Query 027687
Match_columns 220
No_of_seqs 12 out of 14
Neff 1.7
Searched_HMMs 46136
Date Fri Mar 29 13:40:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027687.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027687hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02960 alpha-amylase 75.2 3 6.6E-05 43.0 3.6 47 3-51 5-51 (897)
2 PF05266 DUF724: Protein of un 60.4 1.1E+02 0.0023 26.0 9.8 110 100-211 67-183 (190)
3 PRK09568 DNA primase large sub 56.8 56 0.0012 29.9 7.5 73 126-209 10-92 (306)
4 PRK12525 RNA polymerase sigma 51.4 1.1E+02 0.0023 23.3 7.5 22 194-215 146-167 (168)
5 PF05848 CtsR: Firmicute trans 50.3 85 0.0018 26.4 7.1 82 106-218 66-150 (152)
6 PF15412 Nse4-Nse3_bdg: Bindin 49.7 8.8 0.00019 26.6 1.0 36 104-140 10-45 (56)
7 PRK12527 RNA polymerase sigma 49.1 1.1E+02 0.0024 22.8 7.6 42 175-216 112-155 (159)
8 PF04703 FaeA: FaeA-like prote 42.6 39 0.00085 24.2 3.5 44 122-170 4-47 (62)
9 TIGR00831 a_cpa1 Na+/H+ antipo 39.7 48 0.001 31.1 4.5 36 150-185 486-521 (525)
10 PF08463 EcoEI_R_C: EcoEI R pr 39.5 1.3E+02 0.0029 23.2 6.3 63 123-186 3-79 (164)
11 PF03701 UPF0181: Uncharacteri 38.2 52 0.0011 23.9 3.5 30 126-159 16-45 (51)
12 PF09548 Spore_III_AB: Stage I 37.6 2.2E+02 0.0047 23.0 8.3 89 118-215 61-152 (170)
13 PF05008 V-SNARE: Vesicle tran 34.8 1.1E+02 0.0024 21.1 4.7 42 170-212 31-72 (79)
14 PF06819 Arc_PepC: Archaeal Pe 34.1 17 0.00038 29.3 0.6 58 115-172 45-108 (110)
15 TIGR00425 CBF5 rRNA pseudourid 32.7 36 0.00078 30.9 2.4 25 112-136 36-60 (322)
16 PRK12523 RNA polymerase sigma 32.4 1E+02 0.0022 23.5 4.6 39 177-215 128-168 (172)
17 PRK11924 RNA polymerase sigma 32.1 1E+02 0.0022 22.6 4.4 40 177-216 134-175 (179)
18 PF08148 DSHCT: DSHCT (NUC185) 31.4 87 0.0019 25.4 4.2 45 176-220 131-178 (180)
19 PF03238 ESAG1: ESAG protein; 31.0 33 0.00072 31.0 1.9 24 128-153 7-32 (231)
20 PF15005 IZUMO: Izumo sperm-eg 30.3 2.7E+02 0.0058 23.5 7.0 60 129-188 44-107 (160)
21 PF05794 Tcp11: T-complex prot 29.4 76 0.0016 28.3 3.9 31 157-188 118-158 (441)
22 TIGR02787 codY_Gpos GTP-sensin 29.2 1.1E+02 0.0024 27.8 4.9 81 132-216 137-221 (251)
23 PF05761 5_nucleotid: 5' nucle 28.8 1.7E+02 0.0037 27.8 6.2 65 149-214 321-385 (448)
24 PRK07037 extracytoplasmic-func 28.7 1.3E+02 0.0029 22.3 4.5 35 181-215 122-158 (163)
25 PLN00091 photosystem I reactio 28.0 36 0.00078 29.3 1.5 42 87-128 89-134 (160)
26 PF00727 IL4: Interleukin 4 Th 27.8 31 0.00066 28.1 1.0 25 114-138 92-116 (117)
27 PTZ00238 expression site-assoc 27.3 46 0.001 31.4 2.2 25 127-153 103-129 (326)
28 PTZ00436 60S ribosomal protein 27.1 3E+02 0.0064 26.5 7.4 59 154-212 101-168 (357)
29 PRK04217 hypothetical protein; 26.6 1.6E+02 0.0035 23.2 4.8 44 175-218 49-94 (110)
30 COG3923 PriC Primosomal replic 25.9 2.1E+02 0.0045 25.2 5.8 97 115-215 38-164 (175)
31 PRK12529 RNA polymerase sigma 25.1 3.2E+02 0.007 21.1 6.8 39 175-213 134-174 (178)
32 PRK12528 RNA polymerase sigma 24.9 3E+02 0.0064 20.5 6.6 40 175-214 120-161 (161)
33 COG2761 FrnE Predicted dithiol 24.1 4.9E+02 0.011 23.1 7.8 50 164-213 114-180 (225)
34 PLN03244 alpha-amylase; Provis 23.9 62 0.0013 33.9 2.6 42 7-51 9-54 (872)
35 PF13747 DUF4164: Domain of un 23.8 3.2E+02 0.007 20.6 6.4 16 196-211 48-63 (89)
36 COG3579 PepC Aminopeptidase C 23.7 1.6E+02 0.0034 28.9 5.1 37 145-181 169-215 (444)
37 PRK12547 RNA polymerase sigma 22.8 1.9E+02 0.0041 21.9 4.5 35 182-216 126-162 (164)
38 COG3937 Uncharacterized conser 22.5 2.9E+02 0.0062 22.6 5.6 51 124-181 2-56 (108)
39 TIGR01806 CM_mono2 chorismate 22.4 2.3E+02 0.0049 22.0 4.9 26 151-180 43-68 (114)
40 PRK07764 DNA polymerase III su 22.0 7.4E+02 0.016 25.4 9.6 23 108-130 169-191 (824)
41 PF10130 PIN_2: PIN domain; I 21.8 2.5E+02 0.0054 22.4 5.1 45 160-212 44-89 (133)
42 KOG2546 Abl interactor ABI-1, 21.8 3.7E+02 0.008 26.8 7.2 70 36-135 362-431 (483)
43 PF10271 Tmp39: Putative trans 21.5 58 0.0013 31.2 1.8 43 123-165 179-225 (423)
44 PF05120 GvpG: Gas vesicle pro 21.3 3.7E+02 0.008 20.3 6.2 67 138-210 6-72 (79)
45 COG0393 Uncharacterized conser 21.2 1.4E+02 0.003 24.1 3.6 52 123-174 32-84 (108)
46 PRK00967 hypothetical protein; 21.1 1.5E+02 0.0032 23.0 3.6 48 122-169 31-79 (105)
47 KOG4797 Transcriptional regula 20.8 2.5E+02 0.0055 23.5 5.1 59 126-201 46-104 (123)
48 PRK12531 RNA polymerase sigma 20.5 2.2E+02 0.0049 22.2 4.6 33 183-215 156-190 (194)
49 COG3140 Uncharacterized protei 20.4 1.4E+02 0.003 22.4 3.2 29 126-154 16-44 (60)
50 PF08312 cwf21: cwf21 domain; 20.3 3E+02 0.0065 18.9 4.7 33 180-212 11-43 (46)
51 cd02867 PseudoU_synth_TruB_4 P 20.1 68 0.0015 29.4 1.9 24 113-136 3-26 (312)
52 TIGR02952 Sig70_famx2 RNA poly 20.1 2.1E+02 0.0046 21.1 4.2 33 182-214 136-170 (170)
53 PRK09637 RNA polymerase sigma 20.1 2.2E+02 0.0047 22.3 4.5 35 181-215 119-155 (181)
No 1
>PLN02960 alpha-amylase
Probab=75.21 E-value=3 Score=43.01 Aligned_cols=47 Identities=17% Similarity=0.232 Sum_probs=35.4
Q ss_pred cccccccCCCCCCccccccccccCCCCCCccccceeeecCCCCCCCCCC
Q 027687 3 ATFFPFLSQPNSPLFNHFTSKNQTSRNPSQRSYNSIKCSNTSNNSTPVP 51 (220)
Q Consensus 3 sT~l~~ls~pnp~~l~h~t~~~~ts~~~~~~~~fsikC~~ts~~s~~~~ 51 (220)
|+|+.|--+|||+..+|.-.+.-++.|..++..|-|+| ++.+.++.+
T Consensus 5 ~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~c--~~~~~~~~~ 51 (897)
T PLN02960 5 SLFLRFPRPPNPLVHAEPRRLGASRVNLPRKIGFKITC--FAAPRPRQP 51 (897)
T ss_pred ccccccCCCCCccccccCCCCCccccCCccccccceee--ccCCCCCcc
Confidence 56777888999999988866666777777888999999 555544443
No 2
>PF05266 DUF724: Protein of unknown function (DUF724); InterPro: IPR007930 This family contains several uncharacterised proteins found exclusively in Arabidopsis thaliana.
