RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18072
(174 letters)
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 126 bits (318), Expect = 7e-36
Identities = 57/77 (74%), Positives = 68/77 (88%)
Query: 3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLI 62
L CRFY +K+PE +D+VMV V+ I EMGAYV LLEY++IEGMIL+SELS+RRIRSINKLI
Sbjct: 5 LDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLI 64
Query: 63 RVGKTEPVVVIRVDKEK 79
RVG+ E VVV+RVDKEK
Sbjct: 65 RVGRHEVVVVLRVDKEK 81
Score = 64.7 bits (158), Expect = 7e-13
Identities = 33/91 (36%), Positives = 54/91 (59%), Gaps = 5/91 (5%)
Query: 80 VMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEA 139
V+ T +K G++ + A++ IK I++ GG F+V+ P+VV DE +L +E+AE
Sbjct: 230 VIVTTCSDKDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGG-DEEDLEELLEKAEE 288
Query: 140 ENAEV----AADDDEDEEDFDNERDGDEGED 166
E E + D+DE++ED + E D DEG+
Sbjct: 289 EEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319
>gnl|CDD|239899 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of
translation Initiation Factor 2, S1-like RNA-binding
domain. S1-like RNA-binding domains are found in a wide
variety of RNA-associated proteins. Eukaryotic and
archaeal Initiation Factor 2 (e- and aIF2,
respectively) are heterotrimeric proteins with three
subunits (alpha, beta, and gamma). IF2 plays a crucial
role in the process of translation initiation. The IF2
gamma subunit contains a GTP-binding site. The IF2 beta
and gamma subunits together are thought to be
responsible for binding methionyl-initiator tRNA. The
ternary complex consisting of IF2, GTP, and the
methionyl-initiator tRNA binds to the small subunit of
the ribosome, as part of a pre-initiation complex that
scans the mRNA to find the AUG start codon. The
IF2-bound GTP is hydrolyzed to GDP when the
methionyl-initiator tRNA binds the AUG start codon, at
which time the IF2 is released with its bound GDP. The
large ribosomal subunit then joins with the small
subunit to complete the initiation complex, which is
competent to begin translation. The IF2a subunit is a
major site of control of the translation initiation
process, via phosphorylation of a specific serine
residue. This alpha subunit is well conserved in
eukaryotes and archaea but is not present in bacteria.
IF2 is a cold-shock-inducible protein.
Length = 76
Score = 113 bits (286), Expect = 1e-33
Identities = 51/67 (76%), Positives = 58/67 (86%)
Query: 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72
PE ++V+VTV SIA+MGAYV LLEY NIEGMILLSELSRRRIRSI KL++VG+ E V V
Sbjct: 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKV 60
Query: 73 IRVDKEK 79
IRVDKEK
Sbjct: 61 IRVDKEK 67
>gnl|CDD|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit
(eIF-2alpha) [Translation, ribosomal structure and
biogenesis].
Length = 269
Score = 92.4 bits (230), Expect = 3e-23
Identities = 26/75 (34%), Positives = 44/75 (58%)
Query: 5 CRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRV 64
R +YPE ++V+ TV +A+ GAYV L EY EG I +SE++ +++I ++
Sbjct: 1 MRMKRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKE 60
Query: 65 GKTEPVVVIRVDKEK 79
G+ V+RVD ++
Sbjct: 61 GQKVVAKVLRVDPKR 75
Score = 30.0 bits (68), Expect = 0.56
Identities = 10/45 (22%), Positives = 19/45 (42%)
Query: 80 VMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTA 124
+ P+ + L++A + I++LGG PK+V
Sbjct: 224 RIDVQAPDYKKAEEVLEKAAEAAIKTIKKLGGEGTFIREPKLVGE 268
>gnl|CDD|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit
alpha; Validated.
Length = 262
Score = 61.8 bits (151), Expect = 5e-12
Identities = 24/70 (34%), Positives = 42/70 (60%)
Query: 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEP 69
+++PE ++V+ TV + + GA+V L EY EG I +SE++ +++I ++ G+
Sbjct: 3 KEWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVV 62
Query: 70 VVVIRVDKEK 79
VIRVD K
Sbjct: 63 CKVIRVDPRK 72
>gnl|CDD|216000 pfam00575, S1, S1 RNA binding domain. The S1 domain occurs in a
wide range of RNA associated proteins. It is
structurally similar to cold shock protein which binds
nucleic acids. The S1 domain has an OB-fold structure.
Length = 74
Score = 57.7 bits (140), Expect = 8e-12
Identities = 27/68 (39%), Positives = 42/68 (61%), Gaps = 2/68 (2%)
Query: 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71
PE DVV TV + + GA+V L N +EG I +SE+S R+ +++++VG V
Sbjct: 1 KPEEGDVVKGTVTRVTKGGAFVDLG--NGVEGFIPISEISDDRVEDPDEVLKVGDEVEVK 58
Query: 72 VIRVDKEK 79
V++VDKE+
Sbjct: 59 VLKVDKER 66
>gnl|CDD|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain.
Length = 72
Score = 54.9 bits (133), Expect = 8e-11
Identities = 29/66 (43%), Positives = 42/66 (63%), Gaps = 2/66 (3%)
Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
EV DVV TV I GA+V L N +EG+I +SELS +R++ ++++VG V V+
Sbjct: 1 EVGDVVEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVL 58
Query: 74 RVDKEK 79
VD+EK
Sbjct: 59 SVDEEK 64
>gnl|CDD|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding
domain. Found in a wide variety of RNA-associated
proteins. Originally identified in S1 ribosomal
protein. This superfamily also contains the Cold Shock
Domain (CSD), which is a homolog of the S1 domain. Both
domains are members of the
Oligonucleotide/oligosaccharide Binding (OB) fold.
Length = 65
Score = 45.1 bits (107), Expect = 4e-07
Identities = 21/61 (34%), Positives = 37/61 (60%), Gaps = 2/61 (3%)
Query: 19 VMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE 78
V V+SI + G +V L + +EG++ +SELS + ++ +++ +VG V V+ VD E
Sbjct: 1 VTGKVVSITKFGVFVELED--GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPE 58
Query: 79 K 79
K
Sbjct: 59 K 59
>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate
reductase/S1 RNA-binding domain protein; Reviewed.
Length = 647
Score = 45.3 bits (108), Expect = 4e-06
Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 3/71 (4%)
Query: 9 AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTE 68
EKYP V +V+ V+ IA GA+V L ++G++ +S++S +RI ++ G+
Sbjct: 557 EEKYP-VGSIVLGKVVRIAPFGAFVELEP--GVDGLVHISQISWKRIDKPEDVLSEGEEV 613
Query: 69 PVVVIRVDKEK 79
++ VD E+
Sbjct: 614 KAKILEVDPEE 624
Score = 37.2 bits (87), Expect = 0.002
Identities = 31/107 (28%), Positives = 55/107 (51%), Gaps = 16/107 (14%)
Query: 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNI----EGMILLSELSRRRIRSINKLIRVG 65
EK D+V TV+S+ E +V ++ EG+I L EL+ I S+ + ++VG
Sbjct: 297 EKQIRRGDIVKGTVVSVNENEVFV------DVGYKSEGVIPLRELTLDEISSLKESVKVG 350
Query: 66 KTEPVVVIRVDKEKVMTTVTPEKADGLKA---LQEAID---TIKAKI 106
V V++++ E ++ ++AD KA L+EA + +K K+
Sbjct: 351 DEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKV 397
Score = 36.1 bits (84), Expect = 0.005
Identities = 19/66 (28%), Positives = 37/66 (56%), Gaps = 3/66 (4%)
Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
E DVV V + + GA+V + ++G++ +SE+S R+ + +++VG V ++
Sbjct: 476 EEGDVVEGEVKRLTDFGAFVDI---GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYIL 532
Query: 74 RVDKEK 79
+DKE
Sbjct: 533 DIDKEN 538
>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 565
Score = 44.8 bits (107), Expect = 6e-06
Identities = 26/72 (36%), Positives = 45/72 (62%), Gaps = 4/72 (5%)
Query: 9 AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS-RRRIRSINKLIRVGKT 67
+KYP V V V +I + GA+V L E IEG++ +SE+S ++ + +K++ VG+
Sbjct: 281 EKKYP-VGSKVKGKVTNITDYGAFVELEE--GIEGLVHVSEMSWTKKNKHPSKVVSVGQE 337
Query: 68 EPVVVIRVDKEK 79
V+V+ +D+EK
Sbjct: 338 VEVMVLEIDEEK 349
Score = 41.7 bits (99), Expect = 7e-05
Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 3/72 (4%)
Query: 8 YAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKT 67
+A+K+ +V TV + + GA+V L + +EG+I SELSR R+ ++++VG
Sbjct: 454 FAKKHK-KGSIVTGTVTEVKDKGAFVEL--EDGVEGLIRASELSRDRVEDATEVLKVGDE 510
Query: 68 EPVVVIRVDKEK 79
VI +D++
Sbjct: 511 VEAKVINIDRKN 522
Score = 39.4 bits (93), Expect = 4e-04
Identities = 28/72 (38%), Positives = 42/72 (58%), Gaps = 4/72 (5%)
Query: 9 AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS-RRRIRSINKLIRVGKT 67
AEKYP V DVV V +I + GA+V L I+G++ LS++S ++ +L + G
Sbjct: 368 AEKYP-VGDVVEGKVKNITDFGAFVGLEG--GIDGLVHLSDISWDKKGEEAVELYKKGDE 424
Query: 68 EPVVVIRVDKEK 79
VV++VD EK
Sbjct: 425 VEAVVLKVDVEK 436
Score = 35.1 bits (82), Expect = 0.014
Identities = 20/66 (30%), Positives = 39/66 (59%), Gaps = 3/66 (4%)
Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
E VV V +I + GA+V L ++G++ ++++S +R+ ++++ VG V V+
Sbjct: 200 EEGQVVEGVVKNITDYGAFVDL---GGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVL 256
Query: 74 RVDKEK 79
+ DKEK
Sbjct: 257 KFDKEK 262
>gnl|CDD|240193 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal
protein S1 (RPS1) domain. RPS1 is a component of the
small ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria,
the tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains
have been identified in plants and humans, however
these lack the N-terminal HMBPP reductase domain. This
CD includes S1 repeat 3 (ec3) of the Escherichia coli
RPS1. Autoantibodies to double-stranded DNA from
patients with systemic lupus erythematosus cross-react
with the human RPS1 homolog.
Length = 68
Score = 41.5 bits (98), Expect = 7e-06
Identities = 22/65 (33%), Positives = 41/65 (63%), Gaps = 3/65 (4%)
Query: 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74
DVV TV SI + GA+V L ++G++ +S++S R++ ++++ VG V V++
Sbjct: 1 EGDVVEGTVKSITDFGAFVDL---GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLK 57
Query: 75 VDKEK 79
+DKE+
Sbjct: 58 IDKER 62
>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.
