RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 038122
(130 letters)
>1gtk_A Porphobilinogen deaminase; lyase, biosynthesis of linear
tetrapyrrole, all alpha/beta; HET: DPM; 1.66A
{Escherichia coli} SCOP: c.94.1.1 d.50.2.1 PDB: 1ah5_A*
2ypn_A* 1ypn_A* 1pda_A*
Length = 313
Score = 164 bits (418), Expect = 1e-51
Identities = 57/176 (32%), Positives = 71/176 (40%), Gaps = 47/176 (26%)
Query: 2 EEALINGEIDIAVHSMKDVPTYLLDKTILPCNLQRE------------------------ 37
E AL+ DIAVHSMKDVP L +RE
Sbjct: 67 EVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVG 126
Query: 38 -----------------------GNVQARLRKLNEGVIQATLSALAGLKCLNMTENVTNI 74
GNV RL KL+ G A + A+AGLK L + +
Sbjct: 127 TSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAA 186
Query: 75 LPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETRQAVVCERAFLGTLDGSC 130
LP + L AV QGA+GI C +D + + L +LNH ET V ERA L+G C
Sbjct: 187 LPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEGGC 242
>3ecr_A Porphobilinogen deaminase; heme biosynthesis, porphobilinogen
hinge, alternative splicing, cytoplasm, disease
mutation, porphyrin biosynthesis; HET: DPM; 2.18A {Homo
sapiens} PDB: 3eq1_A*
Length = 364
Score = 156 bits (397), Expect = 5e-48
Identities = 50/180 (27%), Positives = 73/180 (40%), Gaps = 51/180 (28%)
Query: 2 EEALINGEIDIAVHSMKDVPTYLLDKTILPCNLQRE------------------------ 37
E AL E+D+ VHS+KD+PT L + +RE
Sbjct: 85 EHALEKNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLETLPEKS 144
Query: 38 --------------------------GNVQARLRKLNE-GVIQATLSALAGLKCLNMTEN 70
GN+ RLRKL+E A + A AGL+ +
Sbjct: 145 VVGTSSLRRAAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQEFSAIILATAGLQRMGWHNR 204
Query: 71 VTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETRQAVVCERAFLGTLDGSC 130
V IL ++ + AV QGA+G+ + D+ + +G L+ ET + ERAFL L+G C
Sbjct: 205 VGQILHPEECMYAVGQGALGVEVRAKDQDILDLVGVLHDPETLLRCIAERAFLRHLEGGC 264
>2o6y_A Putative histidine ammonia-lyase; methylidene imidazolone
prosthetic group; HET: MDO; 1.50A {Rhodobacter
sphaeroides} PDB: 2o7b_A* 2o7d_A* 2o7e_A* 2o78_A*
2o7f_A*
Length = 521
Score = 29.9 bits (68), Expect = 0.22
Identities = 14/61 (22%), Positives = 22/61 (36%), Gaps = 4/61 (6%)
Query: 56 LSALAGLKCLNMTENVTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETRQA 115
L +A C + IL I L +AQ A + C S ++ L + R+
Sbjct: 439 LGTIAARLCREKIDRWAEILAIL--ALCLAQ-AAELRCGSGLDGVSPAGKKL-VQALREQ 494
Query: 116 V 116
Sbjct: 495 F 495
>2qve_A Tyrosine aminomutase; MIO, enediyne, transferase; HET: MDO 247;
2.00A {Streptomyces globisporus} PDB: 2rjr_A* 2rjs_A*
2ohy_A* 3kdz_A* 3kdy_A*
Length = 526
Score = 28.4 bits (64), Expect = 0.70
Identities = 10/61 (16%), Positives = 23/61 (37%), Gaps = 6/61 (9%)
Query: 56 LSALAGLKCLNMTENVTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETRQA 115
+ ++ + N IL ++ LA AQ + + ++ + +E R+
Sbjct: 434 MGLISARNARRVLSNNNKILAVE--YLAAAQ---AVDISGRFDGLSPAAKAT-YEAVRRL 487
Query: 116 V 116
V
Sbjct: 488 V 488
>1gkm_A Histidase, HAL, histidine ammonia-lyase; histidine degradation;
HET: MDO; 1.0A {Pseudomonas putida} SCOP: a.127.1.2 PDB:
1b8f_A* 1gkj_A* 1eb4_A* 1gk3_A 1gk2_A
Length = 507
Score = 28.0 bits (63), Expect = 0.92
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 54 ATLSALAGLKCLNMTENVTNILPIDDMLLAVAQG 87
+++ AG + M EN +L I+ L QG
Sbjct: 415 VSMAPAAGKRLWEMAENTRGVLAIE--WLGACQG 446
>3unv_A ADMH; MIO, lyase; HET: KWS SFE PHE; 1.54A {Pantoea agglomerans}
Length = 547
Score = 28.0 bits (63), Expect = 1.0
Identities = 5/32 (15%), Positives = 11/32 (34%), Gaps = 2/32 (6%)
Query: 56 LSALAGLKCLNMTENVTNILPIDDMLLAVAQG 87
+A + +N+ + + LL Q
Sbjct: 459 FGLVAARRVREQLKNLKYVFSFE--LLCACQA 488
>3krt_A Crotonyl COA reductase; structural genomics, protein structure
