RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 022559
(295 letters)
>gnl|CDD|216717 pfam01812, 5-FTHF_cyc-lig, 5-formyltetrahydrofolate cyclo-ligase
family. 5-formyltetrahydrofolate cyclo-ligase or
methenyl-THF synthetase EC:6.3.3.2 catalyzes the
interchange of 5-formyltetrahydrofolate (5-FTHF) to
5-10-methenyltetrahydrofolate, this requires ATP and
Mg2+. 5-FTHF is used in chemotherapy where it is
clinically known as Leucovorin.
Length = 182
Score = 109 bits (275), Expect = 2e-29
Identities = 40/174 (22%), Positives = 75/174 (43%), Gaps = 21/174 (12%)
Query: 96 KWIIRKRI---WDLMEVQNIAQNPRPVHHRIPNFVGASVAAKNLTGLEEFRVAGCVKVNP 152
K +RK++ + + A R +H ++P+FVGA A RVA V V
Sbjct: 1 KQELRKQLLAKRRALSEEERAAASRALHQKLPSFVGAQKAK---------RVALYVSVKG 51
Query: 153 DSPQKQVRLLTLSGGKKLLTPQPRLRTGFFSVLDSSMLSPSTINEAC-TSVGVAKYGKQI 211
+ +++ L L GK +L P+PR +G + + + + +++
Sbjct: 52 EIDTRELIELLLEEGKLVLLPRPRPDSGLVVRITPYYPETGLPSGPYGLPEPIEEEQREL 111
Query: 212 GLDEIIKVDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDDSTPVVT 265
L+ ++DL+++ VA + + G RLG+G G+ + L+ G V
Sbjct: 112 ALN---QIDLVLVPGVAFD-RQGYRLGRGGGYYDRYLARLQGHG----PLTVGL 157
>gnl|CDD|223290 COG0212, COG0212, 5-formyltetrahydrofolate cyclo-ligase [Coenzyme
metabolism].
Length = 191
Score = 83.5 bits (207), Expect = 2e-19
Identities = 41/168 (24%), Positives = 68/168 (40%), Gaps = 14/168 (8%)
Query: 99 IRKRIWDLMEVQNIAQNPRPVHHRIPNFVGASVAAKNLTGLEEFRVAGCVKVNPDSPQKQ 158
+ + L+ + IA +P H A + A + + +A V N + +
Sbjct: 4 TKSALRKLLLERRIALSPEERHEADQR--IAKLLASLIEVKKAKTIALYVPFNGEIDTRP 61
Query: 159 VRLLTLSGGKKLLTPQPRLRTGFFSVLDSSMLSPSTINEACTSVGVAKYGKQIGLDEIIK 218
+ L GK+LL P+ R F L P N + +YG++I EI
Sbjct: 62 LIRQALRRGKRLLLPKLRDYKLLFLRYIPDPLQPLIKN-RFGILEPGEYGRKIPPPEI-- 118
Query: 219 VDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDD-STPVVT 265
DL+++ VA + + G RLG G G+ + RY+ + TP V
Sbjct: 119 -DLVLVPLVAFDKQ-GYRLGYGGGYYD------RYLANLRGRKTPTVG 158
>gnl|CDD|147807 pfam05851, Lentivirus_VIF, Lentivirus virion infectivity factor
(VIF). This family consists of several feline specific
Lentivirus virion infectivity factor (VIF) proteins. VIF
is essential for productive FIV infection of host target
cells in vitro.