Members of this protein family are polyribonucleotide
nucleotidyltransferase, also called polynucleotide
phosphorylase. Some members have been shown also to have
additional functions as guanosine pentaphosphate
synthetase and as poly(A) polymerase (see model
TIGR02696 for an exception clade, within this family)
[Transcription, Degradation of RNA].
Length = 684
Score = 43.3 bits (103), Expect = 3e-05
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72
PEV + V+ I + GA+V +L +G++ +SE++ R+ + +++ G V V
Sbjct: 616 PEVGKIYEGKVVRIMDFGAFVEIL--PGKDGLVHISEIANERVEKVEDVLKEGDEVKVKV 673
Query: 73 IRVDK 77
+ +DK
Sbjct: 674 LEIDK 678
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 42.3 bits (101), Expect = 4e-05
Identities = 18/65 (27%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72
PEV ++ V+ I + GA+V +L +G++ +SE++ R+ + +++ G V V
Sbjct: 619 PEVGEIYEGKVVRIVDFGAFVEIL--PGKDGLVHISEIADERVEKVEDVLKEGDEVKVKV 676
Query: 73 IRVDK 77
+ +DK
Sbjct: 677 LEIDK 681
>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal
structure and biogenesis].
Length = 541
Score = 41.9 bits (99), Expect = 6e-05
Identities = 21/66 (31%), Positives = 42/66 (63%), Gaps = 3/66 (4%)
Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
EV +VV V +I + GA+V + ++G++ +SE+S +R+ +++++VG V VI
Sbjct: 191 EVGEVVEGVVKNITDYGAFVDI---GGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVI 247
Query: 74 RVDKEK 79
+D+E+
Sbjct: 248 SLDEER 253
Score = 36.9 bits (86), Expect = 0.003
Identities = 21/71 (29%), Positives = 42/71 (59%), Gaps = 3/71 (4%)
Query: 9 AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTE 68
+KYP V D V V ++ + GA+V + +EG++ +SE+S + +++++VG+
Sbjct: 272 EKKYP-VGDKVEGKVTNLTDYGAFVEI--EEGVEGLVHVSEISWTKKNVPSEVVKVGQEV 328
Query: 69 PVVVIRVDKEK 79
V V+ +D E+
Sbjct: 329 EVKVLDIDPER 339
Score = 34.2 bits (79), Expect = 0.028
Identities = 29/110 (26%), Positives = 52/110 (47%), Gaps = 19/110 (17%)
Query: 7 FYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNI----EGMILLSELSRRRIRSINKLI 62
+++ E DVV TV+SI + G V +I EG+I +SE S + ++
Sbjct: 13 DKSDEEFEPGDVVKGTVVSIEKDGVLV------DIGGKSEGVIPISEFS---NEPVEDVV 63
Query: 63 RVGKTEPVVVIRVDKEKVMTTVTPEKA------DGLKALQEAIDTIKAKI 106
+VG V+V+RV+ + ++ KA + L+ E + ++ KI
Sbjct: 64 QVGDEVEVLVLRVEDGEGELVLSRRKAERERAWEKLEEAFENGEIVEGKI 113
Score = 33.0 bits (76), Expect = 0.057
Identities = 28/71 (39%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 9 AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTE 68
A+K+P V DVV V SI + GA+V L I+G++ LS+LS R + + G
Sbjct: 358 ADKHP-VGDVVEGKVKSITDFGAFVELEG--GIDGLVHLSDLSWDRPGEEAEKYKKGDEV 414
Query: 69 PVVVIRVDKEK 79
V+ VDKEK
Sbjct: 415 EAKVLAVDKEK 425
Score = 32.7 bits (75), Expect = 0.078
Identities = 30/107 (28%), Positives = 52/107 (48%), Gaps = 13/107 (12%)
Query: 8 YAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKT 67
++EKY VV V S+ + GA+V L +EG+I LSELSR ++VG
Sbjct: 443 FSEKYK-KGSVVKGKVKSVKDKGAFVEL--GGGVEGLIRLSELSRDV-------LKVGDE 492
Query: 68 EPVVVIRVDK--EKVMTTVTPEK-ADGLKALQEAIDTIKAKIEQLGG 111
VV+ +DK K++ ++ + + +AL+ + + + G
Sbjct: 493 VEAVVVSIDKKNRKILLSIKALERKEEKEALESYNKDDDSSLGDILG 539
>gnl|CDD|239918 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase
(PNPase), ), S1-like RNA-binding domain. PNPase is a
polyribonucleotide nucleotidyl transferase that
degrades mRNA. It is a trimeric multidomain protein.
The C-terminus contains the S1 domain which binds
ssRNA. This family is classified based on the S1
domain. PNPase nonspecifically removes the 3'
nucleotides from mRNA, but is stalled by
double-stranded RNA structures such as a stem-loop.
Evidence shows that a minimum of 7-10 unpaired
nucleotides at the 3' end, is required for PNPase
degradation. It is suggested that PNPase also
dephosphorylates the RNA 5' end. This additional
activity may regulate the 5'-dependent activity of
RNaseE in vivo.
Length = 68
Score = 38.7 bits (91), Expect = 8e-05
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 22 TVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK 77
V+ I + GA+V +L +G++ +SELS R+ + +++VG V VI VD
Sbjct: 7 KVVKIKDFGAFVEILP--GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD 60
>gnl|CDD|240203 cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5: Rrp5 is
a trans-acting factor important for biogenesis of both
the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has
two distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of
A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6)
and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 70
Score = 37.6 bits (88), Expect = 2e-04
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 22 TVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVM 81
T++ + G V YNN++G + SELS I+ + RVG+ V V+ D E+
Sbjct: 7 TIVKVKPNGCIVSF--YNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQR 64
Query: 82 TTVT 85
++
Sbjct: 65 LLLS 68
>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 390
Score = 39.9 bits (94), Expect = 3e-04
Identities = 28/101 (27%), Positives = 54/101 (53%), Gaps = 7/101 (6%)
Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
EV DVV V+ + + +V++ Y +EG+I +SELS I IN +++VG V V+
Sbjct: 16 EVGDVVTGEVLKVEDKQVFVNIEGYK-VEGVIPISELSNDHIEDINDVVKVGDELEVYVL 74
Query: 74 RVDKEKVMTTVTPEKADGLKA---LQEAID---TIKAKIEQ 108
+V+ + ++ + + KA L+E + ++ K+ +
Sbjct: 75 KVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTE 115
Score = 34.5 bits (80), Expect = 0.021
Identities = 22/70 (31%), Positives = 43/70 (61%), Gaps = 3/70 (4%)
Query: 9 AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTE 68
EK PE DV+ TV + + GA+V +L +EG++ +S++S + I + ++++ G+
Sbjct: 272 EEKLPE-GDVIEGTVKRLTDFGAFVEVLP--GVEGLVHISQISHKHIATPSEVLEEGQEV 328
Query: 69 PVVVIRVDKE 78
V V+ V++E
Sbjct: 329 KVKVLEVNEE 338
Score = 34.1 bits (79), Expect = 0.023
Identities = 20/66 (30%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
+ DVV TV + + GA+V + ++G++ +SELS R+ ++++ VG+ V V+
Sbjct: 191 KEGDVVEGTVARLTDFGAFVDI---GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVL 247
Query: 74 RVDKEK 79
+D E
Sbjct: 248 SIDWET 253
>gnl|CDD|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal
protein S1 (RPS1) domain. RPS1 is a component of the
small ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria,
the tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains
have been identified in plants and humans, however
these lack the N-terminal HMBPP reductase domain. This
CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1
homolog. Autoantibodies to double-stranded DNA from
patients with systemic lupus erythematosus cross-react
with the human RPS1 homolog.
Length = 69
Score = 36.1 bits (84), Expect = 8e-04
Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 17 DVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76
VV TV + GA+V L I G++ +S+++ +R++ + +++ G V V+ +D
Sbjct: 2 SVVEGTVTRLKPFGAFVELG--GGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID 59
Query: 77 KEK 79
Sbjct: 60 ARG 62
>gnl|CDD|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional.
Length = 491
Score = 37.0 bits (86), Expect = 0.003
Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 17 DVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76
DVV TV +A GA+V L +EGM+ +SELS R++ ++ + VG T V V+ ++
Sbjct: 204 DVVEGTVTRLAPFGAFVELAP--GVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIE 261
Query: 77 KEK 79
+ K
Sbjct: 262 RAK 264
Score = 34.3 bits (79), Expect = 0.023
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS-RRRIRSINKLIRVGKTEPVVV 72
+ D V V+ +A GA+V +L IEG++ +SE+S RR+ ++ G V +
Sbjct: 291 KAGDKVTGKVVRLAPFGAFVEILP--GIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKI 348
Query: 73 IRVDKEK 79
+D K
Sbjct: 349 KDIDPAK 355
>gnl|CDD|240213 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 is a
trans-acting factor important for biogenesis of both
the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has
two distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of
A0-A2. This CD includes S. cerevisiae S1 repeat 12
(sc12). Rrp5 is found in eukaryotes but not in
prokaryotes or archaea.
Length = 77
Score = 34.6 bits (80), Expect = 0.003
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
+V + TV + + G ++ + + N+ G+ SE+S R+ +KL RVG V+
Sbjct: 1 KVGQKIDGTVRRVEDYGVFIDI-DGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVL 59
Query: 74 RVDKEK 79
++D EK
Sbjct: 60 KIDAEK 65
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 36.4 bits (85), Expect = 0.004
Identities = 21/65 (32%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72
EV +V TV+ I + GA+V LL +G++ +S+L++ R+ + +++ G V V
Sbjct: 617 VEVGEVYEGTVVRIVDFGAFVELL--PGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKV 674
Query: 73 IRVDK 77
I +DK
Sbjct: 675 IEIDK 679
>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1. This model describes
ribosomal protein S1, RpsA. This protein is found in
most bacterial genomes in a single copy, but is not
present in the Mycoplasmas. It is heterogeneous with
respect to the number of repeats of the S1 RNA binding
domain described by PFAM model pfam00575: six repeats in
E. coli and most other bacteria, four in Bacillus
subtilis and some other species. rpsA is an essential
gene in E. coli but not in B. subtilis. It is associated
with the cytidylate kinase gene cmk in many species, and
fused to it in Treponema pallidum. RpsA is proposed
(Medline:97323001) to assist in mRNA degradation. This
model provides trusted hits to most long form (6 repeat)
examples of RpsA. Among homologs with only four repeats
are some to which other (perhaps secondary) functions
have been assigned [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 516
Score = 35.9 bits (83), Expect = 0.008
Identities = 25/84 (29%), Positives = 48/84 (57%), Gaps = 9/84 (10%)
Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
+ DVV V +I + GA+V L ++G++ ++++S +R++ ++ ++VG+ V VI
Sbjct: 186 KEGDVVKGVVKNITDFGAFVDL---GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVI 242
Query: 74 RVDKEKVMTTVTPEKADGLKALQE 97
+ DKEK ++ LK L E
Sbjct: 243 KFDKEKGRISL------SLKQLGE 260
Score = 34.3 bits (79), Expect = 0.022
Identities = 26/70 (37%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 8 YAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKT 67
+A KY V VV V I + GA+V L +EG+I SELS R I+VG
Sbjct: 440 FAAKYK-VGSVVKGKVTEIKDFGAFVEL--PGGVEGLIRNSELSENRDEDKTDEIKVGDE 496
Query: 68 EPVVVIRVDK 77
V+ +DK
Sbjct: 497 VEAKVVDIDK 506
Score = 33.6 bits (77), Expect = 0.049
Identities = 19/72 (26%), Positives = 42/72 (58%), Gaps = 4/72 (5%)
Query: 9 AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS-RRRIRSINKLIRVGKT 67
+K+P V D + V ++ + G +V + E IEG++ +SE+S ++ +K+++ G
Sbjct: 267 EKKFP-VGDKITGRVTNLTDYGVFVEIEE--GIEGLVHVSEMSWVKKNSHPSKVVKKGDE 323
Query: 68 EPVVVIRVDKEK 79
V+++ +D E+
Sbjct: 324 VEVMILDIDPER 335
>gnl|CDD|115196 pfam06524, NOA36, NOA36 protein. This family consists of several
NOA36 proteins which contain 29 highly conserved
cysteine residues. The function of this protein is
unknown.
