Query gi|254780252|ref|YP_003064665.1| 30S ribosomal protein S17 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 79
No_of_seqs 106 out of 1566
Neff 5.4
Searched_HMMs 39220
Date Tue May 24 08:35:21 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780252.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00142 rps17 ribosomal prote 100.0 7.3E-33 1.9E-37 201.2 11.1 78 1-78 1-78 (84)
2 COG0186 RpsQ Ribosomal protein 100.0 7.2E-33 1.8E-37 201.2 10.3 78 1-78 6-83 (87)
3 PRK05610 rpsQ 30S ribosomal pr 100.0 3.4E-32 8.7E-37 197.5 11.0 78 1-78 4-81 (84)
4 PRK08572 rps17p 30S ribosomal 100.0 5.2E-31 1.3E-35 191.0 10.3 76 3-78 29-105 (108)
5 TIGR03630 arch_S17P archaeal r 100.0 9.5E-31 2.4E-35 189.5 9.8 74 3-76 27-101 (102)
6 TIGR03635 S17_bact 30S ribosom 100.0 2.8E-30 7E-35 187.0 9.2 71 3-73 1-71 (71)
7 pfam00366 Ribosomal_S17 Riboso 100.0 3.5E-29 8.8E-34 180.9 8.8 69 8-76 1-69 (69)
8 KOG1740 consensus 99.9 1.5E-26 3.8E-31 166.5 1.9 74 3-76 2-75 (107)
9 PTZ00241 40S ribosomal protein 99.9 7.1E-25 1.8E-29 157.2 8.3 75 3-77 68-143 (158)
10 KOG1728 consensus 99.8 3.3E-22 8.4E-27 142.6 3.4 75 3-77 68-144 (156)
11 KOG3447 consensus 99.2 1.7E-12 4.3E-17 89.1 1.6 74 3-76 10-84 (150)
12 cd04466 S1_YloQ_GTPase S1_YloQ 44.1 27 0.0007 16.5 4.1 49 6-63 1-50 (68)
13 TIGR02375 pseudoazurin pseudoa 41.6 21 0.00055 17.1 2.4 23 40-62 10-33 (123)
14 PRK10409 hydrogenase isoenzyme 41.1 19 0.00048 17.4 2.0 52 7-68 6-59 (90)
15 TIGR00074 hypC_hupF hydrogenas 32.4 25 0.00063 16.7 1.5 51 8-67 7-61 (88)
16 TIGR01017 rpsD_bact ribosomal 30.5 29 0.00073 16.4 1.6 16 46-61 136-151 (217)
17 pfam09493 DUF2389 Tryptophan-r 28.5 45 0.0012 15.3 2.3 18 61-78 6-23 (60)
18 TIGR01751 crot-CoA-red crotony 26.7 30 0.00077 16.3 1.1 19 41-59 185-203 (409)
19 pfam06107 DUF951 Bacterial pro 24.8 59 0.0015 14.7 3.0 26 50-76 1-26 (57)
20 TIGR02228 sigpep_I_arch signal 24.2 61 0.0016 14.6 3.6 31 47-77 64-96 (175)
21 PRK12565 30S ribosomal protein 22.8 43 0.0011 15.4 1.3 17 46-62 124-140 (197)
22 CHL00113 rps4 ribosomal protei 22.7 43 0.0011 15.4 1.3 17 46-62 125-141 (201)
23 PRK05338 rplS 50S ribosomal pr 22.2 67 0.0017 14.4 3.3 19 4-22 40-61 (112)
24 COG3655 Predicted transcriptio 20.9 41 0.0011 15.5 0.9 14 48-61 54-67 (73)
No 1
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=100.00 E-value=7.3e-33 Score=201.18 Aligned_cols=78 Identities=46% Similarity=0.773 Sum_probs=76.5
Q ss_pred CCCEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEEEEEE
Q ss_conf 973479999996089861999997188786413087351038986886604068789999637754320399997640
Q gi|254780252|r 1 MPKRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEESAPISKKKSWLVIDSEG 78 (79)
Q Consensus 1 m~~k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vHD~~~~~~~GD~V~i~e~rPiSK~K~~~vve~~~ 78 (79)
||+++|.|+|+|++|+|||+|++++.++||+|+|+++++++|+||||+|+|++||.|.|+|||||||+|+|.|+|+..
