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= 004950
(722 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IBV|A Chain A, Karyopherin Cytosolic State
pdb|3IBV|B Chain B, Karyopherin Cytosolic State
pdb|3ICQ|T Chain T, Karyopherin Nuclear State
pdb|3ICQ|U Chain U, Karyopherin Nuclear State
Length = 980
Score = 191 bits (486), Expect = 1e-48, Method: Compositional matrix adjust.
Identities = 156/653 (23%), Positives = 305/653 (46%), Gaps = 45/653 (6%)
Query: 82 DTTFSIVQFLSGYVATMKSLSPLKE---EQRLHAGQILEVILTQIRYDPMYRNNLDVLDK 138
+T+ ++ FLS + +++ S KE + +LE I+ +++YD + D
Sbjct: 347 ETSTAVFPFLSDLLVSLRKESSSKELSASLKEFLKSLLEAIIKKMKYDESQEWD----DD 402
Query: 139 IGIEEEDRMVEYRKDLLVLLRSVGRVAPEVTQVF----IRNSLANAVTFSADRNVEEVEA 194
EEE E RK L + ++ + + + I +SL+ A T S + + + +E
Sbjct: 403 PDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEF 462
Query: 195 ALTLLYALGESMSE-----EAMRTGAGHLSELVPMLLQTKLPCHSNRLVALVYLETVTRY 249
AL Y GE + + LS+++ ++ +++ H + LV L+Y+E + RY
Sbjct: 463 ALYETYIFGEGLRGPDAFFNEVDKSPTVLSQILALVTTSQVCRHPHPLVQLLYMEILVRY 522
Query: 250 MKFIQEHTQYIPVVLAAFLDERGIHHPNVHVSRRASYLFMRVVKLLKAKLVPFIENILQS 309
F + IP ++ F+ RGIH+ N V RA YLF R VK +K ++V + E+ L
Sbjct: 523 ASFFDYESAAIPALIEYFVGPRGIHNTNERVRPRAWYLFYRFVKSIKKQVVNYTESSLAM 582
Query: 310 LQD----TIARFTSMNYASKELSGSEDGS------HIFEAIGLLIGMEDVPPEKQSDYLS 359
L D +++ T M+ L+ S S ++FE +G+LI ++ PE+Q+ Y
Sbjct: 583 LGDLLNISVSPVTDMDAPVPTLNSSIRNSDFNSQLYLFETVGVLISSGNLTPEEQALYCD 642
Query: 360 SLLTPLCQQVQTMLLDAKMLNPEESTAKFXXXXXXXXXXXXLSKGFNERLVTSSRPAIGL 419
SL+ L + +A + + + +KGF R S A
Sbjct: 643 SLINALIGKA-----NAALSSDLSALENIISVYCSLMAIGNFAKGFPAR--GSEEVAWLA 695
Query: 420 MFKQTLDVLLQILVVFPKVEPLRCKVTSFIHRMVDTLGASVFPYLPKALEQLLAESEPKE 479
F + D + IL E +R V R+++ +G + P +P+ + LL + E
Sbjct: 696 SFNKASDEIFLILDRMGFNEDIRGAVRFTSGRIINVVGPDMLPKVPQLISILLNSIDMNE 755
Query: 480 MAGFLVLLNQLICKFNTLVHDILDEVFPAIAGRIFNIIPRDAFPSGPGTNTEEIREVQEL 539
+ L ++QLI + + +I + + P + RIF+ + A P G T++ + +L
Sbjct: 756 LVDVLSFISQLIHIYKDNMMEITNRMLPTLLMRIFSSL--SAAPQG----TDDAVKQNDL 809
Query: 540 QRTLYTFLHVIATHDLSSVFLSPKSRGYLDPIMQLLLYTSCNHKDYLVRKACVQIFIRLI 599
+++ +F+ + S+ + +++ Y DP++ +L+ + + +K+ + + +++
Sbjct: 810 RKSYISFILQLLNKGFGSILFTEENQVYFDPLINSILHFANLVGEPATQKSSIALVSKMV 869
Query: 600 KDWCARPFVEEKVPGFQSFMIEAFAMNCCLYSVLDKSFEFGDANTLVLFGEIVLAQKVMY 659
W + + + GF++F + + C ++ +F D +LV+ GE+ QK++
Sbjct: 870 SLWGGK----DGIAGFENFTLSLTPL--CFEMPVNPNFNTRDGQSLVVLGELAGLQKIIL 923
Query: 660 EKFGNDFLVHFVTKGFPSAHCPPDLAEQYCQKLQGNDIKALKSFYQSLIEKLR 712
EK G+ + + VT FP+ + P +A +Y Q L D ++ K F+Q I+ L+
Sbjct: 924 EKLGDIYKSYLVTVYFPTVNFPDVMASEYLQALSNLDSRSFKQFFQKFIQALK 976
>pdb|3ICE|A Chain A, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|B Chain B, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|C Chain C, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|D Chain D, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|E Chain E, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|F Chain F, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
Length = 422
Score = 38.1 bits (87), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 34/115 (29%), Positives = 58/115 (50%), Gaps = 18/115 (15%)