Length = 314
Score = 34.5 bits (79), Expect = 0.016
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 146 ADDDEDEE--DFDNERDGDEGEDEEEGEN 172
+DDDE D+D E DGD+ ++E+ +
Sbjct: 273 SDDDEGSSSNDYDEEEDGDDDDNEDNDDT 301
>gnl|CDD|224023 COG1098, VacB, Predicted RNA binding protein (contains ribosomal
protein S1 domain) [Translation, ribosomal structure
and biogenesis].
Length = 129
Score = 33.8 bits (78), Expect = 0.016
Identities = 15/67 (22%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72
+V + + I GA+V L G++ +SE++ ++ I+ ++VG+ V V
Sbjct: 3 MKVGSKLKGKITGITPYGAFVEL--EGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKV 60
Query: 73 IRVDKEK 79
+ +D+
Sbjct: 61 LDIDENG 67
>gnl|CDD|240192 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1:
Ribosomal protein S1 (RPS1) domain. RPS1 is a component
of the small ribosomal subunit thought to be involved
in the recognition and binding of mRNA's during
translation initiation. The bacterial RPS1 domain
architecture consists of 4-6 tandem S1 domains. In some
bacteria, the tandem S1 array is located C-terminal to
a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains
have been identified in plants and humans, however
these lack the N-terminal HMBPP reductase domain. This
CD includes S1 repeat 1 of the Escherichia coli and
Homo sapiens RPS1 (ec1 and hs1, respectively).
Autoantibodies to double-stranded DNA from patients
with systemic lupus erythematosus cross-react with the
human RPS1 homolog.
Length = 70
Score = 32.1 bits (74), Expect = 0.023
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 17 DVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76
D+V TV+S+ + V + EG+I +SE S I + ++VG V V+RV+
Sbjct: 2 DIVKGTVVSVDDDEVLVDIGYK--SEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVE 59
Query: 77 KE 78
E
Sbjct: 60 DE 61
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 33.4 bits (77), Expect = 0.050
Identities = 16/93 (17%), Positives = 36/93 (38%)
Query: 82 TTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAEN 141
P K L + K V+ +D+ + + + ++
Sbjct: 87 AAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDD 146
Query: 142 AEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+ DD++D+ED D++ DE E+++E + +
Sbjct: 147 IDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELE 179
Score = 30.3 bits (69), Expect = 0.49
Identities = 16/98 (16%), Positives = 38/98 (38%)
Query: 77 KEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMER 136
K + E KA ++ + + + + A D+ +L
Sbjct: 89 KAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDID 148
Query: 137 AEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+ ++ + DDD+D+ D ++E + E E+ +++D
Sbjct: 149 DDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDD 186
Score = 28.4 bits (64), Expect = 2.1
Identities = 13/99 (13%), Positives = 35/99 (35%)
Query: 76 DKEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQME 135
+ ++ D K ++ K V D+ + +
Sbjct: 87 AAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDD 146
Query: 136 RAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+ ++ E +DD+D++ D + + E ++ E+ ++D
Sbjct: 147 IDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDD 185
>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region. The domain
is found in the primary vegetative sigma factor. The
function of this domain is unclear and can be removed
without loss of function.
Length = 211
Score = 32.9 bits (76), Expect = 0.053
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 137 AEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
A A A + + DEED +++ D DE EDE++ E D
Sbjct: 35 AAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEAD 72
Score = 32.2 bits (74), Expect = 0.084
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 137 AEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
A A A AA + E +E+ + D D+ +++E+ E E
Sbjct: 34 AAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEA 71
Score = 31.0 bits (71), Expect = 0.20
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 137 AEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
A A + D+ED ED D++ + ++ +DEEE +
Sbjct: 38 AATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLG 74
Score = 30.6 bits (70), Expect = 0.30
Identities = 17/46 (36%), Positives = 24/46 (52%)
Query: 124 ASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEE 169
A+ A A +E E DDD+++ED D+E + D G D EE
Sbjct: 34 AAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLGPDPEE 79
Score = 26.8 bits (60), Expect = 5.7
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 141 NAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
NA AA E +E D ++ +D++E E+ED
Sbjct: 33 NAAAAAATAAAIESELDEEDLEDDDDDDEDEDED 66
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This is
a family of uncharacterized proteins.
Length = 449
Score = 33.0 bits (75), Expect = 0.054
Identities = 13/40 (32%), Positives = 27/40 (67%)
Query: 135 ERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
E A E + DDD+D+++ +++ D D+ ED+E+ +++D
Sbjct: 47 EEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDD 86
Score = 31.9 bits (72), Expect = 0.14
Identities = 12/39 (30%), Positives = 27/39 (69%)
Query: 136 RAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
R + AE A ++ED+++ D++ D DE ED+++ ++++
Sbjct: 39 RKLGKEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDE 77
Score = 30.0 bits (67), Expect = 0.71
Identities = 14/40 (35%), Positives = 27/40 (67%)
Query: 135 ERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+ AE E E DD+ED++D D+E + D+ +D++E + ++
Sbjct: 43 KEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDE 82
Score = 29.2 bits (65), Expect = 1.0
Identities = 12/39 (30%), Positives = 25/39 (64%)
Query: 129 ELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDE 167
E A + E + E+ + D+DED++D D++ D ++ +D+
Sbjct: 47 EEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDD 85
Score = 29.2 bits (65), Expect = 1.1
Identities = 14/48 (29%), Positives = 27/48 (56%)
Query: 127 EAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
EAE E + E + DD+++++D D++ + DE ED+++ D
Sbjct: 44 EAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHD 91
Score = 29.2 bits (65), Expect = 1.2
Identities = 14/43 (32%), Positives = 29/43 (67%)
Query: 132 RQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
R++ + E A DDDE+++D D++ D D+ +D+++ ++ED
Sbjct: 39 RKLGKEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDED 81
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 33.3 bits (76), Expect = 0.060
Identities = 26/109 (23%), Positives = 44/109 (40%), Gaps = 11/109 (10%)
Query: 76 DKEKVMTTVTPEKADGLKALQEA---IDTIKAKIEQLGGVFQVQMAPKVVTASDEAELAR 132
E+ + + EK G A +D + +IE G +A ++ A + R
Sbjct: 151 PLEEAVALLVREKLTGDAPPDSAGKVLDLWRDEIEDKAGEDLDGLAAEIDDQQAFARVVR 210
Query: 133 QM--------ERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
M E + E A ++D D++ DN D + G +E EG +E
Sbjct: 211 DMLGSMDMAEETGDDGIEEDADEEDGDDDQPDNNEDSEAGREESEGSDE 259
Score = 29.0 bits (65), Expect = 1.3
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 123 TASDEAELA-RQMERAEAENAEVAADDDEDEEDFDNERDGD 162
+ DEAE + E E + AE + D + DE D D E G+
Sbjct: 260 SEEDEAEATDGEGEEGEMDAAEASEDSESDESDEDTETPGE 300
>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid).
Members of this family are bacterial proteins with a
conserved motif [KR]FYDLN, sometimes flanked by a pair
of CXXC motifs, followed by a long region of low
complexity sequence in which roughly half the residues
are Asp and Glu, including multiple runs of five or more
acidic residues. The function of members of this family
is unknown.
Length = 104
Score = 31.5 bits (72), Expect = 0.064
Identities = 11/59 (18%), Positives = 27/59 (45%)
Query: 116 QMAPKVVTASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
A A+ + E + ++ + DDD+ + D++ D D+ +D+ +++D
Sbjct: 45 APAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDDDVDLDDDDDDFLEDDDD 103
Score = 25.7 bits (57), Expect = 6.2
Identities = 8/48 (16%), Positives = 24/48 (50%)
Query: 127 EAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
E +R + A+ D++++++ ++ D D+ +D+ ++D
Sbjct: 39 EVAKSRAPAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDD 86
>gnl|CDD|239908 cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs8_sc7: Rrp5
Homo sapiens S1 repeat 8 (hs8) and Saccharomyces
cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a
trans-acting factor important for biogenesis of both
the 40S and 60S eukaryotic ribosomal subunits. Rrp5
has two distinct regions, an N-terminal region
containing tandemly repeated S1 RNA-binding domains (12
S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in
H. sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of
A0-A2. This CD includes H. sapiens S1 repeat 8 and S.
cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but
not in prokaryotes or archaea.
Length = 83
Score = 30.2 bits (69), Expect = 0.12
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 2/63 (3%)
Query: 23 VISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMT 82
V +I G +V L + G+ S +S + + + G++ V VD+EK
Sbjct: 22 VRNITPYGVFVEFL--GGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79
Query: 83 TVT 85
++
Sbjct: 80 LLS 82
>gnl|CDD|180908 PRK07252, PRK07252, hypothetical protein; Provisional.
Length = 120
Score = 31.2 bits (71), Expect = 0.12
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 22 TVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76
T+ I GA+V L N G+I +SE+ I +I++L++VG+ V V+ D
Sbjct: 10 TITGIKPYGAFVAL--ENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFD 62
>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin. Nucleoplasmins are also
known as chromatin decondensation proteins. They bind to
core histones and transfer DNA to them in a reaction
that requires ATP. This is thought to play a role in the
assembly of regular nucleosomal arrays.
