RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|255764510|ref|YP_003065448.2| uroporphyrinogen-III synthase
[Candidatus Liberibacter asiaticus str. psy62]
(232 letters)
>3mw8_A Uroporphyrinogen-III synthase; structural genomics, joint center
for structural genomics, J protein structure initiative,
PSI-2, lyase; 1.65A {Shewanella amazonensis}
Length = 240
Score = 86.4 bits (213), Expect = 6e-18
Identities = 33/240 (13%), Positives = 73/240 (30%), Gaps = 11/240 (4%)
Query: 1 MYIVITRPIKKALRTQEKIQKMGYIPVMMPLSYFIHDRES-VFLAMQQSYGAIAITSSES 59
M +++TRP K + + ++ PL + L + S+ +
Sbjct: 2 MKLLLTRPEGKNAAMASALDALAIPYLVEPLLSVEAAAVTQAQLDELSRADILIFISTSA 61
Query: 60 LSTLPANFCR---HTPIFAIGEASACLARQKGFTQIFHGKDNSINLAKIIVEQKVLFTPQ 116
+S +A+G+A+A +G T D+ + + + +
Sbjct: 62 VSFATPWLKDQWPKATYYAVGDATADALALQGITAERSPADSQATEGLLTLPSLEQVSGK 121
Query: 117 KPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETTMKNLLQNA--DAILFYA 174
+ +I G R D L + ++ Y + Q+ D I+ +
Sbjct: 122 QIVIVRGKGGREAM-ADGLRLRGANVSYLEVYQRACPPLDAPASVSRWQSFGIDTIVVTS 180
Query: 175 RSSVLYFFSL----PLPAKISAAFLCLSNNIASAIPASYKNVVTVACFPKETSLLKLLPL 230
+ +L + S + + VT A + ++L L +
Sbjct: 181 GEVLENLINLVPKDSFAWLRDCHIIVPSARVETQARKKGLRRVTNAGAANQAAVLDALGM 240
>1jr2_A Uroporphyrinogen-III synthase; heme biosynthesis, HEAM
biosynthesis, lyase; 1.84A {Homo sapiens} SCOP:
c.113.1.1
Length = 286
Score = 72.5 bits (177), Expect = 8e-14
Identities = 36/255 (14%), Positives = 77/255 (30%), Gaps = 32/255 (12%)
Query: 3 IVITRPIKKAL---RTQEKIQKMGYIPVMMPL---SYFIHDRESVFLAMQQSYGAIAITS 56
+++ + ++ G ++P+ + S L+ + YG + TS
Sbjct: 25 LLLKDAKEDDCGQDPYIRELGLYGLEATLIPVLSFEFLSLPSFSEKLSHPEDYGGLIFTS 84
Query: 57 SESLSTL----------------PANFCRHTPIFAIGEASACLARQKGFTQIFHGKDNSI 100
++ ++ +G A+A L + G N+
Sbjct: 85 PRAVEAAELCLEQNNKTEVWERSLKEKWNAKSVYVVGNATASLVSKIGLDTEGETCGNAE 144
Query: 101 NLAKIIVEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETTM 160
LA+ I ++ PL++ G + L + I + I Y + + +
Sbjct: 145 KLAEYICSRES---SALPLLFPCGNLKREILPKALKDKGIAMESITVYQTVAHPGIQGNL 201
Query: 161 KNLLQNA---DAILFYARSSVLYFFSL----PLPAKISAAFLCLSNNIASAIPASYKNVV 213
+ +I F++ S + Y F + A A+ A V
Sbjct: 202 NSYYSQQGVPASITFFSPSGLTYSLKHIQELSGDNIDQIKFAAIGPTTARALAAQGLPVS 261
Query: 214 TVACFPKETSLLKLL 228
A P +L +
Sbjct: 262 CTAESPTPQALATGI 276
>3p9z_A Uroporphyrinogen III cosynthase (HEMD); MCSG, PSI2, structural
genomics, protein structure initiativ midwest center for
structural genomics; HET: MSE; 2.10A {Helicobacter
pylori}
Length = 229
Score = 59.7 bits (144), Expect = 6e-10
Identities = 32/190 (16%), Positives = 64/190 (33%), Gaps = 14/190 (7%)
Query: 48 SYGAIAITSSES--------LSTLPANFCRHTPIFAIGEASACLARQKGFTQIFHGKDNS 99
+ A+ TS + ++ ++ P +A+ E +A + F F G+
Sbjct: 37 PFNALIFTSKNAVFSLLETLKNSPKLKMLQNIPAYALSEPTAKTLQDHHFKVAFMGEKAH 96
Query: 100 INLAKIIVEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETT 159
K V++ +K ++YL K + L+EH I + Y ++ +
Sbjct: 97 ---GKEFVQEIFPLLEKKSVLYLRAKEIVSSLDTILLEHGIDFKQAVVYENKLKHLTLSE 153
Query: 160 MKNLLQN-ADAILFYARSSVLYFFSLPLPAKISAAFLCLSNNIASAIPASYKNVVTVACF 218
L ++F A S F + + + N A + +A
Sbjct: 154 QNALKPKEKSILIFTAISHAKAFLHY-FEFLENYTAISIGNTTALYLQEQGIPSY-IAKK 211
Query: 219 PKETSLLKLL 228
P + L+L
Sbjct: 212 PSLEACLELA 221
>1wcw_A Uroporphyrinogen III synthase; congenital erythropoietic porphyria,
structural genomics, riken structural
