Query 029522
Match_columns 192
No_of_seqs 136 out of 214
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 14:15:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029522.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029522hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03763 Remorin_C: Remorin, C 100.0 2.1E-29 4.6E-34 196.2 13.8 101 77-187 11-111 (111)
2 PF03766 Remorin_N: Remorin, N 99.2 7.3E-12 1.6E-16 88.5 3.8 52 35-90 5-57 (57)
3 PF03763 Remorin_C: Remorin, C 97.9 0.00016 3.5E-09 56.7 9.7 20 92-111 2-21 (111)
4 PRK09174 F0F1 ATP synthase sub 70.2 69 0.0015 27.4 13.9 53 113-165 98-150 (204)
5 PRK14471 F0F1 ATP synthase sub 58.7 88 0.0019 25.1 8.3 6 102-107 48-53 (164)
6 PRK13454 F0F1 ATP synthase sub 57.3 1.1E+02 0.0024 25.3 12.5 35 116-150 79-113 (181)
7 cd03404 Band_7_HflK Band_7_Hfl 54.7 1.1E+02 0.0024 26.1 8.7 52 127-178 190-241 (266)
8 KOG4661 Hsp27-ERE-TATA-binding 53.5 77 0.0017 32.5 8.5 61 100-162 641-708 (940)
9 PRK14474 F0F1 ATP synthase sub 51.9 1.7E+02 0.0036 25.7 9.6 27 100-126 43-70 (250)
10 PRK13453 F0F1 ATP synthase sub 51.5 1.3E+02 0.0029 24.5 9.6 10 117-126 74-83 (173)
11 TIGR01933 hflK HflK protein. H 50.6 1.6E+02 0.0034 25.1 9.8 63 113-177 151-213 (261)
12 PRK14473 F0F1 ATP synthase sub 48.2 1.4E+02 0.0031 23.9 8.3 10 101-110 47-56 (164)
13 PF10211 Ax_dynein_light: Axon 43.0 2E+02 0.0044 24.2 14.7 97 79-177 78-183 (189)
14 PF12856 Apc9: Anaphase-promot 42.3 21 0.00045 27.9 2.2 15 94-108 44-58 (100)
15 PF12925 APP_E2: E2 domain of 41.6 2.4E+02 0.0051 24.5 9.2 72 85-166 33-105 (193)
16 PF10376 Mei5: Double-strand r 40.3 2.5E+02 0.0055 24.5 9.5 51 113-163 138-188 (221)
17 PRK13455 F0F1 ATP synthase sub 39.6 2.1E+02 0.0046 23.4 12.5 43 114-156 73-115 (184)
18 PRK13428 F0F1 ATP synthase sub 38.2 3E+02 0.0066 26.1 9.6 70 112-181 31-103 (445)
19 CHL00019 atpF ATP synthase CF0 36.3 2.4E+02 0.0052 23.1 9.6 70 112-181 54-126 (184)
20 TIGR03321 alt_F1F0_F0_B altern 34.4 3E+02 0.0066 23.7 10.5 68 112-179 35-105 (246)
21 KOG2412 Nuclear-export-signal 33.6 5.2E+02 0.011 26.2 11.3 25 141-165 250-274 (591)
22 KOG0163 Myosin class VI heavy 31.4 7E+02 0.015 26.9 11.8 14 112-125 952-965 (1259)
23 PF04888 SseC: Secretion syste 29.9 1.1E+02 0.0023 26.9 4.9 61 121-189 4-64 (306)
24 KOG4055 Uncharacterized conser 29.8 3.2E+02 0.0069 24.2 7.6 29 137-165 109-137 (213)
25 PRK13665 hypothetical protein; 29.5 1.4E+02 0.003 27.8 5.7 27 112-138 233-259 (316)
26 PRK14475 F0F1 ATP synthase sub 29.5 3.1E+02 0.0066 22.2 12.5 11 116-126 65-75 (167)
27 PF12127 YdfA_immunity: SigmaW 29.3 1.3E+02 0.0029 28.0 5.5 27 112-138 228-254 (316)
28 KOG3654 Uncharacterized CH dom 25.7 2.1E+02 0.0046 28.9 6.5 33 119-162 406-440 (708)
29 PF00430 ATP-synt_B: ATP synth 25.5 2.9E+02 0.0062 20.6 9.3 35 120-154 51-85 (132)
30 PRK10930 FtsH protease regulat 23.2 5.4E+02 0.012 24.5 8.6 56 121-176 253-308 (419)
31 CHL00118 atpG ATP synthase CF0 23.0 3.9E+02 0.0086 21.3 12.4 40 117-156 71-110 (156)
32 PF11875 DUF3395: Domain of un 22.8 4.2E+02 0.0091 21.5 7.1 34 132-165 14-47 (151)
33 PRK02463 OxaA-like protein pre 22.5 1.1E+02 0.0024 27.9 3.8 23 169-191 120-142 (307)
34 KOG4001 Axonemal dynein light 22.4 5.8E+02 0.013 23.0 9.8 88 83-175 147-246 (259)
35 PF07291 MauE: Methylamine uti 22.4 49 0.0011 27.8 1.3 14 178-192 97-110 (184)
36 KOG1103 Predicted coiled-coil 22.3 7.5E+02 0.016 24.2 10.4 43 112-154 159-211 (561)
37 KOG0996 Structural maintenance 22.2 1.1E+03 0.024 26.2 13.2 62 120-185 556-618 (1293)
38 PRK11029 FtsH protease regulat 20.6 4.4E+02 0.0095 24.3 7.2 21 145-165 262-282 (334)
39 COG4582 Uncharacterized protei 20.6 1.6E+02 0.0035 26.4 4.2 31 160-191 102-132 (244)
No 1
>PF03763 Remorin_C: Remorin, C-terminal region ; InterPro: IPR005516 Remorin binds both simple and complex galaturonides. The N-terminal region of remorin is proline rich, while the C-terminal region has been predicted to form a coiled-coil, that is expected to interact with other macromolecules, most likely DNA. Functional similarities between the behavior of the proteins and viral proteins involved in intercellular communication have been noted [].
