RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10208
(143 letters)
>3mad_A Sphingosine-1-phosphate lyase; carboxy-lyase activity, pyridoxal
phosphate; HET: LLP; 2.00A {Symbiobacterium
thermophilum} PDB: 3maf_A* 3mau_A* 3mbb_A*
Length = 514
Score = 136 bits (343), Expect = 7e-39
Identities = 41/141 (29%), Positives = 75/141 (53%), Gaps = 3/141 (2%)
Query: 3 YVNTTRSIIETVKYIEKELRSMDGLFIFGTPATSVIALGSDVFHIYRLSSGLNKRGWNTN 62
Y++ TR I++ ++ +R++ L I G P VIA+ SD +IY++ + RGW N
Sbjct: 375 YLDATRRILQAADRLKAGVRAIPSLKILGDP-LWVIAVASDELNIYQVMEEMAGRGWRLN 433
Query: 63 SLQFPVGIHICITHMHTQPGVADKFISDVREELAIIMQNPGLQLEGVMAMYGKSHSIPDR 122
L P H+ +T HT+PGV D+F++D+++ +A + +P + G+ +YG + + P
Sbjct: 434 GLHRPPAFHVALTLRHTEPGVVDRFLADLQDAVAQVRAHPE-KATGMAPVYGMAAAAPPE 492
Query: 123 SIIGDFTRYYIDATYYTPDSK 143
++ +ID Y
Sbjct: 493 -LVRQVLTGFIDLLYEVHHHH 512
>3mc6_A Sphingosine-1-phosphate lyase; carboxy-lyase activity, pyridoxyl
phosphate; HET: LLP; 3.15A {Saccharomyces cerevisiae}
Length = 497
Score = 132 bits (333), Expect = 1e-37
Identities = 36/141 (25%), Positives = 66/141 (46%), Gaps = 5/141 (3%)
Query: 3 YVNTTRSIIETVKYIEKELR-SMDGLFIFGTPATSVIALGSDVFHIYRLSSGLNKRGWNT 61
Y+ + + I+ +K ++ ++ L I G P SVI+ S +I+ LS L+K+GW+
Sbjct: 343 YIESCQEIVGAAMKFKKYIQENIPDLDIMGNPRYSVISFSSKTLNIHELSDRLSKKGWHF 402
Query: 62 NSLQFPVGIHICITHMHTQPGVADKFISDVREELAIIMQNPG--LQLEGVMAMYGKSHSI 119
N+LQ PV +H+ T + V D+ +R + + +G A+YG + S+
Sbjct: 403 NALQKPVALHMAFTRLS--AHVVDEICDILRTTVQELKSESNSKPSPDGTSALYGVAGSV 460
Query: 120 PDRSIIGDFTRYYIDATYYTP 140
+ ++DA Y
Sbjct: 461 KTAGVADKLIVGFLDALYKLG 481
>3hbx_A GAD 1, glutamate decarboxylase 1; calmodulin-binding, lyase,
pyridoxal phosphate; HET: LLP; 2.67A {Arabidopsis
thaliana}
Length = 502
Score = 98.2 bits (244), Expect = 5e-25
Identities = 22/133 (16%), Positives = 47/133 (35%), Gaps = 9/133 (6%)
Query: 3 YVNTTRSIIETVKYIEKELRSMDGLFIF----GTPATSVIALGSDVFHIYRLSSGLNKRG 58
Y N + E + + + L + I G P + S + +S L + G
Sbjct: 340 YRNVMENCRENMIVLREGLEKTERFNIVSKDEGVPLVAFSLKDSSCHTEFEISDMLRRYG 399
Query: 59 WNTNSLQF-PVGIHICITHMHTQPGV----ADKFISDVREELAIIMQNPGLQLEGVMAMY 113
W + P HI + + + A++ + D+ + + + + P + +
Sbjct: 400 WIVPAYTMPPNAQHITVLRVVIREDFSRTLAERLVIDIEKVMRELDELPSRVIHKISLGQ 459
Query: 114 GKSHSIPDRSIIG 126
KS S D ++
Sbjct: 460 EKSESNSDNLMVT 472
>2dgk_A GAD-beta, GADB, glutamate decarboxylase beta; gadbd1-14,
autoinhibition, substituted aldamine, lyase; HET: PLP;
1.90A {Escherichia coli} PDB: 2dgm_A* 1pmo_A* 2dgl_A*
1pmm_A* 3fz6_A* 3fz7_A 3fz8_A* 1xey_A*
Length = 452
Score = 78.5 bits (193), Expect = 4e-18
