Query 033398
Match_columns 120
No_of_seqs 100 out of 238
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 13:25:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033398.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033398hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00074 60S ribosomal protein 100.0 8.9E-62 1.9E-66 363.1 12.9 115 1-117 1-115 (135)
2 KOG1790 60s ribosomal protein 100.0 2.8E-55 6.1E-60 322.4 5.9 114 1-116 1-114 (121)
3 PLN03166 60S ribosomal protein 100.0 5.9E-53 1.3E-57 300.4 9.0 96 1-96 1-96 (96)
4 PF01199 Ribosomal_L34e: Ribos 100.0 5.9E-52 1.3E-56 294.2 4.8 94 1-96 1-94 (94)
5 COG2174 RPL34A Ribosomal prote 100.0 5.3E-45 1.2E-49 257.9 8.8 92 9-102 2-93 (93)
6 PRK04059 rpl34e 50S ribosomal 100.0 3.8E-42 8.2E-47 241.8 8.6 83 10-94 3-85 (88)
7 COG1381 RecO Recombinational D 64.3 2.9 6.4E-05 33.5 0.7 30 40-87 153-182 (251)
8 KOG1842 FYVE finger-containing 61.4 2.9 6.3E-05 37.7 0.2 36 39-89 178-213 (505)
9 PRK00085 recO DNA repair prote 58.2 3.7 8.1E-05 31.8 0.3 30 40-87 148-177 (247)
10 PF14471 DUF4428: Domain of un 57.6 9 0.00019 24.2 1.9 30 43-90 1-30 (51)
11 KOG1819 FYVE finger-containing 51.0 3.3 7.2E-05 38.5 -1.1 34 39-87 899-932 (990)
12 PTZ00218 40S ribosomal protein 45.4 21 0.00044 23.4 2.2 37 33-90 7-44 (54)
13 PF01412 ArfGap: Putative GTPa 42.6 16 0.00035 25.9 1.5 37 38-95 10-46 (116)
14 KOG3815 Transcription factor D 40.0 48 0.001 27.6 4.2 39 36-87 31-69 (322)
15 COG1571 Predicted DNA-binding 40.0 14 0.00031 32.7 1.1 12 40-51 349-360 (421)
16 PRK00420 hypothetical protein; 38.3 15 0.00033 26.9 0.9 14 42-55 24-37 (112)
17 TIGR00613 reco DNA repair prot 34.6 24 0.00053 27.1 1.5 33 39-89 145-177 (241)
18 PHA02565 49 recombination endo 34.6 34 0.00074 26.7 2.3 14 41-54 20-33 (157)
19 COG5347 GTPase-activating prot 33.2 6.1 0.00013 33.6 -2.2 36 32-86 11-46 (319)
20 PRK00415 rps27e 30S ribosomal 33.1 60 0.0013 21.5 3.0 34 18-52 7-41 (59)
21 COG3813 Uncharacterized protei 33.0 26 0.00057 24.6 1.3 34 43-79 43-77 (84)
22 COG2906 Bfd Bacterioferritin-a 32.9 47 0.001 22.3 2.4 19 80-100 35-53 (63)
23 smart00105 ArfGap Putative GTP 32.7 29 0.00063 24.5 1.5 27 42-87 4-30 (112)
24 PF11022 DUF2611: Protein of u 31.3 54 0.0012 22.3 2.6 18 98-115 52-69 (71)
25 smart00064 FYVE Protein presen 30.1 25 0.00055 22.1 0.8 39 41-94 10-48 (68)
26 PF09889 DUF2116: Uncharacteri 28.0 33 0.00071 22.6 1.1 11 42-52 4-14 (59)
27 PF13408 Zn_ribbon_recom: Reco 27.7 22 0.00048 21.3 0.2 14 41-54 5-18 (58)
28 PF13248 zf-ribbon_3: zinc-rib 26.7 31 0.00067 18.6 0.6 10 42-51 17-26 (26)
29 PF02865 STAT_int: STAT protei 24.5 71 0.0015 23.4 2.4 17 89-105 105-121 (124)
30 PF06689 zf-C4_ClpX: ClpX C4-t 24.0 53 0.0012 19.6 1.4 32 42-89 2-33 (41)
31 PRK08061 rpsN 30S ribosomal pr 24.0 58 0.0013 21.6 1.7 19 72-92 31-49 (61)
32 PF10764 Gin: Inhibitor of sig 23.7 44 0.00094 20.8 1.0 15 77-91 15-29 (46)
33 PLN00209 ribosomal protein S27 23.1 93 0.002 22.1 2.7 37 14-51 28-65 (86)
34 PF13005 zf-IS66: zinc-finger 22.7 38 0.00081 20.0 0.5 16 42-57 3-18 (47)
35 PTZ00083 40S ribosomal protein 22.3 95 0.0021 22.0 2.6 37 14-51 27-64 (85)
36 PF05340 DUF740: Protein of un 21.4 82 0.0018 29.4 2.6 27 66-93 11-37 (603)
37 PF10367 Vps39_2: Vacuolar sor 21.3 67 0.0015 21.2 1.6 14 40-53 77-90 (109)
38 PRK05342 clpX ATP-dependent pr 20.8 76 0.0016 27.5 2.2 30 41-87 9-38 (412)
39 PF11314 DUF3117: Protein of u 20.6 72 0.0016 20.7 1.5 20 15-34 13-35 (51)
40 COG1198 PriA Primosomal protei 20.3 86 0.0019 29.7 2.6 26 27-52 419-446 (730)
41 PF13085 Fer2_3: 2Fe-2S iron-s 20.2 23 0.0005 25.6 -0.9 16 41-56 54-69 (110)
No 1
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=100.00 E-value=8.9e-62 Score=363.14 Aligned_cols=115 Identities=63% Similarity=0.956 Sum_probs=112.1
Q ss_pred CccceeccCCCCCCCCCceeEEeecCCCceEEEeeecCCCCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCC
Q 033398 1 MVQRLTYRTRHSYATKSNQHRVVKTPGGKLVYQSTKKRASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGG 80 (120)
Q Consensus 1 m~~R~t~rrr~~Y~TrSnk~~~vrTPGGrlv~~y~KK~~~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG 80 (120)
|+||||||||++|||+||+++++|||||+|||||++|+++.|+|||||.+|+||+++||.+++ +|++++++|+|||||
T Consensus 1 M~qR~t~rrr~~YnTrSnk~r~vrTPGGrlV~~y~KK~~~~pkC~~cg~~L~GI~~~Rp~e~~--rlsK~~KtvsRaYGG 78 (135)
T PTZ00074 1 MAQRVTYRRRNSYNTRSNKVRLVKTPGGRLVVQKRKKKSSGPKCGDCGKVLAGIKALRPTEYK--QLSRRERTVSRAYGG 78 (135)
T ss_pred CCcceEecccCCCCCCCCeeEEEECCCCceEEEEeccCCCCCCCCCCCCccCCccCCchHHHH--HccccCCCccCCCcc
Confidence 999999999999999999999999999999999999999999999999999999999999999 999999999999999
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033398 81 VLSGGAVRERIIRAFLVEEQKIVKKVLKIQKAKEKLA 117 (120)
Q Consensus 81 ~lC~kcVr~rIvrAFL~EEqkivk~v~~~~~~~~~~~ 117 (120)
++||+||+|||++|||+||||||++|++++++++++.
