Query 025742
Match_columns 248
No_of_seqs 145 out of 187
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 09:02:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025742.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025742hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04640 PLATZ: PLATZ transcri 100.0 2.4E-39 5.2E-44 244.5 5.9 72 74-145 1-72 (72)
2 PF00643 zf-B_box: B-box zinc 96.7 0.00076 1.7E-08 44.6 1.2 37 33-73 5-42 (42)
3 cd00021 BBOX B-Box-type zinc f 95.1 0.016 3.4E-07 37.1 2.0 36 33-72 2-38 (39)
4 smart00336 BBOX B-Box-type zin 94.2 0.038 8.3E-07 35.8 2.3 35 33-71 5-40 (42)
5 PF12855 Ecl1: Life-span regul 85.7 0.17 3.7E-06 35.2 -0.7 29 122-150 6-37 (43)
6 PF03884 DUF329: Domain of unk 82.2 0.12 2.6E-06 38.0 -2.8 28 123-150 3-35 (57)
7 PF10013 DUF2256: Uncharacteri 71.7 1.1 2.5E-05 31.3 -0.2 23 122-144 8-39 (42)
8 PRK01343 zinc-binding protein; 69.0 1.6 3.6E-05 32.2 0.1 28 122-149 9-37 (57)
9 PF09889 DUF2116: Uncharacteri 62.0 2.3 4.9E-05 31.5 -0.3 26 123-148 4-29 (59)
10 PF02207 zf-UBR: Putative zinc 61.6 4.1 8.9E-05 30.1 1.0 33 44-76 11-48 (71)
11 PF13240 zinc_ribbon_2: zinc-r 61.2 3.6 7.8E-05 24.9 0.5 16 125-140 2-17 (23)
12 PRK00418 DNA gyrase inhibitor; 54.6 3.6 7.8E-05 30.9 -0.3 29 122-150 6-39 (62)
13 COG4338 Uncharacterized protei 53.9 1.1 2.4E-05 32.6 -3.0 24 121-144 11-43 (54)
14 PF13248 zf-ribbon_3: zinc-rib 49.6 8.6 0.00019 23.5 0.9 19 122-140 2-20 (26)
15 cd02340 ZZ_NBR1_like Zinc fing 48.7 11 0.00025 25.7 1.5 27 47-73 15-43 (43)
16 COG3024 Uncharacterized protei 47.2 6.1 0.00013 30.1 -0.1 28 123-150 8-40 (65)
17 KOG4367 Predicted Zn-finger pr 46.8 7.4 0.00016 39.6 0.4 35 31-69 223-259 (699)
18 KOG2177 Predicted E3 ubiquitin 45.1 11 0.00024 31.2 1.1 38 33-75 88-127 (386)
19 PF01412 ArfGap: Putative GTPa 41.8 7.6 0.00017 31.2 -0.3 50 43-93 10-72 (116)
20 PF06467 zf-FCS: MYM-type Zinc 40.0 6.4 0.00014 25.8 -0.8 24 121-144 5-40 (43)
21 smart00396 ZnF_UBR1 Putative z 39.8 33 0.00072 25.6 2.9 30 41-70 8-42 (71)
22 PF04570 DUF581: Protein of un 30.5 16 0.00034 27.0 -0.1 28 122-149 16-52 (58)
23 PF04438 zf-HIT: HIT zinc fing 30.3 13 0.00029 23.8 -0.5 20 124-144 4-29 (30)
24 COG4068 Uncharacterized protei 29.8 15 0.00033 27.7 -0.3 23 122-144 8-30 (64)
25 cd02341 ZZ_ZZZ3 Zinc finger, Z 29.1 37 0.0008 23.9 1.6 27 47-73 16-48 (48)
26 PF08002 DUF1697: Protein of u 26.2 36 0.00078 28.3 1.3 30 79-109 16-48 (137)
27 PHA03301 envelope glycoprotein 24.5 1E+02 0.0022 28.4 3.8 12 219-230 188-199 (226)
28 smart00105 ArfGap Putative GTP 24.4 21 0.00046 28.5 -0.4 43 45-88 2-57 (112)
29 PLN00209 ribosomal protein S27 24.4 85 0.0018 25.1 2.9 59 64-145 20-85 (86)
30 smart00746 TRASH metallochaper 21.9 46 0.00099 18.8 0.8 10 136-145 24-33 (39)
31 TIGR00412 redox_disulf_2 small 21.7 1.3E+02 0.0028 21.9 3.3 33 80-113 32-66 (76)
32 KOG4582 Uncharacterized conser 21.6 61 0.0013 30.2 2.0 29 47-75 168-199 (278)
33 KOG0704 ADP-ribosylation facto 21.6 76 0.0016 31.4 2.6 44 45-88 18-73 (386)
34 KOG3362 Predicted BBOX Zn-fing 21.0 60 0.0013 28.5 1.6 28 120-147 116-148 (156)
35 PRK05707 DNA polymerase III su 20.1 77 0.0017 29.9 2.3 94 16-110 2-113 (328)
No 1
