Query 009145
Match_columns 542
No_of_seqs 93 out of 105
Neff 2.7
Searched_HMMs 46136
Date Thu Mar 28 20:58:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009145.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009145hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0314 Predicted E3 ubiquitin 99.7 1.1E-17 2.3E-22 174.8 10.3 186 1-205 258-445 (448)
2 KOG1902 Putative signal transd 97.1 0.0017 3.6E-08 68.3 8.8 31 365-395 402-432 (441)
3 KOG1902 Putative signal transd 94.2 0.12 2.5E-06 55.0 7.0 63 157-226 267-347 (441)
4 KOG4849 mRNA cleavage factor I 92.8 0.43 9.4E-06 51.1 8.2 28 364-395 463-490 (498)
5 COG5180 PBP1 Protein interacti 92.6 0.26 5.7E-06 54.2 6.6 8 178-185 517-524 (654)
6 TIGR01642 U2AF_lg U2 snRNP aux 91.5 0.092 2E-06 54.4 1.6 10 514-523 255-264 (509)
7 KOG1049 Polyadenylation factor 89.0 3.3 7.1E-05 46.2 10.8 31 192-222 276-309 (538)
8 PF04564 U-box: U-box domain; 87.2 0.45 9.8E-06 38.8 2.3 28 3-31 44-71 (73)
9 KOG2888 Putative RNA binding p 86.6 0.37 8E-06 51.3 1.9 24 365-388 330-353 (453)
10 KOG1924 RhoA GTPase effector D 86.3 5.4 0.00012 46.8 10.7 29 155-183 503-531 (1102)
11 COG5180 PBP1 Protein interacti 85.5 1.8 3.8E-05 48.1 6.3 16 7-22 211-227 (654)
12 KOG2375 Protein interacting wi 85.2 2.2 4.8E-05 49.2 7.1 15 392-406 708-722 (756)
13 KOG0132 RNA polymerase II C-te 78.4 33 0.00071 40.5 13.0 8 42-49 464-471 (894)
14 KOG0117 Heterogeneous nuclear 73.1 14 0.0003 41.0 8.1 8 199-206 380-387 (506)
15 PF06495 Transformer: Fruit fl 69.7 8.4 0.00018 38.0 5.0 13 166-178 119-131 (182)
16 KOG1984 Vesicle coat complex C 59.6 22 0.00047 42.3 6.7 20 200-219 16-36 (1007)
17 KOG0132 RNA polymerase II C-te 56.9 31 0.00066 40.7 7.2 18 15-32 514-531 (894)
18 smart00504 Ubox Modified RING 52.0 9.6 0.00021 29.0 1.7 20 8-27 44-63 (63)
19 KOG3875 Peroxisomal biogenesis 47.3 47 0.001 35.8 6.2 6 193-198 54-59 (362)
20 KOG2375 Protein interacting wi 40.5 61 0.0013 38.0 6.3 6 190-195 576-581 (756)
21 KOG2236 Uncharacterized conser 40.5 1.8E+02 0.0039 32.8 9.5 122 137-260 323-481 (483)
22 KOG3088 Secretory carrier memb 38.5 96 0.0021 33.1 6.9 9 289-297 84-92 (313)
23 KOG3875 Peroxisomal biogenesis 37.5 38 0.00082 36.4 3.8 30 183-213 54-84 (362)
24 KOG0835 Cyclin L [General func 36.8 27 0.00059 37.6 2.7 11 109-119 85-95 (367)
25 KOG3263 Nucleic acid binding p 36.8 16 0.00036 36.2 1.0 11 289-299 25-35 (196)
26 KOG1984 Vesicle coat complex C 35.4 1.2E+02 0.0027 36.5 7.7 14 173-186 118-131 (1007)
27 KOG0147 Transcriptional coacti 35.3 21 0.00045 40.3 1.6 32 364-395 88-119 (549)
28 PF15336 Auts2: Autism suscept 34.2 1.1E+02 0.0025 31.0 6.4 7 250-256 152-158 (212)
29 TIGR01622 SF-CC1 splicing fact 30.1 36 0.00079 35.2 2.3 12 433-444 131-142 (457)
30 KOG3263 Nucleic acid binding p 29.9 39 0.00084 33.7 2.3 30 365-395 14-44 (196)
31 KOG0796 Spliceosome subunit [R 27.6 12 0.00026 39.7 -1.6 17 134-151 146-162 (319)
32 KOG1847 mRNA splicing factor [ 26.8 25 0.00054 40.8 0.5 19 278-296 718-736 (878)
33 KOG0199 ACK and related non-re 26.7 1.2E+02 0.0027 36.2 5.8 20 186-205 922-941 (1039)
34 KOG0796 Spliceosome subunit [R 26.7 69 0.0015 34.2 3.6 11 20-30 5-15 (319)
35 TIGR01628 PABP-1234 polyadenyl 25.2 3E+02 0.0064 29.8 8.1 8 22-29 193-200 (562)
