Query psy13877
Match_columns 114
No_of_seqs 122 out of 341
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 22:41:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13877.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13877hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0482|consensus 99.8 3.9E-21 8.4E-26 169.2 1.3 67 1-67 205-289 (721)
2 KOG0480|consensus 99.5 3E-15 6.5E-20 134.0 4.3 86 1-98 181-284 (764)
3 smart00350 MCM minichromosome 99.4 1.6E-13 3.4E-18 117.2 6.4 53 1-56 61-128 (509)
4 COG1241 MCM2 Predicted ATPase 99.2 1.7E-11 3.6E-16 110.0 6.4 73 2-77 154-253 (682)
5 KOG0479|consensus 99.2 2E-11 4.3E-16 109.6 5.4 67 14-80 180-271 (818)
6 PTZ00111 DNA replication licen 99.1 5.9E-11 1.3E-15 109.2 5.8 50 7-56 286-370 (915)
7 KOG0477|consensus 99.0 3.4E-10 7.4E-15 102.2 3.7 69 2-75 318-413 (854)
8 KOG0478|consensus 98.4 2.1E-07 4.5E-12 84.8 3.9 46 11-56 293-353 (804)
9 KOG0481|consensus 98.4 3.3E-07 7.3E-12 82.0 4.0 43 14-56 202-259 (729)
10 cd04486 YhcR_OBF_like YhcR_OBF 81.2 1.9 4.1E-05 28.8 2.9 25 45-69 44-69 (78)
11 COG2871 NqrF Na+-transporting 79.8 1.8 3.8E-05 37.5 2.9 27 31-57 230-265 (410)
12 smart00739 KOW KOW (Kyprides, 56.7 19 0.0004 18.5 2.8 22 46-68 2-23 (28)
13 COG4043 Preprotein translocase 55.6 4.1 8.8E-05 30.0 0.1 23 45-67 33-64 (111)
14 cd04482 RPA2_OBF_like RPA2_OBF 53.6 13 0.00029 25.2 2.4 17 45-61 47-64 (91)
15 CHL00143 rpl3 ribosomal protei 39.0 44 0.00094 26.8 3.6 38 25-63 77-119 (207)
16 PF00970 FAD_binding_6: Oxidor 38.8 20 0.00043 23.3 1.4 14 45-58 81-94 (99)
17 PRK03760 hypothetical protein; 38.4 22 0.00048 25.5 1.7 11 45-55 105-115 (117)
18 PRK11507 ribosome-associated p 36.0 29 0.00064 23.4 1.9 14 43-56 50-63 (70)
19 smart00276 GLECT Galectin. Gal 34.9 60 0.0013 22.8 3.4 30 39-70 4-35 (128)
20 COG2012 RPB5 DNA-directed RNA 32.8 27 0.0006 24.4 1.4 12 45-56 54-65 (80)
21 PF12249 AftA_C: Arabinofurano 32.5 52 0.0011 26.1 3.0 42 35-77 22-84 (178)
22 PF08021 FAD_binding_9: Sidero 31.5 25 0.00054 24.8 1.0 14 45-58 101-114 (117)
23 PF02769 AIRS_C: AIR synthase 30.9 32 0.00069 23.8 1.5 11 47-57 1-11 (153)
24 cd04088 EFG_mtEFG_II EFG_mtEFG 30.5 1.5E+02 0.0032 18.8 4.7 28 28-56 44-71 (83)
25 KOG3416|consensus 30.1 32 0.00069 26.1 1.4 13 44-56 60-72 (134)
26 COG0611 ThiL Thiamine monophos 29.2 41 0.00089 28.4 2.1 23 45-67 147-171 (317)
27 cd06188 NADH_quinone_reductase 28.6 1.2E+02 0.0025 23.8 4.4 19 39-57 116-140 (283)
28 cd04487 RecJ_OBF2_like RecJ_OB 28.4 66 0.0014 21.0 2.6 18 45-62 43-61 (73)
29 PF07425 Pardaxin: Pardaxin; 27.7 25 0.00053 20.6 0.4 12 93-104 22-33 (33)
30 KOG1749|consensus 27.4 61 0.0013 24.7 2.5 32 46-78 94-134 (143)
31 PF07287 DUF1446: Protein of u 27.2 80 0.0017 27.0 3.5 27 24-61 277-307 (362)
32 PF02643 DUF192: Uncharacteriz 27.1 20 0.00044 25.0 -0.1 11 45-55 97-107 (108)
33 PF01191 RNA_pol_Rpb5_C: RNA p 26.8 56 0.0012 22.1 2.1 18 45-62 48-65 (74)
34 PF02080 TrkA_C: TrkA-C domain 26.8 36 0.00079 20.7 1.1 17 40-56 41-58 (71)
35 PRK08051 fre FMN reductase; Va 26.4 80 0.0017 23.9 3.1 30 45-74 79-114 (232)
36 KOG2241|consensus 25.8 56 0.0012 27.1 2.3 14 41-56 186-199 (255)
37 TIGR03595 Obg_CgtA_exten Obg f 25.0 55 0.0012 21.4 1.7 12 45-56 53-64 (69)
38 PF13567 DUF4131: Domain of un 24.8 1.2E+02 0.0026 20.4 3.5 11 46-56 129-139 (176)
39 COG2375 ViuB Siderophore-inter 24.6 91 0.002 25.8 3.3 34 45-78 121-159 (265)
40 cd06193 siderophore_interactin 24.5 91 0.002 23.7 3.1 35 45-79 98-137 (235)
41 COG3450 Predicted enzyme of th 24.5 1.4E+02 0.003 21.8 3.9 40 12-54 53-94 (116)
42 PF14801 GCD14_N: tRNA methylt 24.4 50 0.0011 21.5 1.4 14 46-59 6-19 (54)
43 PRK09570 rpoH DNA-directed RNA 23.7 62 0.0013 22.3 1.8 15 45-59 51-65 (79)
44 cd04496 SSB_OBF SSB_OBF: A sub 23.3 54 0.0012 21.1 1.4 12 45-56 61-72 (100)
45 cd04092 mtEFG2_II_like mtEFG2_ 22.5 2.2E+02 0.0047 18.1 4.8 27 29-56 45-71 (83)
46 PRK14105 selenophosphate synth 22.2 63 0.0014 26.4 1.9 22 39-60 158-179 (345)
47 PRK06863 single-stranded DNA-b 22.0 69 0.0015 24.6 2.0 44 45-89 69-121 (168)
48 TIGR00621 ssb single stranded 21.8 72 0.0016 23.8 2.0 35 45-79 68-111 (164)
49 cd06190 T4MO_e_transfer_like T 21.0 1.2E+02 0.0025 22.6 3.0 28 46-73 75-108 (232)
50 cd06189 flavin_oxioreductase N 20.8 1.1E+02 0.0024 22.7 2.9 13 45-57 75-87 (224)
51 PF02874 ATP-synt_ab_N: ATP sy 20.7 69 0.0015 19.8 1.5 12 45-56 58-69 (69)
52 cd02691 PurM-like2 AIR synthas 20.6 71 0.0015 26.6 1.9 16 44-59 158-173 (346)
53 TIGR03625 L3_bact 50S ribosoma 20.4 1.2E+02 0.0026 24.2 3.1 38 25-63 74-116 (202)
54 TIGR00739 yajC preprotein tran 20.3 70 0.0015 21.8 1.5 12 45-56 37-48 (84)
No 1
>KOG0482|consensus
Probab=99.81 E-value=3.9e-21 Score=169.16 Aligned_cols=67 Identities=51% Similarity=0.877 Sum_probs=65.2
Q ss_pred CCCcccccCCCCccceEEEecCceeeeceEeeeeccCCCCCCCC---------------CCCCCcEEEEEc---CCCCcc
Q psy13877 1 MCPSEDCQVNKSGGRLYLQTRGSKFVKFQELKVQEHTSNQPLQM---------------GSSPAQVVKLTN---PPVQTG 62 (114)
Q Consensus 1 ~Cps~~C~~n~s~G~l~L~~r~SkF~dfQeVrIQE~peeVP~G~---------------~~kPGD~V~lTG---p~p~tg 62 (114)
.|||+.|+.|+.+|+|+|++|+|||++|||+++||++++||.|| .|+|||+|.|+| |.||+|
T Consensus 205 ~CpS~eC~~n~~~G~L~lqtRgSKFikfQe~kmQEls~qVPvG~IPRsltv~~~ge~tr~~~PGDvV~vsGiFLP~pytG 284 (721)
T KOG0482|consen 205 ECPSEECRTNKAGGRLYLQTRGSKFIKFQEVKMQELSDQVPVGHIPRSLTVHVYGEMTRKCQPGDVVVVSGIFLPIPYTG 284 (721)
T ss_pred hCChHHhhhcccCCeEEEEecccccchhhhhhHHHHhccCCCCccCceeEEEEecccceecCCCCEEEEeeeecccchhh
Confidence 49999999999999999999999999999999999999999999 589999999999 999999
Q ss_pred eeeee
Q psy13877 63 QKMIV 67 (114)
Q Consensus 63 f~a~~ 67 (114)
|++++
T Consensus 285 fr~~~ 289 (721)
T KOG0482|consen 285 FRALK 289 (721)
T ss_pred HHHHH
Confidence 99987
No 2
>KOG0480|consensus
Probab=99.55 E-value=3e-15 Score=133.99 Aligned_cols=86 Identities=22% Similarity=0.414 Sum_probs=69.8
Q ss_pred CCCcccccCCCCccceEEEecCceeeeceEeeeeccCCCCCCCC---------------CCCCCcEEEEEc---CCCCcc
Q psy13877 1 MCPSEDCQVNKSGGRLYLQTRGSKFVKFQELKVQEHTSNQPLQM---------------GSSPAQVVKLTN---PPVQTG 62 (114)
Q Consensus 1 ~Cps~~C~~n~s~G~l~L~~r~SkF~dfQeVrIQE~peeVP~G~---------------~~kPGD~V~lTG---p~p~tg 62 (114)
.|||+.|. ++-+|.+....|+|+|||+|||||+.+++|.|+ .|+|||+|+||| .+|+..
