RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032125
(147 letters)
>gnl|CDD|177799 PLN00210, PLN00210, 40S ribosomal protein S16; Provisional.
Length = 141
Score = 282 bits (723), Expect = e-100
Identities = 136/140 (97%), Positives = 139/140 (99%)
Query: 8 TESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKAFEPILLLGRHRFNGV 67
TESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELV+PEILRFKAFEPILLLGRHRF GV
Sbjct: 2 TESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVQPEILRFKAFEPILLLGRHRFAGV 61
Query: 68 DMRIRVKGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRR 127
DMRIRVKGGGHTSQIYAIRQSIAKALVA+YQKYVDEQSKKEIKDIL+RYDRTLLVADPRR
Sbjct: 62 DMRIRVKGGGHTSQIYAIRQSIAKALVAYYQKYVDEQSKKEIKDILLRYDRTLLVADPRR 121
Query: 128 CEPKKFGGRGARARFQKSYR 147
CEPKKFGGRGARARFQKSYR
Sbjct: 122 CEPKKFGGRGARARFQKSYR 141
>gnl|CDD|185437 PTZ00086, PTZ00086, 40S ribosomal protein S16; Provisional.
Length = 147
Score = 249 bits (639), Expect = 7e-87
Identities = 96/147 (65%), Positives = 120/147 (81%)
Query: 1 MATAAPKTESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKAFEPILLLG 60
MA K + VQ FG+KKTAVAV +G+GLI++NG P++L+ PE LR K FEP+LL+G
Sbjct: 1 MAEKTTKLKQVQTFGKKKTAVAVALVTKGKGLIRVNGVPLDLINPETLRAKVFEPLLLVG 60
Query: 61 RHRFNGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTL 120
+ RF+ +D+R+RV+GGG +Q YAIRQ+IAK LVA+YQKYVDE +K E+KD L+ YDR+L
Sbjct: 61 KERFSRLDIRVRVRGGGQVAQAYAIRQAIAKGLVAYYQKYVDEATKAELKDKLLAYDRSL 120
Query: 121 LVADPRRCEPKKFGGRGARARFQKSYR 147
LVADPRRCEPKKFGG GARARFQKSYR
Sbjct: 121 LVADPRRCEPKKFGGPGARARFQKSYR 147
>gnl|CDD|179041 PRK00474, rps9p, 30S ribosomal protein S9P; Reviewed.
Length = 134
Score = 160 bits (406), Expect = 2e-51
Identities = 65/137 (47%), Positives = 89/137 (64%), Gaps = 7/137 (5%)
Query: 11 VQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKAFEPILLLGRHRFNGVDMR 70
V G++KTA+A + G+G ++ING P+EL+EPE+ R K EP++L G + VD+
Sbjct: 5 VITSGKRKTAIARATIREGKGRVRINGVPLELIEPELARLKIMEPLILAGEDLRSKVDID 64
Query: 71 IRVKGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEP 130
+ V+GGG Q A R +IA+ LV + E+KD + YDRTLLV DPRR EP
Sbjct: 65 VNVEGGGIMGQADAARTAIARGLVEWTG-------DMELKDAFLAYDRTLLVGDPRRTEP 117
Query: 131 KKFGGRGARARFQKSYR 147
KK+GG+GARA+ QKSYR
Sbjct: 118 KKWGGKGARAKRQKSYR 134
>gnl|CDD|201193 pfam00380, Ribosomal_S9, Ribosomal protein S9/S16. This family
includes small ribosomal subunit S9 from prokaryotes and
S16 from eukaryotes.
Length = 121
Score = 151 bits (385), Expect = 1e-48
Identities = 58/134 (43%), Positives = 73/134 (54%), Gaps = 14/134 (10%)
Query: 15 GRKKTAVAVTYCKRGRGLIKINGCPI-ELVEPEILRFKAFEPILLLGRHRFNGVDMRIRV 73
GR+KTAVA + K G G I ING P+ E E LR K EP+ L G D+ + V
Sbjct: 1 GRRKTAVARVWLKPGSGKITINGKPLEEYFPNETLRMKILEPLELTGT--LGKFDIVVTV 58
Query: 74 KGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKF 133
KGGG + Q AIR +IA+ALVA+ + + E+K LL DPRR E KK+
Sbjct: 59 KGGGISGQAGAIRLAIARALVAYDPEL-----RPELKK------AGLLTRDPRRKERKKY 107
Query: 134 GGRGARARFQKSYR 147
G + AR R Q S R
Sbjct: 108 GLKKARKRPQFSKR 121
>gnl|CDD|132666 TIGR03627, arch_S9P, archaeal ribosomal protein S9P. This model
describes exclusively the archaeal ribosomal protein
S9P. Homologous eukaryotic and bacterial ribosomal
proteins are excluded from this model [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 130
Score = 142 bits (360), Expect = 1e-44
Identities = 65/133 (48%), Positives = 84/133 (63%), Gaps = 8/133 (6%)
Query: 15 GRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKAFEPILLLGRHRFNGVDMRIRVK 74
G++KTA+A + G+G ++ING P+EL PE+ R K EP++L G VD+ ++V
Sbjct: 6 GKRKTAIARATIREGKGRVRINGVPVELYPPELARLKIMEPLILAGDIA-KEVDIDVKVS 64
Query: 75 GGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFG 134
GGG Q A R +IA+ LV F KE++D YDRTLLV DPRR EPKK G
Sbjct: 65 GGGIMGQADAARTAIARGLVEFTGD-------KELRDAFRAYDRTLLVNDPRRKEPKKPG 117
Query: 135 GRGARARFQKSYR 147
GRGARA+ QKSYR
Sbjct: 118 GRGARAKRQKSYR 130
>gnl|CDD|223181 COG0103, RpsI, Ribosomal protein S9 [Translation, ribosomal
structure and biogenesis].
