Query 041883
Match_columns 33
No_of_seqs 59 out of 61
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 11:42:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041883.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041883hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0687 PotD Spermidine/putres 98.6 3.8E-08 8.2E-13 61.3 3.0 26 8-33 124-149 (363)
2 PRK10682 putrescine transporte 98.0 2.7E-06 5.9E-11 52.4 2.0 22 11-32 126-147 (370)
3 PRK09501 potD spermidine/putre 98.0 4.9E-06 1.1E-10 50.9 2.0 23 10-32 121-143 (348)
4 PF13416 SBP_bac_8: Bacterial 97.6 4.2E-05 9E-10 43.9 2.0 26 8-33 79-105 (281)
5 TIGR03850 bind_CPR_0540 carboh 97.4 6.2E-05 1.4E-09 46.3 1.1 25 9-33 147-171 (437)
6 PRK09474 malE maltose ABC tran 97.3 0.00019 4.2E-09 43.7 2.3 25 9-33 125-149 (396)
7 PRK10974 glycerol-3-phosphate 97.1 0.00015 3.1E-09 45.3 0.6 25 9-33 133-157 (438)
8 COG1653 UgpB ABC-type sugar tr 96.7 0.00044 9.5E-09 41.0 0.2 26 8-33 133-158 (433)
9 TIGR03851 chitin_NgcE carbohyd 96.7 0.00066 1.4E-08 42.4 0.8 25 9-33 149-173 (450)
10 PRK11622 hypothetical protein; 96.2 0.0035 7.7E-08 39.7 2.0 23 11-33 147-169 (401)
11 TIGR01276 thiB thiamine ABC tr 95.9 0.0072 1.6E-07 36.2 2.3 21 12-32 96-116 (309)
12 TIGR01254 sfuA ABC transporter 95.4 0.0098 2.1E-07 35.7 1.6 22 11-32 95-116 (304)
13 PRK11205 tbpA thiamine transpo 94.7 0.025 5.4E-07 34.4 2.0 19 14-32 119-137 (330)
14 PF02030 Lipoprotein_8: Hypoth 94.5 0.019 4.2E-07 39.8 1.2 19 14-32 142-160 (493)
15 PF13343 SBP_bac_6: Bacterial 94.3 0.04 8.8E-07 31.8 2.2 26 5-32 41-66 (242)
16 TIGR03227 PhnS 2-aminoethylpho 93.2 0.071 1.5E-06 33.3 2.0 20 12-32 131-150 (367)
17 PRK15046 2-aminoethylphosphona 92.2 0.12 2.7E-06 31.8 2.1 24 8-33 123-146 (349)
18 PF01547 SBP_bac_1: Bacterial 92.0 0.076 1.7E-06 30.1 1.0 19 13-33 107-125 (315)
19 COG2182 MalE Maltose-binding p 88.2 0.15 3.3E-06 34.3 0.1 24 9-32 137-160 (420)
20 TIGR03261 phnS2 putative 2-ami 82.4 0.66 1.4E-05 28.3 0.9 24 9-32 112-135 (334)
21 COG4143 TbpA ABC-type thiamine 79.9 0.85 1.8E-05 30.6 0.8 20 14-33 123-142 (336)
22 PF02446 Glyco_hydro_77: 4-alp 77.6 1.4 3.1E-05 29.6 1.4 15 7-21 243-258 (496)
23 PF00877 NLPC_P60: NlpC/P60 fa 73.6 1.4 3E-05 23.0 0.4 9 15-23 1-9 (105)
24 PRK10838 spr outer membrane li 70.5 1.3 2.9E-05 27.0 -0.1 10 14-23 78-87 (190)
25 PRK14508 4-alpha-glucanotransf 68.3 1.6 3.4E-05 29.8 -0.1 14 8-21 256-270 (497)
26 TIGR02219 phage_NlpC_fam putat 67.8 1.6 3.6E-05 24.4 -0.1 9 15-23 10-18 (134)
27 PLN03236 4-alpha-glucanotransf 63.3 2.4 5.1E-05 30.8 0.0 16 7-22 325-341 (745)
28 PF07494 Reg_prop: Two compone 59.7 5.7 0.00012 16.6 0.9 9 8-16 13-21 (24)
29 COG0791 Spr Cell wall-associat 59.1 2.8 6.1E-05 24.1 -0.2 9 15-23 87-95 (197)
30 PF06970 RepA_N: Replication i 57.6 7.4 0.00016 20.6 1.3 13 3-15 39-51 (76)
31 PLN02950 4-alpha-glucanotransf 57.1 3.5 7.7E-05 30.2 0.0 16 7-22 512-528 (909)
32 PF03664 Glyco_hydro_62: Glyco 54.9 11 0.00024 25.0 2.0 21 11-31 87-107 (271)
33 PF05199 GMC_oxred_C: GMC oxid 54.5 4.3 9.3E-05 21.6 0.1 14 4-17 102-115 (144)
34 cd00005 CBM9 Family 9 carbohyd 44.6 10 0.00022 22.2 0.6 19 8-26 167-185 (186)
35 PF01123 Stap_Strp_toxin: Stap 42.4 16 0.00035 19.8 1.1 12 12-23 59-70 (87)
36 PF14433 SUKH-3: SUKH-3 immuni 41.2 17 0.00037 20.2 1.1 12 7-18 108-119 (142)
37 PRK02106 choline dehydrogenase 41.1 14 0.0003 24.6 0.9 16 2-17 483-498 (560)
38 PLN00055 photosystem II reacti 40.3 3.9 8.4E-05 22.5 -1.5 14 10-26 30-43 (73)
39 PRK13914 invasion associated s 39.7 9.4 0.0002 26.6 -0.1 10 14-23 377-386 (481)
40 PF13186 SPASM: Iron-sulfur cl 39.1 13 0.00029 17.0 0.5 13 6-18 9-21 (64)
41 PF00737 PsbH: Photosystem II 39.0 2.3 5.1E-05 22.1 -2.4 13 10-25 15-27 (52)
42 PF12396 DUF3659: Protein of u 37.5 33 0.00071 17.8 1.8 14 2-15 40-54 (64)
43 CHL00066 psbH photosystem II p 37.0 4.6 0.0001 22.2 -1.5 14 10-26 30-43 (73)
44 PF05075 DUF684: Protein of un 36.6 26 0.00056 22.6 1.6 13 18-30 239-252 (345)
45 PF07522 DRMBL: DNA repair met 33.9 29 0.00063 18.6 1.3 11 9-19 72-82 (110)
46 PF13540 RCC1_2: Regulator of 33.0 20 0.00044 15.5 0.5 9 7-15 14-22 (30)
47 TIGR01810 betA choline dehydro 32.4 28 0.0006 23.0 1.2 14 4-17 480-493 (532)
48 TIGR01898 cas_TM1791_cmr6 CRIS 31.4 12 0.00026 21.9 -0.5 12 13-24 28-39 (176)
49 PF08261 Carcinustatin: Carcin 31.2 18 0.00039 12.6 0.1 6 16-21 2-7 (8)
50 TIGR00971 3a0106s03 sulfate/th 31.0 36 0.00077 21.4 1.5 16 15-31 98-113 (315)
51 COG0655 WrbA Multimeric flavod 29.8 22 0.00047 20.8 0.4 16 8-23 75-90 (207)
52 smart00706 TECPR Beta propelle 29.6 41 0.00089 14.5 1.2 10 9-18 17-26 (35)
53 COG2113 ProX ABC-type proline/ 29.5 25 0.00055 22.7 0.7 16 10-25 143-158 (302)
54 KOG3135 1,4-benzoquinone reduc 29.4 24 0.00052 22.6 0.5 16 9-24 70-85 (203)
55 PF14903 WG_beta_rep: WG conta 29.1 22 0.00047 14.9 0.2 9 5-13 2-10 (35)
56 PF12481 DUF3700: Aluminium in 28.9 27 0.00058 22.6 0.7 14 8-24 150-163 (228)
57 PF03358 FMN_red: NADPH-depend 27.5 47 0.001 17.8 1.5 17 8-24 70-86 (152)
58 COG3807 Uncharacterized protei 26.2 31 0.00067 21.6 0.6 12 4-16 153-164 (171)
59 PRK14510 putative bifunctional 26.0 21 0.00046 27.0 -0.1 15 7-21 985-1000(1221)
60 PF01436 NHL: NHL repeat; Int 24.5 32 0.0007 14.5 0.4 10 7-16 9-18 (28)
61 PF10637 Ofd1_CTDD: Oxoglutara 24.1 75 0.0016 20.4 2.1 24 7-30 205-228 (266)
62 KOG4565 E93 protein involved i 24.0 32 0.00069 22.0 0.4 13 7-19 141-153 (206)
63 PF00736 EF1_GNE: EF-1 guanine 23.5 1.1E+02 0.0023 16.5 2.4 19 7-25 28-51 (89)
64 PRK10343 RNA-binding protein Y 23.0 68 0.0015 17.9 1.6 11 21-31 79-89 (97)
65 PF07598 DUF1561: Protein of u 22.9 22 0.00048 26.0 -0.5 11 9-19 291-301 (632)
66 TIGR00253 RNA_bind_YhbY putati 22.6 72 0.0016 17.6 1.6 11 21-31 77-87 (95)
67 PRK10852 thiosulfate transport 21.6 65 0.0014 20.8 1.5 15 15-30 115-129 (338)
68 PF13365 Trypsin_2: Trypsin-li 21.5 50 0.0011 16.3 0.8 10 7-16 111-120 (120)
69 PRK11792 queF 7-cyano-7-deazag 21.4 77 0.0017 20.9 1.8 14 19-32 187-200 (273)
70 cd01910 Wali7 This domain is p 20.9 53 0.0012 20.8 1.0 14 6-19 210-223 (224)
71 PF00235 Profilin: Profilin; 20.7 57 0.0012 17.3 1.0 11 6-16 21-31 (121)
72 PF14827 Cache_3: Sensory doma 20.5 67 0.0015 17.0 1.2 9 8-16 98-106 (116)
73 cd01936 Ntn_CA Cephalosporin a 20.4 28 0.00061 23.4 -0.4 11 13-23 5-15 (469)
74 cd08355 Glo_EDI_BRP_like_14 Th 20.0 81 0.0018 15.8 1.4 10 7-16 110-119 (122)
No 1
>COG0687 PotD Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]
Probab=98.60 E-value=3.8e-08 Score=61.32 Aligned_cols=26 Identities=23% Similarity=0.358 Sum_probs=23.9
Q ss_pred CCCCcEEEeeecccceEEEEeCCCCC
Q 041883 8 DPRDKIWAASHRWGTVVIAYKKKASH 33 (33)
Q Consensus 8 d~~G~iwgvPyrWG~t~IaYr~dkf~ 33 (33)
+..|..|+|||.||+++|+||++++.
