RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5439
(381 letters)
>2nzw_A Alpha1,3-fucosyltransferase; FUCT, GT 10; 1.90A {Helicobacter
pylori} SCOP: c.87.1.11 PDB: 2nzx_A* 2nzy_A*
Length = 371
Score = 137 bits (345), Expect = 4e-37
Identities = 37/241 (15%), Positives = 73/241 (30%), Gaps = 14/241 (5%)
Query: 133 FVWALYFLECPYHTQHVAHNDVFNWTATYRSDSDIVTPYEKWVYYDDRHKQMPLDKMKNY 192
++ + + +H ++ + S + P + H +
Sbjct: 119 YLRMPLYYDRLHHKAESVNDTTAPYKLKDNSLYALKKPSHCFKEK---HPNLCAVVNDES 175
Query: 193 AANKTHKVAWFVSNCGAKNNRLQYAHELGKYIEVDIYGSCGSKKCPRISKCFRLLDTKYK 252
K ++ SN A R + L V G K ++YK
Sbjct: 176 DPLKRGFASFVASNPNA-PIRNAFYDALNSIEPVT-GGGSVRNTLGYNVKNKNEFLSQYK 233
Query: 253 FYLAFENSNCVDYITEKLYINGLSHNVLPIVMGARPEDYKKAAPMNSYIHVDDFPSAKHL 312
F L FEN+ Y+TEK+ + + +PI G+ K S+++V DF +
Sbjct: 234 FNLCFENTQGYGYVTEKII-DAYFSHTIPIYWGS--PSVAKDFNPKSFVNVHDFKNFDEA 290
Query: 313 AEYLNKLDANDTLYNSYFRWKGTGEFVNTFFW------CRLCAMLHDSFPIKSYSDINEW 366
+Y+ L + Y ++ ++ A + N +
Sbjct: 291 IDYIKYLHTHKNAYLDMLYENPLNTLDGKAYFYQNLSFKKILAFFKTILENDTIYHDNPF 350
Query: 367 W 367
Sbjct: 351 I 351
>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 = 35.8 bits (82), Expect = 0.026
Identities = 35/207 (16%), Positives = 58/207 (28%), Gaps = 85/207 (41%)
Query: 43 MKNGTRKPTP---------AQINPRTNRRDSKLWPKEDPGQDRIVNQLMYVPNNYDSKNV 93
++N P+P Q+ N+ +S L P ++
Sbjct: 328 LENNEGVPSPMLSISNLTQEQVQDYVNKTNSHL-----PAGKQVE--------------- 367
Query: 94 KKILLFNALTSWNVKLGSSMFSNCPVNACALTTN----KAES-------PF-----VWAL 137
I L N + V G P + L KA S PF ++
Sbjct: 368 --ISLVNGAKNLVVS-GP------PQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSN 418
Query: 138 YFLE--CPYHTQHVA------HNDVFNWTATYRSDSDIVTPYEKWVY-----YDDRHK-- 182
FL P+H+ + + D+ ++ + DI P VY D R
Sbjct: 419 RFLPVASPFHSHLLVPASDLINKDLVKNNVSFNA-KDIQIP----VYDTFDGSDLRVLSG 473
Query: 183 -----------QMPLDKMKNYAANKTH 198
++P+ TH
Sbjct: 474 SISERIVDCIIRLPVKWETTTQFKATH 500
>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 = 35.2 bits (80), Expect = 0.039
Identities = 35/199 (17%), Positives = 63/199 (31%), Gaps = 43/199 (21%)
Query: 171 YEKWVY--YDDRHKQMPLDKMKNYAANKTHKVAWFVSNCGAKNN--RLQYAHEL------ 220
Y+ ++ +Q P + Y + + + AK N RLQ +L
Sbjct: 91 YK-FLMSPIKTEQRQ-PSMMTRMY--IEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLE 146
Query: 221 ---GKYIEVDIYGSCGS-KKCPRISKCFRLLDTKYK-------FYLAFENSNCVDYITEK 269
K + + G GS K + C L K + F+L +N N + + E
Sbjct: 147 LRPAKNVLI--DGVLGSGKTWVALDVC---LSYKVQCKMDFKIFWLNLKNCNSPETVLEM 201
Query: 270 LYINGLSHNVLPIVMGARPEDYKKAAPMNSYIHVDDFPSAKHLAEYLNKLDANDTLYNSY 329
L L + + P D+ + + + Y N L + N+
Sbjct: 202 L--QKLLYQIDP--NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNA- 256
Query: 330 FRWKGTGEFVNTF-FWCRL 347
+ N F C++
Sbjct: 257 -------KAWNAFNLSCKI 268
Score = 33.7 bits (76), Expect = 0.12
Identities = 43/362 (11%), Positives = 99/362 (27%), Gaps = 85/362 (23%)
Query: 19 DPEYSEGDDSYVETDFSFEEKYWFMKNGTRKPTPAQINPRT-----NRRDSKLWPKEDPG 73
DP ++ D ++ R+ ++ N +++K W +
Sbjct: 210 DPNWTSRSDHSSNIKLRIHS----IQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS 265
Query: 74 -------QDR-IVNQLMYVPNNYDSKNVKKILLFNALTSWNVKLGSSMFSNC-------- 117
+ + + + L + I L + + S+
Sbjct: 266 CKILLTTRFKQVTDFL-------SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL 318
Query: 118 PVNACALTTNKAESPFVWAL---YFLECPYHTQHVAHNDVFNWTATYRSDSDIVTPYEKW 174
