Query psy4919
Match_columns 96
No_of_seqs 103 out of 248
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 21:09:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4919.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4919hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3561|consensus 99.9 2.6E-24 5.6E-29 187.4 4.0 86 3-89 70-176 (803)
2 KOG3558|consensus 99.6 1E-15 2.2E-20 132.7 5.7 69 23-92 116-225 (768)
3 KOG3560|consensus 98.8 3.7E-09 8E-14 91.0 4.9 47 28-75 113-176 (712)
4 KOG3559|consensus 98.7 1.7E-08 3.6E-13 85.2 4.4 55 20-75 73-144 (598)
5 PF00989 PAS: PAS fold; Inter 96.2 0.0084 1.8E-07 37.0 3.7 34 26-60 1-40 (113)
6 PF08446 PAS_2: PAS fold; Int 90.3 0.39 8.5E-06 32.5 3.3 41 36-76 15-75 (110)
7 PF13426 PAS_9: PAS domain; PD 83.2 0.71 1.5E-05 27.7 1.3 21 39-60 4-30 (104)
8 PF14598 PAS_11: PAS domain; P 82.9 1 2.2E-05 30.3 2.1 33 36-69 2-53 (111)
9 PF08448 PAS_4: PAS fold; Int 78.1 2.9 6.3E-05 25.3 2.8 21 32-53 1-21 (110)
10 TIGR02040 PpsR-CrtJ transcript 77.1 4.7 0.0001 32.0 4.5 43 29-71 136-195 (442)
11 PF08447 PAS_3: PAS fold; Int 76.9 0.93 2E-05 27.4 0.3 25 49-73 1-45 (91)
12 smart00091 PAS PAS domain. PAS 76.4 6.3 0.00014 18.7 3.4 23 30-53 5-27 (67)
13 TIGR00229 sensory_box PAS doma 73.6 12 0.00025 20.4 4.3 31 29-60 6-42 (124)
14 cd00130 PAS PAS domain; PAS mo 73.2 4.3 9.3E-05 20.8 2.4 23 37-60 3-31 (103)
15 TIGR02040 PpsR-CrtJ transcript 65.4 6.8 0.00015 31.1 3.0 37 33-71 4-57 (442)
16 PF13596 PAS_10: PAS domain; P 61.4 21 0.00045 22.6 4.2 23 30-53 3-25 (106)
17 KOG3753|consensus 55.9 14 0.00031 34.6 3.6 51 32-82 187-254 (1114)
18 KOG4175|consensus 54.2 15 0.00033 29.3 3.1 22 23-44 159-180 (268)
19 PF13986 DUF4224: Domain of un 47.6 41 0.0009 19.9 3.6 28 21-50 2-40 (47)
20 KOG3883|consensus 46.5 13 0.00029 28.5 1.7 20 25-44 75-94 (198)
21 smart00564 PQQ beta-propeller 43.9 29 0.00063 17.6 2.3 18 34-51 13-30 (33)
22 PF10411 DsbC_N: Disulfide bon 43.6 26 0.00057 21.1 2.4 18 35-53 22-39 (57)
23 PF02743 Cache_1: Cache domain 43.1 18 0.00038 22.1 1.6 17 36-53 53-69 (81)
24 PF08534 Redoxin: Redoxin; In 42.8 35 0.00076 22.7 3.2 19 39-58 118-136 (146)
25 PRK13560 hypothetical protein; 42.5 29 0.00063 28.8 3.2 31 29-60 207-243 (807)
26 PRK10060 RNase II stability mo 42.0 45 0.00098 28.6 4.3 29 31-60 116-150 (663)
27 PRK13557 histidine kinase; Pro 41.4 43 0.00093 26.3 3.8 34 27-60 31-72 (540)
28 PF01011 PQQ: PQQ enzyme repea 41.2 38 0.00083 18.4 2.6 20 34-53 7-26 (38)
29 PF13188 PAS_8: PAS domain; PD 40.1 44 0.00095 19.1 2.9 28 28-57 3-36 (64)
30 COG1908 FrhD Coenzyme F420-red 39.8 74 0.0016 23.3 4.6 23 30-53 45-71 (132)
31 TIGR02966 phoR_proteo phosphat 38.5 53 0.0011 23.7 3.7 32 28-60 8-45 (333)
32 TIGR02938 nifL_nitrog nitrogen 37.8 38 0.00082 25.9 3.0 34 26-60 4-43 (494)
33 PRK09776 putative diguanylate 35.9 49 0.0011 29.1 3.7 28 32-60 289-322 (1092)
34 PRK11408 hypothetical protein; 35.6 57 0.0012 24.1 3.5 43 33-75 29-89 (145)
35 PF13359 DDE_Tnp_4: DDE superf 35.6 33 0.00072 23.3 2.1 17 38-55 32-48 (158)
36 PF14097 SpoVAE: Stage V sporu 35.5 57 0.0012 25.0 3.6 38 14-51 30-67 (180)
37 PF08168 NUC205: NUC205 domain 33.8 46 0.001 20.1 2.3 13 39-53 19-31 (44)
38 PF08269 Cache_2: Cache domain 32.2 57 0.0012 20.7 2.7 31 21-52 34-71 (95)
39 PF10946 DUF2625: Protein of u 31.0 73 0.0016 24.8 3.6 43 33-75 106-166 (208)
40 cd03014 PRX_Atyp2cys Peroxired 30.8 82 0.0018 20.8 3.4 28 39-67 113-140 (143)
41 PRK11091 aerobic respiration c 30.6 81 0.0018 27.0 4.1 32 28-60 157-194 (779)
42 COG3828 Uncharacterized protei 29.4 49 0.0011 26.3 2.4 28 46-73 183-213 (239)
43 PRK11073 glnL nitrogen regulat 29.3 63 0.0014 24.2 2.9 33 27-60 8-46 (348)
44 PF09756 DDRGK: DDRGK domain; 29.1 38 0.00082 25.7 1.7 21 32-53 137-157 (188)
45 COG1066 Sms Predicted ATP-depe 29.1 67 0.0015 27.8 3.3 30 46-75 120-168 (456)
46 PF09266 VirDNA-topo-I_N: Vira 28.7 11 0.00024 24.0 -1.1 24 18-41 33-57 (58)
47 COG2202 AtoS FOG: PAS/PAC doma 28.6 98 0.0021 18.3 3.2 31 29-60 115-151 (232)
48 PF09902 DUF2129: Uncharacteri 28.0 33 0.00072 22.3 1.1 30 46-75 20-53 (71)
49 PRK11006 phoR phosphate regulo 26.9 64 0.0014 25.4 2.7 30 30-60 102-137 (430)
50 PF06018 CodY: CodY GAF-like d 24.3 1.6E+02 0.0035 22.1 4.4 32 21-53 20-51 (177)
51 PF06523 DUF1106: Protein of u 23.4 1.3E+02 0.0029 20.3 3.4 40 33-73 31-80 (91)
52 PF09511 RNA_lig_T4_1: RNA lig 22.1 68 0.0015 23.8 1.9 21 33-53 51-72 (221)
53 PRK02302 hypothetical protein; 21.8 50 0.0011 22.5 1.1 30 46-75 26-59 (89)
54 PRK02886 hypothetical protein; 21.8 50 0.0011 22.4 1.1 30 46-75 24-57 (87)
55 PLN03220 uncharacterized prote 21.8 57 0.0012 23.0 1.4 21 54-74 78-103 (105)
56 PRK11360 sensory histidine kin 21.7 1.3E+02 0.0029 23.6 3.5 31 29-60 265-301 (607)
57 PLN03219 uncharacterized prote 21.5 66 0.0014 22.7 1.6 22 54-75 80-106 (108)
58 cd04895 ACT_ACR_1 ACT domain-c 21.0 1.5E+02 0.0032 19.0 3.1 26 49-74 44-71 (72)
59 COG0159 TrpA Tryptophan syntha 20.7 1.3E+02 0.0028 24.1 3.3 22 23-44 158-179 (265)
60 smart00706 TECPR Beta propelle 20.7 1.1E+02 0.0024 16.1 2.2 15 37-52 19-33 (35)
61 cd03015 PRX_Typ2cys Peroxiredo 20.3 1.9E+02 0.0041 20.1 3.8 32 38-71 122-153 (173)
62 PRK00522 tpx lipid hydroperoxi 20.1 1.9E+02 0.0041 20.3 3.8 32 38-70 133-164 (167)
No 1
>KOG3561|consensus
Probab=99.89 E-value=2.6e-24 Score=187.42 Aligned_cols=86 Identities=53% Similarity=0.778 Sum_probs=80.3
Q ss_pred cccccC--CCCCCCCCCCCCCCChHHHHHHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC-----------chh
Q psy4919 3 ESQERT--GNTSTDGTYKPSFLTDQELKHLILEAADGFLFVVACDTGRVVVTG------LGLPCSD-----------SVD 63 (96)
Q Consensus 3 k~~rg~--~~~~~~~~~kPsfls~~el~~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d-----------p~D 63 (96)
|.+||. .+++.+.+|||+||+++||++|||||||||||||+| +|+||||| |||+|+| |+|
T Consensus 70 r~~k~~~~~~~~~~~d~KpSflS~~eL~~LmLeAlDGF~fvV~c-dG~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d 148 (803)
T KOG3561|consen 70 RLIKEQESENSSIDQDYKPSFLSNDELTHLILEALDGFLFVVNC-DGRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLD 148 (803)
T ss_pred HHHhhhhcccccccccccccccchHHHHHHHHHHhcCeEEEEec-CceEEEEecchHHhhCcCHHHHhcchHHHhcCccc
Confidence 456764 677889999999999999999999999999999999 69999999 9999999 999
Q ss_pred HHHHHHHhC--CCCCCCcccccccccce
Q psy4919 64 IEKVREQLS--TQEPQNAGRILDLKTGT 89 (96)
Q Consensus 64 ~~e~~eqL~--~~~~~~~~r~~d~kt~~ 89 (96)
.+++|+||+ ..+.+...|+++.|+++
T Consensus 149 ~~~~~~ql~~r~~e~~f~~r~l~~~~~~ 176 (803)
T KOG3561|consen 149 NDKPREQLSPRSNEHTFNCRLLDGKTGP 176 (803)
T ss_pred cCcccccccccccccccchhhhccCCCC
Confidence 999999999 77789999999999997
No 2
>KOG3558|consensus
Probab=99.60 E-value=1e-15 Score=132.66 Aligned_cols=69 Identities=32% Similarity=0.485 Sum_probs=63.1
Q ss_pred ChHHHHHHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC-----------chhHHHHHHHhCCCC----------
Q psy4919 23 TDQELKHLILEAADGFLFVVACDTGRVVVTG------LGLPCSD-----------SVDIEKVREQLSTQE---------- 75 (96)
Q Consensus 23 s~~el~~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d-----------p~D~~e~~eqL~~~~---------- 75 (96)
.++.++.+||||||||+|||+. +|+++||| ||++|.| ||||+||+|||....
