Query 000530
Match_columns 1440
No_of_seqs 156 out of 324
Neff 3.4
Searched_HMMs 46136
Date Mon Apr 1 18:12:06 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000530.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000530hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00509 TFS2N Domain in the 99.4 1.9E-13 4.1E-18 125.8 4.7 58 171-228 17-74 (75)
2 cd00183 TFIIS_I N-terminal dom 99.4 6.5E-13 1.4E-17 122.1 5.6 58 171-228 19-76 (76)
3 KOG1886 BAH domain proteins [T 99.2 6.8E-12 1.5E-16 146.2 6.0 264 1-272 192-461 (464)
4 TIGR01385 TFSII transcription 99.2 4E-11 8.6E-16 134.9 10.6 63 172-234 20-82 (299)
5 PF08711 Med26: TFIIS helical 99.2 9.6E-12 2.1E-16 106.8 2.5 52 177-228 1-53 (53)
6 KOG1105 Transcription elongati 98.7 1.1E-08 2.4E-13 115.0 6.6 60 171-230 21-81 (296)
7 PLN02976 amine oxidase 97.5 0.0007 1.5E-08 89.4 13.2 105 115-232 1256-1361(1713)
8 KOG1793 Uncharacterized conser 96.6 0.0047 1E-07 72.6 7.4 122 95-227 159-290 (417)
9 KOG2821 RNA polymerase II tran 94.7 0.0096 2.1E-07 71.0 0.3 58 172-231 24-81 (433)
10 PF11467 LEDGF: Lens epitheliu 93.7 0.056 1.2E-06 54.2 3.2 59 170-228 20-80 (106)
11 COG5139 Uncharacterized conser 88.4 1 2.2E-05 52.3 6.6 53 176-228 233-287 (397)
12 KOG1984 Vesicle coat complex C 45.8 6.5E+02 0.014 34.3 16.7 26 1164-1189 21-46 (1007)
13 KOG0260 RNA polymerase II, lar 28.9 5.2E+02 0.011 36.3 12.3 11 434-444 401-411 (1605)
14 PF14726 RTTN_N: Rotatin, an a 27.9 48 0.001 33.5 2.6 52 170-221 45-96 (98)
15 PF06371 Drf_GBD: Diaphanous G 25.9 1.1E+02 0.0024 32.0 5.0 93 120-221 86-183 (187)
16 KOG4464 Signaling protein RIC- 24.6 1.7E+02 0.0036 36.6 6.6 61 123-185 169-229 (532)
No 1
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=99.40 E-value=1.9e-13 Score=125.82 Aligned_cols=58 Identities=45% Similarity=0.652 Sum_probs=56.0
Q ss_pred hHHHHHHHHHHhcCCCCcHHhhhhcCCCcccccccCCCCHHHHHHHHHHHHHHHHHHH
Q 000530 171 VEEFLLILLRALDKLPVNLNALQMCNIGKSVNHLRTHKNVEIQKKARSLVDTWKKRVE 228 (1440)
Q Consensus 171 ~ee~lLeLLraLkkLPVTvelLksT~IGKtVnkLRKH~neEI~kLAk~LVkkWKKlVd 228 (1440)
.++.|+++|++|+.+|||+++|+.|+||+.||+||||.|++|+++|+.||++||++|+
T Consensus 17 ~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~A~~Li~~WK~~v~ 74 (75)
T smart00509 17 EVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred CHHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhc
Confidence 3689999999999999999999999999999999999999999999999999999985
No 2
>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Probab=99.36 E-value=6.5e-13 Score=122.12 Aligned_cols=58 Identities=47% Similarity=0.696 Sum_probs=55.8
Q ss_pred hHHHHHHHHHHhcCCCCcHHhhhhcCCCcccccccCCCCHHHHHHHHHHHHHHHHHHH
Q 000530 171 VEEFLLILLRALDKLPVNLNALQMCNIGKSVNHLRTHKNVEIQKKARSLVDTWKKRVE 228 (1440)
