Query 014840
Match_columns 417
No_of_seqs 182 out of 239
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 09:01:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014840.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014840hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2673 Uncharacterized conser 100.0 3.2E-47 6.8E-52 385.8 10.7 265 46-344 55-321 (485)
2 KOG2330 Splicing factor 3b, su 99.9 5.9E-24 1.3E-28 215.7 6.6 82 166-290 251-333 (500)
3 smart00581 PSP proline-rich do 99.9 1.7E-23 3.8E-28 160.5 5.7 42 182-223 1-42 (54)
4 PF04046 PSP: PSP; InterPro: 99.8 3.6E-21 7.9E-26 144.7 5.1 38 186-223 1-38 (48)
5 COG5182 CUS1 Splicing factor 3 99.8 8.1E-19 1.8E-23 174.8 6.2 81 166-289 258-341 (429)
6 KOG2673 Uncharacterized conser 98.6 1.7E-08 3.7E-13 104.6 3.5 137 138-277 1-141 (485)
7 PF00098 zf-CCHC: Zinc knuckle 97.3 0.00011 2.4E-09 45.4 1.5 18 126-143 1-18 (18)
8 PF14392 zf-CCHC_4: Zinc knuck 91.7 0.062 1.3E-06 40.2 0.5 19 125-143 31-49 (49)
9 smart00343 ZnF_C2HC zinc finge 90.6 0.12 2.7E-06 33.7 1.0 18 127-144 1-18 (26)
10 COG5082 AIR1 Arginine methyltr 90.2 0.14 3.1E-06 48.9 1.4 19 124-142 59-77 (190)
11 PF13696 zf-CCHC_2: Zinc knuck 87.7 0.25 5.5E-06 35.1 1.0 20 125-144 8-27 (32)
12 PTZ00368 universal minicircle 86.2 0.59 1.3E-05 41.4 2.7 22 125-146 27-48 (148)
13 PTZ00368 universal minicircle 85.8 0.42 9E-06 42.3 1.5 20 126-145 1-20 (148)
14 PF15288 zf-CCHC_6: Zinc knuck 77.0 1.5 3.3E-05 32.7 1.5 20 126-145 2-23 (40)
15 COG5082 AIR1 Arginine methyltr 73.2 1.7 3.6E-05 41.8 1.2 18 125-142 97-114 (190)
16 PF13917 zf-CCHC_3: Zinc knuck 70.8 2.7 5.8E-05 31.5 1.5 19 125-143 4-22 (42)
17 KOG4400 E3 ubiquitin ligase in 69.6 2.2 4.8E-05 41.2 1.1 19 126-144 144-162 (261)
18 KOG4400 E3 ubiquitin ligase in 63.0 3.4 7.3E-05 40.0 1.0 23 125-147 92-114 (261)
19 TIGR03290 CoB_CoM_SS_C CoB--Co 56.2 3.9 8.4E-05 36.2 0.1 76 126-210 46-122 (144)
20 PF12353 eIF3g: Eukaryotic tra 45.6 12 0.00025 33.6 1.4 19 124-143 105-123 (128)
21 KOG2044 5'-3' exonuclease HKE1 39.8 12 0.00026 42.9 0.8 50 95-144 218-279 (931)
22 KOG0119 Splicing factor 1/bran 35.3 19 0.0004 39.5 1.2 19 126-144 286-304 (554)
23 COG5222 Uncharacterized conser 32.7 23 0.0005 36.9 1.4 23 125-147 176-198 (427)
24 KOG0119 Splicing factor 1/bran 32.2 12 0.00025 41.0 -0.8 20 125-144 261-280 (554)
25 PRK02220 4-oxalocrotonate taut 29.5 83 0.0018 23.4 3.6 24 8-31 2-26 (61)
26 PF15127 DUF4565: Protein of u 29.0 48 0.001 28.8 2.5 28 12-39 53-80 (91)
27 KOG0109 RNA-binding protein LA 28.1 29 0.00064 36.0 1.2 25 124-148 159-183 (346)
28 smart00647 IBR In Between Ring 26.7 38 0.00081 25.1 1.3 17 125-141 48-64 (64)
29 KOG2560 RNA splicing factor - 26.1 15 0.00033 39.9 -1.2 19 124-142 111-129 (529)
30 PF05515 Viral_NABP: Viral nuc 25.6 47 0.001 30.3 2.0 18 125-142 62-79 (124)
31 TIGR02663 nifX nitrogen fixati 24.5 31 0.00067 29.7 0.6 26 187-212 93-118 (119)
32 PRK02289 4-oxalocrotonate taut 24.0 1.3E+02 0.0028 22.9 3.8 24 8-31 2-26 (60)
33 COG4866 Uncharacterized conser 22.3 64 0.0014 33.0 2.3 29 11-39 151-179 (294)
34 PF14787 zf-CCHC_5: GAG-polypr 20.5 56 0.0012 24.1 1.1 21 126-146 3-23 (36)
No 1
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=100.00 E-value=3.2e-47 Score=385.85 Aligned_cols=265 Identities=34% Similarity=0.567 Sum_probs=216.8
Q ss_pred CCccccccceeeecceeccCCCCCceeeEEeccccccccCCCCCCCCCCCCccccccccccccCCCCCCcCCCcccccCC
Q 014840 46 PNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDA 125 (417)
Q Consensus 46 ~~e~~e~G~~~~fpa~~v~~~~~~a~sF~~D~~~~~~~n~~~~~~~~~~VPlYdr~~~~~L~s~Dg~s~~e~~~Ei~~~~ 125 (417)
..+++++++.+|+| +++++.+...++||++++....--++..+.+.. + ||.++.+|.+.+++.+++++..|.+ .
