Query 025998
Match_columns 245
No_of_seqs 142 out of 205
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 02:29:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025998.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025998hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02701 zf-Dof: Dof domain, z 100.0 1.2E-38 2.5E-43 235.7 3.9 62 9-70 2-63 (63)
2 PF12760 Zn_Tnp_IS1595: Transp 94.1 0.051 1.1E-06 37.1 2.7 28 12-45 18-45 (46)
3 TIGR02159 PA_CoA_Oxy4 phenylac 93.5 0.029 6.3E-07 47.1 0.8 34 12-47 105-140 (146)
4 COG3677 Transposase and inacti 93.2 0.064 1.4E-06 44.2 2.4 35 13-49 31-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 91.3 0.13 2.8E-06 34.6 1.6 31 12-44 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 89.2 0.46 9.9E-06 32.1 2.9 37 13-49 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 86.4 0.59 1.3E-05 31.3 2.1 35 14-48 2-39 (39)
8 cd00202 ZnF_GATA Zinc finger D 83.1 1 2.2E-05 32.3 2.2 42 14-58 1-42 (54)
9 PF13453 zf-TFIIB: Transcripti 82.5 0.38 8.2E-06 32.1 -0.1 37 14-55 1-37 (41)
10 TIGR01384 TFS_arch transcripti 80.2 2.8 6.1E-05 32.2 3.9 39 12-50 62-103 (104)
11 PHA02998 RNA polymerase subuni 78.1 2.4 5.2E-05 38.2 3.3 39 11-49 142-183 (195)
12 PF04216 FdhE: Protein involve 77.3 1.2 2.5E-05 40.2 1.2 36 13-48 212-249 (290)
13 PF04981 NMD3: NMD3 family ; 74.6 1.8 3.8E-05 38.2 1.6 37 15-51 1-49 (236)
14 PF14690 zf-ISL3: zinc-finger 68.3 2.7 5.8E-05 27.8 1.0 32 12-43 2-47 (47)
15 KOG2906 RNA polymerase III sub 67.2 5.2 0.00011 33.1 2.6 45 4-48 57-104 (105)
16 smart00401 ZnF_GATA zinc finge 64.8 5.6 0.00012 28.1 2.1 39 12-53 3-41 (52)
17 TIGR00244 transcriptional regu 61.7 6.3 0.00014 34.1 2.3 45 14-58 2-49 (147)
18 PF06220 zf-U1: U1 zinc finger 59.6 3.8 8.3E-05 27.6 0.5 17 35-51 1-17 (38)
19 PHA00626 hypothetical protein 56.6 8.1 0.00018 29.2 1.8 36 14-51 2-37 (59)
20 PRK00464 nrdR transcriptional 56.1 8.1 0.00018 33.1 2.0 44 14-57 2-48 (154)
21 PF09526 DUF2387: Probable met 53.2 11 0.00024 28.7 2.1 32 11-45 7-38 (71)
22 PRK00432 30S ribosomal protein 52.8 8.1 0.00018 27.4 1.3 26 12-45 20-45 (50)
23 PF14599 zinc_ribbon_6: Zinc-r 49.5 6.8 0.00015 29.1 0.5 14 11-24 47-60 (61)
24 PRK03564 formate dehydrogenase 48.2 13 0.00027 35.3 2.1 10 38-47 253-262 (309)
25 TIGR01562 FdhE formate dehydro 44.2 15 0.00033 34.6 2.0 34 13-47 225-262 (305)
26 PF06827 zf-FPG_IleRS: Zinc fi 39.9 12 0.00027 23.2 0.5 28 12-44 1-28 (30)
27 PF07282 OrfB_Zn_ribbon: Putat 39.1 28 0.00061 24.7 2.3 33 10-49 26-58 (69)
28 COG1997 RPL43A Ribosomal prote 37.7 23 0.00049 28.7 1.8 42 11-59 34-75 (89)
29 TIGR00686 phnA alkylphosphonat 35.3 27 0.00058 29.1 1.9 31 13-51 3-33 (109)
30 PRK14892 putative transcriptio 34.9 30 0.00065 27.9 2.1 37 7-47 16-52 (99)
31 TIGR02443 conserved hypothetic 34.3 30 0.00066 26.0 1.9 32 10-44 7-38 (59)
32 PRK10220 hypothetical protein; 31.1 36 0.00078 28.5 2.0 32 12-51 3-34 (111)
33 PF08274 PhnA_Zn_Ribbon: PhnA 30.2 25 0.00053 23.0 0.7 28 13-48 3-30 (30)
34 PF14354 Lar_restr_allev: Rest 30.0 51 0.0011 22.9 2.4 35 11-45 2-37 (61)
35 TIGR03655 anti_R_Lar restricti 29.9 51 0.0011 23.0 2.3 32 13-45 2-34 (53)
36 COG1327 Predicted transcriptio 29.5 35 0.00075 30.0 1.8 44 14-57 2-48 (156)
37 PF08273 Prim_Zn_Ribbon: Zinc- 26.1 49 0.0011 22.8 1.7 32 12-45 3-34 (40)
38 PF01807 zf-CHC2: CHC2 zinc fi 25.7 46 0.001 25.7 1.7 29 13-45 34-62 (97)
39 smart00661 RPOL9 RNA polymeras 24.5 55 0.0012 21.8 1.7 33 14-51 2-34 (52)
40 PRK00420 hypothetical protein; 23.9 59 0.0013 26.9 2.0 28 12-47 23-50 (112)
41 PF06044 DRP: Dam-replacing fa 22.7 34 0.00073 32.1 0.5 32 13-48 32-64 (254)
42 PTZ00255 60S ribosomal protein 21.3 71 0.0015 25.7 2.0 39 11-59 35-76 (90)
