Query 040162
Match_columns 395
No_of_seqs 158 out of 190
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 05:42:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040162.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040162hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14327 CSTF2_hinge: Hinge do 99.8 1.7E-21 3.8E-26 157.8 2.9 68 4-71 12-79 (84)
2 PF14304 CSTF_C: Transcription 99.4 6.2E-13 1.3E-17 99.1 4.3 36 360-395 7-42 (46)
3 KOG0108 mRNA cleavage and poly 98.9 9.8E-09 2.1E-13 105.1 11.2 73 6-78 126-200 (435)
4 PF14483 Cut8_M: Cut8 dimerisa 66.3 9.5 0.00021 27.7 3.5 35 10-47 2-36 (38)
5 PF14555 UBA_4: UBA-like domai 57.6 24 0.00052 25.3 4.4 31 25-55 2-33 (43)
6 KOG0132 RNA polymerase II C-te 54.2 4.1E+02 0.0089 31.0 18.5 118 149-287 618-737 (894)
7 PF14377 DUF4414: Domain of un 53.4 25 0.00054 29.9 4.5 38 354-391 8-66 (108)
8 PF07319 DnaI_N: Primosomal pr 47.6 41 0.0009 27.9 4.9 49 9-58 2-52 (94)
9 smart00727 STI1 Heat shock cha 46.7 23 0.00049 24.8 2.8 28 22-53 12-39 (41)
10 PF01434 Peptidase_M41: Peptid 38.0 27 0.00058 32.6 2.6 52 17-68 157-208 (213)
11 PF09030 Creb_binding: Creb bi 34.5 14 0.0003 32.5 0.2 39 18-56 51-90 (104)
12 PF11304 DUF3106: Protein of u 34.5 77 0.0017 27.2 4.6 34 354-387 40-86 (107)
13 PF08158 NUC130_3NT: NUC130/3N 33.1 60 0.0013 25.1 3.4 44 15-64 5-48 (52)
14 PF10044 Ret_tiss: Retinal tis 32.8 73 0.0016 27.5 4.2 34 13-46 53-87 (95)
15 PF03562 MltA: MltA specific i 31.6 23 0.0005 32.8 1.1 26 27-52 130-155 (158)
16 PF13919 ASXH: Asx homology do 29.5 45 0.00097 30.1 2.5 19 371-389 40-58 (138)
17 PF11304 DUF3106: Protein of u 28.0 1.4E+02 0.0029 25.7 5.1 19 375-393 56-74 (107)
18 KOG4402 Uncharacterized conser 27.8 1.8E+02 0.0038 27.0 6.0 43 13-67 93-136 (144)
19 PF08898 DUF1843: Domain of un 26.3 1.2E+02 0.0026 24.0 4.0 31 27-61 16-46 (53)
20 PRK10733 hflB ATP-dependent me 24.6 81 0.0018 34.4 3.8 59 17-75 536-594 (644)
21 COG3275 LytS Putative regulato 22.1 87 0.0019 34.4 3.4 37 11-47 364-400 (557)
No 1
>PF14327 CSTF2_hinge: Hinge domain of cleavage stimulation factor subunit 2; PDB: 4EBA_G.
Probab=99.83 E-value=1.7e-21 Score=157.77 Aligned_cols=68 Identities=50% Similarity=0.728 Sum_probs=56.3
Q ss_pred CCCCCCchhhhhcCCCHHHHHHHHHHHHHHHhhCHHHHHHHHHhCCchHHHHHHHHHHhcCCCCCCCC
Q 040162 4 KQVAGDGLPANLAGMSKNQLYEIMTQMKSLIEQNEQQARQILIQNPLLTKALFQAQIMLGMVKPPQVI 71 (395)
Q Consensus 4 ~~~apD~IS~tLasmpP~QL~ELLsqMK~Li~qnP~qARqLL~qNPQLAyALfQAqLlMGmVDp~~Vl 71 (395)
+..+.|.|+++|++|+++||||||++||.|+.+||++||+||.+||||+||||||+|+||+||++.+.
