Query 030987
Match_columns 168
No_of_seqs 116 out of 267
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 07:33:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030987.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030987hhsearch_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 6.3E-32 1.4E-36 238.4 8.9 137 7-151 66-207 (467)
2 PF13716 CRAL_TRIO_2: Divergen 99.9 7.3E-28 1.6E-32 184.4 9.4 121 19-141 2-124 (149)
3 smart00516 SEC14 Domain in hom 99.8 1.5E-18 3.2E-23 131.9 9.5 113 25-140 14-134 (158)
4 cd00170 SEC14 Sec14p-like lipi 99.7 1.8E-17 3.9E-22 123.5 8.5 120 19-140 9-136 (157)
5 KOG1470 Phosphatidylinositol t 99.5 3.8E-14 8.3E-19 123.1 9.4 129 6-138 86-220 (324)
6 PF00650 CRAL_TRIO: CRAL/TRIO 99.5 5E-14 1.1E-18 107.1 5.2 126 14-140 2-136 (159)
7 KOG1471 Phosphatidylinositol t 98.7 4E-08 8.8E-13 83.6 8.6 124 12-136 88-230 (317)
8 PF03721 UDPG_MGDP_dh_N: UDP-g 81.8 0.48 1E-05 38.0 0.2 113 15-131 19-139 (185)
9 PF10928 DUF2810: Protein of u 69.6 2.6 5.7E-05 27.7 1.1 18 97-114 19-36 (54)
10 KOG1826 Ras GTPase activating 68.3 2.6 5.7E-05 45.1 1.4 119 6-127 1549-1668(2724)
11 PF07872 DUF1659: Protein of u 63.8 3.9 8.4E-05 25.9 1.1 28 17-44 7-35 (47)
12 PF13986 DUF4224: Domain of un 57.1 18 0.00038 23.0 3.3 26 8-35 17-42 (47)
13 PRK11020 hypothetical protein; 55.1 7 0.00015 29.7 1.3 32 82-113 67-98 (118)
14 KOG2925 Predicted translation 39.3 33 0.00071 27.5 2.9 44 95-153 50-98 (167)
15 PF11385 DUF3189: Protein of u 39.3 60 0.0013 25.4 4.4 50 17-71 48-97 (148)
16 COG0381 WecB UDP-N-acetylgluco 38.6 48 0.001 30.1 4.2 73 64-145 202-274 (383)
17 PF09949 DUF2183: Uncharacteri 38.2 43 0.00092 24.5 3.2 48 52-110 51-98 (100)
18 PF04666 Glyco_transf_54: N-Ac 37.8 2.1E+02 0.0046 24.9 8.0 84 20-114 41-129 (297)
19 KOG2633 Hismacro and SEC14 dom 32.4 0.81 1.8E-05 37.9 -7.4 38 9-46 13-50 (200)
20 PF04079 DUF387: Putative tran 30.8 58 0.0013 25.7 3.1 35 7-41 109-144 (159)
21 PF00025 Arf: ADP-ribosylation 30.3 1.9E+02 0.0042 22.1 6.0 58 29-91 114-173 (175)
22 PF13905 Thioredoxin_8: Thiore 29.8 59 0.0013 21.9 2.7 11 65-75 33-43 (95)
23 TIGR00281 segregation and cond 27.7 56 0.0012 26.5 2.6 35 7-41 114-149 (186)
24 PF01243 Pyridox_oxidase: Pyri 26.8 75 0.0016 20.9 2.8 32 9-40 3-34 (89)
25 PF02350 Epimerase_2: UDP-N-ac 24.2 93 0.002 27.2 3.5 71 64-143 178-249 (346)
26 PF10954 DUF2755: Protein of u 23.2 59 0.0013 23.9 1.7 31 121-160 5-35 (100)
27 PRK03298 hypothetical protein; 22.9 1.5E+02 0.0033 25.0 4.4 37 18-56 134-170 (224)
28 TIGR01001 metA homoserine O-su 22.9 5.3E+02 0.011 22.7 8.6 91 12-110 12-106 (300)
29 PF06933 SSP160: Special lobe- 20.9 69 0.0015 29.9 2.1 34 91-124 423-456 (756)
No 1
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=99.97 E-value=6.3e-32 Score=238.38 Aligned_cols=137 Identities=27% Similarity=0.413 Sum_probs=128.7
Q ss_pred ChhhhHhHHHhc--CCEEEecc--CCCCCeEEEEEeecCCC-CCCCHHHHHHHHHHhhcCcCCCCCeEEEEEcCCccccc
Q 030987 7 SESEQEELIDRL--EIFKIHGR--DKQGRKILRIIGKFFPA-RLLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQRSE 81 (168)
Q Consensus 7 s~~e~~~di~~~--~ily~~G~--D~~GrPVvV~~a~~lP~-~~~d~e~ll~Yvv~~~Ld~~~~~~yvlVy~htg~~~~~ 81 (168)
+.+++|.|+.+| +++...|. |++||+|+|+.+|++|+ +++|.-+++.|.+ +++|++++++|++||||.|+ .+.
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 PKEDPFYDIARHEREILQVIGDAKDKQGRKIIVVYACRLPSSSELDDIRLISYLV-YTIDKYVENDYTLVYFHHGL-PSD 143 (467)
T ss_pred cccccHHHHHHhhhheeeeccCcccccCCeeEEEEEecCCchhhhhhHHHHHHHH-HHHHHHHhccceeeehhcCC-ccc
Confidence 678899999999 99988877 99999999999999999 6788889999999 66999999999999999999 799
Q ss_pred CcccHHHHHHHHHhcChhhhhccceEEEEcCChHHHHHHHHhchhhcccccccceecCceeeeeeehhhH
Q 030987 82 NFAGISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGYVSLLPFFNFYYCFNLLY 151 (168)
Q Consensus 82 n~P~~~wL~~~y~~L~~~ykKNLkalYIVHPt~~~K~~l~~~~pFissk~~~kv~~l~~~~~~~~~~~~~ 151 (168)
|+|.++|+.++|..+||+++||+||+|+|||||++|++|.+++||||.||.+|++ |+.|+.+|.