Query: 106 EEQRLHAGQILEVILTQIRYDPMYRNNLDVLDKIGIEEEDRMVEYRKDLLVLLRSVGRVA 165
E QRL G+++ +D ++ V + + IE+ R+VE++KD+++LL S+ R+A
Sbjct: 221 EXQRLVKGEVVAST-----FDEPASRHVQVAEXV-IEKAKRLVEHKKDVIILLDSITRLA 274
Query: 166 -------PEVTQVFIRNSLANAVT-----FSADRNVEEVEAALTLLYALGESMSE 208
P +V ANA+ F A RNVEE + + AL ++ S+
Sbjct: 275 RAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSK 329
>pdb|1PV4|A Chain A, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|B Chain B, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|C Chain C, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|D Chain D, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|E Chain E, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|F Chain F, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
Length = 419
Score = 37.7 bits (86), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 34/115 (29%), Positives = 58/115 (50%), Gaps = 18/115 (15%)
Query: 106 EEQRLHAGQILEVILTQIRYDPMYRNNLDVLDKIGIEEEDRMVEYRKDLLVLLRSVGRVA 165
E QRL G+++ +D ++ V + + IE+ R+VE++KD+++LL S+ R+A
Sbjct: 218 EXQRLVKGEVVAST-----FDEPASRHVQVAEXV-IEKAKRLVEHKKDVIILLDSITRLA 271
Query: 166 -------PEVTQVFIRNSLANAVT-----FSADRNVEEVEAALTLLYALGESMSE 208
P +V ANA+ F A RNVEE + + AL ++ S+
Sbjct: 272 RAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSK 326
>pdb|2HT1|A Chain A, The Closed Ring Structure Of The Rho Transcription
Termination Factor In Complex With Nucleic Acid In The
Motor Domains
pdb|2HT1|B Chain B, The Closed Ring Structure Of The Rho Transcription
Termination Factor In Complex With Nucleic Acid In The
Motor Domains
Length = 433
Score = 37.4 bits (85), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 15/83 (18%)
Query: 141 IEEEDRMVEYRKDLLVLLRSVGRVA-------PEVTQVFIRNSLANAVT-----FSADRN 188
IE+ R+VE++KD+++LL S+ R+A P +V ANA+ F A RN
Sbjct: 269 IEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARN 328
Query: 189 VEEVEAALTLLYAL---GESMSE 208
VEE + + AL G M E
Sbjct: 329 VEEGGSLTIIATALIDTGSKMDE 351
>pdb|1PVO|A Chain A, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|B Chain B, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|C Chain C, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|D Chain D, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|E Chain E, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|F Chain F, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1XPR|A Chain A, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|B Chain B, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|C Chain C, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|D Chain D, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|E Chain E, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|F Chain F, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPU|A Chain A, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|B Chain B, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|C Chain C, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|D Chain D, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|E Chain E, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|F Chain F, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPO|A Chain A, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|B Chain B, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|C Chain C, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|D Chain D, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|E Chain E, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|F Chain F, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
