RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 018252
(359 letters)
>2cw6_A Hydroxymethylglutaryl-COA lyase, mitochondrial; HMG-COA lyase,
ketogenic enzyme; HET: 3HG; 2.10A {Homo sapiens} PDB:
3mp3_A* 3mp4_A 3mp5_A*
Length = 298
Score = 386 bits (994), Expect = e-135
Identities = 141/222 (63%), Positives = 171/222 (77%)
Query: 123 IPRFVKIVEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADA 182
+P+ VKIVEVGPRDGLQNEKN V T VK++LI L +GL V+E TSFVSPKWVPQ+ D
Sbjct: 2 LPKRVKIVEVGPRDGLQNEKNIVSTPVKIKLIDMLSEAGLSVIETTSFVSPKWVPQMGDH 61
Query: 183 RDVMEAVRDLEGARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLV 242
+V++ ++ G PVLTPNLKGFEAA+AAGAKEV IF +ASE F+K NINCSIE+S
Sbjct: 62 TEVLKGIQKFPGINYPVLTPNLKGFEAAVAAGAKEVVIFGAASELFTKKNINCSIEESFQ 121
Query: 243 RYRAVAHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGV 302
R+ A+ AA+ +I VRGYVSC +GCP EG I P+KVA V K+ + MGC+EISLGDTIGV
Sbjct: 122 RFDAILKAAQSANISVRGYVSCALGCPYEGKISPAKVAEVTKKFYSMGCYEISLGDTIGV 181
Query: 303 GTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQ 344
GTPG + ML AVM VP+ LAVH HDTYGQ+L N L++LQ
Sbjct: 182 GTPGIMKDMLSAVMQEVPLAALAVHCHDTYGQALANTLMALQ 223
>1ydo_A HMG-COA lyase; TIM-barrel protein, structural genomics, PSI,
protein struct initiative, northeast structural genomics
consortium, NESG,; 2.71A {Bacillus subtilis subsp}
Length = 307
Score = 385 bits (991), Expect = e-134
Identities = 93/222 (41%), Positives = 132/222 (59%)
Query: 123 IPRFVKIVEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADA 182
P+ V I EVGPRDGLQNE + T K+ I +L +GL +E TSFV PKW+P L DA
Sbjct: 3 YPKKVTIKEVGPRDGLQNEPVWIATEDKITWINQLSRTGLSYIEITSFVHPKWIPALRDA 62
Query: 183 RDVMEAVRDLEGARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLV 242
DV + + +G L PN +G E A+ G E +F SASE ++ NIN S +SL
Sbjct: 63 IDVAKGIDREKGVTYAALVPNQRGLENALEGGINEACVFMSASETHNRKNINKSTSESLH 122
Query: 243 RYRAVAHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGV 302
+ V + A+ ++ R Y+S V GCP E +P +V +++ L + G E+SLGDTIG
Sbjct: 123 ILKQVNNDAQKANLTTRAYLSTVFGCPYEKDVPIEQVIRLSEALFEFGISELSLGDTIGA 182
Query: 303 GTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQ 344
P V +LEA++A P ++A+H HDT G +L N++ +LQ
Sbjct: 183 ANPAQVETVLEALLARFPANQIALHFHDTRGTALANMVTALQ 224
>1ydn_A Hydroxymethylglutaryl-COA lyase; TIM-barrel protein, structural
genomics, PSI, protein struct initiative; 2.30A
{Brucella melitensis}
Length = 295
Score = 384 bits (990), Expect = e-134
Identities = 124/222 (55%), Positives = 156/222 (70%)
Query: 123 IPRFVKIVEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADA 182
+ V+IVE+ RDGLQNEK VPT K+ LI RL G +EATSFVSPKWVPQLAD+
Sbjct: 1 MAEHVEIVEMAARDGLQNEKRFVPTADKIALINRLSDCGYARIEATSFVSPKWVPQLADS 60
Query: 183 RDVMEAVRDLEGARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLV 242
R+VM +R +G R VL PN+KG+EAA AA A E+A+F SASE FSK+NINC+I +S+
Sbjct: 61 REVMAGIRRADGVRYSVLVPNMKGYEAAAAAHADEIAVFISASEGFSKANINCTIAESIE 120
Query: 243 RYRAVAHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGV 302
R V AA + +RGYVSCVV CP +G + P VA V ++L +GC E+SLGDTIG
