Query gi|254781141|ref|YP_003065554.1| hypothetical protein CLIBASIA_05225 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 196
No_of_seqs 124 out of 155
Neff 6.0
Searched_HMMs 39220
Date Mon May 30 06:50:58 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781141.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd07321 Extradiol_Dioxygenase_ 74.9 4.8 0.00012 20.7 3.9 42 92-133 11-53 (77)
2 pfam07746 LigA Aromatic-ring-o 74.1 6.1 0.00015 20.0 4.3 42 94-135 9-50 (88)
3 cd07925 LigA_like_1 The A subu 72.4 6.8 0.00017 19.6 4.3 43 93-135 23-65 (106)
4 cd07921 PCA_45_Doxase_A_like S 70.6 7.9 0.0002 19.2 4.2 43 93-135 23-65 (106)
5 PRK13378 protocatechuate 4,5-d 66.9 10 0.00026 18.4 4.3 44 92-135 33-76 (117)
6 cd07924 PCA_45_Doxase_A The A 64.5 11 0.00029 18.1 4.3 43 93-135 31-73 (121)
7 PRK13377 protocatechuate 4,5-d 63.2 12 0.00031 18.0 4.3 43 93-135 34-76 (129)
8 pfam08855 DUF1825 Domain of un 63.0 9.2 0.00023 18.8 3.3 44 82-126 52-95 (108)
9 cd07923 Gallate_dioxygenase_C 61.8 13 0.00033 17.8 4.2 44 93-136 15-58 (94)
10 pfam08506 Cse1 Cse1. This doma 60.7 13 0.00034 17.7 6.3 23 25-47 200-222 (370)
11 PRK06800 fliH flagellar assemb 58.9 14 0.00037 17.5 8.4 101 33-133 24-137 (229)
12 KOG1991 consensus 58.7 14 0.00037 17.4 4.3 116 4-121 334-500 (1010)
13 COG0587 DnaE DNA polymerase II 58.3 15 0.00038 17.4 4.5 54 71-125 683-736 (1139)
14 pfam01244 Peptidase_M19 Membra 57.6 15 0.00038 17.3 4.5 28 105-132 287-314 (316)
15 TIGR00084 ruvA Holliday juncti 56.8 11 0.00028 18.3 2.8 28 98-125 167-194 (217)
16 COG3184 Uncharacterized protei 53.9 17 0.00044 16.9 5.9 97 22-125 21-118 (183)
17 PRK13379 protocatechuate 4,5-d 52.5 18 0.00046 16.8 4.2 44 93-136 35-78 (119)
18 TIGR02389 RNA_pol_rpoA2 DNA-di 50.8 19 0.00048 16.7 3.2 45 92-142 288-332 (397)
19 pfam04695 Pex14_N Peroxisomal 49.9 16 0.0004 17.2 2.7 39 85-123 5-43 (79)
20 cd07922 CarBa CarBa is the A s 47.9 21 0.00054 16.3 3.3 35 93-127 14-48 (81)
21 pfam09440 eIF3_N eIF3 subunit 47.5 22 0.00055 16.3 5.7 46 79-127 81-130 (133)
22 pfam02787 CPSase_L_D3 Carbamoy 46.6 19 0.00049 16.6 2.8 25 103-127 60-84 (122)
23 cd06549 GH18_trifunctional GH1 42.0 26 0.00067 15.7 3.4 25 93-117 83-107 (298)
24 pfam10302 DUF2407 Putative mem 40.8 17 0.00043 17.0 1.7 18 106-123 119-138 (252)
25 cd02874 GH18_CFLE_spore_hydrol 40.6 27 0.0007 15.6 3.3 25 93-117 82-106 (313)
26 KOG0455 consensus 40.2 7.4 0.00019 19.4 -0.2 48 86-133 180-231 (364)
27 pfam06382 DUF1074 Protein of u 39.8 28 0.00072 15.5 4.3 61 91-161 75-140 (187)
28 COG2355 Zn-dependent dipeptida 39.7 28 0.00072 15.5 4.6 43 91-137 270-312 (313)
29 TIGR02302 aProt_lowcomp conser 38.9 29 0.00074 15.4 7.2 113 72-193 506-622 (899)
30 PRK13367 protocatechuate 4,5-d 38.9 29 0.00074 15.4 4.0 55 84-143 323-378 (418)
31 pfam03359 GKAP Guanylate-kinas 38.2 30 0.00076 15.3 6.2 70 114-183 233-312 (342)
32 pfam07499 RuvA_C RuvA, C-termi 38.0 29 0.00073 15.5 2.5 25 102-126 2-26 (47)
33 pfam01793 Glyco_transf_15 Glyc 35.7 26 0.00067 15.7 2.1 29 89-117 73-101 (274)
34 PRK13901 ruvA Holliday junctio 35.4 25 0.00065 15.8 1.9 24 102-125 143-166 (196)
35 pfam04877 Hairpins HrpZ. HrpZ 35.0 33 0.00085 15.0 4.4 11 11-21 166-176 (277)
36 TIGR01991 HscA Fe-S protein as 34.8 30 0.00076 15.3 2.2 10 131-140 523-532 (628)
37 pfam11867 DUF3387 Domain of un 34.5 34 0.00087 15.0 2.9 136 48-190 170-313 (333)
38 KOG2629 consensus 34.4 25 0.00063 15.9 1.8 95 14-116 103-198 (300)
39 PTZ00217 flap endonuclease-1; 33.0 36 0.00092 14.8 3.2 29 92-125 299-328 (394)
40 PHA00542 putative Cro-like pro 31.6 38 0.00097 14.6 2.8 39 89-127 4-44 (82)
41 COG5656 SXM1 Importin, protein 31.6 28 0.00072 15.5 1.7 38 9-46 337-379 (970)
42 pfam10929 DUF2811 Protein of u 31.2 39 0.00098 14.6 5.0 47 75-124 6-52 (57)
43 cd02876 GH18_SI-CLP Stabilin-1 31.0 39 0.00099 14.6 3.3 28 93-120 87-114 (318)
44 KOG4472 consensus 30.8 33 0.00085 15.0 1.9 30 89-118 151-180 (399)
45 COG5020 KTR1 Mannosyltransfera 30.8 33 0.00085 15.0 1.9 30 89-118 151-180 (399)
46 pfam00816 Histone_HNS H-NS his 30.6 39 0.001 14.5 3.7 21 100-120 23-43 (91)
47 KOG1992 consensus 30.2 24 0.00061 16.0 1.1 113 10-126 331-456 (960)
48 pfam11198 DUF2857 Protein of u 30.1 40 0.001 14.5 2.3 30 159-188 116-145 (181)
49 pfam08069 Ribosomal_S13_N Ribo 28.5 43 0.0011 14.3 3.0 33 89-123 21-53 (60)
50 pfam01371 Trp_repressor Trp re 28.4 43 0.0011 14.3 3.4 56 82-145 2-59 (88)
51 COG3722 MtlR Transcriptional r 28.1 43 0.0011 14.3 4.0 35 88-122 80-116 (174)
52 PRK05672 dnaE2 error-prone DNA 27.8 44 0.0011 14.2 4.7 60 66-125 666-725 (1050)
53 TIGR03253 oxalate_frc formyl-C 27.4 20 0.00052 16.5 0.3 32 91-122 292-325 (415)
54 KOG0139 consensus 27.2 45 0.0011 14.2 7.2 85 35-119 291-378 (398)
55 PHA02512 minor structural prot 26.9 45 0.0012 14.1 9.3 48 73-123 147-198 (844)
56 PRK05398 formyl-coenzyme A tra 26.5 22 0.00056 16.2 0.4 33 91-123 293-327 (416)
57 pfam06401 Alpha-2-MRAP_C Alpha 25.4 48 0.0012 13.9 3.5 29 91-124 106-134 (205)
58 cd06548 GH18_chitinase The GH1 25.0 49 0.0013 13.9 3.4 27 94-120 105-131 (322)
59 pfam01471 PG_binding_1 Putativ 24.9 49 0.0013 13.9 1.9 36 102-137 4-39 (57)
60 PRK03525 crotonobetainyl-CoA:c 24.2 20 0.0005 16.6 -0.2 11 177-187 391-401 (405)
61 cd02875 GH18_chitobiase Chitob 24.1 51 0.0013 13.8 3.4 28 93-120 91-118 (358)
62 pfam04587 ADP_PFK_GK ADP-speci 23.6 49 0.0012 13.9 1.7 33 92-124 259-291 (444)
63 pfam02375 JmjN jmjN domain. 23.4 53 0.0013 13.7 2.0 20 92-114 9-28 (34)
64 pfam09388 SpoOE-like Spo0E lik 23.3 53 0.0013 13.7 3.0 25 100-124 7-31 (45)
65 cd06545 GH18_3CO4_chitinase Th 23.1 53 0.0014 13.7 3.4 28 93-120 78-105 (253)
66 PRK13795 hypothetical protein; 22.9 54 0.0014 13.6 3.0 37 80-121 423-459 (630)
67 pfam07862 Nif11 Nitrogen fixat 22.7 51 0.0013 13.8 1.7 23 94-116 15-42 (49)
68 TIGR02990 ectoine_eutA ectoine 22.6 50 0.0013 13.8 1.6 24 113-136 154-178 (239)
69 TIGR01245 trpD anthranilate ph 22.1 56 0.0014 13.5 4.4 40 80-124 12-53 (331)
70 KOG0031 consensus 22.0 42 0.0011 14.3 1.1 43 85-127 102-146 (171)
71 cd01938 ADPGK_ADPPFK ADP-depen 21.9 56 0.0014 13.5 2.0 34 92-125 253-286 (445)
72 TIGR01420 pilT_fam twitching m 21.7 14 0.00036 17.5 -1.4 14 29-42 158-171 (350)
73 PRK07668 hypothetical protein; 21.6 57 0.0015 13.5 3.1 34 97-130 4-37 (248)
74 pfam10932 DUF2783 Protein of u 21.5 57 0.0015 13.4 3.4 40 89-134 3-42 (60)
75 TIGR01926 peroxid_rel uncharac 21.5 55 0.0014 13.5 1.6 21 109-129 141-161 (179)
76 KOG1546 consensus 20.4 46 0.0012 14.1 1.1 37 103-139 87-131 (362)
77 pfam00531 Death Death domain. 20.2 61 0.0016 13.3 3.4 26 100-125 9-34 (83)
78 TIGR01369 CPSaseII_lrg carbamo 20.2 61 0.0016 13.3 4.7 46 76-130 468-518 (1089)
No 1
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=74.92 E-value=4.8 Score=20.68 Aligned_cols=42 Identities=19% Similarity=0.173 Sum_probs=34.3
Q ss_pred CC-CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHH
Q ss_conf 65-8989999999999999997599989997205999999999
Q gi|254781141|r 92 QT-KDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAY 133 (196)
Q Consensus 92 e~-~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~ 133 (196)
++ .||+.++.|..+-..|...+|.|++|...|.+--...+++
T Consensus 11 ~l~~~p~~rerF~~D~~a~l~~~~Lt~ee~~al~~~D~~~L~~ 53 (77)
T cd07321 11 QLLVKPEVKERFKADPEAVLAEYGLTPEEKAALLARDVGALYV 53 (77)
T ss_pred HHCCCHHHHHHHHHCHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9837999999998299999987699999999988568999999
No 2
>pfam07746 LigA Aromatic-ring-opening dioxygenase LigAB, LigA subunit. This is a family of aromatic ring opening dioxygenases which catalyse the ring-opening reaction of protocatechuate and related compounds.
Probab=74.13 E-value=6.1 Score=19.98 Aligned_cols=42 Identities=14% Similarity=0.165 Sum_probs=36.4
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHH
Q ss_conf 898999999999999999759998999720599999999999
Q gi|254781141|r 94 KDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAYYA 135 (196)
Q Consensus 94 ~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~A 135 (196)
.+|+-++.|..+-..|...+|.|++|...|.+-..+.+++-.
T Consensus 9 ~~~~~R~~F~~D~eay~~~~~Lt~eqr~av~~rD~~~L~~~G 50 (88)
T pfam07746 9 IKAENRERFLADEEAYLDEYGLTEEQKAAVRARDWNGLIALG 50 (88)
T ss_pred CCHHHHHHHHHCHHHHHHHCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf 879999999839999987279999999999826699999945
No 3
>cd07925 LigA_like_1 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB). The proteins of unknown function in this subfamily are similar to the A subunit of the Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds.
