RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254781179|ref|YP_003065592.1| D-alanine--D-alanine ligase
[Candidatus Liberibacter asiaticus str. psy62]
(300 letters)
>1iow_A DD-ligase, DDLB, D-ALA\:D-Ala ligase; glycogen phosphorylase, cell
WALL, peptidoglycan synthesis, vancomycin, ADP binding;
HET: ADP PHY; 1.90A {Escherichia coli} SCOP: c.30.1.2
d.142.1.1 PDB: 1iov_A* 2dln_A*
Length = 306
Score = 246 bits (628), Expect = 6e-66
Identities = 105/304 (34%), Positives = 160/304 (52%), Gaps = 13/304 (4%)
Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLVLAHLKPDLAFNVLHGN 61
AVL+GG S+EREVSL+SG A + L + G +D L + F LHG
Sbjct: 6 AVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKSMGFQKVFIALHGR 65
Query: 62 FGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQ 121
GEDG +Q +LEL+ +PYT SG++ASALSMDK+RSK + G+PV P + + R +
Sbjct: 66 GGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKLLWQGAGLPVAPWVALTRAEFEKG 125
Query: 122 HL---------ISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYV 172
+ P ++KP + GSS+G+ + + + L ++ H +++LIE+++
Sbjct: 126 LSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAENA--LQDALRLAFQHDEEVLIEKWL 183
Query: 173 DGIELTCGVMGDASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAF 232
G E T ++G+ L I P FY YE K+ S + + PA + +Q L
Sbjct: 184 SGPEFTVAILGEEILPSIRI-QPSGTFYDYEAKFLSDETQYFCPAGLEASQEANLQALVL 242
Query: 233 LAHQAIGCRGISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELLLWM 292
A +GC+G R D + D + + LE N PGMT S+ P A AG SF +L++ +
Sbjct: 243 KAWTTLGCKGWGRIDVMLDS-DGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRI 301
Query: 293 VEDA 296
+E A
Sbjct: 302 LELA 305
>3lwb_A D-alanine--D-alanine ligase; DDL, D-alanyl--D-alanine ligase,
RV2981C, structural genomics, TB structural genomics
consortium, TBSGC; 2.10A {Mycobacterium tuberculosis}
Length = 373
Score = 235 bits (601), Expect = 7e-63
Identities = 93/356 (26%), Positives = 150/356 (42%), Gaps = 65/356 (18%)
Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDR--------------------- 40
AV+ GG S+E +S S + L+ F V + +
Sbjct: 14 AVVFGGRSNEHAISCVSAGSILRNLDSRRFDVIAVGITPAGSWVLTDANPDALTITNREL 73
Query: 41 --------------------------SVGLVLAHLKPDLAFNVLHGNFGEDGLVQAILEL 74
G D+ F VLHG +GEDG +Q +LEL
Sbjct: 74 PQVKSGSGTELALPADPRRGGQLVSLPPGAGEVLESVDVVFPVLHGPYGEDGTIQGLLEL 133
Query: 75 LEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQHL----ISPPYVI 130
+PY +G+LASA+ MDK +K+++++ G+PV ++ + P +
Sbjct: 134 AGVPYVGAGVLASAVGMDKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERLGLPVFV 193
Query: 131 KPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDAS---- 186
KP +GGSS+G+ + L + + H ++++E + G EL CGV+
Sbjct: 194 KPARGGSSIGVSRVSSWD--QLPAAVARARRHDPKVIVEAAISGRELECGVLEMPDGTLE 251
Query: 187 -LDVTEIAVP-----KSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGC 240
+ EI V + FY + KY + +PAK+ + + +++LA A AI C
Sbjct: 252 ASTLGEIRVAGVRGREDSFYDFATKYLDDAAELDVPAKVDDQVAEAIRQLAIRAFAAIDC 311
Query: 241 RGISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296
RG++R DF EIN PG T +S++P M A +G + LL M+E
Sbjct: 312 RGLARVDFFLTD--DGPVINEINTMPGFTTISMYPRMWAASGVDYPTLLATMIETT 365
>3k3p_A D-alanine--D-alanine ligase; D-alanyl-alanine synthetase,
ATP-binding, cell shape, cell W biogenesis/degradation,
magnesium, manganese; 2.23A {Streptococcus mutans}
Length = 383
Score = 233 bits (596), Expect = 3e-62
Identities = 90/334 (26%), Positives = 150/334 (44%), Gaps = 42/334 (12%)
Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLVLAH------------- 48
+L GG S+ER+VS+ S ++ A+ F V + ++ +
Sbjct: 41 VLLYGGRSAERDVSVLSAESVMRAINYDNFLVKTYFITQAGDFIKTQEFDSQPSETDKLM 100
Query: 49 -----------------LKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILASALSM 91
+ + F VLHG GEDG +Q LE+L++PY + IL+S+++M
Sbjct: 101 TNDTIIASQKIKPSDIYEEEAVVFPVLHGPMGEDGSIQGFLEVLKMPYVGTNILSSSVAM 160
Query: 92 DKMRSKQVVSSCGVPVCPSILVNRFTMDSQHLISP-------PYVIKPLKGGSSLGIIVI 144
DK+ + QV+ S + + + ++ P +KP GSS+GI
Sbjct: 161 DKITTNQVLESATTIPQVAYVALIEGEPLESKLAEVEEKLIYPVFVKPANMGSSVGISKA 220
Query: 145 KKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDASLDVTEI--AVPKSDFYSY 202
+ L + + + ++LIEQ VD E+ G++G+ + T V FY Y
Sbjct: 221 ENRTD--LKQAIALALKYDSRVLIEQGVDAREIEVGILGNTDVKTTLPGEIVKDVAFYDY 278
Query: 203 ELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEI 262
E KY T +PA+I I ++++ A A + +GC G+SR DF KV+ E+
Sbjct: 279 EAKYIDNKITMAIPAEIDPVIVEKMRDYAATAFRTLGCCGLSRCDFFLTE-DGKVYLNEL 337
Query: 263 NVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296
N PG T S++P + G S+ L+ +V A
Sbjct: 338 NTMPGFTQWSMYPLLWENMGLSYSVLIEELVSLA 371
>1e4e_A Vancomycin/teicoplanin A-type resistance protein VANA; ligase, cell
WALL, antibiotic resistance, membrane, plasmid; HET: ADP
PHY; 2.5A {Enterococcus faecium} SCOP: c.30.1.2
d.142.1.1 PDB: 1e4e_B*
Length = 343
Score = 221 bits (563), Expect = 2e-58
Identities = 85/337 (25%), Positives = 143/337 (42%), Gaps = 45/337 (13%)
Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDR--------------------- 40
A+L GG S E +VS+ S A+ + ++ I + +
Sbjct: 7 AILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSGVWKMCEKPCAEWENENCYS 66
Query: 41 --------------SVGLVLAHLKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILA 86
D+AF+ LHG GEDG +Q + EL IP+ I +
Sbjct: 67 AVLSPDKKMHGLLVKKNHEYEINHVDVAFSALHGKSGEDGSIQGLFELSGIPFVGCDIQS 126
Query: 87 SALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQHLISPPYVIKPLKGGSSLGIIVIKK 146
SA+ MDK + V + G+ ++N+ + P +KP + GSS G+ +
Sbjct: 127 SAICMDKSLTYIVAKNAGIATPAFWVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNS 186
Query: 147 DQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDAS----LDVTEIAVPKSDF--- 199
LD S+ + ++LIEQ V G E+ C V+G+++ +V +I + F
Sbjct: 187 ADE--LDYAIESARQYDSKILIEQAVSGCEVGCAVLGNSAALVVGEVDQIRLQYGIFRIH 244
Query: 200 YSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFW 259
E + S N+ +PA + + +Q ++ +GCRG++R D + ++
Sbjct: 245 QEVEPEKGSENAVITVPADLSAEERGRIQETVKKIYKTLGCRGLARVDMFLQD-NGRIVL 303
Query: 260 LEINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296
E+N PG T S +P M A AG S EL+ ++ A
Sbjct: 304 NEVNTLPGFTSYSRYPRMMAAAGISLPELIDRLIVLA 340
>1ehi_A LMDDL2, D-alanine:D-lactate ligase; ATP-binding. grAsp motif for
ATP.; HET: ADP PHY; 2.38A {Leuconostoc mesenteroides}
SCOP: c.30.1.2 d.142.1.1
Length = 377
Score = 220 bits (561), Expect = 3e-58
Identities = 85/348 (24%), Positives = 155/348 (44%), Gaps = 56/348 (16%)
Query: 2 AVLMGGISSEREVSLSSGKACASALEDAG------------------------------- 30
A++ GG SSE +VS S + +A+E G
Sbjct: 7 ALIFGGNSSEHDVSKRSAQNFYNAIEATGKYEIIVFAIAQNGFFLDTESSKKILALEDEQ 66
Query: 31 -------FKVSQIDVDRSVGLVLAHLKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSG 83
V D + + + D+ F V+HGN GEDG +Q + +LL+ PY +
Sbjct: 67 PIVDAFMKTVDASDPLARIHALKSAGDFDIFFPVVHGNLGEDGTLQGLFKLLDKPYVGAP 126
Query: 84 ILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQHL------ISPPYVIKPLKGGS 137
+ A+S DK +K++++ G+ I+V+ + ++ + +K GS
Sbjct: 127 LRGHAVSFDKALTKELLTVNGIRNTKYIVVDPESANNWSWDKIVAELGNIVFVKAANQGS 186
Query: 138 SLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGI-ELTCGVMGDASLDVTEIAV-- 194
S+GI + + S S+ + ++LIE+ V+G EL GV+G+ V+EI
Sbjct: 187 SVGISRVTNAEE--YTEALSDSFQYDYKVLIEEAVNGARELEVGVIGNDQPLVSEIGAHT 244
Query: 195 -----PKSDFYSYELKYSSLNSTHVL-PAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDF 248
+Y Y K+ ++ H PA++ ++ KEV+++A A++ + RG +R DF
Sbjct: 245 VPNQGSGDGWYDYNNKFVDNSAVHFQIPAQLSPEVTKEVKQMALDAYKVLNLRGEARMDF 304
Query: 249 LFDPLSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296
L D + + E N PG T +S+F + Y+ + +L+ +++
Sbjct: 305 LLDE-NNVPYLGEPNTLPGFTNMSLFKRLWDYSDINNAKLVDMLIDYG 351
>2i87_A D-alanine-D-alanine ligase; APO; 2.00A {Staphylococcus aureus
subsp} PDB: 2i8c_A* 2i80_A*
Length = 364
Score = 178 bits (451), Expect = 2e-45
Identities = 83/338 (24%), Positives = 143/338 (42%), Gaps = 46/338 (13%)
Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLVL--------------- 46
++ GG S+E EVS+ + + +A++ + V I +
Sbjct: 7 CIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELH 66
Query: 47 -----------------AHLKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILASAL 89
+ D F +LHG GEDG +Q + E+L++PY +G+L++A
Sbjct: 67 LENGEALEISQLLKESSSGQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAAS 126
Query: 90 SMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQHL---------ISPPYVIKPLKGGSSLG 140
SMDK+ KQ+ G+P P I R + ++ P +KP GSS+G
Sbjct: 127 SMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVG 186
Query: 141 IIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGV--MGDASLDVTEIAVPKSD 198
I + + + ++ +L+IEQ V+ E+ V V
Sbjct: 187 ISKCNNEAELKEGI--KEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVA 244
Query: 199 FYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVF 258
FY Y+ KY +PA + D+ ++ +A A +A C G+ R+DF +++
Sbjct: 245 FYDYKSKYKDGKVQLQIPADLDEDVQLTLRNMALEAFKATDCSGLVRADFFVTE-DNQIY 303
Query: 259 WLEINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296
E N PG T S++P++ G S+ EL+ ++E A
Sbjct: 304 INETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELA 341
>3e5n_A D-alanine-D-alanine ligase A; bacterial blight; 2.00A {Xanthomonas
oryzae PV}
Length = 386
Score = 176 bits (447), Expect = 5e-45
Identities = 85/347 (24%), Positives = 154/347 (44%), Gaps = 55/347 (15%)
Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRS-------------------- 41
++ GG S+E EVSL S + AL+ F+ I +D+
Sbjct: 26 GLIFGGKSAEHEVSLQSARNILDALDPQRFEPVLIGIDKQGQWHVNDPDSFLLHADDPAR 85
Query: 42 -----------------------VGLVLAHLKPDLAFNVLHGNFGEDGLVQAILELLEIP 78
+ A + D+ F ++HG GEDG +Q +L + +P
Sbjct: 86 IALHRSGRGVALLPGAQQQQLRPIQPEQALAQIDVVFPIVHGTLGEDGSLQGLLRMANLP 145
Query: 79 YTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQHL------ISPPYVIKP 132
+ SG+L SA++MDK +K+V+ + V P + +R T + + P +KP
