Query psy7214
Match_columns 201
No_of_seqs 117 out of 203
Neff 2.5
Searched_HMMs 46136
Date Fri Aug 16 21:03:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7214.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7214hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01215 COX5B: Cytochrome c o 100.0 1.2E-33 2.6E-38 227.0 6.3 74 1-74 61-136 (136)
2 PLN02294 cytochrome c oxidase 100.0 6.1E-33 1.3E-37 231.4 8.4 76 1-76 89-167 (174)
3 cd00924 Cyt_c_Oxidase_Vb Cytoc 100.0 3.8E-32 8.2E-37 207.5 8.0 68 1-68 29-97 (97)
4 KOG3352|consensus 100.0 5.3E-31 1.2E-35 216.2 7.3 69 1-69 83-152 (153)
5 PTZ00043 cytochrome c oxidase 99.9 3.4E-26 7.4E-31 199.9 7.8 75 3-77 131-212 (268)
6 PF10276 zf-CHCC: Zinc-finger 96.0 0.011 2.4E-07 39.6 3.6 36 26-61 1-40 (40)
7 KOG3456|consensus 94.5 0.031 6.7E-07 45.5 2.6 40 22-61 73-115 (120)
8 COG4391 Uncharacterized protei 80.9 2.6 5.6E-05 31.2 3.7 44 18-63 15-61 (62)
9 PF04216 FdhE: Protein involve 54.1 11 0.00024 32.8 2.6 34 35-69 218-256 (290)
10 COG5189 SFP1 Putative transcri 53.6 5.6 0.00012 38.0 0.7 16 46-61 393-409 (423)
11 COG4647 AcxC Acetone carboxyla 51.5 6.3 0.00014 33.6 0.6 12 49-60 68-79 (165)
12 PF09845 DUF2072: Zn-ribbon co 45.2 8 0.00017 32.0 0.3 11 51-61 1-12 (131)
13 PF09723 Zn-ribbon_8: Zinc rib 44.8 30 0.00065 22.5 2.9 16 52-67 6-22 (42)
14 KOG3507|consensus 43.9 9.7 0.00021 28.3 0.5 15 45-59 31-46 (62)
15 smart00834 CxxC_CXXC_SSSS Puta 43.7 31 0.00067 21.2 2.7 11 53-63 7-18 (41)
16 PF13912 zf-C2H2_6: C2H2-type 42.7 15 0.00033 20.8 1.2 11 51-61 1-12 (27)
17 COG3357 Predicted transcriptio 40.9 12 0.00025 29.9 0.6 19 50-68 57-76 (97)
18 PF08882 Acetone_carb_G: Aceto 38.6 28 0.00061 28.3 2.5 19 42-60 15-33 (112)
19 COG3364 Zn-ribbon containing p 38.3 12 0.00027 30.4 0.4 11 51-61 2-13 (112)
20 PF03604 DNA_RNApol_7kD: DNA d 36.0 17 0.00036 23.3 0.7 16 46-61 12-28 (32)
21 PF13719 zinc_ribbon_5: zinc-r 34.4 28 0.0006 22.3 1.5 14 48-61 22-36 (37)
22 TIGR02605 CxxC_CxxC_SSSS putat 32.9 37 0.0008 22.2 2.0 13 52-64 6-19 (52)
23 PF13465 zf-H2C2_2: Zinc-finge 32.3 29 0.00062 20.4 1.2 13 49-61 12-25 (26)
24 smart00659 RPOLCX RNA polymera 31.6 29 0.00062 23.4 1.3 16 46-61 14-30 (44)
25 PF09526 DUF2387: Probable met 31.6 66 0.0014 23.7 3.3 37 29-65 6-45 (71)
26 PF06397 Desulfoferrod_N: Desu 30.8 41 0.00089 22.3 1.9 21 48-68 3-24 (36)
27 PF12172 DUF35_N: Rubredoxin-l 29.5 29 0.00062 21.7 1.0 10 51-60 11-21 (37)
28 COG1326 Uncharacterized archae 28.0 33 0.00072 30.4 1.4 50 35-87 15-72 (201)
29 PF10571 UPF0547: Uncharacteri 27.5 20 0.00044 21.9 -0.0 11 51-61 14-25 (26)
30 PRK03564 formate dehydrogenase 24.5 77 0.0017 29.2 3.1 31 37-67 234-269 (309)
