Query 045147
Match_columns 113
No_of_seqs 102 out of 245
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 10:17:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045147.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045147hhsearch_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 1.8E-28 3.9E-33 160.5 4.0 49 32-80 10-58 (58)
2 PF09889 DUF2116: Uncharacteri 95.7 0.015 3.3E-07 38.3 3.4 31 39-78 4-34 (59)
3 PF12855 Ecl1: Life-span regul 94.8 0.015 3.3E-07 36.1 1.3 31 36-72 4-34 (43)
4 PF06467 zf-FCS: MYM-type Zinc 93.2 0.072 1.6E-06 31.1 2.0 34 38-71 6-42 (43)
5 COG4068 Uncharacterized protei 92.0 0.15 3.2E-06 34.4 2.5 33 39-82 9-41 (64)
6 COG2075 RPL24A Ribosomal prote 90.2 0.27 5.7E-06 33.4 2.4 32 39-70 4-38 (66)
7 PRK01343 zinc-binding protein; 88.3 0.39 8.4E-06 31.6 2.0 38 38-85 9-46 (57)
8 PF03884 DUF329: Domain of unk 87.1 0.25 5.5E-06 32.3 0.6 35 40-80 4-38 (57)
9 PRK00418 DNA gyrase inhibitor; 85.5 0.56 1.2E-05 31.3 1.6 42 38-85 6-47 (62)
10 smart00746 TRASH metallochaper 78.3 3.4 7.3E-05 20.8 2.8 32 41-72 1-35 (39)
11 PRK00807 50S ribosomal protein 73.8 3.4 7.4E-05 26.2 2.3 34 39-72 2-38 (52)
12 PF00412 LIM: LIM domain; Int 70.2 3.1 6.7E-05 24.9 1.5 25 40-66 28-52 (58)
13 PRK14891 50S ribosomal protein 68.1 4.5 9.7E-05 30.7 2.3 36 38-73 4-42 (131)
14 PF04945 YHS: YHS domain; Int 67.7 2.9 6.3E-05 25.1 1.0 32 43-74 5-38 (47)
15 PF02069 Metallothio_Pro: Prok 63.9 5.5 0.00012 25.8 1.8 32 39-72 8-39 (52)
16 PF12156 ATPase-cat_bd: Putati 60.8 28 0.0006 23.8 5.0 47 40-86 2-51 (88)
17 cd00472 Ribosomal_L24e_L24 Rib 59.6 8.7 0.00019 24.7 2.2 35 39-73 4-41 (54)
18 COG3024 Uncharacterized protei 54.0 7.4 0.00016 26.4 1.2 42 38-85 7-48 (65)
19 PF06906 DUF1272: Protein of u 47.4 16 0.00035 24.2 2.0 30 39-69 6-36 (57)
20 PF04181 RPAP2_Rtr1: Rtr1/RPAP 45.2 29 0.00062 22.9 3.0 32 43-74 27-72 (79)
21 smart00132 LIM Zinc-binding do 42.9 27 0.00058 18.6 2.2 23 40-63 1-23 (39)
22 PHA03073 late transcription fa 41.7 17 0.00036 28.2 1.5 39 33-72 44-86 (150)
23 PF04640 PLATZ: PLATZ transcri 36.0 17 0.00036 24.8 0.7 24 36-68 47-70 (72)
24 PTZ00033 60S ribosomal protein 33.9 47 0.001 25.0 2.9 35 39-73 4-45 (125)
25 PF01246 Ribosomal_L24e: Ribos 32.6 37 0.0008 23.0 1.9 35 39-73 4-41 (71)
26 PF08394 Arc_trans_TRASH: Arch 30.1 53 0.0012 19.8 2.2 32 41-72 1-33 (37)
27 PF01753 zf-MYND: MYND finger; 29.0 37 0.0008 19.2 1.3 15 59-73 16-30 (37)
28 cd01224 PH_Collybistin Collybi 28.6 26 0.00057 25.5 0.7 17 42-59 31-47 (109)
29 KOG4357 Uncharacterized conser 27.3 25 0.00054 27.3 0.4 16 48-63 111-127 (164)
