Query 030117
Match_columns 182
No_of_seqs 133 out of 241
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 08:47:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030117.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030117hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04570 DUF581: Protein of un 99.9 8.3E-28 1.8E-32 168.7 4.9 51 85-135 8-58 (58)
2 PF09889 DUF2116: Uncharacteri 95.2 0.023 5E-07 40.4 3.1 29 94-131 4-32 (59)
3 PF12855 Ecl1: Life-span regul 94.6 0.019 4.1E-07 38.5 1.4 32 91-128 4-35 (43)
4 PF06467 zf-FCS: MYM-type Zinc 94.3 0.031 6.7E-07 35.2 1.8 34 93-126 6-42 (43)
5 COG2075 RPL24A Ribosomal prote 91.5 0.16 3.5E-06 37.2 2.4 32 94-125 4-38 (66)
6 COG4068 Uncharacterized protei 90.3 0.26 5.7E-06 35.9 2.5 32 94-136 9-40 (64)
7 PRK00418 DNA gyrase inhibitor; 81.4 0.97 2.1E-05 32.6 1.6 37 93-135 6-42 (62)
8 PF03884 DUF329: Domain of unk 81.3 0.51 1.1E-05 33.4 0.1 33 95-133 4-36 (57)
9 smart00746 TRASH metallochaper 79.8 2.7 5.9E-05 22.8 2.8 33 96-128 1-36 (39)
10 PF04945 YHS: YHS domain; Int 79.3 1.2 2.5E-05 29.0 1.4 32 98-130 5-39 (47)
11 PRK01343 zinc-binding protein; 77.4 1.7 3.8E-05 30.9 1.9 31 94-134 10-40 (57)
12 PRK14891 50S ribosomal protein 76.7 2.1 4.5E-05 35.1 2.4 35 94-128 5-42 (131)
13 PRK00807 50S ribosomal protein 76.4 2.6 5.5E-05 28.9 2.4 34 94-127 2-38 (52)
14 PF04640 PLATZ: PLATZ transcri 70.7 2.1 4.5E-05 31.5 0.9 23 92-123 48-70 (72)
15 cd00472 Ribosomal_L24e_L24 Rib 65.7 6 0.00013 27.6 2.4 35 94-128 4-41 (54)
16 PF00412 LIM: LIM domain; Int 65.0 4.3 9.4E-05 26.1 1.5 25 95-121 28-52 (58)
17 PF02069 Metallothio_Pro: Prok 60.3 6.5 0.00014 27.5 1.8 32 94-127 8-39 (52)
18 PF11809 DUF3330: Domain of un 57.1 4.6 0.0001 30.0 0.6 36 94-130 12-50 (70)
19 PF15279 SOBP: Sine oculis-bin 52.3 13 0.00027 33.9 2.7 33 96-130 2-38 (306)
20 PHA03073 late transcription fa 49.3 11 0.00024 31.5 1.7 35 93-128 49-87 (150)
21 COG3024 Uncharacterized protei 48.7 9.4 0.0002 28.1 1.1 36 93-134 7-42 (65)
22 PF06906 DUF1272: Protein of u 44.9 17 0.00037 26.1 1.9 31 94-125 6-37 (57)
23 PF04181 RPAP2_Rtr1: Rtr1/RPAP 42.7 29 0.00063 24.8 2.9 41 90-130 17-73 (79)
24 PF01753 zf-MYND: MYND finger; 41.2 21 0.00045 22.0 1.7 15 114-128 16-30 (37)
25 PF01246 Ribosomal_L24e: Ribos 39.9 25 0.00053 25.8 2.1 35 94-128 4-41 (71)
26 PF12156 ATPase-cat_bd: Putati 39.7 58 0.0013 24.0 4.1 41 95-135 2-45 (88)
27 smart00132 LIM Zinc-binding do 34.0 40 0.00086 19.4 2.1 23 95-118 1-23 (39)
28 PF08394 Arc_trans_TRASH: Arch 33.7 43 0.00094 21.9 2.3 32 96-127 1-33 (37)
29 PF10367 Vps39_2: Vacuolar sor 31.7 34 0.00073 24.2 1.7 25 93-118 78-102 (109)
