Query 018130
Match_columns 360
No_of_seqs 193 out of 357
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 06:23:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018130.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018130hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2897 DNA-binding protein YL 100.0 4.6E-60 1E-64 462.4 18.1 348 9-359 3-387 (390)
2 PF05764 YL1: YL1 nuclear prot 100.0 1.4E-47 2.9E-52 362.0 19.3 215 14-237 1-239 (240)
3 PF08265 YL1_C: YL1 nuclear pr 99.5 3.2E-15 6.9E-20 99.2 2.1 30 266-295 1-30 (30)
4 KOG4137 Uncharacterized conser 99.3 2.1E-12 4.5E-17 106.1 3.6 47 256-302 41-87 (102)
5 COG5195 Uncharacterized conser 99.2 8.4E-12 1.8E-16 104.0 3.7 81 222-302 20-103 (118)
6 KOG2897 DNA-binding protein YL 96.6 0.0007 1.5E-08 68.2 0.7 86 188-274 220-313 (390)
7 PF04438 zf-HIT: HIT zinc fing 96.4 0.0013 2.8E-08 43.8 0.9 29 265-293 2-30 (30)
8 PF04795 PAPA-1: PAPA-1-like c 94.6 0.11 2.5E-06 42.6 6.4 59 194-252 17-89 (89)
9 KOG0526 Nucleosome-binding fac 89.8 0.19 4E-06 53.3 2.1 36 24-59 440-475 (615)
10 PF10446 DUF2457: Protein of u 89.6 0.19 4.2E-06 52.1 2.0 7 9-15 12-18 (458)
11 PF05764 YL1: YL1 nuclear prot 86.3 3.8 8.2E-05 39.3 8.5 7 240-246 231-237 (240)
12 KOG3362 Predicted BBOX Zn-fing 80.3 0.83 1.8E-05 41.0 1.2 40 257-296 110-149 (156)
13 KOG4317 Predicted Zn-finger pr 73.2 1.4 2.9E-05 44.3 0.6 29 266-294 8-37 (383)
14 PF13824 zf-Mss51: Zinc-finger 72.5 2.6 5.6E-05 32.0 1.8 29 267-295 1-34 (55)
15 KOG3064 RNA-binding nuclear pr 71.7 2.9 6.3E-05 41.0 2.4 7 28-34 187-193 (303)
16 KOG2857 Predicted MYND Zn-fing 70.4 2.3 5.1E-05 38.2 1.4 36 266-301 6-42 (157)
17 PF10446 DUF2457: Protein of u 63.6 4.8 0.00011 42.1 2.3 7 280-286 354-360 (458)
18 PF09866 DUF2093: Uncharacteri 55.0 6.4 0.00014 28.4 1.0 26 266-291 8-38 (42)
19 TIGR00986 3a0801s05tom22 mitoc 48.5 9.8 0.00021 34.2 1.4 27 45-72 19-45 (145)
20 PF06524 NOA36: NOA36 protein; 44.6 12 0.00025 37.0 1.4 6 42-47 247-252 (314)
21 PF05565 Sipho_Gp157: Siphovir 41.9 74 0.0016 28.6 6.1 63 188-255 62-124 (162)
22 PF04281 Tom22: Mitochondrial 34.5 23 0.0005 31.5 1.5 7 66-72 37-43 (137)
23 TIGR01299 synapt_SV2 synaptic 33.8 35 0.00076 38.0 3.2 35 22-57 25-59 (742)
24 PF02724 CDC45: CDC45-like pro 32.1 27 0.00059 38.0 1.9 14 263-276 553-566 (622)
25 PF04147 Nop14: Nop14-like fam 31.6 27 0.00059 39.4 1.9 6 19-24 262-267 (840)
26 COG3908 Uncharacterized protei 30.2 24 0.00052 28.2 0.8 26 266-291 31-61 (77)
27 PF12253 CAF1A: Chromatin asse 25.4 43 0.00093 27.0 1.5 13 53-65 46-58 (77)
28 PF03153 TFIIA: Transcription 23.7 27 0.00058 35.1 0.0 7 66-72 308-314 (375)
29 PF04147 Nop14: Nop14-like fam 22.5 39 0.00085 38.2 1.0 6 288-293 670-675 (840)
30 PF09457 RBD-FIP: FIP domain ; 22.4 1.7E+02 0.0037 21.6 4.0 18 187-204 1-18 (48)
No 1
>KOG2897 consensus DNA-binding protein YL1 and related proteins [General function prediction only]
Probab=100.00 E-value=4.6e-60 Score=462.45 Aligned_cols=348 Identities=37% Similarity=0.484 Sum_probs=265.2
Q ss_pred CCCcccccccccccccHHHHHHHhhhhhhhhhhhhhcccchhcccccccc-ccccccccCCCCCCCC--CCCChhhhhhh
Q 018130 9 EDAPVFLDRSSRVTRGKRMNKLLDDENEEDEAFWNQDALKEEENDDNYEE-EQEIADEFDSDFDEDE--PEPDEEVENEV 85 (360)
Q Consensus 9 ~~~~l~~~R~rRstAGnRM~kLL~eE~e~De~f~~~~~F~Eee~D~ey~~-e~e~eD~~DSDFd~dE--~e~dde~E~E~ 85 (360)
..++|+++|++|+||||+|++||++|+++|+++|+|++|.|+++|++|++ +.+.+|++||||++|+ +++|++.+++.
