RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1153
(195 letters)
>gnl|CDD|204038 pfam08712, Nfu_N, Scaffold protein Nfu/NifU N terminal. This
domain is found at the N terminus of NifU and NifU
related proteins, and in the human Nfu protein. Both of
these proteins are thought to be involved in the the
assembly of iron-sulphur clusters.
Length = 87
Score = 104 bits (261), Expect = 2e-29
Identities = 37/67 (55%), Positives = 42/67 (62%), Gaps = 1/67 (1%)
Query: 34 PGQTIDFPTGQAAYCSPLGKLLFRIEGVKSVFFGHDFITVTKQDDDVDWKLLKPEIFATI 93
P T +F A SPL + LF+I GVKSVFFG DFITVTK DD DW LKPE+ I
Sbjct: 22 PEGTFEFKNADEAEASPLAQALFKIPGVKSVFFGDDFITVTK-ADDADWDDLKPEVLEAI 80
Query: 94 MDFFSSG 100
M+ SG
Sbjct: 81 MEHLESG 87
>gnl|CDD|214919 smart00932, Nfu_N, Scaffold protein Nfu/NifU N terminal. This
domain is found at the N terminus of NifU and NifU
related proteins, and in the human Nfu protein. Both of
these proteins are thought to be involved in the the
assembly of iron-sulphur clusters.
Length = 88
Score = 96.4 bits (241), Expect = 2e-26
Identities = 39/68 (57%), Positives = 48/68 (70%), Gaps = 2/68 (2%)
Query: 34 PGQTIDFPT-GQAAYCSPLGKLLFRIEGVKSVFFGHDFITVTKQDDDVDWKLLKPEIFAT 92
PG + +F + +AA SPL + LF I GVKSVFFG DFITVTK DVDW+ LKPE+ +
Sbjct: 22 PGGSAEFKSADEAAEASPLAQKLFEIPGVKSVFFGPDFITVTK-YPDVDWEDLKPEVLSV 80
Query: 93 IMDFFSSG 100
IM+ F SG
Sbjct: 81 IMEHFESG 88
>gnl|CDD|223766 COG0694, COG0694, Thioredoxin-like proteins and domains
[Posttranslational modification, protein turnover,
chaperones].
Length = 93
Score = 89.7 bits (223), Expect = 9e-24
Identities = 33/73 (45%), Positives = 50/73 (68%), Gaps = 2/73 (2%)
Query: 117 EDDDETVQMIKELLDTRIRPTVQEDGGDIQFISFQG--GVVKLKMQGSCTSCPSSVVTLK 174
E D E ++ ++E+LD +IRP + DGGD++ + GVV L++ G+C+ CPSS VTLK
Sbjct: 5 ETDAELLERVEEVLDEKIRPQLAMDGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLK 64
Query: 175 NGVQNMLQFYIPE 187
NG++ L+ IPE
Sbjct: 65 NGIERQLKEEIPE 77
Score = 37.7 bits (88), Expect = 5e-04
Identities = 13/31 (41%), Positives = 21/31 (67%), Gaps = 2/31 (6%)
Query: 2 IKELLDTRIRPTVQEDGGDIQFISFQ--DGV 30
++E+LD +IRP + DGGD++ + DGV
Sbjct: 14 VEEVLDEKIRPQLAMDGGDVELVGIDEEDGV 44
>gnl|CDD|144628 pfam01106, NifU, NifU-like domain. This is an alignment of the
carboxy-terminal domain. This is the only common region
between the NifU protein from nitrogen-fixing bacteria
and rhodobacterial species. The biochemical function of
NifU is unknown.
Length = 68
Score = 85.4 bits (212), Expect = 2e-22
Identities = 27/62 (43%), Positives = 43/62 (69%), Gaps = 1/62 (1%)
Query: 126 IKELLDTRIRPTVQEDGGDIQFISFQGGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYI 185
I+E++D IRP +Q DGGDI+ + G +VK+++QG+C C SS +TLK G++ L+ +
Sbjct: 1 IEEVIDE-IRPMLQRDGGDIELVDVDGDIVKVRLQGACGGCMSSTMTLKGGIERKLRERL 59
Query: 186 PE 187
E
Sbjct: 60 GE 61
Score = 34.1 bits (79), Expect = 0.004
Identities = 12/29 (41%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 2 IKELLDTRIRPTVQEDGGDIQFISFQDGV 30
I+E++D IRP +Q DGGDI+ + +
Sbjct: 1 IEEVIDE-IRPMLQRDGGDIELVDVDGDI 28
>gnl|CDD|233679 TIGR02000, NifU_proper, Fe-S cluster assembly protein NifU. Three
different but partially homologous Fe-S cluster assembly
systems have been described: Isc, Suf, and Nif. The
latter is associated with donation of an Fe-S cluster to
nitrogenase in a number of nitrogen-fixing species.
