVRAVSTSQVRDLNRI 61 (174)
Q Consensus 44 G~QIr~~Nls~LEeW~~~ 61 (174)
|....- |+..|+.||..
T Consensus 116 G~P~~~-~LD~LQ~wfe~ 132 (182)
T PF01017_consen 116 GAPFDS-SLDQLQNWFES 132 (182)
T ss_dssp TSS-----THHHHHHHHH
T ss_pred CCCChh-hhHHHHHHHHH
Confidence 444455 78888888887
No 20
>PRK10391 oriC-binding nucleoid-associated protein; Provisional
Probab=27.09 E-value=30 Score=24.61 Aligned_cols=25 Identities=20% Similarity=0.380 Sum_probs=20.5
Q ss_pred hhhhcccC--ChhHHHHHHH-HhccCCH
Q psy13278 69 SQLLQARK--TQEDVNTVCE-MCNKMST 93 (174)
Q Consensus 69 ~~LLQ~~K--t~~D~~~i~~-~C~~L~~ 93 (174)
-.|||.|| +.+.++-+.+ .+++|+.
T Consensus 5 eyLlkfRkcss~eTLEkv~e~~~y~L~~ 32 (71)
T PRK10391 5 DYLLKFRKISSLESLEKLFDHLNYTLTD 32 (71)
T ss_pred HHHHHHHhcCcHHHHHHHHHHhhcccCC
Confidence 35899999 7888888884 8899986
No 21
>PF05361 PP1_inhibitor: PKC-activated protein phosphatase-1 inhibitor; InterPro: IPR008025 Contractility of vascular smooth muscle depends on phosphorylation of myosin light chains, and is modulated by hormonal control of myosin phosphatase activity. Signaling pathways activate kinases such as PKC or Rho-dependent kinases that phosphorylate the myosin phosphatase inhibitor protein called CPI-17. Phosphorylation of CPI-17 at Thr-38 enhances its inhibitory potency 1000-fold, creating a molecular switch for regulating contraction [].; GO: 0042325 regulation of phosphorylation, 0005737 cytoplasm; PDB: 2RLT_A 1J2M_A 1K5O_A 1J2N_A.
Probab=26.70 E-value=1.4e+02 Score=24.05 Aligned_cols=60 Identities=18% Similarity=0.331 Sum_probs=44.9
Q ss_pred HHHHHHhhcCchHhhhhhhcccC--C--hhHHHHHHHHhccCCHHH-HHHHHH-hcCCCCCCCCCCCHHHHHHHHHHHh
Q psy13278 54 QVRDLNRIKSVHKVASQLLQARK--T--QEDVNTVCEMCNKMSTNQ-IIKLLN-LYTPADDYEERISQSFIHLIQEKLK 126 (174)
Q Consensus 54 ~LEeW~~~~~lhiQa~~LLQ~~K--t--~~D~~~i~~~C~~L~~~Q-i~klL~-~Y~P~~~~E~~ip~~~i~~v~~~~~ 126 (174)
.+|+|.-. |.-.|-++.- . .=|++.+.++-+.=--.+ |+.+|+ .+.| ..+||+-+-.+++
T Consensus 50 ~vE~WId~-----qL~eLy~~~e~~~p~EIDIDeLLDl~sdeeR~~~LqelL~~C~~p--------tE~FI~ELL~kLk 115 (144)
T PF05361_consen 50 DVEEWIDE-----QLQELYDCQEDEMPEEIDIDELLDLESDEERRRKLQELLQDCPKP--------TEDFIQELLSKLK 115 (144)
T ss_dssp HHHHHHHH-----HHHHCSSSSSTTS-SSSHHHHHHCTSSTTHHHHHHHHHHTTCSST--------THHHHHHHHHHCT
T ss_pred HHHHHHHH-----HHHHHhcCCCCCCCCcccHHHHhcCCchHHHHHHHHHHHhhcCCC--------HHHHHHHHHHHHH
Confidence 68999999 9999999976 3 247999998877665556 888884 5555 2468887777775
No 22
>smart00335 ANX Annexin repeats.
