RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2242
(246 letters)
>2gmh_A Electron transfer flavoprotein-ubiquinone oxidoreductase; HET: BHG
FAD UQ5; 2.50A {Sus scrofa} SCOP: c.3.1.2 d.16.1.8
d.58.1.6 PDB: 2gmj_A*
Length = 584
Score = 238 bits (608), Expect = 2e-75
Identities = 120/190 (63%), Positives = 147/190 (77%), Gaps = 2/190 (1%)
Query: 5 DFNTYGGSFLYHLNEPSPLVAVGFVVGLDYTNPYLSPFKEFQRFKTHPAVRPVFEGGKRI 64
D +TYGGSFLYHLNE PL+A+GFVVGLDY NPYLSPF+EFQR+K HP+++P EGGKRI
Sbjct: 267 DRHTYGGSFLYHLNEGEPLLALGFVVGLDYQNPYLSPFREFQRWKHHPSIKPTLEGGKRI 326
Query: 65 AYGARALNEGGLQAIPRLTFPGGCLVGCTAGFLNVPKIKGTHNAMKSGMLAAEATYEALA 124
AYGARALNEGG Q+IP+LTFPGG L+GC+ GF+NVPKIKGTH AMKSG LAAE+ + L
Sbjct: 327 AYGARALNEGGFQSIPKLTFPGGLLIGCSPGFMNVPKIKGTHTAMKSGTLAAESIFNQLT 386
Query: 125 EAGDEVST-GLEPKSYEDKIKSSWIYKELKEVRNCRPSFHSKLGLWGGLAYSGA-SIMMK 182
+ T GL YED +K+SW++KEL VRN RPS H LG++GG+ Y+G + +
Sbjct: 387 SENLQSKTIGLHVTEYEDNLKNSWVWKELYSVRNIRPSCHGILGVYGGMIYTGIFYWIFR 446
Query: 183 GIEPWTFKWN 192
G+EPWT K
Sbjct: 447 GMEPWTLKHK 456
Score = 133 bits (336), Expect = 4e-36
Identities = 47/53 (88%), Positives = 50/53 (94%)
Query: 194 VYEYVPLEDGSGERLQINAQNCIHCKTCDIKDPTQNINWVVPEGGGGPAYNGM 246
VYE+VPLE G G RLQINAQNC+HCKTCDIKDP+QNINWVVPEGGGGPAYNGM
Sbjct: 532 VYEFVPLEQGDGFRLQINAQNCVHCKTCDIKDPSQNINWVVPEGGGGPAYNGM 584
>3atr_A Conserved archaeal protein; saturating double bonds, archaeal
membrane precursor, like 2 geranylgeranylglyceryl
phosphate; HET: FDA; 1.80A {Sulfolobus acidocaldarius}
PDB: 3atq_A*
Length = 453
Score = 70.2 bits (172), Expect = 4e-14
Identities = 25/134 (18%), Positives = 48/134 (35%), Gaps = 11/134 (8%)
Query: 26 VGFVVGLDYTNPYLSPFKEFQRFKTHPAVRPVFEGGKRIAYGARALNEGGLQAIPRLTFP 85
VG + P + + ++++ P + K + G + + + +
Sbjct: 229 VGLGIQGGMGYPSIHEY--YKKY--LDKYAPDVDKSKLLVKGGALVPTRRP--LYTMAWN 282
Query: 86 GGCLVGCTAGFLNVPKIKGTHNAMKSGMLAAEATYEALAEAGDEVSTGLEPKSYEDKIKS 145
G ++G + +N G +AM SG AA+A A E GD ++GL +
Sbjct: 283 GIIVIGDSGFTVNPVHGGGKGSAMISGYCAAKAILSAF-ETGDFSASGL--WDMNICYVN 339
Query: 146 SW--IYKELKEVRN 157
+ L R
Sbjct: 340 EYGAKQASLDIFRR 353
>3cgv_A Geranylgeranyl reductase related protein; NP_393992.1,
geranylgeranyl bacteriochlorophyll reductase- like FIXC
homolog; HET: MSE FAD UNL; 1.60A {Thermoplasma
acidophilum dsm 1728} PDB: 3oz2_A*
Length = 397
Score = 54.6 bits (132), Expect = 5e-09
Identities = 32/125 (25%), Positives = 52/125 (41%), Gaps = 8/125 (6%)
Query: 26 VGFVVGLDYTNPYLSPFKEFQRFKTHPAVRPVFEGGKRIAYGARALNEGGLQAIPRLTFP 85
VG +++ + RF + P + G+ I ++ + +T P
Sbjct: 223 VGIGSSINWIHNRFELKNYLDRFIEN---HPGLKKGQDIQLVTGGVSVSKV--KMPITMP 277
Query: 86 GGCLVGCTAGFLNVPKIKGTHNAMKSGMLAAEATYEALAEAGDEVSTGLEPKSYEDKIKS 145