Probab=60.38 E-value=1.1e+02 Score=26.03 Aligned_cols=110 Identities=23% Similarity=0.221 Sum_probs=69.1
Q ss_pred CCCccccceeeccccccCCcchhHHHHHHHHHHhhhcccchhhHHHhhhhHHHHHHHHHH--HHHhhcchhhHHHHHHHH
Q 027687 100 PPNFEVGWKRTKEISLEKPIGFVIMDFLEKLQGLMERDYGSTALLAKVGELVAERAREEA--EVLRDEGKVEERMVTELS 177 (220)
Q Consensus 100 ppnfeigwkRTkei~Lekp~G~vI~dflekle~Lm~r~fGS~~Llak~geiVaERAreEa--EvLrdegkVeermvtElf 177 (220)
|..-=..|.+|. -.||+ .||=|......|..|+.-..+++.++...-..=.+-.+.++ ..|-.+=+.-|+-+.||-
T Consensus 67 ~~~~f~~~~~tl-~~LE~-~GFnV~~l~~RL~kLL~lk~~~~~~~e~~k~le~~~~~~~~~~~~~e~~i~~Le~ki~el~ 144 (190)
T PF05266_consen 67 SRSSFESLMKTL-SELEE-HGFNVKFLRSRLNKLLSLKDDQEKLLEERKKLEKKIEEKEAELKELESEIKELEMKILELQ 144 (190)
T ss_pred cHHHHHHHHHHH-HHHHH-cCCccHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Confidence 333333455443 24777 89999999999999999999999998865443333333322 222233334466677777
Q ss_pred HHHHHH-----HHhHHHHHHHhhhhHHHHHHHHHHHHHH
Q 027687 178 RVLRLM-----EMDMAMVKAAVKEETLSERLEQAKARCR 211 (220)
Q Consensus 178 RVLrLm-----eMDlamVkAavKEeTl~ERle~ArarCr 211 (220)
|-..+| ++|....+.-+..+.+++.++.++-+-+
T Consensus 145 ~~~~~~~~~ke~~~~ei~~lks~~~~l~~~~~~~e~~F~ 183 (190)
T PF05266_consen 145 RQAAKLKEKKEAKDKEISRLKSEAEALKEEIENAELEFQ 183 (190)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 754333 3565555566667777777777776653
No 3
>PRK09568 DNA primase large subunit; Reviewed
Probab=56.80 E-value=56 Score=29.87 Aligned_cols=73 Identities=15% Similarity=0.313 Sum_probs=48.9
Q ss_pred HHHHHHHhhhcccchhhHHHhhh---hHHHHHHHHHHHHHhhcchh-------hHHHHHHHHHHHHHHHHhHHHHHHHhh
Q 027687 126 FLEKLQGLMERDYGSTALLAKVG---ELVAERAREEAEVLRDEGKV-------EERMVTELSRVLRLMEMDMAMVKAAVK 195 (220)
Q Consensus 126 flekle~Lm~r~fGS~~Llak~g---eiVaERAreEaEvLrdegkV-------eermvtElfRVLrLmeMDlamVkAavK 195 (220)
||....+.+.+ ||.|.-|+... ..+.|||.|-++.-...|.+ ++-++.=+-|+| =++++
T Consensus 10 Fl~~a~~~v~~-~~~g~~L~~ll~~~~~~v~rA~eRv~~al~~~~~~~~~~~~~~vlsy~~a~~l----------vs~~~ 78 (306)
T PRK09568 10 FIKSLEDELKK-YGGGITLSDLLLNSTTLIDQAKDRIQKIKSGEELPHYVSYNEPVLVFYTTLLS----------LAILN 78 (306)
T ss_pred ChHHHHHHHHh-hcCCCcHHHHHcCcHHHHHHHHHHHHHHhccCCccCccccchhHHHHHHHHHH----------HHHcC
Confidence 78888888887 99996555553 77888998888888887777 443333322332 34566
Q ss_pred hhHHHHHHHHHHHH
Q 027687 196 EETLSERLEQAKAR 209 (220)
Q Consensus 196 EeTl~ERle~Arar 209 (220)
+..|-+|.-.|.|+
T Consensus 79 d~~l~~R~A~~Eak 92 (306)
T PRK09568 79 DLRLIRKYAHKEAK 92 (306)
T ss_pred ChHHHHHHHHHHHH
Confidence 66777776655543
No 4
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=51.40 E-value=1.1e+02 Score=23.35 Aligned_cols=22 Identities=18% Similarity=0.223 Sum_probs=19.6
Q ss_pred hhhhHHHHHHHHHHHHHHHHhH
Q 027687 194 VKEETLSERLEQAKARCRQAIL 215 (220)
Q Consensus 194 vKEeTl~ERle~ArarCrqAIl 215 (220)
+.+.|++.||..|++.|++++.
T Consensus 146 is~~tV~~~l~ra~~~~~~~~~ 167 (168)
T PRK12525 146 VSLSRIHQYMVEAFKCCYQGFQ 167 (168)
T ss_pred CCHHHHHHHHHHHHHHHHHhhc
Confidence 5678999999999999999874
No 5
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=50.33 E-value=85 Score=26.39 Aligned_cols=82 Identities=27% Similarity=0.424 Sum_probs=53.4
Q ss_pred cceeeccccccCCcchhHHHHHHHHHHhhhcccchhhHHHhhhhHHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHH
Q 027687 106 GWKRTKEISLEKPIGFVIMDFLEKLQGLMERDYGSTALLAKVGELVAERAREEAEVLRDEGKVEERMVTELSRVLRLMEM 185 (220)
Q Consensus 106 gwkRTkei~Lekp~G~vI~dflekle~Lm~r~fGS~~Llak~geiVaERAreEaEvLrdegkVeermvtElfRVLrLmeM 185 (220)
||=|-..+++..+. |+++.+...++. .+-...|..=+.-|.++|.+.+|=
T Consensus 66 GyIRI~rv~~~~~~-----~~~~~l~~~ig~------------~is~~~a~~ii~~L~e~~~it~RE------------- 115 (152)
T PF05848_consen 66 GYIRIVRVPLDDEE-----DLLDHLIESIGD------------SISQQDAEDIIQRLLEEGLITERE------------- 115 (152)
T ss_dssp -EEEEEEEEESTCH-----HHHHHHHCCS-S---------------HHHHHHHHHHHHHTTSS-HHH-------------
T ss_pred ceEEEEEEccCCcH-----HHHHHHHHHhcC------------cCCHHHHHHHHHHHHHCCCCCHHH-------------
Confidence 88888888888754 445544444322 233344555567788999998874
Q ss_pred hHHHHHHHhhhhHHH---HHHHHHHHHHHHHhHhhc
Q 027687 186 DMAMVKAAVKEETLS---ERLEQAKARCRQAILVAN 218 (220)
Q Consensus 186 DlamVkAavKEeTl~---ERle~ArarCrqAIlva~ 218 (220)
-.|+++|+..++|. +.=++.||+.-++++...
T Consensus 116 -a~l~~~~i~~~~L~~~~~~rd~lRA~ilk~mL~~L 150 (152)
T PF05848_consen 116 -ANLMKAAISDETLNVDLPDRDELRARILKAMLLRL 150 (152)
T ss_dssp -HHHHHHHT-HHHH-S-TTHHHHHHHHHHHHHHHHH
T ss_pred -HHHHHHHhhHHhcCCCccchHHHHHHHHHHHHHHh
Confidence 46788999999988 666788899888887654
No 6
>PF15412 Nse4-Nse3_bdg: Binding domain of Nse4/EID3 to Nse3-MAGE
Probab=49.69 E-value=8.8 Score=26.58 Aligned_cols=36 Identities=17% Similarity=0.373 Sum_probs=32.0
Q ss_pred cccceeeccccccCCcchhHHHHHHHHHHhhhcccch
Q 027687 104 EVGWKRTKEISLEKPIGFVIMDFLEKLQGLMERDYGS 140 (220)
Q Consensus 104 eigwkRTkei~Lekp~G~vI~dflekle~Lm~r~fGS 140 (220)
++|.++++.+.+. ..|+=+-+|+.+|-..|...+..
T Consensus 10 dla~~ka~~lk~~-~~~fd~deFv~~l~~fm~~~~~~ 45 (56)
T PF15412_consen 10 DLAAEKARNLKFG-GSGFDVDEFVSKLKTFMGGNRFE 45 (56)
T ss_pred HHHHHHHHHhccC-CCccCHHHHHHHHHHHhCcccCC
Confidence 5788899999999 89999999999999999996654
No 7
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=49.07 E-value=1.1e+02 Score=22.82 Aligned_cols=42 Identities=10% Similarity=0.191 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHhHHHHHHH--hhhhHHHHHHHHHHHHHHHHhHh
Q 027687 175 ELSRVLRLMEMDMAMVKAA--VKEETLSERLEQAKARCRQAILV 216 (220)
Q Consensus 175 ElfRVLrLmeMDlamVkAa--vKEeTl~ERle~ArarCrqAIlv 216 (220)
++|....+-+|..+-|... +.+.|+..|+..|+++||+.|.-
T Consensus 112 ~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~ 155 (159)
T PRK12527 112 DSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155 (159)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 4555556677777777654 57899999999999999998764
No 8
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=42.63 E-value=39 Score=24.24 Aligned_cols=44 Identities=30% Similarity=0.292 Sum_probs=34.9
Q ss_pred hHHHHHHHHHHhhhcccchhhHHHhhhhHHHHHHHHHHHHHhhcchhhH
Q 027687 122 VIMDFLEKLQGLMERDYGSTALLAKVGELVAERAREEAEVLRDEGKVEE 170 (220)
Q Consensus 122 vI~dflekle~Lm~r~fGS~~Llak~geiVaERAreEaEvLrdegkVee 170 (220)
-|.+|+... ..--+|.=+|.+-++-.-.||-=.+.|.+||+|+.
