RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10962
(196 letters)
>gnl|CDD|132463 TIGR03422, mito_frataxin, frataxin. Frataxin is a mitochondrial
protein, mutation of which leads to the disease
Friedreich's ataxia. Its orthologs are widely
distributed in the bacteria, associated with the ISC
system for iron-sulfur cluster assembly, and designated
CyaY. This exception-type model allows those examples of
frataxin per se that score above the trusted cutoff to
the CyaY equivalog-type model (TIGR03421) to be named
appropriately.
Length = 97
Score = 145 bits (369), Expect = 9e-46
Identities = 49/99 (49%), Positives = 61/99 (61%), Gaps = 4/99 (4%)
Query: 77 EYEVICNETLESLTDYFDVIVEENTHLENADVTYGDGVLTVNFGNPHGTYVINRQTPNKQ 136
EY + +E L+ L D + + E L+ DV Y GVLT+ GTYVIN+Q PNKQ
Sbjct: 1 EYHKVADEYLDHLLDKLEELGESRPDLD-FDVEYSSGVLTLELP-SVGTYVINKQPPNKQ 58
Query: 137 IWLSSPTSGPKRYDFDPSRNIWIYKHDNKSLHDLLQEEI 175
IWLSSP SGPKRYD+ WIY D SL +LL+EE+
Sbjct: 59 IWLSSPVSGPKRYDYV--NGEWIYLRDGSSLTELLEEEL 95
>gnl|CDD|216529 pfam01491, Frataxin_Cyay, Frataxin-like domain. This family
contains proteins that have a domain related to the
globular C-terminus of Frataxin the protein that is
mutated in Friedreich's ataxia. This domain is found in
a family of bacterial proteins. The function of this
domain is currently unknown. It has been suggested that
this family is involved in iron transport.
Length = 107
Score = 129 bits (328), Expect = 2e-39
Identities = 43/109 (39%), Positives = 61/109 (55%), Gaps = 6/109 (5%)
Query: 77 EYEVICNETLESLTDYFDVIVEENTHLENADVTYGDGVLTVNFGNPHGTYVINRQTPNKQ 136
E+ + +ETL+S+ D + + +E+ + DV GVLT+ F N G VIN+Q P KQ
Sbjct: 5 EFHQLADETLDSIEDALEELADESD--ADIDVERSGGVLTLTFEN-GGQIVINKQPPLKQ 61
Query: 137 IWLSSPTSGPKRYDFDPSRNIWIYKHDNKSLHDLLQEEIVTIVTSNVDF 185
IWL+SP SG +D+D WI D + L +LL EE+ VDF
Sbjct: 62 IWLASP-SGGFHFDYD--GGQWIDTRDGEELFELLSEELSEQAGEPVDF 107
>gnl|CDD|238280 cd00503, Frataxin, Frataxin is a nuclear-encoded mitochondrial
protein implicated in Friedreich's ataxia (FRDA), an
human autosomal recessive neurodegenerative disease;
Frataxin is found in eukaryotes and in purple bacteria;
lack of frataxin causes iron to accumulate in the
mitochondrial matrix suggesting that frataxin is
involved in mitochondrial iron homeostasis and possibly
in iron transport; the domain has an alpha-beta fold
consisting of two helices flanking an antiparallel beta
sheet.
