Query psy15467
Match_columns 241
No_of_seqs 193 out of 1461
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 21:48:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15467.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15467hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1470|consensus 100.0 2.4E-35 5.2E-40 256.6 10.8 180 3-192 51-244 (324)
2 KOG1471|consensus 100.0 1.1E-34 2.5E-39 257.2 10.3 191 3-193 47-259 (317)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 9.8E-30 2.1E-34 203.0 7.7 149 33-190 3-159 (159)
4 smart00516 SEC14 Domain in hom 100.0 4.7E-28 1E-32 193.1 13.4 140 47-191 14-157 (158)
5 cd00170 SEC14 Sec14p-like lipi 99.9 2.5E-26 5.4E-31 181.2 13.7 139 48-190 16-157 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.4 2.4E-13 5.2E-18 107.7 6.1 133 46-190 7-143 (149)
7 PF03765 CRAL_TRIO_N: CRAL/TRI 98.2 1.5E-07 3.2E-12 62.1 -0.6 21 3-23 33-53 (55)
8 KOG4406|consensus 97.8 0.00019 4.2E-09 64.9 9.8 130 37-179 80-211 (467)
9 PF14213 DUF4325: Domain of un 64.9 35 0.00077 23.3 6.2 51 98-149 16-68 (74)
10 PF14555 UBA_4: UBA-like domai 57.7 4.2 9.1E-05 24.9 0.4 19 4-22 18-36 (43)
11 PF03641 Lysine_decarbox: Poss 52.0 43 0.00094 25.6 5.4 42 135-177 86-132 (133)
12 COG2961 ComJ Protein involved 48.7 13 0.00029 32.2 2.1 28 134-161 237-264 (279)
13 PF04378 RsmJ: Ribosomal RNA s 43.5 17 0.00036 31.4 2.0 34 129-162 201-234 (245)
14 TIGR02364 dha_pts dihydroxyace 41.0 1.4E+02 0.0031 22.7 6.7 51 97-155 59-109 (125)
15 TIGR00730 conserved hypothetic 40.0 87 0.0019 25.4 5.7 66 107-178 105-175 (178)
16 KOG1534|consensus 39.9 75 0.0016 27.1 5.2 63 83-146 76-145 (273)
17 PF01740 STAS: STAS domain; I 35.0 93 0.002 22.6 4.8 50 100-151 49-98 (117)
18 PF11964 SpoIIAA-like: SpoIIAA 31.8 1E+02 0.0022 22.0 4.5 57 97-155 30-87 (109)
19 cd07042 STAS_SulP_like_sulfate 31.4 1.8E+02 0.0039 20.2 6.1 50 100-151 42-91 (107)
20 PF02875 Mur_ligase_C: Mur lig 31.2 1.5E+02 0.0031 20.6 5.1 30 97-131 11-40 (91)
21 cd07043 STAS_anti-anti-sigma_f 27.9 2E+02 0.0044 19.6 5.9 51 100-152 39-89 (99)
22 PF00627 UBA: UBA/TS-N domain; 27.4 26 0.00057 20.4 0.5 17 5-21 20-36 (37)
23 PRK14484 phosphotransferase ma 27.0 2.9E+02 0.0063 21.1 6.3 48 98-155 58-105 (124)
24 TIGR02886 spore_II_AA anti-sig 26.6 2.4E+02 0.0051 20.0 6.4 51 100-152 40-90 (106)
25 KOG4178|consensus 24.8 2.4E+02 0.0052 25.4 6.2 82 48-144 67-149 (322)
26 TIGR00377 ant_ant_sig anti-ant 24.4 2.6E+02 0.0056 19.7 5.7 51 98-152 42-94 (108)
27 COG1219 ClpX ATP-dependent pro 23.9 35 0.00075 30.9 0.8 19 4-22 147-165 (408)
28 smart00165 UBA Ubiquitin assoc 20.9 48 0.001 19.0 0.8 19 4-22 18-36 (37)
No 1
>KOG1470|consensus
Probab=100.00 E-value=2.4e-35 Score=256.62 Aligned_cols=180 Identities=20% Similarity=0.216 Sum_probs=154.8
Q ss_pred ccchhhhcCCCChhhHhhcCcCccccccc----c---------cccCCCcccccCCCCCCCCCCeEEEEEeccCCCCCCc
Q psy15467 3 SMGKKLRRDTIDQERPLRSLPVPAQLVES----P---------LLSGGHLQVSPTPDGLTPGGHQNPILRLCVSSRLEPN 69 (241)
Q Consensus 3 ~llRFLrArkfdv~kA~~~L~~~~~~~~~----~---------~l~~g~~~~l~~~~~~d~~G~~vii~r~~~~~~~~~~ 69 (241)
++|||||||+||+++|.+||..++.|+.+ . -++.|..+.++ +|++||||+|+|+..+.+...+
T Consensus 51 cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~~~~~Ev~~e~~tGK~yi~G----~D~~gRPVl~~~~~~~~qn~~t 126 (324)
T KOG1470|consen 51 CLLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEVIEADEVAAELETGKAYILG----HDKDGRPVLYLRPRPHRQNTKT 126 (324)
T ss_pred HHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCccccCHHHHHHHhhcCcEEEec----ccCCCCeEEEEecCCCCCCCCC
Confidence 68999999999999999999999999754 1 34668888887 4589999999987754443332
Q ss_pred hhhhccchhhhHHHHHhhhhhhccCCccccEEEEEeCCCCcc-ccCHHHHHHHHHHHHhhhhhhcceEEEEeCChHHHHH
Q psy15467 70 VDLRQSDATSDHDIRTSGLLLVDTKIQYSGFVFLLDWNQTSI-YASPTLLRTMISGLQDCYPARFKAIHFINEPVQVDVL 148 (241)
Q Consensus 70 ~~~~~~~~~~~~~i~~~E~l~~~~~~~~~g~v~I~D~~g~s~-~~~~~~~k~~~~~~q~~yP~rl~~i~ivN~P~~~~~~ 148 (241)
... ...+.+++||.++.....+++.+++++|++|+|+ +++...+|.++.++|+|||+||+..+++|+||+|+.+
T Consensus 127 ~~~-----~~r~~Vy~mE~Ai~~lp~~qe~~~~L~D~~~fs~sN~d~~~~k~~~~~lq~hYPErLg~a~l~~~P~iF~~~ 201 (324)
T KOG1470|consen 127 QKE-----LERLLVYTLENAILFLPPGQEQFVWLFDLTGFSMSNPDIKFLKELLHILQDHYPERLGKALLVNAPWIFQPF 201 (324)
T ss_pred HHH-----HHHHHHHHHHHHHHhCCCCcceEEEEEecccCcccCCCcHHHHHHHHHHHHhChHHhhhhhhcCChHHHHHH
Confidence 211 2345677899988877778899999999999998 6889999999999999999999999999999999999
Q ss_pred HHHHhhhcChhhcCceEEeCCChHHHhccCCCCCCCcccCCCcc
Q psy15467 149 LALVKPFLKEKTRDKIIVHGQNLDSLYGYLPRDILPIEIFNGSI 192 (241)
Q Consensus 149 ~~lik~fl~~k~~~ki~~~~~~~~~L~~~i~~~~LP~eyGG~~~ 192 (241)
|+++|||++|+|++||.|+ .+.+.+.++||+++||..|||...
