Query 033016
Match_columns 129
No_of_seqs 104 out of 317
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 08:46:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033016.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033016hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2118 DNA-binding protein [G 100.0 6.7E-41 1.5E-45 245.5 13.5 116 1-121 1-116 (116)
2 KOG3431 Apoptosis-related prot 100.0 6.7E-41 1.5E-45 248.3 12.8 123 2-128 1-124 (129)
3 PRK04239 hypothetical protein; 100.0 1E-39 2.3E-44 238.2 12.8 110 4-121 1-110 (110)
4 PF01984 dsDNA_bind: Double-st 100.0 3.4E-38 7.3E-43 228.7 3.6 107 9-120 1-107 (107)
5 cd02987 Phd_like_Phd Phosducin 85.4 0.74 1.6E-05 35.3 2.6 17 5-21 39-55 (175)
6 cd02988 Phd_like_VIAF Phosduci 73.1 3.3 7.2E-05 32.3 2.7 17 5-21 60-76 (192)
7 smart00753 PAM PCI/PINT associ 66.4 6.9 0.00015 25.8 2.8 50 46-95 10-59 (88)
8 smart00088 PINT motif in prote 66.4 6.9 0.00015 25.8 2.8 50 46-95 10-59 (88)
9 PF01399 PCI: PCI domain; Int 61.1 5.4 0.00012 26.4 1.5 22 75-96 75-96 (105)
10 KOG1672 ATP binding protein [P 52.5 13 0.00029 30.3 2.6 19 1-19 34-52 (211)
11 cd00390 Urease_gamma Urease ga 46.2 62 0.0013 23.4 5.0 45 58-107 16-61 (96)
12 PF02114 Phosducin: Phosducin; 43.0 22 0.00047 29.4 2.5 18 4-21 101-118 (265)
13 PRK14981 DNA-directed RNA poly 40.4 1.4E+02 0.003 21.5 6.2 56 44-108 53-109 (112)
14 PF15248 DUF4587: Domain of un 39.4 14 0.00031 25.6 0.8 18 73-90 6-23 (76)
15 PRK01294 lipase chaperone; Pro 39.2 2.4E+02 0.0051 24.2 8.3 64 44-108 250-313 (336)
16 PF14237 DUF4339: Domain of un 35.7 28 0.0006 20.8 1.6 19 87-105 7-25 (45)
17 PF03280 Lipase_chap: Proteoba 35.3 1.5E+02 0.0033 23.0 6.1 62 44-107 124-185 (195)
18 PF06628 Catalase-rel: Catalas 35.0 66 0.0014 21.0 3.5 13 51-63 16-28 (68)
19 PF00392 GntR: Bacterial regul 33.9 99 0.0021 19.3 4.1 31 73-103 1-34 (64)
20 PRK13242 ureA urease subunit g 33.7 59 0.0013 23.7 3.3 35 55-89 16-51 (100)
21 TIGR00193 urease_gam urease, g 32.2 66 0.0014 23.5 3.3 36 54-89 15-51 (102)
22 PRK13241 ureA urease subunit g 31.5 69 0.0015 23.4 3.3 46 56-106 17-63 (100)
23 PF09682 Holin_LLH: Phage holi 31.0 1.1E+02 0.0023 21.7 4.3 48 58-107 54-101 (108)
24 PF10587 EF-1_beta_acid: Eukar 30.0 62 0.0013 18.5 2.3 17 3-19 10-26 (28)
25 PF08369 PCP_red: Proto-chloro 28.9 40 0.00086 20.7 1.5 16 56-75 2-17 (45)
26 PF13767 DUF4168: Domain of un 27.9 1.8E+02 0.004 19.1 7.1 64 5-77 15-78 (78)
27 COG0831 UreA Urea amidohydrola 26.2 92 0.002 22.7 3.2 41 50-90 11-52 (100)
28 PF02697 DUF217: Uncharacteriz 25.7 1.5E+02 0.0032 20.0 3.9 54 55-108 6-62 (71)
29 PF00547 Urease_gamma: Urease, 25.3 80 0.0017 23.0 2.7 44 57-105 18-62 (99)
30 KOG2351 RNA polymerase II, fou 24.6 66 0.0014 24.6 2.3 20 89-108 110-129 (134)
31 PF04552 Sigma54_DBD: Sigma-54 23.1 78 0.0017 24.3 2.5 32 74-105 102-133 (160)
32 PF10256 Erf4: Golgin subfamil 22.3 74 0.0016 22.4 2.1 22 88-109 24-45 (118)
33 KOG4449 Translocase of outer m 20.7 69 0.0015 20.9 1.5 13 54-66 2-14 (53)
34 PRK13192 bifunctional urease s 20.5 1.3E+02 0.0027 24.7 3.3 35 55-89 16-51 (208)
No 1
>COG2118 DNA-binding protein [General function prediction only]
Probab=100.00 E-value=6.7e-41 Score=245.47 Aligned_cols=116 Identities=44% Similarity=0.683 Sum_probs=102.5
Q ss_pred CCchHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhhhccCchhHHHHHHH
Q 033016 1 MADPELEAIRQRRMQELMAQQGVGSQQNSEQHQKAQEDAKREADERRQMMLSQILSTEARERLARIALVKPEKARGVEDI 80 (129)
Q Consensus 1 m~d~eLe~IR~~rl~ELq~~~~~~~~~~~~~~~~~qee~~~~~ee~k~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~ 80 (129)
|+|+||++||++||+|||++++.. .+...++++++.+.+++|++||++||||+||+||+||+||+||+|++||+|
T Consensus 1 mdd~eLEeIRrrkl~eLQrq~~~~-----~~~~~q~eq~r~~~eaqkqaiLrqiLtpeAreRL~~irLvRPe~AeavE~q 75 (116)