Length = 105
Score = 122 bits (309), Expect = 1e-36
Identities = 37/109 (33%), Positives = 54/109 (49%), Gaps = 8/109 (7%)
Query: 77 EYEVICNETLESLTDYFDVIVEENTHLENADVTYGDGVLTVNFGNPHGTYVINRQTPNKQ 136
E+ + ++ L + D EE + DV GVLT+ FGN T VINRQ P +Q
Sbjct: 5 EFHRLADDLLLKIEDTL----EEQDDDADIDVETQGGVLTLTFGN-GSTIVINRQEPLRQ 59
Query: 137 IWLSSPTSGPKRYDFDPSRNIWIYKHDNKSLHDLLQEEIVTIVTSNVDF 185
IWL+S G +D+ + WI + L +LL+EE +V+F
Sbjct: 60 IWLASK-VGGYHFDYKNGK--WICTRSGEELWELLEEECSAQSGEDVEF 105
>gnl|CDD|163255 TIGR03421, FeS_CyaY, iron donor protein CyaY. Members of this
protein family are the iron-sulfur cluster (FeS)
metabolism protein CyaY, a homolog of eukaryotic
frataxin. ISC is one of several bacterial systems for
FeS assembly; we find by Partial Phylogenetic Profiling
vs. the ISC system that CyaY most like work with the ISC
system for FeS cluster biosynthesis. A study of of cyaY
mutants in Salmonella enterica bears this out. Although
the trusted cutoff is set low enough to include
eukaryotic frataxin sequences, a narrower,
exception-type model (TIGR03421) identifies identifies
members of that specific set [Biosynthesis of cofactors,
prosthetic groups, and carriers, Other].
Length = 102
Score = 78.8 bits (195), Expect = 2e-19
Identities = 30/109 (27%), Positives = 45/109 (41%), Gaps = 10/109 (9%)
Query: 77 EYEVICNETLESLTDYFDVIVEENTHLENADVTYGDGVLTVNFGNPHGTYVINRQTPNKQ 136
E+ + L+++ + D + D GVLT+ F N +IN+Q P Q
Sbjct: 4 EFHQLAEALLDAIEEAID------DADADIDCERAGGVLTLTFEN-GSQIIINKQEPLHQ 56
Query: 137 IWLSSPTSGPKRYDFDPSRNIWIYKHDNKSLHDLLQEEIVTIVTSNVDF 185
IWL++ SG +D+D WI D + L LL V F
Sbjct: 57 IWLAAK-SGGFHFDYD--GGAWIDTRDGEELWALLARACSEQAGEPVVF 102
>gnl|CDD|224876 COG1965, CyaY, Protein implicated in iron transport, frataxin
homolog [Inorganic ion transport and metabolism].
Length = 106
Score = 78.2 bits (193), Expect = 4e-19
Identities = 31/98 (31%), Positives = 44/98 (44%), Gaps = 8/98 (8%)
Query: 77 EYEVICNETLESLTDYFDVIVEENTHLENADVTYGDGVLTVNFGNPHGTYVINRQTPNKQ 136
E+ + + L + D D +E + D GVLT+ F N +IN+Q P +Q
Sbjct: 5 EFHRLADALLLKIEDQLDEQDDEG----DIDCEIQGGVLTLTFDN-GSQIIINKQEPLQQ 59
Query: 137 IWLSSPTSGPKRYDFDPSRNIWIYKHDNKSLHDLLQEE 174
IWL+S G Y FD WI + DLL+E
Sbjct: 60 IWLASKVGG---YHFDYKNGEWISTRSGEEFWDLLEEA 94
>gnl|CDD|234765 PRK00446, cyaY, frataxin-like protein; Provisional.
Length = 105
Score = 47.2 bits (113), Expect = 2e-07
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 113 GVLTVNFGNPHGT-YVINRQTPNKQIWLSSPTSGPKRYDFDPSRNIWIYKHDNKSLHDLL 171
GVLT+ F N G+ +INRQ P ++WL++ + G + FD WI + LL
Sbjct: 36 GVLTLTFEN--GSKIIINRQEPLHELWLAAKSGG---FHFDYKDGEWICDRSGEEFWALL 90
Query: 172 QEEI 175
+E
Sbjct: 91 EEAA 94
>gnl|CDD|134546 PRK01379, cyaY, frataxin-like protein; Provisional.
