RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2966
(237 letters)
>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 = 44.5 bits (104), Expect = 2e-05
Identities = 23/165 (13%), Positives = 54/165 (32%), Gaps = 47/165 (28%)
Query: 75 AFD-NCFTMM---YILVLEYVGPSWRTFVANMSIAIFFTLAASLLPWIAYYVANWQYL-C 129
AF+ +C ++ + V +++ + T ++ ++ T + + L C
Sbjct: 261 AFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVK-----SLLLKY--LDC 313
Query: 130 VITSL--------PLLVAVITPWIVPESARWLVSQGRVDEAVVIMKRFEKINNKKVDPKL 181
L P +++I I A W ++ +N K+ +
Sbjct: 314 RPQDLPREVLTTNPRRLSIIAESIRDGLATW--------------DNWKHVNCDKLTTII 359
Query: 182 ---YQQLKETCQRQAKQEIDGKRYSVLDLFRTPRLRNITCLLIVI 223
L+ R+ + L +F P +I +L+ +
Sbjct: 360 ESSLNVLEPAEYRK--------MFDRLSVF--PPSAHIPTILLSL 394
>2gfp_A EMRD, multidrug resistance protein D; membrane protein, multidrug
transporter; 3.50A {Escherichia coli}
Length = 375
Score = 41.1 bits (97), Expect = 2e-04
Identities = 11/70 (15%), Positives = 22/70 (31%), Gaps = 5/70 (7%)
Query: 6 AQDTLPTLAQAIFFCGAIVGGLVFGWVADHFGRIPALVGTNLTGFVAGVATAFASTFWQF 65
Q + + V L +G ++D GR P ++ +A + S+
Sbjct: 37 VQSVM-----GAYLLTYGVSQLFYGPISDRVGRRPVILVGMSIFMLATLVAVTTSSLTVL 91
Query: 66 AICRFFVGLA 75
G+
Sbjct: 92 IAASAMQGMG 101
>1pw4_A Glycerol-3-phosphate transporter; transmembrane, inner membrane,
major facilitator superfamily, secondary active membrane
transporter; 3.30A {Escherichia coli} SCOP: f.38.1.1
Length = 451
Score = 38.5 bits (90), Expect = 0.001
Identities = 15/140 (10%), Positives = 39/140 (27%), Gaps = 11/140 (7%)
Query: 24 VGGLVFGWVADHFG-RI---PALVGTNLTGFVAGVATAFASTFWQFAICRFFVGLAFDNC 79
+ G V+D R+ L+ G S+ + F G
Sbjct: 77 FSKFIMGSVSDRSNPRVFLPAGLILAAAVMLFMGFVPWATSSIAVMFVLLFLCGWFQGMG 136
Query: 80 FTMMYILVLEYVGPSWRTFVA---NMSIAIFFTLAASLLPWIAYYVANWQYLCVITSLPL 136
+ ++ + R + N + + + L + +W + +
Sbjct: 137 WPPCGRTMVHWWSQKERGGIVSVWNCAHNVGGGIPPLLFLLGMAWFNDWHAALYMPAFCA 196
Query: 137 LVAVITPWIV----PESARW 152
++ + + + P+S
Sbjct: 197 ILVALFAFAMMRDTPQSCGL 216
Score = 35.8 bits (83), Expect = 0.010
Identities = 20/148 (13%), Positives = 46/148 (31%), Gaps = 14/148 (9%)
Query: 16 AIFFCGAIVGGLVFGWVADHF-----GRIPALVGTNLTGFVAGVATAFASTFWQFAICRF 70
++ I G L+ GW++D G T +T A IC
Sbjct: 295 FLYEYAGIPGTLLCGWMSDKVFRGNRGATGVFFMTLVTIATIVYWMNPAGNPTVDMICMI 354
Query: 71 FVGLAFDNCFTMMYILVLEYVGP-------SWRTFVANMSIAIFFTLAASLLPWIAYYVA 123
+G ++ + LE + + ++ + + ++
Sbjct: 355 VIGFLIYGPVMLIGLHALELAPKKAAGTAAGFTGLFGYLGGSVAASAIVGYT--VDFFGW 412
Query: 124 NWQYLCVITSLPLLVAVITPWIVPESAR 151
+ ++ +I L V ++ ++ E R
