Query 047104
Match_columns 80
No_of_seqs 27 out of 29
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 07:39:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047104.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047104hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06592 DUF1138: Protein of u 100.0 7.3E-58 1.6E-62 298.7 6.2 73 3-75 1-73 (73)
2 PF02936 COX4: Cytochrome c ox 97.3 0.00028 6E-09 49.7 3.8 47 4-53 75-121 (142)
3 cd00922 Cyt_c_Oxidase_IV Cytoc 97.0 0.0013 2.7E-08 46.1 4.7 54 4-69 75-129 (136)
4 KOG4075 Cytochrome c oxidase, 94.0 0.1 2.2E-06 38.9 4.3 41 8-53 106-146 (167)
5 PRK14750 kdpF potassium-transp 74.9 4 8.6E-05 23.0 2.5 27 1-27 1-27 (29)
6 PF06295 DUF1043: Protein of u 69.5 5.1 0.00011 27.4 2.6 23 5-27 1-23 (128)
7 PRK14748 kdpF potassium-transp 64.1 10 0.00022 21.4 2.7 27 1-27 1-27 (29)
8 PF12454 Ecm33: GPI-anchored c 62.3 4.9 0.00011 23.8 1.2 18 1-18 2-19 (40)
9 PRK14759 potassium-transportin 58.9 14 0.0003 20.8 2.6 28 1-28 1-28 (29)
10 TIGR03039 PS_II_CP47 photosyst 57.8 4.1 8.9E-05 34.9 0.5 14 63-76 51-64 (504)
11 PLN00068 photosystem II CP47 c 56.5 3.8 8.2E-05 35.1 0.1 14 63-76 51-64 (508)
12 CHL00062 psbB photosystem II 4 55.4 3.9 8.5E-05 35.0 0.0 14 63-76 51-64 (504)
13 KOG2309 60s ribosomal protein 53.6 5.3 0.00012 31.6 0.5 18 49-68 185-202 (248)
14 PF08750 CNP1: CNP1-like famil 49.5 6.4 0.00014 27.9 0.3 36 39-75 4-40 (139)
15 PF10883 DUF2681: Protein of u 45.7 23 0.00051 23.6 2.6 25 1-25 1-27 (87)
16 PF04286 DUF445: Protein of un 41.2 34 0.00073 24.9 3.0 30 6-37 1-32 (367)
17 PF09604 Potass_KdpF: F subuni 39.1 49 0.0011 17.7 2.7 24 5-28 1-24 (25)
18 PF08507 COPI_assoc: COPI asso 37.5 40 0.00087 22.7 2.7 38 5-47 89-126 (136)
19 PF04238 DUF420: Protein of un 34.8 52 0.0011 23.0 3.0 27 7-33 41-67 (133)
20 PF06416 DUF1076: Protein of u 34.1 23 0.00051 25.1 1.2 12 63-75 102-113 (113)
21 TIGR00769 AAA ADP/ATP carrier 34.1 41 0.0009 27.6 2.8 24 4-27 134-157 (472)
22 PF10661 EssA: WXG100 protein 33.3 43 0.00094 23.7 2.5 26 4-30 119-144 (145)
23 cd03513 CrtW_beta-carotene-ket 33.1 30 0.00065 25.7 1.7 29 5-44 154-182 (225)
24 COG3205 Predicted membrane pro 32.9 67 0.0014 21.3 3.1 32 34-65 38-69 (72)
25 PF03201 HMD: H2-forming N5,N1 31.7 48 0.001 22.9 2.4 26 7-32 10-35 (98)
26 PF10731 Anophelin: Thrombin i 30.8 48 0.001 21.6 2.2 17 1-17 1-17 (65)
27 TIGR00694 thiM hydroxyethylthi 29.2 46 0.001 24.3 2.1 32 35-68 57-88 (249)
28 TIGR02115 potass_kdpF K+-trans 28.9 75 0.0016 17.2 2.4 23 6-28 1-23 (26)
29 PF12301 CD99L2: CD99 antigen 28.2 66 0.0014 23.6 2.8 24 6-29 120-143 (169)
30 PF02529 PetG: Cytochrome B6-F 27.8 61 0.0013 19.1 2.0 21 6-28 14-34 (37)
31 KOG1741 Mitochondrial/chloropl 27.3 56 0.0012 22.9 2.1 28 38-65 37-64 (103)
32 COG4733 Phage-related protein, 24.6 38 0.00081 31.3 1.1 27 12-40 298-324 (952)
33 KOG2822 Sphingoid base-phospha 24.2 39 0.00086 28.4 1.1 13 51-63 133-145 (407)
34 PRK11677 hypothetical protein; 23.8 74 0.0016 22.5 2.3 26 1-26 1-26 (134)
35 PF06916 DUF1279: Protein of u 23.7 62 0.0013 20.7 1.7 19 7-25 60-78 (91)
36 PF03947 Ribosomal_L2_C: Ribos 23.6 31 0.00068 24.0 0.4 27 40-68 79-106 (130)
37 PF12072 DUF3552: Domain of un 22.1 80 0.0017 22.7 2.2 21 6-26 6-26 (201)
38 PF11839 DUF3359: Protein of u 22.1 64 0.0014 22.0 1.6 19 4-22 3-21 (96)
39 KOG2214 Predicted esterase of 21.9 27 0.00058 30.4 -0.3 53 5-69 317-371 (543)
40 PF07179 SseB: SseB protein N- 21.8 98 0.0021 19.0 2.3 27 49-75 91-117 (124)
41 PRK09993 C-lysozyme inhibitor; 21.3 76 0.0017 23.4 2.0 33 42-74 42-77 (153)
42 PF13283 NfrA_C: Bacteriophage 20.7 51 0.0011 24.4 1.0 16 61-76 17-32 (176)
43 PF09158 MotCF: Bacteriophage 20.7 47 0.001 23.1 0.8 9 67-75 27-35 (103)
44 PRK03854 opgC glucans biosynth 20.4 80 0.0017 23.8 2.0 27 9-35 345-375 (375)
45 cd01169 HMPP_kinase 4-amino-5- 20.4 1.4E+02 0.0031 20.6 3.1 40 28-70 67-106 (242)
No 1
>PF06592 DUF1138: Protein of unknown function (DUF1138); InterPro: IPR009515 This family consists of several hypothetical short plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.
