RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9025
(361 letters)
>gnl|CDD|237999 cd00038, CAP_ED, effector domain of the CAP family of transcription
factors; members include CAP (or cAMP receptor protein
(CRP)), which binds cAMP, FNR (fumarate and nitrate
reduction), which uses an iron-sulfur cluster to sense
oxygen) and CooA, a heme containing CO sensor. In all
cases binding of the effector leads to conformational
changes and the ability to activate transcription.
Cyclic nucleotide-binding domain similar to CAP are also
present in cAMP- and cGMP-dependent protein kinases
(cAPK and cGPK) and vertebrate cyclic nucleotide-gated
ion-channels. Cyclic nucleotide-monophosphate binding
domain; proteins that bind cyclic nucleotides (cAMP or
cGMP) share a structural domain of about 120 residues;
the best studied is the prokaryotic catabolite gene
activator, CAP, where such a domain is known to be
composed of three alpha-helices and a distinctive
eight-stranded, antiparallel beta-barrel structure;
three conserved glycine residues are thought to be
essential for maintenance of the structural integrity of
the beta-barrel; CooA is a homodimeric transcription
factor that belongs to CAP family; cAMP- and
cGMP-dependent protein kinases (cAPK and cGPK) contain
two tandem copies of the cyclic nucleotide-binding
domain; cAPK's are composed of two different subunits, a
catalytic chain and a regulatory chain, which contains
both copies of the domain; cGPK's are single chain
enzymes that include the two copies of the domain in
their N-terminal section; also found in vertebrate
cyclic nucleotide-gated ion-channels.
Length = 115
Score = 97.0 bits (242), Expect = 8e-25
Identities = 38/117 (32%), Positives = 56/117 (47%), Gaps = 8/117 (6%)
Query: 123 LFQDCDEALLRELVLKLRPVLYLPGDYICRKGEVGKEMYIVKTGQVQVV-----SGETVL 177
LF D+ L EL L + G+ I R+G+ +YIV +G V+V E ++
Sbjct: 1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIV 60
Query: 178 ATLTEGSVFGEISLLALAGTNRRTADVRSHGFSNLFVLNKDDLNEAIEYYPNAQEVL 234
L G +FGE++LL G R+A VR+ S L VL + D ++ YP L
Sbjct: 61 GFLGPGDLFGELALL---GNGPRSATVRALTDSELLVLPRSDFRRLLQEYPELARRL 114
>gnl|CDD|197516 smart00100, cNMP, Cyclic nucleotide-monophosphate binding domain.
Catabolite gene activator protein (CAP) is a prokaryotic
homologue of eukaryotic cNMP-binding domains, present in
ion channels, and cNMP-dependent kinases.
Length = 120
Score = 94.8 bits (236), Expect = 7e-24
Identities = 35/114 (30%), Positives = 56/114 (49%), Gaps = 6/114 (5%)
Query: 123 LFQDCDEALLRELVLKLRPVLYLPGDYICRKGEVGKEMYIVKTGQVQVVS-----GETVL 177
LF++ D LREL L PV Y G+ I R+G+VG YI+ +G+V+V E ++
Sbjct: 1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIV 60
Query: 178 ATLTEGSVFGEISLLALAGTNRRTADVRSHGFSNLFVLNKDDLNEAIEYYPNAQ 231
TL G FGE++LL + +A + + L ++ D + + P
Sbjct: 61 GTLGPGDFFGELALLTNSRR-AASAAAVALELATLLRIDFRDFLQLLPELPQLL 113
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 71.2 bits (175), Expect = 1e-15
Identities = 31/93 (33%), Positives = 48/93 (51%), Gaps = 8/93 (8%)
Query: 141 PVLYLPGDYICRKGEVGKEMYIVKTGQVQVVS-----GETVLATLTEGSVFGEISLLALA 195
+ G+ I R+G+ +YIV +G+V+V E +LA L G FGE++LL
Sbjct: 1 LRSFKKGEVIFREGDPADSLYIVLSGKVKVYKLDEDGREQILAFLGPGDFFGELALL--- 57
Query: 196 GTNRRTADVRSHGFSNLFVLNKDDLNEAIEYYP 228
G R+A V + S L V+ ++D E +E P
Sbjct: 58 GGEPRSATVVALTDSELLVIPREDFLELLEQDP 90
>gnl|CDD|223736 COG0664, Crp, cAMP-binding proteins - catabolite gene activator and
regulatory subunit of cAMP-dependent protein kinases
[Signal transduction mechanisms].
