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= 025981
(245 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3J2I|B Chain B, Structure Of Late Pre-60s Ribosomal Subunits With Nuclear
Export Factor Arx1 Bound At The Peptide Exit Tunnel
Length = 245
Score = 376 bits (965), Expect = e-105, Method: Compositional matrix adjust.
Identities = 175/244 (71%), Positives = 208/244 (85%)
Query: 1 MATRLMFENSCEVGVFSKLTNAYCLVAIGGSESFYSTFEAELADVFPVVKTSIGGTRIIG 60
MATR FENS E+GVFSKLTN YCLVA+GGSE+FYS FEAEL D P+V T+I GTRIIG
Sbjct: 1 MATRTQFENSNEIGVFSKLTNTYCLVAVGGSENFYSAFEAELGDAIPIVHTTIAGTRIIG 60
Query: 61 RLCAGNKNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALGNCIACNDHVALTHTD 120
R+ AGN+ GLL+P TTDQELQHLRNSLPD V +QR+EERLSALGN I CND+VAL H D
Sbjct: 61 RMTAGNRRGLLVPTQTTDQELQHLRNSLPDSVKIQRVEERLSALGNVICCNDYVALVHPD 120
Query: 121 LDRETEEMIADVLGVEVFRQTIAGNILVGSYCSFSNRGGLVHPHTSIEDLDELSTLLQVP 180
+DRETEE+I+DVLGVEVFRQTI+GNILVGSYCS SN+GGLVHP TS++D +ELS+LLQVP
Sbjct: 121 IDRETEELISDVLGVEVFRQTISGNILVGSYCSLSNQGGLVHPQTSVQDQEELSSLLQVP 180
Query: 181 LVAGTVNRGSEVIAAGLTVNDWTAFCGSDTTATELSVIESVFKLREAQPSALVDEMRKSL 240
LVAGTVNRGS V+ AG+ VND+ A G DTTA ELSVIES+F+L++AQP ++ +R +L
Sbjct: 181 LVAGTVNRGSSVVGAGMVVNDYLAVTGLDTTAPELSVIESIFRLQDAQPESISGNLRDTL 240
Query: 241 IDSY 244
I++Y
Sbjct: 241 IETY 244
>pdb|1G62|A Chain A, Crystal Structure Of S.Cerevisiae Eif6
pdb|2X7N|B Chain B, Mechanism Of Eif6s Anti-Association Activity
Length = 224
Score = 357 bits (915), Expect = 4e-99, Method: Compositional matrix adjust.
Identities = 168/224 (75%), Positives = 193/224 (86%)
Query: 1 MATRLMFENSCEVGVFSKLTNAYCLVAIGGSESFYSTFEAELADVFPVVKTSIGGTRIIG 60
MATR FENS E+GVFSKLTN YCLVA+GGSE+FYS FEAEL D P+V T+I GTRIIG
Sbjct: 1 MATRTQFENSNEIGVFSKLTNTYCLVAVGGSENFYSAFEAELGDAIPIVHTTIAGTRIIG 60
Query: 61 RLCAGNKNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALGNCIACNDHVALTHTD 120
R+ AGN+ GLL+P TTDQELQHLRNSLPD V +QR+EERLSALGN I CND+VAL H D
Sbjct: 61 RMTAGNRRGLLVPTQTTDQELQHLRNSLPDSVKIQRVEERLSALGNVICCNDYVALVHPD 120
Query: 121 LDRETEEMIADVLGVEVFRQTIAGNILVGSYCSFSNRGGLVHPHTSIEDLDELSTLLQVP 180
+DRETEE+I+DVLGVEVFRQTI+GNILVGSYCS SN+GGLVHP TS++D +ELS+LLQVP
Sbjct: 121 IDRETEELISDVLGVEVFRQTISGNILVGSYCSLSNQGGLVHPQTSVQDQEELSSLLQVP 180
Query: 181 LVAGTVNRGSEVIAAGLTVNDWTAFCGSDTTATELSVIESVFKL 224
LVAGTVNRGS V+ AG+ VND+ A G DTTA ELSVIES+F+L
Sbjct: 181 LVAGTVNRGSSVVGAGMVVNDYLAVTGLDTTAPELSVIESIFRL 224
>pdb|4A18|J Chain J, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|J Chain J, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|J Chain J, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|J Chain J, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 248
Score = 342 bits (877), Expect = 1e-94, Method: Compositional matrix adjust.