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=100.00 E-value=2.4e-39 Score=244.54 Aligned_cols=72 Identities=67% Similarity=1.146 Sum_probs=71.1
Q ss_pred EeccccceeeechhhhhhcccceeeEEECCcEEEEeeCCCCCCCCCCCCCcccccccccCCCCeeeeecccc
Q 025742 74 RRSSYHNVVRVNEIQKFIDISCVQTYIINSAKIVFLNERPQPRPGKGVTNTCEICCRSLLDSFRFCSLGCKL 145 (248)
Q Consensus 74 RRssYhdVVRv~DIqkllD~S~IQtYvINsakVVFLn~RPq~r~~kg~~~~Ce~C~R~L~D~~rFCSL~CKv 145 (248)
|||||||||||.|||||||||+||||+|||+||||||+|||+++++++++.|++|+|+|+|+|+||||+|||
T Consensus 1 Rr~sY~dVVrv~di~kl~D~s~IQtY~iNs~kVVfLn~Rpq~~~~~~~~~~C~~C~R~L~d~~~fCSl~CKv 72 (72)
T PF04640_consen 1 RRYSYHDVVRVSDIQKLLDCSGIQTYVINSAKVVFLNPRPQSRPSKGSGNICETCHRSLQDPYRFCSLSCKV 72 (72)
T ss_pred CcccccceEEHHHhHhhccccccEEEEeCCceEEEEccCCcCCCCCCCCCccCCCCCCCCCCCeEEeeeEEC
Confidence 899999999999999999999999999999999999999999999999999999999999999999999997
No 2
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=96.67 E-value=0.00076 Score=44.60 Aligned_cols=37 Identities=38% Similarity=0.904 Sum_probs=29.7
Q ss_pred CCccCCCCCCCCcceecccCCCccCCcchhc-CCCCCceeEE
Q 025742 33 PCVVHGDSNKSECNMFCLDCMGNAFCSYCLI-NHKDHRVVQI 73 (248)
Q Consensus 33 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~-~H~~HrvlQI 73 (248)
.|..|.. .+.++||.+|.. .+|..|.. .|++|.++.|
T Consensus 5 ~C~~H~~---~~~~~~C~~C~~-~~C~~C~~~~H~~H~~~~i 42 (42)
T PF00643_consen 5 KCPEHPE---EPLSLFCEDCNE-PLCSECTVSGHKGHKIVPI 42 (42)
T ss_dssp B-SSTTT---SBEEEEETTTTE-EEEHHHHHTSTTTSEEEEC
T ss_pred cCccCCc---cceEEEecCCCC-ccCccCCCCCCCCCEEeEC
Confidence 6888864 348899999998 89999977 4999988764
No 3
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=95.09 E-value=0.016 Score=37.11 Aligned_cols=36 Identities=31% Similarity=0.626 Sum_probs=27.9
Q ss_pred CCccCCCCCCCCcceecccCCCccCCcchhc-CCCCCceeE
Q 025742 33 PCVVHGDSNKSECNMFCLDCMGNAFCSYCLI-NHKDHRVVQ 72 (248)
Q Consensus 33 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~-~H~~HrvlQ 72 (248)
.|..|.. +...+||.+|.. .+|..|.. .|++|.++-
T Consensus 2 ~C~~H~~---~~~~~fC~~~~~-~iC~~C~~~~H~~H~~~~ 38 (39)
T cd00021 2 LCDEHGE---EPLSLFCETDRA-LLCVDCDLSVHSGHRRVP 38 (39)
T ss_pred CCCccCC---cceEEEeCccCh-hhhhhcChhhcCCCCEee
Confidence 4788843 246899999988 89999964 599987754
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=94.22 E-value=0.038 Score=35.76 Aligned_cols=35 Identities=37% Similarity=0.868 Sum_probs=27.7
Q ss_pred CCccCCCCCCCCcceecccCCCccCCcchhc-CCCCCcee
Q 025742 33 PCVVHGDSNKSECNMFCLDCMGNAFCSYCLI-NHKDHRVV 71 (248)
Q Consensus 33 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~-~H~~Hrvl 71 (248)
.|..|.. ....+||.+|.. .+|..|.. .|++|.++
T Consensus 5 ~C~~h~~---~~~~~~C~~c~~-~iC~~C~~~~H~~H~~~ 40 (42)
T smart00336 5 KCDSHGD---EPAEFFCEECGA-LLCRTCDEAEHRGHTVV 40 (42)
T ss_pred cCCCCCC---CceEEECCCCCc-ccccccChhhcCCCcee
Confidence 5888853 335899999997 89999976 59898765
No 5
>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=85.72 E-value=0.17 Score=35.23 Aligned_cols=29 Identities=24% Similarity=0.663 Sum_probs=24.5
Q ss_pred CCccccccccc---CCCCeeeeeccccCceec
Q 025742 122 TNTCEICCRSL---LDSFRFCSLGCKLGAMKR 150 (248)
Q Consensus 122 ~~~Ce~C~R~L---~D~~rFCSL~CKv~~~~~ 150 (248)
.+.|.+|+|-+ .+...|||-.|++.....
