Query 003096
Match_columns 848
No_of_seqs 233 out of 440
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 16:56:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003096.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003096hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2169 Zn-finger transcriptio 100.0 5.1E-39 1.1E-43 370.8 23.5 358 13-463 1-394 (636)
2 PF14324 PINIT: PINIT domain; 99.8 3E-18 6.5E-23 166.0 10.1 135 140-290 1-144 (144)
3 PF02891 zf-MIZ: MIZ/SP-RING z 99.6 3.6E-17 7.7E-22 133.4 1.5 42 381-422 7-48 (50)
4 PF02037 SAP: SAP domain; Int 98.0 4.2E-06 9.1E-11 64.1 3.5 35 12-46 1-35 (35)
5 KOG2169 Zn-finger transcriptio 97.9 5E-05 1.1E-09 89.9 11.9 449 381-847 22-542 (636)
6 smart00513 SAP Putative DNA-bi 97.9 1.4E-05 3.1E-10 60.8 4.0 34 13-46 2-35 (35)
7 PF11789 zf-Nse: Zinc-finger o 96.6 0.0011 2.3E-08 56.2 1.6 52 336-420 2-53 (57)
8 KOG1973 Chromatin remodeling p 96.2 0.0027 5.8E-08 68.4 2.4 52 95-154 216-268 (274)
9 PF00628 PHD: PHD-finger; Int 95.9 0.0031 6.7E-08 50.8 1.0 49 100-153 1-50 (51)
10 COG5034 TNG2 Chromatin remodel 94.0 0.029 6.4E-07 60.2 2.1 49 98-154 221-270 (271)
11 KOG1844 PHD Zn-finger proteins 93.1 0.048 1E-06 62.6 2.2 56 96-160 84-140 (508)
12 smart00249 PHD PHD zinc finger 93.1 0.098 2.1E-06 39.9 3.2 44 102-151 4-47 (47)
13 PF13831 PHD_2: PHD-finger; PD 88.1 0.11 2.4E-06 40.5 -0.7 35 110-152 2-36 (36)
14 KOG4323 Polycomb-like PHD Zn-f 85.9 0.33 7.1E-06 56.4 1.1 54 98-154 171-224 (464)
15 PF07498 Rho_N: Rho terminatio 83.6 1.4 3.1E-05 35.4 3.6 35 12-46 2-38 (43)
16 PF12949 HeH: HeH/LEM domain; 73.3 2.3 5E-05 33.4 1.8 28 13-40 2-31 (35)
17 KOG2979 Protein involved in DN 72.7 1 2.2E-05 49.0 -0.5 51 336-419 167-217 (262)
18 KOG4259 Putative nucleic acid- 65.7 6.7 0.00015 42.2 3.8 35 13-47 7-41 (260)
19 PF10208 Armet: Degradation ar 57.4 8.1 0.00018 39.4 2.6 35 12-46 104-140 (154)
20 PF02837 Glyco_hydro_2_N: Glyc 43.6 70 0.0015 31.1 6.6 65 188-277 72-138 (167)
21 KOG0957 PHD finger protein [Ge 36.3 37 0.00079 40.5 3.8 59 96-158 118-183 (707)
22 TIGR00599 rad18 DNA repair pro 34.0 47 0.001 38.6 4.3 36 13-48 267-302 (397)
23 PLN03124 poly [ADP-ribose] pol 25.9 49 0.0011 40.7 2.7 38 13-50 3-40 (643)
24 COG3683 ABC-type uncharacteriz 24.6 1.3E+02 0.0027 32.6 5.1 76 228-307 89-170 (213)
25 PRK03298 hypothetical protein; 22.8 1.4E+02 0.003 32.4 5.1 41 443-483 21-61 (224)
26 PF08531 Bac_rhamnosid_N: Alph 22.8 44 0.00095 33.8 1.4 47 229-277 15-64 (172)
27 COG5222 Uncharacterized conser 21.2 33 0.00072 38.5 0.2 50 381-435 279-331 (427)
28 PF13670 PepSY_2: Peptidase pr 20.2 1.6E+02 0.0034 26.3 4.2 21 443-463 42-62 (83)
29 KOG0825 PHD Zn-finger protein 20.2 53 0.0011 41.2 1.5 63 98-167 215-282 (1134)
No 1
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=100.00 E-value=5.1e-39 Score=370.78 Aligned_cols=358 Identities=20% Similarity=0.310 Sum_probs=262.4
Q ss_pred hhcCHHHHHHHH-HHcCCCCCC--CHHHHHHHHHHhcCchh---HHHHHHHHHHhh-c--cccchhhhhhcCCCCCcccc
Q 003096 13 VNFRMKELKDVL-TKLGLPKQG--KKQDLVDRIFHQLSDEG---VARIIDDTYRKM-Q--ISEAADLAIMGQSGLDICNV 83 (848)
Q Consensus 13 ~sFRV~ELk~lL-~~lGl~KsG--rKqEL~dRil~lL~~~~---v~~~I~elYrk~-q--~~~~~~~a~~~q~~~~~s~v 83 (848)
+++||+||+.++ ++.++.+.| +|++|+-|++.++...+ ++++|+++|++. . ...+.++..+. ..
T Consensus 1 m~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~r~l~~~~~~~~~~~q~~i~~~~~~~~~~~~~~~~~~~~~~----~~--- 73 (636)
T KOG2169|consen 1 MSLRVSSLQVLLSGAIGRSFPGQVNKHKLAPRALTLVGSGCKPYLQMVIKELYQRQYPNGQQQPIDLPAVK----LH--- 73 (636)
T ss_pred CCcccccccccchhhhccccccccchhhhhhhhhcccccCCchhhhhhhhhhhhhhccccccccccccccc----cC---
Confidence 468999999999 778999999 99999999999999886 689999999853 1 11111211111 00
Q ss_pred ccccccccccCCCCccccCCCCCCCCCCceeeCCCccccccccccccCCCCcccc--ccCCCCcccccccccccCCchhh
Q 003096 84 KVEMEAEDSLNLGGKIFCPCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEE--IRLLPPLFFCETCRIKRADPFWI 161 (848)
Q Consensus 84 ~~~~~~~~~~~~~~~vRCiCGSSl~s~~mIQC~~~~C~v~QH~sCv~Ip~Kp~~~--ipvhPdvFyCe~CRLKr~dPFy~ 161 (848)
+. .. ++..... |....|..-..++...+.+ -+.+|++ ||++ .|||+
T Consensus 74 -~~------~~--------~~~~~~~----------~~~~~~~~~~~~~~~~l~g~~~~~~~~~------~~~~-~~~y~ 121 (636)
T KOG2169|consen 74 -PN------VV--------PPFYPLL----------WQLLRHPTQQPVTPSSLLGPPLPFHPDV------KLKK-LPFYD 121 (636)
T ss_pred -Cc------cc--------Cccccch----------hcccccCCCCCCCcccccCCCCcCCCcc------cccC-Cchhe
Confidence 00 00 0000000 0111111100111111111 1357888 7885 99999
Q ss_pred hhhhccCceEeeeccCCCCCCCCCceeEEEEEeCHhhHHhhcC---------CCcEEEEEEEecCCCccccccCCCceEE
Q 003096 162 TVAHLVSPMKLVASNIPTDGTNPLQKAEAAFHLTKAHSDLLQN---------TEYDVQAWCILLNDKVSFRMQWPLHAEL 232 (848)
Q Consensus 162 ~i~~Ll~P~~L~~s~i~~dG~~~~Q~~e~~F~LT~~q~~lL~~---------~~y~vQlrCi~l~d~v~~~~~wP~~~el 232 (848)
++..+++|+.+..+..+ +++...+.|+||++++..+.. .++.+ |+. +..++++.+||.+..+
T Consensus 122 ~l~~~~~p~~~~~~~~~-----~~~~~~~~f~lt~~~~~~i~~~~~~~~~~k~~~~~---~~~-~~s~p~e~~~p~~~~~ 192 (636)
T KOG2169|consen 122 VLSELIKPHVLHSSNSP-----SLSESPFLFALTPEQVSGISSRPDVLPGSKSEGSV---CLM-ETSCPQEDHFPPNVQV 192 (636)
T ss_pred ecccccCceeecCcCCC-----Ccccccchhhcchhhhhhcccccccccccccccce---eec-cccCccccccCceeEE
Confidence 99999999999876542 566778899999999875531 22333 555 6678899999999999
Q ss_pred EEcCeEeeecc--CCCcccCCCCCCCCCCc-ccc--cccCc-ccEEEEEEe--ecceEEEEEEEEeecCHHHHHHhcccC
Q 003096 233 QVNGLLVRTVN--RPGTQLLGSNGRDDGAL-ITL--YIGEG-VNQISLSGC--DIRNFCFGVRLVKRQTVAQVLSLVPKE 304 (848)
Q Consensus 233 ~VNg~~v~~~~--RPg~~~~g~ngR~d~pi-IT~--~i~~g-~N~I~is~~--d~r~y~~~V~LVk~~t~eqll~~I~~~ 304 (848)
+||+..+.+.. -|.....-+.+|...|. ||. ++..- .|.+.+.|. ..+.|.+++|+|+.+|.++||++++..