31 PHA00616 hypothetical protein 24.0 18 0.00038 24.9 -0.8 11 51-61 1-12 (44)
32 COG1545 Predicted nucleic-acid 23.4 38 0.00083 27.2 0.9 16 46-61 22-40 (140)
33 cd06404 PB1_aPKC PB1 domain is 21.6 77 0.0017 24.5 2.2 23 55-77 36-58 (83)
34 PF04405 ScdA_N: Domain of Unk 21.5 28 0.0006 24.4 -0.2 18 158-175 16-33 (56)
35 COG2007 RPS8A Ribosomal protei 20.3 1.2E+02 0.0025 25.3 3.1 40 148-187 24-68 (127)
36 PF00096 zf-C2H2: Zinc finger, 20.1 59 0.0013 17.6 1.0 9 53-61 2-11 (23)
No 1
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=100.00 E-value=1.2e-33 Score=227.05 Aligned_cols=74 Identities=41% Similarity=0.862 Sum_probs=50.6
Q ss_pred CCCCCCCCCCCCCCCCCCeeeecCCCceeEeeeC-CCCCcceEEEEEecCCceee-cCCcEEEEEEecCCCCcccc
Q psy7214 1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVC-EEDQYHIVWMWVEADMPRRC-ACGHWFKLKLICRGGVHVAI 74 (201)
Q Consensus 1 DPFDMkPLks~~GTKEDPiLVPS~~deRIVGCtG-peDSH~VvWf~L~KGkP~RC-ECGqwFKLv~vG~~g~~~~~ 74 (201)
|||||+|+++++||+||||||||++++|||||+| ++|+|+|+||||++|+|+|| +||+||||+++|+++++|.|
T Consensus 61 D~Fd~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~~~sH~v~W~~l~~g~~~RCpeCG~~fkL~~vg~~~~~h~h 136 (136)
T PF01215_consen 61 DPFDMKPLKAPFGTKEDPILVPSYFDERIVGCTGEPDDSHDVIWFWLHKGKPQRCPECGQVFKLKYVGPEGDHHHH 136 (136)
T ss_dssp -TT--S--B----SSSS-CEEEESSSCEEEEESSSTT-SSS-EEEEEETTSEEEETTTEEEEEEEE----------
T ss_pred CcccccCccCCCCCccCCeEccCCCCceEEeeccCCCCcceeEEEEEeCCCccCCCCCCeEEEEEEcCCCCCCCCC
Confidence 8999999988899999999999999999999999 66888999999999999999 89999999999999988864
No 2
>PLN02294 cytochrome c oxidase subunit Vb
Probab=99.98 E-value=6.1e-33 Score=231.35 Aligned_cols=76 Identities=29% Similarity=0.630 Sum_probs=74.0
Q ss_pred CCCCCCCCCCCCCCCCCCeeeecCCCceeEeeeC--CCCCcceEEEEEecCCceee-cCCcEEEEEEecCCCCccccCC
Q psy7214 1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVC--EEDQYHIVWMWVEADMPRRC-ACGHWFKLKLICRGGVHVAIGS 76 (201)
Q Consensus 1 DPFDMkPLks~~GTKEDPiLVPS~~deRIVGCtG--peDSH~VvWf~L~KGkP~RC-ECGqwFKLv~vG~~g~~~~~gs 76 (201)
|||||+++++++||+||||||||++++|||||+| ++|+|+|+||||++|+|+|| |||+||||+++|++++|+.||-
T Consensus 89 D~Fd~~~~~gp~GTke~P~lVpS~~d~RiVGCtg~~~eDsh~v~Wf~L~kGkp~RCpeCG~~fkL~~vG~~~~~~~h~d 167 (174)
T PLN02294 89 KLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVGPGGPPDGHGD 167 (174)
T ss_pred CccccccccCCCCCccCCcEeccCCCceEEeeCCCCCCCCceeEEEEecCCCceeCCCCCCEEEEEEeCCCCCCCCCCC
Confidence 8999999999999999999999999999999999 89999999999999999999 8999999999999999999875
No 3
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=99.97 E-value=3.8e-32 Score=207.46 Aligned_cols=68 Identities=49% Similarity=1.023 Sum_probs=65.0