T Consensus 124 ~d~g~~y~vPy~~g~t~i~Yn~~~~~ 149 (363)
T COG0687 124 FDPGNKYSVPYFWGTTGIAYNTDKVK 149 (363)
T ss_pred CCCCCEeeeeEEeeeeEEEEeccccC
Confidence 56799999999999999999999974
No 2
>PRK10682 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional
Probab=98.04 E-value=2.7e-06 Score=52.41 Aligned_cols=22 Identities=27% Similarity=0.457 Sum_probs=21.0
Q ss_pred CcEEEeeecccceEEEEeCCCC
Q 041883 11 DKIWAASHRWGTVVIAYKKKAS 32 (33)
Q Consensus 11 G~iwgvPyrWG~t~IaYr~dkf 32 (33)
|+.||+||.||+++|+||+++|
T Consensus 126 g~~y~vP~~~~~~~l~YN~~~~ 147 (370)
T PRK10682 126 DNKYAMPYMWATTGIGYNVDKV 147 (370)
T ss_pred CCeEeeeeEecceEEEEehHHh
Confidence 8899999999999999999986
No 3
>PRK09501 potD spermidine/putrescine ABC transporter periplasmic substrate-binding protein; Reviewed
Probab=97.95 E-value=4.9e-06 Score=50.91 Aligned_cols=23 Identities=17% Similarity=0.369 Sum_probs=21.0
Q ss_pred CCcEEEeeecccceEEEEeCCCC
Q 041883 10 RDKIWAASHRWGTVVIAYKKKAS 32 (33)
Q Consensus 10 ~G~iwgvPyrWG~t~IaYr~dkf 32 (33)
+|+.|++||.||+++|+||+++|
T Consensus 121 ~~~~y~vP~~~~~~~i~YN~d~v 143 (348)
T PRK09501 121 PNNDYSIPYIWGATAIGVNSDAI 143 (348)
T ss_pred CCCceEeeeeccceEEEEcHHHc
Confidence 36789999999999999999977
No 4
>PF13416 SBP_bac_8: Bacterial extracellular solute-binding protein; PDB: 2FNC_A 1ELJ_A 3TTM_B 3TTK_C 2W7Y_A 3RPW_A 2GHB_C 2GHA_A 1POY_3 1POT_A ....
Probab=97.60 E-value=4.2e-05 Score=43.90 Aligned_cols=26 Identities=19% Similarity=0.340 Sum_probs=23.2
Q ss_pred CCCCcEEEeeecccc-eEEEEeCCCCC
Q 041883 8 DPRDKIWAASHRWGT-VVIAYKKKASH 33 (33)
Q Consensus 8 d~~G~iwgvPyrWG~-t~IaYr~dkf~ 33 (33)
..+|++||+|+.+++ .++.||++.|+
T Consensus 79 ~~~G~~y~~P~~~~~~~~~~yn~d~~~ 105 (281)
T PF13416_consen 79 TYDGKLYGVPFDYGTPYGLYYNKDLLK 105 (281)
T ss_dssp EETTEESEEEEEEEEEEEEEEETTTHS
T ss_pred CCCCeEEEEEEeeccceEEEEchhhcc
Confidence 458999999999997 89999999874
No 5
>TIGR03850 bind_CPR_0540 carbohydrate ABC transporter substrate-binding protein, CPR_0540 family. Members of this protein are the substrate-binding protein of a predicted carbohydrate transporter operon, together with permease subunits of ABC transporter homology families. This substrate-binding protein frequently co-occurs in genomes with a family of disaccharide phosphorylases, TIGR02336, suggesting that the molecule transported will include beta-D-galactopyranosyl-(1-3)-N-acetyl-D-glucosamine and related carbohydrates. Members of this family are sporadically strain by strain, often in species with a human host association, including Propionibacterium acnes and Clostridium perfringens, and Bacillus cereus.
Probab=97.40 E-value=6.2e-05 Score=46.34 Aligned_cols=25 Identities=16% Similarity=0.163 Sum_probs=22.9
Q ss_pred CCCcEEEeeecccceEEEEeCCCCC
Q 041883 9 PRDKIWAASHRWGTVVIAYKKKASH 33 (33)
Q Consensus 9 ~~G~iwgvPyrWG~t~IaYr~dkf~ 33 (33)
.+|++||+|+..++.++.||+|.|+
T Consensus 147 ~~g~~ygvP~~~~~~~l~yNkdl~~ 171 (437)
T TIGR03850 147 GDGKTYLAPMFYSPTGLFYNKTLFE 171 (437)
T ss_pred CCCeEEEEEeecceEEEEEcHHHHH
Confidence 3899999999999999999999874
No 6
>PRK09474 malE maltose ABC transporter periplasmic protein; Reviewed
Probab=97.30 E-value=0.00019 Score=43.69 Aligned_cols=25 Identities=12% Similarity=0.088 Sum_probs=23.1
Q ss_pred CCCcEEEeeecccceEEEEeCCCCC
Q 041883 9 PRDKIWAASHRWGTVVIAYKKKASH 33 (33)
Q Consensus 9 ~~G~iwgvPyrWG~t~IaYr~dkf~ 33 (33)
.+|++||+|+...+.++.||+|.|+
T Consensus 125 ~dg~~YgvP~~~~~~~l~ynkdl~~ 149 (396)
T PRK09474 125 YNGKLIGYPIAVEALSLIYNKDLVP 149 (396)
T ss_pred ECCEEEEEeeeccceeEEEehhhcc
Confidence 4799999999999999999999874
No 7
>PRK10974 glycerol-3-phosphate transporter periplasmic binding protein; Provisional
Probab=97.13 E-value=0.00015 Score=45.35 Aligned_cols=25 Identities=20% Similarity=0.239 Sum_probs=22.7
Q ss_pred CCCcEEEeeecccceEEEEeCCCCC
Q 041883 9 PRDKIWAASHRWGTVVIAYKKKASH 33 (33)
Q Consensus 9 ~~G~iwgvPyrWG~t~IaYr~dkf~ 33 (33)
-+|++||+|+...+.++.||||.|+
T Consensus 133 ~~G~~YglP~~~~~~~l~YNkdlf~ 157 (438)
T PRK10974 133 KTGHLLSQPFNSSTPVLYYNKDAFK 157 (438)
T ss_pred CCCcEEEeeccCCCceEEEcHHHHH
Confidence 3799999999999999999998773
No 8
>COG1653 UgpB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=96.72 E-value=0.00044 Score=40.98 Aligned_cols=26 Identities=15% Similarity=0.198 Sum_probs=23.2
Q ss_pred CCCCcEEEeeecccceEEEEeCCCCC
Q 041883 8 DPRDKIWAASHRWGTVVIAYKKKASH 33 (33)
Q Consensus 8 d~~G~iwgvPyrWG~t~IaYr~dkf~ 33 (33)
..||++||+|..+.+.++.||+|.|+
T Consensus 133 ~~dG~~y~~P~~~~~~~~~ynkdlf~ 158 (433)
T COG1653 133 TYDGKLYGVPFNSSTPALFYNKDLFK 158 (433)
T ss_pred eeCCEEeeccccccCceEEEeHHHHH
Confidence 34899999999999999999999774
No 9
>TIGR03851 chitin_NgcE carbohydrate ABC transporter, N-acetylglucosamine/diacetylchitobiose-binding protein. Members of this protein family are the substrate-binding protein, a lipid-anchored protein of Gram-positive bacteria in all examples found so far, that include NgcE of the chitin-degrader, Streptomyces olivaceoviridis, and close homologs from other species likely to share the same function. NgcE binds both N-acetylglucosamine and the chitin dimer, N,N'-diacetylchitobiose.
