Query 032490
Match_columns 139
No_of_seqs 108 out of 289
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 14:45:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032490.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032490hhsearch_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-30 7.8E-35 214.4 8.1 126 5-132 64-194 (467)
2 PF13716 CRAL_TRIO_2: Divergen 99.9 3.7E-27 8E-32 172.1 9.9 110 19-131 2-113 (149)
3 smart00516 SEC14 Domain in hom 99.7 8.9E-18 1.9E-22 122.0 9.2 105 25-132 14-126 (158)
4 cd00170 SEC14 Sec14p-like lipi 99.7 1.5E-16 3.4E-21 113.6 8.1 111 19-131 9-127 (157)
5 KOG1470 Phosphatidylinositol t 99.5 2.5E-13 5.4E-18 111.5 9.5 118 6-127 86-209 (324)
6 PF00650 CRAL_TRIO: CRAL/TRIO 99.4 2.4E-13 5.3E-18 98.7 5.6 116 14-131 2-127 (159)
7 KOG1471 Phosphatidylinositol t 98.6 1.6E-07 3.5E-12 76.1 8.8 119 12-131 88-225 (317)
8 KOG1826 Ras GTPase activating 96.1 0.0024 5.3E-08 62.5 1.5 128 6-137 1549-1677(2724)
9 PF10928 DUF2810: Protein of u 77.7 1.3 2.7E-05 27.3 1.1 18 98-115 20-37 (54)
10 PF09949 DUF2183: Uncharacteri 74.5 5.8 0.00013 27.4 3.9 46 53-109 52-97 (100)
11 PF07872 DUF1659: Protein of u 71.6 2.6 5.6E-05 25.2 1.4 27 18-44 8-35 (47)
12 PF13986 DUF4224: Domain of un 71.6 7.5 0.00016 23.2 3.4 26 8-35 17-42 (47)
13 PF03721 UDPG_MGDP_dh_N: UDP-g 65.6 1.9 4.1E-05 32.7 -0.1 109 15-127 19-135 (185)
14 PRK11020 hypothetical protein; 65.1 3.7 8.1E-05 29.3 1.3 18 98-115 83-100 (118)
15 PF08412 Ion_trans_N: Ion tran 48.8 18 0.00039 23.9 2.4 43 81-123 10-52 (77)
16 PF06057 VirJ: Bacterial virul 39.5 85 0.0018 24.3 5.2 73 28-113 27-106 (192)
17 PF13905 Thioredoxin_8: Thiore 35.7 48 0.001 21.2 2.9 16 61-76 28-44 (95)
18 COG4822 CbiK Cobalamin biosynt 34.9 97 0.0021 24.9 4.9 66 28-111 108-174 (265)
19 PF11385 DUF3189: Protein of u 34.3 1.1E+02 0.0024 22.5 4.9 26 17-42 48-73 (148)
20 PF06933 SSP160: Special lobe- 33.0 23 0.00051 31.0 1.3 17 94-110 426-442 (756)
21 PF01243 Pyridox_oxidase: Pyri 30.6 64 0.0014 20.2 2.8 32 9-40 3-34 (89)
22 PF04666 Glyco_transf_54: N-Ac 30.5 3.1E+02 0.0066 22.6 8.0 83 21-114 42-129 (297)
23 KOG2283 Clathrin coat dissocia 29.4 2.2E+02 0.0047 24.8 6.6 71 36-112 22-114 (434)
24 PF02350 Epimerase_2: UDP-N-ac 28.4 75 0.0016 26.3 3.5 47 64-113 178-224 (346)
25 PF00025 Arf: ADP-ribosylation 28.0 2.4E+02 0.0051 20.4 6.4 59 29-91 114-173 (175)
26 PF04079 DUF387: Putative tran 27.9 67 0.0015 23.9 2.9 33 9-41 111-144 (159)
27 PF10340 DUF2424: Protein of u 27.0 1E+02 0.0023 26.3 4.2 39 66-111 121-161 (374)
28 KOG2633 Hismacro and SEC14 dom 26.0 1.1 2.4E-05 34.9 -7.2 37 9-45 13-49 (200)
29 TIGR00281 segregation and cond 24.0 74 0.0016 24.4 2.5 33 9-41 116-149 (186)
30 PHA02894 hypothetical protein; 21.6 52 0.0011 22.5 1.1 16 100-115 58-73 (97)
31 PF05846 Chordopox_A15: Chordo 21.3 59 0.0013 22.3 1.3 17 99-115 41-57 (90)
32 TIGR01001 metA homoserine O-su 20.2 5.1E+02 0.011 21.5 9.1 91 12-110 12-106 (300)
No 1
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=99.96 E-value=3.6e-30 Score=214.39 Aligned_cols=126 Identities=29% Similarity=0.407 Sum_probs=118.4
Q ss_pred CCChhhhHHHHHhc--CcEEEecc--CCCCCeEEEEEcccCCC-cCCCHHHHHHHHHHHhhcccCCCCeEEEEEecCccc
Q 032490 5 VVSESEQEELIDRL--EIFKIHGR--DKQGRKILRIIGKFFPA-RLLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQR 79 (139)
Q Consensus 5 ~i~~~e~~~~i~~~--~ily~~G~--D~~GrpVvvi~a~~~p~-~~~d~e~ll~y~~~~~ld~~~~~~y~lVy~~tg~~~ 79 (139)
.-+.+++|+|+.++ +++...|. |++||+|+|+.||++|+ +++|.-+++.|.++ ++|++++++|++||||.|+ .