Identities = 22/130 (16%), Positives = 42/130 (32%), Gaps = 16/130 (12%)
Query: 3 YVNTTRSIIETVKYIEKELRSMDG--LFIFGTPATSVIALGS-------DVFHIYRLSSG 53
Y + + Y+ E+ + G P + A+ + +Y LS
Sbjct: 325 YTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSER 384
Query: 54 LNKRGWNTNSLQFP-VGIHICITHMHTQPG----VADKFISDVREELAIIMQNPGLQLEG 108
L RGW + I + + + G A+ + D + L + +P LQ
Sbjct: 385 LRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIA 444
Query: 109 VMAMYGKSHS 118
+ H+
Sbjct: 445 QQNSF--KHT 452
>3f9t_A TDC, L-tyrosine decarboxylase MFNA; NP_247014.1, L-tyrosine
decarboxylase MFNA (EC 4.1.1.25), ST genomics; HET: PLP;
2.11A {Methanocaldococcus jannaschii}
Length = 397
Score = 76.6 bits (189), Expect = 2e-17
Identities = 14/91 (15%), Positives = 29/91 (31%), Gaps = 4/91 (4%)
Query: 3 YVNTTRSIIETVKYIEKELRSMDGLFIFGTPATSVIALGSDVFHIYRLSSGLNKRGWNTN 62
+E Y+ K+L+ P +++A+ + + L RG +
Sbjct: 307 QRKIVNECMENTLYLYKKLKEN-NFKPVIEPILNIVAIEDE--DYKEVCKKLRDRGIYVS 363
Query: 63 SLQFPVGIHICITHMHTQPGVADKFISDVRE 93
+ I + H + D FI +
Sbjct: 364 VCNCVKALRIVVMP-HIKREHIDNFIEILNS 393
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 34.8 bits (79), Expect = 0.006
Identities = 23/149 (15%), Positives = 49/149 (32%), Gaps = 37/149 (24%)
Query: 2 SYVNTTRSIIETVKYIEKELRSMDGLFIFGTPATSVIALGSDVFHIYRLSSGLNKRGWNT 61
S + + +I + I+ ELR L ++ L +V N
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRR---LLKSKPYENCLLVL-LNV--------------QNA 256
Query: 62 NSLQ-FPVGIHICITHMHTQ-PGVADKFISDVREELAIIMQNPGL---QLEGVMAMY--G 114
+ F + I +T T+ V D + +++ + L +++ ++ Y
Sbjct: 257 KAWNAFNLSCKILLT---TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDC 313
Query: 115 KSHSIPDR---------SIIGDFTRYYID 134
+ +P SII + R +
Sbjct: 314 RPQDLPREVLTTNPRRLSIIAESIRDGLA 342
Score = 31.7 bits (71), Expect = 0.073
Identities = 23/142 (16%), Positives = 47/142 (33%), Gaps = 37/142 (26%)
Query: 5 NTTRSIIETVKYIEK---ELRSMDGLFIFGTPAT--SVIALGSDVFHIYRLSSGLNKRGW 59
N +R ++ + + ELR + I G + + +AL DV Y++
Sbjct: 130 NVSR--LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVAL--DVCLSYKVQC------- 178
Query: 60 NTNSLQFPVGIH-ICITHMHTQPGVADKFISDVREELAIIMQNPGLQLEGVMAMYGK-SH 117
+ I + + + ++ E + ++Q Q++ S
Sbjct: 179 -----KMDFKIFWLNLKNCNSP------------ETVLEMLQKLLYQIDPNWTSRSDHSS 221
Query: 118 SIPDR--SIIGDFTRYYIDATY 137
+I R SI + R Y
Sbjct: 222 NIKLRIHSIQAELRRLLKSKPY 243
>3cai_A Possible aminotransferase; RV3778C; 1.80A {Mycobacterium
tuberculosis}
Length = 406
Score = 31.8 bits (73), Expect = 0.055
Identities = 10/47 (21%), Positives = 17/47 (36%), Gaps = 2/47 (4%)
Query: 14 VKYIEKELRSMDGLFIFGTPA--TSVIALGSDVFHIYRLSSGLNKRG 58