T Consensus 193 ~vn~~~~~l~~~~~~~n~~~~~~~~~~~P~n~t~~~~~~~~~~~~~~~~~~~~~~~~ysl~~~~v~~~t~~~llq~~~~~ 272 (636)
T KOG2169|consen 193 KVNNSPCQLPFGYMPNNKHGLEPKRPSRPGNITSLSRLSVTTPNQITVLWTAQGGKSYSLSVYFVEGLTSKDLLQRLKQN 272 (636)
T ss_pred EecCCcceeeccccCCCCcccccCCCCCCCcCcccccccccccccceEEEEeccCcccceEEEEecccCHHHHHHHHhcc
Confidence 99999998541 11111112235777788 999 44444 488998885 579999999999999999999999875
Q ss_pred CCC-CChHHHHHHHHHhhCCccCCCCCCCCCceeeeeceEEEecCCCCcccccccccccCcCcccccchhhccccccccc
Q 003096 305 TAG-EVFEDALTRVRRCFGGVATGNEDGDSDLEIIADSIIVNLRCPKVFSEENSDVLLFGIPFDCTFHWLFLTCNWQMSG 383 (848)
Q Consensus 305 ~~g-~~~edal~rIkr~l~~~~~~n~d~D~DlEIv~~s~~VSL~CP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lS~ 383 (848)
.+. ..++.+++.|++.+ .+++|.||++++++|||.|| |++
T Consensus 273 ~~~~~~~~~s~~~~~~~l--------~~~~d~~i~tt~~~vSL~CP-------------------------------l~~ 313 (636)
T KOG2169|consen 273 GKINRNLSQSDALIKKKL--------TAGPDSEIATTSLRVSLNCP-------------------------------LSK 313 (636)
T ss_pred CCccCchhHhHHHhhccc--------ccCCcccceeccceeEecCC-------------------------------ccc
Confidence 332 23466777777443 44566689999999999999 999
Q ss_pred cceeccccccCcCcccccCHHHHHHHhcCCCCceee-------cchhhhhhhHHHHHHHhhhhhcCCCCeeEEEEccCCc
Q 003096 384 SRIRVAGRFKPCVHTGCFDLETFVELNQRTRKASYS-------FILLFLSMFRIFKLIKVGKMRNFADDLTEIEVKHDGS 456 (848)
Q Consensus 384 ~RI~vP~Rg~~C~HlQCFDLetFL~mNer~~tW~C~-------~~~L~l~ID~yf~~IL~s~l~~~~~dv~eIev~~DGS 456 (848)
+||++|||+..|+|+|||||.+||+||++++||+|+ |++|+ ||+||..|| .++..+++||++.+||+
T Consensus 314 ~Rm~~P~r~~~CkHlQcFD~~~~lq~n~~~pTW~CPVC~~~~~~e~l~--iD~~~~~iL----~~~~~~~~ev~~~~dGs 387 (636)
T KOG2169|consen 314 MRMSLPARGHTCKHLQCFDALSYLQMNEQKPTWRCPVCQKAAPFEGLI--IDGYFLNIL----QSCQANVEEVEVSEDGS 387 (636)
T ss_pred ceeecCCcccccccceecchhhhHHhccCCCeeeCccCCccccccchh--hhHHHHHHH----hhccCCCcceEecCCCc
Confidence 999999999999999999999999999999999984 88899 999999999 67888899999999999
Q ss_pred EEEeecC
Q 003096 457 WRVKCKG 463 (848)
Q Consensus 457 W~v~~~~ 463 (848)
|++...+
T Consensus 388 w~pi~~~ 394 (636)
T KOG2169|consen 388 WKPIPEE 394 (636)
T ss_pred eecCccc
Confidence 9966544
No 2
>PF14324 PINIT: PINIT domain; PDB: 3I2D_A.
Probab=99.75 E-value=3e-18 Score=165.98 Aligned_cols=135 Identities=27% Similarity=0.433 Sum_probs=84.2
Q ss_pred cCCCCcccccccccccCCchhhhhhhccCceEeeeccCCCCCCCCCceeEEEEEeCHhhHHhhcC--CCcEEEEEEEec-
Q 003096 140 RLLPPLFFCETCRIKRADPFWITVAHLVSPMKLVASNIPTDGTNPLQKAEAAFHLTKAHSDLLQN--TEYDVQAWCILL- 216 (848)
Q Consensus 140 pvhPdvFyCe~CRLKr~dPFy~~i~~Ll~P~~L~~s~i~~dG~~~~Q~~e~~F~LT~~q~~lL~~--~~y~vQlrCi~l- 216 (848)
|++|++ +|| .+|||+++ ++|.|+.+..... ...+...+.|+||++|+++|++ ..|+|+|+|...