T Consensus 64 ~~p~ed~fyd~~~H~~ei~qvi~~~~D~~gr~iivv~a~rlp~~~eld~~~li~~~v~-~id~~Ve~DYt~vYfh~gl-~ 141 (467)
T KOG4406|consen 64 IEPKEDPFYDIARHEREILQVIGDAKDKQGRKIIVVYACRLPSSSELDDIRLISYLVY-TIDKYVENDYTLVYFHHGL-P 141 (467)
T ss_pred cCcccccHHHHHHhhhheeeeccCcccccCCeeEEEEEecCCchhhhhhHHHHHHHHH-HHHHHHhccceeeehhcCC-c
Confidence 34668899999999 99988766 99999999999999999 77898889999998 6999999999999999999 7
Q ss_pred CcCcccHHHHHHHHHhcChhhHhccceEEEEcCChHHHHHHHHhcchhccCCC
Q 032490 80 SENFAGISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVG 132 (139)
Q Consensus 80 ~~n~p~~~wl~~~y~~l~~~~kknLk~lyiVHPt~~~K~~~~~~~pfi~s~~~ 132 (139)
+.|+|+++|+.++|..+||+|+|||||+|+|||+||+|++|.+++||||.+.+
T Consensus 142 s~nkp~l~~l~~aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~ 194 (467)
T KOG4406|consen 142 SDNKPYLQLLFDAYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFT 194 (467)
T ss_pred ccccchHHHHHHHHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhh
Confidence 99999999999999999999999999999999999999999999999998765
No 2
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.94 E-value=3.7e-27 Score=172.15 Aligned_cols=110 Identities=27% Similarity=0.426 Sum_probs=86.2
Q ss_pred CcEEEeccCCCCCeEEEEEcccCCCcCCCHHHHHHHHHHHhh-cccCCCCeEEEEEecCcccCcCcccHHHHHHHHHhcC
Q 032490 19 EIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVY-PRLGKKAFTVLYVHTGVQRSENFAGISALRSIYDAIP 97 (139)
Q Consensus 19 ~ily~~G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~~~~~l-d~~~~~~y~lVy~~tg~~~~~n~p~~~wl~~~y~~l~ 97 (139)
.+++.+|+|++||||+++.++++ +...|+|+++.|++++ + +.+.+++|+||||++++ +..|.|+++|++++|+.++
T Consensus 2 ~~~~~gG~d~~g~pV~~~~~~~~-~~~~~~~~ll~yl~~~-l~~~~~~~~f~vVid~~~~-~~~~~~~~~~l~~~~~~l~ 78 (149)
T PF13716_consen 2 IFFYPGGRDREGRPVVVFIASRL-PSSDDLERLLLYLLST-LSEEVVDKPFSVVIDHTGF-SRSSEPSLSWLKQLYKLLP 78 (149)
T ss_dssp SE-EEEEEBTTS-EEEEEEGGG--C-TTHHHHHHHHHHHH-H-TTTTTS-EEEEEE-TT---GGG---HHHHHHTTTSS-
T ss_pred eEEEecccCCCcCEEEEEECCcC-cchhhHHHHHHHHHHh-hhHHhcCCCEEEEEEcCCC-ccccCCchHHHHHHHHHHH
Confidence 46789999999999999999999 4345999999999985 6 88899999999999999 7889999999999999999
Q ss_pred hhhHhccceEEEEcCChHHHHHH-HHhcchhccCC
Q 032490 98 ANVKENLQAVYFVHPGLQARLFL-ATFGRLFFNGV 131 (139)
Q Consensus 98 ~~~kknLk~lyiVHPt~~~K~~~-~~~~pfi~s~~ 131 (139)
+.+++||+++|||||++|+|+++ ...+++++++.
T Consensus 79 ~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~ 113 (149)
T PF13716_consen 79 RKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKF 113 (149)
T ss_dssp HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT
T ss_pred HHHhhceEEEEEECCCHHHHHHHHHHhcccccccc
Confidence 99999999999999999999999 55566666654
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=99.74 E-value=8.9e-18 Score=122.04 Aligned_cols=105 Identities=27% Similarity=0.420 Sum_probs=92.5
Q ss_pred ccCCCCCeEEEEEcccCCCcCCCHHHHHHHHHHHhhccc--------CCCCeEEEEEecCcccCcCcccHHHHHHHHHhc
Q 032490 25 GRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRL--------GKKAFTVLYVHTGVQRSENFAGISALRSIYDAI 96 (139)
Q Consensus 25 G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~~~~~ld~~--------~~~~y~lVy~~tg~~~~~n~p~~~wl~~~y~~l 96 (139)
|.|++||||+++.+++++.+..+.+.+++|++. ++|.. ..+.+++|++.++. +..+ ++.+|++++++.+
T Consensus 14 g~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~~-~~e~~~~~~~~~~~~~~~~~i~D~~~~-~~~~-~~~~~lk~~~~~~ 90 (158)
T smart00516 14 GYDKDGRPVLIFRAGRFDLKSVTLEELLRYLVY-VLEKILQREKKTGGIEGFTVIFDLKGL-SMSN-PDLSVLRKILKIL 90 (158)
T ss_pred CCCCCcCEEEEEeccccccCcCCHHHHHHHHHH-HHHHHHHHHhcCCCeeeEEEEEECCCC-Cccc-ccHHHHHHHHHHH
Confidence 799999999999999998877899999998887 45533 23578999999998 5544 7899999999999
Q ss_pred ChhhHhccceEEEEcCChHHHHHHHHhcchhccCCC
Q 032490 97 PANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVG 132 (139)
Q Consensus 97 ~~~~kknLk~lyiVHPt~~~K~~~~~~~pfi~s~~~ 132 (139)
+..|+++|+++|||||+++++++|++++||++.++.
T Consensus 91 ~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~ 126 (158)
T smart00516 91 QDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTR 126 (158)
T ss_pred HHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhh
Confidence 999999999999999999999999999999988754
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=99.68 E-value=1.5e-16 Score=113.55 Aligned_cols=111 Identities=25% Similarity=0.354 Sum_probs=90.6
Q ss_pred CcEEEeccCCCCCeEEEEEcccCC-CcCCCHHHHHHHHHHHhhcccCC------CCeEEEEEecCcccCcCcc-cHHHHH
Q 032490 19 EIFKIHGRDKQGRKILRIIGKFFP-ARLLSVEVLKRYLSERVYPRLGK------KAFTVLYVHTGVQRSENFA-GISALR 90 (139)
Q Consensus 19 ~ily~~G~D~~GrpVvvi~a~~~p-~~~~d~e~ll~y~~~~~ld~~~~------~~y~lVy~~tg~~~~~n~p-~~~wl~ 90 (139)
++.+.+|.|++||||+++..+... ....+.+.+++|.+. .+|.... +.+++|++.++. +..+.. ..+|++
T Consensus 9 ~~~~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~-~~e~~~~~~~~~~~~~~~i~D~~~~-~~~~~~~~~~~~k 86 (157)
T cd00170 9 KVGYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVY-TLEKLLQEDDEQVEGFVVIIDLKGL-SLSHLLPDPSLLK 86 (157)
T ss_pred cccccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHH-HHHHHHhhhhhcccceEEEEECCCC-ChhccchhHHHHH
Confidence 566566779999999999998433 345666888888776 4654322 478999999998 555553 789999
Q ss_pred HHHHhcChhhHhccceEEEEcCChHHHHHHHHhcchhccCC
Q 032490 91 SIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGV 131 (139)
Q Consensus 91 ~~y~~l~~~~kknLk~lyiVHPt~~~K~~~~~~~pfi~s~~ 131 (139)
++++.++..|++||+++|||||+++++++|++++||++.+.