Sbjct: 121 RLSPVIGAAINDGLAIRGYVSCVVECPYDGPVTPQAVASVTEQLFSLGCHEVSLGDTIGR 180
Query: 303 GTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQ 344
GTP TV ML+AV+A+ P LA H HDT G++L NI +SL+
Sbjct: 181 GTPDTVAAMLDAVLAIAPAHSLAGHYHDTGGRALDNIRVSLE 222
>2ftp_A Hydroxymethylglutaryl-COA lyase; structural genomics, PSI, protein
structure initiativ midwest center for structural
genomics, MCSG; 2.40A {Pseudomonas aeruginosa}
Length = 302
Score = 384 bits (988), Expect = e-134
Identities = 124/222 (55%), Positives = 161/222 (72%)
Query: 123 IPRFVKIVEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADA 182
+P+ V++VEVGPRDGLQNEK + K+ L+ L ++GL +E SFVSPKWVPQ+A +
Sbjct: 5 LPKKVRLVEVGPRDGLQNEKQPIEVADKIRLVDDLSAAGLDYIEVGSFVSPKWVPQMAGS 64
Query: 183 RDVMEAVRDLEGARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLV 242
+V +R G L PNLKGFEAA+ +G KEVA+FA+ASEAFS+ NINCSI+DSL
Sbjct: 65 AEVFAGIRQRPGVTYAALAPNLKGFEAALESGVKEVAVFAAASEAFSQRNINCSIKDSLE 124
Query: 243 RYRAVAHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGV 302
R+ V AA+ + VRGY+SCV+GCP +G + P +VA+VA+EL MGC+E+SLGDTIGV
Sbjct: 125 RFVPVLEAARQHQVRVRGYISCVLGCPYDGDVDPRQVAWVARELQQMGCYEVSLGDTIGV 184
Query: 303 GTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQ 344
GT G ++EAV + VP E+LA H HDTYGQ+L NI SL
Sbjct: 185 GTAGATRRLIEAVASEVPRERLAGHFHDTYGQALANIYASLL 226
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 58.1 bits (140), Expect = 2e-09
Identities = 66/359 (18%), Positives = 90/359 (25%), Gaps = 147/359 (40%)
Query: 36 GMGMGSCWIEGSSCSTSNSYDEDYDEYT--REAFPWRR---HTRDMSHGDSFSRRTVSLG 90
GMGM + Y ++ W R H +D ++G FS + +
Sbjct: 1630 GMGM-----------------DLYKTSKAAQDV--WNRADNHFKD-TYG--FSILDIVIN 1667
Query: 91 RNHK----MFG--SACDI---YNSNC--NDKDIRDITNKFLKGI-PRFVKIVEVGPRDGL 138
N FG I Y++ D + T K K I + L
Sbjct: 1668 -NPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLL 1726
Query: 139 QNEKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADARDVMEAVRDL--EGAR 196
+ T P L A DL +G
Sbjct: 1727 SATQFTQP---------ALT--------LME----------------KAAFEDLKSKG-- 1751
Query: 197 LPVLTPNLKGF------E-AAIAAGAKEVAIFASASEAFSKSNINCSIED--SLVRYR-- 245
L P F E AA+A+ A + SIE +V YR
Sbjct: 1752 ---LIPADATFAGHSLGEYAALASLA----------DVM-------SIESLVEVVFYRGM 1791
Query: 246 AVAHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVA----------YVAKELHDMGCF-EI 294
+ A + Y AI P +VA V + G EI
Sbjct: 1792 TMQVAVPRDELGRSNYGMI--------AINPGRVAASFSQEALQYVVERVGKRTGWLVEI 1843
Query: 295 ----SLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNI-LISLQVSPM 348
G L A+ V V L I +I LQ S
Sbjct: 1844 VNYNVENQQYVAA--GD----LRALDTVTNVLNFI---------KLQKIDIIELQKSLS 1887
Score = 43.5 bits (102), Expect = 9e-05
Identities = 49/293 (16%), Positives = 85/293 (29%), Gaps = 101/293 (34%)
Query: 80 DSFSRRTVSLGRNHKMFGS-ACDI---YNSNCNDKDIRDITNKFLKGIPRFVKIVEVGPR 135
D++S R ++L +H GS + S +++ +F K +P P
Sbjct: 2 DAYSTRPLTL--SH---GSLEHVLLVPTASFFIASQLQE---QFNKILPE--------PT 45
Query: 136 DGL--QNEKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADARDVMEAVRDLE 193
+G +E PT EL+ + + +VS L + V