P +P ++ + + H + T S +++ P E
Sbjct: 319 PREVLTT------NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYR 372
Query: 175 VYYDD-----RHKQMPLD-------KMKNY----AANKTHKVAWFVSNCGAKNNRLQYAH 218
+D +P + NK HK + + K + +
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYS--LVEKQPKESTISI-P 429
Query: 219 ELGKYIEVDIYGSCGSKKCPRISKCFRLLDTKYKFYLAFENSNCVDYITEKLYINGLSHN 278
+ Y+E+ K R + Y F++ + + ++ + + + H+
Sbjct: 430 SI--YLEL-------KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHH 480
Query: 279 VLPIVMGARPEDYKKAAPMNSYIHVD-DFPSAK--HLAEYLNKL-DANDTL-----YNSY 329
+ I R ++ + +D F K H + N +TL Y Y
Sbjct: 481 LKNIEHPERMTLFRM-------VFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPY 533
Query: 330 FR 331
Sbjct: 534 IC 535
>3k4h_A Putative transcriptional regulator; structural genomics, protein
structure INI NEW YORK structural genomix research
consortium; HET: MAL; 2.80A {Bacillus cytotoxicus nvh
391-98}
Length = 292
Score = 32.1 bits (74), Expect = 0.27
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 271 YINGLSHNVLPIVMGARPEDYKKAAPMNSYIHVDDFPSAKHLAEYL 316
I L P V+ +P D K Y+ D++ +A+ +AEYL
Sbjct: 84 IIQYLHEQNFPFVLIGKPYDRKDEIT---YVDNDNYTAAREVAEYL 126
>3jr7_A Uncharacterized EGV family protein COG1307; structural genomics,
PSI2, MCSG, protein struct initiative; HET: PG6; 2.00A
{Ruminococcus gnavus}
Length = 298
Score = 30.7 bits (70), Expect = 0.75
Identities = 5/34 (14%), Positives = 10/34 (29%), Gaps = 1/34 (2%)
Query: 25 GDDSYVE-TDFSFEEKYWFMKNGTRKPTPAQINP 57
D + + EE + T + +P
Sbjct: 52 EDTQWTDDDSLKQEELLLKIAESTSCAKTSCPSP 85
>3huu_A Transcription regulator like protein; PSI-II, NYSGXRC, LAC I, STR
genomics, protein structure initiative; 1.95A
{Staphylococcus haemolyticus}
Length = 305
Score = 30.6 bits (70), Expect = 0.80
Identities = 9/46 (19%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 271 YINGLSHNVLPIVMGARPEDYKKAAPMNSYIHVDDFPSAKHLAEYL 316
+ L+ +P ++ + +Y+ +I D+ +A L +YL
Sbjct: 98 IEHLLNEFKVPYLIVGKSLNYENI----IHIDNDNIDAAYQLTQYL 139
>3fdj_A DEGV family protein; GUT microbiome, structural genomics, PSI-2,
protein ST initiative, midwest center for structural
genomics, MCSG; HET: MSE P6G PG4; 1.80A {Eubacterium
eligens}
Length = 278
Score = 30.2 bits (69), Expect = 0.90
Identities = 1/34 (2%), Positives = 8/34 (23%), Gaps = 1/34 (2%)
Query: 25 GDDSYVE-TDFSFEEKYWFMKNGTRKPTPAQINP 57
++ + + ++ + A
Sbjct: 32 DNEEFCDDGQLDIHRMLDILEKHKGRSYTACPGI 65
>2iks_A DNA-binding transcriptional dual regulator; escherichia coli
structural genomics, PSI-2, protein structure
initiative; 1.85A {Escherichia coli}
Length = 293
Score = 29.8 bits (68), Expect = 1.4
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 4/50 (8%)
Query: 267 TEKLYINGLSHNVLPIVMGARPEDYKKAAPMNSYIHVDDFPSAKHLAEYL 316
E + +++ PIV R D + + + D A+ LAE L
Sbjct: 88 PEHPFYQRWANDPFPIVALDRALDREHF----TSVVGADQDDAEMLAEEL 133
>3hs3_A Ribose operon repressor; PSI-II, NYSGXRC, periplasmic binding
protein, structural genomics, protein structure
initiative; 1.60A {Lactobacillus acidophilus}
Length = 277
Score = 29.5 bits (67), Expect = 1.8
Identities = 16/99 (16%), Positives = 28/99 (28%), Gaps = 24/99 (24%)
Query: 250 KYKFYLAFENSNCVD-------YITEKLYINGLSHNVLPIVMGARPEDYKKAAPMNSYIH 302
KY+ + +N VD I ++N P+VM I
Sbjct: 55 KYQNAIINFENNNVDGIITSAFTIPPNFHLN------TPLVMYDSANINDDI----VRIV 104