T Consensus 1 M~~k~~~G~VvS~km~KTv~V~V~r~~~Hp~Y~K~i~r~kky~aHDe~n~~~~GD~V~I~e~rPiSK~Krw~v~~I~~ 78 (84)
T CHL00142 1 MPIKERIGTVVSNKMQKTIVVAVENRVSHPRYGKIITKTKKYKAHDEENECNIGDQVLIQETRPLSKTKRWILKEILS 78 (84)
T ss_pred CCCEEEEEEEEECCCCCCEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCEEEEEEEEEE
T ss_conf 995069999996789984899999999658775799997989999997889999899999988888871699999996
No 2
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.2e-33 Score=201.20 Aligned_cols=78 Identities=50% Similarity=0.808 Sum_probs=75.8
Q ss_pred CCCEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEEEEEE
Q ss_conf 973479999996089861999997188786413087351038986886604068789999637754320399997640
Q gi|254780252|r 1 MPKRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEESAPISKKKSWLVIDSEG 78 (79)
Q Consensus 1 m~~k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vHD~~~~~~~GD~V~i~e~rPiSK~K~~~vve~~~ 78 (79)
|++|+|.|+|+|++|+|||+|++++.++||+|+|+++++++|+||||+|+|++||.|.|+|||||||||+|+|+|+.+
T Consensus 6 ~~~k~l~G~VvS~Km~KTvvV~ve~~~~hp~Y~K~v~r~kK~~aHde~~~~k~GD~V~I~EtRPLSKtK~~~vv~i~~ 83 (87)
T COG0186 6 VRGRVLEGVVVSDKMDKTVVVEVERKVYHPKYGKYVRRSKKYHAHDECNEAKVGDIVRIAETRPLSKTKRFVVVEIVE 83 (87)
T ss_pred CCCEEEEEEEEECCCCEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCCEEEEEEEEE
T ss_conf 483089999997568624999999999535612799987525766632337889999999824467753099999764
No 3
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=99.98 E-value=3.4e-32 Score=197.47 Aligned_cols=78 Identities=53% Similarity=0.894 Sum_probs=76.0
Q ss_pred CCCEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEEEEEE
Q ss_conf 973479999996089861999997188786413087351038986886604068789999637754320399997640
Q gi|254780252|r 1 MPKRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEESAPISKKKSWLVIDSEG 78 (79)
Q Consensus 1 m~~k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vHD~~~~~~~GD~V~i~e~rPiSK~K~~~vve~~~ 78 (79)
|++|+|.|+|+|++|+||++|++++.++||+|+|+++++++|+||||+|+|++||.|.|.|||||||+|+|+|+|+..
T Consensus 4 ~~rr~l~G~VvS~km~KTvvV~v~r~~~hpkY~K~~~r~kk~~aHDe~n~~~~GD~V~I~e~rPiSK~K~~~vv~I~~ 81 (84)
T PRK05610 4 NPRKTLQGVVVSDKMDKTIVVLVERRVKHPLYGKIVKRSKKYKAHDENNECKIGDVVKIMETRPLSKTKRWRLVEIVE 81 (84)
T ss_pred CCCCEEEEEEEECCCCCCEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCEEEEEEEEEE
T ss_conf 787589999992689872999999999768755899861899998999978999899999886778852899999995
No 4
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=99.97 E-value=5.2e-31 Score=190.97 Aligned_cols=76 Identities=38% Similarity=0.565 Sum_probs=72.6
Q ss_pred CEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEECCC-CCCCCCCCEEEEEECCCCCCCEEEEEEEEEE
Q ss_conf 347999999608986199999718878641308735103898688-6604068789999637754320399997640
Q gi|254780252|r 3 KRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDE-NNKYKVGDFVSIEESAPISKKKSWLVIDSEG 78 (79)
Q Consensus 3 ~k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vHD~-~~~~~~GD~V~i~e~rPiSK~K~~~vve~~~ 78 (79)
.|+|.|+|+|++|+|||+|+++|+++||+|+||++++++|+|||| +++|++||.|+|+|||||||+|+|+|+|+..
