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= 032030
(148 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2HF9|A Chain A, Crystal Structure Of Hypb From Methanocaldococcus
Jannaschii In The Triphosphate Form
pdb|2HF9|B Chain B, Crystal Structure Of Hypb From Methanocaldococcus
Jannaschii In The Triphosphate Form
Length = 226
Score = 52.4 bits (124), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 39/87 (44%), Positives = 52/87 (59%), Gaps = 5/87 (5%)
Query: 35 LEELSNLFKADLLLCESGGDNLA-ANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ-AD 92
LE+L NL + DLL E+ G+ + A+F I+ I G D I + PGI + AD
Sbjct: 111 LEDL-NLDEIDLLFIENVGNLICPADFDLGTHKRIVVISTTEGDDTIEKH--PGIMKTAD 167
Query: 93 LLVINKTDLASAIGADLAVMERDALRM 119
L+VINK DLA A+GAD+ ME DA R+
Sbjct: 168 LIVINKIDLADAVGADIKKMENDAKRI 194
>pdb|2HF8|A Chain A, Crystal Structure Of Hypb From Methanocaldococcus
Jannaschii In The Triphosphate Form, In Complex With
Zinc
pdb|2HF8|B Chain B, Crystal Structure Of Hypb From Methanocaldococcus
Jannaschii In The Triphosphate Form, In Complex With
Zinc
Length = 226
Score = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 38/87 (43%), Positives = 51/87 (58%), Gaps = 5/87 (5%)
Query: 35 LEELSNLFKADLLLCESGGDNLA-ANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ-AD 92
LE+L NL + DLL E+ G+ + A+F I+ I G D I + PGI + AD
Sbjct: 111 LEDL-NLDEIDLLFIENVGNLICPADFDLGTHKRIVVISTTEGDDTIEKH--PGIXKTAD 167
Query: 93 LLVINKTDLASAIGADLAVMERDALRM 119
L+VINK DLA A+GAD+ E DA R+
Sbjct: 168 LIVINKIDLADAVGADIKKXENDAKRI 194
>pdb|2WSM|A Chain A, Crystal Structure Of Hydrogenase Maturation Factor Hypb
From Archaeoglobus Fulgidus
pdb|2WSM|B Chain B, Crystal Structure Of Hydrogenase Maturation Factor Hypb
From Archaeoglobus Fulgidus
Length = 221
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 31/80 (38%), Positives = 43/80 (53%), Gaps = 2/80 (2%)
Query: 38 LSNLFKADLLLCESGGDNLAANFSRELAD-YIIYIIDVSGGDKIPRKGGPGITQADLLVI 96
L DLLL E+ G NL +L + Y + ++ V+ GD + K ADL+VI
Sbjct: 103 LKKFSDCDLLLIENVG-NLICPVDFDLGENYRVVMVSVTEGDDVVEKHPEIFRVADLIVI 161
Query: 97 NKTDLASAIGADLAVMERDA 116
NK LA A+GAD+ M+ DA
Sbjct: 162 NKVALAEAVGADVEKMKADA 181
>pdb|1ZRT|D Chain D, Rhodobacter Capsulatus Cytochrome Bc1 Complex With
Stigmatellin Bound
pdb|1ZRT|Q Chain Q, Rhodobacter Capsulatus Cytochrome Bc1 Complex With
Stigmatellin Bound
Length = 258
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 48 LCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGA 107
L + GG L F RE A + IID G++ RK + D+ T + +G
Sbjct: 48 LADDGGPQLDPTFVREYAAGLDTIIDKDSGEERDRK------ETDMF---PTRVGDGMGP 98
Query: 108 DLAVMER 114
DL+VM +
Sbjct: 99 DLSVMAK 105
>pdb|1OAO|C Chain C, Nizn[fe4s4] And Nini[fe4s4] Clusters In Closed And Open
Alpha Subunits Of Acetyl-Coa SynthaseCARBON MONOXIDE
Dehydrogenase
pdb|1OAO|D Chain D, Nizn[fe4s4] And Nini[fe4s4] Clusters In Closed And Open
Alpha Subunits Of Acetyl-Coa SynthaseCARBON MONOXIDE
Dehydrogenase
pdb|2Z8Y|M Chain M, Xenon-Bound Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL-Coa Synthase(CodhACS) FROM MOORELLA
Thermoacetica
pdb|2Z8Y|N Chain N, Xenon-Bound Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL-Coa Synthase(CodhACS) FROM MOORELLA
Thermoacetica
pdb|2Z8Y|O Chain O, Xenon-Bound Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL-Coa Synthase(CodhACS) FROM MOORELLA
Thermoacetica
pdb|2Z8Y|P Chain P, Xenon-Bound Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL-Coa Synthase(CodhACS) FROM MOORELLA
Thermoacetica
pdb|3I01|M Chain M, Native Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL- Coa Synthase From Moorella
Thermoacetica, Water-Bound C-Cluster.
pdb|3I01|N Chain N, Native Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL- Coa Synthase From Moorella
Thermoacetica, Water-Bound C-Cluster.
pdb|3I01|O Chain O, Native Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL- Coa Synthase From Moorella
Thermoacetica, Water-Bound C-Cluster.
