RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10165
(337 letters)
>gnl|CDD|223176 COG0098, RpsE, Ribosomal protein S5 [Translation, ribosomal
structure and biogenesis].
Length = 181
Score = 102 bits (257), Expect = 3e-26
Identities = 52/169 (30%), Positives = 86/169 (50%), Gaps = 1/169 (0%)
Query: 115 GKLTARDLNRGQIIGIDTFDGFDTRILEYKAVFCMKKNSGRYRTVSTLVVTGNGQGLAGF 174
GK+ + G I D ++++ V + K GR S LVV G+ G GF
Sbjct: 3 GKIATIEFKSGLPIKEPEVDELLEKVVDINRVSKVVK-GGRRFRFSALVVVGDRNGRVGF 61
Query: 175 ALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDFYTQFGKTKIFVEKKPEGTGLIC 234
+GK+ E ++R A A + +I V R HT+ H+ + G K+ ++ PEGTG+I
Sbjct: 62 GIGKAKEVPEAIRKAIEDAKKNIIEVPRGNGHTIPHEVIGKHGAVKVLLKPAPEGTGIIA 121
Query: 235 HRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQQKSHQQLAEE 283
++ + + GIKD+ AK GS NP +V+A F L + ++ + +A +
Sbjct: 122 GGAVRAVLELAGIKDVLAKSLGSRNPINVVRATFDALKKLRTPEDVAAK 170
>gnl|CDD|234790 PRK00550, rpsE, 30S ribosomal protein S5; Validated.
Length = 168
Score = 88.6 bits (221), Expect = 3e-21
Identities = 45/130 (34%), Positives = 73/130 (56%), Gaps = 1/130 (0%)
Query: 154 GRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDFY 213
GR + S LVV G+G+G GF GK+ E ++R A A + +I V T+ H+
Sbjct: 30 GRRFSFSALVVVGDGKGRVGFGYGKAREVPEAIRKAVEDAKKNMIKVPL-VGGTIPHEVI 88
Query: 214 TQFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQ 273
+FG K+ ++ EGTG+I ++ + + G+KD+ AK GS NP +V+A F L Q
Sbjct: 89 GKFGAAKVLLKPASEGTGVIAGGAVRAVLELAGVKDVLAKSLGSNNPINVVRATFDALKQ 148
Query: 274 QKSHQQLAEE 283
+S +++A +
Sbjct: 149 LRSPEEVAAK 158
>gnl|CDD|130093 TIGR01021, rpsE_bact, ribosomal protein S5, bacterial/organelle
type. This model finds chloroplast ribosomal protein S5
as well as bacterial ribosomal protein S5. A candidate
mitochondrial form (Saccharomyces cerevisiae YBR251W and
its homolog) differs substantially and is not included
in this model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 154
Score = 84.3 bits (209), Expect = 8e-20
Identities = 48/137 (35%), Positives = 75/137 (54%), Gaps = 1/137 (0%)
Query: 154 GRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDFY 213
GR + S LVV G+G+G GF GK+ E +++ A A + LI V K T+ H+
Sbjct: 19 GRRFSFSALVVVGDGKGRVGFGFGKAKEVPDAIKKAVEAARKNLINVPLTKG-TIPHEVI 77
Query: 214 TQFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQ 273
+ G K+ ++ GTG+I ++ I + G+KDI AK GS NP +V+A F L++
Sbjct: 78 GRSGAAKVLLKPASPGTGVIAGGAVRAILELAGVKDILAKSLGSNNPINVVRATFDALLK 137
Query: 274 QKSHQQLAEEQQLHLVE 290
KS + +AE + + E
Sbjct: 138 LKSPEDVAELRGKPVEE 154
>gnl|CDD|190724 pfam03719, Ribosomal_S5_C, Ribosomal protein S5, C-terminal domain.
Length = 74
Score = 74.0 bits (183), Expect = 5e-17
Identities = 24/67 (35%), Positives = 40/67 (59%)
Query: 216 FGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQQK 275
FG K+ ++ P GTG+I ++ + + GIKD+ AK GS NP +VKA F L + +
Sbjct: 5 FGAVKVLLKPAPRGTGIIAGGAVRAVLELAGIKDVLAKSLGSRNPINVVKATFDALKKLR 64
Query: 276 SHQQLAE 282
+ +++A
Sbjct: 65 TPEEVAA 71
>gnl|CDD|235213 PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed.
