Query 028657
Match_columns 206
No_of_seqs 121 out of 384
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 14:57:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028657.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028657hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4406 CDC42 Rho GTPase-activ 100.0 3.6E-35 7.8E-40 260.5 10.6 177 7-188 66-265 (467)
2 PF13716 CRAL_TRIO_2: Divergen 100.0 1.3E-33 2.7E-38 222.3 12.0 145 19-168 2-149 (149)
3 smart00516 SEC14 Domain in hom 99.8 4.5E-20 9.7E-25 144.8 11.6 128 25-160 14-151 (158)
4 cd00170 SEC14 Sec14p-like lipi 99.8 3.7E-19 8.1E-24 137.5 10.1 135 19-160 9-152 (157)
5 KOG1470 Phosphatidylinositol t 99.7 3E-17 6.5E-22 143.9 12.3 145 6-156 86-235 (324)
6 PF00650 CRAL_TRIO: CRAL/TRIO 99.6 5.7E-16 1.2E-20 121.6 7.3 141 14-160 2-154 (159)
7 KOG1471 Phosphatidylinositol t 99.1 3.7E-10 8E-15 99.0 9.1 150 13-171 89-259 (317)
8 KOG1826 Ras GTPase activating 97.2 0.0002 4.4E-09 74.3 2.6 161 6-171 1549-1710(2724)
9 KOG2633 Hismacro and SEC14 dom 96.6 1.2E-05 2.6E-10 66.7 -9.8 180 10-194 14-198 (200)
10 PF13986 DUF4224: Domain of un 60.8 14 0.00031 23.4 3.3 25 9-35 18-42 (47)
11 PF03641 Lysine_decarbox: Poss 59.7 16 0.00035 28.0 4.1 63 86-151 64-133 (133)
12 PF07872 DUF1659: Protein of u 54.9 7.9 0.00017 24.6 1.4 26 18-43 8-34 (47)
13 PF10928 DUF2810: Protein of u 51.8 8.5 0.00018 25.1 1.1 19 98-116 20-38 (54)
14 PF11385 DUF3189: Protein of u 43.5 61 0.0013 25.7 5.1 51 17-72 48-98 (148)
15 PF03721 UDPG_MGDP_dh_N: UDP-g 38.6 8.5 0.00018 31.3 -0.5 96 15-114 19-122 (185)
16 PF04079 DUF387: Putative tran 34.6 45 0.00098 26.6 3.1 35 7-41 109-144 (159)
17 PF01243 Pyridox_oxidase: Pyri 30.4 73 0.0016 21.5 3.3 33 9-41 3-35 (89)
18 PF08412 Ion_trans_N: Ion tran 29.0 54 0.0012 23.1 2.4 43 82-124 11-53 (77)
19 TIGR00281 segregation and cond 28.2 54 0.0012 27.0 2.6 35 7-41 114-149 (186)
20 PRK11020 hypothetical protein; 28.0 42 0.0009 25.6 1.7 19 98-116 83-101 (118)
21 PF02350 Epimerase_2: UDP-N-ac 25.6 2.5E+02 0.0054 24.9 6.7 71 64-146 178-249 (346)
22 TIGR01001 metA homoserine O-su 25.5 3.6E+02 0.0078 24.0 7.4 93 12-111 12-107 (300)
23 PF06057 VirJ: Bacterial virul 24.1 2.7E+02 0.0059 23.1 6.1 74 28-114 27-107 (192)
24 PF09949 DUF2183: Uncharacteri 23.1 1.8E+02 0.0038 21.4 4.3 49 51-110 50-98 (100)
No 1
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=100.00 E-value=3.6e-35 Score=260.49 Aligned_cols=177 Identities=27% Similarity=0.426 Sum_probs=163.7
Q ss_pred ChhhHHHHHHhc--CcEEEecc--CCCCCeEEEEEeecCCC-CCCCHHHHHHHHHHHhhcccCCCCeEEEEEcCCcccCc
Q 028657 7 SESEQEELIDRL--EIFKIHGR--DKQGRKILRIIGKFFPA-RLLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQRSE 81 (206)
Q Consensus 7 s~~e~~~~i~~~--~i~y~~G~--D~~GrpVvvi~a~~~p~-~~~d~e~ll~y~l~~ll~~~~~~~y~lVy~~tg~~~~~ 81 (206)
++++.|.++.++ +++.+.|. |++||+|+++.||++|. +++|.-+++.|+.++ .|++++++|++||||.|+ ++.
T Consensus 66 p~ed~fyd~~~H~~ei~qvi~~~~D~~gr~iivv~a~rlp~~~eld~~~li~~~v~~-id~~Ve~DYt~vYfh~gl-~s~ 143 (467)
T KOG4406|consen 66 PKEDPFYDIARHEREILQVIGDAKDKQGRKIIVVYACRLPSSSELDDIRLISYLVYT-IDKYVENDYTLVYFHHGL-PSD 143 (467)
T ss_pred cccccHHHHHHhhhheeeeccCcccccCCeeEEEEEecCCchhhhhhHHHHHHHHHH-HHHHHhccceeeehhcCC-ccc
Confidence 457889999998 89988866 99999999999999999 578888899999995 899999999999999999 599
Q ss_pred CCCcHHHHHHHHHhcchhHHhccceEEEEcCChHHHHHHHHhccccccCcCcccCcEEEeCChhHHHhhcccccccCChh
Q 028657 82 NFAGISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGLYGKLRYVNRLDYLWEHVRRHEVEIPEF 161 (206)
Q Consensus 82 n~p~~~~L~~~y~~L~~~~kknLk~lyiVHPt~~~k~~~~~~~~~fis~~~k~~~KI~yv~~l~eL~~~I~~~ql~iP~~ 161 (206)
|+|+++|+.++|..++++++||||++|+|||+|++|.+|.+|+ ||+| .||.+||+|+++++||.++|..++|.+|+.
