RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 030930
(169 letters)
>gnl|CDD|235358 PRK05179, rpsM, 30S ribosomal protein S13; Validated.
Length = 122
Score = 177 bits (452), Expect = 2e-58
Identities = 66/121 (54%), Positives = 88/121 (72%), Gaps = 2/121 (1%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVS 106
AR+ GV+IP NKR+ +L YI+G+GRTRA++IL + + KD+++EEL IR+E+
Sbjct: 2 ARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEID 61
Query: 107 K-YMIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKRVAIAGKK 165
K Y +EGDLRR ++ I+RL +I CYRG+RH +GLP RGQ TK N RT KG R IAGKK
Sbjct: 62 KNYKVEGDLRREVSMNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKTIAGKK 121
Query: 166 K 166
K
Sbjct: 122 K 122
>gnl|CDD|223177 COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal
structure and biogenesis].
Length = 121
Score = 157 bits (400), Expect = 2e-50
Identities = 60/120 (50%), Positives = 84/120 (70%), Gaps = 2/120 (1%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEV- 105
AR+ GV+IP NKR+ +L YI+G+GR RA++I + +K +++EEE+ +RD +
Sbjct: 2 ARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQ 61
Query: 106 SKYMIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKRVAIAGKK 165
+KY++EGDLRR + I+RL +I CYRGIRH +GLP RGQ TK N RT KG R +A KK
Sbjct: 62 NKYLVEGDLRREVRMDIKRLMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGVAKKK 121
>gnl|CDD|213840 TIGR03631, bact_S13, 30S ribosomal protein S13. This model
describes bacterial ribosomal protein S13, to the
exclusion of the homologous archaeal S13P and eukaryotic
ribosomal protein S18. This model identifies some (but
not all) instances of chloroplast and mitochondrial S13,
which is of bacterial type [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 113
Score = 156 bits (398), Expect = 3e-50
Identities = 65/112 (58%), Positives = 85/112 (75%), Gaps = 2/112 (1%)
Query: 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEV-S 106
R+ GV+IPNNKR+E +L YI+G+GRTRAR+IL + +K KD++EEEL IR+E+ +
Sbjct: 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEA 60
Query: 107 KYMIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKR 158
KY +EGDLRR +L I+RL +I CYRG+RH +GLP RGQ TK N RT KG R
Sbjct: 61 KYKVEGDLRREVSLNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGPR 112
>gnl|CDD|144128 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18. This family
includes ribosomal protein S13 from prokaryotes and S18
from eukaryotes.
Length = 106
Score = 148 bits (376), Expect = 5e-47
Identities = 52/106 (49%), Positives = 72/106 (67%), Gaps = 1/106 (0%)
Query: 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVSK 107
R+ + NK+IE +L YI G+GR +A QIL + ++K +++EEE+ IRD +S
Sbjct: 1 RILNTNLDGNKKIEIALTYIKGIGRRKANQILKKAGVDKDKRVGELTEEEIDRIRDIISN 60
Query: 108 YMIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQHTKNNCRT 153
Y++E DLRR I RLK+I+CYRG+RHI+GLP RGQ TK N RT
Sbjct: 61 YVVENDLRRKIRNDIERLKKIRCYRGLRHIRGLPVRGQRTKTNART 106
>gnl|CDD|177059 CHL00137, rps13, ribosomal protein S13; Validated.
Length = 122
Score = 133 bits (337), Expect = 5e-41
Identities = 60/121 (49%), Positives = 86/121 (71%), Gaps = 2/121 (1%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEV- 105
R+ GV++P NKRIEY+L YI+G+G T A++IL ++ + TKD+++E++ +R+ +
Sbjct: 2 VRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIE 61
Query: 106 SKYMIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKRVAIAGKK 165
Y +EGDLRRF +L I+RL EI CYRG RH GLP RGQ T+ N RT +G + +AGKK
Sbjct: 62 ENYQVEGDLRRFESLNIKRLMEINCYRGRRHRLGLPVRGQRTRTNARTRRGAKKTVAGKK 121
Query: 166 K 166
K
Sbjct: 122 K 122
>gnl|CDD|235215 PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed.