Q ss_pred CCCCCCCCCCCCCCCCCCeeeecCCCceeEeeeCCCCCcceEEEEEecCCceee-cCCcEEEEEEecCC
Q psy7214 1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHWFKLKLICRG 68 (201)
Q Consensus 1 DPFDMkPLks~~GTKEDPiLVPS~~deRIVGCtGpeDSH~VvWf~L~KGkP~RC-ECGqwFKLv~vG~~ 68 (201)
|+|||+|+.+++||++|||||||++++|||||+|++|+|+|+||||++|+|+|| +||+||||++++++
T Consensus 29 d~f~~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~~~h~v~W~~l~~g~~~rC~eCG~~fkL~~v~~~ 97 (97)
T cd00924 29 DDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCICEPDSHDVIWMWLEKGKPKRCPECGHVFKLVDVGPP 97 (97)
T ss_pred ccccccccccCCCCccCCeEecCCCCCeEEeeeCCCCCceEEEEEEeCCCceeCCCCCcEEEEEECCCC
Confidence 789999999888999999999999999999999988899999999999999999 69999999999864
No 4
>KOG3352|consensus
Probab=99.97 E-value=5.3e-31 Score=216.25 Aligned_cols=69 Identities=46% Similarity=0.939 Sum_probs=66.7
Q ss_pred CCCCCCCCCCCCCCCCCCeeeecCCCceeEeeeCCCCCcceEEEEEecCCceee-cCCcEEEEEEecCCC
Q psy7214 1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHWFKLKLICRGG 69 (201)
Q Consensus 1 DPFDMkPLks~~GTKEDPiLVPS~~deRIVGCtGpeDSH~VvWf~L~KGkP~RC-ECGqwFKLv~vG~~g 69 (201)
|||||+.+++++||++|||||||++|+|||||.|++|+|+|+||||+||+++|| ||||||||+.+|+++
T Consensus 83 d~~d~k~~~~~~GTkedP~lV~S~~d~RiVGC~c~eD~~~V~Wmwl~Kge~~rc~eCG~~fkL~~v~~~~ 152 (153)
T KOG3352|consen 83 DPFDMKVPRGPSGTKEDPNLVPSYYDKRIVGCGCEEDSHAVVWMWLEKGETQRCPECGHYFKLVPVGPVN 152 (153)
T ss_pred CccccccccCCCCcccCCccccccCCceEEeecccCCCcceEEEEEEcCCcccCCcccceEEeeecCCCC
Confidence 799999669999999999999999999999999999999999999999999998 999999999999876
No 5
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=99.93 E-value=3.4e-26 Score=199.91 Aligned_cols=75 Identities=25% Similarity=0.422 Sum_probs=69.8
Q ss_pred CCCCCCCCCCCCCCCCeeeecCCCceeEeeeC--CCCCcceEEEEEecCCceee-cCCcEEEEEE----ecCCCCccccC
Q psy7214 3 YYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVC--EEDQYHIVWMWVEADMPRRC-ACGHWFKLKL----ICRGGVHVAIG 75 (201)
Q Consensus 3 FDMkPLks~~GTKEDPiLVPS~~deRIVGCtG--peDSH~VvWf~L~KGkP~RC-ECGqwFKLv~----vG~~g~~~~~g 75 (201)
+.++++.+++||+|||+||||++++|||||+| ++|+|+|+|||+++|+++|| +||+||||++ ++++++|++.-
T Consensus 131 Lk~~~~~GPfGTkEdPiLVpSy~deRyVGCTGg~~EDeH~VvWFwLrEGkpqRCpECGqVFKLVr~~~s~~dg~dp~~~d 210 (268)
T PTZ00043 131 LKSSSFVGPFGTIENPVLVPSVGTERVVGCTGGTGEHEHVPLWFRCREGFLYRCGECDQIFMLVRVLYSLPDGEDPFPND 210 (268)
T ss_pred cCcCCCCCCCCCccCCeEeccCCCceEEeccCCCccCCceeEEEEecCCCCccCCCCCcEEEEEEEEeecCCCCCCCCCC
Confidence 45678899999999999999999999999999 78899999999999999999 9999999999 99999999876
Q ss_pred Cc
Q psy7214 76 SN 77 (201)
Q Consensus 76 s~ 77 (201)
-.
