RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17621
(448 letters)
>gnl|CDD|219818 pfam08393, DHC_N2, Dynein heavy chain, N-terminal region 2.
Dyneins are described as motor proteins of eukaryotic
cells, as they can convert energy derived from the
hydrolysis of ATP to force and movement along
cytoskeletal polymers, such as microtubules. This region
is found C-terminal to the dynein heavy chain N-terminal
region 1 (pfam08385) in many members of this family. No
functions seem to have been attributed specifically to
this region.
Length = 408
Score = 214 bits (547), Expect = 4e-65
Identities = 97/307 (31%), Positives = 144/307 (46%), Gaps = 76/307 (24%)
Query: 138 LVVKKGEDRGFQ-LGDLSEMLLQLEDSCMNLQSMAGSAYIGPFLPVVQEWEKRLSVVSEV 196
+ +D G L E++ L+D+ + LQSM S Y+ PF EWEK+L+++ EV
Sbjct: 160 FELVPYKDTGTYLLKGWDEIIELLDDNLVTLQSMKASPYVKPFEEEADEWEKKLNLIQEV 219
Query: 197 LYTWIQLQRKWLYLEGVEDELKTVKRWSSDIREMPQCKALEKYLKDFKKSVALFVELKHE 256
L W+++QRKW+YLE + SSDI+ K L + K F
Sbjct: 220 LELWLKVQRKWVYLEPIFS--------SSDIK-----KQLPEESKRFSNV---------- 256
Query: 257 ALRERHWTELMKKTGVEDELKTVKRWSSDIREMPQCKALEKYLKDFKKSVALFIMWETHK 316
++ W +LMKK +K
Sbjct: 257 ---DKEWKKLMKK--------------------------------------------ANK 269
Query: 317 NPRVIEQCLVPNRLEHLEQLKDGLEACEKSLQDYLTDKRNAFPRFFFISDDELLSILGSS 376
+P V+E C +P LE LE+L + LE +KSL +YL KR+AFPRF+F+S+D+LL IL S
Sbjct: 270 DPNVLEVCNIPGLLEKLEKLNEQLEKIQKSLNEYLESKRSAFPRFYFLSNDDLLEILSQS 329
Query: 377 S-PTAIQEHIVKMFDNVQSLKMADSESPGVKTISAMISCENEVMDFRTPQLTFGEIEQWM 435
PTA+Q H+ K+F+ + SL+ + I+ MIS E E + P G +E W+
Sbjct: 330 KDPTAVQPHLKKLFEGISSLEFDEEN----NNITGMISSEGEEVPLSKPVSVEGNVEDWL 385
Query: 436 TRVLDEM 442
+ EM
Sbjct: 386 NELEKEM 392
Score = 64.1 bits (157), Expect = 4e-11
Identities = 25/91 (27%), Positives = 46/91 (50%), Gaps = 11/91 (12%)
Query: 195 EVLYTWIQLQRKWLYL-----------EGVEDELKTVKRWSSDIREMPQCKALEKYLKDF 243
++ W + +W +E LK +++ ++R+ + L+K + DF
Sbjct: 18 DLYSEWSESIEEWKNTPWSTIDPEELESEIEKFLKQLRKLPKNLRQYEVAEELKKKIDDF 77
Query: 244 KKSVALFVELKHEALRERHWTELMKKTGVED 274
KKS+ L +LK+ AL+ERHW ++ K G +D
Sbjct: 78 KKSLPLIEDLKNPALKERHWEQIFKLLGFKD 108
Score = 30.2 bits (69), Expect = 2.2
Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 9/86 (10%)
Query: 231 PQCKALEKYLKDFKK---SVALFVELKHEALRERHWTEL----MKKTGVEDELKTVKRWS 283
+ + LEK LK KK + + E E + W+ + ++ +E LK +++
Sbjct: 1 EELQELEKELKPLKKLWDLYSEWSESIEE-WKNTPWSTIDPEELESE-IEKFLKQLRKLP 58
Query: 284 SDIREMPQCKALEKYLKDFKKSVALF 309
++R+ + L+K + DFKKS+ L
Sbjct: 59 KNLRQYEVAEELKKKIDDFKKSLPLI 84
>gnl|CDD|193250 pfam12774, AAA_6, Hydrolytic ATP binding site of dynein motor
region D1. the 380 kDa motor unit of dynein belongs to
the AAA class of chaperone-like ATPases. The core of
the 380 kDa motor unit contains a concatenated chain of
six AAA modules, of which four correspond to the ATP
binding sites with P-loop signatures described
previously, and two are modules in which the P loop has
been lost in evolution. This particular family is the
D1 unit of the motor and contains the hydrolytic ATP
binding site.
Length = 231
Score = 45.8 bits (108), Expect = 1e-05
Identities = 17/28 (60%), Positives = 20/28 (71%)
Query: 35 NCGEGMDFLAFGKILSGLSQCGAWGCFD 62
NC E MD+ + G I GL+Q GAWGCFD
Sbjct: 64 NCSEQMDYKSCGNIYKGLAQTGAWGCFD 91
>gnl|CDD|218353 pfam04963, Sigma54_CBD, Sigma-54 factor, core binding domain. This
domain makes a direct interaction with the core RNA
polymerase, to form an enhancer dependent holoenzyme.