43 PF11378 DUF3181: Protein of u 21.0 42 0.00091 26.9 0.6 11 55-65 56-66 (87)
44 PRK03976 rpl37ae 50S ribosomal 20.9 67 0.0014 25.8 1.8 40 11-60 35-77 (90)
45 KOG2463 Predicted RNA-binding 20.7 29 0.00062 34.1 -0.4 37 12-63 242-278 (376)
46 PF01873 eIF-5_eIF-2B: Domain 20.0 89 0.0019 25.9 2.4 29 13-45 94-122 (125)
No 1
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=100.00 E-value=1.2e-38 Score=235.67 Aligned_cols=62 Identities=77% Similarity=1.535 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCCccccccCCCCccCCCCCCC
Q 025998 9 VETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAKS 70 (245)
Q Consensus 9 ~e~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRnVPVGgG~RKnk~s~s 70 (245)
+++.++||||+|.+|||||||||+++||||||++|+||||+||+||||||||||||+|+++|
T Consensus 2 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg~Rk~k~~~s 63 (63)
T PF02701_consen 2 PEQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGGCRKNKRSSS 63 (63)
T ss_pred CccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCCcccCCcCCC
Confidence 56789999999999999999999999999999999999999999999999999999998875
No 2
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=94.08 E-value=0.051 Score=37.08 Aligned_cols=28 Identities=39% Similarity=0.893 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 025998 12 APSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRR 45 (245)
Q Consensus 12 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 45 (245)
+..||+|.+. +...+.+ ..+|.|++|++
T Consensus 18 g~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 3679999998 6666665 78999999985
No 3
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=93.51 E-value=0.029 Score=47.13 Aligned_cols=34 Identities=26% Similarity=0.791 Sum_probs=26.5
Q ss_pred CCCCCCCCCCCceeeeeccc--CCCCCccccccccccc
Q 025998 12 APSCPRCASPNTKFCYYNNY--SLSQPRYFCKGCRRYW 47 (245)
Q Consensus 12 ~~~CPRC~S~nTKFcYyNNy--~~~QPR~fCk~CrRyW 47 (245)
...||||.|.+|+.. +.+ +.++.-|.|++|+.=+
T Consensus 105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcH
Confidence 369999999999965 555 4457779999998643
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.21 E-value=0.064 Score=44.15 Aligned_cols=35 Identities=34% Similarity=0.704 Sum_probs=28.0
Q ss_pred CCCCCCCCCCceeeeecccCCCCCccccccccccccc
Q 025998 13 PSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTK 49 (245)
Q Consensus 13 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~ 49 (245)
..||+|.+.+ +-=++-+.....||.|++|++-|+.
T Consensus 31 ~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 31 VNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred CcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence 6899999999 3334555555999999999999874
No 5
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=91.26 E-value=0.13 Score=34.59 Aligned_cols=31 Identities=45% Similarity=0.819 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCceeeeecccCCC-CCcccccccc
Q 025998 12 APSCPRCASPNTKFCYYNNYSLS-QPRYFCKGCR 44 (245)
Q Consensus 12 ~~~CPRC~S~nTKFcYyNNy~~~-QPR~fCk~Cr 44 (245)
.+.||+|.|.+. -|=|-.+.. ..||+|++|+
T Consensus 5 ~v~CP~C~s~~~--v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEG--VKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCc--ceeCCCCCCCCEeEecCcCC
Confidence 468999999871 123444433 5899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=89.17 E-value=0.46 Score=32.10 Aligned_cols=37 Identities=27% Similarity=0.815 Sum_probs=27.9
Q ss_pred CCCCCCCCCCceeeeecccCCCCC---ccccccccccccc
Q 025998 13 PSCPRCASPNTKFCYYNNYSLSQP---RYFCKGCRRYWTK 49 (245)
Q Consensus 13 ~~CPRC~S~nTKFcYyNNy~~~QP---R~fCk~CrRyWT~ 49 (245)
.+||+|...+.-|-..+-.+...| -|.|.+|...|..