T Consensus 116 ~e~~l~~~iLqsLDGFVm~l~~-dG~~lYiSEtVS~yLGLSQvELTG~SvFDfiHP~DheE~~eqL~l~~~~p~~~es~~ 194 (768)
T KOG3558|consen 116 LEQHLGDHILQSLDGFVMALTQ-DGDFLYISETVSIYLGLSQVELTGSSVFDFIHPCDHEEIAEQLGLRLTTPEVKESTD 194 (768)
T ss_pred hhhhhhhhHHhhccceEEEEcc-CCCEEEEechhHhhhCccceeeecchhhhccCccCHHHHHHHhccccCCCccccccc
Confidence 3667999999999999999998 99999999 9999999 999999999987643
Q ss_pred --------------CCCcccccccccceeec
Q psy4919 76 --------------PQNAGRILDLKTGTVKK 92 (96)
Q Consensus 76 --------------~~~~~r~~d~kt~~~~~ 92 (96)
+++|||++|+|++.||.
T Consensus 195 ~~teRsFflRMKsTLT~RGRtlnlKSa~yKv 225 (768)
T KOG3558|consen 195 TSTERSFFLRMKSTLTKRGRTLNLKSAGYKV 225 (768)
T ss_pred CccceeEEEEeeeeeccCCceeeeeccceeE
Confidence 68999999999998874
No 3
>KOG3560|consensus
Probab=98.83 E-value=3.7e-09 Score=91.04 Aligned_cols=47 Identities=32% Similarity=0.496 Sum_probs=44.2
Q ss_pred HHHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC-----------chhHHHHHHHhCCCC
Q psy4919 28 KHLILEAADGFLFVVACDTGRVVVTG------LGLPCSD-----------SVDIEKVREQLSTQE 75 (96)
Q Consensus 28 ~~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d-----------p~D~~e~~eqL~~~~ 75 (96)
+.++||||+||++||++ +|.|+|+| ||+.|+| .+|+++|+.||.+.-
T Consensus 113 ge~lLqsLnGF~lVvt~-eg~ifyAS~tIedYLGFhQSDV~HQsVYdlIHseDR~dfqrQLhwa~ 176 (712)
T KOG3560|consen 113 GELLLQSLNGFALVVTA-EGEIFYASATIEDYLGFHQSDVMHQSVYDLIHSEDRQDFQRQLHWAM 176 (712)
T ss_pred hHHHHHhcCCeEEEEec-CceEEEehhhHHhhhcccccchhhhhHHHHhhhhhHHHHHHHHhhcc
Confidence 46899999999999999 99999999 9999999 999999999999853
No 4
>KOG3559|consensus
Probab=98.69 E-value=1.7e-08 Score=85.22 Aligned_cols=55 Identities=31% Similarity=0.506 Sum_probs=50.6
Q ss_pred CCCChHHHHHHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC-----------chhHHHHHHHhCCCC
Q psy4919 20 SFLTDQELKHLILEAADGFLFVVACDTGRVVVTG------LGLPCSD-----------SVDIEKVREQLSTQE 75 (96)
Q Consensus 20 sfls~~el~~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d-----------p~D~~e~~eqL~~~~ 75 (96)
-.=++.|++..+|+.||||+|||.. +|+|+|+| ||++|.+ |-||+++-.+|.-.+
T Consensus 73 ~~g~~~elgshlLqtLDGF~fvva~-dGkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~demna~L~~h~ 144 (598)
T KOG3559|consen 73 LDGVDKELGSHLLQTLDGFIFVVAP-DGKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDEMNAVLTAHQ 144 (598)
T ss_pred ccchHHHHHHhHHHhhcceEEEEeC-CCCEEEEecceeeeecceeeEeecchhhhhhcccchHHHHHHHhhhh
Confidence 3445899999999999999999998 99999999 9999999 999999999998776
No 5
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....
Probab=96.17 E-value=0.0084 Score=37.03 Aligned_cols=34 Identities=29% Similarity=0.447 Sum_probs=27.5
Q ss_pred HHHHHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC
Q psy4919 26 ELKHLILEAADGFLFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 26 el~~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
|.-.-+++++.-.+++++. +|+|+|++ +||.+.+
T Consensus 1 e~~~~i~~~~~~~i~~~d~-~g~I~~~N~a~~~l~g~~~~~ 40 (113)
T PF00989_consen 1 ERYRAILENSPDGIFVIDE-DGRILYVNQAAEELLGYSREE 40 (113)
T ss_dssp HHHHHHHHCSSSEEEEEET-TSBEEEECHHHHHHHSS-HHH
T ss_pred CHHHHHHhcCCceEEEEeC-cCeEEEECHHHHHHHccCHHH
Confidence 3445678889999999996 99999999 8888766
No 6
>PF08446 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3S7O_A 2O9B_A 3S7P_A 1ZTU_A 3S7N_A 3S7Q_A 2O9C_A 2OOL_A 3C2W_G 3NHQ_B ....
Probab=90.25 E-value=0.39 Score=32.46 Aligned_cols=41 Identities=29% Similarity=0.500 Sum_probs=32.0
Q ss_pred cccEEEEecCCCcEEEEc------cCCC---CCC-----------chhHHHHHHHhCCCCC
Q psy4919 36 DGFLFVVACDTGRVVVTG------LGLP---CSD-----------SVDIEKVREQLSTQEP 76 (96)
Q Consensus 36 dGFl~Vvs~~~G~IlyvS------Lg~~---q~d-----------p~D~~e~~eqL~~~~~ 76 (96)
-|||+|+..++++|+++| ||.. ..+ +.....+++.+.....
T Consensus 15 hG~LLa~d~~~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~~~~l~~~~~~~~~ 75 (110)
T PF08446_consen 15 HGALLALDPDDLRIVQASENIAELLGIPPELPEELLGRPLSELLGAESAERLREALQSESL 75 (110)
T ss_dssp TSEEEEEETTTTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCCHHHHHHHCTCCCC
T ss_pred CEEEEEEECCCCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHHHHHHHHhhhccCc
Confidence 499999987789999999 8988 444 5667788888877554
No 7
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=83.17 E-value=0.71 Score=27.69 Aligned_cols=21 Identities=19% Similarity=0.580 Sum_probs=14.9
Q ss_pred EEEEecCCCcEEEEc------cCCCCCC
Q psy4919 39 LFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 39 l~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
++++.. +|.|+|++ +||++.+
T Consensus 4 i~i~d~-~g~i~~~N~~~~~~~g~~~~~ 30 (104)
T PF13426_consen 4 IFILDP-DGRILYVNPAFERLFGYSREE 30 (104)
T ss_dssp EEEEET-TSBEEEE-HHHHHHHTS-HHH
T ss_pred EEEECC-cCcEEehhHHHHHHHCcCHHH
Confidence 466776 89999999 7777655
No 8
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=82.86 E-value=1 Score=30.34 Aligned_cols=33 Identities=15% Similarity=0.366 Sum_probs=26.4
Q ss_pred cccEEEEecCCCcEEEEc-------cCCCCCC-----------chhHHH-HHH
Q psy4919 36 DGFLFVVACDTGRVVVTG-------LGLPCSD-----------SVDIEK-VRE 69 (96)
Q Consensus 36 dGFl~Vvs~~~G~IlyvS-------Lg~~q~d-----------p~D~~e-~~e 69 (96)
+-|..-.+. +|+|+|+. |||.+.| |+|... +++
T Consensus 2 ~~F~trhs~-dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~ 53 (111)
T PF14598_consen 2 EEFTTRHSL-DGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQ 53 (111)
T ss_dssp -EEEEEEET-TSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHH
T ss_pred ceEEEEECC-CcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHH
Confidence 458888998 99999998 8999988 999997 543
No 9
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.