T Consensus 6 ~~yC~~Cdk~~~~~~~~~lYCSe~Cr~~D~~~ 37 (43)
T PF12855_consen 6 NDYCIVCDKQIDPPDDGSLYCSEECRLKDQEK 37 (43)
T ss_pred hhHHHHhhccccCCCCCccccCHHHHhHhhhc
Confidence 46799999999 678999999999876554
No 6
>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=82.24 E-value=0.12 Score=38.01 Aligned_cols=28 Identities=43% Similarity=0.816 Sum_probs=17.3
Q ss_pred CcccccccccCC----CCe-eeeeccccCceec
Q 025742 123 NTCEICCRSLLD----SFR-FCSLGCKLGAMKR 150 (248)
Q Consensus 123 ~~Ce~C~R~L~D----~~r-FCSL~CKv~~~~~ 150 (248)
..|-+|++...- +|+ |||-.||+..+.+
T Consensus 3 v~CP~C~k~~~~~~~n~~rPFCS~RCk~iDLg~ 35 (57)
T PF03884_consen 3 VKCPICGKPVEWSPENPFRPFCSERCKLIDLGR 35 (57)
T ss_dssp EE-TTT--EEE-SSSSS--SSSSHHHHHHHHS-
T ss_pred ccCCCCCCeecccCCCCcCCcccHhhcccCHHH
Confidence 469999998865 564 9999999876654
No 7
>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=71.70 E-value=1.1 Score=31.29 Aligned_cols=23 Identities=30% Similarity=0.967 Sum_probs=19.7
Q ss_pred CCcccccccccC---------CCCeeeeeccc
Q 025742 122 TNTCEICCRSLL---------DSFRFCSLGCK 144 (248)
Q Consensus 122 ~~~Ce~C~R~L~---------D~~rFCSL~CK 144 (248)
..+|.+|+|.+. |..+|||-.|.
T Consensus 8 ~K~C~~C~rpf~WRKKW~~~Wd~VkYCS~rCR 39 (42)
T PF10013_consen 8 SKICPVCGRPFTWRKKWARCWDEVKYCSDRCR 39 (42)
T ss_pred CCcCcccCCcchHHHHHHHhchhhccHHHHhc
Confidence 457999999996 56899999996
No 8
>PRK01343 zinc-binding protein; Provisional
Probab=69.05 E-value=1.6 Score=32.21 Aligned_cols=28 Identities=25% Similarity=0.600 Sum_probs=22.3
Q ss_pred CCcccccccccCCC-CeeeeeccccCcee
Q 025742 122 TNTCEICCRSLLDS-FRFCSLGCKLGAMK 149 (248)
Q Consensus 122 ~~~Ce~C~R~L~D~-~rFCSL~CKv~~~~ 149 (248)
...|-+|++..... .-|||-.|++..+.
T Consensus 9 ~~~CP~C~k~~~~~~rPFCS~RC~~iDLg 37 (57)
T PRK01343 9 TRPCPECGKPSTREAYPFCSERCRDIDLN 37 (57)
T ss_pred CCcCCCCCCcCcCCCCcccCHHHhhhhHH
Confidence 45699999987755 58999999976554
No 9
>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=62.03 E-value=2.3 Score=31.51 Aligned_cols=26 Identities=23% Similarity=0.608 Sum_probs=22.2
Q ss_pred CcccccccccCCCCeeeeeccccCce
Q 025742 123 NTCEICCRSLLDSFRFCSLGCKLGAM 148 (248)
Q Consensus 123 ~~Ce~C~R~L~D~~rFCSL~CKv~~~ 148 (248)
..|..||..+...-.|||-.|+=...
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCREEYR 29 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHHHHHH
Confidence 47999999999889999999985443
No 10
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 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. The N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=61.62 E-value=4.1 Score=30.15 Aligned_cols=33 Identities=36% Similarity=0.622 Sum_probs=23.5
Q ss_pred CcceecccCCC---ccCCcch-hc-CCCCCceeEEEec
Q 025742 44 ECNMFCLDCMG---NAFCSYC-LI-NHKDHRVVQIRRS 76 (248)
Q Consensus 44 E~N~FCldC~~---~~~C~~C-l~-~H~~HrvlQIRRs 76 (248)
+-...|++|.. .++|..| .. .|.+|+++.++-.
