Query 033107
Match_columns 127
No_of_seqs 113 out of 312
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 09:53:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033107.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033107hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK04239 hypothetical protein; 100.0 1.2E-37 2.6E-42 228.6 12.5 108 4-116 1-109 (110)
2 COG2118 DNA-binding protein [G 100.0 6.8E-37 1.5E-41 226.2 13.2 112 1-117 1-114 (116)
3 KOG3431 Apoptosis-related prot 100.0 7.4E-34 1.6E-38 212.7 11.5 111 2-116 1-114 (129)
4 PF01984 dsDNA_bind: Double-st 100.0 4.7E-35 1E-39 212.9 3.3 103 9-116 1-105 (107)
5 cd02987 Phd_like_Phd Phosducin 87.4 0.51 1.1E-05 36.3 2.6 17 5-21 39-55 (175)
6 cd02988 Phd_like_VIAF Phosduci 77.8 2.1 4.6E-05 33.5 2.7 16 5-20 60-75 (192)
7 smart00088 PINT motif in prote 64.4 6.1 0.00013 26.1 2.2 51 46-96 10-60 (88)
8 smart00753 PAM PCI/PINT associ 64.4 6.1 0.00013 26.1 2.2 51 46-96 10-60 (88)
9 KOG1672 ATP binding protein [P 60.9 7.7 0.00017 31.9 2.6 19 1-19 34-52 (211)
10 PF01399 PCI: PCI domain; Int 56.5 5.6 0.00012 26.2 0.9 22 75-96 75-96 (105)
11 PF09756 DDRGK: DDRGK domain; 54.9 8.6 0.00019 30.7 1.9 34 76-123 129-162 (188)
12 PF02114 Phosducin: Phosducin; 49.0 15 0.00033 30.4 2.5 19 3-21 100-118 (265)
13 PHA01632 hypothetical protein 48.5 31 0.00067 23.4 3.5 35 89-123 23-62 (64)
14 PF13932 GIDA_assoc_3: GidA as 47.5 16 0.00034 24.7 2.0 35 55-103 37-71 (72)
15 PF10587 EF-1_beta_acid: Eukar 43.1 28 0.00061 20.2 2.3 17 3-19 10-26 (28)
16 TIGR02574 stabl_TIGR02574 puta 40.1 49 0.0011 21.5 3.4 56 67-123 2-57 (63)
17 PF09720 Unstab_antitox: Putat 38.0 54 0.0012 20.3 3.3 52 68-122 2-53 (54)
18 cd00390 Urease_gamma Urease ga 37.0 92 0.002 22.8 4.7 44 58-106 16-60 (96)
19 PF13833 EF-hand_8: EF-hand do 36.1 48 0.001 19.7 2.7 23 94-116 22-44 (54)
20 cd05029 S-100A6 S-100A6: S-100 35.6 32 0.00069 23.6 2.1 26 91-116 45-70 (88)
21 PF14237 DUF4339: Domain of un 35.5 28 0.00061 20.9 1.6 19 87-105 7-25 (45)
22 PF11829 DUF3349: Protein of u 33.5 33 0.0007 24.9 1.9 32 90-124 32-63 (96)
23 PRK14981 DNA-directed RNA poly 33.4 1.9E+02 0.004 20.9 5.9 57 44-109 53-110 (112)
24 PRK01294 lipase chaperone; Pro 32.1 3.2E+02 0.007 23.4 8.0 63 44-107 250-312 (336)
25 PF05871 ESCRT-II: ESCRT-II co 31.4 42 0.00091 25.5 2.3 61 54-124 29-89 (139)
26 PF08369 PCP_red: Proto-chloro 31.2 35 0.00076 21.2 1.5 16 56-75 2-17 (45)
27 PF00392 GntR: Bacterial regul 30.8 1E+02 0.0022 19.3 3.8 32 73-104 1-35 (64)
28 PF03280 Lipase_chap: Proteoba 28.6 2.3E+02 0.005 22.0 6.1 61 44-106 124-184 (195)
29 PF15248 DUF4587: Domain of un 27.0 31 0.00066 24.2 0.8 18 73-90 6-23 (76)
30 PF08708 PriCT_1: Primase C te 26.7 1.6E+02 0.0035 18.8 4.2 36 72-109 33-68 (71)
31 PRK13242 ureA urease subunit g 26.3 88 0.0019 23.1 3.1 35 55-89 16-51 (100)
32 TIGR00193 urease_gam urease, g 25.1 97 0.0021 22.9 3.2 36 54-89 15-51 (102)
33 PRK13241 ureA urease subunit g 24.8 99 0.0021 22.8 3.2 45 56-105 17-62 (100)
34 PF11964 SpoIIAA-like: SpoIIAA 24.2 50 0.0011 22.1 1.5 30 90-119 7-38 (109)
35 PF04552 Sigma54_DBD: Sigma-54 24.0 71 0.0015 24.7 2.4 31 74-104 102-132 (160)
36 KOG2351 RNA polymerase II, fou 23.3 70 0.0015 24.7 2.2 23 89-111 110-132 (134)
37 PF14493 HTH_40: Helix-turn-he 22.9 1.4E+02 0.003 20.2 3.5 55 51-111 10-67 (91)
38 cd05026 S-100Z S-100Z: S-100Z 22.8 64 0.0014 22.0 1.8 30 76-107 54-83 (93)
39 COG1610 Uncharacterized conser 22.5 73 0.0016 25.0 2.2 61 51-120 11-71 (148)
40 cd03312 CIMS_N_terminal_like C 22.3 1.5E+02 0.0033 25.3 4.3 45 71-124 14-63 (360)
41 PF13767 DUF4168: Domain of un 21.8 2.5E+02 0.0054 18.6 6.2 64 5-77 15-78 (78)
42 COG1390 NtpE Archaeal/vacuolar 21.4 4.2E+02 0.0091 21.0 8.3 70 44-119 57-128 (194)
43 KOG3561 Aryl-hydrocarbon recep 21.1 1.6E+02 0.0036 28.6 4.6 54 69-122 54-125 (803)
44 KOG2582 COP9 signalosome, subu 21.1 73 0.0016 28.7 2.2 24 72-95 330-353 (422)
45 TIGR00136 gidA glucose-inhibit 20.7 94 0.002 29.1 2.9 41 54-108 575-615 (617)
46 COG2517 Predicted RNA-binding 20.3 1.7E+02 0.0037 24.2 4.0 47 74-121 13-60 (219)
47 PF06375 BLVR: Bovine leukaemi 20.3 34 0.00074 26.7 0.0 19 1-19 1-19 (154)
48 PF00547 Urease_gamma: Urease, 20.0 1.1E+02 0.0024 22.5 2.6 33 57-89 18-51 (99)
No 1
>PRK04239 hypothetical protein; Provisional
Probab=100.00 E-value=1.2e-37 Score=228.59 Aligned_cols=108 Identities=39% Similarity=0.456 Sum_probs=92.9
Q ss_pred hHHHHHHHHHHHHHHHHcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHhchhhccCchhHHHHHHHHHH
Q 033107 4 PELEAIRQRRMQELMAQQGVGSQQNSEQHQKAQEDAKREADERRQMMLSQILSTEARERLARIALVKPEKARGVEDIILR 83 (127)
Q Consensus 4 ~ELeaIR~rRl~ELq~q~~~~~~~~~ee~~q~qee~~~~~ee~r~~iL~qiLt~eAreRL~rI~lVKPE~A~~VE~~Liq 83 (127)
+||++||++||+|||+++|+++ ++ .+++++++++.++++++||++||||+||+||+||+|||||+|++||+|||+
T Consensus 1 ~ELe~IR~~rl~eLq~q~~~~~-~~----~~~~~~~~~~~e~qk~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~liq 75 (110)
T PRK04239 1 EELEEIRRRKLEELQKQAQEQQ-QA----QEEQEEAQAQAEAQKQAILRQILTPEARERLNRIKLVKPEFAEQVEQQLIQ 75 (110)
T ss_pred ChHHHHHHHHHHHHHHHhccCC-cc----hhhHHHHHHHHHHHHHHHHHHHCCHHHHHHHHhhhhcCHHHHHHHHHHHHH
Confidence 4899999999999998887422 22 123456667779999999999999999999999999999999999999999
Q ss_pred HHHcCCCCCCCChHHHHHHHHHhhhhhc-CCeeE
Q 033107 84 SAQMGQIVEKVPLCLLRTQCWMDAQIIS-QNIVY 116 (127)
Q Consensus 84 laq~Gql~~kI~e~~Lk~iL~~~~q~~~-~~i~~ 116 (127)
||++|+|++||||++||+||..++.++. .+|.+
T Consensus 76 lAq~G~i~~ki~e~~L~~lL~~v~~~kre~~I~r 109 (110)
T PRK04239 76 LAQSGRIQGPIDDEQLKEILEQLTPQKREFKITR 109 (110)
T ss_pred HHHcCCCCCCcCHHHHHHHHHHHhhcccCcCccc
Confidence 9999999999999999999999985543 56654
No 2
