Query 039845
Match_columns 210
No_of_seqs 15 out of 17
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 02:34:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039845.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039845hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0307 Vesicle coat complex C 67.5 1.1E+02 0.0023 33.1 12.6 151 20-179 466-655 (1049)
2 cd02414 jag_KH jag_K homology 52.0 3.6 7.8E-05 29.4 -0.6 38 4-41 2-42 (77)
3 PF13518 HTH_28: Helix-turn-he 48.5 41 0.0009 21.1 4.0 34 129-183 11-44 (52)
4 PF08625 Utp13: Utp13 specific 38.6 49 0.0011 26.9 3.8 73 90-183 10-85 (141)
5 PRK13453 F0F1 ATP synthase sub 35.6 1.3E+02 0.0028 24.5 5.9 35 45-79 8-42 (173)
6 PF07311 Dodecin: Dodecin; In 33.0 29 0.00062 25.6 1.6 17 91-107 14-30 (66)
7 TIGR01610 phage_O_Nterm phage 32.3 1.1E+02 0.0024 22.7 4.6 47 89-141 3-58 (95)
8 PF00954 S_locus_glycop: S-loc 32.1 21 0.00045 26.5 0.7 15 182-196 90-104 (110)
9 TIGR02698 CopY_TcrY copper tra 31.3 45 0.00097 26.2 2.5 26 163-195 105-130 (130)
10 TIGR03342 dsrC_tusE_dsvC sulfu 25.4 61 0.0013 25.8 2.3 21 162-182 43-63 (108)
11 TIGR03707 PPK2_P_aer polyphosp 24.9 1.3E+02 0.0027 26.4 4.4 102 24-132 97-227 (230)
12 COG2920 DsrC Dissimilatory sul 24.4 66 0.0014 26.4 2.4 44 140-183 18-67 (111)
13 PRK11508 sulfur transfer prote 21.7 78 0.0017 25.3 2.3 21 162-182 44-64 (109)
14 PF04051 TRAPP: Transport prot 21.5 59 0.0013 25.8 1.6 34 29-62 24-58 (152)
15 COG0203 RplQ Ribosomal protein 21.1 27 0.00059 28.7 -0.4 20 19-40 87-106 (116)
16 PF00627 UBA: UBA/TS-N domain; 21.1 1.6E+02 0.0035 18.2 3.2 25 124-150 8-33 (37)
17 PF05186 Dpy-30: Dpy-30 motif; 21.1 78 0.0017 21.2 1.9 15 162-176 27-41 (42)
18 PF02044 Bombesin: Bombesin-li 21.0 34 0.00074 19.2 0.1 9 33-41 5-13 (14)
19 PF04358 DsrC: DsrC like prote 21.0 84 0.0018 24.8 2.3 30 153-182 28-64 (109)
No 1
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=67.48 E-value=1.1e+02 Score=33.07 Aligned_cols=151 Identities=17% Similarity=0.101 Sum_probs=89.9
Q ss_pred eCCCCcchhhhHh---hhhhchhhhHHHHHHHhhhhhhhHHHHHHHHHHHH---------------HHHHHHHhhccchh
Q 039845 20 NRSDSGYTRGLIE---KVGFLMGRDVASLVLEACIRLRIWELVETLIVHGL---------------LLCILKYFLCPLQD 81 (210)
Q Consensus 20 ~~s~~~y~rvLie---K~G~~mgRdv~~lVl~~~vsL~~WelVe~Li~~gl---------------lL~iLk~FL~psk~ 81 (210)
|.+.++- +.+++ +.-...+.|.-++|.++-|.=.+=+.||..++.-. +-++..=++.=.+.
