Query 029035
Match_columns 200
No_of_seqs 110 out of 215
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 06:26:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029035.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029035hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0836 F-actin capping protei 100.0 6.1E-75 1.3E-79 501.9 14.4 190 5-194 2-281 (282)
2 PF01267 F-actin_cap_A: F-acti 100.0 3E-73 6.5E-78 498.4 12.6 181 11-191 1-271 (271)
3 PF01115 F_actin_cap_B: F-acti 91.2 5.3 0.00012 35.2 12.0 83 12-102 1-96 (242)
4 KOG2477 Uncharacterized conser 54.5 13 0.00029 36.3 3.4 68 103-173 483-552 (628)
5 PF07661 MORN_2: MORN repeat v 52.8 14 0.0003 19.5 2.0 15 103-117 4-18 (22)
6 KOG3174 F-actin capping protei 47.5 2.1E+02 0.0045 25.6 9.9 42 133-174 211-252 (275)
7 PF08265 YL1_C: YL1 nuclear pr 41.6 12 0.00026 22.6 0.6 14 83-96 9-22 (30)
8 PLN03113 DNA ligase 1; Provisi 41.0 57 0.0012 33.2 5.6 32 7-41 260-291 (744)
9 PF08146 BP28CT: BP28CT (NUC21 36.9 16 0.00035 29.6 0.9 39 138-182 31-69 (153)
10 PF13708 Methyltransf_27: Meth 35.1 1.5E+02 0.0033 24.7 6.6 68 6-76 23-94 (194)
11 PF12466 GDH_N: Glutamate dehy 29.6 18 0.0004 25.1 0.1 16 161-176 36-51 (60)
12 PF06972 DUF1296: Protein of u 26.1 96 0.0021 21.8 3.2 33 25-59 2-34 (60)
13 cd05795 Ribosomal_P0_L10e Ribo 25.4 14 0.00029 30.5 -1.4 37 136-172 5-41 (175)
14 cd05796 Ribosomal_P0_like Ribo 24.7 15 0.00033 29.9 -1.3 38 136-173 5-42 (163)
15 PF14969 DUF4508: Domain of un 23.8 1E+02 0.0023 23.6 3.3 36 6-41 14-49 (98)
16 cd00495 Ribosomal_L25_TL5_CTC 23.4 1.3E+02 0.0027 21.9 3.6 47 47-100 44-90 (91)
17 PF08863 YolD: YolD-like prote 23.3 61 0.0013 23.0 1.9 17 103-119 45-61 (92)
18 PF01267 F-actin_cap_A: F-acti 23.1 52 0.0011 29.2 1.7 106 42-153 107-237 (271)
19 COG5104 PRP40 Splicing factor 20.2 96 0.0021 30.1 2.9 67 105-175 305-377 (590)
No 1
>KOG0836 consensus F-actin capping protein, alpha subunit [Cytoskeleton]
Probab=100.00 E-value=6.1e-75 Score=501.86 Aligned_cols=190 Identities=36% Similarity=0.650 Sum_probs=186.8
Q ss_pred ccCChhhHHHHHHHHhhcCCCCcHHHHHHHHHHhhCCChhhHHHHhhhHHHHhhhcceeeEcCCCCCeEEEccccccCCC
Q 029035 5 VELNPKQKKEIAKWFLLNSPAGEIQYVAKDLRLVLNDNEVYDEAVSESFPIYNKSHMICLQMPAGAGDVLVTSFGELGEN 84 (200)
Q Consensus 5 ~~~s~~ek~~ii~~fl~~aPPGE~~eV~~Dlr~l~~~d~~~~~~i~~a~~~yn~~~~~~v~~~g~~~~viis~~n~l~~~ 84 (200)
.+||+++|++||++||++||||||++|++|||.|+.+|.++++++.+||++||++||+||+++|+.++||||+||+++++
T Consensus 2 ~~lS~~~k~rii~kfi~~APPGEfneVf~Dlr~ll~~d~l~~e~~~~A~~qYn~~~~vpv~i~g~~~~viIS~~n~lg~~ 81 (282)
T KOG0836|consen 2 SELSDAEKVRIISKFILHAPPGEFNEVFNDLRLLLSNDELLKEAAHEAFAQYNVDQMVPVEIDGGANQVIISEYNDLGNN 81 (282)
T ss_pred CcccHHHHHHHHHHHHhhCCChHHHHHHHHHHHHhcchhHHHHHHHHHHHHhchhcceeEecCCCCCceEEecccccCcc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecCCCCeEEEEecccc--------------------------------------------------------------
