Query psy4218
Match_columns 520
No_of_seqs 169 out of 222
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 19:50:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4218.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4218hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2560|consensus 100.0 2E-158 4E-163 1223.0 19.0 485 1-517 1-514 (529)
2 PF11708 Slu7: Pre-mRNA splici 100.0 3.2E-84 7E-89 635.7 18.8 228 158-401 1-238 (239)
3 PF00098 zf-CCHC: Zinc knuckle 89.6 0.19 4.2E-06 31.7 1.3 17 117-133 2-18 (18)
4 PF14392 zf-CCHC_4: Zinc knuck 71.6 1.5 3.2E-05 33.8 0.3 17 116-132 32-48 (49)
5 PF15288 zf-CCHC_6: Zinc knuck 63.9 3.1 6.7E-05 31.7 0.7 17 117-133 3-21 (40)
6 COG5082 AIR1 Arginine methyltr 61.9 3.6 7.9E-05 40.7 1.0 24 116-141 98-121 (190)
7 PF13917 zf-CCHC_3: Zinc knuck 56.1 4.9 0.00011 30.8 0.6 19 115-133 4-22 (42)
8 PTZ00368 universal minicircle 47.7 9.1 0.0002 35.2 1.1 19 116-134 130-148 (148)
9 KOG0119|consensus 45.2 9.5 0.00021 42.7 1.0 19 116-134 262-280 (554)
10 COG2947 Uncharacterized conser 44.8 11 0.00023 36.2 1.1 56 261-326 77-136 (156)
11 smart00343 ZnF_C2HC zinc finge 44.1 10 0.00022 25.3 0.6 16 118-133 2-17 (26)
12 COG5082 AIR1 Arginine methyltr 44.0 9.6 0.00021 37.8 0.7 23 110-132 55-77 (190)
13 PF14787 zf-CCHC_5: GAG-polypr 40.1 16 0.00035 27.4 1.2 26 115-140 2-27 (36)
14 PTZ00368 universal minicircle 36.7 19 0.00041 33.1 1.4 23 115-137 77-99 (148)
15 PF07535 zf-DBF: DBF zinc fing 26.8 24 0.00052 27.9 0.3 10 114-123 4-13 (49)
16 KOG3490|consensus 23.9 25 0.00054 32.1 -0.1 18 111-129 21-38 (111)
17 PF09524 Phg_2220_C: Conserved 23.8 24 0.00052 30.1 -0.2 18 165-182 25-43 (74)
18 TIGR02220 phg_TIGR02220 phage 22.7 26 0.00056 30.1 -0.2 18 164-181 27-45 (77)
19 PTZ00076 60S ribosomal protein 22.3 68 0.0015 33.2 2.5 40 26-74 154-193 (253)
20 PF10593 Z1: Z1 domain; Inter 21.0 1E+02 0.0023 31.1 3.6 37 148-194 165-209 (239)
21 PF04184 ST7: ST7 protein; In 20.1 26 0.00055 39.6 -1.0 29 39-67 351-384 (539)
No 1
>KOG2560|consensus
Probab=100.00 E-value=2.1e-158 Score=1222.99 Aligned_cols=485 Identities=53% Similarity=0.805 Sum_probs=420.4
Q ss_pred CCCCCCCCchhHhhhccCCCCCCccccCHHHHHHHHHHHHHHhcCCCCCcccccCCCCCCCcccccccCCcccCCCCCCc
Q psy4218 1 MASTSTNVPVSEILRTKASEDDEPKKKSREDWRKAKELEEARKAGTAPAAVDEHGRDINPHIPQYISSAPWYFGSKGPTL 80 (520)
Q Consensus 1 m~~~~~~~~~s~~~~~~~~~~~~~~~~sre~~rk~keLeeaRKaG~aPa~~De~GkeiNPHIPqYIs~aPWY~~~~~p~L 80 (520)
|+.+.++.|+|...... ...++++||++||++++|||+||||+|||+||+.|++||||||+|||++|||+.+.+|+|