T Consensus 181 ~C~np~C~---nrr~f~l~~~~s~f~D~QkIrIQE~~~E~p~GsiPRtvdviLr~dlVe~~~pGD~v~~TGiliVvpdv~ 257 (764)
T KOG0480|consen 181 KCPNPVCS---NRRSFTLDRSSSRFLDWQKIRIQELQAEIPRGSIPRTVDVILRGDLVETAQPGDKVDITGILIVVPDVS 257 (764)
T ss_pred cCCCcccc---CCceeeeecccceeeeeeeeehhhhhhhCCCCCCCceeEEEEhhhhHhhcCCCCEEEEEEEEEEecChH
Confidence 49999994 566899999999999999999999999999999 589999999999 667643
Q ss_pred eeeeeecCCCCCcchhhhhhhcCCccccccchhhhh
Q psy13877 63 QKMIVLTNNSNPPALEEKKFDRGIYNNEGLIASKLM 98 (114)
Q Consensus 63 f~a~~l~n~v~~~~~~~~~~~~g~~~~~g~~~~~~~ 98 (114)
. +..|.++.+.- ||+...+|++|++-+
T Consensus 258 ~--------l~~pgsk~~n~-r~~~~~~~i~~lkal 284 (764)
T KOG0480|consen 258 Q--------LGGPGSKAENN-RGGETGDGITGLKAL 284 (764)
T ss_pred H--------hcCCccccccc-cCCCcccceeeehhc
Confidence 3 44455666533 366556899998765
No 3
>smart00350 MCM minichromosome maintenance proteins.
Probab=99.44 E-value=1.6e-13 Score=117.25 Aligned_cols=53 Identities=30% Similarity=0.616 Sum_probs=48.4
Q ss_pred CCCcccccCCCCccceEEEecCceeeeceEeeeeccCCCCCCCC---------------CCCCCcEEEEEc
Q psy13877 1 MCPSEDCQVNKSGGRLYLQTRGSKFVKFQELKVQEHTSNQPLQM---------------GSSPAQVVKLTN 56 (114)
Q Consensus 1 ~Cps~~C~~n~s~G~l~L~~r~SkF~dfQeVrIQE~peeVP~G~---------------~~kPGD~V~lTG 56 (114)
.|+++.| +++++|.++...|+|+|||+|+|||.|+++|.|+ .++|||+|.|+|
T Consensus 61 ~C~~~~C---~~~~~f~l~~~~s~~~D~Q~I~iQE~~e~~p~G~~Prsi~v~l~~dLvd~~~PGD~V~i~G 128 (509)
T smart00350 61 VCPPREC---QSPTPFSLNHERSTFIDFQKIKLQESPEEVPAGQLPRSVDVILDGDLVDKAKPGDRVEVTG 128 (509)
T ss_pred cCCCCcC---CCCCceEeccCCCeEEEEEEEEEEcCcccCCCCCCCcEEEEEEcccccCcccCCCEEEEEE
Confidence 3888778 4566799999999999999999999999999999 589999999999
No 4
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=99.22 E-value=1.7e-11 Score=109.97 Aligned_cols=73 Identities=26% Similarity=0.328 Sum_probs=60.9
Q ss_pred CCcccccCCCCccceEEEecCceeeeceEeeeeccCCCCCCCC---------------CCCCCcEEEEEc---CCC----
Q psy13877 2 CPSEDCQVNKSGGRLYLQTRGSKFVKFQELKVQEHTSNQPLQM---------------GSSPAQVVKLTN---PPV---- 59 (114)
Q Consensus 2 Cps~~C~~n~s~G~l~L~~r~SkF~dfQeVrIQE~peeVP~G~---------------~~kPGD~V~lTG---p~p---- 59 (114)
|++ | ....+++|.+..+.|+|+|||+|+|||.|+.+|+|+ .++|||+|.+|| +.|
T Consensus 154 C~~--~-~~~~~~~~~~~~~~s~f~d~Q~vkiQE~pe~~p~g~~Prs~~vil~~dlv~~~~pGdrV~itGi~~~~~~~~~ 230 (682)
T COG1241 154 CEN--C-GKFGKGPLKLVPRKSEFIDFQKVKIQELPELVPGGELPRSIEVILEDDLVDSVRPGDRVKITGVVRIVPSRSL 230 (682)
T ss_pred CCC--c-cccCCCceEEecCcceeeeceEEEEecCcccCCCCCCCceEEEEEecCcccccCCCCEEEEEEEEeccccccc
Confidence 777 4 223678999999999999999999999999999998 589999999999 444
Q ss_pred -----CcceeeeeecCCCCCcch
Q psy13877 60 -----QTGQKMIVLTNNSNPPAL 77 (114)
Q Consensus 60 -----~tgf~a~~l~n~v~~~~~ 77 (114)
...|+.++.+|++.....