Length = 146
Score = 31.5 bits (72), Expect = 0.12
Identities = 16/31 (51%), Positives = 21/31 (67%)
Query: 139 AENAEVAADDDEDEEDFDNERDGDEGEDEEE 169
A + + DD+EDEE+ D+E D DE E EEE
Sbjct: 108 ASEEDESDDDEEDEEEEDDEEDDDEDESEEE 138
Score = 27.7 bits (62), Expect = 2.5
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 142 AEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
A + D+DEED + E D ++ +++E E E
Sbjct: 108 ASEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 32.3 bits (73), Expect = 0.13
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 131 ARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
AR + + + DD+DE++ + D D+ ED+EE E E+
Sbjct: 137 ARHLAEEDMSPRDNFVIDDDDEDE---DEDDDDEEDDEEEEEEE 177
Score = 30.8 bits (69), Expect = 0.38
Identities = 12/25 (48%), Positives = 20/25 (80%)
Query: 147 DDDEDEEDFDNERDGDEGEDEEEGE 171
DDD+++ED D++ + D+ E+EEE E
Sbjct: 154 DDDDEDEDEDDDDEEDDEEEEEEEE 178
Score = 28.1 bits (62), Expect = 2.8
Identities = 14/23 (60%), Positives = 18/23 (78%)
Query: 147 DDDEDEEDFDNERDGDEGEDEEE 169
D+DEDE+D D E D +E E+EEE
Sbjct: 157 DEDEDEDDDDEEDDEEEEEEEEE 179
Score = 28.1 bits (62), Expect = 3.4
Identities = 13/30 (43%), Positives = 22/30 (73%)
Query: 140 ENAEVAADDDEDEEDFDNERDGDEGEDEEE 169
+N + DD++++ED D+E D +E E+EEE
Sbjct: 149 DNFVIDDDDEDEDEDDDDEEDDEEEEEEEE 178
>gnl|CDD|181215 PRK08059, PRK08059, general stress protein 13; Validated.
Length = 123
Score = 30.8 bits (70), Expect = 0.13
Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 8/85 (9%)
Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
EV VV V I GA+V L E +G++ +SE++ ++ I+ + VG V V+
Sbjct: 6 EVGSVVTGKVTGIQPYGAFVALDE--ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVL 63
Query: 74 RVDKEKVMTTVTPEKADGLKALQEA 98
VD+EK +++ ++A +EA
Sbjct: 64 SVDEEKGKISLS------IRATEEA 82
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 32.0 bits (73), Expect = 0.14
Identities = 14/61 (22%), Positives = 24/61 (39%)
Query: 114 QVQMAPKVVTASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
Q + K A++ E + ++ D+D E D D+ D ED E+ +
Sbjct: 228 QPKKQAKSSKRRTIAQIDGIDSDDEGDGSDDDDDEDAIESDLDDSDDDVSDEDGEDLFDT 287
Query: 174 D 174
D
Sbjct: 288 D 288
>gnl|CDD|240190 cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain of a
transcription accessory factor called Tex, which has
been characterized in Bordetella pertussis and
Pseudomonas aeruginosa. The tex gene is essential in
Bortella pertusis and is named for its role in toxin
expression. Tex has two functional domains, an
N-terminal domain homologous to the Escherichia coli
maltose repression protein, which is a poorly defined
transcriptional factor, and a C-terminal S1 RNA-binding
domain. Tex is found in prokaryotes, eukaryotes, and
archaea.
Length = 68
Score = 29.5 bits (67), Expect = 0.17
Identities = 15/58 (25%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 22 TVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79
V ++ + GA+V + + G+I +S+++ R + + ++ VG V VI +D+E+
Sbjct: 7 VVTNVTDFGAFVDIGVKQD--GLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEER 62
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 31.9 bits (72), Expect = 0.18
Identities = 14/53 (26%), Positives = 28/53 (52%)
Query: 122 VTASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+ A ++ E + + + D +E+EE+ + E + +E E+EEE E E+
Sbjct: 837 LNAENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEE 889
Score = 29.6 bits (66), Expect = 1.1
Identities = 26/94 (27%), Positives = 38/94 (40%), Gaps = 13/94 (13%)
Query: 93 KALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAAD----- 147
K E K E G +V + E EL + + EA+ E D
Sbjct: 800 KVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAE-NQGEAKQDEKGVDGGGGS 858
Query: 148 ---DDEDEEDFDNERDGDEGED----EEEGENED 174
D E+EE+ + E + +E E+ EEE ENE+
Sbjct: 859 DGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEE 892
Score = 27.7 bits (61), Expect = 3.6
Identities = 24/109 (22%), Positives = 41/109 (37%), Gaps = 17/109 (15%)
Query: 75 VDKEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQM 134
++ E++ G + +T K + E G + P E E +
Sbjct: 649 GERPTEAEGENGEESGGEAEQEGETET-KGENESEGEI------PAERKGEQEGEGEIEA 701
Query: 135 ERAEAENAEVA----------ADDDEDEEDFDNERDGDEGEDEEEGENE 173
+ A+ + A A+ EDE + + +G+E EDE EGE E
Sbjct: 702 KEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAE 750
Score = 26.5 bits (58), Expect = 8.6
Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 104 AKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADD----DEDEEDFDNER 159
AK+ LG + + +A T E + AE EN E + + E E +NE
Sbjct: 622 AKVMALGDLSKGDVAEAEHTGERTGEEGERPTEAEGENGEESGGEAEQEGETETKGENES 681
Query: 160 DGDEGEDEEEGENED 174
+G+ E +GE E
Sbjct: 682 EGEI-PAERKGEQEG 695
Score = 26.5 bits (58), Expect = 9.9
Identities = 10/53 (18%), Positives = 19/53 (35%)
Query: 122 VTASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+ + AE + E + + + + D E + GE E EN+
Sbjct: 791 MKGDEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQG 843
>gnl|CDD|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed.
Length = 318
Score = 31.3 bits (71), Expect = 0.22
Identities = 37/146 (25%), Positives = 63/146 (43%), Gaps = 30/146 (20%)
Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
EV +VV+ TV I GA++ + + G++ +SE+S I + + + V V++I
Sbjct: 195 EVGEVVVGTVRGIKPYGAFIDI---GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMII 251
Query: 74 RVDKEKVMTTVT-----PEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEA 128
+D E+ +++ PE D LK Q+ D A + A
Sbjct: 252 DLDAERGRISLSTKQLEPEPGDMLKDPQKVFDK----------------------AEEMA 289
Query: 129 ELARQMERAEAENAEVAADDDEDEED 154
RQM A+AE E ++ E+E
Sbjct: 290 AKYRQMLLAQAEGGEEPEEEMEEEVA 315
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 31.1 bits (71), Expect = 0.24
Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 125 SDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
E EL + +A DDD++E D + + + + ED+E+ +++D
Sbjct: 105 DIEEELQDEPRYDDAYRDLEEDDDDDEESD-EEDEESSKSEDDEDDDDDD 153
>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 = 30.5 bits (69), Expect = 0.32
Identities = 12/48 (25%), Positives = 21/48 (43%)
Query: 126 DEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
D+ E + +R E + ADD + D D+ D + +D E+
Sbjct: 99 DDEEDEIKRKRIEEDARNSDADDSDSSSDSDSSDDDSDDDDSEDETAA 146
>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 = 30.5 bits (69), Expect = 0.34
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 103 KAKIEQLGGVFQVQMAPKVVTASDEAELARQME----RAEAENAEVAADDDEDEEDFDNE 158
KA + F+ ++ D E +E EAE+ + + DE+EE+ + E
Sbjct: 125 KAGKKLALSKFKRKVGLFTEEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEE 184
Query: 159 RDGDEGEDEEEGEN 172
D D +D+++ ++
Sbjct: 185 EDEDFDDDDDDDDD 198
Score = 26.6 bits (59), Expect = 7.1
Identities = 22/102 (21%), Positives = 46/102 (45%), Gaps = 2/102 (1%)
Query: 72 VIRVDKEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELA 131
V+ ++K+ + + E + I K+ L + A V ++ +
Sbjct: 119 VMGINKKAGKKLALSKFKRKVGLFTEEEEDIDEKLSMLEKKLKELEAEDVD--EEDEKDE 176
Query: 132 RQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
+ E E E+ + DDD+D++D++ E D GED++ ++E
Sbjct: 177 EEEEEEEEEDEDFDDDDDDDDDDYNAENYFDNGEDDDYDDDE 218
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 30.7 bits (69), Expect = 0.36
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 123 TASDEAELA-RQMERAEAENAEVAADDDEDEEDFDNERDGD 162
+A E+E R+ E E E + DD DE D D+E G+
Sbjct: 239 SAPQESEATDRESESGEEEMVQSDQDDLPDESDDDSETPGE 279
Score = 28.8 bits (64), Expect = 1.8
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 129 ELARQMERAEAENAEVAADDDEDEEDFDNERDGDEG-EDEEEGENED 174
E+ R ME AE DD E E++ D + D E EE+GE E
Sbjct: 192 EMLRSMELAEE-----MGDDTESEDEEDGDDDQPTENEQEEQGEGEG 233
Score = 27.6 bits (61), Expect = 4.2
Identities = 14/46 (30%), Positives = 21/46 (45%)
Query: 129 ELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
ELA +M E DDD+ E+ E+ EGE +E ++
Sbjct: 198 ELAEEMGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQE 243
>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 = 30.5 bits (69), Expect = 0.39
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 131 ARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
R+ + EV D+DE+EE +E + +EGED EE ++
Sbjct: 357 KRRARLDPIDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQS 400
Score = 26.6 bits (59), Expect = 9.0
Identities = 30/133 (22%), Positives = 49/133 (36%), Gaps = 25/133 (18%)
Query: 38 YNNIEGMILLSELSRRRI-RSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKADGLKALQ 96
Y + + EL RRR+ I L+R + + V K + +T + D +A
Sbjct: 310 YKPLRSRV---ELRRRRVNDVIRPLVREHNNDQLNV----KLRNPSTKESKMRDKRRARL 362
Query: 97 EAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADDDEDEEDFD 156
+ ID ++++ DE E R E E E + + + ED
Sbjct: 363 DPID--FEEVDED---------------EDEEEEQRSDEHEEEEGEDSEEEGSQSREDGS 405
Query: 157 NERDGDEGEDEEE 169
+E D G D E
Sbjct: 406 SESSSDVGSDSES 418
>gnl|CDD|225094 COG2183, Tex, Transcriptional accessory protein [Transcription].
Length = 780
Score = 30.7 bits (70), Expect = 0.41
Identities = 17/68 (25%), Positives = 40/68 (58%), Gaps = 2/68 (2%)
Query: 18 VVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK 77
++ TV ++ + GA+V + + +G++ +S+LS + ++ N++++VG V VI VD
Sbjct: 661 ILEGTVRNVVDFGAFVDIGVHQ--DGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDT 718
Query: 78 EKVMTTVT 85
+ ++
Sbjct: 719 ARKRIALS 726
>gnl|CDD|225731 COG3190, FliO, Flagellar biogenesis protein [Cell motility and
secretion].