T Consensus 12 ~~~~~~~Is~~l~~l~~~ql~ell~~mK~l~~~~p~~ar~lL~~nPqLa~Al~qa~l~lg~vd~~v~~ 79 (84)
T PF14327_consen 12 PQSAPDAISQTLSSLPPEQLYELLSQMKQLAQQNPEQARQLLQQNPQLAYALFQALLLLGMVDPDVVQ 79 (84)
T ss_dssp ---HHHHHHTTSSTSHHHHHHHHHHHHHHHHC----HHHHHHHS-THHHHHHHHHHHHTSS-SSSCHH
T ss_pred ccCcHHHHHHHHHhCCHHHHHHHHHHHHHHHHhCHHHHHHHHHHCcHHHHHHHHHHHHhCCCCHHHHH
Confidence 45678999999999999999999999999999999999999999999999999999999999985544
No 2
>PF14304 CSTF_C: Transcription termination and cleavage factor C-terminal; PDB: 2J8P_A.
Probab=99.36 E-value=6.2e-13 Score=99.12 Aligned_cols=36 Identities=58% Similarity=0.886 Sum_probs=31.5
Q ss_pred HHHHHHHHHcCCHHHHhcCChHHHHHHHHHHHHHhC
Q 040162 360 EQALLQQVMSLSPEQISLLPPEQRNQVLQLQQILRQ 395 (395)
Q Consensus 360 ~~aLl~QVl~Lt~eqI~~LPp~qR~QIl~Lr~ql~~ 395 (395)
++|||+|||+||+||||+||++||++|++||++|.+
T Consensus 7 q~aLl~QVL~Lt~eQI~~LPp~qR~~I~~Lr~ql~~ 42 (46)
T PF14304_consen 7 QAALLMQVLQLTPEQINALPPDQRQQILQLRQQLMR 42 (46)
T ss_dssp HHHHHHHHHTS-HHHHHTS-HHHHTHHHHHHHHHH-
T ss_pred HHHHHHHHHcCCHHHHHhCCHHHHHHHHHHHHHHHh
Confidence 459999999999999999999999999999999974
No 3
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=98.89 E-value=9.8e-09 Score=105.11 Aligned_cols=73 Identities=21% Similarity=0.231 Sum_probs=68.0
Q ss_pred CCCCchhhhhcCCCHHHHHHHHHHHHHHH-hhCHHHHHHHHHhCCchHHH-HHHHHHHhcCCCCCCCCCCCCCCc
Q 040162 6 VAGDGLPANLAGMSKNQLYEIMTQMKSLI-EQNEQQARQILIQNPLLTKA-LFQAQIMLGMVKPPQVIPSVQPPA 78 (395)
Q Consensus 6 ~apD~IS~tLasmpP~QL~ELLsqMK~Li-~qnP~qARqLL~qNPQLAyA-LfQAqLlMGmVDp~~Vl~~~qp~~ 78 (395)
.+.|.+...++++++++++|+++++|.++ ..++..++++|..+|+++|+ +++++.+++++|+++++..+.+.+
T Consensus 126 ~a~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~i~~s~~~~~~~~p~~~l~~~~~~~ 200 (435)
T KOG0108|consen 126 DALKGNGSGVSNEPPSQLFELLSQGANNTNKSNPTPNPSGLTIPPAIVVKNIPQSLVKLTLAKPFTALYILRPYA 200 (435)
T ss_pred ccccccccccccCCccccccccchhhhhccccCCCcCccccccCchhhhccchhhhhhhhccChHhhhcccchhh
Confidence 45688999999999999999999999999 78999999999999999999 999999999999999998877665
No 4
>PF14483 Cut8_M: Cut8 dimerisation domain; PDB: 3Q5W_A 3Q5X_A.