T Consensus 4 ~Il~~i~~~-----~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~ 47 (62)
T PF04703_consen 4 KILEYIKEQ-----NGPLKTREIADALGLSIYQARYYLEKLEKEGKVER 47 (62)
T ss_dssp CHHHHHHHH-----TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE
T ss_pred HHHHHHHHc-----CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 366777766 33457888999999999999999999999999964
No 9
>TIGR00831 a_cpa1 Na+/H+ antiporter, bacterial form. This model is specific for the bacterial members of this family.
Probab=39.72 E-value=48 Score=31.12 Aligned_cols=36 Identities=31% Similarity=0.389 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHH
Q 027687 150 LVAERAREEAEVLRDEGKVEERMVTELSRVLRLMEM 185 (220)
Q Consensus 150 iVaERAreEaEvLrdegkVeermvtElfRVLrLmeM 185 (220)
.+.+.-|++...|+++|++++.++.++.|-|.+.|.
T Consensus 486 ~~l~~er~~l~~~~~~~~i~~~~~~~~~~~ld~~e~ 521 (525)
T TIGR00831 486 YVLDAKRSAVVDLRAGGLISQEVLLELMRELDLKEA 521 (525)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhhHHHH
Confidence 455777889999999999999999999888865553
No 10
>PF08463 EcoEI_R_C: EcoEI R protein C-terminal; InterPro: IPR013670 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. Type III restriction endonucleases (3.1.21.5 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) [, ]. This entry represents the C-terminal domain found in both the R subunit of type I enzymes and the Res subunit of type III enzymes. The type I enzyme represented is EcoEI, which recognises 5'-GAGN(7)ATGC-3; the R protein (HsdR) is required for both nuclease and ATPase activity [, ]. ; GO: 0003677 DNA binding, 0003824 catalytic activity, 0006304 DNA modification
Probab=39.52 E-value=1.3e+02 Score=23.18 Aligned_cols=63 Identities=17% Similarity=0.267 Sum_probs=41.5
Q ss_pred HHHHHHHHHHhhhcccchhhHHHhhhhHHHHHHHHHHHHHhh-----cchhhHHHHHH--------HHHHHHHH-HHh
Q 027687 123 IMDFLEKLQGLMERDYGSTALLAKVGELVAERAREEAEVLRD-----EGKVEERMVTE--------LSRVLRLM-EMD 186 (220)
Q Consensus 123 I~dflekle~Lm~r~fGS~~Llak~geiVaERAreEaEvLrd-----egkVeermvtE--------lfRVLrLm-eMD 186 (220)
..||++++++.|...+.+-+-|.++=.- ..-.+++.+.|.. +...+++.+.+ ||.+||-+ -||
T Consensus 3 ~~~y~e~~~~~l~~~~~~~~al~~i~~~-~~~~~~~L~eL~~~l~~~~~~~~~~~l~~~~~~~~~dl~~~ir~i~g~d 79 (164)
T PF08463_consen 3 AEDYRERFRKYLREHFDDIEALRKIWSN-PPLTEADLKELEEKLIDPEELFTEEDLWETYEAIDADLFDFIRHILGLD 79 (164)
T ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHcC-cccCHHHHHHHHHhCcccccccCHHHHHhhcccccCCHHHHHHHHHhcC
Confidence 3689999999999998887777665433 2222333333333 33455555544 99999988 888
No 11
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=38.21 E-value=52 Score=23.86 Aligned_cols=30 Identities=37% Similarity=0.520 Sum_probs=23.6
Q ss_pred HHHHHHHhhhcccchhhHHHhhhhHHHHHHHHHH
Q 027687 126 FLEKLQGLMERDYGSTALLAKVGELVAERAREEA 159 (220)
Q Consensus 126 flekle~Lm~r~fGS~~Llak~geiVaERAreEa 159 (220)
-.|++..||..--+|++-++ +||+..|++.
T Consensus 16 AvE~Iq~LMaqGmSsgEAI~----~VA~~iRe~~ 45 (51)
T PF03701_consen 16 AVERIQELMAQGMSSGEAIA----IVAQEIREEH 45 (51)
T ss_pred HHHHHHHHHHhcccHHHHHH----HHHHHHHHHH
Confidence 36899999999999998776 5666666653
No 12
>PF09548 Spore_III_AB: Stage III sporulation protein AB (spore_III_AB); InterPro: IPR014198 This entry represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=37.65 E-value=2.2e+02 Score=22.96 Aligned_cols=89 Identities=22% Similarity=0.303 Sum_probs=52.5
Q ss_pred CcchhHHHHHHHHHHhhhcccchhhHHHhhhhHHHHHHHHHHHHHhhcchhhH---HHHHHHHHHHHHHHHhHHHHHHHh
Q 027687 118 PIGFVIMDFLEKLQGLMERDYGSTALLAKVGELVAERAREEAEVLRDEGKVEE---RMVTELSRVLRLMEMDMAMVKAAV 194 (220)
Q Consensus 118 p~G~vI~dflekle~Lm~r~fGS~~Llak~geiVaERAreEaEvLrdegkVee---rmvtElfRVLrLmeMDlamVkAav 194 (220)
..+.-+.+|+..+.+.|.+.=|.+ +.+--++..+.+..+....+ .++.++.+.|=-.+.|...=.=..
T Consensus 61 ~~~~~~~~~f~~~a~~L~~~~~~~---------~~~~w~~~~~~~~~~~~L~~~d~e~L~~lg~~LG~~D~~~Q~k~i~l 131 (170)
T PF09548_consen 61 RSEGPIGEFFERVAERLEKNEGES---------FAEAWEEAVEKLLKESALKKEDKEILLELGKSLGYSDREMQEKHIEL 131 (170)
T ss_pred cccchHHHHHHHHHHHHHcCCCCC---------HHHHHHHHHHhhhhcCCCCHHHHHHHHHHHHHHccCCHHHHHHHHHH
Confidence 344567788888888887765553 23334455555555555533 344455555544444433333334
Q ss_pred hhhHHHHHHHHHHHHHHHHhH
Q 027687 195 KEETLSERLEQAKARCRQAIL 215 (220)
Q Consensus 195 KEeTl~ERle~ArarCrqAIl 215 (220)
-.+-|...+++||+.+++-.-
T Consensus 132 ~~~~L~~~~~~a~~~~~~~~K 152 (170)
T PF09548_consen 132 YLEQLEQQLEEAREEAKKKGK 152 (170)
T ss_pred HHHHHHHHHHHHHHHHHhccc
Confidence 467788899999998876443
No 13
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=34.79 E-value=1.1e+02 Score=21.13 Aligned_cols=42 Identities=17% Similarity=0.371 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 027687 170 ERMVTELSRVLRLMEMDMAMVKAAVKEETLSERLEQAKARCRQ 212 (220)
Q Consensus 170 ermvtElfRVLrLmeMDlamVkAavKEeTl~ERle~ArarCrq 212 (220)
++-+.|.-..|.-||+.+..+-++.+ ..+..||...|..+..
T Consensus 31 e~~l~ea~~~l~qMe~E~~~~p~s~r-~~~~~kl~~yr~~l~~ 72 (79)
T PF05008_consen 31 ERDLDEAEELLKQMELEVRSLPPSER-NQYKSKLRSYRSELKK 72 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHCTS-HHHH-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHH-HHHHHHHHHHHHHHHH
Confidence 45567777888999999888866555 6788999998888754
No 14
>PF06819 Arc_PepC: Archaeal Peptidase A24 C-terminal Domain; InterPro: IPR009639 This region is of unknown function found at the C terminus of some archael proteins that have multiple transmembrane domains and are predicted to be aspartic peptidases belonging to the MEROPS peptidase subfamily A24A (type 4 prepilin peptidase 1.
Probab=34.11 E-value=17 Score=29.27 Aligned_cols=58 Identities=22% Similarity=0.362 Sum_probs=39.4
Q ss_pred ccCCcchhH--HHHHHHHHHhhhcccchhh----HHHhhhhHHHHHHHHHHHHHhhcchhhHHH
Q 027687 115 LEKPIGFVI--MDFLEKLQGLMERDYGSTA----LLAKVGELVAERAREEAEVLRDEGKVEERM 172 (220)
Q Consensus 115 Lekp~G~vI--~dflekle~Lm~r~fGS~~----Llak~geiVaERAreEaEvLrdegkVeerm 172 (220)
.+|..|++. .||+++|..++.-.=|+.. ++...|+=..+--=|....|++|||+++.+
T Consensus 45 ~~k~~~v~~d~~~~~~r~k~~l~~~~~~~l~g~~i~~~~~EGLs~E~IE~Lk~Lv~eGKi~nef 108 (110)
T PF06819_consen 45 YEKDDGVYRDRSSFFKRFKFALKTEDGSALTGEKIISTDAEGLSKEDIEKLKKLVEEGKIENEF 108 (110)
T ss_pred EEeCCcEEEecccHHHHHHHHHHhcccccccCCeEEeccccCCCHHHHHHHHHHHHcCCCcccc
Confidence 455555333 7899999999988666552 233445555555566777889999998764
No 15
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=32.66 E-value=36 Score=30.85 Aligned_cols=25 Identities=16% Similarity=0.327 Sum_probs=22.5
Q ss_pred cccccCCcchhHHHHHHHHHHhhhc
Q 027687 112 EISLEKPIGFVIMDFLEKLQGLMER 136 (220)
Q Consensus 112 ei~Lekp~G~vI~dflekle~Lm~r 136 (220)
-|.+.||.|+.=.|.+.++..++..
