Query 046374
Match_columns 420
No_of_seqs 132 out of 701
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 11:28:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046374.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046374hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03140 DUF247: Plant protein 100.0 1E-105 3E-110 818.5 32.0 373 16-407 1-391 (391)
2 PRK10404 hypothetical protein; 80.2 3.8 8.2E-05 34.0 5.0 19 390-409 79-97 (101)
3 KOG3110 Riboflavin kinase [Coe 68.9 3.5 7.6E-05 35.8 2.1 58 33-90 65-137 (153)
4 PHA02103 hypothetical protein 65.2 20 0.00044 29.9 5.7 69 262-333 23-101 (135)
5 PRK10132 hypothetical protein; 57.5 11 0.00023 31.8 2.9 26 383-409 77-103 (108)
6 PF12911 OppC_N: N-terminal TM 55.2 18 0.0004 26.0 3.6 34 383-416 8-41 (56)
7 PF07438 DUF1514: Protein of u 54.3 14 0.00031 27.9 2.8 21 392-412 2-22 (66)
8 PF14579 HHH_6: Helix-hairpin- 45.3 1.6E+02 0.0034 23.5 8.2 84 249-340 1-86 (90)
9 COG4575 ElaB Uncharacterized c 42.6 18 0.0004 30.1 2.0 22 386-408 77-99 (104)
10 PF15103 G0-G1_switch_2: G0/G1 39.9 35 0.00076 28.2 3.3 26 394-419 28-53 (102)
11 PF05957 DUF883: Bacterial pro 34.6 41 0.00089 27.1 2.9 19 389-408 71-89 (94)
12 PF00690 Cation_ATPase_N: Cati 31.9 32 0.00068 25.9 1.8 58 339-402 5-68 (69)
13 PF09820 AAA-ATPase_like: Pred 30.5 52 0.0011 32.2 3.5 61 335-398 221-282 (284)
14 PF04971 Lysis_S: Lysis protei 30.0 89 0.0019 24.0 3.8 37 378-414 19-56 (68)
15 PF05421 DUF751: Protein of un 28.2 93 0.002 23.4 3.6 30 387-416 30-59 (61)
16 PF14770 TMEM18: Transmembrane 28.1 66 0.0014 27.7 3.2 46 365-413 55-100 (123)
17 PF08181 DegQ: DegQ (SacQ) fam 22.6 1.1E+02 0.0023 21.1 2.7 30 53-82 1-30 (46)
18 cd00925 Cyt_c_Oxidase_VIa Cyto 22.6 85 0.0018 25.3 2.7 26 389-414 13-38 (86)
19 PF10961 DUF2763: Protein of u 22.2 1.3E+02 0.0029 24.4 3.8 27 389-415 13-42 (91)
20 PHA02947 S-S bond formation pa 22.2 86 0.0019 29.5 3.0 19 388-406 175-194 (215)
21 PF09069 EF-hand_3: EF-hand; 20.7 1.4E+02 0.0031 24.2 3.7 55 56-111 3-76 (90)
22 PF04531 Phage_holin_1: Bacter 20.6 1.2E+02 0.0026 24.1 3.2 24 386-409 6-29 (84)
No 1
>PF03140 DUF247: Plant protein of unknown function; InterPro: IPR004158 The function of the plant proteins constituting this family is unknown.
Probab=100.00 E-value=1.2e-105 Score=818.54 Aligned_cols=373 Identities=38% Similarity=0.668 Sum_probs=316.8
Q ss_pred eeccCchhhhcccCCCCCCceeEeeCccCCCCchhccccHHHHHHHHHHHHhcC---CCHHHHHHHHHHhhhHHhhhccC
Q 046374 16 LEKVPRIFREKKAKKNCFDPFVVSIGPYHHGKPELQFMEKHKLTMAQQYVSNNL---HMLEELYKKVLDVAKPARECYSD 92 (420)
Q Consensus 16 I~rVP~~lr~~~~n~~aY~P~~VSIGPyHhg~~~L~~mE~~K~~~l~~~l~r~~---~~l~~~~~~i~~~e~~~R~~Y~~ 92 (420)
|||||+++|+ .|++||+|++|||||||||+++|+.||++|++|++.|++|++ .++++++++|+++|++||+|| +
T Consensus 1 I~rVP~~lr~--~~~~~Y~P~~VsIGPyH~g~~~L~~mE~~K~~~l~~~l~~~~~~~~~l~~~~~~i~~~e~~~R~~Y-~ 77 (391)
T PF03140_consen 1 IYRVPESLRD--VNPKAYTPQVVSIGPYHHGKPDLQEMEEHKLRYLHRFLKRSGAPAESLEDYVEAIRSLEEEARACY-A 77 (391)
T ss_pred CcCCCHHHcc--CCchhcCCceEEeCCCCCCchhhhhhHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHHHHHHh-c
Confidence 8999999997 599999999999999999999999999999999999999998 899999999999999999999 6
Q ss_pred CCccCCCCHHHHHHHHHHHHHHHHHHHHHhhh--ccccc-ccccchhHHHHHHHHhhhcCCCcHHHHHHHHhcccc-chh
Q 046374 93 EDSIKKFDDKQFIRMMVLDGCFVLQFIYCFAQ--DKRDL-LKMKSNIAACVQRDLLLLENQLPFPVLKELMSFRFS-EDQ 168 (420)
Q Consensus 93 ~~~~~~~~~~~f~~MmllDgCFiLe~l~~~~~--~~~~~-~~~~~~~~~~i~~DllLLENQIPffVL~~L~~~~~~-~~~ 168 (420)
++.. ++++++|++||++|||||||+|++... +..+. .....|....|.+||+|||||||||||++||++... ...