Length = 103
Score = 45.3 bits (107), Expect = 8e-07
Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 77 EYEVICNETLESLTDYFDVIVEENTHLENADVTYGDGVLTVNFGNPHGTYVINRQTPNKQ 136
E+ I T+ + D +EE + DV +L N G YVIN+Q+ K+
Sbjct: 5 EFSKIAETTIAYIADK----IEEQDKEASIDVDLQGDIL--NLDTDKGIYVINKQSAAKE 58
Query: 137 IWLSSPTSGPKRYDFD 152
IWLSSP SGP + ++
Sbjct: 59 IWLSSPVSGPYHFFYE 74
>gnl|CDD|237379 PRK13412, fkp, bifunctional
fucokinase/L-fucose-1-P-guanylyltransferase;
Provisional.
Length = 974
Score = 31.3 bits (71), Expect = 0.30
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 14/74 (18%)
Query: 72 SISLPEYEVICNETLESLTDYF---DVIVEENTHLEN---ADVT-YG---DGVLTVNFGN 121
S+ LP YE I ++ E L DV + L++ ADV YG D L N
Sbjct: 136 SLQLPLYERIMSKAPEGLHTLIASGDVYIRSEQPLQDIPEADVVCYGLWVDPSLATN--- 192
Query: 122 PHGTYVINRQTPNK 135
HG +V +R++P +
Sbjct: 193 -HGVFVSSRKSPER 205
>gnl|CDD|181731 PRK09257, PRK09257, aromatic amino acid aminotransferase;
Provisional.
Length = 396
Score = 30.9 bits (71), Expect = 0.37
Identities = 6/16 (37%), Positives = 11/16 (68%)
Query: 128 INRQTPNKQIWLSSPT 143
+ R P+ ++W+S PT
Sbjct: 114 LKRAFPDAKVWVSDPT 129
>gnl|CDD|131679 TIGR02631, xylA_Arthro, xylose isomerase, Arthrobacter type. This
model describes a D-xylose isomerase that is also active
as a D-glucose isomerase. It is tetrameric and dependent
on a divalent cation Mg2+, Co2+ or Mn2+ as characterized
in Arthrobacter. Members of this family differ
substantially from the D-xylose isomerases of family
TIGR02630.
Length = 382
Score = 29.4 bits (66), Expect = 1.1
Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 5/39 (12%)
Query: 140 SSPTSGPKRYDFDPSRN-----IWIYKHDNKSLHDLLQE 173
S GP+ +D+ PSR +W ++ +L+E
Sbjct: 275 SGGYQGPRHFDYKPSRTEDYDGVWASAKGCMRMYLILKE 313
>gnl|CDD|217943 pfam04180, LTV, Low temperature viability protein. The
low-temperature viability protein LTV1 is involved in
ribosome biogenesis 40S subunit production.
Length = 426
Score = 28.8 bits (64), Expect = 1.8
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 72 SISLPEYEVICNETLESLTDYFDVIVEENTHLEN 105
S+ + E L +L D F+ EE ++L +
Sbjct: 315 DQSMSSSALDRTEKLTTLDDRFEKAEEEYSNLYD 348
>gnl|CDD|111000 pfam02057, Glyco_hydro_59, Glycosyl hydrolase family 59.
Length = 669
Score = 28.1 bits (62), Expect = 3.2
Identities = 14/66 (21%), Positives = 28/66 (42%), Gaps = 3/66 (4%)
Query: 118 NFGNPHGTYVIN---RQTPNKQIWLSSPTSGPKRYDFDPSRNIWIYKHDNKSLHDLLQEE 174
N + T+V+ + P Q+W + +R F ++W+ +L ++E
Sbjct: 387 NVSHQFATFVLKGSFSEIPELQVWYTKLGKPSERLLFKQLDSLWLLDSSGSFTLELEEDE 446
Query: 175 IVTIVT 180
I T+ T
Sbjct: 447 IFTLTT 452
>gnl|CDD|199873 cd06254, M14_ASTE_ASPA_like_4, Peptidase M14 Succinylglutamate
desuccinylase (ASTE)/aspartoacylase (ASPA)-like;
uncharacterized subgroup. A functionally
uncharacterized subgroup of the Succinylglutamate
desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily
which is part of the M14 family of
metallocarboxypeptidases. ASTE catalyzes the fifth and
last step in arginine catabolism by the arginine
succinyltransferase pathway, and aspartoacylase (ASPA,
also known as aminoacylase 2, and ACY-2; EC:3.5.1.15)
cleaves N-acetyl L-aspartic acid (NAA) into aspartate
and acetate. NAA is abundant in the brain, and
hydrolysis of NAA by ASPA may help maintain white
matter. ASPA is an NAA scavenger in other tissues.
