BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 044684
(545 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NPE|A Chain A, Structure Of Vp14 In Complex With Oxygen
Length = 529
Score = 630 bits (1624), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 312/526 (59%), Positives = 377/526 (71%), Gaps = 9/526 (1%)
Query: 23 HLNPLQKLAASALDKIEDSLIG-FFEKGKSLPKTVDPTVQISGNFAPVQECPVHHGLQVV 81
LN Q+ AA+ALD E+ + E+ LP T DP VQI+GNFAPV E P H L V
Sbjct: 8 QLNLFQRAAAAALDAFEEGFVANVLERPHGLPSTADPAVQIAGNFAPVGERPPVHELPVS 67
Query: 82 GRIPDCLRGVYVRNGANPMFVPSGGHHLFDGDGMIHAVTLGHANQASYSCRYTQTSRLVQ 141
GRIP + GVY RNGANP F P GHHLFDGDGM+HA+ + + SY+CR+T+T+RL Q
Sbjct: 68 GRIPPFIDGVYARNGANPCFDPVAGHHLFDGDGMVHALRIRNGAAESYACRFTETARLRQ 127
Query: 142 EAKYGKPVFPKPIXXXXXXXXXXXXXXFMARAGAGLVDGSRGMGVANAGLVYFHGSLLAM 201
E G+PVFPK I F ARA GLVD S G GVANAGLVYF+G LLAM
Sbjct: 128 ERAIGRPVFPKAIGELHGHSGIARLALFYARAACGLVDPSAGTGVANAGLVYFNGRLLAM 187
Query: 202 SEDDLPYRVKIKPDGDLETIGRFSFDDQLDCPMIAHPKVDPVTSDLHALSYNVVRKPYLK 261
SEDDLPY V++ DGDLET+GR+ FD QL C MIAHPK+DP T +LHALSY+V+++PYLK
Sbjct: 188 SEDDLPYHVRVADDGDLETVGRYDFDGQLGCAMIAHPKLDPATGELHALSYDVIKRPYLK 247
Query: 262 YFRFGGSNDGKKSRDVDVTLDQPTMIHDFAITENCVIIPDHQVVFKLSEMIRGGSPVIFD 321
YF F DG KS DV++ L+QPTMIHDFAITEN V++PDHQVVFKL EM+RGGSPV+ D
Sbjct: 248 YFYF--RPDGTKSDDVEIPLEQPTMIHDFAITENLVVVPDHQVVFKLQEMLRGGSPVVLD 305
Query: 322 KNKTSRFGVLSKNDADESGIQWIDVPNCFCFHLWNAWEENNDDGDRNVVVIGSCMDPPDS 381
KTSRFGVL K+ AD S + W+DVP+CFCFHLWNAWE D+ VVVIGSCM P DS
Sbjct: 306 AAKTSRFGVLPKHAADASEMAWVDVPDCFCFHLWNAWE---DEATGEVVVIGSCMTPADS 362
Query: 382 VFNEHQDPVRSELSEIRLNLKTGESTRRVVV---SGMNLEAGQVNRALLGQKTRYVYLAI 438
+FNE + + S L+EIRL+ +TG STRR V+ +NLE G VNR LLG++TRY YLA+
Sbjct: 363 IFNESDERLESVLTEIRLDARTGRSTRRAVLPPSQQVNLEVGMVNRNLLGRETRYAYLAV 422
Query: 439 ADPWPKCSGIAKVDLGTGEVTKFMYGAHRFGGEPMFVPQNSKNVGSGREDEGFIMGFVRD 498
A+PWPK SG AKVDL TGE+TKF YG RFGGEP FVP + ED+G+++ FV D
Sbjct: 423 AEPWPKVSGFAKVDLSTGELTKFEYGEGRFGGEPCFVPMDPAAAHPRGEDDGYVLTFVHD 482
Query: 499 ERREESEMVIVKASSMEQVASVKLPRRVPYGFHGTFISEQELSGQV 544
ER SE+++V A+ M A+V+LP RVP+GFHGTFI+ QEL Q
Sbjct: 483 ERAGTSELLVVNAADMRLEATVQLPSRVPFGFHGTFITGQELEAQA 528
>pdb|2BIW|A Chain A, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Native Enzyme
pdb|2BIW|B Chain B, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Native Enzyme
pdb|2BIW|C Chain C, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Native Enzyme
pdb|2BIW|D Chain D, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Native Enzyme
pdb|2BIX|A Chain A, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Fe-Free Apoenzyme
pdb|2BIX|B Chain B, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Fe-Free Apoenzyme
Length = 490
Score = 113 bits (282), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 127/485 (26%), Positives = 203/485 (41%), Gaps = 65/485 (13%)
Query: 80 VVGRIPDCLRGVYVRNGANPMFVPSGGH---HLFDGDGMIHAVTLGHANQASYSCRYTQT 136
V G IP L+G RNG P + G H FDGDGM+ A + + ++ +T
