Query psy12041
Match_columns 153
No_of_seqs 145 out of 1211
Neff 7.6
Searched_HMMs 46136
Date Fri Aug 16 17:07:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12041.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12041hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12781 AAA_9: ATP-binding dy 100.0 2E-46 4.3E-51 292.5 4.2 141 1-153 7-153 (228)
2 KOG3595|consensus 99.9 2.5E-23 5.4E-28 195.0 9.4 140 2-152 1078-1225(1395)
3 COG5245 DYN1 Dynein, heavy cha 98.7 2.5E-08 5.4E-13 93.5 4.8 129 12-151 2464-2600(3164)
4 KOG3595|consensus 96.4 0.0023 4.9E-08 61.7 2.8 55 54-108 1299-1353(1395)
5 PF03028 Dynein_heavy: Dynein 95.8 0.019 4E-07 51.7 5.8 121 13-148 102-229 (707)
6 PHA02244 ATPase-like protein 91.0 0.58 1.3E-05 39.5 5.6 72 76-149 175-259 (383)
7 PF12774 AAA_6: Hydrolytic ATP 87.4 1.8 3.9E-05 33.9 5.7 118 25-150 30-166 (231)
8 TIGR02640 gas_vesic_GvpN gas v 76.1 5.7 0.00012 31.4 4.7 72 76-149 100-183 (262)
9 PF07728 AAA_5: AAA domain (dy 42.9 25 0.00054 24.3 2.6 65 76-142 60-138 (139)
10 TIGR02902 spore_lonB ATP-depen 42.2 27 0.00059 30.7 3.1 67 81-149 175-261 (531)
11 PRK05783 hypothetical protein; 40.3 12 0.00026 24.8 0.5 16 30-45 13-29 (84)
12 PF00158 Sigma54_activat: Sigm 36.9 20 0.00043 26.5 1.3 64 81-147 93-166 (168)
13 PF05386 TEP1_N: TEP1 N-termin 31.7 26 0.00055 18.6 0.8 14 11-24 11-24 (30)
14 COG1828 PurS Phosphoribosylfor 30.8 22 0.00048 23.5 0.6 16 30-45 12-28 (83)
15 PF14987 NADHdh_A3: NADH dehyd 28.6 25 0.00055 23.1 0.6 13 33-45 71-83 (84)
16 TIGR01650 PD_CobS cobaltochela 25.5 1.1E+02 0.0025 25.3 4.0 68 76-145 129-213 (327)
17 cd01262 PH_PDK1 3-Phosphoinosi 24.4 23 0.00049 23.8 -0.2 20 28-47 66-85 (89)
18 PRK07003 DNA polymerase III su 21.8 1.2E+02 0.0025 28.5 3.7 55 86-149 122-176 (830)
19 PF13711 DUF4160: Domain of un 21.7 83 0.0018 19.3 2.0 19 121-139 1-19 (66)
20 PRK12758 DNA topoisomerase IV 21.2 64 0.0014 30.4 1.9 26 11-38 85-110 (869)
21 cd00187 TOP4c DNA Topoisomeras 20.4 67 0.0015 27.8 1.8 28 10-38 49-79 (445)
22 smart00434 TOP4c DNA Topoisome 20.2 67 0.0014 27.7 1.7 27 11-38 69-98 (445)
No 1
>PF12781 AAA_9: ATP-binding dynein motor region D5; PDB: 3VKG_A 3VKH_C 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A.
Probab=100.00 E-value=2e-46 Score=292.50 Aligned_cols=141 Identities=43% Similarity=0.730 Sum_probs=118.8
Q ss_pred CcccchhCCCCCCcchhhhhHhhhcCCCcceEecCcchHHHHHHhhhhcchhHHHHHHHHhhhhhhchHHHHHhhHHHHh
Q psy12041 1 MISQWNSEGLPPDELSIQNGILSTRGCHFPLCIDPQTQALKWIRNREDKNNLKVSYKLKLAESTAIDIDNLREGYRPVAK 80 (153)
Q Consensus 1 ~i~~w~~~gLp~d~~s~ena~i~~~~~~~Pl~iDP~~~~~~wl~~~~~~~~~~i~~~~~~~~~~~~~~~~~r~~ye~a~~ 80 (153)
.+++|+.+|||.|++|+|||+|+.+|.||||+||||+||.+||++++ ++++.+++ +.+.++.+.+ |.|++
T Consensus 7 ~i~~W~~~GLP~D~~siENa~i~~~~~r~PLiIDPq~qa~~wi~~~~-~~~l~v~~--------~~~~~~~~~l-e~air 76 (228)
T PF12781_consen 7 EIRQWISQGLPSDQLSIENAIILKNSRRWPLIIDPQGQANKWIKNMY-KNDLEVTS--------FSDSNFLKQL-ENAIR 76 (228)
T ss_dssp ---HHHHCT--SSHHHHHHHHHCCC-SSEEEEESTTTCHHHHHHHHC-CCCEEEEE--------TTSTCHHHHH-HHHHH
T ss_pred chhhHHhcCCCCCchHHhhHHHHhhcCCCceEECCchHHHHHHHHhh-hhcccccc--------cchHhHHHHH-HHHHH
Confidence 47899999999999999999999999999999999999999999985 55688888 8999999999 99999
