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= 048807
(757 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 35.8 bits (81), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 35/133 (26%), Positives = 56/133 (42%), Gaps = 12/133 (9%)
Query: 453 MC-RHGRINSAVEFFQEVTRKGLCANAVTYTILITAFCNVNNFQEAIKWFDDMSRA---- 507
MC + G + A+ + E R G+ + Y +L+ C++ +SR
Sbjct: 35 MCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYV-CSLAEAATESSPNPGLSRGFDIF 93
Query: 508 -GCSADSVV--YFTLISGLCQAGRMNDASL---VVSKLKEAGFRPDIVCYNHLISGFCKK 561
D VV T +G A +D + +V ++K G +P + Y + GFC+K
Sbjct: 94 KQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRK 153
Query: 562 KMLDKAYEVLQEM 574
DKAYEV M
Sbjct: 154 GDADKAYEVDAHM 166
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 34/184 (18%), Positives = 68/184 (36%), Gaps = 37/184 (20%)
Query: 564 LDKAYEVLQEMEDIGMTPNSVTYNTLISFLSKSGNFSAARRVLKKMVKEGLVPTVVTYGA 623
L + +++ ++M + PN T+ + A ++K+M G+ P + +YG
Sbjct: 86 LSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGP 145
Query: 624 LIHAFCVNGHVDEAMKIFKELSSSSNVSPNTVIYNILIDSLCKNNQVELALSLMEEMKVK 683
+ FC G D+A ++ + S V + +L S+
Sbjct: 146 ALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSM------------------- 186
Query: 684 EVRPNTNTYNAMFKGLRQKNMLDKAFKLMDRMIEHACHPDYISMEILTEWL-SEAGQTEK 742
+T NA DK +K + R+ + + +++ EW SE
Sbjct: 187 ------DTKNA-----------DKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSEVATKTG 229
Query: 743 LKKF 746
+KK+
Sbjct: 230 VKKW 233
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 30/148 (20%), Positives = 59/148 (39%), Gaps = 11/148 (7%)
Query: 577 IGMTPNSVTYNTLISFLSKSGNFSAARRVLKKMVKEGLVPTVVTYGALIHAFCV------ 630
I +P ++ L SK G+ A R+ + + G+ + Y L++ +
Sbjct: 21 IQQSPEALLKQKL-DMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATE 79
Query: 631 ---NGHVDEAMKIFKELSSSSNVSPNTVIYNILIDSLCKNNQVELALSLMEEMKVKEVRP 687
N + IFK++ V PN + + E+A ++++MK ++P
Sbjct: 80 SSPNPGLSRGFDIFKQMIVD-KVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQP 138
Query: 688 NTNTYNAMFKGLRQKNMLDKAFKLMDRM 715
+Y G +K DKA+++ M
Sbjct: 139 RLRSYGPALFGFCRKGDADKAYEVDAHM 166
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 536 VSKLKEAGFRPDIVCYNHLISGFCKKKMLDKAYEV 570
V + K G +P + Y + GFC+K DKAYEV
Sbjct: 128 VKQXKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162
>pdb|3E4B|A Chain A, Crystal Structure Of Algk From Pseudomonas Fluorescens
Wcs374r
pdb|3E4B|B Chain B, Crystal Structure Of Algk From Pseudomonas Fluorescens
Wcs374r
pdb|3E4B|C Chain C, Crystal Structure Of Algk From Pseudomonas Fluorescens
Wcs374r
pdb|3E4B|D Chain D, Crystal Structure Of Algk From Pseudomonas Fluorescens
Wcs374r
Length = 452
Score = 33.1 bits (74), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 39/171 (22%), Positives = 74/171 (43%), Gaps = 16/171 (9%)
Query: 478 AVTYTILITAFCNVNNFQEAIKWFDDMSRAGCSADSVVYFTLISGLCQAGRMNDASLVVS 537
A+ Y +F NVN Q+ +W A ++Y T G + V
Sbjct: 113 AMLYLQYPHSFPNVNAQQQISQWQAAGYPEAGLAQVLLYRT-------QGTYDQHLDDVE 165
Query: 538 KLKEAGFRPDIVCYNHLISGFCKKKMLDKAYEVLQEMEDIGMTPNSVTYNTLISFLSKSG 597
++ +A +CY L + + KK+ ++ E+L++ME G++ +VT + S G
Sbjct: 166 RICKAALNTTDICYVELATVYQKKQQPEQQAELLKQME-AGVSRGTVTAQRVDSVARVLG 224
Query: 598 NFS-------AARRVLKKMVKEGLVPTVVTYGALIHAFCVNGHVDEAMKIF 641
+ + A+ +L+K+ G + V+ L++ F G V++ MK
Sbjct: 225 DATLGTPDEKTAQALLEKIAP-GYPASWVSLAQLLYDFPELGDVEQMMKYL 274
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 551 YNHLISGFCKKKMLDKAYEVLQEMEDIGMTPNSVTYNTLISFLSKSGNFSAA-RRVLKKM 609
YN ++ G+ ++ + VL ++D G+TP+ ++Y + + + + R L++M
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQM 227
Query: 610 VKEGL 614
+EGL
Sbjct: 228 SQEGL 232
>pdb|1UED|A Chain A, Crystal Structure Of Oxyc A Cytochrome P450 Implicated In
An Oxidative C-C Coupling Reaction During Vancomycin
Biosynthesis.
