RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5701
(125 letters)
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 106 bits (267), Expect = 4e-28
Identities = 52/104 (50%), Positives = 70/104 (67%), Gaps = 2/104 (1%)
Query: 8 IAAETHGHVGADLASLCSEAALQQIREKMDL--IDLEDDQIDAEILASLAVTMENFRYAM 65
+A THG VGADLA+L EAA+ +R + I+ E ++I AE+L L VTM++F A+
Sbjct: 373 LAEVTHGFVGADLAALAKEAAMAALRRFIREGKINFEAEEIPAEVLKELKVTMKDFMEAL 432
Query: 66 GKSSPSALRETIVEVPNITWEDIGGLEGVKRELQELVQPSLWSP 109
PSA+RE +VEVPN+ W DIGGLE VK+EL+E V+ L P
Sbjct: 433 KMVEPSAIREVLVEVPNVRWSDIGGLEEVKQELREAVEWPLKHP 476
Score = 48.0 bits (114), Expect = 2e-07
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 8 IAAETHGHVGADLASLCSEAALQQIREKMDLIDLED-DQIDAEILASLAVTMENFRYAMG 66
+A T G+ GAD+ ++C EAA+ +RE + E + + E L L V M +F A+
Sbjct: 649 LAEMTEGYTGADIEAVCREAAMAALRESIGSPAKEKLEVGEEEFLKDLKVEMRHFLEALK 708
Query: 67 KSSPSALRETI 77
K PS +E +
Sbjct: 709 KVKPSVSKEDM 719
Score = 36.4 bits (84), Expect = 0.002
Identities = 16/41 (39%), Positives = 27/41 (65%), Gaps = 1/41 (2%)
Query: 70 PSALRETI-VEVPNITWEDIGGLEGVKRELQELVQPSLWSP 109
+RE I +VP +T+EDIGGL+ K +++E+V+ + P
Sbjct: 161 EKPVREEIERKVPKVTYEDIGGLKEAKEKIREMVELPMKHP 201
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 71.0 bits (174), Expect = 1e-15
Identities = 35/95 (36%), Positives = 52/95 (54%), Gaps = 13/95 (13%)
Query: 8 IAAETHGHVGADLASLCSEAALQQIREKMDLIDLEDDQIDAEILASLAVTMENFRYAMGK 67
+AA T G GADL +L EAAL+++R +D + + VT ++F A+ K
Sbjct: 177 LAARTVGKSGADLGALAKEAALRELRRAID-----------LVGEYIGVTEDDFEEALKK 225
Query: 68 SSPSALRETIVEVPNITWEDIGGLEGVKRELQELV 102
PS R + E ++T +DIGGLE K EL+E +
Sbjct: 226 VLPS--RGVLFEDEDVTLDDIGGLEEAKEELKEAI 258
Score = 31.7 bits (72), Expect = 0.067
Identities = 23/57 (40%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 8 IAAETHGHVGADLASLCSEAALQQIREKMDLIDLEDDQIDA--EILASLAVTMENFR 62
+A T G+ GAD+A+L EAAL+ +RE DD +DA +I S VT E ++
Sbjct: 439 LAEITEGYSGADIAALVREAALEALREARRREVTLDDFLDALKKIKPS--VTYEEWK 493
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 39.8 bits (94), Expect = 1e-04
Identities = 17/33 (51%), Positives = 24/33 (72%)
Query: 77 IVEVPNITWEDIGGLEGVKRELQELVQPSLWSP 109
++E PN+T+EDIGGLE RE++E V+ L P
Sbjct: 122 VIESPNVTYEDIGGLEEQIREVREAVELPLKKP 154
Score = 39.0 bits (92), Expect = 2e-04
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 8 IAAETHGHVGADLASLCSEAALQQIREKMDLIDLED 43
+A T G GADL ++C+EA + IR+ + +ED
Sbjct: 329 LAELTEGASGADLKAICTEAGMFAIRDDRTEVTMED 364
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 37.6 bits (88), Expect = 7e-04
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 66 GKSSPSALRETIVEVPNITWEDIGGLEGVKRELQELVQPSLWSP 109
+ P + E P++T+EDIGGL+ +E++E+V+ L +P
Sbjct: 131 PEVDPRVSVMEVEEKPDVTYEDIGGLDEQIQEIREVVELPLKNP 174
Score = 33.8 bits (78), Expect = 0.016
Identities = 16/36 (44%), Positives = 24/36 (66%)
Query: 8 IAAETHGHVGADLASLCSEAALQQIREKMDLIDLED 43
+A T G GADL ++C+EA + IRE+ D + +ED
Sbjct: 349 LARLTEGFSGADLKAICTEAGMFAIRERRDEVTMED 384