T Consensus 3 ~t~~~~~~RSrRanaGnKls~LLe~E~ed~~~~t~q~s~~e~~~DeEyE~~~~e~eDe~DsDfs~d~~~~~sDe~sed~~ 82 (390)
T KOG2897|consen 3 NTEMLAAGRSRRANAGNKLSKLLESEEEDDEYSTTQGSFSEDSHDEEYEGEESEEEDEVDSDFSIDETSNESDEESEDDK 82 (390)
T ss_pred cchhhhhccccccccchHHHHHhhhhhhhhHHhhhhccccccccchhhhhhhhhhccccccccchhhccccCcccccccc
Confidence 34689999999999999999999999999999999999999999999994 5889999999999983 22233222222
Q ss_pred hhhhhhhccccCCCCCcchhhhhhccccC-CCCCCccccCccccCCCCC-----CCCCCCccccccchhhhHHHHHHHHH
Q 018130 86 DERVWTKKRLIFPGKPLTKKKKKKKILSK-LDSPDKDVKSNEQSILPEN-----HDVPNDVEGERIIRKSTRTAVVVRQA 159 (360)
Q Consensus 86 ~Er~~rKKr~~~~~k~~~~~kKKkk~~~~-~~~~~~~kk~~e~~~~~~~-----~~~~~~~~~~~~~RkStR~st~~r~~ 159 (360)
.+....+++++...+. .+|+++++.+ +.--++..++.+......+ ..+.....+...+|+|+|+|||.+.+
T Consensus 83 ~~~d~~~k~~vl~~~~---rkkr~k~~~k~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~RkS~R~St~~~t~ 159 (390)
T KOG2897|consen 83 EEEDEDAKRKVLRTKE---RKKRKKALKKRAANLPAADKKPKFGGTAERSEEPNNEVQKEGKDPVHRRKSERTSTVEKTQ 159 (390)
T ss_pred cccccccccchhhhHH---hhhhhhhhcccccccccccCCCCcCCcccccccchHHHHhhccCcccccchhhhHHHhhhh
Confidence 1111223333322111 1111111110 0000111111111111111 12222333345689999999999988
Q ss_pred HHHHHHHHHHhhcccccccccccCC-CCCHHHHHHHHHHHHHHhHHHHHHHHHhHHHHHHHHhhhcccccCCeeEEEec-
Q 018130 160 ERDAIRAALQATMKPIKRKKEGEEK-RMTQEEMLLEAAQTEIMNLRNLERVLAREEEVKKRAIVHKAVYTGPQLRYLSK- 237 (360)
Q Consensus 160 erE~~R~~~~~~~k~~krKk~~~~~-~lTQEElL~EA~~TE~~N~~SL~~~~~~EeekKk~~~~~k~~~~gP~ir~~S~- 237 (360)
+....|.+.+...+++++|++..+. .+||||||.||++||.+|+.||+.+.++|+.+|++++.+|+.+.||+|+|||.
T Consensus 160 ~~~e~rs~~e~~~r~r~rK~~~~E~~~~TQeE~l~eAk~TE~~Nl~SLe~~~~~ee~~Kkk~~~~kr~~~~P~i~~~S~t 239 (390)
T KOG2897|consen 160 EETELRSKEEKDGRPRRRKKKFNEPKMGTQEERLLEAKKTEAMNLLSLEIVAAREEDDKKKAAMKKRQEKGPIITYHSLT 239 (390)
T ss_pred hHHHHhhhhhccccchhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCceeEEeec
Confidence 8777777766667776666655554 45999999999999999999999999999999998888899999999999999
Q ss_pred ----------------------CC-c--eeeEeecCCccccccCCCCCCCC-CCcccccCCCCcccCCCCCCCCCCCHHH
Q 018130 238 ----------------------DG-Y--SYLEFSKGVSFQSELSTTSVPYP-ERAVCAVTGLPAKYRDPKTGLPYATKEA 291 (360)
Q Consensus 238 ----------------------~~-~--~~i~f~d~~~~~~~~~~~~~~~P-~k~~C~iTg~~a~Y~DP~T~lpy~~~~~ 291 (360)
.| | +|+++.+.++|.+.|+...+|.| ...+|+|||+||+|+||+|||||+|+.|
T Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~G~~~q~~~t~~~e~~~~s~~~~~~~p~~~~~~~C~iTg~PA~Y~DPVT~lPy~ta~A 319 (390)
T KOG2897|consen 240 KPAAFEPERGRKPAKNTVRLFPDGRCEQTFMTESGEASFLSEFPTKSPPKPRERVVCVITGRPARYLDPVTGLPYSTAQA 319 (390)
T ss_pred chhhcccccccccccccccccCCCcccceeeecccchhhhhcCCccCCCCCcccccccccCCcccccCcccCCcchhHHH
Confidence 44 4 67788888999999998888877 8899999999999999999999999999
Q ss_pred HHHHHHcccccchhhhccCCchhhhhhcccccccccccccccCCCCccccccccccccccCCcccccc
Q 018130 292 FKIIRERFVDKSSGIRKAMDMGTLFDSLSRKGFMATRRRSKSSNKNEKSYLRYSARFRRFPSLEIEVS 359 (360)
Q Consensus 292 fk~ir~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 359 (360)
||+||+.|.+++.++.+.+.|..|+++|...++.+..+|+..+.-.....+...++|--....+.++|
T Consensus 320 FKviRe~y~~~~~~~~~~de~~~l~~tl~~~p~~q~~kr~~l~~s~~~~~~~~i~~~~~~e~~~es~s 387 (390)