Length = 250
Score = 36.8 bits (85), Expect = 0.008
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 97 WIIRKRIWDLMEVQNIAQNPRPVHHRIPNFVGASVAA 133
WI K +WD +E QNI + P P VG + A
Sbjct: 121 WIKTKFMWDDIESQNICKGGEPSPGWGPGMVGVVIKA 157
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 32.7 bits (75), Expect = 0.22
Identities = 29/122 (23%), Positives = 39/122 (31%), Gaps = 33/122 (27%)
Query: 61 YEAERLSMDAK------ARDLMAETSKRETESGAEDDPKSWKWI-------------IRK 101
+E ER A+ A AE + S DDP +W+ +R
Sbjct: 423 WEGERRERLARRRAAQLAAASEAEVEQPLLLSSGPDDPALERWLQRQLGQEGERLAILRD 482
Query: 102 RIWDLMEVQNIAQNPRPVHHRIPNFVGASVAAKNLTGLEEFR--VAGCVKVNPDSPQKQV 159
R+W + Q H R+ N S L L R G V V S +
Sbjct: 483 RLWSDITWQR--------HDRVLNLANRS----LLWALGPLRAVPEGGVTVLCSSQEDSD 530
Query: 160 RL 161
RL
Sbjct: 531 RL 532
>gnl|CDD|133457 cd06848, GCS_H, Glycine cleavage H-protein. Glycine cleavage
H-proteins are part of the glycine cleavage system (GCS)
found in bacteria, archea and the mitochondria of
eukaryotes. GCS is a multienzyme complex consisting of 4
different components (P-, H-, T- and L-proteins) which
catalyzes the oxidative cleavage of glycine. The
H-protein shuttles the methylamine group of glycine from
the P-protein (glycine dehydrogenase) to the T-protein
(aminomethyltransferase) via a lipoyl group, attached to
a completely conserved lysine residue.
Length = 96
Score = 28.7 bits (65), Expect = 1.2
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 10/46 (21%)
Query: 202 VGVAKYGKQIGLDEIIKVDLIVIGSVAVNPKTGARLGKGEGFAELE 247
VG+ Y Q L +I+ V+L P+ G + KG+ F +E
Sbjct: 18 VGITDYA-QDLLGDIVFVEL---------PEVGTEVKKGDPFGSVE 53
>gnl|CDD|236200 PRK08245, PRK08245, hypothetical protein; Validated.
Length = 240
Score = 29.1 bits (66), Expect = 2.6
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 13/52 (25%)
Query: 114 QNPRPVHHRIPNFVGASV------AAKNLTGLEEFRVAGCVKVNPDSPQKQV 159
+ RP+ P VG + A ++L E F +P+SPQ+
Sbjct: 37 RGVRPLRPGGPRMVGPAFTLRFVPAREDLNTPESFA-------DPESPQRAA 81
>gnl|CDD|224190 COG1271, CydA, Cytochrome bd-type quinol oxidase, subunit 1 [Energy
production and conversion].
Length = 457
Score = 29.1 bits (66), Expect = 3.1
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 248 YGMLRYMGAIDDSTPVVTSGKCGFCRIFLPLFYLVLFILFVY 289
YG+L+ D + VT+G F I + Y VL I VY
Sbjct: 393 YGVLK----TDVVSSAVTAGSVLFSLILFMVLYTVLLIAEVY 430
>gnl|CDD|192193 pfam08986, DUF1889, Domain of unknown function (DUF1889). This
domain is found in a set of hypothetical bacterial
proteins.
Length = 119
Score = 27.8 bits (61), Expect = 3.1
Identities = 13/33 (39%), Positives = 23/33 (69%), Gaps = 1/33 (3%)
Query: 181 FFSVLDSSMLSPSTINEACTSVGVAKYGKQIGL 213
F +D S +PS++NE+ T+ G+ KY K++G+
Sbjct: 31 FIGAMDVSAPTPSSMNES-TAKGIFKYLKELGV 62
>gnl|CDD|233985 TIGR02727, MTHFS_bact, 5,10-methenyltetrahydrofolate synthetase.
This enzyme, 5,10-methenyltetrahydrofolate synthetase,
is also called 5-formyltetrahydrofolate cycloligase.
Function of bacterial proteins in this family was
inferred originally from the known activity of
eukaryotic homologs. Recently, activity was shown
explicitly for the member from Mycoplasma pneumonia.
