Query 027059
Match_columns 229
No_of_seqs 117 out of 1156
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 04:23:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027059.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027059hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13816 ribosome-binding fact 100.0 8E-34 1.7E-38 231.7 15.2 121 68-201 3-130 (131)
2 TIGR00082 rbfA ribosome-bindin 100.0 2.5E-33 5.3E-38 223.6 15.0 114 64-192 1-114 (114)
3 PRK13815 ribosome-binding fact 100.0 2.2E-33 4.7E-38 226.7 14.8 111 68-192 3-113 (122)
4 PRK00521 rbfA ribosome-binding 100.0 3.9E-33 8.4E-38 223.3 15.3 117 63-193 1-117 (120)
5 PRK13818 ribosome-binding fact 100.0 1.4E-32 2.9E-37 221.8 15.2 114 68-195 3-117 (121)
6 PRK13817 ribosome-binding fact 100.0 5.7E-32 1.2E-36 217.5 14.6 110 68-192 3-112 (119)
7 COG0858 RbfA Ribosome-binding 100.0 1.4E-31 3.1E-36 215.3 13.8 116 64-193 1-117 (118)
8 PF02033 RBFA: Ribosome-bindin 100.0 1.4E-29 3.1E-34 196.7 10.4 104 69-186 1-104 (104)
9 KOG4700 Uncharacterized homolo 99.6 3.2E-14 6.9E-19 122.7 11.2 116 63-191 25-140 (207)
10 PF10446 DUF2457: Protein of u 74.1 2.9 6.3E-05 41.2 3.1 26 172-197 28-53 (458)
11 PF10934 DUF2634: Protein of u 58.8 26 0.00056 27.9 5.2 45 69-132 62-106 (112)
12 PTZ00248 eukaryotic translatio 57.2 45 0.00097 31.6 7.3 52 137-194 237-291 (319)
13 cd03030 GRX_SH3BGR Glutaredoxi 51.9 63 0.0014 24.8 6.2 59 125-184 2-79 (92)
14 PF10446 DUF2457: Protein of u 51.2 19 0.00041 35.7 3.9 21 175-195 27-47 (458)
15 COG5129 MAK16 Nuclear protein 32.7 41 0.00089 31.0 2.8 25 166-190 212-236 (303)
16 PF00085 Thioredoxin: Thioredo 32.3 84 0.0018 22.3 4.0 24 154-177 61-84 (103)
17 PF04931 DNA_pol_phi: DNA poly 31.6 25 0.00055 36.4 1.5 42 139-190 592-633 (784)
18 PF01842 ACT: ACT domain; Int 31.5 1.5E+02 0.0033 19.4 5.2 40 110-149 25-65 (66)
19 PF14088 DUF4268: Domain of un 27.1 1.7E+02 0.0036 23.5 5.3 45 123-167 50-95 (140)
20 PHA00415 25 baseplate wedge su 27.0 1.8E+02 0.004 23.8 5.5 44 72-135 69-117 (131)
21 PTZ00254 40S ribosomal protein 26.4 1.9E+02 0.0042 26.5 6.1 62 111-174 143-207 (249)
22 KOG2321 WD40 repeat protein [G 25.4 64 0.0014 33.4 3.0 19 169-187 493-511 (703)
23 COG1438 ArgR Arginine represso 23.8 44 0.00096 28.4 1.4 100 64-192 2-117 (150)
24 PF06213 CobT: Cobalamin biosy 23.5 52 0.0011 29.9 1.9 45 141-190 163-207 (282)
25 PF09840 DUF2067: Uncharacteri 22.5 1.7E+02 0.0036 25.7 4.7 33 125-157 34-66 (190)
26 PF03517 Voldacs: Regulator of 22.1 1.1E+02 0.0023 24.9 3.3 36 163-200 75-110 (135)
27 cd02974 AhpF_NTD_N Alkyl hydro 22.0 1.6E+02 0.0034 22.7 4.0 40 151-194 9-48 (94)
28 PF13103 TonB_2: TonB C termin 21.8 2.7E+02 0.0059 19.8 5.1 41 110-150 26-67 (85)
29 PRK10824 glutaredoxin-4; Provi 21.7 1.1E+02 0.0023 24.7 3.1 33 152-185 58-90 (115)
30 PF04965 GPW_gp25: Gene 25-lik 21.6 1.9E+02 0.0042 21.4 4.4 43 70-132 42-86 (99)
31 cd04886 ACT_ThrD-II-like C-ter 20.8 2.6E+02 0.0056 18.3 4.8 37 111-147 24-66 (73)
32 PF05764 YL1: YL1 nuclear prot 20.1 1.8E+02 0.0038 26.1 4.5 18 177-194 9-26 (240)
No 1
>PRK13816 ribosome-binding factor A; Provisional
Probab=100.00 E-value=8e-34 Score=231.67 Aligned_cols=121 Identities=31% Similarity=0.544 Sum_probs=108.4
Q ss_pred HHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCc-------hhHHH
Q 027059 68 RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDD-------RGKEV 140 (229)
Q Consensus 68 ~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~-------~~~~~ 140 (229)
+|+.||+++|+++||++|+++. .||++.++||||+|+||+||++||||||++|+. .+++.
T Consensus 3 ~R~~Rv~~~Irreis~il~~ei-------------~dprl~~~vtVT~V~vS~DL~~AkVyvs~lg~~~~~~~~~~~~~~ 69 (131)
T PRK13816 3 QRLKRMADSVQRELSELIRQEL-------------KDPRLGGLVTISSVKVSPDLGYADVYVTVMGRELSDDQNEVAHRE 69 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc-------------cCcccCCceEEeEEEECCCCCeEEEEEEecCCccccccchhHHHH
Confidence 5999999999999999997532 377776789999999999999999999999863 34567
Q ss_pred HHHHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHhHhhhhccCc
Q 027059 141 AIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEKEAAKSKNK 201 (229)
Q Consensus 141 vl~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e~~~~~~~~~ 201 (229)
++++|++++||||+.||++|+||++|+|+|++|+|++++.+|++||+++.+++++++++++
T Consensus 70 ~l~~L~~a~g~iR~~L~krl~lR~~PeL~F~~D~s~e~~~~I~~Ll~~i~~~~~~~~~~~~ 130 (131)
T PRK13816 70 TLDVLNKASGFLRTELSRRIKTRITPRLRFHYDKTNAYGNYMFGLIEKAVQDLPKRESDDE 130 (131)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCeECCEEEEEECCChhHHHHHHHHHHHHHhhhhccccccc
Confidence 8999999999999999999999999999999999999999999999999988776666653
No 2
>TIGR00082 rbfA ribosome-binding factor A. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'terminal helix region of 16S rRNA. Mutants lacking rbfA have a cold-sensitive phenotype.
