Query 029236
Match_columns 196
No_of_seqs 144 out of 1040
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 09:41:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029236.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029236hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0139 HisI Phosphoribosyl-AM 100.0 2E-57 4.3E-62 355.9 12.8 104 52-155 6-110 (111)
2 PRK00051 hisI phosphoribosyl-A 100.0 2.4E-57 5.2E-62 361.6 13.0 105 52-156 2-106 (125)
3 PRK02759 bifunctional phosphor 100.0 4.1E-55 8.8E-60 371.7 13.2 123 53-180 4-143 (203)
4 PLN02346 histidine biosynthesi 100.0 3.1E-54 6.6E-59 379.1 15.2 136 17-154 7-144 (271)
5 PF01502 PRA-CH: Phosphoribosy 100.0 7E-46 1.5E-50 273.8 9.5 75 79-153 1-75 (75)
6 KOG4311 Histidinol dehydrogena 100.0 5.7E-41 1.2E-45 298.6 7.1 173 1-181 78-273 (359)
7 cd04474 RPA1_DBD_A RPA1_DBD_A: 44.4 89 0.0019 23.4 5.9 57 62-118 34-92 (104)
8 cd00495 Ribosomal_L25_TL5_CTC 39.8 45 0.00099 24.5 3.6 33 61-95 21-53 (91)
9 PF09137 Glucodextran_N: Gluco 34.6 61 0.0013 29.3 4.3 27 112-138 92-118 (269)
10 PRK05943 50S ribosomal protein 34.0 48 0.0011 24.8 3.0 32 61-95 22-54 (94)
11 TIGR02196 GlrX_YruB Glutaredox 31.8 55 0.0012 21.0 2.7 25 63-92 49-73 (74)
12 KOG3953 SOCS box protein SSB-1 29.8 48 0.001 30.0 2.7 61 93-153 108-181 (242)
13 PF14076 DUF4258: Domain of un 27.2 2E+02 0.0042 19.2 6.1 34 83-116 15-52 (73)
14 PF01386 Ribosomal_L25p: Ribos 23.0 1.2E+02 0.0026 22.4 3.4 31 61-93 19-49 (88)
15 PF00905 Transpeptidase: Penic 22.1 87 0.0019 27.0 2.9 17 66-82 2-18 (304)
16 TIGR03577 EF_0830 conserved hy 21.9 75 0.0016 25.7 2.2 20 74-93 89-108 (115)
17 PF03413 PepSY: Peptidase prop 21.1 1.4E+02 0.003 19.3 3.1 19 61-79 44-62 (64)
18 PRK05618 50S ribosomal protein 20.6 1.1E+02 0.0024 25.9 3.1 33 61-95 24-56 (197)
No 1
>COG0139 HisI Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]
Probab=100.00 E-value=2e-57 Score=355.90 Aligned_cols=104 Identities=47% Similarity=0.868 Sum_probs=100.2
Q ss_pred HHhhccccCCCCeEEEEEEeCCCCcEEEEEecCHHHHHHHHHcCeEEEEeCCCCcceecCCCCCCeEEEEEeeecCCCCe
Q 029236 52 RLLDSVKWDNKGLAVAIAQNVDTGAILMQGFANRDALATTISSRKATFYSRSRSTLWTKGETSQNFINVQDIFLDCDRDS 131 (196)
Q Consensus 52 ~~l~~i~~d~~GLiPaIvQD~~tg~VLMlaymN~EAl~~Tl~TG~~~yySRSR~~lW~KGetSGn~Q~V~~I~~DCD~Da 131 (196)
.++..++|+++|||||||||+.||+|||+||||+|||++|++||++|||||||++||.|||||||+|+|++|++|||+||
T Consensus 6 ~~~~~~~~~~~gLvpaIvQd~~t~eVLMlaymN~eAl~kTleTg~~~y~SRSR~~lW~KGetSG~~q~v~~i~~DCD~Da 85 (111)
T COG0139 6 ALLDELDFDKDGLVPAIVQDAETGEVLMLAYMNEEALAKTLETGEAHYYSRSRQELWTKGETSGHTQKVVEIRLDCDGDA 85 (111)
T ss_pred hhhhhcccCCCCeEEEEEEecCCCcEEEEEecCHHHHHHHHhcCeEEEEEcchhhheccccccCceEEEEEEEcCCCCCE
Confidence 35678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEeeCC-CCccCCCCccccccc
Q 029236 132 IIYLGKPDG-PTCHTGSETCYYTSV 155 (196)
