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= 004627
(741 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2FUG|3 Chain 3, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus
pdb|2FUG|C Chain C, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus
pdb|2FUG|L Chain L, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus
pdb|2FUG|U Chain U, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus
pdb|3I9V|3 Chain 3, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Oxidized, 2 MolASU
pdb|3I9V|C Chain C, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Oxidized, 2 MolASU
pdb|3IAM|3 Chain 3, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Reduced, 2 MolASU,
WITH BOUND NADH
pdb|3IAM|C Chain C, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Reduced, 2 MolASU,
WITH BOUND NADH
pdb|3IAS|3 Chain 3, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Oxidized, 4 MolASU,
RE-Refined To 3.15 Angstrom Resolution
pdb|3IAS|C Chain C, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Oxidized, 4 MolASU,
RE-Refined To 3.15 Angstrom Resolution
pdb|3IAS|L Chain L, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Oxidized, 4 MolASU,
RE-Refined To 3.15 Angstrom Resolution
pdb|3IAS|U Chain U, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Oxidized, 4 MolASU,
RE-Refined To 3.15 Angstrom Resolution
pdb|3M9S|3 Chain 3, Crystal Structure Of Respiratory Complex I From Thermus
Thermophilus
pdb|3M9S|C Chain C, Crystal Structure Of Respiratory Complex I From Thermus
Thermophilus
pdb|2YBB|3 Chain 3, Fitted Model For Bovine Mitochondrial Supercomplex
I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)
pdb|4HEA|3 Chain 3, Crystal Structure Of The Entire Respiratory Complex I From
Thermus Thermophilus
pdb|4HEA|D Chain D, Crystal Structure Of The Entire Respiratory Complex I From
Thermus Thermophilus
Length = 783
Score = 230 bits (586), Expect = 3e-60, Method: Compositional matrix adjust.
Identities = 192/670 (28%), Positives = 280/670 (41%), Gaps = 90/670 (13%)
Query: 70 IEVFVDGYPLKIPKGFTVLQACEVAGVDIPRFCYHSRLSIAGNCRMCLV----------- 118
+ V V+ +++P G +V+ A AG D+P FC LS G CRMCLV
Sbjct: 2 VRVKVNDRIVEVPPGTSVMDAVFHAGYDVPLFCSEKHLSPIGACRMCLVRIGLPKKGPDG 61
Query: 119 ----------EVEKSPKPVASCAMPALPGMKIKTDTPLAKKAREGVMEFLLMNHPLDCPI 168
E++ PK ASC GM + T + + ++A+ G++EF L+NHPLDCP
Sbjct: 62 KPLLNEKGEPEIQWQPKLAASCVTAVADGMVVDTLSDVVREAQAGMVEFTLLNHPLDCPT 121
Query: 169 CDQGGECDLQDQSMAFGSDRGRFT------------EMKRSVVDKN--LGPLVKTVMTRC 214
CD+GG C+LQD+++ +G + E R VDK+ L P V RC
Sbjct: 122 CDKGGACELQDRTVEYGLYEKYYQKGPLELPVYTRFEFTRRHVDKHHPLSPFVILDRERC 181
Query: 215 IQCTRCVRFATEVAGVQDLGMLGRGSGEEIGTYVEKLMTSELSGNVIDICPVGALTSKPF 274
I C RCVR+ EV G + L + RG IGT ++ + S SGN+ DICPVGAL
Sbjct: 182 IHCKRCVRYFEEVPGDEVLDFIERGVHTFIGT-MDFGLPSGFSGNITDICPVGALLDLTA 240
Query: 275 AFKARNWELKGTETIDVTDAVGSNIRIDSRGPEVMRILPRLNEDINEEWISDKTRFCYDG 334
F+ARNWE++ T T VG I D+R E++RI R ++NE WI D RF ++
Sbjct: 241 RFRARNWEMEETPTTCALCPVGCGITADTRSGELLRIRAREVPEVNEIWICDAGRFGHEW 300
Query: 335 LKSQRLNDPMIRGADGRFKAVNWRDALAVVAEVMLQAKPEEIVGIAGRLSDAESMMALKD 394
RL P++R +GR W +A + E + +A+ EE+ + E + +
Sbjct: 301 ADQNRLKTPLVR-KEGRLVEATWEEAFLALKEGLKEARGEEVGLYLAHDATLEEGLLASE 359