T COG2118 1 MDDEELEEIRRRKLAELQRQAKLE-----EQREAQEEQARQEEEAQKQAILRQILTPEARERLARVRLVRPELAEAVENQ 75 (116)
T ss_pred CChHHHHHHHHHHHHHHHHhhhhH-----HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHhhhcCHHHHHHHHHH
Confidence 788899999999999999977311 121234455556668999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCccCCHHHHHHHHHHhhhhccccceeEEeee
Q 033016 81 ILRSAQMGQIVEKVSEERLISLLEQINTQTTKQTKVTIQRR 121 (129)
Q Consensus 81 Liqlaq~G~l~~kitd~~L~~iL~~i~~~~~k~~~I~~~Rr 121 (129)
||+||++|+|++||||++||+||++|+++++++++|+|+||
T Consensus 76 Li~LaqtGri~~~I~e~~lk~IL~~i~~~~rre~kI~~~rk 116 (116)
T COG2118 76 LIQLAQTGRITHKIDEEELKEILERISPQTRREFKIRRRRK 116 (116)
T ss_pred HHHHHHcCCCCCCCCHHHHHHHHHHHhHHhccchheecccC
Confidence 99999999999999999999999999998888999999876
No 2
>KOG3431 consensus Apoptosis-related protein/predicted DNA-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=6.7e-41 Score=248.32 Aligned_cols=123 Identities=50% Similarity=0.741 Sum_probs=105.9
Q ss_pred CchHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhhhccCchhHHHHHHHH
Q 033016 2 ADPELEAIRQRRMQELMAQQGVGSQQNSEQHQKAQEDAKREADERRQMMLSQILSTEARERLARIALVKPEKARGVEDII 81 (129)
Q Consensus 2 ~d~eLe~IR~~rl~ELq~~~~~~~~~~~~~~~~~qee~~~~~ee~k~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~L 81 (129)
+|+||++||++||++|++.+|++++...+ ++..++. +.+++|++||+|||++.||+||+||+|||||||.+||+||
T Consensus 1 ~D~eL~AiR~qRlaqlqa~~G~~~~~~~q---~a~q~~~-~q~e~r~~~lsQvLdqqAr~RLsrlAlvkpekAq~VE~~l 76 (129)
T KOG3431|consen 1 MDPELQAIRAQRLAQLQANSGGANDAAQQ---QANQEQQ-EQEEMRQSMLSQVLDQQARERLSRLALVKPEKAQAVENYL 76 (129)
T ss_pred CchHHHHHHHHHHHHhhhhcCCCcccccc---chhhhhh-hHHHHHHhHHHHHhhHHHHHHHHhhhhcCHHHHHHHHHHH
Confidence 58899999999999999999865543221 1122222 3789999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCccCCHHHHHHHHHHhhhhc-cccceeEEeeeCCcCCCC
Q 033016 82 LRSAQMGQIVEKVSEERLISLLEQINTQT-TKQTKVTIQRRRSVLEDD 128 (129)
Q Consensus 82 iqlaq~G~l~~kitd~~L~~iL~~i~~~~-~k~~~I~~~Rr~~~~DdD 128 (129)
|+||++|+|++||||++||.||++|+.++ .+.|+|+|.||+...|||
T Consensus 77 irma~~gQvs~Kise~~lisiLe~is~Qt~qk~tkV~f~RRr~~~Ddd 124 (129)
T KOG3431|consen 77 IRMAQTGQVSHKISEAELISILEKISAQTNQKNTKVKFDRRRFNDDDD 124 (129)
T ss_pred HHHHHhCCccccccHHHHHHHHHHHHHhhccccceeeeeccccccCcc
Confidence 99999999999999999999999999998 678999999998544444
No 3
>PRK04239 hypothetical protein; Provisional
Probab=100.00 E-value=1e-39 Score=238.22 Aligned_cols=110 Identities=45% Similarity=0.648 Sum_probs=94.6
Q ss_pred hHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhhhccCchhHHHHHHHHHH
Q 033016 4 PELEAIRQRRMQELMAQQGVGSQQNSEQHQKAQEDAKREADERRQMMLSQILSTEARERLARIALVKPEKARGVEDIILR 83 (129)
Q Consensus 4 ~eLe~IR~~rl~ELq~~~~~~~~~~~~~~~~~qee~~~~~ee~k~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~Liq 83 (129)
+||++||++||+|||+++|+++++ .+++++++++.++++++||++||||+||+||+||+|||||+|++||+|||+
T Consensus 1 ~ELe~IR~~rl~eLq~q~~~~~~~-----~~~~~~~~~~~e~qk~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~liq 75 (110)
T PRK04239 1 EELEEIRRRKLEELQKQAQEQQQA-----QEEQEEAQAQAEAQKQAILRQILTPEARERLNRIKLVKPEFAEQVEQQLIQ 75 (110)
T ss_pred ChHHHHHHHHHHHHHHHhccCCcc-----hhhHHHHHHHHHHHHHHHHHHHCCHHHHHHHHhhhhcCHHHHHHHHHHHHH
Confidence 489999999999999888743221 233456667789999999999999999999999999999999999999999
Q ss_pred HHhcCCCCccCCHHHHHHHHHHhhhhccccceeEEeee
Q 033016 84 SAQMGQIVEKVSEERLISLLEQINTQTTKQTKVTIQRR 121 (129)
Q Consensus 84 laq~G~l~~kitd~~L~~iL~~i~~~~~k~~~I~~~Rr 121 (129)
|||+|+|++||||++||+||++|+++ ++ .++|+||
T Consensus 76 lAq~G~i~~ki~e~~L~~lL~~v~~~-kr--e~~I~r~ 110 (110)
T PRK04239 76 LAQSGRIQGPIDDEQLKEILEQLTPQ-KR--EFKITRR 110 (110)
T ss_pred HHHcCCCCCCcCHHHHHHHHHHHhhc-cc--CcCcccC
Confidence 99999999999999999999999975 44 4445554