Length = 149
Score = 74.1 bits (183), Expect = 2e-17
Identities = 41/132 (31%), Positives = 62/132 (46%), Gaps = 30/132 (22%)
Query: 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS- 106
R+ G ++ K +EY+L I G+GR AR I L ++ N +S+EE+ I + +
Sbjct: 11 RIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALED 70
Query: 107 ----------------------KYMIEGDL---RRFNALAIRRLKEIQCYRGIRHIQGLP 141
++I DL R + I R+K+I+ YRGIRH GL
Sbjct: 71 PAEEGIPSWMLNRRKDYETGEDLHLIGSDLILTVRED---INRMKKIRSYRGIRHELGLK 127
Query: 142 CRGQHTKNNCRT 153
RGQ T++ RT
Sbjct: 128 VRGQRTRSTGRT 139
>gnl|CDD|213839 TIGR03629, arch_S13P, archaeal ribosomal protein S13P. This model
describes exclusively the archaeal ribosomal protein
S13P. It excludes the homologous eukaryotic 40S
ribosomal protein S18 and bacterial 30S ribosomal
protein S13 [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 144
Score = 72.3 bits (178), Expect = 8e-17
Identities = 44/140 (31%), Positives = 65/140 (46%), Gaps = 25/140 (17%)
Query: 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107
R+ ++ NK +EY+L I G+GR AR I L ++ N + +EE+ + + V
Sbjct: 7 RIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVEN 66
Query: 108 Y----------------------MIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQ 145
Y +I DL I R+K+I+ YRGIRH GL RGQ
Sbjct: 67 YEYGIPSWLLNRRKDYETGEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVRGQ 126
Query: 146 HTKNNCRTLKGKRVAIAGKK 165
TK+ R G+ V ++ KK
Sbjct: 127 RTKSTGRR--GRTVGVSRKK 144
>gnl|CDD|185469 PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisional.
Length = 154
Score = 50.0 bits (120), Expect = 3e-08
Identities = 36/131 (27%), Positives = 62/131 (47%), Gaps = 26/131 (19%)
Query: 59 KRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEE---LITIRDEVSKYMI---- 110
+++ Y+L I G+GR A + ++ K +++ EE ++ I ++ I
Sbjct: 26 RKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKIPDWF 85
Query: 111 ---EGDLRR-------FNALAIR------RLKEIQCYRGIRHIQGLPCRGQHTKNNCRTL 154
+ D + N L + RLK+I+ +RG+RH GL RGQHTK R
Sbjct: 86 LNRQRDPKDGKNSHLTSNMLDTKLREDLERLKKIRLHRGLRHHWGLRVRGQHTKTTGR-- 143
Query: 155 KGKRVAIAGKK 165
+G+ V ++ KK
Sbjct: 144 RGRTVGVSRKK 154
>gnl|CDD|219216 pfam06883, RNA_pol_Rpa2_4, RNA polymerase I, Rpa2 specific
domain. This domain is found between domain 3
(pfam04565) and domain 5 (pfam04565), but shows no
homology to domain 4 of Rpb2. The external domains in
multisubunit RNA polymerase (those most distant from
the active site) are known to demonstrate more sequence
variability.
Length = 58
Score = 26.4 bits (59), Expect = 1.7
Identities = 9/19 (47%), Positives = 10/19 (52%), Gaps = 2/19 (10%)
Query: 33 PVSKQPQYPGLSI--QCAR 49
P S QYPGL + AR
Sbjct: 37 PPSNGGQYPGLYLFSTPAR 55
>gnl|CDD|235807 PRK06460, PRK06460, hypothetical protein; Provisional.
Length = 376
Score = 27.9 bits (62), Expect = 2.5
Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 1 MVQTLAMPV-----APALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSI 45
V+ + P+ LS +C + + L+ +A+ S P++++P G I
Sbjct: 135 FVENITNPLLRVVDITELSKVCKENGSILIVDATFSTPINQKPLELGADI 184
>gnl|CDD|217035 pfam02441, Flavoprotein, Flavoprotein. This family contains
diverse flavoprotein enzymes. This family includes
epidermin biosynthesis protein, EpiD, which has been
shown to be a flavoprotein that binds FMN. This enzyme
catalyzes the removal of two reducing equivalents from
the cysteine residue of the C-terminal meso-lanthionine
of epidermin to form a --C==C-- double bond. This family
also includes the B chain of dipicolinate synthase a
small polar molecule that accumulates to high
concentrations in bacterial endospores, and is thought
to play a role in spore heat resistance, or the
maintenance of heat resistance. dipicolinate synthase
catalyzes the formation of dipicolinic acid from
dihydroxydipicolinic acid. This family also includes
phenyl-acrylic acid decarboxylase (EC:4.1.1.-).