NifU, described here, consists of an N-terminal domain
(pfam01592) and a C-terminal domain (pfam01106).
Homologs with an equivalent domain archictecture from
Helicobacter and Campylobacter, however, are excluded
from this model by a high trusted cutoff. The model,
therefore, is specific for NifU involved in nitrogenase
maturation. The related model TIGR01999 homologous to
the N-terminus of this model describes IscU from the Isc
system as in E. coli, Saccharomyces cerevisiae, and Homo
sapiens [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other, Central intermediary metabolism,
Nitrogen fixation].
Length = 290
Score = 54.5 bits (131), Expect = 4e-09
Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 3/61 (4%)
Query: 123 VQMIKELLDT--RIRPTVQEDGGDIQFISFQGGVVKLKMQGSCTSCPSSVVTLKNGVQNM 180
VQ I+ + +RP +Q DGGD++ G +V + + G+C+ C S +TLK G+Q
Sbjct: 218 VQRIQLIQKVLEEVRPVLQADGGDVELYDVDGKIVYVVLTGACSGCSMSTMTLK-GIQQR 276
Query: 181 L 181
L
Sbjct: 277 L 277
Score = 27.1 bits (60), Expect = 6.3
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 10 IRPTVQEDGGDIQFIS 25
+RP +Q DGGD++
Sbjct: 231 VRPVLQADGGDVELYD 246
>gnl|CDD|132384 TIGR03341, YhgI_GntY, IscR-regulated protein YhgI. IscR
(TIGR02010) is an iron-sulfur cluster-binding
transcriptional regulator (see Genome Property
GenProp0138). Members of this protein family include
YhgI, whose expression is under control of IscR, and
show sequence similarity to IscA, a known protein of
iron-sulfur cluster biosynthesis. These two lines of
evidence strongly suggest a role as an iron-sulfur
cluster biosynthesis protein. An older study designated
this protein GntY and suggested a role for it and for
the product of an adjacent gene, based on
complementation studies, in gluconate utilization
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 190
Score = 36.9 bits (86), Expect = 0.003
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 1/73 (1%)
Query: 118 DDDETVQMIKELLDTRIRPTVQEDGGDIQFISFQG-GVVKLKMQGSCTSCPSSVVTLKNG 176
DD + I +L + I P + GG + + GV L+ G C C VTLK+G
Sbjct: 102 DDAPLEERINYVLQSEINPQLASHGGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDG 161
Query: 177 VQNMLQFYIPETT 189
V+ L PE
Sbjct: 162 VEKTLLERFPELK 174
>gnl|CDD|183027 PRK11190, PRK11190, Fe/S biogenesis protein NfuA; Provisional.
Length = 192
Score = 30.4 bits (69), Expect = 0.37
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 118 DDDETVQMIKELLDTRIRPTVQEDGGDIQFISF-QGGVVKLKMQGSCTSCPSSVVTLKNG 176
DD ++ ++ +L ++I P + GG + + + G L+ G C C VTLK G
Sbjct: 103 DDAPLMERVEYVLQSQINPQLAGHGGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEG 162
Query: 177 VQNML 181
++ L
Sbjct: 163 IEKQL 167
>gnl|CDD|172310 PRK13772, PRK13772, formimidoylglutamase; Provisional.
Length = 314
Score = 30.1 bits (68), Expect = 0.64
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 100 GLPVLTDAQPSSDTVIHEDDDETVQM-----IKELLDTRIRPTVQEDGGDIQFISFQGGV 154
GLP L DA D V + D E+ Q + E+L RP V G ++ + ++QG
Sbjct: 81 GLPALADA---GDVVCDDGDLESAQAALAEVVAEVLAAGARPLVLGGGHEVAWGTWQGLR 137
Query: 155 VKLKMQGSC 163
L QG
Sbjct: 138 AHLDAQGDR 146
>gnl|CDD|146279 pfam03557, Bunya_G1, Bunyavirus glycoprotein G1. Bunyavirus has
three genomic segments: small (S), middle-sized (M), and
large (L). The S segment encodes the nucleocapsid and a
non-structural protein. The M segment codes for two
glycoproteins, G1 and G2, and another non-structural
protein (NSm). The L segment codes for an RNA
polymerase. This family contains the G1 glycoprotein
which is the viral attachment protein.