T Consensus 11 q~~y~C~tC~~~~~~~iC~~CF~~~~H~gH~~~~~~~~ 48 (71)
T PF02207_consen 11 QIFYRCLTCSLDESSGICEECFANSCHEGHRVVYYRSS 48 (71)
T ss_dssp -EEEEETTTBSSTT-BBEHHHHCTSGGGGSSEEEEE--
T ss_pred CEEEECccCCCCCCEEEchhhCCCCCcCCCcEEEEEeC
Confidence 45566999986 4699999 44 7999998877654
No 11
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=61.20 E-value=3.6 Score=24.90 Aligned_cols=16 Identities=31% Similarity=0.870 Sum_probs=14.3
Q ss_pred ccccccccCCCCeeee
Q 025742 125 CEICCRSLLDSFRFCS 140 (248)
Q Consensus 125 Ce~C~R~L~D~~rFCS 140 (248)
|..|+..|.+...||+
T Consensus 2 Cp~CG~~~~~~~~fC~ 17 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCP 17 (23)
T ss_pred CcccCCCCCCcCcchh
Confidence 7889999999999986
No 12
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=54.60 E-value=3.6 Score=30.87 Aligned_cols=29 Identities=31% Similarity=0.660 Sum_probs=22.0
Q ss_pred CCcccccccccC---C-CC-eeeeeccccCceec
Q 025742 122 TNTCEICCRSLL---D-SF-RFCSLGCKLGAMKR 150 (248)
Q Consensus 122 ~~~Ce~C~R~L~---D-~~-rFCSL~CKv~~~~~ 150 (248)
+-.|-+|++.+. + +| -|||-.||+..+.+
T Consensus 6 ~v~CP~C~k~~~w~~~~~~rPFCS~RCk~IDLg~ 39 (62)
T PRK00418 6 TVNCPTCGKPVEWGEISPFRPFCSKRCQLIDLGE 39 (62)
T ss_pred cccCCCCCCcccccCCCCcCCcccHHHHhhhHHH
Confidence 457999999874 2 45 79999999766553
No 13
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.88 E-value=1.1 Score=32.62 Aligned_cols=24 Identities=29% Similarity=0.881 Sum_probs=20.8
Q ss_pred CCCcccccccccC---------CCCeeeeeccc
Q 025742 121 VTNTCEICCRSLL---------DSFRFCSLGCK 144 (248)
Q Consensus 121 ~~~~Ce~C~R~L~---------D~~rFCSL~CK 144 (248)
.+.+|++|+|.+. |..+|||-.|+
T Consensus 11 p~KICpvCqRPFsWRkKW~~cWDeVKyCSeRCr 43 (54)
T COG4338 11 PDKICPVCQRPFSWRKKWARCWDEVKYCSERCR 43 (54)
T ss_pred chhhhhhhcCchHHHHHHHHHHHHHHHHHHHHH
Confidence 3679999999985 57899999999
No 14
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.60 E-value=8.6 Score=23.52 Aligned_cols=19 Identities=21% Similarity=0.539 Sum_probs=15.7
Q ss_pred CCcccccccccCCCCeeee
Q 025742 122 TNTCEICCRSLLDSFRFCS 140 (248)
Q Consensus 122 ~~~Ce~C~R~L~D~~rFCS 140 (248)
...|..|+..+.+..+||+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~ 20 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCP 20 (26)
T ss_pred cCCCcccCCcCCcccccCh
Confidence 3468999998888899996
No 15
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=48.70 E-value=11 Score=25.68 Aligned_cols=27 Identities=30% Similarity=0.697 Sum_probs=20.3
Q ss_pred eecccCCCccCCcchhc--CCCCCceeEE
Q 025742 47 MFCLDCMGNAFCSYCLI--NHKDHRVVQI 73 (248)
Q Consensus 47 ~FCldC~~~~~C~~Cl~--~H~~HrvlQI 73 (248)
.-|+.|..--+|..|.. .|..|+.++|
T Consensus 15 y~C~~C~d~dLC~~C~~~~~H~~H~f~~~ 43 (43)
T cd02340 15 YKCLVCPDYDLCESCEAKGVHPEHAMLKI 43 (43)
T ss_pred EECCCCCCccchHHhhCcCCCCCCCEEeC
Confidence 44888876679999955 5878887754
No 16
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.22 E-value=6.1 Score=30.05 Aligned_cols=28 Identities=29% Similarity=0.586 Sum_probs=21.8
Q ss_pred CcccccccccCC----C-CeeeeeccccCceec
Q 025742 123 NTCEICCRSLLD----S-FRFCSLGCKLGAMKR 150 (248)
Q Consensus 123 ~~Ce~C~R~L~D----~-~rFCSL~CKv~~~~~ 150 (248)
--|-+|++.+.- + +-|||-.||+-.+.+
T Consensus 8 v~CP~Cgkpv~w~~~s~frPFCSkRCklIDLg~ 40 (65)
T COG3024 8 VPCPTCGKPVVWGEESPFRPFCSKRCKLIDLGE 40 (65)
T ss_pred ccCCCCCCcccccccCCcCcchhHhhhhcchhh
Confidence 459999998863 4 579999999766653
No 17
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=46.77 E-value=7.4 Score=39.56 Aligned_cols=35 Identities=29% Similarity=0.705 Sum_probs=27.9
Q ss_pred CCCCccCCCCCCCCcceecccCCCccCCcchhc--CCCCCc
Q 025742 31 FIPCVVHGDSNKSECNMFCLDCMGNAFCSYCLI--NHKDHR 69 (248)
Q Consensus 31 F~~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~--~H~~Hr 69 (248)
-..|..|... ...|||+.|.. ++|..|+. .|..|.