30 PF10367 Vps39_2: Vacuolar sor 25.9 57 0.0012 21.3 1.9 25 38-63 78-102 (109)
31 PF10013 DUF2256: Uncharacteri 24.9 22 0.00048 22.2 -0.2 30 39-71 9-41 (42)
32 KOG4739 Uncharacterized protei 23.9 14 0.00031 30.2 -1.5 39 25-63 24-69 (233)
33 COG3350 Uncharacterized conser 21.4 90 0.002 20.4 2.2 32 43-74 7-41 (53)
No 1
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=99.95 E-value=1.8e-28 Score=160.50 Aligned_cols=49 Identities=55% Similarity=1.120 Sum_probs=47.0
Q ss_pred CCCchhhhcCcCCCCCCCCCCCeeEEcCCCcccChhhHHHHHHHHHHHH
Q 045147 32 YQEPHFLDSCFLCRKPLGYNSDIFMYRGNTPFCSKECRQEQIEMDEAKE 80 (113)
Q Consensus 32 ~~~~~FL~~C~~C~K~L~~~~DIymYrGe~AFCS~ECR~~qI~~DE~~E 80 (113)
.++.+||++|++|+|+|.+++||||||||+||||.|||++||++||++|
T Consensus 10 ~~~~~FL~~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~~qi~~de~~E 58 (58)
T PF04570_consen 10 FPSEHFLSFCYLCKKKLDPGKDIYMYRGDKAFCSEECRSQQILMDEEKE 58 (58)
T ss_pred CCcHHHHHHHHccCCCCCCCCCeeeeccccccccHHHHHHHHHHHHhcC
Confidence 4778999999999999999999999999999999999999999999976
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=95.65 E-value=0.015 Score=38.25 Aligned_cols=31 Identities=32% Similarity=0.768 Sum_probs=25.1
Q ss_pred hcCcCCCCCCCCCCCeeEEcCCCcccChhhHHHHHHHHHH
Q 045147 39 DSCFLCRKPLGYNSDIFMYRGNTPFCSKECRQEQIEMDEA 78 (113)
Q Consensus 39 ~~C~~C~K~L~~~~DIymYrGe~AFCS~ECR~~qI~~DE~ 78 (113)
..|-.|.+++.+ |..|||.+||+.....-+.
T Consensus 4 kHC~~CG~~Ip~---------~~~fCS~~C~~~~~k~qk~ 34 (59)
T PF09889_consen 4 KHCPVCGKPIPP---------DESFCSPKCREEYRKRQKR 34 (59)
T ss_pred CcCCcCCCcCCc---------chhhhCHHHHHHHHHHHHH
Confidence 469999999986 5899999999987655444
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=94.79 E-value=0.015 Score=36.10 Aligned_cols=31 Identities=32% Similarity=0.786 Sum_probs=24.9
Q ss_pred hhhhcCcCCCCCCCCCCCeeEEcCCCcccChhhHHHH
Q 045147 36 HFLDSCFLCRKPLGYNSDIFMYRGNTPFCSKECRQEQ 72 (113)
Q Consensus 36 ~FL~~C~~C~K~L~~~~DIymYrGe~AFCS~ECR~~q 72 (113)
.|+++|-.|-|.+.+. -.+..+||++||..-
T Consensus 4 ~F~~yC~~Cdk~~~~~------~~~~lYCSe~Cr~~D 34 (43)
T PF12855_consen 4 AFNDYCIVCDKQIDPP------DDGSLYCSEECRLKD 34 (43)
T ss_pred hhhhHHHHhhccccCC------CCCccccCHHHHhHh
Confidence 6999999999999553 235678999999764
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=93.17 E-value=0.072 Score=31.10 Aligned_cols=34 Identities=26% Similarity=0.707 Sum_probs=22.1
Q ss_pred hhcCcCCCCCCCCCCC--eeEEcCC-CcccChhhHHH
Q 045147 38 LDSCFLCRKPLGYNSD--IFMYRGN-TPFCSKECRQE 71 (113)
Q Consensus 38 L~~C~~C~K~L~~~~D--IymYrGe-~AFCS~ECR~~ 71 (113)
...|..|++.+....+ +..+.|. .-|||..|+..