Sbjct: 38 VEGSIPPDLQGTLYRNG--PGLLEIGDRPLKHPFDGDGMVTAFKFPGDGRVHFQSKFVRT 95
Query: 137 SRLVQEAKYGKPVFPKPIXXXXXXXXXXXXXXFMARAGAGLVDG---SRGMGVANAGLVY 193
V+E K GK ++ F ++ G + R +AN + Y
Sbjct: 96 QGYVEEQKAGKMIY---------------RGVFGSQPAGGWLKTIFDLRLKNIANTNITY 140
Query: 194 FHGSLLAMSEDDLPYRVKIKPDGDLETIGRFSFDDQL--DCPMIAHPKVDPVTS----DL 247
+ LLA+ E P+R++ +L TIG L P+ AHP++DP ++
Sbjct: 141 WGDRLLALWEGGQPHRLE---PSNLATIGLDDLGGILAEGQPLSAHPRIDPASTFDGGQP 197
Query: 248 HALSYNVVRKPYLKYFRFGGSNDGKKSRDVDVTLDQPTMIHDFAITENCVIIPDHQVVFK 307
+++++ GK R T IHDFAIT + I + V
Sbjct: 198 CYVTFSIKSSLSSTLTLLELDPQGKLLRQKTETFPGFAFIHDFAITPHYAIFLQNNVTLN 257
Query: 308 ----LSEMIRGGSPVIFDKNKTSRFGVLSKNDADESGIQWIDVPNCFCFHLWNAWEENND 363
L + G V F +K ++ +L D E I+ I V F FH NA+EEN
Sbjct: 258 GLPYLFGLRGAGECVQFHPDKPAQI-ILVPRDGGE--IKRIPVQAGFVFHHANAFEENG- 313
Query: 364 DGDRNVVVIGSCMDP-----PDSVFN----EHQDPVRSELSEIRLNLKTGESTRRVVVSG 414
+++ C + D F ++ DP +L ++ ++++VS
Sbjct: 314 ----KIILDSICYNSLPQVDTDGDFRSTNFDNLDP--GQLWRFTIDPAAATVEKQLMVS- 366
Query: 415 MNLEAGQVNRALLGQKTRYVYLAIADPW---PKCSGIAKVDLGTGEVTKFMYGAHRFGGE 471
E V+ +G+ RYVY+ A I KVDL +G T + H F GE
Sbjct: 367 RCCEFPVVHPQQVGRPYRYVYMGAAHHSTGNAPLQAILKVDLESGTETLRSFAPHGFAGE 426
Query: 472 PMFVPQNSKNVGSGREDEGFIMGFVRDERREESEMVIVKASSME--QVASVKLPRRVPYG 529
P+FVP+ G ED+G+++ + SE+VI+ A + +A++KL +PY
Sbjct: 427 PIFVPRP----GGVAEDDGWLLCLIYKADLHRSELVILDAQDITAPAIATLKLKHHIPYP 482
Query: 530 FHGTF 534
HG++
Sbjct: 483 LHGSW 487
>pdb|3FSN|A Chain A, Crystal Structure Of Rpe65 At 2.14 Angstrom Resolution
pdb|3FSN|B Chain B, Crystal Structure Of Rpe65 At 2.14 Angstrom Resolution
pdb|3KVC|A Chain A, Crystal Structure Of Bovine Rpe65 At 1.9 Angstrom
Resolution
pdb|3KVC|B Chain B, Crystal Structure Of Bovine Rpe65 At 1.9 Angstrom
Resolution
pdb|4F2Z|A Chain A, Crystal Structure Of Rpe65 In A Lipid Environment
pdb|4F2Z|E Chain E, Crystal Structure Of Rpe65 In A Lipid Environment
pdb|4F30|A Chain A, Structure Of Rpe65: P6522 Crystal Form Grown In Ammonium
Phosphate Solution
pdb|4F3A|A Chain A, Structure Of Rpe65: P6522 Crystal Form, Iridium Derivative
pdb|4F3D|A Chain A, Structure Of Rpe65: P65 Crystal Form Grown In
Fos-Choline-10
pdb|4F3D|B Chain B, Structure Of Rpe65: P65 Crystal Form Grown In
Fos-Choline-10
Length = 533
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 114/551 (20%), Positives = 203/551 (36%), Gaps = 118/551 (21%)
Query: 66 FAPVQECPVHHGLQVVGRIPDCLRGVYVRNGANPMFVPSGG-HHLFDGDGMIHAVTLGHA 124
F V+E V GRIP L G +R G V S +HLFDG ++H
Sbjct: 16 FETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEG 75
Query: 125 NQASYSCRYTQTSRLVQE--------AKYGKPVFPKPIXXXXXXXXXXXXXXFMARAGAG 176
+Y R+ +T V+ ++G FP P +
Sbjct: 76 -HVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDP----------------CKNIFSR 118
Query: 177 LVDGSRGMGVANAGLVYFH---GSLLAMSEDDLPYRVKIKPDGDLETIGRFSFDDQLDCP 233
RG+ V + LV + A +E + + K+ P+ LETI + + +
Sbjct: 119 FFSYFRGVEVTDNALVNIYPVGEDYYACTETN--FITKVNPE-TLETIKQVDLCNYVSVN 175