Query: 303 VDDFPSAKHLAEYLNK-------LDANDTLYNSYFRWKG 334
++ K + L+K +L R +
Sbjct: 105 SNNTKGGKESIKLLSKKIEKVLIQHWPLSLPTIRERIEA 143
>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein
structure initiative II(PSI II), NYSGXRC, 11232D),
structural genomics; 2.53A {Corynebacterium glutamicum}
Length = 366
Score = 29.5 bits (67), Expect = 2.1
Identities = 7/37 (18%), Positives = 15/37 (40%), Gaps = 4/37 (10%)
Query: 280 LPIVMGARPEDYKKAAPMNSYIHVDDFPSAKHLAEYL 316
LP V+ +P + +I ++ + A+ L
Sbjct: 152 LPAVIADQPAREEGM----PFIAPNNRKAIAPAAQAL 184
>3gv0_A Transcriptional regulator, LACI family; transcription regulator,
PSI-II, structural genomics structure initiative; 2.35A
{Agrobacterium tumefaciens str}
Length = 288
Score = 29.1 bits (66), Expect = 2.3
Identities = 7/46 (15%), Positives = 16/46 (34%), Gaps = 4/46 (8%)
Query: 271 YINGLSHNVLPIVMGARPEDYKKAAPMNSYIHVDDFPSAKHLAEYL 316
+ ++ +P V R + + ++ D+ A E L
Sbjct: 81 RVRFMTERNMPFVTHGRSDMGIEH----AFHDFDNEAYAYEAVERL 122
>4dqv_A Probable peptide synthetase NRP (peptide synthase; GXXGXXG motif,
rossmann fold, short chain dehydrogenase/REDU family,
reductase; 2.30A {Mycobacterium tuberculosis}
Length = 478
Score = 29.1 bits (65), Expect = 2.6
Identities = 16/113 (14%), Positives = 34/113 (30%), Gaps = 13/113 (11%)
Query: 118 PVNACA-----LTTNKAESPFVWALYFLECPYHTQHVAHNDVFNWTATYRSDSDIVTPYE 172
PV A L A S + H + ++ +W + +
Sbjct: 330 PVTFVAEAIAVLGARVAGSSLAGFATYHVMNPHDDGIGLDEYVDWLIEAGYPIRRIDDFA 389
Query: 173 KWV--------YYDDRHKQMPLDKMKNYAANKTHKVAWFVSNCGAKNNRLQYA 217
+W+ DR ++ + M + ++ + C A +R + A
Sbjct: 390 EWLQRFEASLGALPDRQRRHSVLPMLLASNSQRLQPLKPTRGCSAPTDRFRAA 442
>3p8c_F ABL interactor 2; actin polymerization, protein binding; 2.29A
{Homo sapiens}
Length = 159
Score = 28.0 bits (62), Expect = 3.1
Identities = 9/44 (20%), Positives = 17/44 (38%)
Query: 171 YEKWVYYDDRHKQMPLDKMKNYAANKTHKVAWFVSNCGAKNNRL 214
Y + Y KQ L++ K Y VA+ ++ ++
Sbjct: 33 YCENNYIQSADKQRALEETKAYTTQSLASVAYLINTLANNVLQM 76
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 28.7 bits (64), Expect = 4.2
Identities = 9/26 (34%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 100 NALTSWNV--KLGSSMFSNCPVNACA 123
N +++W + SS PV ACA
Sbjct: 1082 NTMSAWVNMLLISSSGPIKTPVGACA 1107
>2dt8_A DEGV family protein; fatty acid binding, structural genomics,
NPPSFA, natio project on protein structural and
functional analyses; HET: PLM; 1.48A {Thermus
thermophilus}
Length = 280
Score = 27.9 bits (63), Expect = 4.8
Identities = 7/34 (20%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 25 GDDSYVE-TDFSFEEKYWFMKNGTRKPTPAQINP 57
Y + + + E + ++ G PT +Q +P
Sbjct: 33 SGAIYRDWEEITPTEIFQKVREGAAFPTTSQPSP 66
>3lup_A DEGV family protein; PSI-2, MCSG, structural genomics, fatty acid
binding, protei structure initiative; HET: ELA; 2.65A
{Streptococcus agalactiae}
Length = 285
Score = 27.9 bits (63), Expect = 5.0
Identities = 5/34 (14%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 25 GDDSYVE-TDFSFEEKYWFMKNGTRKPTPAQINP 57
+Y+E + + ++ Y + P +Q +
Sbjct: 36 DGKTYIEGQNLTLDQYYDKLAASKELPKTSQPSL 69
>3r8s_E 50S ribosomal protein L4; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_C
1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E
2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E*
2qbk_E* 2qov_E 2qox_E 2qoz_E* ...