Length = 214
Score = 57.9 bits (140), Expect = 7e-10
Identities = 37/148 (25%), Positives = 61/148 (41%), Gaps = 15/148 (10%)
Query: 117 TLSKVQLFQDCDEALLRELVLKLRPVLYLPGDYICRKGEVGKEMYIVKTGQVQVV----- 171
L + L LL L LKL G+ + +GE +YI+ +G V++
Sbjct: 1 ALKENPLLNLLPSELLELLALKLEVRKLPKGEVLFTEGEEADSLYIILSGIVKLYANTED 60
Query: 172 SGETVLATLTEGSVFGEISLLALAGTNRRTADVRSHGFSNLFVLNKDDLNEAIEYYPNAQ 231
E +L L G FGE++LL G + R+A + + + + D E + P
Sbjct: 61 GREIILGFLGPGDFFGELALL---GGDPRSASAVALTDVEVLEIPRKDFLELLAESPKL- 116
Query: 232 EVLKKKARQLIKENAARERVSQPKLSTM 259
A L++ A R R + +LS +
Sbjct: 117 ------ALALLRLLARRLRQALERLSLL 138
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 57.2 bits (138), Expect = 7e-09
Identities = 46/200 (23%), Positives = 87/200 (43%), Gaps = 20/200 (10%)
Query: 91 SEDENKILNNLPLKLKTDVAINVHIQTLSKVQLFQDCDEALLRELVLKLRPVLYLPGDYI 150
S ++ ++++ LP + + ++ + + KV LF+ +L LV K++ P + +
Sbjct: 349 SLNQQQLIDQLPKSICKSICQHLFLPVVEKVYLFKGVSREILLLLVTKMKAEYIPPREDV 408
Query: 151 CRKGEVGKEMYIVKTGQVQVV----SGETVLATLTEGSVFGEISLLALAGTNRRTADVRS 206
+ E ++YIV +G+V+++ E V+ TL G +FGE+ L ++ R+
Sbjct: 409 IMQNEAPDDVYIVVSGEVEIIDSEGEKERVVGTLGCGDIFGEVGALC---CRPQSFTFRT 465
Query: 207 HGFSNLFVLNKDDLNEAIEYYPNAQEVLKKKARQLIKENAARERVSQPKLSTMDASSVLL 266
S L L L EA++ V+ K Q +L ++ +L
Sbjct: 466 KTLSQLLRLKTSTLIEAMQTRQEDNVVILKNFLQ-----------HHKELHDLNVGDLLG 514
Query: 267 DRKGE--EPKQAPKLLPIVM 284
D GE +P A LL +
Sbjct: 515 DNGGEHDDPNMASNLLTVAS 534
>gnl|CDD|178459 PLN02868, PLN02868, acyl-CoA thioesterase family protein.
Length = 413
Score = 37.8 bits (88), Expect = 0.007
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 118 LSKVQLFQDCDEALLRELVLKLRPVLYLPGDYICRKGEVGKEMYIVKTGQVQV 170
L V L Q + L+++ + P Y G+Y+ R+GE G +Y + G+ +V
Sbjct: 10 LGSVPLLQRLPSSSLKKIAEVVVPKRYGKGEYVVREGEPGDGLYFIWKGEAEV 62
>gnl|CDD|218351 pfam04961, FTCD_C, Formiminotransferase-cyclodeaminase. Members of
this family are thought to be Formiminotransferase-
cyclodeaminase enzymes EC:4.3.1.4. This domain is found
in the C-terminus of the bifunctional animal members of
the family.
Length = 176
Score = 32.5 bits (75), Expect = 0.15
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 11/65 (16%)
Query: 23 EQVRGDIESGVDEDEEY-----------HDSDSEKERRERFIQERIRHLAHVFTERAQKI 71
E++R ++ + DED E +++ EK RE IQE ++ A V E A+
Sbjct: 62 EELREELLALADEDAEAFNAVMAAYKLPKETEEEKAAREAAIQEALKQAAEVPLEVARAA 121
Query: 72 KRILD 76
+L
Sbjct: 122 LEVLK 126
>gnl|CDD|225457 COG2905, COG2905, Predicted signal-transduction protein containing
cAMP-binding and CBS domains [Signal transduction
mechanisms].