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 36.3 bits (84), Expect = 0.002
Identities = 16/36 (44%), Positives = 24/36 (66%)
Query: 8 IAAETHGHVGADLASLCSEAALQQIREKMDLIDLED 43
IA T G GADL ++C+EA + IRE+ D + ++D
Sbjct: 320 IAKMTEGASGADLKAICTEAGMFAIREERDYVTMDD 355
Score = 34.8 bits (80), Expect = 0.005
Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 66 GKSSPSALRETIVEVPNITWEDIGGLEGVKRELQELVQPSLWSP 109
P + E PN+++EDIGGLE RE++E V+ L P
Sbjct: 102 TSKDPLVKGMEVEERPNVSYEDIGGLEEQIREIREAVELPLKHP 145
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 35.7 bits (83), Expect = 0.003
Identities = 16/36 (44%), Positives = 21/36 (58%)
Query: 8 IAAETHGHVGADLASLCSEAALQQIREKMDLIDLED 43
+A T G GADLA+L +EAAL R+ I + D
Sbjct: 252 VARRTPGFSGADLANLLNEAALLAARKNKTEITMND 287
Score = 29.6 bits (67), Expect = 0.43
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 65 MGKSSPSALRETIVEVPNITWEDIGGLEGVKRELQELV 102
GKS L E E P +T++D+ G++ K EL E+V
Sbjct: 37 FGKSKAKLLNE---EKPKVTFKDVAGIDEAKEELMEIV 71
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 34.2 bits (79), Expect = 0.011
Identities = 17/36 (47%), Positives = 20/36 (55%)
Query: 8 IAAETHGHVGADLASLCSEAALQQIREKMDLIDLED 43
IA T G GADLA+L +EAAL R I + D
Sbjct: 347 IARGTPGFSGADLANLLNEAALLAARRNKKEITMRD 382
Score = 25.7 bits (57), Expect = 7.6
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 69 SPSALRETIVEVPNITWEDIGGLEGVKRELQELVQPSLWSPSK 111
S + + + +T+ D+ G++ K EL ELV L +P K
Sbjct: 133 GKSKAKLYLEDQVKVTFADVAGVDEAKEELSELVDF-LKNPKK 174
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 32.4 bits (74), Expect = 0.042
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 11/47 (23%)
Query: 79 EVPNITWEDIGGLEGVKRELQE-----LVQPSLWS------PSKVLM 114
E P++T+ DIGGL+ K+E++E L P L+ P VL+
Sbjct: 138 EKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLL 184
Score = 27.4 bits (61), Expect = 2.5
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 17 GADLASLCSEAALQQIRE 34
AD+A++C EA +Q +R+
Sbjct: 352 AADIAAICQEAGMQAVRK 369
>gnl|CDD|182885 PRK10991, fucI, L-fucose isomerase; Provisional.
Length = 588
Score = 30.4 bits (69), Expect = 0.21
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 9 AAETHGHVGADLASLCS 25
T+GHVGADL +L S
Sbjct: 527 GVLTYGHVGADLITLAS 543
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 30.4 bits (69), Expect = 0.23
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 83 ITWEDIGGLEGVKRELQELV 102
IT+ DI G+E K E +E+V
Sbjct: 180 ITFRDIAGIEEAKEEFEEVV 199
Score = 29.6 bits (67), Expect = 0.42
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 8 IAAETHGHVGADLASLCSEAALQQIREK-----MDLIDLEDDQIDAEI 50
IA T G GADLA+L +EAA+ R K M ID D++ A +
Sbjct: 380 IARRTPGFSGADLANLLNEAAILTARRKKATITMKEIDTAIDRVIAGL 427
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 30.1 bits (68), Expect = 0.28
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 79 EVPNITWEDIGGL 91
EVP++T+ DIGGL
Sbjct: 175 EVPDVTYADIGGL 187
>gnl|CDD|180601 PRK06520, PRK06520,
5-methyltetrahydropteroyltriglutamate--homocysteine
methyltransferase; Provisional.