T Consensus 144 nkp~l~~l~~aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~------Y~n~lseL~ 207 (467)
T KOG4406|consen 144 NKPYLQLLFDAYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKII------YFNSLSELF 207 (467)
T ss_pred ccchHHHHHHHHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeE------EeehHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999 777777764
No 2
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.95 E-value=7.3e-28 Score=184.42 Aligned_cols=121 Identities=26% Similarity=0.406 Sum_probs=93.7
Q ss_pred CCEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHHhhcCcCCCCCeEEEEEcCCcccccCcccHHHHHHHHHhcCh
Q 030987 19 EIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQRSENFAGISALRSIYDAIPA 98 (168)
Q Consensus 19 ~ily~~G~D~~GrPVvV~~a~~lP~~~~d~e~ll~Yvv~~~Ld~~~~~~yvlVy~htg~~~~~n~P~~~wL~~~y~~L~~ 98 (168)
.+++.+|+|++||||+++.++++| +..|+|+++.|+++++.+.+.+++|++|+++++. +..|.|+++|++++|+.+|+
T Consensus 2 ~~~~~gG~d~~g~pV~~~~~~~~~-~~~~~~~ll~yl~~~l~~~~~~~~f~vVid~~~~-~~~~~~~~~~l~~~~~~l~~ 79 (149)
T PF13716_consen 2 IFFYPGGRDREGRPVVVFIASRLP-SSDDLERLLLYLLSTLSEEVVDKPFSVVIDHTGF-SRSSEPSLSWLKQLYKLLPR 79 (149)
T ss_dssp SE-EEEEEBTTS-EEEEEEGGG-C--TTHHHHHHHHHHHHH-TTTTTS-EEEEEE-TT---GGG---HHHHHHTTTSS-H
T ss_pred eEEEecccCCCcCEEEEEECCcCc-chhhHHHHHHHHHHhhhHHhcCCCEEEEEEcCCC-ccccCCchHHHHHHHHHHHH
Confidence 466889999999999999999994 4459999999999653388899999999999999 67899999999999999999
Q ss_pred hhhhccceEEEEcCChHHHHHH-HHhchhhcccc-cccceecCce
Q 030987 99 NVKENLQAVYFVHPGLQARLFL-ATFGRLFFNGV-GGYVSLLPFF 141 (168)
Q Consensus 99 ~ykKNLkalYIVHPt~~~K~~l-~~~~pFissk~-~~kv~~l~~~ 141 (168)
++++||+++|+|||++++|.++ .+.+++.++++ .+||+.++.+
T Consensus 80 ~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~sl 124 (149)
T PF13716_consen 80 KYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSSL 124 (149)
T ss_dssp HHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESST
T ss_pred HHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECCH
Confidence 9999999999999999999999 66677789999 8997755544
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=99.77 E-value=1.5e-18 Score=131.94 Aligned_cols=113 Identities=25% Similarity=0.391 Sum_probs=99.8
Q ss_pred ccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHHhhcCcC--------CCCCeEEEEEcCCcccccCcccHHHHHHHHHhc
Q 030987 25 GRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRL--------GKKAFTVLYVHTGVQRSENFAGISALRSIYDAI 96 (168)
Q Consensus 25 G~D~~GrPVvV~~a~~lP~~~~d~e~ll~Yvv~~~Ld~~--------~~~~yvlVy~htg~~~~~n~P~~~wL~~~y~~L 96 (168)
|.|++||||+++.+++++.+..+.+++++|++ .++|.. ..+.+++|++.++. +..+ ++.+|++++++.+
T Consensus 14 g~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~-~~~e~~~~~~~~~~~~~~~~~i~D~~~~-~~~~-~~~~~lk~~~~~~ 90 (158)
T smart00516 14 GYDKDGRPVLIFRAGRFDLKSVTLEELLRYLV-YVLEKILQREKKTGGIEGFTVIFDLKGL-SMSN-PDLSVLRKILKIL 90 (158)
T ss_pred CCCCCcCEEEEEeccccccCcCCHHHHHHHHH-HHHHHHHHHHhcCCCeeeEEEEEECCCC-Cccc-ccHHHHHHHHHHH
Confidence 79999999999999999887789999999888 445533 23578999999998 4444 7899999999999
Q ss_pred ChhhhhccceEEEEcCChHHHHHHHHhchhhcccccccceecCc
Q 030987 97 PANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGYVSLLPF 140 (168)
Q Consensus 97 ~~~ykKNLkalYIVHPt~~~K~~l~~~~pFissk~~~kv~~l~~ 140 (168)
+..|++||+++|||||++++++++++++||+++++.+||+.+..
T Consensus 91 ~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~ 134 (158)
T smart00516 91 QDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGN 134 (158)
T ss_pred HHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCC
Confidence 99999999999999999999999999999999999999996654
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=99.72 E-value=1.8e-17 Score=123.54 Aligned_cols=120 Identities=24% Similarity=0.321 Sum_probs=98.6
Q ss_pred CCEEEeccCCCCCeEEEEEeec-CCCCCCCHHHHHHHHHHhhcCcCCC------CCeEEEEEcCCcccccCcc-cHHHHH
Q 030987 19 EIFKIHGRDKQGRKILRIIGKF-FPARLLSVEVLKRYLSERVYPRLGK------KAFTVLYVHTGVQRSENFA-GISALR 90 (168)
Q Consensus 19 ~ily~~G~D~~GrPVvV~~a~~-lP~~~~d~e~ll~Yvv~~~Ld~~~~------~~yvlVy~htg~~~~~n~P-~~~wL~ 90 (168)
++.+.+|.|++||||+++..+. -+.+..+.++++++.+ .++|.... +.+++|++.+|. +..+.. +.++++
T Consensus 9 ~~~~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~-~~~e~~~~~~~~~~~~~~~i~D~~~~-~~~~~~~~~~~~k 86 (157)
T cd00170 9 KVGYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLV-YTLEKLLQEDDEQVEGFVVIIDLKGL-SLSHLLPDPSLLK 86 (157)
T ss_pred cccccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHH-HHHHHHHhhhhhcccceEEEEECCCC-ChhccchhHHHHH
Confidence 5665566799999999999984 3334456688888877 34554322 479999999998 455553 778999
Q ss_pred HHHHhcChhhhhccceEEEEcCChHHHHHHHHhchhhcccccccceecCc
Q 030987 91 SIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGYVSLLPF 140 (168)
Q Consensus 91 ~~y~~L~~~ykKNLkalYIVHPt~~~K~~l~~~~pFissk~~~kv~~l~~ 140 (168)
++++.++..|++||+++|+|||++++++++++++||+++++.+||+.+..