T Consensus 144 nkp~l~~l~~aYke~Dr~~~KNlKalYvvHptwfikvi~n~~k-plIS--~KF~rKi~Y~n~lseL~~~l~l~rL~lP~~ 220 (467)
T KOG4406|consen 144 NKPYLQLLFDAYKELDRNFKKNLKALYVVHPTWFIKVIWNLFK-PLIS--LKFTRKIIYFNSLSELFEALKLNRLKLPPE 220 (467)
T ss_pred ccchHHHHHHHHHHHHHHHhhhhhheEEecHHHHHHHHHHHHh-hhcc--hhhhceeEEeehHHHHHHhhhhhhhcCChh
Confidence 9999999999999999999999999999999999999998885 8999 999999999999999999999999999999
Q ss_pred HHhhhhhhccC------------------CCccCCccCCCccccC
Q 028657 162 VMDHDEDLEYR------------------PMMDYGLESDHRRVYG 188 (206)
Q Consensus 162 V~~~d~~l~~~------------------p~~~~g~~~~~~~~~~ 188 (206)
|++||+.++.. |.++||+.+++....+
T Consensus 221 v~~~D~~~~s~~~~~a~~p~~~~~pr~pl~t~qFgvpLqf~~~~~ 265 (467)
T KOG4406|consen 221 VLKHDDKLLSKAKTPAPPPEKMTPPRPPLPTQQFGVPLQFIPEKN 265 (467)
T ss_pred hhhhhhcccccccCCCCCcccCCCCCCCCchhhcCccHHHhcccC
Confidence 99999998763 4899999999876443
No 2
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=100.00 E-value=1.3e-33 Score=222.27 Aligned_cols=145 Identities=30% Similarity=0.463 Sum_probs=112.7
Q ss_pred CcEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHHHhhcccCCCCeEEEEEcCCcccCcCCCcHHHHHHHHHhcch
Q 028657 19 EIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQRSENFAGISALRSIYDAIPA 98 (206)
Q Consensus 19 ~i~y~~G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~l~~ll~~~~~~~y~lVy~~tg~~~~~n~p~~~~L~~~y~~L~~ 98 (206)
.+++.+|+|++||||++++++++ ....|+|+++.|++.++.+.+.+++|+||+++++.+ ..+.|+++|++++|+.+|+
T Consensus 2 ~~~~~gG~d~~g~pV~~~~~~~~-~~~~~~~~ll~yl~~~l~~~~~~~~f~vVid~~~~~-~~~~~~~~~l~~~~~~l~~ 79 (149)
T PF13716_consen 2 IFFYPGGRDREGRPVVVFIASRL-PSSDDLERLLLYLLSTLSEEVVDKPFSVVIDHTGFS-RSSEPSLSWLKQLYKLLPR 79 (149)
T ss_dssp SE-EEEEEBTTS-EEEEEEGGG--C-TTHHHHHHHHHHHHH-TTTTTS-EEEEEE-TT---GGG---HHHHHHTTTSS-H
T ss_pred eEEEecccCCCcCEEEEEECCcC-cchhhHHHHHHHHHHhhhHHhcCCCEEEEEEcCCCc-cccCCchHHHHHHHHHHHH
Confidence 46788999999999999999999 434699999999999643788899999999999995 8899999999999999999
Q ss_pred hHHhccceEEEEcCChHHHHHHHHhccccccCcCcc-cCcEEEeCChhHHHhhcccccc--cCChhHHhhhhh
Q 028657 99 NVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGL-YGKLRYVNRLDYLWEHVRRHEV--EIPEFVMDHDED 168 (206)
Q Consensus 99 ~~kknLk~lyiVHPt~~~k~~~~~~~~~fis~~~k~-~~KI~yv~~l~eL~~~I~~~ql--~iP~~V~~~d~~ 168 (206)
.+++||+++||+||++++|.+++.+.+++.+ .++ ++||+|++++++|.++|+.+|| .|| .|++||++
T Consensus 80 ~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~--~~~~~~kv~~~~sl~~L~~~i~~~qL~~~lp-~~~~~d~~ 149 (149)
T PF13716_consen 80 KYKKNLKKVYIVHPNWFLKKILATLLRPFVS--SKFWKKKVVYVSSLSELSKHIDPSQLPESLP-GVLQYDHE 149 (149)
T ss_dssp HHHHTEEEEEEES--HHHHHHHHHTTTTGGG--GTT--TTEEEESSTCGGGGTSGGGG-------HHH-----
T ss_pred HHhhceEEEEEECCCHHHHHHHHHHhccccc--ccccceEEEEECCHHHHHhhCCHHHhcccCC-CEEecCcC
Confidence 9999999999999999999999778889889 999 9999999999999999999999 999 99999975
No 3
>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=99.83 E-value=4.5e-20 Score=144.84 Aligned_cols=128 Identities=27% Similarity=0.443 Sum_probs=111.9
Q ss_pred ccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHHHhhcc--------cCCCCeEEEEEcCCcccCcCCCcHHHHHHHHHhc
Q 028657 25 GRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPR--------LGKKAFTVLYVHTGVQRSENFAGISALRSIYDAI 96 (206)
Q Consensus 25 G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~l~~ll~~--------~~~~~y~lVy~~tg~~~~~n~p~~~~L~~~y~~L 96 (206)
|.|++||||+++.+++++.+..+.+.+++|+... ++. ...+.+++|++.+|.+ ..+ ++.+|++++++.+
T Consensus 14 g~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~~~-~e~~~~~~~~~~~~~~~~~i~D~~~~~-~~~-~~~~~lk~~~~~~ 90 (158)
T smart00516 14 GYDKDGRPVLIFRAGRFDLKSVTLEELLRYLVYV-LEKILQREKKTGGIEGFTVIFDLKGLS-MSN-PDLSVLRKILKIL 90 (158)
T ss_pred CCCCCcCEEEEEeccccccCcCCHHHHHHHHHHH-HHHHHHHHhcCCCeeeEEEEEECCCCC-ccc-ccHHHHHHHHHHH
Confidence 6999999999999999988778999888887763 332 2335789999999985 544 8899999999999
Q ss_pred chhHHhccceEEEEcCChHHHHHHHHhccccccCcCcccCcEEEeCC--hhHHHhhcccccccCCh
Q 028657 97 PANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGLYGKLRYVNR--LDYLWEHVRRHEVEIPE 160 (206)
Q Consensus 97 ~~~~kknLk~lyiVHPt~~~k~~~~~~~~~fis~~~k~~~KI~yv~~--l~eL~~~I~~~ql~iP~ 160 (206)
+..|++||+++|||||+++++++|+++ ++|++ +++++||+++++ .++|.++|+.++ ||.
T Consensus 91 ~~~yp~~l~~i~ivn~p~~~~~~~~~~-~~~l~--~~~~~ki~~~~~~~~~~L~~~i~~~~--lP~ 151 (158)
T smart00516 91 QDHYPERLGKVLIINPPWFFRVLWKII-KPFLD--EKTREKIRFVGNDSKEELLEYIDPEQ--LPE 151 (158)
T ss_pred HHHhHHHhCeEEEECCCHHHHHHHHHH-HhhcC--hhhhccEEEeCCCCHHHHHhhCCHhh--CcH
Confidence 999999999999999999999999877 58899 999999999998 899999999885 887
No 4
>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=99.80 E-value=3.7e-19 Score=137.52 Aligned_cols=135 Identities=24% Similarity=0.372 Sum_probs=110.4
Q ss_pred CcEEEeccCCCCCeEEEEEeecCCC-CCCCHHHHHHHHHHHhhcccC------CCCeEEEEEcCCcccCcCCC-cHHHHH
Q 028657 19 EIFKIHGRDKQGRKILRIIGKFFPA-RLLSVEVLKRYLSERVYPRLG------KKAFTVLYVHTGVQRSENFA-GISALR 90 (206)
Q Consensus 19 ~i~y~~G~D~~GrpVvvi~a~~~p~-~~~d~e~ll~y~l~~ll~~~~------~~~y~lVy~~tg~~~~~n~p-~~~~L~ 90 (206)
++.+.+|.|++||||+++..+.... ...+.+.++.+.... ++... .+.+++|++.+|.+ ..+.. ..++++
T Consensus 9 ~~~~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~~-~e~~~~~~~~~~~~~~~i~D~~~~~-~~~~~~~~~~~k 86 (157)
T cd00170 9 KVGYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYT-LEKLLQEDDEQVEGFVVIIDLKGLS-LSHLLPDPSLLK 86 (157)
T ss_pred cccccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHHH-HHHHHhhhhhcccceEEEEECCCCC-hhccchhHHHHH
Confidence 5666667799999999999984333 445657777776653 44222 24789999999995 55543 789999
Q ss_pred HHHHhcchhHHhccceEEEEcCChHHHHHHHHhccccccCcCcccCcEEEeCC-hhHHHhhcccccccCCh
Q 028657 91 SIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGLYGKLRYVNR-LDYLWEHVRRHEVEIPE 160 (206)
Q Consensus 91 ~~y~~L~~~~kknLk~lyiVHPt~~~k~~~~~~~~~fis~~~k~~~KI~yv~~-l~eL~~~I~~~ql~iP~ 160 (206)
++++.++..|++||+++|||||+++++++|+++ ++|++ +++++||+++++ .++|.++|+.++ ||.