T Consensus 202 wkiikpflDp~t~~Kv~F~-~~~~~l~~~~d~~~l~s~~GG~~~ 244 (324)
T KOG1470|consen 202 WKIIKPFLDPKTASKVKFV-EPKDDLSEYFDESQLPSLFGGKLL 244 (324)
T ss_pred HHHhhhccChhhhceeEEe-cChhHHHhhCCccccchhhCCCcc
Confidence 9999999999999999999 467789999999999999999543
No 2
>KOG1471|consensus
Probab=100.00 E-value=1.1e-34 Score=257.21 Aligned_cols=191 Identities=29% Similarity=0.341 Sum_probs=147.5
Q ss_pred ccchhhhcCCCChhhHhhcCcCccccccc----ccccC----CCcc--cccCCCCCCCCCCeEEEEEeccCCCCCCchhh
Q psy15467 3 SMGKKLRRDTIDQERPLRSLPVPAQLVES----PLLSG----GHLQ--VSPTPDGLTPGGHQNPILRLCVSSRLEPNVDL 72 (241)
Q Consensus 3 ~llRFLrArkfdv~kA~~~L~~~~~~~~~----~~l~~----g~~~--~l~~~~~~d~~G~~vii~r~~~~~~~~~~~~~ 72 (241)
+||||||||+||+++|.+||..+++|+.. +++.. ..+. ......+.+++|+++.+-+.+..+.+..-...
T Consensus 47 ~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~~g~~~~~~l~~~~ 126 (317)
T KOG1471|consen 47 NLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFEDFEEDDELLKYYPQGLHGVDKEGRPVYIERLGKIDPKGLLKRT 126 (317)
T ss_pred HHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhccccchhhhhhccccccccCCCCCEEEEeccCCCCcccceeec
Confidence 68999999999999999999887777643 23322 1111 11223458899999999999987765532211
Q ss_pred hc---cchhhhH----HHHHhhhhhhccCCccccEEEEEeCCCCcc----ccCHHHHHHHHHHHHhhhhhhcceEEEEeC
Q psy15467 73 RQ---SDATSDH----DIRTSGLLLVDTKIQYSGFVFLLDWNQTSI----YASPTLLRTMISGLQDCYPARFKAIHFINE 141 (241)
Q Consensus 73 ~~---~~~~~~~----~i~~~E~l~~~~~~~~~g~v~I~D~~g~s~----~~~~~~~k~~~~~~q~~yP~rl~~i~ivN~ 141 (241)
.. .+..... ....+|.+.+..+.+++|++.|+|++|+++ +..++.+++++.++|++||+|++++||||+
T Consensus 127 ~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G~~~~~~~~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~ 206 (317)
T KOG1471|consen 127 GSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKGVSLSHLLKPAPTLLKKILKILQDNYPERLKRIHIINA 206 (317)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCCCcchhHHHHHHHHHHHHHHHHHHhCHHhhceEEEEcC
Confidence 00 0000000 111345555555678999999999999996 467889999999999999999999999999
Q ss_pred ChHHHHHHHHHhhhcChhhcCceE-EeCCChHHHhccCCCCCCCcccCCCccc
Q psy15467 142 PVQVDVLLALVKPFLKEKTRDKII-VHGQNLDSLYGYLPRDILPIEIFNGSII 193 (241)
Q Consensus 142 P~~~~~~~~lik~fl~~k~~~ki~-~~~~~~~~L~~~i~~~~LP~eyGG~~~~ 193 (241)
|++|+++|+++||||+++|++||+ +++++.++|.++||+++||.+|||++..
T Consensus 207 P~~f~~~~~~ikpfL~~kt~~ki~~~~~~~~~~L~k~i~~~~LP~~yGG~~~~ 259 (317)
T KOG1471|consen 207 PTIFSALWKVVKPFLDEKTRKKIHVLHSKDKESLLKYIPPEVLPEEYGGTCGD 259 (317)
T ss_pred chhHHHHHHHHhccCCHHHHhhheecCCCchhhhhhhCCHhhCccccCCCccc
Confidence 999999999999999999999999 6666778999999999999999997654
No 3
>PF00650 CRAL_TRIO: CRAL/TRIO domain; InterPro: IPR001251 This entry defines the C-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1OLM_E 1O6U_E 3Q8G_A 3B7Q_B 3B7Z_A ....
Probab=99.96 E-value=9.8e-30 Score=203.01 Aligned_cols=149 Identities=28% Similarity=0.358 Sum_probs=111.5
Q ss_pred cccCCCcccccCCCCCCCCCCeEEEEEeccCCCCCCchhhhccchhhhHHHHHhhhhhhc-cC-CccccEEEEEeCCCCc
Q psy15467 33 LLSGGHLQVSPTPDGLTPGGHQNPILRLCVSSRLEPNVDLRQSDATSDHDIRTSGLLLVD-TK-IQYSGFVFLLDWNQTS 110 (241)
Q Consensus 33 ~l~~g~~~~l~~~~~~d~~G~~vii~r~~~~~~~~~~~~~~~~~~~~~~~i~~~E~l~~~-~~-~~~~g~v~I~D~~g~s 110 (241)
+.+.|..+..+ .|++|++|+++|+++.++...+.... ....++++|.++.. ++ .+.+|+++|+|++|++
T Consensus 3 ~~~~~~~~~~g----~D~~gr~v~~~~~~~~~~~~~~~~~~-----~~~~~~~~E~~~~~~~~~~~~~~~~~iiD~~g~~ 73 (159)
T PF00650_consen 3 ILKSGPFYLHG----RDKDGRPVIYIRLGRFDPKKFSPEDV-----IRFFVYLLERMLKRMPEGGQVEGIVVIIDLSGFS 73 (159)
T ss_dssp HHTTSCEEEEE----E-TTS-EEEEEEGTT--HHTS-HHHH-----HHHHHHHHHHHHHTHHHTSHHH-EEEEEE-TT--
T ss_pred HHCCeeEEECC----CCCCcCEEEEEEcccCCCCcCCHHHH-----HHHHHHHHHHHHhhhcccccceeEEEEEeCCCce
Confidence 34455555444 46899999999999877665543222 22345567776643 32 5899999999999999
Q ss_pred c-ccC---HHHHHHHHHHHHhhhhhhcceEEEEeCChHHHHHHHHHhhhcChhhcCceEEeCC-Ch-HHHhccCCCCCCC
Q psy15467 111 I-YAS---PTLLRTMISGLQDCYPARFKAIHFINEPVQVDVLLALVKPFLKEKTRDKIIVHGQ-NL-DSLYGYLPRDILP 184 (241)
Q Consensus 111 ~-~~~---~~~~k~~~~~~q~~yP~rl~~i~ivN~P~~~~~~~~lik~fl~~k~~~ki~~~~~-~~-~~L~~~i~~~~LP 184 (241)
+ +++ .+.+|.++.++|++||+|++++|+||+|++++++|+++++||++++++||+++++ +. ++|.++||+++||
T Consensus 74 ~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~~l~~~i~~~~lP 153 (159)
T PF00650_consen 74 LSNFDWWPISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSDWKAKLKEYIDPEQLP 153 (159)