Query: 234 -MIAHPKV--DPVTSDL-------HALSYNVVRKPYLKYFRFGGSNDGKKSRDVDVTLD- 282
AHP + D ++ +++YN+V+ P L+ D ++ V
Sbjct: 176 GATAHPHIENDGTVYNIGNCFGKNFSIAYNIVKIPPLQ----ADKEDPISKSEIVVQFPC 231
Query: 283 ----QPTMIHDFAITENCVIIPDHQVVFKLSEMIRGGSPV------IFDKNKTSRFGVLS 332
+P+ +H F +T N ++ + V L + + S F+ N+T GV
Sbjct: 232 SDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNET--MGVWL 289
Query: 333 KNDADESGIQWIDVPNCFCFHLWNAWEENNDDGDRNVVVIG-SCMDPPDSVFNE-HQDPV 390
+ AD+ ++I+ N + +N + N D +++ C + V+N + +
Sbjct: 290 -HIADKKRKKYIN--NKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANL 346
Query: 391 RSELSEIRLNLKTG--ESTRRVVV--------SGMNL----------------------- 417
R E++ N + RR V+ +G NL
Sbjct: 347 RENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPE 406
Query: 418 ----------EAGQVNRALLGQK-TRYVY-LAIADPWPKCSGIAKVDLGTGEVTKFMYGA 465
E Q+N G K Y Y L + P + K+++ T E T
Sbjct: 407 VLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVP--DRLCKLNVKTKE-TWVWQEP 463
Query: 466 HRFGGEPMFVPQNSKNVGSGREDEGFIMGFVRD--ERREESEMVIVKASSMEQVASVKLP 523
+ EP+FV + + ED+G ++ V ++ + ++I+ A + +VA ++
Sbjct: 464 DSYPSEPIFV----SHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVE 519
Query: 524 RRVPYGFHGTF 534
+P FHG F
Sbjct: 520 INIPVTFHGLF 530
>pdb|4F7Z|A Chain A, Conformational Dynamics Of Exchange Protein Directly
Activated By Camp
Length = 999
Score = 33.5 bits (75), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 26/102 (25%), Positives = 44/102 (43%), Gaps = 3/102 (2%)
Query: 252 YNVVRKPYLKYFRFGGSNDGKKSRDVDVTLDQPTMIHDFAITENCVIIPDHQVVFKLSEM 311
+N V + L Y FG N K + ++D+ L + I + +TE C+ + V L +
Sbjct: 776 FNCVHELELIYHTFGRHNFKKTTANLDLFLRRFNEIQFWVVTEVCLCSQLSKRVQLLKKF 835
Query: 312 IRGGSPVIFDKNKTSRFGV---LSKNDADESGIQWIDVPNCF 350
I+ + KN S F + LS + W +P+ F
Sbjct: 836 IKIAAHCKEYKNLNSFFAIVMGLSNVAVSRLALTWEKLPSKF 877
>pdb|2BYV|E Chain E, Structure Of The Camp Responsive Exchange Factor Epac2 In
Its Auto-Inhibited State
Length = 999
Score = 33.5 bits (75), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 26/102 (25%), Positives = 44/102 (43%), Gaps = 3/102 (2%)
Query: 252 YNVVRKPYLKYFRFGGSNDGKKSRDVDVTLDQPTMIHDFAITENCVIIPDHQVVFKLSEM 311
+N V + L Y FG N K + ++D+ L + I + +TE C+ + V L +
Sbjct: 776 FNCVHELELIYHTFGRHNFKKTTANLDLFLRRFNEIQFWVVTEVCLCSQLSKRVQLLKKF 835
Query: 312 IRGGSPVIFDKNKTSRFGV---LSKNDADESGIQWIDVPNCF 350
I+ + KN S F + LS + W +P+ F
Sbjct: 836 IKIAAHCKEYKNLNSFFAIVMGLSNVAVSRLALTWEKLPSKF 877
>pdb|3CF6|E Chain E, Structure Of Epac2 In Complex With Cyclic-Amp And Rap
Length = 694
Score = 33.5 bits (75), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 26/102 (25%), Positives = 44/102 (43%), Gaps = 3/102 (2%)
Query: 252 YNVVRKPYLKYFRFGGSNDGKKSRDVDVTLDQPTMIHDFAITENCVIIPDHQVVFKLSEM 311
+N V + L Y FG N K + ++D+ L + I + +TE C+ + V L +
Sbjct: 471 FNCVHELELIYHTFGRHNFKKTTANLDLFLRRFNEIQFWVVTEVCLCSQLSKRVQLLKKF 530
Query: 312 IRGGSPVIFDKNKTSRFGV---LSKNDADESGIQWIDVPNCF 350
I+ + KN S F + LS + W +P+ F
Sbjct: 531 IKIAAHCKEYKNLNSFFAIVMGLSNVAVSRLALTWEKLPSKF 572