Q 029035 85 EYLDPRTAQVAIVDHVKQ-------------------------------------------------------------- 102 (200)
Q Consensus 85 ~y~Dp~~k~~f~~Dhl~~-------------------------------------------------------------- 102 (200)
|||||+++++|+|||+++
T Consensus 82 rf~Dp~~k~sFk~dhl~kea~d~qp~~~~~~~~E~~r~~l~~~l~~y~~~hy~~~~t~~vkk~dg~~~~l~icIesh~y~ 161 (282)
T KOG0836|consen 82 RFLDPVNKKSFKYDHLRKEAEDVQPYEAEINIIEIWRYALDAQLKKYVSDHYPKGVTFVVKKSDGEQETLTICIESHQYQ 161 (282)
T ss_pred eecchhhceeeeHHHHHHHhccCCCcchhhhhhHHHHHHHHHHHHHHHHhccCCCceEEEeccCCcceEEEEEEeecccC
Confidence 999999999999999997
Q ss_pred ----------------------------eeeEEEeeceEEEeecccccccccccCCcccHHHHHHHHHHHHHHHHHHHHH
Q 029035 103 ----------------------------VGAHYFEEGNVQLDAKHECGDSTLFQSPDDSAISISNILRHHETEYLASLEV 154 (200)
Q Consensus 103 ----------------------------v~vHYyEdGNVqL~s~k~~~~s~~~~~~~~~a~~ivk~I~~~E~~~q~~L~e 154 (200)
|||||||||||||.++|++.+|+.+++..+.|++|+++|+++||+||++|++
T Consensus 162 pkNfwNG~WRS~w~~~v~~~~~l~G~i~vqvHYyEdGNV~l~s~Kd~qds~~vsn~~q~a~e~~~iI~~~Eneyq~ai~e 241 (282)
T KOG0836|consen 162 PKNFWNGRWRSEWNYDVQPTTELKGRIKVQVHYYEDGNVQLVSSKDIQDSLTVSNEVQTAKEFIKIIEEAENEYQAAISE 241 (282)
T ss_pred cccccCCceeeeeeeccCchheeeeEEEEEEEEEecCcEEEEecCcchhhheeechHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999
Q ss_pred HhccCChhhhhhhhccCCCCCCcccCCccccchhhHHHhh
Q 029035 155 SYSNLPDNTFKDLRRKLPVTRTLFPWHNTSQFSLTREITK 194 (200)
Q Consensus 155 ~~~~Lse~~FK~LRR~LPvTRsKi~W~ki~~yrlg~d~~~ 194 (200)
+|++|||+|||+||||||||||||||+||++||||++|..
T Consensus 242 ~yq~lsD~tFKaLRRqLPVTRtkIdW~kilsy~igke~~~ 281 (282)
T KOG0836|consen 242 NYQTLSDTTFKALRRQLPVTRTKIDWNKILSYRIGKEMQN 281 (282)
T ss_pred HHHhcChhHHHHHHhhCCceeeeccHHHhhhHHHHHHhcc
Confidence 9999999999999999999999999999999999999865
No 2
>PF01267 F-actin_cap_A: F-actin capping protein alpha subunit; InterPro: IPR002189 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. The actin filament system, a prominent part of the cytoskeleton in eukaryotic cells, is both a static structure and a dynamic network that can undergo rearrangements: it is thought to be involved in processes such as cell movement and phagocytosis [], as well as muscle contraction. The F-actin capping protein binds in a calcium-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike gelsolin and severin this protein does not sever actin filaments. The F-actin capping protein is a heterodimer composed of two unrelated subunits: alpha and beta (see IPR001698 from INTERPRO). Neither of the subunits shows sequence similarity to other filament-capping proteins []. The alpha subunit is a protein of about 268 to 286 amino acid residues whose sequence is well conserved in eukaryotic species [].; GO: 0003779 actin binding, 0030036 actin cytoskeleton organization, 0008290 F-actin capping protein complex; PDB: 1MQ1_D 1MWN_X 2KBM_Y 2KZ7_A 3AAE_C 3AA6_A 3LK4_G 1IZN_A 3AA7_A 3AAA_A ....