Probab=100.00 E-value=2.5e-33 Score=223.62 Aligned_cols=114 Identities=35% Similarity=0.643 Sum_probs=104.4
Q ss_pred CCChHHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHHH
Q 027059 64 MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIA 143 (229)
Q Consensus 64 M~~~~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~ 143 (229)
|+ ++|+.||+++|+++||++|+++. .||++ ++||||+|+||+||++||||||++|++..++.+++
T Consensus 1 m~-~~R~~Rv~~~i~~eis~il~~~i-------------~dp~~-~~vtVt~V~lS~Dl~~AkVyvs~~~~~~~~~~~l~ 65 (114)
T TIGR00082 1 MA-SYRKERVESDIIREINRILIREI-------------KDPRV-GMLTVTKVEVSKDLQHAKVFVDCYGDEEAIDRVVK 65 (114)
T ss_pred Cc-cHHHHHHHHHHHHHHHHHHHHhc-------------cCCCC-CeEEEeEEEECCCCCEEEEEEEECCChhhHHHHHH
Confidence 54 57999999999999999998642 37777 47999999999999999999999998777788999
Q ss_pred HHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHh
Q 027059 144 GLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAE 192 (229)
Q Consensus 144 aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e 192 (229)
+|++++|+||+.||++|+||++|+|+|++|+++|++.+|++||+++.++
T Consensus 66 ~L~~~~g~iR~~l~k~l~lR~~P~L~F~~D~s~e~~~~i~~ll~~i~~~ 114 (114)
T TIGR00082 66 ALNKAKGFIRSLLGQAMRLRKTPELHFVKDNSLDKGMRIENLINSLKKE 114 (114)
T ss_pred HHHHHHHHHHHHHHhhCCceECCEEEEEecCcHHHHHHHHHHHHHhhhC
Confidence 9999999999999999999999999999999999999999999998753
No 3
>PRK13815 ribosome-binding factor A; Provisional
Probab=100.00 E-value=2.2e-33 Score=226.69 Aligned_cols=111 Identities=35% Similarity=0.610 Sum_probs=102.8
Q ss_pred HHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHHHHHHH
Q 027059 68 RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKS 147 (229)
Q Consensus 68 ~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~aL~~ 147 (229)
+|++||+++|+++||++|+++. +||++ ++||||+|+||+||++||||||++|++..++.++++|++
T Consensus 3 ~R~~Rv~~~Ir~eis~il~~~i-------------~dprl-~~vtVt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~~L~~ 68 (122)
T PRK13815 3 KRSEKVAEAIHELISGLLVKGL-------------KDPRI-GFVTITGVKVTDDLHLATIYFTVIGDDEAKKSTEAGLNS 68 (122)
T ss_pred hHHHHHHHHHHHHHHHHHHHhC-------------cCCCC-CceEEeEEEECCCCCEEEEEEEECCCchhHHHHHHHHHH
Confidence 5999999999999999998542 37777 479999999999999999999999877666789999999
Q ss_pred hhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHh
Q 027059 148 KAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAE 192 (229)
Q Consensus 148 aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e 192 (229)
++|+||+.||++|+||++|+|+|++|+++|++.+|++||++++++
T Consensus 69 a~g~iR~~l~~~l~lR~~PeL~F~~D~s~e~~~~I~~lL~~i~~~ 113 (122)
T PRK13815 69 ARGFIRKELGKVLRMRYAPELIFKYDESQEYGNRIDSLLKEIGTE 113 (122)
T ss_pred HHHHHHHHHHHhCCCeECCEEEEEECCChHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999865
No 4
>PRK00521 rbfA ribosome-binding factor A; Validated
Probab=100.00 E-value=3.9e-33 Score=223.34 Aligned_cols=117 Identities=48% Similarity=0.749 Sum_probs=108.1
Q ss_pred cCCChHHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHH
Q 027059 63 CMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAI 142 (229)
Q Consensus 63 ~M~~~~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl 142 (229)
||+.++|++||+++|+++|+++|+++. .||+++ .||||+|++|+||++|+||||++|++.+.+.++
T Consensus 1 ~~~~~~R~~Rv~~~i~~~is~il~~~i-------------~d~~~~-~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~ 66 (120)
T PRK00521 1 MMAESQRALRVAEQIQRELAEILQREI-------------KDPRLG-MVTVTDVEVSPDLAHAKVYVTVLGDEEDKEEAL 66 (120)
T ss_pred CCCccHHHHHHHHHHHHHHHHHHHHHc-------------cCCCCC-eeEEEEEEECCCCCEEEEEEEECCCchhHHHHH
Confidence 688899999999999999999998532 367765 799999999999999999999999777778899
Q ss_pred HHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHhH
Q 027059 143 AGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEK 193 (229)
Q Consensus 143 ~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e~ 193 (229)
++|++++|+||+.||++|+||++|+|+|++|++++++.+|++||+++++++
T Consensus 67 ~~L~~~~~~iR~~la~~l~lr~~P~L~F~~D~s~e~~~~i~~lL~~i~~~~ 117 (120)
T PRK00521 67 AALKKAAGFLRSELGKRLRLRYVPELRFVYDESLEYGNRIDELLRKAKKED 117 (120)
T ss_pred HHHHHhHHHHHHHHHhhCCCccCCEEEEEECCCHHHHHHHHHHHHHHHhhh
Confidence 999999999999999999999999999999999999999999999998764
No 5
>PRK13818 ribosome-binding factor A; Provisional
Probab=100.00 E-value=1.4e-32 Score=221.78 Aligned_cols=114 Identities=29% Similarity=0.452 Sum_probs=102.3
Q ss_pred HHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCch-hHHHHHHHHH
Q 027059 68 RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDR-GKEVAIAGLK 146 (229)
Q Consensus 68 ~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~-~~~~vl~aL~ 146 (229)
+|++||+++|+++||++|+++. +||+++ +||||+|+||+||++||||||++|+++ .++.++++|+
T Consensus 3 ~R~~Rv~~~i~reis~ii~~ei-------------~Dprl~-~vtVt~V~lS~Dl~~AkVyvs~~~~~~~~~~~~~~~L~ 68 (121)
T PRK13818 3 HRIGRVEGEILRELTKILRKNI-------------RDPRLS-DVTITAVECTNDLSYATVYYSLLTEDEAKEKEVQEGLE 68 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHhC-------------cCCCcC-ceEEeEEEECCCCCEEEEEEEeCCCchhHHHHHHHHHH
Confidence 6999999999999999998532 478874 799999999999999999999998543 3467889999
Q ss_pred HhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHhHhh
Q 027059 147 SKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEKEA 195 (229)
Q Consensus 147 ~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e~~~ 195 (229)
+++||||+.||++|+||++|+|+|++|+|++++.+|++||+++.+++.+
T Consensus 69 ~a~g~iR~~la~~l~lR~~P~L~F~~D~s~e~~~~I~~Ll~~i~~~~~~ 117 (121)
T PRK13818 69 KAKGMMRHLLGQTLTVYKVPELIFKRDNSVAYGSKIDRLIAEVKKQDQE 117 (121)