36 KOG1049 Polyadenylation factor 25.2 9.8E+02 0.021 27.6 12.1 13 387-399 484-496 (538)
37 KOG4368 Predicted RNA binding 24.2 2.3E+02 0.0051 33.0 7.3 20 166-185 320-340 (757)
38 KOG2295 C2H2 Zn-finger protein 22.7 1.4E+02 0.003 34.5 5.1 11 175-185 550-564 (648)
39 KOG0151 Predicted splicing reg 22.4 43 0.00093 39.3 1.3 16 14-29 556-571 (877)
40 KOG4594 Sequence-specific sing 22.1 2.3E+02 0.0049 30.6 6.3 67 178-262 113-206 (354)
41 KOG2888 Putative RNA binding p 21.8 31 0.00067 37.5 0.1 15 424-438 401-415 (453)
42 KOG2416 Acinus (induces apopto 20.5 14 0.00031 42.3 -2.8 16 364-379 696-711 (718)
No 1
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.73 E-value=1.1e-17 Score=174.79 Aligned_cols=186 Identities=45% Similarity=0.632 Sum_probs=162.1
Q ss_pred CcccCCcccccccCCCChhHHHHHHHHHhhcCCCCccCCCccceeccccccCCCCCCCCCCCCcccccccccc-CCCCCC
Q 009145 1 MCVCGATNILADDLLPNKTLRNTINRILESGNNSSAENAGSTFQVQDMESARCPPPPKVPSPTMSAASKGEQK-LSAGDK 79 (542)
Q Consensus 1 kCvCga~~VLaDDL~PN~tLR~TI~~~L~~~~~sS~en~Gs~~~~~dm~S~~~~~~pk~~Spt~SaAsk~E~K-~s~~~~ 79 (542)
+|+|++..+|+|+|.|+++||++|+.+|+.+ |++.+|+++.++.+++++..| +.+|..+++++++|.++.+ ....++
T Consensus 258 ~~~c~~~~~~~~~~~~p~~~r~~~n~~~a~~-n~~~~~~~~~~~~~~~~~~~~-p~~k~v~~~~~~~s~~~~~~~~~~~~ 335 (448)
T KOG0314|consen 258 MCVCGASNVLADDLLPPKTLRDTINRILASG-NSSGENSGSSQRTQDPESLRC-PPPKALSPTTSVASPGEKKPLPSNNN 335 (448)
T ss_pred CCcchhhcccccccCCchhhHHHHHHHHhhh-cccccCcccccccCCCccccC-CcccccCCcccccCCCCcccCCcCCC
Confidence 5999999999999999999999999999999 999999999999999999999 8899999999999998877 777777
Q ss_pred CCCccccccccccccccccccccccCCcccccchhhhhcccccccccCCCCCCccc-hHHHHhhhccchHHHHhhhhccC
Q 009145 80 ETPIAMETTDVGKAVITATQSVEKVPPAAKVVDVSEATLESASVKEPASQGSAPMV-DEEVQQKMASGEAAKKKKKKKVR 158 (542)
Q Consensus 80 esp~lq~~te~~k~~sa~~~s~ek~~k~~k~~DvsE~T~es~~vKE~~~~g~a~~v-~ee~qqk~a~~e~~KKKKKKk~r 158 (542)
.+......-+..++......+.+- .+.+.++.+..+..+.++|+.++.-.++++ .++++|++..++..+-..|++
T Consensus 336 ~~s~d~~~p~~~~~~~~~~~~~~g--~~~~~~~~sa~~~~~~~~~~~~~~~~~t~~P~~~~~~~~~~~~~~~~~~~~~-- 411 (448)
T KOG0314|consen 336 PTSTDPQFPEGAEITSGYDVSPPG--FVPKPVDASAPWQGSSAVKEASVSILNTQAPKEEMPQQVAAGEPLKEEEKKP-- 411 (448)
T ss_pred ccccCCCCCCCCCCCCCCCCCCCC--CCCCccccccccccccccCCCCCCcCCCCCCccccccccccCCCccccccCc--
Confidence 777766666666665555444432 566889999999999999999999888888 799999999988866666553
Q ss_pred CCCCccCCCCCCCccccCCCCCCCCCCCCCCCCCCCCccCcccCccC
Q 009145 159 APANDLQWKTPQDLAAESCMMPLGPSAYNPPAAYNPYWTGIQPGMEG 205 (542)
Q Consensus 159 ~p~nd~qwk~~~d~a~~~YmMP~gP~~~~~~~g~NPyw~G~~Pgm~G 205 (542)
|+|++.|||.++|+. ..|+|..||++|++++++|
T Consensus 412 ------------~~a~~~~~~~~~~~~-~~~~~~~p~~~~~~~~~~~ 445 (448)
T KOG0314|consen 412 ------------DLAGPDYMMKMGPGP-QYFNGKQPGFNGVQSGFNG 445 (448)
T ss_pred ------------ccccchhhcccCCcc-ccCCCCCCCCCccccCCCC
Confidence 899999999999999 8899999999999988775
No 2
>KOG1902 consensus Putative signal transduction protein involved in RNA splicing [Signal transduction mechanisms; RNA processing and modification]
Probab=97.15 E-value=0.0017 Score=68.34 Aligned_cols=31 Identities=58% Similarity=0.860 Sum_probs=17.5
Q ss_pred CCccchhhhhHHHHHHHHHHHHHhhhhhccc
Q 009145 365 RDRDYDYEYDREREREREREREKERERDRNH 395 (542)
Q Consensus 365 ~dr~~d~~~~r~r~~~~~~~~~~~~~~~r~~ 395 (542)
+|++.|..++++|+|.+++|+|.++.-+|..
