RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11025
(535 letters)
>gnl|CDD|220380 pfam09751, Es2, Nuclear protein Es2. This entry is of a family of
proteins of approximately 500 residues with alternating
regions of low complexity and conservation where the
domain similarities are strong. Apart from a predicted
coiled-coil domain, no other known functional domains
have been characterized. The protein appears to be
expressed in the nucleus and particularly highly in the
pons sub-region of the brain. The protein is clearly
necessary for normal development of the nervous system.
Length = 390
Score = 168 bits (428), Expect = 3e-47
Identities = 92/277 (33%), Positives = 134/277 (48%), Gaps = 30/277 (10%)
Query: 47 EIIERDFFPDLEKLHAQNDFLDAMELNDVQKLRELYAKYSNSTPYVDRCESSPATFETPE 106
+IIERDFFPDL KL AQN++LDA+E D +++RE+ K ++ E +P F TP
Sbjct: 17 KIIERDFFPDLLKLRAQNEYLDAVESGDKERIREIQRKLTSLMG--KSTEVTPGRFRTPS 74
Query: 107 ---HFTSLEEAGSADHEASVRSQG---------SCSSKKSTSGKYQ-----SLNEFLSTH 149
+ GS G S + + + SL+EF + +
Sbjct: 75 SSSGLRNTPNPGSPSTSGDHTPMGGDTPRSVVSSETEGEEEGKGKKKDDNLSLDEFQAKY 134
Query: 150 TSEDNQSFEDIIEHAKKKHRIKYPWLYCGEDEAPENTSRFLELPSMQEQIDQAK-----D 204
TSEDN SFE+++E +K R K+ WLY E E ++ L LPS++EQ +
Sbjct: 135 TSEDNASFEELLEKQNEKRREKHAWLYEAEKEHNRKIAQRLALPSIEEQTKLGIKSLAIE 194
Query: 205 KDRDRRIQTWKFVNKNSAMYTPDGVELTKDEQIEMARNRMSINHSGTRLH--VNPFDEQQ 262
+ + TWK+ KNS M+ PDGVE + E I+ A I H TR NPF +
Sbjct: 195 DNPAANLDTWKYKAKNSLMFMPDGVEDSPLETIQAAARAPEIVHKNTRFSQEYNPFPKSP 254
Query: 263 SKEALHDLAKTQAISSLSGKIGVDGKEITLNSTPRNR 299
SK A+ + +A + ++G DGK + TPR
Sbjct: 255 SKSAIQEAIAGKARAKDG-EVGEDGK---GSETPRVN 287
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 36.0 bits (83), Expect = 0.057
Identities = 29/116 (25%), Positives = 36/116 (31%), Gaps = 37/116 (31%)
Query: 125 SQGSCSSKKSTSGKYQSLNEFLSTHTSE---DNQSFEDIIEHAKKKHRIKYPW------- 174
GSCS + +EF + Q ED+ H RI PW
Sbjct: 2033 QNGSCSIVDQRFLYEKYESEFEEGESEGALDPQQIEEDLFNHIVWAPRIWRPWGFLFDCI 2092
Query: 175 --------------------LYCGEDEAPENTSRFLELPSMQEQIDQAKDKDRDRR 210
+Y EDE EN S FL+ +MQ Q RDR
Sbjct: 2093 ERPNELGFPYWARSFRGKRIIYDEEDELQENDSEFLQSGTMQYQT-------RDRS 2141
>gnl|CDD|132282 TIGR03238, dnd_assoc_3, DNA phosphorothioation-dependent
restriction protein DptF. A DNA sulfur modification
(phosphorothioation) system, dnd (degradation during
electrophoresis), is sparsely and sporadically
distributed among the bacteria. This protein is one
member of a three-gene restriction enzyme cassette that
depends on DNA phosphorothioation [DNA metabolism,
Restriction/modification].
Length = 504
Score = 31.4 bits (71), Expect = 1.4
Identities = 22/110 (20%), Positives = 31/110 (28%), Gaps = 33/110 (30%)
Query: 112 EEAGSADHEASVRSQGSCSSKKSTSGKYQSLN----------------EFLS------TH 149
+E G S G SS +T + ++ F T
Sbjct: 107 QEFGYTALNKFKDSIGLFSSSVTTCDHFDFISFEDYPKFELTEEGPQSTFFLKLLNKITA 166
Query: 150 TSEDNQSFEDIIEHAKKKHRIKYPWLYCGEDEAPENTSRFLELPSMQEQI 199
E N + E KK R Y FL+ P +Q+QI
Sbjct: 167 KEEGNPFYLAYQEDVNKKVRTMVQENY-----------EFLQEPYVQKQI 205
>gnl|CDD|225461 COG2909, MalT, ATP-dependent transcriptional regulator
[Transcription].
