Query psy1265
Match_columns 384
No_of_seqs 148 out of 1125
Neff 3.1
Searched_HMMs 46136
Date Fri Aug 16 16:02:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1265.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1265hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00075 rpl21 ribosomal prote 100.0 1.1E-38 2.3E-43 269.4 15.3 107 208-318 2-108 (108)
2 PRK05573 rplU 50S ribosomal pr 100.0 4.7E-38 1E-42 262.8 15.0 102 209-314 1-102 (103)
3 TIGR00061 L21 ribosomal protei 100.0 5.6E-37 1.2E-41 256.1 14.3 101 210-314 1-101 (101)
4 COG0261 RplU Ribosomal protein 100.0 4.7E-37 1E-41 258.3 13.4 103 209-315 1-103 (103)
5 PRK12278 50S ribosomal protein 100.0 2.9E-36 6.4E-41 280.6 15.5 107 209-319 1-107 (221)
6 PF00829 Ribosomal_L21p: Ribos 100.0 3.8E-36 8.2E-41 247.9 9.1 96 209-308 1-96 (96)
7 KOG1686|consensus 99.9 1.8E-25 3.9E-30 197.9 11.7 129 177-317 3-131 (151)
8 KOG1686|consensus 91.0 0.03 6.6E-07 51.1 -2.1 84 171-264 67-151 (151)
9 PF07498 Rho_N: Rho terminatio 75.2 1.7 3.7E-05 31.5 1.4 20 335-354 5-24 (43)
10 PF02311 AraC_binding: AraC-li 55.4 18 0.00039 28.4 3.8 22 211-232 34-55 (136)
11 PF12791 RsgI_N: Anti-sigma fa 55.1 24 0.00052 26.1 4.2 37 208-252 5-41 (56)
12 PF11356 Pilus_PilP: Type IV p 54.2 16 0.00034 28.8 3.3 26 204-229 36-62 (87)
13 COG0662 {ManC} Mannose-6-phosp 51.0 22 0.00049 30.3 3.9 22 211-232 68-89 (127)
14 PF06249 EutQ: Ethanolamine ut 42.7 39 0.00085 31.1 4.3 27 213-246 108-134 (152)
15 PF07883 Cupin_2: Cupin domain 37.9 51 0.0011 24.0 3.6 21 212-232 31-51 (71)
16 PF04351 PilP: Pilus assembly 30.8 53 0.0012 29.2 3.2 26 206-231 88-114 (149)
17 COG3168 PilP Tfp pilus assembl 30.2 75 0.0016 30.1 4.1 27 206-232 107-133 (170)
18 PHA03325 nuclear-egress-membra 29.8 37 0.0008 35.8 2.3 45 336-383 34-78 (418)
19 PRK08433 flagellar motor switc 29.6 2.5E+02 0.0055 24.6 7.0 77 192-279 17-98 (111)
20 PRK09943 DNA-binding transcrip 29.3 73 0.0016 28.5 3.8 22 211-232 139-160 (185)
21 PF05896 NQRA: Na(+)-transloca 26.6 89 0.0019 31.1 4.2 57 218-283 27-84 (257)
22 cd04867 TGS_YchF_C TGS_YchF_C: 26.5 30 0.00066 29.2 0.9 19 212-230 63-81 (83)
23 PF01927 Mut7-C: Mut7-C RNAse 23.6 29 0.00062 30.6 0.2 10 73-82 132-141 (147)
24 PF15377 DUF4604: Domain of un 22.3 19 0.00041 32.4 -1.2 27 85-115 1-28 (158)
25 TIGR00632 vsr DNA mismatch end 21.0 39 0.00084 29.9 0.5 11 3-13 61-71 (117)
26 PF11213 DUF3006: Protein of u 20.6 1.1E+02 0.0023 24.2 2.9 32 208-245 9-42 (71)
No 1
>CHL00075 rpl21 ribosomal protein L21
Probab=100.00 E-value=1.1e-38 Score=269.37 Aligned_cols=107 Identities=28% Similarity=0.406 Sum_probs=103.5
Q ss_pred ceEEEEEECCEEEEEccCCEEEEcCCCCCCCCCCeEEeceEEEEeCCCceEEcccccCCceeEEEEEEEeeecCCeeEEE
Q psy1265 208 RLFAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVGGADFTLVGRPLLTPGLVNVTGTIIEKDLSHTRTNF 287 (384)
Q Consensus 208 ~MYAIVeIGGKQYKVt~GDvI~VEr~ll~aevGDkI~LdKVLLVGs~d~TlIGrPyLega~AkVeAtVVEh~KgkKViVF 287 (384)
.|||||++|||||||++||+|.||+ +++++||.|.|++|||+++++.+.+|+|||++ |+|+|+|+||++++|+++|
T Consensus 2 ~myAIi~~gGkQykV~~Gd~i~vek--l~~~~G~~i~l~~VL~~~~~~~~~iG~P~v~~--a~V~a~V~~h~r~~Ki~vf 77 (108)
