Query 007230
Match_columns 612
No_of_seqs 180 out of 238
Neff 3.0
Searched_HMMs 46136
Date Thu Mar 28 20:44:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007230.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007230hhsearch_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 1.9E-45 4.2E-50 385.2 11.7 262 241-538 55-320 (485)
2 KOG2330 Splicing factor 3b, su 99.9 2.3E-23 5.1E-28 218.5 7.3 83 359-484 249-332 (500)
3 smart00581 PSP proline-rich do 99.9 2.3E-22 4.9E-27 160.6 5.7 42 377-418 1-42 (54)
4 PF04046 PSP: PSP; InterPro: 99.8 3.6E-20 7.8E-25 145.1 5.1 38 381-418 1-38 (48)
5 COG5182 CUS1 Splicing factor 3 99.7 5.1E-18 1.1E-22 174.9 6.3 82 360-484 257-341 (429)
6 KOG2673 Uncharacterized conser 98.6 2.1E-08 4.5E-13 107.7 4.0 137 333-472 1-141 (485)
7 PF00098 zf-CCHC: Zinc knuckle 97.0 0.00032 6.9E-09 45.5 1.5 18 321-338 1-18 (18)
8 PF14392 zf-CCHC_4: Zinc knuck 89.6 0.12 2.7E-06 40.3 0.5 19 320-338 31-49 (49)
9 smart00343 ZnF_C2HC zinc finge 87.5 0.27 5.9E-06 33.6 1.0 17 322-338 1-17 (26)
10 COG5082 AIR1 Arginine methyltr 87.3 0.29 6.3E-06 48.8 1.4 20 318-337 58-77 (190)
11 PF13696 zf-CCHC_2: Zinc knuck 85.5 0.38 8.3E-06 35.9 0.9 20 320-339 8-27 (32)
12 PTZ00368 universal minicircle 82.5 1 2.2E-05 41.5 2.6 22 320-341 27-48 (148)
13 PTZ00368 universal minicircle 80.5 0.89 1.9E-05 41.9 1.5 20 321-340 1-20 (148)
14 PF15288 zf-CCHC_6: Zinc knuck 72.3 2.3 4.9E-05 33.4 1.5 19 320-338 1-21 (40)
15 COG5082 AIR1 Arginine methyltr 66.7 2.8 6E-05 42.1 1.2 18 320-337 97-114 (190)
16 PF13917 zf-CCHC_3: Zinc knuck 60.7 5.3 0.00011 31.4 1.5 19 320-338 4-22 (42)
17 KOG4400 E3 ubiquitin ligase in 60.6 4.1 8.9E-05 41.0 1.1 19 321-339 144-162 (261)
18 KOG4400 E3 ubiquitin ligase in 50.6 7.1 0.00015 39.4 1.0 23 320-342 92-114 (261)
19 TIGR03290 CoB_CoM_SS_C CoB--Co 43.3 7.9 0.00017 35.8 -0.0 76 321-405 46-122 (144)
20 PF12353 eIF3g: Eukaryotic tra 38.0 17 0.00037 34.1 1.3 19 319-338 105-123 (128)
21 KOG2044 5'-3' exonuclease HKE1 35.5 15 0.00033 43.8 0.7 21 319-339 259-279 (931)
22 KOG0119 Splicing factor 1/bran 27.5 30 0.00064 39.6 1.2 20 320-339 285-304 (554)
23 KOG0132 RNA polymerase II C-te 26.8 1.5E+02 0.0033 35.9 6.7 31 579-610 782-812 (894)
24 COG5222 Uncharacterized conser 25.1 38 0.00083 36.9 1.5 23 320-342 176-198 (427)
25 KOG0109 RNA-binding protein LA 21.4 47 0.001 36.1 1.3 25 318-342 158-182 (346)
No 1
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=100.00 E-value=1.9e-45 Score=385.24 Aligned_cols=262 Identities=34% Similarity=0.583 Sum_probs=213.4
Q ss_pred CCccccccceeeeceeeccCCCCCceeeEEecccccccCCCCCCCCCCCCCcccccccccccCCCCCCCcCCCcccccCC
Q 007230 241 PNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDA 320 (612)
Q Consensus 241 ~~e~~esG~etyfPal~vg~~~ssavsFwvDkq~~~~~n~~~~~~d~~eVPlYdr~~~~~L~s~Dg~sn~E~~lEi~~~~ 320 (612)
..+++++++.+|+| +++.......++||++++....--+++.+.+... ||.++.+|.+.+++-+++++..|.+..