Probab=66.25 E-value=9.5 Score=27.70 Aligned_cols=35 Identities=29% Similarity=0.402 Sum_probs=27.5
Q ss_pred chhhhhcCCCHHHHHHHHHHHHHHHhhCHHHHHHHHHh
Q 040162 10 GLPANLAGMSKNQLYEIMTQMKSLIEQNEQQARQILIQ 47 (395)
Q Consensus 10 ~IS~tLasmpP~QL~ELLsqMK~Li~qnP~qARqLL~q 47 (395)
.+.+-|..|+.++|..+ ++.+|..+|+-++++-..
T Consensus 2 pl~RlLE~Ld~~qL~~l---L~~l~~~HPei~~~i~~~ 36 (38)
T PF14483_consen 2 PLPRLLETLDKDQLQSL---LQSLCERHPEIQQEIRSI 36 (38)
T ss_dssp -HHHHHTTS-HHHHHHH---HHHHHHHSTHHHHHHHTT
T ss_pred ChhHHHHHcCHHHHHHH---HHHHHHhChhHHHHHHhh
Confidence 36788999999999999 677888899888877544
No 5
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=57.62 E-value=24 Score=25.29 Aligned_cols=31 Identities=32% Similarity=0.279 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHhCC-chHHHH
Q 040162 25 EIMTQMKSLIEQNEQQARQILIQNP-LLTKAL 55 (395)
Q Consensus 25 ELLsqMK~Li~qnP~qARqLL~qNP-QLAyAL 55 (395)
|+|.++..++..+.+.|+.+|..|- +|-.||
T Consensus 2 e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av 33 (43)
T PF14555_consen 2 EKIAQFMSITGADEDVAIQYLEANNWDLEAAV 33 (43)
T ss_dssp HHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHH
Confidence 6788888888889999999999987 665554
No 6
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=54.21 E-value=4.1e+02 Score=30.96 Aligned_cols=118 Identities=25% Similarity=0.383 Sum_probs=65.9
Q ss_pred CCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCcCCCCCCCCCCCCCCCCCC
Q 040162 149 HALQVPQQLKGRPNAPLTTMSLPQPSQHSSMPPISHHSASQPPSLHQPQMPAASSQLQPPLQSTGPPHMPLQPPLPQQPR 228 (395)
Q Consensus 149 ~~~~~~qq~kg~~~~q~~~~s~~q~sQ~p~~~~~~~~s~sq~~p~~~~~~pt~ssq~qqplq~~g~~~~~lQpplP~~pr 228 (395)
.|.+.+-.--||.....++...+-.++.+-+++.....-.+++|+.+..+.+ .||-+-|+---.+|.|.|+.=.
T Consensus 618 PnpPpP~~~Pg~np~~pPpg~~pP~~pPp~~Ppm~~pp~~pppp~~p~~~~~------Pp~~~~~~~~p~~~~p~Pp~~~ 691 (894)
T KOG0132|consen 618 PNPPPPPLRPGYNPYPPPPGFMPPTSPPPGQPPMGIPPQTPPPPMFPQGFNA------PPLGFQGGAAPMSQRPMPPRGG 691 (894)
T ss_pred CCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCccCCCC------CCCcccccCCCcccCCCCCCCC
Confidence 3444455556777777777787777775555554333333335677777776 2344445544455666443222
Q ss_pred CCCcCCc--cccCCCCCCCccccCCCCccCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCC
Q 040162 229 PASMQSF--HQYAPHVGSTVGFQHPAAQQRSSQPMYHSGPNPPASIGPSFQQGQPPVPSQP 287 (395)
Q Consensus 229 pp~~p~f--hQ~~~q~~~~~gfqh~~a~~~l~Qpmfh~g~~p~as~gp~f~qgQp~lPsQp 287 (395)
+--|++- |+-++ | +|.+-++ |+|-.| -..|+.|+.-+++--.|.