T ss_pred HhHHHHHHHHHhhCCCeECCEEEEEeCCChHHHHHHHHHHHHHHhhhhh
Confidence 9999999999999999999999999999999999999999999865433
No 6
>PRK13817 ribosome-binding factor A; Provisional
Probab=99.98 E-value=5.7e-32 Score=217.48 Aligned_cols=110 Identities=28% Similarity=0.491 Sum_probs=100.4
Q ss_pred HHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHHHHHHH
Q 027059 68 RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKS 147 (229)
Q Consensus 68 ~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~aL~~ 147 (229)
+|++||+++|+++||++|+++. .||+++ +||||+|+||+||++||||||++|+. +.+.++++|++
T Consensus 3 ~R~~Rv~~~I~reis~il~~ei-------------~dp~l~-~vtVt~V~vS~Dl~~AkVyvs~~~~~-~~~~~~~~L~~ 67 (119)
T PRK13817 3 QRQQRVADLIHQQLAELLKKEV-------------RDSRLS-KISLTAVSISPDLKQAKVFYSLLENQ-NEKEVQKALNK 67 (119)
T ss_pred hHHHHHHHHHHHHHHHHHHHhc-------------cCCCCC-ceEEeEEEECCCCCEEEEEEEECCCc-cHHHHHHHHHH
Confidence 5999999999999999997532 377774 79999999999999999999999865 45668999999
Q ss_pred hhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHh
Q 027059 148 KAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAE 192 (229)
Q Consensus 148 aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e 192 (229)
++|+||+.||++|+||++|+|+|++|+++|++.+|++||+++.++
T Consensus 68 a~g~iR~~l~~~l~lR~~PeL~F~~D~s~e~~~~I~~Ll~~l~~~ 112 (119)
T PRK13817 68 ATGYLRHLLAQATVLRYVPKLEFVYDESIERAHRISLLIERALKK 112 (119)
T ss_pred hHHHHHHHHHHhCCCeECCEEEEEEcCchHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999754
No 7
>COG0858 RbfA Ribosome-binding factor A [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.4e-31 Score=215.34 Aligned_cols=116 Identities=42% Similarity=0.714 Sum_probs=105.2
Q ss_pred CCChHHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecC-CchhHHHHH
Q 027059 64 MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFG-DDRGKEVAI 142 (229)
Q Consensus 64 M~~~~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g-~~~~~~~vl 142 (229)
|+...|.+|++++|+++|+++|+++ + +||+++. ++||+|+||+||++|+||||++| .....+.++
T Consensus 1 M~~~~R~~rv~e~i~~~l~~il~~e--i-----------kDprl~~-~~Vt~V~vS~Dl~~A~Vyvt~l~~~~~~~~~~~ 66 (118)
T COG0858 1 MAKSTRAKRVAEQIQKELAEILQRE--I-----------KDPRLGL-VTVTDVEVSKDLSHAKVYVTVLGDEESSKAEIL 66 (118)
T ss_pred CCccHHHHHHHHHHHHHHHHHHHHH--c-----------cCCCcCc-eEEEEEEEcCCCceEEEEEEecCCchhhHHHHH
Confidence 6777799999999999999999863 2 3888855 66999999999999999999999 444678889
Q ss_pred HHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHhH
Q 027059 143 AGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEK 193 (229)
Q Consensus 143 ~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e~ 193 (229)
++|++|+|+||+.||++++||++|+|+|++|+|++++.+|++||+++++.+
T Consensus 67 ~~L~~A~g~ir~~l~~~~~lr~~PeL~F~~D~s~~~~~ki~~Ll~~l~~~~ 117 (118)
T COG0858 67 AALNKAKGFIRSELGKRLRLRKTPELHFVYDDSIENGNKIDALLNDLKKAD 117 (118)
T ss_pred HHHHHhHHHHHHHHHHhCCeEeCCeEEEEeCcccchHHHHHHHHHHhhhcC
Confidence 999999999999999999999999999999999999999999999998654
No 8
>PF02033 RBFA: Ribosome-binding factor A; InterPro: IPR000238 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 [, ]. Ribosome-binding factor A [] (gene rbfA) is a bacterial protein that associates with free 30S ribosomal subunits. It does not associate with 30S subunits that are part of 70S ribosomes or polysomes. It is essential for efficient processing of 16S rRNA. Ribosome-binding factor A is a protein of from 13 to 15 Kd which is found in most bacteria. A putative chloroplastic form seems to exist in plants.; GO: 0006364 rRNA processing; PDB: 2R1C_A 2DYJ_B 2KZF_A 2E7G_A 1JOS_A 1KKG_A 1PA4_A.
Probab=99.96 E-value=1.4e-29 Score=196.74 Aligned_cols=104 Identities=40% Similarity=0.680 Sum_probs=90.4
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHHHHHHHh
Q 027059 69 RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSK 148 (229)
Q Consensus 69 R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~aL~~a 148 (229)
|++|++++|+++|+++|.++. .||++ ++||||+|++|+|+++|+|||+++|++.+.+.++++|+++
T Consensus 1 R~~Rv~~~i~~~i~~il~~~~-------------~d~~l-~~vtIt~V~ls~Dl~~a~Vy~~~~~~~~~~~~~~~~L~~~ 66 (104)
T PF02033_consen 1 RQQRVESLIQREISEILQREI-------------KDPRL-KLVTITRVELSPDLSHAKVYVSILGDEEEQEEVLEALNKA 66 (104)
T ss_dssp THHHHHHHHHHHHHHHHCTCT-------------SSCGH-HCEEEEEEEECTTSSEEEEEEEESSSHHHHHHHHHHHHHT
T ss_pred ChHHHHHHHHHHHHHHHHhhc-------------cCcCc-ceEEEEEEEECCCCCEEEEEEEEecCchhHHHHHHHHHHH
Confidence 789999999999999998652 26666 5799999999999999999999998888889999999999
Q ss_pred hHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHH
Q 027059 149 AKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAIL 186 (229)
Q Consensus 149 ag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LL 186 (229)
+|+||+.||++|+||++|+|+|++|++++++.+|++||
T Consensus 67 ~~~iR~~l~~~l~lr~~P~L~F~~D~~~e~~~~i~~ll 104 (104)
T PF02033_consen 67 AGFIRHELAKRLNLRRVPELRFVYDDSIEKAARIEKLL 104 (104)
T ss_dssp HHHHHHHHHHHTTSSSG-EEEEEESTTTSSS------S
T ss_pred HHHHHHHHHhhcCCCcCCEEEEEECCCHHHHHHHHHhC
Confidence 99999999999999999999999999999999999986
No 9
>KOG4700 consensus Uncharacterized homolog of ribosome-binding factor A [General function prediction only]
Probab=99.55 E-value=3.2e-14 Score=122.74 Aligned_cols=116 Identities=21% Similarity=0.271 Sum_probs=101.0
Q ss_pred cCCChHHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHH
Q 027059 63 CMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAI 142 (229)
Q Consensus 63 ~M~~~~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl 142 (229)
|--+.+|...++.++.+.|+++|+.+..- ..+ .+-.|.|++|++++|++.+.|||.+-++.+ ..++.