Q Consensus 132 LL~~V~q~G-~aCHtG~~SCF~~~~ 155 (196)
||++|+|.| ||||||++||||+.+
T Consensus 86 ll~~V~q~gg~aCHtG~~SCF~~~~ 110 (111)
T COG0139 86 LLLLVEQIGGPACHTGTRSCFYRAV 110 (111)
T ss_pred EEEEEEeCCCCcccCCCcccccccC
Confidence 999999965 899999999999864
No 2
>PRK00051 hisI phosphoribosyl-AMP cyclohydrolase; Reviewed
Probab=100.00 E-value=2.4e-57 Score=361.64 Aligned_cols=105 Identities=42% Similarity=0.810 Sum_probs=102.4
Q ss_pred HHhhccccCCCCeEEEEEEeCCCCcEEEEEecCHHHHHHHHHcCeEEEEeCCCCcceecCCCCCCeEEEEEeeecCCCCe
Q 029236 52 RLLDSVKWDNKGLAVAIAQNVDTGAILMQGFANRDALATTISSRKATFYSRSRSTLWTKGETSQNFINVQDIFLDCDRDS 131 (196)
Q Consensus 52 ~~l~~i~~d~~GLiPaIvQD~~tg~VLMlaymN~EAl~~Tl~TG~~~yySRSR~~lW~KGetSGn~Q~V~~I~~DCD~Da 131 (196)
.+++.++||++|||||||||+.||+|||+||||+|||++||+||++|||||||++||+|||||||+|+|++|++|||+||
T Consensus 2 ~~~~~l~~~~~GLipaivqd~~tg~VLMlaymn~eAl~~Tl~tg~~~y~SRSR~~lW~KGetSG~~q~v~~i~~DCD~D~ 81 (125)
T PRK00051 2 KILDRLKFDADGLVPAIAQDAETGEVLMVAWMNEEALAKTLETGRAHYWSRSRQKLWRKGETSGHVQKVHEVRLDCDGDA 81 (125)
T ss_pred cHhhccccCCCCcEEEEEEECCCCCEEEEEEcCHHHHHHHHhcCcEEEEeCccCcccCCCCCcCCeEEEEEEEecCCCCE
Confidence 36778999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEeeCCCCccCCCCcccccccc
Q 029236 132 IIYLGKPDGPTCHTGSETCYYTSVL 156 (196)
Q Consensus 132 LL~~V~q~G~aCHtG~~SCF~~~~~ 156 (196)
||++|+|.|||||||++||||+++.
T Consensus 82 Ll~~V~q~G~aCHtg~~SCF~~~~~ 106 (125)
T PRK00051 82 VLLKVEQVGAACHTGRRSCFYRKLE 106 (125)
T ss_pred EEEEEEecCCcccCCCCCccceeec
Confidence 9999999999999999999999985
No 3
>PRK02759 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed
Probab=100.00 E-value=4.1e-55 Score=371.73 Aligned_cols=123 Identities=44% Similarity=0.796 Sum_probs=114.3
Q ss_pred HhhccccCCC-CeEEEEEEeCCCCcEEEEEecCHHHHHHHHHcCeEEEEeCCCCcceecCCCCCCeEEEEEeeecCCCCe
Q 029236 53 LLDSVKWDNK-GLAVAIAQNVDTGAILMQGFANRDALATTISSRKATFYSRSRSTLWTKGETSQNFINVQDIFLDCDRDS 131 (196)
Q Consensus 53 ~l~~i~~d~~-GLiPaIvQD~~tg~VLMlaymN~EAl~~Tl~TG~~~yySRSR~~lW~KGetSGn~Q~V~~I~~DCD~Da 131 (196)
+++.|+||++ |||||||||+.||+|||+||||+|||++|++||++|||||||++||+|||||||+|+|++|++|||+||
T Consensus 4 ~~~~l~~~~~~gLip~ivqd~~tg~vLml~ymn~eal~~Tl~tg~~~~~SRSr~~lW~KGetSG~~q~v~~i~~DCD~D~ 83 (203)
T PRK02759 4 QIEELDFDKNDGLIPAIVQDALTGEVLMLGYMNREALEKTLETGEVTFFSRSKQRLWTKGETSGNTQKVVSIRLDCDNDT 83 (203)
T ss_pred hhhccCcCCCCCcEEEEEEECCCCCEEEEEecCHHHHHHHHhcCcEEEEeCCCCcccCCCCCCCCeEEEEEEEecCCCCe
Confidence 5678999997 999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEeeCCCCccCCCCccccccc----------------ccccccCCCCccccccccccccCCC
Q 029236 132 IIYLGKPDGPTCHTGSETCYYTSV----------------LDALKDQPVGSFISLAHTAVLFGIP 180 (196)
Q Consensus 132 LL~~V~q~G~aCHtG~~SCF~~~~----------------~~~~~~~~~g~~~a~~~~~~lf~~~ 180 (196)
||++|+|.|||||||++||||+.+ .++....|.||| |++||...