Sbjct: 146 FVGSGVLGSAVAMDKDMAKRVLRDARLAVAPFVCFDRHTAAHADVDTLIAQLGLPLFVKP 205
Query: 133 LKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDAS---LDV 189
GSS+G+ ++ + + + ++L+E V G E+ C V+G+A
Sbjct: 206 ANQGSSVGVSQVRTAD--AFAAALALALAYDHKVLVEAAVAGREIECAVLGNAVPHASVC 263
Query: 190 TEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFL 249
E+ V + + S + V+PA I + +Q++A A+QA+GC G++R D
Sbjct: 264 GEVVVHDAFYSYATKYISEHGAEIVIPADIDAQTQQRIQQIAVQAYQALGCAGMARVDVF 323
Query: 250 FDPLSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296
++ E+N PG T +S++P++ +G +R L+ ++E A
Sbjct: 324 LCA-DGRIVINEVNTLPGFTRISVYPKLWQASGLDYRGLITRLIELA 369
>3i12_A D-alanine-D-alanine ligase A; D-alanyl-alanine synthetase A, ADP
binding protein, csgid, ATP-binding, cell shape; HET:
ADP; 2.20A {Salmonella typhimurium}
Length = 364
Score = 157 bits (398), Expect = 2e-39
Identities = 79/347 (22%), Positives = 152/347 (43%), Gaps = 55/347 (15%)
Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLVL--------------- 46
++ GG S+E EVSL S K A++ F V + +D++ +
Sbjct: 7 GIVFGGKSAEHEVSLQSAKNIVDAIDKTRFDVVLLGIDKAGQWHVNDAENYLQNADDPAH 66
Query: 47 ----------------------------AHLKPDLAFNVLHGNFGEDGLVQAILELLEIP 78
D+ F ++HG GEDG +Q +L + +P
Sbjct: 67 IALRPSAISLAQVPGKHQHQLINAQNGQPLPTVDVIFPIVHGTLGEDGSLQGMLRVANLP 126
Query: 79 YTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQHL------ISPPYVIKP 132
+ S +L+SA MDK +K+++ G+ + P I + R + + P +KP
Sbjct: 127 FVGSDVLSSAACMDKDVAKRLLRDAGLNIAPFITLTRTNRHAFSFAEVESRLGLPLFVKP 186
Query: 133 LKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDAS---LDV 189
GSS+G+ + + + ++ ++++EQ + G E+ C V+G+ +
Sbjct: 187 ANQGSSVGVSKVANEAQYQQA--VALAFEFDHKVVVEQGIKGREIECAVLGNDNPQASTC 244
Query: 190 TEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFL 249
EI + + + V+PA+IP ++ +++ +A A+Q +GC G++R D
Sbjct: 245 GEIVLNSEFYAYDTKYIDDNGAQVVVPAQIPSEVNDKIRAIAIQAYQTLGCAGMARVDVF 304
Query: 250 FDPLSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296
+V EIN PG T +S++P++ +G + +L+ ++E A
Sbjct: 305 LTA-DNEVVINEINTLPGFTNISMYPKLWQASGLGYTDLISRLIELA 350
>2fb9_A D-alanine:D-alanine ligase; 1.90A {Thermus caldophilus} PDB:
2zdh_A* 2yzg_A 2yzn_A* 2yzm_A* 2zdg_A* 2zdq_A*
Length = 322
Score = 157 bits (397), Expect = 3e-39
Identities = 95/318 (29%), Positives = 152/318 (47%), Gaps = 27/318 (8%)
Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKV---------------------SQIDVDR 40
++ GG+S E EVSL S + + + + +
Sbjct: 7 LLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEH 66
Query: 41 SVGLVLAHLKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVV 100
L+ + D+ F +LHG FGEDG VQ LELL PY +G+ ASAL MDK SK+V+
Sbjct: 67 PFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVL 126
Query: 101 SSCGVPVCPSILVNRFTMDSQHLISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSW 160
+ GVPV P + R PP+ +KP GSS+GI +++ Q + L +
Sbjct: 127 AQAGVPVVPWV-AVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLE-AALALAFR 184
Query: 161 NHGDQLLIEQYVDGIELTCGVMGDASLDVTEIAV--PKSDFYSYELKYSSLNSTHVLPAK 218
++ + EL GV+G+ + + + ++ FY YE KY+ + ++PA
Sbjct: 185 YDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAP 244
Query: 219 IPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFPEMA 278
+ + VQ LA A++ +G RG++R DF +++ E+N PG TP S++P +
Sbjct: 245 LDPGTQETVQELALKAYKVLGVRGMARVDFFLA--EGELYLNELNTIPGFTPTSMYPRLF 302
Query: 279 AYAGYSFRELLLWMVEDA 296
G ++ ELL +VE A
Sbjct: 303 EAGGVAYPELLRRLVELA 320
>1z2n_X Inositol 1,3,4-trisphosphate 5/6-kinase; inositol phosphate kinase,
ATP-grAsp, transferase; HET: ADP; 1.20A {Entamoeba
histolytica hm-1} PDB: 1z2o_X* 1z2p_X*
Length = 324
Score = 148 bits (374), Expect = 1e-36
Identities = 37/320 (11%), Positives = 88/320 (27%), Gaps = 37/320 (11%)
Query: 5 MGGISSEREVSLS-------SGKACASALEDAGFKVSQIDVDRSVGLVLAHLKP-DLAFN 56
+G +++++ VSL S F+++ I D ++ L +P +
Sbjct: 3 LGSMTTKQTVSLFIWLPESKQKTLFISTKNHTQFELNNIIFDVTLSTELPDKEPNAIITK 62
Query: 57 VLHGNFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRF 116
H ++ + + + ++ +P+ S V
Sbjct: 63 RTHPVGKMADEMRKYEKDHPKVLFLESSAIHDMMSSREEINALLIKNNIPIPNSFSVKSK 122
Query: 117 TMDSQHL----ISPPYVIKPLKGGSSLGIIVIK-----KDQSIPLDLLQSSSWNHGDQLL 167
Q L + P+++KP + +K + + + + +
Sbjct: 123 EEVIQLLQSKQLILPFIVKPENAQGTFNAHQMKIVLEQEGIDDIHFPCLCQHYINHNNKI 182
Query: 168 IEQYVDGIELTCGV-------------------MGDASLDVTEIAVPKSDFYSYELKYSS 208
++ + G L + V
Sbjct: 183 VKVFCIGNTLKWQTRTSLPNVHRCGIKSVDFNNQHLEDILSWPEGVIDKQDIIENSANRF 242
Query: 209 LNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEINVQPGM 268
+ P + L E++ LA+ A+G + DF+ + +++NV P
Sbjct: 243 GSKILEDPILLNLTSEAEMRDLAYKVRCALGV-QLCGIDFIKENEQGNPLVVDVNVFPSY 301
Query: 269 TPVSIFPEMAAYAGYSFREL 288
F + E+
Sbjct: 302 GGKVDFDWFVEKVALCYTEV 321
>2pvp_A D-alanine-D-alanine ligase; 2.40A {Helicobacter pylori SS1}
Length = 367
Score = 136 bits (343), Expect = 5e-33
Identities = 71/337 (21%), Positives = 129/337 (38%), Gaps = 49/337 (14%)
Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKV----------------------SQIDVD 39
VL GG S E E+S+ S A L+D +QI
Sbjct: 24 CVLFGGASFEHEISIVSAIALKGVLKDRIKYFIFLDENHHFYLIEESNMHSKYFAQIKEK 83
Query: 40 RSVGLVLAH-------------LKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILA 86
+ L+L H ++ L N++HG GEDG + ++LE I + I A
Sbjct: 84 KLPPLILTHNGLLKNSFLGAKIIELPLVINLVHGGDGEDGKLASLLEFYRIAFIGPRIEA 143
Query: 87 SALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDS---QHLISPPYVIKPLKGGSSLGIIV 143
S LS +K +K G+ +L+N + + P+++KP GSSLG+ V
Sbjct: 144 SVLSYNKYLTKLYAKDLGIKTLDYVLLNEKNRANALDLMNFNFPFIVKPSNAGSSLGVNV 203
Query: 144 IKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGI---ELTCGVMGDASLDVTEIAVPKSDFY 200
+K+++ + S++ + ++LIE ++ G+ L + K +F
Sbjct: 204 VKEEKELIY--ALDSAFEYSKEVLIEPFIQGVKEYNLAGCKIKKDFCFSYIEEPNKQEFL 261
Query: 201 SYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWL 260
++ KY + A + + ++++ + + I R DF +V+
Sbjct: 262 DFKQKYLDFSRNKAPKASLSNALEEQLKENFKKLYSDLFDGAIIRCDFFVI--ENEVYLN 319
Query: 261 EINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDAS 297
EIN PG +F + + L + +
Sbjct: 320 EINPIPGSLANYLFDDF----KTTLENLAQSLPKTPK 352
>2q7d_A Inositol-tetrakisphosphate 1-kinase; inositol kinase, ITPK1,
inositol 1,3,4- 5/6-kinase, inositol phosphate,
inositolphosphate, polyphosphate; HET: ANP; 1.60A {Homo
sapiens} PDB: 2qb5_A* 2odt_X
Length = 346
Score = 126 bits (316), Expect = 8e-30
Identities = 43/302 (14%), Positives = 98/302 (32%), Gaps = 33/302 (10%)
Query: 6 GGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSV-----GLVLAHLKPDLAFNVLHG 60
G SE+++ + +A A G +V Q+++ R + V+ H K
Sbjct: 22 GYWLSEKKIKKLNFQAFAELCRKRGMEVVQLNLSRPIEEQGPLDVIIH-KLTDVILEADQ 80
Query: 61 NFGEDGLVQAILELLEIPYTHSGIL----ASALSMDKMRSKQVVSSCGVPV-------CP 109
N + + + + + +L A +D+ +S +++ + P
Sbjct: 81 NDSQSLELVHRFQEYIDAHPETIVLDPLPAIRTLLDRSKSYELIRKIEAYMEDDRICSPP 140
Query: 110 SILVNRFTMDS------QHLISPPYVIKPLKGGSSLGIIVIKKDQ----SIPLDLLQSSS 159
+ + D ++ ++ P++ K + + + +
Sbjct: 141 FMELTSLCGDDTMRLLEKNGLTFPFICKTRVAHGTNSHEMAIVFNQEGLNAIQPPCVVQN 200
Query: 160 WNHGDQLLIEQYVDGIELTCGVM-----GDASLDVTEIAVPKSDFYSYELKYSSLNSTHV 214
+ + + +L + +V G T A E S S S L
Sbjct: 201 FINHNAVLYKVFVVGESYTVVQRPSLKNFSAGTSDRESIFFNSHNVSKPESSSVLTELDK 260
Query: 215 LPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEINVQPGMTPVSIF 274
+ + ++ L+ QA+G + D + + + + ++IN PG VS F
Sbjct: 261 IEGVFERPSDEVIRELSRALRQALGVS-LFGIDIIINNQTGQHAVIDINAFPGYEGVSEF 319
Query: 275 PE 276
Sbjct: 320 FT 321
>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane
protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP:
c.30.1.5 d.142.1.3 PDB: 1px2_A*
Length = 422
Score = 88.5 bits (219), Expect = 1e-18
Identities = 36/257 (14%), Positives = 74/257 (28%), Gaps = 29/257 (11%)
Query: 23 ASALEDAGFKVSQIDVDRSVGLVLAHLKPDLAFNVLHGNF-GEDGLVQAILELLEIPYTH 81
A + GF V ++V R+ V+ LKPD H +G ++++ L+ Y
Sbjct: 154 LVAHANGGFSVD-MEVLRNGVKVVRSLKPDFVLIRQHAFSMARNGDYRSLVIGLQ--YAG 210
Query: 82 SGILASALSMDKMRSKQVVSS-----CGVPVCPSILVNRFTMDSQHLISP-----PYVIK 131
+ S S+ K V + + T H P V+K
Sbjct: 211 IPSVNSLHSVYNFCDKPWVFAQMVRLHKKLGTEEFPLIDQTFYPNHKEMLSSTTYPVVVK 270
Query: 132 PLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGI-ELTCGVMGDASLDVT 190
S +G + + + S E ++D ++ +G
Sbjct: 271 MGHAHSGMGKVKVDNQHD--FQDIASVVALTKTYATAEPFIDAKYDVRVQKIGQNYKAYM 328
Query: 191 EIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLF 250
++ + N+ + +I + + + G I + L
Sbjct: 329 RT-SVSGNWKT--------NTGSAMLEQIAMS--DRYKLWVDTCSEIFGGLDICAVEALH 377
Query: 251 DPLSRKVFWLEINVQPG 267
+ +E+
Sbjct: 378 GK-DGRDHIIEVVGSSM 393
>2p0a_A Synapsin-3, synapsin III; neurotransmitter release, schizophrenia,
vesicle transport, structural genomics, structural
genomics consortium, SGC; HET: ANP; 1.90A {Homo sapiens}
Length = 344
Score = 75.6 bits (185), Expect = 1e-14
Identities = 28/283 (9%), Positives = 70/283 (24%), Gaps = 28/283 (9%)
Query: 24 SALEDAGFKVSQIDVDRSVGLVLAHLKPDLAFNVLHGNFGEDGLVQ-AILELLE---IPY 79
+A G V V +V KPD H G +++ L+ +P
Sbjct: 59 AAYVTGGCMVDMQVVRNGTKVVSRSFKPDFILVRQHAYSMALGEDYRSLVIGLQYGGLPA 118
Query: 80 THSGILASALSMDKMRSKQVVSSCGVPVCPSILVNR------FTMDSQHLISPPYVIKPL 133
+S + + K + + P P V+K
Sbjct: 119 VNS-LYSVYNFCSKPWVFSQLIKIFHSLGPEKFPLVEQTFFPNHKPMVTAPHFPVVVKLG 177
Query: 134 KGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDASLDVTEIA 193
+ +G I ++ + S E ++D ++
Sbjct: 178 HAHAGMGKIKVENQLDFQD--ITSVVAMAKTYATTEAFIDSKYDIRIQKIGSNYKAYMRT 235
Query: 194 VPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPL 253
++ + + + + + + G I +
Sbjct: 236 SISGNWKANTGSAML----------EQVAMTERYRLWVDSCSEMFGGLDICAVKAVHSK- 284
Query: 254 SRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296
+ + +E+ + + + E +L++ +
Sbjct: 285 DGRDYIIEVMD----SSMPLIGEHVEEDRQLMADLVVSKMSQL 323
>3hbl_A Pyruvate carboxylase; TIM barrel, ligase; HET: BTI ADP; 2.71A
{Staphylococcus aureus subsp} PDB: 3bg5_A* 3ho8_A*
3hb9_A*
Length = 1150