T Consensus 29 GriL~G~VvS~Km~KTvvV~ver~~~hpkY~K~irr~~k~~aHd~e~~~~~~GD~V~I~E~RPlSKtK~w~vv~v~e 105 (108)
T PRK08572 29 GQVLEGTVVSDKMHKTVVVEREYYHYIPKYERYEKRRSRIHAHNPECIDVKVGDTVKIAECRPLSKTKSFVVVEKKE 105 (108)
T ss_pred EEEEEEEEEECCCCCEEEEEEEEEEEECCCCEEEEEECCEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEEEEEE
T ss_conf 78999999978799809999999998414655999812588778634668899999999844677860699999986
No 5
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=99.97 E-value=9.5e-31 Score=189.54 Aligned_cols=74 Identities=35% Similarity=0.556 Sum_probs=71.3
Q ss_pred CEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEECCC-CCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf 347999999608986199999718878641308735103898688-66040687899996377543203999976
Q gi|254780252|r 3 KRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDE-NNKYKVGDFVSIEESAPISKKKSWLVIDS 76 (79)
Q Consensus 3 ~k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vHD~-~~~~~~GD~V~i~e~rPiSK~K~~~vve~ 76 (79)
.|+|.|+|+|++|+|||+|+++|+++||+|+||++++++|+|||| +++|++||.|+|+|||||||+|+|+|+|.
T Consensus 27 Gril~G~VvS~Km~KTvvV~ver~~~hpkY~k~~kr~kk~~aHd~~~~~~kvGD~V~I~E~RPlSKtK~~~Vvek 101 (102)
T TIGR03630 27 GQILEGVVVSDKMNKTVVVEREYLYYDRKYERYERRRSKIHAHNPPCIDVKEGDIVIIGETRPLSKTKSFVVLGK 101 (102)
T ss_pred EEEEEEEEEECCCCCEEEEEEEEEEECCCCCCEEEECCCEEEECCCCCCCCCCCEEEEEEEECCCCCEEEEEEEC
T ss_conf 789999999787996399999999872664607896320788897567789999999998003667457899871
No 6
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=99.97 E-value=2.8e-30 Score=187.00 Aligned_cols=71 Identities=56% Similarity=0.942 Sum_probs=69.7
Q ss_pred CEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEE
Q ss_conf 34799999960898619999971887864130873510389868866040687899996377543203999
Q gi|254780252|r 3 KRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEESAPISKKKSWLV 73 (79)
Q Consensus 3 ~k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vHD~~~~~~~GD~V~i~e~rPiSK~K~~~v 73 (79)
||+|.|+|+|++|+||++|+++|+++||+|+|+++++++|+||||+|+|++||.|.|+|||||||+|+|.|
T Consensus 1 kk~l~G~Vvs~km~KTv~V~v~r~~~hpkY~K~~~r~kk~~aHde~n~~~~GD~V~I~e~rPiSK~K~w~l 71 (71)
T TIGR03635 1 RKTLQGVVVSDKMDKTIVVLVERRVKHPLYGKIVKRTKKYHAHDENNECKVGDVVRIIETRPLSKTKRWRL 71 (71)
T ss_pred CCEEEEEEEECCCCCCEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCEEEEC
T ss_conf 97899999916898739999999997587458999838999979999789998999998867888548389
No 7
>pfam00366 Ribosomal_S17 Ribosomal protein S17.