T Consensus 402 ~~~~~~~~~~~~~~r~~~~e~e~e~~~~r~~ 432 (441)
T KOG1902|consen 402 RDRPRDNRRDRERDRGRDRERERERLCDRDR 432 (441)
T ss_pred cccchhhhhhhhhhcccchhhhhhhhccccc
Confidence 3566666666666665555555555544443
No 3
>KOG1902 consensus Putative signal transduction protein involved in RNA splicing [Signal transduction mechanisms; RNA processing and modification]
Probab=94.24 E-value=0.12 Score=55.00 Aligned_cols=63 Identities=22% Similarity=0.276 Sum_probs=32.2
Q ss_pred cCCCCCccCCCCCCCccccC--------CCCC-CCCCCCCCCCCCCCCccC-----cccCccCCCCCCCCCC----CCCC
Q 009145 157 VRAPANDLQWKTPQDLAAES--------CMMP-LGPSAYNPPAAYNPYWTG-----IQPGMEGYMGPFAGAM----PYMP 218 (542)
Q Consensus 157 ~r~p~nd~qwk~~~d~a~~~--------YmMP-~gP~~~~~~~g~NPyw~G-----~~Pgm~GymGPf~gpM----P~mG 218 (542)
-+.|+--.+|-.+.++.-+- |-.+ |+|+. ||+|--| +.|+++| |+|++|+| ||--
T Consensus 267 G~~p~~~h~~Pg~~~~~r~q~~~~rf~g~~L~v~~Pg~------~~~y~~~f~nm~p~p~~~g-~~p~pgm~~p~~p~~q 339 (441)
T KOG1902|consen 267 GDYPPEFHQRPGYLKDPRYQEVDRRFSGVRLDVFLPGS------YNDYVREFHNMGPPPPWQG-MPPYPGMEQPPHPYYQ 339 (441)
T ss_pred CCCCcccccCCCcCCCccccccccccCceecccccCcc------cccccchhhhcCCCccccC-cCCcCCcccCCCCccc
Confidence 34455556777666655542 2233 55655 4444322 3455555 56666665 3444
Q ss_pred CCCCCCCC
Q 009145 219 YGMGPLDM 226 (542)
Q Consensus 219 YgmgP~gM 226 (542)
|..+|++|
T Consensus 340 ~~~~~~~~ 347 (441)
T KOG1902|consen 340 HHAPPPQA 347 (441)
T ss_pred cCCCCccc
Confidence 44444443
No 4
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=92.76 E-value=0.43 Score=51.13 Aligned_cols=28 Identities=50% Similarity=0.669 Sum_probs=18.5
Q ss_pred CCCccchhhhhHHHHHHHHHHHHHhhhhhccc
Q 009145 364 DRDRDYDYEYDREREREREREREKERERDRNH 395 (542)
Q Consensus 364 d~dr~~d~~~~r~r~~~~~~~~~~~~~~~r~~ 395 (542)
-.||-.||- ++|-+|+|||+|++++|++
T Consensus 463 ~~drhddY~----~er~re~erhrDrdrdr~~ 490 (498)
T KOG4849|consen 463 FNDRHDDYI----IERFREQERHRDRDRDRLA 490 (498)
T ss_pred hhhhHHHHH----HHHHHhhhhhhhhhhhhhh
Confidence 355555543 4455577888888888876
No 5
>COG5180 PBP1 Protein interacting with poly(A)-binding protein [RNA processing and modification]
Probab=92.62 E-value=0.26 Score=54.22 Aligned_cols=8 Identities=25% Similarity=0.235 Sum_probs=4.5
Q ss_pred CCCCCCCC
Q 009145 178 MMPLGPSA 185 (542)
Q Consensus 178 mMP~gP~~ 185 (542)
.|+|||..
T Consensus 517 ~~~M~~~m 524 (654)
T COG5180 517 GMNMGGMM 524 (654)
T ss_pred cCCcccee
Confidence 45666555
No 6
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=91.51 E-value=0.092 Score=54.37 Aligned_cols=10 Identities=50% Similarity=1.125 Sum_probs=5.8
Q ss_pred cCCCCCCCCC
Q 009145 514 RKPSRYEPSP 523 (542)
Q Consensus 514 Rkpsrye~sp 523 (542)
++|..|.++|
T Consensus 255 ~r~~~~~~~~ 264 (509)
T TIGR01642 255 RRPHDYIPVP 264 (509)
T ss_pred cCccccCCcc
Confidence 3566676554
No 7
>KOG1049 consensus Polyadenylation factor I complex, subunit FIP1 [RNA processing and modification]
Probab=89.04 E-value=3.3 Score=46.20 Aligned_cols=31 Identities=23% Similarity=0.230 Sum_probs=17.7
Q ss_pred CCCCccCcccCccCCCCCC---CCCCCCCCCCCC
Q 009145 192 YNPYWTGIQPGMEGYMGPF---AGAMPYMPYGMG 222 (542)
Q Consensus 192 ~NPyw~G~~Pgm~GymGPf---~gpMP~mGYgmg 222 (542)
++|.-+++.|++.++.++- ..+||+|-.+..
T Consensus 276 ~~~~~~~~~~~~r~g~~~~~~~~~~~p~~~a~p~ 309 (538)
T KOG1049|consen 276 AEPSSNSQAPGARSGSGEPSGMSEPPPSMEAGPS 309 (538)
T ss_pred cCCCCCccCccccCCCCCCCCCCCCCCCcCCCCC
Confidence 4566667777777765532 334455555433
No 8
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=87.22 E-value=0.45 Score=38.78 Aligned_cols=28 Identities=21% Similarity=0.426 Sum_probs=22.0
Q ss_pred ccCCcccccccCCCChhHHHHHHHHHhhc
Q 009145 3 VCGATNILADDLLPNKTLRNTINRILESG 31 (542)
Q Consensus 3 vCga~~VLaDDL~PN~tLR~TI~~~L~~~ 31 (542)
+|+. .+..+||+||..||..|.+|+++.