Score = 58.5 bits (141), Expect = 2e-09
Identities = 29/184 (15%), Positives = 70/184 (38%), Gaps = 21/184 (11%)
Query: 92 DKMRSKQVVSSCGVPVCPSILVNRFTMDSQHL------ISPPYVIKPLKGGSSLGIIVIK 145
DK++++ +PV P + + P +IK GG G+ +++
Sbjct: 118 DKVKARTTAIKADLPVIPGT--DGPIKSYELAKEFAEEAGFPLMIKATSGGGGKGMRIVR 175
Query: 146 KDQSIPLDLLQSSS----WNHGDQLLIEQYVDG-IELTCGVMGDASLDVTEIAVPKSDFY 200
++ + ++ S ++ IE+Y+D + V+GD ++ + + + D
Sbjct: 176 EESELEDAFHRAKSEAEKSFGNSEVYIERYIDNPKHIEVQVIGDEHGNI--VHLFERDC- 232
Query: 201 SYELKYSSLNSTHVLPA-KIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFW 259
++ V P+ + + + + A + I +FL + F+
Sbjct: 233 --SVQRRHQKVVEVAPSVGLSPTLRQRICDAAIQLMENIKYVNAGTVEFLVSG--DEFFF 288
Query: 260 LEIN 263
+E+N
Sbjct: 289 IEVN 292
>2qf7_A Pyruvate carboxylase protein; multi-domain, multi-functional,
biotin-dependent, ligase; HET: KCX COA SAP; 2.00A
{Rhizobium etli cfn 42}
Length = 1165
Score = 55.5 bits (133), Expect = 1e-08
Identities = 33/186 (17%), Positives = 71/186 (38%), Gaps = 21/186 (11%)
Query: 91 MDKMRSKQVVSSCGVPVCPSILVNRFTMDSQHL------ISPPYVIKPLKGGSSLGIIVI 144
+K+ ++ + S GVPV P+ D + I P ++K GG G+ VI
Sbjct: 133 GNKVAARNLAISVGVPVVPA--TEPLPDDMAEVAKMAAAIGYPVMLKASWGGGGRGMRVI 190
Query: 145 KKDQSIPLDLLQ----SSSWNHGDQLLIEQYVDG---IELTCGVMGDASLDVTEIAVPKS 197
+ + + ++ + + + D++ +E+ V+ +E ++GD +V +
Sbjct: 191 RSEADLAKEVTEAKREAMAAFGKDEVYLEKLVERARHVESQ--ILGDTHGNVVHLFERDC 248
Query: 198 DFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKV 257
K L +E+ + A G ++L D + K
Sbjct: 249 SVQRRNQKVVERAPAPYLSE----AQRQELAAYSLKIAGATNYIGAGTVEYLMDADTGKF 304
Query: 258 FWLEIN 263
+++E+N
Sbjct: 305 YFIEVN 310
>1uc8_A LYSX, lysine biosynthesis enzyme; alpha-aminoadipate pathway, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; 2.00A {Thermus thermophilus} SCOP:
c.30.1.6 d.142.1.7 PDB: 1uc9_A*
Length = 280
Score = 53.0 bits (126), Expect = 7e-08
Identities = 45/293 (15%), Positives = 82/293 (27%), Gaps = 33/293 (11%)
Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDR-SVGLVLAHLKPDLAFNVLHG 60
A+L I + + E G ++ V + L + + L
Sbjct: 3 AILYDRIRPD-------ERMLFERAEALGLPYKKVYVPALPMVLGERPKELEGVTVALER 55
Query: 61 NFG--EDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTM 118
L L IP + DK + ++ G+P + L
Sbjct: 56 CVSQSRGLAAARYLTALGIPVVNR-PEVIEACGDKWATSVALAKAGLPQPKTALATDREE 114
Query: 119 DSQHLISP--PYVIKPLKGGSSLGIIVIKKDQSIPLDLLQSS--SWNHGDQLLIEQYVDG 174
+ + + P V+KP+ G I++YV+
Sbjct: 115 ALRLMEAFGYPVVLKPVIGSWGRLXXXXXXXXXXXXXXXXXXVLGGFQHQLFYIQEYVEK 174
Query: 175 IELTCGVMGDASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLA 234
V + I + + + + + + +EV RL+ A
Sbjct: 175 PGRDIRVFVVGERAIAAIYRRSAHWITNTARGGQAENCP---------LTEEVARLSVKA 225
Query: 235 HQAIGCRGISRSDFLFDPLSRKVFWLEINVQPGM------TPVSIFPEMAAYA 281
+A+G G+ D R + E+N T V I E+ YA
Sbjct: 226 AEAVGG-GVVAVDLFESE--RGLLVNEVNHTMEFKNSVHTTGVDIPGEILKYA 275
>1ulz_A Pyruvate carboxylase N-terminal domain; biotin carboxylase, ligase;
2.20A {Aquifex aeolicus VF5} SCOP: b.84.2.1 c.30.1.1
d.142.1.2
Length = 451
Score = 51.0 bits (122), Expect = 3e-07
Identities = 46/240 (19%), Positives = 87/240 (36%), Gaps = 20/240 (8%)
Query: 36 IDVDRSVGLVLAHLKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILASALSMDKMR 95
++ R + + + D G E+ + E I + L DK R
Sbjct: 60 LNKQRIIN-LALEVGADAIHPGY-GFLAENAEFAKMCEEAGITFIGPHWKVIELMGDKAR 117
Query: 96 SKQVVSSCGVPVCPSILVNRFTMDSQHL------ISPPYVIKPLKGGSSLGIIVIKKDQS 149
SK+V+ GVPV P + + I P ++K GG GI + + ++
Sbjct: 118 SKEVMKKAGVPVVPGS--DGVLKSLEEAKALAREIGYPVLLKATAGGGGRGIRICRNEEE 175
Query: 150 IPLDLLQ----SSSWNHGDQLLIEQYVDG-IELTCGVMGDASLDVTEIAVPKSDFYSYEL 204
+ + Q + LL+E++++ + V+GD +V I + + D S +
Sbjct: 176 LVKNYEQASREAEKAFGRGDLLLEKFIENPKHIEYQVLGDKHGNV--IHLGERD-CSIQR 232
Query: 205 KYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEINV 264
+ L P + + + A + IG +F+ D F +E+N
Sbjct: 233 RNQKLVEIAPSLILTP-EKREYYGNIVTKAAKEIGYYNAGTMEFIADQEGNLYF-IEMNT 290
>3ouz_A Biotin carboxylase; structural genomics, center for structural
genomics of infec diseases, csgid, alpha-beta fold,
cytosol, LIG; HET: MSE ADP SRT TLA; 1.90A {Campylobacter
jejuni subsp}
Length = 446
Score = 50.5 bits (121), Expect = 5e-07
Identities = 45/221 (20%), Positives = 84/221 (38%), Gaps = 16/221 (7%)
Query: 60 GNFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMD 119
G E+ I I + + A L DK ++KQV+ GVPV P +
Sbjct: 87 GFLSENQNFVEICAKHNIKFIGPSVEAMNLMSDKSKAKQVMQRAGVPVIPGSDGALAGAE 146
Query: 120 SQHLISP----PYVIKPLKGGSSLGIIVIKKDQSIPLDLLQ----SSSWNHGDQLLIEQY 171
+ ++ P ++K GG G+ V++ ++ + + + + +E+Y
Sbjct: 147 AAKKLAKEIGYPVILKAAAGGGGRGMRVVENEKDLEKAYWSAESEAMTAFGDGTMYMEKY 206
Query: 172 VDG-IELTCGVMGDASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPA-KIPLDIYKEVQR 229
+ + V+GD+ +V I V + D ++ PA + +
Sbjct: 207 IQNPRHIEVQVIGDSFGNV--IHVGERD---CSMQRRHQKLIEESPAILLDEKTRTRLHE 261
Query: 230 LAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEINVQPGMTP 270
A A +AIG G +FL D F +E+N + +
