RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16139
(466 letters)
>gnl|CDD|222296 pfam13660, DUF4147, Domain of unknown function (DUF4147). This
domain is frequently found at the N-terminus of proteins
carrying the glycerate kinase-like domain MOFRL,
pfam05161.
Length = 227
Score = 251 bits (644), Expect = 1e-81
Identities = 95/240 (39%), Positives = 137/240 (57%), Gaps = 18/240 (7%)
Query: 7 IYEAAVSAVNGQNLIQANVHLEKNKLIIRDQTVLIKNNVYLIGFGKAVLGMAVEIEAMFR 66
I++AAV+A + + ++ + L+ L + ++G GKA MA E
Sbjct: 6 IFDAAVAAADPERAVRRALPLDPAGLSKYG-------RIVVVGAGKAAAAMAAAAEEAL- 57
Query: 67 PQRLKGILSVPFGSVGILKPQFNKNSEIEIRECARNNLPDEASCQNTQLIQNFVKHCTED 126
RL+G++ +G L IE+ E A + +PDEA + + I V TED
Sbjct: 58 GDRLEGLVVTRYGHAVPLPR-------IEVLE-AGHPVPDEAGVRAARRILELVSGLTED 109
Query: 127 DVVLVLISGGGSACLSSPKSPLSLEDKLKTIKLLVQSGANIKELNKVRKKLSDVKGGQLA 186
D+VLVLISGGGSA L +P ++LEDK + L+ SGA+I+E+N VRK LS +KGG+LA
Sbjct: 110 DLVLVLISGGGSALLPAPAEGITLEDKQAVTRALLASGADIQEINAVRKHLSRIKGGRLA 169
Query: 187 EIVYPATLVSLIISDIVGDPLQDIASGPTVLNEDLWSDARDIVIKYGLQNKVSKSVMTIL 246
PA +VSLIISD+ GD L IASGPTV + ++DA I+ +YGL+ + +SV L
Sbjct: 170 RAAAPARVVSLIISDVPGDDLSVIASGPTVPDPTTFADALAILERYGLE--LPESVRAHL 227
>gnl|CDD|225254 COG2379, GckA, Putative glycerate kinase [Carbohydrate transport
and metabolism].
Length = 422
Score = 226 bits (579), Expect = 2e-69
Identities = 116/306 (37%), Positives = 168/306 (54%), Gaps = 25/306 (8%)
Query: 7 IYEAAVSAVNGQNLIQANVHLEKNKLIIRDQTVLIKNNVYLIGFGKAVLGMAVEIEAMFR 66
+++AAV+A + + A++ L + +T +IG GKA MA E ++
Sbjct: 13 LFDAAVAAADPYRALAAHL----PVLPPKGRT-------IVIGAGKASAEMARAFEEHWK 61
Query: 67 PQRLKGILSVPFGSVGILKPQFNKNSEIEIRECARNNLPDEASCQNTQLIQNFVKHCTED 126
L G++ P+G G IE+ E A + +PDEAS + ++ + V TED
Sbjct: 62 GP-LAGVVVTPYGYGGPCP-------RIEVIE-AGHPVPDEASLKASRRLLELVSGLTED 112
Query: 127 DVVLVLISGGGSACLSSPKSPLSLEDKLKTIKLLVQSGANIKELNKVRKKLSDVKGGQLA 186
D+V+VLISGGGSA L P ++LED + + L++SGA I E+N VRK LS VKGG+LA
Sbjct: 113 DLVIVLISGGGSALLELPAEGITLEDLIAVNRALLKSGAPISEMNTVRKHLSRVKGGRLA 172
Query: 187 EIVYPATLVSLIISDIVGDPLQDIASGPTVLNEDLWSDARDIVIKYGLQNKVSKSVMTIL 246
PA +VSLIISD+ GD IASGPTV + DA ++ +YG+ + +SV L
Sbjct: 173 AAAKPAKVVSLIISDVPGDDPSVIASGPTVPDPTTREDALAVLERYGIA--LPESVRAHL 230
Query: 247 ---SHETPHQDTKYFENVHNHIIGNNRAALLGAKWKAESLGFQTVILSSDIEGLGDDICR 303
ETP + F NV N II +NR +L A +A +LGF+ VIL IEG ++ R
Sbjct: 231 ESERAETPKPGDERFANVENRIIASNRLSLEAAASEARALGFKAVILGDTIEGEAREVGR 290
Query: 304 GYVDLV 309
+ +
Sbjct: 291 VHASIA 296
>gnl|CDD|238116 cd00194, UBA, Ubiquitin Associated domain. The UBA domain is a
commonly occurring sequence motif in some members of the
ubiquitination pathway, UV excision repair proteins, and
certain protein kinases. Although its specific role is
so far unknown, it has been suggested that UBA domains
are involved in conferring protein target specificity.