T Consensus 223 ~~~ct~h~~e---~~smyc~~ck~-pvc~~clee~khs~he 259 (699)
T KOG4367|consen 223 VSTCTDHELE---NHSMYCVQCKM-PVCYQCLEEGKHSSHE 259 (699)
T ss_pred hhhccCCCCC---CceEEEEecCC-hHHHHHHHhhcccchh
Confidence 4489999763 36799999987 89999998 577774
No 18
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.15 E-value=11 Score=31.18 Aligned_cols=38 Identities=26% Similarity=0.656 Sum_probs=30.0
Q ss_pred CCccCCCCCCCCcceecccCCCccCCcchh--cCCCCCceeEEEe
Q 025742 33 PCVVHGDSNKSECNMFCLDCMGNAFCSYCL--INHKDHRVVQIRR 75 (248)
Q Consensus 33 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl--~~H~~HrvlQIRR 75 (248)
.|..|... ..+||..|.. .+|..|. ..|.+|.++.+..
T Consensus 88 ~c~~~~~~----~~~~c~~~~~-~~c~~c~~~~~h~~h~~~~~~~ 127 (386)
T KOG2177|consen 88 LCEKHGEE----LKLFCEEDEK-LLCVLCRESGEHRGHPVLPLEE 127 (386)
T ss_pred hhhhcCCc----ceEEeccccc-ccCCCCCCcccccCCccccHHH
Confidence 67777543 6799999987 8999996 3799998877643
No 19
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=41.83 E-value=7.6 Score=31.16 Aligned_cols=50 Identities=20% Similarity=0.350 Sum_probs=30.1
Q ss_pred CCcceecccCCCc-----------cCCcchhcCCCC--CceeEEEeccccceeeechhhhhhcc
Q 025742 43 SECNMFCLDCMGN-----------AFCSYCLINHKD--HRVVQIRRSSYHNVVRVNEIQKFIDI 93 (248)
Q Consensus 43 nE~N~FCldC~~~-----------~~C~~Cl~~H~~--HrvlQIRRssYhdVVRv~DIqkllD~ 93 (248)
..-|..|.||... -+|..|...|+. .++-+| |+.-.|-....||+.+...
T Consensus 10 ~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~V-kSi~~d~w~~~ev~~~~~~ 72 (116)
T PF01412_consen 10 KPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRV-KSITMDNWSPEEVQRMREG 72 (116)
T ss_dssp STTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--E-EETTTS---HHHHHHHHHS
T ss_pred CcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhc-cccccCCCCHHHHHHHHHH
Confidence 4578999999642 289999887863 334444 7788888888888887554
No 20
>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=40.01 E-value=6.4 Score=25.78 Aligned_cols=24 Identities=29% Similarity=0.693 Sum_probs=14.9
Q ss_pred CCCcccccccccCC------------CCeeeeeccc
Q 025742 121 VTNTCEICCRSLLD------------SFRFCSLGCK 144 (248)
Q Consensus 121 ~~~~Ce~C~R~L~D------------~~rFCSL~CK 144 (248)
....|..|++.+.. ...|||..|.