Y+ LRS+ + + G P V++ R+ L G
Sbjct: 312 FDYLMVSLRSLPLVMLIGRPEAQIPVVSFAVHKVPADRVVQRLADNG 358
>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 = 30.0 bits (67), Expect = 0.26
Identities = 27/140 (19%), Positives = 48/140 (34%), Gaps = 40/140 (28%)
Query: 14 VKYIEKELR-SMDGLFIFGTPATSVIALGSDVFH-------IYRLSSGLNKRG--WNTNS 63
+ + E++L+ S L + +P FH ++ L K +N
Sbjct: 407 IPFSERKLKFSNRFLPVA-SP-----------FHSHLLVPASDLINKDLVKNNVSFNAKD 454
Query: 64 LQFPVGIHICITHMHTQPGVAD--KFISDVREELA-IIMQNPGLQLEGVMAMYGKSHSI- 119
+Q PV T G +D + E + I++ P ++ E +H +
Sbjct: 455 IQIPV--------YDTFDG-SDLRVLSGSISERIVDCIIRLP-VKWETTTQF-KATHILD 503
Query: 120 --PDR-SIIGDFTRYYIDAT 136
P S +G T D T
Sbjct: 504 FGPGGASGLGVLTHRNKDGT 523
>1xfc_A Alanine racemase; alpha-beta barrel, beta-structure for C-terminal
domain, INT aldimine form, isomerase; HET: PLP; 1.90A
{Mycobacterium tuberculosis}
Length = 384
Score = 27.5 bits (62), Expect = 1.6
Identities = 9/59 (15%), Positives = 18/59 (30%), Gaps = 13/59 (22%)
Query: 63 SLQFPVGIHICI-THMH---TQPGVADKFISDVREELAIIMQNPGLQLEGVMAMYGKSH 117
+ + + T ++ P + L M ++L G+M SH
Sbjct: 123 RTGRTATVTVKVDTGLNRNGVGPAQFPAML----TALRQAMAEDAVRLRGLM-----SH 172
>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 = 27.2 bits (59), Expect = 1.8
Identities = 6/34 (17%), Positives = 17/34 (50%), Gaps = 8/34 (23%)
Query: 12 ETVKYIEKELRSMDGLFIFGT-PATSVIALGSDV 44
+ +K ++ L+ L+ + PA +A+ + +
Sbjct: 20 QALKKLQASLK----LYADDSAPA---LAIKATM 46
Score = 26.1 bits (56), Expect = 3.7
Identities = 6/33 (18%), Positives = 12/33 (36%), Gaps = 12/33 (36%)
Query: 105 QLEGVMAMYGKSHSIPDRS-IIGDFTRYYIDAT 136
+L+ + +Y D + + I AT
Sbjct: 24 KLQASLKLYA-----DDSAPALA------IKAT 45
>1kmj_A Selenocysteine lyase; persulfide perselenide NIFS pyridoxal
phosphate, structural PSI, protein structure initiative;
HET: PLP; 2.00A {Escherichia coli} SCOP: c.67.1.3 PDB:
1i29_A* 1jf9_A* 1kmk_A* 1c0n_A*
Length = 406
Score = 27.1 bits (61), Expect = 2.1
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 14 VKYIEKELRSMDGLFIFGTPA-TSVIALGSDVFHIYRLSSGLNKRG 58
+ Y +L S+ L ++G VIA H Y + S L+ G
Sbjct: 310 MHYALSQLESVPDLTLYGPQNRLGVIAFNLGKHHAYDVGSFLDNYG 355
>2e7y_A TRNAse Z; tRNA maturation, metallo-beta-lactaMSe, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; 1.97A {Thermotoga
maritima} SCOP: d.157.1.7 PDB: 1ww1_A
Length = 280
Score = 26.9 bits (60), Expect = 2.3
Identities = 3/8 (37%), Positives = 6/8 (75%)
Query: 71 HICITHMH 78
++ +TH H
Sbjct: 43 YVFLTHGH 50
>3zwf_A Zinc phosphodiesterase ELAC protein 1; beta-lactamase, hydrolase,
metal-binding, tRNA processing, zinc-binding,
