Query 025596
Match_columns 250
No_of_seqs 78 out of 80
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 07:27:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025596.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025596hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG4735 Uncharacterized protei 100.0 9E-50 2E-54 349.7 11.3 187 9-243 20-208 (211)
2 PRK10236 hypothetical protein; 100.0 2E-42 4.2E-47 309.8 14.1 171 8-239 58-230 (237)
3 COG4735 Uncharacterized protei 98.3 3.5E-06 7.6E-11 75.3 8.6 91 28-134 1-100 (211)
4 PF03981 Ubiq_cyt_C_chap: Ubiq 97.7 6.7E-05 1.5E-09 61.0 5.8 53 14-97 7-60 (141)
5 PF02173 pKID: pKID domain; I 67.7 3.6 7.8E-05 28.7 1.5 13 34-46 18-30 (41)
6 PF04542 Sigma70_r2: Sigma-70 46.2 36 0.00078 23.3 3.8 33 38-73 5-37 (71)
7 PRK09535 btuC corrinoid ABC tr 44.9 44 0.00096 32.6 5.3 38 196-233 282-320 (366)
8 cd01915 CODH Carbon monoxide d 44.4 68 0.0015 33.5 6.9 51 33-85 100-154 (613)
9 TIGR02989 Sig-70_gvs1 RNA poly 43.6 30 0.00066 27.5 3.5 36 37-75 9-44 (159)
10 cd06406 PB1_P67 A PB1 domain i 39.0 24 0.00052 27.6 2.1 20 33-52 18-37 (80)
11 cd06134 RNaseT DEDDh 3'-5' exo 32.9 41 0.0009 28.8 2.8 33 41-73 151-188 (189)
12 TIGR03869 F420-0_ABCperm propo 32.4 93 0.002 29.7 5.3 42 196-237 240-282 (325)
13 PF05461 ApoL: Apolipoprotein 30.0 1.5E+02 0.0033 28.2 6.3 41 32-73 28-69 (313)
14 PRK09777 fecD iron-dicitrate t 29.5 1.1E+02 0.0024 29.1 5.3 38 197-234 237-275 (318)
15 cd07679 F-BAR_PACSIN2 The F-BA 29.0 34 0.00074 32.0 1.7 47 7-60 200-249 (258)
16 cd02642 R3H_encore_like R3H do 28.9 86 0.0019 22.6 3.5 44 11-54 3-49 (63)
17 PRK07247 DNA polymerase III su 28.6 89 0.0019 27.4 4.2 35 37-73 132-168 (195)
18 PRK14082 hypothetical protein; 28.5 46 0.001 25.3 2.1 16 58-73 33-48 (65)
19 cd02646 R3H_G-patch R3H domain 28.3 67 0.0014 22.9 2.8 44 13-56 1-46 (58)
20 PF08708 PriCT_1: Primase C te 28.1 1.2E+02 0.0026 21.9 4.2 54 4-64 7-60 (71)
21 PF07498 Rho_N: Rho terminatio 27.8 97 0.0021 20.9 3.4 29 41-69 9-37 (43)
22 cd00014 CH Calponin homology d 27.6 1.1E+02 0.0023 22.8 4.0 24 39-63 64-87 (107)
23 PF11470 TUG-UBL1: GLUT4 regul 25.0 46 0.001 24.8 1.5 20 35-54 16-35 (65)
24 PF04281 Tom22: Mitochondrial 24.6 2E+02 0.0044 24.5 5.5 35 192-235 79-113 (137)
25 PF02037 SAP: SAP domain; Int 24.2 1.6E+02 0.0034 19.0 3.7 28 40-69 7-34 (35)
26 PRK12513 RNA polymerase sigma 23.3 74 0.0016 26.5 2.6 35 37-74 34-68 (194)
27 PRK09643 RNA polymerase sigma 22.7 1.1E+02 0.0023 25.9 3.5 36 37-75 35-70 (192)
28 PF01335 DED: Death effector d 22.5 2.8E+02 0.0061 20.6 5.4 12 38-49 1-12 (84)
29 PRK03784 vtamin B12-transporte 22.4 1.8E+02 0.0039 27.9 5.3 40 196-235 246-286 (331)
30 PHA02564 V virion protein; Pro 21.7 92 0.002 26.7 2.9 40 42-84 88-127 (141)
31 cd00045 DED The Death Effector 21.5 1.6E+02 0.0035 22.1 3.9 22 38-67 1-22 (77)
32 smart00530 HTH_XRE Helix-turn- 20.9 1.7E+02 0.0038 17.5 3.5 26 29-54 29-54 (56)
33 KOG2805 tRNA (5-methylaminomet 20.8 78 0.0017 31.1 2.5 41 35-75 49-92 (377)
34 PF02836 Glyco_hydro_2_C: Glyc 20.5 77 0.0017 28.7 2.3 38 14-51 36-73 (298)
35 COG0609 FepD ABC-type Fe3+-sid 20.1 1.4E+02 0.0029 28.6 4.0 36 194-229 246-282 (334)
No 1
>COG4735 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00 E-value=9e-50 Score=349.70 Aligned_cols=187 Identities=24% Similarity=0.390 Sum_probs=173.6
Q ss_pred HHHHHHHHHHHHhhhhhhh-hhhhcCCCccHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCccc
Q 025596 9 REDFIASLESRFLFLAADA-RSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGSWE 87 (250)
Q Consensus 9 r~~~~~~ie~rf~flaAD~-~t~lRG~~~sYReVLldVc~kLkV~~s~~lsT~dLEaeIfl~lL~~~~~~~~~~~~~awe 87 (250)
-..+...|.++++.+++|+ .+.|||.|+.||+||+|+|||||++|+++++|.+||+.++++++++ +|+
T Consensus 20 ~~ky~k~ia~elq~~gg~s~anflr~~G~lyk~il~d~~~~Lk~k~~k~~~tt~Iee~ll~~il~~-----------~l~ 88 (211)
T COG4735 20 VCKYLKRIAEELQTTGGLSAANFLRDLGQLYKKILCDEKDKLKVKVQKELGTTEIEEPLLLQILRN-----------PLE 88 (211)
T ss_pred HHHHHHhhHHHHHHhccHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHhhccccccchhHHHHHHh-----------HHH
Confidence 3456778999999999999 6999999999999999999999999999999999999999999999 999
Q ss_pred CCCchhhhhHHHhhhhhHHHHHHHhhhcCchhHHHHHHhcchHHHHHHHHH-HHHHHhhHHHHHHHhhHHHHHHHHHhhh
Q 025596 88 NSEASDAQNSLELGLSQWKVQALAAFNAGAVELKSMMLKGGGIYTLVKIYQ-LLMRNLSGKFFLEAANYQIKKEVLKKGG 166 (250)
Q Consensus 88 k~~~~~e~~sl~~~l~~~~~~~la~~~lg~~~~~~~llkggsa~av~~i~~-~l~~~ls~q~a~~~A~Yq~ak~~l~~Gg 166 (250)
||+.. +.+++++.+. . .+.+ |..|+.+++|.|++||.+..+|+
T Consensus 89 km~~~-~~~e~~~~l~----------------------------------~~~v~~-i~e~~~vl~a~~l~ak~~~~~~S 132 (211)
T COG4735 89 KMLKG-GKAEAVDSLD----------------------------------APNVLE-IEEQLQVLIADYLVAKKALGKGS 132 (211)
T ss_pred HHhHH-HHHHHHHHhc----------------------------------chhHHH-HHHHHHHHHHHHHHHHHHhccch
Confidence 99998 6666554443 3 3445 88999999999999999999999
Q ss_pred HHHHHhHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHhhhc
Q 025596 167 QLAAINLESRAALLAAKQGFAGAATKYLGLRNMVALLGPVLWGTFLADVVIQMLGTDYARILRAIYAFAQIRITRTY 243 (250)
Q Consensus 167 ~~aa~~l~~~~a~~~A~rG~~~~Aary~~~Rs~~~llGPilW~w~~aDL~~~~igt~Y~riIpaI~alAqIRltRt~ 243 (250)
..+|.+++|++|+|+++|||++.|+ |+++||+|+|.|||||+||.+|++||++|||||||||+||++||||++|..