Probab=100.00 E-value=3e-73 Score=498.42 Aligned_cols=181 Identities=38% Similarity=0.706 Sum_probs=161.4
Q ss_pred hHHHHHHHHhhcCCCCcHHHHHHHHHHhhCCChhhHHHHhhhHHHHhhhcceeeEcCCCCCeEEEccccccCCCeeecCC
Q 029035 11 QKKEIAKWFLLNSPAGEIQYVAKDLRLVLNDNEVYDEAVSESFPIYNKSHMICLQMPAGAGDVLVTSFGELGENEYLDPR 90 (200)
Q Consensus 11 ek~~ii~~fl~~aPPGE~~eV~~Dlr~l~~~d~~~~~~i~~a~~~yn~~~~~~v~~~g~~~~viis~~n~l~~~~y~Dp~ 90 (200)
||.+||++||++||||||++|++|||.|++||.++++.+++||++||++||+||++||.+++||||+||+++++||+||+
T Consensus 1 ek~~ii~~fl~~aPPGE~~~V~~Dlr~l~~dd~~~~~~i~~a~~~yn~~q~~~v~~~~~~~~viis~~n~~~~~ry~Dp~ 80 (271)
T PF01267_consen 1 EKVEIISSFLLQAPPGEFNEVFNDLRTLLGDDSLLKEGIAEAFEQYNEEQFIPVKLPGSDHKVIISKYNKLGGNRYFDPR 80 (271)
T ss_dssp HHHHHHHHHHHT--TT-HHHHHHHHHHHHT-HHHHHHHSHHHHHHHHHHTTEEE--TTSSS-EEE-GGGBESTTEEEETT
T ss_pred CHHHHHHHHHHcCCCccHHHHHHHHHHHhCCchhHHHHHHHHHHHHHHHCcEEEEeCCCCcceEEecccccCCCeEEEec
Confidence 68999999999999999999999999999999999999999999999999999999998899999999999999999999
Q ss_pred CCeEEEEecccc--------------------------------------------------------------------
Q 029035 91 TAQVAIVDHVKQ-------------------------------------------------------------------- 102 (200)
Q Consensus 91 ~k~~f~~Dhl~~-------------------------------------------------------------------- 102 (200)
++++|.|||+++
T Consensus 81 ~~~~F~~DHl~~~~~d~e~~~~~~~~~e~~R~~l~~~l~~Yv~~hy~~g~~~V~~~~~~~~~~l~i~I~~~k~n~~Nfwn 160 (271)
T PF01267_consen 81 SKKSFSVDHLKQKASDVEPYEPPDEELESYRDALDKALEKYVKEHYPSGACGVYPKSEEDKETLVICIVAHKYNPKNFWN 160 (271)
T ss_dssp TTEEEEEETTTTEEEEEEE-----TSSHHHHHHHHHHHHHHHHHHSTTEEEEEEEEEETTEEEEEEEEEEEEEEGGGTEE
T ss_pred cCcEEEEeeeccEEccCccccccccchHHHHHHHHHHHHHHHHHhccCceeEEEeccCCCccEEEEEEEecccccccccC
Confidence 999999999998
Q ss_pred ----------------------eeeEEEeeceEEEeecccccccccccCCcccHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 029035 103 ----------------------VGAHYFEEGNVQLDAKHECGDSTLFQSPDDSAISISNILRHHETEYLASLEVSYSNLP 160 (200)
Q Consensus 103 ----------------------v~vHYyEdGNVqL~s~k~~~~s~~~~~~~~~a~~ivk~I~~~E~~~q~~L~e~~~~Ls 160 (200)
|+|||||||||||+++|++..++.++++.++|++||++|+++|++||++|+++|++||
T Consensus 161 G~WrS~w~~~~~~~~~l~G~I~V~vHYyEdGNVqL~~~k~~~~~~~~~~~~~~a~~iv~~I~~~E~~~q~~L~e~~~~ls 240 (271)
T PF01267_consen 161 GRWRSEWTVDFSSSGTLSGKIKVQVHYYEDGNVQLNSSKEVSETVSVSNDEQFASDIVKAIKEAENKYQTSLNESYNNLS 240 (271)
T ss_dssp EEEEEEEEEEEETTEEEEEEEEEEEEE-TTEEEEEEEEEEEEEEEE--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ceeeEEEEEecCCCceEEEEEEeeEEEEeecEEEEEEccccceeeccCChhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999999999999988888889999999999999999999999999999
Q ss_pred hhhhhhhhccCCCCCCcccCCccccchhhHH
Q 029035 161 DNTFKDLRRKLPVTRTLFPWHNTSQFSLTRE 191 (200)
Q Consensus 161 e~~FK~LRR~LPvTRsKi~W~ki~~yrlg~d 191 (200)
+++||+|||+||||||||||+||++||||+|
T Consensus 241 ~~tFK~LRR~LPVTRsKi~W~ki~~yrlg~d 271 (271)
T PF01267_consen 241 EKTFKALRRQLPVTRSKINWNKIGNYRLGKD 271 (271)
T ss_dssp HTHHHHHS-SS-TTTSS-SHHHHHTTTS---
T ss_pred HHHHHHhhhhCCCCCCcccccccccEEecCC
Confidence 9999999999999999999999999999997
No 3
>PF01115 F_actin_cap_B: F-actin capping protein, beta subunit; InterPro: IPR001698 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. The actin filament system, a prominent part of the cytoskeleton in eukaryotic cells, is both a static structure and a dynamic network that can undergo rearrangements: it is thought to be involved in processes such as cell movement and phagocytosis [], as well as muscle contraction. The F-actin capping protein binds in a calcium-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike gelsolin (see IPR007122 from INTERPRO) and severin this protein does not sever actin filaments. The F-actin capping protein is a heterodimer composed of two unrelated subunits: alpha and beta. Neither of the subunits shows sequence similarity to other filament-capping proteins []. The beta subunit is a protein of about 280 amino acid residues whose sequence is well conserved in eukaryotic species [].; GO: 0003779 actin binding, 0030036 actin cytoskeleton organization, 0005737 cytoplasm, 0008290 F-actin capping protein complex; PDB: 3AAE_D 3LK4_Q 2KXP_B 2KZ7_B 3AA1_B 3LK2_B 3AA7_B 3AAA_B 1IZN_B 3AA0_B ....