Length = 130
Score = 141 bits (358), Expect = 2e-44
Identities = 56/140 (40%), Positives = 75/140 (53%), Gaps = 14/140 (10%)
Query: 9 ESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEP-EILRFKAFEPILLLGRHRFNGV 67
+ V G++K+AVA G+G I +NG P+EL P E LR K +P+LL G
Sbjct: 4 DQVYTTGKRKSAVARVRLVPGKGKITVNGRPLELYFPRETLRMKIMQPLLLTGT--VGKF 61
Query: 68 DMRIRVKGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRR 127
D+ + VKGGG + Q AIR IA+ALV + E++ L + LL DPRR
Sbjct: 62 DIDVTVKGGGISGQAGAIRHGIARALVEYDP---------ELRPALKKAG--LLTRDPRR 110
Query: 128 CEPKKFGGRGARARFQKSYR 147
E KK+G + AR R Q S R
Sbjct: 111 VERKKYGLKKARRRPQFSKR 130
>gnl|CDD|178888 PRK00132, rpsI, 30S ribosomal protein S9; Reviewed.
Length = 130
Score = 77.4 bits (192), Expect = 3e-19
Identities = 48/134 (35%), Positives = 63/134 (47%), Gaps = 14/134 (10%)
Query: 15 GRKKTAVAVTYCKRGRGLIKINGCPIELVEP-EILRFKAFEPILLLGRHRFNGVDMRIRV 73
GR+KTAVA K G G I +NG +E P E LR +P+ L D+ + V
Sbjct: 10 GRRKTAVARVRLKPGSGKITVNGRDLEEYFPRETLRMVVRQPLELTET--EGKFDVYVTV 67
Query: 74 KGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKF 133
KGGG + Q AIR IA+AL+ + D + +K L D R E KK+
Sbjct: 68 KGGGISGQAGAIRHGIARALLEY-----DPDLRPALK------KAGFLTRDARMVERKKY 116
Query: 134 GGRGARARFQKSYR 147
G + AR Q S R
Sbjct: 117 GLKKARRAPQFSKR 130
>gnl|CDD|214357 CHL00079, rps9, ribosomal protein S9.
Length = 130
Score = 54.1 bits (131), Expect = 3e-10
Identities = 50/139 (35%), Positives = 66/139 (47%), Gaps = 23/139 (16%)
Query: 15 GRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKA------FEPILLLGRHRFNGVD 68
GR+KTAVA G G I ING P E E L++ P+ LLG N D
Sbjct: 9 GRRKTAVAQVRLVPGSGEIIINGKPAE----EYLQYNPNYLNAIKAPLKLLGLE--NKYD 62
Query: 69 MRIRVKGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRC 128
+ ++VKGGG T Q AIR +A+AL + +++K +K L D R
Sbjct: 63 IIVKVKGGGLTGQAEAIRLGLARALCKI-----NPENRKSLK------KEGFLTRDARIK 111
Query: 129 EPKKFGGRGARARFQKSYR 147
E KK+G + AR Q S R
Sbjct: 112 ERKKYGLKKARKAPQFSKR 130
>gnl|CDD|227642 COG5337, CotH, Spore coat assembly protein [Cell envelope
biogenesis, outer membrane].
Length = 473
Score = 29.9 bits (67), Expect = 0.52
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 65 NGV---DMRIRVKGGGHTSQI----YAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYD 117
+GV D+ IR+KG H I S L++F KY D + + I + R
Sbjct: 90 DGVTILDVGIRLKGQSHIQDFKKKSSHIDVSTWPLLISFD-KYKDGRGYRGITLLAERKG 148
Query: 118 RTLL 121
+L+
Sbjct: 149 PSLM 152
>gnl|CDD|232801 TIGR00054, TIGR00054, RIP metalloprotease RseP. Members of this
nearly universal bacterial protein family are regulated
intramembrane proteolysis (RIP) proteases. Older and
synonymous gene symbols include yaeL in E. coli, mmpA in
Caulobacter crescentus, etc. This family includes a
region that hits the PDZ domain, found in a number of
proteins targeted to the membrane by binding to a
peptide ligand. The N-terminal region of this family
contains a perfectly conserved motif HEXGH as found in a
number of metalloproteinases, where the Glu is the
active site and the His residues coordinate the metal
cation [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 419
Score = 27.5 bits (61), Expect = 3.0
Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 45 PEILRFKAFE------PILLLGRHRFNGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQ 98
P+IL+FK I L G + G+D + VK ++ + KA++ F
Sbjct: 43 PKILKFKKNGTEYAISLIPLGGYVKMKGLDKEMEVKPPETDGDLFNNKSVFQKAIIIFAG 102
Query: 99 KYVD 102
+
Sbjct: 103 PLAN 106
>gnl|CDD|216561 pfam01545, Cation_efflux, Cation efflux family. Members of this
family are integral membrane proteins, that are found to
increase tolerance to divalent metal ions such as
cadmium, zinc, and cobalt. These proteins are thought to
be efflux pumps that remove these ions from cells.