T CHL00075 2 MTYAIIEAGGKQLWVEPGRFYDINH--FPLEPGTKILLNRVLLIRNESEILIGKPWLEN--ATVKGRILHHFRGKKITVY 77 (108)
T ss_pred cEEEEEEECCEEEEEeCCCEEEEEE--cCCCCCCEEEEEEEEEEecCCCeEECCcEecC--cEEEEEEEeecCCCCEEEE
Confidence 5999999999999999999999999 78999999999999999999899999999999 8999999999999999999
Q ss_pred EeCCCCCcccccCccCcceEEEEeEEEeccc
Q psy1265 288 RKIPRKRHTRFRFFRTQLTMIRINEIEIIEK 318 (384)
Q Consensus 288 KkKRRKrYRRk~GHRQ~yTrLRIteI~l~gk 318 (384)
||||||+|+|++||||+||+|+|++|..+++
T Consensus 78 K~krRK~yrrk~GHRQ~~T~i~I~~I~~~g~ 108 (108)
T CHL00075 78 KMRPKKKTRKKQGHRQKLTRFLIDSISFNGK 108 (108)
T ss_pred EeCCCCCccCCCccCCCcEEEEEEEEEcCCC
Confidence 9999999999999999999999999998763
No 2
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=100.00 E-value=4.7e-38 Score=262.77 Aligned_cols=102 Identities=30% Similarity=0.495 Sum_probs=100.1
Q ss_pred eEEEEEECCEEEEEccCCEEEEcCCCCCCCCCCeEEeceEEEEeCCCceEEcccccCCceeEEEEEEEeeecCCeeEEEE
Q psy1265 209 LFAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVGGADFTLVGRPLLTPGLVNVTGTIIEKDLSHTRTNFR 288 (384)
Q Consensus 209 MYAIVeIGGKQYKVt~GDvI~VEr~ll~aevGDkI~LdKVLLVGs~d~TlIGrPyLega~AkVeAtVVEh~KgkKViVFK 288 (384)
|||||++||+||||++||+|.||+ +++++||.|.|++|||+++++++.+|+|+|++ |+|+|+|++|++++|+++||
T Consensus 1 MyAIi~~gGkQykV~~Gd~i~v~~--l~~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~--a~V~A~V~~~~k~~Ki~vfK 76 (103)
T PRK05573 1 MYAIIKTGGKQYKVEEGDVIKVEK--LDAEVGDTVEFDEVLLVGGGEEVKIGAPYVEG--AKVTAEVVEHGRGKKVIVFK 76 (103)
T ss_pred CEEEEEECCEEEEEeCCCEEEEcc--cCCCCCCEEEEeEEEEEeCCCCEEECCeEcCC--CEEEEEEEeccCCCcEEEEE
Confidence 899999999999999999999999 68999999999999999999999999999999 89999999999999999999
Q ss_pred eCCCCCcccccCccCcceEEEEeEEE
Q psy1265 289 KIPRKRHTRFRFFRTQLTMIRINEIE 314 (384)
Q Consensus 289 kKRRKrYRRk~GHRQ~yTrLRIteI~ 314 (384)
|||||+|+|++||||++|+|+|++|.
T Consensus 77 ~krRK~y~r~~GHRQ~~T~i~I~~I~ 102 (103)
T PRK05573 77 YKRRKNYRKKQGHRQPYTKVKITSIN 102 (103)
T ss_pred EcCCCCccccCCccCCcEEEEEEEEe
Confidence 99999999999999999999999996
No 3
>TIGR00061 L21 ribosomal protein L21. Eubacterial and chloroplast.
Probab=100.00 E-value=5.6e-37 Score=256.06 Aligned_cols=101 Identities=21% Similarity=0.393 Sum_probs=98.6
Q ss_pred EEEEEECCEEEEEccCCEEEEcCCCCCCCCCCeEEeceEEEEeCCCceEEcccccCCceeEEEEEEEeeecCCeeEEEEe
Q psy1265 210 FAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVGGADFTLVGRPLLTPGLVNVTGTIIEKDLSHTRTNFRK 289 (384)
Q Consensus 210 YAIVeIGGKQYKVt~GDvI~VEr~ll~aevGDkI~LdKVLLVGs~d~TlIGrPyLega~AkVeAtVVEh~KgkKViVFKk 289 (384)
||||++||+||||++||+|.||+ +++++||.|.|++|||+++++++.+|+|+|++ |+|+|+|++|++++|+++|||
T Consensus 1 yAIi~~gGkQykV~~Gd~i~Ve~--l~~~~G~~i~l~~VLlv~~~~~~~iG~P~l~~--a~V~a~V~~~~r~~Ki~vfK~ 76 (101)
T TIGR00061 1 YAIVEIGGKQYKVEEGQTVRIEK--LDAAPGDTVEFDKVLMVNKGGDVKIGKPYVEG--AKVVAEVEKHGRGKKVKVYKY 76 (101)
T ss_pred CEEEEECCEEEEEeCCCEEEEcc--cCCCCCCEEEEEEEEEEecCCCeEECCeEcCC--CEEEEEEEeecCCCCEEEEEe
Confidence 89999999999999999999999 78999999999999999999999999999999 799999999999999999999
Q ss_pred CCCCCcccccCccCcceEEEEeEEE
Q psy1265 290 IPRKRHTRFRFFRTQLTMIRINEIE 314 (384)
Q Consensus 290 KRRKrYRRk~GHRQ~yTrLRIteI~ 314 (384)
||||+|+|++||||+||+|+|++|.