T Consensus 133 ~qla~~l~~~~a~q~lg~Gl~~ga~-~~~~rtl~~l~GPvgw~l~ga~~~~~~~g~~YrvtIPai~~lA~lRl~~~~ 208 (211)
T COG4735 133 YQLAVILQNAVALQTLGQGLLRGAA-YGLVRTLFSLGGPVGWALFGADLGWRAIGTNYRVTIPAIFQLAQLRLTRAA 208 (211)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhhhh-hhHHHHHHHhcchHHHHHHHHHHHHHhhcccccccHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999888 999999999999999999999999999999999999999999999999863
No 2
>PRK10236 hypothetical protein; Provisional
Probab=100.00 E-value=2e-42 Score=309.81 Aligned_cols=171 Identities=20% Similarity=0.307 Sum_probs=132.0
Q ss_pred hHHHHHHHHHHHHhhhhhhh-hhhhcCCCccHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCcc
Q 025596 8 EREDFIASLESRFLFLAADA-RSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGSW 86 (250)
Q Consensus 8 ~r~~~~~~ie~rf~flaAD~-~t~lRG~~~sYReVLldVc~kLkV~~s~~lsT~dLEaeIfl~lL~~~~~~~~~~~~~aw 86 (250)
|-...-+.||.||||||||+ +|+|||+||+|||||+|||||||||||+++||++||+|||+|++++ +|
T Consensus 58 ~~~~yw~~Ia~elq~fGgnt~~n~lRG~Gv~YreIL~DVc~~LKV~y~~~~st~~iE~~il~kll~~-----------a~ 126 (237)
T PRK10236 58 QHRRNWQLIAGELQHFGGDSIANKLRGHGKLYRAILLDVSKRLKLKADKEMSTFEIEQQLLEQFLRN-----------TW 126 (237)
T ss_pred hHHHHHHHHHHHHHHhcchHHHHHHhcCCccHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHH-----------HH
Confidence 34445579999999999999 5799999999999999999999999999999999999999999999 99
Q ss_pred cCCCchhhhhHHHhhhhhHHHHHHHhhhcCchhHHHHHHhcchHHHHHHHHHHHHHHhhHHHHHHHhhHHHHHHHHHhhh
Q 025596 87 ENSEASDAQNSLELGLSQWKVQALAAFNAGAVELKSMMLKGGGIYTLVKIYQLLMRNLSGKFFLEAANYQIKKEVLKKGG 166 (250)
Q Consensus 87 ek~~~~~e~~sl~~~l~~~~~~~la~~~lg~~~~~~~llkggsa~av~~i~~~l~~~ls~q~a~~~A~Yq~ak~~l~~Gg 166 (250)
+|||++ |+++|+..++. .+ +. ...+.+.++..- +.+.+ +.+|+.||++.-+.
T Consensus 127 ~kms~e-E~~~L~~~l~~----~l--~~--~~~~~~~ll~~~-----~~~~~----------~~gf~~y~l~~iv~---- 178 (237)
T PRK10236 127 KKMDEE-HKQEFLHAVDA----RV--NE--LEELLPLLMKDK-----LLAKG----------VSHLLSSQLTRILR---- 178 (237)
T ss_pred HHCCHH-HHHHHHHHHhh----hc--cC--cccchHHHHHHH-----HHHHh----------hcchHHHHHHHHHH----
Confidence 999999 99999999985 22 11 223455543321 11222 34555555443322
Q ss_pred HHHHHhHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhHhHHHHHHHHH-HHHHHhhccchhHHHHHHHHHHHHHH
Q 025596 167 QLAAINLESRAALLAAKQGFAGAATKYLGLRNMVALLGPVLWGTFLA-DVVIQMLGTDYARILRAIYAFAQIRI 239 (250)
Q Consensus 167 ~~aa~~l~~~~a~~~A~rG~~~~Aary~~~Rs~~~llGPilW~w~~a-DL~~~~igt~Y~riIpaI~alAqIRl 239 (250)
|.++.+..++|++ |+++ |+|||+|+.+.+ |++ ||+||||||||++||.+|.