Probab=72.44 E-value=6.8 Score=19.63 Aligned_cols=43 Identities=19% Similarity=0.270 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHH
Q ss_conf 5898999999999999999759998999720599999999999
Q gi|254781141|r 93 TKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAYYA 135 (196)
Q Consensus 93 ~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~A 135 (196)
+..|+-++.|+.+=..|...+|.|+++...|.|-..+.+|+-.
T Consensus 23 l~~~~nRe~F~ade~Ay~d~~~Lt~eqk~aV~~RD~~~ll~~G 65 (106)
T cd07925 23 FNDAANREAFLADEEAYCEKFGLTPEQKQAVRNRDVLRMLEAG 65 (106)
T ss_pred HCCHHHHHHHHHCHHHHHHHCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf 7779889999829999998769999999999973699999906
No 4
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit.
Probab=70.64 E-value=7.9 Score=19.22 Aligned_cols=43 Identities=19% Similarity=0.227 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHH
Q ss_conf 5898999999999999999759998999720599999999999
Q gi|254781141|r 93 TKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAYYA 135 (196)
Q Consensus 93 ~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~A 135 (196)
+..|+-++.|+.+=..|...+|.|+++...|.|-..+.+|+..
T Consensus 23 l~~~~nRe~F~ade~Ay~d~~~Lt~eqk~aV~~RD~~~ll~~G 65 (106)
T cd07921 23 LNKAENREAFKADEEAYCDKFGLTEEQKQAVLDRDWLRLLELG 65 (106)
T ss_pred HCCHHHHHHHHHCHHHHHHHCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf 7779889999819999998769999999999973699999906
No 5
>PRK13378 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=66.93 E-value=10 Score=18.42 Aligned_cols=44 Identities=20% Similarity=0.269 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHH
Q ss_conf 65898999999999999999759998999720599999999999
Q gi|254781141|r 92 QTKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAYYA 135 (196)
Q Consensus 92 e~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~A 135 (196)
.+..|+-++.|..+=..|...+|.|+++-..|.|-..+.+|+-.
T Consensus 33 Sl~~~~nRe~F~ade~AY~d~~~Lteeqr~aV~~RD~~~ll~lG 76 (117)
T PRK13378 33 SFNDAANRAAFLADEAAYCRKYGLNEEQKEAIRNRDVLQLLAAG 76 (117)
T ss_pred HHCCHHHHHHHHHCHHHHHHHCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf 96679999999829999998769999999999973799999946
No 6
>cd07924 PCA_45_Doxase_A The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit. The A subunit is the non-catalytic subunit of Protocatechuate (PCA) 4,5-dioxygenase (LigAB), which is composed of A and B subunits that form a tetramer. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As a member of the Class III extradiol dioxygenase family, LigAB uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon.
Probab=64.54 E-value=11 Score=18.12 Aligned_cols=43 Identities=9% Similarity=0.021 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHH
Q ss_conf 5898999999999999999759998999720599999999999
Q gi|254781141|r 93 TKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAYYA 135 (196)
Q Consensus 93 ~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~A 135 (196)
+..|+-++.|..+=..|...+|.|+++-..|.|-..+.+|+-.
T Consensus 31 L~~~~nRe~F~ade~Ay~d~~~Lteeqk~aV~~RD~~~li~lG 73 (121)
T cd07924 31 LMKAENRERFKADERAYLDKWPMTEEQKQAVLARDYNRMLALG 73 (121)
T ss_pred HCCHHHHHHHHHCHHHHHHHCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf 7679889999839999998769999999999974799999926
No 7
>PRK13377 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=63.16 E-value=12 Score=17.96 Aligned_cols=43 Identities=9% Similarity=-0.011 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHH
Q ss_conf 5898999999999999999759998999720599999999999
Q gi|254781141|r 93 TKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAYYA 135 (196)
Q Consensus 93 ~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~A 135 (196)
+..|+-++.|+.+=..|...+|.|+++-..|.|-..+.+|+-.
T Consensus 34 L~~~~nRe~F~aDe~AY~d~~~Lteeqk~aV~~RD~~~li~lG 76 (129)
T PRK13377 34 LMKAENRARFKADERAYLDEWPMTEEQKQAVLARDLNRCIALG 76 (129)
T ss_pred HCCHHHHHHHHHCHHHHHHHCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf 7679899999819999998769999999999973799999926
No 8
>pfam08855 DUF1825 Domain of unknown function (DUF1825). This uncharacterized family of proteins are principally found in cyanobacteria.
Probab=63.00 E-value=9.2 Score=18.78 Aligned_cols=44 Identities=14% Similarity=0.216 Sum_probs=33.4
Q ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCH
Q ss_conf 999999958365898999999999999999759998999720599
Q gi|254781141|r 82 ENQQLEHLFPQTKDPAQRENFFKNLFRIGNILGFQKEEMVDITDH 126 (196)
Q Consensus 82 e~~~L~e~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~ 126 (196)
-++.+..++ .++|+--|...+..|.+.+.-.||++++|+.+.|.
T Consensus 52 KQki~y~Rl-sLSdDpeA~~mke~i~~sa~~mG~~~~dm~~~F~~ 95 (108)
T pfam08855 52 RQRIFYKRL-ELSDDFEAKMMKEQLKTQLNQFGFTPTNLLEMFDQ 95 (108)
T ss_pred HHHHHHHHH-HHCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf 999999997-65589889999999999999859982159999999
No 9
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=61.79 E-value=13 Score=17.80 Aligned_cols=44 Identities=23% Similarity=0.363 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHH
Q ss_conf 58989999999999999997599989997205999999999999
Q gi|254781141|r 93 TKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAYYAQ 136 (196)
Q Consensus 93 ~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~Am 136 (196)
+..|+-++.|..+=..|...+|.|+|+-..|-+-..+.+|+..-
T Consensus 15 l~~~~nRe~F~ade~Ay~d~~~Lt~eqk~av~~RDw~~mi~~Gg 58 (94)
T cd07923 15 LIEPAHRERFLEDPEALFDEAGLTEEERTLIRNRDWIGMIRYGV 58 (94)
T ss_pred HCCHHHHHHHHHCHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf 77788899997099999987699999999999616999998376
No 10
>pfam08506 Cse1 Cse1. This domain is present in Cse1 nuclear export receptor proteins. Cse1 mediates the nuclear export of importin alpha. This domain contains HEAT repeats.
Probab=60.69 E-value=13 Score=17.67 Aligned_cols=23 Identities=22% Similarity=0.173 Sum_probs=18.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99918999943899999999999
Q gi|254781141|r 25 DDSSPTLEKTYPETYHRIRYLRQ 47 (196)
Q Consensus 25 ~~p~~~L~~~DP~~Y~~~k~~~~ 47 (196)
-+.|++|++.||++|+|..-+--
T Consensus 200 Re~DeElFED~P~EyIRrDlEGS 222 (370)
T pfam08506 200 RESDEELFEDDPIEYIRRDLEGS 222 (370)
T ss_pred CHHHHHHHCCCHHHHHHHHCCCC
T ss_conf 67779886679899998733347
No 11
>PRK06800 fliH flagellar assembly protein H; Validated
Probab=58.91 E-value=14 Score=17.47 Aligned_cols=101 Identities=10% Similarity=0.045 Sum_probs=48.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHCCCCCCH---------HHHHH
Q ss_conf 9438999999999999999999999999999999999999999--999999999999958365898---------99999
Q gi|254781141|r 33 KTYPETYHRIRYLRQKALNIINHFVETGRNPDNIAKELDSEIL--EKKLIAENQQLEHLFPQTKDP---------AQREN 101 (196)
Q Consensus 33 ~~DP~~Y~~~k~~~~~~~~~~~~~~~e~q~~~q~q~~~q~~~~--q~~l~~e~~~L~e~iPe~~D~---------~k~~~ 101 (196)
=-|||+-.....+++...+.+...+.....-..+-..+|+..- .+.|..+...+.+.+-||--. +.-..
T Consensus 24 y~~~i~~~~ee~e~~~d~~eL~~~Q~~L~~e~~~l~~eqQ~l~~e~~~l~aek~~~~~~~~e~~~~~e~~r~~fekekqq 103 (229)
T PRK06800 24 FPKPIEVEEEEEEIQVDHEELLAQQKSLHKELNQLRQEQQKLERERQQLLADREQFQMHVQEQMKEIEAARQQFQKEQQE 103 (229)
T ss_pred CCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 36702354312620226999999999999999999999999999999999889999999999999999999999999999
Q ss_pred HHHHHHHHH--HHCCCCHHHHHHHCCHHHHHHHH
Q ss_conf 999999999--97599989997205999999999
Q gi|254781141|r 102 FFKNLFRIG--NILGFQKEEMVDITDHRLLSLAY 133 (196)
Q Consensus 102 ~~~~i~~~~--~~~Gfs~eEi~~v~D~R~i~vl~ 133 (196)
.+..+.+++ .+....+.=|++..|.|.+.||-
T Consensus 104 ~~~~~t~~LwdeSi~LAEkIV~QaiDtRql~vlP 137 (229)
T PRK06800 104 TAYEWTELLWDQSFQLAEKIVNQAVDTRLLDVLP 137 (229)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999878889999999864377887889
No 12
>KOG1991 consensus
Probab=58.70 E-value=14 Score=17.45 Aligned_cols=116 Identities=15% Similarity=0.137 Sum_probs=59.8
Q ss_pred HHHHHHHHHHHHHHHHHHC-----CCCCCCHHHHHHHHHHHHHHHHHHH-------------------HH-HHHHHHHHH
Q ss_conf 9999999999999997320-----6899918999943899999999999-------------------99-999999999
Q gi|254781141|r 4 QAKILAQSAEALAQLINHH-----IPDDSSPTLEKTYPETYHRIRYLRQ-------------------KA-LNIINHFVE 58 (196)
Q Consensus 4 ~a~~~aq~~~~l~q~~~~~-----~p~~p~~~L~~~DP~~Y~~~k~~~~-------------------~~-~~~~~~~~~ 58 (196)
.+..+..+.+-+.-++..- -++.-+++|+++||.+|.|.+...- .+ ++.++.+.+
T Consensus 334 ~~~twkll~PHl~~ii~~vIFPlmc~~d~deelwe~DP~EYiR~~~Di~ed~~sp~~Aa~~~l~~~~~KR~ke~l~k~l~ 413 (1010)
T KOG1991 334 HASTWKLLKPHLQVIIQDVIFPLMCFNDEDEELWEEDPYEYIRKKFDIFEDGYSPDTAALDFLTTLVSKRGKETLPKILS 413 (1010)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCHHHHHHHCCCHHCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf 89899874259999998742331078813187774197999985373104567974789999999998403222266999
Q ss_pred HHHHHHHHHHHH---------HHHH------HHH------HHHHHHH--HHHHHCCCCCCHHHHHHHHHHHHHHHH---H
Q ss_conf 999999999999---------9999------999------9999999--999958365898999999999999999---7
Q gi|254781141|r 59 TGRNPDNIAKEL---------DSEI------LEK------KLIAENQ--QLEHLFPQTKDPAQRENFFKNLFRIGN---I 112 (196)
Q Consensus 59 e~q~~~q~q~~~---------q~~~------~q~------~l~~e~~--~L~e~iPe~~D~~k~~~~~~~i~~~~~---~ 112 (196)
=.-.+-..-.+. ..-+ ... -.+.+.+ .....+|+|++|--- +++..+.++. +
T Consensus 414 F~~~Il~~~~~~~~~~~~~rqkdGAL~~vgsl~~~L~K~s~~~~~mE~flv~hVfP~f~s~~g~--Lrarac~vl~~~~~ 491 (1010)
T KOG1991 414 FIVDILTRYKEASPPNKNPRQKDGALRMVGSLASILLKKSPYKSQMEYFLVNHVFPEFQSPYGY--LRARACWVLSQFSS 491 (1010)
T ss_pred HHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCHHH--HHHHHHHHHHHHHH
T ss_conf 9999997511369976573665218999999999980687067899999998731753283267--89999999998774
Q ss_pred CCCCHHHHH
Q ss_conf 599989997
Q gi|254781141|r 113 LGFQKEEMV 121 (196)
Q Consensus 113 ~Gfs~eEi~ 121 (196)
.-|+++-+-
T Consensus 492 ~df~d~~~l 500 (1010)
T KOG1991 492 IDFKDPNNL 500 (1010)
T ss_pred CCCCCHHHH
T ss_conf 368874789
No 13
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=58.25 E-value=15 Score=17.40 Aligned_cols=54 Identities=19% Similarity=0.163 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCC
Q ss_conf 9999999999999999995836589899999999999999975999899972059
Q gi|254781141|r 71 DSEILEKKLIAENQQLEHLFPQTKDPAQRENFFKNLFRIGNILGFQKEEMVDITD 125 (196)
Q Consensus 71 q~~~~q~~l~~e~~~L~e~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D 125 (196)
-.+...-|--.|...|-.+|- +++++.-.+++..+++-+...||+.+-...+.|
T Consensus 683 IAq~~agfSlgeAD~LRRAMg-KK~~~~m~~~r~~F~~Ga~~~G~~~~~a~~ifd 736 (1139)
T COG0587 683 IAQVLAGFSLGEADLLRRAMG-KKKAEEMEKQREKFIEGAVKNGYDKEFAEKIFD 736 (1139)
T ss_pred HHHHHCCCCCHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 999971899426789999871-477899999999999789876999899999999
No 14
>pfam01244 Peptidase_M19 Membrane dipeptidase (Peptidase family M19).
