Query psy2272
Match_columns 276
No_of_seqs 164 out of 515
Neff 2.4
Searched_HMMs 46136
Date Fri Aug 16 20:29:12 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2272.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2272hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00329 eukaryotic translatio 100.0 4.7E-38 1E-42 267.2 11.6 100 1-101 41-140 (155)
2 KOG3403|consensus 100.0 6.2E-38 1.3E-42 263.1 6.6 105 1-105 41-145 (145)
3 PLN00208 translation initiatio 100.0 1.4E-34 3.1E-39 243.7 11.5 95 1-95 41-140 (145)
4 smart00652 eIF1a eukaryotic tr 100.0 3.6E-29 7.9E-34 192.1 9.6 70 1-70 14-83 (83)
5 cd04456 S1_IF1A_like S1_IF1A_l 100.0 1.7E-28 3.7E-33 186.9 9.5 69 1-69 9-78 (78)
6 PRK04012 translation initiatio 100.0 1.9E-28 4.2E-33 194.7 9.8 71 1-71 30-100 (100)
7 cd05793 S1_IF1A S1_IF1A: Trans 100.0 2.1E-28 4.5E-33 185.8 9.4 69 1-69 9-77 (77)
8 TIGR00523 eIF-1A eukaryotic/ar 99.9 4.9E-28 1.1E-32 191.9 9.6 71 1-71 28-99 (99)
9 cd05792 S1_eIF1AD_like S1_eIF1 99.9 2.4E-26 5.1E-31 176.6 9.4 69 1-69 9-78 (78)
10 COG0361 InfA Translation initi 99.9 1.7E-25 3.7E-30 171.8 6.4 59 1-59 16-75 (75)
11 TIGR00008 infA translation ini 99.9 2.5E-22 5.5E-27 151.5 7.2 54 1-54 14-68 (68)
12 PF01176 eIF-1a: Translation i 99.8 9.9E-22 2.1E-26 143.4 5.0 54 1-54 12-65 (65)
13 PRK12442 translation initiatio 99.8 4.8E-21 1E-25 151.1 7.4 56 1-56 16-72 (87)
14 CHL00010 infA translation init 99.6 6.1E-16 1.3E-20 117.2 6.9 58 1-58 16-74 (78)
15 KOG2925|consensus 99.6 5.8E-16 1.3E-20 133.7 6.4 76 2-77 32-111 (167)
16 PRK00276 infA translation init 99.6 1.3E-15 2.8E-20 113.2 7.1 55 2-56 17-72 (72)
17 cd04451 S1_IF1 S1_IF1: Transla 99.3 6.4E-12 1.4E-16 90.3 6.6 53 2-54 11-64 (64)
18 cd04466 S1_YloQ_GTPase S1_YloQ 97.4 0.00057 1.2E-08 48.1 6.4 51 4-56 10-61 (68)
19 PRK00098 GTPase RsgA; Reviewed 94.4 0.13 2.7E-06 46.7 6.8 50 4-55 10-60 (298)
20 PRK12289 GTPase RsgA; Reviewed 93.5 0.2 4.3E-06 47.4 6.3 53 4-56 18-77 (352)
21 cd01854 YjeQ_engC YjeQ/EngC. 93.0 0.29 6.3E-06 44.1 6.4 51 4-57 8-59 (287)
22 PRK12288 GTPase RsgA; Reviewed 92.9 0.33 7.1E-06 45.7 6.8 51 4-57 49-101 (347)
23 PRK01889 GTPase RsgA; Reviewed 83.7 2.4 5.2E-05 39.8 5.6 51 4-59 38-93 (356)
24 cd00164 S1_like S1_like: Ribos 75.4 8.2 0.00018 25.1 4.6 48 5-52 11-63 (65)
25 PF03749 SfsA: Sugar fermentat 67.3 38 0.00082 30.6 8.3 67 5-73 5-90 (215)
26 COG0509 GcvH Glycine cleavage 64.5 3.8 8.1E-05 35.2 1.4 39 19-57 3-47 (131)
27 cd04721 BAH_plant_1 BAH, or Br 58.8 12 0.00027 30.9 3.5 38 26-63 3-55 (130)
28 cd06530 S26_SPase_I The S26 Ty 58.1 9.7 0.00021 27.6 2.5 28 31-58 14-44 (85)
29 COG1162 Predicted GTPases [Gen 56.8 23 0.00049 34.0 5.3 50 4-56 14-67 (301)
30 TIGR00230 sfsA sugar fermentat 56.8 39 0.00085 31.0 6.6 65 5-71 19-100 (232)
31 PF13533 Biotin_lipoyl_2: Biot 56.6 11 0.00024 26.2 2.4 35 17-61 5-39 (50)
32 PF00717 Peptidase_S24: Peptid 54.8 4 8.7E-05 28.3 -0.0 28 31-59 11-38 (70)
33 TIGR02754 sod_Ni_protease nick 52.7 16 0.00034 27.1 2.8 28 31-58 12-42 (90)
34 COG0048 RpsL Ribosomal protein 51.0 26 0.00057 30.4 4.2 35 7-44 59-93 (129)
35 PRK00347 putative DNA-binding 49.6 59 0.0013 29.7 6.5 65 5-71 17-100 (234)
36 cd06462 Peptidase_S24_S26 The 48.7 21 0.00046 24.9 2.8 28 31-58 14-41 (84)
37 cd00319 Ribosomal_S12_like Rib 47.9 30 0.00064 28.6 3.9 32 7-41 38-69 (95)
38 PF10017 Methyltransf_33: Hist 46.5 87 0.0019 25.4 6.5 36 26-71 77-113 (127)
39 CHL00051 rps12 ribosomal prote 46.3 32 0.00068 29.6 4.0 32 7-41 53-84 (123)
40 TIGR00981 rpsL_bact ribosomal 42.9 38 0.00082 29.2 4.0 33 7-42 53-85 (124)
41 cd06555 ASCH_PF0470_like ASC-1 41.3 81 0.0017 26.1 5.6 51 3-65 16-67 (109)
42 PRK05163 rpsL 30S ribosomal pr 41.2 43 0.00093 28.9 4.1 32 7-41 53-84 (124)
43 cd03368 Ribosomal_S12 S12-like 40.6 44 0.00095 28.2 3.9 33 7-42 51-83 (108)
44 PF00164 Ribosom_S12_S23: Ribo 40.3 43 0.00093 28.6 3.9 34 7-43 52-85 (122)
45 PF03459 TOBE: TOBE domain; I 39.9 35 0.00077 23.6 2.9 38 6-43 22-59 (64)
46 TIGR00638 Mop molybdenum-pteri 37.9 61 0.0013 22.4 3.8 41 4-44 20-62 (69)
47 PF09795 Atg31: Autophagy-rela 31.1 21 0.00045 31.9 0.7 28 224-251 70-97 (160)
48 cd06529 S24_LexA-like Peptidas 30.4 33 0.00072 24.1 1.5 27 31-58 14-40 (81)
49 CHL00141 rpl24 ribosomal prote 30.0 71 0.0015 25.1 3.4 33 27-59 5-37 (83)
50 PF11302 DUF3104: Protein of u 29.2 69 0.0015 25.5 3.2 27 29-55 4-37 (75)
51 PF04014 Antitoxin-MazE: Antid 27.6 23 0.0005 24.1 0.3 30 14-43 4-33 (47)
52 KOG2107|consensus 26.9 84 0.0018 28.7 3.7 49 3-69 102-150 (179)
53 PF11948 DUF3465: Protein of u 26.8 1.4E+02 0.003 26.0 4.8 50 4-53 58-108 (131)
54 PTZ00115 40S ribosomal protein 26.5 87 0.0019 30.3 3.9 32 7-41 149-180 (290)
55 PRK01191 rpl24p 50S ribosomal 26.4 89 0.0019 26.6 3.6 32 28-59 43-74 (120)
56 cd05685 S1_Tex S1_Tex: The C-t 26.2 1.4E+02 0.003 19.9 3.9 44 8-52 17-66 (68)
57 COG2996 Predicted RNA-bindinin 26.2 53 0.0012 31.7 2.5 32 27-60 111-142 (287)
58 TIGR02228 sigpep_I_arch signal 25.8 52 0.0011 28.2 2.1 43 13-57 29-72 (158)
59 PRK12281 rplX 50S ribosomal pr 25.3 96 0.0021 24.0 3.3 31 29-59 5-35 (76)
60 TIGR02227 sigpep_I_bact signal 24.8 57 0.0012 27.2 2.2 27 31-57 34-63 (163)
61 PRK08577 hypothetical protein; 24.2 57 0.0012 26.4 2.0 34 19-55 15-48 (136)
62 PTZ00067 40S ribosomal S23; Pr 24.0 1.5E+02 0.0033 26.2 4.6 34 7-41 70-104 (143)
63 COG2002 AbrB Regulators of sta 23.6 90 0.0019 24.1 2.9 38 19-58 16-53 (89)
64 PF07065 D123: D123; InterPro 22.7 1.3E+02 0.0028 28.4 4.3 29 47-76 10-39 (299)
65 PF04717 Phage_base_V: Phage-r 22.6 1.8E+02 0.0039 21.3 4.2 56 3-58 9-71 (79)
66 cd04482 RPA2_OBF_like RPA2_OBF 22.3 1.7E+02 0.0036 22.7 4.2 38 3-40 15-57 (91)
67 PF09038 53-BP1_Tudor: Tumour 20.9 1.5E+02 0.0034 25.5 4.0 30 3-44 29-58 (122)
68 PF09902 DUF2129: Uncharacteri 20.7 91 0.002 24.2 2.4 22 48-69 2-23 (71)
69 cd05696 S1_Rrp5_repeat_hs4 S1_ 20.4 1.9E+02 0.0041 20.9 3.9 47 7-53 18-69 (71)
70 TIGR01439 lp_hng_hel_AbrB loop 20.0 76 0.0016 20.3 1.6 25 18-42 8-32 (43)
No 1
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=100.00 E-value=4.7e-38 Score=267.19 Aligned_cols=100 Identities=73% Similarity=1.216 Sum_probs=93.6
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccCCCCeEEEEEecCHhHHHHHHHcCCCCcccccccccc
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEARNLKTYGEFPETVRINDTVT 80 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDYQD~KGDIIyRYt~DEIR~LKk~GeLPEeFkiNEtdt 80 (276)
||||++|+|+|+||++|||||||||||+|||++||+|+|+|||||++||+|||||+++||++|+++|+||++|+||++++
T Consensus 41 ~LGn~~f~V~c~dG~~rLa~I~GKmRK~IWI~~GD~VlVel~~yd~~KgdIi~Ry~~devr~Lk~~g~~P~~~~~~~~~~ 120 (155)
T PTZ00329 41 MLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDIILVSLRDFQDSKADVILKYTPDEARALKQHGELPETAKINETDI 120 (155)
T ss_pred EcCCCEEEEEECCCCEEEEEeeccceeeEEecCCCEEEEeccCCCCCEEEEEEEcCHHHHHHHHHcCCCCcceeeccccc
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCeeecCCCCCccc
Q psy2272 81 FVEEGYDEDIEFGDEISDDEE 101 (276)
Q Consensus 81 fg~~~~dd~ieFd~~~d~~~d 101 (276)
|++++ +++|+|.+++|++++
T Consensus 121 ~~~~~-~~~~~f~~~~~~~~~ 140 (155)
T PTZ00329 121 FDDEG-DDGIEFQDDESDEEA 140 (155)
T ss_pred cCcCc-CCCeEEecccccccc
Confidence 98664 778999876655543
No 2
>KOG3403|consensus
Probab=100.00 E-value=6.2e-38 Score=263.05 Aligned_cols=105 Identities=73% Similarity=1.181 Sum_probs=101.0
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccCCCCeEEEEEecCHhHHHHHHHcCCCCcccccccccc
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEARNLKTYGEFPETVRINDTVT 80 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDYQD~KGDIIyRYt~DEIR~LKk~GeLPEeFkiNEtdt 80 (276)
|||||+++|.|+||++|+|||+||+||||||++||||||.+++||++|||||++|++||+|.||++|+||+++++||+++
T Consensus 41 mLGnGr~e~~CfDGvkR~~hiRGklrkkVwi~~GDIiLv~lRD~qd~kaDvilKY~~dEar~LK~~Gelpe~~k~Ne~~~ 120 (145)
T KOG3403|consen 41 MLGNGRLEASCFDGVKRLCHIRGKLRKKVWINQGDIILVGLRDYQDDKADVILKYMPDEARILKAYGELPENAKINETDT 120 (145)
T ss_pred hhcCCcEEEEEecchhhhhhhhccceeeEeecCCCEEEEeeecccccccceehhhChHHHHHHHhcCcCCcccccccccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCeeecCCCCCcccccch
Q psy2272 81 FVEEGYDEDIEFGDEISDDEEGNAV 105 (276)
Q Consensus 81 fg~~~~dd~ieFd~~~d~~~d~~~i 105 (276)
|+.+++||++.|+++.+++||+|++
T Consensus 121 ~~~e~~d~~~~~~~~~~~~ed~d~~ 145 (145)
T KOG3403|consen 121 FGVEDDDDDIDFDDIEDDDEDIDDI 145 (145)
T ss_pred cCccCCccccccccccccccccccC
Confidence 9999888899999988888877764
No 3
>PLN00208 translation initiation factor (eIF); Provisional
Probab=100.00 E-value=1.4e-34 Score=243.75 Aligned_cols=95 Identities=71% Similarity=1.168 Sum_probs=87.4
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccCCCCeEEEEEecCHhHHHHHHHcCCCCcccccccccc
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEARNLKTYGEFPETVRINDTVT 80 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDYQD~KGDIIyRYt~DEIR~LKk~GeLPEeFkiNEtdt 80 (276)
||||++|+|+|+||++|||||||||||+|||++||+|+|++|+||++||||||||+++||++|+++|+||+.|.+|++++