T Consensus 55 qqd~l~~te~a~~~-fr~~~qe~~t~s~wl~~~~~ek~gedl~~~e~~t----dr~~a~~l~sq~~s~tvek~~~v~~~~ 129 (485)
T KOG2673|consen 55 QQDLLGVTEKAFPP-FRYRMQELGTPSFWLKNAELEKSGEDLYLGEDST----DRETAVGLISQNKSVTVEKSKLVNKCD 129 (485)
T ss_pred HHHHhhcccccccc-hhhhHHhhcCchhhhhhcccccChhhhccccccc----cccceecccccccchhhhhhhhhccCc
Confidence 34567778888888 8898888888999999997776666666666553 999999999999999889887766544
Q ss_pred CceecCCCCCCCCCCCCCccCHHHHHHHHHHHHhhhccCCCCCCCceEeeccccccccCCCCCCCCHHHHHHhCCCCCCC
Q 007230 321 SRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDP 400 (612)
Q Consensus 321 ~rCFNCGs~eHsLrDCP~PRD~a~In~aRKeF~~krnq~~~sr~GdrYYEgk~e~k~~~fkPGkLS~ELReALGm~~ndp 400 (612)
+ |||||++.|+|+|||+|+|+++|+++||+++..++| |||....-++++|||||+||.+||.|||+.+++|
T Consensus 130 ~-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 130 P-CFNCGGTPHSLRDCPRPFDFSRIQRARKEKMVFRNQ--------RYYQDTEQGREDHFKPGVLSGNTRSALGLSPGDP 200 (485)
T ss_pred c-ccccCCCCCccccCCCccccHHHHHHHHhhccccce--------eeeeecchhhhcccCCcccchhHHHhhcCCCCCc
Confidence 4 999999999999999999999999999999877765 8998776669999999999999999999999999
Q ss_pred hHHHHHHHhcCCCCCCCCCCCCCCCCCeeeecCCCccCCCCCccccccCCCCCCCeeeeecCCCCCC-CCCCcchhcccc
Q 007230 401 PPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPASKRKMTTEFPGINAP-IPENADERLWAA 479 (612)
Q Consensus 401 PPWLyrMrrlGyPPgYp~~a~~~q~SGLtIF~Dg~~k~d~EDGEi~e~~~pe~~rkKiV~fPGFNaP-iPeGad~~~Wg~ 479 (612)
|+|+||||++||||||+.++ ..+.+||+||+... ..++|+.| ...+|+++.+|++.|||||.+ .|+...++.|..