The domain, a compact three helix bundle, has a
conserved GFP-loop and the proline is thought to be
critical for binding. The UBA domain is distinct from
the conserved three helical domain seen in the
N-terminus of EF-TS and eukaryotic NAC proteins.
Length = 38
Score = 30.9 bits (71), Expect = 0.081
Identities = 11/27 (40%), Positives = 12/27 (44%), Gaps = 1/27 (3%)
Query: 436 MGFTDENEVRRALRKAANEPNHACLLL 462
MGF E R+ALR N A L
Sbjct: 11 MGF-SREEARKALRATNNNVERAVEWL 36
>gnl|CDD|221489 pfam12252, SidE, Dot/Icm substrate protein. This family of proteins
is found in bacteria. Proteins in this family are
typically between 397 and 1543 amino acids in length.
This family is the SidE protein in the Dot/Icm pathway of
Legionella pneumophila bacteria. There is little
literature describing the family.
Length = 1443
Score = 34.5 bits (79), Expect = 0.14
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 305 YVDLVAWIDQLRKQRTIQVGKDKNNIKEQDMEQ---NLQQVANQATIDELTKKMKVKNNK 361
+ D A I+ LR +R + G K+ + D+++ NLQ V NQ+ + L ++ N+
Sbjct: 1213 FFDTTADIEVLRNERIKKHGSSKDPLDLSDLDKLSGNLQGV-NQSLVSILITTIRSSLNQ 1271
Query: 362 KKKKSFDYKSPHCNQFLIQIE 382
K K+F+ + Q +
Sbjct: 1272 MKPKTFEMQEKEIQQNFELLA 1292
>gnl|CDD|198164 smart01096, CPSase_L_D3, Carbamoyl-phosphate synthetase large
chain, oligomerisation domain. Carbamoyl-phosphate
synthase catalyses the ATP-dependent synthesis of
carbamyl-phosphate from glutamine or ammonia and
bicarbonate. The carbamoyl-phosphate synthase (CPS)
enzyme in prokaryotes is a heterodimer of a small and
large chain.
Length = 124
Score = 31.3 bits (72), Expect = 0.36
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 19/61 (31%)
Query: 407 FQDIV---KKL-GLDKEELDLDIAENYLVKIKKMGFTD----------ENEVRRALRKAA 452
++IV K+L +ELD D+ L K K++GF+D E EV RALRK
Sbjct: 43 IKEIVELEKELKKGGLDELDADL----LRKAKRLGFSDRQIAKLLGVTEAEV-RALRKEL 97
Query: 453 N 453
Sbjct: 98 G 98
>gnl|CDD|197551 smart00165, UBA, Ubiquitin associated domain. Present in Rad23,
SNF1-like kinases. The newly-found UBA in p62 is known
to bind ubiquitin.