Length = 137
Score = 29.7 bits (67), Expect = 0.41
Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 46 LLSELSRRRIRSINKLIR------VGKTEPVVVIRVDKEKVMTTVTPEKADGLKALQEAI 99
L+ L R + + ++ +G E VV++ V ++++ VT ++ L L
Sbjct: 44 LVKRLGRAPLFKGSSGLKILASRSLGSRESVVLVEVGDKRLVLGVTAQQITLLHTLPPNA 103
Query: 100 DT 101
Sbjct: 104 PL 105
>gnl|CDD|234285 TIGR03625, L3_bact, 50S ribosomal protein L3, bacterial. This
model describes bacterial (and mitochondrial and
chloroplast) class of ribosomal protein L3. A separate
model describes the archaeal form, where both belong to
Pfam family pfam00297. The name is phrased to meet the
needs of bacterial genome annotation. Organellar forms
typically will have transit peptides, N-terminal to the
region modeled here.
Length = 202
Score = 30.1 bits (69), Expect = 0.46
Identities = 17/41 (41%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 65 GKTEPVVVIRVDKEKVMTTVTPEKADGLKALQEAIDTIKAK 105
GK PV VI V V T EK DG A+Q K K
Sbjct: 17 GKAVPVTVIEVGPNVVTQVKTVEK-DGYSAVQLGFGEKKEK 56
>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha
subunit. The alpha-subunit of the TRAP complex (TRAP
alpha) is a single-spanning membrane protein of the
endoplasmic reticulum (ER) which is found in proximity
of nascent polypeptide chains translocating across the
membrane.
Length = 281
Score = 30.1 bits (68), Expect = 0.48
Identities = 14/48 (29%), Positives = 24/48 (50%)
Query: 124 ASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGE 171
A E EAE+ V D++++ ++E + E E++EEGE
Sbjct: 25 KGPFASAQDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGE 72
>gnl|CDD|221931 pfam13136, DUF3984, Protein of unknown function (DUF3984). This
family of proteins is functionally uncharacterized. This
family of proteins is found in eukaryotes. Proteins in
this family are typically between 393 and 442 amino
acids in length.
Length = 301
Score = 30.1 bits (68), Expect = 0.56
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 135 ERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEE 169
E AE A + DD+ D+E + ++ DE E
Sbjct: 240 EDIRAEMA--SIDDESFSSLSDSESESEDEIDEAE 272
>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 = 30.3 bits (68), Expect = 0.63
Identities = 14/48 (29%), Positives = 22/48 (45%)
Query: 127 EAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+ + E E E A + E+E + +E DGD E EE+ E +
Sbjct: 460 QESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEEDAERRN 507
Score = 29.5 bits (66), Expect = 0.92
Identities = 19/56 (33%), Positives = 31/56 (55%)
Query: 119 PKVVTASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
K + S E+ E E E+ E +++E+EE+ + E + +EGEDEEE E +
Sbjct: 422 SKASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVE 477
Score = 28.0 bits (62), Expect = 3.3
Identities = 13/52 (25%), Positives = 21/52 (40%)
Query: 123 TASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
S E E + E E E + +++EE+ + E D E+ E D
Sbjct: 442 EESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGD 493
Score = 27.6 bits (61), Expect = 4.3
Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 5/55 (9%)
Query: 124 ASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGD-----EGEDEEEGENE 173
+E E + + +E E E +++E E D +E + + +G+ EE E+
Sbjct: 449 EEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEEDA 503
>gnl|CDD|240196 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal
protein S1 (RPS1) domain. RPS1 is a component of the
small ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria,
the tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains
have been identified in plants and humans, however
these lack the N-terminal HMBPP reductase domain. This
CD includes S1 repeat 6 (ec6) of the Escherichia coli
RPS1. Autoantibodies to double-stranded DNA from
patients with systemic lupus erythematosus cross-react
with the human RPS1 homolog.
Length = 73
Score = 28.0 bits (63), Expect = 0.69
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 2/69 (2%)
Query: 17 DVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76
+V V + GA V L + +EG + +ELSR R+ + +VG + VD
Sbjct: 2 SIVTGKVTEVDAKGATVKLGD--GVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVD 59
Query: 77 KEKVMTTVT 85
++ +++
Sbjct: 60 RKNRKISLS 68
>gnl|CDD|219240 pfam06957, COPI_C, Coatomer (COPI) alpha subunit C-terminus. This
family represents the C-terminus (approximately 500
residues) of the eukaryotic coatomer alpha subunit.
Coatomer (COPI) is a large cytosolic protein complex
which forms a coat around vesicles budding from the
Golgi apparatus. Such coatomer-coated vesicles have been
proposed to play a role in many distinct steps of
intracellular transport. Note that many family members
also contain the pfam04053 domain.
Length = 421
Score = 29.8 bits (67), Expect = 0.80
Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 10/73 (13%)
Query: 111 GVFQVQMAPKV-VTASDEAELARQMERAEAENAEVAADD-------DEDEEDFDNERDG- 161
G F+ + +A+ + A A+ A + DD DE+ + DG
Sbjct: 2 GFFEGGLLSLGGQSATARQPTVGGDKAAAADFAVMGGDDWGEDADLGLDEDGYLEGEDGL 61
Query: 162 -DEGEDEEEGENE 173
D+ E E G+ E
Sbjct: 62 LDDEEGPEGGDEE 74
>gnl|CDD|165194 PHA02858, PHA02858, EIF2a-like PKR inhibitor; Provisional.
Length = 86
Score = 28.1 bits (63), Expect = 0.80
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMIL-LSELSRRRIRSINKLIRVGKTEPV 70
+P + +V ++ + + YV L++Y +E +I+ ++ R + K + VGKT V
Sbjct: 13 FPNINEVTK-GIVFVKDNIFYVKLIDYG-LEALIVNYVNVNADRAEKLKKKL-VGKTINV 69
Query: 71 VVIRVDKEK 79
VIR DK K
Sbjct: 70 QVIRTDKLK 78
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi. This family includes
the fifth essential DNA polymerase in yeast EC:2.7.7.7.
Pol5p is localised exclusively to the nucleolus and
binds near or at the enhancer region of rRNA-encoding
DNA repeating units.
Length = 784
Score = 29.8 bits (67), Expect = 0.84
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 138 EAENAEVAADDDEDEE---DFDNERDGDEGEDEEEGENED 174
E E+ DDDEDE + +GED EE E ED
Sbjct: 650 EDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQED 689
Score = 28.7 bits (64), Expect = 1.7
Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 7/79 (8%)
Query: 91 GLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADDDE 150
+ LQ +D +KA ++ +E E + + + E D +
Sbjct: 621 TNEGLQLILDVLKADE-------NKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSES 673
Query: 151 DEEDFDNERDGDEGEDEEE 169
+ E + + DE ED+ E
Sbjct: 674 ESESDGEDGEEDEQEDDAE 692
>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 = 29.6 bits (67), Expect = 0.85
Identities = 18/78 (23%), Positives = 35/78 (44%)
Query: 97 EAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADDDEDEEDFD 156
E + K + L F+ E + + + + E+ E DD E+EE+
Sbjct: 290 EEEEDSKESADDLDDEFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDV 349
Query: 157 NERDGDEGEDEEEGENED 174
+ D +E E++E+ ++ED
Sbjct: 350 DLSDEEEDEEDEDSDDED 367
Score = 28.4 bits (64), Expect = 2.0
Identities = 17/59 (28%), Positives = 34/59 (57%), Gaps = 11/59 (18%)
Query: 127 EAELARQM-----ERAEAENAEVAADDDEDE------EDFDNERDGDEGEDEEEGENED 174
EAE R+M + E E+++ +ADD +DE ++F + ++ E+EE+G +++
Sbjct: 275 EAERLRRMRGEEEDDEEEEDSKESADDLDDEFEPDDDDNFGLGQGEEDEEEEEDGVDDE 333
Score = 28.0 bits (63), Expect = 2.7
Identities = 16/48 (33%), Positives = 27/48 (56%)
Query: 122 VTASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEE 169
V DE + +E E + ++DE++ED D+E D +E E+E+E
Sbjct: 330 VDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKE 377
Score = 27.7 bits (62), Expect = 4.4
Identities = 7/38 (18%), Positives = 21/38 (55%)
Query: 137 AEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+ ++ ++D D D + + + ++ +DE++ E E+
Sbjct: 336 EDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEE 373
>gnl|CDD|220102 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a
nuclear protein involved in bud-site selection. It plays
a role in positioning the proximal bud pole signal. More
recently it has been shown to be involved in ribosome
biogenesis.
Length = 424
Score = 29.4 bits (66), Expect = 0.95
Identities = 13/79 (16%), Positives = 38/79 (48%)
Query: 93 KALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADDDEDE 152
K ++ +++I ++++ G+ K + +++ E ++ ++ E + +DE +
Sbjct: 123 KPVKNVLESIMEGLDKILGIETKAKKGKAKKKTKKSKKKEAKESSDKDDEEESESEDESK 182
Query: 153 EDFDNERDGDEGEDEEEGE 171
+ E D D+ E+E+
Sbjct: 183 SEESAEDDSDDEEEEDSDS 201
>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27. This protein forms
the C subunit of DNA polymerase delta. It carries the
essential residues for binding to the Pol1 subunit of
polymerase alpha, from residues 293-332, which are
characterized by the motif D--G--VT, referred to as the
DPIM motif. The first 160 residues of the protein form
the minimal domain for binding to the B subunit, Cdc1,
of polymerase delta, the final 10 C-terminal residues,
362-372, being the DNA sliding clamp, PCNA, binding
motif.
Length = 427
Score = 29.4 bits (66), Expect = 1.0
Identities = 22/100 (22%), Positives = 35/100 (35%), Gaps = 1/100 (1%)
Query: 76 DKEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQME 135
KE +TV E + ++ A+ L SD E + E
Sbjct: 232 KKEASESTVKEESEEESGKRDVILEDESAEPTGLDEDEDEDEPKPSGERSDSEEETEEKE 291
Query: 136 RAEAENAE-VAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+ + + + + D+DEDEE E E+ EE E
Sbjct: 292 KEKRKRLKKMMEDEDEDEEMEIVPESPVEEEESEEPEPPP 331
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 29.5 bits (67), Expect = 1.0
Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 14/80 (17%)
Query: 90 DGLKALQEAI-DTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADD 148
G+K L + I+ P+ EA + + ++ +
Sbjct: 319 LGVKELCWDLMTFIEE-------------NPREEAEEAEAPEKVEFMWDDYHREQLEEVE 365
Query: 149 DEDEEDFDNERDGDEGEDEE 168
+ED++D+D++ D D+ E E
Sbjct: 366 EEDDDDWDDDWDEDDDEGVE 385
Score = 26.4 bits (59), Expect = 8.7
Identities = 8/46 (17%), Positives = 19/46 (41%)
Query: 129 ELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
E R+ +V D+ + E + ++ +D ++ +ED
Sbjct: 334 ENPREEAEEAEAPEKVEFMWDDYHREQLEEVEEEDDDDWDDDWDED 379
>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional.