Length = 871
Score = 29.6 bits (67), Expect = 1.3
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 8/63 (12%)
Query: 108 QPSSDTVIHEDDDETVQMI--KELLDTRIRPTVQEDGGDIQFISFQGGVVKLKMQGSCTS 165
+PSS + E++ ET+ +I K++L T ++ GDI++ +F + L+ +G C
Sbjct: 709 EPSS--LRLEENHETITVIDYKKILGTI---KMKAILGDIRYKTFAESI-DLEAEGKCVG 762
Query: 166 CPS 168
C +
Sbjct: 763 CIN 765
>gnl|CDD|227434 COG5103, CDC39, Cell division control protein, negative regulator
of transcription [Cell division and chromosome
partitioning / Transcription].
Length = 2005
Score = 28.0 bits (62), Expect = 3.5
Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 11/64 (17%)
Query: 88 EIFATIMDFFSSGLP------VLTDAQPS-----SDTVIHEDDDETVQMIKELLDTRIRP 136
IF ++ F++G P VL P S V+ +D +++ L+ ++ P
Sbjct: 407 RIFEELLMGFANGAPNSFVFVVLFRTHPEMMLQKSRLVLAKDGIPVSRLLDIFLEHKMLP 466
Query: 137 TVQE 140
V
Sbjct: 467 LVSN 470
>gnl|CDD|238507 cd01036, ClC_euk, Chloride channel, ClC. These domains are found
in the eukaryotic halogen ion (Cl-, Br- and I-) channel
proteins that perform a variety of functions including
cell volume regulation, membrane potential
stabilization, charge compensation necessary for the
acidification of intracellular organelles, signal
transduction and transepithelial transport. They are
also involved in many pathophysiological processes and
are responsible for a number of human diseases. These
proteins belong to the ClC superfamily of chloride ion
channels, which share the unique double-barreled
architecture and voltage-dependent gating mechanism.
The gating is conferred by the permeating anion itself,
acting as the gating charge. Some proteins possess long
C-terminal cytoplasmic regions containing two CBS
(cystathionine beta synthase) domains of putative
regulatory function.
Length = 416
Score = 28.1 bits (63), Expect = 3.5
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 45 AAYCSPLGKLLFRIEGVKSVF 65
+A+ +P+G LLF +E V + F
Sbjct: 160 SAFGAPIGGLLFVLEEVSTFF 180
>gnl|CDD|222818 PHA01075, PHA01075, major capsid protein.
Length = 408
Score = 27.7 bits (61), Expect = 4.0
Identities = 31/106 (29%), Positives = 47/106 (44%), Gaps = 16/106 (15%)
Query: 1 MIKELLDTRIRPTVQEDGGDI--QFISFQD--GVLE-------EPGQTIDFPTGQAAYCS 49
+ LLDT+I T Q G D ISF D GV + + +IDF Y S
Sbjct: 246 LKSYLLDTKIANTFQIAGIDFTDHVISFDDLGGVFKVTKEFKLQNQDSIDFLRAYGDYQS 305
Query: 50 PLGKLLFRIEGVKSVFFGHDFITVTKQDDDVDWKLLKPEIFATIMD 95
LG + V +V F +D + + +V+ K +++A I+D
Sbjct: 306 QLGDTI----PVGAV-FTYDVSKLKEFTGNVEEIKPKSDLYAFILD 346
Score = 26.9 bits (59), Expect = 8.4
Identities = 17/39 (43%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 122 TVQMIKELLDTRIRPTVQEDGGDI--QFISFQ--GGVVK 156
T + LLDT+I T Q G D ISF GGV K
Sbjct: 243 TDSLKSYLLDTKIANTFQIAGIDFTDHVISFDDLGGVFK 281
>gnl|CDD|147830 pfam05892, Tricho_coat, Trichovirus coat protein. This family
consists of several coat proteins which are specific to
the ssRNA positive-strand, no DNA stage viruses such as
the Trichovirus and Vitivirus.