Sbjct: 413 DGGFMVMIGGSILAVILLIVVMIGEKRR 440
>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 = 36.2 bits (83), Expect = 0.009
Identities = 25/128 (19%), Positives = 39/128 (30%), Gaps = 47/128 (36%)
Query: 1 LNWVCAQDTLPT---LAQAIFFCGAIVGGLV----FGWVADHFGRIPALVGTNL---TGF 50
L W+ P L C I G++ + A G P + + L TG
Sbjct: 216 LEWLENPSNTPDKDYLLSIPISCPLI--GVIQLAHYVVTAKLLGFTPGELRSYLKGATGH 273
Query: 51 VAGVATAFASTFWQFAICRFFVGLAFDNCFTMMYILVLEYVGPSWRTFVANMSIAIFFTL 110
G+ TA A +A SW +F ++ AI
Sbjct: 274 SQGLVTAVA--------------IA---------------ETDSWESFFVSVRKAI---- 300
Query: 111 AASLLPWI 118
++L +I
Sbjct: 301 --TVLFFI 306
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 33.2 bits (75), Expect = 0.041
Identities = 12/60 (20%), Positives = 25/60 (41%), Gaps = 18/60 (30%)
Query: 147 PESAR-WLVSQGRVDEAVVIMKRFEKINNKKVDPKLYQQLKETCQRQAKQEIDG--KRYS 203
PES R W R ++ + + + Q+ +E +AK++++ +R S
Sbjct: 84 PESIRKW-----REEQRKRLQELDAASKVME------QEWRE----KAKKDLEEWNQRQS 128
>3p5n_A RIBU, riboflavin uptake protein; transporter, alpha-helical bundle,
transport protein; HET: RBF; 3.60A {Staphylococcus
aureus}
Length = 189
Score = 32.5 bits (74), Expect = 0.074
Identities = 25/143 (17%), Positives = 54/143 (37%), Gaps = 3/143 (2%)
Query: 36 FGRIPALVGTNLTGFVAGVATAFASTFWQFAICRF-FVGLAFDNCFTMMYILVLEYVGPS 94
F +P+L+ T G VAG+ A + VG + ++L + +
Sbjct: 46 FSDVPSLLATFTFGPVAGIIVALVKNLLNYLFSMGDPVGPFANFLAGASFLLTAYAIYKN 105
Query: 95 WRTFVANMSIAIFFTLAASLLPWIAYYVANWQYLCVITSLPLLVAVITPWIVPESARWLV 154
R+ + ++ I T+ +++ I Y +I +L + + IV + +
Sbjct: 106 KRSTKSLITGLIIATIVMTIVLSILNYFVLLPLYGMIFNLADIANNLKVIIVSGIIPFNI 165
Query: 155 SQGRVDEAV--VIMKRFEKINNK 175
+G V V ++ +R +
Sbjct: 166 IKGIVISIVFILLYRRLANFLKR 188
>1m1j_A Fibrinogen alpha subunit; coiled coils, disulfide rings,
fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus
gallus} SCOP: h.1.8.1 PDB: 1ei3_A
Length = 491
Score = 33.0 bits (74), Expect = 0.076
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 156 QGRVDEAVVIMKRFEKINNKKVDPKLYQQLKETCQRQAKQEIDGKRY 202
Q + E VV MKR E +D K+ + K +C R ++D + Y
Sbjct: 138 QNSIQEQVVEMKRLEV----DIDIKI-RACKGSCARSFDYQVDKEGY 179
>2cfq_A Lactose permease; transport, transport mechanism, lactose/H+
symport, sugar transport, transmembrane, formylation;
2.95A {Escherichia coli} SCOP: f.38.1.2 PDB: 1pv7_A*
1pv6_A 2cfp_A 2v8n_A 2y5y_A*
Length = 417
Score = 32.2 bits (73), Expect = 0.12
Identities = 18/165 (10%), Positives = 47/165 (28%), Gaps = 9/165 (5%)
Query: 13 LAQAIFFCGAIVGGLVFGWVADHFGRIPALVGTNLTGFVAGVA--------TAFASTFWQ 64
