Query 043997
Match_columns 222
No_of_seqs 152 out of 946
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 10:26:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043997.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043997hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14244 UBN2_3: gag-polypepti 99.9 1.1E-21 2.3E-26 151.6 10.9 111 8-127 6-117 (152)
2 PF14223 UBN2: gag-polypeptide 99.7 7.9E-17 1.7E-21 119.3 9.4 86 90-175 1-109 (119)
3 PF14227 UBN2_2: gag-polypepti 99.5 5.1E-14 1.1E-18 104.2 9.1 84 89-175 1-107 (119)
4 PF13961 DUF4219: Domain of un 99.2 1.9E-11 4.1E-16 66.2 2.2 26 15-40 1-27 (27)
5 PF00098 zf-CCHC: Zinc knuckle 98.3 2.7E-07 5.9E-12 44.9 1.6 17 198-214 1-18 (18)
6 PF13696 zf-CCHC_2: Zinc knuck 97.2 0.00015 3.2E-09 40.3 0.8 18 198-215 9-27 (32)
7 PF14787 zf-CCHC_5: GAG-polypr 96.4 0.0018 3.8E-08 36.8 1.3 24 198-221 3-27 (36)
8 smart00343 ZnF_C2HC zinc finge 96.0 0.0036 7.7E-08 33.2 1.1 17 199-215 1-18 (26)
9 PF13917 zf-CCHC_3: Zinc knuck 95.3 0.0096 2.1E-07 35.4 1.3 18 196-213 3-21 (42)
10 PF15288 zf-CCHC_6: Zinc knuck 95.2 0.0097 2.1E-07 34.8 1.2 19 197-215 1-22 (40)
11 PF14392 zf-CCHC_4: Zinc knuck 94.6 0.014 3E-07 36.0 0.7 18 197-214 31-49 (49)
12 PF03564 DUF1759: Protein of u 94.3 0.28 6.2E-06 36.9 7.6 54 68-125 28-85 (145)
13 COG5082 AIR1 Arginine methyltr 94.0 0.027 5.9E-07 44.5 1.5 15 198-212 98-113 (190)
14 COG5082 AIR1 Arginine methyltr 93.6 0.031 6.8E-07 44.2 1.1 20 194-213 57-77 (190)
15 KOG4400 E3 ubiquitin ligase in 87.4 0.34 7.3E-06 40.6 1.8 18 198-215 144-162 (261)
16 PTZ00368 universal minicircle 87.4 0.29 6.3E-06 37.3 1.2 17 198-214 130-147 (148)
17 KOG2560 RNA splicing factor - 86.6 0.14 3.1E-06 45.5 -0.9 22 196-217 111-133 (529)
18 KOG0109 RNA-binding protein LA 84.8 0.4 8.7E-06 40.5 0.9 20 196-215 159-179 (346)
19 COG5222 Uncharacterized conser 83.8 0.47 1E-05 40.2 0.8 17 199-215 178-195 (427)
20 PTZ00368 universal minicircle 82.8 0.77 1.7E-05 34.9 1.7 18 199-216 79-97 (148)
21 KOG0341 DEAD-box protein abstr 79.3 0.89 1.9E-05 40.3 1.0 20 196-215 569-589 (610)
22 KOG3926 F-box proteins [Amino 76.0 8.6 0.00019 32.5 5.8 127 12-174 163-292 (332)
23 PF12353 eIF3g: Eukaryotic tra 70.8 1.8 3.9E-05 32.3 0.7 21 195-216 104-125 (128)
24 KOG0119 Splicing factor 1/bran 69.4 2.4 5.2E-05 38.4 1.2 18 198-215 286-304 (554)
25 KOG4400 E3 ubiquitin ligase in 68.2 2.5 5.5E-05 35.3 1.1 23 197-219 92-115 (261)
26 PF03732 Retrotrans_gag: Retro 67.3 14 0.00031 24.8 4.6 15 131-145 82-96 (96)
27 COG5179 TAF1 Transcription ini 67.3 4.9 0.00011 37.7 2.7 21 195-215 935-958 (968)
28 PF07904 Eaf7: Chromatin modif 65.1 9.5 0.00021 26.6 3.3 19 86-104 40-58 (91)
29 KOG2044 5'-3' exonuclease HKE1 64.8 3.6 7.8E-05 39.5 1.5 22 196-217 259-281 (931)
30 KOG0119 Splicing factor 1/bran 58.1 5.4 0.00012 36.3 1.3 20 196-215 260-280 (554)
31 KOG3794 CBF1-interacting corep 53.8 4.4 9.6E-05 35.7 0.1 21 195-215 122-145 (453)
32 TIGR03859 PQQ_PqqD coenzyme PQ 47.9 53 0.0012 22.1 4.7 29 77-105 31-59 (81)
33 KOG2673 Uncharacterized conser 46.3 9.8 0.00021 34.3 1.0 17 199-215 130-147 (485)
34 PF02764 Diphtheria_T: Diphthe 46.2 12 0.00026 28.0 1.3 25 9-33 68-93 (180)
35 PF11248 DUF3046: Protein of u 37.3 46 0.00099 21.6 2.8 38 67-104 20-58 (63)
36 smart00647 IBR In Between Ring 37.0 20 0.00044 22.3 1.2 15 198-212 49-64 (64)
37 PF06689 zf-C4_ClpX: ClpX C4-t 36.5 13 0.00029 21.7 0.3 10 198-207 2-11 (41)
38 COG1644 RPB10 DNA-directed RNA 33.5 16 0.00034 23.6 0.2 9 198-206 5-13 (63)
39 COG3167 PilO Tfp pilus assembl 33.2 1.4E+02 0.0031 23.9 5.5 62 97-167 59-122 (211)
40 PF13376 OmdA: Bacteriocin-pro 30.9 1E+02 0.0022 19.6 3.8 27 78-104 6-32 (63)
41 PF01194 RNA_pol_N: RNA polyme 30.5 26 0.00056 22.5 0.9 9 198-206 5-13 (60)
42 PLN00032 DNA-directed RNA poly 29.8 23 0.00049 23.5 0.5 9 198-206 5-13 (71)
43 PF01485 IBR: IBR domain; Int 28.4 25 0.00055 21.8 0.6 14 199-212 50-64 (64)
44 KOG3497 DNA-directed RNA polym 27.9 19 0.00041 23.0 -0.1 10 198-207 5-14 (69)
45 KOG0107 Alternative splicing f 27.2 31 0.00068 27.2 1.0 17 198-214 101-118 (195)
46 PF05402 PqqD: Coenzyme PQQ sy 26.7 1.7E+02 0.0037 18.4 5.6 35 74-108 14-48 (68)
47 PRK04016 DNA-directed RNA poly 26.2 28 0.0006 22.5 0.4 9 198-206 5-13 (62)
48 PF08354 DUF1729: Domain of un 22.3 49 0.0011 20.9 1.0 29 12-41 1-29 (57)
49 PRK07758 hypothetical protein; 22.2 44 0.00096 23.5 0.9 21 200-220 10-30 (95)
50 KOG2999 Regulator of Rac1, req 21.8 3.2E+02 0.0068 25.9 6.4 37 135-178 471-508 (713)
51 PF13427 DUF4111: Domain of un 20.8 3.2E+02 0.0069 19.4 5.7 41 114-154 36-76 (106)
52 PF02023 SCAN: SCAN domain; I 20.6 1.9E+02 0.0041 20.1 3.9 38 131-174 46-83 (95)
53 PF02671 PAH: Paired amphipath 20.3 1.2E+02 0.0025 17.8 2.4 30 144-174 1-30 (47)
54 COG1198 PriA Primosomal protei 20.3 55 0.0012 31.8 1.4 22 195-216 460-482 (730)
55 PF10122 Mu-like_Com: Mu-like 20.2 50 0.0011 20.4 0.7 25 196-220 23-49 (51)