T Consensus 79 ~lC~~CVr~rIirAFLiEEqKivkkv~k~~~~~~k~~ 115 (135)
T PTZ00074 79 VLCHKCVRDRIVRAFLVEEQKIVKQVLKEKAKQKKQK 115 (135)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999999999999999999999766643
No 2
>KOG1790 consensus 60s ribosomal protein L34 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-55 Score=322.41 Aligned_cols=114 Identities=67% Similarity=0.999 Sum_probs=110.9
Q ss_pred CccceeccCCCCCCCCCceeEEeecCCCceEEEeeecCCCCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCC
Q 033398 1 MVQRLTYRTRHSYATKSNQHRVVKTPGGKLVYQSTKKRASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGG 80 (120)
Q Consensus 1 m~~R~t~rrr~~Y~TrSnk~~~vrTPGGrlv~~y~KK~~~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG 80 (120)
|+|||||++|++|||+||++++++||||+||++|.+|.++.|+|||||..|+||+++||.+++ ++|++.|+|||||||
T Consensus 1 mvqrlty~rrlsYnT~SNk~r~vrTPg~~lv~q~~kK~~~~pkc~~c~~~l~Gi~~~RPk~~~--rlsk~~KtVsRayGG 78 (121)
T KOG1790|consen 1 MVQRLTYRRRLSYNTRSNKTRLVRTPGGRLVYQYVKKKAKLPKCGDCGMRLQGIPALRPKELM--RLSKSHKTVSRAYGG 78 (121)
T ss_pred CchhHHhHhhcccccccCccccccCCCceehhHhhHhhccCCCCCcCCcccCCCCCcCHHHHH--HHhhhHHHhhhhccc
Confidence 999999999999999999999999999999999999999999999999999999999999999 999999999999999
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033398 81 VLSGGAVRERIIRAFLVEEQKIVKKVLKIQKAKEKL 116 (120)
Q Consensus 81 ~lC~kcVr~rIvrAFL~EEqkivk~v~~~~~~~~~~ 116 (120)
++|++||+|||++||||||||||+++++++...++.
T Consensus 79 ~~ca~~vrerI~rAFLi~EQkIV~k~~~~~~~~~~~ 114 (121)
T KOG1790|consen 79 VLCAKCVRERIIRAFLIEEQKIVKKVLKAQEALKEL 114 (121)
T ss_pred cchHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999998766553
No 3
>PLN03166 60S ribosomal protein L34; Provisional
Probab=100.00 E-value=5.9e-53 Score=300.36 Aligned_cols=96 Identities=97% Similarity=1.430 Sum_probs=94.4
Q ss_pred CccceeccCCCCCCCCCceeEEeecCCCceEEEeeecCCCCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCC
Q 033398 1 MVQRLTYRTRHSYATKSNQHRVVKTPGGKLVYQSTKKRASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGG 80 (120)
Q Consensus 1 m~~R~t~rrr~~Y~TrSnk~~~vrTPGGrlv~~y~KK~~~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG 80 (120)
|+||||||||++|||+||+++++|||||+||+||++|++++|+|||||.+|+||+++||.|+++.+|||++|+|||||||
T Consensus 1 m~~r~t~rrr~~YnT~Snk~r~vkTPGGrlv~~y~kK~~~~pkC~~cg~~L~Gi~~~Rp~~~~~~~lsK~~K~vsRaYGG 80 (96)
T PLN03166 1 MVQRLTYRKRHSYATKSNQHRVVKTPGGKLVYQTTKKRASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGG 80 (96)
T ss_pred CCcceEEeeccCccCcCCeeEEEECCCCcEEEEEeccCCCCCcCCCCCCccCCccCCChhhhhhhhcccCcCccccCcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999766899999999999999
Q ss_pred cchHHHHHHHHHHHHH
Q 033398 81 VLSGGAVRERIIRAFL 96 (120)
Q Consensus 81 ~lC~kcVr~rIvrAFL 96 (120)
++||+||+|+|++|||
T Consensus 81 ~lc~~cvr~rIvrAFL 96 (96)
T PLN03166 81 VLSGSAVRERIIRAFL 96 (96)
T ss_pred cccHHHHHHHHHHHhC
Confidence 9999999999999998
No 4
>PF01199 Ribosomal_L34e: Ribosomal protein L34e; InterPro: IPR008195 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaebacterial ribosomal proteins belong to the L34e family. These include, vertebrate L34, mosquito L31 [], plant L34 [], yeast putative ribosomal protein YIL052c and archaebacterial L34e.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_i 3IZS_i 4A19_L 4A1D_L 4A18_L 4A1B_L.