Probab=91.17 E-value=5.3 Score=35.22 Aligned_cols=83 Identities=18% Similarity=0.238 Sum_probs=48.4
Q ss_pred HHHHHHHHhhcCCCCcHHHHHHHHHHhhCCChhhHHHHhhhHHHHhhhcceeeEc-CCCCCeEEEccccccCC-------
Q 029035 12 KKEIAKWFLLNSPAGEIQYVAKDLRLVLNDNEVYDEAVSESFPIYNKSHMICLQM-PAGAGDVLVTSFGELGE------- 83 (200)
Q Consensus 12 k~~ii~~fl~~aPPGE~~eV~~Dlr~l~~~d~~~~~~i~~a~~~yn~~~~~~v~~-~g~~~~viis~~n~l~~------- 83 (200)
|.+-+-.|+..=||-.+.+-+++|..|.++ +.+.+...+ +|-..|.- +.....+|.|.||+.++
T Consensus 1 k~d~aLdLlRRlpP~~ie~nl~~l~~L~Pd---l~edLLssV-----D~PLkv~~d~~~~k~yL~CdYNRDgDSYRSPwS 72 (242)
T PF01115_consen 1 KLDAALDLLRRLPPKKIEKNLSNLIDLVPD---LTEDLLSSV-----DQPLKVARDKETGKDYLLCDYNRDGDSYRSPWS 72 (242)
T ss_dssp HHHHHHHHHTTS-GGGHHHHHHHHHHHSGG---GHHHHHHHS---------EEEEETTTTEEEEESGGGEETTEEE-TTT
T ss_pred ChhHHHHHHhhCChHHHHHHHHHHHHHHHH---HHHHHHHhC-----CCcceEEEchhhCCeeEeecccCCcccccCCCC
Confidence 456677899999999999999999999873 344444333 33333333 33446799999999643
Q ss_pred CeeecCCC-----CeEEEEecccc
Q 029035 84 NEYLDPRT-----AQVAIVDHVKQ 102 (200)
Q Consensus 84 ~~y~Dp~~-----k~~f~~Dhl~~ 102 (200)
++|+-|-. --.+.-++|++
T Consensus 73 NkY~P~~~~~~~~dg~~PS~~LR~ 96 (242)
T PF01115_consen 73 NKYYPPLEGDDLEDGPVPSERLRK 96 (242)
T ss_dssp --EES--S-----S-----HHHHH
T ss_pred cccCCCccccccCCCCCChHHHHH
Confidence 46665555 45565666665
No 4
>KOG2477 consensus Uncharacterized conserved protein [Function unknown]
Probab=54.48 E-value=13 Score=36.34 Aligned_cols=68 Identities=12% Similarity=0.176 Sum_probs=42.6
Q ss_pred eeeEEEeeceEEEeecccccccccccCC--cccHHHHHHHHHHHHHHHHHHHHHHhccCChhhhhhhhccCCC
Q 029035 103 VGAHYFEEGNVQLDAKHECGDSTLFQSP--DDSAISISNILRHHETEYLASLEVSYSNLPDNTFKDLRRKLPV 173 (200)
Q Consensus 103 v~vHYyEdGNVqL~s~k~~~~s~~~~~~--~~~a~~ivk~I~~~E~~~q~~L~e~~~~Lse~~FK~LRR~LPv 173 (200)
.+|-|||..+--=.--+..-+.+.+.-+ +....-|=++|.++|.+|---.+...-.+|. |+||+++|-
T Consensus 483 ~dviFyE~a~~l~rrpH~~IeCIPvpqeig~map~YFKkAI~esE~Ews~~~nkkliets~---k~lR~~IpK 552 (628)
T KOG2477|consen 483 LDVIFYENAPSLQRRPHTAIECIPVPQEIGSMAPAYFKKAISESEEEWSHRKNKKLIETSK---KALRKMIPK 552 (628)
T ss_pred CCeEEEeccCccccCCceeEEEeechHHhhhhhhHHHHHHHhhhHHHHHhhhHHHHHHhhH---HHHHHhccc
Confidence 8999999876422222333334433322 2334467799999999995444444444443 999999984
No 5
>PF07661 MORN_2: MORN repeat variant; InterPro: IPR011652 This entry represents an apparent variant of the IPR003409 from INTERPRO repeat.
Probab=52.78 E-value=14 Score=19.46 Aligned_cols=15 Identities=20% Similarity=0.507 Sum_probs=11.5
Q ss_pred eeeEEEeeceEEEee
Q 029035 103 VGAHYFEEGNVQLDA 117 (200)
Q Consensus 103 v~vHYyEdGNVqL~s 117 (200)
....||++|+++-..
