RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10239
(100 letters)
>gnl|CDD|215741 pfam00135, COesterase, Carboxylesterase family.
Length = 510
Score = 39.2 bits (92), Expect = 9e-05
Identities = 22/88 (25%), Positives = 28/88 (31%), Gaps = 5/88 (5%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATIINEYTDWERPVQHPVNIRD 60
E E + E E LS I + EYTD RD
Sbjct: 321 YVLPDPTELSELLNEDFLELLPELLPGAPE---LSRIADALKEEYTDDPDDN--SEESRD 375
Query: 61 ETLEALSDAMVVAPSVNTADLHSSARSV 88
++ LSD + V P A +SA S
Sbjct: 376 ALVDLLSDYLFVCPIRLAAARLASAGSP 403
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 36.1 bits (83), Expect = 0.001
Identities = 16/28 (57%), Positives = 27/28 (96%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRN 29
++E++EEEEEEE+++EEE+++EEEE+ N
Sbjct: 863 SEEEEEEEEEEEEEEEEEEEEEEEEEEN 890
Score = 35.0 bits (80), Expect = 0.003
Identities = 17/34 (50%), Positives = 27/34 (79%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLS 35
+ E++EEEEEEE+++EEE+++EEEE+ LS
Sbjct: 862 DSEEEEEEEEEEEEEEEEEEEEEEEEEENEEPLS 895
Score = 25.3 bits (55), Expect = 6.9
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKR 28
+E++EEEEEEE++ EE E E R
Sbjct: 877 EEEEEEEEEEEEENEEPLSLEWPETR 902
>gnl|CDD|184954 PRK14992, PRK14992, tetrathionate reductase subunit C;
Provisional.
Length = 335
Score = 33.6 bits (77), Expect = 0.007
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 39 ATIINEYTDWERPVQHPVNIRDETLEALSDAM---VVAPSVNTADLHSSAR 86
A + Y W + E AL A+ + AP TADLH +AR
Sbjct: 31 AALFACYLHWRKKDAAT-----EENRALLIAVTCAITAPLALTADLHQTAR 76
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 33.0 bits (76), Expect = 0.014
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRN 29
K +EE +EE ++K+EEKKKEE E +
Sbjct: 273 LKAAEEERQEEAQEKKEEKKKEEREAKL 300
Score = 28.8 bits (65), Expect = 0.37
Identities = 9/30 (30%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKRNM 30
+E+++EE + EKK+E++K++ E + +
Sbjct: 275 AAEEERQEEAQ-EKKEEKKKEEREAKLAKL 303
Score = 28.4 bits (64), Expect = 0.57
Identities = 11/33 (33%), Positives = 22/33 (66%), Gaps = 7/33 (21%)
Query: 3 KEKKEEEEE-------EEKKKEEEKKKEEEEKR 28
++KKEE E EE++K EEK+++++ ++
Sbjct: 290 EKKKEEREAKLAKLSPEEQRKLEEKERKKQARK 322
Score = 27.6 bits (62), Expect = 1.1
Identities = 15/39 (38%), Positives = 25/39 (64%), Gaps = 8/39 (20%)
Query: 1 MNKEKKEEEEEEEKKK-------EEEKKKEEEE-KRNMR 31
+EKKEE+++EE++ EE++K EE+E K+ R
Sbjct: 283 EAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKERKKQAR 321
Score = 26.8 bits (60), Expect = 1.9
Identities = 14/35 (40%), Positives = 26/35 (74%), Gaps = 5/35 (14%)
Query: 2 NKEKKEEEEE-----EEKKKEEEKKKEEEEKRNMR 31
+K ++EEEE+ EE+++EE ++K+EE+K+ R
Sbjct: 262 DKTREEEEEKILKAAEEERQEEAQEKKEEKKKEER 296
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 32.1 bits (74), Expect = 0.026
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEE 26
EEEEEE+++EEE++ EEE
Sbjct: 298 AAAAEEEEEEEEEEEEEEPSEEE 320
Score = 31.4 bits (72), Expect = 0.051
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEE 26
+ EEEEE+++EEE+++ EE
Sbjct: 297 QAAAAEEEEEEEEEEEEEEPSEE 319
Score = 28.7 bits (65), Expect = 0.37
Identities = 12/22 (54%), Positives = 17/22 (77%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEE 24
+EEEEEEE+++EEE +EE
Sbjct: 299 AAAEEEEEEEEEEEEEEPSEEE 320
Score = 25.2 bits (56), Expect = 7.7
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 7 EEEEEEEKKKEEEKKKEEEEK 27
+ EE+++EEE+++EEE
Sbjct: 297 QAAAAEEEEEEEEEEEEEEPS 317
Score = 24.8 bits (55), Expect = 8.7
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 7 EEEEEEEKKKEEEKKKEEEEK 27
+ E+++EEE+++EEEE
Sbjct: 296 AQAAAAEEEEEEEEEEEEEEP 316
Score = 24.8 bits (55), Expect = 9.0
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
KE + + +EEE+++EEEE+
Sbjct: 289 KEVLSAQAQAAAAEEEEEEEEEEEE 313
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is
functionally equivalent to L7/L12 in bacteria and the
P1 and P2 proteins in eukaryotes. L12p is homologous to
P1 and P2 but is not homologous to bacterial L7/L12. It
is located in the L12 stalk, with proteins L10, L11,
and 23S rRNA. L12p is the only protein in the ribosome
to occur as multimers, always appearing as sets of
dimers. Recent data indicate that most archaeal species
contain six copies of L12p (three homodimers), while
eukaryotes have four copies (two heterodimers), and
bacteria may have four or six copies (two or three
homodimers), depending on the species. The organization
of proteins within the stalk has been characterized
primarily in bacteria, where L7/L12 forms either two or
three homodimers and each homodimer binds to the
extended C-terminal helix of L10. L7/L12 is attached to
the ribosome through L10 and is the only ribosomal
protein that does not directly interact with rRNA.
Archaeal L12p is believed to function in a similar
fashion. However, hybrid ribosomes containing the large
subunit from E. coli with an archaeal stalk are able to
bind archaeal and eukaryotic elongation factors but not
bacterial elongation factors. In several mesophilic and
thermophilic archaeal species, the binding of 23S rRNA
to protein L11 and to the L10/L12p pentameric complex
was found to be temperature-dependent and cooperative.
Length = 106
Score = 30.9 bits (70), Expect = 0.036
Identities = 18/24 (75%), Positives = 22/24 (91%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEE 26
E+K EE+EEEKKKEEEK++EEEE
Sbjct: 74 AEEKAEEKEEEKKKEEEKEEEEEE 97
Score = 24.8 bits (54), Expect = 7.3
Identities = 12/21 (57%), Positives = 17/21 (80%)
Query: 7 EEEEEEEKKKEEEKKKEEEEK 27
EE+ ++KEEEKKKEEE++
Sbjct: 72 AAAEEKAEEKEEEKKKEEEKE 92
Score = 24.4 bits (53), Expect = 8.4
Identities = 11/21 (52%), Positives = 18/21 (85%)
Query: 7 EEEEEEEKKKEEEKKKEEEEK 27
EE+ E+K+EE+KK+EE+E+
Sbjct: 73 AAEEKAEEKEEEKKKEEEKEE 93
>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase.
Length = 1066
Score = 31.8 bits (72), Expect = 0.041
Identities = 17/27 (62%), Positives = 20/27 (74%), Gaps = 2/27 (7%)
Query: 4 EKKE--EEEEEEKKKEEEKKKEEEEKR 28
EKK EEE E KKK+EEK KE+E K+
Sbjct: 9 EKKILTEEELERKKKKEEKAKEKELKK 35
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 30.7 bits (70), Expect = 0.051
Identities = 11/23 (47%), Positives = 18/23 (78%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEE 26
EE++EE+++EEEK++ EEE
Sbjct: 74 AAAAEEKKEEEEEEEEKEESEEE 96
Score = 29.5 bits (67), Expect = 0.11
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEE 26
EE++E+++EEE+K+E EE
Sbjct: 73 AAAAAEEKKEEEEEEEEKEESEE 95
Score = 26.5 bits (59), Expect = 1.8
Identities = 13/17 (76%), Positives = 16/17 (94%)
Query: 3 KEKKEEEEEEEKKKEEE 19
+EKKEEEEEEE+K+E E
Sbjct: 78 EEKKEEEEEEEEKEESE 94
Score = 25.7 bits (57), Expect = 2.6
Identities = 11/17 (64%), Positives = 16/17 (94%)
Query: 3 KEKKEEEEEEEKKKEEE 19
++K+EEEEEEEK++ EE
Sbjct: 79 EKKEEEEEEEEKEESEE 95
Score = 25.3 bits (56), Expect = 4.4
Identities = 11/17 (64%), Positives = 15/17 (88%)
Query: 3 KEKKEEEEEEEKKKEEE 19
E+K+EEEEEE++KEE
Sbjct: 77 AEEKKEEEEEEEEKEES 93
Score = 25.3 bits (56), Expect = 4.7
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 7 EEEEEEEKKKEEEKKKEEEEK 27
EEKK+EEE+++E+EE
Sbjct: 73 AAAAAEEKKEEEEEEEEKEES 93
Score = 24.9 bits (55), Expect = 6.5
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 7 EEEEEEEKKKEEEKKKEEEEK 27
E+KKEEE+++EE+E+
Sbjct: 72 AAAAAAEEKKEEEEEEEEKEE 92
>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional.
