Query 047331
Match_columns 102
No_of_seqs 136 out of 578
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 10:05:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047331.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047331hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02221 asparaginyl-tRNA synt 99.9 2.1E-24 4.6E-29 184.8 6.1 65 37-101 201-265 (572)
2 KOG0554 Asparaginyl-tRNA synth 99.8 4.6E-19 1E-23 148.6 4.4 33 1-35 25-57 (446)
3 PLN02532 asparagine-tRNA synth 99.7 2.7E-17 5.9E-22 142.9 3.6 64 37-101 265-328 (633)
4 PLN02603 asparaginyl-tRNA synt 99.4 5.9E-13 1.3E-17 114.5 4.9 33 1-35 112-144 (565)
5 PTZ00425 asparagine-tRNA ligas 99.3 2.6E-12 5.7E-17 111.2 5.3 34 1-34 86-119 (586)
6 cd04318 EcAsnRS_like_N EcAsnRS 99.1 9.8E-11 2.1E-15 75.9 4.2 53 1-55 4-63 (82)
7 cd04321 ScAspRS_mt_like_N ScAs 98.9 3.4E-09 7.3E-14 69.9 5.2 51 1-54 4-62 (86)
8 COG0017 AsnS Aspartyl/asparagi 98.9 2.7E-09 5.9E-14 90.2 5.1 31 1-35 21-51 (435)
9 cd04322 LysRS_N LysRS_N: N-ter 98.8 1.2E-08 2.7E-13 69.3 5.4 51 1-55 4-65 (108)
10 cd04100 Asp_Lys_Asn_RS_N Asp_L 98.7 2E-08 4.4E-13 65.4 5.0 51 1-55 4-63 (85)
11 cd04323 AsnRS_cyto_like_N AsnR 98.7 1.6E-08 3.5E-13 66.0 3.2 51 1-55 4-62 (84)
12 cd04319 PhAsnRS_like_N PhAsnRS 98.6 2.7E-08 5.9E-13 67.2 3.6 50 1-54 4-62 (103)
13 cd04316 ND_PkAspRS_like_N ND_P 98.6 3E-08 6.6E-13 67.5 3.5 51 1-55 17-77 (108)
14 cd04320 AspRS_cyto_N AspRS_cyt 98.6 5.3E-08 1.2E-12 65.4 3.4 35 1-38 4-38 (102)
15 cd04317 EcAspRS_like_N EcAspRS 98.5 8.4E-08 1.8E-12 67.3 3.3 50 1-54 19-76 (135)
16 TIGR00457 asnS asparaginyl-tRN 98.4 3.9E-07 8.5E-12 76.3 4.0 34 1-36 21-54 (453)
17 PRK05159 aspC aspartyl-tRNA sy 97.9 1.1E-05 2.4E-10 67.1 3.6 32 1-36 21-52 (437)
18 TIGR00458 aspS_arch aspartyl-t 97.9 1.2E-05 2.7E-10 66.8 3.5 32 1-36 17-48 (428)
19 PRK00476 aspS aspartyl-tRNA sy 97.9 1.3E-05 2.9E-10 69.5 3.7 50 1-54 22-78 (588)
20 PRK00484 lysS lysyl-tRNA synth 97.8 1.5E-05 3.3E-10 67.6 3.9 32 1-36 59-90 (491)
21 PLN02903 aminoacyl-tRNA ligase 97.8 1.8E-05 3.9E-10 70.0 3.8 50 1-54 77-135 (652)
22 TIGR00499 lysS_bact lysyl-tRNA 97.8 2.3E-05 4.9E-10 66.7 3.9 32 1-36 58-89 (496)
23 PRK03932 asnC asparaginyl-tRNA 97.8 2.1E-05 4.6E-10 65.8 3.4 32 1-34 21-52 (450)
24 PRK12445 lysyl-tRNA synthetase 97.7 2.7E-05 5.9E-10 66.5 3.7 33 1-37 70-102 (505)
25 PLN02502 lysyl-tRNA synthetase 97.7 2.8E-05 6.2E-10 67.3 3.7 51 1-55 113-176 (553)
26 TIGR00459 aspS_bact aspartyl-t 97.7 2.8E-05 6.2E-10 67.7 3.7 31 1-35 20-50 (583)
27 PRK12820 bifunctional aspartyl 97.7 3.6E-05 7.8E-10 68.6 3.7 32 1-36 23-54 (706)
28 PLN02850 aspartate-tRNA ligase 97.6 4E-05 8.6E-10 65.9 3.0 33 1-37 86-118 (530)
29 PTZ00401 aspartyl-tRNA synthet 97.6 6.8E-05 1.5E-09 64.9 3.9 31 1-35 83-113 (550)
30 PRK02983 lysS lysyl-tRNA synth 97.4 0.0002 4.4E-09 66.1 5.3 33 1-37 656-688 (1094)
31 KOG0555 Asparaginyl-tRNA synth 97.4 7.1E-05 1.5E-09 64.5 1.8 31 1-35 128-158 (545)
32 PTZ00385 lysyl-tRNA synthetase 97.1 0.00051 1.1E-08 61.0 3.6 34 1-38 112-145 (659)
33 PF01336 tRNA_anti-codon: OB-f 96.9 0.00091 2E-08 40.8 2.7 31 1-35 3-34 (75)
34 PTZ00417 lysine-tRNA ligase; P 96.8 0.0011 2.4E-08 58.0 3.3 34 1-37 137-170 (585)
35 COG0173 AspS Aspartyl-tRNA syn 96.6 0.0017 3.7E-08 57.2 3.0 31 1-35 20-50 (585)
36 PF00458 WHEP-TRS: WHEP-TRS do 94.2 0.061 1.3E-06 34.2 3.0 25 77-101 2-26 (56)
37 cd00938 HisRS_RNA HisRS_RNA bi 91.9 0.18 4E-06 31.2 2.6 26 76-101 3-28 (45)
38 KOG1885 Lysyl-tRNA synthetase 91.6 0.19 4.1E-06 44.4 3.4 32 1-35 109-140 (560)
39 cd00939 MetRS_RNA MetRS_RNA bi 88.1 0.51 1.1E-05 29.2 2.4 23 78-100 3-25 (45)
40 KOG0556 Aspartyl-tRNA syntheta 86.6 0.73 1.6E-05 40.4 3.3 31 1-35 87-117 (533)
41 COG1190 LysU Lysyl-tRNA synthe 83.2 1.3 2.8E-05 39.0 3.3 31 1-35 66-96 (502)
42 cd04489 ExoVII_LU_OBF ExoVII_L 82.5 2.1 4.4E-05 26.5 3.3 32 2-36 5-36 (78)
43 cd00935 GlyRS_RNA GlyRS_RNA bi 75.9 2.8 6E-05 25.1 2.2 27 74-100 2-28 (51)
44 cd04483 hOBFC1_like hOBFC1_lik 75.8 5 0.00011 27.0 3.7 30 1-34 2-31 (92)
45 COG5235 RFA2 Single-stranded D 68.4 4.7 0.0001 32.7 2.6 24 2-27 72-95 (258)
46 cd01200 WHEPGMRS_RNA EPRS-like 68.4 3.9 8.3E-05 23.4 1.6 22 79-100 3-24 (42)
47 cd04485 DnaE_OBF DnaE_OBF: A s 68.0 11 0.00024 22.4 3.7 32 2-35 3-37 (84)
48 cd04478 RPA2_DBD_D RPA2_DBD_D: 66.8 14 0.0003 23.7 4.2 30 2-35 5-34 (95)
49 KOG2411 Aspartyl-tRNA syntheta 66.3 5.8 0.00013 35.7 2.9 31 1-35 52-82 (628)
50 cd04490 PolII_SU_OBF PolII_SU_ 58.1 19 0.00042 23.4 3.7 31 2-35 5-35 (79)
51 cd00936 WEPRS_RNA WEPRS_RNA bi 56.0 8.5 0.00018 23.1 1.6 23 78-100 3-25 (50)
52 cd05694 S1_Rrp5_repeat_hs2_sc2 54.2 11 0.00023 24.1 1.9 18 1-22 8-25 (74)
53 KOG4141 DNA repair and recombi 51.4 14 0.0003 29.6 2.5 39 2-43 82-127 (222)
54 cd03524 RPA2_OBF_family RPA2_O 50.8 14 0.0003 20.9 1.9 37 2-40 3-41 (75)
55 PLN02734 glycyl-tRNA synthetas 43.4 23 0.00051 32.3 3.0 32 69-100 5-36 (684)
56 PF15279 SOBP: Sine oculis-bin 42.2 7.2 0.00016 32.2 -0.4 29 1-35 1-29 (306)
57 PRK13159 cytochrome c-type bio 40.0 1.1E+02 0.0023 23.1 5.7 53 1-56 56-124 (155)
58 PRK05672 dnaE2 error-prone DNA 38.8 41 0.00089 31.9 3.9 32 1-35 958-991 (1046)
59 COG4085 Predicted RNA-binding 38.7 62 0.0013 25.7 4.3 50 1-52 56-116 (204)
60 PRK13165 cytochrome c-type bio 37.8 67 0.0015 24.3 4.3 53 1-56 62-131 (160)
61 cd04492 YhaM_OBF_like YhaM_OBF 37.4 69 0.0015 19.2 3.6 19 15-35 19-37 (83)
62 PF10451 Stn1: Telomere regula 34.1 79 0.0017 25.2 4.3 68 15-82 87-163 (256)
63 KOG1276 Protoporphyrinogen oxi 33.8 23 0.00051 31.3 1.4 16 1-18 48-63 (491)
64 PRK07373 DNA polymerase III su 33.0 68 0.0015 27.5 4.0 32 2-35 286-320 (449)
65 PF01834 XRCC1_N: XRCC1 N term 31.5 50 0.0011 25.0 2.7 40 16-57 55-101 (153)
66 PRK13150 cytochrome c-type bio 29.8 1.2E+02 0.0026 22.9 4.5 53 1-56 62-131 (159)
67 cd04482 RPA2_OBF_like RPA2_OBF 29.5 89 0.0019 20.7 3.4 32 1-35 3-35 (91)
68 cd05707 S1_Rrp5_repeat_sc11 S1 29.0 53 0.0012 19.7 2.1 20 1-24 4-23 (68)
69 COG0691 SmpB tmRNA-binding pro 27.9 41 0.00089 25.6 1.7 24 1-25 30-56 (153)
70 PF14954 LIX1: Limb expression 26.5 41 0.00089 27.4 1.5 21 15-35 59-79 (252)
71 PF06902 Fer4_19: Divergent 4F 25.7 64 0.0014 20.5 2.1 49 29-83 5-54 (64)
72 cd05689 S1_RPS1_repeat_ec4 S1_ 25.7 52 0.0011 19.8 1.6 19 2-24 8-26 (72)
73 PF08206 OB_RNB: Ribonuclease 25.2 1.1E+02 0.0024 18.6 3.0 37 10-51 5-43 (58)
74 PF10642 Tom5: Mitochondrial i 24.8 81 0.0018 19.6 2.4 17 65-81 6-22 (49)
75 PF11829 DUF3349: Protein of u 24.6 61 0.0013 22.6 2.0 21 64-84 69-89 (96)
76 PF09259 Fve: Fungal immunomod 24.2 44 0.00095 24.0 1.2 40 9-49 67-109 (111)
77 PF15072 DUF4539: Domain of un 22.9 1.5E+02 0.0031 20.1 3.5 31 2-36 8-38 (86)
78 PRK14450 acylphosphatase; Prov 22.3 44 0.00095 22.2 0.9 9 1-9 30-38 (91)
79 CHL00173 cpeA phycoerythrin al 22.3 1.2E+02 0.0025 22.9 3.2 39 48-92 5-43 (164)
80 PRK00624 glycine cleavage syst 22.2 1.4E+02 0.0031 21.0 3.5 22 14-35 32-54 (114)
81 TIGR03077 not_gcvH glycine cle 21.8 1.5E+02 0.0033 20.7 3.6 22 14-35 30-52 (110)
82 TIGR03824 FlgM_jcvi flagellar 21.5 1.7E+02 0.0037 19.4 3.6 42 42-83 37-78 (95)
83 KOG3360 Acylphosphatase [Energ 21.3 46 0.00099 23.7 0.8 10 1-10 36-45 (98)
84 cd05698 S1_Rrp5_repeat_hs6_sc5 21.1 94 0.002 18.5 2.1 27 1-36 4-30 (70)
85 PF13742 tRNA_anti_2: OB-fold 20.5 1.8E+02 0.0039 19.4 3.6 31 3-36 28-58 (99)
86 PRK14441 acylphosphatase; Prov 20.3 50 0.0011 22.2 0.8 8 1-8 33-40 (93)
87 PF02728 Cu_amine_oxidN3: Copp 20.2 1.5E+02 0.0032 19.7 3.1 29 66-94 1-29 (101)
No 1
>PLN02221 asparaginyl-tRNA synthetase
Probab=99.90 E-value=2.1e-24 Score=184.84 Aligned_cols=65 Identities=63% Similarity=0.954 Sum_probs=62.5
Q ss_pred CCCCCCCceeEeeehhhhhHHHHHhhcCCCCCChhhHHHHHHHHHHhhHHHHHhhhchhhhhhhh
Q 047331 37 NGCGGAGEMFQVTTLLSEAEKLEKELMKNPPPSEADREAAKLFVKEKGEGVAKLKSKKASKEVLL 101 (102)
Q Consensus 37 sdcEGage~fqVTTLl~kae~~~~~~~~~~~~~~~~iea~ka~v~ekg~~V~~lK~~~s~ke~~~ 101 (102)
++|||+||||+||||.++..+.++++++++|+++.|+||+|++|+|+|+.|++||++++||+++.