Q ss_pred cCCceeEEEecccc-cCccchhccceeeE-----EecCCeeeecCCCeeEEEeecCCCCCCCHhhhcceEEEEEEeecC
Q psy12041 81 RGALLFFVFSDISN-VNPMYQYSLESYLE-----VPYGDKEVDYDVNFRLYLTTKIPNPTFDPSLYTKATVINYSVTAQ 153 (153)
Q Consensus 81 ~Gs~l~~li~~l~~-idp~y~~~L~~~i~-----i~~g~k~i~~~~~F~l~l~t~~~~~~~~~~~~~~~~~inft~t~~ 153 (153)
+|+ +++|+|+++ +||++.++|.+.+. |++|++.++|+|+|||||+|+.+||||+|++++++|+||||+|++
T Consensus 77 ~G~--~llIe~v~e~~dp~l~plL~k~~~~~g~~i~igd~~v~~~~~FrL~L~T~~~~p~~~pe~~s~vtviNFtvt~~ 153 (228)
T PF12781_consen 77 FGK--PLLIENVGESLDPILDPLLRKNIIKSGKFIKIGDKEVDYNPNFRLYLTTKLPNPHYPPEVSSKVTVINFTVTQE 153 (228)
T ss_dssp CT---EEEEC-GCSCHHCTCHHHHTTT-EE-SSEEESSSSEEE--SS-EEEEEESSTTSHHHHHHHHCSEEEE----CH
T ss_pred cCC--eeeecccccccChhhhhhhcchhccCCceEEecCeEEEeeccceEEEeecCCCCCCChhhhceeeEEEEEecHH
Confidence 999 999999977 99999999998764 999999999999999999999999999999999999999999973
No 2
>KOG3595|consensus
Probab=99.89 E-value=2.5e-23 Score=194.97 Aligned_cols=140 Identities=39% Similarity=0.677 Sum_probs=133.9
Q ss_pred cccchhCCCCCCcchhhhhHhhhcCCCcceEecCcchHHHHHHhhhhcchhHHHHHHHHhhhhhhchHHHHHhhHHHHhc
Q psy12041 2 ISQWNSEGLPPDELSIQNGILSTRGCHFPLCIDPQTQALKWIRNREDKNNLKVSYKLKLAESTAIDIDNLREGYRPVAKR 81 (153)
Q Consensus 2 i~~w~~~gLp~d~~s~ena~i~~~~~~~Pl~iDP~~~~~~wl~~~~~~~~~~i~~~~~~~~~~~~~~~~~r~~ye~a~~~ 81 (153)
+..|...|+|.|++|+|||+++.++.+||++||||+|+..||+++++.++..+.+ ..+.++.+.+ +.++++
T Consensus 1078 ~~~w~~~~lp~~~~s~en~~i~~~~~~~~l~id~q~q~~~~i~~~~~~~~~~~i~--------~~~~~~l~~l-e~a~~~ 1148 (1395)
T KOG3595|consen 1078 ILNWNIRGLPADDLSIENGIIITNSNRWPLIIDPQGQANEWIKNKESENKLQVIS--------FNEKEFLRQL-ENALRF 1148 (1395)
T ss_pred hcchhhccCcccccchhHHHHHhccCCCceeecchhhhhHhHhhhhhhcccceee--------ccchhHHHHH-HhHhcc
Confidence 5789999999999999999999999999999999999999999999889999988 9999999999 999999
Q ss_pred CCceeEEEecccc-cCccchhccceeeE-------EecCCeeeecCCCeeEEEeecCCCCCCCHhhhcceEEEEEEeec
Q psy12041 82 GALLFFVFSDISN-VNPMYQYSLESYLE-------VPYGDKEVDYDVNFRLYLTTKIPNPTFDPSLYTKATVINYSVTA 152 (153)
Q Consensus 82 Gs~l~~li~~l~~-idp~y~~~L~~~i~-------i~~g~k~i~~~~~F~l~l~t~~~~~~~~~~~~~~~~~inft~t~ 152 (153)
|. .++++++.+ +||.+++.+.+... +.+|++.++++++|++|++|+++|||+.|+++++++++||++|.
T Consensus 1149 g~--~il~~~~~e~~d~~l~~ll~~~~~~~g~~~~~~~gd~~~~~~~~f~~~~~t~~~~~~~~p~~~~~~~~v~f~~t~ 1225 (1395)
T KOG3595|consen 1149 GE--PVLIEDVNEELDPALEPLLLKETFKQGGRVLIKLGDKEIDLNPDFRLYITTKLRNPHYLPELSARVTLVNFTVTP 1225 (1395)
T ss_pred CC--ceeccchhhhhchhhhhhcccceeeccCeEeeecCceeeecCCCeeEEEeecccCcccChhhhhceeEEEeEech
Confidence 99 999999966 99999999998655 99999999999999999999999999999999999999999985
No 3
>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]
Probab=98.65 E-value=2.5e-08 Score=93.55 Aligned_cols=129 Identities=7% Similarity=0.049 Sum_probs=115.2
Q ss_pred CCcchhhhhHhhhcCC-CcceEecCcchHHHHHHhhhhcchhHHHHHHHHhhhhhhchHHHHHhhHHHHhcCCceeEEEe
Q psy12041 12 PDELSIQNGILSTRGC-HFPLCIDPQTQALKWIRNREDKNNLKVSYKLKLAESTAIDIDNLREGYRPVAKRGALLFFVFS 90 (153)
Q Consensus 12 ~d~~s~ena~i~~~~~-~~Pl~iDP~~~~~~wl~~~~~~~~~~i~~~~~~~~~~~~~~~~~r~~ye~a~~~Gs~l~~li~ 90 (153)
..++++||..|.++.. ..|+++||..+...-+++++++++-...+ +.+..+...+ +.|.+.|+ ..+|.