Probab=78.13 E-value=2.9 Score=25.30 Aligned_cols=21 Identities=29% Similarity=0.536 Sum_probs=17.3
Q ss_pred HHhhcccEEEEecCCCcEEEEc
Q psy4919 32 LEAADGFLFVVACDTGRVVVTG 53 (96)
Q Consensus 32 LeAldGFl~Vvs~~~G~IlyvS 53 (96)
|+++.--++|+.. +|+|+|+.
T Consensus 1 l~~~p~~i~v~D~-~~~i~~~N 21 (110)
T PF08448_consen 1 LDSSPDGIFVIDP-DGRIVYAN 21 (110)
T ss_dssp HHHCSSEEEEEET-TSBEEEE-
T ss_pred CCCCCceeEEECC-CCEEEEEH
Confidence 4677778899998 99999999
No 10
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=77.14 E-value=4.7 Score=32.04 Aligned_cols=43 Identities=26% Similarity=0.352 Sum_probs=30.0
Q ss_pred HHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC-----------chhHHHHHHHh
Q psy4919 29 HLILEAADGFLFVVACDTGRVVVTG------LGLPCSD-----------SVDIEKVREQL 71 (96)
Q Consensus 29 ~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d-----------p~D~~e~~eqL 71 (96)
..+++++.=.++++..++|+|+|+. +||...+ |.|.+.++..+
T Consensus 136 ~~l~e~~~~~i~~~d~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l 195 (442)
T TIGR02040 136 RVVLEVSSDAVLLVDMSTGRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTL 195 (442)
T ss_pred HHHHhhCCceEEEEECCCCEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHH
Confidence 3455665556666664479999998 8888755 67777766665
No 11
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=76.91 E-value=0.93 Score=27.43 Aligned_cols=25 Identities=20% Similarity=0.395 Sum_probs=17.5
Q ss_pred EEEEc------cCCCCCC--------------chhHHHHHHHhCC
Q psy4919 49 VVVTG------LGLPCSD--------------SVDIEKVREQLST 73 (96)
Q Consensus 49 IlyvS------Lg~~q~d--------------p~D~~e~~eqL~~ 73 (96)
|+|+| +||++.+ |+|++.+.+.+..
T Consensus 1 ~i~~s~~~~~i~G~~~~~~~~~~~~~~~~~ihpdD~~~~~~~~~~ 45 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEIGKPDFEEWLERIHPDDRERVRQAIQQ 45 (91)
T ss_dssp -EEE-THHHHHHTS-HHHHTCBEHHHHHHHB-TTTHHHHHHHHHH
T ss_pred CEEEeHHHHHHhCCCHHHhccCCHHHHHhhcCHHHHHHHHHHHHH
Confidence 68999 8988855 8998888877655
No 12
>smart00091 PAS PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
Probab=76.37 E-value=6.3 Score=18.74 Aligned_cols=23 Identities=30% Similarity=0.491 Sum_probs=17.1
Q ss_pred HHHHhhcccEEEEecCCCcEEEEc
Q psy4919 30 LILEAADGFLFVVACDTGRVVVTG 53 (96)
Q Consensus 30 l~LeAldGFl~Vvs~~~G~IlyvS 53 (96)
.+++++...++++.. .|.+++++
T Consensus 5 ~~~~~~~~~~~~~~~-~~~~~~~~ 27 (67)
T smart00091 5 AILESLPDGIFVLDL-DGRILYAN 27 (67)
T ss_pred HHHhhCCceEEEEcC-CCeEEEEC
Confidence 355666666777776 99999987
No 13
>TIGR00229 sensory_box PAS domain S-box. The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.
Probab=73.58 E-value=12 Score=20.38 Aligned_cols=31 Identities=16% Similarity=0.433 Sum_probs=22.3
Q ss_pred HHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC
Q psy4919 29 HLILEAADGFLFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 29 ~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
..+++++...++++.. +|.|+|+. +|+...+
T Consensus 6 ~~~~~~~~~~~~~~d~-~~~i~~~n~~~~~~~g~~~~~ 42 (124)
T TIGR00229 6 RAIFESSPDAIIVIDL-EGNILYVNPAFEEIFGYSAEE 42 (124)
T ss_pred HHHHhhCCceEEEEcC-CCcEEEEchHHHHHhCCChHH
Confidence 3456666666777776 99999998 7776543
No 14
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=73.22 E-value=4.3 Score=20.81 Aligned_cols=23 Identities=22% Similarity=0.407 Sum_probs=16.9
Q ss_pred ccEEEEecCCCcEEEEc------cCCCCCC
Q psy4919 37 GFLFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 37 GFl~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
.+++++.. +|.++|++ +|+.+.+
T Consensus 3 ~~i~~~d~-~~~~~~~n~~~~~~~g~~~~~ 31 (103)
T cd00130 3 DGVIVLDL-DGRILYANPAAEQLLGYSPEE 31 (103)
T ss_pred ceEEEECC-CCcEEEECHHHHHHhCCCHHH
Confidence 45677776 99999998 7766543
No 15
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=65.45 E-value=6.8 Score=31.13 Aligned_cols=37 Identities=24% Similarity=0.191 Sum_probs=27.6
Q ss_pred HhhcccEEEEecCCCcEEEEc------cCCCCCC-----------chhHHHHHHHh
Q psy4919 33 EAADGFLFVVACDTGRVVVTG------LGLPCSD-----------SVDIEKVREQL 71 (96)
Q Consensus 33 eAldGFl~Vvs~~~G~IlyvS------Lg~~q~d-----------p~D~~e~~eqL 71 (96)
.|.|| ++++.. +|+|+|+. +||.+++ |+|++++...|
T Consensus 4 ~~~d~-~~~~d~-~g~i~~~n~~~~~~~g~~~~el~G~~~~~~~~~~~~~~~~~~~ 57 (442)
T TIGR02040 4 TAADV-TLLLDA-EGVVREVAANPHHPSFEQLSEWEGRRWEEIVTAESVEKFELRL 57 (442)
T ss_pred ccCcE-EEEECC-CCcEEEEEECCCcccccccccCCCCcHhHhhCcchHHHHHHHH
Confidence 34565 557776 89999996 9998877 77777776665
No 16
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=61.40 E-value=21 Score=22.63 Aligned_cols=23 Identities=17% Similarity=0.024 Sum_probs=19.8
Q ss_pred HHHHhhcccEEEEecCCCcEEEEc
Q psy4919 30 LILEAADGFLFVVACDTGRVVVTG 53 (96)
Q Consensus 30 l~LeAldGFl~Vvs~~~G~IlyvS 53 (96)
-+|++++.=+++|.. +++|.|.+
T Consensus 3 ~il~s~~~~i~~vD~-~~~I~~~n 25 (106)
T PF13596_consen 3 NILDSMPIGIIFVDR-NLRIRYFN 25 (106)
T ss_dssp HHHHHSSSEEEEEET-TSBEEEE-
T ss_pred HHHhcCCCCEEEEcC-CCeEEEeC
Confidence 478889988999997 99999999
No 17
>KOG3753|consensus
Probab=55.92 E-value=14 Score=34.62 Aligned_cols=51 Identities=18% Similarity=0.146 Sum_probs=41.2
Q ss_pred HHhhcccEEEEecCCCcEEEEc------cCCCCCC-----------chhHHHHHHHhCCCCCCCcccc
Q psy4919 32 LEAADGFLFVVACDTGRVVVTG------LGLPCSD-----------SVDIEKVREQLSTQEPQNAGRI 82 (96)
Q Consensus 32 LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d-----------p~D~~e~~eqL~~~~~~~~~r~ 82 (96)
.+..|-|..||+--+|+|||+| ||+...= |.|+..++.+++...+....+.