T Consensus 466 d~~~~~~-q~~~~~~~~~~~s~~~d~d~~Is~alitgd~~~aV~~cl~~~~~a~AliiA~~gg~el~~~t~~~Y~~k~~~ 544 (1049)
T KOG0307|consen 466 DTSIFSE-QFVPEPKGSGNISLDSDIDGLISEALITGDFKSAVELCLEANKMADALIIAHAGGTELLESTRDKYLAKSNS 544 (1049)
T ss_pred cccccch-hhcccCCCCcccCCCCcHHHHHHHHHHhccHHHHHHHHHhhhHHHHHHHHHhcCCHHHHHHHHHHHHHHhCC
Confidence 3333333 66666 44456777888888888888888999998888765 22222112222211
Q ss_pred hhhhH----H-----------HHHHHHHHHHHHHHHHhccCCchhHHHHHHHHHHHHHHHHhcCCChhhHHHHHHHhcCC
Q 039845 82 AYGSM----G-----------SVRMEWESQALLAIEKASDENPSRKQLCLAKEASILLMVAHDGFSISELCLRYLLASSN 146 (210)
Q Consensus 82 ay~sm----~-----------~Vr~~We~~A~LAIekas~knl~kK~~~vAk~AaiLLmva~DgFt~sElCLHyL~AS~n 146 (210)
-|+.. + .|+ .||+.-...-+.+.+ +|-.++--.-+=.|+.+-| .+.+.||-|+ ++|+
T Consensus 545 k~s~li~a~v~~d~~~~ve~~~~k-~Wke~la~i~t~~~~----~~~~elc~~Lg~rl~~~g~--~~~~a~lcYi-~ags 616 (1049)
T KOG0307|consen 545 KLSRLIYAMVNRDLDDYVETCEVK-QWKETLAAICTYAQT----DEFSELCDMLGDRLENAGD--LTSAAILCYI-CAGS 616 (1049)
T ss_pred hHHHHHHHHHhhhHHHHHhhcchh-hHHHHHHHHHHhcch----hhHHHHHHHHHHHHhhccc--hhhhhhHHhh-hccC
Confidence 13221 1 223 377766655555554 5666666556667777777 7888999999 8899
Q ss_pred cchhHHHHhhhc---cchhhHHHHH---HHHHHhhhcCC
Q 039845 147 IDEVMLSSAISN---LNGMSLIRYL---GKWLKKFETFP 179 (210)
Q Consensus 147 vDe~vL~aaVse---Ldg~~LiRYL---~KWl~KY~rFp 179 (210)
+|..|-.=+.++ +++.++--++ -+=.+|.+.|+
T Consensus 617 v~k~v~~w~~~~~~~~~~~~y~~~~e~l~~~~~~l~~~~ 655 (1049)
T KOG0307|consen 617 VDKLVEIWLKALDLELAPTSYQDLAEDLMELTLKLAQFS 655 (1049)
T ss_pred hhhhHHHHHHhcccccchHHHHHHHHHHHHHHhhhhhcc
Confidence 998775444443 3454444444 34444444444
No 2
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=52.01 E-value=3.6 Score=29.39 Aligned_cols=38 Identities=21% Similarity=0.439 Sum_probs=25.3
Q ss_pred hHHHhhcchhcceEeeeCCC---CcchhhhHhhhhhchhhh
Q 039845 4 PYLEKISEKVGISTRINRSD---SGYTRGLIEKVGFLMGRD 41 (210)
Q Consensus 4 ~~le~i~~k~gis~~~~~s~---~~y~rvLieK~G~~mgRd 41 (210)
+|||++-++.|+...++-.. .=...+--+..|.+|||+
T Consensus 2 ~~L~~il~~mg~~~~v~~~~~~~~i~i~i~~~~~g~LIGk~ 42 (77)
T cd02414 2 EFLEEVLELMGIEADVDVEEEGDTVEVNISGDDIGLLIGKR 42 (77)
T ss_pred hHHHHHHHHcCCCcEEEEEecCCEEEEEEecCCCCeEECCC
Confidence 68888888888766653222 123444457889999985
No 3
>PF13518 HTH_28: Helix-turn-helix domain
Probab=48.53 E-value=41 Score=21.06 Aligned_cols=34 Identities=18% Similarity=0.390 Sum_probs=24.8
Q ss_pred cCCChhhHHHHHHHhcCCcchhHHHHhhhccchhhHHHHHHHHHHhhhcCCcccc
Q 039845 129 DGFSISELCLRYLLASSNIDEVMLSSAISNLNGMSLIRYLGKWLKKFETFPQIAI 183 (210)
Q Consensus 129 DgFt~sElCLHyL~AS~nvDe~vL~aaVseLdg~~LiRYL~KWl~KY~rFpqa~~ 183 (210)
+|-|..|+|-++=+ |. +-+..|+++|+..-..+.