Length = 610
Score = 33.5 bits (77), Expect = 0.16
Identities = 39/176 (22%), Positives = 58/176 (32%), Gaps = 41/176 (23%)
Query: 132 LRELVLKLRPVLYLPGDYICRKGEVGKEMYIVKTGQVQVVS-GETVLATLTEGSVFGEIS 190
L +L+ L Y G+ I G +Y+++ G V+V S G VL L G +FG S
Sbjct: 23 LEQLMGALEVKYYRKGEIIIYAGSPVHYLYVIRKGVVEVRSDGGEVLDRLAAGDLFGFSS 82
Query: 191 LLALAGTNRRTADVRSHGFSNLFVLNKDDLNEAIEYYP---------------------- 228
L R A S ++L K + +E P
Sbjct: 83 LFTELNKQRYMAAEED---SLCYLLPKSVFMQLMEENPEFADFFLRSLAKRLRDIADRLA 139
Query: 229 --NAQEVLKKKARQLIKENAARERVSQPKLSTMDA----------SSVLLDRKGEE 272
E + + ++ A P+ S DA S V+LD G
Sbjct: 140 EQGESEFILTRVGEVKTLPA---VTVSPQASIQDAARKMKDEGVSSLVVLDDSGPL 192
>gnl|CDD|233823 TIGR02339, thermosome_arch, thermosome, various subunits, archaeal.
Thermosome is the name given to the archaeal rather
than eukaryotic form of the group II chaperonin
(counterpart to the group I chaperonin, GroEL/GroES, in
bacterial), a torroidal, ATP-dependent molecular
chaperone that assists in the folding or refolding of
nascent or denatured proteins. Various homologous
subunits, one to five per archaeal genome, may be
designated alpha, beta, etc., but phylogenetic analysis
does not show distinct alpha subunit and beta subunit
lineages traceable to ancient paralogs [Protein fate,
Protein folding and stabilization].
Length = 519
Score = 30.8 bits (70), Expect = 1.1
Identities = 16/49 (32%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 92 EDENKILNNLPLKL-KTDVAINVHIQTLSKVQLFQDCDEALLRELVLKL 139
E+ L + PL++ KT++ + I ++Q F D +EA+L+E+V K+
Sbjct: 230 ENAKIALLDAPLEVEKTEIDAEIRITDPDQIQKFLDQEEAMLKEMVDKI 278
>gnl|CDD|236969 PRK11753, PRK11753, DNA-binding transcriptional dual regulator Crp;
Provisional.
Length = 211
Score = 29.9 bits (68), Expect = 1.4
Identities = 24/113 (21%), Positives = 47/113 (41%), Gaps = 14/113 (12%)
Query: 150 ICRKGEVGKEMYIVKTGQVQVVSG-----ETVLATLTEGSVFGEISLLALAGTNRRTADV 204
+ GE + +Y + G V V+ E +L+ L +G GE+ L R+A V
Sbjct: 31 LIHAGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGL--FEEGQERSAWV 88
Query: 205 RSHGFSNLFVLNKDDLNEAIEYYPNAQEVLKKKARQLIKENAARERVSQPKLS 257
R+ + ++ + I+ P ++L + Q+ A R + + K+
Sbjct: 89 RAKTACEVAEISYKKFRQLIQVNP---DILMALSAQM----ARRLQNTSRKVG 134
>gnl|CDD|227656 COG5353, COG5353, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 161
Score = 29.8 bits (67), Expect = 1.5
Identities = 29/132 (21%), Positives = 48/132 (36%), Gaps = 20/132 (15%)
Query: 142 VLYLPGDYICRKGEVGKEMYIVKTGQVQVVSGETVLATLTEGSVFGEISLLALAGTNRRT 201
+ L K K + + + + + ET LAT + ++ N +
Sbjct: 18 AIILSIALFFWKSM--KPYHEAEEQAIDLATEETDLATADQFDLY-----------NGKE 64
Query: 202 ADVRSHGFSNLFVLNKDDLNEAIEYYPNAQEVLKKKARQLIKENAARERVSQPKLSTMDA 261
G LNK + + ++ KKA Q I E AR +S+ K +
Sbjct: 65 VYYVIVG------LNKKGEEIIVWVPKDDGKIYSKKASQGISEEDARAIISKEKA-VKEI 117
Query: 262 SSVLLDRKGEEP 273
SV L R+ E+P
Sbjct: 118 KSVTLGREKEKP 129
>gnl|CDD|173170 PRK14707, PRK14707, hypothetical protein; Provisional.