T Consensus 201 P~~~yRMR~lGYPPg~L~~s-~~e~s~i~if~eet-~~~dee~e--se~PP~~~~~K~~~f~gfn~~~~p~~~~e~~ke~ 276 (485)
T KOG2673|consen 201 PEWKYRMRRLGYPPGYLRKS-DMEVSGIKIFSEET-FQFDEELE--SETPPEPQGTKPVVFPGFNPKGTPPNDREDSKEA 276 (485)
T ss_pred hHHHHHHhhccCCchhhhhh-hcccccceeecccc-cccCcccC--CCCCCCCCCCCCcccCCCCCCCCCCCChhhcccc
Confidence 99999999999999999987 56899999997222 12223332 334678899999999999999 999999888876
Q ss_pred CCCCCCcccccccccccCCCCCccccccccccccc--cccCCCCCCCCCCCCCCCCCCC-CC
Q 007230 480 RPSSSDSSRDRSHHRLNHHSESISRGRYHEQRWSR--DYRDDGPPGVDPVSSYPPRYGG-YD 538 (612)
Q Consensus 480 ~P~~~d~~r~~~~~~~~~~~e~~~R~~~~~qr~~~--d~rd~gppg~~~~~s~~pr~g~-~~ 538 (612)
..|+|+.--+. .+-.++ ++++|+|.|.++..+++++||. +|
T Consensus 277 ---~r~~s~s~~q~---------------~l~~~~l~~k~~dl~~~~e~s~~~~~~~~t~~D 320 (485)
T KOG2673|consen 277 ---PRDASCSVDQD---------------ALTLSRLEKKQRDLPAGLEQSESAPSDSGTEVD 320 (485)
T ss_pred ---cchhhhhhhHH---------------HhhhhHHHHHhhhcccccccccCCCcccCCccc
Confidence 23444321111 111223 7889999999999999999998 55
No 2
>KOG2330 consensus Splicing factor 3b, subunit 2 [RNA processing and modification]
Probab=99.88 E-value=2.3e-23 Score=218.49 Aligned_cols=83 Identities=33% Similarity=0.619 Sum_probs=77.6
Q ss_pred CCCCCCCceEeecc-ccccccCCCCCCCCHHHHHHhCCCCCCChHHHHHHHhcCCCCCCCCCCCCCCCCCeeeecCCCcc
Q 007230 359 NSASRNPMRYYQNS-AGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIK 437 (612)
Q Consensus 359 ~~~sr~GdrYYEgk-~e~k~~~fkPGkLS~ELReALGm~~ndpPPWLyrMrrlGyPPgYp~~a~~~q~SGLtIF~Dg~~k 437 (612)
-.++.+|+.||+++ .+..+++.+||.||+|||.||||+.+.|||||++||++|+|||||+
T Consensus 249 p~lt~~Ge~yyegke~e~~~k~k~PG~iS~eLr~aLgmp~g~pPPWl~aMqryGpPpsYPd------------------- 309 (500)
T KOG2330|consen 249 PYLTKFGELYYEGKELEAMVKEKKPGDISDELRIALGMPVGTPPPWLIAMQRYGPPPSYPD------------------- 309 (500)
T ss_pred cceeecceeeecchhHHHHHhhcCccchhHHHHHHhCCCCCCCChHHHHhhhcCCCCCCCc-------------------
Confidence 34789999999998 5677899999999999999999999999999999999999999996
Q ss_pred CCCCCccccccCCCCCCCeeeeecCCCCCCCCCCcchhccccCCCCC
Q 007230 438 EGQEDGEIIETGRPASKRKMTTEFPGINAPIPENADERLWAARPSSS 484 (612)
Q Consensus 438 ~d~EDGEi~e~~~pe~~rkKiV~fPGFNaPiPeGad~~~Wg~~P~~~ 484 (612)
+++||+|+|||+|+. ||+||++|
T Consensus 310 ---------------------lkIpGLNapIPeg~s---~Gyh~gGW 332 (500)
T KOG2330|consen 310 ---------------------LKIPGLNAPIPEGCS---FGYHAGGW 332 (500)
T ss_pred ---------------------ccCCCCCCCCCcccc---cccccCCC
Confidence 789999999999998 99999988
No 3
>smart00581 PSP proline-rich domain in spliceosome associated proteins.