Length = 195
Score = 27.3 bits (61), Expect = 4.7
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 9/42 (21%)
Query: 33 EPGQTIDFPTG---------QAAYCSPLGKLLFRIEGVKSVF 65
EP DF +G +A + LFR EG KSVF
Sbjct: 141 EPEVMFDFNSGLNLLILTKQEAKVIQNMNSRLFRTEGAKSVF 182
>gnl|CDD|223154 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 27.3 bits (61), Expect = 5.2
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 45 AAYCSPLGKLLFRIEGVKSV 64
+ P G+ F +EGV S+
Sbjct: 251 LPFLEPDGRWDFGLEGVDSI 270
>gnl|CDD|233046 TIGR00603, rad25, DNA repair helicase rad25. All proteins in this
family for which functions are known are DNA-DNA
helicases used for the initiation of nucleotide excision
repair and transacription as part of the TFIIH
complex.This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 732
Score = 27.5 bits (61), Expect = 5.6
Identities = 12/38 (31%), Positives = 18/38 (47%)
Query: 9 RIRPTVQEDGGDIQFISFQDGVLEEPGQTIDFPTGQAA 46
RI PT +E + S +D ++ +PG T GQ
Sbjct: 139 RIDPTEEESLQTPTYGSKEDFIINKPGFTGGASAGQLE 176
>gnl|CDD|239068 cd02248, Peptidase_C1A, Peptidase C1A subfamily (MEROPS database
nomenclature); composed of cysteine peptidases (CPs)
similar to papain, including the mammalian CPs
(cathepsins B, C, F, H, L, K, O, S, V, X and W). Papain
is an endopeptidase with specific substrate preferences,
primarily for bulky hydrophobic or aromatic residues at
the S2 subsite, a hydrophobic pocket in papain that
accommodates the P2 sidechain of the substrate (the
second residue away from the scissile bond). Most
members of the papain subfamily are endopeptidases. Some
exceptions to this rule can be explained by specific
details of the catalytic domains like the occluding loop
in cathepsin B which confers an additional
carboxydipeptidyl activity and the mini-chain of
cathepsin H resulting in an N-terminal exopeptidase
activity. Papain-like CPs have different functions in
various organisms. Plant CPs are used to mobilize
storage proteins in seeds. Parasitic CPs act
extracellularly to help invade tissues and cells, to
hatch or to evade the host immune system. Mammalian CPs
are primarily lysosomal enzymes with the exception of
cathepsin W, which is retained in the endoplasmic
reticulum. They are responsible for protein degradation
in the lysosome. Papain-like CPs are synthesized as
inactive proenzymes with N-terminal propeptide regions,
which are removed upon activation. In addition to its
inhibitory role, the propeptide is required for proper
folding of the newly synthesized enzyme and its
stabilization in denaturing pH conditions. Residues
within the propeptide region also play a role in the
transport of the proenzyme to lysosomes or acidified
vesicles. Also included in this subfamily are proteins
classified as non-peptidase homologs, which lack
peptidase activity or have missing active site residues.
Length = 210
Score = 26.8 bits (60), Expect = 5.7
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 151 QGGVVKLKMQGSCTSC 166
+G V +K QGSC SC
Sbjct: 9 KGAVTPVKDQGSCGSC 24
>gnl|CDD|99968 cd03794, GT1_wbuB_like, This family is most closely related to the
GT1 family of glycosyltransferases. wbuB in E. coli is
involved in the biosynthesis of the O26 O-antigen. It
has been proposed to function as an
N-acetyl-L-fucosamine (L-FucNAc) transferase.
Length = 394
Score = 27.2 bits (61), Expect = 6.7
Identities = 11/53 (20%), Positives = 19/53 (35%), Gaps = 10/53 (18%)
Query: 93 IMDFFSSGLPVLTDAQPSSDTVI----------HEDDDETVQMIKELLDTRIR 135
+ ++ ++G PVL S ++ D + I ELLD
Sbjct: 316 LFEYMAAGKPVLASVDGESAELVEEAGAGLVVPPGDPEALAAAILELLDDPEE 368
>gnl|CDD|227252 COG4915, XpaC, 5-bromo-4-chloroindolyl phosphate hydrolysis protein
[General function prediction only].
