RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5351
(65 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 31.7 bits (73), Expect = 0.003
Identities = 10/14 (71%), Positives = 13/14 (92%)
Query: 2 VEVWFQNRRTKWRK 15
V+VWFQNRR KW++
Sbjct: 44 VKVWFQNRRAKWKR 57
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved
in the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 28.7 bits (65), Expect = 0.041
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 2 VEVWFQNRRTKWRKKH 17
V++WFQNRR K ++
Sbjct: 44 VKIWFQNRRAKLKRSE 59
>gnl|CDD|240285 PTZ00135, PTZ00135, 60S acidic ribosomal protein P0; Provisional.
Length = 310
Score = 30.0 bits (68), Expect = 0.047
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 18 AAEMATAKRKQDQVEESEEEEEDD 41
AA A A EE EEEE+D
Sbjct: 281 AAAAAAAAAAAAPAEEEEEEEDDM 304
Score = 28.1 bits (63), Expect = 0.23
Identities = 12/24 (50%), Positives = 12/24 (50%)
Query: 18 AAEMATAKRKQDQVEESEEEEEDD 41
AA A A E EEEEEDD
Sbjct: 280 AAAAAAAAAAAAAPAEEEEEEEDD 303
Score = 27.7 bits (62), Expect = 0.28
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 18 AAEMATAKRKQDQVEESEEEEEDD 41
AA A A EEEEE+D
Sbjct: 279 AAAAAAAAAAAAAAPAEEEEEEED 302
Score = 25.7 bits (57), Expect = 1.4
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 17 HAAEMATAKRKQDQVEESEEEEEDD 41
AA A A +EEEEE++
Sbjct: 277 AAAAAAAAAAAAAAAAPAEEEEEEE 301
Score = 25.0 bits (55), Expect = 3.4
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 18 AAEMATAKRKQDQVEESEEEEEDDY 42
AA A A EE EEE++ +
Sbjct: 282 AAAAAAAAAAAPAEEEEEEEDDMGF 306
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 27.2 bits (61), Expect = 0.17
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 2 VEVWFQNRRTKWR 14
V+VWFQNRR KW+
Sbjct: 45 VKVWFQNRRAKWK 57
>gnl|CDD|223903 COG0833, LysP, Amino acid transporters [Amino acid transport and
metabolism].
Length = 541
Score = 28.0 bits (63), Expect = 0.22
Identities = 10/34 (29%), Positives = 21/34 (61%)
Query: 6 FQNRRTKWRKKHAAEMATAKRKQDQVEESEEEEE 39
+ TK+ + ++ T +R+ D++EE E+EE+
Sbjct: 498 LYKKTTKFVRLEEIDLDTGRREYDELEEQEDEEK 531
>gnl|CDD|100111 cd05833, Ribosomal_P2, Ribosomal protein P2. This subfamily
represents the eukaryotic large ribosomal protein P2.
Eukaryotic P1 and P2 are functionally equivalent to the
bacterial protein L7/L12, but are not homologous to
L7/L12. P2 is located in the L12 stalk, with proteins
P1, P0, L11, and 28S rRNA. P1 and P2 are the only
proteins in the ribosome to occur as multimers, always
appearing as sets of heterodimers. Recent data indicate
that eukaryotes have four copies (two heterodimers),
while most archaeal species contain six copies of L12p
(three homodimers). Bacteria may have four or six copies
of L7/L12 (two or three homodimers) depending on the
species. Experiments using S. cerevisiae P1 and P2
indicate that P1 proteins are positioned more internally
with limited reactivity in the C-terminal domains, while
P2 proteins seem to be more externally located and are
more likely to interact with other cellular components.
In lower eukaryotes, P1 and P2 are further subdivided
into P1A, P1B, P2A, and P2B, which form P1A/P2B and
P1B/P2A heterodimers. Some plants have a third
P-protein, called P3, which is not homologous to P1 and
P2. In humans, P1 and P2 are strongly autoimmunogenic.