T Consensus 4 ~~~~yy~nG~l~~~~ 18 (22)
T PF07661_consen 4 EWKFYYENGKLKSEG 18 (22)
T ss_pred eEEEEeCCCCEEEEE
Confidence 356899999987654
No 6
>KOG3174 consensus F-actin capping protein, beta subunit [Cytoskeleton]
Probab=47.49 E-value=2.1e+02 Score=25.60 Aligned_cols=42 Identities=14% Similarity=0.158 Sum_probs=36.9
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhccCChhhhhhhhccCCCC
Q 029035 133 SAISISNILRHHETEYLASLEVSYSNLPDNTFKDLRRKLPVT 174 (200)
Q Consensus 133 ~a~~ivk~I~~~E~~~q~~L~e~~~~Lse~~FK~LRR~LPvT 174 (200)
....+-+.|++.|++...-|++.|-.=+...|-.+|-.+|+.
T Consensus 211 Hian~gklve~~et~mr~~l~~iYfgkTkdi~~~~Rs~~~~a 252 (275)
T KOG3174|consen 211 HIANQGKLVEDMETKMRNLLNEIYFGKTKDISNQLRSPQALA 252 (275)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccChHHHhhccchhhhh
Confidence 345678999999999999999999999999999999887764
No 7
>PF08265 YL1_C: YL1 nuclear protein C-terminal domain; InterPro: IPR013272 This domain is found at the C terminus in proteins of the YL1 family []. These proteins have been shown to be DNA-binding and may be transcription factors []. This domain is also found in proteins that do not belong to the YL1 family.
Probab=41.59 E-value=12 Score=22.64 Aligned_cols=14 Identities=29% Similarity=0.401 Sum_probs=11.6
Q ss_pred CCeeecCCCCeEEE
Q 029035 83 ENEYLDPRTAQVAI 96 (200)
Q Consensus 83 ~~~y~Dp~~k~~f~ 96 (200)
..+|.||+++.-|.
T Consensus 9 pA~Y~DP~T~l~Y~ 22 (30)
T PF08265_consen 9 PARYRDPKTGLPYA 22 (30)
T ss_pred CccccCCCCCCccc
Confidence 47899999998763
No 8
>PLN03113 DNA ligase 1; Provisional
Probab=41.01 E-value=57 Score=33.21 Aligned_cols=32 Identities=25% Similarity=0.326 Sum_probs=26.4
Q ss_pred CChhhHHHHHHHHhhcCCCCcHHHHHHHHHHhhCC
Q 029035 7 LNPKQKKEIAKWFLLNSPAGEIQYVAKDLRLVLND 41 (200)
Q Consensus 7 ~s~~ek~~ii~~fl~~aPPGE~~eV~~Dlr~l~~~ 41 (200)
-|.+.|..++..|+..+.|-|..-+ +|.|+++
T Consensus 260 ~sq~~K~~~i~~Ll~~~~~~E~k~l---iR~l~g~ 291 (744)
T PLN03113 260 DSQEKKKNRIKALLVAATDCEPLYL---IRLLQTK 291 (744)
T ss_pred cCHHHHHHHHHHHHHhCCHHHHHHH---HHHHhcc
Confidence 4667899999999999999998887 6666654
No 9
>PF08146 BP28CT: BP28CT (NUC211) domain; InterPro: IPR012954 This C-terminal domain is found in BAP28-like nucleolar proteins []. The bap28 mutation leads to abnormalities in the brain, starting at midsomitogenesis stages. Mutant zebrafish embryos display excessive apoptosis, especially in the central nervous system (CNS) that results in death. The mutation affects a gene that encodes a large protein with high similarity to the uncharacterised human protein BAP28 and lower similarity to yeast Utp10. Utp10 is a component of a nucleolar U3 small nucleolar RNA-containing RNP complex that is required for transcription of ribosomal DNA and for processing of 18 S rRNA. Zebrafish Bap28 is also required for rRNA transcription and processing, with a major effect on 18S rRNA maturation. Bap28 is therefore required for cell survival in the CNS through its role in rRNA synthesis and processing [].
Probab=36.87 E-value=16 Score=29.56 Aligned_cols=39 Identities=18% Similarity=0.333 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHHHhccCChhhhhhhhccCCCCCCcccCCc
Q 029035 138 SNILRHHETEYLASLEVSYSNLPDNTFKDLRRKLPVTRTLFPWHN 182 (200)
Q Consensus 138 vk~I~~~E~~~q~~L~e~~~~Lse~~FK~LRR~LPvTRsKi~W~k 182 (200)
...|.+.|...-..+.+.--.|||.+|| |+-.+-++|..