T Consensus 25 r~~d~~r~~~Ln~Ll~~~itdvlaTgava-~~l-----------~~l~vqiS~V~vt~dFS~~~vYWm~~~~ge-N~e~e 91 (207)
T KOG4700|consen 25 RRLDDKKVVQLNRLLEERITDVLATGAVA-EML-----------GRLQVQISRVRVTRDFSQVSVYWMCRGDGE-NSEIE 91 (207)
T ss_pred hccchHHHHHHHHHHHHHHHHHHhchHHH-HHH-----------hhcceeEEEEEeccchhhheeEEEecCCcc-HHHHH
Confidence 44567899999999999999999974321 111 134699999999999999999999987765 56788
Q ss_pred HHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHH
Q 027059 143 AGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKA 191 (229)
Q Consensus 143 ~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~ 191 (229)
+.|++.++.||+.|.+.++|+.||+|.|+-|++.--..+|++||++++-
T Consensus 92 ~~L~rs~~~~rh~l~~~~~~g~vP~IkFV~DK~~~~l~e~d~ll~~aD~ 140 (207)
T KOG4700|consen 92 DFLERSKHQIRHRLEESIGIGTVPEIKFVGDKALLMLQEMDKLLREADY 140 (207)
T ss_pred HHHHHHHHHHHHHHHHHhccccCCceEEecchHHHHHHHHHHHHHHhcc
Confidence 9999999999999999999999999999999999999999999999963
No 10
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=74.10 E-value=2.9 Score=41.18 Aligned_cols=26 Identities=8% Similarity=0.249 Sum_probs=17.8
Q ss_pred EcCchhHHHHHHHHHHHHHHhHhhhh
Q 027059 172 EDESFERGSRVIAILDRIKAEKEAAK 197 (229)
Q Consensus 172 ~D~S~E~a~rId~LLd~i~~e~~~~~ 197 (229)
+++.+.+...|-+|=.++++|-...+
T Consensus 28 i~DtlkKE~~IRkLgeEaEEEA~~EE 53 (458)
T PF10446_consen 28 INDTLKKENAIRKLGEEAEEEAEEEE 53 (458)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHhhcc
Confidence 57778888888777777665544444
No 11
>PF10934 DUF2634: Protein of unknown function (DUF2634); InterPro: IPR020288 This entry is represented by the Bacteriophage EJ-1, Orf60. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Bacteriophage EJ-1, Orf60 function has not been characterised. It has been shown to be simialr to XkdS (P54331 from SWISSPROT), which is encoded on a phage-like element (prophage) of PSBX found in Bacillus subtilis.
Probab=58.76 E-value=26 Score=27.87 Aligned_cols=45 Identities=22% Similarity=0.327 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEec
Q 027059 69 RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVF 132 (229)
Q Consensus 69 R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~ 132 (229)
-..-+.++|+|.|.++|..||++ ..|....++.+....+|.+++.
T Consensus 62 ~~~~~~sEi~r~I~EaL~~d~rI-------------------~~V~~f~f~~~~~~l~v~f~V~ 106 (112)
T PF10934_consen 62 PREYVESEIEREIEEALLQDPRI-------------------TSVENFSFEWEGDSLYVSFTVT 106 (112)
T ss_pred ChHHHHHHHHHHHHHHHhcCCCc-------------------ceEEEEEEEEECCEEEEEEEEE
Confidence 45668899999999999877654 3466666666667777777664
No 12
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=57.16 E-value=45 Score=31.60 Aligned_cols=52 Identities=15% Similarity=0.303 Sum_probs=32.6
Q ss_pred hHHHHHHHHHHhhHHHHHHHHhcc---CCcccceEEEEEcCchhHHHHHHHHHHHHHHhHh
Q 027059 137 GKEVAIAGLKSKAKYVRSQLGRRM---KLRLTPEIRFIEDESFERGSRVIAILDRIKAEKE 194 (229)
Q Consensus 137 ~~~~vl~aL~~aag~IR~~LakrL---~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e~~ 194 (229)
+++...+.|+++...|+..+.+.= .+++-|++- -+ . +. .. .++|.++..+.+
T Consensus 237 d~k~g~~~l~~a~~~i~~~i~~~gG~~~~~~~p~~v--~~-~-~~-~~-~~~~~~~~~~~~ 291 (319)
T PTZ00248 237 DKDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEVV--GG-D-EE-DL-EELLEKAEEEEE 291 (319)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHcCCeEEEEECCEEe--cc-h-hH-HH-HHHHHHHhhhhc
Confidence 345677888888888888886654 377778752 11 1 11 22 677777765444
No 13
>cd03030 GRX_SH3BGR Glutaredoxin (GRX) family, SH3BGR (SH3 domain binding glutamic acid-rich protein) subfamily; a recently-identified subfamily composed of SH3BGR and similar proteins possessing significant sequence similarity to GRX, but without a redox active CXXC motif. The SH3BGR gene was cloned in an effort to identify genes mapping to chromosome 21, which could be involved in the pathogenesis of congenital heart disease affecting Down syndrome newborns. Several human SH3BGR-like (SH3BGRL) genes have been identified since, mapping to different locations in the chromosome. Of these, SH3BGRL3 was identified as a tumor necrosis factor (TNF) alpha inhibitory protein and was also named TIP-B1. Upregulation of expression of SH3BGRL3 is associated with differentiation. It has been suggested that it functions as a regulator of differentiation-related signal transduction pathways.