genomics/proteomics initiative; 1.30A {Thermus
thermophilus} PDB: 1wd7_A 1wcx_A
Length = 261
Score = 50.4 bits (120), Expect = 3e-07
Identities = 34/244 (13%), Positives = 70/244 (28%), Gaps = 27/244 (11%)
Query: 1 MYIVITRPIKKALRTQEKIQKMGYIPVMMPLSYF----IHDRESVFLAMQQSYGAIAITS 56
+ + ++ + +K+G+ P++ P+ + + A+ Q T+
Sbjct: 9 VRVAYAGL-RRKEAFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRALAQGVDLFLATT 67
Query: 57 SESLSTL----------PANFCRHTPIFAIGEASACLARQKGFTQIFHGKDNSINLAKII 106
+ L A G +A ++ G G S +L ++
Sbjct: 68 GVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLL 127
Query: 107 VEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETTMKNLLQN 166
+ + + L GKP E+ L E + + Y ++ L
Sbjct: 128 PQGR-----GVAALQLYGKPLPL-LENALAERGYRVLPLMPYRHLPDPEGILRLEEALLR 181
Query: 167 A--DAILFYARSSVLYFFSLPLPAKISAAFLCLSNNIASAIPASYKNV----VTVACFPK 220
DA+ F A V + F K L + + + V +
Sbjct: 182 GEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDE 241
Query: 221 ETSL 224
L
Sbjct: 242 TERL 245
>3d8t_A Uroporphyrinogen-III synthase; heme biosynthesis, lyase; 1.60A
{Thermus thermophilus} PDB: 3d8r_A 3d8s_A 3d8n_A
Length = 286
Score = 48.1 bits (114), Expect = 2e-06
Identities = 36/244 (14%), Positives = 67/244 (27%), Gaps = 27/244 (11%)
Query: 1 MYIVITRPIKKALRTQEKIQKMGYIPVMMPLS--YFIHDRESVFLAMQ--QSYGAIAITS 56
M I ++ + +K+G+ P++ P+ + E + Q T+
Sbjct: 34 MRIAYAGL-RRKEEFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRELAQGVDLFLATT 92
Query: 57 SESLSTLPANFCRH----------TPIFAIGEASACLARQKGFTQIFHGKDNSINLAKII 106
+ L A G +A ++ G G S +L ++
Sbjct: 93 GVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLL 152
Query: 107 VEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYP--ETTMKNLL 164
+ + + L GKP E+ L E + + Y L
Sbjct: 153 PQGR-----GVAALQLYGKPLPL-LENALAERGYRVLPLMPYRHLPDPEGILRLEEAVLR 206
Query: 165 QNADAILFYARSSVLYFFSLPLPAKISAAFLCLSNNIASAIPASYKNV----VTVACFPK 220
DA+ F A V + F K L + + + V +
Sbjct: 207 GEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDE 266
Query: 221 ETSL 224
L
Sbjct: 267 TERL 270
>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 = 33.8 bits (77), Expect = 0.031
Identities = 44/271 (16%), Positives = 76/271 (28%), Gaps = 105/271 (38%)
Query: 9 IKKALRTQEKIQKMGY---IPVMMPL-------SYFI-------HDRESVFLAMQQ---- 47
I + L Y IP+ PL Y + E ++
Sbjct: 215 ILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGE-----LRSYLKG 269
Query: 48 ----SYG---AIAITSSESLSTLPANFCRHTPI---FAIGEASACLARQKGFTQIFHGKD 97
S G A+AI ++S + + I F IG + +
Sbjct: 270 ATGHSQGLVTAVAIAETDSWESFFVSV--RKAITVLFFIGVRC-----YEAYPNTS---- 318
Query: 98 NSINLAKIIVEQKV---LFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVID---CYYSQ 151
L I+E + P P++ + + + + ++ ++ +
Sbjct: 319 ----LPPSILEDSLENNEGVPS-PMLSISNLTQ-----EQVQDY------VNKTNSHLPA 362
Query: 152 D----IAYPETTMKNLLQNADAILFYARSSV-------LYFFSLPLPAKISAAFLCLSNN 200
I+ L N A++ V LY +L L K A S
Sbjct: 363 GKQVEIS---------LVNG------AKNLVVSGPPQSLYGLNLTL-RKAKAP----SGL 402
Query: 201 IASAIPASYKNVVTVACF-----PKETSLLK 226
S IP S + + F P + LL
Sbjct: 403 DQSRIPFSERKLKFSNRFLPVASPFHSHLLV 433
Score = 31.5 bits (71), Expect = 0.16
Identities = 31/208 (14%), Positives = 56/208 (26%), Gaps = 63/208 (30%)
Query: 48 SYGAIAIT------SSESLSTLPANFCRH----TPIFAIGEASAC----LARQKGFTQIF 93
S+G++ S S L F + T FA + + + G+