T Consensus 231 ~~~~~~~~~~~~~~a~~v~~~~~ 253 (682)
T COG1241 231 SGRRKGPVFEIYLEANSVEKLDK 253 (682)
T ss_pred ccccCCceEEEEEEEEEEEeccc
Confidence 334788888888776664
No 5
>KOG0479|consensus
Probab=99.19 E-value=2e-11 Score=109.62 Aligned_cols=67 Identities=18% Similarity=0.223 Sum_probs=59.1
Q ss_pred cceEEEecCceeeeceEeeeeccCCCCCCCC---------------CCCCCcEEEEEc-----CC-----CCcceeeeee
Q psy13877 14 GRLYLQTRGSKFVKFQELKVQEHTSNQPLQM---------------GSSPAQVVKLTN-----PP-----VQTGQKMIVL 68 (114)
Q Consensus 14 G~l~L~~r~SkF~dfQeVrIQE~peeVP~G~---------------~~kPGD~V~lTG-----p~-----p~tgf~a~~l 68 (114)
-.|......|+|.|||.|.|||+||..|+|+ ++||||+|.|.| |. ...+|++++|
T Consensus 180 N~L~TEyGlS~ykDHQtitiQEmPE~APaGQLPRSVDvilddDLVD~~KPGDRV~ivG~yr~Lp~k~~g~tsg~FRTvli 259 (818)
T KOG0479|consen 180 NLLETEYGLSVYKDHQTITIQEMPEKAPAGQLPRSVDVILDDDLVDRVKPGDRVNIVGIYRSLPGKSNGNTSGTFRTVLI 259 (818)
T ss_pred CeeeEeecceeeecccEEEeeeccccCCCCCCCcceeEEecccccccCCCCCeeEEEEEEeeccCccCCcccceeEEEEE
Confidence 4688889999999999999999999999999 689999999999 32 2344999999
Q ss_pred cCCCCCcchhhh
Q psy13877 69 TNNSNPPALEEK 80 (114)
Q Consensus 69 ~n~v~~~~~~~~ 80 (114)
+|||.+++.+++
T Consensus 260 aNni~~l~ke~~ 271 (818)
T KOG0479|consen 260 ANNIELLSKEAA 271 (818)
T ss_pred eccHHhhccccc
Confidence 999999998754
No 6
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=99.13 E-value=5.9e-11 Score=109.20 Aligned_cols=50 Identities=12% Similarity=0.076 Sum_probs=44.6
Q ss_pred ccCCCCccceEEEecCceeeeceEeeeeccCCCCCCCC-----------------------------------CCCCCcE
Q psy13877 7 CQVNKSGGRLYLQTRGSKFVKFQELKVQEHTSNQPLQM-----------------------------------GSSPAQV 51 (114)
Q Consensus 7 C~~n~s~G~l~L~~r~SkF~dfQeVrIQE~peeVP~G~-----------------------------------~~kPGD~ 51 (114)
|..|+++++|.|+.+.|+|+|||+|+|||.|+.+|.|+ .|+|||+
T Consensus 286 C~~C~~~~~f~l~~~~s~f~D~Q~IklQE~pe~vp~G~~P~~~~~~~~~~~~~~~~~~~~rsi~v~l~dDLVD~v~PGDr 365 (915)
T PTZ00111 286 CNECNSKYTFELNHNMCVYSTKKIVKLLQSNSSLNNPDKDGLDNSVDNSGLNGEIYMKDNEVINLNLYDDLIDSVKTGDR 365 (915)
T ss_pred CCCCCCCCCeEEccCccEEEeeeEEEEeeCcccCCCCCCCccccccccccccccccccCCceEEEEEecchhccCCCCCE
Confidence 44447889999999999999999999999999998763 4799999
Q ss_pred EEEEc
Q psy13877 52 VKLTN 56 (114)
Q Consensus 52 V~lTG 56 (114)
|+|||
T Consensus 366 V~VtG 370 (915)
T PTZ00111 366 VTVVG 370 (915)
T ss_pred EEEEE
Confidence 99999
No 7
>KOG0477|consensus
Probab=98.97 E-value=3.4e-10 Score=102.24 Aligned_cols=69 Identities=19% Similarity=0.419 Sum_probs=59.0
Q ss_pred CCcccccCCCCccceEEEecCceeeeceEeeeeccCCCCCCCC---------------CCCCCcEEEEEc--CCCCcc--
Q psy13877 2 CPSEDCQVNKSGGRLYLQTRGSKFVKFQELKVQEHTSNQPLQM---------------GSSPAQVVKLTN--PPVQTG-- 62 (114)
Q Consensus 2 Cps~~C~~n~s~G~l~L~~r~SkF~dfQeVrIQE~peeVP~G~---------------~~kPGD~V~lTG--p~p~tg-- 62 (114)
||+ | +++|+|.++++...|.+||+|+|||.|..||+|. .|+|||.|.+|| ..-|.|
T Consensus 318 C~~--c---qSkGpf~vn~e~TvyrnYQritiQEspg~v~~GrlPRsk~vILl~DLvD~~kpGdEievTGIy~nn~d~sL 392 (854)
T KOG0477|consen 318 CPE--C---QSKGPFEVNVEETVYRNYQRITIQESPGTVPAGRLPRSKEVILLADLVDSCKPGDEIEVTGIYTNNFDGSL 392 (854)
T ss_pred Ccc--c---cCCCCCccchhhhhhcccceeeeccCCCcCCCCccccchhheehhhhhhhcCCCcceEEeeeecccccccc
Confidence 666 6 7899999999999999999999999999999999 589999999999 333333
Q ss_pred --------eeeeeecCCCCCc
Q psy13877 63 --------QKMIVLTNNSNPP 75 (114)
Q Consensus 63 --------f~a~~l~n~v~~~ 75 (114)
|.+++++|.|.--
T Consensus 393 N~kngFpvfatvi~ANhV~~k 413 (854)
T KOG0477|consen 393 NTKNGFPVFATVIEANHVVKK 413 (854)
T ss_pred cccCCccccceeheehhhhhh
Confidence 7889999976543
No 8
>KOG0478|consensus
Probab=98.41 E-value=2.1e-07 Score=84.75 Aligned_cols=46 Identities=24% Similarity=0.304 Sum_probs=42.8
Q ss_pred CCccceEEEecCceeeeceEeeeeccCCCCCCCC---------------CCCCCcEEEEEc
Q psy13877 11 KSGGRLYLQTRGSKFVKFQELKVQEHTSNQPLQM---------------GSSPAQVVKLTN 56 (114)
Q Consensus 11 ~s~G~l~L~~r~SkF~dfQeVrIQE~peeVP~G~---------------~~kPGD~V~lTG 56 (114)
+.+-.|.|....|.|.|-|-||+||.|+.+|.|+ .++|||+|.|||
T Consensus 293 ~~~~~~~Lihnrs~F~dkQviklqEspd~~p~g~tPhtv~v~~~~dLVD~v~pGDrv~VTG 353 (804)
T KOG0478|consen 293 GTTNSFQLLHNRSEFADKQVIKLQESPDDMPEGSTPHTVSVVLHNDLVDKVRPGDRVEVTG 353 (804)
T ss_pred cCcccceeehhhhhhcccceeeeeeccccCcCCCCCceEEEEEehhhhhccCCCCeEEEEE
Confidence 5555699999999999999999999999999999 689999999999
No 9
>KOG0481|consensus
Probab=98.36 E-value=3.3e-07 Score=82.05 Aligned_cols=43 Identities=26% Similarity=0.297 Sum_probs=41.0
Q ss_pred cceEEEecCceeeeceEeeeeccCCCCCCCC---------------CCCCCcEEEEEc
Q psy13877 14 GRLYLQTRGSKFVKFQELKVQEHTSNQPLQM---------------GSSPAQVVKLTN 56 (114)
Q Consensus 14 G~l~L~~r~SkF~dfQeVrIQE~peeVP~G~---------------~~kPGD~V~lTG 56 (114)