Probab=100.00 E-value=7.3e-58 Score=298.68 Aligned_cols=73 Identities=78% Similarity=1.319 Sum_probs=72.4
Q ss_pred cchhhhhHHHHHHHHHHHHHHHhccccccCCCCcccCchhhHHHHHHHhhhCCCccCCCeeecccccceeeee
Q 047104 3 TKYIVGSLIGSCALAYAFDQIIAEKKIFGGTTPKTVSDKEWWEETDKKFQAWPRVAGPPVVMNPISRQNFIVK 75 (80)
Q Consensus 3 ~kyIv~s~~~sfa~Ay~c~~~vs~~k~fGGt~P~TvtnkeW~~aT~~k~qaWPR~agpPVvmNPisrqnfivk 75 (80)
+||||+||+|||++||+||++++++|+|||++||||+|||||+|||+||||||||||||||||||||||||||
T Consensus 1 ~kyIi~al~gsfa~ay~c~~~vs~~K~FGGt~p~Tv~~keW~~aT~~K~qaWPR~agpPVvmNPisrqnfivk 73 (73)
T PF06592_consen 1 TKYIIGALAGSFAVAYVCDQYVSDKKIFGGTTPHTVSNKEWWKATDKKFQAWPREAGPPVVMNPISRQNFIVK 73 (73)
T ss_pred CcEEeehHHHHHHHHHHHHHHHhcccccCCCCCCccccHHHHHHHHHHHhhCcccCCCCeeeccccccceecC
Confidence 6999999999999999999999999999999999999999999999999999999999999999999999998
No 2
>PF02936 COX4: Cytochrome c oxidase subunit IV; InterPro: IPR004203 Cytochrome c oxidase, a 13 sub-unit complex (1.9.3.1 from EC) is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit IV. The Dictyostelium discoideum (Slime mould) member of this family is called COX VI. The Saccharomyces cerevisiae protein YGX6_YEAST appears to be the yeast COX IV subunit.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3ABK_Q 3AG1_Q 3ASN_Q 1OCZ_D 2EIN_Q 2OCC_D 2YBB_O 3AG3_D 1OCO_Q 1V55_Q ....
Probab=97.33 E-value=0.00028 Score=49.72 Aligned_cols=47 Identities=17% Similarity=0.231 Sum_probs=31.6
Q ss_pred chhhhhHHHHHHHHHHHHHHHhccccccCCCCcccCchhhHHHHHHHhhh
Q 047104 4 KYIVGSLIGSCALAYAFDQIIAEKKIFGGTTPKTVSDKEWWEETDKKFQA 53 (80)
Q Consensus 4 kyIv~s~~~sfa~Ay~c~~~vs~~k~fGGt~P~TvtnkeW~~aT~~k~qa 53 (80)
|.|++++...++++.+...++ +..-.+.+|||+++ ||.+++.+++-.
T Consensus 75 k~v~~~~~~~i~~s~~l~~~~--r~~~~~~~P~T~~~-Ew~ea~~~~m~~ 121 (142)
T PF02936_consen 75 KKVFGGVFIFIGFSVLLFIWQ--RSYVYPPLPHTFSK-EWQEAQNERMLD 121 (142)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH--HHHT-----GGGSH-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH--HHHhCCCCCCCcCH-HHHHHHHHHHHH
Confidence 567887777777776544444 44466789999999 999999999954
No 3
>cd00922 Cyt_c_Oxidase_IV Cytochrome c oxidase subunit IV. 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 IV is the largest of the nuclear-encoded subunits. It binds ATP at the matrix side, leading to an allosteric inhibition of enzyme activity at high intramitochondrial ATP/ADP ratios. In mammals, subunit IV has a lung-specific isoform and a ubiquitously expressed isoform.
Probab=97.05 E-value=0.0013 Score=46.14 Aligned_cols=54 Identities=22% Similarity=0.410 Sum_probs=40.5
Q ss_pred chhhhhHHHHHHHHHHHHHHHhcccccc-CCCCcccCchhhHHHHHHHhhhCCCccCCCeeeccccc
Q 047104 4 KYIVGSLIGSCALAYAFDQIIAEKKIFG-GTTPKTVSDKEWWEETDKKFQAWPRVAGPPVVMNPISR 69 (80)
Q Consensus 4 kyIv~s~~~sfa~Ay~c~~~vs~~k~fG-Gt~P~TvtnkeW~~aT~~k~qaWPR~agpPVvmNPisr 69 (80)
|.|++.++...+++.++..++. .|. |-.|+|+++ ||.++..+++.+- -+|||.+
T Consensus 75 k~v~~~~~~~i~~s~~~~~~~r---~~~~~~~P~T~t~-Ewqea~~er~~~~--------~~NPitG 129 (136)
T cd00922 75 KTVFGGVLAFIGITGVIFGLQR---AFVYGPKPHTFTE-EWQEAQLERMLDM--------KVNPITG 129 (136)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH---HhccCCCCCCcCH-HHHHHHHHHHHHh--------CCCCCcc
Confidence 6778888777777775554443 355 999999999 9999999999753 4677653
No 4
>KOG4075 consensus Cytochrome c oxidase, subunit IV/COX5b [Energy production and conversion]
Probab=94.02 E-value=0.1 Score=38.87 Aligned_cols=41 Identities=17% Similarity=0.276 Sum_probs=29.9
Q ss_pred hhHHHHHHHHHHHHHHHhccccccCCCCcccCchhhHHHHHHHhhh
Q 047104 8 GSLIGSCALAYAFDQIIAEKKIFGGTTPKTVSDKEWWEETDKKFQA 53 (80)
Q Consensus 8 ~s~~~sfa~Ay~c~~~vs~~k~fGGt~P~TvtnkeW~~aT~~k~qa 53 (80)
..++.+|+++++.+..+- -.|-+|+|+++ ||.++-++++-.
T Consensus 106 ~~~f~Gl~~~v~l~~~v~----vy~~~P~Tf~~-Ewq~kq~erml~ 146 (167)
T KOG4075|consen 106 AGFFLGLTISVILFGKVR----VYGPLPKTFNK-EWQEKQLERMLD 146 (167)
T ss_pred HHHHHHHHHHHHHHHhhe----ecCCCCcchhH-HHHHHHHHHHHH
Confidence 445555555555554444 67899999988 999999999854
No 5
>PRK14750 kdpF potassium-transporting ATPase subunit F; Provisional
Probab=74.86 E-value=4 Score=23.03 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=24.0
Q ss_pred CccchhhhhHHHHHHHHHHHHHHHhcc
Q 047104 1 MATKYIVGSLIGSCALAYAFDQIIAEK 27 (80)
Q Consensus 1 m~~kyIv~s~~~sfa~Ay~c~~~vs~~ 27 (80)
|+...|.|++..-+.+.|.|+-++.-+
T Consensus 1 Ms~~vi~g~llv~lLl~YLvYAL~naE 27 (29)
T PRK14750 1 MNFSIVCGALLVLLLLGYLVYALFNAE 27 (29)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHcCcc
Confidence 788899999999999999999887644
No 6
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=69.50 E-value=5.1 Score=27.37 Aligned_cols=23 Identities=9% Similarity=0.320 Sum_probs=19.6
Q ss_pred hhhhhHHHHHHHHHHHHHHHhcc
Q 047104 5 YIVGSLIGSCALAYAFDQIIAEK 27 (80)
Q Consensus 5 yIv~s~~~sfa~Ay~c~~~vs~~ 27 (80)
||+.++++++++.|++..+...+
T Consensus 1 y~~i~lvvG~iiG~~~~r~~~~~ 23 (128)
T PF06295_consen 1 YAIIGLVVGLIIGFLIGRLTSSN 23 (128)
T ss_pred ChHHHHHHHHHHHHHHHHHhccc
Confidence 89999999999999988776554
No 7
>PRK14748 kdpF potassium-transporting ATPase subunit F; Provisional
Probab=64.12 E-value=10 Score=21.38 Aligned_cols=27 Identities=26% Similarity=0.338 Sum_probs=23.8
Q ss_pred CccchhhhhHHHHHHHHHHHHHHHhcc
Q 047104 1 MATKYIVGSLIGSCALAYAFDQIIAEK 27 (80)
Q Consensus 1 m~~kyIv~s~~~sfa~Ay~c~~~vs~~ 27 (80)
|++..|+|.+.+-..+.|.++-++.-+
T Consensus 1 Ms~~vi~G~ilv~lLlgYLvyALi~aE 27 (29)
T PRK14748 1 MSAGVITGVLLVFLLLGYLVYALINAE 27 (29)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence 889999999999999999999887643
No 8
>PF12454 Ecm33: GPI-anchored cell wall organization protein
Probab=62.27 E-value=4.9 Score=23.79 Aligned_cols=18 Identities=28% Similarity=0.331 Sum_probs=13.2
Q ss_pred CccchhhhhHHHHHHHHH
Q 047104 1 MATKYIVGSLIGSCALAY 18 (80)
Q Consensus 1 m~~kyIv~s~~~sfa~Ay 18 (80)
-..||++++|++.-+++.