They play a significant role in the etiology and
pathogenesis of systemic lupus erythema (SLE). In
addition, the ribosome-inactivating protein
trichosanthin (TCS) interacts with human P0, P1, and P2,
with its primary binding site in the C-terminal region
of P2. TCS inactivates the ribosome by depurinating a
specific adenine in the sarcin-ricin loop of 28S rRNA.
Length = 109
Score = 26.8 bits (60), Expect = 0.43
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 18 AAEMATAKRKQDQVEESEEEEEDD 41
AA A A +K+++ EESEEE +DD
Sbjct: 79 AAAAAAAAKKEEKKEESEEESDDD 102
>gnl|CDD|179150 PRK00876, nadE, NAD synthetase; Reviewed.
Length = 326
Score = 27.2 bits (61), Expect = 0.51
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 43 RHSDNAAKRLRRELAAHCGVQ 63
R S + RL RE+A H GV+
Sbjct: 70 RDSSPESLRLGREVAEHLGVE 90
>gnl|CDD|100109 cd05831, Ribosomal_P1, Ribosomal protein P1. This subfamily
represents the eukaryotic large ribosomal protein P1.
Eukaryotic P1 and P2 are functionally equivalent to the
bacterial protein L7/L12, but are not homologous to
L7/L12. P1 is located in the L12 stalk, with proteins
P2, P0, L11, and 28S rRNA. P1 and P2 are the only
proteins in the ribosome to occur as multimers, always
appearing as sets of heterodimers. Recent data indicate
that eukaryotes have four copies (two heterodimers),
while most archaeal species contain six copies of L12p
(three homodimers) and bacteria may have four or six
copies (two or three homodimers), depending on the
species. Experiments using S. cerevisiae P1 and P2
indicate that P1 proteins are positioned more
internally with limited reactivity in the C-terminal
domains, while P2 proteins seem to be more externally
located and are more likely to interact with other
cellular components. In lower eukaryotes, P1 and P2 are
further subdivided into P1A, P1B, P2A, and P2B, which
form P1A/P2B and P1B/P2A heterodimers. Some plant
species have a third P-protein, called P3, which is not
homologous to P1 and P2. In humans, P1 and P2 are
strongly autoimmunogenic. They play a significant role
in the etiology and pathogenesis of systemic lupus
erythema (SLE). In addition, the ribosome-inactivating
protein trichosanthin (TCS) interacts with human P0,
P1, and P2, with its primary binding site located in
the C-terminal region of P2. TCS inactivates the
ribosome by depurinating a specific adenine in the
sarcin-ricin loop of 28S rRNA.
Length = 103
Score = 26.5 bits (59), Expect = 0.53
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 18 AAEMATAKRKQDQVEESEEEEEDD 41
AA A +K+++ EE EEE +DD
Sbjct: 74 AAAAAAEAKKEEKKEEEEEESDDD 97
>gnl|CDD|215973 pfam00527, E7, E7 protein, Early protein.
Length = 92
Score = 25.7 bits (57), Expect = 1.2
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 30 QVEESEEEEEDDYRHSDNAAKRL 52
Q+++SEEEEED+ A++
Sbjct: 26 QLDDSEEEEEDEEDRGQPPAQQP 48
>gnl|CDD|178597 PLN03026, PLN03026, histidinol-phosphate aminotransferase;
Provisional.
Length = 380
Score = 26.2 bits (58), Expect = 1.2
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 42 YRHSDNAAKRLRRELAAHCGVQ 63
Y + D ++RLR LA G++
Sbjct: 81 YVYPDPESRRLRAALAEDSGLE 102
>gnl|CDD|173589 PTZ00398, PTZ00398, phosphoenolpyruvate carboxylase; Provisional.