>COG2118 DNA-binding protein [General function prediction only]
Probab=100.00 E-value=6.8e-37 Score=226.19 Aligned_cols=112 Identities=38% Similarity=0.505 Sum_probs=95.5
Q ss_pred CCchHHHHHHHHHHHHHHHHcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHhchhhccCchhHHHHHHH
Q 033107 1 MADPELEAIRQRRMQELMAQQGVGSQQNSEQHQKAQEDAKREADERRQMMLSQILSTEARERLARIALVKPEKARGVEDI 80 (127)
Q Consensus 1 M~D~ELeaIR~rRl~ELq~q~~~~~~~~~ee~~q~qee~~~~~ee~r~~iL~qiLt~eAreRL~rI~lVKPE~A~~VE~~ 80 (127)
|||+||++||++||+|||++++. . ++...+++++..+.+++|++||++||||+||+||+||+|||||+|++||++
T Consensus 1 mdd~eLEeIRrrkl~eLQrq~~~----~-~~~~~q~eq~r~~~eaqkqaiLrqiLtpeAreRL~~irLvRPe~AeavE~q 75 (116)
T COG2118 1 MDDEELEEIRRRKLAELQRQAKL----E-EQREAQEEQARQEEEAQKQAILRQILTPEARERLARVRLVRPELAEAVENQ 75 (116)
T ss_pred CChHHHHHHHHHHHHHHHHhhhh----H-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHhhhcCHHHHHHHHHH
Confidence 78889999999999999997731 1 121223445555668999999999999999999999999999999999999
Q ss_pred HHHHHHcCCCCCCCChHHHHHHHHHhhhh--hcCCeeEe
Q 033107 81 ILRSAQMGQIVEKVPLCLLRTQCWMDAQI--ISQNIVYL 117 (127)
Q Consensus 81 Liqlaq~Gql~~kI~e~~Lk~iL~~~~q~--~~~~i~~~ 117 (127)
||+||++|+|++||||++||+||..++.. .+.+|+|-
T Consensus 76 Li~LaqtGri~~~I~e~~lk~IL~~i~~~~rre~kI~~~ 114 (116)
T COG2118 76 LIQLAQTGRITHKIDEEELKEILERISPQTRREFKIRRR 114 (116)
T ss_pred HHHHHHcCCCCCCCCHHHHHHHHHHHhHHhccchheecc
Confidence 99999999999999999999999999776 33577764
No 3
>KOG3431 consensus Apoptosis-related protein/predicted DNA-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=7.4e-34 Score=212.67 Aligned_cols=111 Identities=41% Similarity=0.587 Sum_probs=94.6
Q ss_pred CchHHHHHHHHHHHHHHHHcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHhchhhccCchhHHHHHHHH
Q 033107 2 ADPELEAIRQRRMQELMAQQGVGSQQNSEQHQKAQEDAKREADERRQMMLSQILSTEARERLARIALVKPEKARGVEDII 81 (127)
Q Consensus 2 ~D~ELeaIR~rRl~ELq~q~~~~~~~~~ee~~q~qee~~~~~ee~r~~iL~qiLt~eAreRL~rI~lVKPE~A~~VE~~L 81 (127)
+|+||++||++||++|++.+|++++.+. +++..++. +.+++|+++|+|||++.||+||+||+|||||||++||+||
T Consensus 1 ~D~eL~AiR~qRlaqlqa~~G~~~~~~~---q~a~q~~~-~q~e~r~~~lsQvLdqqAr~RLsrlAlvkpekAq~VE~~l 76 (129)
T KOG3431|consen 1 MDPELQAIRAQRLAQLQANSGGANDAAQ---QQANQEQQ-EQEEMRQSMLSQVLDQQARERLSRLALVKPEKAQAVENYL 76 (129)
T ss_pred CchHHHHHHHHHHHHhhhhcCCCccccc---cchhhhhh-hHHHHHHhHHHHHhhHHHHHHHHhhhhcCHHHHHHHHHHH
Confidence 5889999999999999998885443221 12222222 3789999999999999999999999999999999999999
Q ss_pred HHHHHcCCCCCCCChHHHHHHHHHhhhhhc---CCeeE
Q 033107 82 LRSAQMGQIVEKVPLCLLRTQCWMDAQIIS---QNIVY 116 (127)
Q Consensus 82 iqlaq~Gql~~kI~e~~Lk~iL~~~~q~~~---~~i~~ 116 (127)
|+||++|+|++||||++|+.||.+++.+-+ -+|+|
T Consensus 77 irma~~gQvs~Kise~~lisiLe~is~Qt~qk~tkV~f 114 (129)
T KOG3431|consen 77 IRMAQTGQVSHKISEAELISILEKISAQTNQKNTKVKF 114 (129)
T ss_pred HHHHHhCCccccccHHHHHHHHHHHHHhhccccceeee
Confidence 999999999999999999999999987663 37777
No 4
>PF01984 dsDNA_bind: Double-stranded DNA-binding domain; InterPro: IPR002836 This protein family is found in archaea and eukaryota. The human TFAR19 (TF-1 cell apoptosis-related protein 19) encodes a protein which shares significant homology to the corresponding proteins of species ranging from yeast to mice. TFAR19 exhibits a ubiquitous expression pattern and its expression is up-regulated in the tumour cells undergoing apoptosis. TFAR19 may play a general role in the apoptotic process []. Also included in this family is a DNA-binding protein from the archaea, Methanobacterium thermoautotrophicum.; GO: 0003677 DNA binding; PDB: 1EIJ_A 2K6B_A 2CRU_A 1YYB_A 2JXN_A 2FH0_A.
Probab=100.00 E-value=4.7e-35 Score=212.90 Aligned_cols=103 Identities=43% Similarity=0.556 Sum_probs=84.4
Q ss_pred HHHHHHHHHHHHcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHhchhhccCchhHHHHHHHHHHHHHcC
Q 033107 9 IRQRRMQELMAQQGVGSQQNSEQHQKAQEDAKREADERRQMMLSQILSTEARERLARIALVKPEKARGVEDIILRSAQMG 88 (127)
Q Consensus 9 IR~rRl~ELq~q~~~~~~~~~ee~~q~qee~~~~~ee~r~~iL~qiLt~eAreRL~rI~lVKPE~A~~VE~~Liqlaq~G 88 (127)
||++||+|||++++.++.. ..++++++++.+++++++|++||||+||+||+||+|||||+|.+||+|||+||++|
T Consensus 1 iR~~rl~Elq~~~~~~~~~-----~~~~~~~~~~~ee~~~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~Liqlaq~G 75 (107)
T PF01984_consen 1 IRRRRLAELQQQQGQQQQK-----QQQQEEQREQQEEQRRAILRQILTPEARERLNRIKLVKPEKARQVENQLIQLAQSG 75 (107)
T ss_dssp HHHHHHHHCCHTSS-SSST-----CHHCHHCHCCCHHCCHHHHHTCB-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred CchHHHHHHHhccccccch-----hhhHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHcC
Confidence 8999999999887521111 12345566777999999999999999999999999999999999999999999999
Q ss_pred CCCCCCChHHHHHHHHHhhhhhc--CCeeE
Q 033107 89 QIVEKVPLCLLRTQCWMDAQIIS--QNIVY 116 (127)
Q Consensus 89 ql~~kI~e~~Lk~iL~~~~q~~~--~~i~~ 116 (127)
+|++||||++||+||..++.+.. .+|+|
T Consensus 76 ~l~~kI~d~~L~~iL~~i~~~~~~~~~I~~ 105 (107)
T PF01984_consen 76 QLRGKIDDEQLKEILEQISEQKQKETKIKI 105 (107)
T ss_dssp SSSS-B-HHHHHHHHHHHCCC-SS-SS-S-
T ss_pred CCCCCcCHHHHHHHHHHHhhcccCCCeeee
Confidence 99999999999999999988777 68887
No 5
>cd02987 Phd_like_Phd Phosducin (Phd)-like family, Phd subfamily; Phd is a cytosolic regulator of G protein functions. It specifically binds G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane. This impedes the formation of a functional G protein trimer (G protein alphabetagamma), thereby inhibiting G protein-mediated signal transduction. Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=87.36 E-value=0.51 Score=36.27 Aligned_cols=17 Identities=41% Similarity=0.548 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHc
Q 033107 5 ELEAIRQRRMQELMAQQ 21 (127)
Q Consensus 5 ELeaIR~rRl~ELq~q~ 21 (127)
+|+.+|++||+||++..
