Query psy8200
Match_columns 530
No_of_seqs 328 out of 582
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 21:12:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8200.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8200hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07851 TMPIT: TMPIT-like pro 100.0 3.2E-61 6.9E-66 492.8 5.6 169 304-480 92-274 (330)
2 PF04707 PRELI: PRELI-like fam 100.0 2.3E-49 5.1E-54 369.1 22.6 153 105-259 3-157 (157)
3 KOG3336|consensus 100.0 2.2E-45 4.7E-50 343.6 17.8 162 97-260 6-172 (185)
4 KOG4758|consensus 100.0 5.3E-48 1.1E-52 363.8 -3.0 139 317-457 4-146 (220)
5 KOG3337|consensus 100.0 6.1E-38 1.3E-42 293.8 9.2 162 95-260 9-170 (201)
6 PF07851 TMPIT: TMPIT-like pro 100.0 2E-34 4.3E-39 295.7 -1.2 85 1-85 155-250 (330)
7 PF09788 Tmemb_55A: Transmembr 100.0 3.8E-31 8.1E-36 261.4 7.0 70 453-522 41-113 (256)
8 KOG4684|consensus 100.0 4.2E-31 9.2E-36 254.9 5.3 75 448-522 51-128 (275)
9 KOG4758|consensus 99.9 1.1E-28 2.4E-33 233.2 -2.8 88 1-89 43-137 (220)
10 PF10698 DUF2505: Protein of u 96.0 0.42 9E-06 44.9 16.0 117 127-249 38-155 (159)
11 PF02121 IP_trans: Phosphatidy 94.1 1.7 3.6E-05 44.8 14.7 112 136-252 54-232 (254)
12 PF11331 DUF3133: Protein of u 93.7 0.037 8E-07 42.8 1.6 37 470-506 2-43 (46)
13 cd07815 SRPBCC_PITP Lipid-bind 88.5 9.9 0.00021 39.2 13.3 40 139-178 55-95 (251)
14 PF13719 zinc_ribbon_5: zinc-r 82.9 0.91 2E-05 33.2 2.0 30 474-503 2-34 (37)
15 cd08890 SRPBCC_PITPNC1_like Li 81.2 29 0.00062 35.9 12.6 53 124-178 37-94 (250)
16 PF13717 zinc_ribbon_4: zinc-r 72.3 2.7 5.9E-05 30.7 1.8 30 474-503 2-34 (36)
17 cd08889 SRPBCC_PITPNM1-2_like 65.7 23 0.00049 36.8 7.5 63 137-204 56-119 (260)
18 PRK00398 rpoP DNA-directed RNA 63.7 7.1 0.00015 29.5 2.7 36 474-511 3-38 (46)
19 PF10122 Mu-like_Com: Mu-like 61.6 5 0.00011 31.9 1.5 39 472-510 2-40 (51)
20 PRK03824 hypA hydrogenase nick 60.9 5.8 0.00013 36.9 2.1 16 473-488 69-84 (135)
21 TIGR02098 MJ0042_CXXC MJ0042 f 55.8 7.8 0.00017 27.9 1.6 29 475-503 3-34 (38)
22 PRK02935 hypothetical protein; 54.9 9.1 0.0002 34.8 2.2 41 471-515 67-107 (110)
23 PRK12380 hydrogenase nickel in 53.2 8.9 0.00019 34.6 1.9 14 414-427 4-17 (113)
24 TIGR00100 hypA hydrogenase nic 52.1 9.7 0.00021 34.4 2.0 16 414-429 4-19 (115)
25 PF11023 DUF2614: Protein of u 50.2 7.2 0.00016 35.7 0.8 41 471-515 66-106 (114)
26 cd08888 SRPBCC_PITPNA-B_like L 49.4 63 0.0014 33.6 7.5 57 137-198 54-113 (258)
27 COG5028 Vesicle coat complex C 48.8 8.5 0.00019 45.1 1.3 56 444-503 173-230 (861)
28 PF01396 zf-C4_Topoisom: Topoi 48.4 8.6 0.00019 28.5 0.9 25 494-519 1-25 (39)
29 COG4416 Com Mu-like prophage p 47.4 7 0.00015 31.6 0.3 38 472-509 2-39 (60)
30 TIGR01206 lysW lysine biosynth 47.2 13 0.00027 29.9 1.7 28 475-502 3-30 (54)
31 PRK00564 hypA hydrogenase nick 46.9 12 0.00027 33.9 1.9 12 414-425 4-15 (117)
32 PF03604 DNA_RNApol_7kD: DNA d 46.5 12 0.00025 27.0 1.3 20 496-519 2-21 (32)
33 PRK00415 rps27e 30S ribosomal 45.4 29 0.00063 28.5 3.5 41 470-513 7-47 (59)
34 PF15354 KAAG1: Kidney-associa 45.3 43 0.00094 28.5 4.6 61 248-321 20-84 (84)
35 KOG3668|consensus 45.0 75 0.0016 33.0 7.2 36 136-171 54-89 (269)
36 PRK03681 hypA hydrogenase nick 43.8 15 0.00033 33.2 1.9 13 414-426 4-16 (114)
37 PF13719 zinc_ribbon_5: zinc-r 43.1 17 0.00038 26.5 1.8 26 494-519 2-29 (37)
38 cd08868 START_STARD1_3_like Ch 41.1 3.4E+02 0.0074 26.2 11.6 96 117-223 76-180 (208)
39 smart00834 CxxC_CXXC_SSSS Puta 40.0 18 0.00038 26.0 1.4 28 475-502 6-34 (41)
40 PF04810 zf-Sec23_Sec24: Sec23 39.5 9.7 0.00021 28.2 -0.0 35 474-508 2-38 (40)
41 PF02150 RNA_POL_M_15KD: RNA p 37.3 16 0.00035 26.6 0.8 33 474-507 1-33 (35)
42 TIGR01206 lysW lysine biosynth 36.6 30 0.00065 27.7 2.3 29 494-523 2-31 (54)
43 cd08904 START_STARD6-like Lipi 36.0 4.5E+02 0.0097 26.1 12.6 116 119-246 75-203 (204)
44 PF06827 zf-FPG_IleRS: Zinc fi 35.8 30 0.00065 23.8 2.0 27 476-502 3-29 (30)
45 COG1198 PriA Primosomal protei 34.7 30 0.00064 40.8 2.9 38 470-507 431-475 (730)
46 PTZ00408 NAD-dependent deacety 32.6 22 0.00048 36.1 1.2 42 468-509 111-152 (242)
47 PRK03824 hypA hydrogenase nick 32.3 26 0.00056 32.6 1.6 33 493-525 69-118 (135)
48 PF09723 Zn-ribbon_8: Zinc rib 32.1 27 0.00059 26.1 1.4 28 475-502 6-34 (42)
49 KOG2824|consensus 30.7 47 0.001 34.9 3.2 35 470-504 236-272 (281)
50 PRK08351 DNA-directed RNA poly 29.5 22 0.00048 29.3 0.5 24 473-504 2-25 (61)
51 PF01155 HypA: Hydrogenase exp 29.0 23 0.00051 31.8 0.7 27 473-503 69-95 (113)
52 TIGR02605 CxxC_CxxC_SSSS putat 28.9 32 0.00069 26.3 1.3 28 475-502 6-34 (52)
53 PF10891 DUF2719: Protein of u 28.0 29 0.00063 30.0 1.0 21 486-507 15-35 (81)
54 cd00729 rubredoxin_SM Rubredox 28.0 35 0.00076 24.6 1.3 24 475-502 3-26 (34)
55 PF14369 zf-RING_3: zinc-finge 27.8 31 0.00066 25.2 1.0 26 476-502 4-29 (35)
56 PF06839 zf-GRF: GRF zinc fing 27.7 22 0.00047 26.9 0.2 27 496-523 2-33 (45)
57 TIGR00155 pqiA_fam integral me 27.2 45 0.00097 36.5 2.5 33 471-503 10-42 (403)
58 PF07282 OrfB_Zn_ribbon: Putat 27.0 40 0.00087 27.1 1.6 25 476-502 30-54 (69)
59 PF07295 DUF1451: Protein of u 26.9 44 0.00095 31.8 2.1 45 463-509 101-145 (146)
60 PRK11827 hypothetical protein; 25.9 53 0.0011 27.0 2.1 37 471-509 5-41 (60)
61 COG2835 Uncharacterized conser 25.8 54 0.0012 27.0 2.1 36 471-508 5-40 (60)
62 PTZ00083 40S ribosomal protein 25.8 80 0.0017 27.7 3.3 43 469-514 30-72 (85)
63 PRK12495 hypothetical protein; 24.6 34 0.00074 34.8 1.0 27 473-503 41-67 (226)
64 COG0675 Transposase and inacti 23.8 56 0.0012 32.7 2.3 21 475-502 310-330 (364)
65 PF09788 Tmemb_55A: Transmembr 23.4 43 0.00092 34.8 1.4 38 472-509 155-192 (256)
66 PLN00209 ribosomal protein S27 23.0 99 0.0021 27.2 3.3 43 469-514 31-73 (86)
67 PRK12860 transcriptional activ 22.9 47 0.001 33.0 1.5 34 468-501 128-161 (189)
68 PRK03681 hypA hydrogenase nick 22.4 54 0.0012 29.6 1.7 26 474-502 70-95 (114)
69 TIGR00595 priA primosomal prot 22.2 59 0.0013 36.4 2.3 39 470-508 209-254 (505)
70 KOG3312|consensus 22.2 50 0.0011 32.0 1.5 54 312-374 107-163 (186)
71 PF14353 CpXC: CpXC protein 22.0 82 0.0018 28.4 2.8 33 475-507 2-51 (128)
72 PRK00564 hypA hydrogenase nick 21.9 40 0.00088 30.6 0.8 13 474-486 71-83 (117)
73 COG5608 LEA14-like dessication 21.8 55 0.0012 31.7 1.7 51 320-384 69-119 (161)
74 PRK15103 paraquat-inducible me 21.7 48 0.001 36.4 1.5 30 474-503 10-39 (419)
75 PF09332 Mcm10: Mcm10 replicat 21.5 28 0.00061 37.5 -0.3 12 472-483 250-261 (344)
76 KOG1984|consensus 21.4 57 0.0012 39.2 2.1 59 444-504 310-370 (1007)
77 PF05624 LSR: Lipolysis stimul 21.2 45 0.00097 26.2 0.8 7 515-521 34-40 (49)
78 PRK06393 rpoE DNA-directed RNA 21.2 29 0.00063 28.9 -0.2 25 472-504 3-27 (64)
79 PF05191 ADK_lid: Adenylate ki 21.0 35 0.00077 25.0 0.2 28 475-502 2-29 (36)
80 PRK03988 translation initiatio 20.9 79 0.0017 29.8 2.5 35 474-508 102-137 (138)
81 PF05876 Terminase_GpA: Phage 20.3 87 0.0019 35.6 3.2 34 492-525 198-240 (557)
No 1
>PF07851 TMPIT: TMPIT-like protein; InterPro: IPR012926 A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this. ; GO: 0016021 integral to membrane
Probab=100.00 E-value=3.2e-61 Score=492.79 Aligned_cols=169 Identities=46% Similarity=0.731 Sum_probs=149.8
Q ss_pred CCCCCCceeeecCcc-----------cccCcceEEe--eceeeecccccceeeeec-cchhhHHHHHHHhhhhHhhhhcc
Q psy8200 304 MSPSGTSLSLIDKNW-----------TEGADYERVE--SPILCHDGESIQGSHVTS-RDELSFMFLLVWYYCTLTIRESI 369 (530)
Q Consensus 304 ~s~~g~~~sLi~~~~-----------~yk~dYekve--~~ilc~~gesiqgsHv~~-~~d~~~~fl~~~~y~tlt~re~i 369 (530)
+.+||.++++++|++ +|||||||++ .++++..+..+..+...+ .+|++|+||||||||||||||||
T Consensus 92 PkkNGlyL~liLGnVNVsll~k~~kf~yKdEYEkFKl~~tii~l~~~~~~~~~~~~r~~d~~~~f~lvwyY~tLtiRE~I 171 (330)
T PF07851_consen 92 PKKNGLYLRLILGNVNVSLLSKQAKFKYKDEYEKFKLYLTIILLLFAVALLFLLNYRVLDQLFNFLLVWYYCTLTIRESI 171 (330)
T ss_pred CCCCCcccceecccccceecccccccchhhhHHHHHHHHHHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456888888888775 8999999988 466666666656666665 59999999999999999999999
Q ss_pred cccCCCccchhhhhhHHHHHhhcceEEecCCCccccccHhhHHHHHHHHHHHHHhHhhhhcchhhhhhhcCccCCCcccc
Q psy8200 370 LKVNGSRIKGWWRMHHFISTVCSAVLLIWPNSVTWHLFRPQFMVFNVYISVVQALQFWYQQGVLYRLKALGERHNMDITI 449 (530)
Q Consensus 370 l~~ngs~i~~ww~~hhy~s~~~~~~~l~wp~~~~~~~f~~~f~~f~~~~~~vq~lq~~YQ~~~ly~~~alg~~~~md~tv 449 (530)
|++|||||||||+.|||+|+++|||+||||||++||+||+|||.|++|||+||+||||||||||||||||||+|+||||+
T Consensus 172 L~~NGS~Ik~WW~~HHy~s~~~s~v~Ltwp~~~~~~~fr~~fl~f~~~~~~vq~lQ~~YQ~~~Ly~l~AlG~~~~mdvt~ 251 (330)
T PF07851_consen 172 LIVNGSRIKGWWVFHHYISTFLSGVMLTWPDGEAYQKFRPQFLLFSLYQSVVQFLQYRYQRGCLYRLRALGKRHNMDVTV 251 (330)
T ss_pred hccCCCcchHHHHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHhccCccceeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCcceEEeccc
Q psy8200 450 EGQNPIPPDELPPPYQASQPGQVPMVTCRVC 480 (530)
Q Consensus 450 egf~s~~~~~~~p~~~~~~~~~~p~v~c~vc 480 (530)
|||+|..-. .-.+..|++.|-..