G LVG A ++ G NA+ SGM AA+ T EA+ E+ D + + YE IK
Sbjct: 278 GLMLVGDAARLIDPITGGGIANAIVSGMYAAQVTKEAI-ESNDYSPQMM--QKYEKLIKE 334
Query: 146 SWIYK 150
+ K
Sbjct: 335 RFERK 339
>3nix_A Flavoprotein/dehydrogenase; structural genomics, PSI-2, NES protein
structure initiative, northeast structural genomics
consortium; HET: FAD; 2.60A {Cytophaga hutchinsonii}
Length = 421
Score = 48.6 bits (116), Expect = 6e-07
Identities = 24/124 (19%), Positives = 44/124 (35%), Gaps = 9/124 (7%)
Query: 23 LVAVGFVVGLDYTNPY-LSPFKEFQRF-KTHPAVRPVFEGGKRIAYGARALNEGGLQAIP 80
+VGFV Y + Y +P + + + F+ + + +
Sbjct: 226 NTSVGFVGEPSYFDEYTGTPEERMRAMIANEGHIAERFKSEEFLFEPRTIEGYAI--SAS 283
Query: 81 RLTFPGGCLVGCTAGFLNVPKIKGTHNAMKSGMLAAEATYEALAEAGDEVSTGLEPKSYE 140
+L G L G FL+ G AM+SG + + L G+EV+ K +
Sbjct: 284 KLYGDGFVLTGNATEFLDPIFSSGATFAMESGSKGGKLAVQFL--KGEEVN---WEKDFV 338
Query: 141 DKIK 144
+ +
Sbjct: 339 EHMM 342
>3i3l_A Alkylhalidase CMLS; flavin-dependent halogenase, chloramphenicol
biosynthesis, halogenation reaction, structural
genomics; HET: FAD; 2.20A {Streptomyces venezuelae}
Length = 591
Score = 37.6 bits (87), Expect = 0.003
Identities = 19/128 (14%), Positives = 37/128 (28%), Gaps = 8/128 (6%)
Query: 23 LVAVGFVVGLDYTNPY-LSPFKEFQR--FKTHPAVRPVFEGGKRIAYGARALNEGGLQAI 79
L +VG VV + F + G +++ +
Sbjct: 245 LYSVGLVVDRSKSAEVREQGADAFYSSTLAKCAKAMDILGGAEQVDEVRIVQDWSY--DT 302
Query: 80 PRLTFPGGCLVGCTAGFLNVPKIKGTHNAMKSGMLAAEATYEALAEAGDEVSTGLEPKSY 139
+ L G A F + +G H A +S + AA A ++ + Y
Sbjct: 303 EVFSADRFFLCGDAACFTDPLFSQGVHLASQSAVSAAAAIDRITRHGDEKDAV---HAWY 359
Query: 140 EDKIKSSW 147
+ ++
Sbjct: 360 NRTYREAY 367
>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 = 37.7 bits (87), Expect = 0.003
Identities = 31/163 (19%), Positives = 56/163 (34%), Gaps = 43/163 (26%)
Query: 43 KEFQRFKTHPAVRPVFEGGKRI---AYGARALNEGGLQAI-----PRLTFPGGCLVGCTA 94
+ +KT A + V+ YG + I LT G G
Sbjct: 1633 MDL--YKTSKAAQDVWNRADNHFKDTYGFS------ILDIVINNPVNLTIHFGGEKGK-- 1682
Query: 95 GFLNVPKIKGTHNAMK-SGMLAAEATYEALAEAGDEVSTGLEPKSYEDKIK--------- 144
+I+ ++AM ++ + E + + +E ST +S + +
Sbjct: 1683 ------RIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPAL 1736
Query: 145 ---SSWIYKELKE--VRNCRPSF--HSKLGLWGGLAYSGASIM 180
+++LK + +F HS LG + LA S A +M
Sbjct: 1737 TLMEKAAFEDLKSKGLIPADATFAGHS-LGEYAALA-SLADVM 1777
Score = 35.4 bits (81), Expect = 0.016
Identities = 46/236 (19%), Positives = 76/236 (32%), Gaps = 101/236 (42%)
Query: 19 EPSPLVAVGFVVGL---------DYTNPYLSPFKEFQRFKTHPAVRPVFEGGKRIAY--G 67
PSP++++ L + TN +L PA + V I+ G
Sbjct: 334 VPSPMLSI---SNLTQEQVQDYVNKTNSHL------------PAGKQVE-----ISLVNG 373