Length = 2710
Score = 30.1 bits (67), Expect = 2.2
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 298 RCGSKSLNKRPHRRVNRSASADTYFHPKQQRRLLHQTPT 336
RC ++ + P+ RV A D F P+Q + LL + P+
Sbjct: 2196 RCFAERVRSLPYSRVTARAMQDGRFDPEQTKLLLQRMPS 2234
>gnl|CDD|240177 cd05156, ChoK_euk, Choline Kinase (ChoK) in eukaryotes. The ChoK
subfamily is part of a larger superfamily that includes
the catalytic domains of other kinases, such as the
typical serine/threonine/tyrosine protein kinases (PKs),
RIO kinases, actin-fragmin kinase (AFK), and
phosphoinositide 3-kinase (PI3K). It is composed of
bacterial and eukaryotic choline kinases, as well as
eukaryotic ethanolamine kinase. ChoK catalyzes the
transfer of the gamma-phosphoryl group from ATP (or CTP)
to its substrate, choline, producing phosphorylcholine
(PCho), a precursor to the biosynthesis of two major
membrane phospholipids, phosphatidylcholine (PC) and
sphingomyelin (SM). Although choline is the preferred
substrate, ChoK also shows substantial activity towards
ethanolamine and its N-methylated derivatives. ChoK
plays an important role in cell signaling pathways and
the regulation of cell growth. Along with PCho, it is
involved in malignant transformation through Ras
oncogenes in various human cancers such as breast, lung,
colon, prostate, neuroblastoma, and hepatic lymphoma. In
mammalian cells, there are three ChoK isoforms (A-1,
A-2, and B) which are active in homo or heterodimeric
forms.
Length = 302
Score = 29.2 bits (66), Expect = 3.0
Identities = 16/64 (25%), Positives = 23/64 (35%)
Query: 38 EYHDSDSEKERRERFIQERIRHLAHVFTERAQKIKRILDFPPTPSSSTTLSSSSEDENKI 97
+ H ER + I L + + A+ + I+D LS EDE K
Sbjct: 104 KLHSIVVPLSPEERDLTPAIWKLLKQWLDLAETVIEIVDSDSEKLLEVELSLFLEDEAKY 163
Query: 98 LNNL 101
L L
Sbjct: 164 LRFL 167
>gnl|CDD|224780 COG1867, TRM1, N2,N2-dimethylguanosine tRNA methyltransferase
[Translation, ribosomal structure and biogenesis].
Length = 380
Score = 29.2 bits (66), Expect = 3.2
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 237 KARQLIKENAARERVSQPKLSTMDASSVLLDRKG 270
KA +LIKEN ++ DA+++L +
Sbjct: 87 KAVELIKENVRLNSGEDAEVINKDANALLHELHR 120
>gnl|CDD|233265 TIGR01085, murE, UDP-N-acetylmuramyl-tripeptide synthetase. Most
members of this family are EC 6.3.2.13,
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,
6-diaminopimelate ligase. An exception is Staphylococcus
aureus, in which diaminopimelate is replaced by lysine
in the peptidoglycan and MurE is EC 6.3.2.7. The
Mycobacteria, part of the closest neighboring branch
outside of the low-GC Gram-positive bacteria, use
diaminopimelate. A close homolog, scoring just below the
trusted cutoff, is found (with introns) in Arabidopsis
thaliana. Its role is unknown [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 464
Score = 29.2 bits (66), Expect = 3.6
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 17 RKESVPEQVRGDIESGVDEDEEYHDSDSEKERRE 50
R E PEQ+ DI +G+ E E+ +RR+
Sbjct: 397 RGED-PEQIIADILAGISEKEKVV---IIADRRQ 426
>gnl|CDD|234585 PRK00035, hemH, ferrochelatase; Reviewed.
Length = 333
Score = 29.0 bits (66), Expect = 3.9
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 9/60 (15%)
Query: 52 FIQERIRHLAHVFTERAQKIKRILDFPPTP--SSSTTLSSSSEDENKILNNLPLKLKTDV 109
I+E + L +A + RI+ P P S STT S ED + L L L+ +
Sbjct: 106 SIEEALEAL------KADGVDRIVVLPLYPQYSYSTTA-SYFEDLARALAKLRLQPEIRF 158
>gnl|CDD|178745 PLN03206, PLN03206, phosphoribosylformylglycinamidine synthase;
Provisional.