T Consensus 87 ~~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~-~~~l~--~~~~~ki~~~~~~~~~L~~~i~~~~--Lp~ 152 (157)
T cd00170 87 KILKILQDNYPERLKAVYIINPPWFFKVLWKIV-KPFLS--EKTRKKIVFLGSDKEELLKYIDKEQ--LPE 152 (157)
T ss_pred HHHHHHHHhChHhhCeEEEECCCHhHHHHHHHH-HHhcC--HhhhhhEEEecCCHHHHHhhCChhh--CcH
Confidence 999999999999999999999999999999887 58899 999999999999 999999999986 665
No 5
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=99.73 E-value=3e-17 Score=143.91 Aligned_cols=145 Identities=19% Similarity=0.239 Sum_probs=121.1
Q ss_pred CChhhHHHHHHhcCcEEEeccCCCCCeEEEEEeecCCCCCCCHH---HHHHHHHHHhhc--ccCCCCeEEEEEcCCcccC
Q 028657 6 VSESEQEELIDRLEIFKIHGRDKQGRKILRIIGKFFPARLLSVE---VLKRYLSERVYP--RLGKKAFTVLYVHTGVQRS 80 (206)
Q Consensus 6 is~~e~~~~i~~~~i~y~~G~D~~GrpVvvi~a~~~p~~~~d~e---~ll~y~l~~ll~--~~~~~~y~lVy~~tg~~~~ 80 (206)
+..+|...++ +.|..|.+|.|+.||||+++.++.-..+..+.+ +++.|++++... .-+++.++++++.+|.+ .
T Consensus 86 ~~~~Ev~~e~-~tGK~yi~G~D~~gRPVl~~~~~~~~qn~~t~~~~~r~~Vy~mE~Ai~~lp~~qe~~~~L~D~~~fs-~ 163 (324)
T KOG1470|consen 86 IEADEVAAEL-ETGKAYILGHDKDGRPVLYLRPRPHRQNTKTQKELERLLVYTLENAILFLPPGQEQFVWLFDLTGFS-M 163 (324)
T ss_pred cCHHHHHHHh-hcCcEEEecccCCCCeEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCcceEEEEEecccCc-c
Confidence 5566666666 678888999999999999999986666545544 555555554322 23467799999999995 4
Q ss_pred cCCCcHHHHHHHHHhcchhHHhccceEEEEcCChHHHHHHHHhccccccCcCcccCcEEEeCChhHHHhhcccccc
Q 028657 81 ENFAGISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGLYGKLRYVNRLDYLWEHVRRHEV 156 (206)
Q Consensus 81 ~n~p~~~~L~~~y~~L~~~~kknLk~lyiVHPt~~~k~~~~~~~~~fis~~~k~~~KI~yv~~l~eL~~~I~~~ql 156 (206)
..++++.++-+...|+.+|+++|+..+++||+|++..+|+.+ +||++ +++..||+|+.+..+|.++|+.+++
T Consensus 164 -sN~d~~~~k~~~~~lq~hYPErLg~a~l~~~P~iF~~~wkii-kpflD--p~t~~Kv~F~~~~~~l~~~~d~~~l 235 (324)
T KOG1470|consen 164 -SNPDIKFLKELLHILQDHYPERLGKALLVNAPWIFQPFWKII-KPFLD--PKTASKVKFVEPKDDLSEYFDESQL 235 (324)
T ss_pred -cCCCcHHHHHHHHHHHHhChHHhhhhhhcCChHHHHHHHHHh-hhccC--hhhhceeEEecChhHHHhhCCcccc
Confidence 477999999999999999999999999999999999999887 69999 9999999999999999999999973
No 6
>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=99.63 E-value=5.7e-16 Score=121.56 Aligned_cols=141 Identities=23% Similarity=0.310 Sum_probs=103.6
Q ss_pred HHHhcCcEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHH---HHhhc---c-cCCCCeEEEEEcCCcccCcCCCc-
Q 028657 14 LIDRLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLS---ERVYP---R-LGKKAFTVLYVHTGVQRSENFAG- 85 (206)
Q Consensus 14 ~i~~~~i~y~~G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~l---~~ll~---~-~~~~~y~lVy~~tg~~~~~n~p~- 85 (206)
++.+.+..+..|.|++||||+++..+++.......+.+.+++. +..+. . ...+.+++|++.+|.+ ..+.+.
T Consensus 2 ~~~~~~~~~~~g~D~~gr~v~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~~~~iiD~~g~~-~~~~~~~ 80 (159)
T PF00650_consen 2 EILKSGPFYLHGRDKDGRPVIYIRLGRFDPKKFSPEDVIRFFVYLLERMLKRMPEGGQVEGIVVIIDLSGFS-LSNFDWW 80 (159)
T ss_dssp HHHTTSCEEEEEE-TTS-EEEEEEGTT--HHTS-HHHHHHHHHHHHHHHHHTHHHTSHHH-EEEEEE-TT---HHHHHCH
T ss_pred HHHCCeeEEECCCCCCcCEEEEEEcccCCCCcCCHHHHHHHHHHHHHHHHhhhcccccceeEEEEEeCCCce-Eeccccc
Confidence 5778999999999999999999999887776555554444443 32221 1 2346789999999994 544442
Q ss_pred -HHHHHHHHHhcchhHHhccceEEEEcCChHHHHHHHHhccccccCcCcccCcEEEeCCh---hHHHhhcccccccCCh
Q 028657 86 -ISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGLYGKLRYVNRL---DYLWEHVRRHEVEIPE 160 (206)
Q Consensus 86 -~~~L~~~y~~L~~~~kknLk~lyiVHPt~~~k~~~~~~~~~fis~~~k~~~KI~yv~~l---~eL~~~I~~~ql~iP~ 160 (206)
.+.++.+.+.++..|+++++++||+|++++++++|+++. +|++ +++.+||+++.+- ++|.++|+.++ ||.