T Consensus 1 ~~~~~~------~Fk-~sPFY~~~-~~i~~~~~~~~~~-----~~r~~~~~~F~L~~~~~~~l~~~~~~~~v~L~c~~~~ 67 (144)
T PF14324_consen 1 PVHPDL------RFK-PSPFYKVL-RLIHPTPLLPASS-----SGRQTCSFSFKLSPDQVELLKSSNPSYQVYLFCGKFC 67 (144)
T ss_dssp -------------B---BTTEEEE-EEEEEEEEEE--E-----EEEEEEEEEE---HHHHHHHHSTT--EEEEEEEEESS
T ss_pred CCCCcc------Eec-cCCCccee-EEcCCcccccccc-----CCCCeEEEEEEECHHHHHHHhcCCCCeEEEEEEeccc
Confidence 356777 699 59999988 8888888776432 2456788999999999999976 789999999884
Q ss_pred --CCCccccccCCCceEEEEcCeEeeeccCCCcccCCCCCCCCCCcccccccCc---ccEEEEEEe-ecceEEEEEEEEe
Q 003096 217 --NDKVSFRMQWPLHAELQVNGLLVRTVNRPGTQLLGSNGRDDGALITLYIGEG---VNQISLSGC-DIRNFCFGVRLVK 290 (848)
Q Consensus 217 --~d~v~~~~~wP~~~el~VNg~~v~~~~RPg~~~~g~ngR~d~piIT~~i~~g---~N~I~is~~-d~r~y~~~V~LVk 290 (848)
+....+.++||.+++|+|||+.|++..| .+++|+|...++.||++++.. .|+|+|+|. +.+.|+++|||||
T Consensus 68 ~~~~~~~q~i~FP~~~evkvN~~~v~~~~~---glknKpGt~rPvdIT~~l~~~~~~~N~i~v~y~~~~~~Y~~~vylVk 144 (144)
T PF14324_consen 68 LSESSGNQPIEFPPPCEVKVNGKQVKLNNR---GLKNKPGTARPVDITPYLRLSPPQTNRIEVTYANTKKKYYVYVYLVK 144 (144)
T ss_dssp -SS-GGGB-----SSEEEEETTEE--S--S---S-TTS-GGGS-EE-GGG---S-SS-EEEEEEEEEESS-EEEEEEEEE
T ss_pred cCCCCCccccccCCCeEEEEeCEEcccCcc---CCCCCCCCCCCcccchhhcccCCCCeEEEEEEeCCCCeEEEEEEEEC
Confidence 3456788999999999999999997655 456778875455599999876 999999996 7899999999997
No 3
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=99.64 E-value=3.6e-17 Score=133.43 Aligned_cols=42 Identities=48% Similarity=0.641 Sum_probs=31.1
Q ss_pred ccccceeccccccCcCcccccCHHHHHHHhcCCCCceeecch
Q 003096 381 MSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKASYSFIL 422 (848)
Q Consensus 381 lS~~RI~vP~Rg~~C~HlQCFDLetFL~mNer~~tW~C~~~~ 422 (848)
||++||++|+||+.|+|+|||||++||++|+++++|+||+.+
T Consensus 7 ls~~~i~~P~Rg~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~ 48 (50)
T PF02891_consen 7 LSFQRIRIPVRGKNCKHLQCFDLESFLESNQRTPKWKCPICN 48 (50)
T ss_dssp TTSSB-SSEEEETT--SS--EEHHHHHHHHHHS---B-TTT-
T ss_pred CCCCEEEeCccCCcCcccceECHHHHHHHhhccCCeECcCCc
Confidence 999999999999999999999999999999999999998763
No 4
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=98.04 E-value=4.2e-06 Score=64.05 Aligned_cols=35 Identities=37% Similarity=0.647 Sum_probs=31.3
Q ss_pred HhhcCHHHHHHHHHHcCCCCCCCHHHHHHHHHHhc
Q 003096 12 LVNFRMKELKDVLTKLGLPKQGKKQDLVDRIFHQL 46 (848)
Q Consensus 12 l~sFRV~ELk~lL~~lGl~KsGrKqEL~dRil~lL 46 (848)
+..++|+|||..|...|++.+|+|+||++|+.++|
T Consensus 1 l~~l~v~eLk~~l~~~gL~~~G~K~~Li~Rl~~~l 35 (35)
T PF02037_consen 1 LSKLTVAELKEELKERGLSTSGKKAELIERLKEHL 35 (35)
T ss_dssp TTTSHHHHHHHHHHHTTS-STSSHHHHHHHHHHHH
T ss_pred CCcCcHHHHHHHHHHCCCCCCCCHHHHHHHHHHhC
Confidence 35789999999999999999999999999998864
No 5
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=97.94 E-value=5e-05 Score=89.95 Aligned_cols=449 Identities=13% Similarity=0.021 Sum_probs=268.9
Q ss_pred ccccceeccccccCcCcccccC--HHHHHHHhc--CCCCcee-------ecchhhhhhhHHHHHHHhhhhhcCCC-CeeE
Q 003096 381 MSGSRIRVAGRFKPCVHTGCFD--LETFVELNQ--RTRKASY-------SFILLFLSMFRIFKLIKVGKMRNFAD-DLTE 448 (848)
Q Consensus 381 lS~~RI~vP~Rg~~C~HlQCFD--LetFL~mNe--r~~tW~C-------~~~~L~l~ID~yf~~IL~s~l~~~~~-dv~e 448 (848)
+...+.++.+|+..|.+.+|+. ..-+-+..+ +..+|.+ +..-.. ...++..+- ..++.... -+..
T Consensus 22 ~~~~~~~~~~r~l~~~~~~~~~~~q~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~-~~~~~~~~~~~~~ 98 (636)
T KOG2169|consen 22 GQVNKHKLAPRALTLVGSGCKPYLQMVIKELYQRQYPNGQQQPIDLPAVKLHPNV--VPPFYPLLW-QLLRHPTQQPVTP 98 (636)
T ss_pred cccchhhhhhhhhcccccCCchhhhhhhhhhhhhhccccccccccccccccCCcc--cCccccchh-cccccCCCCCCCc
Confidence 6678999999999999999998 555555554 3345553 111222 444555553 23344333 4666
Q ss_pred EEEcc---CCcEEEeecCCC-----CCCCCccCCCCccccccccccccceeeeeeccC----CceeeeEec-------cC
Q 003096 449 IEVKH---DGSWRVKCKGEN-----NNLAEWHSPDGSTYAARSEVVSNSETKQLVNSG----QTIIARIKK-------NL 509 (848)
Q Consensus 449 Iev~~---DGSW~v~~~~E~-----~~~~~w~~pdg~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~-------~~ 509 (848)
..+.. +..|+++.++.. .++..|+...........+....+...+.+.++ +.+.-+.|. ..
T Consensus 99 ~~l~g~~~~~~~~~~~~~~~~y~~l~~~~~p~~~~~~~~~~~~~~~~~f~lt~~~~~~i~~~~~~~~~~k~~~~~~~~~~ 178 (636)
T KOG2169|consen 99 SSLLGPPLPFHPDVKLKKLPFYDVLSELIKPHVLHSSNSPSLSESPFLFALTPEQVSGISSRPDVLPGSKSEGSVCLMET 178 (636)
T ss_pred ccccCCCCcCCCcccccCCchheecccccCceeecCcCCCCcccccchhhcchhhhhhcccccccccccccccceeeccc
Confidence 77766 799999987764 778899988888873333333233322222221 222223333 34
Q ss_pred CcceEEccCCCCCC---CccccccccCCcceeEecccCCCCCCCCCCC---CcccCCCCC-------ccccCCCCCCCCC
Q 003096 510 SANVDVSKYWSTSP---NKHMSYHVENNSEKIITMSSSASGCSRDEED---PTVNQDTNS-------RKDLNDIPHRIDP 576 (848)
Q Consensus 510 ~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~sss~~~~~~~~~~---~~~~~~~~~-------~~~~~~~~~~~~~ 576 (848)
++.||...+..... .+.++-.+.+...+..++....++.-++..+ .++..+... ...-.++...+..