T Consensus 11 ~g~s~~~~a~~~gi-s~--------------------~tv~~w~~~y~~~G~~~l 44 (52)
T PF13518_consen 11 EGESVREIAREFGI-SR--------------------STVYRWIKRYREGGIEGL 44 (52)
T ss_pred cCCCHHHHHHHHCC-CH--------------------hHHHHHHHHHHhcCHHHh
Confidence 67799999888875 33 346789999998754444
No 4
>PF08625 Utp13: Utp13 specific WD40 associated domain; InterPro: IPR013934 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp13 is a nucleolar protein and component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA []. Upt13 is also a component of the Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome []. Components of the Pwp2 complex are: Utp1 (Pwp2), Utp6, Utp12 (Dip2), Utp13, Utp18, and Utp21. The relationship between the Pwp2 complex and the t-Utps complex [] that also associates with the 5' end of nascent pre-18S rRNA is unclear. ; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=38.56 E-value=49 Score=26.87 Aligned_cols=73 Identities=16% Similarity=0.241 Sum_probs=46.2
Q ss_pred HHHHHHHHHHHHHHhccCCchhHHHHHHHHHHHHHHHHhcCCChhhHHHHHHHhcCCcchhHHHHhhhccch---hhHHH
Q 039845 90 RMEWESQALLAIEKASDENPSRKQLCLAKEASILLMVAHDGFSISELCLRYLLASSNIDEVMLSSAISNLNG---MSLIR 166 (210)
Q Consensus 90 r~~We~~A~LAIekas~knl~kK~~~vAk~AaiLLmva~DgFt~sElCLHyL~AS~nvDe~vL~aaVseLdg---~~LiR 166 (210)
.+.|++|..+|++.-.- ++-..+-++. +. ... ..+.+-+.-+...|.+|+. ..|++
T Consensus 10 ~~~y~~Al~LAl~L~~P----~~ll~i~~~~-----~~-~~~-----------~~~~~g~~~l~~~i~~L~~~~l~~LL~ 68 (141)
T PF08625_consen 10 QKDYKEALRLALKLDHP----FRLLKILKDL-----LE-TEE-----------DEDSIGSEELDEVIKKLDDEQLEKLLR 68 (141)
T ss_pred hhhHHHHHHHHHhcCCc----HHHHHHHHHH-----Hh-ccc-----------ccccchHHHHHHHHHhcCHHHHHHHHH
Confidence 68899999999987543 3333331111 11 000 0011123567788999999 99999
Q ss_pred HHHHHHHhhhcCCcccc
Q 039845 167 YLGKWLKKFETFPQIAI 183 (210)
Q Consensus 167 YL~KWl~KY~rFpqa~~ 183 (210)
|...|-..-+.+.-||.
