RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3489
(129 letters)
>gnl|CDD|236598 PRK09631, PRK09631, DNA topoisomerase IV subunit A; Provisional.
Length = 635
Score = 29.7 bits (67), Expect = 0.45
Identities = 26/117 (22%), Positives = 53/117 (45%), Gaps = 15/117 (12%)
Query: 2 ELLQDFYETTLEALKDAKNDRLWFKTNTKL---GKLYFDREDFNKLSRI-------LKQL 51
E LQ + LE + ++++ KT ++ ++Y E + + LK
Sbjct: 318 EHLQKVLKMELELERAKLLEKIFAKTLEQIFIEERIYKRIETISSEEDVISIVLSELKPF 377
Query: 52 HQSCQTDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKKLYELIQVKSSEQNIMD 108
+ D E+D++ LL+I I ++ KN K+++ L + ++KS E+N+
Sbjct: 378 KEELSRDVTEEDIEN---LLKIPIRRISLFDIDKNQKEIRILNK--ELKSVEKNLKS 429
>gnl|CDD|214929 smart00947, Pro_CA, Carbonic anhydrase. Carbonic anhydrases (CA)
are zinc metalloenzymes which catalyze the reversible
hydration of carbon dioxide. In Escherichia coli, CA
(gene cynT) is involved in recycling carbon dioxide
formed in the bicarbonate-dependent decomposition of
cyanate by cyanase (gene cynS). By this action, it
prevents the depletion of cellular bicarbonate. In
photosynthetic bacteria and plant chloroplast, CA is
essential to inorganic carbon fixation. Prokaryotic and
plant chloroplast CA are structurally and evolutionary
related and form a family distinct from the one which
groups the many different forms of eukaryotic CA's.
Length = 154
Score = 28.6 bits (65), Expect = 0.62
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 99 VKSSEQNIMDDPFIREHIE 117
V+ +N+ P IRE +
Sbjct: 115 VRDQVENLRTSPAIREAVA 133
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 28.3 bits (64), Expect = 1.3
Identities = 31/132 (23%), Positives = 53/132 (40%), Gaps = 25/132 (18%)
Query: 4 LQDFYETTLEALKDAKNDRLWFKTNTKLGKLYFDREDFNK--LSRILKQLHQSCQTDDGE 61
L + + + L +A DRL K +LG + D +K L + K+L Q DD E
Sbjct: 217 LPEELKEIRDLLNEALKDRL--KKLKELGVIVSISPDVSKKELLGLQKKLQQEIANDDSE 274
Query: 62 DDLKKGTQLLEIYA-----------LEIQMYTAQKNNKKLKKLYELIQVKS---SEQNIM 107
G + + I A LE Q A + L++L E + + + ++
Sbjct: 275 -----GYEAISILAEAMKLRHAVELLETQGVEALRR--YLERLREEARSSGGSKASKRLV 327
Query: 108 DDPFIREHIEDL 119
+DP R+ +
Sbjct: 328 EDPRFRKAVRKA 339
>gnl|CDD|215206 PLN02362, PLN02362, hexokinase.
Length = 509
Score = 28.3 bits (63), Expect = 1.4
Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 31 LGKLYFDREDFNKLSRILKQLHQSCQTDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKL 90
+G+ R + ++ +LK+L ++C+T G + Q+++ A+E+ A + KL
Sbjct: 24 VGRRVKSRRKWRRVVGVLKELEEACETPVG-----RLRQVVDAMAVEMHAGLASEGGSKL 78
Query: 91 KKL 93
K L
Sbjct: 79 KML 81
>gnl|CDD|128949 smart00709, Zpr1, Duplicated domain in the epidermal growth factor-
and elongation factor-1alpha-binding protein Zpr1. Also
present in archaeal proteins.