T Consensus 201 s~~EGg~e~F~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 265 (572)
T PLN02221 201 SDCEGAGEMFQVTTLINYTERLEQDLIDNPPPTEADVEAARLIVKERGEVVAQLKAAKASKEEIT 265 (572)
T ss_pred ccCCCCccceeeeecccccccccccccccCcccchhhhhhhhhhhhhcchhhhhhccccchhhhh
Confidence 99999999999999999888889999999999999999999999999999999999999999864
No 2
>KOG0554 consensus Asparaginyl-tRNA synthetase (mitochondrial) [Translation, ribosomal structure and biogenesis]
Probab=99.76 E-value=4.6e-19 Score=148.56 Aligned_cols=33 Identities=48% Similarity=0.896 Sum_probs=32.1
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|+|||||+|.+| +++|++||||||.++||||++
T Consensus 25 i~GWvKsvr~~~--~~~Fl~i~DGs~~~~lQvVv~ 57 (446)
T KOG0554|consen 25 IGGWVKSVRKLK--KVTFLDINDGSCPSPLQVVVD 57 (446)
T ss_pred ecchhhhccccc--ceEEEEecCCCCCcceEEEec
Confidence 689999999999 999999999999999999998
No 3
>PLN02532 asparagine-tRNA synthetase
Probab=99.67 E-value=2.7e-17 Score=142.91 Aligned_cols=64 Identities=34% Similarity=0.449 Sum_probs=55.2
Q ss_pred CCCCCCCceeEeeehhhhhHHHHHhhcCCCCCChhhHHHHHHHHHHhhHHHHHhhhchhhhhhhh
Q 047331 37 NGCGGAGEMFQVTTLLSEAEKLEKELMKNPPPSEADREAAKLFVKEKGEGVAKLKSKKASKEVLL 101 (102)
Q Consensus 37 sdcEGage~fqVTTLl~kae~~~~~~~~~~~~~~~~iea~ka~v~ekg~~V~~lK~~~s~ke~~~ 101 (102)
||||||||||+||||.++.++.++. ....++.+.+++++++++++|+++|.+||++++|||++.
T Consensus 265 s~~EGa~elF~v~t~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 (633)
T PLN02532 265 TDATGFGEMFRVTTLLGKSDDKEEK-KPVHETEGISLEAVKAAIKEKTNLVEELKRSESNREALV 328 (633)
T ss_pred cCCCccccccceecccccccccccc-ccccccccccchhhhhhhhcccccccccccccccccccc
Confidence 9999999999999999877643222 234678899999999999999999999999999999874
No 4
>PLN02603 asparaginyl-tRNA synthetase
Probab=99.36 E-value=5.9e-13 Score=114.54 Aligned_cols=33 Identities=45% Similarity=0.893 Sum_probs=31.3
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|+|||+++|.+| +++||+|+|||+..+||||++
T Consensus 112 v~GwV~~iR~~g--~~~Fi~l~Dgs~~~~lQ~v~~ 144 (565)
T PLN02603 112 VMGWVRTLRAQS--SVTFIEVNDGSCLSNMQCVMT 144 (565)
T ss_pred EEEEEEEEEeCC--CeEEEEEECCCCCEeEEEEEE
Confidence 589999999999 999999999999999999995
No 5
>PTZ00425 asparagine-tRNA ligase; Provisional
Probab=99.30 E-value=2.6e-12 Score=111.19 Aligned_cols=34 Identities=47% Similarity=0.844 Sum_probs=31.0
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEE
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLV 34 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv 34 (102)
|+|||+++|.+|+++++||+||||||..++|||+
T Consensus 86 l~GWv~~iR~~g~~~~~Fv~lrDgsg~~~iQiVv 119 (586)
T PTZ00425 86 VCGWSKAVRKQGGGRFCFVNLNDGSCHLNLQIIV 119 (586)
T ss_pred EEEEEeehhhcCCceEEEEEEECCCCCcceEEEE
Confidence 5899999999995569999999999999999986
No 6
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial
Probab=99.10 E-value=9.8e-11 Score=75.90 Aligned_cols=53 Identities=36% Similarity=0.683 Sum_probs=41.4
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecCCC-------CCCCceeEeeehhhhh
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNGC-------GGAGEMFQVTTLLSEA 55 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~sdc-------EGage~fqVTTLl~ka 55 (102)
|+|||+++|.+| +++|++|+|||+.+++|+|++.... -..|+..+|+-.+.+.
T Consensus 4 v~Gwv~~~R~~g--~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~ 63 (82)
T cd04318 4 VNGWVRSVRDSK--KISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLVKS 63 (82)
T ss_pred EEEeEEEEEcCC--cEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEEeC
Confidence 579999999999 8999999999999999999985322 1345666666655443
No 7
>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for
Probab=98.89 E-value=3.4e-09 Score=69.93 Aligned_cols=51 Identities=24% Similarity=0.300 Sum_probs=39.2
Q ss_pred CceeEeceec-CCCCeeEEEEEeCCCCCCceeEEEecC-------CCCCCCceeEeeehhhh
Q 047331 1 LAGWVKIGRK-QDKDWLAFFEVNDGSCFDNLQVLVERN-------GCGGAGEMFQVTTLLSE 54 (102)
Q Consensus 1 v~GWVks~R~-~k~g~~~Fl~lnDGS~~~~LQvVv~~s-------dcEGage~fqVTTLl~k 54 (102)
|.|||+++|. +| +++|++|+|||+ ..+|+|+++. ..-..|..+.||--+..
T Consensus 4 v~Gwv~~~R~~~~--~~~Fi~LrD~~g-~~iQvv~~~~~~~~~~~~~l~~~s~V~V~G~v~~ 62 (86)
T cd04321 4 LNGWIDRKPRIVK--KLSFADLRDPNG-DIIQLVSTAKKDAFSLLKSITAESPVQVRGKLQL 62 (86)
T ss_pred EEEeEeeEeCCCC--ceEEEEEECCCC-CEEEEEECCCHHHHHHHhcCCCCcEEEEEEEEEe
Confidence 5799999999 67 899999999999 6799999742 12345677777765444
No 8
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=98.86 E-value=2.7e-09 Score=90.16 Aligned_cols=31 Identities=35% Similarity=0.670 Sum_probs=29.3
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|+|||+++|.+| +++||.|+||||+ +|+|++
T Consensus 21 v~GWV~~~R~~g--~i~Fi~lrDgsg~--iQ~v~~ 51 (435)
T COG0017 21 VRGWVHNKRDLG--KIIFLVLRDGSGF--IQAVVP 51 (435)
T ss_pred EEEEeeeecccC--CeEEEEEEcCCcE--EEEEEE
Confidence 589999999999 8999999999999 999984
No 9
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=98.79 E-value=1.2e-08 Score=69.30 Aligned_cols=51 Identities=25% Similarity=0.338 Sum_probs=39.5
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecCCC-----------CCCCceeEeeehhhhh
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNGC-----------GGAGEMFQVTTLLSEA 55 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~sdc-----------EGage~fqVTTLl~ka 55 (102)
|+|||+++|.+| +++||+|+|||. .+|+|+...++ -.-|+.+.|+-.+.+.
T Consensus 4 v~GwV~~~R~~g--~~~Fi~lrd~~~--~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~ 65 (108)
T cd04322 4 VAGRIMSKRGSG--KLSFADLQDESG--KIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKT 65 (108)
T ss_pred EEEEEEEEecCC--CeEEEEEEECCe--EEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEec
Confidence 589999999999 899999999994 59999975431 3447777777655444
No 10
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=98.73 E-value=2e-08 Score=65.38 Aligned_cols=51 Identities=33% Similarity=0.537 Sum_probs=38.7
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecCCCC---------CCCceeEeeehhhhh
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNGCG---------GAGEMFQVTTLLSEA 55 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~sdcE---------Gage~fqVTTLl~ka 55 (102)
|+|||+++|.+| +++|++|+||++ .+|+|++.++.+ -.|+.++|+--+...
T Consensus 4 i~Gwv~~~R~~g--~~~Fi~Lrd~~~--~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~ 63 (85)
T cd04100 4 LAGWVHSRRDHG--GLIFIDLRDGSG--IVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKR 63 (85)
T ss_pred EEEEEehhccCC--CEEEEEEEeCCe--eEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEEC
Confidence 589999999999 899999999995 599999854322 236667776655443
No 11
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with
Probab=98.68 E-value=1.6e-08 Score=66.00 Aligned_cols=51 Identities=29% Similarity=0.414 Sum_probs=39.5
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecCCC--------CCCCceeEeeehhhhh
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNGC--------GGAGEMFQVTTLLSEA 55 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~sdc--------EGage~fqVTTLl~ka 55 (102)
|+|||+++|.+| +++|++|+|||+. +|+++..... -..|...+|+--+.+.
T Consensus 4 v~Gwv~~~R~~g--~~~Fi~LrD~~~~--iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~v~~~ 62 (84)
T cd04323 4 VFGWVHRLRSQK--KLMFLVLRDGTGF--LQCVLSKKLVTEFYDAKSLTQESSVEVTGEVKED 62 (84)
T ss_pred EEEEEEEEecCC--CcEEEEEEcCCeE--EEEEEcCCcchhHHHHhcCCCcCEEEEEEEEEEC
Confidence 579999999998 8999999999987 9999974321 1246677777655554
No 12
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.