30 KOG4357 Uncharacterized conser 31.2 20 0.00043 30.1 0.5 16 103-118 111-127 (164)
31 PTZ00033 60S ribosomal protein 30.1 50 0.0011 26.9 2.6 35 94-128 4-45 (125)
32 cd01224 PH_Collybistin Collybi 23.9 37 0.0008 26.8 0.8 21 94-115 28-48 (109)
33 PF08600 Rsm1: Rsm1-like; Int 21.8 34 0.00074 25.4 0.3 17 93-113 19-35 (91)
No 1
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=99.94 E-value=8.3e-28 Score=168.67 Aligned_cols=51 Identities=59% Similarity=1.083 Sum_probs=48.0
Q ss_pred CCCCchhHhhccccccCCCCCCCceeEEcCCccccChhHHHHHHHHHHHHh
Q 030117 85 DFLETPHFLRTCGLCKRRLVPGRDIYMYRGDSAFCSLECRQQQMNQDERKQ 135 (182)
Q Consensus 85 ~~~e~~~FL~~C~lCkK~L~~gkDIYMYRGe~AFCS~ECR~qqI~~DE~~E 135 (182)
...++.+||++|++|+|+|.+++||||||||+||||.|||++||++||++|
T Consensus 8 ~~~~~~~FL~~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~~qi~~de~~E 58 (58)
T PF04570_consen 8 SPFPSEHFLSFCYLCKKKLDPGKDIYMYRGDKAFCSEECRSQQILMDEEKE 58 (58)
T ss_pred CCCCcHHHHHHHHccCCCCCCCCCeeeeccccccccHHHHHHHHHHHHhcC
Confidence 345788999999999999999999999999999999999999999999986
No 2
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=95.15 E-value=0.023 Score=40.36 Aligned_cols=29 Identities=31% Similarity=0.918 Sum_probs=23.4
Q ss_pred hccccccCCCCCCCceeEEcCCccccChhHHHHHHHHH
Q 030117 94 RTCGLCKRRLVPGRDIYMYRGDSAFCSLECRQQQMNQD 131 (182)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYRGe~AFCS~ECR~qqI~~D 131 (182)
+.|-.|.+.+.+ |..|||.+||+.....-
T Consensus 4 kHC~~CG~~Ip~---------~~~fCS~~C~~~~~k~q 32 (59)
T PF09889_consen 4 KHCPVCGKPIPP---------DESFCSPKCREEYRKRQ 32 (59)
T ss_pred CcCCcCCCcCCc---------chhhhCHHHHHHHHHHH
Confidence 469999999964 58999999998776543
No 3
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=94.56 E-value=0.019 Score=38.49 Aligned_cols=32 Identities=34% Similarity=0.760 Sum_probs=25.4
Q ss_pred hHhhccccccCCCCCCCceeEEcCCccccChhHHHHHH
Q 030117 91 HFLRTCGLCKRRLVPGRDIYMYRGDSAFCSLECRQQQM 128 (182)
Q Consensus 91 ~FL~~C~lCkK~L~~gkDIYMYRGe~AFCS~ECR~qqI 128 (182)
.|+.+|-.|-|.+....| +..+||++||..-.
T Consensus 4 ~F~~yC~~Cdk~~~~~~~------~~lYCSe~Cr~~D~ 35 (43)
T PF12855_consen 4 AFNDYCIVCDKQIDPPDD------GSLYCSEECRLKDQ 35 (43)
T ss_pred hhhhHHHHhhccccCCCC------CccccCHHHHhHhh
Confidence 799999999999955333 46679999997643
No 4
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=94.25 E-value=0.031 Score=35.20 Aligned_cols=34 Identities=29% Similarity=0.709 Sum_probs=22.0
Q ss_pred hhccccccCCCCCCCc--eeEEcCC-ccccChhHHHH
Q 030117 93 LRTCGLCKRRLVPGRD--IYMYRGD-SAFCSLECRQQ 126 (182)
Q Consensus 93 L~~C~lCkK~L~~gkD--IYMYRGe-~AFCS~ECR~q 126 (182)
...|..|++.+....+ +..|.|. .-|||..|+..