T Consensus 41 ~lGn~~~~V~c~dG~~rLa~IpGKmRKrIWI~~GD~VlVel~~~d~~KgdIv~ry~~dqvr~Lkk~G~~P~~f~~~~~~~ 120 (145)
T PLN00208 41 MLGNGRCEALCIDGTKRLCHIRGKMRKKVWIAAGDIILVGLRDYQDDKADVILKYMPDEARLLKAYGELPENTRLNEGIA 120 (145)
T ss_pred EcCCCEEEEEECCCCEEEEEEeccceeeEEecCCCEEEEEccCCCCCEEEEEEEcCHHHHHHHHHcCCCCcceeeccccc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ---cc--cCCCCCCeeecCC
Q psy2272 81 ---FV--EEGYDEDIEFGDE 95 (276)
Q Consensus 81 ---fg--~~~~dd~ieFd~~ 95 (276)
|. .+++|+.|+|+++
T Consensus 121 ~~~~~~~~~~~~~~~~f~~~ 140 (145)
T PLN00208 121 GDLDEEEDGEGDDYIEFEDE 140 (145)
T ss_pred cccccccCcccCcceeeccc
Confidence 41 1224667888863
No 4
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=99.96 E-value=3.6e-29 Score=192.13 Aligned_cols=70 Identities=64% Similarity=1.080 Sum_probs=69.2
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccCCCCeEEEEEecCHhHHHHHHHcCCCC
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEARNLKTYGEFP 70 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDYQD~KGDIIyRYt~DEIR~LKk~GeLP 70 (276)
++||++|+|+|+||++++|||||||||+|||++||+|+|++|||+++||||+|||+++|+++|+++|+||
T Consensus 14 ~lG~~~~~V~~~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~~~~vk~L~k~g~wp 83 (83)
T smart00652 14 MLGNGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDPWDFQDVKADIIYKYTKDEVRWLKKEGELP 83 (83)
T ss_pred EcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEecCCCCCEEEEEEEeCHHHHHHHHHcCCCC
Confidence 6899999999999999999999999999999999999999999999999999999999999999999998
No 5
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=99.95 E-value=1.7e-28 Score=186.87 Aligned_cols=69 Identities=46% Similarity=0.830 Sum_probs=67.4
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccC-CCCeEEEEEecCHhHHHHHHHcCCC
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDY-QDAKADVILKYTPDEARNLKTYGEF 69 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDY-QD~KGDIIyRYt~DEIR~LKk~GeL 69 (276)
++||++|+|+|+||+++||||||||||+|||++||+|+|+|||| +++||||+|||++|||++|+++|+|
T Consensus 9 ~lG~~~~~V~~~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~~~vk~L~k~g~w 78 (78)
T cd04456 9 MLGNNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIVDPIEEGEDVKADIIFVYCKDHVRSLKKEGFL 78 (78)
T ss_pred ECCCCEEEEEECCCCEEEEEEchhhccCEEEcCCCEEEEEecccCCCceEEEEEEeCHHHHHHHHHcCcC
Confidence 68999999999999999999999999999999999999999999 6889999999999999999999987
No 6
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=99.95 E-value=1.9e-28 Score=194.73 Aligned_cols=71 Identities=39% Similarity=0.821 Sum_probs=69.7
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccCCCCeEEEEEecCHhHHHHHHHcCCCCc
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEARNLKTYGEFPE 71 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDYQD~KGDIIyRYt~DEIR~LKk~GeLPE 71 (276)
||||++|+|+|+||+++||||||||||+|||++||+|+|++|||+++||||+|||+++|+++|+++|+||+
T Consensus 30 ~lG~~~~~V~~~dG~~~la~i~GK~Rk~IwI~~GD~VlVe~~~~~~~kg~Iv~r~~~~qv~~L~~~g~~~~ 100 (100)
T PRK04012 30 MLGANRVRVRCMDGVERMGRIPGKMKKRMWIREGDVVIVAPWDFQDEKADIIWRYTKPQVDWLRRKGYISE 100 (100)
T ss_pred EcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEecccCCCEEEEEEEcCHHHHHHHHHcCCCCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999985
No 7
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=99.95 E-value=2.1e-28 Score=185.76 Aligned_cols=69 Identities=70% Similarity=1.221 Sum_probs=67.6
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccCCCCeEEEEEecCHhHHHHHHHcCCC
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEARNLKTYGEF 69 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDYQD~KGDIIyRYt~DEIR~LKk~GeL 69 (276)
++||++|+|+|+||++++|||||||||+|||++||+|+|++|||+++||+|+|||+++|+++|+++|+|
T Consensus 9 ~~g~~~~~V~~~~g~~~la~i~gK~rk~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~~~v~~L~~~g~i 77 (77)
T cd05793 9 MLGNGRLEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVAPWDFQDDKADIIYKYTPDEVRWLKRKGEL 77 (77)
T ss_pred EcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEeccccCCEEEEEEEcCHHHHHHHHHcCcC
Confidence 589999999999999999999999999999999999999999999999999999999999999999985
No 8
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=99.95 E-value=4.9e-28 Score=191.91 Aligned_cols=71 Identities=41% Similarity=0.847 Sum_probs=69.5
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccCC-CCeEEEEEecCHhHHHHHHHcCCCCc
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQ-DAKADVILKYTPDEARNLKTYGEFPE 71 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDYQ-D~KGDIIyRYt~DEIR~LKk~GeLPE 71 (276)
|+||++|+|+|+||+++||||||||||+|||++||+|+|+|||++ +.||+|+|||+++||++|+++|+||+
T Consensus 28 ~lG~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~GD~VlVsp~d~~~~~kg~Iv~r~~~~qv~~L~~~g~~p~ 99 (99)
T TIGR00523 28 MLGAGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIVKPWEFQGDDKCDIVWRYTKTQVEWLKRKGYLKE 99 (99)
T ss_pred EcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEEccCCCCccEEEEEEcCHHHHHHHHHcCCCCC
Confidence 689999999999999999999999999999999999999999999 88999999999999999999999995
No 9
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=99.93 E-value=2.4e-26 Score=176.60 Aligned_cols=69 Identities=29% Similarity=0.500 Sum_probs=67.2
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccCCC-CeEEEEEecCHhHHHHHHHcCCC
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQD-AKADVILKYTPDEARNLKTYGEF 69 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDYQD-~KGDIIyRYt~DEIR~LKk~GeL 69 (276)
++||++|+|+|+||.++||+|||||||+|||++||+|||+||++|+ .||||+++|+++|+++|+++|+|
T Consensus 9 ~~G~n~~~V~~~dG~~~l~~iP~KfRk~iWIkrGd~VlV~p~~~~~kvkgeIv~i~~~~qvk~L~k~g~W 78 (78)
T cd05792 9 SKGNNLHEVETPNGSRYLVSMPTKFRKNIWIKRGDFVLVEPIEEGDKVKAEIVKILTRDHVKYIKEEGLW 78 (78)
T ss_pred cCCCcEEEEEcCCCCEEEEEechhhcccEEEEeCCEEEEEecccCCceEEEEEEEECHHHHHHHHHcCCC
Confidence 6899999999999999999999999999999999999999999996 69999999999999999999987
No 10
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=1.7e-25 Score=171.84 Aligned_cols=59 Identities=41% Similarity=0.741 Sum_probs=57.7
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccc-eeeeecCCEEEEEeccCCCCeEEEEEecCHhH
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILKYTPDE 59 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRK-KVWIk~GDiVLVEprDYQD~KGDIIyRYt~DE 59 (276)
||||++|+|+|+||++++||||||||| +|||.+||+|+|+|||||++||||+|||+++|
T Consensus 16 ~L~~~~f~v~~edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~~~~ 75 (75)
T COG0361 16 MLPNGRFRVELENGHERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVYRYKKDE 75 (75)
T ss_pred ecCCCEEEEEecCCcEEEEEccCcchheeEEeCCCCEEEEEecccccccccEEEEecCCC
Confidence 699999999999999999999999999 99999999999999999999999999999875
No 11
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=99.87 E-value=2.5e-22 Score=151.50 Aligned_cols=54 Identities=26% Similarity=0.407 Sum_probs=52.8
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccc-eeeeecCCEEEEEeccCCCCeEEEEEe
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILK 54 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRK-KVWIk~GDiVLVEprDYQD~KGDIIyR 54 (276)
+|||++|+|+|+||++++||||||||+ +|||.+||.|+|++||||++||+||||
T Consensus 14 ~L~~~~f~V~l~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~spyd~tkgrIi~R 68 (68)
T TIGR00008 14 SLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDKVKVELSPYDLTRGRITYR 68 (68)
T ss_pred ECCCCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEECcccCCcEeEEeC
Confidence 689999999999999999999999997 999999999999999999999999997
No 12
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=99.85 E-value=9.9e-22 Score=143.39 Aligned_cols=54 Identities=43% Similarity=0.867 Sum_probs=48.8
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccCCCCeEEEEEe
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILK 54 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDYQD~KGDIIyR 54 (276)
||||++|+|+|+||++++|+||||||++|||++||+|+|++|+|+++||+||||
T Consensus 12 ~lG~~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~~~d~~kG~Ii~r 65 (65)
T PF01176_consen 12 MLGNNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPSPYDKVKGRIIYR 65 (65)
T ss_dssp EESSSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEESTTCTTEEEEEEE
T ss_pred ECCCCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEecccCCCeEEEEEC
Confidence 589999999999999999999999999999999999999999999999999997
No 13
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=99.84 E-value=4.8e-21 Score=151.07 Aligned_cols=56 Identities=21% Similarity=0.365 Sum_probs=54.9
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccc-eeeeecCCEEEEEeccCCCCeEEEEEecC
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILKYT 56 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRK-KVWIk~GDiVLVEprDYQD~KGDIIyRYt 56 (276)
+|||++|.|+|+||++++|||+||||+ +|||.+||.|+|++||||++||+|||||.
