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= 041604
(162 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1J6Q|A Chain A, Solution Structure And Characterization Of The Heme
Chaperone Ccme
pdb|1LM0|A Chain A, Solution Structure And Characterization Of The Heme
Chaperone Ccme
Length = 136
Score = 77.8 bits (190), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 51/150 (34%), Positives = 72/150 (48%), Gaps = 26/150 (17%)
Query: 12 NFQDQLVFYVTPSEALEKYQSNPSK----NKFRLGGLVLEGSVAHPASSSEMEFVVTD-L 66
+ L + TPSE + K + R+GG+V GS+ +S ++F V D L
Sbjct: 4 DLNSNLNLFYTPSEIVNGKTDTGVKPEAGQRIRVGGMVTVGSMVRDPNSLHVQFAVHDSL 63
Query: 67 VTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDV 126
+ILV Y LPDLFREG +V +G + D +AT+V
Sbjct: 64 GGEILVTYDDLLPDLFREGQGIVAQGVL---------------------GEDGKLAATEV 102
Query: 127 LAKHDEKYMPQEVAAAIEKNKKMLEEQQQE 156
LAKHDE YMP EVA A+ + + L+ QQ+
Sbjct: 103 LAKHDENYMPPEVAEAMGQKHEKLDYSQQK 132
>pdb|1SR3|A Chain A, Solution Structure Of The Heme Chaperone Ccme Of
Escherichia Coli
Length = 136
Score = 72.8 bits (177), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 48/135 (35%), Positives = 66/135 (48%), Gaps = 26/135 (19%)
Query: 18 VFYVTPSEAL----EKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVR 73
+FY TP E L E Q + R+GG+V+ GSV +S ++ F + D + V
Sbjct: 7 LFY-TPGEILYGKRETQQMPEVGQRLRVGGMVMPGSVQRDPNSLKVTFTIYDAEGSVDVS 65
Query: 74 YQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEK 133
Y+G LPDLFREG VVV+G ++ + A +VLAKHDE
Sbjct: 66 YEGILPDLFREGQGVVVQGELE---------------------KGNHILAKEVLAKHDEN 104
Query: 134 YMPQEVAAAIEKNKK 148
Y P EV A+E N +
Sbjct: 105 YTPPEVEKAMEANHR 119
>pdb|2KCT|A Chain A, Solution Nmr Structure Of The Ob-Fold Domain Of Heme
Chaperone Ccme From Desulfovibrio Vulgaris. Northeast
Structural Genomics Target Dvr115g
Length = 94
Score = 32.0 bits (71), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 70 ILVRYQGSLPDLFREGHSVVVEGFIKP 96
+ V Y+G++PD F+ G V++EG + P
Sbjct: 45 VWVLYKGAVPDTFKPGVEVIIEGGLAP 71
>pdb|2Y6P|A Chain A, Evidence For A Two-Metal-Ion-Mechanism In The
Kdo-Cytidylyltransferase Kdsb
pdb|2Y6P|B Chain B, Evidence For A Two-Metal-Ion-Mechanism In The
Kdo-Cytidylyltransferase Kdsb
pdb|2Y6P|C Chain C, Evidence For A Two-Metal-Ion-Mechanism In The
Kdo-Cytidylyltransferase Kdsb
Length = 234
Score = 30.8 bits (68), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 10/74 (13%)
Query: 53 PASSSEMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSE 112
P+ S + +VV DL D+++ YQG P ++ E IK I E++ K E+ V+
Sbjct: 71 PSGSDRVLYVVRDLDVDLIINYQGDEPFVYEED--------IKLIFRELE--KGERVVTL 120
Query: 113 NARSRDCFFSATDV 126
+ ++ + DV
Sbjct: 121 ARKDKEAYERPEDV 134
>pdb|3U60|A Chain A, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
Length = 195
Score = 26.6 bits (57), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 76 GSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENA 114
G LP + +E +V + F+K +T KNVK +K + + A
Sbjct: 148 GKLPLVLKELKGLVTDDFLKEVT---KNVKEQKQLKKLA 183
>pdb|3U5Z|A Chain A, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|K Chain K, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U61|A Chain A, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
Length = 199
Score = 26.6 bits (57), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 76 GSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENA 114
G LP + +E +V + F+K +T KNVK +K + + A
Sbjct: 148 GKLPLVLKELKGLVTDDFLKEVT---KNVKEQKQLKKLA 183
>pdb|2Y7I|A Chain A, Structural Basis For High Arginine Specificity In
Salmonella Typhimurium Periplasmic Binding Protein
Stm4351.
pdb|2Y7I|B Chain B, Structural Basis For High Arginine Specificity In
Salmonella Typhimurium Periplasmic Binding Protein
Stm4351
Length = 229
Score = 26.2 bits (56), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 30/68 (44%)
Query: 90 VEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKM 149
V G + I + +KN + E A D + + + D + QE+ AA++K K
Sbjct: 157 VFGDVAAIGKWLKNNPDYAIMDERASDPDYYGKGLGIAVRKDNDALLQEINAALDKVKAS 216
Query: 150 LEEQQQEE 157
E Q +E
Sbjct: 217 PEYAQMQE 224
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
0.314 0.131 0.359
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,454,593
Number of Sequences: 62578
Number of extensions: 161720
Number of successful extensions: 431
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 420
Number of HSP's gapped (non-prelim): 12
length of query: 162
length of database: 14,973,337
effective HSP length: 91
effective length of query: 71
effective length of database: 9,278,739
effective search space: 658790469
effective search space used: 658790469
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)