T Consensus 692 ~~~m~P~~~~~g~p--g-----~~~~PPP----P~~~~~----gpgG~~f~P~~~~~~~~~ 737 (894)
T KOG0132|consen 692 MRHMPPPPSHRGGP--G-----GHGIPPP----PFFDRG----GPGGPPFPPENPRGRLQR 737 (894)
T ss_pred CCCCCCCCCCCCCC--C-----CCCCCCC----ccccCC----CCCCCCCCCCCccccccc
Confidence 2223333 55441 1 3333333 888888 457888987777655543
No 7
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=53.43 E-value=25 Score=29.88 Aligned_cols=38 Identities=29% Similarity=0.606 Sum_probs=30.5
Q ss_pred CCChHHHHHHHHHHH---------------------cCCHHHHhcCChHHHHHHHHHHH
Q 040162 354 SLSPEMEQALLQQVM---------------------SLSPEQISLLPPEQRNQVLQLQQ 391 (395)
Q Consensus 354 ~~~~~~~~aLl~QVl---------------------~Lt~eqI~~LPp~qR~QIl~Lr~ 391 (395)
-|.+|++.++|.+-+ ++.+|-++.||++=|+.|++--.
T Consensus 8 aLPeDiR~Evl~~~~~~~~~~~~~~~~~~~~~~~~~~I~pefL~ALP~diR~EVl~qe~ 66 (108)
T PF14377_consen 8 ALPEDIREEVLAQQQRERRAQASQRQSPQSSAPQPSQIDPEFLAALPPDIREEVLAQER 66 (108)
T ss_pred HCCHHHHHHHHHHHHhhccchhcccCcccccCCCccccCHHHHHhCCHHHHHHHHHHHH
Confidence 477888888887766 34588899999999999997544
No 8
>PF07319 DnaI_N: Primosomal protein DnaI N-terminus; InterPro: IPR009928 This entry represents the N terminus (approximately 120 residues) of bacterial primosomal DnaI proteins, although one family member appears to be of viral origin. DnaI is one of the components of the Bacillus subtilis replication restart primosome, and is required for the DnaB75-dependent loading of the DnaC helicase [].; PDB: 2K7R_A.
Probab=47.61 E-value=41 Score=27.94 Aligned_cols=49 Identities=18% Similarity=0.348 Sum_probs=29.2
Q ss_pred CchhhhhcC-CCHHHHHHHHHHHHHHHhhCHHHHHHHHHhC-CchHHHHHHH
Q 040162 9 DGLPANLAG-MSKNQLYEIMTQMKSLIEQNEQQARQILIQN-PLLTKALFQA 58 (395)
Q Consensus 9 D~IS~tLas-mpP~QL~ELLsqMK~Li~qnP~qARqLL~qN-PQLAyALfQA 58 (395)
|.|.++|.+ +....+-+-..+|+.-+..|| ..++||.+| ++|+...+.-
T Consensus 2 e~I~~~l~~~~~~~~~~~~~~~l~~~vl~dp-~V~~Fl~~h~~eLt~~~i~r 52 (94)
T PF07319_consen 2 ESIGDSLKQLMKRRNFEERYEQLKQEVLSDP-EVQAFLQEHQPELTQEMIER 52 (94)
T ss_dssp --TT-S----S---HHHHHHHHHHHHHTT-H-HHHHHHHHSTTT--HHHHHH
T ss_pred ccHHHHHHHHHhcccHHHHHHHHHHHHHcCH-HHHHHHHHhHHhcCHHHHHH
Confidence 567788888 445666677778888777787 589999999 9999876653
No 9
>smart00727 STI1 Heat shock chaperonin-binding motif.