Probab=99.86 E-value=2.3e-22 Score=160.65 Aligned_cols=42 Identities=52% Similarity=1.112 Sum_probs=40.7
Q ss_pred ccCCCCCCCCHHHHHHhCCCCCCChHHHHHHHhcCCCCCCCC
Q 007230 377 YDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLD 418 (612)
Q Consensus 377 ~~~fkPGkLS~ELReALGm~~ndpPPWLyrMrrlGyPPgYp~ 418 (612)
|++||||+||++||+||||.++++||||++||++|||||||+
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=99.80 E-value=3.6e-20 Score=145.07 Aligned_cols=38 Identities=66% Similarity=1.307 Sum_probs=37.0
Q ss_pred CCCCCCHHHHHHhCCCCCCChHHHHHHHhcCCCCCCCC
Q 007230 381 RPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLD 418 (612)
Q Consensus 381 kPGkLS~ELReALGm~~ndpPPWLyrMrrlGyPPgYp~ 418 (612)
|||+||++||+||||.++++||||++||++||||||++
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=99.72 E-value=5.1e-18 Score=174.94 Aligned_cols=82 Identities=38% Similarity=0.651 Sum_probs=71.6
Q ss_pred CCCCCCceEeecc-ccccccCCCCCCCCHHHHHHhCCCCCCChHHHHHHHhcCCCCCCCCCCCCCCCCCeeeecCCCccC
Q 007230 360 SASRNPMRYYQNS-AGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKE 438 (612)
Q Consensus 360 ~~sr~GdrYYEgk-~e~k~~~fkPGkLS~ELReALGm~~ndpPPWLyrMrrlGyPPgYp~~a~~~q~SGLtIF~Dg~~k~ 438 (612)
-.+.||+.||+++ ...-.++.+||.||+|||+||||.+++|||||.+||++|+|||||+
T Consensus 257 ~L~~fGe~y~e~~n~~~~vk~krPG~IS~eLrealgi~~g~pPPWlf~Mq~~G~PpsYPD-------------------- 316 (429)
T COG5182 257 YLSKFGEFYEEVDNDYRFVKKKRPGAISAELREALGIDSGTPPPWLFNMQKHGMPPSYPD-------------------- 316 (429)
T ss_pred ccccccceeeccchHHHHHhccCCcchHHHHHHHhCCCCCCCChHHHhhhhcCCCCCCcc--------------------
Confidence 3688999999998 4445689999999999999999999999999999999999999996
Q ss_pred CCCCccccccCCCCCCCeeeeecCCCC-CCCC-CCcchhccccCCCCC
Q 007230 439 GQEDGEIIETGRPASKRKMTTEFPGIN-APIP-ENADERLWAARPSSS 484 (612)
Q Consensus 439 d~EDGEi~e~~~pe~~rkKiV~fPGFN-aPiP-eGad~~~Wg~~P~~~ 484 (612)
+++||+| +|+| +|.- ||+.|+.|
T Consensus 317 --------------------lkIpGlNW~~~pL~Gdv---yG~~~p~~ 341 (429)
T COG5182 317 --------------------LKIPGLNWAPIPLEGDV---YGYQPPGW 341 (429)
T ss_pred --------------------ccCCCCCCCCccccccc---ccccCCCc
Confidence 6799999 8888 5544 77777766
No 6
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=98.62 E-value=2.1e-08 Score=107.73 Aligned_cols=137 Identities=22% Similarity=0.363 Sum_probs=102.4
Q ss_pred CCCCCCccCHHHHHHHHHHHHhhhccCCCCCCCceEeeccccccccCCCCCCCCHHHHHHhCCCCCCChHHHHHHHhcCC
Q 007230 333 LKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGY 412 (612)
Q Consensus 333 LrDCP~PRD~a~In~aRKeF~~krnq~~~sr~GdrYYEgk~e~k~~~fkPGkLS~ELReALGm~~ndpPPWLyrMrrlGy 412 (612)
+++||.|+| ++|+..|++++.+-...+..-++.+|+......+...+.+|.|| ++.++|+-.+.+.+|++++||++|+
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 478999999 99999999999864433344466888877777788999999999 8899999999999999999999999
Q ss_pred CCCCCCCCCCCCCCCeeeec-CCCccCCCCCccccccCCCCCCCeeeeecC--CCC-CCCCCCc
Q 007230 413 PPGYLDSEDDDQPSGITIYA-DGEIKEGQEDGEIIETGRPASKRKMTTEFP--GIN-APIPENA 472 (612)
Q Consensus 413 PPgYp~~a~~~q~SGLtIF~-Dg~~k~d~EDGEi~e~~~pe~~rkKiV~fP--GFN-aPiPeGa 472 (612)
|+.|++.+. .+.+|..+|. +...+-..++|.+-.......+.++.|.++ =|| .-.|.++
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 999999654 4578998884 211122345565544444455566666666 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=97.03 E-value=0.00032 Score=45.54 Aligned_cols=18 Identities=50% Similarity=1.315 Sum_probs=16.6
Q ss_pred CceecCCCCCCCCCCCCC
Q 007230 321 SRCFNCGSYSHSLKECPK 338 (612)
Q Consensus 321 ~rCFNCGs~eHsLrDCP~ 338 (612)
..|||||..+|..++||+
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 479999999999999995
No 8
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=89.61 E-value=0.12 Score=40.34 Aligned_cols=19 Identities=58% Similarity=1.183 Sum_probs=17.5
Q ss_pred CCceecCCCCCCCCCCCCC
Q 007230 320 ASRCFNCGSYSHSLKECPK 338 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~ 338 (612)
...||+||..+|..++||+
T Consensus 31 p~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ChhhcCCCCcCcCHhHcCC
Confidence 5789999999999999995
No 9
>smart00343 ZnF_C2HC zinc finger.