Length = 894
Score = 31.2 bits (71), Expect = 1.5
Identities = 36/262 (13%), Positives = 71/262 (27%), Gaps = 62/262 (23%)
Query: 301 AASTVLEKGAKSLEELKPDAALTLYSRAAD----VAHGEDNYKQAAEYISRNREAASTVL 356
A T++ + L+ L + VA + ++A +
Sbjct: 433 EAETLIARLEHFLKAPMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLA-------- 484
Query: 357 EKGAKSLEELKSDAALT---LYSRAADVAHGEDNYKQAAEYISRAARM------------ 401
L +L A + S + AH QA + +A +M
Sbjct: 485 ------LVQLPEAAYRSRIVALSVLGEAAHIRGELTQALALMQQAEQMARQHDVYHLALW 538
Query: 402 --CVRVK-----------EFDKAADLIRQEIGYHQESEHLLAIGRLAVALVLVQLARGDT 448
+ + E +KA +LIR++ + L R + ++L
Sbjct: 539 SLLQQSEILEAQGQVARAEQEKAFNLIREQHLEQKPRHEFLVRIRAQLLRAWLRLD-LAE 597
Query: 449 VAAEKAFK---EWGNCCEAPERCESGSSSFSFSLG------------KAGYHQESEHLLA 493
A + + S + F G + H+
Sbjct: 598 AEARLGIEVGSVYTPQPLLSRLALSMLAELEFLRGDLDKALAQLDELERLLLNGQYHVDY 657
Query: 494 IGRLAVALVLVQLARGDTVAAE 515
+ +++ LA+GD A
Sbjct: 658 LAAAYKVKLILWLAQGDKELAA 679
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 31.2 bits (71), Expect = 1.8
Identities = 25/111 (22%), Positives = 44/111 (39%), Gaps = 4/111 (3%)
Query: 312 SLEELKPDAALTLYSRAADVAHGEDNYKQAA--EYISRNREAASTVLEKGAKSLEELKSD 369
LE D + + ED + E + RE ++ + +++EE K +
Sbjct: 479 ELEAELEDLEEEVEEVEERLERAEDLVEAEDRIERLEERREDLEELIAERRETIEE-KRE 537
Query: 370 AALTLYSRAADV-AHGEDNYKQAAEYISRAARMCVRVKEFDKAADLIRQEI 419
A L RAA++ A E+ + AAE A V E + +++ I
Sbjct: 538 RAEELRERAAELEAEAEEKREAAAEAEEEAEEAREEVAELNSKLAELKERI 588
>gnl|CDD|220036 pfam08837, DUF1810, Protein of unknown function (DUF1810). This is
a family of uncharacterized proteins. The structure of
one of the members in this family has been solved and it
adopts a mainly alpha helical structure.
Length = 139
Score = 29.4 bits (67), Expect = 2.3
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 7/42 (16%)
Query: 296 PRNREAASTVLEKGAKSLEEL--KPDAA-----LTLYSRAAD 330
PR RE +L +S EE+ PD +TL++ AA
Sbjct: 72 PRLRECTELLLAVEGRSAEEIFGSPDDLKLRSSMTLFAAAAP 113
>gnl|CDD|223861 COG0790, COG0790, FOG: TPR repeat, SEL1 subfamily [General function
prediction only].
Length = 292
Score = 29.6 bits (66), Expect = 3.8
Identities = 18/93 (19%), Positives = 29/93 (31%), Gaps = 10/93 (10%)
Query: 318 PDAALTLYSRAADVAHGEDNYKQ-AAEYISRNREAASTVLEKGAKSLEELKSDAALTLYS 376
AL Y +AA + + E + A V K+L + AA
Sbjct: 129 LVKALKYYEKAAKLGNVEAALAMYRLGLAYLSGLQALAVAYDDKKALYLYR-KAAELGNP 187
Query: 377 RAADV-----AHGED---NYKQAAEYISRAARM 401
A + G + K+A + +AA
Sbjct: 188 DAQLLLGRMYEKGLGVPRDLKKAFRWYKKAAEQ 220
>gnl|CDD|227285 COG4949, COG4949, Uncharacterized membrane-anchored protein
conserved in bacteria [Function unknown].