T Consensus 78 ~~~~-~~~~~~f~~MmllDgCFlLe~~~~~~~~~~~~d~~~~~~~~~~~~i~~Dl~LLENQIPffVL~~L~~l~~~~~~~ 156 (391)
T PF03140_consen 78 EDID-DMSSDEFVEMMLLDGCFLLEFFLRYSRSDGENDPGIFSRPWLLSAIRRDLLLLENQIPFFVLEKLFELLFGSKSD 156 (391)
T ss_pred cccc-ccCHHHHHHHHHHHHHHHHHHHHhhhhccccccccccccccccccchhheeeecccchHHHHHHHHHHhcccccC
Confidence 6543 699999999999999999999998766 22233 334457777799999999999999999999999872 111
Q ss_pred HhHHHHHHHHhhcCchhhhhhhhhhhhhhhccccCCCCCCCCChhHHHHHHhccCCCCC--CCCCC------CCCCCccc
Q 046374 169 WKKMLSNFVAQIRGPVKINKSFSRKAQAQADHQLIHFEDEPAHLLEVVRTQLIEKSAYT--IPPPS------CSDWSSYR 240 (420)
Q Consensus 169 ~~~~~~~f~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~HlLdL~~~~~~~~~~~~--~~~~~------~~~~~~~~ 240 (420)
+...+..++ .+||....+...+ .......+++|||||+|.+++|++... .+... ...+..||
T Consensus 157 ~~~~l~~l~---------~~~~~~~~~~~~~-~~~~~~~~~~HlL~L~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~ 226 (391)
T PF03140_consen 157 VDESLIDLV---------LKFFYKHWPSWPP-DEPISNPEPHHLLDLLRMSLLPSPPSSSPTPPRPPRSNGEKPPPKRIR 226 (391)
T ss_pred ccchHHHHH---------HhHhccccccccc-cccccCCCCCChHHHHHHHhccccCCcccCCCCcccccccccccccCC
Confidence 122222222 3455222211111 123455679999999999999932211 11111 13567999
Q ss_pred CHHHHHHcCCeEeeCCCC-CceeeEEeccccceEEEcCceeecCchhHHHhhHHHHHhcCCCCCCcceeeHHHHHHhhcC
Q 046374 241 STKELKAVGIHFRPSKTR-KFTDVTFISMFFEAFLKLPPITIDDSTESMLLNMVAYEACPEGPDDFGVSSYVCFMDSLID 319 (420)
Q Consensus 241 sAteL~~aGVkfk~~~~~-~llDi~F~~~~~~g~L~IP~L~id~~Te~llrNLiA~Eq~~~~~~~~~vtsYv~fM~~LI~ 319 (420)
|||||++|||+||++++. +++||+|++ |+|+||+|.||++|+++||||||||||+. ..+.+||||+.||++||+
T Consensus 227 sA~eL~~aGV~fk~~~~~~~~lDv~F~~----G~L~IP~L~id~~T~~~lrNLiA~Eq~~~-~~~~~vtsY~~fm~~Li~ 301 (391)
T PF03140_consen 227 SATELREAGVKFKPSETDRSLLDVKFKK----GVLEIPPLYIDDNTESLLRNLIAFEQCHP-PTGSYVTSYVFFMDSLIN 301 (391)
T ss_pred CHHHHHhCCcEEeeccCccccccceecC----CEEEeCeEEECCcchHHHhHHHHHHHHhc-cCCchHhHHHHHHHHHhC
Confidence 999999999999999876 599999974 89999999999999999999999999964 445699999999999999
Q ss_pred CHHhHHHHHHCCcccCCCCChHHHHHHHHHhhccCCCC--CcchHHHHHHHHhhccchhhhHHHHhhccccCChHHHHHH
Q 046374 320 HAEDVKELRSKGILFNFLGSDQQVADLFNQIADNLVPN--PYAYAVVKHRIEKHYKNKIKIWLAEWFHTHFSSPWTVIAF 397 (420)
Q Consensus 320 t~eDV~lL~~kgIi~~~lgsdeeva~lFn~L~~~~~~~--~~~y~~v~~~l~~~~~~~~~~w~a~l~~~yf~npW~~is~ 397 (420)
|++||++|+++|||+|++||||||++|||+||++++.+ .++|.+++++||+||++||++|+|+++|+||+|||+++|+
T Consensus 302 t~~DV~lL~~kgIi~~~l~~d~eva~~F~~L~~~v~~~~~~~~~~~v~~~l~~~~~~~~~~~~a~l~~~yf~~pw~~is~ 381 (391)
T PF03140_consen 302 TPEDVELLRRKGIIVNWLGSDEEVAKLFNGLCKGVVFDVDDSYYSDVCEDLNKYYQSRWNRWWAWLRRKYFSNPWTFISL 381 (391)