>pdb|2B2X|A Chain A, Vla1 Rdeltah I-Domain Complexed With A Quadruple Mutant
Of The Aqc2 Fab
pdb|2B2X|B Chain B, Vla1 Rdeltah I-Domain Complexed With A Quadruple Mutant
Of The Aqc2 Fab
Length = 223
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 55 TVDPTVQISGNFAPVQECPVHHGLQVV 81
+V PT Q+ +FAPVQEC + +V
Sbjct: 2 SVSPTFQVVNSFAPVQECSTQLDIVIV 28
>pdb|3UOT|A Chain A, Crystal Structure Of Mdc1 Fha Domain In Complex With A
Phosphorylated Peptide From The Mdc1 N-Terminus
pdb|3UOT|B Chain B, Crystal Structure Of Mdc1 Fha Domain In Complex With A
Phosphorylated Peptide From The Mdc1 N-Terminus
Length = 122
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 47 EKGKSLPKTVDPTVQI---SGNFAPVQECPVHHGLQVVGRIPDC 87
+ +SL V+P ++ SG P ++ P+H G VVGR PDC
Sbjct: 3 QSSESLRCNVEPVGRLHIFSGAHGPEKDFPLHLGKNVVGRXPDC 46
>pdb|3UMZ|A Chain A, Crystal Structure Of The Human Mdc1 Fha Domain
pdb|3UMZ|B Chain B, Crystal Structure Of The Human Mdc1 Fha Domain
pdb|3UNM|A Chain A, Crystal Structure Of The Human Mdc1 Fha Domain
pdb|3UNM|B Chain B, Crystal Structure Of The Human Mdc1 Fha Domain
pdb|3UNN|A Chain A, Monomeric Structure Of The Human Mdc1 Fha Domain In
Complex With An Mdc1 Phospho-T4 Peptide
Length = 113
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 63 SGNFAPVQECPVHHGLQVVGRIPDC 87
SG P ++ P+H G VVGR+PDC
Sbjct: 13 SGAHGPEKDFPLHLGKNVVGRMPDC 37
>pdb|3UN0|B Chain B, Crystal Structure Of Mdc1 Fha Domain
pdb|3UN0|A Chain A, Crystal Structure Of Mdc1 Fha Domain
Length = 115
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 63 SGNFAPVQECPVHHGLQVVGRIPDC 87
SG P ++ P+H G VVGR+PDC
Sbjct: 15 SGAHGPEKDFPLHLGKNVVGRMPDC 39
>pdb|3IZB|D Chain D, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5C|E Chain E, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|E Chain E, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 261
Score = 28.5 bits (62), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 25/107 (23%), Positives = 46/107 (42%), Gaps = 18/107 (16%)
Query: 406 STRRVVVSGMNLEAGQVNRALLGQK-TRYVY------LAIADPWPKCSGIAKVDLGTGEV 458
+ R+ + + G+V + LG+K YV + DP K + K+DL +G++
Sbjct: 110 AVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKI 169
Query: 459 TKFMYGAHRFGGEPMFVPQNSKNVG-------SGREDEGFIMGFVRD 498
T F+ +F + +N+G R D GF + ++D
Sbjct: 170 TDFI----KFDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKD 212
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.138 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,066,134
Number of Sequences: 62578
Number of extensions: 753877
Number of successful extensions: 1413
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1393
Number of HSP's gapped (non-prelim): 19
length of query: 545
length of database: 14,973,337
effective HSP length: 104
effective length of query: 441
effective length of database: 8,465,225
effective search space: 3733164225
effective search space used: 3733164225
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)