T Consensus 2 a~~Ky~lpAlaaag~a~A 19 (40)
T PF12454_consen 2 AFSKYLLPALAAAGAAAA 19 (40)
T ss_pred chHHHHHHHHHHHHHHHH
Confidence 078999999877655554
No 9
>PRK14759 potassium-transporting ATPase subunit F; Provisional
Probab=58.93 E-value=14 Score=20.75 Aligned_cols=28 Identities=14% Similarity=0.256 Sum_probs=23.2
Q ss_pred CccchhhhhHHHHHHHHHHHHHHHhccc
Q 047104 1 MATKYIVGSLIGSCALAYAFDQIIAEKK 28 (80)
Q Consensus 1 m~~kyIv~s~~~sfa~Ay~c~~~vs~~k 28 (80)
|.-.|+++++++...++|...-++.-++
T Consensus 1 m~~~~~l~~~va~~L~vYL~~ALlrPEr 28 (29)
T PRK14759 1 MILDYSLAGAVSLGLLIYLTYALLRPER 28 (29)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHhCccc
Confidence 6677999999999999999888776543
No 10
>TIGR03039 PS_II_CP47 photosystem II chlorophyll-binding protein CP47.
Probab=57.82 E-value=4.1 Score=34.90 Aligned_cols=14 Identities=43% Similarity=0.648 Sum_probs=12.2
Q ss_pred eecccccceeeeec
Q 047104 63 VMNPISRQNFIVKS 76 (80)
Q Consensus 63 vmNPisrqnfivk~ 76 (80)
|+|||-||++|+=+
T Consensus 51 vlnPM~eQGlIlLP 64 (504)
T TIGR03039 51 VLNPMWRQGMYVLP 64 (504)
T ss_pred cCCCchhccceeeh
Confidence 79999999999843
No 11
>PLN00068 photosystem II CP47 chlorophyll A apoprotein; Provisional
Probab=56.49 E-value=3.8 Score=35.14 Aligned_cols=14 Identities=36% Similarity=0.650 Sum_probs=12.0
Q ss_pred eecccccceeeeec
Q 047104 63 VMNPISRQNFIVKS 76 (80)
Q Consensus 63 vmNPisrqnfivk~ 76 (80)
|+|||-||++|+=+
T Consensus 51 vlnPM~eQGlilLP 64 (508)
T PLN00068 51 VLDPMWRQGMFVIP 64 (508)
T ss_pred ccCCchhcccchhh
Confidence 79999999999743
No 12
>CHL00062 psbB photosystem II 47 kDa protein
Probab=55.42 E-value=3.9 Score=35.00 Aligned_cols=14 Identities=36% Similarity=0.650 Sum_probs=12.0
Q ss_pred eecccccceeeeec
Q 047104 63 VMNPISRQNFIVKS 76 (80)
Q Consensus 63 vmNPisrqnfivk~ 76 (80)
|+|||-||++|+=+
T Consensus 51 vlnPM~eQGlIlLP 64 (504)
T CHL00062 51 VLDPMWRQGMFVIP 64 (504)
T ss_pred cCCcchhccchhhh
Confidence 79999999999743
No 13
>KOG2309 consensus 60s ribosomal protein L2/L8 [Translation, ribosomal structure and biogenesis]
Probab=53.59 E-value=5.3 Score=31.56 Aligned_cols=18 Identities=56% Similarity=1.095 Sum_probs=15.2
Q ss_pred HHhhhCCCccCCCeeecccc
Q 047104 49 KKFQAWPRVAGPPVVMNPIS 68 (80)
Q Consensus 49 ~k~qaWPR~agpPVvmNPis 68 (80)
.|...|||+-| |.|||+.
T Consensus 185 ~Krn~wPrvRG--VAMnPVe 202 (248)
T KOG2309|consen 185 AKRNCWPRVRG--VAMNPVE 202 (248)
T ss_pred hhcCCchhhcc--eeccccc
Confidence 46789999988 9999973
No 14
>PF08750 CNP1: CNP1-like family; InterPro: IPR014861 This group of proteins are likely to be lipoproteins. CNP1 (cryptic neisserial protein) has been expressed in Escherichia coli and shown to be localised periplasmicly [].
Probab=49.54 E-value=6.4 Score=27.95 Aligned_cols=36 Identities=28% Similarity=0.482 Sum_probs=28.9
Q ss_pred CchhhHHHHHHHhhhCCCccCC-Ceeecccccceeeee
Q 047104 39 SDKEWWEETDKKFQAWPRVAGP-PVVMNPISRQNFIVK 75 (80)
Q Consensus 39 tnkeW~~aT~~k~qaWPR~agp-PVvmNPisrqnfivk 75 (80)
.+++|.+.. ..+-+||+++.= |+-++|-+++.|-|=
T Consensus 4 ~~~~w~E~~-~~LPp~P~~~~l~~f~v~~~~~~~f~ID 40 (139)
T PF08750_consen 4 ADKPWKEAE-VPLPPAPQDANLLPFDVSPTSPLKFFID 40 (139)
T ss_pred cCCCCEecc-cCCCCCCCcCCccEEECCCCCCceEEEc
Confidence 356776554 489999999877 999999999999874
No 15
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=45.72 E-value=23 Score=23.65 Aligned_cols=25 Identities=28% Similarity=0.323 Sum_probs=15.8
Q ss_pred CccchhhhhHHHHH--HHHHHHHHHHh
Q 047104 1 MATKYIVGSLIGSC--ALAYAFDQIIA 25 (80)
Q Consensus 1 m~~kyIv~s~~~sf--a~Ay~c~~~vs 25 (80)
|-+.+|+++++|.| .++|+++..=.