T KOG2897|consen 320 FKVIRERYKKHLRSIRGNDEMPNLFKTLKALPSPQEQKRVPLPTSGPITSGPLIASSAGLEVMAESTS 387 (390)
T ss_pred HHHHHHHHHHHhhhcccchhhhhHHHhhccCCCCCcCccccCcCcCcccccchhhhhhcchhhhhhhc
Confidence 99999999999999999999999999999999999999999998888887888888776655555554
No 2
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=100.00 E-value=1.4e-47 Score=361.97 Aligned_cols=215 Identities=44% Similarity=0.572 Sum_probs=154.5
Q ss_pred cccccccccccHHHHHHHhhhhhhhhhhhhhcc-cchhcccccccccccccccc--CCCCCCCCCCC---Chh--hhhhh
Q 018130 14 FLDRSSRVTRGKRMNKLLDDENEEDEAFWNQDA-LKEEENDDNYEEEQEIADEF--DSDFDEDEPEP---DEE--VENEV 85 (360)
Q Consensus 14 ~~~R~rRstAGnRM~kLL~eE~e~De~f~~~~~-F~Eee~D~ey~~e~e~eD~~--DSDFd~dE~e~---dde--~E~E~ 85 (360)
|++|++||||||||++||++|+++|++||++.+ |+||++|++|+++++++|++ |||||+|++++ +++ +|.++
T Consensus 1 v~~R~rRsnaGnrm~~LL~~E~e~de~~~~~~~~f~Eee~D~ef~~~~~eed~~~~Dsdf~~se~de~~~~~e~e~e~~~ 80 (240)
T PF05764_consen 1 VATRPRRSNAGNRMKKLLEEELEEDEFFWNQYGLFQEEEDDEEFESEEEEEDEEEDDSDFDDSEDDEDESDDEEEGEKEL 80 (240)
T ss_pred CCCcccccchhHHHHHHHHHHHhhhhhhhhhcccccccCCCccccCCCccccccccccccCccccCCCCCcccchhhhHH
Confidence 689999999999999999999999999999765 99999999999987777776 99999987632 222 22222
Q ss_pred --hhhhhhhccccCCCCCcchhhhhhccccCC----CCCCccccCccccCCCCCCCCCCCccccccchhhhHHHHH----
Q 018130 86 --DERVWTKKRLIFPGKPLTKKKKKKKILSKL----DSPDKDVKSNEQSILPENHDVPNDVEGERIIRKSTRTAVV---- 155 (360)
Q Consensus 86 --~Er~~rKKr~~~~~k~~~~~kKKkk~~~~~----~~~~~~kk~~e~~~~~~~~~~~~~~~~~~~~RkStR~st~---- 155 (360)
+++..+|++++..++..|..+++++....+ ...+++++.+.. ..|+++.. ..++|+|+|++|+
T Consensus 81 ~~~ek~~kkk~~~~~~~~~p~~~k~k~~~~~~~~~~~~~~~~k~~~~~-----~~~~~~~~--~~~~R~S~R~st~~~~~ 153 (240)
T PF05764_consen 81 RREEKLKKKKRRKKKAYKEPAKKKKKKPPQAAKKDSAAAPKPKKKKER-----QSWAPTLL--DSPRRKSTRSSTVANKQ 153 (240)
T ss_pred HHHHHHHHhhhcccccchhhhhhcccccccccccccccCCCCcccccc-----ccCccccc--ccchhhhHHHHHHHHHH
Confidence 233333333333332222222221111111 111222222222 12444332 3458999999887
Q ss_pred ---HHHHHHHHHHHHHHhhcccccccccccCCCCCHHHHHHHHHHHHHHhHHHHHHHHHhHHHHHH---HHhhhcccccC
Q 018130 156 ---VRQAERDAIRAALQATMKPIKRKKEGEEKRMTQEEMLLEAAQTEIMNLRNLERVLAREEEVKK---RAIVHKAVYTG 229 (360)
Q Consensus 156 ---~r~~erE~~R~~~~~~~k~~krKk~~~~~~lTQEElL~EA~~TE~~N~~SL~~~~~~EeekKk---~~~~~k~~~~g 229 (360)
.++++++.+++.+++.| .++++....++|||||||+||++||++|++||++|+++|+++|+ .+.++|.++.|
T Consensus 154 ~~~~rlke~e~~r~~~~~~~--~~~k~~~~~~~lTQeElL~EAk~TE~~N~~SL~~~~~~EeekKk~~~~~~~~K~~~~G 231 (240)
T PF05764_consen 154 ATYERLKEREEKRKKRQARM--KKKKKKQEERPLTQEELLEEAKETEEENLKSLNKYEELEEEKKKAQRQAQKKKKIYTG 231 (240)
T ss_pred HHHHHHHHHHHHHHHHHHhh--hcccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCC
Confidence 58899998888888777 35666778899999999999999999999999999999999998 66777777899
Q ss_pred CeeEEEec
Q 018130 230 PQLRYLSK 237 (360)
Q Consensus 230 P~ir~~S~ 237 (360)
|+|+|||+
T Consensus 232 P~ir~~S~ 239 (240)
T PF05764_consen 232 PVIRYHSR 239 (240)
T ss_pred CeEEEEeC
Confidence 99999996
No 3
>PF08265 YL1_C: YL1 nuclear protein C-terminal domain; InterPro: IPR013272 This domain is found at the C terminus in proteins of the YL1 family []. These proteins have been shown to be DNA-binding and may be transcription factors []. This domain is also found in proteins that do not belong to the YL1 family.