Identities = 158/241 (65%), Positives = 197/241 (81%)
Query: 1 MATRLMFENSCEVGVFSKLTNAYCLVAIGGSESFYSTFEAELADVFPVVKTSIGGTRIIG 60
MA R FENS ++GVF KLT+AYCLV++G SE+FYS FE+EL PV+ TSIGGTRI+G
Sbjct: 4 MARRCQFENSNDIGVFCKLTSAYCLVSVGASENFYSVFESELVPHIPVIHTSIGGTRIVG 63
Query: 61 RLCAGNKNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALGNCIACNDHVALTHTD 120
R+ GNKNGLL+P+T D EL+++RNSLPD V V+RIEE+LSALGNC+ ND+VAL H D
Sbjct: 64 RVTCGNKNGLLVPNTCNDNELRNIRNSLPDNVRVRRIEEKLSALGNCVVANDYVALIHPD 123
Query: 121 LDRETEEMIADVLGVEVFRQTIAGNILVGSYCSFSNRGGLVHPHTSIEDLDELSTLLQVP 180
LDRE+EE+IAD LGVEVFR TIA N+LVG+YC +NRGGLVHP S+E+LDEL+ LLQ+P
Sbjct: 124 LDRESEEIIADTLGVEVFRTTIANNVLVGTYCVINNRGGLVHPLASVEELDELANLLQIP 183
Query: 181 LVAGTVNRGSEVIAAGLTVNDWTAFCGSDTTATELSVIESVFKLREAQPSALVDEMRKSL 240
L AGT+NRGS+VI AGL VNDW AFCG DTT+TE+SV+E++FKL E + + +EMRK
Sbjct: 184 LCAGTINRGSDVIGAGLVVNDWAAFCGLDTTSTEISVVENIFKLNEMKDENMDNEMRKDF 243
Query: 241 I 241
+
Sbjct: 244 V 244
>pdb|4ADX|I Chain I, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 222
Score = 104 bits (260), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 72/227 (31%), Positives = 111/227 (48%), Gaps = 5/227 (2%)
Query: 1 MATRLMFENSCEVGVFSKLTNAYCLVAIGGSESFYSTFEAELADVFPVVKTSIGGTRIIG 60
M R+ + +GV+ +T++ L+ E F L V+K SI G+ + G
Sbjct: 1 MIRRINLSGNPNLGVYISVTDSVALIPQNTPEKFEGVLREALE--VEVLKVSISGSSLNG 58
Query: 61 RLCAGNKNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALGNCIACNDHVALTHTD 120
L GN NG ++ + D+E+ L + + V RI ER +A+GN + ND+ A+
Sbjct: 59 ALAVGNSNGFVVSNQAMDREIDALAAAGVEAV---RIPERFTAVGNLVLANDNGAVASPL 115
Query: 121 LDRETEEMIADVLGVEVFRQTIAGNILVGSYCSFSNRGGLVHPHTSIEDLDELSTLLQVP 180
L + ++I DVL V+V T+AG +VGS + +NRG L++P S E++ + L V
Sbjct: 116 LSDDALQVIGDVLEVDVKVSTLAGLNIVGSMGAATNRGALLNPQASSEEIGIIEDTLGVE 175
Query: 181 LVAGTVNRGSEVIAAGLTVNDWTAFCGSDTTATELSVIESVFKLREA 227
GTVN G +I A N G +TT EL+ IE E
Sbjct: 176 ADVGTVNHGVTLIGACSVANSNGVLVGEETTGPELARIEEALGFLEG 222
>pdb|1G61|A Chain A, Crystal Structure Of M.Jannaschii Eif6
pdb|1G61|B Chain B, Crystal Structure Of M.Jannaschii Eif6
Length = 228
Score = 103 bits (257), Expect = 8e-23, Method: Compositional matrix adjust.