T Consensus 84 ll~~V~~~G~aCHtg~~sCF~~~~~~~~~~~~L~~L~~~I~~Rk~~~pe~SY-----T~~L~~~G 143 (203)
T PRK02759 84 LLVLVEPIGPACHTGTRSCFYREKKAAPPWDFLSQLEQLIAERKNAPPEGSY-----TAKLFASG 143 (203)
T ss_pred EEEEEEecCCcCCCCCCCCCCCcccccchhhHHHHHHHHHHHHHhCCCCCcH-----HHHHHhCc
Confidence 999999999999999999999953 113557788999 99999763
No 4
>PLN02346 histidine biosynthesis bifunctional protein hisIE
Probab=100.00 E-value=3.1e-54 Score=379.08 Aligned_cols=136 Identities=72% Similarity=1.152 Sum_probs=120.3
Q ss_pred CCCcccccccc-cc-cceeeccccCCCCCCcchhHHHHHhhccccCCCCeEEEEEEeCCCCcEEEEEecCHHHHHHHHHc
Q 029236 17 TGSDRCRDNDM-KR-NCLVFASSTESNSNPVLQSKVDRLLDSVKWDNKGLAVAIAQNVDTGAILMQGFANRDALATTISS 94 (196)
Q Consensus 17 ~~~~~~~~~~~-~~-~~i~~~s~~~~~~~~~~~~~~~~~l~~i~~d~~GLiPaIvQD~~tg~VLMlaymN~EAl~~Tl~T 94 (196)
-|..+|..+.. +. .....-| .-..+++.+..++.+++.|+||++|||||||||+.||+||||||||+|||++||+|
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~gLipaivQd~~tg~VLml~ymn~eal~~Tl~t 84 (271)
T PLN02346 7 SPASPCRRDRKISAASKAAAGS--KTLAEPALEPKVESLLDSVKWDDKGLAVAIAQNVDTGAILMQGFANREAISATISS 84 (271)
T ss_pred ccccccccchhhcccccccccc--cCccccccchhHHHHHHhcCcCCCCCEEEEEEECCCCCEEEEEecCHHHHHHHHhc
Confidence 36778866553 22 2222222 22345688999999999999999999999999999999999999999999999999
Q ss_pred CeEEEEeCCCCcceecCCCCCCeEEEEEeeecCCCCeEEEEEeeCCCCccCCCCcccccc
Q 029236 95 RKATFYSRSRSTLWTKGETSQNFINVQDIFLDCDRDSIIYLGKPDGPTCHTGSETCYYTS 154 (196)
Q Consensus 95 G~~~yySRSR~~lW~KGetSGn~Q~V~~I~~DCD~DaLL~~V~q~G~aCHtG~~SCF~~~ 154 (196)
|++|||||||++||+|||||||+|+|++|++|||+|+|||+|+|.||+||||++||||++
T Consensus 85 g~~~y~SRSR~~LW~KGetSG~~q~v~~i~~DCD~D~ll~~V~~~G~aCHtg~~SCF~~~ 144 (271)
T PLN02346 85 RKATFYSRSRSGLWTKGETSGNFINVHDIYLDCDRDSIIYLGTPDGPTCHTGAETCYYTS 144 (271)
T ss_pred CcEEEEeCCCCccccCCCCcCCeEEEEEEEecCCCCeEEEEEEecCCcccCCCCCCcCcc
Confidence 999999999999999999999999999999999999999999999999999999999985
No 5
>PF01502 PRA-CH: Phosphoribosyl-AMP cyclohydrolase; InterPro: IPR002496 Phosphoribosyl-AMP cyclohydrolase 3.5.4.19 from EC catalyses the third step in the histidine biosynthetic pathway: 5-phosphoribosyl-AMP + H2O = 5-(5-phospho-D-ribosylaminoformimino)-1-(5-phospho-ribosyl) imidazole-4-carboxamide It requires Zn2+ ions for activity [].; GO: 0004635 phosphoribosyl-AMP cyclohydrolase activity, 0000105 histidine biosynthetic process; PDB: 1ZPS_B.