T Consensus 36 ~l~i~KP~g~tS~~~v~~vr~~~~~ 60 (322)
T TIGR00425 36 VVNLDKPSGPSSHEVVAWVRRILNV 60 (322)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhcc
Confidence 4789999999999999999998863
No 16
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=32.42 E-value=1e+02 Score=23.46 Aligned_cols=39 Identities=23% Similarity=0.203 Sum_probs=27.9
Q ss_pred HHHHHHHHHhHHHHHHH--hhhhHHHHHHHHHHHHHHHHhH
Q 027687 177 SRVLRLMEMDMAMVKAA--VKEETLSERLEQAKARCRQAIL 215 (220)
Q Consensus 177 fRVLrLmeMDlamVkAa--vKEeTl~ERle~ArarCrqAIl 215 (220)
|..-.+-+|..+-|-.. +.+.|+..||-.|+++|+..+-
T Consensus 128 ~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~ 168 (172)
T PRK12523 128 FLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALY 168 (172)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 33333445666655543 5789999999999999998764
No 17
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=32.12 E-value=1e+02 Score=22.62 Aligned_cols=40 Identities=15% Similarity=0.150 Sum_probs=29.0
Q ss_pred HHHHHHHHHhHHHHHHH--hhhhHHHHHHHHHHHHHHHHhHh
Q 027687 177 SRVLRLMEMDMAMVKAA--VKEETLSERLEQAKARCRQAILV 216 (220)
Q Consensus 177 fRVLrLmeMDlamVkAa--vKEeTl~ERle~ArarCrqAIlv 216 (220)
|....+-+|..+-|-.. +.+.|+..++..|+++||+.+.-
T Consensus 134 ~~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~ 175 (179)
T PRK11924 134 FLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEA 175 (179)
T ss_pred hhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 33334556666655443 57899999999999999998753
No 18
>PF08148 DSHCT: DSHCT (NUC185) domain; InterPro: IPR012961 This C-terminal domain is found in DOB1/SK12/helY-like DEAD box helicases [].; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; PDB: 4A4Z_A 2XGJ_B 3L9O_A.
Probab=31.41 E-value=87 Score=25.38 Aligned_cols=45 Identities=22% Similarity=0.293 Sum_probs=29.9
Q ss_pred HHHHHHHHHHhHHHHHHH---hhhhHHHHHHHHHHHHHHHHhHhhcCC
Q 027687 176 LSRVLRLMEMDMAMVKAA---VKEETLSERLEQAKARCRQAILVANSF 220 (220)
Q Consensus 176 lfRVLrLmeMDlamVkAa---vKEeTl~ERle~ArarCrqAIlva~s~ 220 (220)
+.|.+|-++-=+..|..| .....|.++.++|....+.-|..+.|+
T Consensus 131 iVR~~rRl~dlLrql~~aa~~~g~~~L~~~~~~a~~~i~R~iV~~~SL 178 (180)
T PF08148_consen 131 IVRWIRRLIDLLRQLANAAKIIGDPELAEKAREAIDLIRRDIVFASSL 178 (180)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCCT-HHHHHHHHHHHHHHSHCCCC---T
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccCCccccccc
Confidence 345555555445555555 788999999999999988888777664
No 19
>PF03238 ESAG1: ESAG protein; InterPro: IPR004922 Trypanosoma brucei is the causative agent of sleeping sickness in humans and nagana in cattle. The parasite lives extracellularly in the blood and tissue fluids of the mammalian host, and is transmitted by the bite of infected tsetse. Each variant surface glycoprotein (Vsg) expression site (ES) in bloodstream-form T. brucei is a polycistronic transcription unit containing several distinct expression site-associated genes (esag), in addition to a single vsg gene. They are co-transcribed with the gene encoding the VSG protein, forming the surface coat of the parasite. ESAG1 genes from different ESs encode a highly polymorphic family of membrane-associated glycoproteins, whose function is unknown [].
Probab=31.00 E-value=33 Score=30.99 Aligned_cols=24 Identities=54% Similarity=0.862 Sum_probs=19.9
Q ss_pred HHHHHhhhcccch--hhHHHhhhhHHHH
Q 027687 128 EKLQGLMERDYGS--TALLAKVGELVAE 153 (220)
Q Consensus 128 ekle~Lm~r~fGS--~~Llak~geiVaE 153 (220)
+|||.|+ -||. |.|+||||+..||
T Consensus 7 dKLEKLI--SyGN~MGDLVaKvGGLFAe 32 (231)
T PF03238_consen 7 DKLEKLI--SYGNEMGDLVAKVGGLFAE 32 (231)
T ss_pred hhHHHHH--HcCcchhhHHHhccchhHH
Confidence 6888888 5775 7899999999876
No 20
>PF15005 IZUMO: Izumo sperm-egg fusion
Probab=30.29 E-value=2.7e+02 Score=23.51 Aligned_cols=60 Identities=18% Similarity=0.240 Sum_probs=48.5
Q ss_pred HHHHhhhcccchhhHHHhhhh----HHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHHhHH
Q 027687 129 KLQGLMERDYGSTALLAKVGE----LVAERAREEAEVLRDEGKVEERMVTELSRVLRLMEMDMA 188 (220)
Q Consensus 129 kle~Lm~r~fGS~~Llak~ge----iVaERAreEaEvLrdegkVeermvtElfRVLrLmeMDla 188 (220)
-+++++.+.|-..+.++.|++ -|+.-...+..-|.+...=++-++.||+.+++...--++
T Consensus 44 ~m~~~~~~~~~~~a~~g~vd~~~L~~va~~~~~~lkrl~~s~~kg~~ll~EL~~~r~~~~~~lk 107 (160)
T PF15005_consen 44 EMEDFFFLPYAEDAFMGVVDEDTLDKVAWSFKNQLKRLTDSDLKGEPLLKELVWMRQNQKKELK 107 (160)
T ss_pred HhhCccccccchhhhhhhccHHHHHHHHHHHHHHHHHHhcCCcccchHHHHHHHHHHHHHHHHH
Confidence 356667778888899999886 466777789999999999999999999999987765444
No 21
>PF05794 Tcp11: T-complex protein 11; InterPro: IPR008862 This family consists of several eukaryotic T-complex protein 11 (Tcp11) related sequences. Tcp11 is only expressed in fertile adult mammalian testes and is thought to be important in sperm function and fertility. The family also contains the Saccharomyces cerevisiae Sok1 protein which is known to suppress cyclic AMP-dependent protein kinase mutants [].
Probab=29.36 E-value=76 Score=28.31 Aligned_cols=31 Identities=29% Similarity=0.470 Sum_probs=22.1
Q ss_pred HHHHHHhhc----------chhhHHHHHHHHHHHHHHHHhHH
Q 027687 157 EEAEVLRDE----------GKVEERMVTELSRVLRLMEMDMA 188 (220)
Q Consensus 157 eEaEvLrde----------gkVeermvtElfRVLrLmeMDla 188 (220)
++++.|+++ +.+-+ .+..+|.+|.+|-+|+|
T Consensus 118 ~~v~~l~~~~~~~~~~~~~~~~V~-~lr~if~~le~MklD~A 158 (441)
T PF05794_consen 118 EEVKALVEKIEEGCTESSATDIVD-GLRFIFEILELMKLDMA 158 (441)
T ss_pred HHHHHHHHHHHhccccCCHHHHHH-HHHHHHHHHHHHHHHHH
Confidence 456666653 23333 56789999999999997
No 22
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=29.17 E-value=1.1e+02 Score=27.82 Aligned_cols=81 Identities=16% Similarity=0.254 Sum_probs=52.9
Q ss_pred Hhhhcccchh----hHHHhhhhHHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHHhHHHHHHHhhhhHHHHHHHHHH
Q 027687 132 GLMERDYGST----ALLAKVGELVAERAREEAEVLRDEGKVEERMVTELSRVLRLMEMDMAMVKAAVKEETLSERLEQAK 207 (220)
Q Consensus 132 ~Lm~r~fGS~----~Llak~geiVaERAreEaEvLrdegkVeermvtElfRVLrLmeMDlamVkAavKEeTl~ERle~Ar 207 (220)
.|+=-|||+| ++|-...+-..|.||..+-|=.+=+-.-=-=+.-+-++|+.+.-| .+-+.+..|.+|+--.|
T Consensus 137 DliLaEy~aTVVG~Eilr~~~~~iEee~Rkka~Vq~Ai~tLSySEleAv~~IL~~L~~~----egrlse~eLAerlGVSR 212 (251)
T TIGR02787 137 DLVLAEYAATVVGMELLRAQAEEIEEEARKKAAVQMAINTLSYSELEAVEHIFEELDGN----EGLLVASKIADRVGITR 212 (251)
T ss_pred cchhhhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHhHHHHHHHHHHHhccc----cccccHHHHHHHHCCCH
Confidence 3445567766 677777778888888888776665544322222333344444332 13467788999999999
Q ss_pred HHHHHHhHh
Q 027687 208 ARCRQAILV 216 (220)
Q Consensus 208 arCrqAIlv 216 (220)
.-||+|+..