T Consensus 77 krrK~y~r~~GHRQ~~T~i~I~~I~ 101 (101)
T TIGR00061 77 RRRKHSRKKQGHRQPYTKVKVTKIV 101 (101)
T ss_pred CCCCCccCCCccCCCcEEEEEEEeC
Confidence 9999999999999999999999983
No 4
>COG0261 RplU Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.7e-37 Score=258.29 Aligned_cols=103 Identities=30% Similarity=0.483 Sum_probs=100.7
Q ss_pred eEEEEEECCEEEEEccCCEEEEcCCCCCCCCCCeEEeceEEEEeCCCceEEcccccCCceeEEEEEEEeeecCCeeEEEE
Q psy1265 209 LFAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVGGADFTLVGRPLLTPGLVNVTGTIIEKDLSHTRTNFR 288 (384)
Q Consensus 209 MYAIVeIGGKQYKVt~GDvI~VEr~ll~aevGDkI~LdKVLLVGs~d~TlIGrPyLega~AkVeAtVVEh~KgkKViVFK 288 (384)
|||||++|||||+|++||+|.||+ +++++|+.|.|++|||+++++.+.+|+||+++ |.|.|+|++|.|++||++||
T Consensus 1 mYAii~tGGKQykV~~G~~i~vEk--l~~e~g~~v~f~~VL~v~~~~~v~iG~P~v~g--a~V~aeV~~hgr~kKV~i~K 76 (103)
T COG0261 1 MYAIIKTGGKQYKVEEGDVIKVEK--LDAEPGDKVEFDEVLMVGGGEEVKIGAPYVEG--AKVTAEVVEHGRGKKVIIFK 76 (103)
T ss_pred CeEEEEECCEEEEEecCCEEEEEE--cCCCCCCEEEEEEEEEEcCCCceEECCceecC--cEEEEEEhhhCCCceEEEEE
Confidence 899999999999999999999999 89999999999999999999999999999999 89999999999999999999
Q ss_pred eCCCCCcccccCccCcceEEEEeEEEe
Q psy1265 289 KIPRKRHTRFRFFRTQLTMIRINEIEI 315 (384)
Q Consensus 289 kKRRKrYRRk~GHRQ~yTrLRIteI~l 315 (384)
|||||+|+|++||||+||+|+|++|.+
T Consensus 77 ~k~rK~~~rk~GHRQ~yT~vkI~~I~~ 103 (103)
T COG0261 77 YKRRKNYRKKQGHRQPYTRVKITGIVA 103 (103)
T ss_pred eccCcCcccccCcccceEEEEEEEeeC
Confidence 999999999999999999999999963
No 5
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=100.00 E-value=2.9e-36 Score=280.58 Aligned_cols=107 Identities=31% Similarity=0.484 Sum_probs=104.1
Q ss_pred eEEEEEECCEEEEEccCCEEEEcCCCCCCCCCCeEEeceEEEEeCCCceEEcccccCCceeEEEEEEEeeecCCeeEEEE
Q psy1265 209 LFAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVGGADFTLVGRPLLTPGLVNVTGTIIEKDLSHTRTNFR 288 (384)
Q Consensus 209 MYAIVeIGGKQYKVt~GDvI~VEr~ll~aevGDkI~LdKVLLVGs~d~TlIGrPyLega~AkVeAtVVEh~KgkKViVFK 288 (384)
|||||++|||||||++||+|.||+ +..++||+|.|++|||+++++++.||+|||++ ++|+|+|++|++++||++||
T Consensus 1 MyAVI~~gGKQykV~~Gd~i~Vek--l~~~~G~~i~~~~VL~v~~~~~~~iG~P~v~~--a~V~A~V~~~~kg~Ki~vfK 76 (221)
T PRK12278 1 MFAVIKTGGKQYKVQAGDLLRVEK--LAAEAGETVQFGEVLMLGEGDNVTVGAPFVDG--AAVQAEVIEQIKGDKVIHFK 76 (221)
T ss_pred CEEEEEeCCEEEEEeCCCEEEEec--cCCCCCCEEEEeEEEEEecCCCeEECCeEecC--CEEEEEEEeecCCCCEEEEE
Confidence 999999999999999999999999 78999999999999999999999999999999 79999999999999999999
Q ss_pred eCCCCCcccccCccCcceEEEEeEEEecccc
Q psy1265 289 KIPRKRHTRFRFFRTQLTMIRINEIEIIEKV 319 (384)
Q Consensus 289 kKRRKrYRRk~GHRQ~yTrLRIteI~l~gkv 319 (384)
|||||+|+|++||||+||+|||++|..+|..
T Consensus 77 ~krRK~yrrk~GHRQ~~T~i~I~~I~~~g~~ 107 (221)
T PRK12278 77 KRRRQSSRRTKGHRQLLTLVRITEILASGAD 107 (221)
T ss_pred eCCCCCcccCCCcCCCcEEEEEEEEEcCCcc
Confidence 9999999999999999999999999998864
No 6
>PF00829 Ribosomal_L21p: Ribosomal prokaryotic L21 protein; InterPro: IPR001787 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 L21 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L21 is known to bind to the 23S rRNA in the presence of L20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Bacterial L21. Marchantia polymorpha chloroplast L21. Cyanelle L21. Plant chloroplast L21 (nuclear-encoded). Bacterial L21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XG0_V 2X9S_V 2XG2_V 3UZ1_2 2Y19_V 2WDL_V 3V23_V 2WRO_V 2WRL_V 2Y11_V ....