T Consensus 252 eG~~s~~~~--------~L~fLlPfLf~~~~ 274 (330)
T PF07851_consen 252 EGFQSWMWR--------GLTFLLPFLFFGQF 274 (330)
T ss_pred cccccchhc--------cHHHHHHHHHHHHH
Confidence 999987763 12356777766653
No 2
>PF04707 PRELI: PRELI-like family; InterPro: IPR006797 These proteins contain a conserved region found in the yeast YLR168C gene MSF1 product. The function of this protein is unknown, though it is thought to be involved in intra-mitochondrial protein sorting. GFP-tagged MSF1 localizes to mitochondria and is required for wild-type respiratory growth []. This region is also found in a number of other eukaryotic proteins. The PRELI/MSF1 domain is an eukaryotic protein module which occurs in stand-alone form in several proteins, including the human PRELI protein and the yeast MSF1 protein, and as an amino-terminal domain in an orthologous group of proteins typified by human SEC14L1, which is conserved in all animals. In this group of proteins, the PRELI/MSF1 domain co-occurs with the CRAL-TRIO (see PDOC50191 from PROSITEDOC) and the GOLD domains (see PDOC50866 from PROSITEDOC). The PRELI/MSF1 domain is approximately 170 residues long and is predicted to assume a globular alpha + beta fold with six beta strands and four alpha helices. It has been suggested that the PRELI/MSF1 domain may have a function associated with cellular membrane [].
Probab=100.00 E-value=2.3e-49 Score=369.07 Aligned_cols=153 Identities=34% Similarity=0.613 Sum_probs=147.7
Q ss_pred HHHhhhhcCCCCCCCCceeeeeeeeeeecCCCceEEEEEEEeeccChhHHHHHHhCC-ceEEEEEEEEEeCCCCEEEEEE
Q psy8200 105 VHEAYERRFPTCPLIPLLVGCEVLSDETSEDTSERITERRFKLIVEAPYLIKKIIGV-DFVYFLQRNELDWRNRTLEIES 183 (530)
Q Consensus 105 Vt~AywrKYPN~P~~pHVlsvDVLeR~vd~dG~l~tteRLi~~~~~lP~WlkKilG~-~~v~~vEeS~VDpk~rtL~i~T 183 (530)
|++|||+|||| |++|||+++|||+|++|+||++++ +||+++++++|+|++||+|. +.+|++|+|+|||++|+|+++|
T Consensus 3 V~~a~w~kYPn-p~~~hVl~~Dvl~r~vd~~g~l~t-~Rl~~~~~~~P~w~~kl~g~~~~~~~~E~S~vD~~~k~l~~~t 80 (157)
T PF04707_consen 3 VTSAFWRKYPN-PYSPHVLSVDVLDREVDPDGKLHT-KRLITKKNNLPRWLKKLIGVDSECYIIEESIVDPKNKTLTTKT 80 (157)
T ss_pred hHHHHHhhCCC-CCCCceeEEEEEEEEEcCCCcEEE-eeeeeeecCchHHHHHHhCcCceEEEEEEEEEECCCCEEEEEE
Confidence 99999999998 999999999999999999998776 79999999999999999995 5699999999999999999999
Q ss_pred EeccccceEEEEEEEEEEeCCCCCCccEEEEEEEEEEec-chhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcc
Q psy8200 184 KNETFSNRVIVLEKCRYFVHPENPDWTCFEQNAELDVKS-FFGFENTIEKLAMKQYITNISKGKEILEHHVEVLKGE 259 (530)
Q Consensus 184 rNlSfss~~~V~E~c~Y~phPeNP~wT~f~QeA~I~iss-f~Gf~s~IEk~~~krf~~Na~KGregmE~VL~~L~~e 259 (530)
+|+||++++.|+|+|+|+|||+||+||+|+|+|+|+++| ++||+++||++++++|++|++|||+|||++|++|++|
T Consensus 81 ~Nls~~~~~~v~E~~~Y~~~p~np~~T~~~q~a~i~~~~~~~~~~~~iE~~~~~~f~~na~kgr~~~e~vi~~l~~~ 157 (157)
T PF04707_consen 81 RNLSFSSFLSVEETCVYKPHPDNPNWTLFKQEATISIKGSFSGFSSRIEKFSVSRFKSNAKKGREGMEWVIKKLEEE 157 (157)
T ss_pred EEcccCceeEEEEEEEEEECCCCCCcceEEEEEEEEEeCchhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999999999999987 7799999999999999999999999999999999875
No 3
>KOG3336|consensus
Probab=100.00 E-value=2.2e-45 Score=343.64 Aligned_cols=162 Identities=26% Similarity=0.402 Sum_probs=151.4
Q ss_pred eeeccchh---HHHhhhhcCCCCCCCCceeeeeeeeeeecCCCceEEEEEEEeeccChhHHHHHHhCCce-EEEEEEEEE
Q psy8200 97 VSVSRNHP---VHEAYERRFPTCPLIPLLVGCEVLSDETSEDTSERITERRFKLIVEAPYLIKKIIGVDF-VYFLQRNEL 172 (530)
Q Consensus 97 ~~hs~~hp---Vt~AywrKYPN~P~~pHVlsvDVLeR~vd~dG~l~tteRLi~~~~~lP~WlkKilG~~~-v~~vEeS~V 172 (530)
-.|.|||| |++|.|+|||| |+++||+++|||+|++|+.|+||+ +|||+.++.+|+|+.+++|.+. +|+.|.|+|
T Consensus 6 seh~F~hPwE~Vt~A~w~KyPn-p~~~hVi~VDvl~R~l~~~GkL~T-eRlit~~~~~P~w~~~LiG~a~~~yv~E~SvV 83 (185)
T KOG3336|consen 6 SEHIFDHPWETVTAAAWRKYPN-PINTHVIGVDVLDRKLDDSGKLHT-ERLITIHQGLPSWIHKLIGGANTCYVREVSVV 83 (185)
T ss_pred ccccccCcHHHHHHHHHHhCCC-CCCCceEEEeeeeeeeccCceEEE-eeeeeeccCCcHHHHHHhCcccceEEEEEEEE
Confidence 35566666 99999999998 999999999999999999997777 7999999999999999999755 688999999
Q ss_pred eCCCCEEEEEEEeccccceEEEEEEEEEEeCCCCCCccEEEEEEEEEEecc-hhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q psy8200 173 DWRNRTLEIESKNETFSNRVIVLEKCRYFVHPENPDWTCFEQNAELDVKSF-FGFENTIEKLAMKQYITNISKGKEILEH 251 (530)
Q Consensus 173 Dpk~rtL~i~TrNlSfss~~~V~E~c~Y~phPeNP~wT~f~QeA~I~issf-~Gf~s~IEk~~~krf~~Na~KGregmE~ 251 (530)
||+.|+|+++|+|+||++++.|+|+.+|.|||+||+||+|+|+|.|++++. -.|++++|++++++|.+||.|||+|||+
T Consensus 84 D~~~ksm~L~t~Nltf~~~l~vdE~l~Y~PhP~dpskTv~~QEa~it~~~~~~~ls~~~E~~~~s~fs~NA~KGreg~e~ 163 (185)
T KOG3336|consen 84 DPKRKSMTLKTCNLTFSDFLSVDERLTYSPHPEDPSKTVLKQEAIITIKGPLVSLSEYVEQWSASRFSQNASKGREGFEW 163 (185)
T ss_pred cCccceEEEEecccccccceEeeeEEEecCCCCCcccceeeeeeEEEEecchhhHHHHHHHHHHHHHhhcccccHHHHHH
Confidence 999999999999999999999999999999999999999999999999874 3689999999999999999999999999
Q ss_pred HHHHHHccC
Q psy8200 252 HVEVLKGEG 260 (530)
Q Consensus 252 VL~~L~~eg 260 (530)
||+.++.+-
T Consensus 164 Vl~~~n~e~ 172 (185)
T KOG3336|consen 164 VLKKINAEV 172 (185)
T ss_pred HHHHHHHHH
Confidence 999998763
No 4
>KOG4758|consensus
Probab=100.00 E-value=5.3e-48 Score=363.81 Aligned_cols=139 Identities=51% Similarity=0.818 Sum_probs=122.6
Q ss_pred cccccCcceEEee---ceeeeccccc-ceeeeeccchhhHHHHHHHhhhhHhhhhcccccCCCccchhhhhhHHHHHhhc
Q psy8200 317 NWTEGADYERVES---PILCHDGESI-QGSHVTSRDELSFMFLLVWYYCTLTIRESILKVNGSRIKGWWRMHHFISTVCS 392 (530)
Q Consensus 317 ~~~yk~dYekve~---~ilc~~gesi-qgsHv~~~~d~~~~fl~~~~y~tlt~re~il~~ngs~i~~ww~~hhy~s~~~~ 392 (530)
+.+|||+|+|||. ++....+.+- |..|.. ..|+.|+|+|||||||||||||||+.| |||||||+.|||+|+.+|
T Consensus 4 k~~~Kd~~ek~K~~~~~~~~~is~~~~~~l~~R-~~~~af~fllvwyycTltiresil~~n-srikgww~~hh~Vst~~s 81 (220)
T KOG4758|consen 4 EEEVKQIIDEVKELHDSAASFISFSSQQELNLR-QKASAFDFLLVWYYCTLTIRESILPKN-SRIKGWWARHHLVSTETS 81 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHheeehhhhcccch-hhhhHHHHHHhhhhhhhc
Confidence 4689999999885 3332222222 233322 468899999999999999999999999 999999999999999999
Q ss_pred ceEEecCCCccccccHhhHHHHHHHHHHHHHhHhhhhcchhhhhhhcCccCCCcccccCCCCCCC
Q psy8200 393 AVLLIWPNSVTWHLFRPQFMVFNVYISVVQALQFWYQQGVLYRLKALGERHNMDITIEGQNPIPP 457 (530)
Q Consensus 393 ~~~l~wp~~~~~~~f~~~f~~f~~~~~~vq~lq~~YQ~~~ly~~~alg~~~~md~tvegf~s~~~ 457 (530)
|+||+||+|..||+||+||+.|+++||+||+||++||||||||++|||++|.||+|+|||+|..=
T Consensus 82 gvlltwPqG~~~q~Fr~qf~~fsl~~s~vq~lq~~Yqrg~lYRlkalger~~~d~Tvegf~SwmW 146 (220)
T KOG4758|consen 82 GVLLTWPQGRFYQKFRNQFLVFSLYQSVVQFLQYYYQRGCLYRLKALGERHFMDLTVEGFQSWMW 146 (220)
T ss_pred ceeecCCCcHHHHHHHhHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhccChhHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999998654
No 5
>KOG3337|consensus
Probab=100.00 E-value=6.1e-38 Score=293.76 Aligned_cols=162 Identities=21% Similarity=0.369 Sum_probs=147.4
Q ss_pred EEeeeccchhHHHhhhhcCCCCCCCCceeeeeeeeeeecCCCceEEEEEEEeeccChhHHHHHHhCCceEEEEEEEEEeC
Q psy8200 95 HSVSVSRNHPVHEAYERRFPTCPLIPLLVGCEVLSDETSEDTSERITERRFKLIVEAPYLIKKIIGVDFVYFLQRNELDW 174 (530)
Q Consensus 95 ~~~~hs~~hpVt~AywrKYPN~P~~pHVlsvDVLeR~vd~dG~l~tteRLi~~~~~lP~WlkKilG~~~v~~vEeS~VDp 174 (530)
+.+..+|+ .|.+|||.|||| |+++||++.|||+|+||+||++.+ +||+.+++++|+|+.+++....+|++|+|+|||
T Consensus 9 t~lp~s~d-~VssAfw~RYPN-pySkHVlSeDvleR~Vt~dg~L~T-~RLLvKqgRlPrWasrll~i~~v~viE~SVvdp 85 (201)
T KOG3337|consen 9 TVLPSSWD-QVSSAFWQRYPN-PYSKHVLSEDVLEREVTDDGTLVT-KRLLVKQGRLPRWASRLLDIQVVYVIEESVVDP 85 (201)
T ss_pred CcccCcHH-HHHHHHHHhCCC-ccccccccHHHHhhhcCcccceeh-hhhHHhcCCCchhhhhhcccceeEEeeeeecCc
Confidence 34566676 499999999998 999999999999999999999887 699999999999999999999999999999999
Q ss_pred CCCEEEEEEEeccccceEEEEEEEEEEeCCCCCCccEEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q psy8200 175 RNRTLEIESKNETFSNRVIVLEKCRYFVHPENPDWTCFEQNAELDVKSFFGFENTIEKLAMKQYITNISKGKEILEHHVE 254 (530)
Q Consensus 175 k~rtL~i~TrNlSfss~~~V~E~c~Y~phPeNP~wT~f~QeA~I~issf~Gf~s~IEk~~~krf~~Na~KGregmE~VL~ 254 (530)
.+++|.++|+|++|.++|.|+|.|+|..+.+|+.|+.=..++.+ ++..||+.++++++++.+|++|..|.+.||+++|+
T Consensus 86 ~nqtmkTyTrNldH~~lm~v~Erc~y~~ssdns~ti~d~~~kfv-ss~~~G~~r~Vqe~sl~rFkenv~ktrkGl~yvlq 164 (201)
T KOG3337|consen 86 VNQTMKTYTRNLDHARLMVVEERCVYCVSSDNSGTIEDRREKFV-SSSLFGVSRAVQEFSLARFKENVTKTRKGLEYVLQ 164 (201)
T ss_pred cccceeeeeeccccceeeEEEEEEEEEecCCCCcchhHHHHHHh-hhhhhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence 99999999999999999999999999999999877654444333 34558999999999999999999999999999999
Q ss_pred HHHccC
Q psy8200 255 VLKGEG 260 (530)
Q Consensus 255 ~L~~eg 260 (530)
++.++.