T Consensus 1 ~~~~~~~~~~sn~~k~~---~~~~k~Ksr~dhrk~~eleE~rkag~aPaevDe~g~~iNphIP~yis~aPwY~~s~~ptL 77 (529)
T KOG2560|consen 1 MSRNNENRSTSNRNKMQ---LQQAKKKSREDHRKRKELEEARKAGLAPAEVDEKGKDINPHIPEYISKAPWYVHSEGPTL 77 (529)
T ss_pred CCccccccccchhhHHH---HHHHhhhhhhhhhhhHHHHHHHHhcCCchhhcCCCCCCCccccccccCCCceecccCccc
Confidence 78888888888865433 568899999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCCCCCccchhhhccCccccccccccccccccccccCCCCccccccCcccccccccCCccCcccccccccccc
Q psy4218 81 QHQRIQPDQEKPRASLDEWYKRGVDTTSQAKKFRKGACENCGAMTHKKKDCLERPRKVLAKYSNAQIACDEFVQPKLIQD 160 (520)
Q Consensus 81 kHQR~~~~~~~~~~~i~~wy~RG~~~~~~atKyRKGACeNCGAmtHkkKDClERPRK~GAk~tg~~Ia~DE~iq~~~~ld 160 (520)
+|||+|++....++.++.||.||.+.++++||||||||+|||||||++|||||||||+||+|||.+|++||+||+.+.+|
T Consensus 78 kHQr~~~~epk~m~~~~ewy~rG~kk~~~atkyRKGACeNCGAmtHk~KDCmERPRK~gAk~t~~Nia~De~iq~~~~~d 157 (529)
T KOG2560|consen 78 KHQRPWKEEPKIMGIKDEWYDRGKKKGSVATKYRKGACENCGAMTHKVKDCMERPRKVGAKYTDLNIAPDEKIQSVLELD 157 (529)
T ss_pred cccCCCccCCccccccchhhhcccccchHHHHHhhhhhhhhhhhhcchHHHhhcchhhcccCCCcccCcccccccccccc
Confidence 99999987666667789999999988899999999999999999999999999999999999999999999999889999
Q ss_pred cccccCcCCCCCcccHHHHHHHHHHHHHHH-HHHHHhhhhcccccCCCCCCCCCCCCCCCccchhhhccccCCCCC--cc
Q psy4218 161 YDSKRDRWAGYDPSNHKAIVEHYQKIEEAK-RELRADKLDAGVSIDNRGSKEGDEDKDDLEEDEDKYVDEVDMPGT--KV 237 (520)
Q Consensus 161 yDaKRDRWnGYDp~ey~~Vveeyek~e~~r-~~~k~~~l~~~~~~~~~~~~~~~~~~~~~d~DedkY~de~d~~g~--~~ 237 (520)
||+||||||||||++|++||++|+++++++ +.+++++++.. . ...+++++.++-|+++|+|.++|++. .+
T Consensus 158 yD~KRDRWnGYdps~y~~vIe~yEk~eeak~K~l~~~q~~~d-----~--~~~d~eE~~~~~dee~y~D~a~~~k~v~~~ 230 (529)
T KOG2560|consen 158 YDGKRDRWNGYDPSEYKEVIERYEKLEEAKIKGLKEQQKNGD-----E--ALWDTEEGIEDLDEELYADFADMLKTVRDT 230 (529)
T ss_pred cccccccccCCChHHHHHHHHHHHHHHHHHHHHHHHhhccCc-----c--cccccccccchhhHHhhhhhhccccccccc
Confidence 999999999999999999999999999999 56666653211 0 01122333445588999999999998 67
Q ss_pred CccccccccccccccchHHHhhccCCCCCccCCCcccccCCCCCCCCCCCCCCccCCCccccccchHHHHHHHHHHHHHH
Q psy4218 238 DSKQRITVRNLRIREDTAKYLRNLDPNSAYYDPKTRSMRDNPYETVANPEDVDYAGENFVRFSGDTRKHATAQLFAWEAY 317 (520)
Q Consensus 238 d~k~r~tvrnLRIREDtAKYL~NLd~nSA~YDPKTRsMRdnP~~~~~~~~~~~faGdnF~R~SGda~e~~~lQ~FAWeA~ 317 (520)
+++++||||||||||||||||+|||+|||||||||||||+||+++ .+|.+..|.|+||||+||++.+|++||+|||+|+
T Consensus 231 d~~s~iTvrnLRiRED~AkYL~nld~Nsa~YDPKSRsMReep~~~-~~~~e~~~~gdnfvr~SGe~~~~~qlq~FAweA~ 309 (529)
T KOG2560|consen 231 DDGSRITVRNLRIREDTAKYLRNLDVNSAYYDPKSRSMREEPLPG-KDPNEDEYSGDNFVRNSGEALEFNQLQMFAWEAF 309 (529)
