Query 040998
Match_columns 117
No_of_seqs 106 out of 463
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 02:51:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040998.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040998hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14392 zf-CCHC_4: Zinc knuck 99.6 1.8E-16 3.8E-21 91.8 3.1 44 59-102 1-49 (49)
2 PF14111 DUF4283: Domain of un 99.6 6.2E-16 1.3E-20 107.0 2.8 57 2-58 97-153 (153)
3 PF00098 zf-CCHC: Zinc knuckle 97.5 5.1E-05 1.1E-09 34.9 1.5 17 86-102 2-18 (18)
4 PF13696 zf-CCHC_2: Zinc knuck 96.6 0.0013 2.7E-08 34.6 1.3 24 85-108 9-32 (32)
5 smart00343 ZnF_C2HC zinc finge 94.7 0.015 3.3E-07 28.6 0.8 19 86-104 1-19 (26)
6 PF15288 zf-CCHC_6: Zinc knuck 94.2 0.045 9.9E-07 30.1 2.1 23 85-107 2-26 (40)
7 PF13917 zf-CCHC_3: Zinc knuck 92.7 0.063 1.4E-06 29.9 1.1 20 83-102 3-22 (42)
8 COG5082 AIR1 Arginine methyltr 90.5 0.12 2.6E-06 37.7 1.0 23 79-101 55-77 (190)
9 COG5082 AIR1 Arginine methyltr 89.9 0.16 3.4E-06 37.1 1.2 17 85-101 98-114 (190)
10 KOG0109 RNA-binding protein LA 89.7 0.18 4E-06 39.2 1.5 21 85-105 161-181 (346)
11 PF14787 zf-CCHC_5: GAG-polypr 89.6 0.3 6.5E-06 26.2 1.8 22 84-105 2-23 (36)
12 PTZ00368 universal minicircle 88.4 0.28 6E-06 33.8 1.5 19 84-102 129-147 (148)
13 KOG4400 E3 ubiquitin ligase in 87.9 0.27 5.8E-06 37.1 1.3 25 78-103 138-162 (261)
14 KOG2044 5'-3' exonuclease HKE1 84.5 0.7 1.5E-05 40.4 2.2 29 77-105 253-281 (931)
15 COG5222 Uncharacterized conser 83.8 0.58 1.3E-05 36.7 1.3 22 85-106 177-198 (427)
16 PF01191 RNA_pol_Rpb5_C: RNA p 79.9 2.6 5.5E-05 26.2 2.9 43 13-55 30-72 (74)
17 PTZ00368 universal minicircle 77.2 1.8 3.9E-05 29.7 1.9 20 85-104 78-97 (148)
18 PF10083 DUF2321: Uncharacteri 73.2 1.8 3.9E-05 30.7 1.0 31 62-93 46-77 (158)
19 PLN00032 DNA-directed RNA poly 72.7 1.6 3.5E-05 26.9 0.6 14 83-96 3-17 (71)
20 PRK09570 rpoH DNA-directed RNA 72.0 4.1 8.9E-05 25.6 2.4 35 13-47 33-67 (79)
21 KOG2560 RNA splicing factor - 71.8 0.93 2E-05 37.3 -0.7 20 85-104 113-132 (529)
22 PF01194 RNA_pol_N: RNA polyme 70.8 2 4.4E-05 25.6 0.8 11 83-93 3-13 (60)
23 PRK04016 DNA-directed RNA poly 69.8 2.1 4.5E-05 25.8 0.6 11 83-93 3-13 (62)
24 KOG4285 Mitotic phosphoprotein 69.7 6.1 0.00013 31.1 3.3 70 1-74 189-259 (350)
25 KOG4400 E3 ubiquitin ligase in 69.3 3.4 7.4E-05 31.1 1.9 25 83-107 163-187 (261)
26 COG1644 RPB10 DNA-directed RNA 69.1 2.1 4.5E-05 25.7 0.5 14 83-96 3-17 (63)
27 KOG0125 Ataxin 2-binding prote 68.9 7.2 0.00016 31.0 3.6 43 9-52 96-138 (376)
28 PF14605 Nup35_RRM_2: Nup53/35 67.1 9.8 0.00021 21.7 3.1 33 9-43 1-33 (53)
29 COG2012 RPB5 DNA-directed RNA 65.0 10 0.00023 23.8 3.1 41 15-55 38-78 (80)
30 KOG3497 DNA-directed RNA polym 64.3 2.4 5.2E-05 25.5 0.2 11 83-93 3-13 (69)
31 COG4306 Uncharacterized protei 61.0 3.7 8.1E-05 28.3 0.6 29 64-93 48-77 (160)
32 PF00076 RRM_1: RNA recognitio 60.7 14 0.0003 20.8 3.1 32 12-44 1-32 (70)
33 KOG0119 Splicing factor 1/bran 60.2 5.4 0.00012 33.3 1.5 18 86-103 287-304 (554)
34 KOG0341 DEAD-box protein abstr 58.1 3.8 8.2E-05 33.7 0.3 22 85-106 571-592 (610)
35 COG5179 TAF1 Transcription ini 56.3 7.7 0.00017 33.6 1.8 27 84-110 937-965 (968)
36 KOG2985 Uncharacterized conser 52.2 4.1 9E-05 31.2 -0.3 34 80-113 77-110 (306)
37 smart00647 IBR In Between Ring 50.1 10 0.00022 21.6 1.2 18 83-100 47-64 (64)
38 PF00567 TUDOR: Tudor domain; 46.1 42 0.0009 20.9 3.8 46 49-94 65-121 (121)
39 COG1998 RPS31 Ribosomal protei 46.1 14 0.0003 21.3 1.3 17 75-91 7-26 (51)
40 PRK13130 H/ACA RNA-protein com 45.9 13 0.00028 21.8 1.2 30 85-115 6-43 (56)
41 smart00769 WHy Water Stress an 42.8 37 0.0008 21.5 3.1 32 52-83 14-45 (100)
42 KOG2673 Uncharacterized conser 39.8 16 0.00034 30.3 1.2 19 87-105 131-149 (485)
43 PF05515 Viral_NABP: Viral nuc 39.6 18 0.00039 24.7 1.3 19 85-103 63-81 (124)
44 KOG4399 C2HC-type Zn-finger pr 39.5 14 0.00031 28.5 0.9 22 84-105 261-282 (325)
45 KOG3794 CBF1-interacting corep 38.2 17 0.00037 29.6 1.1 23 84-106 124-148 (453)
46 PRK09698 D-allose kinase; Prov 38.2 70 0.0015 24.0 4.5 89 12-101 81-187 (302)
47 COG1940 NagC Transcriptional r 36.4 38 0.00082 25.6 2.8 78 21-102 92-190 (314)
48 PLN03111 DNA-directed RNA poly 35.6 32 0.0007 25.4 2.2 39 13-53 162-200 (206)
49 PF01485 IBR: IBR domain; Int 35.0 15 0.00033 20.8 0.4 18 83-100 47-64 (64)
50 KOG0119 Splicing factor 1/bran 35.0 23 0.00049 29.8 1.4 22 85-106 262-283 (554)
51 PF14259 RRM_6: RNA recognitio 34.6 89 0.0019 17.6 4.5 33 12-45 1-33 (70)
52 COG1241 MCM2 Predicted ATPase 33.7 2.3E+02 0.005 24.8 7.3 32 8-43 82-114 (682)
53 PTZ00061 DNA-directed RNA poly 33.4 37 0.0008 25.1 2.2 34 13-46 161-194 (205)
54 PF12322 T4_baseplate: T4 bact 32.2 1.1E+02 0.0024 22.4 4.6 69 14-86 50-124 (205)
55 PF05172 Nup35_RRM: Nup53/35/4 31.3 39 0.00084 22.0 1.8 31 9-41 6-36 (100)
56 PF06130 PduL: Propanediol uti 31.0 1.3E+02 0.0028 18.4 4.1 45 22-67 13-58 (71)
57 PF12353 eIF3g: Eukaryotic tra 26.7 38 0.00083 23.0 1.3 22 82-104 104-125 (128)
58 PF13248 zf-ribbon_3: zinc-rib 26.3 42 0.00091 16.1 1.0 8 85-92 3-10 (26)
59 PRK10123 wcaM putative colanic 25.7 27 0.00058 27.7 0.4 42 12-53 376-417 (464)
60 PF14599 zinc_ribbon_6: Zinc-r 25.3 43 0.00094 19.9 1.1 21 74-94 38-58 (61)
61 PF14803 Nudix_N_2: Nudix N-te 24.9 29 0.00063 18.1 0.3 8 85-92 1-8 (34)
62 PF13240 zinc_ribbon_2: zinc-r 22.8 35 0.00076 16.1 0.3 10 83-92 12-21 (23)
63 PF14205 Cys_rich_KTR: Cystein 22.7 41 0.00089 19.7 0.7 15 79-93 23-37 (55)
64 KOG0109 RNA-binding protein LA 22.6 1.7E+02 0.0038 23.1 4.2 89 12-107 5-107 (346)
65 KOG0107 Alternative splicing f 21.4 54 0.0012 24.0 1.2 19 84-102 100-118 (195)
66 PF01570 Flavi_propep: Flavivi 21.3 28 0.00061 22.3 -0.2 14 100-113 49-62 (87)
67 smart00661 RPOL9 RNA polymeras 20.9 45 0.00097 18.3 0.6 13 85-97 1-13 (52)
68 PRK01202 glycine cleavage syst 20.9 1.4E+02 0.003 20.0 3.1 61 6-69 11-77 (127)
69 PF09297 zf-NADH-PPase: NADH p 20.7 44 0.00096 16.7 0.5 14 84-97 3-16 (32)
70 smart00362 RRM_2 RNA recogniti 20.7 1.5E+02 0.0033 15.7 4.2 33 12-45 2-34 (72)
71 PF05575 V_cholerae_RfbT: Vibr 20.3 2E+02 0.0043 21.1 4.0 33 34-71 103-135 (286)