Sbjct: 46 EGFAADDE----PTTP-AELVGKFLG----------YVS-----SLVEPSKV-------- 77
Query: 194 GARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLVR--YRAVAHAA 251
G VL L FE G ++ A+ + + + + L++ A A
Sbjct: 78 GQFDQVLNLCLTEFENCYLEG-NDIHALAAKLLQENDTTLVKT--KELIKNYITARIMAK 134
Query: 252 KVLSIPVRGYVSCVVGCPVEGAIPPSKV--AYVAKELHDMGCFEISLGDTIGVGTPGTVV 309
+ S + A + F G G G
Sbjct: 135 RPFDKK-----------------SNSALFRAVGEGNAQLVAIF----G---GQGNTDD-- 168
Query: 310 PMLEAVMAVVPVEKLAVHLHDTYG-------QSLPNILISLQVSPMHAKPCFT 355
E+L L+ TY + L L + + A+ FT
Sbjct: 169 ----------YFEELR-DLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFT 210
Score = 35.0 bits (80), Expect = 0.041
Identities = 75/421 (17%), Positives = 119/421 (28%), Gaps = 188/421 (44%)
Query: 4 LEEPLGLDKLP----------SMSTIDRIQRFSS--NACRPSGDGMGMGSCWIEGSS--- 48
LE P P S I IQ + + G G +++G++
Sbjct: 219 LENP---SNTPDKDYLLSIPISCPLIGVIQ-LAHYVVTAKLLGFTPGELRSYLKGATGHS 274
Query: 49 --------CSTSNSYDEDYDEYTREA----FPW---RRHTRDMSHGDSFSRRTV------ 87
+ ++S+ E + R+A F + R + +++ ++
Sbjct: 275 QGLVTAVAIAETDSW-ESFFVSVRKAITVLF-FIGVRCY-------EAYPNTSLPPSILE 325
Query: 88 -SLGRNHK----MFGSACDIYNSNCNDKDIRDI---TNKFLKG-----I-----PR-FVK 128
SL N M + SN + ++D TN L I + V
Sbjct: 326 DSLENNEGVPSPML--SI----SNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLV- 378
Query: 129 IVEV-G-PRD--GLQN--EKNTVPTGV---KVELIRRLVSSGLPVVEATSFVSPKWVPQL 179
V G P+ GL K P+G+ ++ R F
Sbjct: 379 ---VSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERK-----LKFS-NRF--------- 420
Query: 180 ADARDVMEAVRDLEGARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIED 239
LPV +P F + + A ++ I
Sbjct: 421 -----------------LPVASP----FHSHLLVPASDL------------------INK 441
Query: 240 SLVRYRAVAHAAKVLSIPV---------RGY--------VSCVVGCPV--EGAIPPSKVA 280
LV+ V+ AK + IPV R V C++ PV E
Sbjct: 442 DLVK-NNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQ----- 495
Query: 281 YVAKELH--DMGCFEISLGDTIGVGT------PGTVVPMLEAVMAVVPVEKLAVHLHDTY 332
K H D G G G+G GT V V+ L ++ D Y
Sbjct: 496 --FKATHILDFG-----PGGASGLGVLTHRNKDGTGV-------RVIVAGTLDINPDDDY 541
Query: 333 G 333
G
Sbjct: 542 G 542
>1nvm_A HOA, 4-hydroxy-2-oxovalerate aldolase; sequestered tunnel,
substrate channeling; HET: NAD; 1.70A {Pseudomonas SP}
SCOP: a.5.7.1 c.1.10.5
Length = 345
Score = 43.8 bits (104), Expect = 4e-05
Identities = 40/226 (17%), Positives = 76/226 (33%), Gaps = 33/226 (14%)
Query: 127 VKIVEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEAT------SFVSPKWVPQLA 180
+ I +V RDG ++ + R L + + +E +
Sbjct: 9 LYISDVTLRDGSHAIRHQYTLDDVRAIARALDKAKVDSIEVAHGDGLQGSSFNYGFGRHT 68
Query: 181 DARDVMEAVRDLEGARLPVLTPNLKG----FEAAIAAGAKEVAIFASASEAFSKSNINCS 236
D + ++ A++ L G + A AGA+ V + +C+
Sbjct: 69 DLEYIEAVAGEISHAQIATLLLPGIGSVHDLKNAYQAGARVVRVA-----------THCT 117
Query: 237 IEDSLVRYRAVAHAAKVLSIPVRGYVSCVVG-CPVEGAIPPSKVAYVAKELHDMGCFEIS 295
D V + + +A R VG + IP K+A K + G I
Sbjct: 118 EAD--VSKQHIEYA--------RNLGMDTVGFLMMSHMIPAEKLAEQGKLMESYGATCIY 167
Query: 296 LGDTIGVGTPGTVVPMLEAVMAVVPVE-KLAVHLHDTYGQSLPNIL 340
+ D+ G + + + A AV+ E ++ +H H + N +