T ss_pred CCCceeeeecceechhHHHHHHhcCCcccccCccccccccCCCCC-CChhhhhhcccceeeccchhhhHHHHHHHHHHHh
Confidence 889999999999999999999999999999999999999999998 7889999999999999999999999999999999
Q ss_pred hCCCceeeecCCCHHHHHhHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCChhhhhhhhccceeeeccccceee-------
Q psy4218 318 EKGVDVHVLAEPTKLELLKKEYEEKKEEFKKEVSSSVIDKYGGAEHLQAPPKALLLAQTEDYVEYSRYGKVIK------- 390 (520)
Q Consensus 318 ~kG~dvhl~AnPT~~Ell~Ke~k~kke~~k~~~k~~ileKYGg~e~l~~~p~elll~qtE~yvEY~~~G~vik------- 390 (520)
.+|++||+||+||++|||++.|+.+++.|+.+++++||+||||.+|++.+|++|||+|||.||+|++.|+|||
T Consensus 310 ~kG~~~H~~A~Ptk~Ell~k~~k~kke~lK~q~kq~il~kYG~~~~~d~~p~elll~qte~~iey~rkg~v~KG~e~~~~ 389 (529)
T KOG2560|consen 310 DKGVDVHMQADPTKLELLYKENKVKKETLKKQTKQEILDKYGGGEHKDLPPKELLLAQTEEYIEYSRKGKVIKGQEKIVP 389 (529)
T ss_pred cccceeeeecCcHHHHHHHHHhHHHHHHHHHHHHHHHHhhcCCccccccChHhhhccccHHHHHHhhccceecccccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred -------cccCCCccccC-----CCcccccccch-------hhhhhhccccccCCCCCCCCCCCCCCCCCchhhhhhhHH
Q psy4218 391 -------MYIPTIIPVYG-----GPGGIMECGDT-------REAGLATSSVVGASLGPPPGIMNRPEHQDEDEEDSGHKK 451 (520)
Q Consensus 391 -------v~~nNHtsVWG-----g~WGY~CChs~-------Ge~G~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 451 (520)
||+|||||||| |+|||+||||| |.+|++|....... ....+...++.+.++.++...
T Consensus 390 ~S~yeedV~~~nht~vwgs~w~~~rwgykcc~~f~~~syctg~~g~e~~~~~~~~---~~~~~~~~~~~~~~e~k~~~~- 465 (529)
T KOG2560|consen 390 KSKYEEDVYINNHTSVWGSFWKEGRWGYKCCHQFIKNSYCTGSAGIEAVAEELSK---ASRKEASKEPPKKVEEKEMER- 465 (529)
T ss_pred cccchhheeccccchhhhhhhhccchhHHHHHHHHhhhcccCccchhHHhHHHhh---hhhhhccCCChhhhHHhhhhc-
Confidence 99999999999 99999999999 99999996422111 011111122222222222111
Q ss_pred hhhhhhhhhhhHHHhhhcHHHHHHHHHHHHHHHHHHHHHhhhcccccccccCCCCCCCChhhhccc
Q psy4218 452 QKKNKKSKKKKKEKEKSAEEKMKEALKKEEEEQREADRLLRMDERKRSYNSMISVKEPTMDSDRGN 517 (520)
Q Consensus 452 ~~~~~~~~~~~~~~~~~~~~kl~~Al~~e~~r~~~~~~~~~~derkR~YNs~~~~~~~teeeM~~~ 517 (520)
++.....+.+++++.|-.+++.++. .|||||+|||||++ +||+||||||
T Consensus 466 ------~~~~~~~~~~~~~~~~~ss~~~~e~----------~d~rkr~yn~~y~~-~~t~~emeay 514 (529)
T KOG2560|consen 466 ------WGERKPEDLDSNEESLPSSLSKEEE----------KDERKRKYNSMYSN-APTEEEMEAY 514 (529)
T ss_pred ------ccccchhhhccccccccccccchhh----------hhhhcccccccccC-CCCHHHHHHH
Confidence 1111223334555556666666552 69999999999999 9999999998
No 2