T Consensus 179 s~p~e~~~p~~~~~~vn~~~~~l~~~~~~~n~~~~~~~~~~~P~n~t~~~~~~~~~~~~~~~~~~~~~~~~ysl~~~~v~ 258 (636)
T KOG2169|consen 179 SCPQEDHFPPNVQVKVNNSPCQLPFGYMPNNKHGLEPKRPSRPGNITSLSRLSVTTPNQITVLWTAQGGKSYSLSVYFVE 258 (636)
T ss_pred cCccccccCceeEEEecCCcceeeccccCCCCcccccCCCCCCCcCcccccccccccccceEEEEeccCcccceEEEEec
Confidence 67777666544333 1222222223444445555555555555555 444443322 3344466667777
Q ss_pred CCCCCCCCCC-CCCCccEEEecCCCcccCccC-CCcccCCCCC-----CCCCCCCCCcccccCCCCCCCCCCCccCCCCC
Q 003096 577 IFGTGNQTDG-LIGDTDIIVLSDSEEDNDHLA-PSTSYQSYHP-----IDSAPDGICESYFEDPAFDGGDGPCFGPFNGT 649 (848)
Q Consensus 577 ~~~~~~~~~~-~~~~~~~ivlsds~~~~~~~~-~~~~~~~~~~-----~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~ 649 (848)
.++..+...+ -.......+++.++......+ .+.-|+-.++ +.-+-.+.--.|-..+.....- .||.+--=.
T Consensus 259 ~~t~~~llq~~~~~~~~~~~~~~s~~~~~~~l~~~~d~~i~tt~~~vSL~CPl~~~Rm~~P~r~~~CkHl-QcFD~~~~l 337 (636)
T KOG2169|consen 259 GLTSKDLLQRLKQNGKINRNLSQSDALIKKKLTAGPDSEIATTSLRVSLNCPLSKMRMSLPARGHTCKHL-QCFDALSYL 337 (636)
T ss_pred ccCHHHHHHHHhccCCccCchhHhHHHhhcccccCCcccceeccceeEecCCcccceeecCCcccccccc-eecchhhhH
Confidence 7766555222 225556666788887755555 5555554444 3344455556666666655531 244433112
Q ss_pred cCcccccCcCCCCCCCCCCcceeeccccccccccccCCC--CCcccCCCCCCCCCCCCccccCCCCcCCCCccccccccc
Q 003096 650 VDAVGLSNWSYPSGTQAGSSFQVFDAVSNVSDVFVDLDH--PSVACSLPMNGYKSPSKSTLTCDSGVLDSPVCHSNIDIG 727 (848)
Q Consensus 650 ~~~~~~~~w~~~s~~~~~~~~q~~~s~~dvsd~~v~~~H--~~i~c~~~~~~y~~~~~~tl~~~~~~~d~~~~~~~~d~~ 727 (848)
......+-|.+| -.+....|.-+-.|..+.+.|.+++| ..|.|... -+|+...-..-++-...+++.+ +.+
T Consensus 338 q~n~~~pTW~CP-VC~~~~~~e~l~iD~~~~~iL~~~~~~~~ev~~~~d-Gsw~pi~~~~~~~~~~~~~~~~-----~~~ 410 (636)
T KOG2169|consen 338 QMNEQKPTWRCP-VCQKAAPFEGLIIDGYFLNILQSCQANVEEVEVSED-GSWKPIPEEAEADISVLDGPDV-----GVN 410 (636)
T ss_pred HhccCCCeeeCc-cCCccccccchhhhHHHHHHHhhccCCCcceEecCC-CceecCccccccccccCCCCCC-----CCC
Confidence 456788999998 56777889999999999999999997 57888766 4553222221111111122222 111
Q ss_pred ccccccccccccccccCCCCCCcceeeccCCCCccc-----c-ccCCCCCCCCCceEEEeCCccCC-CCCCCCccccccc
Q 003096 728 EQLIDISEQLIENTLPFVREDPSIGHFVPSQPTALF-----S-ESNSGNYTSENWISLRLGSTCAD-TGSHSQSATTNAL 800 (848)
Q Consensus 728 ~~~~~~~~~lvdn~l~f~~~dpslqiflp~~p~~~~-----~-~~~s~~~~~~dwisl~l~~~~~~-~g~~~~~~~~~~~ 800 (848)
..|...|+.+++.++....++.+.-|.+.. . |-+.++-..++|.+...+-+... .|.+...++..+.
T Consensus 411 ------~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~r~~~~~ss~~~p~~~~~~~~~~~p~~~s~~ 484 (636)
T KOG2169|consen 411 ------GSGSLRNTSGQGLDPSGGNKKQGPGPGDITLPSSSPEEDVPSPQRSESQSSSEGGPSPSPEKGPHTTPATPSQV 484 (636)
T ss_pred ------CccccccccccccCccccccccCCCCCcccCCCCCccccCCcccCccCcccccCCCCCccccCCCCCCCCCCCc
Confidence 048899999999999999999877666522 1 33666678899999888876211 3778888888877
Q ss_pred ccCCccCCCCCcc----------CC--CCccccCCCccccCCCCCCCCCCCcccccccC
Q 003096 801 ELRSSCRPSGASL----------RG--DPKCTRTNDAKIFDGPFSFPRQPRSVRQKVHL 847 (848)
Q Consensus 801 ~~~~~~~~~~a~~----------~~--~~~~~~~~~~~~~~~~f~~~~q~rs~~~~~~l 847 (848)
...+.++...-+. .+ ........ ..+...+|+.|+++++++++++.
T Consensus 485 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~p~~~~~~~~~~~~ 542 (636)
T KOG2169|consen 485 TFSPGSGTSDGSQDPPGATPASSSSESMPVTPPMP-QNGQLNSGSSPVTPGSVPPGMNA 542 (636)
T ss_pred eeCCCCcccccccCCcccccccccCcccccccccc-ccccCCCCCCcCCCCCcCCCcCc
Confidence 7777777661111 11 22222333 55889999999999999988764
No 6
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=97.89 E-value=1.4e-05 Score=60.84 Aligned_cols=34 Identities=44% Similarity=0.740 Sum_probs=31.8
Q ss_pred hhcCHHHHHHHHHHcCCCCCCCHHHHHHHHHHhc
Q 003096 13 VNFRMKELKDVLTKLGLPKQGKKQDLVDRIFHQL 46 (848)
Q Consensus 13 ~sFRV~ELk~lL~~lGl~KsGrKqEL~dRil~lL 46 (848)
..++++|||..|...|++.+|+|+||++|+.+++
T Consensus 2 ~~l~~~~Lk~~l~~~gl~~~G~K~~Lv~Rl~~~~ 35 (35)
T smart00513 2 AKLKVSELKDELKKRGLSTSGTKAELVDRLLEAL 35 (35)
T ss_pred CcCcHHHHHHHHHHcCCCCCCCHHHHHHHHHHhC
Confidence 5689999999999999999999999999998875
No 7
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.57 E-value=0.0011 Score=56.24 Aligned_cols=52 Identities=21% Similarity=0.432 Sum_probs=35.1
Q ss_pred eeeeeceEEEecCCCCcccccccccccCcCcccccchhhccccccccccceeccccccCcCcccccCHHHHHHHhcCCCC
Q 003096 336 EIIADSIIVNLRCPKVFSEENSDVLLFGIPFDCTFHWLFLTCNWQMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRK 415 (848)
Q Consensus 336 EIv~~s~~VSL~CP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lS~~RI~vP~Rg~~C~HlQCFDLetFL~mNer~~t 415 (848)
||+.+..+++++|| ||+..|+-|++++.|.| .||-++.+++-++...