Probab=98.64 E-value=2.7e-08 Score=67.24 Aligned_cols=50 Identities=24% Similarity=0.341 Sum_probs=38.4
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecC-C--------CCCCCceeEeeehhhh
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERN-G--------CGGAGEMFQVTTLLSE 54 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~s-d--------cEGage~fqVTTLl~k 54 (102)
|.|||+++|.+| +++|++|+|||+. +|+|++.. + .-..|+.+.|+-.+.+
T Consensus 4 v~Gwv~~~R~~g--k~~Fi~lrD~~g~--iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~ 62 (103)
T cd04319 4 LAGWVYRKREVG--KKAFIVLRDSTGI--VQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKA 62 (103)
T ss_pred EEEEEEeEEcCC--CeEEEEEecCCee--EEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEE
Confidence 579999999999 8999999999976 99999742 1 1134667777765544
No 13
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=98.63 E-value=3e-08 Score=67.51 Aligned_cols=51 Identities=22% Similarity=0.295 Sum_probs=38.0
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecCCC----------CCCCceeEeeehhhhh
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNGC----------GGAGEMFQVTTLLSEA 55 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~sdc----------EGage~fqVTTLl~ka 55 (102)
|+|||+++|.+| +++|++|+|||+. +|+|++.... -..|....|+-.+.+.
T Consensus 17 v~Gwv~~~R~~g--~~~Fi~LrD~~g~--iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~ 77 (108)
T cd04316 17 VAGWVHEIRDLG--GIKFVILRDREGI--VQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAE 77 (108)
T ss_pred EEEEEEeeeccC--CeEEEEEecCCee--EEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeC
Confidence 579999999999 8999999999985 9999973211 1235566666654443
No 14
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=98.57 E-value=5.3e-08 Score=65.44 Aligned_cols=35 Identities=20% Similarity=0.305 Sum_probs=29.8
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecCC
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNG 38 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~sd 38 (102)
|+|||+++|.+++. +.|++|+|||.. +|+|++..+
T Consensus 4 i~Gwv~~~R~~g~k-~~Fi~LrD~sg~--iQ~v~~~~~ 38 (102)
T cd04320 4 IRARVHTSRAQGAK-LAFLVLRQQGYT--IQGVLAASA 38 (102)
T ss_pred EEEEEEEeecCCCc-eEEEEEecCCce--EEEEEeCCc
Confidence 57999999998644 999999999954 999998544
No 15
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=98.51 E-value=8.4e-08 Score=67.32 Aligned_cols=50 Identities=26% Similarity=0.412 Sum_probs=37.4
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecCCC--------CCCCceeEeeehhhh
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNGC--------GGAGEMFQVTTLLSE 54 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~sdc--------EGage~fqVTTLl~k 54 (102)
|+|||+++|.+| +++|++|+||++. +|+|+..++. --.|....|+--+..
T Consensus 19 i~Gwv~~~R~~g--k~~Fi~LrD~~g~--~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~ 76 (135)
T cd04317 19 LCGWVQRRRDHG--GLIFIDLRDRYGI--VQVVFDPEEAPEFELAEKLRNESVIQVTGKVRA 76 (135)
T ss_pred EEEeEehhcccC--CEEEEEEecCCee--EEEEEeCCchhHHHHHhCCCCccEEEEEEEEEC
Confidence 589999999999 8999999999965 9999974321 123556666664443
No 16
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=98.35 E-value=3.9e-07 Score=76.34 Aligned_cols=34 Identities=32% Similarity=0.740 Sum_probs=31.6
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEec
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVER 36 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~ 36 (102)
|.|||+++|.+| ++.|++|+||||.+.+|+|++.
T Consensus 21 v~Gwv~~~R~~~--~~~F~~lrD~~~~g~iQ~v~~~ 54 (453)
T TIGR00457 21 VSGWVRTKRSSK--KIIFLELNDGSSLGPIQAVING 54 (453)
T ss_pred EEEEeEEEEcCC--CeEEEEEECCCCCccEEEEEeC
Confidence 579999999888 9999999999999999999974
No 17
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=97.88 E-value=1.1e-05 Score=67.08 Aligned_cols=32 Identities=41% Similarity=0.628 Sum_probs=29.5
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEec
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVER 36 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~ 36 (102)
|.|||+++|.+| ++.|++|+|||+. +|+|++.
T Consensus 21 i~GrV~~~R~~g--k~~Fl~LrD~~g~--iQ~v~~~ 52 (437)
T PRK05159 21 LAGWVHEIRDLG--GIAFLILRDRSGI--IQVVVKK 52 (437)
T ss_pred EEEEeEeeecCC--CeEEEEEEcCCcE--EEEEEeC
Confidence 579999999999 8999999999986 9999973
No 18
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=97.86 E-value=1.2e-05 Score=66.79 Aligned_cols=32 Identities=25% Similarity=0.401 Sum_probs=29.5
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEec
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVER 36 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~ 36 (102)
|.|||+++|.+| ++.||+|+|||+. +|+|++.
T Consensus 17 i~G~v~~~R~~g--~~~Fi~lrd~~g~--iQ~v~~~ 48 (428)
T TIGR00458 17 FMGWVHEIRDLG--GLIFVLLRDREGL--IQITAPA 48 (428)
T ss_pred EEEEEEEEecCC--CcEEEEEEeCCee--EEEEEEC
Confidence 579999999999 8999999999985 9999974
No 19
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=97.85 E-value=1.3e-05 Score=69.53 Aligned_cols=50 Identities=26% Similarity=0.421 Sum_probs=37.6
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecC-------CCCCCCceeEeeehhhh
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERN-------GCGGAGEMFQVTTLLSE 54 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~s-------dcEGage~fqVTTLl~k 54 (102)
|+|||+++|.+| ++.||+|+|||+. +|+|+... ..-..|...+|+-.+.+
T Consensus 22 l~GwV~~~R~~g--~l~Fi~LrD~~g~--iQ~v~~~~~~~~~~~~~l~~es~V~V~G~v~~ 78 (588)
T PRK00476 22 LCGWVHRRRDHG--GLIFIDLRDREGI--VQVVFDPDAEAFEVAESLRSEYVIQVTGTVRA 78 (588)
T ss_pred EEEEEEEEEeCC--CeEEEEEEeCCce--EEEEEeCCHHHHHHHhCCCCCCEEEEEEEEEe
Confidence 579999999999 8999999999997 99999731 01123556666665544
No 20
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=97.85 E-value=1.5e-05 Score=67.59 Aligned_cols=32 Identities=31% Similarity=0.422 Sum_probs=29.4
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEec
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVER 36 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~ 36 (102)
|.|||.++|.+| ++.|++|+|||+. +|||++.
T Consensus 59 v~G~v~~~R~~g--~~~Fi~lrD~~g~--iQ~v~~~ 90 (491)
T PRK00484 59 VAGRVMLKRVMG--KASFATLQDGSGR--IQLYVSK 90 (491)
T ss_pred EEEEEEEEecCC--ceEEEEEEcCCcc--EEEEEEC
Confidence 579999999999 8999999999984 9999974
No 21
>PLN02903 aminoacyl-tRNA ligase
Probab=97.80 E-value=1.8e-05 Score=69.96 Aligned_cols=50 Identities=24% Similarity=0.367 Sum_probs=38.8
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecCC---------CCCCCceeEeeehhhh
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNG---------CGGAGEMFQVTTLLSE 54 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~sd---------cEGage~fqVTTLl~k 54 (102)
|+|||+++|.+| ++.||+|+|+++. +|||+...+ .-..|...+|+-.+.+
T Consensus 77 l~GWV~~~R~~G--~l~FidLRD~~G~--iQvV~~~~~~~~~~~~~~~L~~esvV~V~G~V~~ 135 (652)
T PLN02903 77 LCGWVDLHRDMG--GLTFLDVRDHTGI--VQVVTLPDEFPEAHRTANRLRNEYVVAVEGTVRS 135 (652)
T ss_pred EEEEEEEEecCC--CcEEEEEEcCCcc--EEEEEeCCccHHHHHHHhcCCCCCEEEEEEEEEe
Confidence 589999999999 8999999999987 899997432 1223666777765543
No 22
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=97.78 E-value=2.3e-05 Score=66.69 Aligned_cols=32 Identities=25% Similarity=0.377 Sum_probs=29.1
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEec
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVER 36 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~ 36 (102)
|.|||+++|.+| +++|++|+|||+. ||+|+++
T Consensus 58 v~Grv~~~R~~g--k~~F~~l~D~~g~--iQ~~~~~ 89 (496)
T TIGR00499 58 IAGRIMARRSMG--KATFITLQDESGQ--IQLYVNK 89 (496)
T ss_pred EEEEEEEEecCC--CeEEEEEEcCCcc--EEEEEEC
Confidence 579999999998 9999999999965 9999974
No 23
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=97.76 E-value=2.1e-05 Score=65.79 Aligned_cols=32 Identities=44% Similarity=0.935 Sum_probs=26.6
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEE
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLV 34 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv 34 (102)
|.|||+++|.+| +++|++|+|||+...+|++.
T Consensus 21 i~G~v~~~R~~g--~~~Fi~lrD~~g~iq~~~~~ 52 (450)
T PRK03932 21 VRGWVRTKRDSG--KIAFLQLRDGSCFKQLQVVK 52 (450)
T ss_pred EEEEEEEEEeCC--CeEEEEEECCCCcEEEEEEc
Confidence 589999999998 99999999999974344443
No 24
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=97.73 E-value=2.7e-05 Score=66.47 Aligned_cols=33 Identities=24% Similarity=0.301 Sum_probs=29.7
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecC
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERN 37 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~s 37 (102)
|.|||.++|.+| +++|++|+|||+. ||||+++.
T Consensus 70 v~Grv~~~R~~G--k~~F~~lrD~~g~--iQ~~~~~~ 102 (505)
T PRK12445 70 VAGRMMTRRIMG--KASFVTLQDVGGR--IQLYVARD 102 (505)
T ss_pred EEEEEEEEecCC--CcEEEEEEeCCcc--EEEEEECC
Confidence 579999999999 8999999999974 99999853
No 25
>PLN02502 lysyl-tRNA synthetase
Probab=97.73 E-value=2.8e-05 Score=67.26 Aligned_cols=51 Identities=22% Similarity=0.342 Sum_probs=38.7
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecCCC-------------CCCCceeEeeehhhhh
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNGC-------------GGAGEMFQVTTLLSEA 55 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~sdc-------------EGage~fqVTTLl~ka 55 (102)
|.|||.++|.+| ++.|++|+|||+. |||++...+. ---|+...|+--+.+.
T Consensus 113 v~GrV~~~R~~G--k~~F~~LrD~~g~--iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t 176 (553)
T PLN02502 113 VAGRIMAKRAFG--KLAFYDLRDDGGK--IQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKT 176 (553)
T ss_pred EEEEEEEEecCC--CeEEEEEecCCcc--EEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEec
Confidence 579999999999 9999999999975 9999974321 1236677776654443
No 26
>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.
Probab=97.72 E-value=2.8e-05 Score=67.74 Aligned_cols=31 Identities=39% Similarity=0.656 Sum_probs=29.0
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|.|||+++|.+| ++.|++|+|+|+. +|||++
T Consensus 20 l~GwV~~~R~~G--kl~Fi~LrD~sg~--iQvv~~ 50 (583)
T TIGR00459 20 LAGWVNRRRDLG--GLIFIDLRDRSGI--VQVVCD 50 (583)
T ss_pred EEEEEEEEEcCC--CcEEEEEEeCCcc--EEEEEe
Confidence 579999999999 8999999999995 999997
No 27
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=97.68 E-value=3.6e-05 Score=68.57 Aligned_cols=32 Identities=34% Similarity=0.594 Sum_probs=29.6
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEec
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVER 36 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~ 36 (102)
|+|||.++|.+| ++.||+|+|+++. +|||++.
