RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14005
(226 letters)
>gnl|CDD|214485 smart00044, CYCc, Adenylyl- / guanylyl cyclase, catalytic domain.
Present in two copies in mammalian adenylyl cyclases.
Eubacterial homologues are known. Two residues (Asn,
Arg) are thought to be involved in catalysis. These
cyclases have important roles in a diverse range of
cellular processes.
Length = 194
Score = 205 bits (525), Expect = 1e-67
Identities = 83/175 (47%), Positives = 107/175 (61%), Gaps = 32/175 (18%)
Query: 40 VPAENFDSVTIYFSDIVGFTNISADSSPMEVVNMLNTLYKLFDSRIRKYDVYKVETIGDA 99
VPAE++D+VTI FSDIVGFT++ + S+P +VVN+LN LY FD I ++ YKV+TIGDA
Sbjct: 29 VPAESYDNVTILFSDIVGFTSLCSTSTPEQVVNLLNDLYSRFDQIIDRHGGYKVKTIGDA 88
Query: 100 YMVVSGLPQRNGKSPGTAISFYIRNIGSFGGLGTKGFFRPFSGTLHVGEIATMSLDLLVG 159
YMV SGLP+ H IA +LD++
Sbjct: 89 YMVASGLPEEALV-------------------------------DHAELIADEALDMVEE 117
Query: 160 IEHFKIPHRPNDKLEIRVGINTGPCVAGVVGTTMPRYCLFGDTINTASRMESAGD 214
++ + HR + L +R+GI+TGP VAGVVG MPRYCLFGDT+N ASRMESAGD
Sbjct: 118 LKTVLVQHR-EEGLRVRIGIHTGPVVAGVVGIRMPRYCLFGDTVNLASRMESAGD 171
>gnl|CDD|201086 pfam00211, Guanylate_cyc, Adenylate and Guanylate cyclase catalytic
domain.
Length = 184
Score = 187 bits (478), Expect = 1e-60
Identities = 75/175 (42%), Positives = 98/175 (56%), Gaps = 34/175 (19%)
Query: 40 VPAENFDSVTIYFSDIVGFTNISADSSPMEVVNMLNTLYKLFDSRIRKYDVYKVETIGDA 99
V A+++D+VTI F+DIVGFT +S+ SP E+V +LN LY FD + K+ VYKV+TIGDA
Sbjct: 1 VYAQSYDNVTILFADIVGFTALSSRHSPEELVRLLNDLYTRFDELLDKHGVYKVKTIGDA 60
Query: 100 YMVVSGLPQRNGKSPGTAISFYIRNIGSFGGLGTKGFFRPFSGTLHVGEIATMSLDLLVG 159
YM SGLP+ H +A M+LD+L
Sbjct: 61 YMAASGLPEP--------------------------------SPAHAQTLAEMALDMLEA 88
Query: 160 IEHFKIPHRPNDKLEIRVGINTGPCVAGVVGTTMPRYCLFGDTINTASRMESAGD 214
I+ I L +RVGI+TGP VAGV+G PRY ++GDT+N ASRMES G
Sbjct: 89 IKSVNIHSFEG--LRVRVGIHTGPVVAGVIGARRPRYDVWGDTVNLASRMESTGV 141
>gnl|CDD|143636 cd07302, CHD, cyclase homology domain. Catalytic domains of the
mononucleotidyl cyclases (MNC's), also called cyclase
homology domains (CHDs), are part of the class III
nucleotidyl cyclases. This class includes eukaryotic and
prokaryotic adenylate cyclases (AC's) and guanylate
cyclases (GC's). They seem to share a common catalytic
mechanism in their requirement for two magnesium ions to
bind the polyphosphate moiety of the nucleotide.
Length = 177
Score = 159 bits (404), Expect = 2e-49
Identities = 53/166 (31%), Positives = 76/166 (45%), Gaps = 32/166 (19%)
Query: 48 VTIYFSDIVGFTNISADSSPMEVVNMLNTLYKLFDSRIRKYDVYKVETIGDAYMVVSGLP 107
VT+ F+DIVGFT +S P E+V +LN + FD I ++ +TIGDA M V GLP
Sbjct: 2 VTVLFADIVGFTALSERLGPEELVELLNEYFSAFDEIIERHGGTVDKTIGDAVMAVFGLP 61
Query: 108 QRNGKSPGTAISFYIRNIGSFGGLGTKGFFRPFSGTLHVGEIATMSLDLLVGIEHFKIPH 167
+ A+ +L++ +
Sbjct: 62 GAHEDHAERAVR--------------------------------AALEMQEALAELNAER 89
Query: 168 RPNDKLEIRVGINTGPCVAGVVGTTMPRYCLFGDTINTASRMESAG 213
L +R+GI+TGP VAGVVG+ P Y + GDT+N A+R+ES
Sbjct: 90 EGGPPLRLRIGIHTGPVVAGVVGSERPEYTVIGDTVNLAARLESLA 135
>gnl|CDD|143637 cd07556, Nucleotidyl_cyc_III, Class III nucleotidyl cyclases.