Sbjct: 168 MADSGGAMSMNDIRDRMRAFKAVLKPETQVGMHAHHNLSLGVANSI 213
>3dxi_A Putative aldolase; TIM barrel, 11107N, PSI2, NYSGXRC, structural
genomics, protein structure initiative; 2.04A
{Bacteroides vulgatus atcc 8482}
Length = 320
Score = 39.7 bits (93), Expect = 9e-04
Identities = 26/227 (11%), Positives = 57/227 (25%), Gaps = 29/227 (12%)
Query: 127 VKIVEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEAT-------SFVSPKWVPQL 179
+KI++ RDG + + I + + +E ++ +
Sbjct: 3 LKILDCTLRDGGYYTNWDFNSKIVDAYILAMNELPIDYLEVGYRNKPSKEYMGKFGYTPV 62
Query: 180 ADARDVMEAVRDLEGARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIED 239
+ + + ++ ++ + I ++
Sbjct: 63 SVLKHLRNIST----KKIAIM------LNEKNTTPEDLNHLLLPIIGLVDMIRIAIDPQN 112
Query: 240 SLVRYRAVAHAAKVLSIPVRGYVSCVVGCPVEGA--IPPSKVAYVAKELHDMGCFEISLG 297
G+ VG V + D +
Sbjct: 113 IDRAIVLAKAIKT------MGF---EVGFNVMYMSKWAEMNGFLSKLKAIDKIADLFCMV 163
Query: 298 DTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQ 344
D+ G TP V +L+ V V + H HD L N + ++
Sbjct: 164 DSFGGITPKEVKNLLKEVRKYTHVP-VGFHGHDNLQLGLINSITAID 209
>2yvq_A Carbamoyl-phosphate synthase; conserved hypothetical protein,
structural genomics, NPPSFA; 1.98A {Homo sapiens}
Length = 143
Score = 32.1 bits (74), Expect = 0.10
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 11/59 (18%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNIL 340
VA++LH+ G F++ T T L A VP +A + SL +I
Sbjct: 42 VAEQLHNEG-FKL-------FATEATSD-WLNA--NNVPATPVAWPSQEGQNPSLSSIR 89
>1rqb_A Transcarboxylase 5S subunit; TIM-barrel, carbamylated lysine,
transfera; HET: KCX; 1.90A {Propionibacterium
freudenreichii subspshermanii} SCOP: a.5.7.2 c.1.10.5
PDB: 1rqe_A 1rqh_A* 1rr2_A* 1u5j_A* 1s3h_A*
Length = 539
Score = 31.5 bits (72), Expect = 0.42
Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 9/66 (13%)
Query: 281 YV--AKELHDMGCFEISLGDTIGVGTP---GTVVPML-EAVMAVVPVEKLAVHLHDTYGQ 334
YV A +L DMG I+L D + P ++ + + + +H H T G
Sbjct: 177 YVKLAGQLLDMGADSIALKDMAALLKPQPAYDIIKAIKDTYGQKTQIN---LHCHSTTGV 233
Query: 335 SLPNIL 340
+ +++
Sbjct: 234 TEVSLM 239
>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 = 31.1 bits (71), Expect = 0.67
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNIL 340
+AKEL G +++ D G+ P ++ + + V + + +H HDT G L
Sbjct: 697 LAKELEREGFHILAIKDMAGLLKPKAAYELIGELKSAVDL-PIHLHTHDTSGNGLLTYK 754
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.9 bits (66), Expect = 0.78
Identities = 9/52 (17%), Positives = 18/52 (34%), Gaps = 24/52 (46%)
Query: 187 EAVRDLEGARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIE 238
+A++ L+ A L + + SA A + I ++E
Sbjct: 20 QALKKLQ-ASLKLYADD-------------------SAP-ALA---IKATME 47
Score = 28.8 bits (63), Expect = 2.0
Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 19/48 (39%)
Query: 141 EKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLA-DARDVME 187
EK +++L +S L + P LA A ME
Sbjct: 18 EKQA---------LKKLQAS-L------KLYADDSAPALAIKA--TME 47
>1wxx_A TT1595, hypothetical protein TTHA1280; thermus thermophillus,
methyltransferase, adoMet, structural genomics; 1.80A