T Consensus 179 --------~~i~~~~lG~gL~---------r~~~-l~GPIGw~itg~wdla----gpAyRVTIPaviqIA~Lrq 230 (237)
T PRK10236 179 --------THAAMSVLGHGLL---------RGAG-LGGPVGAALNGVKAVS----GSAYRVTIPAVLQIACLRR 230 (237)
T ss_pred --------HHHHHHHhhhhHH---------HHhh-ccCchhHHhhhhHHhc----CCeeeeecchHHHHHHHHH
Confidence 3344555777776 6665 999999994443 555 9999999999999999975
No 3
>COG4735 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.28 E-value=3.5e-06 Score=75.27 Aligned_cols=91 Identities=23% Similarity=0.253 Sum_probs=81.3
Q ss_pred hhhhcCC--CccHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCcccCCCchhhhhHHHhhhhhH
Q 025596 28 RSTLRGW--RPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGSWENSEASDAQNSLELGLSQW 105 (250)
Q Consensus 28 ~t~lRG~--~~sYReVLldVc~kLkV~~s~~lsT~dLEaeIfl~lL~~~~~~~~~~~~~awek~~~~~e~~sl~~~l~~~ 105 (250)
+|++||+ ..+||+-+.||||+++++++.-..|-++|.+.|+|.+.+ .|++.+.. +.+.|....++
T Consensus 1 lt~~l~~~~~~k~r~g~~~~~ky~k~ia~elq~~gg~s~anflr~~G~-----------lyk~il~d-~~~~Lk~k~~k- 67 (211)
T COG4735 1 LTVLLGRSEQFKYREGLIQVCKYLKRIAEELQTTGGLSAANFLRDLGQ-----------LYKKILCD-EKDKLKVKVQK- 67 (211)
T ss_pred CchhhccchhhHHHhhHHHHHHHHHhhHHHHHHhccHHHHHHHHHHHH-----------HHHHcCHH-HHHHHHHHHHH-
Confidence 3677876 999999999999999999999999999999999999999 99999998 88888888887
Q ss_pred HHHHHHhhhcCc-------hhHHHHHHhcchHHHHH
Q 025596 106 KVQALAAFNAGA-------VELKSMMLKGGGIYTLV 134 (250)
Q Consensus 106 ~~~~la~~~lg~-------~~~~~~llkggsa~av~ 134 (250)
.+..+.+.+ +||...++|||++.+++
T Consensus 68 ---~~~tt~Iee~ll~~il~~~l~km~~~~~~e~~~ 100 (211)
T COG4735 68 ---ELGTTEIEEPLLLQILRNPLEKMLKGGKAEAVD 100 (211)
T ss_pred ---hhccccccchhHHHHHHhHHHHHhHHHHHHHHH
Confidence 677777766 89999999999886654
No 4
>PF03981 Ubiq_cyt_C_chap: Ubiquinol-cytochrome C chaperone ; InterPro: IPR021150 Saccharomyces cerevisiae ubiquinol-cytochrome C chaperone is required for assembly of coenzyme QF-2-cytochrome C reductase. It appears to be found in a number of different organisms including Homo sapiens, Caenorhabditis elegans and Rhizobium meliloti. This entry also contains bacterial proteins belonging to the UPF0174 family.
Probab=97.73 E-value=6.7e-05 Score=60.99 Aligned_cols=53 Identities=17% Similarity=0.227 Sum_probs=42.3
Q ss_pred HHHHHHHhhhhhhh-hhhhcCCCccHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCcccCCCch
Q 025596 14 ASLESRFLFLAADA-RSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGSWENSEAS 92 (250)
Q Consensus 14 ~~ie~rf~flaAD~-~t~lRG~~~sYReVLldVc~kLkV~~s~~lsT~dLEaeIfl~lL~~~~~~~~~~~~~awek~~~~ 92 (250)
|++++||+++.... +.+.| ||..+ .+.+++|+++|.++.+| ++++|.+.
T Consensus 7 dt~~~~f~~~~lh~~l~~~R----------------Lk~~~---~~~~~~~q~l~~~~~~d-----------~~~~l~~~ 56 (141)
T PF03981_consen 7 DTFAGRFQMLGLHVWLVLRR----------------LKAEG---KEGKELEQALFDKFFED-----------MDERLREM 56 (141)
T ss_pred cCHHHHHHHHHHHHHHHHHH----------------Hcccc---ccHHHHHHHHHHHHHHH-----------HHHHHHHh
Confidence 57899999999998 45545 77776 44699999999999999 88888776
Q ss_pred hhhhH
Q 025596 93 DAQNS 97 (250)
Q Consensus 93 ~e~~s 97 (250)
+.++
T Consensus 57 -gv~d 60 (141)
T PF03981_consen 57 -GVGD 60 (141)
T ss_pred -cCcc
Confidence 4444
No 5
>PF02173 pKID: pKID domain; InterPro: IPR003102 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB [].; GO: 0005515 protein binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1KDX_B.
Probab=67.67 E-value=3.6 Score=28.66 Aligned_cols=13 Identities=46% Similarity=0.810 Sum_probs=11.5
Q ss_pred CCccHHHHHHHHH
Q 025596 34 WRPSYRNVLLAVR 46 (250)
Q Consensus 34 ~~~sYReVLldVc 46 (250)
++||||.||-|+.
T Consensus 18 RRPSYRKIlndLs 30 (41)
T PF02173_consen 18 RRPSYRKILNDLS 30 (41)
T ss_dssp TSTHHHHHHHHHH
T ss_pred hCchHHHHHHHhc
Confidence 6999999999874
No 6
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=46.23 E-value=36 Score=23.26 Aligned_cols=33 Identities=24% Similarity=0.384 Sum_probs=27.6
Q ss_pred HHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhh
Q 025596 38 YRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQE 73 (250)
Q Consensus 38 YReVLldVc~kLkV~~s~~lsT~dLEaeIfl~lL~~ 73 (250)
|...+..+|.+. ++.....+|+-+|.|+++++.
T Consensus 5 ~~~~l~~~~~~~---~~~~~~~eD~~qe~~~~l~~~ 37 (71)
T PF04542_consen 5 YYPLLYRYARRY---TGDPEDAEDLVQEAFIKLWRA 37 (71)
T ss_dssp THHHHHHHHHTC---TTCSSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH---hCCHhhHHHHhhHHHHHHHhh
Confidence 677788888888 555568999999999999987
No 7
>PRK09535 btuC corrinoid ABC transporter permease; Reviewed
Probab=44.86 E-value=44 Score=32.61 Aligned_cols=38 Identities=18% Similarity=0.200 Sum_probs=29.7
Q ss_pred HHHHHHhHhHHHHH-HHHHHHHHHhhccchhHHHHHHHH
Q 025596 196 LRNMVALLGPVLWG-TFLADVVIQMLGTDYARILRAIYA 233 (250)
Q Consensus 196 ~Rs~~~llGPilW~-w~~aDL~~~~igt~Y~riIpaI~a 233 (250)
+=..-++.|||+|+ -..--++-...|+||+..+|....