T Consensus 165 k~fg~a 170 (201)
T KOG3337|consen 165 KLFGEA 170 (201)
T ss_pred HHhccc
Confidence 998664
No 6
>PF07851 TMPIT: TMPIT-like protein; InterPro: IPR012926 A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this. ; GO: 0016021 integral to membrane
Probab=99.98 E-value=2e-34 Score=295.75 Aligned_cols=85 Identities=54% Similarity=1.018 Sum_probs=76.0
Q ss_pred CeEEEeeehhhhhhhceeeecCCCccchhhhhHHHHHhhhceEeecCCCcchhcchhhhhhHHhhhh-----------hc
Q psy8200 1 MFLLVWYYCTLTIRESILKVNGSRIKGWWRMHHFISTVCSAVLLIWPNSVTWHLFRPQFMVFNVYIR-----------GL 69 (530)
Q Consensus 1 ~f~~~~~y~~l~~re~il~~ngs~i~~ww~~hhy~s~~~~~~~l~wp~~~~~~~f~~~f~~f~~~~~-----------~~ 69 (530)
+|||||||||||||||||++|||||||||+.|||+|+++|||+||||||++||+||+|||+|++||| |.
T Consensus 155 ~f~lvwyY~tLtiRE~IL~~NGS~Ik~WW~~HHy~s~~~s~v~Ltwp~~~~~~~fr~~fl~f~~~~~~vq~lQ~~YQ~~~ 234 (330)
T PF07851_consen 155 NFLLVWYYCTLTIRESILIVNGSRIKGWWVFHHYISTFLSGVMLTWPDGEAYQKFRPQFLLFSLYQSVVQFLQYRYQRGC 234 (330)
T ss_pred HHHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 5899999999999999999999999999999999999999999999999999999999999998877 55
Q ss_pred ccceeeeeccceeccC
Q psy8200 70 IPKSLYMSEADWERGT 85 (530)
Q Consensus 70 ~~~~~~~~~~~~~~~~ 85 (530)
+|++.++|+|+.||-+
T Consensus 235 Ly~l~AlG~~~~mdvt 250 (330)
T PF07851_consen 235 LYRLRALGKRHNMDVT 250 (330)
T ss_pred HHHHHHhccCccceee
Confidence 6666666666655544
No 7
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=99.97 E-value=3.8e-31 Score=261.36 Aligned_cols=70 Identities=63% Similarity=1.223 Sum_probs=66.1
Q ss_pred CCCCCCCCCCCCCC---CCCCCcceEEecccceeeeecceeeeEEEeCCCCCccccCCCCCCCCceEeccCCC
Q psy8200 453 NPIPPDELPPPYQA---SQPGQVPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNAPAGKKYVRCPYGV 522 (530)
Q Consensus 453 ~s~~~~~~~p~~~~---~~~~~~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~p~gk~~~rc~c~~ 522 (530)
.++++||+||||++ ++++++|+|+|||||++||||||+|||||||++||||||||+|||||||||||||-
T Consensus 41 ~~~~~~e~pppy~~~~s~~~~~~p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpGKKYVRCPCNC 113 (256)
T PF09788_consen 41 PPVGPGEPPPPYSPLGSPESGGAPVVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPGKKYVRCPCNC 113 (256)
T ss_pred CCCCCCCCCCCCCcccCCCCCCCceEEeecCCceecccCccceeeEECCCCCccccccCCCCCCeeEecCCce
Confidence 57889999999996 45589999999999999999999999999999999999999999999999999994
No 8
>KOG4684|consensus
Probab=99.96 E-value=4.2e-31 Score=254.91 Aligned_cols=75 Identities=59% Similarity=1.035 Sum_probs=69.4
Q ss_pred cccCCCCCCCCCCCCCCCCCC---CCCcceEEecccceeeeecceeeeEEEeCCCCCccccCCCCCCCCceEeccCCC
Q psy8200 448 TIEGQNPIPPDELPPPYQASQ---PGQVPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNAPAGKKYVRCPYGV 522 (530)
Q Consensus 448 tvegf~s~~~~~~~p~~~~~~---~~~~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~p~gk~~~rc~c~~ 522 (530)
+.|+-..+.|+|.||||++.. +|++|+|+|||||.+||+|||++||||||.+||||||||||||||||||||||-
T Consensus 51 f~~~vp~~~P~E~PpPY~~lts~~~g~~PmvtCRVCq~~i~~egk~~QHVVKC~~CnEATPIrnAPpGKKYVRCPCNC 128 (275)
T KOG4684|consen 51 FDKKVPQLFPHERPPPYLALTSAMLGQFPMVTCRVCQVAISLEGKNQQHVVKCHSCNEATPIRNAPPGKKYVRCPCNC 128 (275)
T ss_pred CcccCcccCCCCCCCcchhccccccCCCceEeehhhhHHhccccccceeeEeecccCccccCCCCCCCCceeecCCcE
Confidence 345667889999999999854 499999999999999999999999999999999999999999999999999994
No 9
>KOG4758|consensus
Probab=99.94 E-value=1.1e-28 Score=233.21 Aligned_cols=88 Identities=55% Similarity=0.899 Sum_probs=82.6
Q ss_pred CeEEEeeehhhhhhhceeeecCCCccchhhhhHHHHHhhhceEeecCCCcchhcchhhhhhHHhhhh-------hcccce
Q psy8200 1 MFLLVWYYCTLTIRESILKVNGSRIKGWWRMHHFISTVCSAVLLIWPNSVTWHLFRPQFMVFNVYIR-------GLIPKS 73 (530)
Q Consensus 1 ~f~~~~~y~~l~~re~il~~ngs~i~~ww~~hhy~s~~~~~~~l~wp~~~~~~~f~~~f~~f~~~~~-------~~~~~~ 73 (530)
+|+|||||||||||||||++| |||||||..|||+|+++||+||+||+|+.||+||+||+.|++||| ++|.+.
T Consensus 43 ~fllvwyycTltiresil~~n-srikgww~~hh~Vst~~sgvlltwPqG~~~q~Fr~qf~~fsl~~s~vq~lq~~Yqrg~ 121 (220)
T KOG4758|consen 43 DFLLVWYYCTLTIRESILPKN-SRIKGWWARHHLVSTETSGVLLTWPQGRFYQKFRNQFLVFSLYQSVVQFLQYYYQRGC 121 (220)
T ss_pred HHHHHHHHheeehhhhcccch-hhhhHHHHHHhhhhhhhcceeecCCCcHHHHHHHhHHHHHHHHHHHHHHHHHHHhcch
Confidence 489999999999999999999 999999999999999999999999999999999999999999999 458899
Q ss_pred eeeeccceeccCCccc
Q psy8200 74 LYMSEADWERGTHAMT 89 (530)
Q Consensus 74 ~~~~~~~~~~~~~~~~ 89 (530)
||+.||..||..-+.|
T Consensus 122 lYRlkalger~~~d~T 137 (220)
T KOG4758|consen 122 LYRLKALGERHFMDLT 137 (220)
T ss_pred HHHHHHHHHhccChhH
Confidence 9999999999765544
No 10
>PF10698 DUF2505: Protein of unknown function (DUF2505); InterPro: IPR019639 This entry represents proteins found Actinobacteria and Proteobacteria. The function is not known.
Probab=96.02 E-value=0.42 Score=44.90 Aligned_cols=117 Identities=15% Similarity=0.022 Sum_probs=75.2
Q ss_pred eeeeeecCCCceEEEEEEEeeccChhHHHHHHhCCceEEEEEEEEEeC-CCCEEEEEEEeccccceEEEEEEEEEEeCCC
Q psy8200 127 VLSDETSEDTSERITERRFKLIVEAPYLIKKIIGVDFVYFLQRNELDW-RNRTLEIESKNETFSNRVIVLEKCRYFVHPE 205 (530)
Q Consensus 127 VLeR~vd~dG~l~tteRLi~~~~~lP~WlkKilG~~~v~~vEeS~VDp-k~rtL~i~TrNlSfss~~~V~E~c~Y~phPe 205 (530)
+.+-.++.||...+++|-+.. -.+|..++|+++.+...-.++.+ .| .+...+-...=-....-+.+.=+++..+
T Consensus 38 ~~~~~~~~~g~~v~~~~~v~~-~~lP~~~~k~v~~~l~v~~~e~w-~~~~~g~~~g~~~~~~~G~P~~~~G~~~L~~--- 112 (159)
T PF10698_consen 38 VESFEVDGDGVRVTVRQTVPA-DKLPSAARKFVGGDLRVTRTETW-TPLDDGRRTGTFTVSIPGAPVSISGTMRLRP--- 112 (159)
T ss_pred EEEEEEcCCeEEEEEEEecCh-hhCCHHHHHhcCCCeEEEEEEEE-ecCCCCeEEEEEEEEecCceEEEEEEEEEec---
Confidence 344556777755555443433 38999999999976554444555 55 3444443322223356677777888888
Q ss_pred CCCccEEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhHHHHH
Q psy8200 206 NPDWTCFEQNAELDVKSFFGFENTIEKLAMKQYITNISKGKEIL 249 (530)
Q Consensus 206 NP~wT~f~QeA~I~issf~Gf~s~IEk~~~krf~~Na~KGregm 249 (530)
+.+.|...-++.++++ +..++++||+++.+...+...+-.+..
T Consensus 113 ~~~gt~~~~~g~v~v~-VPlvGgkiE~~v~~~~~~~~~~e~~~~ 155 (159)
T PF10698_consen 113 DGGGTRLTVEGEVKVK-VPLVGGKIEKAVAENLRKLLEAEQEFT 155 (159)
T ss_pred CCCCEEEEEEEEEEEE-EccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 3467888888888764 335679999999988777766654443
No 11
>PF02121 IP_trans: Phosphatidylinositol transfer protein; InterPro: IPR001666 Phosphatidylinositol transfer protein (PITP) is a ubiquitous cytosolic protein, thought to be involved in transport of phospholipids from their site of synthesis in the endoplasmic reticulum and Golgi to other cell membranes []. More recently, PITP has been shown to be an essential component of the polyphosphoinositide synthesis machinery and is hence required for proper signalling by epidermal growth factor and f-Met-Leu-Phe, as well as for exocytosis. The role of PITP in polyphosphoinositide synthesis may also explain its involvement in intracellular vesicular traffic [].; GO: 0006810 transport, 0005622 intracellular; PDB: 1T27_A 1KCM_A 2A1L_A 1UW5_C.