Q Consensus 171 ~ee~lLeLLraLkkLPVTvelLksT~IGKtVnkLRKH~neEI~kLAk~LVkkWKKlVd 228 (1440)
..+.|+++|+.|+.+|||+++|++|+||+.||+||||.+++|+++|+.||++||++|+
T Consensus 19 ~~~~~~~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~i~~~A~~Lv~~Wk~~v~ 76 (76)
T cd00183 19 EVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD 76 (76)
T ss_pred CHHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcC
Confidence 4789999999999999999999999999999999999999999999999999999873
No 3
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=99.23 E-value=6.8e-12 Score=146.22 Aligned_cols=264 Identities=15% Similarity=-0.021 Sum_probs=221.5
Q ss_pred CCcccCCCCCCCCCCCCCCccccCCCCCCCCCCCCCCCccccccccccCcCCCcccccccccccCCCCCCCCccchhhHH
Q 000530 1 MHATVPSGGRSPKPMNGPTSTSQLKPGSDGAQNSASFPSQVKGKKRERGDQSSEPVKRERSSKMEDGNSGHSRTETNLKT 80 (1440)
Q Consensus 1 Mha~vQ~GGrSPk~lngpts~q~lK~gsd~~qn~~Sf~sq~KgkKRer~~q~~~~~kr~r~~k~dd~~~~~~~~~~~lk~ 80 (1440)
||...++..+....++.+.-+|+ |..++ +-+++-+..++++.+...-.++|.++.|+.+.-...+.-..-.-+
T Consensus 192 ~~~~~~p~~~~t~~~~~~~~~~~-~s~~~------~~~r~ss~~~~~~~e~~~~~t~~~~~~k~~g~~~~~v~~~~~~~s 264 (464)
T KOG1886|consen 192 RGTLPDPKKVQTLNAAASKRSQQ-KSEIS------SLSRASSSVDGEILESFDLLTGRSDRDKVLGKLLEVVWQNSCSTS 264 (464)
T ss_pred CCCCCCccccccccccccceecc-ccccc------cccccccccccccccCCCCCCCcccccccccccchhhcccccccc
Confidence 56778888999999888888887 66555 335667889999999999999999999999988777755555778
Q ss_pred HHhhhcccCCccchHHHHHHHHHhcccccccccccchhhHHHHHHHhcChhhHHHHHHHhcChhhHHHHHHHHhhcccCC
Q 000530 81 EIAKITEKGGLVDYDGVEKLVQLMVPERNDKKIDLVCRSLLAGVVAATDKFDCLNWFVQLRGLLVFDEWLQEVHKGKIGD 160 (1440)
Q Consensus 81 ei~~l~~~GGl~~~e~V~klV~LM~~~~~~kki~L~~R~~l~~Vi~~T~~qd~L~rFvql~Gl~vL~eWLqEa~Kgk~Gd 160 (1440)
++..-+++|++..-+.|..++.||++.....++||.++..++.++..+-...||-+|..++|..+..+|.|++|.....+
T Consensus 265 ~~~~~~~~~~~~p~~~v~~~~~le~~s~~s~a~d~~~~~~~~~~l~~~~k~~~~l~~~~ln~~~~~~e~~~~l~~p~~p~ 344 (464)
T KOG1886|consen 265 EAKPAGDQGSLWPNPSVSPCGALEQPSHASLAKDLESYLGLRETLVLLLKGQALLKPEPLNPGETKPEPKQELHPPSFPD 344 (464)
T ss_pred ccCCCcccccCCCCcccchhhhhhhhhhhhHhhhhhhhhhhhhHHHhhhcchhhhccccCCCcccCchhhhhccCCCCCC
Confidence 88888999999999999999999999998889999999888888888888999999999999999999999999999999
Q ss_pred CCCCCCCCCChHHHHHHHHHHhcCCCCcHHhhhhcCCCcccccccCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCc
Q 000530 161 AGSPRDGDKSVEEFLLILLRALDKLPVNLNALQMCNIGKSVNHLRTHKNVEIQKKARSLVDTWKKRVEAEMDARPRLPEV 240 (1440)
Q Consensus 161 ~~sP~~~dks~ee~lLeLLraLkkLPVTvelLksT~IGKtVnkLRKH~neEI~kLAk~LVkkWKKlVd~Ek~~kp~~~e~ 240 (1440)
+..+.+..+-+.+..+.++..|..++..++++...++++.+++|+-|..++|..-+..+|..|+.++...+..++..++-
T Consensus 345 ~~~~~~~~~~~~d~~~~l~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~~~~~~~~~~~~~~~q~ 424 (464)
T KOG1886|consen 345 GQSSPSSMKLNDDDYDGLCVGLELTAGSLYLYCGQEGLICAGHLPCPMLPEVKLSPVAAVHREGLLLAPSSVPKGTPFQH 424 (464)