T Consensus 2 di~i~~~~~~~~CP-------------------------------iT~~~~~~PV~s~~C~H--~fek~aI~~~i~~~~~ 48 (57)
T PF11789_consen 2 DIVIEGGTISLKCP-------------------------------ITLQPFEDPVKSKKCGH--TFEKEAILQYIQRNGS 48 (57)
T ss_dssp -----SSB--SB-T-------------------------------TTSSB-SSEEEESSS----EEEHHHHHHHCTTTS-
T ss_pred ceEEeccEeccCCC-------------------------------CcCChhhCCcCcCCCCC--eecHHHHHHHHHhcCC
Confidence 46667789999999 99999999999999999 7999999998877777
Q ss_pred ceeec
Q 003096 416 ASYSF 420 (848)
Q Consensus 416 W~C~~ 420 (848)
-+||.
T Consensus 49 ~~CPv 53 (57)
T PF11789_consen 49 KRCPV 53 (57)
T ss_dssp EE-SC
T ss_pred CCCCC
Confidence 77764
No 8
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=96.18 E-value=0.0027 Score=68.45 Aligned_cols=52 Identities=25% Similarity=0.667 Sum_probs=43.1
Q ss_pred CCCccccCCCCCCCCCCceeeCCCccc-cccccccccCCCCccccccCCCCcccccccccc
Q 003096 95 LGGKIFCPCGTSLPSESKIQCVDPRCL-VQQHISCVIIPEKPMEEIRLLPPLFFCETCRIK 154 (848)
Q Consensus 95 ~~~~vRCiCGSSl~s~~mIQC~~~~C~-v~QH~sCv~Ip~Kp~~~ipvhPdvFyCe~CRLK 154 (848)
++...+|+|. ...++.||.|+++.|. -|+|..||++-.+| .+.+||+.|+-.
T Consensus 216 ~~e~~yC~Cn-qvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~P-------kgkWyC~~C~~~ 268 (274)
T KOG1973|consen 216 PDEPTYCICN-QVSYGKMIGCDNPGCPIEWFHFTCVGLKTKP-------KGKWYCPRCKAE 268 (274)
T ss_pred CCCCEEEEec-ccccccccccCCCCCCcceEEEeccccccCC-------CCcccchhhhhh
Confidence 3457789998 5668999999999999 79999999997554 456999999755
No 9
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=95.90 E-value=0.0031 Score=50.79 Aligned_cols=49 Identities=37% Similarity=0.674 Sum_probs=37.9
Q ss_pred cc-CCCCCCCCCCceeeCCCccccccccccccCCCCccccccCCCCccccccccc
Q 003096 100 FC-PCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRI 153 (848)
Q Consensus 100 RC-iCGSSl~s~~mIQC~~~~C~v~QH~sCv~Ip~Kp~~~ipvhPdvFyCe~CRL 153 (848)
+| +|+.....+.||+|.. |..|+|..|+.++.+..+. ....|+|+.|+-
T Consensus 1 ~C~vC~~~~~~~~~i~C~~--C~~~~H~~C~~~~~~~~~~---~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDS--CNRWYHQECVGPPEKAEEI---PSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBST--TSCEEETTTSTSSHSHHSH---HSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCC--CChhhCcccCCCChhhccC---CCCcEECcCCcC
Confidence 35 7888777899999998 9999999999997543221 223899999864
No 10
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=93.99 E-value=0.029 Score=60.22 Aligned_cols=49 Identities=22% Similarity=0.690 Sum_probs=38.7
Q ss_pred ccccCCCCCCCCCCceeeCCCcccc-ccccccccCCCCccccccCCCCcccccccccc
Q 003096 98 KIFCPCGTSLPSESKIQCVDPRCLV-QQHISCVIIPEKPMEEIRLLPPLFFCETCRIK 154 (848)
Q Consensus 98 ~vRCiCGSSl~s~~mIQC~~~~C~v-~QH~sCv~Ip~Kp~~~ipvhPdvFyCe~CRLK 154 (848)
..+|.|. +...+.||.|+++.|.. |+|..||++-..| --.+||+-|+-+
T Consensus 221 ~lYCfCq-qvSyGqMVaCDn~nCkrEWFH~~CVGLk~pP-------KG~WYC~eCk~~ 270 (271)
T COG5034 221 ELYCFCQ-QVSYGQMVACDNANCKREWFHLECVGLKEPP-------KGKWYCPECKKA 270 (271)
T ss_pred eeEEEec-ccccccceecCCCCCchhheeccccccCCCC-------CCcEeCHHhHhc
Confidence 5679994 34468999999999997 9999999985422 246899999754
No 11
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=93.14 E-value=0.048 Score=62.55 Aligned_cols=56 Identities=25% Similarity=0.356 Sum_probs=46.6
Q ss_pred CCccccCCCCCCC-CCCceeeCCCccccccccccccCCCCccccccCCCCcccccccccccCCchh
Q 003096 96 GGKIFCPCGTSLP-SESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIKRADPFW 160 (848)
Q Consensus 96 ~~~vRCiCGSSl~-s~~mIQC~~~~C~v~QH~sCv~Ip~Kp~~~ipvhPdvFyCe~CRLKr~dPFy 160 (848)
...++|.|+.... .+.|++|+. |..|||.-|+++.... .|+.|+|+.|+.. ...-+
T Consensus 84 ~~~~~c~c~~~~~~~g~~i~c~~--c~~Wqh~~C~g~~~~~------~p~~y~c~~c~~~-~~~~~ 140 (508)
T KOG1844|consen 84 REISRCDCGLEDDMEGLMIQCDW--CGRWQHKICCGSFKST------KPDKYVCEICTPR-NKEVE 140 (508)
T ss_pred CcccccccccccCCCceeeCCcc--cCcccCceeeeecCCC------Cchhceeeeeccc-cccch
Confidence 4578999999988 899999999 9999999999986432 2899999999887 34444
No 12
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=88.13 E-value=0.11 Score=40.47 Aligned_cols=35 Identities=29% Similarity=0.637 Sum_probs=18.9
Q ss_pred CCceeeCCCccccccccccccCCCCccccccCCCCcccccccc
Q 003096 110 ESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCR 152 (848)
Q Consensus 110 ~~mIQC~~~~C~v~QH~sCv~Ip~Kp~~~ipvhPdvFyCe~CR 152 (848)
+.+|+|.. |.+..|..|+++...+ ..+.++|..|+
T Consensus 2 n~ll~C~~--C~v~VH~~CYGv~~~~------~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDN--CNVAVHQSCYGVSEVP------DGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SS--S--EEEHHHHT-SS--------SS-----HHH-
T ss_pred CceEEeCC--CCCcCChhhCCcccCC------CCCcEECCcCC
Confidence 45899998 9999999999997532 23348898885
No 14
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=85.87 E-value=0.33 Score=56.36 Aligned_cols=54 Identities=22% Similarity=0.313 Sum_probs=39.9
Q ss_pred ccccCCCCCCCCCCceeeCCCccccccccccccCCCCccccccCCCCcccccccccc
Q 003096 98 KIFCPCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIK 154 (848)
Q Consensus 98 ~vRCiCGSSl~s~~mIQC~~~~C~v~QH~sCv~Ip~Kp~~~ipvhPdvFyCe~CRLK 154 (848)
...|.||......+||+|.. |..|.|..|+....++++-- -.--+|||..|+=.