Length = 449
Score = 29.4 bits (66), Expect = 1.1
Identities = 14/75 (18%), Positives = 32/75 (42%)
Query: 100 DTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADDDEDEEDFDNER 159
D+ + E ++ + + + E ++E +AE AE A E ++E
Sbjct: 372 DSAEYDQEAEDAKVAELISQREEEEALQREAEERLEAEQAERAEEDARLRELYPLPEDEF 431
Query: 160 DGDEGEDEEEGENED 174
+ ++ +E + E E+
Sbjct: 432 EDEDELEEAQPEEEE 446
>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT. This family
consists of several bacterial cobalamin biosynthesis
(CobT) proteins. CobT is involved in the transformation
of precorrin-3 into cobyrinic acid.
Length = 282
Score = 29.0 bits (65), Expect = 1.1
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 9/82 (10%)
Query: 99 IDTIKAKIEQLGGVFQVQMAPKVVT-----ASDEA-ELARQMERAEAENAEVAADDDEDE 152
D +++L Q A V + D A EL + E A++E+ E D+D+ +
Sbjct: 175 EDKAGKDLDRLAACVDDQQAFARVVRDMLSSMDMAEELGDEPESADSEDNE---DEDDPK 231
Query: 153 EDFDNERDGDEGEDEEEGENED 174
ED D+++ +E + +ED
Sbjct: 232 EDEDDDQGEEEESGSSDSLSED 253
>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 = 29.3 bits (66), Expect = 1.2
Identities = 14/26 (53%), Positives = 17/26 (65%)
Query: 149 DEDEEDFDNERDGDEGEDEEEGENED 174
+ ED + ERD +E EDEEE E ED
Sbjct: 378 ALEIEDANTERDDEEEEDEEEEEEED 403
Score = 27.0 bits (60), Expect = 5.7
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 135 ERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+ + E D++E+EE+ ++E E D+EE E +D
Sbjct: 383 DANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDD 422
>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This nucleolar
family of proteins are involved in 60S ribosomal
biogenesis. They are specifically involved in the
processing beyond the 27S stage of 25S rRNA maturation.
This family contains sequences that bear similarity to
the glioma tumour suppressor candidate region gene 2
protein (p60). This protein has been found to interact
with herpes simplex type 1 regulatory proteins.
Length = 387
Score = 28.9 bits (65), Expect = 1.2
Identities = 7/43 (16%), Positives = 17/43 (39%)
Query: 129 ELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGE 171
E E +E ++ +D+ + +++ + E E E
Sbjct: 225 EKMAPEASRLDEMSEGLLEESDDDGEEESDDESAWEGFESEYE 267
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 29.0 bits (65), Expect = 1.3
Identities = 12/48 (25%), Positives = 22/48 (45%)
Query: 124 ASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGE 171
+ +A E EA +D D+DE ++E + +E ++E E
Sbjct: 5 VNTQANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEEAESP 52
Score = 27.5 bits (61), Expect = 4.7
Identities = 27/102 (26%), Positives = 41/102 (40%), Gaps = 23/102 (22%)
Query: 64 VGKTEPVVVIRVDKEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVT 123
V K E + ++R E V ++ D E ID I AK E+
Sbjct: 631 VNKDELLQMVRYGAEMVFSSKDSTITD------EDIDRIIAKGEE--------------- 669
Query: 124 ASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGE 165
AEL +M++ + + DD + DFD+E D DE +
Sbjct: 670 --ATAELDAKMKKFTEDAIKFKMDDTAELYDFDDEDDKDENK 709
>gnl|CDD|234510 TIGR04225, CshA_fibril_rpt, CshA-type fibril repeat. Many proteins
with this repeat are LPXTG-anchored surface proteins of
Firmicutes species, but the repeat occurs more broadly.
Members include CshA from Streptococcus gordonii.
Length = 103
Score = 27.6 bits (62), Expect = 1.4
Identities = 12/26 (46%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 64 VGKTEPVVVIRVDKE--KVMTTVTPE 87
VG PV V RVDK T TP
Sbjct: 77 VGTATPVTVQRVDKNGTPATATYTPT 102
>gnl|CDD|236126 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 486
Score = 28.9 bits (65), Expect = 1.6
Identities = 30/102 (29%), Positives = 51/102 (50%), Gaps = 14/102 (13%)
Query: 22 TVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVM 81
V SI GA+V L ++G++ +SELS + I ++++ VG+ V V+ VD ++
Sbjct: 215 VVSSIVNFGAFVDL---GGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRER 271
Query: 82 TTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVT 123
+++ LKA QE A+ +G Q+ P VT
Sbjct: 272 VSLS------LKATQEDPWQQFARTHAIG-----QIVPGKVT 302
Score = 26.9 bits (60), Expect = 6.9
Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 30 GAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79
GA+V + E IEG++ +SEL+ R + ++++VG V VI +D E+
Sbjct: 308 GAFVRVEE--GIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLER 355
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 28.9 bits (65), Expect = 1.6
Identities = 21/115 (18%), Positives = 44/115 (38%), Gaps = 6/115 (5%)
Query: 66 KTEPVVVIRVDKEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTAS 125
+ V ++ E G K +K ++E + + + TA
Sbjct: 1274 APKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTAR 1333
Query: 126 DEAELARQMERAEAENAEVAA------DDDEDEEDFDNERDGDEGEDEEEGENED 174
+ R + + ++++ + D E+D D+E D E ED+E+ E++D
Sbjct: 1334 KKKSKTRVKQASASQSSRLLRRPRKKKSDSSSEDDDDSEVDDSEDEDDEDDEDDD 1388
>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa). Members of this
family of proteins are part of the yeast nuclear pore
complex-associated pre-60S ribosomal subunit. The family
functions as a highly conserved exonuclease that is
required for the 5'-end maturation of 5.8S and 25S
rRNAs, demonstrating that 5'-end processing also has a
redundant pathway. Nop25 binds late pre-60S ribosomes,
accompanying them from the nucleolus to the nuclear
periphery; and there is evidence for both physical and
functional links between late 60S subunit processing and
export.
Length = 134
Score = 28.1 bits (63), Expect = 1.7
Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 127 EAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+ EL +Q++ + + ++D++E+ + E D +DE EG E
Sbjct: 62 KQELEKQLKERKEALKLLEEENDDEEDA-ETEDTEDVEDDEWEGFPEP 108
>gnl|CDD|215079 PLN00151, PLN00151, potassium transporter; Provisional.
Length = 852
Score = 28.6 bits (64), Expect = 1.8
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 147 DDDEDEEDFDNERDGDE---GEDEEEGE 171
DD ED D++ D + G EEE +
Sbjct: 35 DDSEDPASLDDDDDDRDSGGGMLEEEED 62
>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF)
Superfamily; Provisional.
Length = 844
Score = 28.7 bits (64), Expect = 1.8
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 140 ENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
+ DDD+DE DF E D D+ + GE+
Sbjct: 81 NQRKSLDDDDDDEFDFLYEDDEDDAGNATSGESS 114
>gnl|CDD|226908 COG4531, ZnuA, ABC-type Zn2+ transport system, periplasmic
component/surface adhesin [Inorganic ion transport and
metabolism].
Length = 318
Score = 28.5 bits (64), Expect = 1.9
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 83 TVTPEKADGLKALQEAIDTIKAKIEQLGG--VF-QVQMAPKVVTA 124
TV+PE G K L E I+ ++++ VF + Q PKVV
Sbjct: 235 TVSPEVQPGAKRLAE----IRTQLKEQKATCVFAEPQFRPKVVET 275
Score = 27.8 bits (62), Expect = 2.9
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 8/54 (14%)
Query: 120 KVVTASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
KVVT +D + + R A D E+E D ++ G + + + + +E
Sbjct: 101 KVVTLADLPGVKPLLFRE--------AHDHEEEHDHGHDHAGADHKGDHDHHHE 146
>gnl|CDD|107272 cd06277, PBP1_LacI_like_1, Ligand-binding domain of uncharacterized
DNA-binding regulatory proteins that are members of the
LacI-GalR family of bacterial transcription repressors.
This group includes the ligand-binding domain of
uncharacterized DNA-binding regulatory proteins that are
members of the LacI-GalR family of bacterial
transcription repressors. The LacI-GalR family
repressors are composed of two functional domains: an
N-terminal HTH (helix-turn-helix) domain, which is
responsible for the DNA-binding specificity, and a
C-terminal ligand-binding domain, which is homologous to
the sugar-binding domain of ABC-type transport systems
that contain the type I periplasmic binding protein-like
fold. As also observed in the periplasmic binding
proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 268
Score = 28.0 bits (63), Expect = 2.1
Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 7/82 (8%)
Query: 35 LLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI--RVDKEKVMTTVTPEKADGL 92
LE ++G+ILL +S I ++ +G P V++ + EK +T +
Sbjct: 53 FLEDGKVDGIILLGGIST---EYIKEIKELGI--PFVLVDHYIPNEKADCVLTDNYSGAY 107
Query: 93 KALQEAIDTIKAKIEQLGGVFQ 114
A + I+ KI +G
Sbjct: 108 AATEYLIEKGHRKIGFVGDPLY 129
>gnl|CDD|219939 pfam08619, Nha1_C, Alkali metal cation/H+ antiporter Nha1 C
terminus. The C terminus of the plasma membrane Nha1
antiporter plays an important role in the immediate cell
response to hypo-osmotic shock which prevents an
execessive loss of ions and water. This domain is found
with pfam00999.
Length = 430
Score = 28.2 bits (63), Expect = 2.3
Identities = 15/52 (28%), Positives = 20/52 (38%)
Query: 123 TASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
EA R+ + + D ED D ERD + +DEEE E
Sbjct: 359 LLGSEASERRKNREPSSSSPPSRPRSRRDSEDEDTERDDSDSDDEEETPAER 410
>gnl|CDD|223052 PHA03346, PHA03346, US22 family homolog; Provisional.
Length = 520
Score = 28.2 bits (63), Expect = 2.3
Identities = 10/49 (20%), Positives = 19/49 (38%)
Query: 124 ASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGEN 172
A LA E DDDE +++ D++ + + +E+
Sbjct: 405 ADGGGGLAPPPEPPRPPPPPFPDDDDEGDDEDDDDWEDLGFDLDEDDVY 453
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 28.4 bits (64), Expect = 2.4
Identities = 23/83 (27%), Positives = 34/83 (40%), Gaps = 12/83 (14%)
Query: 76 DKEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDE--AELARQ 133
+ E+ + V P+KA A+ AI KAK + Q + D A +A
Sbjct: 602 EPEEQVAEVDPKKA----AVAAAIARAKAKKAEQ------QANAEPEEPVDPRKAAVAAA 651
Query: 134 MERAEAENAEVAADDDEDEEDFD 156
+ RA+A A + E EE D
Sbjct: 652 IARAKARKAAQQQANAEPEEAED 674
Score = 27.2 bits (61), Expect = 4.8
Identities = 13/68 (19%), Positives = 19/68 (27%), Gaps = 5/68 (7%)
Query: 88 KADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQME-RAEAENAEVAA 146
A A+ A+ +KAK + K D + + E R A A
Sbjct: 481 AAKDKDAVAAALARVKAKKAAA----TQPIVIKAGARPDNSAVIAAREARKAQARARQAE 536
Query: 147 DDDEDEED 154
D
Sbjct: 537 KQAAAAAD 544
>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional.
