RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy111
(85 letters)
>2wvv_A Alpha-L-fucosidase; alpha-L-fucose, hydrolase, glycoside hydrolase
family 29; 1.73A {Bacteroides thetaiotaomicron} PDB:
2xii_A* 2xib_A* 2wvv_B 2wvt_A* 2wvu_A* 2wvs_A*
Length = 450
Score = 63.3 bits (154), Expect = 1e-13
Identities = 19/88 (21%), Positives = 36/88 (40%), Gaps = 14/88 (15%)
Query: 2 VVVNDRW---------CNTCLCKHGGYLTCEDKYNPGKFQSRKF-----ENCFTLDKYSW 47
V +N R ++ G Y + ++ P + K E C T+ + W
Sbjct: 223 VAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQW 282
Query: 48 GYRRDANIDDILNMTEVLQTMMNTVSFG 75
GY +D ++ + EV+ +++ VS G
Sbjct: 283 GYHKDWSLSYVKTPIEVIDRIVHAVSMG 310
>2zxd_A Alpha-L-fucosidase, putative; TIM barrel, hydrolase; HET: ZXD;
2.15A {Thermotoga maritima} PDB: 2zwy_A* 2zx5_A* 2zx6_A*
2zx7_A* 2zwz_A* 2zx9_A* 2zxa_A* 2zxb_A* 2zx8_A* 1hl9_A*
1hl8_A* 1odu_A* 2wsp_A*
Length = 455
Score = 48.1 bits (114), Expect = 2e-08
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 2 VVVNDRWCNTCLCKHGGYLTCEDKYN-PGKFQSRKFENCFTLDKYSWGYRRDANIDDILN 60
VNDRW H + T E N PG K+E + S+GY R+ + +L+
Sbjct: 249 GSVNDRWGV----PHWDFKTAEYHVNYPGDLPGYKWEFTRGIGL-SFGYNRNEGPEHMLS 303
Query: 61 MTEVLQTMMNTVSFG 75
+ +++ T+++ VS G
Sbjct: 304 VEQLVYTLVDVVSKG 318
>3eyp_A Putative alpha-L-fucosidase; structural genomics, hydrolase,
lipoprotein, PSI-2, protein initiative; 1.90A
{Bacteroides thetaiotaomicron}
Length = 469
Score = 36.1 bits (83), Expect = 4e-04
Identities = 10/87 (11%), Positives = 23/87 (26%), Gaps = 18/87 (20%)
Query: 5 NDRWCNTCLCKHG----------------GYLTCEDKYNPGKFQSRKFENCFTLDKYSWG 48
+ RW + G Y ++ E ++ SW
Sbjct: 205 DVRWMGNEAGEAGDPCWATTDSVAIRDEAQYYKGLNEGMLDGDAYIPAETDVSIRP-SWF 263
Query: 49 YRRDANIDDILNMTEVLQTMMNTVSFG 75
Y + + + ++ E+ +V
Sbjct: 264 YHAEED-SRVKSVRELWDIYCTSVGRN 289
>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 = 29.8 bits (66), Expect = 0.082
Identities = 11/70 (15%), Positives = 24/70 (34%), Gaps = 18/70 (25%)
Query: 31 FQSRKFENCF----------TLDKYSWGYR-----RDANIDDILNMTEVLQTMMNTVSFG 75
+S+ +ENC + ++ + R + D L+ ++ S
Sbjct: 238 LKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMT 297
Query: 76 ---DKTLSIL 82
D+ S+L
Sbjct: 298 LTPDEVKSLL 307
>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 = 28.1 bits (62), Expect = 0.30
Identities = 9/56 (16%), Positives = 22/56 (39%), Gaps = 8/56 (14%)
Query: 20 LTCEDKYNPGKFQSRK-FENC-FTLDKYSWGYRRDANIDDILNMTEVLQTMMNTVS 73
+ E + GK ++ K F+ Y++ + +L+ T+ Q + +
Sbjct: 1691 MIFETIVD-GKLKTEKIFKEINEHSTSYTFR-----SEKGLLSATQFTQPALTLME 1740
>2vf7_A UVRA2, excinuclease ABC, subunit A.; DNA-binding protein,
nucleotide-binding, zinc-binding domain, SOS response,
metal-binding; HET: ADP; 2.30A {Deinococcus radiodurans}