T ss_dssp HHHHHCHHHHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTCHCHHHCCCSTGGGSB
T ss_pred EeccccchhhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcccHHHHHhhCCHhHCc
Confidence 7 455 8899999999999999999999999999999999999999999999999999953 44 6899999999999
Q ss_pred cccCCC
Q psy15467 185 IEIFNG 190 (241)
Q Consensus 185 ~eyGG~ 190 (241)
.+|||+
T Consensus 154 ~~~GG~ 159 (159)
T PF00650_consen 154 VEYGGT 159 (159)
T ss_dssp GGGTSS
T ss_pred hhcCCC
Confidence 999995
No 4
>smart00516 SEC14 Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.95 E-value=4.7e-28 Score=193.11 Aligned_cols=140 Identities=27% Similarity=0.372 Sum_probs=121.6
Q ss_pred CCCCCCCeEEEEEeccCCCCCCchhhhccchhhhHHHHHhhhhhhc--cCCccccEEEEEeCCCCcc-ccCHHHHHHHHH
Q psy15467 47 GLTPGGHQNPILRLCVSSRLEPNVDLRQSDATSDHDIRTSGLLLVD--TKIQYSGFVFLLDWNQTSI-YASPTLLRTMIS 123 (241)
Q Consensus 47 ~~d~~G~~vii~r~~~~~~~~~~~~~~~~~~~~~~~i~~~E~l~~~--~~~~~~g~v~I~D~~g~s~-~~~~~~~k~~~~ 123 (241)
|.|++||+|++++++..++...+.... +...+.++|.++.+ +..+++|+++|+|++|+++ +++++.+|+++.
T Consensus 14 g~D~~GrpV~~~~~~~~~~~~~~~~~~-----~~~~~~~~e~~~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~lk~~~~ 88 (158)
T smart00516 14 GYDKDGRPVLIFRAGRFDLKSVTLEEL-----LRYLVYVLEKILQREKKTGGIEGFTVIFDLKGLSMSNPDLSVLRKILK 88 (158)
T ss_pred CCCCCcCEEEEEeccccccCcCCHHHH-----HHHHHHHHHHHHHHHhcCCCeeeEEEEEECCCCCcccccHHHHHHHHH
Confidence 478999999999999877655544332 23345567777765 5678999999999999997 688999999999
Q ss_pred HHHhhhhhhcceEEEEeCChHHHHHHHHHhhhcChhhcCceEEeCCC-hHHHhccCCCCCCCcccCCCc
Q psy15467 124 GLQDCYPARFKAIHFINEPVQVDVLLALVKPFLKEKTRDKIIVHGQN-LDSLYGYLPRDILPIEIFNGS 191 (241)
Q Consensus 124 ~~q~~yP~rl~~i~ivN~P~~~~~~~~lik~fl~~k~~~ki~~~~~~-~~~L~~~i~~~~LP~eyGG~~ 191 (241)
.+|++||+|++++||||+|+++.++|+++++|+++++++||++++++ .++|.++||+++||.+|||++
T Consensus 89 ~~~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~L~~~i~~~~lP~~~GG~~ 157 (158)
T smart00516 89 ILQDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGNDSKEELLEYIDPEQLPEELGGTL 157 (158)
T ss_pred HHHHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCCCCHHHHHhhCCHhhCcHhhCCCC
Confidence 99999999999999999999999999999999999999999999642 689999999999999999974
No 5
>cd00170 SEC14 Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.94 E-value=2.5e-26 Score=181.20 Aligned_cols=139 Identities=32% Similarity=0.444 Sum_probs=116.0
Q ss_pred CCCCCCeEEEEEeccCCCCCCchhhhccchhhhHHHHHhhhhhhccCCccccEEEEEeCCCCcc-cc--CHHHHHHHHHH
Q psy15467 48 LTPGGHQNPILRLCVSSRLEPNVDLRQSDATSDHDIRTSGLLLVDTKIQYSGFVFLLDWNQTSI-YA--SPTLLRTMISG 124 (241)
Q Consensus 48 ~d~~G~~vii~r~~~~~~~~~~~~~~~~~~~~~~~i~~~E~l~~~~~~~~~g~v~I~D~~g~s~-~~--~~~~~k~~~~~ 124 (241)
.|++|++|++++++..+....... ...+...+..+|.++.++..+.+|+++|+|++|+++ ++ +++.+|+++..
T Consensus 16 ~D~~gr~V~~~~~~~~~~~~~~~~----~~~~~~~~~~~e~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~~~~k~~~~~ 91 (157)
T cd00170 16 RDKEGRPVLIIRAGNKDLSKSLDS----EELLRYLVYTLEKLLQEDDEQVEGFVVIIDLKGLSLSHLLPDPSLLKKILKI 91 (157)
T ss_pred CCCCcCEEEEEecCCcchhhcCCH----HHHHHHHHHHHHHHHhhhhhcccceEEEEECCCCChhccchhHHHHHHHHHH
Confidence 579999999999995333222110 112334455678877776666689999999999997 44 77889999999
Q ss_pred HHhhhhhhcceEEEEeCChHHHHHHHHHhhhcChhhcCceEEeCCChHHHhccCCCCCCCcccCCC
Q psy15467 125 LQDCYPARFKAIHFINEPVQVDVLLALVKPFLKEKTRDKIIVHGQNLDSLYGYLPRDILPIEIFNG 190 (241)
Q Consensus 125 ~q~~yP~rl~~i~ivN~P~~~~~~~~lik~fl~~k~~~ki~~~~~~~~~L~~~i~~~~LP~eyGG~ 190 (241)
+|++||+|++++|+||+|+++.++|+++++|+++++++||++++++.++|.++||+++||.+|||+
T Consensus 92 ~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~L~~~i~~~~Lp~~~GG~ 157 (157)
T cd00170 92 LQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSDKEELLKYIDKEQLPEEYGGT 157 (157)
T ss_pred HHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCCHHHHHhhCChhhCcHhhCCC
Confidence 999999999999999999999999999999999999999999963389999999999999999995
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.42 E-value=2.4e-13 Score=107.74 Aligned_cols=133 Identities=16% Similarity=0.183 Sum_probs=86.7
Q ss_pred CCCCCCCCeEEEEEeccCCCCCCchhhhccchhhhHHHHHhhhhhhccCCccccEEEEEeCCCCcc--ccCHHHHHHHHH
Q psy15467 46 DGLTPGGHQNPILRLCVSSRLEPNVDLRQSDATSDHDIRTSGLLLVDTKIQYSGFVFLLDWNQTSI--YASPTLLRTMIS 123 (241)
Q Consensus 46 ~~~d~~G~~vii~r~~~~~~~~~~~~~~~~~~~~~~~i~~~E~l~~~~~~~~~g~v~I~D~~g~s~--~~~~~~~k~~~~ 123 (241)
+|.|++|+||+++..... +...+.. ..+.+.+. .+.+ +....++++|+|++|++. ..+...++++..