T Consensus 87 ~~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~ 127 (157)
T cd00170 87 KILKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKT 127 (157)
T ss_pred HHHHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhh
Confidence 99999999999999999999999999999999999988764
No 5
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=99.47 E-value=2.5e-13 Score=111.51 Aligned_cols=118 Identities=19% Similarity=0.254 Sum_probs=93.3
Q ss_pred CChhhhHHHHHhcCcEEEeccCCCCCeEEEEEcccCCCcCCCHHHHHHHHHHHhhcc------cCCCCeEEEEEecCccc
Q 032490 6 VSESEQEELIDRLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPR------LGKKAFTVLYVHTGVQR 79 (139)
Q Consensus 6 i~~~e~~~~i~~~~ily~~G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~~~~~ld~------~~~~~y~lVy~~tg~~~ 79 (139)
+...|.-.++ +.|-.|.+|.|++||||+++.++.-..+..+.+.+.++++. +|+. -+++.++++++.+|+ +
T Consensus 86 ~~~~Ev~~e~-~tGK~yi~G~D~~gRPVl~~~~~~~~qn~~t~~~~~r~~Vy-~mE~Ai~~lp~~qe~~~~L~D~~~f-s 162 (324)
T KOG1470|consen 86 IEADEVAAEL-ETGKAYILGHDKDGRPVLYLRPRPHRQNTKTQKELERLLVY-TLENAILFLPPGQEQFVWLFDLTGF-S 162 (324)
T ss_pred cCHHHHHHHh-hcCcEEEecccCCCCeEEEEecCCCCCCCCCHHHHHHHHHH-HHHHHHHhCCCCcceEEEEEecccC-c
Confidence 3344433334 34666788999999999999998444444565555555554 3442 367789999999999 5
Q ss_pred CcCcccHHHHHHHHHhcChhhHhccceEEEEcCChHHHHHHHHhcchh
Q 032490 80 SENFAGISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLF 127 (139)
Q Consensus 80 ~~n~p~~~wl~~~y~~l~~~~kknLk~lyiVHPt~~~K~~~~~~~pfi 127 (139)
..| ++++.++.+..+|+..|+++|...+|+||.|++..+|++.+|||
T Consensus 163 ~sN-~d~~~~k~~~~~lq~hYPErLg~a~l~~~P~iF~~~wkiikpfl 209 (324)
T KOG1470|consen 163 MSN-PDIKFLKELLHILQDHYPERLGKALLVNAPWIFQPFWKIIKPFL 209 (324)
T ss_pred ccC-CCcHHHHHHHHHHHHhChHHhhhhhhcCChHHHHHHHHHhhhcc
Confidence 555 68999999999999999999999999999999999999999998
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=99.42 E-value=2.4e-13 Score=98.69 Aligned_cols=116 Identities=23% Similarity=0.301 Sum_probs=84.2
Q ss_pred HHHhcCcEEEeccCCCCCeEEEEEcccCCCcCCCHHHHHHHHHHHhhcc--------cCCCCeEEEEEecCcccCcCccc
Q 032490 14 LIDRLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPR--------LGKKAFTVLYVHTGVQRSENFAG 85 (139)
Q Consensus 14 ~i~~~~ily~~G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~~~~~ld~--------~~~~~y~lVy~~tg~~~~~n~p~ 85 (139)
++.+.+..+..|.|++||||+++-.+++.......+.+.++++. ++|. ...+.+++|++.+|+ +..+.+.
T Consensus 2 ~~~~~~~~~~~g~D~~gr~v~~~~~~~~~~~~~~~~~~~~~~~~-~~E~~~~~~~~~~~~~~~~~iiD~~g~-~~~~~~~ 79 (159)
T PF00650_consen 2 EILKSGPFYLHGRDKDGRPVIYIRLGRFDPKKFSPEDVIRFFVY-LLERMLKRMPEGGQVEGIVVIIDLSGF-SLSNFDW 79 (159)
T ss_dssp HHHTTSCEEEEEE-TTS-EEEEEEGTT--HHTS-HHHHHHHHHH-HHHHHHHTHHHTSHHH-EEEEEE-TT---HHHHHC
T ss_pred HHHCCeeEEECCCCCCcCEEEEEEcccCCCCcCCHHHHHHHHHH-HHHHHHhhhcccccceeEEEEEeCCCc-eEecccc
Confidence 57788999999999999999999998877655555555555544 2332 123578999999999 5555542
Q ss_pred --HHHHHHHHHhcChhhHhccceEEEEcCChHHHHHHHHhcchhccCC
Q 032490 86 --ISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGV 131 (139)
Q Consensus 86 --~~wl~~~y~~l~~~~kknLk~lyiVHPt~~~K~~~~~~~pfi~s~~ 131 (139)
.+.++.+.+.++..|+++++.+||+|++++++++|++++||++.++
T Consensus 80 ~~~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~ 127 (159)
T PF00650_consen 80 WPISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKT 127 (159)
T ss_dssp HHHHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHH
T ss_pred chhhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhh
Confidence 7888999999999999999999999999999999999999998764
No 7
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=98.64 E-value=1.6e-07 Score=76.06 Aligned_cols=119 Identities=13% Similarity=0.111 Sum_probs=83.6
Q ss_pred HHHHHhcCcEEEeccCCCCCeEEEEEcccCCCcC----CC-----------HHHHHHHHHHHhhcc--cCCCCeEEEEEe
Q 032490 12 EELIDRLEIFKIHGRDKQGRKILRIIGKFFPARL----LS-----------VEVLKRYLSERVYPR--LGKKAFTVLYVH 74 (139)
Q Consensus 12 ~~~i~~~~ily~~G~D~~GrpVvvi~a~~~p~~~----~d-----------~e~ll~y~~~~~ld~--~~~~~y~lVy~~ 74 (139)
..++.+..-....|.|++|+||++--....-.+. .. .++.+..+.....+. -.....+.|.+.
T Consensus 88 ~~~~~~~~~~~~~~~~~~g~~v~~~~~g~~~~~~l~~~~~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl 167 (317)
T KOG1471|consen 88 DDELLKYYPQGLHGVDKEGRPVYIERLGKIDPKGLLKRTGSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDL 167 (317)
T ss_pred chhhhhhccccccccCCCCCEEEEeccCCCCcccceeeccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEEC
Confidence 3444443334467999999999997665553221 12 233333332211111 235567889999
Q ss_pred cCcccCcC--cccHHHHHHHHHhcChhhHhccceEEEEcCChHHHHHHHHhcchhccCC
Q 032490 75 TGVQRSEN--FAGISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGV 131 (139)
Q Consensus 75 tg~~~~~n--~p~~~wl~~~y~~l~~~~kknLk~lyiVHPt~~~K~~~~~~~pfi~s~~ 131 (139)
.|. +-.+ .+....++++...++..|+++++++||||..+++.++|++++||+..+.
