RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy759
(230 letters)
>gnl|CDD|218493 pfam05199, GMC_oxred_C, GMC oxidoreductase. This domain found
associated with pfam00732.
Length = 139
Score = 158 bits (402), Expect = 1e-49
Identities = 52/145 (35%), Positives = 71/145 (48%), Gaps = 6/145 (4%)
Query: 74 PRSRGKVLLKDSHPLTPPLIHANFFNDTRDLDVIVEGIKMAIELSKTKAFQSIGSTLHKA 133
PRSRG+V L S PL P+I N+ +D DL + +++A + L
Sbjct: 1 PRSRGRVTLSSSDPLGLPVIDPNYLSDPADLAALRAALRLARRILAAA-----LVELTPG 55
Query: 134 PIPGCSQYTFGSDAYWGCSVRHITTQLHHQCGTCKMGPRWDSSAVVDPQLKVYGVDNLRV 193
P+ SD +R H GTC+MG VVDP L+V+GVDNLRV
Sbjct: 56 PVEVVPGAAEASDDEILEYIRAAAVTSWHPMGTCRMGAD-PDDGVVDPDLRVHGVDNLRV 114
Query: 194 VDASIIPVIPGGHTVAVVYMIAEKA 218
VDAS+ P P G+ +Y +AE+A
Sbjct: 115 VDASVFPSSPSGNPTLTIYALAERA 139
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 125 bits (316), Expect = 2e-33
Identities = 47/160 (29%), Positives = 81/160 (50%), Gaps = 7/160 (4%)
Query: 65 WSIWPMILYPRSRGKVLLKDSHPLTPPLIHANFFNDTRDLDVIVEGIKMAIELSKTKAFQ 124
+++ + P+SRG V L+ P P+I N+ + D + GI++ E+ A
Sbjct: 383 FTLHVGPMRPKSRGSVTLRSPDPDNRPVIDPNYLSAEGDRAIFRAGIRLTREIIGQPALD 442
Query: 125 SIGSTLHKAPIPGCSQYTFGSDAYWGCSVRHITTQLHHQCGTCKMGPRWDSSAVVDPQLK 184
+ AP P + +D ++R + +H GTC+MG ++ V DP L+
Sbjct: 443 AR-RKAELAPGPRVT-----TDEDISAAIRFLARTAYHPMGTCRMG-SDPAAVVDDPYLR 495
Query: 185 VYGVDNLRVVDASIIPVIPGGHTVAVVYMIAEKASDMIKK 224
V+G++NLRVVDAS++P G + + +AE+A+D I
Sbjct: 496 VHGLENLRVVDASVMPTSTGVNPNLTIIALAERAADHILG 535
>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 119 bits (301), Expect = 3e-31
Identities = 60/163 (36%), Positives = 81/163 (49%), Gaps = 15/163 (9%)
Query: 69 PMILYPRSRGKVLLKDSHPLTPPLIHANFFNDTRDLDVIVEGIKMAIELSKTKAFQSI-G 127
PM SRG V LK + P P I N+ + +D + I++ E+ A G
Sbjct: 388 PM--RSPSRGSVKLKSADPRAHPSILFNYMSTEQDWREFRDAIRLTREIMAQPALDPYRG 445
Query: 128 STLHKAPIPGCS-QYTFGSDAYWGCSVRHITTQLHHQCGTCKMGPRWDSSAVVDPQLKVY 186
+ PG Q +D VR +H TCKMG D AVVDP+ +V+
Sbjct: 446 REIS----PGADVQ----TDEEIDAFVREHAETAYHPSCTCKMGT--DPMAVVDPEGRVH 495
Query: 187 GVDNLRVVDASIIPVIPGGHTVAVVYMIAEKASDMIK-KTWLP 228
GV+ LRVVDASI+P I G+ A MIAEKA+D+I+ +T L
Sbjct: 496 GVEGLRVVDASIMPTITNGNLNAPTIMIAEKAADLIRGRTPLA 538
>gnl|CDD|233581 TIGR01810, betA, choline dehydrogenase. Choline dehydrogenase
catalyzes the conversion of exogenously supplied choline
into the intermediate glycine betaine aldehyde, as part
of a two-step oxidative reaction leading to the
formation of osmoprotectant betaine. This enzymatic
system can be found in both gram-positive and
gram-negative bacteria. As in Escherichia coli ,
Staphylococcus xylosus , and Sinorhizobium meliloti,
this enzyme is found associated in a transciptionally
co-induced gene cluster with betaine aldehyde
dehydrogenase, the second catalytic enzyme in this
reaction. Other gram-positive organisms have been shown
to employ a different enzymatic system, utlizing a
soluable choline oxidase or type III alcohol
dehydrogenase instead of choline dehydrogenase. This
enzyme is a member of the GMC oxidoreductase family
(pfam00732 and pfam05199), sharing a common
evoluntionary origin and enzymatic reaction with alcohol
dehydrogenase. Outgrouping from this model, Caulobacter
crescentus shares sequence homology with choline
dehydrogenase, yet other genes participating in this
enzymatic reaction have not currently been identified
[Cellular processes, Adaptations to atypical
conditions].