Probab=94.07 E-value=1.7 Score=44.76 Aligned_cols=112 Identities=15% Similarity=0.197 Sum_probs=74.0
Q ss_pred CceEEEEEEEeeccChhHHHHHHhCCceEEEEEEEEE-eCCCCEEEEEEEeccccceEEEEEEEEEEeCC---CC-----
Q psy8200 136 TSERITERRFKLIVEAPYLIKKIIGVDFVYFLQRNEL-DWRNRTLEIESKNETFSNRVIVLEKCRYFVHP---EN----- 206 (530)
Q Consensus 136 G~l~tteRLi~~~~~lP~WlkKilG~~~v~~vEeS~V-Dpk~rtL~i~TrNlSfss~~~V~E~c~Y~phP---eN----- 206 (530)
|.=..|+++..+...+|+|+++++..+...+.|++.- .|-.+|.- | |--+.+|-...|+ .|.++- ||
T Consensus 54 ~~GqYT~K~y~l~sklP~~ir~l~P~~~l~v~E~aWNaYPy~~T~~--t-~~~~~kF~i~IET-~~~~d~G~~eNv~~L~ 129 (254)
T PF02121_consen 54 GKGQYTHKIYHLASKLPSWIRALLPKGALYVHEKAWNAYPYCKTVY--T-NPYMDKFSIKIET-MHKPDNGTSENVFNLS 129 (254)
T ss_dssp -EEEEEEEEEEETTTS-HHHHTTSTTTTTEEEEEEEEETTEEEEEE--E-ETTTGGEEEEEEE-EEESSSS--TTTT---
T ss_pred CceeeEEEEEEecccChHHHHHhCCCceEEEEEEEecccceEEEEE--e-cCCCCceEEEEEE-EEcCCCCCcCcccCCC
Confidence 4445568999999999999999998877888888885 67666544 3 3344777777777 455542 11
Q ss_pred --------------------------------------------CCcc----------EEE--EEEEEEEecchhHHHHH
Q psy8200 207 --------------------------------------------PDWT----------CFE--QNAELDVKSFFGFENTI 230 (530)
Q Consensus 207 --------------------------------------------P~wT----------~f~--QeA~I~issf~Gf~s~I 230 (530)
++|- .+. .-.++++ .+|||.+++
T Consensus 130 ~~~lk~reV~~IDI~~d~i~~~dyk~~eDp~~f~S~ktgRGPL~~~W~~~~~~~~~~PiMc~YKlv~v~f-~~~GlQ~~v 208 (254)
T PF02121_consen 130 PEELKKREVVFIDIANDPISPKDYKEEEDPTKFKSKKTGRGPLKEDWRKEWKKNGKKPIMCCYKLVTVEF-KWWGLQTKV 208 (254)
T ss_dssp HHHHTTSEEEEE-TTGGGS-CCC--GGG-CCC---TTT------TTHHHHHCTSSSS--EEEEEEEEEEE---TTTHHHH
T ss_pred HHHhcCceEEEEEecCCcccccccCcccCchheEecCCCCCCCCcchhhhhhhcCCCCEEEEEEEEEEEe-eeechHHHH
Confidence 2331 111 1223333 357999999
Q ss_pred HHHHHHHH-HHHHHhH-HHHHHHH
Q psy8200 231 EKLAMKQY-ITNISKG-KEILEHH 252 (530)
Q Consensus 231 Ek~~~krf-~~Na~KG-regmE~V 252 (530)
|++..+.. +.-..++ |+++-|+
T Consensus 209 E~~I~~~~~r~i~~~~HRq~fcw~ 232 (254)
T PF02121_consen 209 ENFIHKQILRRIFLNFHRQAFCWI 232 (254)
T ss_dssp HHHHHHHH-HHHHHHHHHHHHHTH
T ss_pred HHHHHHhhhhHHHHHHHHHHheeh
Confidence 99999988 8777776 7776554
No 12
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=93.70 E-value=0.037 Score=42.82 Aligned_cols=37 Identities=27% Similarity=0.767 Sum_probs=31.6
Q ss_pred CCcceEEecccceeeeec-----ceeeeEEEeCCCCCccccC
Q psy8200 470 GQVPMVTCRVCQAMIDIS-----GKRDQHVVKCVHCNEATPV 506 (530)
Q Consensus 470 ~~~p~v~c~vc~~~i~~~-----~~~~q~vv~c~~c~eat~~ 506 (530)
||.|+|.|.-|..++.+. +++.|+-++|+.|.|+--+
T Consensus 2 GGAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~ 43 (46)
T PF11331_consen 2 GGAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSF 43 (46)
T ss_pred CCCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEE
Confidence 799999999999998875 3566999999999997543
No 13
>cd07815 SRPBCC_PITP Lipid-binding SRPBCC domain of Class I and Class II Phosphatidylinositol Transfer Proteins. This family includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of the phosphatidylinositol transfer protein (PITP) family of lipid transfer proteins. This family of proteins includes Class 1 PITPs (PITPNA/PITPalpha and PITPNB/PITPbeta, Drosophila vibrator and related proteins), Class IIA PITPs (PITPNM1/PITPalphaI/Nir2, PITPNM2/PITPalphaII/Nir3, Drosophila RdgB, and related proteins), and Class IIB PITPs (PITPNC1/RdgBbeta and related proteins). The PITP family belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns
Probab=88.54 E-value=9.9 Score=39.18 Aligned_cols=40 Identities=10% Similarity=0.060 Sum_probs=31.6
Q ss_pred EEEEEEEeeccChhHHHHHHhCCceEEEEEEEE-EeCCCCE
Q psy8200 139 RITERRFKLIVEAPYLIKKIIGVDFVYFLQRNE-LDWRNRT 178 (530)
Q Consensus 139 ~tteRLi~~~~~lP~WlkKilG~~~v~~vEeS~-VDpk~rt 178 (530)
-+|+++..+...+|+|++.++......+.|++. -.|-.+|
T Consensus 55 qYT~Kiyhl~sklP~w~~~~~P~~al~v~EkaWNaYPy~~T 95 (251)
T cd07815 55 QYTHKIYHLGSKLPSWLRALAPKSALTIEEKSWNAYPYCKT 95 (251)
T ss_pred eeEEEEEEccccchhHHHHhCCccceEEEhhhhCCCCceeE
Confidence 345799999999999999999877777777766 4566555
No 14
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=82.89 E-value=0.91 Score=33.20 Aligned_cols=30 Identities=23% Similarity=0.674 Sum_probs=24.9
Q ss_pred eEEecccceeeeecce---eeeEEEeCCCCCcc
Q psy8200 474 MVTCRVCQAMIDISGK---RDQHVVKCVHCNEA 503 (530)
Q Consensus 474 ~v~c~vc~~~i~~~~~---~~q~vv~c~~c~ea 503 (530)
.+.|..|++..+|... ...--|+|++|.+.
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCcE
Confidence 4789999999999887 56778999999864
No 15
>cd08890 SRPBCC_PITPNC1_like Lipid-binding SRPBCC domain of mammalian PITPNC1,and related proteins (Class IIB PITPs). This subgroup includes the N-terminal SRPBCC (START/RHO_alpha_C /PITP /Bet_v1/CoxG/CalC) domain of mammalian Class IIB phosphatidylinositol transfer protein (PITP), PITPNC1/RdgBbeta, and related proteins. These are metazoan proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. Mammalian PITPNC1 contains an amino-terminal SRPBCC PITP-like domain and a short carboxyl-terminal domain. It is a cytoplasmic protein, and is ubiquitously
Probab=81.18 E-value=29 Score=35.88 Aligned_cols=53 Identities=19% Similarity=0.193 Sum_probs=33.1
Q ss_pred eeeeeeee--ecC-CC-ceEEEEEEEeeccChhHHHHHHhCCceEEEEEEEE-EeCCCCE
Q psy8200 124 GCEVLSDE--TSE-DT-SERITERRFKLIVEAPYLIKKIIGVDFVYFLQRNE-LDWRNRT 178 (530)
Q Consensus 124 svDVLeR~--vd~-dG-~l~tteRLi~~~~~lP~WlkKilG~~~v~~vEeS~-VDpk~rt 178 (530)
+++||.-. .|+ .| +.+| ++++.+...+|+|++.++... ..+.|++. .-|-.+|
T Consensus 37 GVEvl~Nep~~~~~~~~GqYT-~K~~hl~sklP~w~r~~~P~~-l~v~EkaWNaYPy~~T 94 (250)
T cd08890 37 GVEVVQNEPCEDPEHGNGQFT-EKRVYLNSRLPSWARAVVPKI-FYVTEKAWNYYPYTIT 94 (250)
T ss_pred cEEEEeccccccCCCCcccee-EEEEEccccChhHHHHhCCcc-eEEehhhhccCCceee
Confidence 45565543 222 22 4555 677889999999999999754 44555554 2355444
No 16
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=72.27 E-value=2.7 Score=30.66 Aligned_cols=30 Identities=30% Similarity=0.740 Sum_probs=23.8
Q ss_pred eEEecccceeeeecce---eeeEEEeCCCCCcc
Q psy8200 474 MVTCRVCQAMIDISGK---RDQHVVKCVHCNEA 503 (530)
Q Consensus 474 ~v~c~vc~~~i~~~~~---~~q~vv~c~~c~ea 503 (530)
.|.|..|++..+|+.. .+-..|+|++|++.
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred EEECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 3789999999998876 45567899999864
No 17
>cd08889 SRPBCC_PITPNM1-2_like Lipid-binding SRPBCC domain of mammalian PITPNM1-2 and related proteins (Class IIA PITPs). This subgroup includes an N-terminal SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of mammalian Class II phosphatidylinositol transfer protein (PITPs), PITPNM1/PITPalphaI/Nir2 (PYK2 N-terminal domain-interacting receptor2) and PITPNM2/PITPalphaII/Nir3), Drosophila RdgB, and related proteins. These are membrane associated multidomain proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. Ablation of the mouse gene en
Probab=65.71 E-value=23 Score=36.82 Aligned_cols=63 Identities=11% Similarity=0.055 Sum_probs=40.5
Q ss_pred ceEEEEEEEeeccChhHHHHHHhCCceEEEEEEEE-EeCCCCEEEEEEEeccccceEEEEEEEEEEeCC
Q psy8200 137 SERITERRFKLIVEAPYLIKKIIGVDFVYFLQRNE-LDWRNRTLEIESKNETFSNRVIVLEKCRYFVHP 204 (530)
Q Consensus 137 ~l~tteRLi~~~~~lP~WlkKilG~~~v~~vEeS~-VDpk~rtL~i~TrNlSfss~~~V~E~c~Y~phP 204 (530)
+.+| +++..+...+|+|++.++......+.|++. .-|-.+| +++ |--|.++....|+. |.++-
T Consensus 56 GqYT-~Kiyhl~sklP~wl~~~~P~~al~v~EkaWNaYPy~~T--~yt-~~~~~kF~i~IET~-h~~d~ 119 (260)
T cd08889 56 GQYT-HKIYHIGSHIPGWFRAILPKSALRVEEEAWNAYPYTRT--RYT-CPFVEKFSLDIETY-YFDDA 119 (260)
T ss_pred ceeE-EEEEEccccChHHHHHhCCCcceEEehhHhCCCCceEE--EEe-cCCccceEEEEEEE-EcCCC
Confidence 4554 799999999999999999766566666665 3466555 232 33345555445544 55543
No 18
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=63.69 E-value=7.1 Score=29.50 Aligned_cols=36 Identities=19% Similarity=0.432 Sum_probs=27.8
Q ss_pred eEEecccceeeeecceeeeEEEeCCCCCccccCCCCCC
Q psy8200 474 MVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNAPA 511 (530)
Q Consensus 474 ~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~p~ 511 (530)
...|..|++.++++.... .++|+.|+..-.++..++
T Consensus 3 ~y~C~~CG~~~~~~~~~~--~~~Cp~CG~~~~~~~~~~ 38 (46)
T PRK00398 3 EYKCARCGREVELDEYGT--GVRCPYCGYRILFKERPP 38 (46)
T ss_pred EEECCCCCCEEEECCCCC--ceECCCCCCeEEEccCCC
Confidence 467999999999987775 789999987665555444
No 19
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=61.58 E-value=5 Score=31.91 Aligned_cols=39 Identities=18% Similarity=0.520 Sum_probs=31.8
Q ss_pred cceEEecccceeeeecceeeeEEEeCCCCCccccCCCCC
Q psy8200 472 VPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNAP 510 (530)
Q Consensus 472 ~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~p 510 (530)
+..+.|..|+.+.--.|...+--+||++|....-++..-
T Consensus 2 ~~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~ 40 (51)
T PF10122_consen 2 LKEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATS 40 (51)
T ss_pred CcceeccchhHHHhhhcCccEEEEECCCCCccceEeccC
Confidence 357899999999988888888999999998766655543
No 20
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.95 E-value=5.8 Score=36.87 Aligned_cols=16 Identities=19% Similarity=0.559 Sum_probs=11.8
Q ss_pred ceEEecccceeeeecc
Q psy8200 473 PMVTCRVCQAMIDISG 488 (530)
Q Consensus 473 p~v~c~vc~~~i~~~~ 488 (530)
+...|+.|++...+++
T Consensus 69 ~~~~C~~CG~~~~~~~ 84 (135)
T PRK03824 69 AVLKCRNCGNEWSLKE 84 (135)
T ss_pred eEEECCCCCCEEeccc
Confidence 4678888888777763
No 21
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=55.78 E-value=7.8 Score=27.89 Aligned_cols=29 Identities=17% Similarity=0.617 Sum_probs=19.7
Q ss_pred EEecccceeeeeccee---eeEEEeCCCCCcc
Q psy8200 475 VTCRVCQAMIDISGKR---DQHVVKCVHCNEA 503 (530)
Q Consensus 475 v~c~vc~~~i~~~~~~---~q~vv~c~~c~ea 503 (530)
+.|..|.+.+.|.... +...|+|++|.+.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 6788888887777532 2336888888754
No 22
>PRK02935 hypothetical protein; Provisional
Probab=54.86 E-value=9.1 Score=34.75 Aligned_cols=41 Identities=27% Similarity=0.701 Sum_probs=35.5
Q ss_pred CcceEEecccceeeeecceeeeEEEeCCCCCccccCCCCCCCCce
Q psy8200 471 QVPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNAPAGKKY 515 (530)
Q Consensus 471 ~~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~p~gk~~ 515 (530)
.++.|.|.-|+...-.-|+.+ .|.+|||---+.+.-.||.|
T Consensus 67 kavqV~CP~C~K~TKmLGrvD----~CM~C~~PLTLd~~legkef 107 (110)
T PRK02935 67 KAVQVICPSCEKPTKMLGRVD----ACMHCNQPLTLDRSLEGKEF 107 (110)
T ss_pred cceeeECCCCCchhhhcccee----ecCcCCCcCCcCccccccCc
Confidence 566889999999998888865 89999998888888889876
No 23
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=53.21 E-value=8.9 Score=34.58 Aligned_cols=14 Identities=21% Similarity=0.204 Sum_probs=10.6
Q ss_pred HHHHHHHHHHhHhh
Q psy8200 414 FNVYISVVQALQFW 427 (530)
Q Consensus 414 f~~~~~~vq~lq~~ 427 (530)
+|+.+++++.+.-.