T Consensus 168 ~G~-~~~~~~~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~P~~f~~~~~~ikpfL~~kt 225 (317)
T KOG1471|consen 168 KGV-SLSHLLKPAPTLLKKILKILQDNYPERLKRIHIINAPTIFSALWKVVKPFLDEKT 225 (317)
T ss_pred CCC-cchhHHHHHHHHHHHHHHHHHHhCHHhhceEEEEcCchhHHHHHHHHhccCCHHH
Confidence 998 4443 3778889999999999999999999999999999999999999998654
No 8
>KOG1826 consensus Ras GTPase activating protein RasGAP/neurofibromin [Defense mechanisms]
Probab=96.12 E-value=0.0024 Score=62.51 Aligned_cols=128 Identities=16% Similarity=0.060 Sum_probs=101.2
Q ss_pred CChhhhHHHHHhcCcEEEeccCCCCCeEEEEEcccCCCcCCCHHHHHHHHHHHhhcccCCCCeEEEEEecCcccCcCccc
Q 032490 6 VSESEQEELIDRLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQRSENFAG 85 (139)
Q Consensus 6 i~~~e~~~~i~~~~ily~~G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~~~~~ld~~~~~~y~lVy~~tg~~~~~n~p~ 85 (139)
+.+.|+|--++..-+.|+.| .+.|.|+.++++++.--+..+-+ ++.|+..-++.+.+.-++.++.+-|.. ..+++--
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-SENGLKNFYLVSRRKFLKECSDD-ILIFLVELCLKPKVHFPGEVREDPTPI-EFDYSFL 1625 (2724)
T ss_pred HhhhhHHHHHHHHHHHHHhh-hhccCcchhhHhHHHHHhhcCcH-HHHHHHHHHcCccccCcceeeecCCcC-CccHHHH
Confidence 46788999999999999999 99999999999986655555433 444544434677888999999987777 3344444
Q ss_pred HHHHHH-HHHhcChhhHhccceEEEEcCChHHHHHHHHhcchhccCCCCCccc
Q 032490 86 ISALRS-IYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGSESE 137 (139)
Q Consensus 86 ~~wl~~-~y~~l~~~~kknLk~lyiVHPt~~~K~~~~~~~pfi~s~~~~~~~~ 137 (139)
.+++.. ++...+.-..+|..++|+++.+.|.|.....--+ |+-+++|++.|
T Consensus 1626 tsf~~~~~f~vr~~va~e~~~a~~di~~n~~lK~~~~l~dr-iL~~L~~~k~~ 1677 (2724)
T KOG1826|consen 1626 TSFLYLKWFKVRPHVANENKHAVGDINCNSFLKETTKLHDR-ILGQLGQPKME 1677 (2724)
T ss_pred HHHHhhhheeechhhhhhcccccccccchHHHHHHHHHHHH-HHhhcCCCcee
Confidence 555554 6777888899999999999999999999988888 88899999876
No 9
>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=77.72 E-value=1.3 Score=27.28 Aligned_cols=18 Identities=22% Similarity=0.464 Sum_probs=13.4
Q ss_pred hhhHhccceEEEEcCChH
Q 032490 98 ANVKENLQAVYFVHPGLQ 115 (139)
Q Consensus 98 ~~~kknLk~lyiVHPt~~ 115 (139)
-+.||.++.+.||||..-
T Consensus 20 GkLKKsVrGLvvVHPmTa 37 (54)
T PF10928_consen 20 GKLKKSVRGLVVVHPMTA 37 (54)
T ss_dssp HHHHHHTTS-EEE-SSSH
T ss_pred HHHHhhhceeEEEechHH
Confidence 367999999999999764
No 10
>PF09949 DUF2183: Uncharacterized conserved protein (DUF2183); InterPro: IPR019236 This domain, found in various bacterial and fungal proteins, has no known function.
Probab=74.52 E-value=5.8 Score=27.41 Aligned_cols=46 Identities=20% Similarity=0.270 Sum_probs=36.6
Q ss_pred HHHHHHhhcccCCCCeEEEEEecCcccCcCcccHHHHHHHHHhcChhhHhccceEEE
Q 032490 53 RYLSERVYPRLGKKAFTVLYVHTGVQRSENFAGISALRSIYDAIPANVKENLQAVYF 109 (139)
Q Consensus 53 ~y~~~~~ld~~~~~~y~lVy~~tg~~~~~n~p~~~wl~~~y~~l~~~~kknLk~lyi 109 (139)
...+.++++.+.+.+|++|-+.+.. .| +.|..+-++|+.+++++||
T Consensus 52 ~~~i~~i~~~fP~~kfiLIGDsgq~-----Dp------eiY~~ia~~~P~~i~ai~I 97 (100)
T PF09949_consen 52 RDNIERILRDFPERKFILIGDSGQH-----DP------EIYAEIARRFPGRILAIYI 97 (100)
T ss_pred HHHHHHHHHHCCCCcEEEEeeCCCc-----CH------HHHHHHHHHCCCCEEEEEE
Confidence 3344456778899999999996533 23 7899999999999999998
No 11
>PF07872 DUF1659: Protein of unknown function (DUF1659); InterPro: IPR012454 This family consists of hypothetical bacterial proteins of unknown function
Probab=71.64 E-value=2.6 Score=25.17 Aligned_cols=27 Identities=19% Similarity=0.278 Sum_probs=19.9
Q ss_pred cCcEEEeccCCCCCeEEEEEc-ccCCCc
Q 032490 18 LEIFKIHGRDKQGRKILRIIG-KFFPAR 44 (139)
Q Consensus 18 ~~ily~~G~D~~GrpVvvi~a-~~~p~~ 44 (139)
+.+-++.|.|..|.||+---. +++.+.
T Consensus 8 L~l~~~~G~d~~Gkpi~k~ks~~nvk~~ 35 (47)
T PF07872_consen 8 LRLKYQTGVDENGKPIFKTKSFSNVKPD 35 (47)
T ss_pred EEEEEEcccCCCCCEEEEeeehhhcCCC
Confidence 567788899999999987544 355443
No 12
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=71.56 E-value=7.5 Score=23.20 Aligned_cols=26 Identities=27% Similarity=0.256 Sum_probs=20.1
Q ss_pred hhhhHHHHHhcCcEEEeccCCCCCeEEE
Q 032490 8 ESEQEELIDRLEIFKIHGRDKQGRKILR 35 (139)
Q Consensus 8 ~~e~~~~i~~~~ily~~G~D~~GrpVvv 35 (139)
.+.+...+.++||-+..+ ++|+|+|.