Probab=99.53 E-value=3.2e-15 Score=99.15 Aligned_cols=30 Identities=73% Similarity=1.336 Sum_probs=28.7
Q ss_pred cccccCCCCcccCCCCCCCCCCCHHHHHHH
Q 018130 266 AVCAVTGLPAKYRDPKTGLPYATKEAFKII 295 (360)
Q Consensus 266 ~~C~iTg~~a~Y~DP~T~lpy~~~~~fk~i 295 (360)
++|+|||+||+|+||.|||||+|+++|++|
T Consensus 1 k~C~iTglpA~Y~DP~T~l~Y~n~~ayk~i 30 (30)
T PF08265_consen 1 KYCDITGLPARYRDPKTGLPYANSEAYKII 30 (30)
T ss_pred CcccccCCCccccCCCCCCcccCHHHhhcC
Confidence 589999999999999999999999999986
No 4
>KOG4137 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.28 E-value=2.1e-12 Score=106.15 Aligned_cols=47 Identities=43% Similarity=0.727 Sum_probs=43.6
Q ss_pred CCCCCCCCCCcccccCCCCcccCCCCCCCCCCCHHHHHHHHHccccc
Q 018130 256 STTSVPYPERAVCAVTGLPAKYRDPKTGLPYATKEAFKIIRERFVDK 302 (360)
Q Consensus 256 ~~~~~~~P~k~~C~iTg~~a~Y~DP~T~lpy~~~~~fk~ir~~~~~~ 302 (360)
.++++..|.+++|+||||||.|.||.|||.|+|.++|+.|+++..+.
T Consensus 41 ~appSv~PakKycDvTGLpapYtdP~t~Lry~naeiY~~i~empsd~ 87 (102)
T KOG4137|consen 41 EAPPSVKPAKKYCDVTGLPAPYTDPNTGLRYHNAEIYKLICEMPSDR 87 (102)
T ss_pred cCCCccccchhhccccCCcccccCCCccceeccHHHHHHHHHCCchH
Confidence 56778889999999999999999999999999999999999988765
No 5
>COG5195 Uncharacterized conserved protein [Function unknown]
Probab=99.21 E-value=8.4e-12 Score=104.00 Aligned_cols=81 Identities=28% Similarity=0.443 Sum_probs=58.4
Q ss_pred hhcccccCCeeEEEecCC-ceeeEeec--CCccccccCCCCCCCCCCcccccCCCCcccCCCCCCCCCCCHHHHHHHHHc
Q 018130 222 VHKAVYTGPQLRYLSKDG-YSYLEFSK--GVSFQSELSTTSVPYPERAVCAVTGLPAKYRDPKTGLPYATKEAFKIIRER 298 (360)
Q Consensus 222 ~~k~~~~gP~ir~~S~~~-~~~i~f~d--~~~~~~~~~~~~~~~P~k~~C~iTg~~a~Y~DP~T~lpy~~~~~fk~ir~~ 298 (360)
.++..+.||.-|+.+..- -+-++..+ ...-...+.++++..|.+++|+|||+||.|+||.|||.|+|.++|+.|+++
T Consensus 20 fk~~~Yk~~~rr~ktlrQli~~~~i~ne~sk~~Y~sieappSv~P~~KyCDvTGL~a~Yt~P~t~lrYhn~eiY~lI~el 99 (118)
T COG5195 20 FKKSTYKGKNRRFKTLRQLIPRLTIENESSKHRYLSIEAPPSVKPRMKYCDVTGLPAPYTCPNTGLRYHNSEIYKLICEL 99 (118)
T ss_pred ccCccccCcccchhhHHHHccccccccccccceeEeecCCCccccccccccccCCcccccCCCcCceeccHHHHHHhhcC
Confidence 456667788777765521 01112222 111122345677788999999999999999999999999999999999998
Q ss_pred cccc
Q 018130 299 FVDK 302 (360)
Q Consensus 299 ~~~~ 302 (360)
....
T Consensus 100 psg~ 103 (118)
T COG5195 100 PSGR 103 (118)
T ss_pred CCch
Confidence 8765
No 6
>KOG2897 consensus DNA-binding protein YL1 and related proteins [General function prediction only]
Probab=96.57 E-value=0.0007 Score=68.17 Aligned_cols=86 Identities=20% Similarity=0.196 Sum_probs=51.4
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHhHHHHHHHHhhh--cccccCCeeEEEecCC--ceeeEeecCCccccc----cCCCC
Q 018130 188 QEEMLLEAAQTEIMNLRNLERVLAREEEVKKRAIVH--KAVYTGPQLRYLSKDG--YSYLEFSKGVSFQSE----LSTTS 259 (360)
Q Consensus 188 QEElL~EA~~TE~~N~~SL~~~~~~EeekKk~~~~~--k~~~~gP~ir~~S~~~--~~~i~f~d~~~~~~~----~~~~~ 259 (360)
+...+..+..+..+|+.||..+..++-++....... +....|+.-+-.+..+ .+|..-.+....+.. +| +.