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=3.4e-38 Score=228.74 Aligned_cols=107 Identities=50% Similarity=0.750 Sum_probs=86.3
Q ss_pred HHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhhhccCchhHHHHHHHHHHHHhcC
Q 033016 9 IRQRRMQELMAQQGVGSQQNSEQHQKAQEDAKREADERRQMMLSQILSTEARERLARIALVKPEKARGVEDIILRSAQMG 88 (129)
Q Consensus 9 IR~~rl~ELq~~~~~~~~~~~~~~~~~qee~~~~~ee~k~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~Liqlaq~G 88 (129)
||++||+|||++.++++.. ..++++++++.++++++||++||||+||+||+||+|||||+|.+||+|||+||++|
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 8999999999887622211 23345566777999999999999999999999999999999999999999999999
Q ss_pred CCCccCCHHHHHHHHHHhhhhccccceeEEee
Q 033016 89 QIVEKVSEERLISLLEQINTQTTKQTKVTIQR 120 (129)
Q Consensus 89 ~l~~kitd~~L~~iL~~i~~~~~k~~~I~~~R 120 (129)
+|++||||++||+||++|+..++++++|+|+|
T Consensus 76 ~l~~kI~d~~L~~iL~~i~~~~~~~~~I~~~R 107 (107)
T PF01984_consen 76 QLRGKIDDEQLKEILEQISEQKQKETKIKIKR 107 (107)
T ss_dssp SSSS-B-HHHHHHHHHHHCCC-SS-SS-S---
T ss_pred CCCCCcCHHHHHHHHHHHhhcccCCCeeeeeC
Confidence 99999999999999999998877779999987
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=85.43 E-value=0.74 Score=35.34 Aligned_cols=17 Identities=41% Similarity=0.548 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHh
Q 033016 5 ELEAIRQRRMQELMAQQ 21 (129)
Q Consensus 5 eLe~IR~~rl~ELq~~~ 21 (129)
+|+.+|++||+||++..
T Consensus 39 ~l~~~R~~R~~el~~~~ 55 (175)
T cd02987 39 FLQQYREQRMQEMHAKL 55 (175)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 89999999999999764
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=73.09 E-value=3.3 Score=32.34 Aligned_cols=17 Identities=35% Similarity=0.487 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHh
Q 033016 5 ELEAIRQRRMQELMAQQ 21 (129)
Q Consensus 5 eLe~IR~~rl~ELq~~~ 21 (129)
.|+.+|++||+||++..
T Consensus 60 ~Le~yR~kRl~el~~~~ 76 (192)
T cd02988 60 FLEEYRRKRLAEMKALA 76 (192)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 69999999999999643
No 7
>smart00753 PAM PCI/PINT associated module.
Probab=66.45 E-value=6.9 Score=25.81 Aligned_cols=50 Identities=20% Similarity=0.211 Sum_probs=30.1
Q ss_pred HHHHHHHHhCCHHHHHHHhhhhccCchhHHHHHHHHHHHHhcCCCCccCC
Q 033016 46 RRQMMLSQILSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVS 95 (129)
Q Consensus 46 ~k~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~Liqlaq~G~l~~kit 95 (129)
.+...+.++..+-..=.++.|+-.=+=-...||..|+.|+..|.|.++|+
T Consensus 10 ~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID 59 (88)
T smart00753 10 IRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKID 59 (88)
T ss_pred HHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEc
Confidence 34445555555443333333332211112369999999999999999986
No 8
>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=66.45 E-value=6.9 Score=25.81 Aligned_cols=50 Identities=20% Similarity=0.211 Sum_probs=30.1
Q ss_pred HHHHHHHHhCCHHHHHHHhhhhccCchhHHHHHHHHHHHHhcCCCCccCC
Q 033016 46 RRQMMLSQILSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVS 95 (129)
Q Consensus 46 ~k~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~Liqlaq~G~l~~kit 95 (129)
.+...+.++..+-..=.++.|+-.=+=-...||..|+.|+..|.|.++|+
T Consensus 10 ~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID 59 (88)
T smart00088 10 IRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKID 59 (88)
T ss_pred HHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEc
Confidence 34445555555443333333332211112369999999999999999986
No 9
>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=61.12 E-value=5.4 Score=26.37 Aligned_cols=22 Identities=27% Similarity=0.415 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHhcCCCCccCCH
Q 033016 75 RGVEDIILRSAQMGQIVEKVSE 96 (129)
Q Consensus 75 ~~VE~~Liqlaq~G~l~~kitd 96 (129)
..||..|+.|+..|.|.++|+.