T Consensus 55 qqd~l~~te~a~~~-fr~~~qe~~t~s~wl~~~~~ek~gedl~~~e~~-t---dr~~a~~l~sq~~s~tvek~~~v~~-~ 128 (485)
T KOG2673|consen 55 QQDLLGVTEKAFPP-FRYRMQELGTPSFWLKNAELEKSGEDLYLGEDS-T---DRETAVGLISQNKSVTVEKSKLVNK-C 128 (485)
T ss_pred HHHHhhcccccccc-hhhhHHhhcCchhhhhhcccccChhhhcccccc-c---cccceecccccccchhhhhhhhhcc-C
Confidence 56788888888888 999999999999999999888666666666554 2 9999999999999999998877654 4
Q ss_pred CceecCCCCCCCCCCCCCccCHHHHHHHHHHHHHhhccCCCCCCCceeeecccCccccCCCCCcCCHHHHHHhCCCCCCC
Q 014840 126 SRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDP 205 (417)
Q Consensus 126 ~~CFNCG~~~HsLrdCP~PRd~a~In~~Rk~f~~~r~q~~~sr~GdrYYe~k~e~k~~~~kPG~LS~eLReALGm~~~~p 205 (417)
-.|||||++.|+|+|||+|+|+++|+.+||+++..++| |||.....++++|||||+||.+||.|||+.+++|
T Consensus 129 ~~CFNC~g~~hsLrdC~rp~d~s~I~r~rkek~~~rnq--------ry~~~teq~re~h~KPG~lS~~~R~al~l~~~d~ 200 (485)
T KOG2673|consen 129 DPCFNCGGTPHSLRDCPRPFDFSRIQRARKEKMVFRNQ--------RYYQDTEQGREDHFKPGVLSGNTRSALGLSPGDP 200 (485)
T ss_pred ccccccCCCCCccccCCCccccHHHHHHHHhhccccce--------eeeeecchhhhcccCCcccchhHHHhhcCCCCCc
Confidence 55999999999999999999999999999999887774 8998876669999999999999999999999999
Q ss_pred hHHHHHHHhcCCCCCCCCCCCCCCCCCceeecCCCccCCCCCcchhccCCCCCCCeeeeecCCCCCC-CCCCcchhcccc
Q 014840 206 PPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPASKRKMTTEFPGINAP-IPENADERLWAA 284 (417)
Q Consensus 206 PPWL~~Mr~~GyPPgYp~~a~~~q~SGl~IF~Dg~~~~~~EDgEi~e~~~~~~~~kk~V~fPGFNaP-iP~g~d~~~w~~ 284 (417)
|+|+||||++||||||+.++ ..+.+||+||+... .++|.|+.....++++.+|+|.|||||.+ .|++..++.|..
T Consensus 201 P~~~yRMR~lGYPPg~L~~s-~~e~s~i~if~eet---~~~dee~ese~PP~~~~~K~~~f~gfn~~~~p~~~~e~~ke~ 276 (485)
T KOG2673|consen 201 PEWKYRMRRLGYPPGYLRKS-DMEVSGIKIFSEET---FQFDEELESETPPEPQGTKPVVFPGFNPKGTPPNDREDSKEA 276 (485)
T ss_pred hHHHHHHhhccCCchhhhhh-hcccccceeecccc---cccCcccCCCCCCCCCCCCCcccCCCCCCCCCCCChhhcccc
Confidence 99999999999999999977 67899999997222 22223333334678899999999999999 999999888886
Q ss_pred CCCCCCcccccccccccCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCC-CCC
Q 014840 285 RPSSSDSSRDRSHHRLNHHSESISRGRYHEQRWSRDYRDDGPPGVDPVSSYPPRYGG-YDY 344 (417)
Q Consensus 285 ~P~~~~~~r~~~~~~~~~~~e~~~r~~~~~~r~~~~~rd~gppg~~~~~s~~pr~~~-~d~ 344 (417)
+ .++|+.--+.. .-.-...++++++|.|+++..++++++|. +|+
T Consensus 277 ~---r~~s~s~~q~~-------------l~~~~l~~k~~dl~~~~e~s~~~~~~~~t~~D~ 321 (485)