T Consensus 211 pd 212 (268)
T PTZ00043 211 PD 212 (268)
T ss_pred Cc
Confidence 43
No 6
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=95.96 E-value=0.011 Score=39.63 Aligned_cols=36 Identities=22% Similarity=0.386 Sum_probs=29.7
Q ss_pred CceeEeeeC--CCCCcceEEEEEec-CCceee-cCCcEEE
Q psy7214 26 KSRLVGCVC--EEDQYHIVWMWVEA-DMPRRC-ACGHWFK 61 (201)
Q Consensus 26 deRIVGCtG--peDSH~VvWf~L~K-GkP~RC-ECGqwFK 61 (201)
+.|+|-|.| .+-.|-.+|+.|.+ +++..| .||.-|+
T Consensus 1 ~~~~v~CdG~~~~lgHPrVyl~l~~~~~~~~CpYCg~~yv 40 (40)
T PF10276_consen 1 DGRRVSCDGGGGALGHPRVYLNLDDEPGPVVCPYCGTRYV 40 (40)
T ss_dssp -SSEEEEEESSTTSCCCCEEEE-TTTTCEEEETTTTEEEE
T ss_pred CCcEEEeCCCCCCCCCCeEEEecCCCCCeEECCCCCCEEC
Confidence 468999999 46889999999999 478999 7999885
No 7
>KOG3456|consensus
Probab=94.45 E-value=0.031 Score=45.48 Aligned_cols=40 Identities=23% Similarity=0.382 Sum_probs=35.8
Q ss_pred ecCCCceeEeeeC--CCCCcceEEEEEecCCceee-cCCcEEE
Q psy7214 22 RSAFKSRLVGCVC--EEDQYHIVWMWVEADMPRRC-ACGHWFK 61 (201)
Q Consensus 22 PS~~deRIVGCtG--peDSH~VvWf~L~KGkP~RC-ECGqwFK 61 (201)
|+--+.|+|.|-| ++=-|-.+|+.|.+..++-| .||--|.
T Consensus 73 p~e~d~RVV~CdGg~~aLGHPkvyInLDk~~~~~CgYCGlrf~ 115 (120)
T KOG3456|consen 73 PIEVDGRVVACDGGTPALGHPKVYINLDKPGPHICGYCGLRFV 115 (120)
T ss_pred hhhccceEEEecCCCCCCCCCeEEEEcCCCCCcccccchhhhh
Confidence 4556999999999 78899999999999999999 8998775
No 8
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.89 E-value=2.6 Score=31.18 Aligned_cols=44 Identities=11% Similarity=0.197 Sum_probs=32.9
Q ss_pred CeeeecCCCceeEeeeC--CCCCcceEEEEEecCCceee-cCCcEEEEE
Q psy7214 18 PNLVRSAFKSRLVGCVC--EEDQYHIVWMWVEADMPRRC-ACGHWFKLK 63 (201)
Q Consensus 18 PiLVPS~~deRIVGCtG--peDSH~VvWf~L~KGkP~RC-ECGqwFKLv 63 (201)
++.|.+.. --+-|.| ++-+|-=+|+-+.+..-.-| .||..|+|.
T Consensus 15 ~~~I~~~~--~~l~C~g~~~p~~HPrV~L~mg~~gev~CPYC~t~y~l~ 61 (62)
T COG4391 15 HETIEIGD--LPLMCPGPEPPNDHPRVFLDMGDEGEVVCPYCSTRYRLN 61 (62)
T ss_pred ceEEEeCC--eeEEcCCCCCCCCCCEEEEEcCCCCcEecCccccEEEec
Confidence 44454432 2367999 57899999999966567899 699999985
No 9
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=54.09 E-value=11 Score=32.77 Aligned_cols=34 Identities=12% Similarity=0.206 Sum_probs=16.9
Q ss_pred CCCCcceEEEEEecCC----ceee-cCCcEEEEEEecCCC
Q psy7214 35 EEDQYHIVWMWVEADM----PRRC-ACGHWFKLKLICRGG 69 (201)
Q Consensus 35 peDSH~VvWf~L~KGk----P~RC-ECGqwFKLv~vG~~g 69 (201)
+.+.+.-.|+.-.+++ ..-| .|++|+|..+ .+.+
T Consensus 218 g~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd-~~~~ 256 (290)
T PF04216_consen 218 GNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVD-REKD 256 (290)
T ss_dssp ---SS-EEE--------SEEEEEETTTTEEEEEEE-TTT-
T ss_pred CCCCCcceeeEecCCCCcEEEEECCcccchHHHHh-hhhC
Confidence 5566666666423333 3779 6999999999 4433
No 10
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=53.64 E-value=5.6 Score=38.00 Aligned_cols=16 Identities=38% Similarity=0.891 Sum_probs=14.3
Q ss_pred EecCCceeec-CCcEEE
Q psy7214 46 VEADMPRRCA-CGHWFK 61 (201)
Q Consensus 46 L~KGkP~RCE-CGqwFK 61 (201)
.-+++|.||| |+.-||
T Consensus 393 ~~~~KPYrCevC~KRYK 409 (423)
T COG5189 393 SAKDKPYRCEVCDKRYK 409 (423)
T ss_pred cccCCceeccccchhhc
Confidence 6688999996 999998
No 11
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=51.53 E-value=6.3 Score=33.57 Aligned_cols=12 Identities=50% Similarity=1.071 Sum_probs=10.2
Q ss_pred CCceeecCCcEE
Q psy7214 49 DMPRRCACGHWF 60 (201)
Q Consensus 49 GkP~RCECGqwF 60 (201)
++..||+||+.|
T Consensus 68 ~rv~rcecghsf 79 (165)
T COG4647 68 KRVIRCECGHSF 79 (165)
T ss_pred ccEEEEeccccc
Confidence 457999999987
No 12
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=45.23 E-value=8 Score=31.99 Aligned_cols=11 Identities=45% Similarity=1.365 Sum_probs=9.5
Q ss_pred ceee-cCCcEEE
Q psy7214 51 PRRC-ACGHWFK 61 (201)
Q Consensus 51 P~RC-ECGqwFK 61 (201)
|+|| .||..|.
