Query psy4401
Match_columns 147
No_of_seqs 150 out of 606
Neff 4.8
Searched_HMMs 46136
Date Sat Aug 17 00:36:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4401.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4401hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3563|consensus 99.8 5.5E-20 1.2E-24 160.2 4.7 57 1-57 216-275 (454)
2 KOG3562|consensus 99.8 6.2E-20 1.3E-24 151.8 1.5 55 1-55 56-113 (277)
3 KOG2294|consensus 99.7 2.4E-18 5.1E-23 148.6 4.4 52 1-52 175-230 (454)
4 PF00250 Fork_head: Fork head 99.7 6.8E-19 1.5E-23 127.7 0.5 50 1-50 44-96 (96)
5 cd00059 FH Forkhead (FH), also 99.7 3E-18 6.6E-23 120.5 2.8 35 1-35 44-78 (78)
6 smart00339 FH FORKHEAD. FORKHE 99.7 4E-17 8.8E-22 117.1 2.6 39 1-39 44-82 (89)
7 COG5025 Transcription factor o 99.0 1.8E-10 3.9E-15 106.3 2.0 37 1-37 380-416 (610)
8 KOG4385|consensus 98.9 5.7E-11 1.2E-15 107.0 -2.7 113 1-125 411-524 (581)
9 COG5025 Transcription factor o 98.4 3.4E-07 7.4E-12 84.9 4.4 39 1-39 129-167 (610)
10 PF12317 IFT46_B_C: Intraflage 25.9 46 0.001 27.8 1.8 24 14-37 53-76 (214)
11 COG4009 Uncharacterized protei 20.2 56 0.0012 23.7 1.1 22 109-131 32-55 (88)
No 1
>KOG3563|consensus
Probab=99.79 E-value=5.5e-20 Score=160.18 Aligned_cols=57 Identities=49% Similarity=0.759 Sum_probs=53.3
Q ss_pred CccccccccccCCCceEeccCCCCCCCCceeeecCcc---ccccCCccccccCCCcchhh
Q psy4401 1 MRVNSIRHNLSLNKCFVKVPRSKDQPGKGGFWKLDLQ---KLEEGGGRYRNVRRKSSDIQ 57 (147)
Q Consensus 1 ~WkNSIRHNLSLn~~F~Kv~r~~~~~GKg~~W~l~~~---~~~~g~~rrr~~r~~~~~~~ 57 (147)
.|||||||.||+|+||+||+|.++.||||+||+|+|+ +|++|++.||+||.|..+..
T Consensus 216 RWQNSIRHSLSFNDCFVKVaRSPDKPGKGSfWTLHpdsGNMFENGCYLRRQKRFK~ekk~ 275 (454)
T KOG3563|consen 216 RWQNSIRHSLSFNDCFVKVARSPDKPGKGSFWTLHPDSGNMFENGCYLRRQKRFKCEKKE 275 (454)
T ss_pred HHHhhhhhhccccceeeeccCCCCCCCCccceeecCCcCcccccchhehhhhhhhhhhhh
Confidence 3999999999999999999999999999999999999 99999999999998876543
No 2
>KOG3562|consensus
Probab=99.77 E-value=6.2e-20 Score=151.76 Aligned_cols=55 Identities=44% Similarity=0.793 Sum_probs=50.5
Q ss_pred CccccccccccCCCceEeccCCCCCCCCceeeecCcc---ccccCCccccccCCCcch
Q psy4401 1 MRVNSIRHNLSLNKCFVKVPRSKDQPGKGGFWKLDLQ---KLEEGGGRYRNVRRKSSD 55 (147)
Q Consensus 1 ~WkNSIRHNLSLn~~F~Kv~r~~~~~GKg~~W~l~~~---~~~~g~~rrr~~r~~~~~ 55 (147)
.||||+|||||+|+||+||||..+++|||+||+|+|. +|++|.+.|||||.+..+
T Consensus 56 rWQNSLRHNLSFNDCFIKiPRr~drpGKGsyWalHP~a~dMFENGS~LRRrKRFrv~k 113 (277)
T KOG3562|consen 56 RWQNSLRHNLSFNDCFIKIPRRPDRPGKGSYWALHPSAFDMFENGSLLRRRKRFRVLK 113 (277)
T ss_pred HHHHHhhccccccceeeecCCCCCCCCCccceeeccchhhhcccchHHHHhhhhhhcc