72 KOG3116 Predicted C3H1-type Zn 20.1 28 0.00061 24.7 -0.4 21 84-104 27-47 (177)
No 1
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=99.63 E-value=1.8e-16 Score=91.83 Aligned_cols=44 Identities=43% Similarity=0.889 Sum_probs=40.0
Q ss_pred EccCCCceeEEEEe---ce--EEEEeeccCCcccccccccccCCCCCCC
Q 040998 59 IALDKPLCLQFLLD---GR--IQKVEYESLPINCFNCGKYGHVSIGCPE 102 (117)
Q Consensus 59 idl~kPL~~~v~v~---g~--~~~v~YE~lp~~C~~Cg~~GH~~~~C~~ 102 (117)
+|+++||...+.+. |. ++.|+|||||.||++||.+||..++|++
T Consensus 1 id~~kPL~~~i~v~~~~g~~~~~~v~YE~lp~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 1 IDVSKPLRREIKVKFPEGESFWVKVKYERLPRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred CCCCCcccceEEEEeCCCcEEEEEEEECCcChhhcCCCCcCcCHhHcCC
Confidence 58999999998885 43 6899999999999999999999999985
No 2
>PF14111 DUF4283: Domain of unknown function (DUF4283)
Probab=99.58 E-value=6.2e-16 Score=107.01 Aligned_cols=57 Identities=26% Similarity=0.579 Sum_probs=54.3
Q ss_pred ccccceEeEEEEecCCCccccccchhhhhhhccccEEEEeccCCCccccceEEEEEE
Q 040998 2 SDKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVK 58 (117)
Q Consensus 2 ~~~l~~~~~WVri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y~Rv~V~ 58 (117)
++.++++++||||+|||++||+++++++||+.+|+|+++|.++.+..+++|+||+|+
T Consensus 97 ~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t~~~~~~~~~Rv~V~ 153 (153)
T PF14111_consen 97 EVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENTLKRTRLDFARVRVE 153 (153)
T ss_pred ccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCCCCcccccEEEEEEC
Confidence 467889999999999999999999999999999999999999999999999999985
No 3
>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=97.54 E-value=5.1e-05 Score=34.92 Aligned_cols=17 Identities=53% Similarity=1.450 Sum_probs=15.8
Q ss_pred ccccccccccCCCCCCC
Q 040998 86 NCFNCGKYGHVSIGCPE 102 (117)
Q Consensus 86 ~C~~Cg~~GH~~~~C~~ 102 (117)
.|+.||..||...+||.
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 69999999999999984
No 4
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=96.57 E-value=0.0013 Score=34.62 Aligned_cols=24 Identities=38% Similarity=0.769 Sum_probs=20.5
Q ss_pred cccccccccccCCCCCCCCCCCCC
Q 040998 85 INCFNCGKYGHVSIGCPENGDGEE 108 (117)
Q Consensus 85 ~~C~~Cg~~GH~~~~C~~~~~~~~ 108 (117)
..|..|+.-||...+||...+.+|
T Consensus 9 Y~C~~C~~~GH~i~dCP~~~Pk~e 32 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPTNKPKGE 32 (32)
T ss_pred CEeecCCCCCccHhHCCCCCCCCC
Confidence 689999999999999999665543
No 5
>smart00343 ZnF_C2HC zinc finger.
Probab=94.65 E-value=0.015 Score=28.63 Aligned_cols=19 Identities=47% Similarity=1.288 Sum_probs=16.3
Q ss_pred ccccccccccCCCCCCCCC
Q 040998 86 NCFNCGKYGHVSIGCPENG 104 (117)
Q Consensus 86 ~C~~Cg~~GH~~~~C~~~~ 104 (117)
.|+.||..||...+|+...
T Consensus 1 ~C~~CG~~GH~~~~C~~~~ 19 (26)
T smart00343 1 KCYNCGKEGHIARDCPKXX 19 (26)
T ss_pred CCccCCCCCcchhhCCccc
Confidence 4999999999999998443
No 6
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=94.15 E-value=0.045 Score=30.12 Aligned_cols=23 Identities=35% Similarity=0.836 Sum_probs=19.0
Q ss_pred cccccccccccCC--CCCCCCCCCC
Q 040998 85 INCFNCGKYGHVS--IGCPENGDGE 107 (117)
Q Consensus 85 ~~C~~Cg~~GH~~--~~C~~~~~~~ 107 (117)
..|..||-+||.. +.||......
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~~~~ 26 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYCWSG 26 (40)
T ss_pred ccccccccccccccCccCCCCCCCC
Confidence 3699999999987 7899987653
No 7
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=92.67 E-value=0.063 Score=29.86 Aligned_cols=20 Identities=35% Similarity=0.974 Sum_probs=17.8
Q ss_pred CCcccccccccccCCCCCCC
Q 040998 83 LPINCFNCGKYGHVSIGCPE 102 (117)
Q Consensus 83 lp~~C~~Cg~~GH~~~~C~~ 102 (117)
-...|..|+..||..-+|+.
T Consensus 3 ~~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 3 ARVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCCcCcccCCCCcchhhCCC
Confidence 34689999999999999995
No 8
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=90.51 E-value=0.12 Score=37.65 Aligned_cols=23 Identities=39% Similarity=0.911 Sum_probs=19.6
Q ss_pred eeccCCcccccccccccCCCCCC
Q 040998 79 EYESLPINCFNCGKYGHVSIGCP 101 (117)
Q Consensus 79 ~YE~lp~~C~~Cg~~GH~~~~C~ 101 (117)
.+-.-..+|+.||..||...+||
T Consensus 55 ~~~~~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 55 AIREENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred cccccccccchhcccCcccccCC
Confidence 44445689999999999999999
No 9
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=89.94 E-value=0.16 Score=37.05 Aligned_cols=17 Identities=47% Similarity=1.202 Sum_probs=15.3
Q ss_pred cccccccccccCCCCCC
Q 040998 85 INCFNCGKYGHVSIGCP 101 (117)
Q Consensus 85 ~~C~~Cg~~GH~~~~C~ 101 (117)
..|++||..||...+|+
T Consensus 98 ~~C~~Cg~~GH~~~dC~ 114 (190)
T COG5082 98 KKCYNCGETGHLSRDCN 114 (190)
T ss_pred cccccccccCccccccC
Confidence 68999999999999994
No 10
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=89.70 E-value=0.18 Score=39.20 Aligned_cols=21 Identities=43% Similarity=0.980 Sum_probs=18.9
Q ss_pred cccccccccccCCCCCCCCCC
Q 040998 85 INCFNCGKYGHVSIGCPENGD 105 (117)
Q Consensus 85 ~~C~~Cg~~GH~~~~C~~~~~ 105 (117)
.-|+.||+-||.+++||....
T Consensus 161 ~~cyrcGkeghwskEcP~~~~ 181 (346)
T KOG0109|consen 161 SGCYRCGKEGHWSKECPVDRT 181 (346)
T ss_pred HHheeccccccccccCCccCC
Confidence 579999999999999998754
No 11
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=89.62 E-value=0.3 Score=26.22 Aligned_cols=22 Identities=36% Similarity=0.566 Sum_probs=13.6
Q ss_pred CcccccccccccCCCCCCCCCC
Q 040998 84 PINCFNCGKYGHVSIGCPENGD 105 (117)
Q Consensus 84 p~~C~~Cg~~GH~~~~C~~~~~ 105 (117)
|..|+.|++-.|...+|....+
T Consensus 2 ~~~CprC~kg~Hwa~~C~sk~d 23 (36)
T PF14787_consen 2 PGLCPRCGKGFHWASECRSKTD 23 (36)
T ss_dssp --C-TTTSSSCS-TTT---TCC
T ss_pred CccCcccCCCcchhhhhhhhhc
Confidence 5689999999999999988764
No 12
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=88.39 E-value=0.28 Score=33.82 Aligned_cols=19 Identities=47% Similarity=1.260 Sum_probs=11.9
Q ss_pred CcccccccccccCCCCCCC
Q 040998 84 PINCFNCGKYGHVSIGCPE 102 (117)
Q Consensus 84 p~~C~~Cg~~GH~~~~C~~ 102 (117)
+..|+.|+..||...+||.