Probab=87.54 E-value=0.27 Score=33.64 Aligned_cols=17 Identities=47% Similarity=1.365 Sum_probs=15.8
Q ss_pred ceecCCCCCCCCCCCCC
Q 007230 322 RCFNCGSYSHSLKECPK 338 (612)
Q Consensus 322 rCFNCGs~eHsLrDCP~ 338 (612)
.||+||..+|..++||.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 49999999999999995
No 10
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=87.27 E-value=0.29 Score=48.84 Aligned_cols=20 Identities=40% Similarity=1.154 Sum_probs=18.2
Q ss_pred cCCCceecCCCCCCCCCCCC
Q 007230 318 DDASRCFNCGSYSHSLKECP 337 (612)
Q Consensus 318 ~~~~rCFNCGs~eHsLrDCP 337 (612)
.....|||||+.+|..+|||
T Consensus 58 ~~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 58 EENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccccchhcccCcccccCC
Confidence 34689999999999999999
No 11
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=85.45 E-value=0.38 Score=35.95 Aligned_cols=20 Identities=30% Similarity=0.881 Sum_probs=18.1
Q ss_pred CCceecCCCCCCCCCCCCCc
Q 007230 320 ASRCFNCGSYSHSLKECPKP 339 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~P 339 (612)
.-.|+-|+..+|-++|||..
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCEeecCCCCCccHhHCCCC
Confidence 46799999999999999983
No 12
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=82.51 E-value=1 Score=41.54 Aligned_cols=22 Identities=36% Similarity=0.925 Sum_probs=17.3
Q ss_pred CCceecCCCCCCCCCCCCCccC
Q 007230 320 ASRCFNCGSYSHSLKECPKPRD 341 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PRD 341 (612)
...||||+..+|..++||.+++
T Consensus 27 ~~~C~~Cg~~GH~~~~Cp~~~~ 48 (148)
T PTZ00368 27 ARPCYKCGEPGHLSRECPSAPG 48 (148)
T ss_pred CccCccCCCCCcCcccCcCCCC
Confidence 5678888888888888888663
No 13
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=80.53 E-value=0.89 Score=41.95 Aligned_cols=20 Identities=35% Similarity=1.022 Sum_probs=18.1
Q ss_pred CceecCCCCCCCCCCCCCcc
Q 007230 321 SRCFNCGSYSHSLKECPKPR 340 (612)
Q Consensus 321 ~rCFNCGs~eHsLrDCP~PR 340 (612)
+.||||+..+|..++||.+.
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=72.31 E-value=2.3 Score=33.38 Aligned_cols=19 Identities=42% Similarity=1.081 Sum_probs=16.8
Q ss_pred CCceecCCCCCCCC--CCCCC
Q 007230 320 ASRCFNCGSYSHSL--KECPK 338 (612)
Q Consensus 320 ~~rCFNCGs~eHsL--rDCP~ 338 (612)
+.+|-|||+.+|.- +.||.