Length = 204
Score = 26.7 bits (59), Expect = 7.4
Identities = 27/116 (23%), Positives = 51/116 (43%), Gaps = 15/116 (12%)
Query: 53 KLLFRIEGVKSVFFGHDFITVTKQDDDVDWKLLK--PEIFATIMDFFSSGLPV---LTDA 107
KLL + + ++ + + ++K+ +K +K P+ F +FF S L LT+
Sbjct: 89 KLLKQEKSLQVFEQVNGGLEISKRI----YKYVKQEPKRFYKAEEFFYSHLDNMVELTEK 144
Query: 108 ------QPSSDTVIHEDDDETVQMIKELLDTRIRPTVQEDGGDIQFISFQGGVVKL 157
QP I++D ET ++KEL + + + D+ + F+ KL
Sbjct: 145 YAFLKKQPVKSKEINQDLSETRILLKELSRSIEKDLHELLMDDVNVLDFELDFAKL 200
>gnl|CDD|235363 PRK05198, PRK05198, 2-dehydro-3-deoxyphosphooctonate aldolase;
Provisional.
Length = 264
Score = 26.6 bits (60), Expect = 7.4
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 12/44 (27%)
Query: 88 EIFATIMDFFSSGLPVLTDAQPSSDTVIHEDDDETVQMIKELLD 131
+I + + F G+PVLTD +HE + + E++D
Sbjct: 71 KILQEVKETF--GVPVLTD--------VHEPEQ--AAPVAEVVD 102
>gnl|CDD|220370 pfam09734, Tau95, RNA polymerase III transcription factor (TF)IIIC
subunit. TFIIIC1 is a multisubunit DNA binding factor
that serves as a dynamic platform for assembly of
pre-initiation complexes on class III genes. This entry
represents the tau 95 subunit which holds a key position
in TFIIIC, exerting both upstream and downstream
influence on the TFIIIC-DNA complex by rendering the
complex more stable. Once bound to tDNA-intragenic
promoter elements, TFIIIC directs the assembly of TFIIIB
on the DNA, which in turn recruits the RNA polymerase
III (pol III) and activates multiple rounds of
transcription.
Length = 303
Score = 27.0 bits (60), Expect = 7.4
Identities = 14/63 (22%), Positives = 21/63 (33%), Gaps = 1/63 (1%)
Query: 72 TVTKQDDDVDWKLLKPEIFA-TIMDFFSSGLPVLTDAQPSSDTVIHEDDDETVQMIKELL 130
V Q K T + + V T+ P + DE VQ++K L
Sbjct: 178 EVADQSGGKTVVNGKKRRKLTTAVIDDDTDPVVPTEPGPLKLLSLDPVLDELVQILKALF 237
Query: 131 DTR 133
+ R
Sbjct: 238 EER 240
>gnl|CDD|225033 COG2122, COG2122, Uncharacterized conserved protein [Function
unknown].
Length = 256
Score = 26.7 bits (59), Expect = 8.7
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 125 MIKELLDTRIRPTVQEDGGDIQFISFQGGVVKL 157
++ LL + + ++GGDI + + VV L
Sbjct: 101 ALEALLAAGAKEAIVDNGGDIALHNDRSVVVGL 133
>gnl|CDD|181392 PRK08332, PRK08332, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1740
Score = 27.0 bits (59), Expect = 8.8
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 9/44 (20%)
Query: 124 QMIKELLDTRIRPTVQEDGGDIQFISFQGGVVKLKMQGSCTSCP 167
+ I+ELL P E +G +V+L+M+ C +CP
Sbjct: 1696 EKIRELLGVVYCPVCYEK---------EGKLVELRMESGCATCP 1730
>gnl|CDD|224698 COG1784, COG1784, Predicted membrane protein [Function unknown].
Length = 395
Score = 26.6 bits (59), Expect = 9.9
Identities = 10/40 (25%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 83 KLLKPEIFATIMDFFSSGLPVLTDAQPSS-DTVIHEDDDE 121
+LLK ++ S LP ++ AQ + + + DD++
Sbjct: 217 RLLKSSFAGSLAGALVSFLPGVSPAQAALLASKLTGDDED 256
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 0.139 0.408
Gapped
Lambda K H
0.267 0.0821 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,071,357
Number of extensions: 941309
Number of successful extensions: 899
Number of sequences better than 10.0: 1
Number of HSP's gapped: 895
Number of HSP's successfully gapped: 33
Length of query: 195
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 103
Effective length of database: 6,857,034
Effective search space: 706274502
Effective search space used: 706274502
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 (21.7 bits)
S2: 56 (25.2 bits)