T Consensus 81 ~~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~-~~l~--~~~~~ki~~~~~~~~~~~l~~~i~~~~--lP~ 154 (159)
T PF00650_consen 81 PISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVK-PFLS--PKTREKIVFHSGSDWKAKLKEYIDPEQ--LPV 154 (159)
T ss_dssp HHHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHG-GGS---HHHHCTEEEECTTCHCHHHCCCSTGGG--SBG
T ss_pred hhhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHH-hhcC--HhhheeEEEECCcccHHHHHhhCCHhH--Cch
Confidence 888999999999999999999999999999999998884 8899 9999999999553 57999999885 776
No 7
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=99.10 E-value=3.7e-10 Score=98.95 Aligned_cols=150 Identities=13% Similarity=0.135 Sum_probs=109.5
Q ss_pred HHHHhcCcEEEeccCCCCCeEEEEEeecCCCCC----CC-----------HHHHHHHHHHHhhcc--cCCCCeEEEEEcC
Q 028657 13 ELIDRLEIFKIHGRDKQGRKILRIIGKFFPARL----LS-----------VEVLKRYLSERVYPR--LGKKAFTVLYVHT 75 (206)
Q Consensus 13 ~~i~~~~i~y~~G~D~~GrpVvvi~a~~~p~~~----~d-----------~e~ll~y~l~~ll~~--~~~~~y~lVy~~t 75 (206)
+++.+..-....|.|++|+||++-.....-.+. .. .++....+....... -..+..+.|++..
T Consensus 89 ~~~~~~~~~~~~~~~~~g~~v~~~~~g~~~~~~l~~~~~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~ 168 (317)
T KOG1471|consen 89 DELLKYYPQGLHGVDKEGRPVYIERLGKIDPKGLLKRTGSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLK 168 (317)
T ss_pred hhhhhhccccccccCCCCCEEEEeccCCCCcccceeeccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECC
Confidence 344443334457999999999998776553321 11 223332222211111 2356689999999
Q ss_pred CcccCcCC--CcHHHHHHHHHhcchhHHhccceEEEEcCChHHHHHHHHhccccccCcCcccCcEE--EeCChhHHHhhc
Q 028657 76 GVQRSENF--AGISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGLYGKLR--YVNRLDYLWEHV 151 (206)
Q Consensus 76 g~~~~~n~--p~~~~L~~~y~~L~~~~kknLk~lyiVHPt~~~k~~~~~~~~~fis~~~k~~~KI~--yv~~l~eL~~~I 151 (206)
|++ ..+. +..+.++++...++..|++++++++|||.++++.++|++++ ||++ +++++||+ .-++.++|.++|
T Consensus 169 G~~-~~~~~~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~P~~f~~~~~~ik-pfL~--~kt~~ki~~~~~~~~~~L~k~i 244 (317)
T KOG1471|consen 169 GVS-LSHLLKPAPTLLKKILKILQDNYPERLKRIHIINAPTIFSALWKVVK-PFLD--EKTRKKIHVLHSKDKESLLKYI 244 (317)
T ss_pred CCc-chhHHHHHHHHHHHHHHHHHHhCHHhhceEEEEcCchhHHHHHHHHh-ccCC--HHHHhhheecCCCchhhhhhhC
Confidence 995 5444 77899999999999999999999999999999999999885 8999 99999999 345789999999
Q ss_pred ccccccCChhHHhhhhhhcc
Q 028657 152 RRHEVEIPEFVMDHDEDLEY 171 (206)
Q Consensus 152 ~~~ql~iP~~V~~~d~~l~~ 171 (206)
+++. ||. +|......
T Consensus 245 ~~~~--LP~---~yGG~~~~ 259 (317)
T KOG1471|consen 245 PPEV--LPE---EYGGTCGD 259 (317)
T ss_pred CHhh--Ccc---ccCCCccc
Confidence 9985 777 66654443
No 8
>KOG1826 consensus Ras GTPase activating protein RasGAP/neurofibromin [Defense mechanisms]
Probab=97.18 E-value=0.0002 Score=74.32 Aligned_cols=161 Identities=16% Similarity=-0.007 Sum_probs=129.1
Q ss_pred CChhhHHHHHHhcCcEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHHHhhcccCCCCeEEEEEcCCcccCcCCCc
Q 028657 6 VSESEQEELIDRLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQRSENFAG 85 (206)
Q Consensus 6 is~~e~~~~i~~~~i~y~~G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~l~~ll~~~~~~~y~lVy~~tg~~~~~n~p~ 85 (206)
+++.|++--+++.-++|+.| .+.|.|+.++++++.--++.+-+.++.+... ++.+.+.-++.++-+-+... .+++--
T Consensus 1549 lheKe~fitL~~~i~~~~~G-sen~~k~~~lvs~r~fl~~~s~~il~~l~~L-~~kp~~hf~~evreD~T~~~-~d~sfl 1625 (2724)
T KOG1826|consen 1549 LHEKEEFITLAKVIQFYANG-SENGLKNFYLVSRRKFLKECSDDILIFLVEL-CLKPKVHFPGEVREDPTPIE-FDYSFL 1625 (2724)
T ss_pred HhhhhHHHHHHHHHHHHHhh-hhccCcchhhHhHHHHHhhcCcHHHHHHHHH-HcCccccCcceeeecCCcCC-ccHHHH
Confidence 67889999999999999999 9999999999997766655555555555555 36778889999998877664 345545
Q ss_pred HHHHHH-HHHhcchhHHhccceEEEEcCChHHHHHHHHhccccccCcCcccCcEEEeCChhHHHhhcccccccCChhHHh
Q 028657 86 ISALRS-IYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGLYGKLRYVNRLDYLWEHVRRHEVEIPEFVMD 164 (206)
Q Consensus 86 ~~~L~~-~y~~L~~~~kknLk~lyiVHPt~~~k~~~~~~~~~fis~~~k~~~KI~yv~~l~eL~~~I~~~ql~iP~~V~~ 164 (206)
-++++. ++...+.-..+|-.++|+++.+.|.|...+.-.|.+-. -|--++..+.+..-.|.++|+.+|..+|...+-
T Consensus 1626 tsf~~~~~f~vr~~va~e~~~a~~di~~n~~lK~~~~l~driL~~--L~~~k~~~f~e~P~kl~e~id~~~q~~~~~t~~ 1703 (2724)
T KOG1826|consen 1626 TSFLYLKWFKVRPHVANENKHAVGDINCNSFLKETTKLHDRILGQ--LGQPKMEFFNEIPIKLREHIDDYPQLYEFMTRH 1703 (2724)
T ss_pred HHHHhhhheeechhhhhhcccccccccchHHHHHHHHHHHHHHhh--cCCCceeehhcCCHHHHHHHhhhhhhhhHHHHH