Length = 1832
Score = 31.6 bits (72), Expect = 0.052
Identities = 11/39 (28%), Positives = 26/39 (66%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATII 42
+ EE+ +++KKKE++K++E + + R ++E +I+
Sbjct: 739 DSVEEKTKKKKKKEKKKEEEYKREEKARIEIAEAWDSIL 777
Score = 26.6 bits (59), Expect = 2.5
Identities = 12/24 (50%), Positives = 19/24 (79%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEE 26
K+KKE+++EEE K+EE+ + E E
Sbjct: 748 KKKKEKKKEEEYKREEKARIEIAE 771
Score = 25.8 bits (57), Expect = 4.7
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHL 34
N+EK EE+ E ++ K K ++ K N L
Sbjct: 1552 NQEKNIEEDYAESDIKKRKNK-KQYKSNTEAEL 1583
Score = 25.4 bits (56), Expect = 6.3
Identities = 11/23 (47%), Positives = 18/23 (78%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEE 24
K+KK+E+++EE+ K EEK + E
Sbjct: 746 KKKKKKEKKKEEEYKREEKARIE 768
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 30.4 bits (69), Expect = 0.054
Identities = 12/23 (52%), Positives = 18/23 (78%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEE 26
EEEEEE+++EEE+++E EE
Sbjct: 72 AAAAEEEEEEEEEEEEEEEESEE 94
Score = 29.2 bits (66), Expect = 0.17
Identities = 13/23 (56%), Positives = 19/23 (82%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEE 26
EEEEEEE+++EEE+++ EEE
Sbjct: 73 AAAEEEEEEEEEEEEEEEESEEE 95
Score = 28.1 bits (63), Expect = 0.47
Identities = 12/25 (48%), Positives = 19/25 (76%)
Query: 6 KEEEEEEEKKKEEEKKKEEEEKRNM 30
EEEEE+++EEE+++EE E+ M
Sbjct: 73 AAAEEEEEEEEEEEEEEEESEEEAM 97
Score = 26.2 bits (58), Expect = 1.9
Identities = 13/23 (56%), Positives = 19/23 (82%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEE 25
+EEEEEEE+++EEE++ EEE
Sbjct: 73 AAAEEEEEEEEEEEEEEEESEEE 95
Score = 24.6 bits (54), Expect = 7.0
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 8 EEEEEEKKKEEEKKKEEEEK 27
E+++EEE+++EEEE+
Sbjct: 71 AAAAAEEEEEEEEEEEEEEE 90
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 30.4 bits (69), Expect = 0.10
Identities = 12/47 (25%), Positives = 26/47 (55%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATIINEYTDWE 49
K+++ + KK+EE+KKKE E+ + +E ++Y+ ++
Sbjct: 562 ALKEQKRLRKLKKQEEKKKKELEKLEKAKIPPAEFFKRQEDKYSAFD 608
Score = 28.8 bits (65), Expect = 0.41
Identities = 10/26 (38%), Positives = 19/26 (73%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKR 28
+ +KEE+E +++K K K++EEK+
Sbjct: 554 QREKEEKEALKEQKRLRKLKKQEEKK 579
>gnl|CDD|218734 pfam05758, Ycf1, Ycf1. The chloroplast genomes of most higher
plants contain two giant open reading frames designated
ycf1 and ycf2. Although the function of Ycf1 is unknown,
it is known to be an essential gene.
Length = 832
Score = 30.4 bits (69), Expect = 0.12
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATII 42
KE K + EEK K+EEKK++ + + R ++E TI
Sbjct: 650 KKEFKILDYTEEKTKKEEKKEKNKREEKERIEIAETWDTIP 690
Score = 26.1 bits (58), Expect = 3.2
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEK 27
E++EEE + E + E K ++E+
Sbjct: 233 EEREEETDVEIETTSETKGTKQEQ 256
Score = 25.7 bits (57), Expect = 5.4
Identities = 13/47 (27%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 6 KEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEI-LATIINEYTDWERP 51
EE+E+ +K ++ +K + +EK++ E T++ +Y W RP
Sbjct: 268 SEEKEDPDKTEDLDKLEILKEKKDEELFWFEKPWPTLLFDYKRWNRP 314
>gnl|CDD|212055 cd11486, SLC5sbd_SGLT1, Na(+)/glucose cotransporter SGLT1;solute
binding domain. Human SGLT1 (hSGLT1) is a
high-affinity/low-capacity glucose transporter, which
can also transport galactose. In the transport
mechanism, two Na+ ions first bind to the extracellular
side of the transporter and induce a conformational
change in the glucose binding site. This results in an
increased affinity for glucose. A second conformational
change in the transporter follows, bringing the Na+ and
glucose binding sites to the inner surface of the
membrane. Glucose is then released, followed by the Na+
ions. In the process, hSGLT1 is also able to transport
water and urea and may be a major pathway for transport
of these across the intestinal brush-border membrane.
hSGLT1 is encoded by the SLC5A1 gene and expressed
mostly in the intestine, but also in the trachea,
kidney, heart, brain, testis, and prostate. The
WHO/UNICEF oral rehydration solution (ORS) for the
treatment of secretory diarrhea contains salt and
glucose. The glucose, along with sodium ions, is
transported by hSGLT1 and water is either co-transported
along with these or follows by osmosis. Mutations in
SGLT1 are associated with intestinal glucose galactose
malabsorption (GGM). Up-regulation of intestinal SGLT1
may protect against enteric infections. SGLT1 is
expressed in colorectal, head and neck, and prostate
tumors. Epidermal growth factor receptor (EGFR)
functions in cell survival by stabilizing SGLT1, and
thereby maintaining intracellular glucose levels. SGLT1
is predicted to have 14 membrane-spanning regions. This
subgroup belongs to the solute carrier 5
(SLC5)transporter family.
Length = 635
Score = 30.2 bits (68), Expect = 0.13
Identities = 7/30 (23%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 2 NKEKKEE---EEEEEKKKEEEKKKEEEEKR 28
+ E++ + ++ E + E E + +EE K+
Sbjct: 540 STEERIDLDADDWTEDEDENEMETDEERKK 569
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 29.9 bits (68), Expect = 0.15
Identities = 13/25 (52%), Positives = 21/25 (84%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
K+++EE++E++KK KKKEEEE+
Sbjct: 421 KKREEEKKEKKKKAFAGKKKEEEEE 445
Score = 29.9 bits (68), Expect = 0.18
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEK 27
EKK EEE++EKKK+ K++EE+
Sbjct: 417 EKAEKKREEEKKEKKKKAFAGKKKEEE 443
Score = 29.1 bits (66), Expect = 0.31
Identities = 13/25 (52%), Positives = 21/25 (84%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
++K+EEE++E+KKK KK+EEE+
Sbjct: 420 EKKREEEKKEKKKKAFAGKKKEEEE 444
Score = 28.7 bits (65), Expect = 0.37
Identities = 18/25 (72%), Positives = 24/25 (96%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
+KKEEEEEEEK+K+EE+K+EEEE+
Sbjct: 437 GKKKEEEEEEEKEKKEEEKEEEEEE 461
Score = 28.7 bits (65), Expect = 0.42
Identities = 18/25 (72%), Positives = 24/25 (96%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
K+K+EEEEEE++KKEEEK++EEEE
Sbjct: 438 KKKEEEEEEEKEKKEEEKEEEEEEA 462
Score = 28.3 bits (64), Expect = 0.52
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
EK E++ EEEKK++++K ++K
Sbjct: 416 VEKAEKKREEEKKEKKKKAFAGKKK 440
Score = 28.3 bits (64), Expect = 0.52
Identities = 15/25 (60%), Positives = 23/25 (92%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
KK+EEEEEE+K+++E++KEEEE+
Sbjct: 436 AGKKKEEEEEEEKEKKEEEKEEEEE 460
Score = 27.6 bits (62), Expect = 1.1
Identities = 10/28 (35%), Positives = 20/28 (71%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNM 30
K ++E++E+++K +KK+EEEE+
Sbjct: 422 KREEEKKEKKKKAFAGKKKEEEEEEEKE 449
Score = 27.6 bits (62), Expect = 1.2
Identities = 18/25 (72%), Positives = 24/25 (96%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
KEKKEEE+EEE+++ EE+K+EEEEK
Sbjct: 448 KEKKEEEKEEEEEEAEEEKEEEEEK 472
Score = 27.6 bits (62), Expect = 1.2
Identities = 10/26 (38%), Positives = 18/26 (69%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKR 28
+K E++ EE+KKE++KK +K+
Sbjct: 415 IVEKAEKKREEEKKEKKKKAFAGKKK 440
Score = 27.6 bits (62), Expect = 1.2
Identities = 11/25 (44%), Positives = 21/25 (84%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
K++K+++ KKKEEE+++E+E+K
Sbjct: 427 KKEKKKKAFAGKKKEEEEEEEKEKK 451
Score = 27.6 bits (62), Expect = 1.2
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
K KK E+ E+K++EE+K+K+++ +
Sbjct: 410 KKIKKIVEKAEKKREEEKKEKKKKAFAGKK 439
Score = 27.2 bits (61), Expect = 1.3
Identities = 12/25 (48%), Positives = 21/25 (84%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
K+K +++E+++EEEK+K+EEEK
Sbjct: 431 KKKAFAGKKKEEEEEEEKEKKEEEK 455
Score = 27.2 bits (61), Expect = 1.5
Identities = 12/25 (48%), Positives = 24/25 (96%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
+E+++E++EEEK++EEE+ +EE+E+
Sbjct: 444 EEEEKEKKEEEKEEEEEEAEEEKEE 468
Score = 27.2 bits (61), Expect = 1.6
Identities = 8/27 (29%), Positives = 19/27 (70%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRN 29
K +K+ EEE+++KK++ +++E+
Sbjct: 418 KAEKKREEEKKEKKKKAFAGKKKEEEE 444
Score = 26.8 bits (60), Expect = 1.8
Identities = 12/25 (48%), Positives = 24/25 (96%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
+E++E+E++EE+K+EEE++ EEE++
Sbjct: 443 EEEEEKEKKEEEKEEEEEEAEEEKE 467
Score = 26.8 bits (60), Expect = 2.1
Identities = 11/27 (40%), Positives = 22/27 (81%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRN 29
K++EEEEE++KE++++++EEE+
Sbjct: 435 FAGKKKEEEEEEEKEKKEEEKEEEEEE 461
Score = 26.4 bits (59), Expect = 2.4
Identities = 7/28 (25%), Positives = 22/28 (78%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNM 30
+E++++E++++ ++K++EEEE++
Sbjct: 423 REEEKKEKKKKAFAGKKKEEEEEEEKEK 450
Score = 26.4 bits (59), Expect = 2.4
Identities = 9/27 (33%), Positives = 22/27 (81%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRN 29
K+KK ++++++EEE+K+++EE++
Sbjct: 430 KKKKAFAGKKKEEEEEEEKEKKEEEKE 456
Score = 26.0 bits (58), Expect = 3.3
Identities = 12/29 (41%), Positives = 25/29 (86%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNM 30
K+++E+EEEEE+ +EE++++EE++K+
Sbjct: 449 EKKEEEKEEEEEEAEEEKEEEEEKKKKQA 477
Score = 26.0 bits (58), Expect = 3.6
Identities = 14/25 (56%), Positives = 24/25 (96%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
K+++EEEEE+EKK+EE++++EEE +
Sbjct: 439 KKEEEEEEEKEKKEEEKEEEEEEAE 463
Score = 26.0 bits (58), Expect = 4.0
Identities = 10/26 (38%), Positives = 21/26 (80%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKR 28
KEKK++ +KK+EEE++++E+++
Sbjct: 428 KEKKKKAFAGKKKEEEEEEEKEKKEE 453
Score = 26.0 bits (58), Expect = 4.1
Identities = 11/25 (44%), Positives = 21/25 (84%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
K +++EEE+++E+EKK+EE+E+
Sbjct: 433 KAFAGKKKEEEEEEEKEKKEEEKEE 457
Score = 25.3 bits (56), Expect = 6.6
Identities = 5/26 (19%), Positives = 19/26 (73%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKR 28
++ +++ EEE+K+K+++ ++++
Sbjct: 417 EKAEKKREEEKKEKKKKAFAGKKKEE 442
Score = 24.9 bits (55), Expect = 8.2
Identities = 13/28 (46%), Positives = 24/28 (85%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKR 28
KE++EEEE+E+K++E+E+++EE E+
Sbjct: 438 KKKEEEEEEEKEKKEEEKEEEEEEAEEE 465
Score = 24.9 bits (55), Expect = 8.6
Identities = 8/26 (30%), Positives = 19/26 (73%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKR 28
KK ++ E+ +K+ E++K+E++K+
Sbjct: 408 ATKKIKKIVEKAEKKREEEKKEKKKK 433
>gnl|CDD|162338 TIGR01398, FlhA, flagellar biosynthesis protein FlhA. This model
describes flagellar biosynthesis protein FlhA, one of a
large number of genes associated with the biosynthesis
of functional bacterial flagella. Homologs of many such
proteins, including FlhA, function in type III protein
secretion systems. A separate model describes InvA
(Salmonella enterica), LcrD (Yersinia enterocolitica),
HrcV (Xanthomonas), etc., all of which score below the
noise cutoff for this model [Cellular processes,
Chemotaxis and motility].