Probab=57.61 E-value=15 Score=17.33 Aligned_cols=28 Identities=21% Similarity=0.163 Sum_probs=11.5
Q ss_pred HHHHHHHHCCCCHHHHHHHCCHHHHHHH
Q ss_conf 9999999759998999720599999999
Q gi|254781141|r 105 NLFRIGNILGFQKEEMVDITDHRLLSLA 132 (196)
Q Consensus 105 ~i~~~~~~~Gfs~eEi~~v~D~R~i~vl 132 (196)
+|.+.+...|||++||..|.--..+.++
T Consensus 287 ~l~~~L~~rG~se~~i~ki~g~N~lRvl 314 (316)
T pfam01244 287 NLTAELLRRGYSEAEIEKILGGNWLRVL 314 (316)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf 9999999869899999999856399984
No 15
>TIGR00084 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR000085 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure . In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB.; GO: 0003678 DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=56.80 E-value=11 Score=18.28 Aligned_cols=28 Identities=18% Similarity=0.325 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHCC
Q ss_conf 9999999999999975999899972059
Q gi|254781141|r 98 QRENFFKNLFRIGNILGFQKEEMVDITD 125 (196)
Q Consensus 98 k~~~~~~~i~~~~~~~Gfs~eEi~~v~D 125 (196)
.....+.++...+.++||.+.||+.+..
T Consensus 167 ~~~~~y~E~~~aL~sLGY~~~Ei~~~l~ 194 (217)
T TIGR00084 167 AEAARYDELFEALVSLGYKPQEIQKALK 194 (217)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 1021188999999972988889999998
No 16
>COG3184 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.91 E-value=17 Score=16.93 Aligned_cols=97 Identities=13% Similarity=0.026 Sum_probs=50.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHH
Q ss_conf 068999189999438999999999999999999999999-9999999999999999999999999999583658989999
Q gi|254781141|r 22 HIPDDSSPTLEKTYPETYHRIRYLRQKALNIINHFVETG-RNPDNIAKELDSEILEKKLIAENQQLEHLFPQTKDPAQRE 100 (196)
Q Consensus 22 ~~p~~p~~~L~~~DP~~Y~~~k~~~~~~~~~~~~~~~e~-q~~~q~q~~~q~~~~q~~l~~e~~~L~e~iPe~~D~~k~~ 100 (196)
-.-.+|...-.-+|-+.-.++.-----.-+....+.-+. +.+.++--+..-......++.-.++.+..-|+|+|=
T Consensus 21 af~~p~~~q~v~~~~~~aa~~ai~~~~~~~~fd~i~~q~a~~l~~~liqa~p~~~~~i~~r~~ekal~lA~~~~dl---- 96 (183)
T COG3184 21 AFATPPSDQDVAEDLDTAARQAIAAKNATELFDAILPQYAQMLAAELIQAKPDQQALILERYDEKALKLAPRRADL---- 96 (183)
T ss_pred HCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCHHHH----
T ss_conf 0358851388999899999999998188711003207899999988764495789999999999999865008775----
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHCC
Q ss_conf 9999999999975999899972059
Q gi|254781141|r 101 NFFKNLFRIGNILGFQKEEMVDITD 125 (196)
Q Consensus 101 ~~~~~i~~~~~~~Gfs~eEi~~v~D 125 (196)
++..+.-|+ --||.+||+.++.
T Consensus 97 -e~e~~~~Ya--~~FT~eEl~ai~a 118 (183)
T COG3184 97 -EREAALLYA--KIFTEEELNAITA 118 (183)
T ss_pred -HHHHHHHHH--HHCCHHHHHHHHH
T ss_conf -199999999--8647999999999
No 17
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=52.54 E-value=18 Score=16.79 Aligned_cols=44 Identities=16% Similarity=0.191 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHH
Q ss_conf 58989999999999999997599989997205999999999999
Q gi|254781141|r 93 TKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAYYAQ 136 (196)
Q Consensus 93 ~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~Am 136 (196)
+..|+-++.|+.+=..|...+|.|++|-..|-+-..+.+++..-
T Consensus 35 l~~~~~Re~F~aDe~Ay~d~~~LTeEqk~aV~~RDw~~li~~Gg 78 (119)
T PRK13379 35 MIRAPWRDRFLQDAEALMQEADLTEQEKELIRARDWLGLVQYGA 78 (119)
T ss_pred HCCHHHHHHHHHCHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf 67788899998399999977599999999999615999998476
No 18
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''; InterPro: IPR012757 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=50.77 E-value=19 Score=16.69 Aligned_cols=45 Identities=18% Similarity=0.025 Sum_probs=38.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf 658989999999999999997599989997205999999999999999997
Q gi|254781141|r 92 QTKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAYYAQIGLQSQ 142 (196)
Q Consensus 92 e~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~Am~y~~~~ 142 (196)
=+.-++-|+....++..++.++|.++ .|=|++++.-|.|-|+-..
T Consensus 288 VLGIEAAR~AII~E~~~tL~EQGL~d------VDiRHlmLvAD~MT~~G~V 332 (397)
T TIGR02389 288 VLGIEAARNAIIEEIKRTLEEQGLDD------VDIRHLMLVADLMTWDGEV 332 (397)
T ss_pred HCCHHHHHHHHHHHHHHHHHHCCCCH------HHHHHHHHHHHHCCCCCEE
T ss_conf 30668999999999999986428860------2489898886510788548
No 19
>pfam04695 Pex14_N Peroxisomal membrane anchor protein (Pex14p) conserved region. Family of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N-terminus of the protein.
Probab=49.88 E-value=16 Score=17.20 Aligned_cols=39 Identities=18% Similarity=0.269 Sum_probs=32.6
Q ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 999958365898999999999999999759998999720
Q gi|254781141|r 85 QLEHLFPQTKDPAQRENFFKNLFRIGNILGFQKEEMVDI 123 (196)
Q Consensus 85 ~L~e~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v 123 (196)
.+..+++=+.||.++..=...=+.|+.+-|.+++||...
T Consensus 5 li~~Av~FL~~p~V~~sp~~~k~~FL~sKgLt~~eI~~a 43 (79)
T pfam04695 5 LVESAVKFLQDPSVRDSPLEKKIEFLESKGLTEEEIDEA 43 (79)
T ss_pred HHHHHHHHHCCHHHHCCCHHHHHHHHHHCCCCHHHHHHH
T ss_conf 999999995680020085899999999759999999999
No 20
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=47.95 E-value=21 Score=16.32 Aligned_cols=35 Identities=20% Similarity=0.236 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHH
Q ss_conf 58989999999999999997599989997205999
Q gi|254781141|r 93 TKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHR 127 (196)
Q Consensus 93 ~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R 127 (196)
++||..-+.+..+-......||.|++|...+.+.-
T Consensus 14 ~r~p~~~e~~~~dp~av~e~y~Lt~~E~~AL~eg~ 48 (81)
T cd07922 14 FKDPGLIERFQDDPSAVFEEYGLTPAERAALREGT 48 (81)
T ss_pred HCCHHHHHHHHHCHHHHHHHCCCCHHHHHHHHCCC
T ss_conf 36988899987498998775289989999986388
No 21
>pfam09440 eIF3_N eIF3 subunit 6 N terminal domain. This is the N terminal domain of subunit 6 translation initiation factor eIF3.
Probab=47.47 E-value=22 Score=16.27 Aligned_cols=46 Identities=15% Similarity=0.170 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHH---HHHHHH-HHCCCCHHHHHHHCCHH
Q ss_conf 99999999995836589899999999---999999-97599989997205999
Q gi|254781141|r 79 LIAENQQLEHLFPQTKDPAQRENFFK---NLFRIG-NILGFQKEEMVDITDHR 127 (196)
Q Consensus 79 l~~e~~~L~e~iPe~~D~~k~~~~~~---~i~~~~-~~~Gfs~eEi~~v~D~R 127 (196)
++++...+.+.+ .||++...+++ ....|+ ..+||+.+-|+++|+.-
T Consensus 81 l~~~~~~i~~~l---~d~~v~~~lrsdk~~nl~~L~~~~~it~e~i~aLY~~a 130 (133)
T pfam09440 81 LQEEVAPIVKFL---EDPEVIKNLRSDKKANLEFLEEEHGITSEMVNALYKFA 130 (133)
T ss_pred HHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 999889999996---59999999882489999999986199999999999877
No 22
>pfam02787 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain.
Probab=46.63 E-value=19 Score=16.60 Aligned_cols=25 Identities=16% Similarity=0.312 Sum_probs=19.6
Q ss_pred HHHHHHHHHHCCCCHHHHHHHCCHH
Q ss_conf 9999999997599989997205999
Q gi|254781141|r 103 FKNLFRIGNILGFQKEEMVDITDHR 127 (196)
Q Consensus 103 ~~~i~~~~~~~Gfs~eEi~~v~D~R 127 (196)
-.++...++.+||||..|+.+...-
T Consensus 60 ~~~~l~~aK~~GFSD~~IA~l~~~~ 84 (122)
T pfam02787 60 SDDLLLKAKKLGFSDAQIAKLLGVT 84 (122)
T ss_pred CHHHHHHHHHHCCCHHHHHHHHCCC
T ss_conf 9999999999499989999883986
No 23
>cd06549 GH18_trifunctional GH18 domain of an uncharacterized family of bacterial proteins, which share a common three-domain architecture: an N-terminal glycosyl hydrolase family 18 (GH18) domain, a glycosyl transferase family 2 domain, and a C-terminal polysaccharide deacetylase domain.
Probab=42.01 E-value=26 Score=15.73 Aligned_cols=25 Identities=20% Similarity=0.204 Sum_probs=22.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCH
Q ss_conf 5898999999999999999759998
Q gi|254781141|r 93 TKDPAQRENFFKNLFRIGNILGFQK 117 (196)
Q Consensus 93 ~~D~~k~~~~~~~i~~~~~~~Gfs~ 117 (196)
++||+.++++..+|..++..+||.-
T Consensus 83 L~d~~~R~~~i~~i~~~~~~~~~dG 107 (298)
T cd06549 83 LADPSARAKFIANIAAYLERNQADG 107 (298)
T ss_pred HCCHHHHHHHHHHHHHHHHHCCCCE
T ss_conf 3799999999999999999829983
No 24
>pfam10302 DUF2407 Putative membrane protein (DUF2407). This is a family of proteins found in fungi. The function is not known. There is a characteristic GFDRL sequence motif.
Probab=40.77 E-value=17 Score=17.00 Aligned_cols=18 Identities=17% Similarity=0.008 Sum_probs=13.6
Q ss_pred HHHH--HHHCCCCHHHHHHH
Q ss_conf 9999--99759998999720
Q gi|254781141|r 106 LFRI--GNILGFQKEEMVDI 123 (196)
Q Consensus 106 i~~~--~~~~Gfs~eEi~~v 123 (196)
.+-| +.+.|||++||+.+
T Consensus 119 ~rGFDRLlsaGFs~~EV~~L 138 (252)
T pfam10302 119 PRGFDRLLSAGFSPAEVSLL 138 (252)
T ss_pred CCCHHHHHHCCCCHHHHHHH
T ss_conf 74487898758999999999
No 25
>cd02874 GH18_CFLE_spore_hydrolase Cortical fragment-lytic enzyme (CFLE) is a peptidoglycan hydrolase involved in bacterial endospore germination. CFLE is expressed as an inactive preprotein (called SleB) in the forespore compartment of sporulating cells. SleB translocates across the forespore inner membrane and is deposited as a mature enzyme in the cortex layer of the spore. As part of a sensory mechanism capable of initiating germination, CFLE degrades a spore-specific peptidoglycan constituent called muramic-acid delta-lactam that comprises the outer cortex. CFLE has a C-terminal glycosyl hydrolase family 18 (GH18) catalytic domain as well as two N-terminal LysM peptidoglycan-binding domains. In addition to SleB, this family includes YaaH, YdhD, and YvbX from Bacillus subtilis.