T ss_pred CccCccccccCchhHHHHHHhhhhhccchhhhcccccceeccccCCCCCCCcCcccccccchhhhcccceeccCCCCccC
Confidence 99988888888899999999999999999999999999999999999999999999999999999999998877665544
Q ss_pred cCCCC------CCCCCcccccccccccccCCCCCCccc
Q 000530 241 PHSGN------RQTGASTEVAIKSLVTQPASSKTGAVK 272 (1440)
Q Consensus 241 s~~gn------~~s~~~~~~~~ks~v~q~s~sk~~svk 272 (1440)
...++ |+++.+.+ +.+.......+.+..++|
T Consensus 425 ~~~~~k~~~~~ret~~~~e-a~~~~~~~~~a~~~~~~k 461 (464)
T KOG1886|consen 425 PPWPEKRLCSPRETGVNGE-AICGVLPLLVAHAGTTCK 461 (464)
T ss_pred CCChhhcccCccccCCchh-cccCCchhhhhccccccc
Confidence 44444 44555444 333333333444444443
No 4
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=99.21 E-value=4e-11 Score=134.89 Aligned_cols=63 Identities=33% Similarity=0.523 Sum_probs=59.4
Q ss_pred HHHHHHHHHHhcCCCCcHHhhhhcCCCcccccccCCCCHHHHHHHHHHHHHHHHHHHHHhhcC
Q 000530 172 EEFLLILLRALDKLPVNLNALQMCNIGKSVNHLRTHKNVEIQKKARSLVDTWKKRVEAEMDAR 234 (1440)
Q Consensus 172 ee~lLeLLraLkkLPVTvelLksT~IGKtVnkLRKH~neEI~kLAk~LVkkWKKlVd~Ek~~k 234 (1440)
++.||++|++|+.++||+++|++|+||+.||+||||.+++|++||+.||++||++|+.++..+
T Consensus 20 ~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~v~~~k~~~ 82 (299)
T TIGR01385 20 VEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDKNKSDH 82 (299)
T ss_pred HHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhhhcccC
Confidence 678999999999999999999999999999999999999999999999999999999875433
No 5
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=99.17 E-value=9.6e-12 Score=106.81 Aligned_cols=52 Identities=44% Similarity=0.802 Sum_probs=47.8
Q ss_pred HHHHHhcCCCCcHHhhhhcCCCcccccccCC-CCHHHHHHHHHHHHHHHHHHH
Q 000530 177 ILLRALDKLPVNLNALQMCNIGKSVNHLRTH-KNVEIQKKARSLVDTWKKRVE 228 (1440)
Q Consensus 177 eLLraLkkLPVTvelLksT~IGKtVnkLRKH-~neEI~kLAk~LVkkWKKlVd 228 (1440)
++|+.|+.+|||+++|++|+||+.|+.|||| .+++|+++|+.||++||++|+
T Consensus 1 ~iL~~L~~l~it~~~L~~T~IGk~V~~l~k~~~~~~i~~~A~~Li~~Wk~~v~ 53 (53)
T PF08711_consen 1 EILKVLEKLPITVELLKSTGIGKAVNKLRKHSENPEIRKLAKELIKKWKRIVD 53 (53)
T ss_dssp HHHHHHHCSS-SHHHHHHHSHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHH-
T ss_pred CHHHHhhcCCCCHHHHHhCChhHHHHHHHcCCCCHHHHHHHHHHHHHHhHhcC
Confidence 5899999999999999999999999999999 999999999999999999985
No 6
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=98.75 E-value=1.1e-08 Score=114.98 Aligned_cols=60 Identities=42% Similarity=0.608 Sum_probs=56.5
Q ss_pred hHHHHHHHHHHhcCCCCcHHhhhhcCCCcccc-cccCCCCHHHHHHHHHHHHHHHHHHHHH
Q 000530 171 VEEFLLILLRALDKLPVNLNALQMCNIGKSVN-HLRTHKNVEIQKKARSLVDTWKKRVEAE 230 (1440)
Q Consensus 171 ~ee~lLeLLraLkkLPVTvelLksT~IGKtVn-kLRKH~neEI~kLAk~LVkkWKKlVd~E 230 (1440)
+.+.+|++|..|+++|||+++|++|+||+.|| .|++|.|++|.++|+.||+.||++|+..