{Thermus thermophilus} SCOP: b.122.1.9 c.66.1.51 PDB:
1wxw_A 2cww_A*
Length = 382
Score = 30.4 bits (69), Expect = 0.89
Identities = 14/57 (24%), Positives = 24/57 (42%)
Query: 181 DARDVMEAVRDLEGARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSI 237
D R+ + G R + GF +A G +EV S++EA ++ N +
Sbjct: 197 DQRENRLYMERFRGERALDVFSYAGGFALHLALGFREVVAVDSSAEALRRAEENARL 253
>3oa3_A Aldolase; structural genomics, seattle structural genomics center
for infectious disease, ssgcid, pathogenic fungus; 1.60A
{Coccidioides immitis}
Length = 288
Score = 29.6 bits (67), Expect = 1.3
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 21/60 (35%)
Query: 171 VSPKWVPQLADARDVMEAVRDLEGARLPVLT----------PNLKGFEA--AIAAGAKEV 218
V P +V + AV+ L+G ++ V + K EA A+ GA E+
Sbjct: 93 VRPDYVSR---------AVQYLQGTQVGVTCVIGFHEGTYSTDQKVSEAKRAMQNGASEL 143
>3r12_A Deoxyribose-phosphate aldolase; TIM beta/alpha-barrel, structural
genomics, joint center for structural genomics, JCSG;
HET: MSE CIT; 1.75A {Thermotoga maritima} PDB: 1o0y_A*
3r13_A*
Length = 260
Score = 29.5 bits (67), Expect = 1.3
Identities = 15/64 (23%), Positives = 22/64 (34%), Gaps = 21/64 (32%)
Query: 167 ATSFVSPKWVPQLADARDVMEAVRDLEGARLPV----------LTPNLKGFEA--AIAAG 214
V+P +V A +LEG + V K EA A+ +G
Sbjct: 74 HGVCVNPCYVKL---------AREELEGTDVKVVTVVGFPLGANETRTKAHEAIFAVESG 124
Query: 215 AKEV 218
A E+
Sbjct: 125 ADEI 128
>3ivs_A Homocitrate synthase, mitochondrial; TIM barrel, metalloprotein,
transferase, claisen condensatio acid biosynthesis;
2.24A {Schizosaccharomyces pombe} PDB: 3ivt_A* 3ivu_A*
3mi3_A*
Length = 423
Score = 29.9 bits (68), Expect = 1.5
Identities = 38/215 (17%), Positives = 74/215 (34%), Gaps = 21/215 (9%)
Query: 124 PRFVKIVEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATS-FVSPKWVPQLADA 182
I+E R+G Q T K+++ + L + G+ +E TS S
Sbjct: 37 VNNFSIIESTLREGEQFANAFFDTEKKIQIAKALDNFGVDYIELTSPVASE------QSR 90
Query: 183 RDVMEAVRDLEGARLPVLT-PNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSL 241
+D + ++ ++ A+ G V + S+ K + + +
Sbjct: 91 QDCEAICKLGLKCKILTHIRCHMDDARVAVETGVDGVDVVIGTSQYLRKYSHGKDMTYII 150
Query: 242 VR-YRAVAHAAKVLSIPVRGYVSCVVGCPVEGAI--PPSKVAYVAKELHDMGCFEISLGD 298
+ K I VR S E + + + K + +G + + D
Sbjct: 151 DSATEVINFV-KSKGIEVR--FSS------EDSFRSDLVDLLSLYKAVDKIGVNRVGIAD 201
Query: 299 TIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYG 333
T+G TP V ++ + VV + + H H+ G
Sbjct: 202 TVGCATPRQVYDLIRTLRGVVSCD-IECHFHNDTG 235
>3bg3_A Pyruvate carboxylase, mitochondrial; TIM barrel, ATP-binding,
biotin, disease mutation, gluconeogenesis, ligase, lipid
synthesis, manganese; HET: KCX BTI; 2.80A {Homo sapiens}
PDB: 3bg9_A
Length = 718
Score = 29.6 bits (67), Expect = 1.7
Identities = 22/88 (25%), Positives = 33/88 (37%), Gaps = 20/88 (22%)
Query: 270 VEGAI--------PPSKV----AYV--AKELHDMGCFEISLGDTIGVGTP---GTVVPML 312
VE AI P Y+ A+EL G + + D G+ P +V L
Sbjct: 240 VEAAISYTGDVADPSRTKYSLQYYMGLAEELVRAGTHILCIKDMAGLLKPTACTMLVSSL 299
Query: 313 EAVMAVVPVEKLAVHLHDTYGQSLPNIL 340
+P+ +H HDT G + +L
Sbjct: 300 RDRFPDLPLH---IHTHDTSGAGVAAML 324