Length = 974
Score = 26.3 bits (58), Expect = 1.3
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 18 AAEMATAKRKQDQVEESEEEEEDDYRHS-DNAAKRLRR 54
AE A R++ E S + + + S N + L +
Sbjct: 127 YAEWAHRIRRRRAFERSFTDNDRIFTESLKNTIEMLLQ 164
>gnl|CDD|165587 PHA03343, PHA03343, US22 family homolog; Provisional.
Length = 578
Score = 26.1 bits (57), Expect = 1.3
Identities = 11/31 (35%), Positives = 13/31 (41%)
Query: 9 RRTKWRKKHAAEMATAKRKQDQVEESEEEEE 39
R +K E A A E+ EEEEE
Sbjct: 95 ERPFRKKGPGGETAAAAAAAAAAEKGEEEEE 125
>gnl|CDD|215562 PLN03078, PLN03078, Putative tRNA pseudouridine synthase;
Provisional.
Length = 513
Score = 26.0 bits (57), Expect = 1.6
Identities = 11/27 (40%), Positives = 20/27 (74%)
Query: 14 RKKHAAEMATAKRKQDQVEESEEEEED 40
R K + EM++++ +++ E SEE+EED
Sbjct: 265 RAKSSKEMSSSESEENHGEISEEDEED 291
>gnl|CDD|235440 PRK05387, PRK05387, histidinol-phosphate aminotransferase;
Provisional.
Length = 353
Score = 25.5 bits (57), Expect = 1.8
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 35 EEEEEDDYR-HSDNAAKRLRRELAAHCGVQ 63
DD R + D A LR+ +AA+ G+
Sbjct: 47 RAALGDDLRLYPDPNADALRQAIAAYYGLD 76
>gnl|CDD|204792 pfam11947, DUF3464, Protein of unknown function (DUF3464). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 137 to
196 amino acids in length.
Length = 149
Score = 25.4 bits (56), Expect = 1.8
Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 6 FQNRR-TKWRKKHAAEMATAKRKQDQVEESEEEEEDDYRHSDNAAKRLRRELAAHCGV 62
F+ +R K K + A AK K Q + + + + R+ R +A G+
Sbjct: 10 FEPKRSRKKGVKALRKAAVAKSKDKQKKPKSKRAASESGIPKVVSNRMARRVAFFSGI 67
>gnl|CDD|178993 PRK00378, PRK00378, nucleoid-associated protein NdpA; Validated.
Length = 334
Score = 25.6 bits (57), Expect = 1.9
Identities = 12/30 (40%), Positives = 13/30 (43%)
Query: 28 QDQVEESEEEEEDDYRHSDNAAKRLRRELA 57
+ E E E D S A RLR ELA
Sbjct: 64 AQALREYREGELDFLAFSRAATGRLRDELA 93
>gnl|CDD|235672 PRK06012, flhA, flagellar biosynthesis protein FlhA; Validated.
Length = 697
Score = 25.5 bits (57), Expect = 2.1
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 9 RRTKWRKKHAAEMATAKRKQDQVEESEEEEEDDYRHSD 46
R + R+K AAE+A + ++++ E EEE DD D
Sbjct: 324 YRLRKREKKAAELAAEEAEEEEAAEPEEESWDDVLPVD 361
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 25.1 bits (55), Expect = 2.3
Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 2 VEVWFQNRRTKWRKKHAAEMATAKRKQDQVEESEEEEEDDYRHSDN 47
V++WFQN+R K +KK + ++ ++ EE++ +
Sbjct: 95 VQIWFQNKRAKEKKKRSGKV----EQRPGEEEADLAKIGSLSTGQI 136
>gnl|CDD|233290 TIGR01141, hisC, histidinol-phosphate aminotransferase.
Alternate names: histidinol-phosphate transaminase;
imidazole acetol-phosphate transaminase
Histidinol-phosphate aminotransferase is a
pyridoxal-phosphate dependent enzyme [Amino acid
biosynthesis, Histidine family].