Length = 413
Score = 28.0 bits (62), Expect = 2.5
Identities = 8/45 (17%), Positives = 14/45 (31%)
Query: 127 EAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGE 171
E A + N + ++ ED E + E E +
Sbjct: 146 PHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSP 190
Score = 26.9 bits (59), Expect = 7.0
Identities = 5/50 (10%), Positives = 11/50 (22%), Gaps = 1/50 (2%)
Query: 125 SDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
S E+ A + + E + + E+
Sbjct: 127 SPESP-ASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSP 175
Score = 26.5 bits (58), Expect = 9.1
Identities = 7/40 (17%), Positives = 12/40 (30%)
Query: 135 ERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
E A E+ + + + D E + E E
Sbjct: 148 EPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEP 187
>gnl|CDD|239911 cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec2_hs2:
Ribosomal protein S1 (RPS1) domain. RPS1 is a component
of the small ribosomal subunit thought to be involved
in the recognition and binding of mRNA's during
translation initiation. The bacterial RPS1 domain
architecture consists of 4-6 tandem S1 domains. In some
bacteria, the tandem S1 array is located C-terminal to
a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain.While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains
have been identified in plants and humans, however
these lack the N-terminal HMBPP reductase domain. This
CD includes S1 repeat 2 of the Escherichia coli and
Homo sapiens RPS1 (ec2 and hs2, respectively).
Autoantibodies to double-stranded DNA from patients
with systemic lupus erythematosus cross-react with the
human RPS1 homolog.
Length = 67
Score = 26.3 bits (59), Expect = 2.6
Identities = 12/64 (18%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV 75
++V V + G V + + + S++ R + +++ VGK +I +
Sbjct: 1 GEIVEGKVTEKVKGGLIV---DIEGVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEI 55
Query: 76 DKEK 79
D+E+
Sbjct: 56 DRER 59
>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit
[Transcription / DNA replication, recombination, and
repair / Chromatin structure and dynamics].
Length = 1001
Score = 28.1 bits (62), Expect = 2.7
Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 117 MAPKVVTASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGED----EEEGEN 172
M + + E + E + + ++ +D+E +E + DE E+ EE+GE+
Sbjct: 924 MVGSDDESDESEEEVSEYEASSDDESDETDEDEESDE-SSEDLSEDESENDSSDEEDGED 982
Query: 173 ED 174
D
Sbjct: 983 WD 984
Score = 28.1 bits (62), Expect = 2.8
Identities = 11/39 (28%), Positives = 25/39 (64%)
Query: 135 ERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
E E E ++ +++D ++E ++ D ++GED +E E++
Sbjct: 951 ETDEDEESDESSEDLSEDESENDSSDEEDGEDWDELESK 989
>gnl|CDD|217373 pfam03115, Astro_capsid, Astrovirus capsid protein precursor. This
product is encoded by astrovirus ORF2, one of the three
astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein
undergoes an intracellular cleavage to form a 79kD
protein. Subsequently, extracellular trypsin cleavage
yields the three proteins forming the infectious virion.
Length = 787
Score = 27.8 bits (62), Expect = 3.1
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 124 ASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGEN 172
E ++ + E E+ E D++DE D + D E E++ EN
Sbjct: 664 DPYEDLISLEETDTEDESTE----DEDDELDRFDLHDSSGSEPEDDDEN 708
>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor
[Transcription].
Length = 392
Score = 27.7 bits (61), Expect = 3.1
Identities = 14/53 (26%), Positives = 21/53 (39%)
Query: 122 VTASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
V A++ E + EV + EE + D E EE+ ENE+
Sbjct: 279 VGAAEIENKEVSEGDKEQQQEEVENAEAHKEEVQSDRPDEIGEEKEEDDENEE 331
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 28.0 bits (62), Expect = 3.2
Identities = 14/48 (29%), Positives = 21/48 (43%)
Query: 126 DEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
D E ++ A N E ED+ ++D E EDEEE ++
Sbjct: 3915 DLLETEQKSNEQSAANNESDLVSKEDDNKALEDKDRQEKEDEEEMSDD 3962
Score = 28.0 bits (62), Expect = 3.2
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 139 AENAEVAADDDEDEEDFDNERDGDEGEDEEEGE 171
AE+ ++D+D E+ NE D D +E E
Sbjct: 3824 AEDITNTLNEDDDLEELANEEDTANQSDLDESE 3856
Score = 27.3 bits (60), Expect = 6.1
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 126 DEAELARQMERAEAENAEVAADDDED----EEDFDNERDGDEGEDEEEGENED 174
DE +E + N + AA+++ D E+D D D E E+E E D
Sbjct: 3909 DEPNEEDLLETEQKSNEQSAANNESDLVSKEDDNKALEDKDRQEKEDEEEMSD 3961
Score = 26.9 bits (59), Expect = 7.4
Identities = 9/26 (34%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 149 DEDEEDFDNERDGDEGEDEEEGENED 174
DE++E+ D E+D + +DE+ E +
Sbjct: 4017 DENKEEADAEKD-EPMQDEDPLEENN 4041
>gnl|CDD|218421 pfam05086, Dicty_REP, Dictyostelium (Slime Mold) REP protein. This
family consists of REP proteins from Dictyostelium
(Slime molds). REP protein is likely involved in
transcription regulation and control of DNA replication,
specifically amplification of plasmid at low copy
numbers. The formation of homomultimers may be required
for their regulatory activity.
Length = 910
Score = 27.9 bits (62), Expect = 3.3
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 145 AADDDEDEEDFDNERDGDEGEDEEE 169
+DD+ +ED D + D DE EDE+E
Sbjct: 886 ENEDDDADEDEDQDEDEDEDEDEDE 910
Score = 27.5 bits (61), Expect = 4.2
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 140 ENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
+ DDD DE++ D DE EDE+E E+E
Sbjct: 882 SQFQENEDDDADEDE-----DQDEDEDEDEDEDE 910
>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R. This family consists of an
exoribonuclease, ribonuclease R, also called VacB. It is
one of the eight exoribonucleases reported in E. coli
and is broadly distributed throughout the bacteria. In
E. coli, double mutants of this protein and
polynucleotide phosphorylase are not viable. Scoring
between trusted and noise cutoffs to the model are
shorter, divergent forms from the Chlamydiae, and
divergent forms from the Campylobacterales (including
Helicobacter pylori) and Leptospira interrogans
[Transcription, Degradation of RNA].
Length = 709
Score = 28.0 bits (63), Expect = 3.4
Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 15/88 (17%)
Query: 3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS----------- 51
+ +EK E + V + + G +V L E N IEG++ +S L
Sbjct: 618 KKAEYMSEKIGEEFEGV---ISGVTSFGLFVEL-ENNTIEGLVHISTLKDDYYVFDEKGL 673
Query: 52 RRRIRSINKLIRVGKTEPVVVIRVDKEK 79
K+ R+G V V++ D +
Sbjct: 674 ALVGERTGKVFRLGDRVKVRVVKADLDT 701
>gnl|CDD|222918 PHA02687, PHA02687, ORF061 late transcription factor VLTF-4;
Provisional.
Length = 231
Score = 27.7 bits (61), Expect = 3.5
Identities = 10/48 (20%), Positives = 23/48 (47%)
Query: 127 EAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+ A + E++ ++ DD D+++ + E + +EE G+ E
Sbjct: 92 KKAKADKPEKSPKAVEKLCPPDDRDDKNEEKEPTEEAQRNEESGDAEG 139
>gnl|CDD|130083 TIGR01010, BexC_CtrB_KpsE, polysaccharide export inner-membrane
protein, BexC/CtrB/KpsE family. This family contains
gamma proteobacterial proteins involved in capsule
polysaccharide export [Transport and binding proteins,
Carbohydrates, organic alcohols, and acids].
Length = 362
Score = 27.8 bits (62), Expect = 3.7
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 35 LLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPEKADGLK 93
LL+Y + S ++ I+ L + E +IRV + + ++TPE+ +
Sbjct: 193 LLKYQIKNKVFDPKAQSSAQLSLISTL----EGE---LIRVQAQLAQLRSITPEQNPQVP 245
Query: 94 ALQEAIDTIKAKIEQ 108
+LQ I +++ +I++
Sbjct: 246 SLQARIKSLRKQIDE 260
>gnl|CDD|227504 COG5177, COG5177, Uncharacterized conserved protein [Function
unknown].
Length = 769
Score = 27.7 bits (61), Expect = 3.8
Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 8/69 (11%)
Query: 103 KAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGD 162
KA + + +Q + A + + E+ A DDD+ +E+ + E GD
Sbjct: 378 KAAVPKGTSFYQAKWAEDEEEEDGQC--------NDEESTMSAIDDDDPKENDNEEVAGD 429
Query: 163 EGEDEEEGE 171
E ++ E
Sbjct: 430 EESAIDDNE 438
>gnl|CDD|177748 PLN00144, PLN00144, acetylornithine transaminase.
Length = 382
Score = 27.4 bits (61), Expect = 3.9
Identities = 21/63 (33%), Positives = 27/63 (42%), Gaps = 14/63 (22%)
Query: 33 VHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKADGL 92
V +EY N+E + KLI+ GKT V V V E + T E GL
Sbjct: 148 VTFVEYGNLE--------------AARKLIQKGKTAAVFVEPVQGEGGIYPATKEFLQGL 193
Query: 93 KAL 95
+AL
Sbjct: 194 RAL 196
>gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal
protein S1; Provisional.
Length = 863
Score = 27.8 bits (61), Expect = 4.0
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS-RRRIRSINKLIRVGKTEPVVVI 73
V DVV V IA+ GA++ L E IEG+ +SE S ++ + ++++G +++
Sbjct: 578 VNDVVKGRVTKIADFGAFIELAE--GIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMIL 635
Query: 74 RVD 76
D
Sbjct: 636 GYD 638
>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional.
Length = 991
Score = 27.7 bits (61), Expect = 4.1
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 130 LARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEE 169
LA ++E + + +DD++ E+ ++E D DE + E
Sbjct: 340 LAMEIEAVRLPDDPIIVEDDDESEEIESECDPDEDKSGAE 379
>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A. The CAF-1
or chromatin assembly factor-1 consists of three
subunits, and this is the first, or A. The A domain is
uniquely required for the progression of S phase in
mouse cells, independent of its ability to promote
histone deposition but dependent on its ability to
interact with HP1 - heterochromatin protein 1-rich
heterochromatin domains next to centromeres that are
crucial for chromosome segregation during mitosis. This
HP1-CAF-1 interaction module functions as a built-in
replication control for heterochromatin, which, like a
control barrier, has an impact on S-phase progression in
addition to DNA-based checkpoints.