Probab=51.94 E-value=63 Score=24.81 Aligned_cols=59 Identities=20% Similarity=0.264 Sum_probs=32.8
Q ss_pred EEEEEEecCCch----hHHHHHHHHHHh-----------hHHHHHHHHhccCC----cccceEEEEEcCchhHHHHHHH
Q 027059 125 VKVYVSVFGDDR----GKEVAIAGLKSK-----------AKYVRSQLGRRMKL----RLTPEIRFIEDESFERGSRVIA 184 (229)
Q Consensus 125 AKVYvSi~g~~~----~~~~vl~aL~~a-----------ag~IR~~LakrL~l----R~vPeL~Fv~D~S~E~a~rId~ 184 (229)
.+||+|.+.+.. +.+.+...|++. ....|.++-++.+- +.+|.| |+-|.-+--...+.+
T Consensus 2 i~vY~ts~~g~~~~k~~~~~v~~lL~~k~I~f~eiDI~~d~~~r~em~~~~~~~~g~~tvPQI-Fi~~~~iGg~ddl~~ 79 (92)
T cd03030 2 IKVYIASSSGSTEIKKRQQEVLGFLEAKKIEFEEVDISMNEENRQWMRENVPNENGKPLPPQI-FNGDEYCGDYEAFFE 79 (92)
T ss_pred EEEEEecccccHHHHHHHHHHHHHHHHCCCceEEEecCCCHHHHHHHHHhcCCCCCCCCCCEE-EECCEEeeCHHHHHH
Confidence 589999886642 234455555543 34455566555543 566666 765555444434333
No 14
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=51.18 E-value=19 Score=35.69 Aligned_cols=21 Identities=10% Similarity=0.173 Sum_probs=10.0
Q ss_pred chhHHHHHHHHHHHHHHhHhh
Q 027059 175 SFERGSRVIAILDRIKAEKEA 195 (229)
Q Consensus 175 S~E~a~rId~LLd~i~~e~~~ 195 (229)
++.-..+.+..|.+|-+|-++
T Consensus 27 Ti~DtlkKE~~IRkLgeEaEE 47 (458)
T PF10446_consen 27 TINDTLKKENAIRKLGEEAEE 47 (458)
T ss_pred cHHHHHHHHHHHhhhhHHHHH
Confidence 344444555555555544433
No 15
>COG5129 MAK16 Nuclear protein with HMG-like acidic region [General function prediction only]
Probab=32.71 E-value=41 Score=31.01 Aligned_cols=25 Identities=12% Similarity=0.195 Sum_probs=17.3
Q ss_pred ceEEEEEcCchhHHHHHHHHHHHHH
Q 027059 166 PEIRFIEDESFERGSRVIAILDRIK 190 (229)
Q Consensus 166 PeL~Fv~D~S~E~a~rId~LLd~i~ 190 (229)
-+|.|+-|++-..-..+..|.+=+-
T Consensus 212 ~elE~vtdD~e~e~~~~~dlekWl~ 236 (303)
T COG5129 212 TELEAVTDDSEKEKTKKKDLEKWLG 236 (303)
T ss_pred ceeEeeccccccchhhHHHHHHHhc
Confidence 3577888887777777776666554
No 16
>PF00085 Thioredoxin: Thioredoxin; InterPro: IPR013766 Thioredoxins [, , , ] are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of two cysteine thiol groups to a disulphide, accompanied by the transfer of two electrons and two protons. The net result is the covalent interconversion of a disulphide and a dithiol. In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses the reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide; reduced thioredoxin then directly reduces the disulphide in the substrate protein []. Thioredoxin is present in prokaryotes and eukaryotes and the sequence around the redox-active disulphide bond is well conserved. All thioredoxins contain a cis-proline located in a loop preceding beta-strand 4, which makes contact with the active site cysteines, and is important for stability and function []. Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase []. Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins. A number of eukaryotic proteins contain domains evolutionary related to thioredoxin, most of them are protein disulphide isomerases (PDI). PDI (5.3.4.1 from EC) [, , ] is an endoplasmic reticulum multi-functional enzyme that catalyses the formation and rearrangement of disulphide bonds during protein folding []. All PDI contains two or three (ERp72) copies of the thioredoxin domain, each of which contributes to disulphide isomerase activity, but which are functionally non-equivalent []. Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity []. The various forms of PDI which are currently known are: PDI major isozyme; a multifunctional protein that also function as the beta subunit of prolyl 4-hydroxylase (1.14.11.2 from EC), as a component of oligosaccharyl transferase (2.4.1.119 from EC), as thyroxine deiodinase (3.8.1.4 from EC), as glutathione-insulin transhydrogenase (1.8.4.2 from EC) and as a thyroid hormone-binding protein ERp60 (ER-60; 58 Kd microsomal protein). ERp60 was originally thought to be a phosphoinositide-specific phospholipase C isozyme and later to be a protease. ERp72. ERp5. Bacterial proteins that act as thiol:disulphide interchange proteins that allows disulphide bond formation in some periplasmic proteins also contain a thioredoxin domain. These proteins include: Escherichia coli DsbA (or PrfA) and its orthologs in Vibrio cholerae (TtcpG) and Haemophilus influenzae (Por). E. coli DsbC (or XpRA) and its orthologues in Erwinia chrysanthemi and H. influenzae. E. coli DsbD (or DipZ) and its H. influenzae orthologue. E. coli DsbE (or CcmG) and orthologues in H. influenzae. Rhodobacter capsulatus (Rhodopseudomonas capsulata) (HelX), Rhiziobiacae (CycY and TlpA). This entry represents the thioredoxin domain.; GO: 0045454 cell redox homeostasis; PDB: 3ED3_B 1EP7_A 1EP8_B 1TOF_A 2OE3_B 2OE1_B 2OE0_B 1V98_A 3H79_A 3CXG_A ....
Probab=32.28 E-value=84 Score=22.30 Aligned_cols=24 Identities=17% Similarity=0.339 Sum_probs=20.1
Q ss_pred HHHHhccCCcccceEEEEEcCchh
Q 027059 154 SQLGRRMKLRLTPEIRFIEDESFE 177 (229)
Q Consensus 154 ~~LakrL~lR~vPeL~Fv~D~S~E 177 (229)
..++++++++.+|.+.|+.+....
T Consensus 61 ~~l~~~~~v~~~Pt~~~~~~g~~~ 84 (103)
T PF00085_consen 61 KELCKKYGVKSVPTIIFFKNGKEV 84 (103)
T ss_dssp HHHHHHTTCSSSSEEEEEETTEEE
T ss_pred chhhhccCCCCCCEEEEEECCcEE
Confidence 468899999999999998876544
No 17
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=31.58 E-value=25 Score=36.41 Aligned_cols=42 Identities=17% Similarity=0.293 Sum_probs=26.5
Q ss_pred HHHHHHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHH
Q 027059 139 EVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIK 190 (229)
Q Consensus 139 ~~vl~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~ 190 (229)
+.++..|-+.+.++|+...+-.+. ++|.| ...-++.||+.+.