Length = 211
Score = 48.0 bits (115), Expect = 1e-06
Identities = 30/115 (26%), Positives = 52/115 (45%), Gaps = 9/115 (7%)
Query: 153 SGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQR---------Y 203
SGR +VV GN G G GK+ + ++R A A +I V+R
Sbjct: 66 SGRRVRFRVVVVVGNRDGYVGVGQGKAKQVGPAIRKAIRNAKLNIIKVRRGCGSWECGCG 125
Query: 204 KDHTVLHDFYTQFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGST 258
+ H+V + G ++ ++ P G GL+ + +++ + GIKD+ + G T
Sbjct: 126 EPHSVPFKVTGKAGSVEVTLKPAPRGLGLVAGDVAKKVLELAGIKDVWTRTFGET 180
>gnl|CDD|177060 CHL00138, rps5, ribosomal protein S5; Validated.
Length = 143
Score = 46.5 bits (111), Expect = 2e-06
Identities = 32/118 (27%), Positives = 61/118 (51%), Gaps = 1/118 (0%)
Query: 139 RILEYKAVFCMKKNSGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLI 198
R+++ K V + K G+ + +VV GN G G +GK+ + + +++ A A + LI
Sbjct: 27 RVIQIKRVSKVVK-GGKKLSFRAIVVIGNENGWVGVGVGKADDVQNAVKKAVTDAKKNLI 85
Query: 199 YVQRYKDHTVLHDFYTQFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEG 256
+ K +++ H+ FG K+ + G+G+I ++ + + GIK+I AK G
Sbjct: 86 TIPLTKSNSIPHNITGIFGAAKVILRPSAPGSGVIAGGSVRIVLELAGIKNILAKQLG 143
>gnl|CDD|233235 TIGR01020, rpsE_arch, ribosomal protein S5(archaeal
type)/S2(eukaryote cytosolic type). This model finds
eukaryotic ribosomal protein S2 as well as archaeal
ribosomal protein S5 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 212
Score = 46.3 bits (110), Expect = 5e-06
Identities = 35/142 (24%), Positives = 60/142 (42%), Gaps = 10/142 (7%)
Query: 126 QIIGIDTFDGFDTRILEYKAVFCMKKNSGRYRTVSTLVVTGNGQGLAGFALGKSVEGRAS 185
+I+ D + +L+ V M SGR VV GN G G +GK+ E +
Sbjct: 40 EIVDYLLPDLNEEEVLDVSLVQRMTD-SGRRTRFRAFVVVGNRDGYVGLGIGKAKEVAPA 98
Query: 186 MRNAKNRAGQKLIYVQRY---------KDHTVLHDFYTQFGKTKIFVEKKPEGTGLICHR 236
+R A A +I V+R + H+V + G ++ + P G GL+
Sbjct: 99 IRKAIINAKLNIIPVRRGCGSWECGCGRPHSVPFKVTGKCGSVRVRLIPAPRGLGLVAGD 158
Query: 237 IIQEICKAVGIKDIRAKVEGST 258
+ +++ + GI D+ + G T
Sbjct: 159 VAKKVLRLAGIDDVWTQTRGET 180
>gnl|CDD|144065 pfam00333, Ribosomal_S5, Ribosomal protein S5, N-terminal domain.
Length = 67
Score = 30.7 bits (70), Expect = 0.13
Identities = 18/50 (36%), Positives = 23/50 (46%)
Query: 153 SGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQR 202
GR + LVV G+ G G GK+ E ++R A A LI V R
Sbjct: 18 GGRRFSFRALVVVGDKNGHVGLGEGKAKEVPGAIRKAIEDAKLNLIEVPR 67
>gnl|CDD|235716 PRK06149, PRK06149, hypothetical protein; Provisional.