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~~ 40 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWRE 40 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeCC
Confidence 379999977777666666655555 4999999999963
No 7
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=86.39 E-value=0.59 Score=31.33 Aligned_cols=35 Identities=29% Similarity=0.811 Sum_probs=23.9
Q ss_pred CCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 025998 14 SCPRCASPNTKFCYYNNYSLSQPR---YFCKGCRRYWT 48 (245)
Q Consensus 14 ~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT 48 (245)
+||.|...+.-|=-.+..+..-|- |.|.+|..-|+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 699999987666555665555553 89999999885
No 8
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=83.06 E-value=1 Score=32.27 Aligned_cols=42 Identities=26% Similarity=0.651 Sum_probs=29.4
Q ss_pred CCCCCCCCCceeeeecccCCCCCcccccccccccccCCccccccC
Q 025998 14 SCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPV 58 (245)
Q Consensus 14 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRnVPV 58 (245)
.|-.|....|..=.-. ...+..+|-+|.-||.+.|..|.+-.
T Consensus 1 ~C~~C~~~~Tp~WR~g---~~~~~~LCNaCgl~~~k~~~~rp~~~ 42 (54)
T cd00202 1 ACSNCGTTTTPLWRRG---PSGGSTLCNACGLYWKKHGVMRPLSK 42 (54)
T ss_pred CCCCCCCCCCcccccC---CCCcchHHHHHHHHHHhcCCCCCccc
Confidence 3777888777422221 24677899999999999997665543
No 9
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=82.52 E-value=0.38 Score=32.06 Aligned_cols=37 Identities=24% Similarity=0.588 Sum_probs=27.2
Q ss_pred CCCCCCCCCceeeeecccCCCCCcccccccccccccCCcccc
Q 025998 14 SCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRN 55 (245)
Q Consensus 14 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRn 55 (245)
+||+|...-...-+ ..-+-+.|.+|.-.|=..|.+..
T Consensus 1 ~CP~C~~~l~~~~~-----~~~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-----GDVEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred CcCCCCcccceEEE-----CCEEEEECCCCCeEEccHHHHHH
Confidence 69999985554444 23566889999999988776654
No 10
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=80.19 E-value=2.8 Score=32.16 Aligned_cols=39 Identities=21% Similarity=0.652 Sum_probs=28.4
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCc---ccccccccccccC
Q 025998 12 APSCPRCASPNTKFCYYNNYSLSQPR---YFCKGCRRYWTKG 50 (245)
Q Consensus 12 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~G 50 (245)
...||+|...+.-|=..+-.+...|- |.|..|+-.|+.+
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 57999998776665555555444343 9999999999875
No 11
>PHA02998 RNA polymerase subunit; Provisional
Probab=78.05 E-value=2.4 Score=38.18 Aligned_cols=39 Identities=23% Similarity=0.573 Sum_probs=33.7
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCc---cccccccccccc
Q 025998 11 TAPSCPRCASPNTKFCYYNNYSLSQPR---YFCKGCRRYWTK 49 (245)
Q Consensus 11 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~ 49 (245)
...+||+|...++-|=-.|-.+...|- |.|..|..-|.-
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 557999999999998888888888775 899999999964
No 12
>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=77.30 E-value=1.2 Score=40.18 Aligned_cols=36 Identities=22% Similarity=0.572 Sum_probs=18.1
Q ss_pred CCCCCCCCCC-ceeeeecc-cCCCCCcccccccccccc
Q 025998 13 PSCPRCASPN-TKFCYYNN-YSLSQPRYFCKGCRRYWT 48 (245)
Q Consensus 13 ~~CPRC~S~n-TKFcYyNN-y~~~QPR~fCk~CrRyWT 48 (245)
..||.|...+ .++-||.. -....--+.|+.|+.|+-
T Consensus 212 ~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 212 IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp TS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred CCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 5899999855 45666633 333333499999999983
No 13
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=74.56 E-value=1.8 Score=38.16 Aligned_cols=37 Identities=32% Similarity=0.861 Sum_probs=26.7
Q ss_pred CCCCCCCCce-------eeeecccCCCC-C----cccccccccccccCC
Q 025998 15 CPRCASPNTK-------FCYYNNYSLSQ-P----RYFCKGCRRYWTKGG 51 (245)
Q Consensus 15 CPRC~S~nTK-------FcYyNNy~~~Q-P----R~fCk~CrRyWT~GG 51 (245)
||+|...... =||...+.+.. | -.+|+.|.||+..|.