T Consensus 187 ~kn~DsF~~~vS~~dG~iLyis~q~a~ilg~krDv~s~a~FvdflapqD~~vF~sfta~~~lp~ws~~ 254 (1114)
T KOG3753|consen 187 VKNADSFVVAVSFLDGRILYISEQAALILGCKRDVLSSAKFVDFLAPQDVGVFYSFTARYKLPLWSMG 254 (1114)
T ss_pred cccccceEEEEeccCCcEEEeechhhhhccCchhhhccchhhhhcchhhhhhhhhccccccCcccccc
Confidence 4556999999999999999999 7766533 9999999999988776554444
No 18
>KOG4175|consensus
Probab=54.23 E-value=15 Score=29.35 Aligned_cols=22 Identities=45% Similarity=0.705 Sum_probs=17.9
Q ss_pred ChHHHHHHHHHhhcccEEEEec
Q psy4919 23 TDQELKHLILEAADGFLFVVAC 44 (96)
Q Consensus 23 s~~el~~l~LeAldGFl~Vvs~ 44 (96)
+.+|=-.++-+|.|+|++|||.
T Consensus 159 TtdeRmell~~~adsFiYvVSr 180 (268)
T KOG4175|consen 159 TTDERMELLVEAADSFIYVVSR 180 (268)
T ss_pred ChHHHHHHHHHhhcceEEEEEe
Confidence 3455566888999999999997
No 19
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=47.63 E-value=41 Score=19.91 Aligned_cols=28 Identities=50% Similarity=0.838 Sum_probs=21.2
Q ss_pred CCChHHHHHHH-----------HHhhcccEEEEecCCCcEE
Q psy4919 21 FLTDQELKHLI-----------LEAADGFLFVVACDTGRVV 50 (96)
Q Consensus 21 fls~~el~~l~-----------LeAldGFl~Vvs~~~G~Il 50 (96)
|||++|+..|- |.. .|+-|++.. +|+.+
T Consensus 2 fLT~~El~elTG~k~~~~Q~~~L~~-~Gi~~~~~~-~G~p~ 40 (47)
T PF13986_consen 2 FLTDEELQELTGYKRPSKQIRWLRR-NGIPFVVRA-DGRPI 40 (47)
T ss_pred CCCHHHHHHHHCCCCHHHHHHHHHH-CCCeeEECC-CCCEE
Confidence 78888886653 555 599999998 88654
No 20
>KOG3883|consensus
Probab=46.46 E-value=13 Score=28.55 Aligned_cols=20 Identities=35% Similarity=0.464 Sum_probs=18.5
Q ss_pred HHHHHHHHHhhcccEEEEec
Q psy4919 25 QELKHLILEAADGFLFVVAC 44 (96)
Q Consensus 25 ~el~~l~LeAldGFl~Vvs~ 44 (96)
+||...++++.|||++|-++
T Consensus 75 ~eLprhy~q~aDafVLVYs~ 94 (198)
T KOG3883|consen 75 QELPRHYFQFADAFVLVYSP 94 (198)
T ss_pred hhhhHhHhccCceEEEEecC
Confidence 68889999999999999987
No 21
>smart00564 PQQ beta-propeller repeat. Beta-propeller repeat occurring in enzymes with pyrrolo-quinoline quinone (PQQ) as cofactor, in Ire1p-like Ser/Thr kinases, and in prokaryotic dehydrogenases.
Probab=43.85 E-value=29 Score=17.57 Aligned_cols=18 Identities=28% Similarity=0.636 Sum_probs=11.6
Q ss_pred hhcccEEEEecCCCcEEE
Q psy4919 34 AADGFLFVVACDTGRVVV 51 (96)
Q Consensus 34 AldGFl~Vvs~~~G~Ily 51 (96)
..+|.|+++..++|+++.
T Consensus 13 ~~~g~l~a~d~~~G~~~W 30 (33)
T smart00564 13 STDGTLYALDAKTGEILW 30 (33)
T ss_pred cCCCEEEEEEcccCcEEE
Confidence 346667777766676654
No 22
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=43.59 E-value=26 Score=21.12 Aligned_cols=18 Identities=22% Similarity=0.268 Sum_probs=15.0
Q ss_pred hcccEEEEecCCCcEEEEc
Q psy4919 35 ADGFLFVVACDTGRVVVTG 53 (96)
Q Consensus 35 ldGFl~Vvs~~~G~IlyvS 53 (96)
+.|+.-|+.. .|.|+|++
T Consensus 22 i~GlyeV~~~-~~~i~Y~~ 39 (57)
T PF10411_consen 22 IPGLYEVVLK-GGGILYVD 39 (57)
T ss_dssp STTEEEEEE--TTEEEEEE
T ss_pred CCCeEEEEEC-CCeEEEEc
Confidence 5898888885 89999998
No 23
>PF02743 Cache_1: Cache domain; InterPro: IPR004010 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions [].; GO: 0016020 membrane; PDB: 3C8C_A 3LIB_D 3LIA_A 3LI8_A 3LI9_A.
Probab=43.14 E-value=18 Score=22.15 Aligned_cols=17 Identities=24% Similarity=0.675 Sum_probs=14.4
Q ss_pred cccEEEEecCCCcEEEEc
Q psy4919 36 DGFLFVVACDTGRVVVTG 53 (96)
Q Consensus 36 dGFl~Vvs~~~G~IlyvS 53 (96)
.|++|+++. +|.|++=+
T Consensus 53 ~g~~~ivd~-~G~ii~hp 69 (81)
T PF02743_consen 53 NGYAFIVDK-NGTIIAHP 69 (81)
T ss_dssp TBEEEEEET-TSBBCE-S
T ss_pred CEEEEEEEC-CCCEEEeC
Confidence 799999997 99999855
No 24
>PF08534 Redoxin: Redoxin; InterPro: IPR013740 This redoxin domain is found in peroxiredoxin, thioredoxin and glutaredoxin proteins. Peroxiredoxins (Prxs) constitute a family of thiol peroxidases that reduce hydrogen peroxide, peroxinitrite, and hydroperoxides using a strictly conserved cysteine []. Chloroplast thioredoxin systems in plants regulate the enzymes involved in photosynthetic carbon assimilation []. It is thought that redoxins have a large role to play in anti-oxidant defence. Cadmium-sensitive proteins are also regulated via thioredoxin and glutaredoxin thiol redox systems [].; GO: 0016491 oxidoreductase activity; PDB: 2H30_A 1TP9_A 1Y25_A 1XVQ_A 2B1K_A 2G0F_A 2B1L_B 3K8N_A 1Z5Y_E 3OR5_A ....
Probab=42.84 E-value=35 Score=22.67 Aligned_cols=19 Identities=26% Similarity=0.408 Sum_probs=16.3
Q ss_pred EEEEecCCCcEEEEccCCCC
Q psy4919 39 LFVVACDTGRVVVTGLGLPC 58 (96)
Q Consensus 39 l~Vvs~~~G~IlyvSLg~~q 58 (96)
.++|.. +|+|+|+..|...
T Consensus 118 ~~lId~-~G~V~~~~~g~~~ 136 (146)
T PF08534_consen 118 TFLIDK-DGKVVYRHVGPDP 136 (146)
T ss_dssp EEEEET-TSBEEEEEESSBT
T ss_pred EEEEEC-CCEEEEEEeCCCC
Confidence 688886 9999999988776
No 25
>PRK13560 hypothetical protein; Provisional
Probab=42.50 E-value=29 Score=28.81 Aligned_cols=31 Identities=13% Similarity=0.135 Sum_probs=24.6
Q ss_pred HHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC
Q psy4919 29 HLILEAADGFLFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 29 ~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
..+++++...++++.. +|+|+|++ +||+..+
T Consensus 207 ~~l~e~~~~~i~~~d~-~g~i~~~N~~~~~~~G~~~~e 243 (807)
T PRK13560 207 QQLLDNIADPAFWKDE-DAKVFGCNDAACLACGFRREE 243 (807)
T ss_pred HHHHhhCCCeEEEEcC-CCCEEEEhHHHHHHhCCCHHH
Confidence 3566777777788887 99999999 8888765
No 26
>PRK10060 RNase II stability modulator; Provisional
Probab=41.98 E-value=45 Score=28.59 Aligned_cols=29 Identities=17% Similarity=0.375 Sum_probs=21.2
Q ss_pred HHHhhcccEEEEecCCCcEEEEc------cCCCCCC
Q psy4919 31 ILEAADGFLFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 31 ~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
+++.++--++++.. +|+|+|+. +||+..+
T Consensus 116 v~~~~~~gI~i~D~-~g~I~~~N~a~~~l~Gy~~~e 150 (663)
T PRK10060 116 VVSEANSVIVILDS-RGNIQRFNRLCEEYTGLKEHD 150 (663)
T ss_pred HHhhCCceEEEEeC-CCCEEEEcHHHHHHHCcCHHH
Confidence 45555444666776 99999999 8887665
No 27
>PRK13557 histidine kinase; Provisional
Probab=41.40 E-value=43 Score=26.32 Aligned_cols=34 Identities=12% Similarity=0.155 Sum_probs=21.6
Q ss_pred HHHHHHHhhcccEEEEec--CCCcEEEEc------cCCCCCC
Q psy4919 27 LKHLILEAADGFLFVVAC--DTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 27 l~~l~LeAldGFl~Vvs~--~~G~IlyvS------Lg~~q~d 60 (96)
+-..+++++.--++|+.. .+|.|+|++ +||+..+
T Consensus 31 ~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e 72 (540)
T PRK13557 31 IFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEE 72 (540)
T ss_pred HHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHH
Confidence 334445555444455543 279999999 8887765
No 28
>PF01011 PQQ: PQQ enzyme repeat family.; InterPro: IPR002372 Pyrrolo-quinoline quinone (PQQ) is a redox coenzyme, which serves as a cofactor for a number of enzymes (quinoproteins) and particularly for some bacterial dehydrogenases [, ]. A number of bacterial quinoproteins belong to this family. Enzymes in this group have repeats of a beta propeller.; PDB: 1H4I_C 1H4J_E 1W6S_A 2YH3_A 3PRW_A 3P1L_A 3Q7M_A 3Q7O_A 3Q7N_A 1G72_A ....