+ A +++ +FG ++D G L+ V +
Sbjct: 47 IIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVG 106
Query: 65 FAICRFFVGLAFDNCFTMMYILVLEYVGPSWRTF-VANMSIAIFFTLAASLLPWIAYYVA 123
+ ++G F+ + + + S F A M + + L AS++ +
Sbjct: 107 SIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALGASIVGIMFTINN 166
Query: 124 NWQYLCVITSLPLLVAVITPWIVPESARWLVSQGRVDEAVVIMKR 168
+ + +L ++ + V+ +
Sbjct: 167 QFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLK 211
Score = 31.8 bits (72), Expect = 0.19
Identities = 11/93 (11%), Positives = 28/93 (30%)
Query: 27 LVFGWVADHFGRIPALVGTNLTGFVAGVATAFASTFWQFAICRFFVGLAFDNCFTMMYIL 86
+ + G AL+ V + ++FA++ + I + +
Sbjct: 277 FFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKY 336
Query: 87 VLEYVGPSWRTFVANMSIAIFFTLAASLLPWIA 119
+ + + + F LA + +A
Sbjct: 337 ITSQFEVRFSATIYLVCFCFFKQLAMIFMSVLA 369
>2psd_A Renilla-luciferin 2-monooxygenase; alpha/beta-hydrolase,
luciferase, oxidoreductase; 1.40A {Renilla reniformis}
PDB: 2pse_A 2psj_A* 2psh_A 2psf_A
Length = 318
Score = 29.3 bits (66), Expect = 0.88
Identities = 28/166 (16%), Positives = 47/166 (28%), Gaps = 26/166 (15%)
Query: 8 DTLPTLAQAIFFC---GAIVGGLVFGWVADHFGRIPALVGTNLTGFVAGVATAFASTFWQ 64
+ L + IF GA + F + +H RI A+V V +
Sbjct: 105 ELLNLPKKIIFVGHDWGAALA---FHYAYEHQDRIKAIVHMESVVDVIESWDEWPDIEED 161
Query: 65 FAICRFFVG--LAFDNCFTMMYIL------------VLEYVGP---SWRTFVANMSIAIF 107
A+ + G + +N F + +L Y+ P +S
Sbjct: 162 IALIKSEEGEKMVLENNFFVETVLPSKIMRKLEPEEFAAYLEPFKEKGEVRRPTLSWPRE 221
Query: 108 FTLAASLLPWIAYYVANWQYLCVITSLPLLVAVIT--PWIVPESAR 151
L P + V N+ + S L I P +
Sbjct: 222 IPLVKGGKPDVVQIVRNYNAY-LRASDDLPKLFIESDPGFFSNAIV 266
>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR),
beta-hairpin, alpha-solenoi transport protein; 2.60A
{Bos taurus}
Length = 291
Score = 29.3 bits (65), Expect = 0.96
Identities = 9/63 (14%), Positives = 21/63 (33%)
Query: 134 LPLLVAVITPWIVPESARWLVSQGRVDEAVVIMKRFEKINNKKVDPKLYQQLKETCQRQA 193
L L + + + + L+ R+D A +K+ + + +L
Sbjct: 121 LRTLHQGDSLECMAMTVQILLKLDRLDLARKELKKMQDQDEDATLTQLATAWVSLAAGGE 180
Query: 194 KQE 196
K +
Sbjct: 181 KLQ 183
>3o7q_A L-fucose-proton symporter; transporter, multi-PASS membrane protei
transport protein; HET: BNG; 3.14A {Escherichia coli}
PDB: 3o7p_A*
Length = 438
Score = 28.7 bits (64), Expect = 1.6
Identities = 15/122 (12%), Positives = 35/122 (28%), Gaps = 12/122 (9%)
Query: 8 DTLPTLAQAIFFCGAIVGGLVFGWVADHFGRIPALV---GTNLTGFVAGVATAFASTFWQ 64
+ L Q+ F+ G + + G + ++ G A +
Sbjct: 60 NFQAGLIQSAFYFGYFIIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTL 119
