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= 029958
(185 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1HPC|A Chain A, Refined Structures At 2 Angstroms And 2.2 Angstroms Of The
Two Forms Of The H-Protein, A Lipoamide-Containing
Protein Of The Glycine Decarboxylase
pdb|1HPC|B Chain B, Refined Structures At 2 Angstroms And 2.2 Angstroms Of The
Two Forms Of The H-Protein, A Lipoamide-Containing
Protein Of The Glycine Decarboxylase
pdb|1DXM|A Chain A, Reduced Form Of The H Protein From Glycine Decarboxylase
Complex
pdb|1DXM|B Chain B, Reduced Form Of The H Protein From Glycine Decarboxylase
Complex
pdb|1HTP|A Chain A, Refined Structures At 2 Angstroms And 2.2 Angstroms Of The
Two Forms Of The H-Protein, A Lipoamide-Containing
Protein Of The Glycine Decarboxylase Complex
Length = 131
Score = 47.0 bits (110), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 36/129 (27%), Positives = 57/129 (44%), Gaps = 3/129 (2%)
Query: 52 ANGLCVIGLAPTHVAFKDEGGITAVDFNVGKSDRSGFKVTGKRKKNAQHFESNTAVCKVC 111
+N L + AP+H K EG + + D G V + + V
Sbjct: 1 SNVLDGLKYAPSHEWVKHEGSVATIGITDHAQDHLGEVVFVELPEPGVSVTKGKGFGAVE 60
Query: 112 TNNDSYIVRCCVKGSLLEVNNRLIKQPGLLNSSADREGYIAIIMPKPADWLKIKSSLLGL 171
+ + V + G ++EVN L +PGL+NSS +G++ I P D L+ SLLG
Sbjct: 61 SVKATSDVNSPISGEVIEVNTGLTGKPGLINSSPYEDGWMIKIKPTSPDELE---SLLGA 117
Query: 172 EDYKRKREE 180
++Y + EE
Sbjct: 118 KEYTKFCEE 126
>pdb|1ONL|A Chain A, Crystal Structure Of Thermus Thermophilus Hb8 H-Protein Of
The Glycine Cleavage System
pdb|1ONL|B Chain B, Crystal Structure Of Thermus Thermophilus Hb8 H-Protein Of
The Glycine Cleavage System
pdb|1ONL|C Chain C, Crystal Structure Of Thermus Thermophilus Hb8 H-Protein Of
The Glycine Cleavage System
Length = 128
Score = 30.8 bits (68), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 102 ESNTAVCKVCTNNDSYIVRCCVKGSLLEVNNRLIKQPGLLNSSADREGYIAIIMPK 157
E+ V V T +D Y V G ++EVN L K P L+N EG+I + P+
Sbjct: 54 EAVAVVESVKTASDIY---APVAGEIVEVNLALEKTPELVNQDPYGEGWIFRLKPR 106
>pdb|3OZ6|A Chain A, Crystal Structure Of Mapk From Cryptosporidium Parvum,
Cgd2_1960
pdb|3OZ6|B Chain B, Crystal Structure Of Mapk From Cryptosporidium Parvum,
Cgd2_1960
Length = 388
Score = 30.0 bits (66), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 9/69 (13%)
Query: 33 AYFAPDFLKPGHDQYV---------YRHANGLCVIGLAPTHVAFKDEGGITAVDFNVGKS 83
A + L+P H QYV Y H+ GL + P+++ E + DF + +S
Sbjct: 99 AVIRANILEPVHKQYVVYQLIKVIKYLHSGGLLHRDMKPSNILLNAECHVKVADFGLSRS 158
Query: 84 DRSGFKVTG 92
+ +VT
Sbjct: 159 FVNIRRVTN 167
>pdb|3MXU|A Chain A, Crystal Structure Of Glycine Cleavage System Protein H
From Henselae
Length = 143
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 35/88 (39%)
Query: 64 HVAFKDEGGITAVDFNVGKSDRSGFKVTGKRKKNAQHFESNTAVCKVCTNNDSYIVRCCV 123
H EG + V ++ G V +N A V + + V +
Sbjct: 31 HEWLSVEGQVVTVGITDYAQEQLGDLVFIDLPQNGTKLSKGDAAAVVESVKAASDVYAPL 90
Query: 124 KGSLLEVNNRLIKQPGLLNSSADREGYI 151
G ++E+N L + P L+N A+ EG++
Sbjct: 91 DGEVVEINAALAESPELVNQKAETEGWL 118
>pdb|2EDG|A Chain A, Solution Structure Of The Gcv_h Domain From Mouse Glycine
Length = 130
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 123 VKGSLLEVNNRLIKQPGLLNSSADREGY-IAIIMPKPAD 160