T Consensus 6 ~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~~~ 42 (43)
T PF06467_consen 6 MKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCLSS 42 (43)
T ss_dssp CEE-TTT--EEECCC----EE-TTTTSCCSSHHHHHH
T ss_pred CCcCcccCCcccCCCccccccccCcccChhCHHHHhh
Confidence 3579999999955555 6777765 78999999875
No 5
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=91.47 E-value=0.16 Score=37.20 Aligned_cols=32 Identities=38% Similarity=0.986 Sum_probs=28.3
Q ss_pred hccccccCCCCCCCceeEEcCCc---cccChhHHH
Q 030117 94 RTCGLCKRRLVPGRDIYMYRGDS---AFCSLECRQ 125 (182)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYRGe~---AFCS~ECR~ 125 (182)
..|++|.+.|.||.-|+--|.|. -|||..|+.
T Consensus 4 ~~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k 38 (66)
T COG2075 4 RVCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEK 38 (66)
T ss_pred eEecCcCCccCCCceEEEEecCCeEEEEechhHHH
Confidence 46999999999999988878885 499999998
No 6
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=90.28 E-value=0.26 Score=35.90 Aligned_cols=32 Identities=34% Similarity=0.808 Sum_probs=24.4
Q ss_pred hccccccCCCCCCCceeEEcCCccccChhHHHHHHHHHHHHhh
Q 030117 94 RTCGLCKRRLVPGRDIYMYRGDSAFCSLECRQQQMNQDERKQK 136 (182)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYRGe~AFCS~ECR~qqI~~DE~~Ek 136 (182)
+.|--|.|.|.+| .-|||+||+ +|+..|++-+
T Consensus 9 ~HC~VCg~aIp~d---------e~~CSe~C~--eil~ker~R~ 40 (64)
T COG4068 9 RHCVVCGKAIPPD---------EQVCSEECG--EILNKERKRQ 40 (64)
T ss_pred ccccccCCcCCCc---------cchHHHHHH--HHHHHHHHHH
Confidence 4588999999754 469999997 5777776644
No 7
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=81.41 E-value=0.97 Score=32.63 Aligned_cols=37 Identities=22% Similarity=0.501 Sum_probs=25.4
Q ss_pred hhccccccCCCCCCCceeEEcCCccccChhHHHHHHHHHHHHh
Q 030117 93 LRTCGLCKRRLVPGRDIYMYRGDSAFCSLECRQQQMNQDERKQ 135 (182)
Q Consensus 93 L~~C~lCkK~L~~gkDIYMYRGe~AFCS~ECR~qqI~~DE~~E 135 (182)
...|--|+|... +..-.-| .+|||..|+ .|.+-++..
T Consensus 6 ~v~CP~C~k~~~-w~~~~~~---rPFCS~RCk--~IDLg~W~~ 42 (62)
T PRK00418 6 TVNCPTCGKPVE-WGEISPF---RPFCSKRCQ--LIDLGEWAA 42 (62)
T ss_pred cccCCCCCCccc-ccCCCCc---CCcccHHHH--hhhHHHHHc
Confidence 457999999974 2222334 489999987 577777653
No 8
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=81.25 E-value=0.51 Score=33.41 Aligned_cols=33 Identities=18% Similarity=0.415 Sum_probs=17.7
Q ss_pred ccccccCCCCCCCceeEEcCCccccChhHHHHHHHHHHH
Q 030117 95 TCGLCKRRLVPGRDIYMYRGDSAFCSLECRQQQMNQDER 133 (182)
Q Consensus 95 ~C~lCkK~L~~gkDIYMYRGe~AFCS~ECR~qqI~~DE~ 133 (182)
.|--|+|.... .+-.= -.+|||..|| .|.+-.+
T Consensus 4 ~CP~C~k~~~~-~~~n~---~rPFCS~RCk--~iDLg~W 36 (57)
T PF03884_consen 4 KCPICGKPVEW-SPENP---FRPFCSERCK--LIDLGRW 36 (57)
T ss_dssp E-TTT--EEE--SSSSS-----SSSSHHHH--HHHHS-S
T ss_pred cCCCCCCeecc-cCCCC---cCCcccHhhc--ccCHHHH
Confidence 58889998843 22222 3699999998 4655444
No 9
>smart00746 TRASH metallochaperone-like domain.
Probab=79.75 E-value=2.7 Score=22.85 Aligned_cols=33 Identities=27% Similarity=0.734 Sum_probs=20.8
Q ss_pred cccccCCCC-CCCc-eeEEcCC-ccccChhHHHHHH
Q 030117 96 CGLCKRRLV-PGRD-IYMYRGD-SAFCSLECRQQQM 128 (182)
Q Consensus 96 C~lCkK~L~-~gkD-IYMYRGe-~AFCS~ECR~qqI 128 (182)
|..|++.+. +... .+.+.|. .-|||.+|.....
