Query psy3941
Match_columns 83
No_of_seqs 129 out of 1144
Neff 8.5
Searched_HMMs 46136
Date Fri Aug 16 21:15:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3941.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3941hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00725 3HCDH: 3-hydroxyacyl- 100.0 2.7E-32 5.9E-37 156.8 4.8 80 1-81 18-97 (97)
2 KOG2304|consensus 100.0 4.7E-29 1E-33 161.6 6.7 82 1-82 217-298 (298)
3 COG1250 FadB 3-hydroxyacyl-CoA 100.0 3.3E-28 7.1E-33 163.5 7.6 83 1-83 203-285 (307)
4 PRK09260 3-hydroxybutyryl-CoA 99.9 7E-28 1.5E-32 160.4 7.7 81 1-83 202-282 (288)
5 PRK08293 3-hydroxybutyryl-CoA 99.9 7.6E-28 1.6E-32 160.3 7.7 81 1-82 206-287 (287)
6 PRK07819 3-hydroxybutyryl-CoA 99.9 1.2E-27 2.6E-32 159.7 7.5 80 1-81 207-286 (286)
7 PRK06035 3-hydroxyacyl-CoA deh 99.9 1.4E-27 3.1E-32 159.1 7.6 80 1-81 206-290 (291)
8 PRK05808 3-hydroxybutyryl-CoA 99.9 1.8E-27 3.9E-32 158.0 7.5 80 1-81 203-282 (282)
9 PLN02545 3-hydroxybutyryl-CoA 99.9 3.8E-27 8.2E-32 157.3 7.9 82 1-83 204-285 (295)
10 PRK07530 3-hydroxybutyryl-CoA 99.9 5.2E-27 1.1E-31 156.4 7.8 82 1-83 204-285 (292)
11 TIGR02279 PaaC-3OHAcCoADH 3-hy 99.9 4.1E-26 8.8E-31 161.8 7.7 81 1-82 205-286 (503)
12 TIGR02437 FadB fatty oxidation 99.9 9.8E-25 2.1E-29 159.6 7.6 81 1-82 513-593 (714)
13 PRK11730 fadB multifunctional 99.9 1E-24 2.2E-29 159.5 7.7 81 1-82 513-593 (715)
14 TIGR02440 FadJ fatty oxidation 99.9 1.5E-24 3.2E-29 158.4 7.5 78 1-82 505-582 (699)
15 PRK08269 3-hydroxybutyryl-CoA 99.9 2.3E-24 4.9E-29 145.6 7.8 81 1-82 200-283 (314)
16 TIGR02441 fa_ox_alpha_mit fatt 99.9 3.2E-24 7E-29 157.3 7.3 78 1-82 535-614 (737)
17 PRK11154 fadJ multifunctional 99.9 4.3E-24 9.2E-29 156.2 7.4 78 1-82 510-587 (708)
18 PRK08268 3-hydroxy-acyl-CoA de 99.9 6.8E-24 1.5E-28 150.6 7.8 82 1-82 207-288 (507)
19 PRK06130 3-hydroxybutyryl-CoA 99.9 8.3E-23 1.8E-27 137.0 7.2 81 1-83 201-284 (311)
20 PRK08268 3-hydroxy-acyl-CoA de 99.8 5.7E-19 1.2E-23 125.6 7.1 68 1-69 433-500 (507)
21 TIGR02279 PaaC-3OHAcCoADH 3-hy 99.8 1.6E-18 3.5E-23 123.2 7.0 68 1-69 432-499 (503)
22 TIGR02440 FadJ fatty oxidation 99.7 1.4E-16 3E-21 116.8 7.0 67 1-69 626-696 (699)
23 PRK11154 fadJ multifunctional 99.7 2.1E-16 4.6E-21 116.0 7.0 67 1-69 633-703 (708)
24 TIGR02441 fa_ox_alpha_mit fatt 99.6 3.2E-16 7E-21 115.5 6.8 67 1-69 663-734 (737)
25 PRK11730 fadB multifunctional 99.6 1.8E-15 3.9E-20 111.2 7.0 66 1-69 642-711 (715)
26 TIGR02437 FadB fatty oxidation 99.6 4.6E-15 1E-19 109.1 6.9 66 1-69 642-711 (714)
27 PRK07066 3-hydroxybutyryl-CoA 99.6 1.3E-15 2.7E-20 103.5 2.4 82 1-82 205-297 (321)
28 KOG1683|consensus 99.4 5.5E-14 1.2E-18 96.2 3.0 69 7-83 196-264 (380)
29 KOG1683|consensus 98.9 2.5E-10 5.4E-15 78.5 0.3 62 1-69 311-376 (380)
30 PRK06129 3-hydroxyacyl-CoA deh 98.9 4.1E-09 8.9E-14 71.1 6.0 65 1-66 204-274 (308)
31 PRK07531 bifunctional 3-hydrox 98.3 5.9E-07 1.3E-11 64.3 3.6 49 1-49 202-254 (495)
32 KOG2305|consensus 92.2 0.58 1.2E-05 31.5 5.4 32 1-32 206-240 (313)
33 PF02762 Cbl_N3: CBL proto-onc 61.2 2.1 4.5E-05 23.8 -0.4 19 59-83 60-78 (86)
34 PF02493 MORN: MORN repeat; I 52.5 5.4 0.00012 16.1 0.2 13 71-83 8-20 (23)
35 smart00345 HTH_GNTR helix_turn 50.5 12 0.00027 18.2 1.4 24 56-79 36-59 (60)
36 PF05157 T2SE_Nter: Type II se 48.9 12 0.00026 20.7 1.3 24 1-24 1-24 (109)
37 TIGR01323 nitrile_alph nitrile 43.1 14 0.00031 23.7 1.1 27 1-28 10-36 (185)
38 PF14419 SPOUT_MTase_2: AF2226 42.2 13 0.00027 23.6 0.8 14 20-33 131-144 (173)
39 PHA02930 hypothetical protein; 40.4 12 0.00026 20.1 0.4 9 75-83 29-37 (81)
40 PRK11402 DNA-binding transcrip 40.0 17 0.00036 23.6 1.2 26 54-79 47-72 (241)
41 PF13300 DUF4078: Domain of un 37.3 14 0.00031 20.9 0.4 10 74-83 31-40 (88)
42 PF08672 APC2: Anaphase promot 36.4 33 0.00072 17.8 1.7 48 25-73 4-54 (60)
43 cd07377 WHTH_GntR Winged helix 36.4 30 0.00065 17.1 1.6 24 56-79 41-64 (66)
44 TIGR02404 trehalos_R_Bsub treh 36.2 21 0.00046 22.9 1.2 26 54-79 38-63 (233)
45 smart00540 LEM in nuclear memb 35.5 47 0.001 16.3 2.1 20 8-28 7-26 (44)
46 PF10415 FumaraseC_C: Fumarase 35.3 18 0.00038 18.5 0.6 16 2-17 33-48 (55)
47 PRK10079 phosphonate metabolis 35.1 22 0.00049 23.0 1.2 26 54-79 49-74 (241)
48 KOG1785|consensus 34.2 31 0.00068 25.2 1.8 19 59-83 314-332 (563)
49 cd08323 CARD_APAF1 Caspase act 34.0 26 0.00056 19.6 1.1 18 1-18 23-40 (86)
50 PRK14999 histidine utilization 33.7 23 0.00051 22.9 1.1 25 55-79 51-75 (241)
51 TIGR02325 C_P_lyase_phnF phosp 33.6 25 0.00054 22.5 1.2 25 55-79 47-71 (238)
52 PF09003 Phage_integ_N: Bacter 33.3 13 0.00029 20.4 -0.1 12 71-82 21-32 (75)
53 PF02979 NHase_alpha: Nitrile 33.2 19 0.00041 23.2 0.6 29 1-30 16-44 (188)
54 PF15606 Toxin_55: Putative to 33.1 90 0.0019 17.2 4.1 34 38-73 24-57 (77)
55 PF13319 DUF4090: Protein of u 33.1 92 0.002 17.3 5.2 70 9-79 2-84 (84)
56 TIGR02018 his_ut_repres histid 31.3 28 0.00061 22.3 1.2 26 54-79 39-64 (230)
57 PF01881 Cas_Cas6: CRISPR asso 30.9 40 0.00087 20.4 1.7 21 57-78 129-149 (155)
58 PRK09764 DNA-binding transcrip 30.6 30 0.00065 22.4 1.2 26 54-79 43-68 (240)
59 smart00698 MORN Possible plasm 28.6 21 0.00046 15.2 0.2 12 71-82 10-21 (26)
60 PF12367 PFO_beta_C: Pyruvate 27.9 35 0.00076 18.2 1.0 28 3-31 21-51 (67)
61 PF07882 Fucose_iso_N2: L-fuco 27.1 47 0.001 21.4 1.6 17 2-18 43-59 (181)
62 COG2188 PhnF Transcriptional r 27.0 35 0.00076 22.2 1.0 26 54-79 45-70 (236)
63 PRK11234 nfrB bacteriophage N4 26.9 31 0.00068 26.6 0.9 22 1-22 686-707 (727)
64 PF00392 GntR: Bacterial regul 26.9 25 0.00053 17.9 0.3 23 57-79 41-63 (64)
65 PF05813 Orthopox_F7: Orthopox 26.6 28 0.00061 18.7 0.4 9 75-83 30-38 (82)
66 PF04967 HTH_10: HTH DNA bindi 25.7 30 0.00066 17.5 0.5 6 77-82 16-21 (53)
67 PF01081 Aldolase: KDPG and KH 25.3 55 0.0012 21.1 1.7 22 5-26 107-132 (196)
68 PF09722 DUF2384: Protein of u 25.0 98 0.0021 15.1 2.3 33 12-45 11-50 (54)
69 PF12637 TSCPD: TSCPD domain; 23.2 1.3E+02 0.0028 16.9 2.8 23 3-27 52-74 (95)
70 KOG4742|consensus 23.2 78 0.0017 21.8 2.2 25 58-82 68-92 (286)
71 smart00445 LINK Link (Hyaluron 23.1 69 0.0015 18.3 1.6 15 6-20 31-45 (94)
72 PF12525 DUF3726: Protein of u 22.7 1.1E+02 0.0024 16.9 2.4 34 14-48 13-53 (80)
73 PF13121 DUF3976: Domain of un 22.5 25 0.00054 16.7 -0.2 10 71-80 13-22 (41)
74 PRK13677 hypothetical protein; 22.2 57 0.0012 19.6 1.2 13 3-15 7-19 (125)
75 cd00279 YlxR Ylxr homologs; gr 22.2 42 0.00091 18.4 0.6 12 69-80 32-43 (79)
76 PRK10333 5-formyltetrahydrofol 21.6 32 0.00069 21.6 0.1 7 74-80 129-135 (182)
77 smart00052 EAL Putative diguan 21.6 59 0.0013 20.3 1.3 27 1-27 206-232 (241)
78 TIGR02727 MTHFS_bact 5,10-meth 21.6 32 0.00069 21.4 0.1 7 74-80 135-141 (181)
79 PF09925 DUF2157: Predicted me 21.5 82 0.0018 18.9 1.9 21 2-23 5-25 (145)
80 PF13466 STAS_2: STAS domain 21.2 94 0.002 16.1 1.9 41 25-66 34-75 (80)
81 PRK06552 keto-hydroxyglutarate 21.1 1.9E+02 0.004 18.8 3.6 68 5-79 115-187 (213)
82 PF12623 Hen1_L: RNA repair, l 20.7 77 0.0017 21.3 1.7 17 7-23 198-214 (245)
83 cd03515 Link_domain_TSG_6_like 20.4 94 0.002 17.8 1.8 15 6-20 30-44 (93)
84 PF00193 Xlink: Extracellular 20.0 69 0.0015 18.0 1.2 14 7-20 31-44 (92)
No 1
>PF00725 3HCDH: 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; InterPro: IPR006108 3-hydroxyacyl-CoA dehydrogenase (1.1.1.35 from EC) (HCDH) [] is an enzyme involved in fatty acid metabolism, it catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA. Most eukaryotic cells have 2 fatty-acid beta-oxidation systems, one located in mitochondria and the other in peroxisomes. In peroxisomes 3-hydroxyacyl-CoA dehydrogenase forms, with enoyl-CoA hydratase (ECH) and 3,2-trans-enoyl-CoA isomerase (ECI) a multifunctional enzyme where the N-terminal domain bears the hydratase/isomerase activities and the C-terminal domain the dehydrogenase activity. There are two mitochondrial enzymes: one which is monofunctional and the other which is, like its peroxisomal counterpart, multifunctional. In Escherichia coli (gene fadB) and Pseudomonas fragi (gene faoA) HCDH is part of a multifunctional enzyme which also contains an ECH/ECI domain as well as a 3-hydroxybutyryl-CoA epimerase domain []. There are two major region of similarities in the sequences of proteins of the HCDH family, the first one located in the N-terminal, corresponds to the NAD-binding site, the second one is located in the centre of the sequence. This represents the C-terminal domain which is also found in lambda crystallin. Some proteins include two copies of this domain.; GO: 0003857 3-hydroxyacyl-CoA dehydrogenase activity, 0016491 oxidoreductase activity, 0006631 fatty acid metabolic process, 0055114 oxidation-reduction process; PDB: 3MOG_A 2WTB_A 3ADP_A 3ADO_A 1WDL_B 2D3T_B 1WDK_A 1WDM_B 3K6J_A 1ZCJ_A ....