Probab=40.57 E-value=27 Score=15.58 Aligned_cols=25 Identities=16% Similarity=0.539 Sum_probs=20.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCH
Q ss_conf 5898999999999999999759998
Q gi|254781141|r 93 TKDPAQRENFFKNLFRIGNILGFQK 117 (196)
Q Consensus 93 ~~D~~k~~~~~~~i~~~~~~~Gfs~ 117 (196)
.+||+++++|..+|.+++..+||.-
T Consensus 82 ls~~~~R~~fi~siv~~~~~~~fDG 106 (313)
T cd02874 82 LSNPEARQRLINNILALAKKYGYDG 106 (313)
T ss_pred HCCHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 6799999999999999999819985
No 26
>KOG0455 consensus
Probab=40.22 E-value=7.4 Score=19.39 Aligned_cols=48 Identities=15% Similarity=0.324 Sum_probs=39.0
Q ss_pred HHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCH----HHHHHHCCHHHHHHHH
Q ss_conf 99958365898999999999999999759998----9997205999999999
Q gi|254781141|r 86 LEHLFPQTKDPAQRENFFKNLFRIGNILGFQK----EEMVDITDHRLLSLAY 133 (196)
Q Consensus 86 L~e~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~----eEi~~v~D~R~i~vl~ 133 (196)
|--.+-||+|-+....-.+++...++.+|||+ ++++++-=+|-+.+|-
T Consensus 180 LsYifne~s~gk~~~~sfsdvVk~AKklGYTEPDPRDDLnGmDVARKvtIl~ 231 (364)
T KOG0455 180 LSYIFNELSDGKPGTLSFSDVVKAAKKLGYTEPDPRDDLNGMDVARKVTILA 231 (364)
T ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 7888777605998756599999999972899999642346511344432311
No 27
>pfam06382 DUF1074 Protein of unknown function (DUF1074). This family consists of several proteins which appear to be specific to Drosophila melanogaster. The function of this family is unknown.
Probab=39.84 E-value=28 Score=15.51 Aligned_cols=61 Identities=13% Similarity=0.179 Sum_probs=37.1
Q ss_pred CCCCCHHHHHH----HHHHHHHHHHH-CCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 36589899999----99999999997-5999899972059999999999999999974300112320369843478
Q gi|254781141|r 91 PQTKDPAQREN----FFKNLFRIGNI-LGFQKEEMVDITDHRLLSLAYYAQIGLQSQKLSEDAYHKIRHKPFVNIT 161 (196)
Q Consensus 91 Pe~~D~~k~~~----~~~~i~~~~~~-~Gfs~eEi~~v~D~R~i~vl~~Am~y~~~~~~k~~a~kk~~~~p~~~~~ 161 (196)
|-++-.+++.- .-+=|++|-+. +|+|++|| |.+-|+.|.+|-.+.+.+-+.++++.++-++
T Consensus 75 p~yK~qKv~~vTnNgYLNflrefkKk~~gLsPqdm----------v~~aAkaW~~LS~aeke~fk~kkp~tv~~k~ 140 (187)
T pfam06382 75 PIYKRQKVARVTNNGYLNFMTEYKKRFYGLSPQDM----------VHYAAKQWTQLSMAEKEAFKSKKPSTITLKS 140 (187)
T ss_pred CHHHHHHEEECCCCCHHHHHHHHHHHHCCCCHHHH----------HHHHHHHHHHHHHHHHHHHCCCCCCEEEECC
T ss_conf 33432010001356316999999988639988999----------9999999887658889886147998478638
No 28
>COG2355 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]
Probab=39.66 E-value=28 Score=15.49 Aligned_cols=43 Identities=19% Similarity=0.083 Sum_probs=27.4
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 36589899999999999999975999899972059999999999999
Q gi|254781141|r 91 PQTKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAYYAQI 137 (196)
Q Consensus 91 Pe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~Am~ 137 (196)
+.|.|+. ...++...+..-||+++||..+.--..+.|+...|.
T Consensus 270 ~gled~~----~l~~l~~~L~~~G~~e~~i~~i~~~N~lRV~~~~~~ 312 (313)
T COG2355 270 DGLEDVG----KLPNLTAALIERGYSEEEIEKIAGENWLRVLKEVWG 312 (313)
T ss_pred HHHCCHH----HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 1012756----779999999976999999999998769999999736
No 29
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302; InterPro: IPR012683 Members of this family are bacterial proteins from the alphaproteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted to be outside the membrane. Bradyrhizobium japonicum contains two tandem copies that are, together, homologous to the single members found in other species. .
Probab=38.95 E-value=29 Score=15.42 Aligned_cols=113 Identities=12% Similarity=0.043 Sum_probs=61.9
Q ss_pred HHHHHHHHHHHHHHHHHH-CCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999995-8365898999999999999999759998999720599999999999999999743001123
Q gi|254781141|r 72 SEILEKKLIAENQQLEHL-FPQTKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAYYAQIGLQSQKLSEDAYH 150 (196)
Q Consensus 72 ~~~~q~~l~~e~~~L~e~-iPe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~Am~y~~~~~~k~~a~k 150 (196)
..++.+.+..=.++-+-+ -=+.++-+++=--..+-..-++..|=|+|||..++|- ||+||.- -+..- +..
T Consensus 506 DdaLRd~ad~lW~~AlgIEdGdlS~AerrLR~AQ~AL~dALergASdeEI~~Ltd~-----LR~Amq~-ymr~l---Aqq 576 (899)
T TIGR02302 506 DDALRDVADYLWEVALGIEDGDLSAAERRLRDAQDALKDALERGASDEEIKKLTDE-----LRKAMQE-YMREL---AQQ 576 (899)
T ss_pred CCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH-----HHHHHHH-HHHHH---HHH
T ss_conf 60488998777664441036764179999999999999997438888899999999-----9999999-99999---999
Q ss_pred HCCCCCCC-CCCCCC--CCCCCCHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf 20369843-478877--87632148999999999761999999750
Q gi|254781141|r 151 KIRHKPFV-NITTNK--AKNHRRITSQEKAIQKLYQTGSLYDSLEI 193 (196)
Q Consensus 151 k~~~~p~~-~~~~~~--~~~~~~~~~~~ka~~rL~ksG~v~DA~al 193 (196)
..+++-.. .+--+. .=....-.+==..+.+|..||+-+.|--|
T Consensus 577 ~~~NP~~~a~p~dpN~~vlrqqDL~~M~dqiEnLaRsG~rdqA~Ql 622 (899)
T TIGR02302 577 LRKNPAALARPEDPNAKVLRQQDLQKMMDQIENLARSGDRDQAKQL 622 (899)
T ss_pred HHHCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf 8605597718888735664688899999999975067887899999
No 30
>PRK13367 protocatechuate 4,5-dioxygenase; Provisional
Probab=38.87 E-value=29 Score=15.41 Aligned_cols=55 Identities=24% Similarity=0.238 Sum_probs=42.9
Q ss_pred HHHHHHC-CCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999958-36589899999999999999975999899972059999999999999999974
Q gi|254781141|r 84 QQLEHLF-PQTKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAYYAQIGLQSQK 143 (196)
Q Consensus 84 ~~L~e~i-Pe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~Am~y~~~~~ 143 (196)
.-|...| |+|+ +.|..+-..+....|.|+||-.-|..-.-+-+++....|.=+.+
T Consensus 323 ~flh~li~p~~R-----~rf~~d~ea~~~e~~Lt~ee~~li~~rdw~gli~yGv~ff~leK 378 (418)
T PRK13367 323 RFLHRLIEPAWR-----ERFLADPEALFDEAGLSEEERDLIRRRDWRGLIHYGVIFFLLEK 378 (418)
T ss_pred HHHHHHCCHHHH-----HHHHHCHHHHHHHCCCCHHHHHHHHCCCHHHHHHHCHHHHHHHH
T ss_conf 999996483779-----99862989898763999899999860548899983326999998
No 31
>pfam03359 GKAP Guanylate-kinase-associated protein (GKAP) protein.
Probab=38.21 E-value=30 Score=15.34 Aligned_cols=70 Identities=14% Similarity=0.133 Sum_probs=39.0
Q ss_pred CCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH---------HHCCCCCCCCCCCCCCC-CCCCHHHHHHHHHHHHH
Q ss_conf 999899972059999999999999999974300112---------32036984347887787-63214899999999976
Q gi|254781141|r 114 GFQKEEMVDITDHRLLSLAYYAQIGLQSQKLSEDAY---------HKIRHKPFVNITTNKAK-NHRRITSQEKAIQKLYQ 183 (196)
Q Consensus 114 Gfs~eEi~~v~D~R~i~vl~~Am~y~~~~~~k~~a~---------kk~~~~p~~~~~~~~~~-~~~~~~~~~ka~~rL~k 183 (196)
--|-+++.+.-|-=.+.|=+=-|+|++|..-+...= ++..+.+..++...+.+ .+...+.|..+++||..
T Consensus 233 ~~t~~DL~GFWDm~~lqiedv~~kF~~l~~lk~n~W~~~~~p~~~kk~~k~~~~~~~~~r~~s~ds~dk~RqeARkRL~A 312 (342)
T pfam03359 233 RTTSQDLAGFWDMLQLQIEDVDKKFDELQQLKANDWQKKVPPPVPKKPAKGPIVKPAISREKSLDSSDRQRQEARSRLAA 312 (342)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf 88646778788989854998999999999998769863788999988889999998865344554157789999999999
No 32
>pfam07499 RuvA_C RuvA, C-terminal domain. Homologous recombination is a crucial process in all living organisms. In bacteria, this process the RuvA, RuvB, and RuvC proteins are involved. More specifically the proteins process the Holliday junction DNA. RuvA is comprised of three distinct domains. The domain represents the C-terminal domain and plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB. Within the Holliday junction, the C-terminal domain makes no interaction with DNA.
Probab=38.01 E-value=29 Score=15.47 Aligned_cols=25 Identities=12% Similarity=0.163 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHCCH
Q ss_conf 9999999999759998999720599
Q gi|254781141|r 102 FFKNLFRIGNILGFQKEEMVDITDH 126 (196)
Q Consensus 102 ~~~~i~~~~~~~Gfs~eEi~~v~D~ 126 (196)
...+....+.++||+..|+..+...
T Consensus 2 ~~~da~~AL~~LGy~~~ea~~av~~ 26 (47)
T pfam07499 2 ALEEAVSALLALGYKEKEAEKAVAK 26 (47)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 5889999999939989999999999
No 33
>pfam01793 Glyco_transf_15 Glycolipid 2-alpha-mannosyltransferase. This is a family of alpha-1,2 mannosyl-transferases involved in N-linked and O-linked glycosylation of proteins. Some of the enzymes in this family have been shown to be involved in O- and N-linked glycan modifications in the Golgi.
Probab=35.74 E-value=26 Score=15.73 Aligned_cols=29 Identities=17% Similarity=0.185 Sum_probs=22.5
Q ss_pred HCCCCCCHHHHHHHHHHHHHHHHHCCCCH
Q ss_conf 58365898999999999999999759998
Q gi|254781141|r 89 LFPQTKDPAQRENFFKNLFRIGNILGFQK 117 (196)
Q Consensus 89 ~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~ 117 (196)
.+|+|-|..++.+.+..+.+-+..||.|.
T Consensus 73 ~~P~~id~~k~~~~~~~~~~~~i~yg~s~ 101 (274)
T pfam01793 73 SYPEWIDQDKAAESREKMGEKGIIYGDSE 101 (274)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCCH
T ss_conf 79998598999999999887098765425
No 34
>PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional
Probab=35.36 E-value=25 Score=15.80 Aligned_cols=24 Identities=21% Similarity=0.217 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHCC
Q ss_conf 999999999975999899972059
Q gi|254781141|r 102 FFKNLFRIGNILGFQKEEMVDITD 125 (196)
Q Consensus 102 ~~~~i~~~~~~~Gfs~eEi~~v~D 125 (196)
...++...+.++||+..++..+.+
T Consensus 143 ~~~e~~~AL~~LGy~~~~a~~al~ 166 (196)
T PRK13901 143 KFKELEQSIVNMGFDRKLVNSAIK 166 (196)
T ss_pred CHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 489999999984999899999999
No 35
>pfam04877 Hairpins HrpZ. HrpZ from the plant pathogen Pseudomonas syringae binds to lipid bilayers and forms a cation-conducting pore in vivo. This pore-forming activity may allow nutrient release or delivery of virulence factors during bacterial colonisation of host plants. The family of hairpinN proteins, Harpin, has been merged into this family. HrpN is a virulence determinant which elicits lesion formation in Arabidopsis and tobacco and triggers systemic resistance in Arabidopsis.