No 1
>PF14244 UBN2_3: gag-polypeptide of LTR copia-type
Probab=99.87 E-value=1.1e-21 Score=151.62 Aligned_cols=111 Identities=31% Similarity=0.527 Sum_probs=93.8
Q ss_pred CCCCCCcccC-ChHHHHHHHHHHhhccccccccccCccCCCCCCcCchHhhhhhHHhhhhhHHHHHHHHHhchHHHHhhh
Q 043997 8 SQPAIPRFVG-HYDHWSMLMDNFMRSKEYWGLVETGYDEPASGSVLMDAHQKMTDELKLKDLKVKNYLFQAIDRTILDTI 86 (222)
Q Consensus 8 ~~~~i~~l~G-NY~~W~~~m~~~L~~~~lw~~v~~~~~~p~~~~~~t~~~~~~~~~~~~~d~~a~~~I~~sl~~~~~~~i 86 (222)
.....++|+| ||..|+..|+.+|.++++|++|+|..+.|+.+. ..+++|.+.|.++++||.++|+++++..|
T Consensus 6 ~~i~~~kL~g~NY~~W~~~~~~~L~~~~l~~~i~g~~~~P~~~~-------~~~~~W~~~d~~v~swl~~sis~~i~~~i 78 (152)
T PF14244_consen 6 QPITSIKLNGSNYLSWSQQMEMALRGKGLWGFIDGTIPKPPETD-------PAYEKWERKDQLVLSWLLNSISPDILSTI 78 (152)
T ss_pred CcccccCCCCccHHHHHHHHHHHHHhCCCcccccCccccccccc-------hhhhhHHHhhhHHHHHHHHhhcHHHHhhh
Confidence 3444689999 999999999999999999999999887775321 34566689999999999999999999999
Q ss_pred ccccchHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhhcc
Q 043997 87 RKKDTAKEIWDAMKKKFEGNARVKKSQLQALRREFETLEMK 127 (222)
Q Consensus 87 ~~~~tAke~W~~L~~~y~~~~~~~~~~l~~l~~~~~~~~m~ 127 (222)
..++||+++|++|+++|...+. .+++.+|+.+|..++..
T Consensus 79 ~~~~tak~~W~~L~~~f~~~~~--~~r~~~L~~~l~~~kq~ 117 (152)
T PF14244_consen 79 IFCETAKEIWDALKERFSQKSN--ASRVFQLRNELHSLKQG 117 (152)
T ss_pred HhhhhHHHHHHHHHHHhhcccH--HHHHHHHHHHHHHHhhC
Confidence 9999999999999999998873 24556677777777633
No 2
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=99.70 E-value=7.9e-17 Score=119.31 Aligned_cols=86 Identities=40% Similarity=0.692 Sum_probs=81.7
Q ss_pred cchHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhhcccCC-----------------------hhHHHHHHHHhhcccc
Q 043997 90 DTAKEIWDAMKKKFEGNARVKKSQLQALRREFETLEMKSGE-----------------------EDVKIVEKILRTLTEK 146 (222)
Q Consensus 90 ~tAke~W~~L~~~y~~~~~~~~~~l~~l~~~~~~~~m~~~e-----------------------~d~~~v~~lL~~Lp~~ 146 (222)
+||+++|++|++.|++.+.++.+++..|+.+|..++|.+++ +|.++|.++|++||++
T Consensus 1 ~tA~e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L~~~g~~i~d~~~v~~iL~~Lp~~ 80 (119)
T PF14223_consen 1 KTAKEAWDALKKRYEGQSKVKQARVQQLKSQLENLKMKDGESVDEYISRLKEIVDELRAIGKPISDEDLVSKILRSLPPS 80 (119)
T ss_pred ChHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhhhhhhcCCcccchhHHHHHHhcCCch
Confidence 58999999999999999998889999999999999998876 8999999999999999
Q ss_pred hhHHHHHHhhcCCCCCCCHHHHHHHHHHh
Q 043997 147 FNDIVCSIEESKDIDSLSEEAEVKEDEVK 175 (222)
Q Consensus 147 ~~~~~~~i~~~~~~~~lt~~ev~~~l~~~ 175 (222)
|++++++|...++++.+|+++++++|+.+
T Consensus 81 y~~~~~~i~~~~~~~~~t~~el~~~L~~~ 109 (119)
T PF14223_consen 81 YDTFVTAIRNSKDLPKMTLEELISRLLAE 109 (119)
T ss_pred hHHHHHHHHhcCCCCcCCHHHHHHHHHHH
Confidence 99999999999999989999999999993
No 3
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type
Probab=99.53 E-value=5.1e-14 Score=104.19 Aligned_cols=84 Identities=31% Similarity=0.406 Sum_probs=74.3
Q ss_pred ccchHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhhcccCC-----------------------hhHHHHHHHHhhccc
Q 043997 89 KDTAKEIWDAMKKKFEGNARVKKSQLQALRREFETLEMKSGE-----------------------EDVKIVEKILRTLTE 145 (222)
Q Consensus 89 ~~tAke~W~~L~~~y~~~~~~~~~~l~~l~~~~~~~~m~~~e-----------------------~d~~~v~~lL~~Lp~ 145 (222)
|+||+++|++|+..|++.+..+.. .|.++|..++|.+|. +|++++..||.+||+
T Consensus 1 ~~ta~~~W~~L~~~y~~~~~~~~~---~l~~kl~~~k~~~~~~v~~hi~~~~~l~~~L~~~g~~i~d~~~~~~lL~sLP~ 77 (119)
T PF14227_consen 1 CKTAKEMWDKLKKKYEKKSFANKI---YLLRKLYSLKMDEGGSVRDHINEFRSLVNQLKSLGVPIDDEDKVIILLSSLPP 77 (119)
T ss_pred CCCHHHHHHHHHHHHcCCCHHHHH---HHHHHHHHhHhccchhHHHHHHHHHHHHHhhccccccchHHHHHHHHHHcCCH
Confidence 689999999999999999875433 467899999998764 899999999999999
Q ss_pred chhHHHHHHhhcCCCCCCCHHHHHHHHHHh
Q 043997 146 KFNDIVCSIEESKDIDSLSEEAEVKEDEVK 175 (222)
Q Consensus 146 ~~~~~~~~i~~~~~~~~lt~~ev~~~l~~~ 175 (222)
+|++++++|.+..+...+|+++|+++|.++
T Consensus 78 sy~~~~~~l~~~~~~~~~tl~~v~~~L~~e 107 (119)
T PF14227_consen 78 SYDSFVTALLYSKPEDELTLEEVKSKLLQE 107 (119)
T ss_pred hHHHHHHHHHccCCCCCcCHHHHHHHHHHH
Confidence 999999999998766789999999999994
No 4
>PF13961 DUF4219: Domain of unknown function (DUF4219)
Probab=99.15 E-value=1.9e-11 Score=66.19 Aligned_cols=26 Identities=31% Similarity=0.920 Sum_probs=24.9
Q ss_pred ccC-ChHHHHHHHHHHhhccccccccc
Q 043997 15 FVG-HYDHWSMLMDNFMRSKEYWGLVE 40 (222)
Q Consensus 15 l~G-NY~~W~~~m~~~L~~~~lw~~v~ 40 (222)
||| ||..|+.+|+.+|++++||++|+
T Consensus 1 l~g~NY~~W~~~M~~~L~~~~lW~vVe 27 (27)
T PF13961_consen 1 LDGTNYSTWKIRMKAYLESQDLWDVVE 27 (27)
T ss_pred CCccCHHHHHHHHHHHHHHcchhhhhC
Confidence 799 99999999999999999999985
No 5
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.34 E-value=2.7e-07 Score=44.90 Aligned_cols=17 Identities=18% Similarity=0.208 Sum_probs=15.3
Q ss_pred CCCCCCCCCCccc-cccc
Q 043997 198 KGSSNCHSTWKAQ-DVSF 214 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~~ 214 (222)
+.||+||+.||++ |||.