Sbjct: 12 SHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYV-SS 70
Query: 94 HGKDNSINLAKIIVEQKVL--FTPQKPLIYLGGKPRNFH--FEDYLIEHKIPL----RVI 145
+ + + ++ L F YL G + H L E+ L +I
Sbjct: 71 LVEPSKVGQFDQVL-NLCLTEFENC----YLEGN--DIHALAAKLLQENDTTLVKTKELI 123
Query: 146 DCYY-----SQDIAYPETTMKNLLQNA---DAILFYARSSVL--------YFFSL----- 184
Y ++ + + + L + +A L A + YF L
Sbjct: 124 KNYITARIMAKR-PFDKKSNSALFRAVGEGNAQL-VA---IFGGQGNTDDYFEELRDLYQ 178
Query: 185 -------PLPAKISAAFLCLSNNIASAI 205
L + L A
Sbjct: 179 TYHVLVGDLIKFSAETLSELIRTTLDAE 206
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 29.0 bits (64), Expect = 0.86
Identities = 38/183 (20%), Positives = 69/183 (37%), Gaps = 33/183 (18%)
Query: 38 RESVFLAMQQSYGAIAITSSESLSTLPANFCRHTPIFAIGEASACLARQKGFTQIFHGKD 97
+ES M + I+SS + T P C A++ + G I GK
Sbjct: 1077 QESFINTMSAWVNMLLISSSGPIKT-PVGAC----------ATSVESVDIGVETILSGK- 1124
Query: 98 NSINLAKI-IVEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEH-KIPLRVIDCYYSQDIAY 155
A+I IV F + + K + E++ EH + P +++
Sbjct: 1125 -----ARICIVGGYDDFQEEGSFEFGNMKATSNTLEEF--EHGRTP---------AEMSR 1168
Query: 156 PETTMKNLLQNADA--ILFYARSSVLYFFSLPLPAKISAAFLCLSNNIASAIPASYKNVV 213
P TT +N A I ++ + +P+ ++ A ++ I ++PA K ++
Sbjct: 1169 PATTTRNGFMEAQGAGIQIIMQADLALKMGVPIYGIVAMA-ATATDKIGRSVPAPGKGIL 1227
Query: 214 TVA 216
T A
Sbjct: 1228 TTA 1230
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1
PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C*
2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3dxj_C* 3eql_C*
1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C 1l9z_C 1i6v_C*
Length = 1119
Score = 27.8 bits (61), Expect = 2.4
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 1 MYIVITRPIKKALRTQEKIQKMGYIPVMMPLSYFI 35
+Y + K +E +G+IP+M FI
Sbjct: 94 LYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSFI 128
>1ivz_A Hypothetical protein 1110008I14RIK; structural genomics, SEA
domain, mucin 16, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.41.1
Length = 132
Score = 26.3 bits (57), Expect = 6.2
Identities = 22/56 (39%), Positives = 26/56 (46%), Gaps = 9/56 (16%)
Query: 149 YSQDIAYPETT----MKNLLQNADAILFYARSSVLYFFSLPLPAKISAAFLCLSNN 200
YSQDIA P TT K ++NA LF S YF + AF +SNN
Sbjct: 25 YSQDIAQPSTTKYQQTKRSIENALNQLFRNSSIKSYFSDCQV-----LAFRSVSNN 75
>1tzf_A Glucose-1-phosphate cytidylyltransferase; nucleotidyltransferase,
mixed alpha/beta fold; HET: C5G; 2.10A {Salmonella
enterica subsp} SCOP: c.68.1.13 PDB: 1wvc_A*
Length = 259
Score = 25.8 bits (55), Expect = 8.2
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 117 KPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYY 149
KP++ +GGKP +H H I +I C Y
Sbjct: 25 KPMVEIGGKPILWHIMKMYSVHGIKDFIICCGY 57
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
0.325 0.138 0.405
Gapped
Lambda K H
0.267 0.0530 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,874,483
Number of extensions: 79832
Number of successful extensions: 328
Number of sequences better than 10.0: 1
Number of HSP's gapped: 316
Number of HSP's successfully gapped: 15
Length of query: 232
Length of database: 5,693,230
Length adjustment: 89
Effective length of query: 143
Effective length of database: 3,535,514
Effective search space: 505578502
Effective search space used: 505578502
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.4 bits)