Probab=35.01 E-value=33 Score=15.01 Aligned_cols=11 Identities=18% Similarity=0.413 Sum_probs=4.4
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999732
Q gi|254781141|r 11 SAEALAQLINH 21 (196)
Q Consensus 11 ~~~~l~q~~~~ 21 (196)
++..|+||+.+
T Consensus 166 ml~eIaQFMDd 176 (277)
T pfam04877 166 MLKEIAQFMDD 176 (277)
T ss_pred HHHHHHHHHHC
T ss_conf 99999998613
No 36
>TIGR01991 HscA Fe-S protein assembly chaperone HscA; InterPro: IPR010236 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 HscA chaperone protein from the SUF system. HscA (or Hsc66) is a specialised bacterial Hsp70-class molecular chaperone that participates in the assembly of iron-sulphur cluster proteins. HscA resembles DnaK, but belongs to a separate clade. HscA interacts with IscU, which is believed to serve as a template for Fe-S cluster formation. The HscA-IscU interaction is facilitated by the J-type co-chaperone protein HscB (or Hsc20), which binds to both HscA and IscU, bringing them into contact with each other. HscA recognises a conserved LPPVK sequence motif at positions 99-103 of IscU .; GO: 0005524 ATP binding, 0016887 ATPase activity, 0051082 unfolded protein binding, 0016226 iron-sulfur cluster assembly.
Probab=34.83 E-value=30 Score=15.34 Aligned_cols=10 Identities=0% Similarity=-0.300 Sum_probs=4.1
Q ss_pred HHHHHHHHHH
Q ss_conf 9999999999
Q gi|254781141|r 131 LAYYAQIGLQ 140 (196)
Q Consensus 131 vl~~Am~y~~ 140 (196)
||+|+|-|-.
T Consensus 523 MlkDs~s~a~ 532 (628)
T TIGR01991 523 MLKDSLSYAE 532 (628)
T ss_pred HHHHHHHHHH
T ss_conf 9998876578
No 37
>pfam11867 DUF3387 Domain of unknown function (DUF3387). This domain is functionally uncharacterized. This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with pfam04851, pfam04313.
Probab=34.54 E-value=34 Score=14.96 Aligned_cols=136 Identities=14% Similarity=0.137 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 99999999999999999999999999999999999999999-------58365898999999999999999759998999
Q gi|254781141|r 48 KALNIINHFVETGRNPDNIAKELDSEILEKKLIAENQQLEH-------LFPQTKDPAQRENFFKNLFRIGNILGFQKEEM 120 (196)
Q Consensus 48 ~~~~~~~~~~~e~q~~~q~q~~~q~~~~q~~l~~e~~~L~e-------~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi 120 (196)
=+.+-++.+....-........-+...+.+.|+.-..+-.. .|-|+-+ -.++..+-..-|..+|.|++|+
T Consensus 170 laiE~L~kLL~~~Ik~~~~~N~v~~~~FsE~Le~~i~~Y~nr~it~aevieELi~---lakel~~e~~rg~~lGLs~eEl 246 (333)
T pfam11867 170 LALELLKKLLNDEIKSRSKTNLVQSKKFSERLEEAINKYHNRAITTAEVIEELIK---LAKEIREADKRGEELGLSEEEI 246 (333)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH---HHHHHHHHHHHHHHCCCCHHHH
T ss_conf 7999999999999999970068989999999999999998077749999999999---9999998886235259998999
Q ss_pred HHHCCHHHHHH-HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCHHHH
Q ss_conf 72059999999-99999999997430011232036984347887787632148999999999761999999
Q gi|254781141|r 121 VDITDHRLLSL-AYYAQIGLQSQKLSEDAYHKIRHKPFVNITTNKAKNHRRITSQEKAIQKLYQTGSLYDS 190 (196)
Q Consensus 121 ~~v~D~R~i~v-l~~Am~y~~~~~~k~~a~kk~~~~p~~~~~~~~~~~~~~~~~~~ka~~rL~ksG~v~DA 190 (196)
+ .||.=.--- ....|--+.+..-...-+..++....+ -=..+.+.++.-|..-+.=|+|-|=.-|-
T Consensus 247 A-FYDaLa~~~sa~~~~g~e~L~~iA~el~~~vr~~~~i---DW~~re~vrAklR~~vkrlL~k~gYPPd~ 313 (333)
T pfam11867 247 A-FYDALADNESAVREMGDDKLKKIAKELVEKLRKNVTV---DWQKRESVRAKLRVLVKRILRKYGYPPDK 313 (333)
T ss_pred H-HHHHHHCCHHHHHHCCCHHHHHHHHHHHHHHHHCCCC---CCCCCHHHHHHHHHHHHHHHHHCCCCCHH
T ss_conf 9-9999964416888758289999999999999865884---76300748999999999999985989226
No 38
>KOG2629 consensus
Probab=34.41 E-value=25 Score=15.88 Aligned_cols=95 Identities=13% Similarity=0.111 Sum_probs=44.6
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 99999732068999189999438999999999999999999999999999999999999999999999999999958365
Q gi|254781141|r 14 ALAQLINHHIPDDSSPTLEKTYPETYHRIRYLRQKALNIINHFVETGRNPDNIAKELDSEILEKKLIAENQQLEHLFPQT 93 (196)
Q Consensus 14 ~l~q~~~~~~p~~p~~~L~~~DP~~Y~~~k~~~~~~~~~~~~~~~e~q~~~q~q~~~q~~~~q~~l~~e~~~L~e~iPe~ 93 (196)
.+..++.+-+-.++.+.|...++. .-..+......++++..+..++.+....+|. .+-.-|......|. -.-
T Consensus 103 ~~K~YV~P~~l~~~~~k~e~~k~~----Ld~~~~~~~~~~~~l~~~va~v~q~~~~qq~-Els~~L~~l~~~~~---~~s 174 (300)
T KOG2629 103 FVKSYVLPRFLGESKDKLEADKRQ----LDDQFDKAAKSLNALMDEVAQVSQLLATQQS-ELSRALASLKNTLV---QLS 174 (300)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH---HHH
T ss_conf 999988887607651167777888----8899999999999999999999999999999-99999999997777---753
Q ss_pred CCHHHHHHHHHHHHHHHHH-CCCC
Q ss_conf 8989999999999999997-5999
Q gi|254781141|r 94 KDPAQRENFFKNLFRIGNI-LGFQ 116 (196)
Q Consensus 94 ~D~~k~~~~~~~i~~~~~~-~Gfs 116 (196)
+|-++.+.+.+.|-.-+.+ .-|+
T Consensus 175 ~~~~k~esei~~Ik~lvln~~~f~ 198 (300)
T KOG2629 175 RNIEKLESEINTIKQLVLNMSNFA 198 (300)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 019888878888889985343357
No 39
>PTZ00217 flap endonuclease-1; Provisional
Probab=33.02 E-value=36 Score=14.80 Aligned_cols=29 Identities=14% Similarity=0.124 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHHHHHHHHHH-HCCCCHHHHHHHCC
Q ss_conf 65898999999999999999-75999899972059
Q gi|254781141|r 92 QTKDPAQRENFFKNLFRIGN-ILGFQKEEMVDITD 125 (196)
Q Consensus 92 e~~D~~k~~~~~~~i~~~~~-~~Gfs~eEi~~v~D 125 (196)
+|+.| -...|++|+. +.|||++-|.+..+
T Consensus 299 ~w~~p-----d~e~l~~fL~~e~~Fse~Rv~~~~~ 328 (394)
T PTZ00217 299 KWSEP-----DIEGLKKFLVEEKNFNEERVEKGIE 328 (394)
T ss_pred CCCCC-----CHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf 08999-----9899999976466979899999999
No 40
>PHA00542 putative Cro-like protein
Probab=31.59 E-value=38 Score=14.65 Aligned_cols=39 Identities=26% Similarity=0.273 Sum_probs=28.5
Q ss_pred HCCCCCC--HHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHH
Q ss_conf 5836589--89999999999999997599989997205999
Q gi|254781141|r 89 LFPQTKD--PAQRENFFKNLFRIGNILGFQKEEMVDITDHR 127 (196)
Q Consensus 89 ~iPe~~D--~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R 127 (196)
.+|+..+ |...++--.+|+..+...|||..+|..+++-+
T Consensus 4 ~~~~~~~~~~~~y~k~P~E~V~aLi~~G~tQ~qI~~~tgv~ 44 (82)
T PHA00542 4 AMPATTPTIPAAYTQRPDELVCALIRAGWSQEQIADATDVS 44 (82)
T ss_pred CCCCCCCCCHHHHHCCHHHHHHHHHHCCCCHHHHHHHHCCC
T ss_conf 66788997437653298999999998225699999860877
No 41
>COG5656 SXM1 Importin, protein involved in nuclear import [Posttranslational modification, protein turnover, chaperones]
Probab=31.57 E-value=28 Score=15.52 Aligned_cols=38 Identities=18% Similarity=0.152 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHH-----CCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999732-----0689991899994389999999999
Q gi|254781141|r 9 AQSAEALAQLINH-----HIPDDSSPTLEKTYPETYHRIRYLR 46 (196)
Q Consensus 9 aq~~~~l~q~~~~-----~~p~~p~~~L~~~DP~~Y~~~k~~~ 46 (196)
+-+.+.+.=++.+ .-+++-.++|++.||.+|.+....+
T Consensus 337 ~l~ePhlq~ii~~vIfPllc~see~eElfEnDp~eyirry~df 379 (970)
T COG5656 337 RLMEPHLQYIISGVIFPLLCLSEEEEELFENDPDEYIRRYYDF 379 (970)
T ss_pred HHHCCHHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHCCH
T ss_conf 6634279999873024220787305877724989999974211
No 42
>pfam10929 DUF2811 Protein of unknown function (DUF2811). This is a bacterial family of uncharacterized proteins.
Probab=31.15 E-value=39 Score=14.60 Aligned_cols=47 Identities=11% Similarity=0.016 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHC
Q ss_conf 99999999999999583658989999999999999997599989997205
Q gi|254781141|r 75 LEKKLIAENQQLEHLFPQTKDPAQRENFFKNLFRIGNILGFQKEEMVDIT 124 (196)
Q Consensus 75 ~q~~l~~e~~~L~e~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~ 124 (196)
.-+.|.+.....++..|.|--- .-+.+.|..|+...|.++-.+..+|
T Consensus 6 iPe~L~~am~~fie~hP~WDQy---Rl~~aALa~FL~QnG~~~r~vtr~Y 52 (57)
T pfam10929 6 IPEALQQAMKDFIESHPNWDQY---RLIQAALAGFLLQNGCQDRAVTRLY 52 (57)
T ss_pred CCHHHHHHHHHHHHHCCCCHHH---HHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf 6299999999999839994099---9999999999998488622889998
No 43
>cd02876 GH18_SI-CLP Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl hydrolase family 18 (GH18) domain but lacks a chitin-binding domain. The catalytic amino acids of the GH18 domain are not conserved in SI-CLP, similar to the chitolectins YKL-39, YKL-40, and YM1/2. Human SI-CLP is sorted to late endosomes and secretory lysosomes in alternatively activated macrophages.