T Consensus 69 ~ir~WNTNsr~~~vAQ~ 85 (141)
T PF08625_consen 69 FIRDWNTNSRTSHVAQR 85 (141)
T ss_pred HHHHhhcccccHHHHHH
Confidence 99999887777666653
No 5
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=35.59 E-value=1.3e+02 Score=24.50 Aligned_cols=35 Identities=26% Similarity=0.258 Sum_probs=29.2
Q ss_pred HHHHhhhhhhhHHHHHHHHHHHHHHHHHHHhhccc
Q 039845 45 LVLEACIRLRIWELVETLIVHGLLLCILKYFLCPL 79 (210)
Q Consensus 45 lVl~~~vsL~~WelVe~Li~~gllL~iLk~FL~ps 79 (210)
.||-+..++..|..+=++|.-.+++.+|++|+-|+
T Consensus 8 ~~~~~~~~~~~~t~~~~iInFliL~~lL~~~l~~p 42 (173)
T PRK13453 8 FVLGAAGGVEWGTVIVTVLTFIVLLALLKKFAWGP 42 (173)
T ss_pred HHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36677788888888888888889999999998766
No 6
>PF07311 Dodecin: Dodecin; InterPro: IPR009923 This entry represents proteins with a Dodecin-like topology. Dodecin flavoprotein is a small dodecameric flavin-binding protein from Halobacterium salinarium (Halobacterium halobium) that contains two flavins stacked in a single binding pocket between two tryptophan residues to form an aromatic tetrade []. Dodecin binds riboflavin, although it appears to have a broad specificity for flavins. Lumichrome, a molecule associated with flavin metabolism, appears to be a ligand of dodecin, which could act as a waste-trapping device. ; PDB: 2VYX_L 2DEG_F 2V18_K 2V19_D 2UX9_B 2CZ8_E 2V21_F 2CC8_A 2CCB_A 2VX9_A ....
Probab=33.04 E-value=29 Score=25.62 Aligned_cols=17 Identities=29% Similarity=0.503 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHhccC
Q 039845 91 MEWESQALLAIEKASDE 107 (210)
Q Consensus 91 ~~We~~A~LAIekas~k 107 (210)
+.|++|+..||++|++.
T Consensus 14 ~S~edAv~~Av~~A~kT 30 (66)
T PF07311_consen 14 KSWEDAVQNAVARASKT 30 (66)
T ss_dssp SHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHhhc
Confidence 57999999999999864
No 7
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=32.27 E-value=1.1e+02 Score=22.66 Aligned_cols=47 Identities=13% Similarity=0.070 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHHhccCCchhHHHHHHHHHHHHHHHH---------hcCCChhhHHHHHH
Q 039845 89 VRMEWESQALLAIEKASDENPSRKQLCLAKEASILLMVA---------HDGFSISELCLRYL 141 (210)
Q Consensus 89 Vr~~We~~A~LAIekas~knl~kK~~~vAk~AaiLLmva---------~DgFt~sElCLHyL 141 (210)
+..+|-..+...++..+..++ .+++|.+|+.++ .|..|..|+|-.+-
T Consensus 3 ~~~g~t~~~~~~~e~l~~~~l------~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g 58 (95)
T TIGR01610 3 LSNGYTRMANELQEALPGADL------SGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTG 58 (95)
T ss_pred cccchhhhhHHHHHHHHhCCC------CHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHC
Confidence 455666667777766554443 457788888776 78899999997665
No 8
>PF00954 S_locus_glycop: S-locus glycoprotein family; InterPro: IPR000858 In Brassicaceae, self-incompatible plants have a self/non-self recognition system, which involves the inability of flowering plants to achieve self-fertilisation. This is sporophytically controlled by multiple alleles at a single locus (S). There are a total of 50 different S alleles in Brassica oleracea. S-locus glycoproteins, as well as S-receptor kinases, are in linkage with the S-alleles []. Most of the proteins within this family contain apple-like domain (IPR003609 from INTERPRO), which is predicted to possess protein- and/or carbohydrate-binding functions.; GO: 0048544 recognition of pollen
Probab=32.14 E-value=21 Score=26.53 Aligned_cols=15 Identities=33% Similarity=0.786 Sum_probs=12.5
