Query 031743
Match_columns 153
No_of_seqs 115 out of 1074
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 04:44:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031743.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031743hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01038 L22_arch ribosomal p 100.0 8.2E-60 1.8E-64 364.0 16.2 148 4-152 1-148 (150)
2 PTZ00178 60S ribosomal protein 100.0 7.5E-59 1.6E-63 367.3 16.3 151 1-152 1-151 (181)
3 PRK04223 rpl22p 50S ribosomal 100.0 2.1E-58 4.5E-63 357.2 16.1 148 1-152 3-150 (153)
4 COG0091 RplV Ribosomal protein 100.0 1.2E-42 2.6E-47 259.5 9.8 115 4-152 1-116 (120)
5 CHL00034 rpl22 ribosomal prote 100.0 6.5E-40 1.4E-44 244.1 13.2 110 10-152 5-115 (117)
6 PRK00565 rplV 50S ribosomal pr 100.0 3.6E-38 7.9E-43 232.8 12.5 107 13-152 1-108 (112)
7 TIGR01044 rplV_bact ribosomal 100.0 2E-38 4.3E-43 231.2 10.5 102 17-151 1-103 (103)
8 KOG3353 60S ribosomal protein 100.0 4.1E-40 8.8E-45 258.7 -2.2 145 7-152 1-145 (175)
9 cd00336 Ribosomal_L22 Ribosoma 100.0 1.1E-35 2.3E-40 216.3 12.2 104 15-151 1-105 (105)
10 PF00237 Ribosomal_L22: Riboso 100.0 1.6E-36 3.6E-41 220.8 7.5 103 17-152 1-104 (105)
11 PRK12279 50S ribosomal protein 100.0 1.6E-35 3.5E-40 250.4 12.3 107 13-152 1-109 (311)
12 KOG1711 Mitochondrial/chloropl 99.9 7.3E-24 1.6E-28 170.9 7.0 114 4-152 63-178 (218)
13 PRK11235 bifunctional antitoxi 70.8 18 0.00038 25.3 5.6 65 27-112 14-79 (80)
14 TIGR01999 iscU FeS cluster ass 67.3 37 0.00079 25.0 7.1 70 14-106 53-122 (124)
15 PRK11325 scaffold protein; Pro 65.2 35 0.00075 25.3 6.6 70 13-105 54-123 (127)
16 COG3077 RelB DNA-damage-induci 60.4 16 0.00035 26.1 3.9 34 29-63 19-52 (88)
17 PF04221 RelB: RelB antitoxin; 57.3 15 0.00032 25.2 3.2 35 27-62 14-48 (83)
18 PF01713 Smr: Smr domain; Int 56.0 14 0.0003 24.8 2.9 36 36-71 3-40 (83)
19 KOG3361 Iron binding protein i 55.3 11 0.00024 29.3 2.4 34 29-62 96-129 (157)
20 PF13852 DUF4197: Protein of u 55.1 25 0.00054 28.5 4.6 20 30-49 84-103 (202)
21 TIGR03419 NifU_clost FeS clust 52.5 90 0.0019 22.8 7.5 70 13-105 48-118 (121)
22 PF12637 TSCPD: TSCPD domain; 51.1 79 0.0017 22.3 6.2 36 15-50 26-66 (95)
23 COG1094 Predicted RNA-binding 46.3 18 0.00038 29.5 2.4 30 21-50 59-89 (194)
24 PF06738 DUF1212: Protein of u 44.7 72 0.0016 24.6 5.6 49 13-61 51-104 (193)
25 TIGR02384 RelB_DinJ addiction 42.3 50 0.0011 22.9 4.0 35 27-62 15-49 (83)
26 COG0822 IscU NifU homolog invo 41.8 39 0.00085 26.0 3.7 86 14-105 56-143 (150)
27 PF11116 DUF2624: Protein of u 41.3 21 0.00046 25.3 1.9 26 17-42 24-49 (85)
28 PF01466 Skp1: Skp1 family, di 40.1 37 0.00081 22.9 3.0 21 29-49 36-56 (78)
29 PHA02754 hypothetical protein; 37.0 39 0.00084 22.6 2.5 26 27-52 2-27 (67)
30 smart00463 SMR Small MutS-rela 37.0 29 0.00063 23.1 2.0 23 36-58 6-28 (80)
31 PF04703 FaeA: FaeA-like prote 36.9 41 0.00088 22.2 2.7 26 25-51 14-39 (62)
32 PF03793 PASTA: PASTA domain; 35.0 26 0.00057 22.0 1.5 15 36-50 6-20 (63)
33 PF07778 CENP-I: Mis6 ; Inter 34.1 41 0.00088 31.1 3.1 46 39-113 56-101 (511)
34 cd06664 IscU_like Iron-sulfur 33.4 1E+02 0.0022 22.1 4.6 41 14-54 50-90 (123)
35 TIGR02000 NifU_proper Fe-S clu 26.9 3.2E+02 0.0069 23.2 7.2 70 14-105 54-123 (290)
36 PF01592 NifU_N: NifU-like N t 26.7 2.4E+02 0.0052 20.5 5.7 71 13-105 52-122 (126)
37 PF04921 XAP5: XAP5, circadian 25.1 1.8E+02 0.0038 24.4 5.1 96 43-146 86-185 (239)
38 PF04485 NblA: Phycobilisome d 24.5 1.5E+02 0.0033 19.2 3.7 24 28-51 11-34 (53)
39 COG3812 Uncharacterized protei 24.3 43 0.00094 26.7 1.3 27 90-116 43-69 (193)
40 TIGR01994 SUF_scaf_2 SUF syste 20.9 2.4E+02 0.0053 20.9 4.8 79 14-100 53-136 (137)
No 1
>TIGR01038 L22_arch ribosomal protein L22(archaeal)/L17(eukaryotic/archaeal). This model describes the ribosomal protein of the eukaryotic cytosol and of the Archaea, variously designated as L17, L22, and L23. The corresponding bacterial homolog, described by a separate model, is designated L22.