Probab=96.68 E-value=0.00066 Score=42.44 Aligned_cols=25 Identities=12% Similarity=0.008 Sum_probs=22.6
Q ss_pred CCCcEEEeeecccceEEEEeCCCCC
Q 041883 9 PRDKIWAASHRWGTVVIAYKKKASH 33 (33)
Q Consensus 9 ~~G~iwgvPyrWG~t~IaYr~dkf~ 33 (33)
.+|++||+|+...+.++.||++.|+
T Consensus 149 ~dG~~ygvP~~~~~~~l~YNkdl~~ 173 (450)
T TIGR03851 149 FDGKPYALNYVYTVYGLWYSATLFE 173 (450)
T ss_pred ECCEEEEEeecceeeEEEEcHHHHH
Confidence 4799999999999999999998763
No 10
>PRK11622 hypothetical protein; Provisional
Probab=96.18 E-value=0.0035 Score=39.67 Aligned_cols=23 Identities=13% Similarity=0.099 Sum_probs=20.5
Q ss_pred CcEEEeeecccceEEEEeCCCCC
Q 041883 11 DKIWAASHRWGTVVIAYKKKASH 33 (33)
Q Consensus 11 G~iwgvPyrWG~t~IaYr~dkf~ 33 (33)
++.|++||.++.++|+||+|+|.
T Consensus 147 ~~~y~~P~~~~~~~l~YN~d~~~ 169 (401)
T PRK11622 147 TEGLEAPWGGAQLVFIYDSARTP 169 (401)
T ss_pred CCceEeeccCCeEEEEEchHhcC
Confidence 45699999999999999999873
No 11
>TIGR01276 thiB thiamine ABC transporter, periplasmic binding protein. This model finds the thiamine (and thiamine pyrophosphate) ABC transporter periplasmic binding protein ThiB in proteobacteria. Completed genomes having this protein (E. coli, Vibrio cholera, Haemophilus influenzae) also have the permease ThiP, described by TIGRFAMs equivalog model TIGR01253.
Probab=95.89 E-value=0.0072 Score=36.25 Aligned_cols=21 Identities=14% Similarity=0.180 Sum_probs=18.8
Q ss_pred cEEEeeecccceEEEEeCCCC
Q 041883 12 KIWAASHRWGTVVIAYKKKAS 32 (33)
Q Consensus 12 ~iwgvPyrWG~t~IaYr~dkf 32 (33)
.-+++||.||+++|+||++++
T Consensus 96 ~~~~~p~~~~~~~i~yn~~~~ 116 (309)
T TIGR01276 96 NDTFVPFDYGYFAFVYDKNKL 116 (309)
T ss_pred CCeEEEEeeEEEEEEECcccc
Confidence 348999999999999999876
No 12
>TIGR01254 sfuA ABC transporter periplasmic binding protein, thiB subfamily. The model describes thiamine ABC transporter, periplasmic protein in bacteria and archae. The protein belongs to the larger ABC transport system. It consists of at least three components: the thiamine binding periplasmic protein; an inner membrane permease; an ATP-binding subunit. It has been experimentally demonstrated that the mutants in the various steps in the de novo synthesis of the thiamine and the biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate (TMP) or thiamine pyrophosphate (TPP).
Probab=95.38 E-value=0.0098 Score=35.68 Aligned_cols=22 Identities=18% Similarity=0.280 Sum_probs=18.9
Q ss_pred CcEEEeeecccceEEEEeCCCC
Q 041883 11 DKIWAASHRWGTVVIAYKKKAS 32 (33)
Q Consensus 11 G~iwgvPyrWG~t~IaYr~dkf 32 (33)
...+++||.||.++|+||+++|
T Consensus 95 ~~~~~~p~~~~~~~i~yn~~~~ 116 (304)
T TIGR01254 95 NNATFLPFDYGYVAFVYDKNKL 116 (304)
T ss_pred CCCeEEEEeeeeEEEEEchHHh
Confidence 3447899999999999999876
No 13
>PRK11205 tbpA thiamine transporter substrate binding subunit; Provisional
Probab=94.71 E-value=0.025 Score=34.39 Aligned_cols=19 Identities=16% Similarity=0.221 Sum_probs=17.5
Q ss_pred EEeeecccceEEEEeCCCC
Q 041883 14 WAASHRWGTVVIAYKKKAS 32 (33)
Q Consensus 14 wgvPyrWG~t~IaYr~dkf 32 (33)
+++||.||.++|+||++++
T Consensus 119 ~~~~~~~~~~~l~yn~~~~ 137 (330)
T PRK11205 119 TFVPYDYGYFAFVYDKEKL 137 (330)
T ss_pred ceeeEeeeeEEEEEccccc
Confidence 5799999999999999976
No 14
>PF02030 Lipoprotein_8: Hypothetical lipoprotein (MG045 family)
Probab=94.47 E-value=0.019 Score=39.77 Aligned_cols=19 Identities=21% Similarity=0.476 Sum_probs=17.3
Q ss_pred EEeeecccceEEEEeCCCC
Q 041883 14 WAASHRWGTVVIAYKKKAS 32 (33)
Q Consensus 14 wgvPyrWG~t~IaYr~dkf 32 (33)
|||||-||-.+||||-.+.
T Consensus 142 Y~IPYF~QDLvfaY~~eki 160 (493)
T PF02030_consen 142 YGIPYFWQDLVFAYNGEKI 160 (493)
T ss_pred hcccceeeeeEEEEccccc
Confidence 8999999999999997764
No 15
>PF13343 SBP_bac_6: Bacterial extracellular solute-binding protein; PDB: 2QRY_D 1XVX_A 1SI1_A 1SI0_A 1Q35_A 1Y9U_A 2OWS_A 2OWT_A 2VP1_A 2VOZ_A ....
Probab=94.28 E-value=0.04 Score=31.79 Aligned_cols=26 Identities=31% Similarity=0.359 Sum_probs=21.3
Q ss_pred CccCCCCcEEEeeecccceEEEEeCCCC
Q 041883 5 GEIDPRDKIWAASHRWGTVVIAYKKKAS 32 (33)
Q Consensus 5 G~id~~G~iwgvPyrWG~t~IaYr~dkf 32 (33)
+..|++|..+ ||.++..+|+|+++++
T Consensus 41 ~~~d~~g~~~--~~~~~~~~i~yN~~~~ 66 (242)
T PF13343_consen 41 SFKDPDGYWV--PYGYGPVVIAYNTDKL 66 (242)
T ss_dssp GGBHTTSSSE--EEEEEEEEEEEETTTS
T ss_pred hccCCCCeEE--EEEEEEEEEEEEhhhc
Confidence 3446677655 9999999999999986
No 16
>TIGR03227 PhnS 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate binding protein. This ABC transporter periplasmic substrate binding protein component is found in a region of the salmonella typhimurium LT2 genome responsible for the catabolism of 2-aminoethylphosphonate via the phnWX pathway (GenProp0238). The protein contains a match to pfam01547 for the "Bacterial extracellular solute-binding protein" domain.
Probab=93.22 E-value=0.071 Score=33.29 Aligned_cols=20 Identities=20% Similarity=0.227 Sum_probs=17.3
Q ss_pred cEEEeeecccceEEEEeCCCC
Q 041883 12 KIWAASHRWGTVVIAYKKKAS 32 (33)
Q Consensus 12 ~iwgvPyrWG~t~IaYr~dkf 32 (33)
..|. ||.|+.++|+||++++
T Consensus 131 g~~~-p~~~~~~~i~YN~d~~ 150 (367)
T TIGR03227 131 GLWA-PFVKNYFSFAINPKLL 150 (367)
T ss_pred CeEE-EEeeceeEEEEchhhc
Confidence 3564 9999999999999986
No 17
>PRK15046 2-aminoethylphosphonate ABC transporter substrate-binding protein; Provisional
Probab=92.24 E-value=0.12 Score=31.79 Aligned_cols=24 Identities=17% Similarity=0.216 Sum_probs=19.5
Q ss_pred CCCCcEEEeeecccceEEEEeCCCCC
Q 041883 8 DPRDKIWAASHRWGTVVIAYKKKASH 33 (33)
Q Consensus 8 d~~G~iwgvPyrWG~t~IaYr~dkf~ 33 (33)
|++|. | +||.++.++|+||+++|+
T Consensus 123 d~~g~-~-~~~~~~~~~l~Yn~~~~~ 146 (349)
T PRK15046 123 DADGT-Y-APFVNNYLSFIYNPKVLK 146 (349)
T ss_pred CCCCC-E-EeeecceeEEEEchhhcc
Confidence 45675 3 699999999999999873
No 18
>PF01547 SBP_bac_1: Bacterial extracellular solute-binding protein; InterPro: IPR006059 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins and a high affinity periplasmic solute-binding protein. In Gram-positive bacteria, which are surrounded by a single membrane and therefore have no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute through the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped into eight family clusters [], which generally correlate with the nature of the solute bound. Family 1 includes the maltose/maltodextrin-binding proteins of Enterobacteriaceae (gene malE) [] and Streptococcus pneumoniae malX; multiple oligosaccharide binding protein of Streptococcus mutans (gene msmE); Escherichia coli glycerol-3-phosphate-binding protein; Serratia marcescens iron-binding protein (gene sfuA) and the homologous proteins (gene fbp) from Haemophilus influenzae and Neisseria; and the E. coli thiamine-binding protein (gene tbpA).; GO: 0005215 transporter activity, 0006810 transport; PDB: 3CFZ_A 2THI_A 3THI_A 4THI_A 1O7T_C 1D9Y_A 1URG_A 1URS_A 1URD_B 3OMB_A ....