Query: 395 FLNRMGSNNVWCEGTGAQSNADLRSGYIMNTSISGLEKADCFLLVGTQPRVEAAMVNARI 454
+ + ++ +G A + S+ L +AD F LV P EA +++ R+
Sbjct: 360 LAKALKTPHLDFQGRTAAP-----ASLFPPASLEDLLQAD-FALVLGDPTEEAPILHLRL 413
Query: 455 RKTVR--ANNAKVGYIGPATDLNYDHQHLGTGPKTLLEIAEGRHPFF------------- 499
+ VR + + P DL + K L A R P
Sbjct: 414 SEFVRDLKPPHRYNHGTPFADLQIKERMPRRTDKMAL-FAPYRAPLMKWAAIHEVHRPGE 472
Query: 500 ----------------------SAISNAKNPVIIVGAGLFERKDKDAIFSTVEAIAKKGN 537
A AKNPV+I+GAG+ + TV A +
Sbjct: 473 EREILLALLGDKEGSEMVAKAKEAWEKAKNPVLILGAGVLQ--------DTVAAERARLL 524
Query: 538 VIRPDWNXXXXXXXXXXXXXXXXXXXXPESSNSIESAKFVYLMGADDVDLEKLPNDAFVV 597
R S + +Y E L FVV
Sbjct: 525 AERKGAKVLAMTPAANARGLEAMGVLPGAKGASWDEPGALYAYYGFVPPEEALKGKRFVV 584
Query: 598 YQGHHGDHGVYR-ANVILPASAFSEKEGTYENTEGCTQQTLPAVPTVGDARDDWKIIRAL 656
H R A+V+LPA F EK G N EG PA G+A +++ L
Sbjct: 585 MHLSHLHPLAERYAHVVLPAPTFYEKRGHLVNLEGRVLPLSPAPIENGEAEGALQVLALL 644
Query: 657 SEVAGMRLPY 666
+E G+R P+
Sbjct: 645 AEALGVRPPF 654
>pdb|1FEH|A Chain A, Fe-Only Hydrogenase From Clostridium Pasteurianum
pdb|1C4A|A Chain A, Binding Of Exogenously Added Carbon Monoxide At The Active
Site Of The Fe-Only Hydrogenase (Cpi) From Clostridium
Pasteurianum
pdb|1C4C|A Chain A, Binding Of Exogenously Added Carbon Monoxide At The Active
Site Of The Fe-Only Hydrogenase (Cpi) From Clostridium
Pasteurianum
pdb|3C8Y|A Chain A, 1.39 Angstrom Crystal Structure Of Fe-Only Hydrogenase
Length = 574
Score = 54.3 bits (129), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 50/215 (23%), Positives = 85/215 (39%), Gaps = 8/215 (3%)
Query: 72 VFVDGYPLKIPKGFTVLQACEVAGVDIPRFCYHSRLSIAGN-CRMCLVEVEKSPKPVASC 130
+ ++G + T+L+ +DI C+ + + N C +C VEVE + V +C
Sbjct: 4 IIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTG-LVTAC 62
Query: 131 AMPALPGMKIKTDTPLAKKAREGVMEFLLMNHPLDCPICDQGGECDLQDQSMAFGSDRGR 190
GM I T++ + + + LL H C C++ C+ + + + +
Sbjct: 63 DTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASK 122
Query: 191 --FTEMKRSVVDKNLGPLVKTVMTRCIQCTRCVRFATEVAGVQDLGMLGRGSGEEIGTYV 248
+ K VD+ L T+C+ C RCV + + L + IG
Sbjct: 123 PFLPKDKTEYVDERSKSLT-VDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAED 181
Query: 249 EKLMTSE---LSGNVIDICPVGALTSKPFAFKARN 280
EK L G I CPV AL+ K + +N
Sbjct: 182 EKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKN 216
>pdb|2IV2|X Chain X, Reinterpretation Of Reduced Form Of Formate Dehydrogenase
H From E. Coli
pdb|1AA6|A Chain A, Reduced Form Of Formate Dehydrogenase H From E. Coli
pdb|1FDI|A Chain A, Oxidized Form Of Formate Dehydrogenase H From E. Coli
Complexed With The Inhibitor Nitrite
pdb|1FDO|A Chain A, Oxidized Form Of Formate Dehydrogenase H From E. Coli
Length = 715
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 41/86 (47%)
Query: 610 ANVILPASAFSEKEGTYENTEGCTQQTLPAVPTVGDARDDWKIIRALSEVAGMRLPYDTI 669
A+VILP++++ E EG + + Q+ AV D + DW+II ++ G + Y+
Sbjct: 439 ADVILPSTSWGEHEGVFTAADRGFQRFFKAVEPKWDLKTDWQIISEIATRMGYPMHYNNT 498
Query: 670 GGIRSRIRTVAPNLLHVDEREPATLG 695
I +R + P+ + LG
Sbjct: 499 QEIWDELRHLCPDFYGATYEKMGELG 524
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 36/139 (25%), Positives = 58/139 (41%), Gaps = 13/139 (9%)