>PF11708 Slu7: Pre-mRNA splicing Prp18-interacting factor; InterPro: IPR021715 The spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and U5) and proteins, catalyses the excision of introns from pre-mRNAs in two successive trans-esterification reactions. Step 2 depends upon integral spliceosome constituents such as U5 snRNA and Prp8 and non-spliceosomal proteins Prp16, Slu7, Prp18, and Prp22. ATP hydrolysis by the DEAH-box enzyme Prp16 promotes a conformational change in the spliceosome that leads to protection of the 3'ss from targeted RNase H cleavage. This change, which probably reflects binding of the 3'ss PyAG in the catalytic centre of the spliceosome, requires the ordered recruitment of Slu7, Prp18, and Prp22 to the spliceosome. There is a close functional relationship between Prp8, Prp18, and Slu7, and Prp18 interacts with Slu7, so that together they recruit Prp22 to the spliceosome. Most members of the family carry a zinc-finger of the CCHC-type upstream of this domain.
Probab=100.00 E-value=3.2e-84 Score=635.67 Aligned_cols=228 Identities=62% Similarity=0.999 Sum_probs=210.9
Q ss_pred ccccccccCcCCCCCcccHHHHHHHHHHHHHHHHHHHHhhhhcccccCCCCCCCCCCCCCCCccchhhhccccCCCCCcc
Q psy4218 158 IQDYDSKRDRWAGYDPSNHKAIVEHYQKIEEAKRELRADKLDAGVSIDNRGSKEGDEDKDDLEEDEDKYVDEVDMPGTKV 237 (520)
Q Consensus 158 ~ldyDaKRDRWnGYDp~ey~~Vveeyek~e~~r~~~k~~~l~~~~~~~~~~~~~~~~~~~~~d~DedkY~de~d~~g~~~ 237 (520)
.+||||||||||||||++|++||++|+++++++++++++++.. ...+.+.+++++++|++..+|+ ++
T Consensus 1 ~l~yDaKRDRWnGYd~~ey~~vve~~e~~e~~r~~~~~~~~~~-----------~~~d~d~~~e~~~~~~~~~d~~--~~ 67 (239)
T PF11708_consen 1 ELDYDAKRDRWNGYDPEEYKEVVEEYEKIEEARKKLKAEKLED-----------DSDDEDEEDEDEELYLDEADMG--KK 67 (239)
T ss_pred CCCccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHhhhccc-----------ccccchhhhhhhhcccchhhcc--cc
Confidence 3799999999999999999999999999999999988766521 1223455666778999999997 67
Q ss_pred CccccccccccccccchHHHhhccCCCCCccCCCcccccCCCCCCCCCCCCCCccCCCccccccchHHHHHHHHHHHHHH
Q psy4218 238 DSKQRITVRNLRIREDTAKYLRNLDPNSAYYDPKTRSMRDNPYETVANPEDVDYAGENFVRFSGDTRKHATAQLFAWEAY 317 (520)
Q Consensus 238 d~k~r~tvrnLRIREDtAKYL~NLd~nSA~YDPKTRsMRdnP~~~~~~~~~~~faGdnF~R~SGda~e~~~lQ~FAWeA~ 317 (520)
++++++|+|||||||||||||+|||+|||||||||||||+||+ .++++++|+|+||||.|||+.+|.+||+|||+|+
T Consensus 68 ~~k~~~t~rnLRiREDtAkYL~NLd~nsa~YDPKSRsmrd~p~---~~~~~~~~~gdnFvR~sGea~e~~~lq~FAWea~ 144 (239)
T PF11708_consen 68 DSKTRITVRNLRIREDTAKYLLNLDSNSAYYDPKSRSMRDNPA---KDPGDVLFAGDNFVRLSGEAQEFEKLQRFAWEAA 144 (239)
T ss_pred ccccccccccccccccHHHHHHhCCCCCccCCCCccccccCCC---CChhhccccccCceeccccHHHHHHHHHHHHHHH