Confidence 3999999999999999999999999999999999998 789999999988766544
No 3
>KOG2294|consensus
Probab=99.72 E-value=2.4e-18 Score=148.63 Aligned_cols=52 Identities=54% Similarity=0.934 Sum_probs=45.3
Q ss_pred CccccccccccCCCceEeccCCCCCCCCceeeecCcc----ccccCCccccccCCC
Q psy4401 1 MRVNSIRHNLSLNKCFVKVPRSKDQPGKGGFWKLDLQ----KLEEGGGRYRNVRRK 52 (147)
Q Consensus 1 ~WkNSIRHNLSLn~~F~Kv~r~~~~~GKg~~W~l~~~----~~~~g~~rrr~~r~~ 52 (147)
.||||||||||||+||+||+|..+++|||+||+|+++ +|.+|.++||+++.+
T Consensus 175 gWqNSIRHNLSLn~cF~Kvpr~~~~~gKg~~W~ldP~~~~~~~~~g~~~rr~~~~~ 230 (454)
T KOG2294|consen 175 GWKNSIRHNLSLNKCFVKVPRERGRPGKGNYWTLDPDDENNMFDNGSFRRRRRSKS 230 (454)
T ss_pred cchhhcccccccccCccccCCcccCCCCCCccccCcchhccccccccccccccccc
Confidence 4999999999999999999999998999999999998 566677877766433
No 4
>PF00250 Fork_head: Fork head domain; InterPro: IPR001766 The fork head protein of Drosophila melanogaster, a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors []. Instead, it contains a distinct type of DNA-binding region, containing around 100 amino acids, which has since been identified in a number of transcription factors (including D. melanogaster FD1-5, mammalian HNF-3, human HTLF, Saccharomyces cerevisiae HCM1, etc.). This is referred to as the fork head domain but is also known as a 'winged helix' [, , ]. The fork head domain binds B-DNA as a monomer [], but shows no similarity to previously identified DNA-binding motifs. Although the domain is found in several different transcription factors, a common function is their involvement in early developmental decisions of cell fates during embryogenesis [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2UZK_A 2K86_A 1JXS_A 2C6Y_A 2A3S_A 2D2W_A 2KIU_A 1VTN_C 2A07_J 2AS5_F ....
Probab=99.72 E-value=6.8e-19 Score=127.73 Aligned_cols=50 Identities=56% Similarity=0.971 Sum_probs=43.0
Q ss_pred CccccccccccCCCceEeccCCCCCCCCceeeecCcc---ccccCCccccccC
Q psy4401 1 MRVNSIRHNLSLNKCFVKVPRSKDQPGKGGFWKLDLQ---KLEEGGGRYRNVR 50 (147)
Q Consensus 1 ~WkNSIRHNLSLn~~F~Kv~r~~~~~GKg~~W~l~~~---~~~~g~~rrr~~r 50 (147)
.||||||||||+|+||+||++..+.+|||+||+|+++ .+.++.++++++|
T Consensus 44 ~WknSIRHnLS~~~~F~kv~~~~~~~gkg~~W~i~~~~~~~~~~~~~~~~~~~ 96 (96)
T PF00250_consen 44 GWKNSIRHNLSLNKCFVKVPRDPSEPGKGSYWTIDPEAIEEFEKGRFKRRRKR 96 (96)
T ss_dssp HHHHHHHHHHHHSTTEEEESCCTSSSSSSEEEEE-CTHHHHHHHSCCSSSSSS
T ss_pred hhhhHHhhhccccceeeecCcCCCCCCCceeEEeCHHHHHHHhcchhhhhhcc
Confidence 4999999999999999999998877899999999999 6667777776654
No 5