Confidence 566665 88889999999999999999999999876554454423 666788999999999999999999999998888
Q ss_pred hhhhhcc
Q 028657 165 HDEDLEY 171 (206)
Q Consensus 165 ~d~~l~~ 171 (206)
-+++++-
T Consensus 1704 ~~edlkv 1710 (2724)
T KOG1826|consen 1704 AFEDLKV 1710 (2724)
T ss_pred HHhhccc
Confidence 8887753
No 9
>KOG2633 consensus Hismacro and SEC14 domain-containing proteins [Chromatin structure and dynamics; Transcription]
Probab=96.58 E-value=1.2e-05 Score=66.67 Aligned_cols=180 Identities=26% Similarity=0.297 Sum_probs=132.9
Q ss_pred hHHHHHHhcCcEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHHHhhcccCCCCeEEEEEcC---CcccCcCCCcH
Q 028657 10 EQEELIDRLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLGKKAFTVLYVHT---GVQRSENFAGI 86 (206)
Q Consensus 10 e~~~~i~~~~i~y~~G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~l~~ll~~~~~~~y~lVy~~t---g~~~~~n~p~~ 86 (206)
++++++....+|-..+.++.|.-+.-..+..++.+.+-+.....+.-......-.+.+..+.++|+ |.....+.+.+
T Consensus 14 ~~~~~~~~l~~f~~~~~~~~~i~lwr~d~~~l~v~avvl~~g~~~~~ai~~aagp~l~~e~~~~~~c~tG~ak~t~~~~L 93 (200)
T KOG2633|consen 14 EIFSNITSLEVFKIDKPDNGGISLWRGDGKTLEVDAVVLLGGKGVDEAIHRAAGPELPLECAYLHGCRTGAAKSTGGYGL 93 (200)
T ss_pred hhhccccccchhhccCccccCeeEeecccccccceeeeeccCcchhHHHHHhcCCcchHHHHhhcCCCCCeeEecCCCCC
Confidence 456677788888888999999999999999998853322211111111011223445556666666 66555677788
Q ss_pred HHHHHHHHhcchhHHhccceEEEEcCChHHHHHHHHhccccccCcCcccCcEEEeCChhHHHhhcccccccCC--hhHHh
Q 028657 87 SALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGLYGKLRYVNRLDYLWEHVRRHEVEIP--EFVMD 164 (206)
Q Consensus 87 ~~L~~~y~~L~~~~kknLk~lyiVHPt~~~k~~~~~~~~~fis~~~k~~~KI~yv~~l~eL~~~I~~~ql~iP--~~V~~ 164 (206)
...+-++...|+.+.+++...|.+|++......+++- ..+| +....||. .......++......++.| .++..
T Consensus 94 pak~vIHtvgP~~~~d~~~~~~~L~~~~rs~L~la~~--~~ls--~iAf~~I~-sg~~gyP~e~aa~~~l~ti~~~f~~~ 168 (200)
T KOG2633|consen 94 PAKRVIHTVGPRWKEDKLQECYFLHSCYRSCLDLAIE--KLLS--SIAFPKIS-SGRVGYPWEDAAKIELETIRVFFVKN 168 (200)
T ss_pred ceeEEEEecCchhhccchHHHHHHHHHHHHHHHHHHH--hccc--eeeeeeee-ccccCccHHHHHHHHHHHHHHHHhhC
Confidence 8888889999999999999999999999888877554 3356 77778888 7777777777777777788 67777
Q ss_pred hhhhhccCCCccCCccCCCccccCCCCCCC
Q 028657 165 HDEDLEYRPMMDYGLESDHRRVYGAPAVDS 194 (206)
Q Consensus 165 ~d~~l~~~p~~~~g~~~~~~~~~~~~~~~~ 194 (206)
+|..|+..|+++|+.|..+..+..+...|.
T Consensus 169 ~d~~l~~~~f~~~d~e~~~~~l~~~~~~~~ 198 (200)
T KOG2633|consen 169 KDSSLKTVPFLDYDSESYGAYLPEYAPSDA 198 (200)
T ss_pred CCceEEEEEEeccCCchHHHHHhhhccccc
Confidence 887789999999999999999888777654
No 10
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=60.75 E-value=14 Score=23.45 Aligned_cols=25 Identities=28% Similarity=0.270 Sum_probs=19.6
Q ss_pred hhHHHHHHhcCcEEEeccCCCCCeEEE
Q 028657 9 SEQEELIDRLEIFKIHGRDKQGRKILR 35 (206)
Q Consensus 9 ~e~~~~i~~~~i~y~~G~D~~GrpVvv 35 (206)
+.+-..|.++||.+..+. .|||+|.
T Consensus 18 ~~Q~~~L~~~Gi~~~~~~--~G~p~V~ 42 (47)
T PF13986_consen 18 SKQIRWLRRNGIPFVVRA--DGRPIVT 42 (47)
T ss_pred HHHHHHHHHCCCeeEECC--CCCEEee
Confidence 456778899999997655 5999975
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=59.70 E-value=16 Score=27.96 Aligned_cols=63 Identities=14% Similarity=0.256 Sum_probs=43.6
Q ss_pred HHHHHHHHHhcch-hHHhccc-eEEEEcCC-hHHHHHHHHh----ccccccCcCcccCcEEEeCChhHHHhhc
Q 028657 86 ISALRSIYDAIPA-NVKENLQ-AVYFVHPG-LQARLFLATF----GRLFFNGVGGLYGKLRYVNRLDYLWEHV 151 (206)
Q Consensus 86 ~~~L~~~y~~L~~-~~kknLk-~lyiVHPt-~~~k~~~~~~----~~~fis~~~k~~~KI~yv~~l~eL~~~I 151 (206)
++.|..+++.+.- +...+-+ -+++++.+ +|-.. ++.+ ..-|++ +.-...+.++++.+++.+.|
T Consensus 64 ~GTl~El~~~~~~~~l~~~~~~Piil~~~~g~w~~l-~~~l~~~~~~g~i~--~~~~~~~~~~d~~~e~~~~i 133 (133)
T PF03641_consen 64 IGTLDELFEALTLMQLGRHNKVPIILLNIDGFWDPL-LEFLDRMIEEGFIS--PDDLDLLHFVDDPEEALEYI 133 (133)
T ss_dssp HHHHHHHHHHHHHHHTTSSTS-EEEEEECGGCCHHH-HHHHHHHHHTTSSS--HHHHCCEEEESSHHHHHHHH
T ss_pred CchHHHHHHHHHHHhhccccCCCEEEeCCcchHHHH-HHHHHHHHHCCCCC--HHHCCeEEEeCCHHHHHhhC
Confidence 3457777777763 4444556 79999975 54443 3333 345778 88889999999999987765
No 12
>PF07872 DUF1659: Protein of unknown function (DUF1659); InterPro: IPR012454 This family consists of hypothetical bacterial proteins of unknown function
Probab=54.93 E-value=7.9 Score=24.56 Aligned_cols=26 Identities=19% Similarity=0.293 Sum_probs=19.2
Q ss_pred cCcEEEeccCCCCCeEEEEEe-ecCCC
Q 028657 18 LEIFKIHGRDKQGRKILRIIG-KFFPA 43 (206)
Q Consensus 18 ~~i~y~~G~D~~GrpVvvi~a-~~~p~ 43 (206)
+.+-|+.|.|..|.||+--.. +++..