T Consensus 220 k~~~~kr~~~~P~i~~~S~t~~~~~~~~~~~~~~~~~~~~~~~G~~~q~~~t~~~e~~~~s~~~~~~~p~~~~~~~C-~i 298 (390)
T KOG2897|consen 220 KAAMKKRQEKGPIITYHSLTKPAAFEPERGRKPAKNTVRLFPDGRCEQTFMTESGEASFLSEFPTKSPPKPRERVVC-VI 298 (390)
T ss_pred HHHHHhhhccCCceeEEeecchhhcccccccccccccccccCCCcccceeeecccchhhhhcCCccCCCCCcccccc-cc
Confidence 777778888899999999998888776655432222 2223676666666554 233332222212111 11 11
Q ss_pred CCCCCCcccccCCCC
Q 018130 260 VPYPERAVCAVTGLP 274 (360)
Q Consensus 260 ~~~P~k~~C~iTg~~ 274 (360)
...|....-+|||+|
T Consensus 299 Tg~PA~Y~DPVT~lP 313 (390)
T KOG2897|consen 299 TGRPARYLDPVTGLP 313 (390)
T ss_pred cCCcccccCcccCCc
Confidence 236778889999999
No 7
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=96.41 E-value=0.0013 Score=43.82 Aligned_cols=29 Identities=45% Similarity=0.902 Sum_probs=23.6
Q ss_pred CcccccCCCCcccCCCCCCCCCCCHHHHH
Q 018130 265 RAVCAVTGLPAKYRDPKTGLPYATKEAFK 293 (360)
Q Consensus 265 k~~C~iTg~~a~Y~DP~T~lpy~~~~~fk 293 (360)
..+|.|=|.+++|++|..+++|.+++.||
T Consensus 2 ~~~C~vC~~~~kY~Cp~C~~~~CSl~C~k 30 (30)
T PF04438_consen 2 RKLCSVCGNPAKYRCPRCGARYCSLACYK 30 (30)
T ss_dssp -EEETSSSSEESEE-TTT--EESSHHHHH
T ss_pred cCCCccCcCCCEEECCCcCCceeCcEeEC
Confidence 46899999999999999999999999996
No 8
>PF04795 PAPA-1: PAPA-1-like conserved region; InterPro: IPR006880 This is a group of proteins with a conserved C-terminal region which is found in PAPA-1, a PAP-1 binding protein, Q9C086 from SWISSPROT.
Probab=94.62 E-value=0.11 Score=42.62 Aligned_cols=59 Identities=17% Similarity=0.276 Sum_probs=39.7
Q ss_pred HHHHHHHHhHHHHHHHHHhHHHHHHH-----------H---hhhcccccCCeeEEEecCCceeeEeecCCccc
Q 018130 194 EAAQTEIMNLRNLERVLAREEEVKKR-----------A---IVHKAVYTGPQLRYLSKDGYSYLEFSKGVSFQ 252 (360)
Q Consensus 194 EA~~TE~~N~~SL~~~~~~EeekKk~-----------~---~~~k~~~~gP~ir~~S~~~~~~i~f~d~~~~~ 252 (360)
-++..|+.-...+|+|+.....+++. . ........-|+|||+|+..+++|+|+.++.||
T Consensus 17 ~eKk~EEeK~eTInKLLkkqa~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~IR~v~~~~G~~vs~P~~~~~P 89 (89)
T PF04795_consen 17 SEKKLEEEKMETINKLLKKQATRKKREPKDKEGEEDSAQEKKRRAPKPNPPMIRWVSNKNGSRVSVPEEMGLP 89 (89)
T ss_pred HHHHHHHHHHHHHHHHHhhhccccccchhhhhhhhhccccccccccCCCCCEEEEEECCCceEEEecCCCCCC
Confidence 34556777777888888655421110 0 11123367799999999999999999887654
No 9
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=89.84 E-value=0.19 Score=53.29 Aligned_cols=36 Identities=14% Similarity=0.362 Sum_probs=15.5
Q ss_pred cHHHHHHHhhhhhhhhhhhhhcccchhccccccccc
Q 018130 24 GKRMNKLLDDENEEDEAFWNQDALKEEENDDNYEEE 59 (360)
Q Consensus 24 GnRM~kLL~eE~e~De~f~~~~~F~Eee~D~ey~~e 59 (360)
--.++.|+++..++++.--+...=..++.|++|.-.
T Consensus 440 D~~~~~~~~e~~~~edd~~d~~~de~~e~Dedf~~~ 475 (615)
T KOG0526|consen 440 DEYLATLKAEDRDEEDDSDDSSTDEDEEEDEDFKPG 475 (615)
T ss_pred chHHhhhccccchhhhcccccccccchhhhhhcccC
Confidence 345666665544333221111222224556666643
No 10
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=89.59 E-value=0.19 Score=52.09 Aligned_cols=7 Identities=29% Similarity=0.064 Sum_probs=3.7
Q ss_pred CCCcccc
Q 018130 9 EDAPVFL 15 (360)
Q Consensus 9 ~~~~l~~ 15 (360)
++.||-.
T Consensus 12 ~ddWi~~ 18 (458)
T PF10446_consen 12 EDDWIRQ 18 (458)
T ss_pred hhhhhhc
Confidence 3457743
No 11
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=86.34 E-value=3.8 Score=39.26 Aligned_cols=7 Identities=0% Similarity=0.164 Sum_probs=3.9
Q ss_pred ceeeEee
Q 018130 240 YSYLEFS 246 (360)
Q Consensus 240 ~~~i~f~ 246 (360)
+++|.|.
T Consensus 231 GP~ir~~ 237 (240)
T PF05764_consen 231 GPVIRYH 237 (240)
T ss_pred CCeEEEE
Confidence 3666654
No 12
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=80.28 E-value=0.83 Score=41.03 Aligned_cols=40 Identities=28% Similarity=0.415 Sum_probs=34.6
Q ss_pred CCCCCCCCCcccccCCCCcccCCCCCCCCCCCHHHHHHHH
Q 018130 257 TTSVPYPERAVCAVTGLPAKYRDPKTGLPYATKEAFKIIR 296 (360)
Q Consensus 257 ~~~~~~P~k~~C~iTg~~a~Y~DP~T~lpy~~~~~fk~ir 296 (360)
++++..|.++.|.|-|.+.+|.|-.-|-.||++.|+++=.