T Consensus 39 ~l~~~R~~R~~el~~~~ 55 (175)
T cd02987 39 FLQQYREQRMQEMHAKL 55 (175)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 89999999999998754
No 6
>cd02988 Phd_like_VIAF Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis. It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=77.81 E-value=2.1 Score=33.51 Aligned_cols=16 Identities=38% Similarity=0.522 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHH
Q 033107 5 ELEAIRQRRMQELMAQ 20 (127)
Q Consensus 5 ELeaIR~rRl~ELq~q 20 (127)
.|+.+|++||+||++.
T Consensus 60 ~Le~yR~kRl~el~~~ 75 (192)
T cd02988 60 FLEEYRRKRLAEMKAL 75 (192)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 6999999999999864
No 7
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=64.36 E-value=6.1 Score=26.05 Aligned_cols=51 Identities=20% Similarity=0.189 Sum_probs=30.3
Q ss_pred HHHHHHHHhCCHHHHHHhchhhccCchhHHHHHHHHHHHHHcCCCCCCCCh
Q 033107 46 RRQMMLSQILSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVPL 96 (127)
Q Consensus 46 ~r~~iL~qiLt~eAreRL~rI~lVKPE~A~~VE~~Liqlaq~Gql~~kI~e 96 (127)
.+...+.++..+-..=.++.|+-.=+=-...||..|+.|+..|.|.++|+.
T Consensus 10 ~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~ 60 (88)
T smart00088 10 IRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQ 60 (88)
T ss_pred HHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcC
Confidence 344455555554433333333221111123599999999999999999873
No 8
>smart00753 PAM PCI/PINT associated module.
Probab=64.36 E-value=6.1 Score=26.05 Aligned_cols=51 Identities=20% Similarity=0.189 Sum_probs=30.3
Q ss_pred HHHHHHHHhCCHHHHHHhchhhccCchhHHHHHHHHHHHHHcCCCCCCCCh
Q 033107 46 RRQMMLSQILSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVPL 96 (127)
Q Consensus 46 ~r~~iL~qiLt~eAreRL~rI~lVKPE~A~~VE~~Liqlaq~Gql~~kI~e 96 (127)
.+...+.++..+-..=.++.|+-.=+=-...||..|+.|+..|.|.++|+.
T Consensus 10 ~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~ 60 (88)
T smart00753 10 IRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQ 60 (88)
T ss_pred HHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcC
Confidence 344455555554433333333221111123599999999999999999873
No 9
>KOG1672 consensus ATP binding protein [Posttranslational modification, protein turnover, chaperones; Energy production and conversion]
Probab=60.94 E-value=7.7 Score=31.91 Aligned_cols=19 Identities=32% Similarity=0.705 Sum_probs=17.5
Q ss_pred CCchHHHHHHHHHHHHHHH
Q 033107 1 MADPELEAIRQRRMQELMA 19 (127)
Q Consensus 1 M~D~ELeaIR~rRl~ELq~ 19 (127)
|++++|+-+|++||++|..
T Consensus 34 ~d~~dle~lr~qRl~~lkk 52 (211)
T KOG1672|consen 34 MDEDDLEVLREQRLEQLKK 52 (211)
T ss_pred CCchhHHHhHHHHHHHHHH
Confidence 7889999999999999975
No 10
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=56.49 E-value=5.6 Score=26.22 Aligned_cols=22 Identities=27% Similarity=0.347 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHcCCCCCCCCh
Q 033107 75 RGVEDIILRSAQMGQIVEKVPL 96 (127)
Q Consensus 75 ~~VE~~Liqlaq~Gql~~kI~e 96 (127)
..||..|+.|+..|.|.++||.
T Consensus 75 ~~vE~~l~~~I~~~~i~~~ID~ 96 (105)
T PF01399_consen 75 EEVESILIDLISNGLIKAKIDQ 96 (105)
T ss_dssp HHHHHHHHHHHHTTSSEEEEET
T ss_pred HHHHHHHHHHHHCCCEEEEEEC
Confidence 8999999999999999999875
No 11
>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=54.89 E-value=8.6 Score=30.72 Aligned_cols=34 Identities=18% Similarity=0.301 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHcCCCCCCCChHHHHHHHHHhhhhhcCCeeEeecccch
Q 033107 76 GVEDIILRSAQMGQIVEKVPLCLLRTQCWMDAQIISQNIVYLSDNEIR 123 (127)
Q Consensus 76 ~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~~q~~~~~i~~~~~~~~~ 123 (127)
.|-+.|-.|-..|.|+|-|||. |+..|||++|+.
T Consensus 129 ~~i~ri~~L~~~g~ltGv~Ddr--------------GkfIyIs~eE~~ 162 (188)
T PF09756_consen 129 DVINRIQELEAEGRLTGVIDDR--------------GKFIYISEEEME 162 (188)
T ss_dssp HHHHHHHHHHHHSSS-EEE-TT----------------EEE-------
T ss_pred HHHHHHHHHHHCCCceeeEcCC--------------CCeEEecHHHHH
Confidence 4568888888999999977663 889999988864
No 12
>PF02114 Phosducin: Phosducin; InterPro: IPR024253 The outer and inner segments of vertebrate rod photoreceptor cells contain phosducin, a soluble phosphoprotein that complexes with the beta/gamma-subunits of the GTP-binding protein, transducin. Light-induced changes in cyclic nucleotide levels modulate the phosphorylation of phosducin by protein kinase A []. The protein is thought to participate in the regulation of visual phototransduction or in the integration of photo-receptor metabolism. Similar proteins have been isolated from the pineal gland and it is believed that the functional role of the protein is the same in both retina and pineal gland []. This entry represents a domain found in members of the phosducin family. This domain has a thioredoxin-like fold [].; PDB: 2DBC_A 1A0R_P 1B9Y_C 1B9X_C 2TRC_P 3EVI_B.
Probab=48.97 E-value=15 Score=30.37 Aligned_cols=19 Identities=42% Similarity=0.536 Sum_probs=15.2
Q ss_pred chHHHHHHHHHHHHHHHHc
Q 033107 3 DPELEAIRQRRMQELMAQQ 21 (127)
Q Consensus 3 D~ELeaIR~rRl~ELq~q~ 21 (127)
|+-|+..|++||+||+++.
T Consensus 100 eefL~~yR~qRm~El~~~~ 118 (265)
T PF02114_consen 100 EEFLEQYREQRMQELKQKL 118 (265)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3468999999999998543
No 13
>PHA01632 hypothetical protein
Probab=48.51 E-value=31 Score=23.43 Aligned_cols=35 Identities=23% Similarity=0.032 Sum_probs=27.4
Q ss_pred CCCCCCChHHHHHHHHHh-----hhhhcCCeeEeecccch
Q 033107 89 QIVEKVPLCLLRTQCWMD-----AQIISQNIVYLSDNEIR 123 (127)
Q Consensus 89 ql~~kI~e~~Lk~iL~~~-----~q~~~~~i~~~~~~~~~ 123 (127)
+++.+-|+++|+..|.++ +=...|+|+.+..+|.-
T Consensus 23 qvp~kpteeelrkvlpkilkdyanmie~gk~ki~ds~ewg 62 (64)
T PHA01632 23 QVPQKPTEEELRKVLPKILKDYANMIENGKIKILDSKEWG 62 (64)
T ss_pred hcCCCCCHHHHHHHHHHHHHHHHHHHhcCceEEecccccc
Confidence 678899999999999866 33345899999887753
No 14
>PF13932 GIDA_assoc_3: GidA associated domain 3; PDB: 3CES_C 3CP2_A 3G05_A 3CP8_A 2ZXI_B 2ZXH_A.