Probab=100.00 E-value=5.9e-52 Score=294.20 Aligned_cols=94 Identities=60% Similarity=0.980 Sum_probs=78.7
Q ss_pred CccceeccCCCCCCCCCceeEEeecCCCceEEEeeecCCCCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCC
Q 033398 1 MVQRLTYRTRHSYATKSNQHRVVKTPGGKLVYQSTKKRASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGG 80 (120)
Q Consensus 1 m~~R~t~rrr~~Y~TrSnk~~~vrTPGGrlv~~y~KK~~~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG 80 (120)
||||||||+|++|||+||+++++|||||+|||||++|+++.|+|||||.+|+||+++||.|++ +|+|++++|||||||
T Consensus 1 M~~rvt~rrr~~Y~TrSnk~~~vrTPGGrlv~~y~kK~~~~pkC~~cg~~L~Gi~~~rp~~~~--rl~k~~k~vsRaYGG 78 (94)
T PF01199_consen 1 MVQRVTYRRRPSYNTRSNKRRYVRTPGGRLVYHYIKKKPKKPKCGDCGKPLNGIPALRPVELR--RLSKRQKTVSRAYGG 78 (94)
T ss_dssp -HHHHHHHHSS-STTCSGSSEEEE-SSSEEEEEE-S--TT--BSTSSS-BSSSS-SS-SSTTG--TS-CHCH--CCTSSS
T ss_pred CCcceeeccCCCccCccceEEEeEcCCCcEEEEeccccCCCCCcCccCCcccccccccHHHHh--hcccCCCCCCCCCCc
Confidence 999999999999999999999999999999999999999999999999999999999999999 999999999999999
Q ss_pred cchHHHHHHHHHHHHH
Q 033398 81 VLSGGAVRERIIRAFL 96 (120)
Q Consensus 81 ~lC~kcVr~rIvrAFL 96 (120)
++||+||+|+|++|||
T Consensus 79 ~lc~~cvr~rI~rAFL 94 (94)
T PF01199_consen 79 SLCHKCVRERIKRAFL 94 (94)
T ss_dssp S-HHHHHHHHHHHHHH
T ss_pred cchHHHHHHHHHHHhC
Confidence 9999999999999998
No 5
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.3e-45 Score=257.88 Aligned_cols=92 Identities=49% Similarity=0.868 Sum_probs=90.7
Q ss_pred CCCCCCCCCceeEEeecCCCceEEEeeecCCCCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHHH
Q 033398 9 TRHSYATKSNQHRVVKTPGGKLVYQSTKKRASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAVR 88 (120)
Q Consensus 9 rr~~Y~TrSnk~~~vrTPGGrlv~~y~KK~~~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcVr 88 (120)
.+++|+|+||++++||||||++|+||++|+++.|+|++||.+|+||+++||.|+. ++|+++|+|+|||||++|++||+
T Consensus 2 ~rp~YrSRS~rr~~vkTPgGr~v~h~~kK~~~~p~C~~cg~pL~Gi~r~RP~e~~--r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 2 PRPAYRSRSNRRRYVKTPGGRTVIHYEKKKPTIPKCAICGRPLGGIPRGRPREFR--RLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred CCcccccccceeEEEECCCCcEEEeeeeccCCCCcccccCCccCCccCCCcHHHH--hccccccCcCCCcCceecHHHHH
Confidence 5899999999999999999999999999999999999999999999999999999 99999999999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q 033398 89 ERIIRAFLVEEQKI 102 (120)
Q Consensus 89 ~rIvrAFL~EEqki 102 (120)
++|++|||+|||+|
T Consensus 80 ~~i~~a~r~~~~ki 93 (93)
T COG2174 80 ERIKRAFRIEEQKI 93 (93)
T ss_pred HHHHHHHHHHHhcC
Confidence 99999999999986
No 6
>PRK04059 rpl34e 50S ribosomal protein L34e; Validated
Probab=100.00 E-value=3.8e-42 Score=241.80 Aligned_cols=83 Identities=31% Similarity=0.622 Sum_probs=81.5
Q ss_pred CCCCCCCCceeEEeecCCCceEEEeeecCCCCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHHHH
Q 033398 10 RHSYATKSNQHRVVKTPGGKLVYQSTKKRASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAVRE 89 (120)
Q Consensus 10 r~~Y~TrSnk~~~vrTPGGrlv~~y~KK~~~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcVr~ 89 (120)
++.|||+||++++||||||+|||||++|+++.|+|||||.+|+||+++||.|++ +|||++|+|||||||++||+||+|
T Consensus 3 ~p~YnT~Snk~r~vrTPGGrlv~~y~kK~~~~pkC~~c~~~L~Gi~~~Rp~~~~--rlsK~~K~vsRaYGG~lc~~cvr~ 80 (88)
T PRK04059 3 APRYRSRSLRRVYVRTPGGRTVIHYERKKPSKAKCAICGKPLNGVPRGRPVEIR--KLGKTEKRPERPYGGYLCPKCLKR 80 (88)
T ss_pred CccccccCCceEEEECCCCCEEEEEeccCCCCCcCCCCCCccCCccCcchHHHH--hcccccCCcccCcCceecHHHHHH
Confidence 689999999999999999999999999999999999999999999999999999 999999999999999999999999
Q ss_pred HHHHH
Q 033398 90 RIIRA 94 (120)
Q Consensus 90 rIvrA 94 (120)
+|+.+
T Consensus 81 rI~~~ 85 (88)
T PRK04059 81 LIKAK 85 (88)
T ss_pred HHHHH
Confidence 99876
No 7
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=64.25 E-value=2.9 Score=33.53 Aligned_cols=30 Identities=17% Similarity=0.284 Sum_probs=23.7
Q ss_pred CCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHH
Q 033398 40 SGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAV 87 (120)
Q Consensus 40 ~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcV 87 (120)
.-..|+.||.+++= -.+++.+||.+|+.|.