T ss_pred cHhhHHHHHhCCeEecCCCCcHHHHHHHHHHhccCCCCCccHHHHHHHHHHHHHhcChHHHHHHHHhhhhcCCcHHHHHH
Confidence 99999999999999999999999999999999999876 5789999999999999999999999999999999999999
Q ss_pred HHHHHHHHHH
Q 046374 398 FAATFALFLS 407 (420)
Q Consensus 398 ~aA~~ll~lT 407 (420)
+||+++|+||
T Consensus 382 ~aa~~ll~lT 391 (391)
T PF03140_consen 382 VAAIILLLLT 391 (391)
T ss_pred HHHHHHHHhC
Confidence 9999999997
No 2
>PRK10404 hypothetical protein; Provisional
Probab=80.24 E-value=3.8 Score=34.03 Aligned_cols=19 Identities=32% Similarity=0.557 Sum_probs=13.9
Q ss_pred ChHHHHHHHHHHHHHHHHHH
Q 046374 390 SPWTVIAFFAATFALFLSAI 409 (420)
Q Consensus 390 npW~~is~~aA~~ll~lT~~ 409 (420)
|||..+++. |.++|++.++
T Consensus 79 ~Pw~avGia-agvGlllG~L 97 (101)
T PRK10404 79 KPWQGIGVG-AAVGLVLGLL 97 (101)
T ss_pred CcHHHHHHH-HHHHHHHHHH
Confidence 999999865 4467766654
No 3
>KOG3110 consensus Riboflavin kinase [Coenzyme transport and metabolism]
Probab=68.95 E-value=3.5 Score=35.84 Aligned_cols=58 Identities=22% Similarity=0.315 Sum_probs=42.4
Q ss_pred CCceeEeeC--ccCCCCc---hhccccHHHHHHHHHHHHh-------c---CCCHHHHHHHHHHhhhHHhhhc
Q 046374 33 FDPFVVSIG--PYHHGKP---ELQFMEKHKLTMAQQYVSN-------N---LHMLEELYKKVLDVAKPARECY 90 (420)
Q Consensus 33 Y~P~~VSIG--PyHhg~~---~L~~mE~~K~~~l~~~l~r-------~---~~~l~~~~~~i~~~e~~~R~~Y 90 (420)
--|.++||| ||..++. ++..+++.|.-+...-++- . =.++++++++|....+.|++.-
T Consensus 65 v~kMvmSIGwNP~Y~N~~Kt~E~hlih~f~~DFYge~l~~~IvGyiRpe~nf~slesLi~~I~~Di~vA~~~l 137 (153)
T KOG3110|consen 65 VFKMVMSIGWNPYYKNKKKTMELHLIHDFGEDFYGETLKVIIVGYIRPELNFDSLESLIEAIHGDIEVAKKVL 137 (153)
T ss_pred ceeEEEEcccCcccCCcccceeeeeehhcccchhhheeeEEEEEeeccccCcchHHHHHHHHHhhHHHHHHhh
Confidence 458999999 8887763 5666666666665554432 1 2468999999999999999876
No 4
>PHA02103 hypothetical protein
Probab=65.22 E-value=20 Score=29.88 Aligned_cols=69 Identities=19% Similarity=0.361 Sum_probs=46.3
Q ss_pred eeEEeccccceE--EEcCceeecCchhHHHhhHHHHHhcCC-CC----CCc---ceeeHHHHHHhhcCCHHhHHHHHHCC
Q 046374 262 DVTFISMFFEAF--LKLPPITIDDSTESMLLNMVAYEACPE-GP----DDF---GVSSYVCFMDSLIDHAEDVKELRSKG 331 (420)
Q Consensus 262 Di~F~~~~~~g~--L~IP~L~id~~Te~llrNLiA~Eq~~~-~~----~~~---~vtsYv~fM~~LI~t~eDV~lL~~kg 331 (420)
.|.|..+|...+ -+||.+..|....-+-|=.+-+|.|.. ++ +.. ++-+|-.. .-..+|-|++-.+-|
T Consensus 23 ~~~fsdkf~d~t~~~e~pai~~~~~~~ei~rl~~f~~kck~~yp~gkgg~~df~~ipdyyry---f~ee~e~ie~we~yg 99 (135)
T PHA02103 23 KMHFSDKFSDATLEYEIPAIDADRTKAEIVRLITFMDKCKAEYPRGKGGQADFNHIPDYYRY---FGEEAEGVELWEEYG 99 (135)
T ss_pred EEecccccCcceeEEeccccccchhhHHHHHHHHHHHHHHhhCCCCCCCccccccChHHHHH---hcccchhhhHHHHhC