T Consensus 1 Mi~l~iv~~~~~v~~~i~~y~~~k~~k 27 (87)
T PF10883_consen 1 MINLQIVGGVGAVVALILAYLWWKVKK 27 (87)
T ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66778876665544 45677776543
No 16
>PF04286 DUF445: Protein of unknown function (DUF445); InterPro: IPR007383 This entry contains proteins of unknown function. They are predicted to be transmembrane proteins with 2 or 3 TM domains.
Probab=41.24 E-value=34 Score=24.91 Aligned_cols=30 Identities=33% Similarity=0.514 Sum_probs=17.9
Q ss_pred hhhhHHHHHHHHHHHHHHHhccccccCC-CC-cc
Q 047104 6 IVGSLIGSCALAYAFDQIIAEKKIFGGT-TP-KT 37 (80)
Q Consensus 6 Iv~s~~~sfa~Ay~c~~~vs~~k~fGGt-~P-~T 37 (80)
+++|++|+++=-++..-++. |++||. +| ||
T Consensus 1 ~~~a~iG~~tnw~Av~~lFr--~Plg~~~ip~~~ 32 (367)
T PF04286_consen 1 AEGALIGYITNWFAVKMLFR--KPLGGIPIPFHT 32 (367)
T ss_pred CchhHhHHHHHHHHHHHHhh--CCCcccCCCccc
Confidence 45777777766666666664 235544 66 44
No 17
>PF09604 Potass_KdpF: F subunit of K+-transporting ATPase (Potass_KdpF); InterPro: IPR011726 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 F subunit (KdpF) of a P-type K+-translocating ATPase (Kdp). KdpF is a very small integral membrane peptide. The kdpABC operon of Escherichia coli codes for the high affinity K+-translocating Kdp complex []. KdpF is found upstream of the KdpA subunit (IPR004623 from INTERPRO). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation. More information about this protein can be found at Protein of the Month: ATP Synthases [].
Probab=39.09 E-value=49 Score=17.66 Aligned_cols=24 Identities=21% Similarity=0.645 Sum_probs=19.0
Q ss_pred hhhhhHHHHHHHHHHHHHHHhccc
Q 047104 5 YIVGSLIGSCALAYAFDQIIAEKK 28 (80)
Q Consensus 5 yIv~s~~~sfa~Ay~c~~~vs~~k 28 (80)
+|++.+++...++|....++.-+|
T Consensus 1 ~~l~~~v~~~L~~YL~~aLl~PEr 24 (25)
T PF09604_consen 1 YILGGIVAVALFVYLFYALLRPER 24 (25)
T ss_pred ChHHHHHHHHHHHHHHHHHhCccc
Confidence 578888888889999888776554
No 18
>PF08507 COPI_assoc: COPI associated protein; InterPro: IPR013714 Proteins in this family co-localise with COPI vesicle coat proteins []. In yeast it is a Golgi membrane protein involved in vesicular trafficking, interacting with TVP18 [].
Probab=37.51 E-value=40 Score=22.68 Aligned_cols=38 Identities=18% Similarity=0.273 Sum_probs=30.3
Q ss_pred hhhhhHHHHHHHHHHHHHHHhccccccCCCCcccCchhhHHHH
Q 047104 5 YIVGSLIGSCALAYAFDQIIAEKKIFGGTTPKTVSDKEWWEET 47 (80)
Q Consensus 5 yIv~s~~~sfa~Ay~c~~~vs~~k~fGGt~P~TvtnkeW~~aT 47 (80)
.++|.+....++.|++-.++..++ .|+.+.+++|...-
T Consensus 89 ~i~g~~~~~~G~~~i~l~~~~~~~-----~~~~~r~~~~~~~~ 126 (136)
T PF08507_consen 89 IIIGLLLFLVGVIYIILGFFCPIK-----EPESMREQEIALSS 126 (136)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCC-----CchhcCcccccccc
Confidence 567888888899999999988875 78888887776543
No 19
>PF04238 DUF420: Protein of unknown function (DUF420); InterPro: IPR007352 This is a predicted membrane protein with four transmembrane helices.
Probab=34.76 E-value=52 Score=22.99 Aligned_cols=27 Identities=19% Similarity=0.333 Sum_probs=22.3
Q ss_pred hhhHHHHHHHHHHHHHHHhccccccCC
Q 047104 7 VGSLIGSCALAYAFDQIIAEKKIFGGT 33 (80)
Q Consensus 7 v~s~~~sfa~Ay~c~~~vs~~k~fGGt 33 (80)
...+.+.|.+.|+..+++.+.+.|||.
T Consensus 41 a~~ls~lFlv~Yl~~~~~~g~~~f~g~ 67 (133)
T PF04238_consen 41 AFVLSALFLVSYLYYHFLGGSTPFGGP 67 (133)
T ss_pred HHHHHHHHHHHHHHHHHhcCCcccCCC
Confidence 345677899999999999888889875
No 20
>PF06416 DUF1076: Protein of unknown function (DUF1076); InterPro: IPR010489 This entry is represented by Bacteriophage 2851, Orf74 (EP2851_74). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2KKX_A 2KKY_A.
Probab=34.14 E-value=23 Score=25.06 Aligned_cols=12 Identities=33% Similarity=0.695 Sum_probs=9.0
Q ss_pred eecccccceeeee
Q 047104 63 VMNPISRQNFIVK 75 (80)
Q Consensus 63 vmNPisrqnfivk 75 (80)
..|+. |||||+|
T Consensus 102 ~fd~~-~~~F~ik 113 (113)
T PF06416_consen 102 YFDTT-KGNFIIK 113 (113)
T ss_dssp EEETT-TTEEEES
T ss_pred eecCC-CCeEEeC
Confidence 34555 9999997
No 21
>TIGR00769 AAA ADP/ATP carrier protein family. These proteins are members of the ATP:ADP Antiporter (AAA) Family (TC 2.A.12), which consists of nucleotide transporters that have 12 GES predicted transmembrane regions. One protein from Rickettsia prowazekii functions to take up ATP from the eukaryotic cell cytoplasm into the bacterium in exchange for ADP. Five AAA family paralogues are encoded within the genome of R. prowazekii. This organism transports UMP and GMP but not CMP, and it seems likely that one or more of the AAA family paralogues are responsible. The genome of Chlamydia trachomatis encodes two AAA family members, Npt1 and Npt2, which catalyse ATP/ADP exchange and GTP, CTP, ATP and UTP uptake probably employing a proton symport mechanism. Two homologous adenylate translocators of Arabidopsis thaliana are postulated to be localized to the intracellular plastid membrane where they function as ATP importers.