T Consensus 4 lsi~~~iv~~v~~~ 17 (113)
T PRK12380 4 LSLCQSAVEIIQRQ 17 (113)
T ss_pred HHHHHHHHHHHHHH
Confidence 67888888887643
No 24
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=52.12 E-value=9.7 Score=34.41 Aligned_cols=16 Identities=0% Similarity=0.036 Sum_probs=10.6
Q ss_pred HHHHHHHHHHhHhhhh
Q psy8200 414 FNVYISVVQALQFWYQ 429 (530)
Q Consensus 414 f~~~~~~vq~lq~~YQ 429 (530)
+|+.++++..+.-.-+
T Consensus 4 ~sia~~iv~~v~~~a~ 19 (115)
T TIGR00100 4 LSLAEAMLEIVEEQAE 19 (115)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5778888877654433
No 25
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=50.18 E-value=7.2 Score=35.71 Aligned_cols=41 Identities=27% Similarity=0.666 Sum_probs=36.2
Q ss_pred CcceEEecccceeeeecceeeeEEEeCCCCCccccCCCCCCCCce
Q psy8200 471 QVPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNAPAGKKY 515 (530)
Q Consensus 471 ~~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~p~gk~~ 515 (530)
..+.|.|.-|+...-.-|+.+ .|.+|+|---+.+.-.||.|
T Consensus 66 kav~V~CP~C~K~TKmLGr~D----~CM~C~~pLTLd~~legkef 106 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRVD----ACMHCKEPLTLDPSLEGKEF 106 (114)
T ss_pred cceeeECCCCCChHhhhchhh----ccCcCCCcCccCchhhcchh
Confidence 446889999999999999885 79999998889999999976
No 26
>cd08888 SRPBCC_PITPNA-B_like Lipid-binding SRPBCC domain of mammalian PITPNA, -B, and related proteins (Class I PITPs). This subgroup includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of mammalian Class 1 phosphatidylinositol transfer proteins (PITPs), PITPNA/PITPalpha and PITPNB/PITPbeta, Drosophila vibrator, and related proteins. These are single domain proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. In addition, PITPNB transfers sphingomyelin in vitro, with a low affinity. PITPNA is found chiefly in the nucleus and cy
Probab=49.39 E-value=63 Score=33.60 Aligned_cols=57 Identities=16% Similarity=0.208 Sum_probs=37.0
Q ss_pred ceEEEEEEEeeccChhHHHHHHhCCceEEEEEEEE-EeCCCCEEEEEEEeccc--cceEEEEEEE
Q psy8200 137 SERITERRFKLIVEAPYLIKKIIGVDFVYFLQRNE-LDWRNRTLEIESKNETF--SNRVIVLEKC 198 (530)
Q Consensus 137 ~l~tteRLi~~~~~lP~WlkKilG~~~v~~vEeS~-VDpk~rtL~i~TrNlSf--ss~~~V~E~c 198 (530)
+.+ |+++..+...+|+|++.++-.....+.|++. -.|-.+| +.+ | .| .++....|+.
T Consensus 54 GqY-T~Kiyhl~sklP~wir~~~P~~al~v~EkaWNaYPy~~T--~yt-~-~~~k~~F~i~IET~ 113 (258)
T cd08888 54 GQY-THKIYHLQSKVPGFVRMLAPEGSLEIHEKAWNAYPYCRT--IIT-N-EYMKEDFLIIIETW 113 (258)
T ss_pred cee-EEEEEEccccchhHHHHhCCCcceEEehhhhcCCCceEE--EEe-c-CCcCccEEEEEEEE
Confidence 344 5799999999999999998655555566665 3455554 344 5 44 3455555554
No 27
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=48.80 E-value=8.5 Score=45.08 Aligned_cols=56 Identities=23% Similarity=0.454 Sum_probs=42.0
Q ss_pred CCcccccCCCCCCCCCCCCCCCCCCCCCcceEEecccceeee-ecceeeeE-EEeCCCCCcc
Q psy8200 444 NMDITIEGQNPIPPDELPPPYQASQPGQVPMVTCRVCQAMID-ISGKRDQH-VVKCVHCNEA 503 (530)
Q Consensus 444 ~md~tvegf~s~~~~~~~p~~~~~~~~~~p~v~c~vc~~~i~-~~~~~~q~-vv~c~~c~ea 503 (530)
+.-+++.-|+..-++|+|+|-.-... .+.||.|++-|| +.---+|. +++|+.|+-.
T Consensus 173 PfgLVI~Pf~~l~~e~~~vpl~~d~~----ivRCrrCrsYiNPfv~fi~~g~kw~CNiC~~k 230 (861)
T COG5028 173 PFGLVIRPFLELYPEEDPVPLVEDGS----IVRCRRCRSYINPFVQFIEQGRKWRCNICRSK 230 (861)
T ss_pred CceEEeehhhhcCccCCCCccCCCCc----chhhhhhHhhcCceEEEecCCcEEEEeecccc
Confidence 44577777888888888888765432 689999999999 44444454 9999999753
No 28
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=48.44 E-value=8.6 Score=28.49 Aligned_cols=25 Identities=28% Similarity=0.736 Sum_probs=20.8
Q ss_pred EEeCCCCCccccCCCCCCCCceEecc
Q psy8200 494 VVKCVHCNEATPVKNAPAGKKYVRCP 519 (530)
Q Consensus 494 vv~c~~c~eat~~~~~p~gk~~~rc~ 519 (530)
|++|+.|+..--+|....| +|+-|.
T Consensus 1 ~~~CP~Cg~~lv~r~~k~g-~F~~Cs 25 (39)
T PF01396_consen 1 VEKCPKCGGPLVLRRGKKG-KFLGCS 25 (39)
T ss_pred CcCCCCCCceeEEEECCCC-CEEECC
Confidence 5789999977778888888 888885
No 29
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=47.39 E-value=7 Score=31.57 Aligned_cols=38 Identities=16% Similarity=0.394 Sum_probs=27.1
Q ss_pred cceEEecccceeeeecceeeeEEEeCCCCCccccCCCC
Q psy8200 472 VPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNA 509 (530)
Q Consensus 472 ~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~ 509 (530)
+..+.|+-|..+.-=-+-.----+||++|.|..-+..+
T Consensus 2 ~~tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~~~~ 39 (60)
T COG4416 2 MQTIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEFYIK 39 (60)
T ss_pred ceeeehHHHhHHHHhcccceeeeecCCccceeeeeecc
Confidence 45799999998875444444467899999887655443
No 30
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=47.15 E-value=13 Score=29.88 Aligned_cols=28 Identities=25% Similarity=0.571 Sum_probs=20.4
Q ss_pred EEecccceeeeecceeeeEEEeCCCCCc
Q psy8200 475 VTCRVCQAMIDISGKRDQHVVKCVHCNE 502 (530)
Q Consensus 475 v~c~vc~~~i~~~~~~~q~vv~c~~c~e 502 (530)
..|.+|.+.|++++...=-.|.|+.|.-
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGa 30 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGA 30 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCC
Confidence 4688888888887765555678888863
No 31
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.94 E-value=12 Score=33.87 Aligned_cols=12 Identities=17% Similarity=0.346 Sum_probs=8.5
Q ss_pred HHHHHHHHHHhH
Q psy8200 414 FNVYISVVQALQ 425 (530)
Q Consensus 414 f~~~~~~vq~lq 425 (530)
+|+.++++..+.
T Consensus 4 ~si~~~il~~v~ 15 (117)
T PRK00564 4 YSVVSSLIALCE 15 (117)
T ss_pred HHHHHHHHHHHH
Confidence 577777777664
No 32
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=46.45 E-value=12 Score=26.99 Aligned_cols=20 Identities=30% Similarity=0.816 Sum_probs=10.3
Q ss_pred eCCCCCccccCCCCCCCCceEecc
Q psy8200 496 KCVHCNEATPVKNAPAGKKYVRCP 519 (530)
Q Consensus 496 ~c~~c~eat~~~~~p~gk~~~rc~ 519 (530)
+|+.|+.-..|++..+ ||||
T Consensus 2 ~C~~Cg~~~~~~~~~~----irC~ 21 (32)
T PF03604_consen 2 ICGECGAEVELKPGDP----IRCP 21 (32)
T ss_dssp BESSSSSSE-BSTSST----SSBS
T ss_pred CCCcCCCeeEcCCCCc----EECC
Confidence 3566665555554433 5665
No 33
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=45.38 E-value=29 Score=28.45 Aligned_cols=41 Identities=22% Similarity=0.495 Sum_probs=31.3
Q ss_pred CCcceEEecccceeeeecceeeeEEEeCCCCCccccCCCCCCCC
Q psy8200 470 GQVPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNAPAGK 513 (530)
Q Consensus 470 ~~~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~p~gk 513 (530)
+.|--|.|..|...--|.++ -|.+|+|..|+. .|..|--||
T Consensus 7 S~F~~VkCp~C~n~q~vFsh-a~t~V~C~~Cg~--~L~~PtGGK 47 (59)
T PRK00415 7 SRFLKVKCPDCGNEQVVFSH-ASTVVRCLVCGK--TLAEPTGGK 47 (59)
T ss_pred CeEEEEECCCCCCeEEEEec-CCcEEECcccCC--CcccCCCcc
Confidence 46778999999988777665 689999999974 455554454
No 34
>PF15354 KAAG1: Kidney-associated antigen 1
Probab=45.32 E-value=43 Score=28.47 Aligned_cols=61 Identities=25% Similarity=0.343 Sum_probs=34.7
Q ss_pred HHHHHHHHHHc--cCcccccCCCCCCCccc--ccccccccCCCCcccccccccccccCCCCCCCCCceeeecCccccc
Q psy8200 248 ILEHHVEVLKG--EGITHVPQWQPPKNMEI--CDELNKLDLKTDISVEENHLDRMRRQGSMSPSGTSLSLIDKNWTEG 321 (530)
Q Consensus 248 gmE~VL~~L~~--eg~~~~~rw~~~~~~~~--~~~~~~~~lR~dvsf~~~h~~~a~~~g~~s~~g~~~sLi~~~~~yk 321 (530)
++.+-|.+... .+..|+|||+|+-..+. +.|..+ . . .-..+|..++...+.++.+++++.|
T Consensus 20 alh~~lrqvagpga~aahlpr~~pp~laa~r~~ap~l~---------q--~--~~rt~gags~petn~k~tnpqvkek 84 (84)
T PF15354_consen 20 ALHDRLRQVAGPGAGAAHLPRGTPPRLAAPRGEAPPLS---------Q--R--PHRTQGAGSPPETNEKLTNPQVKEK 84 (84)
T ss_pred HHHHHHHHhcCCcchhhcCCCCCCcccccccccCCCCC---------C--C--cccccCCCCCccccccccCcccccC
Confidence 44455566655 45679999999865511 111110 0 0 1245566666666767777776654
No 35
>KOG3668|consensus
Probab=44.95 E-value=75 Score=33.01 Aligned_cols=36 Identities=11% Similarity=0.171 Sum_probs=27.8
Q ss_pred CceEEEEEEEeeccChhHHHHHHhCCceEEEEEEEE
Q psy8200 136 TSERITERRFKLIVEAPYLIKKIIGVDFVYFLQRNE 171 (530)
Q Consensus 136 G~l~tteRLi~~~~~lP~WlkKilG~~~v~~vEeS~ 171 (530)
|.--.|+++..++..+|+|+++++-.+...+.|+|.