Probab=100.00 E-value=8.2e-60 Score=364.01 Aligned_cols=148 Identities=53% Similarity=0.765 Sum_probs=146.1
Q ss_pred ccCCCCCCCceEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCC
Q 031743 4 YSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGR 83 (153)
Q Consensus 4 ys~~~~~~~~~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr 83 (153)
||++++||+++++|.++++++||+|+++||++||||++++|+++|++|+++|+||||++|++|+||++|+++ ++|++||
T Consensus 1 ys~~~~~~~~~akA~~~~~riS~kk~r~va~~IrG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~-~~~~~gR 79 (150)
T TIGR01038 1 YSYKPEDPTKSAKARGRNLRVSFKNARETARAIRGMELDKARKYLEDVIEMKRAVPFRRYNGKVGHRRGLKE-WGWTAGR 79 (150)
T ss_pred CCcCCCCCCeeEEEEeCCCcccHHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccc-cccccCC
Confidence 899999999999999999999999999999999999999999999999999999999999999999999999 6999999
Q ss_pred CcchhhHHHHHHHHHHHHHHHHcCCCCCCeEEEEEEECCCccccCccccCCCCcccccccceeEEEEEe
Q 031743 84 WPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINRMFLVLFHLCLIFL 152 (153)
Q Consensus 84 ~p~KaA~~i~klL~sa~aNA~~kgld~d~L~I~~i~v~kG~~~kr~~pRA~GRa~~~~k~~~hI~ivl~ 152 (153)
||+|+|+.|+|||+||++||+++|+|+|+|||.||+||+|+++||++|||+||++|+++++|||||+|+
T Consensus 80 ~P~Kaa~~i~klL~sA~aNA~~~gld~d~L~I~~i~vnkg~~~kR~~prA~GRa~~~~k~~~HI~Iil~ 148 (150)
T TIGR01038 80 YPVKAAKFILKVLQNAEANAEYKGLDVEKLVIIHIQANKGPKIRRWMPRAFGRATPYNSSPTHIELVVE 148 (150)
T ss_pred CchHHHHHHHHHHHHHHHHHHhcCCChhHeEEEEEEECCCCccCCCCCccCCCCCcccCCCceEEEEEe
Confidence 999999999999999999999999999999999999999999999999999999999999999999986
No 2
>PTZ00178 60S ribosomal protein L17; Provisional
Probab=100.00 E-value=7.5e-59 Score=367.32 Aligned_cols=151 Identities=64% Similarity=0.995 Sum_probs=148.7
Q ss_pred CccccCCCCCCCceEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCC
Q 031743 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNG 80 (153)
Q Consensus 1 ~~~ys~~~~~~~~~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~ 80 (153)
||+||++.+||+++++|.++++++||+|+++||++||||++++|+++|++||++|++|||+|||+|+||++|+.+ |+.+
T Consensus 1 ~~~Ys~~~~n~~~~akA~~~~~riSpkk~r~Va~~IRGk~v~~A~~~L~~Vi~~k~~VPf~r~~~~vgh~~~~~~-~~~~ 79 (181)
T PTZ00178 1 MVKYARKPQNPSKSAKAKGSDLRVHFKNTYETARAIKGMKLARAQKYLEDVLAKKRCVPFRRFNGGVGRTAQAKE-FGHT 79 (181)
T ss_pred CCccccCCCCCCceEEEEeCCcccchHHHHHHHHHHcCCcHHHHHHHHHHHHhccccccceeecCCccccccccc-cccc
Confidence 899999998899999999999999999999999999999999999999999999999999999999999999988 6889
Q ss_pred CCCCcchhhHHHHHHHHHHHHHHHHcCCCCCCeEEEEEEECCCccccCccccCCCCcccccccceeEEEEEe
Q 031743 81 QGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINRMFLVLFHLCLIFL 152 (153)
Q Consensus 81 ~gr~p~KaA~~i~klL~sa~aNA~~kgld~d~L~I~~i~v~kG~~~kr~~pRA~GRa~~~~k~~~hI~ivl~ 152 (153)
+||||+|+|..|+|+|+||++||+++|+|+|+|||.||.||+|++++|++|||+|||+|+++++|||||+|+
T Consensus 80 ~GR~P~KaA~~i~KlL~SA~aNAe~~gld~d~L~I~~i~v~kG~~lKR~~pRA~GRA~~i~k~t~HI~Ivl~ 151 (181)
T PTZ00178 80 QGRWPEKSVKFVLSLLKNAEANAEAKGLDVEKLVISHVQVNRAPRGRRRTYRAHGRINPFMSSPCHIELIAT 151 (181)
T ss_pred cCcCcHHHHHHHHHHHHHHHHHHHhcCCChhHeEEEEEEECCCcccCCCCCccCCCcCcccCCceeEEEEEE
Confidence 999999999999999999999999999999999999999999999999999999999999999999999985
No 3
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=100.00 E-value=2.1e-58 Score=357.18 Aligned_cols=148 Identities=39% Similarity=0.546 Sum_probs=144.9
Q ss_pred CccccCCCCCCCceEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCC
Q 031743 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNG 80 (153)
Q Consensus 1 ~~~ys~~~~~~~~~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~ 80 (153)
|++||+++ +++++++|.++++++||+|+++||++||||++++|+++|++|+++|+||||++|++|+||++|+ ++|+
T Consensus 3 ~~~ys~~~-~~~~~akA~~~~~rvS~kk~r~va~~IRG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~---~~~~ 78 (153)
T PRK04223 3 RINYSVKA-DPEKTAKAMGRELPISPKHSVEIAREIRGMKLDEAKAYLEDVIALKRAVPFKRHNKKVGHRKGI---DGWP 78 (153)
T ss_pred ccccccCC-CCCceEEEEeCCCccChHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccc---cccc
Confidence 67899999 6999999999999999999999999999999999999999999999999999999999999999 6789
Q ss_pred CCCCcchhhHHHHHHHHHHHHHHHHcCCCCCCeEEEEEEECCCccccCccccCCCCcccccccceeEEEEEe
Q 031743 81 QGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINRMFLVLFHLCLIFL 152 (153)
Q Consensus 81 ~gr~p~KaA~~i~klL~sa~aNA~~kgld~d~L~I~~i~v~kG~~~kr~~pRA~GRa~~~~k~~~hI~ivl~ 152 (153)
+||||+|+|++|+|+|+||++||+++|+|+|+|||+||+||+|++++|++|||+||++|+.+++|||||+|+
T Consensus 79 ~gr~PkKaa~~i~KlL~sA~aNA~~~gld~d~L~I~~i~v~kg~~~kR~~prA~GRa~~~~k~~sHI~Iil~ 150 (153)
T PRK04223 79 AGRYPVKAAKAFLKLLENAEANAEYKGLDTEKLVIVHIAAHKGRVIKGYMPRAFGRATPKNTETVNIEVILE 150 (153)
T ss_pred cCCCchHHHHHHHHHHHHHHHHHHhcCCChhHeEEEEEEECCCCCCCCcCcccCCCCCcccCCCceEEEEEE
Confidence 999999999999999999999999999999999999999999999999999999999999999999999986
No 4
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-42 Score=259.49 Aligned_cols=115 Identities=36% Similarity=0.460 Sum_probs=111.9
Q ss_pred ccCCCCCCCceEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCC
Q 031743 4 YSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGR 83 (153)
Q Consensus 4 ys~~~~~~~~~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr 83 (153)
||+..+ |+++++|.++++++||+|+++||++||||++++|+++|+ |.
T Consensus 1 y~~~~~-~~~~akA~~r~~riSpkk~r~Va~~IrG~~v~~A~~~L~---------------------------~~----- 47 (120)
T COG0091 1 YSAKVE-PEMEAKAKARYLRISPKKARLVADLIRGKKVAEALAILE---------------------------FV----- 47 (120)
T ss_pred CCcccc-hhhhhHhhhccCcCChHHHHHHHHHHcCCcHHHHHHHHH---------------------------hC-----
Confidence 788786 899999999999999999999999999999999999999 77
Q ss_pred CcchhhHHHHHHHHHHHHHHHH-cCCCCCCeEEEEEEECCCccccCccccCCCCcccccccceeEEEEEe
Q 031743 84 WPVKSAKFILDLLKNAESNAEV-KGLDVDALYISHIQVNQAQKQRRRTYRAHGRINRMFLVLFHLCLIFL 152 (153)
Q Consensus 84 ~p~KaA~~i~klL~sa~aNA~~-kgld~d~L~I~~i~v~kG~~~kr~~pRA~GRa~~~~k~~~hI~ivl~ 152 (153)
|+|+|+.|+|+|+||++||++ +|||+|+|||.||+||+|+++||++|||+||++++++++|||||+|+
T Consensus 48 -pkKaa~~v~KvL~sA~aNAe~n~gLd~d~L~V~~i~v~~gp~lKR~~pRA~GRa~~i~k~tshItvvv~ 116 (120)
T COG0091 48 -PKKAAKLVKKVLESAIANAENNKGLDPDKLVVSHIAVDKGPVLKRFMPRARGRATRINKRTSHITVVVR 116 (120)