T Consensus 23 l~GWV~~~R~~G--~l~FidLRD~~G~--iQvV~~~ 54 (706)
T PRK12820 23 LAGWVDAFRDHG--ELLFIHLRDRNGF--IQAVFSP 54 (706)
T ss_pred EEEEEEEEEcCC--CcEEEEEEeCCcc--EEEEEeC
Confidence 589999999999 8999999999997 9999974
No 28
>PLN02850 aspartate-tRNA ligase
Probab=97.62 E-value=4e-05 Score=65.90 Aligned_cols=33 Identities=21% Similarity=0.211 Sum_probs=29.4
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecC
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERN 37 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~s 37 (102)
|+|||.++|.+| +++||+|+|++.. +|+|+..+
T Consensus 86 v~Grv~~~R~~g--k~~Fl~Lrd~~~~--iQ~v~~~~ 118 (530)
T PLN02850 86 IRGRVHTIRGKG--KSAFLVLRQSGFT--VQCVVFVS 118 (530)
T ss_pred EEEEEEEEccCC--CeEEEEEEeCCcC--EEEEEECC
Confidence 589999999999 8999999999875 99999743
No 29
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=97.58 E-value=6.8e-05 Score=64.93 Aligned_cols=31 Identities=29% Similarity=0.409 Sum_probs=28.7
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|+|||.++|.+| +++||+|+||++. +|+|+.
T Consensus 83 v~Grv~~~R~~G--k~~Fl~LRd~~~~--iQ~v~~ 113 (550)
T PTZ00401 83 IRARVSTTRKKG--KMAFMVLRDGSDS--VQAMAA 113 (550)
T ss_pred EEEEEEEEecCC--CeEEEEEEeCCcC--EEEEEE
Confidence 589999999999 8999999999995 999985
No 30
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=97.44 E-value=0.0002 Score=66.14 Aligned_cols=33 Identities=30% Similarity=0.283 Sum_probs=29.8
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecC
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERN 37 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~s 37 (102)
|.|||.++|.+| ++.|++|+|+|.. ||+|+++.
T Consensus 656 v~Grv~~~R~~G--~~~F~~lrD~~g~--iQ~v~~~~ 688 (1094)
T PRK02983 656 VSGRVLRIRDYG--GVLFADLRDWSGE--LQVLLDAS 688 (1094)
T ss_pred EEEEEEEEeeCC--CeEEEEEEeCCee--EEEEEECC
Confidence 579999999999 8999999999965 99999854
No 31
>KOG0555 consensus Asparaginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=97.40 E-value=7.1e-05 Score=64.51 Aligned_cols=31 Identities=39% Similarity=0.694 Sum_probs=29.5
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|.|||..+|++| ++.||.|+||+.+ ||+|+.
T Consensus 128 v~gWVhrlR~qk--~l~FivLrdg~gf--lqCVl~ 158 (545)
T KOG0555|consen 128 VFGWVHRLRRQK--SLIFIVLRDGTGF--LQCVLS 158 (545)
T ss_pred eehhhHhhhhcC--ceEEEEEecCCce--EEEEEc
Confidence 579999999999 8999999999999 999997
No 32
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=97.06 E-value=0.00051 Score=61.05 Aligned_cols=34 Identities=24% Similarity=0.231 Sum_probs=30.3
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecCC
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNG 38 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~sd 38 (102)
|.|||.++|.+| +++|++|+|++.. +|+++.+.+
T Consensus 112 vaGrV~~~R~~G--k~~F~~LrD~~G~--IQvv~~~~~ 145 (659)
T PTZ00385 112 VAGRVTSVRDIG--KIIFVTIRSNGNE--LQVVGQVGE 145 (659)
T ss_pred EEEEEEeeeccC--CeEEEEEEECCce--EEEEEECCc
Confidence 579999999999 8999999999986 999997543
No 33
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=96.90 E-value=0.00091 Score=40.84 Aligned_cols=31 Identities=29% Similarity=0.481 Sum_probs=26.3
Q ss_pred CceeEece-ecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIG-RKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~-R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|.|||.++ |..+ ++.|+.|.||| ..+|+++-
T Consensus 3 v~G~V~~~~~~~~--~~~~~~l~D~t--g~i~~~~~ 34 (75)
T PF01336_consen 3 VEGRVTSIRRSGG--KIVFFTLEDGT--GSIQVVFF 34 (75)
T ss_dssp EEEEEEEEEEEET--TEEEEEEEETT--EEEEEEEE
T ss_pred EEEEEEEEEcCCC--CEEEEEEEECC--ccEEEEEc
Confidence 57999999 5555 89999999999 45899886
No 34
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=96.78 E-value=0.0011 Score=57.96 Aligned_cols=34 Identities=21% Similarity=0.286 Sum_probs=27.9
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecC
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERN 37 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~s 37 (102)
|.|||.++|.+|+ ++.|++|.|.++. |||++++.
T Consensus 137 v~Grv~~~R~~G~-k~~F~~L~d~~g~--iQv~~~~~ 170 (585)
T PTZ00417 137 VTGRIMRVSASGQ-KLRFFDLVGDGAK--IQVLANFA 170 (585)
T ss_pred EEEEEEeeecCCC-CCEEEEEEeCCee--EEEEEECC
Confidence 5799999999972 3999999776663 99999854
No 35
>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=96.58 E-value=0.0017 Score=57.23 Aligned_cols=31 Identities=32% Similarity=0.650 Sum_probs=29.1
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
+.|||...|..| .+.||+|+|=+.+ +|||++
T Consensus 20 L~GWV~r~Rd~G--gliFiDLRDr~Gi--vQvv~~ 50 (585)
T COG0173 20 LSGWVHRRRDHG--GLIFIDLRDREGI--VQVVFD 50 (585)
T ss_pred EEeeeeeccccC--CeEEEEcccCCCe--EEEEEC
Confidence 579999999999 7999999999998 899997
No 36
>PF00458 WHEP-TRS: WHEP-TRS domain; InterPro: IPR000738 A conserved domain of 46 amino acids, called WHEP-TRS has been shown [] to exist in a number of higher eukaryote aminoacyl-transfer RNA synthetases. This domain is present one to six times in the several enzymes. There are three copies in mammalian multifunctional aminoacyl-tRNA synthetase in a region that separates the N-terminal glutamyl-tRNA synthetase domain from the C-terminal prolyl-tRNA synthetase domain, and six copies in the intercatalytic region of the Drosophila enzyme. The domain is found at the N-terminal extremity of the mammalian tryptophanyl- tRNA synthetase and histidyl-tRNA synthetase, and the mammalian, insect, nematode and plant glycyl- tRNA synthetases []. This domain could contain a central alpha-helical region and may play a role in the association of tRNA-synthetases into multienzyme complexes.; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation; PDB: 1R1B_A 1D2D_A 1X59_A 1FYJ_A 2ZT8_A 2ZXF_A 2ZT7_A 2ZT6_A 2PME_A 2ZT5_A ....
Probab=94.16 E-value=0.061 Score=34.20 Aligned_cols=25 Identities=36% Similarity=0.469 Sum_probs=20.4
Q ss_pred HHHHHHhhHHHHHhhhchhhhhhhh
Q 047331 77 KLFVKEKGEGVAKLKSKKASKEVLL 101 (102)
Q Consensus 77 ka~v~ekg~~V~~lK~~~s~ke~~~ 101 (102)
.+.|.++|+.|.+||++++.+++|.
T Consensus 2 ~~~I~~QG~~VR~LKa~ka~k~~i~ 26 (56)
T PF00458_consen 2 EAQIAAQGDKVRKLKAEKADKEEID 26 (56)
T ss_dssp HHHHHHHHHHHHHHHHTT--HHHHH
T ss_pred hHHHHHHHHHHHHHHccCCcHHHHH
Confidence 5789999999999999999998764
No 37
>cd00938 HisRS_RNA HisRS_RNA binding domain. This short RNA-binding domain is found at the N-terminus of HisRS in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). This domain consists of a helix- turn- helix structure, which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes.
Probab=91.89 E-value=0.18 Score=31.16 Aligned_cols=26 Identities=50% Similarity=0.465 Sum_probs=22.5
Q ss_pred HHHHHHHhhHHHHHhhhchhhhhhhh
Q 047331 76 AKLFVKEKGEGVAKLKSKKASKEVLL 101 (102)
Q Consensus 76 ~ka~v~ekg~~V~~lK~~~s~ke~~~ 101 (102)
....|.++|+.|.+||+.+++++.|.
T Consensus 3 l~~~I~~QGe~VRkLKa~KA~k~~i~ 28 (45)
T cd00938 3 LEEAVKLQGELVRKLKAEKASKEQIA 28 (45)
T ss_pred HHHHHHHHHHHHHHHHHccCCHHHHH
Confidence 45679999999999999999998763
No 38
>KOG1885 consensus Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=91.62 E-value=0.19 Score=44.37 Aligned_cols=32 Identities=25% Similarity=0.483 Sum_probs=28.4
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|.|-|.++|.+| .++.|++|.+|..- |||++.
T Consensus 109 vaGRI~s~R~sG-sKL~Fydl~~~g~k--lQvm~~ 140 (560)
T KOG1885|consen 109 VAGRIHSKRESG-SKLVFYDLHGDGVK--LQVMAN 140 (560)
T ss_pred eeeeEeeeeccC-CceEEEEEecCCeE--EEEEEe
Confidence 579999999998 67999999999655 999998
No 39
>cd00939 MetRS_RNA MetRS_RNA binding domain. This short RNA-binding domain is found at the C-terminus of MetRS in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). It is repeated in Drosophila MetRS. This domain consists of a helix-turn-helix structure, which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes.
Probab=88.09 E-value=0.51 Score=29.18 Aligned_cols=23 Identities=48% Similarity=0.510 Sum_probs=20.3
Q ss_pred HHHHHhhHHHHHhhhchhhhhhh
Q 047331 78 LFVKEKGEGVAKLKSKKASKEVL 100 (102)
Q Consensus 78 a~v~ekg~~V~~lK~~~s~ke~~ 100 (102)
..|.++|+.|.+||++++.++.|
T Consensus 3 ~~I~~QGekVR~LKa~ka~k~~i 25 (45)
T cd00939 3 KEVAEQGNKVRKLKASKADKSVW 25 (45)
T ss_pred HHHHHHHHHHHHHHhccCcHHHH
Confidence 56889999999999999988765
No 40
>KOG0556 consensus Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=86.60 E-value=0.73 Score=40.41 Aligned_cols=31 Identities=26% Similarity=0.372 Sum_probs=27.8
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|+|.|.+-|..| +.+||.|++|.+. +|+++.
T Consensus 87 vRgrVhtsr~~G--K~~FlvLRq~~~t--VQ~~~~ 117 (533)
T KOG0556|consen 87 VRGRVHTSRLKG--KLCFLVLRQQGST--VQCLVA 117 (533)
T ss_pred EEEEEeeccccc--eEEEEEEeccCce--EEEEEE
Confidence 578888999998 9999999999987 899985
No 41
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=83.20 E-value=1.3 Score=38.98 Aligned_cols=31 Identities=29% Similarity=0.394 Sum_probs=28.3
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|.|-|.++|.+| +.+|++|.|+|.- ||+.++
T Consensus 66 vAGRi~~~R~~G--K~~F~~i~d~~gk--iQ~yi~ 96 (502)
T COG1190 66 VAGRIMTIRNMG--KASFADLQDGSGK--IQLYVN 96 (502)
T ss_pred EecceeeecccC--ceeEEEEecCCce--EEEEEe
Confidence 468899999999 9999999999994 999998
No 42
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=82.49 E-value=2.1 Score=26.51 Aligned_cols=32 Identities=13% Similarity=0.272 Sum_probs=24.0
Q ss_pred ceeEeceecCCCCeeEEEEEeCCCCCCceeEEEec
Q 047331 2 AGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVER 36 (102)
Q Consensus 2 ~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~ 36 (102)
.|=|-++|..++| .+|+.|.|++.. +.+++-+
T Consensus 5 ~g~v~~i~~tk~g-~~~~~L~D~~~~--i~~~~f~ 36 (78)
T cd04489 5 EGEISNLKRPSSG-HLYFTLKDEDAS--IRCVMWR 36 (78)
T ss_pred EEEEecCEECCCc-EEEEEEEeCCeE--EEEEEEc
Confidence 4667777766666 999999999843 7776653
No 43
>cd00935 GlyRS_RNA GlyRS_RNA binding domain. This short RNA-binding domain is found at the N-terminus of GlyRS in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). This domain consists of a helix-turn-helix structure , which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes.