T Consensus 87 ~~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~ 136 (157)
T cd00170 87 KILKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGS 136 (157)
T ss_pred HHHHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecC
Confidence 99999999999999999999999999999999999999999999996554
No 5
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=99.53 E-value=3.8e-14 Score=123.10 Aligned_cols=129 Identities=19% Similarity=0.240 Sum_probs=103.1
Q ss_pred CChhhhHhHHHhcCCEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHHhhcCc------CCCCCeEEEEEcCCccc
Q 030987 6 VSESEQEELIDRLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPR------LGKKAFTVLYVHTGVQR 79 (168)
Q Consensus 6 is~~e~~~di~~~~ily~~G~D~~GrPVvV~~a~~lP~~~~d~e~ll~Yvv~~~Ld~------~~~~~yvlVy~htg~~~ 79 (168)
+...|.-.+++ .|-.|.+|.|+.||||+++.++.-+.+..+.+.+.++++ .+|+. -+++.++++++.+|. +
T Consensus 86 ~~~~Ev~~e~~-tGK~yi~G~D~~gRPVl~~~~~~~~qn~~t~~~~~r~~V-y~mE~Ai~~lp~~qe~~~~L~D~~~f-s 162 (324)
T KOG1470|consen 86 IEADEVAAELE-TGKAYILGHDKDGRPVLYLRPRPHRQNTKTQKELERLLV-YTLENAILFLPPGQEQFVWLFDLTGF-S 162 (324)
T ss_pred cCHHHHHHHhh-cCcEEEecccCCCCeEEEEecCCCCCCCCCHHHHHHHHH-HHHHHHHHhCCCCcceEEEEEecccC-c
Confidence 44445444444 466668899999999999999855445456555555554 34442 367889999999999 5
Q ss_pred ccCcccHHHHHHHHHhcChhhhhccceEEEEcCChHHHHHHHHhchhhcccccccceec
Q 030987 80 SENFAGISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGYVSLL 138 (168)
Q Consensus 80 ~~n~P~~~wL~~~y~~L~~~ykKNLkalYIVHPt~~~K~~l~~~~pFissk~~~kv~~l 138 (168)
.+| |+++.++.+...|+..|+++|...+++||+|.+..+|.+.+||+.++...||...
T Consensus 163 ~sN-~d~~~~k~~~~~lq~hYPErLg~a~l~~~P~iF~~~wkiikpflDp~t~~Kv~F~ 220 (324)
T KOG1470|consen 163 MSN-PDIKFLKELLHILQDHYPERLGKALLVNAPWIFQPFWKIIKPFLDPKTASKVKFV 220 (324)
T ss_pred ccC-CCcHHHHHHHHHHHHhChHHhhhhhhcCChHHHHHHHHHhhhccChhhhceeEEe
Confidence 555 6899999999999999999999999999999999999999999999999999833
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=99.47 E-value=5e-14 Score=107.10 Aligned_cols=126 Identities=23% Similarity=0.289 Sum_probs=91.5
Q ss_pred HHHhcCCEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHH---HhhcCc----CCCCCeEEEEEcCCcccccCccc-
Q 030987 14 LIDRLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLS---ERVYPR----LGKKAFTVLYVHTGVQRSENFAG- 85 (168)
Q Consensus 14 di~~~~ily~~G~D~~GrPVvV~~a~~lP~~~~d~e~ll~Yvv---~~~Ld~----~~~~~yvlVy~htg~~~~~n~P~- 85 (168)
++.+.+..+..|.|++||||+++-.+++..+....+.+.++++ ...+.. -..+..++|++.+|. +..+.+.
T Consensus 2 ~~~~~~~~~~~g~D~~gr~v~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~~~~iiD~~g~-~~~~~~~~ 80 (159)
T PF00650_consen 2 EILKSGPFYLHGRDKDGRPVIYIRLGRFDPKKFSPEDVIRFFVYLLERMLKRMPEGGQVEGIVVIIDLSGF-SLSNFDWW 80 (159)
T ss_dssp HHHTTSCEEEEEE-TTS-EEEEEEGTT--HHTS-HHHHHHHHHHHHHHHHHTHHHTSHHH-EEEEEE-TT---HHHHHCH
T ss_pred HHHCCeeEEECCCCCCcCEEEEEEcccCCCCcCCHHHHHHHHHHHHHHHHhhhcccccceeEEEEEeCCCc-eEeccccc
Confidence 5778899999999999999999999877554444444444444 332211 223678999999999 5555543
Q ss_pred -HHHHHHHHHhcChhhhhccceEEEEcCChHHHHHHHHhchhhcccccccceecCc
Q 030987 86 -ISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGYVSLLPF 140 (168)
Q Consensus 86 -~~wL~~~y~~L~~~ykKNLkalYIVHPt~~~K~~l~~~~pFissk~~~kv~~l~~ 140 (168)
.+-++.+.+.++..|+++++++|+++++++++++|++++||++++..+||+-+.+
T Consensus 81 ~~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~ 136 (159)
T PF00650_consen 81 PISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSG 136 (159)
T ss_dssp HHHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECT
T ss_pred hhhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECC
Confidence 7788999999999999999999999999999999999999999999999997644
No 7
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=98.75 E-value=4e-08 Score=83.64 Aligned_cols=124 Identities=12% Similarity=0.105 Sum_probs=90.9
Q ss_pred HhHHHhcCCEEEeccCCCCCeEEEEEeecCCCCC----CC-----------HHHHHHHHHHhhcCc--CCCCCeEEEEEc
Q 030987 12 EELIDRLEIFKIHGRDKQGRKILRIIGKFFPARL----LS-----------VEVLKRYLSERVYPR--LGKKAFTVLYVH 74 (168)
Q Consensus 12 ~~di~~~~ily~~G~D~~GrPVvV~~a~~lP~~~----~d-----------~e~ll~Yvv~~~Ld~--~~~~~yvlVy~h 74 (168)
..++.+..-....|.|++|+|+.+-.....-.+. .. .++.+..+.....+. -..+..+.|.+.