>cd00059 FH Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
Probab=99.71 E-value=3e-18 Score=120.51 Aligned_cols=35 Identities=74% Similarity=1.278 Sum_probs=33.3
Q ss_pred CccccccccccCCCceEeccCCCCCCCCceeeecC
Q psy4401 1 MRVNSIRHNLSLNKCFVKVPRSKDQPGKGGFWKLD 35 (147)
Q Consensus 1 ~WkNSIRHNLSLn~~F~Kv~r~~~~~GKg~~W~l~ 35 (147)
.||||||||||+|+||+||+|..+.+|||+||+||
T Consensus 44 gWknSIRHnLS~n~~F~kv~r~~~~~gkg~~W~i~ 78 (78)
T cd00059 44 GWQNSIRHNLSLNKCFVKVPREPDEPGKGSYWTLD 78 (78)
T ss_pred CCccceeEecccccceEECCCCCCCCCCCCeeeeC
Confidence 59999999999999999999998778999999986
No 6
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=99.65 E-value=4e-17 Score=117.10 Aligned_cols=39 Identities=64% Similarity=1.079 Sum_probs=36.3
Q ss_pred CccccccccccCCCceEeccCCCCCCCCceeeecCcccc
Q psy4401 1 MRVNSIRHNLSLNKCFVKVPRSKDQPGKGGFWKLDLQKL 39 (147)
Q Consensus 1 ~WkNSIRHNLSLn~~F~Kv~r~~~~~GKg~~W~l~~~~~ 39 (147)
.||||||||||+|+||+||+|..+.+|||+||+|++++.
T Consensus 44 ~WknSIRHnLS~n~~F~kv~~~~~~~gkg~~W~i~~~~~ 82 (89)
T smart00339 44 GWQNSIRHNLSLNDCFVKVPREGDRPGKGSYWTLDPDAE 82 (89)
T ss_pred ccccccccccchhhceeecCcCCCCCCCCCEEEECccHH
Confidence 599999999999999999999888789999999999854
No 7
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=98.97 E-value=1.8e-10 Score=106.30 Aligned_cols=37 Identities=70% Similarity=1.090 Sum_probs=36.1
Q ss_pred CccccccccccCCCceEeccCCCCCCCCceeeecCcc
Q psy4401 1 MRVNSIRHNLSLNKCFVKVPRSKDQPGKGGFWKLDLQ 37 (147)
Q Consensus 1 ~WkNSIRHNLSLn~~F~Kv~r~~~~~GKg~~W~l~~~ 37 (147)
+||||||||||||++|.||||....+|||+||+++.+
T Consensus 380 ~w~nSiRhnlSlNksf~kvP~sa~~pGKg~fw~i~~s 416 (610)
T COG5025 380 AWQNSIRHNLSLNKSFEKVPRSASQPGKGCFWKIDYS 416 (610)
T ss_pred ccCchhhhhhhhccccccCCCCcCCCCCcccCccChh
Confidence 6999999999999999999999999999999999998
No 8
>KOG4385|consensus
Probab=98.93 E-value=5.7e-11 Score=107.04 Aligned_cols=113 Identities=20% Similarity=0.253 Sum_probs=69.1
Q ss_pred CccccccccccCCCceEeccCCCCCCCCceeeecCccccccCCccccccC-CCcchhhhhcccCCCCCCCCCCCCcccCC
Q psy4401 1 MRVNSIRHNLSLNKCFVKVPRSKDQPGKGGFWKLDLQKLEEGGGRYRNVR-RKSSDIQHRKQAHRPKPAPSENLNTAYTN 79 (147)
Q Consensus 1 ~WkNSIRHNLSLn~~F~Kv~r~~~~~GKg~~W~l~~~~~~~g~~rrr~~r-~~~~~~~~~~~~~~~~~~ps~~~~~~~~~ 79 (147)
||||+||||||||+||++|+. -||.-|++|...|. +||-.+ ...-..-.......+++.+..+.-.+..+
T Consensus 411 TWKnAVRHNLSLHKCF~RVEn-----vkgavwtvDe~e~~----krr~~k~~g~~sl~~n~~~~~~~~~~~~a~l~~al~ 481 (581)
T KOG4385|consen 411 TWKNAVRHNLSLHKCFVRVEN-----VKGAVWTVDEREFQ----KRRPQKITGSPSLIGNMATLLGNGGAPNAALQAALA 481 (581)
T ss_pred hHhHHHhhhhHHHHHHHHHHH-----Hhcceeeeehhhhh----hhcCccccCchhhhcccccccCCCcchhHHHHHHhh