T Consensus 129 ~~~C~~Cg~~gH~~~dCp~ 147 (148)
T PTZ00368 129 DKTCYNCGQTGHLSRDCPD 147 (148)
T ss_pred CCccccCCCcCcccccCCC
Confidence 3566666666666666664
No 13
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=87.86 E-value=0.27 Score=37.06 Aligned_cols=25 Identities=44% Similarity=1.002 Sum_probs=19.0
Q ss_pred EeeccCCcccccccccccCCCCCCCC
Q 040998 78 VEYESLPINCFNCGKYGHVSIGCPEN 103 (117)
Q Consensus 78 v~YE~lp~~C~~Cg~~GH~~~~C~~~ 103 (117)
+.+.+- .+||.||..||...+|+..
T Consensus 138 ~~~~~~-~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 138 VDGPKP-AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred ccCCCC-CccCCCCcCCcchhhCCCC
Confidence 344444 6799999999999999854
No 14
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=84.50 E-value=0.7 Score=40.40 Aligned_cols=29 Identities=28% Similarity=0.649 Sum_probs=25.4
Q ss_pred EEeeccCCcccccccccccCCCCCCCCCC
Q 040998 77 KVEYESLPINCFNCGKYGHVSIGCPENGD 105 (117)
Q Consensus 77 ~v~YE~lp~~C~~Cg~~GH~~~~C~~~~~ 105 (117)
.+.+...|.-|+.||..||..++|.-...
T Consensus 253 E~~~P~~~~~C~~cgq~gh~~~dc~g~~~ 281 (931)
T KOG2044|consen 253 EEFFPNKPRRCFLCGQTGHEAKDCEGKPR 281 (931)
T ss_pred eeecCCCcccchhhcccCCcHhhcCCcCC
Confidence 45569999999999999999999998855
No 15
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=83.77 E-value=0.58 Score=36.71 Aligned_cols=22 Identities=41% Similarity=0.955 Sum_probs=19.7
Q ss_pred cccccccccccCCCCCCCCCCC
Q 040998 85 INCFNCGKYGHVSIGCPENGDG 106 (117)
Q Consensus 85 ~~C~~Cg~~GH~~~~C~~~~~~ 106 (117)
..||.||.-||...+|+.....
T Consensus 177 Y~CyRCGqkgHwIqnCpTN~Dp 198 (427)
T COG5222 177 YVCYRCGQKGHWIQNCPTNQDP 198 (427)
T ss_pred eeEEecCCCCchhhcCCCCCCC
Confidence 6899999999999999987653
No 16
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=79.89 E-value=2.6 Score=26.22 Aligned_cols=43 Identities=21% Similarity=0.285 Sum_probs=31.6
Q ss_pred EecCCCccccccchhhhhhhccccEEEEeccCCCccccceEEE
Q 040998 13 KLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRI 55 (117)
Q Consensus 13 ri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y~Rv 55 (117)
+...||.-+-+..+++.+|-.-|.++++...+......-+-|+
T Consensus 30 ~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR~ 72 (74)
T PF01191_consen 30 KPEQLPKILSSDPVARYLGAKPGDVVKIIRKSETAGEYVTYRL 72 (74)
T ss_dssp -TTCSSEEETTSHHHHHTT--TTSEEEEEEEETTTSEEEEEEE
T ss_pred ChhhCCcccccChhhhhcCCCCCCEEEEEecCCCCCCcEEEEE
Confidence 4567999999999999999999999999998765433333344
No 17
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=77.17 E-value=1.8 Score=29.73 Aligned_cols=20 Identities=45% Similarity=1.200 Sum_probs=11.9
Q ss_pred cccccccccccCCCCCCCCC
Q 040998 85 INCFNCGKYGHVSIGCPENG 104 (117)
Q Consensus 85 ~~C~~Cg~~GH~~~~C~~~~ 104 (117)
..|+.|+..||...+|+...
T Consensus 78 ~~C~~Cg~~GH~~~~C~~~~ 97 (148)
T PTZ00368 78 RSCYNCGQTGHISRECPNRA 97 (148)
T ss_pred cccCcCCCCCcccccCCCcc
Confidence 45666666666666665543
No 18
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=73.20 E-value=1.8 Score=30.69 Aligned_cols=31 Identities=32% Similarity=0.656 Sum_probs=22.0
Q ss_pred CCCceeEEEEeceE-EEEeeccCCccccccccc
Q 040998 62 DKPLCLQFLLDGRI-QKVEYESLPINCFNCGKY 93 (117)
Q Consensus 62 ~kPL~~~v~v~g~~-~~v~YE~lp~~C~~Cg~~ 93 (117)
+.|++....++|.. +.-.|+ .|.+|+.||+-
T Consensus 46 ~~~IrG~y~v~gv~~~g~~~~-~PsYC~~CGkp 77 (158)
T PF10083_consen 46 STPIRGDYHVEGVFGLGGHYE-APSYCHNCGKP 77 (158)
T ss_pred CCCCCCceecCCeeeeCCCCC-CChhHHhCCCC
Confidence 34555555666653 457888 99999999974
No 19
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=72.66 E-value=1.6 Score=26.89 Aligned_cols=14 Identities=50% Similarity=1.405 Sum_probs=10.8
Q ss_pred CCccccccccc-ccC
Q 040998 83 LPINCFNCGKY-GHV 96 (117)
Q Consensus 83 lp~~C~~Cg~~-GH~ 96 (117)
+|..||.||++ ||.
T Consensus 3 iPVRCFTCGkvig~~ 17 (71)
T PLN00032 3 IPVRCFTCGKVIGNK 17 (71)
T ss_pred CceeecCCCCCcHHH
Confidence 58899999985 443
No 20
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=71.98 E-value=4.1 Score=25.63 Aligned_cols=35 Identities=26% Similarity=0.357 Sum_probs=30.1
Q ss_pred EecCCCccccccchhhhhhhccccEEEEeccCCCc
Q 040998 13 KLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSA 47 (117)
Q Consensus 13 ri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~ 47 (117)
+...||.-+-+..+++.+|-.-|.++++...+...
T Consensus 33 ~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R~S~ta 67 (79)
T PRK09570 33 KPEQLPKIKASDPVVKAIGAKPGDVIKIVRKSPTA 67 (79)
T ss_pred CHHHCCceeccChhhhhcCCCCCCEEEEEECCCCC
Confidence 34568999999999999999999999998887543
No 21
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=71.78 E-value=0.93 Score=37.31 Aligned_cols=20 Identities=35% Similarity=0.595 Sum_probs=18.1
Q ss_pred cccccccccccCCCCCCCCC
Q 040998 85 INCFNCGKYGHVSIGCPENG 104 (117)
Q Consensus 85 ~~C~~Cg~~GH~~~~C~~~~ 104 (117)
.+|.+||-+||..+.|-.+.
T Consensus 113 GACeNCGAmtHk~KDCmERP 132 (529)
T KOG2560|consen 113 GACENCGAMTHKVKDCMERP 132 (529)
T ss_pred hhhhhhhhhhcchHHHhhcc
Confidence 79999999999999997764
No 22
>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=70.83 E-value=2 Score=25.62 Aligned_cols=11 Identities=55% Similarity=1.603 Sum_probs=7.9
Q ss_pred CCccccccccc
Q 040998 83 LPINCFNCGKY 93 (117)
Q Consensus 83 lp~~C~~Cg~~ 93 (117)
.|..||.||++
T Consensus 3 iPVRCFTCGkv 13 (60)
T PF01194_consen 3 IPVRCFTCGKV 13 (60)
T ss_dssp -SSS-STTTSB
T ss_pred CceecCCCCCC
Confidence 58899999985
No 23
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=69.76 E-value=2.1 Score=25.76 Aligned_cols=11 Identities=55% Similarity=1.603 Sum_probs=9.5
Q ss_pred CCccccccccc
Q 040998 83 LPINCFNCGKY 93 (117)
Q Consensus 83 lp~~C~~Cg~~ 93 (117)
.|..||.||++
T Consensus 3 iPvRCFTCGkv 13 (62)
T PRK04016 3 IPVRCFTCGKV 13 (62)
T ss_pred CCeEecCCCCC
Confidence 58899999985
No 24
>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]
Probab=69.73 E-value=6.1 Score=31.10 Aligned_cols=70 Identities=17% Similarity=0.265 Sum_probs=46.7
Q ss_pred CccccceEeEEEEecCCCccccccchhhhhhhccccEEEEeccCCCccccceEEEEEEEccCCCcee-EEEEece
Q 040998 1 TSDKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKPLCL-QFLLDGR 74 (117)
Q Consensus 1 ~~~~l~~~~~WVri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y~Rv~V~idl~kPL~~-~v~v~g~ 74 (117)
|+.+.+-...||.++|.|..- -+++...=+..|++++.... .+++|. ++|-.=.++..|.|.+ +..|+|.