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 3444443434467999999999988775442211 12 233333222111111 245678999999
Q ss_pred CCcccccC--cccHHHHHHHHHhcChhhhhccceEEEEcCChHHHHHHHHhchhhcccccccce
Q 030987 75 TGVQRSEN--FAGISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGYVS 136 (168)
Q Consensus 75 tg~~~~~n--~P~~~wL~~~y~~L~~~ykKNLkalYIVHPt~~~K~~l~~~~pFissk~~~kv~ 136 (168)
.|.+ -.+ .+...-++++...++..|++++++++|||.++++.++|++++||++++..+|||
T Consensus 168 ~G~~-~~~~~~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~ 230 (317)
T KOG1471|consen 168 KGVS-LSHLLKPAPTLLKKILKILQDNYPERLKRIHIINAPTIFSALWKVVKPFLDEKTRKKIH 230 (317)
T ss_pred CCCc-chhHHHHHHHHHHHHHHHHHHhCHHhhceEEEEcCchhHHHHHHHHhccCCHHHHhhhe
Confidence 9984 343 478889999999999999999999999999999999999999999999999999
No 8
>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=81.81 E-value=0.48 Score=38.04 Aligned_cols=113 Identities=10% Similarity=0.075 Sum_probs=77.4
Q ss_pred HHhcCCEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHH--h---hc---CcCCCCCeEEEEEcCCcccccCcccH
Q 030987 15 IDRLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSE--R---VY---PRLGKKAFTVLYVHTGVQRSENFAGI 86 (168)
Q Consensus 15 i~~~~ily~~G~D~~GrPVvV~~a~~lP~~~~d~e~ll~Yvv~--~---~L---d~~~~~~yvlVy~htg~~~~~n~P~~ 86 (168)
+++.|.- +.|.|.+-+.|=-+.....|-.+..++.++.-.+. . +. +.+.+.|+++|..-|.. ..++.|++
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 4555533 56888877666566666677777778888775541 1 01 11456799999999988 67889999
Q ss_pred HHHHHHHHhcChhhhhccceEEEEcCChHHHHHHHHhchhhcccc
Q 030987 87 SALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGV 131 (168)
Q Consensus 87 ~wL~~~y~~L~~~ykKNLkalYIVHPt~~~K~~l~~~~pFissk~ 131 (168)
+++.++-+.+.+..++ .+++++-.|...-+.=..+.|.+...-
T Consensus 97 s~v~~a~~~i~~~l~~--~~lvV~~STvppGtt~~~~~~ile~~~ 139 (185)
T PF03721_consen 97 SYVESAIESIAPVLRP--GDLVVIESTVPPGTTEELLKPILEKRS 139 (185)
T ss_dssp HHHHHHHHHHHHHHCS--CEEEEESSSSSTTHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHhh--cceEEEccEEEEeeehHhhhhhhhhhc
Confidence 9999999999988777 789999998888887778888886543
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=69.61 E-value=2.6 Score=27.66 Aligned_cols=18 Identities=22% Similarity=0.423 Sum_probs=13.1
Q ss_pred ChhhhhccceEEEEcCCh
Q 030987 97 PANVKENLQAVYFVHPGL 114 (168)
Q Consensus 97 ~~~ykKNLkalYIVHPt~ 114 (168)
=-+.||..+.|.||||..
T Consensus 19 mGkLKKsVrGLvvVHPmT 36 (54)
T PF10928_consen 19 MGKLKKSVRGLVVVHPMT 36 (54)
T ss_dssp HHHHHHHTTS-EEE-SSS
T ss_pred HHHHHhhhceeEEEechH
Confidence 356899999999999953
No 10
>KOG1826 consensus Ras GTPase activating protein RasGAP/neurofibromin [Defense mechanisms]
Probab=68.30 E-value=2.6 Score=45.05 Aligned_cols=119 Identities=16% Similarity=0.040 Sum_probs=89.4
Q ss_pred CChhhhHhHHHhcCCEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHHhhcCcCCCCCeEEEEEcCCcccccCccc
Q 030987 6 VSESEQEELIDRLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQRSENFAG 85 (168)
Q Consensus 6 is~~e~~~di~~~~ily~~G~D~~GrPVvV~~a~~lP~~~~d~e~ll~Yvv~~~Ld~~~~~~yvlVy~htg~~~~~n~P~ 85 (168)
+.+.|+|--++..-+.|+.| .+.|.|+...++++.--+..+ ++++.|+...++.+.+.-++-++-+-|.. ..++.--
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-SENGLKNFYLVSRRKFLKECS-DDILIFLVELCLKPKVHFPGEVREDPTPI-EFDYSFL 1625 (2724)
T ss_pred HhhhhHHHHHHHHHHHHHhh-hhccCcchhhHhHHHHHhhcC-cHHHHHHHHHHcCccccCcceeeecCCcC-CccHHHH
Confidence 35678888898889999999 899999999999755444333 46788887677788889999999998887 3333322
Q ss_pred HHHHHH-HHHhcChhhhhccceEEEEcCChHHHHHHHHhchhh
Q 030987 86 ISALRS-IYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLF 127 (168)
Q Consensus 86 ~~wL~~-~y~~L~~~ykKNLkalYIVHPt~~~K~~l~~~~pFi 127 (168)
-+++.. ++...+.-..+|-.+++...-+-|.|....+-.+.+
T Consensus 1626 tsf~~~~~f~vr~~va~e~~~a~~di~~n~~lK~~~~l~driL 1668 (2724)
T KOG1826|consen 1626 TSFLYLKWFKVRPHVANENKHAVGDINCNSFLKETTKLHDRIL 1668 (2724)
T ss_pred HHHHhhhheeechhhhhhcccccccccchHHHHHHHHHHHHHH
Confidence 333333 555677778899999999999999999776544443
No 11
>PF07872 DUF1659: Protein of unknown function (DUF1659); InterPro: IPR012454 This family consists of hypothetical bacterial proteins of unknown function
Probab=63.84 E-value=3.9 Score=25.94 Aligned_cols=28 Identities=18% Similarity=0.266 Sum_probs=20.6
Q ss_pred hcCCEEEeccCCCCCeEEEEEe-ecCCCC
Q 030987 17 RLEIFKIHGRDKQGRKILRIIG-KFFPAR 44 (168)
Q Consensus 17 ~~~ily~~G~D~~GrPVvV~~a-~~lP~~ 44 (168)
.+.+-++.|.|..|.||+---. +++.+.