T Consensus 153 ~l~~Ca~cg~~~~~------------------~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 153 NLTSCARCGTPVDP------------------VYFSPKSGGFLCSKCA 182 (251)
T ss_pred chHHHhCcCCcCCC------------------cceeeccCcccchhcc
Confidence 34569999987553 2678999999999996
No 8
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=61.43 E-value=2.9 Score=37.66 Aligned_cols=36 Identities=22% Similarity=0.329 Sum_probs=27.8
Q ss_pred CCCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHHHH
Q 033398 39 ASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAVRE 89 (120)
Q Consensus 39 ~~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcVr~ 89 (120)
.+++-|++|+.+.. |.+ .++-.|--|+++|+.|.+.
T Consensus 178 s~V~~CP~Ca~~F~-l~r--------------RrHHCRLCG~VmC~~C~k~ 213 (505)
T KOG1842|consen 178 SSVQFCPECANSFG-LTR--------------RRHHCRLCGRVMCRDCSKF 213 (505)
T ss_pred Ccccccccccchhh-hHH--------------HhhhhhhcchHHHHHHHHh
Confidence 56778999988753 221 2678899999999999974
No 9
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=58.19 E-value=3.7 Score=31.77 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHH
Q 033398 40 SGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAV 87 (120)
Q Consensus 40 ~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcV 87 (120)
....|+.||.++.. -..+-..||.+|..|-
T Consensus 148 ~l~~C~~Cg~~~~~------------------~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 148 DLDHCAVCGAPGDH------------------RYFSPKEGGAVCSECG 177 (247)
T ss_pred chhhHhcCCCCCCc------------------eEEecccCCccccccc
Confidence 33469999998761 1356678999999995
No 10
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=57.55 E-value=9 Score=24.19 Aligned_cols=30 Identities=20% Similarity=0.422 Sum_probs=20.0
Q ss_pred CCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHHHHH
Q 033398 43 KCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAVRER 90 (120)
Q Consensus 43 kC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcVr~r 90 (120)
+|+.||..+.=+.. ...=.|++|..|....
T Consensus 1 ~C~iCg~kigl~~~------------------~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKR------------------FKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccc------------------eeccCccchHHHHHHh
Confidence 49999988654322 1112479999999875
No 11
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=50.98 E-value=3.3 Score=38.50 Aligned_cols=34 Identities=18% Similarity=0.376 Sum_probs=25.9
Q ss_pred CCCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHH
Q 033398 39 ASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAV 87 (120)
Q Consensus 39 ~~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcV 87 (120)
...+.|-.|..+++.+.+ ++-.|--||.+|++|-
T Consensus 899 ~~a~~cmacq~pf~afrr---------------rhhcrncggifcg~cs 932 (990)
T KOG1819|consen 899 EDAEQCMACQMPFNAFRR---------------RHHCRNCGGIFCGKCS 932 (990)
T ss_pred CcchhhhhccCcHHHHHH---------------hhhhcccCceeecccc
Confidence 346678888877765443 5778999999999995
No 12
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=45.39 E-value=21 Score=23.37 Aligned_cols=37 Identities=24% Similarity=0.454 Sum_probs=26.5
Q ss_pred EeeecCCCCCC-CCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHHHHH
Q 033398 33 QSTKKRASGPK-CPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAVRER 90 (120)
Q Consensus 33 ~y~KK~~~~pk-C~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcVr~r 90 (120)
-+.++-+++.+ |..||.+ .-+-|.||=.+|--|.||.
T Consensus 7 shpr~yGkGsr~C~vCg~~---------------------~gliRkygL~~CRqCFRe~ 44 (54)
T PTZ00218 7 THPRTYGKGSRQCRVCSNR---------------------HGLIRKYGLNVCRQCFREN 44 (54)
T ss_pred CCCCcCCCCCCeeecCCCc---------------------chhhhhcCcchhhHHHHHh
Confidence 34455566544 8889874 2355789999999999985
No 13
>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=42.62 E-value=16 Score=25.94 Aligned_cols=37 Identities=22% Similarity=0.299 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHHHHHHHHHH
Q 033398 38 RASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAVRERIIRAF 95 (120)
Q Consensus 38 ~~~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcVr~rIvrAF 95 (120)
.+.-..|+|||.+= | . =++=.||-.+|..|- .|-|.|
T Consensus 10 ~~~N~~CaDCg~~~-------p-~-----------w~s~~~GiflC~~Ca--g~HR~l 46 (116)
T PF01412_consen 10 KPGNKVCADCGAPN-------P-T-----------WASLNYGIFLCLECA--GIHRSL 46 (116)
T ss_dssp STTCTB-TTT-SBS---------------------EEETTTTEEE-HHHH--HHHHHH
T ss_pred CcCcCcCCCCCCCC-------C-C-----------EEEeecChhhhHHHH--HHHHHh
Confidence 45556799998442 1 1 334459999999997 344443
No 14
>KOG3815 consensus Transcription factor Doublesex [Transcription]
Probab=40.02 E-value=48 Score=27.63 Aligned_cols=39 Identities=23% Similarity=0.342 Sum_probs=25.6
Q ss_pred ecCCCCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHH
Q 033398 36 KKRASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAV 87 (120)
Q Consensus 36 KK~~~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcV 87 (120)
++....|+|+.| ..+|+.. .|+=. .-+=.|..+-|++|.