T Consensus 7 gG~d~~g~pV~~~~~~~~-~~~~~~~-----~ll~yl~~---~l~~--~~~~~~f~vVid~~~~~~~~~~~~~~l~~~~~ 75 (149)
T PF13716_consen 7 GGRDREGRPVVVFIASRL-PSSDDLE-----RLLLYLLS---TLSE--EVVDKPFSVVIDHTGFSRSSEPSLSWLKQLYK 75 (149)
T ss_dssp EEEBTTS-EEEEEEGGG--C-TTHHH-----HHHHHHHH---HH-T--TTTTS-EEEEEE-TT--GGG---HHHHHHTTT
T ss_pred cccCCCcCEEEEEECCcC-cchhhHH-----HHHHHHHH---hhhH--HhcCCCEEEEEEcCCCccccCCchHHHHHHHH
Confidence 457899999999987765 2221110 01222222 2211 134577999999999986 356778999999
Q ss_pred HHHhhhhhhcceEEEEeCChHHHHHH-HHHhhhcChhh-cCceEEeCCChHHHhccCCCCCCCcccCCC
Q psy15467 124 GLQDCYPARFKAIHFINEPVQVDVLL-ALVKPFLKEKT-RDKIIVHGQNLDSLYGYLPRDILPIEIFNG 190 (241)
Q Consensus 124 ~~q~~yP~rl~~i~ivN~P~~~~~~~-~lik~fl~~k~-~~ki~~~~~~~~~L~~~i~~~~LP~eyGG~ 190 (241)
.++..|+.+++.+++||+.+++..++ .+.+++.+++. ..||.++ ++.++|.++||+++||++.||.
T Consensus 76 ~l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~-~sl~~L~~~i~~~qL~~~lp~~ 143 (149)
T PF13716_consen 76 LLPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYV-SSLSELSKHIDPSQLPESLPGV 143 (149)
T ss_dssp SS-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEE-SSTCGGGGTSGGGG------HH
T ss_pred HHHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEE-CCHHHHHhhCCHHHhcccCCCE
Confidence 99999999999999999999999999 66678889998 9999998 5899999999999999999963
No 7
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=98.25 E-value=1.5e-07 Score=62.12 Aligned_cols=21 Identities=24% Similarity=0.325 Sum_probs=18.7
Q ss_pred ccchhhhcCCCChhhHhhcCc
Q psy15467 3 SMGKKLRRDTIDQERPLRSLP 23 (241)
Q Consensus 3 ~llRFLrArkfdv~kA~~~L~ 23 (241)
+||||||||+||+++|++||.
T Consensus 33 ~llRFLRARkf~v~~A~~mL~ 53 (55)
T PF03765_consen 33 FLLRFLRARKFDVEKAFKMLK 53 (55)
T ss_dssp HHHHHHHHTTT-HHHHHHHHH
T ss_pred HHHHHHHHccCCHHHHHHHHH
Confidence 689999999999999999984
No 8
>KOG4406|consensus
Probab=97.77 E-value=0.00019 Score=64.88 Aligned_cols=130 Identities=18% Similarity=0.192 Sum_probs=85.8
Q ss_pred CCcccccCCCCCCCCCCeEEEEEeccCCCCCCchhhhccchhhhHHHHHhhhhhhccCCccccEEEEEeCCCCccc--cC
Q psy15467 37 GHLQVSPTPDGLTPGGHQNPILRLCVSSRLEPNVDLRQSDATSDHDIRTSGLLLVDTKIQYSGFVFLLDWNQTSIY--AS 114 (241)
Q Consensus 37 g~~~~l~~~~~~d~~G~~vii~r~~~~~~~~~~~~~~~~~~~~~~~i~~~E~l~~~~~~~~~g~v~I~D~~g~s~~--~~ 114 (241)
+.+.+.+ ++.|++|++|+++-..+..... ..+. .+ .....++.++..++. .++.+.=-.|.... -.
T Consensus 80 ei~qvi~--~~~D~~gr~iivv~a~rlp~~~-eld~-~~--li~~~v~~id~~Ve~------DYt~vYfh~gl~s~nkp~ 147 (467)
T KOG4406|consen 80 EILQVIG--DAKDKQGRKIIVVYACRLPSSS-ELDD-IR--LISYLVYTIDKYVEN------DYTLVYFHHGLPSDNKPY 147 (467)
T ss_pred heeeecc--CcccccCCeeEEEEEecCCchh-hhhh-HH--HHHHHHHHHHHHHhc------cceeeehhcCCcccccch
Confidence 4444443 2358999999988877653321 1111 11 122334444554443 25566555666542 23
Q ss_pred HHHHHHHHHHHHhhhhhhcceEEEEeCChHHHHHHHHHhhhcChhhcCceEEeCCChHHHhccCC
Q psy15467 115 PTLLRTMISGLQDCYPARFKAIHFINEPVQVDVLLALVKPFLKEKTRDKIIVHGQNLDSLYGYLP 179 (241)
Q Consensus 115 ~~~~k~~~~~~q~~yP~rl~~i~ivN~P~~~~~~~~lik~fl~~k~~~ki~~~~~~~~~L~~~i~ 179 (241)
...+.+...-+-.+|---++++|+|++-|+..++|+++|||++.|-.+||+-. +..++|.+++.
T Consensus 148 l~~l~~aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~-n~lseL~~~l~ 211 (467)
T KOG4406|consen 148 LQLLFDAYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYF-NSLSELFEALK 211 (467)
T ss_pred HHHHHHHHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEe-ehHHHHHHhhh
Confidence 34444455555566888899999999999999999999999999999999987 46889988765
No 9
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=64.85 E-value=35 Score=23.26 Aligned_cols=51 Identities=16% Similarity=0.253 Sum_probs=34.2
Q ss_pred ccEEEEEeCCCCccccCHHHHHHHHHHHHhhhh--hhcceEEEEeCChHHHHHH
Q psy15467 98 SGFVFLLDWNQTSIYASPTLLRTMISGLQDCYP--ARFKAIHFINEPVQVDVLL 149 (241)
Q Consensus 98 ~g~v~I~D~~g~s~~~~~~~~k~~~~~~q~~yP--~rl~~i~ivN~P~~~~~~~ 149 (241)
.|-.+++|++|++ .++.+++-.++.-+...|| .--+.+.++|+......+.