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 8999999999999999999874
No 10
>KOG1672 consensus ATP binding protein [Posttranslational modification, protein turnover, chaperones; Energy production and conversion]
Probab=52.47 E-value=13 Score=30.30 Aligned_cols=19 Identities=32% Similarity=0.705 Sum_probs=17.4
Q ss_pred CCchHHHHHHHHHHHHHHH
Q 033016 1 MADPELEAIRQRRMQELMA 19 (129)
Q Consensus 1 m~d~eLe~IR~~rl~ELq~ 19 (129)
|++++|+-+|.+||++|..
T Consensus 34 ~d~~dle~lr~qRl~~lkk 52 (211)
T KOG1672|consen 34 MDEDDLEVLREQRLEQLKK 52 (211)
T ss_pred CCchhHHHhHHHHHHHHHH
Confidence 7789999999999999985
No 11
>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=46.16 E-value=62 Score=23.42 Aligned_cols=45 Identities=40% Similarity=0.464 Sum_probs=36.7
Q ss_pred HHHHHHhh-hhccCchhHHHHHHHHHHHHhcCCCCccCCHHHHHHHHHHhh
Q 033016 58 EARERLAR-IALVKPEKARGVEDIILRSAQMGQIVEKVSEERLISLLEQIN 107 (129)
Q Consensus 58 eAreRL~r-I~lvkPe~A~~VE~~Liqlaq~G~l~~kitd~~L~~iL~~i~ 107 (129)
=|+.|++| |+|-.||-...|=++++-.|..|+ |=++|.++-..+=
T Consensus 16 lA~~R~~rGlkLN~pEAvAlIs~~v~E~aRdG~-----svaelm~~g~~~L 61 (96)
T cd00390 16 LARKRLARGLKLNYPEAVALIADEILEGARDGK-----SVAELMSLGKTVL 61 (96)
T ss_pred HHHHHHHcCcccCcHHHHHHHHHHHHHHhhcCC-----CHHHHHHHHhhhC
Confidence 36777775 999999999999999999999997 6667776665554
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=43.00 E-value=22 Score=29.40 Aligned_cols=18 Identities=44% Similarity=0.516 Sum_probs=15.2
Q ss_pred hHHHHHHHHHHHHHHHHh
Q 033016 4 PELEAIRQRRMQELMAQQ 21 (129)
Q Consensus 4 ~eLe~IR~~rl~ELq~~~ 21 (129)
+-|+..|++||+||+++.
T Consensus 101 efL~~yR~qRm~El~~~~ 118 (265)
T PF02114_consen 101 EFLEQYREQRMQELKQKL 118 (265)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 468999999999998654
No 13
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=40.44 E-value=1.4e+02 Score=21.50 Aligned_cols=56 Identities=16% Similarity=0.219 Sum_probs=40.1
Q ss_pred HHHHHHHHHHh-CCHHHHHHHhhhhccCchhHHHHHHHHHHHHhcCCCCccCCHHHHHHHHHHhhh
Q 033016 44 DERRQMMLSQI-LSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVSEERLISLLEQINT 108 (129)
Q Consensus 44 ee~k~~iL~qi-Lt~eAreRL~rI~lvkPe~A~~VE~~Liqlaq~G~l~~kitd~~L~~iL~~i~~ 108 (129)
.+.++.++... |++.....|.||--.-+|-++.| +- .+...+||++|.+||+-|+.