Probab=99.97 E-value=2.7e-32 Score=156.84 Aligned_cols=80 Identities=50% Similarity=0.915 Sum_probs=73.2
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYN 80 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~ 80 (83)
|++||++||++||++++.++|||+|||+++|.+|++++.++.+.+.+.+++ +.++|++++++|+++|++|+|+|+|||+
T Consensus 18 l~~egvas~~~ID~~~~~~~G~p~Gpf~l~D~~Gl~~~~~~~~~~~~~~~~-~~~~~~~~l~~mv~~g~~G~k~g~Gfy~ 96 (97)
T PF00725_consen 18 LVEEGVASPEDIDRAMRYGLGFPMGPFELADLVGLDVVYHILEYLAAALGD-RAFRPSPLLKEMVEEGRLGRKSGKGFYD 96 (97)
T ss_dssp HHHTTSSSHHHHHHHHHHHHTHSSTHHHHHHHHHHHHHHHHHHHHHHHHCC-GGGSS-HHHHHHHHTT--BGGGTBSSSB
T ss_pred HHHHcCCCHHHHHHHHHHhCCCCCccchHHHHhCchHHHHHHHHHHHhcCC-CcCCchHHHHHHHHCCCCcCcCCCccee
Confidence 578999999999999999999999999999999999999999999999887 3578899999999999999999999999
Q ss_pred c
Q psy3941 81 Y 81 (83)
Q Consensus 81 y 81 (83)
|
T Consensus 97 Y 97 (97)
T PF00725_consen 97 Y 97 (97)
T ss_dssp E
T ss_pred C
Confidence 8
No 2
>KOG2304|consensus
Probab=99.96 E-value=4.7e-29 Score=161.59 Aligned_cols=82 Identities=76% Similarity=1.331 Sum_probs=78.7
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYN 80 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~ 80 (83)
|++.|.+|-+|||.||+.|.|+|||||++.|++|||++..+++-+.+.++++..|+|+|++.+++++|++|+|+|+|||+
T Consensus 217 ~yerGdAskeDIDtaMklGagyPMGPfEL~DyvGLDt~kfvmdgwhe~~pe~~~f~psPll~klVaegklGrKtg~GfY~ 296 (298)
T KOG2304|consen 217 MYERGDASKEDIDTAMKLGAGYPMGPFELADYVGLDTCKFVMDGWHEGYPEDSLFAPSPLLDKLVAEGKLGRKTGEGFYK 296 (298)
T ss_pred HHHhcCCcHhhHHHHHhccCCCCCChHHHHHHhhHHHHHHHHHHHHhcCCcccccCCChHHHHHHhccccccccCcccee
Confidence 57889999999999999999999999999999999999999999999998778899999999999999999999999999
Q ss_pred cC
Q psy3941 81 YK 82 (83)
Q Consensus 81 y~ 82 (83)
|.
T Consensus 297 Yk 298 (298)
T KOG2304|consen 297 YK 298 (298)
T ss_pred cC
Confidence 95
No 3
>COG1250 FadB 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]
Probab=99.95 E-value=3.3e-28 Score=163.55 Aligned_cols=83 Identities=46% Similarity=0.897 Sum_probs=77.7
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYN 80 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~ 80 (83)
|++||+++|++||.+++.++|||||||+++|.+|+|+++++++.+.+.+++.+.+.+++++++|++.|++|+|+|+|||+
T Consensus 203 l~~eGva~~e~ID~~~~~~~G~pmGpf~l~D~~GlD~~~~i~~~~~~~~~~~~~~~~~~~~~~~v~~g~lG~Ksg~GfY~ 282 (307)
T COG1250 203 LLEEGVATPEEIDAAMRQGLGLPMGPFELADLIGLDVMLHIMKVLNETLGDDPYYRPPPLLRKLVEAGRLGRKSGKGFYD 282 (307)
T ss_pred HHHhCCCCHHHHHHHHHhccCCCccHHHHHHHHhHHHHHHHHHHHHHhcCCCccccccHHHHHHHhcccccccCCCccee
Confidence 57899999999999999999999999999999999999999999998888546778899999999999999999999999
Q ss_pred cCC
Q psy3941 81 YKK 83 (83)
Q Consensus 81 y~~ 83 (83)
|++
T Consensus 283 y~~ 285 (307)
T COG1250 283 YRG 285 (307)
T ss_pred ccc
Confidence 973
No 4
>PRK09260 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=99.95 E-value=7e-28 Score=160.44 Aligned_cols=81 Identities=42% Similarity=0.770 Sum_probs=76.7
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYN 80 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~ 80 (83)
|++||+++|++||.+++.|+|||+|||+++|.+|++++.++.+.+.+.+++ +|.|++++.+|+++|++|+|+|+|||+
T Consensus 202 ~~~~gv~~~~~iD~~~~~g~g~p~Gp~~~~D~~Gl~~~~~~~~~l~~~~~~--~~~~~~~l~~~~~~g~~G~k~g~Gfy~ 279 (288)
T PRK09260 202 MLQEGVATAEDIDKAIRLGLNFPMGPLELGDLVGLDTRLNNLKYLHETLGE--KYRPAPLLEKYVKAGRLGRKTGRGVYD 279 (288)
T ss_pred HHHcCCCCHHHHHHHHHhCCCCCCCHHHHHHHhhHHHHHHHHHHHHHHhCC--CCCCCHHHHHHHHCCCCccccCCEEEE
Confidence 578999999999999999999999999999999999999999999988875 788999999999999999999999999
Q ss_pred cCC
Q psy3941 81 YKK 83 (83)
Q Consensus 81 y~~ 83 (83)
|++
T Consensus 280 y~~ 282 (288)
T PRK09260 280 YTN 282 (288)
T ss_pred CCC
Confidence 974
No 5
>PRK08293 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=99.95 E-value=7.6e-28 Score=160.28 Aligned_cols=81 Identities=41% Similarity=0.762 Sum_probs=75.3
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCC-CchHHHHHHHHCCCCCcccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLF-KPVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~-~~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
|++||++||++||++++.++|+|+|||+++|.+|+|++.++++++++.+++ +++ .+++++++|+++|++|+|+|+|||
T Consensus 206 l~~~g~a~~~~iD~a~~~~~g~~~Gp~~~~D~~Gld~~~~~~~~~~~~~~~-~~~~~~~~~l~~~v~~g~~G~k~g~Gfy 284 (287)
T PRK08293 206 LWAKGVADPETIDKTWMIATGAPMGPFGILDIVGLDTAYNITSNWAEATDD-ENAKKAAALLKEYIDKGKLGVATGEGFY 284 (287)
T ss_pred HHHcCCCCHHHHHHHHHhccCCCcCHHHHHHHhchHHHHHHHHHHHHHhCC-cccccchHHHHHHHHCCCCcccCCCccc
Confidence 578999999999999999999999999999999999999999999998876 343 378999999999999999999999
Q ss_pred ccC
Q psy3941 80 NYK 82 (83)
Q Consensus 80 ~y~ 82 (83)
+|+
T Consensus 285 ~y~ 287 (287)
T PRK08293 285 NYP 287 (287)
T ss_pred cCc
Confidence 995
No 6
>PRK07819 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=99.95 E-value=1.2e-27 Score=159.71 Aligned_cols=80 Identities=51% Similarity=0.839 Sum_probs=76.2
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYN 80 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~ 80 (83)
|++||++||+|||++++.++|||+|||+++|.+|++++.++.+.+++.+++ ++|.|++++++|+++|++|+|+|+|||+
T Consensus 207 ll~eGv~~~~dID~~~~~g~G~p~Gpf~~~D~~Gld~~~~~~~~l~~~~~~-~~~~p~~~l~~~v~~g~~G~k~g~GfY~ 285 (286)
T PRK07819 207 MVESGFATAEDIDKAMVLGCAHPMGPLRLSDLVGLDTVKAIADSMYEEFKE-PLYAPPPLLLRMVEAGLLGKKSGRGFYT 285 (286)
T ss_pred HHHhCCCCHHHHHHHHHhCCCCCCCHHHHHHHhccHHHHHHHHHHHHHcCC-CCCCCCHHHHHHHHCCCCcccCCCEecc
Confidence 589999999999999999999999999999999999999999999998875 5788999999999999999999999999
Q ss_pred c
Q psy3941 81 Y 81 (83)
Q Consensus 81 y 81 (83)
|
T Consensus 286 y 286 (286)
T PRK07819 286 Y 286 (286)
T ss_pred C
Confidence 8
No 7
>PRK06035 3-hydroxyacyl-CoA dehydrogenase; Validated
Probab=99.94 E-value=1.4e-27 Score=159.13 Aligned_cols=80 Identities=39% Similarity=0.681 Sum_probs=76.0
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccc-----c
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKS-----G 75 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~-----g 75 (83)
|++||++||+|||++++.++|+|+|||+++|.+|+|++.++++.+++.+++ +++.+++++++|+++|++|+|+ |
T Consensus 206 ~~~~g~a~~~~iD~~~~~~~g~~~Gp~~~~D~~Gl~~~~~~~~~l~~~~~~-~~~~~~~~l~~~v~~g~~G~k~~~~~~g 284 (291)
T PRK06035 206 SFEIGIATIKDIDEMCKLAFGFPMGPFELMDIIGIDTVYHIAEYLYEETGD-PQFIPPNSLKQMVLNGYVGDKKVKYGSK 284 (291)
T ss_pred HHHcCCCCHHHHHHHHhhcCCCccCHHHHHHHhhHHHHHHHHHHHHHHcCC-CcCCccHHHHHHHHCCCCcCCCCCCCCC
Confidence 578999999999999999999999999999999999999999999999875 5788999999999999999999 9
Q ss_pred cccccc
Q psy3941 76 EGFYNY 81 (83)
Q Consensus 76 ~GfY~y 81 (83)
+|||+|
T Consensus 285 ~Gfy~y 290 (291)
T PRK06035 285 GGWFDY 290 (291)
T ss_pred ceeeec
Confidence 999998
No 8
>PRK05808 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=99.94 E-value=1.8e-27 Score=157.98 Aligned_cols=80 Identities=41% Similarity=0.748 Sum_probs=76.1
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYN 80 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~ 80 (83)
|++||+++|+|||+++++|+|||+|||+++|.+|++++.++++.+++.+++ ++|.|++++++|+++|++|+|+|+|||+
T Consensus 203 ~~~~gv~~~~diD~~~~~g~g~p~Gp~~~~D~~Gl~~~~~~~~~l~~~~~~-~~~~~~~~l~~~~~~g~~G~k~g~Gfy~ 281 (282)
T PRK05808 203 VLAEGVATAEDIDEGMKLGCNHPIGPLALADLIGLDTCLAIMEVLYEGFGD-SKYRPCPLLRKMVAAGWLGRKTGRGFYD 281 (282)
T ss_pred HHHhCCCCHHHHHHHHHhCCCCCCCHHHHHHHhhhHHHHHHHHHHHHHcCC-CcCCCCHHHHHHHHCCCCccccCCcccC
Confidence 579999999999999999999999999999999999999999999999875 4788999999999999999999999999
Q ss_pred c
Q psy3941 81 Y 81 (83)
Q Consensus 81 y 81 (83)
|
T Consensus 282 y 282 (282)
T PRK05808 282 Y 282 (282)
T ss_pred C
Confidence 8
No 9
>PLN02545 3-hydroxybutyryl-CoA dehydrogenase
Probab=99.94 E-value=3.8e-27 Score=157.25 Aligned_cols=82 Identities=44% Similarity=0.735 Sum_probs=77.3
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYN 80 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~ 80 (83)
|++||++++++||+++++++|||+|||+++|.+|++++.++++.+++.+++ ++|.|++++.+|+++|++|+|+|+|||+
T Consensus 204 ~~~~gv~~~~~iD~~~~~g~g~~~Gp~~~~D~~Gl~~~~~~~~~l~~~~~~-~~~~~~~~l~~~~~~g~~G~k~g~Gfy~ 282 (295)
T PLN02545 204 ALYTGVASKEDIDTGMKLGTNHPMGPLHLADFIGLDTCLSIMKVLHEGLGD-SKYRPCPLLVQYVDAGRLGRKSGRGVYH 282 (295)
T ss_pred HHHcCCCCHHHHHHHHHhccCCCCCHHHHHHHhchHHHHHHHHHHHHHcCC-CcCCCCHHHHHHHHCCCCcccCCCeeeE
Confidence 578999999999999999999999999999999999999999999998875 4788999999999999999999999999
Q ss_pred cCC
Q psy3941 81 YKK 83 (83)
Q Consensus 81 y~~ 83 (83)
|+.
T Consensus 283 y~~ 285 (295)
T PLN02545 283 YDG 285 (295)
T ss_pred CCC
Confidence 964
No 10
>PRK07530 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=99.94 E-value=5.2e-27 Score=156.40 Aligned_cols=82 Identities=45% Similarity=0.751 Sum_probs=77.0
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYN 80 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~ 80 (83)
|++||+++|++||.++++++|||+|||+++|.+|++++.++.+++++.+++ ++|.|++++.+|+++|++|+|+|+|||+
T Consensus 204 ~~~~g~~~~~~iD~~~~~g~g~~~GP~~~~D~~Gl~~~~~~~~~~~~~~~~-~~~~p~~~l~~~v~~g~~G~k~g~Gfy~ 282 (292)
T PRK07530 204 TLYEGVGSVEAIDTAMKLGANHPMGPLELADFIGLDTCLSIMQVLHDGLAD-SKYRPCPLLVKYVEAGWLGRKTGRGFYD 282 (292)
T ss_pred HHHhCCCCHHHHHHHHHhCCCCCCCHHHHHHHhhhHHHHHHHHHHHHHcCC-CcCCCCHHHHHHHHCCCCccccCCEeee
Confidence 578999999999999999999999999999999999999999999998875 4788999999999999999999999999
Q ss_pred cCC
Q psy3941 81 YKK 83 (83)
Q Consensus 81 y~~ 83 (83)
|++
T Consensus 283 y~~ 285 (292)
T PRK07530 283 YRG 285 (292)
T ss_pred CCC
Confidence 953
No 11
>TIGR02279 PaaC-3OHAcCoADH 3-hydroxyacyl-CoA dehydrogenase PaaC. This 3-hydroxyacyl-CoA dehydrogenase is involved in the degradation of phenylacetic acid, presumably in steps following the opening of the phenyl ring. The sequences included in this model are all found in aparrent operons with other related genes such as paaA, paaB, paaD, paaE, paaF and paaN. Some genomes contain these other genes without an apparent paaC in the same operon - possibly in these cases a different dehydrogenase involved in fatty acid degradation may fill in the needed activity. This enzyme has domains which are members of the pfam02737 and pfam00725 families.