T Consensus 54 g~GqyThKIyhl~sk~P~~~r~l~Pk~al~v~EesW 89 (269)
T KOG3668|consen 54 GSGQYTHKIYHLGSKVPAWLRSLLPKGALIVHEESW 89 (269)
T ss_pred CccceEEEEEEecccchHHHHHhCCccceEEeeecc
Confidence 344556899999999999999999766555666655
No 36
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=43.83 E-value=15 Score=33.19 Aligned_cols=13 Identities=0% Similarity=0.130 Sum_probs=9.4
Q ss_pred HHHHHHHHHHhHh
Q psy8200 414 FNVYISVVQALQF 426 (530)
Q Consensus 414 f~~~~~~vq~lq~ 426 (530)
+|+.+++++.+.-
T Consensus 4 ~si~~~iv~~v~~ 16 (114)
T PRK03681 4 ITLCQRALELIEQ 16 (114)
T ss_pred HHHHHHHHHHHHH
Confidence 5778888887653
No 37
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=43.12 E-value=17 Score=26.49 Aligned_cols=26 Identities=38% Similarity=0.943 Sum_probs=20.9
Q ss_pred EEeCCCCCccccCCCC--CCCCceEecc
Q psy8200 494 VVKCVHCNEATPVKNA--PAGKKYVRCP 519 (530)
Q Consensus 494 vv~c~~c~eat~~~~~--p~gk~~~rc~ 519 (530)
-+.|++|+-.--|... |++.+-||||
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~ 29 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCP 29 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECC
Confidence 4789999988777665 6777799998
No 38
>cd08868 START_STARD1_3_like Cholesterol-binding START domain of mammalian STARD1, -3 and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD1 (also known as StAR) and STARD3 (also known as metastatic lymph node 64/MLN64). The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. This STARD1-like subfamily has a high affinity for cholesterol. STARD1/StAR can reduce macrophage lipid content and inflammatory status. It plays an essential role in steroidogenic tissues: transferring the steroid precursor, cholesterol, from the outer to the inner mitochondrial membrane, across the aqueous space. Mutations in the gene encoding STARD1/StAR can cause lipid congenital adrenal hyperplasia (CAH), an autosomal recessive disorder characterized by a steroid synth
Probab=41.15 E-value=3.4e+02 Score=26.23 Aligned_cols=96 Identities=15% Similarity=0.126 Sum_probs=54.9
Q ss_pred CCCCceeeeeeeeeeecCCCceEEEEEEEeeccChhHHHHHHhCCceEEEEEEEEEeCCCCEEEEEEEeccc------cc
Q psy8200 117 PLIPLLVGCEVLSDETSEDTSERITERRFKLIVEAPYLIKKIIGVDFVYFLQRNELDWRNRTLEIESKNETF------SN 190 (530)
Q Consensus 117 P~~pHVlsvDVLeR~vd~dG~l~tteRLi~~~~~lP~WlkKilG~~~v~~vEeS~VDpk~rtL~i~TrNlSf------ss 190 (530)
-..+++...++|++ +|++..+... .....+| |. +-+.|.+.+.... -+. ..+.+..+...| .+
T Consensus 76 ~Wd~~~~~~~~i~~-~d~~~~i~y~----~~~~~~~-~~--vs~RDfV~~r~~~-~~~--~~~~i~~~sv~h~~~P~~~g 144 (208)
T cd08868 76 SWNPTVLECKIIQV-IDDNTDISYQ----VAAEAGG-GL--VSPRDFVSLRHWG-IRE--NCYLSSGVSVEHPAMPPTKN 144 (208)
T ss_pred eecCcccceEEEEE-ecCCcEEEEE----EecCcCC-Cc--ccccceEEEEEEE-ecC--CeEEEEEEeccCCCCCCCCC
Confidence 34678888999988 4555443331 1111222 22 1223444432221 222 345555555555 45
Q ss_pred eEEEEEE---EEEEeCCCCCCccEEEEEEEEEEecc
Q psy8200 191 RVIVLEK---CRYFVHPENPDWTCFEQNAELDVKSF 223 (530)
Q Consensus 191 ~~~V~E~---c~Y~phPeNP~wT~f~QeA~I~issf 223 (530)
++.++-. -.++|.++++++|.++..+..+.+|.
T Consensus 145 ~VR~~~~~~~~~i~p~~~~~~~t~v~~~~~~Dp~G~ 180 (208)
T cd08868 145 YVRGENGPGCWILRPLPNNPNKCNFTWLLNTDLKGW 180 (208)
T ss_pred eEEEeccccEEEEEECCCCCCceEEEEEEEECCCCC
Confidence 5666644 25678888889999999999988776
No 39
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=39.98 E-value=18 Score=26.05 Aligned_cols=28 Identities=18% Similarity=0.534 Sum_probs=21.9
Q ss_pred EEecccceeeeecceee-eEEEeCCCCCc
Q psy8200 475 VTCRVCQAMIDISGKRD-QHVVKCVHCNE 502 (530)
Q Consensus 475 v~c~vc~~~i~~~~~~~-q~vv~c~~c~e 502 (530)
..|..|++.+++..... ...+.|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 47889999888776554 66788999987
No 40
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=39.54 E-value=9.7 Score=28.24 Aligned_cols=35 Identities=26% Similarity=0.521 Sum_probs=20.7
Q ss_pred eEEecccceeeeecceeeeE--EEeCCCCCccccCCC
Q psy8200 474 MVTCRVCQAMIDISGKRDQH--VVKCVHCNEATPVKN 508 (530)
Q Consensus 474 ~v~c~vc~~~i~~~~~~~q~--vv~c~~c~eat~~~~ 508 (530)
.+.|+.|++.||--=+.+.. .-+|+-|+..+++..
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp~ 38 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLPP 38 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--EEE--G
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCCcCCCCC
Confidence 47899999999877666654 789999999888754
No 41
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=37.28 E-value=16 Score=26.56 Aligned_cols=33 Identities=21% Similarity=0.592 Sum_probs=24.5
Q ss_pred eEEecccceeeeecceeeeEEEeCCCCCccccCC
Q psy8200 474 MVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVK 507 (530)
Q Consensus 474 ~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~ 507 (530)
+..|.-|..+...+....-.+ +|..|.-.-||.
T Consensus 1 m~FCp~C~nlL~p~~~~~~~~-~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 1 MRFCPECGNLLYPKEDKEKRV-ACRTCGYEEPIS 33 (35)
T ss_dssp --BETTTTSBEEEEEETTTTE-EESSSS-EEE-S
T ss_pred CeeCCCCCccceEcCCCccCc-CCCCCCCccCCC
Confidence 457999999999888888777 999998766664
No 42
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=36.64 E-value=30 Score=27.75 Aligned_cols=29 Identities=24% Similarity=0.588 Sum_probs=23.4
Q ss_pred EEeCCCCCccccCCCCCCCCceEecc-CCCC
Q psy8200 494 VVKCVHCNEATPVKNAPAGKKYVRCP-YGVG 523 (530)
Q Consensus 494 vv~c~~c~eat~~~~~p~gk~~~rc~-c~~~ 523 (530)
..+|+.|.+.-.+..+..|. -|-|| |+..
T Consensus 2 ~~~CP~CG~~iev~~~~~Ge-iV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGE-LVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEecCCCccCC-EEeCCCCCCE
Confidence 46899999998887766666 78999 8764
No 43
>cd08904 START_STARD6-like Lipid-binding START domain of mammalian STARD6 and related proteins. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD6 and related domains. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD6 is expressed in male germ cells of normal rats, and in the steroidogenic Leydig cells of perinatal hypothyroid testes. It may play a pivotal role in the steroidogenesis as well as in the spermatogenesis of normal rats. STARD6 has also been detected in the rat nervous system, and may participate in neurosteroid synthesis.
Probab=36.02 E-value=4.5e+02 Score=26.12 Aligned_cols=116 Identities=16% Similarity=0.125 Sum_probs=65.2
Q ss_pred CCceeeeeeeeeeecCCCceEEEEEEEeeccChhHHHHHHhCC-ceEEEEEEEEEeCCCCEEEEEEEeccccc------e
Q psy8200 119 IPLLVGCEVLSDETSEDTSERITERRFKLIVEAPYLIKKIIGV-DFVYFLQRNELDWRNRTLEIESKNETFSN------R 191 (530)
Q Consensus 119 ~pHVlsvDVLeR~vd~dG~l~tteRLi~~~~~lP~WlkKilG~-~~v~~vEeS~VDpk~rtL~i~TrNlSfss------~ 191 (530)
.+.+...++|++ +|+|.-+... +. +.+...+++. |.+.+.- .-...+.+..+.+..+.|.+ +
T Consensus 75 d~~~~~~~iie~-Id~~T~I~~~-~~-------~~~~~~~vspRDfV~vr~--~~r~~~~~~ii~~~sv~Hp~~Pp~~g~ 143 (204)
T cd08904 75 DKSLQVYKMLQR-IDSDTFICHT-IT-------QSFAMGSISPRDFVDLVH--IKRYEGNMNIVSSVSVEYPQCPPSSNY 143 (204)
T ss_pred cccccceeeEEE-eCCCcEEEEE-ec-------ccccCCcccCceEEEEEE--EEEeCCCEEEEEEEecccCCCCCCCCc
Confidence 457888888888 7777654432 11 1122233432 3333322 21223355666666666655 2
Q ss_pred EEEEE---EEEEEeCCCCCCccEEEEEEEEEEecchhHHHHHHHHHH---HHHHHHHHhHH
Q psy8200 192 VIVLE---KCRYFVHPENPDWTCFEQNAELDVKSFFGFENTIEKLAM---KQYITNISKGK 246 (530)
Q Consensus 192 ~~V~E---~c~Y~phPeNP~wT~f~QeA~I~issf~Gf~s~IEk~~~---krf~~Na~KGr 246 (530)
+..+= -+..+|.|++|+.|.|+--...|.+|..+ .+.|+++.. --|.+|++||.
T Consensus 144 VRa~n~~~G~~i~pl~~~p~~t~l~~~~~~DlkG~lP-~~vv~~~~~~~~~~f~~~~~~~~ 203 (204)
T cd08904 144 IRGYNHPCGYVCSPLPENPAYSKLVMFVQPELRGNLS-RSVIEKTMPTNLVNLILDAKDGI 203 (204)
T ss_pred EEEeeeccEEEEEECCCCCCceEEEEEEEeCCCCCCC-HHHHHHHhHHHHHHHHHHHHHhc
Confidence 32221 23456888899888887777788787633 445555543 35777777763
No 44
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=35.77 E-value=30 Score=23.79 Aligned_cols=27 Identities=22% Similarity=0.554 Sum_probs=20.6
Q ss_pred EecccceeeeecceeeeEEEeCCCCCc
Q psy8200 476 TCRVCQAMIDISGKRDQHVVKCVHCNE 502 (530)
Q Consensus 476 ~c~vc~~~i~~~~~~~q~vv~c~~c~e 502 (530)
.|..|...|.-.+....+..-|++|.+
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred cCccCCCcceEeEecCCCCeECcCCcC
Confidence 489999999999999999999999975
No 45
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=34.66 E-value=30 Score=40.77 Aligned_cols=38 Identities=21% Similarity=0.594 Sum_probs=29.7
Q ss_pred CCcceEEecccceeeeec-------ceeeeEEEeCCCCCccccCC
Q psy8200 470 GQVPMVTCRVCQAMIDIS-------GKRDQHVVKCVHCNEATPVK 507 (530)
Q Consensus 470 ~~~p~v~c~vc~~~i~~~-------~~~~q~vv~c~~c~eat~~~ 507 (530)
|-.|++.|+.|++...+. -+++++..+|..|+-..|+.
T Consensus 431 Gys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p 475 (730)
T COG1198 431 GYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIP 475 (730)
T ss_pred CccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCC
Confidence 677899999999987543 35556789999999876554
No 46
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=32.55 E-value=22 Score=36.09 Aligned_cols=42 Identities=14% Similarity=0.305 Sum_probs=30.3
Q ss_pred CCCCcceEEecccceeeeecceeeeEEEeCCCCCccccCCCC
Q psy8200 468 QPGQVPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNA 509 (530)
Q Consensus 468 ~~~~~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~ 509 (530)
.-|++-...|..|....+........+-+|+.|++..++||.
T Consensus 111 lHG~~~~~~C~~C~~~~~~~~~~~~~~p~C~~Cg~~g~lrP~ 152 (242)
T PTZ00408 111 MHGELLKVRCTATGHVFDWTEDVVHGSSRCKCCGCVGTLRPH 152 (242)
T ss_pred ecCccceEEECCCCcccCchhhhhcCCCccccCCCCCCCCCC
Confidence 347888889999998877654333346789888877777764
No 47
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.27 E-value=26 Score=32.58 Aligned_cols=33 Identities=24% Similarity=0.623 Sum_probs=25.0
Q ss_pred EEEeCCCCCccccCCCCCCC----------------CceEecc-CCCCCc
Q psy8200 493 HVVKCVHCNEATPVKNAPAG----------------KKYVRCP-YGVGMT 525 (530)
Q Consensus 493 ~vv~c~~c~eat~~~~~p~g----------------k~~~rc~-c~~~~~ 525 (530)
-+.+|..|+...++..+|.+ ..+.+|| |+..-.
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~ 118 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDF 118 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCc
Confidence 56899999988888765444 6789999 775433
No 48
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=32.13 E-value=27 Score=26.08 Aligned_cols=28 Identities=18% Similarity=0.520 Sum_probs=23.9
Q ss_pred EEecccceeeeecceeee-EEEeCCCCCc
Q psy8200 475 VTCRVCQAMIDISGKRDQ-HVVKCVHCNE 502 (530)
Q Consensus 475 v~c~vc~~~i~~~~~~~q-~vv~c~~c~e 502 (530)
-.|..|++.+++.-+.++ ..+.|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 479999999988877777 7889999987
No 49
>KOG2824|consensus
Probab=30.75 E-value=47 Score=34.87 Aligned_cols=35 Identities=26% Similarity=0.695 Sum_probs=25.2
Q ss_pred CCcceEEecccceeeeecc--eeeeEEEeCCCCCccc
Q psy8200 470 GQVPMVTCRVCQAMIDISG--KRDQHVVKCVHCNEAT 504 (530)
Q Consensus 470 ~~~p~v~c~vc~~~i~~~~--~~~q~vv~c~~c~eat 504 (530)
|++-++-|..|.=-=-+-- ..+-.+++|..|||--
T Consensus 236 Gg~rFlpC~~C~GS~kv~~~~~~~~~~~rC~~CNENG 272 (281)
T KOG2824|consen 236 GGARFLPCSNCHGSCKVHEEEEDDGGVLRCLECNENG 272 (281)
T ss_pred CCcceEecCCCCCceeeeeeccCCCcEEECcccCCCC
Confidence 7889999999974322221 3344799999999965
No 50
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=29.50 E-value=22 Score=29.25 Aligned_cols=24 Identities=21% Similarity=0.628 Sum_probs=18.5
Q ss_pred ceEEecccceeeeecceeeeEEEeCCCCCccc
Q psy8200 473 PMVTCRVCQAMIDISGKRDQHVVKCVHCNEAT 504 (530)
Q Consensus 473 p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat 504 (530)
+..+|+.|..+.+ ++ +|++|...+
T Consensus 2 ~~kAC~~C~~i~~--~~------~CP~Cgs~~ 25 (61)
T PRK08351 2 TEKACRHCHYITT--ED------RCPVCGSRD 25 (61)
T ss_pred chhhhhhCCcccC--CC------cCCCCcCCc
Confidence 3468999999984 22 599999866
No 51
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=28.98 E-value=23 Score=31.79 Aligned_cols=27 Identities=19% Similarity=0.490 Sum_probs=18.0
Q ss_pred ceEEecccceeeeecceeeeEEEeCCCCCcc
Q psy8200 473 PMVTCRVCQAMIDISGKRDQHVVKCVHCNEA 503 (530)
Q Consensus 473 p~v~c~vc~~~i~~~~~~~q~vv~c~~c~ea 503 (530)
+...|+.|++..+++... ..||.|+..