T Consensus 44 ~t~~-~l~~~~l~pn~~Lk~~I~~~~~~~ 71 (73)
T PF04564_consen 44 FTRQ-PLSESDLIPNRALKSAIEEWCAEN 71 (73)
T ss_dssp TT-S-B-SGGGSEE-HHHHHHHHHHHHHC
T ss_pred CCCC-cCCcccceECHHHHHHHHHHHHHc
Confidence 4544 788899999999999999999876
No 9
>KOG2888 consensus Putative RNA binding protein [General function prediction only]
Probab=86.61 E-value=0.37 Score=51.29 Aligned_cols=24 Identities=54% Similarity=1.006 Sum_probs=10.1
Q ss_pred CCccchhhhhHHHHHHHHHHHHHh
Q 009145 365 RDRDYDYEYDREREREREREREKE 388 (542)
Q Consensus 365 ~dr~~d~~~~r~r~~~~~~~~~~~ 388 (542)
+++|||+++-++|.+++||+|++|
T Consensus 330 r~~Dy~~erg~~r~~erER~rerd 353 (453)
T KOG2888|consen 330 REKDYERERGRDRYRERERDRERD 353 (453)
T ss_pred ccccCCcccCcchhhhhhhhhhcc
Confidence 334555444344433444444333
No 10
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=86.34 E-value=5.4 Score=46.79 Aligned_cols=29 Identities=21% Similarity=0.189 Sum_probs=13.0
Q ss_pred hccCCCCCccCCCCCCCccccCCCCCCCC
Q 009145 155 KKVRAPANDLQWKTPQDLAAESCMMPLGP 183 (542)
Q Consensus 155 Kk~r~p~nd~qwk~~~d~a~~~YmMP~gP 183 (542)
|=..++++-++....--+-.-..++|+-|
T Consensus 503 Ki~~l~ae~~al~s~~~~~~~~~~iP~PP 531 (1102)
T KOG1924|consen 503 KIKLLEAEKQALSSPSQLLPIDGGIPPPP 531 (1102)
T ss_pred hcccCchhhhhccCcccCCCCCCCCCCCC
Confidence 43455555555543333332334555433
No 11
>COG5180 PBP1 Protein interacting with poly(A)-binding protein [RNA processing and modification]
Probab=85.51 E-value=1.8 Score=48.07 Aligned_cols=16 Identities=25% Similarity=0.295 Sum_probs=10.0
Q ss_pred cccccccC-CCChhHHH
Q 009145 7 TNILADDL-LPNKTLRN 22 (542)
Q Consensus 7 ~~VLaDDL-~PN~tLR~ 22 (542)
-+|.+||- +=++.|-.
T Consensus 211 RGl~~DDSGldeEDlYS 227 (654)
T COG5180 211 RGLGNDDSGLDEEDLYS 227 (654)
T ss_pred cCccccccCcchhhhhh
Confidence 36677777 66666643
No 12
>KOG2375 consensus Protein interacting with poly(A)-binding protein [RNA processing and modification]
Probab=85.23 E-value=2.2 Score=49.16 Aligned_cols=15 Identities=27% Similarity=0.273 Sum_probs=7.7
Q ss_pred hcccCCCCcCcCCCC
Q 009145 392 DRNHHHRTESSSKHS 406 (542)
Q Consensus 392 ~r~~~~rs~~~~~~~ 406 (542)
-.+|+|-+..++.+-
T Consensus 708 ~~~~~~~s~~ss~~~ 722 (756)
T KOG2375|consen 708 SFSHSNASTSSSLKA 722 (756)
T ss_pred cccccccCccccccc
Confidence 345555555555443
No 13
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=78.44 E-value=33 Score=40.47 Aligned_cols=8 Identities=38% Similarity=0.389 Sum_probs=4.0
Q ss_pred cceecccc
Q 009145 42 TFQVQDME 49 (542)
Q Consensus 42 ~~~~~dm~ 49 (542)
+++++|.+
T Consensus 464 M~~RqdA~ 471 (894)
T KOG0132|consen 464 MVRRQDAE 471 (894)
T ss_pred EeehhHHH
Confidence 45555444
No 14
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=73.11 E-value=14 Score=41.00 Aligned_cols=8 Identities=63% Similarity=0.891 Sum_probs=6.0
Q ss_pred cccCccCC
Q 009145 199 IQPGMEGY 206 (542)
Q Consensus 199 ~~Pgm~Gy 206 (542)
++|+|+|+
T Consensus 380 ~~P~~y~~ 387 (506)
T KOG0117|consen 380 SQPGMYGT 387 (506)
T ss_pred cCCccccC
Confidence 68888875
No 15
>PF06495 Transformer: Fruit fly transformer protein; InterPro: IPR010519 This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster [].; GO: 0006397 mRNA processing, 0046660 female sex differentiation, 0005634 nucleus
Probab=69.74 E-value=8.4 Score=37.98 Aligned_cols=13 Identities=8% Similarity=-0.194 Sum_probs=6.0
Q ss_pred CCCCCCccccCCC
Q 009145 166 WKTPQDLAAESCM 178 (542)
Q Consensus 166 wk~~~d~a~~~Ym 178 (542)
|-+....-.+.|.