T Consensus 282 ~a~aVa~~G~IgFVGLivPHiaR~l~g~~~r~llp~S~L 320 (366)
T PRK09535 282 TAAAVAVAGVIGFVGLIVPHVMRLLVGPDHRILLPTSAL 320 (366)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHhCcCcchHHHHHHH
Confidence 33456789999999 555677777789999999998654
No 8
>cd01915 CODH Carbon monoxide dehydrogenase (CODH) is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA, respectively. CODH has two types of metal clusters, a cubane [Fe4-S4] center (B-cluster) similar to that of hybrid cluster protein (HCP) and a Ni-Fe-S center (C-cluster) where carbon monoxide oxidation occurs. Bifunctional CODH forms a heterotetramer with acetyl-CoA synthase (ACS) consisting of two CODH and two ACS subunits while monofunctional CODH forms a homodimer. Bifunctional CODH reduces carbon dioxide to carbon monoxide and ACS then synthesizes acetyl-CoA from carbon monoxide, CoA, and a methyl group donated by another protein (CoFeSP), while monofunctional CODH oxidizes carbon monoxide to carbon dioxide. CODH and ACS each have a metal cluster referred to as the C- and A-clusters, respectively.
Probab=44.45 E-value=68 Score=33.54 Aligned_cols=51 Identities=20% Similarity=0.227 Sum_probs=39.9
Q ss_pred CCCccHH----HHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCc
Q 025596 33 GWRPSYR----NVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGS 85 (250)
Q Consensus 33 G~~~sYR----eVLldVc~kLkV~~s~~lsT~dLEaeIfl~lL~~~~~~~~~~~~~a 85 (250)
|+. .|+ +=|..||++|+|+.+. -+..|+=.|+=..+|+||.+.......+.
T Consensus 100 g~~-~y~I~d~~KL~~~A~~~gi~t~g-~~~~eiA~~va~~~l~d~~~~~~~~~~~~ 154 (613)
T cd01915 100 GKT-DYEIKDEEKLKALAKRLGIDTEG-KSINEIAVEVAEIALEDFGRPREEPSRWV 154 (613)
T ss_pred CCC-CCccCCHHHHHHHHHHcCCCcCC-CCHHHHHHHHHHHHHHHhcCCCCcchhhH
Confidence 554 465 8899999999999776 67899999999999999986544344443
No 9
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=43.63 E-value=30 Score=27.55 Aligned_cols=36 Identities=17% Similarity=0.253 Sum_probs=28.3
Q ss_pred cHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhh
Q 025596 37 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 75 (250)
Q Consensus 37 sYReVLldVc~kLkV~~s~~lsT~dLEaeIfl~lL~~~~ 75 (250)
.|+..|..+|.++.. +....||+.+|.|+++++...
T Consensus 9 ~~~~~l~~~~~~~~~---~~~~aEDivQe~~l~l~~~~~ 44 (159)
T TIGR02989 9 RHQRSLRAFVRSLVP---DRDDADDVLQETFVTAWRKFD 44 (159)
T ss_pred HhHHHHHHHHHHHcC---ChhhHHHHHHHHHHHHHHHHH
Confidence 477788888888843 445679999999999998743
No 10
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=38.96 E-value=24 Score=27.63 Aligned_cols=20 Identities=25% Similarity=0.474 Sum_probs=18.8
Q ss_pred CCCccHHHHHHHHHhhcCCC
Q 025596 33 GWRPSYRNVLLAVRKNLNIP 52 (250)
Q Consensus 33 G~~~sYReVLldVc~kLkV~ 52 (250)
..+++|.++.-.|++|||+|
T Consensus 18 p~~~~y~~L~~ki~~kLkl~ 37 (80)
T cd06406 18 ARGLSYATLLQKISSKLELP 37 (80)
T ss_pred CCCCCHHHHHHHHHHHhCCC
Confidence 56999999999999999998
No 11
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=32.87 E-value=41 Score=28.82 Aligned_cols=33 Identities=18% Similarity=0.234 Sum_probs=24.1
Q ss_pred HHHHHHhhcCCCC---CCCCChH--HHHHHHHHHHHhh
Q 025596 41 VLLAVRKNLNIPC---SSKLSTE--DLEAEIFLHLLQE 73 (250)
Q Consensus 41 VLldVc~kLkV~~---s~~lsT~--dLEaeIfl~lL~~ 73 (250)
-|-++|++++|+. ..+..-. ..-+++|++++++
T Consensus 151 ~L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 151 VLAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred cHHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 3888999999985 3344433 4557999999887
No 12
>TIGR03869 F420-0_ABCperm proposed F420-0 ABC transporter, permease protein. his small clade of ABC-type transporter permease protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (TIGR03868) and an ATPase (TIGR03873). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with an F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this permease protein is a component of a F420-0 (that is, F420 lacking only the polyglutamate tail) transporter.