T Consensus 171 c~vC~~g~~~~~NrmlqC~~--C~~~fHq~Chqp~i~~~l~~-D~~~~w~C~~C~~~ 224 (464)
T KOG4323|consen 171 CSVCYCGGPGAGNRMLQCDK--CRQWYHQACHQPLIKDELAG-DPFYEWFCDVCNRG 224 (464)
T ss_pred eeeeecCCcCccceeeeecc--cccHHHHHhccCCCCHhhcc-CccceEeehhhccc
Confidence 56678888888789999999 99999999999876654311 12245667777443
No 15
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=83.65 E-value=1.4 Score=35.36 Aligned_cols=35 Identities=26% Similarity=0.499 Sum_probs=26.8
Q ss_pred HhhcCHHHHHHHHHHcCCCCCC--CHHHHHHHHHHhc
Q 003096 12 LVNFRMKELKDVLTKLGLPKQG--KKQDLVDRIFHQL 46 (848)
Q Consensus 12 l~sFRV~ELk~lL~~lGl~KsG--rKqEL~dRil~lL 46 (848)
|....+.||+.+...+|++..+ ||+||+..|+...
T Consensus 2 L~~~~~~eL~~iAk~lgI~~~~~~~K~eLI~~Il~~q 38 (43)
T PF07498_consen 2 LKSMTLSELREIAKELGIEGYSKMRKQELIFAILKAQ 38 (43)
T ss_dssp HHCS-HHHHHHHHHCTT-TTGCCS-HHHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHHHHH
Confidence 5677899999999999996543 7999999998753
No 16
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=73.33 E-value=2.3 Score=33.38 Aligned_cols=28 Identities=32% Similarity=0.614 Sum_probs=20.4
Q ss_pred hhcCHHHHHHHHHHcCC--CCCCCHHHHHH
Q 003096 13 VNFRMKELKDVLTKLGL--PKQGKKQDLVD 40 (848)
Q Consensus 13 ~sFRV~ELk~lL~~lGl--~KsGrKqEL~d 40 (848)
.+++|.|||.+|...|. +.+.||.||+.
T Consensus 2 ~sltV~~Lk~iL~~~~I~~ps~AkKaeLv~ 31 (35)
T PF12949_consen 2 KSLTVAQLKRILDEHGIEFPSNAKKAELVA 31 (35)
T ss_dssp TT--SHHHHHHHHHHT---SSS--SHHHHH
T ss_pred CcCcHHHHHHHHHHcCCCCCCCCCHHHHHH
Confidence 57899999999999875 78899999984
No 17
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=72.71 E-value=1 Score=48.97 Aligned_cols=51 Identities=18% Similarity=0.208 Sum_probs=41.8
Q ss_pred eeeeeceEEEecCCCCcccccccccccCcCcccccchhhccccccccccceeccccccCcCcccccCHHHHHHHhcCCCC
Q 003096 336 EIIADSIIVNLRCPKVFSEENSDVLLFGIPFDCTFHWLFLTCNWQMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRK 415 (848)
Q Consensus 336 EIv~~s~~VSL~CP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lS~~RI~vP~Rg~~C~HlQCFDLetFL~mNer~~t 415 (848)
|+...+-.+|++|| +|+.-|.-|.+++.|.|. ||-..-.++-....+
T Consensus 167 e~~i~~e~fs~rdP-------------------------------is~~~I~nPviSkkC~Hv--ydrDsI~~~l~~~~~ 213 (262)
T KOG2979|consen 167 EELIGQEVFSNRDP-------------------------------ISKKPIVNPVISKKCGHV--YDRDSIMQILCDEIT 213 (262)
T ss_pred HHHhhhhhhcccCc-------------------------------hhhhhhhchhhhcCcCcc--hhhhhHHHHhccCce
Confidence 55667889999999 999999999999999998 777777776655556
Q ss_pred ceee
Q 003096 416 ASYS 419 (848)
Q Consensus 416 W~C~ 419 (848)
=+||
T Consensus 214 i~CP 217 (262)
T KOG2979|consen 214 IRCP 217 (262)
T ss_pred eecc
Confidence 6664
No 18
>KOG4259 consensus Putative nucleic acid-binding protein Hcc-1/proliferation associated cytokine-inducible protein, contains SAP domain [Cell cycle control, cell division, chromosome partitioning]
Probab=65.74 E-value=6.7 Score=42.21 Aligned_cols=35 Identities=31% Similarity=0.527 Sum_probs=31.7
Q ss_pred hhcCHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcC
Q 003096 13 VNFRMKELKDVLTKLGLPKQGKKQDLVDRIFHQLS 47 (848)
Q Consensus 13 ~sFRV~ELk~lL~~lGl~KsGrKqEL~dRil~lL~ 47 (848)
..++|.|||.=|..-||...|.|.||++|+.+-+.
T Consensus 7 kklkVa~LkeeLa~rGL~~~GNK~EL~~RLtaa~e 41 (260)
T KOG4259|consen 7 KKLKVAELKEELAERGLSTAGNKAELVSRLTAATE 41 (260)
T ss_pred hhccHHHHHHHHHHhcccccCChHHHHHHHHHHHH
Confidence 46799999999999999999999999999877654
No 19
>PF10208 Armet: Degradation arginine-rich protein for mis-folding; InterPro: IPR019345 This entry represents Armet proteins (aka mesencephalic astrocyte-derived neurotrophic factor or arginine-rich protein). Armet is a small protein of approximately 170 residues which contains four di-sulphide bridges that are highly conserved from nematodes to humans. Armet is a soluble protein resident in the endoplasmic reticulum and induced by ER stress. It appears to be involved with dealing with mis-folded proteins in the ER, thus in quality control of ER stress []. Armet from Rattus norvegicus (Rat) selectively promotes the survival of dopaminergic neurons of the ventral mid-brain. It modulates GABAergic transmission to the dopaminergic neurons of the substantia nigra, and enhances spontaneous, as well as evoked, GABAergic inhibitory postsynaptic currents in dopaminergic neurons [].; PDB: 2KVE_A 2KVD_A 2W51_A 2W50_B 2RQY_A.