T Consensus 2464 ~tDy~lEN~~i~~~~qd~~~~L~dpss~ivt~~~~~y~~kkail~s--------f~e~~f~~~L-~~a~r~gs--~~iI~ 2532 (3164)
T COG5245 2464 STDYGLENSRIRKDLQDLTAVLNDPSSKIVTSQRQMYDEKKAILGS--------FREMEFAFGL-SQARREGS--DKIIG 2532 (3164)
T ss_pred cchhcchhhHHHhhccccHhHhcCcHHHHHHhhHHHhccchhhhhh--------hhhHHHHHHH-HHHHHhcc--ceEec
Confidence 4568999988887765 78899999999999999998877766666 7888999999 99999999 99999
Q ss_pred cccccCccchhcccee-------eEEecCCeeeecCCCeeEEEeecCCCCCCCHhhhcceEEEEEEee
Q psy12041 91 DISNVNPMYQYSLESY-------LEVPYGDKEVDYDVNFRLYLTTKIPNPTFDPSLYTKATVINYSVT 151 (153)
Q Consensus 91 ~l~~idp~y~~~L~~~-------i~i~~g~k~i~~~~~F~l~l~t~~~~~~~~~~~~~~~~~inft~t 151 (153)
+.+.+||...+.++.. +++.+|+.+|+..-.|.+|..+..+.-..+.-.++++.+|||+..
T Consensus 2533 daE~~d~~i~rlIk~ef~s~~~eV~v~i~~~eI~~S~~~~vf~~se~~Sgdm~~~~~k~l~~v~Fvs~ 2600 (3164)
T COG5245 2533 DAEALDEEIGRLIKEEFKSNLSEVKVMINPPEIVRSTVEAVFWLSEGRSGDMGSIEWKQLIQVMFVSK 2600 (3164)
T ss_pred chhhhhhhhhhhhhHHHhcCCceEEEEECCCeeEEecceeEEEEeecCCCchhHHHHHHhHhhheehh
Confidence 9999999998888754 559999999999999999999999999999999999999999864
No 4
>KOG3595|consensus
Probab=96.38 E-value=0.0023 Score=61.68 Aligned_cols=55 Identities=47% Similarity=0.826 Sum_probs=52.9
Q ss_pred HHHHHHHhhhhhhchHHHHHhhHHHHhcCCceeEEEecccccCccchhccceeeE
Q psy12041 54 VSYKLKLAESTAIDIDNLREGYRPVAKRGALLFFVFSDISNVNPMYQYSLESYLE 108 (153)
Q Consensus 54 i~~~~~~~~~~~~~~~~~r~~ye~a~~~Gs~l~~li~~l~~idp~y~~~L~~~i~ 108 (153)
+..|+.++..++.+++..|..|++++.+|+.+||.+.++..++|||+++|.+++.
T Consensus 1299 i~~k~~e~~~~e~~i~~~r~~y~p~a~~~~~l~~~~~~l~~i~~myq~sl~~f~~ 1353 (1395)
T KOG3595|consen 1299 IKEKLEEAEETEKEIDAAREQYRPLAIHSSILYFSISDLANIHPMYQYSLKWFLN 1353 (1395)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhHHHHhHhhhheehhhccccChHHHHHHHHHHH
Confidence 8889999999999999999999999999999999999999999999999998765
No 5
>PF03028 Dynein_heavy: Dynein heavy chain and region D6 of dynein motor; InterPro: IPR004273 Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein is composed of a number of ATP-binding large subunits, intermediate size subunits and small subunits (see IPR001372 from INTERPRO). This family represents the C-terminal region of dynein heavy chain. The dynein heavy chain also exhibits ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. ; GO: 0003777 microtubule motor activity, 0007018 microtubule-based movement, 0030286 dynein complex; PDB: 3VKG_A 3VKH_C 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A.
Probab=95.85 E-value=0.019 Score=51.71 Aligned_cols=121 Identities=20% Similarity=0.316 Sum_probs=66.6
Q ss_pred CcchhhhhHhhhcCCCcceE--e----cCcchHHHHHHhhh-hcchhHHHHHHHHhhhhhhchHHHHHhhHHHHhcCCce
Q psy12041 13 DELSIQNGILSTRGCHFPLC--I----DPQTQALKWIRNRE-DKNNLKVSYKLKLAESTAIDIDNLREGYRPVAKRGALL 85 (153)
Q Consensus 13 d~~s~ena~i~~~~~~~Pl~--i----DP~~~~~~wl~~~~-~~~~~~i~~~~~~~~~~~~~~~~~r~~ye~a~~~Gs~l 85 (153)
..+++++.+- ..+...|++ . ||........++.. .+..+.+.+ ++. -......+.+ +.|++.|.