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~ 49 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGGR 49 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCEECCCE
Confidence 7788765444 37888777654 2 278999999999843
No 14
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=68.26 E-value=2.7 Score=27.79 Aligned_cols=32 Identities=38% Similarity=0.927 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCcee-eeeccc-------------CCCCCccccccc
Q 025998 12 APSCPRCASPNTKF-CYYNNY-------------SLSQPRYFCKGC 43 (245)
Q Consensus 12 ~~~CPRC~S~nTKF-cYyNNy-------------~~~QPR~fCk~C 43 (245)
...||.|.+...+. -++... .+..+|++|++|
T Consensus 2 ~~~Cp~Cg~~~~~~~g~~~r~i~~l~~~~~~~~L~i~~~R~~C~~C 47 (47)
T PF14690_consen 2 PPRCPHCGSPSVHRHGYKTRRIRHLPIGGRPVYLRIRKRRYRCKNC 47 (47)
T ss_pred CccCCCcCCCceECCceEEEEEeecccCCEEEEEEEEeEEEECcCC
Confidence 46899999876221 111110 345678888877
No 15
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=67.22 E-value=5.2 Score=33.12 Aligned_cols=45 Identities=27% Similarity=0.706 Sum_probs=38.0
Q ss_pred CCCCCCCCCCCCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 025998 4 KWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPR---YFCKGCRRYWT 48 (245)
Q Consensus 4 ~~~~~~e~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT 48 (245)
.|+-.......||+|.....-|--+|-.+..-|- |.|-.|.--|-
T Consensus 57 a~~nv~~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 57 AWENVDQTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred cccchhhccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 5666667778999999999998888888888876 89999998884
No 16
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=64.85 E-value=5.6 Score=28.09 Aligned_cols=39 Identities=28% Similarity=0.640 Sum_probs=28.7
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCcccccccccccccCCcc
Q 025998 12 APSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSL 53 (245)
Q Consensus 12 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtL 53 (245)
...|-.|....|..=.- ...-++.+|-+|.-||.+.|.+
T Consensus 3 ~~~C~~C~~~~T~~WR~---g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 3 GRSCSNCGTTETPLWRR---GPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCcCCCCCCCCCcccc---CCCCCCcEeecccHHHHHcCCC
Confidence 46899999888853211 2223369999999999998886
No 17
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=61.74 E-value=6.3 Score=34.07 Aligned_cols=45 Identities=22% Similarity=0.347 Sum_probs=33.2
Q ss_pred CCCCCCCCCceeeee---cccCCCCCcccccccccccccCCccccccC
Q 025998 14 SCPRCASPNTKFCYY---NNYSLSQPRYFCKGCRRYWTKGGSLRNVPV 58 (245)
Q Consensus 14 ~CPRC~S~nTKFcYy---NNy~~~QPR~fCk~CrRyWT~GGtLRnVPV 58 (245)
+||.|...+||+-=- ...+.-+-|.-|.+|.+-||-==.+-..|+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l 49 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPP 49 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeecccccc
Confidence 699999999998643 444555678999999999886555444443
No 18
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=59.59 E-value=3.8 Score=27.59 Aligned_cols=17 Identities=41% Similarity=1.171 Sum_probs=7.1
Q ss_pred CCcccccccccccccCC
Q 025998 35 QPRYFCKGCRRYWTKGG 51 (245)
Q Consensus 35 QPR~fCk~CrRyWT~GG 51 (245)
+|||||.=|..|.|..-
T Consensus 1 m~ryyCdyC~~~~~~d~ 17 (38)
T PF06220_consen 1 MPRYYCDYCKKYLTHDS 17 (38)
T ss_dssp --S-B-TTT--B-S--S
T ss_pred CcCeecccccceecCCC
Confidence 69999999999997654
No 19
>PHA00626 hypothetical protein
Probab=56.58 E-value=8.1 Score=29.17 Aligned_cols=36 Identities=28% Similarity=0.393 Sum_probs=24.4
Q ss_pred CCCCCCCCCceeeeecccCCCCCcccccccccccccCC
Q 025998 14 SCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGG 51 (245)
Q Consensus 14 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GG 51 (245)
.||+|.|.+.-=|-.= ....-||.|+.|.=.+|+..