-+|.+.++.|+|+|+|.+++||.||.||.|+ .+.||.+|+|+|
T Consensus 202 DPyii~pdks~~vD~QtLKLQE~pe~VP~GE~PRhl~L~~dRyL~~kvvPG~RvtI~G 259 (729)
T KOG0481|consen 202 DPYIIMPDKSKCVDQQTLKLQELPEDVPVGEMPRHLQLFCDRYLTNKVVPGNRVTIMG 259 (729)
T ss_pred CCEEEcccccceeehhheehhhCcccCCcCcCcchhhhhhhHHHhccccCCceEEEEE
Confidence 4689999999999999999999999999999 589999999999
No 10
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=81.20 E-value=1.9 Score=28.81 Aligned_cols=25 Identities=12% Similarity=0.147 Sum_probs=19.7
Q ss_pred CCCCCcEEEEEc-CCCCcceeeeeec
Q psy13877 45 GSSPAQVVKLTN-PPVQTGQKMIVLT 69 (114)
Q Consensus 45 ~~kPGD~V~lTG-p~p~tgf~a~~l~ 69 (114)
.+++||+|.|+| ...|.|...|..+
T Consensus 44 ~~~~Gd~V~vtG~v~ey~g~tql~~~ 69 (78)
T cd04486 44 DVAVGDLVRVTGTVTEYYGLTQLTAV 69 (78)
T ss_pred CCCCCCEEEEEEEEEeeCCeEEEccC
Confidence 478999999999 8888886665533
No 11
>COG2871 NqrF Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF [Energy production and conversion]
Probab=79.79 E-value=1.8 Score=37.50 Aligned_cols=27 Identities=15% Similarity=0.415 Sum_probs=21.1
Q ss_pred eeeeccCC---CCCCCC------CCCCCcEEEEEcC
Q psy13877 31 LKVQEHTS---NQPLQM------GSSPAQVVKLTNP 57 (114)
Q Consensus 31 VrIQE~pe---eVP~G~------~~kPGD~V~lTGp 57 (114)
|||--+|- ++|.|. .++|||+|+|+||
T Consensus 230 vRIAtPPp~~~~~PpG~mSSyi~sLKpGDKvtisGP 265 (410)
T COG2871 230 VRIATPPPRNPDAPPGQMSSYIWSLKPGDKVTISGP 265 (410)
T ss_pred EEeccCCCCCCCCCccceeeeEEeecCCCeEEEecc
Confidence 56655543 678888 6899999999994
No 12
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=56.73 E-value=19 Score=18.52 Aligned_cols=22 Identities=18% Similarity=0.098 Sum_probs=15.5
Q ss_pred CCCCcEEEEEcCCCCcceeeeee
Q psy13877 46 SSPAQVVKLTNPPVQTGQKMIVL 68 (114)
Q Consensus 46 ~kPGD~V~lTGp~p~tgf~a~~l 68 (114)
..+||.|.|++ -|+.|+.+.++
T Consensus 2 ~~~G~~V~I~~-G~~~g~~g~i~ 23 (28)
T smart00739 2 FEVGDTVRVIA-GPFKGKVGKVL 23 (28)
T ss_pred CCCCCEEEEeE-CCCCCcEEEEE
Confidence 47999999988 23666666553
No 13
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=55.63 E-value=4.1 Score=29.97 Aligned_cols=23 Identities=9% Similarity=0.108 Sum_probs=18.2
Q ss_pred CCCCCcEEEEEc---------CCCCcceeeee
Q psy13877 45 GSSPAQVVKLTN---------PPVQTGQKMIV 67 (114)
Q Consensus 45 ~~kPGD~V~lTG---------p~p~tgf~a~~ 67 (114)
+++|||.+.|+| ...|..|++|.
T Consensus 33 ~ik~GD~IiF~~~~l~v~V~~vr~Y~tF~~ml 64 (111)
T COG4043 33 QIKPGDKIIFNGDKLKVEVIDVRVYDTFEEML 64 (111)
T ss_pred CCCCCCEEEEcCCeeEEEEEEEeehhHHHHHH
Confidence 589999999997 34677787763
No 14
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=53.59 E-value=13 Score=25.22 Aligned_cols=17 Identities=18% Similarity=-0.005 Sum_probs=14.6
Q ss_pred CCCCCcEEEEEc-CCCCc
Q psy13877 45 GSSPAQVVKLTN-PPVQT 61 (114)
Q Consensus 45 ~~kPGD~V~lTG-p~p~t 61 (114)
.+++||+|.+.| +..|.
T Consensus 47 ~l~~Gd~V~v~G~v~~y~ 64 (91)
T cd04482 47 LLIPGDEVTVYGSVRPGT 64 (91)
T ss_pred CCCCCCEEEEEEEEecCC
Confidence 378999999999 77776
No 15
>CHL00143 rpl3 ribosomal protein L3; Validated
Probab=39.04 E-value=44 Score=26.76 Aligned_cols=38 Identities=16% Similarity=0.277 Sum_probs=27.9
Q ss_pred eeeceEeeeeccCCCCCCCC-----CCCCCcEEEEEcCCCCcce
Q psy13877 25 FVKFQELKVQEHTSNQPLQM-----GSSPAQVVKLTNPPVQTGQ 63 (114)
Q Consensus 25 F~dfQeVrIQE~peeVP~G~-----~~kPGD~V~lTGp~p~tgf 63 (114)
+..+-|+|+.+ .+++|.|+ -..|||.|+++|..---||
T Consensus 77 ~r~l~Efrv~~-~~~~~vG~~l~v~~F~~Gq~VDV~g~sKGKGF 119 (207)
T CHL00143 77 LKYLKEFRVKS-SEEFEVGQPLTVDAFSVGQLVNVSGKSIGKGF 119 (207)
T ss_pred ceEEEEEEcCC-cccCCCCCEEEhhhccCCCEEEEEEEecCCcc
Confidence 34567889977 45599999 4799999999994333344
No 16
>PF00970 FAD_binding_6: Oxidoreductase FAD-binding domain; InterPro: IPR008333 These sequences contain an oxidoreductase FAD-binding domain. To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [] and of pig NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+ reductase []: the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).; PDB: 1JB9_A 3LVB_A 3LO8_A 1FRN_A 1FND_A 1BX1_A 1FNC_A 1FNB_A 1BX0_A 1FRQ_A ....
Probab=38.85 E-value=20 Score=23.34 Aligned_cols=14 Identities=21% Similarity=0.387 Sum_probs=12.3
Q ss_pred CCCCCcEEEEEcCC
Q psy13877 45 GSSPAQVVKLTNPP 58 (114)
Q Consensus 45 ~~kPGD~V~lTGp~ 58 (114)
.+++||+|.|.||.
T Consensus 81 ~l~~Gd~v~i~gP~ 94 (99)
T PF00970_consen 81 QLKPGDEVEIRGPY 94 (99)
T ss_dssp TSCTTSEEEEEEEE
T ss_pred hCCCCCEEEEEEcc
Confidence 68999999999963
No 17
>PRK03760 hypothetical protein; Provisional
Probab=38.37 E-value=22 Score=25.54 Aligned_cols=11 Identities=0% Similarity=-0.033 Sum_probs=9.0
Q ss_pred CCCCCcEEEEE
Q psy13877 45 GSSPAQVVKLT 55 (114)
Q Consensus 45 ~~kPGD~V~lT 55 (114)
+++|||+|.+.