T Consensus 5 ~~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~ 40 (43)
T PF06467_consen 5 KMKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCL 40 (43)
T ss_dssp SCEE-TTT--EEECCC----EE-TTTTSCCSSHHHH
T ss_pred cCCcCcccCCcccCCCccccccccCcccChhCHHHH
Confidence 35689999887732 1489999885
No 21
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=39.75 E-value=33 Score=25.60 Aligned_cols=30 Identities=30% Similarity=0.541 Sum_probs=22.2
Q ss_pred CCCCcceecccCCCc---cCCcchhc--CCCCCce
Q 025742 41 NKSECNMFCLDCMGN---AFCSYCLI--NHKDHRV 70 (248)
Q Consensus 41 ~knE~N~FCldC~~~---~~C~~Cl~--~H~~Hrv 70 (248)
.++|....|++|... .+|..|.. .|.+|++
T Consensus 8 ~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~~ 42 (71)
T smart00396 8 TGGEVIYRCKTCGLDPTCVLCSDCFRSNCHKGHDY 42 (71)
T ss_pred CCCCEEEECcCCCCCCCEeEChHHCCCCCCCCCCE
Confidence 356666779999753 58888855 6999973
No 22
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=30.50 E-value=16 Score=27.03 Aligned_cols=28 Identities=29% Similarity=0.670 Sum_probs=21.5
Q ss_pred CCcccccccccC---CC--C----eeeeeccccCcee
Q 025742 122 TNTCEICCRSLL---DS--F----RFCSLGCKLGAMK 149 (248)
Q Consensus 122 ~~~Ce~C~R~L~---D~--~----rFCSL~CKv~~~~ 149 (248)
-..|..|.|.|. |. | -|||..|.-..|.
T Consensus 16 L~~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~~qi~ 52 (58)
T PF04570_consen 16 LSFCYLCKKKLDPGKDIYMYRGDKAFCSEECRSQQIL 52 (58)
T ss_pred HHHHHccCCCCCCCCCeeeeccccccccHHHHHHHHH
Confidence 368999999998 32 3 4999999866554
No 23
>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=30.31 E-value=13 Score=23.78 Aligned_cols=20 Identities=35% Similarity=0.929 Sum_probs=12.4
Q ss_pred cccccccccCC------CCeeeeeccc
Q 025742 124 TCEICCRSLLD------SFRFCSLGCK 144 (248)
Q Consensus 124 ~Ce~C~R~L~D------~~rFCSL~CK 144 (248)
.|.+|+. ... ..+||||.|.
T Consensus 4 ~C~vC~~-~~kY~Cp~C~~~~CSl~C~ 29 (30)
T PF04438_consen 4 LCSVCGN-PAKYRCPRCGARYCSLACY 29 (30)
T ss_dssp EETSSSS-EESEE-TTT--EESSHHHH
T ss_pred CCccCcC-CCEEECCCcCCceeCcEeE
Confidence 4777776 321 3689999984
No 24
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=29.85 E-value=15 Score=27.72 Aligned_cols=23 Identities=22% Similarity=0.641 Sum_probs=20.7
Q ss_pred CCcccccccccCCCCeeeeeccc
Q 025742 122 TNTCEICCRSLLDSFRFCSLGCK 144 (248)
Q Consensus 122 ~~~Ce~C~R~L~D~~rFCSL~CK 144 (248)
...|.+|+..+...-+|||-.|.
T Consensus 8 H~HC~VCg~aIp~de~~CSe~C~ 30 (64)
T COG4068 8 HRHCVVCGKAIPPDEQVCSEECG 30 (64)
T ss_pred CccccccCCcCCCccchHHHHHH
Confidence 35799999999988999999997
No 25
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=29.11 E-value=37 Score=23.89 Aligned_cols=27 Identities=33% Similarity=0.894 Sum_probs=19.0
Q ss_pred eecccCC--CccCCcchhc---CCC-CCceeEE
Q 025742 47 MFCLDCM--GNAFCSYCLI---NHK-DHRVVQI 73 (248)
Q Consensus 47 ~FCldC~--~~~~C~~Cl~---~H~-~HrvlQI 73 (248)
.-|+.|. .--+|..|.. .|+ +|+++.|
T Consensus 16 ~~C~~C~~~d~DlC~~C~~~~~~H~~~H~~~~i 48 (48)
T cd02341 16 YHCSECDDGDFDLCQDCVVKGESHQEDHWLVKI 48 (48)
T ss_pred EECCCCCCCCCccCHHHHhCcCCCCCCCceeeC
Confidence 4488888 5579999954 353 6777664
No 26