Query: 65 FAICRFFVGLAFDNCFTMMYILVLEYV---GPSWRTFVANMSIA-IFFTLAASLLPWIAY 120
F + F + + +V GP + +++A F + A +
Sbjct: 120 FLVGLFIIAA----GLGCLETAANPFVTVLGPE-SSGHFRLNLAQTFNSFGAIIAVVFGQ 174
Query: 121 YV 122
+
Sbjct: 175 SL 176
>1g2r_A Hypothetical cytosolic protein; NUSA-INFB operon, structural
genomics, PSI, protein structure initiative; 1.35A
{Streptococcus pneumoniae} SCOP: d.192.1.1
Length = 100
Score = 27.4 bits (61), Expect = 1.7
Identities = 6/33 (18%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 167 KRFEKINNKKVDPKLYQQLKETCQRQ-AKQEID 198
K F + + +V+ Y +L + ++E+
Sbjct: 66 KVFNRSFSMEVEESFYDELIAYVDHKVKRRELG 98
>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter,
lipid flippase, hydrolase, inner membrane, lipid
transport, membrane; 5.50A {Vibrio cholerae}
Length = 582
Score = 28.7 bits (65), Expect = 1.8
Identities = 3/31 (9%), Positives = 9/31 (29%)
Query: 88 LEYVGPSWRTFVANMSIAIFFTLAASLLPWI 118
Y+ V + + A + + +
Sbjct: 17 WTYIRLYKAGLVVSTIALVINAAADTYMISL 47
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 28.1 bits (62), Expect = 1.9
Identities = 8/17 (47%), Positives = 8/17 (47%), Gaps = 4/17 (23%)
Query: 86 LVLE--YV--GPSWRTF 98
LVL V WRTF
Sbjct: 50 LVLSDKLVDTRSEWRTF 66
>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION
channel, transport protein, casse protein; 2.00A {Homo
sapiens} PDB: 2onj_A* 2hyd_A
Length = 578
Score = 28.3 bits (64), Expect = 2.2
Identities = 8/38 (21%), Positives = 15/38 (39%)
Query: 87 VLEYVGPSWRTFVANMSIAIFFTLAASLLPWIAYYVAN 124
L++V P A + + I L+P + Y +
Sbjct: 5 YLQFVKPYKYRIFATIIVGIIKFGIPMLIPLLIKYAID 42
>3b60_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter,
lipid flippase, hydrolase, inner membrane, lipid
transport, membrane; HET: ANP; 3.70A {Salmonella
typhimurium} SCOP: c.37.1.12 f.37.1.1 PDB: 3b5y_A*
3b5z_A* 3b5w_A
Length = 582
Score = 27.9 bits (63), Expect = 3.4
Identities = 3/61 (4%), Positives = 17/61 (27%), Gaps = 7/61 (11%)
Query: 88 LEYVGPSWRTFVANMSIAIFFTLAASLLPWIAYYV-------ANWQYLCVITSLPLLVAV 140
+ P + I + + + + + + L + + + + +
Sbjct: 17 WPTIAPFKAGLIVAGIALILNAASDTFMLSLLKPLLDDGFGKTDRSVLLWMPLVVIGLMI 76
Query: 141 I 141
+
Sbjct: 77 L 77
>2kat_A Uncharacterized protein; NESG, structure, structural genomics,
PSI-2, protein structure initiative; NMR {Bordetella
parapertussis}
Length = 115
Score = 26.5 bits (59), Expect = 3.6
Identities = 8/44 (18%), Positives = 19/44 (43%)
Query: 153 LVSQGRVDEAVVIMKRFEKINNKKVDPKLYQQLKETCQRQAKQE 196
L QG A + + D ++ ++L+ +R A+++
Sbjct: 63 LQGQGDRAGARQAWESGLAAAQSRGDQQVVKELQVFLRRLARED 106