Q ss_pred ccCCCCCccccCccc
Q 039845 182 AIDNPSTLYPCNCIP 196 (210)
Q Consensus 182 ~~~~~~~~~~~~~~~ 196 (210)
++||..+...|+|+|
T Consensus 90 g~C~~~~~~~C~Cl~ 104 (110)
T PF00954_consen 90 GICNSNNSPKCSCLP 104 (110)
T ss_pred cEeCCCCCCceECCC
Confidence 678888778899986
No 9
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=31.28 E-value=45 Score=26.22 Aligned_cols=26 Identities=35% Similarity=0.535 Sum_probs=18.8
Q ss_pred hHHHHHHHHHHhhhcCCccccCCCCCccccCcc
Q 039845 163 SLIRYLGKWLKKFETFPQIAIDNPSTLYPCNCI 195 (210)
Q Consensus 163 ~LiRYL~KWl~KY~rFpqa~~~~~~~~~~~~~~ 195 (210)
+=+..|.++|++.++- .-+--||||+
T Consensus 105 eele~L~~li~~~~~~-------~~~~~~~~~~ 130 (130)
T TIGR02698 105 TDIEKLEKLLSEKKST-------AVEEVPCNCI 130 (130)
T ss_pred HHHHHHHHHHHhcccC-------CCccccCCCC
Confidence 4467888899887653 3456799996
No 10
>TIGR03342 dsrC_tusE_dsvC sulfur relay protein, TusE/DsrC/DsvC family. Members of this protein family may be described as TusE, a partner to TusBCD in a sulfur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Other members are DsrC, a functionally similar protein in species where the sulfur relay system exists primarily for sulfur metabolism rather than tRNA base modification. Some members of this family are known explicitly as the gamma subunit of sulfite reductases.
Probab=25.36 E-value=61 Score=25.78 Aligned_cols=21 Identities=14% Similarity=0.490 Sum_probs=16.2
Q ss_pred hhHHHHHHHHHHhhhcCCccc
Q 039845 162 MSLIRYLGKWLKKFETFPQIA 182 (210)
Q Consensus 162 ~~LiRYL~KWl~KY~rFpqa~ 182 (210)
.+.|+|++.+-.+|...|..+
T Consensus 43 w~vI~~lR~~y~e~~~~P~~R 63 (108)
T TIGR03342 43 WEVINFLRDFYAEYNISPAVR 63 (108)
T ss_pred HHHHHHHHHHHHHHCCCCcHH
Confidence 678888888888888877654
No 11
>TIGR03707 PPK2_P_aer polyphosphate kinase 2, PA0141 family. Members of this protein family are designated polyphosphate kinase 2 (PPK2) after the characterized protein in Pseudomonas aeruginosa. This family comprises one of three well-separated clades in the larger family described by Pfam model pfam03976. PA0141 from this family has been shown capable of operating in reverse, with GDP preferred (over ADP) as a substrate, producing GTP (or ATP) by transfer of a phosphate residue from polyphosphate. Most species with a member of this family also encode a polyphosphate kinase 1 (PPK1).
Probab=24.89 E-value=1.3e+02 Score=26.45 Aligned_cols=102 Identities=18% Similarity=0.249 Sum_probs=61.6
Q ss_pred CcchhhhHhhhhhchhhhHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHhhccchh-hhhhHHHHH----HHH-----
Q 039845 24 SGYTRGLIEKVGFLMGRDVASLVLEACIRLRIWELVETLIVHGLLLCILKYFLCPLQD-AYGSMGSVR----MEW----- 93 (210)
Q Consensus 24 ~~y~rvLieK~G~~mgRdv~~lVl~~~vsL~~WelVe~Li~~gllL~iLk~FL~psk~-ay~sm~~Vr----~~W----- 93 (210)
|=|.++|++++.-.++...-..-++ +|=+-=+.|..+|. .|+||||..|++ --+-+.... +.|
T Consensus 97 SwY~~~lv~rv~~~~~~~~~~~~~~-----~I~~FEr~L~~~G~--~IlKfflhIsk~eQ~kRl~~r~~~p~k~Wk~~~~ 169 (230)
T TIGR03707 97 SWYNRAGVERVMGFCTDEEYEEFLR-----QVPEFERMLVRDGI--HLFKYWLSVSREEQLRRFKARIDDPLKQWKLSPM 169 (230)
T ss_pred chhhhHHHHHhcCCCCHHHHHHHHH-----HHHHHHHHHHHCCC--EEEEEEEECCHHHHHHHHHHHhcCCcccccCCHH
Confidence 5699999999987777665444443 22223356778885 578999999944 344444332 333
Q ss_pred --------H---HHHHHHHHHhccCC--------chhHHHHHHHHHHHHHHHHhcCCC
Q 039845 94 --------E---SQALLAIEKASDEN--------PSRKQLCLAKEASILLMVAHDGFS 132 (210)
Q Consensus 94 --------e---~~A~LAIekas~kn--------l~kK~~~vAk~AaiLLmva~DgFt 132 (210)
. +++-.+|++.+... .-|++..+.+.-.|+=.+-+|++.