T Consensus 69 ~~~~C~~Cg~~~~~~~~~----~~CP~Cgs~ 95 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEFD----FSCPRCGSP 95 (113)
T ss_dssp -EEEETTTS-EEECHHCC----HH-SSSSSS
T ss_pred CcEECCCCCCEEecCCCC----CCCcCCcCC
Confidence 467888898888887665 458888754
No 52
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=28.88 E-value=32 Score=26.26 Aligned_cols=28 Identities=18% Similarity=0.558 Sum_probs=21.4
Q ss_pred EEecccceeeeecceeee-EEEeCCCCCc
Q psy8200 475 VTCRVCQAMIDISGKRDQ-HVVKCVHCNE 502 (530)
Q Consensus 475 v~c~vc~~~i~~~~~~~q-~vv~c~~c~e 502 (530)
-.|..|+..+++.-..+. -.+.|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 479999998888755443 4578999996
No 53
>PF10891 DUF2719: Protein of unknown function (DUF2719); InterPro: IPR020122 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf56; it is a family of uncharacterised viral proteins.
Probab=28.03 E-value=29 Score=30.02 Aligned_cols=21 Identities=29% Similarity=0.575 Sum_probs=15.9
Q ss_pred ecceeeeEEEeCCCCCccccCC
Q psy8200 486 ISGKRDQHVVKCVHCNEATPVK 507 (530)
Q Consensus 486 ~~~~~~q~vv~c~~c~eat~~~ 507 (530)
...+.+| ||.|..|+=..|+.
T Consensus 15 ~~~~~~q-VV~C~~C~FVAPmS 35 (81)
T PF10891_consen 15 EADEENQ-VVYCPKCYFVAPMS 35 (81)
T ss_pred cccccCC-EEEccccceecccE
Confidence 3444455 99999999998864
No 54
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=28.02 E-value=35 Score=24.60 Aligned_cols=24 Identities=25% Similarity=0.497 Sum_probs=15.8
Q ss_pred EEecccceeeeecceeeeEEEeCCCCCc
Q psy8200 475 VTCRVCQAMIDISGKRDQHVVKCVHCNE 502 (530)
Q Consensus 475 v~c~vc~~~i~~~~~~~q~vv~c~~c~e 502 (530)
-.|++|++..+-+. .--+|+.|+.
T Consensus 3 ~~C~~CG~i~~g~~----~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEGEE----APEKCPICGA 26 (34)
T ss_pred EECCCCCCEeECCc----CCCcCcCCCC
Confidence 36999998876332 1238888874
No 55
>PF14369 zf-RING_3: zinc-finger
Probab=27.80 E-value=31 Score=25.16 Aligned_cols=26 Identities=23% Similarity=0.629 Sum_probs=17.6
Q ss_pred EecccceeeeecceeeeEEEeCCCCCc
Q psy8200 476 TCRVCQAMIDISGKRDQHVVKCVHCNE 502 (530)
Q Consensus 476 ~c~vc~~~i~~~~~~~q~vv~c~~c~e 502 (530)
-|=.|...|.+... .+..+.|+.|+.
T Consensus 4 wCh~C~~~V~~~~~-~~~~~~CP~C~~ 29 (35)
T PF14369_consen 4 WCHQCNRFVRIAPS-PDSDVACPRCHG 29 (35)
T ss_pred eCccCCCEeEeCcC-CCCCcCCcCCCC
Confidence 37778888888655 233347888874
No 56
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=27.74 E-value=22 Score=26.86 Aligned_cols=27 Identities=26% Similarity=0.728 Sum_probs=18.3
Q ss_pred eCCCCCccc----cC-CCCCCCCceEeccCCCC
Q psy8200 496 KCVHCNEAT----PV-KNAPAGKKYVRCPYGVG 523 (530)
Q Consensus 496 ~c~~c~eat----~~-~~~p~gk~~~rc~c~~~ 523 (530)
+|. |++-. .- ..+=+|++|.+||-...
T Consensus 2 ~C~-Cg~~~~~~~s~k~~~N~GR~Fy~C~~~~~ 33 (45)
T PF06839_consen 2 KCP-CGEPAVRRTSKKTGPNPGRRFYKCPNYKD 33 (45)
T ss_pred CCC-CCCEeEEEEEeCCCCCCCCcceECCCCCC
Confidence 566 66533 23 45668999999996654
No 57
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=27.16 E-value=45 Score=36.46 Aligned_cols=33 Identities=12% Similarity=0.494 Sum_probs=27.3
Q ss_pred CcceEEecccceeeeecceeeeEEEeCCCCCcc
Q psy8200 471 QVPMVTCRVCQAMIDISGKRDQHVVKCVHCNEA 503 (530)
Q Consensus 471 ~~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~ea 503 (530)
..+.+.|..|..+.++..-..-+...|++|+..
T Consensus 10 ~~~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~ 42 (403)
T TIGR00155 10 AAKHILCSQCDMLVALPRIESGQKAACPRCGTT 42 (403)
T ss_pred CCCeeeCCCCCCcccccCCCCCCeeECCCCCCC
Confidence 344788999999999987777778999999854
No 58
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=27.02 E-value=40 Score=27.07 Aligned_cols=25 Identities=28% Similarity=0.596 Sum_probs=18.3
Q ss_pred EecccceeeeecceeeeEEEeCCCCCc
Q psy8200 476 TCRVCQAMIDISGKRDQHVVKCVHCNE 502 (530)
Q Consensus 476 ~c~vc~~~i~~~~~~~q~vv~c~~c~e 502 (530)
+|-.|++...- ...+.+..|+.|+.
T Consensus 30 ~C~~CG~~~~~--~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 30 TCPRCGHRNKK--RRSGRVFTCPNCGF 54 (69)
T ss_pred CccCccccccc--ccccceEEcCCCCC
Confidence 47788877655 56777888888864
No 59
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=26.86 E-value=44 Score=31.78 Aligned_cols=45 Identities=11% Similarity=0.389 Sum_probs=32.7
Q ss_pred CCCCCCCCCcceEEecccceeeeecceeeeEEEeCCCCCccccCCCC
Q psy8200 463 PYQASQPGQVPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNA 509 (530)
Q Consensus 463 ~~~~~~~~~~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~ 509 (530)
-|++.+-.|.=+..|..|++.+.+... .+.-.|+.|+--.-.|.|
T Consensus 101 ~Y~sGE~~g~G~l~C~~Cg~~~~~~~~--~~l~~Cp~C~~~~F~R~~ 145 (146)
T PF07295_consen 101 VYHSGEVVGPGTLVCENCGHEVELTHP--ERLPPCPKCGHTEFTRQP 145 (146)
T ss_pred CeecCcEecCceEecccCCCEEEecCC--CcCCCCCCCCCCeeeeCC
Confidence 355433335558899999999999863 569999999976655543
No 60
>PRK11827 hypothetical protein; Provisional
Probab=25.92 E-value=53 Score=26.96 Aligned_cols=37 Identities=22% Similarity=0.480 Sum_probs=27.2
Q ss_pred CcceEEecccceeeeecceeeeEEEeCCCCCccccCCCC
Q psy8200 471 QVPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNA 509 (530)
Q Consensus 471 ~~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~ 509 (530)
.+-.+.|.+|......... .|. ..|..|+-|-||+.-
T Consensus 5 LLeILaCP~ckg~L~~~~~-~~~-Lic~~~~laYPI~dg 41 (60)
T PRK11827 5 LLEIIACPVCNGKLWYNQE-KQE-LICKLDNLAFPLRDG 41 (60)
T ss_pred HHhheECCCCCCcCeEcCC-CCe-EECCccCeeccccCC
Confidence 3456899999988776433 343 449999999999863
No 61
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=25.83 E-value=54 Score=27.02 Aligned_cols=36 Identities=19% Similarity=0.622 Sum_probs=27.8
Q ss_pred CcceEEecccceeeeecceeeeEEEeCCCCCccccCCC
Q psy8200 471 QVPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKN 508 (530)
Q Consensus 471 ~~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~ 508 (530)
.+-.+.|.+|..-....-.+. +.-|..|+.|-||+.
T Consensus 5 LLeiLaCP~~kg~L~~~~~~~--~L~c~~~~~aYpI~d 40 (60)
T COG2835 5 LLEILACPVCKGPLVYDEEKQ--ELICPRCKLAYPIRD 40 (60)
T ss_pred hheeeeccCcCCcceEeccCC--EEEecccCceeeccc
Confidence 345789999998866544333 888999999999975
No 62
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=25.81 E-value=80 Score=27.71 Aligned_cols=43 Identities=23% Similarity=0.420 Sum_probs=31.9
Q ss_pred CCCcceEEecccceeeeecceeeeEEEeCCCCCccccCCCCCCCCc
Q psy8200 469 PGQVPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNAPAGKK 514 (530)
Q Consensus 469 ~~~~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~p~gk~ 514 (530)
..-|=-|.|..|...=-|.+ .-|.||+|..|+. .|-.|--||-
T Consensus 30 nS~Fm~VkCp~C~n~q~VFS-hA~t~V~C~~Cg~--~L~~PTGGKa 72 (85)
T PTZ00083 30 NSYFMDVKCPGCSQITTVFS-HAQTVVLCGGCSS--QLCQPTGGKA 72 (85)
T ss_pred CCeEEEEECCCCCCeeEEEe-cCceEEEccccCC--EeeccCCCCe
Confidence 34677899999998766665 4689999999974 5555555553
No 63
>PRK12495 hypothetical protein; Provisional
Probab=24.62 E-value=34 Score=34.81 Aligned_cols=27 Identities=22% Similarity=0.443 Sum_probs=22.3
Q ss_pred ceEEecccceeeeecceeeeEEEeCCCCCcc
Q psy8200 473 PMVTCRVCQAMIDISGKRDQHVVKCVHCNEA 503 (530)
Q Consensus 473 p~v~c~vc~~~i~~~~~~~q~vv~c~~c~ea 503 (530)
--..|.+|+.-|- ..+.|+.|..|.+.
T Consensus 41 sa~hC~~CG~PIp----a~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 41 TNAHCDECGDPIF----RHDGQEFCPTCQQP 67 (226)
T ss_pred chhhcccccCccc----CCCCeeECCCCCCc
Confidence 3457999999988 45899999999975
No 64
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.78 E-value=56 Score=32.71 Aligned_cols=21 Identities=29% Similarity=0.673 Sum_probs=17.9
Q ss_pred EEecccceeeeecceeeeEEEeCCCCCc
Q psy8200 475 VTCRVCQAMIDISGKRDQHVVKCVHCNE 502 (530)
Q Consensus 475 v~c~vc~~~i~~~~~~~q~vv~c~~c~e 502 (530)
..|..|++ .++.+.+|++|..
T Consensus 310 ~~C~~cg~-------~~~r~~~C~~cg~ 330 (364)
T COG0675 310 KTCPCCGH-------LSGRLFKCPRCGF 330 (364)
T ss_pred ccccccCC-------ccceeEECCCCCC
Confidence 36999999 6688999999987
No 65
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=23.35 E-value=43 Score=34.75 Aligned_cols=38 Identities=18% Similarity=0.429 Sum_probs=33.1
Q ss_pred cceEEecccceeeeecceeeeEEEeCCCCCccccCCCC
Q psy8200 472 VPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNA 509 (530)
Q Consensus 472 ~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~ 509 (530)
.--++|-.|...+-...-.+....+|++|.+.+.+.+.
