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= 038790
(139 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 34.3 bits (77), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 77 CDHIFHRVCLDQWVGLFRRVTCPLCR 102
C H+FH+VC+DQW L CP+CR
Sbjct: 35 CMHLFHQVCVDQW--LITNKKCPICR 58
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 32.7 bits (73), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 3/61 (4%)
Query: 43 LTVGRYERNN-DNEAVECAVXXXXXXXXXXXXXXXCDHIFHRVCLDQWVGLFRRVTCPLC 101
L R+ NN +E C V C+H FH C+D+W+ R TCP+C
Sbjct: 9 LPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANR--TCPIC 66
Query: 102 R 102
R
Sbjct: 67 R 67
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 32.3 bits (72), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 77 CDHIFHRVCLDQWVGLFRRVTCPLCR 102
C H FH C+D W+G TCPLCR
Sbjct: 27 CGHGFHAECVDMWLG--SHSTCPLCR 50
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 32.3 bits (72), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 77 CDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSR--RAVVENGIEILV 120
C H F C+++W+ R++ CP+CR + S+ V++N I +V
Sbjct: 71 CAHSFCSYCINEWMK--RKIECPICRKDIKSKTYSLVLDNXINKMV 114
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 2/59 (3%)
Query: 54 NEAVECAVXXXXXXXXXXXXXXXCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVV 112
+EC V C+H+FH C+ W L + +CP+CR L +
Sbjct: 13 GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPW--LEQHDSCPVCRKSLTGQNTAT 69
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 31.6 bits (70), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 77 CDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSR--RAVVENGIEILV 120
C H F C+++W+ R++ CP+CR + S+ V++N I +V
Sbjct: 71 CAHSFCSYCINEWMK--RKIECPICRKDIKSKTYSLVLDNCINKMV 114
>pdb|4EPO|C Chain C, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|G Chain G, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|H Chain H, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|K Chain K, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|L Chain L, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
Length = 149
Score = 31.6 bits (70), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 77 CDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSR--RAVVENGIEILV 120
C H F C+++W+ R++ CP+CR + S+ V++N I +V
Sbjct: 82 CAHSFCSYCINEWMK--RKIECPICRKDIKSKTYSLVLDNCINKMV 125
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 30.0 bits (66), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 77 CDHIFHRVCLDQWVGLFRRVTCPLC 101
C H FHR CL +W+ + R CPLC
Sbjct: 36 CKHAFHRKCLIKWLEV--RKVCPLC 58
>pdb|2L0B|A Chain A, Solution Nmr Structure Of Zinc Finger Domain Of E3
Ubiquitin-Protein Ligase Praja-1 From Homo Sapiens,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4710b
Length = 91
Score = 28.9 bits (63), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 77 CDHIFHRVCLDQWVGLFRRVTCPLCR 102
C H FH+ C+ W L + TCP+CR
Sbjct: 61 CHHYFHKPCVSIW--LQKSGTCPVCR 84
>pdb|1BCC|A Chain A, Cytochrome Bc1 Complex From Chicken
pdb|3BCC|A Chain A, Stigmatellin And Antimycin Bound Cytochrome Bc1 Complex
From Chicken
pdb|2BCC|A Chain A, Stigmatellin-Bound Cytochrome Bc1 Complex From Chicken
Length = 446
Score = 27.7 bits (60), Expect = 2.0, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 17 KFLIQNSLFGHRIGMHGVPAEIGEELLTVGR 47
K ++N+L H G V +IG ELLT GR
Sbjct: 358 KNFLRNALVSHLDGTTPVCEDIGRELLTYGR 388
>pdb|1CHC|A Chain A, Structure Of The C3hc4 Domain By 1h-Nuclear Magnetic
Resonance Spectroscopy; A New Structural Class Of Zinc-
Finger
Length = 68
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 77 CDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVVENGIE 117
C H F VC+ +W+ + TCPLC+ ++S +E+ E
Sbjct: 24 CLHAFCYVCITRWIR--QNPTCPLCKVPVESVVHTIESDSE 62
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 27.3 bits (59), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 77 CDHIFHRVCLDQWVGLFRRVTCPLCR 102
C+H FH C+ WV R CPLC+