T ss_pred -hHHHHHHHHHHHHHHHhhHHhccCCChHHEEEEEEEeCCCceeeeecccccCccccccCCCceEEEEEe
Confidence 999999999999999999998 79999999999999999999999999999999999999999999986
No 5
>CHL00034 rpl22 ribosomal protein L22
Probab=100.00 E-value=6.5e-40 Score=244.08 Aligned_cols=110 Identities=25% Similarity=0.317 Sum_probs=106.5
Q ss_pred CCCceEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcchhh
Q 031743 10 NPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSA 89 (153)
Q Consensus 10 ~~~~~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA 89 (153)
.++++++|.++++++||+|+++||++||||++++|+.||+ |. |+|+|
T Consensus 5 ~~~~~~~A~~~~ir~SpkK~r~va~~IRG~~v~~A~~~L~---------------------------~~------pkk~a 51 (117)
T CHL00034 5 KSTTEVYALAKYIRMSAHKARRVIDQIRGRSYEEALMILE---------------------------FM------PYRAC 51 (117)
T ss_pred CCCceEEEEeCCcccCHHHHHHHHHHHcCCcHHHHHHHHH---------------------------HC------cHHHH
Confidence 4678999999999999999999999999999999999999 78 99999
Q ss_pred HHHHHHHHHHHHHHH-HcCCCCCCeEEEEEEECCCccccCccccCCCCcccccccceeEEEEEe
Q 031743 90 KFILDLLKNAESNAE-VKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINRMFLVLFHLCLIFL 152 (153)
Q Consensus 90 ~~i~klL~sa~aNA~-~kgld~d~L~I~~i~v~kG~~~kr~~pRA~GRa~~~~k~~~hI~ivl~ 152 (153)
+.|+|+|+||++||+ ++|+|+|+|||.||+||+|+++||++|||+||++++++++|||+|+|+
T Consensus 52 ~~i~klL~sA~aNA~~~~gld~d~L~I~~i~v~~G~~~KR~~prArGRa~~i~k~~sHI~Vvl~ 115 (117)
T CHL00034 52 YPILKLVYSAAANASHNMGLNKANLFISKAEVDEGPTLKRFRPRAQGRSYPIKKPTCHITIVLK 115 (117)
T ss_pred HHHHHHHHHHHHHHHHccCCCccceEEEEEEECCCCccCCCCcccCCCCCcccCCCccEEEEEe
Confidence 999999999999995 589999999999999999999999999999999999999999999986
No 6
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=100.00 E-value=3.6e-38 Score=232.83 Aligned_cols=107 Identities=30% Similarity=0.404 Sum_probs=104.1
Q ss_pred ceEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcchhhHHH
Q 031743 13 KSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFI 92 (153)
Q Consensus 13 ~~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA~~i 92 (153)
++++|.++++++||+|+++||++||||++++|+.+|+ |. |+|+|+.|
T Consensus 1 ~~~~A~~~~~~~SpkK~~~v~~~IrG~~v~~A~~~L~---------------------------~~------pkk~a~~i 47 (112)
T PRK00565 1 MEAKAKARYVRVSPRKARLVADLIRGKKVEEALAILK---------------------------FS------PKKAARLV 47 (112)
T ss_pred CceEEEeCccccCHHHHHHHHHHHcCCcHHHHHHHHH---------------------------HC------cHhHHHHH
Confidence 4689999999999999999999999999999999999 76 99999999
Q ss_pred HHHHHHHHHHHHH-cCCCCCCeEEEEEEECCCccccCccccCCCCcccccccceeEEEEEe
Q 031743 93 LDLLKNAESNAEV-KGLDVDALYISHIQVNQAQKQRRRTYRAHGRINRMFLVLFHLCLIFL 152 (153)
Q Consensus 93 ~klL~sa~aNA~~-kgld~d~L~I~~i~v~kG~~~kr~~pRA~GRa~~~~k~~~hI~ivl~ 152 (153)
+|+|+||++||++ +|+|+|+|||.+++||+|+++||++|||+||++++++++|||+|+|+
T Consensus 48 ~k~L~sA~aNA~~~~g~d~~~L~I~~~~v~~G~~~Kr~~~rArGR~~~i~k~~~hi~vvL~ 108 (112)
T PRK00565 48 KKVLKSAIANAENNHGLDIDNLVVKEAYVDEGPTLKRFRPRARGRASRIRKRTSHITVVVA 108 (112)
T ss_pred HHHHHHHHHHHHhccCCChhHeEEEEEEECCCCccCCCCCCcCCCCCccccCCccEEEEEE
Confidence 9999999999998 89999999999999999999999999999999999999999999985
No 7
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=100.00 E-value=2e-38 Score=231.25 Aligned_cols=102 Identities=30% Similarity=0.391 Sum_probs=98.6
Q ss_pred EeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcchhhHHHHHHH
Q 031743 17 ARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLL 96 (153)
Q Consensus 17 A~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA~~i~klL 96 (153)
|.++++++||+|+++||++||||++++|+.||+ |. |+|+|..|+|+|
T Consensus 1 a~~r~~r~SpkK~~~va~~IrG~~v~~A~~~L~---------------------------f~------pkk~a~~i~klL 47 (103)
T TIGR01044 1 AKARFVRISPRKARLVADLIRGKSVSQALDILR---------------------------FT------PKKAAPLIKKVL 47 (103)
T ss_pred CcccccccCHHHHHHHHHHHcCCcHHHHHHHHh---------------------------hC------CHhHHHHHHHHH
Confidence 567999999999999999999999999999999 76 999999999999
Q ss_pred HHHHHHHH-HcCCCCCCeEEEEEEECCCccccCccccCCCCcccccccceeEEEEE
Q 031743 97 KNAESNAE-VKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINRMFLVLFHLCLIF 151 (153)
Q Consensus 97 ~sa~aNA~-~kgld~d~L~I~~i~v~kG~~~kr~~pRA~GRa~~~~k~~~hI~ivl 151 (153)
+||++||+ ++|+|+|+|||.|++||+|+++||++|||+||++++++++|||+|+|
T Consensus 48 ~sA~aNA~~~~~ld~~~L~I~~~~v~~G~~~kr~~~rarGRa~~i~k~~~hi~vvl 103 (103)
T TIGR01044 48 ASAIANAEHNYGLDADNLVVVTIFVDEGPTLKRIRPRAKGRASRIRKRTSHITVVV 103 (103)
T ss_pred HHHHHHHHHccCCChHheEEEEEEECCCCcccCCCCCCCCCCCcccCCCccEEEeC
Confidence 99999996 58999999999999999999999999999999999999999999986
No 8
>KOG3353 consensus 60S ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.1e-40 Score=258.71 Aligned_cols=145 Identities=65% Similarity=0.984 Sum_probs=141.9
Q ss_pred CCCCCCceEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcc
Q 031743 7 EPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPV 86 (153)
Q Consensus 7 ~~~~~~~~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~ 86 (153)
+|+++++.++|++.++++|+|++++.+..|+++++..|+.+|++|+..++|+||.+|++|+|++.|+++ |+|.+||||+
T Consensus 1 ~~~~~~k~~karg~~lrv~fKn~r~~~~~i~~~~~~~a~~~l~~v~~~~~c~p~~~~~~g~g~~~q~k~-~~~~~~rwpk 79 (175)
T KOG3353|consen 1 DPENPTKSCKARGSNLRVHFKNTRETAQTIKCMELLKATVYLKDVILQKICVPFRRYNGGVGRTAQAKQ-WGWTQGRWPK 79 (175)
T ss_pred CccccchhhhcccccEEEEeccCcccchhhcCcccccceeeeccchhhcccccceecCCCcCccchhhh-hccccCcccc
Confidence 478999999999999999999999999999999999999999999999999999999999999999999 6999999999
Q ss_pred hhhHHHHHHHHHHHHHHHHcCCCCCCeEEEEEEECCCccccCccccCCCCcccccccceeEEEEEe
Q 031743 87 KSAKFILDLLKNAESNAEVKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINRMFLVLFHLCLIFL 152 (153)
Q Consensus 87 KaA~~i~klL~sa~aNA~~kgld~d~L~I~~i~v~kG~~~kr~~pRA~GRa~~~~k~~~hI~ivl~ 152 (153)
|+|++++-+|+||++||+.+|+|+|.|+|.||+||++|++.|+++|||||.+++.+.+|||++||+
T Consensus 80 ksaefll~~LkN~esnaElkgldVDsLvIehiqvnkApKm~~rtyraHg~in~y~ssP~hie~il~ 145 (175)
T KOG3353|consen 80 KSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILT 145 (175)
T ss_pred hHHHHHHHHHHhhhhcccccCcCcceeEeeehhhcccchhhhHHHHhhcccccccCChHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999998875
No 9
>cd00336 Ribosomal_L22 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.