Probab=99.93 E-value=4.1e-26 Score=161.76 Aligned_cols=81 Identities=41% Similarity=0.702 Sum_probs=75.1
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhC-CCCCCCCchHHHHHHHHCCCCCcccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKF-PENPLFKPVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~-~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
|+++|+++|++||++++.++|||||||+++|.+|+|+++++.+.+.+.+ ++ ++|.|++++++|+++|++|+|||+|||
T Consensus 205 l~e~g~a~~~~ID~al~~~~G~~mGPf~l~D~~Gldv~~~v~~~~~~~~~~~-~~~~p~~~~~~~v~~G~lG~KtG~GfY 283 (503)
T TIGR02279 205 ALEEQVAAPAVLDAALRDGAGFPMGPFELTDLIGHDVNFAVTCSVFNAFWQD-RRFLPSLVQQELVIAGRLGRKSGLGVY 283 (503)
T ss_pred HHHcCCCCHHHHHHHHHhcCCCCcCHHHHHHHhhhHHHHHHHHHHHHHhcCC-CCCCCcHHHHHHHHCCCCccccCCEee
Confidence 5789999999999999999999999999999999999999999988764 43 578889999999999999999999999
Q ss_pred ccC
Q psy3941 80 NYK 82 (83)
Q Consensus 80 ~y~ 82 (83)
+|+
T Consensus 284 ~y~ 286 (503)
T TIGR02279 284 DYR 286 (503)
T ss_pred eCC
Confidence 996
No 12
>TIGR02437 FadB fatty oxidation complex, alpha subunit FadB. Members represent alpha subunit of multifunctional enzyme complex of the fatty acid degradation cycle. Activities include: enoyl-CoA hydratase (EC 4.2.1.17), dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8), 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35), 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A representative is E. coli FadB. This model excludes the FadJ family represented by SP:P77399.
Probab=99.91 E-value=9.8e-25 Score=159.62 Aligned_cols=81 Identities=36% Similarity=0.558 Sum_probs=73.1
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYN 80 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~ 80 (83)
|++|| ++|++||++++.++|||+|||+++|.+|||++.++.+.+.+.+++.....+++++++|+++|++|+|+|+|||+
T Consensus 513 l~~eG-~~~~~ID~a~~~~~G~p~GPf~l~D~~Gld~~~~i~~~~~~~~~~~~~~~~~~~l~~~v~~G~lG~K~g~GfY~ 591 (714)
T TIGR02437 513 LLRDG-ADFVRIDKVMEKQFGWPMGPAYLLDVVGIDTGHHAQAVMAEGFPDRMGKDGRDAIDALFEAKRLGQKNGKGFYA 591 (714)
T ss_pred HHHCC-CCHHHHHHHHHhcCCCccCHHHHHHhhhHHHHHHHHHHHHHhcCcccccchhHHHHHHHHCCCCcccCCCEEEe
Confidence 57899 89999999999999999999999999999999999999998887522234578999999999999999999999
Q ss_pred cC
Q psy3941 81 YK 82 (83)
Q Consensus 81 y~ 82 (83)
|+
T Consensus 592 y~ 593 (714)
T TIGR02437 592 YE 593 (714)
T ss_pred cc
Confidence 95
No 13
>PRK11730 fadB multifunctional fatty acid oxidation complex subunit alpha; Reviewed
Probab=99.91 E-value=1e-24 Score=159.52 Aligned_cols=81 Identities=36% Similarity=0.590 Sum_probs=73.8
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYN 80 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~ 80 (83)
|++|| ++|++||++++.++|||+|||+++|.+|+|++.++.+.+...+++.....+++++++|+++|++|+|+|+|||+
T Consensus 513 lv~~G-a~~e~ID~a~~~~~G~~~GP~~~~D~~Gld~~~~~~~~~~~~~~~~~~~~~~~~l~~~v~~G~~G~k~g~GfY~ 591 (715)
T PRK11730 513 LLRDG-ADFRQIDKVMEKQFGWPMGPAYLLDVVGIDTAHHAQAVMAEGFPDRMKKDYRDAIDVLFEAKRFGQKNGKGFYR 591 (715)
T ss_pred HHHcC-CCHHHHHHHHHhhCCCccCHHHHHHhhchHHHHHHHHHHHHhcCCccccchhHHHHHHHHCCCCccccCCEeEe
Confidence 57899 99999999999999999999999999999999999999998887632234679999999999999999999999
Q ss_pred cC
Q psy3941 81 YK 82 (83)
Q Consensus 81 y~ 82 (83)
|+
T Consensus 592 y~ 593 (715)
T PRK11730 592 YE 593 (715)
T ss_pred cc
Confidence 95
No 14
>TIGR02440 FadJ fatty oxidation complex, alpha subunit FadJ. Members represent alpha subunit of multifunctional enzyme complex of the fatty acid degradation cycle. Plays a minor role in aerobic beta-oxidation of fatty acids. FadJI complex is necessary for anaerobic growth on short-chain acids with nitrate as an electron acceptor. Activities include: enoyl-CoA hydratase (EC 4.2.1.17),3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35), 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A representative is E. coli FadJ (aka YfcX). This model excludes the FadB of TIGR02437 equivalog.
Probab=99.91 E-value=1.5e-24 Score=158.40 Aligned_cols=78 Identities=33% Similarity=0.569 Sum_probs=73.6
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYN 80 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~ 80 (83)
|++||+ +|++||++++ ++|||+|||+++|.+|+|++.++.+.+.+.+++ ++.+++++++|+++|++|+|||+|||+
T Consensus 505 l~~~G~-~~~dID~a~~-~~G~p~GPf~l~D~vGld~~~~i~~~l~~~~~~--~~~~~~~l~~~v~~G~lG~ksg~GfY~ 580 (699)
T TIGR02440 505 LLLEGE-PVEHIDKALV-KFGFPVGPITLLDEVGIDVGAKISPILEAELGE--RFKAPAVFDKLLSDDRKGRKNGKGFYL 580 (699)
T ss_pred HHHCCC-CHHHHHHHHH-HcCCCcCHHHHHHHhchHHHHHHHHHHHHhcCC--CCCCcHHHHHHHHCCCCcccCCcEEEe
Confidence 578995 9999999998 899999999999999999999999999999886 788889999999999999999999999
Q ss_pred cC
Q psy3941 81 YK 82 (83)
Q Consensus 81 y~ 82 (83)
|+
T Consensus 581 y~ 582 (699)
T TIGR02440 581 YG 582 (699)
T ss_pred CC
Confidence 96
No 15
>PRK08269 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=99.91 E-value=2.3e-24 Score=145.64 Aligned_cols=81 Identities=32% Similarity=0.569 Sum_probs=75.7
Q ss_pred CcccCCCCHHHHHHHHHhccCCC---cchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCcccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYP---MGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEG 77 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p---~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~G 77 (83)
|+++|+++|++||.+++.++||| +|||+++|.+|++++.++.+.+.+.+++ ++|.|++++++|+++|++|+|+|+|
T Consensus 200 l~e~g~~~~e~iD~a~~~g~G~~~~~~Gpf~~~D~~Gld~~~~~~~~l~~~~~~-~~~~p~~~l~~~v~~g~~G~ksG~G 278 (314)
T PRK08269 200 MVEEGVASAEDIDKAIRTGFGLRFAVLGLLEFIDWGGCDILYYASRYLAGEIGP-DRFAPPAIVVRNMEEGRDGLRTGAG 278 (314)
T ss_pred HHHhCCCCHHHHHHHHHhCCCCCccCcCHHHHHHhhhHHHHHHHHHHHHHHhCC-CCCCCCHHHHHHHHCCCCcccCCCc
Confidence 46889899999999999999999 5999999999999999999999988875 4788999999999999999999999
Q ss_pred ccccC
Q psy3941 78 FYNYK 82 (83)
Q Consensus 78 fY~y~ 82 (83)
||+|+
T Consensus 279 fY~y~ 283 (314)
T PRK08269 279 FYDYA 283 (314)
T ss_pred ceeCC
Confidence 99995
No 16
>TIGR02441 fa_ox_alpha_mit fatty acid oxidation complex, alpha subunit, mitochondrial. Members represent alpha subunit of mitochondrial multifunctional fatty acid degradation enzyme complex. Subunit activities include: enoyl-CoA hydratase (EC 4.2.1.17) & 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35). Some characterization in human, pig, and rat. The beta subunit has activity: acetyl-CoA C-acyltransferase (EC 2.3.1.16).
Probab=99.90 E-value=3.2e-24 Score=157.33 Aligned_cols=78 Identities=35% Similarity=0.639 Sum_probs=71.9
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCC--CchHHHHHHHHCCCCCccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLF--KPVDALNKLVDEGKLGVKSGEGF 78 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~--~~~~~l~~~~~~g~~G~k~g~Gf 78 (83)
|++||+ +|++||++++ ++|||+|||+++|.+|+|++.++.+.+.+.+++ ++ .+++++.+|+++|++|+|+|+||
T Consensus 535 lv~eGv-~~~~ID~a~~-~~G~p~GP~~l~D~vGld~~~~v~~~l~~~~~~--~~~~~~~~~l~~~v~~G~~G~k~G~Gf 610 (737)
T TIGR02441 535 LLQEGV-DPKKLDKLTT-KFGFPVGAATLADEVGVDVAEHVAEDLGKAFGE--RFGGGSAELLSELVKAGFLGRKSGKGI 610 (737)
T ss_pred HHHcCC-CHHHHHHHHH-HcCCCCCHHHHHHHhhHHHHHHHHHHHHHhcCc--ccccccCHHHHHHHHCCCCcccCCCee
Confidence 588996 9999999985 899999999999999999999999999988875 55 36899999999999999999999
Q ss_pred cccC
Q psy3941 79 YNYK 82 (83)
Q Consensus 79 Y~y~ 82 (83)
|+|+
T Consensus 611 Y~y~ 614 (737)
T TIGR02441 611 FIYQ 614 (737)
T ss_pred EEcC
Confidence 9996
No 17
>PRK11154 fadJ multifunctional fatty acid oxidation complex subunit alpha; Reviewed
Probab=99.90 E-value=4.3e-24 Score=156.17 Aligned_cols=78 Identities=35% Similarity=0.588 Sum_probs=73.4
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYN 80 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~ 80 (83)
|++||+ +|++||.+++ ++|||+|||+++|.+|+|++.++.+.+.+.+++ +|.+++++++|+++|++|+|+|+|||+
T Consensus 510 lv~eGv-~~~dID~a~~-~~G~p~GPf~~~D~~Gld~~~~i~~~l~~~~~~--~~~~~~~l~~~v~~g~~G~k~g~GfY~ 585 (708)
T PRK11154 510 LLLEGE-PIEHIDAALV-KFGFPVGPITLLDEVGIDVGTKIIPILEAALGE--RFSAPAAFDKLLNDDRKGRKNGRGFYL 585 (708)
T ss_pred HHHcCC-CHHHHHHHHH-HcCCCCCHHHHHHHhhhHHHHHHHHHHHHHcCC--CCCCCHHHHHHHHCCCCcccCCceEEE
Confidence 578996 9999999999 899999999999999999999999999998874 788889999999999999999999999
Q ss_pred cC
Q psy3941 81 YK 82 (83)
Q Consensus 81 y~ 82 (83)
|+
T Consensus 586 y~ 587 (708)
T PRK11154 586 YG 587 (708)
T ss_pred CC
Confidence 97
No 18
>PRK08268 3-hydroxy-acyl-CoA dehydrogenase; Validated
Probab=99.90 E-value=6.8e-24 Score=150.58 Aligned_cols=82 Identities=40% Similarity=0.781 Sum_probs=74.4
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYN 80 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~ 80 (83)
|+++|+++|++||.+++.++|||||||+++|.+|+|+..++.+.+.+.+...++|.+++++++|++.|++|+|+|+|||+
T Consensus 207 l~~~g~~~~~~iD~al~~~~G~~mGPf~l~D~~Gldv~~~v~~~~~~~~~~~~~~~~~~~~~~lv~~g~lG~ksG~GfY~ 286 (507)
T PRK08268 207 VLEEGVADPATIDAILREAAGFRMGPFELMDLIGLDVNHAVMESVYRQFYQEPRFRPSLIQQELVAAGRLGRKSGQGFYR 286 (507)
T ss_pred HHHcCCCCHHHHHHHHHhcCCCCcCHHHHHHHhchHHHHHHHHHHHHHhcCCCcCCccHHHHHHHHCCCCccccCCeeeE
Confidence 57899899999999999999999999999999999999999998887642225788899999999999999999999999
Q ss_pred cC
Q psy3941 81 YK 82 (83)
Q Consensus 81 y~ 82 (83)
|+
T Consensus 287 y~ 288 (507)
T PRK08268 287 YA 288 (507)
T ss_pred CC
Confidence 95
No 19
>PRK06130 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=99.88 E-value=8.3e-23 Score=137.02 Aligned_cols=81 Identities=33% Similarity=0.539 Sum_probs=75.3
Q ss_pred CcccCCCCHHHHHHHHHhccCCC---cchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCcccccc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYP---MGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEG 77 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p---~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~G 77 (83)
|+++|+++|++||.+++.++||| +|||+++|.+|++++.++.+.+++.+++ ++.+++++++|+++|++|+|+|+|
T Consensus 201 l~~~g~~~~~~id~~~~~~~g~~~~~~Gp~~~~D~~Gl~~~~~~~~~l~~~~~~--~~~~~~~l~~~~~~g~~G~~~g~g 278 (311)
T PRK06130 201 LLEKGVASAEDIDEVVKWSLGIRLALTGPLEQRDMNGLDVHLAVASYLYQDLEN--RTTPSPLLEEKVEAGELGAKSGQG 278 (311)
T ss_pred HHHcCCCCHHHHHHHHHhcCCCCccCCCHHHHhhhhccchHHHHHHHHHHhcCC--cCCCCHHHHHHHHcCCccccCCCc
Confidence 46888899999999999999999 6999999999999999999999988864 788899999999999999999999
Q ss_pred ccccCC
Q psy3941 78 FYNYKK 83 (83)
Q Consensus 78 fY~y~~ 83 (83)
||+|++
T Consensus 279 fy~y~~ 284 (311)
T PRK06130 279 FYAWPP 284 (311)
T ss_pred CccCCC
Confidence 999973
No 20
>PRK08268 3-hydroxy-acyl-CoA dehydrogenase; Validated
Probab=99.78 E-value=5.7e-19 Score=125.56 Aligned_cols=68 Identities=31% Similarity=0.601 Sum_probs=64.1
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCC
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGK 69 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~ 69 (83)
|++|||+||+|||++|+.|+|||+|||+++|.+|++++.++++++++.+++ ++|+|++++++|+++|+
T Consensus 433 ll~eGvas~~dID~a~~~g~G~p~GP~~~~D~~Gld~~~~~~~~l~~~~g~-~~~~p~~ll~~~v~~G~ 500 (507)
T PRK08268 433 IAQQGIASPADIDLAMRLGLNYPLGPLAWGDRLGAARILRVLENLQALYGD-PRYRPSPWLRRRAALGL 500 (507)
T ss_pred HHHcCCCCHHHHHHHHHhcCCCCcCHHHHHHHhCHHHHHHHHHHHHHHhCC-CcCCcCHHHHHHHHcCC
Confidence 589999999999999999999999999999999999999999999999885 58899999999999886
No 21
>TIGR02279 PaaC-3OHAcCoADH 3-hydroxyacyl-CoA dehydrogenase PaaC. This 3-hydroxyacyl-CoA dehydrogenase is involved in the degradation of phenylacetic acid, presumably in steps following the opening of the phenyl ring. The sequences included in this model are all found in aparrent operons with other related genes such as paaA, paaB, paaD, paaE, paaF and paaN. Some genomes contain these other genes without an apparent paaC in the same operon - possibly in these cases a different dehydrogenase involved in fatty acid degradation may fill in the needed activity. This enzyme has domains which are members of the pfam02737 and pfam00725 families.