Probab=32.37 E-value=93 Score=29.69 Aligned_cols=42 Identities=14% Similarity=0.153 Sum_probs=31.3
Q ss_pred HHHHHHhHhHHHHH-HHHHHHHHHhhccchhHHHHHHHHHHHH
Q 025596 196 LRNMVALLGPVLWG-TFLADVVIQMLGTDYARILRAIYAFAQI 237 (250)
Q Consensus 196 ~Rs~~~llGPilW~-w~~aDL~~~~igt~Y~riIpaI~alAqI 237 (250)
+=+.-++.|||+++ -..--++=+..|++|+..+|+...+.-+
T Consensus 240 ~a~~va~vG~I~FvGLi~Phiar~l~g~~~~~ll~~s~l~Ga~ 282 (325)
T TIGR03869 240 TGALVSVSGAIGFVGLILPHAVRLLTGPRHRLLLPVSALAGAV 282 (325)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHH
Confidence 34556889999999 5555666667789999999988765443
No 13
>PF05461 ApoL: Apolipoprotein L; InterPro: IPR008405 Apo L belongs to the high density lipoprotein family that plays a central role in cholesterol transport. The cholesterol content of membranes is important in cellular processes such as modulating gene transcription and signal transduction both in the adult brain and during neurodevelopment. There are six apo L genes located in close proximity to each other on chromosome 22q12 in humans. 22q12 is a confirmed high-susceptibility locus for schizophrenia and close to the region associated with velocardiofacial syndrome that includes symptoms of schizophrenia []. The various functions of apoL are still not entirely clear. Apolipoprotein L-I has been identified as a trypanolytic agent [] and displays similar phylogenetic distribution to the programmed cell death protein Bcl-2 and BH-3 domain-containing proteins, suggesting a possible role in apoptosis [].; GO: 0008289 lipid binding, 0006869 lipid transport, 0042157 lipoprotein metabolic process, 0005576 extracellular region
Probab=30.03 E-value=1.5e+02 Score=28.23 Aligned_cols=41 Identities=17% Similarity=0.238 Sum_probs=29.1
Q ss_pred cCCCccHHHHHHHHHhhcCCCCCCCCChH-HHHHHHHHHHHhh
Q 025596 32 RGWRPSYRNVLLAVRKNLNIPCSSKLSTE-DLEAEIFLHLLQE 73 (250)
Q Consensus 32 RG~~~sYReVLldVc~kLkV~~s~~lsT~-dLEaeIfl~lL~~ 73 (250)
|-+--.-|+.|.+.|..+..+- +.++.+ ..+.+.||+.+.+
T Consensus 28 rde~d~l~~~L~~l~~~~~~~d-~~~~~~~~~~~~~FL~~Fp~ 69 (313)
T PF05461_consen 28 RDEADALREALKELTEDMDSED-KDRSQKDQQDRERFLKEFPQ 69 (313)
T ss_pred hhhHHHHHHHHHHHHhhhhccc-cchhHHHHHHHHHHHHHhHH
Confidence 4555666788888888777664 555555 4558999998877
No 14
>PRK09777 fecD iron-dicitrate transporter subunit FecD; Reviewed
Probab=29.49 E-value=1.1e+02 Score=29.08 Aligned_cols=38 Identities=18% Similarity=0.237 Sum_probs=28.9
Q ss_pred HHHHHhHhHHHHHH-HHHHHHHHhhccchhHHHHHHHHH
Q 025596 197 RNMVALLGPVLWGT-FLADVVIQMLGTDYARILRAIYAF 234 (250)
Q Consensus 197 Rs~~~llGPilW~w-~~aDL~~~~igt~Y~riIpaI~al 234 (250)
=+.-++.|||+++- ..--++-+..|++++..+|....+
T Consensus 237 a~~vs~vG~I~FvGLi~Phiar~l~g~~~~~~l~~s~l~ 275 (318)
T PRK09777 237 ATGVAACGPISFIGLVVPHLMRSLVGGRHRRLLPVSALT 275 (318)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHHHhCcCcchHHHHHHHH
Confidence 34568899999994 445667667789999999976554
No 15
>cd07679 F-BAR_PACSIN2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Protein kinase C and Casein kinase Substrate in Neurons 2 (PACSIN2). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins, also called Synaptic dynamin-associated proteins (Syndapins), act as regulators of cytoskeletal and membrane dynamics. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSIN 2 or Syndapin II is expressed ubiquitously and is involved in the regulation of tubulin polymerization. It associates with Golgi membranes and forms a complex with dynamin II which is crucial in promoting vesicle formation from the trans-Golgi network. PACSIN 2 contains an N-terminal F-BAR domain and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave su
Probab=29.01 E-value=34 Score=32.02 Aligned_cols=47 Identities=19% Similarity=0.338 Sum_probs=31.2
Q ss_pred hhHHHHHHHHHHHHhhh---hhhhhhhhcCCCccHHHHHHHHHhhcCCCCCCCCChH
Q 025596 7 EEREDFIASLESRFLFL---AADARSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTE 60 (250)
Q Consensus 7 ~~r~~~~~~ie~rf~fl---aAD~~t~lRG~~~sYReVLldVc~kLkV~~s~~lsT~ 60 (250)
..+..|++.-++=|..+ --|=.+. .|++|+++|++|+|.|++.++..
T Consensus 200 ~~~~~y~e~m~~~fe~~Q~~E~eRi~F-------~K~~l~~~~~~l~i~~~~~~~~i 249 (258)
T cd07679 200 QTTPQYMENMEQVFEQCQQFEEKRLRF-------FREVLLEVQKHLDLSNVASYKNI 249 (258)
T ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHccchhhhhHHHH
Confidence 44666777666554332 3333333 46899999999999999976544
No 16
>cd02642 R3H_encore_like R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=28.87 E-value=86 Score=22.64 Aligned_cols=44 Identities=23% Similarity=0.312 Sum_probs=36.0
Q ss_pred HHHHHHHHHHhhhhhhh-hhhh--cCCCccHHHHHHHHHhhcCCCCC
Q 025596 11 DFIASLESRFLFLAADA-RSTL--RGWRPSYRNVLLAVRKNLNIPCS 54 (250)
Q Consensus 11 ~~~~~ie~rf~flaAD~-~t~l--RG~~~sYReVLldVc~kLkV~~s 54 (250)
.|+-.+|+.|.=|..|. ...+ ..-.+.+|-++-+||+..+....
T Consensus 3 ~~~l~~E~~i~~Fi~~~~~~~~~f~pm~sy~RllvH~la~~~gL~s~ 49 (63)
T cd02642 3 LFVLKLEKDLLAFIKDSTRQSLELPPMNSYYRLLAHRVAQYYGLDHN 49 (63)
T ss_pred hHHHHHHHHHHHHHhCCCCCeeEcCCCCcHHHHHHHHHHHHhCCeeE
Confidence 48888999999999998 4444 45588999999999999887643
No 17
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=28.60 E-value=89 Score=27.40 Aligned_cols=35 Identities=26% Similarity=0.332 Sum_probs=29.5
Q ss_pred cHHHHHHHHHhhcCCCCCCCCChHHHH--HHHHHHHHhh
Q 025596 37 SYRNVLLAVRKNLNIPCSSKLSTEDLE--AEIFLHLLQE 73 (250)
Q Consensus 37 sYReVLldVc~kLkV~~s~~lsT~dLE--aeIfl~lL~~ 73 (250)
+|| |-++|++++|++..+-...|-+ ++||+++++.