Probab=30.99 E-value=39 Score=14.58 Aligned_cols=28 Identities=21% Similarity=0.247 Sum_probs=23.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 5898999999999999999759998999
Q gi|254781141|r 93 TKDPAQRENFFKNLFRIGNILGFQKEEM 120 (196)
Q Consensus 93 ~~D~~k~~~~~~~i~~~~~~~Gfs~eEi 120 (196)
.+||+.++++..+|+++.+.+||.-=.|
T Consensus 87 ls~~~~R~~~i~~iv~~~~~~gfDGidi 114 (318)
T cd02876 87 LNDEQEREKLIKLLVTTAKKNHFDGIVL 114 (318)
T ss_pred HCCHHHHHHHHHHHHHHHHHHCCCCEEE
T ss_conf 6399999999999999999819985888
No 44
>KOG4472 consensus
Probab=30.79 E-value=33 Score=15.03 Aligned_cols=30 Identities=17% Similarity=0.251 Sum_probs=25.6
Q ss_pred HCCCCCCHHHHHHHHHHHHHHHHHCCCCHH
Q ss_conf 583658989999999999999997599989
Q gi|254781141|r 89 LFPQTKDPAQRENFFKNLFRIGNILGFQKE 118 (196)
Q Consensus 89 ~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~e 118 (196)
-+|+|-|..++.....++.+-+.-||.|+-
T Consensus 151 ~~P~~Id~~~~~e~~~~~~~~~i~Yg~s~S 180 (399)
T KOG4472 151 NFPEWIDEDKAAESLDDMADEGILYGGSES 180 (399)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCCHH
T ss_conf 796101569999999987643954368589
No 45
>COG5020 KTR1 Mannosyltransferase [Carbohydrate transport and metabolism]
Probab=30.79 E-value=33 Score=15.03 Aligned_cols=30 Identities=17% Similarity=0.251 Sum_probs=25.6
Q ss_pred HCCCCCCHHHHHHHHHHHHHHHHHCCCCHH
Q ss_conf 583658989999999999999997599989
Q gi|254781141|r 89 LFPQTKDPAQRENFFKNLFRIGNILGFQKE 118 (196)
Q Consensus 89 ~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~e 118 (196)
-+|+|-|..++.....++.+-+.-||.|+-
T Consensus 151 ~~P~~Id~~~~~e~~~~~~~~~i~Yg~s~S 180 (399)
T COG5020 151 NFPEWIDEDKAAESLDDMADEGILYGGSES 180 (399)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCCHH
T ss_conf 796101569999999987643954368589
No 46
>pfam00816 Histone_HNS H-NS histone family.
Probab=30.59 E-value=39 Score=14.54 Aligned_cols=21 Identities=14% Similarity=0.267 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHCCCCHHHH
Q ss_conf 999999999999759998999
Q gi|254781141|r 100 ENFFKNLFRIGNILGFQKEEM 120 (196)
Q Consensus 100 ~~~~~~i~~~~~~~Gfs~eEi 120 (196)
..-...|...+..+|||.+||
T Consensus 23 ~~a~~~i~~~~~~~glt~~el 43 (91)
T pfam00816 23 AAALAEIRELAAEYGLTLEEL 43 (91)
T ss_pred HHHHHHHHHHHHHHCCCHHHH
T ss_conf 999999999999909999998
No 47
>KOG1992 consensus
Probab=30.19 E-value=24 Score=16.00 Aligned_cols=113 Identities=18% Similarity=0.150 Sum_probs=53.4
Q ss_pred HHHHHHHHHHHH-CCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999732-068----999189999438999999999999999999999999999999999999999999999999
Q gi|254781141|r 10 QSAEALAQLINH-HIP----DDSSPTLEKTYPETYHRIRYLRQKALNIINHFVETGRNPDNIAKELDSEILEKKLIAENQ 84 (196)
Q Consensus 10 q~~~~l~q~~~~-~~p----~~p~~~L~~~DP~~Y~~~k~~~~~~~~~~~~~~~e~q~~~q~q~~~q~~~~q~~l~~e~~ 84 (196)
+.-+.++++.+. -.| .+-+++|+|.||++|+|..-+=-+---+++....-...+...- +...-..+..+.+
T Consensus 331 ~~~~vl~~i~e~VvlpN~~lR~eDeElFED~pleYiRRDlEGsDvdTRRR~a~dlvrgL~~~f----e~~vt~v~~~~v~ 406 (960)
T KOG1992 331 EGENVLAQICEKVVLPNLILREEDEELFEDNPLEYIRRDLEGSDVDTRRRAAIDLVRGLCKNF----EGQVTGVFSSEVQ 406 (960)
T ss_pred CCHHHHHHHHHHHCCCCCCCCHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH----CCHHHHHHHHHHH
T ss_conf 354899999986532510010536877356889999875346775325779999999999870----2244778999999
Q ss_pred HHHHH---C--CCCCCHHHHHHHHHHHHHHHHH--CCCCH-HHHHHHCCH
Q ss_conf 99995---8--3658989999999999999997--59998-999720599
Q gi|254781141|r 85 QLEHL---F--PQTKDPAQRENFFKNLFRIGNI--LGFQK-EEMVDITDH 126 (196)
Q Consensus 85 ~L~e~---i--Pe~~D~~k~~~~~~~i~~~~~~--~Gfs~-eEi~~v~D~ 126 (196)
.|+.. - -+|++...+=-+...+.--|.+ -|.|. .++.++.|.
T Consensus 407 ~~l~~y~~nPS~nWk~kd~aiyL~talaik~~t~~~Gvtstn~lvdv~~F 456 (960)
T KOG1992 407 RLLDQYSKNPSGNWKKKDRAIYLVTALAIKGQTAKHGVTSTNELVDVVDF 456 (960)
T ss_pred HHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCHHHCCEEECCCCCCHHHH
T ss_conf 89887323887453301014335678886032210451212323458899
No 48
>pfam11198 DUF2857 Protein of unknown function (DUF2857). This is a bacterial family of uncharacterized proteins.
Probab=30.14 E-value=40 Score=14.49 Aligned_cols=30 Identities=13% Similarity=0.017 Sum_probs=15.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHCCHH
Q ss_conf 478877876321489999999997619999
Q gi|254781141|r 159 NITTNKAKNHRRITSQEKAIQKLYQTGSLY 188 (196)
Q Consensus 159 ~~~~~~~~~~~~~~~~~ka~~rL~ksG~v~ 188 (196)
.+|-+..+.+......=..++.+.+.+.+.
T Consensus 116 ~~GR~~~~~ee~~~~lW~~W~~~~~~~~~~ 145 (181)
T pfam11198 116 RKGRPPALDEEQEAALWRAWQQLRSKPDVE 145 (181)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf 999999998688999999999989864888
No 49
>pfam08069 Ribosomal_S13_N Ribosomal S13/S15 N-terminal domain. This domain is found at the N-terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021.
Probab=28.50 E-value=43 Score=14.31 Aligned_cols=33 Identities=12% Similarity=0.123 Sum_probs=23.4
Q ss_pred HCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 58365898999999999999999759998999720
Q gi|254781141|r 89 LFPQTKDPAQRENFFKNLFRIGNILGFQKEEMVDI 123 (196)
Q Consensus 89 ~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v 123 (196)
.-|+|.+- ..+.....|.++++ .|+|+-+|+.+
T Consensus 21 ~~P~W~~~-~~~eve~~I~klak-kG~~pSqIG~i 53 (60)
T pfam08069 21 TPPEWLKY-SPEEVEELIVKLAK-KGLTPSQIGVI 53 (60)
T ss_pred CCCCCCCC-CHHHHHHHHHHHHH-CCCCHHHHHHH
T ss_conf 89865568-99999999999998-79988897356
No 50
>pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
Probab=28.37 E-value=43 Score=14.29 Aligned_cols=56 Identities=11% Similarity=0.061 Sum_probs=41.9
Q ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHH--HHHHHHHHHHHHHHH
Q ss_conf 9999999583658989999999999999997599989997205999999--999999999997430
Q gi|254781141|r 82 ENQQLEHLFPQTKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLS--LAYYAQIGLQSQKLS 145 (196)
Q Consensus 82 e~~~L~e~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~--vl~~Am~y~~~~~~k 145 (196)
+-+.|.++|=...+++-...|..+| +|+.|+.++..-=.|. +|+..+-|+++....
T Consensus 2 ~~d~l~~ail~l~~~ee~~~f~~dl--------~T~~E~~ala~R~~va~~LL~~~~syreI~~~~ 59 (88)
T pfam01371 2 EWDALFEALLKLENQEECYAFLTDL--------LTPDEREALAQRLRIAKELLRGELSQREIAQEL 59 (88)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHH--------CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 5999999999749999999999983--------999999999999999999997899899999985
No 51
>COG3722 MtlR Transcriptional regulator [Transcription]
Probab=28.15 E-value=43 Score=14.27 Aligned_cols=35 Identities=20% Similarity=0.317 Sum_probs=21.6
Q ss_pred HHCCC--CCCHHHHHHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf 95836--589899999999999999975999899972
Q gi|254781141|r 88 HLFPQ--TKDPAQRENFFKNLFRIGNILGFQKEEMVD 122 (196)
Q Consensus 88 e~iPe--~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~ 122 (196)
-.||. |.|-+---+.+..+-+-+.+|||+|++|-+
T Consensus 80 Gvi~~~~y~Diehl~~lre~Ln~d~~ey~FtDd~ild 116 (174)
T COG3722 80 GVIDRWEYEDIEHLMALREELNHDGEEYGFTDDEILD 116 (174)
T ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHH
T ss_conf 5661888862899999999965665214766589886
No 52
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=27.82 E-value=44 Score=14.23 Aligned_cols=60 Identities=13% Similarity=-0.059 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCC
Q ss_conf 999999999999999999999995836589899999999999999975999899972059
Q gi|254781141|r 66 IAKELDSEILEKKLIAENQQLEHLFPQTKDPAQRENFFKNLFRIGNILGFQKEEMVDITD 125 (196)
Q Consensus 66 ~q~~~q~~~~q~~l~~e~~~L~e~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D 125 (196)
+|-.+-.+.+.-+--.+...|..+|=-+++++.-.+++..+++-+...||+++....|.|
T Consensus 666 EQvM~ia~~~aGfslgeAD~lRramgsKK~~~~m~~~~~~f~~g~~~~g~~~~~a~~i~~ 725 (1050)
T PRK05672 666 EQVMQIAIDAAGFTPGEADQLRRAMAAWRRVGRLERLRERLVDGMLARGYTGEFAERIFE 725 (1050)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 999999999749998999999999875437222889999998679875999999999999
No 53
>TIGR03253 oxalate_frc formyl-CoA transferase. This enzyme, formyl-CoA transferase, transfers coenzyme A from formyl-CoA to oxalate. It forms a pathway, together with oxalyl-CoA decarboxylase, for oxalate degradation; decarboxylation by the latter gene regenerates formyl-CoA. The two enzymes typically are encoded by a two-gene operon.
Probab=27.38 E-value=20 Score=16.47 Aligned_cols=32 Identities=19% Similarity=0.295 Sum_probs=11.7
Q ss_pred CCCCCHHHHHHHHHHHHHHHHH--CCCCHHHHHH
Q ss_conf 3658989999999999999997--5999899972
Q gi|254781141|r 91 PQTKDPAQRENFFKNLFRIGNI--LGFQKEEMVD 122 (196)
Q Consensus 91 Pe~~D~~k~~~~~~~i~~~~~~--~Gfs~eEi~~ 122 (196)
|.|.++..+.....+|...... ..+|-+|+..