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 5679999999976555 6777765 58999999875
No 5
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=92.05 E-value=0.15 Score=34.40 Aligned_cols=33 Identities=30% Similarity=0.658 Sum_probs=25.6
Q ss_pred hcCcCCCCCCCCCCCeeEEcCCCcccChhhHHHHHHHHHHHHhh
Q 045147 39 DSCFLCRKPLGYNSDIFMYRGNTPFCSKECRQEQIEMDEAKERS 82 (113)
Q Consensus 39 ~~C~~C~K~L~~~~DIymYrGe~AFCS~ECR~~qI~~DE~~Ek~ 82 (113)
+.|--|.+.+.++ .-|||++|+ +|+..|++.+.
T Consensus 9 ~HC~VCg~aIp~d---------e~~CSe~C~--eil~ker~R~r 41 (64)
T COG4068 9 RHCVVCGKAIPPD---------EQVCSEECG--EILNKERKRQR 41 (64)
T ss_pred ccccccCCcCCCc---------cchHHHHHH--HHHHHHHHHHH
Confidence 5699999999875 579999997 46776665544
No 6
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=90.18 E-value=0.27 Score=33.41 Aligned_cols=32 Identities=28% Similarity=0.713 Sum_probs=28.4
Q ss_pred hcCcCCCCCCCCCCCeeEEcCCC---cccChhhHH
Q 045147 39 DSCFLCRKPLGYNSDIFMYRGNT---PFCSKECRQ 70 (113)
Q Consensus 39 ~~C~~C~K~L~~~~DIymYrGe~---AFCS~ECR~ 70 (113)
..|.+|.++|.||..|.--++|. =|||..|+.
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 47999999999999988888885 499999998
No 7
>PRK01343 zinc-binding protein; Provisional
Probab=88.29 E-value=0.39 Score=31.63 Aligned_cols=38 Identities=32% Similarity=0.633 Sum_probs=26.7
Q ss_pred hhcCcCCCCCCCCCCCeeEEcCCCcccChhhHHHHHHHHHHHHhhhcc
Q 045147 38 LDSCFLCRKPLGYNSDIFMYRGNTPFCSKECRQEQIEMDEAKERSWKK 85 (113)
Q Consensus 38 L~~C~~C~K~L~~~~DIymYrGe~AFCS~ECR~~qI~~DE~~Ek~~~~ 85 (113)
...|-.|+|+... -..+|||..||. |.+-.+......+
T Consensus 9 ~~~CP~C~k~~~~--------~~rPFCS~RC~~--iDLg~W~~e~Y~I 46 (57)
T PRK01343 9 TRPCPECGKPSTR--------EAYPFCSERCRD--IDLNRWLSGSYVI 46 (57)
T ss_pred CCcCCCCCCcCcC--------CCCcccCHHHhh--hhHHHHhCCCccc
Confidence 4679999998752 235999999985 5666665554444
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=87.09 E-value=0.25 Score=32.33 Aligned_cols=35 Identities=29% Similarity=0.723 Sum_probs=18.3
Q ss_pred cCcCCCCCCCCCCCeeEEcCCCcccChhhHHHHHHHHHHHH
Q 045147 40 SCFLCRKPLGYNSDIFMYRGNTPFCSKECRQEQIEMDEAKE 80 (113)
Q Consensus 40 ~C~~C~K~L~~~~DIymYrGe~AFCS~ECR~~qI~~DE~~E 80 (113)
.|-.|+|..... +-. .-.+|||..|| .|.+-.+..