Probab=57.38 E-value=8.1 Score=39.40 Aligned_cols=35 Identities=37% Similarity=0.489 Sum_probs=29.7
Q ss_pred HhhcCHHHHHHHHHHcCCCCCCC--HHHHHHHHHHhc
Q 003096 12 LVNFRMKELKDVLTKLGLPKQGK--KQDLVDRIFHQL 46 (848)
Q Consensus 12 l~sFRV~ELk~lL~~lGl~KsGr--KqEL~dRil~lL 46 (848)
|..+||+|||.||..-|..=.|- |.|++.||.++-
T Consensus 104 l~KlrVk~LK~iL~~~g~~C~GC~EK~dfv~ri~el~ 140 (154)
T PF10208_consen 104 LKKLRVKQLKKILDDWGEDCKGCLEKSDFVRRIEELK 140 (154)
T ss_dssp TTTTCHHHHHHHHHHHTTT-SS-CSHHHHHHHCHCCC
T ss_pred HhhCcHHHHHHHHHHcCCCCCCccchHHHHHHHHHHh
Confidence 56789999999999999999995 999999998753
No 20
>PF02837 Glyco_hydro_2_N: Glycosyl hydrolases family 2, sugar binding domain; InterPro: IPR006104 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities; beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. This domain has a jelly-roll fold [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3DEC_A 3OB8_A 3OBA_A 3CMG_A 3FN9_C 2VZU_A 2X09_A 2VZO_A 2X05_A 2VZV_B ....
Probab=43.62 E-value=70 Score=31.12 Aligned_cols=65 Identities=25% Similarity=0.218 Sum_probs=42.5
Q ss_pred eEEEEEeCHhhHHhhcCCCcEEEEEEEecCCCccccccCCCceEEEEcCeEeeeccCCCcccCCCCCCCCCCc-cccccc
Q 003096 188 AEAAFHLTKAHSDLLQNTEYDVQAWCILLNDKVSFRMQWPLHAELQVNGLLVRTVNRPGTQLLGSNGRDDGAL-ITLYIG 266 (848)
Q Consensus 188 ~e~~F~LT~~q~~lL~~~~y~vQlrCi~l~d~v~~~~~wP~~~el~VNg~~v~~~~RPg~~~~g~ngR~d~pi-IT~~i~ 266 (848)
.+..|.|.++. ...++.|..-.++ ..++|.|||+.|-.. . .+....-+ ||.+++
T Consensus 72 Yr~~f~lp~~~------~~~~~~L~f~gv~----------~~a~v~vNG~~vg~~-~--------~~~~~~~~dIt~~l~ 126 (167)
T PF02837_consen 72 YRRTFTLPADW------KGKRVFLRFEGVD----------YAAEVYVNGKLVGSH-E--------GGYTPFEFDITDYLK 126 (167)
T ss_dssp EEEEEEESGGG------TTSEEEEEESEEE----------SEEEEEETTEEEEEE-E--------STTS-EEEECGGGSS
T ss_pred EEEEEEeCchh------cCceEEEEeccce----------EeeEEEeCCeEEeee-C--------CCcCCeEEeChhhcc
Confidence 46689998854 2445555543332 347899999999631 1 12222223 999999
Q ss_pred Ccc-cEEEEEEe
Q 003096 267 EGV-NQISLSGC 277 (848)
Q Consensus 267 ~g~-N~I~is~~ 277 (848)
.|. |.|.|...
T Consensus 127 ~g~~N~l~V~v~ 138 (167)
T PF02837_consen 127 PGEENTLAVRVD 138 (167)
T ss_dssp SEEEEEEEEEEE
T ss_pred CCCCEEEEEEEe
Confidence 997 99999874
No 21
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=36.33 E-value=37 Score=40.51 Aligned_cols=59 Identities=24% Similarity=0.483 Sum_probs=38.0
Q ss_pred CCccccCCCCC--CCCCCceeeCCCccccccccccccCCCCccccccC-----CCCcccccccccccCCc
Q 003096 96 GGKIFCPCGTS--LPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRL-----LPPLFFCETCRIKRADP 158 (848)
Q Consensus 96 ~~~vRCiCGSS--l~s~~mIQC~~~~C~v~QH~sCv~Ip~Kp~~~ipv-----hPdvFyCe~CRLKr~dP 158 (848)
.+.+-|+|=.. ...+.+|||++ |++..|-+||+..++. +|+. .-.-+||+-|+.--..|
T Consensus 118 k~~iCcVClg~rs~da~ei~qCd~--CGi~VHEgCYGv~dn~--si~s~~s~~stepWfCeaC~~Gvs~P 183 (707)
T KOG0957|consen 118 KAVICCVCLGQRSVDAGEILQCDK--CGINVHEGCYGVLDNV--SIPSGSSDCSTEPWFCEACLYGVSLP 183 (707)
T ss_pred cceEEEEeecCccccccceeeccc--cCceeccccccccccc--ccCCCCccCCCCchhhhhHhcCCCCC
Confidence 45577888432 33577899999 9999999999976322 2221 11346777776553334
No 22
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.00 E-value=47 Score=38.55 Aligned_cols=36 Identities=22% Similarity=0.245 Sum_probs=32.5
Q ss_pred hhcCHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCc
Q 003096 13 VNFRMKELKDVLTKLGLPKQGKKQDLVDRIFHQLSD 48 (848)
Q Consensus 13 ~sFRV~ELk~lL~~lGl~KsGrKqEL~dRil~lL~~ 48 (848)
..++.+.||..|..|||+-+|-|+.|+.|--+++--
T Consensus 267 ~~l~~~~lr~kL~~lglpt~G~r~~l~~Rh~e~~~l 302 (397)
T TIGR00599 267 SLLTDSQIRKKLSELGLSTNGTRQLLQKRHNEWETL 302 (397)
T ss_pred hhcCHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHH
Confidence 457889999999999999999999999999888763
No 23
>PLN03124 poly [ADP-ribose] polymerase; Provisional
Probab=25.89 E-value=49 Score=40.66 Aligned_cols=38 Identities=29% Similarity=0.513 Sum_probs=34.3
Q ss_pred hhcCHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCchh
Q 003096 13 VNFRMKELKDVLTKLGLPKQGKKQDLVDRIFHQLSDEG 50 (848)
Q Consensus 13 ~sFRV~ELk~lL~~lGl~KsGrKqEL~dRil~lL~~~~ 50 (848)
..++|.||++-|..=||+-.|.|.+|+.|.-+.+..+.