Probab=46.71 E-value=23 Score=24.78 Aligned_cols=28 Identities=32% Similarity=0.506 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHhCCchHH
Q 040162 22 QLYEIMTQMKSLIEQNEQQARQILIQNPLLTK 53 (395)
Q Consensus 22 QL~ELLsqMK~Li~qnP~qARqLL~qNPQLAy 53 (395)
++-.++.+|. .||+.++.++..||++.-
T Consensus 12 ~~~~~l~~~~----~nP~~~~~~~~~nP~~~~ 39 (41)
T smart00727 12 QVQSLLQDMQ----QNPDMLAQMLQENPQLLQ 39 (41)
T ss_pred HHHHHHHHHH----HCHHHHHHHHHhCHHhHh
Confidence 4555555554 499999999988998864
No 10
>PF01434 Peptidase_M41: Peptidase family M41 This is family M41 in the peptidase classification. ; InterPro: IPR000642 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The peptidase M41 family belong to a larger family of zinc metalloproteases. This family includes the cell division protein FtsH, and the yeast mitochondrial respiratory chain complexes assembly protein, which is a putative ATP-dependent protease required for assembly of the mitochondrial respiratory chain and ATPase complexes. FtsH is an integral membrane protein, which seems to act as an ATP-dependent zinc metallopeptidase that binds one zinc ion.; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0006508 proteolysis; PDB: 4EIW_C 2DHR_E 1IY1_A 1IY2_A 1IY0_A 1IXZ_A 2CE7_F 2CEA_F 3KDS_E 2QZ4_A ....
Probab=37.96 E-value=27 Score=32.62 Aligned_cols=52 Identities=23% Similarity=0.216 Sum_probs=43.4
Q ss_pred CCCHHHHHHHHHHHHHHHhhCHHHHHHHHHhCCchHHHHHHHHHHhcCCCCC
Q 040162 17 GMSKNQLYEIMTQMKSLIEQNEQQARQILIQNPLLTKALFQAQIMLGMVKPP 68 (395)
Q Consensus 17 smpP~QL~ELLsqMK~Li~qnP~qARqLL~qNPQLAyALfQAqLlMGmVDp~ 68 (395)
.++.+-...+-..++.++...-++|++||..|-...-+|..+++.-+.++.+
T Consensus 157 ~~s~~~~~~i~~ev~~lL~~a~~~a~~iL~~~r~~l~~la~~Lle~~~L~~~ 208 (213)
T PF01434_consen 157 PMSEETRALIDREVRKLLEEAYARAKEILEENREALEALAEALLEKETLSGE 208 (213)
T ss_dssp SS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHSEEEHH
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCeeCHH
Confidence 3455545566688999999999999999999999999999999998887754
No 11
>PF09030 Creb_binding: Creb binding; InterPro: IPR014744 This entry represents the interlocking domain of the eukaryotic nuclear receptor coactivators CREBP and p300. The interlocking domain forms a 3-helical non-globular array that forms interlocked heterodimers with its target. Nuclear receptors are ligand-activated transcription factors involved in the regulation of many processes, including development, reproduction and homeostasis. Nuclear receptor coactivators act to modulate the function of nuclear receptors. Coactivators associate with promoters and enhancers primarily through protein-protein contacts to facilitate the interaction between DNA-bound transcription factors and the transcription machinery. Many of these coactivators are structurally related, including CBP (CREB-binding protein) and p300 []. CBP and p300 both have histone acetyltransferase activity (2.3.1.48 from EC). CBP/p300 proteins function synergistically to activate transcription, acting to remodel chromatin and to recruit RNA polymerase II and the basal transcription machinery. CBP is required for proper cell cycle control, differentiation and apoptosis. The interaction of CBP/p300 with transcription factors involves several small domains. The IBiD domain in the C-terminal of CBP is responsible for CBP interaction with IRF-3, as well as with the adenoviral oncoprotein E1A, TIF-2 coactivator, and the IRF homologue KSHV IRF-1 []. ; GO: 0003713 transcription coactivator activity, 0004402 histone acetyltransferase activity, 0006355 regulation of transcription, DNA-dependent, 0016573 histone acetylation, 0000123 histone acetyltransferase complex, 0005634 nucleus; PDB: 2KKJ_A 2C52_A 1JJS_A 2L14_A 1KBH_B 1ZOQ_C.