Length = 368
Score = 29.7 bits (67), Expect = 0.30
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 13/55 (23%)
Query: 21 ASLCSEAALQQIREKMDLIDLEDDQIDAEIL--------ASLAVTME----NFRY 63
A LCS+ QQIRE+ D D E +I A +L A L + + NFR
Sbjct: 195 AYLCSDDQRQQIRERGDDPD-ELARIYARVLNKALAGKPADLTIGLHVCRGNFRS 248
>gnl|CDD|219562 pfam07766, LETM1, LETM1-like protein. Members of this family are
inner mitochondrial membrane proteins which play a role
in potassium and hydrogen ion exchange. Deletion of
LETM1 is thought to be involved in the development of
Wolf-Hirschhorn syndrome in humans.
Length = 268
Score = 29.2 bits (66), Expect = 0.54
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 12/55 (21%)
Query: 20 LASLCSEAALQ----------QIREKMDLIDLEDDQIDAEILASLAVTMENFRYA 64
L +LC L Q+REK+ I +D I E + SL+ E +YA
Sbjct: 176 LVALCKYLELHPFGTDNMLRFQLREKLRSIKADDRAIAREGVHSLSP--EELQYA 228
>gnl|CDD|239618 cd03556, L-fucose_isomerase, L-fucose isomerase (FucIase); FucIase
converts L-fucose, an aldohexose, to its ketose form,
which prepares it for aldol cleavage (similar to the
isomerization of glucose during glycolysis). L-fucose
(or 6-deoxy-L-galactose) is found in blood group
determinants as well as in various oligo- and
polysaccharides, and glycosides in mammals, bacteria and
plants.
Length = 584
Score = 29.0 bits (65), Expect = 0.57
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 10 AETHGHVGADLASLCS 25
A THGH+GADL +L S
Sbjct: 524 AITHGHIGADLITLAS 539
>gnl|CDD|235394 PRK05297, PRK05297, phosphoribosylformylglycinamidine synthase;
Provisional.
Length = 1290
Score = 29.0 bits (66), Expect = 0.61
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 14/59 (23%)
Query: 51 LASLAVTMENFR------YAMGKSSPSAL-------RETIVE-VPNITWEDIGGLEGVK 95
+A AVT ++ AMG+ +P AL R + E + NI IG L+ +K
Sbjct: 672 VADCAVTAASYDGYAGEAMAMGERTPVALLDAAASARMAVGEALTNIAAAPIGDLKRIK 730
>gnl|CDD|216326 pfam01142, TruD, tRNA pseudouridine synthase D (TruD). TruD is
responsible for synthesis of pseudouridine from
uracil-13 in transfer RNAs. The structure of TruD
reveals an overall V-shaped molecule which contains an
RNA-binding cleft.
Length = 336
Score = 27.2 bits (61), Expect = 2.4
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 42 EDDQIDAEILASLAVTMENFRYAMGK-SSPSALRETIVEVPNITWE 86
E +++ EILA +T E+F + K R ++ N++W+
Sbjct: 267 EAGELEQEILAEEGITPEDFE-LLPKLGLKGERRPLRLKPENLSWQ 311
>gnl|CDD|233819 TIGR02307, RNA_lig_RNL2, RNA ligase, Rnl2 family. Members of this
family ligate (seal breaks in) RNA. Members so far
include phage proteins that can counteract a host
defense of cleavage of specific tRNA molecules,
trypanosome ligases involved in RNA editing, but no
prokaryotic host proteins [Mobile and extrachromosomal
element functions, Prophage functions, Transcription,
RNA processing].
Length = 325
Score = 27.1 bits (60), Expect = 2.5
Identities = 23/115 (20%), Positives = 39/115 (33%), Gaps = 24/115 (20%)
Query: 14 GHVGADLASLCSEAALQQIREKMDLIDLED---DQIDAEILASLA--------------- 55
G C + + + K L + +++A L
Sbjct: 204 LRNGNRTIIKCKNSKFSEKKNKAGKPILAKVVLSEAQNKLVALLLCYVTENRLNNVLSKI 263
Query: 56 --VTMENFRYAMGKSSPSALRETIVEVPNITWEDIGGLEGVKREL----QELVQP 104
++F MG + AL+E + E P IT + +KR L QEL++P
Sbjct: 264 GTEPPKDFGMVMGLLAQDALKEFLRETPGITNTQADNRKLIKRSLVFMAQELLRP 318
>gnl|CDD|233903 TIGR02512, FeFe_hydrog_A, [FeFe] hydrogenase, group A. This model
describes iron-only hydrogenases of anaerobic and
microaerophilic bacteria and protozoa. This model is
narrower, and covers a longer stretch of sequence, than
pfam02906. This family represents a division among
families that belong to pfam02906, which also includes
proteins such as nuclear prelamin A recognition factor
in animals. Note that this family shows some
heterogeneity in terms of periplasmic, cytosolic, or
hydrogenosome location, NAD or NADP dependence, and
overal protein protein length.