Members of this family from alpha- and
gamma-proteobacteria, designated ygfA, are often found
in an operon with 6S structural RNA, and show a similar
pattern of high expression during stationary phase. The
function may be to deplete folate to slow 1-carbon
biosynthetic metabolism [Central intermediary
metabolism, One-carbon metabolism].
Length = 179
Score = 28.0 bits (63), Expect = 3.8
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 212 GLDEIIKVDLIVIGSVAVNPKTGARLGKGEGF 243
++DLI++ VA + + G RLG G G+
Sbjct: 109 EPVPPDEIDLIIVPGVAFD-RRGYRLGYGGGY 139
>gnl|CDD|217431 pfam03219, TLC, TLC ATP/ADP transporter.
Length = 491
Score = 28.7 bits (65), Expect = 3.9
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 275 FLPLFYLVLFILFVYCI 291
FLP+ ++ ILF Y I
Sbjct: 26 FLPMALMMFCILFNYNI 42
>gnl|CDD|233766 TIGR02181, GRX_bact, Glutaredoxin, GrxC family. Glutaredoxins
are thioltransferases (disulfide reductases) which
utilize glutathione and NADPH as cofactors. Oxidized
glutathione is regenerated by glutathione reductase.
Together these components compose the glutathione
system. Glutaredoxins utilize the CXXC motif common to
thioredoxins and are involved in multiple cellular
processes including protection from redox stress,
reduction of critical enzymes such as ribonucleotide
reductase and the generation of reduced sulfur for iron
sulfur cluster formation. Glutaredoxins are capable of
reduction of mixed disulfides of glutathione as well as
the formation of glutathione mixed disulfides. This
family of glutaredoxins includes the E. coli protein
GrxC (Grx3) which appears to have a secondary role in
reducing ribonucleotide reductase (in the absence of
GrxA) possibly indicating a role in the reduction of
other protein disulfides [Energy metabolism, Electron
transport].
Length = 79
Score = 26.8 bits (60), Expect = 4.3
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 50 ARNGVAFDESAYEAERLSMDAKARDLMAETSKRET 84
+ GV F E R+ D RD M + S R T
Sbjct: 20 SSKGVTFTEI-----RVDGDPALRDEMMQRSGRRT 49
>gnl|CDD|176261 cd08301, alcohol_DH_plants, Plant alcohol dehydrogenase.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and aldehydes
or ketones. Alcohol dehydrogenase in the liver converts
ethanol and NAD+ to acetaldehyde and NADH, while in
yeast and some other microorganisms ADH catalyzes the
conversion acetaldehyde to ethanol in alcoholic
fermentation. There are 7 vertebrate ADH 7 classes, 6
of which have been identified in humans. Class III,
glutathione-dependent formaldehyde dehydrogenase, has
been identified as the primordial form and exists in
diverse species, including plants, micro-organisms,
vertebrates, and invertebrates. Class I, typified by
liver dehydrogenase, is an evolving form. Gene
duplication and functional specialization of ADH into
ADH classes and subclasses created numerous forms in
vertebrates. For example, the A, B and C (formerly
alpha, beta, gamma) human class I subunits have high
overall structural similarity, but differ in the
substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48) , then the alcohol, which allows the transfer
of a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 369
Score = 28.4 bits (64), Expect = 4.6
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 14/51 (27%)
Query: 115 NPRPVHHRIPNFVGASVAAKNLTGLEEFRV--AGCV-KVNPDSPQKQVRLL 162
N +P++H FVG S E+ V GCV K+NP++P +V LL
Sbjct: 129 NGKPIYH----FVGTST-------FSEYTVVHVGCVAKINPEAPLDKVCLL 168
>gnl|CDD|237734 PRK14500, PRK14500, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MoaC/MobA;
Provisional.