T Consensus 110 a~p~~KP~r~fCaVCG~~S~ysC~~CG~kyCsv~C~~~Hn 149 (156)
T KOG3362|consen 110 AKPSFKPLRKFCAVCGYDSKYSCVNCGTKYCSVRCLKTHN 149 (156)
T ss_pred cCCCCCCcchhhhhcCCCchhHHHhcCCceeechhhhhcc
Confidence 3445568899999999999999999999999999998643
No 13
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=73.20 E-value=1.4 Score=44.33 Aligned_cols=29 Identities=21% Similarity=0.605 Sum_probs=25.2
Q ss_pred cccccCCC-CcccCCCCCCCCCCCHHHHHH
Q 018130 266 AVCAVTGL-PAKYRDPKTGLPYATKEAFKI 294 (360)
Q Consensus 266 ~~C~iTg~-~a~Y~DP~T~lpy~~~~~fk~ 294 (360)
-.|.|-|. ++.|+||+-++|||++-||+-
T Consensus 8 ~~C~ic~vq~~~YtCPRCn~~YCsl~CYr~ 37 (383)
T KOG4317|consen 8 LACGICGVQKREYTCPRCNLLYCSLKCYRN 37 (383)
T ss_pred eeccccccccccccCCCCCccceeeeeecC
Confidence 47888775 599999999999999999974
No 14
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=72.52 E-value=2.6 Score=32.05 Aligned_cols=29 Identities=21% Similarity=0.461 Sum_probs=23.0
Q ss_pred ccccCCC----CcccCCCCCCCCCC-CHHHHHHH
Q 018130 267 VCAVTGL----PAKYRDPKTGLPYA-TKEAFKII 295 (360)
Q Consensus 267 ~C~iTg~----~a~Y~DP~T~lpy~-~~~~fk~i 295 (360)
+|+|++. .-.|.+|..|+||+ +.++++.=
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGipthcS~ehw~~D 34 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIPTHCSEEHWEDD 34 (55)
T ss_pred CCCCCccccccccCCcCCCCCCcCccCHHHHHHh
Confidence 5999999 89999999999964 55555543
No 15
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=71.65 E-value=2.9 Score=40.98 Aligned_cols=7 Identities=43% Similarity=0.601 Sum_probs=3.1
Q ss_pred HHHHhhh
Q 018130 28 NKLLDDE 34 (360)
Q Consensus 28 ~kLL~eE 34 (360)
+++|++.
T Consensus 187 nK~l~~~ 193 (303)
T KOG3064|consen 187 NKALEAR 193 (303)
T ss_pred HHHHHhh
Confidence 3445443
No 16
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=70.39 E-value=2.3 Score=38.17 Aligned_cols=36 Identities=28% Similarity=0.471 Sum_probs=29.8
Q ss_pred cccccCCC-CcccCCCCCCCCCCCHHHHHHHHHcccc
Q 018130 266 AVCAVTGL-PAKYRDPKTGLPYATKEAFKIIRERFVD 301 (360)
Q Consensus 266 ~~C~iTg~-~a~Y~DP~T~lpy~~~~~fk~ir~~~~~ 301 (360)
..|.|--. +.+|+||.-..||+++-+||+=+..+..
T Consensus 6 ~tC~ic~e~~~KYKCpkC~vPYCSl~CfKiHk~tPq~ 42 (157)
T KOG2857|consen 6 TTCVICLESEIKYKCPKCSVPYCSLPCFKIHKSTPQC 42 (157)
T ss_pred eeehhhhcchhhccCCCCCCccccchhhhhccCCccc
Confidence 57888765 4699999999999999999998884433
No 17
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=63.60 E-value=4.8 Score=42.08 Aligned_cols=7 Identities=43% Similarity=0.994 Sum_probs=3.6
Q ss_pred CCCCCCC
Q 018130 280 PKTGLPY 286 (360)
Q Consensus 280 P~T~lpy 286 (360)
|.|..||
T Consensus 354 PR~p~~f 360 (458)
T PF10446_consen 354 PRTPNPF 360 (458)
T ss_pred CCCCCcc
Confidence 4455555
No 18
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=55.01 E-value=6.4 Score=28.38 Aligned_cols=26 Identities=42% Similarity=0.654 Sum_probs=21.4
Q ss_pred cccccCCCC-----cccCCCCCCCCCCCHHH
Q 018130 266 AVCAVTGLP-----AKYRDPKTGLPYATKEA 291 (360)
Q Consensus 266 ~~C~iTg~~-----a~Y~DP~T~lpy~~~~~ 291 (360)
-.|+|||.+ =+|=...-+-||++.++
T Consensus 8 V~CAVTg~~IpLd~LrYWsv~~QEaYa~~~~ 38 (42)
T PF09866_consen 8 VRCAVTGQPIPLDELRYWSVDRQEAYASAEA 38 (42)
T ss_pred EEEEeeCCcccHHHhccCChhhhhcccCHHH
Confidence 479999998 57888888888888765
No 19
>TIGR00986 3a0801s05tom22 mitochondrial import receptor subunit Tom22. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tom22 proteins.