T Consensus 102 ~~~~l~~~~~-~s~~~~Pil~~~s~g~Dp~~~i~~lA~~~~~~~~~~~~is-lG~----~~~~~a~~~l-~~a~~~G~-- 172 (707)
T PF03028_consen 102 PPFDLESIYE-ESSPTTPILFILSPGSDPSSEIEQLAKKKGFGNKKLQSIS-LGS----GQGPEAEKAL-KEAAKEGH-- 172 (707)
T ss_dssp ----HHHHHH-CTTTTC-EEEEE-TT--THHHHHHHHHCTT-----EEEEE-TTS----HHHHHHHHHH-HHHHHHTS--
T ss_pred CCCCHHHHHH-hcCCCCceEEEeCCCCChHHHHHHHHHHHhhhhhheeecC-CCC----chHHHHHHHH-HHHhcCCe--
Confidence 3455665543 556788863 3 66666655555442 012222221 221 1222334444 99999999
Q ss_pred eEEEecccccCccchhccceeeEEecCCeeeecCCCeeEEEeecCCCCCCCHhhhcceEEEEE
Q psy12041 86 FFVFSDISNVNPMYQYSLESYLEVPYGDKEVDYDVNFRLYLTTKIPNPTFDPSLYTKATVINY 148 (153)
Q Consensus 86 ~~li~~l~~idp~y~~~L~~~i~i~~g~k~i~~~~~F~l~l~t~~~~~~~~~~~~~~~~~inf 148 (153)
-++++|++...+ +-+.|.+.+.-.-. +.+++|||||++ .+.+.+|..+..+...|-|
T Consensus 173 Wv~L~N~HL~~~-wl~~Le~~l~~~~~----~~h~~FRL~lt~-~~~~~~P~~lL~~s~kv~~ 229 (707)
T PF03028_consen 173 WVLLQNCHLAPS-WLPQLEKKLESLSP----EIHPNFRLFLTS-EPSPSFPISLLQSSIKVTY 229 (707)
T ss_dssp EEEEETGGGGCC-CHHCHHHHHHC-SS----TTSTT-EEEEEE-ESSTTS-HHHHHCSEEEEE
T ss_pred EEEcccchhHHH-HHHHHHHHHhcccc----ccccceEEEEEe-cCcccCCHHHHHcccceee
Confidence 999999986433 33455544321111 789999999998 5888999999877666654
No 6
>PHA02244 ATPase-like protein
Probab=90.99 E-value=0.58 Score=39.49 Aligned_cols=72 Identities=17% Similarity=0.290 Sum_probs=53.2
Q ss_pred HHHHhcCCceeEEEecccccCccchhccceeeE---EecCCeeeecCCCeeEEEeecCC----------CCCCCHhhhcc
Q psy12041 76 RPVAKRGALLFFVFSDISNVNPMYQYSLESYLE---VPYGDKEVDYDVNFRLYLTTKIP----------NPTFDPSLYTK 142 (153)
Q Consensus 76 e~a~~~Gs~l~~li~~l~~idp~y~~~L~~~i~---i~~g~k~i~~~~~F~l~l~t~~~----------~~~~~~~~~~~ 142 (153)
-.+++.|. .+++.++...+|-.+..|..-+. +...+..+..+++||++.++... ...+++.+..|
T Consensus 175 l~A~~~Gg--vLiLDEId~a~p~vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~~~~G~~~~y~G~k~L~~AllDR 252 (383)
T PHA02244 175 YEAFKKGG--LFFIDEIDASIPEALIIINSAIANKFFDFADERVTAHEDFRVISAGNTLGKGADHIYVARNKIDGATLDR 252 (383)
T ss_pred HHHhhcCC--EEEEeCcCcCCHHHHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCCCccCcccccCCCcccCHHHHhh
Confidence 45678899 99999999877655443333221 44456678889999999999863 35568999999
Q ss_pred eEEEEEE
Q psy12041 143 ATVINYS 149 (153)
Q Consensus 143 ~~~inft 149 (153)
..+|+|.
T Consensus 253 Fv~I~~d 259 (383)
T PHA02244 253 FAPIEFD 259 (383)
T ss_pred cEEeeCC
Confidence 9999874
No 7
>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A.