T Consensus 17 ~~~Q~~~L~~~Gi~~~~~--~~G~p~V~ 42 (47)
T PF13986_consen 17 PSKQIRWLRRNGIPFVVR--ADGRPIVT 42 (47)
T ss_pred HHHHHHHHHHCCCeeEEC--CCCCEEee
Confidence 355677899999998855 45999985
No 13
>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=65.65 E-value=1.9 Score=32.72 Aligned_cols=109 Identities=10% Similarity=0.099 Sum_probs=70.5
Q ss_pred HHhcCcEEEeccCCCCCeEEEEEcccCCCcCCCHHHHHHHHHH--Hh---h--c-ccCCCCeEEEEEecCcccCcCcccH
Q 032490 15 IDRLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSE--RV---Y--P-RLGKKAFTVLYVHTGVQRSENFAGI 86 (139)
Q Consensus 15 i~~~~ily~~G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~~~--~~---l--d-~~~~~~y~lVy~~tg~~~~~n~p~~ 86 (139)
+++.|.- +.|+|.+-..|=-+.....|-.+..++.++.-.+. ++ . + .+.+-++++|..-|.. ..++.|++
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 LAEKGHQ-VIGVDIDEEKVEALNNGELPIYEPGLDELLKENVSAGRLRATTDIEEAIKDADVVFICVPTPS-DEDGSPDL 96 (185)
T ss_dssp HHHTTSE-EEEE-S-HHHHHHHHTTSSSS-CTTHHHHHHHHHHTTSEEEESEHHHHHHH-SEEEE----EB-ETTTSBET
T ss_pred HHhCCCE-EEEEeCChHHHHHHhhccccccccchhhhhccccccccchhhhhhhhhhhccceEEEecCCCc-cccCCccH
Confidence 4555633 66888877766666667777777778877765541 00 0 1 1455688888888888 67889999
Q ss_pred HHHHHHHHhcChhhHhccceEEEEcCChHHHHHHHHhcchh
Q 032490 87 SALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLF 127 (139)
Q Consensus 87 ~wl~~~y~~l~~~~kknLk~lyiVHPt~~~K~~~~~~~pfi 127 (139)
+++.++-+.+....++ .+++|+-.|...-+.=..+.|.+
T Consensus 97 s~v~~a~~~i~~~l~~--~~lvV~~STvppGtt~~~~~~il 135 (185)
T PF03721_consen 97 SYVESAIESIAPVLRP--GDLVVIESTVPPGTTEELLKPIL 135 (185)
T ss_dssp HHHHHHHHHHHHHHCS--CEEEEESSSSSTTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhh--cceEEEccEEEEeeehHhhhhhh
Confidence 9999999999888777 78889887766655555555544
No 14
>PRK11020 hypothetical protein; Provisional
Probab=65.11 E-value=3.7 Score=29.32 Aligned_cols=18 Identities=22% Similarity=0.464 Sum_probs=15.2
Q ss_pred hhhHhccceEEEEcCChH
Q 032490 98 ANVKENLQAVYFVHPGLQ 115 (139)
Q Consensus 98 ~~~kknLk~lyiVHPt~~ 115 (139)
-+.+|.++.+.||||-.-
T Consensus 83 GkLKKSVrGLVVVHPMTa 100 (118)
T PRK11020 83 GKLKKSVRGLVVVHPMTA 100 (118)
T ss_pred HHHhhcccceeEecCchH
Confidence 357999999999999653
No 15
>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=48.76 E-value=18 Score=23.90 Aligned_cols=43 Identities=12% Similarity=0.182 Sum_probs=25.2
Q ss_pred cCcccHHHHHHHHHhcChhhHhccceEEEEcCChHHHHHHHHh
Q 032490 81 ENFAGISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATF 123 (139)
Q Consensus 81 ~n~p~~~wl~~~y~~l~~~~kknLk~lyiVHPt~~~K~~~~~~ 123 (139)
.|.-++..+.+-..+...+-|.-=..-+|+||....|.+|.++
T Consensus 10 ~nk~sl~~f~S~~ai~~E~~R~~~~~~~IIHP~S~fR~~WD~~ 52 (77)
T PF08412_consen 10 DNKFSLRVFGSKKAIEKEKERQRSSGPWIIHPFSKFRFYWDLI 52 (77)
T ss_pred cCHHHHHHHccHHHHHHHHHHHhcCCCeEEcCCccHHHHHHHH
Confidence 4555555544444333333222224568999999999988654
No 16
>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=39.54 E-value=85 Score=24.33 Aligned_cols=73 Identities=22% Similarity=0.392 Sum_probs=51.4
Q ss_pred CCCCeEEEEEcc-cCCCc------CCCHHHHHHHHHHHhhcccCCCCeEEEEEecCcccCcCcccHHHHHHHHHhcChhh
Q 032490 28 KQGRKILRIIGK-FFPAR------LLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQRSENFAGISALRSIYDAIPANV 100 (139)
Q Consensus 28 ~~GrpVvvi~a~-~~p~~------~~d~e~ll~y~~~~~ld~~~~~~y~lVy~~tg~~~~~n~p~~~wl~~~y~~l~~~~ 100 (139)
+.|-|||-+-+. +|=.+ .-|+++++.+... +-....+++|-+.-|+. - +--+|..||...
T Consensus 27 ~~G~~VvGvdsl~Yfw~~rtP~~~a~Dl~~~i~~y~~----~w~~~~vvLiGYSFGAD---v------lP~~~nrLp~~~ 93 (192)
T PF06057_consen 27 KQGVPVVGVDSLRYFWSERTPEQTAADLARIIRHYRA----RWGRKRVVLIGYSFGAD---V------LPFIYNRLPAAL 93 (192)
T ss_pred HCCCeEEEechHHHHhhhCCHHHHHHHHHHHHHHHHH----HhCCceEEEEeecCCch---h------HHHHHhhCCHHH
Confidence 457777777773 44331 1357777766543 46788899998877772 3 337899999999
Q ss_pred HhccceEEEEcCC
Q 032490 101 KENLQAVYFVHPG 113 (139)
Q Consensus 101 kknLk~lyiVHPt 113 (139)
|++++.+.++-|+
T Consensus 94 r~~v~~v~Ll~p~ 106 (192)
T PF06057_consen 94 RARVAQVVLLSPS 106 (192)
T ss_pred HhheeEEEEeccC
Confidence 9999999887654
No 17
>PF13905 Thioredoxin_8: Thioredoxin-like; PDB: 1FG4_A 1I5G_A 1OC8_B 1O6J_A 1OC9_B 1O81_A 3FKF_A 1O85_A 1O7U_A 1O8W_A ....
Probab=35.73 E-value=48 Score=21.19 Aligned_cols=16 Identities=13% Similarity=0.281 Sum_probs=9.0
Q ss_pred cccC-CCCeEEEEEecC
Q 032490 61 PRLG-KKAFTVLYVHTG 76 (139)
Q Consensus 61 d~~~-~~~y~lVy~~tg 76 (139)
+.+. +.++.+|+.+..
T Consensus 28 ~~~~~~~~v~~v~Vs~d 44 (95)
T PF13905_consen 28 KKYKKKDDVEFVFVSLD 44 (95)
T ss_dssp HHHTTTTTEEEEEEE-S
T ss_pred HHhCCCCCEEEEEEEeC
Confidence 3344 667777777654
No 18
>COG4822 CbiK Cobalamin biosynthesis protein CbiK, Co2+ chelatase [Coenzyme metabolism]
Probab=34.89 E-value=97 Score=24.94 Aligned_cols=66 Identities=21% Similarity=0.294 Sum_probs=40.1
Q ss_pred CCCCeEEEEEcccCCCcCCCHHHHHHHHHHHhhcccCCCCeEEEEEecCcccCcCcccHHHHHHHHHhcChhhHhc-cce
Q 032490 28 KQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQRSENFAGISALRSIYDAIPANVKEN-LQA 106 (139)
Q Consensus 28 ~~GrpVvvi~a~~~p~~~~d~e~ll~y~~~~~ld~~~~~~y~lVy~~tg~~~~~n~p~~~wl~~~y~~l~~~~kkn-Lk~ 106 (139)
+-|||++++. -|.+.++.-+.+ .+++..+..-++..+|+.. . ++ ..+|..||.-++++ -..
T Consensus 108 kig~PlLy~k--------~DYe~~v~aik~-~~ppl~k~e~~vlmgHGt~-h----~s----~~~YacLd~~~~~~~f~~ 169 (265)
T COG4822 108 KIGRPLLYYK--------NDYEICVEAIKD-QIPPLNKDEILVLMGHGTD-H----HS----NAAYACLDHVLDEYGFDN 169 (265)
T ss_pred ecCCceeech--------hhHHHHHHHHHH-hcCCcCcCeEEEEEecCCC-c----cH----HHHHHHHHHHHHhcCCCc
Confidence 5689998875 478888877765 3555555555544455433 2 22 26777777777666 235
Q ss_pred EEEEc
Q 032490 107 VYFVH 111 (139)
Q Consensus 107 lyiVH 111 (139)
++|+.