Query: 339 RLNDPMIRGA-DGRFKAVNWRDALAVVAEVMLQAK----PEEIVGI-AGRLSDAESMMAL 392
RL PMIR G+ + V+W +AL VAE + K P+ I + R + E+ +
Sbjct: 61 RLKTPMIRRQRGGKLEPVSWDEALNYVAERLSAIKEKYGPDAIQTTGSSRGTGNETNYVM 120
Query: 393 KDFLNR-MGSNNVWC-----EGTGAQSNADLRSGYIMNTSISGLEKADCFLLVGTQPRVE 446
+ F +G+NNV C G M+ +I+ ++ D + G P
Sbjct: 121 QKFARAVIGTNNVDCCARVXHGPSVAGLHQSVGNGAMSNAINEIDNTDLVFVFGYNPADS 180
Query: 447 AAMVNARIRKTVRANNAKV 465
+V + R N AK+
Sbjct: 181 HPIVANHVINAKR-NGAKI 198
>pdb|3O5A|A Chain A, Crystal Structure Of Partially Reduced Periplasmic Nitrate
Reductase From Cupriavidus Necator Using Ionic Liquids
Length = 802
Score = 35.8 bits (81), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 610 ANVILPASAFSEKEGTYENTEGCTQQTLPAVPTVGDARDD-WKII 653
A+++LP++ + EKEG Y N E TQ V G+AR D W+++
Sbjct: 493 ADLVLPSAMWVEKEGAYGNAERRTQFWHQLVDAPGEARSDLWQLV 537
>pdb|3ML1|A Chain A, Crystal Structure Of The Periplasmic Nitrate Reductase
From Cupriavidus Necator
Length = 802
Score = 35.8 bits (81), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 610 ANVILPASAFSEKEGTYENTEGCTQQTLPAVPTVGDARDD-WKII 653
A+++LP++ + EKEG Y N E TQ V G+AR D W+++
Sbjct: 493 ADLVLPSAMWVEKEGAYGNAERRTQFWHQLVDAPGEARSDLWQLV 537
>pdb|2NYA|A Chain A, Crystal Structure Of The Periplasmic Nitrate Reductase
(Nap) From Escherichia Coli
pdb|2NYA|F Chain F, Crystal Structure Of The Periplasmic Nitrate Reductase
(Nap) From Escherichia Coli
Length = 792
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 610 ANVILPASAFSEKEGTYENTEGCTQQTLPAVPTVGDARDD-WKIIR 654
A++ILP + + EKEG Y N E TQ V G+A+ D W++++
Sbjct: 483 ADLILPTAMWVEKEGAYGNAERRTQFWRQQVQAPGEAKSDLWQLVQ 528
>pdb|1OGY|A Chain A, Crystal Structure Of The Heterodimeric Nitrate Reductase
From Rhodobacter Sphaeroides
pdb|1OGY|C Chain C, Crystal Structure Of The Heterodimeric Nitrate Reductase
From Rhodobacter Sphaeroides
pdb|1OGY|E Chain E, Crystal Structure Of The Heterodimeric Nitrate Reductase
From Rhodobacter Sphaeroides
pdb|1OGY|G Chain G, Crystal Structure Of The Heterodimeric Nitrate Reductase
From Rhodobacter Sphaeroides
pdb|1OGY|I Chain I, Crystal Structure Of The Heterodimeric Nitrate Reductase
From Rhodobacter Sphaeroides
pdb|1OGY|K Chain K, Crystal Structure Of The Heterodimeric Nitrate Reductase
From Rhodobacter Sphaeroides
pdb|1OGY|M Chain M, Crystal Structure Of The Heterodimeric Nitrate Reductase
From Rhodobacter Sphaeroides
pdb|1OGY|O Chain O, Crystal Structure Of The Heterodimeric Nitrate Reductase
From Rhodobacter Sphaeroides
Length = 802
Score = 35.4 bits (80), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 579 LMGADDVDLEKLPN----DAFVVYQGHHGDHGVYRANVILPASAFSEKEGTYENTEGCTQ 634
+ A ++D E P + F+V + A+++LPA+ + EKEG Y N E T
Sbjct: 458 MQAAPNIDQETYPGYRNPENFIVVSDAYPTVTGRAADLVLPAAMWVEKEGAYGNAERRTH 517
Query: 635 QTLPAVPTVGDARDD-WKII 653
V G+AR D W+++
Sbjct: 518 FWHQLVEAPGEARSDLWQLM 537
>pdb|1FRR|A Chain A, Crystal Structure Of [2fe-2s] Ferredoxin I From Equisetum
Arvense At 1.8 Angstroms Resolution
pdb|1FRR|B Chain B, Crystal Structure Of [2fe-2s] Ferredoxin I From Equisetum
Arvense At 1.8 Angstroms Resolution
Length = 95
Score = 34.3 bits (77), Expect = 0.26, Method: Composition-based stats.