T Consensus 213 s~ireAlrk 221 (251)
T TIGR02787 213 SVIVNALRK 221 (251)
T ss_pred HHHHHHHHH
Confidence 999999853
No 23
>PF05761 5_nucleotid: 5' nucleotidase family; InterPro: IPR008380 This family includes a 5'-nucleotidase, 3.1.3.5 from EC, specific for purines (IMP and GMP) []. These enzymes are members of the Haloacid Dehalogenase (HAD) superfamily. HAD members are recognised by three short motifs {hhhhDxDx(T/V)}, {hhhh(T/S)}, and either {hhhh(D/E)(D/E)x(3-4)(G/N)} or {hhhh(G/N)(D/E)x(3-4)(D/E)} (where "h" stands for a hydrophobic residue). Crystal structures of many HAD enzymes has verified PSI-PRED predictions of secondary structural elements which show each of the "hhhh" sequences of the motifs as part of beta sheets. This subfamily of enzymes is part of "Subfamily I" of the HAD superfamily by virtue of a "cap" domain in between motifs 1 and 2. This subfamily's cap domain has a different predicted secondary structure than all other known HAD enzymes and thus has been designated "subfamily IG", the domain appears to consist of a mixed alpha/beta fold.; PDB: 2BDE_A 2XCW_A 2XCX_A 2XCV_A 2XJB_A 2JCM_A 2XJE_A 2J2C_A 2XJF_A 2XJD_A ....
Probab=28.81 E-value=1.7e+02 Score=27.83 Aligned_cols=65 Identities=12% Similarity=0.204 Sum_probs=49.3
Q ss_pred hHHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHHhHHHHHHHhhhhHHHHHHHHHHHHHHHHh
Q 027687 149 ELVAERAREEAEVLRDEGKVEERMVTELSRVLRLMEMDMAMVKAAVKEETLSERLEQAKARCRQAI 214 (220)
Q Consensus 149 eiVaERAreEaEvLrdegkVeermvtElfRVLrLmeMDlamVkAavKEeTl~ERle~ArarCrqAI 214 (220)
..|++....|++++..+-...++ +.+|-..+..++..+..++..-+..+..+.+.+.++..+++.
T Consensus 321 ~~Ii~ELe~Ei~~~~~~~~~~~~-l~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 385 (448)
T PF05761_consen 321 AAIIPELEQEIEIWNSKKYRFEE-LQELEELLEELQDHLDQLRSSSELRPDISELRKERRELRREM 385 (448)
T ss_dssp EEE-TTHHHHHHHHHHTHHHHHH-HHHHHHHCHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEEehhhhhhhhhhhhcchhhhH-HHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHH
Confidence 35677888999999988877777 778888888888887777766777777777777777776654
No 24
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=28.73 E-value=1.3e+02 Score=22.31 Aligned_cols=35 Identities=17% Similarity=0.222 Sum_probs=27.2
Q ss_pred HHHHHhHHHHHHH--hhhhHHHHHHHHHHHHHHHHhH
Q 027687 181 RLMEMDMAMVKAA--VKEETLSERLEQAKARCRQAIL 215 (220)
Q Consensus 181 rLmeMDlamVkAa--vKEeTl~ERle~ArarCrqAIl 215 (220)
.+-+|..+-|.+. +.+.|++.++..|+++||+.+.
T Consensus 122 ~~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~ 158 (163)
T PRK07037 122 RLHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLD 158 (163)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 4456666666554 5789999999999999998763
No 25
>PLN00091 photosystem I reaction center subunit V (PsaG); Provisional
Probab=27.96 E-value=36 Score=29.34 Aligned_cols=42 Identities=36% Similarity=0.528 Sum_probs=32.4
Q ss_pred hhhhhccCCCCCCCCCccccceeecc----ccccCCcchhHHHHHH
Q 027687 87 RERRARTGLVKPEPPNFEVGWKRTKE----ISLEKPIGFVIMDFLE 128 (220)
Q Consensus 87 r~r~~rt~l~~~eppnfeigwkRTke----i~Lekp~G~vI~dfle 128 (220)
|+.-.|+.-+|.--.-||-|=.|-|| +.-+.|.|+.|+|-|-
T Consensus 89 R~~v~kq~P~qnG~Thfeagd~ra~E~~sllksnDPaGFtiVDVlA 134 (160)
T PLN00091 89 RENVAKQVPEQNGLTHFEAGDDRAKEYVSLLKSNDPVGFNIVDVLA 134 (160)
T ss_pred hhhHhhhCCCcCCceeeecccHHHHHHHhhhccCCCCcceeehhhh
Confidence 44445665567777889999999887 4578999999999874
No 26
>PF00727 IL4: Interleukin 4 This family is a subset of the SCOP family; InterPro: IPR002354 Cytokines are protein messengers that carry information from cell to cell []. Interleukin is one such molecule, and participates in several B-cell activation processes: e.g., it enhances production and secretion of IgG1 and IgE []; it induces expression of class II major histocompatability complex (MHC) molecules on resting B-cells; and it regulates expression of the low affinity Fc receptor for IgE on lymphocytes and monocytes. Interleukin-4 (IL4) has a compact, globular fold (similar to other cytokines), stabilised by 3 disulphide bonds []. One half of the structure is dominated by a 4 alpha-helix bundle with a left-handed twist []. The helices are anti-parallel, with 2 overhand connections, which fall into a 2-stranded anti-parallel beta-sheet [].; GO: 0005136 interleukin-4 receptor binding, 0008083 growth factor activity, 0006955 immune response, 0005576 extracellular region; PDB: 1HIK_A 1HZI_A 1ITI_A 2INT_A 1RCB_A 1CYL_A 3QB7_A 1BBN_A 2B8Z_A 1ITM_A ....
Probab=27.79 E-value=31 Score=28.11 Aligned_cols=25 Identities=28% Similarity=0.595 Sum_probs=18.1
Q ss_pred cccCCcchhHHHHHHHHHHhhhccc
Q 027687 114 SLEKPIGFVIMDFLEKLQGLMERDY 138 (220)
Q Consensus 114 ~Lekp~G~vI~dflekle~Lm~r~f 138 (220)
|....+--..-||||+|...|++.|
T Consensus 92 ~Vne~~~ttLkdFLe~Lk~imq~ky 116 (117)
T PF00727_consen 92 PVNEAKQTTLKDFLERLKTIMQEKY 116 (117)
T ss_dssp ---SSSEEEHHHHHHHHHHHHHHHH
T ss_pred CCCccchhhHHHHHHHHHHHHHhhc
Confidence 3445555568899999999999876
No 27
>PTZ00238 expression site-associated gene (ESAG); Provisional
Probab=27.32 E-value=46 Score=31.39 Aligned_cols=25 Identities=52% Similarity=0.799 Sum_probs=19.5
Q ss_pred HHHHHHhhhcccch--hhHHHhhhhHHHH
Q 027687 127 LEKLQGLMERDYGS--TALLAKVGELVAE 153 (220)
Q Consensus 127 lekle~Lm~r~fGS--~~Llak~geiVaE 153 (220)
-+|||.|+. ||. |.|+||||+..||
T Consensus 103 hDKLEKLIS--yGN~MGDLVaKvGGLFae 129 (326)
T PTZ00238 103 HDKLEKLIS--YGNAMGDLVAKVGGLFAE 129 (326)
T ss_pred chhHHHHHH--hcchhhhHHHHhchhhHH
Confidence 467777775 554 7899999999876
No 28
>PTZ00436 60S ribosomal protein L19-like protein; Provisional
Probab=27.09 E-value=3e+02 Score=26.48 Aligned_cols=59 Identities=25% Similarity=0.270 Sum_probs=36.3
Q ss_pred HHHHHHHHHhhcchhhHHHHHHHHHH--------HHHHHHhHHHHHH-HhhhhHHHHHHHHHHHHHHH
Q 027687 154 RAREEAEVLRDEGKVEERMVTELSRV--------LRLMEMDMAMVKA-AVKEETLSERLEQAKARCRQ 212 (220)
Q Consensus 154 RAreEaEvLrdegkVeermvtElfRV--------LrLmeMDlamVkA-avKEeTl~ERle~ArarCrq 212 (220)
-.|.+.-.|||+|+++-.+-.+|++- .+-|..-+.-.|+ ..++..|.+.++.-|++-+|
T Consensus 101 aLRRlLKklRd~gKIDkh~YR~LYrKAKGn~FKNK~~L~e~I~k~KaE~~R~K~L~dQ~eArR~k~~~ 168 (357)
T PTZ00436 101 ILRRLLRKYREEKKIDRHIYRELYVKAKGNVFRNKRNLMEHIHKVKNEKKKERQLAEQLAAKRLKDEQ 168 (357)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhcCCccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 35788999999999999999999653 3333223333332 23444555555554444433
No 29
>PRK04217 hypothetical protein; Provisional
Probab=26.56 E-value=1.6e+02 Score=23.22 Aligned_cols=44 Identities=16% Similarity=0.189 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhHHHHHH--HhhhhHHHHHHHHHHHHHHHHhHhhc
Q 027687 175 ELSRVLRLMEMDMAMVKA--AVKEETLSERLEQAKARCRQAILVAN 218 (220)
Q Consensus 175 ElfRVLrLmeMDlamVkA--avKEeTl~ERle~ArarCrqAIlva~ 218 (220)
|+++.+..-++..+-|.. -+...|+..+|..|++.+++++.-..