T Consensus 170 D~~~~~~yd~y~~a~e~~l~~T~t~~APW~iI~a~dk~~a~l~v~~~i~~~l~~~~~~ 227 (230)
T TIGR03707 170 DLASLDRWDDYSRAKDEMFARTDTPEAPWTVVRSDDKKRARLNAIRHILSRLDYEGKD 227 (230)
T ss_pred HHHHHHhHHHHHHHHHHHHHhcCCCCCCeEEEcCCCHHHHHHHHHHHHHHhCCCcCCC
Confidence 2 23344445544432 345566676666777777777764
No 12
>COG2920 DsrC Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]
Probab=24.40 E-value=66 Score=26.44 Aligned_cols=44 Identities=20% Similarity=0.385 Sum_probs=33.0
Q ss_pred HHHhcCCcchhHHHHhhhccch------hhHHHHHHHHHHhhhcCCcccc
Q 039845 140 YLLASSNIDEVMLSSAISNLNG------MSLIRYLGKWLKKFETFPQIAI 183 (210)
Q Consensus 140 yL~AS~nvDe~vL~aaVseLdg------~~LiRYL~KWl~KY~rFpqa~~ 183 (210)
||..+.+-||-|-.++-.+.++ -.++||+++.-.+|..=|-.+|
T Consensus 18 yL~~~~dW~E~vAe~lA~~e~i~LT~eHWevv~fvR~fy~ef~tsPaiRM 67 (111)
T COG2920 18 YLKDSEDWSEKVAEALAEREGIELTEEHWEVVRFVREFYEEFNTSPAIRM 67 (111)
T ss_pred hhcChhhhCHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHCCCchHHH
Confidence 6777887888775544444444 7899999999999988887766
No 13
>PRK11508 sulfur transfer protein TusE; Provisional
Probab=21.70 E-value=78 Score=25.27 Aligned_cols=21 Identities=24% Similarity=0.577 Sum_probs=15.2
Q ss_pred hhHHHHHHHHHHhhhcCCccc
Q 039845 162 MSLIRYLGKWLKKFETFPQIA 182 (210)
Q Consensus 162 ~~LiRYL~KWl~KY~rFpqa~ 182 (210)
.+.|+||+.+-.+|...|..+
T Consensus 44 W~VI~~lR~~y~e~~~~P~~R 64 (109)
T PRK11508 44 WEVVRFVRDFYLEFNTSPAIR 64 (109)
T ss_pred HHHHHHHHHHHHHHCCCCcHH
Confidence 667888887777777777643
No 14
>PF04051 TRAPP: Transport protein particle (TRAPP) component; InterPro: IPR007194 TRAPP plays a key role in the targeting and/or fusion of ER-to-Golgi transport vesicles with their acceptor compartment. TRAPP is a large multimeric protein that contains at least 10 subunits. This family contains many TRAPP family proteins. The Bet3 subunit is one of the better characterised TRAPP proteins and has a dimeric structure [] with hydrophobic channels. The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues. Bet3 is proposed to localise TRAPP to the Golgi [].; PDB: 2J3R_A 1WC9_A 2J3T_A 2PWN_A 2J3W_E 1WC8_A 3CUE_N 2C0J_B 3KXC_A 2CFH_A ....