Probab=87.38 E-value=1.8 Score=33.92 Aligned_cols=118 Identities=12% Similarity=0.113 Sum_probs=68.0
Q ss_pred cCCCcceEecCcchHHHH-HH---hhhhcchhHHHHHHHHhhhhhhchHHHHHhhHHHHhcCCceeEEEecccccCccch
Q psy12041 25 RGCHFPLCIDPQTQALKW-IR---NREDKNNLKVSYKLKLAESTAIDIDNLREGYRPVAKRGALLFFVFSDISNVNPMYQ 100 (153)
Q Consensus 25 ~~~~~Pl~iDP~~~~~~w-l~---~~~~~~~~~i~~~~~~~~~~~~~~~~~r~~ye~a~~~Gs~l~~li~~l~~idp~y~ 100 (153)
+....+.+.=|.|.|..= +| +.. +.-.-+.. +.+ ..+...+..++.-+++.|+ -.+++++..+++-.-
T Consensus 30 ~~~~~~~~~GpagtGKtetik~La~~l-G~~~~vfn----c~~-~~~~~~l~ril~G~~~~Ga--W~cfdefnrl~~~vL 101 (231)
T PF12774_consen 30 SLNLGGALSGPAGTGKTETIKDLARAL-GRFVVVFN----CSE-QMDYQSLSRILKGLAQSGA--WLCFDEFNRLSEEVL 101 (231)
T ss_dssp CTTTEEEEESSTTSSHHHHHHHHHHCT-T--EEEEE----TTS-SS-HHHHHHHHHHHHHHT---EEEEETCCCSSHHHH
T ss_pred ccCCCCCCcCCCCCCchhHHHHHHHHh-CCeEEEec----ccc-cccHHHHHHHHHHHhhcCc--hhhhhhhhhhhHHHH
Confidence 455677788887766322 22 221 22121111 001 3455667777799999999 999999999885433
Q ss_pred hcccee------------eEEecCCeeeecCCCeeEEEeecC---CCCCCCHhhhcceEEEEEEe
Q psy12041 101 YSLESY------------LEVPYGDKEVDYDVNFRLYLTTKI---PNPTFDPSLYTKATVINYSV 150 (153)
Q Consensus 101 ~~L~~~------------i~i~~g~k~i~~~~~F~l~l~t~~---~~~~~~~~~~~~~~~inft~ 150 (153)
..+... -.+.+.++++..+++..+|++... .+.++|+++.+....|.+..
T Consensus 102 S~i~~~i~~i~~al~~~~~~~~~~g~~i~l~~~~~iFiT~np~y~gr~~LP~nLk~lFRpvam~~ 166 (231)
T PF12774_consen 102 SVISQQIQSIQDALRAKQKSFTLEGQEIKLNPNCGIFITMNPGYAGRSELPENLKALFRPVAMMV 166 (231)
T ss_dssp HHHHHHHHHHHHHHHCTSSEEEETTCEEE--TT-EEEEEE-B-CCCC--S-HHHCTTEEEEE--S
T ss_pred HHHHHHHHHHHHhhcccccccccCCCEEEEccceeEEEeeccccCCcccCCHhHHHHhheeEEeC
Confidence 333221 227778999999999999998752 23678999988888887653
No 8
>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN. Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).
Probab=76.09 E-value=5.7 Score=31.38 Aligned_cols=72 Identities=18% Similarity=0.260 Sum_probs=50.1
Q ss_pred HHHHhcCCceeEEEecccccCccchhccceeeE---EecC-----CeeeecCCCeeEEEeecCCC----CCCCHhhhcce
Q psy12041 76 RPVAKRGALLFFVFSDISNVNPMYQYSLESYLE---VPYG-----DKEVDYDVNFRLYLTTKIPN----PTFDPSLYTKA 143 (153)
Q Consensus 76 e~a~~~Gs~l~~li~~l~~idp~y~~~L~~~i~---i~~g-----~k~i~~~~~F~l~l~t~~~~----~~~~~~~~~~~ 143 (153)
..|++.|. .++++++...+|-.+..|..-+. +.+. +..+..+++||++.++.... ...++.++.|+
T Consensus 100 ~~A~~~g~--~lllDEi~r~~~~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~~~g~~~l~~aL~~R~ 177 (262)
T TIGR02640 100 TLAVREGF--TLVYDEFTRSKPETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVEYAGVHETQDALLDRL 177 (262)
T ss_pred HHHHHcCC--EEEEcchhhCCHHHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCccccceecccHHHHhhc
Confidence 45778899 99999999988876665544332 2222 34577889999999887543 24477888888
Q ss_pred EEEEEE
Q psy12041 144 TVINYS 149 (153)
Q Consensus 144 ~~inft 149 (153)
..+.+.
T Consensus 178 ~~i~i~ 183 (262)
T TIGR02640 178 ITIFMD 183 (262)
T ss_pred EEEECC
Confidence 776543
No 9
>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []. The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=42.95 E-value=25 Score=24.33 Aligned_cols=65 Identities=23% Similarity=0.423 Sum_probs=38.9
Q ss_pred HHHHhcCCceeEEEecccccCccchhccc-----eeeEEecCCeeeecCC------CeeEEEeecCCC---CCCCHhhhc
Q psy12041 76 RPVAKRGALLFFVFSDISNVNPMYQYSLE-----SYLEVPYGDKEVDYDV------NFRLYLTTKIPN---PTFDPSLYT 141 (153)
Q Consensus 76 e~a~~~Gs~l~~li~~l~~idp~y~~~L~-----~~i~i~~g~k~i~~~~------~F~l~l~t~~~~---~~~~~~~~~ 141 (153)
-.+++.|. .++++++...+|-+...|. +.+.+..++..+..++ +|+++.++.... ..+++.+.+
T Consensus 60 ~~a~~~~~--il~lDEin~a~~~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~l~~al~~ 137 (139)
T PF07728_consen 60 VRAMRKGG--ILVLDEINRAPPEVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKELSPALLD 137 (139)
T ss_dssp CTTHHEEE--EEEESSCGG--HHHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTTTCHHHHT
T ss_pred ccccccee--EEEECCcccCCHHHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCcCCHHHHh
Confidence 45667888 9999999876654443332 2333445555555554 599999997555 467777766
Q ss_pred c
Q psy12041 142 K 142 (153)
Q Consensus 142 ~ 142 (153)
|
T Consensus 138 R 138 (139)
T PF07728_consen 138 R 138 (139)
T ss_dssp T
T ss_pred h
Confidence 5
No 10
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=42.19 E-value=27 Score=30.69 Aligned_cols=67 Identities=21% Similarity=0.333 Sum_probs=46.4
Q ss_pred cCCceeEEEecccccCccchhccceeeE---EecC-------Ce----------eeecCCCeeEEEeecCCCCCCCHhhh
Q psy12041 81 RGALLFFVFSDISNVNPMYQYSLESYLE---VPYG-------DK----------EVDYDVNFRLYLTTKIPNPTFDPSLY 140 (153)
Q Consensus 81 ~Gs~l~~li~~l~~idp~y~~~L~~~i~---i~~g-------~k----------~i~~~~~F~l~l~t~~~~~~~~~~~~ 140 (153)
.|. .+.|++++.+++..+..|-+.+. +++. ++ .-.+..+|++...|...-..++|.+.