T KOG2673|consen 277 P---RDASCSVDQDA-------------LTLSRLEKKQRDLPAGLEQSESAPSDSGTEVDD 321 (485)
T ss_pred c---chhhhhhhHHH-------------hhhhHHHHHhhhcccccccccCCCcccCCcccc
Confidence 2 34443211111 11111237889999999999999999998 666
No 2
>KOG2330 consensus Splicing factor 3b, subunit 2 [RNA processing and modification]
Probab=99.89 E-value=5.9e-24 Score=215.69 Aligned_cols=82 Identities=33% Similarity=0.638 Sum_probs=76.0
Q ss_pred CCCCCceeeecc-cCccccCCCCCcCCHHHHHHhCCCCCCChHHHHHHHhcCCCCCCCCCCCCCCCCCceeecCCCccCC
Q 014840 166 ASRNPMRYYQNS-AGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEG 244 (417)
Q Consensus 166 ~sr~GdrYYe~k-~e~k~~~~kPG~LS~eLReALGm~~~~pPPWL~~Mr~~GyPPgYp~~a~~~q~SGl~IF~Dg~~~~~ 244 (417)
-+.+|+.||+++ .+..+++.+||.||+|||.||||+.+.|||||++||++|+|||||+
T Consensus 251 lt~~Ge~yyegke~e~~~k~k~PG~iS~eLr~aLgmp~g~pPPWl~aMqryGpPpsYPd--------------------- 309 (500)
T KOG2330|consen 251 LTKFGELYYEGKELEAMVKEKKPGDISDELRIALGMPVGTPPPWLIAMQRYGPPPSYPD--------------------- 309 (500)
T ss_pred eeecceeeecchhHHHHHhhcCccchhHHHHHHhCCCCCCCChHHHHhhhcCCCCCCCc---------------------
Confidence 468999999998 5677899999999999999999999999999999999999999996
Q ss_pred CCCcchhccCCCCCCCeeeeecCCCCCCCCCCcchhccccCCCCCC
Q 014840 245 QEDGEIIETGRPASKRKMTTEFPGINAPIPENADERLWAARPSSSD 290 (417)
Q Consensus 245 ~EDgEi~e~~~~~~~~kk~V~fPGFNaPiP~g~d~~~w~~~P~~~~ 290 (417)
++|||+|+|||+|+. ||++|++|.
T Consensus 310 -------------------lkIpGLNapIPeg~s---~Gyh~gGWG 333 (500)
T KOG2330|consen 310 -------------------LKIPGLNAPIPEGCS---FGYHAGGWG 333 (500)
T ss_pred -------------------ccCCCCCCCCCcccc---cccccCCCc
Confidence 789999999999998 888888773
No 3
>smart00581 PSP proline-rich domain in spliceosome associated proteins.
Probab=99.88 E-value=1.7e-23 Score=160.47 Aligned_cols=42 Identities=52% Similarity=1.112 Sum_probs=40.8
Q ss_pred ccCCCCCcCCHHHHHHhCCCCCCChHHHHHHHhcCCCCCCCC
Q 014840 182 YDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLD 223 (417)
Q Consensus 182 ~~~~kPG~LS~eLReALGm~~~~pPPWL~~Mr~~GyPPgYp~ 223 (417)
|++||||+||++||+||||.++++||||++||++|||||||+
T Consensus 1 ~~~~kPG~lS~~LR~ALG~~~~~pPPWl~~Mq~~G~PPsYp~ 42 (54)
T smart00581 1 FKHFKPGRISDELREALGLPPGQPPPWLYRMRRLGYPPGYPR 42 (54)
T ss_pred CCCccCCcCCHHHHHHcCCCCCCCChHHHHHHHHCCCCCCcc
Confidence 578999999999999999999999999999999999999996
No 4
>PF04046 PSP: PSP; InterPro: IPR006568 PSP is a proline-rich domain of unknown function found in spliceosome associated proteins.