Probab=21.52 E-value=59 Score=25.83 Aligned_cols=34 Identities=21% Similarity=0.401 Sum_probs=23.3
Q ss_pred hhHhhhhhchhhhHHHHHHHh-hhhhhhHHHHHHH
Q 039845 29 GLIEKVGFLMGRDVASLVLEA-CIRLRIWELVETL 62 (210)
Q Consensus 29 vLieK~G~~mgRdv~~lVl~~-~vsL~~WelVe~L 62 (210)
--+|++|+.||.++++....- -.+-.+.+..+++
T Consensus 24 ~~Le~~G~~vG~rl~E~~~~~~~~~~r~~~~~~~~ 58 (152)
T PF04051_consen 24 KRLERMGYNVGQRLAERLLRRRKNSPRFTDILDIL 58 (152)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCSSTCSTSSHHHHH
T ss_pred HHHHHHHHHHhHHHHHHHHHHhccCcccCCHHHHH
Confidence 344999999999999988766 3334455544443
No 15
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=21.12 E-value=27 Score=28.65 Aligned_cols=20 Identities=45% Similarity=0.732 Sum_probs=15.8
Q ss_pred eeCCCCcchhhhHhhhhhchhh
Q 039845 19 INRSDSGYTRGLIEKVGFLMGR 40 (210)
Q Consensus 19 ~~~s~~~y~rvLieK~G~~mgR 40 (210)
.-.-.+|||||| |+||--|-
T Consensus 87 y~~R~GGYtRIl--K~g~R~GD 106 (116)
T COG0203 87 YAERNGGYTRIL--KLGFRRGD 106 (116)
T ss_pred hcCCCCCeeEEE--ecCCCCCC
Confidence 346678999999 89987664
No 16
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=21.12 E-value=1.6e+02 Score=18.24 Aligned_cols=25 Identities=24% Similarity=0.339 Sum_probs=16.1
Q ss_pred HHHHhcCCChhhHHHHHHHhcC-Ccchh
Q 039845 124 LMVAHDGFSISELCLRYLLASS-NIDEV 150 (210)
Q Consensus 124 Lmva~DgFt~sElCLHyL~AS~-nvDe~ 150 (210)
.++.- ||+-. .|...|.+++ |+|.+
T Consensus 8 ~L~~m-Gf~~~-~~~~AL~~~~~nve~A 33 (37)
T PF00627_consen 8 QLMEM-GFSRE-QAREALRACNGNVERA 33 (37)
T ss_dssp HHHHH-TS-HH-HHHHHHHHTTTSHHHH
T ss_pred HHHHc-CCCHH-HHHHHHHHcCCCHHHH
Confidence 33444 88755 9999998887 45444
No 17
>PF05186 Dpy-30: Dpy-30 motif; InterPro: IPR007858 This motif is about 40 residues long and is probably formed of two alpha-helices. It is found in the Dpy-30 proteins, hence the motifs name. Dpy-30 from Caenorhabditis elegans is an essential component of dosage compensation machinery and loss of dpy-30 activity results in XX-specific lethality; in XO animals, Dpy-30 is required for developmental processes other than dosage compensation []. In yeast, the homologue of DPY-30, Saf19p, functions as part of the Set1 complex that is necessary for the methylation of histone H3 at lysine residue 4; Set1 is a key part of epigenetic developmental control []. There is also a human homologue of Dpy-30 []. This Dpy-30 region may be a dimerisation motif analogous that found in the cAMP-dependent protein kinase regulator, type II PKA, R subunit IPR003117 from INTERPRO.; PDB: 3G36_D.
Probab=21.06 E-value=78 Score=21.17 Aligned_cols=15 Identities=27% Similarity=0.476 Sum_probs=12.2
Q ss_pred hhHHHHHHHHHHhhh
Q 039845 162 MSLIRYLGKWLKKFE 176 (210)
Q Consensus 162 ~~LiRYL~KWl~KY~ 176 (210)
.+=++||+.||-++.