T Consensus 1 k~kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 1 KVKCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred CccccccccccccccCccCCC
Confidence 36899999999988 78998
No 15
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=66.66 E-value=2.8 Score=42.09 Aligned_cols=18 Identities=33% Similarity=1.075 Sum_probs=16.4
Q ss_pred CCceecCCCCCCCCCCCC
Q 007230 320 ASRCFNCGSYSHSLKECP 337 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP 337 (612)
...|+|||..+|.-+||+
T Consensus 97 ~~~C~~Cg~~GH~~~dC~ 114 (190)
T COG5082 97 PKKCYNCGETGHLSRDCN 114 (190)
T ss_pred ccccccccccCccccccC
Confidence 378999999999999995
No 16
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=60.74 E-value=5.3 Score=31.45 Aligned_cols=19 Identities=42% Similarity=0.915 Sum_probs=17.6
Q ss_pred CCceecCCCCCCCCCCCCC
Q 007230 320 ASRCFNCGSYSHSLKECPK 338 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~ 338 (612)
...|-||+..+|--.+||.
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 5789999999999999994
No 17
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=60.56 E-value=4.1 Score=41.05 Aligned_cols=19 Identities=32% Similarity=1.104 Sum_probs=17.8
Q ss_pred CceecCCCCCCCCCCCCCc
Q 007230 321 SRCFNCGSYSHSLKECPKP 339 (612)
Q Consensus 321 ~rCFNCGs~eHsLrDCP~P 339 (612)
..|||||..+|.-.+||++
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred CccCCCCcCCcchhhCCCC
Confidence 5699999999999999987
No 18
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=50.56 E-value=7.1 Score=39.37 Aligned_cols=23 Identities=39% Similarity=0.985 Sum_probs=20.6
Q ss_pred CCceecCCCCCCCCCCCCCccCH
Q 007230 320 ASRCFNCGSYSHSLKECPKPRDK 342 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PRD~ 342 (612)
...||||+...|..++||.+...
T Consensus 92 ~~~c~~C~~~gH~~~~c~~~~~~ 114 (261)
T KOG4400|consen 92 AAACFNCGEGGHIERDCPEAGKE 114 (261)
T ss_pred chhhhhCCCCccchhhCCcccCc
Confidence 68899999999999999997665
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=43.26 E-value=7.9 Score=35.81 Aligned_cols=76 Identities=18% Similarity=0.247 Sum_probs=40.6
Q ss_pred CceecCCCCCCCCCCCCCccCHH-HHHHHHHHHHhhhccCCCCCCCceEeeccccccccCCCCCCCCHHHHHHhCCCCCC
Q 007230 321 SRCFNCGSYSHSLKECPKPRDKD-AVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELD 399 (612)
Q Consensus 321 ~rCFNCGs~eHsLrDCP~PRD~a-~In~aRKeF~~krnq~~~sr~GdrYYEgk~e~k~~~fkPGkLS~ELReALGm~~nd 399 (612)
-.|+.||. -..-||.-.+.. .|...|+... +.+... ..+. ..++.-. ..-..+.-..+..+||+++|++ .
T Consensus 46 ~~C~~Cg~---C~~~CP~~i~~~~~i~~~R~~~~-~~g~~~-~~~~-~~~~~~~-~~g~~~~~~~~~~~lr~~~g~~--~ 116 (144)
T TIGR03290 46 WMCTTCYT---CQERCPRDVKITDIIKALRNLAA-KKGFMA-KAHR-KTASFVL-KTGHAVPINDEIKELRKELGLD--E 116 (144)
T ss_pred CcCcCcCc---hhhhcCCCCCHHHHHHHHHHHHH-HcCCCC-HHHH-HHHHHHH-HHCCCCCccHHHHHHHHHcCCC--C
Confidence 47888886 566899988876 4444454432 221110 0000 0111100 0012345556778899999986 4
Q ss_pred ChHHHH
Q 007230 400 PPPWLH 405 (612)
Q Consensus 400 pPPWLy 405 (612)
.|+|..