Length = 37
Score = 28.6 bits (65), Expect = 0.63
Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 436 MGFTDENEVRRALRKAANEPNHA 458
MGF+ E E +ALR A A
Sbjct: 11 MGFSRE-EALKALRAANGNVERA 32
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 378
Score = 31.8 bits (72), Expect = 0.84
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 427 ENYLVKIKKMGFTDENEVRRALRKAANEPNHAC-LLLVGEP 466
E + +I +MG+ + EV RALR A N P+ A LL G P
Sbjct: 157 ETTIEEIMEMGY-EREEVERALRAAFNNPDRAVEYLLTGIP 196
>gnl|CDD|235393 PRK05294, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1066
Score = 32.0 bits (74), Expect = 0.90
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 18/60 (30%)
Query: 407 FQDIV---KKLGLDKEELDLDIAENYLVKIKKMGFTD----------ENEVRRALRKAAN 453
++IV ++L + LD + L + K++GF+D E+EV R LRKA
Sbjct: 463 IEEIVELEEELKENGLPLDAE----LLREAKRLGFSDARIAKLLGVTEDEV-RKLRKALG 517
>gnl|CDD|237654 PRK14278, PRK14278, chaperone protein DnaJ; Provisional.
Length = 378
Score = 31.2 bits (71), Expect = 1.1
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 206 PLQDIASGPTVLNEDLWSDARDIVIKYGLQNKVSKSVMTILSHETPHQDTKYFENVHNHI 265
P+ D A G TV E + +I I G Q SV+T+ PH + ++H H+
Sbjct: 272 PMVDAALGTTVTVEAILDGPSEITIPPGTQ---PGSVITLRGRGMPHLRSGGRGDLHAHV 328
>gnl|CDD|237506 PRK13785, PRK13785, adenylosuccinate synthetase; Provisional.
Length = 454
Score = 30.9 bits (70), Expect = 1.5
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 202 IVGDPLQDIASGPTVLNEDLWSDARDIVIKY 232
IVG L D G V DL+ DA D+V++Y
Sbjct: 5 IVGSQLGDEGKGGVV---DLYGDAADVVVRY 32
>gnl|CDD|234423 TIGR03972, rSAM_TYW1, wyosine biosynthesis protein TYW1. Members
of this protein family are the archaeal protein TWY1, a
radical SAM protein that catalyzes the second step in
creating the wye-bases, wyosine and derivatives such as
wybutosine, for tRNA base modification [Protein
synthesis, tRNA and rRNA base modification].
Length = 297
Score = 30.7 bits (70), Expect = 1.6
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 414 LGLDKEELDLD---IAENYLVKIKK--MGFTDENEVRRALRKAANEPNHACLLLVGEP 466
+G + +E D I E + +K G+ +V R + A EP H + L GEP
Sbjct: 73 VGEEWDETKDDPEDIVEESIKAQRKLLSGYKGNPKVDREKWEEALEPKHVAISLSGEP 130
>gnl|CDD|129467 TIGR00370, TIGR00370, sensor histidine kinase inhibitor, KipI
family. [Hypothetical proteins, Conserved].
Length = 202
Score = 29.8 bits (67), Expect = 1.9
Identities = 18/46 (39%), Positives = 23/46 (50%), Gaps = 6/46 (13%)
Query: 45 VYLIGF--GKAVLG-MAVEIEAMFRPQRLKGILSVPFGSVGILKPQ 87
VY++GF G LG + + P+R SVP GSVGI Q
Sbjct: 118 VYMLGFQPGFPYLGGLPERLHT---PRRASPRPSVPAGSVGIGGLQ 160
>gnl|CDD|180831 PRK07088, PRK07088, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 764
Score = 30.5 bits (69), Expect = 2.4
Identities = 14/56 (25%), Positives = 24/56 (42%)
Query: 314 QLRKQRTIQVGKDKNNIKEQDMEQNLQQVANQATIDELTKKMKVKNNKKKKKSFDY 369
Q ++ IQ KD N + N Q VA + + +L K+ ++ + DY
Sbjct: 62 QTAIEKVIQNSKDNNGNNTKKTNPNWQYVAARLYVFDLYKEARINRHYNSFGYGDY 117
>gnl|CDD|201355 pfam00627, UBA, UBA/TS-N domain. This small domain is composed of
three alpha helices. This family includes the previously
defined UBA and TS-N domains. The UBA-domain (ubiquitin
associated domain) is a novel sequence motif found in
several proteins having connections to ubiquitin and the
ubiquitination pathway. The structure of the UBA domain
consists of a compact three helix bundle. This domain is
found at the N terminus of EF-TS hence the name TS-N.