The centre of this domain contains a very weak
similarity to a helix-turn-helix motif which may
represent the other DNA binding domain.
Length = 195
Score = 29.1 bits (66), Expect = 3.5
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 9/34 (26%)
Query: 256 EALRERHWTELMKKTGVEDELKTVKRWSSDIREM 289
E L R + L + GV++E D+REM
Sbjct: 116 ELLARRDFATLKRICGVDEE---------DLREM 140
>gnl|CDD|227680 COG5391, COG5391, Phox homology (PX) domain protein [Intracellular
trafficking and secretion / General function prediction
only].
Length = 524
Score = 29.8 bits (67), Expect = 3.8
Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 331 EHLEQLKDGLEACEKSLQDYLTDKRNAFPRFFFISDDELLSILGSSSPTAIQEHIVKMFD 390
+ E+L++ L EK Q+ + +N FF + + +L IL S + + ++ +
Sbjct: 454 QDKEKLEEQLAIAEKDAQEINEELKNELKFFFSVRNSDLEKILKSVA-----DSHIEWAE 508
Query: 391 N 391
Sbjct: 509 E 509
>gnl|CDD|227652 COG5349, COG5349, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 126
Score = 28.1 bits (63), Expect = 4.0
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 34 PNCGEGMDFLAFGKILSGLSQCG 56
P CGEG F F K++ CG
Sbjct: 25 PRCGEGRLFRGFLKVVPACEACG 47
>gnl|CDD|225244 COG2369, COG2369, Uncharacterized protein, homolog of phage Mu
protein gp30 [Function unknown].
Length = 432
Score = 29.5 bits (66), Expect = 4.3
Identities = 18/73 (24%), Positives = 22/73 (30%), Gaps = 6/73 (8%)
Query: 252 ELKHEALRERHWTELMKKTGVEDELKTVKRWSSDIREM-PQCKALEKYL-KDFKKSVALF 309
E + E L K TG E K VK S + M F +A+
Sbjct: 269 EKEVEKLE---NVAKDKDTGEAREEK-VKLISKKRKSMKKGIGWDYNVGSAAFGTDMAVI 324
Query: 310 IMWETHKNPRVIE 322
KN R E
Sbjct: 325 RNLILVKNKRYQE 337
>gnl|CDD|218792 pfam05880, Fiji_64_capsid, Fijivirus 64 kDa capsid protein. This
family consists of several Fijivirus 64 kDa capsid
proteins.
Length = 559
Score = 29.4 bits (66), Expect = 4.7
Identities = 12/67 (17%), Positives = 25/67 (37%), Gaps = 4/67 (5%)
Query: 329 RLEHLEQLKDGLEACEKSLQDYLTDKRNAFPRFFFISDDELLSILGSS----SPTAIQEH 384
+ E L++L D L + S ++ + FF + LG++ S +
Sbjct: 66 KTELLKRLHDRLSTVDTSTLPNISQFKEHITSFFQNEIQPIFQTLGNNEIDPSFVGVTTF 125
Query: 385 IVKMFDN 391
+ +F
Sbjct: 126 GLSLFAT 132
>gnl|CDD|177877 PLN02233, PLN02233, ubiquinone biosynthesis methyltransferase.
Length = 261
Score = 29.1 bits (65), Expect = 4.9
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 71 TKKAIYDFGKTSKPRT----EWMLDNIGMTVLAANGVWWTAEVENVFSKIR 117
++ +I DF K+++P T EWM+DN+ + V G+ E E + S I
Sbjct: 176 SRVSILDFNKSTQPFTTSMQEWMIDNVVVPVATGYGL--AKEYEYLKSSIN 224
>gnl|CDD|233451 TIGR01531, glyc_debranch, glycogen debranching enzymye. glycogen
debranching enzyme possesses two different catalytic
activities; oligo-1,4-->1,4-glucantransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site
directed mutagenesis studies in S. cerevisiae indicate
that the transferase and glucosidase activities are
independent and located in different regions of the
polypeptide chain. Proteins in this model belong to the
larger alpha-amylase family. The model covers eukaryotic
proteins with a seed composed of human, nematode and
yeast sequences. Yeast seed sequence is well
characterized. The model is quite rigorous; either query
sequence yields large bit score or it fails to hit the
model altogether. There doesn't appear to be any middle
ground [Energy metabolism, Biosynthesis and degradation
of polysaccharides].
Length = 1464
Score = 29.4 bits (66), Expect = 5.1
Identities = 14/42 (33%), Positives = 18/42 (42%)
Query: 162 DSCMNLQSMAGSAYIGPFLPVVQEWEKRLSVVSEVLYTWIQL 203
D + L S+A + L + EWE RL V E Y I
Sbjct: 110 DKFLPLDSIALQTVLAKLLGPLSEWEPRLRVAKEKGYNMIHF 151
>gnl|CDD|215640 PLN03232, PLN03232, ABC transporter C family member; Provisional.