Probab=75.86 E-value=2.8 Score=25.13 Aligned_cols=27 Identities=33% Similarity=0.368 Sum_probs=20.4
Q ss_pred HHHHHHHHHhhHHHHHhhhchhhhhhh
Q 047331 74 EAAKLFVKEKGEGVAKLKSKKASKEVL 100 (102)
Q Consensus 74 ea~ka~v~ekg~~V~~lK~~~s~ke~~ 100 (102)
+..+..|..+|+.|..||++++.+.++
T Consensus 2 ~~l~~~v~~qg~~vR~lk~~~a~~~~~ 28 (51)
T cd00935 2 APLRAAVKEQGDLVRKLKEEGAPDVDI 28 (51)
T ss_pred hHHHHHHHHhhHHHHhhccccCcHHHH
Confidence 346788899999999998877666444
No 44
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=75.85 E-value=5 Score=26.97 Aligned_cols=30 Identities=23% Similarity=0.381 Sum_probs=24.5
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEE
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLV 34 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv 34 (102)
|-|+|++++... .+..+.|.|||.. +-+++
T Consensus 2 ivG~V~sv~~~~--~~~~~tLdDgTG~--Ie~~~ 31 (92)
T cd04483 2 ILGTVVSRRERE--TFYSFGVDDGTGV--VNCVC 31 (92)
T ss_pred eEEEEEEEEecC--CeEEEEEecCCce--EEEEE
Confidence 459999999988 7888999999974 55544
No 45
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=68.39 E-value=4.7 Score=32.67 Aligned_cols=24 Identities=21% Similarity=0.268 Sum_probs=22.2
Q ss_pred ceeEeceecCCCCeeEEEEEeCCCCC
Q 047331 2 AGWVKIGRKQDKDWLAFFEVNDGSCF 27 (102)
Q Consensus 2 ~GWVks~R~~k~g~~~Fl~lnDGS~~ 27 (102)
-||||++..+- .-.|+.|-||+..
T Consensus 72 VGvvrni~~~t--tn~~~~iEDGTG~ 95 (258)
T COG5235 72 VGVVRNIKTST--TNSMFVIEDGTGS 95 (258)
T ss_pred EEEEEeeeecc--cceEEEEecCCce
Confidence 49999999999 8899999999976
No 46
>cd01200 WHEPGMRS_RNA EPRS-like_RNA binding domain. This short RNA-binding domain is found in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). It is found in three copies in the mammalian bifunctional EPRS in a region that separates the N-terminal GluRS from the C-terminal ProRS. In the Drosophila EPRS, this domain is repeated six times. It is found at the N-terminus of TrpRS, HisRS and GlyR and at the C-terminus of MetRS. This domain consists of a helix- turn- helix structure, which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes.
Probab=68.38 E-value=3.9 Score=23.36 Aligned_cols=22 Identities=45% Similarity=0.585 Sum_probs=17.1
Q ss_pred HHHHhhHHHHHhhhchhhhhhh
Q 047331 79 FVKEKGEGVAKLKSKKASKEVL 100 (102)
Q Consensus 79 ~v~ekg~~V~~lK~~~s~ke~~ 100 (102)
.|.++|+.|..||++++.+.++
T Consensus 3 ~i~~qg~~vR~lK~~~a~k~~~ 24 (42)
T cd01200 3 KIAEQGDLVRKLKAEKAPKEEI 24 (42)
T ss_pred HHHHhHHHHHhccccCCCHHHH
Confidence 5778888888888887776554
No 47
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=67.96 E-value=11 Score=22.44 Aligned_cols=32 Identities=31% Similarity=0.391 Sum_probs=21.5
Q ss_pred ceeEecee--cCCCC-eeEEEEEeCCCCCCceeEEEe
Q 047331 2 AGWVKIGR--KQDKD-WLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 2 ~GWVks~R--~~k~g-~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
.|.|.+.+ ..++| .+.|+.|.|+|.. +.+++-
T Consensus 3 ~g~v~~~~~~~~k~g~~~~~~~l~D~tg~--~~~~~f 37 (84)
T cd04485 3 AGLVTSVRRRRTKKGKRMAFVTLEDLTGS--IEVVVF 37 (84)
T ss_pred EEEEEEeEEEEcCCCCEEEEEEEEeCCCe--EEEEEC
Confidence 46676543 33444 5899999999987 555554
No 48
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=66.83 E-value=14 Score=23.75 Aligned_cols=30 Identities=20% Similarity=0.204 Sum_probs=23.8
Q ss_pred ceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 2 AGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 2 ~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
-|||+++...+ ...-+.|.|||.. +-+.+=
T Consensus 5 vG~V~~~~~~~--~~~~~tL~D~TG~--I~~~~W 34 (95)
T cd04478 5 VGVVRNVEEQS--TNITYTIDDGTGT--IEVRQW 34 (95)
T ss_pred EEEEEeeeEcc--cEEEEEEECCCCc--EEEEEe
Confidence 49999999887 6788899999964 565553
No 49
>KOG2411 consensus Aspartyl-tRNA synthetase, mitochondrial [Translation, ribosomal structure and biogenesis]
Probab=66.26 E-value=5.8 Score=35.67 Aligned_cols=31 Identities=32% Similarity=0.713 Sum_probs=27.4
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|+||+--.|.+| .+.|..|+|-... +|+.++
T Consensus 52 l~GWl~~~~~~k--~~~F~~LRD~~G~--vq~lls 82 (628)
T KOG2411|consen 52 LCGWLELHRVHK--MLTFFNLRDAYGI--VQQLLS 82 (628)
T ss_pred Eeeeeeeeeccc--cceEEEeeccCcc--eEEEec
Confidence 589999999998 8999999998876 788776
No 50
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=58.13 E-value=19 Score=23.40 Aligned_cols=31 Identities=23% Similarity=0.263 Sum_probs=24.9
Q ss_pred ceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 2 AGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 2 ~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
.|=|.++|.+|+|+- |+.|.|.|.. +.+++-
T Consensus 5 ~GiI~~v~~TK~g~~-~~~leD~~G~--~Ev~~F 35 (79)
T cd04490 5 IGMVNDVRSTKNGHR-IVELEDTTGR--ITVLLT 35 (79)
T ss_pred EEEEeEEEEcCCCCE-EEEEECCCCE--EEEEEe
Confidence 467778877788888 9999999987 677765
No 51
>cd00936 WEPRS_RNA WEPRS_RNA binding domain. This short RNA-binding domain is found in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). It is found in multiple copies in eukaryotic bifunctional glutamyl-prolyl-tRNA synthetases (EPRS) in a region that separates the N-terminal glutamyl-tRNA synthetase (GluRS) from the C-terminal prolyl-tRNA synthetase (ProRS). It is also found at the N-terminus of vertebrate tryptophanyl-tRNA synthetases (TrpRS). This domain consists of a helix-turn-helix structure, which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes.
Probab=56.03 E-value=8.5 Score=23.10 Aligned_cols=23 Identities=39% Similarity=0.478 Sum_probs=16.8
Q ss_pred HHHHHhhHHHHHhhhchhhhhhh
Q 047331 78 LFVKEKGEGVAKLKSKKASKEVL 100 (102)
Q Consensus 78 a~v~ekg~~V~~lK~~~s~ke~~ 100 (102)
..|.++|+.|..||++++.+.++
T Consensus 3 ~~i~~qge~VR~LK~~~a~k~~~ 25 (50)
T cd00936 3 KKIAAQGDLVRELKAKKAPKEEI 25 (50)
T ss_pred HHHHhchHHHhhhccccCchHHH
Confidence 35678888888888877766554
No 52
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=54.17 E-value=11 Score=24.15 Aligned_cols=18 Identities=17% Similarity=0.340 Sum_probs=15.2
Q ss_pred CceeEeceecCCCCeeEEEEEe
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVN 22 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~ln 22 (102)
|.|||+++...| .|+++.