>1ub3_A Aldolase protein; schiff base, deoxyribose phosphate,
carbinolamine, structural genomics, riken structural
genomics/proteomics initiative; HET: HPD; 1.40A {Thermus
thermophilus} SCOP: c.1.10.1 PDB: 1j2w_A*
Length = 220
Score = 29.1 bits (66), Expect = 2.1
Identities = 12/64 (18%), Positives = 16/64 (25%), Gaps = 21/64 (32%)
Query: 167 ATSFVSPKWVPQLADARDVMEAVRDLEGARLPV----------LTPNLKGFEA--AIAAG 214
+ P +V A + +K EA A A G
Sbjct: 34 YGLCIPPSYVAW---------VRARYPHAPFRLVTVVGFPLGYQEKEVKALEAALACARG 84
Query: 215 AKEV 218
A EV
Sbjct: 85 ADEV 88
>3ble_A Citramalate synthase from leptospira interrogans; TIM barrel,
licmsn, substrate specificity, acyltransferase,
amino-acid biosynthesis; 2.00A {Leptospira interrogans}
PDB: 3blf_A 3bli_A*
Length = 337
Score = 29.0 bits (66), Expect = 2.2
Identities = 12/43 (27%), Positives = 21/43 (48%)
Query: 298 DTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNIL 340
DT+GV +P +++++ P H H+ Y S+ N L
Sbjct: 190 DTLGVLSPEETFQGVDSLIQKYPDIHFEFHGHNDYDLSVANSL 232
>3ngj_A Deoxyribose-phosphate aldolase; lyase, structural genomics,
structural genomics center for infectious disease,
ssgcid; 1.70A {Entamoeba histolytica}
Length = 239
Score = 28.7 bits (65), Expect = 2.5
Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 21/64 (32%)
Query: 167 ATSFVSPKWVPQLADARDVMEAVRDLEGARLPV----------LTPNLKGFEA--AIAAG 214
A+ V+P WVP L+G + V +K +E A+ G
Sbjct: 58 ASVCVNPTWVPL---------CAELLKGTGVKVCTVIGFPLGATPSEVKAYETKVAVEQG 108
Query: 215 AKEV 218
A+EV
Sbjct: 109 AEEV 112
>3l6d_A Putative oxidoreductase; structural genomics, protein structure
initiative, oxidoredu PSI-2; HET: MSE; 1.90A
{Pseudomonas putida}
Length = 306
Score = 28.8 bits (65), Expect = 2.8
Identities = 6/37 (16%), Positives = 12/37 (32%), Gaps = 1/37 (2%)
Query: 178 QLADARDVMEAVRDLEGARLPVLTPNLKGFEAAIAAG 214
+ +++ G PV + + A A G
Sbjct: 245 HADAFAHIAQSLHAQ-GVWTPVFDAVCQVVQRAAAMG 280
>2hs5_A Putative transcriptional regulator GNTR; APC6050, rhodococcus SP.
RH structural genomics, PSI-2, protein structure
initiative; 2.20A {Rhodococcus SP} SCOP: a.4.5.6
a.78.1.1
Length = 239
Score = 28.4 bits (64), Expect = 3.1
Identities = 16/87 (18%), Positives = 26/87 (29%), Gaps = 13/87 (14%)
Query: 152 ELIRRLVSSGLPVVEAT--SFVSPKWVPQLADARDVMEAVRDLEGARLPVLTPN---LKG 206
E + L+ L E FV P D ++ R +E A + P L
Sbjct: 70 EAFQILIEDRLVAHELNRGVFVRV---PTAEDITELYICRRVVECAGVNGFDPATGDLSR 126
Query: 207 FEAAI-----AAGAKEVAIFASASEAF 228
A+ ++ +A F
Sbjct: 127 VAEALDLADERYAVEDWTGVGTADIHF 153
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 28.7 bits (64), Expect = 4.1
Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 21/74 (28%)
Query: 142 KNTVPTGVK-----VELIRRLVSSGLPVVEATSFVSPKWVPQLADARDVMEAVRDL---- 192
K + TG E+++ L+ G VV TS S + V + + +
Sbjct: 477 KYVLITGAGKGSIGAEVLQGLLQGGAKVVVTTSRFS----------KQVTDYYQSIYAKY 526
Query: 193 --EGARLPVLTPNL 204
+G+ L V+ N
Sbjct: 527 GAKGSTLIVVPFNQ 540
>1n7k_A Deoxyribose-phosphate aldolase; A.pernix, tetramer, alpha-beta TIM
barrel, riken S genomics/proteomics initiative, RSGI,