Probab=100.00 E-value=1.1e-35 Score=216.34 Aligned_cols=104 Identities=44% Similarity=0.587 Sum_probs=99.7
Q ss_pred EEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcchhhHHHHH
Q 031743 15 CKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILD 94 (153)
Q Consensus 15 ~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA~~i~k 94 (153)
++|..+++++||||+++++++||||+++||+++|+ |. |+|+|..|+|
T Consensus 1 ~~a~~~~i~~S~kK~~~v~~~Irg~~v~~A~~~L~---------------------------~~------~kk~a~~i~k 47 (105)
T cd00336 1 AKAKGRYLRISPKKARLVARLIRGMSVDEALAQLE---------------------------FV------PKKAAKIILK 47 (105)
T ss_pred CEEEEccCccCHHHHHHHHHHHcCCcHHHHHHHHH---------------------------hC------CHHHHHHHHH
Confidence 47889999999999999999999999999999999 78 9999999999
Q ss_pred HHHHHHHHHHHcC-CCCCCeEEEEEEECCCccccCccccCCCCcccccccceeEEEEE
Q 031743 95 LLKNAESNAEVKG-LDVDALYISHIQVNQAQKQRRRTYRAHGRINRMFLVLFHLCLIF 151 (153)
Q Consensus 95 lL~sa~aNA~~kg-ld~d~L~I~~i~v~kG~~~kr~~pRA~GRa~~~~k~~~hI~ivl 151 (153)
+|+||.+||++++ +|+|+|||.|++||+|++++|++|||+||++++++++|||+|+|
T Consensus 48 ~l~sa~~nA~~~~~~~~~~L~I~~~~v~~g~~~kr~~~rarGR~~~~~k~~~hi~ivl 105 (105)
T cd00336 48 LLKSAEANAENNGLDDPDKLYIKHIQVNKGPTLKRRRPRARGRANPIRKRTCHITVVL 105 (105)
T ss_pred HHHHHHHhHHHcCCCCccceEEEEEEECCCCcccCCCcCCCCCCcccccCceeEEEeC
Confidence 9999999999865 56999999999999999999999999999999999999999986
No 10
>PF00237 Ribosomal_L22: Ribosomal protein L22p/L17e; InterPro: IPR001063 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 L22 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L22 is known to bind 23S rRNA. It belongs to a family of ribosomal proteins which includes: bacterial L22; algal and plant chloroplast L22 (in legumes L22 is encoded in the nucleus instead of the chloroplast); cyanelle L22; archaebacterial L22; mammalian L17; plant L17 and yeast YL17.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3CD6_R 1Q7Y_S 1VQ6_R 1YI2_R 1QVF_Q 3CCR_R 3CCU_R 3CCL_R 1YJ9_R 3CCQ_R ....
Probab=100.00 E-value=1.6e-36 Score=220.77 Aligned_cols=103 Identities=41% Similarity=0.514 Sum_probs=99.3
Q ss_pred EeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcchhhHHHHHHH
Q 031743 17 ARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLL 96 (153)
Q Consensus 17 A~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA~~i~klL 96 (153)
|.++++++||||++++|++||||++++|+.+|+ |. |+|+|..|+++|
T Consensus 1 A~~~~i~~S~kk~~~v~~~Irg~~v~~A~~~L~---------------------------~~------~~k~a~~i~k~L 47 (105)
T PF00237_consen 1 AKLRNIRISPKKLREVARLIRGMSVDEAIAQLK---------------------------FV------PKKAAKFILKLL 47 (105)
T ss_dssp EEEEEESS-HHHHHHHHHHHTTSBHHHHHHHHH---------------------------HH------SSHHHHHHHHHH
T ss_pred CccccccCCHHHHHHHHHHHcCCCHHHHHHHHH---------------------------hC------cHHHHHHHHhhH
Confidence 678999999999999999999999999999999 66 999999999999
Q ss_pred HHHHHHHH-HcCCCCCCeEEEEEEECCCccccCccccCCCCcccccccceeEEEEEe
Q 031743 97 KNAESNAE-VKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINRMFLVLFHLCLIFL 152 (153)
Q Consensus 97 ~sa~aNA~-~kgld~d~L~I~~i~v~kG~~~kr~~pRA~GRa~~~~k~~~hI~ivl~ 152 (153)
+||.+||+ ++|+|+|+|||.+++||+|+.++|++|||+||++++++++|||+|+|+
T Consensus 48 ~~a~~nA~~~~g~d~~~L~I~~~~v~~g~~~kr~~~rArGR~~~~~k~~~hi~vvl~ 104 (105)
T PF00237_consen 48 KSAIANAENNKGLDPDNLYISEIWVNKGPYLKRIRPRARGRAGPIRKRTSHITVVLK 104 (105)
T ss_dssp HHHHHHHHHHCTSTCGGEEEEEEEEEEEEEEEEEEEECTTEEEEEEEEEEEEEEEEE
T ss_pred HHHHhhcccccccccCceEEEEEEEEecccccCCCcCcCCCccCeecCceEEEEEEe
Confidence 99999999 799999999999999999999999999999999999999999999986
No 11
>PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional
Probab=100.00 E-value=1.6e-35 Score=250.38 Aligned_cols=107 Identities=28% Similarity=0.413 Sum_probs=104.2
Q ss_pred ceEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcchhhHHH
Q 031743 13 KSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFI 92 (153)
Q Consensus 13 ~~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA~~i 92 (153)
|+++|.++++++||+|+++||++||||++++|+.+|+ |. |+|+|..|
T Consensus 1 M~akA~~r~iriSpkK~R~Va~~IRGk~v~~Al~~L~---------------------------~~------PkKaA~~I 47 (311)
T PRK12279 1 MTNKVIQRNIHISHRKASLVIDLVRNKPVHEAIRILS---------------------------NT------PKKFAPIV 47 (311)
T ss_pred CceEEEeCCcccCHHHHHHHHHHHcCCcHHHHHHHHH---------------------------hC------CHHHHHHH
Confidence 4689999999999999999999999999999999999 78 99999999
Q ss_pred HHHHHHHHHHHH--HcCCCCCCeEEEEEEECCCccccCccccCCCCcccccccceeEEEEEe
Q 031743 93 LDLLKNAESNAE--VKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINRMFLVLFHLCLIFL 152 (153)
Q Consensus 93 ~klL~sa~aNA~--~kgld~d~L~I~~i~v~kG~~~kr~~pRA~GRa~~~~k~~~hI~ivl~ 152 (153)
+|||+||++||+ ++|||+|+|||.||+||+|+++||++|||+||++++++++|||||+|+
T Consensus 48 ~KlLkSA~ANAe~~n~gld~d~L~I~~~~VdkGp~lKR~~PRArGRA~~i~KrtsHItIvl~ 109 (311)
T PRK12279 48 LKLLNSAISNVQHNSKDMDPSKLYIYKIVANQGPTMKRTLPRAKGSADQLFKRTTHLEIVLS 109 (311)
T ss_pred HHHHHHHHHHHHHhhcCCChhHeEEEEEEECCCCcccCCCCccCCCCCcccCCCccEEEEEe
Confidence 999999999999 489999999999999999999999999999999999999999999985
No 12
>KOG1711 consensus Mitochondrial/chloroplast ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=7.3e-24 Score=170.90 Aligned_cols=114 Identities=26% Similarity=0.305 Sum_probs=106.0
Q ss_pred ccCCCCCCCceEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCC
Q 031743 4 YSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGR 83 (153)
Q Consensus 4 ys~~~~~~~~~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr 83 (153)
|++.|.- .++.|....++.|+||++.+|++|+||++++|+.+|+ |+
T Consensus 63 l~~~p~~--~eVya~~~~Ik~S~kK~~~l~~lirgm~v~~AL~Ql~---------------------------~s----- 108 (218)
T KOG1711|consen 63 LPFEPKR--PEVYACSKSIKSSPKKVWLLARLIRGMSVEEALMQLE---------------------------FS----- 108 (218)
T ss_pred CCCCCcc--hhHHHHHHHHHhCHHHHHHHHHHHcCCCHHHHHHHhh---------------------------cc-----
Confidence 4555432 5777888999999999999999999999999999999 99
Q ss_pred CcchhhHHHHHHHHHHHHHHHH-cCCCCCCeEE-EEEEECCCccccCccccCCCCcccccccceeEEEEEe
Q 031743 84 WPVKSAKFILDLLKNAESNAEV-KGLDVDALYI-SHIQVNQAQKQRRRTYRAHGRINRMFLVLFHLCLIFL 152 (153)
Q Consensus 84 ~p~KaA~~i~klL~sa~aNA~~-kgld~d~L~I-~~i~v~kG~~~kr~~pRA~GRa~~~~k~~~hI~ivl~ 152 (153)
++|+|+.|.++|.+|.+||.+ +|||+++|+| .++++++|..+||..++|+||.+++++++|||+++|.