T Consensus 3 ~~~~v~~l~~~l~~~~~~~~g~k~~l~~rl~~~~~~e~ 40 (643)
T PLN03124 3 NKLKVDELRAALAKRGLDTTGLKAALVRRLDDAIAEDA 40 (643)
T ss_pred ccchhHHHHHHHHhcCCcccccchHHHHHHHhhhhhhh
Confidence 45899999999999999999999999999998887543
No 24
>COG3683 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=24.59 E-value=1.3e+02 Score=32.56 Aligned_cols=76 Identities=21% Similarity=0.276 Sum_probs=45.1
Q ss_pred CceEEEEcCeEeeeccCCCcccCCCCCCCCCCcccc------cccCcccEEEEEEeecceEEEEEEEEeecCHHHHHHhc
Q 003096 228 LHAELQVNGLLVRTVNRPGTQLLGSNGRDDGALITL------YIGEGVNQISLSGCDIRNFCFGVRLVKRQTVAQVLSLV 301 (848)
Q Consensus 228 ~~~el~VNg~~v~~~~RPg~~~~g~ngR~d~piIT~------~i~~g~N~I~is~~d~r~y~~~V~LVk~~t~eqll~~I 301 (848)
..-.|..||+.++..+||.+. +.+-.++..+|.= .+....++++|...|+. |+.++...+. +.-.+...+
T Consensus 89 yFt~I~~~gk~vk~~~~p~~~--~~~~~d~ql~~~F~i~la~p~~l~~~~l~~~~YDpT-yY~amdY~~d-~~~~~~~~l 164 (213)
T COG3683 89 YFTFIRDNGKKVKYSPRPTHY--GAKRKDNQLLIYFSIPLAEPQPLKGATLSFGTYDPT-YYVAMDYAKD-SDITVFGKL 164 (213)
T ss_pred hhhhheeCCceeeccCCCchh--cccccCCEEEEEEecCcccccccCCceEEEEecCCe-eEEEEeeccc-ccccchhhh
Confidence 346788999999977667543 3333333333321 22233557777777775 5578888876 444444556
Q ss_pred ccCCCC
Q 003096 302 PKETAG 307 (848)
Q Consensus 302 ~~~~~g 307 (848)
+++.++
T Consensus 165 ~~~c~~ 170 (213)
T COG3683 165 PKNCKG 170 (213)
T ss_pred hhcCce
Confidence 655444
No 25
>PRK03298 hypothetical protein; Provisional
Probab=22.81 E-value=1.4e+02 Score=32.45 Aligned_cols=41 Identities=22% Similarity=0.259 Sum_probs=33.4
Q ss_pred CCCeeEEEEccCCcEEEeecCCCCCCCCccCCCCccccccc
Q 003096 443 ADDLTEIEVKHDGSWRVKCKGENNNLAEWHSPDGSTYAARS 483 (848)
Q Consensus 443 ~~dv~eIev~~DGSW~v~~~~E~~~~~~w~~pdg~~~~~~~ 483 (848)
+.--.=|.||+|||--+..+.+..+--.|.+|..++.+..+
T Consensus 21 ~~~~RLiiiK~DGsvlVH~d~~~~kPlNW~pp~~~~~~~~~ 61 (224)
T PRK03298 21 PSARRLLLVKADGSVSVHADDRAYKPLNWMSPPCTLTEEPP 61 (224)
T ss_pred CCCceEEEEccCCeEEEecCCCCCCCcccCCCCeEEEEEec
Confidence 34445689999999999998777777889999988887664
No 26
>PF08531 Bac_rhamnosid_N: Alpha-L-rhamnosidase N-terminal domain; InterPro: IPR013737 This domain is found in bacterial rhamnosidase A and B enzymes and is probably involved in substrate recognition. ; PDB: 2OKX_B.
Probab=22.79 E-value=44 Score=33.81 Aligned_cols=47 Identities=30% Similarity=0.204 Sum_probs=24.6
Q ss_pred ceEEEEcCeEeeec-cCCCcccCCCCCC--CCCCcccccccCcccEEEEEEe
Q 003096 229 HAELQVNGLLVRTV-NRPGTQLLGSNGR--DDGALITLYIGEGVNQISLSGC 277 (848)
Q Consensus 229 ~~el~VNg~~v~~~-~RPg~~~~g~ngR--~d~piIT~~i~~g~N~I~is~~ 277 (848)
..++.|||+.|-.- ..|+.... ..| -+.-.||.+++.|.|.|-+...
T Consensus 15 ~Y~l~vNG~~V~~~~l~P~~t~y--~~~~~Y~tyDVt~~L~~G~N~iav~lg 64 (172)
T PF08531_consen 15 RYELYVNGERVGDGPLAPGWTDY--DKRVYYQTYDVTPYLRPGENVIAVWLG 64 (172)
T ss_dssp EEEEEETTEEEEEE--------B--TTEEEEEEEE-TTT--TTEEEEEEEEE
T ss_pred eEEEEECCEEeeCCccccccccC--CCceEEEEEeChHHhCCCCCEEEEEEe
Confidence 36899999999732 12432210 111 1122399999999999998753
No 27
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=21.20 E-value=33 Score=38.53 Aligned_cols=50 Identities=14% Similarity=0.010 Sum_probs=32.6
Q ss_pred ccccceeccccccCcCcccccCHHHHHHHhcCCCCcee---ecchhhhhhhHHHHHHH
Q 003096 381 MSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKASY---SFILLFLSMFRIFKLIK 435 (848)
Q Consensus 381 lS~~RI~vP~Rg~~C~HlQCFDLetFL~mNer~~tW~C---~~~~L~l~ID~yf~~IL 435 (848)
+.+..++-|+|..-|.|+-|=.+- +..---.-+.| .-.++. +|++.-+|-
T Consensus 279 lc~~Llrnp~kT~cC~~~fc~eci---~~al~dsDf~CpnC~rkdvl--ld~l~pD~d 331 (427)
T COG5222 279 LCHCLLRNPMKTPCCGHTFCDECI---GTALLDSDFKCPNCSRKDVL--LDGLTPDID 331 (427)
T ss_pred chhhhhhCcccCccccchHHHHHH---hhhhhhccccCCCcccccch--hhccCccHH
Confidence 999999999999999999774432 21111122444 444567 777766664
No 28
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=20.24 E-value=1.6e+02 Score=26.27 Aligned_cols=21 Identities=24% Similarity=0.561 Sum_probs=17.5
Q ss_pred CCCeeEEEEccCCcEEEeecC
Q 003096 443 ADDLTEIEVKHDGSWRVKCKG 463 (848)
Q Consensus 443 ~~dv~eIev~~DGSW~v~~~~ 463 (848)
.-+|.+|+++.||.|.++.-.
T Consensus 42 G~~v~~ve~~~~g~yev~~~~ 62 (83)
T PF13670_consen 42 GYQVREVEFDDDGCYEVEARD 62 (83)
T ss_pred CCceEEEEEcCCCEEEEEEEE
Confidence 349999999999999998443
No 29
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=20.19 E-value=53 Score=41.17 Aligned_cols=63 Identities=19% Similarity=0.474 Sum_probs=44.5
Q ss_pred cccc-CCCCCCCCCCceeeCCCccccc-cccccccCCCCccccccCCCCccccccccccc---CCchhhhhhhcc
Q 003096 98 KIFC-PCGTSLPSESKIQCVDPRCLVQ-QHISCVIIPEKPMEEIRLLPPLFFCETCRIKR---ADPFWITVAHLV 167 (848)
Q Consensus 98 ~vRC-iCGSSl~s~~mIQC~~~~C~v~-QH~sCv~Ip~Kp~~~ipvhPdvFyCe~CRLKr---~dPFy~~i~~Ll 167 (848)
...| +|+...+-+.||-|.. |+.- -|+-|+..+.. ++| -..|||..|.+.. .--||..++.++
T Consensus 215 ~~~C~IC~~~DpEdVLLLCDs--CN~~~YH~YCLDPdl~---eiP--~~eWYC~NC~dL~~~eh~~~~~~~~~~~ 282 (1134)
T KOG0825|consen 215 EVKCDICTVHDPEDVLLLCDS--CNKVYYHVYCLDPDLS---ESP--VNEWYCTNCSLLEITEHKDFTLKTEELI 282 (1134)
T ss_pred cccceeeccCChHHhheeecc--cccceeeccccCcccc---ccc--ccceecCcchhhhhhhhhHHHHHHHHHh
Confidence 4566 7888888899999998 9975 99999877532 232 3679999997652 223555555444
Done!