T Consensus 117 ~p~~~~ 122 (144)
T TIGR03290 117 IPPTTH 122 (144)
T ss_pred CCCccc
Confidence 577763
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=37.95 E-value=17 Score=34.06 Aligned_cols=19 Identities=26% Similarity=0.672 Sum_probs=17.1
Q ss_pred CCCceecCCCCCCCCCCCCC
Q 007230 319 DASRCFNCGSYSHSLKECPK 338 (612)
Q Consensus 319 ~~~rCFNCGs~eHsLrDCP~ 338 (612)
....|.+|++ +|--..||.
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 4578999997 999999997
No 21
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=35.51 E-value=15 Score=43.80 Aligned_cols=21 Identities=38% Similarity=0.917 Sum_probs=18.1
Q ss_pred CCCceecCCCCCCCCCCCCCc
Q 007230 319 DASRCFNCGSYSHSLKECPKP 339 (612)
Q Consensus 319 ~~~rCFNCGs~eHsLrDCP~P 339 (612)
+..+||-||+.+|.++||.--
T Consensus 259 ~~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 259 KPRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred CcccchhhcccCCcHhhcCCc
Confidence 357899999999999999743
No 22
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=27.51 E-value=30 Score=39.59 Aligned_cols=20 Identities=25% Similarity=0.580 Sum_probs=18.1
Q ss_pred CCceecCCCCCCCCCCCCCc
Q 007230 320 ASRCFNCGSYSHSLKECPKP 339 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~P 339 (612)
...|++||..+|..+||+..
T Consensus 285 ~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 285 TNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred cccccccCCcccccccCCCc
Confidence 34899999999999999987
No 23
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=26.85 E-value=1.5e+02 Score=35.86 Aligned_cols=31 Identities=32% Similarity=0.391 Sum_probs=19.0
Q ss_pred CCCCccccccccchhhhccchhhccccCCCCC
Q 007230 579 PDYDLDRYRDDYSREYLSRSMDEYDRFRPRGR 610 (612)
Q Consensus 579 ~~~~~~r~~~~~~~~~s~r~~d~~~~~~~~~~ 610 (612)
.+.+..||..+.+||-|.|++ |=||-+||+|
T Consensus 782 g~~~Rer~G~~~~Rd~~~Rd~-r~~~~~~rrR 812 (894)
T KOG0132|consen 782 GARDRERYGNDDRRDDSNRDR-RSDRREHRRR 812 (894)
T ss_pred cchhhhhhcCCcccccccccc-cccccccccc
Confidence 344555666677777788844 3466666655
No 24
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=25.08 E-value=38 Score=36.89 Aligned_cols=23 Identities=30% Similarity=0.896 Sum_probs=19.5
Q ss_pred CCceecCCCCCCCCCCCCCccCH
Q 007230 320 ASRCFNCGSYSHSLKECPKPRDK 342 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PRD~ 342 (612)
.-.||-||+.+|-++.||---|-
T Consensus 176 gY~CyRCGqkgHwIqnCpTN~Dp 198 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPTNQDP 198 (427)
T ss_pred ceeEEecCCCCchhhcCCCCCCC
Confidence 35799999999999999986553
No 25
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=21.41 E-value=47 Score=36.06 Aligned_cols=25 Identities=44% Similarity=0.884 Sum_probs=22.7
Q ss_pred cCCCceecCCCCCCCCCCCCCccCH
Q 007230 318 DDASRCFNCGSYSHSLKECPKPRDK 342 (612)
Q Consensus 318 ~~~~rCFNCGs~eHsLrDCP~PRD~ 342 (612)
-+..-|.-||-++|--++||.+++-
T Consensus 158 gDq~~cyrcGkeghwskEcP~~~~~ 182 (346)
T KOG0109|consen 158 GDQSGCYRCGKEGHWSKECPVDRTG 182 (346)
T ss_pred CCHHHheeccccccccccCCccCCC
Confidence 4578899999999999999999986
Done!