T Consensus 170 v~v~~ 174 (265)
T COG4822 170 VFVAA 174 (265)
T ss_pred eEEEE
Confidence 55544
No 19
>PF11385 DUF3189: Protein of unknown function (DUF3189); InterPro: IPR021525 This family of proteins with unknown function appears to be restricted to Firmicutes
Probab=34.31 E-value=1.1e+02 Score=22.54 Aligned_cols=26 Identities=15% Similarity=0.121 Sum_probs=20.4
Q ss_pred hcCcEEEeccCCCCCeEEEEEcccCC
Q 032490 17 RLEIFKIHGRDKQGRKILRIIGKFFP 42 (139)
Q Consensus 17 ~~~ily~~G~D~~GrpVvvi~a~~~p 42 (139)
+.|-++..|.|..|++|.++-.+..+
T Consensus 48 d~G~l~y~G~De~gn~VY~lG~~~~~ 73 (148)
T PF11385_consen 48 DIGRLIYMGTDEYGNEVYILGRKNNG 73 (148)
T ss_pred cCceEEEEEEcCCCCEEEEEecCChH
Confidence 44656667999999999988877664
No 20
>PF06933 SSP160: Special lobe-specific silk protein SSP160; InterPro: IPR009701 This family consists of several special lobe-specific silk protein SSP160 sequences which appear to be specific to Chironomus (Midge) species.
Probab=33.00 E-value=23 Score=30.99 Aligned_cols=17 Identities=18% Similarity=0.278 Sum_probs=13.2
Q ss_pred HhcChhhHhccceEEEE
Q 032490 94 DAIPANVKENLQAVYFV 110 (139)
Q Consensus 94 ~~l~~~~kknLk~lyiV 110 (139)
..=-|+||||+|.+||-
T Consensus 426 ksgvrryrknik~vyip 442 (756)
T PF06933_consen 426 KSGVRRYRKNIKYVYIP 442 (756)
T ss_pred HHhHHHHhcCCcEEEeC
Confidence 33457899999999883
No 21
>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=30.62 E-value=64 Score=20.17 Aligned_cols=32 Identities=16% Similarity=0.167 Sum_probs=25.4
Q ss_pred hhhHHHHHhcCcEEEeccCCCCCeEEEEEccc
Q 032490 9 SEQEELIDRLEIFKIHGRDKQGRKILRIIGKF 40 (139)
Q Consensus 9 ~e~~~~i~~~~ily~~G~D~~GrpVvvi~a~~ 40 (139)
.|...-|++.+++..+-.|.+|+|.+..+.-.
T Consensus 3 ~~~~~~l~~~~~~~laTv~~dG~P~~~~v~~~ 34 (89)
T PF01243_consen 3 EEIREFLEESKYCVLATVDEDGRPHASPVWFV 34 (89)
T ss_dssp HHHHHHHHSTSEEEEEEEETTSEEEEEEEEEE
T ss_pred HHHHHHhcCCCEEEEEEECCCCCEEEEEEeee
Confidence 34556688889999999999999988877743
No 22
>PF04666 Glyco_transf_54: N-Acetylglucosaminyltransferase-IV (GnT-IV) conserved region; InterPro: IPR006759 The complex-type of oligosaccharides are synthesised through elongation by glycosyltransferases after trimming of the precursor oligosaccharides transferred to proteins in the endoplasmic reticulum. N-Acetylglucosaminyltransferases (GnTs) take part in the formation of branches in the biosynthesis of complex-type sugar chains. In vertebrates, six GnTs, designated as GnT-I to -VI, which catalyse the transfer of GlcNAc to the core mannose residues of Asn-linked sugar chains, have been identified. GnT-IV (2.4.1.145 from EC) catalyzes the transfer of GlcNAc from UDP-GlcNAc to the GlcNAc1-2Man1-3 arm of core oligosaccharide [Gn2(22)core oligosaccharide] and forms a GlcNAc1-4(GlcNAc1-2)Man1-3 structure on the core oligosaccharide (Gn3(2,4,2)core oligosaccharide). In some members the conserved region occupies all but the very N-terminal, where there is a signal sequence on all members. For other members the conserved region does not occupy the entire protein but is still to the N-terminal end of the protein [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0005975 carbohydrate metabolic process, 0016020 membrane
Probab=30.54 E-value=3.1e+02 Score=22.55 Aligned_cols=83 Identities=11% Similarity=0.125 Sum_probs=44.9
Q ss_pred EEEeccCCCCCeEEEEEcccCCCcCCCHHHHHHHHHHHhhcccC---CCCeEEEEEecCcccCcCcccHHHHHHHHHhcC
Q 032490 21 FKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLG---KKAFTVLYVHTGVQRSENFAGISALRSIYDAIP 97 (139)
Q Consensus 21 ly~~G~D~~GrpVvvi~a~~~p~~~~d~e~ll~y~~~~~ld~~~---~~~y~lVy~~tg~~~~~n~p~~~wl~~~y~~l~ 97 (139)
-+..|..+.|.+++|=++.--..+.--+..-+.= +++.+. .++-+||++-... +..|..++.+.+.
T Consensus 42 ~~~~g~~~~~~~L~IGIpTV~R~~~sYL~~TL~S----Ll~~ls~~Er~~i~IvVllAd~-------Dp~~~~~~~~~i~ 110 (297)
T PF04666_consen 42 ALLAGKPRTGKKLCIGIPTVKREKESYLLDTLAS----LLDGLSPEERKDIVIVVLLADT-------DPDYHPSVAQNIS 110 (297)
T ss_pred ceEcCCCCCCCeEEEEecccccCCCchHHHHHHH----HHHhCCHHHhcCeEEEEEecCC-------ChhhhHHHHHHHH
Confidence 3456899999886665554222222122233332 344443 3355666665544 2346666666666
Q ss_pred hhhHhccc--eEEEEcCCh
Q 032490 98 ANVKENLQ--AVYFVHPGL 114 (139)
Q Consensus 98 ~~~kknLk--~lyiVHPt~ 114 (139)
.++..-+. -+-||||..
