RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11737
(125 letters)
>gnl|CDD|221996 pfam13232, Complex1_LYR_1, Complex1_LYR-like. This is a family
of proteins carrying the LYR motif of family
Complex1_LYR, pfam05347, likely to be involved in Fe-S
cluster biogenesis in mitochondria.
Length = 61
Score = 55.7 bits (135), Expect = 9e-12
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 29 RVLGLYKAWIRQATLIPIDYDVPKSEEQIKEKIRSEFLKHKHVTDIRIIDMLVIKGQMEL 88
VL LY+ +R A P E I+ +IR EF K+K +TD I+ L+ +G+ +L
Sbjct: 2 EVLSLYRQLLRAARKFPD----YNFREYIRRRIRDEFRKNKDLTDPEKIEKLLKEGKKQL 57
Query: 89 RE 90
Sbjct: 58 EL 59
>gnl|CDD|203236 pfam05347, Complex1_LYR, Complex 1 protein (LYR family).
Proteins in this family have been identified as a
component of the higher eukaryotic NADH complex. In
Saccharomyces cerevisiae, the Isd11 protein has been
shown to play a role in Fe/S cluster biogenesis in
mitochondria. We have named this family LYR after a
highly conserved tripeptide motif close to the
N-terminus of these proteins.
Length = 59
Score = 54.5 bits (132), Expect = 2e-11
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 29 RVLGLYKAWIRQATLIPIDYDVPKSEEQIKEKIRSEFLKHKHVTDIRIIDMLVIKGQMEL 88
VL LY+ +R+A P + E + +IR EF K+K++TD I+ L+ +G+ +L
Sbjct: 2 EVLSLYRQLLREARKFP----DYNAREYFRRRIRDEFRKNKNLTDPEKIEALLKEGKKQL 57
Query: 89 RE 90
Sbjct: 58 EV 59
>gnl|CDD|221997 pfam13233, Complex1_LYR_2, Complex1_LYR-like. This is a family
of proteins carrying the LYR motif of family
Complex1_LYR, pfam05347, likely to be involved in Fe-S
cluster biogenesis in mitochondria.
Length = 97
Score = 42.4 bits (100), Expect = 3e-06
Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 30 VLGLYKAWIRQATLIPIDYDVPKSEEQIKEKIRSEFLKHKHVTDIRIIDMLVIKGQMELR 89
VL LY+ +R+ P+ Y++ S + +R EF +H TD D L + E
Sbjct: 1 VLRLYRELLRELPKYPLRYNLLSSLSLGRRYVRKEFRRHAGATD----DELAKEFLQEAE 56
Query: 90 ETASLFK 96
+ K
Sbjct: 57 NYLAYLK 63
>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd). All
proteins in this family for which functions are known
are DNA-dependent ATPases that function in the process
of transcription-coupled DNA repair in which the repair
of the transcribed strand of actively transcribed genes
is repaired at a higher rate than the repair of
non-transcribed regions of the genome and than the
non-transcribed strand of the same gene. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). This family is
closely related to the RecG and UvrB families [DNA
metabolism, DNA replication, recombination, and repair].
Length = 926
Score = 28.1 bits (63), Expect = 1.5
Identities = 16/72 (22%), Positives = 24/72 (33%), Gaps = 21/72 (29%)
Query: 48 YDVPKSEEQIKEKIRSE-------FLKHKHVTDI-RIIDML----------VIKGQM--- 86
+ + E ++E IR E F H + I ++ L + GQM
Sbjct: 640 FVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTEN 699
Query: 87 ELRETASLFKHK 98
EL E F
Sbjct: 700 ELEEVMLEFYKG 711
>gnl|CDD|215498 PLN02920, PLN02920, pantothenate kinase 1.
Length = 398
Score = 27.5 bits (61), Expect = 1.9
Identities = 26/67 (38%), Positives = 33/67 (49%), Gaps = 12/67 (17%)
Query: 58 KEKIRSEFLKHKHVTDIRIIDMLV--IKGQME-----LRET--ASLFKHKGQIMSYWKET 108
K K E L+ H + R+IDMLV I G M+ L T AS F G+ +S KE
Sbjct: 209 KCKSFDELLELSHQGNNRVIDMLVGDIYGGMDYSKIGLSSTTIASSF---GKAISDNKEL 265
Query: 109 LEPKPTD 115
+ KP D
Sbjct: 266 EDYKPED 272
>gnl|CDD|236553 PRK09535, btuC, corrinoid ABC transporter permease; Reviewed.
Length = 366
Score = 26.3 bits (58), Expect = 5.9
Identities = 10/44 (22%), Positives = 18/44 (40%)
Query: 19 LSTTKADARVRVLGLYKAWIRQATLIPIDYDVPKSEEQIKEKIR 62
++ T V +GL P + VP++ + I +IR
Sbjct: 52 VAVTTHGVPVLSVGLSLPAPDLEYASPFSFAVPETAQTIVLQIR 95
>gnl|CDD|182607 PRK10638, PRK10638, glutaredoxin 3; Provisional.
Length = 83
Score = 25.2 bits (55), Expect = 6.0
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 44 IPIDYDVPKSEEQIKEKIRSE----FLKHKHV 71
IPID D K EE IK R+ F+ +H+
Sbjct: 32 IPIDGDAAKREEMIKRSGRTTVPQIFIDAQHI 63
>gnl|CDD|218015 pfam04300, FBA, F-box associated region. Members of this family
are associated with F-box domains, hence the name FBA.
This domain is probably involved in binding other
proteins that will be targeted for ubiquitination. Human
FBXO2 is involved in binding to N-glycosylated proteins.
Length = 184
Score = 25.6 bits (56), Expect = 7.1
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 94 LFKHKGQIMSYWKETLEPKPTD 115
F+H GQ +WK + T+
Sbjct: 156 HFEHGGQDTQFWKGWFGARVTN 177
>gnl|CDD|223867 COG0796, MurI, Glutamate racemase [Cell envelope biogenesis,
outer membrane].
Length = 269
Score = 25.6 bits (57), Expect = 9.1
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 8/34 (23%)
Query: 51 PKSEEQIKEKIRS--EFLKHKHVTDIRIIDMLVI 82
KSEE+I+E+ +FL + I LVI
Sbjct: 46 EKSEEEIRERTLEIVDFLLERG------IKALVI 73
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.133 0.378
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,216,589
Number of extensions: 544398
Number of successful extensions: 535
Number of sequences better than 10.0: 1
Number of HSP's gapped: 533
Number of HSP's successfully gapped: 26
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.3 bits)