T Consensus 105 gi~~Gd~v~~~ 115 (117)
T PRK03760 105 KVEVGDEIEWI 115 (117)
T ss_pred CCCCCCEEEEe
Confidence 58999999763
No 18
>PRK11507 ribosome-associated protein; Provisional
Probab=36.03 E-value=29 Score=23.42 Aligned_cols=14 Identities=14% Similarity=0.162 Sum_probs=11.8
Q ss_pred CCCCCCCcEEEEEc
Q psy13877 43 QMGSSPAQVVKLTN 56 (114)
Q Consensus 43 G~~~kPGD~V~lTG 56 (114)
|..++|||.|.|.|
T Consensus 50 gkKl~~GD~V~~~g 63 (70)
T PRK11507 50 RCKIVAGQTVSFAG 63 (70)
T ss_pred CCCCCCCCEEEECC
Confidence 33799999999987
No 19
>smart00276 GLECT Galectin. Galectin - galactose-binding lectin
Probab=34.91 E-value=60 Score=22.79 Aligned_cols=30 Identities=17% Similarity=0.137 Sum_probs=19.0
Q ss_pred CCCCCCCCCCCcEEEEEc-CCCC-cceeeeeecC
Q psy13877 39 NQPLQMGSSPAQVVKLTN-PPVQ-TGQKMIVLTN 70 (114)
Q Consensus 39 eVP~G~~~kPGD~V~lTG-p~p~-tgf~a~~l~n 70 (114)
.+|.| .+||+.|.|+| +.+. ..|.--..++
T Consensus 4 ~lp~~--l~~G~~i~i~G~~~~~~~~F~inl~~~ 35 (128)
T smart00276 4 PIPGG--LKPGQTLTVRGIVLPDAKRFSINLLTG 35 (128)
T ss_pred cCCCC--CCCCCEEEEEEEECCCCCEEEEEeecC
Confidence 35555 89999999999 4443 3454433333
No 20
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=32.78 E-value=27 Score=24.39 Aligned_cols=12 Identities=42% Similarity=0.830 Sum_probs=10.9
Q ss_pred CCCCCcEEEEEc
Q psy13877 45 GSSPAQVVKLTN 56 (114)
Q Consensus 45 ~~kPGD~V~lTG 56 (114)
+++|||+|.|+=
T Consensus 54 gak~GdvVkIvR 65 (80)
T COG2012 54 GAKPGDVVKIVR 65 (80)
T ss_pred cCCCCcEEEEEe
Confidence 599999999987
No 21
>PF12249 AftA_C: Arabinofuranosyltransferase A C terminal; InterPro: IPR020959 The arabinofuranosyltransferase enzyme AftA is involved in cell wall arabinan biosynthesis in bacteria []. It catalyses the addition of the first key arabinofuranosyl residue from the sugar donor beta-D-arabinofuranosyl-1-monophosphoryldecaprenol to the galactan domain of the cell wall, thus priming the galactan for further elaboration by the arabinofuranosyltransferases. As this enzyme is important for cell growth and is found in some important pathogens, such as Mycobacterium tuberculosis, it represents a potential target for the devlopment of new antibacterial drugs. This entry represents the C-terminal domain of AftA.; GO: 0016757 transferase activity, transferring glycosyl groups, 0044038 cell wall macromolecule biosynthetic process, 0005886 plasma membrane, 0016021 integral to membrane
Probab=32.49 E-value=52 Score=26.06 Aligned_cols=42 Identities=26% Similarity=0.347 Sum_probs=34.1
Q ss_pred ccCCCCCCCC---------------CCCCCcEEEEEc------CCCCcceeeeeecCCCCCcch
Q psy13877 35 EHTSNQPLQM---------------GSSPAQVVKLTN------PPVQTGQKMIVLTNNSNPPAL 77 (114)
Q Consensus 35 E~peeVP~G~---------------~~kPGD~V~lTG------p~p~tgf~a~~l~n~v~~~~~ 77 (114)
|+.+..|+|. +-.|-|.|.||- -.||-||.++- +.+.||++.
T Consensus 22 ~RaDr~P~~a~~yY~~id~~I~~~tG~~~~~tVvLT~d~~FlsyyPY~gFQalT-sHYANPLae 84 (178)
T PF12249_consen 22 ERADRRPPDAERYYPEIDAAIREQTGRPPDDTVVLTDDYSFLSYYPYWGFQALT-SHYANPLAE 84 (178)
T ss_pred cccccCCCchHHhHHHHHHHHHHhcCCCCCCeEEEeccccceEecccccccccc-hhhcCchhh
Confidence 5677788887 347889999998 67999999987 677888874
No 22
>PF08021 FAD_binding_9: Siderophore-interacting FAD-binding domain; InterPro: IPR013113 Proteins in this entry are siderophore-interacting FAD-binding proteins. This entry includes the vibriobactin utilization protein ViuB, which is involved in the removal of iron from iron-vibriobactin complexes, as well as several hypothetical proteins.; PDB: 2GPJ_A.
Probab=31.47 E-value=25 Score=24.81 Aligned_cols=14 Identities=29% Similarity=0.525 Sum_probs=9.3
Q ss_pred CCCCCcEEEEEcCC
Q psy13877 45 GSSPAQVVKLTNPP 58 (114)
Q Consensus 45 ~~kPGD~V~lTGp~ 58 (114)
.++|||.|.|+||.
T Consensus 101 ~A~pGd~v~v~gP~ 114 (117)
T PF08021_consen 101 SARPGDRVGVTGPR 114 (117)
T ss_dssp H--TT-EEEEEEEE
T ss_pred hCCCCCEEEEeCCC
Confidence 58999999999953
No 23
>PF02769 AIRS_C: AIR synthase related protein, C-terminal domain; InterPro: IPR010918 This entry includes Hydrogen expression/formation protein, HypE, which may be involved in the maturation of NifE hydrogenase; AIR synthase and FGAM synthase, which are involved in de novo purine biosynthesis; and selenide, water dikinase, an enzyme which synthesizes selenophosphate from selenide and ATP.; PDB: 2Z1F_A 2Z1E_A 2YXZ_D 2V9Y_A 2HS0_A 2HRU_A 2HS3_A 3D54_A 1VK3_A 2HS4_A ....
Probab=30.89 E-value=32 Score=23.85 Aligned_cols=11 Identities=18% Similarity=0.516 Sum_probs=10.2
Q ss_pred CCCcEEEEEcC
Q psy13877 47 SPAQVVKLTNP 57 (114)
Q Consensus 47 kPGD~V~lTGp 57 (114)
+|||.|.++|+
T Consensus 1 k~GD~i~~~g~ 11 (153)
T PF02769_consen 1 KPGDLIIVTGS 11 (153)
T ss_dssp STTEEEEEECS
T ss_pred CCCCEEEEECC
Confidence 69999999996
No 24
>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl
Probab=30.53 E-value=1.5e+02 Score=18.83 Aligned_cols=28 Identities=4% Similarity=0.049 Sum_probs=18.5
Q ss_pred ceEeeeeccCCCCCCCCCCCCCcEEEEEc
Q psy13877 28 FQELKVQEHTSNQPLQMGSSPAQVVKLTN 56 (114)
Q Consensus 28 fQeVrIQE~peeVP~G~~~kPGD~V~lTG 56 (114)
-++|.+-...+.+|. +.+.+||.|.++|
T Consensus 44 v~~l~~~~g~~~~~v-~~~~aGdI~~i~g 71 (83)
T cd04088 44 VGRLLRMHGKKQEEV-EEAGAGDIGAVAG 71 (83)
T ss_pred eeEEEEEcCCCceEC-CEeCCCCEEEEEC
Confidence 444554545545554 3588999999999
No 25
>KOG3416|consensus
Probab=30.14 E-value=32 Score=26.13 Aligned_cols=13 Identities=23% Similarity=0.460 Sum_probs=11.5
Q ss_pred CCCCCCcEEEEEc
Q psy13877 44 MGSSPAQVVKLTN 56 (114)
Q Consensus 44 ~~~kPGD~V~lTG 56 (114)
...+|||.|.|||
T Consensus 60 ~~~~PGDIirLt~ 72 (134)
T KOG3416|consen 60 CLIQPGDIIRLTG 72 (134)
T ss_pred cccCCccEEEecc
Confidence 3579999999999
No 26
>COG0611 ThiL Thiamine monophosphate kinase [Coenzyme metabolism]
Probab=29.20 E-value=41 Score=28.39 Aligned_cols=23 Identities=22% Similarity=0.534 Sum_probs=16.9
Q ss_pred CCCCCcEEEEEc--CCCCcceeeee
Q psy13877 45 GSSPAQVVKLTN--PPVQTGQKMIV 67 (114)
Q Consensus 45 ~~kPGD~V~lTG--p~p~tgf~a~~ 67 (114)
.++|||.|.+|| -.+..|+..+.
T Consensus 147 gAkpGD~v~vtG~lG~saagl~ll~ 171 (317)
T COG0611 147 GAKPGDLVAVTGTLGRSAAGLELLL 171 (317)
T ss_pred CCCCCCEEEEcCCCchhHHHHHHHh
Confidence 699999999999 44555554443
No 27
>cd06188 NADH_quinone_reductase Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase, and has NADH and FAD binding sites. (Na+-NQR) is distinct from H+-translocating NADH:quinone oxidoreductases and noncoupled NADH:quinone oxidoreductases. The NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain of this group typically contains an iron-sulfur cluster binding domain.