structural genomics,; 2.00A {Aeropyrum pernix} SCOP:
c.1.10.1
Length = 234
Score = 27.9 bits (63), Expect = 4.2
Identities = 9/64 (14%), Positives = 19/64 (29%), Gaps = 21/64 (32%)
Query: 167 ATSFVSPKWVPQLADARDVMEAVRDLEGARLPV----------LTPNLKGFEA--AIAAG 214
+ ++P + + E + + +K EA + AG
Sbjct: 51 RCAVLTPVYTVK---------ISGLAEKLGVKLCSVIGFPLGQAPLEVKLVEAQTVLEAG 101
Query: 215 AKEV 218
A E+
Sbjct: 102 ATEL 105
>2ztj_A Homocitrate synthase; (beta/alpha)8 TIM barrel, substrate complex,
amino-acid BIOS lysine biosynthesis, transferase; HET:
AKG; 1.80A {Thermus thermophilus} PDB: 2ztk_A* 2zyf_A*
3a9i_A*
Length = 382
Score = 28.3 bits (64), Expect = 4.3
Identities = 41/207 (19%), Positives = 70/207 (33%), Gaps = 31/207 (14%)
Query: 135 RDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATS-FVSPKWVPQLADARDVMEAVRDLE 193
R+G Q EK T KVE+ + L G+ +E T+ SP +D
Sbjct: 12 REGEQFEKANFSTQDKVEIAKALDEFGIEYIEVTTPVASP------QSRKDAEVLASLGL 65
Query: 194 GARLPVLT-PNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLVR-YRAVAHAA 251
A++ L + A+ G + + + S+ + ++ I + +A+
Sbjct: 66 KAKVVTHIQCRLDAAKVAVETGVQGIDLLFGTSK-YLRAPHGRDIPRIIEEAKEVIAYI- 123
Query: 252 KVLSIPVRGYVSCVVGCPVEGAIPP-----SKVAYVAK--ELHDMGCFEISLGDTIGVGT 304
R VE S+ + E + L DT+GV T
Sbjct: 124 -------REA-----APHVEVRFSAEDTFRSEEQDLLAVYEAVAPYVDRVGLADTVGVAT 171
Query: 305 PGTVVPMLEAVMAVVPVE-KLAVHLHD 330
P V ++ V VV + H H+
Sbjct: 172 PRQVYALVREVRRVVGPRVDIEFHGHN 198
>2nx9_A Oxaloacetate decarboxylase 2, subunit alpha; carboxyltransferase
structure, B enzymes, Zn2+ binding site, TIM-barrel
fold, lyase; 1.70A {Vibrio cholerae}
Length = 464
Score = 28.3 bits (64), Expect = 4.9
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 281 YV--AKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVV--PVEKLAVHLHDTYGQSL 336
+V A++L ++G I+L D G+ TP ++ + V + +H H T G +
Sbjct: 160 WVDVAQQLAELGVDSIALKDMAGILTPYAAEELVSTLKKQVDVELH---LHCHSTAGLAD 216
Query: 337 PNIL 340
+L
Sbjct: 217 MTLL 220
>1nw9_B Caspase 9, apoptosis-related cysteine protease; XIAP, caspase
inhibition, caspase activation, dimerization; 2.40A
{Homo sapiens} SCOP: c.17.1.1 PDB: 1jxq_A* 2ar9_A
Length = 277
Score = 27.8 bits (61), Expect = 6.0
Identities = 12/63 (19%), Positives = 19/63 (30%), Gaps = 7/63 (11%)
Query: 74 RDMSHGDSFSRRTVSLGRNHKMFGSACDIYNSNCNDKDIRDITNKF-------LKGIPRF 126
+D D +S G +Y ++ + I N F L G P+
Sbjct: 83 QDHGALDCCVVVILSHGCQASHLQFPGAVYGTDGCPVSVEKIVNIFNGTSCPSLGGKPKL 142
Query: 127 VKI 129
I
Sbjct: 143 FFI 145
>2nwi_A Hypothetical protein; structural genomics, unknown function, PSI-2,
protein structure initiative; 2.20A {Archaeoglobus
fulgidus} SCOP: d.190.1.3
Length = 172
Score = 27.2 bits (60), Expect = 7.0
Identities = 14/83 (16%), Positives = 26/83 (31%), Gaps = 11/83 (13%)
Query: 120 LKGIPRFVKIVEVGPRDGLQNEKNTVPTGVKVELIRR---LVSSGLPVVEATSFVSPKWV 176
+ V+ +E + + E+ R L ++G +A SF K +
Sbjct: 24 VTQKKVEVETLEQKIIRADRELAELLEIDEGDEVNYRVVYLRANGEIYAKAISFTPLKRL 83
Query: 177 PQLADARDVMEAVRDLEGARLPV 199
DL A +P+
Sbjct: 84 EN--------SFREDLMRADIPI 98