catabolism; 1.70A {Homo sapiens}
Length = 368
Score = 27.1 bits (60), Expect = 2.3
Identities = 5/8 (62%), Positives = 6/8 (75%)
Query: 71 HICITHMH 78
I ITH+H
Sbjct: 55 KIFITHLH 62
>1vfs_A Alanine racemase; TIM-barrel, greek-KEY motief, isomerase; HET: KCX
DCS; 1.90A {Streptomyces lavendulae} SCOP: b.49.2.2
c.1.6.1 PDB: 1vfh_A* 1vft_A*
Length = 386
Score = 27.1 bits (61), Expect = 2.5
Identities = 9/55 (16%), Positives = 15/55 (27%), Gaps = 13/55 (23%)
Query: 67 PVGIHICI-THMH---TQPGVADKFISDVREELAIIMQNPGLQLEGVMAMYGKSH 117
I + T + QP + + +Q+ GV SH
Sbjct: 123 TARIQLKADTGLGRNGCQPADWAELV----GAAVAAQAEGTVQVTGVW-----SH 168
>3sy1_A UPF0001 protein YGGS; engineered protein, structural genomics,
PSI-biology, protei structure initiative; HET: MES;
1.47A {Escherichia coli} PDB: 1w8g_A*
Length = 245
Score = 25.6 bits (57), Expect = 5.7
Identities = 7/24 (29%), Positives = 15/24 (62%)
Query: 89 SDVREELAIIMQNPGLQLEGVMAM 112
+++ E A + + P L+L G+ A+
Sbjct: 144 AELDELAAAVAELPRLRLRGLSAI 167
>3cpg_A Uncharacterized protein; unknown protein, TIM barrel, monomer,
structural genomics, PSI-2, protein structure
initiative; 1.71A {Bifidobacterium adolescentis
ATCC15703}
Length = 282
Score = 25.7 bits (57), Expect = 5.7
Identities = 5/24 (20%), Positives = 11/24 (45%)
Query: 89 SDVREELAIIMQNPGLQLEGVMAM 112
+ I G++L+G+M +
Sbjct: 181 AHAIRIAQKIGTLDGIELQGLMTI 204
>2cbn_A Ribonuclease Z; phosphodiesterase beta lactamase tRNAse Z,
hydrolase, metal- binding, endonuclease, tRNA
processing, zinc; 2.9A {Escherichia coli} SCOP:
d.157.1.7
Length = 306
Score = 25.8 bits (57), Expect = 6.1
Identities = 4/8 (50%), Positives = 6/8 (75%)
Query: 71 HICITHMH 78
I I+H+H
Sbjct: 60 KIFISHLH 67
>1t3i_A Probable cysteine desulfurase; PLP-binding enzyme, transferase;
HET: 2OS PLP; 1.80A {Synechocystis SP} SCOP: c.67.1.3
Length = 420
Score = 25.9 bits (58), Expect = 6.1
Identities = 7/52 (13%), Positives = 21/52 (40%), Gaps = 5/52 (9%)
Query: 12 ETVKYIEKELRSMDGLFIFGTPA-----TSVIALGSDVFHIYRLSSGLNKRG 58
E Y+ + L + L ++G ++ + H +++ +++ G
Sbjct: 312 ELTHYLWQGLGQIPQLRLYGPNPKHGDRAALASFNVAGLHASDVATMVDQDG 363
>2rff_A Putative nucleotidyltransferase; NP_343093.1,
nucleotidyltransferase domain, structural genomics;
HET: MSE; 1.40A {Sulfolobus solfataricus P2}
Length = 111
Score = 25.0 bits (54), Expect = 6.2
Identities = 9/43 (20%), Positives = 20/43 (46%)
Query: 2 SYVNTTRSIIETVKYIEKELRSMDGLFIFGTPATSVIALGSDV 44
S + + E V+ + +++ ++IFG+ A SD+
Sbjct: 11 SQIRMLKLAKEIVEEVASSFPNLEEVYIFGSRARGDYLDTSDI 53
>4a3q_A Alanine racemase 1; isomerase, PLP-dependent enzymes; HET: PLP;