T Consensus 31 ~~~~r~p~CaRC--rnHG~~~---------~LKGH--k~~C~~~~C~C~kC~ 69 (322)
T KOG3815|consen 31 APSARGPKCARC--ENHGVLS---------RLKGH--KRSCPYRDCPCEKCG 69 (322)
T ss_pred ccccccchhhhh--hccCcce---------eccCC--CCCCCCCCCCchHhc
Confidence 355677899999 4567553 22111 123469999999997
No 15
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=39.96 E-value=14 Score=32.71 Aligned_cols=12 Identities=42% Similarity=0.960 Sum_probs=8.6
Q ss_pred CCCCCCCCCCCC
Q 033398 40 SGPKCPVTGKRI 51 (120)
Q Consensus 40 ~~pkC~~cg~~L 51 (120)
..|+|+.||..+
T Consensus 349 ~~p~Cp~Cg~~m 360 (421)
T COG1571 349 VNPVCPRCGGRM 360 (421)
T ss_pred cCCCCCccCCch
Confidence 457888888764
No 16
>PRK00420 hypothetical protein; Validated
Probab=38.25 E-value=15 Score=26.91 Aligned_cols=14 Identities=29% Similarity=0.648 Sum_probs=11.0
Q ss_pred CCCCCCCCCCCCcc
Q 033398 42 PKCPVTGKRIQGIP 55 (120)
Q Consensus 42 pkC~~cg~~L~GI~ 55 (120)
..|+.||.+|-+..
T Consensus 24 ~~CP~Cg~pLf~lk 37 (112)
T PRK00420 24 KHCPVCGLPLFELK 37 (112)
T ss_pred CCCCCCCCcceecC
Confidence 56999999887654
No 17
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=34.58 E-value=24 Score=27.12 Aligned_cols=33 Identities=24% Similarity=0.392 Sum_probs=21.4
Q ss_pred CCCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHHHH
Q 033398 39 ASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAVRE 89 (120)
Q Consensus 39 ~~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcVr~ 89 (120)
+....|+.||. ..+.. ..+=..||.+|..|-..
T Consensus 145 p~l~~C~~cg~-~~~~~-----------------~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 145 LDLDKCAVCGS-KEDLI-----------------YFSMTYGGALCRQCGEK 177 (241)
T ss_pred cccCccCCCCC-cCCCc-----------------eEchhcCeEEChhhCcc
Confidence 34456999997 44311 23345799999999754
No 18
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=34.55 E-value=34 Score=26.71 Aligned_cols=14 Identities=21% Similarity=0.610 Sum_probs=11.3
Q ss_pred CCCCCCCCCCCCCc
Q 033398 41 GPKCPVTGKRIQGI 54 (120)
Q Consensus 41 ~pkC~~cg~~L~GI 54 (120)
.-.|+.|+.+|.|-
T Consensus 20 ~G~CaiC~~~l~~~ 33 (157)
T PHA02565 20 NGICPLCKRELDGD 33 (157)
T ss_pred CCcCCCCCCccCCC
Confidence 45799999998873
No 19
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=33.24 E-value=6.1 Score=33.58 Aligned_cols=36 Identities=22% Similarity=0.228 Sum_probs=25.4
Q ss_pred EEeeecCCCCCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHH
Q 033398 32 YQSTKKRASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGA 86 (120)
Q Consensus 32 ~~y~KK~~~~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kc 86 (120)
..+++....--+|+|||.+- |. =+|=.||=+||-.|
T Consensus 11 l~~l~~~~~Nk~CaDCga~~---P~----------------W~S~nlGvfiCi~C 46 (319)
T COG5347 11 LKLLKSDSSNKKCADCGAPN---PT----------------WASVNLGVFLCIDC 46 (319)
T ss_pred HHHHhhccccCccccCCCCC---Cc----------------eEecccCeEEEeec
Confidence 34456667777899999875 21 23456899999888
No 20
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=33.13 E-value=60 Score=21.51 Aligned_cols=34 Identities=24% Similarity=0.340 Sum_probs=25.9
Q ss_pred ceeEEeecCC-CceEEEeeecCCCCCCCCCCCCCCC
Q 033398 18 NQHRVVKTPG-GKLVYQSTKKRASGPKCPVTGKRIQ 52 (120)
Q Consensus 18 nk~~~vrTPG-Grlv~~y~KK~~~~pkC~~cg~~L~ 52 (120)
.....|+=|| +...+.| -.-.+...|..||..|.