Length = 532
Score = 105 bits (263), Expect = 3e-26
Identities = 74/221 (33%), Positives = 106/221 (47%), Gaps = 32/221 (14%)
Query: 5 EGLAYVNTKYNVFPDDLPDIEFIFTAVSLASDGGVSLRQEMGITDHLYNSVYSSVDRKDS 64
EG +V + +V D P+I++ F V++ DG + + G H
Sbjct: 337 EGGGFVRSNDDV---DYPNIQYHFLPVAIRYDGTKAPK-AHGFQVH-------------- 378
Query: 65 WSIWPMILYPRSRGKVLLKDSHPLTPPLIHANFFNDTRDLDVIVEGIKMAIELSKTKAFQ 124
+ PM Y SRG V +K P P I N+ + D E I++ E+ K KA
Sbjct: 379 --VGPM--YSNSRGHVKIKSKDPFEKPEIVFNYMSHEEDWREFREAIRVTREILKQKALD 434
Query: 125 SIGSTLHKAP--IPGCSQYTFGSDAYWGCSVRHITTQLHHQCGTCKMGPRWDSSAVVDPQ 182
++ PG T + RH T L H CGTCKMGP D +VVDP+
Sbjct: 435 -----PYRGGEISPGPEVQT--DEEIDEFVRRHGETAL-HPCGTCKMGPASDEMSVVDPE 486
Query: 183 LKVYGVDNLRVVDASIIPVIPGGHTVAVVYMIAEKASDMIK 223
+V+G++ LRVVDASI+P I G+ A V M+ EKA+D+I+
Sbjct: 487 TRVHGMEGLRVVDASIMPRITNGNLNAPVIMMGEKAADIIR 527
>gnl|CDD|234421 TIGR03970, Rv0697, dehydrogenase, Rv0697 family. This model
describes a set of dehydrogenases belonging to the
glucose-methanol-choline oxidoreductase (GMC
oxidoreductase) family. Members of the present family
are restricted to Actinobacterial genome contexts
containing also members of families TIGR03962 and
TIGR03969 (the mycofactocin system), and are proposed to
be uniform in function.
Length = 487
Score = 91.0 bits (226), Expect = 3e-21
Identities = 53/151 (35%), Positives = 74/151 (49%), Gaps = 18/151 (11%)
Query: 74 PRSRGKVLLKDSHPLTPPLIHANFFNDTRDLDVIVEGIKMAIELSKTKAFQSIGSTLHKA 133
P SRG++ L + P PP I + + D + G +A EL
Sbjct: 352 PHSRGRIRLASADPADPPRIEHRYDSSAADRAALRAGAALAHELLG-----------SPE 400
Query: 134 PIPGCSQYTFGSDAYWGCSVRHITTQLHHQCGTCKMGPRWDSSAVVDPQLKVYGVDNLRV 193
P +A W + R T+Q H CG+C+MG R D AVVD + +V GV+ L V
Sbjct: 401 LGPLLEPAVREGEASWVLA-RLATSQ--HLCGSCRMGGRDDPGAVVDARCRVRGVEGLWV 457
Query: 194 VDASIIPVIP--GGHTVAVVYMIAEKASDMI 222
VD SI+PVIP G H AV M+AE+A++ +
Sbjct: 458 VDGSILPVIPSRGPHATAV--MVAERAAEFL 486
>gnl|CDD|215420 PLN02785, PLN02785, Protein HOTHEAD.
Length = 587
Score = 59.0 bits (143), Expect = 3e-10
Identities = 46/158 (29%), Positives = 65/158 (41%), Gaps = 24/158 (15%)
Query: 71 ILYPRSRGKVLLKDSHPLTPPLIHANFFNDTRDLDVIVEGIKMAIELSKTKAF----QSI 126
I P S G + L +++ P + N+F +DL V GI+ ++ KT F Q
Sbjct: 421 IAGPISTGHLSLINTNVDDNPSVTFNYFKHPQDLQRCVYGIRTIEKIVKTNHFTNFTQCD 480
Query: 127 GSTLHKAP----------IPGCSQYTFGSDAYWGCSVRHITTQLHHQCGTCKMGPRWDSS 176
T+ K IP + T + + C IT +H G C +G
Sbjct: 481 KQTMEKVLNMSVKANINLIPKHTNDTKSLEQF--CKDTVITIWHYH--GGCHVG------ 530
Query: 177 AVVDPQLKVYGVDNLRVVDASIIPVIPGGHTVAVVYMI 214
VVD KV GV LRV+D S PG + A V M+
Sbjct: 531 KVVDQNYKVLGVSRLRVIDGSTFDESPGTNPQATVMMM 568
>gnl|CDD|217220 pfam02771, Acyl-CoA_dh_N, Acyl-CoA dehydrogenase, N-terminal
domain. The N-terminal domain of Acyl-CoA dehydrogenase
is an all-alpha domain.