Probab=48.51 E-value=9.8 Score=34.25 Aligned_cols=27 Identities=30% Similarity=0.677 Sum_probs=14.3
Q ss_pred cccchhccccccccccccccccCCCCCC
Q 018130 45 DALKEEENDDNYEEEQEIADEFDSDFDE 72 (360)
Q Consensus 45 ~~F~Eee~D~ey~~e~e~eD~~DSDFd~ 72 (360)
-++..+++|++|.+. +.+|.+||||++
T Consensus 19 ~~~~~~~~~~~~td~-~se~~~d~~~~~ 45 (145)
T TIGR00986 19 TVVEPEEDDEDFTDV-DSEDSVDSDFES 45 (145)
T ss_pred ccccccccccccccc-cccccccccccc
Confidence 345556667777653 233335555633
No 20
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=44.61 E-value=12 Score=37.04 Aligned_cols=6 Identities=0% Similarity=-0.186 Sum_probs=2.5
Q ss_pred hhhccc
Q 018130 42 WNQDAL 47 (360)
Q Consensus 42 ~~~~~F 47 (360)
|+++.|
T Consensus 247 ~~y~~y 252 (314)
T PF06524_consen 247 SGYGSY 252 (314)
T ss_pred ccccch
Confidence 444443
No 21
>PF05565 Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840 This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophage. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage [].
Probab=41.93 E-value=74 Score=28.61 Aligned_cols=63 Identities=11% Similarity=0.062 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHhHHHHHHHHhhhcccccCCeeEEEecCCceeeEeecCCcccccc
Q 018130 188 QEEMLLEAAQTEIMNLRNLERVLAREEEVKKRAIVHKAVYTGPQLRYLSKDGYSYLEFSKGVSFQSEL 255 (360)
Q Consensus 188 QEElL~EA~~TE~~N~~SL~~~~~~EeekKk~~~~~k~~~~gP~ir~~S~~~~~~i~f~d~~~~~~~~ 255 (360)
...+|++-+..-+.++.+|..|+... .......++.||...+.-+.+.+.+.+.|...+|..|
T Consensus 62 E~krL~~rkk~~e~~~~~Lk~yL~~~-----m~~~g~~ki~t~~~tisirk~~~sv~I~de~~iP~~y 124 (162)
T PF05565_consen 62 EIKRLQERKKSIENRIDRLKEYLLDA-----MEAAGIKKIKTPLFTISIRKNPPSVEIDDEEKIPDEY 124 (162)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHcCCceeecCceEEEEecCCCCeEeeChHHCCHHH
Confidence 45566777777778888999888543 2233455667888777666655555555555555444
No 22
>PF04281 Tom22: Mitochondrial import receptor subunit Tom22 ; InterPro: IPR005683 The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family represents the Tom22 proteins []. The N-terminal region of Tom22 has been shown to have chaperone-like activity, and the C-terminal region faces the intermembrane face []. ; GO: 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane
Probab=34.45 E-value=23 Score=31.55 Aligned_cols=7 Identities=43% Similarity=0.648 Sum_probs=3.4
Q ss_pred cCCCCCC
Q 018130 66 FDSDFDE 72 (360)
Q Consensus 66 ~DSDFd~ 72 (360)
.|||+++
T Consensus 37 ~~sd~~d 43 (137)
T PF04281_consen 37 TDSDISD 43 (137)
T ss_pred ccccccc
Confidence 3555544
No 23
>TIGR01299 synapt_SV2 synaptic vesicle protein SV2. This model describes a tightly conserved subfamily of the larger family of sugar (and other) transporters described by pfam model pfam00083. Members of this subfamily include closely related forms SV2A and SV2B of synaptic vesicle protein from vertebrates and a more distantly related homolog (below trusted cutoff) from Drosophila melanogaster. Members are predicted to have two sets of six transmembrane helices.
Probab=33.85 E-value=35 Score=37.95 Aligned_cols=35 Identities=23% Similarity=0.499 Sum_probs=23.2
Q ss_pred cccHHHHHHHhhhhhhhhhhhhhcccchhccccccc
Q 018130 22 TRGKRMNKLLDDENEEDEAFWNQDALKEEENDDNYE 57 (360)
Q Consensus 22 tAGnRM~kLL~eE~e~De~f~~~~~F~Eee~D~ey~ 57 (360)
.|+++..+-++.. .|+-.-.+|.-|+||++|++|-
T Consensus 25 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 59 (742)
T TIGR01299 25 HAAKKVNKALDRA-QDEYSQRSYSRFEDEDDDDDFP 59 (742)
T ss_pred HHHHHHHHHHHHh-hHHHhhhhHhhhcccccccCCC
Confidence 4566777777654 2222234578899999999994
No 24
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=32.07 E-value=27 Score=38.03 Aligned_cols=14 Identities=36% Similarity=0.491 Sum_probs=8.8
Q ss_pred CCCcccccCCCCcc
Q 018130 263 PERAVCAVTGLPAK 276 (360)
Q Consensus 263 P~k~~C~iTg~~a~ 276 (360)
.....|.|.|..++
T Consensus 553 ~~~~~~lVvGv~~~ 566 (622)
T PF02724_consen 553 EERGTYLVVGVSAP 566 (622)
T ss_pred CCCCeEEEEEeccC
Confidence 34567778888433
No 25
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=31.62 E-value=27 Score=39.41 Aligned_cols=6 Identities=17% Similarity=0.235 Sum_probs=2.4
Q ss_pred cccccc
Q 018130 19 SRVTRG 24 (360)
Q Consensus 19 rRstAG 24 (360)
+|+.+.