+ G + EVN L + PGL+N S +G+ I + + P++
Sbjct: 73 LSGEVTEVNEALAENPGLVNKSCYEDGWLIKMTLSDPSE 111
>pdb|1ZKO|A Chain A, Crystal Structure Of Glycine Cleavage System H Protein
(Tm0212) From Thermotoga Maritima At 1.65 A Resolution
pdb|1ZKO|B Chain B, Crystal Structure Of Glycine Cleavage System H Protein
(Tm0212) From Thermotoga Maritima At 1.65 A Resolution
Length = 136
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 119 VRCCVKGSLLEVNNRLIKQPGLLNSSADREGYI 151
V + G ++EVN +L +P L+N + EG++
Sbjct: 77 VYAPLSGKIVEVNEKLDTEPELINKDPEGEGWL 109
>pdb|2KA7|A Chain A, Nmr Solution Structure Of Tm0212 At 40 C
Length = 124
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 119 VRCCVKGSLLEVNNRLIKQPGLLNSSADREGYI 151
V + G ++EVN +L +P L+N + EG++
Sbjct: 65 VYAPLSGKIVEVNEKLDTEPELINKDPEGEGWL 97
>pdb|3IFT|A Chain A, Crystal Structure Of Glycine Cleavage System Protein H
From Mycobacterium Tuberculosis, Using X-Rays From The
Compact L Source
Length = 142
Score = 27.3 bits (59), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%)
Query: 123 VKGSLLEVNNRLIKQPGLLNSSADREGYIAIIMPKPADWLKIKSSLLGLEDYKRKR 178
+ G + EVN+ L P L+NS G++ I +D ++S+L L D + R
Sbjct: 82 ISGKVSEVNSDLDGTPQLVNSDPYGAGWLLDIQVDSSDVAALESALTTLLDAEAYR 137
>pdb|3KLR|A Chain A, Bovine H-Protein At 0.88 Angstrom Resolution
Length = 125
Score = 27.3 bits (59), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 123 VKGSLLEVNNRLIKQPGLLNSSADREGY-IAIIMPKPAD 160
+ G + E+N L + PGL+N S +G+ I + P++
Sbjct: 68 LSGEVTEINKALAENPGLVNKSCYEDGWLIKMTFSNPSE 106
>pdb|3HGB|A Chain A, Crystal Structure Of Glycine Cleavage System Protein H
From Mycobacterium Tuberculosis
Length = 155
Score = 27.3 bits (59), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%)
Query: 123 VKGSLLEVNNRLIKQPGLLNSSADREGYIAIIMPKPADWLKIKSSLLGLEDYKRKR 178
+ G + EVN+ L P L+NS G++ I +D ++S+L L D + R
Sbjct: 95 ISGKVSEVNSDLDGTPQLVNSDPYGAGWLLDIQVDSSDVAALESALTTLLDAEAYR 150
>pdb|3AUX|A Chain A, Crystal Structure Of Rad50 Bound To Adp
pdb|3AUY|A Chain A, Crystal Structure Of Rad50 Bound To Adp
pdb|3AUY|B Chain B, Crystal Structure Of Rad50 Bound To Adp
pdb|3AV0|B Chain B, Crystal Structure Of Mre11-Rad50 Bound To Atp S
Length = 371
Score = 26.9 bits (58), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 45/97 (46%), Gaps = 8/97 (8%)
Query: 88 FKVTGKRKKNAQHFESNTAVCKVCTNNDSYIVRCCVKGSLLEVNNRL-IKQPGLLNSSAD 146
F+V G K + ++S K+ N Y VN L + + LNS
Sbjct: 75 FEVNGNNYKIIREYDSGRGGAKLYKNGKPYATTISAVNK--AVNEILGVDRNMFLNSIYI 132
Query: 147 REGYIAIIMP-KPADWLKIKSSLLGLEDYKRKREECF 182
++G IA + KP++ L+ + LLG++++ E+C+
Sbjct: 133 KQGEIAKFLSLKPSEKLETVAKLLGIDEF----EKCY 165
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 0.138 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,027,648
Number of Sequences: 62578
Number of extensions: 251128
Number of successful extensions: 674
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 665
Number of HSP's gapped (non-prelim): 11
length of query: 185
length of database: 14,973,337
effective HSP length: 93
effective length of query: 92
effective length of database: 9,153,583
effective search space: 842129636
effective search space used: 842129636
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: 48 (23.1 bits)