Probab=100.00 E-value=3.8e-36 Score=247.95 Aligned_cols=96 Identities=41% Similarity=0.607 Sum_probs=93.4
Q ss_pred eEEEEEECCEEEEEccCCEEEEcCCCCCCCCCCeEEeceEEEEeCCCceEEcccccCCceeEEEEEEEeeecCCeeEEEE
Q psy1265 209 LFAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVGGADFTLVGRPLLTPGLVNVTGTIIEKDLSHTRTNFR 288 (384)
Q Consensus 209 MYAIVeIGGKQYKVt~GDvI~VEr~ll~aevGDkI~LdKVLLVGs~d~TlIGrPyLega~AkVeAtVVEh~KgkKViVFK 288 (384)
|||||+++|+||||++||+|.||+ +++++||+|.|++||++++++++.+|+|||++ |+|+|+|++|++++|+++||
T Consensus 1 myAIi~~ggkQykV~~gd~i~v~~--l~~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~--a~V~a~V~~~~k~~Ki~v~K 76 (96)
T PF00829_consen 1 MYAIIEIGGKQYKVEEGDVIDVER--LDAEVGDKIELDKVLLIGSEDFTLIGRPYLEG--AKVEATVLEHGKGKKIIVFK 76 (96)
T ss_dssp -EEEEESSSEEEEESSSEEEEEES--TSSSTTSEEEETTEEEEETSSSTCSSSSSSSS--SEEEEEEEEEEEEEEEEEEE
T ss_pred CEEEEEECCEEEEEeCCCEEEECC--cCcCCCCEEEEEEEEEEecCCCeEECCccCCC--cEEEEEEEeccCCCcEEEEE
Confidence 899999999999999999999998 59999999999999999999999999999999 89999999999999999999
Q ss_pred eCCCCCcccccCccCcceEE
Q psy1265 289 KIPRKRHTRFRFFRTQLTMI 308 (384)
Q Consensus 289 kKRRKrYRRk~GHRQ~yTrL 308 (384)
|||||+|+|++||||+||+|
T Consensus 77 ~krRK~y~r~~GhRq~~T~i 96 (96)
T PF00829_consen 77 KKRRKRYRRKQGHRQPYTRI 96 (96)
T ss_dssp EETTTTEEEEEEEEEEEEEE
T ss_pred ECCccccccCCccCCCeEEC
Confidence 99999999999999999986
No 7
>KOG1686|consensus
Probab=99.93 E-value=1.8e-25 Score=197.91 Aligned_cols=129 Identities=29% Similarity=0.296 Sum_probs=118.0
Q ss_pred hcCcccccccCCCchhHHHHHHHHHHhcCCCceEEEEEECCEEEEEccCCEEEEcCCCCCCCCCCeEEeceEEEEeCCCc
Q psy1265 177 TKGTEIVSTKLSSVPVYLNLVNNQIERNEQGRLFAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVGGADF 256 (384)
Q Consensus 177 a~~~~~v~~PL~~s~~vle~Vn~~I~~~~~~~MYAIVeIGGKQYKVt~GDvI~VEr~ll~aevGDkI~LdKVLLVGs~d~ 256 (384)
+...+.++++|++.... +..+++.||||.+||+||||..||.|+.++ +.+++++|+|.|++|||+|+.++
T Consensus 3 ~~~e~v~vg~l~s~~~~---------~~kr~~~favv~v~srq~kvs~gd~iy~eg-~~p~nv~d~i~l~kVlLvg~~~~ 72 (151)
T KOG1686|consen 3 ASSETVTVGRLASACSH---------SIKRPSGFAVVSVGSRQRKVSSGDTIYTEG-LKPKNVLDSIPLPKVLLVGPVEE 72 (151)
T ss_pred ccceeEEEeccchhhhh---------ccccCCccEEEEEcceeEEecCCCeeeecC-ccccccccccccceEEEecCcce
Confidence 44455667888876442 246789999999999999999999999999 78999999999999999999999
Q ss_pred eEEcccccCCceeEEEEEEEeeecCCeeEEEEeCCCCCcccccCccCcceEEEEeEEEecc
Q psy1265 257 TLVGRPLLTPGLVNVTGTIIEKDLSHTRTNFRKIPRKRHTRFRFFRTQLTMIRINEIEIIE 317 (384)
Q Consensus 257 TlIGrPyLega~AkVeAtVVEh~KgkKViVFKkKRRKrYRRk~GHRQ~yTrLRIteI~l~g 317 (384)
|.+|+|.|+. |+|.|.|+|+....|+++||+|++|.|+|.+||||..|+|||++|....