Probab=26.62 E-value=47 Score=20.78 Aligned_cols=32 Identities=22% Similarity=0.357 Sum_probs=24.7
Q ss_pred HHHHHHHHhccCCHHHHHHHHHhcCCCCCCCCCC
Q psy13278 80 DVNTVCEMCNKMSTNQIIKLLNLYTPADDYEERI 113 (174)
Q Consensus 80 D~~~i~~~C~~L~~~Qi~klL~~Y~P~~~~E~~i 113 (174)
|-+.+.++...-|+.|+.+|...|. .-|...+
T Consensus 3 de~~l~~il~~rs~~~~~~i~~~Y~--~~~~~~L 34 (53)
T smart00335 3 DEKTLIEILASRSNAQLQAIKQAYK--KRYGKDL 34 (53)
T ss_pred CHHHHHHHHHcCCHHHHHHHHHHHH--HHhCccH
Confidence 5567778878889999999999998 4444443
No 23
>cd08336 DED_FADD Death Effector Domain found in Fas-Associated via Death Domain. Death Effector Domain (DED) found in Fas-Associated via Death Domain (FADD). DEDs comprise a subfamily of the Death Domain (DD) superfamily. FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor and its DED recruits the initiator caspases 8 and 10 to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. 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 incl
Probab=26.15 E-value=2.2e+02 Score=20.06 Aligned_cols=75 Identities=11% Similarity=0.208 Sum_probs=50.3
Q ss_pred HHHHHHHH--h-hhhhHHhhhccccccccccccccchhHHHHHHhhcCchHhhhh-hhcccC-ChhHHHHHHHHhccCCH
Q psy13278 19 ASQLLQAR--K-TQEDVNTVCEMCNKMSTNQVRAVSTSQVRDLNRIKSVHKVASQ-LLQARK-TQEDVNTVCEMCNKMST 93 (174)
Q Consensus 19 fsQLf~~i--~-~fNdl~s~~~lCs~~~G~QIr~~Nls~LEeW~~~~~lhiQa~~-LLQ~~K-t~~D~~~i~~~C~~L~~ 93 (174)
|.++++-| . +-.|+.+.+-+|.-.-| -+++|...... +.-. |-...+ +++|.+-+-+.|..+.-
T Consensus 3 fr~lL~~Is~~L~~~dl~~lKFLc~d~i~-------~~~le~~~s~l----~lf~~Le~~~~i~~~nl~~L~~lL~~i~R 71 (82)
T cd08336 3 FLALLLSISNSLSDSELESLKFLCRDKIG-------KRKLEKVQSGL----QLFSALMERNLISPENTAFLRELLQSIKR 71 (82)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHhhhhcC-------hHhhhccCCHH----HHHHHHHHcCCCCcchHHHHHHHHHHcCH
Confidence 56677777 2 67788888888865333 33445433332 2222 222345 88999999999999998
Q ss_pred HHHHHHHHhcC
Q psy13278 94 NQIIKLLNLYT 104 (174)
Q Consensus 94 ~Qi~klL~~Y~ 104 (174)
.++.+.+..|.
T Consensus 72 ~DL~~~i~~y~ 82 (82)
T cd08336 72 DDLIQKLQQFE 82 (82)
T ss_pred HHHHHHHHhcC
Confidence 89999998884
No 24
>PF13808 DDE_Tnp_1_assoc: DDE_Tnp_1-associated
Probab=25.09 E-value=1.1e+02 Score=21.73 Aligned_cols=58 Identities=9% Similarity=0.230 Sum_probs=37.3
Q ss_pred ccccccccccccchhHHHHHHhhcCchHhhhhhhcccC-ChhHHHHHHHHhccCCHHHHHHHHHhc
Q psy13278 39 CNKMSTNQVRAVSTSQVRDLNRIKSVHKVASQLLQARK-TQEDVNTVCEMCNKMSTNQIIKLLNLY 103 (174)
Q Consensus 39 Cs~~~G~QIr~~Nls~LEeW~~~~~lhiQa~~LLQ~~K-t~~D~~~i~~~C~~L~~~Qi~klL~~Y 103 (174)
|....|.. +...+++|++.+. -...+.|.++. .++. +++..+-..|.|.++.+.+..+