T Consensus 53 ~elve~L~~~~~l~e~~a~~I~nL~P~~~dElrai---~~------~~~~~~~~e~l~~ILd~l~k 109 (112)
T PRK14981 53 EELVEELLELEKMKEKTAVKIADILPETRDELRAI---FA------KERYTLSPEELDEILDIVKK 109 (112)
T ss_pred HHHHHHHHHccCCCHHHHHHHHhcCCCCHHHHHHH---HH------HhccCCCHHHHHHHHHHHHH
Confidence 34555666666 58888888988876665555554 32 33568999999999998864
No 14
>PF15248 DUF4587: Domain of unknown function (DUF4587)
Probab=39.37 E-value=14 Score=25.59 Aligned_cols=18 Identities=44% Similarity=0.512 Sum_probs=15.7
Q ss_pred hHHHHHHHHHHHHhcCCC
Q 033016 73 KARGVEDIILRSAQMGQI 90 (129)
Q Consensus 73 ~A~~VE~~Liqlaq~G~l 90 (129)
|...||-+|+|.||+-||
T Consensus 6 KEDmvElMlmQNAQMHQi 23 (76)
T PF15248_consen 6 KEDMVELMLMQNAQMHQI 23 (76)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 567899999999998876
No 15
>PRK01294 lipase chaperone; Provisional
Probab=39.19 E-value=2.4e+02 Score=24.16 Aligned_cols=64 Identities=17% Similarity=0.251 Sum_probs=49.8
Q ss_pred HHHHHHHHHHhCCHHHHHHHhhhhccCchhHHHHHHHHHHHHhcCCCCccCCHHHHHHHHHHhhh
Q 033016 44 DERRQMMLSQILSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVSEERLISLLEQINT 108 (129)
Q Consensus 44 ee~k~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~Liqlaq~G~l~~kitd~~L~~iL~~i~~ 108 (129)
.+....+..+.+.|||-+||..+.--+-..-..|..|+-+-.+-- =..-+|+++-..-|.++-.
T Consensus 250 ~~~~~~~r~~~vG~EaA~RL~~Ld~qr~~wq~r~~~Y~~~R~~I~-~~~~ls~~~k~~aI~~LR~ 313 (336)
T PRK01294 250 PQELRLMRAQLVGPEAAQRLEQLDQQRAAWQQRYDDYLAQRAQIL-NAAGLSPQDRQAQIAQLRQ 313 (336)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCCCHHHHHHHHHHHHH
Confidence 344667889999999999999999999999999999997766422 1256777777777777754
No 16
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=35.68 E-value=28 Score=20.78 Aligned_cols=19 Identities=32% Similarity=0.261 Sum_probs=16.4
Q ss_pred cCCCCccCCHHHHHHHHHH
Q 033016 87 MGQIVEKVSEERLISLLEQ 105 (129)
Q Consensus 87 ~G~l~~kitd~~L~~iL~~ 105 (129)
.|+=.||+|.++|+.++..
T Consensus 7 ~g~~~GP~s~~el~~l~~~ 25 (45)
T PF14237_consen 7 NGQQQGPFSLEELRQLISS 25 (45)
T ss_pred CCeEECCcCHHHHHHHHHc
Confidence 5777899999999999875
No 17
>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=35.29 E-value=1.5e+02 Score=23.00 Aligned_cols=62 Identities=18% Similarity=0.259 Sum_probs=44.9
Q ss_pred HHHHHHHHHHhCCHHHHHHHhhhhccCchhHHHHHHHHHHHHhcCCCCccCCHHHHHHHHHHhh
Q 033016 44 DERRQMMLSQILSTEARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVSEERLISLLEQIN 107 (129)
Q Consensus 44 ee~k~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~Liqlaq~G~l~~kitd~~L~~iL~~i~ 107 (129)
++.+..+....+.|||-+||..+---+-..-..|..|+-...+-- ..-+|+++-..-|..+-
T Consensus 124 ~~~~~~~r~~~vg~eaA~RL~~ld~~~~~w~~r~~~Y~~~r~~I~--~~~ls~~~kq~~i~~Lr 185 (195)
T PF03280_consen 124 EQELRAARAQLVGPEAAQRLAQLDQQRAQWQQRLDSYLQERDQIL--NSGLSEEEKQQQIAQLR 185 (195)
T ss_dssp HHHHHHHHHCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--TT---CCHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCCHHHHHHHHHHHH
Confidence 445667888999999999999999999999999999998887643 45556555555555553
No 18
>PF06628 Catalase-rel: Catalase-related immune-responsive; InterPro: IPR010582 Catalases (1.11.1.6 from EC) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects []. Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (IPR000763 from INTERPRO) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (IPR007760 from INTERPRO) that are found in bacteria []. This entry represents a small conserved region within catalase enzymes that carries the immune-responsive amphipathic octa-peptide that is recognised by T cells [].; PDB: 2CAH_A 1NM0_A 1H7K_A 1E93_A 1H6N_A 3HB6_A 2CAG_A 1M85_A 1MQF_A 1A4E_C ....