T Consensus 132 ~~~--L~~La~~~gi~~~~HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 132 NLK--LQTVADFLGIKGRGHNSLEDARMTARVYESFLES 168 (195)
T ss_pred CCC--HHHHHHhcCCCCCCcCCHHHHHHHHHHHHHHHhh
Confidence 454 8899999999998888877766 7899999987
No 18
>PRK14082 hypothetical protein; Provisional
Probab=28.50 E-value=46 Score=25.31 Aligned_cols=16 Identities=31% Similarity=0.640 Sum_probs=14.4
Q ss_pred ChHHHHHHHHHHHHhh
Q 025596 58 STEDLEAEIFLHLLQE 73 (250)
Q Consensus 58 sT~dLEaeIfl~lL~~ 73 (250)
.-||||+||=++++++
T Consensus 33 eREDLeQElk~Ki~eK 48 (65)
T PRK14082 33 EREDLEQELKIKIIEK 48 (65)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 3689999999999988
No 19
>cd02646 R3H_G-patch R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=28.28 E-value=67 Score=22.86 Aligned_cols=44 Identities=16% Similarity=0.208 Sum_probs=34.4
Q ss_pred HHHHHHHHhhhhhhhhhhhcC--CCccHHHHHHHHHhhcCCCCCCC
Q 025596 13 IASLESRFLFLAADARSTLRG--WRPSYRNVLLAVRKNLNIPCSSK 56 (250)
Q Consensus 13 ~~~ie~rf~flaAD~~t~lRG--~~~sYReVLldVc~kLkV~~s~~ 56 (250)
|+.|+.+|+-|-+|....+.= =.+.-|.++-++|+.+++.+.+.
T Consensus 1 ~~~i~~~i~~F~~~~~~~~~fppm~~~~R~~vH~lA~~~~L~S~S~ 46 (58)
T cd02646 1 IEDIKDEIEAFLLDSRDSLSFPPMDKHGRKTIHKLANCYNLKSKSR 46 (58)
T ss_pred ChHHHHHHHHHHhCCCceEecCCCCHHHHHHHHHHHHHcCCccccc
Confidence 467899999888888554432 27788999999999999987654
No 20
>PF08708 PriCT_1: Primase C terminal 1 (PriCT-1); InterPro: IPR014820 This alpha helical domain is found at the C-terminal of primases.
Probab=28.13 E-value=1.2e+02 Score=21.85 Aligned_cols=54 Identities=19% Similarity=0.279 Sum_probs=38.5
Q ss_pred hhhhhHHHHHHHHHHHHhhhhhhhhhhhcCCCccHHHHHHHHHhhcCCCCCCCCChHHHHH
Q 025596 4 QDLEEREDFIASLESRFLFLAADARSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEA 64 (250)
Q Consensus 4 ~~~~~r~~~~~~ie~rf~flaAD~~t~lRG~~~sYReVLldVc~kLkV~~s~~lsT~dLEa 64 (250)
++.-+|..++=.+-.++.+-+.|--. ..++.+.+.|..++-.|+..|+-.|++.
T Consensus 7 ~~~g~RN~~lf~~a~~~~~~~v~~~~-------~~~~~v~~~~~~~N~~~~~PL~~~Ev~~ 60 (71)
T PF08708_consen 7 IVEGGRNCTLFRLARRLAYRGVDQEE-------QFRQEVLSLAQAINSNFSPPLPESEVKA 60 (71)
T ss_pred CCCCCcHHHHHHHHHHHHHhCCCHhH-------HHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence 34556777776666666555554433 6777888899999988888888888765
No 21
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=27.79 E-value=97 Score=20.92 Aligned_cols=29 Identities=28% Similarity=0.290 Sum_probs=21.7
Q ss_pred HHHHHHhhcCCCCCCCCChHHHHHHHHHH
Q 025596 41 VLLAVRKNLNIPCSSKLSTEDLEAEIFLH 69 (250)
Q Consensus 41 VLldVc~kLkV~~s~~lsT~dLEaeIfl~ 69 (250)
=|.++|+.++|+..+++.-.||=.+|+-.
T Consensus 9 eL~~iAk~lgI~~~~~~~K~eLI~~Il~~ 37 (43)
T PF07498_consen 9 ELREIAKELGIEGYSKMRKQELIFAILKA 37 (43)
T ss_dssp HHHHHHHCTT-TTGCCS-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCCcCCHHHHHHHHHHH
Confidence 37889999999999999988776666544
No 22
>cd00014 CH Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
Probab=27.64 E-value=1.1e+02 Score=22.80 Aligned_cols=24 Identities=29% Similarity=0.495 Sum_probs=18.9
Q ss_pred HHHHHHHHhhcCCCCCCCCChHHHH
Q 025596 39 RNVLLAVRKNLNIPCSSKLSTEDLE 63 (250)
Q Consensus 39 ReVLldVc~kLkV~~s~~lsT~dLE 63 (250)
-+..+++|+++|||.. ..+++||-
T Consensus 64 i~~~l~~~~~~gi~~~-~~~~~Dl~ 87 (107)
T cd00014 64 INLALNFAEKLGVPVV-NFDAEDLV 87 (107)
T ss_pred HHHHHHHHHHcCCcee-ccCHHHHh
Confidence 3567888888888877 77888886
No 23
>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.
Probab=25.04 E-value=46 Score=24.77 Aligned_cols=20 Identities=20% Similarity=0.218 Sum_probs=14.7
Q ss_pred CccHHHHHHHHHhhcCCCCC
Q 025596 35 RPSYRNVLLAVRKNLNIPCS 54 (250)
Q Consensus 35 ~~sYReVLldVc~kLkV~~s 54 (250)
.-+-.+||.++|+|+|++-+
T Consensus 16 ~~~l~~VL~eac~k~~l~~~ 35 (65)
T PF11470_consen 16 NTTLNQVLEEACKKFGLDPS 35 (65)
T ss_dssp TSBHHHHHHHHHHHTT--GG
T ss_pred CCCHHHHHHHHHHHcCCCcc
Confidence 34567999999999998854
No 24
>PF04281 Tom22: Mitochondrial import receptor subunit Tom22 ; InterPro: IPR005683 The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family represents the Tom22 proteins []. The N-terminal region of Tom22 has been shown to have chaperone-like activity, and the C-terminal region faces the intermembrane face []. ; GO: 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane
Probab=24.60 E-value=2e+02 Score=24.55 Aligned_cols=35 Identities=9% Similarity=0.190 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhHhHHHHHHHHHHHHHHhhccchhHHHHHHHHHH
Q 025596 192 KYLGLRNMVALLGPVLWGTFLADVVIQMLGTDYARILRAIYAFA 235 (250)
Q Consensus 192 ry~~~Rs~~~llGPilW~w~~aDL~~~~igt~Y~riIpaI~alA 235 (250)
-+...++++.|.|-++|+.+--=+. -.+|.+|++.