Probab=99.76 E-value=1.6e-18 Score=123.21 Aligned_cols=68 Identities=31% Similarity=0.542 Sum_probs=63.8
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCC
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGK 69 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~ 69 (83)
|++||+++|+|||++|++|+|||+|||+++|.+|+|++.++++++++.+++ ++|+|++++++++..|.
T Consensus 432 ll~eGvas~~dID~a~~~g~G~P~GP~~~~D~~Gld~~~~~l~~l~~~~~~-~~~~p~~~L~~~v~~g~ 499 (503)
T TIGR02279 432 AVLQGVASAQDIDTAMRLGVNYPYGPLAWAAQLGWQRILRVLENLQHHYGE-ERYRPSSLLRRRALLGS 499 (503)
T ss_pred HHHcCCCCHHHHHHHHHhCCCCCcCHHHHHHHhCHHHHHHHHHHHHHHcCC-CcCCcCHHHHHHHHcCC
Confidence 589999999999999999999999999999999999999999999999985 57899999999998875
No 22
>TIGR02440 FadJ fatty oxidation complex, alpha subunit FadJ. Members represent alpha subunit of multifunctional enzyme complex of the fatty acid degradation cycle. Plays a minor role in aerobic beta-oxidation of fatty acids. FadJI complex is necessary for anaerobic growth on short-chain acids with nitrate as an electron acceptor. Activities include: enoyl-CoA hydratase (EC 4.2.1.17),3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35), 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A representative is E. coli FadJ (aka YfcX). This model excludes the FadB of TIGR02437 equivalog.
Probab=99.67 E-value=1.4e-16 Score=116.82 Aligned_cols=67 Identities=30% Similarity=0.575 Sum_probs=62.6
Q ss_pred CcccCC-CCHHHHHHHHHhccCCCc---chhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCC
Q psy3941 1 MYERGD-ASPRDIDTAMKLGAGYPM---GPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGK 69 (83)
Q Consensus 1 ll~egv-~~~~~ID~a~~~g~G~p~---GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~ 69 (83)
||+||| ++|+|||+++++|+|||+ |||+++|.+|++++.++++.+++.+++ +|.|++++.+|+++|.
T Consensus 626 ll~eGvva~~~dID~~~~~g~G~p~~~~Gpf~~~D~~Gld~~~~~~~~l~~~~g~--~~~p~~~L~~~~~~~~ 696 (699)
T TIGR02440 626 CLDEGVIRSPRDGDIGAIFGIGFPPFLGGPFRYIDTLGADNVVKILERLQTQYGD--RFTPCQRLVAMAAEKQ 696 (699)
T ss_pred HHHCCCcCCHHHHHHHHHhcCCCCCCcCCHHHHHHHhCHHHHHHHHHHHHHHcCC--CcCCCHHHHHHHHcCC
Confidence 589998 799999999999999996 999999999999999999999998875 8899999999999875
No 23
>PRK11154 fadJ multifunctional fatty acid oxidation complex subunit alpha; Reviewed
Probab=99.66 E-value=2.1e-16 Score=115.99 Aligned_cols=67 Identities=27% Similarity=0.556 Sum_probs=62.9
Q ss_pred CcccCC-CCHHHHHHHHHhccCCCc---chhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCC
Q psy3941 1 MYERGD-ASPRDIDTAMKLGAGYPM---GPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGK 69 (83)
Q Consensus 1 ll~egv-~~~~~ID~a~~~g~G~p~---GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~ 69 (83)
||+||| ++|+|||.++++|+|||+ |||+++|.+|++++.++++.+++.+++ +|.|++++.+|+++|+
T Consensus 633 ll~eGvva~~~dID~~~~~G~G~p~~~gGp~~~~D~~Gld~~~~~~~~l~~~~~~--~~~p~~~l~~~~~~~~ 703 (708)
T PRK11154 633 CLDEGIIRSARDGDIGAVFGIGFPPFLGGPFRYMDSLGAGEVVAILERLAAQYGD--RFTPCERLVEMAERGE 703 (708)
T ss_pred HHHCCCcCCHHHHHHHHHhcCCCCCccCCHHHHHHHhCHHHHHHHHHHHHHhcCC--ccCCCHHHHHHHHcCC
Confidence 589998 799999999999999997 999999999999999999999999875 7899999999999886
No 24
>TIGR02441 fa_ox_alpha_mit fatty acid oxidation complex, alpha subunit, mitochondrial. Members represent alpha subunit of mitochondrial multifunctional fatty acid degradation enzyme complex. Subunit activities include: enoyl-CoA hydratase (EC 4.2.1.17) & 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35). Some characterization in human, pig, and rat. The beta subunit has activity: acetyl-CoA C-acyltransferase (EC 2.3.1.16).
Probab=99.65 E-value=3.2e-16 Score=115.46 Aligned_cols=67 Identities=30% Similarity=0.509 Sum_probs=62.5
Q ss_pred CcccCC-CCHHHHHHHHHhccCCCc---chhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHC-CC
Q psy3941 1 MYERGD-ASPRDIDTAMKLGAGYPM---GPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDE-GK 69 (83)
Q Consensus 1 ll~egv-~~~~~ID~a~~~g~G~p~---GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~-g~ 69 (83)
||+||| ++|+|||.++++|+|||+ |||+++|.+|+++++++++.+++.+++ +|.|++++.+|+++ |+
T Consensus 663 lLeEGV~a~~~DID~a~~~G~GfP~~~gGP~~~aD~~Gld~v~~~~~~l~~~~g~--~~~p~~lL~~~~~~~g~ 734 (737)
T TIGR02441 663 CLEEGILASPSEGDIGAVFGLGFPPFLGGPFRFVDLYGADKLVDKMEKYAAAYGV--QFTPCQLLLDHAKSPGK 734 (737)
T ss_pred HhhcCccCCHHHHHHHHHhCCCCCCccCCHHHHHHHhCHHHHHHHHHHHHHHhCC--CcCCCHHHHHHHHhcCC
Confidence 589999 699999999999999996 999999999999999999999998885 89999999999987 75
No 25
>PRK11730 fadB multifunctional fatty acid oxidation complex subunit alpha; Reviewed
Probab=99.61 E-value=1.8e-15 Score=111.22 Aligned_cols=66 Identities=27% Similarity=0.517 Sum_probs=59.2
Q ss_pred CcccCC-CCHHHHHHHHHhccCCCc---chhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCC
Q psy3941 1 MYERGD-ASPRDIDTAMKLGAGYPM---GPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGK 69 (83)
Q Consensus 1 ll~egv-~~~~~ID~a~~~g~G~p~---GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~ 69 (83)
||+||+ ++|+|||.++++|+|||+ |||+++|.+|+++++++++.+. .+++ +|.|++++++|+++|+
T Consensus 642 ll~eGvva~~~dID~a~~~g~G~p~~~gGPf~~~D~~Gld~~~~~~~~~~-~~~~--~~~p~~~L~~~v~~~~ 711 (715)
T PRK11730 642 CLEEGIVASPAEADMALVYGLGFPPFRGGAFRYLDTLGVANYVALADKYA-HLGP--LYQVPEGLREMAANGE 711 (715)
T ss_pred HHhcCCcCCHHHHHHHHHhCCCCCCCcCCHHHHHHHhCHHHHHHHHHHHH-HcCC--CCCCCHHHHHHHHcCC
Confidence 589997 799999999999999997 9999999999999999999765 4653 7899999999998875
No 26
>TIGR02437 FadB fatty oxidation complex, alpha subunit FadB. Members represent alpha subunit of multifunctional enzyme complex of the fatty acid degradation cycle. Activities include: enoyl-CoA hydratase (EC 4.2.1.17), dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8), 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35), 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A representative is E. coli FadB. This model excludes the FadJ family represented by SP:P77399.
Probab=99.58 E-value=4.6e-15 Score=109.13 Aligned_cols=66 Identities=23% Similarity=0.478 Sum_probs=59.3
Q ss_pred CcccC-CCCHHHHHHHHHhccCCCc---chhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCC
Q psy3941 1 MYERG-DASPRDIDTAMKLGAGYPM---GPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGK 69 (83)
Q Consensus 1 ll~eg-v~~~~~ID~a~~~g~G~p~---GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~ 69 (83)
||+|| +++|+|||.++++|+|||+ |||+++|.+|++++.++++.+. .+++ +|.|++++.+|+++|+
T Consensus 642 ll~eGiva~~~dID~~~~~G~Gfp~~~gGP~~~~D~~Gl~~~~~~~~~~~-~~g~--~~~p~~~l~~~~~~g~ 711 (714)
T TIGR02437 642 CLEEGIVATAAEADMGLVYGLGFPPFRGGAFRYLDSIGVANFVALADQYA-ELGA--LYQVTAKLREMAKNGQ 711 (714)
T ss_pred HHhCCCcCCHHHHHHHHHhCCCCCCccCCHHHHHHHhCHHHHHHHHHHHH-HhCC--CCCCCHHHHHHHHcCC
Confidence 58999 5699999999999999997 9999999999999999999654 6764 7899999999998875
No 27
>PRK07066 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=99.56 E-value=1.3e-15 Score=103.54 Aligned_cols=82 Identities=22% Similarity=0.400 Sum_probs=64.3
Q ss_pred CcccCCCCHHHHHHHHHhccCCC---cchhhhhhhhcHHH-HHHHHHHHHHhCCCC-CCCCchHHHHHHHH------CCC
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYP---MGPFELADYVGHDT-TKFIIDGWHKKFPEN-PLFKPVDALNKLVD------EGK 69 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p---~GPf~~~D~vGld~-~~~~~~~l~~~~~~~-~~~~~~~~l~~~~~------~g~ 69 (83)
|++||++|++|||++++.|+|+| +|||+++|.+|+|. +.+..+++.+.+.+. ..+..+++..++++ ++.
T Consensus 205 lv~eGvas~edID~a~~~g~g~r~~~~Gpf~~~Dl~Gld~g~~~~~~~~g~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~ 284 (321)
T PRK07066 205 LVNEGVATTGEIDDAIRFGAGIRWSFMGTFLTYTLAGGDAGMRHFMQQFGPALELPWTKLVAPELTDALIDRVVEGTAEQ 284 (321)
T ss_pred HHHhCCCCHHHHHHHHHhCCCCCccCcCHHHHhhhcChHHHHHHHHHHhhhhhhHHHHhcCCCcccHHHHHHHHHHHHHH
Confidence 58999999999999999999998 89999999999998 667777776554321 01344555555555 588
Q ss_pred CCccccccccccC
Q psy3941 70 LGVKSGEGFYNYK 82 (83)
Q Consensus 70 ~G~k~g~GfY~y~ 82 (83)
+|.++..++++|.
