RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018338
(357 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 = 138 bits (350), Expect = 1e-39
Identities = 53/203 (26%), Positives = 92/203 (45%), Gaps = 25/203 (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 GLDEIIKVDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDDSTPVVTSVHDYQ 271
L+ ++DL+++ VA + + G RLG+G G+ + L+ G V + + Q
Sbjct: 112 ALN---QIDLVLVPGVAFD-RQGYRLGRGGGYYDRYLARLQGHG----PLTVGLAYDE-Q 162
Query: 272 LVDDIPVEKLLIHDVPVDIICTP 294
LV+ +P E HDVPVD I T
Sbjct: 163 LVERLPQEP---HDVPVDEIVTE 182
>gnl|CDD|223290 COG0212, COG0212, 5-formyltetrahydrofolate cyclo-ligase [Coenzyme
metabolism].
Length = 191
Score = 119 bits (300), Expect = 3e-32
Identities = 57/201 (28%), Positives = 87/201 (43%), Gaps = 17/201 (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-STPVVTSVHDYQLVDDIP 277
DL+++ VA + + G RLG G G+ + RY+ + TP V +D QLVD +P
Sbjct: 119 -DLVLVPLVAFDKQ-GYRLGYGGGYYD------RYLANLRGRKTPTVGIAYDCQLVDHLP 170
Query: 278 VEKLLIHDVPVDIICTPTQVI 298
E HDVP+D I T VI
Sbjct: 171 REP---HDVPLDAIVTEEGVI 188
>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 = 51.9 bits (125), Expect = 6e-08
Identities = 28/83 (33%), Positives = 42/83 (50%), Gaps = 12/83 (14%)
Query: 212 GLDEIIKVDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDDSTPVVTSVHDYQ 271
++DLI++ VA + + G RLG G G+ Y R++ + + D+Q
Sbjct: 109 EPVPPDEIDLIIVPGVAFD-RRGYRLGYGGGY----YD--RFLARL--KGITIGLAFDFQ 159
Query: 272 LVDDIPVEKLLIHDVPVDIICTP 294
LVD++P E HDVPVD I T
Sbjct: 160 LVDELPREP---HDVPVDAIITE 179
>gnl|CDD|178408 PLN02812, PLN02812, 5-formyltetrahydrofolate cyclo-ligase.
Length = 211
Score = 38.5 bits (90), Expect = 0.002
Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 16/88 (18%)
Query: 219 VDLIVIGSVAVNPKTGARLGKGEGFAELEY-----GMLRYMGAIDDSTPVVTSV-HDYQL 272
+DL+++ +A + G RLG+G G+ Y P++ ++ + Q+
Sbjct: 132 LDLLLLPGLAFDRS-GRRLGRGGGY----YDTFLSKYQELAKEKGWKQPLLVALSYSPQI 186
Query: 273 VDD--IPVEKLLIHDVPVDIICTPTQVI 298
+D+ +PV++ DV VD + TP+ VI
Sbjct: 187 LDEGSVPVDE---TDVLVDALVTPSGVI 211
>gnl|CDD|182385 PRK10333, PRK10333, 5-formyltetrahydrofolate cyclo-ligase family
protein; Provisional.
Length = 182
Score = 36.4 bits (84), Expect = 0.009
Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 9/80 (11%)
Query: 218 KVDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDDSTPVVTSVHDYQLVDDIP 277
++D+++ VA + + G RLG G GF + ++ PV HD QLV+ +P
Sbjct: 109 RLDVLITPLVAFD-EYGQRLGMGGGFYDRTLQNWQHYKT----QPV-GYAHDCQLVEKLP 162
Query: 278 VEKLLIHDVPVDIICTPTQV 297
VE+ D+P+ + TP++V
Sbjct: 163 VEEW---DIPLPAVVTPSKV 179
>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 = 36.4 bits (84), Expect = 0.015
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 = 31.9 bits (73), Expect = 0.50
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 = 28.3 bits (64), Expect = 2.2
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|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 = 28.8 bits (65), Expect = 5.0
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|236200 PRK08245, PRK08245, hypothetical protein; Validated.
Length = 240
Score = 28.3 bits (64), Expect = 5.1
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|192193 pfam08986, DUF1889, Domain of unknown function (DUF1889). This
domain is found in a set of hypothetical bacterial
proteins.
Length = 119
Score = 27.4 bits (60), Expect = 5.1
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|212667 cd10170, HSP70_NBD, Nucleotide-binding domain of the HSP70 family.
HSP70 (70-kDa heat shock protein) family chaperones
assist in protein folding and assembly and can direct
incompetent "client" proteins towards degradation.
Typically, HSP70s have a nucleotide-binding domain (NBD)
and a substrate-binding domain (SBD). The nucleotide
sits in a deep cleft formed between the two lobes of the
NBD. The two subdomains of each lobe change conformation
between ATP-bound, ADP-bound, and nucleotide-free
states. ATP binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
HSP70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). Some HSP70 family members are not
chaperones but instead, function as NEFs to remove ADP
from their HSP70 chaperone partners during the ATP
hydrolysis cycle, some may function as both chaperones
and NEFs.
Length = 369
Score = 28.3 bits (64), Expect = 5.7
Identities = 17/59 (28%), Positives = 24/59 (40%), Gaps = 1/59 (1%)
Query: 284 HDVPVDIICTPTQVIFTNTTIPKPQGIYWDKLSPEKLGQIRILRELKGRIEQETGKEQT 342
D V V IP P + K SPE++ + IL++LK E G+ T
Sbjct: 75 DDPLVQSAKKVIGVDRGAPIIPVPVELGGKKYSPEEVSAL-ILKKLKEDAEAYLGEPVT 132
>gnl|CDD|215552 PLN03051, PLN03051, acyl-activating enzyme; Provisional.
Length = 499
Score = 28.2 bits (63), Expect = 6.6
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 294 PTQVIFTNTTIPKPQGIYWDKLSP 317
T ++F++ T +P+ I W LSP
Sbjct: 121 VTNILFSSGTTGEPKAIPWTHLSP 144
>gnl|CDD|237904 PRK15080, PRK15080, ethanolamine utilization protein EutJ;
Provisional.
Length = 267
Score = 27.9 bits (63), Expect = 7.9
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 320 LGQIRILRELKGRIEQETGKE 340
+G + I+R LK +E++ G+E
Sbjct: 67 IGAVTIVRRLKATLEEKLGRE 87
>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 = 8.2
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
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
0.316 0.134 0.389
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: 18,499,521
Number of extensions: 1821218
Number of successful extensions: 1397
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1385
Number of HSP's successfully gapped: 20
Length of query: 357
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 259
Effective length of database: 6,590,910
Effective search space: 1707045690
Effective search space used: 1707045690
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 (21.6 bits)
S2: 60 (27.4 bits)