Class III nucleotidyl cyclases are the largest, most
diverse group of nucleotidyl cyclases (NC's) containing
prokaryotic and eukaryotic proteins. They can be divided
into two major groups; the mononucleotidyl cyclases
(MNC's) and the diguanylate cyclases (DGC's). The
MNC's, which include the adenylate cyclases (AC's) and
the guanylate cyclases (GC's), have a conserved cyclase
homology domain (CHD), while the DGC's have a conserved
GGDEF domain, named after a conserved motif within this
subgroup. Their products, cyclic guanylyl and adenylyl
nucleotides, are second messengers that play important
roles in eukaryotic signal transduction and prokaryotic
sensory pathways.
Length = 133
Score = 110 bits (278), Expect = 3e-31
Identities = 54/166 (32%), Positives = 77/166 (46%), Gaps = 40/166 (24%)
Query: 48 VTIYFSDIVGFTNISADSSPMEVVNMLNTLYKLFDSRIRKYDVYKVETIGDAYMVVSGLP 107
VTI F+DIVGFT+++ P E +LN L FDS IR+ K++TIGD +MVVSGL
Sbjct: 2 VTILFADIVGFTSLADALGPDEGDELLNELAGRFDSLIRRSGDLKIKTIGDEFMVVSGL- 60
Query: 108 QRNGKSPGTAISFYIRNIGSFGGLGTKGFFRPFSGTLHVGEIATMSLDLLVGIEHFKIPH 167
P A+ + D+ +
Sbjct: 61 ----DHPAAAV--------------------------------AFAEDMREAVSALNQSE 84
Query: 168 RPNDKLEIRVGINTGPCVAGVVGTTMPRYCLFGDTINTASRMESAG 213
+ +R+GI+TGP V GV+G + P+Y ++G +N ASRMES
Sbjct: 85 GNP--VRVRIGIHTGPVVVGVIG-SRPQYDVWGALVNLASRMESQA 127
>gnl|CDD|225025 COG2114, CyaA, Adenylate cyclase, family 3 (some proteins contain
HAMP domain) [Signal transduction mechanisms].
Length = 227
Score = 81.0 bits (200), Expect = 9e-19
Identities = 37/176 (21%), Positives = 62/176 (35%), Gaps = 41/176 (23%)
Query: 37 DFQVPAENFDSVTIYFSDIVGFTNISADSSPMEVVNMLNTLYKLFDSRIRKYDVYKVETI 96
VT+ F+DIVG T +S +V +LN + + ++ V+ I
Sbjct: 36 LLARGGAGDRRVTLLFADIVGSTELSESLGDEALVELLNLYFDAVAEVVARHGGRVVKFI 95
Query: 97 GDAYMVVSGLPQRNGKSPGTAISFYIRNIGSFGGLGTKGFFRPFSGTLHVGEIATMSLDL 156
GD ++ V G P + A+ ++ +
Sbjct: 96 GDGFLAVFGRPSPLEDAVACAL-----------------------------DLQLALRNP 126
Query: 157 LVGIEHFKIPHRPNDKLEIRVGINTGPCVAGVVGTTMPRYCLFGDTINTASRMESA 212
L + L +R+GI+TG V G G Y + G +N A+R+ES
Sbjct: 127 LAR--------LRRESLRVRIGIHTGEVVVGNTG----GYTVVGSAVNQAARLESL 170
>gnl|CDD|197275 cd09178, PLDc_N_Snf2_like, N-terminal putative catalytic domain of
uncharacterized HKD family nucleases fused to putative
helicases from the Snf2-like family. N-terminal
putative catalytic domain of uncharacterized archaeal
and prokaryotic HKD family nucleases fused to putative
helicases from the Snf2-like family, which belong to the
DNA/RNA helicase superfamily II (SF2). Although
Snf2-like family enzymes do not possess helicase
activity, they contain a helicase-like region, where
seven helicase-related sequence motifs are found,
similar to those in DEAD/DEAH box helicases, which
represent the biggest family within the SF2 superfamily.