Probab=28.58 E-value=1.2e+02 Score=23.78 Aligned_cols=19 Identities=21% Similarity=0.433 Sum_probs=15.2
Q ss_pred CCCCCC------CCCCCcEEEEEcC
Q psy13877 39 NQPLQM------GSSPAQVVKLTNP 57 (114)
Q Consensus 39 eVP~G~------~~kPGD~V~lTGp 57 (114)
.+|.|. .+++||.|.|+||
T Consensus 116 ~~~~G~~S~~L~~l~~Gd~v~i~gP 140 (283)
T cd06188 116 DIPPGIGSSYIFNLKPGDKVTASGP 140 (283)
T ss_pred CCCCceehhHHhcCCCCCEEEEECc
Confidence 366666 5899999999994
No 28
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=28.40 E-value=66 Score=21.02 Aligned_cols=18 Identities=17% Similarity=0.296 Sum_probs=13.2
Q ss_pred CCCCCcEEEEEc-CCCCcc
Q psy13877 45 GSSPAQVVKLTN-PPVQTG 62 (114)
Q Consensus 45 ~~kPGD~V~lTG-p~p~tg 62 (114)
.+++||+|.++| +....|
T Consensus 43 ~l~~Gd~V~v~G~v~~~~G 61 (73)
T cd04487 43 EVEVGDIVRVTGEVEPRDG 61 (73)
T ss_pred CCCCCCEEEEEEEEecCCe
Confidence 378999999999 433444
No 29
>PF07425 Pardaxin: Pardaxin; InterPro: IPR009990 This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin []. Pardaxin has also been found to have a shark repellent action [].; GO: 0005576 extracellular region; PDB: 1XC0_A 2KNS_A.
Probab=27.66 E-value=25 Score=20.61 Aligned_cols=12 Identities=42% Similarity=0.745 Sum_probs=9.2
Q ss_pred chhhhhhhCCCC
Q psy13877 93 IASKLMKKGGQD 104 (114)
Q Consensus 93 ~~~~~~~~~~~~ 104 (114)
.|++|-++|||.
T Consensus 22 vgsalsssggqe 33 (33)
T PF07425_consen 22 VGSALSSSGGQE 33 (33)
T ss_dssp HHHHCTTTCCG-
T ss_pred HHHHHhcccCCC
Confidence 478888999984
No 30
>KOG1749|consensus
Probab=27.38 E-value=61 Score=24.66 Aligned_cols=32 Identities=13% Similarity=-0.011 Sum_probs=24.9
Q ss_pred CCCCcEEEEEc---------CCCCcceeeeeecCCCCCcchh
Q psy13877 46 SSPAQVVKLTN---------PPVQTGQKMIVLTNNSNPPALE 78 (114)
Q Consensus 46 ~kPGD~V~lTG---------p~p~tgf~a~~l~n~v~~~~~~ 78 (114)
+.--|+|.+.| -.|-..|+.++++| |+++++-
T Consensus 94 ieendevlv~gfgrkg~avgdipgvrfkvvkv~~-vsl~alf 134 (143)
T KOG1749|consen 94 IEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVSG-VSLLALF 134 (143)
T ss_pred eccCCeeeeeccCccCccccCCCceEEEEEEEcC-cChhhhh
Confidence 45678888887 46777799999999 8887653
No 31
>PF07287 DUF1446: Protein of unknown function (DUF1446); InterPro: IPR010839 This family consists of several bacterial and plant proteins of around 400 residues in length. The function of this family is unknown.
Probab=27.22 E-value=80 Score=27.05 Aligned_cols=27 Identities=15% Similarity=0.412 Sum_probs=18.9
Q ss_pred eeeeceEeeeeccCCCCCCCCCCCCCcEEEEEc----CCCCc
Q psy13877 24 KFVKFQELKVQEHTSNQPLQMGSSPAQVVKLTN----PPVQT 61 (114)
Q Consensus 24 kF~dfQeVrIQE~peeVP~G~~~kPGD~V~lTG----p~p~t 61 (114)
.-.||-.++++|..+ |+|.|+| |.|++
T Consensus 277 vv~D~~~v~~~q~~~-----------~rVrVsG~~g~p~p~t 307 (362)
T PF07287_consen 277 VVLDLSNVRFEQVGE-----------DRVRVSGARGRPPPPT 307 (362)
T ss_pred EEEEeeeeEEEEeCC-----------CeEEEECCccCCCCCc
Confidence 556677777776543 7899999 66664
No 32
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=27.07 E-value=20 Score=24.98 Aligned_cols=11 Identities=18% Similarity=0.344 Sum_probs=5.3
Q ss_pred CCCCCcEEEEE
Q psy13877 45 GSSPAQVVKLT 55 (114)
Q Consensus 45 ~~kPGD~V~lT 55 (114)
++++||+|.+.
T Consensus 97 ~i~~Gd~v~~~ 107 (108)
T PF02643_consen 97 GIKVGDRVRIE 107 (108)
T ss_dssp T--TT-EEE--
T ss_pred CCCCCCEEEec
Confidence 68999999863
No 33
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=26.82 E-value=56 Score=22.13 Aligned_cols=18 Identities=33% Similarity=0.637 Sum_probs=12.1
Q ss_pred CCCCCcEEEEEcCCCCcc
Q psy13877 45 GSSPAQVVKLTNPPVQTG 62 (114)
Q Consensus 45 ~~kPGD~V~lTGp~p~tg 62 (114)
+++|||+|.|+-..+-+|
T Consensus 48 g~k~GdVvkI~R~S~taG 65 (74)
T PF01191_consen 48 GAKPGDVVKIIRKSETAG 65 (74)
T ss_dssp T--TTSEEEEEEEETTTS
T ss_pred CCCCCCEEEEEecCCCCC
Confidence 699999999998444444
No 34
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=26.82 E-value=36 Score=20.73 Aligned_cols=17 Identities=6% Similarity=-0.013 Sum_probs=11.6
Q ss_pred CCCCC-CCCCCcEEEEEc
Q psy13877 40 QPLQM-GSSPAQVVKLTN 56 (114)
Q Consensus 40 VP~G~-~~kPGD~V~lTG 56 (114)
+|.++ .+++||.+.+.|
T Consensus 41 ~p~~~~~l~~gD~l~v~g 58 (71)
T PF02080_consen 41 IPDGDTVLQAGDILIVVG 58 (71)
T ss_dssp S--TT-BE-TTEEEEEEE
T ss_pred CCCCCCEECCCCEEEEEE
Confidence 45555 689999999988
No 35
>PRK08051 fre FMN reductase; Validated
Probab=26.45 E-value=80 Score=23.89 Aligned_cols=30 Identities=3% Similarity=0.140 Sum_probs=19.2
Q ss_pred CCCCCcEEEEEcC------CCCcceeeeeecCCCCC
Q psy13877 45 GSSPAQVVKLTNP------PVQTGQKMIVLTNNSNP 74 (114)
Q Consensus 45 ~~kPGD~V~lTGp------~p~tgf~a~~l~n~v~~ 74 (114)
.++|||+|.|.|| .+..+-+.+.+++++=.