Probab=100.00 E-value=7e-46 Score=273.81 Aligned_cols=75 Identities=47% Similarity=0.914 Sum_probs=66.5
Q ss_pred EEEecCHHHHHHHHHcCeEEEEeCCCCcceecCCCCCCeEEEEEeeecCCCCeEEEEEeeCCCCccCCCCccccc
Q 029236 79 MQGFANRDALATTISSRKATFYSRSRSTLWTKGETSQNFINVQDIFLDCDRDSIIYLGKPDGPTCHTGSETCYYT 153 (196)
Q Consensus 79 MlaymN~EAl~~Tl~TG~~~yySRSR~~lW~KGetSGn~Q~V~~I~~DCD~DaLL~~V~q~G~aCHtG~~SCF~~ 153 (196)
|+||||+|||++||+||++|||||||++||+|||||||+|+|++|++|||+||||++|+|.||+||||++|||||
T Consensus 1 Mlaymn~eal~~Tl~tg~~~y~SRSR~~lW~KGetSG~~q~v~~i~~DCD~D~ll~~V~~~G~aCHtg~~SCF~r 75 (75)
T PF01502_consen 1 MLAYMNKEALEKTLETGRATYYSRSRNRLWRKGETSGNTQKVVEIRLDCDGDALLFKVEQVGPACHTGRRSCFYR 75 (75)
T ss_dssp EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS--E
T ss_pred CceecCHHHHHHHHHhCcEEEEEccCCcEeeEECCCCCEEEEEEEEecCCCCeEEEEEEeCCCCccCCCCCCcCc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999996
No 6
>KOG4311 consensus Histidinol dehydrogenase [Amino acid transport and metabolism]
Probab=100.00 E-value=5.7e-41 Score=298.57 Aligned_cols=173 Identities=48% Similarity=0.687 Sum_probs=143.7
Q ss_pred Ccccccccccceeecc--CCCccccc---ccccc------cceeeccccCCCCCCcchhHHHHHhhccccCCC-CeEEEE
Q 029236 1 MAVSYSQCVQSLKVSL--TGSDRCRD---NDMKR------NCLVFASSTESNSNPVLQSKVDRLLDSVKWDNK-GLAVAI 68 (196)
Q Consensus 1 ~a~~~~~~~~~~~~~~--~~~~~~~~---~~~~~------~~i~~~s~~~~~~~~~~~~~~~~~l~~i~~d~~-GLiPaI 68 (196)
||+|+.+-.|++-+++ .|.++-.+ -.|.. +-.+++= ..++++....+++.+|+.++||+. ||+.++
T Consensus 78 ~~~Sq~A~~~~~~~s~~niPker~v~~e~g~F~~q~~v~~sfsv~~~--v~~K~~~k~~l~d~~L~~i~tDr~dgl~~tl 155 (359)
T KOG4311|consen 78 MAVSQNALAQSLARSSCNIPKERVVVEENGSFRDQKLVSRSFSVFAC--VDNKNIAKQALVDNLLDRIKTDRKDGLVATL 155 (359)
T ss_pred HHHhHHHHHHHHHHhhccCCCcceecccCCccchHHHHhhccceeee--eccchHHHHHHHHHHHHHhccCCCCCeEEEE
Confidence 7889999999998888 44443211 12322 2222222 235567788899999999999975 665554
Q ss_pred EEeCCCCcEEEEEecCHHHHHHHHHcCeEEEEeCCCCcceecCCCCCCeEEEEEeeecCCCCeEEEEEeeCCC-CccCCC
Q 029236 69 AQNVDTGAILMQGFANRDALATTISSRKATFYSRSRSTLWTKGETSQNFINVQDIFLDCDRDSIIYLGKPDGP-TCHTGS 147 (196)
Q Consensus 69 vQD~~tg~VLMlaymN~EAl~~Tl~TG~~~yySRSR~~lW~KGetSGn~Q~V~~I~~DCD~DaLL~~V~q~G~-aCHtG~ 147 (196)
| -.++|.|||++|.||||+.+||.+|+++||||||++||.|||||||+|++.+|++|||+|||.|.|.|.|+ +||+|+
T Consensus 156 v-v~~~g~~Lglvysskes~a~ti~~g~gvy~SRsR~~lW~KGetSgn~q~ll~i~vDCD~D~l~f~v~q~g~gfCHl~t 234 (359)
T KOG4311|consen 156 V-VVDTGAVLGLVYSSKESLATTISSGKGVYFSRSRSTLWTKGETSGNFQNLLDIYVDCDRDSLIFLVTQDGPGFCHLGT 234 (359)
T ss_pred E-ehhhhhhhhhhcccHHHHHHHHhcCcceEEecccceeeeccccCcCceeeEEEeeccCccceEEEEecCCCcccccCc
Confidence 4 45899999999999999999999999999999999999999999999999999999999999999999998 999999
Q ss_pred Cccccccc----------ccccccCCCCccccccccccccCCCC
Q 029236 148 ETCYYTSV----------LDALKDQPVGSFISLAHTAVLFGIPE 181 (196)
Q Consensus 148 ~SCF~~~~----------~~~~~~~~~g~~~a~~~~~~lf~~~~ 181 (196)
.+||+... .++++.+|.|+| |.|||+|+.