Probab=41.16 E-value=38 Score=18.37 Aligned_cols=20 Identities=30% Similarity=0.639 Sum_probs=17.0
Q ss_pred hhcccEEEEecCCCcEEEEc
Q psy4919 34 AADGFLFVVACDTGRVVVTG 53 (96)
Q Consensus 34 AldGFl~Vvs~~~G~IlyvS 53 (96)
..+|.|+.+..++|+++.--
T Consensus 7 ~~~g~l~AlD~~TG~~~W~~ 26 (38)
T PF01011_consen 7 TPDGYLYALDAKTGKVLWKF 26 (38)
T ss_dssp TTTSEEEEEETTTTSEEEEE
T ss_pred CCCCEEEEEECCCCCEEEee
Confidence 46899999999999998754
No 29
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=40.09 E-value=44 Score=19.11 Aligned_cols=28 Identities=11% Similarity=0.409 Sum_probs=18.3
Q ss_pred HHHHHHhhcccEEEEecCCCcEEEEc------cCCC
Q psy4919 28 KHLILEAADGFLFVVACDTGRVVVTG------LGLP 57 (96)
Q Consensus 28 ~~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~ 57 (96)
-+.+++++.--++|+. +|+|+|+. +||.
T Consensus 3 ~~~l~~~~~~~i~i~d--~~~i~~~N~~~~~l~g~~ 36 (64)
T PF13188_consen 3 YRSLFDNSPDGILIID--GGRIIYVNPAFEELFGYS 36 (64)
T ss_dssp HHHHHCCSSSEEEEEE--TSBEEEE-HHHHHHHCS-
T ss_pred HHHHHHcCccceEEEE--CCChHHhhHHHHHHhCCC
Confidence 3456666655666665 56999999 8887
No 30
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=39.82 E-value=74 Score=23.27 Aligned_cols=23 Identities=30% Similarity=0.638 Sum_probs=17.5
Q ss_pred HHHHhh----cccEEEEecCCCcEEEEc
Q psy4919 30 LILEAA----DGFLFVVACDTGRVVVTG 53 (96)
Q Consensus 30 l~LeAl----dGFl~Vvs~~~G~IlyvS 53 (96)
++|+|+ ||. ||+.|.-|.+=|.|
T Consensus 45 fvl~Al~~GaDGV-~v~GC~~geCHy~~ 71 (132)
T COG1908 45 FVLKALRKGADGV-LVAGCKIGECHYIS 71 (132)
T ss_pred HHHHHHHcCCCeE-EEecccccceeeec
Confidence 556655 674 56777899999999
No 31
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR. Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154).
Probab=38.51 E-value=53 Score=23.66 Aligned_cols=32 Identities=22% Similarity=0.233 Sum_probs=25.7
Q ss_pred HHHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC
Q psy4919 28 KHLILEAADGFLFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 28 ~~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
-..+++++.-=++++.. +|+|+|++ +|+...+
T Consensus 8 l~~~~~~~~~~i~~~d~-~g~i~~~N~~~~~~~g~~~~~ 45 (333)
T TIGR02966 8 FRAAAQALPDAVVVLDE-EGQIEWCNPAAERLLGLRWPD 45 (333)
T ss_pred HHHHHHhCcCcEEEECC-CCcEEEEcHHHHHHhCCChHH
Confidence 35667777777788887 99999999 9997765
No 32
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
Probab=37.78 E-value=38 Score=25.95 Aligned_cols=34 Identities=9% Similarity=0.105 Sum_probs=24.3
Q ss_pred HHHHHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC
Q psy4919 26 ELKHLILEAADGFLFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 26 el~~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
++-..+++++.--++++.. +|+++|++ +||++.+
T Consensus 4 ~~~~~i~~~~~~~i~~~d~-~g~~~~~N~~~~~~~G~~~~~ 43 (494)
T TIGR02938 4 EAYRQTVDQAPLAISITDL-KANILYANDAFTRITGYTKEE 43 (494)
T ss_pred HHHHHHHHhCCceEEEECC-CCcEEEEchhheeecCCCHHH
Confidence 3444566666666677776 99999999 7776654
No 33
>PRK09776 putative diguanylate cyclase; Provisional
Probab=35.94 E-value=49 Score=29.07 Aligned_cols=28 Identities=18% Similarity=0.223 Sum_probs=20.2
Q ss_pred HHhhcccEEEEecCCCcEEEEc------cCCCCCC
Q psy4919 32 LEAADGFLFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 32 LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
+++..--++++.. +|+|+|++ +||+..+
T Consensus 289 ~e~~~~~i~~~d~-dG~i~~~N~~~~~l~G~~~~e 322 (1092)
T PRK09776 289 MEYSAIGMALVGT-EGQWLQVNKALCQFLGYSQEE 322 (1092)
T ss_pred HHhCCceEEEEcC-CCcEEehhHHHHHHhCCCHHH
Confidence 3444334577787 99999999 8887765
No 34
>PRK11408 hypothetical protein; Provisional
Probab=35.63 E-value=57 Score=24.15 Aligned_cols=43 Identities=26% Similarity=0.347 Sum_probs=30.8
Q ss_pred HhhcccEEE----EecCCCcEEEEc---cCCCCC-----C------chhHHHHHHHhCCCC
Q psy4919 33 EAADGFLFV----VACDTGRVVVTG---LGLPCS-----D------SVDIEKVREQLSTQE 75 (96)
Q Consensus 33 eAldGFl~V----vs~~~G~IlyvS---Lg~~q~-----d------p~D~~e~~eqL~~~~ 75 (96)
.|++||..+ +..+-|.|.|.. |..-+. + ..|.+++++-|....
T Consensus 29 DviGG~FAiNgG~lg~~~G~v~Y~aPDtL~WE~l~~gYSeFl~Wal~gdl~~FY~~lRW~g 89 (145)
T PRK11408 29 DVIGGFFALNGGGLGEDVGEVYYFAPDTLKWESLELGYSEFLGWALSGDLEDFYEDLRWEG 89 (145)
T ss_pred ccccceEEeccCccCCCCCeEEEeCCCccceeccCCcHHHHHHHHHcCCHHHHHHhccccc
Confidence 488999876 455689999999 332222 2 888888888877754
No 35
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=35.56 E-value=33 Score=23.26 Aligned_cols=17 Identities=24% Similarity=0.485 Sum_probs=13.4
Q ss_pred cEEEEecCCCcEEEEccC
Q psy4919 38 FLFVVACDTGRVVVTGLG 55 (96)
Q Consensus 38 Fl~Vvs~~~G~IlyvSLg 55 (96)
+++|++. +|+|+||+.|
T Consensus 32 ~q~v~d~-~g~i~~v~~~ 48 (158)
T PF13359_consen 32 VQIVCDP-DGRIIYVSVG 48 (158)
T ss_pred EEEEEec-cceeEeeecc
Confidence 5567777 9999999933
No 36
>PF14097 SpoVAE: Stage V sporulation protein AE1
Probab=35.50 E-value=57 Score=24.98 Aligned_cols=38 Identities=26% Similarity=0.300 Sum_probs=30.3
Q ss_pred CCCCCCCCCChHHHHHHHHHhhcccEEEEecCCCcEEE
Q psy4919 14 DGTYKPSFLTDQELKHLILEAADGFLFVVACDTGRVVV 51 (96)
Q Consensus 14 ~~~~kPsfls~~el~~l~LeAldGFl~Vvs~~~G~Ily 51 (96)
.+.-.|+.|+-+|+-.|+++|-.==++|+--|.|.+=+
T Consensus 30 ~S~GNPT~lsG~elV~lIk~a~~DPV~VMfDD~G~~g~ 67 (180)
T PF14097_consen 30 QSAGNPTPLSGEELVELIKQAPHDPVLVMFDDKGFIGE 67 (180)
T ss_pred ccCCCCCcCCHHHHHHHHHhCCCCCEEEEEeCCCCCCC
Confidence 45558999999999999999997777777666776533
No 37
>PF08168 NUC205: NUC205 domain; InterPro: IPR012584 This domain is found in a novel family of nucleolar proteins [].; GO: 0005634 nucleus
Probab=33.77 E-value=46 Score=20.14 Aligned_cols=13 Identities=15% Similarity=0.386 Sum_probs=10.3
Q ss_pred EEEEecCCCcEEEEc
Q psy4919 39 LFVVACDTGRVVVTG 53 (96)
Q Consensus 39 l~Vvs~~~G~IlyvS 53 (96)
|+-+++ +| ++|.|
T Consensus 19 L~~L~S-DG-Ciyet 31 (44)
T PF08168_consen 19 LMSLSS-DG-CIYET 31 (44)
T ss_pred EEEecc-CC-ceeee
Confidence 344888 99 99999
No 38
>PF08269 Cache_2: Cache domain; InterPro: IPR013163 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions []. This entry is composed of the type 2 Cache domain.; PDB: 2QHK_A 4EXO_A.