The structure of EF-TS is known and this domain is
implicated in its interaction with EF-TU. The domain has
been found in non EF-TS proteins such as alpha-NAC and
MJ0280.
Length = 37
Score = 26.6 bits (60), Expect = 2.8
Identities = 8/27 (29%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 432 KIKKMGFTDENEVRRALRKAANEPNHA 458
++++MGF E ++ALR A
Sbjct: 8 QLREMGF-SREEAKKALRATNGNVERA 33
>gnl|CDD|107029 PHA01351, PHA01351, putative minor structural protein.
Length = 1070
Score = 29.9 bits (67), Expect = 3.3
Identities = 14/28 (50%), Positives = 21/28 (75%)
Query: 414 LGLDKEELDLDIAENYLVKIKKMGFTDE 441
L +K ++DLD A++YL ++KK G TDE
Sbjct: 1028 LLFEKHKIDLDTAQSYLQQLKKYGLTDE 1055
>gnl|CDD|218293 pfam04855, SNF5, SNF5 / SMARCB1 / INI1. SNF5 is a component of the
yeast SWI/SNF complex, which is an ATP-dependent
nucleosome-remodelling complex that regulates the
transcription of a subset of yeast genes. SNF5 is a key
component of all SWI/SNF-class complexes characterized
so far. This family consists of the conserved region of
SNF5, including a direct repeat motif. SNF5 is essential
for the assembly promoter targeting and chromatin
remodelling activity of the SWI-SNF complex. SNF5 is
also known as SMARCB1, for SWI/SNF-related,
matrix-associated, actin-dependent regulator of
chromatin, subfamily b, member 1, and also INI1 for
integrase interactor 1. Loss-of function mutations in
SNF5 are thought to contribute to oncogenesis in
malignant rhabdoid tumours (MRTs).
Length = 228
Score = 29.2 bits (66), Expect = 3.4
Identities = 20/70 (28%), Positives = 29/70 (41%), Gaps = 7/70 (10%)
Query: 34 IRDQTVLIKNNVYLIGF---GKAVLGMAVEIEAMFRPQRLKGILSVPFGSVGILKPQFNK 90
IR+Q + K ++ +G G + EI A F P L G P P+ +
Sbjct: 153 IREQLLKFKKSLCELGHLFDGSPIED--DEIRAAFLPGPLAGTRRDPDQLADEWTPRLEE 210
Query: 91 NS--EIEIRE 98
+ EIE RE
Sbjct: 211 LTDAEIERRE 220
>gnl|CDD|240430 PTZ00473, PTZ00473, Plasmodium Vir superfamily; Provisional.
Length = 420
Score = 29.4 bits (66), Expect = 4.4
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 357 VKNNKKKKKSFDYKSPHCNQFLIQIELNSVFVALIEMSAKLVRFNDASVVFQDIVK 412
V+ K++ FD S H F E + +++ K + + + +DI+K
Sbjct: 88 VEWFYNKQEKFDVFSNHLESFNYDFEYL-IQKNILKNFNKFKKLYENNYELEDIMK 142
>gnl|CDD|222979 PHA03093, PHA03093, EEV glycoprotein; Provisional.