Length = 424
Score = 29.9 bits (67), Expect = 4.0
Identities = 33/133 (24%), Positives = 52/133 (39%), Gaps = 30/133 (22%)
Query: 349 REAASTVLEKGAKSLEELKSDAALTLYSRAADVAHGE--------------DNYKQAAEY 394
R + +L + + EL++ AAL+LY A A+ ++ E+
Sbjct: 236 RRDSQALLAELTRLAAELEARAALSLYRFGASRAYDGIVLERLEALRETPVPGHETMGEF 295
Query: 395 ISR----AARMCVRVKE--------FDKAADLIRQEIGYHQESEH--LLAI--GRLAVAL 438
+ R A R C V+E +A L+R I E ++ LL R + L
Sbjct: 296 LERRLAPAMRTCQSVEERQANLSRKLARATALLRTWIDVELERQNQELLNSMDARAQLQL 355
Query: 439 VLVQLARGDTVAA 451
L Q G +VAA
Sbjct: 356 RLQQTVEGLSVAA 368
>gnl|CDD|227301 COG4966, PilW, Tfp pilus assembly protein PilW [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 318
Score = 29.4 bits (66), Expect = 5.3
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 373 TLYSRAADVAHGEDNYKQAAEYISRAARM 401
LY+ AD A ++N + A E I+R RM
Sbjct: 43 QLYTTLADRASLQENGRFALELITRDLRM 71
>gnl|CDD|240167 cd05144, RIO2_C, RIO kinase family; RIO2, C-terminal catalytic
domain. The RIO kinase catalytic domain family is part
of a larger superfamily, that includes the catalytic
domains of other kinases such as the typical
serine/threonine/tyrosine protein kinases (PKs),
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase (PI3K). RIO kinases are
atypical protein serine kinases containing a kinase
catalytic signature, but otherwise show very little
sequence similarity to typical PKs. Serine kinases
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine residues in protein substrates. The RIO
catalytic domain is truncated compared to the catalytic
domains of typical PKs, with deletions of the loops
responsible for substrate binding. RIO2 is present in
archaea and eukaryotes. It contains an N-terminal winged
helix (wHTH) domain and a C-terminal RIO kinase
catalytic domain. The wHTH domain is primarily seen in
DNA-binding proteins, although some wHTH domains may be
involved in RNA recognition. RIO2 is essential for
survival and is necessary for rRNA cleavage during 40S
ribosomal subunit maturation. The biological substrates
of RIO2 are still unknown.
Length = 198
Score = 28.6 bits (65), Expect = 6.4
Identities = 13/24 (54%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 266 ALHDLAKTQAISSLSGKIGVDGKE 289
ALH L K + SL +IGV GKE
Sbjct: 6 ALHTLVKRGVVESLGNQIGV-GKE 28
>gnl|CDD|234467 TIGR04094, adjacent_YSIRK, YSIRK-targeted surface antigen
transcriptional regulator. Bacteria whose genomes
encode only one protein with the YSIRK variant form of
signal peptide (TIGR01168) were examined for conserved
genes near that one tagged protein. This protein is
found adjacent to at various classes of repetitive or
low-complexity YSIRK proteins (whether unique in genome
or not), in a range of species (Enterococcus faecalis
X98, Ruminococcus torques, Coprobacillus sp. D7,
Lysinibacillus fusiformis ZC1, Streptococcus equi subsp.
equi 4047, etc). The affliated YSIRK proteins include
Streptococcal protective antigen (see PMID:19865839) and
proteins with the Rib/alpha/Esp surface antigen repeat
(see TIGR02331). The last quarter of this protein has an
AraC family helix-turn-helix (HTH)transcriptional
regulator domain.
Length = 383
Score = 28.9 bits (65), Expect = 6.6
Identities = 14/46 (30%), Positives = 28/46 (60%)
Query: 43 QKIAEIIERDFFPDLEKLHAQNDFLDAMELNDVQKLRELYAKYSNS 88
+K E+ +++F + H +N L+ ++ D+Q+L+EL + SNS
Sbjct: 157 EKSEELSKQNFTSETYLFHYENQILELVKKGDIQQLKELVFQLSNS 202
>gnl|CDD|226404 COG3887, COG3887, Predicted signaling protein consisting of a
modified GGDEF domain and a DHH domain [Signal
transduction mechanisms].