Probab=99.96 E-value=2.1e-29 Score=196.20 Aligned_cols=101 Identities=54% Similarity=0.724 Sum_probs=88.2
Q ss_pred CCCchhhHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029522 77 TEGSVNRDAVLARVETEKRISLIRAWEESEKSQAENNRKAAVEAELKKIEEQLEKKKAEYVEKMKNKMALIHKEAEEKRA 156 (192)
Q Consensus 77 ~~gs~~rd~~lakve~Ekr~akI~AWEeaEKaKa~n~kKAKAEA~mrKiE~KLEkkRA~a~EKm~nKiA~a~kkAEekRA 156 (192)
.|.-.+...+..||+++. ++|.+|| |+||++++++|+++|++||++|++++|+|+|+|+.||++|+++|+
T Consensus 11 aWe~ae~aK~~~r~~ree--~~I~aWE--------n~qkaKaea~m~k~E~klEkkra~a~ek~~nkia~~~~~Aee~Ra 80 (111)
T PF03763_consen 11 AWEEAEKAKINNRYEREE--AKIQAWE--------NLQKAKAEAEMRKIEEKLEKKRAKALEKMKNKIARAHKKAEEKRA 80 (111)
T ss_pred HHHHHHHHHHHHHHHHHH--hHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444555666666555 7777777 788899999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhHHHHHHHHHHHHhcCCCCCCCc
Q 029522 157 MIEAKRGEDLLKAEELAAKYRATGSAPKKLL 187 (192)
Q Consensus 157 ~aEAkr~ee~~Ka~EkA~kiRaTGk~P~k~~ 187 (192)
+++++|+++++++.++|++||+||++|++||
T Consensus 81 ~aea~r~~~~~k~~ekA~~~R~tG~~P~~~f 111 (111)
T PF03763_consen 81 AAEARRGEEIAKAEEKAAKIRATGKVPSKCF 111 (111)
T ss_pred HHHHHHhhHHHhHHHHHHHHHhCCCCCcccC
Confidence 9999999999999999999999999997743
No 2
>PF03766 Remorin_N: Remorin, N-terminal region ; InterPro: IPR005518 Remorin binds both simple and complex galaturonides. The N-terminal region of remorin is proline rich, while the C-terminal region has been predicted to form a coiled-coil, that is expected to interact with other macromolecules, most likely DNA. Functional similarities between the behavior of the proteins and viral proteins involved in intercellular communication have been noted [].
Probab=99.23 E-value=7.3e-12 Score=88.48 Aligned_cols=52 Identities=67% Similarity=1.069 Sum_probs=44.6
Q ss_pred CCccccCCCCCCCCCCCCCccccceeeecCC-CCCCCCCCCCCCCCchhhHHHHHHH
Q 029522 35 KDVADDKTVIPSPPAEDKPEESKALAVVDKA-PEAEPPAGEKSTEGSVNRDAVLARV 90 (192)
Q Consensus 35 ~~~~~e~~~~p~p~~~~~~~~skal~~v~~~-~~~~~~~~~~~~~gs~~rd~~lakv 90 (192)
+|++++++++|||. +.+.||||||+||++. ++ +..+++++||+|||.+|++|
T Consensus 5 ~dva~ek~~~PpP~-~~k~ddSKAl~vVek~~~e---pa~eK~s~GS~dRDa~LA~v 57 (57)
T PF03766_consen 5 KDVAEEKSVIPPPA-EEKPDDSKALVVVEKKVPE---PAEEKPSEGSIDRDAALARV 57 (57)
T ss_pred hhhccccCCCCCCC-CCCCCccceEEEeeccCCC---ccccccCCCcchhhhhhhcC
Confidence 78999999988776 6778999999999985 45 46678889999999999985
No 3
>PF03763 Remorin_C: Remorin, C-terminal region ; InterPro: IPR005516 Remorin binds both simple and complex galaturonides. The N-terminal region of remorin is proline rich, while the C-terminal region has been predicted to form a coiled-coil, that is expected to interact with other macromolecules, most likely DNA. Functional similarities between the behavior of the proteins and viral proteins involved in intercellular communication have been noted [].
Probab=97.86 E-value=0.00016 Score=56.69 Aligned_cols=20 Identities=35% Similarity=0.542 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHhhHH
Q 029522 92 TEKRISLIRAWEESEKSQAE 111 (192)
Q Consensus 92 ~Ekr~akI~AWEeaEKaKa~ 111 (192)
.++++++|.+||+++++|+.
T Consensus 2 ~~~~~a~a~aWe~ae~aK~~ 21 (111)
T PF03763_consen 2 KEEVEAKADAWEEAEKAKIN 21 (111)
T ss_pred cHHHHhHHHHHHHHHHHHHH
Confidence 35678999999999999996
No 4
>PRK09174 F0F1 ATP synthase subunit B'; Validated
Probab=70.23 E-value=69 Score=27.37 Aligned_cols=53 Identities=23% Similarity=0.248 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029522 113 NRKAAVEAELKKIEEQLEKKKAEYVEKMKNKMALIHKEAEEKRAMIEAKRGED 165 (192)
Q Consensus 113 ~kKAKAEA~mrKiE~KLEkkRA~a~EKm~nKiA~a~kkAEekRA~aEAkr~ee 165 (192)
..+..++..+...|.+|..-|.++.+-+.+-...++...+..+..+++.-...
T Consensus 98 ~~k~eAe~~~~~ye~~L~~Ar~eA~~Ii~~Ar~ea~~~~e~~~~~a~~ea~~~ 150 (204)
T PRK09174 98 RLKQEADAAVAAYEQELAQARAKAHSIAQAAREAAKAKAEAERAAIEASLEKK 150 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666666666666666666666666555555555555555444443333
No 5
>PRK14471 F0F1 ATP synthase subunit B; Provisional
Probab=58.68 E-value=88 Score=25.07 Aligned_cols=6 Identities=17% Similarity=0.302 Sum_probs=2.4
Q ss_pred HHHHHH
Q 029522 102 WEESEK 107 (192)
Q Consensus 102 WEeaEK 107 (192)
.+++++
T Consensus 48 l~~A~~ 53 (164)
T PRK14471 48 LASAEE 53 (164)
T ss_pred HHHHHH
Confidence 344433
No 6
>PRK13454 F0F1 ATP synthase subunit B'; Provisional
Probab=57.29 E-value=1.1e+02 Score=25.32 Aligned_cols=35 Identities=20% Similarity=0.142 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029522 116 AAVEAELKKIEEQLEKKKAEYVEKMKNKMALIHKE 150 (192)
Q Consensus 116 AKAEA~mrKiE~KLEkkRA~a~EKm~nKiA~a~kk 150 (192)
..++..+..+|.+|.+-|.++.+-+.+-...+.+.