Confidence 456766665555 579999999999999999999999952 22 111 23344332 235667777777777
Q ss_pred cc
Q 046374 332 IL 333 (420)
Q Consensus 332 Ii 333 (420)
|=
T Consensus 100 ve 101 (135)
T PHA02103 100 VE 101 (135)
T ss_pred cc
Confidence 64
No 5
>PRK10132 hypothetical protein; Provisional
Probab=57.55 E-value=11 Score=31.80 Aligned_cols=26 Identities=23% Similarity=0.524 Sum_probs=16.6
Q ss_pred hhcccc-CChHHHHHHHHHHHHHHHHHH
Q 046374 383 WFHTHF-SSPWTVIAFFAATFALFLSAI 409 (420)
Q Consensus 383 l~~~yf-~npW~~is~~aA~~ll~lT~~ 409 (420)
...+|- .|||..+++.| .+++++.++
T Consensus 77 ~~~~~V~~~Pw~svgiaa-gvG~llG~L 103 (108)
T PRK10132 77 CADTFVRERPWCSVGTAA-AVGIFIGAL 103 (108)
T ss_pred HHHHHHHhCcHHHHHHHH-HHHHHHHHH
Confidence 334454 49999998754 466666554
No 6
>PF12911 OppC_N: N-terminal TM domain of oligopeptide transport permease C
Probab=55.21 E-value=18 Score=25.95 Aligned_cols=34 Identities=9% Similarity=0.139 Sum_probs=25.7
Q ss_pred hhccccCChHHHHHHHHHHHHHHHHHHhHHhhcc
Q 046374 383 WFHTHFSSPWTVIAFFAATFALFLSAIQTYWAVK 416 (420)
Q Consensus 383 l~~~yf~npW~~is~~aA~~ll~lT~~QT~~sv~ 416 (420)
.++.+++|+..++|++.-+++++++++--+++=+
T Consensus 8 ~~~~f~~nk~a~~gl~il~~~vl~ai~~p~~~p~ 41 (56)
T PF12911_consen 8 AWRRFRRNKLAVIGLIILLILVLLAIFAPFISPY 41 (56)
T ss_pred HHHHHHhCchHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 3457778999999988888888888777666543
No 7
>PF07438 DUF1514: Protein of unknown function (DUF1514); InterPro: IPR009999 This entry is represented by Bacteriophage phi PVL, Orf60. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several Staphylococcus aureus and related bacteriophage proteins of around 65 residues in length. The function of this family is unknown.
Probab=54.27 E-value=14 Score=27.87 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHhHH
Q 046374 392 WTVIAFFAATFALFLSAIQTY 412 (420)
Q Consensus 392 W~~is~~aA~~ll~lT~~QT~ 412 (420)
|-++|.+.|+++|++-.+|+-
T Consensus 2 WIiiSIvLai~lLI~l~~ns~ 22 (66)
T PF07438_consen 2 WIIISIVLAIALLISLSVNSE 22 (66)
T ss_pred hhhHHHHHHHHHHHHHhhhHH
Confidence 899999999999999888864
No 8
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=45.33 E-value=1.6e+02 Score=23.48 Aligned_cols=84 Identities=19% Similarity=0.192 Sum_probs=56.3
Q ss_pred CCeEeeCC-CCCceeeEEeccccceEEEcCceeecCchhHHHhhHHHHHhcCCCCCCcceeeHHHHHHhh-cCCHHhHHH
Q 046374 249 GIHFRPSK-TRKFTDVTFISMFFEAFLKLPPITIDDSTESMLLNMVAYEACPEGPDDFGVSSYVCFMDSL-IDHAEDVKE 326 (420)
Q Consensus 249 GVkfk~~~-~~~llDi~F~~~~~~g~L~IP~L~id~~Te~llrNLiA~Eq~~~~~~~~~vtsYv~fM~~L-I~t~eDV~l 326 (420)
||++.|.+ ..+-.+-+..+. .+.+.+|=-.|..-.+.....+++-=+ . + .++|+..|...+ --+..+++.