T Consensus 16 ~~~~V~lDF~gv~-~~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I 68 (74)
T PF14213_consen 16 EGEKVVLDFEGVE-SITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMI 68 (74)
T ss_pred cCCeEEEECCCcc-cccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHH
Confidence 4545899999995 4566777666666666666 3345677777766555444
No 10
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=57.71 E-value=4.2 Score=24.88 Aligned_cols=19 Identities=16% Similarity=0.151 Sum_probs=15.3
Q ss_pred cchhhhcCCCChhhHhhcC
Q psy15467 4 MGKKLRRDTIDQERPLRSL 22 (241)
Q Consensus 4 llRFLrArkfdv~kA~~~L 22 (241)
...||.+.+||++.|+..+
T Consensus 18 A~~~L~~~~wdle~Av~~y 36 (43)
T PF14555_consen 18 AIQYLEANNWDLEAAVNAY 36 (43)
T ss_dssp HHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHH
Confidence 3579999999999999865
No 11
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=52.02 E-value=43 Score=25.63 Aligned_cols=42 Identities=19% Similarity=0.253 Sum_probs=35.2
Q ss_pred eEEEEeCChHHHHHHHHH-----hhhcChhhcCceEEeCCChHHHhcc
Q psy15467 135 AIHFINEPVQVDVLLALV-----KPFLKEKTRDKIIVHGQNLDSLYGY 177 (241)
Q Consensus 135 ~i~ivN~P~~~~~~~~li-----k~fl~~k~~~ki~~~~~~~~~L~~~ 177 (241)
-+.++|..-+.+.++.++ ..|+++...+.++++ ++.+++.++
T Consensus 86 Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~-d~~~e~~~~ 132 (133)
T PF03641_consen 86 PIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFV-DDPEEALEY 132 (133)
T ss_dssp EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEE-SSHHHHHHH
T ss_pred CEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEe-CCHHHHHhh
Confidence 699999987888888876 569999999999999 588877654
No 12
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=48.67 E-value=13 Score=32.15 Aligned_cols=28 Identities=21% Similarity=0.312 Sum_probs=24.2
Q ss_pred ceEEEEeCChHHHHHHHHHhhhcChhhc
Q psy15467 134 KAIHFINEPVQVDVLLALVKPFLKEKTR 161 (241)
Q Consensus 134 ~~i~ivN~P~~~~~~~~lik~fl~~k~~ 161 (241)
.++.+||+||.+..-+..+-|+|...+.
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~L~ 264 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTLLA 264 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHHhc
Confidence 5899999999999999999999876543
No 13
>PF04378 RsmJ: Ribosomal RNA small subunit methyltransferase D, RsmJ; InterPro: IPR007473 This is a bacterial protein of unknown function, possibly secreted.; PDB: 2OO3_A.
Probab=43.45 E-value=17 Score=31.36 Aligned_cols=34 Identities=24% Similarity=0.266 Sum_probs=23.5
Q ss_pred hhhhcceEEEEeCChHHHHHHHHHhhhcChhhcC
Q psy15467 129 YPARFKAIHFINEPVQVDVLLALVKPFLKEKTRD 162 (241)
Q Consensus 129 yP~rl~~i~ivN~P~~~~~~~~lik~fl~~k~~~ 162 (241)
..+.=.++.|||+||-+....+-+-|+|.+.+.+
T Consensus 201 ~gm~GSGm~iiNPPw~l~~~l~~~l~~L~~~L~~ 234 (245)
T PF04378_consen 201 RGMNGSGMLIINPPWTLDEELEEILPWLAETLAQ 234 (245)
T ss_dssp -S--EEEEEEES--TTHHHHHHHHHHHHHHHSST
T ss_pred CceecceEEEEcCCccHHHHHHHHHHHHHHHhCc
Confidence 3344468999999999999999888888766554
No 14
>TIGR02364 dha_pts dihydroxyacetone kinase, phosphotransfer subunit. In E. coli and many other bacteria, unlike the yeasts and a few bacteria such as Citrobacter freundii, the dihydroxyacetone kinase (also called glycerone kinase) transfers a phosphate from a phosphoprotein rather than from ATP and contains multiple subunits. This protein, which resembles proteins of PTS transport systems, is found with its gene adjacent to
Probab=41.02 E-value=1.4e+02 Score=22.72 Aligned_cols=51 Identities=14% Similarity=0.264 Sum_probs=34.3
Q ss_pred cccEEEEEeCCCCccccCHHHHHHHHHHHHhhhhhhcceEEEEeCChHHHHHHHHHhhh
Q psy15467 97 YSGFVFLLDWNQTSIYASPTLLRTMISGLQDCYPARFKAIHFINEPVQVDVLLALVKPF 155 (241)
Q Consensus 97 ~~g~v~I~D~~g~s~~~~~~~~k~~~~~~q~~yP~rl~~i~ivN~P~~~~~~~~lik~f 155 (241)
-.|++++.|+ |-|. .....++.+++ +.+.+.+..+|.|.+...+...+..-
T Consensus 59 ~dgVlvl~DL-Ggs~----~n~e~a~~~l~---~~~~~~v~g~nlPlvega~~aa~~~~ 109 (125)
T TIGR02364 59 ADGVLIFYDL-GSAV----MNAEMAVELLE---DEDRDKVHLVDAPLVEGAFAAAVEAQ 109 (125)
T ss_pred CCCEEEEEcC-CCcH----hHHHHHHHHhc---cccccEEEEechhHHHHHHHHHHHHc
Confidence 4789999999 5442 11112333332 35557899999999999888877543
No 15
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=40.04 E-value=87 Score=25.42 Aligned_cols=66 Identities=20% Similarity=0.109 Sum_probs=46.9
Q ss_pred CCCccccCHHHHHHHHHHHHhhhhhhcceEEEEeCChHHHHHHHHH-----hhhcChhhcCceEEeCCChHHHhccC
Q psy15467 107 NQTSIYASPTLLRTMISGLQDCYPARFKAIHFINEPVQVDVLLALV-----KPFLKEKTRDKIIVHGQNLDSLYGYL 178 (241)
Q Consensus 107 ~g~s~~~~~~~~k~~~~~~q~~yP~rl~~i~ivN~P~~~~~~~~li-----k~fl~~k~~~ki~~~~~~~~~L~~~i 178 (241)
.|++ |...+-.++...|-... -+-+.++|..-+++.+.+++ ..|++++-.+.++++ ++.+++.+++
T Consensus 105 GG~G---TL~El~e~~~~~qlg~~--~kPiil~n~~g~~~~l~~~l~~~~~~gfi~~~~~~~~~~~-d~~~e~~~~i 175 (178)