Probab=99.96 E-value=3.5e-29 Score=180.95 Aligned_cols=69 Identities=49% Similarity=0.720 Sum_probs=68.0
Q ss_pred EEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf 999960898619999971887864130873510389868866040687899996377543203999976
Q gi|254780252|r 8 GMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEESAPISKKKSWLVIDS 76 (79)
Q Consensus 8 G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vHD~~~~~~~GD~V~i~e~rPiSK~K~~~vve~ 76 (79)
|+|+|++|+||++|+++++++||+|+|+++++++|+||||.|.|++||.|.|+|||||||+|+|.|+|+
T Consensus 1 G~Vvs~km~KTv~V~v~~~~~h~ky~k~~~r~kk~~aHde~n~~~~GD~V~I~e~RPiSKtK~~~vv~I 69 (69)
T pfam00366 1 GVVVSDKMEKTIVVRVERLVPHPKYGKYEKRTKKYPAHDPPCFRKVGDVVKIGECRPLSKTKRFRVVRV 69 (69)
T ss_pred CEEEECCCCCCEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCEEEEEEEC
T ss_conf 999847899869999999998387788999835899999978899999999998857889642999989
No 8
>KOG1740 consensus
Probab=99.92 E-value=1.5e-26 Score=166.49 Aligned_cols=74 Identities=36% Similarity=0.682 Sum_probs=71.6
Q ss_pred CEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf 34799999960898619999971887864130873510389868866040687899996377543203999976
Q gi|254780252|r 3 KRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEESAPISKKKSWLVIDS 76 (79)
Q Consensus 3 ~k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vHD~~~~~~~GD~V~i~e~rPiSK~K~~~vve~ 76 (79)
++.+.|+|+|.+|+||++|+|+++.+||+|+||.+++++|+|||+.|.|++||.|+|..|||+||+|+|.++|+
T Consensus 2 m~~~vg~VvS~kmqKTv~V~V~rl~~n~~ynryv~~~~kymahD~~n~cnvGD~VrlepsRPlSk~K~f~i~eI 75 (107)
T KOG1740 2 MKNVVGTVVSNKMQKTVKVRVDRLFFNPKYNRYVKRTSKYMAHDDKNQCNVGDRVRLEPSRPLSKTKHFIIAEI 75 (107)
T ss_pred CCCCEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHHEEECCCCCCCCCCCEEEECCCCCCCCCCEEEHHHH
T ss_conf 76520001331467406898640102678888988764103307634355465577546885553430445999
No 9
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=99.91 E-value=7.1e-25 Score=157.23 Aligned_cols=75 Identities=28% Similarity=0.437 Sum_probs=72.0
Q ss_pred CEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEEC-CCCCCCCCCCEEEEEECCCCCCCEEEEEEEEE
Q ss_conf 3479999996089861999997188786413087351038986-88660406878999963775432039999764
Q gi|254780252|r 3 KRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVH-DENNKYKVGDFVSIEESAPISKKKSWLVIDSE 77 (79)
Q Consensus 3 ~k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vH-D~~~~~~~GD~V~i~e~rPiSK~K~~~vve~~ 77 (79)
.|+|.|+|+|++|++||+|+.++++|.+||++|++++++++|| .||.++++||+|+|+||||||||++|+|+++.
T Consensus 68 G~Il~G~V~s~Km~rTIVirrdyl~yi~KY~Ryekr~~ni~aH~spcf~vk~GD~V~igECRPLSKTV~F~VlkV~ 143 (158)
T PTZ00241 68 GRILRGVVISTKMKRTIIIRRDYLHFIKKYNRYEKRHKNLPVHCSPAFDVKEGDIVVVGQCRPLSKTVRFNVLKVV 143 (158)
T ss_pred EEEEEEEEEEECCCCEEEEEEEEEEEEHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCEEEEEEEEEE
T ss_conf 5789999997258710799987652000213333145641110888622787999999874616617889999996
No 10
>KOG1728 consensus
Probab=99.85 E-value=3.3e-22 Score=142.57 Aligned_cols=75 Identities=28% Similarity=0.402 Sum_probs=70.4
Q ss_pred CEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEEC--CCCCCCCCCCEEEEEECCCCCCCEEEEEEEEE
Q ss_conf 3479999996089861999997188786413087351038986--88660406878999963775432039999764
Q gi|254780252|r 3 KRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVH--DENNKYKVGDFVSIEESAPISKKKSWLVIDSE 77 (79)
Q Consensus 3 ~k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vH--D~~~~~~~GD~V~i~e~rPiSK~K~~~vve~~ 77 (79)
-++|.|+|.++||++||+|+.++++|.+||++|.+|++++.|| ++..+.++||+|+++||||||||++|+|+.+.