T Consensus 16 ~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~ 72 (87)
T PRK12442 16 VLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred ECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEECcccCCceeEEEEec
Confidence 589999999999999999999999999 99999999999999999999999999997
No 14
>CHL00010 infA translation initiation factor 1
Probab=99.63 E-value=6.1e-16 Score=117.23 Aligned_cols=58 Identities=28% Similarity=0.412 Sum_probs=54.7
Q ss_pred CCCCceEEEEeCCCCEEEEEecccccc-eeeeecCCEEEEEeccCCCCeEEEEEecCHh
Q psy2272 1 MLGNGRLEAMCFDGTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILKYTPD 58 (276)
Q Consensus 1 MLGNgrfEVeC~DG~kRLAhIpGKMRK-KVWIk~GDiVLVEprDYQD~KGDIIyRYt~D 58 (276)
++|++.|.|+|+||+.++|+++||||+ ++|+..||+|.|++|++++++|+|||||.+.
T Consensus 16 ~lg~~~y~V~~~~g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~~ 74 (78)
T CHL00010 16 SLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRNK 74 (78)
T ss_pred EcCCCEEEEEeCCCCEEEEEeccceecCCcccCCCCEEEEEEcccCCCeEEEEEEecCC
Confidence 368999999999999999999999998 7999999999999999999999999999753
No 15
>KOG2925|consensus
Probab=99.62 E-value=5.8e-16 Score=133.71 Aligned_cols=76 Identities=25% Similarity=0.453 Sum_probs=71.9
Q ss_pred CCCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccC---CC-CeEEEEEecCHhHHHHHHHcCCCCccccccc
Q psy2272 2 LGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDY---QD-AKADVILKYTPDEARNLKTYGEFPETVRIND 77 (276)
Q Consensus 2 LGNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDY---QD-~KGDIIyRYt~DEIR~LKk~GeLPEeFkiNE 77 (276)
.||++|+|+-.+|...|+.||.||||+|||++|++|+|.|+.+ +. .||.|.|.+..|+++.|++.|+||+.|+.+-
T Consensus 32 rGsnlheV~danGq~~lvsmP~KfRksiWiRRg~FvvVdpiee~~~g~KVkgeI~yVl~~d~vr~lqk~g~WPe~F~d~a 111 (167)
T KOG2925|consen 32 RGSNLHEVMDANGQNSLVSMPAKFRKSIWIRRGSFVVVDPIEEEKSGSKVKGEICYVLFFDQVRLLQKSGEWPEIFKDTA 111 (167)
T ss_pred CCcchhhhhhcCCceeeeeCCHhhhhceEEeeCCEEEEccccccccCCccceEEEEEEccHHHHHHHHcCCcchhhhhcc
Confidence 5999999999999999999999999999999999999999999 54 4999999999999999999999999997653
No 16
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=99.61 E-value=1.3e-15 Score=113.20 Aligned_cols=55 Identities=29% Similarity=0.431 Sum_probs=52.6
Q ss_pred CCCceEEEEeCCCCEEEEEecccccc-eeeeecCCEEEEEeccCCCCeEEEEEecC
Q psy2272 2 LGNGRLEAMCFDGTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILKYT 56 (276)
Q Consensus 2 LGNgrfEVeC~DG~kRLAhIpGKMRK-KVWIk~GDiVLVEprDYQD~KGDIIyRYt 56 (276)
+||+.|.|.|+||..++|+++||||+ ++|+.+||+|+|++|++++++|+|||||.
T Consensus 17 ~~~~~y~V~~~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~r~~ 72 (72)
T PRK00276 17 LPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITYRHK 72 (72)
T ss_pred cCCCEEEEEeCCCCEEEEEEccceeeCCcccCCCCEEEEEEcccCCCeEEEEEEeC
Confidence 67889999999999999999999997 99999999999999999999999999984
No 17
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=99.30 E-value=6.4e-12 Score=90.31 Aligned_cols=53 Identities=28% Similarity=0.448 Sum_probs=50.1
Q ss_pred CCCceEEEEeCCCCEEEEEecccccc-eeeeecCCEEEEEeccCCCCeEEEEEe
Q psy2272 2 LGNGRLEAMCFDGTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILK 54 (276)
Q Consensus 2 LGNgrfEVeC~DG~kRLAhIpGKMRK-KVWIk~GDiVLVEprDYQD~KGDIIyR 54 (276)
+||+.|.|+|+||..++|+++||||+ ++|+..||+|+++++++++.+|.||||
T Consensus 11 ~~g~~~~V~~~~g~~~~c~~rGklr~~~~~~~vGD~V~~~~~~~~~~~g~I~~~ 64 (64)
T cd04451 11 LPNAMFRVELENGHEVLAHISGKMRMNYIRILPGDRVKVELSPYDLTKGRIVYR 64 (64)
T ss_pred eCCCEEEEEeCCCCEEEEEECceeecCCcccCCCCEEEEEEeecCCCEEEEEEC
Confidence 56789999999999999999999996 899999999999999999889999997
No 18
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=97.44 E-value=0.00057 Score=48.11 Aligned_cols=51 Identities=27% Similarity=0.277 Sum_probs=41.0
Q ss_pred CceEEEEeCCCCEEEEEecccccc-eeeeecCCEEEEEeccCCCCeEEEEEecC
Q psy2272 4 NGRLEAMCFDGTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILKYT 56 (276)
Q Consensus 4 NgrfEVeC~DG~kRLAhIpGKMRK-KVWIk~GDiVLVEprDYQD~KGDIIyRYt 56 (276)
++.+.|.+.+|....|.++|++++ ..++..||.|++++.+ ...+-|+..+.
T Consensus 10 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~VGD~V~~~~~~--~~~~~I~~vl~ 61 (68)
T cd04466 10 GGFYYVETEDGKIYECRLRGKFRKDKNPPAVGDRVEFEPED--DGEGVIEEILP 61 (68)
T ss_pred CCEEEEEeCCCeEEEEEEccccccCCCCCCCCcEEEEEECC--CCcEEEEEEec
Confidence 467889998788999999999986 6889999999999754 34566665553
No 19
>PRK00098 GTPase RsgA; Reviewed
Probab=94.44 E-value=0.13 Score=46.65 Aligned_cols=50 Identities=22% Similarity=0.250 Sum_probs=39.6
Q ss_pred CceEEEEeCCCCEEEEEecccccc-eeeeecCCEEEEEeccCCCCeEEEEEec
Q psy2272 4 NGRLEAMCFDGTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILKY 55 (276)
Q Consensus 4 NgrfEVeC~DG~kRLAhIpGKMRK-KVWIk~GDiVLVEprDYQD~KGDIIyRY 55 (276)
++.+.|.+.+|....|.++|++|+ +.-+..||.|+|++. ++..|-|...+
T Consensus 10 ~~~~~v~~~~~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~--~~~~g~i~~i~ 60 (298)
T PRK00098 10 GGFYYVESEDGQVYQCRARGKFRKKTNTPAVGDRVEFSAE--NNDEGVILEIH 60 (298)
T ss_pred CCEEEEEECCCCEEEEEeccccccCCCCcCCCCEEEEEEC--CCCcEEEEEEe
Confidence 578899988899999999999986 566789999999874 34557665444
No 20
>PRK12289 GTPase RsgA; Reviewed
Probab=93.46 E-value=0.2 Score=47.40 Aligned_cols=53 Identities=17% Similarity=0.237 Sum_probs=41.4
Q ss_pred CceEEEEeCCC------CEEEEEecccccc-eeeeecCCEEEEEeccCCCCeEEEEEecC
Q psy2272 4 NGRLEAMCFDG------TKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILKYT 56 (276)
Q Consensus 4 NgrfEVeC~DG------~kRLAhIpGKMRK-KVWIk~GDiVLVEprDYQD~KGDIIyRYt 56 (276)
++.|.|.+.+| ...+|..+|++|+ ..-+..||.|.+++.++++.+|-|...+.