Length = 346
Score = 25.3 bits (56), Expect = 2.4
Identities = 9/34 (26%), Positives = 15/34 (44%)
Query: 31 VEESEEEEEDDYRHSDNAAKRLRRELAAHCGVQN 64
E E + +R+ D L++ LA + GV
Sbjct: 38 KEALRAEADKLHRYPDPDPAELKQALADYYGVDP 71
>gnl|CDD|184829 PRK14807, PRK14807, histidinol-phosphate aminotransferase;
Provisional.
Length = 351
Score = 25.2 bits (55), Expect = 2.9
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 43 RHSDNAAKRLRRELAAHCGV 62
+ D A++LR ELA +C V
Sbjct: 55 IYPDPTAEKLREELARYCSV 74
>gnl|CDD|179920 PRK05054, PRK05054, exoribonuclease II; Provisional.
Length = 644
Score = 24.8 bits (55), Expect = 2.9
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 6 FQNRRTKWRKKHA 18
F R++WRK+HA
Sbjct: 344 FCLARSEWRKQHA 356
>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase
component YidC; Validated.
Length = 429
Score = 25.2 bits (55), Expect = 3.0
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 3/59 (5%)
Query: 3 EVWFQNRRTKWRKKHAAEMATAKRKQDQVEESEEEEE-DDYRHSDNAAK--RLRRELAA 58
E+ +N K + A A++K+ + E E + + AA R R AA
Sbjct: 324 ELHAENAEIKKTRTAEKNEAKARKKEIAQKRRAAEREINREARQERAAAMARARARRAA 382
>gnl|CDD|179559 PRK03321, PRK03321, putative aminotransferase; Provisional.
Length = 352
Score = 24.9 bits (55), Expect = 3.1
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 43 RHSDNAAKRLRRELAAHCGV 62
R+ D A LR LA H GV
Sbjct: 53 RYPDMGAVELRAALAEHLGV 72
>gnl|CDD|223080 COG0001, HemL, Glutamate-1-semialdehyde aminotransferase [Coenzyme
metabolism].
Length = 432
Score = 24.5 bits (54), Expect = 3.9
Identities = 8/25 (32%), Positives = 9/25 (36%)
Query: 36 EEEEDDYRHSDNAAKRLRRELAAHC 60
EE Y D +RL L A
Sbjct: 319 MTEEGVYERLDALGERLAEGLRAAA 343
>gnl|CDD|233358 TIGR01327, PGDH, D-3-phosphoglycerate dehydrogenase. This model
represents a long form of D-3-phosphoglycerate
dehydrogenase, the serA gene of one pathway of serine
biosynthesis. Shorter forms, scoring between trusted and
noise cutoff, include SerA from E. coli [Amino acid
biosynthesis, Serine family].
Length = 525
Score = 24.6 bits (54), Expect = 4.6
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 22 ATAKRKQDQVEESEEEEEDDYRHS 45
A AK + VEES+ E DY++
Sbjct: 388 AVAKERGITVEESKSESSPDYKNY 411
>gnl|CDD|165706 PLN00138, PLN00138, large subunit ribosomal protein LP2;
Provisional.
Length = 113
Score = 24.2 bits (52), Expect = 4.7
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 18 AAEMATAKRKQDQVEESEEEEED 40
AA A +K+++VEE EE ++D
Sbjct: 84 AAAPAAEAKKEEKVEEKEESDDD 106
>gnl|CDD|165442 PHA03171, PHA03171, UL37 tegument protein; Provisional.
Length = 499
Score = 24.3 bits (52), Expect = 5.1
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 10/59 (16%)
Query: 7 QNRRTKWRKKHA---AEMATAKRKQDQVE-------ESEEEEEDDYRHSDNAAKRLRRE 55
Q RR + +++H E + +R +D E EEE++D D A+ E
Sbjct: 48 QQRRHRLQRQHGVIDGENSETERPRDLTAALFAEAGEEAEEEDNDRECPDTEAEEEDEE 106
>gnl|CDD|216484 pfam01411, tRNA-synt_2c, tRNA synthetases class II (A). Other tRNA
synthetase sub-families are too dissimilar to be
included. This family includes only alanyl-tRNA
synthetases.