T Consensus 119 v~VPp~gf~~~y~ 131 (182)
T PF06495_consen 119 VDVPPPGFEYAYG 131 (182)
T ss_pred ccCCCcccccccC
Confidence 5554433344444
No 16
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=59.63 E-value=22 Score=42.31 Aligned_cols=20 Identities=30% Similarity=0.390 Sum_probs=9.1
Q ss_pred ccCccC-CCCCCCCCCCCCCC
Q 009145 200 QPGMEG-YMGPFAGAMPYMPY 219 (542)
Q Consensus 200 ~Pgm~G-ymGPf~gpMP~mGY 219 (542)
.|++|| +.++.+..|++|.+
T Consensus 16 ~~~~~~g~~~~~a~~~~~~~~ 36 (1007)
T KOG1984|consen 16 PPNFYGGSSNSLAQAMPNGSI 36 (1007)
T ss_pred CCCcCCCCCchhhhhccCCcc
Confidence 444444 44444445544444
No 17
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=56.87 E-value=31 Score=40.68 Aligned_cols=18 Identities=17% Similarity=0.302 Sum_probs=9.7
Q ss_pred CCChhHHHHHHHHHhhcC
Q 009145 15 LPNKTLRNTINRILESGN 32 (542)
Q Consensus 15 ~PN~tLR~TI~~~L~~~~ 32 (542)
||-.-|......|++..+
T Consensus 514 IP~~kLt~dl~~~~egam 531 (894)
T KOG0132|consen 514 IPWEKLTDDLEAWCEGAM 531 (894)
T ss_pred eehHhcCHHHHHhhhhce
Confidence 444445455556666653
No 18
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=52.03 E-value=9.6 Score=29.04 Aligned_cols=20 Identities=30% Similarity=0.591 Sum_probs=17.4
Q ss_pred ccccccCCCChhHHHHHHHH
Q 009145 8 NILADDLLPNKTLRNTINRI 27 (542)
Q Consensus 8 ~VLaDDL~PN~tLR~TI~~~ 27 (542)
.+..+||+||..|+..|.++
T Consensus 44 ~~~~~~l~~~~~l~~~i~~~ 63 (63)
T smart00504 44 PLTHEDLIPNLALKSAIQEW 63 (63)
T ss_pred CCChhhceeCHHHHHHHHhC
Confidence 67789999999999999853
No 19
>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]
Probab=47.32 E-value=47 Score=35.75 Aligned_cols=6 Identities=50% Similarity=0.661 Sum_probs=2.3
Q ss_pred CCCccC
Q 009145 193 NPYWTG 198 (542)
Q Consensus 193 NPyw~G 198 (542)
+||-+|
T Consensus 54 ~s~~~g 59 (362)
T KOG3875|consen 54 ISYVTG 59 (362)
T ss_pred CccccC
Confidence 344333
No 20
>KOG2375 consensus Protein interacting with poly(A)-binding protein [RNA processing and modification]
Probab=40.53 E-value=61 Score=38.02 Aligned_cols=6 Identities=50% Similarity=1.016 Sum_probs=4.1
Q ss_pred CCCCCC
Q 009145 190 AAYNPY 195 (542)
Q Consensus 190 ~g~NPy 195 (542)
+|||||
T Consensus 576 ~~~~P~ 581 (756)
T KOG2375|consen 576 PGYNPQ 581 (756)
T ss_pred CCCCcc
Confidence 567776
No 21
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.50 E-value=1.8e+02 Score=32.79 Aligned_cols=122 Identities=14% Similarity=0.061 Sum_probs=0.0
Q ss_pred HHHHhhhccchHHHHhhhhccCCCCC-------ccC--CCCCCCccc-------------------cCCCCCCCCCCCCC
Q 009145 137 EEVQQKMASGEAAKKKKKKKVRAPAN-------DLQ--WKTPQDLAA-------------------ESCMMPLGPSAYNP 188 (542)
Q Consensus 137 ee~qqk~a~~e~~KKKKKKk~r~p~n-------d~q--wk~~~d~a~-------------------~~YmMP~gP~~~~~ 188 (542)
+......+.-.+.++|+++|.+...| ..+ ||...-++. -.+--|=-+..|+.
T Consensus 323 DDEkEaeak~~kKQrk~r~~~k~~~nd~~~~~~~~~~ean~~Ssn~p~~~~y~~r~~~~gf~rp~s~~~q~pP~~~q~~~ 402 (483)
T KOG2236|consen 323 DDEKEAEAKQMKKQRKRRSKVKFSDNDPVKVKTEVEGEANRTSSNQPAPQMYRGRDQNRGFKRPRSNHGQKPPQSAQNSF 402 (483)
T ss_pred hHHHHHHHHHHHHHhhcccccccccCCCCccccccccccccccccCCcccccCCcccccCCCCcccccCCCCCccccccc
Q ss_pred CCCC--CCCccCcccCccCCCCCCCCCC---CCCCCCCCCCC--CcCCCCCCCCcccccCCCCCCCCC-CCChhhhc-CC
Q 009145 189 PAAY--NPYWTGIQPGMEGYMGPFAGAM---PYMPYGMGPLD--MAFGGVMPQEPFAAQGYMMPVVPP-QRDLAEFG-MG 259 (542)