T Consensus 21 n~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~~ 81 (296)
T KOG1105|consen 21 NVEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDKS 81 (296)
T ss_pred cHHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhcc
Confidence 46899999999999999999999999999999 6668999999999999999999999874
No 7
>PLN02976 amine oxidase
Probab=97.50 E-value=0.0007 Score=89.39 Aligned_cols=105 Identities=23% Similarity=0.299 Sum_probs=86.2
Q ss_pred cchhhHHHHHHHhcChhhHHHHHHHhcChhhHHHHHHHHhhcccCCCCCCCCCCCChHHHHHHHHHHhcCCCCcHHhhhh
Q 000530 115 LVCRSLLAGVVAATDKFDCLNWFVQLRGLLVFDEWLQEVHKGKIGDAGSPRDGDKSVEEFLLILLRALDKLPVNLNALQM 194 (1440)
Q Consensus 115 L~~R~~l~~Vi~~T~~qd~L~rFvql~Gl~vL~eWLqEa~Kgk~Gd~~sP~~~dks~ee~lLeLLraLkkLPVTvelLks 194 (1440)
.+||.-|+.-+..--...+...-++..||.+|++||-+.. +|. -..++...|+.|-.++.++.+|+.
T Consensus 1256 ~~gr~~~~~~~~~~~~~~~~~~a~~~~gl~~l~~w~~~~~-~~~------------~~~l~~~~~~ll~~~~~d~~a~r~ 1322 (1713)
T PLN02976 1256 TAGRLHLAKELLNLPVETLKSFAGTKEGLATLNSWILDSM-GKD------------GTQLLRHCVRLLVLVSTDLLAVRL 1322 (1713)
T ss_pred cccHHHHHHHHHhCCHHHHHHHhcccchHHHHHHHHHHHh-ccc------------HHHHHHHHHHHHhhcchhHHHHHh
Confidence 5888666666654454555556678999999999998774 331 246888888888889999999999
Q ss_pred cCCCcccc-cccCCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 000530 195 CNIGKSVN-HLRTHKNVEIQKKARSLVDTWKKRVEAEMD 232 (1440)
Q Consensus 195 T~IGKtVn-kLRKH~neEI~kLAk~LVkkWKKlVd~Ek~ 232 (1440)
..|||+|+ ++.-|.+.+|+.+|++|++.|.+++..++.
T Consensus 1323 sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~~~~~~~~ 1361 (1713)
T PLN02976 1323 SGIGKTVKEKVCVHTSRDIRAIASQLVSVWLEVFRREKA 1361 (1713)
T ss_pred ccchHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHhhh
Confidence 99999996 567899999999999999999999999885
No 8
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.57 E-value=0.0047 Score=72.63 Aligned_cols=122 Identities=25% Similarity=0.385 Sum_probs=86.4
Q ss_pred HHHHHHHHHhcccccccc-cccch-----h-hHHHHHHHhcChhhHHHHHHHhcChhhHHHHHHHHhhcccCCCCCCCCC
Q 000530 95 DGVEKLVQLMVPERNDKK-IDLVC-----R-SLLAGVVAATDKFDCLNWFVQLRGLLVFDEWLQEVHKGKIGDAGSPRDG 167 (1440)
Q Consensus 95 e~V~klV~LM~~~~~~kk-i~L~~-----R-~~l~~Vi~~T~~qd~L~rFvql~Gl~vL~eWLqEa~Kgk~Gd~~sP~~~ 167 (1440)
+.|..|+..|...-+.-. .+.-+ . -+|--|.+--.++.+...||.-+=|..|.+||.=+- |+.-|.-
T Consensus 159 ~~v~~l~~~m~~aa~~D~~~N~e~kPA~~Klk~Lp~v~~vL~k~~L~et~LDngvL~~lk~WLePLP-----D~SLPal- 232 (417)
T KOG1793|consen 159 DEVSRLMERMEDAAEKDRELNREGKPATQKLKLLPLVVAVLSKKALQETFLDNGVLDSLKEWLEPLP-----DGSLPAL- 232 (417)
T ss_pred HHHHHHHHHHHHHHHHHHhhccccCchHHHHhccHHHHHHHhhhhHHHHHHhhhHHHHHHHHhccCC-----CCCCcch-
Confidence 788899999975432210 11111 1 122233333345788889999999999999995332 2222322