T Consensus 109 -~kK~a~~i~~~l~~A~~nA~~~~gl~~~~l~v~~~~t~~~g~~~Krl~~hargr~~ii~~~yvhi~v~L~ 178 (218)
T KOG1711|consen 109 -DKKAAKTIAEVLLSARANAVHNHGLDPDSLLVVAEATVGQGNELKRLKVHARGRFGIIRRPYVHIFVKLE 178 (218)
T ss_pred -hHHHHHHHHHHHHHHHhhhHHhcCCCccceEEEEeeecccchhhhheeeeccCcccceecceeeEEEEEe
Confidence 999999999999999999975 8999999999 9999999999999999999999999999999999985
No 13
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=70.78 E-value=18 Score=25.30 Aligned_cols=65 Identities=14% Similarity=0.216 Sum_probs=47.6
Q ss_pred hHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcchhhHHHHHHHHHHHHHHHH-
Q 031743 27 KNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEV- 105 (153)
Q Consensus 27 kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA~~i~klL~sa~aNA~~- 105 (153)
+.+.++++.+ |++..+|+..+-.-+....-+||.--. +--.-..++...+++++|-..
T Consensus 14 ~~A~~vl~~l-Gls~S~Ai~~fl~qi~~~~~iPF~~~~--------------------~s~ed~~~l~~~re~~~~~~~~ 72 (80)
T PRK11235 14 ARAYAVLEKL-GVTPSEALRLLLQYVAENGRLPFKTVL--------------------LSDEDAALLETVRERLANPQKG 72 (80)
T ss_pred HHHHHHHHHh-CCCHHHHHHHHHHHHHHhCCCCCCCCC--------------------CCHHHHHHHHHHHHHHhCCCCC
Confidence 3567788888 999999999999889999999997542 333466778888888877532
Q ss_pred cCCCCCC
Q 031743 106 KGLDVDA 112 (153)
Q Consensus 106 kgld~d~ 112 (153)
...+.|+
T Consensus 73 ~~~~~d~ 79 (80)
T PRK11235 73 IRVTLDD 79 (80)
T ss_pred eeeecCc
Confidence 1244444
No 14
>TIGR01999 iscU FeS cluster assembly scaffold IscU. This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms.
Probab=67.33 E-value=37 Score=25.00 Aligned_cols=70 Identities=14% Similarity=0.144 Sum_probs=48.3
Q ss_pred eEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcchhhHHHH
Q 031743 14 SCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFIL 93 (153)
Q Consensus 14 ~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA~~i~ 93 (153)
.++-.+..--+|.-=+-.++++|.|++++||.++..+.+....-+| .. -.++|....
T Consensus 53 d~~f~~~GC~~s~Asas~~~e~i~Gktl~ea~~i~~~~i~~~lg~p---------------------~~--r~~CA~l~~ 109 (124)
T TIGR01999 53 DAKFKTFGCGSAIASSSLATELIKGKSLEEALKIKNTEIAKELSLP---------------------PV--KLHCSLLAE 109 (124)
T ss_pred EEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHhccHHHHHHHcCCC---------------------cc--cchHHHHHH
Confidence 3444445555666667889999999999999999875433211111 01 256899999
Q ss_pred HHHHHHHHHHHHc
Q 031743 94 DLLKNAESNAEVK 106 (153)
Q Consensus 94 klL~sa~aNA~~k 106 (153)
+.|+.|..+....
T Consensus 110 ~al~~a~~~y~~~ 122 (124)
T TIGR01999 110 DAIKAAIKDYKSK 122 (124)
T ss_pred HHHHHHHHHHHHh
Confidence 9999998887543
No 15
>PRK11325 scaffold protein; Provisional
Probab=65.24 E-value=35 Score=25.31 Aligned_cols=70 Identities=13% Similarity=0.115 Sum_probs=50.4
Q ss_pred ceEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcchhhHHH
Q 031743 13 KSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFI 92 (153)
Q Consensus 13 ~~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA~~i 92 (153)
..++-.+..--+|-==+-.++.+++|++++||..+..+.+....-+| .. -.++|...
T Consensus 54 ~d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~~~~i~~~lg~p---------------------~~--r~~CA~la 110 (127)
T PRK11325 54 EDAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKNTDIAEELALP---------------------PV--KIHCSILA 110 (127)
T ss_pred EEEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHcCCC---------------------cc--cchHHHHH
Confidence 34555566667777778899999999999999999886543221111 11 25689999
Q ss_pred HHHHHHHHHHHHH
Q 031743 93 LDLLKNAESNAEV 105 (153)
Q Consensus 93 ~klL~sa~aNA~~ 105 (153)
.+.|+.|+.+...
T Consensus 111 ~~al~~a~~~y~~ 123 (127)
T PRK11325 111 EDAIKAAIADYKS 123 (127)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999888654
No 16
>COG3077 RelB DNA-damage-inducible protein J [DNA replication, recombination, and repair]
Probab=60.43 E-value=16 Score=26.06 Aligned_cols=34 Identities=21% Similarity=0.309 Sum_probs=29.4
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHHhccccccceee
Q 031743 29 TRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRF 63 (153)
Q Consensus 29 ~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~ 63 (153)
+..|+..+ |+++.+|+.++=.=+.....+||.-.
T Consensus 19 A~~Vl~~m-Glt~S~airm~L~~va~~~~lPfdl~ 52 (88)
T COG3077 19 ATAVLEEM-GLTISDAIRMFLTKVAREGALPFDLR 52 (88)
T ss_pred HHHHHHHh-CCCHHHHHHHHHHHHHHcCCCCcccc
Confidence 56677777 99999999999888899999999765
No 17
>PF04221 RelB: RelB antitoxin; InterPro: IPR007337 Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. Several toxin/antitoxin pairs may occur in a single species. RelE and RelB form a toxin-antitoxin system; RelE represses translation, probably through binding ribosomes [, ]. RelB stably binds RelE, presumably deactivating it.; PDB: 2KC8_B 2K29_A.
Probab=57.27 E-value=15 Score=25.24 Aligned_cols=35 Identities=17% Similarity=0.309 Sum_probs=24.8
Q ss_pred hHHHHHHHHHhCCCHHHHHHHHHHHHhcccccccee
Q 031743 27 KNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTR 62 (153)
Q Consensus 27 kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r 62 (153)
..+..|+..+ |++..+|+..+-.=+.....+||.-
T Consensus 14 ~~a~~il~~~-Glt~s~ai~~fl~qiv~~~~iPF~~ 48 (83)
T PF04221_consen 14 EEAEAILEEL-GLTLSDAINMFLKQIVREGGIPFEL 48 (83)
T ss_dssp HHHHHHHHHT-T--HHHHHHHHHHHHHHHSS-S---
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHHHHHhCCCCccc
Confidence 3567778877 9999999999988888999999864
No 18
>PF01713 Smr: Smr domain; InterPro: IPR002625 This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 (P23909 from SWISSPROT) protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2, P94545 from SWISSPROT [].; PDB: 3QD7_X 2D9I_A 3FAU_A 2VKC_A 2ZQE_A.
Probab=55.96 E-value=14 Score=24.83 Aligned_cols=36 Identities=25% Similarity=0.398 Sum_probs=25.0
Q ss_pred HhCCCHHHHHHHHHHHHhc--cccccceeecCCCcccc
Q 031743 36 IRKLPLTKAKRYLEDVMAH--KQAIPFTRFCGGVGRTA 71 (153)
Q Consensus 36 IRG~~v~~A~~~L~~V~~k--k~~vPf~r~~~~v~~~~ 71 (153)
+.||++++|+..|++.+.. .+-+...+---|.|+++
T Consensus 3 LHG~~~~eA~~~l~~~l~~~~~~~~~~~~II~G~G~hS 40 (83)
T PF01713_consen 3 LHGLTVEEALRALEEFLDEARQRGIRELRIITGKGNHS 40 (83)
T ss_dssp -TTS-HHHHHHHHHHHHHHHHHTTHSEEEEE--STCTC
T ss_pred CCCCcHHHHHHHHHHHHHHHHHcCCCEEEEEeccCCCC
Confidence 4699999999999999865 45566666667777665
No 19
>KOG3361 consensus Iron binding protein involved in Fe-S cluster formation [Energy production and conversion]
Probab=55.27 E-value=11 Score=29.27 Aligned_cols=34 Identities=12% Similarity=0.189 Sum_probs=28.8
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHHhcccccccee
Q 031743 29 TRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTR 62 (153)
Q Consensus 29 ~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r 62 (153)
.......|+||+++||..+=+.=|+|+.|.|=-+
T Consensus 96 SS~aTewvkgkt~dea~kIkNteIAKeL~LPPVK 129 (157)
T KOG3361|consen 96 SSLATEWVKGKTLDEALKIKNTEIAKELSLPPVK 129 (157)
T ss_pred hHHHHHHHccccHHHHHhcccHHHHHhccCCchh
Confidence 4456778999999999999999999999997433
No 20
>PF13852 DUF4197: Protein of unknown function (DUF4197)
Probab=55.08 E-value=25 Score=28.50 Aligned_cols=20 Identities=25% Similarity=0.321 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCHHHHHHHHH
Q 031743 30 RETAHAIRKLPLTKAKRYLE 49 (153)
Q Consensus 30 ~~va~~IRG~~v~~A~~~L~ 49 (153)
-.+.++|+.|++++|..+|.