Q Consensus 189 ~~g~--NPyw~G~~Pgm~GymGPf~gpM---P~mGYgmgP~g--MpfgG~mP~dPfam~G~GmP~vpP-~Rn~A~fg-rG 259 (542)
+-+| |+|..=+++- |-|.-|+.-+- |.+-++.+.|+ |||++ ||+...-++.-++|..|| .-+....| ++
T Consensus 403 ~p~~~~~s~p~pq~qN-yppp~p~f~m~~~hP~~~~p~~~~g~~~P~~~-mpp~~P~~~~pppP~~pp~p~~~~~q~q~~ 480 (483)
T KOG2236|consen 403 HPSSSDNSGPSPQQQN-YPPPSPSFPMFQPHPPESNPPANFGQANPFNQ-MPPAYPHQQSPPPPPPPPPPNSPMNQMQNP 480 (483)
T ss_pred CccccCCCCCCcccCC-CCCCCCCCCccCCCCCCCCCcccccccCcccc-CCCCCccccCCCCCCCCCCCCChhhcccCC
Q ss_pred C
Q 009145 260 M 260 (542)
Q Consensus 260 m 260 (542)
+
T Consensus 481 ~ 481 (483)
T KOG2236|consen 481 S 481 (483)
T ss_pred C
No 22
>KOG3088 consensus Secretory carrier membrane protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=38.48 E-value=96 Score=33.06 Aligned_cols=9 Identities=44% Similarity=0.722 Sum_probs=4.0
Q ss_pred hhhcccccc
Q 009145 289 RRGEREFSR 297 (542)
Q Consensus 289 Rr~Ere~~r 297 (542)
.|||++.-+
T Consensus 84 dRREr~~a~ 92 (313)
T KOG3088|consen 84 DRRERALAR 92 (313)
T ss_pred hHHHHHHhh
Confidence 444544433
No 23
>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.53 E-value=38 Score=36.41 Aligned_cols=30 Identities=23% Similarity=0.243 Sum_probs=12.4
Q ss_pred CCCCCCCCCCCCCccCcccCccCCC-CCCCCC
Q 009145 183 PSAYNPPAAYNPYWTGIQPGMEGYM-GPFAGA 213 (542)
Q Consensus 183 P~~~~~~~g~NPyw~G~~Pgm~Gym-GPf~gp 213 (542)
++++.+..+.|-+.+|. -|++||+ |+|+|.
T Consensus 54 ~s~~~g~~~mN~f~~~~-~~~~G~Gyg~YGgG 84 (362)
T KOG3875|consen 54 ISYVTGHYSMNTFVPGS-GYNYGSGYGPYGGG 84 (362)
T ss_pred CccccCCcccccccCCc-ccccCCCCCCcCCC
Confidence 44433334444443332 1344544 555444
No 24
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=36.79 E-value=27 Score=37.58 Aligned_cols=11 Identities=18% Similarity=0.132 Sum_probs=5.2
Q ss_pred cccchhhhhcc
Q 009145 109 KVVDVSEATLE 119 (542)
Q Consensus 109 k~~DvsE~T~e 119 (542)
++-||.-.+|-
T Consensus 85 r~rdVinVFh~ 95 (367)
T KOG0835|consen 85 RIRDVINVFHY 95 (367)
T ss_pred cHhHHHHHHHH
Confidence 34555554443
No 25
>KOG3263 consensus Nucleic acid binding protein [General function prediction only]
Probab=36.77 E-value=16 Score=36.19 Aligned_cols=11 Identities=64% Similarity=0.848 Sum_probs=5.2
Q ss_pred hhhcccccccc
Q 009145 289 RRGEREFSRDR 299 (542)
Q Consensus 289 Rr~Ere~~rdr 299 (542)
|++|+.++||+
T Consensus 25 RrrErsRsREr 35 (196)
T KOG3263|consen 25 RRRERSRSRER 35 (196)
T ss_pred HHHHHHhhhhh
Confidence 44455444443
No 26
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.43 E-value=1.2e+02 Score=36.48 Aligned_cols=14 Identities=29% Similarity=0.207 Sum_probs=8.4
Q ss_pred cccCCCCCCCCCCC
Q 009145 173 AAESCMMPLGPSAY 186 (542)
Q Consensus 173 a~~~YmMP~gP~~~ 186 (542)
++.++...+||+.+
T Consensus 118 ~~p~~~~~~gpp~g 131 (1007)
T KOG1984|consen 118 AGPSSGSGTGPPSG 131 (1007)
T ss_pred cCCCCCCcCCCCCC
Confidence 44556666676664
No 27
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=35.26 E-value=21 Score=40.29 Aligned_cols=32 Identities=38% Similarity=0.621 Sum_probs=17.3
Q ss_pred CCCccchhhhhHHHHHHHHHHHHHhhhhhccc
Q 009145 364 DRDRDYDYEYDREREREREREREKERERDRNH 395 (542)
Q Consensus 364 d~dr~~d~~~~r~r~~~~~~~~~~~~~~~r~~ 395 (542)
|.||+.|+.++|.|.-.++|+|++.+++++..