T Consensus 27 ~DPi~~La~~Ll~~~ 41 (42)
T PF05186_consen 27 EDPIEFLAEYLLKHN 41 (42)
T ss_dssp SSHHHHHHHHHHHHG
T ss_pred CChHHHHHHHHHHhC
Confidence 566889999998875
No 18
>PF02044 Bombesin: Bombesin-like peptide; InterPro: IPR000874 Bombesin-like peptides comprise a large family of peptides which were initially isolated from amphibian skin, where they stimulate smooth muscle contraction. They were later found to be widely distributed in mammalian neural and endocrine cells. The amphibian peptides which belong to this family are currently classified into three subfamilies [, ]; the Bombesin group, which includes bombesin and alytesin; the Ranatensin group, which includes ranatensins, litorin, and Rohdei litorin; and the Phyllolitorin group, which includes Leu(8)- and Phe(8)-phyllolitorins. In mammals and birds two categories of bombesin-like peptides are known [, ], gastrin-releasing peptide (GRP), which stimulates the release of gastrin as well as other gastrointestinal hormones, and neuromedin B (NMB), a neuropeptide whose function is not yet clear. Bombesin-like peptides, like many other active peptides, are synthesized as larger protein precursors that are enzymatically converted to their mature forms. The final peptides are eight to fourteen residues long.; GO: 0007218 neuropeptide signaling pathway; PDB: 1C9A_A 1C98_A.
Probab=21.00 E-value=34 Score=19.20 Aligned_cols=9 Identities=44% Similarity=0.947 Sum_probs=3.9
Q ss_pred hhhhchhhh
Q 039845 33 KVGFLMGRD 41 (210)
Q Consensus 33 K~G~~mgRd 41 (210)
-+|.+||++
T Consensus 5 AvGh~Mgkk 13 (14)
T PF02044_consen 5 AVGHFMGKK 13 (14)
T ss_dssp HHHCT----
T ss_pred ceeeeeccC
Confidence 478999986
No 19
>PF04358 DsrC: DsrC like protein; InterPro: IPR007453 DsrC (P45573 from SWISSPROT) has been observed to co-purify with Desulphovibrio vulgaris dissimilatory sulphite reductase []. However, DsrC appears to be only loosely associated to the sulphite reductase, which suggests that it may not be an integral part of the dissimilatory sulphite reductase. Many proteins in this entry are found in organisms such as Escherichia coli and Haemophilus influenzae which do not contain dissimilatory sulphite reductases but can synthesise assimilatory sirohaem sulphite and nitrite reductases. It is speculated that DsrC may be involved in the assembly, folding or stabilisation of sirohaem proteins []. The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds []. Also included in this entry is TusE, a partner to TusBCD in a sulphur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Many proteins in this entry are annotated as the third (gamma) subunit of dissimilatory sulphite reductase ; PDB: 2V4J_F 2A5W_C 1SAU_A 1JI8_A 1YX3_A.
Probab=20.98 E-value=84 Score=24.83 Aligned_cols=30 Identities=23% Similarity=0.562 Sum_probs=19.9
Q ss_pred HHhhhccch-------hhHHHHHHHHHHhhhcCCccc
Q 039845 153 SSAISNLNG-------MSLIRYLGKWLKKFETFPQIA 182 (210)
Q Consensus 153 ~aaVseLdg-------~~LiRYL~KWl~KY~rFpqa~ 182 (210)
+.++|+-+| .++|+||++.-.+|...|..+
T Consensus 28 A~~lA~~egI~Ltd~HW~vI~flR~~y~~~~~~P~~R 64 (109)
T PF04358_consen 28 AEALAKEEGIELTDEHWEVIRFLRDYYQEYGVSPAIR 64 (109)
T ss_dssp HHHHHHCTT-S--HHHHHHHHHHHHHHHHHSS---HH
T ss_pred HHHHHHHcCCCCCHHHHHHHHHHHHHHHHHCCCCcHH
Confidence 445555555 778999999988888888654
Done!