Probab=99.83 E-value=3.6e-21 Score=144.68 Aligned_cols=38 Identities=66% Similarity=1.307 Sum_probs=37.0
Q ss_pred CCCcCCHHHHHHhCCCCCCChHHHHHHHhcCCCCCCCC
Q 014840 186 RPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLD 223 (417)
Q Consensus 186 kPG~LS~eLReALGm~~~~pPPWL~~Mr~~GyPPgYp~ 223 (417)
|||+||++||+||||.++++||||++||++||||||++
T Consensus 1 kPG~lS~~LR~ALg~~~~~~PPwl~~M~~~G~PP~y~~ 38 (48)
T PF04046_consen 1 KPGKLSDELREALGMQENDPPPWLYRMRRLGYPPGYPD 38 (48)
T ss_pred CCcccCHHHHHHcCCCCCCCChHHHHHHhcCCCCCCcc
Confidence 79999999999999999999999999999999999975
No 5
>COG5182 CUS1 Splicing factor 3b, subunit 2 [RNA processing and modification]
Probab=99.75 E-value=8.1e-19 Score=174.76 Aligned_cols=81 Identities=38% Similarity=0.667 Sum_probs=70.3
Q ss_pred CCCCCceeeecc-cCccccCCCCCcCCHHHHHHhCCCCCCChHHHHHHHhcCCCCCCCCCCCCCCCCCceeecCCCccCC
Q 014840 166 ASRNPMRYYQNS-AGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEG 244 (417)
Q Consensus 166 ~sr~GdrYYe~k-~e~k~~~~kPG~LS~eLReALGm~~~~pPPWL~~Mr~~GyPPgYp~~a~~~q~SGl~IF~Dg~~~~~ 244 (417)
-+.||+.||+++ .....++.+||.||+|||+||||.+++|||||.+||++|+|||||+
T Consensus 258 L~~fGe~y~e~~n~~~~vk~krPG~IS~eLrealgi~~g~pPPWlf~Mq~~G~PpsYPD--------------------- 316 (429)
T COG5182 258 LSKFGEFYEEVDNDYRFVKKKRPGAISAELREALGIDSGTPPPWLFNMQKHGMPPSYPD--------------------- 316 (429)
T ss_pred cccccceeeccchHHHHHhccCCcchHHHHHHHhCCCCCCCChHHHhhhhcCCCCCCcc---------------------
Confidence 468999999998 4445689999999999999999999999999999999999999996
Q ss_pred CCCcchhccCCCCCCCeeeeecCCCC-CCCC-CCcchhccccCCCCC
Q 014840 245 QEDGEIIETGRPASKRKMTTEFPGIN-APIP-ENADERLWAARPSSS 289 (417)
Q Consensus 245 ~EDgEi~e~~~~~~~~kk~V~fPGFN-aPiP-~g~d~~~w~~~P~~~ 289 (417)
++|||+| +++| +|.- ||+.|+.|
T Consensus 317 -------------------lkIpGlNW~~~pL~Gdv---yG~~~p~~ 341 (429)
T COG5182 317 -------------------LKIPGLNWAPIPLEGDV---YGYQPPGW 341 (429)
T ss_pred -------------------ccCCCCCCCCccccccc---ccccCCCc
Confidence 7899999 8888 5544 67666655
No 6
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=98.63 E-value=1.7e-08 Score=104.64 Aligned_cols=137 Identities=22% Similarity=0.358 Sum_probs=102.5
Q ss_pred CCCCCCccCHHHHHHHHHHHHHhhccCCCCCCCceeeecccCccccCCCCCcCCHHHHHHhCCCCCCChHHHHHHHhcCC
Q 014840 138 LKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGY 217 (417)
Q Consensus 138 LrdCP~PRd~a~In~~Rk~f~~~r~q~~~sr~GdrYYe~k~e~k~~~~kPG~LS~eLReALGm~~~~pPPWL~~Mr~~Gy 217 (417)
+++||.|+| ++|+..|.+++.+-..-...-++.+++..........+.+|.|| ++.++|+-.+.+.+|++++||++|+
T Consensus 1 ~~~cp~~~n-~~i~~~~d~~~e~~~eis~q~~~e~~~d~~~d~~~~r~esg~i~-~qqd~l~~te~a~~~fr~~~qe~~t 78 (485)
T KOG2673|consen 1 MKDCPMPRN-ARISEKRDEYMEACGEISNQNFQERLHDELVDERRGRFESGVIS-EQQDLLGVTEKAFPPFRYRMQELGT 78 (485)
T ss_pred CCcCCCccc-cccCcchhHHHHHhhhcCCcchhhhccchhhhhhhccccccccc-hHHHHhhcccccccchhhhHHhhcC
Confidence 579999999 99999999998764332333456788877777888999999999 8899999999999999999999999
Q ss_pred CCCCCCCCCCCCCCCceeecCCCc-cCCCCCcchhccCCCCCCCeeeeecC--CCC-CCCCCCc
Q 014840 218 PPGYLDSEDDDQPSGITIYADGEI-KEGQEDGEIIETGRPASKRKMTTEFP--GIN-APIPENA 277 (417)
Q Consensus 218 PPgYp~~a~~~q~SGl~IF~Dg~~-~~~~EDgEi~e~~~~~~~~kk~V~fP--GFN-aPiP~g~ 277 (417)
|+.|++.+. .+.+|..||.-... +-..+.|.+..+.....+.++.|.++ =|| .-.|.++
T Consensus 79 ~s~wl~~~~-~ek~gedl~~~e~~tdr~~a~~l~sq~~s~tvek~~~v~~~~~CFNC~g~~hsL 141 (485)
T KOG2673|consen 79 PSFWLKNAE-LEKSGEDLYLGEDSTDRETAVGLISQNKSVTVEKSKLVNKCDPCFNCGGTPHSL 141 (485)
T ss_pred chhhhhhcc-cccChhhhccccccccccceecccccccchhhhhhhhhccCccccccCCCCCcc
Confidence 999998544 45788888842222 22456666655555555566666666 444 4456655
No 7
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=97.32 E-value=0.00011 Score=45.43 Aligned_cols=18 Identities=50% Similarity=1.315 Sum_probs=16.5
Q ss_pred CceecCCCCCCCCCCCCC
Q 014840 126 SRCFNCGSYSHSLKECPK 143 (417)
Q Consensus 126 ~~CFNCG~~~HsLrdCP~ 143 (417)
..|||||..+|..++||+
T Consensus 1 ~~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 1 RKCFNCGEPGHIARDCPK 18 (18)
T ss_dssp SBCTTTSCSSSCGCTSSS
T ss_pred CcCcCCCCcCcccccCcc
Confidence 379999999999999995
No 8
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=91.74 E-value=0.062 Score=40.18 Aligned_cols=19 Identities=58% Similarity=1.183 Sum_probs=17.5
Q ss_pred CCceecCCCCCCCCCCCCC
Q 014840 125 ASRCFNCGSYSHSLKECPK 143 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~ 143 (417)
...||+||..+|..++||+
T Consensus 31 p~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ChhhcCCCCcCcCHhHcCC
Confidence 4789999999999999985
No 9
>smart00343 ZnF_C2HC zinc finger.