Q ss_pred CCChHHHHHHHHHHhcCCCCcH-HhhhhcCCCcccccccCCCC--HHHHHHHHHHHHHHHHHH
Q 000530 168 DKSVEEFLLILLRALDKLPVNL-NALQMCNIGKSVNHLRTHKN--VEIQKKARSLVDTWKKRV 227 (1440)
Q Consensus 168 dks~ee~lLeLLraLkkLPVTv-elLksT~IGKtVnkLRKH~n--eEI~kLAk~LVkkWKKlV 227 (1440)
.-=..||..|..|||-. ++|++..+|+.|=-|.||+. .+++.+|..||.+|-.-|
T Consensus 233 -----~Ir~~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI 290 (417)
T KOG1793|consen 233 -----NIRKSLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPI 290 (417)
T ss_pred -----HHHHHHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccc
Confidence 23356788888999999 99999999999999999965 489999999999997665
No 9
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription]
Probab=94.67 E-value=0.0096 Score=70.99 Aligned_cols=58 Identities=31% Similarity=0.406 Sum_probs=53.1
Q ss_pred HHHHHHHHHHhcCCCCcHHhhhhcCCCcccccccCCCCHHHHHHHHHHHHHHHHHHHHHh
Q 000530 172 EEFLLILLRALDKLPVNLNALQMCNIGKSVNHLRTHKNVEIQKKARSLVDTWKKRVEAEM 231 (1440)
Q Consensus 172 ee~lLeLLraLkkLPVTvelLksT~IGKtVnkLRKH~neEI~kLAk~LVkkWKKlVd~Ek 231 (1440)
...++..|..|-.+|+++++|.+|.+|++|+.||||. .+..+|..|+..||+.|..+-
T Consensus 24 pkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~~v~~d~ 81 (433)
T KOG2821|consen 24 PKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKDLVLVDF 81 (433)
T ss_pred HHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHHhccccc
Confidence 4688999999999999999999999999999999999 689999999999999985443
No 10
>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. ; PDB: 3F9K_K 3HPG_G 3U88_C 3HPH_H 2B4J_D 1Z9E_A.
Probab=93.65 E-value=0.056 Score=54.21 Aligned_cols=59 Identities=27% Similarity=0.225 Sum_probs=47.9
Q ss_pred ChHHHHHHHHHHhcCCCCcHHhhhhc-CCCcccccccCC-CCHHHHHHHHHHHHHHHHHHH
Q 000530 170 SVEEFLLILLRALDKLPVNLNALQMC-NIGKSVNHLRTH-KNVEIQKKARSLVDTWKKRVE 228 (1440)
Q Consensus 170 s~ee~lLeLLraLkkLPVTvelLksT-~IGKtVnkLRKH-~neEI~kLAk~LVkkWKKlVd 228 (1440)
.....||++|..|..|+||..+|+.+ .+=-++++||++ .|..|++.|..|+.+.|.++-
T Consensus 20 ~Dv~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lYnkfK~~f~ 80 (106)
T PF11467_consen 20 PDVKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELYNKFKSLFL 80 (106)
T ss_dssp E-HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHhC
Confidence 44689999999999999999988765 588889999998 588999999999999999995
No 11
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=88.43 E-value=1 Score=52.26 Aligned_cols=53 Identities=25% Similarity=0.501 Sum_probs=45.2
Q ss_pred HHHHHHhcCCCCcHHhhhhcCCCccccccc--CCCCHHHHHHHHHHHHHHHHHHH
Q 000530 176 LILLRALDKLPVNLNALQMCNIGKSVNHLR--THKNVEIQKKARSLVDTWKKRVE 228 (1440)
Q Consensus 176 LeLLraLkkLPVTvelLksT~IGKtVnkLR--KH~neEI~kLAk~LVkkWKKlVd 228 (1440)
-.||..|++|||-.|+|++..||+.|==.. |....+|+.+|+.||..|-.-|.