T Consensus 30 ~a~l~G~~----~~~~i~~~~~~~~--~~l~~~l~~~~~~PS~-~Ti~rvl~~ld~~~l~~~~~~W 88 (90)
T PF13808_consen 30 CAVLCGAD----SWREIAEWARAHE--EWLRKRLGLPRGVPSH-DTIRRVLSRLDPEALEEAFRSW 88 (90)
T ss_pred HHHHHccc----cHHHHHHHHHHhH--HHHHHhcCCCCCCCcH-HHHHHHHHHCCHHHHHHHHHHH
Confidence 44445555 6779999999853 23444555533 3333 6666666778888888887654
No 25
>COG1535 EntB Isochorismate hydrolase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=24.51 E-value=35 Score=28.88 Aligned_cols=78 Identities=18% Similarity=0.225 Sum_probs=44.8
Q ss_pred cccccchhHHHHHHhhcCch-HhhhhhhcccC-ChhHHHHHHHHhc-cCC--HHHHHHHHHhcCCCCCC----CCCCCHH
Q psy13278 46 QVRAVSTSQVRDLNRIKSVH-KVASQLLQARK-TQEDVNTVCEMCN-KMS--TNQIIKLLNLYTPADDY----EERISQS 116 (174)
Q Consensus 46 QIr~~Nls~LEeW~~~~~lh-iQa~~LLQ~~K-t~~D~~~i~~~C~-~L~--~~Qi~klL~~Y~P~~~~----E~~ip~~ 116 (174)
++.. |+.+|..||+.+|+- +=+|| -.. +++|-.-+.++.- -|+ |.| +++...-.|..+. +-+-+.=
T Consensus 55 ~li~-Ni~~Lr~~~~~~giPVvyTaq---p~~qs~~draLL~d~WGpgl~~~p~~-~~vv~~l~P~~~D~vL~kwrYsAF 129 (218)
T COG1535 55 QLIA-NIAKLRIWCKQAGIPVVYTAQ---PGEQSPEDRALLKDFWGPGLTASPEQ-QKVVDELAPGADDTVLTKWRYSAF 129 (218)
T ss_pred HHHH-HHHHHHHHHHHcCCcEEEEec---CCcCCHHHHHHHHHhcCCCCCCChhh-hhhHHhcCCCCCceEEeeeehhhh
Confidence 5667 999999999999982 22222 222 7888777777642 233 333 5666666663222 2233333
Q ss_pred HHHHHHHHHhhC
Q psy13278 117 FIHLIQEKLKER 128 (174)
Q Consensus 117 ~i~~v~~~~~~r 128 (174)
.-+.+-+++++.
T Consensus 130 ~~s~Llq~lr~~ 141 (218)
T COG1535 130 HRSPLLQMLREK 141 (218)
T ss_pred hcChHHHHHHHc
Confidence 333455555543
No 26
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=24.46 E-value=1.5e+02 Score=23.20 Aligned_cols=73 Identities=12% Similarity=0.162 Sum_probs=53.7
Q ss_pred hhHHHHHHhhcCch----HhhhhhhcccC---ChhHHHHHHHHhccCCHHHHHHHHHhcCCCCCCCC----CC-------
Q psy13278 52 TSQVRDLNRIKSVH----KVASQLLQARK---TQEDVNTVCEMCNKMSTNQIIKLLNLYTPADDYEE----RI------- 113 (174)
Q Consensus 52 ls~LEeW~~~~~lh----iQa~~LLQ~~K---t~~D~~~i~~~C~~L~~~Qi~klL~~Y~P~~~~E~----~i------- 113 (174)
...+++|.+.++-. +++.+.+|-.- +.+.+..|.+. ..+++.++..+++-|.= =..++ .|
T Consensus 7 ~~~~~~i~~~~~~~~~~ll~~L~~vQ~~~g~ip~~~~~~iA~~-l~v~~~~v~~v~tFY~~-f~~~p~gk~~I~VC~g~~ 84 (154)
T PRK07539 7 LAAIEREIAKYPRPRSAVIPALKIVQEQRGWVPDEAIEAVADY-LGMPAIDVEEVATFYSM-IFRQPVGRHVIQVCTSTP 84 (154)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHhCCCCHHHHHHHHHH-hCcCHHHHHHHHHHHhh-hCcCCCCCEEEEEcCCch
Confidence 45788888887752 88888888654 77888888888 67999999999988862 11111 12
Q ss_pred -----CHHHHHHHHHHHh
Q psy13278 114 -----SQSFIHLIQEKLK 126 (174)
Q Consensus 114 -----p~~~i~~v~~~~~ 126 (174)
..++++++.+.+.
