RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2439
(146 letters)
>3sj5_A Methyl-accepting chemotaxis protein; no or O2-sensing protein,
signaling protein; HET: HEM; 1.67A {Caldanaerobacter
subterraneus} PDB: 3nvr_A* 3tf0_A* 1u4h_A* 1u56_A*
3m0b_A* 1u55_A* 3tf1_A* 1xbn_A* 3nvu_A* 3eee_A* 3iqb_A*
3lah_A* 3lai_A*
Length = 188
Score = 56.4 bits (136), Expect = 7e-11
Identities = 13/81 (16%), Positives = 24/81 (29%), Gaps = 7/81 (8%)
Query: 69 GIILAIAFQKL---EYGDDVWLKVLKKAGCKVS-CFNTHHIYPDIYMPDLATACASVIEG 124
G + + K YG+DV + LK G + D + + +
Sbjct: 3 GTFVG-TWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKT-- 59
Query: 125 DLTSEYFMEFFGKCFVRYFSN 145
G+ ++ FS
Sbjct: 60 GKNVNEIWREVGRQNIKTFSE 80
Score = 54.8 bits (132), Expect = 3e-10
Identities = 11/67 (16%), Positives = 20/67 (29%), Gaps = 3/67 (4%)
Query: 2 EYGDDVWLKVLKKAGCKVS-CFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKC 60
YG+DV + LK G + D + + + G+
Sbjct: 16 LYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKT--GKNVNEIWREVGRQ 73
Query: 61 FVRYFSN 67
++ FS
Sbjct: 74 NIKTFSE 80
>2kii_A Putative uncharacterized protein; H-NOX, unknown function; HET:
HEM; NMR {Shewanella oneidensis} PDB: 2kil_A*
Length = 181
Score = 53.1 bits (127), Expect = 1e-09
Identities = 10/66 (15%), Positives = 28/66 (42%), Gaps = 2/66 (3%)
Query: 2 EYGDDVWLKVLKKAGCKVSCFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCF 61
+ G VW ++L+K K + + Y + + + A + ++ + ++ FG+
Sbjct: 16 QCGMSVWNELLEKHAPKDRVYVSAKSYAESELFSIVQDVAQRL--NMPIQDVVKAFGQFL 73
Query: 62 VRYFSN 67
++
Sbjct: 74 FNGLAS 79
>3tfg_A ALR2278 protein; heme-based sensor domain, GAS binding, signaling
protein; HET: HEM; 1.90A {Nostoc SP} PDB: 3tfd_A*
3tfe_A* 3tff_A* 2o09_A* 2o0c_A* 2o0g_A* 3l6j_A* 3tf8_A*
3tf9_A* 3tfa_A*
Length = 189
Score = 51.9 bits (124), Expect = 3e-09
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 2 EYGDDVWLKVLKKAGCK-VSCFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKC 60
+G+D W + +KAG + + F Y D L A + V+ +E + FG+
Sbjct: 16 HHGEDTWEAIKQKAGLEDIDFFVGMEAYSDDVTYHLVGAASEVL--GKPAEEWWIAFGEY 73
Query: 61 FVRYFSNLG 69
+V Y S G
Sbjct: 74 WVTYTSEEG 82
>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 = 33.4 bits (75), Expect = 0.013
Identities = 11/51 (21%), Positives = 16/51 (31%), Gaps = 26/51 (50%)
Query: 75 AFQKLEYGDDVWLKVLKKAGCKVSCFNTHHIYPDIYMPDLATACA--SVIE 123
A +KL+ LK +Y D A A A + +E
Sbjct: 21 ALKKLQ-------ASLK-----------------LYADDSAPALAIKATME 47
Score = 32.2 bits (72), Expect = 0.030
Identities = 11/40 (27%), Positives = 15/40 (37%), Gaps = 16/40 (40%)
Query: 10 KVLKK--AGCKVSCFNTHHIYPDIYMPDLATACA--SVIE 45
+ LKK A K +Y D A A A + +E
Sbjct: 20 QALKKLQASLK------------LYADDSAPALAIKATME 47
>1m5w_A Pyridoxal phosphate biosynthetic protein PDXJ; TIM barrel,
protein-substrate complex, multi-binding states; HET:
DXP; 1.96A {Escherichia coli} SCOP: c.1.24.1 PDB: 1ho1_A
1ho4_A* 1ixn_A* 1ixo_A* 1ixp_A 1ixq_A 3f4n_A*
Length = 243
Score = 30.9 bits (71), Expect = 0.12
Identities = 13/38 (34%), Positives = 14/38 (36%), Gaps = 5/38 (13%)
Query: 9 LKVLKKAGCKVSCFNTHHIYPDIYMPDLATAC-ASVIE 45
K L AG +VS F I D A A IE
Sbjct: 120 CKRLADAGIQVSLF----IDADEEQIKAAAEVGAPFIE 153
Score = 30.9 bits (71), Expect = 0.12
Identities = 13/38 (34%), Positives = 14/38 (36%), Gaps = 5/38 (13%)