Length = 113
Score = 29.4 bits (67), Expect = 0.59
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 194 VDASIIPVIPGGHTVAVVYMIAEKASDMIKKTWLP 228
DAS+ + H+ V I ++ K+ +LP
Sbjct: 74 ADASV-GLALSVHSSLVAPPILRFGTEEQKEKYLP 107
>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM2 of Nop13p
encoded by YNL175c from Saccharomyces cerevisiae. It
shares high sequence similarity with nucleolar protein
12 (Nop12p). Both Nop12p and Nop13p are not essential
for growth. However, unlike Nop12p that is localized to
the nucleolus, Nop13p localizes primarily to the
nucleolus but is also present in the nucleoplasm to a
lesser extent. Nop13p contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). .
Length = 73
Score = 28.6 bits (64), Expect = 0.60
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 9/43 (20%)
Query: 4 CEGLAYVNTKYNVFPDDLPDIEFIFTAVSLASDGGVSLRQEMG 46
C+G A+V D +IEF A+ G +LR E G
Sbjct: 39 CKGFAFV---------DFEEIEFATNALKGKHLNGRALRVEYG 72
>gnl|CDD|178530 PLN02942, PLN02942, dihydropyrimidinase.
Length = 486
Score = 30.2 bits (68), Expect = 0.96
Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 6/48 (12%)
Query: 177 AVVDPQLKVYGVDNLRVVDASIIPVIPGG---HT-VAVVYMIAEKASD 220
V P LKV D++RV+DA+ V+PGG HT +A+ +M E D
Sbjct: 33 VAVAPNLKV--PDDVRVIDATGKFVMPGGIDPHTHLAMPFMGTETIDD 78
>gnl|CDD|217064 pfam02487, CLN3, CLN3 protein. This is a family of proteins from
the CLN3 gene. A missense mutation of glutamic acid (E)
to lysine (K) at position 295 in the human protein has
been implicated in Juvenile neuronal ceroid
lipofuscinosis (Batten disease).
Length = 409
Score = 29.0 bits (65), Expect = 2.4
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 6 GLAYVNTKYNVFPDDLPDI-EFIFTAVSLASDGGVSLRQEMGITDH 50
G +YVNT +N+ + PD+ EF A S++ GV+L + + H
Sbjct: 357 GASYVNTFHNIHKEVDPDVREFAMGAASISDSLGVNLAALLALPLH 402
>gnl|CDD|143651 cd07935, RHD-n_NFkB1, N-terminal sub-domain of the Rel homology
domain (RHD) of nuclear factor of kappa B1 (NF-kappa
B1). Proteins containing the Rel homology domain (RHD)
are metazoan transcription factors. The RHD is composed
of two structural sub-domains; this model characterizes
the N-terminal RHD sub-domain of the NF-kappa B1 family
of transcription factors, a class I member of the
NF-kappa B family. In class I NF-kappa Bs, the RHD
domain co-occurs with C-terminal ankyrin repeats.
NF-kappa B1 is commonly referred to as p105 or p50
(proteolytically processed form). NF-kappa B proteins
are part of a protein complex that acts as a
transcription factor, which is responsible for
regulating a host of cellular responses to a variety of
stimuli. This complex tightly regulates the expression
of a large number of genes, and is involved in processes
such as adaptive and innate immunity, stress response,
inflammation, cell adhesion, proliferation and
apoptosis. The cytosolic NF-kappa B complex is activated
via phosphorylation of the ankyrin-repeat containing
inhibitory protein I-kappa B, which dissociates from the
complex and exposes the nuclear localization signal of
the heterodimer (NF-kappa B and REL). NF-kappa B1 is
involved in the canonical NF-kappa B signaling pathway
which is activated by many agonists and is essential in
immune and inflammatory responses, as well as cell
survival. p105 is involved in its own specific NF-kappa
B signaling pathway which is also implicated in immune
and inflammatory responses. p105 may also act as an
I-kappa B due to its C-terminal ankyrin repeats. It is
also involved in mitogen-activated protein kinase (MAPK)
signaling as its degradation leads to the activation of
TPL-2, a MAPK kinase kinase which activates ERK
pathways.