initiative, NYSGXRC, PSI-2; 2.19A {Streptomyces
coelicolor} PDB: 3hzz_A
Length = 456
Score = 27.1 bits (60), Expect = 1.7
Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 82 LAVAQGAIGIACTSNDKKM--AKYLG 105
A+A GA I S+ +K + +G
Sbjct: 248 FALAGGANPICVVSSPQKAEICRAMG 273
>2yii_A Phenylalanine ammonia-lyase; HET: MDO; 2.18A {Taxus wallichiana
var} PDB: 3nz4_A*
Length = 705
Score = 27.1 bits (60), Expect = 2.0
Identities = 5/32 (15%), Positives = 13/32 (40%), Gaps = 2/32 (6%)
Query: 56 LSALAGLKCLNMTENVTNILPIDDMLLAVAQG 87
L+ ++ K + + ++ L A+ Q
Sbjct: 482 LALISARKTEEALDILKLMIASH--LTAMCQA 511
>2nyn_A Phenylalanine/histidine ammonia-lyase; methylidene imidazolone
prosthetic group; HET: MDO; 1.90A {Anabaena variabilis}
PDB: 3czo_A* 2nyf_A*
Length = 565
Score = 27.0 bits (59), Expect = 2.0
Identities = 4/32 (12%), Positives = 8/32 (25%), Gaps = 2/32 (6%)
Query: 56 LSALAGLKCLNMTENVTNILPIDDMLLAVAQG 87
+ + N + I L+ Q
Sbjct: 455 QGYTSATLARRSVDIFQNYVAIA--LMFGVQA 484
>1y2m_A Phenylalanine ammonia-lyase; alpha helices; HET: MSE; 1.60A
{Rhodosporidium toruloides} PDB: 1t6j_A* 1t6p_A*
Length = 716
Score = 27.0 bits (60), Expect = 2.1
Identities = 5/32 (15%), Positives = 13/32 (40%), Gaps = 2/32 (6%)
Query: 56 LSALAGLKCLNMTENVTNILPIDDMLLAVAQG 87
L+ ++ + + ++ +L L V Q
Sbjct: 505 LALISARRTTESNDVLSLLLATH--LYCVLQA 534
>3uog_A Alcohol dehydrogenase; structural genomics, protein structure
initiative, PSI-biolo YORK structural genomics research
consortium; 2.20A {Sinorhizobium meliloti 1021}
Length = 363
Score = 26.4 bits (59), Expect = 3.3
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 82 LAVAQGAIGIACTSNDKKMAK 102
+A A GA I +S+ +K+ +
Sbjct: 208 IAKATGAEVIVTSSSREKLDR 228
>4a0s_A Octenoyl-COA reductase/carboxylase; oxidoreductase, transferase,
cinnabaramide PKS biosynthesis; HET: CO8 NAP; 1.90A
{Streptomyces SP} PDB: 4a10_A
Length = 447
Score = 25.9 bits (57), Expect = 4.0
Identities = 6/21 (28%), Positives = 9/21 (42%)
Query: 82 LAVAQGAIGIACTSNDKKMAK 102
G I +A S+ +K A
Sbjct: 240 FVKNGGGIPVAVVSSAQKEAA 260
>2y7p_A LYSR-type regulatory protein; transcription regulator,
DNA-binding, transcription, transcr factor,
transcription regulation; HET: SAL PEU; 1.85A
{Burkholderia SP} PDB: 2y7k_A* 2y84_A 2y7w_A 2y7r_A
Length = 218
Score = 24.9 bits (55), Expect = 7.5
Identities = 4/21 (19%), Positives = 13/21 (61%)
Query: 1 TEEALINGEIDIAVHSMKDVP 21
+E + +G +D+A+ + ++
Sbjct: 49 LKEDMESGAVDLALGLLPELQ 69
>3dpi_A NAD+ synthetase; ssgcid, decode, structural genomics, PSI, protein
structure initiative; 2.20A {Burkholderia pseudomallei}
Length = 285
Score = 25.0 bits (55), Expect = 8.8
Identities = 17/112 (15%), Positives = 36/112 (32%), Gaps = 31/112 (27%)
Query: 9 EIDIAVHSMKD-VPTYLLDKTILPCNLQREGNVQARLRKLNEGVIQATLSALAGLKCL-- 65
++ A +M + L GN++AR R + Q ++ +
Sbjct: 114 DVKPAADAMLAALAAGGLAYLDHAQQDFVLGNIKARER----MIAQYAVAGARNGVVIGT 169
Query: 66 -NMTENVT-----------NILPIDDMLLAVAQGAIGIACTSNDKKMAKYLG 105
+ E+V ++LP+ L + + +A+ LG
Sbjct: 170 DHAAESVMGFFTKFGDGGADVLPLAG--LTKRRV----------RALARMLG 209
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
0.318 0.134 0.378
Gapped
Lambda K H
0.267 0.0634 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,895,586
Number of extensions: 103141
Number of successful extensions: 304
Number of sequences better than 10.0: 1
Number of HSP's gapped: 302
Number of HSP's successfully gapped: 26
Length of query: 130
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 47
Effective length of database: 4,384,350
Effective search space: 206064450
Effective search space used: 206064450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.0 bits)