RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 048067
(75 letters)
>gnl|CDD|235586 PRK05738, rplW, 50S ribosomal protein L23; Reviewed.
Length = 92
Score = 37.0 bits (87), Expect = 6e-05
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 34 KLYGLEIEKVRTLNKQGMKKRREGCLVTG--PNYKKAYRTLKK 74
KL+G+++E V TLN +G KR G ++KKA TL +
Sbjct: 42 KLFGVKVESVNTLNVKGKTKRFGR--RIGKRSDWKKAIVTLAE 82
>gnl|CDD|144021 pfam00276, Ribosomal_L23, Ribosomal protein L23.
Length = 90
Score = 34.6 bits (80), Expect = 6e-04
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 30 HAASKLYGLEIEKVRTLNKQGMKKRREGCLVTGPNYKKAYRTLKKP 75
A ++G+++EKV TL G KR L +YKKA TL++
Sbjct: 37 DAVEHIFGVKVEKVNTLILPGKVKRNGQYLGRKKSYKKAIVTLEEG 82
>gnl|CDD|223167 COG0089, RplW, Ribosomal protein L23 [Translation, ribosomal
structure and biogenesis].
Length = 94
Score = 34.1 bits (79), Expect = 0.001
Identities = 18/42 (42%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 34 KLYGLEIEKVRTLN-KQGMKKRREGCLVTGPNYKKAYRTLKK 74
+L+G+++EKV TLN K K+ + +YKKAY TLK+
Sbjct: 43 ELFGVKVEKVNTLNTKGKTKRAGVKRIGLRKDYKKAYVTLKE 84
>gnl|CDD|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed.
Length = 324
Score = 27.0 bits (60), Expect = 0.72
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 27 KTMHAASKLYGLEIEKVRTLNKQGMKKRREG 57
+T+ KL+GL E+VR + ++ M K R G
Sbjct: 283 RTLDQIGKLFGLSRERVRQIEREVMSKLRNG 313
>gnl|CDD|237250 PRK12893, PRK12893, allantoate amidohydrolase; Reviewed.
Length = 412
Score = 25.6 bits (57), Expect = 2.3
Identities = 11/21 (52%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 35 LYGLEIEKVRTLNKQGMKKRR 55
L LE+ VRTLN G++ RR
Sbjct: 101 LAALEV--VRTLNDAGIRTRR 119
>gnl|CDD|132675 TIGR03636, L23_arch, archaeal ribosomal protein L23. This model
describes the archaeal ribosomal protein L23P and
rigorously excludes the bacterial counterpart L23. In
order to capture every known instance of archaeal L23P,
the trusted cutoff is set lower than a few of the
highest scoring eukaryotic cytosolic ribosomal
counterparts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 77
Score = 24.9 bits (55), Expect = 2.4
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 13/42 (30%)
Query: 34 KLYGLEIEKVRTLNKQGMKKRREGCLVTGPNYKKAYRTLKKP 75
KL+ +++EKV T L+T KKAY L +
Sbjct: 36 KLFDVKVEKVNT-------------LITPRGEKKAYVKLAEE 64
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse
gyrase, found in both archaeal and bacterial
thermophiles. This enzyme, a fusion of a type I
topoisomerase domain and a helicase domain, introduces
positive supercoiling to increase the melting
temperature of DNA double strands. Generally, these
gyrases are encoded as a single polypeptide. An
exception was found in Methanopyrus kandleri, where
enzyme is split within the topoisomerase domain,
yielding a heterodimer of gene products designated RgyB
and RgyA [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1171
Score = 25.6 bits (56), Expect = 3.0
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 6 IDFPMKLLMPSSFENIKEIAFKTMHAASKLYGLEIEKVRTLNKQGMKKRREGCLV 60
+D +KLL S E + E A+K + KLY K R + + ++ GCL+
Sbjct: 218 VDKLLKLLGFS--EELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLI 270
>gnl|CDD|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH. A sigma
factor is a DNA-binding protein protein that binds to
the DNA-directed RNA polymerase core to produce the
holoenzyme capable of initiating transcription at
specific sites. Different sigma factors act in
vegetative growth, heat shock, extracytoplasmic
functions (ECF), etc. This model represents the clade of
sigma factors called RpoH and further restricted to the
Proteobacteria. This protein may be called sigma-32,
sigma factor H, heat shock sigma factor, and alternative
sigma factor RpoH. Note that in some species the single
locus rpoH may be replaced by two or more differentially
regulated stress response sigma factors [Cellular
processes, Adaptations to atypical conditions,
Transcription, Transcription factors].