pdb|1UED|B Chain B, Crystal Structure Of Oxyc A Cytochrome P450 Implicated In
An Oxidative C-C Coupling Reaction During Vancomycin
Biosynthesis
Length = 406
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 26/60 (43%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 197 DRDAFN-VLDEMLDRESQFPVNELTGDIVFYALMRREHVKNSVTDEELVGLVSKFAEHGV 255
D AFN LD +L R+ P + L G IV R+H N VTDEEL GL + GV
Sbjct: 195 DSAAFNRYLDNLLARQRADPDDGLLGMIV------RDHGDN-VTDEELKGLCTALILGGV 247
>pdb|4ELJ|A Chain A, Crystal Structure Of The Inactive Retinoblastoma Protein
Phosphorylated At T373
Length = 656
Score = 30.4 bits (67), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 42/96 (43%), Gaps = 8/96 (8%)
Query: 90 RALSFFNFLQSNLPTEANTSSLSYAYQAVFELAIRERM---SPESLFDLYKACKDQNIPL 146
+A F+ ++S + E N + + E I E + S LFDL K KD+ PL
Sbjct: 452 KAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAWLSDSPLFDLIKQSKDREGPL 511
Query: 147 SINSATLLIRFFGKVSMYDYSLLVYNELDNNLRNTH 182
S +L F+ KV Y + L N L L + H
Sbjct: 512 KSTSLSL---FYKKV--YRLAYLRLNTLCERLLSEH 542
>pdb|3BBP|A Chain A, Rab6-Gtp:gcc185 Rab Binding Domain Complex
pdb|3BBP|B Chain B, Rab6-Gtp:gcc185 Rab Binding Domain Complex
pdb|3BBP|C Chain C, Rab6-Gtp:gcc185 Rab Binding Domain Complex
Length = 211
Score = 30.4 bits (67), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 480 TYTILITAFCNVNNFQEAIKWFDDMSRAGCSADSVV 515
T +++ NVN+FQ+ KW DD+ R +D ++
Sbjct: 90 TVAVVVYDITNVNSFQQTTKWIDDV-RTERGSDVII 124
>pdb|3CWZ|A Chain A, Strucure Of Rab6(Gtp)-R6ip1 Complex
Length = 188
Score = 29.3 bits (64), Expect = 8.4, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 480 TYTILITAFCNVNNFQEAIKWFDDM 504
T +++ NVN+FQ+ KW DD+
Sbjct: 80 TVAVVVYDITNVNSFQQTTKWIDDV 104
>pdb|2GIL|A Chain A, Structure Of The Extremely Slow Gtpase Rab6a In The Gtp
Bound Form At 1.8 Resolution
pdb|2GIL|B Chain B, Structure Of The Extremely Slow Gtpase Rab6a In The Gtp
Bound Form At 1.8 Resolution
pdb|2GIL|C Chain C, Structure Of The Extremely Slow Gtpase Rab6a In The Gtp
Bound Form At 1.8 Resolution
pdb|2GIL|D Chain D, Structure Of The Extremely Slow Gtpase Rab6a In The Gtp
Bound Form At 1.8 Resolution
Length = 162
Score = 29.3 bits (64), Expect = 8.4, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 480 TYTILITAFCNVNNFQEAIKWFDDM 504
T +++ NVN+FQ+ KW DD+
Sbjct: 75 TVAVVVYDITNVNSFQQTTKWIDDV 99
>pdb|3BG0|B Chain B, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG0|C Chain C, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG0|F Chain F, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG0|G Chain G, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|B Chain B, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|C Chain C, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|F Chain F, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|G Chain G, Architecture Of A Coat For The Nuclear Pore Membrane
Length = 442
Score = 29.3 bits (64), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 6/46 (13%)
Query: 29 NSPLPQVSESSIIITQALDVLLQTPD--NEWTSSPQIKNLLFSSTS 72
++P PQ+SESS++ ALD + +T N W ++ ++LF S
Sbjct: 94 SNPYPQISESSLLFKDALDYMEKTSSDYNLW----KLSSILFDPVS 135
>pdb|3IKO|B Chain B, Crystal Structure Of The Heterotrimeric
Sec13-Nup145c-Nup84 Nucleoporin Complex
pdb|3IKO|E Chain E, Crystal Structure Of The Heterotrimeric
Sec13-Nup145c-Nup84 Nucleoporin Complex
pdb|3IKO|H Chain H, Crystal Structure Of The Heterotrimeric
Sec13-Nup145c-Nup84 Nucleoporin Complex
Length = 442
Score = 29.3 bits (64), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 6/46 (13%)
Query: 29 NSPLPQVSESSIIITQALDVLLQTPD--NEWTSSPQIKNLLFSSTS 72
++P PQ+SESS++ ALD + +T N W ++ ++LF S
Sbjct: 94 SNPYPQISESSLLFKDALDYMEKTSSDYNLW----KLSSILFDPVS 135
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
0.321 0.135 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,876,158
Number of Sequences: 62578
Number of extensions: 767206
Number of successful extensions: 1882
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1861
Number of HSP's gapped (non-prelim): 31
length of query: 757
length of database: 14,973,337
effective HSP length: 106
effective length of query: 651
effective length of database: 8,340,069
effective search space: 5429384919
effective search space used: 5429384919
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)