T Consensus 175 ~gG--~L~IdEI~~L~~~~q~~LL~~Le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~rlI~ATt~~p~~L~paLr 252 (531)
T TIGR02902 175 HGG--VLFIDEIGELHPVQMNKLLKVLEDRKVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRNPEEIPPALR 252 (531)
T ss_pred CCc--EEEEechhhCCHHHHHHHHHHHHhCeeeeccccccccCcccccchhhhcccCcccceEEEEEecCCcccCChHHh
Confidence 456 88999999999988877654432 2221 10 01245689999888765567899999
Q ss_pred cceEEEEEE
Q psy12041 141 TKATVINYS 149 (153)
Q Consensus 141 ~~~~~inft 149 (153)
+|+..|.|.
T Consensus 253 sR~~~I~f~ 261 (531)
T TIGR02902 253 SRCVEIFFR 261 (531)
T ss_pred hhhheeeCC
Confidence 998877663
No 11
>PRK05783 hypothetical protein; Provisional
Probab=40.25 E-value=12 Score=24.80 Aligned_cols=16 Identities=13% Similarity=0.418 Sum_probs=11.0
Q ss_pred ceEecCcchHHH-HHHh
Q psy12041 30 PLCIDPQTQALK-WIRN 45 (153)
Q Consensus 30 Pl~iDP~~~~~~-wl~~ 45 (153)
|=+.||||.|+. =|.+
T Consensus 13 ~gVlDPqG~aI~~aL~~ 29 (84)
T PRK05783 13 DSVRDPEGETIQRYVIE 29 (84)
T ss_pred CCCcCchHHHHHHHHHH
Confidence 457899999854 3433
No 12
>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....
Probab=36.89 E-value=20 Score=26.49 Aligned_cols=64 Identities=23% Similarity=0.371 Sum_probs=42.4
Q ss_pred cCCceeEEEecccccCccchhccceeeE----EecCCeeeecCCCeeEEEeecCC------CCCCCHhhhcceEEEE
Q psy12041 81 RGALLFFVFSDISNVNPMYQYSLESYLE----VPYGDKEVDYDVNFRLYLTTKIP------NPTFDPSLYTKATVIN 147 (153)
Q Consensus 81 ~Gs~l~~li~~l~~idp~y~~~L~~~i~----i~~g~k~i~~~~~F~l~l~t~~~------~~~~~~~~~~~~~~in 147 (153)
.|. .+.+++++.+.|-.|.-|-..+. ..+|+. -....+.|+..+|..+ +-.|.++++-+.+++.
T Consensus 93 ~~G--tL~Ld~I~~L~~~~Q~~Ll~~l~~~~~~~~g~~-~~~~~~~RiI~st~~~l~~~v~~g~fr~dLy~rL~~~~ 166 (168)
T PF00158_consen 93 NGG--TLFLDEIEDLPPELQAKLLRVLEEGKFTRLGSD-KPVPVDVRIIASTSKDLEELVEQGRFREDLYYRLNVFT 166 (168)
T ss_dssp TTS--EEEEETGGGS-HHHHHHHHHHHHHSEEECCTSS-SEEE--EEEEEEESS-HHHHHHTTSS-HHHHHHHTTEE
T ss_pred cce--EEeecchhhhHHHHHHHHHHHHhhchhcccccc-ccccccceEEeecCcCHHHHHHcCCChHHHHHHhceEe
Confidence 455 78899999999988877766554 445543 2444579999999754 3688999988776653
No 13
>PF05386 TEP1_N: TEP1 N-terminal domain; InterPro: IPR008850 Telomerase protein component 1 (TP1/TLP1) or TEP1 is a protein component of two ribonucleoprotein (RNP) complexes: vaults and telomerase. Vaults are large RNP particles with a barrel-like structure (IPR002499 from INTERPRO). The telomerase RNP replenishes incomplete chromosome termini due to DNA replication. Mammalian TEP1 is an RNA-binding protein and is required for the association of vault RNA with the vault particle [, ]. The N-terminal part of TEP1 contains 4 copies of the TEP1 N-terminal repeat in tandem. The repeat is composed of 30 amino acids and occurs in combination with the TROVE (IPR008858 from INTERPRO) and NACHT (IPR007111 from INTERPRO) domains and with WD-40 repeats (see IPR001680 from INTERPRO) in the C-terminal part.