T Consensus 235 ~~Cfg~~~~gL~~LEs~l~~Rk~~aPeeSy-----TrRLftD~a 273 (359)
T KOG4311|consen 235 ETCFGTSVFGLYSLESILSKRKETAPEESY-----TRRLFTDDA 273 (359)
T ss_pred ceeeeeechhhhhHHHHHHHhhhcCCchhh-----HHHhhCChH
Confidence 99999964 357889999999 999999975
No 7
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large 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). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=44.37 E-value=89 Score=23.42 Aligned_cols=57 Identities=19% Similarity=0.097 Sum_probs=43.5
Q ss_pred CCeEEEEEEeCCCCcEEEEEecCH-HHHHHHHHcCeEEEEeCCCCccee-cCCCCCCeE
Q 029236 62 KGLAVAIAQNVDTGAILMQGFANR-DALATTISSRKATFYSRSRSTLWT-KGETSQNFI 118 (196)
Q Consensus 62 ~GLiPaIvQD~~tg~VLMlaymN~-EAl~~Tl~TG~~~yySRSR~~lW~-KGetSGn~Q 118 (196)
..++..++.|-++|++=...|-+. +.+...|+.|+++|+++=+-+-.. +--+.+|..
T Consensus 34 g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~~V~~a~~~y~~~~~~y 92 (104)
T cd04474 34 GKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYISKGSVKVANKKFNTLKNDY 92 (104)
T ss_pred cEEEEEEEEECCCCEEEEEEehHHHHHhhcccccccEEEEeccEEeeccccCCCCCCcE
Confidence 347799999988999988888653 567889999999999998766653 344455543
No 8
>cd00495 Ribosomal_L25_TL5_CTC Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is found only in bacteria and some plastids. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L
Probab=39.75 E-value=45 Score=24.55 Aligned_cols=33 Identities=9% Similarity=0.056 Sum_probs=23.0
Q ss_pred CCCeEEEEEEeCCCCcEEEEEecCHHHHHHHHHcC
Q 029236 61 NKGLAVAIAQNVDTGAILMQGFANRDALATTISSR 95 (196)
Q Consensus 61 ~~GLiPaIvQD~~tg~VLMlaymN~EAl~~Tl~TG 95 (196)
++|+||+|+--.. .+- +.-.++.-.|.+.+.+.
T Consensus 21 ~~G~iPavvYG~~-~~~-~~i~v~~~~l~k~l~~~ 53 (91)
T cd00495 21 RAGKVPAVIYGKG-KEP-ISISVDEKELEKLLRKE 53 (91)
T ss_pred HCCCCCEEEECCC-CCC-EEEEEcHHHHHHHHhhc
Confidence 5799999995432 233 34478888888887653
No 9
>PF09137 Glucodextran_N: Glucodextranase, domain N; InterPro: IPR015220 Glucodextranase domain N, uniquely found in bacterial and archaeal glucoamylases and glucodextranases, adopts a structure consisting of 17 antiparallel beta-strands. These beta-strands are divided into two beta-sheets, and one of the beta-sheets is wrapped by an extended polypeptide, which appears to stabilise the domain. This domain, together with glycoside hydrolase domain A (IPR011613 from INTERPRO), is mainly involved with catalytic activity, hydrolysing alpha-1,6-glucosidic linkages of dextran to release beta-D-glucose from the non-reducing end via an inverting reaction mechanism []. ; PDB: 1UG9_A 1ULV_A 1LF6_B 1LF9_A.
Probab=34.64 E-value=61 Score=29.32 Aligned_cols=27 Identities=22% Similarity=0.335 Sum_probs=23.2
Q ss_pred CCCCCeEEEEEeeecCCCCeEEEEEee
Q 029236 112 ETSQNFINVQDIFLDCDRDSIIYLGKP 138 (196)
Q Consensus 112 etSGn~Q~V~~I~~DCD~DaLL~~V~q 138 (196)
...|.++..++|..|-++|+||+.|.-
T Consensus 92 d~~gry~i~k~i~tDP~rd~ll~~v~f 118 (269)
T PF09137_consen 92 DKQGRYRITKEIFTDPDRDVLLMRVTF 118 (269)
T ss_dssp ETTSSEEEEEEEEE-TTSSEEEEEEEE
T ss_pred cCCCCEEEEEEEECCCCCCEEEEEEEE
Confidence 457889999999999999999999864
No 10
>PRK05943 50S ribosomal protein L25; Reviewed
Probab=33.95 E-value=48 Score=24.83 Aligned_cols=32 Identities=13% Similarity=0.021 Sum_probs=23.3
Q ss_pred CCCeEEEEEEeCCCC-cEEEEEecCHHHHHHHHHcC
Q 029236 61 NKGLAVAIAQNVDTG-AILMQGFANRDALATTISSR 95 (196)
Q Consensus 61 ~~GLiPaIvQD~~tg-~VLMlaymN~EAl~~Tl~TG 95 (196)
++|+||+|+-- -| +- +-..+++..|.+.+.++
T Consensus 22 ~~G~vPaViYG--~~~~~-~~i~v~~~el~k~l~~~ 54 (94)
T PRK05943 22 RAGKFPAIIYG--GNEAP-VSIVLDHKDVINLQAKA 54 (94)
T ss_pred HCCCCCEEEEC--CCCCc-EEEEEcHHHHHHHHhcC
Confidence 57999999944 44 33 45578999999888643
No 11
>TIGR02196 GlrX_YruB Glutaredoxin-like protein, YruB-family. This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon. Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system.