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~~FCs~~c~~~~~ 36 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVFYFCSSKCLSKFK 36 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEEEEeCHHHHHHHH
Confidence 677888885 3322 2234442 4799999987543
No 10
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=79.29 E-value=1.2 Score=28.99 Aligned_cols=32 Identities=28% Similarity=0.641 Sum_probs=21.7
Q ss_pred cccCCCCCC--CceeEEcCC-ccccChhHHHHHHHH
Q 030117 98 LCKRRLVPG--RDIYMYRGD-SAFCSLECRQQQMNQ 130 (182)
Q Consensus 98 lCkK~L~~g--kDIYMYRGe-~AFCS~ECR~qqI~~ 130 (182)
-|...| ++ ...+.|+|. --|||.+|++.....
T Consensus 5 vcg~~v-~~~~~~~~~y~G~~Y~FCS~~C~~~F~~~ 39 (47)
T PF04945_consen 5 VCGMKV-PGNAAYSVEYNGRTYYFCSEGCKEKFEAN 39 (47)
T ss_dssp GGG-BE------EEEEETTEEEEESSHHHHHHHHCS
T ss_pred CCCCEE-ccCccEEEEECCEEEEEcCHHHHHHHHHC
Confidence 477788 33 466788887 589999999876543
No 11
>PRK01343 zinc-binding protein; Provisional
Probab=77.40 E-value=1.7 Score=30.90 Aligned_cols=31 Identities=26% Similarity=0.587 Sum_probs=22.7
Q ss_pred hccccccCCCCCCCceeEEcCCccccChhHHHHHHHHHHHH
Q 030117 94 RTCGLCKRRLVPGRDIYMYRGDSAFCSLECRQQQMNQDERK 134 (182)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYRGe~AFCS~ECR~qqI~~DE~~ 134 (182)
..|--|+|... + = ..+|||..||. |.+-.+.
T Consensus 10 ~~CP~C~k~~~-~----~---~rPFCS~RC~~--iDLg~W~ 40 (57)
T PRK01343 10 RPCPECGKPST-R----E---AYPFCSERCRD--IDLNRWL 40 (57)
T ss_pred CcCCCCCCcCc-C----C---CCcccCHHHhh--hhHHHHh
Confidence 57999999874 1 1 35999999985 6666654
No 12
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=76.74 E-value=2.1 Score=35.09 Aligned_cols=35 Identities=26% Similarity=0.516 Sum_probs=27.4
Q ss_pred hccccccCCCCCCCceeEEcCC---ccccChhHHHHHH
Q 030117 94 RTCGLCKRRLVPGRDIYMYRGD---SAFCSLECRQQQM 128 (182)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYRGe---~AFCS~ECR~qqI 128 (182)
..|++|..+|-||.-|-.-|.| --|||..|....+
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~f~ 42 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNYD 42 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHHHH
Confidence 4799999999999876555655 3599999976554
No 13
>PRK00807 50S ribosomal protein L24e; Validated
Probab=76.42 E-value=2.6 Score=28.94 Aligned_cols=34 Identities=32% Similarity=0.786 Sum_probs=27.2
Q ss_pred hccccccCCCCCCCceeEEcCC---ccccChhHHHHH
Q 030117 94 RTCGLCKRRLVPGRDIYMYRGD---SAFCSLECRQQQ 127 (182)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYRGe---~AFCS~ECR~qq 127 (182)
..|..|..+|.||.-+..++.| --|||..|....