T Consensus 88 ~~~Re~~rsrsr~r~~~rsRsr~~srDr~~~~ 119 (549)
T KOG0147|consen 88 DYDRERDRSRSRDRQLRRSRSRASSRDRRRSD 119 (549)
T ss_pred ccccceehhhccccccchhhhhhhhcccccCC
Confidence 66666666655555434555555444444433
No 28
>PF15336 Auts2: Autism susceptibility gene 2 protein
Probab=34.24 E-value=1.1e+02 Score=31.04 Aligned_cols=7 Identities=29% Similarity=0.529 Sum_probs=3.6
Q ss_pred CCChhhh
Q 009145 250 QRDLAEF 256 (542)
Q Consensus 250 ~Rn~A~f 256 (542)
||-...|
T Consensus 152 hRtPpsF 158 (212)
T PF15336_consen 152 HRTPPSF 158 (212)
T ss_pred CCCCCCC
Confidence 5555545
No 29
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=30.06 E-value=36 Score=35.20 Aligned_cols=12 Identities=17% Similarity=0.218 Sum_probs=6.0
Q ss_pred cceeeecCchhh
Q 009145 433 SVFSRISFPEEE 444 (542)
Q Consensus 433 svFsRiSfpee~ 444 (542)
.=|+=|-|-..+
T Consensus 131 kg~afVeF~~~e 142 (457)
T TIGR01622 131 KGVAYVEFYDVE 142 (457)
T ss_pred ceEEEEEECCHH
Confidence 345556665333
No 30
>KOG3263 consensus Nucleic acid binding protein [General function prediction only]
Probab=29.85 E-value=39 Score=33.70 Aligned_cols=30 Identities=50% Similarity=0.787 Sum_probs=15.8
Q ss_pred CCccchhhhh-HHHHHHHHHHHHHhhhhhccc
Q 009145 365 RDRDYDYEYD-REREREREREREKERERDRNH 395 (542)
Q Consensus 365 ~dr~~d~~~~-r~r~~~~~~~~~~~~~~~r~~ 395 (542)
+||++.+.++ |.|++.|+||| .++++++--
T Consensus 14 R~Re~~R~~~dRrrErsRsREr-~~~rrdr~~ 44 (196)
T KOG3263|consen 14 RDRERRRSRRDRRRERSRSRER-RDRRRDRYE 44 (196)
T ss_pred hhHHHhhhHHHHHHHHHhhhhh-hhhhccccc
Confidence 4455544433 55556666666 455555443
No 31
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=27.61 E-value=12 Score=39.65 Aligned_cols=17 Identities=41% Similarity=0.360 Sum_probs=9.3
Q ss_pred cchHHHHhhhccchHHHH
Q 009145 134 MVDEEVQQKMASGEAAKK 151 (542)
Q Consensus 134 ~v~ee~qqk~a~~e~~KK 151 (542)
.| ++-|..+..-|.+|+
T Consensus 146 ~V-eeaq~~~~e~E~lk~ 162 (319)
T KOG0796|consen 146 NV-EEAQKAMKEVEELKA 162 (319)
T ss_pred CH-HHHHHHHHHHHHHHH
Confidence 44 344455556666665
No 32
>KOG1847 consensus mRNA splicing factor [RNA processing and modification]
Probab=26.84 E-value=25 Score=40.79 Aligned_cols=19 Identities=26% Similarity=0.359 Sum_probs=8.1
Q ss_pred hHHHHHHHHHhhhhccccc
Q 009145 278 KADVRRKRENERRGEREFS 296 (542)
Q Consensus 278 k~~~~RkrE~eRr~Ere~~ 296 (542)
+++...++.+.|+|-|.++
T Consensus 718 ee~k~~~~~rhrkRhrkrS 736 (878)
T KOG1847|consen 718 EEDKYHSRSRHRKRHRKRS 736 (878)
T ss_pred hhhhhhhhHhHhhhhcccc
Confidence 4444444444444444333
No 33
>KOG0199 consensus ACK and related non-receptor tyrosine kinases [Signal transduction mechanisms]
Probab=26.70 E-value=1.2e+02 Score=36.21 Aligned_cols=20 Identities=25% Similarity=0.207 Sum_probs=13.6
Q ss_pred CCCCCCCCCCccCcccCccC
Q 009145 186 YNPPAAYNPYWTGIQPGMEG 205 (542)
Q Consensus 186 ~~~~~g~NPyw~G~~Pgm~G 205 (542)
|.+.+||-+|-||+++|-+|
T Consensus 922 ~p~l~~~P~rg~~~~~~~~~ 941 (1039)
T KOG0199|consen 922 YPQLNGYPNRGNGFQAYGYG 941 (1039)
T ss_pred CccccCCCCccccccccccc
Confidence 34577788887777776544
No 34
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=26.68 E-value=69 Score=34.20 Aligned_cols=11 Identities=18% Similarity=0.610 Sum_probs=5.3
Q ss_pred HHHHHHHHHhh
Q 009145 20 LRNTINRILES 30 (542)
Q Consensus 20 LR~TI~~~L~~ 30 (542)
+|+-|+.++.+
T Consensus 5 mR~mLdqLMGs 15 (319)
T KOG0796|consen 5 MRAMLDQLMGS 15 (319)
T ss_pred HHHHHHHHhCC
Confidence 44445555543
No 35
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=25.24 E-value=3e+02 Score=29.84 Aligned_cols=8 Identities=0% Similarity=0.443 Sum_probs=3.6
Q ss_pred HHHHHHHh
Q 009145 22 NTINRILE 29 (542)
Q Consensus 22 ~TI~~~L~ 29 (542)
+.|+.++.
T Consensus 193 e~L~~~F~ 200 (562)
T TIGR01628 193 DKLRELFA 200 (562)
T ss_pred HHHHHHHH
Confidence 44444444
No 36
>KOG1049 consensus Polyadenylation factor I complex, subunit FIP1 [RNA processing and modification]
Probab=25.19 E-value=9.8e+02 Score=27.63 Aligned_cols=13 Identities=31% Similarity=0.662 Sum_probs=5.6
Q ss_pred HhhhhhcccCCCC
Q 009145 387 KERERDRNHHHRT 399 (542)
Q Consensus 387 ~~~~~~r~~~~rs 399 (542)
+-..+++|..||-
T Consensus 484 ~~~~~d~~~~~r~ 496 (538)
T KOG1049|consen 484 SSVDKDRHREHRR 496 (538)
T ss_pred hccchhhcchhhh
Confidence 3344444444443
No 37
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=24.24 E-value=2.3e+02 Score=33.04 Aligned_cols=20 Identities=20% Similarity=0.275 Sum_probs=10.0
Q ss_pred CCCCCCccccCCCCC-CCCCC
Q 009145 166 WKTPQDLAAESCMMP-LGPSA 185 (542)
Q Consensus 166 wk~~~d~a~~~YmMP-~gP~~ 185 (542)
|..+.+--..+|-.+ |+++.