In addition to the helicase-like region, members of this
family also contain an N-terminal putative catalytic
domain with one copy of the conserved HKD motif
(H-x-K-x(4)-D, where x represents any amino acid
residue), and have been classified as members of the
phospholipase D (PLD, EC 3.1.4.4) superfamily.
Length = 134
Score = 30.6 bits (70), Expect = 0.28
Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 8/45 (17%)
Query: 135 GFFRPFSGTLHVGE--IATMSLDLLVGIEHFKIPHRPNDKLEIRV 177
G+F SG + E L +L+GIE K K+EIRV
Sbjct: 29 GYFY-LSGFRLLKEELENFEKLRILIGIELIK-----EGKVEIRV 67
>gnl|CDD|178450 PLN02859, PLN02859, glutamine-tRNA ligase.
Length = 788
Score = 31.3 bits (71), Expect = 0.44
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 5/55 (9%)
Query: 1 MKKKKKKQERSELKPDESYPHDLSGNINRVHLIPFVDFQVPAENFD-SVTIYFSD 54
+KKKK+K + E K S L P+ F P ENF ++FSD
Sbjct: 191 VKKKKEKPAKVEEKKVAVAAAPPSEE----ELNPYSIFPQPEENFKVHTEVFFSD 241
>gnl|CDD|185592 PTZ00389, PTZ00389, 40S ribosomal protein S7; Provisional.
Length = 184
Score = 29.6 bits (67), Expect = 0.86
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 8/59 (13%)
Query: 2 KKKKKKQERSELKPD--------ESYPHDLSGNINRVHLIPFVDFQVPAENFDSVTIYF 52
KK KK E SEL+ E+ DL ++ + + + V + +V ++
Sbjct: 1 IKKLKKAEPSELEKQVAKALFELEASSKDLKADLKNLKISSVKEVTVGKDKKKAVVVFV 59
>gnl|CDD|187734 cd09765, Csx14_I-U, CRISPR/Cas system-associated protein Csx14.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Protein containing C-terminal alpha-helical domain
resembling Cas8a2, also known as GSU0052.
Length = 272
Score = 29.9 bits (67), Expect = 0.93
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 154 LDLL--VGIEHFKIPHRPNDKLEIRVGINTGPCVAGVVGTTM 193
L+LL VG++ F+ P R L R G GP V V
Sbjct: 211 LELLAFVGLQRFR-PLRLQANLRYRYGAWFGPLVPTVAARAA 251
>gnl|CDD|149213 pfam08003, Methyltransf_9, Protein of unknown function (DUF1698).
This family contains many hypothetical proteins. It also
includes two putative methyltransferase proteins.
Length = 315
Score = 29.7 bits (67), Expect = 1.3
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 23 LSGNINRVHLIPFVDFQVPA-ENFDSV 48
L GN R HL+P Q+PA E FD+V
Sbjct: 160 LLGNDQRAHLLPLGIEQLPALEAFDTV 186
>gnl|CDD|236572 PRK09566, nirA, ferredoxin-nitrite reductase; Reviewed.
Length = 513
Score = 29.6 bits (67), Expect = 1.4
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 9/56 (16%)
Query: 161 EHFKIPHRPNDKLEI--------RVGINTGPCVAGVVGTTMPRYCLFGDTINTASR 208
++ IP+ P++ LE + + GP G+V T +YC F I T +R
Sbjct: 359 QNVIIPNIPDENLETFLAEPLLQKFSLEPGPLARGLVSCTGNQYCNFA-LIETKNR 413
>gnl|CDD|220590 pfam10130, PIN_2, PIN domain. Members of this family of
bacterial domains are predicted to be RNases (from
similarities to 5'-exonucleases).
Length = 133
Score = 28.5 bits (64), Expect = 1.5
Identities = 10/52 (19%), Positives = 21/52 (40%), Gaps = 4/52 (7%)
Query: 29 RVHLIPFVDFQVPAENFDSVTIYFSDIVGFTNISADSSPMEVVNMLNTLYKL 80
+ + P ++ VP D Y +V + +S + E+ L+ L+
Sbjct: 20 LIFVAPRLELFVPEFAVDEAEKYLEALVRKSKLSEE----ELQEALDLLFTK 67
>gnl|CDD|226803 COG4360, APA2, ATP adenylyltransferase
(5',5'''-P-1,P-4-tetraphosphate phosphorylase II)
[Nucleotide transport and metabolism].