T Consensus 285 ~~~~~~~~~~~~r 297 (321)
T PRK07066 285 QGPRSIKALERYR 297 (321)
T ss_pred cCCCCHHHHHHHH
Confidence 9999999999874
No 28
>KOG1683|consensus
Probab=99.44 E-value=5.5e-14 Score=96.21 Aligned_cols=69 Identities=30% Similarity=0.555 Sum_probs=60.4
Q ss_pred CCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccccccccCC
Q psy3941 7 ASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGEGFYNYKK 83 (83)
Q Consensus 7 ~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~GfY~y~~ 83 (83)
++|.+||.... -||||+||+++.|.+|+|+..++...+...+++ + +.++++++++.|+||++|||.|++
T Consensus 196 ~~p~~iD~~~t-~fGf~~g~~~L~d~~gfdv~eal~~gl~~~~~~--r-----~~eel~~~~~~g~kT~kg~y~y~~ 264 (380)
T KOG1683|consen 196 ADPWLIDSLIT-KFGFRVGERALADGVGFDVAEALAVGLGDEIGP--R-----IEEELLEKGRAGIKTGKGIYPYAR 264 (380)
T ss_pred CCHHHHHHHHH-hcCccccHHHHhhccCccHHHHHhhccchhccc--h-----hHHHHHHHHhhhhhccCccccccc
Confidence 89999999998 599999999999999999999888776555442 2 688899999999999999999974
No 29
>KOG1683|consensus
Probab=98.91 E-value=2.5e-10 Score=78.49 Aligned_cols=62 Identities=32% Similarity=0.567 Sum_probs=55.3
Q ss_pred CcccCCC-CHHHHHHHHHhccCCCc---chhhhhhhhcHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHCCC
Q psy3941 1 MYERGDA-SPRDIDTAMKLGAGYPM---GPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGK 69 (83)
Q Consensus 1 ll~egv~-~~~~ID~a~~~g~G~p~---GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~ 69 (83)
+++||+. +|.++|.+.+.|+|||. |||.+.|.+|++.++..++.++ .|+|+.++.++..+++
T Consensus 311 ~l~EGi~~~~~~~Di~~v~G~gfp~~~GGp~~~~d~~G~~ki~~~l~~~~-------~f~P~~~l~~~a~~~~ 376 (380)
T KOG1683|consen 311 CLLEGLKASPSDGDIASVFGLGFPPFRGGPMRFVDLYGADKIVSRLQKWS-------SFEPCQLLKDHAKSGK 376 (380)
T ss_pred HHHHHHhcCccccceeeeeccCCCCcCCCceeeeeccChHHHHHHHHHHh-------cCCHHHHHHHHHhhhc
Confidence 3689994 99999999999999996 9999999999999999998864 3889999999988753
No 30
>PRK06129 3-hydroxyacyl-CoA dehydrogenase; Validated
Probab=98.90 E-value=4.1e-09 Score=71.06 Aligned_cols=65 Identities=29% Similarity=0.347 Sum_probs=56.1
Q ss_pred CcccCCCCHHHHHHHHHhccCCC---cchhhhhhhh---cHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHH
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYP---MGPFELADYV---GHDTTKFIIDGWHKKFPENPLFKPVDALNKLVD 66 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p---~GPf~~~D~v---Gld~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~ 66 (83)
|+++|++|+++||.+++.++|++ +|||.++|.. |++........++....+ +.+.++++++++++
T Consensus 204 l~~~g~~~~~~id~~~~~~~g~~~~~~gp~~~~d~~~~~g~~~~~~k~~~l~~~~~~-~~~~~~~~~~~~~~ 274 (308)
T PRK06129 204 LVADGVASVDDIDAVIRDGLGLRWSFMGPFETIDLNAPGGVADYAQRYGPMYRRMAA-ERGQPVPWDGELVA 274 (308)
T ss_pred HHHcCCCCHHHHHHHHHhccCCCccCcCHHHHHhccccccHHHHHHHHHHHHHhhcc-ccCCCchhhHHHHH
Confidence 46889999999999999999998 8999999987 899999988888888765 35667788888776
No 31
>PRK07531 bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase; Validated
Probab=98.31 E-value=5.9e-07 Score=64.27 Aligned_cols=49 Identities=20% Similarity=0.370 Sum_probs=40.7
Q ss_pred CcccCCCCHHHHHHHHHhccCCC---cchhhhhhhhcH-HHHHHHHHHHHHhC
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYP---MGPFELADYVGH-DTTKFIIDGWHKKF 49 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p---~GPf~~~D~vGl-d~~~~~~~~l~~~~ 49 (83)
|+++|++|+++||.+++.++|++ +|||+.+|.+|+ +.+.+.++++.+.+
T Consensus 202 L~~~g~~s~~~id~~~~~g~g~~~~~~Gpf~~~dl~g~~~g~~~~~~~~~~~~ 254 (495)
T PRK07531 202 LVKDGIATTEEIDDVIRYSFGLRWAQMGLFETYRIAGGEAGMRHFLAQFGPCL 254 (495)
T ss_pred HHHcCCCCHHHHHHHHhhccCCCccccchHHHHHhcCcHHHHHHHHHHhchhh
Confidence 46789999999999999998875 799999999984 45777777776554
No 32
>KOG2305|consensus
Probab=92.24 E-value=0.58 Score=31.53 Aligned_cols=32 Identities=31% Similarity=0.532 Sum_probs=27.4
Q ss_pred CcccCCCCHHHHHHHHHhccCCC---cchhhhhhh
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYP---MGPFELADY 32 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p---~GPf~~~D~ 32 (83)
|+..|+.+..|+|+.|-.|+|.+ .||++.+..
T Consensus 206 LvasGil~v~dvD~VmS~GLG~RYAflG~lET~HL 240 (313)
T KOG2305|consen 206 LVASGILNVNDVDAVMSAGLGPRYAFLGPLETAHL 240 (313)
T ss_pred HHHccCcchhhHHHHHhcCCCcchhcccchhhhhc
Confidence 46789889999999999999987 399997654
No 33
>PF02762 Cbl_N3: CBL proto-oncogene N-terminus, SH2-like domain; InterPro: IPR014742 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the SH2-like domain.; PDB: 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B ....
Probab=61.19 E-value=2.1 Score=23.84 Aligned_cols=19 Identities=37% Similarity=0.761 Sum_probs=12.6
Q ss_pred HHHHHHHHCCCCCccccccccccCC
Q psy3941 59 DALNKLVDEGKLGVKSGEGFYNYKK 83 (83)
Q Consensus 59 ~~l~~~~~~g~~G~k~g~GfY~y~~ 83 (83)
++.+.+++-.+ +|||.|++
T Consensus 60 ~L~qaLidG~r------eG~ylyP~ 78 (86)
T PF02762_consen 60 SLYQALIDGSR------EGFYLYPD 78 (86)
T ss_dssp -HHHHHHHHHH------TTSS-EET
T ss_pred hHHHHHHhccc------cceEECCC
Confidence 67777887554 69999875
No 34
>PF02493 MORN: MORN repeat; InterPro: IPR003409 The MORN (Membrane Occupation and Recognition Nexus) motif is found in multiple copies in several proteins including junctophilins (). The function of this motif is unknown.; PDB: 1H3I_B 1MT6_A 1N6C_A 3OS5_A 3M53_A 3M55_A 3CBP_A 4E47_B 3M58_A 3CBO_A ....
Probab=52.51 E-value=5.4 Score=16.13 Aligned_cols=13 Identities=38% Similarity=0.815 Sum_probs=9.2
Q ss_pred CccccccccccCC
Q psy3941 71 GVKSGEGFYNYKK 83 (83)
Q Consensus 71 G~k~g~GfY~y~~ 83 (83)
|.+.|.|-|.|++
T Consensus 8 g~~~G~G~~~~~~ 20 (23)
T PF02493_consen 8 GKKHGYGVYTFPD 20 (23)
T ss_dssp TEEECEEEEE-TT
T ss_pred CcccccEEEEeCC
Confidence 6778888888764
No 35
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=50.50 E-value=12 Score=18.18 Aligned_cols=24 Identities=29% Similarity=0.516 Sum_probs=17.2
Q ss_pred CchHHHHHHHHCCCCCcccccccc
Q psy3941 56 KPVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 56 ~~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
+....++.|.+.|..-...|+|++
T Consensus 36 tv~~~l~~L~~~g~i~~~~~~g~~ 59 (60)
T smart00345 36 TVREALSRLEAEGLVQRRPGSGTF 59 (60)
T ss_pred HHHHHHHHHHHCCCEEEecCCeeE
Confidence 455667778888887777777765
No 36
>PF05157 T2SE_Nter: Type II secretion system (T2SS), protein E, N-terminal domain; InterPro: IPR007831 This domain is found at the N terminus of members of the general secretory system II protein E. Proteins in this subfamily are typically involved in Type IV pilus biogenesis (e.g. Q9X4G8 from SWISSPROT), though some are involved in other processes; for instance aggregation in Myxococcus xanthus (e.g. Q9RF11 from SWISSPROT) [].; GO: 0005524 ATP binding, 0006810 transport; PDB: 2D27_A 2D28_C.
Probab=48.94 E-value=12 Score=20.71 Aligned_cols=24 Identities=25% Similarity=0.300 Sum_probs=16.9
Q ss_pred CcccCCCCHHHHHHHHHhccCCCc
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPM 24 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~ 24 (83)
|+++|.+|.+++-.++-.-+|.|.
T Consensus 1 Lv~~g~ise~~l~~~la~~~~l~~ 24 (109)
T PF05157_consen 1 LVELGLISEDQLLEALAEQLGLPF 24 (109)
T ss_dssp -HHTT-S-HHHHHHHHHHHHT--B
T ss_pred CccCCCCCHHHHHHHHHHHhCCCe
Confidence 688999999999999988899984
No 37
>TIGR01323 nitrile_alph nitrile hydratase, alpha subunit. This model describes both iron- and cobalt-containing nitrile hydratase alpha chains. It excludes the thiocyanate hydrolase gamma subunit of Thiobacillus thioparus, a sequence that appears to have evolved from within the family of nitrile hydratase alpha subunits but which differs by several indels and a more rapid accumulation of point mutations.
Probab=43.09 E-value=14 Score=23.69 Aligned_cols=27 Identities=19% Similarity=0.241 Sum_probs=20.4
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhh
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFE 28 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~ 28 (83)
|.+.|++++++||+.+.. +--.+||.-
T Consensus 10 l~eKGli~~~~id~~i~~-~~~~~gP~n 36 (185)
T TIGR01323 10 LKSKGLIPEGAVDQLTSL-YENEWGPEN 36 (185)
T ss_pred HHHcCCCCHHHHHHHHHH-HHhccCCcc
Confidence 457888899999998874 666667753
No 38
>PF14419 SPOUT_MTase_2: AF2226-like SPOUT RNA Methylase fused to THUMP
Probab=42.16 E-value=13 Score=23.60 Aligned_cols=14 Identities=57% Similarity=1.042 Sum_probs=12.1
Q ss_pred cCCCcchhhhhhhh
Q psy3941 20 AGYPMGPFELADYV 33 (83)
Q Consensus 20 ~G~p~GPf~~~D~v 33 (83)
-|.|+|.|.++|++
T Consensus 131 eGiP~GlfRfAd~V 144 (173)
T PF14419_consen 131 EGIPRGLFRFADYV 144 (173)
T ss_pred cCCChhHHHHhhhh
Confidence 37899999999986
No 39
>PHA02930 hypothetical protein; Provisional
Probab=40.39 E-value=12 Score=20.06 Aligned_cols=9 Identities=67% Similarity=1.398 Sum_probs=7.1
Q ss_pred cccccccCC
Q psy3941 75 GEGFYNYKK 83 (83)
Q Consensus 75 g~GfY~y~~ 83 (83)
|+|+|+|.+
T Consensus 29 geg~~dykn 37 (81)
T PHA02930 29 GEGCYDYKN 37 (81)
T ss_pred Ccccccccc
Confidence 469999964
No 40
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=40.03 E-value=17 Score=23.55 Aligned_cols=26 Identities=27% Similarity=0.355 Sum_probs=19.8
Q ss_pred CCCchHHHHHHHHCCCCCcccccccc
Q psy3941 54 LFKPVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 54 ~~~~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
+.++...+..|+++|..=++.|+|-|
T Consensus 47 R~TvR~Al~~L~~eGli~r~~G~GTf 72 (241)
T PRK11402 47 RITIRKAISDLVADGVLIRWQGKGTF 72 (241)
T ss_pred HHHHHHHHHHHHHCCCEEEecCceeE
Confidence 34455667788888988888888866
No 41
>PF13300 DUF4078: Domain of unknown function (DUF4078)
Probab=37.29 E-value=14 Score=20.85 Aligned_cols=10 Identities=50% Similarity=1.132 Sum_probs=7.2
Q ss_pred ccccccccCC
Q psy3941 74 SGEGFYNYKK 83 (83)
Q Consensus 74 ~g~GfY~y~~ 83 (83)
-|-|||.+++
T Consensus 31 ~Gvgfy~FS~ 40 (88)
T PF13300_consen 31 HGVGFYAFSK 40 (88)
T ss_pred HcceeeecCC
Confidence 3459999874
No 42
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=36.39 E-value=33 Score=17.83 Aligned_cols=48 Identities=21% Similarity=0.209 Sum_probs=28.5
Q ss_pred chhhhhhhhcHHHHHHHHHHHHHhCCCCCCC---CchHHHHHHHHCCCCCcc
Q psy3941 25 GPFELADYVGHDTTKFIIDGWHKKFPENPLF---KPVDALNKLVDEGKLGVK 73 (83)
Q Consensus 25 GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~---~~~~~l~~~~~~g~~G~k 73 (83)
|.++-.+..-++.++..++-+...-+. ..+ +...+|.+++++|++=..