Length = 185
Score = 28.6 bits (64), Expect = 4.6
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 9/66 (13%)
Query: 353 KKMKVKNNKKKKKSFDYKSPHCNQFLIQIELNSVFVALIEMSAKL-VRFNDASVVFQDIV 411
K+K K NKKK K C I+I + ++LI ++A L ++ N + +
Sbjct: 21 DKLKKKKNKKKVK--------CIGICIRISIIISILSLIAITATLALQLNKCKSANESAI 72
Query: 412 KKLGLD 417
LD
Sbjct: 73 TDAALD 78
>gnl|CDD|204184 pfam09265, Cytokin-bind, Cytokinin dehydrogenase 1, FAD and
cytokinin binding. Members of this family adopt an
alpha+beta sandwich structure with an antiparallel
beta-sheet, in a ferredoxin-like fold. They are
predominantly found in plant cytokinin dehydrogenase 1,
where they are capable of binding both FAD and cytokinin
substrates. The substrate displays a 'plug-into-socket'
binding mode that seals the catalytic site and precisely
positions the carbon atom undergoing oxidation in close
contact with the reactive locus of the flavin.
Length = 280
Score = 28.8 bits (65), Expect = 5.0
Identities = 18/75 (24%), Positives = 24/75 (32%), Gaps = 8/75 (10%)
Query: 208 QDIASGPT---VLNEDLWSDARDIVIKYGLQNKVSKSVMTILSHETP--HQDTKYFENVH 262
SGP +N W D VI V V + S D + EN +
Sbjct: 166 NTNNSGPILVYPMNRSKWDDRMSAVIPDE---DVFYLVGLLRSAVPSAGPSDLEALENQN 222
Query: 263 NHIIGNNRAALLGAK 277
I+ A +G K
Sbjct: 223 RRILEFCEGAGIGYK 237
>gnl|CDD|224960 COG2049, DUR1, Allophanate hydrolase subunit 1 [Amino acid
transport and metabolism].
Length = 223
Score = 28.7 bits (65), Expect = 5.8
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 45 VYLIGF--GKAVL-GMAVEIEAMFRPQRLKGILSVPFGSVGI 83
VY++GF G L G+ E + P+R + S+P GSVGI
Sbjct: 125 VYMLGFAPGFPYLGGLD---ERLATPRRAEPRTSIPAGSVGI 163
>gnl|CDD|151462 pfam11015, DUF2853, Protein of unknown function (DUF2853). This
bacterial family of proteins has no known function.
Length = 102
Score = 26.8 bits (60), Expect = 8.4
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 16/56 (28%)
Query: 410 IVKKLGL-------------DKEELDLDIAENYLVKIKKMGFTDENEVRRALRKAA 452
+ K LG D +EL+ + EN+L IKK+G DE E+ A+ K
Sbjct: 22 VTKGLGPSIYNRDSSTVSASDPKELE-RVKENFL--IKKLGLADEAELDAAINKVC 74
>gnl|CDD|179586 PRK03512, PRK03512, thiamine-phosphate pyrophosphorylase;
Provisional.
Length = 211
Score = 27.7 bits (62), Expect = 9.6
Identities = 12/39 (30%), Positives = 24/39 (61%), Gaps = 6/39 (15%)
Query: 306 VDLVAWIDQLRKQ--RTIQVG-KDKNNIKEQDMEQNLQQ 341
VD V WI++L RT+Q+ KD+ +++++E ++
Sbjct: 19 VDSVQWIERLLDAGVRTLQLRIKDR---RDEEVEADVVA 54
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
0.317 0.134 0.374
Gapped
Lambda K H
0.267 0.0865 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,393,974
Number of extensions: 2326845
Number of successful extensions: 2635
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2627
Number of HSP's successfully gapped: 49
Length of query: 466
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 366
Effective length of database: 6,502,202
Effective search space: 2379805932
Effective search space used: 2379805932
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: 61 (27.0 bits)