Probab=34.96 E-value=66 Score=20.95 Aligned_cols=13 Identities=62% Similarity=0.859 Sum_probs=7.5
Q ss_pred HHHhCCHHHHHHH
Q 033016 51 LSQILSTEARERL 63 (129)
Q Consensus 51 L~qiLt~eAreRL 63 (129)
|-.+|+++.++||
T Consensus 16 ly~~l~~~er~~l 28 (68)
T PF06628_consen 16 LYRVLSDEERERL 28 (68)
T ss_dssp HHHHSSHHHHHHH
T ss_pred HHHHCCHHHHHHH
Confidence 3336666666664
No 19
>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=33.93 E-value=99 Score=19.27 Aligned_cols=31 Identities=16% Similarity=0.236 Sum_probs=24.7
Q ss_pred hHHHHHHHHHHHHhcCCCC--ccC-CHHHHHHHH
Q 033016 73 KARGVEDIILRSAQMGQIV--EKV-SEERLISLL 103 (129)
Q Consensus 73 ~A~~VE~~Liqlaq~G~l~--~ki-td~~L~~iL 103 (129)
++++|-+.|.....+|.+. .++ |+.+|-+.+
T Consensus 1 l~~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~ 34 (64)
T PF00392_consen 1 LYEQIYDQLRQAILSGRLPPGDRLPSERELAERY 34 (64)
T ss_dssp HHHHHHHHHHHHHHTTSS-TTSBE--HHHHHHHH
T ss_pred CHHHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHh
Confidence 4678999999999999999 688 888887665
No 20
>PRK13242 ureA urease subunit gamma; Provisional
Probab=33.72 E-value=59 Score=23.71 Aligned_cols=35 Identities=29% Similarity=0.389 Sum_probs=30.0
Q ss_pred CCHHHHHHHhh-hhccCchhHHHHHHHHHHHHhcCC
Q 033016 55 LSTEARERLAR-IALVKPEKARGVEDIILRSAQMGQ 89 (129)
Q Consensus 55 Lt~eAreRL~r-I~lvkPe~A~~VE~~Liqlaq~G~ 89 (129)
.-.=|+.|++| |+|-.||-...|-++++-.|..|.
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 21
>TIGR00193 urease_gam urease, gamma subunit. Nomenclature for the various subunits of urease in Helicobacter differs from nomenclature in most other species.
Probab=32.20 E-value=66 Score=23.54 Aligned_cols=36 Identities=28% Similarity=0.350 Sum_probs=30.4
Q ss_pred hCCHHHHHHHhh-hhccCchhHHHHHHHHHHHHhcCC
Q 033016 54 ILSTEARERLAR-IALVKPEKARGVEDIILRSAQMGQ 89 (129)
Q Consensus 54 iLt~eAreRL~r-I~lvkPe~A~~VE~~Liqlaq~G~ 89 (129)
..-.=|+.|++| |+|-.||-...|-++++-.|..|.
T Consensus 15 ~a~~lA~rR~~rGlkLN~pEAvAlIs~~v~E~aRdG~ 51 (102)
T TIGR00193 15 YAGELAKKRKARGVKLNYPEAVAYISAHIMEGARDGK 51 (102)
T ss_pred HHHHHHHHHHHcCcccCcHHHHHHHHHHHHHHhhcCC
Confidence 334447888876 999999999999999999999994
No 22
>PRK13241 ureA urease subunit gamma; Provisional
Probab=31.50 E-value=69 Score=23.35 Aligned_cols=46 Identities=28% Similarity=0.360 Sum_probs=36.0
Q ss_pred CHHHHHHHhh-hhccCchhHHHHHHHHHHHHhcCCCCccCCHHHHHHHHHHh
Q 033016 56 STEARERLAR-IALVKPEKARGVEDIILRSAQMGQIVEKVSEERLISLLEQI 106 (129)
Q Consensus 56 t~eAreRL~r-I~lvkPe~A~~VE~~Liqlaq~G~l~~kitd~~L~~iL~~i 106 (129)
-.=|+.|++| |+|-.||-...|-++++-.|..|. |=++|.++-.++
T Consensus 17 ~~lA~~R~~rGlkLN~pEAvAlI~~~v~E~aRdG~-----svaelm~~g~~~ 63 (100)
T PRK13241 17 ALLAERRKARGLKLNYPEAVALISDALLEGARDGK-----TVAELMSYGRTV 63 (100)
T ss_pred HHHHHHHHHcCcccCcHHHHHHHHHHHHHHhhCCC-----CHHHHHHHhhhh
Confidence 3447888886 999999999999999999999994 445666555444
No 23
>PF09682 Holin_LLH: Phage holin protein (Holin_LLH); InterPro: IPR010026 This entry represents the Bacteriophage LL-H, Orf107, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=31.02 E-value=1.1e+02 Score=21.70 Aligned_cols=48 Identities=21% Similarity=0.191 Sum_probs=36.8
Q ss_pred HHHHHHhhhhccCchhHHHHHHHHHHHHhcCCCCccCCHHHHHHHHHHhh
Q 033016 58 EARERLARIALVKPEKARGVEDIILRSAQMGQIVEKVSEERLISLLEQIN 107 (129)
Q Consensus 58 eAreRL~rI~lvkPe~A~~VE~~Liqlaq~G~l~~kitd~~L~~iL~~i~ 107 (129)
.|-|-+..-..--+||-...=+++......-.| ++||++|..+.|..-
T Consensus 54 ~aveq~~~~~~~G~~K~~~A~~~v~~~L~~~gi--~~t~~~i~~~IEaAV 101 (108)
T PF09682_consen 54 NAVEQVAKEGGKGEEKKAEAVQYVKERLKKKGI--KVTDEQIEGAIEAAV 101 (108)
T ss_pred HHHHHHHhccCCcHHHHHHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHH
Confidence 344555555556788888888888888877777 999999999998754
No 24
>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=30.01 E-value=62 Score=18.53 Aligned_cols=17 Identities=41% Similarity=0.577 Sum_probs=13.6
Q ss_pred chHHHHHHHHHHHHHHH
Q 033016 3 DPELEAIRQRRMQELMA 19 (129)
Q Consensus 3 d~eLe~IR~~rl~ELq~ 19 (129)
|+|-+.||+.||++...