T Consensus 189 te~~~d~~D~WVTVfGFppg~--~s~vL~~F~~cG~Vvkhv~~-~ngNwM-hirYssr~~A~KALskng~ii~g~ 259 (350)
T KOG4285|consen 189 TEEEADAADTWVTVFGFPPGQ--VSIVLNLFSRCGEVVKHVTP-SNGNWM-HIRYSSRTHAQKALSKNGTIIDGD 259 (350)
T ss_pred cccccccccceEEEeccCccc--hhHHHHHHHhhCeeeeeecC-CCCceE-EEEecchhHHHHhhhhcCeeeccc
Confidence 345566778999999999985 34555566789999997666 444433 2344456677888865 4455543
No 25
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=69.25 E-value=3.4 Score=31.06 Aligned_cols=25 Identities=40% Similarity=0.822 Sum_probs=22.6
Q ss_pred CCcccccccccccCCCCCCCCCCCC
Q 040998 83 LPINCFNCGKYGHVSIGCPENGDGE 107 (117)
Q Consensus 83 lp~~C~~Cg~~GH~~~~C~~~~~~~ 107 (117)
.+..|+.|+..||...+|+.....+
T Consensus 163 ~~~~c~~c~~~~h~~~~C~~~~~~~ 187 (261)
T KOG4400|consen 163 KGGTCFRCGKVGHGSRDCPSKQKSK 187 (261)
T ss_pred CCCccccCCCcceecccCCcccccc
Confidence 4899999999999999999998763
No 26
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=69.11 E-value=2.1 Score=25.75 Aligned_cols=14 Identities=57% Similarity=1.528 Sum_probs=10.8
Q ss_pred CCccccccccc-ccC
Q 040998 83 LPINCFNCGKY-GHV 96 (117)
Q Consensus 83 lp~~C~~Cg~~-GH~ 96 (117)
.|..||.||+. ||.
T Consensus 3 iPiRCFsCGkvi~~~ 17 (63)
T COG1644 3 IPVRCFSCGKVIGHK 17 (63)
T ss_pred CceEeecCCCCHHHH
Confidence 58899999974 554
No 27
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=68.89 E-value=7.2 Score=31.03 Aligned_cols=43 Identities=16% Similarity=0.369 Sum_probs=32.4
Q ss_pred eEEEEecCCCccccccchhhhhhhccccEEEEeccCCCccccce
Q 040998 9 VAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKF 52 (117)
Q Consensus 9 ~~WVri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y 52 (117)
|=-+.+.|||+.|++.+...+.+ ..|+|++|+.-.+.+....|
T Consensus 96 pkRLhVSNIPFrFRdpDL~aMF~-kfG~VldVEIIfNERGSKGF 138 (376)
T KOG0125|consen 96 PKRLHVSNIPFRFRDPDLRAMFE-KFGKVLDVEIIFNERGSKGF 138 (376)
T ss_pred CceeEeecCCccccCccHHHHHH-hhCceeeEEEEeccCCCCcc
Confidence 34567889999999999876665 89999999876654434444
No 28
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=67.13 E-value=9.8 Score=21.68 Aligned_cols=33 Identities=27% Similarity=0.536 Sum_probs=26.9
Q ss_pred eEEEEecCCCccccccchhhhhhhccccEEEEecc
Q 040998 9 VAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFN 43 (117)
Q Consensus 9 ~~WVri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~ 43 (117)
+-||-+.|.|.... +.++....+ +|++.++...
T Consensus 1 ~~wI~V~Gf~~~~~-~~vl~~F~~-fGeI~~~~~~ 33 (53)
T PF14605_consen 1 STWISVSGFPPDLA-EEVLEHFAS-FGEIVDIYVP 33 (53)
T ss_pred CcEEEEEeECchHH-HHHHHHHHh-cCCEEEEEcC
Confidence 46999999998874 567778885 9999998776
No 29
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=65.04 E-value=10 Score=23.82 Aligned_cols=41 Identities=20% Similarity=0.340 Sum_probs=32.1
Q ss_pred cCCCccccccchhhhhhhccccEEEEeccCCCccccceEEE
Q 040998 15 SNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRI 55 (117)
Q Consensus 15 ~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y~Rv 55 (117)
..||--..+..+++.+|...|.++++-..+......-|-|+
T Consensus 38 ~qLPkI~~~DPva~~lgak~GdvVkIvRkS~TaGe~v~YR~ 78 (80)
T COG2012 38 EQLPKIKASDPVAKALGAKPGDVVKIVRKSPTAGESVYYRL 78 (80)
T ss_pred HHCCcccccChhHHHccCCCCcEEEEEecCCCCCceEEEEE
Confidence 45788888999999999999999999888755444444454
No 30
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=64.34 E-value=2.4 Score=25.47 Aligned_cols=11 Identities=64% Similarity=1.630 Sum_probs=9.4
Q ss_pred CCccccccccc
Q 040998 83 LPINCFNCGKY 93 (117)
Q Consensus 83 lp~~C~~Cg~~ 93 (117)
.|..||.||++
T Consensus 3 iPiRCFtCGKv 13 (69)
T KOG3497|consen 3 IPIRCFTCGKV 13 (69)
T ss_pred eeeEeeecccc
Confidence 58899999986
No 31
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.02 E-value=3.7 Score=28.32 Aligned_cols=29 Identities=28% Similarity=0.628 Sum_probs=18.3
Q ss_pred CceeEEEEeceE-EEEeeccCCccccccccc
Q 040998 64 PLCLQFLLDGRI-QKVEYESLPINCFNCGKY 93 (117)
Q Consensus 64 PL~~~v~v~g~~-~~v~YE~lp~~C~~Cg~~ 93 (117)
|++....++|.. +-=.|| .|.||.+||.-
T Consensus 48 sirgd~~vegvlglg~dye-~psfchncgs~ 77 (160)
T COG4306 48 SIRGDYYVEGVLGLGGDYE-PPSFCHNCGSR 77 (160)
T ss_pred cccccceeeeeeccCCCCC-CcchhhcCCCC
Confidence 444444555432 334676 79999999975
No 32
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=60.72 E-value=14 Score=20.81 Aligned_cols=32 Identities=16% Similarity=0.195 Sum_probs=22.9
Q ss_pred EEecCCCccccccchhhhhhhccccEEEEeccC
Q 040998 12 IKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNT 44 (117)
Q Consensus 12 Vri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~ 44 (117)
|-|.|||..+-.+. ++.+-+..|.+..+....
T Consensus 1 l~v~nlp~~~t~~~-l~~~f~~~g~i~~~~~~~ 32 (70)
T PF00076_consen 1 LYVGNLPPDVTEEE-LRDFFSQFGKIESIKVMR 32 (70)
T ss_dssp EEEESETTTSSHHH-HHHHHHTTSTEEEEEEEE
T ss_pred cEEcCCCCcCCHHH-HHHHHHHhhhcccccccc
Confidence 45789999885544 445555699998877766
No 33
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=60.17 E-value=5.4 Score=33.30 Aligned_cols=18 Identities=50% Similarity=1.027 Sum_probs=16.4
Q ss_pred ccccccccccCCCCCCCC
Q 040998 86 NCFNCGKYGHVSIGCPEN 103 (117)
Q Consensus 86 ~C~~Cg~~GH~~~~C~~~ 103 (117)
.|+.||-+||...+|+..
T Consensus 287 ~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 287 VCKICGPLGHISIDCKVN 304 (554)
T ss_pred cccccCCcccccccCCCc
Confidence 899999999999999887
No 34
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=58.14 E-value=3.8 Score=33.69 Aligned_cols=22 Identities=32% Similarity=0.706 Sum_probs=19.5
Q ss_pred cccccccccccCCCCCCCCCCC
Q 040998 85 INCFNCGKYGHVSIGCPENGDG 106 (117)
Q Consensus 85 ~~C~~Cg~~GH~~~~C~~~~~~ 106 (117)
.-|..||-+||-..+||+..+-
T Consensus 571 kGCayCgGLGHRItdCPKle~~ 592 (610)
T KOG0341|consen 571 KGCAYCGGLGHRITDCPKLEAQ 592 (610)
T ss_pred cccccccCCCcccccCchhhhh
Confidence 5699999999999999987654
No 35
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=56.29 E-value=7.7 Score=33.57 Aligned_cols=27 Identities=33% Similarity=0.843 Sum_probs=20.9
Q ss_pred CcccccccccccC--CCCCCCCCCCCCCc
Q 040998 84 PINCFNCGKYGHV--SIGCPENGDGEEPQ 110 (117)
Q Consensus 84 p~~C~~Cg~~GH~--~~~C~~~~~~~~~~ 110 (117)
-..|..||.+||. .+.||.-...+-++
T Consensus 937 tr~C~nCGQvGHmkTNK~CP~f~s~~~~a 965 (968)
T COG5179 937 TRTCGNCGQVGHMKTNKACPKFSSKDNPA 965 (968)
T ss_pred ceecccccccccccccccCccccCCCCCC
Confidence 4789999999996 46799877665443
No 36
>KOG2985 consensus Uncharacterized conserved protein [Function unknown]
Probab=52.21 E-value=4.1 Score=31.23 Aligned_cols=34 Identities=24% Similarity=0.525 Sum_probs=25.2
Q ss_pred eccCCcccccccccccCCCCCCCCCCCCCCcccC
Q 040998 80 YESLPINCFNCGKYGHVSIGCPENGDGEEPQDEN 113 (117)
Q Consensus 80 YE~lp~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~ 113 (117)
-|-...-|..||..||....|.......|+..+.