Length = 678
Score = 29.9 bits (68), Expect = 0.16
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEE 26
+ K+EEE E K +E+ EEEE
Sbjct: 312 RSKQEEEAAAEAAKAQEEAAEEEE 335
Score = 28.4 bits (64), Expect = 0.50
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEK 27
+++EE E K +EE +EEEE
Sbjct: 311 RRSKQEEEAAAEAAKAQEEAAEEEEES 337
>gnl|CDD|224881 COG1970, MscL, Large-conductance mechanosensitive channel [Cell
envelope biogenesis, outer membrane].
Length = 130
Score = 29.6 bits (67), Expect = 0.16
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEE 25
+NK +++ E+EE + EE
Sbjct: 94 INKLRRKLEKEEPEAPAPAPPAEEV 118
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 30.0 bits (67), Expect = 0.19
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
K ++E E E+EK+KE E+++E E +R +
Sbjct: 595 KAREEREREKEKEKEREREREREAERAAK 623
Score = 27.0 bits (59), Expect = 2.1
Identities = 11/26 (42%), Positives = 20/26 (76%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKR 28
K K+E E++ +++E EK+KE+E +R
Sbjct: 587 KAKREAEQKAREEREREKEKEKERER 612
Score = 27.0 bits (59), Expect = 2.2
Identities = 11/25 (44%), Positives = 19/25 (76%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
++K EE E EK+KE+E+++E E +
Sbjct: 593 EQKAREEREREKEKEKERERERERE 617
Score = 26.6 bits (58), Expect = 2.3
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 5 KKEEEEEEEKKKEEEKKKEEEEKR 28
KK EE E+ K+E E+K EE +R
Sbjct: 579 KKREEAVEKAKREAEQKAREERER 602
Score = 25.4 bits (55), Expect = 7.6
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
+K+EE E+ K++ E+K +EE E+ +
Sbjct: 579 KKREEAVEKAKREAEQKAREEREREKEK 606
>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein. This
protein is covalently attached to the terminii of
replicating DNA in vivo.
Length = 548
Score = 29.6 bits (67), Expect = 0.21
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 7 EEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATIIN 43
E EEEEE+++E +++EEEE+ R E+ AT+
Sbjct: 304 EPEEEEEEEEEVPEEEEEEEEEEERTFEEEVRATVAE 340
>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein. The
Ligand-gated Ion Channel (LIC) Family of
Neurotransmitter Receptors TC 1.A.9)Members of the LIC
family of ionotropic neurotransmitter receptors are
found only in vertebrate and invertebrate animals. They
exhibit receptor specificity for (1)acetylcholine, (2)
serotonin, (3) glycine, (4) glutamate and (5)
g-aminobutyric acid (GABA). All of these receptor
channels are probably hetero- orhomopentameric. The
best characterized are the nicotinic acetyl-choline
receptors which are pentameric channels of a2bgd
subunit composition. All subunits arehomologous. The
three dimensional structures of the protein complex in
both the open and closed configurations have been
solved at 0.9 nm resolution.The channel protein
complexes of the LIC family preferentially transport
cations or anions depending on the channel (e.g., the
acetylcholine receptors are cationselective while
glycine receptors are anion selective) [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 459
Score = 29.3 bits (66), Expect = 0.25
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 24 EEEKRNMRYHLSEILATIINEYTDWERPVQ--HPVNIR 59
K N++ ++L ++ Y RPV PV +
Sbjct: 21 GNAKSNLKEVERKLLDELLKNYDARVRPVFGGPPVTVS 58
>gnl|CDD|217286 pfam02919, Topoisom_I_N, Eukaryotic DNA topoisomerase I, DNA
binding fragment. Topoisomerase I promotes the
relaxation of DNA superhelical tension by introducing a
transient single-stranded break in duplex DNA and are
vital for the processes of replication, transcription,
and recombination. This family may be more than one
structural domain.
Length = 215
Score = 29.1 bits (66), Expect = 0.25
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEK 27
KEKK+ +EEKK +E+K + EE
Sbjct: 97 AEKEKKKAMSKEEKKAIKEEKDKLEEP 123
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 29.1 bits (66), Expect = 0.29
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
K +K+ E+EE +K +KK E K
Sbjct: 420 KAEKKAEKEEAEKAAAKKKAEAAAK 444
Score = 28.0 bits (63), Expect = 0.74
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKR 28
EKK E+EE EK ++K + +K
Sbjct: 422 EKKAEKEEAEKAAAKKKAEAAAKKA 446
Score = 26.8 bits (60), Expect = 2.1
Identities = 8/27 (29%), Positives = 18/27 (66%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRN 29
K +K++ + E+K ++EE +K +K+
Sbjct: 413 KLRKKQRKAEKKAEKEEAEKAAAKKKA 439
Score = 26.8 bits (60), Expect = 2.1
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 2 NKEKKEE--EEEEEKKKEEEKKKEEEEKRN 29
K++K E E+EE +K KKK E +
Sbjct: 416 KKQRKAEKKAEKEEAEKAAAKKKAEAAAKK 445
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 28.4 bits (64), Expect = 0.29
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEE 26
EE+KKEEE+++EE++
Sbjct: 59 AAAAAAAAEEEKKEEEEEEEEDD 81
Score = 24.9 bits (55), Expect = 5.4
Identities = 6/23 (26%), Positives = 15/23 (65%)
Query: 8 EEEEEEKKKEEEKKKEEEEKRNM 30
+++++E+++EEEE +M
Sbjct: 61 AAAAAAEEEKKEEEEEEEEDDDM 83
Score = 24.5 bits (54), Expect = 7.3
Identities = 7/17 (41%), Positives = 14/17 (82%)
Query: 3 KEKKEEEEEEEKKKEEE 19
+EE++EEE+++EE+
Sbjct: 64 AAAEEEKKEEEEEEEED 80
>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 = 28.1 bits (63), Expect = 0.42
Identities = 7/24 (29%), Positives = 16/24 (66%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEE 26
E ++E+KKEEE+++ +++
Sbjct: 74 AAAAAAEAKKEEKKEEEEEESDDD 97
Score = 24.6 bits (54), Expect = 6.6
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 12 EEKKKEEEKKKEEEEKRNM 30
+ K+EEKK+EEEE+ +
Sbjct: 78 AAEAKKEEKKEEEEEESDD 96
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 28.5 bits (64), Expect = 0.42
Identities = 12/23 (52%), Positives = 18/23 (78%)
Query: 6 KEEEEEEEKKKEEEKKKEEEEKR 28
K+E EE++++EEEK EEE+ R
Sbjct: 155 KKERAEEKEREEEEKAAEEEKAR 177
Score = 28.5 bits (64), Expect = 0.48
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
EK ++E EEK++EEE+K EEEK
Sbjct: 152 EKIKKERAEEKEREEEEKAAEEEKAREE 179
Score = 27.8 bits (62), Expect = 0.87
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRN 29
K KKE EE+E+++EE+ +EE+ +
Sbjct: 153 KIKKERAEEKEREEEEKAAEEEKAREE 179
Score = 26.2 bits (58), Expect = 2.6
Identities = 13/23 (56%), Positives = 18/23 (78%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEE 25
+ +++E EEEEK EEEK +EEE
Sbjct: 158 RAEEKEREEEEKAAEEEKAREEE 180
>gnl|CDD|238356 cd00660, Topoisomer_IB_N, Topoisomer_IB_N: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the monomeric yeast and human topo I
and heterodimeric topo I from Leishmania donvanni. Topo
I enzymes are divided into: topo type IA (bacterial)
and type IB (eukaryotic). Topo I relaxes superhelical
tension in duplex DNA by creating a single-strand nick,
the broken strand can then rotate around the unbroken
strand to remove DNA supercoils and, the nick is
religated, liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit re-ligation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I play putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain.
Length = 215
Score = 28.4 bits (64), Expect = 0.49
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
KEKK+ +EEKK +E+K++ EE
Sbjct: 98 KEKKKAMSKEEKKAIKEEKEKLEEP 122
>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein. The YqfQ-like protein family
includes the B. subtilis YqfQ protein, also known as
VrrA, which is functionally uncharacterized. This family
of proteins is found in bacteria. Proteins in this
family are typically between 146 and 237 amino acids in
length. There are two conserved sequence motifs: QYGP
and PKLY.
Length = 155
Score = 28.2 bits (63), Expect = 0.49
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 6 KEEEEEEEKKKEEEKKKEEEEKRN 29
+E +E E++ E K E +EK+
Sbjct: 103 EESTDETEQEDPPETKTESKEKKK 126
Score = 27.4 bits (61), Expect = 0.89
Identities = 7/30 (23%), Positives = 18/30 (60%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
+E +EE +E ++++ + K E +++ R
Sbjct: 98 EEETEEESTDETEQEDPPETKTESKEKKKR 127
Score = 27.4 bits (61), Expect = 1.0
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKR 28
+ + + E +E+KK+E K K E+EK
Sbjct: 113 DPPETKTESKEKKKREVPKPKTEKEKP 139
Score = 26.3 bits (58), Expect = 2.6
Identities = 8/26 (30%), Positives = 16/26 (61%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEK 27
+ ++ E+E+ E K E ++KK+ E
Sbjct: 105 STDETEQEDPPETKTESKEKKKREVP 130
Score = 24.7 bits (54), Expect = 8.1
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEK 27
E ++E+ E K + +EKKK E K
Sbjct: 108 ETEQEDPPETKTESKEKKKREVPK 131
>gnl|CDD|150884 pfam10278, Med19, Mediator of RNA pol II transcription subunit 19.