Sbjct: 262 TAIKAAKAIGYEGAGTFEFLVDKNLDFYF-IEMNTRLQVEH 301
>3df7_A Putative ATP-grAsp superfamily protein; putative protein, PSI-II,
nysgrc., structural genomics, protein structure
initiative; 1.87A {Archaeoglobus fulgidus}
Length = 305
Score = 49.8 bits (118), Expect = 8e-07
Identities = 36/242 (14%), Positives = 75/242 (30%), Gaps = 42/242 (17%)
Query: 50 KPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCP 109
K D + + + E S A A++ DK + +
Sbjct: 69 KSDAFLIIAPEDDFLLYTLTKKAEK-YCENLGSSSRAIAVTSDKWELYKKLRGEVQVPQT 127
Query: 110 SILVNRFTMDSQHLISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIE 169
S+ ++IKP + GI D + +
Sbjct: 128 SLRPLDC----------KFIIKPRTACAGEGIGFS---------------DEVPDGHIAQ 162
Query: 170 QYVDGIELTCGVMGDASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQR 229
++++GI L+ + + + + + Y + V+PA+I ++ +EV
Sbjct: 163 EFIEGINLSVSLAVGEDVKCLSVNEQIINNFRY--------AGAVVPARISDEVKREVVE 214
Query: 230 LAFLAHQAIG-CRGISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFREL 288
A A + + G D ++ + + +EIN + + G S +L
Sbjct: 215 EAVRAVECVEGLNGYVGVDIVYSD---QPYVIEINARLTTP----VVAFSRAYGASVADL 267
Query: 289 LL 290
L
Sbjct: 268 LA 269
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 44.5 bits (105), Expect = 3e-05
Identities = 30/148 (20%), Positives = 47/148 (31%), Gaps = 55/148 (37%)
Query: 10 SEREVSLSSGKACASA------LEDAGFKVSQIDVDRSVGLVLAHLKP---DLAFNVLHG 60
SER++ S+ ++ L A I+ D LV ++ D+ V
Sbjct: 410 SERKLKFSNRFLPVASPFHSHLLVPA---SDLINKD----LVKNNVSFNAKDIQIPVYDT 462
Query: 61 NFGED----------GLVQAILEL-------LEIPYTH---------SGILASALSMDKM 94
G D +V I+ L + TH SG+ L+
Sbjct: 463 FDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGL--GVLT---H 517
Query: 95 RSKQVVSSCGVPVCPSILVNRFTMDSQH 122
R+K GV V I+ T+D
Sbjct: 518 RNKD---GTGVRV---IVAG--TLDINP 537
Score = 36.1 bits (83), Expect = 0.009
Identities = 55/390 (14%), Positives = 99/390 (25%), Gaps = 184/390 (47%)
Query: 5 MGGISSEREVSLSSGK------------ACASALEDAGFKVS---------QIDVDRSV- 42
M S+ R ++LS G AS L++ F D +
Sbjct: 1 MDAYST-RPLTLSHGSLEHVLLVPTASFFIASQLQEQ-FNKILPEPTEGFAADDEPTTPA 58
Query: 43 -------GLVLAHLKPDLAFNVLHGNFGEDGLVQAILELL------------EIPYTHSG 83
G V + ++P + G +L L +I H+
Sbjct: 59 ELVGKFLGYVSSLVEPS-----------KVGQFDQVLNLCLTEFENCYLEGNDI---HA- 103
Query: 84 ILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQHLISPPYVIKPLKGGSSLGIIV 143
LA+ L + + + ++ N T ++ + P+ K +S
Sbjct: 104 -LAAKLLQE--------NDTTLVKTKELIKNYIT--ARIMAKRPFD----KKSNSA---- 144
Query: 144 IKKDQSIPLDLLQSSSWNH-------GDQLLIEQYVDGIEL----------------TCG 180
L ++ + G Q + Y + EL
Sbjct: 145 ----------LFRAVGEGNAQLVAIFGGQGNTDDYFE--ELRDLYQTYHVLVGDLIKFSA 192
Query: 181 VM--------GDAS------LDV-----TEIAVPKSDFYSYELKYSSLNSTHV-LPAKIP 220
DA L++ P D+ L S + P I
Sbjct: 193 ETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDY---------LLSIPISCPL-IG 242
Query: 221 LDIYKEVQRLAFLAHQAIGCR-----------------G----------ISRSDFL--FD 251
+ +Q LAH + + G I+ +D F
Sbjct: 243 V-----IQ----LAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFF 293
Query: 252 PLSRKV----FWLEINVQPGMTPVSIFPEM 277
RK F++ + S+ P +
Sbjct: 294 VSVRKAITVLFFIGVRCYEAYPNTSLPPSI 323
Score = 34.1 bits (78), Expect = 0.036
Identities = 46/291 (15%), Positives = 86/291 (29%), Gaps = 147/291 (50%)
Query: 62 FGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPV---------CPSIL 112
D L++ E L S ++ + L +K+ ++ G+ + P
Sbjct: 183 LVGD-LIKFSAETL------SELIRTTLDAEKVFTQ------GLNILEWLENPSNTP--- 226
Query: 113 VNRFTMDSQHLISPP-------------YVI-------KP------LKG--GSSLGIIV- 143
D +L+S P YV+ P LKG G S G++
Sbjct: 227 ------DKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTA 280
Query: 144 ---------------IKK-----------------DQSIPLDLLQSSSWNHG-------- 163
++K + S+P +L+ S +
Sbjct: 281 VAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILE-DSLENNEGVPSPML 339
Query: 164 -------DQLLIEQYVD------------GIELTCGVMGDASLDVTEIAVPKSDFYSYEL 204
+Q+ + YV+ I L V G +L V+ P+S Y L
Sbjct: 340 SISNLTQEQV--QDYVNKTNSHLPAGKQVEISL---VNGAKNLVVS--GPPQS-LYGLNL 391
Query: 205 KYSSL-NSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLS 254
+ + ++IP +R +++ FL P++
Sbjct: 392 TLRKAKAPSGLDQSRIPFS-----ERKLKFSNR-----------FL--PVA 424
Score = 33.0 bits (75), Expect = 0.083
Identities = 31/172 (18%), Positives = 60/172 (34%), Gaps = 62/172 (36%)
Query: 146 KDQSIPLDLLQSSS-----WNHGDQLLIEQY----VD-----GIELTCGVMGDASLDVTE 191
++Q + +DL ++S WN D + Y +D + LT G+ + E
Sbjct: 1627 QEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRE 1686
Query: 192 IAVPKSDFYSYELKYSSLNSTHVLPAKIPLD-IYKEVQR----LAFLAHQAIGCRGISRS 246
YS++ ++ K+ + I+KE+ F + + + +S +
Sbjct: 1687 -------------NYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGL----LSAT 1729
Query: 247 DFLFDPLSRKVFWLEINVQPGMTPVS-----------IFPEMAAYAGYSFRE 287
F QP +T + + P A +AG+S E
Sbjct: 1730 QF---------------TQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGE 1766