T Consensus 73 T~~grpvv~~--vtv~aVv~e~g~~~kvvhfk~k~~k~tr~~~~~~qe~t~LrIt~it~ie 131 (151)
T KOG1686|consen 73 TRIGRPVVKK--VTVHAVVEEYGLLFKVVHFKSKQWKVTRRDLGHRQEATELRITCITGIE 131 (151)
T ss_pred eEecCccccc--ceEEEEeeeccccccEEEEEecchhhhhhhhcccCcccEEEEeeeeeee
Confidence 9999999999 8999999999999999999999999999999999999999999998755
No 8
>KOG1686|consensus
Probab=91.04 E-value=0.03 Score=51.05 Aligned_cols=84 Identities=33% Similarity=0.385 Sum_probs=65.9
Q ss_pred CCchhhhcCcccccccCCCchhHHHHHHHHHHhcCCCceEEEEEECCEEEEEccCCEEEEcC-CCCCCCCCCeEEeceEE
Q psy1265 171 PSSSEFTKGTEIVSTKLSSVPVYLNLVNNQIERNEQGRLFAIIHVLGRQTKVTPNDIIIVDS-NSFAPLNGDKIKFEKVL 249 (384)
Q Consensus 171 ps~~efa~~~~~v~~PL~~s~~vle~Vn~~I~~~~~~~MYAIVeIGGKQYKVt~GDvI~VEr-~ll~aevGDkI~LdKVL 249 (384)
+.+.+|+-++ +.++.+++-++--.+++..|++++...+|+|++.-|..-..- +.++...++-|++.+++
T Consensus 67 vg~~~~T~~g----------rpvv~~vtv~aVv~e~g~~~kvvhfk~k~~k~tr~~~~~~qe~t~LrIt~it~ie~e~~~ 136 (151)
T KOG1686|consen 67 VGPVEETRIG----------RPVVKKVTVHAVVEEYGLLFKVVHFKSKQWKVTRRDLGHRQEATELRITCITGIELEKVL 136 (151)
T ss_pred ecCcceeEec----------CcccccceEEEEeeeccccccEEEEEecchhhhhhhhcccCcccEEEEeeeeeeeeccce
Confidence 5566677666 455555555554456789999999999999999998887662 12566789999999999
Q ss_pred EEeCCCceEEccccc
Q psy1265 250 LVGGADFTLVGRPLL 264 (384)
Q Consensus 250 LVGs~d~TlIGrPyL 264 (384)
+++..+|+.+|.|.+
T Consensus 137 ~v~~~nf~~vgk~~l 151 (151)
T KOG1686|consen 137 LVGAPNFTAVGKPLL 151 (151)
T ss_pred eccCccceeeccccC
Confidence 999999999999864
No 9
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=75.25 E-value=1.7 Score=31.53 Aligned_cols=20 Identities=10% Similarity=0.029 Sum_probs=16.5
Q ss_pred ccHHHHHHHHHhcCCchhhh
Q psy1265 335 CLQTQYNLILENQGKTYMAS 354 (384)
Q Consensus 335 ~~~aEL~~mar~~g~~~~as 354 (384)
++..||.+||++.|+++++.
T Consensus 5 ~~~~eL~~iAk~lgI~~~~~ 24 (43)
T PF07498_consen 5 MTLSELREIAKELGIEGYSK 24 (43)
T ss_dssp S-HHHHHHHHHCTT-TTGCC
T ss_pred CCHHHHHHHHHHcCCCCCCc
Confidence 78999999999999998875
No 10
>PF02311 AraC_binding: AraC-like ligand binding domain; InterPro: IPR003313 This entry defines the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The crystal structure of the arabinose-binding and dimerization domain of the Escherichia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1XJA_B 2ARA_A 2AAC_B 2ARC_A.
Probab=55.40 E-value=18 Score=28.38 Aligned_cols=22 Identities=18% Similarity=0.593 Sum_probs=16.9
Q ss_pred EEEEECCEEEEEccCCEEEEcC
Q psy1265 211 AIIHVLGRQTKVTPNDIIIVDS 232 (384)
Q Consensus 211 AIVeIGGKQYKVt~GDvI~VEr 232 (384)
+.+.++|++|.|.+||++.++.
T Consensus 34 ~~~~~~~~~~~l~~g~~~li~p 55 (136)
T PF02311_consen 34 GTLHIDGQEYPLKPGDLFLIPP 55 (136)
T ss_dssp EEEEETTEEEEE-TT-EEEE-T
T ss_pred EEEEECCEEEEEECCEEEEecC
Confidence 4578999999999999999986
No 11
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=55.07 E-value=24 Score=26.15 Aligned_cols=37 Identities=16% Similarity=0.312 Sum_probs=28.9
Q ss_pred ceEEEEEECCEEEEEccCCEEEEcCCCCCCCCCCeEEeceEEEEe
Q psy1265 208 RLFAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVG 252 (384)
Q Consensus 208 ~MYAIVeIGGKQYKVt~GDvI~VEr~ll~aevGDkI~LdKVLLVG 252 (384)
..||||-+. .|+++.|.+ ..+.++|++|.|+..-...
T Consensus 5 ~~~aiVlT~-------dGeF~~ik~-~~~~~vG~eI~~~~~~~~~ 41 (56)
T PF12791_consen 5 KKYAIVLTP-------DGEFIKIKR-KPGMEVGQEIEFDEKDIIN 41 (56)
T ss_pred CCEEEEEcC-------CCcEEEEeC-CCCCcccCEEEEechhhcc
Confidence 568888776 688889988 4579999999998755443
No 12
>PF11356 Pilus_PilP: Type IV pilus biogenesis; InterPro: IPR022753 Type IV pili are required for auto-agglutination, twitching motility, biofilm formation, adherence and DNA uptake during transformation []. PilP is an inner membrane protein, required for pilus expression and transformation []. PilP interacts with PilQ which suggests that the two proteins may have coordinated activity in functions such as pilus extrusion/retraction []. ; PDB: 3OSS_C 2LNV_A.
