RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12858
(131 letters)
>1pj5_A N,N-dimethylglycine oxidase; channelling, FAD binding, folate
binding, amine oxidase, oxidoreductase; HET: FAD; 1.61A
{Arthrobacter globiformis} SCOP: b.44.2.1 c.3.1.2
d.16.1.5 d.250.1.1 PDB: 1pj6_A* 1pj7_A* 3gsi_A*
Length = 830
Score = 117 bits (295), Expect = 6e-32
Identities = 29/108 (26%), Positives = 48/108 (44%), Gaps = 12/108 (11%)
Query: 5 KDYFIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYG 64
K+ FIGK AL+ + ++ +RL +D + G EP++ +Q VG +TSA YG
Sbjct: 725 KESFIGKGALEGRTEEASARRLRCLTIDDGRSI----VLGKEPVFYKEQAVGYVTSAAYG 780
Query: 65 FTMKKLIGLGYIRHPSEQNVTNDFVTEGTYTLDVAGNRFQASAHIYPP 112
+T+ K I Y+ + ++ G R A+ P
Sbjct: 781 YTVAKPIAYSYLP--------GTVSVGDSVDIEYFGRRITATVTEDPL 820
>3tfi_A GCVT-like aminomethyltransferase protein; demethylase, THF; 1.60A
{Candidatus pelagibacter ubique} PDB: 3tfh_A 3tfj_A*
Length = 369
Score = 60.2 bits (147), Expect = 5e-12
Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 8 FIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYGFTM 67
F+GK L+ K +G QK+L + + N+ +G + SA Y
Sbjct: 274 FLGKEKLKEIKLKGPQKKLRGVKIDIKEISLTGSKN---IYDENNNVIGELRSACYSPHF 330
Query: 68 KKLIGLGYIRHP 79
+K+IG+ I+
Sbjct: 331 QKVIGIAMIKKS 342
>3ttg_A Putative aminomethyltransferase; structural genomics, PSI-biology,
midwest center for structu genomics, MCSG; 2.00A
{Leptospirillum rubarum}
Length = 355
Score = 57.6 bits (140), Expect = 5e-11
Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 8/77 (10%)
Query: 5 KDYFIGKAALQRQKDQG-VQKRLVMFVAED---LDPDTDVWLWGSEPIYRNDQFVGTITS 60
K ++G+ + R K QG + + L F E + V L+ ++ G +T
Sbjct: 257 KGCYVGQEPVTRLKFQGHLNRSLAGFRLEGGPFPKMEFPVTLFNP----KDGNEAGILTR 312
Query: 61 AGYGFTMKKLIGLGYIR 77
+ IGLGYI+
Sbjct: 313 TSSSDILGSGIGLGYIK 329
>1yx2_A Aminomethyltransferase; glycine cleavage system T protein,
alpha-beta, beta-barrel, structural genomics, PSI,
protein structure initiative; 2.08A {Bacillus subtilis}
Length = 365
Score = 57.1 bits (139), Expect = 7e-11
Identities = 20/102 (19%), Positives = 41/102 (40%), Gaps = 20/102 (19%)
Query: 8 FIGKAALQRQKDQGVQKRLVMFVAED---LDPDTDVWLWGSEPIYRNDQFVGTITSAGYG 64
F GK+ L QK+ G +++LV + +++N + VG +T+
Sbjct: 270 FFGKSVLSEQKENGAKRKLVGLEMIEKGIPRHGY--------EVFQNGKSVGKVTTGTQS 321
Query: 65 FTMKKLIGLGYIRHPSEQNVTNDFVTEGT-YTLDVAGNRFQA 105
T+ K +GL + ++ GT +++ +A
Sbjct: 322 PTLGKNVGLAL--------IDSETSEIGTVVDVEIRKKLVKA 355
>1v5v_A Aminomethyltransferase; glycine-cleavage sytem, structural riken
structural genomics/proteomics initiative, RSGI; 1.50A
{Pyrococcus horikoshii} SCOP: b.44.2.1 d.250.1.1
Length = 401
Score = 56.9 bits (138), Expect = 8e-11
Identities = 28/102 (27%), Positives = 46/102 (45%), Gaps = 15/102 (14%)
Query: 5 KDYFIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYG 64
KD FIGK AL +QK++GV ++LV F D +Y N + +G +TS
Sbjct: 295 KD-FIGKDALLKQKERGVGRKLVHFKMIDKGI-----PREGYKVYANGEMIGEVTSGTLS 348
Query: 65 FTMKKLIGLGYIRHPSEQNVTNDFVTEGT-YTLDVAGNRFQA 105
+ IG+ + V ++ G +++ G R +A
Sbjct: 349 PLLNVGIGIAF--------VKEEYAKPGIEIEVEIRGQRKKA 382
>1wsr_A Aminomethyltransferase; glycine-cleavage sytem; 2.00A {Homo
sapiens} PDB: 1wsv_A*
Length = 375
Score = 56.7 bits (138), Expect = 1e-10
Identities = 26/119 (21%), Positives = 42/119 (35%), Gaps = 24/119 (20%)
Query: 8 FIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYGFTM 67
F G + Q VQ+R V + E S + +GT+TS ++