Probab=47.45 E-value=16 Score=24.70 Aligned_cols=35 Identities=34% Similarity=0.454 Sum_probs=24.5
Q ss_pred CCHHHHHHhchhhccCchhHHHHHHHHHHHHHcCCCCCCCChHHHHHHH
Q 033107 55 LSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVPLCLLRTQC 103 (127)
Q Consensus 55 Lt~eAreRL~rI~lVKPE~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL 103 (127)
|+.|++++|+++ ||. .+++..+|.| ||-..+..||
T Consensus 37 LS~E~~ekL~~~---rP~----------Ti~~A~rI~G-vtPa~i~~Ll 71 (72)
T PF13932_consen 37 LSNEAREKLEKI---RPR----------TIGQASRIPG-VTPAAISLLL 71 (72)
T ss_dssp --CHHHHHHHHH-----S----------CHHHHTTSTT-S-HHHHHHHH
T ss_pred cHHHHHHHHHhc---CCC----------CHHHHHhCCC-CCHHHHHHHh
Confidence 789999999885 565 3567889998 8888888776
No 15
>PF10587 EF-1_beta_acid: Eukaryotic elongation factor 1 beta central acidic region; InterPro: IPR018940 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This region is found in the centre of the beta subunits of Elongation factor-1. More information about these proteins can be found at Protein of the Month: Elongation Factors [].
Probab=43.11 E-value=28 Score=20.25 Aligned_cols=17 Identities=41% Similarity=0.577 Sum_probs=14.0
Q ss_pred chHHHHHHHHHHHHHHH
Q 033107 3 DPELEAIRQRRMQELMA 19 (127)
Q Consensus 3 D~ELeaIR~rRl~ELq~ 19 (127)
|+|-+.||+.|+++...
T Consensus 10 d~ea~r~reeRla~y~a 26 (28)
T PF10587_consen 10 DEEAERIREERLAAYAA 26 (28)
T ss_pred cHHHHHHHHHHHHHHHc
Confidence 67888999999998753
No 16
>TIGR02574 stabl_TIGR02574 putative addiction module component, TIGR02574 family. Members of this family are bacterial proteins, typically are about 75 amino acids long, always found as part of a pair (at least) of two small genes. The other in the pair always belongs to a subfamily of the larger family pfam05016 (although not necessarily scoring above the designated cutoff), which contains plasmid stabilization proteins. It is likely that this protein and its pfam05016 member partner comprise some form of addiction module, although these gene pairs usually are found on the bacterial main chromosome.
Probab=40.13 E-value=49 Score=21.46 Aligned_cols=56 Identities=20% Similarity=-0.050 Sum_probs=43.9
Q ss_pred hccCchhHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHhhhhhcCCeeEeecccch
Q 033107 67 ALVKPEKARGVEDIILRSAQMGQIVEKVPLCLLRTQCWMDAQIISQNIVYLSDNEIR 123 (127)
Q Consensus 67 ~lVKPE~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~~q~~~~~i~~~~~~~~~ 123 (127)
+|.-+||+..||..+-.+.. ..-...+++....++-..+....+|+++|++-.++.
T Consensus 2 ~L~~~ERl~Lve~LwdSL~~-~~~~~~~~~~~~~el~~R~~~~~~g~~~~i~~eev~ 57 (63)
T TIGR02574 2 ALSPDERIQLVEDIWDSIAA-EAKHLILTEAQKAELDRRLADYKADPSKASPWEEVR 57 (63)
T ss_pred CCCHHHHHHHHHHHHHHhcc-CcccCCCCHHHHHHHHHHHHHHHcCCcCCCCHHHHH
Confidence 45668999999998887774 233445778888888889999999999999877764
No 17
>PF09720 Unstab_antitox: Putative addiction module component; InterPro: IPR013406 This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilisation proteins (IPR007712 from INTERPRO). It is likely that this protein and its partner comprise some form of addiction module - a pair of genes consisting of a stable toxin and an unstable antitoxin which mediate programmed cell death [] - although these gene pairs are usually found on the bacterial main chromosome.
Probab=37.97 E-value=54 Score=20.33 Aligned_cols=52 Identities=15% Similarity=-0.024 Sum_probs=42.5
Q ss_pred ccCchhHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHhhhhhcCCeeEeecccc
Q 033107 68 LVKPEKARGVEDIILRSAQMGQIVEKVPLCLLRTQCWMDAQIISQNIVYLSDNEI 122 (127)
Q Consensus 68 lVKPE~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~~q~~~~~i~~~~~~~~ 122 (127)
|--.||+..||..+-.+... ...+++.-..++-..+....+|+..+++-+++
T Consensus 2 L~~~er~~L~e~L~~sl~~~---~~~~~~~w~~el~rR~~~~~~G~~~~i~~eev 53 (54)
T PF09720_consen 2 LPPEERAELAEELWDSLDDP---DSEVEAWWKEELERRLAEYESGKVQGIPWEEV 53 (54)
T ss_pred cCHHHHHHHHHHHHHHhccc---cccCcHHHHHHHHHHHHHHHcCCCCCCcHHHh
Confidence 34468889999988888775 23789999999999999999999999987664
No 18
>cd00390 Urease_gamma Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of external and internally-generated urea as a nitrogen source. The enzyme consists of three subunits, alpha, beta and gamma, which can exist as separate proteins or can be fused on a single protein chain. The alpha-beta-gamma heterotrimer forms multimers, mainly trimers. The large alpha subunit is the catalytic domain containing an active site with a bi-nickel center complexed by a carbamylated lysine. The beta and gamma subunits play a role in subunit association to form the higher order trimers.
Probab=36.96 E-value=92 Score=22.79 Aligned_cols=44 Identities=34% Similarity=0.345 Sum_probs=35.6
Q ss_pred HHHHHhch-hhccCchhHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHh
Q 033107 58 EARERLAR-IALVKPEKARGVEDIILRSAQMGQIVEKVPLCLLRTQCWMD 106 (127)
Q Consensus 58 eAreRL~r-I~lVKPE~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~ 106 (127)
=|+.|++| ++|-.||-..-|=++++-.|..|+ |=++|.++-..+
T Consensus 16 lA~~R~~rGlkLN~pEAvAlIs~~v~E~aRdG~-----svaelm~~g~~~ 60 (96)
T cd00390 16 LARKRLARGLKLNYPEAVALIADEILEGARDGK-----SVAELMSLGKTV 60 (96)
T ss_pred HHHHHHHcCcccCcHHHHHHHHHHHHHHhhcCC-----CHHHHHHHHhhh
Confidence 36777775 999999999999999999999997 666676665543
No 19
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=36.09 E-value=48 Score=19.68 Aligned_cols=23 Identities=4% Similarity=-0.257 Sum_probs=20.3
Q ss_pred CChHHHHHHHHHhhhhhcCCeeE
Q 033107 94 VPLCLLRTQCWMDAQIISQNIVY 116 (127)
Q Consensus 94 I~e~~Lk~iL~~~~q~~~~~i~~ 116 (127)
+|++++..|+...-..++|.|.|
T Consensus 22 ~s~~e~~~l~~~~D~~~~G~I~~ 44 (54)
T PF13833_consen 22 LSEEEVDRLFREFDTDGDGYISF 44 (54)
T ss_dssp SCHHHHHHHHHHHTTSSSSSEEH
T ss_pred CCHHHHHHHHHhcccCCCCCCCH
Confidence 89999999999888888888876
No 20
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=35.58 E-value=32 Score=23.59 Aligned_cols=26 Identities=8% Similarity=-0.121 Sum_probs=16.8
Q ss_pred CCCCChHHHHHHHHHhhhhhcCCeeE
Q 033107 91 VEKVPLCLLRTQCWMDAQIISQNIVY 116 (127)
Q Consensus 91 ~~kI~e~~Lk~iL~~~~q~~~~~i~~ 116 (127)
..++|++++.+++..+-..++|.|.|
T Consensus 45 g~k~t~~ev~~m~~~~D~d~dG~Idf 70 (88)
T cd05029 45 GSKLQDAEIAKLMEDLDRNKDQEVNF 70 (88)
T ss_pred CCCCCHHHHHHHHHHhcCCCCCCCcH
Confidence 35567777777776666566666665
No 21
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=35.48 E-value=28 Score=20.91 Aligned_cols=19 Identities=26% Similarity=0.043 Sum_probs=16.4
Q ss_pred cCCCCCCCChHHHHHHHHH
Q 033107 87 MGQIVEKVPLCLLRTQCWM 105 (127)
Q Consensus 87 ~Gql~~kI~e~~Lk~iL~~ 105 (127)
.|+=.||+|.++|+.+++.