T Consensus 1 PH~Ct~Cg~~f~ 12 (131)
T PF09845_consen 1 PHQCTKCGRVFE 12 (131)
T ss_pred CcccCcCCCCcC
Confidence 7899 8999985
No 13
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=44.84 E-value=30 Score=22.55 Aligned_cols=16 Identities=38% Similarity=0.779 Sum_probs=10.6
Q ss_pred eee-cCCcEEEEEEecC
Q psy7214 52 RRC-ACGHWFKLKLICR 67 (201)
Q Consensus 52 ~RC-ECGqwFKLv~vG~ 67 (201)
.|| +||+.|....-..
T Consensus 6 y~C~~Cg~~fe~~~~~~ 22 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSIS 22 (42)
T ss_pred EEeCCCCCEEEEEEEcC
Confidence 578 6888887655433
No 14
>KOG3507|consensus
Probab=43.91 E-value=9.7 Score=28.28 Aligned_cols=15 Identities=27% Similarity=0.497 Sum_probs=12.8
Q ss_pred EEecCCceee-cCCcE
Q psy7214 45 WVEADMPRRC-ACGHW 59 (201)
Q Consensus 45 ~L~KGkP~RC-ECGqw 59 (201)
.|..+.+-|| |||+-
T Consensus 31 ~lk~~D~irCReCG~R 46 (62)
T KOG3507|consen 31 TLKRGDVIRCRECGYR 46 (62)
T ss_pred cccCCCcEehhhcchH
Confidence 3788999999 99973
No 15
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=43.65 E-value=31 Score=21.20 Aligned_cols=11 Identities=55% Similarity=1.343 Sum_probs=5.9
Q ss_pred ee-cCCcEEEEE
Q psy7214 53 RC-ACGHWFKLK 63 (201)
Q Consensus 53 RC-ECGqwFKLv 63 (201)
+| +||+.|.+.
T Consensus 7 ~C~~Cg~~fe~~ 18 (41)
T smart00834 7 RCEDCGHTFEVL 18 (41)
T ss_pred EcCCCCCEEEEE
Confidence 55 555555544
No 16
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=42.69 E-value=15 Score=20.83 Aligned_cols=11 Identities=45% Similarity=1.168 Sum_probs=8.6
Q ss_pred ceee-cCCcEEE
Q psy7214 51 PRRC-ACGHWFK 61 (201)
Q Consensus 51 P~RC-ECGqwFK 61 (201)
|.+| .|+..|.