Sbjct: 274 FPGAKVIVPQLKGRVQRRRVGLMCEGAPMRA-----HSPILNMEGTKIGTVTSGCPSPSL 328
Query: 68 KKLIGLGYIRHPSEQNVTNDFVTEGT-YTLDVAGNRFQASAHIYPPLSNVQVARPYVPQ 125
KK + +GY V ++ GT ++V + A V P+VP
Sbjct: 329 KKNVAMGY--------VPCEYSRPGTMLLVEVRRKQQMA----------VVSKMPFVPT 369
>3gir_A Aminomethyltransferase; glycine cleavage system, aminotransferase,
structural genomics; 1.60A {Bartonella henselae}
Length = 393
Score = 54.1 bits (131), Expect = 8e-10
Identities = 22/122 (18%), Positives = 38/122 (31%), Gaps = 29/122 (23%)
Query: 8 FIGKAALQRQKDQGVQKRLVMFVAEDLDP---DTDVWLWGSEPIYRNDQFVGTITSAGYG 64
F G A +G + V + P ++ I G +TS G+G
Sbjct: 292 FYGAKAFLESLQKGPSRCRVGLKPQTRQPIRAGAVLFDNEGNRI-------GVVTSGGFG 344
Query: 65 FTMKKLIGLGYIRHPSEQNVTNDFVTEGT-YTLDVAGNRFQASAHIYPPLSNVQVARPYV 123
+ + +GY V + EGT ++ G + + P+V
Sbjct: 345 PSFDGPVAMGY--------VPVAWKVEGTEVFTELRGKKIAL----------SVHSLPFV 386
Query: 124 PQ 125
Q
Sbjct: 387 EQ 388
>1vlo_A Aminomethyltransferase; NP417381, tetrahydrofolat dependent) of
glycine cleavage system, structural genomics, protein
structure initiative; HET: MSE; 1.70A {Escherichia coli
K12} SCOP: b.44.2.1 d.250.1.1 PDB: 3a8j_A* 3a8i_A*
3a8k_A*
Length = 381
Score = 52.5 bits (127), Expect = 3e-09
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 8 FIGKAALQRQKDQGVQKRLVMFVAED---LDPDTDVWLWGSEPIYRNDQFVGTITSAGYG 64
FIG+ AL+ Q++ G ++LV V + L + V ++ +Q G ITS +
Sbjct: 276 FIGREALEVQREHGT-EKLVGLVMTEKGVLRNELPVRFTDAQ----GNQHEGIITSGTFS 330
Query: 65 FTMKKLIGLGYI 76
T+ I L +
Sbjct: 331 PTLGYSIALARV 342
>1wos_A Aminomethyltransferase; T-protein; 1.84A {Thermotoga maritima}
SCOP: b.44.2.1 d.250.1.1 PDB: 1woo_A* 1wop_A* 1wor_A
Length = 364
Score = 52.5 bits (127), Expect = 3e-09
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 13/75 (17%)
Query: 5 KDYFIGKAALQRQKDQGVQKRLVMFVAED---LDPDTDVWLWGSEPIYRNDQFVGTITSA 61
KD F+GK AL + K + V+++LV + +N + VG ITS
Sbjct: 262 KD-FVGKEALLKAK-EKVERKLVALELSGKRIARKGY--------EVLKNGERVGEITSG 311
Query: 62 GYGFTMKKLIGLGYI 76
+ T+ K I L +
Sbjct: 312 NFSPTLGKSIALALV 326
>2gag_A Heterotetrameric sarcosine oxidase alpha-subunit; flavoenzyme,
electron transfer, folate-ME enzyme, oxidoreductase;
HET: NAD FAD FMN; 1.85A {Stenotrophomonas maltophilia}
PDB: 2gah_A* 1x31_A* 1vrq_A* 3ad7_A* 3ad8_A* 3ad9_A*
3ada_A*
Length = 965
Score = 36.1 bits (83), Expect = 0.002
Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 6/78 (7%)
Query: 5 KDYFIGKAALQR-QKDQGVQKRLVMFVAED----LDPDTDVWLWGSEPIYRNDQFVGTIT 59
KD FIG + R + +K+LV + D L + + G +T
Sbjct: 851 KD-FIGNRSYSRADNAREDRKQLVSVLPVDKSLRLPEGAALVASDALASEGITPMEGWVT 909
Query: 60 SAGYGFTMKKLIGLGYIR 77
S+ + + GL I+
Sbjct: 910 SSYDSPNLGRTFGLALIK 927
>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 = 32.5 bits (73), Expect = 0.035
Identities = 19/114 (16%), Positives = 34/114 (29%), Gaps = 29/114 (25%)
Query: 28 MFVAEDLD-----PDTD------VWLWGSEPIYRNDQFVGTITSAGYGFTMKKLIGLGYI 76
+ E++D D W S+ +FV + Y F M +
Sbjct: 45 ILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPI--KTEQ 102
Query: 77 RHPSEQNVTNDFVTEGTYTLDVAGNRFQASAHIYPPLSNVQVARPYVPQVVNKI 130
R PS T ++ + +R ++ V+R Q K+
Sbjct: 103 RQPSMM--TRMYIEQ--------RDRLYNDNQVFAKY---NVSR---LQPYLKL 140
>1nc5_A Hypothetical protein YTER; structural genomics, helix barrel, PSI,
protein structure initiative, midwest center for
structural genomics, MCSG; 1.60A {Bacillus subtilis}
SCOP: a.102.1.6 PDB: 2d8l_A* 2gh4_A*
Length = 373
Score = 27.4 bits (60), Expect = 1.4