T Consensus 4 ~CP~C~k~~~~~-~~n---~~rPFCS~RCk--~iDLg~W~~ 38 (57)
T PF03884_consen 4 KCPICGKPVEWS-PEN---PFRPFCSERCK--LIDLGRWAN 38 (57)
T ss_dssp E-TTT--EEE-S-SSS---S--SSSSHHHH--HHHHS-SSS
T ss_pred cCCCCCCeeccc-CCC---CcCCcccHhhc--ccCHHHHhc
Confidence 588899988642 111 23799999998 455554433
No 9
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=85.47 E-value=0.56 Score=31.32 Aligned_cols=42 Identities=31% Similarity=0.687 Sum_probs=28.1
Q ss_pred hhcCcCCCCCCCCCCCeeEEcCCCcccChhhHHHHHHHHHHHHhhhcc
Q 045147 38 LDSCFLCRKPLGYNSDIFMYRGNTPFCSKECRQEQIEMDEAKERSWKK 85 (113)
Q Consensus 38 L~~C~~C~K~L~~~~DIymYrGe~AFCS~ECR~~qI~~DE~~Ek~~~~ 85 (113)
.-.|-.|+|+..-. .---| .+|||..|+ .|.+-++......+
T Consensus 6 ~v~CP~C~k~~~w~-~~~~~---rPFCS~RCk--~IDLg~W~~e~y~I 47 (62)
T PRK00418 6 TVNCPTCGKPVEWG-EISPF---RPFCSKRCQ--LIDLGEWAAEEKRI 47 (62)
T ss_pred cccCCCCCCccccc-CCCCc---CCcccHHHH--hhhHHHHHcCCccc
Confidence 45799999997521 11122 599999997 46777776655555
No 10
>smart00746 TRASH metallochaperone-like domain.
Probab=78.30 E-value=3.4 Score=20.84 Aligned_cols=32 Identities=25% Similarity=0.554 Sum_probs=20.0
Q ss_pred CcCCCCCCC-CCCC-eeEEcC-CCcccChhhHHHH
Q 045147 41 CFLCRKPLG-YNSD-IFMYRG-NTPFCSKECRQEQ 72 (113)
Q Consensus 41 C~~C~K~L~-~~~D-IymYrG-e~AFCS~ECR~~q 72 (113)
|..|+..+. +... .+.+.| ..-|||.+|....
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~~FCs~~c~~~~ 35 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVFYFCSSKCLSKF 35 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEEEEeCHHHHHHH
Confidence 677888886 3321 222333 2369999998754
No 11
>PRK00807 50S ribosomal protein L24e; Validated
Probab=73.79 E-value=3.4 Score=26.18 Aligned_cols=34 Identities=21% Similarity=0.571 Sum_probs=26.8
Q ss_pred hcCcCCCCCCCCCCCeeEEcCC---CcccChhhHHHH
Q 045147 39 DSCFLCRKPLGYNSDIFMYRGN---TPFCSKECRQEQ 72 (113)
Q Consensus 39 ~~C~~C~K~L~~~~DIymYrGe---~AFCS~ECR~~q 72 (113)
..|..|..++.|+..+-..+.| --|||..|....
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 4699999999988877666655 359999997654
No 12
>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=70.21 E-value=3.1 Score=24.85 Aligned_cols=25 Identities=32% Similarity=0.892 Sum_probs=18.4
Q ss_pred cCcCCCCCCCCCCCeeEEcCCCcccCh
Q 045147 40 SCFLCRKPLGYNSDIFMYRGNTPFCSK 66 (113)
Q Consensus 40 ~C~~C~K~L~~~~DIymYrGe~AFCS~ 66 (113)
.|..|+++|..+ +.|+ ..+++||..
T Consensus 28 ~C~~C~~~l~~~-~~~~-~~~~~~C~~ 52 (58)
T PF00412_consen 28 KCSKCGKPLNDG-DFYE-KDGKPYCKD 52 (58)
T ss_dssp BETTTTCBTTTS-SEEE-ETTEEEEHH
T ss_pred ccCCCCCccCCC-eeEe-ECCEEECHH
Confidence 589999999865 4444 555899864
No 13
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=68.13 E-value=4.5 Score=30.70 Aligned_cols=36 Identities=11% Similarity=0.277 Sum_probs=28.1
Q ss_pred hhcCcCCCCCCCCCCCeeEEcCCC---cccChhhHHHHH
Q 045147 38 LDSCFLCRKPLGYNSDIFMYRGNT---PFCSKECRQEQI 73 (113)
Q Consensus 38 L~~C~~C~K~L~~~~DIymYrGe~---AFCS~ECR~~qI 73 (113)
+..|++|..+|-||..+-.-|.|. -|||..|....+
T Consensus 4 ~e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~f~ 42 (131)
T PRK14891 4 TRTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNYD 42 (131)
T ss_pred eeeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHHHH
Confidence 357999999999998766556553 599999976654
No 14
>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=67.71 E-value=2.9 Score=25.08 Aligned_cols=32 Identities=28% Similarity=0.614 Sum_probs=20.6
Q ss_pred CCCCCC-CCCCCeeEEcCCC-cccChhhHHHHHH
Q 045147 43 LCRKPL-GYNSDIFMYRGNT-PFCSKECRQEQIE 74 (113)
Q Consensus 43 ~C~K~L-~~~~DIymYrGe~-AFCS~ECR~~qI~ 74 (113)
-|...| ........|+|.. -|||.+|++.-..