T Consensus 85 C~~~Ga~~l~~~l~~~L~ 102 (154)
T PRK07539 85 CWLRGGEAILAALKKKLG 102 (154)
T ss_pred HHHCCHHHHHHHHHHHhC
Confidence 4678888888876
No 27
>KOG0098|consensus
Probab=23.63 E-value=55 Score=27.84 Aligned_cols=88 Identities=19% Similarity=0.197 Sum_probs=52.5
Q ss_pred cchhccchhhhhHHHHHHHHHHHHh--hhhhHHh-hhccccccccccccccchhHHHHHHhhcCch-HhhhhhhcccCCh
Q psy13278 3 TSQVRDLNRIKSVHKVASQLLQARK--TQEDVNT-VCEMCNKMSTNQVRAVSTSQVRDLNRIKSVH-KVASQLLQARKTQ 78 (174)
Q Consensus 3 ~~~~~~~~~~~~v~q~fsQLf~~i~--~fNdl~s-~~~lCs~~~G~QIr~~Nls~LEeW~~~~~lh-iQa~~LLQ~~Kt~ 78 (174)
++.|-|+.+-.|..-+-++|.-.+- ..|=.+. ..|-|....--.+++ ++=|.|||+||+. ++++. ||.
T Consensus 82 alLVydit~r~sF~hL~~wL~D~rq~~~~NmvImLiGNKsDL~~rR~Vs~---EEGeaFA~ehgLifmETSa-----kt~ 153 (216)
T KOG0098|consen 82 ALLVYDITRRESFNHLTSWLEDARQHSNENMVIMLIGNKSDLEARREVSK---EEGEAFAREHGLIFMETSA-----KTA 153 (216)
T ss_pred eEEEEEccchhhHHHHHHHHHHHHHhcCCCcEEEEEcchhhhhccccccH---HHHHHHHHHcCceeehhhh-----hhh
Confidence 5678899999999888888888662 2333222 222233222223333 6789999999983 44433 255
Q ss_pred hHHHHHHHHhccCCHHHHHHHHHh
Q psy13278 79 EDVNTVCEMCNKMSTNQIIKLLNL 102 (174)
Q Consensus 79 ~D~~~i~~~C~~L~~~Qi~klL~~ 102 (174)
+.+++.+.- +..+|.+.++.
T Consensus 154 ~~VEEaF~n----ta~~Iy~~~q~ 173 (216)
T KOG0098|consen 154 ENVEEAFIN----TAKEIYRKIQD 173 (216)
T ss_pred hhHHHHHHH----HHHHHHHHHHh
Confidence 566665532 23566666643
No 28
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=23.55 E-value=1.7e+02 Score=21.94 Aligned_cols=38 Identities=16% Similarity=0.307 Sum_probs=31.6
Q ss_pred HhccCCHHHHHHHHHhcCCCCCCCCCCCHHHHHHHHHHHhhCC
Q psy13278 87 MCNKMSTNQIIKLLNLYTPADDYEERISQSFIHLIQEKLKERP 129 (174)
Q Consensus 87 ~C~~L~~~Qi~klL~~Y~P~~~~E~~ip~~~i~~v~~~~~~r~ 129 (174)
+..-++..+|.+.|..|.. .+||+++...|..-.++-+
T Consensus 51 ~~~G~~~e~i~~~L~~~S~-----~~lP~~v~~~i~~w~~~~g 88 (129)
T PF13625_consen 51 ASAGLTAEEIIEFLERYSK-----NPLPQNVEQSIEDWARRYG 88 (129)
T ss_pred HHcCCCHHHHHHHHHHHcC-----CCCCHHHHHHHHHHHHhcC
Confidence 4456888999999999995 6899999999998887543
No 29
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=23.30 E-value=38 Score=22.85 Aligned_cols=14 Identities=7% Similarity=0.256 Sum_probs=11.3
Q ss_pred chhHHHHHHhhcCc
Q psy13278 51 STSQVRDLNRIKSV 64 (174)
Q Consensus 51 Nls~LEeW~~~~~l 64 (174)
..+.|.+||.++|+
T Consensus 46 ~~~~l~~~lD~~gI 59 (64)
T PF09494_consen 46 DPSKLKEWLDSQGI 59 (64)
T ss_pred CHHHHHHHHHHCCc
Confidence 77888888888775
No 30