T Consensus 31 ~~~v~~vE~~v~~~~~~lV~KLnE~~FR------PlF~~l~dWA~ 69 (153)
T PF08146_consen 31 LEDVDEVESSVISAFVSLVLKLNEATFR------PLFLKLVDWAT 69 (153)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcccchhH------hHHHHHHHHHc
Confidence 5678889999999999999999999999 77777799974
No 10
>PF13708 Methyltransf_27: Methyltransferase domain
Probab=35.13 E-value=1.5e+02 Score=24.70 Aligned_cols=68 Identities=9% Similarity=0.159 Sum_probs=46.0
Q ss_pred cCChhhHHHHHHHHhh-cCCCCcHHHHHHHHHHhhCC-ChhhHHHHhhhHHHHhhhcce--eeEcCCCCCeEEEc
Q 029035 6 ELNPKQKKEIAKWFLL-NSPAGEIQYVAKDLRLVLND-NEVYDEAVSESFPIYNKSHMI--CLQMPAGAGDVLVT 76 (200)
Q Consensus 6 ~~s~~ek~~ii~~fl~-~aPPGE~~eV~~Dlr~l~~~-d~~~~~~i~~a~~~yn~~~~~--~v~~~g~~~~viis 76 (200)
-||.+.+.++-+.|-. ..||=....|+.=+..|..+ +..+.+++.++|..-....-+ |.++. .++||.
T Consensus 23 ~m~~~~r~~~~~~l~~~~~p~ft~~NI~~t~~~l~~~r~~~~~~~v~~vF~~Ls~~yKTN~~~~~g---kkiIi~ 94 (194)
T PF13708_consen 23 FMSAQARDEWDKQLEEDDPPEFTEENIYSTFEQLHANRGEIFERGVIDVFRSLSWDYKTNSPCKFG---KKIIIN 94 (194)
T ss_pred HhCHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHHHCHHHHHHHHHHHHHHHhchhhccCCCeeec---cceeec
Confidence 4677777777777774 55556667777778888776 667788899988876544333 55554 456664
No 11
>PF12466 GDH_N: Glutamate dehydrogenase N terminal; InterPro: IPR024727 Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia []. This entry represents a domain found in the N-terminal region of a bacterial family of putative GDHs.
Probab=29.59 E-value=18 Score=25.14 Aligned_cols=16 Identities=31% Similarity=0.733 Sum_probs=13.7
Q ss_pred hhhhhhhhccCCCCCC
Q 029035 161 DNTFKDLRRKLPVTRT 176 (200)
Q Consensus 161 e~~FK~LRR~LPvTRs 176 (200)
|-.|-+||.+-|+.||
T Consensus 36 epVfaALRkryPaa~Q 51 (60)
T PF12466_consen 36 EPVFAALRKRYPAARQ 51 (60)
T ss_pred hHHHHHHHHhCcHHHH
Confidence 3479999999999887
No 12
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=26.14 E-value=96 Score=21.78 Aligned_cols=33 Identities=6% Similarity=0.089 Sum_probs=27.0
Q ss_pred CCcHHHHHHHHHHhhCCChhhHHHHhhhHHHHhhh
Q 029035 25 AGEIQYVAKDLRLVLNDNEVYDEAVSESFPIYNKS 59 (200)
Q Consensus 25 PGE~~eV~~Dlr~l~~~d~~~~~~i~~a~~~yn~~ 59 (200)
|.....++.+|+.+++. -..+.|-.+|.+.|++
T Consensus 2 P~~~rk~VQ~iKEiv~~--hse~eIya~L~ecnMD 34 (60)
T PF06972_consen 2 PAASRKTVQSIKEIVGC--HSEEEIYAMLKECNMD 34 (60)
T ss_pred ChHHHHHHHHHHHHhcC--CCHHHHHHHHHHhCCC
Confidence 56678899999999996 3668888888888875
No 13
>cd05795 Ribosomal_P0_L10e Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). These eukaryotic and archaeal P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.