T Consensus 79 ~eA~~~~~eye~~L~~Ar~EA~~ii~~A~~ea~~~ 113 (181)
T PRK13454 79 QKAVEAEKAYNKALADARAEAQRIVAETRAEIQAE 113 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444444444433333333
No 7
>cd03404 Band_7_HflK Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma membranes lack cholesterol and are unlikely to have lipid raft domains. Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Escherichia coli HflK is an integral membrane protein which may localize to the plasma membrane. HflK associates with another band 7 family member (HflC) to form an HflKC complex. HflKC interacts with FtsH in a large complex termed the FtsH holo-enzyme. FtsH is an AAA ATP-dependent protease which exerts progressive proteolysis against membrane-embedded and soluble substrate proteins. HflKC can modulate the activity of FtsH. HflKC plays a role in the decision between lysogenic and lytic cycle growth during la
Probab=54.73 E-value=1.1e+02 Score=26.06 Aligned_cols=52 Identities=19% Similarity=0.132 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHh
Q 029522 127 EQLEKKKAEYVEKMKNKMALIHKEAEEKRAMIEAKRGEDLLKAEELAAKYRA 178 (192)
Q Consensus 127 ~KLEkkRA~a~EKm~nKiA~a~kkAEekRA~aEAkr~ee~~Ka~EkA~kiRa 178 (192)
.+.++.++++...-...+..++..|+..+..+++.+....++++-.|..|+.
T Consensus 190 q~~~~~~~eae~~a~~~~~~A~~ea~~~~~~A~a~~~~~~~~ae~~a~~~~~ 241 (266)
T cd03404 190 QDRERLINEAEAYANEVVPKARGEAARIIQEAEAYKEEVIAEAQGEAARFES 241 (266)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 3345666666444444668888888899999999999999888888877664
No 8
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=53.46 E-value=77 Score=32.51 Aligned_cols=61 Identities=30% Similarity=0.438 Sum_probs=36.6
Q ss_pred HHHHHHHHhhHH------HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 029522 100 RAWEESEKSQAE------NNRKAAVEAELKKIE-EQLEKKKAEYVEKMKNKMALIHKEAEEKRAMIEAKR 162 (192)
Q Consensus 100 ~AWEeaEKaKa~------n~kKAKAEA~mrKiE-~KLEkkRA~a~EKm~nKiA~a~kkAEekRA~aEAkr 162 (192)
.+||..++..+. ..|..++|.+ +|| +.||+.|.+.++.-...-.+||+.-++-|-+-+.-+
T Consensus 641 a~~ERee~eRl~~erlrle~qRQrLERE--rmErERLEreRM~ve~eRr~eqeRihreReelRrqqetlr 708 (940)
T KOG4661|consen 641 AAVEREELERLKAERLRLERQRQRLERE--RMERERLERERMKVEEERRDEQERIHREREELRRQQETLR 708 (940)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHhhccceee
Confidence 567766655442 2222222222 222 467788888888878888888888777766555433
No 9
>PRK14474 F0F1 ATP synthase subunit B; Provisional
Probab=51.88 E-value=1.7e+02 Score=25.70 Aligned_cols=27 Identities=19% Similarity=0.465 Sum_probs=12.1
Q ss_pred HHHHHHHHhhHH-HHHHHHHHHHHHHHH
Q 029522 100 RAWEESEKSQAE-NNRKAAVEAELKKIE 126 (192)
Q Consensus 100 ~AWEeaEKaKa~-n~kKAKAEA~mrKiE 126 (192)
..+++++..+.. +......+.+|...+
T Consensus 43 ~~l~~Ae~~~~eA~~~~~e~e~~l~~a~ 70 (250)
T PRK14474 43 NRWQDAEQRQQEAGQEAERYRQKQQSLE 70 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555554443 333333444444443
No 10
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=51.54 E-value=1.3e+02 Score=24.51 Aligned_cols=10 Identities=20% Similarity=0.318 Sum_probs=3.9
Q ss_pred HHHHHHHHHH
Q 029522 117 AVEAELKKIE 126 (192)
Q Consensus 117 KAEA~mrKiE 126 (192)
..+.+|....
T Consensus 74 e~e~~l~~a~ 83 (173)
T PRK13453 74 ENKQKLKETQ 83 (173)
T ss_pred HHHHHHHHHH
Confidence 3333443333
No 11
>TIGR01933 hflK HflK protein. HflK and HflC are paralogs encoded by tandem genes in Proteobacteria, spirochetes, and some other bacterial lineages. The HflKC complex is anchored in the membrane and exposed to the periplasm. The complex is not active as a protease, but rather binds to and appears to modulate the ATP-dependent protease FtsH. The overall function of HflKC is not fully described.//Regulation of FtsH by HflKC appears to be negative (PubMed:8947034,PubMed:96367)
Probab=50.61 E-value=1.6e+02 Score=25.08 Aligned_cols=63 Identities=11% Similarity=0.088 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Q 029522 113 NRKAAVEAELKKIEEQLEKKKAEYVEKMKNKMALIHKEAEEKRAMIEAKRGEDLLKAEELAAKYR 177 (192)
Q Consensus 113 ~kKAKAEA~mrKiE~KLEkkRA~a~EKm~nKiA~a~kkAEekRA~aEAkr~ee~~Ka~EkA~kiR 177 (192)
.+++ .+..+.- +...++.++++...-...+..+...|+..+..+++.+..+..+++=.|..++
T Consensus 151 v~~a-~~~~~~a-~q~~~~~~~~ae~~~~~~~~~a~~~a~~~~~~Aea~~~~~~~~a~g~a~~~~ 213 (261)
T TIGR01933 151 VKEA-FDDVIIA-REDEERYINEAEAYANEVVPKARGDAQRIIEEARGYKERRINRAKGDVARFT 213 (261)
T ss_pred HHHH-HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHH
Confidence 3333 4555443 3334677777765555556777777887777777777777777655555543
No 12
>PRK14473 F0F1 ATP synthase subunit B; Provisional
Probab=48.19 E-value=1.4e+02 Score=23.86 Aligned_cols=10 Identities=20% Similarity=0.398 Sum_probs=4.6
Q ss_pred HHHHHHHhhH
Q 029522 101 AWEESEKSQA 110 (192)
Q Consensus 101 AWEeaEKaKa 110 (192)
..++++..+.
T Consensus 47 ~l~~Ae~~~~ 56 (164)
T PRK14473 47 SLRDAEKVRE 56 (164)
T ss_pred HHHHHHHHHH
Confidence 4455544433
No 13
>PF10211 Ax_dynein_light: Axonemal dynein light chain; InterPro: IPR019347 Axonemal dynein light chain proteins play a dynamic role in flagellar and cilial motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains [].