T Consensus 111 ~~f~~~i~sG~l~VI~~p~ 129 (297)
T PF04666_consen 111 TRFADHIESGLLEVISPPP 129 (297)
T ss_pred HHhHHHHHhCceEEEeccc
Confidence 66666664 356777653
No 23
>KOG2283 consensus Clathrin coat dissociation kinase GAK/PTEN/Auxilin and related tyrosine phosphatases [Signal transduction mechanisms; General function prediction only]
Probab=29.43 E-value=2.2e+02 Score=24.85 Aligned_cols=71 Identities=21% Similarity=0.295 Sum_probs=52.9
Q ss_pred EEcccCCCcCC------CHHHHHHHHHHHhhcccCCCCeEEEEEe----------------cCcccCcCcccHHHHHHHH
Q 032490 36 IIGKFFPARLL------SVEVLKRYLSERVYPRLGKKAFTVLYVH----------------TGVQRSENFAGISALRSIY 93 (139)
Q Consensus 36 i~a~~~p~~~~------d~e~ll~y~~~~~ld~~~~~~y~lVy~~----------------tg~~~~~n~p~~~wl~~~y 93 (139)
|+|.-+|+..+ +++.+.+|+-. +.. +.|.+--+. -|+ ...|.|++..|..+=
T Consensus 22 IIamsfPa~~~es~yRN~l~dV~~fL~s----~H~-~~y~vyNL~~er~yd~~~f~g~V~~~~~-~Dh~~P~L~~l~~~c 95 (434)
T KOG2283|consen 22 IIAMSFPAEGIESLYRNNLEDVVLFLDS----KHK-DHYKVYNLSSERLYDPSRFHGRVARFGF-DDHNPPPLELLCPFC 95 (434)
T ss_pred EEEEeCCCCcchhhhcCCHHHHHHHHhh----ccC-CceEEEecCccccCCccccccceeecCC-CCCCCCcHHHHHHHH
Confidence 67777888532 47887777643 233 555544444 356 578999999999999
Q ss_pred HhcChhhHhccceEEEEcC
Q 032490 94 DAIPANVKENLQAVYFVHP 112 (139)
Q Consensus 94 ~~l~~~~kknLk~lyiVHP 112 (139)
+.++.-.....+.+.+||.
T Consensus 96 ~~~~~WL~~d~~nVvvvHC 114 (434)
T KOG2283|consen 96 KSMDNWLSEDPKNVVVVHC 114 (434)
T ss_pred HCHHHHHhcCccceEEEEc
Confidence 9999999999999999996
No 24
>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=28.36 E-value=75 Score=26.29 Aligned_cols=47 Identities=13% Similarity=0.316 Sum_probs=28.0
Q ss_pred CCCCeEEEEEecCcccCcCcccHHHHHHHHHhcChhhHhccceEEEEcCC
Q 032490 64 GKKAFTVLYVHTGVQRSENFAGISALRSIYDAIPANVKENLQAVYFVHPG 113 (139)
Q Consensus 64 ~~~~y~lVy~~tg~~~~~n~p~~~wl~~~y~~l~~~~kknLk~lyiVHPt 113 (139)
..++|+++.+|.-. +..+.....-+.++...|... +++.-++.+|++
T Consensus 178 ~~~~~iLvt~H~~t-~~~~~~~~~~i~~~l~~L~~~--~~~~vi~~~hn~ 224 (346)
T PF02350_consen 178 APKPYILVTLHPVT-NEDNPERLEQILEALKALAER--QNVPVIFPLHNN 224 (346)
T ss_dssp TTSEEEEEE-S-CC-CCTHH--HHHHHHHHHHHHHH--TTEEEEEE--S-
T ss_pred cCCCEEEEEeCcch-hcCChHHHHHHHHHHHHHHhc--CCCcEEEEecCC
Confidence 77899999999877 433233355555555555555 699999999933
No 25
>PF00025 Arf: ADP-ribosylation factor family The prints entry specific to Sar1 proteins The Prosite entry specific to Sar1 proteins; InterPro: IPR006689 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. This entry represents a branch of the small GTPase superfamily that includes the ADP ribosylation factor Arf, Arl (Arf-like), Arp (Arf-related proteins) and the remotely related Sar (Secretion-associated and Ras-related) proteins. Arf proteins are major regulators of vesicle biogenesis in intracellular traffic []. They cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other. The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2-beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N terminus. In GDP-bound Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.; GO: 0005525 GTP binding; PDB: 2H57_B 2W83_B 3N5C_B 2J5X_A 3LVR_E 2BAO_A 3LVQ_E 2A5F_A 3PCR_B 1E0S_A ....
Probab=28.00 E-value=2.4e+02 Score=20.44 Aligned_cols=59 Identities=22% Similarity=0.235 Sum_probs=37.1
Q ss_pred CCCeEEEEEcccCCCcCCCHHHHHHHHHHHhhcccC-CCCeEEEEEecCcccCcCcccHHHHHH
Q 032490 29 QGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLG-KKAFTVLYVHTGVQRSENFAGISALRS 91 (139)
Q Consensus 29 ~GrpVvvi~a~~~p~~~~d~e~ll~y~~~~~ld~~~-~~~y~lVy~~tg~~~~~n~p~~~wl~~ 91 (139)
.+-|++++..+.=..+.++.+.+..++. ++.+. ..++.++-+.... ...-...+.||.+
T Consensus 114 ~~~piLIl~NK~D~~~~~~~~~i~~~l~---l~~l~~~~~~~v~~~sa~~-g~Gv~e~l~WL~~ 173 (175)
T PF00025_consen 114 KDIPILILANKQDLPDAMSEEEIKEYLG---LEKLKNKRPWSVFSCSAKT-GEGVDEGLEWLIE 173 (175)
T ss_dssp TTSEEEEEEESTTSTTSSTHHHHHHHTT---GGGTTSSSCEEEEEEBTTT-TBTHHHHHHHHHH
T ss_pred ccceEEEEeccccccCcchhhHHHhhhh---hhhcccCCceEEEeeeccC-CcCHHHHHHHHHh
Confidence 4779888777633334467777665542 45565 6777777666655 4455566888865
No 26
>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=27.94 E-value=67 Score=23.91 Aligned_cols=33 Identities=21% Similarity=0.199 Sum_probs=23.1
Q ss_pred hhhHHHHHhcCcEEEeccC-CCCCeEEEEEcccC
Q 032490 9 SEQEELIDRLEIFKIHGRD-KQGRKILRIIGKFF 41 (139)
Q Consensus 9 ~e~~~~i~~~~ily~~G~D-~~GrpVvvi~a~~~ 41 (139)
....+.+-+.|++...|.. .-|||+.+-.+..|
T Consensus 111 ~~~i~~L~e~glI~~~gr~~~~Grp~ly~tT~~F 144 (159)
T PF04079_consen 111 DSVIKTLLERGLIEEVGRKDTPGRPILYGTTDKF 144 (159)
T ss_dssp HCHHHHHHHTTSEEEEEE-TTTT--EEEEE-HHH
T ss_pred HHHHHHHHHCCCEEecCcCCCCCCCeEeehhHHH
Confidence 4556778899999999855 46999999888655
No 27
>PF10340 DUF2424: Protein of unknown function (DUF2424); InterPro: IPR019436 Sterol homeostasis in eukaryotic cells relies on the reciprocal interconversion of free sterols and steryl esters. In Saccharomyces cerevisiae (Baker's yeast) sterol acetylation requires the acetyltransferase Atf2, whereas deacetylation requires Say1, a membrane-anchored deacetylase with a putative active site in the ER lumen. Lack of Say1 results in the secretion of acetylated sterols into the culture medium, indicating that the substrate specificity of Say1 determines whether acetylated sterols are secreted from the cells or whether they are deacetylated and retained. In S. cerevisiae cells lacking Say1 or Atf2 are sensitive against the plant-derived allylbenzene eugenol and both Say1 and Atf2 affect pregnenolone toxicity, indicating that lipid acetylation acts as a detoxification pathway []. Homologues of Say1 are present in the mammalian genome and can functionally substitute for Say1 in yeast demonstrating that part of this pathway has been evolutionarily conserved [].