Probab=31.69 E-value=26 Score=18.56 Aligned_cols=14 Identities=50% Similarity=0.679 Sum_probs=11.6
Q ss_pred CCCcchhhhhHhhh
Q psy12041 11 PPDELSIQNGILST 24 (153)
Q Consensus 11 p~d~~s~ena~i~~ 24 (153)
-+|-+|+||-++.+
T Consensus 11 hpdILSLeNrCLat 24 (30)
T PF05386_consen 11 HPDILSLENRCLAT 24 (30)
T ss_pred CcchhhhhhhHHHh
Confidence 37899999988765
No 14
>COG1828 PurS Phosphoribosylformylglycinamidine (FGAM) synthase, PurS component [Nucleotide transport and metabolism]
Probab=30.83 E-value=22 Score=23.53 Aligned_cols=16 Identities=19% Similarity=0.528 Sum_probs=10.9
Q ss_pred ceEecCcchHHH-HHHh
Q psy12041 30 PLCIDPQTQALK-WIRN 45 (153)
Q Consensus 30 Pl~iDP~~~~~~-wl~~ 45 (153)
|=+.||||+|+. -|..
T Consensus 12 ~~VlDPqG~ti~~aL~~ 28 (83)
T COG1828 12 PGVLDPEGETIEKALHR 28 (83)
T ss_pred CcccCchhHHHHHHHHH
Confidence 457899999853 3443
No 15
>PF14987 NADHdh_A3: NADH dehydrogenase 1 alpha subcomplex subunit 3
Probab=28.58 E-value=25 Score=23.08 Aligned_cols=13 Identities=38% Similarity=0.989 Sum_probs=11.2
Q ss_pred ecCcchHHHHHHh
Q psy12041 33 IDPQTQALKWIRN 45 (153)
Q Consensus 33 iDP~~~~~~wl~~ 45 (153)
-||||-..+|||+
T Consensus 71 qdpqGPsLewLK~ 83 (84)
T PF14987_consen 71 QDPQGPSLEWLKK 83 (84)
T ss_pred CCCCCCcHHHHhc
Confidence 3789999999987
No 16
>TIGR01650 PD_CobS cobaltochelatase, CobS subunit. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.
Probab=25.45 E-value=1.1e+02 Score=25.32 Aligned_cols=68 Identities=13% Similarity=0.210 Sum_probs=45.7
Q ss_pred HHHHhcCCceeEEEecccccCccchh----ccc--eeeEEecCCeeeecCCCeeEEEeecCCC-----------CCCCHh
Q psy12041 76 RPVAKRGALLFFVFSDISNVNPMYQY----SLE--SYLEVPYGDKEVDYDVNFRLYLTTKIPN-----------PTFDPS 138 (153)
Q Consensus 76 e~a~~~Gs~l~~li~~l~~idp~y~~----~L~--~~i~i~~g~k~i~~~~~F~l~l~t~~~~-----------~~~~~~ 138 (153)
-.|++.|. .++++++...+|-.+. +|. +.+.+.-+++.+.-+|+||++.+.+... -..+..
T Consensus 129 ~~A~~~g~--illlDEin~a~p~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~Gd~~G~y~Gt~~l~~A 206 (327)
T TIGR01650 129 PWALQHNV--ALCFDEYDAGRPDVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLGDTTGLYHGTQQINQA 206 (327)
T ss_pred hhHHhCCe--EEEechhhccCHHHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcCCCCcceeeeecCCHH
Confidence 55678887 8999999888875444 444 2344444567788899999998886422 123666
Q ss_pred hhcceEE
Q psy12041 139 LYTKATV 145 (153)
Q Consensus 139 ~~~~~~~ 145 (153)
...|..+
T Consensus 207 ~lDRF~i 213 (327)
T TIGR01650 207 QMDRWSI 213 (327)
T ss_pred HHhheee
Confidence 6677754
No 17
>cd01262 PH_PDK1 3-Phosphoinositide dependent protein kinase 1 (PDK1) pleckstrin homology (PH) domain. 3-Phosphoinositide dependent protein kinase 1 (PDK1) pleckstrin homology (PH) domain. PDK1 contains an N-terminal serine/threonine kinase domain followed by a PH domain. Following binding of the PH domain to PtdIns(3,4,5)P3 and PtdIns(3,4)P2, PDK1 activates kinases such as Akt (PKB). PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=24.39 E-value=23 Score=23.80 Aligned_cols=20 Identities=25% Similarity=0.396 Sum_probs=15.8
Q ss_pred CcceEecCcchHHHHHHhhh
Q psy12041 28 HFPLCIDPQTQALKWIRNRE 47 (153)
Q Consensus 28 ~~Pl~iDP~~~~~~wl~~~~ 47 (153)
|.=.+-||.+.|..|++..+
T Consensus 66 rty~leD~~~~a~~W~~~I~ 85 (89)
T cd01262 66 KVYSFEDPKGRASQWKKAIE 85 (89)
T ss_pred ceEEEECCCCCHHHHHHHHH
Confidence 33356899999999998764
No 18
>PRK07003 DNA polymerase III subunits gamma and tau; Validated
Probab=21.84 E-value=1.2e+02 Score=28.52 Aligned_cols=55 Identities=9% Similarity=0.177 Sum_probs=37.3
Q ss_pred eEEEecccccCccchhccceeeEEecCCeeeecCCCeeEEEeecCCCCCCCHhhhcceEEEEEE
Q psy12041 86 FFVFSDISNVNPMYQYSLESYLEVPYGDKEVDYDVNFRLYLTTKIPNPTFDPSLYTKATVINYS 149 (153)
Q Consensus 86 ~~li~~l~~idp~y~~~L~~~i~i~~g~k~i~~~~~F~l~l~t~~~~~~~~~~~~~~~~~inft 149 (153)
.++|++++.++.--.+.|.+.+ -+..++.+++|.|+.. ..+++.+.||+..++|.