Probab=43.04 E-value=2e+02 Score=24.17 Aligned_cols=97 Identities=25% Similarity=0.322 Sum_probs=59.3
Q ss_pred CchhhHHHHHHHHHHHHHHHHHHHHHHHHhhHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029522 79 GSVNRDAVLARVETEKRISLIRAWEESEKSQAE---------NNRKAAVEAELKKIEEQLEKKKAEYVEKMKNKMALIHK 149 (192)
Q Consensus 79 gs~~rd~~lakve~Ekr~akI~AWEeaEKaKa~---------n~kKAKAEA~mrKiE~KLEkkRA~a~EKm~nKiA~a~k 149 (192)
.-.+|+..|.+|..+= ...|.+...--.+-+. +..+...+.++..++.+++....+ +..+.+++..+++
T Consensus 78 ~C~ERGlLL~rvrde~-~~~l~~y~~l~~s~~~f~~rk~l~~e~~~~~l~~~i~~L~~e~~~L~~~-~~~l~~~~e~~ek 155 (189)
T PF10211_consen 78 DCPERGLLLLRVRDEY-RMTLDAYQTLYESSIAFGMRKALQAEQGKQELEEEIEELEEEKEELEKQ-VQELKNKCEQLEK 155 (189)
T ss_pred CcHHHhHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Confidence 3456899999997654 3456665543332222 122344455555555555544433 3456788888899
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHH
Q 029522 150 EAEEKRAMIEAKRGEDLLKAEELAAKYR 177 (192)
Q Consensus 150 kAEekRA~aEAkr~ee~~Ka~EkA~kiR 177 (192)
..++.+...+.++.+++......-..++
T Consensus 156 ~~~e~~~~~~k~~~~ei~~lk~~~~ql~ 183 (189)
T PF10211_consen 156 REEELRQEEEKKHQEEIDFLKKQNQQLK 183 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8888888888888877765555444443
No 14
>PF12856 Apc9: Anaphase-promoting complex subunit 9; InterPro: IPR024274 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. All APC subunits are members of the cullin family proteins, which bind to a ring-finger subunit via a conserved cullin domain [].The APC can be divided in four parts, the third of which is a tetratricopeptide repeat arm (TPR) that contains multiple subunits, including Apc9 []. This entry represents Apc9, one of the subunits of the anaphase-promoting complex.
Probab=42.26 E-value=21 Score=27.94 Aligned_cols=15 Identities=47% Similarity=0.674 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHh
Q 029522 94 KRISLIRAWEESEKS 108 (192)
Q Consensus 94 kr~akI~AWEeaEKa 108 (192)
-++++|.+|+.+|++
T Consensus 44 l~eSkI~~~l~sEra 58 (100)
T PF12856_consen 44 LRESKIKAWLSSERA 58 (100)
T ss_pred HHHHHHHHHHHHHHH
Confidence 456999999999885
No 15
>PF12925 APP_E2: E2 domain of amyloid precursor protein; InterPro: IPR024329 Amyloid-beta precursor protein (APP, or A4) is associated with Alzheimer's disease (AD), because one of its breakdown products, amyloid-beta (A-beta), aggregates to form amyloid or senile plaques [, ]. Mutations in APP or in proteins that process APP have been linked with early-onset, familial AD. Individuals with Down's syndrome carry an extra copy of chromosome 21, which contains the APP gene, and almost invariably develop amyloid plaques and Alzheimer's symptoms. APP is important for the neurogenesis and neuronal regeneration, either through the intact protein, or through its many breakdown products []. APP consists of a large N-terminal extracellular region containing heparin-binding and copper-binding sites, a short hydrophobic transmembrane domain, and a short C-terminal intracellular domain. The N-terminal region is similar in structure to cysteine-rich growth factors and appears to function as a cell surface receptor, contributing to neurite growth, neuronal adhesion, axonogenesis and cell mobility []. APP acts as a kinesin I membrane receptor to mediate the axonal transport of beta-secretase and presenilin 1. The N-terminal domain can regulate neurite outgrowth through its binding to heparin and collagen I and IV, which are components of the extracellular matrix. APP is also coupled to apoptosis-inducing pathways, and is involved in copper homeostasis/oxidative stress through copper ion reduction, where copper-metallated APP induces neuronal death []. The C-terminal intracellular domain appears to be involved in transcription regulation through protein-protein interactions. APP can promote transcription activation through binding to APBB1/Tip60, and may bind to the adaptor protein FE65 to transactivate a wide variety of different promoters. APP can be processed by different sets of enzymes: In the non-amyloidogenic (non-plaque-forming) pathway, APP is cleaved by alpha-secretase to yield a soluble N-terminal sAPP-alpha (neuroprotective) and a membrane-bound CTF-alpha. CTF-alpha is broken-down by presenilin-containing gamma-secretase to yield soluble p3 and membrane-bound AICD (nuclear signalling). In the amyloidogenic pathway (plaque-forming), APP is broken down by beta-secretase to yield soluble sAPP-beta and membrane-bound CTF-beta. CTF-beta is broken down by gamma-secretase to yield soluble amyloid-beta and membrane-bound AICD. Amyloid-beta is required for neuronal function, but can aggregate to form amyloid plaques that seem to disrupt brain cells by clogging points of cell-cell contact. The E2 domain is the largest of the conserved domains in the amyloidogenic glycoproteins. The structure of E2 consists of two coiled-coil sub-structures connected through a continuous helix, and bears an unexpected resemblance to the spectrin family of protein structures. E2 can reversibly dimerise in solution, and the dimerisation occurs along the longest dimension of the molecule in an antiparallel orientation, which enables the N-terminal substructure of one monomer to pack against the C-terminal substructure of a second monomer. The high degree of conservation of residues at the putative dimer interface suggests that the E2 dimer observed in the crystal could be physiologically relevant. Heparin sulphate proteoglycans, the putative ligands for the precursor present in extracellular matrix, bind to E2 at a conserved and positively charged site near the dimer interface [].; PDB: 3K6B_A 3K66_A 1TKN_A 3NYL_A 3NYJ_A 3UMH_A 3UMK_A 3UMI_A 3QMK_B 3PMR_B ....
Probab=41.55 E-value=2.4e+02 Score=24.53 Aligned_cols=72 Identities=19% Similarity=0.383 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 029522 85 AVLARVETEKRISLIRAWEESEKSQAENNRKAAVEAELKKIE-EQLEKKKAEYVEKMKNKMALIHKEAEEKRAMIEAKRG 163 (192)
Q Consensus 85 ~~lakve~Ekr~akI~AWEeaEKaKa~n~kKAKAEA~mrKiE-~KLEkkRA~a~EKm~nKiA~a~kkAEekRA~aEAkr~ 163 (192)
..|...-++++.-.++-|+++|.. + ..|++.+ .+.|.++....++|+..+..+...+..-|-+.++-+.