T Consensus 68 Gril~G~V~k~KmqrTIvvrrdYlHy~~KY~ryekrHkN~svh~SPcFrdi~~gDiVtvGecrPLSKtvrfnVLkv~ 144 (156)
T KOG1728 68 GRILTGTVVKMKMQRTIVVRRDYLHYIKKYNRYEKRHKNMSVHVSPCFRDIQEGDIVTVGECRPLSKTVRFNVLKVI 144 (156)
T ss_pred EEEEEEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHHCCCCCCCCCHHHHCCCCCCEEEEEECCCCCCEEEEEEEEEE
T ss_conf 67887377720006889987565456576647777315876302724410665887987401004314788899985
No 11
>KOG3447 consensus
Probab=99.25 E-value=1.7e-12 Score=89.14 Aligned_cols=74 Identities=30% Similarity=0.309 Sum_probs=64.6
Q ss_pred CEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEECCCCCCCCCCCEEEEEECC-CCCCCEEEEEEEE
Q ss_conf 3479999996089861999997188786413087351038986886604068789999637-7543203999976
Q gi|254780252|r 3 KRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEESA-PISKKKSWLVIDS 76 (79)
Q Consensus 3 ~k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vHD~~~~~~~GD~V~i~e~r-PiSK~K~~~vve~ 76 (79)
.++|.|.++..+|++|+.|++.+...+|.+.+|+++++.|+|||+...|++||.|+|.+-. |.-+..+|.|.++
T Consensus 10 ~~~lmGk~ig~~~q~~akVR~~r~eld~yL~kYf~k~~~yfAhD~~~~c~vGDtVLir~lp~r~t~~V~H~v~~V 84 (150)
T KOG3447 10 AQWLMGKVIGTKMQKTAKVRVTRLELDPYLLKYFNKRKTYFAHDALQQCTVGDTVLIRALPVRRTKHVKHEVAEV 84 (150)
T ss_pred CEEEEEEEEECCCCCCHHEEEEHHHCCHHHHHHHCCCCCEEECCHHHCCCCCCEEEEEECCCCHHHHHHHHHHHH
T ss_conf 278875366012231000465365428899998632321143274341654779988507853122234555653
No 12
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=44.14 E-value=27 Score=16.48 Aligned_cols=49 Identities=22% Similarity=0.352 Sum_probs=25.3
Q ss_pred EEEEEEEECCCCEEEEEEE-EEEECCCCCEEECCCEEEEECCCCCCCCCCCEEEEEECC
Q ss_conf 9999996089861999997-188786413087351038986886604068789999637
Q gi|254780252|r 6 LQGMVVSDKSEKTIIVLVE-RRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEESA 63 (79)
Q Consensus 6 l~G~Vvs~km~KTv~V~v~-r~~~~~ky~K~~~~~kk~~vHD~~~~~~~GD~V~i~e~r 63 (79)
+.|.|++.-. .-..|..+ -..+..+.+-..+ + ..+.+-+||.|.+...-
T Consensus 1 m~G~Vi~~~g-~~y~V~~~~g~~~~c~~RG~~r-------~-~~~~~~vGD~V~~~~~~ 50 (68)
T cd04466 1 MEGLIIKAIG-GFYYVETEDGKIYECRLRGKFR-------K-DKNPPAVGDRVEFEPED 50 (68)
T ss_pred CEEEEEEEEC-CEEEEEECCCCEEEEEEEEEEC-------C-CCCCCCCCEEEEEEECC
T ss_conf 9799999999-9999993999799999734791-------5-79998642399999998
No 13
>TIGR02375 pseudoazurin pseudoazurin; InterPro: IPR012745 Pseudoazurin, also called cupredoxin, is a small, blue periplasmic protein with a single bound copper atom. Pseudoazurin is related to plastocyanins. Several examples of pseudoazurin are encoded by a neighbouring gene for, or have been shown to transfer electrons to, copper-containing nitrite reductases (IPR012746 from INTERPRO) of the same species.; GO: 0005507 copper ion binding.