T Consensus 7 ~L~l~~~~G~d~~Gkpi~k~ks~~nvk~~ 35 (47)
T PF07872_consen 7 SLRLKYQTGVDENGKPIFKTKSFSNVKPD 35 (47)
T ss_pred EEEEEEEcccCCCCCEEEEeeehhhcCCC
Confidence 3567788899999999987666 355443
No 12
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=57.11 E-value=18 Score=22.97 Aligned_cols=26 Identities=27% Similarity=0.253 Sum_probs=19.8
Q ss_pred hhhhHhHHHhcCCEEEeccCCCCCeEEE
Q 030987 8 ESEQEELIDRLEIFKIHGRDKQGRKILR 35 (168)
Q Consensus 8 ~~e~~~di~~~~ily~~G~D~~GrPVvV 35 (168)
.+.+...+.++||-+..+. +|||+|.
T Consensus 17 ~~~Q~~~L~~~Gi~~~~~~--~G~p~V~ 42 (47)
T PF13986_consen 17 PSKQIRWLRRNGIPFVVRA--DGRPIVT 42 (47)
T ss_pred HHHHHHHHHHCCCeeEECC--CCCEEee
Confidence 3456678889999997665 4999985
No 13
>PRK11020 hypothetical protein; Provisional
Probab=55.09 E-value=7 Score=29.75 Aligned_cols=32 Identities=19% Similarity=0.208 Sum_probs=22.4
Q ss_pred CcccHHHHHHHHHhcChhhhhccceEEEEcCC
Q 030987 82 NFAGISALRSIYDAIPANVKENLQAVYFVHPG 113 (168)
Q Consensus 82 n~P~~~wL~~~y~~L~~~ykKNLkalYIVHPt 113 (168)
+.|=.+-+.+.=|.==-+.||..+.|.||||-
T Consensus 67 ~lpF~R~iTK~EQADMGkLKKSVrGLVVVHPM 98 (118)
T PRK11020 67 KLPFSRAITKKEQADMGKLKKSVRGLVVVHPM 98 (118)
T ss_pred cCCcchhccHHHHHhHHHHhhcccceeEecCc
Confidence 33444455555555556789999999999994
No 14
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=39.28 E-value=33 Score=27.49 Aligned_cols=44 Identities=16% Similarity=0.321 Sum_probs=31.8
Q ss_pred hcChhhhhcc----ceEEEEcCChHHHHHHHHhchhhcccccccceecCceeeeeeeh-hhHHH
Q 030987 95 AIPANVKENL----QAVYFVHPGLQARLFLATFGRLFFNGVGGYVSLLPFFNFYYCFN-LLYWT 153 (168)
Q Consensus 95 ~L~~~ykKNL----kalYIVHPt~~~K~~l~~~~pFissk~~~kv~~l~~~~~~~~~~-~~~~~ 153 (168)
.+|.+|||++ ..+.||-|+-..| .+.||. .++.|+-|++ +.||-
T Consensus 50 smP~KfRksiWiRRg~FvvVdpiee~~-------------~g~KVk--geI~yVl~~d~vr~lq 98 (167)
T KOG2925|consen 50 SMPAKFRKSIWIRRGSFVVVDPIEEEK-------------SGSKVK--GEICYVLFFDQVRLLQ 98 (167)
T ss_pred eCCHhhhhceEEeeCCEEEEccccccc-------------cCCccc--eEEEEEEccHHHHHHH
Confidence 4688999987 6778888776554 345665 5667999998 77764
No 15
>PF11385 DUF3189: Protein of unknown function (DUF3189); InterPro: IPR021525 This family of proteins with unknown function appears to be restricted to Firmicutes
Probab=39.27 E-value=60 Score=25.42 Aligned_cols=50 Identities=14% Similarity=0.145 Sum_probs=30.2
Q ss_pred hcCCEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHHhhcCcCCCCCeEEE
Q 030987 17 RLEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLGKKAFTVL 71 (168)
Q Consensus 17 ~~~ily~~G~D~~GrPVvV~~a~~lP~~~~d~e~ll~Yvv~~~Ld~~~~~~yvlV 71 (168)
+.|-++..|.|..|++|.++-.+..+. -.++++.=+. .++. ..++++.+|
T Consensus 48 d~G~l~y~G~De~gn~VY~lG~~~~~~---~~~~al~~l~-~i~~-~~~~~i~~v 97 (148)
T PF11385_consen 48 DIGRLIYMGTDEYGNEVYILGRKNNGK---IVERALKSLL-EILG-IENEEIILV 97 (148)
T ss_pred cCceEEEEEEcCCCCEEEEEecCChHH---HHHHHHHHHH-HHhC-CCCCcEEEE
Confidence 446555679999999999988877642 1445555444 2222 234555444
No 16
>COG0381 WecB UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]