Identities = 12/62 (19%), Positives = 27/62 (43%)
Query: 15 QRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYGFTMKKLIGLG 74
R + + ++ + D +T +W + R+D ++ + S Y + + K I G
Sbjct: 235 NRHVWKNTLQDMIKSICRYQDKETGLWYQIVDKGDRSDNWLESSGSCLYMYAIAKGINKG 294
Query: 75 YI 76
Y+
Sbjct: 295 YL 296
>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 = 27.3 bits (60), Expect = 1.6
Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 16/78 (20%)
Query: 38 TDVWLWGSEPIYRNDQFVGTITSAGYGFTMK-------KLIG--LGYIRHPSEQNVTNDF 88
T + S+ +QF + GF +L+G LGY+ E + F
Sbjct: 24 TASFFIASQ---LQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQF 80
Query: 89 VTEGTYTLDVAGNRFQAS 106
L++ F+
Sbjct: 81 ----DQVLNLCLTEFENC 94
>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 = 26.1 bits (56), Expect = 3.3
Identities = 6/33 (18%), Positives = 12/33 (36%), Gaps = 12/33 (36%)
Query: 15 QRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEP 47
++Q + +Q L ++ D S P
Sbjct: 18 EKQALKKLQASLKLYA-----DD-------SAP 38
Score = 25.3 bits (54), Expect = 5.6
Identities = 6/31 (19%), Positives = 11/31 (35%), Gaps = 9/31 (29%)
Query: 102 RFQASAHIYPPLSNVQVARPYVPQV-VNKII 131
+ QAS +Y S P + + +
Sbjct: 24 KLQASLKLYADDS--------APALAIKATM 46
>4a17_O RPL19, 60S ribosomal protein L5; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila}
Length = 185
Score = 25.8 bits (56), Expect = 4.0
Identities = 12/55 (21%), Positives = 21/55 (38%), Gaps = 10/55 (18%)
Query: 23 QKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYGFTMKKLIGLGYIR 77
QKRL V G + ++ + I+ A +++KLI G +
Sbjct: 7 QKRLAA----------SVLKCGQKRLWLDPNESSEISMANSRASIRKLIKDGLVM 51
>3gzk_A Cellulase; fold from GH9 from CAZY database, glycosidase,
hydrolase; 1.80A {Alicyclobacillus acidocaldarius subsp}
PDB: 3ez8_A 3h2w_A* 3h3k_A* 3rx5_A* 3rx7_A* 3rx8_A*
Length = 537
Score = 25.5 bits (56), Expect = 6.0
Identities = 8/26 (30%), Positives = 8/26 (30%), Gaps = 2/26 (7%)
Query: 87 DFVTEGTYTLDVAGN--RFQASAHIY 110
GTYTL V R Y
Sbjct: 63 ALRVPGTYTLTVGTLEARVVIHRRAY 88
>3uaq_A LBPB B-LOBE; beta barrel, lipoprotein, protein binding; 2.93A
{Moraxella bovis}
Length = 341
Score = 25.2 bits (54), Expect = 7.2
Identities = 12/43 (27%), Positives = 17/43 (39%)
Query: 65 FTMKKLIGLGYIRHPSEQNVTNDFVTEGTYTLDVAGNRFQASA 107
F KKL G + + + +V + GNRF SA
Sbjct: 244 FDAKKLTGTLSTKQKAIASSPETYVDRYDIDATIKGNRFAGSA 286
>3l6v_A GYRA, DNA gyrase subunit A; gyrase A C-terminal domain, GYRA
C-terminal domain, DNA wrapping, beta-strand-bearing
proline, ATP-binding; HET: DNA; 2.19A {Xanthomonas
campestris PV}
Length = 370
Score = 24.9 bits (55), Expect = 9.4
Identities = 7/59 (11%), Positives = 14/59 (23%)
Query: 6 DYFIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYG 64
+ + +R + D + ++ T T GYG
Sbjct: 200 EEVVSLIVSERAGGVEDEVEDESAEEVVETTDGAEPAVIDVADNGDVAYILTATENGYG 258
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 0.417
Gapped
Lambda K H
0.267 0.0691 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,033,479
Number of extensions: 110997
Number of successful extensions: 204
Number of sequences better than 10.0: 1
Number of HSP's gapped: 194
Number of HSP's successfully gapped: 29
Length of query: 131
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 48
Effective length of database: 4,384,350
Effective search space: 210448800
Effective search space used: 210448800
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: 52 (23.9 bits)