T Consensus 320 ~~~~~~prqpp~p~~~~~~P~ 340 (757)
T KOG4368|consen 320 WGQQQPPEQPPYPHHQGGPPH 340 (757)
T ss_pred CCCCCCccCCCCCCcccCCCC
Confidence 555555555555443 44444
No 38
>KOG2295 consensus C2H2 Zn-finger protein [General function prediction only]
Probab=22.73 E-value=1.4e+02 Score=34.50 Aligned_cols=11 Identities=18% Similarity=0.767 Sum_probs=7.4
Q ss_pred cCCCC----CCCCCC
Q 009145 175 ESCMM----PLGPSA 185 (542)
Q Consensus 175 ~~YmM----P~gP~~ 185 (542)
+|||. ||+|..
T Consensus 550 nnYl~Dp~rp~~pe~ 564 (648)
T KOG2295|consen 550 NNYLLDPCRPMDPEV 564 (648)
T ss_pred HhhccCccccCCCcc
Confidence 56744 788776
No 39
>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]
Probab=22.45 E-value=43 Score=39.30 Aligned_cols=16 Identities=25% Similarity=0.380 Sum_probs=9.3
Q ss_pred CCCChhHHHHHHHHHh
Q 009145 14 LLPNKTLRNTINRILE 29 (542)
Q Consensus 14 L~PN~tLR~TI~~~L~ 29 (542)
|.|..+|-..-+.||.
T Consensus 556 ifpe~~l~~l~~~Flg 571 (877)
T KOG0151|consen 556 IFPEDFLIGLQNTFLG 571 (877)
T ss_pred hCcHHHHHHHHHHHhc
Confidence 3455566665666665
No 40
>KOG4594 consensus Sequence-specific single-stranded-DNA-binding protein [Replication, recombination and repair; Transcription; General function prediction only]
Probab=22.12 E-value=2.3e+02 Score=30.59 Aligned_cols=67 Identities=31% Similarity=0.492 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCcc----------------------CcccCccCCCCCCCCCC-CCCCCCCC-CCCCcCCCCCC
Q 009145 178 MMPLGPSAYNPPAAYNPYWT----------------------GIQPGMEGYMGPFAGAM-PYMPYGMG-PLDMAFGGVMP 233 (542)
Q Consensus 178 mMP~gP~~~~~~~g~NPyw~----------------------G~~Pgm~GymGPf~gpM-P~mGYgmg-P~gMpfgG~mP 233 (542)
++++.|+. |+||.. |-||+|-+-|-|....+ |-||--|+ |.+|+-+| |
T Consensus 113 gG~~~PGF------Fqpfm~pRy~ggp~Pp~~g~~~Ppg~~pG~qPllPnsmdPtrqqghpnmgqRMnPPrGmg~mG--p 184 (354)
T KOG4594|consen 113 GGPVPPGF------FQPFMSPRYPGGPRPPRMGGMQPPGGVPGSQPLLPNSMDPTRQQGHPNMGQRMNPPRGMGPMG--P 184 (354)
T ss_pred CCCCCCcc------ccccccccCCCCCCCcccCCCCCCCCCCCCCccCCCCCCcccccCCCCcCCcCCCCCCCCCCC--C
Q ss_pred CCc---ccccCCCCCCCCCCCChhhhcCCCCC
Q 009145 234 QEP---FAAQGYMMPVVPPQRDLAEFGMGMGM 262 (542)
Q Consensus 234 ~dP---fam~G~GmP~vpP~Rn~A~fgrGmgM 262 (542)
+.. ..+..-.+|+.| +|+|
T Consensus 185 qnygggmrpPpnslpg~P----------~~~m 206 (354)
T KOG4594|consen 185 QNYGGGMRPPPNSLPGMP----------GMNM 206 (354)
T ss_pred CCCCCCcCCCCCCCCCCC----------cccc
No 41
>KOG2888 consensus Putative RNA binding protein [General function prediction only]
Probab=21.83 E-value=31 Score=37.46 Aligned_cols=15 Identities=27% Similarity=0.271 Sum_probs=10.1
Q ss_pred hcccccccccceeee
Q 009145 424 AGADKKHKGSVFSRI 438 (542)
Q Consensus 424 ~~~~~k~K~svFsRi 438 (542)
-+-..|.|+.|-.|-
T Consensus 401 h~~~~keks~~r~rs 415 (453)
T KOG2888|consen 401 HDSSNKEKSAVRVRS 415 (453)
T ss_pred ccccchhhhcceecc
Confidence 455677888876654
No 42
>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]
Probab=20.47 E-value=14 Score=42.25 Aligned_cols=16 Identities=50% Similarity=0.702 Sum_probs=7.5
Q ss_pred CCCccchhhhhHHHHH
Q 009145 364 DRDRDYDYEYDRERER 379 (542)
Q Consensus 364 d~dr~~d~~~~r~r~~ 379 (542)
++|||..++++|-++|
T Consensus 696 ~rdr~Re~Rr~rs~er 711 (718)
T KOG2416|consen 696 TRDRDREHRRDRSDER 711 (718)
T ss_pred hhhhhhhhhhcccccc
Confidence 4555555544444433
Done!