Med19 represents a family of conserved proteins which
are members of the multi-protein co-activator Mediator
complex. Mediator is required for activation of RNA
polymerase II transcription by DNA binding
transactivators.
Length = 178
Score = 28.3 bits (63), Expect = 0.55
Identities = 12/26 (46%), Positives = 21/26 (80%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKR 28
K+KK E+++E KKK++EKKK+++
Sbjct: 145 KKKKHEDDKERKKKKKEKKKKKKRHS 170
>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional.
Length = 413
Score = 28.5 bits (64), Expect = 0.57
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRN 29
+KK E+++++KK+++E K E E K
Sbjct: 65 ESKKKSEKKKKKKKEKKEPKSEGETKLG 92
Score = 27.8 bits (62), Expect = 0.79
Identities = 14/29 (48%), Positives = 22/29 (75%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKRN 29
K+KKE++ E KKK E+KKK+++EK+
Sbjct: 54 TKKDKKEDKNNESKKKSEKKKKKKKEKKE 82
Score = 25.1 bits (55), Expect = 7.1
Identities = 8/26 (30%), Positives = 20/26 (76%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEK 27
++K E +++ +KK+++KK+++E K
Sbjct: 59 KEDKNNESKKKSEKKKKKKKEKKEPK 84
Score = 25.1 bits (55), Expect = 7.3
Identities = 14/64 (21%), Positives = 28/64 (43%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATIINEYTDWERPVQHPVNIRDE 61
KE K E +++ +K+++KKKE++E ++ ++ T + P P D
Sbjct: 58 KKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPNEDVDN 117
Query: 62 TLEA 65
Sbjct: 118 AFNK 121
>gnl|CDD|151656 pfam11214, Med2, Mediator complex subunit 2. This family of
mediator complex subunit 2 proteins is conserved in
fungi. Cyclin-dependent kinase CDK8 or Srb10 interacts
with and phosphorylates Med2. Post-translational
modifications of Mediator subunits are important for
regulation of gene expression.
Length = 99
Score = 27.4 bits (61), Expect = 0.65
Identities = 14/22 (63%), Positives = 19/22 (86%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKK 22
+ + KK++EEEE KKKEEE+KK
Sbjct: 78 LVENKKKQEEEERKKKEEEEKK 99
>gnl|CDD|129815 TIGR00732, dprA, DNA protecting protein DprA. Disruption of this
gene in both Haemophilus influenzae and Helicobacter
pylori drastically reduces the efficiency of
transformation with exogenous DNA, but with different
levels of effect on chromosomal (linear) and plasmid
(circular) DNA. This difference suggests the DprA is not
active in recombination, and it has been shown not to
affect DNA binding, leaving the intermediate step in
natural transformation, DNA processing. In Strep.
pneumoniae, inactivation of dprA had no effect on the
uptake of DNA. All of these data indicated that DprA is
required at a later stage in transformation.
Subsequently DprA and RecA were both shown in S.
pneumoniae to be required to protect incoming ssDNA from
immediate degradation. Role of DprA in non-transformable
species is not known. The gene symbol smf was assigned
in E. coli, but without assignment of function [Cellular
processes, DNA transformation].
Length = 220
Score = 28.1 bits (63), Expect = 0.75
Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 9/63 (14%)
Query: 28 RNMRYHLSEILAT---IINEYTDWERPVQHPVNIRDETLEALSDAMVV--AP----SVNT 78
R ++I +++EY +P+++ R+ + LS A++V AP ++ T
Sbjct: 114 RQNSKLAAKIAENGGLLLSEYPPDTKPIKYNFPKRNRIISGLSRAVLVVEAPLKSGALIT 173
Query: 79 ADL 81
A
Sbjct: 174 ARY 176
>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional.
Length = 1627
Score = 28.3 bits (63), Expect = 0.76
Identities = 16/34 (47%), Positives = 23/34 (67%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSE 36
KE+K+EE+ EE K EE ++ EEE++ Y L E
Sbjct: 283 KEEKDEEKSEEVKTEEVDEEFEEEEKGFYYELYE 316
Score = 26.3 bits (58), Expect = 2.8
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYH 33
K+++++EE+ E+ K EE +E EE+ Y+
Sbjct: 280 KEKKEEKDEEKSEEVKTEEVDEEFEEEEKGFYY 312
Score = 26.3 bits (58), Expect = 2.9
Identities = 12/27 (44%), Positives = 20/27 (74%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRN 29
KE KE++EE++++K EE K EE ++
Sbjct: 277 KELKEKKEEKDEEKSEEVKTEEVDEEF 303
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 28.2 bits (62), Expect = 0.81
Identities = 20/65 (30%), Positives = 33/65 (50%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATIINEYTDWERPVQHPVNIRDETL 63
E+ ++E EE+KKK EE KK+EEEK+ + + E + E ++ ++ DE
Sbjct: 1733 EEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKR 1792
Query: 64 EALSD 68
D
Sbjct: 1793 RMEVD 1797
Score = 27.0 bits (59), Expect = 1.7
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKR 28
+ ++ ++ EE+KKK EE KK EE+++
Sbjct: 1661 IKAAEEAKKAEEDKKKAEEAKKAEEDEK 1688
Score = 26.6 bits (58), Expect = 2.5
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKR 28
E+ ++ EE+EKK E KKE EE +
Sbjct: 1678 EEAKKAEEDEKKAAEALKKEAEEAK 1702
Score = 26.6 bits (58), Expect = 2.9
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKR 28
+E K+ EEE + K EE KK EE+K+
Sbjct: 1650 EELKKAEEENKIKAAEEAKKAEEDKK 1675
Score = 25.1 bits (54), Expect = 8.3
Identities = 13/25 (52%), Positives = 20/25 (80%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKR 28
E+ ++ EE++KK EE KK EE+EK+
Sbjct: 1665 EEAKKAEEDKKKAEEAKKAEEDEKK 1689
Score = 25.1 bits (54), Expect = 9.7
Identities = 15/25 (60%), Positives = 18/25 (72%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKR 28
E ++E EE KK EE KKKE EEK+
Sbjct: 1692 EALKKEAEEAKKAEELKKKEAEEKK 1716
>gnl|CDD|218660 pfam05620, DUF788, Protein of unknown function (DUF788). This
family consists of several eukaryotic proteins of
unknown function.
Length = 166
Score = 27.7 bits (62), Expect = 0.82
Identities = 6/27 (22%), Positives = 13/27 (48%)
Query: 5 KKEEEEEEEKKKEEEKKKEEEEKRNMR 31
+ E + + K++E+ EKR +
Sbjct: 140 SLPSSQGAETNETKSKRQEKLEKRGEK 166
>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal.
This domain is found to the N-terminus of bacterial
signal peptidases of the S49 family (pfam01343).
Length = 154
Score = 27.5 bits (62), Expect = 0.84
Identities = 9/27 (33%), Positives = 18/27 (66%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKR 28
K +K+ E+ + K ++++ KKEE + R
Sbjct: 72 EKAEKKAEKAKAKAEKKKAKKEEPKPR 98
Score = 26.0 bits (58), Expect = 3.3
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKR 28
++K++ + E+ EKK E+ K K E++K
Sbjct: 63 LDKKELKAWEKAEKKAEKAKAKAEKKKA 90
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 27.7 bits (62), Expect = 0.97
Identities = 11/25 (44%), Positives = 22/25 (88%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
++K EEEE+E++++EEE+++ EE +
Sbjct: 345 EQKDEEEEQEDEEEEEEEEEPEEPE 369
Score = 27.3 bits (61), Expect = 1.5
Identities = 14/25 (56%), Positives = 22/25 (88%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEE 26
N E+K+EEEE+E ++EEE+++E EE
Sbjct: 343 NPEQKDEEEEQEDEEEEEEEEEPEE 367
Score = 25.8 bits (57), Expect = 4.5
Identities = 12/36 (33%), Positives = 23/36 (63%)
Query: 6 KEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATI 41
++++EEEE++ EEE+++EEE + +L I
Sbjct: 345 EQKDEEEEQEDEEEEEEEEEPEEPEPEEGPPLLTPI 380
Score = 25.8 bits (57), Expect = 5.3
Identities = 11/24 (45%), Positives = 21/24 (87%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEE 26
K+++EE+E+EE+++EEE+ +E E
Sbjct: 347 KDEEEEQEDEEEEEEEEEPEEPEP 370
Score = 25.0 bits (55), Expect = 8.4
Identities = 11/25 (44%), Positives = 21/25 (84%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
E++E+E+EEE+++EEE ++ E E+
Sbjct: 348 DEEEEQEDEEEEEEEEEPEEPEPEE 372
>gnl|CDD|218522 pfam05255, UPF0220, Uncharacterized protein family (UPF0220).
This family of proteins is functionally
uncharacterized.
Length = 165
Score = 27.3 bits (61), Expect = 1.0
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 68 DAMVVAPSVNTADLHSSARSVRCNIRSTFAM 98
DA V + N +D+H + I ST M
Sbjct: 41 DAAVYSKKNNASDVHITFVDWIPGICSTLGM 71
>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 926
Score = 27.6 bits (61), Expect = 1.0
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRN 29
+KE K E E + E K+ EEK
Sbjct: 808 DKEIKIESPSVETEGERCTIKQREEKGI 835
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 27.5 bits (61), Expect = 1.1
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRN 29
E EE E K KEE+ K+EE EK+
Sbjct: 390 DETDASEEAEAKAKEEKLKQEENEKKQ 416
Score = 25.9 bits (57), Expect = 3.9
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKR 28
K++ + EE E K +EEK K+EE ++
Sbjct: 388 VKDETDASEEAEAKAKEEKLKQEENEK 414
>gnl|CDD|149343 pfam08229, SHR3_chaperone, ER membrane protein SH3. This family of
proteins are membrane localised chaperones that are
required for correct plasma membrane localisation of
amino acid permeases (AAPs). SH3 prevents AAPs proteins
from aggregating and assists in their correct folding.
In the absence of SH3, AAPs are retained in the ER.