>2vpq_A Acetyl-COA carboxylase; bacteria, ATP-grAsp domain, biotin
carboxylase, ligase; HET: ANP; 2.1A {Staphylococcus
aureus}
Length = 451
Score = 41.4 bits (97), Expect = 2e-04
Identities = 33/192 (17%), Positives = 71/192 (36%), Gaps = 29/192 (15%)
Query: 89 LSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQHL------ISPPYVIKPLKGGSSLGII 142
K +K + VPV P + D I P +IK GG GI
Sbjct: 111 KMGIKDVAKAEMIKANVPVVPGS--DGLMKDVSEAKKIAKKIGYPVIIKATAGGGGKGIR 168
Query: 143 VIKK----DQSIPLDLLQSSSWNHGDQLLIEQYVDG-IELTCGVMGDASLDVTEIAVPKS 197
V + + + ++ + L +E++++ + ++GD+ +V I + +
Sbjct: 169 VARDEKELETGFRMTEQEAQTAFGNGGLYMEKFIENFRHIEIQIVGDSYGNV--IHLGER 226
Query: 198 DFYSYELKYSSLNSTH-----VLPAK-IPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFD 251
D ++ P+ + + +E+ A A +A+ +F++D
Sbjct: 227 D--------CTIQRRMQKLVEEAPSPILDDETRREMGNAAVRAAKAVNYENAGTIEFIYD 278
Query: 252 PLSRKVFWLEIN 263
K +++E+N
Sbjct: 279 LNDNKFYFMEMN 290
>3lp8_A Phosphoribosylamine-glycine ligase; ssgcid, NIH, niaid, SBRI, UW,
emerald biostructures, ALS collaborative
crystallography; 2.15A {Ehrlichia chaffeensis}
Length = 442
Score = 41.5 bits (97), Expect = 3e-04
Identities = 21/130 (16%), Positives = 47/130 (36%), Gaps = 9/130 (6%)
Query: 64 EDGLVQAILELLE---IPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDS 120
E L+ + + L I A+ L K +K++ G+P
Sbjct: 92 ETPLMNGLSDALTEEGILVFGPSKAAARLESSKGFTKELCMRYGIPTAKYGYFVDTNSAY 151
Query: 121 QHLI--SPPYVIKPLKGGSSLGIIVIKKDQ----SIPLDLLQSSSWNHGDQLLIEQYVDG 174
+ + P V+K G ++ + ++ L+ G ++IE++++G
Sbjct: 152 KFIDKHKLPLVVKADGLAQGKGTVICHTHEEAYNAVDAMLVHHKFGEAGCAIIIEEFLEG 211
Query: 175 IELTCGVMGD 184
E++ + D
Sbjct: 212 KEISFFTLVD 221
>1a9x_A Carbamoyl phosphate synthetase (large chain); amidotransferase,
thioester; HET: CYG ADP; 1.80A {Escherichia coli} SCOP:
a.92.1.1 c.24.1.1 c.30.1.1 c.30.1.1 d.142.1.2 d.142.1.2
PDB: 1ce8_A* 1m6v_A* 1c30_A* 1bxr_A* 1c3o_A* 1cs0_A*
1jdb_B* 1kee_A* 1t36_A*
Length = 1073
Score = 39.5 bits (92), Expect = 0.001
Identities = 32/212 (15%), Positives = 71/212 (33%), Gaps = 21/212 (9%)
Query: 92 DKMRSKQVVSSCGVPVCPSILVNRFT--MDSQHLISPPYVIKPLKGGSSLGIIVIKKDQS 149
D+ R + G+ S + + + + P +I+P G + +
Sbjct: 128 DRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGGIAYNREE 187
Query: 150 IPLDLLQSSSWNHGDQLLIEQYVDG---IELTCGVMGDASLDVTEIAVPKSDFYSYELKY 206
+ + +LLI++ + G E+ + I V + +
Sbjct: 188 FEEICARGLDLSPTKELLIDESLIGWKEYEMEV----VRDKNDNCIIVCSIE-NFDAMGI 242
Query: 207 SSLNSTHVLPAK-IPLDIYKEVQRLAFLAHQAIGCRGISRS-DFLFDPLSRKVFWLEINV 264
+ +S V PA+ + Y+ ++ + + IG + F +P + ++ +E+N
Sbjct: 243 HTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEMNP 302
Query: 265 QP--------GMTPVSIFPEMA-AYAGYSFRE 287
+ T I A GY+ E
Sbjct: 303 RVSRSSALASKATGFPIAKVAAKLAVGYTLDE 334
>2cqy_A Propionyl-COA carboxylase alpha chain, mitochondrial; PCCA, B
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 108
Score = 37.8 bits (87), Expect = 0.003
Identities = 23/97 (23%), Positives = 38/97 (39%), Gaps = 9/97 (9%)
Query: 87 SALSM-DKMRSKQVVSSCGVPVCPSILVNRFTMDSQHLIS----PPYVIKPLKGGSSLGI 141
S+ S DK+ SK + V P + I+ P +IK GG G+
Sbjct: 2 SSGSSGDKIESKLLAKKAEVNTIPGFDGVVKDAEEAVRIAREIGYPVMIKASAGGGGKGM 61
Query: 142 IVIKKDQSIPLDLLQ----SSSWNHGDQLLIEQYVDG 174
+ D+ ++S D+LLIE+++D
Sbjct: 62 RIAWDDEETRDGFRLSSQEAASSFGDDRLLIEKFIDN 98
>3n6r_A Propionyl-COA carboxylase, alpha subunit; protein complex,
biotin-dependent carboxylase, ligase; HET: BTI; 3.20A
{Ruegeria pomeroyi}
Length = 681
Score = 37.6 bits (87), Expect = 0.003
Identities = 22/104 (21%), Positives = 39/104 (37%), Gaps = 13/104 (12%)
Query: 92 DKMRSKQVVSSCGVPVCPSILVNRFTMDSQHL------ISPPYVIKPLKGGSSLGIIVIK 145
DK+ SK++ V P D+ I P +IK GG G+ +
Sbjct: 115 DKITSKKIAQEANVSTVPGY--MGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAW 172
Query: 146 KDQSIPL----DLLQSSSWNHGDQLLIEQYVDG-IELTCGVMGD 184
DQ ++++ D++ IE++V + V+ D
Sbjct: 173 NDQEAREGFQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCD 216
>3jrx_A Acetyl-COA carboxylase 2; BC domain, soraphen A, alternative
splicing, ATP-binding, biotin, fatty acid biosynthesis,
ligase, lipid synthesis; HET: S1A; 2.50A {Homo sapiens}
PDB: 3jrw_A*
Length = 587
Score = 33.9 bits (77), Expect = 0.046
Identities = 31/187 (16%), Positives = 63/187 (33%), Gaps = 4/187 (2%)
Query: 77 IPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQHLISPPYVIKPLKGG 136
+P++ SG+ D + K++ V + +++ I P +IK +GG
Sbjct: 196 LPWSGSGLTVEWTEDDLQQGKRISVPEDVYDKGCVKDVDEGLEAAERIGFPLMIKASEGG 255
Query: 137 SSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDASLDVTEIAVPK 196
GI + + P+ Q S G + + + + D AV
Sbjct: 256 GGKGIRKAESAEDFPILFRQVQSEIPGSPIFLMKLAQHAR---HLEVQILADQYGNAVSL 312
Query: 197 SDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRK 256
+ PL I++ +++ A + +G ++L+
Sbjct: 313 FGRDCSIQRRHQKIVEEAPATIAPLAIFEFMEQCAIRLAKTVGYVSAGTVEYLYSQDGSF 372
Query: 257 VFWLEIN 263
F LE+N
Sbjct: 373 HF-LELN 378
>2dzd_A Pyruvate carboxylase; biotin carboxylase, ligase; 2.40A