Probab=31.76 E-value=55 Score=20.96 Aligned_cols=25 Identities=20% Similarity=0.284 Sum_probs=18.8
Q ss_pred CeEEEEEEeCCCCcEEEEEecCHHHHHHHH
Q 029236 63 GLAVAIAQNVDTGAILMQGFANRDALATTI 92 (196)
Q Consensus 63 GLiPaIvQD~~tg~VLMlaymN~EAl~~Tl 92 (196)
+-+|+++-+ |++ +.|| +.++|+..|
T Consensus 49 ~~vP~~~~~---~~~-~~g~-~~~~i~~~i 73 (74)
T TIGR02196 49 RGVPVIVIG---HKI-IVGF-DPEKLDQLL 73 (74)
T ss_pred CcccEEEEC---CEE-EeeC-CHHHHHHHh
Confidence 457999965 665 7776 889988765
No 12
>KOG3953 consensus SOCS box protein SSB-1, contains SPRY domain [General function prediction only]
Probab=29.77 E-value=48 Score=30.01 Aligned_cols=61 Identities=13% Similarity=0.264 Sum_probs=45.6
Q ss_pred HcCeEEEEeCCCCcceecCCCCCCeEEEEE-----------eeecCCCCeEEEEEeeC--CCCccCCCCccccc
Q 029236 93 SSRKATFYSRSRSTLWTKGETSQNFINVQD-----------IFLDCDRDSIIYLGKPD--GPTCHTGSETCYYT 153 (196)
Q Consensus 93 ~TG~~~yySRSR~~lW~KGetSGn~Q~V~~-----------I~~DCD~DaLL~~V~q~--G~aCHtG~~SCF~~ 153 (196)
.+-+-|=|+=.++.||+.|+-.|-++..-+ +-+|||..+|-|.+.+. |.|--....-|-|-
T Consensus 108 s~~qswGw~l~~~~l~H~g~~~~~yp~~~~~p~~~vp~ri~viLDm~egtl~F~~~~e~LGvAFRgL~~~~LYP 181 (242)
T KOG3953|consen 108 SNSQSWGWDLGRNVLYHDGQVAGLYPALNRQPKYNVPDRILVILDMIEGTLSFAADGEYLGVAFRGLKDKKLYP 181 (242)
T ss_pred CCCCccceecccceeeecCccccccccccCCchhcCCceEEEEEeeccceEEEEECCeEEeeeecCCCCCccee
Confidence 456677899999999999988888777655 67999999999999865 65543333344443
No 13
>PF14076 DUF4258: Domain of unknown function (DUF4258)
Probab=27.19 E-value=2e+02 Score=19.23 Aligned_cols=34 Identities=9% Similarity=0.181 Sum_probs=26.6
Q ss_pred cCHHHHHHHHHcCeEEE----EeCCCCcceecCCCCCC
Q 029236 83 ANRDALATTISSRKATF----YSRSRSTLWTKGETSQN 116 (196)
Q Consensus 83 mN~EAl~~Tl~TG~~~y----ySRSR~~lW~KGetSGn 116 (196)
.+.+-++.+|.+|...+ -.+...++|..+...++
T Consensus 15 Is~~~I~~~l~~g~i~~~~~~~~~~~~~~~~~~~~~~~ 52 (73)
T PF14076_consen 15 ISEEDIEDALENGEIIEDYSDDKRGPCRLYIGGGKEGR 52 (73)
T ss_pred CCHHHHHHHHhcCeEeeecCCCCCCCeEEEEEecCCCC
Confidence 57788999999999986 44555677777777777
No 14
>PF01386 Ribosomal_L25p: Ribosomal L25p family; InterPro: IPR020055 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 [, ]. This entry models the short-form of the ribosomal L25 protein. The long-form has homology to the general stress protein Ctc of Bacillus subtilis, a mesophile, and ribosomal protein TL5 of Thermus thermophilus, a thermophile. Ribosomal protein L25 of Escherichia coli and Haemophilus influenzae appear to be orthologous but consist only of the N-terminal half of Ctc and TL5. Both short (L25-like) and full-length (CTC-like) members of this family bind the E-loop of bacterial 5S rRNA.; GO: 0003735 structural constituent of ribosome, 0008097 5S rRNA binding, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2HGQ_Y 2HGJ_Y 2Y19_Z 2WRL_Z 3KIT_Z 2WH2_Z 2WDN_Z 3V25_Z 3HUZ_Z 3KIY_Z ....