Probab=34.08 E-value=41 Score=27.63 Aligned_cols=24 Identities=25% Similarity=0.351 Sum_probs=21.3
Q ss_pred chhhhhHHHHHHHHHHHHHHHhcc
Q 047104 4 KYIVGSLIGSCALAYAFDQIIAEK 27 (80)
Q Consensus 4 kyIv~s~~~sfa~Ay~c~~~vs~~ 27 (80)
=||+.++-+++++++++|++.+|-
T Consensus 134 FYv~~elw~~~vvS~lFW~fandi 157 (472)
T TIGR00769 134 FYVMAELWGSVVLSLLFWGFANQI 157 (472)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 388999999999999999998874
No 22
>PF10661 EssA: WXG100 protein secretion system (Wss), protein EssA; InterPro: IPR018920 The Wss (WXG100 protein secretion system) in Staphylococcus aureus seems to be encoded by a locus of eight ORFs, called ess (eSAT-6 secretion system) []. This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with YukC and YukAB. Proteins homologous to EssA, YukC, EsaA and YukD were absent from mycobacteria []. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions.
Probab=33.27 E-value=43 Score=23.71 Aligned_cols=26 Identities=23% Similarity=0.249 Sum_probs=14.9
Q ss_pred chhhhhHHHHHHHHHHHHHHHhccccc
Q 047104 4 KYIVGSLIGSCALAYAFDQIIAEKKIF 30 (80)
Q Consensus 4 kyIv~s~~~sfa~Ay~c~~~vs~~k~f 30 (80)
++|+ .++++++++.++..|+.-+++|
T Consensus 119 ~~i~-~~i~g~ll~i~~giy~~~r~~~ 144 (145)
T PF10661_consen 119 PTIL-LSIGGILLAICGGIYVVLRKVW 144 (145)
T ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHhh
Confidence 3444 4455555666666666666665
No 23
>cd03513 CrtW_beta-carotene-ketolase Beta-carotene ketolase/oxygenase (CrtW, also known as CrtO), the carotenoid astaxanthin biosynthetic enzyme, initially catalyzes the addition of two keto groups to carbons C4 and C4' of beta-carotene. Carotenoids are important natural pigments produced by many microorganisms and plants. Astaxanthin is reported to be an antioxidant, an anti-cancer agent, and an immune system stimulant. A number of bacteria and green algae can convert beta-carotene into astaxanthin by using several ketocarotenoids as intermediates and CrtW and a beta-carotene hydroxylase (CrtZ). CrtW initially converts beta-carotene to canthaxanthin via echinenone, and CrtZ initially mediates the conversion of beta-carotene to zeaxanthin via beta-cryptoxanthin. After a few more intermediates are formed, CrtW and CrtZ act in combination to produce astaxanthin. Sequences of this domain family appear to be structurally related to membrane fatty acid desaturases and alkane hydroxylases. Th
Probab=33.05 E-value=30 Score=25.75 Aligned_cols=29 Identities=21% Similarity=0.340 Sum_probs=21.3
Q ss_pred hhhhhHHHHHHHHHHHHHHHhccccccCCCCcccCchhhH
Q 047104 5 YIVGSLIGSCALAYAFDQIIAEKKIFGGTTPKTVSDKEWW 44 (80)
Q Consensus 5 yIv~s~~~sfa~Ay~c~~~vs~~k~fGGt~P~TvtnkeW~ 44 (80)
|++++++++|...| ||..+||+-.|..+.
T Consensus 154 ~~~P~l~~~~~l~~-----------f~T~lpH~~~~~~~~ 182 (225)
T cd03513 154 WALPLILSSLQLFY-----------FGTWLPHRPGRGGFA 182 (225)
T ss_pred HHHHHHHHHHHHHH-----------HHhhcCCCCCCCCCC
Confidence 56788888888877 666699987664443
No 24
>COG3205 Predicted membrane protein [Function unknown]
Probab=32.92 E-value=67 Score=21.31 Aligned_cols=32 Identities=22% Similarity=0.001 Sum_probs=20.6
Q ss_pred CCcccCchhhHHHHHHHhhhCCCccCCCeeec
Q 047104 34 TPKTVSDKEWWEETDKKFQAWPRVAGPPVVMN 65 (80)
Q Consensus 34 ~P~TvtnkeW~~aT~~k~qaWPR~agpPVvmN 65 (80)
+..||.=-=|++.=.+--++|||.+..+-.+|
T Consensus 38 ~~nTV~fYfhEr~W~~~~~~~~R~~~~~~~~~ 69 (72)
T COG3205 38 MVNTVAFYFHERLWSRFEKARPRQATQHFALN 69 (72)
T ss_pred hhcchhHHHHHHHHHHHhhcCCcccccCcccc
Confidence 45677655555543333359999998877666
No 25
>PF03201 HMD: H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase; InterPro: IPR004889 This entry represents the C-terminal domain of H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenases. The N(5),N(10)-methylenetetrahydromethanopterin dehydrogenase system of methanogenic archaea is composed of H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd, represented by this entry) and F420-dependent methylenetetrahydromethanopterin dehydrogenase (IPR002844 from INTERPRO) [, ]. Hmd is an iron-sulphur-cluster-free enzyme that contains an intrinsic CO ligand bound to iron []. This domain is found at the C terminus of two distinct subgroups: one has been experimentally characterised as H2-forming N(5),N(10)-methenyltetrahydromethanopterin dehydrogenase (Hmd or HmdI), and the other one contains isozymes that have not been experimentally characterised (HmdII and HmdIII). Because all three isozyme forms are present in each of the corresponding sequenced genomes, it has been suggested that HmdII and HmdIII may not exhibit Hmd activity and may have a different biological function [].; GO: 0018537 coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity, 0047068 N5,N10-methenyltetrahydromethanopterin hydrogenase activity, 0015948 methanogenesis, 0055114 oxidation-reduction process; PDB: 3F46_A 2B0J_A 3DAG_A 3DAF_A 3H65_A 3F47_A.
Probab=31.66 E-value=48 Score=22.92 Aligned_cols=26 Identities=31% Similarity=0.410 Sum_probs=21.9
Q ss_pred hhhHHHHHHHHHHHHHHHhccccccC
Q 047104 7 VGSLIGSCALAYAFDQIIAEKKIFGG 32 (80)
Q Consensus 7 v~s~~~sfa~Ay~c~~~vs~~k~fGG 32 (80)
++|++-+.++|++++++-...|+.|-
T Consensus 10 Mgs~vTAv~~agiL~Y~~v~t~il~A 35 (98)
T PF03201_consen 10 MGSLVTAVTYAGILDYYDVGTKILGA 35 (98)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHHTS--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 67889999999999999999888873
No 26
>PF10731 Anophelin: Thrombin inhibitor from mosquito; InterPro: IPR018932 Members of this family are all inhibitors of thrombin, the peptidase that is at the end of the blood coagulation cascade and which creates the clot by cleaving fibrinogen. The interaction between thrombin and fibrinogen involves two different areas of contact - via the thrombin active site and via a second substrate-binding site known as an exosite. The inhibitor acts by blocking the exosite, rather than by interacting with the active site. The inhibitors are from mosquitoes that feed on human blood and which, by inhibiting thrombin, prevent the blood from clotting and keep it flowing.