T Consensus 10 d~ea~r~reeRla~y~a 26 (28)
T PF10587_consen 10 DEEAERIREERLAAYAA 26 (28)
T ss_pred cHHHHHHHHHHHHHHHc
Confidence 56788899999988753
No 25
>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=28.94 E-value=40 Score=20.70 Aligned_cols=16 Identities=50% Similarity=0.630 Sum_probs=12.1
Q ss_pred CHHHHHHHhhhhccCchhHH
Q 033016 56 STEARERLARIALVKPEKAR 75 (129)
Q Consensus 56 t~eAreRL~rI~lvkPe~A~ 75 (129)
|+||..+|.+| |-+.+
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 26
>PF13767 DUF4168: Domain of unknown function (DUF4168)
Probab=27.91 E-value=1.8e+02 Score=19.14 Aligned_cols=64 Identities=28% Similarity=0.331 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhhhccCchhHHHH
Q 033016 5 ELEAIRQRRMQELMAQQGVGSQQNSEQHQKAQEDAKREADERRQMMLSQILSTEARERLARIALVKPEKARGV 77 (129)
Q Consensus 5 eLe~IR~~rl~ELq~~~~~~~~~~~~~~~~~qee~~~~~ee~k~~iL~qiLt~eAreRL~rI~lvkPe~A~~V 77 (129)
+++.||+.-..+|+.... +. ..++-......++...|=..-||++-...+....-..|++...|
T Consensus 15 ~ie~ir~~~~~~l~~~~~------~~---~~~~l~~~a~~~~~~~I~~~GLtv~~fN~I~~~~q~Dp~L~~rI 78 (78)
T PF13767_consen 15 EIEPIRQEYQQELQAAED------PE---EIQELQEEAQEEMVEAIEENGLTVERFNEITQAAQSDPELRQRI 78 (78)
T ss_pred HHHHHHHHHHHHHHHccC------HH---HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCHHHHhcC
Confidence 578899998899987322 11 22222233335556667788899999999999988888887654
No 27
>COG0831 UreA Urea amidohydrolase (urease) gamma subunit [Amino acid transport and metabolism]
Probab=26.16 E-value=92 Score=22.68 Aligned_cols=41 Identities=32% Similarity=0.369 Sum_probs=34.4
Q ss_pred HHHHhCCHHHHHHHhh-hhccCchhHHHHHHHHHHHHhcCCC
Q 033016 50 MLSQILSTEARERLAR-IALVKPEKARGVEDIILRSAQMGQI 90 (129)
Q Consensus 50 iL~qiLt~eAreRL~r-I~lvkPe~A~~VE~~Liqlaq~G~l 90 (129)
+|--.+..=|+.|++| ++|-.||-...|-.+|+--|.-|+-
T Consensus 11 Lli~~a~~lA~rR~~RGlKLNypEAvAlIs~~i~EgaRdGkt 52 (100)
T COG0831 11 LLIFTAAELARRRKARGLKLNYPEAVALISAFILEGARDGKT 52 (100)
T ss_pred HHHHHHHHHHHHHHhcCcccCcHHHHHHHHHHHHHhhhcCCc
Confidence 4555556678899887 9999999999999999999999854
No 28
>PF02697 DUF217: Uncharacterized ACR, COG1753; InterPro: IPR003847 This entry is represented by Natrialba phage PhiCh1, Orf96. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=25.71 E-value=1.5e+02 Score=20.01 Aligned_cols=54 Identities=19% Similarity=0.229 Sum_probs=31.2
Q ss_pred CCHHHHHHHhhhhccCchhHHHHHHHHH---HHHhcCCCCccCCHHHHHHHHHHhhh
Q 033016 55 LSTEARERLARIALVKPEKARGVEDIIL---RSAQMGQIVEKVSEERLISLLEQINT 108 (129)
Q Consensus 55 Lt~eAreRL~rI~lvkPe~A~~VE~~Li---qlaq~G~l~~kitd~~L~~iL~~i~~ 108 (129)
++.+|.+||..++--.--+-..|.-+|- ..----.+-|.++|++...+-+.+.+
T Consensus 6 IsdevY~rL~~~K~~~eSFSdvI~rli~~~~~~~~l~~~~g~l~deea~~~~~~i~e 62 (71)
T PF02697_consen 6 ISDEVYERLKKLKREDESFSDVIERLIEKEKKRRDLMDYFGILSDEEADEMEKDIKE 62 (71)
T ss_pred ecHHHHHHHHHHhcCCCCHHHHHHHHHhcccchhHHHHHhccCChhhHHHHHHHHHH
Confidence 7899999999999433334444444433 00000012366778877666666654
No 29
>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=25.29 E-value=80 Score=22.98 Aligned_cols=44 Identities=36% Similarity=0.431 Sum_probs=30.7
Q ss_pred HHHHHHHhh-hhccCchhHHHHHHHHHHHHhcCCCCccCCHHHHHHHHHH
Q 033016 57 TEARERLAR-IALVKPEKARGVEDIILRSAQMGQIVEKVSEERLISLLEQ 105 (129)
Q Consensus 57 ~eAreRL~r-I~lvkPe~A~~VE~~Liqlaq~G~l~~kitd~~L~~iL~~ 105 (129)
.=|+.|+.| ++|-.||-..-|-++++-.|..|+ |=.+|.+.-.+
T Consensus 18 ~lA~~R~~rGlkLN~pEAvAlI~~~v~E~aRdG~-----svaelm~~g~~ 62 (99)
T PF00547_consen 18 ELAQRRLARGLKLNYPEAVALISDEVLEGARDGK-----SVAELMSLGRT 62 (99)
T ss_dssp HHHHHHHHTT--B-HHHHHHHHHHHHHHHHHHTS------HHHHHHHGGG
T ss_pred HHHHHHHHhccccCcHHHHHHHHHHHHHHhhCCC-----cHHHHHHHHHh
Confidence 347788876 999999999999999999999994 34455544333
No 30
>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]
Probab=24.59 E-value=66 Score=24.58 Aligned_cols=20 Identities=20% Similarity=0.521 Sum_probs=17.4
Q ss_pred CCCccCCHHHHHHHHHHhhh
Q 033016 89 QIVEKVSEERLISLLEQINT 108 (129)
Q Consensus 89 ~l~~kitd~~L~~iL~~i~~ 108 (129)
.|.+||+|+.|-+||+.++.