T Consensus 77 ~~arsg~ckRcg~~ghl~fqcRn~~~vke~~~~~ 110 (306)
T KOG2985|consen 77 DEARSGSCKRCGRVGHLTFQCRNFLSVKEDKEKD 110 (306)
T ss_pred chhcccchhhccccchhhHHHhhhhhcccccccc
Confidence 3444467999999999999999887655554433
No 37
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=50.13 E-value=10 Score=21.62 Aligned_cols=18 Identities=28% Similarity=0.514 Sum_probs=14.5
Q ss_pred CCcccccccccccCCCCC
Q 040998 83 LPINCFNCGKYGHVSIGC 100 (117)
Q Consensus 83 lp~~C~~Cg~~GH~~~~C 100 (117)
--.||+.|+...|.-..|
T Consensus 47 ~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 47 GFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred CCeECCCCCCcCCCCCCC
Confidence 357899999999987665
No 38
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=46.11 E-value=42 Score=20.86 Aligned_cols=46 Identities=26% Similarity=0.549 Sum_probs=28.8
Q ss_pred ccceEEEEEEEccCCCceeEEEEe-ceEE----------EEeeccCCcccccccccc
Q 040998 49 RRKFVRIAVKIALDKPLCLQFLLD-GRIQ----------KVEYESLPINCFNCGKYG 94 (117)
Q Consensus 49 ~~~y~Rv~V~idl~kPL~~~v~v~-g~~~----------~v~YE~lp~~C~~Cg~~G 94 (117)
.+.|-|++|..+.......-..+| |... .-++..+|..+..|..-|
T Consensus 65 ~~~w~Ra~I~~~~~~~~~~V~~iD~G~~~~v~~~~l~~l~~~~~~~P~~a~~~~L~g 121 (121)
T PF00567_consen 65 DGRWYRAVITVDIDENQYKVFLIDYGNTEKVSASDLRPLPPEFASLPPQAIKCKLAG 121 (121)
T ss_dssp TSEEEEEEEEEEECTTEEEEEETTTTEEEEEEGGGEEE--HHHCSSSSSCEEEEET-
T ss_pred CCceeeEEEEEecccceeEEEEEecCceEEEcHHHhhhhCHHHhhCChhhEEEEEcC
Confidence 357889999666666665555555 5433 445556778888776544
No 39
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=46.08 E-value=14 Score=21.28 Aligned_cols=17 Identities=24% Similarity=0.407 Sum_probs=12.8
Q ss_pred EEEEee---ccCCccccccc
Q 040998 75 IQKVEY---ESLPINCFNCG 91 (117)
Q Consensus 75 ~~~v~Y---E~lp~~C~~Cg 91 (117)
+|.|+. .++..||..||
T Consensus 7 yY~v~~~kv~rk~~~CPrCG 26 (51)
T COG1998 7 YYEVDDEKVKRKNRFCPRCG 26 (51)
T ss_pred EEEEcCCcEEEccccCCCCC
Confidence 455555 56789999999
No 40
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=45.91 E-value=13 Score=21.82 Aligned_cols=30 Identities=37% Similarity=0.705 Sum_probs=19.9
Q ss_pred cccccccccccCCCCCCC-CC-------CCCCCcccCCC
Q 040998 85 INCFNCGKYGHVSIGCPE-NG-------DGEEPQDENGK 115 (117)
Q Consensus 85 ~~C~~Cg~~GH~~~~C~~-~~-------~~~~~~~~~~~ 115 (117)
..|..||.+.= .+.||. +. +.=+|.|.+||
T Consensus 6 r~C~~CgvYTL-k~~CP~CG~~t~~~~P~rfSp~D~y~~ 43 (56)
T PRK13130 6 RKCPKCGVYTL-KEICPVCGGKTKNPHPPRFSPEDKYGK 43 (56)
T ss_pred eECCCCCCEEc-cccCcCCCCCCCCCCCCCCCCCCccHH
Confidence 56888888876 777776 32 23456677765
No 41
>smart00769 WHy Water Stress and Hypersensitive response.
Probab=42.79 E-value=37 Score=21.47 Aligned_cols=32 Identities=13% Similarity=0.257 Sum_probs=25.9
Q ss_pred eEEEEEEEccCCCceeEEEEeceEEEEeeccC
Q 040998 52 FVRIAVKIALDKPLCLQFLLDGRIQKVEYESL 83 (117)
Q Consensus 52 y~Rv~V~idl~kPL~~~v~v~g~~~~v~YE~l 83 (117)
-+++.+.+.+.+|-+..+.++|..|.+.|.+.
T Consensus 14 ~~~~~l~l~v~NPN~~~l~~~~~~y~l~~~g~ 45 (100)
T smart00769 14 EIEIVLKVKVQNPNPFPIPVNGLSYDLYLNGV 45 (100)
T ss_pred EEEEEEEEEEECCCCCccccccEEEEEEECCE
Confidence 35788888899999888888888888887663
No 42
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=39.75 E-value=16 Score=30.30 Aligned_cols=19 Identities=47% Similarity=0.955 Sum_probs=17.2
Q ss_pred cccccccccCCCCCCCCCC
Q 040998 87 CFNCGKYGHVSIGCPENGD 105 (117)
Q Consensus 87 C~~Cg~~GH~~~~C~~~~~ 105 (117)
||+||-.-|+..+|+.+..
T Consensus 131 CFNC~g~~hsLrdC~rp~d 149 (485)
T KOG2673|consen 131 CFNCGGTPHSLRDCPRPFD 149 (485)
T ss_pred ccccCCCCCccccCCCccc
Confidence 8999999999999998753
No 43
>PF05515 Viral_NABP: Viral nucleic acid binding ; InterPro: IPR008891 This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding proteins (NABP).
Probab=39.56 E-value=18 Score=24.71 Aligned_cols=19 Identities=42% Similarity=0.989 Sum_probs=16.5
Q ss_pred cccccccccccCCCCCCCC
Q 040998 85 INCFNCGKYGHVSIGCPEN 103 (117)
Q Consensus 85 ~~C~~Cg~~GH~~~~C~~~ 103 (117)
..|+.||.+-|....|+..
T Consensus 63 ~~C~~CG~~l~~~~~C~~~ 81 (124)
T PF05515_consen 63 NRCFKCGRYLHNNGNCRRN 81 (124)
T ss_pred CccccccceeecCCcCCCc
Confidence 5799999999999999953
No 44
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=39.51 E-value=14 Score=28.55 Aligned_cols=22 Identities=32% Similarity=0.753 Sum_probs=19.1
Q ss_pred CcccccccccccCCCCCCCCCC
Q 040998 84 PINCFNCGKYGHVSIGCPENGD 105 (117)
Q Consensus 84 p~~C~~Cg~~GH~~~~C~~~~~ 105 (117)
-.+|+.||.+-|....|+.-.+
T Consensus 261 ~~~C~iC~~~~~~R~~C~~~kA 282 (325)
T KOG4399|consen 261 KHGCFICGELDHKRSTCPNIKA 282 (325)
T ss_pred hcceeeccccccccccCccHHH
Confidence 3799999999999999997644
No 45
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=38.25 E-value=17 Score=29.61 Aligned_cols=23 Identities=35% Similarity=0.983 Sum_probs=18.5
Q ss_pred CcccccccccccC--CCCCCCCCCC
Q 040998 84 PINCFNCGKYGHV--SIGCPENGDG 106 (117)
Q Consensus 84 p~~C~~Cg~~GH~--~~~C~~~~~~ 106 (117)
..-|..|+.+||. ..+||.-...
T Consensus 124 NVrC~kChkwGH~n~DreCplf~~~ 148 (453)
T KOG3794|consen 124 NVRCLKCHKWGHINTDRECPLFGKS 148 (453)
T ss_pred eeeEEeecccccccCCccCcchhhc
Confidence 4679999999996 5689987654
No 46
>PRK09698 D-allose kinase; Provisional
Probab=38.18 E-value=70 Score=24.00 Aligned_cols=89 Identities=11% Similarity=0.228 Sum_probs=50.2
Q ss_pred EEecCCCc-cccccchhhhhhhccccEEEEeccCCCccccceE------EEEEEEccCCCceeEEEEeceE---------
Q 040998 12 IKLSNMPH-YYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFV------RIAVKIALDKPLCLQFLLDGRI--------- 75 (117)
Q Consensus 12 Vri~~lP~-~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y~------Rv~V~idl~kPL~~~v~v~g~~--------- 75 (117)
+...++|. .+....+...+.+.+|.|+.++.+......+.+. +-.+-+.+..=+=..+.++|..