Length = 972
Score = 33.4 bits (77), Expect = 0.17
Identities = 17/37 (45%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 38 LPPDPDREAKLIALRDKQF---QGKYRKTPP-LERGW 70
P PD A L+A RD F Q Y PP +ERGW
Sbjct: 540 DAPPPDAAA-LLARRDASFARVQKHYYADPPQIERGW 575
>gnl|CDD|184363 PRK13879, PRK13879, conjugal transfer protein TrbJ; Provisional.
Length = 253
Score = 32.0 bits (73), Expect = 0.32
Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 8/49 (16%)
Query: 27 IRGRELVQQ----TRLPPDPDREAKLIALRDKQF-QGKYRKTPPLERGW 70
IRG + QQ TR+ D D+EA+ A +Q G YRK+P + W
Sbjct: 208 IRGLLIAQQNAIATRMQADADKEAQQAA-AAEQLRSGSYRKSPA--KNW 253
>gnl|CDD|234477 TIGR04120, DNA_lig_bact, DNA ligase, ATP-dependent, PP_1105
family. This model describes a family of ATP-dependent
DNA ligases present in about 12 % of prokaryotic
genomes. It occurs as part of a four-gene system with
an exonuclease, a helicase and a phosphoesterase, with
all four genes clustered or at least the first two and
last two paired. This family resembles DNA ligase I
(see TIGR00574 and pfam01068), and its presumed
function may be in DNA repair, replication, or
recombination.
Length = 526
Score = 28.8 bits (65), Expect = 4.8
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 36 TRLPPDPDREAKLIALRDKQFQGKYRKTPPLERGWSGGKL-GGRSL 80
RL P R AKL L+D +R TP +RGW+ L GG
Sbjct: 8 DRLDYTPSRNAKLALLQDY-----FRTTPDPDRGWALAALTGGLPF 48
>gnl|CDD|234256 TIGR03558, oxido_grp_1, luciferase family oxidoreductase, group 1.
The Pfam domain family pfam00296 is named for
luciferase-like monooxygenases, but the family also
contains several coenzyme F420-dependent enzymes. This
protein family represents a well-resolved clade within
family pfam00296 and shows no restriction to coenzyme
F420-positive species, unlike some other clades within
pfam00296 [Unknown function, Enzymes of unknown
specificity].
Length = 323
Score = 27.8 bits (63), Expect = 7.8
Identities = 14/28 (50%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 109 GRGRGPG--KLTARDLNRGQIIGIDTFD 134
G GR PG LTAR L RG D F
Sbjct: 102 GLGRAPGTDPLTARALRRGLDARADDFP 129
>gnl|CDD|131633 TIGR02584, cas_NE0113, CRISPR-associated protein, NE0113 family.
Members of this minor CRISPR-associated (Cas) protein
family are found in cas gene clusters in Vibrio
vulnificus YJ016, Nitrosomonas europaea ATCC 19718,
Mannheimia succiniciproducens MBEL55E, and
Verrucomicrobium spinosum [Mobile and extrachromosomal
element functions, Other].
Length = 209
Score = 27.5 bits (61), Expect = 7.8
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 3 QIVQGWIWNLGKINIQWPGLSAPVI---RGRELVQQTRLPPDPDREAKLIALRDKQFQG 58
QI+ I+ L + + VI G+ +QQ L PD + L LR FQG
Sbjct: 11 QIITETIYALAQESPPVVPEEIHVITTSDGKRDIQQQLLTPDEAWQGVLAKLRHDYFQG 69
>gnl|CDD|189996 pfam01464, SLT, Transglycosylase SLT domain. This family is
distantly related to pfam00062. Members are found in
phages, type II, type III and type IV secretion systems.
Length = 117
Score = 26.5 bits (59), Expect = 9.1
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 252 AKVEGSTNPQAIVKAFFLGLMQ 273
A+ E NP AI + LGLMQ
Sbjct: 21 AQQESGFNPNAISGSGALGLMQ 42
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
0.317 0.136 0.408
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,521,724
Number of extensions: 1704624
Number of successful extensions: 1452
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1444
Number of HSP's successfully gapped: 25
Length of query: 337
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 240
Effective length of database: 6,635,264
Effective search space: 1592463360
Effective search space used: 1592463360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.6 bits)