T Consensus 1 ~~~C~~C~~~F~ 12 (27)
T PF13912_consen 1 PFECDECGKTFS 12 (27)
T ss_dssp SEEETTTTEEES
T ss_pred CCCCCccCCccC
Confidence 5689 7999884
No 17
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=40.88 E-value=12 Score=29.93 Aligned_cols=19 Identities=37% Similarity=0.723 Sum_probs=13.9
Q ss_pred Cceee-cCCcEEEEEEecCC
Q psy7214 50 MPRRC-ACGHWFKLKLICRG 68 (201)
Q Consensus 50 kP~RC-ECGqwFKLv~vG~~ 68 (201)
+|.|| .||..|.=..+-.+
T Consensus 57 ~Pa~CkkCGfef~~~~ik~p 76 (97)
T COG3357 57 RPARCKKCGFEFRDDKIKKP 76 (97)
T ss_pred cChhhcccCccccccccCCc
Confidence 58999 79999976555433
No 18
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=38.59 E-value=28 Score=28.31 Aligned_cols=19 Identities=37% Similarity=0.971 Sum_probs=14.4
Q ss_pred EEEEEecCCceeecCCcEE
Q psy7214 42 VWMWVEADMPRRCACGHWF 60 (201)
Q Consensus 42 vWf~L~KGkP~RCECGqwF 60 (201)
.|..-.+++.-+|+|||.|
T Consensus 15 l~i~~~~~k~vkc~CGh~f 33 (112)
T PF08882_consen 15 LWIVQKKDKVVKCDCGHEF 33 (112)
T ss_pred EEEEEecCceeeccCCCee
Confidence 4555555678999999987
No 19
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=38.34 E-value=12 Score=30.43 Aligned_cols=11 Identities=45% Similarity=1.331 Sum_probs=9.5
Q ss_pred ceee-cCCcEEE
Q psy7214 51 PRRC-ACGHWFK 61 (201)
Q Consensus 51 P~RC-ECGqwFK 61 (201)
|+|| -||++|-
T Consensus 2 pH~CtrCG~vf~ 13 (112)
T COG3364 2 PHQCTRCGEVFD 13 (112)
T ss_pred Cceecccccccc
Confidence 7999 8999984
No 20
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=36.03 E-value=17 Score=23.31 Aligned_cols=16 Identities=38% Similarity=0.900 Sum_probs=11.7
Q ss_pred EecCCceee-cCCcEEE
Q psy7214 46 VEADMPRRC-ACGHWFK 61 (201)
Q Consensus 46 L~KGkP~RC-ECGqwFK 61 (201)
+..+.+-|| +||+.-.
T Consensus 12 ~~~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 12 LKPGDPIRCPECGHRIL 28 (32)
T ss_dssp BSTSSTSSBSSSS-SEE
T ss_pred cCCCCcEECCcCCCeEE
Confidence 667888999 8998543
No 21
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=34.40 E-value=28 Score=22.27 Aligned_cols=14 Identities=43% Similarity=1.030 Sum_probs=11.4
Q ss_pred cCCceee-cCCcEEE
Q psy7214 48 ADMPRRC-ACGHWFK 61 (201)
Q Consensus 48 KGkP~RC-ECGqwFK 61 (201)
.|...|| .|++.|.
T Consensus 22 ~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 22 GGRKVRCPKCGHVFR 36 (37)
T ss_pred CCcEEECCCCCcEee
Confidence 4667999 7999985
No 22
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=32.86 E-value=37 Score=22.18 Aligned_cols=13 Identities=54% Similarity=1.168 Sum_probs=10.8
Q ss_pred eee-cCCcEEEEEE
Q psy7214 52 RRC-ACGHWFKLKL 64 (201)
Q Consensus 52 ~RC-ECGqwFKLv~ 64 (201)
.+| +||+.|.+..
T Consensus 6 y~C~~Cg~~fe~~~ 19 (52)
T TIGR02605 6 YRCTACGHRFEVLQ 19 (52)
T ss_pred EEeCCCCCEeEEEE
Confidence 589 7999998764
No 23
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=32.33 E-value=29 Score=20.39 Aligned_cols=13 Identities=38% Similarity=1.065 Sum_probs=10.5
Q ss_pred CCceee-cCCcEEE
Q psy7214 49 DMPRRC-ACGHWFK 61 (201)
Q Consensus 49 GkP~RC-ECGqwFK 61 (201)
.+|..| .|+..|.
T Consensus 12 ~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 12 EKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSEEESSSSEEES
T ss_pred CCCCCCCCCcCeeC
Confidence 358999 7999884
No 24
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=31.59 E-value=29 Score=23.39 Aligned_cols=16 Identities=25% Similarity=0.594 Sum_probs=11.9
Q ss_pred EecCCceee-cCCcEEE
Q psy7214 46 VEADMPRRC-ACGHWFK 61 (201)
Q Consensus 46 L~KGkP~RC-ECGqwFK 61 (201)
+..+.+-|| +||+--.
T Consensus 14 ~~~~~~irC~~CG~rIl 30 (44)
T smart00659 14 IKSKDVVRCRECGYRIL 30 (44)
T ss_pred cCCCCceECCCCCceEE
Confidence 446788999 8998443
No 25
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=31.57 E-value=66 Score=23.74 Aligned_cols=37 Identities=24% Similarity=0.536 Sum_probs=24.0
Q ss_pred eEeeeCCC-CCcceEEEEEecCC-ceee-cCCcEEEEEEe
Q psy7214 29 LVGCVCEE-DQYHIVWMWVEADM-PRRC-ACGHWFKLKLI 65 (201)
Q Consensus 29 IVGCtGpe-DSH~VvWf~L~KGk-P~RC-ECGqwFKLv~v 65 (201)
|.|=+||. .+-+.+=||-+.+. -..| +||+...+...