Confidence 799999999999999999987 58999999987652 222111 11112222233334444444333444556
Q ss_pred CCCCCCCCCCccchhHHHHHHhhhhhccccccccchhhcccccCCC
Q psy4401 80 NNSIAPGENLNKLEDKLDDTLMESEISMTDDIDEDLILSNILLSGD 125 (147)
Q Consensus 80 ~~s~~p~~~~~~~~~~~~~~~~~~~~s~~~di~~~~~~~~~~~~~s 125 (147)
+++.+.-.+..+..+-...++. ..+.+|+++.+.+..++.+.+
T Consensus 482 ~~~~~lls~a~~~~~~s~~~Le---~~~~~~~~~~~~~~~sp~~~~ 524 (581)
T KOG4385|consen 482 ENSLPLLSEAGMGNNWSVGELE---FAKHEDVNGSMEHNPSPGGHS 524 (581)
T ss_pred cCccccccchhccCCcchhhHH---HHHHhhcccccccCCCCCCCC
Confidence 6777766666666662222221 255677888888777775333
No 9
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=98.37 E-value=3.4e-07 Score=84.88 Aligned_cols=39 Identities=41% Similarity=0.627 Sum_probs=36.1
Q ss_pred CccccccccccCCCceEeccCCCCCCCCceeeecCcccc
Q psy4401 1 MRVNSIRHNLSLNKCFVKVPRSKDQPGKGGFWKLDLQKL 39 (147)
Q Consensus 1 ~WkNSIRHNLSLn~~F~Kv~r~~~~~GKg~~W~l~~~~~ 39 (147)
.|+|||||||++++.|+||.+..+-+|||+||.+.|..+
T Consensus 129 ~~~~sIr~Nls~~~a~~~i~g~~g~~~~g~~~~igP~~~ 167 (610)
T COG5025 129 RWQNSIRHNLSLNDAFIKIEGRNGAKVKGHFWSIGPGHE 167 (610)
T ss_pred hhhhhhhcccccCceEEEEeccCCccccceeeccCCCcc
Confidence 499999999999999999999998889999999999743
No 10
>PF12317 IFT46_B_C: Intraflagellar transport complex B protein 46 C terminal; InterPro: IPR022088 This entry represents proteins is found in eukaryotes. Proteins are typically between 298 and 416 amino acids in length. It is thought to be a flagellar protein of complex B and like all IFT proteins, it is required for transport of IFT particles into the flagella [].
Probab=25.92 E-value=46 Score=27.80 Aligned_cols=24 Identities=38% Similarity=0.635 Sum_probs=20.0
Q ss_pred CceEeccCCCCCCCCceeeecCcc
Q psy4401 14 KCFVKVPRSKDQPGKGGFWKLDLQ 37 (147)
Q Consensus 14 ~~F~Kv~r~~~~~GKg~~W~l~~~ 37 (147)
+.|+||+|..+.+-.-+.+.+|+-
T Consensus 53 DaFiKVpRPD~~~d~LGL~vLDEP 76 (214)
T PF12317_consen 53 DAFIKVPRPDGKPDNLGLTVLDEP 76 (214)
T ss_pred ccceeccCCCCCccccCCEEecCC
Confidence 689999999877767778888865
No 11
>COG4009 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.19 E-value=56 Score=23.68 Aligned_cols=22 Identities=27% Similarity=0.359 Sum_probs=15.3
Q ss_pred cccccchh--hcccccCCCceeeec
Q psy4401 109 DDIDEDLI--LSNILLSGDSYWIHE 131 (147)
Q Consensus 109 ~di~~~~~--~~~~~~~~ss~~~~~ 131 (147)
-|+++||. +-|++ .++|||++=
T Consensus 32 ~~L~dDde~aIfnI~-gT~Sy~V~F 55 (88)
T COG4009 32 VDLNDDDELAIFNIE-GTSSYYVVF 55 (88)
T ss_pred cccCCCCcEEEEEec-CceeEEEEE
Confidence 57777777 34444 689999863
Done!