Length = 1495
Score = 29.2 bits (65), Expect = 6.1
Identities = 32/117 (27%), Positives = 50/117 (42%), Gaps = 16/117 (13%)
Query: 6 LRINFYFSYLKLTCSTTYKVSKWQTASRPNCGEGMDFLAFGKILSGLSQCGAWGCFDMMT 65
L I FY +YL ST+ +V + + +R + FG+ L+GLS A+ +D M
Sbjct: 1059 LLILFYAAYLYYQ-STSREVRRLDSVTRSPI-----YAQFGEALNGLSSIRAYKAYDRMA 1112
Query: 66 A--NRYWTKKAIYDFGKTSKPRTEWMLDNIGMTVLAANGVWWTAEVENVFSKIRAGN 120
+ + TS R W+ I + L +W TA F+ +R GN
Sbjct: 1113 KINGKSMDNNIRFTLANTSSNR--WL--TIRLETLGGVMIWLTA----TFAVLRNGN 1161
>gnl|CDD|180334 PRK05978, PRK05978, hypothetical protein; Provisional.
Length = 148
Score = 28.0 bits (63), Expect = 6.5
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 34 PNCGEGMDFLAFGKILSGLSQCG 56
P CGEG F AF K + + CG
Sbjct: 37 PACGEGKLFRAFLKPVDHCAACG 59
>gnl|CDD|216209 pfam00946, Mononeg_RNA_pol, Mononegavirales RNA dependent RNA
polymerase. Members of the Mononegavirales including the
Paramyxoviridae, like other non-segmented negative strand
RNA viruses, have an RNA-dependent RNA polymerase
composed of two subunits, a large protein L and a
phosphoprotein P. This is a protein family of the L
protein. The L protein confers the RNA polymerase
activity on the complex. The P protein acts as a
transcription factor.
Length = 1065
Score = 28.8 bits (65), Expect = 6.8
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 344 EKSLQDYLTDKRNAFPRFFFISDDELLSILGSSSPTAIQEHIVKMFDNVQSL 395
E+ L +L D+ PR + SS+PT ++E IV + D +++
Sbjct: 987 EEDLARFLLDREPVMPRV--------AHEIFSSTPTGVRESIVGLLDTTRTI 1030
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.9 bits (65), Expect = 7.2
Identities = 31/132 (23%), Positives = 59/132 (44%), Gaps = 13/132 (9%)
Query: 183 VQEWEKRLSVVSEVLYTWIQLQRKWLYLEGVEDELKTVKRWSSDIREMPQ--CKALEKYL 240
V+E E+RL + +++L+ LE E ELK ++ E K LE+
Sbjct: 587 VEELEERLKELEPFYNEYLELKDAEKELEREEKELKKLEEELDKAFEELAETEKRLEELR 646
Query: 241 KDFKKSVALFVELKHEALRERHWTELMK--------KTGVEDELKTVKRWSSDIREMPQC 292
K+ ++ + E ++E LRE + EL + +E + +K+ ++E +
Sbjct: 647 KELEELEKKYSEEEYEELREEY-LELSRELAGLRAELEELEKRREEIKKTLEKLKE--EL 703
Query: 293 KALEKYLKDFKK 304
+ EK K+ +K
Sbjct: 704 EEREKAKKELEK 715
>gnl|CDD|181562 PRK08840, PRK08840, replicative DNA helicase; Provisional.
Length = 464
Score = 28.4 bits (63), Expect = 8.0
Identities = 17/40 (42%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 406 KTISAMISCENEVMDFRTPQLTFG---EIEQWMTRVLDEM 442
KT AM CEN MD P L F EQ M R+L +
Sbjct: 230 KTTFAMNLCENAAMDQDKPVLIFSLEMPAEQLMMRMLASL 269
>gnl|CDD|234711 PRK00279, adk, adenylate kinase; Reviewed.
Length = 215
Score = 28.2 bits (64), Expect = 8.1
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 228 REMPQCKALEKYLKDFKKSVALFVELK--HEALRER 261
R +PQ +AL++ LK+ + +E+ E L ER
Sbjct: 88 RTIPQAEALDEMLKELGIKLDAVIEIDVPDEELVER 123
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
metabolism, Restriction/modification].
Length = 650
Score = 28.5 bits (64), Expect = 9.2
Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 323 QCLVPNRLEHLEQLKDGLEACEKSLQDYLTDKRNAF--PRFFFISD--DELLSILGS--- 375
+ + L LE LK+ +EA K+L + K NAF R I+D + L
Sbjct: 441 EAEIEELLRQLETLKEAIEALRKTLDEKTKQKINAFELERAITIADKAKKTLKEFREKLL 500
Query: 376 -SSPTAIQEHIVKMF 389
++E I K F
Sbjct: 501 ERKLQQLEEEITKSF 515
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
0.320 0.133 0.408
Gapped
Lambda K H
0.267 0.0808 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,983,126
Number of extensions: 2199311
Number of successful extensions: 1968
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1964
Number of HSP's successfully gapped: 33
Length of query: 448
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 348
Effective length of database: 6,502,202
Effective search space: 2262766296
Effective search space used: 2262766296
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: 61 (27.1 bits)