T Consensus 233 ksL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk~e~~v~r~A~~LV~eWtrpIi 287 (397)
T COG5139 233 KSLLDVLKTLPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTRPII 287 (397)
T ss_pred HHHHHHHhhCCchHHHhhhcCCceEEEEEecCCcccHHHHHHHHHHHHHhhcccc
Confidence 356777888999999999999999997665 45678999999999999987664
No 12
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.78 E-value=6.5e+02 Score=34.31 Aligned_cols=26 Identities=19% Similarity=0.258 Sum_probs=13.5
Q ss_pred CCCCCCCcccccccccCCCCCCCCCC
Q 000530 1164 GGLLNGEVNVRRDFDLNDGPVLDDCS 1189 (1440)
Q Consensus 1164 ~~~Ss~~~~~~RnFDLNdgP~~de~~ 1189 (1440)
+++++.--..+-|--+|--|.+....
T Consensus 21 ~g~~~~~a~~~~~~~~~p~p~~~~~~ 46 (1007)
T KOG1984|consen 21 GGSSNSLAQAMPNGSINPPPPMQGTG 46 (1007)
T ss_pred CCCCchhhhhccCCccCCCCCCCCCC
Confidence 44444444456666677544444444
No 13
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=28.87 E-value=5.2e+02 Score=36.28 Aligned_cols=11 Identities=9% Similarity=0.178 Sum_probs=5.0
Q ss_pred CCCceEEeCCC
Q 000530 434 ANPKIIVKIPN 444 (1440)
Q Consensus 434 ~~~kLIVk~Pn 444 (1440)
++.||-.|+-+
T Consensus 401 ~G~Ridlr~~~ 411 (1605)
T KOG0260|consen 401 NGDRIDLRYHK 411 (1605)
T ss_pred CCcEEEEeecC
Confidence 44444444433
No 14
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=27.92 E-value=48 Score=33.46 Aligned_cols=52 Identities=23% Similarity=0.277 Sum_probs=44.5
Q ss_pred ChHHHHHHHHHHhcCCCCcHHhhhhcCCCcccccccCCCCHHHHHHHHHHHH
Q 000530 170 SVEEFLLILLRALDKLPVNLNALQMCNIGKSVNHLRTHKNVEIQKKARSLVD 221 (1440)
Q Consensus 170 s~ee~lLeLLraLkkLPVTvelLksT~IGKtVnkLRKH~neEI~kLAk~LVk 221 (1440)
+..+.+|++|..|-+.|-...+|+.-..=....+||++-++..+.....|++
T Consensus 45 ~~~~~VL~Ll~~L~~~~~a~~~l~~iG~~~fL~klr~~~~~~~~~~id~il~ 96 (98)
T PF14726_consen 45 PMKEEVLALLLRLLKSPYAAQILRDIGAVRFLSKLRPNVEPNLQAEIDEILD 96 (98)
T ss_pred ccHHHHHHHHHHHHhCcHHHHHHHHccHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence 3468999999999999999999998887777999999988877777777665
No 15
>PF06371 Drf_GBD: Diaphanous GTPase-binding Domain; InterPro: IPR010473 Diaphanous-related formins (Drfs) are a family of formin homology (FH) proteins that act as effectors of Rho small GTPases during growth factor-induced cytoskeletal remodelling, stress fibre formation, and cell division []. Drf proteins are characterised by a variety of shared domains: an N-terminal GTPase-binding domain (GBD), formin-homology domains FH1, FH2 (IPR003104 from INTERPRO) and FH3 (IPR010472 from INTERPRO), and a C-terminal conserved Dia-autoregulatory domain (DAD) that binds the GBD. This entry represents the GBD, which is a bifunctional autoinhibitory domain that interacts with and is regulated by activated Rho family members. Mammalian Drf3 contains a CRIB-like motif within its GBD for binding to Cdc42, which is required for Cdc42 to activate and guide Drf3 towards the cell cortex where it remodels the actin skeleton [].; GO: 0003779 actin binding, 0017048 Rho GTPase binding, 0030036 actin cytoskeleton organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=25.92 E-value=1.1e+02 Score=31.99 Aligned_cols=93 Identities=19% Similarity=0.168 Sum_probs=52.2
Q ss_pred HHHHHHHhcChhhHHHHHHHhcChhhHHHHHHHHhhcccCCCCCCCCCCCChHHHHHHHHHHhc---CCCCcHHhhhhcC
Q 000530 120 LLAGVVAATDKFDCLNWFVQLRGLLVFDEWLQEVHKGKIGDAGSPRDGDKSVEEFLLILLRALD---KLPVNLNALQMCN 196 (1440)
Q Consensus 120 ~l~~Vi~~T~~qd~L~rFvql~Gl~vL~eWLqEa~Kgk~Gd~~sP~~~dks~ee~lLeLLraLk---kLPVTvelLksT~ 196 (1440)
.-+.|...|...+-+..|+..+|+.+|-++|...++..... +. ..+...++|+.|+ +...-++.+-.+.