T Consensus 4 gMLtN~gsl~l~RIh~mLkmf~~~~~~-~~~s~~eL~~fL~~lv~e~~L~~~ 54 (60)
T PF08672_consen 4 GMLTNLGSLPLDRIHSMLKMFPKDPGG-YDISLEELQEFLDRLVEEGKLECS 54 (60)
T ss_dssp HHHHHH-SEEHHHHHHHHHHH-GGG---TT--HHHHHHHHHHHHHTTSEE--
T ss_pred HHhhcCCCCCHHHHHHHHHhccCCCCC-CCCCHHHHHHHHHHHHHCCcEEec
Confidence 556667778889999999877222111 122 234668889998886554
No 43
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=36.37 E-value=30 Score=17.07 Aligned_cols=24 Identities=29% Similarity=0.493 Sum_probs=16.2
Q ss_pred CchHHHHHHHHCCCCCcccccccc
Q psy3941 56 KPVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 56 ~~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
+....+.+|.+.|..-...++|++
T Consensus 41 ~v~~~l~~L~~~G~i~~~~~~~~~ 64 (66)
T cd07377 41 TVREALRELEAEGLVERRPGRGTF 64 (66)
T ss_pred HHHHHHHHHHHCCCEEecCCCeEE
Confidence 345667778888876666666654
No 44
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=36.22 E-value=21 Score=22.92 Aligned_cols=26 Identities=27% Similarity=0.247 Sum_probs=18.9
Q ss_pred CCCchHHHHHHHHCCCCCcccccccc
Q psy3941 54 LFKPVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 54 ~~~~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
+.++...+..|+++|..=++.|+|-|
T Consensus 38 R~TVR~Al~~L~~eGli~r~~G~GTf 63 (233)
T TIGR02404 38 RETVRKALNLLTEAGYIQKIQGKGSI 63 (233)
T ss_pred HHHHHHHHHHHHHCCCEEEeCCceEE
Confidence 44556667778888888888888765
No 45
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=35.54 E-value=47 Score=16.26 Aligned_cols=20 Identities=30% Similarity=0.607 Sum_probs=13.1
Q ss_pred CHHHHHHHHHhccCCCcchhh
Q psy3941 8 SPRDIDTAMKLGAGYPMGPFE 28 (83)
Q Consensus 8 ~~~~ID~a~~~g~G~p~GPf~ 28 (83)
|-+++=.-++ .+|+|.||..
T Consensus 7 Sd~eL~~~L~-~~G~~~gPIt 26 (44)
T smart00540 7 SDAELRAELK-QYGLPPGPIT 26 (44)
T ss_pred CHHHHHHHHH-HcCCCCCCcC
Confidence 3445555555 4899999975
No 46
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=35.30 E-value=18 Score=18.47 Aligned_cols=16 Identities=19% Similarity=0.397 Sum_probs=11.3
Q ss_pred cccCCCCHHHHHHHHH
Q psy3941 2 YERGDASPRDIDTAMK 17 (83)
Q Consensus 2 l~egv~~~~~ID~a~~ 17 (83)
+++|..|.+++|..+.
T Consensus 33 ~~~g~lt~ee~d~ll~ 48 (55)
T PF10415_consen 33 LEEGLLTEEELDELLD 48 (55)
T ss_dssp HHTTSS-HHHHHHHTS
T ss_pred HHcCCCCHHHHHHHcC
Confidence 4677778999998753
No 47
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=35.14 E-value=22 Score=23.00 Aligned_cols=26 Identities=23% Similarity=0.381 Sum_probs=19.7
Q ss_pred CCCchHHHHHHHHCCCCCcccccccc
Q psy3941 54 LFKPVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 54 ~~~~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
+.++...+..|+++|..=++.|+|.|
T Consensus 49 R~TVR~Al~~L~~eGli~r~~G~Gtf 74 (241)
T PRK10079 49 RHTLRRAIDQLVEKGWVQRRQGVGVL 74 (241)
T ss_pred HHHHHHHHHHHHHCCCEEEecCCEEE
Confidence 34456677888888888888888866
No 48
>KOG1785|consensus
Probab=34.18 E-value=31 Score=25.17 Aligned_cols=19 Identities=37% Similarity=0.695 Sum_probs=14.2
Q ss_pred HHHHHHHHCCCCCccccccccccCC
Q psy3941 59 DALNKLVDEGKLGVKSGEGFYNYKK 83 (83)
Q Consensus 59 ~~l~~~~~~g~~G~k~g~GfY~y~~ 83 (83)
++.+.+++--+ +|||-|++
T Consensus 314 pL~QaL~eG~k------eGFYlyPd 332 (563)
T KOG1785|consen 314 PLFQALLEGHK------EGFYLYPD 332 (563)
T ss_pred HHHHHHHhccc------cceEECCC
Confidence 67777777554 79999975
No 49
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effect
Probab=33.95 E-value=26 Score=19.58 Aligned_cols=18 Identities=11% Similarity=0.084 Sum_probs=14.9
Q ss_pred CcccCCCCHHHHHHHHHh
Q psy3941 1 MYERGDASPRDIDTAMKL 18 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~ 18 (83)
|+++||.|.+++|.....
T Consensus 23 L~~~gvlt~~~~e~I~~~ 40 (86)
T cd08323 23 MISDGVLTLDEEEKVKSK 40 (86)
T ss_pred HHhcCCCCHHHHHHHHcC
Confidence 578999999999987764
No 50
>PRK14999 histidine utilization repressor; Provisional
Probab=33.68 E-value=23 Score=22.90 Aligned_cols=25 Identities=36% Similarity=0.413 Sum_probs=18.5
Q ss_pred CCchHHHHHHHHCCCCCcccccccc
Q psy3941 55 FKPVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 55 ~~~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
.++...+..|+++|..=++.|+|-|
T Consensus 51 ~TVR~Al~~L~~eGli~r~~GkGTf 75 (241)
T PRK14999 51 MTINRALRELTDEGWLVRLQGVGTF 75 (241)
T ss_pred HHHHHHHHHHHHCCCEEEecCcEEE
Confidence 3455667778888888888888866
No 51
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=33.64 E-value=25 Score=22.52 Aligned_cols=25 Identities=28% Similarity=0.486 Sum_probs=18.8
Q ss_pred CCchHHHHHHHHCCCCCcccccccc
Q psy3941 55 FKPVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 55 ~~~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
.++...+..|+++|..=++.|+|.|
T Consensus 47 ~TvR~Al~~L~~eGli~r~~G~Gtf 71 (238)
T TIGR02325 47 HTVRRAIAALVERGLLRAEQGRGTF 71 (238)
T ss_pred HHHHHHHHHHHHCCCEEEecCCEEE
Confidence 3455667778888888888888876
No 52
>PF09003 Phage_integ_N: Bacteriophage lambda integrase, N-terminal domain ; InterPro: IPR015094 The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage []. ; GO: 0003677 DNA binding, 0008907 integrase activity, 0015074 DNA integration; PDB: 1Z1G_B 1Z1B_A 2WCC_3 1KJK_A.
Probab=33.35 E-value=13 Score=20.40 Aligned_cols=12 Identities=33% Similarity=1.124 Sum_probs=5.3
Q ss_pred CccccccccccC
Q psy3941 71 GVKSGEGFYNYK 82 (83)
Q Consensus 71 G~k~g~GfY~y~ 82 (83)
..++|+|||.|.
T Consensus 21 dkr~~k~Yy~Yr 32 (75)
T PF09003_consen 21 DKRNGKGYYQYR 32 (75)
T ss_dssp T-----SEEEEE
T ss_pred CcCcceeEEEEe
Confidence 345678999883
No 53
>PF02979 NHase_alpha: Nitrile hydratase, alpha chain; InterPro: IPR004232 Nitrile hydratases (4.2.1.84 from EC) are bacterial enzymes that catalyse the hydration of nitrile compounds to the corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and are normally active as a tetramer, alpha(2)beta(2). Nitrile hydratases contain either a non-haem iron or a non-corrinoid cobalt centre, both types sharing a highly conserved peptide sequence in the alpha subunit (CXLCSC) that provides all the residues involved in coordinating the metal ion. Each type of nitrile hydratase specifically incorporated its metal with the help of activator proteins encoded by flanking regions of the nitrile hydratase genes that are necessary for metal insertion. The Fe-containing enzyme is photo-regulated: in the dark the enzyme is inactivated due to the association of nitric oxide (NO) to the iron, while in the light the enzyme is active by photo-dissociation of NO. The NO is held in place by a claw setting formed through specific oxygen atoms in two modified cysteines and a serine residue in the active site [, ]. The cobalt-containing enzyme is unaffected by NO, but was shown to undergo a similar effect with carbon monoxide [, ]. Fe- and cobalt-containing enzymes also display different inhibition patterns with nitrophenols. Thiocyanate hydrolase (SCNase) is a cobalt-containing metalloenzyme with a cysteine-sulphinic acid ligand that hydrolyses thiocyanate to carbonyl sulphide and ammonia []. The two enzymes, nitrile hydratase and SCNase, are homologous over regions corresponding to almost the entire coding regions of the genes: the beta and alpha subunits of thiocyanate hydrolase were homologous to the amino- and carboxyl-terminal halves of the beta subunit of nitrile hydratase, and the gamma subunit of thiocyanate hydrolase was homologous to the alpha subunit of nitrile hydratase []. This entry represents the structural domain of the alpha subunit of both iron- and cobalt-containing nitrile hydratases; the alpha subunit is a duplication of two structural repeats, each consisting of 4 layers, alpha/beta/beta/alpha []. This structure is also found in the related protein, the gamma subunit of thiocyanate hydrolase (SCNase).; GO: 0003824 catalytic activity, 0046914 transition metal ion binding, 0006807 nitrogen compound metabolic process; PDB: 2DPP_A 3HHT_A 1V29_A 2ZZD_I 2DXC_F 2DXB_F 2DD5_C 2DD4_C 2ZPH_A 2CYZ_A ....
Probab=33.22 E-value=19 Score=23.23 Aligned_cols=29 Identities=24% Similarity=0.418 Sum_probs=20.4
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchhhhh
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPFELA 30 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf~~~ 30 (83)
|++.|++++++||+.+.. +--.+||..-+
T Consensus 16 l~ekg~~~~~~~~~~~~~-~~~~~~P~~Ga 44 (188)
T PF02979_consen 16 LIEKGLITPAEVDRIIET-YESRVGPRNGA 44 (188)
T ss_dssp HHHTTSS-HHHHHHHHHH-HHHTSSHHHHH
T ss_pred HHHcCCCCHHHHHHHHHH-HHhccCccccc
Confidence 467899999999998875 55556776433
No 54
>PF15606 Toxin_55: Putative toxin 55
Probab=33.09 E-value=90 Score=17.18 Aligned_cols=34 Identities=24% Similarity=0.223 Sum_probs=21.2
Q ss_pred HHHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCcc
Q psy3941 38 TKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVK 73 (83)
Q Consensus 38 ~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k 73 (83)
+..++......-+. .-..+++|++|++.|..+.+
T Consensus 24 v~~~~~~~~~~~GK--~~drCd~Lqelid~g~~~~k 57 (77)
T PF15606_consen 24 VYEIISDAFQSGGK--APDRCDVLQELIDCGDISAK 57 (77)
T ss_pred HHHHHHHHHhhcCC--CCcHHHHHHHHHHccCcCHH
Confidence 33444433333333 23568999999999887765
No 55
>PF13319 DUF4090: Protein of unknown function (DUF4090)
Probab=33.09 E-value=92 Score=17.31 Aligned_cols=70 Identities=23% Similarity=0.367 Sum_probs=36.4
Q ss_pred HHHHHHHHHhccCC---Cc--chhhhhhhh-cHHHH------HHHHHHHHHhCCCCCCCCchHHHHHHHHCCCCCccccc
Q psy3941 9 PRDIDTAMKLGAGY---PM--GPFELADYV-GHDTT------KFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGE 76 (83)
Q Consensus 9 ~~~ID~a~~~g~G~---p~--GPf~~~D~v-Gld~~------~~~~~~l~~~~~~~~~~~~~~~l~~~~~~g~~G~k~g~ 76 (83)
|+.||.|+..|.-+ |. --+.+...| ++..- .+.+++-.-..+. .-+.-..+=+.+++.|+-|-|..+
T Consensus 2 ~daiD~AI~~GiDlDGspIP~~~L~LY~~VM~lE~~RqRSGV~~sMR~RiVr~Ga-KH~~q~~Lnq~L~~Ag~~~LK~KE 80 (84)
T PF13319_consen 2 ADAIDAAIAAGIDLDGSPIPPAMLELYNEVMDLEAQRQRSGVSNSMRSRIVRIGA-KHFDQEELNQRLIDAGWEGLKDKE 80 (84)
T ss_pred ccHHHHHHHhCcCCCCCcCCHHHHHHHHHHHHHHhcchhhhhHHHHHHHHHHhcc-ccCCHHHHHHHHHHcCccccchhh
Confidence 56799999988865 33 333333322 33221 1222222222221 123344556667888998888765
Q ss_pred -ccc
Q psy3941 77 -GFY 79 (83)
Q Consensus 77 -GfY 79 (83)
-||
T Consensus 81 IaFf 84 (84)
T PF13319_consen 81 IAFF 84 (84)
T ss_pred hccC
Confidence 444
No 56
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=31.29 E-value=28 Score=22.32 Aligned_cols=26 Identities=31% Similarity=0.445 Sum_probs=19.2
Q ss_pred CCCchHHHHHHHHCCCCCcccccccc
Q psy3941 54 LFKPVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 54 ~~~~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
+.++...+..|+++|..=++.|+|-|
T Consensus 39 R~TVR~Al~~L~~eGli~r~~G~Gtf 64 (230)
T TIGR02018 39 RMTVNRALRELTDAGLLERRQGVGTF 64 (230)
T ss_pred HHHHHHHHHHHHHCCCEEEecCCEEE
Confidence 44566677778888888888888755
No 57
>PF01881 Cas_Cas6: CRISPR associated protein Cas6; InterPro: IPR002743 This entry is represented by Bacteriophage c-st, ORF: CST018. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 3PKM_A 3I4H_X 3QJJ_B 3QJP_A 3QJL_B 3UFC_X.