T Consensus 8 L~l~~~~G~d~~Gkpi~k~ks~~nvk~ 34 (47)
T PF07872_consen 8 LRLKYQTGVDENGKPIFKTKSFSNVKP 34 (47)
T ss_pred EEEEEEcccCCCCCEEEEeeehhhcCC
Confidence 567788899999999976655 34444
No 13
>PF10928 DUF2810: Protein of unknown function (DUF2810); InterPro: IPR021230 This is a bacterial family of uncharacterised proteins. This entry contains YibL (P0ADK8 from SWISSPROT), which comigrates with the mature 50S ribosome subunit. It either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2LF0_A.
Probab=51.82 E-value=8.5 Score=25.06 Aligned_cols=19 Identities=21% Similarity=0.419 Sum_probs=13.8
Q ss_pred hhHHhccceEEEEcCChHH
Q 028657 98 ANVKENLQAVYFVHPGLQA 116 (206)
Q Consensus 98 ~~~kknLk~lyiVHPt~~~ 116 (206)
-+.||..+.+.||||-..+
T Consensus 20 GkLKKsVrGLvvVHPmTal 38 (54)
T PF10928_consen 20 GKLKKSVRGLVVVHPMTAL 38 (54)
T ss_dssp HHHHHHTTS-EEE-SSSHH
T ss_pred HHHHhhhceeEEEechHHH
Confidence 4679999999999996644
No 14
>PF11385 DUF3189: Protein of unknown function (DUF3189); InterPro: IPR021525 This family of proteins with unknown function appears to be restricted to Firmicutes
Probab=43.54 E-value=61 Score=25.66 Aligned_cols=51 Identities=16% Similarity=0.144 Sum_probs=31.7
Q ss_pred hcCcEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHHHhhcccCCCCeEEEE
Q 028657 17 RLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLGKKAFTVLY 72 (206)
Q Consensus 17 ~~~i~y~~G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~l~~ll~~~~~~~y~lVy 72 (206)
+.|-++..|.|..|++|..+-.+.... -.++.+.-++. ++. ..++++.+|-
T Consensus 48 d~G~l~y~G~De~gn~VY~lG~~~~~~---~~~~al~~l~~-i~~-~~~~~i~~vd 98 (148)
T PF11385_consen 48 DIGRLIYMGTDEYGNEVYILGRKNNGK---IVERALKSLLE-ILG-IENEEIILVD 98 (148)
T ss_pred cCceEEEEEEcCCCCEEEEEecCChHH---HHHHHHHHHHH-HhC-CCCCcEEEEe
Confidence 467666789999999998887766543 23444444443 232 3345555554
No 15
>PF03721 UDPG_MGDP_dh_N: UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain; InterPro: IPR001732 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents the N-terminal NAD(+)-binding domain. Structural studies indicate that this domain forms an alpha-beta structure containing the six-stranded parallel beta sheet characteristic of the dinucleotide binding Rossman fold [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 3OJO_A 3OJL_A 1MV8_B 1MUU_A 1MFZ_C 3GG2_D 1DLJ_A 1DLI_A 3G79_B 2Y0E_D ....
Probab=38.64 E-value=8.5 Score=31.32 Aligned_cols=96 Identities=10% Similarity=0.125 Sum_probs=60.7
Q ss_pred HHhcCcEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHHH--h---h--c-ccCCCCeEEEEEcCCcccCcCCCcH
Q 028657 15 IDRLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSER--V---Y--P-RLGKKAFTVLYVHTGVQRSENFAGI 86 (206)
Q Consensus 15 i~~~~i~y~~G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~l~~--l---l--~-~~~~~~y~lVy~~tg~~~~~n~p~~ 86 (206)
+++.|. .+.|+|..-..|=-+.....|..+..++.++.-.... + . . .+.+.++++|..-|... ..+.|++
T Consensus 19 lA~~G~-~V~g~D~~~~~v~~l~~g~~p~~E~~l~~ll~~~~~~~~l~~t~~~~~ai~~adv~~I~VpTP~~-~~~~~Dl 96 (185)
T PF03721_consen 19 LAEKGH-QVIGVDIDEEKVEALNNGELPIYEPGLDELLKENVSAGRLRATTDIEEAIKDADVVFICVPTPSD-EDGSPDL 96 (185)
T ss_dssp HHHTTS-EEEEE-S-HHHHHHHHTTSSSS-CTTHHHHHHHHHHTTSEEEESEHHHHHHH-SEEEE----EBE-TTTSBET
T ss_pred HHhCCC-EEEEEeCChHHHHHHhhccccccccchhhhhccccccccchhhhhhhhhhhccceEEEecCCCcc-ccCCccH
Confidence 455553 3568887766555566667777777777776655420 0 0 0 13356788888888884 6788999
Q ss_pred HHHHHHHHhcchhHHhccceEEEEcCCh
Q 028657 87 SALRSIYDAIPANVKENLQAVYFVHPGL 114 (206)
Q Consensus 87 ~~L~~~y~~L~~~~kknLk~lyiVHPt~ 114 (206)
+++.++-+.+....++ .+++|+-.|.
T Consensus 97 s~v~~a~~~i~~~l~~--~~lvV~~STv 122 (185)
T PF03721_consen 97 SYVESAIESIAPVLRP--GDLVVIESTV 122 (185)
T ss_dssp HHHHHHHHHHHHHHCS--CEEEEESSSS
T ss_pred HHHHHHHHHHHHHHhh--cceEEEccEE
Confidence 9999999999877776 8899998655
No 16
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=34.58 E-value=45 Score=26.64 Aligned_cols=35 Identities=23% Similarity=0.238 Sum_probs=24.8
Q ss_pred ChhhHHHHHHhcCcEEEecc-CCCCCeEEEEEeecC
Q 028657 7 SESEQEELIDRLEIFKIHGR-DKQGRKILRIIGKFF 41 (206)
Q Consensus 7 s~~e~~~~i~~~~i~y~~G~-D~~GrpVvvi~a~~~ 41 (206)
+.+...+.|-+.|++...|. |..|||+++-.+..|
T Consensus 109 ~s~~~i~~L~e~glI~~~gr~~~~Grp~ly~tT~~F 144 (159)
T PF04079_consen 109 NSDSVIKTLLERGLIEEVGRKDTPGRPILYGTTDKF 144 (159)
T ss_dssp --HCHHHHHHHTTSEEEEEE-TTTT--EEEEE-HHH
T ss_pred ChHHHHHHHHHCCCEEecCcCCCCCCCeEeehhHHH
Confidence 34566778889999999997 557999999988766
No 17
>PF01243 Pyridox_oxidase: Pyridoxamine 5'-phosphate oxidase; InterPro: IPR011576 Pyridoxamine 5'-phosphate oxidase (PNPOx; 1.4.3.5 from EC) is a FMN flavoprotein that catalyses the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This reaction serves as the terminal step in the de novo biosynthesis of PLP in Escherichia coli and as a part of the salvage pathway of this coenzyme in both E. coli and mammalian cells [, ]. The binding sites for FMN and for substrate have been highly conserved throughout evolution. This entry represents the FMN-binding domain present in pyridoxamine 5'-phosphate oxidases, as well as in a number of proteins that have not been demonstrated to have enzymatic activity. The FMN-binding domain has a structure consisting of a beta-barrel with Greek key topology, and is related to the ferredoxin reductase-like FAD-binding domain. PNPOx has a different dimerisation mode than that found in flavin reductases, which also carry an FMN-binding domain with a similar topology. ; GO: 0004733 pyridoxamine-phosphate oxidase activity, 0010181 FMN binding, 0055114 oxidation-reduction process; PDB: 2IG6_A 1CI0_A 2HQ7_B 2HTD_B 3EC6_A 1WV4_B 1DNL_A 1G76_A 1G79_A 1G77_A ....