T Consensus 84 ~if~~AI~~Ms~~DA~~IL~ 103 (202)
T PF13852_consen 84 PIFVDAIKSMSIQDAKGILN 103 (202)
T ss_pred HHHHHHHHhCCHHhHHHHhc
Confidence 34678999999999999999
No 21
>TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not.
Probab=52.50 E-value=90 Score=22.82 Aligned_cols=70 Identities=10% Similarity=0.105 Sum_probs=48.2
Q ss_pred ceEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHH-hccccccceeecCCCccccccccCCCCCCCCCcchhhHH
Q 031743 13 KSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVM-AHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKF 91 (153)
Q Consensus 13 ~~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~-~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA~~ 91 (153)
..++-.+..--+|--=+...+++|.|++++||.++..+-+ ..=.-+| .. -.++|..
T Consensus 48 ~d~~f~~~GC~is~Asas~~~e~i~Gk~l~ea~~i~~~~i~~~l~~l~---------------------~~--r~~CA~l 104 (121)
T TIGR03419 48 KDVKFKTFGCGAAIASSSMATEMIKGKTLEEAWELTNKAVAEALDGLP---------------------PV--KMHCSVL 104 (121)
T ss_pred EEEEEEEeccHHHHHHHHHHHHHHcCCCHHHHHHhhhHHHHHHHcCCC---------------------cc--cCHHHHH
Confidence 3445555666667777889999999999999999987422 1100011 11 3568999
Q ss_pred HHHHHHHHHHHHHH
Q 031743 92 ILDLLKNAESNAEV 105 (153)
Q Consensus 92 i~klL~sa~aNA~~ 105 (153)
..+.|+.|..+...
T Consensus 105 a~~al~~a~~~y~~ 118 (121)
T TIGR03419 105 AEEAIHKAINDYRE 118 (121)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999888654
No 22
>PF12637 TSCPD: TSCPD domain; InterPro: IPR024434 The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD, after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulphur cluster. This domain is found at the C terminus of some ribonucleoside-diphosphate reductase enzymes.
Probab=51.06 E-value=79 Score=22.25 Aligned_cols=36 Identities=14% Similarity=-0.019 Sum_probs=27.6
Q ss_pred EEEeeCCcccchhHHHHHHHHH-----hCCCHHHHHHHHHH
Q 031743 15 CKARGSDLRVHFKNTRETAHAI-----RKLPLTKAKRYLED 50 (153)
Q Consensus 15 ~kA~~~~~rvS~kk~~~va~~I-----RG~~v~~A~~~L~~ 50 (153)
+.......--..-.+.-++++| .|+++++.+++|+.
T Consensus 26 vf~~~~~~Gg~~~~~~ai~rliS~~Lr~G~~~~~ii~~L~g 66 (95)
T PF12637_consen 26 VFINVGKAGGCSGNLEAIARLISLALRSGVPPEEIIDQLRG 66 (95)
T ss_pred EEEecCcCCCchHHHHHHHHHHHHHHHcCCCHHHHHHHhcC
Confidence 3333333333388899999999 99999999999994
No 23
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=46.25 E-value=18 Score=29.45 Aligned_cols=30 Identities=33% Similarity=0.489 Sum_probs=27.4
Q ss_pred CcccchhHHHHHHHHH-hCCCHHHHHHHHHH
Q 031743 21 DLRVHFKNTRETAHAI-RKLPLTKAKRYLED 50 (153)
Q Consensus 21 ~~rvS~kk~~~va~~I-RG~~v~~A~~~L~~ 50 (153)
.=+.++-|++.+.++| ||-+.++|+.+|+|
T Consensus 59 ~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL~d 89 (194)
T COG1094 59 EDPLALLKARDVVKAIGRGFPPEKALKLLED 89 (194)
T ss_pred CChHHHHHHHHHHHHHhcCCCHHHHHHHhcC
Confidence 4678899999999999 89999999999996
No 24
>PF06738 DUF1212: Protein of unknown function (DUF1212); InterPro: IPR010619 This entry represents a predicted domain found within a number of hypothetical proteins of unknown function found in eukaryotes, bacteria and archaea. Some of these sequences are predicted to be membrane proteins.
Probab=44.68 E-value=72 Score=24.59 Aligned_cols=49 Identities=16% Similarity=0.164 Sum_probs=32.2
Q ss_pred ceEEEeeCCcccchhHHHH---HHHHH--hCCCHHHHHHHHHHHHhccccccce
Q 031743 13 KSCKARGSDLRVHFKNTRE---TAHAI--RKLPLTKAKRYLEDVMAHKQAIPFT 61 (153)
Q Consensus 13 ~~~kA~~~~~rvS~kk~~~---va~~I--RG~~v~~A~~~L~~V~~kk~~vPf~ 61 (153)
.+.-.+...-.+...+..+ +.+.+ ..++++||.+.|+++...++.-|.|
T Consensus 51 ~t~~~~v~~~~~nl~~l~~v~~l~~~~~~~~~~~~ea~~~L~~I~~~~~~y~~~ 104 (193)
T PF06738_consen 51 RTRVRRVPPRGVNLDKLAAVNRLSRRIVAGQLSLEEAIERLDEIDREPPRYPPW 104 (193)
T ss_pred eEEEEEeCCCCcCHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhCCCCCCHH
Confidence 3333444566666666655 55555 6789999999999986666444443
No 25
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=42.32 E-value=50 Score=22.85 Aligned_cols=35 Identities=20% Similarity=0.288 Sum_probs=28.6
Q ss_pred hHHHHHHHHHhCCCHHHHHHHHHHHHhcccccccee
Q 031743 27 KNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTR 62 (153)
Q Consensus 27 kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r 62 (153)
..+..+++.+ |++..+|+..+=.=+.+.+-+||.-
T Consensus 15 ~~a~~i~~~l-Gl~~s~ai~~fl~qvv~~~~lPF~~ 49 (83)
T TIGR02384 15 KEAYAVFEEL-GLTPSTAIRMFLKQVIREQGLPFDL 49 (83)
T ss_pred HHHHHHHHHh-CCCHHHHHHHHHHHHHHhCCCCCCc
Confidence 3466778888 9999999998887888888888864
No 26
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=41.83 E-value=39 Score=26.02 Aligned_cols=86 Identities=16% Similarity=0.133 Sum_probs=49.0
Q ss_pred eEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCc--chhhHH
Q 031743 14 SCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWP--VKSAKF 91 (153)
Q Consensus 14 ~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p--~KaA~~ 91 (153)
.++=.+...-+|--=+..++++|.|++++||+.+.++.++--+ ..++..+....--.+.++..-+| .+++-.
T Consensus 56 d~~F~~~GC~is~ASss~~te~v~Gkti~EAl~i~~~~~~m~~------~~~~~~~~~l~d~~~l~~v~~~p~r~~C~~L 129 (150)
T COG0822 56 DAKFKGFGCAISIASSSMMTELVKGKTLDEALKITEAFTDMAK------ELGGDPDDRLGDLVALAGVALPPARIKCSLL 129 (150)
T ss_pred EEEeeecCcHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH------HcCCCccchhhhhHhhhhhccccccccchhc
Confidence 4445556666777778889999999999999999854322111 01111111100000111122345 456667
Q ss_pred HHHHHHHHHHHHHH
Q 031743 92 ILDLLKNAESNAEV 105 (153)
Q Consensus 92 i~klL~sa~aNA~~ 105 (153)
-.+.|+.|....+.