T Consensus 7 S~F~~VkCp~C~n~q~vF-sha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 7 SRFLKVKCPDCGNEQVVF-SHASTVVRCLVCGKTLA 41 (59)
T ss_pred CeEEEEECCCCCCeEEEE-ecCCcEEECcccCCCcc
Confidence 3567788898 7777777 45667777999998873
No 21
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.99 E-value=26 Score=24.64 Aligned_cols=34 Identities=35% Similarity=0.621 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCccCCChhh-hhhhccccCCCccccccC
Q 033398 43 KCPVTGKRIQGIPHLRPAE-YKRSRLSRNRRTVNRAYG 79 (120)
Q Consensus 43 kC~~cg~~L~GI~~~Rp~~-~~~~rlsK~~ktvsRaYG 79 (120)
.|++||..|---| .||.. +. +.+-+-++|-|+-|
T Consensus 43 ~CPnCGGelv~RP-~RPaa~L~--r~PASt~Rv~r~~G 77 (84)
T COG3813 43 LCPNCGGELVARP-IRPAAKLA--RYPASTRRVLRPEG 77 (84)
T ss_pred cCCCCCchhhcCc-CChHHHHh--hCchhhhheecccC
Confidence 4888888776544 45544 56 77777888888876
No 22
>COG2906 Bfd Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]
Probab=32.88 E-value=47 Score=22.33 Aligned_cols=19 Identities=37% Similarity=0.462 Sum_probs=15.4
Q ss_pred CcchHHHHHHHHHHHHHHHHH
Q 033398 80 GVLSGGAVRERIIRAFLVEEQ 100 (120)
Q Consensus 80 G~lC~kcVr~rIvrAFL~EEq 100 (120)
|+-|++|++. -+.||.|+-
T Consensus 35 Gs~CGkC~~~--Arevl~e~~ 53 (63)
T COG2906 35 GSQCGKCVRA--AREVLEEAL 53 (63)
T ss_pred ccchHHHHHH--HHHHHHHHH
Confidence 8999999975 678887764
No 23
>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=32.72 E-value=29 Score=24.50 Aligned_cols=27 Identities=22% Similarity=0.171 Sum_probs=18.4
Q ss_pred CCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHH
Q 033398 42 PKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAV 87 (120)
Q Consensus 42 pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcV 87 (120)
-.|+|||.+- | .-++=.||=.+|..|-
T Consensus 4 ~~CaDC~~~~-------p------------~w~s~~~GifvC~~Cs 30 (112)
T smart00105 4 KKCFDCGAPN-------P------------TWASVNLGVFLCIECS 30 (112)
T ss_pred CcccCCCCCC-------C------------CcEEeccceeEhHHhH
Confidence 3599999742 1 1344568888988884
No 24
>PF11022 DUF2611: Protein of unknown function (DUF2611); InterPro: IPR021278 This family is conserved in the Dikarya of Fungi. The function is not known.
Probab=31.28 E-value=54 Score=22.34 Aligned_cols=18 Identities=39% Similarity=0.636 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 033398 98 EEQKIVKKVLKIQKAKEK 115 (120)
Q Consensus 98 EEqkivk~v~~~~~~~~~ 115 (120)
||.+.|++.|++.+++++
T Consensus 52 DeE~fIk~fl~~~~~e~~ 69 (71)
T PF11022_consen 52 DEEKFIKEFLKEHEKEEK 69 (71)
T ss_pred HHHHHHHHHHHHHHHhhh
Confidence 888899999988877544
No 25
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=28.05 E-value=33 Score=22.56 Aligned_cols=11 Identities=55% Similarity=1.050 Sum_probs=8.7
Q ss_pred CCCCCCCCCCC
Q 033398 42 PKCPVTGKRIQ 52 (120)
Q Consensus 42 pkC~~cg~~L~ 52 (120)
-+|..||.+++
T Consensus 4 kHC~~CG~~Ip 14 (59)
T PF09889_consen 4 KHCPVCGKPIP 14 (59)
T ss_pred CcCCcCCCcCC
Confidence 35999998865
No 27
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=27.69 E-value=22 Score=21.31 Aligned_cols=14 Identities=14% Similarity=0.285 Sum_probs=11.1
Q ss_pred CCCCCCCCCCCCCc
Q 033398 41 GPKCPVTGKRIQGI 54 (120)
Q Consensus 41 ~pkC~~cg~~L~GI 54 (120)
...|++||..|.+-
T Consensus 5 ~l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 5 LLRCGHCGSKMTRR 18 (58)
T ss_pred cEEcccCCcEeEEE
Confidence 34699999998873
No 28
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=26.65 E-value=31 Score=18.60 Aligned_cols=10 Identities=30% Similarity=0.806 Sum_probs=6.6
Q ss_pred CCCCCCCCCC
Q 033398 42 PKCPVTGKRI 51 (120)
Q Consensus 42 pkC~~cg~~L 51 (120)
.-|+.||.+|
T Consensus 17 ~fC~~CG~~L 26 (26)
T PF13248_consen 17 KFCPNCGAKL 26 (26)
T ss_pred ccChhhCCCC
Confidence 3477777765
No 29
>PF02865 STAT_int: STAT protein, protein interaction domain; InterPro: IPR013799 The STAT protein (Signal Transducers and Activators of Transcription) family contains transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors, hence they act as signal transducers in the cytoplasm and transcription activators in the nucleus []. Binding of these factors to cell-surface receptors leads to receptor autophosphorylation at a tyrosine, the phosphotyrosine being recognised by the STAT SH2 domain, which mediates the recruitment of STAT proteins from the cytosol and their association with the activated receptor. The STAT proteins are then activated by phosphorylation via members of the JAK family of protein kinases, causing them to dimerise and translocated to the nucleus, where they bind to specific promoter sequences in target genes. In mammals, STATs comprise a family of seven structurally and functionally related proteins: Stat1, Stat2, Stat3, Stat4, Stat5a and Stat5b, Stat6. STAT proteins play a critical role in regulating innate and acquired host immune responses. Dysregulation of at least two STAT signalling cascades (i.e. Stat3 and Stat5) is associated with cellular transformation. Signalling through the JAK/STAT pathway is initiated when a cytokine binds to its corresponding receptor. This leads to conformational changes in the cytoplasmic portion of the receptor, initiating activation of receptor associated members of the JAK family of kinases. The JAKs, in turn, mediate phosphorylation at the specific receptor tyrosine residues, which then serve as docking sites for STATs and other signalling molecules. Once recruited to the receptor, STATs also become phosphorylated by JAKs, on a single tyrosine residue. Activated STATs dissociate from the receptor, dimerise, translocate to the nucleus and bind to members of the GAS (gamma activated site) family of enhancers. The seven STAT proteins identified in mammals range in size from 750 and 850 amino acids. The chromosomal distribution of these STATs, as well as the identification of STATs in more primitive eukaryotes, suggest that this family arose from a single primordial gene. STATs share structurally and functionally conserved domains including: an N-terminal domain that strengthens interactions between STAT dimers on adjacent DNA-binding sites; a coiled-coil STAT domain that is implicated in protein-protein interactions; a DNA-binding domain with an immunoglobulin-like fold similar to p53 tumour suppressor protein; an EF-hand-like linker domain connecting the DNA-binding and SH2 domains; an SH2 domain (IPR000980 from INTERPRO) that acts as a phosphorylation-dependent switch to control receptor recognition and DNA-binding; and a C-terminal transactivation domain []. The crystal structure of the N terminus of Stat4 reveals a dimer. The interface of this dimer is formed by a ring-shaped element consisting of five short helices. Several studies suggest that this N-terminal dimerisation promotes cooperativity of binding to tandem GAS elements and with the transcriptional coactivator CBP/p300. This entry represents the N-terminal domain, which is responsible for protein interactions. This domain has a multi-helical structure that can be subdivided into two structural sub-domains.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0004871 signal transducer activity, 0006355 regulation of transcription, DNA-dependent, 0007165 signal transduction; PDB: 1BGF_A 1YVL_A.