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=26.21 E-value=36 Score=28.26 Aligned_cols=30 Identities=30% Similarity=0.604 Sum_probs=20.9
Q ss_pred cceeeechhhhh---hcccceeeEEECCcEEEEe
Q 025742 79 HNVVRVNEIQKF---IDISCVQTYIINSAKIVFL 109 (248)
Q Consensus 79 hdVVRv~DIqkl---lD~S~IQtYvINsakVVFL 109 (248)
++-|+..|+..+ +-..+|+||+ +|.-|||-
T Consensus 16 ~nki~MaeLr~~l~~~Gf~~V~Tyi-~SGNvvf~ 48 (137)
T PF08002_consen 16 KNKIKMAELREALEDLGFTNVRTYI-QSGNVVFE 48 (137)
T ss_dssp BS---HHHHHHHHHHCT-EEEEEET-TTTEEEEE
T ss_pred CCcccHHHHHHHHHHcCCCCceEEE-eeCCEEEe
Confidence 455777888775 6788999995 88899998
No 27
>PHA03301 envelope glycoprotein L; Provisional
Probab=24.45 E-value=1e+02 Score=28.37 Aligned_cols=12 Identities=42% Similarity=0.443 Sum_probs=9.6
Q ss_pred cccccCCCCCCC
Q 025742 219 ATTKLSPATPPI 230 (248)
Q Consensus 219 ~~~~~~p~tpp~ 230 (248)
..|.+++.||||
T Consensus 188 ~~qp~~~atp~~ 199 (226)
T PHA03301 188 SPQPKSLATPPP 199 (226)
T ss_pred CCCCCCCCCCCC
Confidence 348899998887
No 28
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=24.40 E-value=21 Score=28.49 Aligned_cols=43 Identities=23% Similarity=0.417 Sum_probs=26.9
Q ss_pred cceecccCCCc-----------cCCcchhcCCCCC--ceeEEEeccccceeeechhh
Q 025742 45 CNMFCLDCMGN-----------AFCSYCLINHKDH--RVVQIRRSSYHNVVRVNEIQ 88 (248)
Q Consensus 45 ~N~FCldC~~~-----------~~C~~Cl~~H~~H--rvlQIRRssYhdVVRv~DIq 88 (248)
-|..|.||... -+|..|..-|+.. ++-.| |+.-.|...-.+|+
T Consensus 2 ~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~V-kSl~md~w~~~~i~ 57 (112)
T smart00105 2 GNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKV-RSLTLDTWTEEELR 57 (112)
T ss_pred CCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCee-eecccCCCCHHHHH
Confidence 47889999752 2789998888753 33333 45555555555554
No 29
>PLN00209 ribosomal protein S27; Provisional
Probab=24.37 E-value=85 Score=25.12 Aligned_cols=59 Identities=27% Similarity=0.299 Sum_probs=38.8
Q ss_pred CCCCCceeEEEeccccceeeechhhhhhcccceeeEEECCcEEEEeeCCCCCCCCCCCCCcccccccccCCC-------C
Q 025742 64 NHKDHRVVQIRRSSYHNVVRVNEIQKFIDISCVQTYIINSAKIVFLNERPQPRPGKGVTNTCEICCRSLLDS-------F 136 (248)
Q Consensus 64 ~H~~HrvlQIRRssYhdVVRv~DIqkllD~S~IQtYvINsakVVFLn~RPq~r~~kg~~~~Ce~C~R~L~D~-------~ 136 (248)
.|+..+++|-=+|-+.|| |.-||..||+-.-....+ -.|..|+..|..+ .
T Consensus 20 khK~k~Lv~~PnS~Fm~V-------kCp~C~n~q~VFShA~t~----------------V~C~~Cg~~L~~PTGGKa~l~ 76 (86)
T PLN00209 20 KHKLKRLVQSPNSFFMDV-------KCQGCFNITTVFSHSQTV----------------VVCGSCQTVLCQPTGGKARLT 76 (86)
T ss_pred hhhceeeecCCCCEEEEE-------ECCCCCCeeEEEecCceE----------------EEccccCCEeeccCCCCeEec
Confidence 577788888877777766 567888888744333333 2588888888653 2
Q ss_pred eeeeecccc
Q 025742 137 RFCSLGCKL 145 (248)
Q Consensus 137 rFCSL~CKv 145 (248)
.=||+..|+
T Consensus 77 ~gc~fr~k~ 85 (86)
T PLN00209 77 EGCSFRKKG 85 (86)
T ss_pred CCceEEecC
Confidence 346655553
No 30
>smart00746 TRASH metallochaperone-like domain.
Probab=21.87 E-value=46 Score=18.85 Aligned_cols=10 Identities=50% Similarity=0.999 Sum_probs=7.9
Q ss_pred Ceeeeecccc
Q 025742 136 FRFCSLGCKL 145 (248)
Q Consensus 136 ~rFCSL~CKv 145 (248)
+.|||..|..