Probab=92.04 E-value=0.076 Score=30.11 Aligned_cols=19 Identities=21% Similarity=0.294 Sum_probs=17.2
Q ss_pred EEEeeecccceEEEEeCCCCC
Q 041883 13 IWAASHRWGTVVIAYKKKASH 33 (33)
Q Consensus 13 iwgvPyrWG~t~IaYr~dkf~ 33 (33)
+| +|+. +..++.||+|.|+
T Consensus 107 ~y-vP~~-~~~~~~ynkdl~~ 125 (315)
T PF01547_consen 107 IY-VPYS-GPNGLYYNKDLFE 125 (315)
T ss_dssp ES-EEEE-EEEEEEEETTTHH
T ss_pred EE-EEee-eeeEEEEchhHHH
Confidence 89 9999 8999999999863
No 19
>COG2182 MalE Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism]
Probab=88.23 E-value=0.15 Score=34.31 Aligned_cols=24 Identities=17% Similarity=0.304 Sum_probs=22.2
Q ss_pred CCCcEEEeeecccceEEEEeCCCC
Q 041883 9 PRDKIWAASHRWGTVVIAYKKKAS 32 (33)
Q Consensus 9 ~~G~iwgvPyrWG~t~IaYr~dkf 32 (33)
=+|++||+|.-==+.++.||||.+
T Consensus 137 y~GkiYGlP~~~Et~~L~YNKdlv 160 (420)
T COG2182 137 YKGKLYGLPQAVETLALYYNKDLV 160 (420)
T ss_pred cCCEEEeccHhhhhhhhheecccc
Confidence 389999999999999999999975
No 20
>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate-binding protein. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=82.37 E-value=0.66 Score=28.27 Aligned_cols=24 Identities=4% Similarity=-0.020 Sum_probs=16.4
Q ss_pred CCCcEEEeeecccceEEEEeCCCC
Q 041883 9 PRDKIWAASHRWGTVVIAYKKKAS 32 (33)
Q Consensus 9 ~~G~iwgvPyrWG~t~IaYr~dkf 32 (33)
++|+-+.+++..+.++|+||+++|
T Consensus 112 ~~~~~~~~~~~~~~~~~~yN~~~~ 135 (334)
T TIGR03261 112 AKNPPHWVGMDAWMAAICFNTVEA 135 (334)
T ss_pred CCCCCceEeeeeeEEEEEEehHHH
Confidence 344334556666788999999865
No 21
>COG4143 TbpA ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]
Probab=79.87 E-value=0.85 Score=30.65 Aligned_cols=20 Identities=20% Similarity=0.376 Sum_probs=18.1
Q ss_pred EEeeecccceEEEEeCCCCC
Q 041883 14 WAASHRWGTVVIAYKKKASH 33 (33)
Q Consensus 14 wgvPyrWG~t~IaYr~dkf~ 33 (33)
..+||-+|=..|+|++++++
T Consensus 123 f~~P~DyGy~a~vYd~~~~~ 142 (336)
T COG4143 123 FALPYDYGYFAFVYDKTKLK 142 (336)
T ss_pred cccccccceEEEEEchHHhc
Confidence 38999999999999999874
No 22
>PF02446 Glyco_hydro_77: 4-alpha-glucanotransferase; InterPro: IPR003385 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The enzymes in this entry (2.4.1.25 from EC) belong to the glycoside hydrolase family 77 GH77 from CAZY, and transfer a segment of a (1,4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1,4)-alpha-D-glucan []. They belong to the disproportionating family of enzymes.; GO: 0004134 4-alpha-glucanotransferase activity, 0005975 carbohydrate metabolic process; PDB: 1TZ7_A 2X1I_A 2OWX_A 2OWW_A 1FP9_A 1CWY_A 1ESW_A 1FP8_A 2OWC_A 1X1N_A.
Probab=77.56 E-value=1.4 Score=29.57 Aligned_cols=15 Identities=20% Similarity=0.776 Sum_probs=10.4
Q ss_pred cCCCCcEEEee-eccc
Q 041883 7 IDPRDKIWAAS-HRWG 21 (33)
Q Consensus 7 id~~G~iwgvP-yrWG 21 (33)
.+++|+.||.| |.|=
T Consensus 243 fs~~GQ~WG~P~y~w~ 258 (496)
T PF02446_consen 243 FSPTGQNWGNPPYNWD 258 (496)
T ss_dssp SSSS-EEEEEE-B-HH
T ss_pred CCcccccCCCCCcCHH
Confidence 47899999999 7663
No 23
>PF00877 NLPC_P60: NlpC/P60 family; InterPro: IPR000064 The Escherichia coli NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. The E. coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis 3.4.19.11 from EC. This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family. ; PDB: 3PVQ_B 3GT2_A 3NPF_B 2K1G_A 3I86_A 3S0Q_A 2XIV_A 3PBC_A 3NE0_A 3M1U_B ....
Probab=73.59 E-value=1.4 Score=23.03 Aligned_cols=9 Identities=22% Similarity=0.556 Sum_probs=5.6
Q ss_pred Eeeecccce
Q 041883 15 AASHRWGTV 23 (33)
Q Consensus 15 gvPyrWG~t 23 (33)
|.||+||..
T Consensus 1 G~pY~~Gg~ 9 (105)
T PF00877_consen 1 GTPYVWGGR 9 (105)
T ss_dssp T-BB-TTGE
T ss_pred CCeecCCCC
Confidence 689999964
No 24
>PRK10838 spr outer membrane lipoprotein; Provisional
Probab=70.50 E-value=1.3 Score=26.99 Aligned_cols=10 Identities=20% Similarity=0.109 Sum_probs=8.4
Q ss_pred EEeeecccce
Q 041883 14 WAASHRWGTV 23 (33)
Q Consensus 14 wgvPyrWG~t 23 (33)
=|+||+||.+
T Consensus 78 ~G~pY~~GG~ 87 (190)
T PRK10838 78 KGVRYRLGGS 87 (190)
T ss_pred CCCCccCCCC
Confidence 3789999976
No 25
>PRK14508 4-alpha-glucanotransferase; Provisional
Probab=68.25 E-value=1.6 Score=29.76 Aligned_cols=14 Identities=14% Similarity=0.748 Sum_probs=11.7
Q ss_pred CCCCcEEEee-eccc
Q 041883 8 DPRDKIWAAS-HRWG 21 (33)
Q Consensus 8 d~~G~iwgvP-yrWG 21 (33)
+++|+.||.| |+|=
T Consensus 256 s~~GQ~WG~P~y~w~ 270 (497)
T PRK14508 256 SETGQLWGNPVYNWD 270 (497)
T ss_pred CcccCcCCCCCcCHH
Confidence 6789999999 7773
No 26
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=67.81 E-value=1.6 Score=24.44 Aligned_cols=9 Identities=11% Similarity=0.069 Sum_probs=7.5
Q ss_pred Eeeecccce
Q 041883 15 AASHRWGTV 23 (33)
Q Consensus 15 gvPyrWG~t 23 (33)
|.||+||.+
T Consensus 10 G~pY~~Gg~ 18 (134)
T TIGR02219 10 GTPYRHQAS 18 (134)
T ss_pred CCCeecCCC
Confidence 789999863
No 27
>PLN03236 4-alpha-glucanotransferase; Provisional
Probab=63.28 E-value=2.4 Score=30.78 Aligned_cols=16 Identities=19% Similarity=0.599 Sum_probs=13.1
Q ss_pred cCCCCcEEEee-ecccc
Q 041883 7 IDPRDKIWAAS-HRWGT 22 (33)
Q Consensus 7 id~~G~iwgvP-yrWG~ 22 (33)
.+++|+.||.| |.|-.
T Consensus 325 FS~~GQnWG~P~YnW~~ 341 (745)
T PLN03236 325 FDANGQNWGFPTYDWEE 341 (745)
T ss_pred CCcccCcCCCCCcCHHH
Confidence 47899999999 88843
No 28
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=59.71 E-value=5.7 Score=16.65 Aligned_cols=9 Identities=22% Similarity=0.830 Sum_probs=6.4
Q ss_pred CCCCcEEEe
Q 041883 8 DPRDKIWAA 16 (33)
Q Consensus 8 d~~G~iwgv 16 (33)
|++|.+|=.
T Consensus 13 D~~G~lWig 21 (24)
T PF07494_consen 13 DSDGNLWIG 21 (24)
T ss_dssp -TTSCEEEE
T ss_pred cCCcCEEEE
Confidence 789999953
No 29
>COG0791 Spr Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]
Probab=59.07 E-value=2.8 Score=24.09 Aligned_cols=9 Identities=33% Similarity=0.841 Sum_probs=7.6
Q ss_pred Eeeecccce
Q 041883 15 AASHRWGTV 23 (33)
Q Consensus 15 gvPyrWG~t 23 (33)
|.||+||.+
T Consensus 87 g~pY~~gG~ 95 (197)
T COG0791 87 GTPYRWGGS 95 (197)
T ss_pred CCCeEeCCC
Confidence 389999986
No 30
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=57.63 E-value=7.4 Score=20.59 Aligned_cols=13 Identities=23% Similarity=0.470 Sum_probs=10.7
Q ss_pred CCCccCCCCcEEE
Q 041883 3 DAGEIDPRDKIWA 15 (33)
Q Consensus 3 ~~G~id~~G~iwg 15 (33)
.+|.+|++|.||=
T Consensus 39 kn~wiDe~G~vYi 51 (76)
T PF06970_consen 39 KNGWIDENGNVYI 51 (76)
T ss_pred hcCcCCCCCCEEE
Confidence 3688999999983
No 31
>PLN02950 4-alpha-glucanotransferase
Probab=57.12 E-value=3.5 Score=30.23 Aligned_cols=16 Identities=19% Similarity=0.592 Sum_probs=13.1
Q ss_pred cCCCCcEEEee-ecccc
Q 041883 7 IDPRDKIWAAS-HRWGT 22 (33)
Q Consensus 7 id~~G~iwgvP-yrWG~ 22 (33)
.+++|+.||.| |.|-.