Length = 132
Score = 27.1 bits (61), Expect = 2.8
Identities = 16/37 (43%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 6 AMPVAPA----LSVICNGHNNNLLTNASLSFPVSKQP 38
M VAPA L+ I NG +NLLT A+L+ ++P
Sbjct: 79 LMVVAPATANTLAKIANGIADNLLTRAALAALKERKP 115
>gnl|CDD|240391 PTZ00377, PTZ00377, alanine aminotransferase; Provisional.
Length = 481
Score = 27.6 bits (62), Expect = 3.2
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 38 PQYPGLSIQCARVGGVEIP 56
PQYP S +GG ++P
Sbjct: 171 PQYPLYSAAITLLGGKQVP 189
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 27.1 bits (61), Expect = 5.8
Identities = 10/45 (22%), Positives = 27/45 (60%)
Query: 78 QILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLRRFNALAI 122
+ L +L + I+ D+S++EL+ ++ ++ + + D + A++I
Sbjct: 237 KKLKELGVIVSISPDVSKKELLGLQKKLQQEIANDDSEGYEAISI 281
>gnl|CDD|236111 PRK07843, PRK07843, 3-ketosteroid-delta-1-dehydrogenase;
Reviewed.
Length = 557
Score = 26.9 bits (60), Expect = 7.1
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 13/48 (27%)
Query: 34 VSKQPQYPGLSIQCARVG-GVEIPNNK---------RIEYSLQYIHGV 71
V K P Y G + AR G GV IPNN+ E + Y+H +
Sbjct: 36 VEKAPHYGGST---ARSGGGVWIPNNEVLKRAGVPDTPEAARTYLHSI 80
>gnl|CDD|133455 cd05313, NAD_bind_2_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 2. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
asimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 254
Score = 26.4 bits (59), Expect = 7.7
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 148 KNNCRTLKGKRVAIAG 163
K+ TLKGKRVAI+G
Sbjct: 30 KDRNETLKGKRVAISG 45
>gnl|CDD|232867 TIGR00194, uvrC, excinuclease ABC, C subunit. This family consists
of the DNA repair enzyme UvrC, an ABC excinuclease
subunit which interacts with the UvrA/UvrB complex to
excise UV-damaged nucleotide segments [DNA metabolism,
DNA replication, recombination, and repair].
Length = 574
Score = 26.6 bits (59), Expect = 7.9
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 58 NKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEE 97
++ L I GVG R +++L I K S EE
Sbjct: 536 KASLQSPLLKIPGVGEKRVQKLLKYFGSLKGI-KKASVEE 574
>gnl|CDD|172578 PRK14088, dnaA, chromosomal replication initiation protein;
Provisional.
Length = 440
Score = 26.7 bits (59), Expect = 8.0
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 3/58 (5%)
Query: 71 VGRTRARQILVDLKMENKITKDMSEEELITIRDE---VSKYMIEGDLRRFNALAIRRL 125
V A +L D N++ +ELI I + VS+ I + R AL RR+
Sbjct: 320 VDLKEAILLLKDFIKPNRVKAMDPIDELIEIVAKVTGVSREEILSNSRNVKALLARRI 377
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
0.321 0.136 0.397
Gapped
Lambda K H
0.267 0.0689 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,443,095
Number of extensions: 778800
Number of successful extensions: 784
Number of sequences better than 10.0: 1
Number of HSP's gapped: 772
Number of HSP's successfully gapped: 33
Length of query: 169
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 79
Effective length of database: 6,945,742
Effective search space: 548713618
Effective search space used: 548713618
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 (21.9 bits)
S2: 55 (25.0 bits)