T Consensus 110 SL~nkidD~~le~iL~dls~ 129 (134)
T KOG2351|consen 110 SLENKIDDDELEQILKDLST 129 (134)
T ss_pred ccccccCHHHHHHHHHHHHH
Confidence 45689999999999999974
No 31
>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=23.11 E-value=78 Score=24.33 Aligned_cols=32 Identities=13% Similarity=0.226 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHhcCCCCccCCHHHHHHHHHH
Q 033016 74 ARGVEDIILRSAQMGQIVEKVSEERLISLLEQ 105 (129)
Q Consensus 74 A~~VE~~Liqlaq~G~l~~kitd~~L~~iL~~ 105 (129)
+..|...|-.++....-..|+||++|.++|..
T Consensus 102 ~~~ik~~i~~lI~~Ed~~~PlSD~~i~~~L~~ 133 (160)
T PF04552_consen 102 SEAIKARIKELIEEEDKKKPLSDQEIAELLKE 133 (160)
T ss_dssp -TTH-HHHHHHHTTS-TTS---HHHHHHHHTT
T ss_pred HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHH
Confidence 46788899999999888899999999999963
No 32
>PF10256 Erf4: Golgin subfamily A member 7/ERF4 family; InterPro: IPR019383 Proteins in this entry include Golgin subfamily A member 7 and the Ras modification protein ERF4.
Probab=22.30 E-value=74 Score=22.43 Aligned_cols=22 Identities=23% Similarity=0.424 Sum_probs=19.3
Q ss_pred CCCCccCCHHHHHHHHHHhhhh
Q 033016 88 GQIVEKVSEERLISLLEQINTQ 109 (129)
Q Consensus 88 G~l~~kitd~~L~~iL~~i~~~ 109 (129)
|.|.+.||.+++.+++..|+.-
T Consensus 24 ~~L~~~is~~ef~~iI~~IN~~ 45 (118)
T PF10256_consen 24 GELSGYISPEEFEEIINTINQI 45 (118)
T ss_pred HhhcCCCCHHHHHHHHHHHHHH
Confidence 3488999999999999999965
No 33
>KOG4449 consensus Translocase of outer mitochondrial membrane complex, subunit TOM7 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.67 E-value=69 Score=20.86 Aligned_cols=13 Identities=46% Similarity=0.759 Sum_probs=10.4
Q ss_pred hCCHHHHHHHhhh
Q 033016 54 ILSTEARERLARI 66 (129)
Q Consensus 54 iLt~eAreRL~rI 66 (129)
.|++|+.+||..|
T Consensus 2 klS~esKerl~k~ 14 (53)
T KOG4449|consen 2 KLSEESKERLVKV 14 (53)
T ss_pred ccCHHHHHHHHHH
Confidence 4889999998754
No 34
>PRK13192 bifunctional urease subunit gamma/beta; Reviewed
Probab=20.52 E-value=1.3e+02 Score=24.66 Aligned_cols=35 Identities=34% Similarity=0.435 Sum_probs=30.1
Q ss_pred CCHHHHHHHhh-hhccCchhHHHHHHHHHHHHhcCC
Q 033016 55 LSTEARERLAR-IALVKPEKARGVEDIILRSAQMGQ 89 (129)
Q Consensus 55 Lt~eAreRL~r-I~lvkPe~A~~VE~~Liqlaq~G~ 89 (129)
.-.=|+.|++| |+|-.||-...|-++++-.|..|.
T Consensus 16 a~~lA~~R~~rGlkLN~pEAvAlI~~~v~E~aRdG~ 51 (208)
T PRK13192 16 AAELARKRRARGLKLNYPEAVALIADEVLEAARDGR 51 (208)
T ss_pred HHHHHHHHHHcCcccCcHHHHHHHHHHHHHHhhcCC
Confidence 33447888886 999999999999999999999994
Done!