T Consensus 49 eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~ 94 (110)
T PRK04217 49 EALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGR 94 (110)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 334334344444444433 36789999999999999999886544
No 30
>COG3923 PriC Primosomal replication protein N'' [DNA replication, recombination, and repair]
Probab=25.88 E-value=2.1e+02 Score=25.16 Aligned_cols=97 Identities=23% Similarity=0.243 Sum_probs=52.8
Q ss_pred ccCCcchhHHHHHHHHHHhhhc-----ccchhhHHHhhhhHHHHHHHHHHHHHhh---------cch---------hhHH
Q 027687 115 LEKPIGFVIMDFLEKLQGLMER-----DYGSTALLAKVGELVAERAREEAEVLRD---------EGK---------VEER 171 (220)
Q Consensus 115 Lekp~G~vI~dflekle~Lm~r-----~fGS~~Llak~geiVaERAreEaEvLrd---------egk---------Veer 171 (220)
|=.-+|-++-++|+.+..-|+. +-|+-- -....|||.---++.|.. +.- -.++
T Consensus 38 LFs~~g~~ls~ylqEa~~tL~aL~~~~e~~~l~----q~afLAErLlAQi~Al~relt~~~ir~~~~~p~~i~~~~~~~~ 113 (175)
T COG3923 38 LFSENGQLLSFYLQEAGQTLTALKQAVEQDRLP----QVAFLAERLLAQIEALSRELTTQSIREWDPAPPHIARLYRKLA 113 (175)
T ss_pred HHhhcCchHHHHHHHHHHHHHHHHHHHhccchH----HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCccchhhHHHH
Confidence 4456788899999888776654 222221 112334443333333322 111 1122
Q ss_pred HHHHHHHHHHHHHHhHHH----HHHHhhhhHHHHHH---HHHHHHHHHHhH
Q 027687 172 MVTELSRVLRLMEMDMAM----VKAAVKEETLSERL---EQAKARCRQAIL 215 (220)
Q Consensus 172 mvtElfRVLrLmeMDlam----VkAavKEeTl~ERl---e~ArarCrqAIl 215 (220)
.-.+--|-|.+|.-|++. .+-.|.-++|..-| |+=.||||+|+.
T Consensus 114 qhqd~Errl~~m~~~r~l~l~q~s~~vEqq~lqqel~~~e~RlarCr~Ale 164 (175)
T COG3923 114 QHQDYERRLLAMVQDRRLQLAQQSDLVEQQKLQQELEAYEQRLARCRHALE 164 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 233445666677767655 44455566666554 566799999974
No 31
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=25.08 E-value=3.2e+02 Score=21.06 Aligned_cols=39 Identities=18% Similarity=0.163 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhHHHHHHH--hhhhHHHHHHHHHHHHHHHH
Q 027687 175 ELSRVLRLMEMDMAMVKAA--VKEETLSERLEQAKARCRQA 213 (220)
Q Consensus 175 ElfRVLrLmeMDlamVkAa--vKEeTl~ERle~ArarCrqA 213 (220)
++|..-.+-+|..+-|-+. +.+.|++-|+-.|.++|++.
T Consensus 134 ~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 134 QAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 3344444456777766554 57899999999999999987
No 32
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=24.85 E-value=3e+02 Score=20.53 Aligned_cols=40 Identities=15% Similarity=0.226 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhHHHHHHH--hhhhHHHHHHHHHHHHHHHHh
Q 027687 175 ELSRVLRLMEMDMAMVKAA--VKEETLSERLEQAKARCRQAI 214 (220)
Q Consensus 175 ElfRVLrLmeMDlamVkAa--vKEeTl~ERle~ArarCrqAI 214 (220)
++|..-.+-+|+.+-|... +...|+.-||..|+.+||-|.
T Consensus 120 ~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~ 161 (161)
T PRK12528 120 RAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRCYFAL 161 (161)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhcC
Confidence 3444445566776666554 568999999999999999763
No 33
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=24.15 E-value=4.9e+02 Score=23.13 Aligned_cols=50 Identities=18% Similarity=0.283 Sum_probs=39.9
Q ss_pred hcchhhHHHHHHHHHHHHH-----------------HHHhHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 027687 164 DEGKVEERMVTELSRVLRL-----------------MEMDMAMVKAAVKEETLSERLEQAKARCRQA 213 (220)
Q Consensus 164 degkVeermvtElfRVLrL-----------------meMDlamVkAavKEeTl~ERle~ArarCrqA 213 (220)
..|++-++++.-||.-+=+ +-||.+-+|+.+..++..+++.+.-+.-+|+
T Consensus 114 ~~G~~~~~~~~~lf~AyF~eg~nI~D~dVL~diA~~~GLD~~~~~~~L~s~~~~~avr~d~~~A~e~ 180 (225)
T COG2761 114 LQGKAQDRFLEALFEAYFEEGRNIGDEDVLADIAEEVGLDREEFKADLASDAAKDAVRQDEAAAQEM 180 (225)
T ss_pred HhCchHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHhCCCHHHHHHHHhChHHHHHHHHHHHHHHHC
Confidence 4566778888887765432 5689999999999999999999888877765
No 34
>PLN03244 alpha-amylase; Provisional
Probab=23.94 E-value=62 Score=33.94 Aligned_cols=42 Identities=24% Similarity=0.448 Sum_probs=24.6
Q ss_pred cccCCCCCCccccccccccCCCC----CCccccceeeecCCCCCCCCCC
Q 027687 7 PFLSQPNSPLFNHFTSKNQTSRN----PSQRSYNSIKCSNTSNNSTPVP 51 (220)
Q Consensus 7 ~~ls~pnp~~l~h~t~~~~ts~~----~~~~~~fsikC~~ts~~s~~~~ 51 (220)
+|+.+|||+-|- .....+++-+ |.++..+.|+| ++.+-+|.+
T Consensus 9 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~ 54 (872)
T PLN03244 9 QFSCHPNASNLP-FSEKNRLAINGVNFPKKKIKLKIRC--FAAEQPQQE 54 (872)
T ss_pred ceeecCCCCCCC-cccCCccccccccCCccccccceee--cccCCCchh
Confidence 357899964442 1123444433 44567788999 776655554
No 35
>PF13747 DUF4164: Domain of unknown function (DUF4164)
Probab=23.81 E-value=3.2e+02 Score=20.57 Aligned_cols=16 Identities=38% Similarity=0.594 Sum_probs=10.9
Q ss_pred hhHHHHHHHHHHHHHH
Q 027687 196 EETLSERLEQAKARCR 211 (220)
Q Consensus 196 EeTl~ERle~ArarCr 211 (220)
..-|.++|+++.+||.
T Consensus 48 r~rLa~eLD~~~ar~~ 63 (89)
T PF13747_consen 48 RSRLAQELDQAEARAN 63 (89)
T ss_pred HHHHHHHHHhHHHHHH
Confidence 3456777777777774
No 36
>COG3579 PepC Aminopeptidase C [Amino acid transport and metabolism]
Probab=23.75 E-value=1.6e+02 Score=28.93 Aligned_cols=37 Identities=30% Similarity=0.583 Sum_probs=28.3
Q ss_pred HhhhhHHHHHHHHHHHHHhh---cch-------hhHHHHHHHHHHHH
Q 027687 145 AKVGELVAERAREEAEVLRD---EGK-------VEERMVTELSRVLR 181 (220)
Q Consensus 145 ak~geiVaERAreEaEvLrd---egk-------VeermvtElfRVLr 181 (220)
...-.+..+|.|+-|++||+ ||. +.|.|+.|+|+.|-
T Consensus 169 r~ln~~Ln~~LR~dAqiLR~a~~eg~~~~~v~~~kEe~l~eif~~l~ 215 (444)
T COG3579 169 RELNALLNKLLRQDAQILRDALKEGADDDTVEALKEELLQEIFNFLA 215 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHH
Confidence 34456789999999999996 443 35788899998764
No 37
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=22.82 E-value=1.9e+02 Score=21.88 Aligned_cols=35 Identities=17% Similarity=0.220 Sum_probs=26.1
Q ss_pred HHHHhHHHHHH--HhhhhHHHHHHHHHHHHHHHHhHh
Q 027687 182 LMEMDMAMVKA--AVKEETLSERLEQAKARCRQAILV 216 (220)
Q Consensus 182 LmeMDlamVkA--avKEeTl~ERle~ArarCrqAIlv 216 (220)
+-+|+.+-|-. .+.+.|+..||..|++++|+.+.+
T Consensus 126 ~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 162 (164)
T PRK12547 126 ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKV 162 (164)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 34555555543 367999999999999999987643
No 38
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=22.52 E-value=2.9e+02 Score=22.58 Aligned_cols=51 Identities=27% Similarity=0.330 Sum_probs=34.1
Q ss_pred HHHHHHHHHhhhcccchhhHHHhhhhHHHHHHHHHHHHHhhcchhh----HHHHHHHHHHHH
Q 027687 124 MDFLEKLQGLMERDYGSTALLAKVGELVAERAREEAEVLRDEGKVE----ERMVTELSRVLR 181 (220)
Q Consensus 124 ~dflekle~Lm~r~fGS~~Llak~geiVaERAreEaEvLrdegkVe----ermvtElfRVLr 181 (220)
||+-+-|..+|.--+|++++ ++|++.+=+.-|++.|+++ -++|.||.|=++
T Consensus 2 ~~m~~~l~k~~~~gaG~~a~-------~~ek~~klvDelVkkGeln~eEak~~vddl~~q~k 56 (108)
T COG3937 2 MYMGEGLRKLALIGAGLAAE-------TAEKVQKLVDELVKKGELNAEEAKRFVDDLLRQAK 56 (108)
T ss_pred chHHHHHHHHHHhhccHHHH-------HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence 34455566666666775554 4567777777888888875 367777776554
No 39
>TIGR01806 CM_mono2 chorismate mutase, putative. This model represents a clade of probable chorismate mutases from alpha, beta and gamma proteobacteria as well as Mycobacterium tuberculosis and a clade of nematodes. Although the most likely function for the enzymes represented by this model is as a chorismate mutase, in no species are these enzymes the sole chorismate mutase in the genome. Also, in no case are these enzymes located in a region of the genome proximal to any other enzymes involved in chorismate pathways. Although the Pantoea enzyme has been shown to complement a CM-free mutant of E. coli, this was also shown to be the case with isochorismate-pyruvate lyase which only has a secondary (non-physiologically relevant) chorismate mutase activity. This enzyme is believed to be a homodimer and be localized to the periplasm.