Query: 87 LKVLKKAGCKVSCFNTHHIYPDIYMPDLATAC-ASVIE 123
K L AG +VS F I D A A IE
Sbjct: 120 CKRLADAGIQVSLF----IDADEEQIKAAAEVGAPFIE 153
>3gk0_A PNP synthase, pyridoxine 5'-phosphate synthase; decode, ssgcid,
niaid, SBRI, cytoplasm, pyridoxine biosynthesis,
transferase; HET: DXP; 2.28A {Burkholderia pseudomallei}
Length = 278
Score = 30.6 bits (70), Expect = 0.13
Identities = 15/38 (39%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 9 LKVLKKAGCKVSCFNTHHIYPDIYMPDLATAC-ASVIE 45
K L AG +VS F I PD A A VIE
Sbjct: 148 CKQLADAGVRVSLF----IDPDEAQIRAAHETGAPVIE 181
Score = 30.6 bits (70), Expect = 0.13
Identities = 15/38 (39%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 87 LKVLKKAGCKVSCFNTHHIYPDIYMPDLATAC-ASVIE 123
K L AG +VS F I PD A A VIE
Sbjct: 148 CKQLADAGVRVSLF----IDPDEAQIRAAHETGAPVIE 181
>3nvs_A 3-phosphoshikimate 1-carboxyvinyltransferase; structural genomics,
center for structural genomics of infec diseases, csgid;
HET: S3P SKM GPJ EPE; 1.02A {Vibrio cholerae} PDB:
1g6s_A* 1g6t_A* 1x8r_A* 1x8t_A* 2aa9_A* 2aay_A* 2pq9_A*
1eps_A 1mi4_A* 3fjz_A* 3fjx_A* 2qfs_A* 2qft_A* 2qfq_A*
2qfu_A* 3fk0_A* 3fk1_A* 1q36_A* 3ti2_A* 1p88_A ...
Length = 450
Score = 30.7 bits (70), Expect = 0.14
Identities = 26/144 (18%), Positives = 48/144 (33%), Gaps = 43/144 (29%)
Query: 9 LKVLKKAGCKVSC--FNTHHIYPDIYMPDLATACASVIEGDLTS-EYFMEF----FGKCF 61
L ++++ G +V + I + ++EGD +S YF+ G+
Sbjct: 230 LHIMEQFGVQVINHDYQEFVIPAG---QSYVSPGQFLVEGDASSASYFLAAAAIKGGEVK 286
Query: 62 VRYFSNLGIILAIAFQKLEYGDDVWLKVLKKAGCKVSC----------------FNTHHI 105
V +G + Q GD + L+K G ++ + +HI
Sbjct: 287 VT---GIG---KNSIQ----GDIQFADALEKMGAQIEWGDDYVIARRGELNAVDLDFNHI 336
Query: 106 YPDIYMPDLATACA-----SVIEG 124
PD +AT + I
Sbjct: 337 -PDA-AMTIATTALFAKGTTAIRN 358
>3o6c_A PNP synthase, pyridoxine 5'-phosphate synthase; structural
genomics, IDP90671, center for structural genomic
infectious diseases; HET: MSE; 1.87A {Campylobacter
jejuni subsp} PDB: 3o6d_A*
Length = 260
Score = 29.9 bits (68), Expect = 0.23
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 5/38 (13%)
Query: 9 LKVLKKAGCKVSCFNTHHIYPDIYMPDLATAC-ASVIE 45
++ L+ A +VS F I P + + + A IE
Sbjct: 117 IEKLQNANIEVSLF----INPSLEDIEKSKILKAQFIE 150
Score = 29.9 bits (68), Expect = 0.23
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 5/38 (13%)
Query: 87 LKVLKKAGCKVSCFNTHHIYPDIYMPDLATAC-ASVIE 123
++ L+ A +VS F I P + + + A IE
Sbjct: 117 IEKLQNANIEVSLF----INPSLEDIEKSKILKAQFIE 150
>1jql_B DNA polymerase III, delta subunit; processivity clamp, clamp
loader, DNA replication, AAA+ ATPase, transferase; HET:
DNA; 2.50A {Escherichia coli} SCOP: c.37.1.20
Length = 140
Score = 29.2 bits (65), Expect = 0.26
Identities = 9/61 (14%), Positives = 18/61 (29%), Gaps = 4/61 (6%)
Query: 43 VIEGDLTSEYFMEFFGKCFVRYFSNL--GIILAIAFQKLEYGDD--VWLKVLKKAGCKVS 98
+ L + + L ++L + KL + W L +V+
Sbjct: 79 TLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVT 138
Query: 99 C 99
C
Sbjct: 139 C 139
>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 = 29.4 bits (65), Expect = 0.52
Identities = 26/176 (14%), Positives = 47/176 (26%), Gaps = 51/176 (28%)
Query: 5 DDVW-LKVLKK--AGCKVSCFNTHHIYPDIYMPD-LATACASVIEGD-----LTSEYFME 55
+V K CK+ T + D L+ A + I D LT +
Sbjct: 251 LNVQNAKAWNAFNLSCKI-LLTTR----FKQVTDFLSAATTTHISLDHHSMTLTPDEVKS 305
Query: 56 FFGKCFVRYFSNL------GIILAIAF--QKLEYGDDVW------------------LKV 89