T Consensus 7 ~g~~~GP~s~~el~~l~~~ 25 (45)
T PF14237_consen 7 NGQQQGPFSLEELRQLISS 25 (45)
T ss_pred CCeEECCcCHHHHHHHHHc
Confidence 6777899999999999874
No 22
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=33.48 E-value=33 Score=24.90 Aligned_cols=32 Identities=6% Similarity=-0.098 Sum_probs=22.5
Q ss_pred CCCCCChHHHHHHHHHhhhhhcCCeeEeecccchh
Q 033107 90 IVEKVPLCLLRTQCWMDAQIISQNIVYLSDNEIRI 124 (127)
Q Consensus 90 l~~kI~e~~Lk~iL~~~~q~~~~~i~~~~~~~~~~ 124 (127)
|+..+||+++.++...+...+...+ ++.+|+.
T Consensus 32 L~r~Ltd~ev~~Va~~L~~~~~~~~---~~~dI~~ 63 (96)
T PF11829_consen 32 LRRRLTDDEVAEVAAELAARGDPPV---DRIDIGV 63 (96)
T ss_dssp HTTTS-HHHHHHHHHHHHHHTSS-B---SCCHHHH
T ss_pred hcccCCHHHHHHHHHHHHhcCCCCC---CHHHHHH
Confidence 3466999999999999988777655 5556554
No 23
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=33.38 E-value=1.9e+02 Score=20.94 Aligned_cols=57 Identities=11% Similarity=0.010 Sum_probs=41.7
Q ss_pred HHHHHHHHHHh-CCHHHHHHhchhhccCchhHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHhhhh
Q 033107 44 DERRQMMLSQI-LSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVPLCLLRTQCWMDAQI 109 (127)
Q Consensus 44 ee~r~~iL~qi-Lt~eAreRL~rI~lVKPE~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~~q~ 109 (127)
.+.++.++... |++.....|.||--.-||-+++|= - .++.++||++|.+||.-+.+.
T Consensus 53 ~elve~L~~~~~l~e~~a~~I~nL~P~~~dElrai~---~------~~~~~~~~e~l~~ILd~l~k~ 110 (112)
T PRK14981 53 EELVEELLELEKMKEKTAVKIADILPETRDELRAIF---A------KERYTLSPEELDEILDIVKKY 110 (112)
T ss_pred HHHHHHHHHccCCCHHHHHHHHhcCCCCHHHHHHHH---H------HhccCCCHHHHHHHHHHHHHh
Confidence 45566677766 599999999998766666666543 2 345689999999999877654
No 24
>PRK01294 lipase chaperone; Provisional
Probab=32.14 E-value=3.2e+02 Score=23.42 Aligned_cols=63 Identities=16% Similarity=0.151 Sum_probs=47.5
Q ss_pred HHHHHHHHHHhCCHHHHHHhchhhccCchhHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHhh
Q 033107 44 DERRQMMLSQILSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVPLCLLRTQCWMDA 107 (127)
Q Consensus 44 ee~r~~iL~qiLt~eAreRL~rI~lVKPE~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~~ 107 (127)
.+.+..+..+.+.|||-+||..+---+-..-..|.+|+-+-.+--. ..-+|+++-..-+..+-
T Consensus 250 ~~~~~~~r~~~vG~EaA~RL~~Ld~qr~~wq~r~~~Y~~~R~~I~~-~~~ls~~~k~~aI~~LR 312 (336)
T PRK01294 250 PQELRLMRAQLVGPEAAQRLEQLDQQRAAWQQRYDDYLAQRAQILN-AAGLSPQDRQAQIAQLR 312 (336)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-cCCCCHHHHHHHHHHHH
Confidence 3455678899999999999999998888888999999987655321 24477777666666553
No 25
>PF05871 ESCRT-II: ESCRT-II complex subunit; InterPro: IPR008570 This entry represents the vps25 subunit (vacuolar protein sorting-associated protein 25) of the endosome-associated complex ESCRT-II (Endosomal Sorting Complexes Required for Transport protein II). ESCRT (ESCRT-I, -II, -III) complexes orchestrate efficient sorting of ubiquitinated transmembrane receptors to lysosomes via multivesicular bodies (MVBs) []. ESCRT-II recruits the transport machinery for protein sorting at MVB []. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. ESCRT-II transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo []. ESCRT-II is a trilobal complex composed of two copies of vps25, one copy of vps22 and the C-terminal region of vps36. The crystal structure of vps25 revealed two winged-helix domains, the N-terminal domain of vps25 interacting with vps22 and vps35 [].; PDB: 1W7P_B 1U5T_D 1XB4_D 3HTU_E 3CUQ_C 2ZME_D.
Probab=31.40 E-value=42 Score=25.49 Aligned_cols=61 Identities=16% Similarity=0.156 Sum_probs=36.7
Q ss_pred hCCHHHHHHhchhhccCchhHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHhhhhhcCCeeEeecccchh
Q 033107 54 ILSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVPLCLLRTQCWMDAQIISQNIVYLSDNEIRI 124 (127)
Q Consensus 54 iLt~eAreRL~rI~lVKPE~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~~q~~~~~i~~~~~~~~~~ 124 (127)
||+=-...|+..|.+ .++.+ --+...-.|..+++.+.++.||..+.++ |++.+++++.-+.
T Consensus 29 Il~y~~~~k~~~l~~-----~e~~~---~~lF~N~~I~R~L~~e~~~~Il~~Lv~~--g~aew~~~~~~~~ 89 (139)
T PF05871_consen 29 ILDYCRHHKIFRLSL-----SEALE---SPLFNNESINRRLSPEFIREILDELVQK--GNAEWIDKSKTRC 89 (139)
T ss_dssp HHHHHHHTT-SEEEC-----HHHHC---CCTTEETTTTEE--HHHHHHHHHHHHCT--TSEEECSTTSCEE
T ss_pred HHHHHHHhceeeeec-----ccccC---CCCccCccccCCCCHHHHHHHHHHHHhc--CCeEEeeCCCCEE
Confidence 444445555555552 22222 1233455799999999999999999887 5888885544333
No 26
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=31.18 E-value=35 Score=21.15 Aligned_cols=16 Identities=50% Similarity=0.630 Sum_probs=12.0
Q ss_pred CHHHHHHhchhhccCchhHH
Q 033107 56 STEARERLARIALVKPEKAR 75 (127)
Q Consensus 56 t~eAreRL~rI~lVKPE~A~ 75 (127)
|+||.++|.+| |-+.+
T Consensus 2 ~~eA~~~L~~i----P~fvR 17 (45)
T PF08369_consen 2 TDEAEARLDRI----PFFVR 17 (45)
T ss_dssp -HHHHHHHCTS-----HHHH
T ss_pred CHHHHHHHHHC----CHHHH
Confidence 78999999998 76665
No 27
>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=30.78 E-value=1e+02 Score=19.27 Aligned_cols=32 Identities=9% Similarity=0.074 Sum_probs=25.2
Q ss_pred hHHHHHHHHHHHHHcCCCC--CCC-ChHHHHHHHH
Q 033107 73 KARGVEDIILRSAQMGQIV--EKV-PLCLLRTQCW 104 (127)
Q Consensus 73 ~A~~VE~~Liqlaq~Gql~--~kI-~e~~Lk~iL~ 104 (127)
++++|-+.|.....+|.+. .++ |+.+|-+.+.
T Consensus 1 l~~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~ 35 (64)
T PF00392_consen 1 LYEQIYDQLRQAILSGRLPPGDRLPSERELAERYG 35 (64)
T ss_dssp HHHHHHHHHHHHHHTTSS-TTSBE--HHHHHHHHT
T ss_pred CHHHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhc
Confidence 4678999999999999998 688 8888877664
No 28
>PF03280 Lipase_chap: Proteobacterial lipase chaperone protein; InterPro: IPR004961 The proteobacterial lipase chaperone is a lipase helper protein which may be involved in the folding of extracellular lipase during its passage through the periplasm [].; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016020 membrane; PDB: 2ES4_E.