Probab=90.63 E-value=0.12 Score=33.68 Aligned_cols=18 Identities=44% Similarity=1.309 Sum_probs=16.1
Q ss_pred ceecCCCCCCCCCCCCCc
Q 014840 127 RCFNCGSYSHSLKECPKP 144 (417)
Q Consensus 127 ~CFNCG~~~HsLrdCP~P 144 (417)
.||+||..+|..++||..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 499999999999999844
No 10
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=90.20 E-value=0.14 Score=48.92 Aligned_cols=19 Identities=42% Similarity=1.167 Sum_probs=17.8
Q ss_pred CCCceecCCCCCCCCCCCC
Q 014840 124 DASRCFNCGSYSHSLKECP 142 (417)
Q Consensus 124 ~~~~CFNCG~~~HsLrdCP 142 (417)
....|||||+.+|..+|||
T Consensus 59 ~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 59 ENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred cccccchhcccCcccccCC
Confidence 4689999999999999999
No 11
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=87.73 E-value=0.25 Score=35.11 Aligned_cols=20 Identities=30% Similarity=0.881 Sum_probs=18.1
Q ss_pred CCceecCCCCCCCCCCCCCc
Q 014840 125 ASRCFNCGSYSHSLKECPKP 144 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~P 144 (417)
.-.|+-|+..+|-++|||.-
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCEeecCCCCCccHhHCCCC
Confidence 46899999999999999983
No 12
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=86.17 E-value=0.59 Score=41.38 Aligned_cols=22 Identities=36% Similarity=0.925 Sum_probs=17.1
Q ss_pred CCceecCCCCCCCCCCCCCccC
Q 014840 125 ASRCFNCGSYSHSLKECPKPRD 146 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PRd 146 (417)
...||||+..+|..++||.+++
T Consensus 27 ~~~C~~Cg~~GH~~~~Cp~~~~ 48 (148)
T PTZ00368 27 ARPCYKCGEPGHLSRECPSAPG 48 (148)
T ss_pred CccCccCCCCCcCcccCcCCCC
Confidence 4678888888888888887763
No 13
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=85.84 E-value=0.42 Score=42.35 Aligned_cols=20 Identities=35% Similarity=1.022 Sum_probs=18.1
Q ss_pred CceecCCCCCCCCCCCCCcc
Q 014840 126 SRCFNCGSYSHSLKECPKPR 145 (417)
Q Consensus 126 ~~CFNCG~~~HsLrdCP~PR 145 (417)
+.||||+..+|..++||.+.
T Consensus 1 ~~C~~C~~~GH~~~~c~~~~ 20 (148)
T PTZ00368 1 MVCYRCGGVGHQSRECPNSA 20 (148)
T ss_pred CcCCCCCCCCcCcccCcCCC
Confidence 47999999999999999964
No 14
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=76.99 E-value=1.5 Score=32.67 Aligned_cols=20 Identities=40% Similarity=0.946 Sum_probs=17.0
Q ss_pred CceecCCCCCCCC--CCCCCcc
Q 014840 126 SRCFNCGSYSHSL--KECPKPR 145 (417)
Q Consensus 126 ~~CFNCG~~~HsL--rdCP~PR 145 (417)
.+|-|||+.+|.- +.||.-.
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 5899999999988 7899744
No 15
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=73.21 E-value=1.7 Score=41.79 Aligned_cols=18 Identities=33% Similarity=1.075 Sum_probs=16.4
Q ss_pred CCceecCCCCCCCCCCCC
Q 014840 125 ASRCFNCGSYSHSLKECP 142 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP 142 (417)
...|||||..+|.-+||+
T Consensus 97 ~~~C~~Cg~~GH~~~dC~ 114 (190)
T COG5082 97 PKKCYNCGETGHLSRDCN 114 (190)
T ss_pred ccccccccccCccccccC
Confidence 478999999999999995
No 16
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=70.80 E-value=2.7 Score=31.48 Aligned_cols=19 Identities=42% Similarity=0.915 Sum_probs=17.6
Q ss_pred CCceecCCCCCCCCCCCCC
Q 014840 125 ASRCFNCGSYSHSLKECPK 143 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~ 143 (417)
...|-||++.+|-..+||.