Probab=41.63 E-value=21 Score=17.08 Aligned_cols=23 Identities=26% Similarity=0.177 Sum_probs=18.7
Q ss_pred EEEEECCC-CCCCCCCCEEEEEEC
Q ss_conf 03898688-660406878999963
Q gi|254780252|r 40 KRYAVHDE-NNKYKVGDFVSIEES 62 (79)
Q Consensus 40 kk~~vHD~-~~~~~~GD~V~i~e~ 62 (79)
+..+|.+| ...+..||.|++.++
T Consensus 10 k~~MVFEPA~i~a~pGDtv~FvPt 33 (123)
T TIGR02375 10 KIAMVFEPAYIKAAPGDTVTFVPT 33 (123)
T ss_pred EEEEEECCCEEEECCCCEEEEECC
T ss_conf 047761763366538976877528
No 14
>PRK10409 hydrogenase isoenzymes formation protein; Provisional
Probab=41.11 E-value=19 Score=17.38 Aligned_cols=52 Identities=23% Similarity=0.173 Sum_probs=30.5
Q ss_pred EEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEE--CCCCCCCCCCCEEEEEECCCCCCC
Q ss_conf 99999608986199999718878641308735103898--688660406878999963775432
Q gi|254780252|r 7 QGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAV--HDENNKYKVGDFVSIEESAPISKK 68 (79)
Q Consensus 7 ~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~v--HD~~~~~~~GD~V~i~e~rPiSK~ 68 (79)
-|.+++.. +..++|.+.-.. +.-+-.++ -|+..+.++||+|.+--.--||+.
T Consensus 6 Pg~Iv~I~-~~~A~Vd~~Gv~---------r~V~l~lv~~~~~~~~~~vGDyVLVHvGfAis~i 59 (90)
T PRK10409 6 PGQIRTID-GNQAKVDVCGIQ---------RDVDLTLVGSCDENGQPRVGQWVLVHVGFAMSVI 59 (90)
T ss_pred CEEEEEEC-CCEEEEEECCCE---------EEEEEEEEECCCCCCCCCCCCEEEEECCEEHEEC
T ss_conf 43899985-988999957807---------9998765404567775688989999705001117
No 15
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HUPF/HYPC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process . They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation , . .
Probab=32.39 E-value=25 Score=16.72 Aligned_cols=51 Identities=31% Similarity=0.306 Sum_probs=28.1
Q ss_pred EEEEEECCCC-EEEEEEEEEEECCCCCEEECCCEEEEE---CCCCCCCCCCCEEEEEECCCCCC
Q ss_conf 9999608986-199999718878641308735103898---68866040687899996377543
Q gi|254780252|r 8 GMVVSDKSEK-TIIVLVERRFSHPRFQKTIRRSKRYAV---HDENNKYKVGDFVSIEESAPISK 67 (79)
Q Consensus 8 G~Vvs~km~K-Tv~V~v~r~~~~~ky~K~~~~~kk~~v---HD~~~~~~~GD~V~i~e~rPiSK 67 (79)
|.|+....+. ++.|.+.... +.-+--++ .|+|.+.++||+|++--.--+|+
T Consensus 7 ~qV~~i~~~~~~A~v~~~G~~---------~~v~l~Lv~ksC~~N~~~~~GdyvLvH~G~A~~~ 61 (88)
T TIGR00074 7 GQVVEIDENIDLALVEFKGVK---------REVSLDLVGKSCDENEEVKVGDYVLVHVGFAISV 61 (88)
T ss_pred CEEEEECCCCCEEEECCCCEE---------EEEEEEECCCCCCCCCCCCCCCEEEEEEEHHHHH
T ss_conf 168885499987886015224---------6676412355446785999987763200046632
No 16
>TIGR01017 rpsD_bact ribosomal protein S4; InterPro: IPR005709 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 of 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 , . The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This family consists of organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=30.46 E-value=29 Score=16.37 Aligned_cols=16 Identities=31% Similarity=0.478 Sum_probs=14.0
Q ss_pred CCCCCCCCCCEEEEEE
Q ss_conf 8866040687899996
Q gi|254780252|r 46 DENNKYKVGDFVSIEE 61 (79)
Q Consensus 46 D~~~~~~~GD~V~i~e 61 (79)
=|+..|+.||+|.|.|
T Consensus 136 IPSy~v~~Gd~i~ikE 151 (217)
T TIGR01017 136 IPSYQVRPGDIISIKE 151 (217)
T ss_pred CCEEEECCCCEEEEEE
T ss_conf 2406707998899810
No 17
>pfam09493 DUF2389 Tryptophan-rich protein (DUF2389). Members of this family are small hypothetical proteins of 60 to 100 residues from Cyanobacteria and some Proteobacteria. Prochlorococcus marinus strains have two members, other species one only. Interestingly, of the eight most conserved residues, four are aromatic and three are invariant tryptophans. It appears all species that encode this protein can synthesize tryptophan de novo.