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~~~f 38 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCEKNY 38 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHHHHH
Confidence 4699999999989887766655 469999997654
No 14
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=70.67 E-value=2.1 Score=31.55 Aligned_cols=23 Identities=48% Similarity=0.966 Sum_probs=18.4
Q ss_pred HhhccccccCCCCCCCceeEEcCCccccChhH
Q 030117 92 FLRTCGLCKRRLVPGRDIYMYRGDSAFCSLEC 123 (182)
Q Consensus 92 FL~~C~lCkK~L~~gkDIYMYRGe~AFCS~EC 123 (182)
+...|..|.+.|. |- | -|||..|
T Consensus 48 ~~~~C~~C~R~L~---d~--~----~fCSl~C 70 (72)
T PF04640_consen 48 SGNICETCHRSLQ---DP--Y----RFCSLSC 70 (72)
T ss_pred CCCccCCCCCCCC---CC--C----eEEeeeE
Confidence 6688999999995 33 3 3899988
No 15
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=65.71 E-value=6 Score=27.62 Aligned_cols=35 Identities=29% Similarity=0.785 Sum_probs=28.3
Q ss_pred hccccccCCCCCCCceeEEcCCc---cccChhHHHHHH
Q 030117 94 RTCGLCKRRLVPGRDIYMYRGDS---AFCSLECRQQQM 128 (182)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYRGe~---AFCS~ECR~qqI 128 (182)
..|.+|..+|.||.-+-.-|.|. -|||..|+...+
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~s~Kc~~~~~ 41 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFRFCSSKCEKNFL 41 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEEEECHHHHHHHH
Confidence 46999999999998776667673 599999976554
No 16
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=65.04 E-value=4.3 Score=26.13 Aligned_cols=25 Identities=20% Similarity=0.636 Sum_probs=18.0
Q ss_pred ccccccCCCCCCCceeEEcCCccccCh
Q 030117 95 TCGLCKRRLVPGRDIYMYRGDSAFCSL 121 (182)
Q Consensus 95 ~C~lCkK~L~~gkDIYMYRGe~AFCS~ 121 (182)
.|..|++.|..+. |....++.||..
T Consensus 28 ~C~~C~~~l~~~~--~~~~~~~~~C~~ 52 (58)
T PF00412_consen 28 KCSKCGKPLNDGD--FYEKDGKPYCKD 52 (58)
T ss_dssp BETTTTCBTTTSS--EEEETTEEEEHH
T ss_pred ccCCCCCccCCCe--eEeECCEEECHH
Confidence 5889999996554 444545899865
No 17
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=60.34 E-value=6.5 Score=27.55 Aligned_cols=32 Identities=16% Similarity=0.419 Sum_probs=17.8
Q ss_pred hccccccCCCCCCCceeEEcCCccccChhHHHHH
Q 030117 94 RTCGLCKRRLVPGRDIYMYRGDSAFCSLECRQQQ 127 (182)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYRGe~AFCS~ECR~qq 127 (182)
-.|..|+=.+..... ++ +.-+.|||.+|-..+
T Consensus 8 CaC~~C~C~V~~~~A-i~-~dGk~YCS~aCA~gH 39 (52)
T PF02069_consen 8 CACPSCSCVVSEEEA-IQ-KDGKYYCSEACANGH 39 (52)
T ss_dssp -SSTT----B-TTTS-EE-SSS-EESSHHHHHTS
T ss_pred ecCCCCEeEECchHh-HH-hCCEeeecHHHhccC
Confidence 467888888865433 44 556999999997765
No 18
>PF11809 DUF3330: Domain of unknown function (DUF3330); InterPro: IPR021767 This family of proteins are functionally uncharacterised. This family is only found in bacteria.
Probab=57.14 E-value=4.6 Score=30.04 Aligned_cols=36 Identities=22% Similarity=0.546 Sum_probs=23.4
Q ss_pred hccccccCCCCCCCceeEEcCC---ccccChhHHHHHHHH
Q 030117 94 RTCGLCKRRLVPGRDIYMYRGD---SAFCSLECRQQQMNQ 130 (182)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYRGe---~AFCS~ECR~qqI~~ 130 (182)
..|..|.|.|- -.-.+.--|+ .-||..||-++-...
T Consensus 12 ~sC~vC~KEIP-l~~a~t~E~~eYV~hFCGLeCY~~w~a~ 50 (70)
T PF11809_consen 12 TSCCVCCKEIP-LDAAFTPEAAEYVEHFCGLECYQRWQAR 50 (70)
T ss_pred chHHHHhhhCC-hhhccCcchHHHHHHHhhHHHHHHHHHH
Confidence 46888999884 3333333332 569999997766543
No 19
>PF15279 SOBP: Sine oculis-binding protein
Probab=52.26 E-value=13 Score=33.93 Aligned_cols=33 Identities=30% Similarity=0.586 Sum_probs=20.6
Q ss_pred cccccCCCCCCCceeEEcCC----ccccChhHHHHHHHH
Q 030117 96 CGLCKRRLVPGRDIYMYRGD----SAFCSLECRQQQMNQ 130 (182)
Q Consensus 96 C~lCkK~L~~gkDIYMYRGe----~AFCS~ECR~qqI~~ 130 (182)
|-+||. +++.++ |+=-|| --|||..|..|+-+.