T Consensus 1 ~~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 1 RKCFNCGEPGHIARDCPK 18 (18)
T ss_dssp SBCTTTSCSSSCGCTSSS
T ss_pred CcCcCCCCcCcccccCcc
Confidence 4699999999999 9984
No 6
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=97.17 E-value=0.00015 Score=40.32 Aligned_cols=18 Identities=11% Similarity=-0.007 Sum_probs=16.4
Q ss_pred CCCCCCCCCCccc-ccccC
Q 043997 198 KGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~~~ 215 (222)
-.|+.|++.||++ |||..
T Consensus 9 Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CEeecCCCCCccHhHCCCC
Confidence 4699999999999 99985
No 7
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=96.41 E-value=0.0018 Score=36.80 Aligned_cols=24 Identities=17% Similarity=0.234 Sum_probs=15.8
Q ss_pred CCCCCCCCCCccc-ccccCcccccC
Q 043997 198 KGSSNCHSTWKAQ-DVSFRERVDCN 221 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~~~~~~~~~ 221 (222)
..|+.|+|..|++ +|.+.-++|-|
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~d~~G~ 27 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKTDVDGN 27 (36)
T ss_dssp -C-TTTSSSCS-TTT---TCCCCCE
T ss_pred ccCcccCCCcchhhhhhhhhcccCC
Confidence 4599999999999 99999888754
No 8
>smart00343 ZnF_C2HC zinc finger.
Probab=95.95 E-value=0.0036 Score=33.18 Aligned_cols=17 Identities=18% Similarity=0.161 Sum_probs=15.0
Q ss_pred CCCCCCCCCccc-ccccC
Q 043997 199 GSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 199 ~C~~C~k~GH~~-dC~~~ 215 (222)
+|+.|++.||++ +|+..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 599999999999 99843
No 9
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=95.27 E-value=0.0096 Score=35.41 Aligned_cols=18 Identities=11% Similarity=0.200 Sum_probs=16.3
Q ss_pred cCCCCCCCCCCCccc-ccc
Q 043997 196 SRKGSSNCHSTWKAQ-DVS 213 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~ 213 (222)
.+..|.+|++.||+. .|+
T Consensus 3 ~~~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 3 ARVRCQKCGQKGHWTYECP 21 (42)
T ss_pred CCCcCcccCCCCcchhhCC
Confidence 456799999999999 999
No 10
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=95.22 E-value=0.0097 Score=34.82 Aligned_cols=19 Identities=11% Similarity=0.181 Sum_probs=15.9
Q ss_pred CCCCCCCCCCCccc---ccccC
Q 043997 197 RKGSSNCHSTWKAQ---DVSFR 215 (222)
Q Consensus 197 ~~~C~~C~k~GH~~---dC~~~ 215 (222)
+.+|.+||.+||.. .||-.
T Consensus 1 k~kC~~CG~~GH~~t~k~CP~~ 22 (40)
T PF15288_consen 1 KVKCKNCGAFGHMRTNKRCPMY 22 (40)
T ss_pred CccccccccccccccCccCCCC
Confidence 46899999999998 67654
No 11
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=94.60 E-value=0.014 Score=36.00 Aligned_cols=18 Identities=6% Similarity=0.054 Sum_probs=15.5
Q ss_pred CCCCCCCCCCCccc-cccc
Q 043997 197 RKGSSNCHSTWKAQ-DVSF 214 (222)
Q Consensus 197 ~~~C~~C~k~GH~~-dC~~ 214 (222)
...|++||..||.. +|+.
T Consensus 31 p~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ChhhcCCCCcCcCHhHcCC
Confidence 34599999999999 9973
No 12
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=94.28 E-value=0.28 Score=36.93 Aligned_cols=54 Identities=20% Similarity=0.423 Sum_probs=36.7
Q ss_pred HHHHHHHHHhchHHHHhhhcccc----chHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhh
Q 043997 68 LKVKNYLFQAIDRTILDTIRKKD----TAKEIWDAMKKKFEGNARVKKSQLQALRREFETLE 125 (222)
Q Consensus 68 ~~a~~~I~~sl~~~~~~~i~~~~----tAke~W~~L~~~y~~~~~~~~~~l~~l~~~~~~~~ 125 (222)
..=+.+|...|..+....|..+. +=..+|+.|+++|.....+..+ +..++..+.
T Consensus 28 ~~K~~~L~~~L~G~A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~~~i~~~----~~~~l~~l~ 85 (145)
T PF03564_consen 28 IEKLNYLRSCLKGEAKELIRGLPLSEENYEEAWELLEERYGNPRRIIQA----LLEELRNLP 85 (145)
T ss_pred HHHHHHHHHHhcchHHHHHHcccccchhhHHHHHHHHHHhCCchHHHHH----HHHHHhccc
Confidence 34456777888888888777754 3467999999999887654333 334455444
No 13
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=94.03 E-value=0.027 Score=44.52 Aligned_cols=15 Identities=33% Similarity=0.383 Sum_probs=9.9
Q ss_pred CCCCCCCCCCccc-cc
Q 043997 198 KGSSNCHSTWKAQ-DV 212 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC 212 (222)
++|++||..||+. ||
T Consensus 98 ~~C~~Cg~~GH~~~dC 113 (190)
T COG5082 98 KKCYNCGETGHLSRDC 113 (190)
T ss_pred cccccccccCcccccc
Confidence 4566666666666 66
No 14
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=93.61 E-value=0.031 Score=44.17 Aligned_cols=20 Identities=15% Similarity=0.172 Sum_probs=17.7
Q ss_pred hccCCCCCCCCCCCccc-ccc
Q 043997 194 TTSRKGSSNCHSTWKAQ-DVS 213 (222)
Q Consensus 194 ~~~~~~C~~C~k~GH~~-dC~ 213 (222)
+...+.||+||+.||.+ |||
T Consensus 57 ~~~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 57 REENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred cccccccchhcccCcccccCC
Confidence 35667899999999999 999
No 15
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=87.44 E-value=0.34 Score=40.57 Aligned_cols=18 Identities=11% Similarity=0.102 Sum_probs=16.1
Q ss_pred CCCCCCCCCCccc-ccccC
Q 043997 198 KGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~~~ 215 (222)
..||.||+.||+. +|+.+
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred CccCCCCcCCcchhhCCCC
Confidence 6699999999999 99954
No 16
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=87.37 E-value=0.29 Score=37.26 Aligned_cols=17 Identities=29% Similarity=0.258 Sum_probs=14.3
Q ss_pred CCCCCCCCCCccc-cccc
Q 043997 198 KGSSNCHSTWKAQ-DVSF 214 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~~ 214 (222)
..|++|+..||+. |||.