T Consensus 18 ~~~y~V~~~~~~~~~~~~~~~~~~r~~lk~~~~~~~vGD~V~~~~~~~~~~~~~I~~vlp 77 (352)
T PRK12289 18 ANFYRVQLDEPQNLNPPSLLLCTRRTRLKKIGQQVMVGDRVIVEEPDWQGQRGAIAEVLP 77 (352)
T ss_pred CCEEEEEECCCcccCcceEEEEEcccccccCCCCcccCCEEEEeecCCCCCceEEEEEec
Confidence 46788988764 4789999999997 45588999999998777667776665553
No 21
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=92.96 E-value=0.29 Score=44.10 Aligned_cols=51 Identities=25% Similarity=0.385 Sum_probs=40.4
Q ss_pred CceEEEEeCCCCEEEEEecccccc-eeeeecCCEEEEEeccCCCCeEEEEEecCH
Q psy2272 4 NGRLEAMCFDGTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILKYTP 57 (276)
Q Consensus 4 NgrfEVeC~DG~kRLAhIpGKMRK-KVWIk~GDiVLVEprDYQD~KGDIIyRYt~ 57 (276)
++.|.|.. +|..+.|.++|++++ +.-+..||.|.+++.+ +..|-|...+.+
T Consensus 8 ~~~~~v~~-~~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~~--~~~~~i~~i~~R 59 (287)
T cd01854 8 GGFYDVET-EGGELRCRARGKLRKKGIKPVVGDWVEVEPDD--DGEGVIVRVLPR 59 (287)
T ss_pred CCEEEEEE-CCeEEEEEeccccccCCCCccCCCEEEEEecC--CCcEEEEEEECC
Confidence 46788887 478999999999996 4568999999998754 456877777754
No 22
>PRK12288 GTPase RsgA; Reviewed
Probab=92.88 E-value=0.33 Score=45.70 Aligned_cols=51 Identities=18% Similarity=0.187 Sum_probs=39.5
Q ss_pred CceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccCCC--CeEEEEEecCH
Q psy2272 4 NGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQD--AKADVILKYTP 57 (276)
Q Consensus 4 NgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDYQD--~KGDIIyRYt~ 57 (276)
++.|.|.+.+|..+.|.++|++++ +..||.|.+++.+... ..|-|...+.+
T Consensus 49 ~~~~~v~~~~g~~~~~~~~g~~~~---~~vGD~V~~~~~~~~~~~~~~~I~~il~R 101 (347)
T PRK12288 49 GQHADVEAADGEVHRCNIRRTIRS---LVTGDRVVWRPGKEALEGVSGVVEAVHPR 101 (347)
T ss_pred CCEEEEEeCCCcEEEEEecccCCC---CCCCcEEEEEeCCCcccccceEEEEEecc
Confidence 578999999999999999999975 8899999998553322 24777666543
No 23
>PRK01889 GTPase RsgA; Reviewed
Probab=83.72 E-value=2.4 Score=39.78 Aligned_cols=51 Identities=18% Similarity=0.214 Sum_probs=36.8
Q ss_pred CceEEEEeCCCCEEEEEecccccc-----eeeeecCCEEEEEeccCCCCeEEEEEecCHhH
Q psy2272 4 NGRLEAMCFDGTKRLCHIRGKLRK-----KVWINQGDIILIGLRDYQDAKADVILKYTPDE 59 (276)
Q Consensus 4 NgrfEVeC~DG~kRLAhIpGKMRK-----KVWIk~GDiVLVEprDYQD~KGDIIyRYt~DE 59 (276)
++.|.|...+| +..|.++||++. +--...||.|+++. +..|-|...+.+..
T Consensus 38 ~~~~~v~~~~~-~~~~~~~gk~~~~~~~~~~~~~vGD~V~~~~----~~~g~I~~i~pR~~ 93 (356)
T PRK01889 38 RSGYVVATEEG-EVRAEVSGKWRHEAFPPGDRPAVGDWVLLDN----EKKARIVRLLPRRS 93 (356)
T ss_pred CCEEEEEECCc-EEEEEecchhhccccccCCCCccCcEEEEec----CCceEEEEEECCCc
Confidence 57888988666 567999999984 23367899999985 34677776554443
No 24
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=75.42 E-value=8.2 Score=25.06 Aligned_cols=48 Identities=19% Similarity=0.144 Sum_probs=35.3
Q ss_pred ceEEEEeCCCCEEEEEecccccc-----eeeeecCCEEEEEeccCCCCeEEEE
Q psy2272 5 GRLEAMCFDGTKRLCHIRGKLRK-----KVWINQGDIILIGLRDYQDAKADVI 52 (276)
Q Consensus 5 grfEVeC~DG~kRLAhIpGKMRK-----KVWIk~GDiVLVEprDYQD~KGDII 52 (276)
+.+.|.+.+|.+-+++++.--.. +-++++||.|.+.....+..++.|.
T Consensus 11 ~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ 63 (65)
T cd00164 11 FGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRIS 63 (65)
T ss_pred eeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEe
Confidence 34557778888888887764332 4578999999999998876666654
No 25
>PF03749 SfsA: Sugar fermentation stimulation protein; InterPro: IPR005224 The sugar fermentation stimulation protein is a probable regulatory factor involved in maltose metabolism. It contains a putative DNA-binding domain, and was isolated as a gene which enabled Escherichia coli W3110 (strain MK2001) to use maltose [].
Probab=67.27 E-value=38 Score=30.58 Aligned_cols=67 Identities=19% Similarity=0.221 Sum_probs=48.5
Q ss_pred ceEE--EEeCCCCEEEEEec--ccccceeeeecCCEEEEEeccCC--CCeEEEEEecCH-------------hHHHHHHH
Q psy2272 5 GRLE--AMCFDGTKRLCHIR--GKLRKKVWINQGDIILIGLRDYQ--DAKADVILKYTP-------------DEARNLKT 65 (276)
Q Consensus 5 grfE--VeC~DG~kRLAhIp--GKMRKKVWIk~GDiVLVEprDYQ--D~KGDIIyRYt~-------------DEIR~LKk 65 (276)
+||- |+..||.++.||+| |+|+- -+.+|-.|++++++-. ..+-+++..+.. .=+.++.+
T Consensus 5 nRF~~~v~l~~g~~~~~H~pntGRl~e--ll~pG~~v~l~~~~~~~RKt~y~l~av~~~~~~~V~int~~~N~lv~~~l~ 82 (215)
T PF03749_consen 5 NRFLADVELDDGEEVTAHCPNTGRLKE--LLVPGARVLLSKSDNPKRKTKYTLEAVEKDNGVWVGINTQLPNRLVEEALE 82 (215)
T ss_pred CcEEEEEEECCCCEEEEEcCCCCcchh--hccCCCEEEEEECCCCCCCCcEEEEEEEcCCCeEEEEccchHHHHHHHHHH
Confidence 4454 55567999999997 55554 3449999999999876 456777766655 34778888
Q ss_pred cCCCCccc
Q psy2272 66 YGEFPETV 73 (276)
Q Consensus 66 ~GeLPEeF 73 (276)
.|.+|.--
T Consensus 83 ~~~i~~l~ 90 (215)
T PF03749_consen 83 NGLIPELS 90 (215)
T ss_pred cCCCcccc
Confidence 99998633
No 26
>COG0509 GcvH Glycine cleavage system H protein (lipoate-binding) [Amino acid transport and metabolism]
Probab=64.51 E-value=3.8 Score=35.20 Aligned_cols=39 Identities=31% Similarity=0.727 Sum_probs=32.3
Q ss_pred EEecccccc---eeeeec-C-CEEEEEeccC-CCCeEEEEEecCH
Q psy2272 19 CHIRGKLRK---KVWINQ-G-DIILIGLRDY-QDAKADVILKYTP 57 (276)
Q Consensus 19 AhIpGKMRK---KVWIk~-G-DiVLVEprDY-QD~KGDIIyRYt~ 57 (276)
|.||..|+. +.||+. | +++.|.+++| |+.-|||+|.=-|
T Consensus 3 ~~~p~~l~Y~~~heWvr~e~d~~~tvGiT~~aq~~lGdiv~Velp 47 (131)
T COG0509 3 CNIPDDLKYTAEHEWVRVEGDGTATVGITDYAQDQLGDIVFVELP 47 (131)
T ss_pred ccccccceeccceEEEEecCCCEEEEeCCHHHHHhcCCEEEEEcC
Confidence 467777876 899998 5 7999999999 5789999998543
No 27
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=58.80 E-value=12 Score=30.95 Aligned_cols=38 Identities=21% Similarity=0.143 Sum_probs=27.4
Q ss_pred cceeeeecCCEEEEEecc-------------CC--CCeEEEEEecCHhHHHHH
Q psy2272 26 RKKVWINQGDIILIGLRD-------------YQ--DAKADVILKYTPDEARNL 63 (276)
Q Consensus 26 RKKVWIk~GDiVLVEprD-------------YQ--D~KGDIIyRYt~DEIR~L 63 (276)
|+-+.|+.||.|+|.+.+ .. .....+.|=++++|+..+
T Consensus 3 r~~~~i~vGD~V~v~~~~~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~ 55 (130)
T cd04721 3 RNGVTISVHDFVYVLSEEEDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAA 55 (130)
T ss_pred cCCEEEECCCEEEEeCCCCCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccc
Confidence 457889999999998643 11 125667777888898773
No 28
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=58.15 E-value=9.7 Score=27.65 Aligned_cols=28 Identities=25% Similarity=0.627 Sum_probs=21.4
Q ss_pred eecCCEEEEEeccC---CCCeEEEEEecCHh
Q psy2272 31 INQGDIILIGLRDY---QDAKADVILKYTPD 58 (276)
Q Consensus 31 Ik~GDiVLVEprDY---QD~KGDIIyRYt~D 58 (276)
|..||+|+|.+... ...+||||.-..+.