Confidence 8999999999999999999999999999999999999999996 5788999999999999999999999999999999
Q ss_pred hCCC-ceeeecCCCHHHHHhHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCChhhhhhhhccceeeeccccc---eee---
Q psy4218 318 EKGV-DVHVLAEPTKLELLKKEYEEKKEEFKKEVSSSVIDKYGGAEHLQAPPKALLLAQTEDYVEYSRYGK---VIK--- 390 (520)
Q Consensus 318 ~kG~-dvhl~AnPT~~Ell~Ke~k~kke~~k~~~k~~ileKYGg~e~l~~~p~elll~qtE~yvEY~~~G~---vik--- 390 (520)
++|. +||||||||++|+|+|+|+++|++++.+.+++||+||||++|+..+|++|+|+|||.||||+++|. +++
T Consensus 145 ~kg~~~~hl~AnPT~~E~l~k~~~~kk~~~~~~~k~~ll~kYGg~e~~~~~~~e~~~~qtE~yvey~~~g~~~~~~kSkY 224 (239)
T PF11708_consen 145 KKGGLDVHLQANPTKAELLRKEFKEKKEELKEEKKQSLLEKYGGEEHLDKPPKELLLAQTERYVEYDRSGAEKAKAKSKY 224 (239)
T ss_pred hccCCceeeeeCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccCcchhhhcccccccccccccccccccccccc
Confidence 9999 999999999999999999999999999999999999999999999999999999999999999983 333
Q ss_pred ---cccCCCccccC
Q psy4218 391 ---MYIPTIIPVYG 401 (520)
Q Consensus 391 ---v~~nNHtsVWG 401 (520)
|||||||||||
T Consensus 225 ~EDv~~~NHtsVWG 238 (239)
T PF11708_consen 225 EEDVYINNHTSVWG 238 (239)
T ss_pred hhhhccCCCCeecC
Confidence 99999999999
No 3
>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=89.64 E-value=0.19 Score=31.72 Aligned_cols=17 Identities=41% Similarity=0.919 Sum_probs=15.2
Q ss_pred cccccccCCCCcccccc
Q psy4218 117 ACENCGAMTHKKKDCLE 133 (520)
Q Consensus 117 ACeNCGAmtHkkKDClE 133 (520)
.|-|||.++|..+||-+
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 59999999999999953
No 4
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=71.65 E-value=1.5 Score=33.85 Aligned_cols=17 Identities=35% Similarity=0.903 Sum_probs=15.8
Q ss_pred ccccccccCCCCccccc
Q psy4218 116 GACENCGAMTHKKKDCL 132 (520)
Q Consensus 116 GACeNCGAmtHkkKDCl 132 (520)
..|-+||.++|..++|-
T Consensus 32 ~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECP 48 (49)
T ss_pred hhhcCCCCcCcCHhHcC
Confidence 67999999999999994
No 5
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=63.94 E-value=3.1 Score=31.70 Aligned_cols=17 Identities=47% Similarity=1.068 Sum_probs=14.2
Q ss_pred cccccccCCCCc--ccccc
Q psy4218 117 ACENCGAMTHKK--KDCLE 133 (520)
Q Consensus 117 ACeNCGAmtHkk--KDClE 133 (520)
-|.|||+.+|.+ +.|--
T Consensus 3 kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 3 KCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred cccccccccccccCccCCC
Confidence 499999999998 56754
No 6
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=61.89 E-value=3.6 Score=40.66 Aligned_cols=24 Identities=42% Similarity=0.785 Sum_probs=19.3