Probab=54.21 E-value=16 Score=28.84 Aligned_cols=26 Identities=35% Similarity=0.296 Sum_probs=20.0
Q ss_pred cCCCceEEEEE-ECCEEEEEccCCEEE
Q psy1265 204 NEQGRLFAIIH-VLGRQTKVTPNDIII 229 (384)
Q Consensus 204 ~~~~~MYAIVe-IGGKQYKVt~GDvI~ 229 (384)
...+..+|||. .+|.|+.+..||.|.
T Consensus 36 ~~~~~~~Aii~~~~~~~~~~~~Gd~i~ 62 (87)
T PF11356_consen 36 GGGGRSSAIIRPSGGEQRTYRVGDTIP 62 (87)
T ss_dssp SCSSS-EEEEE-CTTEEEEE-TTEE-S
T ss_pred cCCCceEEEEEeCCCcEEEEECcCEeC
Confidence 35678999999 899999999999983
No 13
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=51.00 E-value=22 Score=30.28 Aligned_cols=22 Identities=14% Similarity=0.347 Sum_probs=20.1
Q ss_pred EEEEECCEEEEEccCCEEEEcC
Q psy1265 211 AIIHVLGRQTKVTPNDIIIVDS 232 (384)
Q Consensus 211 AIVeIGGKQYKVt~GDvI~VEr 232 (384)
|+|.++|+++-|.+||.++|+.
T Consensus 68 g~v~~~~~~~~v~~gd~~~iP~ 89 (127)
T COG0662 68 GKVTIGGEEVEVKAGDSVYIPA 89 (127)
T ss_pred EEEEECCEEEEecCCCEEEECC
Confidence 4578999999999999999997
No 14
>PF06249 EutQ: Ethanolamine utilisation protein EutQ; InterPro: IPR010424 The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear [].; PDB: 2PYT_B 3LWC_A.
Probab=42.70 E-value=39 Score=31.08 Aligned_cols=27 Identities=30% Similarity=0.656 Sum_probs=21.0
Q ss_pred EEECCEEEEEccCCEEEEcCCCCCCCCCCeEEec
Q psy1265 213 IHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFE 246 (384)
Q Consensus 213 VeIGGKQYKVt~GDvI~VEr~ll~aevGDkI~Ld 246 (384)
|.+.|+-|...+||+|++++ |.+|.|.
T Consensus 108 i~~~G~~~~A~~GDvi~iPk-------Gs~I~fs 134 (152)
T PF06249_consen 108 ISIDGQTVTAKPGDVIFIPK-------GSTITFS 134 (152)
T ss_dssp EEETTEEEEEETT-EEEE-T-------T-EEEEE
T ss_pred EEECCEEEEEcCCcEEEECC-------CCEEEEe
Confidence 45889999999999999998 7788885
No 15
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=37.95 E-value=51 Score=23.97 Aligned_cols=21 Identities=24% Similarity=0.491 Sum_probs=18.6
Q ss_pred EEEECCEEEEEccCCEEEEcC
Q psy1265 212 IIHVLGRQTKVTPNDIIIVDS 232 (384)
Q Consensus 212 IVeIGGKQYKVt~GDvI~VEr 232 (384)
.+.++|..+.+.+||.+.++.
T Consensus 31 ~~~~~~~~~~l~~Gd~~~i~~ 51 (71)
T PF07883_consen 31 TLTVDGERVELKPGDAIYIPP 51 (71)
T ss_dssp EEEETTEEEEEETTEEEEEET
T ss_pred EEEEccEEeEccCCEEEEECC
Confidence 345899999999999999997
No 16
>PF04351 PilP: Pilus assembly protein, PilP; InterPro: IPR007446 The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [].; PDB: 2Y4Y_B 2Y4X_A 2IVW_A 2LC4_A.
Probab=30.77 E-value=53 Score=29.21 Aligned_cols=26 Identities=23% Similarity=0.333 Sum_probs=22.6
Q ss_pred CCceEEEEEE-CCEEEEEccCCEEEEc
Q psy1265 206 QGRLFAIIHV-LGRQTKVTPNDIIIVD 231 (384)
Q Consensus 206 ~~~MYAIVeI-GGKQYKVt~GDvI~VE 231 (384)
.+.++|+|+. .|+=|.|..||+|--+
T Consensus 88 ~~~~~ALv~~pdg~v~~V~~G~yiG~n 114 (149)
T PF04351_consen 88 GGQPWALVQDPDGKVYRVKVGDYIGQN 114 (149)
T ss_dssp TTEEEEEEEE-TTEEEEEETTEEETTT
T ss_pred CCEEEEEEEeCCCCEEEecCCCEeccC
Confidence 4579999999 8999999999998444
No 17
>COG3168 PilP Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=30.25 E-value=75 Score=30.08 Aligned_cols=27 Identities=15% Similarity=0.094 Sum_probs=23.7
Q ss_pred CCceEEEEEECCEEEEEccCCEEEEcC
Q psy1265 206 QGRLFAIIHVLGRQTKVTPNDIIIVDS 232 (384)
Q Consensus 206 ~~~MYAIVeIGGKQYKVt~GDvI~VEr 232 (384)
.+..+|+|+..|+-|+|..|++|-.+.