Probab=32.18 E-value=57 Score=20.68 Aligned_cols=31 Identities=29% Similarity=0.514 Sum_probs=16.8
Q ss_pred CCChHHHHHHHHHhh-------cccEEEEecCCCcEEEE
Q psy4919 21 FLTDQELKHLILEAA-------DGFLFVVACDTGRVVVT 52 (96)
Q Consensus 21 fls~~el~~l~LeAl-------dGFl~Vvs~~~G~Ilyv 52 (96)
-++.+|....+.++| +|.+||.+. +|.++.-
T Consensus 34 ~ls~eea~~~a~~~l~~~r~~~~gY~fi~d~-~g~~l~h 71 (95)
T PF08269_consen 34 KLSEEEAQQQAREALRALRYGGDGYFFIYDM-DGVVLAH 71 (95)
T ss_dssp -----TTHHHHHHHHHH--SBTTB--EEE-T-TSBEEEE
T ss_pred CccHHHHHHHHHHHHhccccCCCCeEEEEeC-CCeEEEc
Confidence 466677667776664 588999987 8987764
No 39
>PF10946 DUF2625: Protein of unknown function DUF2625; InterPro: IPR021239 Some members in this family of proteins are annotated as ybfG however currently no function is known.
Probab=31.04 E-value=73 Score=24.80 Aligned_cols=43 Identities=23% Similarity=0.302 Sum_probs=31.3
Q ss_pred HhhcccEEEE----ecCCCcEEEEc---cCCCCCC-----------chhHHHHHHHhCCCC
Q psy4919 33 EAADGFLFVV----ACDTGRVVVTG---LGLPCSD-----------SVDIEKVREQLSTQE 75 (96)
Q Consensus 33 eAldGFl~Vv----s~~~G~IlyvS---Lg~~q~d-----------p~D~~e~~eqL~~~~ 75 (96)
.+++||+.+. ..+.|.|.|.+ |..-+.+ ..|.+++++-|....
T Consensus 106 Dv~GG~FAiNgG~lg~d~G~v~YfAPDtL~WE~l~~~YS~Fl~W~l~gdl~~FY~~lrW~g 166 (208)
T PF10946_consen 106 DVLGGFFAINGGGLGEDPGKVYYFAPDTLEWEPLEIGYSDFLYWALSGDLDEFYEGLRWKG 166 (208)
T ss_pred eccccEEEEccCCcCCCCCeEEEECCCcccccccCCCHHHHHHHHHcCCHHHHHHhhcchH
Confidence 5788888775 33589999999 4444444 888888888877754
No 40
>cd03014 PRX_Atyp2cys Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a bacterial periplasmic peroxidase which differs from other PRXs in that it shows substrate specificity toward alkyl hydroperoxides over hydrogen peroxide. As with all other PRXs, the peroxidatic cysteine (N-terminal) of Tpx is oxidized into a sulfenic acid intermediate upon reaction with peroxides. Tpx is able to resolve this intermediate by forming an intramolecular disulfide bond with a conserved C-terminal cysteine (the resolving cysteine), which can then be reduced by thioredoxin. This differs from the typical 2-cys PRX which resolves the oxidized cysteine by forming an intermolecular disulfide bond with the resolving cysteine from the other subunit of the homodimer. Atypical 2-cys PRX homodimers have a loop-based
Probab=30.80 E-value=82 Score=20.85 Aligned_cols=28 Identities=29% Similarity=0.419 Sum_probs=21.1
Q ss_pred EEEEecCCCcEEEEccCCCCCCchhHHHH
Q psy4919 39 LFVVACDTGRVVVTGLGLPCSDSVDIEKV 67 (96)
Q Consensus 39 l~Vvs~~~G~IlyvSLg~~q~dp~D~~e~ 67 (96)
.|+|.. +|+|+|+.+|+...+.-|.+++
T Consensus 113 ~~iid~-~G~I~~~~~~~~~~~~~~~~~~ 140 (143)
T cd03014 113 VFVIDE-NGKVIYVELVPEITDEPDYEAA 140 (143)
T ss_pred EEEEcC-CCeEEEEEECCCcccCCCHHHH
Confidence 388887 9999999988876665455543
No 41
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=30.55 E-value=81 Score=27.00 Aligned_cols=32 Identities=13% Similarity=0.146 Sum_probs=25.2
Q ss_pred HHHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC
Q psy4919 28 KHLILEAADGFLFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 28 ~~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
-..+++++...++++.. +|+|+|+. +||...+
T Consensus 157 l~~il~~~~~~i~~~D~-~g~i~~~N~a~~~l~G~~~~e 194 (779)
T PRK11091 157 LRSFLDASPDLVYYRNE-DGEFSGCNRAMELLTGKSEKQ 194 (779)
T ss_pred HHHHHhcCcceEEEECC-CCcEEeEcHHHHHHhCcCHHH
Confidence 34567788778889997 99999999 8876544
No 42
>COG3828 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.39 E-value=49 Score=26.25 Aligned_cols=28 Identities=25% Similarity=0.302 Sum_probs=22.5
Q ss_pred CCcEEEEccCCCCCC---chhHHHHHHHhCC
Q psy4919 46 TGRVVVTGLGLPCSD---SVDIEKVREQLST 73 (96)
Q Consensus 46 ~G~IlyvSLg~~q~d---p~D~~e~~eqL~~ 73 (96)
.|+++|-||||..++ |+=...++.-+.+
T Consensus 183 kGRvFYssLGHta~~~~~pe~~~i~~rg~~W 213 (239)
T COG3828 183 KGRVFYSSLGHTASEFAVPEMRTIIRRGILW 213 (239)
T ss_pred CceEEEeccCCCccccccHHHHHHHHHHHHH
Confidence 599999999999988 7777777766544
No 43
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=29.28 E-value=63 Score=24.18 Aligned_cols=33 Identities=9% Similarity=0.000 Sum_probs=24.9
Q ss_pred HHHHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC
Q psy4919 27 LKHLILEAADGFLFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 27 l~~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
...-+++++.=-++|++. +|+|+|+. +||...+
T Consensus 8 ~~~~il~~~~~gi~~~d~-~~~i~~~N~a~~~~~g~~~~~ 46 (348)
T PRK11073 8 DAGQILNSLINSILLLDD-DLAIHYANPAAQQLLAQSSRK 46 (348)
T ss_pred hHHHHHhcCcCeEEEECC-CCeEeeEcHHHHHHhCCCHHH
Confidence 345667777666777786 99999999 8887644
No 44
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=29.07 E-value=38 Score=25.70 Aligned_cols=21 Identities=38% Similarity=0.472 Sum_probs=10.6
Q ss_pred HHhhcccEEEEecCCCcEEEEc
Q psy4919 32 LEAADGFLFVVACDTGRVVVTG 53 (96)
Q Consensus 32 LeAldGFl~Vvs~~~G~IlyvS 53 (96)
|++ +|-|..|..|.|+.||||
T Consensus 137 L~~-~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 137 LEA-EGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHH-HSSS-EEE-TT--EEE--
T ss_pred HHH-CCCceeeEcCCCCeEEec
Confidence 344 566666666899999999
No 45
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=29.06 E-value=67 Score=27.80 Aligned_cols=30 Identities=27% Similarity=0.636 Sum_probs=22.2
Q ss_pred CCcEEEEc--------------cCCCCCC-----chhHHHHHHHhCCCC
Q psy4919 46 TGRVVVTG--------------LGLPCSD-----SVDIEKVREQLSTQE 75 (96)
Q Consensus 46 ~G~IlyvS--------------Lg~~q~d-----p~D~~e~~eqL~~~~ 75 (96)
.|+++||| ||....+ .-+.+.+...+....