pdb|3I01|P Chain P, Native Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL- Coa Synthase From Moorella
Thermoacetica, Water-Bound C-Cluster
Length = 729
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 13 AVETGGCPHAAIREDISINLGPLEELSNLFKADLLLCESGGDNLAA 58
A+ET G I+ D+ IN GP E ++ K D+ + E GG+ A
Sbjct: 305 AMETRGIKLTKIKLDLPINFGPAFEGESIRKGDMYV-EMGGNRTPA 349
>pdb|3I04|M Chain M, Cyanide-Bound Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL-Coa Synthase From Moorella
Thermoacetica, Cyanide-Bound C-Cluster
pdb|3I04|N Chain N, Cyanide-Bound Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL-Coa Synthase From Moorella
Thermoacetica, Cyanide-Bound C-Cluster
pdb|3I04|O Chain O, Cyanide-Bound Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL-Coa Synthase From Moorella
Thermoacetica, Cyanide-Bound C-Cluster
pdb|3I04|P Chain P, Cyanide-Bound Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL-Coa Synthase From Moorella
Thermoacetica, Cyanide-Bound C-Cluster
Length = 728
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 13 AVETGGCPHAAIREDISINLGPLEELSNLFKADLLLCESGGDNLAA 58
A+ET G I+ D+ IN GP E ++ K D+ + E GG+ A
Sbjct: 304 AMETRGIKLTKIKLDLPINFGPAFEGESIRKGDMYV-EMGGNRTPA 348
>pdb|1MJG|M Chain M, Crystal Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL-Coa Synthase(CodhACS) FROM MOORELLA
Thermoacetica (F. Clostridium Thermoaceticum)
pdb|1MJG|N Chain N, Crystal Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL-Coa Synthase(CodhACS) FROM MOORELLA
Thermoacetica (F. Clostridium Thermoaceticum)
pdb|1MJG|O Chain O, Crystal Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL-Coa Synthase(CodhACS) FROM MOORELLA
Thermoacetica (F. Clostridium Thermoaceticum)
pdb|1MJG|P Chain P, Crystal Structure Of Bifunctional Carbon Monoxide
DehydrogenaseACETYL-Coa Synthase(CodhACS) FROM MOORELLA
Thermoacetica (F. Clostridium Thermoaceticum)
Length = 729
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 13 AVETGGCPHAAIREDISINLGPLEELSNLFKADLLLCESGGDNLAA 58
A+ET G I+ D+ IN GP E ++ K D+ + E GG+ A
Sbjct: 305 AMETRGIKLTKIKLDLPINFGPAFEGESIRKGDMYV-EMGGNRTPA 349
>pdb|3PFO|A Chain A, Crystal Structure Of A Putative Acetylornithine
Deacetylase (Rpa2325) From Rhodopseudomonas Palustris
Cga009 At 1.90 A Resolution
pdb|3PFO|B Chain B, Crystal Structure Of A Putative Acetylornithine
Deacetylase (Rpa2325) From Rhodopseudomonas Palustris
Cga009 At 1.90 A Resolution
Length = 433
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 3 NGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLLLCESGG 53
G P+E R +E C A D ++ P E + + F+AD +CE GG
Sbjct: 303 TGDTPQEAXRGIEK--CLADAQATDSFLSENPAELVWSGFQADPAVCEPGG 351
>pdb|2H5E|A Chain A, Crystal Structure Of E.Coli Polypeptide Release Factor Rf3
pdb|2H5E|B Chain B, Crystal Structure Of E.Coli Polypeptide Release Factor Rf3
pdb|2O0F|A Chain A, Docking Of The Modified Rf3 X-Ray Structure Into Cryo-Em
Map Of E.Coli 70s Ribosome Bound With Rf3
pdb|3ZVO|Y Chain Y, Crystal Structure Of The Hybrid State Of Ribosome In
Complex With The Guanosine Triphosphatase Release Factor
3
pdb|3SFS|W Chain W, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
Length = 529
Score = 26.9 bits (58), Expect = 4.7, Method: Composition-based stats.
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 96 INKTDLASAIGADLAVMERDALRMRDGG 123
+N DL +A+G DLA RD L + G
Sbjct: 210 LNNPDLDAAVGEDLAQQLRDELELVKGA 237
>pdb|3UOQ|W Chain W, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
Length = 534
Score = 26.6 bits (57), Expect = 4.8, Method: Composition-based stats.
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 96 INKTDLASAIGADLAVMERDALRMRDGG 123
+N DL +A+G DLA RD L + G
Sbjct: 210 LNNPDLDAAVGEDLAQQLRDELELVKGA 237
>pdb|2Y5W|A Chain A, Crystal Structure Of Drosophila Melanogaster Kinesin-1
Motor Domain Dimer
pdb|2Y5W|B Chain B, Crystal Structure Of Drosophila Melanogaster Kinesin-1
Motor Domain Dimer
pdb|2Y65|A Chain A, Crystal Structure Of Drosophila Melanogaster Kinesin-1
Motor Domain Dimer-Tail Complex
pdb|2Y65|B Chain B, Crystal Structure Of Drosophila Melanogaster Kinesin-1
Motor Domain Dimer-Tail Complex
pdb|2Y65|C Chain C, Crystal Structure Of Drosophila Melanogaster Kinesin-1
Motor Domain Dimer-Tail Complex
pdb|2Y65|D Chain D, Crystal Structure Of Drosophila Melanogaster Kinesin-1
Motor Domain Dimer-Tail Complex
Length = 365
Score = 25.8 bits (55), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 69 IYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIG 106
+Y++D++G +K+ + G G + INK+ SA+G
Sbjct: 234 LYLVDLAGSEKVSKTGAEGTVLDEAKNINKS--LSALG 269
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
0.322 0.142 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,563,803
Number of Sequences: 62578
Number of extensions: 182067
Number of successful extensions: 376
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 362
Number of HSP's gapped (non-prelim): 23
length of query: 148
length of database: 14,973,337
effective HSP length: 90
effective length of query: 58
effective length of database: 9,341,317
effective search space: 541796386
effective search space used: 541796386
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: 47 (22.7 bits)