Probab=24.48 E-value=71 Score=23.41 Aligned_cols=17 Identities=53% Similarity=0.790 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHH
Q 033398 89 ERIIRAFLVEEQKIVKK 105 (120)
Q Consensus 89 ~rIvrAFL~EEqkivk~ 105 (120)
-+||+-.|-+|++||..
T Consensus 105 ~~~I~~~L~~E~~iv~~ 121 (124)
T PF02865_consen 105 ARIIRNCLQEEKRIVQE 121 (124)
T ss_dssp HHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 36899999999999853
No 30
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=24.03 E-value=53 Score=19.58 Aligned_cols=32 Identities=13% Similarity=0.372 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHHHH
Q 033398 42 PKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAVRE 89 (120)
Q Consensus 42 pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcVr~ 89 (120)
..|.-||++-.-+.. =++-+-|+++|..||..
T Consensus 2 ~~CSFCgr~~~~v~~----------------li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGR----------------LISGPNGAYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSS----------------EEEES-SEEEEHHHHHH
T ss_pred CCccCCCCCHHHHhc----------------eecCCCCcEECHHHHHH
Confidence 357778876554332 35667779999999875
No 31
>PRK08061 rpsN 30S ribosomal protein S14; Reviewed
Probab=24.03 E-value=58 Score=21.58 Aligned_cols=19 Identities=32% Similarity=0.420 Sum_probs=15.1
Q ss_pred CccccccCCcchHHHHHHHHH
Q 033398 72 RTVNRAYGGVLSGGAVRERII 92 (120)
Q Consensus 72 ktvsRaYGG~lC~kcVr~rIv 92 (120)
+-+-|.|| ||--|.+|...
T Consensus 31 rgvir~fg--l~R~~FRe~A~ 49 (61)
T PRK08061 31 HSVYRKFG--LCRICFRELAY 49 (61)
T ss_pred cceeccCC--ccHHHHHHHHH
Confidence 46778898 99999988654
No 32
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=23.74 E-value=44 Score=20.78 Aligned_cols=15 Identities=20% Similarity=0.481 Sum_probs=11.9
Q ss_pred ccCCcchHHHHHHHH
Q 033398 77 AYGGVLSGGAVRERI 91 (120)
Q Consensus 77 aYGG~lC~kcVr~rI 91 (120)
.||-.+|..|-++.+
T Consensus 15 I~~~fIC~~CE~~iv 29 (46)
T PF10764_consen 15 IYGKFICSDCEKEIV 29 (46)
T ss_pred EECeEehHHHHHHhc
Confidence 588999999977643
No 33
>PLN00209 ribosomal protein S27; Provisional
Probab=23.08 E-value=93 Score=22.11 Aligned_cols=37 Identities=11% Similarity=0.031 Sum_probs=27.5
Q ss_pred CCCCceeEEeecCC-CceEEEeeecCCCCCCCCCCCCCC
Q 033398 14 ATKSNQHRVVKTPG-GKLVYQSTKKRASGPKCPVTGKRI 51 (120)
Q Consensus 14 ~TrSnk~~~vrTPG-Grlv~~y~KK~~~~pkC~~cg~~L 51 (120)
....-....|+=|| +.+.+.| -.-.+...|..||..|
T Consensus 28 ~~PnS~Fm~VkCp~C~n~q~VF-ShA~t~V~C~~Cg~~L 65 (86)
T PLN00209 28 QSPNSFFMDVKCQGCFNITTVF-SHSQTVVVCGSCQTVL 65 (86)
T ss_pred cCCCCEEEEEECCCCCCeeEEE-ecCceEEEccccCCEe
Confidence 34445677888899 7787777 4456667799999877
No 34
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=22.66 E-value=38 Score=19.97 Aligned_cols=16 Identities=25% Similarity=0.497 Sum_probs=12.5
Q ss_pred CCCCCCCCCCCCccCC
Q 033398 42 PKCPVTGKRIQGIPHL 57 (120)
Q Consensus 42 pkC~~cg~~L~GI~~~ 57 (120)
..|++||..|..|...