T Consensus 1 Gi~v~ppdIn~S~~~~~~~~~--~~~Ir~gl~~Ikglg~~~a~~I~~~R~-~---g--~f~s~~df~~R~~~i~~~~le~ 72 (90)
T PF14579_consen 1 GIKVLPPDINKSDADFTVEDK--NNAIRLGLSAIKGLGEEVAEKIVEERE-N---G--PFKSLEDFIQRLPKINKRQLEA 72 (90)
T ss_dssp T-EEE---TTT-BSS-EEETT---TEEE-BGGGSTTS-HHHHHHHHHHHH-C---S--S-SSHHHHHHHS-TS-HHHHHH
T ss_pred CCEEeCCeecccCCCeEEECC--CCEEeehHhhcCCCCHHHHHHHHHhHh-c---C--CCCCHHHHHHHHhcCCHHHHHH
Confidence 78887754 233335455541 379999999999999999888886555 2 1 488999999999 888999999
Q ss_pred HHHCCcccCCCCCh
Q 046374 327 LRSKGILFNFLGSD 340 (420)
Q Consensus 327 L~~kgIi~~~lgsd 340 (420)
|.+.|.+...-+++
T Consensus 73 Li~aGafd~~~~~~ 86 (90)
T PF14579_consen 73 LIKAGAFDSFGKSR 86 (90)
T ss_dssp HHHTTTTTTCSSCH
T ss_pred HHHCCCccccChhh
Confidence 99999997765444
No 9
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=42.65 E-value=18 Score=30.07 Aligned_cols=22 Identities=27% Similarity=0.508 Sum_probs=14.5
Q ss_pred ccc-CChHHHHHHHHHHHHHHHHH
Q 046374 386 THF-SSPWTVIAFFAATFALFLSA 408 (420)
Q Consensus 386 ~yf-~npW~~is~~aA~~ll~lT~ 408 (420)
+|. -|||..|++-|| ++|++.+
T Consensus 77 ~yV~e~PWq~VGvaAa-VGlllGl 99 (104)
T COG4575 77 DYVRENPWQGVGVAAA-VGLLLGL 99 (104)
T ss_pred HHHHcCCchHHHHHHH-HHHHHHH
Confidence 444 399999988665 4554443
No 10
>PF15103 G0-G1_switch_2: G0/G1 switch protein 2
Probab=39.93 E-value=35 Score=28.23 Aligned_cols=26 Identities=15% Similarity=0.203 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHhHHhhccCCC
Q 046374 394 VIAFFAATFALFLSAIQTYWAVKPGH 419 (420)
Q Consensus 394 ~is~~aA~~ll~lT~~QT~~sv~~~~ 419 (420)
+++-+.|+++.++.+++|+|+=|+..
T Consensus 28 vLGSvLA~~Gvv~GLVEtVCsPFs~~ 53 (102)
T PF15103_consen 28 VLGSVLAFFGVVIGLVETVCSPFSAA 53 (102)
T ss_pred hhhhHHHHHHHHHHHHHHHhCccccC
Confidence 46777889999999999999987764
No 11
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=34.59 E-value=41 Score=27.10 Aligned_cols=19 Identities=21% Similarity=0.613 Sum_probs=12.8
Q ss_pred CChHHHHHHHHHHHHHHHHH
Q 046374 389 SSPWTVIAFFAATFALFLSA 408 (420)
Q Consensus 389 ~npW~~is~~aA~~ll~lT~ 408 (420)
.|||..+++.++ +++++.+
T Consensus 71 e~P~~svgiAag-vG~llG~ 89 (94)
T PF05957_consen 71 ENPWQSVGIAAG-VGFLLGL 89 (94)
T ss_pred HChHHHHHHHHH-HHHHHHH
Confidence 489999877655 5555544
No 12
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 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. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=31.90 E-value=32 Score=25.88 Aligned_cols=58 Identities=22% Similarity=0.314 Sum_probs=29.5
Q ss_pred ChHHHHHHHH-HhhccCCCCCcchHHHHHHHHhhc-----cchhhhHHHHhhccccCChHHHHHHHHHHH
Q 046374 339 SDQQVADLFN-QIADNLVPNPYAYAVVKHRIEKHY-----KNKIKIWLAEWFHTHFSSPWTVIAFFAATF 402 (420)