T Consensus 6 IAGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 6 IAGAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred ecCccCCCCcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 66778863 33344444555554 5899 99998776544
No 26
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=30.77 E-value=41 Score=22.27 Aligned_cols=21 Identities=19% Similarity=0.355 Sum_probs=12.0
Q ss_pred cCCceee-cCCcEEEEEEecCC
Q psy7214 48 ADMPRRC-ACGHWFKLKLICRG 68 (201)
Q Consensus 48 KGkP~RC-ECGqwFKLv~vG~~ 68 (201)
+++..+| .||+...+...|.+
T Consensus 3 ~~~~YkC~~CGniVev~~~g~g 24 (36)
T PF06397_consen 3 KGEFYKCEHCGNIVEVVHDGGG 24 (36)
T ss_dssp TTEEEE-TTT--EEEEEE--SS
T ss_pred cccEEEccCCCCEEEEEECCCC
Confidence 4567899 69999988876643
No 27
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=29.53 E-value=29 Score=21.66 Aligned_cols=10 Identities=40% Similarity=0.976 Sum_probs=5.4
Q ss_pred ceee-cCCcEE
Q psy7214 51 PRRC-ACGHWF 60 (201)
Q Consensus 51 P~RC-ECGqwF 60 (201)
.+|| .||.++
T Consensus 11 ~~rC~~Cg~~~ 21 (37)
T PF12172_consen 11 GQRCRDCGRVQ 21 (37)
T ss_dssp EEE-TTT--EE
T ss_pred EEEcCCCCCEe
Confidence 4899 899985
No 28
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=28.04 E-value=33 Score=30.36 Aligned_cols=50 Identities=20% Similarity=0.200 Sum_probs=27.5
Q ss_pred CCCCcceEEEEEecCC--ceee-cCCcEEE--EEEecCCCCc---cccCCchhhhHhhhcc
Q psy7214 35 EEDQYHIVWMWVEADM--PRRC-ACGHWFK--LKLICRGGVH---VAIGSNWSKWILSSVG 87 (201)
Q Consensus 35 peDSH~VvWf~L~KGk--P~RC-ECGqwFK--Lv~vG~~g~~---~~~gs~~~~~~~~~~~ 87 (201)
++-+|.++=. +|. .-|| +||+++. ++...+-... -.++-|+.+|+-.--|
T Consensus 15 eev~hEVik~---~g~~~lvrC~eCG~V~~~~i~~~k~~~v~viVS~~~~S~~~~vel~~g 72 (201)
T COG1326 15 EEVSHEVIKE---RGREPLVRCEECGTVHPAIIKTPKPVRVRVIVSRHEESFTKEVELDPG 72 (201)
T ss_pred chhhHHHHHh---cCCceEEEccCCCcEeeceeeccccceEEEEEecCCcccceeEecCCC
Confidence 3444565322 344 5999 8999993 3332222211 1356788888754433
No 29
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=27.51 E-value=20 Score=21.91 Aligned_cols=11 Identities=36% Similarity=0.890 Sum_probs=8.8
Q ss_pred ceee-cCCcEEE
Q psy7214 51 PRRC-ACGHWFK 61 (201)
Q Consensus 51 P~RC-ECGqwFK 61 (201)
..+| .||+.|.
T Consensus 14 ~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 14 AKFCPHCGYDFE 25 (26)
T ss_pred cCcCCCCCCCCc
Confidence 4789 5999885
No 30
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=24.51 E-value=77 Score=29.18 Aligned_cols=31 Identities=13% Similarity=0.462 Sum_probs=22.3
Q ss_pred CCcceEEEEEecCC----ceee-cCCcEEEEEEecC
Q psy7214 37 DQYHIVWMWVEADM----PRRC-ACGHWFKLKLICR 67 (201)
Q Consensus 37 DSH~VvWf~L~KGk----P~RC-ECGqwFKLv~vG~ 67 (201)
++..+.++.+..+. ..-| .|+.|.|..+...