T Consensus 2 ~CP~CGS~~Ivrcg~c--r~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKTM--RGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeecee--cccCcceEcCCCCCeechhh
Confidence 6999999754322111 11245799999999999864
No 20
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=56.15 E-value=8.1 Score=33.07 Aligned_cols=44 Identities=25% Similarity=0.488 Sum_probs=31.7
Q ss_pred CCCCCCCCCceee---eecccCCCCCcccccccccccccCCcccccc
Q 025998 14 SCPRCASPNTKFC---YYNNYSLSQPRYFCKGCRRYWTKGGSLRNVP 57 (245)
Q Consensus 14 ~CPRC~S~nTKFc---YyNNy~~~QPR~fCk~CrRyWT~GGtLRnVP 57 (245)
+||.|.+..|++- |+-.-++-.-||-|++|.+-++.==++-..+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 7999999987764 4444444556699999999887665554443
No 21
>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=53.18 E-value=11 Score=28.69 Aligned_cols=32 Identities=22% Similarity=0.494 Sum_probs=25.6
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 025998 11 TAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRR 45 (245)
Q Consensus 11 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 45 (245)
.++.||+|.+.+|=..|..|. ..-.-|-.|.=
T Consensus 7 AGa~CP~C~~~D~i~~~~e~~---ve~vECV~CGy 38 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWRENG---VEYVECVECGY 38 (71)
T ss_pred cCccCCCCcCccEEEEEEeCC---ceEEEecCCCC
Confidence 478999999999988888776 55567888853
No 22
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=52.85 E-value=8.1 Score=27.43 Aligned_cols=26 Identities=35% Similarity=0.745 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 025998 12 APSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRR 45 (245)
Q Consensus 12 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 45 (245)
..-||+|.+. |..-.. .|+.|..|..
T Consensus 20 ~~fCP~Cg~~---~m~~~~-----~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSG---FMAEHL-----DRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcc---hheccC-----CcEECCCcCC
Confidence 3489999873 554443 6999999974
No 23
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=49.54 E-value=6.8 Score=29.15 Aligned_cols=14 Identities=36% Similarity=0.733 Sum_probs=6.0
Q ss_pred CCCCCCCCCCCCce
Q 025998 11 TAPSCPRCASPNTK 24 (245)
Q Consensus 11 ~~~~CPRC~S~nTK 24 (245)
-+.+|+.|.|.||+
T Consensus 47 lg~KC~~C~SYNT~ 60 (61)
T PF14599_consen 47 LGHKCSHCGSYNTR 60 (61)
T ss_dssp T----TTTS---EE
T ss_pred hhhcCCCCCCcccC
Confidence 46799999999997
No 24
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=48.20 E-value=13 Score=35.26 Aligned_cols=10 Identities=30% Similarity=0.747 Sum_probs=5.8
Q ss_pred cccccccccc
Q 025998 38 YFCKGCRRYW 47 (245)
Q Consensus 38 ~fCk~CrRyW 47 (245)
+.|..|++|+
T Consensus 253 e~C~~C~~Yl 262 (309)
T PRK03564 253 ESCGDCGTYL 262 (309)
T ss_pred eecccccccc
Confidence 5566665555
No 25
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=44.20 E-value=15 Score=34.60 Aligned_cols=34 Identities=18% Similarity=0.503 Sum_probs=15.7
Q ss_pred CCCCCCCCCCceeeeecccC----CCCCccccccccccc
Q 025998 13 PSCPRCASPNTKFCYYNNYS----LSQPRYFCKGCRRYW 47 (245)
Q Consensus 13 ~~CPRC~S~nTKFcYyNNy~----~~QPR~fCk~CrRyW 47 (245)
.+||.|.+.+ +.-|+.--. ..---..|..|+.|+
T Consensus 225 ~~C~~Cg~~~-~l~y~~~e~~~~~~~~r~e~C~~C~~Yl 262 (305)
T TIGR01562 225 VKCSHCEESK-HLAYLSLEHDAEKAVLKAETCDSCQGYL 262 (305)
T ss_pred ccCCCCCCCC-ceeeEeecCCCCCcceEEeeccccccch
Confidence 4566666543 333443221 111124666666665
No 26
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=39.93 E-value=12 Score=23.18 Aligned_cols=28 Identities=25% Similarity=0.701 Sum_probs=14.9
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCcccccccc
Q 025998 12 APSCPRCASPNTKFCYYNNYSLSQPRYFCKGCR 44 (245)
Q Consensus 12 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~Cr 44 (245)
+.+||||...-.+.-..+ +.-+||..|+
T Consensus 1 G~~C~rC~~~~~~~~~~~-----r~~~~C~rCq 28 (30)
T PF06827_consen 1 GEKCPRCWNYIEDIGING-----RSTYLCPRCQ 28 (30)
T ss_dssp TSB-TTT--BBEEEEETT-----EEEEE-TTTC
T ss_pred CCcCccCCCcceEeEecC-----CCCeECcCCc
Confidence 357999998776655422 2337787775
No 27
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=39.06 E-value=28 Score=24.65 Aligned_cols=33 Identities=30% Similarity=0.611 Sum_probs=25.8
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCccccccccccccc
Q 025998 10 ETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTK 49 (245)
Q Consensus 10 e~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~ 49 (245)
.....||.|.....+ .+.+-.+.|..|...+.+
T Consensus 26 ~TSq~C~~CG~~~~~-------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 26 YTSQTCPRCGHRNKK-------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CCccCccCccccccc-------ccccceEEcCCCCCEECc