T Consensus 592 eiLLslls~~s~llR~~~~~vf~~-~~~~~---------t~~~l~~ll~vl~ 633 (784)
T PF04931_consen 592 EILLSLLSQPSALLRKVSEQVFEA-FCPHL---------TESGLQLLLDVLD 633 (784)
T ss_pred HHHHHHHhCcchHHHHHHHHHHHH-HHhhc---------CHHHHHHHHHHhc
Confidence 345566778888888877766654 46653 2345566666665
No 18
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....
Probab=31.47 E-value=1.5e+02 Score=19.40 Aligned_cols=40 Identities=20% Similarity=0.257 Sum_probs=24.2
Q ss_pred ceEEEEEEEcCCcc-eEEEEEEecCCchhHHHHHHHHHHhh
Q 027059 110 LTTISDVEVSADLQ-VVKVYVSVFGDDRGKEVAIAGLKSKA 149 (229)
Q Consensus 110 lVTVT~VevS~DLs-~AKVYvSi~g~~~~~~~vl~aL~~aa 149 (229)
.+.|..+....+-. .-.+++....+..+.+.+++.|++..
T Consensus 25 ~inI~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 65 (66)
T PF01842_consen 25 GINIDSISQSSDKDGVGIVFIVIVVDEEDLEKLLEELEALP 65 (66)
T ss_dssp TEEEEEEEEEEESSTTEEEEEEEEEEGHGHHHHHHHHHHHT
T ss_pred CCCHHHeEEEecCCCceEEEEEEECCCCCHHHHHHHHHccc
Confidence 36777777766655 33333444445555677888888754
No 19
>PF14088 DUF4268: Domain of unknown function (DUF4268)
Probab=27.09 E-value=1.7e+02 Score=23.50 Aligned_cols=45 Identities=11% Similarity=0.189 Sum_probs=33.8
Q ss_pred ceEEEEEEecCC-chhHHHHHHHHHHhhHHHHHHHHhccCCcccce
Q 027059 123 QVVKVYVSVFGD-DRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPE 167 (229)
Q Consensus 123 s~AKVYvSi~g~-~~~~~~vl~aL~~aag~IR~~LakrL~lR~vPe 167 (229)
+.|.|-+.+-.+ ....+.+.+.|.+.+..|-..+|..|.+...|+
T Consensus 50 ~~~~V~l~I~~~d~~~n~~~fe~L~~~k~~IE~~~g~~l~W~~l~~ 95 (140)
T PF14088_consen 50 KRARVELYIDRPDKEENKEIFEQLKSQKEEIEEEFGEELEWERLDD 95 (140)
T ss_pred CEEEEEEEEcCCCHHHHHHHHHHHHHHHHHHHHHhCCCcEeeeCCC
Confidence 355555555433 334577899999999999999999998777665
No 20
>PHA00415 25 baseplate wedge subunit
Probab=26.98 E-value=1.8e+02 Score=23.85 Aligned_cols=44 Identities=20% Similarity=0.350 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHhc-ChhhhhhhchhhhcccccCCCCceEEEEEEEcCCc----ceEEEEEEecCCc
Q 027059 72 MVAKQIQRELSDMLLT-DKVLQFAVLPEAALGADRYLSSLTTISDVEVSADL----QVVKVYVSVFGDD 135 (229)
Q Consensus 72 RVas~IqreLS~iL~~-Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DL----s~AKVYvSi~g~~ 135 (229)
.....|+..|..+|.+ +|| |++.+|.+.+|- -...|.|++-++.
T Consensus 69 ~~~~~i~~~I~~AI~~~EPR--------------------I~~~~V~v~~~~~~~~l~i~l~y~i~~tn 117 (131)
T PHA00415 69 LTADTIERNIESAIRNYEPR--------------------VYNLNVEVIPVYDDNSIIVTIYFSIIDNP 117 (131)
T ss_pred HHHHHHHHHHHHHHHHhCcC--------------------eeeEEEEEEecCCCCEEEEEEEEEEcCCC
Confidence 4456778888888875 554 567778777773 3456677776655
No 21
>PTZ00254 40S ribosomal protein SA; Provisional
Probab=26.35 E-value=1.9e+02 Score=26.49 Aligned_cols=62 Identities=18% Similarity=0.248 Sum_probs=42.0
Q ss_pred eEEEEEEEcCCcceEEEEEEecCCchh---HHHHHHHHHHhhHHHHHHHHhccCCcccceEEEEEcC
Q 027059 111 TTISDVEVSADLQVVKVYVSVFGDDRG---KEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDE 174 (229)
Q Consensus 111 VTVT~VevS~DLs~AKVYvSi~g~~~~---~~~vl~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~ 174 (229)
-+|.=|+...|++...+-+= +.++. ...++..|.++--.+|-.+.+...|-..|.|-|+-|.
T Consensus 143 PvIal~DTds~p~~VDy~IP--~Ndds~~SI~li~~lLar~Vl~~rG~~~r~~~~~v~~d~f~~r~~ 207 (249)
T PTZ00254 143 PVIALCDTDSPLEYVDIAIP--CNNRGKESIALMYWLLAREVLRLRGTLPRDEEWDVMVDLFFWRDP 207 (249)
T ss_pred CEEEEecCCCCcccCceeeC--CCCchHHHHHHHHHHHHHHHHHhhCccccCCCCCcCceeccccCh
Confidence 35666677777776554442 22222 3445567777777788788888889999999888776
No 22
>KOG2321 consensus WD40 repeat protein [General function prediction only]
Probab=25.43 E-value=64 Score=33.36 Aligned_cols=19 Identities=21% Similarity=0.167 Sum_probs=13.3
Q ss_pred EEEEcCchhHHHHHHHHHH
Q 027059 169 RFIEDESFERGSRVIAILD 187 (229)
Q Consensus 169 ~Fv~D~S~E~a~rId~LLd 187 (229)
.|-.|+.-+.-..+.-+..