Length = 160
Score = 27.2 bits (61), Expect = 1.7
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 16/68 (23%)
Query: 44 LSRILKQLHQSCQTDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKKLYELIQVKSSE 103
LSR+ + L Q+ Q + D + T +K ++ L+KL ELI+ K
Sbjct: 102 LSRVREVLSQAIQETRDDSDPE----------------TKEKIDEFLEKLKELIEGKEPF 145
Query: 104 QNIMDDPF 111
I+DDP
Sbjct: 146 TLILDDPA 153
>gnl|CDD|225559 COG3014, COG3014, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 449
Score = 27.6 bits (61), Expect = 2.3
Identities = 11/53 (20%), Positives = 18/53 (33%), Gaps = 3/53 (5%)
Query: 6 DFYETTLEALKDAKNDRLWFKTNTKLGKLYFDREDFNKLSRILKQLHQSCQTD 58
YE + + K KN LW + + G D+ +L Q +
Sbjct: 42 KAYEQSKQFTKKKKNALLW---DLQNGLSALYARDYATSLGVLDAAEQRFKQQ 91
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 26.8 bits (60), Expect = 3.3
Identities = 18/101 (17%), Positives = 40/101 (39%), Gaps = 14/101 (13%)
Query: 37 DREDFNKLSRILKQLHQSCQTDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKK---- 92
+R+ + ++ + + + + GEDD L + + + + KL +
Sbjct: 213 ERKRLSNSEKLAEAIQNALELLSGEDDTVSALSL--LGRALEALEDLSEYDGKLSELAEL 270
Query: 93 ----LYELIQVKSSEQNIMD----DPFIREHIEDLLRNIRT 125
LYEL + + +D DP E +E+ L +++
Sbjct: 271 LEEALYELEEASEELRAYLDELEFDPNRLEEVEERLFALKS 311
>gnl|CDD|235045 PRK02506, PRK02506, dihydroorotate dehydrogenase 1A; Reviewed.
Length = 310
Score = 26.5 bits (59), Expect = 4.1
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 11/49 (22%)
Query: 6 DFYETTLEALKDAKNDRLWFKTNTK-LG-KL--YFDREDFNKLSRILKQ 50
DF ETT + L++ F TK LG KL YFD F++ + I +
Sbjct: 141 DF-ETTEQILEEV------FTYFTKPLGVKLPPYFDIVHFDQAAAIFNK 182
>gnl|CDD|217516 pfam03367, zf-ZPR1, ZPR1 zinc-finger domain. The zinc-finger
protein ZPR1 is ubiquitous among eukaryotes. It is
indeed known to be an essential protein in yeast. In
quiescent cells, ZPR1 is localised to the cytoplasm. But
in proliferating cells treated with EGF or with other
mitogens, ZPR1 accumulates in the nucleolus. ZPR1
interacts with the cytoplasmic domain of the inactive
EGF receptor (EGFR) and is thought to inhibit the basal
protein tyrosine kinase activity of EGFR. This
interaction is disrupted when cells are treated with
EGF, though by themselves, inactive EGFRs are not
sufficient to sequester ZPR1 to the cytoplasm. Upon
stimulation by EGF, ZPR1 directly binds the eukaryotic
translation elongation factor-1alpha (eEF-1alpha) to
form ZPR1/eEF-1alpha complexes. These move into the
nucleus, localising particularly at the nucleolus.
Indeed, the interaction between ZPR1 and eEF-1alpha has
been shown to be essential for normal cellular
proliferation, and ZPR1 is thought to be involved in
pre-ribosomal RNA expression. The ZPR1 domain consists
of an elongation initiation factor 2-like zinc finger
and a double-stranded beta helix with a helical hairpin
insertion. ZPR1 binds preferentially to GDP-bound eEF1A
but does not directly influence the kinetics of
nucleotide exchange or GTP hydrolysis. The alignment for
this family shows a domain of which there are two copies
in ZPR1 proteins. This family also includes several
hypothetical archaeal proteins (from both Crenarchaeota
and Euryarchaeota), which only contain one copy of the
aligned region. This similarity between ZPR1 and
archaeal proteins was not previously noted.
Length = 160
Score = 26.1 bits (58), Expect = 4.9
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 82 TAQKNNKKLKKLYELIQVKSSEQNIMDDPF 111
T +K ++ L+KL ELI+ K I++DPF
Sbjct: 124 TKKKIDEFLEKLKELIEGKEPFTLILEDPF 153
>gnl|CDD|222957 PHA02994, PHA02994, hypothetical protein; Provisional.