T Consensus 79 ~l~~G~~v~v~gP~G~~~~~~~~~~~~vliagG~Gi 114 (232)
T PRK08051 79 RILKDGEIEVDIPHGDAWLREESERPLLLIAGGTGF 114 (232)
T ss_pred HcCCCCEEEEEcCCCceEccCCCCCcEEEEecCcCc
Confidence 5799999999993 12223345666665543
No 36
>KOG2241|consensus
Probab=25.79 E-value=56 Score=27.11 Aligned_cols=14 Identities=29% Similarity=0.489 Sum_probs=12.1
Q ss_pred CCCCCCCCCcEEEEEc
Q psy13877 41 PLQMGSSPAQVVKLTN 56 (114)
Q Consensus 41 P~G~~~kPGD~V~lTG 56 (114)
|.| +.|||+|+|.|
T Consensus 186 P~g--s~pGdRv~feg 199 (255)
T KOG2241|consen 186 PAG--SKPGDRVTFEG 199 (255)
T ss_pred CCC--CCCCCeeeecC
Confidence 455 88999999999
No 37
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=24.97 E-value=55 Score=21.36 Aligned_cols=12 Identities=17% Similarity=0.515 Sum_probs=10.2
Q ss_pred CCCCCcEEEEEc
Q psy13877 45 GSSPAQVVKLTN 56 (114)
Q Consensus 45 ~~kPGD~V~lTG 56 (114)
++++||.|.|-+
T Consensus 53 G~~~GD~V~Ig~ 64 (69)
T TIGR03595 53 GAKDGDTVRIGD 64 (69)
T ss_pred CCCCCCEEEEcc
Confidence 599999998864
No 38
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=24.79 E-value=1.2e+02 Score=20.39 Aligned_cols=11 Identities=9% Similarity=0.392 Sum_probs=10.4
Q ss_pred CCCCcEEEEEc
Q psy13877 46 SSPAQVVKLTN 56 (114)
Q Consensus 46 ~kPGD~V~lTG 56 (114)
..|||++.++|
T Consensus 129 l~~Gd~i~~~g 139 (176)
T PF13567_consen 129 LQPGDRIRVRG 139 (176)
T ss_pred cCCCCEEEEEE
Confidence 68999999999
No 39
>COG2375 ViuB Siderophore-interacting protein [Inorganic ion transport and metabolism]
Probab=24.61 E-value=91 Score=25.84 Aligned_cols=34 Identities=12% Similarity=0.346 Sum_probs=21.5
Q ss_pred CCCCCcEEEEEcC----CCCcce-eeeeecCCCCCcchh
Q psy13877 45 GSSPAQVVKLTNP----PVQTGQ-KMIVLTNNSNPPALE 78 (114)
Q Consensus 45 ~~kPGD~V~lTGp----~p~tgf-~a~~l~n~v~~~~~~ 78 (114)
.++|||.+.|.|| .|...+ ..+.+.-...+|+..
T Consensus 121 ~a~~GD~l~i~GP~g~~~p~~~~~~~lLigDetAlPAIa 159 (265)
T COG2375 121 TAQPGDTLTIMGPRGSLVPPEAADWYLLIGDETALPAIA 159 (265)
T ss_pred hCCCCCEEEEeCCCCCCCCCCCcceEEEeccccchHHHH
Confidence 6999999999993 333443 344445555555543
No 40
>cd06193 siderophore_interacting Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from transferrin and lactoferrin for bacterial uptake, contributing to pathogen virulence. Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hy
Probab=24.51 E-value=91 Score=23.67 Aligned_cols=35 Identities=11% Similarity=0.325 Sum_probs=23.2
Q ss_pred CCCCCcEEEEEcCC-----CCcceeeeeecCCCCCcchhh
Q psy13877 45 GSSPAQVVKLTNPP-----VQTGQKMIVLTNNSNPPALEE 79 (114)
Q Consensus 45 ~~kPGD~V~lTGp~-----p~tgf~a~~l~n~v~~~~~~~ 79 (114)
.++|||.|.+.||. +...-+.+.+++.+-++.++.
T Consensus 98 ~l~~Gd~v~v~gP~G~~~~~~~~~~~vlia~GtGi~p~~~ 137 (235)
T cd06193 98 SAQPGDTLGIAGPGGSFLPPPDADWYLLAGDETALPAIAA 137 (235)
T ss_pred hCCCCCEEEEECCCCCCCCCCCcceEEEEeccchHHHHHH
Confidence 68999999999931 111224577777777666444
No 41
>COG3450 Predicted enzyme of the cupin superfamily [General function prediction only]
Probab=24.45 E-value=1.4e+02 Score=21.83 Aligned_cols=40 Identities=10% Similarity=0.159 Sum_probs=29.6
Q ss_pred CccceEEEecCceeeeceEeeeeccCCCCCCCC--CCCCCcEEEE
Q psy13877 12 SGGRLYLQTRGSKFVKFQELKVQEHTSNQPLQM--GSSPAQVVKL 54 (114)
Q Consensus 12 s~G~l~L~~r~SkF~dfQeVrIQE~peeVP~G~--~~kPGD~V~l 54 (114)
+.|+|+++.....|..+-+=++-=.+|. |+ .++|||.+.|
T Consensus 53 TpG~~r~~y~~~E~chil~G~v~~T~d~---Ge~v~~~aGD~~~~ 94 (116)
T COG3450 53 TPGKFRVTYDEDEFCHILEGRVEVTPDG---GEPVEVRAGDSFVF 94 (116)
T ss_pred cCccceEEcccceEEEEEeeEEEEECCC---CeEEEEcCCCEEEE
Confidence 5789999999999998766554444442 44 5789999887
No 42
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=24.42 E-value=50 Score=21.49 Aligned_cols=14 Identities=29% Similarity=0.335 Sum_probs=8.9
Q ss_pred CCCCcEEEEEcCCC
Q psy13877 46 SSPAQVVKLTNPPV 59 (114)
Q Consensus 46 ~kPGD~V~lTGp~p 59 (114)
.++||+|+||-|.-
T Consensus 6 f~~GdrVQlTD~Kg 19 (54)
T PF14801_consen 6 FRAGDRVQLTDPKG 19 (54)
T ss_dssp --TT-EEEEEETT-
T ss_pred CCCCCEEEEccCCC
Confidence 57999999998553
No 43
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=23.73 E-value=62 Score=22.31 Aligned_cols=15 Identities=27% Similarity=0.614 Sum_probs=12.2
Q ss_pred CCCCCcEEEEEcCCC
Q psy13877 45 GSSPAQVVKLTNPPV 59 (114)
Q Consensus 45 ~~kPGD~V~lTGp~p 59 (114)
+++|||+|.|+=..+
T Consensus 51 g~k~GdVvkI~R~S~ 65 (79)
T PRK09570 51 GAKPGDVIKIVRKSP 65 (79)
T ss_pred CCCCCCEEEEEECCC
Confidence 599999999987433
No 44
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=23.33 E-value=54 Score=21.06 Aligned_cols=12 Identities=8% Similarity=0.003 Sum_probs=11.2
Q ss_pred CCCCCcEEEEEc
Q psy13877 45 GSSPAQVVKLTN 56 (114)
Q Consensus 45 ~~kPGD~V~lTG 56 (114)
.+++||.|.|+|
T Consensus 61 ~~~kG~~V~v~G 72 (100)
T cd04496 61 YLKKGDLVYVEG 72 (100)
T ss_pred HhCCCCEEEEEE
Confidence 489999999999
No 45
>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n
Probab=22.47 E-value=2.2e+02 Score=18.15 Aligned_cols=27 Identities=15% Similarity=0.043 Sum_probs=17.8
Q ss_pred eEeeeeccCCCCCCCCCCCCCcEEEEEc
Q psy13877 29 QELKVQEHTSNQPLQMGSSPAQVVKLTN 56 (114)
Q Consensus 29 QeVrIQE~peeVP~G~~~kPGD~V~lTG 56 (114)
++|.+-...+.+|. +.+.+||.|.+.|
T Consensus 45 ~~l~~~~g~~~~~v-~~~~aGdI~~i~g 71 (83)
T cd04092 45 SRLLQPFADQYQEI-PSLSAGNIGVITG 71 (83)
T ss_pred eEEEEEECCCceEC-CeeCCCCEEEEEC
Confidence 34444444555554 3588999999998
No 46
>PRK14105 selenophosphate synthetase; Provisional
Probab=22.15 E-value=63 Score=26.45 Aligned_cols=22 Identities=23% Similarity=0.283 Sum_probs=15.9
Q ss_pred CCCCCCCCCCCcEEEEEcCCCC
Q psy13877 39 NQPLQMGSSPAQVVKLTNPPVQ 60 (114)
Q Consensus 39 eVP~G~~~kPGD~V~lTGp~p~ 60 (114)
++.....++|||.|.+||+.=.