Length = 196
Score = 27.3 bits (61), Expect = 1.1
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 3 KEKKEEEEEEEKKKEEEKKK 22
KEEE E +KKE +KKK
Sbjct: 177 AAAKEEESAEGEKKESKKKK 196
Score = 26.1 bits (58), Expect = 3.0
Identities = 7/26 (26%), Positives = 11/26 (42%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEK 27
K +E EE + K++E E
Sbjct: 162 AKLLEEFAAEEAEAAAAAKEEESAEG 187
Score = 25.4 bits (56), Expect = 5.1
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKE 23
+EEE E +K+E KKK+
Sbjct: 175 AAAAAKEEESAEGEKKESKKKK 196
>gnl|CDD|185582 PTZ00373, PTZ00373, 60S Acidic ribosomal protein P2; Provisional.
Length = 112
Score = 27.2 bits (60), Expect = 1.1
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 9 EEEEEKKKEEEKKKEEEEKRNMRYHL 34
+ E KKEE+K++EEEE+ ++ + L
Sbjct: 85 GAKAEAKKEEKKEEEEEEEDDLGFSL 110
>gnl|CDD|184416 PRK13955, mscL, large-conductance mechanosensitive channel;
Provisional.
Length = 130
Score = 27.1 bits (60), Expect = 1.2
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 3 KEKKEEEEEEEKKKEEEKKKE 23
KE+++EEE E KEEE E
Sbjct: 97 KEEEKEEEIPEPTKEEELLGE 117
Score = 26.3 bits (58), Expect = 2.0
Identities = 13/23 (56%), Positives = 14/23 (60%), Gaps = 3/23 (13%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEE 25
KKEEE+EEE E KEEE
Sbjct: 94 TSKKEEEKEEEI---PEPTKEEE 113
Score = 25.6 bits (56), Expect = 3.7
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEE 24
NK ++EEE+E++ E K+EE
Sbjct: 90 FNKLTSKKEEEKEEEIPEPTKEEE 113
Score = 24.4 bits (53), Expect = 9.5
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 14 KKKEEEKKKEEEEKRNMRYHLSEI 37
KKEEEK++E E L EI
Sbjct: 95 SKKEEEKEEEIPEPTKEEELLGEI 118
>gnl|CDD|239570 cd03488, Topoisomer_IB_N_htopoI_like, Topoisomer_IB_N_htopoI_like :
N-terminal DNA binding fragment found in eukaryotic DNA
topoisomerase (topo) IB proteins similar to the
monomeric yeast and human topo I. Topo I enzymes are
divided into: topo type IA (bacterial) and type IB
(eukaryotic). Topo I relaxes superhelical tension in
duplex DNA by creating a single-strand nick, the broken
strand can then rotate around the unbroken strand to
remove DNA supercoils and, the nick is religated,
liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit religation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. This family may represent more than
one structural domain.
Length = 215
Score = 26.9 bits (60), Expect = 1.5
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
KE+K+ +EEKK + +K++ EE+
Sbjct: 98 KEEKKAMSKEEKKAIKAEKEKLEEE 122
>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355). This
family of proteins is found in bacteria and viruses.
Proteins in this family are typically between 180 and
214 amino acids in length.
Length = 125
Score = 26.8 bits (60), Expect = 1.5
Identities = 12/39 (30%), Positives = 24/39 (61%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILA 39
M+ E+K E E E+ +KE E+ + E +R ++ ++L+
Sbjct: 41 MSAEEKAEYELEKLEKELEELEAELARRELKAEAKKMLS 79
>gnl|CDD|239571 cd03489, Topoisomer_IB_N_LdtopoI_like,
Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the heterodimeric topo I from
Leishmania donvanni. Topo I enzymes are divided into:
topo type IA (bacterial) and type IB (eukaryotic). Topo
I relaxes superhelical tension in duplex DNA by creating
a single-strand nick, the broken strand can then rotate
around the unbroken strand to remove DNA supercoils and,
the nick is religated, liberating topo I. These enzymes
regulate the topological changes that accompany DNA
replication, transcription and other nuclear processes.
Human topo I is the target of a diverse set of
anticancer drugs including camptothecins (CPTs). CPTs
bind to the topo I-DNA complex and inhibit re-ligation
of the single-strand nick, resulting in the accumulation
of topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topo I play putative roles in
organizing the kinetoplast DNA network unique to these
parasites. This family may represent more than one
structural domain.
Length = 212
Score = 27.1 bits (60), Expect = 1.5
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
KEKK+ +EEKK +E+K +E E
Sbjct: 95 KEKKKSRTKEEKKALKEEKDKEAEP 119
>gnl|CDD|129022 smart00786, SHR3_chaperone, ER membrane protein SH3. This family
of proteins are membrane localised chaperones that are
required for correct plasma membrane localisation of
amino acid permeases (AAPs). Shr3 prevents AAPs proteins
from aggregating and assists in their correct folding.
In the absence of Shr3, AAPs are retained in the ER.
Length = 196
Score = 27.0 bits (60), Expect = 1.5
Identities = 7/26 (26%), Positives = 11/26 (42%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEK 27
K+K+E EE K+ K+
Sbjct: 162 AKQKEEFAAEERKEALAAAAKKSATP 187
Score = 26.2 bits (58), Expect = 2.7
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
KE+ EE +E KK +K
Sbjct: 165 KEEFAAEERKEALAAAAKKSATPQK 189
Score = 25.8 bits (57), Expect = 4.2
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKR 28
E+KE KK +K E ++K+
Sbjct: 172 ERKEALAAAAKKSATPQKVETKKKK 196
>gnl|CDD|217348 pfam03064, U79_P34, HSV U79 / HCMV P34. This family represents
herpes virus protein U79 and cytomegalovirus early
phosphoprotein P34 (UL112).
Length = 238
Score = 27.1 bits (60), Expect = 1.5
Identities = 11/27 (40%), Positives = 21/27 (77%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRN 29
+++K E+ +K KE+ +KK+EE++RN
Sbjct: 166 QKEKRRVEDSQKHKEDRRKKQEEKRRN 192
>gnl|CDD|219956 pfam08658, Rad54_N, Rad54 N terminal. This is the N terminal of
the DNA repair protein Rad54.
Length = 191
Score = 26.9 bits (60), Expect = 1.6
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYH--LSEIL 38
++ + K EEE+ EK +E E+ + + + H L+EIL
Sbjct: 141 VDDKPKIEEEKAEKDQEPEESETKLSNG-PKVHKSLAEIL 179
>gnl|CDD|240520 cd13156, KOW_RPL6, KOW motif of Ribosomal Protein L6. RPL6
contains KOW motif that has an extra ribosomal role as
an oncogenic. KOW domain is known as an RNA-binding
motif that is shared so far among some families of
ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. .
Length = 152
Score = 26.7 bits (60), Expect = 1.6
Identities = 12/39 (30%), Positives = 24/39 (61%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATI 41
K+KK++E E ++K+++ EE K + + + +LA I
Sbjct: 87 KKKKKKEGEFFEEKKKKYVVSEERKEDQKAVDAALLAAI 125
>gnl|CDD|224403 COG1486, CelF, Alpha-galactosidases/6-phospho-beta-glucosidases,
family 4 of glycosyl hydrolases [Carbohydrate transport
and metabolism].
Length = 442
Score = 26.8 bits (60), Expect = 1.7
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 4/72 (5%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATIINE-YTDWERPVQHPVNIRDE 61
K +KE E +K + +EK +E E++ + SE + IIN + +P + VN+R+
Sbjct: 287 KREKELFELYKKPELKEKPEELEKRIGAGKYSSEYASNIINAIENN--KPSRIYVNVRNN 344
Query: 62 -TLEALSDAMVV 72
+ L D VV
Sbjct: 345 GAITNLPDDAVV 356
>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR). This
family consists of several bovine specific leukaemia
virus receptors which are thought to function as
transmembrane proteins, although their exact function is
unknown.
Length = 561
Score = 27.0 bits (59), Expect = 1.8
Identities = 13/34 (38%), Positives = 26/34 (76%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSE 36
K KK+E++E+EK+++++KKKE E +++ L +
Sbjct: 201 KPKKKEKKEKEKERDKDKKKEVEGFKSLLLALDD 234
Score = 25.0 bits (54), Expect = 9.7
Identities = 11/31 (35%), Positives = 21/31 (67%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMRYH 33
+E++ + EK K E+KK+E+E++ R+H
Sbjct: 85 EEERRHRQRLEKDKREKKKREKEKRGRRRHH 115
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 26.9 bits (60), Expect = 2.0
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
+E++EE EEE +K EE EE +K++ R
Sbjct: 103 RERREEAEEELEKAIEEGDDEEIKKQSKR 131
>gnl|CDD|224968 COG2057, AtoA, Acyl CoA:acetate/3-ketoacid CoA transferase, beta
subunit [Lipid metabolism].
Length = 225
Score = 26.5 bits (59), Expect = 2.0
Identities = 9/51 (17%), Positives = 15/51 (29%), Gaps = 1/51 (1%)
Query: 26 EKRNMRYHLSEILATIINEYTDWERPVQHPVNIRDETLEALSDAMVVAPSV 76
E N+ SE + +N + + AL A V +
Sbjct: 41 EGMNVLLQ-SENGLLGVGPAPLPGEEDADLINAGKQPVTALPGASVFDSAD 90
>gnl|CDD|148679 pfam07218, RAP1, Rhoptry-associated protein 1 (RAP-1). This family
consists of several rhoptry-associated protein 1 (RAP-1)
sequences which appear to be specific to Plasmodium
falciparum.
Length = 790
Score = 27.0 bits (59), Expect = 2.2
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
E++E E +EE ++ EE KKE EK
Sbjct: 241 AEEEEFELDEEHEEAEEDKKEALEK 265
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase;
Provisional.
Length = 330
Score = 26.7 bits (60), Expect = 2.2
Identities = 8/31 (25%), Positives = 19/31 (61%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
++K++ + + +KKKE+++ K + K R
Sbjct: 61 LDKKELKAWHKAQKKKEKQEAKAAKAKSKPR 91
>gnl|CDD|239059 cd02145, BluB, Subfamily of the nitroreductase family that
includes BluB protein in Rhodobacter capsulatus is
involved in the conversion of cobinamide to cobalamin
in Cobalamin (vitamin B12) biosynthesis.
Nitroreductases typically reduce their substrates by
using NAD(P)H as electron donor and often use FMN as a
cofactor.
Length = 196
Score = 26.4 bits (59), Expect = 2.3
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 48 WERPVQH--PVNIRDETLEALSDAMVVAPSV 76
W R V+H P + +E LE L A APSV
Sbjct: 6 WRRDVRHFFPDPVPEEVLERLLAAAHHAPSV 36
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 26.6 bits (59), Expect = 2.3
Identities = 10/31 (32%), Positives = 25/31 (80%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
+ K K+++++ EE+++++ KK++EEE+R +
Sbjct: 189 LKKLKQQQQKREEERRKQRKKQQEEEERKQK 219
>gnl|CDD|222613 pfam14235, DUF4337, Domain of unknown function (DUF4337). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 187 and 201 amino
acids in length. There is a single completely conserved
residue Q that may be functionally important.