Length = 202
Score = 28.3 bits (63), Expect = 2.8
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 20 DLPDIEFIFTAVSLASDGGVSLRQEMGITDHLYNS 54
DL + +FTA S GG + R E ++D +Y+S
Sbjct: 167 DLSVVRLMFTAFLPDSTGGFTRRLEPVVSDAIYDS 201
>gnl|CDD|143293 cd05885, Ig2_Necl-4, Second immunoglobulin (Ig)-like domain of
nectin-like molecule-4 (Necl-4, also known as cell
adhesion molecule 4 (CADM4)). Ig2_Necl-4: second
immunoglobulin (Ig)-like domain of nectin-like
molecule-4 (Necl-4, also known as cell adhesion
molecule 4 (CADM4)). Nectin-like molecules have similar
domain structures to those of nectins. At least five
nectin-like molecules have been identified
(Necl-1-Necl-5). These have an extracellular region
containing three Ig-like domains, one transmembrane
region, and one cytoplasmic region. Ig domains are
likely to participate in ligand binding and
recognition. Necl-4 is expressed on Schwann cells, and
plays a key part in initiating peripheral nervous
system (PNS) myelination. In injured peripheral nerve
cells, the mRNA signal for both Necl-4 and Necl-5 was
observed to be elevated. Necl-4 participates in
cell-cell adhesion and is proposed to play a role in
tumor suppression.
Length = 80
Score = 26.9 bits (59), Expect = 3.1
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 38 GVSLRQEMGITDHLYNSVYSSVDRKDSWSI 67
GV +QE G T + N++ VDRKD +I
Sbjct: 28 GVISQQENGKTVSVSNTIRFPVDRKDDGAI 57
>gnl|CDD|128502 smart00206, NTR, Tissue inhibitor of metalloproteinase family.
Form complexes with metalloproteinases, such as
collagenases, and irreversibly inactivate them.
Length = 172
Score = 27.8 bits (62), Expect = 3.4
Identities = 14/40 (35%), Positives = 17/40 (42%), Gaps = 5/40 (12%)
Query: 18 PDDLPDIEFIFTAVSLASDGGVSLR----QEMGITDHLYN 53
D L DI FI+T S S G L +E I L +
Sbjct: 50 FDKLGDIRFIYTPAS-ESLCGYKLESQNKEEYLIAGRLED 88
>gnl|CDD|184593 PRK14258, PRK14258, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 261
Score = 28.1 bits (62), Expect = 3.8
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 9/53 (16%)
Query: 91 PLIHANFFNDTRDLDVIVEGIKMAIELSKTKAFQSIGSTLHKAPIPGCSQYTF 143
P I N + D I+EG+ M I SK A IG + GC + TF
Sbjct: 6 PAIKVNNLSFYYDTQKILEGVSMEIYQSKVTAI--IGPS-------GCGKSTF 49
>gnl|CDD|131515 TIGR02462, pyranose_ox, pyranose oxidase. Pyranose oxidase (also
called glucose 2-oxidase) converts D-glucose and
molecular oxygen to 2-dehydro-D-glucose and hydrogen
peroxide. Peroxide production is believed to be
important to the wood rot fungi in which this enzyme is
found for lignin degradation.
Length = 544
Score = 27.5 bits (61), Expect = 6.0
Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 1/64 (1%)
Query: 162 HQCGTCKMGPRWDSSAVVDPQLKVYGVDNLRVVDASIIPVIPGGHTVAVVYMIAEKASDM 221
H GT ++G + + V + KV+ NL V IP G + A K+++
Sbjct: 480 HLAGTTRIGFD-EQTTVANTDSKVHNFKNLYVGGNGNIPTAFGANPTLTSMCYAIKSAEY 538
Query: 222 IKKT 225
I
Sbjct: 539 IINN 542
>gnl|CDD|226199 COG3673, COG3673, Uncharacterized conserved protein [Function
unknown].
Length = 423
Score = 27.2 bits (60), Expect = 7.1
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 2/46 (4%)
Query: 62 KDSWSIWPMILYPRSRGKVLLKDSHPLTPPLIHANFF--NDTRDLD 105
D ++ M+L +R V L + L P + N TR D
Sbjct: 253 VDDTTLTDMVLSKSARHAVALDERRKLFPLTLWDNIDALGRTRQFD 298
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 0.137 0.429
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,660,500
Number of extensions: 1053488
Number of successful extensions: 799
Number of sequences better than 10.0: 1
Number of HSP's gapped: 793
Number of HSP's successfully gapped: 18
Length of query: 230
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 136
Effective length of database: 6,768,326
Effective search space: 920492336
Effective search space used: 920492336
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 (25.9 bits)