Probab=27.04 E-value=1e+02 Score=26.27 Aligned_cols=39 Identities=21% Similarity=0.358 Sum_probs=26.6
Q ss_pred CCeEEEEEecCcccC-cCc-ccHHHHHHHHHhcChhhHhccceEEEEc
Q 032490 66 KAFTVLYVHTGVQRS-ENF-AGISALRSIYDAIPANVKENLQAVYFVH 111 (139)
Q Consensus 66 ~~y~lVy~~tg~~~~-~n~-p~~~wl~~~y~~l~~~~kknLk~lyiVH 111 (139)
.+-+|||+|+|. .. ... ..+.+|..+|+.|+.. ++.++.
T Consensus 121 ~DpVlIYlHGGG-Y~l~~~p~qi~~L~~i~~~l~~~------SILvLD 161 (374)
T PF10340_consen 121 SDPVLIYLHGGG-YFLGTTPSQIEFLLNIYKLLPEV------SILVLD 161 (374)
T ss_pred CCcEEEEEcCCe-eEecCCHHHHHHHHHHHHHcCCC------eEEEEe
Confidence 478999999974 21 122 2378888999998833 676665
No 28
>KOG2633 consensus Hismacro and SEC14 domain-containing proteins [Chromatin structure and dynamics; Transcription]
Probab=25.96 E-value=1.1 Score=34.93 Aligned_cols=37 Identities=32% Similarity=0.346 Sum_probs=30.6
Q ss_pred hhhHHHHHhcCcEEEeccCCCCCeEEEEEcccCCCcC
Q 032490 9 SEQEELIDRLEIFKIHGRDKQGRKILRIIGKFFPARL 45 (139)
Q Consensus 9 ~e~~~~i~~~~ily~~G~D~~GrpVvvi~a~~~p~~~ 45 (139)
.|+++++.....+-..+.++.|.-+.-..+..+|.+.
T Consensus 13 ~~~~~~~~~l~~f~~~~~~~~~i~lwr~d~~~l~v~a 49 (200)
T KOG2633|consen 13 AEIFSNITSLEVFKIDKPDNGGISLWRGDGKTLEVDA 49 (200)
T ss_pred hhhhccccccchhhccCccccCeeEeeccccccccee
Confidence 4567778888888888999999999999999998854
No 29
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=23.96 E-value=74 Score=24.37 Aligned_cols=33 Identities=18% Similarity=0.171 Sum_probs=26.5
Q ss_pred hhhHHHHHhcCcEEEecc-CCCCCeEEEEEcccC
Q 032490 9 SEQEELIDRLEIFKIHGR-DKQGRKILRIIGKFF 41 (139)
Q Consensus 9 ~e~~~~i~~~~ily~~G~-D~~GrpVvvi~a~~~ 41 (139)
....+.+-+.|++...|+ |..|||+.+-.+..|
T Consensus 116 ~~~l~~L~ergLI~~~Gr~~~~Grp~ly~TT~~F 149 (186)
T TIGR00281 116 YQIVDDLVEKGLVVELGRKDTPGRSFIYETTPKF 149 (186)
T ss_pred HHHHHHHHHCCCeEecCcCCCCCCCeeehhhHHH
Confidence 456778889999998885 567999999888644
No 30
>PHA02894 hypothetical protein; Provisional
Probab=21.62 E-value=52 Score=22.52 Aligned_cols=16 Identities=19% Similarity=0.461 Sum_probs=14.0
Q ss_pred hHhccceEEEEcCChH
Q 032490 100 VKENLQAVYFVHPGLQ 115 (139)
Q Consensus 100 ~kknLk~lyiVHPt~~ 115 (139)
|-|..+++++|+|+.-
T Consensus 58 yf~s~ksVlLVNPs~~ 73 (97)
T PHA02894 58 YFKKFKNIYIVNPRNH 73 (97)
T ss_pred eeecCceEEEECCcHH
Confidence 6788999999999973
No 31
>PF05846 Chordopox_A15: Chordopoxvirus A15 protein; InterPro: IPR008445 This family consists of several Chordopoxvirus A15 like sequences.
Probab=21.27 E-value=59 Score=22.26 Aligned_cols=17 Identities=12% Similarity=0.554 Sum_probs=14.0
Q ss_pred hhHhccceEEEEcCChH
Q 032490 99 NVKENLQAVYFVHPGLQ 115 (139)
Q Consensus 99 ~~kknLk~lyiVHPt~~ 115 (139)
+..+..+++++|+|+.-
T Consensus 41 ~i~~~~ksilLVNPs~~ 57 (90)
T PF05846_consen 41 KIDKDFKSILLVNPSYI 57 (90)
T ss_pred ccccccceEEEECCCHH
Confidence 34579999999999974
No 32
>TIGR01001 metA homoserine O-succinyltransferase. The apparent equivalog from Bacillus subtilis is broken into two tandem reading frames.
Probab=20.20 E-value=5.1e+02 Score=21.53 Aligned_cols=91 Identities=13% Similarity=0.226 Sum_probs=59.2
Q ss_pred HHHHHhcCcEEEeccCC----CCCeEEEEEcccCCCcCCCHHHHHHHHHHHhhcccCCCCeEEEEEecCcccCcCcccHH
Q 032490 12 EELIDRLEIFKIHGRDK----QGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQRSENFAGIS 87 (139)
Q Consensus 12 ~~~i~~~~ily~~G~D~----~GrpVvvi~a~~~p~~~~d~e~ll~y~~~~~ld~~~~~~y~lVy~~tg~~~~~n~p~~~ 87 (139)
..-+++.||+-+. .++ +-||+=+.+-.-+|.+ ++-|.-+.- +|.. ..-+-.+.++.... ......+..
T Consensus 12 ~~~L~~enifvm~-~~ra~~qdirpL~I~ILNLMP~K-~~TE~Q~lR----lL~n-tplqv~i~~~~~~s-h~~k~t~~~ 83 (300)
T TIGR01001 12 VKVLRKENIFVMT-ESRASHQDIRPLEILILNLMPKK-IETENQFLR----LLSN-SPLQVNITLLRTDS-RKSKNTPIE 83 (300)
T ss_pred HHHHHhCCceeec-hhhhccccccceeEEEEecCCcc-HHHHHHHHH----HhcC-CCCceEEEEEEecc-ccCCCCCHH
Confidence 4568888999663 333 4579999999999987 555543322 2322 12223344444443 223444788
Q ss_pred HHHHHHHhcChhhHhccceEEEE
Q 032490 88 ALRSIYDAIPANVKENLQAVYFV 110 (139)
Q Consensus 88 wl~~~y~~l~~~~kknLk~lyiV 110 (139)
.|.+.|+.++.--.++..+++|-
T Consensus 84 hl~~fY~~f~~ik~~~fDGlIIT 106 (300)
T TIGR01001 84 HLNKFYTTFEAVKDRKFDGLIIT 106 (300)
T ss_pred HHHHHhhCHHHHhcCCCCEEEEc
Confidence 99999999999878999998874
Done!