Length = 158
Score = 26.4 bits (59), Expect = 2.3
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 2 NKEKKEEEEE----EEKKKEEEKKKEEEEKRNMRYHLSEILATI 41
KEK E E K KE E + + ++ R+ L+ L I
Sbjct: 80 KKEKARYRSEAKELEAKAKEAEAESDHALHQHHRFALAVALLQI 123
Score = 25.6 bits (57), Expect = 4.3
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKR 28
+ K ++EK + + KE E K
Sbjct: 73 QAKIARYKKEKARYRSEAKELEAKA 97
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 26.5 bits (59), Expect = 2.3
Identities = 16/43 (37%), Positives = 26/43 (60%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATIINE 44
K ++EEEEE + +EEE++++EEEK+ + T I E
Sbjct: 18 EKIEEEEEEEAPEAEEEEEEEDEEEKKEKPGFFDKAKITEIKE 60
>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit
RPA34.5. This is a family of proteins conserved from
yeasts to human. Subunit A34.5 of RNA polymerase I is a
non-essential subunit which is thought to help Pol I
overcome topological constraints imposed on ribosomal
DNA during the process of transcription.
Length = 193
Score = 26.6 bits (59), Expect = 2.4
Identities = 12/29 (41%), Positives = 24/29 (82%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
+EKKE+++++E KKE+++KK+++EK
Sbjct: 152 EEKKEKKKKKEVKKEKKEKKDKKEKMVEP 180
Score = 25.8 bits (57), Expect = 4.4
Identities = 14/26 (53%), Positives = 22/26 (84%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEK 27
+ + EEEE++EKKK++E KKE++EK
Sbjct: 145 KEAEVEEEEKKEKKKKKEVKKEKKEK 170
>gnl|CDD|169939 PRK09517, PRK09517, multifunctional thiamine-phosphate
pyrophosphorylase/synthase/phosphomethylpyrimidine
kinase; Provisional.
Length = 755
Score = 26.9 bits (59), Expect = 2.4
Identities = 8/36 (22%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 39 ATIINEYTDWERPVQHPVNIRDETLEALS-DAMVVA 73
A ++ W +H + D + A S D ++ A
Sbjct: 322 ADTVDLVASWLGSHEHGPVVLDPVMVATSGDRLLDA 357
>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit
[Energy production and conversion].
Length = 470
Score = 26.3 bits (58), Expect = 2.6
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKRNM 30
E++EEEEEEE++ E + EE
Sbjct: 404 EEEEEEEEEEEEAAEAEAPMEEPVPGF 430
Score = 25.5 bits (56), Expect = 5.9
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEE 26
E+ EEEEEE+++EEE+ E E
Sbjct: 399 ERWAEEEEEEEEEEEEEAAEAEA 421
>gnl|CDD|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex. This
entry is characterized by proteins with alternating
conserved and low-complexity regions. Bud13 together
with Snu17p and a newly identified factor,
Pml1p/Ylr016c, form a novel trimeric complex. called
The RES complex, pre-mRNA retention and splicing
complex. Subunits of this complex are not essential for
viability of yeasts but they are required for efficient
splicing in vitro and in vivo. Furthermore,
inactivation of this complex causes pre-mRNA leakage
from the nucleus. Bud13 contains a unique,
phylogenetically conserved C-terminal region of unknown
function.
Length = 141
Score = 26.1 bits (58), Expect = 2.7
Identities = 12/24 (50%), Positives = 21/24 (87%)
Query: 5 KKEEEEEEEKKKEEEKKKEEEEKR 28
+E+ EE+E++KEE+++KEE+EK
Sbjct: 14 IEEKREEKEREKEEKERKEEKEKE 37
Score = 26.1 bits (58), Expect = 2.7
Identities = 9/26 (34%), Positives = 21/26 (80%)
Query: 5 KKEEEEEEEKKKEEEKKKEEEEKRNM 30
+++ EE+E +K+E+E+K+E+E++
Sbjct: 15 EEKREEKEREKEEKERKEEKEKEWGK 40
Score = 25.3 bits (56), Expect = 5.7
Identities = 11/26 (42%), Positives = 22/26 (84%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEE 26
++ E+K EE+E EK+++E K+++E+E
Sbjct: 12 IDIEEKREEKEREKEEKERKEEKEKE 37
Score = 24.6 bits (54), Expect = 8.9
Identities = 9/25 (36%), Positives = 21/25 (84%)
Query: 6 KEEEEEEEKKKEEEKKKEEEEKRNM 30
EE+ EE+++++EEK+++EE+++
Sbjct: 14 IEEKREEKEREKEEKERKEEKEKEW 38
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). 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 = 309
Score = 26.3 bits (58), Expect = 3.0
Identities = 12/33 (36%), Positives = 23/33 (69%)
Query: 6 KEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEIL 38
+ E+EEEE+++ +K+EEE++ N R + +L
Sbjct: 152 EFEKEEEEQRRLLLQKEEEEQQMNKRKNKQALL 184
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 26.3 bits (58), Expect = 3.3
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEE 26
M ++K +E E E+ +E+EK +EEEE
Sbjct: 155 MLEKKLKELEAEDVDEEDEKDEEEEE 180
Score = 25.5 bits (56), Expect = 5.1
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
EKK +E E E EE++K EEEE+
Sbjct: 156 LEKKLKELEAEDVDEEDEKDEEEEE 180
Score = 24.7 bits (54), Expect = 9.2
Identities = 11/20 (55%), Positives = 18/20 (90%)
Query: 7 EEEEEEEKKKEEEKKKEEEE 26
E+ +EE++K EEE+++EEEE
Sbjct: 166 EDVDEEDEKDEEEEEEEEEE 185
>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed.
Length = 158
Score = 25.9 bits (57), Expect = 3.4
Identities = 12/27 (44%), Positives = 20/27 (74%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKR 28
KE +E EE+E K +++KKE++EK+
Sbjct: 99 QKEVSKETEEKEAIKAKKEKKEKKEKK 125
Score = 24.7 bits (54), Expect = 8.0
Identities = 9/25 (36%), Positives = 19/25 (76%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
++K+ +E EEK+ + KK+++E+K
Sbjct: 98 EQKEVSKETEEKEAIKAKKEKKEKK 122
Score = 24.7 bits (54), Expect = 9.9
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
KE+KE +E E+K+ + KKE++EK+ +
Sbjct: 97 KEQKEVSKETEEKEAIKAKKEKKEKKEKK 125
>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742).
This is a family of fungal proteins of unknown function.
Length = 182
Score = 25.8 bits (57), Expect = 3.5
Identities = 8/40 (20%), Positives = 28/40 (70%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATI 41
+ K+++++++K +++++K+ E++ ++ SE L+T+
Sbjct: 97 KDKDKKDDKKDDKSEKKDEKEAEDKLEDLTKSYSETLSTL 136
Score = 25.0 bits (55), Expect = 6.6
Identities = 10/27 (37%), Positives = 21/27 (77%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEK 27
+ K KKE EE+++ K +++K K++++K
Sbjct: 71 IEKVKKEYEEKQKWKWKKKKSKKKKDK 97
Score = 24.7 bits (54), Expect = 9.5
Identities = 8/26 (30%), Positives = 21/26 (80%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEK 27
K+K +++++++K K+++KK ++ EK
Sbjct: 87 KKKKSKKKKDKDKDKKDDKKDDKSEK 112
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 26.0 bits (57), Expect = 3.6
Identities = 15/27 (55%), Positives = 22/27 (81%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKR 28
N+ KEEE+E+E+ KEE+KKK+E+ K
Sbjct: 100 NESGKEEEKEKEQVKEEKKKKKEKPKE 126
>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase
component YidC; Validated.
Length = 429
Score = 26.0 bits (57), Expect = 3.6
Identities = 7/30 (23%), Positives = 16/30 (53%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKRNM 30
+ K + E+ E + +K+E +K +R +
Sbjct: 332 IKKTRTAEKNEAKARKKEIAQKRRAAEREI 361
>gnl|CDD|235229 PRK04156, gltX, glutamyl-tRNA synthetase; Provisional.
Length = 567
Score = 26.0 bits (58), Expect = 3.6
Identities = 11/30 (36%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 1 MNKEKKEE--EEEEEKKKEEEKKKEEEEKR 28
++ E++ E EE + EEE++K+EE+K
Sbjct: 61 LSLEEQRERLEELAPELLEEEEEKKEEKKG 90
Score = 25.6 bits (57), Expect = 6.0
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 6/35 (17%)
Query: 3 KEKKEEEEEEEKKKEEEKKKE------EEEKRNMR 31
+E E EEE++K+EEKK E+ K MR
Sbjct: 71 EELAPELLEEEEEKKEEKKGLPPLPNAEKGKVVMR 105
>gnl|CDD|215656 pfam00012, HSP70, Hsp70 protein. Hsp70 chaperones help to fold
many proteins. Hsp70 assisted folding involves repeated
cycles of substrate binding and release. Hsp70 activity
is ATP dependent. Hsp70 proteins are made up of two
regions: the amino terminus is the ATPase domain and the
carboxyl terminus is the substrate binding region.
Length = 598
Score = 26.0 bits (58), Expect = 3.7
Identities = 8/26 (30%), Positives = 16/26 (61%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKRN 29
++ ++ EE E++K+KE E +N
Sbjct: 506 IERMVKDAEEYAAEDKKRKERIEAKN 531
Score = 24.9 bits (55), Expect = 9.1
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 8 EEEEEEKKKEEEKKKEEEEKRNMR 31
++E E K+ E+ E++KR R
Sbjct: 503 DDEIERMVKDAEEYAAEDKKRKER 526
>gnl|CDD|206063 pfam13892, DBINO, DNA-binding domain. DBINO is a DNA-binding
domain found on global transcription activator SNF2L1
proteins and chromatin re-modelling proteins.
Length = 140
Score = 25.7 bits (57), Expect = 3.9
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
+++ E+E E+ KKEEE E KR R
Sbjct: 89 RKRAEKEALEQAKKEEE---LREAKRQQR 114
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 26.2 bits (58), Expect = 3.9
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRN 29
K E+ E +++ E ++E E+KR
Sbjct: 247 RKLYGEKRAERVREELREVEREREKKRR 274
>gnl|CDD|217829 pfam03985, Paf1, Paf1. Members of this family are components of
the RNA polymerase II associated Paf1 complex. The Paf1
complex functions during the elongation phase of
transcription in conjunction with Spt4-Spt5 and
Spt16-Pob3i.