T Consensus 2 cdwckh-~rh~~~-y~d~~~g~~~lqfcs~kclnqykm~ 38 (306)
T PF15279_consen 2 CDWCKH-VRHTKS-YVDFQDGERQLQFCSDKCLNQYKMD 38 (306)
T ss_pred ccchhc-ccchhh-eeccccchHHhhhccHHHHhHHHHH
Confidence 667753 434443 554444 359999999986543
No 20
>PHA03073 late transcription factor VLTF-2; Provisional
Probab=49.29 E-value=11 Score=31.54 Aligned_cols=35 Identities=29% Similarity=0.615 Sum_probs=25.4
Q ss_pred hhccccccCCCCCCCceeEE---cCC-ccccChhHHHHHH
Q 030117 93 LRTCGLCKRRLVPGRDIYMY---RGD-SAFCSLECRQQQM 128 (182)
Q Consensus 93 L~~C~lCkK~L~~gkDIYMY---RGe-~AFCS~ECR~qqI 128 (182)
-..|-+|+..|.. .++++= .|. ..|||.=||+-.-
T Consensus 49 ~~~CwfC~q~~~~-~~~~iETl~g~~vg~FCS~ICRDSfa 87 (150)
T PHA03073 49 NDYCWFCKQDLII-APLFIETLKGGAVGYFCSKICRDSFA 87 (150)
T ss_pred CCcEEeecccccc-CceEEEeecCchhhhHhHHHHHHHHH
Confidence 3579999999964 456653 323 6899999998643
No 21
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.69 E-value=9.4 Score=28.06 Aligned_cols=36 Identities=22% Similarity=0.511 Sum_probs=25.3
Q ss_pred hhccccccCCCCCCCceeEEcCCccccChhHHHHHHHHHHHH
Q 030117 93 LRTCGLCKRRLVPGRDIYMYRGDSAFCSLECRQQQMNQDERK 134 (182)
Q Consensus 93 L~~C~lCkK~L~~gkDIYMYRGe~AFCS~ECR~qqI~~DE~~ 134 (182)
-..|-.|.|... +.++==| .+|||..|. .|.+-++.
T Consensus 7 ~v~CP~Cgkpv~-w~~~s~f---rPFCSkRCk--lIDLg~Wa 42 (65)
T COG3024 7 TVPCPTCGKPVV-WGEESPF---RPFCSKRCK--LIDLGEWA 42 (65)
T ss_pred cccCCCCCCccc-ccccCCc---CcchhHhhh--hcchhhhh
Confidence 456999999984 4343344 499999875 67777764
No 22
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=44.86 E-value=17 Score=26.13 Aligned_cols=31 Identities=26% Similarity=0.833 Sum_probs=25.1
Q ss_pred hccccccCCCCCCC-ceeEEcCCccccChhHHH
Q 030117 94 RTCGLCKRRLVPGR-DIYMYRGDSAFCSLECRQ 125 (182)
Q Consensus 94 ~~C~lCkK~L~~gk-DIYMYRGe~AFCS~ECR~ 125 (182)
-.|-.|.+.|.++. |.||.--|=-||. +|-+
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~-~C~e 37 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCA-DCAE 37 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccH-HHHH
Confidence 35889999998887 9999988899985 4543
No 23
>PF04181 RPAP2_Rtr1: Rtr1/RPAP2 family; InterPro: IPR007308 This entry represents a domain found in PAP2 (RNAP II associated polypeptide) protein and the yeast Rtr1 proteins. Its function is not known however it is thought to be a zinc finger.