T Consensus 512 Fs~~GQ~WG~P~ynw~~ 528 (909)
T PLN02950 512 FDKNGQNWGFPTYNWEE 528 (909)
T ss_pred CCcccccCCCCCcCHHH
Confidence 46899999999 88854
No 32
>PF03664 Glyco_hydro_62: Glycosyl hydrolase family 62 ; InterPro: IPR005193 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This is a family of alpha -L-arabinofuranosidases (3.2.1.55 from EC) which are all members of glycoside hydrolase family 62 (GH62 from CAZY). This enzyme hydrolyzed aryl alpha-L-arabinofuranosides and cleaves arabinosyl side chains from arabinoxylan and arabinan.; GO: 0046556 alpha-N-arabinofuranosidase activity, 0046373 L-arabinose metabolic process
Probab=54.89 E-value=11 Score=24.96 Aligned_cols=21 Identities=24% Similarity=0.776 Sum_probs=18.3
Q ss_pred CcEEEeeecccceEEEEeCCC
Q 041883 11 DKIWAASHRWGTVVIAYKKKA 31 (33)
Q Consensus 11 G~iwgvPyrWG~t~IaYr~dk 31 (33)
-++|=.-|+||...++||.+.
T Consensus 87 k~~W~L~yQwg~~~fsY~Ts~ 107 (271)
T PF03664_consen 87 KNIWYLAYQWGPAAFSYSTSS 107 (271)
T ss_pred CcEEEEEEecCCCcceeecCC
Confidence 478999999999999999753
No 33
>PF05199 GMC_oxred_C: GMC oxidoreductase; InterPro: IPR007867 The glucose-methanol-choline (GMC) oxidoreductases are FAD flavoproteins oxidoreductases [, ]. These enzymes include a variety of proteins; choline dehydrogenase (CHD), methanol oxidase (MOX) and cellobiose dehydrogenase (1.1.99.18 from EC) [] which share a number of regions of sequence similarities. The function of this C-terminal conserved domain is not yet known.; GO: 0016614 oxidoreductase activity, acting on CH-OH group of donors, 0055114 oxidation-reduction process; PDB: 3BG7_F 2IGM_D 3BLY_A 3BG6_H 3LSK_A 2IGO_A 3K4B_A 3K4L_B 2IGN_B 3K4M_H ....
Probab=54.54 E-value=4.3 Score=21.56 Aligned_cols=14 Identities=14% Similarity=0.373 Sum_probs=11.0
Q ss_pred CCccCCCCcEEEee
Q 041883 4 AGEIDPRDKIWAAS 17 (33)
Q Consensus 4 ~G~id~~G~iwgvP 17 (33)
.+-+|++++|||+.
T Consensus 102 ~~VvD~~~rv~g~~ 115 (144)
T PF05199_consen 102 TSVVDPDLRVHGVR 115 (144)
T ss_dssp TTSB-TTSBBTTSB
T ss_pred ceeECCCCCeeeee
Confidence 37889999999975
No 34
>cd00005 CBM9 Family 9 carbohydrate-binding module (CBM), plays a role in microbial degradation of cellulose and hemicellulose found in plants; previously called cellulose-binding domain; the binding sites of the CBMs for which structures have been determined are of two general types: flat surfaces comprising predominantly aromatic residues tryptophan and tyrosine and extended shallow grooves; this domain frequently occurs in tandem.
Probab=44.61 E-value=10 Score=22.23 Aligned_cols=19 Identities=21% Similarity=0.597 Sum_probs=16.0
Q ss_pred CCCCcEEEeeecccceEEE
Q 041883 8 DPRDKIWAASHRWGTVVIA 26 (33)
Q Consensus 8 d~~G~iwgvPyrWG~t~Ia 26 (33)
+..+..|+-|.+||++.++
T Consensus 167 ~~~~~~~~~~~~fG~l~L~ 185 (186)
T cd00005 167 DPTNNQYQDTSNFGTLKLE 185 (186)
T ss_pred CCCCCcccChhHcEEEEEc
Confidence 4678999999999998764
No 35
>PF01123 Stap_Strp_toxin: Staphylococcal/Streptococcal toxin, OB-fold domain; InterPro: IPR006173 Staphylococcus aureus is a Gram-positive coccus that grows in clusters or pairs, and is the major cause of nosocomial infections due to its multiple antibiotic resistant nature []. Patients who are immunocompromised (e.g., those suffering from third degree burns or chronic illness) are at risk from deep staphylococcal infections, such as osteomyelitis and pneumonia. Most skin infections are also caused by this bacterium. Many virulence mechanisms are employed by Staphylococci to induce pathogenesis: these can include polysaccharide capsules and exotoxins []. One of the major virulence exotoxins is toxic shock syndrome toxin (TSST), which is secreted by the organism upon successful invasion. It causes a major inflammatory response in the host via superantigenic properties, and is the causative agent of toxic shock syndrome. The structure of the TSST protein was originally determined to 2.5A by means of X-ray crystallography []. The N- and C-terminal domains both contain regions involved in MHC class II association; the C-terminal domain is also implicated in binding the T-cell receptor. Overall, the structure resembles that of Staphylococcal enterotoxin B (SEB), but differs in its N terminus and in the degree to which a long central helix is covered by surface loops []. The region around the carboxyl end of this helix is proposed to govern the superantigenic properties of TSST. An adjacent region along this helix is thought to be critical in the ability of TSST to induce toxic shock syndrome. Most recently, the structures of five mutants of TSST have been determined to 1.95A []. The mutations are in the central alpha-helix, and allow mapping of portions of TSST involved in superantigenicity and lethality.; GO: 0009405 pathogenesis; PDB: 1XXG_A 1KTK_D 1HQR_D 2NTS_A 1FNW_E 1FNU_C 1L0X_B 1FNV_D 1UUP_B 1HA5_C ....
Probab=42.39 E-value=16 Score=19.81 Aligned_cols=12 Identities=17% Similarity=0.238 Sum_probs=10.4
Q ss_pred cEEEeeecccce
Q 041883 12 KIWAASHRWGTV 23 (33)
Q Consensus 12 ~iwgvPyrWG~t 23 (33)
.|+|+||.+.|.
T Consensus 59 DIfG~~Y~~~C~ 70 (87)
T PF01123_consen 59 DIFGLSYYYNCY 70 (87)
T ss_dssp EEEEEEBETTSS
T ss_pred EEEecccccccc
Confidence 489999999885
No 36
>PF14433 SUKH-3: SUKH-3 immunity protein
Probab=41.22 E-value=17 Score=20.16 Aligned_cols=12 Identities=17% Similarity=0.506 Sum_probs=10.3
Q ss_pred cCCCCcEEEeee
Q 041883 7 IDPRDKIWAASH 18 (33)
Q Consensus 7 id~~G~iwgvPy 18 (33)
+|.+|+||++..
T Consensus 108 ide~Grvy~~~~ 119 (142)
T PF14433_consen 108 IDESGRVYGLDD 119 (142)
T ss_pred EeCCCCEEEecC
Confidence 588999999984
No 37
>PRK02106 choline dehydrogenase; Validated
Probab=41.09 E-value=14 Score=24.61 Aligned_cols=16 Identities=13% Similarity=0.441 Sum_probs=13.6
Q ss_pred CCCCccCCCCcEEEee
Q 041883 2 NDAGEIDPRDKIWAAS 17 (33)
Q Consensus 2 ~~~G~id~~G~iwgvP 17 (33)
|..|-+|++++|||++
T Consensus 483 d~~sVVD~~~rV~Gv~ 498 (560)
T PRK02106 483 DPMAVVDPEGRVHGVE 498 (560)
T ss_pred CCCeeECCCCEEeccC
Confidence 4468899999999986
No 38
>PLN00055 photosystem II reaction center protein H; Provisional
Probab=40.34 E-value=3.9 Score=22.46 Aligned_cols=14 Identities=36% Similarity=0.714 Sum_probs=9.5
Q ss_pred CCcEEEeeecccceEEE
Q 041883 10 RDKIWAASHRWGTVVIA 26 (33)
Q Consensus 10 ~G~iwgvPyrWG~t~Ia 26 (33)
-||+ || -||+|+++
T Consensus 30 yGkv--ap-gWGTtp~M 43 (73)
T PLN00055 30 YGKV--AP-GWGTTPLM 43 (73)
T ss_pred cCcc--cC-CccchhHH
Confidence 3554 56 89998763
No 39
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=39.68 E-value=9.4 Score=26.64 Aligned_cols=10 Identities=20% Similarity=0.521 Sum_probs=8.0
Q ss_pred EEeeecccce
Q 041883 14 WAASHRWGTV 23 (33)
Q Consensus 14 wgvPyrWG~t 23 (33)
=|.||+||..
T Consensus 377 lG~PY~wGG~ 386 (481)
T PRK13914 377 LGKAYSWGGN 386 (481)
T ss_pred cCCcccCCCC
Confidence 3789999964
No 40
>PF13186 SPASM: Iron-sulfur cluster-binding domain
Probab=39.10 E-value=13 Score=17.04 Aligned_cols=13 Identities=31% Similarity=0.718 Sum_probs=10.2
Q ss_pred ccCCCCcEEEeee
Q 041883 6 EIDPRDKIWAASH 18 (33)
Q Consensus 6 ~id~~G~iwgvPy 18 (33)
.|++||+|+.-+.