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 5789999999999999995
No 17
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=69.56 E-value=2.2 Score=41.25 Aligned_cols=19 Identities=32% Similarity=1.104 Sum_probs=17.7
Q ss_pred CceecCCCCCCCCCCCCCc
Q 014840 126 SRCFNCGSYSHSLKECPKP 144 (417)
Q Consensus 126 ~~CFNCG~~~HsLrdCP~P 144 (417)
..|||||..+|.-.+||++
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred CccCCCCcCCcchhhCCCC
Confidence 4699999999999999988
No 18
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=62.98 E-value=3.4 Score=40.01 Aligned_cols=23 Identities=39% Similarity=0.985 Sum_probs=20.3
Q ss_pred CCceecCCCCCCCCCCCCCccCH
Q 014840 125 ASRCFNCGSYSHSLKECPKPRDK 147 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PRd~ 147 (417)
...||||+...|..++||.+...
T Consensus 92 ~~~c~~C~~~gH~~~~c~~~~~~ 114 (261)
T KOG4400|consen 92 AAACFNCGEGGHIERDCPEAGKE 114 (261)
T ss_pred chhhhhCCCCccchhhCCcccCc
Confidence 57899999999999999988876
No 19
>TIGR03290 CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, subunit C. The last step in methanogenesis leaves two coenzymes of methanogenesis, CoM and CoB, linked by a disulfide bond. Members of this protein family are the C subunit of the enzyme that reduces the heterodisulfide to CoB-SH and CoM-SH. Similar enzyme complex subunits are found in various other species, but likely act on a different substrate.
Probab=56.20 E-value=3.9 Score=36.24 Aligned_cols=76 Identities=18% Similarity=0.231 Sum_probs=41.0
Q ss_pred CceecCCCCCCCCCCCCCccCHHH-HHHHHHHHHHhhccCCCCCCCceeeecccCccccCCCCCcCCHHHHHHhCCCCCC
Q 014840 126 SRCFNCGSYSHSLKECPKPRDKDA-VNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELD 204 (417)
Q Consensus 126 ~~CFNCG~~~HsLrdCP~PRd~a~-In~~Rk~f~~~r~q~~~sr~GdrYYe~k~e~k~~~~kPG~LS~eLReALGm~~~~ 204 (417)
-.|++||. -..-||.-.+... |...|+... ..+... ..+.. ..+.-. ..-..+.-..+..+||+++|++ .
T Consensus 46 ~~C~~Cg~---C~~~CP~~i~~~~~i~~~R~~~~-~~g~~~-~~~~~-~~~~~~-~~g~~~~~~~~~~~lr~~~g~~--~ 116 (144)
T TIGR03290 46 WMCTTCYT---CQERCPRDVKITDIIKALRNLAA-KKGFMA-KAHRK-TASFVL-KTGHAVPINDEIKELRKELGLD--E 116 (144)
T ss_pred CcCcCcCc---hhhhcCCCCCHHHHHHHHHHHHH-HcCCCC-HHHHH-HHHHHH-HHCCCCCccHHHHHHHHHcCCC--C
Confidence 47999987 6678999999764 444554432 221100 00000 111100 0012345556778899999986 4
Q ss_pred ChHHHH
Q 014840 205 PPPWLH 210 (417)
Q Consensus 205 pPPWL~ 210 (417)
.|+|..
T Consensus 117 ~p~~~~ 122 (144)
T TIGR03290 117 IPPTTH 122 (144)
T ss_pred CCCccc
Confidence 567763
No 20
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=45.58 E-value=12 Score=33.61 Aligned_cols=19 Identities=26% Similarity=0.672 Sum_probs=16.8
Q ss_pred CCCceecCCCCCCCCCCCCC
Q 014840 124 DASRCFNCGSYSHSLKECPK 143 (417)
Q Consensus 124 ~~~~CFNCG~~~HsLrdCP~ 143 (417)
....|.+|++ +|--..||.
T Consensus 105 ~~v~CR~CkG-dH~T~~CPy 123 (128)
T PF12353_consen 105 SKVKCRICKG-DHWTSKCPY 123 (128)
T ss_pred ceEEeCCCCC-CcccccCCc
Confidence 3578999997 999999996
No 21
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=39.84 E-value=12 Score=42.94 Aligned_cols=50 Identities=32% Similarity=0.552 Sum_probs=31.0
Q ss_pred CCccccccccccccCC------CCCCcCCCccccc------CCCceecCCCCCCCCCCCCCc
Q 014840 95 TPLYDRGYALGLTSGD------GSSNLEGGLEIID------DASRCFNCGSYSHSLKECPKP 144 (417)
Q Consensus 95 VPlYdr~~~~~L~s~D------g~s~~e~~~Ei~~------~~~~CFNCG~~~HsLrdCP~P 144 (417)
-|-||-....-|-++| |...-|-.+.|+. +..+||-||+.+|.++||.--
T Consensus 218 ~P~~dPNT~HclyGlDADLImLgLATHE~hF~IlRE~~~P~~~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 218 QPGYDPNTHHCLYGLDADLIMLGLATHEPHFSILREEFFPNKPRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred CCCCCCCceeeeecCCccceeeeccccCCceEEeeeeecCCCcccchhhcccCCcHhhcCCc
Confidence 3667665554443333 4443344443332 357899999999999999743
No 22
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=35.28 E-value=19 Score=39.51 Aligned_cols=19 Identities=26% Similarity=0.600 Sum_probs=17.3
Q ss_pred CceecCCCCCCCCCCCCCc
Q 014840 126 SRCFNCGSYSHSLKECPKP 144 (417)
Q Consensus 126 ~~CFNCG~~~HsLrdCP~P 144 (417)
..||+||..+|..+||+..