T TIGR00730 105 GGFG---TLEELFEVLTWAQLGIH--QKPIILFNVNGHFDGLVEWLKYSIQEGFISESHLKLIHVV-SRPDELIEQV 175 (178)
T ss_pred CCcc---hHHHHHHHHHHHHcCCC--CCCEEEECCcchHHHHHHHHHHHHHCCCCCHHHcCcEEEc-CCHHHHHHHH
Confidence 6665 44555555555555543 36799999887888888765 448888888999998 5888877665
No 16
>KOG1534|consensus
Probab=39.88 E-value=75 Score=27.14 Aligned_cols=63 Identities=11% Similarity=0.202 Sum_probs=43.8
Q ss_pred HHHhhhhhhc------cCCccccEEEEEeCCCCc-cccCHHHHHHHHHHHHhhhhhhcceEEEEeCChHHH
Q psy15467 83 IRTSGLLLVD------TKIQYSGFVFLLDWNQTS-IYASPTLLRTMISGLQDCYPARFKAIHFINEPVQVD 146 (241)
Q Consensus 83 i~~~E~l~~~------~~~~~~g~v~I~D~~g~s-~~~~~~~~k~~~~~~q~~yP~rl~~i~ivN~P~~~~ 146 (241)
++|+|+++++ +.+..++--+|+||-|=- +-....++++++.-++. +-.++-.+|++.++.+++
T Consensus 76 v~cmEyl~~NldwL~~~~Gd~eddylifDcPGQIELytH~pVm~~iv~hl~~-~~F~~c~Vylldsqf~vD 145 (273)
T KOG1534|consen 76 VYCMEYLLENLDWLEEEIGDVEDDYLIFDCPGQIELYTHLPVMPQIVEHLKQ-WNFNVCVVYLLDSQFLVD 145 (273)
T ss_pred hhHHHHHHHHHHHHHhhccCccCCEEEEeCCCeeEEeecChhHHHHHHHHhc-ccCceeEEEEeccchhhh
Confidence 4477776654 233467788999998853 32334568888888887 667788888888876443
No 17
>PF01740 STAS: STAS domain; InterPro: IPR002645 The STAS (Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. The establishment of differential gene expression in sporulating Bacillus subtilis involves four protein components one of which is SpoIIAA (P10727 from SWISSPROT). The four components regulate the sporulation sigma factor F. Early in sporulation, SpoIIAA is in the phosphorylated state (SpoIIAA-P), as a result of the activity of the ATP-dependent protein kinase SpoIIAB (P10728 from SWISSPROT). The site at which this protein is a conserved serine. SpoIIAB is an anti-sigma factor that in its free form inhibits F by binding to it. Competition by SpoIIAA (the anti-anti-sigma factor) for binding to SpoIIAB releases Sigma F activity []. The STAS domain is found in the anti-sigma factor antagonist SpoIIAA.; PDB: 3T6O_B 3LKL_B 1H4Z_A 1H4Y_B 1H4X_B 3NY7_A 3OIZ_A 1T6R_A 1VC1_B 1SBO_A ....
Probab=35.01 E-value=93 Score=22.57 Aligned_cols=50 Identities=12% Similarity=0.137 Sum_probs=35.1
Q ss_pred EEEEEeCCCCccccCHHHHHHHHHHHHhhhhhhcceEEEEeCChHHHHHHHH
Q psy15467 100 FVFLLDWNQTSIYASPTLLRTMISGLQDCYPARFKAIHFINEPVQVDVLLAL 151 (241)
Q Consensus 100 ~v~I~D~~g~s~~~~~~~~k~~~~~~q~~yP~rl~~i~ivN~P~~~~~~~~l 151 (241)
-.+|+||++++. ++.+.+..+..+.++.- .+=..++++|.+.-+...+..
T Consensus 49 ~~vIlD~s~v~~-iDssgi~~L~~~~~~~~-~~g~~~~l~~~~~~v~~~l~~ 98 (117)
T PF01740_consen 49 KNVILDMSGVSF-IDSSGIQALVDIIKELR-RRGVQLVLVGLNPDVRRILER 98 (117)
T ss_dssp SEEEEEETTESE-ESHHHHHHHHHHHHHHH-HTTCEEEEESHHHHHHHHHHH
T ss_pred eEEEEEEEeCCc-CCHHHHHHHHHHHHHHH-HCCCEEEEEECCHHHHHHHHH
Confidence 689999999973 45555555555555544 466789999998877766544
No 18
>PF11964 SpoIIAA-like: SpoIIAA-like; InterPro: IPR021866 This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 120 to 132 amino acids in length. This protein has a single completely conserved residue A that may be functionally important. ; PDB: 2Q3L_B 2OOK_A 3BL4_A.
Probab=31.78 E-value=1e+02 Score=22.00 Aligned_cols=57 Identities=12% Similarity=0.087 Sum_probs=42.3
Q ss_pred cccEEEEEeCC-CCccccCHHHHHHHHHHHHhhhhhhcceEEEEeCChHHHHHHHHHhhh
Q psy15467 97 YSGFVFLLDWN-QTSIYASPTLLRTMISGLQDCYPARFKAIHFINEPVQVDVLLALVKPF 155 (241)
Q Consensus 97 ~~g~v~I~D~~-g~s~~~~~~~~k~~~~~~q~~yP~rl~~i~ivN~P~~~~~~~~lik~f 155 (241)
...+.+++|++ ++. .+++........+... ....++++-+|-.+.+...+.+++.+|
T Consensus 30 ~~~~~ll~d~~~~~~-~~~~~a~~~~~~~~~~-~~~~~~r~AvV~~~~~~~~~~~~~~~~ 87 (109)
T PF11964_consen 30 HGKIRLLVDLRRDFE-GWSPEARWEDAKFGLK-HLKHFRRIAVVGDSEWIRMIANFFAAF 87 (109)
T ss_dssp SSSEEEEEEEC-CEE-EEHHHHHHHHHHHHCC-CCGGEEEEEEE-SSCCCHHHHHHHHHH
T ss_pred CCceEEEEEecCccC-CCCHHHHHHHHHhchh-hhcccCEEEEEECcHHHHHHHHHHHhc
Confidence 35588999998 763 2344555555554444 888899999999999999999999987
No 19
>cd07042 STAS_SulP_like_sulfate_transporter Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function. The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and mammals. They contain 10 to 14 transmembrane helices which form the catalytic core of the protein and a C-terminal extension, the STAS (Sulphate Transporter and AntiSigma factor antagonist) domain which plays a role in the function and regulation of the transport activity. The STAS domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
Probab=31.36 E-value=1.8e+02 Score=20.20 Aligned_cols=50 Identities=20% Similarity=0.129 Sum_probs=32.2
Q ss_pred EEEEEeCCCCccccCHHHHHHHHHHHHhhhhhhcceEEEEeCChHHHHHHHH
Q psy15467 100 FVFLLDWNQTSIYASPTLLRTMISGLQDCYPARFKAIHFINEPVQVDVLLAL 151 (241)
Q Consensus 100 ~v~I~D~~g~s~~~~~~~~k~~~~~~q~~yP~rl~~i~ivN~P~~~~~~~~l 151 (241)
..+|+|+++++. ++.+.+..+..+.+.+-. +=..+++.|++.-+.-++..