Length = 298
Score = 29.1 bits (65), Expect = 1.8
Identities = 19/54 (35%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 2 KKKKKKQERSELKPDESYPHDL-SGNINRVHLIPFVDFQVPAENFDSVTIYFSD 54
K KKK+E P Y DL G+I+ H + F V E+ VT F D
Sbjct: 64 KADKKKREDPSANPFLPYVQDLFVGDISDTHKLLLNKFPVVDEHLLIVTREFED 117
>gnl|CDD|240435 PTZ00485, PTZ00485, aldolase 1-epimerase; Provisional.
Length = 376
Score = 28.4 bits (63), Expect = 3.2
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 72 NMLNTLYKLFDSRIRKYDVYKVETIGDAYMVVSGLPQRNGK 112
N+L T+Y + D V AY ++G+P+RNGK
Sbjct: 158 NVLKTIYDSYIPETSPADATPVNIFNHAYWNLNGIPERNGK 198
>gnl|CDD|234450 TIGR04056, OMP_RagA_SusC, TonB-linked outer membrane protein,
SusC/RagA family. This model describes a distinctive
clade among the TonB-linked outer membrane proteins
(OMP). Members of this family are restricted to the
Bacteriodetes lineage (except for Gemmatimonas
aurantiaca T-27 from the novel phylum Gemmatimonadetes)
and occur in high copy numbers, with over 100 members
from Bacteroides thetaiotaomicron VPI-5482 alone.
Published descriptions of members of this family are
available for RagA from Porphyromonas gingivalis, SusC
from Bacteroides thetaiotaomicron, and OmpW from
Bacteroides caccae. Members form pairs with members of
the SusD/RagB family (pfam07980). Transporter complexes
including these outer membrane proteins are likely to
import large degradation products of proteins (e.g.
RagA) or carbohydrates (e.g. SusC) as nutrients, rather
than siderophores [Transport and binding proteins,
Unknown substrate].
Length = 982
Score = 28.3 bits (64), Expect = 3.8
Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 108 QRNGKSPGTAISFYIRNIGSFGG 130
Q +G+ PG S +IR I SFGG
Sbjct: 129 QSSGE-PGGDASIWIRGISSFGG 150
>gnl|CDD|183259 PRK11652, emrD, multidrug resistance protein D; Provisional.
Length = 394
Score = 27.9 bits (63), Expect = 3.9
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 178 GINTGPCVAGVVGTTMPRYCLFGDTINTASRMESAGDLPS 217
G+ TG V GV+ T+PR G + A+ + + G L S
Sbjct: 107 GLGTG--VGGVMARTLPRDLYEGTQLRHANSLLNMGILVS 144
>gnl|CDD|238615 cd01288, FabZ, FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein
(ACP) dehydratase that primarily catalyzes the
dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP,
the third step in the elongation phase of the bacterial/
plastid, type II, fatty-acid biosynthesis pathway.
Length = 131
Score = 27.1 bits (61), Expect = 4.3
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 153 SLDLLVGIEH--FKIPHRPNDKLEIRV 177
L GI+ F+ P P D+L + V
Sbjct: 72 KLVYFAGIDKARFRKPVVPGDQLILEV 98
>gnl|CDD|220604 pfam10155, DUF2363, Uncharacterized conserved protein (DUF2363).
This is a region of 120 amino acids of a family of
proteins conserved from plants to humans. The function
is not known.
Length = 126
Score = 26.8 bits (60), Expect = 5.8
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 5/46 (10%)
Query: 61 ISADSSP--MEVVNMLNTLYKLFDSRIRKYDVY---KVETIGDAYM 101
I D + +EVVN L+ +KL + Y E I D M
Sbjct: 29 IQMDVTVQSLEVVNRLSKSFKLPREFLHLYIRNCISTCENIKDKQM 74
>gnl|CDD|193572 cd09848, M28_TfR, M28 Zn-peptidase Transferrin Receptor family.
Peptidase M28 family; Transferrin Receptor (TfR)
subfamily. TfRs are homodimeric type II transmembrane
proteins containing three distinct domains:
protease-like, apical or protease-associated (PA), and
helical domains. The protease-like domain is a large
extracellular portion (ectodomain). In TfR, it contains
a binding site for the transferrin molecule and has 28%
identity to membrane glutamate carboxypeptidase II
(mGCP-II or PSMA). The PA domain is inserted between
the first and second strands of the central beta sheet
in the protease-like domain. TfR1 is widely expressed,
and is a key player in the uptake of iron-loaded
transferrin (Tf) into cells. The TfR1 homodimer binds
two molecules of Tf and the complex is then
internalized. TfR1 may also participate in cell growth
and proliferation. TfR2 binds Tf but with a
significantly lower affinity than TfR1. It is expressed
chiefly in hepatocytes, hematopoietic cells, and
duodenal crypt cells; its expression overlaps with that
of hereditary hemochromatosis protein (HFE). TfR2 is
involved in iron homeostasis; in humans, mutations in
TfR2 are associated with a form of hemochromatosis
(HFE3). While related in sequence to peptidase M28
glutamate carboxypeptidase II (also called
prostate-specific membrane antigen or PSMA), TfR lacks
the metal ion coordination centers and protease activity
of that group.