Probab=34.51 E-value=14 Score=32.53 Aligned_cols=39 Identities=28% Similarity=0.423 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHHHHHhh-CHHHHHHHHHhCCchHHHHH
Q 040162 18 MSKNQLYEIMTQMKSLIEQ-NEQQARQILIQNPLLTKALF 56 (395)
Q Consensus 18 mpP~QL~ELLsqMK~Li~q-nP~qARqLL~qNPQLAyALf 56 (395)
+++..|-|||..||.=... .-.++-+||+.||+|--|++
T Consensus 51 ~~q~ALQ~LLrTLkSPsSP~QQQQVLnILkSNPqLMAAFI 90 (104)
T PF09030_consen 51 LPQQALQQLLRTLKSPSSPQQQQQVLNILKSNPQLMAAFI 90 (104)
T ss_dssp -STCHHHHHHHCHCSSSSCHHHHHHHHHHHTSHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCCCCHHHHHHHHHHHhhCHHHHHHHH
Confidence 5899999999999963331 23679999999999988765
No 12
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=34.45 E-value=77 Score=27.21 Aligned_cols=34 Identities=50% Similarity=0.725 Sum_probs=19.1
Q ss_pred CCChHHHHHHHH---HHHcCCHHH----------HhcCChHHHHHHH
Q 040162 354 SLSPEMEQALLQ---QVMSLSPEQ----------ISLLPPEQRNQVL 387 (395)
Q Consensus 354 ~~~~~~~~aLl~---QVl~Lt~eq----------I~~LPp~qR~QIl 387 (395)
.||||+++.+.. .--+||+|+ ++.||+++|+.|.
T Consensus 40 ~mspeqq~r~~~rm~~W~~LspeqR~~~R~~~~~~~~Lpp~qR~~lr 86 (107)
T PF11304_consen 40 SMSPEQQQRLRERMRRWAALSPEQRQQARENYQRFKQLPPEQRQALR 86 (107)
T ss_pred cCCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence 566666664333 444566653 4566777776443
No 13
>PF08158 NUC130_3NT: NUC130/3NT domain; InterPro: IPR012977 This N-terminal domain is found in a novel nucleolar protein family defined by NUC130/133 [].
Probab=33.14 E-value=60 Score=25.06 Aligned_cols=44 Identities=18% Similarity=0.270 Sum_probs=32.3
Q ss_pred hcCCCHHHHHHHHHHHHHHHhhCHHHHHHHHHhCCchHHHHHHHHHHhcC
Q 040162 15 LAGMSKNQLYEIMTQMKSLIEQNEQQARQILIQNPLLTKALFQAQIMLGM 64 (395)
Q Consensus 15 LasmpP~QL~ELLsqMK~Li~qnP~qARqLL~qNPQLAyALfQAqLlMGm 64 (395)
++.--|+++.++-.+++.++.++.. .-+|+|-.++.+|+++++-
T Consensus 5 va~cYp~~~~~Fp~~L~~lL~~~~~------~L~p~lR~~lv~aLiLLRn 48 (52)
T PF08158_consen 5 VAHCYPKETKDFPQELIDLLRNHHT------VLDPDLRMKLVKALILLRN 48 (52)
T ss_pred cccccHHHHHHHHHHHHHHHHhccc------cCCHHHHHHHHHHHHHHHc
Confidence 4445567777777777776666554 4578999999999999874
No 14
>PF10044 Ret_tiss: Retinal tissue protein; InterPro: IPR018737 Rtp is a family of proteins of approximately 112 amino acids in length which is conserved from nematodes to humans. The proposed tertiary structure is of almost entirely alpha helix interrupted only by loops located at proline residues. Three sites in the protein sequence reveal two types of possible post-translation modification. A serine residue, at position 41, is a candidate for protein kinase C phosphorylation. Glycine residues at position 69 and 91 are probable sites for acetylation by covalent amide linkage of myristate via N-myristoyl transferase. Rtp is differentially expressed in the trout retina between parr and smolt developmental stages (smoltification). It is likely to be a house-keeping protein [].