T Consensus 8 v~g~V~si~d~G----~~v~~g 25 (74)
T cd05694 8 LSGCVSSVEDHG----YILDIG 25 (74)
T ss_pred EEEEEEEEeCCE----EEEEeC
Confidence 579999999888 788884
No 53
>KOG4141 consensus DNA repair and recombination protein RAD52/RAD22 [Replication, recombination and repair]
Probab=51.42 E-value=14 Score=29.61 Aligned_cols=39 Identities=18% Similarity=0.327 Sum_probs=31.4
Q ss_pred ceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe-------cCCCCCCC
Q 047331 2 AGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE-------RNGCGGAG 43 (102)
Q Consensus 2 ~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~-------~sdcEGag 43 (102)
+||-.++|++. +-|++.++|-..-.+-++|. ..-|-|.|
T Consensus 82 NGWs~sI~~~~---vd~~d~~~~k~~vg~~a~VrVtLkDGtyhEDiGyG 127 (222)
T KOG4141|consen 82 NGWSSSITSVN---VDFVDEEEGKFSVGVSAIVRVTLKDGTYHEDIGYG 127 (222)
T ss_pred Ccccccceeee---cceeccccCeEEEeEEEEEEEEEecCccccccccc
Confidence 69999999997 99999999986655555554 25688999
No 54
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=50.81 E-value=14 Score=20.94 Aligned_cols=37 Identities=16% Similarity=0.160 Sum_probs=23.3
Q ss_pred ceeEeceecCCC-CeeEEEEEeCCC-CCCceeEEEecCCCC
Q 047331 2 AGWVKIGRKQDK-DWLAFFEVNDGS-CFDNLQVLVERNGCG 40 (102)
Q Consensus 2 ~GWVks~R~~k~-g~~~Fl~lnDGS-~~~~LQvVv~~sdcE 40 (102)
.|-|-+++.... +.+.|+.|.|+| .. +.+++-...++
T Consensus 3 ~g~v~~~~~~~~~~~~~~~~l~D~~~~~--i~~~~~~~~~~ 41 (75)
T cd03524 3 VGIVVAVEEIRTEGKVLIFTLTDGTGGT--IRVTLFGELAE 41 (75)
T ss_pred EEEEEeecccccCCeEEEEEEEcCCCCE--EEEEEEchHHH
Confidence 455666655431 258999999999 55 56666544444
No 55
>PLN02734 glycyl-tRNA synthetase
Probab=43.42 E-value=23 Score=32.27 Aligned_cols=32 Identities=25% Similarity=0.284 Sum_probs=27.0
Q ss_pred ChhhHHHHHHHHHHhhHHHHHhhhchhhhhhh
Q 047331 69 SEADREAAKLFVKEKGEGVAKLKSKKASKEVL 100 (102)
Q Consensus 69 ~~~~iea~ka~v~ekg~~V~~lK~~~s~ke~~ 100 (102)
....|+..++.|+++|+.|..||++++.+.++
T Consensus 5 ~~~~~~~~~~~~~~~~~~~r~l~~~~~~~~~~ 36 (684)
T PLN02734 5 LRDALAEKQAAVTAQGNAVRALKASKADKAEI 36 (684)
T ss_pred HHHHHHHHHHHHHHhHHHHhhhhhccCchHHH
Confidence 45678999999999999999999987776554
No 56
>PF15279 SOBP: Sine oculis-binding protein
Probab=42.16 E-value=7.2 Score=32.20 Aligned_cols=29 Identities=24% Similarity=0.502 Sum_probs=23.3
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|+-|.|.+|..+ .|||+-||-.- ||---+
T Consensus 1 ~cdwckh~rh~~----~y~d~~~g~~~--lqfcs~ 29 (306)
T PF15279_consen 1 VCDWCKHVRHTK----SYVDFQDGERQ--LQFCSD 29 (306)
T ss_pred Cccchhcccchh----heeccccchHH--hhhccH
Confidence 567999999976 89999999866 675443
No 57
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=40.04 E-value=1.1e+02 Score=23.10 Aligned_cols=53 Identities=23% Similarity=0.265 Sum_probs=32.9
Q ss_pred CceeEe--ceecCCCC-eeEEEEEeCCCCCCceeEEEec--CC--CCCC---------CceeEeeehhhhhH
Q 047331 1 LAGWVK--IGRKQDKD-WLAFFEVNDGSCFDNLQVLVER--NG--CGGA---------GEMFQVTTLLSEAE 56 (102)
Q Consensus 1 v~GWVk--s~R~~k~g-~~~Fl~lnDGS~~~~LQvVv~~--sd--cEGa---------ge~fqVTTLl~kae 56 (102)
|.|.|. |++..+.+ .+.| .|.||..- +.|...- .| =||. +..|+-|+||-|-+
T Consensus 56 lGG~V~~GSv~r~~~~~~v~F-~vtD~~~~--v~V~Y~GilPDlFrEGqgVVaeG~~~~g~F~A~~vLAKHd 124 (155)
T PRK13159 56 LGGMVKAGSIQRAADSLKVSF-TVIDKNAA--TQVEYTGILPDLFRDNQSVIANGRMQGGRFVANEVLAKHD 124 (155)
T ss_pred EccEEecCcEEEcCCCcEEEE-EEEcCCcE--EEEEEccCCCccccCCCeEEEEEEEcCCEEEEeEEEecCC
Confidence 457777 77776532 4677 56798543 6666651 00 1111 34899999998876
No 58
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=38.83 E-value=41 Score=31.88 Aligned_cols=32 Identities=22% Similarity=0.399 Sum_probs=25.1
Q ss_pred CceeEeceecC--CCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQ--DKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~--k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|.|++.++|.. |+| ++|+.|.|.+.. +.+++-
T Consensus 958 v~g~i~~~~~~~TkkG-maf~~leD~~g~--~e~~if 991 (1046)
T PRK05672 958 VAGVVTHRQRPGTASG-VTFLTLEDETGM--VNVVVW 991 (1046)
T ss_pred EEEEEEEEEEecCCCc-eEEEEEecCCCC--EEEEEC
Confidence 35777777664 778 999999999988 677664
No 59
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=38.69 E-value=62 Score=25.69 Aligned_cols=50 Identities=24% Similarity=0.334 Sum_probs=34.2
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEecCC------CCC-----CCceeEeeehh
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNG------CGG-----AGEMFQVTTLL 52 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~sd------cEG-----age~fqVTTLl 52 (102)
|.|-|.+.+..-.+.+.||.++||+.- +-+|..|+. -++ -||..+||-+-
T Consensus 56 vkg~V~~~~n~~~~gi~~l~lndgtGt--i~vva~~~tee~l~~n~~~p~~~eGe~veVtGrv 116 (204)
T COG4085 56 VKGEVTADQNAIGGGIESLVLNDGTGT--ITVVASRSTEETLELNEGMPVTVEGEIVEVTGRV 116 (204)
T ss_pred eeeEEEeeecccccceEEEEEECCCCc--EEEEEecChhHhHhhcCCCCccccCcEEEEEEEE
Confidence 457777877444457999999999966 788777522 122 27777887653
No 60
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=37.76 E-value=67 Score=24.29 Aligned_cols=53 Identities=19% Similarity=0.305 Sum_probs=33.6
Q ss_pred CceeEe--ceecCCCC-eeEEEEEeCCCCCCceeEEEe-------c----CCCCCC---CceeEeeehhhhhH
Q 047331 1 LAGWVK--IGRKQDKD-WLAFFEVNDGSCFDNLQVLVE-------R----NGCGGA---GEMFQVTTLLSEAE 56 (102)
Q Consensus 1 v~GWVk--s~R~~k~g-~~~Fl~lnDGS~~~~LQvVv~-------~----sdcEGa---ge~fqVTTLl~kae 56 (102)
|.|.|. |+...+.+ .+.| .|.||... +.|... + --|||. +..|+-|+||-|-+
T Consensus 62 vgG~V~~GSi~r~~~~l~v~F-~vtD~~~~--v~V~Y~GilPDlFrEG~gVVveG~~~~~g~F~A~~vLAKhd 131 (160)
T PRK13165 62 VGGMVMPGSVQRDPNSLKVSF-TLYDAGGS--VTVTYEGILPDLFREGQGIVAQGVLEEGNHIEAKEVLAKHD 131 (160)
T ss_pred EeeEEeCCcEEECCCCeEEEE-EEEcCCeE--EEEEEcccCCccccCCCeEEEEEEECCCCeEEEEEEEecCC
Confidence 357777 77665433 4677 67898543 666654 1 113333 35899999998875
No 61
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=37.38 E-value=69 Score=19.25 Aligned_cols=19 Identities=5% Similarity=-0.083 Sum_probs=15.6
Q ss_pred eeEEEEEeCCCCCCceeEEEe
Q 047331 15 WLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 15 ~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
.+.++.|.|+|.. +.+++-
T Consensus 19 ~~~~~~l~D~tg~--i~~~~f 37 (83)
T cd04492 19 PYLALTLQDKTGE--IEAKLW 37 (83)
T ss_pred cEEEEEEEcCCCe--EEEEEc
Confidence 5899999999987 666664
No 62
>PF10451 Stn1: Telomere regulation protein Stn1; InterPro: IPR018856 The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA. Structural profiling has predicted an OB-fold []. This entry represents the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF6_A 3KF8_A.
Probab=34.08 E-value=79 Score=25.25 Aligned_cols=68 Identities=16% Similarity=0.104 Sum_probs=37.4
Q ss_pred eeEEEEEeCCCCCCceeEEEec--------CCCCCCCceeEeeehhhhhH-HHHHhhcCCCCCChhhHHHHHHHHHH
Q 047331 15 WLAFFEVNDGSCFDNLQVLVER--------NGCGGAGEMFQVTTLLSEAE-KLEKELMKNPPPSEADREAAKLFVKE 82 (102)
Q Consensus 15 ~~~Fl~lnDGS~~~~LQvVv~~--------sdcEGage~fqVTTLl~kae-~~~~~~~~~~~~~~~~iea~ka~v~e 82 (102)
...|+.|.|||....|.+++.. .....-|.+++|+--++.-. +.+-+.+........+++.=+....-
T Consensus 87 ~~~~l~iDD~Sg~~~i~~~~~~~~~~~~~l~~~~~~G~~V~VkG~vsr~~~ql~ve~i~~~~~l~~Ei~fW~~~~~~ 163 (256)
T PF10451_consen 87 DRIILTIDDSSGANTIECKCSKSSYLSMGLPINDLIGKVVEVKGTVSRNERQLDVERIELVRDLNAEIEFWKERMRF 163 (256)
T ss_dssp CEEEEEEE-SSCS-EEEEEEEHHHHHCCCHHCTT-TT-EEEEEEEEESSSEEEEEEEEEEETSCCHHHHHHHHHHHH
T ss_pred ceEEEEEeCCCCceeEEEEEEcccccccCCCccCCCCcEEEEEEEEccCcEEEEEEEEEccCChHHHHHHHHHHHHH
Confidence 6999999999996568888873 12233688888887777211 11122222344455555554444443
No 63
>KOG1276 consensus Protoporphyrinogen oxidase [Coenzyme transport and metabolism]
Probab=33.82 E-value=23 Score=31.27 Aligned_cols=16 Identities=31% Similarity=0.825 Sum_probs=13.0
Q ss_pred CceeEeceecCCCCeeEE
Q 047331 1 LAGWVKIGRKQDKDWLAF 18 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~F 18 (102)
+.|||+|.|..+ .+.|
T Consensus 48 vGGwirS~r~~n--g~if 63 (491)
T KOG1276|consen 48 VGGWIRSDRMQN--GFIF 63 (491)
T ss_pred ccceeeeccCCC--ceee
Confidence 579999988887 6666
No 64
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=33.03 E-value=68 Score=27.54 Aligned_cols=32 Identities=22% Similarity=0.134 Sum_probs=23.2
Q ss_pred ceeEeceecC--CCC-eeEEEEEeCCCCCCceeEEEe
Q 047331 2 AGWVKIGRKQ--DKD-WLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 2 ~GWVks~R~~--k~g-~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
.|+|.++|.. |+| .++|+.|.|.+.. +.+|+-
T Consensus 286 aG~I~~ik~~~TKkG~~maf~~leD~tG~--ie~vvF 320 (449)
T PRK07373 286 VVMLNEVKKIVTKKGDPMAFLQLEDLSGQ--SEAVVF 320 (449)
T ss_pred EEEEEEeEecccCCCCEEEEEEEEECCCC--EEEEEC
Confidence 4777776644 444 6999999999987 566664
No 65
>PF01834 XRCC1_N: XRCC1 N terminal domain; InterPro: IPR002706 DNA-repair protein Xrcc1 functions in the repair of single-strand DNA breaks in mammalian cells and forms a repair complex with beta-Pol, ligase III and PARP []. The NMR solution structure of the Xrcc1 N-terminal domain (Xrcc1 NTD) shows that the structural core is a beta-sandwich with beta-strands connected by loops, three helices and two short two-stranded beta-sheets at each connection side. The Xrcc1 NTD specifically binds single-strand break DNA (gapped and nicked) and a gapped DNA-beta-Pol complex [].; GO: 0003684 damaged DNA binding, 0000012 single strand break repair, 0005634 nucleus; PDB: 3K77_E 3K75_C 3LQC_A 1XNA_A 1XNT_A.