Length = 285
Score = 27.4 bits (61), Expect = 6.6
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 102 VVSGLPQRNGKSPGTAISFYIRNIGSFGGLGTKGFFRPFSGTLHVGEIATMSLDLLV-GI 160
S + + +G P +I F + G FG +G + + +LH+ +SLD V G
Sbjct: 101 TFSDMVKNDGFKPRRSILFASWSAGDFGSVGATEWLEGYLSSLHLKAFTYISLDGAVLGD 160
Query: 161 EHFKIPHRP 169
+ FK P
Sbjct: 161 DSFKASASP 169
>gnl|CDD|182329 PRK10245, adrA, diguanylate cyclase AdrA; Provisional.
Length = 366
Score = 27.1 bits (60), Expect = 7.3
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 125 IGSFGGLGTKGFFRPFSGTLHVGEIATMSLDLLVGIEHFKIPHRPNDKLEIRVGI 179
IG FGG F SGT I MS + G+ ++P+ P L I VG+
Sbjct: 280 IGRFGG---DEFAVIMSGTPAESAITAMS-RVHEGLNTLRLPNAPQVTLRISVGV 330
>gnl|CDD|218537 pfam05284, DUF736, Protein of unknown function (DUF736). This
family consists of several uncharacterized bacterial
proteins of unknown function.
Length = 105
Score = 26.1 bits (58), Expect = 7.8
Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 11/49 (22%)
Query: 124 NIGSFGGLGTKGFFRPFSGTLHVGEIATMSLDLLVGIEHFKIPHRPNDK 172
NIG+F GF G I T++LD + + + N+
Sbjct: 2 NIGTFTRTEDGGF---------TGRIRTLTLDAKIRLV--PNASKTNEN 39
>gnl|CDD|143612 cd07304, Chorismate_synthase, Chorismase synthase, the enzyme
catalyzing the final step of the shikimate pathway.
Chorismate synthase (CS;
5-enolpyruvylshikimate-3-phosphate phospholyase;
1-carboxyvinyl-3-phosphoshikimate phosphate-lyase; E.C.
4.2.3.5) catalyzes the seventh and final step in the
shikimate pathway: the conversion of 5-
enolpyruvylshikimate-3-phosphate (EPSP) to chorismate, a
precursor for the biosynthesis of aromatic compounds.
This process has an absolute requirement for reduced FMN
as a co-factor which is thought to facilitate cleavage
of C-O bonds by transiently donating an electron to the
substrate, having no overall change its redox state.
Depending on the capacity of these enzymes to regenerate
the reduced form of FMN, chorismate synthases are
divided into two classes: Enzymes, mostly from plants
and eubacteria, that sequester CS from the cellular
environment, are monofunctiona,l while those that can
generate reduced FMN at the expense of NADPH, such as
found in fungi and the ciliated protozoan Euglena
gracilis, are bifunctional, having an additional
NADPH:FMN oxidoreductase activity. Recently,
bifunctionality of the Mycobacterium tuberculosis enzyme
(MtCS) was determined by measurements of both chorismate
synthase and NADH:FMN oxidoreductase activities. Since
shikimate pathway enzymes are present in bacteria, fungi
and apicomplexan parasites (such as Toxoplasma gondii,
Plasmodium falciparum, and Cryptosporidium parvum) but
absent in mammals, they are potentially attractive
targets for the development of new therapy against
infectious diseases such as tuberculosis (TB).
Length = 344
Score = 27.0 bits (61), Expect = 9.1
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 98 DAYMVVSGLPQRNGKSPGTAISFYIRN 124
D ++SG+ GK+ GT I+ IRN
Sbjct: 54 DEVEILSGV--FEGKTTGTPIALLIRN 78
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
0.321 0.140 0.412
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,754,648
Number of extensions: 1116972
Number of successful extensions: 897
Number of sequences better than 10.0: 1
Number of HSP's gapped: 890
Number of HSP's successfully gapped: 38
Length of query: 226
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 133
Effective length of database: 6,812,680
Effective search space: 906086440
Effective search space used: 906086440
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: 57 (25.8 bits)