Query: 68 ARALNEGGLQAIPRLTFPGGCLVGCTAGFLNVP--KIKGTHNAMKSGMLAAEATYEALAE 125
A+ L G P + L G LN+ K K A
Sbjct: 374 AKNLVVSG----PPQS-----LYG-----LNLTLRKAK--------------------AP 399
Query: 126 AGDEVSTGLEPKSYEDKIKSSWIYKELKEVRNCR------PSFHSKLGLWGGLAYSGASI 179
+G + S +I S E K + R P FHS L L + +
Sbjct: 400 SGLDQS----------RIPFS----ERKLKFSNRFLPVASP-FHSHL-----LV-PASDL 438
Query: 180 MMKGIEPWTFKWNSVYEYVPLED-GSGERLQINAQNCIHCKTCD--IKDPTQNINW 232
+ K + +N+ +P+ D G L++ + + + D I+ P + W
Sbjct: 439 INKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISE-RIVDCIIRLP---VKW 490
>3e1t_A Halogenase; flavoprotein; HET: FAD; 2.05A {Chondromyces crocatus}
Length = 512
Score = 36.5 bits (84), Expect = 0.007
Identities = 25/118 (21%), Positives = 40/118 (33%), Gaps = 17/118 (14%)
Query: 23 LVAVGFVVGLDYTNPYLSPFKEFQR--FKTHPAVRPVFEGGKRIAYGARALNEGGLQAIP 80
L +VG VV + + P ++ R+ + G ++
Sbjct: 229 LTSVGAVVSREAAEAIKDGHEAALLRYIDRCPIIKEYLAPATRV----TTGDYGEIRIRK 284
Query: 81 RLTF-------PGGCLVGCTAGFLNVPKI--KGTHNAMKSGMLAAEATYEALAEAGDE 129
++ G LVG A F++ P + G H A S +L A A LA E
Sbjct: 285 DYSYCNTSFWKNGMALVGDAACFVD-P-VFSSGVHLATYSALLVARAINTCLAGEMSE 340
>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 = 30.3 bits (67), Expect = 0.36
Identities = 7/33 (21%), Positives = 11/33 (33%), Gaps = 9/33 (27%)
Query: 181 MKGIEPWTFKWNSVYEYVPLEDGSGERLQINAQ 213
+K ++ S+ Y S L I A
Sbjct: 22 LKKLQ------ASLKLYAD---DSAPALAIKAT 45
>3ndn_A O-succinylhomoserine sulfhydrylase; seattle structural genomics
center for infectious disease, S mycobacterium, PLP,
schiff base; HET: LLP; 1.85A {Mycobacterium
tuberculosis}
Length = 414
Score = 28.3 bits (64), Expect = 2.7
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 108 AMKSGMLAAEATYEALAEAGDEV 130
A SGM A + AL AGD +
Sbjct: 101 ATASGMAAVFTSLGALLGAGDRL 123
>3ri6_A O-acetylhomoserine sulfhydrylase; PYR 5'-phosphate,
gamma-elimination, direct sulfhydrylation, CY
metabolism, protein thiocarboxylate, TR; 2.20A
{Wolinella succinogenes}
Length = 430
Score = 27.9 bits (63), Expect = 3.1
Identities = 17/77 (22%), Positives = 22/77 (28%), Gaps = 36/77 (46%)
Query: 57 VFEGGKRIAYGARALNEGGLQAIPRLTFPGGCLVGCTAGFLNVPKIKGTHNAMKSGMLAA 116
E +R+ L G L + A+ SGM A
Sbjct: 86 DLE--QRLK----NL-TGALGVL----------------------------ALGSGMAAI 110
Query: 117 EATYEALAEAGDE-VST 132
LA AGD V+T
Sbjct: 111 STAILTLARAGDSVVTT 127
>2g3m_A Maltase, alpha-glucosidase; hydrolase, glycoside hydrolase family
31, multidomain protein, (beta/alpha)8 barrel, retaining
mechanism; 2.55A {Sulfolobus solfataricus} PDB: 2g3n_A*
Length = 693
Score = 28.1 bits (63), Expect = 3.4
Identities = 17/116 (14%), Positives = 26/116 (22%), Gaps = 21/116 (18%)