Probab=32.76 E-value=73 Score=27.54 Aligned_cols=34 Identities=18% Similarity=0.309 Sum_probs=28.3
Q ss_pred hhhcCCCHHHHHHHHHHHHHHHhh-CHHHHHHHHH
Q 040162 13 ANLAGMSKNQLYEIMTQMKSLIEQ-NEQQARQILI 46 (395)
Q Consensus 13 ~tLasmpP~QL~ELLsqMK~Li~q-nP~qARqLL~ 46 (395)
..|+++++++|++-|.+|.+.+=+ .=++||+|=+
T Consensus 53 ~eLs~Lt~~~L~~~Ik~L~~~aYqLGl~EaKEmtR 87 (95)
T PF10044_consen 53 NELSSLTPDQLIEKIKKLQDEAYQLGLEEAKEMTR 87 (95)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHhHHHHHHHHh
Confidence 459999999999999999988875 6788887643
No 15
>PF03562 MltA: MltA specific insert domain; InterPro: IPR005300 This group of proteins includes MltA; a membrane-bound, murein degrading transglycosylase enzyme which plays an important role in the controlled growth of the stress-bearing sacculus of Escherichia coli [, ].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds; PDB: 2PI8_D 2AE0_X 2PIC_A 2GAE_A 2PJJ_A 3CZB_A 2G6G_A 2PNW_A 2G5D_A.
Probab=31.63 E-value=23 Score=32.81 Aligned_cols=26 Identities=23% Similarity=0.470 Sum_probs=20.7
Q ss_pred HHHHHHHHhhCHHHHHHHHHhCCchH
Q 040162 27 MTQMKSLIEQNEQQARQILIQNPLLT 52 (395)
Q Consensus 27 LsqMK~Li~qnP~qARqLL~qNPQLA 52 (395)
|..+|..+..||+++++||..||-++
T Consensus 130 mq~Ir~wl~~~P~~~~~ll~~N~syV 155 (158)
T PF03562_consen 130 MQAIRAWLRAHPEEADELLNQNPSYV 155 (158)
T ss_dssp HHHHHHHHHHTGGGHHHHHTTS---E
T ss_pred HHHHHHHHHHCHHHHHHHHHhCCCce
Confidence 67789999999999999999999653
No 16
>PF13919 ASXH: Asx homology domain
Probab=29.50 E-value=45 Score=30.07 Aligned_cols=19 Identities=42% Similarity=0.747 Sum_probs=17.7
Q ss_pred CHHHHhcCChHHHHHHHHH
Q 040162 371 SPEQISLLPPEQRNQVLQL 389 (395)
Q Consensus 371 t~eqI~~LPp~qR~QIl~L 389 (395)
.++.-++|++|+|++||+|
T Consensus 40 N~~tw~~L~~eeq~eLl~L 58 (138)
T PF13919_consen 40 NPETWSCLPEEEQQELLKL 58 (138)
T ss_pred CHHHHhcCCHHHHHHHHHh
Confidence 4899999999999999987
No 17
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=27.99 E-value=1.4e+02 Score=25.74 Aligned_cols=19 Identities=37% Similarity=0.382 Sum_probs=10.1
Q ss_pred HhcCChHHHHHHHHHHHHH
Q 040162 375 ISLLPPEQRNQVLQLQQIL 393 (395)
Q Consensus 375 I~~LPp~qR~QIl~Lr~ql 393 (395)
...|+|+||.+|..--+.|
T Consensus 56 W~~LspeqR~~~R~~~~~~ 74 (107)
T PF11304_consen 56 WAALSPEQRQQARENYQRF 74 (107)
T ss_pred HHhCCHHHHHHHHHHHHHH
Confidence 3456666666655544433
No 18
>KOG4402 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.78 E-value=1.8e+02 Score=27.02 Aligned_cols=43 Identities=19% Similarity=0.372 Sum_probs=36.7
Q ss_pred hhhcCCCHHHHHHHHHHHHHHHhh-CHHHHHHHHHhCCchHHHHHHHHHHhcCCCC
Q 040162 13 ANLAGMSKNQLYEIMTQMKSLIEQ-NEQQARQILIQNPLLTKALFQAQIMLGMVKP 67 (395)
Q Consensus 13 ~tLasmpP~QL~ELLsqMK~Li~q-nP~qARqLL~qNPQLAyALfQAqLlMGmVDp 67 (395)
+.|+.++++.|+|.|.+|.+++=+ .=++||++-+. -++|+.|+
T Consensus 93 nel~~lp~~dl~~kIr~iqn~vYqLGl~EaremtRG------------KlLnIl~~ 136 (144)
T KOG4402|consen 93 NELSHLPADDLAKKIRNIQNSVYQLGLEEAREMTRG------------KLLNILKP 136 (144)
T ss_pred HHHhcCCHHHHHHHHHHHHHHHHHHhhHHHHHHhhh------------hhhcccCC
Confidence 569999999999999999998876 57889988776 56788886
No 19
>PF08898 DUF1843: Domain of unknown function (DUF1843); InterPro: IPR014994 This domain is found in functionally uncharacterised proteins. It can be found independently or at the C terminus of the protein.