Q ss_pred ccccccccCCCCccccccCccccccc
Q psy4218 116 GACENCGAMTHKKKDCLERPRKVLAK 141 (520)
Q Consensus 116 GACeNCGAmtHkkKDClERPRK~GAk 141 (520)
--|-|||..+|-..||. |++.+-+
T Consensus 98 ~~C~~Cg~~GH~~~dC~--P~~~~~~ 121 (190)
T COG5082 98 KKCYNCGETGHLSRDCN--PSKDQQK 121 (190)
T ss_pred cccccccccCccccccC--cccccCc
Confidence 35999999999999999 6655544
No 7
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=56.10 E-value=4.9 Score=30.78 Aligned_cols=19 Identities=26% Similarity=0.728 Sum_probs=16.9
Q ss_pred cccccccccCCCCcccccc
Q psy4218 115 KGACENCGAMTHKKKDCLE 133 (520)
Q Consensus 115 KGACeNCGAmtHkkKDClE 133 (520)
.+.|.|||..+|-.-+|--
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 3689999999999999974
No 8
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=47.66 E-value=9.1 Score=35.24 Aligned_cols=19 Identities=37% Similarity=0.952 Sum_probs=15.3
Q ss_pred ccccccccCCCCccccccC
Q psy4218 116 GACENCGAMTHKKKDCLER 134 (520)
Q Consensus 116 GACeNCGAmtHkkKDClER 134 (520)
.+|-|||.++|-.+||.++
T Consensus 130 ~~C~~Cg~~gH~~~dCp~~ 148 (148)
T PTZ00368 130 KTCYNCGQTGHLSRDCPDK 148 (148)
T ss_pred CccccCCCcCcccccCCCC
Confidence 5788888888888888763
No 9
>KOG0119|consensus
Probab=45.24 E-value=9.5 Score=42.71 Aligned_cols=19 Identities=53% Similarity=1.069 Sum_probs=18.1
Q ss_pred ccccccccCCCCccccccC
Q psy4218 116 GACENCGAMTHKKKDCLER 134 (520)
Q Consensus 116 GACeNCGAmtHkkKDClER 134 (520)
-+|.|||...|+.-||-.|
T Consensus 262 ~~c~~cg~~~H~q~~cp~r 280 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGR 280 (554)
T ss_pred ccccccCCCccccccCCcc
Confidence 5899999999999999998
No 10
>COG2947 Uncharacterized conserved protein [Function unknown]
Probab=44.78 E-value=11 Score=36.24 Aligned_cols=56 Identities=27% Similarity=0.345 Sum_probs=33.1
Q ss_pred cCCCCCccCCCcccccCCCCCCCCCCCCCCccCCCccccccchHHHHHHH-HHHHH--H-HhCCCceeee
Q psy4218 261 LDPNSAYYDPKTRSMRDNPYETVANPEDVDYAGENFVRFSGDTRKHATAQ-LFAWE--A-YEKGVDVHVL 326 (520)
Q Consensus 261 Ld~nSA~YDPKTRsMRdnP~~~~~~~~~~~faGdnF~R~SGda~e~~~lQ-~FAWe--A-~~kG~dvhl~ 326 (520)
.||+|-|||||+-- ++|-=.. -+=.|||.--....+..|. .|.|+ + -.+|..+.++
T Consensus 77 ~d~~spYyDPka~~--e~pRW~~--------Vdv~~v~~~~~~vtL~~lK~~~~~~~~~~l~~g~RLSV~ 136 (156)
T COG2947 77 FDPASPYYDPKATP--EDPRWYC--------VDVRFVRKLPRPVTLKELKANPELAEMSLLVKGNRLSVQ 136 (156)
T ss_pred cCCCCcccCccccc--CCCCeeE--------EeeHHHhhcCCCccHHHHhcCcchhhhhhhhccCeeeee
Confidence 79999999999864 6664321 2235777655555565553 34443 2 3566554443
No 11
>smart00343 ZnF_C2HC zinc finger.