Probab=30.89 E-value=40 Score=20.35 Aligned_cols=21 Identities=43% Similarity=0.651 Sum_probs=12.2
Q ss_pred chHHHHHHHHCCCCCccccccc
Q psy3941 57 PVDALNKLVDEGKLGVKSGEGF 78 (83)
Q Consensus 57 ~~~~l~~~~~~g~~G~k~g~Gf 78 (83)
++.+++-+.+.| +|.|+++||
T Consensus 129 ~~ell~~~y~~G-lG~kns~GF 149 (155)
T PF01881_consen 129 DPELLNFAYDAG-LGEKNSQGF 149 (155)
T ss_dssp -HHHHHHHHHH--SSS-GGGT-
T ss_pred CHHHHHHHHHcC-CCCCCCccc
Confidence 356666566666 699999887
No 58
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=30.62 E-value=30 Score=22.43 Aligned_cols=26 Identities=31% Similarity=0.402 Sum_probs=18.7
Q ss_pred CCCchHHHHHHHHCCCCCcccccccc
Q psy3941 54 LFKPVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 54 ~~~~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
+.++...+..|+++|..=++.|+|-|
T Consensus 43 R~TvR~Al~~L~~eGli~r~~G~Gtf 68 (240)
T PRK09764 43 RVTVRQALRQLVEQQILESIQGSGTY 68 (240)
T ss_pred HHHHHHHHHHHHHCCCEEEecCceeE
Confidence 34455667778888888888888765
No 59
>smart00698 MORN Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases.
Probab=28.65 E-value=21 Score=15.16 Aligned_cols=12 Identities=42% Similarity=1.021 Sum_probs=9.0
Q ss_pred CccccccccccC
Q psy3941 71 GVKSGEGFYNYK 82 (83)
Q Consensus 71 G~k~g~GfY~y~ 82 (83)
|.+.|+|-|.|+
T Consensus 10 g~~hG~G~~~~~ 21 (26)
T smart00698 10 GKRHGRGVYTYA 21 (26)
T ss_pred CeEEeeEEEEec
Confidence 677888887775
No 60
>PF12367 PFO_beta_C: Pyruvate ferredoxin oxidoreductase beta subunit C terminal
Probab=27.89 E-value=35 Score=18.22 Aligned_cols=28 Identities=25% Similarity=0.462 Sum_probs=19.3
Q ss_pred ccCCCCHHHHHHHHHhcc---CCCcchhhhhh
Q psy3941 3 ERGDASPRDIDTAMKLGA---GYPMGPFELAD 31 (83)
Q Consensus 3 ~egv~~~~~ID~a~~~g~---G~p~GPf~~~D 31 (83)
+|+ .+|.+.+.|+.... .+|.|.|..-+
T Consensus 21 ~e~-~Dp~d~~~A~~~a~e~d~iplGIfY~~~ 51 (67)
T PF12367_consen 21 DED-HDPSDREAAMEKAREGDKIPLGIFYRNE 51 (67)
T ss_pred CCC-CCchhHHHHHHHHHhcCCceEEEEEeCC
Confidence 444 68888888887654 46778776554
No 61
>PF07882 Fucose_iso_N2: L-fucose isomerase, second N-terminal domain; InterPro: IPR012889 Proteins containing this domain are similar to L-fucose isomerase expressed by Escherichia coli (P11552 from SWISSPROT, 5.3.1.3 from EC). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis, and converts an aldo-hexose to a ketose to prepare it for aldol cleavage. The enzyme is a hexamer, with each subunit being wedge-shaped and composed of three domains. Both domains 1 and 2 contain central parallel beta- sheets with surrounding alpha helices. The active centre is shared between pairs of subunits related along the molecular three-fold axis, with domains 2 and 3 from one subunit providing most of the substrate-contacting residues []. ; GO: 0008736 L-fucose isomerase activity, 0006004 fucose metabolic process, 0005737 cytoplasm; PDB: 3A9R_A 3A9T_C 3A9S_C 1FUI_E.
Probab=27.06 E-value=47 Score=21.36 Aligned_cols=17 Identities=18% Similarity=0.304 Sum_probs=12.5
Q ss_pred cccCCCCHHHHHHHHHh
Q psy3941 2 YERGDASPRDIDTAMKL 18 (83)
Q Consensus 2 l~egv~~~~~ID~a~~~ 18 (83)
++++|++++++++|+.|
T Consensus 43 ~e~~iyD~~E~e~A~~W 59 (181)
T PF07882_consen 43 MEEGIYDEEEFEKALAW 59 (181)
T ss_dssp HHCT-S-HHHHHHHHHH
T ss_pred HHccCCCHHHHHHHHHH
Confidence 36788999999999975
No 62
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=27.00 E-value=35 Score=22.24 Aligned_cols=26 Identities=31% Similarity=0.538 Sum_probs=20.0
Q ss_pred CCCchHHHHHHHHCCCCCcccccccc
Q psy3941 54 LFKPVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 54 ~~~~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
+.++...|..|++.|..=++.|+|-|
T Consensus 45 R~TvRkAL~~L~~eGli~r~~G~Gtf 70 (236)
T COG2188 45 RMTVRKALDELVEEGLIVRRQGKGTF 70 (236)
T ss_pred HHHHHHHHHHHHHCCcEEEEecCeeE
Confidence 44566778888888888888888866
No 63
>PRK11234 nfrB bacteriophage N4 adsorption protein B; Provisional
Probab=26.93 E-value=31 Score=26.64 Aligned_cols=22 Identities=18% Similarity=0.309 Sum_probs=17.9
Q ss_pred CcccCCCCHHHHHHHHHhccCC
Q psy3941 1 MYERGDASPRDIDTAMKLGAGY 22 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~ 22 (83)
|++.|++|.++||.|+....+.
T Consensus 686 Lv~~g~it~~~l~~aL~~Q~~~ 707 (727)
T PRK11234 686 LVTEGVISQETLDRALTIQREL 707 (727)
T ss_pred HHHcCCCCHHHHHHHHHHHHhh
Confidence 5788989999999999875554
No 64
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=26.91 E-value=25 Score=17.95 Aligned_cols=23 Identities=30% Similarity=0.549 Sum_probs=16.8
Q ss_pred chHHHHHHHHCCCCCcccccccc
Q psy3941 57 PVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 57 ~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
....+..|.+.|..=...++|++
T Consensus 41 vr~al~~L~~~g~i~~~~~~G~~ 63 (64)
T PF00392_consen 41 VREALRRLEAEGLIERRPGRGTF 63 (64)
T ss_dssp HHHHHHHHHHTTSEEEETTTEEE
T ss_pred HHHHHHHHHHCCcEEEECCceEE
Confidence 44567777888887777777775
No 65
>PF05813 Orthopox_F7: Orthopoxvirus F7 protein; InterPro: IPR008725 The function of the orthopoxvirus F7L proteins are unknown.
Probab=26.56 E-value=28 Score=18.72 Aligned_cols=9 Identities=67% Similarity=1.398 Sum_probs=6.9
Q ss_pred cccccccCC
Q psy3941 75 GEGFYNYKK 83 (83)
Q Consensus 75 g~GfY~y~~ 83 (83)
|+|+|+|.+
T Consensus 30 ~eg~~~ykn 38 (82)
T PF05813_consen 30 GEGCYDYKN 38 (82)
T ss_pred ccccccccc
Confidence 369999964
No 66
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=25.68 E-value=30 Score=17.54 Aligned_cols=6 Identities=17% Similarity=0.960 Sum_probs=4.8
Q ss_pred cccccC
Q psy3941 77 GFYNYK 82 (83)
Q Consensus 77 GfY~y~ 82 (83)
|||+||
T Consensus 16 GYfd~P 21 (53)
T PF04967_consen 16 GYFDVP 21 (53)
T ss_pred CCCCCC
Confidence 788886
No 67
>PF01081 Aldolase: KDPG and KHG aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related []. They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VCR_A 1FQ0_A 1EUN_A 1EUA_B 1FWR_A 2C0A_B 1WBH_A 1WAU_A 2YW3_B 2YW4_A ....
Probab=25.30 E-value=55 Score=21.10 Aligned_cols=22 Identities=36% Similarity=0.739 Sum_probs=16.5
Q ss_pred CCCCHHHHHHHHHhccC----CCcch
Q psy3941 5 GDASPRDIDTAMKLGAG----YPMGP 26 (83)
Q Consensus 5 gv~~~~~ID~a~~~g~G----~p~GP 26 (83)
|+.||.||-.|+..|+- ||.+.
T Consensus 107 G~~TptEi~~A~~~G~~~vK~FPA~~ 132 (196)
T PF01081_consen 107 GVMTPTEIMQALEAGADIVKLFPAGA 132 (196)
T ss_dssp EESSHHHHHHHHHTT-SEEEETTTTT
T ss_pred CcCCHHHHHHHHHCCCCEEEEecchh
Confidence 66799999999997765 67543
No 68
>PF09722 DUF2384: Protein of unknown function (DUF2384); InterPro: IPR024467 This domain is found predominantly in proteobacterial proteins. Its function in unknown.
Probab=24.96 E-value=98 Score=15.14 Aligned_cols=33 Identities=24% Similarity=0.242 Sum_probs=22.7
Q ss_pred HHHHHHhccCCCc------chhhhhh-hhcHHHHHHHHHHH
Q psy3941 12 IDTAMKLGAGYPM------GPFELAD-YVGHDTTKFIIDGW 45 (83)
Q Consensus 12 ID~a~~~g~G~p~------GPf~~~D-~vGld~~~~~~~~l 45 (83)
-|.|.+| +.-|. =|+++++ ..|...+...+..+
T Consensus 11 ~~~a~~W-l~~p~~~l~g~~Plel~~t~~G~~~V~~~L~~~ 50 (54)
T PF09722_consen 11 EDKARRW-LRTPNPALGGRTPLELLRTEAGAERVLDYLDRI 50 (54)
T ss_pred HHHHHHH-HHChHHHhCCCCHHHHHcChHHHHHHHHHHHHH
Confidence 3556665 55552 5999888 77888887777654
No 69
>PF12637 TSCPD: TSCPD domain; InterPro: IPR024434 The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD, after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulphur cluster. This domain is found at the C terminus of some ribonucleoside-diphosphate reductase enzymes.
Probab=23.25 E-value=1.3e+02 Score=16.85 Aligned_cols=23 Identities=17% Similarity=0.297 Sum_probs=11.9
Q ss_pred ccCCCCHHHHHHHHHhccCCCcchh
Q psy3941 3 ERGDASPRDIDTAMKLGAGYPMGPF 27 (83)
Q Consensus 3 ~egv~~~~~ID~a~~~g~G~p~GPf 27 (83)
+.| +++++|=..++ +..++....
T Consensus 52 r~G-~~~~~ii~~L~-gi~~~~~~~ 74 (95)
T PF12637_consen 52 RSG-VPPEEIIDQLR-GIRCGPSGT 74 (95)
T ss_pred HcC-CCHHHHHHHhc-CCCCCCCCc
Confidence 445 45666555555 455554333
No 70
>KOG4742|consensus
Probab=23.22 E-value=78 Score=21.84 Aligned_cols=25 Identities=20% Similarity=0.464 Sum_probs=19.1
Q ss_pred hHHHHHHHHCCCCCccccccccccC
Q psy3941 58 VDALNKLVDEGKLGVKSGEGFYNYK 82 (83)
Q Consensus 58 ~~~l~~~~~~g~~G~k~g~GfY~y~ 82 (83)
+.+.+.++.+-..|.-.++|||+|+
T Consensus 68 ~~~F~~i~~~~~~g~c~~~gfyty~ 92 (286)
T KOG4742|consen 68 PELFEDIFSKVGSGWCPAKGFYTYD 92 (286)
T ss_pred HHHHHHHhccccCCCCCCCCCcccc
Confidence 4566777777666778889999986
No 71
>smart00445 LINK Link (Hyaluronan-binding).
Probab=23.07 E-value=69 Score=18.32 Aligned_cols=15 Identities=20% Similarity=0.042 Sum_probs=11.8
Q ss_pred CCCHHHHHHHHHhcc
Q psy3941 6 DASPRDIDTAMKLGA 20 (83)
Q Consensus 6 v~~~~~ID~a~~~g~ 20 (83)
++|++++..|++.|+
T Consensus 31 lAs~~QL~~Aw~~Gl 45 (94)
T smart00445 31 LATVGQLYAAWQDGF 45 (94)
T ss_pred eCCHHHHHHHHHhch
Confidence 369999999998643
No 72
>PF12525 DUF3726: Protein of unknown function (DUF3726) ; InterPro: IPR022201 This domain family is found in bacteria and eukaryotes, and is approximately 80 amino acids in length. There is a single completely conserved residue E that may be functionally important.