Length = 270
Score = 25.3 bits (56), Expect = 3.6
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 27 KTMHAASKLYGLEIEKVRTLNKQGMKKRR 55
T+ + YG+ E++R + K MKK +
Sbjct: 237 LTLQELAAEYGVSAERIRQIEKNAMKKLK 265
>gnl|CDD|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit
(eIF-2alpha) [Translation, ribosomal structure and
biogenesis].
Length = 269
Score = 25.0 bits (55), Expect = 4.6
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 60 VTGPNYKKAYRTLKK 74
V P+YKKA L+K
Sbjct: 227 VQAPDYKKAEEVLEK 241
>gnl|CDD|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit
alpha; Validated.
Length = 262
Score = 24.4 bits (54), Expect = 6.3
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 60 VTGPNYKKAYRTLKK 74
VT P+YK A + LKK
Sbjct: 225 VTAPDYKTAEKALKK 239
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 24.4 bits (54), Expect = 6.5
Identities = 10/41 (24%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 13 LMPSSFENIKEIAFKTMHAASKLYGLEIEKVRTLNKQGMKK 53
+ ++ IK++ + + A + GL IE+++ +N+Q + K
Sbjct: 335 FLVRVYDEIKKL-QQELEAIEEETGLTIEELKEINRQ-ISK 373
>gnl|CDD|132354 TIGR03311, Se_dep_Molyb_1, selenium-dependent molybdenum
hydroxylase 1. Members of this protein family show full
length homology to the molybdenum-containing aldehyde
oxido-reductase of Desulfovibrio gigas. Members,
however, are found only within species that have, and
near those genes that encode, a set of predicted
accessory proteins for selenium-dependent molybdenum
hydroxylases. The best known examples of such enzymes
are forms of xanthine dehydrogenase and purine
hydroxylase; this family appears to be another such
enzyme.
Length = 848
Score = 24.4 bits (53), Expect = 7.4
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 26 FKTMHAASKLYGLEIEKVRTLNK 48
+ + L GL EK+R +NK
Sbjct: 366 YDEQRELASLLGLPKEKIRVINK 388
>gnl|CDD|226968 COG4615, PvdE, ABC-type siderophore export system, fused ATPase and
permease components [Secondary metabolites biosynthesis,
transport, and catabolism / Inorganic ion transport and
metabolism].
Length = 546
Score = 24.4 bits (53), Expect = 8.3
Identities = 10/44 (22%), Positives = 14/44 (31%), Gaps = 7/44 (15%)
Query: 8 FPMKLLMPSSFENIKEIA-------FKTMHAASKLYGLEIEKVR 44
P L +F I ++ F A LE+ VR
Sbjct: 286 LPTLLTAQVAFNKIAKLELAPYKADFPRPQAFPDWKTLELRNVR 329
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.135 0.386
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,700,802
Number of extensions: 276843
Number of successful extensions: 260
Number of sequences better than 10.0: 1
Number of HSP's gapped: 256
Number of HSP's successfully gapped: 18
Length of query: 75
Length of database: 10,937,602
Length adjustment: 45
Effective length of query: 30
Effective length of database: 8,941,672
Effective search space: 268250160
Effective search space used: 268250160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.2 bits)