Probab=42.74 E-value=29 Score=24.78 Aligned_cols=41 Identities=27% Similarity=0.420 Sum_probs=23.8
Q ss_pred hhHhhccc--cccCCCCCC--CceeEE--------cCC----ccccChhHHHHHHHH
Q 030117 90 PHFLRTCG--LCKRRLVPG--RDIYMY--------RGD----SAFCSLECRQQQMNQ 130 (182)
Q Consensus 90 ~~FL~~C~--lCkK~L~~g--kDIYMY--------RGe----~AFCS~ECR~qqI~~ 130 (182)
-+....|. +|.+.+... +..|-. .-+ .-|||..|...-..+
T Consensus 17 R~~~~~CGYplC~~~~~~~~~~~~y~i~~~~~~v~~~~~~~~~~fCS~~C~~~s~~~ 73 (79)
T PF04181_consen 17 RNINGLCGYPLCSNPPPKISSRQKYRIDLKANKVYDITERELSKFCSKDCYKASEFY 73 (79)
T ss_pred HHhCCCCCCccCCCCcccccCCCCeEEECCCCeecccccChhcCcCCHHHHHHHHHH
Confidence 34445553 588877655 333322 211 389999998765443
No 24
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=41.20 E-value=21 Score=21.99 Aligned_cols=15 Identities=27% Similarity=0.667 Sum_probs=12.1
Q ss_pred CCccccChhHHHHHH
Q 030117 114 GDSAFCSLECRQQQM 128 (182)
Q Consensus 114 Ge~AFCS~ECR~qqI 128 (182)
....|||.+|+....
T Consensus 16 ~~~~YCs~~Cq~~~w 30 (37)
T PF01753_consen 16 KSVYYCSEECQRADW 30 (37)
T ss_dssp SSSEESSHHHHHHHH
T ss_pred CCEEecCHHHHHHHH
Confidence 457899999998765
No 25
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=39.88 E-value=25 Score=25.80 Aligned_cols=35 Identities=26% Similarity=0.569 Sum_probs=23.7
Q ss_pred hccccccCCCCCCCceeEEcCC---ccccChhHHHHHH
Q 030117 94 RTCGLCKRRLVPGRDIYMYRGD---SAFCSLECRQQQM 128 (182)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYRGe---~AFCS~ECR~qqI 128 (182)
..|.+|..+|.||.-+..-+-| --|||.-|+...+
T Consensus 4 ~~C~Fsg~~I~PG~G~~~Vr~DG~v~~F~s~Kc~~~~~ 41 (71)
T PF01246_consen 4 EKCSFSGYKIYPGHGKMYVRNDGKVFYFCSSKCEKLFK 41 (71)
T ss_dssp EE-TTT-SEE-SSSSEEEE-TTS-EEEESSHHHHHHHH
T ss_pred EEecccCCccCCCCCeEEEecCCCeEEEeCHHHHHHHH
Confidence 4699999999999876544544 3599999987654
No 26
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=39.72 E-value=58 Score=24.05 Aligned_cols=41 Identities=17% Similarity=0.400 Sum_probs=29.4
Q ss_pred ccccccCCCCCCCceeEEcC--CccccChhHHHHH-HHHHHHHh
Q 030117 95 TCGLCKRRLVPGRDIYMYRG--DSAFCSLECRQQQ-MNQDERKQ 135 (182)
Q Consensus 95 ~C~lCkK~L~~gkDIYMYRG--e~AFCS~ECR~qq-I~~DE~~E 135 (182)
.|+.|..++.++..|-+... ++.||-.-|..-. |+.+.-.+
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~~i~~~gL~ 45 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQLIHENGLE 45 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHHHHHHcchH
Confidence 59999999976776666543 4999999998754 44444333
No 27
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=34.02 E-value=40 Score=19.39 Aligned_cols=23 Identities=13% Similarity=0.436 Sum_probs=15.4
Q ss_pred ccccccCCCCCCCceeEEcCCccc
Q 030117 95 TCGLCKRRLVPGRDIYMYRGDSAF 118 (182)
Q Consensus 95 ~C~lCkK~L~~gkDIYMYRGe~AF 118 (182)
.|..|++.|.++ +.++...+..|
T Consensus 1 ~C~~C~~~i~~~-~~~~~~~~~~~ 23 (39)
T smart00132 1 KCAGCGKPIRGG-ELVLRALGKVW 23 (39)
T ss_pred CccccCCcccCC-cEEEEeCCccc
Confidence 488999999655 44554455555
No 28
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=33.72 E-value=43 Score=21.94 Aligned_cols=32 Identities=19% Similarity=0.403 Sum_probs=22.6
Q ss_pred cccccCCCCCCCceeEEcCC-ccccChhHHHHH
Q 030117 96 CGLCKRRLVPGRDIYMYRGD-SAFCSLECRQQQ 127 (182)