Probab=38.58 E-value=48 Score=30.08 Aligned_cols=73 Identities=15% Similarity=0.221 Sum_probs=53.1
Q ss_pred CCCCeEEEEEcCCcccccCcccHHHHHHHHHhcChhhhhccceEEEEcCChHHHHHHHHhchhhcccccccceecCceee
Q 030987 64 GKKAFTVLYVHTGVQRSENFAGISALRSIYDAIPANVKENLQAVYFVHPGLQARLFLATFGRLFFNGVGGYVSLLPFFNF 143 (168)
Q Consensus 64 ~~~~yvlVy~htg~~~~~n~P~~~wL~~~y~~L~~~ykKNLkalYIVHPt~~~K~~l~~~~pFissk~~~kv~~l~~~~~ 143 (168)
.+++|.+|-.|... +.. .++.-+.+++..+..+| +|..-+|=+||.-..|-.. ..-+.+. .+|+.++-+.|
T Consensus 202 ~~~~~iLvT~HRre-N~~--~~~~~i~~al~~i~~~~-~~~~viyp~H~~~~v~e~~---~~~L~~~--~~v~li~pl~~ 272 (383)
T COG0381 202 KDKKYILVTAHRRE-NVG--EPLEEICEALREIAEEY-PDVIVIYPVHPRPRVRELV---LKRLKNV--ERVKLIDPLGY 272 (383)
T ss_pred ccCcEEEEEcchhh-ccc--ccHHHHHHHHHHHHHhC-CCceEEEeCCCChhhhHHH---HHHhCCC--CcEEEeCCcch
Confidence 34569999999887 444 67888888888888888 9999999999994444433 1222222 56888888888
Q ss_pred ee
Q 030987 144 YY 145 (168)
Q Consensus 144 ~~ 145 (168)
++
T Consensus 273 ~~ 274 (383)
T COG0381 273 LD 274 (383)
T ss_pred HH
Confidence 74
No 17
>PF09949 DUF2183: Uncharacterized conserved protein (DUF2183); InterPro: IPR019236 This domain, found in various bacterial and fungal proteins, has no known function.
Probab=38.17 E-value=43 Score=24.48 Aligned_cols=48 Identities=21% Similarity=0.267 Sum_probs=36.7
Q ss_pred HHHHHHhhcCcCCCCCeEEEEEcCCcccccCcccHHHHHHHHHhcChhhhhccceEEEE
Q 030987 52 KRYLSERVYPRLGKKAFTVLYVHTGVQRSENFAGISALRSIYDAIPANVKENLQAVYFV 110 (168)
Q Consensus 52 l~Yvv~~~Ld~~~~~~yvlVy~htg~~~~~n~P~~~wL~~~y~~L~~~ykKNLkalYIV 110 (168)
++..+..+++.+-+.+|++|=+.+.. .| ++|..+-++|+.+++++||=
T Consensus 51 K~~~i~~i~~~fP~~kfiLIGDsgq~-----Dp------eiY~~ia~~~P~~i~ai~IR 98 (100)
T PF09949_consen 51 KRDNIERILRDFPERKFILIGDSGQH-----DP------EIYAEIARRFPGRILAIYIR 98 (100)
T ss_pred HHHHHHHHHHHCCCCcEEEEeeCCCc-----CH------HHHHHHHHHCCCCEEEEEEE
Confidence 44445566778899999999885432 23 46999999999999999983
No 18
>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=37.78 E-value=2.1e+02 Score=24.87 Aligned_cols=84 Identities=11% Similarity=0.120 Sum_probs=48.4
Q ss_pred CEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHHHhhcCcCC---CCCeEEEEEcCCcccccCcccHHHHHHHHHhc
Q 030987 20 IFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLG---KKAFTVLYVHTGVQRSENFAGISALRSIYDAI 96 (168)
Q Consensus 20 ily~~G~D~~GrPVvV~~a~~lP~~~~d~e~ll~Yvv~~~Ld~~~---~~~yvlVy~htg~~~~~n~P~~~wL~~~y~~L 96 (168)
--+..|..+.|.+++|=+..--.++.--+...+. .+++.+. .++-+||.+-+.+ +..|..+..+.+
T Consensus 41 p~~~~g~~~~~~~L~IGIpTV~R~~~sYL~~TL~----SLl~~ls~~Er~~i~IvVllAd~-------Dp~~~~~~~~~i 109 (297)
T PF04666_consen 41 PALLAGKPRTGKKLCIGIPTVKREKESYLLDTLA----SLLDGLSPEERKDIVIVVLLADT-------DPDYHPSVAQNI 109 (297)
T ss_pred cceEcCCCCCCCeEEEEecccccCCCchHHHHHH----HHHHhCCHHHhcCeEEEEEecCC-------ChhhhHHHHHHH
Confidence 3345699999988666665433222222333333 3344443 3455555555544 245677777777
Q ss_pred Chhhhhccc--eEEEEcCCh
Q 030987 97 PANVKENLQ--AVYFVHPGL 114 (168)
Q Consensus 97 ~~~ykKNLk--alYIVHPt~ 114 (168)
..++...+. -+-+|||+.