Probab=30.45 E-value=73 Score=21.47 Aligned_cols=33 Identities=15% Similarity=0.213 Sum_probs=27.4
Q ss_pred hhHHHHHHhcCcEEEeccCCCCCeEEEEEeecC
Q 028657 9 SEQEELIDRLEIFKIHGRDKQGRKILRIIGKFF 41 (206)
Q Consensus 9 ~e~~~~i~~~~i~y~~G~D~~GrpVvvi~a~~~ 41 (206)
+|...-|++.++++.+-.|.+|+|.+..+....
T Consensus 3 ~~~~~~l~~~~~~~laTv~~dG~P~~~~v~~~~ 35 (89)
T PF01243_consen 3 EEIREFLEESKYCVLATVDEDGRPHASPVWFVY 35 (89)
T ss_dssp HHHHHHHHSTSEEEEEEEETTSEEEEEEEEEEE
T ss_pred HHHHHHhcCCCEEEEEEECCCCCEEEEEEeeec
Confidence 566778889999999999999999988877543
No 18
>PF08412 Ion_trans_N: Ion transport protein N-terminal; InterPro: IPR013621 This domain is found to the N terminus of IPR005821 from INTERPRO in voltage- and cyclic nucleotide-gated K/Na ion channels.
Probab=28.99 E-value=54 Score=23.10 Aligned_cols=43 Identities=12% Similarity=0.134 Sum_probs=23.8
Q ss_pred CCCcHHHHHHHHHhcchhHHhccceEEEEcCChHHHHHHHHhc
Q 028657 82 NFAGISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFG 124 (206)
Q Consensus 82 n~p~~~~L~~~y~~L~~~~kknLk~lyiVHPt~~~k~~~~~~~ 124 (206)
|.-++..+++-..+.-.+-|..=...+|+||...+|.+|..+.
T Consensus 11 nk~sl~~f~S~~ai~~E~~R~~~~~~~IIHP~S~fR~~WD~~m 53 (77)
T PF08412_consen 11 NKFSLRVFGSKKAIEKEKERQRSSGPWIIHPFSKFRFYWDLIM 53 (77)
T ss_pred CHHHHHHHccHHHHHHHHHHHhcCCCeEEcCCccHHHHHHHHH
Confidence 4444544433333222222222245679999999999886543
No 19
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=28.16 E-value=54 Score=26.99 Aligned_cols=35 Identities=17% Similarity=0.164 Sum_probs=28.5
Q ss_pred ChhhHHHHHHhcCcEEEecc-CCCCCeEEEEEeecC
Q 028657 7 SESEQEELIDRLEIFKIHGR-DKQGRKILRIIGKFF 41 (206)
Q Consensus 7 s~~e~~~~i~~~~i~y~~G~-D~~GrpVvvi~a~~~ 41 (206)
+.+...+.|-+.|++...|+ |..|||+++-.+..|
T Consensus 114 ~s~~~l~~L~ergLI~~~Gr~~~~Grp~ly~TT~~F 149 (186)
T TIGR00281 114 KSYQIVDDLVEKGLVVELGRKDTPGRSFIYETTPKF 149 (186)
T ss_pred CHHHHHHHHHHCCCeEecCcCCCCCCCeeehhhHHH
Confidence 34567788889999999986 578999999888655
No 20
>PRK11020 hypothetical protein; Provisional
Probab=28.04 E-value=42 Score=25.59 Aligned_cols=19 Identities=21% Similarity=0.419 Sum_probs=15.7
Q ss_pred hhHHhccceEEEEcCChHH
Q 028657 98 ANVKENLQAVYFVHPGLQA 116 (206)
Q Consensus 98 ~~~kknLk~lyiVHPt~~~ 116 (206)
-+.+|..+++.||||-..+
T Consensus 83 GkLKKSVrGLVVVHPMTaL 101 (118)
T PRK11020 83 GKLKKSVRGLVVVHPMTAL 101 (118)
T ss_pred HHHhhcccceeEecCchHH
Confidence 3679999999999996543
No 21
>PF02350 Epimerase_2: UDP-N-acetylglucosamine 2-epimerase; InterPro: IPR003331 UDP-N-acetylglucosamine 2-epimerase 5.1.3.14 from EC catalyses the production of UDP-ManNAc from UDP-GlcNAc. Some of the enzymes is this family are bifunctional. In microorganisms the epimerase is involved in in the synthesis of the capsule precursor UDP-ManNAcA [, ]. The protein from rat liver displays both epimerase and kinase activity [].; GO: 0008761 UDP-N-acetylglucosamine 2-epimerase activity, 0006047 UDP-N-acetylglucosamine metabolic process, 0009103 lipopolysaccharide biosynthetic process; PDB: 1V4V_B 3BEO_B 3DZC_B 3OT5_B 1O6C_B 1VGV_D 1F6D_C.
Probab=25.55 E-value=2.5e+02 Score=24.95 Aligned_cols=71 Identities=13% Similarity=0.311 Sum_probs=37.6
Q ss_pred CCCCeEEEEEcCCcccCcCCCcHHHHHHHHHhcchhHHhccceEEEEcCChHHHHH-HHHhccccccCcCcccCcEEEeC
Q 028657 64 GKKAFTVLYVHTGVQRSENFAGISALRSIYDAIPANVKENLQAVYFVHPGLQARLF-LATFGRLFFNGVGGLYGKLRYVN 142 (206)
Q Consensus 64 ~~~~y~lVy~~tg~~~~~n~p~~~~L~~~y~~L~~~~kknLk~lyiVHPt~~~k~~-~~~~~~~fis~~~k~~~KI~yv~ 142 (206)
..++|.+|.+|.-. +..+...+.-+..+.+.|... +++.-++.+|++=-.+.. ...+ .++ +.++++.