T Consensus 81 ~~~~~~~~~~~~~~~l~~~l~~~~~~pv~v~NDa~aaa~~E~~~~~~~~~~~~~v~lgtGIG~giv~~G~~~~G~~g~ag 160 (302)
T PRK09698 81 ISTPNLPLTALDLYDLADKLENTLNCPVFFSRDVNLQLLWDVKENNLTQQLVLGAYLGTGMGFAVWMNGAPWTGAHGVAG 160 (302)
T ss_pred EecCCCCccccccCCHHHHHHHHhCCCEEEcchHhHHHHHHHHhcCCCCceEEEEEecCceEEEEEECCEEeeCCCCCcc
Confidence 44455554 3444577788888899999888775543222111 1233444554444445555432
Q ss_pred --EEEeeccCCcccccccccccCCCCCC
Q 040998 76 --QKVEYESLPINCFNCGKYGHVSIGCP 101 (117)
Q Consensus 76 --~~v~YE~lp~~C~~Cg~~GH~~~~C~ 101 (117)
-.+.+..-...|. ||..|+.+..|.
T Consensus 161 EiGh~~v~~~~~~C~-CG~~gclE~~~S 187 (302)
T PRK09698 161 ELGHIPLGDMTQHCG-CGNPGCLETNCS 187 (302)
T ss_pred ccCceEeeCCCcccC-CCCccchHhhcC
Confidence 1233333456775 888888877765
No 47
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=36.43 E-value=38 Score=25.64 Aligned_cols=78 Identities=14% Similarity=0.316 Sum_probs=50.5
Q ss_pred ccc-cchhhhhhhccccEEEEeccCCCccccc-------eEEEEEEEccCCCceeEEEEeceE-------------EEEe
Q 040998 21 YYH-KKVLPMVGQVMGEVIHIDFNTRSASRRK-------FVRIAVKIALDKPLCLQFLLDGRI-------------QKVE 79 (117)
Q Consensus 21 ~~~-~~~~~~I~~~iG~~l~vD~~~~~~~~~~-------y~Rv~V~idl~kPL~~~v~v~g~~-------------~~v~ 79 (117)
.|+ .++...|.+.+|.|+.++.+.+....+. -.+.-+-+.+..-+=..+.++|.. ..+.
T Consensus 92 ~~~~~~l~~~L~~~~~~Pv~veNDan~aalaE~~~g~~~~~~~~~~i~~gtGIG~giv~~g~l~~G~~g~age~Gh~~v~ 171 (314)
T COG1940 92 WWNGVDLAEELEARLGLPVFVENDANAAALAEAWFGAGRGIDDVVYITLGTGIGGGIIVNGKLLRGANGNAGEIGHMVVD 171 (314)
T ss_pred ccccccHHHHHHHHHCCCEEEecHHHHHHHHHHHhCCCCCCCCEEEEEEccceeEEEEECCEEeecCCCccccccceEEC
Confidence 444 4578999999999999988765422221 124556677777777777776532 2333
Q ss_pred eccCCcccccccccccCCCCCCC
Q 040998 80 YESLPINCFNCGKYGHVSIGCPE 102 (117)
Q Consensus 80 YE~lp~~C~~Cg~~GH~~~~C~~ 102 (117)
.... | .||..|+.+..+..
T Consensus 172 ~~g~---c-~cG~~GclE~~as~ 190 (314)
T COG1940 172 PDGE---C-GCGRRGCLETYASG 190 (314)
T ss_pred CCCc---c-CCCCCCchHHhccH
Confidence 3333 9 99999988776543
No 48
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=35.60 E-value=32 Score=25.45 Aligned_cols=39 Identities=18% Similarity=0.306 Sum_probs=32.0
Q ss_pred EecCCCccccccchhhhhhhccccEEEEeccCCCccccceE
Q 040998 13 KLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFV 53 (117)
Q Consensus 13 ri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y~ 53 (117)
+...||.-+-+..+++.+|-.-|.++++...+.. .|.|+
T Consensus 162 ~~~qLPrI~~~DPvary~g~k~G~vvkI~R~S~t--aG~~v 200 (206)
T PLN03111 162 KETQLPRIQVSDPIARYYGLKRGQVVKIIRPSET--AGRYV 200 (206)
T ss_pred CHHHCCcccccChhhHhcCCCCCCEEEEEECCCC--CCCce
Confidence 4457899999999999999999999999888654 34443
No 49
>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=35.05 E-value=15 Score=20.76 Aligned_cols=18 Identities=33% Similarity=0.730 Sum_probs=12.3
Q ss_pred CCcccccccccccCCCCC
Q 040998 83 LPINCFNCGKYGHVSIGC 100 (117)
Q Consensus 83 lp~~C~~Cg~~GH~~~~C 100 (117)
...||+.|+..-|....|
T Consensus 47 ~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 47 GTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp CSEECSSSTSESCTTS-H
T ss_pred CCcCccccCcccCCCCCC
Confidence 346888888888875544
No 50
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=35.00 E-value=23 Score=29.76 Aligned_cols=22 Identities=36% Similarity=0.757 Sum_probs=19.6
Q ss_pred cccccccccccCCCCCCCCCCC
Q 040998 85 INCFNCGKYGHVSIGCPENGDG 106 (117)
Q Consensus 85 ~~C~~Cg~~GH~~~~C~~~~~~ 106 (117)
.+|..||.-||..-+|+.+..+
T Consensus 262 ~~c~~cg~~~H~q~~cp~r~~~ 283 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGRIPN 283 (554)
T ss_pred ccccccCCCccccccCCccccc
Confidence 7999999999999999998443
No 51
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=34.58 E-value=89 Score=17.61 Aligned_cols=33 Identities=18% Similarity=0.203 Sum_probs=22.6
Q ss_pred EEecCCCccccccchhhhhhhccccEEEEeccCC
Q 040998 12 IKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTR 45 (117)
Q Consensus 12 Vri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~ 45 (117)
|-|.|||... +++-++..-+..|.+..+.....
T Consensus 1 v~i~nlp~~~-~~~~l~~~f~~~g~v~~v~~~~~ 33 (70)
T PF14259_consen 1 VYISNLPPST-TEEDLRNFFSRFGPVEKVRLIKN 33 (70)
T ss_dssp EEEESSTTT---HHHHHHHCTTSSBEEEEEEEES
T ss_pred CEEeCCCCCC-CHHHHHHHHHhcCCcceEEEEee
Confidence 4688999985 55556667777798877776654
No 52
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=33.70 E-value=2.3e+02 Score=24.81 Aligned_cols=32 Identities=9% Similarity=0.304 Sum_probs=24.8
Q ss_pred EeEEEEecCCCccccccchhhhhh-hccccEEEEecc
Q 040998 8 MVAWIKLSNMPHYYYHKKVLPMVG-QVMGEVIHIDFN 43 (117)
Q Consensus 8 ~~~WVri~~lP~~~~~~~~~~~I~-~~iG~~l~vD~~ 43 (117)
-.+|++|.++|..+ .++.|. ..+|+.+.++-.
T Consensus 82 ~~~~~~~~~~~~~~----~iR~l~s~~igkLV~v~Gi 114 (682)
T COG1241 82 KKIHVRFKNLPNRL----SIRELRSEHIGKLVSVEGI 114 (682)
T ss_pred cceEEEecCCcCCc----ChhhCchhhCCcEEEEEEE
Confidence 46899999999987 556666 588888887553
No 53
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=33.36 E-value=37 Score=25.14 Aligned_cols=34 Identities=24% Similarity=0.274 Sum_probs=29.6
Q ss_pred EecCCCccccccchhhhhhhccccEEEEeccCCC
Q 040998 13 KLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRS 46 (117)
Q Consensus 13 ri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~ 46 (117)
+...||.-+-+..+++.+|-.-|.++++...+..
T Consensus 161 ~~~qLPrI~~~DPvary~g~k~G~vvkI~R~S~t 194 (205)
T PTZ00061 161 KESQLPRIQSADPVARYFGLSKGQVVKIIRPSET 194 (205)
T ss_pred CHHHCCcccccChhhHhcCCCCCCEEEEEECCCC
Confidence 3456899999999999999999999999888754
No 54
>PF12322 T4_baseplate: T4 bacteriophage base plate protein; InterPro: IPR024364 Proteins in this family are found in T4-like viruses. They have a single completely conserved residue S that may be functionally important. The family includes the two base plate proteins from bacteriophage T4: Gp51 and Gp26, encoded by late genes []. Gp26 is a structural component of central hub of the baseplate. It associates with Gp25 (tail lysozyme) in the assembly process. Gp51 is essential for the formation of the central hub of the phage baseplate, playing a catalytic role for the central hub formation. It may be also a structural component of the hub.