Length = 218
Score = 26.2 bits (58), Expect = 5.0
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 86 NNKKLKKLYELIQVKSSEQNIMDDPFIREH---IEDLLRNIRTQVM 128
N KK+K L LI +K+ + I+ D FI ++ ++ LL I + V+
Sbjct: 122 NRKKIKDLIILINMKTCNKKIIKD-FINDNFGSVDTLLSIINSNVL 166
>gnl|CDD|234757 PRK00421, murC, UDP-N-acetylmuramate--L-alanine ligase;
Provisional.
Length = 461
Score = 26.2 bits (59), Expect = 5.8
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 108 DDPFIREHIEDLLRNIRT 125
DDP +RE + + R + T
Sbjct: 219 DDPELRELLPRVSRPVIT 236
>gnl|CDD|225340 COG2719, SpoVR, Uncharacterized conserved protein [Function
unknown].
Length = 495
Score = 26.2 bits (58), Expect = 6.1
Identities = 11/33 (33%), Positives = 13/33 (39%)
Query: 21 DRLWFKTNTKLGKLYFDREDFNKLSRILKQLHQ 53
DR WF L+F RE S I + L
Sbjct: 345 DRYWFPDIAGRDTLFFVREIHKDESFIRQFLTP 377
>gnl|CDD|133383 cd01108, HTH_CueR, Helix-Turn-Helix DNA binding domain of CueR-like
transcription regulators. Helix-turn-helix (HTH)
transcription regulators CueR and ActP, copper efflux
regulators. In Bacillus subtilis, copper induced CueR
regulates the copZA operon, preventing copper toxicity.
In Rhizobium leguminosarum, ActP controls copper
homeostasis; it detects cytoplasmic copper stress and
activates transcription in response to increasing copper
concentrations. These proteins are comprised of two
distinct domains that harbor the regulatory
(effector-binding) site and the active (DNA-binding)
site. Their conserved N-terminal domains contain winged
HTH motifs that mediate DNA binding, while the
C-terminal domains have two conserved cysteines that
define a monovalent copper ion binding site. These
proteins share the N-terminal DNA binding domain with
other transcription regulators of the MerR superfamily
that promote transcription by reconfiguring the spacer
between the -35 and -10 promoter elements.
Length = 127
Score = 25.6 bits (57), Expect = 6.6
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 39 EDFNKLSRILKQLHQSCQTDDGED 62
+ + R L+QL SC DD D
Sbjct: 96 AELQAMRRTLQQLADSCHGDDRPD 119
>gnl|CDD|193517 cd05638, M42, M42 Peptidases, also known as glutamyl aminopeptidase
family. Peptidase M42 family proteins, also known as
glutamyl aminopeptidases (GAP), are co-catalytic
metallopeptidases, found in archaea and bacteria. They
typically bind two zinc or cobalt atoms and include
cellulase and endo-1,4-beta-glucanase (endoglucanase).
Some of the enzymes exhibit typical aminopeptidase
specificity, whereas others are also capable of
N-terminal deblocking activity, i.e. hydrolyzing
acylated N-terminal residues. GAP removes glutamyl
residues from the N-terminus of peptide substrates, but
is also effective against aspartyl and, to a lesser
extent, seryl residues. Lactococcus lactis glutamyl
aminopeptidase (PepA; aminopeptidase A) has high thermal
stability and aids growth of the organism in milk.
Pyrococcus horikoshii contain a thermostable de-blocking
aminopeptidase member of this family, used commercially
for N-terminal protein sequencing.
Length = 332
Score = 25.9 bits (57), Expect = 6.7
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 89 KLKKLYELIQVKSSEQNIMDDPFIREHIEDLLRNIRT 125
LK+L E+ + E I + FI E I+D + ++
Sbjct: 2 LLKELVEIPAISGYEAKIRN--FIIEEIKDWVDEVKV 36
>gnl|CDD|197258 cd09161, PLDc_PaCLS_like_2, Putative catalytic domain, repeat 2, of
Pseudomonas aeruginosa cardiolipin synthase and similar
proteins. Putative catalytic domain, repeat 2, of
Pseudomonas aeruginosa cardiolipin (CL) synthase (PaCLS)
and similar proteins. Although PaCLS and similar
proteins have not been functionally characterized,
members in this subfamily show high sequence homology to
bacterial CL synthases, which catalyze the reversible
phosphatidyl group transfer between two
phosphatidylglycerol molecules to form CL and glycerol.