T Consensus 14 i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~ 44 (85)
T cd06530 14 LQPGDLVLVNKLSYGFREPKRGDVVVFKSPG 44 (85)
T ss_pred ccCCCEEEEEEeecccCCCCCCCEEEEeCCC
Confidence 67899999988877 46788888666555
No 29
>COG1162 Predicted GTPases [General function prediction only]
Probab=56.82 E-value=23 Score=33.97 Aligned_cols=50 Identities=20% Similarity=0.218 Sum_probs=39.4
Q ss_pred CceEEEEeCC---CCEEEEEecccccc-eeeeecCCEEEEEeccCCCCeEEEEEecC
Q psy2272 4 NGRLEAMCFD---GTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILKYT 56 (276)
Q Consensus 4 NgrfEVeC~D---G~kRLAhIpGKMRK-KVWIk~GDiVLVEprDYQD~KGDIIyRYt 56 (276)
.|.|.|.+.+ +....|..+|++|+ ..-...||.|.++...-. |-|...+.
T Consensus 14 ~g~y~v~~~~~~~~~~~~~~~r~~lr~~~~~~vVGD~V~~~~~~~~---g~I~~i~~ 67 (301)
T COG1162 14 AGFYGVRLEEEVDGEVYRCRARGNLRKKDLKPVVGDRVVFEDENNN---GVIEKILP 67 (301)
T ss_pred CCEEEEEEccccccceeeeeeecceeccCccccccCeEEEecCCCc---ceEEEEec
Confidence 4678887774 78899999999999 588889999999887543 66666654
No 30
>TIGR00230 sfsA sugar fermentation stimulation protein. probable regulatory factor involved in maltose metabolism contains a putative DNA binding domain. Isolated as a gene which enabled E.coli strain MK2001 to use maltose.
Probab=56.78 E-value=39 Score=30.96 Aligned_cols=65 Identities=15% Similarity=0.098 Sum_probs=45.7
Q ss_pred ceEEEEeC-CCCEEEEEec--ccccceeeeecCCEEEEEeccCC--CCeEEEEEecC------------HhHHHHHHHcC
Q psy2272 5 GRLEAMCF-DGTKRLCHIR--GKLRKKVWINQGDIILIGLRDYQ--DAKADVILKYT------------PDEARNLKTYG 67 (276)
Q Consensus 5 grfEVeC~-DG~kRLAhIp--GKMRKKVWIk~GDiVLVEprDYQ--D~KGDIIyRYt------------~DEIR~LKk~G 67 (276)
+||-|.+. ||.+..||+| |+|+- -+.+|-.|++++++.. ..+-+++..+. ..=++...+.|
T Consensus 19 nRF~~~V~~~G~~~~aH~pNtGrl~e--ll~pG~~vll~~~~~p~rK~~y~l~~v~~~g~~V~int~~~N~l~~~~l~~~ 96 (232)
T TIGR00230 19 NRFLVDVEVDGRRETAHCPNTGRLTE--LIFPGNDVGLSKSDNGGRKLSYTWEAVQCDGGWVLVNTQLQNRLFKVAIPSS 96 (232)
T ss_pred CCEEEEEEECCeEEEEEcCCCCCChh--hcCCCCEEEEEECCCCCCCCCEEEEEEEECCeEEEEcCccHHHHHHHHHHcC
Confidence 56666654 9999999997 66665 3459999999988764 23455554443 23367777888
Q ss_pred CCCc
Q psy2272 68 EFPE 71 (276)
Q Consensus 68 eLPE 71 (276)
.+|+
T Consensus 97 ~i~~ 100 (232)
T TIGR00230 97 KISE 100 (232)
T ss_pred CCcc
Confidence 8886
No 31
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=56.56 E-value=11 Score=26.19 Aligned_cols=35 Identities=20% Similarity=0.486 Sum_probs=26.2
Q ss_pred EEEEecccccceeeeecCCEEEEEeccCCCCeEEEEEecCHhHHH
Q psy2272 17 RLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEAR 61 (276)
Q Consensus 17 RLAhIpGKMRKKVWIk~GDiVLVEprDYQD~KGDIIyRYt~DEIR 61 (276)
+-+.++|+.. .+.+++||.| +||++++++...+.+
T Consensus 5 I~~~~~G~V~-~v~V~~G~~V---------kkGd~L~~ld~~~~~ 39 (50)
T PF13533_consen 5 IQAPVSGRVE-SVYVKEGQQV---------KKGDVLLVLDSPDLQ 39 (50)
T ss_pred EeCCCCEEEE-EEEecCCCEE---------cCCCEEEEECcHHHH
Confidence 3455667554 4778899888 699999999887765
No 32
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=54.84 E-value=4 Score=28.31 Aligned_cols=28 Identities=21% Similarity=0.493 Sum_probs=16.5
Q ss_pred eecCCEEEEEeccCCCCeEEEEEecCHhH
Q psy2272 31 INQGDIILIGLRDYQDAKADVILKYTPDE 59 (276)
Q Consensus 31 Ik~GDiVLVEprDYQD~KGDIIyRYt~DE 59 (276)
|..||+|+|.+.. ....||||.-...++
T Consensus 11 i~~Gd~v~v~~~~-~~~~gdivv~~~~~~ 38 (70)
T PF00717_consen 11 IKDGDIVLVDPSS-EPKDGDIVVVKIDGD 38 (70)
T ss_dssp SSTTEEEEEEETS----TTSEEEEEETTE
T ss_pred eeCCCEEEEEEcC-CCccCeEEEEEECCc
Confidence 5678888888665 445666666554443
No 33
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=52.65 E-value=16 Score=27.08 Aligned_cols=28 Identities=18% Similarity=0.169 Sum_probs=18.7
Q ss_pred eecCCEEEEEeccC---CCCeEEEEEecCHh
Q psy2272 31 INQGDIILIGLRDY---QDAKADVILKYTPD 58 (276)
Q Consensus 31 Ik~GDiVLVEprDY---QD~KGDIIyRYt~D 58 (276)
++.||+|+|.+... ....|||+.-..++
T Consensus 12 l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~ 42 (90)
T TIGR02754 12 LPPGDRIIVVPWLKIFRVPPIGNVVVVRHPL 42 (90)
T ss_pred cCCCCEEEEEEccccCCCCCCCeEEEEecCC
Confidence 56899999997432 22358888666543
No 34
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=51.05 E-value=26 Score=30.41 Aligned_cols=35 Identities=14% Similarity=0.145 Sum_probs=30.0
Q ss_pred EEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccC
Q psy2272 7 LEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDY 44 (276)
Q Consensus 7 fEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDY 44 (276)
.+|++.||.++.|.|||-=.- |.+-|.|+|+-.--
T Consensus 59 ~RVrL~NG~~VtAyiPg~Gh~---lqEH~~Vli~G~~v 93 (129)
T COG0048 59 ARVRLINGKEVTAYIPGEGHN---LQEHSEVLIRGGRV 93 (129)
T ss_pred EEEEeeCCcEEEEEcCCCCcc---ccccCEEEEecCcc
Confidence 578999999999999997664 99999999986543
No 35
>PRK00347 putative DNA-binding transcriptional regulator; Reviewed
Probab=49.60 E-value=59 Score=29.66 Aligned_cols=65 Identities=18% Similarity=0.231 Sum_probs=43.6
Q ss_pred ceEEEEeC--CCCEEEEEec--ccccceeeeecCCEEEEEeccCCCCeEE----EEEec-----------CHhHHHHHHH
Q psy2272 5 GRLEAMCF--DGTKRLCHIR--GKLRKKVWINQGDIILIGLRDYQDAKAD----VILKY-----------TPDEARNLKT 65 (276)
Q Consensus 5 grfEVeC~--DG~kRLAhIp--GKMRKKVWIk~GDiVLVEprDYQD~KGD----IIyRY-----------t~DEIR~LKk 65 (276)
+||-|.+. ||+...||+| |+|+- -+.+|-.|++++.+-..-|-. .+... ...=+..+.+
T Consensus 17 nRF~~~V~~~~g~~~~aH~pntGRl~e--ll~pG~~v~l~~~~~pkrK~~~~~~l~~~~~~~~V~int~~~N~l~~~~l~ 94 (234)
T PRK00347 17 KRFLADVELDDGEELTAHCPNTGRMTG--LLTPGNTVWLSTSDNPKRKYPHTWELTETPNGRLIGINTALPNKLVEEALE 94 (234)
T ss_pred CCEEEEEEECCCCEEEEEcCCCCCChh--hccCCCEEEEEECCCCCCccceEEEEEEeCCCeEEEECcccHHHHHHHHHH
Confidence 56776665 6999999997 66665 344999999998865433322 33321 2234677788
Q ss_pred cCCCCc
Q psy2272 66 YGEFPE 71 (276)
Q Consensus 66 ~GeLPE 71 (276)
.|.+|.
T Consensus 95 ~~~i~~ 100 (234)
T PRK00347 95 AGLIPE 100 (234)
T ss_pred cCCCcc
Confidence 888885
No 36
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=48.67 E-value=21 Score=24.90 Aligned_cols=28 Identities=25% Similarity=0.622 Sum_probs=22.7
Q ss_pred eecCCEEEEEeccCCCCeEEEEEecCHh
Q psy2272 31 INQGDIILIGLRDYQDAKADVILKYTPD 58 (276)
Q Consensus 31 Ik~GDiVLVEprDYQD~KGDIIyRYt~D 58 (276)
|..||+|+|.+.+-....|+|+.-...+
T Consensus 14 i~~gd~v~i~~~~~~~~~G~iv~~~~~~ 41 (84)
T cd06462 14 IPDGDLVLVDKSSYEPKRGDIVVFRLPG 41 (84)
T ss_pred ccCCCEEEEEecCCCCcCCEEEEEEcCC
Confidence 8899999999987767788888666554
No 37
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=47.88 E-value=30 Score=28.56 Aligned_cols=32 Identities=16% Similarity=0.107 Sum_probs=27.4
Q ss_pred EEEEeCCCCEEEEEecccccceeeeecCCEEEEEe
Q psy2272 7 LEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGL 41 (276)
Q Consensus 7 fEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEp 41 (276)
.+|++.||.++.|+|||-= -.+.+-|.|||.=
T Consensus 38 arV~L~ngk~v~ayIPg~G---h~lqeh~~VLvrG 69 (95)
T cd00319 38 AKVRLTSGYEVTAYIPGEG---HNLQEHSVVLIRG 69 (95)
T ss_pred EEEEccCCCEEEEECCCCC---cccccccEEEEeC
Confidence 5788999999999999977 3688899999875
No 38
>PF10017 Methyltransf_33: Histidine-specific methyltransferase, SAM-dependent; InterPro: IPR019257 This domain is found in methyltransferases and various hypothetical proteins.