Probab=23.04 E-value=1.2e+02 Score=22.42 Aligned_cols=31 Identities=13% Similarity=0.133 Sum_probs=23.2
Q ss_pred CCCeEEEEEEeCCCCcEEEEEecCHHHHHHHHH
Q 029236 61 NKGLAVAIAQNVDTGAILMQGFANRDALATTIS 93 (196)
Q Consensus 61 ~~GLiPaIvQD~~tg~VLMlaymN~EAl~~Tl~ 93 (196)
++|.||+|+ |-.|.=-+...++...|.+.+.
T Consensus 19 ~~G~iPavi--YG~~~~~~~i~v~~~~l~k~~~ 49 (88)
T PF01386_consen 19 REGKIPAVI--YGKGKESIPISVDEKELEKLLR 49 (88)
T ss_dssp HTTEEEEEE--EESSEEEEEEEEEHHHHHHHHT
T ss_pred HcCCceEEE--ECCCCCCEEEEEeHHHHHHHHH
Confidence 479999999 4444334566789999999884
No 15
>PF00905 Transpeptidase: Penicillin binding protein transpeptidase domain; InterPro: IPR001460 This signature identifies a large group of proteins, which include: Beta-lactamase precursor (3.5.2.6 from EC, penicillinase) Peptidoglycan synthetase ftsI (2.4.1.129 from EC, peptidoglycan glycosyltransferase 3) Methicillin resistance mecR1 protein Methicillin resistance blaR1 protein The large number of penicillin binding proteins, which are represented in this group of sequences, are responsible for the final stages of peptidoglycan biosynthesis for cell wall formation. The proteins synthesise cross-linked peptidoglycan from lipid intermediates, and contain a penicillin-sensitive transpeptidase carboxy-terminal domain. The active site serine (residue 337 in P14677 from SWISSPROT) is conserved in all members of this family []. MecR1 and BlaR1 are metallopeptidases belonging to MEROPS peptidase family M56, clan M-. BlaR1 and MecR1 cleave their cognate transcriptional repressors BlaI and MecI, respectively, activating the synthesis of MecA. MecR1 is present in Staphylococcus aureus and Staphylococcus sciuri, whereas BlaR1 (also known as BlaR, PenR1, or PenJ) has been found in Bacillus licheniformis, Staphylococcus epidermidis, Staphylococcus haemolyticus, and several S. aureus strains. These proteins are either plasmid-encoded, chromosomal, or transposon-mediated. MecR1/BlaR1 proteins are made up by homologous N-terminal 330-residue transmembrane metallopeptidase domains linked to extracellular 260-residue homologous PBP-like penicillin sensor moieties. ; GO: 0008658 penicillin binding, 0009273 peptidoglycan-based cell wall biogenesis; PDB: 3FWL_A 3VMA_A 2Z2M_E 2Z2L_E 1QME_A 1RP5_B 2ZC4_E 2ZC3_E 1QMF_A 3HBR_A ....
Probab=22.08 E-value=87 Score=26.98 Aligned_cols=17 Identities=24% Similarity=0.202 Sum_probs=14.1
Q ss_pred EEEEEeCCCCcEEEEEe
Q 029236 66 VAIAQNVDTGAILMQGF 82 (196)
Q Consensus 66 PaIvQD~~tg~VLMlay 82 (196)
.+|+.|+.||+||-++=
T Consensus 2 avVv~d~~TG~IlA~~~ 18 (304)
T PF00905_consen 2 AVVVMDPKTGEILAMVG 18 (304)
T ss_dssp EEEEEETTTTBEEEEEE
T ss_pred EEEEEECCCCcEEEEEe
Confidence 47999999999996653
No 16
>TIGR03577 EF_0830 conserved hypothetical protein EF_0830/AHA_3911. Members of this family of small (about 120 amino acid), relatively rare proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown.