Moreover, PaCLS and other members of this subfamily
contain two HKD motifs (H-x-K-x(4)-D, where x represents
any amino acid residue) that characterizes the
phospholipase D (PLD) superfamily. The two motifs may be
part of the active site and may be involved in
phosphatidyl group transfer.
Length = 176
Score = 25.7 bits (57), Expect = 6.9
Identities = 8/32 (25%), Positives = 14/32 (43%)
Query: 3 LLQDFYETTLEALKDAKNDRLWFKTNTKLGKL 34
L DF + + N LWF+ ++ +L
Sbjct: 140 LEADFAASREVTAAELANRPLWFRLGARVARL 171
>gnl|CDD|99810 cd06214, PA_degradation_oxidoreductase_like, NAD(P) binding domain
of ferredoxin reductase like phenylacetic acid (PA)
degradation oxidoreductase. PA oxidoreductases of E.
coli hydroxylate PA-CoA in the second step of PA
degradation. Members of this group typically fuse a
ferredoxin reductase-like domain with an iron-sulfur
binding cluster domain. Ferredoxins catalyze electron
transfer between an NAD(P)-binding domain of the
alpha/beta class and a discrete (usually N-terminal)
domain which vary in orientation with respect to the
NAD(P) binding domain. The N-terminal portion may
contain a flavin prosthetic group, as in flavoenzymes,
or use flavin as a substrate. Ferredoxin-NADP+
(oxido)reductase is an FAD-containing enzyme that
catalyzes the reversible electron transfer between
NADP(H) and electron carrier proteins such as ferredoxin
and flavodoxin. Isoforms of these flavoproteins (i.e.
having a non-covalently bound FAD as a prosthetic group)
are present in chloroplasts, mitochondria, and bacteria
and participate in a wide variety of redox metabolic
pathways. The C-terminal domain contains most of the
NADP(H) binding residues and the N-terminal domain
interacts non-covalently with the isoalloxazine rings of
the flavin molecule which lies largely in a large gap
betweed the two domains. Ferredoxin-NADP+ reductase
first accepts one electron from reduced ferredoxin to
form a flavin semiquinone intermediate. The enzyme then
accepts a second electron to form FADH2 which then
transfers two electrons and a proton to NADP+ to form
NADPH.
Length = 241
Score = 25.6 bits (57), Expect = 7.9
Identities = 17/57 (29%), Positives = 22/57 (38%), Gaps = 5/57 (8%)
Query: 7 FYETTLEALKDAKNDRL----WFKTNTKLGKLYFDREDFNKLSRILKQLHQSCQTDD 59
F E L LK DRL L R D KL+ +LK L + + D+
Sbjct: 153 FREE-LADLKARYPDRLTVIHVLSREQGDPDLLRGRLDAAKLNALLKNLLDATEFDE 208
>gnl|CDD|218220 pfam04708, Pox_F16, Poxvirus F16 protein.
Length = 216
Score = 25.4 bits (56), Expect = 9.3
Identities = 15/46 (32%), Positives = 29/46 (63%), Gaps = 4/46 (8%)
Query: 86 NNKKLKKLYELIQVKSSEQNIMDDPFIREH---IEDLLRNIRTQVM 128
N KK++ L LI + + ++ I+ D FI ++ ++ LL+ IR+ V+
Sbjct: 122 NRKKIRDLITLINMNTCDKKIIKD-FINDNFGNVDQLLKIIRSNVL 166
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 0.135 0.375
Gapped
Lambda K H
0.267 0.0832 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,458,144
Number of extensions: 563595
Number of successful extensions: 889
Number of sequences better than 10.0: 1
Number of HSP's gapped: 887
Number of HSP's successfully gapped: 78
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
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: 53 (24.0 bits)