Q Consensus 339 sdeeva~lFn-~L~~~~~~~~~~y~~v~~~l~~~~-----~~~~~~w~a~l~~~yf~npW~~is~~aA~~ 402 (420)
+-++|.+.|+ +...|+.. ..+-+....|= ..+-..|+..+. +.|.||+.++=++||++
T Consensus 5 ~~~~v~~~l~t~~~~GLs~-----~ev~~r~~~~G~N~l~~~~~~s~~~~~~-~~f~~~~~~lL~~aail 68 (69)
T PF00690_consen 5 SVEEVLKRLNTSSSQGLSS-----EEVEERRKKYGPNELPEPKKKSLWRIFL-KQFKNPFIILLLIAAIL 68 (69)
T ss_dssp SHHHHHHHHTTBTSSBBTH-----HHHHHHHHHHSSSSTTTTTSSSHHHHHH-HHTTSHHHHHHHHHHHH
T ss_pred CHHHHHHHHCcCCCCCCCH-----HHHHHHHHhcccccccccccCcHHHHHH-HHHHhHHHHHHHHHHHH
Confidence 4566666665 44444421 23333333331 122334444454 45688999876666654
No 13
>PF09820 AAA-ATPase_like: Predicted AAA-ATPase; InterPro: IPR018631 This entry is predicted to be an AAA-ATPase domain []. It is usually found together with IPR012547 from INTERPRO.
Probab=30.46 E-value=52 Score=32.25 Aligned_cols=61 Identities=15% Similarity=0.325 Sum_probs=39.5
Q ss_pred CCCC-ChHHHHHHHHHhhccCCCCCcchHHHHHHHHhhccchhhhHHHHhhccccCChHHHHHHH
Q 046374 335 NFLG-SDQQVADLFNQIADNLVPNPYAYAVVKHRIEKHYKNKIKIWLAEWFHTHFSSPWTVIAFF 398 (420)
Q Consensus 335 ~~lg-sdeeva~lFn~L~~~~~~~~~~y~~v~~~l~~~~~~~~~~w~a~l~~~yf~npW~~is~~ 398 (420)
..+| +++||.++|+...+.+.... ......++|.++|+.-.-.+- -...--.|||.++..+
T Consensus 221 ~~~GFT~~Ev~~ll~~~~~~~~~~~-~~~~~~~~lk~wYdGY~F~~~--~~~~~iYNP~Svl~~l 282 (284)
T PF09820_consen 221 EYFGFTEEEVETLLKYYIENLAEEQ-DREELLEELKEWYDGYHFGES--SEGERIYNPWSVLNYL 282 (284)
T ss_pred hhcCcCHHHHHHHHHHHHHHhhhcc-chHHHHHHHHHHcCCcccCCC--CCCCCEEChHHHHHHh
Confidence 3455 78999999999876654322 456778899998885421111 0013445999998765
No 14
>PF04971 Lysis_S: Lysis protein S ; InterPro: IPR007054 The lysis S protein is a cytotoxic protein forming holes in membranes causing cell lysis. The action of Lysis S is independent of the proportion of acidic phospholipids in the membrane [].
Probab=30.02 E-value=89 Score=24.02 Aligned_cols=37 Identities=22% Similarity=0.531 Sum_probs=24.7
Q ss_pred hHHHHhhccccCChHHHHHHHHHHHHHHHHHH-hHHhh
Q 046374 378 IWLAEWFHTHFSSPWTVIAFFAATFALFLSAI-QTYWA 414 (420)
Q Consensus 378 ~w~a~l~~~yf~npW~~is~~aA~~ll~lT~~-QT~~s 414 (420)
.|...+.-.+-+.-|.+|++++.++.-++|.+ +.+|.
T Consensus 19 ~wl~~lld~~sp~qW~aIGvi~gi~~~~lt~ltN~YFK 56 (68)
T PF04971_consen 19 YWLLQLLDQFSPSQWAAIGVIGGIFFGLLTYLTNLYFK 56 (68)
T ss_pred HHHHHHHhccCcccchhHHHHHHHHHHHHHHHhHhhhh
Confidence 45555554454577999999998887777754 44443
No 15
>PF05421 DUF751: Protein of unknown function (DUF751); InterPro: IPR008470 This family, Ycf33, contains several plant, cyanobacterial and algal chlorplast encoded proteins of unknown function. The family is exclusively found in phototrophic organisms and may therefore play a role in photosynthesis.