T Consensus 79 ~~~~~k~~~~~~g~a~Wi~tTSall---------LgvPl~l~ie 113 (137)
T PF04281_consen 79 TSSAVKSLFSFSGKALWIVTTSALL---------LGVPLALEIE 113 (137)
T ss_pred HHHHHHHHHHhcchhHHHHHHHHHH---------HHHHHHHHHH
Confidence 3455899999999999993222222 2489998775
No 25
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=24.23 E-value=1.6e+02 Score=19.03 Aligned_cols=28 Identities=21% Similarity=0.164 Sum_probs=20.4
Q ss_pred HHHHHHHhhcCCCCCCCCChHHHHHHHHHH
Q 025596 40 NVLLAVRKNLNIPCSSKLSTEDLEAEIFLH 69 (250)
Q Consensus 40 eVLldVc~kLkV~~s~~lsT~dLEaeIfl~ 69 (250)
.=|.+.|+++++|.+.+ -.||-+.|--|
T Consensus 7 ~eLk~~l~~~gL~~~G~--K~~Li~Rl~~~ 34 (35)
T PF02037_consen 7 AELKEELKERGLSTSGK--KAELIERLKEH 34 (35)
T ss_dssp HHHHHHHHHTTS-STSS--HHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCCCC--HHHHHHHHHHh
Confidence 45789999999999887 56666666544
No 26
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=23.30 E-value=74 Score=26.54 Aligned_cols=35 Identities=20% Similarity=0.245 Sum_probs=27.0
Q ss_pred cHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhh
Q 025596 37 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEY 74 (250)
Q Consensus 37 sYReVLldVc~kLkV~~s~~lsT~dLEaeIfl~lL~~~ 74 (250)
.|+..|..+|.+.- ......+|+=+|.|+++++..
T Consensus 34 ~y~~~l~~~~~~~~---~~~~daeDlvQe~fi~l~~~~ 68 (194)
T PRK12513 34 RHRTGLYRFLLRLA---RDRALAEDIFQETWLRVIRAR 68 (194)
T ss_pred HHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHH
Confidence 57777777777763 344568999999999999874
No 27
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=22.73 E-value=1.1e+02 Score=25.89 Aligned_cols=36 Identities=14% Similarity=0.141 Sum_probs=26.2
Q ss_pred cHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhh
Q 025596 37 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 75 (250)
Q Consensus 37 sYReVLldVc~kLkV~~s~~lsT~dLEaeIfl~lL~~~~ 75 (250)
.|...|..+|.++- ......+|+=+|+|+++.+...
T Consensus 35 ~y~~~l~~~~~~~~---~~~~~AeDlvQEvfl~l~~~~~ 70 (192)
T PRK09643 35 RHHRRLWAVARRTS---GTREDAADALQDAMLSAHRAAG 70 (192)
T ss_pred HHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHHHHH
Confidence 46666777776653 3455679999999999997633
No 28
>PF01335 DED: Death effector domain; InterPro: IPR001875 The death effector domain (DED) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DED is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. The dimerisation of DED domains is mediated primarily by electrostatic interactions. DED domains can be found in isolation, or in combination with other domains. Domains associated with DED include: caspase catalytic domains (in caspase-8, -10), death domains (in FADD), nuclear localisation sequences (in DEDD), transmembrane domains (in Bap31 and Bar), nucleotide-binding domains (in Dap3), coiled-coil domains (in Hip and Hippi), SAM domains (in Bar), and E2-binding RING domains (in Bar) []. Several DED-containing proteins are involved in the regulation of apoptosis through their interactions with DED-containing caspases (IPR002398 from INTERPRO), such as caspases 8 and 10 in humans, both of which contain tandem pairs of DEDs. There are many DED-containing modulators of apoptosis, which can either enhance or inhibit caspase activation [].; GO: 0005515 protein binding, 0042981 regulation of apoptosis; PDB: 3CL3_A 2F1S_A 2BBZ_C 2BBR_A 1A1Z_A 2GF5_A 1A1W_A 1N3K_A.
Probab=22.45 E-value=2.8e+02 Score=20.65 Aligned_cols=12 Identities=42% Similarity=0.888 Sum_probs=10.1
Q ss_pred HHHHHHHHHhhc
Q 025596 38 YRNVLLAVRKNL 49 (250)
Q Consensus 38 YReVLldVc~kL 49 (250)
||..|.+|.+.|
T Consensus 1 yr~lL~~I~~~L 12 (84)
T PF01335_consen 1 YRQLLLEISEEL 12 (84)
T ss_dssp HHHHHHHHHHHS
T ss_pred CHHHHHHHHHhc
Confidence 888999988775
No 29
>PRK03784 vtamin B12-transporter permease; Provisional
Probab=22.36 E-value=1.8e+02 Score=27.89 Aligned_cols=40 Identities=18% Similarity=0.056 Sum_probs=29.2
Q ss_pred HHHHHHhHhHHHHH-HHHHHHHHHhhccchhHHHHHHHHHH
Q 025596 196 LRNMVALLGPVLWG-TFLADVVIQMLGTDYARILRAIYAFA 235 (250)
Q Consensus 196 ~Rs~~~llGPilW~-w~~aDL~~~~igt~Y~riIpaI~alA 235 (250)
+=...++.|||+++ -..--++-...|++|+..+|....+.