T Consensus 24 ~~FCs~~c~~ 33 (39)
T smart00746 24 FYFCSSKCLS 33 (39)
T ss_pred EEEeCHHHHH
Confidence 6889988864
No 31
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=21.74 E-value=1.3e+02 Score=21.90 Aligned_cols=33 Identities=6% Similarity=0.328 Sum_probs=22.8
Q ss_pred ceeeechhhhh--hcccceeeEEECCcEEEEeeCCC
Q 025742 80 NVVRVNEIQKF--IDISCVQTYIINSAKIVFLNERP 113 (248)
Q Consensus 80 dVVRv~DIqkl--lD~S~IQtYvINsakVVFLn~RP 113 (248)
.+++++|+... +++.+|-|.+|||..+ +....|
T Consensus 32 ~~~~v~~~~~a~~~~v~~vPti~i~G~~~-~~G~~~ 66 (76)
T TIGR00412 32 EFEKVTDMNEILEAGVTATPGVAVDGELV-IMGKIP 66 (76)
T ss_pred EEEEeCCHHHHHHcCCCcCCEEEECCEEE-EEeccC
Confidence 35666655554 8999999999987655 554433
No 32
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=21.61 E-value=61 Score=30.19 Aligned_cols=29 Identities=21% Similarity=0.588 Sum_probs=23.1
Q ss_pred eecccCCCccCCcchhc---CCCCCceeEEEe
Q 025742 47 MFCLDCMGNAFCSYCLI---NHKDHRVVQIRR 75 (248)
Q Consensus 47 ~FCldC~~~~~C~~Cl~---~H~~HrvlQIRR 75 (248)
+-|+.|...-||..|-. .|..|..|||.+
T Consensus 168 yKC~~C~dYDLCe~Ce~~~~~h~~H~~lR~~t 199 (278)
T KOG4582|consen 168 YKCTVCPDYDLCERCEAGNEHHAAHAMLRLHT 199 (278)
T ss_pred eeecCCCccchhHHhhcCCCCCcccceeeccc
Confidence 44999988779999943 566899999877
No 33
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=21.59 E-value=76 Score=31.43 Aligned_cols=44 Identities=20% Similarity=0.329 Sum_probs=31.7
Q ss_pred cceecccCCCc-----------cCCcchhcCCCC-CceeEEEeccccceeeechhh
Q 025742 45 CNMFCLDCMGN-----------AFCSYCLINHKD-HRVVQIRRSSYHNVVRVNEIQ 88 (248)
Q Consensus 45 ~N~FCldC~~~-----------~~C~~Cl~~H~~-HrvlQIRRssYhdVVRv~DIq 88 (248)
-|-+|++|... -+|..|.--|++ .-+|=..|++=.|--+-.||.
T Consensus 18 eNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~ 73 (386)
T KOG0704|consen 18 ENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELK 73 (386)
T ss_pred cCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHH
Confidence 68899999752 189999888986 345666788777766555553
No 34
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=20.99 E-value=60 Score=28.48 Aligned_cols=28 Identities=18% Similarity=0.476 Sum_probs=18.4
Q ss_pred CCCCcccccccccC-----CCCeeeeeccccCc
Q 025742 120 GVTNTCEICCRSLL-----DSFRFCSLGCKLGA 147 (248)
Q Consensus 120 g~~~~Ce~C~R~L~-----D~~rFCSL~CKv~~ 147 (248)
..-..|.+||-.-. -..+|||++|-..|
T Consensus 116 P~r~fCaVCG~~S~ysC~~CG~kyCsv~C~~~H 148 (156)
T KOG3362|consen 116 PLRKFCAVCGYDSKYSCVNCGTKYCSVRCLKTH 148 (156)
T ss_pred CcchhhhhcCCCchhHHHhcCCceeechhhhhc
Confidence 34567888882111 14799999997544
No 35
>PRK05707 DNA polymerase III subunit delta'; Validated
Probab=20.11 E-value=77 Score=29.91 Aligned_cols=94 Identities=11% Similarity=0.244 Sum_probs=49.1
Q ss_pred CCCCccHHHHhcccCCCCCccCCC---CCCC----------CcceecccCCCc---cCCcchhc-CCCCCc-eeEEEecc
Q 025742 16 DMGPQWLKPMLRASYFIPCVVHGD---SNKS----------ECNMFCLDCMGN---AFCSYCLI-NHKDHR-VVQIRRSS 77 (248)
Q Consensus 16 ~~~P~WL~~LL~t~FF~~C~~H~~---~~kn----------E~N~FCldC~~~---~~C~~Cl~-~H~~Hr-vlQIRRss 77 (248)
|..-|||+..++.-+-..--.|.- +..+ -+-++|.+=... .-|+.|.. ....|+ ++.|..-.
T Consensus 2 ~~~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~ 81 (328)
T PRK05707 2 AEIYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEE 81 (328)
T ss_pred CcCCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccC
Confidence 345699999887655444334422 1111 024556421111 24777744 333443 44443321
Q ss_pred ccceeeechhhhhhcccceeeEEECCcEEEEee
Q 025742 78 YHNVVRVNEIQKFIDISCVQTYIINSAKIVFLN 110 (248)
Q Consensus 78 YhdVVRv~DIqkllD~S~IQtYvINsakVVFLn 110 (248)
=...|+|++|..+++--..=++ .++.|||.|.
T Consensus 82 ~~~~i~id~iR~l~~~~~~~~~-~~~~kv~iI~ 113 (328)
T PRK05707 82 ADKTIKVDQVRELVSFVVQTAQ-LGGRKVVLIE 113 (328)
T ss_pred CCCCCCHHHHHHHHHHHhhccc-cCCCeEEEEC
Confidence 1246899999988654443232 3577888884
Done!