Probab=22.40 E-value=2.3e+02 Score=22.04 Aligned_cols=26 Identities=19% Similarity=0.291 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHhhcchhhHHHHHHHHHHH
Q 027687 151 VAERAREEAEVLRDEGKVEERMVTELSRVL 180 (220)
Q Consensus 151 VaERAreEaEvLrdegkVeermvtElfRVL 180 (220)
|.+++++.++ ++++++..+..+|+.+
T Consensus 43 Vl~~~~~~a~----~~gL~~~~i~~if~~I 68 (114)
T TIGR01806 43 VLDSLRAQAQ----SAGLDPDYVTRFFQAQ 68 (114)
T ss_pred HHHHHHHHhH----cCCCCHHHHHHHHHHH
Confidence 3444444443 3789999999999875
No 40
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=21.99 E-value=7.4e+02 Score=25.45 Aligned_cols=23 Identities=22% Similarity=0.304 Sum_probs=18.1
Q ss_pred eeeccccccCCcchhHHHHHHHH
Q 027687 108 KRTKEISLEKPIGFVIMDFLEKL 130 (220)
Q Consensus 108 kRTkei~Lekp~G~vI~dflekl 130 (220)
+|...+.+.++....|.++|.++
T Consensus 169 SRc~~v~F~~l~~~~l~~~L~~i 191 (824)
T PRK07764 169 SRTHHYPFRLVPPEVMRGYLERI 191 (824)
T ss_pred hheeEEEeeCCCHHHHHHHHHHH
Confidence 56667778888888888888775
No 41
>PF10130 PIN_2: PIN domain; InterPro: IPR019298 This entry represents a set of bacterial and archaeal proteins that are predicted to be RNases (from similarities to 5'-exonucleases).
Probab=21.83 E-value=2.5e+02 Score=22.38 Aligned_cols=45 Identities=24% Similarity=0.380 Sum_probs=28.4
Q ss_pred HHHhhcchhh-HHHHHHHHHHHHHHHHhHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 027687 160 EVLRDEGKVE-ERMVTELSRVLRLMEMDMAMVKAAVKEETLSERLEQAKARCRQ 212 (220)
Q Consensus 160 EvLrdegkVe-ermvtElfRVLrLmeMDlamVkAavKEeTl~ERle~ArarCrq 212 (220)
+.|....++. +.+..-+..+++.+.+ |.++...+-+++|+.+|++
T Consensus 44 ~~I~~k~~l~~~~~~~~l~~l~~~I~i--------v~~~~~~~~~~~A~~~~~~ 89 (133)
T PF10130_consen 44 PKIAKKSKLSEEELEEVLNILFSRIKI--------VPEEIYSENIEEAREIIRD 89 (133)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHhheEE--------ecHHHhHHHHHHHHHHhcC
Confidence 3444444444 4444444444445444 7788889999999999965
No 42
>KOG2546 consensus Abl interactor ABI-1, contains SH3 domain [Signal transduction mechanisms; Cytoskeleton]
Probab=21.76 E-value=3.7e+02 Score=26.80 Aligned_cols=70 Identities=23% Similarity=0.440 Sum_probs=40.2
Q ss_pred ceeeecCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCcccchhhchhhhhhhhhhccCCCCCCCCCccccceeeccccc
Q 027687 36 NSIKCSNTSNNSTPVPAQPEDESFPSPYPNSIATESSDTFPIEKRRKSEILRERRARTGLVKPEPPNFEVGWKRTKEISL 115 (220)
Q Consensus 36 fsikC~~ts~~s~~~~~~~~~~~f~~P~P~s~t~n~~~~f~iekrr~s~i~r~r~~rt~l~~~eppnfeigwkRTkei~L 115 (220)
-+|+-++|+++-++...||.--++|.|+|.+-.. ..+......++-||-+.=
T Consensus 362 ~~i~~~~tsppp~~~~~~~~~~dlppPp~~~~~~------------------~g~ee~st~~~~~~~ap~---------- 413 (483)
T KOG2546|consen 362 RNLNRNDTSPPPSPPSNQPGPDDLPPPPPKSLSD------------------LGREEKSTLPQPPPVAPS---------- 413 (483)
T ss_pred cccccccCCCCCCCccccCCCCCCCCCCCCcccc------------------ccccccccCCCCCCCCCC----------
Confidence 3455666776555554455444444444443221 122244566666665542
Q ss_pred cCCcchhHHHHHHHHHHhhh
Q 027687 116 EKPIGFVIMDFLEKLQGLME 135 (220)
Q Consensus 116 ekp~G~vI~dflekle~Lm~ 135 (220)
-.||+=..||||...+-+
T Consensus 414 --sp~w~p~syLEkVv~iyd 431 (483)
T KOG2546|consen 414 --SPAWVPTSYLEKVVAIYD 431 (483)
T ss_pred --CcccccHHHHHHHHhhcc
Confidence 278999999999987753
No 43
>PF10271 Tmp39: Putative transmembrane protein; InterPro: IPR019397 This is a family of putative, eukaryote, transmembrane proteins but the function is unknown.
Probab=21.55 E-value=58 Score=31.17 Aligned_cols=43 Identities=26% Similarity=0.353 Sum_probs=34.1
Q ss_pred HHHHHHHHHHhhhcc----cchhhHHHhhhhHHHHHHHHHHHHHhhc
Q 027687 123 IMDFLEKLQGLMERD----YGSTALLAKVGELVAERAREEAEVLRDE 165 (220)
Q Consensus 123 I~dflekle~Lm~r~----fGS~~Llak~geiVaERAreEaEvLrde 165 (220)
-.||++-+.+..+.. ++..++..-.....++.+|+|+|.|+++
T Consensus 179 ~~~~l~~~~~~~~~~~~~i~~~~~~~~H~C~~~p~~IR~EV~~Lk~D 225 (423)
T PF10271_consen 179 SRDFLSLLREWLKSPPVQINSQEDMPLHSCSLSPDQIREEVEVLKMD 225 (423)
T ss_pred cchhhHHHHHHhhCCccccccccCCccccCCCCHHHHHHHHHHHHHH
Confidence 578888888887775 3445666777777899999999999986
No 44
>PF05120 GvpG: Gas vesicle protein G ; InterPro: IPR007804 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in water to access oxygen and/or light. Proteins containing this family are involved in the formation of gas vesicles [].