T Consensus 262 ~Ra~ps 267 (840)
T PF04147_consen 262 RRAKPS 267 (840)
T ss_pred cccCCc
Confidence 344443
No 26
>COG3908 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.15 E-value=24 Score=28.19 Aligned_cols=26 Identities=35% Similarity=0.590 Sum_probs=20.5
Q ss_pred cccccCCCC-----cccCCCCCCCCCCCHHH
Q 018130 266 AVCAVTGLP-----AKYRDPKTGLPYATKEA 291 (360)
Q Consensus 266 ~~C~iTg~~-----a~Y~DP~T~lpy~~~~~ 291 (360)
-+|+|||.| -+|-.+.-+-||.+..+
T Consensus 31 V~CAVtgk~IPldeLrYWSvarQEaYv~~a~ 61 (77)
T COG3908 31 VLCAVTGKPIPLDELRYWSVARQEAYVDAAA 61 (77)
T ss_pred EEEEecCCcccHHHhhhcchhhhhccccHHH
Confidence 589999998 57877888888877643
No 27
>PF12253 CAF1A: Chromatin assembly factor 1 subunit A; InterPro: IPR022043 The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A []. The A domain is uniquely required for the progression of S phase in mouse cells [], independent of its ability to promote histone deposition [] but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints [].
Probab=25.36 E-value=43 Score=27.03 Aligned_cols=13 Identities=54% Similarity=0.716 Sum_probs=5.3
Q ss_pred ccccccccccccc
Q 018130 53 DDNYEEEQEIADE 65 (360)
Q Consensus 53 D~ey~~e~e~eD~ 65 (360)
|++++.+++.+|+
T Consensus 46 d~EWeE~e~GEdl 58 (77)
T PF12253_consen 46 DDEWEEEEEGEDL 58 (77)
T ss_pred ccccccCCCCccc
Confidence 4444333334444
No 28
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=23.70 E-value=27 Score=35.13 Aligned_cols=7 Identities=43% Similarity=0.928 Sum_probs=0.0
Q ss_pred cCCCCCC
Q 018130 66 FDSDFDE 72 (360)
Q Consensus 66 ~DSDFd~ 72 (360)
.+||-|+
T Consensus 308 ~~~~~~~ 314 (375)
T PF03153_consen 308 INSDLDD 314 (375)
T ss_dssp -------
T ss_pred ccCCcCC
Confidence 4444443
No 29
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=22.53 E-value=39 Score=38.18 Aligned_cols=6 Identities=33% Similarity=0.711 Sum_probs=2.3
Q ss_pred CHHHHH
Q 018130 288 TKEAFK 293 (360)
Q Consensus 288 ~~~~fk 293 (360)
+...|+
T Consensus 670 ~~~~~k 675 (840)
T PF04147_consen 670 DSDQFK 675 (840)
T ss_pred cchhHH
Confidence 333443
No 30
>PF09457 RBD-FIP: FIP domain ; InterPro: IPR019018 The Rab11 GTPase regulates recycling of internalized plasma membrane receptors and is essential for completion of cytokinesis. A family of Rab11 interacting proteins (FIPs) that conserve a C-terminal Rab-binding domain (RBD) selectively recognise the active form of Rab11. FIPs are diverse in sequence length and composition toward their N-termini, presumably a feature that underpins their specific roles in Rab11-mediated vesicle trafficking. They have been divided into three subfamilies (classe I, II, and III)on the basis of domain architecture. Class I FIPs comprises a subfamily of three proteins (Rip11/pp75/FIP5, Rab-coupling protein (RCP), and FIP2) that possess an N- terminal C2 domain, localize to recycling endosomes, and regulate plasma membrane recycling. The class II subfamily consists of two proteins (FIP3/eferin/arfophilin and FIP4) with tandem EF hands and a proline-rich region. Class II FIPs localize to recycling endosomes, the trans-Golgi network, and have been implicated in the regulation of membrane trafficking during cytokinesis. The class III subfamily consists of a single protein, FIP1, which does not contain obvious homology domains or motifs other than the FIP-RBD [, , , ]. The FIP-RBD domain is also found in Rab6-interacting protein Erc1/Elks. Erc1 is the regulatory subunit of the IKK complex and probably recruits IkappaBalpha/NFKBIA to the complex []. It may be involved in the organisation of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. It may also be involved in vesicle trafficking at the CAZ, as well as in Rab-6 regulated endosomes to Golgi transport []. The FIB-RBD domain consists of an N-terminal long alpha-helix, followed by a 90 degrees bend at a conserved proline residue, a 3(10) helix and a C-terminal short beta-strand, adopting an "L" shape. The long alpha-helix forms a parallel coiled-coil homodimer that symmetrically interacts with two Rab11 molecules on both sides, forming a quaternary Rab11-(FIP)2-Rab11 complex. The Rab11-interacting region of FIP-RBD is confined to the C-terminal 24 amino acids, which cover the C-terminal half of the long alpha-helix and the short beta-strand [, , , ]. This entry represents the FIP-RBD domain.; PDB: 2HV8_E 2D7C_D 2K6S_B 2GZD_D 2GZH_B.
Probab=22.43 E-value=1.7e+02 Score=21.58 Aligned_cols=18 Identities=28% Similarity=0.316 Sum_probs=16.3
Q ss_pred CHHHHHHHHHHHHHHhHH
Q 018130 187 TQEEMLLEAAQTEIMNLR 204 (360)
Q Consensus 187 TQEElL~EA~~TE~~N~~ 204 (360)
|++||+.+....|..|.+
T Consensus 1 s~eeL~~~l~~~e~~~~~ 18 (48)
T PF09457_consen 1 SREELISLLKKQEEENAR 18 (48)
T ss_dssp THHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 789999999999999877
Done!