Probab=28.64 E-value=2.3e+02 Score=22.04 Aligned_cols=61 Identities=13% Similarity=0.107 Sum_probs=43.7
Q ss_pred HHHHHHHHHHhCCHHHHHHhchhhccCchhHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHh
Q 033107 44 DERRQMMLSQILSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVPLCLLRTQCWMD 106 (127)
Q Consensus 44 ee~r~~iL~qiLt~eAreRL~rI~lVKPE~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~ 106 (127)
++.+..+..+.+.|+|-+||..+---+-..-..|..|+....+-- ..-+|+++-..-+..+
T Consensus 124 ~~~~~~~r~~~vg~eaA~RL~~ld~~~~~w~~r~~~Y~~~r~~I~--~~~ls~~~kq~~i~~L 184 (195)
T PF03280_consen 124 EQELRAARAQLVGPEAAQRLAQLDQQRAQWQQRLDSYLQERDQIL--NSGLSEEEKQQQIAQL 184 (195)
T ss_dssp HHHHHHHHHCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--TT---CCHHHHHHHHH
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCCHHHHHHHHHHH
Confidence 455677888999999999999999988899999999999887744 4455655555444443
No 29
>PF15248 DUF4587: Domain of unknown function (DUF4587)
Probab=27.00 E-value=31 Score=24.23 Aligned_cols=18 Identities=44% Similarity=0.512 Sum_probs=15.6
Q ss_pred hHHHHHHHHHHHHHcCCC
Q 033107 73 KARGVEDIILRSAQMGQI 90 (127)
Q Consensus 73 ~A~~VE~~Liqlaq~Gql 90 (127)
|.+.||-+++|-||+-||
T Consensus 6 KEDmvElMlmQNAQMHQi 23 (76)
T PF15248_consen 6 KEDMVELMLMQNAQMHQI 23 (76)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 568899999999998775
No 30
>PF08708 PriCT_1: Primase C terminal 1 (PriCT-1); InterPro: IPR014820 This alpha helical domain is found at the C-terminal of primases.
Probab=26.67 E-value=1.6e+02 Score=18.78 Aligned_cols=36 Identities=8% Similarity=-0.042 Sum_probs=27.2
Q ss_pred hhHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHhhhh
Q 033107 72 EKARGVEDIILRSAQMGQIVEKVPLCLLRTQCWMDAQI 109 (127)
Q Consensus 72 E~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~~q~ 109 (127)
..-+.|...+...-+. ...|+++++++.+..++++.
T Consensus 33 ~~~~~v~~~~~~~N~~--~~~PL~~~Ev~~i~kSi~k~ 68 (71)
T PF08708_consen 33 QFRQEVLSLAQAINSN--FSPPLPESEVKAIAKSIAKW 68 (71)
T ss_pred HHHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHHHHh
Confidence 4455566666666665 59999999999999988764
No 31
>PRK13242 ureA urease subunit gamma; Provisional
Probab=26.32 E-value=88 Score=23.09 Aligned_cols=35 Identities=29% Similarity=0.389 Sum_probs=29.9
Q ss_pred CCHHHHHHhch-hhccCchhHHHHHHHHHHHHHcCC
Q 033107 55 LSTEARERLAR-IALVKPEKARGVEDIILRSAQMGQ 89 (127)
Q Consensus 55 Lt~eAreRL~r-I~lVKPE~A~~VE~~Liqlaq~Gq 89 (127)
.-.=|+.|++| ++|-.||-..-|-++++-.|..|.
T Consensus 16 a~~lA~~R~~rGlkLN~pEAvAlIs~~i~E~aRdG~ 51 (100)
T PRK13242 16 LSDVALKRKNKGLKLNHPEAVAVLSAYVLDGAREGK 51 (100)
T ss_pred HHHHHHHHHHcCcccCcHHHHHHHHHHHHHHhhcCC
Confidence 33447888876 999999999999999999999994
No 32
>TIGR00193 urease_gam urease, gamma subunit. Nomenclature for the various subunits of urease in Helicobacter differs from nomenclature in most other species.
Probab=25.07 E-value=97 Score=22.93 Aligned_cols=36 Identities=28% Similarity=0.350 Sum_probs=30.3
Q ss_pred hCCHHHHHHhch-hhccCchhHHHHHHHHHHHHHcCC
Q 033107 54 ILSTEARERLAR-IALVKPEKARGVEDIILRSAQMGQ 89 (127)
Q Consensus 54 iLt~eAreRL~r-I~lVKPE~A~~VE~~Liqlaq~Gq 89 (127)
..-.=|+.|++| |+|-.||-..-|-++++-.|..|.
T Consensus 15 ~a~~lA~rR~~rGlkLN~pEAvAlIs~~v~E~aRdG~ 51 (102)
T TIGR00193 15 YAGELAKKRKARGVKLNYPEAVAYISAHIMEGARDGK 51 (102)
T ss_pred HHHHHHHHHHHcCcccCcHHHHHHHHHHHHHHhhcCC
Confidence 334457888876 999999999999999999999994
No 33
>PRK13241 ureA urease subunit gamma; Provisional
Probab=24.76 E-value=99 Score=22.80 Aligned_cols=45 Identities=27% Similarity=0.292 Sum_probs=35.3
Q ss_pred CHHHHHHhch-hhccCchhHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHH
Q 033107 56 STEARERLAR-IALVKPEKARGVEDIILRSAQMGQIVEKVPLCLLRTQCWM 105 (127)
Q Consensus 56 t~eAreRL~r-I~lVKPE~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~ 105 (127)
-.=|+.|++| |+|-.||-..-|-++++-.|..|. |=++|.+.-..
T Consensus 17 ~~lA~~R~~rGlkLN~pEAvAlI~~~v~E~aRdG~-----svaelm~~g~~ 62 (100)
T PRK13241 17 ALLAERRKARGLKLNYPEAVALISDALLEGARDGK-----TVAELMSYGRT 62 (100)
T ss_pred HHHHHHHHHcCcccCcHHHHHHHHHHHHHHhhCCC-----CHHHHHHHhhh
Confidence 3447888876 999999999999999999999994 44556555443
No 34
>PF11964 SpoIIAA-like: SpoIIAA-like; InterPro: IPR021866 This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 120 to 132 amino acids in length. This protein has a single completely conserved residue A that may be functionally important. ; PDB: 2Q3L_B 2OOK_A 3BL4_A.
Probab=24.18 E-value=50 Score=22.06 Aligned_cols=30 Identities=17% Similarity=0.049 Sum_probs=21.0
Q ss_pred CCCCCChHHHHHHHHHhhhhh--cCCeeEeec
Q 033107 90 IVEKVPLCLLRTQCWMDAQII--SQNIVYLSD 119 (127)
Q Consensus 90 l~~kI~e~~Lk~iL~~~~q~~--~~~i~~~~~ 119 (127)
+.|++|.+++++++..+.+.. .++|.++-|
T Consensus 7 ~~g~~t~ed~~~~~~~~~~~~~~~~~~~ll~d 38 (109)
T PF11964_consen 7 VSGKLTEEDYKELLPALEELIADHGKIRLLVD 38 (109)
T ss_dssp EEEEE-HHHHHHHHHHHHHHHTTSSSEEEEEE
T ss_pred EeeeeCHHHHHHHHHHHHHHHhcCCceEEEEE
Confidence 357888999999888665553 467887766
No 35
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=23.96 E-value=71 Score=24.69 Aligned_cols=31 Identities=3% Similarity=-0.125 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHcCCCCCCCChHHHHHHHH
Q 033107 74 ARGVEDIILRSAQMGQIVEKVPLCLLRTQCW 104 (127)
Q Consensus 74 A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~ 104 (127)
+..|...|-.++....-..|+||++|.++|.