T Consensus 5 vcg~~v~~~~~~~~~y~G~~Y~FCS~~C~~~F~~ 38 (47)
T PF04945_consen 5 VCGMKVPGNAAYSVEYNGRTYYFCSEGCKEKFEA 38 (47)
T ss_dssp GGG-BE-----EEEEETTEEEEESSHHHHHHHHC
T ss_pred CCCCEEccCccEEEEECCEEEEEcCHHHHHHHHH
Confidence 477777 2223667888864 7999999987543
No 15
>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=63.93 E-value=5.5 Score=25.78 Aligned_cols=32 Identities=16% Similarity=0.413 Sum_probs=17.8
Q ss_pred hcCcCCCCCCCCCCCeeEEcCCCcccChhhHHHH
Q 045147 39 DSCFLCRKPLGYNSDIFMYRGNTPFCSKECRQEQ 72 (113)
Q Consensus 39 ~~C~~C~K~L~~~~DIymYrGe~AFCS~ECR~~q 72 (113)
-.|..|.=-+... +-++.. .+.|||++|-..+
T Consensus 8 CaC~~C~C~V~~~-~Ai~~d-Gk~YCS~aCA~gH 39 (52)
T PF02069_consen 8 CACPSCSCVVSEE-EAIQKD-GKYYCSEACANGH 39 (52)
T ss_dssp -SSTT----B-TT-TSEESS-S-EESSHHHHHTS
T ss_pred ecCCCCEeEECch-HhHHhC-CEeeecHHHhccC
Confidence 4677888888754 555544 5999999997654
No 16
>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=60.75 E-value=28 Score=23.77 Aligned_cols=47 Identities=23% Similarity=0.552 Sum_probs=35.2
Q ss_pred cCcCCCCCCCCCCCeeEEc--CCCcccChhhHHH-HHHHHHHHHhhhccC
Q 045147 40 SCFLCRKPLGYNSDIFMYR--GNTPFCSKECRQE-QIEMDEAKERSWKKS 86 (113)
Q Consensus 40 ~C~~C~K~L~~~~DIymYr--Ge~AFCS~ECR~~-qI~~DE~~Ek~~~~s 86 (113)
.|+.|..++..+..|-+-- .++.||-.-|..- +|+.+.-.+.-+...
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~~i~~~gL~~yY~~r 51 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQLIHENGLESYYQKR 51 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHHHHHHcchHHHHhcc
Confidence 5999999997666665543 3599999999987 666666677666553
No 17
>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=59.62 E-value=8.7 Score=24.73 Aligned_cols=35 Identities=20% Similarity=0.546 Sum_probs=28.3
Q ss_pred hcCcCCCCCCCCCCCeeEEcCCC---cccChhhHHHHH
Q 045147 39 DSCFLCRKPLGYNSDIFMYRGNT---PFCSKECRQEQI 73 (113)
Q Consensus 39 ~~C~~C~K~L~~~~DIymYrGe~---AFCS~ECR~~qI 73 (113)
..|.+|..+|.||..+-.-|.|. -|||..|+...+
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 46999999999998776667774 599999976654
No 18
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.99 E-value=7.4 Score=26.41 Aligned_cols=42 Identities=29% Similarity=0.643 Sum_probs=28.7
Q ss_pred hhcCcCCCCCCCCCCCeeEEcCCCcccChhhHHHHHHHHHHHHhhhcc
Q 045147 38 LDSCFLCRKPLGYNSDIFMYRGNTPFCSKECRQEQIEMDEAKERSWKK 85 (113)
Q Consensus 38 L~~C~~C~K~L~~~~DIymYrGe~AFCS~ECR~~qI~~DE~~Ek~~~~ 85 (113)