Probab=25.40 E-value=14 Score=30.52 Aligned_cols=37 Identities=22% Similarity=0.266 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCChhhhhhhhccCC
Q 029035 136 SISNILRHHETEYLASLEVSYSNLPDNTFKDLRRKLP 172 (200)
Q Consensus 136 ~ivk~I~~~E~~~q~~L~e~~~~Lse~~FK~LRR~LP 172 (200)
.+|+.|+++=.+|..-+.-.|.+|.-..|+.|||.|-
T Consensus 5 ~~v~el~e~l~~~~~v~v~~~~gl~~~ql~~lR~~lr 41 (175)
T cd05795 5 EYVEKLTELLKSYPKVLIVDADNVGSKQLQKIRRSLR 41 (175)
T ss_pred HHHHHHHHHHHhCCEEEEEEecCCChHHHHHHHHHhh
Confidence 4566677766777777778899999999999999985
No 14
>cd05796 Ribosomal_P0_like Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized eukaryotic proteins with similarity to the 60S ribosomal protein P0, including the Saccharomyces cerevisiae protein called mRNA turnover protein 4 (MRT4). MRT4 may be involved in mRNA decay. P0 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. It occupies the L7/L12 stalk of the ribosome. The stalk is known to contain the binding site for elongation factors EF-G and EF-Tu; however, there is disagreement as to whether or not P0 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, P0 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WAS
Probab=24.68 E-value=15 Score=29.89 Aligned_cols=38 Identities=21% Similarity=0.314 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCChhhhhhhhccCCC
Q 029035 136 SISNILRHHETEYLASLEVSYSNLPDNTFKDLRRKLPV 173 (200)
Q Consensus 136 ~ivk~I~~~E~~~q~~L~e~~~~Lse~~FK~LRR~LPv 173 (200)
.+|+.|+++=.+|+.-+.-.|.+|+-.+|+.|||.|.=
T Consensus 5 ~~v~~l~e~l~~y~~v~iv~~~gl~~~ql~~iR~~lr~ 42 (163)
T cd05796 5 KLVENIREAVDKYKYIYVFSVDNMRNNKLKDIRQEWKD 42 (163)
T ss_pred HHHHHHHHHHHhCCEEEEEEecCCCHHHHHHHHHHhcC
Confidence 35566666666677677778999999999999999963
No 15
>PF14969 DUF4508: Domain of unknown function (DUF4508)
Probab=23.84 E-value=1e+02 Score=23.62 Aligned_cols=36 Identities=11% Similarity=0.159 Sum_probs=31.6
Q ss_pred cCChhhHHHHHHHHhhcCCCCcHHHHHHHHHHhhCC
Q 029035 6 ELNPKQKKEIAKWFLLNSPAGEIQYVAKDLRLVLND 41 (200)
Q Consensus 6 ~~s~~ek~~ii~~fl~~aPPGE~~eV~~Dlr~l~~~ 41 (200)
+-|+-++.+++..|+.-|-||.++.+++.+..|.-.
T Consensus 14 ~WS~~QRe~Fl~~Lv~ka~p~~v~~Ll~~l~~l~v~ 49 (98)
T PF14969_consen 14 EWSELQREDFLQDLVEKAVPGKVNGLLDSLENLSVQ 49 (98)
T ss_pred hcCHHHHHHHHHHHHHHhccchHHHHHHHHHhCcCC
Confidence 457889999999999999999999999999988653
No 16
>cd00495 Ribosomal_L25_TL5_CTC Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is found only in bacteria and some plastids. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L
Probab=23.40 E-value=1.3e+02 Score=21.90 Aligned_cols=47 Identities=17% Similarity=0.279 Sum_probs=32.9
Q ss_pred HHHhhhHHHHhhhcceeeEcCCCCCeEEEccccccCCCeeecCCCCeEEEEecc
Q 029035 47 EAVSESFPIYNKSHMICLQMPAGAGDVLVTSFGELGENEYLDPRTAQVAIVDHV 100 (200)
Q Consensus 47 ~~i~~a~~~yn~~~~~~v~~~g~~~~viis~~n~l~~~~y~Dp~~k~~f~~Dhl 100 (200)
..+..++........+.+.++|....|+|-+.- +||.+....++|+.
T Consensus 44 ~~l~k~l~~~~~~~~~~L~i~g~~~~~~ikevQ-------~~pv~~~i~HvDF~ 90 (91)
T cd00495 44 KELEKLLRKEGRSTLIELNIDGKKENVLIKDVQ-------RHPVKDKILHVDFL 90 (91)
T ss_pred HHHHHHHhhcCCceEEEEEECCEEEEEEEehhh-------hccCCCCEEEEecc
Confidence 345555555555556678888876677777653 58999999999875
No 17
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=23.35 E-value=61 Score=23.02 Aligned_cols=17 Identities=29% Similarity=0.421 Sum_probs=13.6
Q ss_pred eeeEEEeeceEEEeecc
Q 029035 103 VGAHYFEEGNVQLDAKH 119 (200)
Q Consensus 103 v~vHYyEdGNVqL~s~k 119 (200)
|.+.||++|+.+=.+.+
T Consensus 45 v~ity~~~g~~~~~~G~ 61 (92)
T PF08863_consen 45 VTITYYEDGYYQSVTGT 61 (92)
T ss_pred EEEEEEECCeeEEEEEE
Confidence 88999999988765544
No 18
>PF01267 F-actin_cap_A: F-actin capping protein alpha subunit; InterPro: IPR002189 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. The actin filament system, a prominent part of the cytoskeleton in eukaryotic cells, is both a static structure and a dynamic network that can undergo rearrangements: it is thought to be involved in processes such as cell movement and phagocytosis [], as well as muscle contraction. The F-actin capping protein binds in a calcium-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike gelsolin and severin this protein does not sever actin filaments. The F-actin capping protein is a heterodimer composed of two unrelated subunits: alpha and beta (see IPR001698 from INTERPRO). Neither of the subunits shows sequence similarity to other filament-capping proteins []. The alpha subunit is a protein of about 268 to 286 amino acid residues whose sequence is well conserved in eukaryotic species [].; GO: 0003779 actin binding, 0030036 actin cytoskeleton organization, 0008290 F-actin capping protein complex; PDB: 1MQ1_D 1MWN_X 2KBM_Y 2KZ7_A 3AAE_C 3AA6_A 3LK4_G 1IZN_A 3AA7_A 3AAA_A ....