T Consensus 3 ~~C~~Cg~~l~~ig~~ 18 (47)
T PF13005_consen 3 RACPDCGGELKEIGEE 18 (47)
T ss_pred CcCCCCCceeeECCce
Confidence 3599999999876653
No 35
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=22.30 E-value=95 Score=22.02 Aligned_cols=37 Identities=14% Similarity=0.159 Sum_probs=27.4
Q ss_pred CCCCceeEEeecCC-CceEEEeeecCCCCCCCCCCCCCC
Q 033398 14 ATKSNQHRVVKTPG-GKLVYQSTKKRASGPKCPVTGKRI 51 (120)
Q Consensus 14 ~TrSnk~~~vrTPG-Grlv~~y~KK~~~~pkC~~cg~~L 51 (120)
....-....|+=|| +.+.+.| -.-.++..|..||..|
T Consensus 27 ~~PnS~Fm~VkCp~C~n~q~VF-ShA~t~V~C~~Cg~~L 64 (85)
T PTZ00083 27 QGPNSYFMDVKCPGCSQITTVF-SHAQTVVLCGGCSSQL 64 (85)
T ss_pred cCCCCeEEEEECCCCCCeeEEE-ecCceEEEccccCCEe
Confidence 34445677888899 7787777 4456667799999877
No 36
>PF05340 DUF740: Protein of unknown function (DUF740); InterPro: IPR008004 This family consists of several uncharacterised plant chloroplastic proteins of unknown function.
Probab=21.37 E-value=82 Score=29.38 Aligned_cols=27 Identities=26% Similarity=0.452 Sum_probs=21.7
Q ss_pred ccccCCCccccccCCcchHHHHHHHHHH
Q 033398 66 RLSRNRRTVNRAYGGVLSGGAVRERIIR 93 (120)
Q Consensus 66 rlsK~~ktvsRaYGG~lC~kcVr~rIvr 93 (120)
..+.+.++|.-.+.| +|+.|++||+..
T Consensus 11 ~~~~C~rHP~~~~~G-vC~~CLrERL~~ 37 (603)
T PF05340_consen 11 SSSRCKRHPSQRFTG-VCPSCLRERLSG 37 (603)
T ss_pred CCCcCcCCCCCCCCe-EChHHHHHHHHh
Confidence 455788999999655 699999999853
No 37
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=21.35 E-value=67 Score=21.21 Aligned_cols=14 Identities=36% Similarity=0.710 Sum_probs=11.2
Q ss_pred CCCCCCCCCCCCCC
Q 033398 40 SGPKCPVTGKRIQG 53 (120)
Q Consensus 40 ~~pkC~~cg~~L~G 53 (120)
....|+.|+++|..
T Consensus 77 ~~~~C~vC~k~l~~ 90 (109)
T PF10367_consen 77 ESTKCSVCGKPLGN 90 (109)
T ss_pred CCCCccCcCCcCCC
Confidence 34569999999976
No 38
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=20.76 E-value=76 Score=27.53 Aligned_cols=30 Identities=13% Similarity=0.251 Sum_probs=21.9
Q ss_pred CCCCCCCCCCCCCccCCChhhhhhhccccCCCccccccCCcchHHHH
Q 033398 41 GPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGGAV 87 (120)
Q Consensus 41 ~pkC~~cg~~L~GI~~~Rp~~~~~~rlsK~~ktvsRaYGG~lC~kcV 87 (120)
..+|.-||++-+.+.. -++.+ |.++|..|+
T Consensus 9 ~~~CSFCGr~~~ev~~----------------li~g~-~~~IC~~Ci 38 (412)
T PRK05342 9 LLYCSFCGKSQHEVRK----------------LIAGP-GVYICDECI 38 (412)
T ss_pred ccccCCCCCChhhccc----------------cccCC-CCcccchHH
Confidence 4479999998766554 23444 678999997
No 39
>PF11314 DUF3117: Protein of unknown function (DUF3117); InterPro: IPR021465 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=20.57 E-value=72 Score=20.67 Aligned_cols=20 Identities=40% Similarity=0.685 Sum_probs=15.0
Q ss_pred CCCceeEEeecC---CCceEEEe
Q 033398 15 TKSNQHRVVKTP---GGKLVYQS 34 (120)
Q Consensus 15 TrSnk~~~vrTP---GGrlv~~y 34 (120)
|+.++-.+.|.| |||||+-.
T Consensus 13 ~kEgR~ivmRvPleGGGRLVvEl 35 (51)
T PF11314_consen 13 TKEGRGIVMRVPLEGGGRLVVEL 35 (51)
T ss_pred eecCceEEEEEecCCCcEEEEEe
Confidence 456777788877 79999864
No 40
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.32 E-value=86 Score=29.67 Aligned_cols=26 Identities=23% Similarity=0.333 Sum_probs=19.9
Q ss_pred CCceEEEeeecCCCCCC--CCCCCCCCC
Q 033398 27 GGKLVYQSTKKRASGPK--CPVTGKRIQ 52 (120)
Q Consensus 27 GGrlv~~y~KK~~~~pk--C~~cg~~L~ 52 (120)
.|.=++.|..+++-.|- |.+||-.+.
T Consensus 419 ~geQ~llflnRRGys~~l~C~~Cg~v~~ 446 (730)
T COG1198 419 RGEQVLLFLNRRGYAPLLLCRDCGYIAE 446 (730)
T ss_pred cCCeEEEEEccCCccceeecccCCCccc
Confidence 36678888888888876 888886544
No 41
>PF13085 Fer2_3: 2Fe-2S iron-sulfur cluster binding domain; PDB: 3P4Q_N 1KFY_N 3CIR_N 3P4R_B 2B76_N 1KF6_B 3P4P_N 3P4S_B 1L0V_B 1ZOY_B ....
Probab=20.22 E-value=23 Score=25.63 Aligned_cols=16 Identities=31% Similarity=0.542 Sum_probs=13.6
Q ss_pred CCCCCCCCCCCCCccC
Q 033398 41 GPKCPVTGKRIQGIPH 56 (120)
Q Consensus 41 ~pkC~~cg~~L~GI~~ 56 (120)
...||.|+..+||.+.
T Consensus 54 ~giCGsCam~ING~~~ 69 (110)
T PF13085_consen 54 SGICGSCAMRINGRPR 69 (110)
T ss_dssp SSSSSTTEEEETTEEE
T ss_pred CCCCCCCEEEECCcee
Confidence 3569999999999885
Done!