T Consensus 107 g~~~~A~i~~~~~v~~V~vG~YlGqN~ 133 (170)
T COG3168 107 GQGVSALIEAPGGVYRVRVGQYLGQNY 133 (170)
T ss_pred CCceEEEEEcCCceEEEeeccEeeccC
Confidence 457899999999999999999996654
No 18
>PHA03325 nuclear-egress-membrane-like protein; Provisional
Probab=29.79 E-value=37 Score=35.77 Aligned_cols=45 Identities=36% Similarity=0.549 Sum_probs=36.2
Q ss_pred cHHHHHHHHHhcCCchhhhhcCCCceeeeecccccCceeEEeeccCCC
Q psy1265 336 LQTQYNLILENQGKTYMASLAQHLPVLVTSSYRRKNSLWFCTQQDTDK 383 (384)
Q Consensus 336 ~~aEL~~mar~~g~~~~as~i~~~~v~~~~~~~~k~~~~~~~~~~~~~ 383 (384)
-..+|+.|.|..|.+-+-+ .+||+-. .|-..-|++.|||.-|.++
T Consensus 34 iS~~YK~~~RAE~kKrlL~--~~LP~~i-~sk~~~n~FiFCt~~D~~~ 78 (418)
T PHA03325 34 ISKAYKGTNRAEGKKRLLS--NHLPDCI-CSKRNTNSFIFCTSRDYRK 78 (418)
T ss_pred HHHHHHHHHhhhhHHHHHH--hhCCccc-ccccccceEEEEecchHHH
Confidence 6788999999999886543 3778777 6778889999999988654
No 19
>PRK08433 flagellar motor switch protein; Validated
Probab=29.57 E-value=2.5e+02 Score=24.63 Aligned_cols=77 Identities=18% Similarity=0.044 Sum_probs=46.7
Q ss_pred hHHHHHHHHHHhcCCCceEEEEEECCEEEEEccCCEEEEcCCCCCCCCCCeEEece-----EEEEeCCCceEEcccccCC
Q psy1265 192 VYLNLVNNQIERNEQGRLFAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEK-----VLLVGGADFTLVGRPLLTP 266 (384)
Q Consensus 192 ~vle~Vn~~I~~~~~~~MYAIVeIGGKQYKVt~GDvI~VEr~ll~aevGDkI~LdK-----VLLVGs~d~TlIGrPyLeg 266 (384)
.+|+++...+..-..-.+-..+++|..+..+. + +++.++||.|.|++ |-++-++--...|.|.+.+
T Consensus 17 ~~~~~~~~~~~~L~~v~VeV~v~LG~t~itl~-------d--lL~Lq~GDVI~Ld~~~~e~v~v~V~g~~~f~G~~G~~~ 87 (111)
T PRK08433 17 TYLEELICDYENLLDIEVDFSAELGTTQISLL-------E--ILKFEKGSVIDLEKPAGESVELYINGRIIGKGEVMVYE 87 (111)
T ss_pred HHHHHhhhhHHHhccceeEEEEEEecccccHH-------H--HhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEEC
Confidence 56666666665555667888888887776654 1 35677777777774 3333333344567777766
Q ss_pred ceeEEEEEEEeee
Q psy1265 267 GLVNVTGTIIEKD 279 (384)
Q Consensus 267 a~AkVeAtVVEh~ 279 (384)
+ +.-+.|.+..
T Consensus 88 ~--k~AVrI~e~i 98 (111)
T PRK08433 88 K--NLAIRINEIL 98 (111)
T ss_pred C--EEEEEEEEec
Confidence 4 3334455544
No 20
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=29.30 E-value=73 Score=28.49 Aligned_cols=22 Identities=5% Similarity=0.297 Sum_probs=19.8
Q ss_pred EEEEECCEEEEEccCCEEEEcC
Q psy1265 211 AIIHVLGRQTKVTPNDIIIVDS 232 (384)
Q Consensus 211 AIVeIGGKQYKVt~GDvI~VEr 232 (384)
+.+.++|+.|.+.+||.+.++.