T Consensus 246 ~a~~va~vG~I~FVGLiaPhiar~l~g~~~~~~l~~s~l~G 286 (331)
T PRK03784 246 VGVSVALAGAIGFIGLVIPHILRLCGLTDHRVLLPGCALAG 286 (331)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHH
Confidence 33456889999999 44555665566899999999876543
No 30
>PHA02564 V virion protein; Provisional
Probab=21.74 E-value=92 Score=26.69 Aligned_cols=40 Identities=20% Similarity=0.258 Sum_probs=31.6
Q ss_pred HHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCC
Q 025596 42 LLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPG 84 (250)
Q Consensus 42 LldVc~kLkV~~s~~lsT~dLEaeIfl~lL~~~~~~~~~~~~~ 84 (250)
...||+.++|+.+..++..|- .+-+|+.--..++.|..|+
T Consensus 88 i~~Vs~~~GV~~~~~idl~d~---~l~~l~~Aii~~EnG~~py 127 (141)
T PHA02564 88 ATAVANAMGVPPQAGLHLDQD---TLAALVTAIIRHENGQQPY 127 (141)
T ss_pred HHHHHHHHCCCCCCcCcCCcH---HHHHHHHHHHHHhcCCCCC
Confidence 567999999999999987765 6777777777777775554
No 31
>cd00045 DED The Death Effector Domain: a protein-protein interaction domain. Death Effector Domains comprise a subfamily of the Death Domain (DD) superfamily. DED-containing proteins include Fas-Associated via Death Domain (FADD), Astrocyte phosphoprotein PEA-15, the initiator caspases (caspase-8 and -10), and FLICE-inhibitory protein (FLIP), among others. These proteins are prominent components of the programmed cell death (apoptosis) pathway. Some members also have non-apoptotic functions such as regulation of insulin signaling (DEDD and PEA15) and cell cycle progression (DEDD). DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes.
Probab=21.52 E-value=1.6e+02 Score=22.06 Aligned_cols=22 Identities=50% Similarity=0.827 Sum_probs=14.9
Q ss_pred HHHHHHHHHhhcCCCCCCCCChHHHHHHHH
Q 025596 38 YRNVLLAVRKNLNIPCSSKLSTEDLEAEIF 67 (250)
Q Consensus 38 YReVLldVc~kLkV~~s~~lsT~dLEaeIf 67 (250)
||+.|.+|.+.| +.+|+|.=.|
T Consensus 1 yr~lL~~Is~~L--------t~~el~~lkF 22 (77)
T cd00045 1 YRRLLLKISKEL--------TSEELEALKF 22 (77)
T ss_pred CHHHHHHHHHHc--------CHHHHHHHHH
Confidence 888999887764 4566665443
No 32
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=20.94 E-value=1.7e+02 Score=17.51 Aligned_cols=26 Identities=19% Similarity=0.176 Sum_probs=18.2
Q ss_pred hhhcCCCccHHHHHHHHHhhcCCCCC
Q 025596 29 STLRGWRPSYRNVLLAVRKNLNIPCS 54 (250)
Q Consensus 29 t~lRG~~~sYReVLldVc~kLkV~~s 54 (250)
...+|....-.+.+..+|+.++++.+
T Consensus 29 ~~~~~~~~~~~~~~~~i~~~~~~~~~ 54 (56)
T smart00530 29 RIENGKRKPSLETLKKLAKALGVSLD 54 (56)
T ss_pred HHHCCCCCCCHHHHHHHHHHhCCChh
Confidence 45567644456667889999998753
No 33
>KOG2805 consensus tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=20.76 E-value=78 Score=31.13 Aligned_cols=41 Identities=24% Similarity=0.282 Sum_probs=32.3
Q ss_pred CccHHHHH---HHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhh
Q 025596 35 RPSYRNVL---LAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 75 (250)
Q Consensus 35 ~~sYReVL---ldVc~kLkV~~s~~lsT~dLEaeIfl~lL~~~~ 75 (250)
+++|..=+ ..||++|+||+-.--=+.|-=..+|..+|++|.
T Consensus 49 ~cp~e~D~~da~~Vc~~LnI~~~~Vnf~kEYW~~Vfs~~L~~Y~ 92 (377)
T KOG2805|consen 49 QCPAERDWKDAKRVCKQLNIPLHQVNFVKEYWNDVFSPFLEEYE 92 (377)
T ss_pred CCCchhhHHHHHHHHHHhCCeeEEEeeHHHHHHHHHHHHHHHHh
Confidence 45554433 458999999998877677777889999999987
No 34
>PF02836 Glyco_hydro_2_C: Glycosyl hydrolases family 2, TIM barrel domain; InterPro: IPR006103 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities; beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. Beta-galactosidase from E. coli has a TIM-barrel-like core surrounded by four other largely beta domains [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3CMG_A 3FN9_C 1YQ2_A 3K4D_B 3LPG_B 3LPF_A 3K4A_B 3K46_B 3GM8_A 3DEC_A ....
Probab=20.48 E-value=77 Score=28.67 Aligned_cols=38 Identities=11% Similarity=0.132 Sum_probs=27.1
Q ss_pred HHHHHHHhhhhhhhhhhhcCCCccHHHHHHHHHhhcCC
Q 025596 14 ASLESRFLFLAADARSTLRGWRPSYRNVLLAVRKNLNI 51 (250)
Q Consensus 14 ~~ie~rf~flaAD~~t~lRG~~~sYReVLldVc~kLkV 51 (250)
+.++..++.+-.=++|.+|-..-.+.+-.++.||++|+
T Consensus 36 ~~~~~d~~l~k~~G~N~iR~~h~p~~~~~~~~cD~~Gi 73 (298)
T PF02836_consen 36 EAMERDLELMKEMGFNAIRTHHYPPSPRFYDLCDELGI 73 (298)
T ss_dssp HHHHHHHHHHHHTT-SEEEETTS--SHHHHHHHHHHT-
T ss_pred HHHHHHHHHHHhcCcceEEcccccCcHHHHHHHhhcCC
Confidence 45677777777666999997656677888999999998
No 35
>COG0609 FepD ABC-type Fe3+-siderophore transport system, permease component [Inorganic ion transport and metabolism]
Probab=20.05 E-value=1.4e+02 Score=28.64 Aligned_cols=36 Identities=22% Similarity=0.385 Sum_probs=27.2
Q ss_pred HHHHHHHHhHhHHHHHHHH-HHHHHHhhccchhHHHH
Q 025596 194 LGLRNMVALLGPVLWGTFL-ADVVIQMLGTDYARILR 229 (250)
Q Consensus 194 ~~~Rs~~~llGPilW~w~~-aDL~~~~igt~Y~riIp 229 (250)
.++=+..++.|||+++=.. --++=..+|+||+.++|
T Consensus 246 llt~~aVa~~G~I~FVGLi~PHiaR~lvg~~~r~lip 282 (334)
T COG0609 246 LLTAAAVSLVGPIGFVGLIAPHIARLLVGNDHRYLLP 282 (334)
T ss_pred HHHHHHHHHhhhHHHHHHhHHHHHHHHhCCCcceeHH
Confidence 3345667899999999444 45555568999999999
Done!