Probab=31.49 E-value=50 Score=24.98 Aligned_cols=40 Identities=25% Similarity=0.544 Sum_probs=23.7
Q ss_pred eEEEEE-eCCCCCCceeEEEecCCCC---CCC---ceeEeeehhhhhHH
Q 047331 16 LAFFEV-NDGSCFDNLQVLVERNGCG---GAG---EMFQVTTLLSEAEK 57 (102)
Q Consensus 16 ~~Fl~l-nDGS~~~~LQvVv~~sdcE---Gag---e~fqVTTLl~kae~ 57 (102)
|.+|+| |.||++ |+|.|.||.+. -.. ..+-.|++.+.+|-
T Consensus 55 I~~IDIGN~gSAf--iEVlVg~S~~~~~~~~~~f~~Ll~~ssfMsp~eS 101 (153)
T PF01834_consen 55 ITSIDIGNEGSAF--IEVLVGRSSWSSTASDQDFEVLLPSSSFMSPSES 101 (153)
T ss_dssp -SEEEEEEEB-SE--EEEEEE-STTS--SSGGGSEEEEEEEESS-HHHH
T ss_pred EEEEeccCCCeEE--EEEEeeccccccccCCCCcEEEEeccCCcCHHHH
Confidence 455666 679999 99999987664 111 24445668888774
No 66
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=29.79 E-value=1.2e+02 Score=22.94 Aligned_cols=53 Identities=21% Similarity=0.285 Sum_probs=33.8
Q ss_pred CceeEe--ceecCCCC-eeEEEEEeCCCCCCceeEEEe-------c----CCCCCC---CceeEeeehhhhhH
Q 047331 1 LAGWVK--IGRKQDKD-WLAFFEVNDGSCFDNLQVLVE-------R----NGCGGA---GEMFQVTTLLSEAE 56 (102)
Q Consensus 1 v~GWVk--s~R~~k~g-~~~Fl~lnDGS~~~~LQvVv~-------~----sdcEGa---ge~fqVTTLl~kae 56 (102)
|.|.|. |+.....+ .+.| .|.||..- +.|... + --|||. +..|+-|+||-|-+
T Consensus 62 vgG~V~~GSv~r~~~~~~v~F-~vtD~~~~--v~V~Y~GilPDlFrEG~gVVveG~~~~~g~F~A~evLAKhd 131 (159)
T PRK13150 62 VGGMVMPGSVRRDPDSLKVNF-SLYDAEGS--VTVSYEGILPDLFREGQGVVVQGTLEKGNHVLAHEVLAKHD 131 (159)
T ss_pred EeeEEeCCcEEECCCCcEEEE-EEEcCCcE--EEEEEeccCCccccCCCeEEEEEEECCCCEEEEeEEEeCCC
Confidence 357777 67665422 4677 67888553 677665 1 113433 35899999998875
No 67
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=29.52 E-value=89 Score=20.70 Aligned_cols=32 Identities=19% Similarity=0.329 Sum_probs=22.0
Q ss_pred CceeEeceecC-CCCeeEEEEEeCCCCCCceeEEEe
Q 047331 1 LAGWVKIGRKQ-DKDWLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 1 v~GWVks~R~~-k~g~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
|.|.|-+.+.. .+| -.|+.|.|.+.. |.+++=
T Consensus 3 v~GeVs~~~~~~~sG-H~yFtlkD~~~~--i~cv~f 35 (91)
T cd04482 3 VTGKVVEEPRTIEGG-HVFFKISDGTGE--IDCAAY 35 (91)
T ss_pred EEEEEeCCeecCCCC-CEEEEEECCCcE--EEEEEE
Confidence 46778877654 334 789999998743 666664
No 68
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=29.01 E-value=53 Score=19.70 Aligned_cols=20 Identities=25% Similarity=0.456 Sum_probs=16.1
Q ss_pred CceeEeceecCCCCeeEEEEEeCC
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDG 24 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDG 24 (102)
+.|+|.++...+ .|++|.+|
T Consensus 4 v~g~V~~v~~~G----v~V~l~~~ 23 (68)
T cd05707 4 VRGFVKNIANNG----VFVTLGRG 23 (68)
T ss_pred EEEEEEEEECcc----EEEEeCCC
Confidence 468999998766 89999875
No 69
>COG0691 SmpB tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones]
Probab=27.93 E-value=41 Score=25.57 Aligned_cols=24 Identities=29% Similarity=0.372 Sum_probs=15.6
Q ss_pred Ccee-EeceecCCCCee--EEEEEeCCC
Q 047331 1 LAGW-VKIGRKQDKDWL--AFFEVNDGS 25 (102)
Q Consensus 1 v~GW-Vks~R~~k~g~~--~Fl~lnDGS 25 (102)
+.|| |||+|..+ .++ +|+.+.+|-
T Consensus 30 L~GtEVKSlRag~-~nl~dsy~~i~~gE 56 (153)
T COG0691 30 LQGTEVKSLRAGK-ANLKDSYARIKKGE 56 (153)
T ss_pred EeeeEeeehhccC-cCcccceEEEeCCe
Confidence 3577 88998854 222 566676665
No 70
>PF14954 LIX1: Limb expression 1
Probab=26.49 E-value=41 Score=27.38 Aligned_cols=21 Identities=29% Similarity=0.679 Sum_probs=18.2
Q ss_pred eeEEEEEeCCCCCCceeEEEe
Q 047331 15 WLAFFEVNDGSCFDNLQVLVE 35 (102)
Q Consensus 15 ~~~Fl~lnDGS~~~~LQvVv~ 35 (102)
-++|+.|.-||||.|.|.--.
T Consensus 59 yVcyVTLPGGSCFGnfq~C~t 79 (252)
T PF14954_consen 59 YVCYVTLPGGSCFGNFQNCPT 79 (252)
T ss_pred eEEEEeCCCCCccCccccCCc
Confidence 579999999999999997554
No 71
>PF06902 Fer4_19: Divergent 4Fe-4S mono-cluster; InterPro: IPR010693 This entry represents bacterial ferredoxins such Ferredoxin-1, -2 and -soy from Streptomyces griseolus and Ferredoxin fas2 from Rhodococcus fascians, plus several bacterial hypothetical proteins that contain three highly conserved cysteine residues. These ferredoxins each bind a 3Fe-4S cluster. Ferredoxin-soy (SoyB) act as electron transport protein for the cytochrome P450-SOY system []. Ferredoxin-1 (SuaB) and Ferredoxin-2 (SubB) act as electron transport proteins for the herbicide-metabolising cytochrome P-450 SU1 and SU2 systems, respectively [, ]. Ferredoxin-fas2 also plays a role in electrontransfer, the fas operon encoding genes involved in cytokinin production and in host plant fasciation (leafy gall).
Probab=25.70 E-value=64 Score=20.54 Aligned_cols=49 Identities=20% Similarity=0.290 Sum_probs=31.9
Q ss_pred ceeEEEecCCCCCCCceeE-eeehhhhhHHHHHhhcCCCCCChhhHHHHHHHHHHh
Q 047331 29 NLQVLVERNGCGGAGEMFQ-VTTLLSEAEKLEKELMKNPPPSEADREAAKLFVKEK 83 (102)
Q Consensus 29 ~LQvVv~~sdcEGage~fq-VTTLl~kae~~~~~~~~~~~~~~~~iea~ka~v~ek 83 (102)
.+.|..++.-|-++|.=.+ .-.+|...++. --.|.+++.+.++.+|..+
T Consensus 5 ~i~V~~d~~~C~hag~Cv~~~p~VFd~~~~~------~v~~d~a~~~~v~~~v~~C 54 (64)
T PF06902_consen 5 DITVTWDRERCIHAGFCVRGAPEVFDQDDEP------WVSPDEASAEEVREAVDRC 54 (64)
T ss_pred cEEEEECcCcccchhhhhcCCCCcccCCCCC------cCCcCccCHHHHHHHHHcC
Confidence 4678888888988887433 44455444321 1266778888888887653
No 72
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=25.67 E-value=52 Score=19.84 Aligned_cols=19 Identities=26% Similarity=0.335 Sum_probs=15.6
Q ss_pred ceeEeceecCCCCeeEEEEEeCC
Q 047331 2 AGWVKIGRKQDKDWLAFFEVNDG 24 (102)
Q Consensus 2 ~GWVks~R~~k~g~~~Fl~lnDG 24 (102)
.|+|.++...+ .|+.|.+|
T Consensus 8 ~g~V~~i~~~G----~fv~l~~~ 26 (72)
T cd05689 8 FGKVTNLTDYG----CFVELEEG 26 (72)
T ss_pred EEEEEEEEeeE----EEEEcCCC
Confidence 58899988877 78899774
No 73
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=25.15 E-value=1.1e+02 Score=18.57 Aligned_cols=37 Identities=19% Similarity=0.320 Sum_probs=20.9
Q ss_pred cCCCCeeEEEEEeCCCCCCceeEEEecCCCCCC--CceeEeeeh
Q 047331 10 KQDKDWLAFFEVNDGSCFDNLQVLVERNGCGGA--GEMFQVTTL 51 (102)
Q Consensus 10 ~~k~g~~~Fl~lnDGS~~~~LQvVv~~sdcEGa--ge~fqVTTL 51 (102)
.+.+| ++|+...| ..-=+.++..+..+| |+...|.-+
T Consensus 5 ~~~~G-fGFv~~~~----~~~DifIp~~~l~~A~~gD~V~v~i~ 43 (58)
T PF08206_consen 5 IHPKG-FGFVIPDD----GGEDIFIPPRNLNGAMDGDKVLVRIT 43 (58)
T ss_dssp E-SSS--EEEEECT-----TEEEEE-HHHHTTS-TT-EEEEEEE
T ss_pred EEcCC-CEEEEECC----CCCCEEECHHHHCCCCCCCEEEEEEe
Confidence 33344 99999988 223567776666666 777666543
No 74
>PF10642 Tom5: Mitochondrial import receptor subunit or translocase; InterPro: IPR019603 This entry represents a short family of yeast proteins. Tom5 is one of three very small translocases of the mitochondrial outer membrane. Tom5 links mitochondrial preprotein receptors to the general import pore []. Although Tom5 has allegedly been identified in vertebrates this could not be confirmed.
Probab=24.82 E-value=81 Score=19.59 Aligned_cols=17 Identities=35% Similarity=0.481 Sum_probs=13.3
Q ss_pred CCCCChhhHHHHHHHHH
Q 047331 65 NPPPSEADREAAKLFVK 81 (102)
Q Consensus 65 ~~~~~~~~iea~ka~v~ 81 (102)
.|.||++++.++++...
T Consensus 6 ~~qpS~eE~k~~e~~A~ 22 (49)
T PF10642_consen 6 PPQPSEEEIKAAEAQAN 22 (49)
T ss_pred CCCCCHHHHHHHHHHHH
Confidence 57889999998877543
No 75
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=24.58 E-value=61 Score=22.64 Aligned_cols=21 Identities=19% Similarity=0.309 Sum_probs=16.2
Q ss_pred CCCCCChhhHHHHHHHHHHhh
Q 047331 64 KNPPPSEADREAAKLFVKEKG 84 (102)
Q Consensus 64 ~~~~~~~~~iea~ka~v~ekg 84 (102)
....|+++||+.+++.....|
T Consensus 69 t~~~P~~~di~RV~~~Laa~G 89 (96)
T PF11829_consen 69 TDELPTPEDIERVRARLAAAG 89 (96)
T ss_dssp CSS-S-HHHHHHHHHHHHTTT
T ss_pred HcCCcCHHHHHHHHHHHHhCC
Confidence 467899999999999888776
No 76
>PF09259 Fve: Fungal immunomodulatory protein Fve; InterPro: IPR015339 This entry represents the FIP-Fve (Fungal Immunomodulatory Protein Fve) is a major fruiting body protein from Flammulina velutipes, a mushroom possessing immunomodulatory activity. It stimulates lymphocyte mitogenesis, suppresses systemic anaphylaxis reactions and oedema, enhances transcription of IL-2, IFN-gamma and TNF-alpha, and haemagglutinates red blood cells. It appears to be a lectin with specificity for complex cell-surface carbohydrates. Fve adopts a tertiary structure consisting of an immunoglobulin-like beta-sandwich, with seven strands arranged in two beta sheets, in a Greek-key topology. It forms a non-covalently linked homodimer containing no Cys, His or Met residues; dimerisation occurs by 3-D domain swapping of the N-terminal helices and is stabilised predominantly by hydrophobic interactions []. ; GO: 0030246 carbohydrate binding, 0002682 regulation of immune system process; PDB: 3KCW_A 1OSY_B 3F3H_B.
Probab=24.24 E-value=44 Score=24.02 Aligned_cols=40 Identities=25% Similarity=0.418 Sum_probs=23.1
Q ss_pred ecCCCCeeEEEEEeCCCCC---CceeEEEecCCCCCCCceeEee
Q 047331 9 RKQDKDWLAFFEVNDGSCF---DNLQVLVERNGCGGAGEMFQVT 49 (102)
Q Consensus 9 R~~k~g~~~Fl~lnDGS~~---~~LQvVv~~sdcEGage~fqVT 49 (102)
.+.|..++-||+-|.|-.+ +.|||.|--.| .|.+|.|-|.