T Consensus 493 dFeVDeds~ey~~l~pv~s 511 (703)
T KOG2321|consen 493 DFEVDEDSEEYRLLAPVAS 511 (703)
T ss_pred ccccCccHHHHhhhchhhh
Confidence 3778887777666666665
No 23
>COG1438 ArgR Arginine repressor [Transcription]
Probab=23.82 E-value=44 Score=28.43 Aligned_cols=100 Identities=22% Similarity=0.389 Sum_probs=54.4
Q ss_pred CCChHHHHHHHHHHH-------HHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcce---EEE------
Q 027059 64 MANPRRVKMVAKQIQ-------RELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQV---VKV------ 127 (229)
Q Consensus 64 M~~~~R~~RVas~Iq-------reLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~---AKV------ 127 (229)
|....|++++.+.|. .||.+.|.. ..+.||.-.||+|++. .||
T Consensus 2 ~kk~~R~~~Ik~iI~~~~i~TQ~Elv~~L~~---------------------~Gi~vTQaTvSRDlkelglvKv~~~~g~ 60 (150)
T COG1438 2 MKKEERLELIKEIITEEKISTQEELVELLQE---------------------EGIEVTQATVSRDLKELGLVKVRNEKGT 60 (150)
T ss_pred CcHHHHHHHHHHHHHhCCCCCHHHHHHHHHH---------------------cCCeEehHHHHHHHHHcCCEEecCCCCc
Confidence 444567777777773 456665542 1366888888888753 222
Q ss_pred EEEecCCchhHHHHHHHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHh
Q 027059 128 YVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAE 192 (229)
Q Consensus 128 YvSi~g~~~~~~~vl~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e 192 (229)
|+-.++.+.... ....+. .++...+ +.+.+.=.+ -++=...-.+.-|.++||.+..+
T Consensus 61 ~~Y~l~~~~~~~-~~~~~~---~~~~~~v---~~vd~~~~~-ivlkT~PG~A~~ia~~lD~~~~~ 117 (150)
T COG1438 61 YVYSLPAELGVP-PTSKLK---RYLKDLV---LSIDRNGNL-IVLKTSPGAAQLIARLLDSLAKD 117 (150)
T ss_pred EEEEeCCccCCC-chhhHH---HHHHHHh---eeeccCCcE-EEEEeCCchHHHHHHHHHhcCch
Confidence 333333322111 122222 2222222 234444443 44555667889999999988755
No 24
>PF06213 CobT: Cobalamin biosynthesis protein CobT; InterPro: IPR006538 These proteins are CobT subunits of the aerobic cobalt chelatase (aerobic cobalamin biosynthesis pathway). Pseudomonas denitrificans CobT has been experimentally characterised [, ]. Aerobic cobalt chelatase consists of three subunits, CobT, CobN (IPR003672 from INTERPRO) and CobS (IPR006537 from INTERPRO). Cobalamin (vitamin B12) can be complexed with metal via the ATP-dependent reactions (aerobic pathway) (e.g., in P. denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in Salmonella typhimurium) [, ]. The corresponding cobalt chelatases are not homologous. However, aerobic cobalt chelatase subunits CobN and CobS are homologous to Mg-chelatase subunits BchH and BchI, respectively []. CobT, too, has been found to be remotely related to the third subunit of Mg-chelatase, BchD (involved in bacteriochlorophyll synthesis, e.g., in Rhodobacter capsulatus) []. Nomenclature note: CobT of the aerobic pathway P. denitrificans is not a homologue of CobT of the anaerobic pathway (Salmonella typhimurium, Escherichia coli). Therefore, annotation of any members of this family as nicotinate-mononucleotide--5,6-dimethylbenzimidazole phosphoribosyltransferases is erroneous.
Probab=23.53 E-value=52 Score=29.88 Aligned_cols=45 Identities=11% Similarity=0.160 Sum_probs=26.5
Q ss_pred HHHHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHH
Q 027059 141 AIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIK 190 (229)
Q Consensus 141 vl~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~ 190 (229)
+...+.-....|-..++++|. .|.-.+++...++..+..||..+.
T Consensus 163 ~~~~~~~~R~~l~~~~g~~L~-----~L~~~~~dq~afa~~~~~ll~~le 207 (282)
T PF06213_consen 163 AEKVVELWRPWLEEKAGKDLD-----GLRDSLDDQAAFARAARDLLEDLE 207 (282)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHhh
Confidence 334444444555555555553 333345677778888888888764
No 25
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=22.46 E-value=1.7e+02 Score=25.66 Aligned_cols=33 Identities=21% Similarity=0.296 Sum_probs=27.9
Q ss_pred EEEEEEecCCchhHHHHHHHHHHhhHHHHHHHH
Q 027059 125 VKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLG 157 (229)
Q Consensus 125 AKVYvSi~g~~~~~~~vl~aL~~aag~IR~~La 157 (229)
-++||.++|.+.+-+.....+.+..+.+|...+
T Consensus 34 n~l~I~i~G~~~eike~~~~Ik~~~~~vr~k~~ 66 (190)
T PF09840_consen 34 NSLKIEIQGYEKEIKEAIRRIKELVRRVRSKYN 66 (190)
T ss_pred CEEEEEEecChHHHHHHHHHHHHHHHHHHHHhc
Confidence 789999999987777778888888888888765
No 26
>PF03517 Voldacs: Regulator of volume decrease after cellular swelling; InterPro: IPR003521 The nucleotide-sensitive chloride conductance regulatory protein (ICln) is found ubiquitously in mammalian (and other) cell types and is postulated to play a critical role in cell volume regulation. Initial studies proposed that ICln was itself a swelling-activated anion channel; however, further studies demonstrated that it is localised primarily to the cell cytoplasm. It has therefore been postulated that activation of cell volume regulation may involve reversible translocation of ICln from the cytoplasm, and its insertion into the plasma membrane. It is not resolved whether the anionic channel involved in cell volume regulation after cell-swelling comprises one or more subunits, and if it does, whether ICln is in fact one of them [].; GO: 0006821 chloride transport, 0006884 cell volume homeostasis; PDB: 1ZYI_A.
Probab=22.08 E-value=1.1e+02 Score=24.94 Aligned_cols=36 Identities=11% Similarity=0.225 Sum_probs=18.4
Q ss_pred cccceEEEEEcCchhHHHHHHHHHHHHHHhHhhhhccC
Q 027059 163 RLTPEIRFIEDESFERGSRVIAILDRIKAEKEAAKSKN 200 (229)
Q Consensus 163 R~vPeL~Fv~D~S~E~a~rId~LLd~i~~e~~~~~~~~ 200 (229)
-.+.+|+|+-.+.-. .-+++|++-+..=-.-..+.+
T Consensus 75 ~~~~El~l~P~~~~~--~~l~~if~Als~C~~LhPD~~ 110 (135)
T PF03517_consen 75 ESSVELRLVPSDPSS--DMLDEIFEALSECQELHPDPD 110 (135)
T ss_dssp -SEEEEEEEES-HHH----HHHHHHHHHHHHH------
T ss_pred ccceEEEEecCcccc--hHHHHHHHHHHHHHHhCCCCc
Confidence 356788888777621 348888888776656555544
No 27
>cd02974 AhpF_NTD_N Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD forming two contiguous TRX-fold subdomain similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The N-terminal TRX-fold subdomain of AhpF NTD is redox inactive, but is proposed to contain an important residue that aids in the catalytic function of the redox-active CXXC motif contained in the C-terminal TRX-
Probab=21.97 E-value=1.6e+02 Score=22.72 Aligned_cols=40 Identities=20% Similarity=0.354 Sum_probs=30.0
Q ss_pred HHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHhHh
Q 027059 151 YVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEKE 194 (229)
Q Consensus 151 ~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e~~ 194 (229)
.+|..++ +|.+-=+|.++.|.+ ++...+.+++.++..-..