--.|-.|.|+..-+ ++=-| .+|||..| +.|.+-++.....++
T Consensus 7 ~v~CP~Cgkpv~w~-~~s~f---rPFCSkRC--klIDLg~Wa~eey~I 48 (65)
T COG3024 7 TVPCPTCGKPVVWG-EESPF---RPFCSKRC--KLIDLGEWAAEEYAI 48 (65)
T ss_pred cccCCCCCCccccc-ccCCc---CcchhHhh--hhcchhhhhccCccc
Confidence 45699999998643 22222 59999988 467777776655554
No 19
>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=47.44 E-value=16 Score=24.19 Aligned_cols=30 Identities=27% Similarity=0.678 Sum_probs=24.1
Q ss_pred hcCcCCCCCCCCCC-CeeEEcCCCcccChhhH
Q 045147 39 DSCFLCRKPLGYNS-DIFMYRGNTPFCSKECR 69 (113)
Q Consensus 39 ~~C~~C~K~L~~~~-DIymYrGe~AFCS~ECR 69 (113)
-.|-.|.+.|.++. |-||.--|=-||. +|-
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~-~C~ 36 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCA-DCA 36 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccH-HHH
Confidence 35888999999988 8999888888884 343
No 20
>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=45.22 E-value=29 Score=22.92 Aligned_cols=32 Identities=25% Similarity=0.445 Sum_probs=20.1
Q ss_pred CCCCCCCCC--CCeeEEc--------CC--C--cccChhhHHHHHH
Q 045147 43 LCRKPLGYN--SDIFMYR--------GN--T--PFCSKECRQEQIE 74 (113)
Q Consensus 43 ~C~K~L~~~--~DIymYr--------Ge--~--AFCS~ECR~~qI~ 74 (113)
+|.+++... ++.|--- -+ . -|||..|...-..
T Consensus 27 lC~~~~~~~~~~~~y~i~~~~~~v~~~~~~~~~~fCS~~C~~~s~~ 72 (79)
T PF04181_consen 27 LCSNPPPKISSRQKYRIDLKANKVYDITERELSKFCSKDCYKASEF 72 (79)
T ss_pred cCCCCcccccCCCCeEEECCCCeecccccChhcCcCCHHHHHHHHH
Confidence 588888766 3333222 11 3 8999999877443
No 21
>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=42.88 E-value=27 Score=18.59 Aligned_cols=23 Identities=17% Similarity=0.411 Sum_probs=15.9
Q ss_pred cCcCCCCCCCCCCCeeEEcCCCcc
Q 045147 40 SCFLCRKPLGYNSDIFMYRGNTPF 63 (113)
Q Consensus 40 ~C~~C~K~L~~~~DIymYrGe~AF 63 (113)
.|..|++.|.++ +.++-.++..|
T Consensus 1 ~C~~C~~~i~~~-~~~~~~~~~~~ 23 (39)
T smart00132 1 KCAGCGKPIRGG-ELVLRALGKVW 23 (39)
T ss_pred CccccCCcccCC-cEEEEeCCccc
Confidence 488899999865 45555555665
No 22
>PHA03073 late transcription factor VLTF-2; Provisional
Probab=41.73 E-value=17 Score=28.24 Aligned_cols=39 Identities=31% Similarity=0.605 Sum_probs=28.3
Q ss_pred CCchhhhcCcCCCCCCCCCCCeeE---EcC-CCcccChhhHHHH
Q 045147 33 QEPHFLDSCFLCRKPLGYNSDIFM---YRG-NTPFCSKECRQEQ 72 (113)
Q Consensus 33 ~~~~FL~~C~~C~K~L~~~~DIym---YrG-e~AFCS~ECR~~q 72 (113)
...+=-+.|-+|+..|... ++++ |.| -..|||.=||+-.