T Consensus 33 ~rLe~~hr~r~~~VmkeW~eaE~~-~---------~~l~~~DPk~Ae~~k~~m~~rFQ~~v~aLE~e~~~er~qL~~~H~ 102 (193)
T PF12925_consen 33 ERLEEKHRERMTKVMKEWSEAEER-Y---------KELPKADPKKAEQFKKEMTQRFQKTVQALEQEAAAERQQLVETHQ 102 (193)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHT-T---------TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-H---------HhchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455688888889999998752 2 1345554 7888999999999999999999998888877777665
Q ss_pred hhH
Q 029522 164 EDL 166 (192)
Q Consensus 164 ee~ 166 (192)
+.+
T Consensus 103 qRV 105 (193)
T PF12925_consen 103 QRV 105 (193)
T ss_dssp HHH
T ss_pred HHH
Confidence 554
No 16
>PF10376 Mei5: Double-strand recombination repair protein ; InterPro: IPR018468 Mei5 is one of a pair of meiosis-specific proteins which facilitate the loading of Dmc1 on to Rad51 on DNA at double-strand breaks during recombination. Recombination is carried out by a large protein complex based around the two RecA homologues, Rad51 and Dmc1 []. This complex may play both a catalytic and a structural role in the interaction between homologous chromosomes during meiosis. Mei5 is seen to contain a coiled-coli region.
Probab=40.30 E-value=2.5e+02 Score=24.53 Aligned_cols=51 Identities=18% Similarity=0.179 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 029522 113 NRKAAVEAELKKIEEQLEKKKAEYVEKMKNKMALIHKEAEEKRAMIEAKRG 163 (192)
Q Consensus 113 ~kKAKAEA~mrKiE~KLEkkRA~a~EKm~nKiA~a~kkAEekRA~aEAkr~ 163 (192)
..|.+++.+++..++.|.+...--+.+++|.+..++..-.+||...+..-.
T Consensus 138 ~ek~kL~~q~~e~~e~lr~L~~~k~~r~Kn~~~~Lq~lI~Kwr~~~q~~l~ 188 (221)
T PF10376_consen 138 EEKRKLEKQVDEKEEELRRLKLVKQYRSKNDLEQLQSLIKKWRSASQEALY 188 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHhhccHHHHHHHHHHHHHHHHHHHH
Confidence 356677899999999999999999999999999999999999977665433
No 17
>PRK13455 F0F1 ATP synthase subunit B; Provisional
Probab=39.64 E-value=2.1e+02 Score=23.41 Aligned_cols=43 Identities=12% Similarity=0.093 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029522 114 RKAAVEAELKKIEEQLEKKKAEYVEKMKNKMALIHKEAEEKRA 156 (192)
Q Consensus 114 kKAKAEA~mrKiE~KLEkkRA~a~EKm~nKiA~a~kkAEekRA 156 (192)
.+..++..+...+.+|..-|.++.+-+.+-...++...++.+.
T Consensus 73 ~~~eA~~~l~e~e~~L~~A~~ea~~Ii~~A~~~a~~~~e~~~~ 115 (184)
T PRK13455 73 LREEAQTLLASYERKQREVQEQADRIVAAAKDEAQAAAEQAKA 115 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555555555555544444444334433333333
No 18
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=38.16 E-value=3e+02 Score=26.11 Aligned_cols=70 Identities=17% Similarity=0.213 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCC
Q 029522 112 NNRKAAVEAELKKIE---EQLEKKKAEYVEKMKNKMALIHKEAEEKRAMIEAKRGEDLLKAEELAAKYRATGS 181 (192)
Q Consensus 112 n~kKAKAEA~mrKiE---~KLEkkRA~a~EKm~nKiA~a~kkAEekRA~aEAkr~ee~~Ka~EkA~kiRaTGk 181 (192)
+..+.++...|...+ .+++..++.|.+.+.+--..++.+-++.+..++..+.+-...+.+.++.|...++
T Consensus 31 ~~R~~~I~~~L~eAe~a~~ea~~~~~~~e~~L~~Ak~ea~~Ii~~A~~~A~~~~~~~~~~A~~ea~~i~~~a~ 103 (445)
T PRK13428 31 AARQDTVRQQLAESATAADRLAEADQAHTKAVEDAKAEAARVVEEAREDAERIAEQLRAQADAEAERIKVQGA 103 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 19
>CHL00019 atpF ATP synthase CF0 B subunit
Probab=36.33 E-value=2.4e+02 Score=23.12 Aligned_cols=70 Identities=14% Similarity=0.141 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCC
Q 029522 112 NNRKAAVEAELKKIE---EQLEKKKAEYVEKMKNKMALIHKEAEEKRAMIEAKRGEDLLKAEELAAKYRATGS 181 (192)
Q Consensus 112 n~kKAKAEA~mrKiE---~KLEkkRA~a~EKm~nKiA~a~kkAEekRA~aEAkr~ee~~Ka~EkA~kiRaTGk 181 (192)
+..+..+...|...+ .+.+...+.|.+++.+-=..++.+-++.+..++..+.+-...+...+..++...+
T Consensus 54 ~~R~~~I~~~l~~Ae~~~~eA~~~~~e~e~~L~~A~~ea~~ii~~A~~~ae~~~~~il~~A~~ea~~~~~~a~ 126 (184)
T CHL00019 54 DNRKQTILNTIRNSEERREEAIEKLEKARARLRQAELEADEIRVNGYSEIEREKENLINQAKEDLERLENYKN 126 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 20
>TIGR03321 alt_F1F0_F0_B alternate F1F0 ATPase, F0 subunit B. CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase.
Probab=34.41 E-value=3e+02 Score=23.67 Aligned_cols=68 Identities=22% Similarity=0.243 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhc
Q 029522 112 NNRKAAVEAELKKIE---EQLEKKKAEYVEKMKNKMALIHKEAEEKRAMIEAKRGEDLLKAEELAAKYRAT 179 (192)
Q Consensus 112 n~kKAKAEA~mrKiE---~KLEkkRA~a~EKm~nKiA~a~kkAEekRA~aEAkr~ee~~Ka~EkA~kiRaT 179 (192)
...+..+...|...+ .+.+..+..|.+++.+--..++.+-++.+..++..+.+-...+.+.+..++..