T Consensus 9 qL~~~f~---~l~~pV~l~~f~~~~-~~~~e~~~ll~e~a~lSd 48 (94)
T cd02974 9 QLKAYLE---RLENPVELVASLDDS-EKSAELLELLEEIASLSD 48 (94)
T ss_pred HHHHHHH---hCCCCEEEEEEeCCC-cchHHHHHHHHHHHHhCC
Confidence 3444444 366667799999988 999999999999875443
No 28
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=21.76 E-value=2.7e+02 Score=19.81 Aligned_cols=41 Identities=12% Similarity=0.197 Sum_probs=24.3
Q ss_pred ceEEEEEEEcCCcceEEEEEEec-CCchhHHHHHHHHHHhhH
Q 027059 110 LTTISDVEVSADLQVVKVYVSVF-GDDRGKEVAIAGLKSKAK 150 (229)
Q Consensus 110 lVTVT~VevS~DLs~AKVYvSi~-g~~~~~~~vl~aL~~aag 150 (229)
+.....|.+++|.+...+-+.-- |+..-.+.++++|+++..
T Consensus 26 ~~~~V~i~i~~dG~v~~~~i~~sSG~~~~D~av~~ai~~~~p 67 (85)
T PF13103_consen 26 LSVTVRITIDPDGRVISVRIVKSSGNPAFDAAVRRAIRRASP 67 (85)
T ss_dssp --EEEEEEE-TTSBEEEEEEEE--S-HHHHHHHHHHHHHH-B
T ss_pred cEEEEEEEECCCCCEEEEEEecCCCCHHHHHHHHHHHHHcCC
Confidence 46678899999999987776443 333334556777775544
No 29
>PRK10824 glutaredoxin-4; Provisional
Probab=21.75 E-value=1.1e+02 Score=24.67 Aligned_cols=33 Identities=18% Similarity=0.368 Sum_probs=22.7
Q ss_pred HHHHHHhccCCcccceEEEEEcCchhHHHHHHHH
Q 027059 152 VRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAI 185 (229)
Q Consensus 152 IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~L 185 (229)
+|..|.++-+++.+|++ |+-.+-+-=...+.++
T Consensus 58 ~~~~l~~~sg~~TVPQI-FI~G~~IGG~ddl~~l 90 (115)
T PRK10824 58 IRAELPKYANWPTFPQL-WVDGELVGGCDIVIEM 90 (115)
T ss_pred HHHHHHHHhCCCCCCeE-EECCEEEcChHHHHHH
Confidence 67777777799999999 7766555444444443
No 30
>PF04965 GPW_gp25: Gene 25-like lysozyme; InterPro: IPR007048 The family of sequences represented by this entry include proteins from Bacteriophage T4 and related phage, which may be structural components of the outer wedge of the baseplate that has acidic lysozyme activity [, ]. They also include anti-adapter protein IraD, from bacteria, that inhibit RpoS proteolysis by regulating RssB activity [].; PDB: 2IA7_A.
Probab=21.59 E-value=1.9e+02 Score=21.40 Aligned_cols=43 Identities=19% Similarity=0.225 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHhc-ChhhhhhhchhhhcccccCCCCceEEEEEEEcCCc-ceEEEEEEec
Q 027059 70 VKMVAKQIQRELSDMLLT-DKVLQFAVLPEAALGADRYLSSLTTISDVEVSADL-QVVKVYVSVF 132 (229)
Q Consensus 70 ~~RVas~IqreLS~iL~~-Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DL-s~AKVYvSi~ 132 (229)
.......++++|.+.|.+ +|+ +.+..|++.++- ...++++++.
T Consensus 42 ~~~~~~~i~~~I~~aI~~~EPR--------------------l~~~~V~~~~~~~~~~~l~~~I~ 86 (99)
T PF04965_consen 42 SPDTRQAIRREIREAIQRFEPR--------------------LKVVSVEVEEDDDEDGKLTFTIS 86 (99)
T ss_dssp -HHHHHHHHHHHHHHHHHH-TT--------------------EEEEEEEEE-TTGGGTEEEEEEE
T ss_pred CHHHHHHHHHHHHHHHHHhCCc--------------------EEEEEEEEEecCCCCCEEEEEEE
Confidence 455666777777777765 554 456777777755 3555555543
No 31
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.75 E-value=2.6e+02 Score=18.29 Aligned_cols=37 Identities=24% Similarity=0.228 Sum_probs=22.8
Q ss_pred eEEEEEEEcCC-----cceEEEEEEecCCc-hhHHHHHHHHHH
Q 027059 111 TTISDVEVSAD-----LQVVKVYVSVFGDD-RGKEVAIAGLKS 147 (229)
Q Consensus 111 VTVT~VevS~D-----Ls~AKVYvSi~g~~-~~~~~vl~aL~~ 147 (229)
+.|+.+...++ ...+.+++++-... .+.+.+++.|++
T Consensus 24 ~nI~~i~~~~~~~~~~~~~~~~~i~v~~~~~~~l~~l~~~l~~ 66 (73)
T cd04886 24 ANIIEVSHDRAFKTLPLGEVEVELTLETRGAEHIEEIIAALRE 66 (73)
T ss_pred CCEEEEEEEeccCCCCCceEEEEEEEEeCCHHHHHHHHHHHHH
Confidence 56677766654 46677888775433 334566666655
No 32
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=20.07 E-value=1.8e+02 Score=26.06 Aligned_cols=18 Identities=28% Similarity=0.453 Sum_probs=13.2
Q ss_pred hHHHHHHHHHHHHHHhHh
Q 027059 177 ERGSRVIAILDRIKAEKE 194 (229)
Q Consensus 177 E~a~rId~LLd~i~~e~~ 194 (229)
..|.+|.+||..-..+++
T Consensus 9 naGnrm~~LL~~E~e~de 26 (240)
T PF05764_consen 9 NAGNRMKKLLEEELEEDE 26 (240)
T ss_pred chhHHHHHHHHHHHhhhh
Confidence 468999999988754333
Done!