T Consensus 42 ~~lilD~~~v~~-iDss~~~~L~~~~~~~~~-~~~~~~l~~~~~~~~~~l~~ 91 (107)
T cd07042 42 KVVILDLSAVNF-IDSTAAEALEELVKDLRK-RGVELYLAGLNPQVRELLER 91 (107)
T ss_pred eEEEEECCCCch-hhHHHHHHHHHHHHHHHH-CCCEEEEecCCHHHHHHHHH
Confidence 578999999973 355555544444433333 34778999999866655544
No 20
>PF02875 Mur_ligase_C: Mur ligase family, glutamate ligase domain This Prosite entry is a subset of the Pfam family.; InterPro: IPR004101 The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages: (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer. Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) [], MurD (6.3.2.9 from EC) [], MurE (6.3.2.13 from EC) [] and MurF (6.3.2.10 from EC) []. These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales []. This entry represents the C-terminal domain from all four stage 2 Mur enzymes: UDP-N-acetylmuramate-L-alanine ligase (MurC), UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD), UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase (MurE), and UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF). This entry also includes the C-terminal domain of folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) []. The C-terminal domain is almost always associated with the cytoplasmic peptidoglycan synthetases, N-terminal domain (see IPR000713 from INTERPRO).; GO: 0005524 ATP binding, 0016874 ligase activity, 0009058 biosynthetic process; PDB: 2Y68_A 3UAG_A 4UAG_A 2UAG_A 1E0D_A 2XPC_A 2WJP_A 2VTE_A 2Y67_A 1EEH_A ....
Probab=31.23 E-value=1.5e+02 Score=20.65 Aligned_cols=30 Identities=23% Similarity=0.575 Sum_probs=24.2
Q ss_pred cccEEEEEeCCCCccccCHHHHHHHHHHHHhhhhh
Q psy15467 97 YSGFVFLLDWNQTSIYASPTLLRTMISGLQDCYPA 131 (241)
Q Consensus 97 ~~g~v~I~D~~g~s~~~~~~~~k~~~~~~q~~yP~ 131 (241)
.+|..+|.|+.. +|..++.++..+.+.+|.
T Consensus 11 ~~~~~vi~D~ah-----Np~s~~a~l~~l~~~~~~ 40 (91)
T PF02875_consen 11 PNGPTVIDDYAH-----NPDSIRALLEALKELYPK 40 (91)
T ss_dssp ETTEEEEEET-------SHHHHHHHHHHHHHHCTT
T ss_pred CCCcEEEEECCC-----CHHHHHHHHHHHHHhccC
Confidence 368999999555 889999999999999884
No 21
>cd07043 STAS_anti-anti-sigma_factors Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation. Anti-anti-sigma factors play an important role in the regulation of several sigma factors and their corresponding anti-sigma factors. Upon dephosphorylation they bind the anti-sigma factor and induce the release of the sigma factor from the anti-sigma factor. In a feedback mechanism the anti-anti-sigma factor can be inactivated via phosphorylation by the anti-sigma factor. Well studied examples from Bacillus subtilis are SpoIIAA (regulating sigmaF and sigmaC which play an important role in sporulation) and RsbV (regulating sigmaB involved in the general stress response). The STAS domain is also found in the C- terminal region of sulphate transporters and stressosomes.
Probab=27.89 E-value=2e+02 Score=19.61 Aligned_cols=51 Identities=14% Similarity=0.169 Sum_probs=33.9
Q ss_pred EEEEEeCCCCccccCHHHHHHHHHHHHhhhhhhcceEEEEeCChHHHHHHHHH
Q psy15467 100 FVFLLDWNQTSIYASPTLLRTMISGLQDCYPARFKAIHFINEPVQVDVLLALV 152 (241)
Q Consensus 100 ~v~I~D~~g~s~~~~~~~~k~~~~~~q~~yP~rl~~i~ivN~P~~~~~~~~li 152 (241)
-.+|+|+++++. ++.+.+..+..+.+.+-. +=+.+.+++.+.-...++..+
T Consensus 39 ~~viid~~~v~~-iDs~g~~~L~~l~~~~~~-~g~~v~i~~~~~~~~~~l~~~ 89 (99)
T cd07043 39 RRLVLDLSGVTF-IDSSGLGVLLGAYKRARA-AGGRLVLVNVSPAVRRVLELT 89 (99)
T ss_pred CEEEEECCCCCE-EcchhHHHHHHHHHHHHH-cCCeEEEEcCCHHHHHHHHHh
Confidence 567899999873 344444445555544443 346799999998777777655
No 22
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=27.43 E-value=26 Score=20.41 Aligned_cols=17 Identities=24% Similarity=0.163 Sum_probs=11.1
Q ss_pred chhhhcCCCChhhHhhc
Q psy15467 5 GKKLRRDTIDQERPLRS 21 (241)
Q Consensus 5 lRFLrArkfdv~kA~~~ 21 (241)
.+-|++++.|+++|.+.
T Consensus 20 ~~AL~~~~~nve~A~~~ 36 (37)
T PF00627_consen 20 REALRACNGNVERAVDW 36 (37)
T ss_dssp HHHHHHTTTSHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHh
Confidence 45567777777777653
No 23
>PRK14484 phosphotransferase mannnose-specific family component IIA; Provisional
Probab=26.96 E-value=2.9e+02 Score=21.10 Aligned_cols=48 Identities=21% Similarity=0.250 Sum_probs=31.3
Q ss_pred ccEEEEEeCCCCccccCHHHHHHHHHHHHhhhhhhcceEEEEeCChHHHHHHHHHhhh
Q psy15467 98 SGFVFLLDWNQTSIYASPTLLRTMISGLQDCYPARFKAIHFINEPVQVDVLLALVKPF 155 (241)
Q Consensus 98 ~g~v~I~D~~g~s~~~~~~~~k~~~~~~q~~yP~rl~~i~ivN~P~~~~~~~~lik~f 155 (241)
+|++++.|+ |-| |.-....+.++ ..- ++++++++|..=..+...+...