Probab=44.14 E-value=10 Score=25.31 Aligned_cols=16 Identities=44% Similarity=1.010 Sum_probs=14.7
Q ss_pred ccccccCCCCcccccc
Q psy4218 118 CENCGAMTHKKKDCLE 133 (520)
Q Consensus 118 CeNCGAmtHkkKDClE 133 (520)
|-+||...|..++|.+
T Consensus 2 C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 2 CYNCGKEGHIARDCPK 17 (26)
T ss_pred CccCCCCCcchhhCCc
Confidence 8899999999999974
No 12
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=44.02 E-value=9.6 Score=37.80 Aligned_cols=23 Identities=35% Similarity=0.696 Sum_probs=19.1
Q ss_pred ccccccccccccccCCCCccccc
Q psy4218 110 AKKFRKGACENCGAMTHKKKDCL 132 (520)
Q Consensus 110 atKyRKGACeNCGAmtHkkKDCl 132 (520)
+..-.--+|-|||-.+|.++||-
T Consensus 55 ~~~~~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 55 AIREENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred cccccccccchhcccCcccccCC
Confidence 33344578999999999999998
No 13
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=40.08 E-value=16 Score=27.38 Aligned_cols=26 Identities=23% Similarity=0.459 Sum_probs=15.7
Q ss_pred cccccccccCCCCccccccCcccccc
Q psy4218 115 KGACENCGAMTHKKKDCLERPRKVLA 140 (520)
Q Consensus 115 KGACeNCGAmtHkkKDClERPRK~GA 140 (520)
.+.|-.||.-.|-..||.-+-...|-
T Consensus 2 ~~~CprC~kg~Hwa~~C~sk~d~~G~ 27 (36)
T PF14787_consen 2 PGLCPRCGKGFHWASECRSKTDVDGN 27 (36)
T ss_dssp --C-TTTSSSCS-TTT---TCCCCCE
T ss_pred CccCcccCCCcchhhhhhhhhcccCC
Confidence 58899999999999999987555553
No 14
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=36.67 E-value=19 Score=33.15 Aligned_cols=23 Identities=30% Similarity=0.788 Sum_probs=18.4
Q ss_pred cccccccccCCCCccccccCccc
Q psy4218 115 KGACENCGAMTHKKKDCLERPRK 137 (520)
Q Consensus 115 KGACeNCGAmtHkkKDClERPRK 137 (520)
.+.|-+||.+.|..+||.++++.
T Consensus 77 ~~~C~~Cg~~GH~~~~C~~~~~~ 99 (148)
T PTZ00368 77 PRSCYNCGQTGHISRECPNRAKG 99 (148)
T ss_pred CcccCcCCCCCcccccCCCcccc
Confidence 35689999999999999887654
No 15
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=26.78 E-value=24 Score=27.86 Aligned_cols=10 Identities=50% Similarity=1.198 Sum_probs=8.3
Q ss_pred cccccccccc
Q psy4218 114 RKGACENCGA 123 (520)
Q Consensus 114 RKGACeNCGA 123 (520)
++|-||||-.
T Consensus 4 k~GYCE~C~~ 13 (49)
T PF07535_consen 4 KPGYCENCRV 13 (49)
T ss_pred CCccCccccc
Confidence 5799999974
No 16
>KOG3490|consensus
Probab=23.87 E-value=25 Score=32.13 Aligned_cols=18 Identities=50% Similarity=0.905 Sum_probs=14.5
Q ss_pred cccccccccccccCCCCcc
Q psy4218 111 KKFRKGACENCGAMTHKKK 129 (520)
Q Consensus 111 tKyRKGACeNCGAmtHkkK 129 (520)
.-|++.-|+||+ |-|-+-
T Consensus 21 ~~F~~dGC~Nc~-~l~mkg 38 (111)
T KOG3490|consen 21 NGFRKDGCENCP-MLNMKG 38 (111)
T ss_pred hhhhhcCCCCch-hhhhcc
Confidence 458999999999 877654
No 17
>PF09524 Phg_2220_C: Conserved phage C-terminus (Phg_2220_C); InterPro: IPR011741 This entry is represented by the C-terminal domain of Bacteriophage r1t, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Probab=23.79 E-value=24 Score=30.09 Aligned_cols=18 Identities=22% Similarity=0.619 Sum_probs=15.7
Q ss_pred cCcCC-CCCcccHHHHHHH
Q psy4218 165 RDRWA-GYDPSNHKAIVEH 182 (520)
Q Consensus 165 RDRWn-GYDp~ey~~Vvee 182 (520)
|.||+ ||+.++++.||+.