Confidence 356689999998877 666777999999876543
No 28
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=37.74 E-value=23 Score=28.67 Aligned_cols=42 Identities=21% Similarity=0.550 Sum_probs=31.2
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCCccccccCC
Q 025998 11 TAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVG 59 (245)
Q Consensus 11 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRnVPVG 59 (245)
+...||-|.+...| -...---.|+.|..-|+.|+-....|.|
T Consensus 34 ~~~~Cp~C~~~~Vk-------R~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 34 AKHVCPFCGRTTVK-------RIATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred cCCcCCCCCCccee-------eeccCeEEcCCCCCeeccccccccchHH
Confidence 34689999998655 1122337899999999999987766655
No 29
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=35.29 E-value=27 Score=29.12 Aligned_cols=31 Identities=29% Similarity=0.787 Sum_probs=24.9
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcccccccccccccCC
Q 025998 13 PSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGG 51 (245)
Q Consensus 13 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GG 51 (245)
+.||.|.|..|- - .+.-+.|..|.-=|...+
T Consensus 3 p~CP~C~seytY---~-----dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTY---H-----DGTQLICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceE---e-----cCCeeECccccccccccc
Confidence 689999997663 1 355699999999999886
No 30
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=34.89 E-value=30 Score=27.89 Aligned_cols=37 Identities=22% Similarity=0.466 Sum_probs=24.2
Q ss_pred CCCCCCCCCCCCCCCCceeeeecccCCCCCccccccccccc
Q 025998 7 PDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYW 47 (245)
Q Consensus 7 ~~~e~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyW 47 (245)
+.......||.|.+ .+--|=... ..+.+.|..|.-|-
T Consensus 16 ~klpt~f~CP~Cge-~~v~v~~~k---~~~h~~C~~CG~y~ 52 (99)
T PRK14892 16 PKLPKIFECPRCGK-VSISVKIKK---NIAIITCGNCGLYT 52 (99)
T ss_pred cCCCcEeECCCCCC-eEeeeecCC---CcceEECCCCCCcc
Confidence 34445568999995 233333333 47889999998884
No 31
>TIGR02443 conserved hypothetical metal-binding protein. 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=34.32 E-value=30 Score=26.03 Aligned_cols=32 Identities=22% Similarity=0.463 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcccccccc
Q 025998 10 ETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCR 44 (245)
Q Consensus 10 e~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~Cr 44 (245)
-.++.||+|...+|=..|..|.- .-.-|-.|.
T Consensus 7 IAGA~CP~C~~~Dtl~~~~e~~~---e~vECv~Cg 38 (59)
T TIGR02443 7 IAGAVCPACSAQDTLAMWKENNI---ELVECVECG 38 (59)
T ss_pred eccccCCCCcCccEEEEEEeCCc---eEEEeccCC
Confidence 35789999999999988866543 335566664
No 32
>PRK10220 hypothetical protein; Provisional
Probab=31.08 E-value=36 Score=28.49 Aligned_cols=32 Identities=31% Similarity=0.808 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCcccccccccccccCC
Q 025998 12 APSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGG 51 (245)
Q Consensus 12 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GG 51 (245)
.+.||.|.|..|- ..+.-+.|..|.-=|+...
T Consensus 3 lP~CP~C~seytY--------~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 3 LPHCPKCNSEYTY--------EDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CCcCCCCCCcceE--------cCCCeEECCcccCcCCccc
Confidence 3689999997663 2355699999999999875
No 33
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=30.24 E-value=25 Score=23.04 Aligned_cols=28 Identities=32% Similarity=0.769 Sum_probs=14.4
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcccccccccccc
Q 025998 13 PSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWT 48 (245)
Q Consensus 13 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT 48 (245)
.+||-|.|..|= ...--+.|..|..=|.
T Consensus 3 p~Cp~C~se~~y--------~D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 3 PKCPLCGSEYTY--------EDGELLVCPECGHEWN 30 (30)
T ss_dssp ---TTT-----E--------E-SSSEEETTTTEEE-
T ss_pred CCCCCCCCccee--------ccCCEEeCCcccccCC
Confidence 589999998775 4566788999987774
No 34
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=30.04 E-value=51 Score=22.85 Aligned_cols=35 Identities=17% Similarity=0.394 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCCceeeeecccCCCC-Cccccccccc
Q 025998 11 TAPSCPRCASPNTKFCYYNNYSLSQ-PRYFCKGCRR 45 (245)
Q Consensus 11 ~~~~CPRC~S~nTKFcYyNNy~~~Q-PR~fCk~CrR 45 (245)
+-.+||.|.+....+.+........ -.-.|..|..