T Consensus 102 ~~~ik~~i~~lI~~Ed~~~PlSD~~i~~~L~ 132 (160)
T PF04552_consen 102 SEAIKARIKELIEEEDKKKPLSDQEIAELLK 132 (160)
T ss_dssp -TTH-HHHHHHHTTS-TTS---HHHHHHHHT
T ss_pred HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHH
Confidence 5678888999999998889999999999996
No 36
>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]
Probab=23.30 E-value=70 Score=24.71 Aligned_cols=23 Identities=9% Similarity=-0.126 Sum_probs=18.5
Q ss_pred CCCCCCChHHHHHHHHHhhhhhc
Q 033107 89 QIVEKVPLCLLRTQCWMDAQIIS 111 (127)
Q Consensus 89 ql~~kI~e~~Lk~iL~~~~q~~~ 111 (127)
-|.+||+|++|-.||..++..++
T Consensus 110 SL~nkidD~~le~iL~dls~lr~ 132 (134)
T KOG2351|consen 110 SLENKIDDDELEQILKDLSTLRT 132 (134)
T ss_pred ccccccCHHHHHHHHHHHHHHHh
Confidence 35678999999999998876653
No 37
>PF14493 HTH_40: Helix-turn-helix domain
Probab=22.87 E-value=1.4e+02 Score=20.18 Aligned_cols=55 Identities=13% Similarity=0.054 Sum_probs=36.4
Q ss_pred HHHhCCHHHHHHhchhhccCchhHHHHHHHHHHHHHcCC-CC--CCCChHHHHHHHHHhhhhhc
Q 033107 51 LSQILSTEARERLARIALVKPEKARGVEDIILRSAQMGQ-IV--EKVPLCLLRTQCWMDAQIIS 111 (127)
Q Consensus 51 L~qiLt~eAreRL~rI~lVKPE~A~~VE~~Liqlaq~Gq-l~--~kI~e~~Lk~iL~~~~q~~~ 111 (127)
+.+=+|.+.-+..-++ +..-|.++|+..+..|. +. .-++++.+..|...+.+.++
T Consensus 10 ~~~G~si~eIA~~R~L------~~sTI~~HL~~~~~~g~~~~~~~~l~~e~~~~I~~~~~~~~~ 67 (91)
T PF14493_consen 10 FQKGLSIEEIAKIRGL------KESTIYGHLAELIESGEPLDIEELLSEEEIKQIEDAIEKLGS 67 (91)
T ss_pred HHcCCCHHHHHHHcCC------CHHHHHHHHHHHHHhCCCCCHHHhCCHHHHHHHHHHHHHcCc
Confidence 3344455544443333 34679999999999998 43 55888888888886655444
No 38
>cd05026 S-100Z S-100Z: S-100Z domain found in proteins similar to S100Z. S100Z is a member of the S100 domain family within the EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100Z group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately.S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control. S100Z is normally expressed in various tissues, with its highest level of expression being in spleen and leukocytes. The function of S100Z remains unclear. Preliminary structural data suggests that S100Z is homodimer, however a heterodimer with S100P has been reported. S100Z is capable of binding calcium ions. When calcium binds to S110Z, the protein experiences a conformational change, which exposes hydrophobic surfac
Probab=22.76 E-value=64 Score=22.00 Aligned_cols=30 Identities=10% Similarity=-0.109 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHcCCCCCCCChHHHHHHHHHhh
Q 033107 76 GVEDIILRSAQMGQIVEKVPLCLLRTQCWMDA 107 (127)
Q Consensus 76 ~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~~ 107 (127)
.|+.++-.+=..| .|.||-+++..++..++
T Consensus 54 ~v~~i~~elD~n~--dG~Idf~EF~~l~~~l~ 83 (93)
T cd05026 54 LVDKIMNDLDSNK--DNEVDFNEFVVLVAALT 83 (93)
T ss_pred HHHHHHHHhCCCC--CCCCCHHHHHHHHHHHH
Confidence 4444444432222 36666666666666553
No 39
>COG1610 Uncharacterized conserved protein [Function unknown]
Probab=22.45 E-value=73 Score=24.97 Aligned_cols=61 Identities=10% Similarity=0.078 Sum_probs=39.9
Q ss_pred HHHhCCHHHHHHhchhhccCchhHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHhhhhhcCCeeEeecc
Q 033107 51 LSQILSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVPLCLLRTQCWMDAQIISQNIVYLSDN 120 (127)
Q Consensus 51 L~qiLt~eAreRL~rI~lVKPE~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~~q~~~~~i~~~~~~ 120 (127)
|+..|-.--..|++.|+|+.-- |-+--=.++ ..++||+++..+|.+.-+++..+|.-.+++
T Consensus 11 lK~AMkakDk~r~~tiRli~AA--------ik~~ei~~r-k~~l~d~~il~vl~k~iKQRrdS~~~y~~a 71 (148)
T COG1610 11 LKEAMKAKDKDRLGTIRLILAA--------IKQEEIDER-KDELDDEEILKVLAKEIKQRRDSAEEYEKA 71 (148)
T ss_pred HHHHHHhhhhhhHHHHHHHHHH--------HHHHHHHcc-CCCCChHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 3444444556788888887532 222222223 466999999999999988888777655543
No 40
>cd03312 CIMS_N_terminal_like CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers the N-terminal barrel, and a few single-barrel sequences most similar to the N-terminal barrel. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Side chains fro
Probab=22.29 E-value=1.5e+02 Score=25.27 Aligned_cols=45 Identities=11% Similarity=-0.019 Sum_probs=34.3
Q ss_pred chhHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHH-----hhhhhcCCeeEeecccchh
Q 033107 71 PEKARGVEDIILRSAQMGQIVEKVPLCLLRTQCWM-----DAQIISQNIVYLSDNEIRI 124 (127)
Q Consensus 71 PE~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~-----~~q~~~~~i~~~~~~~~~~ 124 (127)
+|.-+++|.+= .|++|.++|.+.... +..+..-.|.|++|++.+.
T Consensus 14 reLk~a~e~~~---------~g~i~~~~L~~~~~~~~~~~~~~Q~~~Gl~~it~Gef~~ 63 (360)
T cd03312 14 RELKKALESYW---------KGKISEEELLATAKELRLRHWKLQKEAGIDLIPVGDFSL 63 (360)
T ss_pred HHHHHHHHHHH---------cCCCCHHHHHHHHHHHHHHHHHHHHHcCCCEeccCCchh
Confidence 45566677665 578999999988773 3666777899999999864
No 41
>PF13767 DUF4168: Domain of unknown function (DUF4168)
Probab=21.82 E-value=2.5e+02 Score=18.58 Aligned_cols=64 Identities=28% Similarity=0.334 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHhchhhccCchhHHHH
Q 033107 5 ELEAIRQRRMQELMAQQGVGSQQNSEQHQKAQEDAKREADERRQMMLSQILSTEARERLARIALVKPEKARGV 77 (127)
Q Consensus 5 ELeaIR~rRl~ELq~q~~~~~~~~~ee~~q~qee~~~~~ee~r~~iL~qiLt~eAreRL~rI~lVKPE~A~~V 77 (127)
+++.||+.-..+|+.... +.+ .++-......++...+=..-||++-..++..-.=..|++...|
T Consensus 15 ~ie~ir~~~~~~l~~~~~------~~~---~~~l~~~a~~~~~~~I~~~GLtv~~fN~I~~~~q~Dp~L~~rI 78 (78)
T PF13767_consen 15 EIEPIRQEYQQELQAAED------PEE---IQELQEEAQEEMVEAIEENGLTVERFNEITQAAQSDPELRQRI 78 (78)
T ss_pred HHHHHHHHHHHHHHHccC------HHH---HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCHHHHhcC
Confidence 568899998899886322 111 2222333345566667788899999999998888888877653
No 42
>COG1390 NtpE Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion]
Probab=21.41 E-value=4.2e+02 Score=21.01 Aligned_cols=70 Identities=19% Similarity=0.175 Sum_probs=34.3
Q ss_pred HHHHHHHHHHhCCHHHHHHhchhhccCchhHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHhhhhhc--CCeeEeec
Q 033107 44 DERRQMMLSQILSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVPLCLLRTQCWMDAQIIS--QNIVYLSD 119 (127)
Q Consensus 44 ee~r~~iL~qiLt~eAreRL~rI~lVKPE~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~~q~~~--~~i~~~~~ 119 (127)
+..++.+++..+-...+.+|+...=+=-....+++..|-.++.... ...|..+|.....+.. ..|+|++.