T Consensus 25 ~aRl~eG~t~edf~~VID~ 43 (74)
T PF09524_consen 25 KARLNEGYTLEDFKKVIDN 43 (74)
T ss_pred HHHHHCCCCHHHHHHHHHH
Confidence 67997 9999999999764
No 18
>TIGR02220 phg_TIGR02220 phage conserved hypothetical protein, C-terminal domain. This model represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Probab=22.67 E-value=26 Score=30.08 Aligned_cols=18 Identities=28% Similarity=0.833 Sum_probs=15.9
Q ss_pred ccCcCC-CCCcccHHHHHH
Q psy4218 164 KRDRWA-GYDPSNHKAIVE 181 (520)
Q Consensus 164 KRDRWn-GYDp~ey~~Vve 181 (520)
=|+||+ ||..++++.||+
T Consensus 27 I~aR~~eg~~~~dfk~VId 45 (77)
T TIGR02220 27 IKARWNEGYTLEDFKKVID 45 (77)
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 378998 999999999985
No 19
>PTZ00076 60S ribosomal protein L17; Provisional
Probab=22.27 E-value=68 Score=33.23 Aligned_cols=40 Identities=38% Similarity=0.600 Sum_probs=31.1
Q ss_pred ccCHHHHHHHHHHHHHHhcCCCCCcccccCCCCCCCcccccccCCcccC
Q psy4218 26 KKSREDWRKAKELEEARKAGTAPAAVDEHGRDINPHIPQYISSAPWYFG 74 (520)
Q Consensus 26 ~~sre~~rk~keLeeaRKaG~aPa~~De~GkeiNPHIPqYIs~aPWY~~ 74 (520)
+.||-++|| -+-.||+.|+ +|++|+.|+. --+..+|||-.
T Consensus 154 ~~~r~~~r~--~~~~~~~~~l----~~~~~~~~~~---~~~~~~~~~~~ 193 (253)
T PTZ00076 154 KKTRRNFRK--YFNIAKKFGL----LDENGNLISD---ISALEKPWYEE 193 (253)
T ss_pred HHHHhhHHH--HHHHHHHhCc----cCCCCCcccc---ccccccchhhh
Confidence 456777774 7899999997 5889999987 23457899975
No 20
>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases. This domain is found associated with a helicase domain of superfamily type II [].
Probab=21.02 E-value=1e+02 Score=31.10 Aligned_cols=37 Identities=35% Similarity=0.760 Sum_probs=25.3
Q ss_pred CcccccccccccccccccCcCCCCCcc--c------HHHHHHHHHHHHHHHHHHH
Q psy4218 148 ACDEFVQPKLIQDYDSKRDRWAGYDPS--N------HKAIVEHYQKIEEAKRELR 194 (520)
Q Consensus 148 a~DE~iq~~~~ldyDaKRDRWnGYDp~--e------y~~Vveeyek~e~~r~~~k 194 (520)
++|-++| +-||+||.+. + -..+++.|..+-++-..++
T Consensus 165 ~~DTL~Q----------mgRwFGYR~gY~dl~Ri~~~~~l~~~f~~i~~~~e~lr 209 (239)
T PF10593_consen 165 QYDTLMQ----------MGRWFGYRPGYEDLCRIYMPEELYDWFRHIAEAEEELR 209 (239)
T ss_pred hHHHHHH----------HhhcccCCcccccceEEecCHHHHHHHHHHHHHHHHHH
Confidence 5677776 6799999987 1 1466788877755544443
No 21
>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene. The molecular function of this protein is uncertain.
Probab=20.13 E-value=26 Score=39.62 Aligned_cols=29 Identities=34% Similarity=0.739 Sum_probs=19.7
Q ss_pred HHHHhcCCCCCccc---ccC--CCCCCCcccccc
Q psy4218 39 EEARKAGTAPAAVD---EHG--RDINPHIPQYIS 67 (520)
Q Consensus 39 eeaRKaG~aPa~~D---e~G--keiNPHIPqYIs 67 (520)
|.|-+-|+.||+.. .=. -+.|||+|.|+.
T Consensus 351 e~a~rRGls~ae~~aveAi~RAvefNPHVp~YLL 384 (539)
T PF04184_consen 351 EAASRRGLSPAEMNAVEAIHRAVEFNPHVPKYLL 384 (539)
T ss_pred hhhhhcCCChhHHHHHHHHHHHHHhCCCCchhhh
Confidence 45566777777743 112 369999999974
Done!