PDB: 2vf8_A*
Length = 842
Score = 27.5 bits (62), Expect = 0.47
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 21/49 (42%)
Query: 19 YLTCED----KYNPGKFQSRKFENCFTLD-KYSWGYRRDANIDDILNMT 62
Y C +YN E TL+ +Y R NI D+L +T
Sbjct: 661 YAPCPVCHGTRYNA--------E---TLEVEY-----RGKNIADVLALT 693
>3r38_A UDP-N-acetylglucosamine 1-carboxyvinyltransferase; biosynthesis
and degradation of murein sacculus and peptidog
infectious diseases; 2.23A {Listeria monocytogenes}
PDB: 3sg1_A*
Length = 454
Score = 27.1 bits (61), Expect = 0.56
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 54 NIDDILNMTEVLQTMMNTVSFGDKTLSI 81
N+ D+ + EVL+ + VSF + +++
Sbjct: 71 NLSDVFTINEVLKYLNADVSFVNDEVTV 98
>2yvw_A UDP-N-acetylglucosamine 1-carboxyvinyltransferase; peptidoglycan,
structu genomics, NPPSFA; HET: EPU; 1.81A {Aquifex
aeolicus} PDB: 3swg_A*
Length = 425
Score = 25.9 bits (58), Expect = 1.4
Identities = 6/28 (21%), Positives = 15/28 (53%)
Query: 54 NIDDILNMTEVLQTMMNTVSFGDKTLSI 81
++ D+ N +L+ + + F + T+ I
Sbjct: 55 DLLDVRNTLLLLRELGAELEFLNNTVFI 82
>2r6f_A Excinuclease ABC subunit A; UVRA, nucleotide excision repair, DNA
repair, ABC ATPase, at cassette, DNA damage, DNA
excision; HET: ADP; 3.20A {Geobacillus
stearothermophilus} PDB: 3uwx_A
Length = 972
Score = 25.9 bits (58), Expect = 1.8
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 21/49 (42%)
Query: 19 YLTCE----DKYNPGKFQSRKFENCFTLD-KYSWGYRRDANIDDILNMT 62
Y+ CE +YN E TL+ Y + NI ++L+MT
Sbjct: 776 YVPCEVCHGKRYNR--------E---TLEVTY-----KGKNIAEVLDMT 808
>2ygr_A Uvrabc system protein A; hydrolase, nucleotide excision repair;
3.40A {Mycobacterium tuberculosis} PDB: 3zqj_A
Length = 993
Score = 25.6 bits (57), Expect = 2.6
Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 21/49 (42%)
Query: 19 YLTCE----DKYNPGKFQSRKFENCFTLD-KYSWGYRRDANIDDILNMT 62
Y+ CE +YN R+ TL+ Y + + ++L+M+
Sbjct: 794 YVPCEVCQGARYN------RE-----TLEVHY-----KGKTVSEVLDMS 826
>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA
repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A
{Geobacillus}
Length = 670
Score = 25.2 bits (56), Expect = 3.0
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 21/49 (42%)
Query: 19 YLTCE----DKYNPGKFQSRKFENCFTLD-KYSWGYRRDANIDDILNMT 62
Y+ CE +YN R+ TL+ Y + NI ++L+MT
Sbjct: 474 YVPCEVCHGKRYN------RE-----TLEVTY-----KGKNIAEVLDMT 506
>3pih_A Uvrabc system protein A; hydrolase, ABC ATPase, DNA repair,
nucleotide excision repai hydrolase-DNA complex; HET:
DNA; 2.90A {Thermotoga maritima}
Length = 916
Score = 24.7 bits (55), Expect = 4.0
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 21/49 (42%)
Query: 19 YLTCE----DKYNPGKFQSRKFENCFTLD-KYSWGYRRDANIDDILNMT 62
Y+ C+ +YN R+ TL+ Y + NI DIL+MT