2.15A {Staphylococcus aureus} PDB: 3oo2_A
Length = 382
Score = 25.5 bits (57), Expect = 8.0
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 9/52 (17%)
Query: 67 PVGIHICI-THMHTQPGVADKFISDVREELAIIMQNPGLQLEGVMAMYGKSH 117
+ +HI + T M + G+ D + +E + II Q L EGV +H
Sbjct: 125 KLWLHIKLDTGMG-RLGIKDT--NTYQEVIEIIQQYEQLVFEGVF-----TH 168
>2oze_A ORF delta'; para, walker type atpases, DNA segregation, PSM19035,
plasmid, DNA binding protein; HET: AGS EPE; 1.83A
{Streptococcus pyogenes}
Length = 298
Score = 25.3 bits (56), Expect = 8.1
Identities = 7/27 (25%), Positives = 13/27 (48%), Gaps = 6/27 (22%)
Query: 88 ISDVREELAIIMQNPGLQLEGV-MAMY 113
+ D++E+ NPGL + G +
Sbjct: 201 LIDLQEQF-----NPGLDMIGFVPYLV 222
>2c0j_B R32611_2; palmitate; HET: PLM; 2.20A {Homo sapiens} PDB: 2j3t_B*
Length = 160
Score = 25.2 bits (55), Expect = 8.1
Identities = 12/74 (16%), Positives = 25/74 (33%), Gaps = 12/74 (16%)
Query: 5 NTTRSIIETVKYIEKELRSMDGLFIFGTPATSVIALGSDVFHIY--------RLSSGLNK 56
R ++ +K++ K+L +F S+ + + ++SGL
Sbjct: 58 LAFREELDVLKFLCKDLWVA----VFQKQMDSLRTNHQGTYVLQDNSFPLLLPMASGLQY 113
Query: 57 RGWNTNSLQFPVGI 70
L F G+
Sbjct: 114 LEEAPKFLAFTCGL 127
>1bd0_A Alanine racemase; isomerase, pyridoxal phosphate, alanine
phosphonate; HET: IN5; 1.60A {Geobacillus
stearothermophilus} SCOP: b.49.2.2 c.1.6.1 PDB: 1sft_A*
2sfp_A* 1l6g_A* 1niu_A* 1l6f_A* 1xql_A* 1xqk_A* 1epv_A*
1ftx_A* 3uw6_A
Length = 388
Score = 25.1 bits (56), Expect = 8.9
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 9/56 (16%)
Query: 63 SLQFPVGIHICI-THMHTQPGVADKFISDVREELAIIMQNPGLQLEGVMAMYGKSH 117
S FP+ H+ + T M + GV D+ + + +A+I ++P LEG+ +H
Sbjct: 119 SGPFPIHFHLKMDTGMG-RLGVKDE--EETKRIVALIERHPHFVLEGLY-----TH 166
>1y44_A Ribonuclease Z; zinc-dependent metal hydrolase, hydrolase; HET:
MES; 2.10A {Bacillus subtilis} SCOP: d.157.1.7 PDB:
2fk6_A*
Length = 320
Score = 25.1 bits (55), Expect = 9.0
Identities = 6/8 (75%), Positives = 6/8 (75%)
Query: 71 HICITHMH 78
I ITHMH
Sbjct: 58 KIFITHMH 65
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
0.321 0.138 0.407
Gapped
Lambda K H
0.267 0.0837 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,220,738
Number of extensions: 124536
Number of successful extensions: 252
Number of sequences better than 10.0: 1
Number of HSP's gapped: 243
Number of HSP's successfully gapped: 34
Length of query: 143
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 59
Effective length of database: 4,356,429
Effective search space: 257029311
Effective search space used: 257029311
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 (21.9 bits)
S2: 52 (23.6 bits)