>2qf7_A Pyruvate carboxylase protein; multi-domain, multi-functional,
biotin-dependent, ligase; HET: KCX COA AGS; 2.00A
{Rhizobium etli} PDB: 3tw6_A* 3tw7_A*
Length = 1165
Score = 27.7 bits (62), Expect = 7.5
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 5/61 (8%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVV--PVEKLAVHLHDTYGQSLPNI 339
+A EL G I++ D G+ P + +A+ P+ H HDT G + +
Sbjct: 714 LAVELEKAGAHIIAVKDMAGLLKPAAAKVLFKALREATGLPIH---FHTHDTSGIAAATV 770
Query: 340 L 340
L
Sbjct: 771 L 771
>2odr_C Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 701
Score = 27.6 bits (61), Expect = 7.6
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 208 EAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLVRYRAVAHAAKVLSIPVRGYVSCVVG 267
E A + E + S S+IN I+D ++ + KV I VRG V V
Sbjct: 499 EEAFVSNTTEFKVKVPIVR--SLSDINLKIDDIALKQ--IMSKNKV--IDVRGPVFLNVE 552
Query: 268 CPVE 271
+E
Sbjct: 553 VKIE 556
>3e39_A Putative nitroreductase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; HET: MSE FMN PGE; 1.70A {Desulfovibrio
desulfuricans subsp}
Length = 178
Score = 26.8 bits (60), Expect = 8.4
Identities = 2/31 (6%), Positives = 6/31 (19%), Gaps = 8/31 (25%)
Query: 37 MGMGSCWIEGSSCSTSNSYDEDYDEYTREAF 67
+ +G+ W+
Sbjct: 115 LQLGAVWL--------GEIINQAATLLPALA 137
>2c7p_A Modification methylase HHAI; DNA methyltransferase,
methyltransferase, base flipping, restriction system,
transferase; HET: 5CM A1P SAH EPE CIT; 1.7A {Haemophilus
haemolyticus} SCOP: c.66.1.26 PDB: 10mh_A* 1m0e_A*
1mht_A* 1hmy_A* 1skm_A* 2c7o_A* 2c7q_A* 2hmy_B* 2hr1_A*
3eeo_A* 3mht_A* 4mht_A* 5mht_A* 6mht_A* 7mht_A* 8mht_A*
9mht_A* 2zcj_A* 2z6u_A* 2z6q_A* ...
Length = 327
Score = 27.0 bits (60), Expect = 9.0
Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 9/56 (16%)
Query: 98 SACDIYNSNCNDKDIRDITNKFLKGIPRFVKIV---------EVGPRDGLQNEKNT 144
A ++Y N +K DIT K IP + G + G ++ + T
Sbjct: 44 YAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFPCQAFSISGKQKGFEDSRGT 99
>3ndo_A Deoxyribose-phosphate aldolase; ssgcid, NIH, niaid, SBRI, UW,
emerald biostructures, ALS collaborative
crystallography; HET: GOL; 1.25A {Mycobacterium
smegmatis} PDB: 3ng3_A
Length = 231
Score = 26.8 bits (60), Expect = 9.1
Identities = 15/60 (25%), Positives = 21/60 (35%), Gaps = 22/60 (36%)
Query: 171 VSPKWVPQLADARDVMEAVRDLEGARLPVLT----------PNLKGFEA--AIAAGAKEV 218
VSP V + + L + P +K EA A+AAGA E+
Sbjct: 48 VSPPLVSV----------AAGVAPSGLAIAAVAGFPSGKHVPGIKATEAELAVAAGATEI 97
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.134 0.401
Gapped
Lambda K H
0.267 0.0749 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,615,674
Number of extensions: 353052
Number of successful extensions: 1100
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1095
Number of HSP's successfully gapped: 54
Length of query: 359
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 264
Effective length of database: 4,049,298
Effective search space: 1069014672
Effective search space used: 1069014672
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 (21.7 bits)
S2: 58 (26.1 bits)