Probab=22.71 E-value=1.1e+02 Score=16.88 Aligned_cols=34 Identities=21% Similarity=0.321 Sum_probs=23.6
Q ss_pred HHHHhccCCCcc-------hhhhhhhhcHHHHHHHHHHHHHh
Q psy3941 14 TAMKLGAGYPMG-------PFELADYVGHDTTKFIIDGWHKK 48 (83)
Q Consensus 14 ~a~~~g~G~p~G-------Pf~~~D~vGld~~~~~~~~l~~~ 48 (83)
+|++ |.|++.| -..++...|++.+.+....+...
T Consensus 13 kA~~-Gag~~~G~Ae~aa~~v~wL~~~Gl~G~~~L~~~L~~~ 53 (80)
T PF12525_consen 13 KAFR-GAGLSWGEAEEAANMVAWLEMHGLDGVRHLNNALEFL 53 (80)
T ss_pred HHHH-hcCCCcchHHHHHHHHHHHHHcCCchHHHHHHHHHHh
Confidence 4555 7889865 45567778888888777766443
No 73
>PF13121 DUF3976: Domain of unknown function (DUF3976)
Probab=22.46 E-value=25 Score=16.65 Aligned_cols=10 Identities=30% Similarity=0.710 Sum_probs=6.8
Q ss_pred Cccccccccc
Q psy3941 71 GVKSGEGFYN 80 (83)
Q Consensus 71 G~k~g~GfY~ 80 (83)
+.-+.+|||+
T Consensus 13 ntltkrgfyk 22 (41)
T PF13121_consen 13 NTLTKRGFYK 22 (41)
T ss_pred CeeehhhHHH
Confidence 3446679996
No 74
>PRK13677 hypothetical protein; Provisional
Probab=22.24 E-value=57 Score=19.62 Aligned_cols=13 Identities=38% Similarity=0.547 Sum_probs=9.5
Q ss_pred ccCCCCHHHHHHH
Q psy3941 3 ERGDASPRDIDTA 15 (83)
Q Consensus 3 ~egv~~~~~ID~a 15 (83)
.-||.+|++||+=
T Consensus 7 slGI~~p~~Iery 19 (125)
T PRK13677 7 SLGITNPEDIDRY 19 (125)
T ss_pred hcCCCCHHHHhhh
Confidence 3477788888874
No 75
>cd00279 YlxR Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation
Probab=22.22 E-value=42 Score=18.39 Aligned_cols=12 Identities=33% Similarity=0.506 Sum_probs=9.4
Q ss_pred CCCccccccccc
Q psy3941 69 KLGVKSGEGFYN 80 (83)
Q Consensus 69 ~~G~k~g~GfY~ 80 (83)
..|...|+|+|-
T Consensus 32 ~~~k~~GRGaYv 43 (79)
T cd00279 32 PTGKLPGRGAYV 43 (79)
T ss_pred CCCCCCCCeEEE
Confidence 357788999995
No 76
>PRK10333 5-formyltetrahydrofolate cyclo-ligase family protein; Provisional
Probab=21.63 E-value=32 Score=21.60 Aligned_cols=7 Identities=57% Similarity=1.331 Sum_probs=5.3
Q ss_pred ccccccc
Q psy3941 74 SGEGFYN 80 (83)
Q Consensus 74 ~g~GfY~ 80 (83)
-|+|||+
T Consensus 129 ~GgGyYD 135 (182)
T PRK10333 129 MGGGFYD 135 (182)
T ss_pred CCcchHH
Confidence 4678997
No 77
>smart00052 EAL Putative diguanylate phosphodiesterase. Putative diguanylate phosphodiesterase, present in a variety of bacteria.
Probab=21.63 E-value=59 Score=20.33 Aligned_cols=27 Identities=26% Similarity=0.498 Sum_probs=19.7
Q ss_pred CcccCCCCHHHHHHHHHhccCCCcchh
Q psy3941 1 MYERGDASPRDIDTAMKLGAGYPMGPF 27 (83)
Q Consensus 1 ll~egv~~~~~ID~a~~~g~G~p~GPf 27 (83)
++.+||-++++.+.+...|+-+-.|.|
T Consensus 206 via~gVe~~~~~~~l~~~Gi~~~QG~~ 232 (241)
T smart00052 206 VVAEGVETPEQLDLLRSLGCDYGQGYL 232 (241)
T ss_pred EEEecCCCHHHHHHHHHcCCCEEeece
Confidence 357888899999988887665555643
No 78
>TIGR02727 MTHFS_bact 5,10-methenyltetrahydrofolate synthetase. This enzyme, 5,10-methenyltetrahydrofolate synthetase, is also called 5-formyltetrahydrofolate cycloligase. Function of bacterial proteins in this family was inferred originally from the known activity of eukaryotic homologs. Recently, activity was shown explicitly for the member from Mycoplasma pneumonia. Members of this family from alpha- and gamma-proteobacteria, designated ygfA, are often found in an operon with 6S structural RNA, and show a similar pattern of high expression during stationary phase. The function may be to deplete folate to slow 1-carbon biosynthetic metabolism.
Probab=21.61 E-value=32 Score=21.43 Aligned_cols=7 Identities=43% Similarity=1.217 Sum_probs=5.1
Q ss_pred ccccccc
Q psy3941 74 SGEGFYN 80 (83)
Q Consensus 74 ~g~GfY~ 80 (83)
-|+|||+
T Consensus 135 ~GgGyYD 141 (181)
T TIGR02727 135 YGGGYYD 141 (181)
T ss_pred CCcchHH
Confidence 3678887
No 79
>PF09925 DUF2157: Predicted membrane protein (DUF2157); InterPro: IPR018677 This family of various hypothetical prokaryotic proteins has no known function.
Probab=21.52 E-value=82 Score=18.89 Aligned_cols=21 Identities=19% Similarity=0.368 Sum_probs=17.4
Q ss_pred cccCCCCHHHHHHHHHhccCCC
Q psy3941 2 YERGDASPRDIDTAMKLGAGYP 23 (83)
Q Consensus 2 l~egv~~~~~ID~a~~~g~G~p 23 (83)
+++|+.|+++.+++... ++-+
T Consensus 5 ~~~GlI~~~q~~~i~~~-~~~~ 25 (145)
T PF09925_consen 5 VEQGLITPEQAEAILAF-YGER 25 (145)
T ss_pred HHCCCCCHHHHHHHHHH-hhcc
Confidence 68999999999998885 6653
No 80
>PF13466 STAS_2: STAS domain
Probab=21.17 E-value=94 Score=16.10 Aligned_cols=41 Identities=17% Similarity=0.144 Sum_probs=28.0
Q ss_pred chhhhhhhhcHHHHHHHHHHHHHhCCCCCCC-CchHHHHHHHH
Q psy3941 25 GPFELADYVGHDTTKFIIDGWHKKFPENPLF-KPVDALNKLVD 66 (83)
Q Consensus 25 GPf~~~D~vGld~~~~~~~~l~~~~~~~~~~-~~~~~l~~~~~ 66 (83)
.-.+.+|..|+.......+...+.-.. -.+ .+++.+.++++
T Consensus 34 s~v~~iDsagl~lL~~~~~~~~~~g~~-~~l~~~~~~~~~ll~ 75 (80)
T PF13466_consen 34 SGVEFIDSAGLQLLLAAARRARARGRQ-LRLTGPSPALRRLLE 75 (80)
T ss_pred CCCCeecHHHHHHHHHHHHHHHHCCCe-EEEEcCCHHHHHHHH
Confidence 778899999999999988876553321 112 35566766665
No 81
>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=21.09 E-value=1.9e+02 Score=18.80 Aligned_cols=68 Identities=21% Similarity=0.256 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHhccCCCcchhhhhhhhcHHHHHHHHHHHHHhCCCCC-----CCCchHHHHHHHHCCCCCcccccccc
Q psy3941 5 GDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENP-----LFKPVDALNKLVDEGKLGVKSGEGFY 79 (83)
Q Consensus 5 gv~~~~~ID~a~~~g~G~p~GPf~~~D~vGld~~~~~~~~l~~~~~~~~-----~~~~~~~l~~~~~~g~~G~k~g~GfY 79 (83)
|+.||.|+..|+..|.-+ .+.|- .+.+|++.+..+... +++.+ ... ..-+.+.++.|--+.-.|..++
T Consensus 115 G~~T~~E~~~A~~~Gad~-vklFP-a~~~G~~~ik~l~~~----~p~ip~~atGGI~-~~N~~~~l~aGa~~vavgs~l~ 187 (213)
T PRK06552 115 GCMTVTEIVTALEAGSEI-VKLFP-GSTLGPSFIKAIKGP----LPQVNVMVTGGVN-LDNVKDWFAAGADAVGIGGELN 187 (213)
T ss_pred CcCCHHHHHHHHHcCCCE-EEECC-cccCCHHHHHHHhhh----CCCCEEEEECCCC-HHHHHHHHHCCCcEEEEchHHh
Confidence 667999999998755431 12121 455676655554432 22111 112 3556677777766666665554
No 82
>PF12623 Hen1_L: RNA repair, ligase-Pnkp-associating, region of Hen1; InterPro: IPR024740 This entry represents the N-terminal domain of the bacterial Hen1 protein, which is a 3' terminal RNA ribose 2'-O-methyltransferase that is involved in bacterial RNA repair []. Hen1 forms a heterotetramer with Pnkp. The heterotetramer has been shown to repair transfer RNAs cleaved by ribotoxins in vitro []. The N-terminal domain of Hen1 contributes to the ligase activity of the heterotetramer.
Probab=20.66 E-value=77 Score=21.33 Aligned_cols=17 Identities=18% Similarity=0.554 Sum_probs=15.1
Q ss_pred CCHHHHHHHHHhccCCC
Q psy3941 7 ASPRDIDTAMKLGAGYP 23 (83)
Q Consensus 7 ~~~~~ID~a~~~g~G~p 23 (83)
++.++||+.++.|-||-
T Consensus 198 V~~dEvdKLlr~GegWL 214 (245)
T PF12623_consen 198 VGDDEVDKLLRAGEGWL 214 (245)
T ss_pred eCHHHHHHHHHcCCChh
Confidence 57899999999999984
No 83
>cd03515 Link_domain_TSG_6_like This is the extracellular link domain of the type found in human TSG-6. The link domain is a hyaluronan (HA)-binding domain. TSG-6 is the protein product of tumor necrosis factor-stimulated gene-6. TSG-6 is up-regulated in inflammatory lesions and in the ovary during ovulation. It has a strong anti-inflammatory and chondroprotective effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. Also included in this group are the stabilins: stabilin-1 (FEEL-1, CLEVER-1) and stabilin-2 (FEEL-2). Stabilin-2 functions as the major liver and lymph node-scavenging receptor for HA and related glycosaminoglycans. Stabilin-2 is a scavenger receptor with a broad range of ligands including advanced glycation end (AGE) products, acetylated low density lipoprotein and procollagen peptides. In contrast, stabilin-1 does not bind HA, but binds acetylated low density lipoprotein and AGEs with lower affinity. As AGEs accum
Probab=20.38 E-value=94 Score=17.76 Aligned_cols=15 Identities=27% Similarity=0.281 Sum_probs=12.0
Q ss_pred CCCHHHHHHHHHhcc
Q psy3941 6 DASPRDIDTAMKLGA 20 (83)
Q Consensus 6 v~~~~~ID~a~~~g~ 20 (83)
++|++++-.|++.|+
T Consensus 30 lAs~~QL~~Aw~~G~ 44 (93)
T cd03515 30 LATYSQLSAAQQLGF 44 (93)
T ss_pred cCCHHHHHHHHHcCc
Confidence 469999999998654
No 84
>PF00193 Xlink: Extracellular link domain; InterPro: IPR000538 The link domain [] is a hyaluronan(HA)-binding region found in proteins of vertebrates that are involved in the assembly of extracellular matrix, cell adhesion, and migration. The structure has been shown [] to consist of two alpha helices and two antiparallel beta sheets arranged around a large hydrophobic core similar to that of C-type lectin. This domain contains four conserved cysteines involved in two disulphide bonds. The link domain has also been termed HABM [] (HA binding module) and PTR [] (proteoglycan tandem repeat). Proteins with such a domain include the proteoglycans aggrecan, brevican, neurocan and versican, which are expressed in the CNS; the cartilage link protein (LP), a proteoglycan that together with HA and aggrecan forms multimolecular aggregates; Tumour necrosis factor-inducible protein TSG-6, which may be involved in cell-cell and cell-matrix interactions during inflammation and tumourgenesis; and CD44 antigen, the main cell surface receptor for HA.; GO: 0005540 hyaluronic acid binding, 0007155 cell adhesion; PDB: 1O7B_T 2PF5_C 1O7C_T 2JCQ_A 2JCR_A 2JCP_A 1UUH_B 1POZ_A 2I83_A.
Probab=20.03 E-value=69 Score=18.04 Aligned_cols=14 Identities=43% Similarity=0.650 Sum_probs=9.5
Q ss_pred CCHHHHHHHHHhcc
Q psy3941 7 ASPRDIDTAMKLGA 20 (83)
Q Consensus 7 ~~~~~ID~a~~~g~ 20 (83)
+|++++..|+..||
T Consensus 31 As~~qL~~A~~~G~ 44 (92)
T PF00193_consen 31 ASPEQLEAAWKAGF 44 (92)
T ss_dssp --HHHHHHHHHTT-
T ss_pred CCHHHHHHHHHhhh
Confidence 68999999998644
Done!