T Consensus 120 ~~~vLYVsGEES~~QiklRA~RL~~~~~~l~l~aEt~~e~I~~~l~~~~ 168 (456)
T COG1066 120 RGKVLYVSGEESLQQIKLRADRLGLPTNNLYLLAETNLEDIIAELEQEK 168 (456)
T ss_pred cCcEEEEeCCcCHHHHHHHHHHhCCCccceEEehhcCHHHHHHHHHhcC
Confidence 77999999 8766655 667777777776643
No 46
>PF09266 VirDNA-topo-I_N: Viral DNA topoisomerase I, N-terminal; InterPro: IPR015346 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents a domain foundpredominantly found in viral DNA topoisomerase I, a type IB enzyme. This domain assumes a beta(2)-alpha-beta-alpha-beta(2) fold, with a left-handed crossover between strands beta2 and beta3 []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change; PDB: 3IGC_A 2H7G_X 2H7F_X 1VCC_A.
Probab=28.73 E-value=11 Score=24.03 Aligned_cols=24 Identities=42% Similarity=0.595 Sum_probs=15.4
Q ss_pred CCCCCChHHH-HHHHHHhhcccEEE
Q psy4919 18 KPSFLTDQEL-KHLILEAADGFLFV 41 (96)
Q Consensus 18 kPsfls~~el-~~l~LeAldGFl~V 41 (96)
.|+.|+|-.+ .|-+-||+.|.+||
T Consensus 33 iP~HLtdV~vyeqt~Eea~~gLIfV 57 (58)
T PF09266_consen 33 IPSHLTDVIVYEQTYEEALNGLIFV 57 (58)
T ss_dssp --TT-EEEEEESS-HHHHTTSEEEE
T ss_pred CCcccceEEEeeeeHHHhhccceee
Confidence 4777776554 56778999998887
No 47
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=28.58 E-value=98 Score=18.29 Aligned_cols=31 Identities=26% Similarity=0.460 Sum_probs=22.9
Q ss_pred HHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC
Q psy4919 29 HLILEAADGFLFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 29 ~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
..++++....++++.. +|.++|+. +|+...+
T Consensus 115 ~~~~~~~~~~~~~~d~-~~~~~~~n~~~~~~~g~~~~~ 151 (232)
T COG2202 115 RALLEASPDGIWVLDE-DGRILYANPAAEELLGYSPEE 151 (232)
T ss_pred HHHHhhCCceEEEEeC-CCCEEEeCHHHHHHhCCChHH
Confidence 3466777666677765 89999999 8887555
No 48
>PF09902 DUF2129: Uncharacterized protein conserved in bacteria (DUF2129); InterPro: IPR016979 This is a group of uncharacterised conserved proteins.
Probab=27.96 E-value=33 Score=22.27 Aligned_cols=30 Identities=17% Similarity=0.292 Sum_probs=22.6
Q ss_pred CCcEEEEc--cCCCC--CCchhHHHHHHHhCCCC
Q psy4919 46 TGRVVVTG--LGLPC--SDSVDIEKVREQLSTQE 75 (96)
Q Consensus 46 ~G~IlyvS--Lg~~q--~dp~D~~e~~eqL~~~~ 75 (96)
=|.|.|+| +.|.. .|.+|.+++.+.|..-.
T Consensus 20 fG~i~Y~Skk~kYvvlYvn~~~~e~~~~kl~~l~ 53 (71)
T PF09902_consen 20 FGDIHYVSKKMKYVVLYVNEEDVEEIIEKLKKLK 53 (71)
T ss_pred cccEEEEECCccEEEEEECHHHHHHHHHHHhcCC
Confidence 48899999 55544 45888899888887654
No 49
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=26.89 E-value=64 Score=25.40 Aligned_cols=30 Identities=13% Similarity=0.171 Sum_probs=24.3
Q ss_pred HHHHhhcccEEEEecCCCcEEEEc------cCCCCCC
Q psy4919 30 LILEAADGFLFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 30 l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
.+++++.--++++.. +|+|+|+. +||...+
T Consensus 102 ~~~~~~~~~i~~~d~-~g~i~~~N~~a~~l~g~~~~~ 137 (430)
T PRK11006 102 SGAESLPDAVVLTTE-EGNIFWCNGLAQQLLGFRWPE 137 (430)
T ss_pred HHHHhCCCeEEEEcC-CCceeHHHHHHHHHhCCCChH
Confidence 356777777888887 99999999 9987655
No 50
>PF06018 CodY: CodY GAF-like domain; InterPro: IPR010312 This family consists of several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; GO: 0003677 DNA binding, 0005525 GTP binding; PDB: 2HGV_A 2GX5_D 2B0L_C 2B18_A.
Probab=24.34 E-value=1.6e+02 Score=22.08 Aligned_cols=32 Identities=3% Similarity=0.266 Sum_probs=27.0
Q ss_pred CCChHHHHHHHHHhhcccEEEEecCCCcEEEEc
Q psy4919 21 FLTDQELKHLILEAADGFLFVVACDTGRVVVTG 53 (96)
Q Consensus 21 fls~~el~~l~LeAldGFl~Vvs~~~G~IlyvS 53 (96)
.++.+++...+-+.++.=++||+. .|+|+=.+
T Consensus 20 ~v~F~~ia~vL~dvl~aNvyIis~-kGkiLGy~ 51 (177)
T PF06018_consen 20 PVDFNDIAEVLSDVLEANVYIISR-KGKILGYS 51 (177)
T ss_dssp S--HHHHHHHHHHHHTSEEEEEET-TSBEEEEE
T ss_pred CCCHHHHHHHHHHhhcCcEEEEeC-CccEEEEe
Confidence 466889999999999999999998 99998555
No 51
>PF06523 DUF1106: Protein of unknown function (DUF1106); InterPro: IPR009490 This family consists of several hypothetical bacterial proteins found in Escherichia coli and Citrobacter rodentium. The function of this family is unknown.
Probab=23.37 E-value=1.3e+02 Score=20.33 Aligned_cols=40 Identities=10% Similarity=0.350 Sum_probs=26.6
Q ss_pred HhhcccEEEEecCCCcEEEEccCCCCCC----------chhHHHHHHHhCC
Q psy4919 33 EAADGFLFVVACDTGRVVVTGLGLPCSD----------SVDIEKVREQLST 73 (96)
Q Consensus 33 eAldGFl~Vvs~~~G~IlyvSLg~~q~d----------p~D~~e~~eqL~~ 73 (96)
--|.|.++.+-| ..-|+|+|...++.. .-=.++++|++..
T Consensus 31 grlrgiv~t~kc-s~g~iylsi~v~pnn~~hi~ly~kk~yi~dklkeifpd 80 (91)
T PF06523_consen 31 GRLRGIVLTIKC-SNGIIYLSIKVNPNNSNHIFLYHKKNYIFDKLKEIFPD 80 (91)
T ss_pred eceeeEEEEEEe-cCcEEEEEEEeCCCCcceEEEEecchhHHHHHHHhCCC
Confidence 357899999999 666899995444444 1123467777654
No 52
>PF09511 RNA_lig_T4_1: RNA ligase; InterPro: IPR019039 Members of this family include T4 phage proteins with ATP-dependent RNA ligase activity. Host defence to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. This family also includes fungal tRNA ligases that have adenylyltransferase activity []. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns. Please see the following relevant references: [, ]. ; PDB: 2C5U_B.
Probab=22.14 E-value=68 Score=23.84 Aligned_cols=21 Identities=33% Similarity=0.561 Sum_probs=15.7
Q ss_pred HhhcccEE-EEecCCCcEEEEc
Q psy4919 33 EAADGFLF-VVACDTGRVVVTG 53 (96)
Q Consensus 33 eAldGFl~-Vvs~~~G~IlyvS 53 (96)
+=+||+|+ +...++|.+++.|
T Consensus 51 ~K~dGsli~~~~~~~g~~~~~S 72 (221)
T PF09511_consen 51 EKEDGSLIFIPYLDDGELIVAS 72 (221)
T ss_dssp EE--SEEE-EEEEETTEEEEEE
T ss_pred EecCcEEEEEeeecCCeEEEEe
Confidence 34599999 7777789999999
No 53
>PRK02302 hypothetical protein; Provisional
Probab=21.83 E-value=50 Score=22.51 Aligned_cols=30 Identities=23% Similarity=0.269 Sum_probs=21.8
Q ss_pred CCcEEEEc--cCCCC--CCchhHHHHHHHhCCCC
Q psy4919 46 TGRVVVTG--LGLPC--SDSVDIEKVREQLSTQE 75 (96)
Q Consensus 46 ~G~IlyvS--Lg~~q--~dp~D~~e~~eqL~~~~ 75 (96)
=|.|.|+| +.|.. .+.+|.+++.+.|..-.