T Consensus 110 ~~~f~~~i~sG~l~VI~~p~ 129 (297)
T PF04666_consen 110 STRFADHIESGLLEVISPPP 129 (297)
T ss_pred HHHhHHHHHhCceEEEeccc
Confidence 777777774 366788764
No 19
>KOG2633 consensus Hismacro and SEC14 domain-containing proteins [Chromatin structure and dynamics; Transcription]
Probab=32.39 E-value=0.81 Score=37.87 Aligned_cols=38 Identities=32% Similarity=0.352 Sum_probs=31.7
Q ss_pred hhhHhHHHhcCCEEEeccCCCCCeEEEEEeecCCCCCC
Q 030987 9 SEQEELIDRLEIFKIHGRDKQGRKILRIIGKFFPARLL 46 (168)
Q Consensus 9 ~e~~~di~~~~ily~~G~D~~GrPVvV~~a~~lP~~~~ 46 (168)
.|+++++.....+...+.|+.|.-+--..+..+|.+.+
T Consensus 13 ~~~~~~~~~l~~f~~~~~~~~~i~lwr~d~~~l~v~av 50 (200)
T KOG2633|consen 13 AEIFSNITSLEVFKIDKPDNGGISLWRGDGKTLEVDAV 50 (200)
T ss_pred hhhhccccccchhhccCccccCeeEeecccccccceee
Confidence 45778888888888889999999999999999987543
No 20
>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=30.84 E-value=58 Score=25.72 Aligned_cols=35 Identities=20% Similarity=0.198 Sum_probs=24.0
Q ss_pred ChhhhHhHHHhcCCEEEeccC-CCCCeEEEEEeecC
Q 030987 7 SESEQEELIDRLEIFKIHGRD-KQGRKILRIIGKFF 41 (168)
Q Consensus 7 s~~e~~~di~~~~ily~~G~D-~~GrPVvV~~a~~l 41 (168)
+.+...+.+-+.|++...|+. .-|||+++-....|
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 345667889999999999965 46999999888655
No 21
>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=30.34 E-value=1.9e+02 Score=22.09 Aligned_cols=58 Identities=24% Similarity=0.320 Sum_probs=37.8
Q ss_pred CCCeEEEEEee-cCCCCCCCHHHHHHHHHHhhcCcCC-CCCeEEEEEcCCcccccCcccHHHHHH
Q 030987 29 QGRKILRIIGK-FFPARLLSVEVLKRYLSERVYPRLG-KKAFTVLYVHTGVQRSENFAGISALRS 91 (168)
Q Consensus 29 ~GrPVvV~~a~-~lP~~~~d~e~ll~Yvv~~~Ld~~~-~~~yvlVy~htg~~~~~n~P~~~wL~~ 91 (168)
.+-|++++.-+ -.| +..+.+.+..++. ++.+. ..++.++-..... ..+-..++.||.+
T Consensus 114 ~~~piLIl~NK~D~~-~~~~~~~i~~~l~---l~~l~~~~~~~v~~~sa~~-g~Gv~e~l~WL~~ 173 (175)
T PF00025_consen 114 KDIPILILANKQDLP-DAMSEEEIKEYLG---LEKLKNKRPWSVFSCSAKT-GEGVDEGLEWLIE 173 (175)
T ss_dssp TTSEEEEEEESTTST-TSSTHHHHHHHTT---GGGTTSSSCEEEEEEBTTT-TBTHHHHHHHHHH
T ss_pred ccceEEEEecccccc-CcchhhHHHhhhh---hhhcccCCceEEEeeeccC-CcCHHHHHHHHHh
Confidence 47898888775 444 4466666665542 45565 7788877776665 4555667888875
No 22
>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=29.76 E-value=59 Score=21.88 Aligned_cols=11 Identities=18% Similarity=0.374 Sum_probs=5.2
Q ss_pred CCCeEEEEEcC
Q 030987 65 KKAFTVLYVHT 75 (168)
Q Consensus 65 ~~~yvlVy~ht 75 (168)
++++.+|+.+.
T Consensus 33 ~~~v~~v~Vs~ 43 (95)
T PF13905_consen 33 KDDVEFVFVSL 43 (95)
T ss_dssp TTTEEEEEEE-
T ss_pred CCCEEEEEEEe
Confidence 45555555544
No 23
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=27.73 E-value=56 Score=26.52 Aligned_cols=35 Identities=17% Similarity=0.164 Sum_probs=28.0
Q ss_pred ChhhhHhHHHhcCCEEEecc-CCCCCeEEEEEeecC
Q 030987 7 SESEQEELIDRLEIFKIHGR-DKQGRKILRIIGKFF 41 (168)
Q Consensus 7 s~~e~~~di~~~~ily~~G~-D~~GrPVvV~~a~~l 41 (168)
+.....+.|-+.|++...|+ |..|||+.+-....|
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 34567888999999999885 567999999887544
No 24
>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=26.84 E-value=75 Score=20.94 Aligned_cols=32 Identities=16% Similarity=0.167 Sum_probs=26.1
Q ss_pred hhhHhHHHhcCCEEEeccCCCCCeEEEEEeec
Q 030987 9 SEQEELIDRLEIFKIHGRDKQGRKILRIIGKF 40 (168)
Q Consensus 9 ~e~~~di~~~~ily~~G~D~~GrPVvV~~a~~ 40 (168)
.|...-|++.++...+-.|++|+|-+..++-.
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 35566788889999999999999998888853
No 25
>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=24.22 E-value=93 Score=27.15 Aligned_cols=71 Identities=11% Similarity=0.258 Sum_probs=37.1
Q ss_pred CCCCeEEEEEcCCcccccCcccHHHHHHHHHhcChhhhhccceEEEEcCChHHHH-HHHHhchhhcccccccceecCcee
Q 030987 64 GKKAFTVLYVHTGVQRSENFAGISALRSIYDAIPANVKENLQAVYFVHPGLQARL-FLATFGRLFFNGVGGYVSLLPFFN 142 (168)
Q Consensus 64 ~~~~yvlVy~htg~~~~~n~P~~~wL~~~y~~L~~~ykKNLkalYIVHPt~~~K~-~l~~~~pFissk~~~kv~~l~~~~ 142 (168)
..++|++|.+|..+ ...+.....-+.++.+.|... +|+.-++.+|++=-.+. +...+..+ . .|+.++.+.