Probab=26.25 E-value=1.2e+02 Score=24.02 Aligned_cols=31 Identities=32% Similarity=0.299 Sum_probs=24.6
Q ss_pred HHHHHHHHhhCHHHHHHHHHhCCchHHHHHHHHHH
Q 040162 27 MTQMKSLIEQNEQQARQILIQNPLLTKALFQAQIM 61 (395)
Q Consensus 27 LsqMK~Li~qnP~qARqLL~qNPQLAyALfQAqLl 61 (395)
|.+||.|+. +|++-|.++.+|+-||-....+
T Consensus 16 La~MK~l~~----~aeq~L~~~~~i~~al~~Lk~E 46 (53)
T PF08898_consen 16 LAQMKALAA----QAEQQLAEAGDIAAALEKLKAE 46 (53)
T ss_pred HHHHHHHHH----HHHHHHccchHHHHHHHHHHHH
Confidence 578888764 6888999999999888766543
No 20
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=24.63 E-value=81 Score=34.45 Aligned_cols=59 Identities=29% Similarity=0.327 Sum_probs=50.3
Q ss_pred CCCHHHHHHHHHHHHHHHhhCHHHHHHHHHhCCchHHHHHHHHHHhcCCCCCCCCCCCC
Q 040162 17 GMSKNQLYEIMTQMKSLIEQNEQQARQILIQNPLLTKALFQAQIMLGMVKPPQVIPSVQ 75 (395)
Q Consensus 17 smpP~QL~ELLsqMK~Li~qnP~qARqLL~qNPQLAyALfQAqLlMGmVDp~~Vl~~~q 75 (395)
.++.+-...|-.+.|.++...-++||+||.+|-...-+|..+++...-||.+++-..+.
T Consensus 536 ~~s~~~~~~id~ev~~il~~~~~~a~~iL~~~~~~l~~la~~Lle~etl~~~ei~~i~~ 594 (644)
T PRK10733 536 HMSDETARIIDQEVKALIERNYNRARQLLTDNMDILHAMKDALMKYETIDAPQIDDLMA 594 (644)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhceeCHHHHHHHHh
Confidence 35555556677889999999999999999999999999999999999999877766554
No 21
>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]
Probab=22.10 E-value=87 Score=34.40 Aligned_cols=37 Identities=19% Similarity=0.424 Sum_probs=32.0
Q ss_pred hhhhhcCCCHHHHHHHHHHHHHHHhhCHHHHHHHHHh
Q 040162 11 LPANLAGMSKNQLYEIMTQMKSLIEQNEQQARQILIQ 47 (395)
Q Consensus 11 IS~tLasmpP~QL~ELLsqMK~Li~qnP~qARqLL~q 47 (395)
|..-=+.++|.=||..|..++.+|-.|||.||+|+..
T Consensus 364 ik~LqaQvnPHFLFNaLNTIsa~IR~npdkAreLil~ 400 (557)
T COG3275 364 IKALQAQVNPHFLFNALNTISAVIRRNPDKARELILY 400 (557)
T ss_pred HHHHHhccChHHHHHHHHHHHHHhcCChHHHHHHHHH
Confidence 4444577889999999999999999999999999765
Done!