T Consensus 86 ~~L~v~Lrt~~~~Wv~~Fl~~~G~~~L~~~L~~~~~~~~~~-----~~---~~~~~~~~l~Clkal~n~~~G~~~v~~~~ 157 (187)
T PF06371_consen 86 KSLRVSLRTNPISWVQEFLELGGLEALLNVLSKLNKKKEKS-----EE---DIDIEHECLRCLKALMNTKYGLEAVLSHP 157 (187)
T ss_dssp HHHHHHHHHS-HHHHHHH-HHHHHHHHHHHHHHHHTHHCTC-----TT---CHHHHHHHHHHHHHHTSSHHHHHHHHCSS
T ss_pred HHHHHHhccCCchHHHHhccCCCHHHHHHHHHHhhhhhhhc-----ch---hHHHHHHHHHHHHHHHccHHHHHHHHcCc
Confidence 33556666787888999999999999999998887654222 11 1344444555554 4433334333222
Q ss_pred --CCcccccccCCCCHHHHHHHHHHHH
Q 000530 197 --IGKSVNHLRTHKNVEIQKKARSLVD 221 (1440)
Q Consensus 197 --IGKtVnkLRKH~neEI~kLAk~LVk 221 (1440)
+...+.-|- ..+..++.+|-+|..
T Consensus 158 ~~v~~i~~~L~-s~~~~~r~~~leiL~ 183 (187)
T PF06371_consen 158 DSVNLIALSLD-SPNIKTRKLALEILA 183 (187)
T ss_dssp SHHHHHHHT---TTSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHC-CCCHHHHHHHHHHHH
Confidence 222222222 355677777777653
No 16
>KOG4464 consensus Signaling protein RIC-8/synembryn (regulates neurotransmitter secretion) [Signal transduction mechanisms]
Probab=24.58 E-value=1.7e+02 Score=36.62 Aligned_cols=61 Identities=16% Similarity=0.166 Sum_probs=35.2
Q ss_pred HHHHhcChhhHHHHHHHhcChhhHHHHHHHHhhcccCCCCCCCCCCCChHHHHHHHHHHhcCC
Q 000530 123 GVVAATDKFDCLNWFVQLRGLLVFDEWLQEVHKGKIGDAGSPRDGDKSVEEFLLILLRALDKL 185 (1440)
Q Consensus 123 ~Vi~~T~~qd~L~rFvql~Gl~vL~eWLqEa~Kgk~Gd~~sP~~~dks~ee~lLeLLraLkkL 185 (1440)
..+.+-+-.-....|..+.|+++|+.|| +..++.-.+...|..+- -....+.++|++|-++
T Consensus 169 flltale~~~Rsql~~~l~Gl~~lt~~l-ed~lgidse~n~~~l~p-qe~n~a~EaLK~~FNv 229 (532)
T KOG4464|consen 169 FLLTALETDHRSQLIAELLGLELLTNWL-EDKLGIDSEINVPPLNP-QETNRACEALKVFFNV 229 (532)
T ss_pred HHHHHhhHHHHHHHHHHhcccHHHHHHh-hccccCCCCcCCCCCCH-HHHHHHHHHHHHHhhe
Confidence 3344434333445556699999999999 45555433433444321 1234677788777644
Done!