T Consensus 9 ~I~~dG~v~pC~~ 21 (64)
T PF13186_consen 9 YIDPDGDVYPCCH 21 (64)
T ss_pred EEeeCccEEeCCC
Confidence 4789999998853
No 41
>PF00737 PsbH: Photosystem II 10 kDa phosphoprotein; InterPro: IPR001056 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight phosphoprotein PsbH found in PSII. The phosphorylation site of PsbH is located in the N terminus, where reversible phosphorylation is light-dependent and redox-controlled. PsbH is necessary for the photoprotection of PSII, being required for: (1) the rapid degradation of photodamaged D1 core protein to prevent further oxidative damage to the PSII core, and (2) the insertion of newly synthesised D1 protein into the thylakoid membrane []. PsbH may also regulate the transfer of electrons from D2 (Qa) to D1 (Qb) in the reaction core.; GO: 0042301 phosphate ion binding, 0015979 photosynthesis, 0050821 protein stabilization, 0009523 photosystem II, 0016020 membrane; PDB: 3PRR_H 2AXT_h 3BZ2_H 3BZ1_H 4FBY_W 3PRQ_H 3KZI_H 1S5L_h 3A0H_H 3ARC_H ....
Probab=38.97 E-value=2.3 Score=22.07 Aligned_cols=13 Identities=38% Similarity=0.787 Sum_probs=8.0
Q ss_pred CCcEEEeeecccceEE
Q 041883 10 RDKIWAASHRWGTVVI 25 (33)
Q Consensus 10 ~G~iwgvPyrWG~t~I 25 (33)
-||+ +| -||+|++
T Consensus 15 yGkV--aP-GWGTtpl 27 (52)
T PF00737_consen 15 YGKV--AP-GWGTTPL 27 (52)
T ss_dssp TT----BS-TTTTHHH
T ss_pred CCCc--CC-CccchHH
Confidence 4665 56 8999865
No 42
>PF12396 DUF3659: Protein of unknown function (DUF3659) ; InterPro: IPR022124 This domain family is found in bacteria and eukaryotes, and is approximately 70 amino acids in length.
Probab=37.46 E-value=33 Score=17.85 Aligned_cols=14 Identities=21% Similarity=0.582 Sum_probs=6.5
Q ss_pred CCCCcc-CCCCcEEE
Q 041883 2 NDAGEI-DPRDKIWA 15 (33)
Q Consensus 2 ~~~G~i-d~~G~iwg 15 (33)
|.+|+| |.+|++=|
T Consensus 40 d~~G~I~d~~G~viG 54 (64)
T PF12396_consen 40 DEDGDILDKDGNVIG 54 (64)
T ss_pred CCCCCEECCCCCEEE
Confidence 444443 55555433
No 43
>CHL00066 psbH photosystem II protein H
Probab=37.05 E-value=4.6 Score=22.19 Aligned_cols=14 Identities=36% Similarity=0.714 Sum_probs=9.3
Q ss_pred CCcEEEeeecccceEEE
Q 041883 10 RDKIWAASHRWGTVVIA 26 (33)
Q Consensus 10 ~G~iwgvPyrWG~t~Ia 26 (33)
-||+ || -||+|+++
T Consensus 30 yGkv--ap-gWGTtp~M 43 (73)
T CHL00066 30 YGKV--AP-GWGTTPLM 43 (73)
T ss_pred cCcc--cC-CccchHHH
Confidence 3554 55 79998763
No 44
>PF05075 DUF684: Protein of unknown function (DUF684); InterPro: IPR007767 This family contains uncharacterised proteins from Caenorhabditis elegans.
Probab=36.58 E-value=26 Score=22.64 Aligned_cols=13 Identities=31% Similarity=0.534 Sum_probs=10.2
Q ss_pred ecc-cceEEEEeCC
Q 041883 18 HRW-GTVVIAYKKK 30 (33)
Q Consensus 18 yrW-G~t~IaYr~d 30 (33)
++. ||++|+||..
T Consensus 239 ~~rGgcNv~VYRS~ 252 (345)
T PF05075_consen 239 FNRGGCNVFVYRSK 252 (345)
T ss_pred EeCCCeEEEEEeeC
Confidence 444 6999999984
No 45
>PF07522 DRMBL: DNA repair metallo-beta-lactamase; InterPro: IPR011084 The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in IPR001279 from INTERPRO and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair [].
Probab=33.91 E-value=29 Score=18.58 Aligned_cols=11 Identities=9% Similarity=0.126 Sum_probs=8.7
Q ss_pred CCCcEEEeeec
Q 041883 9 PRDKIWAASHR 19 (33)
Q Consensus 9 ~~G~iwgvPyr 19 (33)
.+..+|+|||.
T Consensus 72 ~~~~~~~VPYS 82 (110)
T PF07522_consen 72 GNVRIYRVPYS 82 (110)
T ss_pred CCceEEEEecc
Confidence 35679999995
No 46
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=32.96 E-value=20 Score=15.48 Aligned_cols=9 Identities=0% Similarity=0.442 Sum_probs=5.9
Q ss_pred cCCCCcEEE
Q 041883 7 IDPRDKIWA 15 (33)
Q Consensus 7 id~~G~iwg 15 (33)
++.+|+||+
T Consensus 14 l~~~g~v~~ 22 (30)
T PF13540_consen 14 LTSDGEVYC 22 (30)
T ss_dssp EE-TTEEEE
T ss_pred EEcCCCEEE
Confidence 466888876
No 47
>TIGR01810 betA choline dehydrogenase. This enzyme is a member of the GMC oxidoreductase family (pfam00732 and pfam05199), sharing a common evoluntionary origin and enzymatic reaction with alcohol dehydrogenase. Outgrouping from this model, Caulobacter crescentus shares sequence homology with choline dehydrogenase, yet other genes participating in this enzymatic reaction have not currently been identified.
Probab=32.40 E-value=28 Score=22.98 Aligned_cols=14 Identities=14% Similarity=0.444 Sum_probs=12.6
Q ss_pred CCccCCCCcEEEee
Q 041883 4 AGEIDPRDKIWAAS 17 (33)
Q Consensus 4 ~G~id~~G~iwgvP 17 (33)
.|-+|++++|||++
T Consensus 480 ~~VVD~~~rV~Gv~ 493 (532)
T TIGR01810 480 MSVVDPETRVHGME 493 (532)
T ss_pred CCccCCCCeEeccC
Confidence 67889999999986
No 48
>TIGR01898 cas_TM1791_cmr6 CRISPR-associated RAMP protein, Cmr6 family. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This family, represented by TM1791 of Thermotoga maritima, is designated Cmr6 [sic], for CRISPR/Cas Ramp Module protein 6. This family is both closely related to and frequently encoded next to the TM1792 family of Cas proteins described by TIGR01867. The two proteins are fused in an example from Methanopyrus kandleri.
Probab=31.44 E-value=12 Score=21.90 Aligned_cols=12 Identities=17% Similarity=0.265 Sum_probs=10.1
Q ss_pred EEEeeecccceE
Q 041883 13 IWAASHRWGTVV 24 (33)
Q Consensus 13 iwgvPyrWG~t~ 24 (33)
++|+||..|+++
T Consensus 28 ~~g~PyIPGSSl 39 (176)
T TIGR01898 28 IYGLPYIPGSAI 39 (176)
T ss_pred ccCcceecCchH
Confidence 689999999863
No 49
>PF08261 Carcinustatin: Carcinustatin peptide
Probab=31.21 E-value=18 Score=12.57 Aligned_cols=6 Identities=17% Similarity=0.484 Sum_probs=4.3
Q ss_pred eeeccc
Q 041883 16 ASHRWG 21 (33)
Q Consensus 16 vPyrWG 21 (33)
-||.+|
T Consensus 2 gpy~fg 7 (8)
T PF08261_consen 2 GPYSFG 7 (8)
T ss_pred Cccccc
Confidence 388777
No 50
>TIGR00971 3a0106s03 sulfate/thiosulfate-binding protein. This model describes binding proteins functionally associated with the sulfate ABC transporter. In the model bacterium E. coli, two different members work with the same transporter; mutation analysis says each enables the uptake of both sulfate and thiosulfate. In many species, a single binding protein is found, and may be referred to in general terms as a sulfate ABC transporter sulfate-binding protein.
Probab=30.96 E-value=36 Score=21.37 Aligned_cols=16 Identities=25% Similarity=0.295 Sum_probs=13.7
Q ss_pred EeeecccceEEEEeCCC
Q 041883 15 AASHRWGTVVIAYKKKA 31 (33)
Q Consensus 15 gvPyrWG~t~IaYr~dk 31 (33)
++||. +.++|+++++.
T Consensus 98 ~~~~~-~~lvl~v~k~~ 113 (315)
T TIGR00971 98 SAPYT-STIVFLVRKGN 113 (315)
T ss_pred CCccc-eeEEEEEeCCC
Confidence 68888 89999999874
No 51
>COG0655 WrbA Multimeric flavodoxin WrbA [General function prediction only]
Probab=29.80 E-value=22 Score=20.80 Aligned_cols=16 Identities=19% Similarity=0.430 Sum_probs=14.1
Q ss_pred CCCCcEEEeeecccce
Q 041883 8 DPRDKIWAASHRWGTV 23 (33)
Q Consensus 8 d~~G~iwgvPyrWG~t 23 (33)
+.||=|+|-|-+||.+
T Consensus 75 ~aD~iI~gsPvy~g~v 90 (207)
T COG0655 75 EADGIIFGSPVYFGNV 90 (207)
T ss_pred HCCEEEEeCCeecCCc
Confidence 4699999999999975
No 52
>smart00706 TECPR Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins.
Probab=29.64 E-value=41 Score=14.52 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=7.0
Q ss_pred CCCcEEEeee
Q 041883 9 PRDKIWAASH 18 (33)
Q Consensus 9 ~~G~iwgvPy 18 (33)
++++||||=.