Probab=23.09 E-value=52 Score=29.20 Aligned_cols=106 Identities=16% Similarity=0.144 Sum_probs=63.6
Q ss_pred ChhhHHHHhhhHHHHhhhcce-----eeEcCCCCC--eEEEccccccCCCeeecCCCCeEEEEec-----------ccc-
Q 029035 42 NEVYDEAVSESFPIYNKSHMI-----CLQMPAGAG--DVLVTSFGELGENEYLDPRTAQVAIVDH-----------VKQ- 102 (200)
Q Consensus 42 d~~~~~~i~~a~~~yn~~~~~-----~v~~~g~~~--~viis~~n~l~~~~y~Dp~~k~~f~~Dh-----------l~~- 102 (200)
-+.++..+..+|.+|-.++|- +...++.+. -+|+-..++.....||-.+++..|.||. +.-
T Consensus 107 ~e~~R~~l~~~l~~Yv~~hy~~g~~~V~~~~~~~~~~l~i~I~~~k~n~~NfwnG~WrS~w~~~~~~~~~l~G~I~V~vH 186 (271)
T PF01267_consen 107 LESYRDALDKALEKYVKEHYPSGACGVYPKSEEDKETLVICIVAHKYNPKNFWNGRWRSEWTVDFSSSGTLSGKIKVQVH 186 (271)
T ss_dssp SHHHHHHHHHHHHHHHHHHSTTEEEEEEEEEETTEEEEEEEEEEEEEEGGGTEEEEEEEEEEEEEETTEEEEEEEEEEEE
T ss_pred hHHHHHHHHHHHHHHHHHhccCceeEEEeccCCCccEEEEEEEecccccccccCceeeEEEEEecCCCceEEEEEEeeEE
Confidence 356778899999999999883 222233222 2332234566789999999999999992 433
Q ss_pred ------eeeEEEeeceEEEeecccccccccccCCcccHHHHHHHHHHHHHHHHHHHH
Q 029035 103 ------VGAHYFEEGNVQLDAKHECGDSTLFQSPDDSAISISNILRHHETEYLASLE 153 (200)
Q Consensus 103 ------v~vHYyEdGNVqL~s~k~~~~s~~~~~~~~~a~~ivk~I~~~E~~~q~~L~ 153 (200)
||..+=++-+..+....+ ... ....++.|-++=.+.+.++.....
T Consensus 187 YyEdGNVqL~~~k~~~~~~~~~~~-~~~-----a~~iv~~I~~~E~~~q~~L~e~~~ 237 (271)
T PF01267_consen 187 YYEDGNVQLNSSKEVSETVSVSND-EQF-----ASDIVKAIKEAENKYQTSLNESYN 237 (271)
T ss_dssp E-TTEEEEEEEEEEEEEEEE--SH-HHH-----HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEeecEEEEEEccccceeeccCCh-hhh-----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 777777776666665443 111 123455555555555555554443
No 19
>COG5104 PRP40 Splicing factor [RNA processing and modification]
Probab=20.20 E-value=96 Score=30.14 Aligned_cols=67 Identities=24% Similarity=0.274 Sum_probs=43.9
Q ss_pred eEEEeeceEEEeecccccccccccCCcccHHHHHHHHHHHHHHHHHHHHHHh------ccCChhhhhhhhccCCCCC
Q 029035 105 AHYFEEGNVQLDAKHECGDSTLFQSPDDSAISISNILRHHETEYLASLEVSY------SNLPDNTFKDLRRKLPVTR 175 (200)
Q Consensus 105 vHYyEdGNVqL~s~k~~~~s~~~~~~~~~a~~ivk~I~~~E~~~q~~L~e~~------~~Lse~~FK~LRR~LPvTR 175 (200)
.||-=|--|+....+.+..= + -...--++++.++.+|++|+.++++.= ...+-..|++|-|.|||-.
T Consensus 305 ~~~~fd~~~ry~~n~~mk~l---~-~~d~L~~f~~~v~~lE~el~~~~~e~k~~~~~~~r~~rd~FrtLLr~l~~~~ 377 (590)
T COG5104 305 NHYVFDSVVRYLKNKEMKPL---D-RKDILFSFIRYVRRLEKELLSAIEERKAAAAQNARHHRDEFRTLLRKLYSEG 377 (590)
T ss_pred hhhhhcccHHHHhhcccCcc---c-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhhh
Confidence 45544444444444444321 0 122345678999999999999998742 3566779999999999853
Done!