T Consensus 26 fG~I~Y~Skk~kYvvlYvn~~~~e~~~~kl~~l~ 59 (89)
T PRK02302 26 YGDIVYHSKRSRYLVLYVNKEDVEQKLEELSKLK 59 (89)
T ss_pred cCcEEEEeccccEEEEEECHHHHHHHHHHHhcCC
Confidence 48899999 54433 34888888888888754
No 54
>PRK02886 hypothetical protein; Provisional
Probab=21.81 E-value=50 Score=22.44 Aligned_cols=30 Identities=23% Similarity=0.308 Sum_probs=21.8
Q ss_pred CCcEEEEc--cCCCC--CCchhHHHHHHHhCCCC
Q psy4919 46 TGRVVVTG--LGLPC--SDSVDIEKVREQLSTQE 75 (96)
Q Consensus 46 ~G~IlyvS--Lg~~q--~dp~D~~e~~eqL~~~~ 75 (96)
=|.|.|+| +.|.. .+.+|.+++.+.|..-.
T Consensus 24 yG~I~Y~Skr~kYvvlYvn~~~~e~~~~kl~~l~ 57 (87)
T PRK02886 24 FGNVHYVSKRLKYAVLYCDMEQVEDIMNKLSSLP 57 (87)
T ss_pred cCcEEEEeccccEEEEEECHHHHHHHHHHHhcCC
Confidence 48899999 54433 34788888888887754
No 55
>PLN03220 uncharacterized protein; Provisional
Probab=21.75 E-value=57 Score=22.95 Aligned_cols=21 Identities=10% Similarity=0.177 Sum_probs=17.9
Q ss_pred cCCCCCC-----chhHHHHHHHhCCC
Q psy4919 54 LGLPCSD-----SVDIEKVREQLSTQ 74 (96)
Q Consensus 54 Lg~~q~d-----p~D~~e~~eqL~~~ 74 (96)
+||.+.+ |||.+.+.+.|+++
T Consensus 78 fGf~~~~G~L~IPCd~~~F~~ll~s~ 103 (105)
T PLN03220 78 FGFNHPMGGLTIPCREEVFLDLIASR 103 (105)
T ss_pred hCCCCCCCCEEeeCCHHHHHHHHHhh
Confidence 7888754 99999999999874
No 56
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=21.67 E-value=1.3e+02 Score=23.57 Aligned_cols=31 Identities=23% Similarity=0.388 Sum_probs=23.0
Q ss_pred HHHHHhhcccEEEEecCCCcEEEEc------cCCCCCC
Q psy4919 29 HLILEAADGFLFVVACDTGRVVVTG------LGLPCSD 60 (96)
Q Consensus 29 ~l~LeAldGFl~Vvs~~~G~IlyvS------Lg~~q~d 60 (96)
..+++++.--++++.. +|+|+|+. +|+.+.+
T Consensus 265 ~~i~~~~~~~i~~~d~-~g~i~~~N~~~~~l~g~~~~~ 301 (607)
T PRK11360 265 ELILESIADGVIAIDR-QGKITTMNPAAEVITGLQRHE 301 (607)
T ss_pred HHHHHhccCeEEEEcC-CCCEEEECHHHHHHhCCChHH
Confidence 3455666556778886 99999999 8887744
No 57
>PLN03219 uncharacterized protein; Provisional
Probab=21.52 E-value=66 Score=22.73 Aligned_cols=22 Identities=14% Similarity=0.160 Sum_probs=18.5
Q ss_pred cCCCCCC-----chhHHHHHHHhCCCC
Q psy4919 54 LGLPCSD-----SVDIEKVREQLSTQE 75 (96)
Q Consensus 54 Lg~~q~d-----p~D~~e~~eqL~~~~ 75 (96)
+||.+.+ |||.+.|+..|+.+.
T Consensus 80 fGf~~~~G~L~IPCd~~~F~~ll~~~~ 106 (108)
T PLN03219 80 CGFHHSMGGLTIPCREESFLHLITSHQ 106 (108)
T ss_pred hCCCCCCCCEEEeCCHHHHHHHHHhhh
Confidence 7887654 999999999998764
No 58
>cd04895 ACT_ACR_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.97 E-value=1.5e+02 Score=18.96 Aligned_cols=26 Identities=27% Similarity=0.277 Sum_probs=19.7
Q ss_pred EEEEc--cCCCCCCchhHHHHHHHhCCC
Q psy4919 49 VVVTG--LGLPCSDSVDIEKVREQLSTQ 74 (96)
Q Consensus 49 IlyvS--Lg~~q~dp~D~~e~~eqL~~~ 74 (96)
++||+ -|..-.||...+++++.|..+
T Consensus 44 vFyV~d~~g~kl~d~~~~~~l~~~L~~~ 71 (72)
T cd04895 44 VFHVTDQLGNKLTDDSLIAYIEKSLGTS 71 (72)
T ss_pred EEEEECCCCCCCCCHHHHHHHHHHhccC
Confidence 57777 455556688999999999764
No 59
>COG0159 TrpA Tryptophan synthase alpha chain [Amino acid transport and metabolism]
Probab=20.70 E-value=1.3e+02 Score=24.08 Aligned_cols=22 Identities=41% Similarity=0.530 Sum_probs=15.3
Q ss_pred ChHHHHHHHHHhhcccEEEEec
Q psy4919 23 TDQELKHLILEAADGFLFVVAC 44 (96)
Q Consensus 23 s~~el~~l~LeAldGFl~Vvs~ 44 (96)
+.++.-..+.++.+||++.||.
T Consensus 158 t~~~rl~~i~~~a~GFiY~vs~ 179 (265)
T COG0159 158 TPDERLKKIAEAASGFIYYVSR 179 (265)
T ss_pred CCHHHHHHHHHhCCCcEEEEec
Confidence 3555556677777888887776
No 60
>smart00706 TECPR Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins.
Probab=20.67 E-value=1.1e+02 Score=16.07 Aligned_cols=15 Identities=13% Similarity=0.297 Sum_probs=12.1
Q ss_pred ccEEEEecCCCcEEEE
Q psy4919 37 GFLFVVACDTGRVVVT 52 (96)
Q Consensus 37 GFl~Vvs~~~G~Ilyv 52 (96)
+.++.|++ +|.|.+-
T Consensus 19 ~~vW~V~~-~g~i~~r 33 (35)
T smart00706 19 DTVWAVNS-DGNIYRR 33 (35)
T ss_pred CeEEEEcC-CCCEEEE
Confidence 67899998 9988763
No 61
>cd03015 PRX_Typ2cys Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides. The functional unit of typical 2-cys PRX is a homodimer. A unique intermolecular redox-active disulfide center is utilized for its activity. Upon reaction with peroxides, its peroxidatic cysteine is oxidized into a sulfenic acid intermediate which is resolved by bonding with the resolving cysteine from the other subunit of the homodimer. This intermolecular disulfide bond is then reduced by thioredoxin, tryparedoxin or AhpF. Typical 2-cys PRXs, like 1-cys PRXs, form decamers which are stabilized by reduction of the active site cysteine. Typical 2-cys PRX interacts through beta strands at one edge of the monomer (B-type interface) to form the functional homodimer, and uses an A-type interface (similar to the dimeric
Probab=20.31 E-value=1.9e+02 Score=20.14 Aligned_cols=32 Identities=9% Similarity=0.051 Sum_probs=22.0
Q ss_pred cEEEEecCCCcEEEEccCCCCCCchhHHHHHHHh
Q psy4919 38 FLFVVACDTGRVVVTGLGLPCSDSVDIEKVREQL 71 (96)
Q Consensus 38 Fl~Vvs~~~G~IlyvSLg~~q~dp~D~~e~~eqL 71 (96)
..|||.. +|+|.|+.++-.+.++ +.+++-+.|
T Consensus 122 ~~~lID~-~G~I~~~~~~~~~~~~-~~~~il~~l 153 (173)
T cd03015 122 GTFIIDP-EGIIRHITVNDLPVGR-SVDETLRVL 153 (173)
T ss_pred EEEEECC-CCeEEEEEecCCCCCC-CHHHHHHHH
Confidence 3799987 9999999976555443 444555554
No 62
>PRK00522 tpx lipid hydroperoxide peroxidase; Provisional
Probab=20.11 E-value=1.9e+02 Score=20.29 Aligned_cols=32 Identities=19% Similarity=0.224 Sum_probs=21.7
Q ss_pred cEEEEecCCCcEEEEccCCCCCCchhHHHHHHH
Q psy4919 38 FLFVVACDTGRVVVTGLGLPCSDSVDIEKVREQ 70 (96)
Q Consensus 38 Fl~Vvs~~~G~IlyvSLg~~q~dp~D~~e~~eq 70 (96)
-.|||.. +|+|.|+..+....+..+.+++-+.
T Consensus 133 ~tfvId~-~G~I~~~~~~~~~~~~~~~~~~l~~ 164 (167)
T PRK00522 133 AVFVLDE-NNKVVYSELVPEITNEPDYDAALAA 164 (167)
T ss_pred EEEEECC-CCeEEEEEECCCcCCCCCHHHHHHH
Confidence 4588987 9999999976655554445554443
Done!