Probab=46.47 E-value=87 Score=25.43 Aligned_cols=36 Identities=25% Similarity=0.367 Sum_probs=23.9
Q ss_pred cceeeeecCCEEEEEeccCCCCeEEEEEecCHhHHHHHHHc-CCCCc
Q psy2272 26 RKKVWINQGDIILIGLRDYQDAKADVILKYTPDEARNLKTY-GEFPE 71 (276)
Q Consensus 26 RKKVWIk~GDiVLVEprDYQD~KGDIIyRYt~DEIR~LKk~-GeLPE 71 (276)
...|-+++|..|. -+..|||++++++.|-+. |+-|.
T Consensus 77 ~~~i~~~~GE~I~----------~e~S~Ky~~~~~~~l~~~aGl~~~ 113 (127)
T PF10017_consen 77 DLTIHFKEGERIH----------TENSYKYSPEEFEALAEQAGLEVE 113 (127)
T ss_pred CceeEECCCCEEE----------EEEeeCcCHHHHHHHHHHCCCeeE
Confidence 3345555665555 456699999999988765 44443
No 39
>CHL00051 rps12 ribosomal protein S12
Probab=46.26 E-value=32 Score=29.62 Aligned_cols=32 Identities=13% Similarity=0.075 Sum_probs=28.0
Q ss_pred EEEEeCCCCEEEEEecccccceeeeecCCEEEEEe
Q psy2272 7 LEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGL 41 (276)
Q Consensus 7 fEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEp 41 (276)
.+|++.||.++.|+|||-=. -+.+-+.|||.-
T Consensus 53 arVrLsngk~v~AyIPGeGh---nlqehs~VLvrG 84 (123)
T CHL00051 53 ARVRLTSGFEITAYIPGIGH---NLQEHSVVLVRG 84 (123)
T ss_pred EEEEccCCCEEEEEcCCCCc---cccccCEEEEeC
Confidence 57889999999999999875 788999999873
No 40
>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle. This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff.
Probab=42.94 E-value=38 Score=29.19 Aligned_cols=33 Identities=15% Similarity=0.100 Sum_probs=28.1
Q ss_pred EEEEeCCCCEEEEEecccccceeeeecCCEEEEEec
Q psy2272 7 LEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLR 42 (276)
Q Consensus 7 fEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEpr 42 (276)
..|++.||.++.|+|||-= --+.+-|.|||.--
T Consensus 53 arVrL~ngk~v~AyIPG~G---hnlqehs~VLvrGG 85 (124)
T TIGR00981 53 ARVRLTNGFEVTAYIPGEG---HNLQEHSVVLIRGG 85 (124)
T ss_pred EEEEeCCCCEEEEEcCCCC---CCccccCEEEEeCC
Confidence 5789999999999999987 36889999999843
No 41
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=41.29 E-value=81 Score=26.06 Aligned_cols=51 Identities=25% Similarity=0.193 Sum_probs=36.9
Q ss_pred CCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccCCC-CeEEEEEecCHhHHHHHHH
Q psy2272 3 GNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQD-AKADVILKYTPDEARNLKT 65 (276)
Q Consensus 3 GNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDYQD-~KGDIIyRYt~DEIR~LKk 65 (276)
|--.+|+.|.|... --|++||.++..-++-.. ....|+....=+.-+.|-+
T Consensus 16 G~KtiEiRlnD~kr------------~~ikvGD~I~f~~~~~~~~l~v~V~~i~~Y~sF~~ll~ 67 (109)
T cd06555 16 GKKTIEIRLNDEKR------------QQIKVGDKILFNDLDTGQQLLVKVVDIRKYDSFRELLE 67 (109)
T ss_pred CCCEEEEEecccch------------hcCCCCCEEEEEEcCCCcEEEEEEEEEEecCCHHHHHH
Confidence 55677888877443 458999999998886543 4788888776666666654
No 42
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=41.15 E-value=43 Score=28.85 Aligned_cols=32 Identities=16% Similarity=0.141 Sum_probs=27.7
Q ss_pred EEEEeCCCCEEEEEecccccceeeeecCCEEEEEe
Q psy2272 7 LEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGL 41 (276)
Q Consensus 7 fEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEp 41 (276)
..|++.||.++.|+|||-=. -+.+-|.|||.-
T Consensus 53 arVrL~ngk~v~AyIPGeGh---nlqehs~VLvrG 84 (124)
T PRK05163 53 ARVRLTNGFEVTAYIPGEGH---NLQEHSVVLIRG 84 (124)
T ss_pred EEEEeCCCCEEEEEcCCCCC---CccccCEEEEeC
Confidence 57899999999999999873 688999999873
No 43
>cd03368 Ribosomal_S12 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions. S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. Antibiotics such as streptomycin bind S12 and cause the ribosome to misread the genetic code.
Probab=40.60 E-value=44 Score=28.19 Aligned_cols=33 Identities=12% Similarity=0.108 Sum_probs=27.9
Q ss_pred EEEEeCCCCEEEEEecccccceeeeecCCEEEEEec
Q psy2272 7 LEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLR 42 (276)
Q Consensus 7 fEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEpr 42 (276)
.+|++.||.++.|+|||-= --+.+-|.|||.=-
T Consensus 51 arV~L~ngk~v~AyIPG~G---hnlqehs~VLvrGG 83 (108)
T cd03368 51 ARVRLSNGKEVTAYIPGEG---HNLQEHSVVLVRGG 83 (108)
T ss_pred EEEEecCCCEEEEEcCCCC---CCccccCEEEEeCC
Confidence 5788999999999999987 35888899998753
No 44
>PF00164 Ribosom_S12_S23: Ribosomal protein S12/S23; InterPro: IPR006032 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S12 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S12 is known to be involved in the translation initiation step. It is a very basic protein of 120 to 150 amino-acid residues. S12 belongs to a family of ribosomal proteins which are grouped on the basis of sequence similarities. This protein is known typically as S12 in bacteria, S23 in eukaryotes and as either S12 or S23 in the Archaea []. Bacterial S12 molecules contain a conserved aspartic acid residue which undergoes a novel post-translational modification, beta-methylthiolation, to form the corresponding 3-methylthioaspartic acid.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZKQ_l 3BBN_L 3PYU_L 3D5A_L 3MS0_L 3MR8_L 3F1G_L 2OW8_m 3PYS_L 2QNH_m ....
Probab=40.27 E-value=43 Score=28.59 Aligned_cols=34 Identities=15% Similarity=0.122 Sum_probs=27.9
Q ss_pred EEEEeCCCCEEEEEecccccceeeeecCCEEEEEecc
Q psy2272 7 LEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRD 43 (276)
Q Consensus 7 fEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprD 43 (276)
..|++.||.+++|+|||-= --+.+-|.|||.=--
T Consensus 52 arVrL~n~k~v~AyIPg~G---hnlqehs~VLVrGgr 85 (122)
T PF00164_consen 52 ARVRLSNGKKVTAYIPGEG---HNLQEHSVVLVRGGR 85 (122)
T ss_dssp EEEEETTSEEEEEEC-SSS---CCSTTTSEEEEEEES
T ss_pred ceeeeccCceEEEEecCCc---ccccccceEEEeccc
Confidence 5789999999999999977 368899999997543
No 45
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=39.88 E-value=35 Score=23.56 Aligned_cols=38 Identities=11% Similarity=0.145 Sum_probs=28.5
Q ss_pred eEEEEeCCCCEEEEEecccccceeeeecCCEEEEEecc
Q psy2272 6 RLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRD 43 (276)
Q Consensus 6 rfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprD 43 (276)
...+.+.+|....|.|+..-..++-+.+||.|.+...+
T Consensus 22 ~v~~~~~~~~~l~a~it~~~~~~L~L~~G~~V~~~ik~ 59 (64)
T PF03459_consen 22 EVTLDLGGGETLTARITPESAEELGLKPGDEVYASIKA 59 (64)
T ss_dssp EEEEEETTSEEEEEEEEHHHHHHCT-STT-EEEEEE-G
T ss_pred EEEEEECCCCEEEEEEcHHHHHHcCCCCCCEEEEEEeh
Confidence 45666777777999999988888889999999887654
No 46
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=37.87 E-value=61 Score=22.44 Aligned_cols=41 Identities=15% Similarity=0.030 Sum_probs=29.2
Q ss_pred CceEEEE--eCCCCEEEEEecccccceeeeecCCEEEEEeccC
Q psy2272 4 NGRLEAM--CFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDY 44 (276)
Q Consensus 4 NgrfEVe--C~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDY 44 (276)
+...+|. +.+|.+..|.|+.+--..+-+.+||.|.+...+.
T Consensus 20 g~~~~v~l~~~~~~~l~a~i~~~~~~~l~l~~G~~v~~~ik~~ 62 (69)
T TIGR00638 20 DVNAEVDLLLGGGTKLTAVITLESVAELGLKPGKEVYAVIKAP 62 (69)
T ss_pred CCeEEEEEEECCCCEEEEEecHHHHhhCCCCCCCEEEEEEECc
Confidence 3444554 5566688899998766677788999888776544
No 47
>PF09795 Atg31: Autophagy-related protein 31; InterPro: IPR018621 Autophagy is an intracellular degradation system that responds to nutrient starvation. Cis1/Atg31 has been shown to be required for autophagosome formation in Saccharomyces cerevisiae (Baker's yeast) []. It interacts with Atg17 [].