T Consensus 178 ~~~~~iLvt~H~~t-~~~~~~~~~~i~~~l~~L~~~--~~~~vi~~~hn~p~~~~~i~~~l--------~~~-~~v~~~~ 245 (346)
T PF02350_consen 178 APKPYILVTLHPVT-NEDNPERLEQILEALKALAER--QNVPVIFPLHNNPRGSDIIIEKL--------KKY-DNVRLIE 245 (346)
T ss_dssp TTSEEEEEE-S-CC-CCTHH--HHHHHHHHHHHHHH--TTEEEEEE--S-HHHHHHHHHHH--------TT--TTEEEE-
T ss_pred cCCCEEEEEeCcch-hcCChHHHHHHHHHHHHHHhc--CCCcEEEEecCCchHHHHHHHHh--------ccc-CCEEEEC
Confidence 67899999999877 333233455555555555444 689999999954444433 3332 334 4888888
Q ss_pred ChhH
Q 028657 143 RLDY 146 (206)
Q Consensus 143 ~l~e 146 (206)
++..
T Consensus 246 ~l~~ 249 (346)
T PF02350_consen 246 PLGY 249 (346)
T ss_dssp ---H
T ss_pred CCCH
Confidence 8754
No 22
>TIGR01001 metA homoserine O-succinyltransferase. The apparent equivalog from Bacillus subtilis is broken into two tandem reading frames.
Probab=25.47 E-value=3.6e+02 Score=23.99 Aligned_cols=93 Identities=14% Similarity=0.219 Sum_probs=59.8
Q ss_pred HHHHHhcCcEEEe---ccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHHHhhcccCCCCeEEEEEcCCcccCcCCCcHHH
Q 028657 12 EELIDRLEIFKIH---GRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQRSENFAGISA 88 (206)
Q Consensus 12 ~~~i~~~~i~y~~---G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~l~~ll~~~~~~~y~lVy~~tg~~~~~n~p~~~~ 88 (206)
...|++.|||... ....+-||+=+.+=.-+|.+ ++.|.-+.-+ +.. ..-+..|-++.... ......+.+.
T Consensus 12 ~~~L~~enifvm~~~ra~~qdirpL~I~ILNLMP~K-~~TE~Q~lRl----L~n-tplqv~i~~~~~~s-h~~k~t~~~h 84 (300)
T TIGR01001 12 VKVLRKENIFVMTESRASHQDIRPLEILILNLMPKK-IETENQFLRL----LSN-SPLQVNITLLRTDS-RKSKNTPIEH 84 (300)
T ss_pred HHHHHhCCceeechhhhccccccceeEEEEecCCcc-HHHHHHHHHH----hcC-CCCceEEEEEEecc-ccCCCCCHHH
Confidence 5678888999764 22345689988898999987 5555433222 211 11222334443332 2235557899
Q ss_pred HHHHHHhcchhHHhccceEEEEc
Q 028657 89 LRSIYDAIPANVKENLQAVYFVH 111 (206)
Q Consensus 89 L~~~y~~L~~~~kknLk~lyiVH 111 (206)
|.++|..++.--.++..+++|-=
T Consensus 85 l~~fY~~f~~ik~~~fDGlIITG 107 (300)
T TIGR01001 85 LNKFYTTFEAVKDRKFDGLIITG 107 (300)
T ss_pred HHHHhhCHHHHhcCCCCEEEEcC
Confidence 99999999887789999999854
No 23
>PF06057 VirJ: Bacterial virulence protein (VirJ); InterPro: IPR010333 This entry contains several bacterial VirJ virulence proteins. VirJ is thought to be involved in the type IV secretion system. It is thought that the substrate proteins localised to the periplasm may associate with the pilus in a manner that is mediated by VirJ, and suggest a two-step process for type IV secretion in Agrobacterium [].
Probab=24.12 E-value=2.7e+02 Score=23.07 Aligned_cols=74 Identities=22% Similarity=0.411 Sum_probs=48.7
Q ss_pred CCCCeEEEEEe-ecCCCC------CCCHHHHHHHHHHHhhcccCCCCeEEEEEcCCcccCcCCCcHHHHHHHHHhcchhH
Q 028657 28 KQGRKILRIIG-KFFPAR------LLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQRSENFAGISALRSIYDAIPANV 100 (206)
Q Consensus 28 ~~GrpVvvi~a-~~~p~~------~~d~e~ll~y~l~~ll~~~~~~~y~lVy~~tg~~~~~n~p~~~~L~~~y~~L~~~~ 100 (206)
+.|-||+-+.+ ++|=.+ .-|+++++.+... +-...++++|=..-|. ..+.-+|..||...
T Consensus 27 ~~G~~VvGvdsl~Yfw~~rtP~~~a~Dl~~~i~~y~~----~w~~~~vvLiGYSFGA---------DvlP~~~nrLp~~~ 93 (192)
T PF06057_consen 27 KQGVPVVGVDSLRYFWSERTPEQTAADLARIIRHYRA----RWGRKRVVLIGYSFGA---------DVLPFIYNRLPAAL 93 (192)
T ss_pred HCCCeEEEechHHHHhhhCCHHHHHHHHHHHHHHHHH----HhCCceEEEEeecCCc---------hhHHHHHhhCCHHH
Confidence 46778888877 444432 1345555554433 3556777665323333 35778899999999
Q ss_pred HhccceEEEEcCCh
Q 028657 101 KENLQAVYFVHPGL 114 (206)
Q Consensus 101 kknLk~lyiVHPt~ 114 (206)
|++++.+..+-|+.
T Consensus 94 r~~v~~v~Ll~p~~ 107 (192)
T PF06057_consen 94 RARVAQVVLLSPST 107 (192)
T ss_pred HhheeEEEEeccCC
Confidence 99999998887754
No 24
>PF09949 DUF2183: Uncharacterized conserved protein (DUF2183); InterPro: IPR019236 This domain, found in various bacterial and fungal proteins, has no known function.
Probab=23.10 E-value=1.8e+02 Score=21.38 Aligned_cols=49 Identities=20% Similarity=0.277 Sum_probs=36.3
Q ss_pred HHHHHHHHhhcccCCCCeEEEEEcCCcccCcCCCcHHHHHHHHHhcchhHHhccceEEEE
Q 028657 51 LKRYLSERVYPRLGKKAFTVLYVHTGVQRSENFAGISALRSIYDAIPANVKENLQAVYFV 110 (206)
Q Consensus 51 ll~y~l~~ll~~~~~~~y~lVy~~tg~~~~~n~p~~~~L~~~y~~L~~~~kknLk~lyiV 110 (206)
.+...+..++..+.+.+|++|=+.+... -.+|..+-++|+.+++++||=
T Consensus 50 ~K~~~i~~i~~~fP~~kfiLIGDsgq~D-----------peiY~~ia~~~P~~i~ai~IR 98 (100)
T PF09949_consen 50 HKRDNIERILRDFPERKFILIGDSGQHD-----------PEIYAEIARRFPGRILAIYIR 98 (100)
T ss_pred HHHHHHHHHHHHCCCCcEEEEeeCCCcC-----------HHHHHHHHHHCCCCEEEEEEE
Confidence 3444555567778899999997665431 267888889999999999983
Done!