T Consensus 130 ~~C~~Cg~~gH~~~dCp~ 147 (148)
T PTZ00368 130 KTCYNCGQTGHLSRDCPD 147 (148)
T ss_pred CccccCCCcCcccccCCC
Confidence 5699999999999 8885
No 17
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=86.64 E-value=0.14 Score=45.53 Aligned_cols=22 Identities=23% Similarity=0.306 Sum_probs=20.0
Q ss_pred cCCCCCCCCCCCccc-ccccCcc
Q 043997 196 SRKGSSNCHSTWKAQ-DVSFRER 217 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~~~~~ 217 (222)
.++-|-|||-.||.. ||-.|||
T Consensus 111 RKGACeNCGAmtHk~KDCmERPR 133 (529)
T KOG2560|consen 111 RKGACENCGAMTHKVKDCMERPR 133 (529)
T ss_pred hhhhhhhhhhhhcchHHHhhcch
Confidence 456799999999999 9999997
No 18
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=84.81 E-value=0.4 Score=40.47 Aligned_cols=20 Identities=10% Similarity=0.225 Sum_probs=17.3
Q ss_pred cCCCCCCCCCCCccc-ccccC
Q 043997 196 SRKGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~~~ 215 (222)
+.-+|+.|||.||+. .||--
T Consensus 159 Dq~~cyrcGkeghwskEcP~~ 179 (346)
T KOG0109|consen 159 DQSGCYRCGKEGHWSKECPVD 179 (346)
T ss_pred CHHHheeccccccccccCCcc
Confidence 455799999999999 99865
No 19
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=83.76 E-value=0.47 Score=40.17 Aligned_cols=17 Identities=6% Similarity=-0.048 Sum_probs=15.9
Q ss_pred CCCCCCCCCccc-ccccC
Q 043997 199 GSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 199 ~C~~C~k~GH~~-dC~~~ 215 (222)
.||.||..||++ .||..
T Consensus 178 ~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 178 VCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred eEEecCCCCchhhcCCCC
Confidence 499999999999 99987
No 20
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=82.83 E-value=0.77 Score=34.90 Aligned_cols=18 Identities=22% Similarity=0.296 Sum_probs=10.6
Q ss_pred CCCCCCCCCccc-ccccCc
Q 043997 199 GSSNCHSTWKAQ-DVSFRE 216 (222)
Q Consensus 199 ~C~~C~k~GH~~-dC~~~~ 216 (222)
.|+.|++.||+. ||+...
T Consensus 79 ~C~~Cg~~GH~~~~C~~~~ 97 (148)
T PTZ00368 79 SCYNCGQTGHISRECPNRA 97 (148)
T ss_pred ccCcCCCCCcccccCCCcc
Confidence 466666666666 665543
No 21
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=79.29 E-value=0.89 Score=40.26 Aligned_cols=20 Identities=20% Similarity=0.223 Sum_probs=16.8
Q ss_pred cCCCCCCCCCCCccc-ccccC
Q 043997 196 SRKGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~~~ 215 (222)
...+|-+||..||.+ |||.-
T Consensus 569 ~~kGCayCgGLGHRItdCPKl 589 (610)
T KOG0341|consen 569 GEKGCAYCGGLGHRITDCPKL 589 (610)
T ss_pred CccccccccCCCcccccCchh
Confidence 345699999999999 99854
No 22
>KOG3926 consensus F-box proteins [Amino acid transport and metabolism]
Probab=76.02 E-value=8.6 Score=32.45 Aligned_cols=127 Identities=11% Similarity=0.236 Sum_probs=70.2
Q ss_pred CCcccCChHHHHHHHHHHhhccccccccccCccCCCCCCcCchHhhhhhHHhhhhhHHHHHHHHHhchHHHHhhhccccc
Q 043997 12 IPRFVGHYDHWSMLMDNFMRSKEYWGLVETGYDEPASGSVLMDAHQKMTDELKLKDLKVKNYLFQAIDRTILDTIRKKDT 91 (222)
Q Consensus 12 i~~l~GNY~~W~~~m~~~L~~~~lw~~v~~~~~~p~~~~~~t~~~~~~~~~~~~~d~~a~~~I~~sl~~~~~~~i~~~~t 91 (222)
-++|-||-..|+.+|.++|.-+.+...++-..+.|. .+|-.+. -.....-|+..+++. .+..+
T Consensus 163 ~~~Lvsn~~~w~~~m~til~~qqv~~~iqi~~~~~~---~ltl~dL---------P~e~vl~Il~rlsDh-----~dL~s 225 (332)
T KOG3926|consen 163 KSVLVSNINLWKERMETILRWQQVLSQIQITEPDPA---GLTLHDL---------PLECVLNILLRLSDH-----RDLES 225 (332)
T ss_pred cccccchHHHHHHHHHHHHHHHHHHHhhcccCCCcC---CCCcccc---------hHHHHHHHHHHccCc-----chHHH
Confidence 356667999999999999999987777776555542 1221110 011122222223221 24568
Q ss_pred hHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhhcccCChhHHHHHHHHh--hcc-cchhHHHHHHhhcCCCCCCCHHHH
Q 043997 92 AKEIWDAMKKKFEGNARVKKSQLQALRREFETLEMKSGEEDVKIVEKILR--TLT-EKFNDIVCSIEESKDIDSLSEEAE 168 (222)
Q Consensus 92 Ake~W~~L~~~y~~~~~~~~~~l~~l~~~~~~~~m~~~e~d~~~v~~lL~--~Lp-~~~~~~~~~i~~~~~~~~lt~~ev 168 (222)
+.++|.+|..+-+ -+.+|+++-+|.+.+ ..+..+|. .-. .+|..+--.+.-. ....|.
T Consensus 226 ~aqa~etl~~l~~---------e~~iWkkLcqfHF~e-----rQi~~~l~l~k~~q~dWkqmyf~L~r~-----yg~keq 286 (332)
T KOG3926|consen 226 LAQAWETLAKLSE---------ERRIWKKLCQFHFNE-----RQIHTILILSKKGQKDWKQMYFQLRRT-----YGVKEQ 286 (332)
T ss_pred HHHhhHHHHHHHH---------HHHHHHHHHHHHhhH-----HHHHHhhhhccccchhHHHHHHHHHHh-----cChHHH
Confidence 8899999988654 124677777776654 22222222 111 2365555555432 224667
Q ss_pred HHHHHH
Q 043997 169 VKEDEV 174 (222)
Q Consensus 169 ~~~l~~ 174 (222)
++.++.