Probab=31.11 E-value=21 Score=31.89 Aligned_cols=28 Identities=39% Similarity=0.624 Sum_probs=21.3
Q ss_pred hCCCCCCCCcccccchhhhhhhhcccCC
Q psy2272 224 LAPKLDSSDTLHLDNWISEEYQLLSYRP 251 (276)
Q Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 251 (276)
+-=-||.+-+|-=-.-||+.|+||||+|
T Consensus 70 IIVdLDe~g~l~~VeLISD~yelLsy~~ 97 (160)
T PF09795_consen 70 IIVDLDESGSLENVELISDQYELLSYKE 97 (160)
T ss_pred EEEEecCCCceeeEEeehhhhhhhhhhh
Confidence 3445677777766678999999999943
No 48
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=30.41 E-value=33 Score=24.09 Aligned_cols=27 Identities=22% Similarity=0.458 Sum_probs=19.3
Q ss_pred eecCCEEEEEeccCCCCeEEEEEecCHh
Q psy2272 31 INQGDIILIGLRDYQDAKADVILKYTPD 58 (276)
Q Consensus 31 Ik~GDiVLVEprDYQD~KGDIIyRYt~D 58 (276)
|..||+|+|++... ...|+|+.-...+
T Consensus 14 i~~gd~lii~~~~~-~~~g~i~~~~~~~ 40 (81)
T cd06529 14 IPDGDLVLVDPSDT-PRDGDIVVARLDG 40 (81)
T ss_pred cCCCCEEEEcCCCC-CCCCCEEEEEECC
Confidence 78888888887654 5677777666554
No 49
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=30.00 E-value=71 Score=25.06 Aligned_cols=33 Identities=18% Similarity=0.199 Sum_probs=26.7
Q ss_pred ceeeeecCCEEEEEeccCCCCeEEEEEecCHhH
Q psy2272 27 KKVWINQGDIILIGLRDYQDAKADVILKYTPDE 59 (276)
Q Consensus 27 KKVWIk~GDiVLVEprDYQD~KGDIIyRYt~DE 59 (276)
.++-|+.||.|.|--=++-...|.|...+...+
T Consensus 5 ~~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~ 37 (83)
T CHL00141 5 KKMHVKIGDTVKIISGSDKGKIGEVLKIIKKSN 37 (83)
T ss_pred eeCcccCCCEEEEeEcCCCCcEEEEEEEEcCCC
Confidence 367899999999888777777899988876644
No 50
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=29.20 E-value=69 Score=25.48 Aligned_cols=27 Identities=19% Similarity=0.229 Sum_probs=19.9
Q ss_pred eeeecCCEEEEEeccCC----C-C--eEEEEEec
Q psy2272 29 VWINQGDIILIGLRDYQ----D-A--KADVILKY 55 (276)
Q Consensus 29 VWIk~GDiVLVEprDYQ----D-~--KGDIIyRY 55 (276)
+-+++||+|+|+..... + + -|+||+--
T Consensus 4 L~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ 37 (75)
T PF11302_consen 4 LSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCE 37 (75)
T ss_pred cccCCCCEEEEecCccccccCCCCcEEEEEEEEe
Confidence 34789999999998732 1 2 68888764
No 51
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=27.57 E-value=23 Score=24.14 Aligned_cols=30 Identities=23% Similarity=0.390 Sum_probs=23.8
Q ss_pred CCEEEEEecccccceeeeecCCEEEEEecc
Q psy2272 14 GTKRLCHIRGKLRKKVWINQGDIILIGLRD 43 (276)
Q Consensus 14 G~kRLAhIpGKMRKKVWIk~GDiVLVEprD 43 (276)
|...-..||-.+++..-|.+||.|.+...+
T Consensus 4 g~s~~v~iPk~~~~~l~l~~Gd~v~i~~~~ 33 (47)
T PF04014_consen 4 GNSGQVTIPKEIREKLGLKPGDEVEIEVEG 33 (47)
T ss_dssp TTCSEEEE-HHHHHHTTSSTTTEEEEEEET
T ss_pred CCCceEECCHHHHHHcCCCCCCEEEEEEeC
Confidence 344556899999999999999999998873
No 52
>KOG2107|consensus
Probab=26.93 E-value=84 Score=28.66 Aligned_cols=49 Identities=18% Similarity=0.418 Sum_probs=37.2
Q ss_pred CCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccCCCCeEEEEEecCHhHHHHHHHcCCC
Q psy2272 3 GNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEARNLKTYGEF 69 (276)
Q Consensus 3 GNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDYQD~KGDIIyRYt~DEIR~LKk~GeL 69 (276)
|+|-|.|.-.|+.=+ |||+..||.|++-+ -|-+|+|-+.-...|.+-+.
T Consensus 102 GtgYfDVrd~dd~WI----------Ri~vekGDlivlPa--------GiyHRFTtt~~n~vkamRlF 150 (179)
T KOG2107|consen 102 GTGYFDVRDKDDQWI----------RIFVEKGDLIVLPA--------GIYHRFTTTPSNYVKAMRLF 150 (179)
T ss_pred cceEEeeccCCCCEE----------EEEEecCCEEEecC--------cceeeeecCchHHHHHHHHh
Confidence 788888887775543 59999999998754 48899988777777666654
No 53
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=26.76 E-value=1.4e+02 Score=25.97 Aligned_cols=50 Identities=20% Similarity=0.193 Sum_probs=32.8
Q ss_pred CceEEEEeCCCCEEEEEecccccce-eeeecCCEEEEEeccCCCCeEEEEE
Q psy2272 4 NGRLEAMCFDGTKRLCHIRGKLRKK-VWINQGDIILIGLRDYQDAKADVIL 53 (276)
Q Consensus 4 NgrfEVeC~DG~kRLAhIpGKMRKK-VWIk~GDiVLVEprDYQD~KGDIIy 53 (276)
-.+|-|.+.+|.+.++-=-=-+--+ =|+++||.|.+-=.=+-+.||-+|+
T Consensus 58 HQ~Fiv~l~~g~tllIahNIDlaprip~l~~GD~V~f~GeYe~n~kggvIH 108 (131)
T PF11948_consen 58 HQRFIVRLSSGQTLLIAHNIDLAPRIPWLQKGDQVEFYGEYEWNPKGGVIH 108 (131)
T ss_pred ceEEEEEeCCCCEEEEEeccCccccCcCcCCCCEEEEEEEEEECCCCCEEE
Confidence 3688999999998875422222223 3799999998876544444666654
No 54
>PTZ00115 40S ribosomal protein S12; Provisional
Probab=26.45 E-value=87 Score=30.33 Aligned_cols=32 Identities=16% Similarity=0.087 Sum_probs=26.9
Q ss_pred EEEEeCCCCEEEEEecccccceeeeecCCEEEEEe
Q psy2272 7 LEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGL 41 (276)
Q Consensus 7 fEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEp 41 (276)
.+|++.+|.++.|+|||-=. -+.+-|.|||.-
T Consensus 149 arVrLsNGk~VtAyIPGeGH---nLQEHs~VLVRG 180 (290)
T PTZ00115 149 ARVRLSTGRTVTVYIPGIGH---NLNTHSVVLVRG 180 (290)
T ss_pred EEEEecCCCEEEEEcCCCCc---ccccCCEEEEeC
Confidence 57889999999999999875 678888888843
No 55
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=26.39 E-value=89 Score=26.57 Aligned_cols=32 Identities=13% Similarity=0.207 Sum_probs=27.2
Q ss_pred eeeeecCCEEEEEeccCCCCeEEEEEecCHhH
Q psy2272 28 KVWINQGDIILIGLRDYQDAKADVILKYTPDE 59 (276)
Q Consensus 28 KVWIk~GDiVLVEprDYQD~KGDIIyRYt~DE 59 (276)
.+.|+.||.|.|--=++-..+|.|+-.+...+
T Consensus 43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~ 74 (120)
T PRK01191 43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRG 74 (120)
T ss_pred cceEeCCCEEEEeecCCCCceEEEEEEEcCCC
Confidence 57899999999998888888999998876654
No 56
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=26.23 E-value=1.4e+02 Score=19.86 Aligned_cols=44 Identities=18% Similarity=0.196 Sum_probs=30.0
Q ss_pred EEEeCCCCEEEEEecccccc-ee-----eeecCCEEEEEeccCCCCeEEEE
Q psy2272 8 EAMCFDGTKRLCHIRGKLRK-KV-----WINQGDIILIGLRDYQDAKADVI 52 (276)
Q Consensus 8 EVeC~DG~kRLAhIpGKMRK-KV-----WIk~GDiVLVEprDYQD~KGDII 52 (276)
-|.+.++..-++|++ .|.. ++ +++.||.|.|....-+..++.|.