Length = 431
Score = 25.9 bits (57), Expect = 4.0
Identities = 8/26 (30%), Positives = 20/26 (76%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEE 26
++ E+ +E+E+EE+++ ++ +EEE
Sbjct: 365 IDFEEVDEDEDEEEEQRSDEHEEEEG 390
Score = 24.7 bits (54), Expect = 9.6
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEE 26
E E+E+EEE+++ +E ++EE E
Sbjct: 369 EVDEDEDEEEEQRSDEHEEEEGE 391
>gnl|CDD|192464 pfam10159, MMtag, Kinase phosphorylation protein. This is a
glycine-rich domain that is the most highly conserved
region of a family of proteins that in vertebrates are
associated with tumours in multiple myelomas. The
region may contain phosphorylation sites for several
protein kinases, as well as N-myristoylation sites and
nuclear localisation signals, so it might act as a
signal molecule in the nucleus.
Length = 78
Score = 25.0 bits (55), Expect = 4.1
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
K + + EE EK KEE ++ +E E+ M
Sbjct: 45 AKGEDDTAEEAEKLKEEIRRIKEAEEEAMA 74
>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein. TolA couples the inner
membrane complex of itself with TolQ and TolR to the
outer membrane complex of TolB and OprL (also called
Pal). Most of the length of the protein consists of
low-complexity sequence that may differ in both length
and composition from one species to another,
complicating efforts to discriminate TolA (the most
divergent gene in the tol-pal system) from paralogs such
as TonB. Selection of members of the seed alignment and
criteria for setting scoring cutoffs are based largely
conserved operon struction. //The Tol-Pal complex is
required for maintaining outer membrane integrity. Also
involved in transport (uptake) of colicins and
filamentous DNA, and implicated in pathogenesis.
Transport is energized by the proton motive force. TolA
is an inner membrane protein that interacts with
periplasmic TolB and with outer membrane porins ompC,
phoE and lamB [Transport and binding proteins, Other,
Cellular processes, Pathogenesis].
Length = 346
Score = 26.0 bits (57), Expect = 4.2
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKR 28
+ K E E E+K KEE KK+ EEE +
Sbjct: 132 AKAKAEAEAEKKAKEEAKKQAEEEAK 157
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 25.9 bits (57), Expect = 4.2
Identities = 7/25 (28%), Positives = 19/25 (76%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKR 28
+++ EE ++++ E+E+ K+ E++R
Sbjct: 86 QQQAEELQQKQAAEQERLKQLEKER 110
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC,
C-terminal domain. This model describes the C-terminal
domain, or longer subunit, of the Firmicutes type VII
secretion protein EssC. This protein (homologous to EccC
in Actinobacteria) and the WXG100 target proteins are
the only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 26.1 bits (58), Expect = 4.3
Identities = 15/68 (22%), Positives = 33/68 (48%), Gaps = 15/68 (22%)
Query: 3 KEKKEEEEEEEKKKE------EEKKKE-----EEEKRNMRYHLSEI--LATIINEYTD-- 47
+EKK+ +++ EK+ ++K+KE E+++ + YH + L ++
Sbjct: 84 REKKKYKKDVEKRNRSYRLYLDKKRKELQALSEKQRHVLHYHNPSVEELKEMVENVNSRI 143
Query: 48 WERPVQHP 55
WE+ +H
Sbjct: 144 WEKTPEHH 151
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 26.0 bits (57), Expect = 4.3
Identities = 12/24 (50%), Positives = 20/24 (83%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEE 26
++EEEEEEE+++EE++ +EEE
Sbjct: 444 SVEEEEEEEEEEEEEEQESEEEEG 467
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 26.2 bits (57), Expect = 4.4
Identities = 8/29 (27%), Positives = 23/29 (79%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNM 30
+ ++ E+E++++++ +EE+++EEEE +
Sbjct: 155 DDDEDEDEDDDDEEDDEEEEEEEEEIKGF 183
Score = 25.4 bits (55), Expect = 7.1
Identities = 7/27 (25%), Positives = 24/27 (88%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEK 27
++ + ++E+E+++ ++++E+++EEEE+
Sbjct: 153 IDDDDEDEDEDDDDEEDDEEEEEEEEE 179
>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain. This is a family of proteins of
approximately 300 residues, found in plants and
vertebrates. They contain a highly conserved DDRGK
motif.
Length = 189
Score = 25.4 bits (56), Expect = 4.5
Identities = 17/26 (65%), Positives = 22/26 (84%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKR 28
KE++E EEE EKKKEEE++KE EE+
Sbjct: 43 KEEEELEEEREKKKEEEERKEREEQA 68
>gnl|CDD|148682 pfam07222, PBP_sp32, Proacrosin binding protein sp32. This family
consists of several mammalian specific proacrosin
binding protein sp32 sequences. sp32 is a sperm specific
protein which is known to bind with with 55- and 53-kDa
proacrosins and the 49-kDa acrosin intermediate. The
exact function of sp32 is unclear, it is thought however
that the binding of sp32 to proacrosin may be involved
in packaging the acrosin zymogen into the acrosomal
matrix.
Length = 243
Score = 25.8 bits (56), Expect = 4.7
Identities = 12/23 (52%), Positives = 19/23 (82%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEE 26
EK+ +EE+EE++ EEE K+EE +
Sbjct: 217 EKQPQEEQEEEEVEEEAKQEEGQ 239
>gnl|CDD|205200 pfam13019, Telomere_Sde2, Telomere stability and silencing. Sde2
has been identified in fission yeast as an important
factor in telomere formation and maintenance. This is a
more N-terminal domain on these nuclear proteins, and is
essential for telomeric silencing and genomic stability.
Length = 163
Score = 25.6 bits (56), Expect = 4.7
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKR 28
E K E K E EKK++E ++
Sbjct: 127 NEAKALAEYLAIKPEMEKKEKEARRK 152
>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510). This
family consists of several hypothetical bacterial
proteins of around 200 residues in length. The function
of this family is unknown.
Length = 214
Score = 25.5 bits (56), Expect = 4.7
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEK 27
N E KE++ + EK+ EE +++ EEE
Sbjct: 74 NSEDKEDKGDAEKEDEESEEENEEED 99
Score = 25.5 bits (56), Expect = 5.6
Identities = 12/26 (46%), Positives = 20/26 (76%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEK 27
++E +EE EEE+++ +E +KE EEK
Sbjct: 88 DEESEEENEEEDEESSDENEKETEEK 113
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 25.9 bits (57), Expect = 4.9
Identities = 14/25 (56%), Positives = 20/25 (80%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEK 27
KE+K+EEEE+ KEEE +EEE++
Sbjct: 44 KEEKKEEEEKTTDKEEEVDEEEEKE 68
>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366). This
family of proteins is found in bacteria and eukaryotes.
Proteins in this family are typically between 227 and
387 amino acids in length.
Length = 213
Score = 25.4 bits (56), Expect = 5.0
Identities = 8/28 (28%), Positives = 12/28 (42%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNM 30
E E + E E ++E E+K M
Sbjct: 131 SVNMTECTGPEPEPEPEPEEEPEKKSGM 158
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 25.6 bits (57), Expect = 5.2
Identities = 13/20 (65%), Positives = 15/20 (75%)
Query: 3 KEKKEEEEEEEKKKEEEKKK 22
KKE+EEEEEKKK + K K
Sbjct: 276 SGKKEKEEEEEKKKIKPKDK 295
>gnl|CDD|116948 pfam08367, M16C_assoc, Peptidase M16C associated. This domain
appears in eukaryotes as well as bacteria and tends to
be found near the C-terminus of the metalloprotease
M16C (pfam05193).
Length = 248
Score = 25.7 bits (57), Expect = 5.3
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKE-EEEKRNMRYHLSEILA 39
++ +E+ EEE++K E+KK EE + L
Sbjct: 4 DETLEEKLNEEEREKLEKKKSSLSEEDKEKIIERGLELE 42
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 25.1 bits (55), Expect = 5.4
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 7 EEEEEEEKKKEEEKKKEEEE 26
E E ++ +EEEK++E EE
Sbjct: 78 EAAAEADEAEEEEKEEEAEE 97
Score = 24.7 bits (54), Expect = 7.7
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEE 26
E +E EE++KEEE ++E ++
Sbjct: 79 AAAEADEAEEEEKEEEAEEESDD 101
Score = 24.3 bits (53), Expect = 9.2
Identities = 8/23 (34%), Positives = 16/23 (69%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEE 26
E E +E E++++EE+ +EE +
Sbjct: 78 EAAAEADEAEEEEKEEEAEEESD 100
>gnl|CDD|235302 PRK04456, PRK04456, acetyl-CoA decarbonylase/synthase complex
subunit beta; Reviewed.
Length = 463
Score = 25.4 bits (56), Expect = 5.9
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEE 25
+ + EEEEEEE+++EEE++ E
Sbjct: 399 VERWAAEEEEEEEEEEEEEEEPVAE 423
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 25.3 bits (56), Expect = 5.9
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 10 EEEEKKKEEEKKKEEEEKR 28
EEE K+E E+ K+ E +R
Sbjct: 260 EEELAKEEAERLKKLEAER 278
>gnl|CDD|219355 pfam07267, Nucleo_P87, Nucleopolyhedrovirus capsid protein P87.
This family consists of several Nucleopolyhedrovirus
capsid protein P87 sequences. P87 is expressed late in
infection and concentrated in infected cell nuclei.
Length = 606
Score = 25.6 bits (56), Expect = 6.1
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKRN 29
E +++ +E+E E+E+K+ EE +N
Sbjct: 373 EDEDDSDEDEVDYEKERKRRREEDKN 398
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 25.4 bits (56), Expect = 6.1
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 2 NKEKKEEEEE-----EEKKKEEEKKKEEEEKRNMRYHLSEILATIINEY 45
+ K EEEEE +EK++E K EEE + + + + E+
Sbjct: 180 AELKAEEEEELERALKEKREELLSKLEEELLARLESKEAALEKQLRLEF 228
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 25.4 bits (56), Expect = 6.3
Identities = 6/28 (21%), Positives = 16/28 (57%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
++ + +E+ K E K + ++++R R
Sbjct: 583 GEETKPQEQPAPKAEAKPERQQDRRKPR 610
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 25.4 bits (56), Expect = 6.3
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
+ KK EE E ++KEE+ + EE R R
Sbjct: 621 EWKKRFEERERRQKEEDILRIIEEYRRER 649
>gnl|CDD|221581 pfam12446, DUF3682, Protein of unknown function (DUF3682). This
domain family is found in eukaryotes, and is typically
between 125 and 136 amino acids in length.