{Geobacillus thermodenitrificans}
Length = 461
Score = 29.2 bits (65), Expect = 1.3
Identities = 16/105 (15%), Positives = 43/105 (40%), Gaps = 9/105 (8%)
Query: 89 LSMDKMRSKQVVSSCGVPVCPSILVNRFTMD----SQHLISPPYVIKPLKGGSSLGIIVI 144
+ DK++++ + G+PV P ++ P +IK GG G+ ++
Sbjct: 117 MFGDKVKARHAAVNAGIPVIPGSDGPVDGLEDVVAFAEAHGYPIIIKAALGGGGRGMRIV 176
Query: 145 KKDQSIPLDLLQ----SSSWNHGDQLLIEQYVDG-IELTCGVMGD 184
+ + + + + D++ +E+ ++ + ++GD
Sbjct: 177 RSKSEVKEAFERAKSEAKAAFGSDEVYVEKLIENPKHIEVQILGD 221
>2cdq_A Aspartokinase; aspartate kinase, amino acid metabolism, ACT domain,
allostery, S-adenosylmethionine, lysine, allosteric
effector, plant; HET: TAR SAM LYS; 2.85A {Arabidopsis
thaliana} SCOP: c.73.1.3 d.58.18.10 d.58.18.10
Length = 510
Score = 28.3 bits (62), Expect = 1.9
Identities = 16/72 (22%), Positives = 27/72 (37%), Gaps = 6/72 (8%)
Query: 24 SALEDAGFKV---SQIDVDRSVGLVLAHLKPDLAFNVLHGNFGEDGLVQAILELLEIPYT 80
L G V SQ ++ ++ + + LH +F E G + ELL P
Sbjct: 441 HVLYTKGVNVQMISQGASKVNISFIVNEAEAEGCVQALHKSFFESG---DLSELLIQPRL 497
Query: 81 HSGILASALSMD 92
+G L ++
Sbjct: 498 GNGSPVRTLQVE 509
>2vob_A Trypanothione synthetase; ligase; 2.3A {Leishmania major} PDB:
2vps_A 2vpm_A
Length = 652
Score = 27.9 bits (62), Expect = 3.0
Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 4/59 (6%)
Query: 112 LVNRFTMDSQHLISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQ 170
++ + L Y KP+ G +I+ D + S +G + +I Q
Sbjct: 529 ILKAEYELTDELRKHGYAKKPIVGRVGSNVIITSGDGVV----HAESGGKYGKRNMIYQ 583
>3ocj_A Putative exported protein; structural genomics, PSI-2, protein
structure initiative, MI center for structural genomics,
MCSG; HET: PLM; 1.39A {Bordetella parapertussis}
Length = 305
Score = 27.5 bits (60), Expect = 3.9
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 3 VLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRS--VGLVLAHLKP 51
++ + R +L + + LE+AGF + + DR+ V+A KP
Sbjct: 255 LVFTRLIQPRWNALRTHAQTRAQLEEAGFTDLRFEDDRARLFPTVIAR-KP 304
>2p8u_A Hydroxymethylglutaryl-COA synthase, cytoplasmic;
hydromethylglutaryl COA, mevalonate pathway, structural
genomics, structural genomics consortium; HET: COA;
2.00A {Homo sapiens}
Length = 478
Score = 27.1 bits (59), Expect = 5.4
Identities = 10/64 (15%), Positives = 15/64 (23%), Gaps = 10/64 (15%)
Query: 8 ISSEREVSLSSG-KACASALEDAGFKVSQIDVDRSVGLVLAHLKPDLAF----NVLHGNF 62
++RE S + +E I L + L F
Sbjct: 66 FCTDREDINSLCMTVVQNLMERNNLSYDCIGR-----LEVGTETIIDKSKSVKTNLMQLF 120
Query: 63 GEDG 66
E G
Sbjct: 121 EESG 124
>2dtx_A Glucose 1-dehydrogenase related protein; rossmann fold,
oxidoreductase; HET: BMA; 1.60A {Thermoplasma
acidophilum} PDB: 2dtd_A* 2dte_A* 2zk7_A
Length = 264
Score = 26.4 bits (58), Expect = 7.8
Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 9/59 (15%)
Query: 19 GKACASALEDAGFKVSQIDVDRSVGLVLAHLKPDL--------AFNVLHGNFGE-DGLV 68
G+A A D G KV + + H++ D+ + + + +G LV
Sbjct: 21 GRAIAERFVDEGSKVIDLSIHDPGEAKYDHIECDVTNPDQVKASIDHIFKEYGSISVLV 79
>1m0w_A Glutathione synthetase; amine/carboxylate ligase, structural
genomics, PSI, protein structure initiative; HET: ANP
3GC; 1.80A {Saccharomyces cerevisiae} SCOP: c.30.1.4
d.142.1.6 PDB: 1m0t_A*
Length = 491
Score = 26.4 bits (58), Expect = 7.9
Identities = 12/45 (26%), Positives = 16/45 (35%), Gaps = 3/45 (6%)
Query: 221 LDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFW--LEIN 263
+Y + A Q GI RSD+L D +E N
Sbjct: 105 WSLYLATLKSAQYKKQNFRL-GIFRSDYLIDKKKGTEQIKQVEFN 148
>3p0b_A TT1467 protein; glycoside hydrolase GH57, glycogen branching,
transferase; 1.35A {Thermus thermophilus} PDB: 1ufa_A
Length = 540
Score = 26.3 bits (57), Expect = 9.4
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 44 LVL-AHLKPDLAFNVLHGNFGEDGLVQAILE 73
LVL AHL P + + FGE+ L +A+ E
Sbjct: 26 LVLHAHL-PYVRAHG-MWPFGEETLYEAMAE 54
>2io8_A Bifunctional glutathionylspermidine synthetase/amidase; ligase,
hydrolase; HET: ADP; 2.10A {Escherichia coli} SCOP:
c.30.1.7 d.3.1.15 d.142.1.8 PDB: 2io7_A* 2io9_A* 2ioa_A*
2iob_A
Length = 619
Score = 26.0 bits (57), Expect = 9.9
Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 119 DSQHLISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQ 170
+ L+ Y +KP+ G I ++ + ++L +S +Q I Q
Sbjct: 521 VNDELVKTGYAVKPIAGRCGSNIDLVSHHE----EVLDKTSGKFAEQKNIYQ 568
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.320 0.137 0.401
Gapped
Lambda K H
0.267 0.0500 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,521,092
Number of extensions: 110982
Number of successful extensions: 467
Number of sequences better than 10.0: 1
Number of HSP's gapped: 425
Number of HSP's successfully gapped: 47
Length of query: 300
Length of database: 5,693,230
Length adjustment: 92
Effective length of query: 208
Effective length of database: 3,462,782
Effective search space: 720258656
Effective search space used: 720258656
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.9 bits)