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4568999966655555432221111 3345888866
No 35
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=29.89 E-value=51 Score=22.98 Aligned_cols=32 Identities=25% Similarity=0.631 Sum_probs=18.5
Q ss_pred CCCCCCCCCCceeeeecccCCCCCccc-cccccc
Q 025998 13 PSCPRCASPNTKFCYYNNYSLSQPRYF-CKGCRR 45 (245)
Q Consensus 13 ~~CPRC~S~nTKFcYyNNy~~~QPR~f-Ck~CrR 45 (245)
.+||.|.+..-.|=+ ......-.+++ |..|..
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 489999996664532 12233333444 777764
No 36
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=29.49 E-value=35 Score=30.03 Aligned_cols=44 Identities=23% Similarity=0.332 Sum_probs=30.5
Q ss_pred CCCCCCCCCceeeeec---ccCCCCCcccccccccccccCCcccccc
Q 025998 14 SCPRCASPNTKFCYYN---NYSLSQPRYFCKGCRRYWTKGGSLRNVP 57 (245)
Q Consensus 14 ~CPRC~S~nTKFcYyN---Ny~~~QPR~fCk~CrRyWT~GGtLRnVP 57 (245)
.||.|.+.+||+-==- .-+.-+-|.-|.+|..-+|-==++--+|
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~ 48 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRP 48 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeecc
Confidence 6999999999985321 2233456788999988888655544444
No 37
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=26.12 E-value=49 Score=22.81 Aligned_cols=32 Identities=19% Similarity=0.688 Sum_probs=18.2
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 025998 12 APSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRR 45 (245)
Q Consensus 12 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 45 (245)
..+||-|.+ ..+|..|-+. ..+-..+|..|..
T Consensus 3 h~pCP~CGG-~DrFri~~d~-~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 3 HGPCPICGG-KDRFRIFDDK-DGRGTWICRQCGG 34 (40)
T ss_dssp EE--TTTT--TTTEEEETT-----S-EEETTTTB
T ss_pred CCCCCCCcC-ccccccCcCc-ccCCCEECCCCCC
Confidence 458999988 5688866543 2347799999943
No 38
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 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 CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=25.70 E-value=46 Score=25.70 Aligned_cols=29 Identities=24% Similarity=0.546 Sum_probs=16.2
Q ss_pred CCCCCCCCCCceeeeecccCCCCCccccccccc
Q 025998 13 PSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRR 45 (245)
Q Consensus 13 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 45 (245)
..||-|+..+..|..+.+- -++.|-+|.+
T Consensus 34 ~~CPfH~d~~pS~~i~~~k----~~~~Cf~Cg~ 62 (97)
T PF01807_consen 34 CLCPFHDDKTPSFSINPDK----NRFKCFGCGK 62 (97)
T ss_dssp E--SSS--SS--EEEETTT----TEEEETTT--
T ss_pred EECcCCCCCCCceEEECCC----CeEEECCCCC
Confidence 4799999887777776543 3799999984
No 39
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.55 E-value=55 Score=21.81 Aligned_cols=33 Identities=18% Similarity=0.442 Sum_probs=20.2
Q ss_pred CCCCCCCCCceeeeecccCCCCCcccccccccccccCC
Q 025998 14 SCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGG 51 (245)
Q Consensus 14 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GG 51 (245)
-||.|.+. .|..... ...|+.|..|...+-.+.