T Consensus 17 fv~l~~~~~g~~~~~-~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ 66 (68)
T cd05685 17 FVDIGVKQDGLIHIS-KMADRFVSHPSDVVSVGDIVEVKVISIDEERGRIS 66 (68)
T ss_pred EEEcCCCCEEEEEHH-HCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEe
Confidence 367777777777765 3332 12 46899999998887776666664
No 57
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=26.22 E-value=53 Score=31.72 Aligned_cols=32 Identities=25% Similarity=0.423 Sum_probs=27.2
Q ss_pred ceeeeecCCEEEEEeccCCCCeEEEEEecCHhHH
Q psy2272 27 KKVWINQGDIILIGLRDYQDAKADVILKYTPDEA 60 (276)
Q Consensus 27 KKVWIk~GDiVLVEprDYQD~KGDIIyRYt~DEI 60 (276)
|.+|.++||.++|.+. -|+|++|.-+.-.+++
T Consensus 111 ~~~wpq~Gd~l~v~l~--~Dkk~Ri~g~~a~~~~ 142 (287)
T COG2996 111 KSLWPQKGDKLLVYLY--VDKKGRIWGTLAIEKI 142 (287)
T ss_pred cccCCCCCCEEEEEEE--EccCCcEEEEecchhH
Confidence 4799999999999987 6789999988776654
No 58
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=25.81 E-value=52 Score=28.15 Aligned_cols=43 Identities=26% Similarity=0.346 Sum_probs=28.4
Q ss_pred CCCEEEEEecccccceeeeecCCEEEEEeccCC-CCeEEEEEecCH
Q psy2272 13 DGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQ-DAKADVILKYTP 57 (276)
Q Consensus 13 DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDYQ-D~KGDIIyRYt~ 57 (276)
.+....+-..+.|.-. +.+||+|++.+.++. ..+||||.=..+
T Consensus 29 ~~~p~v~V~g~SM~Pt--l~~GD~vlv~~~~~~~~~~GDIVvf~~~ 72 (158)
T TIGR02228 29 GPDPVVVVLSGSMEPT--FNTGDLILVTGADPNDIQVGDVITYKSP 72 (158)
T ss_pred CCCcEEEEcCCCCcCC--ccCCCEEEEEecccCCCCCCCEEEEEEC
Confidence 3444444556667654 579999999986554 568998854433
No 59
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=25.31 E-value=96 Score=24.02 Aligned_cols=31 Identities=13% Similarity=0.252 Sum_probs=24.8
Q ss_pred eeeecCCEEEEEeccCCCCeEEEEEecCHhH
Q psy2272 29 VWINQGDIILIGLRDYQDAKADVILKYTPDE 59 (276)
Q Consensus 29 VWIk~GDiVLVEprDYQD~KGDIIyRYt~DE 59 (276)
+-|+.||.|.|--=++....|.|+..+...+
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~ 35 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKKN 35 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCCC
Confidence 5799999999887777677899988876554
No 60
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=24.77 E-value=57 Score=27.22 Aligned_cols=27 Identities=26% Similarity=0.566 Sum_probs=19.9
Q ss_pred eecCCEEEEEeccC---CCCeEEEEEecCH
Q psy2272 31 INQGDIILIGLRDY---QDAKADVILKYTP 57 (276)
Q Consensus 31 Ik~GDiVLVEprDY---QD~KGDIIyRYt~ 57 (276)
|..||+|+|....| +..+||||.-..+
T Consensus 34 l~~Gd~vlv~k~~~~~~~~~rGDiVvf~~~ 63 (163)
T TIGR02227 34 LKEGDRILVNKFAYGTSDPKRGDIVVFKDP 63 (163)
T ss_pred hhCCCEEEEEEeEcCCCCCCCCcEEEEecC
Confidence 56899999998765 3568988765443
No 61
>PRK08577 hypothetical protein; Provisional
Probab=24.20 E-value=57 Score=26.44 Aligned_cols=34 Identities=21% Similarity=0.253 Sum_probs=26.9
Q ss_pred EEecccccceeeeecCCEEEEEeccCCCCeEEEEEec
Q psy2272 19 CHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKY 55 (276)
Q Consensus 19 AhIpGKMRKKVWIk~GDiVLVEprDYQD~KGDIIyRY 55 (276)
..||-.+|+++-|++||.|.+... .++|+|+.+-
T Consensus 15 i~ip~~~r~~l~~~~g~~~~~~~~---~~~~~~~~~~ 48 (136)
T PRK08577 15 ITIPLEIREALGIREGMYVLLIAD---TDKKEIHLEP 48 (136)
T ss_pred EEecHHHHHHcCcCCCCEEEEEEE---CCCCEEEEEE
Confidence 468999999999999999988754 4567777653
No 62
>PTZ00067 40S ribosomal S23; Provisional
Probab=23.98 E-value=1.5e+02 Score=26.22 Aligned_cols=34 Identities=18% Similarity=0.232 Sum_probs=27.5
Q ss_pred EEEEeC-CCCEEEEEecccccceeeeecCCEEEEEe
Q psy2272 7 LEAMCF-DGTKRLCHIRGKLRKKVWINQGDIILIGL 41 (276)
Q Consensus 7 fEVeC~-DG~kRLAhIpGKMRKKVWIk~GDiVLVEp 41 (276)
..|++. ||.++.|.|||-=-- -.|.+-|.|||.-
T Consensus 70 ~rV~L~kngk~vtAyiPg~G~l-h~lqEh~~VLV~G 104 (143)
T PTZ00067 70 VRVQLIKNGKKITAFVPNDGCL-NFINENDEVLVSG 104 (143)
T ss_pred EEEEEccCCcEEEEEeCCCCcc-cccccCCEEEEEe
Confidence 578887 999999999986521 2488999999986
No 63
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=23.58 E-value=90 Score=24.06 Aligned_cols=38 Identities=26% Similarity=0.375 Sum_probs=28.7
Q ss_pred EEecccccceeeeecCCEEEEEeccCCCCeEEEEEecCHh
Q psy2272 19 CHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPD 58 (276)
Q Consensus 19 AhIpGKMRKKVWIk~GDiVLVEprDYQD~KGDIIyRYt~D 58 (276)
.-||-..|+++=|++||.|.+.....+.. =|+-+|.+.
T Consensus 16 IvIPkeiR~~lgi~~Gd~lei~~~~~~~~--ivl~k~~~~ 53 (89)
T COG2002 16 IVIPKEIREALGIKEGDVLEIIVDGDGGR--IVLKKYKPA 53 (89)
T ss_pred EEecHHHHHHhCCCCCCEEEEEEeCCCCE--EEEEECCcc
Confidence 35899999999999999999988755422 445566554
No 64
>PF07065 D123: D123; InterPro: IPR009772 This family contains a number of eukaryotic D123 proteins approximately 330 residues long. It has been shown that mutated variants of D123 exhibit temperature-dependent differences in their degradation rate [].
Probab=22.74 E-value=1.3e+02 Score=28.36 Aligned_cols=29 Identities=21% Similarity=0.260 Sum_probs=24.2
Q ss_pred CeEEEEEecCHhHHHHHHHcC-CCCcccccc
Q psy2272 47 AKADVILKYTPDEARNLKTYG-EFPETVRIN 76 (276)
Q Consensus 47 ~KGDIIyRYt~DEIR~LKk~G-eLPEeFkiN 76 (276)
-|+.|| .+.++=+++|...| .+|++....
T Consensus 10 ~ks~ii-~Lp~~fi~YL~~D~i~lP~~~~~~ 39 (299)
T PF07065_consen 10 IKSKII-PLPEEFIEYLLSDGIVLPEESDPS 39 (299)
T ss_pred cceEEE-eCCHHHHHHHHcCCeECCCCCCcc
Confidence 388888 99999999999999 678766544
No 65
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=22.62 E-value=1.8e+02 Score=21.35 Aligned_cols=56 Identities=18% Similarity=0.111 Sum_probs=29.9
Q ss_pred CCceEEEEeCC-CCE-----E-EEEecccccceeeeecCCEEEEEeccCCCCeEEEEEecCHh
Q psy2272 3 GNGRLEAMCFD-GTK-----R-LCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPD 58 (276)
Q Consensus 3 GNgrfEVeC~D-G~k-----R-LAhIpGKMRKKVWIk~GDiVLVEprDYQD~KGDIIyRYt~D 58 (276)
+.++++|++.+ +.. + +..-.|..+-..--..||-|+|....-+..++=|+-.+..+
T Consensus 9 ~~grvrV~~~~~~~~~s~Wl~~~~~~ag~~g~~~~P~iGeqV~v~~~~Gd~~~~~vlg~l~~~ 71 (79)
T PF04717_consen 9 DKGRVRVRFPDDGDIVSDWLPVLQPRAGGWGFWFPPEIGEQVLVLFPGGDPERPVVLGSLYSD 71 (79)
T ss_dssp TTTEEEEE-B-CTTEEEEEEEE--S-BSSSB------TT-EEEEEEGGCTTTSEEEEEEE--S
T ss_pred CCCEEEEEEecCCCccceEEEeeehhccCCeeEccCCCCcEEEEEccCCcCCCCEEEEEECCC
Confidence 45789999743 332 2 22334544445556789999999977778899998766443
No 66
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=22.26 E-value=1.7e+02 Score=22.68 Aligned_cols=38 Identities=16% Similarity=0.128 Sum_probs=24.2
Q ss_pred CCceEEEEeCC--CCEEEEEeccc--ccc-eeeeecCCEEEEE
Q psy2272 3 GNGRLEAMCFD--GTKRLCHIRGK--LRK-KVWINQGDIILIG 40 (276)
Q Consensus 3 GNgrfEVeC~D--G~kRLAhIpGK--MRK-KVWIk~GDiVLVE 40 (276)
.+|+.-..+.| +....+.-++. +++ ...+++||.|+|.
T Consensus 15 ~sGH~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~ 57 (91)
T cd04482 15 EGGHVFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVY 57 (91)
T ss_pred CCCCEEEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEE
Confidence 34555454444 44555555554 766 7789999988875
No 67
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=20.95 E-value=1.5e+02 Score=25.47 Aligned_cols=30 Identities=17% Similarity=0.241 Sum_probs=23.1
Q ss_pred CCceEEEEeCCCCEEEEEecccccceeeeecCCEEEEEeccC
Q psy2272 3 GNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDY 44 (276)
Q Consensus 3 GNgrfEVeC~DG~kRLAhIpGKMRKKVWIk~GDiVLVEprDY 44 (276)
|+++|.|...||.+. .++.-|+|++.|.|-
T Consensus 29 ~~~kykv~FdDG~~~------------~v~~~div~~dplpl 58 (122)
T PF09038_consen 29 GKNKYKVLFDDGYEC------------RVLGKDIVVCDPLPL 58 (122)
T ss_dssp TTTEEEEEETTS-EE------------EEECCCEEEESSS-T
T ss_pred CCCeEEEEecCCccc------------eeccCcEEEEcceec
Confidence 788999999999875 267789999987766
No 68
>PF09902 DUF2129: Uncharacterized protein conserved in bacteria (DUF2129); InterPro: IPR016979 This is a group of uncharacterised conserved proteins.
Probab=20.67 E-value=91 Score=24.22 Aligned_cols=22 Identities=23% Similarity=0.641 Sum_probs=19.8
Q ss_pred eEEEEEecCHhHHHHHHHcCCC
Q psy2272 48 KADVILKYTPDEARNLKTYGEF 69 (276)
Q Consensus 48 KGDIIyRYt~DEIR~LKk~GeL 69 (276)
.|=|||-|+--+++.|++.|-+
T Consensus 2 ~gliVyl~~~k~~r~L~kfG~i 23 (71)
T PF09902_consen 2 QGLIVYLYSLKDARQLRKFGDI 23 (71)
T ss_pred eEEEEEEechHhHHhHhhcccE
Confidence 4779999999999999999965
No 69
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.36 E-value=1.9e+02 Score=20.88 Aligned_cols=47 Identities=17% Similarity=0.041 Sum_probs=32.5
Q ss_pred EEEEeCCCCEEEEEecccccce-----eeeecCCEEEEEeccCCCCeEEEEE
Q psy2272 7 LEAMCFDGTKRLCHIRGKLRKK-----VWINQGDIILIGLRDYQDAKADVIL 53 (276)
Q Consensus 7 fEVeC~DG~kRLAhIpGKMRKK-----VWIk~GDiVLVEprDYQD~KGDIIy 53 (276)
.-|.+++|..-++|++---..+ =.++.||.|.+....++..++.|..
T Consensus 18 ~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~l 69 (71)
T cd05696 18 AVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQL 69 (71)
T ss_pred EEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEE
Confidence 4577888888888875211111 2378899999999988877666653
No 70
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=20.02 E-value=76 Score=20.31 Aligned_cols=25 Identities=20% Similarity=0.226 Sum_probs=21.8
Q ss_pred EEEecccccceeeeecCCEEEEEec
Q psy2272 18 LCHIRGKLRKKVWINQGDIILIGLR 42 (276)
Q Consensus 18 LAhIpGKMRKKVWIk~GDiVLVEpr 42 (276)
-..||-++|+.+-+..||.|.+...
T Consensus 8 ri~iP~~~r~~l~~~~gd~~~i~~~ 32 (43)
T TIGR01439 8 QIVIPKEIREKLGLKEGDRLEVIRV 32 (43)
T ss_pred eEEecHHHHHHcCcCCCCEEEEEEe
Confidence 3578999999999999999999864
Done!