>2qvb_A Haloalkane dehalogenase 3; RV2579, alpha-beta hydrolase protei
structural genomics consortium, TBSGC, hydrolase; 1.19A
{Mycobacterium tuberculosis} PDB: 2o2i_A 2o2h_A
Length = 297
Score = 27.0 bits (60), Expect = 4.9
Identities = 9/53 (16%), Positives = 13/53 (24%), Gaps = 1/53 (1%)
Query: 25 GGLV-FGWVADHFGRIPALVGTNLTGFVAGVATAFASTFWQFAICRFFVGLAF 76
G + F W H R+ + A + F R G
Sbjct: 109 GSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPM 161
>3afv_A DYP; DYE-decolorizing peroxidase, beta barrel, oxidoreductas
aspartic acid; HET: HEM NAG; 1.40A {Bjerkandera adusta}
PDB: 2d3q_A* 3mm2_A* 3mm3_A* 3mm1_A*
Length = 442
Score = 27.0 bits (59), Expect = 6.3
Identities = 9/53 (16%), Positives = 16/53 (30%), Gaps = 2/53 (3%)
Query: 4 VCAQDTLPTLAQAIFFCGAIVGGLVFG-WVADHFGRIPALVGTNLTGFVAGVA 55
+ + D L Q + G + R G GF+ G++
Sbjct: 123 IGS-DQDDFLDQFTDDISSTFGSSITQVQALSGSARPGDQAGHEHFGFLDGIS 174
>3u1t_A DMMA haloalkane dehalogenase; alpha/beta-hydrolase, hydrolase;
2.20A {Unidentified}
Length = 309
Score = 26.9 bits (60), Expect = 6.5
Identities = 7/66 (10%), Positives = 15/66 (22%), Gaps = 12/66 (18%)
Query: 13 LAQAIFFC---GAIVGGLVFGWVADHFGRIPALVGTNLTGFVAGVATAFASTF-----WQ 64
L + G+++G + R+ A+ +
Sbjct: 95 LDDMVLVIHDWGSVIG---MRHARLNPDRVAAVAFME-ALVPPALPMPSYEAMGPQLGPL 150
Query: 65 FAICRF 70
F R
Sbjct: 151 FRDLRT 156
>3afi_E Haloalkane dehalogenase; A/B-hydrolase, hydrolase; 1.75A
{Bradyrhizobium japonicum} PDB: 3a2m_A* 3a2n_A 3a2l_A*
Length = 316
Score = 26.1 bits (58), Expect = 10.0
Identities = 10/118 (8%), Positives = 20/118 (16%), Gaps = 13/118 (11%)
Query: 13 LAQAIFFC---GAIVGGLVFGWVADHFGRIPALVGTNLTGFVAGVATAFASTFWQFAICR 69
+ A G + F A + L + +
Sbjct: 94 VTSAYLVAQDWGTALA---FHLAARRPDFVRGLAFME------FIRPMPTWQDFHHTEVA 144
Query: 70 FFVGLAFDNCFTMMYILVLEYVGPSWRTFVANMSIAIFFTLAASLLP-WIAYYVANWQ 126
A A + + + L +A Y +
Sbjct: 145 EEQDHAEAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTPFP 202
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
0.331 0.142 0.467
Gapped
Lambda K H
0.267 0.0537 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,861,276
Number of extensions: 227510
Number of successful extensions: 750
Number of sequences better than 10.0: 1
Number of HSP's gapped: 741
Number of HSP's successfully gapped: 47
Length of query: 237
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 146
Effective length of database: 4,160,982
Effective search space: 607503372
Effective search space used: 607503372
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 56 (25.8 bits)