Query: 27 GFVVGLDYTNP-----YLSPFKEFQRFKTH--------PAVRPVFEGGKRIAYGARALNE 73
G V D+ + E+ P F I +L
Sbjct: 286 GTTVYPDFFREDTREWWAGLISEWLSQGVDGIWLDMNEPTD---FSRAIEIRDVLSSLPV 342
Query: 74 GGLQAIPRLTFPGGCLVGCTAGFLNVPKIKGTHNAMKSGMLAAEATYEALAEAGDE 129
TFP K + NA + A AT++ +
Sbjct: 343 QFRDDRLVTTFPDNV---VHYLRGKRVKHEKVRNAY--PLYEAMATFKGFRTSHRN 393
>2cb1_A O-acetyl homoserine sulfhydrylase; PLP enzyme, lyase, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; HET: LLP; 2.0A {Thermus
thermophilus}
Length = 412
Score = 27.9 bits (63), Expect = 3.4
Identities = 18/77 (23%), Positives = 24/77 (31%), Gaps = 36/77 (46%)
Query: 57 VFEGGKRIAYGARALNEGGLQAIPRLTFPGGCLVGCTAGFLNVPKIKGTHNAMKSGMLAA 116
E +R+ AL EG L+A+ + SG A
Sbjct: 60 ALE--ERLK----AL-EGALEAV----------------------------VLASGQAAT 84
Query: 117 EATYEALAEAGDE-VST 132
A AL GDE V+
Sbjct: 85 FAALLALLRPGDEVVAA 101
>2rfv_A Methionine gamma-lyase; pyridoxal-5'-phosphate, PLP-dependent
enzyme; HET: LLP; 1.35A {Citrobacter freundii} PDB:
1y4i_A* 3jwa_A* 3jw9_A* 3jwb_A* 3mkj_A*
Length = 398
Score = 27.9 bits (63), Expect = 3.6
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 108 AMKSGMLAAEATYEALAEAGDEV 130
A SG+ A T L + GD +
Sbjct: 84 ATASGISAITTTLLTLCQQGDHI 106
>1e9y_A Urease subunit alpha; hydrolase, dodecamer; HET: KCX; 3.00A
{Helicobacter pylori} SCOP: b.85.3.1 d.8.1.1 PDB:
1e9z_A*
Length = 238
Score = 27.4 bits (61), Expect = 4.2
Identities = 21/93 (22%), Positives = 25/93 (26%), Gaps = 42/93 (45%)
Query: 35 TNPYLSPFKEFQRFKTH------PA---VRPVFE------------GGKRIAYGARALNE 73
N L +F R KT A VR FE GG R +G AL +
Sbjct: 150 VNRCL----DFDREKTFGKRLDIAAGTAVR--FEPGEEKSVELIDIGGNRRIFGFNALVD 203
Query: 74 GGL------QAIPRLTFPGGCLVGCTAGFLNVP 100
A+ R GF
Sbjct: 204 RQADNESKKIALHRAK---------ERGFHGAK 227
>3top_A Maltase-glucoamylase, intestinal; membrane, hydrolase-hydrolase
inhibitor complex; HET: ACR; 2.88A {Homo sapiens} PDB:
3ton_A*
Length = 908
Score = 27.6 bits (61), Expect = 5.4
Identities = 8/25 (32%), Positives = 10/25 (40%), Gaps = 2/25 (8%)
Query: 105 THNAMKSGMLAAEATYEALAEAGDE 129
HN G TYEA+ E +
Sbjct: 530 VHNLY--GWSQTRPTYEAVQEVTGQ 552
>1gc0_A Methionine gamma-lyase; pyridoxal-5'-phosphate; HET: LLP; 1.70A
{Pseudomonas putida} SCOP: c.67.1.3 PDB: 1gc2_A* 1pg8_A*
1ukj_A* 2o7c_A*
Length = 398
Score = 27.1 bits (61), Expect = 5.8
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 108 AMKSGMLAAEATYEALAEAGDEV 130
A+ SGM A +T L GDEV
Sbjct: 85 ALASGMGAITSTLWTLLRPGDEV 107
>2ctz_A O-acetyl-L-homoserine sulfhydrylase; crystal, O-acetyl homoserine
sulfhydrase, structural genomic structural
genomics/proteomics initiative; HET: PLP; 2.60A {Thermus