T Consensus 35 ~~R~~~I~~~l~~Ae~~~~eA~~~~~e~e~~l~~a~~ea~~i~~~A~~eA~~~~~~i~~~A~~ea~~~~~~ 105 (246)
T TIGR03321 35 DAREKKIAGELADADTKKREAEQERREYEEKNEELDQQREVLLTKAKEEAQAERQRLLDEAREEADEIREK 105 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 21
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=33.63 E-value=5.2e+02 Score=26.19 Aligned_cols=25 Identities=20% Similarity=0.318 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhh
Q 029522 141 KNKMALIHKEAEEKRAMIEAKRGED 165 (192)
Q Consensus 141 ~nKiA~a~kkAEekRA~aEAkr~ee 165 (192)
+.+|..+..++++.|..++.++..+
T Consensus 250 qekiR~~eekqeee~ke~e~~~~k~ 274 (591)
T KOG2412|consen 250 QEKIRAEEEKQEEERKEAEEQAEKE 274 (591)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555566666666666666555443
No 22
>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]
Probab=31.39 E-value=7e+02 Score=26.94 Aligned_cols=14 Identities=29% Similarity=0.434 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHHHH
Q 029522 112 NNRKAAVEAELKKI 125 (192)
Q Consensus 112 n~kKAKAEA~mrKi 125 (192)
..+.+++|.++++.
T Consensus 952 e~k~~k~e~e~kRK 965 (1259)
T KOG0163|consen 952 EKKRAKAEMETKRK 965 (1259)
T ss_pred HHHHHHHHHHHHHH
Confidence 34444555554443
No 23
>PF04888 SseC: Secretion system effector C (SseC) like family ; InterPro: IPR006972 SseC is a secreted protein that forms a complex together with SecB and SecD on the surface of Salmonella typhimurium. All these proteins are secreted by the type III secretion system []. Many mucosal pathogens use type III secretion systems for the injection of effector proteins into target cells. SecB, SseC and SecD are inserted into the target cell membrane. where they form a small pore or translocon [, ]. In addition to SseC, this family includes the bacterial secreted proteins PopB, PepB, YopB and EspD which are thought to be directly involved in pore formation, and type III secretion system translocon.; GO: 0009405 pathogenesis
Probab=29.89 E-value=1.1e+02 Score=26.94 Aligned_cols=61 Identities=11% Similarity=0.166 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCCCCCCcCc
Q 029522 121 ELKKIEEQLEKKKAEYVEKMKNKMALIHKEAEEKRAMIEAKRGEDLLKAEELAAKYRATGSAPKKLLSC 189 (192)
Q Consensus 121 ~mrKiE~KLEkkRA~a~EKm~nKiA~a~kkAEekRA~aEAkr~ee~~Ka~EkA~kiRaTGk~P~k~~gC 189 (192)
.|..+-.++.....+......+++...+. .--....+++.+..+++++.+++|-+ ++.|||
T Consensus 4 ~~~~L~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~e~~~~~~e~~~kaeeaqK~Gi~-~kIf~w 64 (306)
T PF04888_consen 4 LLAELISKSSEESLKSKKEQIERASEAQE-------KKAEEKAEEIEEAQEKAEEAQKAGIF-SKIFGW 64 (306)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHhcChH-HHHHHH
Confidence 34444444444444444444444433333 22233445556667777777777643 333444
No 24
>KOG4055 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.78 E-value=3.2e+02 Score=24.15 Aligned_cols=29 Identities=31% Similarity=0.306 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029522 137 VEKMKNKMALIHKEAEEKRAMIEAKRGED 165 (192)
Q Consensus 137 ~EKm~nKiA~a~kkAEekRA~aEAkr~ee 165 (192)
.+-|+.++...++.||++-|.-.++|..+
T Consensus 109 daefq~r~ek~~kaaEeKTaKKRaKRqk~ 137 (213)
T KOG4055|consen 109 DAEFQIRLEKNQKAAEEKTAKKRAKRQKK 137 (213)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444445555555555444444443
No 25
>PRK13665 hypothetical protein; Provisional
Probab=29.55 E-value=1.4e+02 Score=27.79 Aligned_cols=27 Identities=19% Similarity=0.239 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029522 112 NNRKAAVEAELKKIEEQLEKKKAEYVE 138 (192)
Q Consensus 112 n~kKAKAEA~mrKiE~KLEkkRA~a~E 138 (192)
.+|-.++|+.++=.+.+.|..|+-+.-
T Consensus 233 ~Lq~dQAEADk~iAqAkAEeRRAmAvA 259 (316)
T PRK13665 233 KLQTDQAEADKRIAQAKAEERRAMAVA 259 (316)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467778888777777777777766553
No 26
>PRK14475 F0F1 ATP synthase subunit B; Provisional
Probab=29.47 E-value=3.1e+02 Score=22.21 Aligned_cols=11 Identities=45% Similarity=0.477 Sum_probs=4.1
Q ss_pred HHHHHHHHHHH
Q 029522 116 AAVEAELKKIE 126 (192)
Q Consensus 116 AKAEA~mrKiE 126 (192)
...+.+|....
T Consensus 65 ~~~e~~L~~A~ 75 (167)
T PRK14475 65 ADVKAEREEAE 75 (167)
T ss_pred HHHHHHHHHHH
Confidence 33333333333
No 27
>PF12127 YdfA_immunity: SigmaW regulon antibacterial; InterPro: IPR022853 This entry represents the uncharacterised protein family UPF0365. Its function is not known. The proteins in this family are found in bacteria. They are about 330 amino acids in length and encoded by a gene located in an operon which confers immunity for the host species to a broad range of antibacterial compounds, unlike the specific immunity proteins that are linked to and co-regulated with their antibiotic-synthesis proteins.