Sbjct: 736 YVECDVCKGKRYN------RE-----TLEITY-----KGKNISDILDMT 768
>3h2y_A GTPase family protein; GTP-binding protein YQEH, possibly
involved in replication initiation, csgid, IDP90222;
HET: DGI; 1.80A {Bacillus anthracis str}
Length = 368
Score = 24.2 bits (52), Expect = 7.0
Identities = 15/60 (25%), Positives = 19/60 (31%), Gaps = 11/60 (18%)
Query: 9 CNTCLCKHGGYLTCEDKYNPGKFQSRKFEN-------CFTLDKYSWGYRRDANIDDILNM 61
C C G + EDK G + E CF L Y+ DD L +
Sbjct: 7 CIGC----GVEIQTEDKNEVGYAPASSLEKEQVICQRCFRLKHYNEIQDVSLTDDDFLRI 62
>1z4r_A General control of amino acid synthesis protein 5-like 2; GCN5,
acetyltransferase, SGC, structural genomics, structural
genomics consortium; HET: ACO; 1.74A {Homo sapiens}
SCOP: d.108.1.1 PDB: 1cm0_B*
Length = 168
Score = 23.7 bits (51), Expect = 8.1
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 20 LTCEDKYNPGKFQSRKFENCFTLDKYSW-GYRRD 52
LT D+Y G F+ + F + K + GY +D
Sbjct: 117 LTYADEYAIGYFKKQGFSKDIKVPKSRYLGYIKD 150
>2foj_A Ubiquitin carboxyl-terminal hydrolase 7; MATH domain, hydrolase;
1.60A {Homo sapiens} PDB: 1yze_A 1yy6_A 2foo_A 2fop_A
3mqr_A 3mqs_C 2f1w_A 2f1x_A 2f1y_A 2xxn_A
Length = 155
Score = 23.6 bits (51), Expect = 8.4
Identities = 6/40 (15%), Positives = 16/40 (40%)
Query: 24 DKYNPGKFQSRKFENCFTLDKYSWGYRRDANIDDILNMTE 63
+ + K SR+ + F + WG+ ++ + +
Sbjct: 92 NYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEK 131
>3gt5_A N-acetylglucosamine 2-epimerase; structural genomics, isomerase,
PSI-2; 1.70A {Xylella fastidiosa}
Length = 402
Score = 24.0 bits (51), Expect = 9.0
Identities = 7/35 (20%), Positives = 11/35 (31%)
Query: 16 HGGYLTCEDKYNPGKFQSRKFENCFTLDKYSWGYR 50
GGY + + F + YS G +
Sbjct: 93 TGGYAWTLCDDRVEDDTNHCYGLAFVMLAYSCGLK 127
>2jk9_A SPRY domain-containing SOCS box protein 1; transcription
regulation, transcription; 1.79A {Homo sapiens} PDB:
3f2o_A 2fnj_A 2v24_A 2ihs_A
Length = 212
Score = 23.9 bits (51), Expect = 9.5
Identities = 6/41 (14%), Positives = 11/41 (26%)
Query: 14 CKHGGYLTCEDKYNPGKFQSRKFENCFTLDKYSWGYRRDAN 54
+ G + S + + SWG+ N
Sbjct: 86 RQRGTHAVVGVATADAPLHSVGYTTLVGNNHESWGWDLGRN 126
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
0.323 0.137 0.449
Gapped
Lambda K H
0.267 0.0818 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,286,531
Number of extensions: 61118
Number of successful extensions: 163
Number of sequences better than 10.0: 1
Number of HSP's gapped: 161
Number of HSP's successfully gapped: 26
Length of query: 85
Length of database: 6,701,793
Length adjustment: 53
Effective length of query: 32
Effective length of database: 5,221,980
Effective search space: 167103360
Effective search space used: 167103360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.3 bits)