T Consensus 158 ~~i~r~ga~~GD~I~vTg~lG~ 179 (345)
T PRK14105 158 DILTKAGAKEGDVLILTKPLGT 179 (345)
T ss_pred ceeeCCCCCCCCEEEEeCCChH
Confidence 3333446999999999995544
No 47
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=22.03 E-value=69 Score=24.57 Aligned_cols=44 Identities=11% Similarity=0.031 Sum_probs=29.5
Q ss_pred CCCCCcEEEEEc---CCCCc---c---eeeeeecCCCCCcchhhhhhhcCCccc
Q psy13877 45 GSSPAQVVKLTN---PPVQT---G---QKMIVLTNNSNPPALEEKKFDRGIYNN 89 (114)
Q Consensus 45 ~~kPGD~V~lTG---p~p~t---g---f~a~~l~n~v~~~~~~~~~~~~g~~~~ 89 (114)
.++.||.|.|+| ...|+ | +..-+++..|..+..+.+. ..+||++
T Consensus 69 ~LkKGs~V~VeGrL~~r~w~DkdG~~r~~~eI~a~~i~~L~~r~~~-~~~~~~~ 121 (168)
T PRK06863 69 YLRKGSQVYVEGRLKTRKWQDQNGQDRYTTEIQGDVLQMLGGRNQR-NAGGYGN 121 (168)
T ss_pred HCCCCCEEEEEEEEEeCCccCCCCCEEEEEEEEEeEEEECCCCCcc-ccccccc
Confidence 489999999999 33332 3 5666777778777666543 4456644
No 48
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.81 E-value=72 Score=23.82 Aligned_cols=35 Identities=14% Similarity=0.088 Sum_probs=23.2
Q ss_pred CCCCCcEEEEEc---CCCC---cc---eeeeeecCCCCCcchhh
Q psy13877 45 GSSPAQVVKLTN---PPVQ---TG---QKMIVLTNNSNPPALEE 79 (114)
Q Consensus 45 ~~kPGD~V~lTG---p~p~---tg---f~a~~l~n~v~~~~~~~ 79 (114)
.++.||.|.|+| ...| .| +..-+++.+|..+....
T Consensus 68 ~l~KG~~V~V~G~L~~~~~~~kdG~~~~~~ev~a~~i~~L~~~~ 111 (164)
T TIGR00621 68 YLKKGSLVYVEGRLRTRKWEDQNGQKRSKTEIIADNVQLLDLLG 111 (164)
T ss_pred hCCCCCEEEEEEEEEeceEECCCCcEEEEEEEEEEEEeeccccC
Confidence 479999999999 3333 33 45566667675555443
No 49
>cd06190 T4MO_e_transfer_like Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P. mendocina) to ferredoxin to an iron-containing oxygenase. TmoF is homologous to other mono- and dioxygenase systems within the ferredoxin reductase family.
Probab=20.98 E-value=1.2e+02 Score=22.58 Aligned_cols=28 Identities=14% Similarity=0.392 Sum_probs=18.2
Q ss_pred CCCCcEEEEEcC------CCCcceeeeeecCCCC
Q psy13877 46 SSPAQVVKLTNP------PVQTGQKMIVLTNNSN 73 (114)
Q Consensus 46 ~kPGD~V~lTGp------~p~tgf~a~~l~n~v~ 73 (114)
++|||.|.|.|| .+...-+.+.+++++-
T Consensus 75 ~~~g~~v~v~gP~G~~~~~~~~~~~illIagG~G 108 (232)
T cd06190 75 LEPGDELELDGPYGLAYLRPDEDRDIVCIAGGSG 108 (232)
T ss_pred CCCCCEEEEECCcccceecCCCCCcEEEEeeCcC
Confidence 689999999993 1222335566676553
No 50
>cd06189 flavin_oxioreductase NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN, or riboflavin via NAD(P)H. Flavin is used as a substrate, rather than a tightly bound prosthetic group as in flavoenzymes; weaker binding is due to the absence of a binding site for the AMP moeity of FAD.
Probab=20.85 E-value=1.1e+02 Score=22.67 Aligned_cols=13 Identities=15% Similarity=0.360 Sum_probs=11.3
Q ss_pred CCCCCcEEEEEcC
Q psy13877 45 GSSPAQVVKLTNP 57 (114)
Q Consensus 45 ~~kPGD~V~lTGp 57 (114)
.++|||.|.|.||
T Consensus 75 ~l~~G~~v~i~gP 87 (224)
T cd06189 75 ELKENGLVRIEGP 87 (224)
T ss_pred hccCCCEEEEecC
Confidence 3799999999993
No 51
>PF02874 ATP-synt_ab_N: ATP synthase alpha/beta family, beta-barrel domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR004100 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the N-terminal domain, which forms a closed beta-barrel with Greek-key topology. ; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015992 proton transport, 0046034 ATP metabolic process, 0016469 proton-transporting two-sector ATPase complex; PDB: 1W0K_A 1H8H_B 2WSS_A 1EFR_A 2JIZ_H 1E1Q_A 2V7Q_B 1E79_B 1E1R_C 2XND_C ....
Probab=20.69 E-value=69 Score=19.76 Aligned_cols=12 Identities=33% Similarity=0.429 Sum_probs=10.8
Q ss_pred CCCCCcEEEEEc
Q psy13877 45 GSSPAQVVKLTN 56 (114)
Q Consensus 45 ~~kPGD~V~lTG 56 (114)
++++|++|..||
T Consensus 58 Gl~~G~~V~~tG 69 (69)
T PF02874_consen 58 GLSRGTEVRFTG 69 (69)
T ss_dssp TSBTTCEEEEEE
T ss_pred CCCCCCEEEcCc
Confidence 689999999997
No 52
>cd02691 PurM-like2 AIR synthase (PurM) related protein, archaeal subgroup 2 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two conserved domains and seem to dimerize. The N-terminal domain forms the dimer interface and is a putative ATP binding domain.
Probab=20.61 E-value=71 Score=26.65 Aligned_cols=16 Identities=13% Similarity=0.287 Sum_probs=13.1
Q ss_pred CCCCCCcEEEEEcCCC
Q psy13877 44 MGSSPAQVVKLTNPPV 59 (114)
Q Consensus 44 ~~~kPGD~V~lTGp~p 59 (114)
+.++|||.|.+||+..
T Consensus 158 ~gA~pGD~I~vtg~~G 173 (346)
T cd02691 158 KNAEPGDLILMTEGAG 173 (346)
T ss_pred cCCCCCCEEEEECCcc
Confidence 4699999999999443
No 53
>TIGR03625 L3_bact 50S ribosomal protein L3, bacterial. This model describes bacterial (and mitochondrial and chloroplast) class of ribosomal protein L3. A separate model describes the archaeal form, where both belong to Pfam family pfam00297. The name is phrased to meet the needs of bacterial genome annotation. Organellar forms typically will have transit peptides, N-terminal to the region modeled here.
Probab=20.45 E-value=1.2e+02 Score=24.21 Aligned_cols=38 Identities=16% Similarity=0.121 Sum_probs=27.2
Q ss_pred eeeceEeeeeccCCCCCCCC-----CCCCCcEEEEEcCCCCcce
Q psy13877 25 FVKFQELKVQEHTSNQPLQM-----GSSPAQVVKLTNPPVQTGQ 63 (114)
Q Consensus 25 F~dfQeVrIQE~peeVP~G~-----~~kPGD~V~lTGp~p~tgf 63 (114)
+....|+++.+. +.+|.|+ -..||+.|+++|..---||
T Consensus 74 kr~l~Efrv~~~-~~~~~G~~l~v~~F~~G~~VDV~g~skGKGF 116 (202)
T TIGR03625 74 KRHLREFRVDDL-EGYEVGDEITVDIFEAGQKVDVTGTSKGKGF 116 (202)
T ss_pred CcEEEEEEcCCc-ccCCCCCEEEeeeecCCCEEEEEEEEcCCcc
Confidence 344578888664 5699999 4799999999993333344
No 54
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=20.31 E-value=70 Score=21.76 Aligned_cols=12 Identities=8% Similarity=-0.072 Sum_probs=9.9
Q ss_pred CCCCCcEEEEEc
Q psy13877 45 GSSPAQVVKLTN 56 (114)
Q Consensus 45 ~~kPGD~V~lTG 56 (114)
.++|||+|..+|
T Consensus 37 ~L~~Gd~VvT~g 48 (84)
T TIGR00739 37 SLKKGDKVLTIG 48 (84)
T ss_pred hCCCCCEEEECC
Confidence 378999998877
Done!