T Consensus 287 yad~lh 292 (332)
T KOG3926|consen 287 YADTLH 292 (332)
T ss_pred HHHHHH
Confidence 766665
No 23
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=70.81 E-value=1.8 Score=32.28 Aligned_cols=21 Identities=10% Similarity=0.216 Sum_probs=17.8
Q ss_pred ccCCCCCCCCCCCccc-ccccCc
Q 043997 195 TSRKGSSNCHSTWKAQ-DVSFRE 216 (222)
Q Consensus 195 ~~~~~C~~C~k~GH~~-dC~~~~ 216 (222)
.....|..|+ ..|+- .|||..
T Consensus 104 ~~~v~CR~Ck-GdH~T~~CPyKd 125 (128)
T PF12353_consen 104 KSKVKCRICK-GDHWTSKCPYKD 125 (128)
T ss_pred CceEEeCCCC-CCcccccCCccc
Confidence 4567899996 99999 999973
No 24
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=69.37 E-value=2.4 Score=38.44 Aligned_cols=18 Identities=11% Similarity=0.100 Sum_probs=16.3
Q ss_pred CCCCCCCCCCccc-ccccC
Q 043997 198 KGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~~~ 215 (222)
..|++||-.||+. ||.++
T Consensus 286 n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 286 NVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccCCcccccccCCCc
Confidence 3899999999999 99887
No 25
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=68.16 E-value=2.5 Score=35.29 Aligned_cols=23 Identities=13% Similarity=0.118 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCccc-ccccCcccc
Q 043997 197 RKGSSNCHSTWKAQ-DVSFRERVD 219 (222)
Q Consensus 197 ~~~C~~C~k~GH~~-dC~~~~~~~ 219 (222)
...|++|++.||+. +|+...+..
T Consensus 92 ~~~c~~C~~~gH~~~~c~~~~~~~ 115 (261)
T KOG4400|consen 92 AAACFNCGEGGHIERDCPEAGKEG 115 (261)
T ss_pred chhhhhCCCCccchhhCCcccCcc
Confidence 35699999999999 999986554
No 26
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=67.32 E-value=14 Score=24.82 Aligned_cols=15 Identities=27% Similarity=0.563 Sum_probs=11.2
Q ss_pred hhHHHHHHHHhhccc
Q 043997 131 EDVKIVEKILRTLTE 145 (222)
Q Consensus 131 ~d~~~v~~lL~~Lp~ 145 (222)
+++.+|..|++||.|
T Consensus 82 ~e~~~v~~f~~GL~~ 96 (96)
T PF03732_consen 82 DEEMLVERFIRGLRP 96 (96)
T ss_pred CHHHHHHHHHHCCCC
Confidence 677788888887764
No 27
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=67.31 E-value=4.9 Score=37.69 Aligned_cols=21 Identities=10% Similarity=0.145 Sum_probs=16.9
Q ss_pred ccCCCCCCCCCCCccc---ccccC
Q 043997 195 TSRKGSSNCHSTWKAQ---DVSFR 215 (222)
Q Consensus 195 ~~~~~C~~C~k~GH~~---dC~~~ 215 (222)
..-++|.+||..||++ -||--
T Consensus 935 ~Ttr~C~nCGQvGHmkTNK~CP~f 958 (968)
T COG5179 935 NTTRTCGNCGQVGHMKTNKACPKF 958 (968)
T ss_pred CcceecccccccccccccccCccc
Confidence 3457899999999999 68654
No 28
>PF07904 Eaf7: Chromatin modification-related protein EAF7; InterPro: IPR012423 The Saccharomyces cerevisiae (Baker's yeast) member of this family P53911 from SWISSPROT is part of NuA4, the only essential histone acetyltransferase complex in S. cerevisiae involved in global histone acetylation []. ; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0043189 H4/H2A histone acetyltransferase complex
Probab=65.08 E-value=9.5 Score=26.59 Aligned_cols=19 Identities=21% Similarity=0.648 Sum_probs=16.6
Q ss_pred hccccchHHHHHHHHHHhh
Q 043997 86 IRKKDTAKEIWDAMKKKFE 104 (222)
Q Consensus 86 i~~~~tAke~W~~L~~~y~ 104 (222)
+....|+.+||+.|...|.
T Consensus 40 ~~~~~t~~~IW~kL~~~Yd 58 (91)
T PF07904_consen 40 LNKHFTIDDIWKKLRTLYD 58 (91)
T ss_pred cCCcCCHHHHHHHHHHhcC
Confidence 5667899999999999995
No 29
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=64.76 E-value=3.6 Score=39.49 Aligned_cols=22 Identities=18% Similarity=0.169 Sum_probs=18.3
Q ss_pred cCCCCCCCCCCCccc-ccccCcc
Q 043997 196 SRKGSSNCHSTWKAQ-DVSFRER 217 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~~~~~ 217 (222)
+.++|+-||..||.. ||.--++
T Consensus 259 ~~~~C~~cgq~gh~~~dc~g~~~ 281 (931)
T KOG2044|consen 259 KPRRCFLCGQTGHEAKDCEGKPR 281 (931)
T ss_pred CcccchhhcccCCcHhhcCCcCC
Confidence 445699999999999 9976655
No 30
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=58.13 E-value=5.4 Score=36.25 Aligned_cols=20 Identities=35% Similarity=0.434 Sum_probs=17.7
Q ss_pred cCCCCCCCCCCCccc-ccccC
Q 043997 196 SRKGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~~~ 215 (222)
....|.+||..||.+ ||+.|
T Consensus 260 d~~~c~~cg~~~H~q~~cp~r 280 (554)
T KOG0119|consen 260 DNRACRNCGSTGHKQYDCPGR 280 (554)
T ss_pred ccccccccCCCccccccCCcc
Confidence 346799999999999 99987
No 31
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=53.83 E-value=4.4 Score=35.67 Aligned_cols=21 Identities=10% Similarity=0.140 Sum_probs=17.3
Q ss_pred ccCCCCCCCCCCCccc---ccccC
Q 043997 195 TSRKGSSNCHSTWKAQ---DVSFR 215 (222)
Q Consensus 195 ~~~~~C~~C~k~GH~~---dC~~~ 215 (222)
..+.+|..|++.||.- +||.-
T Consensus 122 VRNVrC~kChkwGH~n~DreCplf 145 (453)
T KOG3794|consen 122 VRNVRCLKCHKWGHINTDRECPLF 145 (453)
T ss_pred eeeeeEEeecccccccCCccCcch
Confidence 4557799999999998 78764
No 32
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=47.86 E-value=53 Score=22.09 Aligned_cols=29 Identities=21% Similarity=0.306 Sum_probs=23.8
Q ss_pred hchHHHHhhhccccchHHHHHHHHHHhhc
Q 043997 77 AIDRTILDTIRKKDTAKEIWDAMKKKFEG 105 (222)
Q Consensus 77 sl~~~~~~~i~~~~tAke~W~~L~~~y~~ 105 (222)
.+...+...+....|..++++.|.+.|..