T Consensus 155 ~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~~ 192 (256)
T PF09788_consen 155 SCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGPR 192 (256)
T ss_pred ceeEECCCCCCcEeccCCCCCccccCCCCceeccccch
Confidence 34699999999999988887899999999999998654
No 66
>PLN00209 ribosomal protein S27; Provisional
Probab=23.04 E-value=99 Score=27.23 Aligned_cols=43 Identities=23% Similarity=0.411 Sum_probs=32.0
Q ss_pred CCCcceEEecccceeeeecceeeeEEEeCCCCCccccCCCCCCCCc
Q psy8200 469 PGQVPMVTCRVCQAMIDISGKRDQHVVKCVHCNEATPVKNAPAGKK 514 (530)
Q Consensus 469 ~~~~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat~~~~~p~gk~ 514 (530)
..-|=-|.|..|...=-|.++ -|.||+|..|+. .|-.|--||-
T Consensus 31 nS~Fm~VkCp~C~n~q~VFSh-A~t~V~C~~Cg~--~L~~PTGGKa 73 (86)
T PLN00209 31 NSFFMDVKCQGCFNITTVFSH-SQTVVVCGSCQT--VLCQPTGGKA 73 (86)
T ss_pred CCEEEEEECCCCCCeeEEEec-CceEEEccccCC--EeeccCCCCe
Confidence 346778999999987666654 689999999974 5555555553
No 67
>PRK12860 transcriptional activator FlhC; Provisional
Probab=22.86 E-value=47 Score=33.02 Aligned_cols=34 Identities=18% Similarity=0.435 Sum_probs=26.4
Q ss_pred CCCCcceEEecccceeeeecceeeeEEEeCCCCC
Q psy8200 468 QPGQVPMVTCRVCQAMIDISGKRDQHVVKCVHCN 501 (530)
Q Consensus 468 ~~~~~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~ 501 (530)
+++-+.+..|+-|..-+=..-...++-.+|+-|+
T Consensus 128 ~s~~L~l~~C~~Cgg~fv~~~~e~~~~f~CplC~ 161 (189)
T PRK12860 128 DAGMLQLARCCRCGGKFVTHAHDLRHNFVCGLCQ 161 (189)
T ss_pred cCCCeeeccCCCCCCCeeccccccCCCCcCCCCC
Confidence 3457889999999987655544556788999999
No 68
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=22.41 E-value=54 Score=29.62 Aligned_cols=26 Identities=23% Similarity=0.666 Sum_probs=14.1
Q ss_pred eEEecccceeeeecceeeeEEEeCCCCCc
Q psy8200 474 MVTCRVCQAMIDISGKRDQHVVKCVHCNE 502 (530)
Q Consensus 474 ~v~c~vc~~~i~~~~~~~q~vv~c~~c~e 502 (530)
...|+.|++.+.+... +...||.|..
T Consensus 70 ~~~C~~Cg~~~~~~~~---~~~~CP~Cgs 95 (114)
T PRK03681 70 ECWCETCQQYVTLLTQ---RVRRCPQCHG 95 (114)
T ss_pred EEEcccCCCeeecCCc---cCCcCcCcCC
Confidence 5566667665555422 2245666663
No 69
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.22 E-value=59 Score=36.42 Aligned_cols=39 Identities=18% Similarity=0.484 Sum_probs=28.3
Q ss_pred CCcceEEecccceeeeec-------ceeeeEEEeCCCCCccccCCC
Q psy8200 470 GQVPMVTCRVCQAMIDIS-------GKRDQHVVKCVHCNEATPVKN 508 (530)
Q Consensus 470 ~~~p~v~c~vc~~~i~~~-------~~~~q~vv~c~~c~eat~~~~ 508 (530)
|-.|.+.|+.|+..+... =++++...+|..|+-..|+..
T Consensus 209 Gya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~ 254 (505)
T TIGR00595 209 GYSKNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPK 254 (505)
T ss_pred cCCCeeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCC
Confidence 567899999999987643 123456789999987766544
No 70
>KOG3312|consensus
Probab=22.19 E-value=50 Score=31.99 Aligned_cols=54 Identities=26% Similarity=0.438 Sum_probs=33.4
Q ss_pred eeecCcccccCcceEEeeceeeecccccce-eeeecc--chhhHHHHHHHhhhhHhhhhcccccCC
Q psy8200 312 SLIDKNWTEGADYERVESPILCHDGESIQG-SHVTSR--DELSFMFLLVWYYCTLTIRESILKVNG 374 (530)
Q Consensus 312 sLi~~~~~yk~dYekve~~ilc~~gesiqg-sHv~~~--~d~~~~fl~~~~y~tlt~re~il~~ng 374 (530)
+++++.+..|- -+..-..||| ||-+-. +-.-..|..+|.-||++||.||-+.=|
T Consensus 107 SiFeGrVVAkL---------PF~Pis~iqglSHRnL~GdD~TDCSfiFLYiLCtmsiRqNlQK~LG 163 (186)
T KOG3312|consen 107 SIFEGRVVAKL---------PFTPISIIQGLSHRNLKGDDMTDCSFIFLYILCTMSIRQNLQKILG 163 (186)
T ss_pred hhhcceeEEec---------CCcchHHHhcccccCCCCCCccchHHHHHHHHHHHHHHHHHHHHhC
Confidence 56666654442 2233345674 565542 223356777889999999999976554
No 71
>PF14353 CpXC: CpXC protein
Probab=22.04 E-value=82 Score=28.39 Aligned_cols=33 Identities=15% Similarity=0.444 Sum_probs=21.9
Q ss_pred EEecccceeeeeccee-----ee------------EEEeCCCCCccccCC
Q psy8200 475 VTCRVCQAMIDISGKR-----DQ------------HVVKCVHCNEATPVK 507 (530)
Q Consensus 475 v~c~vc~~~i~~~~~~-----~q------------~vv~c~~c~eat~~~ 507 (530)
|+|..|++.++++--. .| ..+.|++|++...+.
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 6788888877654321 11 367899998887763
No 72
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.95 E-value=40 Score=30.57 Aligned_cols=13 Identities=15% Similarity=0.575 Sum_probs=6.6
Q ss_pred eEEecccceeeee
Q psy8200 474 MVTCRVCQAMIDI 486 (530)
Q Consensus 474 ~v~c~vc~~~i~~ 486 (530)
...|+.|++...+
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 4455555544443
No 73
>COG5608 LEA14-like dessication related protein [Defense mechanisms]
Probab=21.78 E-value=55 Score=31.74 Aligned_cols=51 Identities=27% Similarity=0.545 Sum_probs=36.2
Q ss_pred ccCcceEEeeceeeecccccceeeeeccchhhHHHHHHHhhhhHhhhhcccccCCCccchhhhhh
Q psy8200 320 EGADYERVESPILCHDGESIQGSHVTSRDELSFMFLLVWYYCTLTIRESILKVNGSRIKGWWRMH 384 (530)
Q Consensus 320 yk~dYekve~~ilc~~gesiqgsHv~~~~d~~~~fl~~~~y~tlt~re~il~~ngs~i~~ww~~h 384 (530)
-|=+|....-.|...+|+..|+.|+-+....-+- =-|+.|-|+||.||+.|
T Consensus 69 tgl~y~vymN~Iki~eG~~~k~~~v~p~S~~tvd--------------v~l~~d~~~~ke~w~~h 119 (161)
T COG5608 69 TGLQYAVYMNDIKIGEGEILKGTTVPPNSRETVD--------------VPLRLDNSKIKEWWVTH 119 (161)
T ss_pred eceEEEEEEcceEeeccccccceEECCCCeEEEE--------------EEEEEehHHHHHHHHHH
Confidence 3446666666778888998999998863221110 24688999999999988
No 74
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=21.72 E-value=48 Score=36.44 Aligned_cols=30 Identities=13% Similarity=0.542 Sum_probs=24.6
Q ss_pred eEEecccceeeeecceeeeEEEeCCCCCcc
Q psy8200 474 MVTCRVCQAMIDISGKRDQHVVKCVHCNEA 503 (530)
Q Consensus 474 ~v~c~vc~~~i~~~~~~~q~vv~c~~c~ea 503 (530)
.+.|..|+.+.+...-.+-+...|++|+-.
T Consensus 10 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~ 39 (419)
T PRK15103 10 HILCPQCDMLVALPRLEHGQKAACPRCGTT 39 (419)
T ss_pred cccCCCCCceeecCCCCCCCeeECCCCCCC
Confidence 377999999999887666667899999853
No 75
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=21.53 E-value=28 Score=37.48 Aligned_cols=12 Identities=33% Similarity=0.764 Sum_probs=7.3
Q ss_pred cceEEeccccee
Q psy8200 472 VPMVTCRVCQAM 483 (530)
Q Consensus 472 ~p~v~c~vc~~~ 483 (530)
.-.|.|++|.+.
T Consensus 250 ~kav~C~~C~yt 261 (344)
T PF09332_consen 250 CKAVTCKQCKYT 261 (344)
T ss_dssp EEEEEETTT--E
T ss_pred EEEEEcCCCCCc
Confidence 457888888654
No 76
>KOG1984|consensus
Probab=21.43 E-value=57 Score=39.17 Aligned_cols=59 Identities=20% Similarity=0.342 Sum_probs=44.4
Q ss_pred CCcccccCCCCCCCCCCCCCCCCCCCCCcceEEecccceeeeecceeeeEE--EeCCCCCccc
Q psy8200 444 NMDITIEGQNPIPPDELPPPYQASQPGQVPMVTCRVCQAMIDISGKRDQHV--VKCVHCNEAT 504 (530)
Q Consensus 444 ~md~tvegf~s~~~~~~~p~~~~~~~~~~p~v~c~vc~~~i~~~~~~~q~v--v~c~~c~eat 504 (530)
++-+++.=|..+.++|.|+|=..-...+ -|.|+.|++-|+..=+-.=.+ +.|+-|+--+
T Consensus 310 PLalvIqPfa~l~p~E~~~~vVd~g~sg--PvRC~RCkaYinPFmqF~~~gr~f~Cn~C~~~n 370 (1007)
T KOG1984|consen 310 PLALVIQPFATLTPNEAPVPVVDLGESG--PVRCNRCKAYINPFMQFIDGGRKFICNFCGSKN 370 (1007)
T ss_pred cceeEecccccCCcccCCCceecCCCCC--CcchhhhhhhcCcceEEecCCceEEecCCCccc
Confidence 4556788899999999998887644333 589999999999766554444 8899987544
No 77
>PF05624 LSR: Lipolysis stimulated receptor (LSR); InterPro: IPR008664 This domain consists of mammalian LISCH7 protein homologues. LISCH7 is a liver-specific BHLH-ZIP transcription factor.
Probab=21.25 E-value=45 Score=26.24 Aligned_cols=7 Identities=71% Similarity=1.545 Sum_probs=4.8
Q ss_pred eEeccCC
Q psy8200 515 YVRCPYG 521 (530)
Q Consensus 515 ~~rc~c~ 521 (530)
||||||-
T Consensus 34 YvrcpcC 40 (49)
T PF05624_consen 34 YVRCPCC 40 (49)
T ss_pred EEECCCC
Confidence 7777764
No 78
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=21.22 E-value=29 Score=28.89 Aligned_cols=25 Identities=20% Similarity=0.535 Sum_probs=19.1
Q ss_pred cceEEecccceeeeecceeeeEEEeCCCCCccc
Q psy8200 472 VPMVTCRVCQAMIDISGKRDQHVVKCVHCNEAT 504 (530)
Q Consensus 472 ~p~v~c~vc~~~i~~~~~~~q~vv~c~~c~eat 504 (530)
.+..+|+.|..+.+ ++ .|+.|+-.+
T Consensus 3 ~~~~AC~~C~~i~~--~~------~Cp~Cgs~~ 27 (64)
T PRK06393 3 VQYRACKKCKRLTP--EK------TCPVHGDEK 27 (64)
T ss_pred chhhhHhhCCcccC--CC------cCCCCCCCc
Confidence 35789999999984 22 899998654
No 79
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=21.04 E-value=35 Score=25.02 Aligned_cols=28 Identities=18% Similarity=0.360 Sum_probs=23.0
Q ss_pred EEecccceeeeecceeeeEEEeCCCCCc
Q psy8200 475 VTCRVCQAMIDISGKRDQHVVKCVHCNE 502 (530)
Q Consensus 475 v~c~vc~~~i~~~~~~~q~vv~c~~c~e 502 (530)
..|..|+...++.-..-+.-.+|..|++
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCC
Confidence 3699999999998888888889999987
No 80
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=20.87 E-value=79 Score=29.83 Aligned_cols=35 Identities=31% Similarity=0.595 Sum_probs=25.9
Q ss_pred eEEeccccee-eeecceeeeEEEeCCCCCccccCCC
Q psy8200 474 MVTCRVCQAM-IDISGKRDQHVVKCVHCNEATPVKN 508 (530)
Q Consensus 474 ~v~c~vc~~~-i~~~~~~~q~vv~c~~c~eat~~~~ 508 (530)
.|.|..|++. -++.-+..-+..+|..|...+|+++
T Consensus 102 yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~~~V~~ 137 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIWVLKCEACGAETPVKP 137 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeEEEEcccCCCCCcCCc
Confidence 7999999873 1222234467899999999999864
No 81
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=20.28 E-value=87 Score=35.60 Aligned_cols=34 Identities=24% Similarity=0.542 Sum_probs=20.7
Q ss_pred eEEEeCCCCCccccCC--------CCCCCCceEecc-CCCCCc
Q psy8200 492 QHVVKCVHCNEATPVK--------NAPAGKKYVRCP-YGVGMT 525 (530)
Q Consensus 492 q~vv~c~~c~eat~~~--------~~p~gk~~~rc~-c~~~~~ 525 (530)
..-|+|++|.|-.+++ .+.++.-+..|| |+..++
T Consensus 198 ~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 198 RYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred EEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCC
Confidence 4456677777766654 114556677787 666554
Done!