Identities = 78/231 (33%), Positives = 118/231 (51%), Gaps = 13/231 (5%)
Query: 1 MATRLMFENSCEVGVFSKLTNAYCLVAIGGSESFYSTFEA-ELADVFPV--VKTSIGGTR 57
M R F +GV + T L+ I F + E+++V ++T+IGG+
Sbjct: 3 MIIRKYFSGIPTIGVLALTTEEITLLPI-----FLDKDDVNEVSEVLETKCLQTNIGGSS 57
Query: 58 IIGRLCAGNKNGLLLPHTTTDQELQHLRNSLPDQ---VVVQRIEERLSALGNCIACNDHV 114
++G L NK GLLLP D+EL ++N L + + V+ I+ + +ALGN I ND
Sbjct: 58 LVGSLSVANKYGLLLPKIVEDEELDRIKNFLKENNLDLNVEIIKSKNTALGNLILTNDKG 117
Query: 115 ALTHTDLDRETEEMIADVLGVEVFRQTIAGNILVGSYCSFSNRGGLVHPHTSIEDLDELS 174
AL +L ++ ++ I D L VEV TIA VGS +N+G L HP ++L+ L
Sbjct: 118 ALISPEL-KDFKKDIEDSLNVEVEIGTIAELPTVGSNAVVTNKGCLTHPLVEDDELEFLK 176
Query: 175 TLLQVPLVA-GTVNRGSEVIAAGLTVNDWTAFCGSDTTATELSVIESVFKL 224
+L +V + GT N+G+ + A + N A G DTT EL +IE L
Sbjct: 177 SLFKVEYIGKGTANKGTTSVGACIIANSKGAVVGGDTTGPELLIIEDALGL 227
>pdb|2AKJ|A Chain A, Structure Of Spinach Nitrite Reductase
Length = 608
Score = 34.3 bits (77), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 51/204 (25%), Positives = 79/204 (38%), Gaps = 42/204 (20%)
Query: 44 DVFPVVKTSIGGTRIIGRLCAGNKNGLLLPHTTTDQELQHLR----NSLPDQVV------ 93
DV PV K + R +G GN+ + + ++ R +P+QV+
Sbjct: 330 DVVPVCKAMLEAFRDLG--FRGNRQKCRMMWLIDELGMEAFRGEVEKRMPEQVLERASSE 387
Query: 94 --VQRIEERLSALGNCIACNDHVALT--HTDLDR----ETEEM--IADVLGVEVFRQTIA 143
VQ+ ER LG ++ H + R E EE+ IADV G R T+
Sbjct: 388 ELVQKDWERREYLGVHPQKQQGLSFVGLHIPVGRLQADEMEELARIADVYGSGELRLTVE 447
Query: 144 GNILVGSYCSFSNRGGLVHPHTSIEDLDELSTLLQVPLVAGTVNRGSEVIAAGLTVNDWT 203
NI++ P+ +D +LL PL+ + ++ GL +
Sbjct: 448 QNIII--------------PNVENSKID---SLLNEPLLKERYSPEPPILMKGLVACTGS 490
Query: 204 AFCGS---DTTATELSVIESVFKL 224
FCG +T A L V E V +L
Sbjct: 491 QFCGQAIIETKARALKVTEEVQRL 514
>pdb|3V9F|A Chain A, Crystal Structure Of The Extracellular Domain Of The
Putative Hybrid Two Component System Bt3049 From B.
Thetaiotaomicron
pdb|3V9F|B Chain B, Crystal Structure Of The Extracellular Domain Of The
Putative Hybrid Two Component System Bt3049 From B.
Thetaiotaomicron
pdb|3V9F|C Chain C, Crystal Structure Of The Extracellular Domain Of The
Putative Hybrid Two Component System Bt3049 From B.
Thetaiotaomicron
pdb|3V9F|D Chain D, Crystal Structure Of The Extracellular Domain Of The
Putative Hybrid Two Component System Bt3049 From B.
Thetaiotaomicron
Length = 781
Score = 28.9 bits (63), Expect = 2.6, Method: Composition-based stats.