T Consensus 44 ~~ns~~~~CwfC~q~~~~~-~~~iETl~g~~vg~FCS~ICRDSf 86 (150)
T PHA03073 44 KTNSDNDYCWFCKQDLIIA-PLFIETLKGGAVGYFCSKICRDSF 86 (150)
T ss_pred ecccCCCcEEeeccccccC-ceEEEeecCchhhhHhHHHHHHHH
Confidence 3344568899999999854 5665 332 3579999999863
No 23
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=36.03 E-value=17 Score=24.75 Aligned_cols=24 Identities=33% Similarity=0.638 Sum_probs=19.1
Q ss_pred hhhhcCcCCCCCCCCCCCeeEEcCCCcccChhh
Q 045147 36 HFLDSCFLCRKPLGYNSDIFMYRGNTPFCSKEC 68 (113)
Q Consensus 36 ~FL~~C~~C~K~L~~~~DIymYrGe~AFCS~EC 68 (113)
.....|..|.+.|. |- .-|||..|
T Consensus 47 ~~~~~C~~C~R~L~---d~------~~fCSl~C 70 (72)
T PF04640_consen 47 GSGNICETCHRSLQ---DP------YRFCSLSC 70 (72)
T ss_pred CCCCccCCCCCCCC---CC------CeEEeeeE
Confidence 56789999999996 22 35899888
No 24
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=33.93 E-value=47 Score=25.00 Aligned_cols=35 Identities=9% Similarity=0.074 Sum_probs=27.2
Q ss_pred hcCcCCCCCCCCCCCeeEEc----CCC---cccChhhHHHHH
Q 045147 39 DSCFLCRKPLGYNSDIFMYR----GNT---PFCSKECRQEQI 73 (113)
Q Consensus 39 ~~C~~C~K~L~~~~DIymYr----Ge~---AFCS~ECR~~qI 73 (113)
..|.+|..+|.||..+=+-+ .|. -||+.-|....+
T Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~~~~~Dgkv~~F~~sKc~~~~~ 45 (125)
T PTZ00033 4 IACEFSHFAVHPGHGRRYVPFAFLSTKPVLTFLRPKCFALYM 45 (125)
T ss_pred eEecCcCCcccCCCCcEeeecccCCCCCEEEEecHHHHHHHH
Confidence 46999999999998765556 553 599999976554
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=32.59 E-value=37 Score=22.95 Aligned_cols=35 Identities=17% Similarity=0.325 Sum_probs=23.9
Q ss_pred hcCcCCCCCCCCCCCeeEEcCC---CcccChhhHHHHH
Q 045147 39 DSCFLCRKPLGYNSDIFMYRGN---TPFCSKECRQEQI 73 (113)
Q Consensus 39 ~~C~~C~K~L~~~~DIymYrGe---~AFCS~ECR~~qI 73 (113)
..|.+|..+|.||..+-.-+-| --|||.-|+...+
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 4699999999999866555555 3599999987754
No 26
>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=30.14 E-value=53 Score=19.78 Aligned_cols=32 Identities=16% Similarity=0.374 Sum_probs=23.4
Q ss_pred CcCCCCCCCCCCCeeEEcCCC-cccChhhHHHH
Q 045147 41 CFLCRKPLGYNSDIFMYRGNT-PFCSKECRQEQ 72 (113)
Q Consensus 41 C~~C~K~L~~~~DIymYrGe~-AFCS~ECR~~q 72 (113)
|-+|.+.|...--+|=+.|.. =||...|..+.
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 788999998655556554432 58999998764
No 27
>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=29.01 E-value=37 Score=19.22 Aligned_cols=15 Identities=27% Similarity=0.753 Sum_probs=12.3
Q ss_pred CCCcccChhhHHHHH
Q 045147 59 GNTPFCSKECRQEQI 73 (113)
Q Consensus 59 Ge~AFCS~ECR~~qI 73 (113)
....|||.+|+....