T Consensus 292 ~rf~~~~~R~~~~~el~~~i~~~~~~~t~~e~~~ 325 (415)
T TIGR03253 292 PAYATPEARQPKLNDIFAFIETYTATKDKFEVTE 325 (415)
T ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
T ss_conf 0015768888989999999999984203999999
No 54
>KOG0139 consensus
Probab=27.22 E-value=45 Score=14.16 Aligned_cols=85 Identities=8% Similarity=-0.029 Sum_probs=56.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 389999999999999999999999999999999999999999999999999---99958365898999999999999999
Q gi|254781141|r 35 YPETYHRIRYLRQKALNIINHFVETGRNPDNIAKELDSEILEKKLIAENQQ---LEHLFPQTKDPAQRENFFKNLFRIGN 111 (196)
Q Consensus 35 DP~~Y~~~k~~~~~~~~~~~~~~~e~q~~~q~q~~~q~~~~q~~l~~e~~~---L~e~iPe~~D~~k~~~~~~~i~~~~~ 111 (196)
--|.|.++|..|-.+.-++|-++.+...+..+.++..--.+..-.-.++-. ....|--+.-++++...-....+++-
T Consensus 291 ~tI~Y~q~R~~FGk~l~d~Q~iQhqiA~~~teiEaaRlL~ynaAr~k~~G~pf~keAAMAKl~ase~A~~~t~qCiq~lG 370 (398)
T KOG0139 291 ETIPYAQERLQFGKRLLDFQGLQHQIADMATEIEAARLLVYNAARMKDQGLPFVKEAAMAKLYASEVATKTTHQCIQWLG 370 (398)
T ss_pred HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 63078999988450466678899999999999999999999999998759964789999987421565778999999970
Q ss_pred HCCCCHHH
Q ss_conf 75999899
Q gi|254781141|r 112 ILGFQKEE 119 (196)
Q Consensus 112 ~~Gfs~eE 119 (196)
..||+.|-
T Consensus 371 G~Gyt~d~ 378 (398)
T KOG0139 371 GVGYTKDF 378 (398)
T ss_pred CCCCCCCC
T ss_conf 34723346
No 55
>PHA02512 minor structural protein; Provisional
Probab=26.93 E-value=45 Score=14.13 Aligned_cols=48 Identities=15% Similarity=0.174 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHH----HHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 9999999999999999583658989999----99999999999759998999720
Q gi|254781141|r 73 EILEKKLIAENQQLEHLFPQTKDPAQRE----NFFKNLFRIGNILGFQKEEMVDI 123 (196)
Q Consensus 73 ~~~q~~l~~e~~~L~e~iPe~~D~~k~~----~~~~~i~~~~~~~Gfs~eEi~~v 123 (196)
-+++..|....+. +---|.|+.-.. .-...|.+|+..-|+|+|+|..-
T Consensus 147 gqfqatl~~N~k~---Aa~~ygDn~ay~~~~~q~fqqieeyg~ahGws~EQI~ak 198 (844)
T PHA02512 147 GQFQATLANNGKL---AAAAYGDNAAYVLANKQTFQQIEDYGAAHGWSHEQIQAK 198 (844)
T ss_pred HHHHHHHHCCHHH---HHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 1268888522666---788737819999989999999998614228988999999
No 56
>PRK05398 formyl-coenzyme A transferase; Provisional
Probab=26.54 E-value=22 Score=16.22 Aligned_cols=33 Identities=27% Similarity=0.277 Sum_probs=15.0
Q ss_pred CCCCCHHHHHHHHHHHHHHHHH--CCCCHHHHHHH
Q ss_conf 3658989999999999999997--59998999720
Q gi|254781141|r 91 PQTKDPAQRENFFKNLFRIGNI--LGFQKEEMVDI 123 (196)
Q Consensus 91 Pe~~D~~k~~~~~~~i~~~~~~--~Gfs~eEi~~v 123 (196)
|.|.++..+.....+|...... ...|-+|+-.+
T Consensus 293 ~rf~t~~~R~~~~~el~~~i~~~~~~~t~~e~~~~ 327 (416)
T PRK05398 293 PAYATPEARQPHIFDIFAEIEKWTATKTKFEAVDI 327 (416)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf 42158899999799999999999825999999987
No 57
>pfam06401 Alpha-2-MRAP_C Alpha-2-macroglobulin RAP, C-terminal domain. The alpha-2-macroglobulin receptor-associated protein (RAP) is a intracellular glycoprotein that binds to the 2-macroglobulin receptor and other members of the low density lipoprotein receptor family. The protein inhibits binding of all currently known ligands of these receptors. Two different studies have provided conflicted domain boundaries.
Probab=25.35 E-value=48 Score=13.94 Aligned_cols=29 Identities=14% Similarity=0.437 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHC
Q ss_conf 3658989999999999999997599989997205
Q gi|254781141|r 91 PQTKDPAQRENFFKNLFRIGNILGFQKEEMVDIT 124 (196)
Q Consensus 91 Pe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~ 124 (196)
-||.+|.+ .+|=..|.+-+||++|+.++-
T Consensus 106 ~eF~ePrV-----q~LW~~A~~~nFs~~ELeSlk 134 (205)
T pfam06401 106 SEFNEPRV-----QGLWKLAQNSNFTEKELESLK 134 (205)
T ss_pred CCCCCHHH-----HHHHHHHHHCCCCHHHHHHHH
T ss_conf 46456689-----999999987699989999999
No 58
>cd06548 GH18_chitinase The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is an eight-stranded alpha/beta barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.
Probab=25.03 E-value=49 Score=13.90 Aligned_cols=27 Identities=19% Similarity=0.279 Sum_probs=24.3
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 898999999999999999759998999
Q gi|254781141|r 94 KDPAQRENFFKNLFRIGNILGFQKEEM 120 (196)
Q Consensus 94 ~D~~k~~~~~~~i~~~~~~~Gfs~eEi 120 (196)
+|++.++.|..++++|...+||.-=+|
T Consensus 105 ~~~~~R~~Fi~s~i~f~~~~~fDGiDi 131 (322)
T cd06548 105 ATEASRAKFADSAVDFIRKYGFDGIDI 131 (322)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCEEE
T ss_conf 599999999999999999729981455
No 59
>pfam01471 PG_binding_1 Putative peptidoglycan binding domain. This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.
Probab=24.90 E-value=49 Score=13.89 Aligned_cols=36 Identities=17% Similarity=-0.004 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 999999999975999899972059999999999999
Q gi|254781141|r 102 FFKNLFRIGNILGFQKEEMVDITDHRLLSLAYYAQI 137 (196)
Q Consensus 102 ~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~Am~ 137 (196)
....|-.++..+||....+++++|......+..--.
T Consensus 4 ~V~~lQ~~L~~~Gy~~~~~dg~~~~~t~~Av~~fQ~ 39 (57)
T pfam01471 4 DVKELQRYLKRLGYYPGPVDGVFGPSTEAAVKAFQR 39 (57)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 999999999997799999999688899999999999
No 60
>PRK03525 crotonobetainyl-CoA:carnitine CoA-transferase; Provisional
Probab=24.21 E-value=20 Score=16.56 Aligned_cols=11 Identities=36% Similarity=0.428 Sum_probs=5.5
Q ss_pred HHHHHHHHCCH
Q ss_conf 99999761999
Q gi|254781141|r 177 AIQKLYQTGSL 187 (196)
Q Consensus 177 a~~rL~ksG~v 187 (196)
.+.+|+.+|=|
T Consensus 391 eI~~L~~~GVI 401 (405)
T PRK03525 391 DIQELVSKGLA 401 (405)
T ss_pred HHHHHHHCCCE
T ss_conf 99999988296
No 61
>cd02875 GH18_chitobiase Chitobiase (also known as di-N-acetylchitobiase) is a lysosomal glycosidase that hydrolyzes the reducing-end N-acetylglucosamine from the chitobiose core of oligosaccharides during the ordered degradation of asparagine-linked glycoproteins in eukaryotes. Chitobiase can only do so if the asparagine that joins the oligosaccharide to protein is previously removed by a glycosylasparaginase. Chitobiase is therefore the final step in the lysosomal degradation of the protein/carbohydrate linkage component of asparagine-linked glycoproteins. The catalytic domain of chitobiase is an eight-stranded alpha/beta barrel fold similar to that of other family 18 glycosyl hydrolases such as hevamine and chitotriosidase.
Probab=24.06 E-value=51 Score=13.78 Aligned_cols=28 Identities=7% Similarity=0.196 Sum_probs=21.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 5898999999999999999759998999
Q gi|254781141|r 93 TKDPAQRENFFKNLFRIGNILGFQKEEM 120 (196)
Q Consensus 93 ~~D~~k~~~~~~~i~~~~~~~Gfs~eEi 120 (196)
..||+.|..|..+.++++..+||.-=+|
T Consensus 91 v~np~~R~~FI~s~V~flrk~~FDGlDl 118 (358)
T cd02875 91 ISNPTYRTQWIQQKVELAKSQFMDGINI 118 (358)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCCEEE
T ss_conf 3898999999999999999819987556
No 62
>pfam04587 ADP_PFK_GK ADP-specific Phosphofructokinase/Glucokinase conserved region. In archaea a novel type of glycolytic pathway exists that is deviant from the classical Embden-Meyerhof pathway. This pathway utilizes two novel proteins: an ADP-dependent Glucokinase and an ADP-dependent Phosphofructokinase. This conserved region is present at the C-terminal of both these proteins. Interestingly this family contains sequences from higher eukaryotes..
Probab=23.55 E-value=49 Score=13.90 Aligned_cols=33 Identities=15% Similarity=0.424 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHC
Q ss_conf 658989999999999999997599989997205
Q gi|254781141|r 92 QTKDPAQRENFFKNLFRIGNILGFQKEEMVDIT 124 (196)
Q Consensus 92 e~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~ 124 (196)
-+.|++.+......|..+..+.|..++||.++.
T Consensus 259 S~~d~~l~~~i~~~ilp~vDSlGmNEqELa~l~ 291 (444)
T pfam04587 259 SIQDRELRKEIVHNVLPMVDSVGMNEQELANLL 291 (444)
T ss_pred CCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHH
T ss_conf 426099999999971420563777989999999
No 63
>pfam02375 JmjN jmjN domain.
Probab=23.42 E-value=53 Score=13.70 Aligned_cols=20 Identities=25% Similarity=0.579 Sum_probs=8.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 65898999999999999999759
Q gi|254781141|r 92 QTKDPAQRENFFKNLFRIGNILG 114 (196)
Q Consensus 92 e~~D~~k~~~~~~~i~~~~~~~G 114 (196)
||+|| -.....|+.+|..+|
T Consensus 9 EF~Dp---~~Yi~~i~~~g~~~G 28 (34)
T pfam02375 9 EFKDP---IKYIEKIRPLGEKYG 28 (34)
T ss_pred HHHCH---HHHHHHHHHHHHHCC
T ss_conf 99689---999999999898859
No 64
>pfam09388 SpoOE-like Spo0E like sporulation regulatory protein. Spore formation is an extreme response to starvation and can also be a component of disease transmission. Sporulation is controlled by an expanded two-component system where starvation signals result in sensor kinase activation and phosphorylation of the master sporulation response regulator Spo0A. Phosphatases such as Spo0E dephosphorylate Spo0A thereby inhibiting sporulation. This is a family of Spo0E-like phosphatases. The structure of a Bacillus anthracis member of this family has revealed an anti-parallel alpha-helical structure.
Probab=23.30 E-value=53 Score=13.68 Aligned_cols=25 Identities=20% Similarity=0.469 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHC
Q ss_conf 9999999999997599989997205
Q gi|254781141|r 100 ENFFKNLFRIGNILGFQKEEMVDIT 124 (196)
Q Consensus 100 ~~~~~~i~~~~~~~Gfs~eEi~~v~ 124 (196)
+..+..|.+.+..+||++.++-..+
T Consensus 7 e~kR~el~~l~~~~gl~~~~vi~~S 31 (45)
T pfam09388 7 EKKRKELIELAEKYGLTDEKVIELS 31 (45)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf 9999999999998099948999998
No 65
>cd06545 GH18_3CO4_chitinase The Bacteroides thetaiotaomicron protein represented by pdb structure 3CO4 is an uncharacterized bacterial member of the family 18 glycosyl hydrolases with homologs found in Flavobacterium, Stigmatella, and Pseudomonas.
Probab=23.08 E-value=53 Score=13.65 Aligned_cols=28 Identities=14% Similarity=0.294 Sum_probs=23.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 5898999999999999999759998999
Q gi|254781141|r 93 TKDPAQRENFFKNLFRIGNILGFQKEEM 120 (196)
Q Consensus 93 ~~D~~k~~~~~~~i~~~~~~~Gfs~eEi 120 (196)
.+||+.+.+|..++.++...+||.-=+|
T Consensus 78 ~~~~~~R~~Fi~~~~~~~~~~~~DGvDi 105 (253)
T cd06545 78 LNDPAKRKALVDKIINYVVSYNLDGIDV 105 (253)
T ss_pred HCCHHHHHHHHHHHHHHHHHCCCCCEEE
T ss_conf 4599999999999999999809972898
No 66
>PRK13795 hypothetical protein; Provisional
Probab=22.95 E-value=54 Score=13.64 Aligned_cols=37 Identities=24% Similarity=0.354 Sum_probs=29.5
Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHH
Q ss_conf 999999999583658989999999999999997599989997
Q gi|254781141|r 80 IAENQQLEHLFPQTKDPAQRENFFKNLFRIGNILGFQKEEMV 121 (196)
Q Consensus 80 ~~e~~~L~e~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~ 121 (196)
..+...+.+.+||.-+ .+..-|..|+...|++++.|.
T Consensus 423 ~~e~~~~k~~~Pe~~~-----kw~~~L~~~a~~~g~~~e~v~ 459 (630)
T PRK13795 423 LAELERLKELHPELYE-----KWNAFLERWAKKMGLSEEWVK 459 (630)
T ss_pred HHHHHHHHHHCHHHHH-----HHHHHHHHHHHHCCCCHHHHH
T ss_conf 5689999866879999-----999999999998299989974
No 67
>pfam07862 Nif11 Nitrogen fixation protein of unknown function. This domain is found in the Cyanobacteria, and may be involved in nitrogen fixation, but no role has been assigned.