Probab=30.84 E-value=48 Score=21.63 Aligned_cols=17 Identities=41% Similarity=0.446 Sum_probs=11.9
Q ss_pred CccchhhhhHHHHHHHH
Q 047104 1 MATKYIVGSLIGSCALA 17 (80)
Q Consensus 1 m~~kyIv~s~~~sfa~A 17 (80)
|++|.|+.|+.-...+|
T Consensus 1 MA~Kl~vialLC~aLva 17 (65)
T PF10731_consen 1 MASKLIVIALLCVALVA 17 (65)
T ss_pred CcchhhHHHHHHHHHHH
Confidence 89999988776544444
No 27
>TIGR00694 thiM hydroxyethylthiazole kinase. This model represents the hydoxyethylthiazole kinase, ThiM, of a number of bacteria, and C-terminal domains of bifunctional thiamine biosynthesis proteins of Saccharomyces cerevisiae and Schizosaccharomyces pombe, in which the N-terminal domain corresponds to the bacterial thiamine-phosphate pyrophosphorylase (EC 2.5.1.3), ThiE.
Probab=29.20 E-value=46 Score=24.33 Aligned_cols=32 Identities=25% Similarity=0.260 Sum_probs=20.9
Q ss_pred CcccCchhhHHHHHHHhhhCCCccCCCeeecccc
Q 047104 35 PKTVSDKEWWEETDKKFQAWPRVAGPPVVMNPIS 68 (80)
Q Consensus 35 P~TvtnkeW~~aT~~k~qaWPR~agpPVvmNPis 68 (80)
|+++.+ |+.+.-.+..+.- ++.+.|||+||.-
T Consensus 57 ~G~l~~-~~~~~i~~~~~~~-~~~~~pvVlDPV~ 88 (249)
T TIGR00694 57 IGTLDK-ESIEAMIAAGKSA-NELGVPVVLDPVG 88 (249)
T ss_pred CCCCCH-HHHHHHHHHHHHH-HhcCCCEEEcccc
Confidence 667755 8877665555332 2336799999974
No 28
>TIGR02115 potass_kdpF K+-transporting ATPase, KdpF subunit. This model describes a very small integral membrane peptide KdpF, a subunit of the K(+)-translocating Kdp complex. It is found upstream of the KdpA subunit (TIGR00680). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation.
Probab=28.93 E-value=75 Score=17.23 Aligned_cols=23 Identities=13% Similarity=0.316 Sum_probs=18.3
Q ss_pred hhhhHHHHHHHHHHHHHHHhccc
Q 047104 6 IVGSLIGSCALAYAFDQIIAEKK 28 (80)
Q Consensus 6 Iv~s~~~sfa~Ay~c~~~vs~~k 28 (80)
|++.+++...+.|.+..++.-+|
T Consensus 1 ii~~~l~~~L~~YL~~aLl~PEr 23 (26)
T TIGR02115 1 IILLVLAVGLFIYLFYALLRPER 23 (26)
T ss_pred CHHHHHHHHHHHHHHHHHhCHHh
Confidence 56788888888999988887654
No 29
>PF12301 CD99L2: CD99 antigen like protein 2; InterPro: IPR022078 This family of proteins is found in eukaryotes. Proteins in this family are typically between 165 and 237 amino acids in length. CD99L2 and CD99 are involved in trans-endothelial migration of neutrophils in vitro and in the recruitment of neutrophils into inflamed peritoneum.
Probab=28.23 E-value=66 Score=23.60 Aligned_cols=24 Identities=21% Similarity=0.133 Sum_probs=12.9
Q ss_pred hhhhHHHHHHHHHHHHHHHhcccc
Q 047104 6 IVGSLIGSCALAYAFDQIIAEKKI 29 (80)
Q Consensus 6 Iv~s~~~sfa~Ay~c~~~vs~~k~ 29 (80)
||++|+.+.+.|-.-+.....||+
T Consensus 120 Ivsav~valvGAvsSyiaYqkKKl 143 (169)
T PF12301_consen 120 IVSAVVVALVGAVSSYIAYQKKKL 143 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcc
Confidence 566666666655544433445553
No 30
>PF02529 PetG: Cytochrome B6-F complex subunit 5; InterPro: IPR003683 This family consists of cytochrome b6/f complex subunit 5 (PetG). The cytochrome bf complex, found in green plants, eukaryotic algae and cyanobacteria, connects photosystem I to photosystem II in the electron transport chain, functioning as a plastoquinol:plastocyanin/cytochrome c6 oxidoreductase []. The purified complex from the unicellular alga Chlamydomonas reinhardtii contains seven subunits; namely four high molecular weight subunits (cytochrome f, Rieske iron-sulphur protein, cytochrome b6, and subunit IV) and three approximately miniproteins (PetG, PetL, and PetX) []. Stoichiometry measurements are consistent with every subunit being present as two copies per b6/f dimer. The absence of PetG affects either the assembly or stability of the cytochrome bf complex in C. reinhardtii [].; GO: 0009512 cytochrome b6f complex; PDB: 1Q90_G 2ZT9_G 1VF5_G 2D2C_G 2E74_G 2E75_G 2E76_G.