Probab=28.53 E-value=45 Score=15.28 Aligned_cols=18 Identities=28% Similarity=0.654 Sum_probs=12.1
Q ss_pred ECCCCCCCEEEEEEEEEE
Q ss_conf 637754320399997640
Q gi|254780252|r 61 ESAPISKKKSWLVIDSEG 78 (79)
Q Consensus 61 e~rPiSK~K~~~vve~~~ 78 (79)
+.+|+.+-+||.|+++.+
T Consensus 6 a~~p~~g~rHF~V~~~~~ 23 (60)
T pfam09493 6 AVKPINGERHFLVVEVGG 23 (60)
T ss_pred CCCCCCCCEEEEEEEEEE
T ss_conf 167438936799999852
No 18
>TIGR01751 crot-CoA-red crotonyl-CoA reductase; InterPro: IPR010085 Crotonyl-CoA reductase is responsible for the conversion of crotonyl-CoA to butyryl-CoA. In serine cycle methylotrophic bacteria this enzyme is involved in the process of acetyl-CoA to glyoxylate , . In other bacteria the enzyme is used to produce butyrate for incorporation into polyketides such as tylosin from Streptomyces fradiae and coronatine from Pseudomonas syringae ..
Probab=26.70 E-value=30 Score=16.25 Aligned_cols=19 Identities=37% Similarity=0.240 Sum_probs=13.2
Q ss_pred EEEECCCCCCCCCCCEEEE
Q ss_conf 3898688660406878999
Q gi|254780252|r 41 RYAVHDENNKYKVGDFVSI 59 (79)
Q Consensus 41 k~~vHD~~~~~~~GD~V~i 59 (79)
+.++|+.-++.+.||.|+|
T Consensus 185 RqL~g~~p~~~KpGD~VLI 203 (409)
T TIGR01751 185 RQLVGWKPAEVKPGDNVLI 203 (409)
T ss_pred HHHCCCCCCCCCCCCCEEE
T ss_conf 4420687776688883798
No 19
>pfam06107 DUF951 Bacterial protein of unknown function (DUF951). This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=24.84 E-value=59 Score=14.66 Aligned_cols=26 Identities=27% Similarity=0.735 Sum_probs=20.4
Q ss_pred CCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf 040687899996377543203999976
Q gi|254780252|r 50 KYKVGDFVSIEESAPISKKKSWLVIDS 76 (79)
Q Consensus 50 ~~~~GD~V~i~e~rPiSK~K~~~vve~ 76 (79)
+.++||+|....-.|= .+..|.|+..
T Consensus 1 ~~~igDiV~mKK~HPC-Gs~~Wei~R~ 26 (57)
T pfam06107 1 EYQIGDIVEMKKPHPC-GTNRWEIIRV 26 (57)
T ss_pred CCCCCCEEEECCCCCC-CCCEEEEEEE
T ss_conf 9656758998489888-8846899990
No 20
>TIGR02228 sigpep_I_arch signal peptidase I; InterPro: IPR001733 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidases belong to MEROPS peptidase family S26 (signal peptidase I family, clan SF), subfamily S26B. Eukaryotic microsomal signal peptidase is involved in the removal of signal peptides from secretory proteins as they pass into the endoplasmic reticulum lumen . The peptidase is more complex than its mitochondrial and bacterial counterparts, containing a number of subunits, ranging from two in the chicken oviduct peptidase, to five in the dog pancreas protein . They share sequence similarity with the bacterial leader peptidases (family S26A), although activity here is mediated by a serine/histidine dyad rather than a serine/lysine dyad . Archaeal signal peptidases also belong to this group. ; GO: 0008233 peptidase activity, 0006465 signal peptide processing, 0006508 proteolysis, 0016020 membrane.