Length = 374
Score = 26.9 bits (60), Expect = 3.0
Identities = 19/79 (24%), Positives = 27/79 (34%), Gaps = 27/79 (34%)
Query: 33 REKMDLIDLEDDQID---------AEILASLAVTMENFRYAMGKSSPSALRETIVEV--- 80
+D L D Q D I + ME +ALR T E+
Sbjct: 252 EAGIDFAKLPDSQFDSPFGEYSGAGAIFGATGGVME-----------AALR-TAYEIVTG 299
Query: 81 ---PNITWEDIGGLEGVKR 96
I ++ + GL+GVK
Sbjct: 300 KELELIEFKAVRGLDGVKE 318
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 26.9 bits (59), Expect = 3.9
Identities = 15/26 (57%), Positives = 17/26 (65%)
Query: 8 IAAETHGHVGADLASLCSEAALQQIR 33
IA T G GADLA+L +EAAL R
Sbjct: 349 IARGTPGFSGADLANLVNEAALFAAR 374
>gnl|CDD|130161 TIGR01089, fucI, L-fucose isomerase. This enzyme catalyzes the
first step in fucose metabolism, and has been
characterized in Escherichia coli and Bacteroides
thetaiotaomicron [Energy metabolism, Sugars].
Length = 587
Score = 26.4 bits (58), Expect = 4.6
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 12 THGHVGADLASLCS 25
T GHVGADL +L S
Sbjct: 529 TIGHVGADLITLAS 542
>gnl|CDD|143169 cd04968, Ig3_Contactin_like, Third Ig domain of contactin.
Ig3_Contactin_like: Third Ig domain of contactins.
Contactins are neural cell adhesion molecules and are
comprised of six Ig domains followed by four
fibronectin type III(FnIII) domains anchored to the
membrane by glycosylphosphatidylinositol. The first
four Ig domains form the intermolecular binding
fragment, which arranges as a compact U-shaped module
via contacts between Ig domains 1 and 4, and between Ig
domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play
a part in the neuronal processes of neurite outgrowth,
axon guidance and fasciculation, and neuronal
migration. This group also includes contactin-1 and
contactin-5. The different contactins show different
expression patterns in the central nervous system.
During development and in adulthood, contactin-2 is
transiently expressed in subsets of central and
peripheral neurons. Contactin-5 is expressed
specifically in the rat postnatal nervous system,
peaking at about 3 weeks postnatal, and a lack of
contactin-5 (NB-2) results in an impairment of neuronal
act ivity in the rat auditory system. Contactin-5 is
highly expressed in the adult human brain in the
occipital lobe and in the amygdala. Contactin-1 is
differentially expressed in tumor tissues and may,
through a RhoA mechanism, facilitate invasion and
metastasis of human lung adenocarcinoma.
Length = 88
Score = 25.1 bits (55), Expect = 7.0
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 60 NFRYAMGKSSPSALR---ETIVEVPNITWEDIGGLE 92
+R G SA ++++PNI +ED G E
Sbjct: 34 KWRKVDGSMPSSAEISMSGAVLKIPNIQFEDEGTYE 69
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 25.9 bits (57), Expect = 8.2
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 17 GADLASLCSEAALQQIREKMDLIDLED 43
GAD+ ++C+EA L +RE+ + D
Sbjct: 390 GADIKAICTEAGLLALRERRMKVTQAD 416
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 0.131 0.373
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,445,662
Number of extensions: 572069
Number of successful extensions: 619
Number of sequences better than 10.0: 1
Number of HSP's gapped: 612
Number of HSP's successfully gapped: 52
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
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: 53 (24.2 bits)