Length = 273
Score = 27.3 bits (61), Expect = 3.1
Identities = 18/91 (19%), Positives = 28/91 (30%), Gaps = 21/91 (23%)
Query: 20 AVAVTYCKRGRGLIKINGCPIELVE--PEILRFKAFEPILL---------------LGRH 62
+A+ G L+K + EL+ P+ L G
Sbjct: 166 LIALLILYTGLRLLKESL--SELLGASPDPELVDEIRDALEKLPGVLGVHDLRVWKSGPK 223
Query: 63 RFNGVDMRIRVKGGGHTSQIYAIRQSIAKAL 93
F VD+ I V + + I I +AL
Sbjct: 224 YF--VDIHIEVDPDLTVEEAHEIADEIERAL 252
>gnl|CDD|219598 pfam07826, IMP_cyclohyd, IMP cyclohydrolase-like protein. This
enzyme is may catalyze the cyclization of
5-formylamidoimidazole-4-carboxamide ribonucleotide to
inosine monophosphate (IMP), a reaction which is
important in de novo purine biosynthesis in archaeal
species. This single domain protein is arranged to form
an overall fold that consists of a four-layered
alpha-beta-beta-alpha core structure. The two
antiparallel beta-sheets pack against each other and are
covered by alpha-helices on one face of the molecule.
The protein is structurally similar to members of the
N-terminal nucleophile (NTN) hydrolase superfamily. A
deep pocket was in fact found on the surface of IMP
cyclohydrolase in a position equivalent to that of
active sites of NTN-hydrolases, but an N-terminal
nucleophile could not be found. Therefore, it is thought
that this enzyme is structurally but not functionally
similar to members of the NTN-hydrolase family.
Length = 200
Score = 26.0 bits (57), Expect = 6.9
Identities = 12/51 (23%), Positives = 16/51 (31%), Gaps = 2/51 (3%)
Query: 24 TYCKRGRGLIKINGCPIELVEPEILRFKAFE-PILLLGR-HRFNGVDMRIR 72
TY I G E L + AFE P+ +G D+
Sbjct: 148 TYEADENQAISFKGKTAEDAAEFALEYAAFEHPVCAAVAELDGDGFDLATE 198
>gnl|CDD|144813 pfam01358, PARP_regulatory, Poly A polymerase regulatory subunit.
Length = 295
Score = 25.9 bits (57), Expect = 8.4
Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 75 GGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPR 126
G GH + + V+ ++VDE+ + +K+ L + LL++D R
Sbjct: 94 GRGHDPSLEGLSD------VSIVTRFVDEKYLRLLKNQL--NLKILLISDIR 137
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 26.3 bits (58), Expect = 8.4
Identities = 29/124 (23%), Positives = 44/124 (35%), Gaps = 32/124 (25%)
Query: 35 INGCPIELVEPEILRFKAFEPILLLGRHRF-NGVDMRIRVKGGGHTSQIYAIR----QSI 89
ING ++ + RF E +LLG F GVD G+ I +
Sbjct: 710 INGSRAKIKK----RFNNGEKAILLGTSSFWEGVDFP------GNGLVCLVIPRLPFANP 759
Query: 90 AKALVAFYQKYVDEQSKKEIKDI---------------LVR--YDRTLLVADPRRCEPKK 132
L Y + ++++ K D L+R DR +V RR K+
Sbjct: 760 KHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVILDRRLVGKR 819
Query: 133 FGGR 136
+G R
Sbjct: 820 YGKR 823
>gnl|CDD|223911 COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms].
Length = 1009
Score = 26.0 bits (58), Expect = 8.6
Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 2/49 (4%)
Query: 45 PEILRFKAFEPILLLGRHRFNGVDMRIRVKGGGHTSQIYAIRQSIAKAL 93
P+ F AF P + G + +G ++R +GG + + +
Sbjct: 638 PDATVF-AFTPPAVDGLGQGSGFPFQLRDRGGDLE-ALRQAANQLLEKA 684
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
0.325 0.140 0.414
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,492,378
Number of extensions: 690328
Number of successful extensions: 928
Number of sequences better than 10.0: 1
Number of HSP's gapped: 915
Number of HSP's successfully gapped: 22
Length of query: 147
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 59
Effective length of database: 7,034,450
Effective search space: 415032550
Effective search space used: 415032550
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.4 bits)