T Consensus 234 ~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~~~~ 269 (309)
T PRK03564 234 QSGKLHYWSLDSEQAAVKAESCGDCGTYLKILYQEK 269 (309)
T ss_pred CCCceeeeeecCCCcceEeeecccccccceeccccc
Confidence 34567777776652 4779 6999999987654
No 31
>PHA00616 hypothetical protein
Probab=24.01 E-value=18 Score=24.93 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=7.6
Q ss_pred ceee-cCCcEEE
Q psy7214 51 PRRC-ACGHWFK 61 (201)
Q Consensus 51 P~RC-ECGqwFK 61 (201)
|.+| +||..|.
T Consensus 1 pYqC~~CG~~F~ 12 (44)
T PHA00616 1 MYQCLRCGGIFR 12 (44)
T ss_pred CCccchhhHHHh
Confidence 4578 7887764
No 32
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=23.44 E-value=38 Score=27.19 Aligned_cols=16 Identities=19% Similarity=0.644 Sum_probs=12.3
Q ss_pred EecCCc--eee-cCCcEEE
Q psy7214 46 VEADMP--RRC-ACGHWFK 61 (201)
Q Consensus 46 L~KGkP--~RC-ECGqwFK 61 (201)
+.+|+. .|| .||++|-
T Consensus 22 l~~~kl~g~kC~~CG~v~~ 40 (140)
T COG1545 22 LKEGKLLGTKCKKCGRVYF 40 (140)
T ss_pred hhhCcEEEEEcCCCCeEEc
Confidence 666774 999 7999873
No 33
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=21.62 E-value=77 Score=24.49 Aligned_cols=23 Identities=30% Similarity=0.265 Sum_probs=20.2
Q ss_pred cCCcEEEEEEecCCCCccccCCc
Q psy7214 55 ACGHWFKLKLICRGGVHVAIGSN 77 (201)
Q Consensus 55 ECGqwFKLv~vG~~g~~~~~gs~ 77 (201)
.=++-|+|+++.++||+..+.|.
T Consensus 36 ~~~q~ft~kw~DEEGDp~tiSS~ 58 (83)
T cd06404 36 HNDQPFTLKWIDEEGDPCTISSQ 58 (83)
T ss_pred CCCCcEEEEEECCCCCceeecCH
Confidence 35789999999999999999874
No 34
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=21.46 E-value=28 Score=24.42 Aligned_cols=18 Identities=39% Similarity=0.829 Sum_probs=15.8
Q ss_pred ccccceeEEEecCCCCcc
Q psy7214 158 VHHFNRFRIRFGSGGNRT 175 (201)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~ 175 (201)
..=|++|+|-|--||||+
T Consensus 16 a~vf~~~gIDfCCgG~~~ 33 (56)
T PF04405_consen 16 ARVFRKYGIDFCCGGNRS 33 (56)
T ss_pred HHHHHHcCCcccCCCCch
Confidence 455999999999999997
No 35
>COG2007 RPS8A Ribosomal protein S8E [Translation, ribosomal structure and biogenesis]
Probab=20.27 E-value=1.2e+02 Score=25.30 Aligned_cols=40 Identities=28% Similarity=0.337 Sum_probs=27.9
Q ss_pred hhhhhCCCCcccccce---eEEEecCCCCcccee--ccCCceeee
Q psy7214 148 SKLVLGRDPKVHHFNR---FRIRFGSGGNRTERL--QGKGNVFQA 187 (201)
Q Consensus 148 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~--~~~~~~~~~ 187 (201)
.|..|||.|..+...- +...-.-|||++-|+ +..+||+..
T Consensus 24 rK~elGreP~~t~ige~~~~~~vr~rGgn~K~r~~~~~~aNV~~p 68 (127)
T COG2007 24 RKFELGREPTETKIGEKRKRKKVRTRGGNFKVRALRAKTANVSDP 68 (127)
T ss_pred hhhhcCCCCcccccCccceEEEEEeecCCeEEEEEEeccceeccc
Confidence 4678999999988754 222334689998886 456777664
No 36
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=20.06 E-value=59 Score=17.64 Aligned_cols=9 Identities=44% Similarity=1.327 Sum_probs=6.7
Q ss_pred ee-cCCcEEE
Q psy7214 53 RC-ACGHWFK 61 (201)
Q Consensus 53 RC-ECGqwFK 61 (201)
+| .||..|.
T Consensus 2 ~C~~C~~~f~ 11 (23)
T PF00096_consen 2 KCPICGKSFS 11 (23)
T ss_dssp EETTTTEEES
T ss_pred CCCCCCCccC
Confidence 68 6888874
Done!