T Consensus 286 n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 286 NVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccCCcccccccCCCc
Confidence 4899999999999999987
No 23
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=32.70 E-value=23 Score=36.91 Aligned_cols=23 Identities=30% Similarity=0.896 Sum_probs=20.0
Q ss_pred CCceecCCCCCCCCCCCCCccCH
Q 014840 125 ASRCFNCGSYSHSLKECPKPRDK 147 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PRd~ 147 (417)
.-.||-||+-+|-++.||---|-
T Consensus 176 gY~CyRCGqkgHwIqnCpTN~Dp 198 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPTNQDP 198 (427)
T ss_pred ceeEEecCCCCchhhcCCCCCCC
Confidence 46899999999999999986654
No 24
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=32.15 E-value=12 Score=40.96 Aligned_cols=20 Identities=40% Similarity=0.866 Sum_probs=18.4
Q ss_pred CCceecCCCCCCCCCCCCCc
Q 014840 125 ASRCFNCGSYSHSLKECPKP 144 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~P 144 (417)
...|-|||..+|.--+||.-
T Consensus 261 ~~~c~~cg~~~H~q~~cp~r 280 (554)
T KOG0119|consen 261 NRACRNCGSTGHKQYDCPGR 280 (554)
T ss_pred cccccccCCCccccccCCcc
Confidence 37999999999999999986
No 25
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=29.53 E-value=83 Score=23.42 Aligned_cols=24 Identities=21% Similarity=0.245 Sum_probs=20.4
Q ss_pred CeEEEE-ecccCHHHHHHHHHHHHH
Q 014840 8 PSVHVI-YNSLTRASKQKLEELLQQ 31 (417)
Q Consensus 8 psv~v~-y~~l~r~sk~kl~e~lq~ 31 (417)
|-|||. .+..|.+.|++|-+.|.+
T Consensus 2 P~i~i~~~~Grs~eqk~~l~~~it~ 26 (61)
T PRK02220 2 PYVHIKLIEGRTEEQLKALVKDVTA 26 (61)
T ss_pred CEEEEEEcCCCCHHHHHHHHHHHHH
Confidence 678888 578999999999988865
No 26
>PF15127 DUF4565: Protein of unknown function (DUF4565)
Probab=28.97 E-value=48 Score=28.85 Aligned_cols=28 Identities=32% Similarity=0.569 Sum_probs=21.0
Q ss_pred EEecccCHHHHHHHHHHHHHHHHHHHhh
Q 014840 12 VIYNSLTRASKQKLEELLQQWSEWQAQF 39 (417)
Q Consensus 12 v~y~~l~r~sk~kl~e~lq~Wsew~a~~ 39 (417)
|.-+.--|=|+.-|..+||||.+=..+.
T Consensus 53 vvlEyA~rLSqEIl~dAlqQWA~~n~kY 80 (91)
T PF15127_consen 53 VVLEYAHRLSQEILSDALQQWAENNIKY 80 (91)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhCccc
Confidence 3445556789999999999998765544
No 27
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=28.06 E-value=29 Score=35.97 Aligned_cols=25 Identities=44% Similarity=0.878 Sum_probs=22.3
Q ss_pred CCCceecCCCCCCCCCCCCCccCHH
Q 014840 124 DASRCFNCGSYSHSLKECPKPRDKD 148 (417)
Q Consensus 124 ~~~~CFNCG~~~HsLrdCP~PRd~a 148 (417)
+..-|.-||-++|--++||.+++-.