Length = 655
Score = 28.8 bits (65), Expect = 7.8
Identities = 29/137 (21%), Positives = 49/137 (35%), Gaps = 43/137 (31%)
Query: 266 ALHDLAKTQAISSLSGKIGVDGKEITLNSTPRNREAASTVLEKGAKSLEE---LKPDAAL 322
L+ +A + L+G I VD K TL + R +AAS + +GA ++ LK D
Sbjct: 480 KKQKLSPIEATALLAG-IIVDTKNFTLRTGSRTFDAASYLRSRGADTILIQKFLKTD--- 535
Query: 323 TLYSRAADVAHGEDNYKQAAEYISRNREAASTVLEKGAKSLEELKSDAALTLYSRAADVA 382
+ Y + +E I ++ K A+ A
Sbjct: 536 ------------FEEYIKRSELI---------------ENARVYKDGIAI---------A 559
Query: 383 HGEDNYKQAAEYISRAA 399
G + + I++AA
Sbjct: 560 TGSKDEAYSNVIIAQAA 576
>gnl|CDD|218819 pfam05942, PaREP1, Archaeal PaREP1/PaREP8 family. This family
consists of several archaeal PaREP1 and PaREP8 proteins
the function of this family is unknown.
Length = 114
Score = 27.2 bits (61), Expect = 9.0
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 6/32 (18%)
Query: 433 RLAVALVLVQLA-----RGDTV-AAEKAFKEW 458
RL A ++ A +GD AAEKAF+ W
Sbjct: 2 RLEEAEKELEEAEELLEKGDLRQAAEKAFQAW 33
Score = 27.2 bits (61), Expect = 9.0
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 6/32 (18%)
Query: 496 RLAVALVLVQLA-----RGDTV-AAEKAFKEW 521
RL A ++ A +GD AAEKAF+ W
Sbjct: 2 RLEEAEKELEEAEELLEKGDLRQAAEKAFQAW 33
>gnl|CDD|238798 cd01557, BCAT_beta_family, BCAT_beta_family: Branched-chain
aminotransferase catalyses the transamination of the
branched-chain amino acids leusine, isoleucine and
valine to their respective alpha-keto acids,
alpha-ketoisocaproate, alpha-keto-beta-methylvalerate
and alpha-ketoisovalerate. The enzyme requires pyridoxal
5'-phosphate (PLP) as a cofactor to catalyze the
reaction. It has been found that mammals have two foms
of the enzyme - mitochondrial and cytosolic forms while
bacteria contain only one form of the enzyme. The
mitochondrial form plays a significant role in skeletal
muscle glutamine and alanine synthesis and in interorgan
nitrogen metabolism.Members of this subgroup are widely
distributed in all three forms of life.
Length = 279
Score = 28.3 bits (64), Expect = 9.5
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 7/46 (15%)
Query: 232 TKDEQIEMAR-----NRMSINHSGTRLHVNPFDEQQSKEALHDLAK 272
T D +I + R R+ N S RL + PF ++ +A+ +L K
Sbjct: 24 TPDGKIVLFRPDENAERL--NRSARRLGLPPFSVEEFIDAIKELVK 67
>gnl|CDD|233223 TIGR00990, 3a0801s09, mitochondrial precursor proteins import
receptor (72 kDa mitochondrial outermembrane protein)
(mitochondrial import receptor for the ADP/ATP carrier)
(translocase of outermembrane tom70). [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 615
Score = 28.8 bits (64), Expect = 9.8
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 363 LEELKSDAALTLYSRAADVAHGEDNYKQAAEYISRAARMCVRVKE 407
L++ D AL L+ RAA++A E QA Y + A R ++V+E
Sbjct: 553 LQQGDVDEALKLFERAAELARTEGELVQAISY-AEATRTQIQVQE 596
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
0.312 0.127 0.357
Gapped
Lambda K H
0.267 0.0670 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,735,043
Number of extensions: 2591702
Number of successful extensions: 2381
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2377
Number of HSP's successfully gapped: 47
Length of query: 535
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 433
Effective length of database: 6,413,494
Effective search space: 2777042902
Effective search space used: 2777042902
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 61 (27.4 bits)