>KOG3242|consensus
Probab=22.29 E-value=1.9e+02 Score=24.45 Aligned_cols=49 Identities=10% Similarity=0.195 Sum_probs=30.5
Q ss_pred hhHHHHHHhhcCch-HhhhhhhcccCChhHHHHHHHHhccCCHHHHHHHHHhcCCCCCCCCCC
Q psy13278 52 TSQVRDLNRIKSVH-KVASQLLQARKTQEDVNTVCEMCNKMSTNQIIKLLNLYTPADDYEERI 113 (174)
Q Consensus 52 ls~LEeW~~~~~lh-iQa~~LLQ~~Kt~~D~~~i~~~C~~L~~~Qi~klL~~Y~P~~~~E~~i 113 (174)
+....|||..|+-. ==..+.++..+|+.|++ .++..-+++|.| .++.++
T Consensus 75 ld~MneWc~ehhg~SGLt~kv~~S~~tl~~aE-----------nevl~yikk~ip--~~~~~l 124 (208)
T KOG3242|consen 75 LDKMNEWCIEHHGNSGLTEKVLASKITLADAE-----------NEVLEYIKKHIP--KGKCPL 124 (208)
T ss_pred HHHHHHHHHHhccchhHHHHHHHhhccHHHHH-----------HHHHHHHHHhCC--CCCCCc
Confidence 56788999987542 22334455555777765 356667788887 444444
No 31
>PF01335 DED: Death effector domain; InterPro: IPR001875 The death effector domain (DED) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DED is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. The dimerisation of DED domains is mediated primarily by electrostatic interactions. DED domains can be found in isolation, or in combination with other domains. Domains associated with DED include: caspase catalytic domains (in caspase-8, -10), death domains (in FADD), nuclear localisation sequences (in DEDD), transmembrane domains (in Bap31 and Bar), nucleotide-binding domains (in Dap3), coiled-coil domains (in Hip and Hippi), SAM domains (in Bar), and E2-binding RING domains (in Bar) []. Several DED-containing proteins are involved in the regulation of apoptosis through their interactions with DED-containing caspases (IPR002398 from INTERPRO), such as caspases 8 and 10 in humans, both of which contain tandem pairs of DEDs. There are many DED-containing modulators of apoptosis, which can either enhance or inhibit caspase activation [].; GO: 0005515 protein binding, 0042981 regulation of apoptosis; PDB: 3CL3_A 2F1S_A 2BBZ_C 2BBR_A 1A1Z_A 2GF5_A 1A1W_A 1N3K_A.
Probab=21.50 E-value=2e+02 Score=19.90 Aligned_cols=76 Identities=16% Similarity=0.228 Sum_probs=46.5
Q ss_pred HHHHHHHHh---hhhhHHhhhccccccccccccccchhHHHHHHhhcCchHhhhhhhcccC-ChhHHHHHHHHhccCCHH
Q psy13278 19 ASQLLQARK---TQEDVNTVCEMCNKMSTNQVRAVSTSQVRDLNRIKSVHKVASQLLQARK-TQEDVNTVCEMCNKMSTN 94 (174)
Q Consensus 19 fsQLf~~i~---~fNdl~s~~~lCs~~~G~QIr~~Nls~LEeW~~~~~lhiQa~~LLQ~~K-t~~D~~~i~~~C~~L~~~ 94 (174)
|.+++.-|. +-.|+-..+-+|.-.-|..-.. .++..-+|... |-...+ +++|..-+-+++..++-.