T Consensus 159 Dq~~cyrcGkeghwskEcP~~~~~r 183 (346)
T KOG0109|consen 159 DQSGCYRCGKEGHWSKECPVDRTGR 183 (346)
T ss_pred CHHHheeccccccccccCCccCCCc
Confidence 3578999999999999999999863
No 28
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=26.74 E-value=38 Score=25.08 Aligned_cols=17 Identities=41% Similarity=0.674 Sum_probs=14.4
Q ss_pred CCceecCCCCCCCCCCC
Q 014840 125 ASRCFNCGSYSHSLKEC 141 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdC 141 (417)
..-||+|+..-|.-..|
T Consensus 48 ~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 48 FSFCFRCKVPWHSPVSC 64 (64)
T ss_pred CeECCCCCCcCCCCCCC
Confidence 47799999999987766
No 29
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=26.07 E-value=15 Score=39.87 Aligned_cols=19 Identities=37% Similarity=0.945 Sum_probs=17.2
Q ss_pred CCCceecCCCCCCCCCCCC
Q 014840 124 DASRCFNCGSYSHSLKECP 142 (417)
Q Consensus 124 ~~~~CFNCG~~~HsLrdCP 142 (417)
++..|-|||.-.|..+||=
T Consensus 111 RKGACeNCGAmtHk~KDCm 129 (529)
T KOG2560|consen 111 RKGACENCGAMTHKVKDCM 129 (529)
T ss_pred hhhhhhhhhhhhcchHHHh
Confidence 3689999999999999994
No 30
>PF05515 Viral_NABP: Viral nucleic acid binding ; InterPro: IPR008891 This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding proteins (NABP).
Probab=25.64 E-value=47 Score=30.26 Aligned_cols=18 Identities=44% Similarity=1.121 Sum_probs=16.5
Q ss_pred CCceecCCCCCCCCCCCC
Q 014840 125 ASRCFNCGSYSHSLKECP 142 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP 142 (417)
-.+||+||.+.|.-..|.
T Consensus 62 ~~~C~~CG~~l~~~~~C~ 79 (124)
T PF05515_consen 62 YNRCFKCGRYLHNNGNCR 79 (124)
T ss_pred hCccccccceeecCCcCC
Confidence 389999999999999999
No 31
>TIGR02663 nifX nitrogen fixation protein NifX. Members of this family are NifX proteins encoded within operons for nitrogen fixation in a number of bacteria. NifX, NafY, and the C-terminal region of NifB all belong to the Pfam family pfam02579 and are involved in MoFe cofactor biosynthesis. NifX is a nitrogenase accessory protein with a role in expression of the MoFe cofactor.
Probab=24.52 E-value=31 Score=29.66 Aligned_cols=26 Identities=27% Similarity=0.658 Sum_probs=17.4
Q ss_pred CCcCCHHHHHHhCCCCCCChHHHHHH
Q 014840 187 PGALDAETRQLLGLGELDPPPWLHRM 212 (417)
Q Consensus 187 PG~LS~eLReALGm~~~~pPPWL~~M 212 (417)
+|.|.+.|.+-..+-.+.|||||.|-
T Consensus 93 ~~~v~eal~~l~~~~~~~~~~w~~~~ 118 (119)
T TIGR02663 93 PESISELLERLQKMLKGNPPPWLRKA 118 (119)
T ss_pred CccHHHHHHHHHHHHcCCCCHHHHhh
Confidence 45566665554455558999999873
No 32
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=24.01 E-value=1.3e+02 Score=22.90 Aligned_cols=24 Identities=17% Similarity=0.266 Sum_probs=20.4
Q ss_pred CeEEEEe-cccCHHHHHHHHHHHHH
Q 014840 8 PSVHVIY-NSLTRASKQKLEELLQQ 31 (417)
Q Consensus 8 psv~v~y-~~l~r~sk~kl~e~lq~ 31 (417)
|-|+|.. +.+|.+.|++|.+.+.+
T Consensus 2 P~i~i~~~~Grs~EqK~~L~~~it~ 26 (60)
T PRK02289 2 PFVRIDLFEGRSQEQKNALAREVTE 26 (60)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHHH
Confidence 6788887 57999999999998865
No 33
>COG4866 Uncharacterized conserved protein [Function unknown]
Probab=22.26 E-value=64 Score=33.03 Aligned_cols=29 Identities=21% Similarity=0.519 Sum_probs=26.3
Q ss_pred EEEecccCHHHHHHHHHHHHHHHHHHHhh
Q 014840 11 HVIYNSLTRASKQKLEELLQQWSEWQAQF 39 (417)
Q Consensus 11 ~v~y~~l~r~sk~kl~e~lq~Wsew~a~~ 39 (417)
..+|+..++.-.+.+-+.|+.|+||+-..
T Consensus 151 ~~~yE~Is~~nl~EV~~FlKkW~e~~~~~ 179 (294)
T COG4866 151 AFVYEKISPQNLKEVLEFLKKWFELESQT 179 (294)
T ss_pred cceeeecCcccHHHHHHHHHHHHHHhccc
Confidence 46899999999999999999999999765
No 34
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=20.53 E-value=56 Score=24.13 Aligned_cols=21 Identities=33% Similarity=0.594 Sum_probs=13.0
Q ss_pred CceecCCCCCCCCCCCCCccC
Q 014840 126 SRCFNCGSYSHSLKECPKPRD 146 (417)
Q Consensus 126 ~~CFNCG~~~HsLrdCP~PRd 146 (417)
..||.|+--.|-.++|-.-.|
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~d 23 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKTD 23 (36)
T ss_dssp -C-TTTSSSCS-TTT---TCC
T ss_pred ccCcccCCCcchhhhhhhhhc
Confidence 579999999999999965544
Done!