Length = 201
Score = 27.6 bits (62), Expect = 5.5
Identities = 14/65 (21%), Positives = 22/65 (33%), Gaps = 21/65 (32%)
Query: 282 IVMGARPEDYKKAAPM-----------------NSYIHVDDF----PSAKHLAEYLNKLD 320
+ ARP+D+ + + I V+ F P K LA+ L +
Sbjct: 83 VTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMA 142
Query: 321 ANDTL 325
D L
Sbjct: 143 LEDVL 147
>3hcw_A Maltose operon transcriptional repressor; RNA-binding, PSI-2,
NYSGXRC, STRU genomics, protein structure initiative;
2.20A {Staphylococcus aureus subsp}
Length = 295
Score = 27.5 bits (62), Expect = 6.7
Identities = 6/46 (13%), Positives = 19/46 (41%), Gaps = 2/46 (4%)
Query: 271 YINGLSHNVLPIVMGARPEDYKKAAPMNSYIHVDDFPSAKHLAEYL 316
L +P ++ +P ++I D+ ++++L ++
Sbjct: 83 IKQMLIDESMPFIVIGKPTS--DIDHQFTHIDNDNILASENLTRHV 126
>2hsg_A Glucose-resistance amylase regulator; CCPA, transcriptional
regulator, transcription regulator; 2.50A {Bacillus
megaterium} SCOP: a.35.1.5 c.93.1.1 PDB: 1rzr_G 2jcg_A
1zvv_A 3oqo_A* 3oqm_A* 3oqn_A*
Length = 332
Score = 27.5 bits (62), Expect = 7.1
Identities = 8/46 (17%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 271 YINGLSHNVLPIVMGARPEDYKKAAPMNSYIHVDDFPSAKHLAEYL 316
++ L + +P+V+ A E + + +D +A + L
Sbjct: 131 HVEELKKSPVPVVLAASIESTNQI----PSVTIDYEQAAFDAVQSL 172
>3fys_A Protein DEGV; fatty acid-binding, EDD fold, fatty acid-binding
protein; HET: PLM; 2.50A {Bacillus subtilis}
Length = 315
Score = 27.2 bits (61), Expect = 8.5
Identities = 7/34 (20%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 25 GDDSYVE-TDFSFEEKYWFMKNGTRKPTPAQINP 57
+++Y E + ++ Y +K PT +Q
Sbjct: 67 REETYREEIELDWKSFYEEVKKHNELPTTSQPPI 100
>3ns4_A Vacuolar protein sorting-associated protein 53; GARP complex
component, helical bundle, membrane tethering C membrane
traffic, VPS51; HET: MSE; 2.90A {Saccharomyces
cerevisiae}
Length = 271
Score = 27.1 bits (59), Expect = 9.6
Identities = 20/108 (18%), Positives = 27/108 (25%), Gaps = 5/108 (4%)
Query: 70 EDPGQDRIVNQLMYVPNNYDSKNVKKILLFNALTSWNVKLGSSMFSNCPVNACALTTNKA 129
D D NN DS +L W++ L M+S +
Sbjct: 129 LDSADDYYETYSKLTNNNPDSAVWSFVLALKG-IPWDLALWKKMWSAYNLETDDTDEGSR 187
Query: 130 ESPFVWALYFLECPYHTQHVAHNDVF----NWTATYRSDSDIVTPYEK 173
F +N NW+ R D I P K
Sbjct: 188 PDSNRDLFIFKWDKVLLGQFENNLARMQDPNWSKFVRQDLKISPPVMK 235
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
0.319 0.134 0.437
Gapped
Lambda K H
0.267 0.0591 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,933,524
Number of extensions: 336966
Number of successful extensions: 651
Number of sequences better than 10.0: 1
Number of HSP's gapped: 647
Number of HSP's successfully gapped: 29
Length of query: 381
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 286
Effective length of database: 4,049,298
Effective search space: 1158099228
Effective search space used: 1158099228
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: 58 (26.4 bits)