T Consensus 67 ~sdGsQkiNFLeYn~GyGiADT~TIQV~VvdPd-tgnse~~iiA 109 (111)
T PF09259_consen 67 ESDGSQKINFLEYNSGYGIADTNTIQVFVVDPD-TGNSEDFIIA 109 (111)
T ss_dssp -TTS-EEEEGGGTTTT--EETTS-EEEEEE-TT-TTT--EEEEE
T ss_pred cCCCCceEeEEEecCCcccccCceEEEEEEcCC-CCCccceEEe
Confidence 3456668999999999854 67899654344 5667777653
No 77
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=22.90 E-value=1.5e+02 Score=20.08 Aligned_cols=31 Identities=16% Similarity=0.020 Sum_probs=26.6
Q ss_pred ceeEeceecCCCCeeEEEEEeCCCCCCceeEEEec
Q 047331 2 AGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVER 36 (102)
Q Consensus 2 ~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~ 36 (102)
.|.|++++.+. .=.|+.|.|-|.- ++..+.|
T Consensus 8 ~v~Iks~~~~~--~D~~v~l~DpTG~--i~~tiH~ 38 (86)
T PF15072_consen 8 VVIIKSIVPSS--EDAFVVLKDPTGE--IRGTIHR 38 (86)
T ss_pred EEEEEEeeccC--CCeEEEEECCCCc--EEEEEeH
Confidence 57899999998 5689999999885 8988874
No 78
>PRK14450 acylphosphatase; Provisional
Probab=22.27 E-value=44 Score=22.20 Aligned_cols=9 Identities=33% Similarity=0.397 Sum_probs=6.4
Q ss_pred CceeEecee
Q 047331 1 LAGWVKIGR 9 (102)
Q Consensus 1 v~GWVks~R 9 (102)
|.|||++..
T Consensus 30 l~G~V~N~~ 38 (91)
T PRK14450 30 LCGYAKNLA 38 (91)
T ss_pred CEEEEEECC
Confidence 579987753
No 79
>CHL00173 cpeA phycoerythrin alpha subunit; Provisional
Probab=22.27 E-value=1.2e+02 Score=22.93 Aligned_cols=39 Identities=21% Similarity=0.250 Sum_probs=26.1
Q ss_pred eeehhhhhHHHHHhhcCCCCCChhhHHHHHHHHHHhhHHHHHhhh
Q 047331 48 VTTLLSEAEKLEKELMKNPPPSEADREAAKLFVKEKGEGVAKLKS 92 (102)
Q Consensus 48 VTTLl~kae~~~~~~~~~~~~~~~~iea~ka~v~ekg~~V~~lK~ 92 (102)
||++++.++.. ---++..+|++++..+..-..-++..+.
T Consensus 5 it~~i~~AD~~------gRyls~~eL~~l~~~~~~a~~rl~aa~~ 43 (164)
T CHL00173 5 ITTTISAADAA------GRFPSSSDLESVQGNIQRAAARLEAAEK 43 (164)
T ss_pred HHHHHHHHHhc------cCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67788888743 3456788888888876666655554443
No 80
>PRK00624 glycine cleavage system protein H; Provisional
Probab=22.16 E-value=1.4e+02 Score=20.98 Aligned_cols=22 Identities=23% Similarity=0.261 Sum_probs=16.0
Q ss_pred CeeEEEEEeC-CCCCCceeEEEe
Q 047331 14 DWLAFFEVND-GSCFDNLQVLVE 35 (102)
Q Consensus 14 g~~~Fl~lnD-GS~~~~LQvVv~ 35 (102)
|.+.|+++.. |+.+..-|.+..
T Consensus 32 G~i~~v~lp~~G~~V~~g~~i~~ 54 (114)
T PRK00624 32 GNILHIDLPSVGSFCKEGEVLVI 54 (114)
T ss_pred CCEEEEECCCCCCEEeCCCEEEE
Confidence 3899999965 887766666554
No 81
>TIGR03077 not_gcvH glycine cleavage protein H-like protein, Chlamydial. The H protein (GcvH) of the glycine cleavage system shuttles the methylamine group of glycine from the P protein to the T protein. Most Chlamydia but lack the P and T proteins, and have a single homolog of GcvH that appears deeply split from canonical GcvH in molecular phylogenetic trees. The protein family modeled here is observed the Chlamydial GcvH homolog, so far always seen as part of a two-gene operon, downstream of a member of the uncharacterized protein family TIGR03076. The function of this protein is unknown.
Probab=21.76 E-value=1.5e+02 Score=20.69 Aligned_cols=22 Identities=23% Similarity=0.274 Sum_probs=16.5
Q ss_pred CeeEEEEEeC-CCCCCceeEEEe
Q 047331 14 DWLAFFEVND-GSCFDNLQVLVE 35 (102)
Q Consensus 14 g~~~Fl~lnD-GS~~~~LQvVv~ 35 (102)
|.+.|+++.+ |+.+..-|.+..
T Consensus 30 G~i~~v~lp~~G~~V~~g~~i~~ 52 (110)
T TIGR03077 30 GNILHIDLPSVGSSCKEGEVLVI 52 (110)
T ss_pred CCEEEEECCCCCCEEcCCCEEEE
Confidence 4899999966 887766666654
No 82
>TIGR03824 FlgM_jcvi flagellar biosynthesis anti-sigma factor FlgM. FlgM interacts with and inhibits the alternative sigma factor sigma(28) FliA. The C-terminus of FlgM contains the sigma(28)-binding domain.
Probab=21.47 E-value=1.7e+02 Score=19.45 Aligned_cols=42 Identities=14% Similarity=0.248 Sum_probs=33.0
Q ss_pred CCceeEeeehhhhhHHHHHhhcCCCCCChhhHHHHHHHHHHh
Q 047331 42 AGEMFQVTTLLSEAEKLEKELMKNPPPSEADREAAKLFVKEK 83 (102)
Q Consensus 42 age~fqVTTLl~kae~~~~~~~~~~~~~~~~iea~ka~v~ek 83 (102)
.++-.+++..-.......+.+...|+...+=|+..|++|.+-
T Consensus 37 ~~d~v~lS~~a~~l~~~~~~~~~~p~v~~~kV~~ik~aI~~G 78 (95)
T TIGR03824 37 SGDSVTLSSAAQQLQSLEAALASSPDVDAEKVAEIKAAIANG 78 (95)
T ss_pred CCCeEEECHHHHHHHHHHHHHhcCchhhHHHHHHHHHHHHcC
Confidence 467888888766666666777778999999999999988764
No 83
>KOG3360 consensus Acylphosphatase [Energy production and conversion]
Probab=21.34 E-value=46 Score=23.65 Aligned_cols=10 Identities=40% Similarity=0.777 Sum_probs=7.2
Q ss_pred CceeEeceec
Q 047331 1 LAGWVKIGRK 10 (102)
Q Consensus 1 v~GWVks~R~ 10 (102)
|+|||++.|.
T Consensus 36 lrGWv~Nt~~ 45 (98)
T KOG3360|consen 36 LRGWVMNTSE 45 (98)
T ss_pred ceEEEEecCC
Confidence 5789888553
No 84
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.14 E-value=94 Score=18.49 Aligned_cols=27 Identities=4% Similarity=0.113 Sum_probs=19.4
Q ss_pred CceeEeceecCCCCeeEEEEEeCCCCCCceeEEEec
Q 047331 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVER 36 (102)
Q Consensus 1 v~GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~ 36 (102)
+.|+|.++...+ .|++|.+| ++.+++.
T Consensus 4 ~~g~V~~v~~~G----~~V~l~~~-----~~gli~~ 30 (70)
T cd05698 4 THGTIVKVKPNG----CIVSFYNN-----VKGFLPK 30 (70)
T ss_pred EEEEEEEEecCc----EEEEECCC-----CEEEEEH
Confidence 368899887655 89999765 4566664
No 85
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=20.53 E-value=1.8e+02 Score=19.41 Aligned_cols=31 Identities=13% Similarity=0.299 Sum_probs=21.5
Q ss_pred eeEeceecCCCCeeEEEEEeCCCCCCceeEEEec
Q 047331 3 GWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVER 36 (102)
Q Consensus 3 GWVks~R~~k~g~~~Fl~lnDGS~~~~LQvVv~~ 36 (102)
|=|-+.+...+ ...|+.|.|+. ..+++++-+
T Consensus 28 GEIs~~~~~~~-gh~YftLkD~~--a~i~~~~~~ 58 (99)
T PF13742_consen 28 GEISNLKRHSS-GHVYFTLKDEE--ASISCVIFR 58 (99)
T ss_pred EEEeecEECCC-ceEEEEEEcCC--cEEEEEEEH
Confidence 33456666433 48999999988 458888764
No 86
>PRK14441 acylphosphatase; Provisional
Probab=20.26 E-value=50 Score=22.16 Aligned_cols=8 Identities=38% Similarity=0.895 Sum_probs=6.2
Q ss_pred CceeEece
Q 047331 1 LAGWVKIG 8 (102)
Q Consensus 1 v~GWVks~ 8 (102)
|.|||++.
T Consensus 33 L~G~V~N~ 40 (93)
T PRK14441 33 VEGWVRNL 40 (93)
T ss_pred cEEEEEEC
Confidence 57999875
No 87
>PF02728 Cu_amine_oxidN3: Copper amine oxidase, N3 domain; InterPro: IPR015802 Amine oxidases (AO) are enzymes that catalyse the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. There are two classes of amine oxidases: flavin-containing (1.4.3.4 from EC) and copper-containing (1.4.3.6 from EC). Copper-containing AO act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor []: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 Copper-containing amine oxidases are found in bacteria, fungi, plants and animals. In prokaryotes, the enzyme enables various amine substrates to be used as sources of carbon and nitrogen [, ]. In eukaryotes they have a broader range of functions, including cell differentiation and growth, wound healing, detoxification and cell signalling []. The copper amine oxidases occur as mushroom-shaped homodimers of 70-95 kDa, each monomer containing a copper ion and a covalently bound redox cofactor, topaquinone (TPQ). TPQ is formed by post-translational modification of a conserved tyrosine residue. The copper ion is coordinated with three histidine residues and two water molecules in a distorted square pyramidal geometry, and has a dual function in catalysis and TPQ biogenesis. The catalytic domain is the largest of the 3-4 domains found in copper amine oxidases, and consists of a beta sandwich of 18 strands in two sheets. The active site is buried and requires a conformational change to allow the substrate access. The two N-terminal domains share a common structural fold, its core consisting of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the stalk, of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other [, ]. This entry represents one (N3) of the two N-terminal domains (N2/N3) that share a similar structure.; GO: 0005507 copper ion binding, 0008131 primary amine oxidase activity, 0048038 quinone binding, 0009308 amine metabolic process, 0055114 oxidation-reduction process; PDB: 1TU5_A 2PNC_B 3MPH_B 3HII_B 3HI7_A 3K5T_A 3HIG_A 1SPU_A 2WGQ_A 2WO0_A ....
Probab=20.22 E-value=1.5e+02 Score=19.73 Aligned_cols=29 Identities=31% Similarity=0.299 Sum_probs=22.4
Q ss_pred CCCChhhHHHHHHHHHHhhHHHHHhhhch
Q 047331 66 PPPSEADREAAKLFVKEKGEGVAKLKSKK 94 (102)
Q Consensus 66 ~~~~~~~iea~ka~v~ekg~~V~~lK~~~ 94 (102)
||.+.+|.+++..++++.-...+.|++.+
T Consensus 1 ppi~~~E~~~~~~~~~~~p~~~~al~~rg 29 (101)
T PF02728_consen 1 PPITLEEFAEAEEIVKADPEFQAALKKRG 29 (101)
T ss_dssp S---HHHHHHHHHHHHTGHHHHHHHHHTT
T ss_pred CCcCHHHHHHHHHHHHHCHHHHHHHHHhC
Confidence 57788899999999998888888888754
Done!