T Consensus 17 ~~~~vW~V~~ 26 (35)
T smart00706 17 PSDTVWAVNS 26 (35)
T ss_pred CCCeEEEEcC
Confidence 4578888754
No 53
>COG2113 ProX ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]
Probab=29.46 E-value=25 Score=22.70 Aligned_cols=16 Identities=25% Similarity=0.651 Sum_probs=14.0
Q ss_pred CCcEEEeeecccceEE
Q 041883 10 RDKIWAASHRWGTVVI 25 (33)
Q Consensus 10 ~G~iwgvPyrWG~t~I 25 (33)
+|+|||.|=-|||+.+
T Consensus 143 ~g~i~g~~pG~g~~~~ 158 (302)
T COG2113 143 GGKIYGIEPGWGCMRV 158 (302)
T ss_pred CCcEEccCCCCchhHH
Confidence 4999999999999864
No 54
>KOG3135 consensus 1,4-benzoquinone reductase-like; Trp repressor binding protein-like/protoplast-secreted protein [General function prediction only]
Probab=29.36 E-value=24 Score=22.56 Aligned_cols=16 Identities=13% Similarity=0.279 Sum_probs=13.9
Q ss_pred CCCcEEEeeecccceE
Q 041883 9 PRDKIWAASHRWGTVV 24 (33)
Q Consensus 9 ~~G~iwgvPyrWG~t~ 24 (33)
-||-++|.|-|+|++.
T Consensus 70 ~D~flFG~PTRfG~~~ 85 (203)
T KOG3135|consen 70 YDGFLFGFPTRFGNMP 85 (203)
T ss_pred ccceeecccccccCcH
Confidence 4899999999999864
No 55
>PF14903 WG_beta_rep: WG containing repeat
Probab=29.06 E-value=22 Score=14.89 Aligned_cols=9 Identities=56% Similarity=0.726 Sum_probs=5.4
Q ss_pred CccCCCCcE
Q 041883 5 GEIDPRDKI 13 (33)
Q Consensus 5 G~id~~G~i 13 (33)
|-+|.+|++
T Consensus 2 G~id~~G~~ 10 (35)
T PF14903_consen 2 GYIDKNGKI 10 (35)
T ss_pred EEEeCCCCE
Confidence 445666665
No 56
>PF12481 DUF3700: Aluminium induced protein ; InterPro: IPR024286 This entry represents a domain found in plant proteins that is approximately 120 amino acids in length. There are two conserved sequence motifs: YGL and LRDR.
Probab=28.88 E-value=27 Score=22.59 Aligned_cols=14 Identities=21% Similarity=0.529 Sum_probs=10.1
Q ss_pred CCCCcEEEeeecccceE
Q 041883 8 DPRDKIWAASHRWGTVV 24 (33)
Q Consensus 8 d~~G~iwgvPyrWG~t~ 24 (33)
|.+|+ +|..||++.
T Consensus 150 d~~G~---vpLyWGi~~ 163 (228)
T PF12481_consen 150 DSDGS---VPLYWGIAA 163 (228)
T ss_pred cCCCC---cceEEEEeC
Confidence 55665 699999863
No 57
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=27.50 E-value=47 Score=17.82 Aligned_cols=17 Identities=24% Similarity=0.302 Sum_probs=13.7
Q ss_pred CCCCcEEEeeecccceE
Q 041883 8 DPRDKIWAASHRWGTVV 24 (33)
Q Consensus 8 d~~G~iwgvPyrWG~t~ 24 (33)
..|+-|++.|-.||...
T Consensus 70 ~aD~iI~~sP~y~~~~s 86 (152)
T PF03358_consen 70 EADGIIFASPVYNGSVS 86 (152)
T ss_dssp HSSEEEEEEEEBTTBE-
T ss_pred cCCeEEEeecEEcCcCC
Confidence 45899999999998763
No 58
>COG3807 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.18 E-value=31 Score=21.56 Aligned_cols=12 Identities=42% Similarity=0.881 Sum_probs=8.8
Q ss_pred CCccCCCCcEEEe
Q 041883 4 AGEIDPRDKIWAA 16 (33)
Q Consensus 4 ~G~id~~G~iwgv 16 (33)
.|.+ .+|+||||
T Consensus 153 ~GWi-~q~eIWGa 164 (171)
T COG3807 153 SGWI-SQGEIWGA 164 (171)
T ss_pred ccee-ecceeecc
Confidence 4555 47999997
No 59
>PRK14510 putative bifunctional 4-alpha-glucanotransferase/glycogen debranching enzyme; Provisional
Probab=25.97 E-value=21 Score=27.02 Aligned_cols=15 Identities=13% Similarity=0.344 Sum_probs=11.5
Q ss_pred cCCCCcEEEe-eeccc
Q 041883 7 IDPRDKIWAA-SHRWG 21 (33)
Q Consensus 7 id~~G~iwgv-PyrWG 21 (33)
++++|+-||. ||.|-
T Consensus 985 fs~~GQ~WG~P~y~w~ 1000 (1221)
T PRK14510 985 FNPEGQNWGLPPYDPR 1000 (1221)
T ss_pred CCcccccCCCcCcCHH
Confidence 4678999999 56664
No 60
>PF01436 NHL: NHL repeat; InterPro: IPR001258 The NHL repeat, named after NCL-1, HT2A and Lin-41, is found largely in a large number of eukaryotic and prokaryotic proteins. For example, the repeat is found in a variety of enzymes of the copper type II, ascorbate-dependent monooxygenase family which catalyse the C terminus alpha-amidation of biological peptides []. In many it occurs in tandem arrays, for example in the ringfinger beta-box, coiled-coil (RBCC) eukaryotic growth regulators []. The 'Brain Tumor' protein (Brat) is one such growth regulator that contains a 6-bladed NHL-repeat beta-propeller [, ]. The NHL repeats are also found in serine/threonine protein kinase (STPK) in diverse range of pathogenic bacteria. These STPK are transmembrane receptors with a intracellular N-terminal kinase domain and extracellular C-terminal sensor domain. In the STPK, PknD, from Mycobacterium tuberculosis, the sensor domain forms a rigid, six-bladed b-propeller composed of NHL repeats with a flexible tether to the transmembrane domain.; GO: 0005515 protein binding; PDB: 3FVZ_A 3FW0_A 1RWL_A 1RWI_A 1Q7F_A.
Probab=24.51 E-value=32 Score=14.53 Aligned_cols=10 Identities=30% Similarity=0.647 Sum_probs=6.4
Q ss_pred cCCCCcEEEe
Q 041883 7 IDPRDKIWAA 16 (33)
Q Consensus 7 id~~G~iwgv 16 (33)
+|++|.||=+
T Consensus 9 v~~~g~i~Va 18 (28)
T PF01436_consen 9 VDSDGNIYVA 18 (28)
T ss_dssp EETTSEEEEE
T ss_pred EeCCCCEEEE
Confidence 3677887743
No 61
>PF10637 Ofd1_CTDD: Oxoglutarate and iron-dependent oxygenase degradation C-term; InterPro: IPR019601 This entry represents the C-terminal degradation domain of oxoglutarate and iron-dependent oxygenase (Ofd1), the domain being conserved from yeasts to humans. Ofd1 is a prolyl 4-hydroxylase-like 2-oxoglutarate-Fe(II) dioxygenase that accelerates the degradation of Sre1N (the N-terminal transcription factor domain of Sre1) in the presence of oxygen []. Yeast Sre1 is the orthologue of mammalian sterol regulatory element binding protein (SREBP), and it responds to changes in oxygen-dependent sterol synthesis as an indirect measure of oxygen availability. However, unlike the prolyl 4-hydroxylases that regulate mammalian hypoxia-inducible factor, Ofd1 uses multiple domains to regulate Sre1N degradation by oxygen; the Ofd1 N-terminal dioxygenase domain is required for oxygen sensing and this Ofd1 C-terminal domain accelerates Sre1N degradation in yeasts []. ; GO: 0005506 iron ion binding, 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0031418 L-ascorbic acid binding, 0055114 oxidation-reduction process; PDB: 3KT4_A 3KT1_A 3KT7_A 3MGU_A.
Probab=24.15 E-value=75 Score=20.36 Aligned_cols=24 Identities=8% Similarity=0.419 Sum_probs=14.1
Q ss_pred cCCCCcEEEeeecccceEEEEeCC
Q 041883 7 IDPRDKIWAASHRWGTVVIAYKKK 30 (33)
Q Consensus 7 id~~G~iwgvPyrWG~t~IaYr~d 30 (33)
-+.|+.+.-+|-.|=+..||||-.
T Consensus 205 ~~ed~~Llt~~p~~N~LsLVlRD~ 228 (266)
T PF10637_consen 205 DDEDEELLTVPPSWNSLSLVLRDE 228 (266)
T ss_dssp -----EEEEE---EEEEEEEEE-T
T ss_pred cCCCceeEEccCCCCeEEEEEecC
Confidence 356789999999999999999953
No 62
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=23.97 E-value=32 Score=22.02 Aligned_cols=13 Identities=15% Similarity=0.470 Sum_probs=10.2
Q ss_pred cCCCCcEEEeeec
Q 041883 7 IDPRDKIWAASHR 19 (33)
Q Consensus 7 id~~G~iwgvPyr 19 (33)
+...+-|||||+.