Probab=27.81 E-value=61 Score=19.10 Aligned_cols=21 Identities=29% Similarity=0.207 Sum_probs=14.0
Q ss_pred hhhhHHHHHHHHHHHHHHHhccc
Q 047104 6 IVGSLIGSCALAYAFDQIIAEKK 28 (80)
Q Consensus 6 Iv~s~~~sfa~Ay~c~~~vs~~k 28 (80)
|-..++|.|+.|| .||-..++
T Consensus 14 i~vtl~Glfv~Ay--~QY~Rg~q 34 (37)
T PF02529_consen 14 IPVTLAGLFVAAY--LQYRRGNQ 34 (37)
T ss_dssp HHHHHHHHHHHHH--HHHCS--T
T ss_pred HHHHHHHHHHHHH--HHHhcccc
Confidence 4557889999999 66655543
No 31
>KOG1741 consensus Mitochondrial/chloroplast ribosomal protein S14/S29 [Translation, ribosomal structure and biogenesis]
Probab=27.27 E-value=56 Score=22.91 Aligned_cols=28 Identities=29% Similarity=0.486 Sum_probs=22.3
Q ss_pred cCchhhHHHHHHHhhhCCCccCCCeeec
Q 047104 38 VSDKEWWEETDKKFQAWPRVAGPPVVMN 65 (80)
Q Consensus 38 vtnkeW~~aT~~k~qaWPR~agpPVvmN 65 (80)
....+|..+-++|+|+=||...|--+.|
T Consensus 37 ~LP~~~r~ea~~kl~alPrns~ptrI~N 64 (103)
T KOG1741|consen 37 ILPEKLRDEAAEKLQALPRNSAPTRIKN 64 (103)
T ss_pred cccHHHHHHHHHHHhcCccccchHHHHH
Confidence 3456899999999999999988844433
No 32
>COG4733 Phage-related protein, tail component [Function unknown]
Probab=24.58 E-value=38 Score=31.30 Aligned_cols=27 Identities=33% Similarity=0.583 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHhccccccCCCCcccCc
Q 047104 12 GSCALAYAFDQIIAEKKIFGGTTPKTVSD 40 (80)
Q Consensus 12 ~sfa~Ay~c~~~vs~~k~fGGt~P~Tvtn 40 (80)
+-.+|+--||+.|-|+ |||+=|+---|
T Consensus 298 aLY~I~qYCDq~vpdG--fGG~EpR~t~N 324 (952)
T COG4733 298 ALYAIAQYCDQTVPDG--FGGTEPRMTCN 324 (952)
T ss_pred HHHHHHHhhcccCCCC--CCCCCcceEEe
Confidence 5678999999999999 99999985433
No 33
>KOG2822 consensus Sphingoid base-phosphate phosphatase [Lipid transport and metabolism]
Probab=24.19 E-value=39 Score=28.43 Aligned_cols=13 Identities=46% Similarity=0.928 Sum_probs=11.4
Q ss_pred hhhCCCccCCCee
Q 047104 51 FQAWPRVAGPPVV 63 (80)
Q Consensus 51 ~qaWPR~agpPVv 63 (80)
-..|||-.+|||+
T Consensus 133 ~~~lPRP~sPPvv 145 (407)
T KOG2822|consen 133 YWCLPRPSSPPVV 145 (407)
T ss_pred eeecCCCCCCCeE
Confidence 4679999999997
No 34
>PRK11677 hypothetical protein; Provisional
Probab=23.75 E-value=74 Score=22.54 Aligned_cols=26 Identities=12% Similarity=0.049 Sum_probs=17.9
Q ss_pred CccchhhhhHHHHHHHHHHHHHHHhc
Q 047104 1 MATKYIVGSLIGSCALAYAFDQIIAE 26 (80)
Q Consensus 1 m~~kyIv~s~~~sfa~Ay~c~~~vs~ 26 (80)
|.--|++.++++++++.|+...+.+.
T Consensus 1 M~W~~a~i~livG~iiG~~~~R~~~~ 26 (134)
T PRK11677 1 MTWEYALIGLVVGIIIGAVAMRFGNR 26 (134)
T ss_pred CcHHHHHHHHHHHHHHHHHHHhhccc
Confidence 44457778888888888876665443
No 35
>PF06916 DUF1279: Protein of unknown function (DUF1279); InterPro: IPR009688 This entry represents the C terminus (approx. 120 residues) of a number of eukaryotic proteins of unknown function.
Probab=23.70 E-value=62 Score=20.68 Aligned_cols=19 Identities=37% Similarity=0.576 Sum_probs=15.3
Q ss_pred hhhHHHHHHHHHHHHHHHh
Q 047104 7 VGSLIGSCALAYAFDQIIA 25 (80)
Q Consensus 7 v~s~~~sfa~Ay~c~~~vs 25 (80)
..+..+.|++||+|...+.
T Consensus 60 ~~~~~~~~~lAy~~~K~~~ 78 (91)
T PF06916_consen 60 KNSSAGTFALAYAIHKLLE 78 (91)
T ss_pred ccccHHHHHHHHHHHhhhh
Confidence 3567899999999987763
No 36
>PF03947 Ribosomal_L2_C: Ribosomal Proteins L2, C-terminal domain; InterPro: IPR022669 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3MRZ_C 3F1H_D 3PYO_C 3F1F_D 3PYV_C 3PYR_C 1VSA_B 3D5B_D 3PYT_C 3MS1_C ....
Probab=23.65 E-value=31 Score=23.99 Aligned_cols=27 Identities=30% Similarity=0.603 Sum_probs=17.0
Q ss_pred chhhHHHHHHHh-hhCCCccCCCeeecccc
Q 047104 40 DKEWWEETDKKF-QAWPRVAGPPVVMNPIS 68 (80)
Q Consensus 40 nkeW~~aT~~k~-qaWPR~agpPVvmNPis 68 (80)
++-+.+|-..++ --||+.-| |+|||++
T Consensus 79 ~~~~~KAG~~r~~g~rP~VRG--vamNpvd 106 (130)
T PF03947_consen 79 EKKLGKAGRNRWLGKRPKVRG--VAMNPVD 106 (130)
T ss_dssp GSB-SSHHHHHHTCCSSS-SG--TCSTTTT
T ss_pred chhhhhhhhccccccCccccc--eeecccc
Confidence 344556666666 44887765 8999986
No 37
>PF12072 DUF3552: Domain of unknown function (DUF3552); InterPro: IPR022711 This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is about 200 amino acids in length. This domain is found associated with PF00013 from PFAM, PF01966 from PFAM. This domain has a single completely conserved residue A that may be functionally important. ; GO: 0008663 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity
Probab=22.11 E-value=80 Score=22.71 Aligned_cols=21 Identities=19% Similarity=0.284 Sum_probs=10.2
Q ss_pred hhhhHHHHHHHHHHHHHHHhc
Q 047104 6 IVGSLIGSCALAYAFDQIIAE 26 (80)
Q Consensus 6 Iv~s~~~sfa~Ay~c~~~vs~ 26 (80)
++.+++.|++++|+.......
T Consensus 6 ~i~~~~vG~~~G~~~~~~~~~ 26 (201)
T PF12072_consen 6 AIVALIVGIGIGYLVRKKINR 26 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344455555555555444433
No 38
>PF11839 DUF3359: Protein of unknown function (DUF3359); InterPro: IPR021793 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Probab=22.09 E-value=64 Score=22.04 Aligned_cols=19 Identities=16% Similarity=0.155 Sum_probs=16.4
Q ss_pred chhhhhHHHHHHHHHHHHH
Q 047104 4 KYIVGSLIGSCALAYAFDQ 22 (80)
Q Consensus 4 kyIv~s~~~sfa~Ay~c~~ 22 (80)
|.++++++.+++++.+|-.