Probab=21.94 E-value=75 Score=25.68 Aligned_cols=20 Identities=20% Similarity=0.463 Sum_probs=16.7
Q ss_pred CCcEEEEEecCHHHHHHHHH
Q 029236 74 TGAILMQGFANRDALATTIS 93 (196)
Q Consensus 74 tg~VLMlaymN~EAl~~Tl~ 93 (196)
-..||.+|||++|.|-+-|.
T Consensus 89 G~~VlGFGFmD~EeLG~rlv 108 (115)
T TIGR03577 89 GKNVLGFGFMDKEELGKRLT 108 (115)
T ss_pred CCeEEeeccccHHHHHHHHH
Confidence 34899999999999977654
No 17
>PF03413 PepSY: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification. ; InterPro: IPR005075 This signature, PepSY, is found in the propeptide of members of the MEROPS peptidase family M4 (clan MA(E)), which contains the thermostable thermolysins (3.4.24.27 from EC), and related thermolabile neutral proteases (bacillolysins) (3.4.24.28 from EC) from various species of Bacillus. It is also in many non-peptidase proteins, including Bacillus subtilis YpeB protein - a regulator of SleB spore cortex lytic enzyme - and a large number of eubacterial and archaeal cell wall-associated and secreted proteins which are mostly annotated as 'hypothetical protein'. Many extracellular bacterial proteases are produced as proenzymes. The propeptides usually have a dual function, i.e. they function as an intramolecular chaperone required for the folding of the polypeptide and as an inhibitor preventing premature activation of the enzyme. Analysis of the propeptide region of the M4 family of peptidases reveals two regions of conservation, the PepSY domain and a second domain, proximate to the N terminus, the FTP domain (IPR011096 from INTERPRO), which is also found in isolation in the propeptide of eukaryotic peptidases belong to MEROPS peptidase family M36. Propeptide domain swapping experiments, for example swapping the propeptide domain of PA protease with that of vibrolysin, both propeptides contain the FTP and PepSY domains, allows the PA protease domain to fold correctly and inhibits the C-terminal autoprocessing activity. However, swapping the propeptide of PA protease for the thermolysin propeptide, does not facilitate the correct folding nor the processing of the chimaeric protein into an active peptidase []. Mutational analysis of the Pseudomonas aeruginosa elastase gene revealed two mutations in the propeptide which resulted in the loss of inhibitory activity but not chaperone activity: A-15V and T-153I (where +1 is defined as the first residue of the mature peptidase). Both mutations resulted in peptidase activity, the T-153V mutation being much less effective than the A-15I mutation [] in activating peptidase activity. The T-153V mutation lies N-terminal to the FTP domain while the A-15I mutation is C-terminal to the PepSY domain. Given the diverse range of other proteins, both domains occur in in isolation, the exact function of each is still unclear; though it has been proposed that the PepSY domain primarily has inhibitory activity and in conjunction with the FTP domain in chaperone activity. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0005576 extracellular region; PDB: 2GU3_A 3NQZ_A 3NQY_A 2KGY_A.
Probab=21.07 E-value=1.4e+02 Score=19.26 Aligned_cols=19 Identities=26% Similarity=0.270 Sum_probs=12.4
Q ss_pred CCCeEEEEEEeCCCCcEEE
Q 029236 61 NKGLAVAIAQNVDTGAILM 79 (196)
Q Consensus 61 ~~GLiPaIvQD~~tg~VLM 79 (196)
.+|-.--+.-|+.||+||-
T Consensus 44 ~~~~~~~v~VDa~tG~Il~ 62 (64)
T PF03413_consen 44 PDGGEYEVYVDAYTGEILS 62 (64)
T ss_dssp TTTEEEEEEEETTT--EEE
T ss_pred CCCCEEEEEEECCCCeEEE
Confidence 3565566678999999984
No 18
>PRK05618 50S ribosomal protein L25/general stress protein Ctc; Reviewed
Probab=20.55 E-value=1.1e+02 Score=25.91 Aligned_cols=33 Identities=12% Similarity=0.116 Sum_probs=24.2
Q ss_pred CCCeEEEEEEeCCCCcEEEEEecCHHHHHHHHHcC
Q 029236 61 NKGLAVAIAQNVDTGAILMQGFANRDALATTISSR 95 (196)
Q Consensus 61 ~~GLiPaIvQD~~tg~VLMlaymN~EAl~~Tl~TG 95 (196)
++|+||+|+ |-.|.==..-.++...|.+.+.++
T Consensus 24 ~~G~VPaVi--YG~~~~~~~i~v~~~~l~k~l~~~ 56 (197)
T PRK05618 24 RAGKVPAVI--YGKGKEPVSISVDEKELIKALKKG 56 (197)
T ss_pred HCCCCcEEE--ECCCCCCEEEEECHHHHHHHHhcC
Confidence 579999999 544422345578999999998654
Done!