T Consensus 141 VskAqsiyGvPHS 153 (206)
T KOG4565|consen 141 VSKAQSIYGVPHS 153 (206)
T ss_pred eecccceeccccc
Confidence 3567889999983
No 63
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=23.50 E-value=1.1e+02 Score=16.51 Aligned_cols=19 Identities=16% Similarity=0.345 Sum_probs=14.0
Q ss_pred cCCCCcEEE-----eeecccceEE
Q 041883 7 IDPRDKIWA-----ASHRWGTVVI 25 (33)
Q Consensus 7 id~~G~iwg-----vPyrWG~t~I 25 (33)
+..+|..|| .|-.+|...|
T Consensus 28 i~~~gl~w~~~~~~epIaFGlk~L 51 (89)
T PF00736_consen 28 IPMEGLKWGEKSKEEPIAFGLKAL 51 (89)
T ss_dssp S-TTTEEEEEEEEEEEECTTEEEE
T ss_pred chhcceeeeeeeeeeeecccEEEE
Confidence 567899999 7888886654
No 64
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=22.96 E-value=68 Score=17.85 Aligned_cols=11 Identities=18% Similarity=0.606 Sum_probs=8.9
Q ss_pred cceEEEEeCCC
Q 041883 21 GTVVIAYKKKA 31 (33)
Q Consensus 21 G~t~IaYr~dk 31 (33)
|-+.+.||+++
T Consensus 79 G~~~vlYR~~~ 89 (97)
T PRK10343 79 GKTLVLYRPTK 89 (97)
T ss_pred CcEEEEEecCC
Confidence 77899999763
No 65
>PF07598 DUF1561: Protein of unknown function (DUF1561); InterPro: IPR011455 This is a family of paralogous proteins in Leptospira interrogans.
Probab=22.89 E-value=22 Score=25.97 Aligned_cols=11 Identities=9% Similarity=0.250 Sum_probs=8.1
Q ss_pred CCCcEEEeeec
Q 041883 9 PRDKIWAASHR 19 (33)
Q Consensus 9 ~~G~iwgvPyr 19 (33)
.=|-=|||||-
T Consensus 291 ~YG~nWGvpYt 301 (632)
T PF07598_consen 291 QYGSNWGVPYT 301 (632)
T ss_pred EecCCCCcccc
Confidence 34677999984
No 66
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=22.60 E-value=72 Score=17.56 Aligned_cols=11 Identities=18% Similarity=0.646 Sum_probs=9.1
Q ss_pred cceEEEEeCCC
Q 041883 21 GTVVIAYKKKA 31 (33)
Q Consensus 21 G~t~IaYr~dk 31 (33)
|-+.+.||+++
T Consensus 77 G~~~vlYR~~~ 87 (95)
T TIGR00253 77 GKTIVLYRPTK 87 (95)
T ss_pred ccEEEEEecCC
Confidence 78899999764
No 67
>PRK10852 thiosulfate transporter subunit; Provisional
Probab=21.63 E-value=65 Score=20.80 Aligned_cols=15 Identities=13% Similarity=0.328 Sum_probs=12.9
Q ss_pred EeeecccceEEEEeCC
Q 041883 15 AASHRWGTVVIAYKKK 30 (33)
Q Consensus 15 gvPyrWG~t~IaYr~d 30 (33)
++|| -++++|++|++
T Consensus 115 ~~p~-~s~lV~vv~kg 129 (338)
T PRK10852 115 SSPF-YSTMAFLVRKG 129 (338)
T ss_pred CCcc-cceEEEEEECC
Confidence 6788 78999999986
No 68
>PF13365 Trypsin_2: Trypsin-like peptidase domain; PDB: 1Y8T_A 2Z9I_A 3QO6_A 1L1J_A 1QY6_A 2O8L_A 3OTP_E 2ZLE_I 1KY9_A 3CS0_A ....
Probab=21.51 E-value=50 Score=16.34 Aligned_cols=10 Identities=10% Similarity=0.295 Sum_probs=7.7
Q ss_pred cCCCCcEEEe
Q 041883 7 IDPRDKIWAA 16 (33)
Q Consensus 7 id~~G~iwgv 16 (33)
+|.+|++.|+
T Consensus 111 ~~~~G~vvGi 120 (120)
T PF13365_consen 111 FDSDGRVVGI 120 (120)
T ss_dssp EETTSEEEEE
T ss_pred ECCCCEEEeC
Confidence 5788888875
No 69
>PRK11792 queF 7-cyano-7-deazaguanine reductase; Provisional
Probab=21.35 E-value=77 Score=20.92 Aligned_cols=14 Identities=36% Similarity=0.807 Sum_probs=12.1
Q ss_pred cccceEEEEeCCCC
Q 041883 19 RWGTVVIAYKKKAS 32 (33)
Q Consensus 19 rWG~t~IaYr~dkf 32 (33)
-||++.|-|+.++.
T Consensus 187 D~~ti~I~Y~~~~i 200 (273)
T PRK11792 187 DWGSVQIRYRGPKI 200 (273)
T ss_pred CeEEEEEEEeCCcc
Confidence 49999999998875
No 70
>cd01910 Wali7 This domain is present in Wali7, a protein of unknown function, expressed in wheat and induced by aluminum. Wali7 has a single domain similar to the glutamine amidotransferase domain of glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). The Wali7 domain is also somewhat similar to the Ntn hydrolase fold of the proteasomal alph and beta subunits.
Probab=20.94 E-value=53 Score=20.77 Aligned_cols=14 Identities=14% Similarity=0.449 Sum_probs=11.3
Q ss_pred ccCCCCcEEEeeec
Q 041883 6 EIDPRDKIWAASHR 19 (33)
Q Consensus 6 ~id~~G~iwgvPyr 19 (33)
.+|++|+++|+-+.
T Consensus 210 ~~~s~g~~cg~~f~ 223 (224)
T cd01910 210 RVDSEGEMCGATFK 223 (224)
T ss_pred cccCcccEecceee
Confidence 46889999998764
No 71
>PF00235 Profilin: Profilin; InterPro: IPR002097 Profilin is a small eukaryotic protein that binds to monomeric actin (G-actin) in a 1:1 ratio thus preventing the polymerisation of actin into filaments (F-actin). It can also in certain circumstance promote actin polymerisation. Profilin also binds to polyphosphoinositides such as PIP2. Overall sequence similarity among profilin from organisms which belong to different phyla (ranging from fungi to mammals) is low, but the N-terminal region is relatively well conserved. That region is thought to be involved in the binding to actin. A protein structurally similar to profilin is present in the genome of Variola virus and Vaccinia virus (gene A42R). Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Ara t 8, Bet v 2, Cyn d 12, Hel a 2, Mer a 1 and Phl p 11.; GO: 0003779 actin binding, 0007010 cytoskeleton organization, 0015629 actin cytoskeleton; PDB: 1ACF_A 3NEC_C 2V8F_B 2V8C_A 2VK3_A 2JKF_A 2JKG_A 1F2K_B 2ACG_A 1YPR_B ....
Probab=20.72 E-value=57 Score=17.31 Aligned_cols=11 Identities=27% Similarity=0.682 Sum_probs=8.1
Q ss_pred ccCCCCcEEEe
Q 041883 6 EIDPRDKIWAA 16 (33)
Q Consensus 6 ~id~~G~iwgv 16 (33)
.++.||.+||.
T Consensus 21 I~~~dG~vwA~ 31 (121)
T PF00235_consen 21 IIGSDGSVWAS 31 (121)
T ss_dssp EEETTSSEEEE
T ss_pred EEcCCCCEEEe
Confidence 45678888884
No 72
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=20.53 E-value=67 Score=17.02 Aligned_cols=9 Identities=22% Similarity=0.372 Sum_probs=5.2
Q ss_pred CCCCcEEEe
Q 041883 8 DPRDKIWAA 16 (33)
Q Consensus 8 d~~G~iwgv 16 (33)
|++|++.|+
T Consensus 98 d~~g~viG~ 106 (116)
T PF14827_consen 98 DSDGKVIGV 106 (116)
T ss_dssp -TTS-EEEE
T ss_pred CCCCcEEEE
Confidence 577888775
No 73
>cd01936 Ntn_CA Cephalosporin acylase (CA) belongs to a family of beta-lactam acylases that includes penicillin G acylase (PGA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and 7-aminocephalosporanic acid (7-ACA), which can be used to synthesize semi-synthetic penicillins and cephalosporins, respectively. While both PGA and CA have a conserved Ntn (N-terminal nucleophile) hydrolase fold and the structural similarity at their active sites is very high, their sequence similarity to other Ntn's is low.
Probab=20.41 E-value=28 Score=23.39 Aligned_cols=11 Identities=9% Similarity=0.302 Sum_probs=8.9
Q ss_pred EEEeeecccce
Q 041883 13 IWAASHRWGTV 23 (33)
Q Consensus 13 iwgvPyrWG~t 23 (33)
.|||||..|.+
T Consensus 5 ~~GvPHi~a~~ 15 (469)
T cd01936 5 TYGVPHIYAKD 15 (469)
T ss_pred CCCCCeEEecC
Confidence 58999988765
No 74
>cd08355 Glo_EDI_BRP_like_14 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins.
Probab=20.03 E-value=81 Score=15.82 Aligned_cols=10 Identities=30% Similarity=0.883 Sum_probs=8.1
Q ss_pred cCCCCcEEEe
Q 041883 7 IDPRDKIWAA 16 (33)
Q Consensus 7 id~~G~iwgv 16 (33)
.||||-+|.+
T Consensus 110 ~DPdG~~~~l 119 (122)
T cd08355 110 RDPEGNLWTF 119 (122)
T ss_pred ECCCCCEEEE
Confidence 4899998876
Done!