Length = 346
Score = 27.9 bits (62), Expect = 5.9
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 7/48 (14%)
Query: 128 GASVAAKNLTGLEEFRVAGCVKVNPDSPQKQVRLLTLSGGKKLLTPQP 175
G +VAA + + C ++P K+ RL+ SGGK L+ P
Sbjct: 120 GVAVAALTIYDM-------CKSISPHIIIKETRLIEKSGGKADLSQTP 160
>gnl|CDD|218709 pfam05707, Zot, Zonular occludens toxin (Zot). This family
consists of bacterial and viral proteins which are very
similar to the Zonular occludens toxin (Zot). Zot is
elaborated by bacteriophages present in toxigenic
strains of Vibrio cholerae. Zot is a single polypeptide
chain of 44.8 kDa, with the ability to reversibly alter
intestinal epithelial tight junctions, allowing the
passage of macromolecules through mucosal barriers.
Length = 183
Score = 27.7 bits (62), Expect = 6.2
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 5/58 (8%)
Query: 84 TESGAEDDPKSWKW--IIRKRIWDLMEVQNIAQNPRPVHHRIPNFVGASVAAKNLTGL 139
+ G + P R WD++ I QNP + +I V V + LT L
Sbjct: 85 SRRGGDKVPPVLDAFSTHRHLGWDIIL---ITQNPSKIDKQIRALVEHHVHCRRLTAL 139
>gnl|CDD|217554 pfam03432, Relaxase, Relaxase/Mobilisation nuclease domain.
Relaxases/mobilisation proteins are required for the
horizontal transfer of genetic information contained on
plasmids that occurs during bacterial conjugation. The
relaxase, in conjunction with several auxiliary
proteins, forms the relaxation complex or relaxosome.
Relaxases nick duplex DNA in a specific manner by
catalyzing trans-esterification.
Length = 240
Score = 27.7 bits (62), Expect = 6.5
Identities = 18/67 (26%), Positives = 24/67 (35%), Gaps = 12/67 (17%)
Query: 47 NNKARNGV--AFDESAYEAERLSMDAKA---RDLMAETSKRETESGAEDDPKSWKWIIRK 101
N KA + A DE LS+D R AE K E + S+K IR+
Sbjct: 122 NYKAYRKLRKANDELELR-HGLSIDEGNPRNRYTEAEKGKAEK------NKTSYKDEIRQ 174
Query: 102 RIWDLME 108
+
Sbjct: 175 ALKKAQA 181
>gnl|CDD|118055 pfam09519, RE_HindVP, HindVP restriction endonuclease. This family
includes the HindVP (recognises GRCGYC bu the cleavage
site is unknown) restriction endonucleases.
Length = 301
Score = 27.8 bits (61), Expect = 6.7
Identities = 16/87 (18%), Positives = 37/87 (42%), Gaps = 14/87 (16%)
Query: 100 RKRIWDLMEVQNIAQNPRPVHHRIPNFVGASVAAKNLTGLEEFRVAGCVK---------V 150
R +W + + A+ + HH+ + + + N + F +G +
Sbjct: 208 RTAVWLYKMLYDFAKYGKINHHKTIDLI-----SYNTKNDKAFASSGMITNVYMKSPELE 262
Query: 151 NPDSPQKQVRLLTLSGGKKLLTPQPRL 177
P + +++ + L GG++LL+P+ R
Sbjct: 263 RPRIKKSEIKNIILGGGQELLSPERRF 289
>gnl|CDD|106284 PRK13324, PRK13324, pantothenate kinase; Reviewed.