T Consensus 58 dGVlVltDL-Gss----p~n~~~a~e~~----~~~-~~v~~~daPlVEGa~~Aav~~~ 105 (124)
T PRK14484 58 DGVLIFFDL-GSA----EMNAEMAIEML----DGE-KKIIIIDAPIVEGAFTAAVLLS 105 (124)
T ss_pred CCeEEEEeC-CCh----HHHHHHHHHhc----CCC-CcEEEECCcHHHHHHHHHHHHc
Confidence 999999999 543 22222333333 222 8899999998777776665443
No 24
>TIGR02886 spore_II_AA anti-sigma F factor antagonist. The anti-sigma F factor antagonist, also called stage II sporulation protein AA, is a protein universal among endospore-forming bacteria, all of which belong to the Firmcutes
Probab=26.62 E-value=2.4e+02 Score=19.98 Aligned_cols=51 Identities=12% Similarity=0.118 Sum_probs=32.4
Q ss_pred EEEEEeCCCCccccCHHHHHHHHHHHHhhhhhhcceEEEEeCChHHHHHHHHH
Q psy15467 100 FVFLLDWNQTSIYASPTLLRTMISGLQDCYPARFKAIHFINEPVQVDVLLALV 152 (241)
Q Consensus 100 ~v~I~D~~g~s~~~~~~~~k~~~~~~q~~yP~rl~~i~ivN~P~~~~~~~~li 152 (241)
-.+|+||++++. ++.+.+..+....+++- .+=..++++|.+.-+.-++...
T Consensus 40 ~~vilDls~v~~-iDssgi~~L~~~~~~~~-~~g~~l~l~~~~~~v~~~l~~~ 90 (106)
T TIGR02886 40 KHLILNLKNVTF-MDSSGLGVILGRYKKIK-NEGGEVIVCNVSPAVKRLFELS 90 (106)
T ss_pred CEEEEECCCCcE-ecchHHHHHHHHHHHHH-HcCCEEEEEeCCHHHHHHHHHh
Confidence 579999999994 23333333333333322 2457899999988888777654
No 25
>KOG4178|consensus
Probab=24.77 E-value=2.4e+02 Score=25.38 Aligned_cols=82 Identities=22% Similarity=0.182 Sum_probs=46.3
Q ss_pred CCCCCCeEEEEEeccCCCCC-CchhhhccchhhhHHHHHhhhhhhccCCccccEEEEEeCCCCccccCHHHHHHHHHHHH
Q psy15467 48 LTPGGHQNPILRLCVSSRLE-PNVDLRQSDATSDHDIRTSGLLLVDTKIQYSGFVFLLDWNQTSIYASPTLLRTMISGLQ 126 (241)
Q Consensus 48 ~d~~G~~vii~r~~~~~~~~-~~~~~~~~~~~~~~~i~~~E~l~~~~~~~~~g~v~I~D~~g~s~~~~~~~~k~~~~~~q 126 (241)
+...|++|+..-++-++..+ +.. ....++.....-+..+++.. +...=.++..|+.++ +...+.
T Consensus 67 la~~~~rviA~DlrGyG~Sd~P~~---~~~Yt~~~l~~di~~lld~L-g~~k~~lvgHDwGai-----------vaw~la 131 (322)
T KOG4178|consen 67 LASRGYRVIAPDLRGYGFSDAPPH---ISEYTIDELVGDIVALLDHL-GLKKAFLVGHDWGAI-----------VAWRLA 131 (322)
T ss_pred hhhcceEEEecCCCCCCCCCCCCC---cceeeHHHHHHHHHHHHHHh-ccceeEEEeccchhH-----------HHHHHH
Confidence 55567777777666554433 221 12223333333233344332 112225556666653 345566
Q ss_pred hhhhhhcceEEEEeCChH
Q psy15467 127 DCYPARFKAIHFINEPVQ 144 (241)
Q Consensus 127 ~~yP~rl~~i~ivN~P~~ 144 (241)
-.||+|+.++..+|.|..
T Consensus 132 ~~~Perv~~lv~~nv~~~ 149 (322)
T KOG4178|consen 132 LFYPERVDGLVTLNVPFP 149 (322)
T ss_pred HhChhhcceEEEecCCCC
Confidence 789999999999999988
No 26
>TIGR00377 ant_ant_sig anti-anti-sigma factor. This superfamily includes small (105-125 residue) proteins related to SpoIIAA of Bacillus subtilis, an anti-anti-sigma factor. SpoIIAA can bind to and inhibit the anti-sigma F factor SpoIIAB. Also, it can be phosphorylated by SpoIIAB on a Ser residue at position 59 of the seed alignment. A similar arrangement is inferred for RsbV, an anti-anti-sigma factor for sigma B. This Ser is fairly well conserved within a motif resembling MXS[STA]G[VIL]X[VIL][VILF] among homologous known or predicted anti-anti-sigma factors. Regions similar to SpoIIAA and apparently homologous, but differing considerably near the phosphorlated Ser of SpoIIAA, appear in a single copy in several longer proteins.
Probab=24.36 E-value=2.6e+02 Score=19.67 Aligned_cols=51 Identities=12% Similarity=0.086 Sum_probs=33.3
Q ss_pred ccEEEEEeCCCCcc--ccCHHHHHHHHHHHHhhhhhhcceEEEEeCChHHHHHHHHH
Q psy15467 98 SGFVFLLDWNQTSI--YASPTLLRTMISGLQDCYPARFKAIHFINEPVQVDVLLALV 152 (241)
Q Consensus 98 ~g~v~I~D~~g~s~--~~~~~~~k~~~~~~q~~yP~rl~~i~ivN~P~~~~~~~~li 152 (241)
..-.+++|+++++. ......+..+...+++ +=+.+.++|.+.-+..++.+.
T Consensus 42 ~~~~vvidls~v~~iDssgl~~L~~~~~~~~~----~~~~~~l~~~~~~~~~~l~~~ 94 (108)
T TIGR00377 42 GPRPIVLDLEDLEFMDSSGLGVLLGRYKQVRR----VGGQLVLVSVSPRVARLLDIT 94 (108)
T ss_pred CCCeEEEECCCCeEEccccHHHHHHHHHHHHh----cCCEEEEEeCCHHHHHHHHHh
Confidence 34569999999984 2333444444443332 346799999988887777654
No 27
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=23.93 E-value=35 Score=30.93 Aligned_cols=19 Identities=32% Similarity=0.358 Sum_probs=17.0
Q ss_pred cchhhhcCCCChhhHhhcC
Q psy15467 4 MGKKLRRDTIDQERPLRSL 22 (241)
Q Consensus 4 llRFLrArkfdv~kA~~~L 22 (241)
|+|-|+|++|||++|-+=+
T Consensus 147 llkLlqaadydV~rAerGI 165 (408)
T COG1219 147 LLKLLQAADYDVERAERGI 165 (408)
T ss_pred HHHHHHHcccCHHHHhCCe
Confidence 7899999999999998744
No 28
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=20.95 E-value=48 Score=19.00 Aligned_cols=19 Identities=32% Similarity=0.214 Sum_probs=12.9
Q ss_pred cchhhhcCCCChhhHhhcC
Q psy15467 4 MGKKLRRDTIDQERPLRSL 22 (241)
Q Consensus 4 llRFLrArkfdv~kA~~~L 22 (241)
.++-|+++++|+++|..-|
T Consensus 18 a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 18 ALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHhCCCHHHHHHHH
Confidence 4556777788887776543
Done!