Probab=28.22 E-value=93 Score=23.39 Aligned_cols=30 Identities=23% Similarity=0.212 Sum_probs=24.5
Q ss_pred ccCChHHHHHHHHHHHHHHHHHHhHHhhcc
Q 046374 387 HFSSPWTVIAFFAATFALFLSAIQTYWAVK 416 (420)
Q Consensus 387 yf~npW~~is~~aA~~ll~lT~~QT~~sv~ 416 (420)
-++||-+.++++++.+..+..+.+|+=+++
T Consensus 30 llk~p~tai~~i~~~~~~~~~l~~tL~aMl 59 (61)
T PF05421_consen 30 LLKNPVTAIALIGILIGGFIFLYFTLRAML 59 (61)
T ss_pred HhcCchHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 347899999999999988888888876654
No 16
>PF14770 TMEM18: Transmembrane protein 18
Probab=28.11 E-value=66 Score=27.70 Aligned_cols=46 Identities=13% Similarity=-0.066 Sum_probs=30.3
Q ss_pred HHHHHhhccchhhhHHHHhhccccCChHHHHHHHHHHHHHHHHHHhHHh
Q 046374 365 KHRIEKHYKNKIKIWLAEWFHTHFSSPWTVIAFFAATFALFLSAIQTYW 413 (420)
Q Consensus 365 ~~~l~~~~~~~~~~w~a~l~~~yf~npW~~is~~aA~~ll~lT~~QT~~ 413 (420)
-+.+|++..+.| +.--+++||.+-=.++|++-++=+|+.+++..+.
T Consensus 55 aE~iN~~~a~nW---~~Fs~qnYFDs~G~Fisvv~s~PlLl~~~ii~~~ 100 (123)
T PF14770_consen 55 AEYINEYAARNW---RSFSKQNYFDSSGVFISVVFSAPLLLNCLIILVN 100 (123)
T ss_pred HHHHHHHHHHHH---HHHhhccCcCCCCeeehHHHHHhHHHHHHHHHHH
Confidence 478888777544 4445579998777888887665555555444443
No 17
>PF08181 DegQ: DegQ (SacQ) family; InterPro: IPR012554 This family consists of the DegQ (formerly sacQ) regulatory peptides. The DegQ family of peptides control the rates of synthesis of a class of both secreted and intracellular degradative enzymes in Bacillus subtilis. DegQ is 46 amino acids long and activates the synthesis of degradative enzymes. The expression of this peptide was shown to be subjected both to catabolite repression and DegS-DegU-mediated control. Thus allowing an increase in the rate of synthesis of degQ under conditions of nitrogen starvation [].
Probab=22.65 E-value=1.1e+02 Score=21.07 Aligned_cols=30 Identities=20% Similarity=0.223 Sum_probs=20.9
Q ss_pred ccHHHHHHHHHHHHhcCCCHHHHHHHHHHh
Q 046374 53 MEKHKLTMAQQYVSNNLHMLEELYKKVLDV 82 (420)
Q Consensus 53 mE~~K~~~l~~~l~r~~~~l~~~~~~i~~~ 82 (420)
||+.|..-+++++-|...++.+-.+.++..
T Consensus 1 mek~~ieelkqll~rle~eirett~sl~ni 30 (46)
T PF08181_consen 1 MEKKKIEELKQLLWRLENEIRETTDSLRNI 30 (46)
T ss_pred CcHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 788899889998887766555554444433
No 18
>cd00925 Cyt_c_Oxidase_VIa Cytochrome c oxidase subunit VIa. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIa is expressed in two tissue-specific isoforms in mammals but not fish. VIa-H is the heart and skeletal muscle isoform; VIa-L is the liver or non-muscle isoform. Mammalian VIa-H induces a slip in CcO (decrease in proton/electron stoichiometry) at high intramitochondrial ATP/ADP ratios, while VIa-L induces a permanent slip i
Probab=22.63 E-value=85 Score=25.30 Aligned_cols=26 Identities=31% Similarity=0.557 Sum_probs=21.5
Q ss_pred CChHHHHHHHHHHHHHHHHHHhHHhh
Q 046374 389 SSPWTVIAFFAATFALFLSAIQTYWA 414 (420)
Q Consensus 389 ~npW~~is~~aA~~ll~lT~~QT~~s 414 (420)
++-|.-||+++|+-+++++++.++..
T Consensus 13 ~~~WkkiS~~va~P~v~l~~~n~y~~ 38 (86)
T cd00925 13 SELWKKISFYVALPAVALCMLNAYLK 38 (86)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHHhh
Confidence 35688999999998898999888754
No 19
>PF10961 DUF2763: Protein of unknown function (DUF2763); InterPro: IPR024491 This entry represents an eukaryotic family of selenoproteins. It includes SelK, which seems to play an important role in protecting cells from endoplasmic reticulum stress-induced apoptosis [] and SelG, which may be involved in regulating the redox state of the cell [].