T Consensus 178 ~~~~~iLvt~H~~t-~~~~~~~~~~i~~~l~~L~~~--~~~~vi~~~hn~p~~~~~i~~~l~~~-~-----~v~~~~~l~ 248 (346)
T PF02350_consen 178 APKPYILVTLHPVT-NEDNPERLEQILEALKALAER--QNVPVIFPLHNNPRGSDIIIEKLKKY-D-----NVRLIEPLG 248 (346)
T ss_dssp TTSEEEEEE-S-CC-CCTHH--HHHHHHHHHHHHHH--TTEEEEEE--S-HHHHHHHHHHHTT--T-----TEEEE----
T ss_pred cCCCEEEEEeCcch-hcCChHHHHHHHHHHHHHHhc--CCCcEEEEecCCchHHHHHHHHhccc-C-----CEEEECCCC
Confidence 78899999999988 333233455666666666655 69999999995333333 33444444 2 566555554
Q ss_pred e
Q 030987 143 F 143 (168)
Q Consensus 143 ~ 143 (168)
|
T Consensus 249 ~ 249 (346)
T PF02350_consen 249 Y 249 (346)
T ss_dssp H
T ss_pred H
Confidence 4
No 26
>PF10954 DUF2755: Protein of unknown function (DUF2755); InterPro: IPR020513 This entry contains membrane proteins with no known function.; GO: 0016021 integral to membrane
Probab=23.16 E-value=59 Score=23.86 Aligned_cols=31 Identities=29% Similarity=0.249 Sum_probs=21.1
Q ss_pred HHhchhhcccccccceecCceeeeeeehhhHHHHHHHHhh
Q 030987 121 ATFGRLFFNGVGGYVSLLPFFNFYYCFNLLYWTFVTFCLI 160 (168)
Q Consensus 121 ~~~~pFissk~~~kv~~l~~~~~~~~~~~~~~~~~~~~~~ 160 (168)
++.+|.++.| ++-++. .-|.+|=.||.||..
T Consensus 5 t~sK~l~~gK--~~~s~t-------~gNiAYAlFVLfcfW 35 (100)
T PF10954_consen 5 TLSKSLFGGK--KRSSST-------PGNIAYALFVLFCFW 35 (100)
T ss_pred cccchhhcCC--CCCCCC-------cchhHHHHHHHHHHH
Confidence 4556777766 333322 469999999999974
No 27
>PRK03298 hypothetical protein; Provisional
Probab=22.95 E-value=1.5e+02 Score=24.97 Aligned_cols=37 Identities=27% Similarity=0.366 Sum_probs=29.6
Q ss_pred cCCEEEeccCCCCCeEEEEEeecCCCCCCCHHHHHHHHH
Q 030987 18 LEIFKIHGRDKQGRKILRIIGKFFPARLLSVEVLKRYLS 56 (168)
Q Consensus 18 ~~ily~~G~D~~GrPVvV~~a~~lP~~~~d~e~ll~Yvv 56 (168)
.|.+-..|+|++|++|+|=+=|+ ..-.-.++|.+|+-
T Consensus 134 ~G~IDil~rD~~G~~V~vEvKRr--~~idaV~QL~RYve 170 (224)
T PRK03298 134 IGPVDLLCRDADGGTVAVEIKRR--GEIDGVEQLTRYLE 170 (224)
T ss_pred CCceeEEEEcCCCCEEEEEEEec--CCccHHHHHHHHHH
Confidence 36777779999999999999888 33224889999996
No 28
>TIGR01001 metA homoserine O-succinyltransferase. The apparent equivalog from Bacillus subtilis is broken into two tandem reading frames.
Probab=22.88 E-value=5.3e+02 Score=22.72 Aligned_cols=91 Identities=14% Similarity=0.234 Sum_probs=58.8
Q ss_pred HhHHHhcCCEEEeccCC----CCCeEEEEEeecCCCCCCCHHHHHHHHHHhhcCcCCCCCeEEEEEcCCcccccCcccHH
Q 030987 12 EELIDRLEIFKIHGRDK----QGRKILRIIGKFFPARLLSVEVLKRYLSERVYPRLGKKAFTVLYVHTGVQRSENFAGIS 87 (168)
Q Consensus 12 ~~di~~~~ily~~G~D~----~GrPVvV~~a~~lP~~~~d~e~ll~Yvv~~~Ld~~~~~~yvlVy~htg~~~~~n~P~~~ 87 (168)
..-|++.||+-+. .++ +-||+=+.+-.-+|.+ ++-|.-+.-+ |.. ..-+--+.+++..+ ...+..+.+
T Consensus 12 ~~~L~~enifvm~-~~ra~~qdirpL~I~ILNLMP~K-~~TE~Q~lRl----L~n-tplqv~i~~~~~~s-h~~k~t~~~ 83 (300)
T TIGR01001 12 VKVLRKENIFVMT-ESRASHQDIRPLEILILNLMPKK-IETENQFLRL----LSN-SPLQVNITLLRTDS-RKSKNTPIE 83 (300)
T ss_pred HHHHHhCCceeec-hhhhccccccceeEEEEecCCcc-HHHHHHHHHH----hcC-CCCceEEEEEEecc-ccCCCCCHH
Confidence 4567888999664 333 3579999999999987 5555433322 221 11222244444443 223444778
Q ss_pred HHHHHHHhcChhhhhccceEEEE
Q 030987 88 ALRSIYDAIPANVKENLQAVYFV 110 (168)
Q Consensus 88 wL~~~y~~L~~~ykKNLkalYIV 110 (168)
.|.+.|+.++.--.++..+++|-
T Consensus 84 hl~~fY~~f~~ik~~~fDGlIIT 106 (300)
T TIGR01001 84 HLNKFYTTFEAVKDRKFDGLIIT 106 (300)
T ss_pred HHHHHhhCHHHHhcCCCCEEEEc
Confidence 99999999988878999998874
No 29
>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=20.94 E-value=69 Score=29.92 Aligned_cols=34 Identities=12% Similarity=0.088 Sum_probs=20.3
Q ss_pred HHHHhcChhhhhccceEEEEcCChHHHHHHHHhc
Q 030987 91 SIYDAIPANVKENLQAVYFVHPGLQARLFLATFG 124 (168)
Q Consensus 91 ~~y~~L~~~ykKNLkalYIVHPt~~~K~~l~~~~ 124 (168)
++-+.=-|+||||+|-+||----..+.++-+++-
T Consensus 423 kaaksgvrryrknik~vyippvmaslnayaalma 456 (756)
T PF06933_consen 423 KAAKSGVRRYRKNIKYVYIPPVMASLNAYAALMA 456 (756)
T ss_pred HHHHHhHHHHhcCCcEEEeChHHHhhHHHHHHHH
Confidence 3444456899999998887433333344444443
Done!