Q Consensus 96 C~lCkK~L~~gkDIYMYRGe-~AFCS~ECR~qq 127 (182)
|-+|.+.|...--+|=+.+. --||+..|..+.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHHH
Confidence 78899999644444555443 359999998764
No 29
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=31.67 E-value=34 Score=24.22 Aligned_cols=25 Identities=12% Similarity=0.324 Sum_probs=17.3
Q ss_pred hhccccccCCCCCCCceeEEcCCccc
Q 030117 93 LRTCGLCKRRLVPGRDIYMYRGDSAF 118 (182)
Q Consensus 93 L~~C~lCkK~L~~gkDIYMYRGe~AF 118 (182)
-..|..|+|+|.. ..+++|--...|
T Consensus 78 ~~~C~vC~k~l~~-~~f~~~p~~~v~ 102 (109)
T PF10367_consen 78 STKCSVCGKPLGN-SVFVVFPCGHVV 102 (109)
T ss_pred CCCccCcCCcCCC-ceEEEeCCCeEE
Confidence 3569999999964 677777532444
No 30
>KOG4357 consensus Uncharacterized conserved protein (involved in mesoderm differentiation in humans) [General function prediction only]
Probab=31.19 E-value=20 Score=30.07 Aligned_cols=16 Identities=38% Similarity=0.912 Sum_probs=13.6
Q ss_pred CCCCCceeEEc-CCccc
Q 030117 103 LVPGRDIYMYR-GDSAF 118 (182)
Q Consensus 103 L~~gkDIYMYR-Ge~AF 118 (182)
+..++-|||++ |+.||
T Consensus 111 i~ddraifm~kdge~a~ 127 (164)
T KOG4357|consen 111 IDDDRAIFMFKDGEQAF 127 (164)
T ss_pred ecCCeEEEEEeChhHHH
Confidence 46789999998 88888
No 31
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=30.07 E-value=50 Score=26.94 Aligned_cols=35 Identities=17% Similarity=0.271 Sum_probs=26.9
Q ss_pred hccccccCCCCCCCceeEEc----CC---ccccChhHHHHHH
Q 030117 94 RTCGLCKRRLVPGRDIYMYR----GD---SAFCSLECRQQQM 128 (182)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYR----Ge---~AFCS~ECR~qqI 128 (182)
..|++|..+|.||.-+-.-+ .| --|||.-|....+
T Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~~~~~Dgkv~~F~~sKc~~~~~ 45 (125)
T PTZ00033 4 IACEFSHFAVHPGHGRRYVPFAFLSTKPVLTFLRPKCFALYM 45 (125)
T ss_pred eEecCcCCcccCCCCcEeeecccCCCCCEEEEecHHHHHHHH
Confidence 47999999999998765556 55 3599999965444
No 32
>cd01224 PH_Collybistin Collybistin pleckstrin homology (PH) domain. Collybistin pleckstrin homology (PH) domain. Collybistin is GEF which induces submembrane clustering of the receptor-associated peripheral membrane protein gephyrin. It consists of an SH3 domain, followed by a RhoGEF(dbH) and PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=23.89 E-value=37 Score=26.76 Aligned_cols=21 Identities=38% Similarity=0.754 Sum_probs=15.6
Q ss_pred hccccccCCCCCCCceeEEcCC
Q 030117 94 RTCGLCKRRLVPGRDIYMYRGD 115 (182)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYRGe 115 (182)
..--+|||.+.. +|.|.|+|-
T Consensus 28 ~~LI~CKkd~~r-~~~~~yKgr 48 (109)
T cd01224 28 HQMVLCKKDLIR-RDHLYYKGR 48 (109)
T ss_pred ceEEEEeccccc-CCcEEEEEE
Confidence 344569999854 689999973
No 33
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=21.82 E-value=34 Score=25.40 Aligned_cols=17 Identities=41% Similarity=1.028 Sum_probs=15.3
Q ss_pred hhccccccCCCCCCCceeEEc
Q 030117 93 LRTCGLCKRRLVPGRDIYMYR 113 (182)
Q Consensus 93 L~~C~lCkK~L~~gkDIYMYR 113 (182)
|-.|..|.|+|+ ++||+
T Consensus 19 ~~~C~~C~Rr~G----LW~f~ 35 (91)
T PF08600_consen 19 LLSCSYCFRRLG----LWMFK 35 (91)
T ss_pred eEEccccCcEee----eeecc
Confidence 889999999994 89997
Done!