Length = 551
Score = 24.1 bits (53), Expect = 5.3
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 17 HAAEMATA----KRKQDQVEESEEEEEDDYRHSDNAAKRLRRELAAH 59
EM A K K+D ++E E EE+ + + RL L
Sbjct: 329 VIEEMGDAYPELKEKEDTIQEILELEEERFAKTLERGLRLLERLIKS 375
>gnl|CDD|226249 COG3726, AhpA, Uncharacterized membrane protein affecting hemolysin
expression [General function prediction only].
Length = 214
Score = 24.0 bits (52), Expect = 6.3
Identities = 11/33 (33%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 6 FQNRRTKWRKKHAAEMATAKRKQDQVEESEEEE 38
Q RRT+W++ +A K++ +ESE++E
Sbjct: 184 LQGRRTRWQQTPNLLLAVKPVKEE--DESEKKE 214
>gnl|CDD|222948 PHA02941, PHA02941, hypothetical protein; Provisional.
Length = 356
Score = 23.8 bits (51), Expect = 7.4
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 20 EMATAKRKQDQVEESEEEEEDD 41
EM ++Q + EE+EEEEE+D
Sbjct: 330 EMLEETQEQQEEEENEEEEEND 351
>gnl|CDD|185582 PTZ00373, PTZ00373, 60S Acidic ribosomal protein P2; Provisional.
Length = 112
Score = 23.7 bits (51), Expect = 8.2
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 22 ATAKRKQDQVEESEEEEEDD 41
A A+ K+++ +E EEEEEDD
Sbjct: 86 AKAEAKKEEKKEEEEEEEDD 105
>gnl|CDD|232931 TIGR00344, alaS, alanine--tRNA ligase. The model describes
alanine--tRNA ligase. This enzyme catalyzes the reaction
(tRNAala + L-alanine + ATP = L-alanyl-tRNAala +
pyrophosphate + AMP) [Protein synthesis, tRNA
aminoacylation].
Length = 851
Score = 23.9 bits (52), Expect = 8.9
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 25 KRKQDQVEESEEEEEDDYRHSDNAAKRLRRELAAHCG 61
K KQ+ VE+ E EE+ + + RL +L G
Sbjct: 343 KEKQEFVEQILELEEERFAKTLERGLRLFEKLLKKLG 379
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 23.7 bits (52), Expect = 9.5
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 18 AAEMATAKRKQDQVEESEEEEEDD 41
A A A ++++ EE EEEEE
Sbjct: 294 AQAQAAAAEEEEEEEEEEEEEEPS 317
>gnl|CDD|185105 PRK15183, PRK15183, Vi polysaccharide biosynthesis protein TviA;
Provisional.
Length = 143
Score = 23.5 bits (50), Expect = 9.8
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 32 EESEEEEEDDYRHSDNAAKRLRRELAAHCGVQ 63
E EE +D + +S + R R+ELA GV+
Sbjct: 98 ESGMEELQDRFMNSSSTMYRWRKELAVKFGVR 129
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 23.6 bits (51), Expect = 9.9
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 28 QDQVEESEEEEEDD 41
D+ EE EEEEE++
Sbjct: 389 DDEEEEDEEEEEEE 402
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
0.313 0.122 0.357
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,282,036
Number of extensions: 236310
Number of successful extensions: 816
Number of sequences better than 10.0: 1
Number of HSP's gapped: 791
Number of HSP's successfully gapped: 98
Length of query: 65
Length of database: 10,937,602
Length adjustment: 36
Effective length of query: 29
Effective length of database: 9,340,858
Effective search space: 270884882
Effective search space used: 270884882
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 (22.0 bits)
S2: 53 (24.1 bits)