Length = 133
Score = 25.2 bits (55), Expect = 6.3
Identities = 8/15 (53%), Positives = 14/15 (93%)
Query: 3 KEKKEEEEEEEKKKE 17
+E++EEEEE EK+++
Sbjct: 96 QEEEEEEEENEKQQQ 110
Score = 25.2 bits (55), Expect = 6.4
Identities = 10/25 (40%), Positives = 17/25 (68%), Gaps = 2/25 (8%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEE 26
++EEEEEE +E EK+++ +E
Sbjct: 91 TGHTRQEEEEEE--EENEKQQQSDE 113
>gnl|CDD|240285 PTZ00135, PTZ00135, 60S acidic ribosomal protein P0; Provisional.
Length = 310
Score = 25.4 bits (56), Expect = 6.3
Identities = 4/19 (21%), Positives = 7/19 (36%)
Query: 8 EEEEEEKKKEEEKKKEEEE 26
+++EEEE
Sbjct: 283 AAAAAAAAAAPAEEEEEEE 301
>gnl|CDD|165287 PHA02984, PHA02984, hypothetical protein; Provisional.
Length = 286
Score = 25.1 bits (55), Expect = 6.6
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 27 KRNMRYHLSEILATIINEYTDWERPVQHPVNI 58
K + +I+ TIINE+ + V + +NI
Sbjct: 21 KEFISKSDEKIIKTIINEFINENHSVLNILNI 52
>gnl|CDD|189037 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Flap endonuclease-1 (FEN1) is
involved in multiple DNA metabolic pathways, including
DNA replication processes (5' flap DNA endonuclease
activity and double stranded DNA 5'-exonuclease
activity) and DNA repair processes (long-patch base
excision repair) in eukaryotes and archaea. Interaction
between FEN1 and PCNA (Proliferating cell nuclear
antigen) is an essential prerequisite to FEN1's DNA
replication functionality and stimulates FEN1 nuclease
activity by 10-50 fold. FEN1 belongs to the
FEN1-EXO1-like family of structure-specific, 5'
nucleases. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain) of variable length (approximately 45 residues in
FEN1 PIN domains) and a H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region.
Both the H3TH domain (not included here) and the helical
arch/clamp region are involved in DNA binding. Nucleases
within this group also have a carboxylate-rich active
site that is involved in binding essential divalent
metal ion cofactors (Mg2+/Mn2+). FEN1 has a C-terminal
extension containing residues forming the consensus
PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1
to PCNA.
Length = 261
Score = 25.2 bits (56), Expect = 6.6
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
+E++EE EE+ ++ +EE EE K R
Sbjct: 96 RERREEAEEKLEEAKEEGDAEEARKYAKR 124
>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota). DNA
Topoisomerase I (eukaryota), DNA topoisomerase V,
Vaccina virus topoisomerase, Variola virus
topoisomerase, Shope fibroma virus topoisomeras.
Length = 391
Score = 25.4 bits (56), Expect = 6.8
Identities = 15/39 (38%), Positives = 25/39 (64%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILAT 40
K E +E++++KK+EEKKK++ E+ R E+ AT
Sbjct: 322 EKLDAEVKEKKKEKKKEEKKKKQIERLEERIEKLEVQAT 360
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 25.2 bits (56), Expect = 7.0
Identities = 7/33 (21%), Positives = 15/33 (45%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYH 33
+ ++ E EE+ ++ E K + E N +
Sbjct: 3 LEALEERNSELEEQIRQLELKLRDLEAENEKLE 35
>gnl|CDD|220735 pfam10408, Ufd2P_core, Ubiquitin elongating factor core. This is
the most conserved part of the core region of Ufd2P
ubiquitin elongating factor or E4, running from helix
alpha-11 to alpha-38. It consists of 31 helices of
variable length connected by loops of variable size
forming a compact unit; the helical packing pattern of
the compact unit consists of five structural repeats
that resemble tandem Armadillo (ARM) repeats. This
domain is involved in ubiquitination as it binds Cdc48p
and escorts ubiquitinated proteins from Cdc48p to the
proteasome for degradation. The core is structurally
similar to the nuclear transporter protein
importin-alpha. The core is associated with the U-box at
the C-terminus, pfam04564, which has ligase activity.
Length = 625
Score = 25.3 bits (56), Expect = 7.0
Identities = 9/47 (19%), Positives = 22/47 (46%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATIINEYTD 47
+ + K+ ++E +++ + E +EE E+R E A + +
Sbjct: 456 LKEIKQLQKELQDRAEWESLSQEEREERESELRQLERQAKSYLQLAN 502
>gnl|CDD|215558 PLN03073, PLN03073, ABC transporter F family; Provisional.
Length = 718
Score = 25.2 bits (55), Expect = 7.3
Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 8/45 (17%)
Query: 3 KEKKEEEE------EEEKKKEEEKKKEEEEKRNMRY--HLSEILA 39
+KK E + E + K E +K++EE +R ++Y H++E+ A
Sbjct: 110 AKKKPEPDDGPLLSERDLAKIERRKRKEERQREVQYQAHVAEMEA 154
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 25.2 bits (55), Expect = 7.3
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 4 EKKEEEEEEEKKKEEEKKKEEEEK 27
EK +EE E +++ EE+++ EEEK
Sbjct: 259 EKLAKEEAERERQAEEQRRREEEK 282
Score = 25.2 bits (55), Expect = 7.4
Identities = 8/35 (22%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 1 MNKEKKEEEEEEEKKKEEE-KKKEEEEKRNMRYHL 34
+ +E++ EE K E+ + K E +++ ++ L
Sbjct: 439 LQEERRLREEAIRAKAEKTARMKAEMKEKTLKMFL 473
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 25.2 bits (56), Expect = 7.9
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 2 NKEKKEEEEEEEKKK---EEEKKKEEEEKRNMRYHLSEILATIINE 44
+E + +E EK K EE+K+K +EE+ + + I E
Sbjct: 536 AEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKE 581
>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein. This family
consists of several Borrelia P83/P100 antigen proteins.
Length = 489
Score = 25.0 bits (54), Expect = 8.1
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMR 31
+E K E+E E K+ E +KK E +++
Sbjct: 310 QESKASEKEAEDKELEAQKKREPVAEDLQ 338
>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 = 24.5 bits (54), Expect = 8.3
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 8 EEEEEEKKKEEEKKKEEEEKRNMRYHL 34
++E+KKEE EEE +M + L
Sbjct: 84 AAAKKEEKKEES---EEESDDDMGFGL 107
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 25.0 bits (55), Expect = 8.4
Identities = 9/36 (25%), Positives = 20/36 (55%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEI 37
E + E++EEE +K + K ++ K+ + + S +
Sbjct: 113 QLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSNL 148
>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97
family. This model family represents the major capsid
protein component of the heads (capsids) of
bacteriophage HK97, phi-105, P27, and related phage.
This model represents one of several analogous families
lacking detectable sequence similarity. The gene
encoding this component is typically located in an
operon encoding the small and large terminase subunits,
the portal protein and the prohead or maturation
protease [Mobile and extrachromosomal element
functions, Prophage functions].
Length = 384
Score = 25.0 bits (55), Expect = 8.5
Identities = 13/50 (26%), Positives = 21/50 (42%)
Query: 1 MNKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATIINEYTDWER 50
+ + E +E K E+EK E EE++ L E + + E E
Sbjct: 4 LREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEE 53
>gnl|CDD|235860 PRK06778, PRK06778, hypothetical protein; Validated.
Length = 289
Score = 24.9 bits (54), Expect = 8.8
Identities = 14/45 (31%), Positives = 17/45 (37%), Gaps = 1/45 (2%)
Query: 2 NKEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATIINEYT 46
EE EKK + +K K+ L E LAT IN
Sbjct: 82 KPATVAVPEETEKKARDVNEKTALLKKKSATELGE-LATSINTIA 125
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 24.9 bits (55), Expect = 9.4
Identities = 5/28 (17%), Positives = 15/28 (53%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNM 30
K ++ +E +K++++ +E+E
Sbjct: 242 KAERLRQEAAAYEKQQKELAKEQEWIRR 269
>gnl|CDD|241486 cd13332, FERM_C_JAK1, Janus kinase 1 FERM domain C-lobe. JAK1 is a
tyrosine kinase protein essential in signaling type I
and type II cytokines. It interacts with the gamma chain
of type I cytokine receptors to elicit signals from the
IL-2 receptor family, the IL-4 receptor family, the
gp130 receptor family, ciliary neurotrophic factor
receptor (CNTF-R), neurotrophin-1 receptor (NNT-1R) and
Leptin-R). It also is involved in transducing a signal
by type I (IFN-alpha/beta) and type II (IFN-gamma)
interferons, and members of the IL-10 family via type II
cytokine receptors. JAK (also called Just Another
Kinase) is a family of intracellular, non-receptor
tyrosine kinases that transduce cytokine-mediated
signals via the JAK-STAT pathway. The JAK family in
mammals consists of 4 members: JAK1, JAK2, JAK3 and
TYK2. JAKs are composed of seven JAK homology (JH)
domains (JH1-JH7) . The C-terminal JH1 domain is the
main catalytic domain, followed by JH2, which is often
referred to as a pseudokinase domain, followed by
JH3-JH4 which is homologous to the SH2 domain, and
lastly JH5-JH7 which is a FERM domain. Named after
Janus, the two-faced Roman god of doorways, JAKs possess
two near-identical phosphate-transferring domains; one
which displays the kinase activity (JH1), while the
other negatively regulates the kinase activity of the
first (JH2). The FERM domain has a cloverleaf tripart
structure (FERM_N, FERM_M, FERM_C/N, alpha-, and
C-lobe/A-lobe,A-lobe, B-lobe, C-lobe/F1, F2, F3). The
C-lobe/F3 within the FERM domain is part of the PH
domain family. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs) , the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 198
Score = 24.8 bits (54), Expect = 9.6
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 3 KEKKEEEEEEEKKKEEEKKKEEEEKRNMRYHLSEILATIINEYT 46
K+K + ++ + K K++E KK+ E N + EI +I E T
Sbjct: 92 KKKGKSKKNKLKGKKDEDKKKAREGWNNFSYFPEITHIVIKEST 135
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
0.305 0.121 0.324
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,028,056
Number of extensions: 440263
Number of successful extensions: 7234
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5257
Number of HSP's successfully gapped: 1560
Length of query: 100
Length of database: 10,937,602
Length adjustment: 66
Effective length of query: 34
Effective length of database: 8,010,238
Effective search space: 272348092
Effective search space used: 272348092
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (22.0 bits)
S2: 53 (24.0 bits)