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= psy4847
(396 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3JTF|A Chain A, The Cbs Domain Pair Structure Of A Magnesium And Cobalt
Efflux Protein From Bordetella Parapertussis In Complex
With Amp
pdb|3JTF|B Chain B, The Cbs Domain Pair Structure Of A Magnesium And Cobalt
Efflux Protein From Bordetella Parapertussis In Complex
With Amp
Length = 129
Score = 51.2 bits (121), Expect = 1e-06, Method: Composition-based stats.
Identities = 33/111 (29%), Positives = 61/111 (54%), Gaps = 13/111 (11%)
Query: 67 ETVSEIMKSGYSRIPVYEDRRTNIVTMFYIKDLALVDPDDNTPLKTLCQFYQNSCYFVFE 126
+ ++ I+++ +SR PVYED R NI+ + KDL + +++L + F+ E
Sbjct: 28 QLLATIIETAHSRFPVYEDDRDNIIGILLAKDLLRYXLEPALDIRSLVR----PAVFIPE 83
Query: 127 DTTLDVLLKQFKEGIKGHMAFVHRVNNEGEGDPFYETVGLITLEDVIEELI 177
L+VLL++F+ + H+A V ++ G GL+T EDV+E+++
Sbjct: 84 VKRLNVLLREFRAS-RNHLAIV--IDEHG------GISGLVTXEDVLEQIV 125
>pdb|3LFR|A Chain A, The Crystal Structure Of A Cbs Domain From A Putative
Metal Ion Transporter Bound To Amp From Pseudomonas
Syringae To 1.55a
pdb|3LFR|B Chain B, The Crystal Structure Of A Cbs Domain From A Putative
Metal Ion Transporter Bound To Amp From Pseudomonas
Syringae To 1.55a
Length = 136
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 36/124 (29%), Positives = 61/124 (49%), Gaps = 17/124 (13%)
Query: 67 ETVSEIMKSGYSRIPVYEDRRTNIVTMFYIKDL---ALVDPDDNTPLKTLCQFYQNSCYF 123
E + ++ + +SR PV + +++ + KDL L D+ +K L + F
Sbjct: 26 EFLPAVIDAAHSRYPVIGESHDDVLGVLLAKDLLPLILKADGDSDDVKKLLR----PATF 81
Query: 124 VFEDTTLDVLLKQFKEGIKGHMAFVHRVNNEGEGDPFYETVGLITLEDVIEELIQAEIMD 183
V E L+VLL++F+ H A V D + GL+T+EDV+E+++ +I D
Sbjct: 82 VPESKRLNVLLREFRAN-HNHXAIVI--------DEYGGVAGLVTIEDVLEQIV-GDIED 131
Query: 184 ETDV 187
E DV
Sbjct: 132 EHDV 135
>pdb|3OI8|A Chain A, The Crystal Structure Of Functionally Unknown Conserved
Protein Domain From Neisseria Meningitidis Mc58
pdb|3OI8|B Chain B, The Crystal Structure Of Functionally Unknown Conserved
Protein Domain From Neisseria Meningitidis Mc58
Length = 156
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 53/105 (50%), Gaps = 16/105 (15%)
Query: 72 IMKSGYSRIPVYEDRRTNIVTMFYIKDLA--LVDPDDNTPLKTLCQFYQNSCYFVFEDTT 129
++ + +SR PV + + ++ + + KDL +P+ LK++ + FV E +
Sbjct: 66 VIDTAHSRFPVIGEDKDEVLGILHAKDLLKYXFNPE-QFHLKSILR----PAVFVPEGKS 120
Query: 130 LDVLLKQFKEGIKGHMAFVHRVNNEGEGDPFYETVGLITLEDVIE 174
L LLK+F+E + H A V D + T GL+T ED+IE
Sbjct: 121 LTALLKEFREQ-RNHXAIV--------IDEYGGTSGLVTFEDIIE 156
>pdb|4HG0|A Chain A, Crystal Structure Of Magnesium And Cobalt Efflux Protein
Corc, Northeast Structural Genomics Consortium (nesg)
Target Er40
Length = 292
Score = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 40/155 (25%), Positives = 67/155 (43%), Gaps = 13/155 (8%)
Query: 24 NDL-EKDEVNIISGALELRRKIVGDVMTKLEDVYMLSYDAILDFETVSEIMKSGYSRIPV 82
NDL ++D + + G ++ + V D+ L + LD E + I++S +SR PV
Sbjct: 47 NDLIDEDTRDXLEGVXDIADQRVRDIXIPRSQXITLKRNQTLD-ECLDVIIESAHSRFPV 105
Query: 83 YEDRRTNIVTMFYIKDLALVDPDDNTPLKTLCQFYQNSCYFVFEDTTLDVLLKQFKEGIK 142
+ + +I + KDL D Q V E +D LK+F+ +
Sbjct: 106 ISEDKDHIEGILXAKDLLPFXRSDAEAFSXDKVLRQ--AVVVPESKRVDRXLKEFRSQ-R 162
Query: 143 GHMAFVHRVNNEGEGDPFYETVGLITLEDVIEELI 177
H A V D F GL+T+ED++E ++
Sbjct: 163 YHXAIVI--------DEFGGVSGLVTIEDILELIV 189
>pdb|3HF7|A Chain A, The Crystal Structure Of A Cbs-Domain Pair With Bound Amp
From Klebsiella Pneumoniae To 2.75a
Length = 130
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 26/109 (23%), Positives = 50/109 (45%), Gaps = 9/109 (8%)
Query: 69 VSEIMKSGYSRIPVYEDRRTNIVTMFYIKDLALVDPDDNTPLKTLCQFYQNSCYFVFEDT 128