K +L ++ + + G W L V
Sbjct: 306 LLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNV 365
Query: 90 LKKAGCKVSCFNTHHIYP-DIYMPDLATACASVIE---GDLTSEYFMEFFGKCFVR 141
L+ A + F+ ++P ++P ++ D+ M K
Sbjct: 366 LEPAEYR-KMFDRLSVFPPSAHIP------TILLSLIWFDVIKSDVMVVVNKLHKY 414
>1ogo_X Dextranase; hydrolase, dextran degradation, glycosidase; HET: BGC
GLC; 1.65A {Penicillium minioluteum} SCOP: b.133.1.1
b.80.1.10 PDB: 1ogm_X*
Length = 574
Score = 27.6 bits (60), Expect = 1.7
Identities = 15/79 (18%), Positives = 26/79 (32%), Gaps = 5/79 (6%)
Query: 72 LAIAFQKLEYGDDVWLKVLKKAGCKVSCFNTHHIYPDIY-----MPDLATACASVIEGDL 126
L +A+ + EY DV +K+L G + + I P D V
Sbjct: 97 LNMAWSQFEYSHDVDVKILATDGSSLGSPSDVVIRPVSISYAISQSDDGGIVIRVPADAN 156
Query: 127 TSEYFMEFFGKCFVRYFSN 145
++ +EF +
Sbjct: 157 GRKFSVEFKTDLYTFLSDG 175
Score = 25.7 bits (55), Expect = 7.8
Identities = 13/71 (18%), Positives = 21/71 (29%), Gaps = 5/71 (7%)
Query: 2 EYGDDVWLKVLKKAGCKVSCFNTHHIYPDIY-----MPDLATACASVIEGDLTSEYFMEF 56
EY DV +K+L G + + I P D V ++ +EF
Sbjct: 105 EYSHDVDVKILATDGSSLGSPSDVVIRPVSISYAISQSDDGGIVIRVPADANGRKFSVEF 164
Query: 57 FGKCFVRYFSN 67
+
Sbjct: 165 KTDLYTFLSDG 175
>1jr3_D DNA polymerase III, delta subunit; processivity, processivity
clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA;
2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB:
1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*
Length = 343
Score = 26.0 bits (57), Expect = 5.8
Identities = 18/118 (15%), Positives = 34/118 (28%), Gaps = 23/118 (19%)
Query: 3 YGDDVWL---------KVLKKAGCKVSCFNTHHIYPDIYMPDLATACAS--------VIE 45
G+D L +V G +T I P+ + + C + +
Sbjct: 24 LGNDPLLLQESQDAVRQVAAAQG--FEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTLL 81
Query: 46 GDLTSEYFMEFFGKCFVRYFSNL--GIILAIAFQKLEYGDDV--WLKVLKKAGCKVSC 99
L + + L ++L + KL + W L +V+C
Sbjct: 82 LLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTC 139
>3ls9_A Triazine hydrolase; atrazine chlorohydrolase TRZN; 1.40A
{Arthrobacter aurescens} PDB: 3lsc_A* 3lsb_A*
Length = 456
Score = 25.7 bits (57), Expect = 6.8
Identities = 9/59 (15%), Positives = 13/59 (22%), Gaps = 21/59 (35%)
Query: 51 EYFMEFFGKCFVRYFSNLGIILAIAFQKLEYGDDVWL-----------KVLKKAGCKVS 98
+G R+ G D VWL AG ++
Sbjct: 246 GMSDHLYGMTPWRFLEKHGWA----------SDRVWLAHAVVPPREEIPEFADAGVAIA 294
>3eyp_A Putative alpha-L-fucosidase; structural genomics, hydrolase,
lipoprotein, PSI-2, protein initiative; 1.90A
{Bacteroides thetaiotaomicron}
Length = 469
Score = 25.7 bits (56), Expect = 7.3
Identities = 7/34 (20%), Positives = 10/34 (29%), Gaps = 1/34 (2%)
Query: 72 LAIAFQKLEYGDDVWLKVLKKAGCKVSCFNT-HH 104
F W++ LK AG + H
Sbjct: 45 STAIFNPTALDCRQWMQTLKAAGIPAAILTAKHA 78
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
0.329 0.144 0.472
Gapped
Lambda K H
0.267 0.0575 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,442,786
Number of extensions: 137371
Number of successful extensions: 416
Number of sequences better than 10.0: 1
Number of HSP's gapped: 410
Number of HSP's successfully gapped: 27
Length of query: 146
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 61
Effective length of database: 4,328,508
Effective search space: 264038988
Effective search space used: 264038988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.5 bits)