Length = 419
Score = 37.4 bits (85), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 15/83 (18%)
Query: 141 IEEEDRMVEYRKDLLVLLRSVGRVA-------PEVTQVFIRNSLANAVT-----FSADRN 188
IE+ R+VE++KD+++LL S+ R+A P +V ANA+ F A RN
Sbjct: 247 IEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARN 306
Query: 189 VEEVEAALTLLYAL---GESMSE 208
VEE + + AL G M E
Sbjct: 307 VEEGGSLTIIATALIDTGSKMDE 329
>pdb|3FDB|A Chain A, Crystal Structure Of A Putative Plp-Dependent
Beta-Cystathionase (Aecd, Dip1736) From Corynebacterium
Diphtheriae At 1.99 A Resolution
Length = 377
Score = 33.9 bits (76), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 32/74 (43%), Gaps = 1/74 (1%)
Query: 648 FGEIVLAQKVMYEKFGNDFLVHFVTKGFPSAHCPPDLAEQYCQKLQGNDIKALKSFYQSL 707
+G L Q+V Y K +DFL+H + K P A P A Y + D S +
Sbjct: 271 YGTDFLNQEVAYLKNNHDFLLHEIPKRIPGAKITPXQA-TYLXWIDFRDTTIEGSPSEFF 329
Query: 708 IEKLRVQQNGSLVF 721
IEK +V N F
Sbjct: 330 IEKAKVAXNDGAWF 343
>pdb|2X1G|F Chain F, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|G Chain G, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 971
Score = 30.0 bits (66), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 29/130 (22%), Positives = 62/130 (47%), Gaps = 16/130 (12%)
Query: 243 LETVTRYMKFIQEHTQYIPVVLAAFLDERGIHHPNVHVSRRASYLFMRVVKLLKAKLVPF 302
LET+ Y ++ E+ YIP + + RG+ N +S +A+ + + + +L P+
Sbjct: 527 LETMGSYCNWLMENPAYIPPAINLLV--RGL---NSSMSAQATLGLKELCRDCQLQLKPY 581
Query: 303 IENILQSLQDTIARFTSMNYASKELSGSEDGSHIFEAIGLLIGMEDVPPEKQSDYLSSLL 362
+ +L + S+N + S D + +IG L+ + + PE+ YL ++
Sbjct: 582 ADPLLNACH------ASLNTGRMKNS---DSVRLMFSIGKLMSL--LRPEEIPKYLDIIV 630
Query: 363 TPLCQQVQTM 372
+P +++Q +
Sbjct: 631 SPCFEELQAI 640
>pdb|3UAU|A Chain A, Crystal Structure Of The Lipoprotein Jlpa
pdb|3UAU|B Chain B, Crystal Structure Of The Lipoprotein Jlpa
Length = 379
Score = 29.6 bits (65), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 7/69 (10%)
Query: 73 FYVMQNCEVDTTFSIVQFLSGYVATMK-SLSPLK-----EEQRLHAGQILEVILTQIRYD 126
+ ++ N ++D+T S Y+AT K +L LK EEQ L + L IL I +
Sbjct: 262 YIILNNFKIDSTLKTEGVFSSYIATAKENLQTLKAQSQNEEQALIFDKAL-AILNNITQN 320
Query: 127 PMYRNNLDV 135
Y+ NLD+
Sbjct: 321 DDYKLNLDL 329
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
0.323 0.137 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,915,978
Number of Sequences: 62578
Number of extensions: 736086
Number of successful extensions: 1620
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1609
Number of HSP's gapped (non-prelim): 8
length of query: 722
length of database: 14,973,337
effective HSP length: 106
effective length of query: 616
effective length of database: 8,340,069
effective search space: 5137482504
effective search space used: 5137482504
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)