Probab=32.23 E-value=1.1e+02 Score=22.43 Aligned_cols=69 Identities=23% Similarity=0.369 Sum_probs=48.6
Q ss_pred ecCCCccccccchhhhhhhccccE-EEEeccCCCccccceEEEEEEEccCC-Cc---eeEEEE-eceEEEEeeccCCcc
Q 040998 14 LSNMPHYYYHKKVLPMVGQVMGEV-IHIDFNTRSASRRKFVRIAVKIALDK-PL---CLQFLL-DGRIQKVEYESLPIN 86 (117)
Q Consensus 14 i~~lP~~~~~~~~~~~I~~~iG~~-l~vD~~~~~~~~~~y~Rv~V~idl~k-PL---~~~v~v-~g~~~~v~YE~lp~~ 86 (117)
+.+||.....--.++..+.++|+. +.+...=.. -|. ++.+.+++++ ++ ...+.. +|..+.++|+.+..+
T Consensus 50 ~~~l~~~~~EylFl~l~~~Sige~~v~~~~~C~~--cg~--~~~~~i~l~~~~l~~~~~~~~~~~~i~i~~ryP~~~~~ 124 (205)
T PF12322_consen 50 FEDLPKFDREYLFLKLRAKSIGETKVPVNYTCPD--CGE--EVKVPINLDQIKLTDGKNEIKLSDGIKIKMRYPSLFEF 124 (205)
T ss_pred cccCChhHHHHHHHHHHHhcCCCccceEEEECCC--CCc--EEEEEecchhcccCCCCcceEecCCEEEEEeCCccccc
Confidence 567888888888999999999998 776655221 233 6777777775 44 333334 456789999987754
No 55
>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []. This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.
Probab=31.26 E-value=39 Score=22.01 Aligned_cols=31 Identities=16% Similarity=0.367 Sum_probs=19.9
Q ss_pred eEEEEecCCCccccccchhhhhhhccccEEEEe
Q 040998 9 VAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHID 41 (117)
Q Consensus 9 ~~WVri~~lP~~~~~~~~~~~I~~~iG~~l~vD 41 (117)
.-||.+.|-|.. ....+++... ..|++++..
T Consensus 6 ~~wVtVFGfp~~-~~~~Vl~~F~-~~G~Ile~~ 36 (100)
T PF05172_consen 6 ETWVTVFGFPPS-ASNQVLRHFS-SFGTILEHF 36 (100)
T ss_dssp CCEEEEE---GG-GHHHHHHHHH-CCS-EECEE
T ss_pred CeEEEEEccCHH-HHHHHHHHHH-hcceEEEee
Confidence 469999999999 4556665655 889998864
No 56
>PF06130 PduL: Propanediol utilisation protein PduL; InterPro: IPR008300 Salmonella enterica subsp. enterica serovar Typhimurium degrades 1,2-propanediol by a pathway that requires coenzyme B12, adenosylcobalamin (AdoCbl). Proteins required for 1,2-propanediol degradation are encoded by the pdu operon []. PduL functions in this pathway, but its exact role is not yet determined. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilization of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilization (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and coregulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR010254 from INTERPRO and IPR009204 from INTERPRO for more details on the propanediol utilization pathway and the pdu operon.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups
Probab=31.00 E-value=1.3e+02 Score=18.36 Aligned_cols=45 Identities=13% Similarity=0.152 Sum_probs=32.7
Q ss_pred cccchhhhhhhccccEEEEeccCCCccc-cceEEEEEEEccCCCcee
Q 040998 22 YHKKVLPMVGQVMGEVIHIDFNTRSASR-RKFVRIAVKIALDKPLCL 67 (117)
Q Consensus 22 ~~~~~~~~I~~~iG~~l~vD~~~~~~~~-~~y~Rv~V~idl~kPL~~ 67 (117)
++++-+..++-.=|+++.+.. +..+.+ +-|-+|+|.++-+.-+.-
T Consensus 13 ms~~da~~l~~~dg~~v~ve~-~~~g~r~~~~~~V~Vrv~~~~~~q~ 58 (71)
T PF06130_consen 13 MSPEDAEKLFGQDGQFVSVEV-TVVGPRGGIFENVRVRVPERFALQM 58 (71)
T ss_pred CCHHHHHHhCCCCCCEEEEEE-eccCCCcceeeeeEEEcCCCcceEE
Confidence 566777778888888888888 555555 777788888776665543
No 57
>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=26.70 E-value=38 Score=22.98 Aligned_cols=22 Identities=23% Similarity=0.495 Sum_probs=18.1
Q ss_pred cCCcccccccccccCCCCCCCCC
Q 040998 82 SLPINCFNCGKYGHVSIGCPENG 104 (117)
Q Consensus 82 ~lp~~C~~Cg~~GH~~~~C~~~~ 104 (117)
..-..|..|+ -.|....||...
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 3447899997 889999999864
No 58
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=26.26 E-value=42 Score=16.10 Aligned_cols=8 Identities=50% Similarity=1.190 Sum_probs=4.8
Q ss_pred cccccccc
Q 040998 85 INCFNCGK 92 (117)
Q Consensus 85 ~~C~~Cg~ 92 (117)
.+|..||.
T Consensus 3 ~~Cp~Cg~ 10 (26)
T PF13248_consen 3 MFCPNCGA 10 (26)
T ss_pred CCCcccCC
Confidence 45666665
No 59
>PRK10123 wcaM putative colanic acid biosynthesis protein; Provisional
Probab=25.71 E-value=27 Score=27.72 Aligned_cols=42 Identities=21% Similarity=0.484 Sum_probs=33.1
Q ss_pred EEecCCCccccccchhhhhhhccccEEEEeccCCCccccceE
Q 040998 12 IKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFV 53 (117)
Q Consensus 12 Vri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y~ 53 (117)
..+|+-|.+++-..+--+--+.+|.-+++..+-...-+|+||
T Consensus 376 lelhn~pqhlflrni~vmqesa~gpalkm~fdlrkdvrg~fm 417 (464)
T PRK10123 376 LELHNKPQHLFLRNINVMQESSVGPALKMNFDLRKDVRGVFM 417 (464)
T ss_pred hhhcCCchhhehhhhhhhhhcccCccceecchhhhhhhceee
Confidence 467899999887777777778899988888777766677775
No 60
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=25.28 E-value=43 Score=19.90 Aligned_cols=21 Identities=29% Similarity=0.661 Sum_probs=9.4
Q ss_pred eEEEEeeccCCcccccccccc
Q 040998 74 RIQKVEYESLPINCFNCGKYG 94 (117)
Q Consensus 74 ~~~~v~YE~lp~~C~~Cg~~G 94 (117)
..-.+.|-.|...|.+||.+.
T Consensus 38 ~~s~v~fH~lg~KC~~C~SYN 58 (61)
T PF14599_consen 38 AKSEVPFHFLGHKCSHCGSYN 58 (61)
T ss_dssp -EEEEE--TT----TTTS---
T ss_pred CccceeeeHhhhcCCCCCCcc
Confidence 345889999999999999863
No 61
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=24.85 E-value=29 Score=18.14 Aligned_cols=8 Identities=38% Similarity=0.841 Sum_probs=3.0
Q ss_pred cccccccc
Q 040998 85 INCFNCGK 92 (117)
Q Consensus 85 ~~C~~Cg~ 92 (117)
.||..||.
T Consensus 1 kfC~~CG~ 8 (34)
T PF14803_consen 1 KFCPQCGG 8 (34)
T ss_dssp -B-TTT--
T ss_pred CccccccC
Confidence 36777764
No 62
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=22.79 E-value=35 Score=16.10 Aligned_cols=10 Identities=40% Similarity=0.693 Sum_probs=6.4
Q ss_pred CCcccccccc
Q 040998 83 LPINCFNCGK 92 (117)
Q Consensus 83 lp~~C~~Cg~ 92 (117)
--.||..||.