Probab=22.22 E-value=1.3e+02 Score=24.35 Aligned_cols=27 Identities=26% Similarity=0.572 Sum_probs=17.1
Q ss_pred CChHH---HHHHHHHHHHHHHHHHhHHhhc
Q 046374 389 SSPWT---VIAFFAATFALFLSAIQTYWAV 415 (420)
Q Consensus 389 ~npW~---~is~~aA~~ll~lT~~QT~~sv 415 (420)
++||. ++-++-+++-+|..+.||+++.
T Consensus 13 rspWrls~I~d~Fwgi~~fI~lFF~Tl~~p 42 (91)
T PF10961_consen 13 RSPWRLSRITDFFWGIINFIVLFFQTLFSP 42 (91)
T ss_pred CCCccHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 35674 4455556666666777777764
No 20
>PHA02947 S-S bond formation pathway protein; Provisional
Probab=22.21 E-value=86 Score=29.54 Aligned_cols=19 Identities=16% Similarity=0.648 Sum_probs=12.2
Q ss_pred cCC-hHHHHHHHHHHHHHHH
Q 046374 388 FSS-PWTVIAFFAATFALFL 406 (420)
Q Consensus 388 f~n-pW~~is~~aA~~ll~l 406 (420)
|++ ||.++++++.++++++
T Consensus 175 ~~~~~W~i~~~~~i~~i~~i 194 (215)
T PHA02947 175 YSNKPWFIVGVVIILIIFVI 194 (215)
T ss_pred cCCCchHHHHHHHHHHHHHH
Confidence 466 9999866655444443
No 21
>PF09069 EF-hand_3: EF-hand; InterPro: IPR015154 Like other EF hand domains, this domain forms a helix-loop-helix motif, though since it does not contain the canonical pattern of calcium binding residues found in many EF hand domains, it does not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (IPR001202 from INTERPRO), enhancing dystroglycan binding []. ; PDB: 1EG3_A 1EG4_A.
Probab=20.71 E-value=1.4e+02 Score=24.17 Aligned_cols=55 Identities=20% Similarity=0.363 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhcCC-----CHHHHHHHHH-------------HhhhHHhhhccCC-CccCCCCHHHHHHHHHHH
Q 046374 56 HKLTMAQQYVSNNLH-----MLEELYKKVL-------------DVAKPARECYSDE-DSIKKFDDKQFIRMMVLD 111 (420)
Q Consensus 56 ~K~~~l~~~l~r~~~-----~l~~~~~~i~-------------~~e~~~R~~Y~~~-~~~~~~~~~~f~~MmllD 111 (420)
.|.||+=+.+.+++. .++.++..+. ..|..+|+|+ .. ....+.+.++|+..|..|
T Consensus 3 dKyRylFslisd~~g~~~~~~l~~lL~d~lqip~~vgE~~aFg~~e~sv~sCF-~~~~~~~~I~~~~Fl~wl~~e 76 (90)
T PF09069_consen 3 DKYRYLFSLISDSNGCMDQRKLGLLLHDVLQIPRAVGEGPAFGYIEPSVRSCF-QQVQLSPKITENQFLDWLMSE 76 (90)
T ss_dssp HHHHHHHHHHS-TTS-B-HHHHHHHHHHHHHHHHHTT-GGGGT--HHHHHHHH-HHTTT-S-B-HHHHHHHHHT-
T ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHhCccccccCcHHHHHHHh-cccCCCCccCHHHHHHHHHhC
Confidence 589999888876532 2344433221 2466778888 32 113456677887666544
No 22
>PF04531 Phage_holin_1: Bacteriophage holin; InterPro: IPR006485 Phage proteins for bacterial lysis typically include a membrane-disrupting protein, or holin, and one or more cell wall degrading enzymes that reach the cell wall because of holin action. Holins are found in a large number of mutually non-homologous families. This entry is represented by the Bacteriophage phi-LC3, holin. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=20.65 E-value=1.2e+02 Score=24.15 Aligned_cols=24 Identities=17% Similarity=0.142 Sum_probs=15.4
Q ss_pred cccCChHHHHHHHHHHHHHHHHHH
Q 046374 386 THFSSPWTVIAFFAATFALFLSAI 409 (420)
Q Consensus 386 ~yf~npW~~is~~aA~~ll~lT~~ 409 (420)
..|.||-..+|+++|+++++.++.
T Consensus 6 vR~kN~~~w~ali~~i~l~vq~~~ 29 (84)
T PF04531_consen 6 VRFKNKAFWVALISAILLLVQQVG 29 (84)
T ss_pred hcccCHHHHHHHHHHHHHHHHHHH
Confidence 456788777777777666655443
Done!