Length = 76
Score = 26.0 bits (58), Expect = 4.3
Identities = 8/23 (34%), Positives = 18/23 (78%)
Query: 147 DDDEDEEDFDNERDGDEGEDEEE 169
+++E+ ED ++E + DE ED+++
Sbjct: 49 EEEEEGEDLESEDEEDEEEDDDD 71
>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation
factor RRN3. This family consists of several eukaryotic
proteins which are homologous to the yeast RRN3 protein.
RRN3 is one of the RRN genes specifically required for
the transcription of rDNA by RNA polymerase I (Pol I) in
Saccharomyces cerevisiae.
Length = 554
Score = 27.3 bits (61), Expect = 4.5
Identities = 9/41 (21%), Positives = 22/41 (53%)
Query: 133 QMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
Q E + ++ E ++++D +++ + +DEEE + E
Sbjct: 219 QNELDDIDDEEEERVLADEDDDDEDDMFDMDDDDEEESDPE 259
Score = 27.3 bits (61), Expect = 4.8
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 141 NAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
E+ DDE+EE + D D+ +D + +++D
Sbjct: 219 QNELDDIDDEEEERVLADEDDDDEDDMFDMDDDD 252
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 27.5 bits (62), Expect = 4.6
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 147 DDDEDEEDFDNERDGDEGEDEEEGENED 174
D EED + E D++E E E+
Sbjct: 174 VDPNAEEDPAHVGSELEELDDDEDEEEE 201
Score = 26.7 bits (60), Expect = 6.9
Identities = 8/48 (16%), Positives = 21/48 (43%)
Query: 127 EAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+ + E + V + +ED +E + + +++EE E ++
Sbjct: 157 DRLENGERRLRELIDGFVDPNAEEDPAHVGSELEELDDDEDEEEEEDE 204
>gnl|CDD|222709 pfam14362, DUF4407, Domain of unknown function (DUF4407). This
family of proteins is found in bacteria. Proteins in
this family are typically between 366 and 597 amino
acids in length. There is a single completely conserved
residue R that may be functionally important.
Length = 297
Score = 26.8 bits (60), Expect = 5.9
Identities = 19/113 (16%), Positives = 33/113 (29%), Gaps = 15/113 (13%)
Query: 77 KEKVMTTVTPEKAD---GLKALQEAIDTIKAKIEQLGGVFQVQMAPK---------VVTA 124
+ +V P+ A + ALQ ID +A++ Q + V
Sbjct: 126 QAQVAAGFRPKIAALTAEIAALQAEIDEAQAEVNAAYQEAQCEAEGTGGTGVAGKGPVYK 185
Query: 125 SDEAELARQM---ERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+L E +A A + + + R E + E D
Sbjct: 186 EKREKLDAAQARLETLKARLDAAIAQLEAQKAALERNRQAAVAEKQARIEAND 238
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 27.1 bits (60), Expect = 6.1
Identities = 7/25 (28%), Positives = 17/25 (68%)
Query: 149 DEDEEDFDNERDGDEGEDEEEGENE 173
++ EE ++ + + ++EE+GE+E
Sbjct: 53 EQKEEKEEDAGEEGDEDEEEQGEDE 77
>gnl|CDD|218889 pfam06088, TLP-20, Nucleopolyhedrovirus telokin-like protein-20
(TLP20). This family consists of several
Nucleopolyhedrovirus telokin-like protein-20 (TLP20)
sequences. The function of this family is unknown but
TLP20 is known to shares some antigenic similarities to
the smooth muscle protein telokin although the amino
acid sequence shows no homologies to telokin.
Length = 162
Score = 26.5 bits (59), Expect = 6.4
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 137 AEAENAEVAADDDEDEEDFDNERDGDEGEDEEE 169
A + ++DEDEED + + G D+
Sbjct: 115 APVPHHSSEDENDEDEEDNADRAGIESGIDDSA 147
>gnl|CDD|221620 pfam12527, DUF3727, Protein of unknown function (DUF3727). This
domain family is found in bacteria and eukaryotes, and
is approximately 100 amino acids in length.
Length = 100
Score = 25.6 bits (57), Expect = 6.9
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 147 DDDEDEEDFDNERDGDEGEDEEEG 170
+ E++E + E + D+ EDEEE
Sbjct: 19 PEPEEDEILELEEEDDDDEDEEEE 42
>gnl|CDD|237603 PRK14083, PRK14083, HSP90 family protein; Provisional.
Length = 601
Score = 26.8 bits (60), Expect = 7.0
Identities = 25/123 (20%), Positives = 43/123 (34%), Gaps = 26/123 (21%)
Query: 30 GAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMT---TVTP 86
G Y + E LL L R R + V R+D ++ +TP
Sbjct: 416 GGYTYDSE--------LLERLPRLR-------------PGLTVERLDPAELTDRLEPLTP 454
Query: 87 EKADGLKALQEAIDTIKAK--IEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEV 144
E+ L+ + A + + F+ P + A+ +R+ E A E ++
Sbjct: 455 EEELALRPFLAEAREVLAPFGCDVVIRHFEPADLPALYLHDRAAQHSREREEAVEEADDL 514
Query: 145 AAD 147
AD
Sbjct: 515 WAD 517
>gnl|CDD|178014 PLN02390, PLN02390, molybdopterin synthase catalytic subunit.
Length = 111
Score = 25.8 bits (57), Expect = 7.1
Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 8/54 (14%)
Query: 53 RRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKADGLKALQEAIDTIKAKI 106
+I ++L V E V + V + +AD L A + ID +KA +
Sbjct: 53 HKIAVAHRLGPVPVGETSVFVAVS--------SVHRADALDACKFLIDELKASV 98
>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2. Transcripts
harbouring premature signals for translation termination
are recognised and rapidly degraded by eukaryotic cells
through a pathway known as nonsense-mediated mRNA decay.
In Saccharomyces cerevisiae, three trans-acting factors
(Upf1 to Upf3) are required for nonsense-mediated mRNA
decay.
Length = 171
Score = 26.2 bits (58), Expect = 7.6
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 140 ENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
+E +DD E++E+ E + DE DEEE + D
Sbjct: 1 SGSESESDDGEEDEELPEEDEDDESSDEEEVDLPD 35
>gnl|CDD|240226 PTZ00007, PTZ00007, (NAP-L) nucleosome assembly protein -L;
Provisional.
Length = 337
Score = 26.7 bits (59), Expect = 8.1
Identities = 6/31 (19%), Positives = 14/31 (45%)
Query: 144 VAADDDEDEEDFDNERDGDEGEDEEEGENED 174
A D+D D +++ D D + + ++
Sbjct: 278 EAIDEDSDYSSDEDDDDYDSYDSSDSASSDS 308
>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation
domain. The centromere protein B (CENP-B) dimerisation
domain is composed of two alpha-helices, which are
folded into an antiparallel configuration. Dimerisation
of CENP-B is mediated by this domain, in which monomers
dimerise to form a symmetrical, antiparallel, four-helix
bundle structure with a large hydrophobic patch in which
23 residues of one monomer form van der Waals contacts
with the other monomer. This CENP-B dimer configuration
may be suitable for capturing two distant CENP-B boxes
during centromeric heterochromatin formation.
Length = 101
Score = 25.5 bits (55), Expect = 8.1
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 140 ENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
E E + D ++EED D+E + D+ ED++E ++E
Sbjct: 7 EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40
>gnl|CDD|222800 PHA00458, PHA00458, single-stranded DNA-binding protein.
Length = 233
Score = 26.3 bits (58), Expect = 8.8
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 146 ADDDEDEEDFDNER-DGDEGEDEEEGENED 174
A + + + D E D D+ E+ EE E+ D
Sbjct: 203 ASEAKARKPQDEEEWDEDDEEESEEDEDGD 232
>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain
fusion protein; Provisional.
Length = 131
Score = 25.7 bits (56), Expect = 9.0
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 124 ASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
A+ AE A + E A+A+ A + + ++ D E + DE DE E +
Sbjct: 66 ATAAAEAAEEAEAADADEDADEAAEADAADEADEEEETDEAVDETADEAD 115
Score = 25.7 bits (56), Expect = 9.4
Identities = 18/51 (35%), Positives = 26/51 (50%)
Query: 124 ASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
A++EAE A E A+ AAD+ ++EE+ D D E + E E D
Sbjct: 72 AAEEAEAADADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEAD 122
>gnl|CDD|237632 PRK14164, PRK14164, heat shock protein GrpE; Provisional.
Length = 218
Score = 26.3 bits (58), Expect = 9.1
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 123 TASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEG 170
T++D AE A EA A+ +DD + + E D D D E+
Sbjct: 22 TSADRAEAAA----EEAALAQGVPEDDPFGDAVEGEIDPDLEADLEDL 65
>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 = 26.2 bits (58), Expect = 9.6
Identities = 14/40 (35%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 135 ERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED 174
E + E E AA+ ++ E+ D E++ +E E+E E E+E+
Sbjct: 63 EEVKEEEKE-AANSEDKEDKGDAEKEDEESEEENEEEDEE 101
>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated.
Length = 325
Score = 26.5 bits (59), Expect = 9.7
Identities = 6/45 (13%), Positives = 16/45 (35%)
Query: 129 ELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENE 173
L +A+ E + +++ + E ++ +EE
Sbjct: 2 TLKVHDLNEDADFDENGVEVFDEKALVEEEPSDNDLAEEELLSQG 46
>gnl|CDD|239917 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 domain.
RNase R is a processive 3' to 5' exoribonuclease, which
is a homolog of RNase II. RNase R degrades RNA with
secondary structure having a 3' overhang of at least 7
nucleotides. RNase R and PNPase play an important role
in the degradation of RNA with extensive secondary
structure, such as rRNA, tRNA, and certain mRNA which
contains repetitive extragenic palindromic sequences.
The C-terminal S1 domain binds ssRNA.
Length = 83
Score = 25.1 bits (56), Expect = 9.8
Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 12/69 (17%)
Query: 22 TVISIAEMGAYVHLLEYNNIEGMILLSELS---------RRRI--RSINKLIRVGKTEPV 70
+ + G +V L +EG++ +S L + K+ R+G V
Sbjct: 8 VISGVTSFGLFVELDN-LTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKV 66
Query: 71 VVIRVDKEK 79
V+RVD ++
Sbjct: 67 RVVRVDLDR 75
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
0.311 0.131 0.344
Gapped
Lambda K H
0.267 0.0685 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,199,830
Number of extensions: 896244
Number of successful extensions: 3550
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2783
Number of HSP's successfully gapped: 516
Length of query: 174
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 84
Effective length of database: 6,945,742
Effective search space: 583442328
Effective search space used: 583442328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 56 (25.4 bits)