Probab=21.28 E-value=3.7e+02 Score=20.34 Aligned_cols=67 Identities=27% Similarity=0.359 Sum_probs=38.9
Q ss_pred cchhhHHHhhhhHHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHHhHHHHHHHhhhhHHHHHHHHHHHHH
Q 027687 138 YGSTALLAKVGELVAERAREEAEVLRDEGKVEERMVTELSRVLRLMEMDMAMVKAAVKEETLSERLEQAKARC 210 (220)
Q Consensus 138 fGS~~Llak~geiVaERAreEaEvLrdegkVeermvtElfRVLrLmeMDlamVkAavKEeTl~ERle~ArarC 210 (220)
+|.--.+..+|+.|.+.|..| +.|.+.|..+ +.+|-+-+.+=|++-+--. -.|+.|..||+.|+++-
T Consensus 6 laPvrgv~wv~e~I~~~Ae~E---~~Dp~~i~~~-L~~L~~~~e~GEIseeEf~--~~E~eLL~rL~~~~~~~ 72 (79)
T PF05120_consen 6 LAPVRGVVWVAEQIQEQAERE---LYDPAAIRRE-LAELQEALEAGEISEEEFE--RREDELLDRLEEARRRE 72 (79)
T ss_pred cchHHHHHHHHHHHHHHHHHH---HcCHHHHHHH-HHHHHHHHHcCCCCHHHHH--HHHHHHHHHHHHHHHHH
Confidence 333344555666666666443 3455555443 3455555555555554433 46888999999988753
No 45
>COG0393 Uncharacterized conserved protein [Function unknown]
Probab=21.18 E-value=1.4e+02 Score=24.15 Aligned_cols=52 Identities=23% Similarity=0.263 Sum_probs=40.6
Q ss_pred HHHHHHHHHHhhhcccch-hhHHHhhhhHHHHHHHHHHHHHhhcchhhHHHHH
Q 027687 123 IMDFLEKLQGLMERDYGS-TALLAKVGELVAERAREEAEVLRDEGKVEERMVT 174 (220)
Q Consensus 123 I~dflekle~Lm~r~fGS-~~Llak~geiVaERAreEaEvLrdegkVeermvt 174 (220)
.-||+.-+..+.+-+-|+ +++|+.+=+...+|.++||+.|-+.+-|.=|+=+
T Consensus 32 ~~d~~agir~i~GGe~~~Y~~~l~~aR~~Al~rm~~~A~~lGAnAVVgvr~d~ 84 (108)
T COG0393 32 GRDIFAGIRDIVGGEIKAYEKMLAEAREEALERMVDEAEALGANAVVGVRFDY 84 (108)
T ss_pred hhhHHHhhhhhhccchHHHHHHHHHHHHHHHHHHHHHHHHhCCCeEEEEEech
Confidence 347777777777665443 7899999999999999999999999887655433
No 46
>PRK00967 hypothetical protein; Provisional
Probab=21.14 E-value=1.5e+02 Score=23.01 Aligned_cols=48 Identities=19% Similarity=0.319 Sum_probs=37.9
Q ss_pred hHHHHHHHHHHhhhcccch-hhHHHhhhhHHHHHHHHHHHHHhhcchhh
Q 027687 122 VIMDFLEKLQGLMERDYGS-TALLAKVGELVAERAREEAEVLRDEGKVE 169 (220)
Q Consensus 122 vI~dflekle~Lm~r~fGS-~~Llak~geiVaERAreEaEvLrdegkVe 169 (220)
++-||...|..+.+-+.++ +++|..+=+.+.+|..++|+.|-+.+-|.
T Consensus 31 ~~~d~~a~~r~~~GGe~~~y~~~l~~aR~eA~~rm~~~A~~~GAnAIIg 79 (105)
T PRK00967 31 IVRDIGAGLKNVVGGEIKGYTEMLTEARDIAIDRMKEEAKQKGANAIVG 79 (105)
T ss_pred hHhHHHHHHhHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHcCCCEEEE
Confidence 3678888888887776654 67888888899999999998887776553
No 47
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=20.76 E-value=2.5e+02 Score=23.45 Aligned_cols=59 Identities=25% Similarity=0.361 Sum_probs=41.9
Q ss_pred HHHHHHHhhhcccchhhHHHhhhhHHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHHhHHHHHHHhhhhHHHH
Q 027687 126 FLEKLQGLMERDYGSTALLAKVGELVAERAREEAEVLRDEGKVEERMVTELSRVLRLMEMDMAMVKAAVKEETLSE 201 (220)
Q Consensus 126 flekle~Lm~r~fGS~~Llak~geiVaERAreEaEvLrdegkVeermvtElfRVLrLmeMDlamVkAavKEeTl~E 201 (220)
.=.|+|.-||- |-.-..=..|||.|+|+.. ++||.--.+.+|-.-.+.|.-+--|+|..
T Consensus 46 IDNKIeQAMDL----------VKtHLmfAVREEVe~Lk~q-------I~eL~er~~~Le~EN~lLk~~~spe~L~q 104 (123)
T KOG4797|consen 46 IDNKIEQAMDL----------VKTHLMFAVREEVEVLKEQ-------IRELEERNSALERENSLLKTLASPEQLAQ 104 (123)
T ss_pred echHHHHHHHH----------HHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHhhCCHHHHHH
Confidence 34677777762 2223344579999999853 67787778888888888888888777754
No 48
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=20.51 E-value=2.2e+02 Score=22.19 Aligned_cols=33 Identities=21% Similarity=0.227 Sum_probs=24.7
Q ss_pred HHHhHHHHHH--HhhhhHHHHHHHHHHHHHHHHhH
Q 027687 183 MEMDMAMVKA--AVKEETLSERLEQAKARCRQAIL 215 (220)
Q Consensus 183 meMDlamVkA--avKEeTl~ERle~ArarCrqAIl 215 (220)
=+|..+-|-. -+.+.|+..||..|+++||+++-
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 3455555544 35788999999999999998763
No 49
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.44 E-value=1.4e+02 Score=22.38 Aligned_cols=29 Identities=28% Similarity=0.351 Sum_probs=22.9
Q ss_pred HHHHHHHhhhcccchhhHHHhhhhHHHHH
Q 027687 126 FLEKLQGLMERDYGSTALLAKVGELVAER 154 (220)
Q Consensus 126 flekle~Lm~r~fGS~~Llak~geiVaER 154 (220)
-+|++.+||..-..||+-++-|+..+-|+
T Consensus 16 AVE~Iq~lMaeGmSsGEAIa~VA~elRe~ 44 (60)
T COG3140 16 AVERIQELMAEGMSSGEAIALVAQELREN 44 (60)
T ss_pred HHHHHHHHHHccccchhHHHHHHHHHHHH
Confidence 36899999999999999888766554443
No 50
>PF08312 cwf21: cwf21 domain; InterPro: IPR013170 The cwf21 domain is found in proteins involved in mRNA splicing. Proteins containing this domain have been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe (Fission yeast) []. In yeast, this domain binds the protein Prp8p [], a large and highly conserved U5 snRNP protein which has been proposed as a protein cofactor at the spliceosomal catalytic centre []. The cwf21 domain is found in, amongst others, the small Cwc21p protein in yeast as well as in the much larger human ortholog SRm300 (serine/arginine repetitive matrix protein). ; PDB: 2E62_A.
Probab=20.27 E-value=3e+02 Score=18.87 Aligned_cols=33 Identities=15% Similarity=0.374 Sum_probs=23.1
Q ss_pred HHHHHHhHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 027687 180 LRLMEMDMAMVKAAVKEETLSERLEQAKARCRQ 212 (220)
Q Consensus 180 LrLmeMDlamVkAavKEeTl~ERle~ArarCrq 212 (220)
+++|++--.|=...+.++++.++++..|++-.+
T Consensus 11 lk~~elrd~LEe~g~~~eeIe~kv~~~R~~L~~ 43 (46)
T PF08312_consen 11 LKCLELRDELEEQGYSEEEIEEKVDELRKKLLE 43 (46)
T ss_dssp HHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHh
Confidence 455666666666667899999999999987644
No 51
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=20.13 E-value=68 Score=29.44 Aligned_cols=24 Identities=25% Similarity=0.463 Sum_probs=22.2
Q ss_pred ccccCCcchhHHHHHHHHHHhhhc
Q 027687 113 ISLEKPIGFVIMDFLEKLQGLMER 136 (220)
Q Consensus 113 i~Lekp~G~vI~dflekle~Lm~r 136 (220)
+.++||.|+.=+|++.++..++..
T Consensus 3 l~i~KP~G~TS~~vv~~lk~~l~~ 26 (312)
T cd02867 3 FAINKPSGITSAQVLNDLKPLFLN 26 (312)
T ss_pred EEEeCCCCCCHHHHHHHHHHHhcc
Confidence 679999999999999999999875
No 52
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=20.07 E-value=2.1e+02 Score=21.11 Aligned_cols=33 Identities=12% Similarity=0.015 Sum_probs=25.3
Q ss_pred HHHHhHHHHHHH--hhhhHHHHHHHHHHHHHHHHh
Q 027687 182 LMEMDMAMVKAA--VKEETLSERLEQAKARCRQAI 214 (220)
Q Consensus 182 LmeMDlamVkAa--vKEeTl~ERle~ArarCrqAI 214 (220)
+-+|..+-|-+. +.+.|+..|+..|++++|+.+
T Consensus 136 ~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l 170 (170)
T TIGR02952 136 GQNLPIAEVARILGKTEGAVKILQFRAIKKLARQM 170 (170)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 446666666554 578999999999999999753
No 53
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=20.06 E-value=2.2e+02 Score=22.31 Aligned_cols=35 Identities=6% Similarity=0.187 Sum_probs=26.2
Q ss_pred HHHHHhHHHHHH--HhhhhHHHHHHHHHHHHHHHHhH
Q 027687 181 RLMEMDMAMVKA--AVKEETLSERLEQAKARCRQAIL 215 (220)
Q Consensus 181 rLmeMDlamVkA--avKEeTl~ERle~ArarCrqAIl 215 (220)
.+-+|+++-|-. .+.+.|+..|+..|++.+++.+.
T Consensus 119 ~~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 119 ELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred HhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 345566655544 35688999999999999999774
Done!