Length = 1307
Score = 29.0 bits (65), Expect = 4.5
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 225 EYYPNAQEVLKKKARQLIKENAARERVSQPKLSTMDASS--VLLDRKGEEPKQAPKLLP 281
EY ++K ++R L++ RER S + T+D S VL+D E +A L P
Sbjct: 541 EYQEQDALLIKPESRDLLQSICDRERCSMAVIGTIDGSGRVVLVDSAAPEKCEANGLPP 599
>gnl|CDD|147980 pfam06109, HlyE, Haemolysin E (HlyE). This family consists of
several enterobacterial haemolysin (HlyE)
proteins.Hemolysin E (HlyE) is a novel pore-forming
toxin of Escherichia coli, Salmonella typhi, and
Shigella flexneri. HlyE is unrelated to the well
characterized pore-forming E. coli hemolysins of the RTX
family, haemolysin A (HlyA), and the enterohaemolysin
encoded by the plasmid borne ehxA gene of E. coli 0157.
However, it is evident that expression of HlyE in the
absence of the RTX toxins is sufficient to give a
hemolytic phenotype in E. coli. HlyE is a protein of 34
kDa that is expressed during anaerobic growth of E.
coli. Anaerobic expression is controlled by the
transcription factor, FNR, such that, upon ingestion and
entry into the anaerobic mammalian intestine, HlyE is
produced and may then contribute to the colonisation of
the host.
Length = 299
Score = 28.5 bits (63), Expect = 5.4
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 7/71 (9%)
Query: 66 ERAQKIKRILDFPPTPSSSTTLSSSSEDENKILNNLPLKLKTDVAINVHIQTLSK-VQLF 124
+K+K + DF +L+++ + NK ++ LKLK ++A I+T ++ + F
Sbjct: 207 ALKEKLKSVKDF------FESLAATVKQANKDIDAAKLKLKDEIAAIGDIKTETETTRFF 260
Query: 125 QDCDEALLREL 135
D D+ +L+ L
Sbjct: 261 VDYDDLMLKLL 271
>gnl|CDD|225939 COG3404, COG3404, Methenyl tetrahydrofolate cyclohydrolase [Amino
acid transport and metabolism].
Length = 208
Score = 27.8 bits (62), Expect = 7.7
Identities = 10/52 (19%), Positives = 25/52 (48%), Gaps = 11/52 (21%)
Query: 23 EQVRGDIESGVDEDEEYH-----------DSDSEKERRERFIQERIRHLAHV 63
++++ ++ + +D+DEE ++ EK R + +Q ++ A V
Sbjct: 67 QKIKAELLALIDKDEEAFNLIMAAYKLPKSTEEEKAARRKALQNALKEAAKV 118
>gnl|CDD|153275 cd07591, BAR_Rvs161p, The Bin/Amphiphysin/Rvs (BAR) domain of
Saccharomyces cerevisiae Reduced viability upon
starvation protein 161 and similar proteins. BAR
domains are dimerization, lipid binding and curvature
sensing modules found in many different proteins with
diverse functions. This subfamily is composed of fungal
proteins with similarity to Saccharomyces cerevisiae
Reduced viability upon starvation protein 161 (Rvs161p)
and Schizosaccharomyces pombe Hob3 (homolog of Bin3). S.
cerevisiae Rvs161p plays a role in regulating cell
polarity, actin cytoskeleton polarization, vesicle
trafficking, endocytosis, bud formation, and the mating
response. It forms a heterodimer with another BAR domain
protein Rvs167p. Rvs161p and Rvs167p share common
functions but are not interchangeable. Their BAR domains
cannot be replaced with each other and the
overexpression of one cannot suppress the mutant
phenotypes of the other. S. pombe Hob3 is important in
regulating filamentous actin localization and may be
required in activating Cdc42 and recruiting it to cell
division sites. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 224
Score = 27.7 bits (62), Expect = 9.0
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 11/53 (20%)
Query: 226 YYPNAQEVLKKKARQLIKENAARERVSQPKLSTMDASSVLLDRKGEEPKQAPK 278
Y+P E +KK+ +L+ +AAR +V + L+D+ E+P + P+
Sbjct: 107 YFPEINEAIKKRNHKLLDYDAARAKVRK-----------LIDKPSEDPTKLPR 148
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
0.314 0.131 0.364
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,976,813
Number of extensions: 1727597
Number of successful extensions: 1514
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1507
Number of HSP's successfully gapped: 43
Length of query: 361
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 263
Effective length of database: 6,590,910
Effective search space: 1733409330
Effective search space used: 1733409330
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: 42 (22.0 bits)
S2: 60 (27.0 bits)