thermophilus} SCOP: c.67.1.3
Length = 421
Score = 27.1 bits (61), Expect = 5.8
Identities = 23/77 (29%), Positives = 26/77 (33%), Gaps = 36/77 (46%)
Query: 57 VFEGGKRIAYGARALNEGGLQAIPRLTFPGGCLVGCTAGFLNVPKIKGTHNAMKSGMLAA 116
V E KR+A AL EGG A+ A SG A
Sbjct: 62 VLE--KRLA----AL-EGGKAAL----------------------------ATASGHAAQ 86
Query: 117 EATYEALAEAGDE-VST 132
LA+AGD VST
Sbjct: 87 FLALTTLAQAGDNIVST 103
>3lpp_A Sucrase-isomaltase; glycoside hydrolase family 31,
alpha-glucosidase membrane, disease mutation, disulfide
bond, glycoprotein, glycosidase; HET: NAG BMA MAN KTL;
2.15A {Homo sapiens} PDB: 3lpo_A*
Length = 898
Score = 27.1 bits (60), Expect = 5.9
Identities = 6/22 (27%), Positives = 10/22 (45%), Gaps = 2/22 (9%)
Query: 105 THNAMKSGMLAAEATYEALAEA 126
H+ G A AT +A+ +
Sbjct: 525 VHSLY--GYSMAIATEQAVQKV 544
>1qgn_A Protein (cystathionine gamma-synthase); methionine biosynthesis,
pyridoxal 5'-phosphate, gamma-famil; HET: PLP; 2.90A
{Nicotiana tabacum} SCOP: c.67.1.3 PDB: 1i41_A* 1i48_A*
1i43_A*
Length = 445
Score = 27.2 bits (61), Expect = 6.4
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 108 AMKSGMLAAEATYEALAEAGDEV 130
M SGM A+ AL AG +
Sbjct: 134 LMASGMCASTVMLLALVPAGGHI 156
>3l4y_A Maltase-glucoamylase, intestinal; glycoside hydrolase family 31,
cell membrane, disulfide bond, glycoprotein,
glycosidase, hydrolase, membrane; HET: NR4 NAG; 1.80A
{Homo sapiens} PDB: 3l4u_A* 3l4v_A* 3l4w_A* 3l4x_A*
3l4t_A* 3l4z_A* 2qmj_A* 2qly_A* 3ctt_A*
Length = 875
Score = 27.1 bits (60), Expect = 7.4
Identities = 29/130 (22%), Positives = 38/130 (29%), Gaps = 17/130 (13%)
Query: 11 GSFLYHLNEPSPLVAV---GFVVGLDYTNPYLSPF--KEFQRFKTHPAV--------RP- 56
++ + +PL+ G V DYTNP + + KEF+ F
Sbjct: 389 KIWVNSSDGVTPLIGEVWPGQTVFPDYTNPNCAVWWTKEFELFHNQVEFDGIWIDMNEVS 448
Query: 57 VFEGGKRIAYGARALNEGGLQAIPRLTFPGGCLVGCTAGFLNVPKIKGTHNAMKSGMLAA 116
F G LN L C C + K HN G A
Sbjct: 449 NFVDGSVSGCSTNNLNNPP-FTPRILDGYLFCKTLCMDAVQHWGKQYDIHNLY--GYSMA 505
Query: 117 EATYEALAEA 126
AT EA
Sbjct: 506 VATAEAAKTV 515
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 0.138 0.440
Gapped
Lambda K H
0.267 0.0596 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,024,895
Number of extensions: 240912
Number of successful extensions: 593
Number of sequences better than 10.0: 1
Number of HSP's gapped: 591
Number of HSP's successfully gapped: 30
Length of query: 246
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 155
Effective length of database: 4,160,982
Effective search space: 644952210
Effective search space used: 644952210
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: 56 (25.6 bits)