Probab=24.16 E-value=61 Score=14.58 Aligned_cols=31 Identities=16% Similarity=0.259 Sum_probs=24.2
Q ss_pred CCCCCCCCCEEEEEECCC--CCCCEEEEEEEEE
Q ss_conf 866040687899996377--5432039999764
Q gi|254780252|r 47 ENNKYKVGDFVSIEESAP--ISKKKSWLVIDSE 77 (79)
Q Consensus 47 ~~~~~~~GD~V~i~e~rP--iSK~K~~~vve~~ 77 (79)
..++.+.||++...+-.+ ..+-.-|+|.|+.
T Consensus 64 ~~~~~~~GDvI~y~~~~~~WyG~~v~HRv~~~~ 96 (175)
T TIGR02228 64 DPEDIQVGDVIVYKSEGKRWYGTPVIHRVIEIK 96 (175)
T ss_pred CHHHCCCCCEEEEEECCCCCCCEEEEEEEEEEE
T ss_conf 766630156799924699523538999999889
No 21
>PRK12565 30S ribosomal protein S4; Provisional
Probab=22.76 E-value=43 Score=15.43 Aligned_cols=17 Identities=29% Similarity=0.409 Sum_probs=14.2
Q ss_pred CCCCCCCCCCEEEEEEC
Q ss_conf 88660406878999963
Q gi|254780252|r 46 DENNKYKVGDFVSIEES 62 (79)
Q Consensus 46 D~~~~~~~GD~V~i~e~ 62 (79)
=|+..|++||.|.+.|.
T Consensus 124 IPSy~vk~GDvI~vkek 140 (197)
T PRK12565 124 IPSYEVKVGDEITLREK 140 (197)
T ss_pred CCCEEECCCCEEEECHH
T ss_conf 88767069999997332
No 22
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=22.74 E-value=43 Score=15.41 Aligned_cols=17 Identities=18% Similarity=0.317 Sum_probs=14.1
Q ss_pred CCCCCCCCCCEEEEEEC
Q ss_conf 88660406878999963
Q gi|254780252|r 46 DENNKYKVGDFVSIEES 62 (79)
Q Consensus 46 D~~~~~~~GD~V~i~e~ 62 (79)
=|+..|++||+|.+.|-
T Consensus 125 IPSy~vk~GDvI~v~~k 141 (201)
T CHL00113 125 IPSYRCKPRDIITIKDK 141 (201)
T ss_pred CCCEEEECCCEEEECCC
T ss_conf 78758427998997534
No 23
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=22.16 E-value=67 Score=14.35 Aligned_cols=19 Identities=21% Similarity=0.485 Sum_probs=15.3
Q ss_pred EEEEEEEEEEC---CCCEEEEE
Q ss_conf 47999999608---98619999
Q gi|254780252|r 4 RVLQGMVVSDK---SEKTIIVL 22 (79)
Q Consensus 4 k~l~G~Vvs~k---m~KTv~V~ 22 (79)
|.|.|+|++.+ .+.|.+|+
T Consensus 40 Q~feGvvI~~~~~G~~~tftvR 61 (112)
T PRK05338 40 QAFEGVVIARRGRGLNETFTVR 61 (112)
T ss_pred EEEEEEEEEEECCCCCCEEEEE
T ss_conf 7568999997378876238899
No 24
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=20.93 E-value=41 Score=15.51 Aligned_cols=14 Identities=14% Similarity=0.199 Sum_probs=11.0
Q ss_pred CCCCCCCCEEEEEE
Q ss_conf 66040687899996
Q gi|254780252|r 48 NNKYKVGDFVSIEE 61 (79)
Q Consensus 48 ~~~~~~GD~V~i~e 61 (79)
.-+|++||++.+..
T Consensus 54 ~LeCqpgDiley~~ 67 (73)
T COG3655 54 ALECQPGDILEYVP 67 (73)
T ss_pred HCCCCHHHEEEEEC
T ss_conf 83898405457716
Done!