T Consensus 3 k~l~sal~~~~~L~~GCAs 21 (96)
T PF11839_consen 3 KLLLSALALAALLLAGCAS 21 (96)
T ss_pred hHHHHHHHHHHHHHhHccC
Confidence 5678899999999999975
No 39
>KOG2214 consensus Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]
Probab=21.94 E-value=27 Score=30.37 Aligned_cols=53 Identities=23% Similarity=0.273 Sum_probs=37.8
Q ss_pred hhhhhHHHHHHHHHHHHHHHhccccccCC-CCcccCchhhHHHHHHHhhhCCCccCCCeeec-cccc
Q 047104 5 YIVGSLIGSCALAYAFDQIIAEKKIFGGT-TPKTVSDKEWWEETDKKFQAWPRVAGPPVVMN-PISR 69 (80)
Q Consensus 5 yIv~s~~~sfa~Ay~c~~~vs~~k~fGGt-~P~TvtnkeW~~aT~~k~qaWPR~agpPVvmN-Pisr 69 (80)
.|=+|+.+||++.+++-..-=-.|-.+|. .|..+++ .|||-.-+++..| |++|
T Consensus 317 LIWSAV~aScs~pgif~~~~Ll~Kd~t~ei~p~~~~~------------~~~r~~dgsl~~d~P~sr 371 (543)
T KOG2214|consen 317 LIWSAVCASCSVPGIFESTPLLAKDLTNEIEPFIVTF------------SEPRFMDGSLDNDLPYSR 371 (543)
T ss_pred ehhHHHHHhcccccccCccHHHHhhccCcEeeccCCc------------cchhhccCcccccCcHHH
Confidence 46789999999988764322222226666 8888887 7898888887764 8877
No 40
>PF07179 SseB: SseB protein N-terminal domain; InterPro: IPR009839 This family consists of several SseB proteins, which appear to be found exclusively in Enterobacteria. SseB is known to enhance serine-sensitivity in Escherichia coli [] and is part of the Salmonella pathogenicity island 2 (SPI-2) translocon [].
Probab=21.75 E-value=98 Score=18.98 Aligned_cols=27 Identities=19% Similarity=0.362 Sum_probs=18.8
Q ss_pred HHhhhCCCccCCCeeecccccceeeee
Q 047104 49 KKFQAWPRVAGPPVVMNPISRQNFIVK 75 (80)
Q Consensus 49 ~k~qaWPR~agpPVvmNPisrqnfivk 75 (80)
.-++.++...+--||+||-+..++++-
T Consensus 91 ~l~~~~~~~~~~giviNP~~~~~~~l~ 117 (124)
T PF07179_consen 91 DLLEMLLNNEGDGIVINPGTPSGFVLP 117 (124)
T ss_pred HHHHHhhcCCCcEEEEECCCCceEEEC
Confidence 344666634446899999999778763
No 41
>PRK09993 C-lysozyme inhibitor; Provisional
Probab=21.28 E-value=76 Score=23.43 Aligned_cols=33 Identities=15% Similarity=0.318 Sum_probs=19.9
Q ss_pred hhHHHH-HHHhhhCCCccCCCeeecccc--cceeee
Q 047104 42 EWWEET-DKKFQAWPRVAGPPVVMNPIS--RQNFIV 74 (80)
Q Consensus 42 eW~~aT-~~k~qaWPR~agpPVvmNPis--rqnfiv 74 (80)
.|.+-. .+++-+|=|++|+.-=|+-++ -|.|+|
T Consensus 42 aw~~mvkg~~LP~WV~~gGtssP~~~V~~~G~~YlV 77 (153)
T PRK09993 42 AFNQMVQGHKLPAWVMKGGTYSPAQTVTLGDETYQV 77 (153)
T ss_pred HHHHHHcCCCCcHHHHcCCCCCchhheeeCCceEEE
Confidence 455444 225789999998822166655 555655
No 42
>PF13283 NfrA_C: Bacteriophage N adsorption protein A C-term
Probab=20.69 E-value=51 Score=24.42 Aligned_cols=16 Identities=31% Similarity=0.461 Sum_probs=13.4
Q ss_pred Ceeecccccceeeeec
Q 047104 61 PVVMNPISRQNFIVKS 76 (80)
Q Consensus 61 PVvmNPisrqnfivk~ 76 (80)
-|---|++.||++++-
T Consensus 17 G~R~KPf~~~nl~l~~ 32 (176)
T PF13283_consen 17 GVRWKPFSDQNLFLAA 32 (176)
T ss_pred eeEeccccceeEEEEE
Confidence 5667799999999975
No 43
>PF09158 MotCF: Bacteriophage T4 MotA, C-terminal; InterPro: IPR015241 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the C-terminal domain of MotA factors, which adopts a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. It contains a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [].; PDB: 1KAF_B.
Probab=20.67 E-value=47 Score=23.14 Aligned_cols=9 Identities=33% Similarity=0.792 Sum_probs=7.1
Q ss_pred cccceeeee
Q 047104 67 ISRQNFIVK 75 (80)
Q Consensus 67 isrqnfivk 75 (80)
+.||||+|+
T Consensus 27 ~~RSN~~i~ 35 (103)
T PF09158_consen 27 IDRSNYEIR 35 (103)
T ss_dssp EETTEEEEE
T ss_pred eeccceEEe
Confidence 359999986
No 44
>PRK03854 opgC glucans biosynthesis protein; Provisional
Probab=20.39 E-value=80 Score=23.84 Aligned_cols=27 Identities=26% Similarity=0.450 Sum_probs=18.3
Q ss_pred hHHHHHHHHHHHHHHHh----ccccccCCCC
Q 047104 9 SLIGSCALAYAFDQIIA----EKKIFGGTTP 35 (80)
Q Consensus 9 s~~~sfa~Ay~c~~~vs----~~k~fGGt~P 35 (80)
.+++++++|++.+.++. -+.+|||..|
T Consensus 345 ~~~~~~~~s~~~y~l~rr~~~lr~lf~g~~~ 375 (375)
T PRK03854 345 GLVFVFGIAFALYEIHLRIPLLRFLFSGKPP 375 (375)
T ss_pred HHHHHHHHHHHHHHHHhccHHHHHHHcCCCC
Confidence 45567777777777554 4678898754
No 45
>cd01169 HMPP_kinase 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of the hydroxyl group of HMP to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate (HMP-P) and then the phophorylation of HMP-P to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine pyrophosphate (HMP-PP), which is the substrate for the thiamine synthase coupling reaction.
Probab=20.36 E-value=1.4e+02 Score=20.56 Aligned_cols=40 Identities=18% Similarity=0.306 Sum_probs=26.8
Q ss_pred ccccCCCCcccCchhhHHHHHHHhhhCCCccCCCeeecccccc
Q 047104 28 KIFGGTTPKTVSDKEWWEETDKKFQAWPRVAGPPVVMNPISRQ 70 (80)
Q Consensus 28 k~fGGt~P~TvtnkeW~~aT~~k~qaWPR~agpPVvmNPisrq 70 (80)
.-|-.-....+.+++.-+.-.+.+...| +.||++||..|.
T Consensus 67 ~~~~~i~~G~l~~~~~~~~i~~~~~~~~---~~~vv~Dpv~~~ 106 (242)
T cd01169 67 IPVDAIKIGMLGSAEIIEAVAEALKDYP---DIPVVLDPVMVA 106 (242)
T ss_pred CCCCEEEECCCCCHHHHHHHHHHHHhCC---CCcEEECCceeC
Confidence 3455555567777777777766665442 469999998653
Done!