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 6/44 (13%)
Query: 77 YPLKIPKGFTVLQACEVAGVDIPRFCYHSRLSIAGNCRMCLVEV 120
+ L +P+G T+L A E AG D+P C AG C CL +V
Sbjct: 13 FTLDVPEGTTILDAAEEAGYDLPFSCR------AGACSSCLGKV 50
>pdb|1VZO|A Chain A, The Structure Of The N-Terminal Kinase Domain Of Msk1
Reveals A Novel Autoinhibitory Conformation For A Dual
Kinase Protein
Length = 355
Score = 32.7 bits (73), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 33/118 (27%), Positives = 57/118 (48%), Gaps = 20/118 (16%)
Query: 297 SNIRIDSRGPEVMRILPRLNEDINEEWISDKTRFCYDGLKSQRLNDP-MIRGAD-GRFKA 354
NI +DS G V+ + +++E+++D+T YD + P ++RG D G KA
Sbjct: 188 ENILLDSNGHVVLT-----DFGLSKEFVADETERAYDFCGTIEYMAPDIVRGGDSGHDKA 242
Query: 355 VNWRDALAVVAEVMLQAKPEEIVG-------IAGRLSDAE-----SMMAL-KDFLNRM 399
V+W ++ E++ A P + G I+ R+ +E M AL KD + R+
Sbjct: 243 VDWWSLGVLMYELLTGASPFTVDGEKNSQAEISRRILKSEPPYPQEMSALAKDLIQRL 300
>pdb|3S6K|A Chain A, Crystal Structure Of Xcnags
Length = 467
Score = 32.3 bits (72), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 45/99 (45%), Gaps = 15/99 (15%)
Query: 369 LQAKPEEIVGIAGRL--SDAESMMALKDFLNRMGSNNVWCEGTGAQSNADLRSGYIMNTS 426
L AK +V + G + D E++ + FL +G + G G Q +A+L + I +
Sbjct: 58 LDAKRFAVVKVGGAVLRDDLEALTSSLSFLQEVGLTPIVLHGAGPQLDAELSAAGIEKQT 117
Query: 427 ISGLEKADCFLLVGTQPRVEAAMVNARIRKTVRANNAKV 465
++GL RV + A +RK +A+N K+
Sbjct: 118 VNGL-------------RVTSPHALAIVRKVFQASNLKL 143
>pdb|1W36|B Chain B, Recbcd:dna Complex
pdb|1W36|E Chain E, Recbcd:dna Complex
pdb|3K70|B Chain B, Crystal Structure Of The Complete Initiation Complex Of
Recbcd
pdb|3K70|E Chain E, Crystal Structure Of The Complete Initiation Complex Of
Recbcd
Length = 1180
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 565 PESSNSIESAKFVYLMGADDVDLEKLPNDAF---VVYQGHHGDHGVYRANVILP 615
PE N++ SA +MG + +D+E L ND VV + G ++R ++P
Sbjct: 606 PERENTLRSALATSMMGLNALDIETLNNDEHAWDVVVEEFDGYRQIWRKRGVMP 659
>pdb|1DWL|A Chain A, The Ferredoxin-Cytochrome Complex Using Heteronuclear Nmr
And Docking Simulation
Length = 59
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 8/60 (13%)
Query: 213 RCIQCTRCVRFATEVAGVQDLGMLGRGSGEEIGTYVEKLMTSELSGNVIDICPVGALTSK 272
CI C CV EV + D GEE T+E + + ID CPV A++ +
Sbjct: 8 ECIGCESCVELCPEVFAMID--------GEEKAMVTAPDSTAECAQDAIDACPVEAISKE 59
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 0.135 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,419,345
Number of Sequences: 62578
Number of extensions: 819370
Number of successful extensions: 1788
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1771
Number of HSP's gapped (non-prelim): 19
length of query: 741
length of database: 14,973,337
effective HSP length: 106
effective length of query: 635
effective length of database: 8,340,069
effective search space: 5295943815
effective search space used: 5295943815
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: 55 (25.8 bits)