T Consensus 130 ~~~al~~ai~~~~~ 143 (150)
T COG0822 130 AWDALKAAIKDYKG 143 (150)
T ss_pred cHHHHHHHHHHhhc
Confidence 77888888887654
No 27
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=41.29 E-value=21 Score=25.33 Aligned_cols=26 Identities=12% Similarity=0.267 Sum_probs=22.7
Q ss_pred EeeCCcccchhHHHHHHHHHhCCCHH
Q 031743 17 ARGSDLRVHFKNTRETAHAIRKLPLT 42 (153)
Q Consensus 17 A~~~~~rvS~kk~~~va~~IRG~~v~ 42 (153)
|.-.+++++.+.+..|++.+||.+++
T Consensus 24 skqy~i~it~~QA~~I~~~lr~k~in 49 (85)
T PF11116_consen 24 SKQYNISITKKQAEQIANILRGKNIN 49 (85)
T ss_pred HHHhCCCCCHHHHHHHHHHHhcCCCC
Confidence 34478999999999999999999973
No 28
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=40.06 E-value=37 Score=22.86 Aligned_cols=21 Identities=14% Similarity=0.289 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCHHHHHHHHH
Q 031743 29 TRETAHAIRKLPLTKAKRYLE 49 (153)
Q Consensus 29 ~~~va~~IRG~~v~~A~~~L~ 49 (153)
+..||+.|+|+++++-.+++.
T Consensus 36 ~~~iA~~i~gks~eeir~~fg 56 (78)
T PF01466_consen 36 CKYIANMIKGKSPEEIRKYFG 56 (78)
T ss_dssp HHHHHHHHTTS-HHHHHHHHT
T ss_pred HHHHHHHhcCCCHHHHHHHcC
Confidence 457899999999999999987
No 29
>PHA02754 hypothetical protein; Provisional
Probab=37.05 E-value=39 Score=22.63 Aligned_cols=26 Identities=27% Similarity=0.399 Sum_probs=23.3
Q ss_pred hHHHHHHHHHhCCCHHHHHHHHHHHH
Q 031743 27 KNTRETAHAIRKLPLTKAKRYLEDVM 52 (153)
Q Consensus 27 kk~~~va~~IRG~~v~~A~~~L~~V~ 52 (153)
-++-|+-++|-.+...+|+..|+|.+
T Consensus 2 skAeEi~k~i~eK~Fke~MRelkD~L 27 (67)
T PHA02754 2 SKAEEIPKAIMEKDFKEAMRELKDIL 27 (67)
T ss_pred ccHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 46889999999999999999999864
No 30
>smart00463 SMR Small MutS-related domain.
Probab=37.02 E-value=29 Score=23.07 Aligned_cols=23 Identities=13% Similarity=0.234 Sum_probs=18.4
Q ss_pred HhCCCHHHHHHHHHHHHhccccc
Q 031743 36 IRKLPLTKAKRYLEDVMAHKQAI 58 (153)
Q Consensus 36 IRG~~v~~A~~~L~~V~~kk~~v 58 (153)
+.||++++|+..|+.-++.-..-
T Consensus 6 LHG~~~~eA~~~l~~~l~~~~~~ 28 (80)
T smart00463 6 LHGLTVEEALTALDKFLNNARLK 28 (80)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHc
Confidence 46999999999999888764443
No 31
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=36.92 E-value=41 Score=22.25 Aligned_cols=26 Identities=38% Similarity=0.493 Sum_probs=21.4
Q ss_pred chhHHHHHHHHHhCCCHHHHHHHHHHH
Q 031743 25 HFKNTRETAHAIRKLPLTKAKRYLEDV 51 (153)
Q Consensus 25 S~kk~~~va~~IRG~~v~~A~~~L~~V 51 (153)
.|-++++||++. |++.-.|..||...
T Consensus 14 ~p~~T~eiA~~~-gls~~~aR~yL~~L 39 (62)
T PF04703_consen 14 GPLKTREIADAL-GLSIYQARYYLEKL 39 (62)
T ss_dssp S-EEHHHHHHHH-TS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHh-CCCHHHHHHHHHHH
Confidence 566899999999 99999999999953
No 32
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=35.02 E-value=26 Score=22.00 Aligned_cols=15 Identities=27% Similarity=0.352 Sum_probs=13.7
Q ss_pred HhCCCHHHHHHHHHH
Q 031743 36 IRKLPLTKAKRYLED 50 (153)
Q Consensus 36 IRG~~v~~A~~~L~~ 50 (153)
+.||++++|.+.|++
T Consensus 6 ~~g~~~~~a~~~l~~ 20 (63)
T PF03793_consen 6 LVGMTYDEAKSILEA 20 (63)
T ss_dssp TTTSBHHHHHHHHHH
T ss_pred cCCCcHHHHHHHHHH
Confidence 579999999999996
No 33
>PF07778 CENP-I: Mis6 ; InterPro: IPR012485 Centromere protein Cenp-I (also known as Mis6) is an essential centromere connector protein acting during G1-S phase of the cell cycle. Mis6 is thought to be required for recruiting Cenp-A, the centromere- specific histone H3 variant; an important event for centromere function and chromosome segregation during mitosis [, ].
Probab=34.08 E-value=41 Score=31.10 Aligned_cols=46 Identities=30% Similarity=0.276 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcchhhHHHHHHHHHHHHHHHHcCCCCCCe
Q 031743 39 LPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDAL 113 (153)
Q Consensus 39 ~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA~~i~klL~sa~aNA~~kgld~d~L 113 (153)
-++++|+++|+++ . .. -+++-...+.+.|+...+.|-..||++|.|
T Consensus 56 ~~l~~ai~~l~~~----------------------~--~~-----~~~~~~~~~~~~i~~l~s~A~~~GL~~~~l 101 (511)
T PF07778_consen 56 DSLEDAIEYLEKV----------------------S--KV-----PSKRRNTSLKSTIKTLESLAYENGLSPEAL 101 (511)
T ss_pred HHHHHHHHHHHhc----------------------c--cc-----ccccccchHHHHHHHHHHHHHHcCCCHHHH
Confidence 6789999999953 0 11 145666788889999999999999998865
No 34
>cd06664 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.
Probab=33.42 E-value=1e+02 Score=22.12 Aligned_cols=41 Identities=17% Similarity=0.194 Sum_probs=32.3
Q ss_pred eEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhc
Q 031743 14 SCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAH 54 (153)
Q Consensus 14 ~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~k 54 (153)
.++-.+..--+|--=+...++.++|++++||..++++.+..
T Consensus 50 d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~~~~~~~ 90 (123)
T cd06664 50 DAKFQGFGCAISIASASLLTELIKGKTLDEALKLLNKDIAM 90 (123)
T ss_pred EEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence 44555566667777788999999999999999999865433
No 35
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=26.86 E-value=3.2e+02 Score=23.22 Aligned_cols=70 Identities=16% Similarity=0.155 Sum_probs=47.4
Q ss_pred eEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcchhhHHHH
Q 031743 14 SCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFIL 93 (153)
Q Consensus 14 ~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA~~i~ 93 (153)
.++-.+..--+|-==+-..+.+|+|++++||.++..+-+... -+++ . .. -.+.|....
T Consensus 54 d~~F~~~GCais~ASAs~~~eli~Gktv~ea~~i~~~di~~~--------L~~l----------p--p~--r~~CA~La~ 111 (290)
T TIGR02000 54 DAGFQTFGCGSAIASSSALTEMIKGLTLDEALKVSNQDIADY--------LGGL----------P--PE--KMHCSVMGQ 111 (290)
T ss_pred EEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHHhhHHHHHHH--------HcCC----------C--hh--hchHHHHHH
Confidence 444455556666667788999999999999999986322211 0011 1 00 256888888
Q ss_pred HHHHHHHHHHHH
Q 031743 94 DLLKNAESNAEV 105 (153)
Q Consensus 94 klL~sa~aNA~~ 105 (153)
+.|+.|..+...