Probab=29.29 E-value=1.3e+02 Score=27.96 Aligned_cols=27 Identities=19% Similarity=0.239 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029522 112 NNRKAAVEAELKKIEEQLEKKKAEYVE 138 (192)
Q Consensus 112 n~kKAKAEA~mrKiE~KLEkkRA~a~E 138 (192)
.+|-.++|+.++-.+.+.|..|+-+.-
T Consensus 228 ~Lq~dQAeADk~iAqAkAEeRRA~AvA 254 (316)
T PF12127_consen 228 KLQTDQAEADKRIAQAKAEERRAMAVA 254 (316)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467777777776666666666655543
No 28
>KOG3654 consensus Uncharacterized CH domain protein [Cytoskeleton]
Probab=25.73 E-value=2.1e+02 Score=28.93 Aligned_cols=33 Identities=39% Similarity=0.512 Sum_probs=18.1
Q ss_pred HHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 029522 119 EAELKK--IEEQLEKKKAEYVEKMKNKMALIHKEAEEKRAMIEAKR 162 (192)
Q Consensus 119 EA~mrK--iE~KLEkkRA~a~EKm~nKiA~a~kkAEekRA~aEAkr 162 (192)
|+++|| +|.+.|.+|-+ ++++|+|-|+-.|..+
T Consensus 406 ear~rkqqleae~e~kree-----------arrkaeeer~~keee~ 440 (708)
T KOG3654|consen 406 EARRRKQQLEAEKEQKREE-----------ARRKAEEERAPKEEEV 440 (708)
T ss_pred HHHHHHHHHHHHHHHHHHH-----------HHHhhHhhhcchhhhh
Confidence 444444 35555555544 4566666666655444
No 29
>PF00430 ATP-synt_B: ATP synthase B/B' CF(0); InterPro: IPR002146 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. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunits B and B' from the F0 complex in F-ATPases found in chloroplasts and in bacterial plasma membranes. The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In bacterial and chloroplast F-ATPases, the peripheral stalk is composed of one copy of the delta subunit (homologous to OSCP in mitochondria), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0045263 proton-transporting ATP synthase complex, coupling factor F(o); PDB: 1L2P_A 2KHK_A 1B9U_A.
Probab=25.51 E-value=2.9e+02 Score=20.60 Aligned_cols=35 Identities=29% Similarity=0.285 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029522 120 AELKKIEEQLEKKKAEYVEKMKNKMALIHKEAEEK 154 (192)
Q Consensus 120 A~mrKiE~KLEkkRA~a~EKm~nKiA~a~kkAEek 154 (192)
..+..++.+|...|.++.+-+.+-...+....+..
T Consensus 51 ~~~~e~~~~l~~a~~ea~~i~~~a~~~a~~~~~~~ 85 (132)
T PF00430_consen 51 QLLAEYEEKLAEAREEAQEIIEEAKEEAEKEKEEI 85 (132)
T ss_dssp HHHHHHHHHHHHHHHHHCHHHHHHCHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333344444444444333333333333333333
No 30
>PRK10930 FtsH protease regulator HflK; Provisional
Probab=23.25 E-value=5.4e+02 Score=24.52 Aligned_cols=56 Identities=13% Similarity=0.093 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Q 029522 121 ELKKIEEQLEKKKAEYVEKMKNKMALIHKEAEEKRAMIEAKRGEDLLKAEELAAKY 176 (192)
Q Consensus 121 ~mrKiE~KLEkkRA~a~EKm~nKiA~a~kkAEekRA~aEAkr~ee~~Ka~EkA~ki 176 (192)
.+...++..++.+.++...-..-+..++..|+.....|++.+...+++++=.|+.|
T Consensus 253 ~v~~Are~~~~~i~eAeayan~iip~A~gea~~ii~~AeAyr~~~i~~AeGda~rF 308 (419)
T PRK10930 253 DAIAARENEQQYIREAEAYTNEVQPRANGQAQRILEEARAYKAQTILEAQGEVARF 308 (419)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHH
Confidence 44444555667777666666666678888888888888888888888887666553
No 31
>CHL00118 atpG ATP synthase CF0 B' subunit; Validated
Probab=23.04 E-value=3.9e+02 Score=21.31 Aligned_cols=40 Identities=15% Similarity=0.134 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029522 117 AVEAELKKIEEQLEKKKAEYVEKMKNKMALIHKEAEEKRA 156 (192)
Q Consensus 117 KAEA~mrKiE~KLEkkRA~a~EKm~nKiA~a~kkAEekRA 156 (192)
.++..+...+.+|..-|.++.+-+.+-...+++..+..++
T Consensus 71 ea~~~~~e~e~~L~~A~~ea~~ii~~A~~~a~~~~~~~~~ 110 (156)
T CHL00118 71 KANELTKQYEQELSKARKEAQLEITQSQKEAKEIVENELK 110 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444445555555554444444444444444433333
No 32
>PF11875 DUF3395: Domain of unknown function (DUF3395); InterPro: IPR024586 Chaperone DnaJ was originally characterised from Escherichia coli as a 41 kDa heat shock protein. DnaJ has a modular structure consisting of a J-domain, a proximal G/F-domain, and a distal zinc finger domain, followed by less conserved C-terminal sequences. Since then, a large number of DnaJ-related proteins containing a J-domain have been characterised from a variety of different organisms. In the genome of Arabidopsis thaliana a total of 89 J-domain proteins have been identified []. This entry represents a C-terminal domain found in some eukaryotic DnaJ-like proteins, including member 11 from the subfamily C1 and protein DnaJ 13 from Arabidopsis. This domain is typically between 147 to 176 amino acids in length.
Probab=22.80 E-value=4.2e+02 Score=21.55 Aligned_cols=34 Identities=18% Similarity=0.212 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029522 132 KKAEYVEKMKNKMALIHKEAEEKRAMIEAKRGED 165 (192)
Q Consensus 132 kRA~a~EKm~nKiA~a~kkAEekRA~aEAkr~ee 165 (192)
.|....+.+..+.+.+...-+.++.+++.++..+
T Consensus 14 ~r~~~~~~~~~~r~eA~~~~~lm~~~a~r~~~~E 47 (151)
T PF11875_consen 14 QREKNKEEIAEKRAEAESAIELMKETAERKQRKE 47 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333333333333444444444444444443
No 33
>PRK02463 OxaA-like protein precursor; Provisional
Probab=22.49 E-value=1.1e+02 Score=27.87 Aligned_cols=23 Identities=26% Similarity=0.336 Sum_probs=18.0
Q ss_pred HHHHHHHHHhcCCCCCCCcCccC
Q 029522 169 AEELAAKYRATGSAPKKLLSCFG 191 (192)
Q Consensus 169 a~EkA~kiRaTGk~P~k~~gCF~ 191 (192)
..|+...||..|--|.+..||++
T Consensus 120 q~em~~lyke~ginp~~~~GCLP 142 (307)
T PRK02463 120 QTELMAAQRENGISMLGGIGCLP 142 (307)
T ss_pred HHHHHHHHHHcCCCCccccchHH
Confidence 35778899999998866568964
No 34
>KOG4001 consensus Axonemal dynein light chain [Cytoskeleton]
Probab=22.45 E-value=5.8e+02 Score=23.04 Aligned_cols=88 Identities=27% Similarity=0.322 Sum_probs=49.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHh-------hHH--HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH
Q 029522 83 RDAVLARVETEKRISLIRAWEESEKS-------QAE--NNRKAAVEAELKKIEE---QLEKKKAEYVEKMKNKMALIHKE 150 (192)
Q Consensus 83 rd~~lakve~Ekr~akI~AWEeaEKa-------Ka~--n~kKAKAEA~mrKiE~---KLEkkRA~a~EKm~nKiA~a~kk 150 (192)
|..+|-++.-|= ...|.|++.-=-+ |+. ...|..++.+.+-+|- .||. .+-.|+.|++...+.