T Consensus 31 ~~g~~Iw~lldg~~tv~eI~~~L~~~Y~~ 59 (81)
T TIGR03859 31 DSAGEILELCDGKRSLAEIIQELAQRFPA 59 (81)
T ss_pred hHHHHHHHHccCCCcHHHHHHHHHHHcCC
Confidence 34556677888889999999999999987
No 33
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=46.31 E-value=9.8 Score=34.28 Aligned_cols=17 Identities=24% Similarity=0.171 Sum_probs=15.0
Q ss_pred CCCCCCCCCccc-ccccC
Q 043997 199 GSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 199 ~C~~C~k~GH~~-dC~~~ 215 (222)
.||+||..-|-. |||-+
T Consensus 130 ~CFNC~g~~hsLrdC~rp 147 (485)
T KOG2673|consen 130 PCFNCGGTPHSLRDCPRP 147 (485)
T ss_pred cccccCCCCCccccCCCc
Confidence 389999999988 99865
No 34
>PF02764 Diphtheria_T: Diphtheria toxin, T domain; InterPro: IPR022405 Diphtheria toxin (2.4.2.36 from EC) is a 58 kDa protein secreted by lysogenic strains of Corynebacterium diphtheriae. The toxin causes the disease diphtheria in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis []. The mechanism of inhibition involves transfer of the ADP-ribose group of NAD to elongation factor-2 (EF-2), rendering EF-2 inactive. The catalysed reaction is as follows: NAD+ + peptide diphthamide = nicotinamide + peptide N-(ADP-D-ribosyl)diphthamide The crystal structure of the diphtheria toxin homodimer has been determined to 2.5A resolution []. The structure reveals a Y-shaped molecule of 3 domains, a catalytic domain (fragment A), whose fold is of the alpha + beta type; a transmembrane (TM) domain, which consists of 9 alpha-helices, 2 pairs of which may participate in pH-triggered membrane insertion and translocation; and a receptor-binding domain, which forms a flattened beta-barrel with a jelly-roll-like topology []. The TM- and receptor binding-domains together constitute fragment B. This entry represents the translocation domain (also known as the T domain) found as the central domain in the Diphtheria toxin protein. The T domain has a multi-helical globin-like fold with two additional helices at N-termini, but which has no counterpart to the first globin helix. This domain is thought to unfold in the membrane []. pH-induced conformational change in the T domain triggers insertion into the endosomal membrane and facilitates the transfer of the catalytic domain into the cytoplasm [, ].; PDB: 1MDT_B 1SGK_A 1F0L_B 1DDT_A 1TOX_B 4AE0_A 1XDT_T 4AE1_A.
Probab=46.17 E-value=12 Score=28.02 Aligned_cols=25 Identities=20% Similarity=0.397 Sum_probs=18.5
Q ss_pred CCCCCcccC-ChHHHHHHHHHHhhcc
Q 043997 9 QPAIPRFVG-HYDHWSMLMDNFMRSK 33 (222)
Q Consensus 9 ~~~i~~l~G-NY~~W~~~m~~~L~~~ 33 (222)
+..-|+|+| ||..|+..|..+....
T Consensus 68 tgtnpvf~~A~~A~WA~n~~qv~~~E 93 (180)
T PF02764_consen 68 TGTNPVFNKAFYAAWAYNMYQVIDHE 93 (180)
T ss_dssp TSS-GGGSHHHHHHHHHHHHHH--HH
T ss_pred cCCchhhhhhHHHHHHHHHHHHHccc
Confidence 345799999 9999999998887643
No 35
>PF11248 DUF3046: Protein of unknown function (DUF3046); InterPro: IPR021408 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=37.26 E-value=46 Score=21.57 Aligned_cols=38 Identities=13% Similarity=0.417 Sum_probs=26.7
Q ss_pred hHHHHHHHHHhch-HHHHhhhccccchHHHHHHHHHHhh
Q 043997 67 DLKVKNYLFQAID-RTILDTIRKKDTAKEIWDAMKKKFE 104 (222)
Q Consensus 67 d~~a~~~I~~sl~-~~~~~~i~~~~tAke~W~~L~~~y~ 104 (222)
...|....+..+. ......|..-..++++|.+|+..|.
T Consensus 20 ~~la~dhvL~~LGgrT~~eAL~~G~dpr~VW~AlC~~~d 58 (63)
T PF11248_consen 20 RSLARDHVLSELGGRTAAEALEAGVDPRDVWRALCDAFD 58 (63)
T ss_pred HHHHHhcchhhcCCcCHHHHHHcCCCHHHHHHHHHHHcC
Confidence 3444455555665 4555667777889999999999874
No 36
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=36.96 E-value=20 Score=22.33 Aligned_cols=15 Identities=13% Similarity=0.443 Sum_probs=12.3
Q ss_pred CCCCCCCCCCccc-cc
Q 043997 198 KGSSNCHSTWKAQ-DV 212 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC 212 (222)
.-|+.|+...|.- .|
T Consensus 49 ~fC~~C~~~~H~~~~C 64 (64)
T smart00647 49 SFCFRCKVPWHSPVSC 64 (64)
T ss_pred eECCCCCCcCCCCCCC
Confidence 4499999999987 66
No 37
>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=36.47 E-value=13 Score=21.68 Aligned_cols=10 Identities=30% Similarity=0.239 Sum_probs=4.9
Q ss_pred CCCCCCCCCC
Q 043997 198 KGSSNCHSTW 207 (222)
Q Consensus 198 ~~C~~C~k~G 207 (222)
..|++||++.
T Consensus 2 ~~CSFCgr~~ 11 (41)
T PF06689_consen 2 KRCSFCGRPE 11 (41)
T ss_dssp -B-TTT--BT
T ss_pred CCccCCCCCH
Confidence 5699999875
No 38
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=33.51 E-value=16 Score=23.56 Aligned_cols=9 Identities=11% Similarity=0.213 Sum_probs=7.6
Q ss_pred CCCCCCCCC
Q 043997 198 KGSSNCHST 206 (222)
Q Consensus 198 ~~C~~C~k~ 206 (222)
.+||-||++
T Consensus 5 iRCFsCGkv 13 (63)
T COG1644 5 VRCFSCGKV 13 (63)
T ss_pred eEeecCCCC
Confidence 469999986
No 39
>COG3167 PilO Tfp pilus assembly protein PilO [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=33.16 E-value=1.4e+02 Score=23.89 Aligned_cols=62 Identities=16% Similarity=0.363 Sum_probs=37.9
Q ss_pred HHHHHHhhchhHHHHHHHHHHHHHHHHhhcccCChhHHHHHHHHhhcccc--hhHHHHHHhhcCCCCCCCHHH
Q 043997 97 DAMKKKFEGNARVKKSQLQALRREFETLEMKSGEEDVKIVEKILRTLTEK--FNDIVCSIEESKDIDSLSEEA 167 (222)
Q Consensus 97 ~~L~~~y~~~~~~~~~~l~~l~~~~~~~~m~~~e~d~~~v~~lL~~Lp~~--~~~~~~~i~~~~~~~~lt~~e 167 (222)
+.|+..|..+.. +.+.+..|+.|+..+ ++.+..+|+.||.+ -.++...|....--.-++|+.