T Consensus 139 ~~~~~~~~~~~l~~Gd~~~~~~ 160 (185)
T PRK09943 139 IVLTINGQDYHLVAGQSYAINT 160 (185)
T ss_pred EEEEECCEEEEecCCCEEEEcC
Confidence 4578999999999999999996
No 21
>PF05896 NQRA: Na(+)-translocating NADH-quinone reductase subunit A (NQRA); InterPro: IPR008703 This family consists of several bacterial Na+-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na+-translocating NADH: ubiquinone oxidoreductase (Na+-NQR) generates an electrochemical Na+ potential driven by aerobic respiration [].; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0006814 sodium ion transport, 0055114 oxidation-reduction process
Probab=26.59 E-value=89 Score=31.09 Aligned_cols=57 Identities=19% Similarity=0.300 Sum_probs=39.0
Q ss_pred EEEEEccCCEEEEcCCCCCCCCCCeEEeceEEEEeCCC-ceEEcccccCCceeEEEEEEEeeecCCe
Q psy1265 218 RQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVGGAD-FTLVGRPLLTPGLVNVTGTIIEKDLSHT 283 (384)
Q Consensus 218 KQYKVt~GDvI~VEr~ll~aevGDkI~LdKVLLVGs~d-~TlIGrPyLega~AkVeAtVVEh~KgkK 283 (384)
+.|-|...|++-+-. .+-+++||+|.....|+.+.++ .+. |... |.++|.+.-||.|
T Consensus 27 ~~~al~~~Df~g~~P-km~VkeGD~Vk~Gq~LF~dK~~p~v~----ftsP----vsG~V~~I~RG~r 84 (257)
T PF05896_consen 27 RTVALLPDDFPGMKP-KMLVKEGDRVKAGQPLFEDKKNPGVK----FTSP----VSGTVKAINRGER 84 (257)
T ss_pred cEEEEcCcccCCCCc-cEEeccCCEEeCCCeeEeeCCCCCcE----EecC----CCeEEEEEecCCC
Confidence 455566777776665 4679999999999999998643 333 3333 4567777665544
No 22
>cd04867 TGS_YchF_C TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the family contain a C-terminal TGS domain. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=26.55 E-value=30 Score=29.19 Aligned_cols=19 Identities=26% Similarity=0.300 Sum_probs=16.7
Q ss_pred EEEECCEEEEEccCCEEEE
Q psy1265 212 IIHVLGRQTKVTPNDIIIV 230 (384)
Q Consensus 212 IVeIGGKQYKVt~GDvI~V 230 (384)
.+.+.||+|.|+.||++.+
T Consensus 63 kir~eGK~Yiv~DGDi~~f 81 (83)
T cd04867 63 KYRQEGKDYVVQDGDIIFF 81 (83)
T ss_pred hhhhhCCceEeeCCeEEEE
Confidence 4678899999999999975
No 23
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=23.56 E-value=29 Score=30.65 Aligned_cols=10 Identities=50% Similarity=0.989 Sum_probs=8.0
Q ss_pred Cccccccccc
Q psy1265 73 TSYWRGSHAL 82 (384)
Q Consensus 73 ~~~~~~~~~~ 82 (384)
.-||.|||--
T Consensus 132 kiyW~GsH~~ 141 (147)
T PF01927_consen 132 KIYWEGSHWR 141 (147)
T ss_pred CEecccccHH
Confidence 4699999964
No 24
>PF15377 DUF4604: Domain of unknown function (DUF4604)
Probab=22.28 E-value=19 Score=32.41 Aligned_cols=27 Identities=33% Similarity=0.837 Sum_probs=20.3
Q ss_pred ccceeeee-cCcceEEEEEEeeeecccccccc
Q psy1265 85 KRNIHYIQ-TEPTYLRRVTIHCLVPRGLIEGP 115 (384)
Q Consensus 85 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 115 (384)
++|++|+. .+|.||+++- -=-|.-+||
T Consensus 1 ~knlsY~~p~eP~FL~klk----~q~g~~~~~ 28 (158)
T PF15377_consen 1 AKNLSYVKPQEPPFLQKLK----AQVGYKEGP 28 (158)
T ss_pred CCCceecCCCCCHHHHHHH----HHhCCCCCc
Confidence 47999999 9999999853 123556666
No 25
>TIGR00632 vsr DNA mismatch endonuclease Vsr. All proteins in this family for which functions are known are G:T mismatch endonucleases that function in a specialized mismatch repair process used usually to repair G:T mismatches in specific sections of the genome. This family was based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Members of this family typically are found near to a DNA cytosine methyltransferase.
Probab=20.99 E-value=39 Score=29.89 Aligned_cols=11 Identities=36% Similarity=1.238 Sum_probs=9.2
Q ss_pred ccccccccccc
Q psy1265 3 ILDTSYWHGSH 13 (384)
Q Consensus 3 ~~~~~~~~~~~ 13 (384)
.+|-.||||.|
T Consensus 61 fVDGcfWHgh~ 71 (117)
T TIGR00632 61 FIHGCFWHGHH 71 (117)
T ss_pred EEcccccccCC
Confidence 36889999987
No 26
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=20.63 E-value=1.1e+02 Score=24.22 Aligned_cols=32 Identities=16% Similarity=0.211 Sum_probs=22.7
Q ss_pred ceEEEEEECCEEEEEccCCEEEEcCCC--CCCCCCCeEEe
Q psy1265 208 RLFAIIHVLGRQTKVTPNDIIIVDSNS--FAPLNGDKIKF 245 (384)
Q Consensus 208 ~MYAIVeIGGKQYKVt~GDvI~VEr~l--l~aevGDkI~L 245 (384)
+-|||+++.+.+ ..+.|++.. .++.+||.+.+
T Consensus 9 ~~~AVl~~~~~~------~~~~vp~~~LP~~~keGDvl~i 42 (71)
T PF11213_consen 9 GDYAVLELEDGE------KEIDVPRSRLPEGAKEGDVLEI 42 (71)
T ss_pred CCEEEEEECCCe------EEEEEEHHHCCCCCCcccEEEE
Confidence 569999998766 355566532 35788998877
Done!