T Consensus 57 ~~~~~~iis~A~le~r~~~Le~~ee~l~~~~~~~~e~L~~i~~~~~------~~~l~~ll~~~~~~~~~~~~iV~~~e 128 (194)
T COG1390 57 ERERQRIISSALLEARRKLLEAKEEILESVFEAVEEKLRNIASDPE------YESLQELLIEALEKLLGGELVVYLNE 128 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcCCcc------hHHHHHHHHHHHHhcCCCCeEEEeCc
Confidence 3334555555555555566655432222233444444443333332 2236667776655544 36666654
No 43
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=21.10 E-value=1.6e+02 Score=28.61 Aligned_cols=54 Identities=15% Similarity=0.031 Sum_probs=34.1
Q ss_pred cCchhHHHHHHHHHHHHHcCCC------------CCCCChHHHHHHHHHhh------hhhcCCeeEeecccc
Q 033107 69 VKPEKARGVEDIILRSAQMGQI------------VEKVPLCLLRTQCWMDA------QIISQNIVYLSDNEI 122 (127)
Q Consensus 69 VKPE~A~~VE~~Liqlaq~Gql------------~~kI~e~~Lk~iL~~~~------q~~~~~i~~~~~~~~ 122 (127)
+||||-.-+...+-.|=..-.. ..-+|+++|+.||=... =--.|+|+|+||+--
T Consensus 54 RK~DK~tVLr~aV~~lr~~k~~~~~~~~~~~d~KpSflS~~eL~~LmLeAlDGF~fvV~cdG~IvyVSeSVT 125 (803)
T KOG3561|consen 54 RKPDKLTVLRMAVDHLRLIKEQESENSSIDQDYKPSFLSNDELTHLILEALDGFLFVVNCDGRIVYVSESVT 125 (803)
T ss_pred cCchHHHHHHHHHHHHHHHhhhhcccccccccccccccchHHHHHHHHHHhcCeEEEEecCceEEEEecchH
Confidence 6999988777665544332221 13367799999876331 111299999999843
No 44
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=21.09 E-value=73 Score=28.75 Aligned_cols=24 Identities=29% Similarity=0.428 Sum_probs=20.4
Q ss_pred hhHHHHHHHHHHHHHcCCCCCCCC
Q 033107 72 EKARGVEDIILRSAQMGQIVEKVP 95 (127)
Q Consensus 72 E~A~~VE~~Liqlaq~Gql~~kI~ 95 (127)
--+..||.+|+||.+.|++...|+
T Consensus 330 a~~qevek~Ilqmie~~~i~a~iN 353 (422)
T KOG2582|consen 330 ASAQEVEKYILQMIEDGEIFASIN 353 (422)
T ss_pred cchHHHHHHHHHHhccCceEEEec
Confidence 346789999999999999987665
No 45
>TIGR00136 gidA glucose-inhibited division protein A. GidA, the longer of two forms of GidA-related proteins, appears to be present in all complete eubacterial genomes so far, as well as Saccharomyces cerevisiae. A subset of these organisms have a closely related protein. GidA is absent in the Archaea. It appears to act with MnmE, in an alpha2/beta2 heterotetramer, in the 5-carboxymethylaminomethyl modification of uridine 34 in certain tRNAs. The shorter, related protein, previously called gid or gidA(S), is now called TrmFO (see model TIGR00137).
Probab=20.73 E-value=94 Score=29.12 Aligned_cols=41 Identities=27% Similarity=0.267 Sum_probs=34.2
Q ss_pred hCCHHHHHHhchhhccCchhHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHhhh
Q 033107 54 ILSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVPLCLLRTQCWMDAQ 108 (127)
Q Consensus 54 iLt~eAreRL~rI~lVKPE~A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~~q 108 (127)
=|+.|++++|+++ ||. .++|.++|.| ||-..+.-||..+.+
T Consensus 575 ~ls~E~~ekL~~~---rP~----------tlgqA~ri~G-vtpa~i~~l~~~l~k 615 (617)
T TIGR00136 575 GLSTEAREKLSKF---RPL----------SIGQASRISG-ITPADISILLVYLKK 615 (617)
T ss_pred chhHHHHHHHhhc---CCC----------CHHHHhcCCC-CCHHHHHHHHHHhcc
Confidence 3789999999875 675 4678889999 999999999988754
No 46
>COG2517 Predicted RNA-binding protein containing a C-terminal EMAP domain [General function prediction only]
Probab=20.33 E-value=1.7e+02 Score=24.22 Aligned_cols=47 Identities=13% Similarity=0.065 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHhhhhhcC-CeeEeeccc
Q 033107 74 ARGVEDIILRSAQMGQIVEKVPLCLLRTQCWMDAQIISQ-NIVYLSDNE 121 (127)
Q Consensus 74 A~~VE~~Liqlaq~Gql~~kI~e~~Lk~iL~~~~q~~~~-~i~~~~~~~ 121 (127)
|..--+.+++.+++|+.+| .+-..+++.|.++...--. .-.||+..|
T Consensus 13 AeK~Ve~~~r~~es~~~~G-~~rk~~ie~lksi~s~lQ~lrY~Yl~pee 60 (219)
T COG2517 13 AEKAVELFIRTIESGGFRG-WDRKRAIEALKSIESELQALRYSYLEPEE 60 (219)
T ss_pred hHHHHHHHHHHHhhcCccc-ccHHHHHHHHHHHHHHHHhheeeccCHHH
Confidence 3333456889999999999 9999999999988665543 666776554
No 47
>PF06375 BLVR: Bovine leukaemia virus receptor (BLVR); InterPro: IPR010474 Bovine leukemia virus (BLV) is one of the most common infectious cattle viruses, with between 30 and 40% of cows in the United States being infected. It is closely related to the human T-cell leukaemia virus type 1 (HTLV-1) and has highly conserved envelope glycoprotein functional domains []. BLV is an oncogenic C-type retrovirus, which results in the animals developing a malignant lymphoma. BLV, like the human and simian T cell leukaemia viruses, is a deltaretrovirus. 182 residues at the amino-terminal of the BLV envelope glycoprotein surface unit encompass the receptor-binding domain. The metabolic activity in B cells, T cells, and thymocytes is indicated by the expression of the BLV-binding receptor []. A candidate gene of the receptor (BLVR) is related, but unique, to a gene family of the delta subunit of the adaptor protein (AP) complex 3, AP-3 []. The AP-3 complex is not clathrin-associated but is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. ; PDB: 4AFI_B.
Probab=20.26 E-value=34 Score=26.69 Aligned_cols=19 Identities=32% Similarity=0.312 Sum_probs=0.0
Q ss_pred CCchHHHHHHHHHHHHHHH
Q 033107 1 MADPELEAIRQRRMQELMA 19 (127)
Q Consensus 1 M~D~ELeaIR~rRl~ELq~ 19 (127)
|+.+||+..|++|++|-..
T Consensus 1 ~~eEEl~rrReaR~~Eq~N 19 (154)
T PF06375_consen 1 QDEEELERRREARKAEQEN 19 (154)
T ss_dssp -------------------
T ss_pred CCHHHHHHHHHHHHHHHHc
Confidence 6778999999999998764
No 48
>PF00547 Urease_gamma: Urease, gamma subunit enzyme!; InterPro: IPR002026 Urease 3.5.1.5 from EC is a nickel-binding enzyme that catalyzes the hydrolysis of urea to carbon dioxide and ammonia []: Urea + H2O = CO2 + 2 NH3 Historically, it was the first enzyme to be crystallized (in 1926). It is mainly found in plantseeds and microorganisms. In plants, urease is a hexamer of identical chains. In bacteria [], it consists of either two or three different subunits (alpha IPR005847 from INTERPRO, beta IPR002019 from INTERPRO and gamma, described in this entry). The structure of the urease complex is known []. This subunit does not appear to take part in the catalytic mechanism.; GO: 0009039 urease activity, 0016151 nickel ion binding, 0006807 nitrogen compound metabolic process; PDB: 3QGA_G 3QGK_M 1E9Y_A 1E9Z_A 1FWF_A 1A5L_A 1EJW_A 1EJR_A 1FWH_A 1EJS_A ....
Probab=20.02 E-value=1.1e+02 Score=22.53 Aligned_cols=33 Identities=36% Similarity=0.480 Sum_probs=26.1
Q ss_pred HHHHHHhch-hhccCchhHHHHHHHHHHHHHcCC
Q 033107 57 TEARERLAR-IALVKPEKARGVEDIILRSAQMGQ 89 (127)
Q Consensus 57 ~eAreRL~r-I~lVKPE~A~~VE~~Liqlaq~Gq 89 (127)
.=|+.|++| ++|-.||-..-|-+.++-.|..|+
T Consensus 18 ~lA~~R~~rGlkLN~pEAvAlI~~~v~E~aRdG~ 51 (99)
T PF00547_consen 18 ELAQRRLARGLKLNYPEAVALISDEVLEGARDGK 51 (99)
T ss_dssp HHHHHHHHTT--B-HHHHHHHHHHHHHHHHHHTS
T ss_pred HHHHHHHHhccccCcHHHHHHHHHHHHHHhhCCC
Confidence 347778876 999999999999999999999994
Done!