Probab=22.70 E-value=51 Score=13.78 Aligned_cols=23 Identities=26% Similarity=0.559 Sum_probs=16.5
Q ss_pred CCHHHHHHHH-----HHHHHHHHHCCCC
Q ss_conf 8989999999-----9999999975999
Q gi|254781141|r 94 KDPAQRENFF-----KNLFRIGNILGFQ 116 (196)
Q Consensus 94 ~D~~k~~~~~-----~~i~~~~~~~Gfs 116 (196)
.||..+.++. .+++.++...||+
T Consensus 15 ~d~~l~~~l~~~~~~~~vi~lA~~~Gf~ 42 (49)
T pfam07862 15 SDPSLREQLKACSDAEEVVALAKEAGFE 42 (49)
T ss_pred CCHHHHHHHHHCCCHHHHHHHHHHCCCC
T ss_conf 3999999998759999999999995998
No 68
>TIGR02990 ectoine_eutA ectoine utilization protein EutA; InterPro: IPR014332 Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include include Mesorhizobium loti, Silicibacter pomeroyi and Sinorhizobium meliloti 1021, where it is known to be induced by ectoine. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens. ,.
Probab=22.64 E-value=50 Score=13.84 Aligned_cols=24 Identities=33% Similarity=0.511 Sum_probs=21.5
Q ss_pred CCCCHH-HHHHHCCHHHHHHHHHHH
Q ss_conf 599989-997205999999999999
Q gi|254781141|r 113 LGFQKE-EMVDITDHRLLSLAYYAQ 136 (196)
Q Consensus 113 ~Gfs~e-Ei~~v~D~R~i~vl~~Am 136 (196)
+||+|| ||+.|+....|.+++.+.
T Consensus 154 lGl~DDREMARIs~~~iv~~A~~~~ 178 (239)
T TIGR02990 154 LGLTDDREMARISPDAIVELAKEAA 178 (239)
T ss_pred CCCCCCHHHHCCCHHHHHHHHHHHC
T ss_conf 5754452432389889999999850
No 69
>TIGR01245 trpD anthranilate phosphoribosyltransferase; InterPro: IPR005940 In many widely different species, including Escherichia coli, Thermotoga maritima, and Archaeoglobus fulgidus, this enzyme is a C-terminal part of a multifunctional protein together with glutamine amidotransferase; the fusion protein is designated anthranilate synthase component II (4.1.3.27 from EC).; GO: 0004048 anthranilate phosphoribosyltransferase activity, 0000162 tryptophan biosynthetic process.
Probab=22.05 E-value=56 Score=13.52 Aligned_cols=40 Identities=18% Similarity=0.155 Sum_probs=30.1
Q ss_pred HHHHHHHHHHC--CCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHC
Q ss_conf 99999999958--3658989999999999999997599989997205
Q gi|254781141|r 80 IAENQQLEHLF--PQTKDPAQRENFFKNLFRIGNILGFQKEEMVDIT 124 (196)
Q Consensus 80 ~~e~~~L~e~i--Pe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~ 124 (196)
.+|...|.+.| ++..|- ....|.--++--|.|++||.+.+
T Consensus 12 ~~ea~~lm~~~~~g~~~~~-----~~aA~L~al~~KGet~~Ei~GfA 53 (331)
T TIGR01245 12 EDEAEQLMKEIMSGEASPA-----QIAAILAALRIKGETPEEIAGFA 53 (331)
T ss_pred HHHHHHHHHHHHCCCCCHH-----HHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 8999999999847898888-----89999999975188999999999
No 70
>KOG0031 consensus
Probab=22.05 E-value=42 Score=14.34 Aligned_cols=43 Identities=16% Similarity=0.167 Sum_probs=24.4
Q ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHHHHCC--CCHHHHHHHCCHH
Q ss_conf 999958365898999999999999999759--9989997205999
Q gi|254781141|r 85 QLEHLFPQTKDPAQRENFFKNLFRIGNILG--FQKEEMVDITDHR 127 (196)
Q Consensus 85 ~L~e~iPe~~D~~k~~~~~~~i~~~~~~~G--fs~eEi~~v~D~R 127 (196)
.++.++-.|-+..++.--...+++.+.+.| |+++||..++..-
T Consensus 102 ~I~~AF~~FD~~~~G~I~~d~lre~Ltt~gDr~~~eEV~~m~r~~ 146 (171)
T KOG0031 102 VILNAFKTFDDEGSGKIDEDYLRELLTTMGDRFTDEEVDEMYREA 146 (171)
T ss_pred HHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHC
T ss_conf 999999841855788657899999998734438999999999858
No 71
>cd01938 ADPGK_ADPPFK ADP-dependent glucokinase (ADPGK) and phosphofructokinase (ADPPFK). ADPGK and ADPPFK are proteins that rely on ADP rather than ATP to donate a phosphoryl group. They are found in certain hyperthermophilic archaea and in higher eukaryotes. A functional ADPGK has been characterized in mouse and is assumed to be desirable during ischemia/hypoxia. ADPGK and ADPPFK contain a large and a small domain with the binding site located in a groove between the domains. Partial domain closing is seen when ADP is bound, and further domain closing is observed when glucose is also bound. The oligomerization state apparently varies depending on the species, with some existing as monomers, some as dimers, and some as tetramers.
Probab=21.95 E-value=56 Score=13.51 Aligned_cols=34 Identities=21% Similarity=0.413 Sum_probs=30.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCC
Q ss_conf 6589899999999999999975999899972059
Q gi|254781141|r 92 QTKDPAQRENFFKNLFRIGNILGFQKEEMVDITD 125 (196)
Q Consensus 92 e~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D 125 (196)
-+.|++.+..+...|.-+..+.|..++||.+++.
T Consensus 253 S~~d~~l~~~i~~~ilp~vdSlGmNEqELa~l~~ 286 (445)
T cd01938 253 STVDEELREEILHEVVPYVDSLGLNEQELANLLQ 286 (445)
T ss_pred CCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHH
T ss_conf 4576999999998725324657788899999999
No 72
>TIGR01420 pilT_fam twitching motility protein; InterPro: IPR006321 These represent the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction . Members of this family may be found in some species that do not have type IV pili but have related structures for DNA uptake and natural transformation. ; GO: 0005524 ATP binding, 0006810 transport.
Probab=21.68 E-value=14 Score=17.52 Aligned_cols=14 Identities=14% Similarity=0.124 Sum_probs=6.8
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 89999438999999
Q gi|254781141|r 29 PTLEKTYPETYHRI 42 (196)
Q Consensus 29 ~~L~~~DP~~Y~~~ 42 (196)
.-|=-||||||+-.
T Consensus 158 HIiTIEDPIEyvh~ 171 (350)
T TIGR01420 158 HIITIEDPIEYVHK 171 (350)
T ss_pred CCEEEECCEEEEEC
T ss_conf 82563177314104
No 73
>PRK07668 hypothetical protein; Validated
Probab=21.60 E-value=57 Score=13.46 Aligned_cols=34 Identities=12% Similarity=0.167 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHH
Q ss_conf 9999999999999997599989997205999999
Q gi|254781141|r 97 AQRENFFKNLFRIGNILGFQKEEMVDITDHRLLS 130 (196)
Q Consensus 97 ~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~ 130 (196)
+.++++-.+++-|+...|-+++||+++-|---+.
T Consensus 4 KE~~~FL~~~r~yL~~~Gkke~dI~~~~eele~H 37 (248)
T PRK07668 4 KEGRKFLDDTRVYLIAKGIKEEDIESFLEDAELH 37 (248)
T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf 4789999999999999189788999999999999
No 74
>pfam10932 DUF2783 Protein of unknown function (DUF2783). This is a bacterial family of uncharacterized protein.
Probab=21.50 E-value=57 Score=13.45 Aligned_cols=40 Identities=25% Similarity=0.457 Sum_probs=29.1
Q ss_pred HCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHH
Q ss_conf 5836589899999999999999975999899972059999999999
Q gi|254781141|r 89 LFPQTKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLSLAYY 134 (196)
Q Consensus 89 ~iPe~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~vl~~ 134 (196)
.-|.+.|| ..|+..+.+. ..|.|+++ +...++|.|++|-.
T Consensus 3 t~pnl~~p---D~fY~~Li~a--H~gLs~~q-S~~lNArLiLlLaN 42 (60)
T pfam10932 3 TTPNLADP---DDFYEALIEA--HRGLSDEQ-SAALNARLILLLAN 42 (60)
T ss_pred CCCCCCCC---HHHHHHHHHH--HCCCCHHH-HHHHHHHHHHHHHH
T ss_conf 88899980---2999999998--62899999-98872899999998
No 75
>TIGR01926 peroxid_rel uncharacterized peroxidase-related enzyme; InterPro: IPR010195 Members of this family are conserved hypothetical proteins of around 200 amino acids in length. Many of them contain an akylhydroperoxidase (AhpD) domain. .
Probab=21.46 E-value=55 Score=13.54 Aligned_cols=21 Identities=24% Similarity=0.366 Sum_probs=12.4
Q ss_pred HHHHCCCCHHHHHHHCCHHHH
Q ss_conf 999759998999720599999
Q gi|254781141|r 109 IGNILGFQKEEMVDITDHRLL 129 (196)
Q Consensus 109 ~~~~~Gfs~eEi~~v~D~R~i 129 (196)
-+...||||.+|-.+...-+|
T Consensus 141 ~Lr~~GfsD~~IlD~~~~~Af 161 (179)
T TIGR01926 141 ALRAAGFSDEEILDLIHVVAF 161 (179)
T ss_pred HHHHCCCCHHHHHHHHHHHHH
T ss_conf 887548995899999999999
No 76
>KOG1546 consensus
Probab=20.39 E-value=46 Score=14.07 Aligned_cols=37 Identities=16% Similarity=0.150 Sum_probs=25.1
Q ss_pred HHHHHHHHHH-CCCCHHHHHHHCCHHHHH-------HHHHHHHHH
Q ss_conf 9999999997-599989997205999999-------999999999
Q gi|254781141|r 103 FKNLFRIGNI-LGFQKEEMVDITDHRLLS-------LAYYAQIGL 139 (196)
Q Consensus 103 ~~~i~~~~~~-~Gfs~eEi~~v~D~R~i~-------vl~~Am~y~ 139 (196)
-..|+..+.+ |||+++.|--++|--.=. =+++||.|-
T Consensus 87 v~~M~~~Lv~rfGFs~ddI~~LtDt~~s~~~~PT~~Nir~Al~wL 131 (362)
T KOG1546 87 VHRMRKLLVERFGFSEDDILMLTDTDESPVRIPTGKNIRRALRWL 131 (362)
T ss_pred HHHHHHHHHHHHCCCHHHEEEEECCCCCCCCCCCHHHHHHHHHHH
T ss_conf 999999999861898334688744777642367277899999999
No 77
>pfam00531 Death Death domain.
Probab=20.20 E-value=61 Score=13.27 Aligned_cols=26 Identities=23% Similarity=0.331 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHCC
Q ss_conf 99999999999975999899972059
Q gi|254781141|r 100 ENFFKNLFRIGNILGFQKEEMVDITD 125 (196)
Q Consensus 100 ~~~~~~i~~~~~~~Gfs~eEi~~v~D 125 (196)
.....+...+|..+|||+.+|..+..
T Consensus 9 ~~~g~~W~~la~~Lgl~~~~i~~i~~ 34 (83)
T pfam00531 9 ELLGKDWRELARKLGLSESEIDEIEQ 34 (83)
T ss_pred HCCHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 32404199999995998999999998
No 78
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains . This entry represents glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=20.16 E-value=61 Score=13.27 Aligned_cols=46 Identities=17% Similarity=0.257 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHH--HCC---CCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHH
Q ss_conf 9999999999999--583---658989999999999999997599989997205999999
Q gi|254781141|r 76 EKKLIAENQQLEH--LFP---QTKDPAQRENFFKNLFRIGNILGFQKEEMVDITDHRLLS 130 (196)
Q Consensus 76 q~~l~~e~~~L~e--~iP---e~~D~~k~~~~~~~i~~~~~~~Gfs~eEi~~v~D~R~i~ 130 (196)
...+.-+.+.... .++ ||. .++..-++.+||||..|+.+..-..-.
T Consensus 468 ~~iV~~e~~l~~~~n~~~~I~~~~---------~e~L~~aK~lGFSD~~iA~~~~~~~~~ 518 (1089)
T TIGR01369 468 KNIVELEKELEELKNKLTGIEELD---------KELLRKAKKLGFSDAQIARLVNVTEAE 518 (1089)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCC---------HHHHHHHHHCCCCHHHHHHHHCCCHHH
T ss_conf 999999999875301244533489---------889999864188878999986897444
Done!