Length = 258
Score = 27.7 bits (61), Expect = 7.6
Identities = 33/159 (20%), Positives = 60/159 (37%), Gaps = 23/159 (14%)
Query: 124 PNFVGASVAAKNLTGLEEF-----RVAGCVKVNPDSPQKQVRLLTLSGGKK--LLTPQPR 176
P F+ +++ +E R+A C+ D P K + ++ L L+T +
Sbjct: 86 PFFISMDTTDLDMSAVEAHQVGADRIASCISAIADHPNKDLLIIDLGTATTFDLVTKDKK 145
Query: 177 LRTGFFSVLDSSMLSPSTINEACTSVGVAKYGKQIGLDEIIKVDLIVIGSVAVNPKTGAR 236
+G S++ LS +N C Q+ I+K ++ + N ++G
Sbjct: 146 YLSG--SIMPGVKLS---LNALCQG------ASQLSSVTIVKPEVAIGYDTKTNIRSGLY 194
Query: 237 LGKGEGFAELEYGMLRYMGAIDDSTPVVTSGKCGFCRIF 275
G EL+ + G+ PV T GF +F
Sbjct: 195 YGHLGALKELKRRSVEEFGS-----PVYTIATGGFAGLF 228
>gnl|CDD|148700 pfam07245, Phlebovirus_G2, Phlebovirus glycoprotein G2. This
family consists of several Phlebovirus glycoprotein G2
sequences. Members of the Bunyaviridae family acquire an
envelope by budding through the lipid bilayer of the
Golgi complex. The budding compartment is thought to be
determined by the accumulation of the two heterodimeric
membrane glycoproteins G1 and G2 in the Golgi.
Length = 504
Score = 27.9 bits (62), Expect = 7.8
Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 16/67 (23%)
Query: 226 SVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDDSTPVVTSGK-CGFCRIFLPLFYLVLF 284
S VNPKTG F+ G++ ++G P+ T GF + +VLF
Sbjct: 440 STVVNPKTGRW-----DFSSWFSGLVDWLGG-----PLKTILVILGFIAL-----GIVLF 484
Query: 285 ILFVYCI 291
+L + +
Sbjct: 485 VLLIILV 491
>gnl|CDD|129679 TIGR00591, phr2, photolyase PhrII. All proteins in this family for
which functions are known are DNA-photolyases used for
the direct repair of UV irradiation induced DNA damage.
Some repair 6-4 photoproducts while others repair
cyclobutane pyrimidine dimers. 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 = 454
Score = 27.4 bits (61), Expect = 9.5
Identities = 8/38 (21%), Positives = 12/38 (31%)
Query: 58 ESAYEAERLSMDAKARDLMAETSKRETESGAEDDPKSW 95
AY R ++D A+D E + W
Sbjct: 316 CGAYWWARTTLDDHAKDKREHLYSLEQLEKSTTHDYLW 353
>gnl|CDD|233122 TIGR00769, AAA, ADP/ATP carrier protein family. These proteins are
members of the ATP:ADP Antiporter (AAA) Family (TC
2.A.12), which consists of nucleotide transporters that
have 12 GES predicted transmembrane regions. One protein
from Rickettsia prowazekii functions to take up ATP from
the eukaryotic cell cytoplasm into the bacterium in
exchange for ADP. Five AAA family paralogues are encoded
within the genome of R. prowazekii. This organism
transports UMP and GMP but not CMP, and it seems likely
that one or more of the AAA family paralogues are
responsible. The genome of Chlamydia trachomatis encodes
two AAA family members, Npt1 and Npt2, which catalyse
ATP/ADP exchange and GTP, CTP, ATP and UTP uptake
probably employing a proton symport mechanism. Two
homologous adenylate translocators of Arabidopsis
thaliana are postulated to be localized to the
intracellular plastid membrane where they function as
ATP importers [Transport and binding proteins,
Nucleosides, purines and pyrimidines].
Length = 472
Score = 27.4 bits (61), Expect = 9.6
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 275 FLPLFYLVLFILFVYCI 291
FLPLF + ILF Y I
Sbjct: 9 FLPLFLMFFCILFNYTI 25
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 0.136 0.396
Gapped
Lambda K H
0.267 0.0497 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,023,903
Number of extensions: 1447636
Number of successful extensions: 1345
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1338
Number of HSP's successfully gapped: 22
Length of query: 295
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 199
Effective length of database: 6,679,618
Effective search space: 1329243982
Effective search space used: 1329243982
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: 59 (27.1 bits)