T Consensus 112 ~Al~~Al~~y~~ 123 (290)
T TIGR02000 112 EALEAAIANYRG 123 (290)
T ss_pred HHHHHHHHHHhc
Confidence 999999888764
No 36
>PF01592 NifU_N: NifU-like N terminal domain; InterPro: IPR002871 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the N-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal and a C-terminal domain (IPR001075 from INTERPRO) []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 3LVL_A 4EB5_C 4EB7_C 1WFZ_A 2Z7E_C 2AZH_A 1XJS_A 1Q48_A 1R9P_A 2KQK_A ....
Probab=26.65 E-value=2.4e+02 Score=20.50 Aligned_cols=71 Identities=18% Similarity=0.185 Sum_probs=44.6
Q ss_pred ceEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcchhhHHH
Q 031743 13 KSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFI 92 (153)
Q Consensus 13 ~~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA~~i 92 (153)
..++-....-.+|--=+-.++.+|.|+++++|..+-.+-+...- ++ -+.. -...+...
T Consensus 52 ~d~~f~~~GC~~~~Asas~~~~~i~gk~l~ea~~i~~~~i~~~l--------~~------------~~~~--~~~~~~l~ 109 (126)
T PF01592_consen 52 KDAKFQGFGCAISIASASMMCELIKGKTLEEALKITAEDIEEAL--------GG------------LPPE--RQHCAELA 109 (126)
T ss_dssp EEEEEEEESSHHHHHHHHHHHHHHTTSBHHHHHCHHHHHHHHHH--------TC-------------CGT--CGHHHHHH
T ss_pred EEEEEEeecChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH--------hc------------cccC--cccHHHHH
Confidence 35555566677777788899999999999999654321111000 00 0111 24567788
Q ss_pred HHHHHHHHHHHHH
Q 031743 93 LDLLKNAESNAEV 105 (153)
Q Consensus 93 ~klL~sa~aNA~~ 105 (153)
...|+.|+++-..
T Consensus 110 ~~al~~av~~y~~ 122 (126)
T PF01592_consen 110 DDALKAAVADYPA 122 (126)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHh
Confidence 8888888887543
No 37
>PF04921 XAP5: XAP5, circadian clock regulator; InterPro: IPR007005 These proteins are found in a wide range of eukaryotes. Their function is uncertain though they are nuclear proteins, possibly with DNA-binding activity.; GO: 0005634 nucleus
Probab=25.15 E-value=1.8e+02 Score=24.41 Aligned_cols=96 Identities=21% Similarity=0.255 Sum_probs=49.9
Q ss_pred HHHHHHHHHHhccccccceeecCCCccccccccCCCCCCCCCcchhhHHHHHHHHHHHHHH-HHcCCCCCCe-EEEEE--
Q 031743 43 KAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNA-EVKGLDVDAL-YISHI-- 118 (153)
Q Consensus 43 ~A~~~L~~V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p~KaA~~i~klL~sa~aNA-~~kgld~d~L-~I~~i-- 118 (153)
|-+..-+.|.+.+-.|||--|. |-||+..++=+ .| ---..+|-++.+.....= +-..+.+|+| ||.+=
T Consensus 86 E~~~~Qe~vK~eeI~I~fsywD-Gs~hrr~v~vK----KG---dtI~~FL~~~r~~l~~~f~el~~vsvd~LM~VkedlI 157 (239)
T PF04921_consen 86 EWLAKQEAVKAEEIEIPFSYWD-GSGHRRTVRVK----KG---DTIWQFLEKCRKQLAKEFRELRRVSVDDLMYVKEDLI 157 (239)
T ss_pred HHHHHHHHHhCCeeEEEEEEEC-CCCCcceEEEc----CC---CCHHHHHHHHHHHHHHHhHHHHhcCHhheeeecccee
Confidence 4445556778888899999775 66777765322 11 111233333333322111 2245666665 33331
Q ss_pred EECCCccccCccccCCCCccccccccee
Q 031743 119 QVNQAQKQRRRTYRAHGRINRMFLVLFH 146 (153)
Q Consensus 119 ~v~kG~~~kr~~pRA~GRa~~~~k~~~h 146 (153)
.-+-=.-+-=+.-+|+|..+|.+....|
T Consensus 158 iPHhy~FY~fI~nka~GksGpLF~fd~~ 185 (239)
T PF04921_consen 158 IPHHYTFYDFIVNKARGKSGPLFDFDVH 185 (239)
T ss_pred ccCCceeeeeeeccccCCCCCeeeccCC
Confidence 1122222234445688999888775554
No 38
>PF04485 NblA: Phycobilisome degradation protein nblA ; InterPro: IPR007574 In the cyanobacterium Synechococcus species PCC 7942 (P35087 from SWISSPROT), nblA triggers degradation of light-harvesting phycobiliproteins in response to deprivation nutrients including nitrogen, phosphorus and sulphur. The mechanism of nblA function is not known, but it has been hypothesised that nblA may act by disrupting phycobilisome structure, activating a protease or tagging phycobiliproteins for proteolysis. Members of this family have also been identified in the chloroplasts of some red algae.; PDB: 3CS5_D 1OJH_L 2QDO_B 2Q8V_A.
Probab=24.52 E-value=1.5e+02 Score=19.16 Aligned_cols=24 Identities=21% Similarity=0.339 Sum_probs=20.2
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHH
Q 031743 28 NTRETAHAIRKLPLTKAKRYLEDV 51 (153)
Q Consensus 28 k~~~va~~IRG~~v~~A~~~L~~V 51 (153)
+.+...+.+..++.++|.++|-++
T Consensus 11 ~L~~~~~qv~~ls~Eqaq~~Lve~ 34 (53)
T PF04485_consen 11 KLRSFKDQVQKLSREQAQELLVEL 34 (53)
T ss_dssp HHHHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCHHHHHHHHHHH
Confidence 567788999999999999999865
No 39
>COG3812 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.27 E-value=43 Score=26.67 Aligned_cols=27 Identities=30% Similarity=0.382 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCeEEE
Q 031743 90 KFILDLLKNAESNAEVKGLDVDALYIS 116 (153)
Q Consensus 90 ~~i~klL~sa~aNA~~kgld~d~L~I~ 116 (153)
+-+..+|.-|.++||.+++|++.|.-.
T Consensus 43 ~~Ls~vL~kaaa~aeak~~D~~~~l~a 69 (193)
T COG3812 43 KNLSAVLAKAAAHAEAKKIDPQVLLTA 69 (193)
T ss_pred HHHHHHHHHHHHhHHhhcCCHHHHHhh
Confidence 345577888999999999999876543
No 40
>TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family. Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.
Probab=20.90 E-value=2.4e+02 Score=20.94 Aligned_cols=79 Identities=14% Similarity=0.184 Sum_probs=45.8
Q ss_pred eEEEeeCCcccchhHHHHHHHHHhCCCHHHHHHHHHH---HHhccccccceeecCCCccccccccCCCCCCCCCc--chh
Q 031743 14 SCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLED---VMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWP--VKS 88 (153)
Q Consensus 14 ~~kA~~~~~rvS~kk~~~va~~IRG~~v~~A~~~L~~---V~~kk~~vPf~r~~~~v~~~~~~~~~~~~~~gr~p--~Ka 88 (153)
.++-.+...-+|--=+..++.+|.|++++||..++++ ++..+...|...--++. .. | .+...|| .|+
T Consensus 53 d~~f~~~GCais~Asas~~~e~i~Gk~~~ea~~l~~~~~~ml~~~~~~~~~~~l~dl---~~----l-~~v~~~p~R~~C 124 (137)
T TIGR01994 53 DIAFEGEGCSISQASASMMTELIKGKTVEEALSLVEAFSEMIQGQETDEDEEKLGDA---EA----L-AGVAKFPARIKC 124 (137)
T ss_pred EEEEEecccHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCCCccccccchH---HH----h-hccccCcchHHH
Confidence 4444455566666677889999999999999998864 33333222211000000 00 1 1112234 778
Q ss_pred hHHHHHHHHHHH
Q 031743 89 AKFILDLLKNAE 100 (153)
Q Consensus 89 A~~i~klL~sa~ 100 (153)
|..-.+.|+.|.
T Consensus 125 a~L~~~al~~al 136 (137)
T TIGR01994 125 ATLAWKALERAL 136 (137)
T ss_pred HHHHHHHHHHHh
Confidence 888888888764
Done!