V ++ S + RI +Y D + ++M +++ + + K + + YFV E T
Sbjct: 27 VRQLTHSPHGRIVLYRDSLDDAISMLRVREAYRLMTEKKEFTKEIMLRAADEIYFVPEGT 86
Query: 129 TLDVLLKQFKEGIKGHMAFVHRVNNEGEGDPFYETVGLITLEDVIEELI 177
L L +F+ K V D + + GL+T+ED++EE++
Sbjct: 87 PLSTQLVKFQRNKKKVGLVV---------DEYGDIQGLVTVEDILEEIV 126
>pdb|3KZV|A Chain A, The Crystal Structure Of A Cytoplasmic Protein With
Unknown Function From Saccharomyces Cerevisiae
Length = 254
Score = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 108 TPLKTLCQFYQNSCYFVFEDTTLDVLLKQF-KEGIKGHMAFVHRVNNEGEGDP 159
PLK L + Y + ++V D T D +LKQ +KGH V N G +P
Sbjct: 39 APLKKLKEKYGDRFFYVVGDITEDSVLKQLVNAAVKGHGKIDSLVANAGVLEP 91
>pdb|3LV9|A Chain A, Crystal Structure Of Cbs Domain Of A Putative Transporter
From Clostridium Difficile 630
Length = 148
Score = 32.3 bits (72), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 30/133 (22%), Positives = 65/133 (48%), Gaps = 18/133 (13%)
Query: 51 KLEDVYMLSYDAILDFETVSE------IMKSGYSRIPVYEDRRTNIVTMFYIKDLALVDP 104
K+ ++ + D + +E+ SE + + G +R PV + +I+ +I+DL
Sbjct: 24 KIREIXVPRTDXVCIYESDSEEKILAILKEEGVTRYPVCRKNKDDILGFVHIRDLYNQKI 83
Query: 105 DDNTPLKTLCQFYQNSCYFVFEDTTLDVLLKQFKEGIKGHMAFVHRVNNEGEGDPFYETV 164
++N K + ++ E+ T+D L++ ++ K +A V D + T
Sbjct: 84 NEN---KIELEEILRDIIYISENLTIDKALERIRKE-KLQLAIVV--------DEYGGTS 131
Query: 165 GLITLEDVIEELI 177
G++T+ED++EE++
Sbjct: 132 GVVTIEDILEEIV 144
>pdb|3NQR|A Chain A, A Putative Cbs Domain-Containing Protein From Salmonella
Typhimurium Lt2
pdb|3NQR|B Chain B, A Putative Cbs Domain-Containing Protein From Salmonella
Typhimurium Lt2
pdb|3NQR|C Chain C, A Putative Cbs Domain-Containing Protein From Salmonella
Typhimurium Lt2
pdb|3NQR|D Chain D, A Putative Cbs Domain-Containing Protein From Salmonella
Typhimurium Lt2
Length = 127
Score = 31.6 bits (70), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 34/133 (25%), Positives = 55/133 (41%), Gaps = 12/133 (9%)
Query: 45 VGDVMTKLEDVYMLSYDAILDFETVSEIMKSGYSRIPVYEDRRTNIVTMFYIKDLALVDP 104
V D+ L + LD E + I++S +SR PV + + +I + KDL
Sbjct: 5 VRDIXIPRSQXITLKRNQTLD-ECLDVIIESAHSRFPVISEDKDHIEGILXAKDLLPFXR 63
Query: 105 DDNTPLKTLCQFYQNSCYFVFEDTTLDVLLKQFKEGIKGHMAFVHRVNNEGEGDPFYETV 164
D + V E +D LK+F+ + H A V D F
Sbjct: 64 SDAEAFSX--DKVLRTAVVVPESKRVDRXLKEFRSQ-RYHXAIVI--------DEFGGVS 112
Query: 165 GLITLEDVIEELI 177
GL+T+ED++E ++
Sbjct: 113 GLVTIEDILELIV 125
>pdb|2NX2|A Chain A, Crystal Structure Of Protein Ypsa From Bacillus Subtilis,
Pfam Duf1273
Length = 181
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 24/107 (22%), Positives = 44/107 (41%), Gaps = 21/107 (19%)
Query: 83 YEDRRTNIVTMFYIKDLALVDPDD-----------------NTPLKTLCQFYQNSCYFVF 125
Y D + ++T FY ++ +P+ + P ++ QF Q + +F+
Sbjct: 70 YPDLKVAVITPFYEQEKNWKEPNKEQYEAVLAQADYEASLTHRPYESPLQFKQKNQFFID 129
Query: 126 EDTTLDVLLKQFKEGIKGHMAFVHRVNNEGEGDPFYETVGLITLEDV 172
+ L +L KEG +M E +G P Y IT++D+
Sbjct: 130 KSDGLLLLYDPEKEGSPKYMLGTAEKRREQDGYPIY----FITMDDL 172
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
0.320 0.135 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,053,481
Number of Sequences: 62578
Number of extensions: 447469
Number of successful extensions: 1024
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 29
Number of HSP's that attempted gapping in prelim test: 1015
Number of HSP's gapped (non-prelim): 31
length of query: 396
length of database: 14,973,337
effective HSP length: 101
effective length of query: 295
effective length of database: 8,652,959
effective search space: 2552622905
effective search space used: 2552622905
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: 52 (24.6 bits)