T Consensus 147 RGlll~rvRDEI-rMt~aAYqtlyeSsvAfGmRKALqae~ek~~~~~~~k~le~~k~~Le~----~ia~~k~K~e~~e~r 221 (259)
T KOG4001|consen 147 RGLLLVRVRDEI-RMTFAAYQTLYESSVAFGMRKALQAENEKTRATTEWKVLEDKKKELEL----KIAQLKKKLETDEIR 221 (259)
T ss_pred cceeEEEehHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhhhHHHHHH----HHHHHHHHHHHHHhh
Confidence 444444455554 4557888864222 211 2233334444433331 1222 234567788888889
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHH
Q 029522 151 AEEKRAMIEAKRGEDLLKAEELAAK 175 (192)
Q Consensus 151 AEekRA~aEAkr~ee~~Ka~EkA~k 175 (192)
-++.|+..|.+..+++....+.-..
T Consensus 222 ~~E~r~ieEkk~~eei~fLk~tN~q 246 (259)
T KOG4001|consen 222 SEEEREIEEKKMKEEIEFLKETNRQ 246 (259)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999998888887666554333
No 35
>PF07291 MauE: Methylamine utilisation protein MauE; InterPro: IPR009908 This entry consists of several bacterial methylamine utilisation MauE proteins. Synthesis of enzymes involved in methylamine oxidation via methylamine dehydrogenase (MADH) is encoded by genes present in the mau cluster. MauE and MauD are specifically involved in the processing, transport, and/or maturation of the beta-subunit and that the absence of each of these proteins leads to production of a non-functional beta-subunit which becomes rapidly degraded [].; GO: 0030416 methylamine metabolic process, 0016021 integral to membrane
Probab=22.39 E-value=49 Score=27.79 Aligned_cols=14 Identities=29% Similarity=0.660 Sum_probs=8.6
Q ss_pred hcCCCCCCCcCccCC
Q 029522 178 ATGSAPKKLLSCFGS 192 (192)
Q Consensus 178 aTGk~P~k~~gCF~~ 192 (192)
..|+.+-. ||||+.
T Consensus 97 ~rg~~~id-CGCfG~ 110 (184)
T PF07291_consen 97 LRGRTDID-CGCFGG 110 (184)
T ss_pred HcCCCCCC-CCCCCC
Confidence 34654434 899973
No 36
>KOG1103 consensus Predicted coiled-coil protein [Function unknown]
Probab=22.26 E-value=7.5e+02 Score=24.24 Aligned_cols=43 Identities=33% Similarity=0.222 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHH
Q 029522 112 NNRKAAVEAELKKIEEQLEKKKAEYV----------EKMKNKMALIHKEAEEK 154 (192)
Q Consensus 112 n~kKAKAEA~mrKiE~KLEkkRA~a~----------EKm~nKiA~a~kkAEek 154 (192)
-.++.|+|-.-+|++++|+.-|.+-. .++.||++....+|++-
T Consensus 159 ~~e~kK~E~~k~Kl~~qLeeEk~RHeqis~mLilEcKka~~KaaEegqKA~ei 211 (561)
T KOG1103|consen 159 IEEKKKAEIAKDKLEMQLEEEKKRHEQISLMLILECKKALLKAAEEGQKAEEI 211 (561)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHH
Confidence 36778889999999999987665532 46777888777777764
No 37
>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]
Probab=22.20 E-value=1.1e+03 Score=26.22 Aligned_cols=62 Identities=21% Similarity=0.347 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhhhhHHHHHHHHHHHHhcCCCCCC
Q 029522 120 AELKKIEEQLEKKKAEYVEKMKNKMALIHKEAEEKRA-MIEAKRGEDLLKAEELAAKYRATGSAPKK 185 (192)
Q Consensus 120 A~mrKiE~KLEkkRA~a~EKm~nKiA~a~kkAEekRA-~aEAkr~ee~~Ka~EkA~kiRaTGk~P~k 185 (192)
.+++.++.+|+++|....... ..+...+.++++.+. ....+-+.+++.+- -.+...|++|+-
T Consensus 556 ~e~~~~~k~l~~~~~e~~~~~-~~~~~~rqrveE~ks~~~~~~s~~kVl~al---~r~kesG~i~Gf 618 (1293)
T KOG0996|consen 556 QELKEKEKELPKLRKEERNLK-SQLNKLRQRVEEAKSSLSSSRSRNKVLDAL---MRLKESGRIPGF 618 (1293)
T ss_pred HHHHHHHHhHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHhhhhhhHHHHHH---HHHHHcCCCCcc
Confidence 367777778888777655444 445566667777776 45555555655544 345678999854
No 38
>PRK11029 FtsH protease regulator HflC; Provisional
Probab=20.63 E-value=4.4e+02 Score=24.30 Aligned_cols=21 Identities=14% Similarity=0.042 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHHHHHHhhhh
Q 029522 145 ALIHKEAEEKRAMIEAKRGED 165 (192)
Q Consensus 145 A~a~kkAEekRA~aEAkr~ee 165 (192)
+.+.+.+.-.|+..++.+.+.
T Consensus 262 AeA~~~a~i~~aegeA~a~~~ 282 (334)
T PRK11029 262 AEAERQGRIMRGEGDAEAAKL 282 (334)
T ss_pred HHHHHHHHHHHhhhHHHHHHH
Confidence 344444444444444444333
No 39
>COG4582 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.56 E-value=1.6e+02 Score=26.40 Aligned_cols=31 Identities=29% Similarity=0.250 Sum_probs=24.3
Q ss_pred HHhhhhHHHHHHHHHHHHhcCCCCCCCcCccC
Q 029522 160 AKRGEDLLKAEELAAKYRATGSAPKKLLSCFG 191 (192)
Q Consensus 160 Akr~ee~~Ka~EkA~kiRaTGk~P~k~~gCF~ 191 (192)
+-|--|.++--+--..+|..-.+|+.|| ||.
T Consensus 102 a~r~GQ~l~edr~is~iRqR~~iPGG~C-~FD 132 (244)
T COG4582 102 APRIGQSLREDRLIALVRQRLSIPGGCC-SFD 132 (244)
T ss_pred chhhHhHhhhhHHHHHHHHHccCCCccc-ccC
Confidence 3355666777788888999999999976 884
Done!