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 47 PVVKTSIGGTRIIGRLCAGNKNGLLLPHTTTDQELQHLRNSL 88
PVV T + RI GRL + KN +P + + EL H +NS
Sbjct: 665 PVVITKV---RIPGRLTSREKNETAIPISEGEIELTHEQNSF 703
>pdb|1HF2|A Chain A, Crystal Structure Of The Bacterial Cell-Division Inhibitor
Minc From T. Maritima
pdb|1HF2|B Chain B, Crystal Structure Of The Bacterial Cell-Division Inhibitor
Minc From T. Maritima
pdb|1HF2|C Chain C, Crystal Structure Of The Bacterial Cell-Division Inhibitor
Minc From T. Maritima
pdb|1HF2|D Chain D, Crystal Structure Of The Bacterial Cell-Division Inhibitor
Minc From T. Maritima
Length = 210
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 30/122 (24%), Positives = 56/122 (45%), Gaps = 21/122 (17%)
Query: 93 VVQRIEERLSALGNCIACNDHVALTHTDLDRETEEMIADV-----LGVEVFRQTIAGNIL 147
V+ I R++ +G A D ++L + ++ ++++ V LG+EV + IL
Sbjct: 24 VLNAISARITQMGGFFAKGDRISLMIENHNKHSQDIPRIVSHLRNLGLEVSQ------IL 77
Query: 148 VGSYCSFSNRGGLVHPHTSIEDLDEL--------STLLQVP--LVAGTVNRGSEVIAAGL 197
VGS V T++E ++ T++ +V G VN+G+E++A G
Sbjct: 78 VGSTVEGKENDLKVQSRTTVESTGKVIKRNIRSGQTVVHSGDVIVFGNVNKGAEILAGGS 137
Query: 198 TV 199
V
Sbjct: 138 VV 139
>pdb|2ZZA|A Chain A, Moritella Profunda Dihydrofolate Reductase Complex With
Nadp+ And Folate
pdb|2ZZA|B Chain B, Moritella Profunda Dihydrofolate Reductase Complex With
Nadp+ And Folate
Length = 162
Score = 27.3 bits (59), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 32/79 (40%), Gaps = 6/79 (7%)
Query: 59 IGRLCAGNKNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALG------NCIACND 112
IGR G N +L T E + +L D VV E L +G C+A D
Sbjct: 51 IGRPLPGRLNIVLSRQTDYQPEGVTVVATLEDAVVAAGDVEELMIIGGATIYNQCLAAAD 110
Query: 113 HVALTHTDLDRETEEMIAD 131
+ LTH +L E + D
Sbjct: 111 RLYLTHIELTTEGDTWFPD 129
>pdb|3IA4|A Chain A, Moritella Profunda Dihydrofolate Reductase (Dhfr) In
Complex With Nadph And Methotrexate (Mtx)
pdb|3IA4|B Chain B, Moritella Profunda Dihydrofolate Reductase (Dhfr) In
Complex With Nadph And Methotrexate (Mtx)
pdb|3IA4|C Chain C, Moritella Profunda Dihydrofolate Reductase (Dhfr) In
Complex With Nadph And Methotrexate (Mtx)
pdb|3IA4|D Chain D, Moritella Profunda Dihydrofolate Reductase (Dhfr) In
Complex With Nadph And Methotrexate (Mtx)
pdb|3IA5|A Chain A, Moritella Profunda Dihydrofolate Reductase (Dhfr)
pdb|3IA5|B Chain B, Moritella Profunda Dihydrofolate Reductase (Dhfr)
Length = 162
Score = 27.3 bits (59), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 32/79 (40%), Gaps = 6/79 (7%)
Query: 59 IGRLCAGNKNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALG------NCIACND 112
IGR G N +L T E + +L D VV E L +G C+A D
Sbjct: 51 IGRPLPGRLNIVLSRQTDYQPEGVTVVATLEDAVVAAGDVEELMIIGGATIYNQCLAAAD 110
Query: 113 HVALTHTDLDRETEEMIAD 131
+ LTH +L E + D
Sbjct: 111 RLYLTHIELTTEGDTWFPD 129
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
0.319 0.134 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,733,292
Number of Sequences: 62578
Number of extensions: 259494
Number of successful extensions: 635
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 615
Number of HSP's gapped (non-prelim): 15
length of query: 245
length of database: 14,973,337
effective HSP length: 96
effective length of query: 149
effective length of database: 8,965,849
effective search space: 1335911501
effective search space used: 1335911501
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)