T Consensus 122 VIIIDEah~LT~~A~NALLKtL--------EEPP~~v~FILaTtd~-~KIp~TIrSRCq~f~Fk 176 (830)
T PRK07003 122 VYMIDEVHMLTNHAFNAMLKTL--------EEPPPHVKFILATTDP-QKIPVTVLSRCLQFNLK 176 (830)
T ss_pred EEEEeChhhCCHHHHHHHHHHH--------HhcCCCeEEEEEECCh-hhccchhhhheEEEecC
Confidence 6778888887653333333221 1244577778888654 56788999999999995
No 19
>PF13711 DUF4160: Domain of unknown function (DUF4160)
Probab=21.69 E-value=83 Score=19.33 Aligned_cols=19 Identities=21% Similarity=0.391 Sum_probs=14.0
Q ss_pred CeeEEEeecCCCCCCCHhh
Q psy12041 121 NFRLYLTTKIPNPTFDPSL 139 (153)
Q Consensus 121 ~F~l~l~t~~~~~~~~~~~ 139 (153)
+|++|+.++..++|-||.+
T Consensus 1 G~~i~~ys~e~~dH~PpHv 19 (66)
T PF13711_consen 1 GIRIYFYSNEGNDHEPPHV 19 (66)
T ss_pred CEEEEEEECCCCCCCCCeE
Confidence 4789999977776666654
No 20
>PRK12758 DNA topoisomerase IV subunit A; Provisional
Probab=21.21 E-value=64 Score=30.37 Aligned_cols=26 Identities=27% Similarity=0.349 Sum_probs=21.0
Q ss_pred CCCcchhhhhHhhhcCCCcceEecCcch
Q psy12041 11 PPDELSIQNGILSTRGCHFPLCIDPQTQ 38 (153)
Q Consensus 11 p~d~~s~ena~i~~~~~~~Pl~iDP~~~ 38 (153)
|..+-|+..|++-+ ++..| +|||||+
T Consensus 85 PHGD~SiydaiV~M-AQ~~~-Lid~qGN 110 (869)
T PRK12758 85 PHGDASIGDALVQL-GQKDL-LIDTQGN 110 (869)
T ss_pred CCchHHHHHHHHHH-hCcCc-EEeccCC
Confidence 77888999997766 55677 9999985
No 21
>cd00187 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth.
Probab=20.36 E-value=67 Score=27.78 Aligned_cols=28 Identities=25% Similarity=0.458 Sum_probs=21.4
Q ss_pred CCCCcchhhhhHhhhc---CCCcceEecCcch
Q psy12041 10 LPPDELSIQNGILSTR---GCHFPLCIDPQTQ 38 (153)
Q Consensus 10 Lp~d~~s~ena~i~~~---~~~~Pl~iDP~~~ 38 (153)
=|..+.|+..|++-+. +.+.| +|||||+
T Consensus 49 hpHGd~Siy~aiV~MAQ~fs~n~p-Lldg~Gn 79 (445)
T cd00187 49 HPHGDSSLYDTIVRMAQDFSNNIP-LLDPQGN 79 (445)
T ss_pred CCCchHHHHHHHHHHhhhccccce-eEeCCCC
Confidence 4788889998877653 35777 7899986
No 22
>smart00434 TOP4c DNA Topoisomerase IV. Bacterial DNA topoisomerase IV, GyrA, ParC
Probab=20.17 E-value=67 Score=27.74 Aligned_cols=27 Identities=22% Similarity=0.455 Sum_probs=19.3
Q ss_pred CCCcchhhhhHhhhc---CCCcceEecCcch
Q psy12041 11 PPDELSIQNGILSTR---GCHFPLCIDPQTQ 38 (153)
Q Consensus 11 p~d~~s~ena~i~~~---~~~~Pl~iDP~~~ 38 (153)
|..+.|+..|++-+. +.++| +|||||+
T Consensus 69 pHGd~Siy~aiV~mAQ~f~~n~p-Ll~~~Gn 98 (445)
T smart00434 69 PHGDSSLYDAIVRMAQDFSNNYP-LLDGQGN 98 (445)
T ss_pred CCchHHHHHHHHHHhcccccccc-eEeCCCC
Confidence 677889988877652 23446 7899986
Done!