T Consensus 59 e~LKs~~q~K~~-~aanL~~lr~Ql~em--------ee~~~~llrQLPs~tEmp~Ll~dv~q~Gl~sgL~fd~ 122 (211)
T COG3167 59 EELKSTYQQKAI-QAANLEALRAQLAEM--------EERFDILLRQLPSDTEMPNLLADVNQAGLSSGLTFDL 122 (211)
T ss_pred HHHHHHHHHHHH-HHhchHHHHHHHHHH--------HHHHHHHHHhCCcccchhHHHHHHHHhhhccCceeec
Confidence 356777765542 346677777777643 35778889999964 556666555443333444443
No 40
>PF13376 OmdA: Bacteriocin-protection, YdeI or OmpD-Associated
Probab=30.89 E-value=1e+02 Score=19.55 Aligned_cols=27 Identities=11% Similarity=0.389 Sum_probs=21.0
Q ss_pred chHHHHhhhccccchHHHHHHHHHHhh
Q 043997 78 IDRTILDTIRKKDTAKEIWDAMKKKFE 104 (222)
Q Consensus 78 l~~~~~~~i~~~~tAke~W~~L~~~y~ 104 (222)
|++++...+.....|++.|+.|...|.
T Consensus 6 vP~dl~~aL~~~p~a~~~f~~l~~~~r 32 (63)
T PF13376_consen 6 VPEDLEAALEANPEAKEFFESLTPSYR 32 (63)
T ss_pred CCHHHHHHHHCCHHHHHHHHHCCHHHH
Confidence 567777777788888888888877664
No 41
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=30.50 E-value=26 Score=22.48 Aligned_cols=9 Identities=11% Similarity=0.198 Sum_probs=6.7
Q ss_pred CCCCCCCCC
Q 043997 198 KGSSNCHST 206 (222)
Q Consensus 198 ~~C~~C~k~ 206 (222)
.+||-|||+
T Consensus 5 VRCFTCGkv 13 (60)
T PF01194_consen 5 VRCFTCGKV 13 (60)
T ss_dssp SS-STTTSB
T ss_pred eecCCCCCC
Confidence 479999996
No 42
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=29.83 E-value=23 Score=23.51 Aligned_cols=9 Identities=11% Similarity=0.198 Sum_probs=7.6
Q ss_pred CCCCCCCCC
Q 043997 198 KGSSNCHST 206 (222)
Q Consensus 198 ~~C~~C~k~ 206 (222)
.+||-|||+
T Consensus 5 VRCFTCGkv 13 (71)
T PLN00032 5 VRCFTCGKV 13 (71)
T ss_pred eeecCCCCC
Confidence 469999996
No 43
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=28.35 E-value=25 Score=21.82 Aligned_cols=14 Identities=14% Similarity=0.408 Sum_probs=10.2
Q ss_pred CCCCCCCCCccc-cc
Q 043997 199 GSSNCHSTWKAQ-DV 212 (222)
Q Consensus 199 ~C~~C~k~GH~~-dC 212 (222)
-|+.|+.+.|.. +|
T Consensus 50 fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 50 FCFKCGEPWHEGVTC 64 (64)
T ss_dssp ECSSSTSESCTTS-H
T ss_pred CccccCcccCCCCCC
Confidence 388888888876 65
No 44
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=27.95 E-value=19 Score=23.04 Aligned_cols=10 Identities=10% Similarity=0.105 Sum_probs=7.8
Q ss_pred CCCCCCCCCC
Q 043997 198 KGSSNCHSTW 207 (222)
Q Consensus 198 ~~C~~C~k~G 207 (222)
.+||-|||.=
T Consensus 5 iRCFtCGKvi 14 (69)
T KOG3497|consen 5 IRCFTCGKVI 14 (69)
T ss_pred eEeeeccccc
Confidence 4699999863
No 45
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=27.22 E-value=31 Score=27.23 Aligned_cols=17 Identities=6% Similarity=-0.097 Sum_probs=14.4
Q ss_pred CCCCCCCCCCccc-cccc
Q 043997 198 KGSSNCHSTWKAQ-DVSF 214 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~~ 214 (222)
..|++||..||+. .|.-
T Consensus 101 ~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 101 GFCYRCGERGHIGRNCKD 118 (195)
T ss_pred cccccCCCcccccccccc
Confidence 4499999999999 8854
No 46
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=26.75 E-value=1.7e+02 Score=18.35 Aligned_cols=35 Identities=17% Similarity=0.297 Sum_probs=20.3
Q ss_pred HHHhchHHHHhhhccccchHHHHHHHHHHhhchhH
Q 043997 74 LFQAIDRTILDTIRKKDTAKEIWDAMKKKFEGNAR 108 (222)
Q Consensus 74 I~~sl~~~~~~~i~~~~tAke~W~~L~~~y~~~~~ 108 (222)
.++.....+...+....|..++-+.|.+.|.....
T Consensus 14 ~Ln~~a~~Iw~~~~g~~t~~ei~~~l~~~y~~~~~ 48 (68)
T PF05402_consen 14 TLNETAAFIWELLDGPRTVEEIVDALAEEYDVDPE 48 (68)
T ss_dssp ---THHHHHHHH--SSS-HHHHHHHHHHHTT--HH
T ss_pred cccHHHHHHHHHccCCCCHHHHHHHHHHHcCCCHH
Confidence 44555666677777778888888888888855443
No 47
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=26.17 E-value=28 Score=22.50 Aligned_cols=9 Identities=11% Similarity=0.198 Sum_probs=7.6
Q ss_pred CCCCCCCCC
Q 043997 198 KGSSNCHST 206 (222)
Q Consensus 198 ~~C~~C~k~ 206 (222)
.+||-|||+
T Consensus 5 vRCFTCGkv 13 (62)
T PRK04016 5 VRCFTCGKV 13 (62)
T ss_pred eEecCCCCC
Confidence 469999996
No 48
>PF08354 DUF1729: Domain of unknown function (DUF1729); InterPro: IPR013565 This domain of unknown function is found in fatty acid synthase beta subunits together with the MaoC-like domain (IPR002539 from INTERPRO) and the Acyltransferase domain (IPR001227 from INTERPRO) []. The domain has been identified in fungi and bacteria. ; GO: 0004318 enoyl-[acyl-carrier-protein] reductase (NADH) activity, 0055114 oxidation-reduction process; PDB: 3HMJ_H 2UV8_I 2VKZ_G.