Mutations in the gene encoding ASPA cause Canavan
disease (CD), a fatal progressive neurodegenerative
disorder involving dysmyelination and spongiform
degeneration of white matter in children. This enzyme
binds zinc which is necessary for activity. Measurement
of elevated NAA levels in urine is used in the diagnosis
of CD.
Length = 291
Score = 27.6 bits (62), Expect = 4.2
Identities = 15/51 (29%), Positives = 20/51 (39%)
Query: 76 PEYEVICNETLESLTDYFDVIVEENTHLENADVTYGDGVLTVNFGNPHGTY 126
V L +TDYF ++ E + V Y L VN G+P Y
Sbjct: 240 AGDTVQKGALLGYVTDYFGNVIAEYRAPFDGVVLYNTATLPVNKGDPLAAY 290
>gnl|CDD|211988 TIGR04265, bac_cardiolipin, cardiolipin synthase. This model is
based on experimentally characterized bacterial
cardiolipin synthases (cls) from E. coli, Staphylococcus
aureus (two), and Bacillus pseudofirmus OF4. This model
describes just one of several homologous but
non-orthologous forms of cls. The cutoff score is set
arbitrarily high to avoid false-positives. Note that
there are two enzymatic activites called cardiolipin
synthase. This model represents type 1, which does not
rely on a CDP-linked donor, but instead does a
reversible transfer of a phosphatidyl group from one
phosphatidylglycerol molecule to another.
Length = 483
Score = 27.8 bits (62), Expect = 4.4
Identities = 12/32 (37%), Positives = 21/32 (65%), Gaps = 3/32 (9%)
Query: 159 IYKHDNKSLHD---LLQEEIVTIVTSNVDFYS 187
IY+++N LH L+ +EI ++ T+N+D S
Sbjct: 392 IYQYENGFLHSKSVLVDDEIASVGTANMDMRS 423
>gnl|CDD|233729 TIGR02103, pullul_strch, alpha-1,6-glucosidases, pullulanase-type.
Members of this protein family include secreted (or
membrane-anchored) pullulanases of Gram-negative
bacteria and pullulanase-type starch debranching enzymes
of plants. Both enzymes hydrolyze alpha-1,6 glycosidic
linkages. Pullulan is an unusual, industrially important
polysaccharide in which short alpha-1,4 chains
(maltotriose) are connected in alpha-1,6 linkages.
Enzymes that cleave alpha-1,6 linkages in pullulan and
release maltotriose are called pullulanases although
pullulan itself may not be the natural substrate. This
family is closely homologous to, but architecturally
different from, the Gram-positive pullulanases of
Gram-positive bacteria (TIGR02102) [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 898
Score = 26.7 bits (59), Expect = 9.3
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 146 PKRYDFDPSRNI-WIYKHDNKSLHDLLQEEIVTIVTS 181
P Y DP+ I ++ KHDN++L D + + S
Sbjct: 641 PAGYAADPTETINYVSKHDNQTLWDAISYKAAAETPS 677
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
0.318 0.133 0.413
Gapped
Lambda K H
0.267 0.0555 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,500,014
Number of extensions: 838931
Number of successful extensions: 776
Number of sequences better than 10.0: 1
Number of HSP's gapped: 761
Number of HSP's successfully gapped: 18
Length of query: 196
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 104
Effective length of database: 6,857,034
Effective search space: 713131536
Effective search space used: 713131536
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.7 bits)