T Consensus 1 yr~lL~~I~~~L~~~e~~~lkfL~~d~i~~~~~~-~~~~~~dlf~~---------Le~~~~i~~~nl~~L~~lL~~i~R~ 70 (84)
T PF01335_consen 1 YRQLLLEISEELTSEELESLKFLCKDHIPRSKLE-EIKSGLDLFEE---------LEKRGLISPDNLSLLKELLKRIGRP 70 (84)
T ss_dssp HHHHHHHHHHHSHHHHHHHHHHHCTTTSTCHCHH-HTSSHHHHHHH---------HHHTTSSSTTBHHHHHHHHHHTT-H
T ss_pred CHHHHHHHHHhcCHHHHHHHHHHHHHHcCchhhh-hhchHHHHHHH---------HHHcCCCCCccHHHHHHHHHHhCHH
Confidence 456666662 6777777777787332222211 12222233322 223345 888999999999999988
Q ss_pred HHHHHHHhcC
Q psy13278 95 QIIKLLNLYT 104 (174)
Q Consensus 95 Qi~klL~~Y~ 104 (174)
.+.+-+..|+
T Consensus 71 DL~~~i~~~~ 80 (84)
T PF01335_consen 71 DLLKKIEEYE 80 (84)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 8988888875
No 32
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.06 E-value=2.9e+02 Score=20.77 Aligned_cols=38 Identities=21% Similarity=0.120 Sum_probs=29.6
Q ss_pred HHHHHHHHhcCCCCC--CCCCCCHHHHHHHHHHHhhCCCC
Q psy13278 94 NQIIKLLNLYTPADD--YEERISQSFIHLIQEKLKERPQS 131 (174)
Q Consensus 94 ~Qi~klL~~Y~P~~~--~E~~ip~~~i~~v~~~~~~r~~~ 131 (174)
.|+.|+|..=+|+.+ .|...|..-|..|++-++..+|+
T Consensus 47 lqVa~mL~eg~tY~~I~~eTGaStaTIsRVkRcl~yGndg 86 (100)
T COG4496 47 LQVAKMLKEGRTYRDIEDETGASTATISRVKRCLNYGNDG 86 (100)
T ss_pred HHHHHHHHcCCCcchhhhccCcchhhHHHHHHHHHcCCcH
Confidence 588888866555554 46799999999999999986663
No 33
>PF02898 NO_synthase: Nitric oxide synthase, oxygenase domain; InterPro: IPR004030 Nitric oxide synthase (1.14.13.39 from EC) (NOS) enzymes produce nitric oxide (NO) by catalysing a five-electron oxidation of a guanidino nitrogen of L-arginine (L-Arg). Oxidation of L-Arg to L-citrulline occurs via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine as an intermediate. 2 mol of O(2) and 1.5 mol of NADPH are consumed per mole of NO formed []. Arginine-derived NO synthesis has been identified in mammals, fish, birds, invertebrates, plants, and bacteria []. Best studied are mammals, where three distinct genes encode NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) and endothelial (eNOS or NOS-3) []. iNOS and nNOS are soluble and found predominantly in the cytosol, while eNOS is membrane associated. The enzymes exist as homodimers, each monomer consisting of two major domains: an N-terminal oxygenase domain, which belongs to the class of haem-thiolate proteins, and a C-terminal reductase domain, which is homologous to NADPH:P450 reductase (1.6.2.4 from EC). The interdomain linker between the oxygenase and reductase domains contains a calmodulin (CaM)-binding sequence. NOSs are the only enzymes known to simultaneously require five bound cofactors animal NOS isozymes are catalytically self-sufficient. The electron flow in the NO synthase reaction is: NADPH --> FAD --> FMN --> haem --> O(2). eNOS localisation to endothelial membranes is mediated by cotranslational N-terminal myristoylation and post-translational palmitoylation []. The subcellular localisation of nNOS in skeletal muscle is mediated by anchoring of nNOS to dystrophin. nNOS contains an additional N-terminal domain, the PDZ domain []. Some bacteria, like Bacillus halodurans, Bacillus subtilis or Deinococcus radiodurans, contain homologs of NOS oxygenase domain. The pattern is directed against the N-terminal haem binding site. This entry represents the oxygenase domain of NOS.; GO: 0004517 nitric-oxide synthase activity, 0006809 nitric oxide biosynthetic process, 0055114 oxidation-reduction process; PDB: 2FBZ_X 2AMO_A 2AN0_A 1M7V_A 2FC1_A 2FC2_B 1M7Z_A 2AN2_A 2ORS_A 1QW5_B ....
Probab=20.03 E-value=82 Score=28.99 Aligned_cols=35 Identities=17% Similarity=0.144 Sum_probs=27.3
Q ss_pred ccchhccchhhhhHHHHHHHHHHHHh-hhhhHHhhh
Q psy13278 2 STSQVRDLNRIKSVHKVASQLLQARK-TQEDVNTVC 36 (174)
Q Consensus 2 ~~~~~~~~~~~~~v~q~fsQLf~~i~-~fNdl~s~~ 36 (174)
++|.|+|.-++++-..+|..|+..++ ++|+-..+.
T Consensus 77 ~~L~V~D~R~~~t~~~~~~al~~Hl~~AtN~G~ir~ 112 (372)
T PF02898_consen 77 SSLQVFDARHVTTAEEMFEALCEHLRYATNGGNIRP 112 (372)
T ss_dssp TG-EEEEETTS-SHHHHHHHHHHHHHHHHGGGS---
T ss_pred ccceeecCCCCCCHHHHHHHHHHHHHHhcCCCccce
Confidence 68999999999999999999999997 888755543
Done!