Sbjct: 48 CNHSFHNCCMSLWVKQNNR--CPLCQ 71
>pdb|1QCR|A Chain A, Crystal Structure Of Bovine Mitochondrial Cytochrome Bc1
Complex, Alpha Carbon Atoms Only
Length = 446
Score = 26.9 bits (58), Expect = 3.2, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 17 KFLIQNSLFGHRIGMHGVPAEIGEELLTVGR 47
K L++N+L H G V +IG LLT GR
Sbjct: 358 KNLLRNALVSHLDGTTPVCEDIGRSLLTYGR 388
>pdb|1BGY|A Chain A, Cytochrome Bc1 Complex From Bovine
pdb|1BGY|M Chain M, Cytochrome Bc1 Complex From Bovine
pdb|1BE3|A Chain A, Cytochrome Bc1 Complex From Bovine
pdb|1L0L|A Chain A, Structure Of Bovine Mitochondrial Cytochrome Bc1 Complex
With A Bound Fungicide Famoxadone
pdb|1L0N|A Chain A, Native Structure Of Bovine Mitochondrial Cytochrome Bc1
Complex
pdb|1NTK|A Chain A, Crystal Structure Of Mitochondrial Cytochrome Bc1 In
Complex With Antimycin A1
pdb|1NTM|A Chain A, Crystal Structure Of Mitochondrial Cytochrome Bc1 Complex
At 2.4 Angstrom
pdb|1NTZ|A Chain A, Crystal Structure Of Mitochondrial Cytochrome Bc1 Complex
Bound With Ubiquinone
pdb|1NU1|A Chain A, Crystal Structure Of Mitochondrial Cytochrome Bc1
Complexed With 2- Nonyl-4-Hydroxyquinoline N-Oxide
(Nqno)
pdb|1PP9|A Chain A, Bovine Cytochrome Bc1 Complex With Stigmatellin Bound
pdb|1PP9|N Chain N, Bovine Cytochrome Bc1 Complex With Stigmatellin Bound
pdb|1PPJ|A Chain A, Bovine Cytochrome Bc1 Complex With Stigmatellin And
Antimycin
pdb|1PPJ|N Chain N, Bovine Cytochrome Bc1 Complex With Stigmatellin And
Antimycin
pdb|2A06|A Chain A, Bovine Cytochrome Bc1 Complex With Stigmatellin Bound
pdb|2A06|N Chain N, Bovine Cytochrome Bc1 Complex With Stigmatellin Bound
pdb|1SQV|A Chain A, Crystal Structure Analysis Of Bovine Bc1 With Uhdbt
pdb|1SQX|A Chain A, Crystal Structure Analysis Of Bovine Bc1 With Stigmatellin
A
pdb|1SQQ|A Chain A, Crystal Structure Analysis Of Bovine Bc1 With Methoxy
Acrylate Stilbene (Moas)
pdb|2FYU|A Chain A, Crystal Structure Of Bovine Heart Mitochondrial Bc1 With
Jg144 Inhibitor
pdb|2YBB|A Chain A, Fitted Model For Bovine Mitochondrial Supercomplex
I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)
pdb|2YBB|AA Chain a, Fitted Model For Bovine Mitochondrial Supercomplex
I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)
Length = 446
Score = 26.9 bits (58), Expect = 3.2, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 17 KFLIQNSLFGHRIGMHGVPAEIGEELLTVGR 47
K L++N+L H G V +IG LLT GR
Sbjct: 358 KNLLRNALVSHLDGTTPVCEDIGRSLLTYGR 388
>pdb|1SQB|A Chain A, Crystal Structure Analysis Of Bovine Bc1 With Azoxystrobin
pdb|1SQP|A Chain A, Crystal Structure Analysis Of Bovine Bc1 With Myxothiazol
Length = 480
Score = 26.9 bits (58), Expect = 3.2, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 17 KFLIQNSLFGHRIGMHGVPAEIGEELLTVGR 47
K L++N+L H G V +IG LLT GR
Sbjct: 392 KNLLRNALVSHLDGTTPVCEDIGRSLLTYGR 422
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 26.6 bits (57), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 77 CDHIFHRVCLDQWVGLFRRVTCPLCR 102
C H F + C+D+W R CP+CR
Sbjct: 32 CAHSFCQKCIDKWSDRHR--NCPICR 55
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 26.6 bits (57), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 77 CDHIFHRVCLDQWVGLFRRVT-CPLCRDFLDSR 108
CDHIF + C+ + + + + CPLC++ + R
Sbjct: 39 CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR 71
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
0.331 0.144 0.480
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,267,976
Number of Sequences: 62578
Number of extensions: 100523
Number of successful extensions: 279
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 266
Number of HSP's gapped (non-prelim): 28
length of query: 139
length of database: 14,973,337
effective HSP length: 89
effective length of query: 50
effective length of database: 9,403,895
effective search space: 470194750
effective search space used: 470194750
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 46 (22.3 bits)