T Consensus 12 ~~~fC~~CG~ 21 (23)
T PF13240_consen 12 DAKFCPNCGT 21 (23)
T ss_pred cCcchhhhCC
Confidence 3467777764
No 63
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=22.68 E-value=41 Score=19.69 Aligned_cols=15 Identities=20% Similarity=0.642 Sum_probs=12.0
Q ss_pred eeccCCccccccccc
Q 040998 79 EYESLPINCFNCGKY 93 (117)
Q Consensus 79 ~YE~lp~~C~~Cg~~ 93 (117)
.-++.|.||..|..-
T Consensus 23 ~LkNfPlyCpKCK~E 37 (55)
T PF14205_consen 23 VLKNFPLYCPKCKQE 37 (55)
T ss_pred eeccccccCCCCCce
Confidence 457789999999764
No 64
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=22.60 E-value=1.7e+02 Score=23.13 Aligned_cols=89 Identities=13% Similarity=0.045 Sum_probs=59.1
Q ss_pred EEecCCCccccccchhhhhhhccccEEEEeccCCCccccceEEEEEEEccCCCc-ee---EEEEeceEEEEeecc-----
Q 040998 12 IKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKPL-CL---QFLLDGRIQKVEYES----- 82 (117)
Q Consensus 12 Vri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y~Rv~V~idl~kPL-~~---~v~v~g~~~~v~YE~----- 82 (117)
.=|.|||-.- ++.-++.+=...|+|++.|.--+ |.=|-|+-+-..+- .+ ...++|+.+.|+-.+
T Consensus 5 LFIGNLp~~~-~~~elr~lFe~ygkVlECDIvKN------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKsk~ 77 (346)
T KOG0109|consen 5 LFIGNLPREA-TEQELRSLFEQYGKVLECDIVKN------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKSKA 77 (346)
T ss_pred hhccCCCccc-chHHHHHHHHhhCceEeeeeecc------cceEEeecccccHHHHhhcccceecceEEEEEeccccCCC
Confidence 3467888876 45556777889999999998653 33455554322221 11 245567767666554
Q ss_pred -----CCcccccccccccCCCCCCCCCCCC
Q 040998 83 -----LPINCFNCGKYGHVSIGCPENGDGE 107 (117)
Q Consensus 83 -----lp~~C~~Cg~~GH~~~~C~~~~~~~ 107 (117)
.+++|+.|.---|-.+.|+...-.|
T Consensus 78 stkl~vgNis~tctn~ElRa~fe~ygpvie 107 (346)
T KOG0109|consen 78 STKLHVGNISPTCTNQELRAKFEKYGPVIE 107 (346)
T ss_pred ccccccCCCCccccCHHHhhhhcccCCcee
Confidence 4589999999999888888775544
No 65
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=21.35 E-value=54 Score=23.98 Aligned_cols=19 Identities=32% Similarity=0.940 Sum_probs=16.8
Q ss_pred CcccccccccccCCCCCCC
Q 040998 84 PINCFNCGKYGHVSIGCPE 102 (117)
Q Consensus 84 p~~C~~Cg~~GH~~~~C~~ 102 (117)
..||+.||.-||....|..
T Consensus 100 ~~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 100 RGFCYRCGERGHIGRNCKD 118 (195)
T ss_pred ccccccCCCcccccccccc
Confidence 3569999999999999987
No 66
>PF01570 Flavi_propep: Flavivirus polyprotein propeptide; InterPro: IPR002535 The Flaviviruses are small enveloped animal viruses containing a single positive strand genomic RNA []. The genome encodes one large ORF, a polyprotein which undergos proteolytic processing into mature viral peptide chains. This entry consists of a propeptide region of approximately 90 amino acids in length.; PDB: 3C6E_C 3C5X_C.
Probab=21.33 E-value=28 Score=22.28 Aligned_cols=14 Identities=50% Similarity=1.097 Sum_probs=6.3
Q ss_pred CCCCCCCCCCcccC
Q 040998 100 CPENGDGEEPQDEN 113 (117)
Q Consensus 100 C~~~~~~~~~~~~~ 113 (117)
||....++||.|++
T Consensus 49 Cp~L~~~eePeDiD 62 (87)
T PF01570_consen 49 CPTLDEGEEPEDID 62 (87)
T ss_dssp E-B-SS-S---S-S
T ss_pred cceecccCCCcccc
Confidence 99999999999875
No 67
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=20.94 E-value=45 Score=18.26 Aligned_cols=13 Identities=23% Similarity=0.353 Sum_probs=8.5
Q ss_pred cccccccccccCC
Q 040998 85 INCFNCGKYGHVS 97 (117)
Q Consensus 85 ~~C~~Cg~~GH~~ 97 (117)
.||..||.+=...
T Consensus 1 ~FCp~Cg~~l~~~ 13 (52)
T smart00661 1 KFCPKCGNMLIPK 13 (52)
T ss_pred CCCCCCCCccccc
Confidence 3788888765443
No 68
>PRK01202 glycine cleavage system protein H; Provisional
Probab=20.91 E-value=1.4e+02 Score=20.05 Aligned_cols=61 Identities=7% Similarity=0.218 Sum_probs=39.1
Q ss_pred ceEeEEEEecCCCccccccchhhhhhhccccEEEEeccCCCcc---ccceEEE---EEEEccCCCceeEE
Q 040998 6 DSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSAS---RRKFVRI---AVKIALDKPLCLQF 69 (117)
Q Consensus 6 ~~~~~WVri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~---~~~y~Rv---~V~idl~kPL~~~v 69 (117)
+.-..||+..+ ..+.-.+.......+|++..++....+.. ...++.| +...++.-|+...+
T Consensus 11 s~~H~Wv~~~~---~~~~vGit~~a~~~lG~i~~v~lp~~G~~v~~g~~~~~IEs~K~~~~i~sPvsG~V 77 (127)
T PRK01202 11 TKSHEWVRVEG---DTATVGITDHAQEQLGDIVFVELPEVGDEVKAGETFGVVESVKAASDIYAPVSGEV 77 (127)
T ss_pred CCCcEEEEEcC---CEEEEeeCHHHHhhcCCeeEEEcCCCCCEecCCCEEEEEEEcceeeeeecCCCeEE
Confidence 33458999887 56677777777889999999997764421 1223332 23346666776544
No 69
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=20.74 E-value=44 Score=16.75 Aligned_cols=14 Identities=21% Similarity=0.320 Sum_probs=6.9
Q ss_pred CcccccccccccCC
Q 040998 84 PINCFNCGKYGHVS 97 (117)
Q Consensus 84 p~~C~~Cg~~GH~~ 97 (117)
..||..||.--+..
T Consensus 3 ~rfC~~CG~~t~~~ 16 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA 16 (32)
T ss_dssp TSB-TTT--BEEE-
T ss_pred CcccCcCCccccCC
Confidence 57899998765433
No 70
>smart00362 RRM_2 RNA recognition motif.
Probab=20.71 E-value=1.5e+02 Score=15.70 Aligned_cols=33 Identities=12% Similarity=0.160 Sum_probs=22.2
Q ss_pred EEecCCCccccccchhhhhhhccccEEEEeccCC
Q 040998 12 IKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTR 45 (117)
Q Consensus 12 Vri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~ 45 (117)
|.+.|||...-. .-++.+-+..|.+..+.....
T Consensus 2 v~i~~l~~~~~~-~~l~~~~~~~g~v~~~~~~~~ 34 (72)
T smart00362 2 LFVGNLPPDVTE-EDLKELFSKFGPIESVKIPKD 34 (72)
T ss_pred EEEcCCCCcCCH-HHHHHHHHhcCCEEEEEEecC
Confidence 567899887744 444556668888777665543
No 71
>PF05575 V_cholerae_RfbT: Vibrio cholerae RfbT protein; InterPro: IPR008890 This family consists of several RfbT proteins from Vibrio cholerae. It has been found that genetic alteration of the rfbT gene is responsible for serotype conversion of V. cholerae O1 [] and determines the difference between the Ogawa and Inaba serotypes, in that the presence of rfbT is sufficient for Inaba-to-Ogawa serotype conversion [].
Probab=20.32 E-value=2e+02 Score=21.14 Aligned_cols=33 Identities=24% Similarity=0.376 Sum_probs=24.3
Q ss_pred cccEEEEeccCCCccccceEEEEEEEccCCCceeEEEE
Q 040998 34 MGEVIHIDFNTRSASRRKFVRIAVKIALDKPLCLQFLL 71 (117)
Q Consensus 34 iG~~l~vD~~~~~~~~~~y~Rv~V~idl~kPL~~~v~v 71 (117)
-|+++++++.|+... .+|+.+.++.||...-..
T Consensus 103 qgkiiaiepltemen-----sirmnvqlnnplvefhhf 135 (286)
T PF05575_consen 103 QGKIIAIEPLTEMEN-----SIRMNVQLNNPLVEFHHF 135 (286)
T ss_pred cCceEEEechhhhhh-----heeeeeeeCCcceeeeec
Confidence 477888888876432 477788899999876544
No 72
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=20.05 E-value=28 Score=24.68 Aligned_cols=21 Identities=24% Similarity=0.597 Sum_probs=18.1
Q ss_pred CcccccccccccCCCCCCCCC
Q 040998 84 PINCFNCGKYGHVSIGCPENG 104 (117)
Q Consensus 84 p~~C~~Cg~~GH~~~~C~~~~ 104 (117)
...|..|-.+||..-+|....
T Consensus 27 ~~rCQKClq~GHWtYECk~kR 47 (177)
T KOG3116|consen 27 SARCQKCLQAGHWTYECKNKR 47 (177)
T ss_pred chhHHHHHhhccceeeecCce
Confidence 458999999999999998753
Done!