T Consensus 2 FCp~Cg~~----l~~~~~~-~~~~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 2 FCPKCGNM----LIPKEGK-EKRRFVCRKCGYEEPIEQ 34 (52)
T ss_pred CCCCCCCc----cccccCC-CCCEEECCcCCCeEECCC
Confidence 48999772 3333221 124899999997665443
No 40
>PRK00420 hypothetical protein; Validated
Probab=23.94 E-value=59 Score=26.88 Aligned_cols=28 Identities=18% Similarity=0.509 Sum_probs=21.6
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCccccccccccc
Q 025998 12 APSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYW 47 (245)
Q Consensus 12 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyW 47 (245)
+..||.|.+.-+++ .+-..||..|...-
T Consensus 23 ~~~CP~Cg~pLf~l--------k~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCGLPLFEL--------KDGEVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCCCcceec--------CCCceECCCCCCee
Confidence 46899999887763 36789999997643
No 41
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=22.71 E-value=34 Score=32.12 Aligned_cols=32 Identities=25% Similarity=0.724 Sum_probs=11.8
Q ss_pred CCCCCCCCC-CceeeeecccCCCCCcccccccccccc
Q 025998 13 PSCPRCASP-NTKFCYYNNYSLSQPRYFCKGCRRYWT 48 (245)
Q Consensus 13 ~~CPRC~S~-nTKFcYyNNy~~~QPR~fCk~CrRyWT 48 (245)
..||+|.+. -.+| .-+.+-.-.+|..|..=.-
T Consensus 32 ~yCP~Cg~~~L~~f----~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 32 MYCPNCGSKPLSKF----ENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp ---TTT--SS-EE------------EEE-TTT--EEE
T ss_pred CcCCCCCChhHhhc----cCCCccceeECCCCchHHh
Confidence 479999997 5554 3344455699999986553
No 42
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=21.32 E-value=71 Score=25.68 Aligned_cols=39 Identities=26% Similarity=0.584 Sum_probs=29.0
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCc---ccccccccccccCCccccccCC
Q 025998 11 TAPSCPRCASPNTKFCYYNNYSLSQPR---YFCKGCRRYWTKGGSLRNVPVG 59 (245)
Q Consensus 11 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~GGtLRnVPVG 59 (245)
....||.|....-| +.. --|+.|.+-++.|.-..+-|.|
T Consensus 35 a~y~CpfCgk~~vk----------R~a~GIW~C~~C~~~~AGGAy~~~T~~~ 76 (90)
T PTZ00255 35 AKYFCPFCGKHAVK----------RQAVGIWRCKGCKKTVAGGAWTLSTPAA 76 (90)
T ss_pred CCccCCCCCCCcee----------eeeeEEEEcCCCCCEEeCCccccccchh
Confidence 45689999876665 222 7899999999988876655554
No 43
>PF11378 DUF3181: Protein of unknown function (DUF3181); InterPro: IPR021518 This family of proteins has no known function.
Probab=20.95 E-value=42 Score=26.94 Aligned_cols=11 Identities=45% Similarity=0.628 Sum_probs=8.4
Q ss_pred cccCCCCccCC
Q 025998 55 NVPVGGGCRKN 65 (245)
Q Consensus 55 nVPVGgG~RKn 65 (245)
+||+|||.++-
T Consensus 56 ~V~lGGG~~~l 66 (87)
T PF11378_consen 56 PVKLGGGKSKL 66 (87)
T ss_pred ccccCCCcccc
Confidence 47899997653
No 44
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=20.95 E-value=67 Score=25.85 Aligned_cols=40 Identities=25% Similarity=0.655 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCc---ccccccccccccCCccccccCCC
Q 025998 11 TAPSCPRCASPNTKFCYYNNYSLSQPR---YFCKGCRRYWTKGGSLRNVPVGG 60 (245)
Q Consensus 11 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~GGtLRnVPVGg 60 (245)
....||.|....-| +.. --|+.|..-|+.|.-..+-|.|-
T Consensus 35 a~y~CpfCgk~~vk----------R~a~GIW~C~~C~~~~AGGAy~~~T~~~~ 77 (90)
T PRK03976 35 AKHVCPVCGRPKVK----------RVGTGIWECRKCGAKFAGGAYTPETPAGK 77 (90)
T ss_pred cCccCCCCCCCceE----------EEEEEEEEcCCCCCEEeCCccccccchhh
Confidence 34689999776655 322 77999999999988877766653
No 45
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=20.74 E-value=29 Score=34.13 Aligned_cols=37 Identities=24% Similarity=0.484 Sum_probs=27.6
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCcccccccccccccCCccccccCCCCcc
Q 025998 12 APSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCR 63 (245)
Q Consensus 12 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRnVPVGgG~R 63 (245)
.++|-.|-+.-+ --+|+||.+|. |+||+.+.|.-+.+
T Consensus 242 iLRCh~Cfsit~----------~m~k~FCp~CG-----~~TL~K~aVsv~~d 278 (376)
T KOG2463|consen 242 ILRCHGCFSITS----------EMPKDFCPSCG-----HKTLTKCAVSVDED 278 (376)
T ss_pred eeEeeeeeEecC----------ccchhcccccC-----CCeeeEEEEEecCC
Confidence 457877876543 37899999995 66999988866554
No 46
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=20.02 E-value=89 Score=25.86 Aligned_cols=29 Identities=31% Similarity=0.566 Sum_probs=20.3
Q ss_pred CCCCCCCCCCceeeeecccCCCCCccccccccc
Q 025998 13 PSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRR 45 (245)
Q Consensus 13 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 45 (245)
..||-|.+++|.+--- ..---..|++|..
T Consensus 94 VlC~~C~spdT~l~k~----~r~~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKE----GRLIFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEE----TTCCEEEETTTSC
T ss_pred EEcCCCCCCccEEEEc----CCEEEEEecccCC
Confidence 5899999999997654 1123366888853
Done!