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 28
>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=28.57 E-value=26 Score=25.46 Aligned_cols=17 Identities=41% Similarity=0.778 Sum_probs=14.2
Q ss_pred cCCCCCCCCCCCeeEEcC
Q 045147 42 FLCRKPLGYNSDIFMYRG 59 (113)
Q Consensus 42 ~~C~K~L~~~~DIymYrG 59 (113)
-+|+|.+.. +|.|.|+|
T Consensus 31 I~CKkd~~r-~~~~~yKg 47 (109)
T cd01224 31 VLCKKDLIR-RDHLYYKG 47 (109)
T ss_pred EEEeccccc-CCcEEEEE
Confidence 569999875 59999997
No 29
>KOG4357 consensus Uncharacterized conserved protein (involved in mesoderm differentiation in humans) [General function prediction only]
Probab=27.25 E-value=25 Score=27.28 Aligned_cols=16 Identities=31% Similarity=0.827 Sum_probs=12.4
Q ss_pred CCCCCCeeEEc-CCCcc
Q 045147 48 LGYNSDIFMYR-GNTPF 63 (113)
Q Consensus 48 L~~~~DIymYr-Ge~AF 63 (113)
++.++-|||++ |+.||
T Consensus 111 i~ddraifm~kdge~a~ 127 (164)
T KOG4357|consen 111 IDDDRAIFMFKDGEQAF 127 (164)
T ss_pred ecCCeEEEEEeChhHHH
Confidence 46678999998 67666
No 30
>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=25.87 E-value=57 Score=21.32 Aligned_cols=25 Identities=28% Similarity=0.555 Sum_probs=17.1
Q ss_pred hhcCcCCCCCCCCCCCeeEEcCCCcc
Q 045147 38 LDSCFLCRKPLGYNSDIFMYRGNTPF 63 (113)
Q Consensus 38 L~~C~~C~K~L~~~~DIymYrGe~AF 63 (113)
-..|..|+|+|+. ..+.+|--...|
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 3569999999985 466666533443
No 31
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=24.86 E-value=22 Score=22.20 Aligned_cols=30 Identities=23% Similarity=0.831 Sum_probs=19.3
Q ss_pred hcCcCCCCCCCCCC---CeeEEcCCCcccChhhHHH
Q 045147 39 DSCFLCRKPLGYNS---DIFMYRGNTPFCSKECRQE 71 (113)
Q Consensus 39 ~~C~~C~K~L~~~~---DIymYrGe~AFCS~ECR~~ 71 (113)
..|-.|.++..=-+ .-+ .++-|||+-||.+
T Consensus 9 K~C~~C~rpf~WRKKW~~~W---d~VkYCS~rCR~~ 41 (42)
T PF10013_consen 9 KICPVCGRPFTWRKKWARCW---DEVKYCSDRCRRR 41 (42)
T ss_pred CcCcccCCcchHHHHHHHhc---hhhccHHHHhccC
Confidence 46778877764211 111 5788999999953
No 32
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=23.94 E-value=14 Score=30.16 Aligned_cols=39 Identities=26% Similarity=0.371 Sum_probs=27.3
Q ss_pred eecccCCCCCchhhhcCcCCCCCCCCCC-------CeeEEcCCCcc
Q 045147 25 YYAGCADYQEPHFLDSCFLCRKPLGYNS-------DIFMYRGNTPF 63 (113)
Q Consensus 25 ~~~~~~~~~~~~FL~~C~~C~K~L~~~~-------DIymYrGe~AF 63 (113)
.+|.|.......+.+.|.+|+|.|.--+ ||+.|=++.++
T Consensus 24 ~HvfC~~C~k~~~~~~C~lCkk~ir~i~l~~slp~~ik~~F~d~~~ 69 (233)
T KOG4739|consen 24 RHVFCEPCLKASSPDVCPLCKKSIRIIQLNRSLPTDIKSYFADPPR 69 (233)
T ss_pred hhhhhhhhcccCCccccccccceeeeeecccccchhHHHHccCcHH
Confidence 3555655556667789999999875433 78888777663
No 33
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=21.43 E-value=90 Score=20.36 Aligned_cols=32 Identities=28% Similarity=0.601 Sum_probs=22.2
Q ss_pred CCCCCCCCCC--CeeEEcCCC-cccChhhHHHHHH
Q 045147 43 LCRKPLGYNS--DIFMYRGNT-PFCSKECRQEQIE 74 (113)
Q Consensus 43 ~C~K~L~~~~--DIymYrGe~-AFCS~ECR~~qI~ 74 (113)
.|+.+|...+ -.+-|+|-. =|||++|-...-.
T Consensus 7 Vcgm~v~~~~a~~k~~Y~GktYYFcse~~~~~F~~ 41 (53)
T COG3350 7 VCGMKVDNENAEYKSSYGGKTYYFCSEECKEKFKD 41 (53)
T ss_pred CcCccccccccceeEEeCCEEEEEeCHHHHHHHHH
Confidence 4778886333 577788854 5999999776443
Done!