Probab=22.26 E-value=49 Score=20.88 Aligned_cols=29 Identities=21% Similarity=0.484 Sum_probs=14.1
Q ss_pred CCcccCChHHHHHHHHHHhhcccccccccc
Q 043997 12 IPRFVGHYDHWSMLMDNFMRSKEYWGLVET 41 (222)
Q Consensus 12 i~~l~GNY~~W~~~m~~~L~~~~lw~~v~~ 41 (222)
||+||.||..|-. --.+-++++|..++.-
T Consensus 1 iPvlD~~f~~wfk-kDSLWQsedl~av~~~ 29 (57)
T PF08354_consen 1 IPVLDEDFEFWFK-KDSLWQSEDLDAVVDQ 29 (57)
T ss_dssp B---STTHHHHHH-SS-SGGGG-GGGSTTS
T ss_pred CCeechhHHHhhc-ccchhhhcccccccCC
Confidence 6888889888843 2344455555555443
No 49
>PRK07758 hypothetical protein; Provisional
Probab=22.18 E-value=44 Score=23.50 Aligned_cols=21 Identities=14% Similarity=0.191 Sum_probs=12.6
Q ss_pred CCCCCCCCcccccccCccccc
Q 043997 200 SSNCHSTWKAQDVSFRERVDC 220 (222)
Q Consensus 200 C~~C~k~GH~~dC~~~~~~~~ 220 (222)
|-.-+.+....|||..|++|-
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~ 30 (95)
T PRK07758 10 CEKGHEYYKSSDCPTCPTCEK 30 (95)
T ss_pred HhcccceeccCCCCCCccccc
Confidence 433333333339999999873
No 50
>KOG2999 consensus Regulator of Rac1, required for phagocytosis and cell migration [Signal transduction mechanisms]
Probab=21.81 E-value=3.2e+02 Score=25.92 Aligned_cols=37 Identities=14% Similarity=0.189 Sum_probs=23.4
Q ss_pred HHHHHHhhcccchhHHHHHHhhcCCCCCCCHHHHHHHHHH-hhhc
Q 043997 135 IVEKILRTLTEKFNDIVCSIEESKDIDSLSEEAEVKEDEV-KTLL 178 (222)
Q Consensus 135 ~v~~lL~~Lp~~~~~~~~~i~~~~~~~~lt~~ev~~~l~~-~~~~ 178 (222)
++...|.+=|.+.+.|++-|+. +|..++. +|.+ +|+.
T Consensus 471 Ql~r~L~~kp~sld~fkskl~~------lsY~eil-~irqsErl~ 508 (713)
T KOG2999|consen 471 QLRRALKRKPQSLDQFKSKLET------LSYREIL-RIRQSERLS 508 (713)
T ss_pred HHHHHhccCCccHHHHHHHHHh------ccHHHHH-HHHHHHhhc
Confidence 3344455667888888887653 5677766 4554 6654
No 51
>PF13427 DUF4111: Domain of unknown function (DUF4111)
Probab=20.81 E-value=3.2e+02 Score=19.36 Aligned_cols=41 Identities=20% Similarity=0.155 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhhcccCChhHHHHHHHHhhcccchhHHHHHH
Q 043997 114 LQALRREFETLEMKSGEEDVKIVEKILRTLTEKFNDIVCSI 154 (222)
Q Consensus 114 l~~l~~~~~~~~m~~~e~d~~~v~~lL~~Lp~~~~~~~~~i 154 (222)
+.+|.+-+..+.-..--+-++-....|..||++|..++..-
T Consensus 36 vL~LcR~~~tl~tg~i~SK~~aa~Wal~~lp~~~~~~i~~A 76 (106)
T PF13427_consen 36 VLNLCRILYTLRTGEIVSKDEAAEWALERLPEEWRPLIQEA 76 (106)
T ss_pred HHHHHHHHHHHHhCCcccHHHHHHHHHHHCCHHHHHHHHHH
Confidence 45566666655532211555667788999999999988643
No 52
>PF02023 SCAN: SCAN domain; InterPro: IPR003309 A number of C2H2-zinc finger proteins contain a highly conserved N-terminal motif termed the SCAN domain. The SCAN domain may play an important role in the assembly and function of this newly defined subclass of transcriptional regulators [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3LHR_B 4E6S_A 2FI2_A 1Y7Q_A.
Probab=20.61 E-value=1.9e+02 Score=20.14 Aligned_cols=38 Identities=24% Similarity=0.251 Sum_probs=23.4
Q ss_pred hhHHHHHHHHhhcccchhHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 043997 131 EDVKIVEKILRTLTEKFNDIVCSIEESKDIDSLSEEAEVKEDEV 174 (222)
Q Consensus 131 ~d~~~v~~lL~~Lp~~~~~~~~~i~~~~~~~~lt~~ev~~~l~~ 174 (222)
-|-.+.+.||..||++-...|.. ..+ . |.+++...+..
T Consensus 46 ~ellvlEQFL~~lP~e~~~wV~e---~~p--~-s~~ea~~Lae~ 83 (95)
T PF02023_consen 46 LELLVLEQFLNILPPEVQTWVRE---RKP--E-SAEEAVALAED 83 (95)
T ss_dssp HHHHHHHHHHHHS-HHHHHHHHT---CS---S-SHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCHHHHHHHHh---cCC--C-CHHHHHHHHHH
Confidence 45677888999999987766543 322 1 56776654443
No 53
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=20.34 E-value=1.2e+02 Score=17.82 Aligned_cols=30 Identities=17% Similarity=0.300 Sum_probs=21.8
Q ss_pred ccchhHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 043997 144 TEKFNDIVCSIEESKDIDSLSEEAEVKEDEV 174 (222)
Q Consensus 144 p~~~~~~~~~i~~~~~~~~lt~~ev~~~l~~ 174 (222)
|..|+.+...|..-.. ..++..+|+.++..
T Consensus 1 p~~Y~~FL~il~~y~~-~~~~~~~v~~~v~~ 30 (47)
T PF02671_consen 1 PEVYNEFLKILNDYKK-GRISRSEVIEEVSE 30 (47)
T ss_dssp HHHHHHHHHHHHHHHC-TCSCHHHHHHHHHH
T ss_pred ChHHHHHHHHHHHHHh-cCCCHHHHHHHHHH
Confidence 4567888887776655 57788888877665
No 54
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.27 E-value=55 Score=31.75 Aligned_cols=22 Identities=9% Similarity=-0.056 Sum_probs=18.2
Q ss_pred ccCCCCCCCCCCCccc-ccccCc
Q 043997 195 TSRKGSSNCHSTWKAQ-DVSFRE 216 (222)
Q Consensus 195 ~~~~~C~~C~k~GH~~-dC~~~~ 216 (222)
....+|++||.....- .||.++
T Consensus 460 ~~~L~CH~Cg~~~~~p~~Cp~Cg 482 (730)
T COG1198 460 TGQLRCHYCGYQEPIPQSCPECG 482 (730)
T ss_pred CCeeEeCCCCCCCCCCCCCCCCC
Confidence 4556799999998888 999874
No 55
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=20.23 E-value=50 Score=20.39 Aligned_cols=25 Identities=8% Similarity=0.170 Sum_probs=17.7
Q ss_pred cCCCCCCCCCCCccc-ccccC-ccccc
Q 043997 196 SRKGSSNCHSTWKAQ-DVSFR-ERVDC 220 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~~~-~~~~~ 220 (222)
-.++|..||...|.. .=+.. |.-+|
T Consensus 23 leIKCpRC~tiN~~~a~~~~~~p~~~~ 49 (51)
T PF10122_consen 23 LEIKCPRCKTINHVRATSPEPEPLSEC 49 (51)
T ss_pred EEEECCCCCccceEeccCCCCCchhhc
Confidence 457899999999998 55444 44443
Done!